-- dump date 20140620_041906 -- class Genbank::CDS -- table cds -- table main -- field 1 id -- field 2 GI -- field 3 GeneID -- field 4 chrom_position -- field 5 chromosome -- field 6 codon_start -- field 7 contig -- field 8 description -- field 9 end_pos -- field 10 gene -- field 11 gene_id -- field 12 name -- field 13 organism -- field 14 product -- field 15 protein_id -- field 16 start_pos -- field 17 strand -- field 18 taxid -- field 19 type -- header -- id GI GeneID chrom_position chromosome codon_start contig description end_pos gene gene_id name organism product protein_id start_pos strand taxid type YP_611162.1 99077903 4074939 27..5300 1 NC_008042.1 PFAM: Hemolysin-type calcium-binding region: (0.15); KEGG: tdn:Tmden_0243 hemolysin-type calcium-binding region, ev=3e-78, 36% identity; hemolysin-type calcium-binding region 5300 4074939 TM1040_3767 Ruegeria sp. TM1040 hemolysin-type calcium-binding region YP_611162.1 27 D 292414 CDS YP_611163.1 99077904 4074940 6566..7546 1 NC_008042.1 KEGG: xcb:XC_2789 hypothetical protein, ev=6e-14, 47% identity; hypothetical protein 7546 4074940 TM1040_3768 Ruegeria sp. TM1040 hypothetical protein YP_611163.1 6566 D 292414 CDS YP_611164.1 99077905 4074941 7780..8247 1 NC_008042.1 hypothetical protein 8247 4074941 TM1040_3769 Ruegeria sp. TM1040 hypothetical protein YP_611164.1 7780 D 292414 CDS YP_611165.1 99077906 4074942 14155..14565 1 NC_008042.1 hypothetical protein 14565 4074942 TM1040_3770 Ruegeria sp. TM1040 hypothetical protein YP_611165.1 14155 D 292414 CDS YP_611166.1 99077907 4074943 complement(15000..16031) 1 NC_008042.1 KEGG: rsp:RSP_3991 hypothetical protein, ev=1e-99, 57% identity; hypothetical protein 16031 4074943 TM1040_3771 Ruegeria sp. TM1040 hypothetical protein YP_611166.1 15000 R 292414 CDS YP_611167.1 99077908 4074944 complement(16148..17152) 1 NC_008042.1 KEGG: jan:Jann_4266 RepA, ev=1e-126, 68% identity; hypothetical protein 17152 4074944 TM1040_3772 Ruegeria sp. TM1040 hypothetical protein YP_611167.1 16148 R 292414 CDS YP_611168.1 99077909 4074945 17636..19045 1 NC_008042.1 PFAM: Cobyrinic acid a,c-diamide synthase: (2.1e-23); KEGG: jan:Jann_4265 cobyrinic acid a,c-diamide synthase, ev=0.0, 75% identity; cobyrinic acid a,c-diamide synthase 19045 4074945 TM1040_3773 Ruegeria sp. TM1040 cobyrinic acid a,c-diamide synthase YP_611168.1 17636 D 292414 CDS YP_611169.1 99077910 4074946 19119..20249 1 NC_008042.1 PFAM: ParB-like nuclease: (6e-05); KEGG: jan:Jann_4264 ParB-like nuclease, ev=1e-48, 36% identity; ParB-like nuclease 20249 4074946 TM1040_3774 Ruegeria sp. TM1040 ParB-like nuclease YP_611169.1 19119 D 292414 CDS YP_611170.1 99077911 4074870 complement(20354..21658) 1 NC_008042.1 PFAM: UDP-glucose/GDP-mannose dehydrogenase: (1.3e-54); KEGG: jan:Jann_0076 UDP-glucose 6-dehydrogenase, ev=0.0, 79% identity; UDP-glucose 6-dehydrogenase 21658 4074870 TM1040_3775 Ruegeria sp. TM1040 UDP-glucose 6-dehydrogenase YP_611170.1 20354 R 292414 CDS YP_611171.1 99077912 4074871 complement(22480..23481) 1 NC_008042.1 PFAM: NAD-dependent epimerase/dehydratase: (4.1e-55) 3-beta hydroxysteroid dehydrogenase/isomerase: (3e-06) dTDP-4-dehydrorhamnose reductase: (0.0013) Male sterility-like: (8.1e-07); KEGG: jan:Jann_0077 NAD-dependent epimerase/dehydratase, ev=1e-126, 67% identity; NAD-dependent epimerase/dehydratase 23481 4074871 TM1040_3776 Ruegeria sp. TM1040 NAD-dependent epimerase/dehydratase YP_611171.1 22480 R 292414 CDS YP_611172.1 99077913 4074872 complement(24265..24642) 1 NC_008042.1 PFAM: helix-turn-helix motif: (2e-07); KEGG: jan:Jann_1232 transcriptional regulator, XRE family, ev=2e-29, 54% identity; XRE family transcriptional regulator 24642 4074872 TM1040_3777 Ruegeria sp. TM1040 XRE family transcriptional regulator YP_611172.1 24265 R 292414 CDS YP_611173.1 99077914 4074873 complement(25175..26596) 1 NC_008042.1 KEGG: rsp:RSP_0834 mannose-6-phosphate isomerase / mannose-1-phosphate guanylyltransferase, ev=0.0, 66% identity; TIGRFAM: Mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase: (4.9e-192); PFAM: mannose-6-phosphate isomerase, type II: (8.6e-88) Nucleotidyl transferase: (2.4e-85) Cupin 2, conserved barrel: (1.3e-12); mannose-1-phosphate guanylyltransferase (GDP) 26596 4074873 TM1040_3778 Ruegeria sp. TM1040 mannose-1-phosphate guanylyltransferase (GDP) YP_611173.1 25175 R 292414 CDS YP_611174.1 99077915 4074874 27852..28736 1 NC_008042.1 PFAM: Domain of unknown function DUF1738: (4.4e-59); KEGG: jan:Jann_3213 antirestriction protein-like, ev=1e-116, 90% identity; hypothetical protein 28736 4074874 TM1040_3779 Ruegeria sp. TM1040 hypothetical protein YP_611174.1 27852 D 292414 CDS YP_611175.1 99077916 4074875 complement(29156..30001) 1 NC_008042.1 KEGG: jan:Jann_0647 hypothetical protein, ev=7e-82, 56% identity; hypothetical protein 30001 4074875 TM1040_3780 Ruegeria sp. TM1040 hypothetical protein YP_611175.1 29156 R 292414 CDS YP_611176.1 99077917 4074876 complement(30047..30502) 1 NC_008042.1 PFAM: Methionine sulfoxide reductase B: (4.5e-58); KEGG: sme:SMc01724 hypothetical protein, ev=8e-54, 61% identity; protein-methionine-S-oxide reductase 30502 4074876 TM1040_3781 Ruegeria sp. TM1040 protein-methionine-S-oxide reductase YP_611176.1 30047 R 292414 CDS YP_611177.1 99077918 4074877 complement(30573..31124) 1 NC_008042.1 PFAM: beta-Ig-H3/fasciclin: (2.9e-41); KEGG: mlo:mlr4813 similar to secreted protein MPB70 (and transforming growth factor-induced protein), ev=3e-56, 64% identity; beta-Ig-H3/fasciclin 31124 4074877 TM1040_3782 Ruegeria sp. TM1040 beta-Ig-H3/fasciclin YP_611177.1 30573 R 292414 CDS YP_611178.1 99077919 4074878 complement(31246..31932) 1 NC_008042.1 KEGG: jan:Jann_0649 hypothetical protein, ev=2e-42, 45% identity; hypothetical protein 31932 4074878 TM1040_3783 Ruegeria sp. TM1040 hypothetical protein YP_611178.1 31246 R 292414 CDS YP_611179.1 99077920 4074879 complement(31929..32483) 1 NC_008042.1 Bacteria have multiple sigma factors which are active under specific conditions; the sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; RNA polymerase sigma factor 32483 4074879 TM1040_3784 Ruegeria sp. TM1040 RNA polymerase sigma factor YP_611179.1 31929 R 292414 CDS YP_611180.1 99077921 4074880 33104..35482 1 NC_008042.1 PFAM: Hemolysin-type calcium-binding region: (0.0021); KEGG: sil:SPO1626 type I secretion target repeat protein, ev=5e-86, 32% identity; hemolysin-type calcium-binding region 35482 4074880 TM1040_3785 Ruegeria sp. TM1040 hemolysin-type calcium-binding region YP_611180.1 33104 D 292414 CDS YP_611181.1 99077922 4074881 35844..36596 1 NC_008042.1 hypothetical protein 36596 4074881 TM1040_3786 Ruegeria sp. TM1040 hypothetical protein YP_611181.1 35844 D 292414 CDS YP_611182.1 99077923 4074882 complement(37024..37380) 1 NC_008042.1 PFAM: nucleic acid binding, OB-fold, tRNA/helicase-type: (0.092); nucleic acid binding, OB-fold, tRNA/helicase-type 37380 4074882 TM1040_3787 Ruegeria sp. TM1040 nucleic acid binding, OB-fold, tRNA/helicase-type YP_611182.1 37024 R 292414 CDS YP_611183.1 99077924 4074883 37746..38255 1 NC_008042.1 KEGG: rsp:RSP_7254 hypothetical protein, ev=2e-23, 45% identity; hypothetical protein 38255 4074883 TM1040_3788 Ruegeria sp. TM1040 hypothetical protein YP_611183.1 37746 D 292414 CDS YP_611184.1 99077925 4074884 38357..38752 1 NC_008042.1 SMART: Staphylococcus nuclease (SNase-like): (3.9e-06); KEGG: jan:Jann_3714 nuclease (SNase-like), ev=3e-21, 46% identity; SNase-like nuclease 38752 4074884 TM1040_3789 Ruegeria sp. TM1040 SNase-like nuclease YP_611184.1 38357 D 292414 CDS YP_611185.1 99077926 4074885 39882..40088 1 NC_008042.1 hypothetical protein 40088 4074885 TM1040_3791 Ruegeria sp. TM1040 hypothetical protein YP_611185.1 39882 D 292414 CDS YP_611186.1 99077927 4074886 40650..41243 1 NC_008042.1 hypothetical protein 41243 4074886 TM1040_3792 Ruegeria sp. TM1040 hypothetical protein YP_611186.1 40650 D 292414 CDS YP_611187.1 99077928 4074887 41230..43440 1 NC_008042.1 PFAM: Relaxase/mobilization nuclease domain: (1.5e-05); KEGG: atc:AGR_pTi_21 T-DNA border endonuclease virD2, ev=1e-18, 33% identity; relaxase/mobilization nuclease domain-containing protein 43440 4074887 TM1040_3793 Ruegeria sp. TM1040 relaxase/mobilization nuclease domain-containing protein YP_611187.1 41230 D 292414 CDS YP_611188.1 99077929 4074888 43437..45443 1 NC_008042.1 PFAM: TRAG protein: (3.6e-71); KEGG: ret:RHE_PA00070 transport secretion system IV, VirD4 protein, ev=2e-77, 34% identity; TRAG protein 45443 4074888 TM1040_3794 Ruegeria sp. TM1040 TRAG protein YP_611188.1 43437 D 292414 CDS YP_611189.1 99077930 4074889 complement(45670..47667) 1 NC_008042.1 PFAM: ATP-binding region, ATPase-like: (5.1e-35) histidine kinase A-like: (2.1e-10); SMART: extracellular solute-binding protein, family 3: (7.6e-22); KEGG: rba:RB9418 signal-transducing histidine kinase, ev=1e-36, 29% identity; periplasmic sensor signal transduction histidine kinase 47667 4074889 TM1040_3795 Ruegeria sp. TM1040 periplasmic sensor signal transduction histidine kinase YP_611189.1 45670 R 292414 CDS YP_611190.1 99077931 4074947 complement(47907..48452) 1 NC_008042.1 hypothetical protein 48452 4074947 TM1040_3796 Ruegeria sp. TM1040 hypothetical protein YP_611190.1 47907 R 292414 CDS YP_611191.1 99077932 4074948 49911..51461 1 NC_008042.1 hypothetical protein 51461 4074948 TM1040_3797 Ruegeria sp. TM1040 hypothetical protein YP_611191.1 49911 D 292414 CDS YP_611192.1 99077933 4074949 52027..52281 1 NC_008042.1 hypothetical protein 52281 4074949 TM1040_3798 Ruegeria sp. TM1040 hypothetical protein YP_611192.1 52027 D 292414 CDS YP_611193.1 99077934 4074950 52469..53038 1 NC_008042.1 hypothetical protein 53038 4074950 TM1040_3799 Ruegeria sp. TM1040 hypothetical protein YP_611193.1 52469 D 292414 CDS YP_611194.1 99077935 4074951 53072..54244 1 NC_008042.1 PFAM: protein of unknown function DUF1625: (2.9e-40); KEGG: mlo:mll2895 hypothetical protein, ev=3e-77, 40% identity; hypothetical protein 54244 4074951 TM1040_3800 Ruegeria sp. TM1040 hypothetical protein YP_611194.1 53072 D 292414 CDS YP_611195.1 99077936 4074952 54278..54745 1 NC_008042.1 hypothetical protein 54745 4074952 TM1040_3801 Ruegeria sp. TM1040 hypothetical protein YP_611195.1 54278 D 292414 CDS YP_611196.1 99077937 4074953 54757..55578 1 NC_008042.1 hypothetical protein 55578 4074953 TM1040_3802 Ruegeria sp. TM1040 hypothetical protein YP_611196.1 54757 D 292414 CDS YP_611197.1 99077938 4074954 55589..56197 1 NC_008042.1 KEGG: sil:SPO3001 hypothetical protein, ev=4e-19, 34% identity; hypothetical protein 56197 4074954 TM1040_3803 Ruegeria sp. TM1040 hypothetical protein YP_611197.1 55589 D 292414 CDS YP_611198.1 99077939 4074955 56206..56622 1 NC_008042.1 hypothetical protein 56622 4074955 TM1040_3804 Ruegeria sp. TM1040 hypothetical protein YP_611198.1 56206 D 292414 CDS YP_611199.1 99077940 4074956 56625..57533 1 NC_008042.1 hypothetical protein 57533 4074956 TM1040_3805 Ruegeria sp. TM1040 hypothetical protein YP_611199.1 56625 D 292414 CDS YP_611200.1 99077941 4074957 57539..58570 1 NC_008042.1 hypothetical protein 58570 4074957 TM1040_3806 Ruegeria sp. TM1040 hypothetical protein YP_611200.1 57539 D 292414 CDS YP_611201.1 99077942 4074958 58658..59440 1 NC_008042.1 hypothetical protein 59440 4074958 TM1040_3807 Ruegeria sp. TM1040 hypothetical protein YP_611201.1 58658 D 292414 CDS YP_611202.1 99077943 4074959 59718..60518 1 NC_008042.1 PFAM: regulatory protein, LuxR: (5.9e-05); LuxR family transcriptional regulator 60518 4074959 TM1040_3808 Ruegeria sp. TM1040 LuxR family transcriptional regulator YP_611202.1 59718 D 292414 CDS YP_611203.1 99077944 4074960 complement(60669..61748) 1 NC_008042.1 PFAM: TrbL/VirB6 plasmid conjugal transfer protein: (3.9e-10); KEGG: lpn:lpg1250 LvhB6, ev=1e-12, 27% identity; TrbL/VirB6 plasmid conjugal transfer protein 61748 4074960 TM1040_3809 Ruegeria sp. TM1040 TrbL/VirB6 plasmid conjugal transfer protein YP_611203.1 60669 R 292414 CDS YP_611204.1 99077945 4074961 complement(61761..62174) 1 NC_008042.1 hypothetical protein 62174 4074961 TM1040_3810 Ruegeria sp. TM1040 hypothetical protein YP_611204.1 61761 R 292414 CDS YP_611205.1 99077946 4074962 complement(62171..62365) 1 NC_008042.1 hypothetical protein 62365 4074962 TM1040_3811 Ruegeria sp. TM1040 hypothetical protein YP_611205.1 62171 R 292414 CDS YP_611206.1 99077947 4074963 complement(62362..63348) 1 NC_008042.1 PFAM: type II secretion system protein E: (3.9e-47); KEGG: ama:AM1313 VirB11 protein, ev=4e-45, 36% identity; type II secretion system protein E 63348 4074963 TM1040_3812 Ruegeria sp. TM1040 type II secretion system protein E YP_611206.1 62362 R 292414 CDS YP_611207.1 99077948 4074964 complement(63353..64732) 1 NC_008042.1 PFAM: conjugation TrbI-like protein: (1.2e-61); KEGG: mlo:mlr9259 conjugal transfer protein, ev=3e-38, 36% identity; conjugation TrbI-like protein 64732 4074964 TM1040_3813 Ruegeria sp. TM1040 conjugation TrbI-like protein YP_611207.1 63353 R 292414 CDS YP_611208.1 99077949 4074965 complement(64729..65424) 1 NC_008042.1 PFAM: Conjugal transfer protein TrbG/VirB9/CagX: (2.8e-41); KEGG: mlo:mlr9258 conjugal transfer protein, trbG, ev=3e-25, 32% identity; conjugal transfer protein TrbG/VirB9/CagX 65424 4074965 TM1040_3814 Ruegeria sp. TM1040 conjugal transfer protein TrbG/VirB9/CagX YP_611208.1 64729 R 292414 CDS YP_611209.1 99077950 4074966 complement(65427..66080) 1 NC_008042.1 PFAM: VirB8: (7.9e-10); KEGG: atc:AGR_pAT_228 virB8 type IV secretion protein, ev=7e-11, 26% identity; VirB8 66080 4074966 TM1040_3815 Ruegeria sp. TM1040 VirB8 YP_611209.1 65427 R 292414 CDS YP_611210.1 99077951 4074967 complement(66097..66906) 1 NC_008042.1 KEGG: xoo:XOO0603 TraF protein, ev=7e-07, 24% identity; hypothetical protein 66906 4074967 TM1040_3816 Ruegeria sp. TM1040 hypothetical protein YP_611210.1 66097 R 292414 CDS YP_611211.1 99077952 4074968 complement(66906..68060) 1 NC_008042.1 PFAM: Lytic transglycosylase, catalytic: (7.1e-19); KEGG: bsu:BG13596 similar to lytic transglycosylase, ev=1e-26, 57% identity; lytic transglycosylase, catalytic 68060 4074968 TM1040_3817 Ruegeria sp. TM1040 lytic transglycosylase, catalytic YP_611211.1 66906 R 292414 CDS YP_611212.1 99077953 4074969 complement(68050..68217) 1 NC_008042.1 hypothetical protein 68217 4074969 TM1040_3818 Ruegeria sp. TM1040 hypothetical protein YP_611212.1 68050 R 292414 CDS YP_611213.1 99077954 4074970 complement(68214..70589) 1 NC_008042.1 PFAM: CagE, TrbE, VirB component of type IV transporter system: (3.2e-19); SMART: ATPase: (1.2e-07); KEGG: ccr:CC2419 type IV secretion system protein B4, putative, ev=1e-100, 34% identity; CagE, TrbE, VirB component of type IV transporter system 70589 4074970 TM1040_3819 Ruegeria sp. TM1040 CagE, TrbE, VirB component of type IV transporter system YP_611213.1 68214 R 292414 CDS YP_611214.1 99077955 4074971 complement(70579..70824) 1 NC_008042.1 PFAM: type IV secretory pathway, VirB3-like: (2.2e-09); type IV secretory pathway, VirB3-like 70824 4074971 TM1040_3820 Ruegeria sp. TM1040 type IV secretory pathway, VirB3-like YP_611214.1 70579 R 292414 CDS YP_611215.1 99077956 4074972 complement(70850..71143) 1 NC_008042.1 PFAM: VIRB2 type IV secretion: (7.3e-06); KEGG: atc:AGR_pAT_220 type IV secretion system protein VirB2, ev=1e-09, 36% identity; VIRB2 type IV secretion 71143 4074972 TM1040_3821 Ruegeria sp. TM1040 VIRB2 type IV secretion YP_611215.1 70850 R 292414 CDS YP_611216.1 99077957 4074973 complement(71140..71754) 1 NC_008042.1 PFAM: Lytic transglycosylase, catalytic: (2.9e-17); KEGG: mta:Moth_1608 lytic transglycosylase, catalytic, ev=1e-24, 41% identity; lytic transglycosylase, catalytic 71754 4074973 TM1040_3822 Ruegeria sp. TM1040 lytic transglycosylase, catalytic YP_611216.1 71140 R 292414 CDS YP_611217.1 99077958 4074974 complement(71798..72151) 1 NC_008042.1 hypothetical protein 72151 4074974 TM1040_3823 Ruegeria sp. TM1040 hypothetical protein YP_611217.1 71798 R 292414 CDS YP_611218.1 99077959 4074975 72319..72615 1 NC_008042.1 hypothetical protein 72615 4074975 TM1040_3824 Ruegeria sp. TM1040 hypothetical protein YP_611218.1 72319 D 292414 CDS YP_611219.1 99077960 4074976 72863..73168 1 NC_008042.1 hypothetical protein 73168 4074976 TM1040_3825 Ruegeria sp. TM1040 hypothetical protein YP_611219.1 72863 D 292414 CDS YP_611220.1 99077961 4074977 73161..73388 1 NC_008042.1 hypothetical protein 73388 4074977 TM1040_3826 Ruegeria sp. TM1040 hypothetical protein YP_611220.1 73161 D 292414 CDS YP_611221.1 99077962 4074978 complement(73530..73781) 1 NC_008042.1 hypothetical protein 73781 4074978 TM1040_3827 Ruegeria sp. TM1040 hypothetical protein YP_611221.1 73530 R 292414 CDS YP_611222.1 99077963 4074979 complement(73771..74475) 1 NC_008042.1 PFAM: short-chain dehydrogenase/reductase SDR: (1.8e-07); KEGG: sme:SMc00136 putative oxidoreductase protein, ev=1e-95, 69% identity; short-chain dehydrogenase/reductase SDR 74475 4074979 TM1040_3828 Ruegeria sp. TM1040 short-chain dehydrogenase/reductase SDR YP_611222.1 73771 R 292414 CDS YP_611223.1 99077964 4074980 74574..75452 1 NC_008042.1 PFAM: regulatory protein, LysR: (3e-16) LysR, substrate-binding: (1e-25); KEGG: mlo:mlr1832 probable transcriptional regulator, ev=7e-75, 51% identity; LysR family transcriptional regulator 75452 4074980 TM1040_3829 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_611223.1 74574 D 292414 CDS YP_611224.1 99077965 4074981 complement(75610..76341) 1 NC_008042.1 hypothetical protein 76341 4074981 TM1040_3830 Ruegeria sp. TM1040 hypothetical protein YP_611224.1 75610 R 292414 CDS YP_611225.1 99077966 4074982 76954..78234 1 NC_008042.1 PFAM: glycosyl transferase, group 1: (5.6e-23); KEGG: ctc:CTC00268 mannosyltransferase, ev=2e-21, 26% identity; glycosyl transferase, group 1 78234 4074982 TM1040_3832 Ruegeria sp. TM1040 glycosyl transferase, group 1 YP_611225.1 76954 D 292414 CDS YP_611226.1 99077967 4074983 complement(78296..79729) 1 NC_008042.1 PFAM: glycosyl transferase, group 1: (0.00036); KEGG: jan:Jann_2029 glycosyl transferase, group 1, ev=7e-59, 47% identity; glycosyl transferase, group 1 79729 4074983 TM1040_3833 Ruegeria sp. TM1040 glycosyl transferase, group 1 YP_611226.1 78296 R 292414 CDS YP_611227.1 99077968 4074984 complement(79812..81131) 1 NC_008042.1 TIGRFAM: Type I secretion membrane fusion protein, HlyD: (2.4e-112); PFAM: secretion protein HlyD: (8.3e-33); KEGG: rru:Rru_B0040 type I secretion membrane fusion protein, HlyD, ev=3e-78, 39% identity; Type I secretion membrane fusion protein, HlyD 81131 4074984 TM1040_3834 Ruegeria sp. TM1040 Type I secretion membrane fusion protein, HlyD YP_611227.1 79812 R 292414 CDS YP_611228.1 99077969 4074985 complement(81194..82906) 1 NC_008042.1 KEGG: rru:Rru_B0039 type I secretion system ATPase, PrtD, ev=1e-152, 50% identity; TIGRFAM: Type I secretion system ATPase, PrtD: (7.7e-257); PFAM: ABC transporter, transmembrane region: (3.5e-12) ABC transporter related: (1.5e-59); SMART: ATPase: (1.8e-19); Type I secretion system ATPase, PrtD 82906 4074985 TM1040_3835 Ruegeria sp. TM1040 Type I secretion system ATPase, PrtD YP_611228.1 81194 R 292414 CDS YP_611229.1 99077970 4074900 83259..83615 1 NC_008042.1 hypothetical protein 83615 4074900 TM1040_3836 Ruegeria sp. TM1040 hypothetical protein YP_611229.1 83259 D 292414 CDS YP_611230.1 99077971 4074901 complement(84226..84423) 1 NC_008042.1 KEGG: rru:Rru_B0036 hypothetical protein, ev=1e-06, 45% identity; hypothetical protein 84423 4074901 TM1040_3838 Ruegeria sp. TM1040 hypothetical protein YP_611230.1 84226 R 292414 CDS YP_611231.1 99077972 4074902 complement(84443..85978) 1 NC_008042.1 PFAM: Methyltransferase type 11: (0.00031); KEGG: ccr:CC1017 hypothetical protein, ev=1e-152, 51% identity; methyltransferase type 11 85978 4074902 TM1040_3839 Ruegeria sp. TM1040 methyltransferase type 11 YP_611231.1 84443 R 292414 CDS YP_611232.1 99077973 4074903 complement(86070..89351) 1 NC_008042.1 PFAM: Hemolysin-type calcium-binding region: (0.97); KEGG: tdn:Tmden_1726 hemolysin-type calcium-binding region, ev=1e-125, 33% identity; hemolysin-type calcium-binding region 89351 4074903 TM1040_3840 Ruegeria sp. TM1040 hemolysin-type calcium-binding region YP_611232.1 86070 R 292414 CDS YP_611233.1 99077974 4074904 89417..89767 1 NC_008042.1 hypothetical protein 89767 4074904 TM1040_3841 Ruegeria sp. TM1040 hypothetical protein YP_611233.1 89417 D 292414 CDS YP_611234.1 99077975 4074905 90028..90330 1 NC_008042.1 PFAM: helix-turn-helix motif: (1.4e-07); KEGG: ccr:CC1006 transcriptional regulator, Cro/CI family, ev=8e-25, 57% identity; XRE family transcriptional regulator 90330 4074905 TM1040_3842 Ruegeria sp. TM1040 XRE family transcriptional regulator YP_611234.1 90028 D 292414 CDS YP_611235.1 99077976 4074906 90406..92100 1 NC_008042.1 KEGG: ccr:CC1005 hypothetical protein, ev=8e-14, 22% identity; hypothetical protein 92100 4074906 TM1040_3843 Ruegeria sp. TM1040 hypothetical protein YP_611235.1 90406 D 292414 CDS YP_611236.1 99077977 4074907 complement(92309..93592) 1 NC_008042.1 KEGG: ccr:CC1003 glyscosyl transferase, group 1 family protein, ev=6e-23, 27% identity; hypothetical protein 93592 4074907 TM1040_3844 Ruegeria sp. TM1040 hypothetical protein YP_611236.1 92309 R 292414 CDS YP_611237.1 99077978 4074908 complement(93592..96000) 1 NC_008042.1 PFAM: glycosyl transferase, group 1: (5.4e-26) Methyltransferase type 11: (3.3e-08); KEGG: syf:Synpcc7942_1902 putative glycosyltransferase, ev=2e-57, 36% identity; glycosyl transferase, group 1 96000 4074908 TM1040_3845 Ruegeria sp. TM1040 glycosyl transferase, group 1 YP_611237.1 93592 R 292414 CDS YP_611238.1 99077979 4074909 complement(96000..97055) 1 NC_008042.1 PFAM: Methyltransferase type 11: (1.9e-12) Methyltransferase type 12: (3.1e-09); KEGG: psp:PSPPH_0956 WbbD, ev=2e-36, 41% identity; methyltransferase type 11 97055 4074909 TM1040_3846 Ruegeria sp. TM1040 methyltransferase type 11 YP_611238.1 96000 R 292414 CDS YP_611239.1 99077980 4074910 complement(97529..100117) 1 NC_008042.1 PFAM: peptidase S8 and S53, subtilisin, kexin, sedolisin: (2.1e-45) Hemolysin-type calcium-binding region: (1.7) Proprotein convertase, P: (2.3e-10); KEGG: ana:all0364 similar to prohormone convertase, ev=1e-106, 39% identity; peptidase S8/S53 subtilisin kexin sedolisin 100117 4074910 TM1040_3847 Ruegeria sp. TM1040 peptidase S8/S53 subtilisin kexin sedolisin YP_611239.1 97529 R 292414 CDS YP_611240.1 99077981 4074911 complement(100442..102199) 1 NC_008042.1 PFAM: ABC transporter, transmembrane region: (4.8e-22) ABC transporter related: (5.6e-57); SMART: ATPase: (4.1e-19); KEGG: atc:AGR_L_552 probable ABC transporter ATP-binding protein Y4GM, ev=1e-157, 51% identity; ABC transporter related 102199 4074911 TM1040_3848 Ruegeria sp. TM1040 ABC transporter related YP_611240.1 100442 R 292414 CDS YP_611241.1 99077982 4074912 complement(102308..102607) 1 NC_008042.1 hypothetical protein 102607 4074912 TM1040_3849 Ruegeria sp. TM1040 hypothetical protein YP_611241.1 102308 R 292414 CDS YP_611242.1 99077983 4074913 complement(102774..103088) 1 NC_008042.1 hypothetical protein 103088 4074913 TM1040_3850 Ruegeria sp. TM1040 hypothetical protein YP_611242.1 102774 R 292414 CDS YP_611243.1 99077984 4074914 103394..103981 1 NC_008042.1 KEGG: sil:SPO0081 hypothetical protein, ev=2e-27, 34% identity; hypothetical protein 103981 4074914 TM1040_3851 Ruegeria sp. TM1040 hypothetical protein YP_611243.1 103394 D 292414 CDS YP_611244.1 99077985 4074915 complement(104093..104719) 1 NC_008042.1 hypothetical protein 104719 4074915 TM1040_3852 Ruegeria sp. TM1040 hypothetical protein YP_611244.1 104093 R 292414 CDS YP_611245.1 99077986 4074916 complement(105732..105923) 1 NC_008042.1 KEGG: rru:Rru_B0036 hypothetical protein, ev=2e-10, 55% identity; hypothetical protein 105923 4074916 TM1040_3853 Ruegeria sp. TM1040 hypothetical protein YP_611245.1 105732 R 292414 CDS YP_611246.1 99077987 4074917 complement(106169..107140) 1 NC_008042.1 KEGG: sil:SPO0082 arabinose 5-phosphate isomerase, ev=8e-97, 60% identity; TIGRFAM: KpsF/GutQ family protein: (8.2e-118); PFAM: CBS: (5.1e-22) sugar isomerase (SIS): (9.7e-33); KpsF/GutQ family protein 107140 4074917 TM1040_3854 Ruegeria sp. TM1040 KpsF/GutQ family protein YP_611246.1 106169 R 292414 CDS YP_611247.1 99077988 4074918 107450..107809 1 NC_008042.1 PFAM: DGPFAETKE: (2.2e-37); KEGG: rba:RB560 hypothetical protein, ev=2e-21, 46% identity; hypothetical protein 107809 4074918 TM1040_3855 Ruegeria sp. TM1040 hypothetical protein YP_611247.1 107450 D 292414 CDS YP_611248.1 99077989 4074919 107815..109062 1 NC_008042.1 PFAM: sigma-70 region 2: (2.9e-08) Sigma-70, region 4 type 2: (7.9e-08); KEGG: sma:SAV1195 putative RNA polymerase ECF-subfamily sigma factor, ev=2e-76, 44% identity; RNA polymerase ECF-subfamily sigma factor 109062 4074919 TM1040_3856 Ruegeria sp. TM1040 RNA polymerase ECF-subfamily sigma factor YP_611248.1 107815 D 292414 CDS YP_611249.1 99077990 4074920 109117..109884 1 NC_008042.1 KEGG: cvi:CV0374 hypothetical protein, ev=4e-36, 35% identity; hypothetical protein 109884 4074920 TM1040_3857 Ruegeria sp. TM1040 hypothetical protein YP_611249.1 109117 D 292414 CDS YP_611250.1 99077991 4074921 complement(109942..111195) 1 NC_008042.1 PFAM: glycosyl transferase, group 1: (1.7e-16); KEGG: jan:Jann_0078 glycosyl transferase, group 1, ev=1e-152, 63% identity; glycosyl transferase, group 1 111195 4074921 TM1040_3858 Ruegeria sp. TM1040 glycosyl transferase, group 1 YP_611250.1 109942 R 292414 CDS YP_611251.1 99077992 4074922 complement(111206..112078) 1 NC_008042.1 TIGRFAM: glucose-1-phosphate thymidylyltransferase: (9.4e-165); PFAM: Nucleotidyl transferase: (4.1e-106); KEGG: jan:Jann_3841 glucose-1-phosphate thymidylyltransferase, ev=1e-124, 77% identity; glucose-1-phosphate thymidylyltransferase 112078 4074922 TM1040_3859 Ruegeria sp. TM1040 glucose-1-phosphate thymidylyltransferase YP_611251.1 111206 R 292414 CDS YP_611252.1 99077993 4074923 complement(112075..112974) 1 NC_008042.1 PFAM: NAD-dependent epimerase/dehydratase: (1.7e-11) polysaccharide biosynthesis protein CapD: (0.0038) dTDP-4-dehydrorhamnose reductase: (4.9e-136) Male sterility-like: (0.00025); KEGG: jan:Jann_3842 dTDP-4-dehydrorhamnose reductase, ev=2e-90, 61% identity; dTDP-4-dehydrorhamnose reductase 112974 4074923 TM1040_3860 Ruegeria sp. TM1040 dTDP-4-dehydrorhamnose reductase YP_611252.1 112075 R 292414 CDS YP_611253.1 99077994 4074924 complement(112986..114038) 1 NC_008042.1 TIGRFAM: dTDP-glucose 4,6-dehydratase: (1.1e-216); PFAM: NAD-dependent epimerase/dehydratase: (3e-96) short-chain dehydrogenase/reductase SDR: (4e-05) 3-beta hydroxysteroid dehydrogenase/isomerase: (3.9e-09) polysaccharide biosynthesis protein CapD: (2.7e-05) dTDP-4-dehydrorhamnose reductase: (1.7e-07) Male sterility-like: (2.5e-08); KEGG: jan:Jann_3843 dTDP-glucose 4,6-dehydratase, ev=1e-150, 72% identity; dTDP-glucose 4,6-dehydratase 114038 4074924 TM1040_3861 Ruegeria sp. TM1040 dTDP-glucose 4,6-dehydratase YP_611253.1 112986 R 292414 CDS YP_611254.1 99077995 4074925 complement(114096..115220) 1 NC_008042.1 PFAM: acyltransferase 3: (7.7e-36); KEGG: ade:Adeh_1161 acyltransferase 3, ev=2e-46, 36% identity; acyltransferase 3 115220 4074925 TM1040_3862 Ruegeria sp. TM1040 acyltransferase 3 YP_611254.1 114096 R 292414 CDS YP_611255.1 99077996 4074926 complement(115225..115773) 1 NC_008042.1 KEGG: jan:Jann_3844 dTDP-4-dehydrorhamnose 3,5-epimerase, ev=1e-69, 63% identity; TIGRFAM: dTDP-4-dehydrorhamnose 3,5-epimerase: (2.3e-77); PFAM: dTDP-4-dehydrorhamnose 3,5-epimerase related: (2.4e-95); dTDP-4-dehydrorhamnose 3,5-epimerase 115773 4074926 TM1040_3863 Ruegeria sp. TM1040 dTDP-4-dehydrorhamnose 3,5-epimerase YP_611255.1 115225 R 292414 CDS YP_611256.1 99077997 4074927 complement(116076..116963) 1 NC_008042.1 PFAM: PfkB: (4e-38); KEGG: jan:Jann_2574 PfkB, ev=3e-69, 51% identity; 2-keto-3-deoxygluconate kinase 116963 4074927 TM1040_3864 Ruegeria sp. TM1040 2-keto-3-deoxygluconate kinase YP_611256.1 116076 R 292414 CDS YP_611257.1 99077998 4074928 complement(116963..118360) 1 NC_008042.1 catalyzes the interconversion of D-glucuronate to D-fructuronate or D-galacturonate to D-tagaturonate; functions in glucuronic and galacturonic metabolism; glucuronate isomerase 118360 4074928 TM1040_3865 Ruegeria sp. TM1040 glucuronate isomerase YP_611257.1 116963 R 292414 CDS YP_611258.1 99077999 4074929 complement(118357..119772) 1 NC_008042.1 PFAM: Mannitol dehydrogenase-like: (1.3e-74) Mannitol dehydrogenase rossman-like: (3e-32); KEGG: spt:SPA1347 putative mannitol dehydrogenase, ev=6e-94, 41% identity; fructuronate reductase 119772 4074929 TM1040_3866 Ruegeria sp. TM1040 fructuronate reductase YP_611258.1 118357 R 292414 CDS YP_611259.1 99078000 4074930 complement(119769..122123) 1 NC_008042.1 PFAM: glycoside hydrolase, family 31: (1.1e-156); KEGG: ypm:YP3545 putative glucosidase, ev=0.0, 55% identity; Alpha-glucosidase 122123 4074930 TM1040_3867 Ruegeria sp. TM1040 Alpha-glucosidase YP_611259.1 119769 R 292414 CDS YP_611260.1 99078001 4074931 complement(122123..123424) 1 NC_008042.1 TIGRFAM: TRAP dicarboxylate transporter- DctM subunit: (1.3e-178); PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit: (5.2e-157); KEGG: vpa:VPA1704 putative integral membrane protein, possible transporter, ev=1e-170, 69% identity; TRAP dicarboxylate transporter- DctM subunit 123424 4074931 TM1040_3868 Ruegeria sp. TM1040 TRAP dicarboxylate transporter- DctM subunit YP_611260.1 122123 R 292414 CDS YP_611261.1 99078002 4074932 complement(123436..123951) 1 NC_008042.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component: (4.7e-29); KEGG: vpa:VPA1703 putative small integral C4-dicarboxylate membrane transport protein, ev=3e-42, 55% identity; tripartite ATP-independent periplasmic transporter DctQ 123951 4074932 TM1040_3869 Ruegeria sp. TM1040 tripartite ATP-independent periplasmic transporter DctQ YP_611261.1 123436 R 292414 CDS YP_611262.1 99078003 4074933 124211..125185 1 NC_008042.1 TIGRFAM: TRAP dicarboxylate transporter, DctP subunit: (5.3e-68); PFAM: TRAP dicarboxylate transporter- DctP subunit: (1.4e-79); KEGG: vvy:VVA1590 TRAP-type C4-dicarboxylate transport system, periplasmic component, ev=4e-95, 56% identity; TRAP dicarboxylate transporter, DctP subunit 125185 4074933 TM1040_3870 Ruegeria sp. TM1040 TRAP dicarboxylate transporter, DctP subunit YP_611262.1 124211 D 292414 CDS YP_611263.1 99078004 4074934 125204..127015 1 NC_008042.1 PFAM: glycoside hydrolase family 2, immunoglobulin-like beta-sandwich: (0.011) glycoside hydrolase family 2, TIM barrel: (3.2e-13) glycoside hydrolase family 2, sugar binding: (1.7e-30); KEGG: sso:SSO3036 beta-glucuronidase, ev=2e-54, 29% identity; Beta-glucuronidase 127015 4074934 TM1040_3871 Ruegeria sp. TM1040 Beta-glucuronidase YP_611263.1 125204 D 292414 CDS YP_611264.1 99078005 4074935 127012..127743 1 NC_008042.1 PFAM: regulatory protein GntR, HTH: (3.9e-20) GntR-like: (2.2e-32); KEGG: vpa:VPA1701 putative transcriptional regulatory protein, ev=2e-72, 57% identity; GntR family transcriptional regulator 127743 4074935 TM1040_3872 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_611264.1 127012 D 292414 CDS YP_611265.1 99078006 4074936 127810..128979 1 NC_008042.1 catalyzes the formation of 2-dehydro-3-deoxy-D-gluconate from mannonate; mannonate dehydratase 128979 4074936 TM1040_3873 Ruegeria sp. TM1040 mannonate dehydratase YP_611265.1 127810 D 292414 CDS YP_611266.1 99078007 4074937 complement(129842..130435) 1 NC_008042.1 hypothetical protein 130435 4074937 TM1040_3874 Ruegeria sp. TM1040 hypothetical protein YP_611266.1 129842 R 292414 CDS YP_611267.1 99078008 4074938 complement(130436..130963) 1 NC_008042.1 hypothetical protein 130963 4074938 TM1040_3875 Ruegeria sp. TM1040 hypothetical protein YP_611267.1 130436 R 292414 CDS YP_611268.1 99078010 4075737 6..827 1 NC_008043.1 KEGG: sil:SPO1791 sulfate/tungstate uptake family ABC transporter, periplasmic substrate-binding protein, ev=4e-45, 66% identity; sulfate/tungstate ABC transporter periplasmic substrate-binding protein 827 4075737 TM1040_3032 Ruegeria sp. TM1040 sulfate/tungstate ABC transporter periplasmic substrate-binding protein YP_611268.1 6 D 292414 CDS YP_611269.1 99078011 4075738 855..1769 1 NC_008043.1 TIGRFAM: Excisionase/Xis, DNA-binding: (5.5e-07); KEGG: mag:amb2274 periplasmic molybdate-binding protein/domain, ev=8e-51, 39% identity; excisionase/Xis, DNA-binding 1769 4075738 TM1040_3033 Ruegeria sp. TM1040 excisionase/Xis, DNA-binding YP_611269.1 855 D 292414 CDS YP_611270.1 99078012 4075739 complement(1785..2594) 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1.4e-19); KEGG: sil:SPO3618 sulfonate ABC transporter, permease protein, , ev=1e-112, 80% identity; binding-protein-dependent transport system inner membrane protein 2594 4075739 TM1040_3034 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_611270.1 1785 R 292414 CDS YP_611271.1 99078013 4075740 complement(2587..3354) 1 NC_008043.1 PFAM: ABC transporter related: (3.8e-50); SMART: ATPase: (4.1e-17); KEGG: bms:BRA0468 ABC transporter, ATP-binding protein, ev=1e-105, 73% identity; ABC transporter 3354 4075740 TM1040_3035 Ruegeria sp. TM1040 ABC transporter YP_611271.1 2587 R 292414 CDS YP_611272.1 99078014 4075741 complement(3409..4425) 1 NC_008043.1 KEGG: sil:SPO3620 sulfonate ABC transporter, periplamic sulfonate-binding protein, ev=1e-119, 66% identity; sulfonate ABC transporter, periplamic sulfonate-binding protein 4425 4075741 TM1040_3036 Ruegeria sp. TM1040 sulfonate ABC transporter, periplamic sulfonate-binding protein YP_611272.1 3409 R 292414 CDS YP_611273.1 99078015 4075742 complement(4480..5145) 1 NC_008043.1 PFAM: regulatory protein GntR, HTH: (1.2e-13); KEGG: jan:Jann_4140 transcriptional regulator, GntR family, ev=2e-27, 37% identity; GntR family transcriptional regulator 5145 4075742 TM1040_3037 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_611273.1 4480 R 292414 CDS YP_611274.1 99078016 4075743 5407..6159 1 NC_008043.1 PFAM: extracellular solute-binding protein, family 3: (1.9e-74); KEGG: ppr:PBPRA0007 amino acid ABC transporter, periplasmic amino acid-binding portion, ev=6e-74, 57% identity; extracellular solute-binding protein 6159 4075743 TM1040_3038 Ruegeria sp. TM1040 extracellular solute-binding protein YP_611274.1 5407 D 292414 CDS YP_611275.1 99078017 4075133 6188..6838 1 NC_008043.1 TIGRFAM: Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine: (3e-25); PFAM: binding-protein-dependent transport systems inner membrane component: (4.1e-22); KEGG: vch:VC0009 polar amino acid transport system permease protein, ev=6e-68, 62% identity; amino acid ABC transporter permease 6838 4075133 TM1040_3039 Ruegeria sp. TM1040 amino acid ABC transporter permease YP_611275.1 6188 D 292414 CDS YP_611276.1 99078018 4075134 6835..7581 1 NC_008043.1 PFAM: ABC transporter related: (9.1e-62); SMART: ATPase: (1.9e-19); KEGG: vch:VC0008 polar amino acid transport system ATP-binding protein, ev=4e-85, 65% identity; ABC transporter 7581 4075134 TM1040_3040 Ruegeria sp. TM1040 ABC transporter YP_611276.1 6835 D 292414 CDS YP_611277.1 99078019 4075135 8058..11189 1 NC_008043.1 PFAM: Hemolysin-type calcium-binding region: (0.00069); KEGG: sil:SPO1626 type I secretion target repeat protein, ev=1e-109, 31% identity; hemolysin-type calcium-binding region 11189 4075135 TM1040_3041 Ruegeria sp. TM1040 hemolysin-type calcium-binding region YP_611277.1 8058 D 292414 CDS YP_611278.1 99078020 4075136 complement(11228..12154) 1 NC_008043.1 PFAM: PfkB: (1.8e-27); KEGG: jan:Jann_2674 PfkB, ev=2e-95, 59% identity; PfkB protein 12154 4075136 TM1040_3042 Ruegeria sp. TM1040 PfkB protein YP_611278.1 11228 R 292414 CDS YP_611279.1 99078021 4075137 12814..13383 1 NC_008043.1 hypothetical protein 13383 4075137 TM1040_3043 Ruegeria sp. TM1040 hypothetical protein YP_611279.1 12814 D 292414 CDS YP_611280.1 99078022 4075138 13418..14599 1 NC_008043.1 PFAM: protein of unknown function DUF1625: (2.9e-35); KEGG: mlo:mll2895 hypothetical protein, ev=2e-63, 35% identity; hypothetical protein 14599 4075138 TM1040_3044 Ruegeria sp. TM1040 hypothetical protein YP_611280.1 13418 D 292414 CDS YP_611281.1 99078023 4075139 14630..15097 1 NC_008043.1 hypothetical protein 15097 4075139 TM1040_3045 Ruegeria sp. TM1040 hypothetical protein YP_611281.1 14630 D 292414 CDS YP_611282.1 99078024 4075140 15109..15927 1 NC_008043.1 hypothetical protein 15927 4075140 TM1040_3046 Ruegeria sp. TM1040 hypothetical protein YP_611282.1 15109 D 292414 CDS YP_611283.1 99078025 4075141 15929..16912 1 NC_008043.1 hypothetical protein 16912 4075141 TM1040_3047 Ruegeria sp. TM1040 hypothetical protein YP_611283.1 15929 D 292414 CDS YP_611284.1 99078026 4075142 complement(16974..17483) 1 NC_008043.1 KEGG: ppu:PP2506 hypothetical protein, ev=1e-08, 30% identity; hypothetical protein 17483 4075142 TM1040_3048 Ruegeria sp. TM1040 hypothetical protein YP_611284.1 16974 R 292414 CDS YP_611285.1 99078027 4075143 complement(17544..19208) 1 NC_008043.1 TIGRFAM: Twin-arginine translocation pathway signal: (0.0035); PFAM: extracellular solute-binding protein, family 5: (5.2e-44); KEGG: sil:SPO3049 dipeptide ABC transporter, periplasmic dipeptide-binding protein, ev=0.0, 56% identity; twin-arginine translocation pathway signal 19208 4075143 TM1040_3049 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_611285.1 17544 R 292414 CDS YP_611286.1 99078028 4075144 complement(19304..20188) 1 NC_008043.1 PFAM: Taurine catabolism dioxygenase TauD/TfdA: (1.8e-54); KEGG: mpa:MAP0238c alpha-ketoglutarate-dependent 2,4-dichlorophenoxyacetate dioxygenase, ev=1e-57, 40% identity; taurine catabolism dioxygenase TauD/TfdA 20188 4075144 TM1040_3050 Ruegeria sp. TM1040 taurine catabolism dioxygenase TauD/TfdA YP_611286.1 19304 R 292414 CDS YP_611287.1 99078029 4075145 complement(20200..21609) 1 NC_008043.1 PFAM: FAD linked oxidase-like: (6.9e-27); KEGG: ret:RHE_CH02042 FAD linked oxidase protein, ev=1e-88, 39% identity; FAD linked oxidase-like protein 21609 4075145 TM1040_3051 Ruegeria sp. TM1040 FAD linked oxidase-like protein YP_611287.1 20200 R 292414 CDS YP_611288.1 99078030 4075146 complement(21606..22877) 1 NC_008043.1 PFAM: amidohydrolase: (0.00015) Amidohydrolase 3: (0.00056); KEGG: jan:Jann_1474 amidohydrolase 3, ev=2e-43, 32% identity; amidohydrolase 22877 4075146 TM1040_3052 Ruegeria sp. TM1040 amidohydrolase YP_611288.1 21606 R 292414 CDS YP_611289.1 99078031 4075147 complement(22874..23665) 1 NC_008043.1 PFAM: Creatininase: (4.9e-29); KEGG: mlo:mlr1298 creatinine amidohydrolase, , ev=6e-46, 39% identity; creatininase 23665 4075147 TM1040_3053 Ruegeria sp. TM1040 creatininase YP_611289.1 22874 R 292414 CDS YP_611290.1 99078032 4075148 complement(23662..24357) 1 NC_008043.1 KEGG: sme:SMc03236 glutamine amidotransferase, ev=4e-30, 34% identity; glutamine amidotransferase 24357 4075148 TM1040_3054 Ruegeria sp. TM1040 glutamine amidotransferase YP_611290.1 23662 R 292414 CDS YP_611291.1 99078033 4075149 24485..24871 1 NC_008043.1 PFAM: Endoribonuclease L-PSP: (3.1e-10); KEGG: jan:Jann_1470 endoribonuclease L-PSP, ev=7e-34, 56% identity; endoribonuclease L-PSP 24871 4075149 TM1040_3055 Ruegeria sp. TM1040 endoribonuclease L-PSP YP_611291.1 24485 D 292414 CDS YP_611292.1 99078034 4075150 complement(25025..25267) 1 NC_008043.1 hypothetical protein 25267 4075150 TM1040_3056 Ruegeria sp. TM1040 hypothetical protein YP_611292.1 25025 R 292414 CDS YP_611293.1 99078035 4075151 complement(25251..25712) 1 NC_008043.1 KEGG: sil:SPO0300 hypothetical protein, ev=2e-50, 67% identity; hypothetical protein 25712 4075151 TM1040_3057 Ruegeria sp. TM1040 hypothetical protein YP_611293.1 25251 R 292414 CDS YP_611294.1 99078036 4075152 complement(25759..26748) 1 NC_008043.1 PFAM: beta-lactamase-like: (1e-23); KEGG: sil:SPO0299 metallo-beta-lactamase family protein, ev=1e-166, 83% identity; beta-lactamase-like protein 26748 4075152 TM1040_3058 Ruegeria sp. TM1040 beta-lactamase-like protein YP_611294.1 25759 R 292414 CDS YP_611295.1 99078037 4075153 complement(26802..28514) 1 NC_008043.1 PFAM: acyl-CoA dehydrogenase-like: (1.2e-34) Acyl-CoA dehydrogenase, type 2-like: (2.5e-06); KEGG: sil:SPO0298 acyl-CoA dehydrogenase family protein, ev=0.0, 78% identity; acyl-CoA dehydrogenase 28514 4075153 TM1040_3059 Ruegeria sp. TM1040 acyl-CoA dehydrogenase YP_611295.1 26802 R 292414 CDS YP_611296.1 99078038 4075154 28710..29681 1 NC_008043.1 TIGRFAM: Sua5/YciO/YrdC/YwlC: (2.8e-70); PFAM: SUA5: (6.6e-23) SUA5/yciO/yrdC-like: (8.5e-59); KEGG: sil:SPO0297 Sua5/YciO/YrdC family protein, ev=1e-121, 72% identity; translation factor SUA5 29681 4075154 TM1040_3060 Ruegeria sp. TM1040 translation factor SUA5 YP_611296.1 28710 D 292414 CDS YP_611297.1 99078039 4075155 29742..30509 1 NC_008043.1 TIGRFAM: phage SPO1 DNA polymerase-related protein: (5.6e-65); PFAM: Uracil-DNA glycosylase superfamily: (5e-31); KEGG: sil:SPO0288 uracil-DNA glycosylase, ev=3e-96, 67% identity; phage SPO1 DNA polymerase-related protein 30509 4075155 TM1040_3061 Ruegeria sp. TM1040 phage SPO1 DNA polymerase-related protein YP_611297.1 29742 D 292414 CDS YP_611298.1 99078040 4075156 30534..31142 1 NC_008043.1 PFAM: metallophosphoesterase: (6.1e-09); KEGG: sil:SPO0289 Ser/Thr protein phosphatase family protein, ev=6e-67, 63% identity; metallophosphoesterase 31142 4075156 TM1040_3062 Ruegeria sp. TM1040 metallophosphoesterase YP_611298.1 30534 D 292414 CDS YP_611299.1 99078041 4075157 31142..31765 1 NC_008043.1 PFAM: Lysine exporter protein (LYSE/YGGA): (1.9e-31); KEGG: sil:SPO0290 transmembrane amino acid efflux protein, ev=1e-64, 63% identity; lysine exporter protein LysE/YggA 31765 4075157 TM1040_3063 Ruegeria sp. TM1040 lysine exporter protein LysE/YggA YP_611299.1 31142 D 292414 CDS YP_611300.1 99078042 4075158 31771..32313 1 NC_008043.1 TIGRFAM: Molybdenum cofactor biosynthesis protein B, proteobacteria: (2.6e-101); PFAM: molybdopterin binding domain: (2.2e-36); KEGG: sil:SPO0291 molybdenum cofactor biosynthesis protein B, ev=3e-84, 83% identity; molybdenum cofactor biosynthesis protein B 32313 4075158 TM1040_3064 Ruegeria sp. TM1040 molybdenum cofactor biosynthesis protein B YP_611300.1 31771 D 292414 CDS YP_611301.1 99078043 4075159 32428..33891 1 NC_008043.1 PFAM: secretion protein HlyD: (0.00049); KEGG: sil:SPO0292 efflux transporter, RND family, MFP subunit, ev=1e-147, 58% identity; secretion protein HlyD 33891 4075159 TM1040_3065 Ruegeria sp. TM1040 secretion protein HlyD YP_611301.1 32428 D 292414 CDS YP_611302.1 99078044 4075160 33952..37365 1 NC_008043.1 PFAM: acriflavin resistance protein: (1.2e-39); KEGG: sil:SPO0293 transporter, AcrB/AcrD/AcrF family, ev=0.0, 74% identity; acriflavin resistance protein 37365 4075160 TM1040_3066 Ruegeria sp. TM1040 acriflavin resistance protein YP_611302.1 33952 D 292414 CDS YP_611303.1 99078045 4075161 complement(37311..37790) 1 NC_008043.1 PFAM: NUDIX hydrolase: (2.2e-22); KEGG: bur:Bcep18194_A5292 NUDIX hydrolase, ev=5e-24, 40% identity; NUDIX hydrolase 37790 4075161 TM1040_3067 Ruegeria sp. TM1040 NUDIX hydrolase YP_611303.1 37311 R 292414 CDS YP_611304.1 99078046 4075162 complement(37867..38652) 1 NC_008043.1 KEGG: sil:SPO0295 hypothetical protein, ev=4e-81, 56% identity; hypothetical protein 38652 4075162 TM1040_3068 Ruegeria sp. TM1040 hypothetical protein YP_611304.1 37867 R 292414 CDS YP_611305.1 99078047 4075163 38804..39424 1 NC_008043.1 PFAM: protein of unknown function DUF179: (1.5e-86); KEGG: sil:SPO0296 transcriptional regulator, ev=2e-58, 63% identity; hypothetical protein 39424 4075163 TM1040_3069 Ruegeria sp. TM1040 hypothetical protein YP_611305.1 38804 D 292414 CDS YP_611306.1 99078048 4075164 39746..40705 1 NC_008043.1 catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis; aspartate carbamoyltransferase catalytic subunit 40705 pyrB 4075164 pyrB Ruegeria sp. TM1040 aspartate carbamoyltransferase catalytic subunit YP_611306.1 39746 D 292414 CDS YP_611307.1 99078049 4075165 40711..41244 1 NC_008043.1 KEGG: sil:SPO0286 hypothetical protein, ev=2e-28, 45% identity; hypothetical protein 41244 4075165 TM1040_3071 Ruegeria sp. TM1040 hypothetical protein YP_611307.1 40711 D 292414 CDS YP_611308.1 99078050 4075166 41351..42661 1 NC_008043.1 TIGRFAM: dihydroorotase, multifunctional complex type: (2.5e-78); PFAM: amidohydrolase: (1.5e-08); KEGG: sil:SPO0284 dihydroorotase, multifunctional complex type, ev=0.0, 84% identity; dihydroorotase 42661 4075166 TM1040_3072 Ruegeria sp. TM1040 dihydroorotase YP_611308.1 41351 D 292414 CDS YP_611309.1 99078051 4075167 42661..43269 1 NC_008043.1 PFAM: protein of unknown function DUF205: (1.7e-50); KEGG: sil:SPO0283 conserved hypothetical protein TIGR00023, ev=3e-76, 67% identity; acyl-phosphate glycerol-3-phosphate acyltransferase 43269 4075167 TM1040_3073 Ruegeria sp. TM1040 acyl-phosphate glycerol-3-phosphate acyltransferase YP_611309.1 42661 D 292414 CDS YP_611310.1 99078052 4075168 43540..44025 1 NC_008043.1 KEGG: sil:SPO0281 hypothetical protein, ev=9e-60, 70% identity; hypothetical protein 44025 4075168 TM1040_3074 Ruegeria sp. TM1040 hypothetical protein YP_611310.1 43540 D 292414 CDS YP_611311.1 99078053 4075169 complement(44125..44379) 1 NC_008043.1 hypothetical protein 44379 4075169 TM1040_3075 Ruegeria sp. TM1040 hypothetical protein YP_611311.1 44125 R 292414 CDS YP_611312.1 99078054 4075170 complement(44581..45951) 1 NC_008043.1 TIGRFAM: glutamate--cysteine ligase: (1.6e-259); PFAM: glutamate--cysteine ligase, GCS2: (7.6e-121); KEGG: sil:SPO3626 glutamate--cysteine ligase, ev=0.0, 84% identity; glutamate--cysteine ligase 45951 4075170 TM1040_3076 Ruegeria sp. TM1040 glutamate--cysteine ligase YP_611312.1 44581 R 292414 CDS YP_611313.1 99078055 4075171 complement(46057..46584) 1 NC_008043.1 KEGG: sil:SPO3627 hypothetical protein, ev=4e-51, 57% identity; hypothetical protein 46584 4075171 TM1040_3077 Ruegeria sp. TM1040 hypothetical protein YP_611313.1 46057 R 292414 CDS YP_611314.1 99078056 4075524 complement(46581..47450) 1 NC_008043.1 PFAM: GCN5-related N-acetyltransferase: (0.0033); KEGG: sil:SPO3628 acetyltransferase, GNAT family, ev=3e-45, 38% identity; N-acetyltransferase GCN5 47450 4075524 TM1040_3078 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_611314.1 46581 R 292414 CDS YP_611315.1 99078057 4075525 complement(47450..48190) 1 NC_008043.1 in Escherichia coli RsmE methylates the N3 position of the U1498 base in 16S rRNA; cells lacking this function can grow, but are outcompeted by wild-type; SAM-dependent m(3)U1498 methyltransferase; 16S ribosomal RNA methyltransferase RsmE 48190 4075525 TM1040_3079 Ruegeria sp. TM1040 16S ribosomal RNA methyltransferase RsmE YP_611315.1 47450 R 292414 CDS YP_611316.1 99078058 4075526 48203..49165 1 NC_008043.1 UbiA prenyltransferase family catalyzes the transfer of a prenyl group to various acceptors with hydrophobic ring structures in the biosynthesis of respiratory quinones, hemes, chlorophylls, vitamin E, and shikonin; 4-hydroxybenzoate polyprenyltransferase 49165 ubiA 4075526 ubiA Ruegeria sp. TM1040 4-hydroxybenzoate polyprenyltransferase YP_611316.1 48203 D 292414 CDS YP_611317.1 99078059 4075527 49247..51208 1 NC_008043.1 PFAM: OmpA/MotB: (3e-26); KEGG: sil:SPO3631 OmpA domain protein, ev=0.0, 58% identity; OmpA/MotB 51208 4075527 TM1040_3081 Ruegeria sp. TM1040 OmpA/MotB YP_611317.1 49247 D 292414 CDS YP_611318.1 99078060 4075528 51205..51525 1 NC_008043.1 KEGG: sil:SPO3632 hypothetical protein, ev=6e-45, 90% identity; hypothetical protein 51525 4075528 TM1040_3082 Ruegeria sp. TM1040 hypothetical protein YP_611318.1 51205 D 292414 CDS YP_611319.1 99078061 4075529 51515..51922 1 NC_008043.1 KEGG: sil:SPO1334 hypothetical protein, ev=1e-23, 47% identity; hypothetical protein 51922 4075529 TM1040_3083 Ruegeria sp. TM1040 hypothetical protein YP_611319.1 51515 D 292414 CDS YP_611320.1 99078062 4075530 52129..52830 1 NC_008043.1 catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine; phosphatidylserine decarboxylase 52830 4075530 TM1040_3084 Ruegeria sp. TM1040 phosphatidylserine decarboxylase YP_611320.1 52129 D 292414 CDS YP_611321.1 99078063 4075531 52823..53590 1 NC_008043.1 KEGG: sil:SPOA0293 CDP-diacylglycerol--serine O-phosphatidyltransferase, ev=4e-76, 53% identity; TIGRFAM: CDP-diacylglycerol--serine O-phosphatidyltransferase: (3.8e-30); PFAM: CDP-alcohol phosphatidyltransferase: (1e-23); CDP-diacylglycerol--serine O-phosphatidyltransferase 53590 4075531 TM1040_3085 Ruegeria sp. TM1040 CDP-diacylglycerol--serine O-phosphatidyltransferase YP_611321.1 52823 D 292414 CDS YP_611322.1 99078064 4075532 53571..54212 1 NC_008043.1 PFAM: UbiE/COQ5 methyltransferase: (0.00018) Methyltransferase type 11: (1.4e-31) Methyltransferase type 12: (2.3e-20); KEGG: sil:SPOA0294 phosphatidylethanolamine N-methyltransferase, ev=5e-71, 62% identity; phosphatidylethanolamine N-methyltransferase/phosphatidyl-N-methylethanolamine N-methyltransferase 54212 4075532 TM1040_3086 Ruegeria sp. TM1040 phosphatidylethanolamine N-methyltransferase/phosphatidyl-N-methylethanolamine N-methyltransferase YP_611322.1 53571 D 292414 CDS YP_611323.1 99078065 4075533 54543..55976 1 NC_008043.1 KEGG: sil:SPO3333 hypothetical protein, ev=1e-61, 41% identity; hypothetical protein 55976 4075533 TM1040_3087 Ruegeria sp. TM1040 hypothetical protein YP_611323.1 54543 D 292414 CDS YP_611324.1 99078066 4075535 56519..57196 1 NC_008043.1 lipoyl-[acyl-carrier protein]-protein-N-lipoyltransferse; lipoate-protein ligase B; transfers lipoate to apolipoproteins; involved in lipoate metabolism; lipoyltransferase 57196 lipB 4075535 lipB Ruegeria sp. TM1040 lipoyltransferase YP_611324.1 56519 D 292414 CDS YP_611325.1 99078067 4075536 57652..59874 1 NC_008043.1 PFAM: GAF: (5.8e-05) ATP-binding region, ATPase-like: (1.4e-25) histidine kinase A-like: (4.9e-06) Phytochrome, central region: (6.4e-12) PAS fold-2: (1.7e-05); KEGG: rpb:RPB_4450 multi-sensor signal transduction histidine kinase, ev=1e-82, 32% identity; multi-sensor signal transduction histidine kinase 59874 4075536 TM1040_3089 Ruegeria sp. TM1040 multi-sensor signal transduction histidine kinase YP_611325.1 57652 D 292414 CDS YP_611326.1 99078068 4075537 59876..60520 1 NC_008043.1 PFAM: Haem oxygenase: (0.00097); heme oxygenase 60520 4075537 TM1040_3090 Ruegeria sp. TM1040 heme oxygenase YP_611326.1 59876 D 292414 CDS YP_611327.1 99078069 4075538 60682..61245 1 NC_008043.1 PFAM: nitrogen-fixing NifU-like: (4.2e-31); KEGG: sil:SPO0382 NifU domain protein, ev=2e-93, 89% identity; nitrogen-fixing NifU-like 61245 4075538 TM1040_3091 Ruegeria sp. TM1040 nitrogen-fixing NifU-like YP_611327.1 60682 D 292414 CDS YP_611328.1 99078070 4075539 61469..62116 1 NC_008043.1 PFAM: peptidase M22, glycoprotease: (1.6e-33); KEGG: rsp:RSP_2213 hypothetical protein, ev=2e-55, 58% identity; peptidase M22, glycoprotease 62116 4075539 TM1040_3092 Ruegeria sp. TM1040 peptidase M22, glycoprotease YP_611328.1 61469 D 292414 CDS YP_611329.1 99078071 4075540 62120..62554 1 NC_008043.1 PFAM: GCN5-related N-acetyltransferase: (2.9e-11); KEGG: sil:SPO0380 ribosomal-protein-alanine acetyltransferase, , ev=2e-36, 55% identity; N-acetyltransferase GCN5 62554 4075540 TM1040_3093 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_611329.1 62120 D 292414 CDS YP_611330.1 99078072 4075541 62691..63686 1 NC_008043.1 PFAM: basic membrane lipoprotein: (3.3e-58); KEGG: sil:SPO0379 sugar ABC transporter, periplasmic sugar-binding protein, ev=1e-147, 77% identity; basic membrane lipoprotein 63686 4075541 TM1040_3094 Ruegeria sp. TM1040 basic membrane lipoprotein YP_611330.1 62691 D 292414 CDS YP_611331.1 99078073 4075542 63876..65405 1 NC_008043.1 PFAM: ABC transporter related: (1.5e-15); SMART: ATPase: (0.0062); KEGG: sil:SPO0378 sugar ABC transporter, ATP-binding protein, ev=0.0, 85% identity; ABC transporter 65405 4075542 TM1040_3095 Ruegeria sp. TM1040 ABC transporter YP_611331.1 63876 D 292414 CDS YP_611332.1 99078074 4075543 65406..66500 1 NC_008043.1 PFAM: inner-membrane translocator: (3.3e-43); KEGG: sil:SPO0377 sugar ABC transporter, permease protein, ev=1e-167, 78% identity; inner-membrane translocator 66500 4075543 TM1040_3096 Ruegeria sp. TM1040 inner-membrane translocator YP_611332.1 65406 D 292414 CDS YP_611333.1 99078075 4075544 66500..67507 1 NC_008043.1 PFAM: inner-membrane translocator: (2.6e-34); KEGG: sil:SPO0376 sugar ABC transporter, permease protein, ev=1e-141, 76% identity; inner-membrane translocator 67507 4075544 TM1040_3097 Ruegeria sp. TM1040 inner-membrane translocator YP_611333.1 66500 D 292414 CDS YP_611334.1 99078076 4075545 67629..68621 1 NC_008043.1 PFAM: protein of unknown function DUF81: (9.7e-36); KEGG: sil:SPO0375 membrane protein, ev=1e-135, 80% identity; hypothetical protein 68621 4075545 TM1040_3098 Ruegeria sp. TM1040 hypothetical protein YP_611334.1 67629 D 292414 CDS YP_611335.1 99078077 4075546 68621..69388 1 NC_008043.1 KEGG: sil:SPO0374 hypothetical protein, ev=4e-89, 65% identity; hypothetical protein 69388 4075546 TM1040_3099 Ruegeria sp. TM1040 hypothetical protein YP_611335.1 68621 D 292414 CDS YP_611336.1 99078078 4075547 complement(69504..70241) 1 NC_008043.1 PFAM: NAD-dependent epimerase/dehydratase: (0.00068) short-chain dehydrogenase/reductase SDR: (1.5e-24); KEGG: jan:Jann_0846 short-chain dehydrogenase/reductase SDR, ev=1e-75, 61% identity; short-chain dehydrogenase/reductase SDR 70241 4075547 TM1040_3100 Ruegeria sp. TM1040 short-chain dehydrogenase/reductase SDR YP_611336.1 69504 R 292414 CDS YP_611337.1 99078079 4075548 complement(70238..71791) 1 NC_008043.1 SMART: ATPase: (9.9e-06); KEGG: sil:SPO0373 helicase, ATP-dependent, , ev=0.0, 89% identity; ATPase 71791 4075548 TM1040_3101 Ruegeria sp. TM1040 ATPase YP_611337.1 70238 R 292414 CDS YP_611338.1 99078080 4075549 complement(71833..72552) 1 NC_008043.1 PFAM: regulatory protein, LuxR: (1.5e-08) Autoinducer-binding: (2.6e-19); KEGG: sil:SPO0371 autoinducer-binding transcriptional regulator LuxR, ev=1e-71, 51% identity; LuxR family transcriptional regulator 72552 4075549 TM1040_3102 Ruegeria sp. TM1040 LuxR family transcriptional regulator YP_611338.1 71833 R 292414 CDS YP_611339.1 99078081 4075550 72590..73012 1 NC_008043.1 hypothetical protein 73012 4075550 TM1040_3103 Ruegeria sp. TM1040 hypothetical protein YP_611339.1 72590 D 292414 CDS YP_611340.1 99078082 4075551 complement(73015..74295) 1 NC_008043.1 TIGRFAM: Crotonyl-CoA reductase: (1.1e-271); PFAM: Alcohol dehydrogenase, zinc-binding: (1.8e-33) Alcohol dehydrogenase GroES-like: (2.6e-15); KEGG: sil:SPO0370 crotonyl-CoA reductase, ev=0.0, 91% identity; crotonyl-CoA reductase 74295 4075551 TM1040_3104 Ruegeria sp. TM1040 crotonyl-CoA reductase YP_611340.1 73015 R 292414 CDS YP_611341.1 99078083 4075552 complement(74421..75851) 1 NC_008043.1 PFAM: phospholipid/glycerol acyltransferase: (3.4e-12); KEGG: sil:SPO0369 acyltransferase family protein, ev=1e-166, 64% identity; glycerol-3-phosphate acyltransferase 75851 4075552 TM1040_3105 Ruegeria sp. TM1040 glycerol-3-phosphate acyltransferase YP_611341.1 74421 R 292414 CDS YP_611342.1 99078084 4075553 76029..78014 1 NC_008043.1 KEGG: sil:SPO0368 methylmalonyl-CoA mutase, ev=0.0, 86% identity; TIGRFAM: methylmalonyl-CoA mutase N-terminal domain: (2e-121) methylmalonyl-CoA mutase C-terminal domain: (1.7e-32); PFAM: methylmalonyl-CoA mutase: (5e-96) cobalamin B12-binding: (2.9e-26); methylmalonyl-CoA mutase 78014 4075553 TM1040_3106 Ruegeria sp. TM1040 methylmalonyl-CoA mutase YP_611342.1 76029 D 292414 CDS YP_611343.1 99078085 4075554 78144..78464 1 NC_008043.1 PFAM: histone-like nucleoid-structuring protein H-NS: (1.2e-25); KEGG: sil:SPO0367 DNA-binding protein, H-NS family, ev=2e-31, 63% identity; histone-like nucleoid-structuring protein H-NS 78464 4075554 TM1040_3107 Ruegeria sp. TM1040 histone-like nucleoid-structuring protein H-NS YP_611343.1 78144 D 292414 CDS YP_611344.1 99078086 4075555 78483..79187 1 NC_008043.1 catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate; purine nucleoside phosphorylase 79187 deoD 4075555 deoD Ruegeria sp. TM1040 purine nucleoside phosphorylase YP_611344.1 78483 D 292414 CDS YP_611345.1 99078087 4075556 complement(79360..80217) 1 NC_008043.1 KEGG: sil:SPO0365 hypothetical protein, ev=1e-137, 80% identity; hypothetical protein 80217 4075556 TM1040_3109 Ruegeria sp. TM1040 hypothetical protein YP_611345.1 79360 R 292414 CDS YP_611346.1 99078088 4075557 complement(80347..81519) 1 NC_008043.1 PFAM: Orn/DAP/Arg decarboxylase 2: (3.5e-28); KEGG: sil:SPO0364 decarboxylase, pyridoxal-dependent, ev=1e-157, 70% identity; ornithine decarboxylase 81519 4075557 TM1040_3110 Ruegeria sp. TM1040 ornithine decarboxylase YP_611346.1 80347 R 292414 CDS YP_611347.1 99078089 4075558 complement(82004..82963) 1 NC_008043.1 PFAM: regulatory protein, LysR: (2.8e-21) LysR, substrate-binding: (7.3e-19); KEGG: reu:Reut_B4718 regulatory protein, LysR:LysR, substrate-binding, ev=7e-47, 36% identity; LysR family transcriptional regulator 82963 4075558 TM1040_3111 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_611347.1 82004 R 292414 CDS YP_611348.1 99078090 4075559 83029..84546 1 NC_008043.1 PFAM: extracellular solute-binding protein, family 5: (4.1e-60); KEGG: pst:PSPTO2576 peptide ABC transporter, periplasmic peptide-binding protein, ev=6e-96, 38% identity; extracellular solute-binding protein 84546 4075559 TM1040_3112 Ruegeria sp. TM1040 extracellular solute-binding protein YP_611348.1 83029 D 292414 CDS YP_611349.1 99078091 4075560 84619..85536 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (6.4e-54); KEGG: pst:PSPTO2575 peptide ABC transporter, permease protein, ev=1e-89, 50% identity; binding-protein-dependent transport systems inner membrane component 85536 4075560 TM1040_3113 Ruegeria sp. TM1040 binding-protein-dependent transport systems inner membrane component YP_611349.1 84619 D 292414 CDS YP_611350.1 99078092 4075561 85541..86449 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1.1e-40); KEGG: psb:Psyr_2265 binding-protein-dependent transport systems inner membrane component, ev=9e-81, 48% identity; binding-protein-dependent transport system inner membrane protein 86449 4075561 TM1040_3114 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_611350.1 85541 D 292414 CDS YP_611351.1 99078093 4074986 86470..88485 1 NC_008043.1 KEGG: eba:ebA5654 ABC transporter, ATP-binding protein, ev=1e-164, 48% identity; TIGRFAM: Oligopeptide/dipeptide ABC transporter, ATP-binding protein-like: (9.3e-30); PFAM: ABC transporter related: (1.8e-69) Oligopeptide/dipeptide ABC transporter-like: (2.8e-28); SMART: ATPase: (3.2e-23); oligopeptide/dipeptide ABC transporter ATP-binding protein-like protein 88485 4074986 TM1040_3115 Ruegeria sp. TM1040 oligopeptide/dipeptide ABC transporter ATP-binding protein-like protein YP_611351.1 86470 D 292414 CDS YP_611352.1 99078094 4074987 88482..89669 1 NC_008043.1 dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE), catalyzes the hydrolysis of N-succinyl-L,Ldiaminopimelate L,L-SDAP to L,L-diaminopimelate and succinate. It is a metalloprotease containing dinuclear active sites. Its structure is similar to the carboxypeptidase G2 from Pseudomonas sp. strain RS-16 and the aminopeptidase from Aeromonas proteolytica.; succinyl-diaminopimelate desuccinylase 89669 4074987 TM1040_3116 Ruegeria sp. TM1040 succinyl-diaminopimelate desuccinylase YP_611352.1 88482 D 292414 CDS YP_611353.1 99078095 4074988 89666..90961 1 NC_008043.1 KEGG: sme:SMb21041 conserved protein, possibly related to processing of cell wall amino acids, ev=2e-33, 29% identity; poly-gamma-glutamate biosynthesis protein 90961 4074988 TM1040_3117 Ruegeria sp. TM1040 poly-gamma-glutamate biosynthesis protein YP_611353.1 89666 D 292414 CDS YP_611354.1 99078096 4074989 91339..91971 1 NC_008043.1 PFAM: phage integrase: (7e-05); KEGG: bps:BPSL0587 phage integrase family protein, ev=2e-64, 54% identity; phage integrase 91971 4074989 TM1040_3118 Ruegeria sp. TM1040 phage integrase YP_611354.1 91339 D 292414 CDS YP_611355.1 99078097 4074990 92141..92704 1 NC_008043.1 hypothetical protein 92704 4074990 TM1040_3119 Ruegeria sp. TM1040 hypothetical protein YP_611355.1 92141 D 292414 CDS YP_611356.1 99078098 4074991 93112..93603 1 NC_008043.1 hypothetical protein 93603 4074991 TM1040_3120 Ruegeria sp. TM1040 hypothetical protein YP_611356.1 93112 D 292414 CDS YP_611357.1 99078099 4074992 complement(93987..94586) 1 NC_008043.1 hypothetical protein 94586 4074992 TM1040_3121 Ruegeria sp. TM1040 hypothetical protein YP_611357.1 93987 R 292414 CDS YP_611358.1 99078100 4074993 complement(95143..96261) 1 NC_008043.1 KEGG: bja:blr2115 hypothetical protein, ev=2e-58, 34% identity; hypothetical protein 96261 4074993 TM1040_3122 Ruegeria sp. TM1040 hypothetical protein YP_611358.1 95143 R 292414 CDS YP_611359.1 99078101 4074994 complement(96406..97101) 1 NC_008043.1 hypothetical protein 97101 4074994 TM1040_3123 Ruegeria sp. TM1040 hypothetical protein YP_611359.1 96406 R 292414 CDS YP_611360.1 99078102 4074995 complement(98105..99355) 1 NC_008043.1 KEGG: spn:SP1145 hypothetical protein, ev=3e-18, 30% identity; hypothetical protein 99355 4074995 TM1040_3124 Ruegeria sp. TM1040 hypothetical protein YP_611360.1 98105 R 292414 CDS YP_611361.1 99078103 4074996 99835..100098 1 NC_008043.1 hypothetical protein 100098 4074996 TM1040_3125 Ruegeria sp. TM1040 hypothetical protein YP_611361.1 99835 D 292414 CDS YP_611362.1 99078104 4074997 complement(100360..101157) 1 NC_008043.1 PFAM: Integrase, catalytic region: (4.6e-37); KEGG: mlo:mll6088 transposase, ev=1e-117, 75% identity; integrase catalytic subunit 101157 4074997 TM1040_3126 Ruegeria sp. TM1040 integrase catalytic subunit YP_611362.1 100360 R 292414 CDS YP_611363.1 99078105 4074998 complement(101190..101456) 1 NC_008043.1 PFAM: transposase IS3/IS911: (2.9e-19); KEGG: ret:RHE_PA00090 probable insertion sequence transposase protein, IS3/IS911 family, ev=2e-34, 77% identity; transposase IS3/IS911 101456 4074998 TM1040_3127 Ruegeria sp. TM1040 transposase IS3/IS911 YP_611363.1 101190 R 292414 CDS YP_611364.1 99078106 4075000 101920..102945 1 NC_008043.1 PFAM: regulatory protein, LacI: (2.3e-06) periplasmic binding protein/LacI transcriptional regulator: (2.2e-12); KEGG: sil:SPO3684 transcriptional regulator, LacI family, ev=1e-163, 85% identity; LacI family transcriptional regulator 102945 4075000 TM1040_3128 Ruegeria sp. TM1040 LacI family transcriptional regulator YP_611364.1 101920 D 292414 CDS YP_611365.1 99078107 4075001 complement(103016..104521) 1 NC_008043.1 PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit: (4.9e-94); KEGG: sil:SPO3695 TRAP dicarboxylate transporter, DctM subunit, , ev=0.0, 82% identity; TRAP dicarboxylate transporter subunit DctM 104521 4075001 TM1040_3129 Ruegeria sp. TM1040 TRAP dicarboxylate transporter subunit DctM YP_611365.1 103016 R 292414 CDS YP_611366.1 99078108 4075002 complement(104518..105138) 1 NC_008043.1 KEGG: sil:SPO3694 hypothetical protein, ev=3e-67, 63% identity; hypothetical protein 105138 4075002 TM1040_3130 Ruegeria sp. TM1040 hypothetical protein YP_611366.1 104518 R 292414 CDS YP_611367.1 99078109 4075003 complement(105191..106237) 1 NC_008043.1 PFAM: TRAP dicarboxylate transporter- DctP subunit: (2.4e-31); KEGG: sil:SPO3693 TRAP dicarboxylate transporter, DctP subunit, ev=1e-153, 75% identity; TRAP dicarboxylate transporter- DctP subunit 106237 4075003 TM1040_3131 Ruegeria sp. TM1040 TRAP dicarboxylate transporter- DctP subunit YP_611367.1 105191 R 292414 CDS YP_611368.1 99078110 4075004 complement(106447..108480) 1 NC_008043.1 TIGRFAM: GGDEF domain: (6.5e-31); PFAM: GGDEF: (5.2e-30) EAL: (6.7e-109); KEGG: mag:amb4494 predicted signal transduction protein containing a membrane domain, ev=8e-90, 35% identity; diguanylate cyclase/phosphodiesterase 108480 4075004 TM1040_3132 Ruegeria sp. TM1040 diguanylate cyclase/phosphodiesterase YP_611368.1 106447 R 292414 CDS YP_611369.1 99078111 4075005 108763..110277 1 NC_008043.1 PFAM: sulfatase: (2.6e-20) type I phosphodiesterase/nucleotide pyrophosphatase: (7.2e-05); KEGG: sil:SPO1083 choline sulfatase, ev=0.0, 80% identity; sulfatase 110277 4075005 TM1040_3133 Ruegeria sp. TM1040 sulfatase YP_611369.1 108763 D 292414 CDS YP_611370.1 99078112 4075006 complement(110420..111265) 1 NC_008043.1 PFAM: flagellin-like: (2.7e-06); KEGG: bmb:BruAb2_1084 flagellin family protein, ev=6e-47, 41% identity; flagellin-like protein 111265 4075006 TM1040_3134 Ruegeria sp. TM1040 flagellin-like protein YP_611370.1 110420 R 292414 CDS YP_611371.1 99078113 4075007 111923..112831 1 NC_008043.1 PFAM: Di-haem cytochrome c peroxidase: (1.5e-48); KEGG: bja:blr1552 methylamine utilization protein precursor, ev=2e-64, 43% identity; cytochrome-c peroxidase 112831 4075007 TM1040_3135 Ruegeria sp. TM1040 cytochrome-c peroxidase YP_611371.1 111923 D 292414 CDS YP_611372.1 99078114 4075008 112844..114946 1 NC_008043.1 TIGRFAM: GGDEF domain: (4.6e-39); PFAM: GGDEF: (1.7e-56) EAL: (3.4e-80) histidine kinase, HAMP region: (6.2e-12); KEGG: ret:RHE_CH02277 sensory box/GGDEF family protein, ev=3e-86, 40% identity; diguanylate cyclase/phosphodiesterase 114946 4075008 TM1040_3136 Ruegeria sp. TM1040 diguanylate cyclase/phosphodiesterase YP_611372.1 112844 D 292414 CDS YP_611373.1 99078115 4075009 complement(114961..117006) 1 NC_008043.1 PFAM: NADH:flavin oxidoreductase/NADH oxidase: (3e-41) FAD-dependent pyridine nucleotide-disulphide oxidoreductase: (0.003); KEGG: jan:Jann_1528 NADH:flavin oxidoreductase/NADH oxidase, ev=0.0, 80% identity; NADH:flavin oxidoreductase 117006 4075009 TM1040_3137 Ruegeria sp. TM1040 NADH:flavin oxidoreductase YP_611373.1 114961 R 292414 CDS YP_611374.1 99078116 4075010 117100..117723 1 NC_008043.1 PFAM: regulatory protein, TetR: (0.00091); KEGG: sil:SPO0168 transcriptional regulator, TetR family, ev=4e-63, 59% identity; TetR family transcriptional regulator 117723 4075010 TM1040_3138 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_611374.1 117100 D 292414 CDS YP_611375.1 99078117 4075011 complement(117760..118725) 1 NC_008043.1 KEGG: bja:bll2873 ABC transporter ATP-binding protein, ev=3e-97, 58% identity; TIGRFAM: Oligopeptide/dipeptide ABC transporter, ATP-binding protein-like: (5.7e-30); PFAM: ABC transporter related: (1.1e-53) Oligopeptide/dipeptide ABC transporter-like: (2.1e-31); SMART: ATPase: (4.9e-18); oligopeptide/dipeptide ABC transporter ATP-binding protein-like protein 118725 4075011 TM1040_3139 Ruegeria sp. TM1040 oligopeptide/dipeptide ABC transporter ATP-binding protein-like protein YP_611375.1 117760 R 292414 CDS YP_611376.1 99078118 4075012 complement(118725..119699) 1 NC_008043.1 KEGG: bja:bll2874 ABC transporter ATP-binding protein, ev=1e-115, 65% identity; TIGRFAM: Oligopeptide/dipeptide ABC transporter, ATP-binding protein-like: (3.8e-26); PFAM: ABC transporter related: (3.8e-62) Oligopeptide/dipeptide ABC transporter-like: (9.6e-26); SMART: ATPase: (1.3e-15); oligopeptide/dipeptide ABC transporter ATP-binding protein-like protein 119699 4075012 TM1040_3140 Ruegeria sp. TM1040 oligopeptide/dipeptide ABC transporter ATP-binding protein-like protein YP_611376.1 118725 R 292414 CDS YP_611377.1 99078119 4075013 complement(119699..120640) 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (3e-42); KEGG: jan:Jann_2825 binding-protein-dependent transport systems inner membrane component, ev=1e-135, 76% identity; binding-protein-dependent transport system inner membrane protein 120640 4075013 TM1040_3141 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_611377.1 119699 R 292414 CDS YP_611378.1 99078120 4075014 complement(120640..121620) 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (3.6e-46); KEGG: jan:Jann_2824 binding-protein-dependent transport systems inner membrane component, ev=1e-136, 74% identity; binding-protein-dependent transport systems inner membrane component 121620 4075014 TM1040_3142 Ruegeria sp. TM1040 binding-protein-dependent transport systems inner membrane component YP_611378.1 120640 R 292414 CDS YP_611379.1 99078121 4075015 complement(121684..123258) 1 NC_008043.1 PFAM: extracellular solute-binding protein, family 5: (1.5e-69); KEGG: jan:Jann_2822 extracellular solute-binding protein, family 5, ev=0.0, 65% identity; extracellular solute-binding protein 123258 4075015 TM1040_3143 Ruegeria sp. TM1040 extracellular solute-binding protein YP_611379.1 121684 R 292414 CDS YP_611380.1 99078122 4075016 complement(123368..124948) 1 NC_008043.1 PFAM: extracellular solute-binding protein, family 5: (5.8e-70); KEGG: jan:Jann_2819 extracellular solute-binding protein, family 5, ev=0.0, 64% identity; extracellular solute-binding protein 124948 4075016 TM1040_3144 Ruegeria sp. TM1040 extracellular solute-binding protein YP_611380.1 123368 R 292414 CDS YP_611381.1 99078123 4075017 complement(125313..125930) 1 NC_008043.1 KEGG: jan:Jann_4169 hypothetical protein, ev=9e-66, 59% identity; hypothetical protein 125930 4075017 TM1040_3145 Ruegeria sp. TM1040 hypothetical protein YP_611381.1 125313 R 292414 CDS YP_611382.1 99078124 4075018 complement(125943..128207) 1 NC_008043.1 PFAM: aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding: (7.8e-06); KEGG: jan:Jann_4168 twin-arginine translocation pathway signal, ev=0.0, 50% identity; aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding 128207 4075018 TM1040_3146 Ruegeria sp. TM1040 aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding YP_611382.1 125943 R 292414 CDS YP_611383.1 99078125 4075019 complement(128211..128669) 1 NC_008043.1 PFAM: ferredoxin: (5.3e-08) [2Fe-2S]-binding: (6.6e-39); KEGG: jan:Jann_4167 (2Fe-2S)-binding, ev=4e-64, 76% identity; (2Fe-2S)-binding protein 128669 4075019 TM1040_3147 Ruegeria sp. TM1040 (2Fe-2S)-binding protein YP_611383.1 128211 R 292414 CDS YP_611384.1 99078126 4075020 complement(128830..129972) 1 NC_008043.1 KEGG: jan:Jann_1361 N-acetylglucosamine-6-phosphate deacetylase, ev=3e-99, 55% identity; TIGRFAM: N-acetylglucosamine-6-phosphate deacetylase: (4e-66); PFAM: amidohydrolase: (0.00092); N-acetylglucosamine 6-phosphate deacetylase 129972 4075020 TM1040_3148 Ruegeria sp. TM1040 N-acetylglucosamine 6-phosphate deacetylase YP_611384.1 128830 R 292414 CDS YP_611385.1 99078127 4075021 complement(129969..130997) 1 NC_008043.1 PFAM: sugar isomerase (SIS): (4.8e-08); KEGG: jan:Jann_1360 glutamine-fructose-6-phosphate transaminase (isomerizing), ev=1e-112, 62% identity; glutamine-fructose-6-phosphate transaminase (isomerizing) 130997 4075021 TM1040_3149 Ruegeria sp. TM1040 glutamine-fructose-6-phosphate transaminase (isomerizing) YP_611385.1 129969 R 292414 CDS YP_611386.1 99078128 4075022 complement(131072..131827) 1 NC_008043.1 PFAM: regulatory protein GntR, HTH: (1e-18) UbiC transcription regulator-associated: (2.7e-46); KEGG: sil:SPO1842 transcriptional regulator, GntR family, ev=3e-80, 61% identity; GntR family transcriptional regulator 131827 4075022 TM1040_3150 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_611386.1 131072 R 292414 CDS YP_611387.1 99078129 4075023 complement(131814..132701) 1 NC_008043.1 PFAM: ATPase, BadF/BadG/BcrA/BcrD type: (1.3e-13); KEGG: jan:Jann_1358 ATPase, BadF/BadG/BcrA/BcrD type, ev=5e-62, 42% identity; BadF/BadG/BcrA/BcrD type ATPase 132701 4075023 TM1040_3151 Ruegeria sp. TM1040 BadF/BadG/BcrA/BcrD type ATPase YP_611387.1 131814 R 292414 CDS YP_611388.1 99078130 4075322 132916..133797 1 NC_008043.1 catalyzes the cleavage of the lactyl ether moiety of N-acetylmuramic acid-6-phosphate (MurNAc-6-P) to form N-acetylglucosamine-6-phosphate (GlcNAc-6-P) and lactate; involved in MurNAc dissimilation pathway; N-acetylmuramic acid 6-phosphate etherase 133797 murQ 4075322 murQ Ruegeria sp. TM1040 N-acetylmuramic acid 6-phosphate etherase YP_611388.1 132916 D 292414 CDS YP_611389.1 99078131 4075323 133822..135075 1 NC_008043.1 PFAM: extracellular solute-binding protein, family 1: (7.3e-19); KEGG: sil:SPO1839 sugar ABC transporter, periplasmic sugar-binding protein, ev=0.0, 77% identity; extracellular solute-binding protein 135075 4075323 TM1040_3153 Ruegeria sp. TM1040 extracellular solute-binding protein YP_611389.1 133822 D 292414 CDS YP_611390.1 99078132 4075324 135160..136074 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (0.00056); KEGG: sil:SPO1838 sugar ABC transporter, permease protein, ev=1e-152, 86% identity; binding-protein-dependent transport system inner membrane protein 136074 4075324 TM1040_3154 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_611390.1 135160 D 292414 CDS YP_611391.1 99078133 4075325 136087..136926 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (2.3e-14); KEGG: sil:SPO1837 sugar ABC transporter, permease protein, ev=1e-141, 91% identity; binding-protein-dependent transport system inner membrane protein 136926 4075325 TM1040_3155 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_611391.1 136087 D 292414 CDS YP_611392.1 99078134 4075326 137006..138040 1 NC_008043.1 PFAM: oxidoreductase-like: (4e-25) dihydrodipicolinate reductase: (0.00054) homoserine dehydrogenase, NAD-binding: (0.00038); KEGG: sil:SPO1836 oxidoreductase, Gfo/Idh/MocA family, ev=1e-160, 80% identity; oxidoreductase-like 138040 4075326 TM1040_3156 Ruegeria sp. TM1040 oxidoreductase-like YP_611392.1 137006 D 292414 CDS YP_611393.1 99078135 4075327 138037..139032 1 NC_008043.1 PFAM: ABC transporter related: (4.1e-54) Transport-associated OB: (7.5e-06); SMART: ATPase: (1.2e-16); KEGG: jan:Jann_1353 ABC transporter related, ev=1e-130, 69% identity; ABC transporter 139032 4075327 TM1040_3157 Ruegeria sp. TM1040 ABC transporter YP_611393.1 138037 D 292414 CDS YP_611394.1 99078136 4075328 139146..139754 1 NC_008043.1 PFAM: regulatory protein, TetR: (2.4e-07); KEGG: sil:SPO1082 HTH-type transcriptional regulator BetI, ev=1e-44, 49% identity; TetR family transcriptional regulator 139754 4075328 TM1040_3158 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_611394.1 139146 D 292414 CDS YP_611395.1 99078137 4075329 139953..140921 1 NC_008043.1 KEGG: sil:SPO2161 hypothetical protein, ev=2e-35, 35% identity; hypothetical protein 140921 4075329 TM1040_3159 Ruegeria sp. TM1040 hypothetical protein YP_611395.1 139953 D 292414 CDS YP_611396.1 99078138 4075330 complement(140996..141958) 1 NC_008043.1 catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer composed of two alpha (AccA) and two beta (AccD) subunits; one of the two catalytic subunits that can form the acetyl CoA carboxylase enzyme together with a carrier protein; acetyl-CoA carboxylase carboxyltransferase subunit alpha 141958 4075330 TM1040_3160 Ruegeria sp. TM1040 acetyl-CoA carboxylase carboxyltransferase subunit alpha YP_611396.1 140996 R 292414 CDS YP_611397.1 99078139 4075331 142179..143012 1 NC_008043.1 PFAM: helix-turn-helix, AraC type: (1e-07) transcription activator, effector binding: (9.1e-39); KEGG: sil:SPO3615 transcriptional regulator, AraC family, ev=1e-101, 64% identity; AraC family transcriptional regulator 143012 4075331 TM1040_3161 Ruegeria sp. TM1040 AraC family transcriptional regulator YP_611397.1 142179 D 292414 CDS YP_611398.1 99078140 4075332 complement(143129..143734) 1 NC_008043.1 PFAM: Lysine exporter protein (LYSE/YGGA): (0.00023); KEGG: sil:SPO3613 transporter, LysE family, ev=1e-86, 78% identity; lysine exporter protein LysE/YggA 143734 4075332 TM1040_3162 Ruegeria sp. TM1040 lysine exporter protein LysE/YggA YP_611398.1 143129 R 292414 CDS YP_611399.1 99078141 4075333 143808..144260 1 NC_008043.1 PFAM: regulatory proteins, AsnC/Lrp: (1.7e-22); KEGG: sil:SPO3612 transcriptional regulator, AsnC family, ev=6e-63, 79% identity; AsnC family transcriptional regulator 144260 4075333 TM1040_3163 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_611399.1 143808 D 292414 CDS YP_611400.1 99078142 4075334 144824..145243 1 NC_008043.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase: (0.00019); KEGG: sil:SPO0917 glyoxalase family protein, ev=2e-33, 57% identity; glyoxalase/bleomycin resistance protein/dioxygenase 145243 4075334 TM1040_3164 Ruegeria sp. TM1040 glyoxalase/bleomycin resistance protein/dioxygenase YP_611400.1 144824 D 292414 CDS YP_611401.1 99078143 4075335 complement(145368..146330) 1 NC_008043.1 PFAM: HpcH/HpaI aldolase: (7.3e-36); KEGG: sil:SPO3608 malyl-CoA lyase, ev=1e-164, 90% identity; citryl-CoA lyase 146330 4075335 TM1040_3165 Ruegeria sp. TM1040 citryl-CoA lyase YP_611401.1 145368 R 292414 CDS YP_611402.1 99078144 4075336 146638..147639 1 NC_008043.1 PFAM: protein of unknown function DUF1611: (1.9e-125); KEGG: sil:SPO3607 hypothetical protein, ev=1e-158, 81% identity; hypothetical protein 147639 4075336 TM1040_3166 Ruegeria sp. TM1040 hypothetical protein YP_611402.1 146638 D 292414 CDS YP_611403.1 99078145 4075337 147745..148710 1 NC_008043.1 PFAM: Mandelate racemase/muconate lactonizing enzyme-like: (8.1e-17); KEGG: sil:SPO3606 mandelate racemase/muconate lactonizing enzyme family protein, ev=1e-151, 84% identity; mandelate racemase/muconate lactonizing-like protein 148710 4075337 TM1040_3167 Ruegeria sp. TM1040 mandelate racemase/muconate lactonizing-like protein YP_611403.1 147745 D 292414 CDS YP_611404.1 99078146 4075338 148721..149581 1 NC_008043.1 PFAM: aminotransferase, class IV: (1.3e-66); KEGG: sil:SPO3604 D-amino acid aminotransferase, , ev=1e-140, 86% identity; aminotransferase, class IV 149581 4075338 TM1040_3168 Ruegeria sp. TM1040 aminotransferase, class IV YP_611404.1 148721 D 292414 CDS YP_611405.1 99078147 4075339 complement(149646..150440) 1 NC_008043.1 PFAM: Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B: (4e-74); KEGG: aci:ACIAD2249 hypothetical protein, ev=1e-74, 51% identity; extradiol ring-cleavage dioxygenase III subunit B 150440 4075339 TM1040_3169 Ruegeria sp. TM1040 extradiol ring-cleavage dioxygenase III subunit B YP_611405.1 149646 R 292414 CDS YP_611406.1 99078148 4075340 complement(150625..150957) 1 NC_008043.1 PFAM: protein of unknown function DUF1244: (1e-44); KEGG: sil:SPO3602 hypothetical protein, ev=1e-41, 77% identity; hypothetical protein 150957 4075340 TM1040_3170 Ruegeria sp. TM1040 hypothetical protein YP_611406.1 150625 R 292414 CDS YP_611407.1 99078149 4075341 151141..152124 1 NC_008043.1 TIGRFAM: K+-dependent Na+/Ca+ exchanger related-protein: (4.5e-76); PFAM: sodium/calcium exchanger membrane region: (2.2e-39); KEGG: son:SO0354 sodium/calcium exchanger, ev=2e-66, 46% identity; K+-dependent Na+/Ca+ exchanger related-protein 152124 4075341 TM1040_3171 Ruegeria sp. TM1040 K+-dependent Na+/Ca+ exchanger related-protein YP_611407.1 151141 D 292414 CDS YP_611408.1 99078150 4075342 complement(152144..153709) 1 NC_008043.1 PFAM: ASPIC/UnbV: (2.9e-15); KEGG: sil:SPO0859 FG-GAP repeat domain protein, ev=0.0, 63% identity; ASPIC/UnbV 153709 4075342 TM1040_3172 Ruegeria sp. TM1040 ASPIC/UnbV YP_611408.1 152144 R 292414 CDS YP_611409.1 99078151 4075343 complement(153696..155003) 1 NC_008043.1 PFAM: ROK: (9.8e-29); KEGG: sil:SPO0860 xylose repressor, , ev=1e-115, 55% identity; ROK domain-containing protein 155003 4075343 TM1040_3173 Ruegeria sp. TM1040 ROK domain-containing protein YP_611409.1 153696 R 292414 CDS YP_611410.1 99078152 4075344 155096..156124 1 NC_008043.1 TIGRFAM: D-xylose ABC transporter, substrate-binding protein: (8.3e-198); PFAM: periplasmic binding protein/LacI transcriptional regulator: (0.0017); KEGG: sil:SPO0861 xylose ABC transporter, periplasmic xylose-binding protein, ev=1e-156, 81% identity; D-xylose ABC transporter, substrate-binding protein 156124 4075344 TM1040_3174 Ruegeria sp. TM1040 D-xylose ABC transporter, substrate-binding protein YP_611410.1 155096 D 292414 CDS YP_611411.1 99078153 4075345 156210..157508 1 NC_008043.1 PFAM: inner-membrane translocator: (1.2e-50); KEGG: sil:SPO0862 xylose ABC transporter, permease protein, ev=0.0, 76% identity; inner-membrane translocator 157508 4075345 TM1040_3175 Ruegeria sp. TM1040 inner-membrane translocator YP_611411.1 156210 D 292414 CDS YP_611412.1 99078154 4075346 157508..158299 1 NC_008043.1 PFAM: ABC transporter related: (8.4e-52); SMART: ATPase: (5.6e-17); KEGG: sil:SPO0863 xylose ABC transporter, ATP-binding protein, ev=1e-117, 86% identity; ABC transporter 158299 4075346 TM1040_3176 Ruegeria sp. TM1040 ABC transporter YP_611412.1 157508 D 292414 CDS YP_611413.1 99078155 4075347 158482..160731 1 NC_008043.1 PFAM: histidine kinase, HAMP region: (1.7e-07) Cache: (4.3e-12) chemotaxis sensory transducer: (1.7e-77); KEGG: ret:RHE_CH00974 methyl-accepting chemotaxis protein, ev=1e-176, 46% identity; methyl-accepting chemotaxis sensory transducer 160731 4075347 TM1040_3177 Ruegeria sp. TM1040 methyl-accepting chemotaxis sensory transducer YP_611413.1 158482 D 292414 CDS YP_611414.1 99078156 4075348 161441..162601 1 NC_008043.1 PFAM: Extracellular ligand-binding receptor: (1e-11); KEGG: bja:blr6548 probable leucine/isoleucine/valine-binding protein precursor, ev=1e-100, 53% identity; extracellular ligand-binding receptor 162601 4075348 TM1040_3178 Ruegeria sp. TM1040 extracellular ligand-binding receptor YP_611414.1 161441 D 292414 CDS YP_611415.1 99078157 4075349 162710..165367 1 NC_008043.1 PFAM: histidine kinase, HAMP region: (1.5e-06) chemotaxis sensory transducer: (1.7e-79); KEGG: ccr:CC0430 methyl-accepting chemotaxis protein McpA, ev=5e-99, 46% identity; methyl-accepting chemotaxis sensory transducer 165367 4075349 TM1040_3179 Ruegeria sp. TM1040 methyl-accepting chemotaxis sensory transducer YP_611415.1 162710 D 292414 CDS YP_611416.1 99078158 4075350 complement(165490..165984) 1 NC_008043.1 KEGG: sil:SPO1053 hypothetical protein, ev=1e-45, 58% identity; hypothetical protein 165984 4075350 TM1040_3180 Ruegeria sp. TM1040 hypothetical protein YP_611416.1 165490 R 292414 CDS YP_611417.1 99078159 4075351 complement(166163..166966) 1 NC_008043.1 PFAM: regulatory protein, LuxR: (2.4e-05); KEGG: sil:SPO2286 autoinducer-binding transcriptional regulator LuxR, ev=5e-07, 23% identity; LuxR family transcriptional regulator 166966 4075351 TM1040_3181 Ruegeria sp. TM1040 LuxR family transcriptional regulator YP_611417.1 166163 R 292414 CDS YP_611418.1 99078160 4075352 complement(167108..168082) 1 NC_008043.1 KEGG: rsp:RSP_3350 lipocalin-related protein, ev=2e-10, 23% identity; hypothetical protein 168082 4075352 TM1040_3182 Ruegeria sp. TM1040 hypothetical protein YP_611418.1 167108 R 292414 CDS YP_611419.1 99078161 4075353 complement(168159..169166) 1 NC_008043.1 hypothetical protein 169166 4075353 TM1040_3183 Ruegeria sp. TM1040 hypothetical protein YP_611419.1 168159 R 292414 CDS YP_611420.1 99078162 4075354 complement(169278..170225) 1 NC_008043.1 PFAM: protein of unknown function DUF6, transmembrane: (1.5e-20); KEGG: bur:Bcep18194_B1695 protein of unknown function DUF6, transmembrane, ev=8e-81, 57% identity; hypothetical protein 170225 4075354 TM1040_3184 Ruegeria sp. TM1040 hypothetical protein YP_611420.1 169278 R 292414 CDS YP_611421.1 99078163 4075355 170270..171157 1 NC_008043.1 PFAM: regulatory protein, LysR: (1.7e-22) LysR, substrate-binding: (1.4e-43); KEGG: pfl:PFL_3389 transcriptional regulator, LysR family, ev=7e-78, 51% identity; LysR family transcriptional regulator 171157 4075355 TM1040_3185 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_611421.1 170270 D 292414 CDS YP_611422.1 99078164 4075356 complement(171207..172082) 1 NC_008043.1 PFAM: regulatory protein, LysR: (2.3e-23); KEGG: sil:SPO0639 transcriptional regulator, LysR family, ev=2e-59, 45% identity; LysR family transcriptional regulator 172082 4075356 TM1040_3186 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_611422.1 171207 R 292414 CDS YP_611423.1 99078165 4075357 172197..172787 1 NC_008043.1 PFAM: metal-dependent phosphohydrolase, HD subdomain: (3.9e-05); KEGG: sil:SPO0638 hypothetical protein, ev=5e-80, 68% identity; metal dependent phosphohydrolase 172787 4075357 TM1040_3187 Ruegeria sp. TM1040 metal dependent phosphohydrolase YP_611423.1 172197 D 292414 CDS YP_611424.1 99078166 4075292 complement(179563..180438) 1 NC_008043.1 PFAM: regulatory protein, LysR: (2.8e-13) LysR, substrate-binding: (1.7e-27); KEGG: sil:SPO3301 transcriptional regulator, LysR family, ev=5e-78, 51% identity; LysR family transcriptional regulator 180438 4075292 TM1040_3188 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_611424.1 179563 R 292414 CDS YP_611425.1 99078167 4075293 180535..180816 1 NC_008043.1 KEGG: sil:SPO3302 hypothetical protein, ev=7e-18, 47% identity; hypothetical protein 180816 4075293 TM1040_3189 Ruegeria sp. TM1040 hypothetical protein YP_611425.1 180535 D 292414 CDS YP_611426.1 99078168 4075294 complement(181083..183857) 1 NC_008043.1 TIGRFAM: formate dehydrogenase, alpha subunit: (1.1e-256); PFAM: ferredoxin: (0.0011) 4Fe-4S ferredoxin, iron-sulfur binding: (9.6e-06) molybdopterin oxidoreductase: (2.5e-108) molydopterin dinucleotide-binding region: (2.4e-41) molybdopterin oxidoreductase Fe4S4 region: (3.7e-22); KEGG: sil:SPO0834 formate dehydrogenase, alpha subunit, ev=0.0, 75% identity; formate dehydrogenase subunit alpha 183857 4075294 TM1040_3190 Ruegeria sp. TM1040 formate dehydrogenase subunit alpha YP_611426.1 181083 R 292414 CDS YP_611427.1 99078169 4075295 complement(183861..185549) 1 NC_008043.1 PFAM: NADH dehydrogenase (ubiquinone), 24 kDa subunit: (9.3e-09) Respiratory-chain NADH dehydrogenase domain, 51 kDa subunit: (1.4e-90); KEGG: sil:SPO0833 formate dehydrogenase, beta subunit, ev=0.0, 82% identity; NADH dehydrogenase (quinone) 185549 4075295 TM1040_3191 Ruegeria sp. TM1040 NADH dehydrogenase (quinone) YP_611427.1 183861 R 292414 CDS YP_611428.1 99078170 4075296 complement(185663..186469) 1 NC_008043.1 PFAM: LysR, substrate-binding: (1.3e-27); KEGG: sil:SPO0832 transcriptional regulator, LysR family, ev=3e-81, 57% identity; LysR family transcriptional regulator 186469 4075296 TM1040_3192 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_611428.1 185663 R 292414 CDS YP_611429.1 99078171 4075297 186865..187434 1 NC_008043.1 KEGG: vch:VCA0032 hypothetical protein, ev=6e-40, 44% identity; hypothetical protein 187434 4075297 TM1040_3193 Ruegeria sp. TM1040 hypothetical protein YP_611429.1 186865 D 292414 CDS YP_611430.1 99078172 4075298 187476..189320 1 NC_008043.1 PFAM: histidine kinase, HAMP region: (4.6e-09) chemotaxis sensory transducer: (1.5e-81); KEGG: ccr:CC0343 methyl-accepting chemotaxis protein McpC, ev=2e-89, 42% identity; methyl-accepting chemotaxis sensory transducer 189320 4075298 TM1040_3194 Ruegeria sp. TM1040 methyl-accepting chemotaxis sensory transducer YP_611430.1 187476 D 292414 CDS YP_611431.1 99078173 4075299 190067..191065 1 NC_008043.1 PFAM: TRAP dicarboxylate transporter- DctP subunit: (2.7e-11); KEGG: dps:DP0483 DctP (periplasmic C4-dicarboxylate binding protein), ev=4e-25, 26% identity; TRAP dicarboxylate transporter- DctP subunit 191065 4075299 TM1040_3195 Ruegeria sp. TM1040 TRAP dicarboxylate transporter- DctP subunit YP_611431.1 190067 D 292414 CDS YP_611432.1 99078174 4075300 191222..191779 1 NC_008043.1 hypothetical protein 191779 4075300 TM1040_3196 Ruegeria sp. TM1040 hypothetical protein YP_611432.1 191222 D 292414 CDS YP_611433.1 99078175 4075301 191776..193065 1 NC_008043.1 TIGRFAM: TRAP dicarboxylate transporter- DctM subunit: (1e-74); PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit: (4.4e-68); KEGG: dps:DP0487 DctM (C4-dicarboxylate permease, large subunit), ev=6e-88, 38% identity; TRAP dicarboxylate transporter- DctM subunit 193065 4075301 TM1040_3197 Ruegeria sp. TM1040 TRAP dicarboxylate transporter- DctM subunit YP_611433.1 191776 D 292414 CDS YP_611434.1 99078176 4075302 193350..194309 1 NC_008043.1 PFAM: dihydrodipicolinate synthetase: (1.2e-09); KEGG: sil:SPOA0267 dihydroxydipicolinate synthase family protein, ev=1e-158, 84% identity; dihydrodipicolinate synthetase 194309 4075302 TM1040_3198 Ruegeria sp. TM1040 dihydrodipicolinate synthetase YP_611434.1 193350 D 292414 CDS YP_611435.1 99078177 4075303 194300..195226 1 NC_008043.1 PFAM: proline racemase: (2.1e-89); KEGG: sil:SPOA0266 proline racemase, , ev=1e-113, 65% identity; proline racemase 195226 4075303 TM1040_3199 Ruegeria sp. TM1040 proline racemase YP_611435.1 194300 D 292414 CDS YP_611436.1 99078178 4075304 195244..196530 1 NC_008043.1 PFAM: FAD dependent oxidoreductase: (1.1e-74); KEGG: sil:SPOA0262 oxidoreductase, FAD-binding, ev=1e-158, 66% identity; D-amino acid dehydrogenase small subunit 196530 4075304 TM1040_3200 Ruegeria sp. TM1040 D-amino acid dehydrogenase small subunit YP_611436.1 195244 D 292414 CDS YP_611437.1 99078179 4075305 196546..197571 1 NC_008043.1 PFAM: proline racemase: (1.5e-190); KEGG: atc:AGR_L_395 hypothetical protein PA1255, ev=1e-155, 77% identity; proline racemase 197571 4075305 TM1040_3201 Ruegeria sp. TM1040 proline racemase YP_611437.1 196546 D 292414 CDS YP_611438.1 99078180 4075306 complement(197964..198293) 1 NC_008043.1 hypothetical protein 198293 4075306 TM1040_3202 Ruegeria sp. TM1040 hypothetical protein YP_611438.1 197964 R 292414 CDS YP_611439.1 99078181 4075307 complement(198295..198681) 1 NC_008043.1 PFAM: response regulator receiver: (9.1e-15); KEGG: rsp:RSP_2433 chemotaxis response regulator, CheY2, ev=8e-40, 60% identity; response regulator receiver protein 198681 4075307 TM1040_3203 Ruegeria sp. TM1040 response regulator receiver protein YP_611439.1 198295 R 292414 CDS YP_611440.1 99078182 4075308 complement(198725..199582) 1 NC_008043.1 PFAM: MCP methyltransferase, CheR-type: (1.6e-78); KEGG: rsp:RSP_2434 MCP methyltransferase, CheR1, ev=4e-66, 46% identity; chemotaxis protein CheR 199582 4075308 TM1040_3204 Ruegeria sp. TM1040 chemotaxis protein CheR YP_611440.1 198725 R 292414 CDS YP_611441.1 99078183 4075309 complement(199579..200067) 1 NC_008043.1 PFAM: CheW-like protein: (3e-29); KEGG: ret:RHE_CH02831 chemotaxis signal transduction protein, ev=1e-30, 48% identity; CheW protein 200067 4075309 TM1040_3205 Ruegeria sp. TM1040 CheW protein YP_611441.1 199579 R 292414 CDS YP_611442.1 99078184 4075310 complement(200051..202186) 1 NC_008043.1 PFAM: CheW-like protein: (4.7e-21) ATP-binding region, ATPase-like: (1.5e-29) Signal transducing histidine kinase, homodimeric: (2.6e-16) Hpt: (6.3e-15); KEGG: ret:RHE_CH00639 chemotaxis two-component sensor histidine kinase protein, ev=0.0, 47% identity; CheA signal transduction histidine kinase 202186 4075310 TM1040_3206 Ruegeria sp. TM1040 CheA signal transduction histidine kinase YP_611442.1 200051 R 292414 CDS YP_611443.1 99078185 4075311 complement(202188..202562) 1 NC_008043.1 PFAM: response regulator receiver: (3.3e-28); KEGG: jan:Jann_2842 response regulator receiver domain protein (CheY-like), ev=4e-36, 61% identity; response regulator receiver protein 202562 4075311 TM1040_3207 Ruegeria sp. TM1040 response regulator receiver protein YP_611443.1 202188 R 292414 CDS YP_611444.1 99078186 4075312 complement(202559..202861) 1 NC_008043.1 hypothetical protein 202861 4075312 TM1040_3208 Ruegeria sp. TM1040 hypothetical protein YP_611444.1 202559 R 292414 CDS YP_611445.1 99078187 4075313 203191..205539 1 NC_008043.1 PFAM: histidine kinase, HAMP region: (1.4e-12) chemotaxis sensory transducer: (1.1e-88); KEGG: ccr:CC0343 methyl-accepting chemotaxis protein McpC, ev=1e-95, 44% identity; methyl-accepting chemotaxis sensory transducer 205539 4075313 TM1040_3209 Ruegeria sp. TM1040 methyl-accepting chemotaxis sensory transducer YP_611445.1 203191 D 292414 CDS YP_611446.1 99078188 4075314 205699..206634 1 NC_008043.1 PFAM: CheB methylesterase: (1.7e-61); KEGG: jan:Jann_2844 CheB methylesterase, ev=4e-48, 40% identity; CheB methylesterase 206634 4075314 TM1040_3210 Ruegeria sp. TM1040 CheB methylesterase YP_611446.1 205699 D 292414 CDS YP_611447.1 99078189 4075315 206661..207224 1 NC_008043.1 PFAM: CheD: (2.5e-30); KEGG: atc:AGR_C_918 chemotaxis protein cheD, ev=1e-43, 51% identity; MCP proteins methylation stimulator CheD 207224 4075315 TM1040_3211 Ruegeria sp. TM1040 MCP proteins methylation stimulator CheD YP_611447.1 206661 D 292414 CDS YP_611448.1 99078190 4075316 207380..208021 1 NC_008043.1 PFAM: regulatory protein, TetR: (1.7e-10); KEGG: sil:SPOA0067 transcriptional regulator, TetR family, ev=4e-44, 42% identity; TetR family transcriptional regulator 208021 4075316 TM1040_3212 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_611448.1 207380 D 292414 CDS YP_611449.1 99078191 4075317 208049..209620 1 NC_008043.1 PFAM: thiamine pyrophosphate enzyme-like TPP-binding: (1.2e-35) thiamine pyrophosphate enzyme, central region: (0.00021) thiamine pyrophosphate enzyme-like TPP binding region: (3.5e-47); KEGG: sil:SPOA0065 thiamine pyrophosphate-dependent enzyme, ev=1e-157, 56% identity; hypothetical protein 209620 4075317 TM1040_3213 Ruegeria sp. TM1040 hypothetical protein YP_611449.1 208049 D 292414 CDS YP_611450.1 99078192 4075318 complement(209629..210435) 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1.7e-08); KEGG: bbr:BB4935 inner membrane component of binding-protein-dependent transport system, ev=1e-108, 69% identity; binding-protein-dependent transport systems inner membrane component 210435 4075318 TM1040_3214 Ruegeria sp. TM1040 binding-protein-dependent transport systems inner membrane component YP_611450.1 209629 R 292414 CDS YP_611451.1 99078193 4075319 complement(210432..211307) 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1e-09); KEGG: bbr:BB4934 inner membrane component of binding-protein-dependent transport system, ev=1e-107, 63% identity; binding-protein-dependent transport systems inner membrane component 211307 4075319 TM1040_3215 Ruegeria sp. TM1040 binding-protein-dependent transport systems inner membrane component YP_611451.1 210432 R 292414 CDS YP_611452.1 99078194 4075320 complement(211368..212645) 1 NC_008043.1 PFAM: extracellular solute-binding protein, family 1: (2.3e-28); KEGG: bbr:BB4933 probable extracellular solute-binding protein, ev=1e-143, 58% identity; extracellular solute-binding protein 212645 4075320 TM1040_3216 Ruegeria sp. TM1040 extracellular solute-binding protein YP_611452.1 211368 R 292414 CDS YP_611453.1 99078195 4075321 complement(212764..213834) 1 NC_008043.1 PFAM: ABC transporter related: (2e-58) TOBE: (3.9e-10) Transport-associated OB: (1.1e-12); SMART: ATPase: (2.1e-12); KEGG: bbr:BB4932 sugar ABC transporter, ATP-binding protein, ev=5e-94, 56% identity; ABC transporter 213834 4075321 TM1040_3217 Ruegeria sp. TM1040 ABC transporter YP_611453.1 212764 R 292414 CDS YP_611454.1 99078196 4075360 complement(214064..215131) 1 NC_008043.1 PFAM: ferredoxin: (4.1e-18) oxidoreductase FAD/NAD(P)-binding: (2.5e-15) Oxidoreductase FAD-binding region: (4.1e-06); KEGG: sme:SMa0752 possible dioxygenase reductase subunit, ev=1e-136, 64% identity; ferredoxin 215131 4075360 TM1040_3218 Ruegeria sp. TM1040 ferredoxin YP_611454.1 214064 R 292414 CDS YP_611455.1 99078197 4075361 complement(215137..216363) 1 NC_008043.1 PFAM: Rieske [2Fe-2S] region: (4.8e-22); KEGG: sme:SMa0751 aromatic-ring hydroxylating dioxygenase, alpha-subunit, ev=1e-169, 68% identity; Rieske (2Fe-2S) protein 216363 4075361 TM1040_3219 Ruegeria sp. TM1040 Rieske (2Fe-2S) protein YP_611455.1 215137 R 292414 CDS YP_611456.1 99078198 4075362 216964..217980 1 NC_008043.1 PFAM: TRAP dicarboxylate transporter- DctP subunit: (6.1e-10); KEGG: sil:SPO1814 TRAP dicarboxylate transporter, DctP subunit, , ev=1e-148, 78% identity; TRAP dicarboxylate transporter- DctP subunit 217980 4075362 TM1040_3220 Ruegeria sp. TM1040 TRAP dicarboxylate transporter- DctP subunit YP_611456.1 216964 D 292414 CDS YP_611457.1 99078199 4075363 218070..218747 1 NC_008043.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component: (1.8e-10); KEGG: sil:SPOA0239 TRAP dicarboxylate transporter, DctQ subunit, ev=6e-70, 62% identity; tripartite ATP-independent periplasmic transporter DctQ 218747 4075363 TM1040_3221 Ruegeria sp. TM1040 tripartite ATP-independent periplasmic transporter DctQ YP_611457.1 218070 D 292414 CDS YP_611458.1 99078200 4075364 218740..220140 1 NC_008043.1 PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit: (1.7e-58); KEGG: sil:SPO1816 TRAP dicarboxylate transporter, DctM subunit, , ev=0.0, 84% identity; TRAP C4-dicarboxylate transport system permease DctM subunit 220140 4075364 TM1040_3222 Ruegeria sp. TM1040 TRAP C4-dicarboxylate transport system permease DctM subunit YP_611458.1 218740 D 292414 CDS YP_611459.1 99078201 4075365 complement(220725..221492) 1 NC_008043.1 KEGG: cvi:CV0102 probable ABC transporter, periplasmic substrate-binding, ev=6e-37, 36% identity; ABC transporter, periplasmic substrate-binding 221492 4075365 TM1040_3223 Ruegeria sp. TM1040 ABC transporter, periplasmic substrate-binding YP_611459.1 220725 R 292414 CDS YP_611460.1 99078202 4075366 complement(221636..222574) 1 NC_008043.1 hypothetical protein 222574 4075366 TM1040_3224 Ruegeria sp. TM1040 hypothetical protein YP_611460.1 221636 R 292414 CDS YP_611461.1 99078203 4075367 complement(222584..224017) 1 NC_008043.1 PFAM: von Willebrand factor, type A: (2e-06); KEGG: sil:SPO2221 von Willebrand factor type A domain protein, ev=3e-84, 41% identity; von Willebrand factor, type A 224017 4075367 TM1040_3225 Ruegeria sp. TM1040 von Willebrand factor, type A YP_611461.1 222584 R 292414 CDS YP_611462.1 99078204 4075368 complement(224021..224833) 1 NC_008043.1 hypothetical protein 224833 4075368 TM1040_3226 Ruegeria sp. TM1040 hypothetical protein YP_611462.1 224021 R 292414 CDS YP_611463.1 99078205 4075369 224962..226599 1 NC_008043.1 PFAM: alpha/beta hydrolase fold: (0.00011) regulatory protein, LuxR: (4.5e-05); KEGG: sil:SPO1388 transcriptional regulator, LuxR family/hydrolase, alpha/beta fold family, ev=3e-31, 26% identity; LuxR family transcriptional regulator 226599 4075369 TM1040_3227 Ruegeria sp. TM1040 LuxR family transcriptional regulator YP_611463.1 224962 D 292414 CDS YP_611464.1 99078206 4075370 complement(226645..227544) 1 NC_008043.1 PFAM: helix-turn-helix, AraC type: (3.3e-06) AraC-type transcriptional regulator-like: (3.9e-33); KEGG: gsu:GSU3127 transcriptional regulator, AraC family, ev=4e-50, 43% identity; AraC family transcriptional regulator 227544 4075370 TM1040_3228 Ruegeria sp. TM1040 AraC family transcriptional regulator YP_611464.1 226645 R 292414 CDS YP_611465.1 99078207 4075371 227859..228323 1 NC_008043.1 PFAM: ferredoxin: (6.4e-12) [2Fe-2S]-binding: (5.1e-28); KEGG: sme:SMb20343 isoquinoline 1-oxidoreductase, alpha ubunit, ev=3e-51, 62% identity; (2Fe-2S)-binding protein 228323 4075371 TM1040_3229 Ruegeria sp. TM1040 (2Fe-2S)-binding protein YP_611465.1 227859 D 292414 CDS YP_611466.1 99078208 4075372 228329..230506 1 NC_008043.1 TIGRFAM: Twin-arginine translocation pathway signal: (6.2e-05); PFAM: aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding: (6e-08); KEGG: hch:HCH_01590 aerobic-type carbon monoxide dehydrogenase large subunit CoxL/CutL-like protein, ev=1e-167, 45% identity; twin-arginine translocation pathway signal 230506 4075372 TM1040_3230 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_611466.1 228329 D 292414 CDS YP_611467.1 99078209 4075373 complement(230751..233225) 1 NC_008043.1 PFAM: response regulator receiver: (0.00049) ATP-binding region, ATPase-like: (7.1e-24) histidine kinase, HAMP region: (2.7e-14) histidine kinase A-like: (1.7e-06); KEGG: ypk:y3864 hypothetical protein, ev=1e-66, 26% identity; periplasmic sensor hybrid histidine kinase 233225 4075373 TM1040_3231 Ruegeria sp. TM1040 periplasmic sensor hybrid histidine kinase YP_611467.1 230751 R 292414 CDS YP_611468.1 99078210 4075374 complement(233222..233956) 1 NC_008043.1 PFAM: response regulator receiver: (4.5e-22) transcriptional regulatory protein-like: (1e-23); KEGG: pae:PA4983 probable two-component response regulator, ev=6e-45, 42% identity; two component transcriptional regulator 233956 4075374 TM1040_3232 Ruegeria sp. TM1040 two component transcriptional regulator YP_611468.1 233222 R 292414 CDS YP_611469.1 99078211 4075375 234200..235180 1 NC_008043.1 TIGRFAM: Phosphonate-binding periplasmic protein: (1.3e-71); KEGG: dde:Dde_3730 phosphonate-binding periplasmic protein, ev=5e-99, 59% identity; phosphonate-binding periplasmic protein 235180 4075375 TM1040_3233 Ruegeria sp. TM1040 phosphonate-binding periplasmic protein YP_611469.1 234200 D 292414 CDS YP_611470.1 99078212 4075376 235287..236060 1 NC_008043.1 KEGG: cyb:CYB_1467 phosphonate ABC transporter, ATP-binding protein, ev=4e-77, 56% identity; TIGRFAM: Phosphonate ABC transporter PhnC, ATP-binding: (3.6e-134); PFAM: ABC transporter related: (1.3e-62); SMART: ATPase: (1.5e-13); phosphonate ABC transporter ATP-binding protein 236060 4075376 TM1040_3234 Ruegeria sp. TM1040 phosphonate ABC transporter ATP-binding protein YP_611470.1 235287 D 292414 CDS YP_611471.1 99078213 4075377 236057..236863 1 NC_008043.1 TIGRFAM: Phosphonate uptake transporter: (2.2e-36); PFAM: binding-protein-dependent transport systems inner membrane component: (1.1e-16); KEGG: cyb:CYB_1468 phosphonate ABC transporter, permease protein, ev=6e-67, 50% identity; phosphonate ABC transporter permease 236863 4075377 TM1040_3235 Ruegeria sp. TM1040 phosphonate ABC transporter permease YP_611471.1 236057 D 292414 CDS YP_611472.1 99078214 4075378 236860..237690 1 NC_008043.1 TIGRFAM: Phosphonate uptake transporter: (2.3e-40); PFAM: binding-protein-dependent transport systems inner membrane component: (2.6e-16); KEGG: rpb:RPB_1925 phosphonate uptake transporter, ev=4e-71, 50% identity; phosphonate ABC transporter permease 237690 4075378 TM1040_3236 Ruegeria sp. TM1040 phosphonate ABC transporter permease YP_611472.1 236860 D 292414 CDS YP_611473.1 99078215 4075379 complement(237883..238554) 1 NC_008043.1 PFAM: DSBA oxidoreductase: (1.5e-07); KEGG: efa:EF1088 hypothetical protein, ev=5e-24, 31% identity; DSBA oxidoreductase 238554 4075379 TM1040_3237 Ruegeria sp. TM1040 DSBA oxidoreductase YP_611473.1 237883 R 292414 CDS YP_611474.1 99078216 4075380 complement(238624..239436) 1 NC_008043.1 KEGG: xft:PD0713 hypothetical protein, ev=9e-58, 45% identity; hypothetical protein 239436 4075380 TM1040_3238 Ruegeria sp. TM1040 hypothetical protein YP_611474.1 238624 R 292414 CDS YP_611475.1 99078217 4075381 complement(239499..240455) 1 NC_008043.1 KEGG: sme:SMc02708 glutathione S-transferase, ev=5e-95, 57% identity; glutathione S-transferase 240455 4075381 TM1040_3239 Ruegeria sp. TM1040 glutathione S-transferase YP_611475.1 239499 R 292414 CDS YP_611476.1 99078218 4075382 240577..241494 1 NC_008043.1 PFAM: regulatory protein, LysR: (7.9e-20) LysR, substrate-binding: (1.6e-60); KEGG: vpa:VPA0216 transcription regulator protein, ev=2e-82, 48% identity; LysR family transcriptional regulator 241494 4075382 TM1040_3240 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_611476.1 240577 D 292414 CDS YP_611477.1 99078219 4075383 242356..242763 1 NC_008043.1 hypothetical protein 242763 4075383 TM1040_3241 Ruegeria sp. TM1040 hypothetical protein YP_611477.1 242356 D 292414 CDS YP_611478.1 99078220 4075384 243791..246433 1 NC_008043.1 PFAM: chemotaxis sensory transducer: (4.7e-59) PAS fold-3: (9.1e-12) PAS fold-4: (0.00012) PAS fold: (0.0014); SMART: PAS: (3.6e-05) PAC motif: (0.01); KEGG: bba:Bd2831 methyl-accepting chemotaxis protein, ev=1e-148, 45% identity; methyl-accepting chemotaxis sensory transducer with Pas/Pac sensor 246433 4075384 TM1040_3242 Ruegeria sp. TM1040 methyl-accepting chemotaxis sensory transducer with Pas/Pac sensor YP_611478.1 243791 D 292414 CDS YP_611479.1 99078221 4075385 246458..247288 1 NC_008043.1 PFAM: MCP methyltransferase, CheR-type: (9.6e-50); KEGG: bba:Bd2830 chemotaxis protein methyltransferase, ev=9e-56, 40% identity; chemotaxis protein CheR 247288 4075385 TM1040_3243 Ruegeria sp. TM1040 chemotaxis protein CheR YP_611479.1 246458 D 292414 CDS YP_611480.1 99078222 4075386 247293..247832 1 NC_008043.1 KEGG: bba:Bd2829 chemotaxis protein, ev=6e-14, 30% identity; MCP proteins methylation stimulator CheD 247832 4075386 TM1040_3244 Ruegeria sp. TM1040 MCP proteins methylation stimulator CheD YP_611480.1 247293 D 292414 CDS YP_611481.1 99078223 4075387 247832..249418 1 NC_008043.1 PFAM: CheW-like protein: (5.2e-16); KEGG: bba:Bd2828 purine-binding chemotaxis protein CheW, ev=6e-67, 29% identity; CheW protein 249418 4075387 TM1040_3245 Ruegeria sp. TM1040 CheW protein YP_611481.1 247832 D 292414 CDS YP_611482.1 99078224 4075388 249743..250009 1 NC_008043.1 PFAM: transposase IS3/IS911: (3.7e-16); KEGG: ret:RHE_PA00090 probable insertion sequence transposase protein, IS3/IS911 family, ev=3e-33, 76% identity; transposase IS3/IS911 250009 4075388 TM1040_3246 Ruegeria sp. TM1040 transposase IS3/IS911 YP_611482.1 249743 D 292414 CDS YP_611483.1 99078225 4075389 250042..250839 1 NC_008043.1 PFAM: Integrase, catalytic region: (4.6e-37); KEGG: mlo:mll6088 transposase, ev=1e-117, 75% identity; integrase catalytic subunit 250839 4075389 TM1040_3247 Ruegeria sp. TM1040 integrase catalytic subunit YP_611483.1 250042 D 292414 CDS YP_611484.1 99078226 4075390 250950..251117 1 NC_008043.1 KEGG: mag:amb0914 transposase and inactivated derivative, ev=1e-09, 53% identity; transposase and inactivated derivative 251117 4075390 TM1040_3248 Ruegeria sp. TM1040 transposase and inactivated derivative YP_611484.1 250950 D 292414 CDS YP_611485.1 99078227 4075391 251153..251410 1 NC_008043.1 KEGG: deh:cbdb_A1487 transposase orfB, ev=1e-20, 59% identity; transposase orfB 251410 4075391 TM1040_3249 Ruegeria sp. TM1040 transposase orfB YP_611485.1 251153 D 292414 CDS YP_611486.1 99078228 4075392 complement(251761..252285) 1 NC_008043.1 PFAM: CBS: (3.4e-30); KEGG: sil:SPOA0034 CBS domain protein, ev=7e-46, 53% identity; signal-transduction protein 252285 4075392 TM1040_3250 Ruegeria sp. TM1040 signal-transduction protein YP_611486.1 251761 R 292414 CDS YP_611487.1 99078229 4075393 252364..252546 1 NC_008043.1 KEGG: sil:SPOA0035 hypothetical protein, ev=6e-08, 50% identity; hypothetical protein 252546 4075393 TM1040_3251 Ruegeria sp. TM1040 hypothetical protein YP_611487.1 252364 D 292414 CDS YP_611488.1 99078230 4075394 complement(252601..253611) 1 NC_008043.1 PFAM: inner-membrane translocator: (2.2e-60); KEGG: ppr:PBPRB0472 sugar ABC transporter (permease), ev=6e-58, 37% identity; inner-membrane translocator 253611 4075394 TM1040_3252 Ruegeria sp. TM1040 inner-membrane translocator YP_611488.1 252601 R 292414 CDS YP_611489.1 99078231 4075395 complement(253608..255110) 1 NC_008043.1 PFAM: ABC transporter related: (8.1e-30); SMART: ATPase: (2.3e-09); KEGG: sma:SAV5319 D-ribose ABC transporter ATP-binding protein, ev=1e-108, 44% identity; ABC transporter 255110 4075395 TM1040_3253 Ruegeria sp. TM1040 ABC transporter YP_611489.1 253608 R 292414 CDS YP_611490.1 99078232 4075396 complement(255172..256242) 1 NC_008043.1 periplasmic sensory protein associated with the TorRS two-component regulatory system; TMAO reductase system periplasmic protein TorT 256242 4075396 TM1040_3254 Ruegeria sp. TM1040 TMAO reductase system periplasmic protein TorT YP_611490.1 255172 R 292414 CDS YP_611491.1 99078233 4075397 complement(256334..257305) 1 NC_008043.1 PFAM: Allophanate hydrolase subunit 2: (1.2e-69); KEGG: bps:BPSS0194 hypothetical protein, ev=1e-105, 57% identity; Urea carboxylase 257305 4075397 TM1040_3255 Ruegeria sp. TM1040 Urea carboxylase YP_611491.1 256334 R 292414 CDS YP_611492.1 99078234 4075398 complement(257295..258170) 1 NC_008043.1 PFAM: Allophanate hydrolase subunit 1: (5.3e-09); KEGG: allophanate hydrolase, subunit 1, ev=1e-113, 64% identity; allophanate hydrolase subunit 1 258170 4075398 TM1040_3256 Ruegeria sp. TM1040 allophanate hydrolase subunit 1 YP_611492.1 257295 R 292414 CDS YP_611493.1 99078235 4075399 complement(258167..259543) 1 NC_008043.1 an AccC homodimer forms the biotin carboxylase subunit of the acetyl CoA carboxylase, an enzyme that catalyzes the formation of malonyl-CoA, which in turn controls the rate of fatty acid metabolism; acetyl-CoA carboxylase biotin carboxylase subunit 259543 4075399 TM1040_3257 Ruegeria sp. TM1040 acetyl-CoA carboxylase biotin carboxylase subunit YP_611493.1 258167 R 292414 CDS YP_611494.1 99078236 4075400 complement(259547..259780) 1 NC_008043.1 PFAM: biotin/lipoyl attachment: (3e-14); KEGG: pae:PA0493 acetyl-CoA carboxylase, ev=4e-13, 48% identity; hypothetical protein 259780 4075400 TM1040_3258 Ruegeria sp. TM1040 hypothetical protein YP_611494.1 259547 R 292414 CDS YP_611495.1 99078237 4075401 complement(259817..260596) 1 NC_008043.1 PFAM: LamB/YcsF: (4.5e-111); KEGG: LamB/YcsF family protein, ev=1e-89, 63% identity; hypothetical protein 260596 4075401 TM1040_3259 Ruegeria sp. TM1040 hypothetical protein YP_611495.1 259817 R 292414 CDS YP_611496.1 99078238 4075402 260876..261793 1 NC_008043.1 PFAM: regulatory protein, LysR: (4.3e-20) LysR, substrate-binding: (2.6e-48); KEGG: transcriptional regulator, LysR family, ev=4e-94, 59% identity; LysR family transcriptional regulator 261793 4075402 TM1040_3260 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_611496.1 260876 D 292414 CDS YP_611497.1 99078239 4075403 complement(261790..262362) 1 NC_008043.1 PFAM: helix-turn-helix motif: (3.1e-15) Cupin 2, conserved barrel: (1.5e-20); KEGG: sil:SPOA0273 DNA-binding protein, , ev=9e-86, 81% identity; XRE family transcriptional regulator 262362 4075403 TM1040_3261 Ruegeria sp. TM1040 XRE family transcriptional regulator YP_611497.1 261790 R 292414 CDS YP_611498.1 99078240 4075404 262509..263786 1 NC_008043.1 catalyzes the formation of succinate semialdehyde and glutamate from 4-aminobutanoate and 2-oxoglutarate; 4-aminobutyrate aminotransferase 263786 4075404 TM1040_3262 Ruegeria sp. TM1040 4-aminobutyrate aminotransferase YP_611498.1 262509 D 292414 CDS YP_611499.1 99078241 4075405 263788..265257 1 NC_008043.1 KEGG: sil:SPOA0275 succinate-semialdehyde dehydrogenase, ev=0.0, 80% identity; TIGRFAM: succinic semialdehyde dehydrogenase: (0); PFAM: aldehyde dehydrogenase: (8.3e-233); succinate semialdehyde dehydrogenase 265257 4075405 TM1040_3263 Ruegeria sp. TM1040 succinate semialdehyde dehydrogenase YP_611499.1 263788 D 292414 CDS YP_611500.1 99078242 4075406 265413..266627 1 NC_008043.1 PFAM: ROK: (3.6e-30); KEGG: jan:Jann_0880 ROK, ev=1e-107, 51% identity; ROK domain-containing protein 266627 4075406 TM1040_3264 Ruegeria sp. TM1040 ROK domain-containing protein YP_611500.1 265413 D 292414 CDS YP_611501.1 99078243 4075407 266624..267874 1 NC_008043.1 PFAM: peptidase M20: (2.6e-23) peptidase dimerisation: (1.4e-05); KEGG: jan:Jann_0881 peptidase M20, ev=1e-138, 57% identity; acetylornithine deacetylase 267874 4075407 TM1040_3265 Ruegeria sp. TM1040 acetylornithine deacetylase YP_611501.1 266624 D 292414 CDS YP_611502.1 99078244 4075408 267890..268942 1 NC_008043.1 KEGG: jan:Jann_0882 periplasmic binding protein/LacI transcriptional regulator, ev=1e-145, 74% identity; periplasmic binding protein/LacI transcriptional regulator 268942 4075408 TM1040_3266 Ruegeria sp. TM1040 periplasmic binding protein/LacI transcriptional regulator YP_611502.1 267890 D 292414 CDS YP_611503.1 99078245 4075409 269124..270077 1 NC_008043.1 PFAM: inner-membrane translocator: (1e-57); KEGG: jan:Jann_0883 inner-membrane translocator, ev=1e-130, 77% identity; inner-membrane translocator 270077 4075409 TM1040_3267 Ruegeria sp. TM1040 inner-membrane translocator YP_611503.1 269124 D 292414 CDS YP_611504.1 99078246 4075410 270091..271302 1 NC_008043.1 KEGG: jan:Jann_0884 hypothetical protein, ev=1e-163, 71% identity; hypothetical protein 271302 4075410 TM1040_3268 Ruegeria sp. TM1040 hypothetical protein YP_611504.1 270091 D 292414 CDS YP_611505.1 99078247 4075411 271299..272042 1 NC_008043.1 PFAM: ABC transporter related: (2.9e-49); SMART: ATPase: (8.5e-19); KEGG: jan:Jann_0885 ABC transporter related, ev=1e-102, 78% identity; ABC transporter 272042 4075411 TM1040_3269 Ruegeria sp. TM1040 ABC transporter YP_611505.1 271299 D 292414 CDS YP_611506.1 99078248 4075412 complement(272076..272879) 1 NC_008043.1 PFAM: short-chain dehydrogenase/reductase SDR: (1.4e-30); KEGG: sil:SPO1015 3-hydroxybutyrate dehydrogenase, , ev=1e-104, 69% identity; short-chain dehydrogenase/reductase SDR 272879 4075412 TM1040_3270 Ruegeria sp. TM1040 short-chain dehydrogenase/reductase SDR YP_611506.1 272076 R 292414 CDS YP_611507.1 99078249 4075413 complement(272876..274402) 1 NC_008043.1 PFAM: AMP-dependent synthetase and ligase: (1e-106); KEGG: rpa:RPA3465 long-chain-fatty-acid CoA ligase, ev=1e-169, 60% identity; AMP-dependent synthetase and ligase 274402 4075413 TM1040_3271 Ruegeria sp. TM1040 AMP-dependent synthetase and ligase YP_611507.1 272876 R 292414 CDS YP_611508.1 99078250 4075414 complement(274399..275559) 1 NC_008043.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation; acetyl-CoA acetyltransferase 275559 4075414 TM1040_3272 Ruegeria sp. TM1040 acetyl-CoA acetyltransferase YP_611508.1 274399 R 292414 CDS YP_611509.1 99078251 4075415 275643..276200 1 NC_008043.1 PFAM: regulatory protein, LuxR: (2.1e-21); SMART: PAS: (4.3e-06); KEGG: sil:SPO1012 transcriptional regulator, LuxR family, ev=1e-50, 54% identity; LuxR family transcriptional regulator 276200 4075415 TM1040_3273 Ruegeria sp. TM1040 LuxR family transcriptional regulator YP_611509.1 275643 D 292414 CDS YP_611510.1 99078252 4075416 complement(276579..276818) 1 NC_008043.1 hypothetical protein 276818 4075416 TM1040_3274 Ruegeria sp. TM1040 hypothetical protein YP_611510.1 276579 R 292414 CDS YP_611511.1 99078253 4075417 276840..277046 1 NC_008043.1 KEGG: eli:ELI_14900 transposase orfB, ev=3e-15, 62% identity; transposase orfB 277046 4075417 TM1040_3275 Ruegeria sp. TM1040 transposase orfB YP_611511.1 276840 D 292414 CDS YP_611512.1 99078254 4075680 277180..277410 1 NC_008043.1 KEGG: deh:cbdb_A1487 transposase orfB, ev=2e-11, 48% identity; transposase orfB 277410 4075680 TM1040_3276 Ruegeria sp. TM1040 transposase orfB YP_611512.1 277180 D 292414 CDS YP_611513.1 99078255 4075681 complement(277819..280044) 1 NC_008043.1 PFAM: response regulator receiver: (3.4e-31) ATP-binding region, ATPase-like: (2.4e-41) histidine kinase A-like: (6.6e-26); KEGG: ccr:CC3102 sensor histidine kinase/response regulator, ev=8e-78, 44% identity; periplasmic sensor hybrid histidine kinase 280044 4075681 TM1040_3277 Ruegeria sp. TM1040 periplasmic sensor hybrid histidine kinase YP_611513.1 277819 R 292414 CDS YP_611514.1 99078256 4075682 complement(280321..281094) 1 NC_008043.1 hypothetical protein 281094 4075682 TM1040_3278 Ruegeria sp. TM1040 hypothetical protein YP_611514.1 280321 R 292414 CDS YP_611515.1 99078257 4075683 281477..281905 1 NC_008043.1 KEGG: sil:SPO2951 hypothetical protein, ev=1e-17, 45% identity; hypothetical protein 281905 4075683 TM1040_3279 Ruegeria sp. TM1040 hypothetical protein YP_611515.1 281477 D 292414 CDS YP_611516.1 99078258 4075684 complement(282061..282978) 1 NC_008043.1 PFAM: protein of unknown function DUF6, transmembrane: (8.3e-09); KEGG: vpa:VPA1215 hypothetical protein, ev=1e-35, 31% identity; hypothetical protein 282978 4075684 TM1040_3280 Ruegeria sp. TM1040 hypothetical protein YP_611516.1 282061 R 292414 CDS YP_611517.1 99078259 4075685 complement(283051..283272) 1 NC_008043.1 TIGRFAM: 4-oxalocrotonate tautomerase family enzyme: (1.3e-16); PFAM: 4-oxalocrotonate tautomerase: (4.1e-18); KEGG: plu:plu0307 hypothetical protein, ev=5e-16, 54% identity; 4-oxalocrotonate tautomerase 283272 4075685 TM1040_3281 Ruegeria sp. TM1040 4-oxalocrotonate tautomerase YP_611517.1 283051 R 292414 CDS YP_611518.1 99078260 4075686 complement(283277..283657) 1 NC_008043.1 KEGG: ccr:CC2974 hypothetical protein, ev=3e-19, 37% identity; hypothetical protein 283657 4075686 TM1040_3282 Ruegeria sp. TM1040 hypothetical protein YP_611518.1 283277 R 292414 CDS YP_611519.1 99078261 4075687 complement(284032..284922) 1 NC_008043.1 PFAM: regulatory protein, LysR: (1.2e-18) LysR, substrate-binding: (3.4e-27); KEGG: hch:HCH_06627 transcriptional regulator, ev=1e-38, 32% identity; LysR family transcriptional regulator 284922 4075687 TM1040_3283 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_611519.1 284032 R 292414 CDS YP_611520.1 99078262 4075688 285111..285689 1 NC_008043.1 PFAM: NADPH-dependent FMN reductase: (0.0023); KEGG: reu:Reut_B4867 flavodoxin/nitric oxide synthase, ev=6e-58, 60% identity; NADPH-dependent FMN reductase 285689 4075688 TM1040_3284 Ruegeria sp. TM1040 NADPH-dependent FMN reductase YP_611520.1 285111 D 292414 CDS YP_611521.1 99078263 4075689 complement(286135..291822) 1 NC_008043.1 TIGRFAM: Outer membrane autotransporter barrel: (1.5e-11); PFAM: Autotransporter beta-domain: (1.7e-19); KEGG: spn:SP1772 cell wall surface anchor family protein, ev=2e-87, 21% identity; Outer membrane autotransporter barrel 291822 4075689 TM1040_3285 Ruegeria sp. TM1040 Outer membrane autotransporter barrel YP_611521.1 286135 R 292414 CDS YP_611522.1 99078264 4075690 292367..292873 1 NC_008043.1 PFAM: phage Tail Collar: (3.5e-20); KEGG: mlo:mll4443 microcystin dependent protein MdpB, ev=4e-50, 55% identity; phage tail Collar 292873 4075690 TM1040_3286 Ruegeria sp. TM1040 phage tail Collar YP_611522.1 292367 D 292414 CDS YP_611523.1 99078265 4075691 292891..293409 1 NC_008043.1 PFAM: phage Tail Collar: (4.3e-26); KEGG: hch:HCH_06045 microcystin-dependent protein, ev=2e-47, 51% identity; phage tail Collar 293409 4075691 TM1040_3287 Ruegeria sp. TM1040 phage tail Collar YP_611523.1 292891 D 292414 CDS YP_611524.1 99078266 4075692 293419..293946 1 NC_008043.1 PFAM: phage Tail Collar: (4.4e-20); KEGG: mlo:mll4441 microcystin dependent protein MdpB, ev=2e-48, 53% identity; phage tail Collar 293946 4075692 TM1040_3288 Ruegeria sp. TM1040 phage tail Collar YP_611524.1 293419 D 292414 CDS YP_611525.1 99078267 4075693 294016..295233 1 NC_008043.1 KEGG: cac:CAC3395 predicted membrane protein, ev=3e-09, 22% identity; hypothetical protein 295233 4075693 TM1040_3289 Ruegeria sp. TM1040 hypothetical protein YP_611525.1 294016 D 292414 CDS YP_611526.1 99078268 4075694 295230..295811 1 NC_008043.1 PFAM: GCN5-related N-acetyltransferase: (1.7e-08); KEGG: mlo:mll4440 contains weak similarity to acetyltransferase, ev=8e-45, 62% identity; N-acetyltransferase GCN5 295811 4075694 TM1040_3290 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_611526.1 295230 D 292414 CDS YP_611527.1 99078269 4075695 complement(295787..296080) 1 NC_008043.1 KEGG: mlo:mlr4438 hypothetical protein, ev=1e-08, 39% identity; hypothetical protein 296080 4075695 TM1040_3291 Ruegeria sp. TM1040 hypothetical protein YP_611527.1 295787 R 292414 CDS YP_611528.1 99078270 4075696 complement(296382..297275) 1 NC_008043.1 hypothetical protein 297275 4075696 TM1040_3292 Ruegeria sp. TM1040 hypothetical protein YP_611528.1 296382 R 292414 CDS YP_611529.1 99078271 4075697 complement(297512..298483) 1 NC_008043.1 PFAM: helix-turn-helix, AraC type: (9.1e-05) ThiJ/PfpI: (6.7e-06); KEGG: atc:AGR_pAT_bx241 transcriptional regulator homolog (GlxA), ev=1e-58, 43% identity; transcriptional regulator 298483 4075697 TM1040_3293 Ruegeria sp. TM1040 transcriptional regulator YP_611529.1 297512 R 292414 CDS YP_611530.1 99078272 4075698 298528..300558 1 NC_008043.1 AcsA; in Sinorhizobium meliloti this enzyme is required for acetoacetate activation; similar to acetyl-CoA synthase; acetoacetyl-CoA synthetase 300558 4075698 TM1040_3294 Ruegeria sp. TM1040 acetoacetyl-CoA synthetase YP_611530.1 298528 D 292414 CDS YP_611531.1 99078273 4075699 300578..301495 1 NC_008043.1 PFAM: protein of unknown function DUF849: (8e-195); KEGG: jan:Jann_3825 protein of unknown function DUF849, ev=1e-148, 82% identity; hypothetical protein 301495 4075699 TM1040_3295 Ruegeria sp. TM1040 hypothetical protein YP_611531.1 300578 D 292414 CDS YP_611532.1 99078274 4075701 303158..304633 1 NC_008043.1 PFAM: BCCT transporter: (2.3e-102); KEGG: cps:CPS_4027 transporter, BCCT family, ev=1e-122, 48% identity; BCCT transporter 304633 4075701 TM1040_3298 Ruegeria sp. TM1040 BCCT transporter YP_611532.1 303158 D 292414 CDS YP_611533.1 99078275 4075702 304724..306997 1 NC_008043.1 TIGRFAM: PAS: (1e-08); PFAM: ATP-binding region, ATPase-like: (1.9e-28) histidine kinase, HAMP region: (0.00021) histidine kinase A-like: (5.9e-09) PAS fold-4: (0.0032); KEGG: son:SO0544 sensory box histidine kinase, ev=7e-56, 33% identity; multi-sensor signal transduction histidine kinase 306997 4075702 TM1040_3299 Ruegeria sp. TM1040 multi-sensor signal transduction histidine kinase YP_611533.1 304724 D 292414 CDS YP_611534.1 99078276 4075703 307142..308299 1 NC_008043.1 PFAM: response regulator receiver: (8.5e-14) ATP-binding region, ATPase-like: (3.8e-33) histidine kinase A-like: (0.00021); KEGG: ret:RHE_CH00624 probable two-component sensor histidine kinase/response regulator hybrid protein, ev=5e-45, 30% identity; response regulator receiver sensor signal transduction histidine kinase 308299 4075703 TM1040_3300 Ruegeria sp. TM1040 response regulator receiver sensor signal transduction histidine kinase YP_611534.1 307142 D 292414 CDS YP_611535.1 99078277 4075704 complement(308585..308794) 1 NC_008043.1 PFAM: Endoribonuclease L-PSP: (0.0046); KEGG: jan:Jann_2297 endoribonuclease L-PSP, ev=4e-24, 81% identity; endoribonuclease L-PSP 308794 4075704 TM1040_3301 Ruegeria sp. TM1040 endoribonuclease L-PSP YP_611535.1 308585 R 292414 CDS YP_611536.1 99078278 4075705 complement(308814..309152) 1 NC_008043.1 KEGG: neu:NE2446 transposase IS4 family, ev=2e-11, 51% identity; hypothetical protein 309152 4075705 TM1040_3302 Ruegeria sp. TM1040 hypothetical protein YP_611536.1 308814 R 292414 CDS YP_611537.1 99078279 4075707 complement(310065..311162) 1 NC_008043.1 PFAM: ABC transporter related: (1.9e-54) TOBE: (0.00078) Transport-associated OB: (8e-05); SMART: ATPase: (1.7e-16); KEGG: rsp:RSP_2870 ABC alpha-glucoside transporter, ATPase subunit AglK, ev=1e-141, 73% identity; ABC transporter 311162 4075707 TM1040_3303 Ruegeria sp. TM1040 ABC transporter YP_611537.1 310065 R 292414 CDS YP_611538.1 99078280 4075708 complement(311182..312834) 1 NC_008043.1 PFAM: alpha amylase, catalytic region: (4.1e-97); SMART: Alpha amylase, catalytic subdomain: (6.3e-132); KEGG: jan:Jann_1949 alpha amylase protein, ev=0.0, 72% identity; alpha amylase 312834 4075708 TM1040_3304 Ruegeria sp. TM1040 alpha amylase YP_611538.1 311182 R 292414 CDS YP_611539.1 99078281 4075709 complement(312880..314028) 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (2.3e-11); KEGG: rsp:RSP_2871 ABC alpha-glucoside transporter, inner membrane subunit AglG, ev=1e-139, 67% identity; binding-protein-dependent transport system inner membrane protein 314028 4075709 TM1040_3305 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_611539.1 312880 R 292414 CDS YP_611540.1 99078282 4075710 complement(314042..315049) 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (0.0022); KEGG: rsp:RSP_2872 ABC alpha-glucoside transporter, inner membrane subunit AglF, ev=1e-123, 67% identity; binding-protein-dependent transport system inner membrane protein 315049 4075710 TM1040_3306 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_611540.1 314042 R 292414 CDS YP_611541.1 99078283 4075711 complement(315194..316543) 1 NC_008043.1 PFAM: extracellular solute-binding protein, family 1: (0.013); KEGG: rsp:RSP_2873 ABC alpha-glucoside transporter, perplasmic substrate-binding protein, ev=0.0, 67% identity; extracellular solute-binding protein 316543 4075711 TM1040_3307 Ruegeria sp. TM1040 extracellular solute-binding protein YP_611541.1 315194 R 292414 CDS YP_611542.1 99078284 4075712 316810..317850 1 NC_008043.1 PFAM: periplasmic binding protein/LacI transcriptional regulator: (3.2e-09); SMART: regulatory protein, LacI: (1.3e-18); KEGG: jan:Jann_1945 transcriptional regulator, LacI family, ev=1e-107, 58% identity; LacI family transcriptional regulator 317850 4075712 TM1040_3308 Ruegeria sp. TM1040 LacI family transcriptional regulator YP_611542.1 316810 D 292414 CDS YP_611543.1 99078285 4075713 317847..319181 1 NC_008043.1 PFAM: glycoside hydrolase, family 1: (5.3e-161); KEGG: jan:Jann_1944 beta-glucosidase, ev=0.0, 69% identity; Beta-glucosidase 319181 4075713 TM1040_3309 Ruegeria sp. TM1040 Beta-glucosidase YP_611543.1 317847 D 292414 CDS YP_611544.1 99078286 4075714 complement(319232..319723) 1 NC_008043.1 RibE; 6,7-diimethyl-8-ribityllumazine synthase; DMRL synthase; lumazine synthase; beta subunit of riboflavin synthase; condenses 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate to generate 6,6-dimethyl-8-lumazine (DMRL); riboflavin synthase then uses 2 molecules of DMRL to produce riboflavin (vitamin B12); involved in the last steps of riboflavin biosynthesis; forms a 60mer (icosahedral shell) in both Bacillus subtilis and Escherichia coli; in Bacillus subtilis this 60mer is associated with the riboflavin synthase subunit (alpha) while in Escherichia coli it is not; riboflavin synthase subunit beta 319723 4075714 TM1040_3310 Ruegeria sp. TM1040 riboflavin synthase subunit beta YP_611544.1 319232 R 292414 CDS YP_611545.1 99078287 4075716 320075..321163 1 NC_008043.1 PFAM: regulatory protein, LacI: (6.5e-08) periplasmic binding protein/LacI transcriptional regulator: (2.2e-13); KEGG: bbr:BB4926 probable LacI-family transcriptional regulator, ev=4e-46, 32% identity; LacI family transcription regulator 321163 4075716 TM1040_3311 Ruegeria sp. TM1040 LacI family transcription regulator YP_611545.1 320075 D 292414 CDS YP_611546.1 99078288 4075717 321168..322187 1 NC_008043.1 KEGG: bbr:BB4927 probable periplasmic solute-binding protein, ev=1e-126, 62% identity; periplasmic solute-binding protein 322187 4075717 TM1040_3312 Ruegeria sp. TM1040 periplasmic solute-binding protein YP_611546.1 321168 D 292414 CDS YP_611547.1 99078289 4075718 322245..323048 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1.5e-13); KEGG: rpa:RPA1477 permease protein, ev=3e-87, 61% identity; binding-protein-dependent transport systems inner membrane component 323048 4075718 TM1040_3313 Ruegeria sp. TM1040 binding-protein-dependent transport systems inner membrane component YP_611547.1 322245 D 292414 CDS YP_611548.1 99078290 4075719 323052..323840 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1.3e-15); KEGG: rpa:RPA1478 permease protein, ev=5e-95, 68% identity; binding-protein-dependent transport systems inner membrane component 323840 4075719 TM1040_3314 Ruegeria sp. TM1040 binding-protein-dependent transport systems inner membrane component YP_611548.1 323052 D 292414 CDS YP_611549.1 99078291 4075720 323837..324865 1 NC_008043.1 PFAM: ABC transporter related: (3.8e-67) Transport-associated OB: (2.6e-10); SMART: ATPase: (3.3e-22); KEGG: rpa:RPA1479 transport system ATP-binding protein, ev=4e-86, 51% identity; ABC transporter 324865 4075720 TM1040_3315 Ruegeria sp. TM1040 ABC transporter YP_611549.1 323837 D 292414 CDS YP_611550.1 99078292 4075721 324875..325687 1 NC_008043.1 PFAM: metallophosphoesterase: (9.7e-16); KEGG: rpb:RPB_4042 metallophosphoesterase, ev=8e-46, 41% identity; metallophosphoesterase 325687 4075721 TM1040_3316 Ruegeria sp. TM1040 metallophosphoesterase YP_611550.1 324875 D 292414 CDS YP_611551.1 99078293 4075722 complement(325731..327014) 1 NC_008043.1 TIGRFAM: TRAP dicarboxylate transporter- DctM subunit: (1.1e-147); PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit: (3.2e-144); KEGG: vpa:VPA1704 integral membrane protein, possible transporter, ev=1e-92, 41% identity; TRAP dicarboxylate transporter- DctM subunit 327014 4075722 TM1040_3317 Ruegeria sp. TM1040 TRAP dicarboxylate transporter- DctM subunit YP_611551.1 325731 R 292414 CDS YP_611552.1 99078294 4075723 complement(327007..327534) 1 NC_008043.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component: (2.3e-27); KEGG: bbr:BB1743 hypothetical protein, ev=1e-16, 36% identity; tripartite ATP-independent periplasmic transporter DctQ 327534 4075723 TM1040_3318 Ruegeria sp. TM1040 tripartite ATP-independent periplasmic transporter DctQ YP_611552.1 327007 R 292414 CDS YP_611553.1 99078295 4075724 complement(327591..328571) 1 NC_008043.1 TIGRFAM: TRAP dicarboxylate transporter, DctP subunit: (2.5e-87); PFAM: TRAP dicarboxylate transporter- DctP subunit: (8e-107); KEGG: bpe:BP2352 periplasmic substrate-binding transport protein, ev=5e-99, 55% identity; TRAP dicarboxylate transporter, DctP subunit 328571 4075724 TM1040_3319 Ruegeria sp. TM1040 TRAP dicarboxylate transporter, DctP subunit YP_611553.1 327591 R 292414 CDS YP_611554.1 99078296 4075725 complement(328688..329566) 1 NC_008043.1 PFAM: 6-phosphogluconate dehydrogenase, NAD-binding: (6.5e-47) NAD-dependent glycerol-3-phosphate dehydrogenase-like: (0.0005); KEGG: bja:bll6323 3-hydroxyisobutyrate dehydrogenase, ev=1e-107, 66% identity; 6-phosphogluconate dehydrogenase 329566 4075725 TM1040_3320 Ruegeria sp. TM1040 6-phosphogluconate dehydrogenase YP_611554.1 328688 R 292414 CDS YP_611555.1 99078297 4075726 complement(329654..331141) 1 NC_008043.1 PFAM: aldehyde dehydrogenase: (3.9e-234); KEGG: mlo:mll2319 aldehyde dehydrogenase, ev=0.0, 75% identity; aldehyde dehydrogenase (acceptor) 331141 4075726 TM1040_3321 Ruegeria sp. TM1040 aldehyde dehydrogenase (acceptor) YP_611555.1 329654 R 292414 CDS YP_611556.1 99078298 4075727 331411..332034 1 NC_008043.1 hypothetical protein 332034 4075727 TM1040_3322 Ruegeria sp. TM1040 hypothetical protein YP_611556.1 331411 D 292414 CDS YP_611557.1 99078299 4075728 complement(332127..333173) 1 NC_008043.1 PFAM: Malate/L-lactate dehydrogenase: (1e-35); KEGG: bma:BMAA1423 malate/L-lactate dehydrogenase family protein, ev=1e-100, 54% identity; malate/L-lactate dehydrogenase 333173 4075728 TM1040_3323 Ruegeria sp. TM1040 malate/L-lactate dehydrogenase YP_611557.1 332127 R 292414 CDS YP_611558.1 99078300 4075729 333330..334019 1 NC_008043.1 PFAM: regulatory protein GntR, HTH: (7.4e-21) GntR-like: (1.1e-10); KEGG: sil:SPOA0261 transcriptional regulator, GntR family, ev=2e-82, 68% identity; GntR family transcriptional regulator 334019 4075729 TM1040_3324 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_611558.1 333330 D 292414 CDS YP_611559.1 99078301 4075730 334135..335655 1 NC_008043.1 PFAM: aldehyde dehydrogenase: (1.8e-16); KEGG: sil:SPOA0260 aldehyde dehydrogenase family protein, ev=0.0, 76% identity; aldehyde dehydrogenase 335655 4075730 TM1040_3325 Ruegeria sp. TM1040 aldehyde dehydrogenase YP_611559.1 334135 D 292414 CDS YP_611560.1 99078302 4075731 336360..336977 1 NC_008043.1 PFAM: Paraquat-inducible protein A: (1.7e-14); KEGG: jan:Jann_1569 paraquat-inducible protein A, ev=1e-42, 44% identity; paraquat-inducible protein A 336977 4075731 TM1040_3326 Ruegeria sp. TM1040 paraquat-inducible protein A YP_611560.1 336360 D 292414 CDS YP_611561.1 99078303 4075732 336974..337579 1 NC_008043.1 PFAM: Paraquat-inducible protein A: (4.3e-65); KEGG: jan:Jann_1570 paraquat-inducible protein A, ev=1e-59, 59% identity; paraquat-inducible protein A 337579 4075732 TM1040_3327 Ruegeria sp. TM1040 paraquat-inducible protein A YP_611561.1 336974 D 292414 CDS YP_611562.1 99078304 4075733 337576..339660 1 NC_008043.1 PFAM: Mammalian cell entry related: (5e-08); KEGG: sil:SPO1249 paraquat-inducible protein, , ev=1e-120, 36% identity; hypothetical protein 339660 4075733 TM1040_3328 Ruegeria sp. TM1040 hypothetical protein YP_611562.1 337576 D 292414 CDS YP_611563.1 99078305 4075734 339662..340219 1 NC_008043.1 PFAM: protein of unknown function DUF330: (2.3e-07); KEGG: jan:Jann_1572 protein of unknown function DUF330, ev=1e-21, 39% identity; hypothetical protein 340219 4075734 TM1040_3329 Ruegeria sp. TM1040 hypothetical protein YP_611563.1 339662 D 292414 CDS YP_611564.1 99078306 4075735 complement(340248..340973) 1 NC_008043.1 PFAM: ABC transporter related: (2.1e-69); SMART: ATPase: (4.6e-21); KEGG: sdy:SDY_2618 ATP-binding component of sulfate permease A protein, ev=3e-69, 57% identity; ABC transporter 340973 4075735 TM1040_3330 Ruegeria sp. TM1040 ABC transporter YP_611564.1 340248 R 292414 CDS YP_611565.1 99078307 4075736 complement(340970..341773) 1 NC_008043.1 TIGRFAM: Sulphate transport system permease protein 2: (2.3e-104) Sulfate ABC transporter, permease protein CysW: (6.8e-129); PFAM: binding-protein-dependent transport systems inner membrane component: (3.7e-11); KEGG: rsp:RSP_3699 ABC sulfate/thiosulfate transporter, inner membrane subunit CysW, ev=1e-81, 57% identity; Sulfate ABC transporter, permease protein CysW 341773 4075736 TM1040_3331 Ruegeria sp. TM1040 Sulfate ABC transporter, permease protein CysW YP_611565.1 340970 R 292414 CDS YP_611566.1 99078308 4075231 complement(341777..342667) 1 NC_008043.1 TIGRFAM: Sulphate transport system permease protein 2: (5.5e-119) Sulfate ABC transporter, permease protein CysT: (1.2e-138); PFAM: binding-protein-dependent transport systems inner membrane component: (1.4e-28); KEGG: sgl:SG1708 sulfate ABC transporter permease component CysT, ev=4e-88, 60% identity; sulfate ABC transporter permease 342667 4075231 TM1040_3332 Ruegeria sp. TM1040 sulfate ABC transporter permease YP_611566.1 341777 R 292414 CDS YP_611567.1 99078309 4075232 complement(342686..343723) 1 NC_008043.1 TIGRFAM: Thiosulphate-binding protein: (6.3e-160); PFAM: extracellular solute-binding protein, family 1: (0.016); KEGG: bmb:BruAb1_1330 hypothetical sulfate ABC transporter, sulfate-binding protein, ev=1e-114, 63% identity; thiosulphate-binding protein 343723 4075232 TM1040_3333 Ruegeria sp. TM1040 thiosulphate-binding protein YP_611567.1 342686 R 292414 CDS YP_611568.1 99078310 4075233 344066..345592 1 NC_008043.1 KEGG: bja:blr7618 hypothetical protein, ev=1e-62, 36% identity; hypothetical protein 345592 4075233 TM1040_3334 Ruegeria sp. TM1040 hypothetical protein YP_611568.1 344066 D 292414 CDS YP_611569.1 99078311 4075234 345607..346299 1 NC_008043.1 PFAM: response regulator receiver: (3.4e-42) transcriptional regulatory protein-like: (1.6e-18); KEGG: bja:blr7619 two-component response regulator, ev=6e-70, 56% identity; two component transcriptional regulator 346299 4075234 TM1040_3335 Ruegeria sp. TM1040 two component transcriptional regulator YP_611569.1 345607 D 292414 CDS YP_611570.1 99078312 4075235 346296..347858 1 NC_008043.1 PFAM: ATP-binding region, ATPase-like: (1.9e-24) histidine kinase, HAMP region: (6.2e-08) histidine kinase A-like: (2.8e-15); KEGG: bja:blr7620 two-component hybrid sensor and regulator, ev=1e-95, 40% identity; periplasmic sensor signal transduction histidine kinase 347858 4075235 TM1040_3336 Ruegeria sp. TM1040 periplasmic sensor signal transduction histidine kinase YP_611570.1 346296 D 292414 CDS YP_611571.1 99078313 4075236 complement(347840..348940) 1 NC_008043.1 PFAM: NADH:flavin oxidoreductase/NADH oxidase: (2.6e-90); KEGG: cvi:CV2245 flavoprotein NADH-dependent oxidoreductase, ev=1e-133, 65% identity; NADH:flavin oxidoreductase 348940 4075236 TM1040_3337 Ruegeria sp. TM1040 NADH:flavin oxidoreductase YP_611571.1 347840 R 292414 CDS YP_611572.1 99078314 4075237 349061..349960 1 NC_008043.1 PFAM: regulatory protein, LysR: (1.2e-16) LysR, substrate-binding: (1.4e-47); KEGG: bur:Bcep18194_B2913 transcriptional regulator, LysR family, ev=2e-97, 62% identity; LysR family transcriptional regulator 349960 4075237 TM1040_3338 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_611572.1 349061 D 292414 CDS YP_611573.1 99078315 4075238 complement(350035..350931) 1 NC_008043.1 PFAM: regulatory protein, LysR: (1.8e-20) LysR, substrate-binding: (5.2e-43); KEGG: pfl:PFL_2646 transcriptional regulator, LysR family, ev=2e-87, 56% identity; LysR family transcriptional regulator 350931 4075238 TM1040_3339 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_611573.1 350035 R 292414 CDS YP_611574.1 99078316 4075239 351039..351881 1 NC_008043.1 KEGG: bur:Bcep18194_C7720 hypothetical protein, ev=2e-86, 56% identity; hypothetical protein 351881 4075239 TM1040_3340 Ruegeria sp. TM1040 hypothetical protein YP_611574.1 351039 D 292414 CDS YP_611575.1 99078317 4075240 complement(352034..352822) 1 NC_008043.1 PFAM: ABC transporter related: (5.8e-43); SMART: ATPase: (5.3e-13); KEGG: jan:Jann_1427 ABC transporter related, ev=1e-110, 77% identity; ABC transporter 352822 4075240 TM1040_3341 Ruegeria sp. TM1040 ABC transporter YP_611575.1 352034 R 292414 CDS YP_611576.1 99078318 4075241 complement(352824..353945) 1 NC_008043.1 PFAM: inner-membrane translocator: (1.9e-72); KEGG: jan:Jann_1426 inner-membrane translocator, ev=1e-157, 74% identity; inner-membrane translocator 353945 4075241 TM1040_3342 Ruegeria sp. TM1040 inner-membrane translocator YP_611576.1 352824 R 292414 CDS YP_611577.1 99078319 4075242 complement(354019..354969) 1 NC_008043.1 PFAM: periplasmic binding protein/LacI transcriptional regulator: (0.0044); KEGG: jan:Jann_1425 periplasmic binding protein/LacI transcriptional regulator, ev=1e-139, 76% identity; periplasmic binding protein/LacI transcriptional regulator 354969 4075242 TM1040_3343 Ruegeria sp. TM1040 periplasmic binding protein/LacI transcriptional regulator YP_611577.1 354019 R 292414 CDS YP_611578.1 99078320 4075243 355156..356160 1 NC_008043.1 PFAM: regulatory protein, LacI: (2.7e-05) periplasmic binding protein/LacI transcriptional regulator: (3.5e-06); KEGG: jan:Jann_1424 transcriptional regulator, LacI family, ev=1e-138, 71% identity; LacI family transcriptional regulator 356160 4075243 TM1040_3344 Ruegeria sp. TM1040 LacI family transcriptional regulator YP_611578.1 355156 D 292414 CDS YP_611579.1 99078321 4075244 complement(356157..357290) 1 NC_008043.1 PFAM: oxidoreductase-like: (6.4e-40) Oxidoreductase-like: (3.2e-10); KEGG: jan:Jann_1423 oxidoreductase-like, ev=1e-179, 80% identity; oxidoreductase-like 357290 4075244 TM1040_3345 Ruegeria sp. TM1040 oxidoreductase-like YP_611579.1 356157 R 292414 CDS YP_611580.1 99078322 4075245 complement(357303..358196) 1 NC_008043.1 PFAM: Xylose isomerase-like TIM barrel: (5.8e-32); KEGG: jan:Jann_1422 xylose isomerase-like, ev=1e-138, 78% identity; xylose isomerase-like TIM barrel 358196 4075245 TM1040_3346 Ruegeria sp. TM1040 xylose isomerase-like TIM barrel YP_611580.1 357303 R 292414 CDS YP_611581.1 99078323 4075246 complement(358216..359319) 1 NC_008043.1 PFAM: oxidoreductase-like: (1.3e-26) Oxidoreductase-like: (0.0011); KEGG: jan:Jann_1421 oxidoreductase-like, ev=1e-154, 71% identity; oxidoreductase-like 359319 4075246 TM1040_3347 Ruegeria sp. TM1040 oxidoreductase-like YP_611581.1 358216 R 292414 CDS YP_611582.1 99078324 4075247 359443..361311 1 NC_008043.1 PFAM: thiamine pyrophosphate enzyme-like TPP-binding: (4.4e-21) thiamine pyrophosphate enzyme, central region: (1.9e-29) thiamine pyrophosphate enzyme-like TPP binding region: (4.2e-06); KEGG: jan:Jann_1420 thiamine pyrophosphate enzyme protein, ev=0.0, 75% identity; thiamine pyrophosphate enzyme, central region 361311 4075247 TM1040_3348 Ruegeria sp. TM1040 thiamine pyrophosphate enzyme, central region YP_611582.1 359443 D 292414 CDS YP_611583.1 99078325 4075248 361412..362386 1 NC_008043.1 PFAM: PfkB: (1e-55); KEGG: jan:Jann_1419 PfkB, ev=1e-112, 62% identity; PfkB protein 362386 4075248 TM1040_3349 Ruegeria sp. TM1040 PfkB protein YP_611583.1 361412 D 292414 CDS YP_611584.1 99078326 4075249 362399..363241 1 NC_008043.1 KEGG: jan:Jann_1418 myo-inositol catabolism IolB protein, ev=1e-128, 76% identity; myo-inositol catabolism IolB protein 363241 4075249 TM1040_3350 Ruegeria sp. TM1040 myo-inositol catabolism IolB protein YP_611584.1 362399 D 292414 CDS YP_611585.1 99078327 4075250 363238..364068 1 NC_008043.1 PFAM: ketose-bisphosphate aldolase, class-II: (6.2e-38); KEGG: jan:Jann_1417 fructose-bisphosphate aldolase, ev=1e-115, 73% identity; fructose-bisphosphate aldolase 364068 4075250 TM1040_3351 Ruegeria sp. TM1040 fructose-bisphosphate aldolase YP_611585.1 363238 D 292414 CDS YP_611586.1 99078328 4075251 364070..365059 1 NC_008043.1 PFAM: oxidoreductase-like: (4e-28) Oxidoreductase-like: (1.8e-09); KEGG: jan:Jann_1416 myo-inositol 2-dehydrogenase, ev=1e-120, 66% identity; myo-inositol 2-dehydrogenase 365059 4075251 TM1040_3352 Ruegeria sp. TM1040 myo-inositol 2-dehydrogenase YP_611586.1 364070 D 292414 CDS YP_611587.1 99078329 4075252 complement(365203..366228) 1 NC_008043.1 PFAM: conserved hypothetical protein 698: (8.6e-58); KEGG: rsp:RSP_4010 conserved hypothetical protein 698, ev=5e-94, 55% identity; hypothetical protein 366228 4075252 TM1040_3353 Ruegeria sp. TM1040 hypothetical protein YP_611587.1 365203 R 292414 CDS YP_611588.1 99078330 4075253 complement(366235..367584) 1 NC_008043.1 PFAM: Di-haem cytochrome c peroxidase: (1.8e-12); KEGG: jan:Jann_3672 di-haem cytochrome c peroxidase, ev=1e-94, 44% identity; di-heme cytochrome c peroxidase 367584 4075253 TM1040_3354 Ruegeria sp. TM1040 di-heme cytochrome c peroxidase YP_611588.1 366235 R 292414 CDS YP_611589.1 99078331 4075254 367612..368055 1 NC_008043.1 PFAM: Sel1-like repeat: (0.0001); KEGG: mca:MCA0405 hypothetical protein, ev=7e-15, 35% identity; Sel1 repeat-containing protein 368055 4075254 TM1040_3355 Ruegeria sp. TM1040 Sel1 repeat-containing protein YP_611589.1 367612 D 292414 CDS YP_611590.1 99078332 4075255 complement(368123..368437) 1 NC_008043.1 PFAM: Stress responsive alpha-beta barrel: (2.3e-12); KEGG: jan:Jann_3925 stress responsive alpha-beta, ev=1e-14, 45% identity; stress responsive alpha-beta barrel 368437 4075255 TM1040_3356 Ruegeria sp. TM1040 stress responsive alpha-beta barrel YP_611590.1 368123 R 292414 CDS YP_611591.1 99078333 4075256 complement(368526..369584) 1 NC_008043.1 PFAM: TRAP dicarboxylate transporter- DctP subunit: (2.7e-40); KEGG: chy:CHY_1301 TRAP dicarboxylate transporter, DctP subunit, ev=1e-41, 34% identity; TRAP dicarboxylate transporter- DctP subunit 369584 4075256 TM1040_3357 Ruegeria sp. TM1040 TRAP dicarboxylate transporter- DctP subunit YP_611591.1 368526 R 292414 CDS YP_611592.1 99078334 4075257 complement(369621..371096) 1 NC_008043.1 TIGRFAM: TRAP dicarboxylate transporter- DctM subunit: (2.6e-125); PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit: (2e-132); KEGG: sme:SMb20444 hypothetical protein, ev=5e-86, 38% identity; TRAP dicarboxylate transporter- DctM subunit 371096 4075257 TM1040_3358 Ruegeria sp. TM1040 TRAP dicarboxylate transporter- DctM subunit YP_611592.1 369621 R 292414 CDS YP_611593.1 99078335 4075258 complement(371096..371686) 1 NC_008043.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component: (8.7e-09); KEGG: bha:BH2672 C4-dicarboxylate transport system (permease small protein), ev=2e-08, 26% identity; tripartite ATP-independent periplasmic transporter DctQ 371686 4075258 TM1040_3359 Ruegeria sp. TM1040 tripartite ATP-independent periplasmic transporter DctQ YP_611593.1 371096 R 292414 CDS YP_611594.1 99078336 4075259 complement(371744..372262) 1 NC_008043.1 PFAM: flavin reductase-like, FMN-binding: (2.9e-38); KEGG: rsp:RSP_2607 nitrilotriacetate monooxygenase component B, ev=7e-43, 56% identity; flavin reductase-like, FMN-binding 372262 4075259 TM1040_3360 Ruegeria sp. TM1040 flavin reductase-like, FMN-binding YP_611594.1 371744 R 292414 CDS YP_611595.1 99078337 4075260 complement(372262..373152) 1 NC_008043.1 PFAM: aldo/keto reductase: (1.3e-38); KEGG: jan:Jann_1942 aldo/keto reductase, ev=1e-107, 65% identity; aldo/keto reductase 373152 4075260 TM1040_3361 Ruegeria sp. TM1040 aldo/keto reductase YP_611595.1 372262 R 292414 CDS YP_611596.1 99078338 4075261 complement(373152..374306) 1 NC_008043.1 PFAM: luciferase-like: (1.2e-05); KEGG: jan:Jann_1941 alkanesulfonate monooxygenase, ev=0.0, 83% identity; alkanesulfonate monooxygenase 374306 4075261 TM1040_3362 Ruegeria sp. TM1040 alkanesulfonate monooxygenase YP_611596.1 373152 R 292414 CDS YP_611597.1 99078339 4075262 374370..375119 1 NC_008043.1 PFAM: regulatory protein GntR, HTH: (6.1e-19) UbiC transcription regulator-associated: (3.3e-15); KEGG: atc:AGR_L_3074 transcription regulator, GntR family, ev=2e-64, 55% identity; GntR family transcriptional regulator 375119 4075262 TM1040_3363 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_611597.1 374370 D 292414 CDS YP_611598.1 99078340 4075263 375128..376234 1 NC_008043.1 PFAM: oxidoreductase-like: (1.4e-19) Oxidoreductase-like: (1.1e-06); KEGG: jan:Jann_1939 oxidoreductase-like, ev=1e-126, 62% identity; oxidoreductase-like 376234 4075263 TM1040_3364 Ruegeria sp. TM1040 oxidoreductase-like YP_611598.1 375128 D 292414 CDS YP_611599.1 99078341 4075264 complement(376336..377040) 1 NC_008043.1 PFAM: protein of unknown function DUF125, transmembrane: (1.7e-76); KEGG: mlo:mlr6622 similar to nodulin 21, ev=1e-64, 58% identity; hypothetical protein 377040 4075264 TM1040_3365 Ruegeria sp. TM1040 hypothetical protein YP_611599.1 376336 R 292414 CDS YP_611600.1 99078342 4075265 complement(377231..378076) 1 NC_008043.1 PFAM: LytTr DNA-binding region: (4.1e-15); KEGG: rsp:RSP_0660 hypothetical protein, ev=4e-11, 32% identity; response regulator receiver protein 378076 4075265 TM1040_3366 Ruegeria sp. TM1040 response regulator receiver protein YP_611600.1 377231 R 292414 CDS YP_611601.1 99078343 4075266 378322..379098 1 NC_008043.1 PFAM: MltA-interacting MipA: (9.4e-33); KEGG: atc:AGR_C_1796 outer membrane protein, ev=9e-17, 27% identity; MltA-interacting MipA 379098 4075266 TM1040_3367 Ruegeria sp. TM1040 MltA-interacting MipA YP_611601.1 378322 D 292414 CDS YP_611602.1 99078344 4075267 379109..380320 1 NC_008043.1 KEGG: bmb:BruAb2_1095 fumarylacetoacetate hydrolase family protein, ev=3e-07, 28% identity; 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1 7-dioic acid hydratase (catechol pathway)-like 380320 4075267 TM1040_3368 Ruegeria sp. TM1040 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1 7-dioic acid hydratase (catechol pathway)-like YP_611602.1 379109 D 292414 CDS YP_611603.1 99078345 4075268 complement(380407..381780) 1 NC_008043.1 PFAM: ABC-1: (1.9e-36); KEGG: rsp:RSP_3305 ubiquinol-cytochrome-c reductase assembly protein, ev=1e-128, 55% identity; hypothetical protein 381780 4075268 TM1040_3369 Ruegeria sp. TM1040 hypothetical protein YP_611603.1 380407 R 292414 CDS YP_611604.1 99078346 4075269 complement(381777..383009) 1 NC_008043.1 KEGG: jan:Jann_2809 DNA photolyase-like protein, ev=1e-89, 47% identity; deoxyribodipyrimidine photo-lyase family protein 383009 4075269 TM1040_3370 Ruegeria sp. TM1040 deoxyribodipyrimidine photo-lyase family protein YP_611604.1 381777 R 292414 CDS YP_611605.1 99078347 4075270 383222..385885 1 NC_008043.1 PFAM: ATP-binding region, ATPase-like: (4.2e-33) histidine kinase A-like: (2.9e-15); KEGG: eba:ebA6722 histidine kinase, ev=3e-60, 46% identity; histidine kinase 385885 4075270 TM1040_3371 Ruegeria sp. TM1040 histidine kinase YP_611605.1 383222 D 292414 CDS YP_611606.1 99078348 4075271 385946..386266 1 NC_008043.1 PFAM: response regulator receiver: (0.00047); KEGG: eba:ebA6722 histidine kinase, ev=1e-11, 37% identity; response regulator receiver protein 386266 4075271 TM1040_3372 Ruegeria sp. TM1040 response regulator receiver protein YP_611606.1 385946 D 292414 CDS YP_611607.1 99078349 4075272 386263..386979 1 NC_008043.1 PFAM: response regulator receiver: (4.3e-40) transcriptional regulatory protein-like: (1.6e-16); KEGG: bja:bll1029 two-component response regulator, ev=2e-53, 47% identity; two component transcriptional regulator 386979 4075272 TM1040_3373 Ruegeria sp. TM1040 two component transcriptional regulator YP_611607.1 386263 D 292414 CDS YP_611608.1 99078350 4075273 complement(387083..388558) 1 NC_008043.1 PFAM: Hemolysin-type calcium-binding region: (0.014); KEGG: bja:bll7673 hypothetical protein, ev=5e-68, 40% identity; hemolysin-type calcium-binding region 388558 4075273 TM1040_3374 Ruegeria sp. TM1040 hemolysin-type calcium-binding region YP_611608.1 387083 R 292414 CDS YP_611609.1 99078351 4075274 389009..390259 1 NC_008043.1 TIGRFAM: sarcosine oxidase, beta subunit family: (1.9e-287); PFAM: FAD dependent oxidoreductase: (1.6e-85); KEGG: sil:SPO1588 sarcosine oxidase, beta subunit family, ev=0.0, 82% identity; sarcosine oxidase subunit beta 390259 4075274 TM1040_3375 Ruegeria sp. TM1040 sarcosine oxidase subunit beta YP_611609.1 389009 D 292414 CDS YP_611610.1 99078352 4075275 390288..390584 1 NC_008043.1 PFAM: Sarcosine oxidase, delta subunit, heterotetrameric: (4.2e-22); KEGG: sil:SPO1587 sarcosine oxidase, delta subunit family, ev=9e-34, 73% identity; sarcosine oxidase, delta subunit, heterotetrameric 390584 4075275 TM1040_3376 Ruegeria sp. TM1040 sarcosine oxidase, delta subunit, heterotetrameric YP_611610.1 390288 D 292414 CDS YP_611611.1 99078353 4075276 390581..393535 1 NC_008043.1 TIGRFAM: sarcosine oxidase, alpha subunit family: (0); PFAM: glycine cleavage T protein (aminomethyl transferase): (1.8e-53); KEGG: sil:SPO1586 sarcosine oxidase, alpha subunit family, ev=0.0, 73% identity; sarcosine oxidase subunit alpha 393535 4075276 TM1040_3377 Ruegeria sp. TM1040 sarcosine oxidase subunit alpha YP_611611.1 390581 D 292414 CDS YP_611612.1 99078354 4075277 393528..394079 1 NC_008043.1 KEGG: sil:SPO1585 sarcosine oxidase, gamma subunit family, ev=2e-35, 42% identity; sarcosine oxidase subunit gamma 394079 4075277 TM1040_3378 Ruegeria sp. TM1040 sarcosine oxidase subunit gamma YP_611612.1 393528 D 292414 CDS YP_611613.1 99078355 4075278 complement(394091..395104) 1 NC_008043.1 PFAM: helix-turn-helix, AraC type: (4.5e-06) ThiJ/PfpI: (0.00013); KEGG: sil:SPO1584 transcriptional regulator, AraC family, ev=2e-89, 51% identity; transcriptional regulator 395104 4075278 TM1040_3379 Ruegeria sp. TM1040 transcriptional regulator YP_611613.1 394091 R 292414 CDS YP_611614.1 99078356 4075279 complement(395104..396009) 1 NC_008043.1 PFAM: regulatory protein, LysR: (2.6e-17) LysR, substrate-binding: (6e-45); KEGG: sil:SPO3192 transcriptional regulator, LysR family, ev=2e-47, 41% identity; LysR family transcriptional regulator 396009 4075279 TM1040_3380 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_611614.1 395104 R 292414 CDS YP_611615.1 99078357 4075280 396121..397569 1 NC_008043.1 PFAM: aldehyde dehydrogenase: (2.1e-186); KEGG: sil:SPO3191 aldehyde dehydrogenase family protein, ev=0.0, 89% identity; aldehyde dehydrogenase 397569 4075280 TM1040_3381 Ruegeria sp. TM1040 aldehyde dehydrogenase YP_611615.1 396121 D 292414 CDS YP_611616.1 99078358 4075281 397569..398549 1 NC_008043.1 PFAM: peptidase M19, renal dipeptidase: (7.8e-102); KEGG: sil:SPO3190 renal dipeptidase family protein, ev=1e-168, 85% identity; peptidase M19, renal dipeptidase 398549 4075281 TM1040_3382 Ruegeria sp. TM1040 peptidase M19, renal dipeptidase YP_611616.1 397569 D 292414 CDS YP_611617.1 99078359 4075282 398618..400162 1 NC_008043.1 PFAM: BCCT transporter: (1.4e-60); KEGG: pha:PSHAa1072 glycine betaine transporter, ev=0.0, 61% identity; BCCT transporter 400162 4075282 TM1040_3383 Ruegeria sp. TM1040 BCCT transporter YP_611617.1 398618 D 292414 CDS YP_611618.1 99078360 4075283 400275..401978 1 NC_008043.1 KEGG: sil:SPO3189 hypothetical protein, ev=0.0, 66% identity; hypothetical protein 401978 4075283 TM1040_3384 Ruegeria sp. TM1040 hypothetical protein YP_611618.1 400275 D 292414 CDS YP_611619.1 99078361 4075284 401975..402625 1 NC_008043.1 KEGG: sil:SPO3188 hypothetical protein, ev=2e-39, 46% identity; hypothetical protein 402625 4075284 TM1040_3385 Ruegeria sp. TM1040 hypothetical protein YP_611619.1 401975 D 292414 CDS YP_611620.1 99078362 4075285 402659..403693 1 NC_008043.1 PFAM: Malate/L-lactate dehydrogenase: (2.7e-29); KEGG: sil:SPO3187 malate/L-lactate dehydrogenase family protein, ev=1e-140, 73% identity; malate/L-lactate dehydrogenase 403693 4075285 TM1040_3386 Ruegeria sp. TM1040 malate/L-lactate dehydrogenase YP_611620.1 402659 D 292414 CDS YP_611621.1 99078363 4075287 404374..407385 1 NC_008043.1 PFAM: aminoglycoside phosphotransferase: (2.5e-18) peptidase M23B: (1.9e-11) aminotransferase class-III: (1.8e-49); KEGG: sil:SPO0791 M23/M37 peptidase/aminotransferase, class III, ev=0.0, 74% identity; hypothetical protein 407385 4075287 TM1040_3387 Ruegeria sp. TM1040 hypothetical protein YP_611621.1 404374 D 292414 CDS YP_611622.1 99078364 4075562 complement(407476..408393) 1 NC_008043.1 PFAM: regulatory protein, LysR: (8e-21) LysR, substrate-binding: (7.8e-29); KEGG: bpm:BURPS1710b_0203 transcriptional regulator, LysR family, ev=6e-70, 48% identity; LysR family transcriptional regulator 408393 4075562 TM1040_3388 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_611622.1 407476 R 292414 CDS YP_611623.1 99078365 4075563 408474..410201 1 NC_008043.1 PFAM: glucose-methanol-choline oxidoreductase: (2.2e-80) GMC oxidoreductase: (4e-48); KEGG: reu:Reut_A3372 glucose-methanol-choline oxidoreductase:FAD dependent oxidoreductase:GMC oxidoreductase, ev=0.0, 62% identity; glucose-methanol-choline oxidoreductase 410201 4075563 TM1040_3389 Ruegeria sp. TM1040 glucose-methanol-choline oxidoreductase YP_611623.1 408474 D 292414 CDS YP_611624.1 99078366 4075564 complement(410234..411202) 1 NC_008043.1 PFAM: aldo/keto reductase: (9.9e-11); KEGG: atc:AGR_L_2607 D-threo-aldose 1-dehydrogenase, ev=3e-84, 53% identity; aldo/keto reductase 411202 4075564 TM1040_3390 Ruegeria sp. TM1040 aldo/keto reductase YP_611624.1 410234 R 292414 CDS YP_611625.1 99078367 4075565 complement(411219..412496) 1 NC_008043.1 PFAM: Mandelate racemase/muconate lactonizing enzyme-like: (7e-08); KEGG: bur:Bcep18194_B0622 mandelate racemase/muconate lactonizing enzyme, ev=0.0, 74% identity; mandelate racemase/muconate lactonizing-like protein 412496 4075565 TM1040_3391 Ruegeria sp. TM1040 mandelate racemase/muconate lactonizing-like protein YP_611625.1 411219 R 292414 CDS YP_611626.1 99078368 4075566 complement(412493..413338) 1 NC_008043.1 PFAM: fumarylacetoacetate (FAA) hydrolase: (6.1e-83); KEGG: jan:Jann_2105 5-carboxymethyl-2-hydroxymuconate delta-isomerase, ev=1e-122, 73% identity; 5-carboxymethyl-2-hydroxymuconate delta-isomerase 413338 4075566 TM1040_3392 Ruegeria sp. TM1040 5-carboxymethyl-2-hydroxymuconate delta-isomerase YP_611626.1 412493 R 292414 CDS YP_611627.1 99078369 4075567 complement(413357..414115) 1 NC_008043.1 PFAM: short-chain dehydrogenase/reductase SDR: (1.1e-25); KEGG: atc:AGR_L_807 oxidoreductase UcpA, ev=1e-89, 70% identity; short-chain dehydrogenase/reductase SDR 414115 4075567 TM1040_3393 Ruegeria sp. TM1040 short-chain dehydrogenase/reductase SDR YP_611627.1 413357 R 292414 CDS YP_611628.1 99078370 4075568 complement(414112..414441) 1 NC_008043.1 PFAM: protein of unknown function DUF718: (1e-64); KEGG: atc:AGR_C_5099 hypothetical protein Cj0488, ev=6e-48, 77% identity; hypothetical protein 414441 4075568 TM1040_3394 Ruegeria sp. TM1040 hypothetical protein YP_611628.1 414112 R 292414 CDS YP_611629.1 99078371 4075569 complement(414441..415550) 1 NC_008043.1 PFAM: Mandelate racemase/muconate lactonizing enzyme-like: (6.2e-15); KEGG: mlo:mll7149 mandelate racemase, ev=1e-144, 68% identity; mandelate racemase/muconate lactonizing-like protein 415550 4075569 TM1040_3395 Ruegeria sp. TM1040 mandelate racemase/muconate lactonizing-like protein YP_611629.1 414441 R 292414 CDS YP_611630.1 99078372 4075570 complement(415555..416649) 1 NC_008043.1 PFAM: ABC transporter related: (1.2e-64) TOBE: (3.8e-05) Transport-associated OB: (0.0017); SMART: ATPase: (2.4e-18); KEGG: bmb:BruAb1_0233 sugar ABC transporter, ATP-binding protein, ev=1e-132, 65% identity; ABC transporter 416649 4075570 TM1040_3396 Ruegeria sp. TM1040 ABC transporter YP_611630.1 415555 R 292414 CDS YP_611631.1 99078373 4075571 complement(416653..417516) 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (4.3e-23); KEGG: sme:SMb21105 sugar uptake ABC transporter permease protein, ev=1e-128, 76% identity; binding-protein-dependent transport system inner membrane protein 417516 4075571 TM1040_3397 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_611631.1 416653 R 292414 CDS YP_611632.1 99078374 4075572 complement(417522..418418) 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (0.00039); KEGG: bms:BR0236 sugar ABC transporter, permease protein, ev=1e-127, 73% identity; binding-protein-dependent transport systems inner membrane component 418418 4075572 TM1040_3398 Ruegeria sp. TM1040 binding-protein-dependent transport systems inner membrane component YP_611632.1 417522 R 292414 CDS YP_611633.1 99078375 4075573 complement(418497..419819) 1 NC_008043.1 PFAM: extracellular solute-binding protein, family 1: (4.1e-18); KEGG: bmb:BruAb1_0230 sugar ABC transporter, periplasmic sugar-binding protein, ev=1e-161, 64% identity; extracellular solute-binding protein 419819 4075573 TM1040_3399 Ruegeria sp. TM1040 extracellular solute-binding protein YP_611633.1 418497 R 292414 CDS YP_611634.1 99078376 4075574 419964..420770 1 NC_008043.1 PFAM: regulatory proteins, IclR: (9.9e-05); KEGG: bur:Bcep18194_B0136 transcriptional regulator, IclR family, ev=4e-58, 45% identity; IclR family transcriptional regulator 420770 4075574 TM1040_3400 Ruegeria sp. TM1040 IclR family transcriptional regulator YP_611634.1 419964 D 292414 CDS YP_611635.1 99078377 4075575 420767..421627 1 NC_008043.1 PFAM: amidohydrolase 2: (5.2e-29); KEGG: amidohydrolase family superfamily, ev=4e-63, 50% identity; amidohydrolase 2 421627 4075575 TM1040_3401 Ruegeria sp. TM1040 amidohydrolase 2 YP_611635.1 420767 D 292414 CDS YP_611636.1 99078378 4075576 complement(421630..422220) 1 NC_008043.1 PFAM: chromosome segregation and condensation protein ScpB: (1.6e-46); KEGG: mlo:mlr9362 hypothetical protein, ev=1e-52, 55% identity; transcriptional regulator 422220 4075576 TM1040_3402 Ruegeria sp. TM1040 transcriptional regulator YP_611636.1 421630 R 292414 CDS YP_611637.1 99078379 4075577 complement(422223..423107) 1 NC_008043.1 PFAM: protein of unknown function DUF1403: (9.8e-77); KEGG: mlo:mlr6196 hypothetical protein, ev=7e-27, 34% identity; hypothetical protein 423107 4075577 TM1040_3403 Ruegeria sp. TM1040 hypothetical protein YP_611637.1 422223 R 292414 CDS YP_611638.1 99078380 4075578 423285..424160 1 NC_008043.1 KEGG: mlo:mll9356 integrase, ev=3e-53, 40% identity; integrase 424160 4075578 TM1040_3404 Ruegeria sp. TM1040 integrase YP_611638.1 423285 D 292414 CDS YP_611639.1 99078381 4075579 complement(424166..425248) 1 NC_008043.1 PFAM: ParB-like nuclease: (2.9e-15); KEGG: rsp:RSP_1422 ParB-like nuclease, ev=1e-74, 46% identity; ParB-like nuclease 425248 4075579 TM1040_3405 Ruegeria sp. TM1040 ParB-like nuclease YP_611639.1 424166 R 292414 CDS YP_611640.1 99078382 4075580 complement(425250..426713) 1 NC_008043.1 PFAM: Cobyrinic acid a,c-diamide synthase: (8e-21); KEGG: rsp:RSP_1423 ParA family ATPase, ev=0.0, 81% identity; cobyrinic acid a,c-diamide synthase 426713 4075580 TM1040_3406 Ruegeria sp. TM1040 cobyrinic acid a,c-diamide synthase YP_611640.1 425250 R 292414 CDS YP_611641.1 99078383 4075581 427302..428594 1 NC_008043.1 PFAM: initiator RepB protein: (0.0063); KEGG: rsp:RSP_1425 plasmid replication initiation protein, ev=1e-153, 64% identity; initiator RepB protein 428594 4075581 TM1040_3407 Ruegeria sp. TM1040 initiator RepB protein YP_611641.1 427302 D 292414 CDS YP_611642.1 99078384 4075582 complement(428668..430182) 1 NC_008043.1 catalyzes the formation of malonyl-CoA from malonate and CoA; malonyl-CoA synthase 430182 4075582 TM1040_3408 Ruegeria sp. TM1040 malonyl-CoA synthase YP_611642.1 428668 R 292414 CDS YP_611643.1 99078385 4075583 430821..431840 1 NC_008043.1 PFAM: helix-turn-helix, AraC type: (5.8e-08); KEGG: sil:SPO1057 transcriptional regulator, AraC family, ev=4e-65, 40% identity; AraC family transcriptional regulator 431840 4075583 TM1040_3409 Ruegeria sp. TM1040 AraC family transcriptional regulator YP_611643.1 430821 D 292414 CDS YP_611644.1 99078386 4075584 431965..432822 1 NC_008043.1 PFAM: NmrA-like: (0.00044); KEGG: sil:SPO1056 hypothetical protein, ev=2e-95, 60% identity; NmrA-like 432822 4075584 TM1040_3410 Ruegeria sp. TM1040 NmrA-like YP_611644.1 431965 D 292414 CDS YP_611645.1 99078387 4075585 432819..433247 1 NC_008043.1 KEGG: sil:SPO1055 membrane protein, , ev=8e-35, 56% identity; hypothetical protein 433247 4075585 TM1040_3411 Ruegeria sp. TM1040 hypothetical protein YP_611645.1 432819 D 292414 CDS YP_611646.1 99078388 4075586 complement(433541..434764) 1 NC_008043.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm; Na(+)-translocating NADH-quinone reductase subunit F 434764 4075586 TM1040_3412 Ruegeria sp. TM1040 Na(+)-translocating NADH-quinone reductase subunit F YP_611646.1 433541 R 292414 CDS YP_611647.1 99078389 4075587 complement(434778..435386) 1 NC_008043.1 Part of the NQR complex which consists of NqrA, NqrB, NqrC, NqrD, NqrE and NqrF; NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm; NqrE is probably involved in the second step, the conversion of ubisemiquinone to ubiquinol.; Na(+)-translocating NADH-quinone reductase subunit E 435386 4075587 TM1040_3413 Ruegeria sp. TM1040 Na(+)-translocating NADH-quinone reductase subunit E YP_611647.1 434778 R 292414 CDS YP_611648.1 99078390 4075588 complement(435386..436039) 1 NC_008043.1 Part of the NQR complex which catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm; Na(+)-translocating NADH-quinone reductase subunit D 436039 4075588 TM1040_3414 Ruegeria sp. TM1040 Na(+)-translocating NADH-quinone reductase subunit D YP_611648.1 435386 R 292414 CDS YP_611649.1 99078391 4075589 complement(436039..436851) 1 NC_008043.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm; Na(+)-translocating NADH-quinone reductase subunit C 436851 4075589 TM1040_3415 Ruegeria sp. TM1040 Na(+)-translocating NADH-quinone reductase subunit C YP_611649.1 436039 R 292414 CDS YP_611650.1 99078392 4075590 complement(436844..438043) 1 NC_008043.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm; Na(+)-translocating NADH-quinone reductase subunit B 438043 4075590 TM1040_3416 Ruegeria sp. TM1040 Na(+)-translocating NADH-quinone reductase subunit B YP_611650.1 436844 R 292414 CDS YP_611651.1 99078393 4075591 complement(438048..439391) 1 NC_008043.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm; Na(+)-translocating NADH-quinone reductase subunit A 439391 4075591 TM1040_3417 Ruegeria sp. TM1040 Na(+)-translocating NADH-quinone reductase subunit A YP_611651.1 438048 R 292414 CDS YP_611652.1 99078394 4075592 439560..440591 1 NC_008043.1 PFAM: ApbE-like lipoprotein: (4.8e-87); KEGG: sil:SPOA0036 thiamin biosynthesis lipoprotein ApbE, ev=5e-79, 48% identity; ApbE-like lipoprotein 440591 4075592 TM1040_3418 Ruegeria sp. TM1040 ApbE-like lipoprotein YP_611652.1 439560 D 292414 CDS YP_611653.1 99078395 4075593 440622..440861 1 NC_008043.1 KEGG: sil:SPOA0037 hypothetical protein, ev=1e-24, 68% identity; hypothetical protein 440861 4075593 TM1040_3419 Ruegeria sp. TM1040 hypothetical protein YP_611653.1 440622 D 292414 CDS YP_611654.1 99078396 4075594 complement(440986..444114) 1 NC_008043.1 TIGRFAM: Hydrophobe/amphiphile efflux-1 HAE1: (0); PFAM: acriflavin resistance protein: (0); KEGG: bms:BRA0334 hydrophobe/amphiphile efflux-1 family protein, ev=0.0, 51% identity; hydrophobe/amphiphile efflux-1 HAE1 444114 4075594 TM1040_3420 Ruegeria sp. TM1040 hydrophobe/amphiphile efflux-1 HAE1 YP_611654.1 440986 R 292414 CDS YP_611655.1 99078397 4075595 complement(444126..445271) 1 NC_008043.1 PFAM: secretion protein HlyD: (2.1e-22); KEGG: bms:BRA0335 HlyD family secretion protein, ev=3e-62, 39% identity; secretion protein HlyD 445271 4075595 TM1040_3421 Ruegeria sp. TM1040 secretion protein HlyD YP_611655.1 444126 R 292414 CDS YP_611656.1 99078398 4075596 445506..445916 1 NC_008043.1 PFAM: WxcM-like: (3.7e-74); KEGG: tel:tlr1343 hypothetical protein, ev=1e-52, 73% identity; hypothetical protein 445916 4075596 TM1040_3422 Ruegeria sp. TM1040 hypothetical protein YP_611656.1 445506 D 292414 CDS YP_611657.1 99078399 4075597 445913..447013 1 NC_008043.1 PFAM: Cys/Met metabolism pyridoxal-phosphate-dependent enzymes: (0.0026) DegT/DnrJ/EryC1/StrS aminotransferase: (9.3e-158) aromatic amino acid beta-eliminating lyase/threonine aldolase: (0.0029); KEGG: tel:tlr1344 probable aminotransferase, ev=1e-123, 59% identity; DegT/DnrJ/EryC1/StrS aminotransferase 447013 4075597 TM1040_3423 Ruegeria sp. TM1040 DegT/DnrJ/EryC1/StrS aminotransferase YP_611657.1 445913 D 292414 CDS YP_611658.1 99078400 4075598 447010..447975 1 NC_008043.1 PFAM: glycosyl transferase, family 2: (1.3e-21); KEGG: mca:MCA1508 glycosyl transferase, group 2 family, ev=5e-21, 27% identity; glycosyl transferase family protein 447975 4075598 TM1040_3424 Ruegeria sp. TM1040 glycosyl transferase family protein YP_611658.1 447010 D 292414 CDS YP_611659.1 99078401 4075599 complement(448036..448977) 1 NC_008043.1 KEGG: xac:XAC1690 hypothetical protein, ev=7e-69, 44% identity; hypothetical protein 448977 4075599 TM1040_3425 Ruegeria sp. TM1040 hypothetical protein YP_611659.1 448036 R 292414 CDS YP_611660.1 99078402 4075600 complement(448974..449903) 1 NC_008043.1 KEGG: xac:XAC1689 hypothetical protein, ev=1e-58, 41% identity; hypothetical protein 449903 4075600 TM1040_3426 Ruegeria sp. TM1040 hypothetical protein YP_611660.1 448974 R 292414 CDS YP_611661.1 99078403 4075601 complement(449905..450579) 1 NC_008043.1 KEGG: xac:XAC1688 hypothetical protein, ev=4e-48, 46% identity; hypothetical protein 450579 4075601 TM1040_3427 Ruegeria sp. TM1040 hypothetical protein YP_611661.1 449905 R 292414 CDS YP_611662.1 99078404 4075602 450816..452498 1 NC_008043.1 PFAM: Tetratricopeptide TPR_2: (0.00021); KEGG: ccr:CC3718 TPR domain protein, ev=2e-85, 38% identity; tetratricopeptide TPR_2 452498 4075602 TM1040_3428 Ruegeria sp. TM1040 tetratricopeptide TPR_2 YP_611662.1 450816 D 292414 CDS YP_611663.1 99078405 4075603 complement(452503..453402) 1 NC_008043.1 PFAM: Rhodanese-like: (2.5e-13); KEGG: sil:SPO0091 rhodanese-like domain protein, ev=1e-153, 86% identity; rhodanese-like protein 453402 4075603 TM1040_3429 Ruegeria sp. TM1040 rhodanese-like protein YP_611663.1 452503 R 292414 CDS YP_611664.1 99078406 4075604 453595..454200 1 NC_008043.1 PFAM: isochorismatase hydrolase: (2.3e-14); KEGG: sil:SPO0093 pyrazinamidase/nicotinamidase, ev=2e-82, 74% identity; nicotinamidase 454200 4075604 TM1040_3430 Ruegeria sp. TM1040 nicotinamidase YP_611664.1 453595 D 292414 CDS YP_611665.1 99078407 4075605 454284..456554 1 NC_008043.1 PFAM: response regulator receiver: (1.9e-30) ATP-binding region, ATPase-like: (1.9e-42) histidine kinase A-like: (1.1e-23) PAS fold-3: (4.6e-10) PAS fold-4: (8.8e-10) PAS fold: (3.1e-13); SMART: PAS: (3.6e-10) PAC motif: (1.9e-08); KEGG: sil:SPO0094 sensory box sensor histidine kinase/response regulator, ev=1e-156, 44% identity; PAS/PAC sensor hybrid histidine kinase 456554 4075605 TM1040_3431 Ruegeria sp. TM1040 PAS/PAC sensor hybrid histidine kinase YP_611665.1 454284 D 292414 CDS YP_611666.1 99078408 4075606 456618..457907 1 NC_008043.1 catalyzes the formation of nictonate and 5-phospho-alpha-D-ribose 1-diphosphate from nicotinate D-ribonucleotide and diphosphate; nicotinate phosphoribosyltransferase 457907 4075606 TM1040_3432 Ruegeria sp. TM1040 nicotinate phosphoribosyltransferase YP_611666.1 456618 D 292414 CDS YP_611667.1 99078409 4075607 complement(457908..458381) 1 NC_008043.1 hypothetical protein 458381 4075607 TM1040_3433 Ruegeria sp. TM1040 hypothetical protein YP_611667.1 457908 R 292414 CDS YP_611668.1 99078410 4075608 complement(458378..459988) 1 NC_008043.1 PFAM: ABC transporter related: (4.5e-61) Oligopeptide/dipeptide ABC transporter-like: (9.6e-05); SMART: ATPase: (8.4e-19); KEGG: sil:SPO0098 peptide/opine/nickel uptake family ABC transporter, ATP-binding protein, ev=0.0, 69% identity; ABC transporter 459988 4075608 TM1040_3434 Ruegeria sp. TM1040 ABC transporter YP_611668.1 458378 R 292414 CDS YP_611669.1 99078411 4075609 complement(459985..460800) 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (2.7e-42); KEGG: sil:SPO0099 peptide/opine/nickel uptake family ABC transporter, permease protein, ev=1e-121, 80% identity; binding-protein-dependent transport systems inner membrane component 460800 4075609 TM1040_3435 Ruegeria sp. TM1040 binding-protein-dependent transport systems inner membrane component YP_611669.1 459985 R 292414 CDS YP_611670.1 99078412 4075610 complement(460797..461744) 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (2.7e-45); KEGG: sil:SPO0100 peptide/opine/nickel uptake family ABC transporter, permease protein, ev=1e-147, 84% identity; binding-protein-dependent transport systems inner membrane component 461744 4075610 TM1040_3436 Ruegeria sp. TM1040 binding-protein-dependent transport systems inner membrane component YP_611670.1 460797 R 292414 CDS YP_611671.1 99078413 4075611 complement(461879..463357) 1 NC_008043.1 PFAM: extracellular solute-binding protein, family 5: (2.4e-87); KEGG: sil:SPO0101 peptide/opine/nickel uptake family ABC transporter, periplasmic substrate-binding protein, ev=0.0, 77% identity; extracellular solute-binding protein 463357 4075611 TM1040_3437 Ruegeria sp. TM1040 extracellular solute-binding protein YP_611671.1 461879 R 292414 CDS YP_611672.1 99078414 4075612 463587..464429 1 NC_008043.1 catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate; 3-methyl-2-oxobutanoate hydroxymethyltransferase 464429 panB 4075612 panB Ruegeria sp. TM1040 3-methyl-2-oxobutanoate hydroxymethyltransferase YP_611672.1 463587 D 292414 CDS YP_611673.1 99078415 4075613 464443..465285 1 NC_008043.1 catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine; pantoate--beta-alanine ligase 465285 panC 4075613 panC Ruegeria sp. TM1040 pantoate--beta-alanine ligase YP_611673.1 464443 D 292414 CDS YP_611674.1 99078416 4075614 465392..466876 1 NC_008043.1 TIGRFAM: glycerol kinase: (6.1e-293); PFAM: carbohydrate kinase, FGGY: (2e-102); KEGG: sil:SPO0104 glycerol kinase, ev=0.0, 75% identity; glycerol kinase 466876 4075614 TM1040_3440 Ruegeria sp. TM1040 glycerol kinase YP_611674.1 465392 D 292414 CDS YP_611675.1 99078417 4075615 complement(466970..468223) 1 NC_008043.1 PFAM: monooxygenase, FAD-binding: (4e-06); KEGG: sil:SPO0105 monooxygenase family protein, ev=0.0, 73% identity; hypothetical protein 468223 4075615 TM1040_3441 Ruegeria sp. TM1040 hypothetical protein YP_611675.1 466970 R 292414 CDS YP_611676.1 99078418 4075616 complement(468295..468849) 1 NC_008043.1 KEGG: sil:SPO0131 isopentyl-diphosphate delta-isomerase, ev=1e-75, 71% identity; TIGRFAM: Isopentenyl-diphosphate delta-isomerase, type 1: (4.2e-35); PFAM: NUDIX hydrolase: (8.5e-26); isopentenyl-diphosphate delta-isomerase 468849 4075616 TM1040_3442 Ruegeria sp. TM1040 isopentenyl-diphosphate delta-isomerase YP_611676.1 468295 R 292414 CDS YP_611677.1 99078419 4075617 complement(468998..469465) 1 NC_008043.1 PFAM: cytochrome c, class I: (7.9e-27); KEGG: sil:SPO0130 cytochrome c family protein, ev=1e-41, 62% identity; cytochrome c, class I 469465 4075617 TM1040_3443 Ruegeria sp. TM1040 cytochrome c, class I YP_611677.1 468998 R 292414 CDS YP_611678.1 99078420 4075618 469717..470052 1 NC_008043.1 hypothetical protein 470052 4075618 TM1040_3444 Ruegeria sp. TM1040 hypothetical protein YP_611678.1 469717 D 292414 CDS YP_611679.1 99078421 4075619 470059..470502 1 NC_008043.1 hypothetical protein 470502 4075619 TM1040_3445 Ruegeria sp. TM1040 hypothetical protein YP_611679.1 470059 D 292414 CDS YP_611680.1 99078422 4075620 complement(470506..470958) 1 NC_008043.1 PFAM: protein of unknown function DUF188: (2e-34); KEGG: sil:SPO3827 YaiI/YqxD family protein, ev=3e-65, 83% identity; hypothetical protein 470958 4075620 TM1040_3446 Ruegeria sp. TM1040 hypothetical protein YP_611680.1 470506 R 292414 CDS YP_611681.1 99078423 4075081 complement(470955..472460) 1 NC_008043.1 catalyzes the conversion of NADPH to NADH; soluble pyridine nucleotide transhydrogenase 472460 4075081 TM1040_3447 Ruegeria sp. TM1040 soluble pyridine nucleotide transhydrogenase YP_611681.1 470955 R 292414 CDS YP_611682.1 99078424 4075082 complement(472465..473310) 1 NC_008043.1 PFAM: esterase: (1.2e-74); KEGG: sil:SPO3829 S-formylglutathione hydrolase, , ev=1e-133, 80% identity; carboxylesterase 473310 4075082 TM1040_3448 Ruegeria sp. TM1040 carboxylesterase YP_611682.1 472465 R 292414 CDS YP_611683.1 99078425 4075083 473527..473868 1 NC_008043.1 PFAM: protein of unknown function DUF861, cupin_3: (2.1e-32); KEGG: sil:SPO3326 hypothetical protein, ev=7e-45, 75% identity; hypothetical protein 473868 4075083 TM1040_3449 Ruegeria sp. TM1040 hypothetical protein YP_611683.1 473527 D 292414 CDS YP_611684.1 99078426 4075084 complement(473885..474808) 1 NC_008043.1 PFAM: Auxin Efflux Carrier: (2.3e-15); KEGG: sil:SPO3843 malonate transporter, , ev=1e-126, 73% identity; auxin efflux carrier 474808 4075084 TM1040_3450 Ruegeria sp. TM1040 auxin efflux carrier YP_611684.1 473885 R 292414 CDS YP_611685.1 99078427 4075085 475100..475750 1 NC_008043.1 PFAM: regulatory protein, TetR: (7.5e-18); KEGG: rsp:RSP_6137 transcriptional regulator, TetR family, ev=2e-58, 58% identity; TetR family transcriptional regulator 475750 4075085 TM1040_3451 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_611685.1 475100 D 292414 CDS YP_611686.1 99078428 4075086 475895..476599 1 NC_008043.1 PFAM: regulatory protein, ArsR: (0.0022); KEGG: sil:SPO3809 transcriptional regulator, ArsR family, ev=3e-67, 58% identity; ArsR family transcriptional regulator 476599 4075086 TM1040_3452 Ruegeria sp. TM1040 ArsR family transcriptional regulator YP_611686.1 475895 D 292414 CDS YP_611687.1 99078429 4075087 476650..476988 1 NC_008043.1 KEGG: jan:Jann_0104 hypothetical protein, ev=6e-41, 79% identity; hypothetical protein 476988 4075087 TM1040_3453 Ruegeria sp. TM1040 hypothetical protein YP_611687.1 476650 D 292414 CDS YP_611688.1 99078430 4075088 complement(477138..477878) 1 NC_008043.1 PFAM: NLP/P60: (2.4e-06); KEGG: sil:SPO3718 NLP/P60 family protein, ev=3e-82, 59% identity; NLP/P60 477878 4075088 TM1040_3454 Ruegeria sp. TM1040 NLP/P60 YP_611688.1 477138 R 292414 CDS YP_611689.1 99078431 4075089 complement(477875..479293) 1 NC_008043.1 PFAM: peptidase M17, leucyl aminopeptidase-like: (4e-101); KEGG: sil:SPO3717 cytosol aminopeptidase family protein, ev=1e-167, 67% identity; leucyl aminopeptidase 479293 4075089 TM1040_3455 Ruegeria sp. TM1040 leucyl aminopeptidase YP_611689.1 477875 R 292414 CDS YP_611690.1 99078432 4075090 complement(479425..479805) 1 NC_008043.1 KEGG: sil:SPO3716 hypothetical protein, ev=4e-39, 65% identity; hypothetical protein 479805 4075090 TM1040_3456 Ruegeria sp. TM1040 hypothetical protein YP_611690.1 479425 R 292414 CDS YP_611691.1 99078433 4075091 479959..480609 1 NC_008043.1 PFAM: carbonic anhydrase: (3.6e-32); KEGG: sil:SPO3715 carbonic anhydrase, , ev=1e-102, 80% identity; carbonate dehydratase 480609 4075091 TM1040_3457 Ruegeria sp. TM1040 carbonate dehydratase YP_611691.1 479959 D 292414 CDS YP_611692.1 99078434 4075092 complement(480673..481824) 1 NC_008043.1 KEGG: sil:SPO3710 hypothetical protein, ev=1e-112, 52% identity; hypothetical protein 481824 4075092 TM1040_3458 Ruegeria sp. TM1040 hypothetical protein YP_611692.1 480673 R 292414 CDS YP_611693.1 99078435 4075093 482089..483111 1 NC_008043.1 catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde; aspartate-semialdehyde dehydrogenase 483111 4075093 TM1040_3459 Ruegeria sp. TM1040 aspartate-semialdehyde dehydrogenase YP_611693.1 482089 D 292414 CDS YP_611694.1 99078436 4075094 483277..484920 1 NC_008043.1 TIGRFAM: conserved hypothetical protein: (5.3e-26); KEGG: sil:SPO3713 hypothetical protein, ev=2e-98, 39% identity; hypothetical protein 484920 4075094 TM1040_3460 Ruegeria sp. TM1040 hypothetical protein YP_611694.1 483277 D 292414 CDS YP_611695.1 99078437 4075095 485089..485412 1 NC_008043.1 hypothetical protein 485412 4075095 TM1040_3461 Ruegeria sp. TM1040 hypothetical protein YP_611695.1 485089 D 292414 CDS YP_611696.1 99078438 4075096 485556..487508 1 NC_008043.1 PFAM: amidohydrolase: (0.0044) Amidohydrolase 3: (1e-100); KEGG: pfl:PFL_2413 conserved hypothetical protein, ev=1e-160, 51% identity; amidohydrolase 3 487508 4075096 TM1040_3462 Ruegeria sp. TM1040 amidohydrolase 3 YP_611696.1 485556 D 292414 CDS YP_611697.1 99078439 4075097 complement(487552..488316) 1 NC_008043.1 PFAM: HpcH/HpaI aldolase: (1.3e-83); KEGG: sil:SPO3686 HpcH/HpaI aldolase family protein, ev=1e-106, 73% identity; 2-dehydro-3-deoxyglucarate aldolase 488316 4075097 TM1040_3463 Ruegeria sp. TM1040 2-dehydro-3-deoxyglucarate aldolase YP_611697.1 487552 R 292414 CDS YP_611698.1 99078440 4075098 complement(488329..489129) 1 NC_008043.1 KEGG: sil:SPOA0024 2-oxo-hepta-3-ene-1,7-dioic acid hydratase, , ev=1e-105, 71% identity; TIGRFAM: 2-oxo-hepta-3-ene-1,7-dioic acid hydratase: (5.1e-149); PFAM: Hydratase/decarboxylase: (3e-90); 2-oxo-hepta-3-ene-1,7-dioic acid hydratase 489129 4075098 TM1040_3464 Ruegeria sp. TM1040 2-oxo-hepta-3-ene-1,7-dioic acid hydratase YP_611698.1 488329 R 292414 CDS YP_611699.1 99078441 4075099 complement(489126..489983) 1 NC_008043.1 PFAM: fumarylacetoacetate (FAA) hydrolase: (1.5e-37); KEGG: sil:SPOA0025 fumarylacetoacetate hydrolase family protein, ev=1e-116, 71% identity; 5-carboxymethyl-2-hydroxymuconate delta-isomerase 489983 4075099 TM1040_3465 Ruegeria sp. TM1040 5-carboxymethyl-2-hydroxymuconate delta-isomerase YP_611699.1 489126 R 292414 CDS YP_611700.1 99078442 4075100 complement(489983..491395) 1 NC_008043.1 PFAM: Pyridoxal-dependent decarboxylase: (7.4e-117); KEGG: sil:SPO3687 decarboxylase, pyridoxal-dependent, ev=0.0, 82% identity; aromatic-L-amino-acid decarboxylase 491395 4075100 TM1040_3466 Ruegeria sp. TM1040 aromatic-L-amino-acid decarboxylase YP_611700.1 489983 R 292414 CDS YP_611701.1 99078443 4075101 complement(491473..492453) 1 NC_008043.1 KEGG: sil:SPO3688 extradiol ring-cleavage dioxygenase family protein, ev=1e-168, 84% identity; TIGRFAM: 3,4-dihydroxyphenylacetate 2,3-dioxygenase HpaD: (4.2e-168); PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase: (5.9e-22); 3,4-dihydroxyphenylacetate 2,3-dioxygenase 492453 4075101 TM1040_3467 Ruegeria sp. TM1040 3,4-dihydroxyphenylacetate 2,3-dioxygenase YP_611701.1 491473 R 292414 CDS YP_611702.1 99078444 4075102 complement(492552..494063) 1 NC_008043.1 KEGG: sil:SPOA0027 5-carboxy-2-hydroxymuconate semialdehyde dehydrogenase, ev=0.0, 78% identity; TIGRFAM: 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase: (0); PFAM: aldehyde dehydrogenase: (1.2e-243); 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase 494063 4075102 TM1040_3468 Ruegeria sp. TM1040 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase YP_611702.1 492552 R 292414 CDS YP_611703.1 99078445 4075103 complement(494060..494455) 1 NC_008043.1 PFAM: 5-carboxymethyl-2-hydroxymuconate isomerase: (1.4e-11); KEGG: sil:SPOA0320 5-carboxymethyl-2-hydroxymuconate delta isomerase, ev=1e-34, 56% identity; 5-carboxymethyl-2-hydroxymuconate isomerase 494455 4075103 TM1040_3469 Ruegeria sp. TM1040 5-carboxymethyl-2-hydroxymuconate isomerase YP_611703.1 494060 R 292414 CDS YP_611704.1 99078446 4075104 494584..495018 1 NC_008043.1 TIGRFAM: Homoprotocatechuate degradation transcriptional regulator HpaR: (2.2e-37); PFAM: regulatory protein, MarR: (1.7e-20); KEGG: sil:SPO3689 transcriptional regulator, MarR family, ev=3e-38, 60% identity; MarR family transcriptional regulator 495018 4075104 TM1040_3470 Ruegeria sp. TM1040 MarR family transcriptional regulator YP_611704.1 494584 D 292414 CDS YP_611705.1 99078447 4075105 complement(495015..496277) 1 NC_008043.1 PFAM: MOFRL: (1.3e-46); KEGG: sil:SPO1564 MOFRL domain protein, ev=3e-96, 49% identity; hydroxypyruvate reductase 496277 4075105 TM1040_3471 Ruegeria sp. TM1040 hydroxypyruvate reductase YP_611705.1 495015 R 292414 CDS YP_611706.1 99078448 4075106 496475..497305 1 NC_008043.1 PFAM: protein of unknown function DUF861, cupin_3: (7.2e-18) Cupin 2, conserved barrel: (2.9e-06); KEGG: bur:Bcep18194_B0211 protein of unknown function DUF861, ev=1e-126, 76% identity; hypothetical protein 497305 4075106 TM1040_3472 Ruegeria sp. TM1040 hypothetical protein YP_611706.1 496475 D 292414 CDS YP_611707.1 99078449 4075107 complement(497379..498818) 1 NC_008043.1 TIGRFAM: uracil-xanthine permease: (6.1e-108); PFAM: Xanthine/uracil/vitamin C permease: (6.3e-97); KEGG: sil:SPO0874 xanthine/uracil permease family protein, ev=0.0, 85% identity; uracil-xanthine permease 498818 4075107 TM1040_3473 Ruegeria sp. TM1040 uracil-xanthine permease YP_611707.1 497379 R 292414 CDS YP_611708.1 99078450 4075108 complement(498896..499402) 1 NC_008043.1 catalyzes the formation of glyoxylate from (S)-ureidoglycolate; ureidoglycolate hydrolase 499402 4075108 TM1040_3474 Ruegeria sp. TM1040 ureidoglycolate hydrolase YP_611708.1 498896 R 292414 CDS YP_611709.1 99078451 4075109 complement(499399..500814) 1 NC_008043.1 PFAM: polysaccharide deacetylase: (2.9e-06); KEGG: rsp:RSP_1554 possible polysaccharide deacetylase, ev=0.0, 74% identity; polysaccharide deacetylase 500814 4075109 TM1040_3475 Ruegeria sp. TM1040 polysaccharide deacetylase YP_611709.1 499399 R 292414 CDS YP_611710.1 99078452 4075110 501014..501370 1 NC_008043.1 PFAM: Transthyretin: (3.6e-59); KEGG: jan:Jann_2609 transthyretin, ev=6e-46, 69% identity; transthyretin 501370 4075110 TM1040_3476 Ruegeria sp. TM1040 transthyretin YP_611710.1 501014 D 292414 CDS YP_611711.1 99078453 4075111 complement(501443..502357) 1 NC_008043.1 PFAM: regulatory protein, LysR: (4.6e-19) LysR, substrate-binding: (2.4e-43); KEGG: sil:SPO0870 transcriptional regulator, LysR family, ev=1e-114, 67% identity; LysR family transcriptional regulator 502357 4075111 TM1040_3477 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_611711.1 501443 R 292414 CDS YP_611712.1 99078454 4075112 502467..503726 1 NC_008043.1 PFAM: protein of unknown function DUF989: (2e-260); KEGG: sil:SPO0869 membrane protein, , ev=1e-179, 74% identity; hypothetical protein 503726 4075112 TM1040_3478 Ruegeria sp. TM1040 hypothetical protein YP_611712.1 502467 D 292414 CDS YP_611713.1 99078455 4075113 503802..505187 1 NC_008043.1 Catalyzes the deamination of guanine; guanine deaminase 505187 4075113 TM1040_3479 Ruegeria sp. TM1040 guanine deaminase YP_611713.1 503802 D 292414 CDS YP_611714.1 99078456 4075120 complement(511757..512116) 1 NC_008043.1 PFAM: response regulator receiver: (0.00015); KEGG: lic:LIC12088 response regulator, ev=1e-10, 44% identity; response regulator receiver protein 512116 4075120 TM1040_3480 Ruegeria sp. TM1040 response regulator receiver protein YP_611714.1 511757 R 292414 CDS YP_611715.1 99078457 4075121 complement(512374..513432) 1 NC_008043.1 PFAM: ABC transporter related: (3.1e-55) Transport-associated OB: (4e-10); SMART: ATPase: (5.9e-14); KEGG: jan:Jann_3840 ABC transporter related, ev=1e-137, 69% identity; ABC transporter 513432 4075121 TM1040_3481 Ruegeria sp. TM1040 ABC transporter YP_611715.1 512374 R 292414 CDS YP_611716.1 99078458 4075122 complement(513488..514279) 1 NC_008043.1 PFAM: regulatory proteins, IclR: (1.8e-32); KEGG: jan:Jann_3839 transcriptional regulator, IclR family, ev=8e-86, 64% identity; IclR family transcriptional regulator 514279 4075122 TM1040_3482 Ruegeria sp. TM1040 IclR family transcriptional regulator YP_611716.1 513488 R 292414 CDS YP_611717.1 99078459 4075123 514420..515673 1 NC_008043.1 PFAM: extracellular solute-binding protein, family 1: (1.4e-30); KEGG: jan:Jann_3838 extracellular solute-binding protein, family 1, ev=1e-164, 67% identity; extracellular solute-binding protein 515673 4075123 TM1040_3483 Ruegeria sp. TM1040 extracellular solute-binding protein YP_611717.1 514420 D 292414 CDS YP_611718.1 99078460 4075124 515908..516735 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (5.4e-05); KEGG: jan:Jann_3837 binding-protein-dependent transport systems inner membrane component, ev=1e-106, 59% identity; binding-protein-dependent transport system inner membrane protein 516735 4075124 TM1040_3484 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_611718.1 515908 D 292414 CDS YP_611719.1 99078461 4075125 516735..517583 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (6e-18); KEGG: jan:Jann_3836 binding-protein-dependent transport systems inner membrane component, ev=1e-126, 78% identity; binding-protein-dependent transport system inner membrane protein 517583 4075125 TM1040_3485 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_611719.1 516735 D 292414 CDS YP_611720.1 99078462 4075126 517580..519646 1 NC_008043.1 PFAM: glycoside hydrolase, clan GH-D: (1.6e-139); KEGG: jan:Jann_3835 glycoside hydrolase, clan GH-D, ev=0.0, 60% identity; glycoside hydrolase, clan GH-D 519646 4075126 TM1040_3486 Ruegeria sp. TM1040 glycoside hydrolase, clan GH-D YP_611720.1 517580 D 292414 CDS YP_611721.1 99078463 4075127 519643..521358 1 NC_008043.1 catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate; dihydroxy-acid dehydratase 521358 4075127 TM1040_3487 Ruegeria sp. TM1040 dihydroxy-acid dehydratase YP_611721.1 519643 D 292414 CDS YP_611722.1 99078464 4075128 521360..522130 1 NC_008043.1 PFAM: short-chain dehydrogenase/reductase SDR: (8.3e-27); KEGG: jan:Jann_3834 short-chain dehydrogenase/reductase SDR, ev=1e-106, 74% identity; short-chain dehydrogenase/reductase SDR 522130 4075128 TM1040_3488 Ruegeria sp. TM1040 short-chain dehydrogenase/reductase SDR YP_611722.1 521360 D 292414 CDS YP_611723.1 99078465 4075129 522127..523041 1 NC_008043.1 PFAM: 2-keto-3-deoxy-galactonokinase: (5.5e-49); KEGG: rsp:RSP_1371 2-dehydro-3-deoxygalactonokinase, ev=1e-77, 49% identity; 2-keto-3-deoxygalactonate kinase 523041 4075129 TM1040_3489 Ruegeria sp. TM1040 2-keto-3-deoxygalactonate kinase YP_611723.1 522127 D 292414 CDS YP_611724.1 99078466 4075130 523050..523655 1 NC_008043.1 catalyzes the formation of D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-galactonate 6-phosphate; functions in galactonate metabolism; 2-dehydro-3-deoxy-6-phosphogalactonate aldolase 523655 4075130 TM1040_3490 Ruegeria sp. TM1040 2-dehydro-3-deoxy-6-phosphogalactonate aldolase YP_611724.1 523050 D 292414 CDS YP_611725.1 99078467 4075131 523652..524497 1 NC_008043.1 PFAM: Senescence marker protein-30 (SMP-30)-like: (3.9e-22) SMP-30/Gluconolaconase/LRE-like region: (7.8e-35); KEGG: jan:Jann_3831 senescence marker protein-30 (SMP-30), ev=2e-84, 55% identity; SMP-30/gluconolaconase/LRE-like region 524497 4075131 TM1040_3491 Ruegeria sp. TM1040 SMP-30/gluconolaconase/LRE-like region YP_611725.1 523652 D 292414 CDS YP_611726.1 99078468 4075132 524505..526412 1 NC_008043.1 PFAM: Glycoside hydrolase, family 42-like: (3.3e-221) Beta-galactosidase trimerisation: (4.6e-51) Beta-galactosidase-like: (4.8e-05); KEGG: jan:Jann_3830 beta-galactosidase, ev=0.0, 62% identity; beta-galactosidase 526412 4075132 TM1040_3492 Ruegeria sp. TM1040 beta-galactosidase YP_611726.1 524505 D 292414 CDS YP_611727.1 99078469 4075172 526566..527798 1 NC_008043.1 PFAM: metallophosphoesterase: (1.1e-15); KEGG: sme:SMc01909 hypothetical protein, ev=5e-91, 43% identity; metallophosphoesterase 527798 4075172 TM1040_3493 Ruegeria sp. TM1040 metallophosphoesterase YP_611727.1 526566 D 292414 CDS YP_611728.1 99078470 4075173 527798..531232 1 NC_008043.1 KEGG: rsp:RSP_3215 hypothetical protein, ev=1e-127, 32% identity; hypothetical protein 531232 4075173 TM1040_3494 Ruegeria sp. TM1040 hypothetical protein YP_611728.1 527798 D 292414 CDS YP_611729.1 99078471 4075174 531293..532558 1 NC_008043.1 TIGRFAM: diaminopimelate decarboxylase: (1.1e-183); PFAM: Orn/DAP/Arg decarboxylase 2: (3.4e-38); KEGG: sil:SPO0334 diaminopimelate decarboxylase, ev=0.0, 88% identity; diaminopimelate decarboxylase 532558 4075174 TM1040_3495 Ruegeria sp. TM1040 diaminopimelate decarboxylase YP_611729.1 531293 D 292414 CDS YP_611730.1 99078472 4075175 532652..535303 1 NC_008043.1 TIGRFAM: conserved hypothetical protein: (1.7e-77); KEGG: sil:SPO0335 hypothetical protein, ev=0.0, 58% identity; hypothetical protein 535303 4075175 TM1040_3496 Ruegeria sp. TM1040 hypothetical protein YP_611730.1 532652 D 292414 CDS YP_611731.1 99078473 4075176 complement(535485..536399) 1 NC_008043.1 TIGRFAM: Zinc finger/thioredoxin : (8.4e-12); KEGG: sil:SPO0336 MJ0042 family finger-like domain protein, ev=2e-57, 43% identity; Zinc finger/thioredoxin 536399 4075176 TM1040_3497 Ruegeria sp. TM1040 Zinc finger/thioredoxin YP_611731.1 535485 R 292414 CDS YP_611732.1 99078474 4075177 536625..537302 1 NC_008043.1 PFAM: ABC transporter related: (8.5e-41); SMART: ATPase: (3e-15); KEGG: sil:SPO0337 cell division ATP-binding protein FtsE, ev=3e-99, 79% identity; ABC transporter 537302 4075177 TM1040_3498 Ruegeria sp. TM1040 ABC transporter YP_611732.1 536625 D 292414 CDS YP_611733.1 99078475 4075178 537299..538192 1 NC_008043.1 PFAM: protein of unknown function DUF214: (0.0015); KEGG: sil:SPO0338 cell division permease protein FtsX, , ev=1e-122, 78% identity; hypothetical protein 538192 4075178 TM1040_3499 Ruegeria sp. TM1040 hypothetical protein YP_611733.1 537299 D 292414 CDS YP_611734.1 99078476 4075179 538189..538938 1 NC_008043.1 PFAM: phospholipid/glycerol acyltransferase: (2.6e-15); KEGG: sil:SPO0339 acyltransferase family protein, ev=1e-97, 70% identity; phospholipid/glycerol acyltransferase 538938 4075179 TM1040_3500 Ruegeria sp. TM1040 phospholipid/glycerol acyltransferase YP_611734.1 538189 D 292414 CDS YP_611735.1 99078477 4075180 538916..539521 1 NC_008043.1 PFAM: pyridoxamine 5'-phosphate oxidase-related, FMN-binding: (4.1e-14); KEGG: jan:Jann_3730 pyridoxamine 5'-phosphate oxidase-related, FMN-binding, ev=5e-61, 59% identity; pyridoxamine 5'-phosphate oxidase-like FMN-binding protein 539521 4075180 TM1040_3501 Ruegeria sp. TM1040 pyridoxamine 5'-phosphate oxidase-like FMN-binding protein YP_611735.1 538916 D 292414 CDS YP_611736.1 99078478 4075181 complement(539572..540084) 1 NC_008043.1 hypothetical protein 540084 4075181 TM1040_3502 Ruegeria sp. TM1040 hypothetical protein YP_611736.1 539572 R 292414 CDS YP_611737.1 99078479 4075182 complement(540098..540412) 1 NC_008043.1 PFAM: Ethyl tert-butyl ether degradation EthD: (2.9e-06); KEGG: sil:SPO0315 hypothetical protein, ev=7e-26, 51% identity; ethyl tert-butyl ether degradation EthD 540412 4075182 TM1040_3503 Ruegeria sp. TM1040 ethyl tert-butyl ether degradation EthD YP_611737.1 540098 R 292414 CDS YP_611738.1 99078480 4075183 complement(540502..541899) 1 NC_008043.1 TIGRFAM: Dihydrolipoamide dehydrogenase: (4.2e-233); PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase: (2.4e-32) glucose-inhibited division protein A: (0.003) fumarate reductase/succinate dehydrogenase flavoprotein-like: (0.0029) pyridine nucleotide-disulphide oxidoreductase dimerisation region: (2.1e-55); KEGG: sil:SPO0340 2-oxoglutarate dehydrogenase, E3 component, dihydrolipoamide dehydrogenase, ev=0.0, 78% identity; dihydrolipoamide dehydrogenase 541899 4075183 TM1040_3504 Ruegeria sp. TM1040 dihydrolipoamide dehydrogenase YP_611738.1 540502 R 292414 CDS YP_611739.1 99078481 4075184 complement(542040..542600) 1 NC_008043.1 KEGG: mlo:mlr7497 hypothetical protein, ev=3e-45, 60% identity; hypothetical protein 542600 4075184 TM1040_3505 Ruegeria sp. TM1040 hypothetical protein YP_611739.1 542040 R 292414 CDS YP_611740.1 99078482 4075185 complement(542597..543007) 1 NC_008043.1 KEGG: jan:Jann_0835 inner membrane protein, ev=3e-49, 69% identity; inner membrane protein 543007 4075185 TM1040_3506 Ruegeria sp. TM1040 inner membrane protein YP_611740.1 542597 R 292414 CDS YP_611741.1 99078483 4075186 complement(543009..543401) 1 NC_008043.1 KEGG: jan:Jann_0835 inner membrane protein, ev=1e-26, 44% identity; inner membrane protein 543401 4075186 TM1040_3507 Ruegeria sp. TM1040 inner membrane protein YP_611741.1 543009 R 292414 CDS YP_611742.1 99078484 4075187 complement(543398..543925) 1 NC_008043.1 hypothetical protein 543925 4075187 TM1040_3508 Ruegeria sp. TM1040 hypothetical protein YP_611742.1 543398 R 292414 CDS YP_611743.1 99078485 4075188 complement(543942..544376) 1 NC_008043.1 hypothetical protein 544376 4075188 TM1040_3509 Ruegeria sp. TM1040 hypothetical protein YP_611743.1 543942 R 292414 CDS YP_611744.1 99078486 4075189 complement(544384..545889) 1 NC_008043.1 component of 2-oxoglutarate dehydrogenase complex; catalyzes the transfer of succinyl coenzyme A to form succinyl CoA as part of the conversion of 2-oxoglutarate to succinyl-CoA; dihydrolipoamide succinyltransferase 545889 4075189 TM1040_3510 Ruegeria sp. TM1040 dihydrolipoamide succinyltransferase YP_611744.1 544384 R 292414 CDS YP_611745.1 99078487 4075190 complement(545904..548855) 1 NC_008043.1 SucA; E1 component of the oxoglutarate dehydrogenase complex which catalyzes the formation of succinyl-CoA from 2-oxoglutarate; SucA catalyzes the reaction of 2-oxoglutarate with dihydrolipoamide succinyltransferase-lipoate to form dihydrolipoamide succinyltransferase-succinyldihydrolipoate and carbon dioxide; 2-oxoglutarate dehydrogenase E1 component 548855 sucA 4075190 sucA Ruegeria sp. TM1040 2-oxoglutarate dehydrogenase E1 component YP_611745.1 545904 R 292414 CDS YP_611746.1 99078488 4075191 complement(549097..549984) 1 NC_008043.1 TIGRFAM: succinyl-CoA synthetase, alpha subunit: (1.7e-145); PFAM: CoA-binding: (3e-51) ATP-citrate lyase/succinyl-CoA ligase: (5.9e-51); KEGG: jan:Jann_0827 succinyl-CoA synthetase, alpha subunit, ev=1e-151, 89% identity; succinyl-CoA synthetase subunit alpha 549984 4075191 TM1040_3512 Ruegeria sp. TM1040 succinyl-CoA synthetase subunit alpha YP_611746.1 549097 R 292414 CDS YP_611747.1 99078489 4075192 complement(550003..550842) 1 NC_008043.1 PFAM: glycosyl transferase, family 25: (2.9e-15); KEGG: jan:Jann_0824 glycosyl transferase, family 25, ev=2e-43, 38% identity; glycosyl transferase family protein 550842 4075192 TM1040_3513 Ruegeria sp. TM1040 glycosyl transferase family protein YP_611747.1 550003 R 292414 CDS YP_611748.1 99078490 4075193 complement(550901..552094) 1 NC_008043.1 catalyzes the interconversion of succinyl-CoA and succinate; succinyl-CoA synthetase subunit beta 552094 sucC 4075193 sucC Ruegeria sp. TM1040 succinyl-CoA synthetase subunit beta YP_611748.1 550901 R 292414 CDS YP_611749.1 99078491 4075194 552295..552765 1 NC_008043.1 hypothetical protein 552765 4075194 TM1040_3515 Ruegeria sp. TM1040 hypothetical protein YP_611749.1 552295 D 292414 CDS YP_611750.1 99078492 4075195 complement(552904..553734) 1 NC_008043.1 hypothetical protein 553734 4075195 TM1040_3516 Ruegeria sp. TM1040 hypothetical protein YP_611750.1 552904 R 292414 CDS YP_611751.1 99078493 4075196 complement(553904..554866) 1 NC_008043.1 Catalyzes the reversible oxidation of malate to oxaloacetate; malate dehydrogenase 554866 4075196 TM1040_3517 Ruegeria sp. TM1040 malate dehydrogenase YP_611751.1 553904 R 292414 CDS YP_611752.1 99078494 4075197 555160..555711 1 NC_008043.1 hypothetical protein 555711 4075197 TM1040_3518 Ruegeria sp. TM1040 hypothetical protein YP_611752.1 555160 D 292414 CDS YP_611753.1 99078495 4075198 complement(555736..556047) 1 NC_008043.1 KEGG: sil:SPO0351 hypothetical protein, ev=5e-29, 61% identity; hypothetical protein 556047 4075198 TM1040_3519 Ruegeria sp. TM1040 hypothetical protein YP_611753.1 555736 R 292414 CDS YP_611754.1 99078496 4075199 556410..557264 1 NC_008043.1 PFAM: HpcH/HpaI aldolase: (1.9e-43); KEGG: sil:SPO0352 citrate lyase, beta subunit, ev=1e-127, 80% identity; citryl-CoA lyase 557264 4075199 TM1040_3520 Ruegeria sp. TM1040 citryl-CoA lyase YP_611754.1 556410 D 292414 CDS YP_611755.1 99078497 4075200 557330..557878 1 NC_008043.1 PFAM: NnrU: (1.5e-16); KEGG: sil:SPO0353 NnrU family protein, ev=2e-69, 67% identity; protein NnrU 557878 4075200 TM1040_3521 Ruegeria sp. TM1040 protein NnrU YP_611755.1 557330 D 292414 CDS YP_611756.1 99078498 4075201 557883..558086 1 NC_008043.1 KEGG: rsp:RSP_0972 hypothetical protein, ev=1e-24, 71% identity; hypothetical protein 558086 4075201 TM1040_3522 Ruegeria sp. TM1040 hypothetical protein YP_611756.1 557883 D 292414 CDS YP_611757.1 99078499 4075202 558088..559128 1 NC_008043.1 KEGG: sil:SPO0355 hypothetical protein, ev=1e-165, 82% identity; hypothetical protein 559128 4075202 TM1040_3523 Ruegeria sp. TM1040 hypothetical protein YP_611757.1 558088 D 292414 CDS YP_611758.1 99078500 4075203 559224..559799 1 NC_008043.1 PFAM: Phosphoglycerate mutase: (2.1e-05); KEGG: jan:Jann_3544 phosphoglycerate mutase, ev=5e-45, 54% identity; phosphoglycerate mutase 559799 4075203 TM1040_3524 Ruegeria sp. TM1040 phosphoglycerate mutase YP_611758.1 559224 D 292414 CDS YP_611759.1 99078501 4075204 560022..560405 1 NC_008043.1 PFAM: succinate dehydrogenase, cytochrome b subunit: (5.3e-41); KEGG: jan:Jann_0811 succinate dehydrogenase, cytochrome b subunit, ev=5e-39, 60% identity; succinate dehydrogenase subunit C 560405 4075204 TM1040_3525 Ruegeria sp. TM1040 succinate dehydrogenase subunit C YP_611759.1 560022 D 292414 CDS YP_611760.1 99078502 4075205 560420..560791 1 NC_008043.1 KEGG: sil:SPO0359 succinate dehydrogenase, hydrophobic membrane anchor protein, ev=8e-32, 53% identity; succinate dehydrogenase subunit D 560791 4075205 TM1040_3526 Ruegeria sp. TM1040 succinate dehydrogenase subunit D YP_611760.1 560420 D 292414 CDS YP_611761.1 99078503 4075206 560816..562624 1 NC_008043.1 part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol; succinate dehydrogenase flavoprotein subunit 562624 sdhA 4075206 sdhA Ruegeria sp. TM1040 succinate dehydrogenase flavoprotein subunit YP_611761.1 560816 D 292414 CDS YP_611762.1 99078504 4075207 562688..563497 1 NC_008043.1 hypothetical protein 563497 4075207 TM1040_3528 Ruegeria sp. TM1040 hypothetical protein YP_611762.1 562688 D 292414 CDS YP_611763.1 99078505 4075208 563494..564360 1 NC_008043.1 hypothetical protein 564360 4075208 TM1040_3529 Ruegeria sp. TM1040 hypothetical protein YP_611763.1 563494 D 292414 CDS YP_611764.1 99078506 4075209 564490..565269 1 NC_008043.1 part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol; the catalytic subunits are similar to fumarate reductase; succinate dehydrogenase iron-sulfur subunit 565269 sdhB 4075209 sdhB Ruegeria sp. TM1040 succinate dehydrogenase iron-sulfur subunit YP_611764.1 564490 D 292414 CDS YP_611765.1 99078507 4075210 complement(566500..567681) 1 NC_008043.1 PFAM: Phytanoyl-CoA dioxygenase: (2.4e-27); KEGG: ret:RHE_CH03702 hypothetical protein, ev=1e-118, 58% identity; phytanoyl-CoA dioxygenase 567681 4075210 TM1040_3531 Ruegeria sp. TM1040 phytanoyl-CoA dioxygenase YP_611765.1 566500 R 292414 CDS YP_611766.1 99078508 4075211 567761..568780 1 NC_008043.1 PFAM: regulatory protein, LacI: (0.00039); KEGG: sco:SCO6986 DNA-binding protein, ev=9e-71, 44% identity; LacI family transcriptional regulator 568780 4075211 TM1040_3532 Ruegeria sp. TM1040 LacI family transcriptional regulator YP_611766.1 567761 D 292414 CDS YP_611767.1 99078509 4075212 complement(569523..570311) 1 NC_008043.1 PFAM: phage integrase: (0.001); phage integrase 570311 4075212 TM1040_3533 Ruegeria sp. TM1040 phage integrase YP_611767.1 569523 R 292414 CDS YP_611768.1 99078510 4075213 570525..570791 1 NC_008043.1 PFAM: transposase IS3/IS911: (2.9e-19); KEGG: ret:RHE_PA00090 probable insertion sequence transposase protein, IS3/IS911 family, ev=2e-34, 77% identity; transposase IS3/IS911 570791 4075213 TM1040_3534 Ruegeria sp. TM1040 transposase IS3/IS911 YP_611768.1 570525 D 292414 CDS YP_611769.1 99078511 4075214 570824..571621 1 NC_008043.1 PFAM: Integrase, catalytic region: (4.6e-37); KEGG: mlo:mll6088 transposase, ev=1e-117, 75% identity; integrase catalytic subunit 571621 4075214 TM1040_3535 Ruegeria sp. TM1040 integrase catalytic subunit YP_611769.1 570824 D 292414 CDS YP_611770.1 99078512 4075215 complement(572581..575973) 1 NC_008043.1 PFAM: helicase-like: (0.0023) type III restriction enzyme, res subunit: (3.3e-47) protein of unknown function DUF450: (4.7e-19) DEAD/DEAH box helicase-like: (2.4e-05); KEGG: mac:MA2418 type I site-specific deoxyribonuclease protein R, ev=0.0, 53% identity; type III restriction enzyme, res subunit 575973 4075215 TM1040_3537 Ruegeria sp. TM1040 type III restriction enzyme, res subunit YP_611770.1 572581 R 292414 CDS YP_611771.1 99078513 4075216 complement(575970..578069) 1 NC_008043.1 PFAM: protein of unknown function DUF262: (5.4e-07) protein of unknown function DUF1524 RloF: (3.3e-42); KEGG: mac:MA2417 hypothetical protein, ev=0.0, 61% identity; hypothetical protein 578069 4075216 TM1040_3538 Ruegeria sp. TM1040 hypothetical protein YP_611771.1 575970 R 292414 CDS YP_611772.1 99078514 4075217 complement(578094..579023) 1 NC_008043.1 KEGG: mac:MA2416 hypothetical protein, ev=5e-53, 36% identity; hypothetical protein 579023 4075217 TM1040_3539 Ruegeria sp. TM1040 hypothetical protein YP_611772.1 578094 R 292414 CDS YP_611773.1 99078515 4075218 complement(579025..580188) 1 NC_008043.1 PFAM: restriction modification system DNA specificity domain: (1.2e-30); KEGG: rba:RB11412 probable type I restriction enzyme EcoBI specificity protein, ev=1e-60, 50% identity; restriction modification system DNA specificity subunit 580188 4075218 TM1040_3540 Ruegeria sp. TM1040 restriction modification system DNA specificity subunit YP_611773.1 579025 R 292414 CDS YP_611774.1 99078516 4075219 complement(580185..581759) 1 NC_008043.1 PFAM: N-6 DNA methylase: (5e-32); KEGG: rba:RB11642 type I restriction enzym, M protein, ev=0.0, 64% identity; N-6 DNA methylase 581759 4075219 TM1040_3541 Ruegeria sp. TM1040 N-6 DNA methylase YP_611774.1 580185 R 292414 CDS YP_611775.1 99078517 4075220 complement(582228..583346) 1 NC_008043.1 PFAM: phage integrase: (0.001); KEGG: aci:ACIAD2657 site-specific tyrosine recombinase, ev=2e-06, 23% identity; phage integrase 583346 4075220 TM1040_3542 Ruegeria sp. TM1040 phage integrase YP_611775.1 582228 R 292414 CDS YP_611776.1 99078518 4075221 complement(583832..584236) 1 NC_008043.1 transcriptional regulator 584236 4075221 TM1040_3544 Ruegeria sp. TM1040 transcriptional regulator YP_611776.1 583832 R 292414 CDS YP_611777.1 99078519 4075222 complement(586363..586938) 1 NC_008043.1 PFAM: BRO-like: (0.002); KEGG: bme:BMEI0899 phage-related DNA binding protein, ev=6e-10, 32% identity; BRO family protein 586938 4075222 TM1040_3546 Ruegeria sp. TM1040 BRO family protein YP_611777.1 586363 R 292414 CDS YP_611778.1 99078520 4075223 complement(587243..589153) 1 NC_008043.1 hypothetical protein 589153 4075223 TM1040_3547 Ruegeria sp. TM1040 hypothetical protein YP_611778.1 587243 R 292414 CDS YP_611779.1 99078521 4075224 complement(589306..590034) 1 NC_008043.1 PFAM: protein of unknown function DUF45: (4.2e-63); KEGG: dvu:DVU1702 hypothetical protein, ev=4e-63, 49% identity; hypothetical protein 590034 4075224 TM1040_3548 Ruegeria sp. TM1040 hypothetical protein YP_611779.1 589306 R 292414 CDS YP_611780.1 99078522 4075225 complement(590038..593316) 1 NC_008043.1 KEGG: dvu:DVU1703 type I restriction-modification enzyme, R subunit, ev=0.0, 59% identity; TIGRFAM: type I site-specific deoxyribonuclease, HsdR family: (3.6e-110); PFAM: type III restriction enzyme, res subunit: (2.7e-13) protein of unknown function DUF450: (1.8e-39); SMART: DEAD/DEAH box helicase-like: (2.5e-08); HsdR family type I site-specific deoxyribonuclease 593316 4075225 TM1040_3549 Ruegeria sp. TM1040 HsdR family type I site-specific deoxyribonuclease YP_611780.1 590038 R 292414 CDS YP_611781.1 99078523 4075226 complement(593428..594681) 1 NC_008043.1 PFAM: restriction modification system DNA specificity domain: (5.3e-17); KEGG: dvu:DVU1705 type I restriction-modification enzyme, S subunit, ev=1e-34, 36% identity; restriction modification system DNA specificity subunit 594681 4075226 TM1040_3550 Ruegeria sp. TM1040 restriction modification system DNA specificity subunit YP_611781.1 593428 R 292414 CDS YP_611782.1 99078524 4075227 complement(594681..596180) 1 NC_008043.1 TIGRFAM: type I restriction-modification system, M subunit: (6.6e-75); PFAM: N-6 DNA methylase: (1.5e-137); KEGG: dvu:DVU1709 type I restriction-modification system, M subunit, ev=0.0, 72% identity; type I restriction-modification system, M subunit 596180 4075227 TM1040_3551 Ruegeria sp. TM1040 type I restriction-modification system, M subunit YP_611782.1 594681 R 292414 CDS YP_611783.1 99078525 4075228 596707..597282 1 NC_008043.1 PFAM: BRO-like: (0.002); KEGG: bme:BMEI0899 phage-related DNA binding protein, ev=6e-10, 32% identity; BRO family protein 597282 4075228 TM1040_3552 Ruegeria sp. TM1040 BRO family protein YP_611783.1 596707 D 292414 CDS YP_611784.1 99078526 4075229 complement(597614..598792) 1 NC_008043.1 PFAM: phage integrase: (0.00022); KEGG: dar:Daro_0788 phage integrase, ev=2e-42, 31% identity; phage integrase 598792 4075229 TM1040_3553 Ruegeria sp. TM1040 phage integrase YP_611784.1 597614 R 292414 CDS YP_611785.1 99078527 4075475 complement(599009..599191) 1 NC_008043.1 PFAM: protein of unknown function DUF329: (8.3e-13); KEGG: jan:Jann_2867 protein of unknown function DUF329, ev=5e-15, 66% identity; hypothetical protein 599191 4075475 TM1040_3554 Ruegeria sp. TM1040 hypothetical protein YP_611785.1 599009 R 292414 CDS YP_611786.1 99078528 4075476 complement(599188..600210) 1 NC_008043.1 KEGG: sil:SPOA0079 ribonuclease, Rne/Rng family, ev=1e-137, 73% identity; ribonuclease 600210 4075476 TM1040_3555 Ruegeria sp. TM1040 ribonuclease YP_611786.1 599188 R 292414 CDS YP_611787.1 99078529 4075477 complement(600207..600788) 1 NC_008043.1 TIGRFAM: maf protein: (1.4e-48); PFAM: Maf-like protein: (3.4e-62); KEGG: rsp:RSP_0625 Maf-like protein, ev=1e-79, 76% identity; maf protein 600788 4075477 TM1040_3556 Ruegeria sp. TM1040 maf protein YP_611787.1 600207 R 292414 CDS YP_611788.1 99078530 4075478 complement(600920..601138) 1 NC_008043.1 stimulates the activities of the other two initiation factors, IF-2 and IF-3; translation initiation factor IF-1 601138 infA 4075478 infA Ruegeria sp. TM1040 translation initiation factor IF-1 YP_611788.1 600920 R 292414 CDS YP_611789.1 99078531 4075479 complement(601223..602101) 1 NC_008043.1 PFAM: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase: (1.6e-07); KEGG: sil:SPOA0076 hydrolase, carbon-nitrogen family, ev=1e-120, 71% identity; nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase 602101 4075479 TM1040_3558 Ruegeria sp. TM1040 nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase YP_611789.1 601223 R 292414 CDS YP_611790.1 99078532 4075480 complement(602195..602782) 1 NC_008043.1 KEGG: sil:SPOA0075 hypothetical protein, ev=8e-80, 72% identity; hypothetical protein 602782 4075480 TM1040_3559 Ruegeria sp. TM1040 hypothetical protein YP_611790.1 602195 R 292414 CDS YP_611791.1 99078533 4075481 complement(602782..603177) 1 NC_008043.1 TIGRFAM: conserved hypothetical protein: (8.1e-41); KEGG: sil:SPOA0074 hypothetical protein, ev=4e-52, 73% identity; hypothetical protein 603177 4075481 TM1040_3560 Ruegeria sp. TM1040 hypothetical protein YP_611791.1 602782 R 292414 CDS YP_611792.1 99078534 4075482 complement(603178..603633) 1 NC_008043.1 PFAM: low molecular weight phosphotyrosine protein phosphatase: (3.3e-12); KEGG: sil:SPOA0073 arsenate reductase, ev=2e-71, 84% identity; protein tyrosine phosphatase 603633 4075482 TM1040_3561 Ruegeria sp. TM1040 protein tyrosine phosphatase YP_611792.1 603178 R 292414 CDS YP_611793.1 99078535 4075483 complement(603637..604116) 1 NC_008043.1 PFAM: Uncharacterised conserved protein UCP032146: (8.4e-77); KEGG: sil:SPOA0072 hypothetical protein, ev=2e-76, 86% identity; hypothetical protein 604116 4075483 TM1040_3562 Ruegeria sp. TM1040 hypothetical protein YP_611793.1 603637 R 292414 CDS YP_611794.1 99078536 4075484 complement(604396..605700) 1 NC_008043.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase 605700 hisD 4075484 hisD Ruegeria sp. TM1040 histidinol dehydrogenase YP_611794.1 604396 R 292414 CDS YP_611795.1 99078537 4075486 606074..606229 1 NC_008043.1 KEGG: sil:SPOA0136 hypothetical protein, ev=5e-08, 71% identity; hypothetical protein 606229 4075486 TM1040_3564 Ruegeria sp. TM1040 hypothetical protein YP_611795.1 606074 D 292414 CDS YP_611796.1 99078538 4075487 606235..607506 1 NC_008043.1 adds enolpyruvyl to UDP-N-acetylglucosamine as a component of cell wall formation; gram-positive bacteria have 2 copies of MurA which are active; UDP-N-acetylglucosamine 1-carboxyvinyltransferase 607506 4075487 TM1040_3565 Ruegeria sp. TM1040 UDP-N-acetylglucosamine 1-carboxyvinyltransferase YP_611796.1 606235 D 292414 CDS YP_611797.1 99078539 4075488 607506..607982 1 NC_008043.1 KEGG: sil:SPOA0138 hypothetical protein, ev=6e-62, 74% identity; hypothetical protein 607982 4075488 TM1040_3566 Ruegeria sp. TM1040 hypothetical protein YP_611797.1 607506 D 292414 CDS YP_611798.1 99078540 4075489 complement(608024..608818) 1 NC_008043.1 TIGRFAM: 3-oxoadipate enol-lactonase: (9.2e-103); PFAM: alpha/beta hydrolase fold: (5.3e-13); KEGG: sil:SPOA0434 3-oxoadipate enol-lactone hydrolase, ev=8e-85, 58% identity; 3-oxoadipate enol-lactonase 608818 4075489 TM1040_3567 Ruegeria sp. TM1040 3-oxoadipate enol-lactonase YP_611798.1 608024 R 292414 CDS YP_611799.1 99078541 4075490 complement(608968..609945) 1 NC_008043.1 PFAM: Pyridoxal-5'-phosphate-dependent enzyme, beta subunit: (1e-64); KEGG: rsp:RSP_2252 threonine dehydratase, ev=1e-135, 76% identity; pyridoxal-5'-phosphate-dependent protein subunit beta 609945 4075490 TM1040_3568 Ruegeria sp. TM1040 pyridoxal-5'-phosphate-dependent protein subunit beta YP_611799.1 608968 R 292414 CDS YP_611800.1 99078542 4075491 complement(609942..610790) 1 NC_008043.1 PFAM: alpha/beta hydrolase fold: (3.6e-13); KEGG: sil:SPOA0436 hydrolase, alpha/beta fold family, ev=4e-70, 50% identity; alpha/beta hydrolase 610790 4075491 TM1040_3569 Ruegeria sp. TM1040 alpha/beta hydrolase YP_611800.1 609942 R 292414 CDS YP_611801.1 99078543 4075492 complement(610813..611502) 1 NC_008043.1 TIGRFAM: haloacid dehalogenase, type II: (1.8e-73) HAD-superfamily hydrolase, subfamily IA, variant 2: (2e-24); PFAM: Haloacid dehalogenase-like hydrolase: (3.8e-26); KEGG: sil:SPOA0437 haloacid dehalogenase, type II, ev=5e-93, 73% identity; haloacid dehalogenase 611502 4075492 TM1040_3570 Ruegeria sp. TM1040 haloacid dehalogenase YP_611801.1 610813 R 292414 CDS YP_611802.1 99078544 4075493 611669..612097 1 NC_008043.1 PFAM: peptidylprolyl isomerase, FKBP-type: (1.6e-27); KEGG: sil:SPOA0438 peptidyl-prolyl cis-trans isomerase, FKBP-type, ev=8e-56, 70% identity; peptidylprolyl isomerase, FKBP-type 612097 4075493 TM1040_3571 Ruegeria sp. TM1040 peptidylprolyl isomerase, FKBP-type YP_611802.1 611669 D 292414 CDS YP_611803.1 99078545 4075494 612350..613423 1 NC_008043.1 KEGG: pca:Pcar_0492 spermidine/putrescine-binding periplasmic protein-like, ev=3e-16, 23% identity; spermidine/putrescine-binding periplasmic protein-like 613423 4075494 TM1040_3572 Ruegeria sp. TM1040 spermidine/putrescine-binding periplasmic protein-like YP_611803.1 612350 D 292414 CDS YP_611804.1 99078546 4075495 613580..614725 1 NC_008043.1 TIGRFAM: Lytic murein transglycosylase: (7.8e-111); PFAM: Peptidoglycan-binding domain 1: (1.6e-10); KEGG: sil:SPO3617 peptidoglycan-binding protein, , ev=1e-128, 60% identity; lytic murein transglycosylase 614725 4075495 TM1040_3573 Ruegeria sp. TM1040 lytic murein transglycosylase YP_611804.1 613580 D 292414 CDS YP_611805.1 99078547 4075496 complement(614751..615059) 1 NC_008043.1 KEGG: jan:Jann_1588 hypothetical protein, ev=3e-16, 45% identity; hypothetical protein 615059 4075496 TM1040_3574 Ruegeria sp. TM1040 hypothetical protein YP_611805.1 614751 R 292414 CDS YP_611806.1 99078548 4075497 complement(615049..616101) 1 NC_008043.1 KEGG: sil:SPOA0095 hypothetical protein, ev=1e-140, 68% identity; hypothetical protein 616101 4075497 TM1040_3575 Ruegeria sp. TM1040 hypothetical protein YP_611806.1 615049 R 292414 CDS YP_611807.1 99078549 4075498 complement(616098..616508) 1 NC_008043.1 KEGG: sil:SPOA0094 hypothetical protein, ev=6e-62, 85% identity; hypothetical protein 616508 4075498 TM1040_3576 Ruegeria sp. TM1040 hypothetical protein YP_611807.1 616098 R 292414 CDS YP_611808.1 99078550 4075499 complement(616505..617992) 1 NC_008043.1 PFAM: FAD linked oxidase-like: (1e-10); KEGG: sil:SPOA0093 FAD binding domain protein, ev=0.0, 80% identity; FAD linked oxidase-like protein 617992 4075499 TM1040_3577 Ruegeria sp. TM1040 FAD linked oxidase-like protein YP_611808.1 616505 R 292414 CDS YP_611809.1 99078551 4075500 618302..621514 1 NC_008043.1 TIGRFAM: Reductive dehalogenase: (3.9e-44); PFAM: ferredoxin: (2e-09) oxidoreductase FAD/NAD(P)-binding: (0.00012) 4Fe-4S ferredoxin, iron-sulfur binding: (0.00044) Oxidoreductase FAD-binding region: (0.00041); KEGG: sil:SPO0589 oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein, ev=0.0, 74% identity; reductive dehalogenase 621514 4075500 TM1040_3578 Ruegeria sp. TM1040 reductive dehalogenase YP_611809.1 618302 D 292414 CDS YP_611810.1 99078552 4075507 complement(628194..629282) 1 NC_008043.1 hypothetical protein 629282 4075507 TM1040_3579 Ruegeria sp. TM1040 hypothetical protein YP_611810.1 628194 R 292414 CDS YP_611811.1 99078553 4075508 complement(629292..630824) 1 NC_008043.1 KEGG: sil:SPO1693 hypothetical protein, ev=1e-107, 42% identity; hypothetical protein 630824 4075508 TM1040_3580 Ruegeria sp. TM1040 hypothetical protein YP_611811.1 629292 R 292414 CDS YP_611812.1 99078554 4075509 complement(631198..632346) 1 NC_008043.1 hypothetical protein 632346 4075509 TM1040_3581 Ruegeria sp. TM1040 hypothetical protein YP_611812.1 631198 R 292414 CDS YP_611813.1 99078555 4075510 complement(632527..632745) 1 NC_008043.1 hypothetical protein 632745 4075510 TM1040_3582 Ruegeria sp. TM1040 hypothetical protein YP_611813.1 632527 R 292414 CDS YP_611814.1 99078556 4075511 complement(632864..633151) 1 NC_008043.1 KEGG: rso:RSc2607 hypothetical protein, ev=7e-09, 53% identity; hypothetical protein 633151 4075511 TM1040_3583 Ruegeria sp. TM1040 hypothetical protein YP_611814.1 632864 R 292414 CDS YP_611815.1 99078557 4075512 complement(633225..633935) 1 NC_008043.1 hypothetical protein 633935 4075512 TM1040_3584 Ruegeria sp. TM1040 hypothetical protein YP_611815.1 633225 R 292414 CDS YP_611816.1 99078558 4075513 complement(634104..635339) 1 NC_008043.1 PFAM: phage integrase: (7e-22); KEGG: rso:RSc2622 probable integrase protein, ev=5e-76, 41% identity; phage integrase 635339 4075513 TM1040_3585 Ruegeria sp. TM1040 phage integrase YP_611816.1 634104 R 292414 CDS YP_611817.1 99078559 4075514 636897..637490 1 NC_008043.1 PFAM: phage integrase: (3.5e-13); KEGG: gox:GOX2485 phage related integrase, ev=2e-21, 41% identity; phage integrase 637490 4075514 TM1040_3588 Ruegeria sp. TM1040 phage integrase YP_611817.1 636897 D 292414 CDS YP_611818.1 99078560 4075516 637924..638838 1 NC_008043.1 PFAM: Sporulation related: (3e-15); KEGG: sil:SPO2738 lipoprotein, , ev=8e-99, 66% identity; sporulation related protein 638838 4075516 TM1040_3589 Ruegeria sp. TM1040 sporulation related protein YP_611818.1 637924 D 292414 CDS YP_611819.1 99078561 4075517 638899..640080 1 NC_008043.1 PFAM: peptidase S11, D-alanyl-D-alanine carboxypeptidase 1: (3.5e-66) Penicillin-binding protein 5-like: (5e-16); KEGG: sil:SPO2739 D-alanyl-D-alanine carboxypeptidase, ev=1e-151, 70% identity; Serine-type D-Ala-D-Ala carboxypeptidase 640080 4075517 TM1040_3590 Ruegeria sp. TM1040 Serine-type D-Ala-D-Ala carboxypeptidase YP_611819.1 638899 D 292414 CDS YP_611820.1 99078562 4075518 640077..640721 1 NC_008043.1 PFAM: thymidylate kinase: (2.9e-57); KEGG: sil:SPO2740 thymidylate kinase, ev=1e-91, 81% identity; thymidylate kinase 640721 4075518 TM1040_3591 Ruegeria sp. TM1040 thymidylate kinase YP_611820.1 640077 D 292414 CDS YP_611821.1 99078563 4075519 640718..641839 1 NC_008043.1 catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the delta' subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA; DNA polymerase III subunit delta' 641839 4075519 TM1040_3592 Ruegeria sp. TM1040 DNA polymerase III subunit delta' YP_611821.1 640718 D 292414 CDS YP_611822.1 99078564 4075520 641900..642703 1 NC_008043.1 PFAM: TatD-related deoxyribonuclease: (4.1e-93); KEGG: sil:SPO2742 hydrolase, TatD family, ev=1e-127, 82% identity; TatD-related deoxyribonuclease 642703 4075520 TM1040_3593 Ruegeria sp. TM1040 TatD-related deoxyribonuclease YP_611822.1 641900 D 292414 CDS YP_611823.1 99078565 4075521 642703..643500 1 NC_008043.1 PFAM: beta-lactamase-like: (3.1e-05); KEGG: jan:Jann_1274 beta-lactamase-like, ev=1e-110, 70% identity; beta-lactamase-like protein 643500 4075521 TM1040_3594 Ruegeria sp. TM1040 beta-lactamase-like protein YP_611823.1 642703 D 292414 CDS YP_611824.1 99078566 4075522 643537..644469 1 NC_008043.1 PFAM: Auxin Efflux Carrier: (4.7e-24); KEGG: sil:SPO2744 malonate transporter, , ev=1e-118, 68% identity; auxin efflux carrier 644469 4075522 TM1040_3595 Ruegeria sp. TM1040 auxin efflux carrier YP_611824.1 643537 D 292414 CDS YP_611825.1 99078567 4075523 644593..645138 1 NC_008043.1 PFAM: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen: (0.00043) Redoxin: (1.9e-35); KEGG: rsp:RSP_2781 peroxiredoxin/glutaredoxin family protein, ev=2e-80, 76% identity; redoxin 645138 4075523 TM1040_3596 Ruegeria sp. TM1040 redoxin YP_611825.1 644593 D 292414 CDS YP_611826.1 99078568 4075024 complement(645205..646596) 1 NC_008043.1 PFAM: peptidase M20: (5e-17); KEGG: bur:Bcep18194_A4728 peptidase M20, ev=1e-135, 54% identity; hypothetical protein 646596 4075024 TM1040_3597 Ruegeria sp. TM1040 hypothetical protein YP_611826.1 645205 R 292414 CDS YP_611827.1 99078569 4075025 complement(646593..648158) 1 NC_008043.1 PFAM: gamma-glutamyltranspeptidase: (1e-69); KEGG: rpa:RPA0776 possible gamma-glutamyltranspeptidase precursor, ev=1e-142, 51% identity; gamma-glutamyltransferase 1 648158 4075025 TM1040_3598 Ruegeria sp. TM1040 gamma-glutamyltransferase 1 YP_611827.1 646593 R 292414 CDS YP_611828.1 99078570 4075026 complement(648155..649138) 1 NC_008043.1 KEGG: psb:Psyr_2263 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal, ev=1e-109, 61% identity; TIGRFAM: Oligopeptide/dipeptide ABC transporter, ATP-binding protein-like: (2.2e-24); PFAM: ABC transporter related: (9.5e-69) Oligopeptide/dipeptide ABC transporter-like: (5.9e-25); SMART: ATPase: (3.7e-23); oligopeptide/dipeptide ABC transporter ATP-binding protein-like protein 649138 4075026 TM1040_3599 Ruegeria sp. TM1040 oligopeptide/dipeptide ABC transporter ATP-binding protein-like protein YP_611828.1 648155 R 292414 CDS YP_611829.1 99078571 4075027 complement(649135..650130) 1 NC_008043.1 KEGG: psb:Psyr_2264 oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal, ev=1e-112, 64% identity; TIGRFAM: Oligopeptide/dipeptide ABC transporter, ATP-binding protein-like: (4.7e-23); PFAM: ABC transporter related: (1.7e-54) Oligopeptide/dipeptide ABC transporter-like: (2.9e-25); SMART: ATPase: (1.1e-15); oligopeptide/dipeptide ABC transporter ATP-binding protein-like protein 650130 4075027 TM1040_3600 Ruegeria sp. TM1040 oligopeptide/dipeptide ABC transporter ATP-binding protein-like protein YP_611829.1 649135 R 292414 CDS YP_611830.1 99078572 4075028 complement(650134..651030) 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (8e-38); KEGG: pst:PSPTO2574 peptide ABC transporter, permease protein, ev=4e-96, 59% identity; binding-protein-dependent transport system inner membrane protein 651030 4075028 TM1040_3601 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_611830.1 650134 R 292414 CDS YP_611831.1 99078573 4075029 complement(651032..651949) 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1.3e-54); KEGG: pst:PSPTO2575 peptide ABC transporter, permease protein, ev=1e-103, 62% identity; binding-protein-dependent transport systems inner membrane component 651949 4075029 TM1040_3602 Ruegeria sp. TM1040 binding-protein-dependent transport systems inner membrane component YP_611831.1 651032 R 292414 CDS YP_611832.1 99078574 4075030 complement(652050..653573) 1 NC_008043.1 PFAM: extracellular solute-binding protein, family 5: (2.8e-75); KEGG: pst:PSPTO2576 peptide ABC transporter, periplasmic peptide-binding protein, ev=1e-143, 49% identity; extracellular solute-binding protein 653573 4075030 TM1040_3603 Ruegeria sp. TM1040 extracellular solute-binding protein YP_611832.1 652050 R 292414 CDS YP_611833.1 99078575 4075031 653725..654486 1 NC_008043.1 PFAM: regulatory proteins, IclR: (9.3e-16); KEGG: rru:Rru_A1344 transcriptional regulator, IclR family, ev=3e-56, 45% identity; IclR family transcriptional regulator 654486 4075031 TM1040_3604 Ruegeria sp. TM1040 IclR family transcriptional regulator YP_611833.1 653725 D 292414 CDS YP_611834.1 99078576 4075032 654670..655857 1 NC_008043.1 PFAM: Cys/Met metabolism pyridoxal-phosphate-dependent enzymes: (2e-05) aromatic amino acid beta-eliminating lyase/threonine aldolase: (0.00022) aminotransferase, class I and II: (1.3e-65); KEGG: sil:SPOA0066 aspartate aminotransferase, , ev=1e-137, 64% identity; aminotransferase 655857 4075032 TM1040_3605 Ruegeria sp. TM1040 aminotransferase YP_611834.1 654670 D 292414 CDS YP_611835.1 99078577 4075033 655964..657247 1 NC_008043.1 PFAM: UDP-glucose/GDP-mannose dehydrogenase: (8.3e-37); KEGG: bbr:BB2925 capsular polysaccharide biosynthesis protein, ev=1e-161, 65% identity; UDP-glucose/GDP-mannose dehydrogenase 657247 4075033 TM1040_3606 Ruegeria sp. TM1040 UDP-glucose/GDP-mannose dehydrogenase YP_611835.1 655964 D 292414 CDS YP_611836.1 99078578 4075034 657267..658217 1 NC_008043.1 PFAM: Asparaginase/glutaminase: (6.5e-73); KEGG: eca:ECA2340 cytoplasmic asparaginase I, ev=3e-50, 38% identity; asparaginase 658217 4075034 TM1040_3607 Ruegeria sp. TM1040 asparaginase YP_611836.1 657267 D 292414 CDS YP_611837.1 99078579 4075035 658318..659745 1 NC_008043.1 TIGRFAM: amino acid carrier protein: (3e-156); PFAM: sodium:alanine symporter: (8.8e-150); KEGG: ppr:PBPRA1278 hypothetical amino acid carrier protein(sodium/alanine symporter), ev=0.0, 71% identity; amino acid carrier protein 659745 4075035 TM1040_3608 Ruegeria sp. TM1040 amino acid carrier protein YP_611837.1 658318 D 292414 CDS YP_611838.1 99078580 4075036 complement(659788..660702) 1 NC_008043.1 PFAM: sugar isomerase (SIS): (0.0046); KEGG: sil:SPO1591 SIS domain protein, ev=3e-33, 30% identity; RpiR family transcriptional regulator 660702 4075036 TM1040_3609 Ruegeria sp. TM1040 RpiR family transcriptional regulator YP_611838.1 659788 R 292414 CDS YP_611839.1 99078581 4075037 complement(660766..664488) 1 NC_008043.1 PFAM: 60 kDa inner membrane insertion protein: (8e-07) pyruvate phosphate dikinase, PEP/pyruvate-binding: (7.4e-10) PEP-utilising enzyme, mobile region: (9.4e-15); SMART: Rhodanese-like: (4e-05); KEGG: gvi:glr2690 similar to phosphoenolpyruvate synthase, ev=9e-28, 25% identity; PEP-utilizing protein 664488 4075037 TM1040_3610 Ruegeria sp. TM1040 PEP-utilizing protein YP_611839.1 660766 R 292414 CDS YP_611840.1 99078582 4075038 664980..665789 1 NC_008043.1 TIGRFAM: Phosphonate-binding periplasmic protein: (5.5e-11); KEGG: ppr:PBPRB1010 hypothetical protein, ev=1e-66, 54% identity; phosphonate-binding periplasmic protein 665789 4075038 TM1040_3611 Ruegeria sp. TM1040 phosphonate-binding periplasmic protein YP_611840.1 664980 D 292414 CDS YP_611841.1 99078583 4075039 665882..668194 1 NC_008043.1 PFAM: response regulator receiver: (1.8e-28) ATP-binding region, ATPase-like: (3.5e-38) histidine kinase A-like: (2.4e-27); KEGG: mlo:mll3725 hybrid sensory histidine kinase, ev=1e-118, 44% identity; periplasmic sensor hybrid histidine kinase 668194 4075039 TM1040_3612 Ruegeria sp. TM1040 periplasmic sensor hybrid histidine kinase YP_611841.1 665882 D 292414 CDS YP_611842.1 99078584 4075040 complement(668225..669037) 1 NC_008043.1 PFAM: ABC-3: (1.5e-75); KEGG: jan:Jann_0315 ABC-3, ev=2e-95, 70% identity; hypothetical protein 669037 4075040 TM1040_3613 Ruegeria sp. TM1040 hypothetical protein YP_611842.1 668225 R 292414 CDS YP_611843.1 99078585 4075041 complement(669034..669783) 1 NC_008043.1 PFAM: ABC transporter related: (2.4e-47); SMART: ATPase: (6e-18); KEGG: sil:SPO0985 zinc ABC transporter, ATP-binding protein, ev=2e-88, 65% identity; ABC transporter 669783 4075041 TM1040_3614 Ruegeria sp. TM1040 ABC transporter YP_611843.1 669034 R 292414 CDS YP_611844.1 99078586 4075042 complement(669789..670259) 1 NC_008043.1 KEGG: jan:Jann_0313 ferric uptake regulator, FUR family, ev=5e-57, 67% identity; ferric uptake regulator family protein 670259 4075042 TM1040_3615 Ruegeria sp. TM1040 ferric uptake regulator family protein YP_611844.1 669789 R 292414 CDS YP_611845.1 99078587 4075043 670359..671495 1 NC_008043.1 PFAM: periplasmic solute binding protein: (2.6e-29); KEGG: jan:Jann_0312 periplasmic solute binding protein, ev=1e-90, 46% identity; periplasmic solute binding protein 671495 4075043 TM1040_3616 Ruegeria sp. TM1040 periplasmic solute binding protein YP_611845.1 670359 D 292414 CDS YP_611846.1 99078588 4075044 671764..672813 1 NC_008043.1 PFAM: homocysteine S-methyltransferase: (1.5e-124); KEGG: rsp:RSP_3347 methionine synthase, 5-methyltetrahydrofolate--homocysteine methyltransferase, ev=1e-152, 77% identity; methionine synthase 672813 4075044 TM1040_3617 Ruegeria sp. TM1040 methionine synthase YP_611846.1 671764 D 292414 CDS YP_611847.1 99078589 4075045 672806..675547 1 NC_008043.1 KEGG: rsp:RSP_3346 5-methyltetrahydrofolate--homocysteine methyltransferase, ev=0.0, 80% identity; TIGRFAM: 5-methyltetrahydrofolate--homocysteine methyltransferase: (0); PFAM: dihydropteroate synthase, DHPS: (2.2e-71) Methionine synthase, B12-binding module, cap: (1.1e-47) Vitamin B12 dependent methionine synthase, activation region: (2.2e-57) cobalamin B12-binding: (3.1e-26); methionine synthase 675547 4075045 TM1040_3618 Ruegeria sp. TM1040 methionine synthase YP_611847.1 672806 D 292414 CDS YP_611848.1 99078590 4075046 675641..676090 1 NC_008043.1 PFAM: thiol-disulphide oxidoreductase DCC: (9.6e-22); KEGG: ret:RHE_CH01012 hypothetical protein, ev=6e-23, 40% identity; thiol-disulfide oxidoreductase DCC 676090 4075046 TM1040_3619 Ruegeria sp. TM1040 thiol-disulfide oxidoreductase DCC YP_611848.1 675641 D 292414 CDS YP_611849.1 99078591 4075047 676087..677670 1 NC_008043.1 PFAM: Saccharopine dehydrogenase: (5.7e-09); KEGG: ret:RHE_CH01011 hypothetical protein, ev=7e-60, 34% identity; saccharopine dehydrogenase 677670 4075047 TM1040_3620 Ruegeria sp. TM1040 saccharopine dehydrogenase YP_611849.1 676087 D 292414 CDS YP_611850.1 99078592 4075048 complement(677733..679253) 1 NC_008043.1 PFAM: aldehyde dehydrogenase: (4.8e-221); KEGG: bha:BH0681 aldehyde dehydrogenase, ev=0.0, 76% identity; aldehyde dehydrogenase 679253 4075048 TM1040_3621 Ruegeria sp. TM1040 aldehyde dehydrogenase YP_611850.1 677733 R 292414 CDS YP_611851.1 99078593 4075049 complement(679401..680360) 1 NC_008043.1 PFAM: helix-turn-helix, Fis-type: (1.3e-14) GAF: (6e-13); KEGG: bmb:BruAb1_0196 transcriptional regulator, Fis family, ev=2e-72, 49% identity; GAF sensor protein 680360 4075049 TM1040_3622 Ruegeria sp. TM1040 GAF sensor protein YP_611851.1 679401 R 292414 CDS YP_611852.1 99078594 4075050 680579..682975 1 NC_008043.1 catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a tetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 2 subfamily; phenylalanyl-tRNA synthetase subunit beta 682975 pheT 4075050 pheT Ruegeria sp. TM1040 phenylalanyl-tRNA synthetase subunit beta YP_611852.1 680579 D 292414 CDS YP_611853.1 99078595 4075051 683214..683663 1 NC_008043.1 KEGG: jan:Jann_0455 hypothetical protein, ev=1e-66, 81% identity; hypothetical protein 683663 4075051 TM1040_3624 Ruegeria sp. TM1040 hypothetical protein YP_611853.1 683214 D 292414 CDS YP_611854.1 99078596 4075052 683660..684190 1 NC_008043.1 KEGG: mlo:mll3172 hypothetical protein, ev=2e-46, 50% identity; hypothetical protein 684190 4075052 TM1040_3625 Ruegeria sp. TM1040 hypothetical protein YP_611854.1 683660 D 292414 CDS YP_611855.1 99078597 4075053 684353..684931 1 NC_008043.1 hypothetical protein 684931 4075053 TM1040_3626 Ruegeria sp. TM1040 hypothetical protein YP_611855.1 684353 D 292414 CDS YP_611856.1 99078598 4075054 complement(684940..685746) 1 NC_008043.1 PFAM: MscS Mechanosensitive ion channel: (1.6e-60); KEGG: sil:SPO3496 mechanosensitive ion channel family protein, ev=1e-114, 75% identity; MscS mechanosensitive ion channel 685746 4075054 TM1040_3627 Ruegeria sp. TM1040 MscS mechanosensitive ion channel YP_611856.1 684940 R 292414 CDS YP_611857.1 99078599 4075055 complement(685988..687112) 1 NC_008043.1 TIGRFAM: alanine dehydrogenase: (2.7e-173); PFAM: D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding: (0.00062) alanine dehydrogenase/PNT-like: (3.2e-83); KEGG: sil:SPO0222 alanine dehydrogenase, ev=1e-180, 84% identity; L-alanine dehydrogenase 687112 4075055 TM1040_3628 Ruegeria sp. TM1040 L-alanine dehydrogenase YP_611857.1 685988 R 292414 CDS YP_611858.1 99078600 4075056 687251..687712 1 NC_008043.1 PFAM: regulatory proteins, AsnC/Lrp: (3.5e-31); KEGG: sil:SPO0223 transcriptional regulator, AsnC family, ev=1e-68, 85% identity; AsnC family transcriptional regulator 687712 4075056 TM1040_3629 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_611858.1 687251 D 292414 CDS YP_611859.1 99078601 4075057 687919..688836 1 NC_008043.1 PFAM: protein of unknown function DUF344: (4.5e-164); KEGG: sil:SPO0224 polyphosphate kinase, , ev=1e-156, 85% identity; hypothetical protein 688836 4075057 TM1040_3630 Ruegeria sp. TM1040 hypothetical protein YP_611859.1 687919 D 292414 CDS YP_611860.1 99078602 4075058 689022..689693 1 NC_008043.1 TIGRFAM: CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase: (1.2e-40); PFAM: CDP-alcohol phosphatidyltransferase: (6.2e-33); KEGG: sil:SPO3635 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, ev=1e-104, 81% identity; CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase 689693 4075058 TM1040_3631 Ruegeria sp. TM1040 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase YP_611860.1 689022 D 292414 CDS YP_611861.1 99078603 4075059 689693..689938 1 NC_008043.1 TIGRFAM: molybdopterin converting factor, subunit 1: (5.7e-33); PFAM: thiamineS: (2.2e-19); KEGG: rsp:RSP_1072 molybdopterin MPT converting factor, subunit 1 protein, ev=2e-33, 86% identity; molybdopterin synthase subunit MoaD 689938 4075059 TM1040_3632 Ruegeria sp. TM1040 molybdopterin synthase subunit MoaD YP_611861.1 689693 D 292414 CDS YP_611862.1 99078604 4075060 689943..690389 1 NC_008043.1 PFAM: molybdopterin biosynthesis MoaE: (5.7e-46); KEGG: sil:SPO3633 molybdopterin converting factor, subunit 2, ev=1e-53, 72% identity; molybdopterin synthase subunit MoaE 690389 4075060 TM1040_3633 Ruegeria sp. TM1040 molybdopterin synthase subunit MoaE YP_611862.1 689943 D 292414 CDS YP_611863.1 99078605 4075062 complement(690768..691682) 1 NC_008043.1 PFAM: regulatory protein, LysR: (1.2e-18) LysR, substrate-binding: (6.8e-33); KEGG: sil:SPO0241 transcriptional regulator, LysR family, ev=1e-76, 47% identity; LysR family transcriptional regulator 691682 4075062 TM1040_3634 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_611863.1 690768 R 292414 CDS YP_611864.1 99078606 4075063 691965..693041 1 NC_008043.1 PFAM: extracellular solute-binding protein, family 1: (0.00012); KEGG: hch:HCH_01471 spermidine/putrescine-binding periplasmic protein, ev=1e-136, 66% identity; extracellular solute-binding protein 693041 4075063 TM1040_3635 Ruegeria sp. TM1040 extracellular solute-binding protein YP_611864.1 691965 D 292414 CDS YP_611865.1 99078607 4075064 693110..694219 1 NC_008043.1 PFAM: ABC transporter related: (1e-61) Transport-associated OB: (9.4e-08); SMART: ATPase: (6.5e-18); KEGG: hch:HCH_01472 ABC-type spermidine/putrescine transport system, ATPase components, ev=1e-115, 59% identity; ABC transporter 694219 4075064 TM1040_3636 Ruegeria sp. TM1040 ABC transporter YP_611865.1 693110 D 292414 CDS YP_611866.1 99078608 4075065 694216..695085 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (3.4e-14); KEGG: hch:HCH_01473 ABC-type spermidine/putrescine transport system, permease component I, ev=1e-114, 72% identity; binding-protein-dependent transport system inner membrane protein 695085 4075065 TM1040_3637 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_611866.1 694216 D 292414 CDS YP_611867.1 99078609 4075066 695082..695942 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (0.001); KEGG: hch:HCH_01474 ABC-type spermidine/putrescine transport system, permease component II, ev=6e-93, 60% identity; binding-protein-dependent transport system inner membrane protein 695942 4075066 TM1040_3638 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_611867.1 695082 D 292414 CDS YP_611868.1 99078610 4075067 complement(696015..697565) 1 NC_008043.1 PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit: (1.4e-52); KEGG: hch:HCH_00746 TRAP-type mannitol/chloroaromatic compound transport system, large permease component, ev=1e-115, 46% identity; TRAP C4-dicarboxylate transport system permease DctM subunit 697565 4075067 TM1040_3639 Ruegeria sp. TM1040 TRAP C4-dicarboxylate transport system permease DctM subunit YP_611868.1 696015 R 292414 CDS YP_611869.1 99078611 4075068 complement(697562..698059) 1 NC_008043.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component: (4.7e-17); KEGG: tcx:Tcr_2006 tripartite ATP-independent periplasmic transporter, DctQ component, ev=2e-27, 43% identity; tripartite ATP-independent periplasmic transporter DctQ 698059 4075068 TM1040_3640 Ruegeria sp. TM1040 tripartite ATP-independent periplasmic transporter DctQ YP_611869.1 697562 R 292414 CDS YP_611870.1 99078612 4075069 complement(698127..699212) 1 NC_008043.1 TIGRFAM: Twin-arginine translocation pathway signal: (0.0068); PFAM: TRAP dicarboxylate transporter- DctP subunit: (3.1e-38); KEGG: tcx:Tcr_2011 TRAP dicarboxylate transporter-DctP subunit, ev=1e-74, 41% identity; twin-arginine translocation pathway signal 699212 4075069 TM1040_3641 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_611870.1 698127 R 292414 CDS YP_611871.1 99078613 4075070 699414..700115 1 NC_008043.1 PFAM: regulatory protein GntR, HTH: (4e-12) UbiC transcription regulator-associated: (2.2e-18); KEGG: rsp:RSP_2932 histidine utilization repressor, GntR family, ev=2e-42, 42% identity; GntR family transcriptional regulator 700115 4075070 TM1040_3642 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_611871.1 699414 D 292414 CDS YP_611872.1 99078614 4075071 700125..700790 1 NC_008043.1 PFAM: cyclic nucleotide-binding: (1.6e-13) regulatory protein, Crp: (1.9e-07); KEGG: sil:SPO1615 cyclic nucleotide-binding protein, ev=3e-56, 48% identity; Crp/FNR family transcriptional regulator 700790 4075071 TM1040_3643 Ruegeria sp. TM1040 Crp/FNR family transcriptional regulator YP_611872.1 700125 D 292414 CDS YP_611873.1 99078615 4075072 700886..701098 1 NC_008043.1 hypothetical protein 701098 4075072 TM1040_3644 Ruegeria sp. TM1040 hypothetical protein YP_611873.1 700886 D 292414 CDS YP_611874.1 99078616 4075073 701101..701532 1 NC_008043.1 PFAM: protein of unknown function DUF395, YeeE/YedE: (1.5e-21); KEGG: jan:Jann_2818 protein of unknown function DUF395, YeeE/YedE, ev=9e-39, 54% identity; hypothetical protein 701532 4075073 TM1040_3645 Ruegeria sp. TM1040 hypothetical protein YP_611874.1 701101 D 292414 CDS YP_611875.1 99078617 4075074 701537..701965 1 NC_008043.1 PFAM: protein of unknown function DUF395, YeeE/YedE: (6.4e-07); KEGG: jan:Jann_2817 protein of unknown function DUF395, YeeE/YedE, ev=2e-37, 57% identity; hypothetical protein 701965 4075074 TM1040_3646 Ruegeria sp. TM1040 hypothetical protein YP_611875.1 701537 D 292414 CDS YP_611876.1 99078618 4075075 701992..702876 1 NC_008043.1 PFAM: beta-lactamase-like: (3.2e-19); KEGG: jan:Jann_2816 beta-lactamase-like, ev=1e-122, 71% identity; beta-lactamase-like protein 702876 4075075 TM1040_3647 Ruegeria sp. TM1040 beta-lactamase-like protein YP_611876.1 701992 D 292414 CDS YP_611877.1 99078619 4075076 702946..704712 1 NC_008043.1 TIGRFAM: sulfate permease: (3.5e-132); PFAM: Sulfate transporter/antisigma-factor antagonist STAS: (9.4e-17) sulphate transporter: (3e-85); KEGG: sil:SPO1956 sulfate permease, ev=0.0, 66% identity; sulfate permease 704712 4075076 TM1040_3648 Ruegeria sp. TM1040 sulfate permease YP_611877.1 702946 D 292414 CDS YP_611878.1 99078620 4075078 704949..705752 1 NC_008043.1 KEGG: sil:SPO0045 phosphomethylpyrimidine kinase, ev=1e-101, 73% identity; TIGRFAM: Phosphomethylpyrimidine kinase type-2: (1.9e-128); PFAM: Phosphomethylpyrimidine kinase type-1: (5.2e-134); phosphomethylpyrimidine kinase type-2 705752 4075078 TM1040_3649 Ruegeria sp. TM1040 phosphomethylpyrimidine kinase type-2 YP_611878.1 704949 D 292414 CDS YP_611879.1 99078621 4075079 705749..706723 1 NC_008043.1 TIGRFAM: Glycine oxidase ThiO: (1.6e-82); PFAM: FAD dependent oxidoreductase: (2.4e-45); KEGG: sil:SPO0046 thiamine biosynthesis oxidoreductase ThiO, , ev=1e-145, 79% identity; glycine oxidase ThiO 706723 4075079 TM1040_3650 Ruegeria sp. TM1040 glycine oxidase ThiO YP_611879.1 705749 D 292414 CDS YP_611880.1 99078622 4075080 706707..706901 1 NC_008043.1 TIGRFAM: thiamine biosynthesis protein ThiS: (1.2e-23); PFAM: thiamineS: (3.9e-15); KEGG: sil:SPO0046.1 thiamine biosynthesis protein ThiS, ev=3e-16, 67% identity; thiamine biosynthesis protein ThiS 706901 4075080 TM1040_3651 Ruegeria sp. TM1040 thiamine biosynthesis protein ThiS YP_611880.1 706707 D 292414 CDS YP_611881.1 99078623 4075621 706904..707674 1 NC_008043.1 functions in thiamine (vitamin B1) biosynthesis; in Bacillus subtilis this enzyme catalyzes the formation of thiazole from dehydroxyglycine and 1-deoxy-D-xylulose-5-phosphate and ThiS-thiocarboxylate; thiazole synthase 707674 thiG 4075621 thiG Ruegeria sp. TM1040 thiazole synthase YP_611881.1 706904 D 292414 CDS YP_611882.1 99078624 4075622 707671..708267 1 NC_008043.1 Condenses 4-methyl-5-(beta-hydroxyethyl)-thiazole monophosphate and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate to form thiamine monophosphate; thiamine-phosphate pyrophosphorylase 708267 thiE 4075622 thiE Ruegeria sp. TM1040 thiamine-phosphate pyrophosphorylase YP_611882.1 707671 D 292414 CDS YP_611883.1 99078625 4075623 708264..709220 1 NC_008043.1 PFAM: UBA/THIF-type NAD/FAD binding fold: (4.3e-59) MoeZ/MoeB: (4.1e-13); KEGG: sil:SPO0049 thiamine biosynthesis protein ThiF, ev=1e-116, 66% identity; UBA/THIF-type NAD/FAD binding fold 709220 4075623 TM1040_3654 Ruegeria sp. TM1040 UBA/THIF-type NAD/FAD binding fold YP_611883.1 708264 D 292414 CDS YP_611884.1 99078626 4075624 709241..710176 1 NC_008043.1 PFAM: NLPA lipoprotein: (0.0025); KEGG: sil:SPO0050 ABC transporter, periplasmic substrate-binding protein, ev=1e-148, 82% identity; NLPA lipoprotein 710176 4075624 TM1040_3655 Ruegeria sp. TM1040 NLPA lipoprotein YP_611884.1 709241 D 292414 CDS YP_611885.1 99078627 4075625 710173..710850 1 NC_008043.1 PFAM: TENA/THI-4 protein: (5.6e-42); KEGG: sil:SPO0051 TENA/THI-4 family protein, ev=6e-96, 78% identity; TenA family transcription regulator 710850 4075625 TM1040_3656 Ruegeria sp. TM1040 TenA family transcription regulator YP_611885.1 710173 D 292414 CDS YP_611886.1 99078628 4075626 710847..711575 1 NC_008043.1 PFAM: ABC transporter related: (1.2e-49); SMART: ATPase: (1.3e-11); KEGG: sil:SPO0052 ABC transporter, ATP-binding protein, ev=3e-87, 69% identity; ABC transporter 711575 4075626 TM1040_3657 Ruegeria sp. TM1040 ABC transporter YP_611886.1 710847 D 292414 CDS YP_611887.1 99078629 4075627 711572..712309 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (3.6e-34); KEGG: sil:SPO0053 ABC transporter, permease protein, ev=1e-104, 80% identity; binding-protein-dependent transport systems inner membrane component 712309 4075627 TM1040_3658 Ruegeria sp. TM1040 binding-protein-dependent transport systems inner membrane component YP_611887.1 711572 D 292414 CDS YP_611888.1 99078630 4075628 complement(712417..712956) 1 NC_008043.1 PFAM: BioY protein: (2.7e-35); KEGG: plu:plu3847 unnamed protein product; similar to biotin synthase, ev=5e-53, 55% identity; BioY protein 712956 4075628 TM1040_3659 Ruegeria sp. TM1040 BioY protein YP_611888.1 712417 R 292414 CDS YP_611889.1 99078631 4075629 complement(712996..713586) 1 NC_008043.1 PFAM: cobalt transport protein: (2.2e-15); KEGG: plu:plu3848 unnamed protein product; similar to hypothetical proteins. transmembrane protein, ev=1e-50, 52% identity; cobalt transport protein 713586 4075629 TM1040_3660 Ruegeria sp. TM1040 cobalt transport protein YP_611889.1 712996 R 292414 CDS YP_611890.1 99078632 4075630 complement(713579..714259) 1 NC_008043.1 PFAM: SMC protein-like: (0.00011) ABC transporter related: (9.1e-51); SMART: ATPase: (8e-16); KEGG: dra:DR2469 cobalt transport system ATP-binding protein, ev=8e-78, 66% identity; ABC transporter 714259 4075630 TM1040_3661 Ruegeria sp. TM1040 ABC transporter YP_611890.1 713579 R 292414 CDS YP_611891.1 99078633 4075631 complement(714370..715461) 1 NC_008043.1 KEGG: sil:SPO0697 molybdate ABC transporter, ATP-binding protein, ev=1e-117, 59% identity; TIGRFAM: Molybdate ABC transporter, ATP-binding protein: (2.2e-144); PFAM: ABC transporter related: (2e-55) TOBE: (3.5e-11); SMART: ATPase: (1.5e-16); molybdate ABC transporter ATP-binding protein 715461 4075631 TM1040_3662 Ruegeria sp. TM1040 molybdate ABC transporter ATP-binding protein YP_611891.1 714370 R 292414 CDS YP_611892.1 99078634 4075632 complement(715458..716150) 1 NC_008043.1 part of ModCBA molybdate transporter; member of ABC superfamily; inner membrane component; regulated by repressor protein ModE; molybdate ABC transporter permease 716150 modB 4075632 modB Ruegeria sp. TM1040 molybdate ABC transporter permease YP_611892.1 715458 R 292414 CDS YP_611893.1 99078635 4075633 complement(716162..716986) 1 NC_008043.1 TIGRFAM: molybdenum ABC transporter, periplasmic molybdate-binding protein: (2.4e-56); PFAM: extracellular solute-binding protein, family 1: (0.014); KEGG: sil:SPO0699 molybdate ABC transporter, periplasmic molybdate-binding protein, ev=8e-60, 53% identity; molybdenum ABC transporter, periplasmic molybdate-binding protein 716986 4075633 TM1040_3664 Ruegeria sp. TM1040 molybdenum ABC transporter, periplasmic molybdate-binding protein YP_611893.1 716162 R 292414 CDS YP_611894.1 99078636 4075634 717409..717669 1 NC_008043.1 KEGG: sil:SPO1811 hypothetical protein, ev=4e-35, 83% identity; hypothetical protein 717669 4075634 TM1040_3665 Ruegeria sp. TM1040 hypothetical protein YP_611894.1 717409 D 292414 CDS YP_611895.1 99078637 4075635 717675..719459 1 NC_008043.1 PFAM: Na+/solute symporter: (3.8e-16); KEGG: sil:SPO1810 sodium/solute symporter family protein, ev=0.0, 85% identity; Na+/solute symporter 719459 4075635 TM1040_3666 Ruegeria sp. TM1040 Na+/solute symporter YP_611895.1 717675 D 292414 CDS YP_611896.1 99078638 4075636 719557..721377 1 NC_008043.1 PFAM: cyclic nucleotide-binding: (4.6e-18) CBS: (7.9e-33) protein of unknown function DUF294, nucleotidyltransferase : (5.8e-172); KEGG: sil:SPO1809 nucleotidyltransferase/CBS/cyclic nucleotide-binding domain protein, ev=0.0, 64% identity; cyclic nucleotide-binding protein 721377 4075636 TM1040_3667 Ruegeria sp. TM1040 cyclic nucleotide-binding protein YP_611896.1 719557 D 292414 CDS YP_611897.1 99078639 4075637 721382..721900 1 NC_008043.1 KEGG: sil:SPO1808 hypothetical protein, ev=1e-52, 56% identity; hypothetical protein 721900 4075637 TM1040_3668 Ruegeria sp. TM1040 hypothetical protein YP_611897.1 721382 D 292414 CDS YP_611898.1 99078640 4075638 721903..723342 1 NC_008043.1 KEGG: sil:SPO1807 exonuclease, DNA polymerase III, epsilon subunit family, ev=1e-118, 49% identity; TIGRFAM: DNA polymerase III, epsilon subunit: (1.2e-22); PFAM: Exonuclease, RNase T and DNA polymerase III: (4.6e-44); SMART: Exonuclease: (7.8e-45); DNA polymerase III, epsilon subunit 723342 4075638 TM1040_3669 Ruegeria sp. TM1040 DNA polymerase III, epsilon subunit YP_611898.1 721903 D 292414 CDS YP_611899.1 99078641 4075639 complement(723351..724298) 1 NC_008043.1 PFAM: alpha/beta hydrolase fold: (1.7e-17); KEGG: rba:RB4968 probable EphA protein-Mycobacterium tuberculosis (strain H37RV), ev=1e-122, 63% identity; alpha/beta hydrolase 724298 4075639 TM1040_3670 Ruegeria sp. TM1040 alpha/beta hydrolase YP_611899.1 723351 R 292414 CDS YP_611900.1 99078642 4075640 724386..725099 1 NC_008043.1 PFAM: protein of unknown function UPF0074: (0.0005) regulatory protein, DeoR: (0.00099) Helix-turn-helix, type 11: (2.2e-10); KEGG: rba:RB4967 probable DeoR-family transcriptional regulator, ev=2e-81, 65% identity; type 11 helix-turn-helix protein 725099 4075640 TM1040_3671 Ruegeria sp. TM1040 type 11 helix-turn-helix protein YP_611900.1 724386 D 292414 CDS YP_611901.1 99078643 4075641 725233..726333 1 NC_008043.1 PFAM: Alcohol dehydrogenase, zinc-binding: (4e-32) Alcohol dehydrogenase GroES-like: (2.4e-26); KEGG: sil:SPOA0430 oxidoreductase, zinc-binding dehydrogenase family, ev=1e-150, 74% identity; zinc-binding alcohol dehydrogenase 726333 4075641 TM1040_3672 Ruegeria sp. TM1040 zinc-binding alcohol dehydrogenase YP_611901.1 725233 D 292414 CDS YP_611902.1 99078644 4075642 726497..727729 1 NC_008043.1 PFAM: Mandelate racemase/muconate lactonizing enzyme-like: (3e-09); KEGG: sil:SPOA0428 mandelate racemase/muconate lactonizing enzyme family protein, ev=0.0, 82% identity; mandelate racemase/muconate lactonizing-like protein 727729 4075642 TM1040_3673 Ruegeria sp. TM1040 mandelate racemase/muconate lactonizing-like protein YP_611902.1 726497 D 292414 CDS YP_611903.1 99078645 4075643 727968..728249 1 NC_008043.1 PFAM: regulatory protein, ArsR: (4.1e-10); KEGG: sil:SPOA0427 transcriptional regulator, ArsR family, ev=5e-23, 61% identity; ArsR family transcriptional regulator 728249 4075643 TM1040_3674 Ruegeria sp. TM1040 ArsR family transcriptional regulator YP_611903.1 727968 D 292414 CDS YP_611904.1 99078646 4075644 complement(728286..729134) 1 NC_008043.1 PFAM: fumarylacetoacetate (FAA) hydrolase: (1.9e-87); KEGG: sme:SMb21112 bifunctional enzyme 2-hydroxyhepta-2,4-diene-1,7-dioatesomerase 5-carboxymethyl-2-oxo-hex-3-ene-1,7-dioatedecarboxylase protein, ev=3e-99, 63% identity; 5-carboxymethyl-2-hydroxymuconate delta-isomerase 729134 4075644 TM1040_3675 Ruegeria sp. TM1040 5-carboxymethyl-2-hydroxymuconate delta-isomerase YP_611904.1 728286 R 292414 CDS YP_611905.1 99078647 4075645 complement(729194..732325) 1 NC_008043.1 PFAM: cyclic nucleotide-binding: (2e-15) ABC transporter, transmembrane region: (1.4e-05); KEGG: sil:SPO0574 ABC transporter, transmembrane ATP-binding protein, , ev=0.0, 67% identity; cyclic nucleotide-binding protein 732325 4075645 TM1040_3676 Ruegeria sp. TM1040 cyclic nucleotide-binding protein YP_611905.1 729194 R 292414 CDS YP_611906.1 99078648 4075646 732480..732869 1 NC_008043.1 KEGG: sil:SPO0573 hypothetical protein, ev=2e-38, 56% identity; hypothetical protein 732869 4075646 TM1040_3677 Ruegeria sp. TM1040 hypothetical protein YP_611906.1 732480 D 292414 CDS YP_611907.1 99078649 4075647 complement(732994..733584) 1 NC_008043.1 PFAM: ThiJ/PfpI: (5.3e-07); KEGG: cvi:CV2336 probable ThiJ/PfpI family protein, ev=9e-39, 46% identity; ThiJ/PfpI 733584 4075647 TM1040_3678 Ruegeria sp. TM1040 ThiJ/PfpI YP_611907.1 732994 R 292414 CDS YP_611908.1 99078650 4075648 complement(733684..734142) 1 NC_008043.1 PFAM: regulatory proteins, AsnC/Lrp: (4.8e-29) regulatory protein, ArsR: (0.0025) Helix-turn-helix, type 11: (0.00089); KEGG: sil:SPO0569 transcriptional regulator, AsnC family, ev=3e-58, 74% identity; AsnC family transcriptional regulator 734142 4075648 TM1040_3679 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_611908.1 733684 R 292414 CDS YP_611909.1 99078651 4075649 734296..737715 1 NC_008043.1 catalyzes the ferredoxin-dependent oxidative decarboxylation of arylpyruvates; 2-oxoacid ferredoxin oxidoreductase 737715 4075649 TM1040_3680 Ruegeria sp. TM1040 2-oxoacid ferredoxin oxidoreductase YP_611909.1 734296 D 292414 CDS YP_611910.1 99078652 4075650 complement(737812..738486) 1 NC_008043.1 PFAM: regulatory protein, TetR: (1.1e-09); KEGG: sil:SPO0566 transcriptional regulator, TetR family, ev=1e-64, 58% identity; TetR family transcriptional regulator 738486 4075650 TM1040_3681 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_611910.1 737812 R 292414 CDS YP_611911.1 99078653 4075651 738877..740649 1 NC_008043.1 KEGG: ret:RHE_PE00042 probable oligopeptide ABC transporter, ATP-binding protein, ev=1e-143, 47% identity; TIGRFAM: Oligopeptide/dipeptide ABC transporter, ATP-binding protein-like: (7.5e-08); PFAM: ABC transporter related: (8.4e-51) Oligopeptide/dipeptide ABC transporter-like: (7.6e-08); SMART: ATPase: (2.3e-17); oligopeptide/dipeptide ABC transporter ATP-binding protein-like protein 740649 4075651 TM1040_3682 Ruegeria sp. TM1040 oligopeptide/dipeptide ABC transporter ATP-binding protein-like protein YP_611911.1 738877 D 292414 CDS YP_611912.1 99078654 4075652 740642..742561 1 NC_008043.1 PFAM: extracellular solute-binding protein, family 5: (1e-35); KEGG: sil:SPO0560 oligopeptide ABC transporter, periplasmic oligopeptide-binding protein, ev=0.0, 72% identity; extracellular solute-binding protein 742561 4075652 TM1040_3683 Ruegeria sp. TM1040 extracellular solute-binding protein YP_611912.1 740642 D 292414 CDS YP_611913.1 99078655 4075653 742561..743589 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (2.5e-24); KEGG: sil:SPO0559 oligopeptide ABC transporter, permease protein, ev=1e-167, 84% identity; binding-protein-dependent transport system inner membrane protein 743589 4075653 TM1040_3684 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_611913.1 742561 D 292414 CDS YP_611914.1 99078656 4075654 743586..744743 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (4.7e-38); KEGG: sil:SPO0558 oligopeptide ABC transporter, permease protein, ev=0.0, 86% identity; binding-protein-dependent transport system inner membrane protein 744743 4075654 TM1040_3685 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_611914.1 743586 D 292414 CDS YP_611915.1 99078657 4075655 744740..746095 1 NC_008043.1 PFAM: L-carnitine dehydratase/bile acid-inducible protein F: (8e-09); KEGG: sil:SPO0264 CaiB/BaiF family protein, ev=1e-147, 62% identity; L-carnitine dehydratase/bile acid-inducible protein F 746095 4075655 TM1040_3686 Ruegeria sp. TM1040 L-carnitine dehydratase/bile acid-inducible protein F YP_611915.1 744740 D 292414 CDS YP_611916.1 99078658 4075656 complement(746168..748522) 1 NC_008043.1 PFAM: MscS Mechanosensitive ion channel: (5.7e-48); KEGG: sil:SPO0557 mechanosensitive ion channel family protein, ev=0.0, 62% identity; MscS mechanosensitive ion channel 748522 4075656 TM1040_3687 Ruegeria sp. TM1040 MscS mechanosensitive ion channel YP_611916.1 746168 R 292414 CDS YP_611917.1 99078659 4075657 748946..750166 1 NC_008043.1 KEGG: sil:SPO0555 hypothetical protein, ev=1e-176, 77% identity; hypothetical protein 750166 4075657 TM1040_3688 Ruegeria sp. TM1040 hypothetical protein YP_611917.1 748946 D 292414 CDS YP_611918.1 99078660 4075658 750163..751407 1 NC_008043.1 PFAM: glycosyl transferase, group 1: (1.9e-34); KEGG: sil:SPO0554 glycosyl transferase, group 1 family protein, ev=1e-169, 74% identity; group 1 glycosyl transferase 751407 4075658 TM1040_3689 Ruegeria sp. TM1040 group 1 glycosyl transferase YP_611918.1 750163 D 292414 CDS YP_611919.1 99078661 4075659 751404..752513 1 NC_008043.1 PFAM: glycosyl transferase, group 1: (4.1e-17); KEGG: sil:SPO0553 glycosyltransferase, group 1, ev=1e-112, 61% identity; group 1 glycosyl transferase 752513 4075659 TM1040_3690 Ruegeria sp. TM1040 group 1 glycosyl transferase YP_611919.1 751404 D 292414 CDS YP_611920.1 99078662 4075660 752510..753094 1 NC_008043.1 PFAM: Phosphoglycerate mutase: (3e-31); KEGG: sil:SPO0552 phosphoglycerate mutase family protein, ev=1e-74, 71% identity; phosphoglycerate mutase 753094 4075660 TM1040_3691 Ruegeria sp. TM1040 phosphoglycerate mutase YP_611920.1 752510 D 292414 CDS YP_611921.1 99078663 4075661 753091..754230 1 NC_008043.1 KEGG: sil:SPO0551 hypothetical protein, ev=1e-130, 64% identity; hypothetical protein 754230 4075661 TM1040_3692 Ruegeria sp. TM1040 hypothetical protein YP_611921.1 753091 D 292414 CDS YP_611922.1 99078664 4075662 754251..755009 1 NC_008043.1 KEGG: sil:SPO0550 hypothetical protein, ev=6e-79, 57% identity; hypothetical protein 755009 4075662 TM1040_3693 Ruegeria sp. TM1040 hypothetical protein YP_611922.1 754251 D 292414 CDS YP_611923.1 99078665 4075663 755010..755489 1 NC_008043.1 KEGG: sil:SPO0549 hypothetical protein, ev=2e-62, 72% identity; hypothetical protein 755489 4075663 TM1040_3694 Ruegeria sp. TM1040 hypothetical protein YP_611923.1 755010 D 292414 CDS YP_611924.1 99078666 4075664 complement(755884..757026) 1 NC_008043.1 TIGRFAM: Phosphonate metabolism PhnM: (8.1e-151); PFAM: amidohydrolase: (0.041) Amidohydrolase 3: (0.0013); KEGG: sil:SPO0476 alkylphosphonate utilization protein PhnM, ev=1e-156, 72% identity; phosphonate metabolism PhnM 757026 4075664 TM1040_3695 Ruegeria sp. TM1040 phosphonate metabolism PhnM YP_611924.1 755884 R 292414 CDS YP_611925.1 99078667 4075665 757079..757762 1 NC_008043.1 PFAM: protein of unknown function DUF1045: (3e-47); KEGG: sil:SPO0475 hypothetical protein, ev=2e-81, 65% identity; hypothetical protein 757762 4075665 TM1040_3696 Ruegeria sp. TM1040 hypothetical protein YP_611925.1 757079 D 292414 CDS YP_611926.1 99078668 4075666 complement(757744..758316) 1 NC_008043.1 TIGRFAM: Phosphonate metabolism, 1,5-bisphosphokinase (PRPP-forming) PhnN: (2.8e-49); SMART: Guanylate kinase/L-type calcium channel region: (3e-08); KEGG: sil:SPO0474 alkylphosphonate utilization protein PhnN, ev=3e-51, 61% identity; phosphonate metabolism 1,5-bisphosphokinase PhnN 758316 4075666 TM1040_3697 Ruegeria sp. TM1040 phosphonate metabolism 1,5-bisphosphokinase PhnN YP_611926.1 757744 R 292414 CDS YP_611927.1 99078669 4075667 complement(758313..759017) 1 NC_008043.1 KEGG: sil:SPO0473 alkylphosphonate utilization protein PhnL, ev=1e-94, 77% identity; TIGRFAM: Phosphonate C-P lyase system, PhnL: (3.9e-139); PFAM: ABC transporter related: (5.7e-53); SMART: ATPase: (3e-11); phosphonate C-P lyase system, PhnL 759017 4075667 TM1040_3698 Ruegeria sp. TM1040 phosphonate C-P lyase system, PhnL YP_611927.1 758313 R 292414 CDS YP_611928.1 99078670 4075668 complement(759088..759858) 1 NC_008043.1 KEGG: sil:SPO0472 alkylphosphonate utilization protein PhnK, ev=1e-126, 88% identity; TIGRFAM: Phosphonate C-P lyase system, PhnK: (1.1e-156); PFAM: ABC transporter related: (1.6e-57); SMART: ATPase: (9.1e-20); phosphonate C-P lyase system protein PhnK 759858 phnK 4075668 phnK Ruegeria sp. TM1040 phosphonate C-P lyase system protein PhnK YP_611928.1 759088 R 292414 CDS YP_611929.1 99078671 4075669 complement(759858..760739) 1 NC_008043.1 PFAM: phosphonate metabolism PhnJ: (1e-209); KEGG: sil:SPO0471 alkylphosphonate utilization protein PhnJ, ev=1e-146, 91% identity; phosphonate metabolism PhnJ 760739 4075669 TM1040_3700 Ruegeria sp. TM1040 phosphonate metabolism PhnJ YP_611929.1 759858 R 292414 CDS YP_611930.1 99078672 4075670 complement(760854..761957) 1 NC_008043.1 PFAM: phosphonate metabolism: (8.1e-225); KEGG: sil:SPO0470 alkylphosphonate utilization protein PhnI, ev=1e-176, 85% identity; phosphonate metabolism protein 761957 4075670 TM1040_3701 Ruegeria sp. TM1040 phosphonate metabolism protein YP_611930.1 760854 R 292414 CDS YP_611931.1 99078673 4075671 complement(761962..762537) 1 NC_008043.1 KEGG: sil:SPO0469 alkylphosphonate utilization protein PhnH, ev=5e-59, 60% identity; carbon-phosphorus lyase complex subunit 762537 phnH 4075671 phnH Ruegeria sp. TM1040 carbon-phosphorus lyase complex subunit YP_611931.1 761962 R 292414 CDS YP_611932.1 99078674 4075672 complement(762537..762989) 1 NC_008043.1 PFAM: phosphonate metabolism PhnG: (2.3e-68); KEGG: sil:SPO0468 alkylphosphonate utilization protein PhnG, ev=1e-42, 59% identity; phosphonate metabolism PhnG 762989 4075672 TM1040_3703 Ruegeria sp. TM1040 phosphonate metabolism PhnG YP_611932.1 762537 R 292414 CDS YP_611933.1 99078675 4075673 763112..763834 1 NC_008043.1 TIGRFAM: Phosphonate C-P lyase system, transcriptional regulator PhnF: (2.2e-76); PFAM: regulatory protein GntR, HTH: (1.1e-18) protein of unknown function UPF0074: (0.0007) UbiC transcription regulator-associated: (9.1e-36) Helix-turn-helix, type 11: (0.0041); KEGG: sil:SPO0467 transcriptional regulator, GntR family, ev=2e-80, 61% identity; GntR family transcriptional regulator 763834 4075673 TM1040_3704 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_611933.1 763112 D 292414 CDS YP_611934.1 99078676 4075674 complement(763884..764498) 1 NC_008043.1 PFAM: transferase hexapeptide repeat: (0.031); KEGG: sil:SPO0784 chloramphenicol acetyltransferase, , ev=7e-95, 79% identity; hexapaptide repeat-containing transferase 764498 4075674 TM1040_3705 Ruegeria sp. TM1040 hexapaptide repeat-containing transferase YP_611934.1 763884 R 292414 CDS YP_611935.1 99078677 4075675 complement(764648..765967) 1 NC_008043.1 TIGRFAM: Phosphonate uptake transporter: (7.5e-36); PFAM: binding-protein-dependent transport systems inner membrane component: (3.2e-11); KEGG: sil:SPO0783 phosphonate ABC transporter, permease protein, ev=0.0, 77% identity; phosphonate ABC transporter permease 765967 4075675 TM1040_3706 Ruegeria sp. TM1040 phosphonate ABC transporter permease YP_611935.1 764648 R 292414 CDS YP_611936.1 99078678 4075676 complement(765971..766849) 1 NC_008043.1 TIGRFAM: Phosphonate uptake transporter: (2.3e-73); PFAM: binding-protein-dependent transport systems inner membrane component: (2.3e-13); KEGG: sil:SPO0782 phosphonate ABC transporter, permease protein, ev=1e-129, 79% identity; phosphonate ABC transporter permease 766849 4075676 TM1040_3707 Ruegeria sp. TM1040 phosphonate ABC transporter permease YP_611936.1 765971 R 292414 CDS YP_611937.1 99078679 4075677 complement(766961..767863) 1 NC_008043.1 TIGRFAM: Phosphonate-binding periplasmic protein: (8.4e-86); KEGG: sil:SPO0781 phosphonate ABC transporter, periplasmic phosphonate-binding protein, ev=1e-145, 83% identity; phosphonate-binding periplasmic protein 767863 4075677 TM1040_3708 Ruegeria sp. TM1040 phosphonate-binding periplasmic protein YP_611937.1 766961 R 292414 CDS YP_611938.1 99078680 4075678 complement(767931..768749) 1 NC_008043.1 KEGG: sil:SPO0780 phosphonate ABC transporter, ATP-binding protein, ev=1e-124, 86% identity; TIGRFAM: Phosphonate ABC transporter PhnC, ATP-binding: (2.3e-131); PFAM: ABC transporter related: (3.2e-56); SMART: ATPase: (2.2e-11); phosphonate ABC transporter ATP-binding protein 768749 4075678 TM1040_3709 Ruegeria sp. TM1040 phosphonate ABC transporter ATP-binding protein YP_611938.1 767931 R 292414 CDS YP_611939.1 99078681 4075679 769037..769717 1 NC_008043.1 PFAM: ribulose-phosphate 3-epimerase: (3.2e-106); KEGG: sil:SPO0779 ribulose-phosphate 3-epimerase, ev=1e-114, 90% identity; ribulose-5-phosphate 3-epimerase 769717 4075679 TM1040_3710 Ruegeria sp. TM1040 ribulose-5-phosphate 3-epimerase YP_611939.1 769037 D 292414 CDS YP_611940.1 99078682 4075418 complement(769944..770234) 1 NC_008043.1 KEGG: sil:SPO0776 conserved hypothetical protein TIGR00369, ev=5e-16, 49% identity; hypothetical protein 770234 4075418 TM1040_3711 Ruegeria sp. TM1040 hypothetical protein YP_611940.1 769944 R 292414 CDS YP_611941.1 99078683 4075419 complement(770332..771564) 1 NC_008043.1 PFAM: protein of unknown function UPF0261: (3e-144); KEGG: sil:SPOA0356 hypothetical protein, ev=1e-175, 74% identity; hypothetical protein 771564 4075419 TM1040_3712 Ruegeria sp. TM1040 hypothetical protein YP_611941.1 770332 R 292414 CDS YP_611942.1 99078684 4075420 complement(771666..773009) 1 NC_008043.1 PFAM: aldehyde dehydrogenase: (3e-218); KEGG: jan:Jann_3507 aldehyde dehydrogenase, ev=0.0, 68% identity; betaine-aldehyde dehydrogenase 773009 4075420 TM1040_3713 Ruegeria sp. TM1040 betaine-aldehyde dehydrogenase YP_611942.1 771666 R 292414 CDS YP_611943.1 99078685 4075421 complement(773015..774634) 1 NC_008043.1 PFAM: protein of unknown function DUF112, transmembrane: (3.1e-111); KEGG: sil:SPO0771 membrane protein, ev=0.0, 83% identity; hypothetical protein 774634 4075421 TM1040_3714 Ruegeria sp. TM1040 hypothetical protein YP_611943.1 773015 R 292414 CDS YP_611944.1 99078686 4075422 complement(774662..775264) 1 NC_008043.1 KEGG: sil:SPO0770 hypothetical protein, ev=3e-62, 59% identity; hypothetical protein 775264 4075422 TM1040_3715 Ruegeria sp. TM1040 hypothetical protein YP_611944.1 774662 R 292414 CDS YP_611945.1 99078687 4075423 complement(775296..776240) 1 NC_008043.1 PFAM: Uncharacterized protein UPF0065: (6.2e-09); KEGG: sil:SPO0769 hypothetical protein, ev=1e-155, 85% identity; hypothetical protein 776240 4075423 TM1040_3716 Ruegeria sp. TM1040 hypothetical protein YP_611945.1 775296 R 292414 CDS YP_611946.1 99078688 4075424 776456..777235 1 NC_008043.1 PFAM: regulatory proteins, IclR: (1.2e-15); KEGG: sil:SPO0768 transcriptional regulator, IclR family, ev=4e-89, 63% identity; IclR family transcriptional regulator 777235 4075424 TM1040_3717 Ruegeria sp. TM1040 IclR family transcriptional regulator YP_611946.1 776456 D 292414 CDS YP_611947.1 99078689 4075425 777265..778632 1 NC_008043.1 PFAM: aminotransferase class-III: (1.2e-110); KEGG: jan:Jann_3512 aminotransferase class-III, ev=0.0, 78% identity; hypothetical protein 778632 4075425 TM1040_3718 Ruegeria sp. TM1040 hypothetical protein YP_611947.1 777265 D 292414 CDS YP_611948.1 99078690 4075426 complement(778782..779498) 1 NC_008043.1 TIGRFAM: Methyltransferase FkbM: (1.7e-15); KEGG: sil:SPO0767 methyltransferase, FkbM family, ev=2e-82, 68% identity; methyltransferase FkbM 779498 4075426 TM1040_3719 Ruegeria sp. TM1040 methyltransferase FkbM YP_611948.1 778782 R 292414 CDS YP_611949.1 99078691 4075427 complement(779668..780957) 1 NC_008043.1 PFAM: glutamine synthetase, catalytic region: (3.5e-56); KEGG: sil:SPO0765 glutamine synthetase family protein, ev=0.0, 84% identity; glutamate--ammonia ligase 780957 4075427 TM1040_3720 Ruegeria sp. TM1040 glutamate--ammonia ligase YP_611949.1 779668 R 292414 CDS YP_611950.1 99078692 4075428 complement(781124..782383) 1 NC_008043.1 PFAM: cytochrome P450: (2.1e-06); KEGG: sil:SPO0764 cytochrome P450 family protein, ev=0.0, 84% identity; cytochrome P450 782383 4075428 TM1040_3721 Ruegeria sp. TM1040 cytochrome P450 YP_611950.1 781124 R 292414 CDS YP_611951.1 99078693 4075429 782475..783194 1 NC_008043.1 PFAM: glutamine amidotransferase class-I: (0.00033); KEGG: sil:SPO0763 glutamine amidotransferase, class I, ev=5e-75, 58% identity; glutamine amidotransferase 783194 4075429 TM1040_3722 Ruegeria sp. TM1040 glutamine amidotransferase YP_611951.1 782475 D 292414 CDS YP_611952.1 99078694 4075430 complement(783160..783810) 1 NC_008043.1 PFAM: regulatory protein GntR, HTH: (3.2e-16) GntR-like: (3.1e-23); KEGG: sil:SPO0762 transcriptional regulator, GntR family, ev=2e-81, 71% identity; GntR family transcriptional regulator 783810 4075430 TM1040_3723 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_611952.1 783160 R 292414 CDS YP_611953.1 99078695 4075431 784063..785055 1 NC_008043.1 with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA; phenylacetate-CoA oxygenase subunit PaaA 785055 paaA 4075431 paaA Ruegeria sp. TM1040 phenylacetate-CoA oxygenase subunit PaaA YP_611953.1 784063 D 292414 CDS YP_611954.1 99078696 4075432 785128..785412 1 NC_008043.1 with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA; involved in phenylacetate degradation; phenylacetate-CoA oxygenase subunit PaaB 785412 paaB 4075432 paaB Ruegeria sp. TM1040 phenylacetate-CoA oxygenase subunit PaaB YP_611954.1 785128 D 292414 CDS YP_611955.1 99078697 4075433 785412..786173 1 NC_008043.1 TIGRFAM: Phenylacetate-CoA oxygenase, PaaI subunit: (5.4e-114); PFAM: phenylacetic acid catabolic: (1.1e-56); KEGG: sil:SPO0755 phenylacetic acid degradation protein PaaI, ev=1e-116, 79% identity; phenylacetate-CoA oxygenase subunit PaaI 786173 4075433 TM1040_3726 Ruegeria sp. TM1040 phenylacetate-CoA oxygenase subunit PaaI YP_611955.1 785412 D 292414 CDS YP_611956.1 99078698 4075434 786301..786777 1 NC_008043.1 TIGRFAM: Phenylacetate-CoA oxygenase, PaaJ subunit: (2.8e-76); PFAM: protein of unknown function DUF59: (6.3e-24); KEGG: sil:SPO0754 phenylacetic acid degradation protein PaaJ, ev=4e-67, 71% identity; phenylacetate-CoA oxygenase subunit PaaJ 786777 4075434 TM1040_3727 Ruegeria sp. TM1040 phenylacetate-CoA oxygenase subunit PaaJ YP_611956.1 786301 D 292414 CDS YP_611957.1 99078699 4075435 786791..787861 1 NC_008043.1 PFAM: ferredoxin: (7.2e-25) oxidoreductase FAD/NAD(P)-binding: (3.7e-17) Oxidoreductase FAD-binding region: (4.3e-09); KEGG: sil:SPO0753 phenylacetic acid degradation oxidoreductase PaaK, ev=1e-158, 76% identity; ferredoxin 787861 4075435 TM1040_3728 Ruegeria sp. TM1040 ferredoxin YP_611957.1 786791 D 292414 CDS YP_611958.1 99078700 4075436 788006..788869 1 NC_008043.1 PFAM: aminotransferase, class IV: (4.4e-26); KEGG: sil:SPO0388 aminotransferase, class IV, ev=1e-125, 74% identity; aminotransferase 788869 4075436 TM1040_3729 Ruegeria sp. TM1040 aminotransferase YP_611958.1 788006 D 292414 CDS YP_611959.1 99078701 4075437 789027..789482 1 NC_008043.1 PFAM: UspA: (2.3e-16); KEGG: sil:SPO0386 universal stress family protein, ev=7e-72, 83% identity; hypothetical protein 789482 4075437 TM1040_3730 Ruegeria sp. TM1040 hypothetical protein YP_611959.1 789027 D 292414 CDS YP_611960.1 99078702 4075438 complement(789799..789975) 1 NC_008043.1 KEGG: sil:SPO0333 lipoprotein, , ev=8e-11, 49% identity; lipoprotein 789975 4075438 TM1040_3731 Ruegeria sp. TM1040 lipoprotein YP_611960.1 789799 R 292414 CDS YP_611961.1 99078703 4075439 complement(790000..791391) 1 NC_008043.1 catalyzes the formation of arginine from (N-L-arginino)succinate; argininosuccinate lyase 791391 4075439 TM1040_3732 Ruegeria sp. TM1040 argininosuccinate lyase YP_611961.1 790000 R 292414 CDS YP_611962.1 99078704 4075440 791412..791975 1 NC_008043.1 PFAM: Redoxin: (3.4e-15); KEGG: sil:SPO0331 thiol:disulfide interchange protein, , ev=5e-63, 64% identity; redoxin 791975 4075440 TM1040_3733 Ruegeria sp. TM1040 redoxin YP_611962.1 791412 D 292414 CDS YP_611963.1 99078705 4075441 792143..792982 1 NC_008043.1 PFAM: EAL: (6.5e-41); KEGG: sil:SPO0327 EAL domain protein, ev=4e-97, 63% identity; diguanylate phosphodiesterase 792982 4075441 TM1040_3734 Ruegeria sp. TM1040 diguanylate phosphodiesterase YP_611963.1 792143 D 292414 CDS YP_611964.1 99078706 4075442 793512..794687 1 NC_008043.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation; in Rhizobia and Ralstonia is involved in PHB biosynthesis; acetyl-CoA acetyltransferase 794687 4075442 TM1040_3735 Ruegeria sp. TM1040 acetyl-CoA acetyltransferase YP_611964.1 793512 D 292414 CDS YP_611965.1 99078707 4075443 794909..795631 1 NC_008043.1 TIGRFAM: Acetoacetyl-CoA reductase: (5e-153); PFAM: short-chain dehydrogenase/reductase SDR: (2.8e-28); KEGG: jan:Jann_0492 acetoacetyl-CoA reductase, ev=1e-115, 84% identity; 3-oxoacyl-ACP reductase 795631 4075443 TM1040_3736 Ruegeria sp. TM1040 3-oxoacyl-ACP reductase YP_611965.1 794909 D 292414 CDS YP_611966.1 99078708 4075444 795993..796931 1 NC_008043.1 Glycine cleavage system transcriptional activator; activates the gcvTHP operon in the presence of glycine and represses the operon in its absence; DNA-binding transcriptional activator GcvA 796931 4075444 TM1040_3737 Ruegeria sp. TM1040 DNA-binding transcriptional activator GcvA YP_611966.1 795993 D 292414 CDS YP_611967.1 99078709 4075445 796938..797849 1 NC_008043.1 PFAM: protein of unknown function DUF6, transmembrane: (4.2e-07); KEGG: sil:SPO0323 membrane protein, , ev=1e-124, 76% identity; hypothetical protein 797849 4075445 TM1040_3738 Ruegeria sp. TM1040 hypothetical protein YP_611967.1 796938 D 292414 CDS YP_611968.1 99078710 4075446 complement(797974..798141) 1 NC_008043.1 PFAM: protein of unknown function DUF465: (5.8e-05); KEGG: sil:SPO0322 hypothetical protein, ev=1e-12, 64% identity; hypothetical protein 798141 4075446 TM1040_3739 Ruegeria sp. TM1040 hypothetical protein YP_611968.1 797974 R 292414 CDS YP_611969.1 99078711 4075447 complement(798374..799162) 1 NC_008043.1 PFAM: methyltransferase small: (3.3e-05); KEGG: sil:SPO0321 hypothetical protein, ev=1e-89, 64% identity; methyltransferase small 799162 4075447 TM1040_3740 Ruegeria sp. TM1040 methyltransferase small YP_611969.1 798374 R 292414 CDS YP_611970.1 99078712 4075448 complement(799155..799382) 1 NC_008043.1 KEGG: sil:SPO0320 hypothetical protein, ev=4e-22, 71% identity; hypothetical protein 799382 4075448 TM1040_3741 Ruegeria sp. TM1040 hypothetical protein YP_611970.1 799155 R 292414 CDS YP_611971.1 99078713 4075449 799434..800444 1 NC_008043.1 PFAM: Polyprenyl synthetase: (1.2e-82); KEGG: sil:SPO0319 decaprenyl diphosphate synthase, ev=1e-151, 84% identity; farnesyltranstransferase 800444 4075449 TM1040_3742 Ruegeria sp. TM1040 farnesyltranstransferase YP_611971.1 799434 D 292414 CDS YP_611972.1 99078714 4075450 complement(800506..801330) 1 NC_008043.1 KEGG: rsp:RSP_1779 4-diphosphocytidyl-2C-methyl-D-erythritol kinase, ev=7e-69, 54% identity; TIGRFAM: 4-diphosphocytidyl-2C-methyl-D-erythritol kinase: (3.7e-18); PFAM: GHMP kinase: (1.1e-06); 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase 801330 4075450 TM1040_3743 Ruegeria sp. TM1040 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase YP_611972.1 800506 R 292414 CDS YP_611973.1 99078715 4075451 complement(801317..803035) 1 NC_008043.1 PFAM: TPR repeat: (0.32) Tetratricopeptide TPR_2: (0.0014); SMART: Tetratricopeptide region: (0.021); KEGG: sil:SPO0317 TPR domain protein, ev=0.0, 63% identity; tetratricopeptide TPR_2 803035 4075451 TM1040_3744 Ruegeria sp. TM1040 tetratricopeptide TPR_2 YP_611973.1 801317 R 292414 CDS YP_611974.1 99078716 4075452 complement(803160..804809) 1 NC_008043.1 PFAM: FAD dependent oxidoreductase: (2.5e-05) electron transfer flavoprotein-ubiquinone oxidoreductase: (2.7e-99); KEGG: sil:SPO0316 electrotransfer ubiquinone oxidoreductase family protein, ev=0.0, 90% identity; electron-transferring-flavoprotein dehydrogenase 804809 4075452 TM1040_3745 Ruegeria sp. TM1040 electron-transferring-flavoprotein dehydrogenase YP_611974.1 803160 R 292414 CDS YP_611975.1 99078717 4075453 complement(805045..805500) 1 NC_008043.1 TIGRFAM: redox-sensitive transcriptional activator SoxR: (2.8e-64); PFAM: regulatory protein, MerR: (1.2e-08); KEGG: sil:SPO0314 redox-sensitive transcriptional activator SoxR, ev=4e-55, 68% identity; MerR family transcriptional regulator 805500 4075453 TM1040_3746 Ruegeria sp. TM1040 MerR family transcriptional regulator YP_611975.1 805045 R 292414 CDS YP_611976.1 99078718 4075454 805646..806026 1 NC_008043.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase: (3.8e-13); KEGG: sil:SPO0313 glyoxalase family protein, ev=4e-42, 60% identity; glyoxalase/bleomycin resistance protein/dioxygenase 806026 4075454 TM1040_3747 Ruegeria sp. TM1040 glyoxalase/bleomycin resistance protein/dioxygenase YP_611976.1 805646 D 292414 CDS YP_611977.1 99078719 4075455 806339..806809 1 NC_008043.1 necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites; arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus; transcription elongation factor GreA 806809 greA 4075455 greA Ruegeria sp. TM1040 transcription elongation factor GreA YP_611977.1 806339 D 292414 CDS YP_611978.1 99078720 4075456 806846..807877 1 NC_008043.1 KEGG: sil:SPO0311 hypothetical protein, ev=1e-101, 62% identity; hypothetical protein 807877 4075456 TM1040_3749 Ruegeria sp. TM1040 hypothetical protein YP_611978.1 806846 D 292414 CDS YP_611979.1 99078721 4075457 807896..808414 1 NC_008043.1 PFAM: GCN5-related N-acetyltransferase: (6.4e-16); KEGG: rsp:RSP_0613 hypothetical protein, ev=1e-51, 57% identity; N-acetyltransferase GCN5 808414 4075457 TM1040_3750 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_611979.1 807896 D 292414 CDS YP_611980.1 99078722 4075458 complement(808645..809904) 1 NC_008043.1 is involved in the formation of active molybdenum cofactor and the chelation of molybdenum; molybdopterin biosynthesis protein MoeA 809904 4075458 TM1040_3751 Ruegeria sp. TM1040 molybdopterin biosynthesis protein MoeA YP_611980.1 808645 R 292414 CDS YP_611981.1 99078723 4075459 complement(809901..810713) 1 NC_008043.1 KEGG: sil:SPO0309 hypothetical protein, ev=1e-100, 66% identity; hypothetical protein 810713 4075459 TM1040_3752 Ruegeria sp. TM1040 hypothetical protein YP_611981.1 809901 R 292414 CDS YP_611982.1 99078724 4075460 complement(810734..811225) 1 NC_008043.1 TIGRFAM: molybdopterin-guanine dinucleotide biosynthesis protein B: (3.9e-66); PFAM: molybdopterin-guanine dinucleotide biosynthesis MobB region: (3.9e-32); KEGG: sil:SPO0308 molybdopterin-guanine dinucleotide biosynthesis protein B, ev=2e-65, 76% identity; molybdopterin-guanine dinucleotide biosynthesis protein B 811225 4075460 TM1040_3753 Ruegeria sp. TM1040 molybdopterin-guanine dinucleotide biosynthesis protein B YP_611982.1 810734 R 292414 CDS YP_611983.1 99078725 4075461 complement(811225..811860) 1 NC_008043.1 in Escherichia coli MobA links a guanosine 5'-phosphate to molydopterin to form molybdopterin guanine dinucleotide during molybdenum cofactor biosynthesis; molybdopterin-guanine dinucleotide biosynthesis protein MobA 811860 mobA 4075461 mobA Ruegeria sp. TM1040 molybdopterin-guanine dinucleotide biosynthesis protein MobA YP_611983.1 811225 R 292414 CDS YP_611984.1 99078726 4075462 complement(811857..812315) 1 NC_008043.1 hypothetical protein 812315 4075462 TM1040_3755 Ruegeria sp. TM1040 hypothetical protein YP_611984.1 811857 R 292414 CDS YP_611985.1 99078727 4075463 complement(812413..813294) 1 NC_008043.1 TIGRFAM: formate dehydrogenase family accessory protein FdhD: (3e-36); PFAM: formate dehydrogenase, subunit FdhD: (1.1e-22); KEGG: sil:SPO0306 formate dehydrogenase accessory protein FdhD, ev=1e-129, 81% identity; formate dehydrogenase family accessory protein FdhD 813294 4075463 TM1040_3756 Ruegeria sp. TM1040 formate dehydrogenase family accessory protein FdhD YP_611985.1 812413 R 292414 CDS YP_611986.1 99078728 4075464 813350..814078 1 NC_008043.1 PFAM: AzlC-like: (5.6e-48); KEGG: sil:SPO0305 AzlC family protein, ev=1e-82, 64% identity; AzlC-like 814078 4075464 TM1040_3757 Ruegeria sp. TM1040 AzlC-like YP_611986.1 813350 D 292414 CDS YP_611987.1 99078729 4075465 814075..814419 1 NC_008043.1 PFAM: branched-chain amino acid transport: (2.7e-10); KEGG: jan:Jann_0460 branched-chain amino acid transport, ev=5e-22, 44% identity; branched-chain amino acid transport 814419 4075465 TM1040_3758 Ruegeria sp. TM1040 branched-chain amino acid transport YP_611987.1 814075 D 292414 CDS YP_611988.1 99078730 4075466 complement(814548..815171) 1 NC_008043.1 KEGG: sil:SPO0304 lipoprotein, , ev=4e-61, 56% identity; lipoprotein 815171 4075466 TM1040_3759 Ruegeria sp. TM1040 lipoprotein YP_611988.1 814548 R 292414 CDS YP_611989.1 99078731 4075467 complement(815201..815335) 1 NC_008043.1 hypothetical protein 815335 4075467 TM1040_3760 Ruegeria sp. TM1040 hypothetical protein YP_611989.1 815201 R 292414 CDS YP_611990.1 99078732 4075469 complement(815638..816594) 1 NC_008043.1 PFAM: protein of unknown function DUF6, transmembrane: (4e-07); KEGG: jan:Jann_0131 protein of unknown function DUF6, transmembrane, ev=3e-89, 52% identity; hypothetical protein 816594 4075469 TM1040_3761 Ruegeria sp. TM1040 hypothetical protein YP_611990.1 815638 R 292414 CDS YP_611991.1 99078733 4075470 complement(816768..817871) 1 NC_008043.1 catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis; 3-isopropylmalate dehydrogenase 817871 4075470 TM1040_3762 Ruegeria sp. TM1040 3-isopropylmalate dehydrogenase YP_611991.1 816768 R 292414 CDS YP_611992.1 99078734 4075471 complement(817967..818992) 1 NC_008043.1 PFAM: Endonuclease/exonuclease/phosphatase: (9.5e-05); KEGG: sil:SPO0213 hypothetical protein, ev=2e-79, 47% identity; endonuclease/exonuclease/phosphatase 818992 4075471 TM1040_3763 Ruegeria sp. TM1040 endonuclease/exonuclease/phosphatase YP_611992.1 817967 R 292414 CDS YP_611993.1 99078735 4075472 complement(818989..819819) 1 NC_008043.1 KEGG: sil:SPO0214 membrane protein, , ev=3e-76, 52% identity; hypothetical protein 819819 4075472 TM1040_3764 Ruegeria sp. TM1040 hypothetical protein YP_611993.1 818989 R 292414 CDS YP_611994.1 99078736 4075473 820294..821019 1 NC_008043.1 PFAM: binding-protein-dependent transport systems inner membrane component: (0.0008); KEGG: sil:SPO1789 sulfate/tungstate uptake family ABC transporter, permease protein, ev=1e-79, 68% identity; binding-protein-dependent transport system inner membrane protein 821019 4075473 TM1040_3765 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_611994.1 820294 D 292414 CDS YP_611995.1 99078737 4075474 821012..821770 1 NC_008043.1 PFAM: ABC transporter related: (1.4e-53); SMART: ATPase: (2.4e-19); KEGG: mag:amb3045 ABC-type polar amino acid transport system, ATPase component, ev=3e-55, 51% identity; ABC transporter 821770 4075474 TM1040_3766 Ruegeria sp. TM1040 ABC transporter YP_611995.1 821012 D 292414 CDS YP_611996.1 99079842 4078745 45..1457 1 NC_008044.1 binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication; can also affect transcription of multiple genes including itself.; chromosomal replication initiation protein 1457 dnaA 4078745 dnaA Ruegeria sp. TM1040 chromosomal replication initiation protein YP_611996.1 45 D 292414 CDS YP_611997.1 99079843 4078746 1739..2860 1 NC_008044.1 binds the polymerase to DNA and acts as a sliding clamp; DNA polymerase III subunit beta 2860 4078746 TM1040_0002 Ruegeria sp. TM1040 DNA polymerase III subunit beta YP_611997.1 1739 D 292414 CDS YP_611998.1 99079844 4078666 2950..4023 1 NC_008044.1 Required for DNA replication; binds preferentially to single-stranded, linear DNA; recombination protein F 4023 recF 4078666 recF Ruegeria sp. TM1040 recombination protein F YP_611998.1 2950 D 292414 CDS YP_611999.1 99079845 4078667 4020..4640 1 NC_008044.1 PFAM: Lysine exporter protein (LYSE/YGGA): (3e-09); KEGG: sil:SPO0152 transporter, LysE family, ev=2e-76, 67% identity; lysine exporter protein LysE/YggA 4640 4078667 TM1040_0004 Ruegeria sp. TM1040 lysine exporter protein LysE/YggA YP_611999.1 4020 D 292414 CDS YP_612000.1 99079846 4078668 complement(4633..5220) 1 NC_008044.1 PFAM: regulatory protein, TetR: (5.9e-13); KEGG: sil:SPO0153 transcriptional regulator, TetR family, ev=2e-57, 58% identity; TetR family transcriptional regulator 5220 4078668 TM1040_0005 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_612000.1 4633 R 292414 CDS YP_612001.1 99079847 4078669 5336..5929 1 NC_008044.1 PFAM: NAD(P)H dehydrogenase (quinone): (1.6e-09) NADPH-dependent FMN reductase: (0.00055); KEGG: sil:SPO0154 NAD(P)H dehydrogenase, quinone family, ev=1e-75, 65% identity; NAD(P)H dehydrogenase (quinone) 5929 4078669 TM1040_0006 Ruegeria sp. TM1040 NAD(P)H dehydrogenase (quinone) YP_612001.1 5336 D 292414 CDS YP_612002.1 99079848 4078670 6015..8432 1 NC_008044.1 negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit B 8432 gyrB 4078670 gyrB Ruegeria sp. TM1040 DNA gyrase subunit B YP_612002.1 6015 D 292414 CDS YP_612003.1 99079849 4078671 complement(8429..9205) 1 NC_008044.1 Involved in DNA double-strand break repair and recombination. Promotes the annealing of complementary single-stranded DNA and by simulation of RAD51 recombinase; DNA repair protein RadC 9205 radC 4078671 radC Ruegeria sp. TM1040 DNA repair protein RadC YP_612003.1 8429 R 292414 CDS YP_612004.1 99079850 4078672 complement(9343..10500) 1 NC_008044.1 chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion; molecular chaperone DnaJ 10500 4078672 TM1040_0009 Ruegeria sp. TM1040 molecular chaperone DnaJ YP_612004.1 9343 R 292414 CDS YP_612005.1 99079851 4078673 complement(10577..12505) 1 NC_008044.1 heat shock protein 70; assists in folding of nascent polypeptide chains; refolding of misfolded proteins; utilizes ATPase activity to help fold; co-chaperones are DnaJ and GrpE; multiple copies in some bacteria; molecular chaperone DnaK 12505 dnaK 4078673 dnaK Ruegeria sp. TM1040 molecular chaperone DnaK YP_612005.1 10577 R 292414 CDS YP_612006.1 99079852 4078674 12713..13315 1 NC_008044.1 PFAM: 2OG-Fe(II) oxygenase: (2.2e-08); KEGG: sil:SPO0042 alkylated DNA repair protein, , ev=8e-75, 68% identity; DNA-N1-methyladenine dioxygenase 13315 4078674 TM1040_0011 Ruegeria sp. TM1040 DNA-N1-methyladenine dioxygenase YP_612006.1 12713 D 292414 CDS YP_612007.1 99079853 4078675 complement(13332..14210) 1 NC_008044.1 KEGG: sil:SPO0040 ABC transporter, permease protein, ev=1e-103, 63% identity; ABC transporter permease 14210 4078675 TM1040_0012 Ruegeria sp. TM1040 ABC transporter permease YP_612007.1 13332 R 292414 CDS YP_612008.1 99079854 4078676 14274..15071 1 NC_008044.1 TIGRFAM: 3'(2'),5'-bisphosphate nucleotidase: (4.7e-88); PFAM: inositol monophosphatase: (1.1e-56); KEGG: sil:SPO0039 3'(2'),5'-bisphosphate nucleotidase, ev=1e-118, 79% identity; 3'(2'),5'-bisphosphate nucleotidase 15071 4078676 TM1040_0013 Ruegeria sp. TM1040 3'(2'),5'-bisphosphate nucleotidase YP_612008.1 14274 D 292414 CDS YP_612009.1 99079855 4078677 15072..15872 1 NC_008044.1 CMP-2-keto-3-deoxyoctulosonic acid synthetase; catalyzes the formation of CMP-3-deoxy-D-manno-octulosonate from CTP and 3-deoxy-D-manno-octulosonate which is incorporated into LPS; 3-deoxy-manno-octulosonate cytidylyltransferase 15872 4078677 TM1040_0014 Ruegeria sp. TM1040 3-deoxy-manno-octulosonate cytidylyltransferase YP_612009.1 15072 D 292414 CDS YP_612010.1 99079856 4078678 16023..16916 1 NC_008044.1 TIGRFAM: UTP-glucose-1-phosphate uridylyltransferase: (3.1e-138); PFAM: Nucleotidyl transferase: (1.7e-12); KEGG: jan:Jann_0218 UTP-glucose-1-phosphate uridylyltransferase, ev=1e-126, 75% identity; UDP-glucose pyrophosphorylase 16916 4078678 TM1040_0015 Ruegeria sp. TM1040 UDP-glucose pyrophosphorylase YP_612010.1 16023 D 292414 CDS YP_612011.1 99079857 4078679 17017..18000 1 NC_008044.1 TIGRFAM: UDP-glucose 4-epimerase: (4.1e-160); PFAM: NAD-dependent epimerase/dehydratase: (5.1e-74) 3-beta hydroxysteroid dehydrogenase/isomerase: (7.7e-09) polysaccharide biosynthesis protein CapD: (1.7e-05) dTDP-4-dehydrorhamnose reductase: (2.2e-05); KEGG: rsp:RSP_0652 UDP-glucose 4-epimerase, ev=1e-124, 67% identity; UDP-galactose 4-epimerase 18000 4078679 TM1040_0016 Ruegeria sp. TM1040 UDP-galactose 4-epimerase YP_612011.1 17017 D 292414 CDS YP_612012.1 99079858 4078680 18017..19078 1 NC_008044.1 KEGG: sil:SPO0037 hypothetical protein, ev=1e-109, 57% identity; hypothetical protein 19078 4078680 TM1040_0017 Ruegeria sp. TM1040 hypothetical protein YP_612012.1 18017 D 292414 CDS YP_612013.1 99079859 4078681 19217..20203 1 NC_008044.1 KEGG: sil:SPO0036 hypothetical protein, ev=1e-147, 73% identity; hypothetical protein 20203 4078681 TM1040_0018 Ruegeria sp. TM1040 hypothetical protein YP_612013.1 19217 D 292414 CDS YP_612014.1 99079860 4078682 20200..21900 1 NC_008044.1 PFAM: glycosyl transferase, family 14: (7.8e-05); KEGG: sil:SPO0035 core-2/I-branching enzyme family protein, ev=0.0, 74% identity; glycosyl transferase family protein 21900 4078682 TM1040_0019 Ruegeria sp. TM1040 glycosyl transferase family protein YP_612014.1 20200 D 292414 CDS YP_612015.1 99079861 4078683 21907..23346 1 NC_008044.1 KEGG: sil:SPO0034 hypothetical protein, ev=0.0, 65% identity; hypothetical protein 23346 4078683 TM1040_0020 Ruegeria sp. TM1040 hypothetical protein YP_612015.1 21907 D 292414 CDS YP_612016.1 99079862 4078684 complement(23420..23884) 1 NC_008044.1 PFAM: phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2: (1.6e-16); KEGG: sil:SPO0077 PTS IIA-like nitrogen-regulatory protein PtsN, ev=2e-58, 74% identity; PTS transporter subunit IIA-like nitrogen-regulatory protein PtsN 23884 4078684 TM1040_0021 Ruegeria sp. TM1040 PTS transporter subunit IIA-like nitrogen-regulatory protein PtsN YP_612016.1 23420 R 292414 CDS YP_612017.1 99079863 4078685 complement(23940..24503) 1 NC_008044.1 TIGRFAM: ribosomal subunit interface protein: (4e-19); PFAM: sigma 54 modulation protein/ribosomal protein S30EA: (5.5e-27); KEGG: sil:SPO0078 ribosomal subunit interface protein, , ev=2e-87, 83% identity; 30S ribosomal protein S30 24503 4078685 TM1040_0022 Ruegeria sp. TM1040 30S ribosomal protein S30 YP_612017.1 23940 R 292414 CDS YP_612018.1 99079864 4076290 24596..24820 1 NC_008044.1 hypothetical protein 24820 4076290 TM1040_0023 Ruegeria sp. TM1040 hypothetical protein YP_612018.1 24596 D 292414 CDS YP_612019.1 99079865 4076291 complement(24823..25581) 1 NC_008044.1 PFAM: ABC transporter related: (3.8e-65); SMART: ATPase: (1.7e-13); KEGG: sil:SPO0079 ABC transporter, ATP-binding protein, ev=1e-122, 87% identity; ABC transporter 25581 4076291 TM1040_0024 Ruegeria sp. TM1040 ABC transporter YP_612019.1 24823 R 292414 CDS YP_612020.1 99079866 4076292 complement(25581..26015) 1 NC_008044.1 PFAM: OstA-like protein: (2.9e-26); KEGG: sil:SPO0080 hypothetical protein, ev=5e-37, 56% identity; OstA-like protein 26015 4076292 TM1040_0025 Ruegeria sp. TM1040 OstA-like protein YP_612020.1 25581 R 292414 CDS YP_612021.1 99079867 4076293 complement(26085..26684) 1 NC_008044.1 KEGG: sil:SPO0081 hypothetical protein, ev=2e-50, 51% identity; hypothetical protein 26684 4076293 TM1040_0026 Ruegeria sp. TM1040 hypothetical protein YP_612021.1 26085 R 292414 CDS YP_612022.1 99079868 4076294 complement(26757..27371) 1 NC_008044.1 PFAM: 3'-5' exonuclease: (4.8e-36); KEGG: sil:SPO0083 exonuclease, , ev=1e-98, 83% identity; 3'-5' exonuclease 27371 4076294 TM1040_0027 Ruegeria sp. TM1040 3'-5' exonuclease YP_612022.1 26757 R 292414 CDS YP_612023.1 99079869 4076295 27635..29086 1 NC_008044.1 TIGRFAM: xylulokinase: (4.1e-214); PFAM: carbohydrate kinase, FGGY: (2.2e-90); KEGG: sil:SPO0855 xylulokinase, ev=1e-173, 62% identity; xylulokinase 29086 4076295 TM1040_0028 Ruegeria sp. TM1040 xylulokinase YP_612023.1 27635 D 292414 CDS YP_612024.1 99079870 4076296 29083..30393 1 NC_008044.1 catalyzes the interconversion of D-xylose to D-xylulose; xylose isomerase 30393 4076296 TM1040_0029 Ruegeria sp. TM1040 xylose isomerase YP_612024.1 29083 D 292414 CDS YP_612025.1 99079871 4076297 30394..31401 1 NC_008044.1 PFAM: Aldose 1-epimerase: (1.6e-57); KEGG: sil:SPO0857 aldose 1-epimerase, ev=3e-63, 42% identity; aldose 1-epimerase 31401 4076297 TM1040_0030 Ruegeria sp. TM1040 aldose 1-epimerase YP_612025.1 30394 D 292414 CDS YP_612026.1 99079872 4076298 31401..32708 1 NC_008044.1 KEGG: sil:SPO0858 methylamine utilization protein MauG, , ev=1e-152, 65% identity; methylamine utilization protein MauG 32708 4076298 TM1040_0031 Ruegeria sp. TM1040 methylamine utilization protein MauG YP_612026.1 31401 D 292414 CDS YP_612027.1 99079873 4076299 complement(32737..34287) 1 NC_008044.1 PFAM: phospholipase D/Transphosphatidylase: (1.5e-05); KEGG: bbr:BB0822 phospholipase D protein, ev=1e-112, 46% identity; phospholipase D/transphosphatidylase 34287 4076299 TM1040_0032 Ruegeria sp. TM1040 phospholipase D/transphosphatidylase YP_612027.1 32737 R 292414 CDS YP_612028.1 99079874 4076300 34629..35831 1 NC_008044.1 PFAM: sodium/hydrogen exchanger: (1.4e-14); KEGG: hch:HCH_01176 NhaP-type Na+/H+ and K+/H+ antiporters with a unique C-terminal domain, ev=4e-75, 42% identity; sodium/hydrogen exchanger 35831 4076300 TM1040_0033 Ruegeria sp. TM1040 sodium/hydrogen exchanger YP_612028.1 34629 D 292414 CDS YP_612029.1 99079875 4076301 complement(35895..36665) 1 NC_008044.1 PFAM: ABC transporter related: (1e-61); SMART: ATPase: (2.3e-18); KEGG: sil:SPO1547 peptide/opine/nickel uptake family ABC transporter, ATP-binding protein, ev=4e-89, 69% identity; ABC transporter 36665 4076301 TM1040_0034 Ruegeria sp. TM1040 ABC transporter YP_612029.1 35895 R 292414 CDS YP_612030.1 99079876 4076302 complement(36662..37519) 1 NC_008044.1 PFAM: ABC transporter related: (1.2e-51); SMART: ATPase: (1.6e-17); KEGG: sil:SPO1546 peptide/opine/nickel uptake family ABC transporter, ATP-binding protein, ev=1e-127, 79% identity; ABC transporter 37519 4076302 TM1040_0035 Ruegeria sp. TM1040 ABC transporter YP_612030.1 36662 R 292414 CDS YP_612031.1 99079877 4076303 complement(37516..38433) 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1.5e-41); KEGG: sil:SPO1545 peptide/opine/nickel uptake family ABC transporter, permease protein, ev=1e-147, 84% identity; binding-protein-dependent transport system inner membrane protein 38433 4076303 TM1040_0036 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_612031.1 37516 R 292414 CDS YP_612032.1 99079878 4076304 complement(38430..39488) 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1.7e-47); KEGG: sil:SPO1544 peptide/opine/nickel uptake family ABC transporter, permease protein, ev=1e-156, 78% identity; binding-protein-dependent transport system inner membrane protein 39488 4076304 TM1040_0037 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_612032.1 38430 R 292414 CDS YP_612033.1 99079879 4076305 complement(39490..41088) 1 NC_008044.1 PFAM: extracellular solute-binding protein, family 5: (6.6e-78); KEGG: sil:SPO1543 peptide/opine/nickel uptake family ABC transporter, periplasmic substrate-binding protein, ev=0.0, 69% identity; extracellular solute-binding protein 41088 4076305 TM1040_0038 Ruegeria sp. TM1040 extracellular solute-binding protein YP_612033.1 39490 R 292414 CDS YP_612034.1 99079880 4076306 complement(41146..42195) 1 NC_008044.1 PFAM: peptidase M19, renal dipeptidase: (2.4e-119); KEGG: sil:SPO1542 renal dipeptidase family protein, ev=1e-118, 61% identity; dipeptidase AC 42195 4076306 TM1040_0039 Ruegeria sp. TM1040 dipeptidase AC YP_612034.1 41146 R 292414 CDS YP_612035.1 99079881 4076307 42535..43575 1 NC_008044.1 PFAM: Alcohol dehydrogenase, zinc-binding: (2.8e-36) Alcohol dehydrogenase GroES-like: (1.9e-38); KEGG: ret:RHE_CH01189 probable alcohol dehydrogenase protein, ev=1e-139, 67% identity; molecular chaperone GroES 43575 4076307 TM1040_0040 Ruegeria sp. TM1040 molecular chaperone GroES YP_612035.1 42535 D 292414 CDS YP_612036.1 99079882 4076308 43680..44879 1 NC_008044.1 PFAM: glucose-inhibited division protein A: (0.0015) fumarate reductase/succinate dehydrogenase flavoprotein-like: (0.0027) HI0933-like protein: (5e-102); KEGG: sil:SPO3436 hypothetical protein, ev=1e-149, 68% identity; hypothetical protein 44879 4076308 TM1040_0041 Ruegeria sp. TM1040 hypothetical protein YP_612036.1 43680 D 292414 CDS YP_612037.1 99079883 4078705 complement(44852..45442) 1 NC_008044.1 PFAM: glutathione S-transferase-like: (1.3e-08); KEGG: jan:Jann_0408 glutathione S-transferase-like, ev=3e-60, 59% identity; glutathione S-transferase 45442 4078705 TM1040_0042 Ruegeria sp. TM1040 glutathione S-transferase YP_612037.1 44852 R 292414 CDS YP_612038.1 99079884 4078706 complement(45518..46546) 1 NC_008044.1 PFAM: DNA polymerase III, delta: (6.8e-05); KEGG: sil:SPO3434 DNA polymerase III delta subunit, ev=1e-147, 75% identity; DNA polymerase III subunit delta 46546 4078706 TM1040_0043 Ruegeria sp. TM1040 DNA polymerase III subunit delta YP_612038.1 45518 R 292414 CDS YP_612039.1 99079885 4078707 complement(46543..47076) 1 NC_008044.1 KEGG: sil:SPO3433 lipoprotein, , ev=8e-35, 50% identity; lipoprotein 47076 4078707 TM1040_0044 Ruegeria sp. TM1040 lipoprotein YP_612039.1 46543 R 292414 CDS YP_612040.1 99079886 4078708 complement(47063..49636) 1 NC_008044.1 leucine--tRNA ligase; LeuRS; class-I aminoacyl-tRNA synthetase; charges leucine by linking carboxyl group to alpha-phosphate of ATP and then transfers aminoacyl-adenylate to its tRNA; due to the large number of codons that tRNA(Leu) recognizes, the leucyl-tRNA synthetase does not recognize the anticodon loop of the tRNA, but instead recognition is dependent on a conserved discriminator base A37 and a long arm; an editing domain hydrolyzes misformed products; in Methanothermobacter thermautotrophicus this enzyme associates with prolyl-tRNA synthetase; leucyl-tRNA synthetase 49636 leuS 4078708 leuS Ruegeria sp. TM1040 leucyl-tRNA synthetase YP_612040.1 47063 R 292414 CDS YP_612041.1 99079887 4078709 complement(49724..50212) 1 NC_008044.1 KEGG: sil:SPO3431 hypothetical protein, ev=3e-48, 61% identity; hypothetical protein 50212 4078709 TM1040_0046 Ruegeria sp. TM1040 hypothetical protein YP_612041.1 49724 R 292414 CDS YP_612042.1 99079888 4078710 50494..51438 1 NC_008044.1 KEGG: sil:SPO3430 outer membrane porin, ev=6e-30, 34% identity; outer membrane porin 51438 4078710 TM1040_0047 Ruegeria sp. TM1040 outer membrane porin YP_612042.1 50494 D 292414 CDS YP_612043.1 99079889 4078711 51557..52213 1 NC_008044.1 TIGRFAM: Protein of unknown function UPF0001: (9.3e-45); PFAM: alanine racemase-like: (7e-09); KEGG: sil:SPO3429 alanine racemase domain protein, ev=3e-99, 82% identity; hypothetical protein 52213 4078711 TM1040_0048 Ruegeria sp. TM1040 hypothetical protein YP_612043.1 51557 D 292414 CDS YP_612044.1 99079890 4078712 complement(52205..52660) 1 NC_008044.1 KEGG: sil:SPO3428 hypothetical protein, ev=6e-62, 72% identity; hypothetical protein 52660 4078712 TM1040_0049 Ruegeria sp. TM1040 hypothetical protein YP_612044.1 52205 R 292414 CDS YP_612045.1 99079891 4078713 complement(52702..53790) 1 NC_008044.1 PFAM: GTP cyclohydrolase II: (4.5e-90); KEGG: sil:SPO3427 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II, ev=1e-145, 71% identity; GTP cyclohydrolase II 53790 4078713 TM1040_0050 Ruegeria sp. TM1040 GTP cyclohydrolase II YP_612045.1 52702 R 292414 CDS YP_612046.1 99079892 4078714 53960..54646 1 NC_008044.1 PFAM: response regulator receiver: (6.9e-38) transcriptional regulatory protein-like: (1.4e-18); KEGG: sil:SPO3426 DNA-binding response regulator, ev=1e-117, 92% identity; two component transcriptional regulator 54646 4078714 TM1040_0051 Ruegeria sp. TM1040 two component transcriptional regulator YP_612046.1 53960 D 292414 CDS YP_612047.1 99079893 4078715 complement(54785..55993) 1 NC_008044.1 PFAM: Taurine catabolism dioxygenase TauD/TfdA: (3.9e-28); KEGG: pfo:Pfl_5234 gamma-butyrobetaine hydroxylase, ev=9e-69, 39% identity; gamma-butyrobetaine,2-oxoglutarate dioxygenase 55993 4078715 TM1040_0052 Ruegeria sp. TM1040 gamma-butyrobetaine,2-oxoglutarate dioxygenase YP_612047.1 54785 R 292414 CDS YP_612048.1 99079894 4078716 56222..57010 1 NC_008044.1 TIGRFAM: exodeoxyribonuclease III: (1.5e-45) exodeoxyribonuclease III (xth): (5.2e-45); PFAM: Endonuclease/exonuclease/phosphatase: (1.8e-39); KEGG: sil:SPO3425 exodeoxyribonuclease III, , ev=1e-130, 82% identity; exodeoxyribonuclease III 57010 4078716 TM1040_0053 Ruegeria sp. TM1040 exodeoxyribonuclease III YP_612048.1 56222 D 292414 CDS YP_612049.1 99079895 4078717 57235..58170 1 NC_008044.1 PFAM: Tetratricopeptide TPR_4: (0.016) Thioredoxin domain: (9e-22); KEGG: sil:SPO3423 thioredoxin, ev=1e-125, 75% identity; thioredoxin domain-containing protein 58170 4078717 TM1040_0054 Ruegeria sp. TM1040 thioredoxin domain-containing protein YP_612049.1 57235 D 292414 CDS YP_612050.1 99079896 4078718 58198..58842 1 NC_008044.1 PFAM: peptidase S16, lon-like: (2.4e-06); KEGG: rsp:RSP_1490 ATP-dependent protease La, LON, ev=2e-86, 73% identity; peptidase S16, lon-like 58842 4078718 TM1040_0055 Ruegeria sp. TM1040 peptidase S16, lon-like YP_612050.1 58198 D 292414 CDS YP_612051.1 99079897 4078719 58839..59024 1 NC_008044.1 PFAM: protein of unknown function DUF343: (2e-16); KEGG: sil:SPO3421 hypothetical protein, ev=5e-20, 78% identity; hypothetical protein 59024 4078719 TM1040_0056 Ruegeria sp. TM1040 hypothetical protein YP_612051.1 58839 D 292414 CDS YP_612052.1 99079898 4078720 complement(59044..60270) 1 NC_008044.1 TIGRFAM: Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family: (2.4e-168); PFAM: monooxygenase, FAD-binding: (4.1e-10); KEGG: sil:SPO3419 ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family, ev=1e-167, 70% identity; 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase 60270 4078720 TM1040_0057 Ruegeria sp. TM1040 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase YP_612052.1 59044 R 292414 CDS YP_612053.1 99079899 4078721 60494..61825 1 NC_008044.1 PFAM: Amidase: (1.7e-76); KEGG: sil:SPO3418 amidase family protein, ev=1e-180, 73% identity; amidase 61825 4078721 TM1040_0058 Ruegeria sp. TM1040 amidase YP_612053.1 60494 D 292414 CDS YP_612054.1 99079900 4078722 61934..63112 1 NC_008044.1 PFAM: aminotransferase, class I and II: (7e-33); KEGG: sil:SPO3417 aminotransferase, classes I and II, ev=0.0, 78% identity; aminotransferase 63112 4078722 TM1040_0059 Ruegeria sp. TM1040 aminotransferase YP_612054.1 61934 D 292414 CDS YP_612055.1 99079901 4078723 63232..66279 1 NC_008044.1 PFAM: cell divisionFtsK/SpoIIIE: (1.4e-78); KEGG: sil:SPO3416 FtsK/SpoIIIE family protein, ev=0.0, 68% identity; DNA translocase FtsK 66279 4078723 TM1040_0060 Ruegeria sp. TM1040 DNA translocase FtsK YP_612055.1 63232 D 292414 CDS YP_612056.1 99079902 4078724 66347..66943 1 NC_008044.1 PFAM: outer membrane lipoprotein carrier protein LolA: (1e-14); KEGG: sil:SPO3415 outer membrane lipoprotein carrier protein LolA, , ev=5e-58, 59% identity; outer membrane lipoprotein carrier protein LolA 66943 4078724 TM1040_0061 Ruegeria sp. TM1040 outer membrane lipoprotein carrier protein LolA YP_612056.1 66347 D 292414 CDS YP_612057.1 99079903 4075959 complement(67002..67589) 1 NC_008044.1 KEGG: sil:SPO3414 lipoprotein, , ev=9e-76, 65% identity; hypothetical protein 67589 4075959 TM1040_0062 Ruegeria sp. TM1040 hypothetical protein YP_612057.1 67002 R 292414 CDS YP_612058.1 99079904 4075960 67820..68146 1 NC_008044.1 TIGRFAM: Hemimethylated DNA-binding region: (1.9e-50); KEGG: sil:SPO3412 hypothetical protein, ev=1e-48, 79% identity; hemimethylated DNA-binding region 68146 4075960 TM1040_0063 Ruegeria sp. TM1040 hemimethylated DNA-binding region YP_612058.1 67820 D 292414 CDS YP_612059.1 99079905 4075961 complement(68184..69761) 1 NC_008044.1 PFAM: gamma-glutamyltranspeptidase: (1.2e-171); KEGG: sil:SPO3411 gamma-glutamyltranspeptidase, , ev=0.0, 74% identity; gamma-glutamyltransferase 2 69761 4075961 TM1040_0064 Ruegeria sp. TM1040 gamma-glutamyltransferase 2 YP_612059.1 68184 R 292414 CDS YP_612060.1 99079906 4075962 complement(70069..70509) 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (0.00013); KEGG: sil:SPO3410 anti-sigma B factor, , ev=5e-37, 54% identity; anti-sigma regulatory factor, serine/threonine protein kinase 70509 4075962 TM1040_0065 Ruegeria sp. TM1040 anti-sigma regulatory factor, serine/threonine protein kinase YP_612060.1 70069 R 292414 CDS YP_612061.1 99079907 4075963 complement(70543..70887) 1 NC_008044.1 TIGRFAM: anti-anti-sigma factor: (1.8e-12); PFAM: Sulfate transporter/antisigma-factor antagonist STAS: (9.8e-21); KEGG: sil:SPO3409 anti-anti-sigma factor, ev=4e-40, 78% identity; anti-sigma-factor antagonist 70887 4075963 TM1040_0066 Ruegeria sp. TM1040 anti-sigma-factor antagonist YP_612061.1 70543 R 292414 CDS YP_612062.1 99079908 4075964 70985..72157 1 NC_008044.1 PFAM: Thiolase: (1.6e-116); KEGG: sil:SPO3408 acetyl-CoA C-acetyltransferase, ev=0.0, 87% identity; Acetyl-CoA C-acetyltransferase 72157 4075964 TM1040_0067 Ruegeria sp. TM1040 Acetyl-CoA C-acetyltransferase YP_612062.1 70985 D 292414 CDS YP_612063.1 99079909 4075965 72257..72724 1 NC_008044.1 SMART: GAF: (3.9e-06); KEGG: jan:Jann_4049 GAF sensor protein, ev=3e-61, 73% identity; GAF sensor protein 72724 4075965 TM1040_0068 Ruegeria sp. TM1040 GAF sensor protein YP_612063.1 72257 D 292414 CDS YP_612064.1 99079910 4075966 72740..73369 1 NC_008044.1 PFAM: Lysine exporter protein (LYSE/YGGA): (1.2e-07); KEGG: sil:SPO3402 transporter, LysE family, ev=2e-88, 79% identity; lysine exporter protein LysE/YggA 73369 4075966 TM1040_0069 Ruegeria sp. TM1040 lysine exporter protein LysE/YggA YP_612064.1 72740 D 292414 CDS YP_612065.1 99079911 4075967 73397..73768 1 NC_008044.1 PFAM: glutathione-dependent formaldehyde-activating, GFA: (1.5e-22); KEGG: sil:SPO3401 hypothetical protein, ev=4e-47, 72% identity; glutathione-dependent formaldehyde-activating protein 73768 4075967 TM1040_0070 Ruegeria sp. TM1040 glutathione-dependent formaldehyde-activating protein YP_612065.1 73397 D 292414 CDS YP_612066.1 99079912 4075968 73920..74855 1 NC_008044.1 TIGRFAM: rarD protein: (6.3e-57); PFAM: protein of unknown function DUF6, transmembrane: (8.6e-12); KEGG: sil:SPO3395 RarD, ev=1e-115, 69% identity; rarD protein 74855 4075968 TM1040_0071 Ruegeria sp. TM1040 rarD protein YP_612066.1 73920 D 292414 CDS YP_612067.1 99079913 4075969 74929..75582 1 NC_008044.1 PFAM: pseudouridine synthase: (8.2e-50); KEGG: sil:SPO3392 ribosomal large subunit pseudouridine synthase A, ev=5e-95, 76% identity; ribosomal large subunit pseudouridine synthase A 75582 4075969 TM1040_0072 Ruegeria sp. TM1040 ribosomal large subunit pseudouridine synthase A YP_612067.1 74929 D 292414 CDS YP_612068.1 99079914 4075970 complement(75566..76279) 1 NC_008044.1 PFAM: helix-turn-helix, AraC type: (1.5e-08); KEGG: pst:PSPTO3805 transcriptional regulator, AraC family, ev=5e-11, 43% identity; AraC family transcriptional regulator 76279 4075970 TM1040_0073 Ruegeria sp. TM1040 AraC family transcriptional regulator YP_612068.1 75566 R 292414 CDS YP_612069.1 99079915 4075971 complement(76421..77863) 1 NC_008044.1 PFAM: aldehyde dehydrogenase: (3.7e-208); KEGG: sil:SPO3382 aldehyde dehydrogenase family protein, ev=0.0, 86% identity; aldehyde dehydrogenase 77863 4075971 TM1040_0074 Ruegeria sp. TM1040 aldehyde dehydrogenase YP_612069.1 76421 R 292414 CDS YP_612070.1 99079916 4075972 78109..78759 1 NC_008044.1 PFAM: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen: (1.2e-73) Redoxin: (0.00011); KEGG: sil:SPO3383 thiol-specific antioxidant protein, ev=2e-93, 76% identity; 1-Cys peroxiredoxin 78759 4075972 TM1040_0075 Ruegeria sp. TM1040 1-Cys peroxiredoxin YP_612070.1 78109 D 292414 CDS YP_612071.1 99079917 4075973 complement(78842..79999) 1 NC_008044.1 KEGG: jan:Jann_4277 lipopolysaccharide biosynthesis protein-like, ev=3e-32, 35% identity; lipopolysaccharide biosynthesis protein-like 79999 4075973 TM1040_0076 Ruegeria sp. TM1040 lipopolysaccharide biosynthesis protein-like YP_612071.1 78842 R 292414 CDS YP_612072.1 99079918 4075974 complement(80070..80933) 1 NC_008044.1 PFAM: glycosyl transferase, family 2: (3.9e-21); KEGG: atc:AGR_L_533 dTDP-Rha:a-D-GlcNAc-diphosphoryl polyprenol, A-3-L-rhamnosyl transferase, ev=6e-61, 46% identity; glycosyl transferase family protein 80933 4075974 TM1040_0077 Ruegeria sp. TM1040 glycosyl transferase family protein YP_612072.1 80070 R 292414 CDS YP_612073.1 99079919 4075975 complement(81035..83170) 1 NC_008044.1 KEGG: sil:SPO3389 polyribonucleotide nucleotidyltransferase, ev=0.0, 89% identity; PFAM: 3' exoribonuclease: (2.5e-47) RNA binding S1: (1.2e-24) KH, type 1: (1.3e-15); SMART: KH: (1.1e-13); polynucleotide phosphorylase 83170 4075975 TM1040_0078 Ruegeria sp. TM1040 polynucleotide phosphorylase YP_612073.1 81035 R 292414 CDS YP_612074.1 99079920 4075976 complement(83364..83552) 1 NC_008044.1 KEGG: jan:Jann_2252 hypothetical protein, ev=6e-11, 55% identity; hypothetical protein 83552 4075976 TM1040_0079 Ruegeria sp. TM1040 hypothetical protein YP_612074.1 83364 R 292414 CDS YP_612075.1 99079921 4075977 complement(83627..84841) 1 NC_008044.1 PFAM: cobalamin synthesis protein, P47K: (3e-91) cobalamin synthesis CobW-like: (3.1e-34); KEGG: jan:Jann_2254 cobalamin synthesis protein, P47K, ev=0.0, 78% identity; cobalamin synthesis protein, P47K 84841 4075977 TM1040_0080 Ruegeria sp. TM1040 cobalamin synthesis protein, P47K YP_612075.1 83627 R 292414 CDS YP_612076.1 99079922 4078747 complement(85005..85274) 1 NC_008044.1 primary rRNA binding protein; helps nucleate assembly of 30S; binds directly to the 16S rRNA and an intersubunit bridge to the 23S rRNA; autoregulates translation through interactions with the mRNA leader sequence; 30S ribosomal protein S15 85274 rpsO 4078747 rpsO Ruegeria sp. TM1040 30S ribosomal protein S15 YP_612076.1 85005 R 292414 CDS YP_612077.1 99079923 4078748 complement(85539..86606) 1 NC_008044.1 KEGG: sil:SPO3839 type I secretion target repeat protein, ev=6e-63, 40% identity; type I secretion target repeat-containing protein 86606 4078748 TM1040_0082 Ruegeria sp. TM1040 type I secretion target repeat-containing protein YP_612077.1 85539 R 292414 CDS YP_612078.1 99079924 4078749 complement(86710..87231) 1 NC_008044.1 PFAM: protein of unknown function DUF1643: (4.2e-41); KEGG: sil:SPO3838 hypothetical protein, ev=3e-68, 71% identity; hypothetical protein 87231 4078749 TM1040_0083 Ruegeria sp. TM1040 hypothetical protein YP_612078.1 86710 R 292414 CDS YP_612079.1 99079925 4078750 complement(87460..88368) 1 NC_008044.1 catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs; tRNA pseudouridine synthase B 88368 truB 4078750 truB Ruegeria sp. TM1040 tRNA pseudouridine synthase B YP_612079.1 87460 R 292414 CDS YP_612080.1 99079926 4078751 complement(88426..89199) 1 NC_008044.1 KEGG: sil:SPO3836 hypothetical protein, ev=1e-88, 68% identity; hypothetical protein 89199 4078751 TM1040_0085 Ruegeria sp. TM1040 hypothetical protein YP_612080.1 88426 R 292414 CDS YP_612081.1 99079927 4078752 complement(89204..89599) 1 NC_008044.1 associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock; ribosome-binding factor A 89599 rbfA 4078752 rbfA Ruegeria sp. TM1040 ribosome-binding factor A YP_612081.1 89204 R 292414 CDS YP_612082.1 99079928 4078753 89693..90502 1 NC_008044.1 catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate reductase 90502 4078753 TM1040_0087 Ruegeria sp. TM1040 dihydrodipicolinate reductase YP_612082.1 89693 D 292414 CDS YP_612083.1 99079929 4078754 complement(90697..90891) 1 NC_008044.1 PFAM: protein of unknown function DUF1674: (2.5e-22); KEGG: sil:SPO3377 hypothetical protein, ev=1e-19, 87% identity; hypothetical protein 90891 4078754 TM1040_0088 Ruegeria sp. TM1040 hypothetical protein YP_612083.1 90697 R 292414 CDS YP_612084.1 99079930 4078755 90990..92264 1 NC_008044.1 PFAM: Fmu (Sun): (1.3e-39) NusB/RsmB/TIM44: (2.1e-07) methyltransferase small: (0.00033) Methyltransferase type 11: (4.5e-05); KEGG: sil:SPO3376 ribosomal RNA small subunit methyltransferase B, , ev=1e-164, 70% identity; hypothetical protein 92264 4078755 TM1040_0089 Ruegeria sp. TM1040 hypothetical protein YP_612084.1 90990 D 292414 CDS YP_612085.1 99079931 4078756 92456..94201 1 NC_008044.1 PFAM: Heparinase II/III-like: (1.7e-14); KEGG: sil:SPO3375 hypothetical protein, ev=0.0, 72% identity; heparinase II/III-like 94201 4078756 TM1040_0090 Ruegeria sp. TM1040 heparinase II/III-like YP_612085.1 92456 D 292414 CDS YP_612086.1 99079932 4078757 94226..95815 1 NC_008044.1 involved in de novo purine biosynthesis; bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase 95815 purH 4078757 purH Ruegeria sp. TM1040 bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase YP_612086.1 94226 D 292414 CDS YP_612087.1 99079933 4078758 95835..96317 1 NC_008044.1 lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis; lipoprotein signal peptidase 96317 4078758 TM1040_0092 Ruegeria sp. TM1040 lipoprotein signal peptidase YP_612087.1 95835 D 292414 CDS YP_612088.1 99079934 4078759 96470..96976 1 NC_008044.1 KEGG: sil:SPO3372 hypothetical protein, ev=3e-39, 46% identity; hypothetical protein 96976 4078759 TM1040_0093 Ruegeria sp. TM1040 hypothetical protein YP_612088.1 96470 D 292414 CDS YP_612089.1 99079935 4078760 97110..98543 1 NC_008044.1 PFAM: peptidase M16-like: (7.5e-35); KEGG: sil:SPO3371 peptidase, M16 family, ev=0.0, 74% identity; peptidase M16-like protein 98543 4078760 TM1040_0094 Ruegeria sp. TM1040 peptidase M16-like protein YP_612089.1 97110 D 292414 CDS YP_612090.1 99079936 4078761 98540..99913 1 NC_008044.1 PFAM: peptidase M16-like: (1.8e-39); KEGG: sil:SPO3370 peptidase, M16 family, ev=1e-157, 63% identity; peptidase M16-like protein 99913 4078761 TM1040_0095 Ruegeria sp. TM1040 peptidase M16-like protein YP_612090.1 98540 D 292414 CDS YP_612091.1 99079937 4078762 complement(100018..102360) 1 NC_008044.1 PFAM: aldehyde dehydrogenase: (1.2e-201); KEGG: sil:SPO3368 aldehyde dehydrogenase family protein, ev=0.0, 78% identity; aldehyde dehydrogenase 102360 4078762 TM1040_0096 Ruegeria sp. TM1040 aldehyde dehydrogenase YP_612091.1 100018 R 292414 CDS YP_612092.1 99079938 4078763 complement(102371..103426) 1 NC_008044.1 KEGG: jan:Jann_0789 deoxyribose-phosphate aldolase, ev=1e-143, 77% identity; TIGRFAM: deoxyribose-phosphate aldolase: (7.9e-38); PFAM: deoxyribose-phosphate aldolase/phospho-2-dehydro-3-deoxyheptonate aldolase: (4.7e-39); deoxyribose-phosphate aldolase 103426 4078763 TM1040_0097 Ruegeria sp. TM1040 deoxyribose-phosphate aldolase YP_612092.1 102371 R 292414 CDS YP_612093.1 99079939 4078764 103637..104599 1 NC_008044.1 TIGRFAM: Twin-arginine translocation pathway signal: (0.078); PFAM: periplasmic solute binding protein: (9e-94); KEGG: sil:SPO3366 zinc/manganese/iron ABC transporter, periplasmic zinc/manganese/iron-binding protein, ev=1e-124, 73% identity; twin-arginine translocation pathway signal 104599 4078764 TM1040_0098 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_612093.1 103637 D 292414 CDS YP_612094.1 99079940 4078765 104599..105405 1 NC_008044.1 PFAM: ABC transporter related: (2.6e-51); SMART: ATPase: (2.9e-16); KEGG: sil:SPO3365 zinc/manganese/iron ABC transporter, ATP-binding protein, ev=1e-116, 80% identity; ABC transporter 105405 4078765 TM1040_0099 Ruegeria sp. TM1040 ABC transporter YP_612094.1 104599 D 292414 CDS YP_612095.1 99079941 4078766 105437..106639 1 NC_008044.1 PFAM: ABC-3: (2.2e-59); KEGG: sil:SPO3364 zinc/manganese/iron ABC transporter, permease protein, ev=1e-178, 81% identity; hypothetical protein 106639 4078766 TM1040_0100 Ruegeria sp. TM1040 hypothetical protein YP_612095.1 105437 D 292414 CDS YP_612096.1 99079942 4078686 106640..107566 1 NC_008044.1 PFAM: ABC-3: (5.6e-26); KEGG: sil:SPO3363 zinc/manganese/iron ABC transporter, permease protein, ev=1e-143, 84% identity; hypothetical protein 107566 4078686 TM1040_0101 Ruegeria sp. TM1040 hypothetical protein YP_612096.1 106640 D 292414 CDS YP_612097.1 99079943 4078687 107657..109591 1 NC_008044.1 This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. Promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex; DNA mismatch repair protein 109591 mutL 4078687 mutL Ruegeria sp. TM1040 DNA mismatch repair protein YP_612097.1 107657 D 292414 CDS YP_612098.1 99079944 4078688 109602..110837 1 NC_008044.1 PFAM: protein of unknown function DUF195: (7.5e-73); KEGG: sil:SPO3361 RmuC domain protein, ev=1e-166, 73% identity; hypothetical protein 110837 4078688 TM1040_0103 Ruegeria sp. TM1040 hypothetical protein YP_612098.1 109602 D 292414 CDS YP_612099.1 99079945 4078689 110834..112147 1 NC_008044.1 PFAM: adenylyl cyclase class-3/4/guanylyl cyclase: (2.1e-14); KEGG: sme:SMa1103 probable adenylate cyclase, ev=2e-64, 36% identity; guanylate cyclase 112147 4078689 TM1040_0104 Ruegeria sp. TM1040 guanylate cyclase YP_612099.1 110834 D 292414 CDS YP_612100.1 99079946 4078690 112226..112549 1 NC_008044.1 KEGG: sil:SPO3310 hypothetical protein, ev=2e-27, 58% identity; hypothetical protein 112549 4078690 TM1040_0105 Ruegeria sp. TM1040 hypothetical protein YP_612100.1 112226 D 292414 CDS YP_612101.1 99079947 4078691 complement(112632..113774) 1 NC_008044.1 PFAM: Saccharopine dehydrogenase: (4.1e-54) 6-phosphogluconate dehydrogenase, NAD-binding: (0.0007); KEGG: sil:SPO3309 saccharopine dehydrogenase, , ev=1e-172, 75% identity; saccharopine dehydrogenase (NADP+, L-glutamate forming) 113774 4078691 TM1040_0106 Ruegeria sp. TM1040 saccharopine dehydrogenase (NADP+, L-glutamate forming) YP_612101.1 112632 R 292414 CDS YP_612102.1 99079948 4078692 complement(113804..114856) 1 NC_008044.1 PFAM: alanine dehydrogenase/PNT-like: (0.00018); KEGG: sil:SPO3307 saccharopine dehydrogenase, , ev=1e-171, 84% identity; saccharopine dehydrogenase 114856 4078692 TM1040_0107 Ruegeria sp. TM1040 saccharopine dehydrogenase YP_612102.1 113804 R 292414 CDS YP_612103.1 99079949 4078693 complement(114868..115482) 1 NC_008044.1 PFAM: glutathione S-transferase-like: (7.7e-07); KEGG: sil:SPO3306 glutathione S-transferase, , ev=5e-73, 67% identity; glutathione S-transferase 115482 4078693 TM1040_0108 Ruegeria sp. TM1040 glutathione S-transferase YP_612103.1 114868 R 292414 CDS YP_612104.1 99079950 4078694 complement(115503..116159) 1 NC_008044.1 PFAM: Phosphoglycerate mutase: (1.4e-20); KEGG: sil:SPO3305 phosphoglycerate mutase family protein, ev=6e-82, 66% identity; phosphoglycerate mutase 116159 4078694 TM1040_0109 Ruegeria sp. TM1040 phosphoglycerate mutase YP_612104.1 115503 R 292414 CDS YP_612105.1 99079951 4078695 complement(116273..116500) 1 NC_008044.1 KEGG: rsp:RSP_1085 hypothetical protein, ev=5e-10, 54% identity; hypothetical protein 116500 4078695 TM1040_0110 Ruegeria sp. TM1040 hypothetical protein YP_612105.1 116273 R 292414 CDS YP_612106.1 99079952 4078696 complement(116589..117308) 1 NC_008044.1 PFAM: response regulator receiver: (9.6e-31) transcriptional regulatory protein-like: (1.3e-16); KEGG: sil:SPO3298 DNA-binding response regulator, ev=1e-113, 88% identity; two component transcriptional regulator 117308 4078696 TM1040_0111 Ruegeria sp. TM1040 two component transcriptional regulator YP_612106.1 116589 R 292414 CDS YP_612107.1 99079953 4078697 complement(117301..119205) 1 NC_008044.1 TIGRFAM: PAS: (0.0022); PFAM: response regulator receiver: (2.5e-05) ATP-binding region, ATPase-like: (7.6e-29) histidine kinase A-like: (0.0016) PAS fold-4: (7.3e-06); KEGG: sil:SPO3297 sensory box histidine kinase/response regulator, ev=0.0, 69% identity; PAS/PAC sensor hybrid histidine kinase 119205 4078697 TM1040_0112 Ruegeria sp. TM1040 PAS/PAC sensor hybrid histidine kinase YP_612107.1 117301 R 292414 CDS YP_612108.1 99079954 4078698 119466..121451 1 NC_008044.1 PFAM: AMP-dependent synthetase and ligase: (7.4e-70); KEGG: sil:SPO3296 AMP-binding enzyme, ev=0.0, 79% identity; AMP-dependent synthetase/ligase 121451 4078698 TM1040_0113 Ruegeria sp. TM1040 AMP-dependent synthetase/ligase YP_612108.1 119466 D 292414 CDS YP_612109.1 99079955 4078699 121536..122354 1 NC_008044.1 PFAM: ABC transporter related: (2.1e-46); SMART: ATPase: (6.8e-10); KEGG: sil:SPO3295 branched-chain amino acid ABC transporter, ATP-binding protein, ev=1e-140, 91% identity; ABC transporter 122354 4078699 TM1040_0114 Ruegeria sp. TM1040 ABC transporter YP_612109.1 121536 D 292414 CDS YP_612110.1 99079956 4078700 122393..123379 1 NC_008044.1 PFAM: inner-membrane translocator: (1.4e-07); KEGG: sil:SPO3294 branched-chain amino acid ABC transporter, permease protein, ev=1e-172, 92% identity; inner-membrane translocator 123379 4078700 TM1040_0115 Ruegeria sp. TM1040 inner-membrane translocator YP_612110.1 122393 D 292414 CDS YP_612111.1 99079957 4078701 complement(123416..123841) 1 NC_008044.1 hypothetical protein 123841 4078701 TM1040_0116 Ruegeria sp. TM1040 hypothetical protein YP_612111.1 123416 R 292414 CDS YP_612112.1 99079958 4078702 123944..124204 1 NC_008044.1 KEGG: sil:SPO3293 hypothetical protein, ev=6e-19, 53% identity; hypothetical protein 124204 4078702 TM1040_0117 Ruegeria sp. TM1040 hypothetical protein YP_612112.1 123944 D 292414 CDS YP_612113.1 99079959 4078703 124243..125319 1 NC_008044.1 PFAM: inner-membrane translocator: (1.8e-21); KEGG: sil:SPO3292 branched-chain amino acid ABC transporter, permease protein, ev=0.0, 90% identity; inner-membrane translocator 125319 4078703 TM1040_0118 Ruegeria sp. TM1040 inner-membrane translocator YP_612113.1 124243 D 292414 CDS YP_612114.1 99079960 4078704 125411..126694 1 NC_008044.1 KEGG: sil:SPO3291 branched-chain amino acid ABC transporter, periplasmic branched-chain amino acid binding protein, , ev=0.0, 78% identity; branched-chain amino acid ABC transporter periplasmic branched-chain amino acid binding protein 126694 4078704 TM1040_0119 Ruegeria sp. TM1040 branched-chain amino acid ABC transporter periplasmic branched-chain amino acid binding protein YP_612114.1 125411 D 292414 CDS YP_612115.1 99079961 4078725 126813..127649 1 NC_008044.1 PFAM: ABC transporter related: (8.6e-31); SMART: ATPase: (9.6e-09); KEGG: sil:SPO3290 branched-chain amino acid ABC transporter, ATP-binding protein, ev=1e-140, 89% identity; ABC transporter 127649 4078725 TM1040_0120 Ruegeria sp. TM1040 ABC transporter YP_612115.1 126813 D 292414 CDS YP_612116.1 99079962 4078726 127666..128883 1 NC_008044.1 KEGG: sil:SPO3289 phenylacetate-CoA ligase, , ev=0.0, 84% identity; phenylacetate-CoA ligase 128883 4078726 TM1040_0121 Ruegeria sp. TM1040 phenylacetate-CoA ligase YP_612116.1 127666 D 292414 CDS YP_612117.1 99079963 4078727 129006..130685 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (9.2e-13); KEGG: sil:SPO3288 ferric iron ABC transporter, permease protein, ev=0.0, 77% identity; binding-protein-dependent transport system inner membrane protein 130685 4078727 TM1040_0122 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_612117.1 129006 D 292414 CDS YP_612118.1 99079964 4078728 complement(130689..131552) 1 NC_008044.1 PFAM: cobalamin synthesis protein, P47K: (2.5e-44); KEGG: jan:Jann_3251 cobalamin synthesis protein, P47K, ev=3e-64, 44% identity; cobalamin synthesis protein, P47K 131552 4078728 TM1040_0123 Ruegeria sp. TM1040 cobalamin synthesis protein, P47K YP_612118.1 130689 R 292414 CDS YP_612119.1 99079965 4078729 complement(131939..132949) 1 NC_008044.1 PFAM: extracellular solute-binding protein, family 1: (1.8e-11); KEGG: sil:SPO3287 ferric iron ABC transporter, periplasmic ferric iron-binding protein, ev=1e-149, 75% identity; extracellular solute-binding protein 132949 4078729 TM1040_0124 Ruegeria sp. TM1040 extracellular solute-binding protein YP_612119.1 131939 R 292414 CDS YP_612120.1 99079966 4078730 complement(133310..133435) 1 NC_008044.1 smallest protein in the large subunit; similar to what is found with protein L31 and L33 several bacterial genomes contain paralogs which may be regulated by zinc; the protein from Thermus thermophilus has a zinc-binding motif and contains a bound zinc ion; the proteins in this group do not have the motif; 50S ribosomal protein L36 133435 rpmJ 4078730 rpmJ Ruegeria sp. TM1040 50S ribosomal protein L36 YP_612120.1 133310 R 292414 CDS YP_612121.1 99079967 4078731 133740..134600 1 NC_008044.1 PFAM: N-formylglutamate amidohydrolase: (2.6e-59); KEGG: rsp:RSP_1399 hypothetical protein, ev=2e-92, 57% identity; N-formylglutamate amidohydrolase 134600 4078731 TM1040_0126 Ruegeria sp. TM1040 N-formylglutamate amidohydrolase YP_612121.1 133740 D 292414 CDS YP_612122.1 99079968 4078732 complement(134637..135908) 1 NC_008044.1 involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function; DNA polymerase IV 135908 4078732 TM1040_0127 Ruegeria sp. TM1040 DNA polymerase IV YP_612122.1 134637 R 292414 CDS YP_612123.1 99079969 4078733 136011..136430 1 NC_008044.1 PFAM: NUDIX hydrolase: (1.9e-16); KEGG: sil:SPO3279 NUDIX domain protein, ev=2e-38, 58% identity; NUDIX hydrolase 136430 4078733 TM1040_0128 Ruegeria sp. TM1040 NUDIX hydrolase YP_612123.1 136011 D 292414 CDS YP_612124.1 99079970 4078734 complement(136844..137569) 1 NC_008044.1 type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase; orotidine 5'-phosphate decarboxylase 137569 4078734 TM1040_0129 Ruegeria sp. TM1040 orotidine 5'-phosphate decarboxylase YP_612124.1 136844 R 292414 CDS YP_612125.1 99079971 4078735 137814..140432 1 NC_008044.1 PFAM: AAA ATPase, central region: (8e-12) Clp, N terminal: (2.9e-07) ATPase associated with various cellular activities, AAA_5: (2.3e-05) ATPase AAA-2: (4.2e-108); SMART: ATPase: (1.5e-14); KEGG: sil:SPO3276 ATP-dependent Clp protease, ATP-binding subunit ClpB, ev=0.0, 85% identity; ATPase AAA 140432 4078735 TM1040_0130 Ruegeria sp. TM1040 ATPase AAA YP_612125.1 137814 D 292414 CDS YP_612126.1 99079972 4078736 140622..142115 1 NC_008044.1 PFAM: ferredoxin-dependent glutamate synthase: (1.7e-82); KEGG: sil:SPO3272 glutamate synthase family protein, ev=0.0, 68% identity; ferredoxin-dependent glutamate synthase 142115 4078736 TM1040_0131 Ruegeria sp. TM1040 ferredoxin-dependent glutamate synthase YP_612126.1 140622 D 292414 CDS YP_612127.1 99079973 4078737 complement(142088..142489) 1 NC_008044.1 hypothetical protein 142489 4078737 TM1040_0132 Ruegeria sp. TM1040 hypothetical protein YP_612127.1 142088 R 292414 CDS YP_612128.1 99079974 4078738 142784..143686 1 NC_008044.1 in Escherichia coli this periplasmic enzyme was found to encode the periplasmic catalytic subunit of an oxidoreductase; sulfite oxidase activity not demonstrated; requires inner membrane anchor protein YedZ; sulfite oxidase subunit YedY 143686 4078738 TM1040_0133 Ruegeria sp. TM1040 sulfite oxidase subunit YedY YP_612128.1 142784 D 292414 CDS YP_612129.1 99079975 4078739 143686..144285 1 NC_008044.1 in Escherichia coli this inner membrane protein was found to anchor the periplasmic catalytic oxidoreductase YedY; sulfite oxidase activity not demonstrated; contains heme; sulfite oxidase subunit YedZ 144285 4078739 TM1040_0134 Ruegeria sp. TM1040 sulfite oxidase subunit YedZ YP_612129.1 143686 D 292414 CDS YP_612130.1 99079976 4078740 144346..144612 1 NC_008044.1 hypothetical protein 144612 4078740 TM1040_0135 Ruegeria sp. TM1040 hypothetical protein YP_612130.1 144346 D 292414 CDS YP_612131.1 99079977 4078741 complement(150726..151112) 1 NC_008044.1 PFAM: response regulator receiver: (5.3e-09); KEGG: lic:LIC13330 response regulator, ev=4e-13, 32% identity; response regulator receiver protein 151112 4078741 TM1040_0136 Ruegeria sp. TM1040 response regulator receiver protein YP_612131.1 150726 R 292414 CDS YP_612132.1 99079978 4078742 complement(151103..152278) 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (4.7e-28) histidine kinase A-like: (1.1e-09); KEGG: rpa:RPA3016 bacteriophytochrome (light-regulated signal transduction histidine kinase), PhyB2, ev=1e-38, 33% identity; histidine kinase 152278 4078742 TM1040_0137 Ruegeria sp. TM1040 histidine kinase YP_612132.1 151103 R 292414 CDS YP_612133.1 99079979 4078743 complement(152275..152919) 1 NC_008044.1 KEGG: nfa:nfa32140 sigma activity regulating serine phosphatase, ev=9e-11, 25% identity; hypothetical protein 152919 4078743 TM1040_0138 Ruegeria sp. TM1040 hypothetical protein YP_612133.1 152275 R 292414 CDS YP_612134.1 99079980 4078744 complement(152904..153326) 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (9e-08); KEGG: bld:BLi00556 RsbT, ev=3e-32, 55% identity; anti-sigma regulatory factor, serine/threonine protein kinase 153326 4078744 TM1040_0139 Ruegeria sp. TM1040 anti-sigma regulatory factor, serine/threonine protein kinase YP_612134.1 152904 R 292414 CDS YP_612135.1 99079981 4078807 complement(153323..153679) 1 NC_008044.1 PFAM: Sulfate transporter/antisigma-factor antagonist STAS: (3.6e-10); KEGG: mpa:MAP0378c hypothetical protein, ev=1e-24, 54% identity; anti-sigma-factor antagonist 153679 4078807 TM1040_0140 Ruegeria sp. TM1040 anti-sigma-factor antagonist YP_612135.1 153323 R 292414 CDS YP_612136.1 99079982 4078808 complement(153682..154578) 1 NC_008044.1 PFAM: Sulfate transporter/antisigma-factor antagonist STAS: (3.7e-11); KEGG: nfa:nfa32110 sigma activity regulator, ev=4e-31, 40% identity; anti-sigma-factor antagonist 154578 4078808 TM1040_0141 Ruegeria sp. TM1040 anti-sigma-factor antagonist YP_612136.1 153682 R 292414 CDS YP_612137.1 99079983 4078809 complement(154810..156234) 1 NC_008044.1 KEGG: rru:Rru_A0400 hypothetical protein, ev=2e-79, 38% identity; hypothetical protein 156234 4078809 TM1040_0142 Ruegeria sp. TM1040 hypothetical protein YP_612137.1 154810 R 292414 CDS YP_612138.1 99079984 4078810 complement(156335..156646) 1 NC_008044.1 PFAM: ETC complex I subunit conserved region: (1.3e-43); KEGG: sil:SPO0482 NADH-ubiquinone oxidoreductase family protein, ev=8e-46, 84% identity; ETC complex I subunit region 156646 4078810 TM1040_0143 Ruegeria sp. TM1040 ETC complex I subunit region YP_612138.1 156335 R 292414 CDS YP_612139.1 99079985 4078811 156843..159035 1 NC_008044.1 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. The beta-hairpin of the Uvr-B subunit is inserted between the strands, where it probes for the presence of a lesion; excinuclease ABC subunit B 159035 4078811 TM1040_0144 Ruegeria sp. TM1040 excinuclease ABC subunit B YP_612139.1 156843 D 292414 CDS YP_612140.1 99079986 4078812 complement(159057..160424) 1 NC_008044.1 KEGG: zmo:ZMO1485 dGTP triphosphohydrolase, ev=1e-125, 52% identity; TIGRFAM: Deoxyguanosinetriphosphate triphosphohydrolase: (4.8e-99); SMART: Metal-dependent phosphohydrolase, HD region: (1.5e-08); deoxyguanosinetriphosphate triphosphohydrolase 160424 4078812 TM1040_0145 Ruegeria sp. TM1040 deoxyguanosinetriphosphate triphosphohydrolase YP_612140.1 159057 R 292414 CDS YP_612141.1 99079987 4078813 complement(160500..161540) 1 NC_008044.1 PFAM: FAD dependent oxidoreductase: (1.2e-31); KEGG: sil:SPO3552 oxidoreductase, FAD-binding, ev=1e-136, 69% identity; FAD dependent oxidoreductase 161540 4078813 TM1040_0146 Ruegeria sp. TM1040 FAD dependent oxidoreductase YP_612141.1 160500 R 292414 CDS YP_612142.1 99079988 4078814 161599..162282 1 NC_008044.1 PFAM: protein of unknown function DUF752: (2e-97); KEGG: sil:SPO3553 hypothetical protein, ev=7e-95, 73% identity; hypothetical protein 162282 4078814 TM1040_0147 Ruegeria sp. TM1040 hypothetical protein YP_612142.1 161599 D 292414 CDS YP_612143.1 99079989 4078815 162286..163173 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (6.6e-06); KEGG: sil:SPO3554 membrane protein, , ev=1e-118, 69% identity; hypothetical protein 163173 4078815 TM1040_0148 Ruegeria sp. TM1040 hypothetical protein YP_612143.1 162286 D 292414 CDS YP_612144.1 99079990 4078816 complement(163129..165096) 1 NC_008044.1 PFAM: Lytic transglycosylase, catalytic: (4.5e-15) Tetratricopeptide TPR_4: (0.051); KEGG: sil:SPO3555 transglycosylase, Slt family, ev=0.0, 61% identity; lytic transglycosylase, catalytic 165096 4078816 TM1040_0149 Ruegeria sp. TM1040 lytic transglycosylase, catalytic YP_612144.1 163129 R 292414 CDS YP_612145.1 99079991 4078817 165208..166107 1 NC_008044.1 catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate synthase 166107 4078817 TM1040_0150 Ruegeria sp. TM1040 dihydrodipicolinate synthase YP_612145.1 165208 D 292414 CDS YP_612146.1 99079992 4078818 complement(166208..167086) 1 NC_008044.1 PFAM: sigma-70 region 2: (1.8e-16) sigma-70 region 4: (1.4e-06) Sigma-70, region 4 type 2: (2.5e-15); KEGG: rpa:RPA1116 RNA polymerase ECF-type sigma factor, ev=4e-88, 55% identity; ECF subfamily RNA polymerase sigma-24 factor 167086 4078818 TM1040_0151 Ruegeria sp. TM1040 ECF subfamily RNA polymerase sigma-24 factor YP_612146.1 166208 R 292414 CDS YP_612147.1 99079993 4078819 complement(167083..167544) 1 NC_008044.1 TIGRFAM: Alkylhydroperoxidase AhpD core: (6.2e-15); PFAM: Carboxymuconolactone decarboxylase: (4.3e-22); KEGG: rpb:RPB_1807 alkylhydroperoxidase, ev=7e-48, 66% identity; alkylhydroperoxidase 167544 4078819 TM1040_0152 Ruegeria sp. TM1040 alkylhydroperoxidase YP_612147.1 167083 R 292414 CDS YP_612148.1 99079994 4078820 complement(167639..168676) 1 NC_008044.1 PFAM: conserved hypothetical protein 698: (2.7e-71); KEGG: rsp:RSP_4010 conserved hypothetical protein 698, ev=1e-112, 65% identity; hypothetical protein 168676 4078820 TM1040_0153 Ruegeria sp. TM1040 hypothetical protein YP_612148.1 167639 R 292414 CDS YP_612149.1 99079995 4078821 complement(168851..169603) 1 NC_008044.1 KEGG: pub:SAR11_1347 hypothetical protein, ev=5e-25, 27% identity; hypothetical protein 169603 4078821 TM1040_0154 Ruegeria sp. TM1040 hypothetical protein YP_612149.1 168851 R 292414 CDS YP_612150.1 99079996 4078822 complement(169615..171393) 1 NC_008044.1 catalyzes the formation of acetyl phosphate and sulfite from 2-sulfoacetaldehyde; is active when grown on taurine as a sole carbon source; sulfoacetaldehyde acetyltransferase 171393 4078822 TM1040_0155 Ruegeria sp. TM1040 sulfoacetaldehyde acetyltransferase YP_612150.1 169615 R 292414 CDS YP_612151.1 99079997 4078823 complement(171551..173017) 1 NC_008044.1 PFAM: regulatory protein GntR, HTH: (4.6e-18) aminotransferase, class I and II: (2.9e-05); KEGG: sil:SPO3562 transcriptional regulator, ev=0.0, 70% identity; GntR family transcriptional regulator 173017 4078823 TM1040_0156 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_612151.1 171551 R 292414 CDS YP_612152.1 99079998 4078824 173159..173482 1 NC_008044.1 PFAM: regulatory protein, ArsR: (9.8e-07); KEGG: sil:SPO3563 transcriptional regulator, ArsR family, ev=7e-26, 60% identity; ArsR family transcriptional regulator 173482 4078824 TM1040_0157 Ruegeria sp. TM1040 ArsR family transcriptional regulator YP_612152.1 173159 D 292414 CDS YP_612153.1 99079999 4078825 173475..174506 1 NC_008044.1 PFAM: permease: (4e-14); KEGG: sil:SPO3564 permease, , ev=1e-132, 72% identity; permease 174506 4078825 TM1040_0158 Ruegeria sp. TM1040 permease YP_612153.1 173475 D 292414 CDS YP_612154.1 99080000 4078767 complement(174832..176232) 1 NC_008044.1 PFAM: aminotransferase class-III: (4.8e-89); KEGG: sil:SPO0673 taurine--pyruvate aminotransferase, ev=0.0, 87% identity; aminotransferase 176232 4078767 TM1040_0159 Ruegeria sp. TM1040 aminotransferase YP_612154.1 174832 R 292414 CDS YP_612155.1 99080001 4078768 176517..177329 1 NC_008044.1 PFAM: protein of unknown function DUF849: (4.3e-13); KEGG: sil:SPO1400 hypothetical protein, ev=2e-58, 51% identity; hypothetical protein 177329 4078768 TM1040_0160 Ruegeria sp. TM1040 hypothetical protein YP_612155.1 176517 D 292414 CDS YP_612156.1 99080002 4078769 177326..178654 1 NC_008044.1 PFAM: aminotransferase class-III: (1.8e-106); KEGG: sil:SPO1401 aminotransferase, class III, ev=0.0, 75% identity; hypothetical protein 178654 4078769 TM1040_0161 Ruegeria sp. TM1040 hypothetical protein YP_612156.1 177326 D 292414 CDS YP_612157.1 99080003 4078770 178748..179851 1 NC_008044.1 PFAM: aromatic amino acid beta-eliminating lyase/threonine aldolase: (1.7e-121) aminotransferase, class I and II: (2.3e-05); KEGG: jan:Jann_2851 threonine aldolase, ev=1e-113, 63% identity; L-threonine aldolase 179851 4078770 TM1040_0162 Ruegeria sp. TM1040 L-threonine aldolase YP_612157.1 178748 D 292414 CDS YP_612158.1 99080004 4078771 complement(179945..180706) 1 NC_008044.1 KEGG: ret:RHE_CH00424 carboxyphosphonoenolpyruvate phosphonomutase protein, ev=5e-68, 51% identity; carboxyphosphonoenolpyruvate phosphonomutase protein 180706 4078771 TM1040_0163 Ruegeria sp. TM1040 carboxyphosphonoenolpyruvate phosphonomutase protein YP_612158.1 179945 R 292414 CDS YP_612159.1 99080005 4078772 complement(180902..181501) 1 NC_008044.1 involved in a recombinational process of DNA repair, independent of the recBC complex; recombination protein RecR 181501 recR 4078772 recR Ruegeria sp. TM1040 recombination protein RecR YP_612159.1 180902 R 292414 CDS YP_612160.1 99080006 4078773 complement(181645..181989) 1 NC_008044.1 PFAM: conserved hypothetical protein 103: (2.4e-36); KEGG: sil:SPO3570 conserved hypothetical protein TIGR00103, ev=2e-45, 77% identity; hypothetical protein 181989 4078773 TM1040_0165 Ruegeria sp. TM1040 hypothetical protein YP_612160.1 181645 R 292414 CDS YP_612161.1 99080007 4078774 complement(182088..183914) 1 NC_008044.1 catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the tau chain serves as a scaffold to help in the dimerizaton of the alpha,epsilon and theta core complex; the gamma chain seems to interact with the delta and delta' subunits to transfer the beta subunit on the DNA; DNA polymerase III subunits gamma and tau 183914 4078774 TM1040_0166 Ruegeria sp. TM1040 DNA polymerase III subunits gamma and tau YP_612161.1 182088 R 292414 CDS YP_612162.1 99080008 4078775 184138..184677 1 NC_008044.1 PFAM: Dual specificity protein phosphatase: (9.1e-05); KEGG: sil:SPO3548 hypothetical protein, ev=3e-49, 59% identity; protein tyrosine phosphatase / dual specificity protein phosphatase 184677 4078775 TM1040_0167 Ruegeria sp. TM1040 protein tyrosine phosphatase / dual specificity protein phosphatase YP_612162.1 184138 D 292414 CDS YP_612163.1 99080009 4078776 complement(184688..185185) 1 NC_008044.1 KEGG: sil:SPO3547 hypothetical protein, ev=4e-21, 42% identity; hypothetical protein 185185 4078776 TM1040_0168 Ruegeria sp. TM1040 hypothetical protein YP_612163.1 184688 R 292414 CDS YP_612164.1 99080010 4078777 complement(185822..187720) 1 NC_008044.1 PFAM: metallophosphoesterase: (5.6e-14) 5'-Nucleotidase-like: (3.8e-21); KEGG: sil:SPO3542 2',3'-cyclic-nucleotide 2'-phosphodiesterase, , ev=1e-134, 44% identity; 5'-nucleotidase 187720 4078777 TM1040_0169 Ruegeria sp. TM1040 5'-nucleotidase YP_612164.1 185822 R 292414 CDS YP_612165.1 99080011 4078778 187981..188964 1 NC_008044.1 PFAM: NUDIX hydrolase: (5e-25); KEGG: sil:SPO3541 hydrolase, NUDIX family, ev=1e-112, 62% identity; NUDIX hydrolase 188964 4078778 TM1040_0170 Ruegeria sp. TM1040 NUDIX hydrolase YP_612165.1 187981 D 292414 CDS YP_612166.1 99080012 4078779 189050..189517 1 NC_008044.1 KEGG: rsp:RSP_0707 hypothetical protein, ev=1e-16, 33% identity; hypothetical protein 189517 4078779 TM1040_0171 Ruegeria sp. TM1040 hypothetical protein YP_612166.1 189050 D 292414 CDS YP_612167.1 99080013 4078780 189692..191749 1 NC_008044.1 TIGRFAM: GGDEF domain: (3.9e-30); PFAM: GGDEF: (3.5e-34) EAL: (7.4e-110) MHYT: (6.7e-07); KEGG: jan:Jann_4149 diguanylate cyclase/phosphodiesterase, ev=0.0, 55% identity; diguanylate cyclase/phosphodiesterase 191749 4078780 TM1040_0172 Ruegeria sp. TM1040 diguanylate cyclase/phosphodiesterase YP_612167.1 189692 D 292414 CDS YP_612168.1 99080014 4078781 191860..192174 1 NC_008044.1 KEGG: nar:Saro_2759 transposase orfA IS5 family element, ev=5e-43, 79% identity; IS5 family transposase 192174 4078781 TM1040_0173 Ruegeria sp. TM1040 IS5 family transposase YP_612168.1 191860 D 292414 CDS YP_612169.1 99080015 4078782 192195..192584 1 NC_008044.1 PFAM: transposase, IS4: (2.1e-13); KEGG: sil:SPOA0134 ISSpo7, transposase, ev=6e-74, 70% identity; IS4 family transposase 192584 4078782 TM1040_0174 Ruegeria sp. TM1040 IS4 family transposase YP_612169.1 192195 D 292414 CDS YP_612170.1 99080016 4078783 complement(192594..195974) 1 NC_008044.1 KEGG: sil:SPO0670 DNA polymerase III, alpha subunit, , ev=0.0, 80% identity; TIGRFAM: DNA polymerase III, alpha subunit: (4.1e-128); PFAM: nucleic acid binding, OB-fold, tRNA/helicase-type: (2e-11); SMART: Phosphoesterase PHP-like: (1e-07); DNA polymerase III subunit alpha 195974 4078783 TM1040_0175 Ruegeria sp. TM1040 DNA polymerase III subunit alpha YP_612170.1 192594 R 292414 CDS YP_612171.1 99080017 4078784 complement(195974..197275) 1 NC_008044.1 KEGG: sil:SPO0671 hypothetical protein, ev=0.0, 68% identity; hypothetical protein 197275 4078784 TM1040_0176 Ruegeria sp. TM1040 hypothetical protein YP_612171.1 195974 R 292414 CDS YP_612172.1 99080018 4078785 complement(197394..197981) 1 NC_008044.1 KEGG: sil:SPO0672 hypothetical protein, ev=9e-57, 58% identity; hypothetical protein 197981 4078785 TM1040_0177 Ruegeria sp. TM1040 hypothetical protein YP_612172.1 197394 R 292414 CDS YP_612173.1 99080019 4078786 complement(198056..198667) 1 NC_008044.1 PFAM: HMG-I and HMG-Y, DNA-binding: (0.062) regulatory protein, TetR: (4.8e-11); KEGG: rpb:RPB_4262 transcriptional regulator, TetR family, ev=5e-24, 35% identity; TetR family transcriptional regulator 198667 4078786 TM1040_0178 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_612173.1 198056 R 292414 CDS YP_612174.1 99080020 4078411 complement(198664..199296) 1 NC_008044.1 PFAM: metal-dependent phosphohydrolase, HD subdomain: (7.9e-08); KEGG: bja:blr7676 hypothetical protein, ev=2e-34, 36% identity; metal dependent phosphohydrolase 199296 4078411 TM1040_0179 Ruegeria sp. TM1040 metal dependent phosphohydrolase YP_612174.1 198664 R 292414 CDS YP_612175.1 99080021 4078412 complement(199436..200230) 1 NC_008044.1 KEGG: sil:SPOA0439 enoyl-(acyl-carrier-protein) reductase, ev=1e-129, 88% identity; enoyl-ACP reductase 200230 4078412 TM1040_0180 Ruegeria sp. TM1040 enoyl-ACP reductase YP_612175.1 199436 R 292414 CDS YP_612176.1 99080022 4078413 complement(200236..201465) 1 NC_008044.1 PFAM: beta-ketoacyl synthase: (1.6e-58); KEGG: sil:SPOA0440 3-oxoacyl-(acyl-carrier-protein) synthase, ev=0.0, 92% identity; 3-oxoacyl-ACP synthase 201465 4078413 TM1040_0181 Ruegeria sp. TM1040 3-oxoacyl-ACP synthase YP_612176.1 200236 R 292414 CDS YP_612177.1 99080023 4078414 complement(201548..202057) 1 NC_008044.1 catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to 2,3-decenoyl-ACP or 3,4-decenoyl-ACP; 3-hydroxydecanoyl-ACP dehydratase 202057 4078414 TM1040_0182 Ruegeria sp. TM1040 3-hydroxydecanoyl-ACP dehydratase YP_612177.1 201548 R 292414 CDS YP_612178.1 99080024 4078415 202285..202713 1 NC_008044.1 PFAM: ferric-uptake regulator: (8.2e-15); KEGG: sil:SPOA0445 transcriptional regulator, Fur family, ev=5e-61, 81% identity; ferric uptake regulator 202713 4078415 TM1040_0183 Ruegeria sp. TM1040 ferric uptake regulator YP_612178.1 202285 D 292414 CDS YP_612179.1 99080025 4078416 complement(202858..203727) 1 NC_008044.1 KEGG: sil:SPOA0001 hypothetical protein, ev=1e-131, 73% identity; hypothetical protein 203727 4078416 TM1040_0184 Ruegeria sp. TM1040 hypothetical protein YP_612179.1 202858 R 292414 CDS YP_612180.1 99080026 4078417 203892..205214 1 NC_008044.1 catalyzes the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine from N6-(dimethylallyl)adenosine (i(6)A); (dimethylallyl)adenosine tRNA methylthiotransferase 205214 4078417 TM1040_0185 Ruegeria sp. TM1040 (dimethylallyl)adenosine tRNA methylthiotransferase YP_612180.1 203892 D 292414 CDS YP_612181.1 99080027 4078418 205559..206137 1 NC_008044.1 PFAM: OmpA/MotB: (1.3e-14); KEGG: sil:SPOA0004 OmpA family protein, ev=7e-59, 58% identity; OmpA/MotB protein 206137 4078418 TM1040_0186 Ruegeria sp. TM1040 OmpA/MotB protein YP_612181.1 205559 D 292414 CDS YP_612182.1 99080028 4078419 206149..206454 1 NC_008044.1 KEGG: sil:SPOA0005 lipoprotein, , ev=1e-22, 53% identity; lipoprotein 206454 4078419 TM1040_0187 Ruegeria sp. TM1040 lipoprotein YP_612182.1 206149 D 292414 CDS YP_612183.1 99080029 4078420 206670..207686 1 NC_008044.1 PFAM: PhoH-like protein: (8.6e-116); KEGG: sil:SPOA0006 PhoH family protein, ev=1e-141, 76% identity; PhoH-like protein 207686 4078420 TM1040_0188 Ruegeria sp. TM1040 PhoH-like protein YP_612183.1 206670 D 292414 CDS YP_612184.1 99080030 4078421 complement(207790..208269) 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (9.9e-16); KEGG: vvu:VV20941 histone acetyltransferase HPA2, ev=4e-25, 44% identity; N-acetyltransferase GCN5 208269 4078421 TM1040_0189 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_612184.1 207790 R 292414 CDS YP_612185.1 99080031 4078422 208272..208856 1 NC_008044.1 PFAM: protein of unknown function UPF0054: (7.6e-31); KEGG: sil:SPOA0008 conserved hypothetical protein TIGR00043, ev=2e-52, 62% identity; hypothetical protein 208856 4078422 TM1040_0190 Ruegeria sp. TM1040 hypothetical protein YP_612185.1 208272 D 292414 CDS YP_612186.1 99080032 4078423 208879..209781 1 NC_008044.1 PFAM: CBS: (1.3e-22) transporter-associated region: (1.4e-18); KEGG: sil:SPOA0009 hemolysin, , ev=1e-115, 70% identity; hypothetical protein 209781 4078423 TM1040_0191 Ruegeria sp. TM1040 hypothetical protein YP_612186.1 208879 D 292414 CDS YP_612187.1 99080033 4078424 209778..211304 1 NC_008044.1 TIGRFAM: apolipoprotein N-acyltransferase: (6e-83); PFAM: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase: (7e-09); KEGG: sil:SPOA0010 apolipoprotein N-acyltransferase, ev=1e-113, 48% identity; apolipoprotein N-acyltransferase 211304 4078424 TM1040_0192 Ruegeria sp. TM1040 apolipoprotein N-acyltransferase YP_612187.1 209778 D 292414 CDS YP_612188.1 99080034 4078425 211416..212597 1 NC_008044.1 catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase; S-adenosylmethionine synthetase 212597 4078425 TM1040_0193 Ruegeria sp. TM1040 S-adenosylmethionine synthetase YP_612188.1 211416 D 292414 CDS YP_612189.1 99080035 4078426 212764..213438 1 NC_008044.1 KEGG: sil:SPOA0013 hypothetical protein, ev=2e-50, 48% identity; hypothetical protein 213438 4078426 TM1040_0194 Ruegeria sp. TM1040 hypothetical protein YP_612189.1 212764 D 292414 CDS YP_612190.1 99080036 4078427 213570..214337 1 NC_008044.1 tRNA (guanine-N(7)-)-methyltransferase; catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA by transferring the methyl residue from S-adenosyl-L-methionine; tRNA (guanine-N(7)-)-methyltransferase 214337 trmB 4078427 trmB Ruegeria sp. TM1040 tRNA (guanine-N(7)-)-methyltransferase YP_612190.1 213570 D 292414 CDS YP_612191.1 99080037 4078428 complement(214406..215035) 1 NC_008044.1 PFAM: nitroreductase: (9.4e-38); KEGG: ccr:CC1449 nitroreductase family protein, ev=8e-63, 59% identity; nitroreductase 215035 4078428 TM1040_0196 Ruegeria sp. TM1040 nitroreductase YP_612191.1 214406 R 292414 CDS YP_612192.1 99080038 4078429 complement(215228..215839) 1 NC_008044.1 Catalyzes the formation of (d)CDP from ATP and (d)CMP; cytidylate kinase 215839 cmk 4078429 cmk Ruegeria sp. TM1040 cytidylate kinase YP_612192.1 215228 R 292414 CDS YP_612193.1 99080039 4078646 complement(215899..216381) 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (1.4e-11); KEGG: bur:Bcep18194_C7224 GCN5-related N-acetyltransferase, ev=5e-19, 44% identity; N-acetyltransferase GCN5 216381 4078646 TM1040_0198 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_612193.1 215899 R 292414 CDS YP_612194.1 99080040 4078647 complement(216374..217726) 1 NC_008044.1 catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis; 3-phosphoshikimate 1-carboxyvinyltransferase 217726 4078647 TM1040_0199 Ruegeria sp. TM1040 3-phosphoshikimate 1-carboxyvinyltransferase YP_612194.1 216374 R 292414 CDS YP_612195.1 99080041 4078648 218325..220001 1 NC_008044.1 in Escherichia coli this protein is involved in binding to the leader sequence of mRNAs and is itself bound to the 30S subunit; autoregulates expression via a C-terminal domain; in most gram negative organisms this protein is composed of 6 repeats of the S1 domain while in gram positive there are 4 repeats; the S1 nucleic acid-binding domain is found associated with other proteins; 30S ribosomal protein S1 220001 rpsA 4078648 rpsA Ruegeria sp. TM1040 30S ribosomal protein S1 YP_612195.1 218325 D 292414 CDS YP_612196.1 99080042 4078649 complement(220102..220743) 1 NC_008044.1 KEGG: ret:RHE_PF00158 hypothetical protein, ev=2e-72, 59% identity; hypothetical protein 220743 4078649 TM1040_0201 Ruegeria sp. TM1040 hypothetical protein YP_612196.1 220102 R 292414 CDS YP_612197.1 99080043 4078650 221101..221388 1 NC_008044.1 This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control; integration host factor subunit beta 221388 ihfB 4078650 ihfB Ruegeria sp. TM1040 integration host factor subunit beta YP_612197.1 221101 D 292414 CDS YP_612198.1 99080044 4078651 221389..221739 1 NC_008044.1 KEGG: sil:SPO0805 hypothetical protein, ev=6e-37, 66% identity; hypothetical protein 221739 4078651 TM1040_0203 Ruegeria sp. TM1040 hypothetical protein YP_612198.1 221389 D 292414 CDS YP_612199.1 99080045 4078652 221741..222388 1 NC_008044.1 catalyzes the formation of 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate from N-(5-phospho-beta-D-ribosyl)-anthranilate in tryptophan biosynthesis; N-(5'-phosphoribosyl)anthranilate isomerase 222388 4078652 TM1040_0204 Ruegeria sp. TM1040 N-(5'-phosphoribosyl)anthranilate isomerase YP_612199.1 221741 D 292414 CDS YP_612200.1 99080046 4078653 222662..223507 1 NC_008044.1 PFAM: regulatory protein, LysR: (5e-17); KEGG: jan:Jann_2521 transcriptional regulator, LysR family, ev=3e-58, 45% identity; LysR family transcriptional regulator 223507 4078653 TM1040_0205 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_612200.1 222662 D 292414 CDS YP_612201.1 99080047 4078654 223721..224980 1 NC_008044.1 catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate; tryptophan synthase subunit beta 224980 4078654 TM1040_0206 Ruegeria sp. TM1040 tryptophan synthase subunit beta YP_612201.1 223721 D 292414 CDS YP_612202.1 99080048 4078655 complement(225112..225483) 1 NC_008044.1 PFAM: helix-turn-helix, HxlR type: (9.1e-25); KEGG: ppr:PBPRB1657 hypothetical transcriptional regulator, ev=3e-36, 55% identity; HxlR family transcriptional regulator 225483 4078655 TM1040_0207 Ruegeria sp. TM1040 HxlR family transcriptional regulator YP_612202.1 225112 R 292414 CDS YP_612203.1 99080049 4078656 225625..226233 1 NC_008044.1 PFAM: NAD(P)H dehydrogenase (quinone): (7.1e-32); KEGG: dde:Dde_1618 flavodoxin-like fold domain protein, ev=1e-61, 57% identity; NAD(P)H dehydrogenase (quinone) 226233 4078656 TM1040_0208 Ruegeria sp. TM1040 NAD(P)H dehydrogenase (quinone) YP_612203.1 225625 D 292414 CDS YP_612204.1 99080050 4078657 226220..226921 1 NC_008044.1 PFAM: glutathione S-transferase-like: (2.6e-15); KEGG: ppr:PBPRB0681 glutathione S-transferase, ev=8e-52, 49% identity; glutathione S-transferase 226921 4078657 TM1040_0209 Ruegeria sp. TM1040 glutathione S-transferase YP_612204.1 226220 D 292414 CDS YP_612205.1 99080051 4078658 226926..227567 1 NC_008044.1 PFAM: DSBA oxidoreductase: (2.6e-37); KEGG: sil:SPO1390 thioredoxin domain protein, DsbA family, ev=3e-69, 59% identity; DSBA oxidoreductase 227567 4078658 TM1040_0210 Ruegeria sp. TM1040 DSBA oxidoreductase YP_612205.1 226926 D 292414 CDS YP_612206.1 99080052 4078659 227730..228554 1 NC_008044.1 PFAM: penicillin-binding protein, transpeptidase: (5.5e-13); KEGG: mca:MCA2220 beta-lactamase, ev=5e-24, 33% identity; beta-lactamase 228554 4078659 TM1040_0211 Ruegeria sp. TM1040 beta-lactamase YP_612206.1 227730 D 292414 CDS YP_612207.1 99080053 4078660 complement(228609..229106) 1 NC_008044.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase: (1.5e-13); KEGG: rba:RB3840 similar to dioxygenase superfamily, ev=9e-69, 73% identity; glyoxalase/bleomycin resistance protein/dioxygenase 229106 4078660 TM1040_0212 Ruegeria sp. TM1040 glyoxalase/bleomycin resistance protein/dioxygenase YP_612207.1 228609 R 292414 CDS YP_612208.1 99080054 4078661 229195..230097 1 NC_008044.1 PFAM: regulatory protein, LysR: (6.3e-19) LysR, substrate-binding: (6.5e-28); KEGG: vpa:VPA0175 transcriptional regulator, LysR family, ev=1e-52, 36% identity; LysR family transcriptional regulator 230097 4078661 TM1040_0213 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_612208.1 229195 D 292414 CDS YP_612209.1 99080055 4078662 complement(230182..230928) 1 NC_008044.1 Enables the recycling of peptidyl-tRNAs produced at termination of translation; peptidyl-tRNA hydrolase 230928 4078662 TM1040_0214 Ruegeria sp. TM1040 peptidyl-tRNA hydrolase YP_612209.1 230182 R 292414 CDS YP_612210.1 99080056 4078663 231109..231594 1 NC_008044.1 hypothetical protein 231594 4078663 TM1040_0215 Ruegeria sp. TM1040 hypothetical protein YP_612210.1 231109 D 292414 CDS YP_612211.1 99080057 4078664 complement(231708..232337) 1 NC_008044.1 the Ctc family of proteins consists of two types, one that contains the N-terminal ribosomal protein L25 domain only which in Escherichia coli binds the 5S rRNA while a subset of proteins contain a C-terminal extension that is involved in the stress response; 50S ribosomal protein L25 232337 4078664 TM1040_0216 Ruegeria sp. TM1040 50S ribosomal protein L25 YP_612211.1 231708 R 292414 CDS YP_612212.1 99080058 4078665 complement(232430..233146) 1 NC_008044.1 KEGG: jan:Jann_1985 hypothetical protein, ev=2e-32, 40% identity; hypothetical protein 233146 4078665 TM1040_0217 Ruegeria sp. TM1040 hypothetical protein YP_612212.1 232430 R 292414 CDS YP_612213.1 99080059 4076251 233213..234322 1 NC_008044.1 PFAM: major facilitator superfamily MFS_1: (7.2e-18); KEGG: jan:Jann_3597 major facilitator superfamily MFS_1, ev=7e-79, 44% identity; major facilitator superfamily transporter 234322 4076251 TM1040_0218 Ruegeria sp. TM1040 major facilitator superfamily transporter YP_612213.1 233213 D 292414 CDS YP_612214.1 99080060 4076252 complement(234369..235532) 1 NC_008044.1 PFAM: FMN-dependent alpha-hydroxy acid dehydrogenase: (1.1e-168); KEGG: sil:SPO0813 L-lactate dehydrogenase, , ev=0.0, 87% identity; L-lactate dehydrogenase (cytochrome) 235532 4076252 TM1040_0219 Ruegeria sp. TM1040 L-lactate dehydrogenase (cytochrome) YP_612214.1 234369 R 292414 CDS YP_612215.1 99080061 4076253 235564..235827 1 NC_008044.1 hypothetical protein 235827 4076253 TM1040_0220 Ruegeria sp. TM1040 hypothetical protein YP_612215.1 235564 D 292414 CDS YP_612216.1 99080062 4076254 236023..237453 1 NC_008044.1 PFAM: response regulator receiver: (2.7e-25) ATP-binding region, ATPase-like: (3.4e-35) histidine kinase A-like: (5.6e-25); KEGG: ccr:CC3219 sensor histidine kinase/response regulator, ev=5e-75, 39% identity; histidine kinase 237453 4076254 TM1040_0221 Ruegeria sp. TM1040 histidine kinase YP_612216.1 236023 D 292414 CDS YP_612217.2 161899031 4076255 complement(237554..238357) 1 NC_008044.1 catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis; tryptophan synthase subunit alpha 238357 trpA 4076255 trpA Ruegeria sp. TM1040 tryptophan synthase subunit alpha YP_612217.2 237554 R 292414 CDS YP_612218.1 99080064 4076256 complement(238456..238968) 1 NC_008044.1 KEGG: sil:SPO0816 hypothetical protein, ev=6e-28, 40% identity; hypothetical protein 238968 4076256 TM1040_0223 Ruegeria sp. TM1040 hypothetical protein YP_612218.1 238456 R 292414 CDS YP_612219.1 99080065 4076257 239155..240252 1 NC_008044.1 translation-associated GTPase; the crystal structure of the Haemophilus influenzae YchF protein showed similarity to the yeast structure (PDB: 1NI3); fluorescence spectroscopy revealed nucleic acid binding; the yeast protein YBR025c interacts with the translation elongation factor eEF1; GTP-dependent nucleic acid-binding protein EngD 240252 4076257 TM1040_0224 Ruegeria sp. TM1040 GTP-dependent nucleic acid-binding protein EngD YP_612219.1 239155 D 292414 CDS YP_612220.1 99080066 4076258 240406..241329 1 NC_008044.1 PFAM: Inosine/uridine-preferring nucleoside hydrolase: (1e-77); KEGG: hch:HCH_02314 inosine-uridine nucleoside N-ribohydrolase, ev=7e-60, 43% identity; inosine/uridine-preferring nucleoside hydrolase 241329 4076258 TM1040_0225 Ruegeria sp. TM1040 inosine/uridine-preferring nucleoside hydrolase YP_612220.1 240406 D 292414 CDS YP_612221.1 99080067 4076259 241515..241712 1 NC_008044.1 forms a complex with SecY and SecG; SecYEG forms a protein-conducting channel to which secA binds and translocates targeted polypeptides across the cytoplasmic membrane, a process driven by ATP and a proton-motive force; preprotein translocase subunit SecE 241712 secE 4076259 secE Ruegeria sp. TM1040 preprotein translocase subunit SecE YP_612221.1 241515 D 292414 CDS YP_612222.1 99080068 4076260 241908..242441 1 NC_008044.1 KEGG: sil:SPO3516 transcription termination/antitermination factor NusG, ev=2e-85, 87% identity; TIGRFAM: transcription termination/antitermination factor NusG: (9.3e-79); PFAM: transcription antitermination protein NusG: (4.7e-41) KOW: (4.4e-09); SMART: NGN: (3.2e-36) KOW (Kyrpides, Ouzounis, Woese) motif: (2.8e-06); transcription antitermination protein nusG 242441 4076260 TM1040_0227 Ruegeria sp. TM1040 transcription antitermination protein nusG YP_612222.1 241908 D 292414 CDS YP_612223.1 99080069 4076261 242545..243768 1 NC_008044.1 PFAM: glycosyl transferase, group 1: (1.6e-23); KEGG: jan:Jann_4272 glycosyl transferase, group 1, ev=4e-27, 31% identity; group 1 glycosyl transferase 243768 4076261 TM1040_0228 Ruegeria sp. TM1040 group 1 glycosyl transferase YP_612223.1 242545 D 292414 CDS YP_612224.1 99080070 4076262 243929..244354 1 NC_008044.1 binds directly to 23S ribosomal RNA; 50S ribosomal protein L11 244354 rplK 4076262 rplK Ruegeria sp. TM1040 50S ribosomal protein L11 YP_612224.1 243929 D 292414 CDS YP_612225.1 99080071 4076263 244356..245054 1 NC_008044.1 in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA; 50S ribosomal protein L1 245054 rplA 4076263 rplA Ruegeria sp. TM1040 50S ribosomal protein L1 YP_612225.1 244356 D 292414 CDS YP_612226.1 99080072 4076264 245198..246118 1 NC_008044.1 KEGG: sil:SPO3511 hypothetical protein, ev=3e-83, 52% identity; hypothetical protein 246118 4076264 TM1040_0231 Ruegeria sp. TM1040 hypothetical protein YP_612226.1 245198 D 292414 CDS YP_612227.1 99080073 4076265 246441..246959 1 NC_008044.1 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit; 50S ribosomal protein L10 246959 rplJ 4076265 rplJ Ruegeria sp. TM1040 50S ribosomal protein L10 YP_612227.1 246441 D 292414 CDS YP_612228.1 99080074 4076266 247040..247417 1 NC_008044.1 present in two forms; L12 is normal, while L7 is aminoacylated at the N-terminal serine; the only multicopy ribosomal protein; 4:1 ratio of L7/L12 per ribosome; two L12 dimers bind L10; critically important for translation efficiency and fidelity; stimulates GTPase activity of translation factors; 50S ribosomal protein L7/L12 247417 rplL 4076266 rplL Ruegeria sp. TM1040 50S ribosomal protein L7/L12 YP_612228.1 247040 D 292414 CDS YP_612229.1 99080075 4076267 247712..251851 1 NC_008044.1 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates; beta subunit is part of the catalytic core which binds with a sigma factor to produce the holoenzyme; DNA-directed RNA polymerase subunit beta 251851 rpoB 4076267 rpoB Ruegeria sp. TM1040 DNA-directed RNA polymerase subunit beta YP_612229.1 247712 D 292414 CDS YP_612230.1 99080076 4076268 251905..256137 1 NC_008044.1 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Subunit beta' binds to sigma factor allowing it to bind to the -10 region of the promoter; DNA-directed RNA polymerase subunit beta' 256137 4076268 TM1040_0235 Ruegeria sp. TM1040 DNA-directed RNA polymerase subunit beta' YP_612230.1 251905 D 292414 CDS YP_612231.1 99080077 4076269 256298..257110 1 NC_008044.1 KEGG: jan:Jann_0572 hypothetical protein, ev=3e-27, 34% identity; hypothetical protein 257110 4076269 TM1040_0236 Ruegeria sp. TM1040 hypothetical protein YP_612231.1 256298 D 292414 CDS YP_612232.1 99080078 4075997 257154..257993 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (1.8e-05); KEGG: sil:SPO3504 membrane protein, , ev=1e-78, 58% identity; hypothetical protein 257993 4075997 TM1040_0237 Ruegeria sp. TM1040 hypothetical protein YP_612232.1 257154 D 292414 CDS YP_612233.1 99080079 4075998 complement(257972..258856) 1 NC_008044.1 KEGG: sil:SPO3502 hypothetical protein, ev=3e-96, 64% identity; hypothetical protein 258856 4075998 TM1040_0238 Ruegeria sp. TM1040 hypothetical protein YP_612233.1 257972 R 292414 CDS YP_612234.1 99080080 4075999 259113..259484 1 NC_008044.1 interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone; located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side; mutations in the S12 gene confer streptomycin resistance; 30S ribosomal protein S12 259484 rpsL 4075999 rpsL Ruegeria sp. TM1040 30S ribosomal protein S12 YP_612234.1 259113 D 292414 CDS YP_612235.1 99080081 4076000 259503..259973 1 NC_008044.1 binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit; 30S ribosomal protein S7 259973 4076000 TM1040_0240 Ruegeria sp. TM1040 30S ribosomal protein S7 YP_612235.1 259503 D 292414 CDS YP_612236.1 99080082 4076001 259995..262115 1 NC_008044.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene; elongation factor G 262115 4076001 TM1040_0241 Ruegeria sp. TM1040 elongation factor G YP_612236.1 259995 D 292414 CDS YP_612237.1 99080083 4076002 262178..263353 1 NC_008044.1 EF-Tu; promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis; when the tRNA anticodon matches the mRNA codon, GTP hydrolysis results; the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts; many prokaryotes have two copies of the gene encoding EF-Tu; elongation factor Tu 263353 4076002 TM1040_0242 Ruegeria sp. TM1040 elongation factor Tu YP_612237.1 262178 D 292414 CDS YP_612238.1 99080084 4076003 263547..264038 1 NC_008044.1 KEGG: jan:Jann_3603 hypothetical protein, ev=1e-23, 45% identity; hypothetical protein 264038 4076003 TM1040_0243 Ruegeria sp. TM1040 hypothetical protein YP_612238.1 263547 D 292414 CDS YP_612239.1 99080085 4076004 264476..264727 1 NC_008044.1 hypothetical protein 264727 4076004 TM1040_0244 Ruegeria sp. TM1040 hypothetical protein YP_612239.1 264476 D 292414 CDS YP_612240.1 99080086 4076005 264947..265261 1 NC_008044.1 NusE; involved in assembly of the 30S subunit; in the ribosome, this protein is involved in the binding of tRNA; in Escherichia coli this protein was also found to be involved in transcription antitermination; NusB/S10 heterodimers bind boxA sequences in the leader RNA of rrn operons which is required for antitermination; binding of NusB/S10 to boxA nucleates assembly of the antitermination complex; 30S ribosomal protein S10 265261 rpsJ 4076005 rpsJ Ruegeria sp. TM1040 30S ribosomal protein S10 YP_612240.1 264947 D 292414 CDS YP_612241.1 99080087 4076006 265280..265999 1 NC_008044.1 binds directly near the 3' end of the 23S rRNA, where it nucleates assembly of the 50S subunit; essential for peptidyltransferase activity; mutations in this gene confer resistance to tiamulin; 50S ribosomal protein L3 265999 rplC 4076006 rplC Ruegeria sp. TM1040 50S ribosomal protein L3 YP_612241.1 265280 D 292414 CDS YP_612242.1 99080088 4076007 265996..266613 1 NC_008044.1 L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA; 50S ribosomal protein L4 266613 rplD 4076007 rplD Ruegeria sp. TM1040 50S ribosomal protein L4 YP_612242.1 265996 D 292414 CDS YP_612243.1 99080089 4076008 266610..266906 1 NC_008044.1 binds third domain of 23S rRNA and protein L29; part of exit tunnel; 50S ribosomal protein L23 266906 rplW 4076008 rplW Ruegeria sp. TM1040 50S ribosomal protein L23 YP_612243.1 266610 D 292414 CDS YP_612244.1 99080090 4076009 267190..267591 1 NC_008044.1 hypothetical protein 267591 4076009 TM1040_0249 Ruegeria sp. TM1040 hypothetical protein YP_612244.1 267190 D 292414 CDS YP_612245.1 99080091 4076010 267658..268230 1 NC_008044.1 KEGG: mlo:mll6838 hypothetical protein, ev=1e-06, 65% identity; hypothetical protein 268230 4076010 TM1040_0250 Ruegeria sp. TM1040 hypothetical protein YP_612245.1 267658 D 292414 CDS YP_612246.1 99080092 4076011 268431..268688 1 NC_008044.1 hypothetical protein 268688 4076011 TM1040_0251 Ruegeria sp. TM1040 hypothetical protein YP_612246.1 268431 D 292414 CDS YP_612247.1 99080093 4076012 268935..269777 1 NC_008044.1 one of the primary rRNA-binding proteins; required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation; 50S ribosomal protein L2 269777 rplB 4076012 rplB Ruegeria sp. TM1040 50S ribosomal protein L2 YP_612247.1 268935 D 292414 CDS YP_612248.1 99080094 4076013 269781..270059 1 NC_008044.1 protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA; 30S ribosomal protein S19 270059 rpsS 4076013 rpsS Ruegeria sp. TM1040 30S ribosomal protein S19 YP_612248.1 269781 D 292414 CDS YP_612249.1 99080095 4076014 270063..270443 1 NC_008044.1 binds specifically to 23S rRNA during the early stages of 50S assembly; makes contact with all 6 domains of the 23S rRNA in the assembled 50S subunit and ribosome; mutations in this gene result in erythromycin resistance; located near peptidyl-transferase center; 50S ribosomal protein L22 270443 rplV 4076014 rplV Ruegeria sp. TM1040 50S ribosomal protein L22 YP_612249.1 270063 D 292414 CDS YP_612250.1 99080096 4076015 270443..271162 1 NC_008044.1 forms a complex with S10 and S14; binds the lower part of the 30S subunit head and the mRNA in the complete ribosome to position it for translation; 30S ribosomal protein S3 271162 rpsC 4076015 rpsC Ruegeria sp. TM1040 30S ribosomal protein S3 YP_612250.1 270443 D 292414 CDS YP_612251.1 99080097 4076016 271175..271588 1 NC_008044.1 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e; 50S ribosomal protein L16 271588 rplP 4076016 rplP Ruegeria sp. TM1040 50S ribosomal protein L16 YP_612251.1 271175 D 292414 CDS YP_612252.1 99080098 4077665 271848..272147 1 NC_008044.1 hypothetical protein 272147 4077665 TM1040_0257 Ruegeria sp. TM1040 hypothetical protein YP_612252.1 271848 D 292414 CDS YP_612253.1 99080099 4077666 272252..272962 1 NC_008044.1 SMART: extracellular solute-binding protein, family 3: (7.5e-06); KEGG: ret:RHE_CH03027 amino acid ABC transporter, substrate-binding protein, ev=2e-42, 41% identity; extracellular solute-binding protein 272962 4077666 TM1040_0258 Ruegeria sp. TM1040 extracellular solute-binding protein YP_612253.1 272252 D 292414 CDS YP_612254.1 99080100 4077667 273110..273730 1 NC_008044.1 TIGRFAM: conserved hypothetical protein: (2.2e-119); KEGG: sil:SPO0491 hypothetical protein, ev=4e-97, 81% identity; hypothetical protein 273730 4077667 TM1040_0259 Ruegeria sp. TM1040 hypothetical protein YP_612254.1 273110 D 292414 CDS YP_612255.1 99080101 4077668 273804..274844 1 NC_008044.1 PFAM: Succinylglutamate desuccinylase/aspartoacylase: (2.1e-71); KEGG: tcx:Tcr_2062 succinylglutamate desuccinylase/aspartoacylase, ev=2e-91, 53% identity; succinylglutamate desuccinylase/aspartoacylase 274844 4077668 TM1040_0260 Ruegeria sp. TM1040 succinylglutamate desuccinylase/aspartoacylase YP_612255.1 273804 D 292414 CDS YP_612256.1 99080102 4077669 complement(274857..275486) 1 NC_008044.1 KEGG: sil:SPO2022 hypothetical protein, ev=7e-42, 46% identity; hypothetical protein 275486 4077669 TM1040_0261 Ruegeria sp. TM1040 hypothetical protein YP_612256.1 274857 R 292414 CDS YP_612257.1 99080103 4077670 275778..275978 1 NC_008044.1 one of the stabilizing components for the large ribosomal subunit; 50S ribosomal protein L29 275978 4077670 TM1040_0262 Ruegeria sp. TM1040 50S ribosomal protein L29 YP_612257.1 275778 D 292414 CDS YP_612258.1 99080104 4077671 275991..276221 1 NC_008044.1 primary binding protein; helps mediate assembly; involved in translation fidelity; 30S ribosomal protein S17 276221 rpsQ 4077671 rpsQ Ruegeria sp. TM1040 30S ribosomal protein S17 YP_612258.1 275991 D 292414 CDS YP_612259.1 99080105 4077672 276322..276690 1 NC_008044.1 binds to the 23S rRNA between the centers for peptidyl transferase and GTPase; 50S ribosomal protein L14 276690 rplN 4077672 rplN Ruegeria sp. TM1040 50S ribosomal protein L14 YP_612259.1 276322 D 292414 CDS YP_612260.1 99080106 4077673 276690..276995 1 NC_008044.1 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel; 50S ribosomal protein L24 276995 rplX 4077673 rplX Ruegeria sp. TM1040 50S ribosomal protein L24 YP_612260.1 276690 D 292414 CDS YP_612261.1 99080107 4077674 276995..277558 1 NC_008044.1 part of 50S and 5S/L5/L18/L25 subcomplex; contacts 5S rRNA and P site tRNA; forms a bridge to the 30S subunit in the ribosome by binding to S13; 50S ribosomal protein L5 277558 rplE 4077674 rplE Ruegeria sp. TM1040 50S ribosomal protein L5 YP_612261.1 276995 D 292414 CDS YP_612262.1 99080108 4077675 277577..277882 1 NC_008044.1 located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit; similar to what is observed with proteins L31 and L33, some proteins in this family contain CXXC motifs that are involved in zinc binding; if two copies are present in a genome, then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc; the proteins in this group do not appear to have the zinc-binding motif; 30S ribosomal protein S14 277882 rpsN 4077675 rpsN Ruegeria sp. TM1040 30S ribosomal protein S14 YP_612262.1 277577 D 292414 CDS YP_612263.1 99080109 4077676 277895..278287 1 NC_008044.1 binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit; 30S ribosomal protein S8 278287 rpsH 4077676 rpsH Ruegeria sp. TM1040 30S ribosomal protein S8 YP_612263.1 277895 D 292414 CDS YP_612264.1 99080110 4077677 278303..278836 1 NC_008044.1 ribosomal protein L6 appears to have arisen as a result of an ancient gene duplication as based on structural comparison of the Bacillus stearothermophilus protein; RNA-binding appears to be in the C-terminal domain; mutations in the L6 gene confer resistance to aminoglycoside antibiotics such as gentamicin and these occur in truncations of the C-terminal domain; it has been localized to a region between the base of the L7/L12 stalk and the central protuberance; 50S ribosomal protein L6 278836 rplF 4077677 rplF Ruegeria sp. TM1040 50S ribosomal protein L6 YP_612264.1 278303 D 292414 CDS YP_612265.1 99080111 4077678 278848..279207 1 NC_008044.1 binds 5S rRNA along with protein L5 and L25; 50S ribosomal protein L18 279207 rplR 4077678 rplR Ruegeria sp. TM1040 50S ribosomal protein L18 YP_612265.1 278848 D 292414 CDS YP_612266.1 99080112 4077679 279375..279938 1 NC_008044.1 located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body; contacts S4 and S8; with S4 and S12 plays a role in translational accuracy; mutations in this gene result in spectinomycin resistance; 30S ribosomal protein S5 279938 rpsE 4077679 rpsE Ruegeria sp. TM1040 30S ribosomal protein S5 YP_612266.1 279375 D 292414 CDS YP_612267.1 99080113 4077680 279951..280139 1 NC_008044.1 L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7; 50S ribosomal protein L30 280139 rpmD 4077680 rpmD Ruegeria sp. TM1040 50S ribosomal protein L30 YP_612267.1 279951 D 292414 CDS YP_612268.1 99080114 4077681 280364..280579 1 NC_008044.1 PFAM: protein of unknown function DUF1127: (2.1e-05); hypothetical protein 280579 4077681 TM1040_0273 Ruegeria sp. TM1040 hypothetical protein YP_612268.1 280364 D 292414 CDS YP_612269.1 99080115 4077682 281136..281606 1 NC_008044.1 late assembly protein; 50S ribosomal protein L15 281606 rplO 4077682 rplO Ruegeria sp. TM1040 50S ribosomal protein L15 YP_612269.1 281136 D 292414 CDS YP_612270.1 99080116 4077683 281717..283081 1 NC_008044.1 forms heterotrimeric complex in the membrane; in bacteria the complex consists of SecY which forms the channel pore and SecE and SecG; the SecG subunit is not essential; in bacteria translocation is driven via the SecA ATPase; preprotein translocase subunit SecY 283081 secY 4077683 secY Ruegeria sp. TM1040 preprotein translocase subunit SecY YP_612270.1 281717 D 292414 CDS YP_612271.1 99080117 4077411 283078..283659 1 NC_008044.1 essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP; adenylate kinase 283659 adk 4077411 adk Ruegeria sp. TM1040 adenylate kinase YP_612271.1 283078 D 292414 CDS YP_612272.1 99080118 4077412 284068..284436 1 NC_008044.1 located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA; makes contact with the large subunit via RNA-protein interactions and via protein-protein interactions with L5; contacts P-site tRNA; 30S ribosomal protein S13 284436 rpsM 4077412 rpsM Ruegeria sp. TM1040 30S ribosomal protein S13 YP_612272.1 284068 D 292414 CDS YP_612273.1 99080119 4077413 284453..284842 1 NC_008044.1 located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA; forms part of the Shine-Dalgarno cleft in the 70S ribosome; interacts with S7 and S18 and IF-3; 30S ribosomal protein S11 284842 4077413 TM1040_0278 Ruegeria sp. TM1040 30S ribosomal protein S11 YP_612273.1 284453 D 292414 CDS YP_612274.1 99080120 4077414 284956..285972 1 NC_008044.1 catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Dimerization of the alpha subunit is the first step in the sequential assembly of subunits to form the holoenzyme; DNA-directed RNA polymerase subunit alpha 285972 4077414 TM1040_0279 Ruegeria sp. TM1040 DNA-directed RNA polymerase subunit alpha YP_612274.1 284956 D 292414 CDS YP_612275.1 99080121 4077415 286119..286544 1 NC_008044.1 is a component of the macrolide binding site in the peptidyl transferase center; 50S ribosomal protein L17 286544 rplQ 4077415 rplQ Ruegeria sp. TM1040 50S ribosomal protein L17 YP_612275.1 286119 D 292414 CDS YP_612276.1 99080122 4077416 286665..287573 1 NC_008044.1 hypothetical protein 287573 4077416 TM1040_0281 Ruegeria sp. TM1040 hypothetical protein YP_612276.1 286665 D 292414 CDS YP_612277.1 99080123 4077417 complement(287589..287927) 1 NC_008044.1 TIGRFAM: alkylphosphonate utilization operon protein PhnA: (1.2e-46); PFAM: PhnA protein: (3.3e-33); KEGG: sil:SPO2122 alkylphosphonate utilization operon protein PhnA, ev=3e-44, 75% identity; alkylphosphonate utilization protein PhnA 287927 4077417 TM1040_0282 Ruegeria sp. TM1040 alkylphosphonate utilization protein PhnA YP_612277.1 287589 R 292414 CDS YP_612278.1 99080124 4077418 complement(288006..288905) 1 NC_008044.1 PFAM: NAD-dependent epimerase/dehydratase: (6.8e-21) 3-beta hydroxysteroid dehydrogenase/isomerase: (9.7e-07) dTDP-4-dehydrorhamnose reductase: (7e-05) Male sterility-like: (0.0029); KEGG: rba:RB3508 probable UDP-glucose 4-epimerase GalE2, ev=1e-100, 59% identity; NAD-dependent epimerase/dehydratase 288905 4077418 TM1040_0283 Ruegeria sp. TM1040 NAD-dependent epimerase/dehydratase YP_612278.1 288006 R 292414 CDS YP_612279.1 99080125 4077419 289070..289723 1 NC_008044.1 PFAM: protein of unknown function DUF161: (2.1e-17); KEGG: rsp:RSP_0447 hypothetical protein, ev=5e-38, 45% identity; hypothetical protein 289723 4077419 TM1040_0284 Ruegeria sp. TM1040 hypothetical protein YP_612279.1 289070 D 292414 CDS YP_612280.1 99080126 4077420 complement(289710..291107) 1 NC_008044.1 TIGRFAM: MATE efflux family protein: (4e-31); PFAM: multi antimicrobial extrusion protein MatE: (7.4e-20); KEGG: jan:Jann_3634 MATE efflux family protein, ev=1e-164, 66% identity; MATE efflux family protein 291107 4077420 TM1040_0285 Ruegeria sp. TM1040 MATE efflux family protein YP_612280.1 289710 R 292414 CDS YP_612281.1 99080127 4077421 291466..292560 1 NC_008044.1 catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, phenylalanine sensitive; phospho-2-dehydro-3-deoxyheptonate aldolase 292560 4077421 TM1040_0286 Ruegeria sp. TM1040 phospho-2-dehydro-3-deoxyheptonate aldolase YP_612281.1 291466 D 292414 CDS YP_612282.1 99080128 4077422 292758..294155 1 NC_008044.1 KEGG: sil:SPO0514 periplasmic serine protease, DO/DeqQ family, ev=1e-169, 65% identity; TIGRFAM: Peptidase S1C, Do: (2.5e-145); PFAM: peptidase S1 and S6, chymotrypsin/Hap: (3.1e-10); SMART: PDZ/DHR/GLGF: (0.00042); peptidase S1C, Do 294155 4077422 TM1040_0287 Ruegeria sp. TM1040 peptidase S1C, Do YP_612282.1 292758 D 292414 CDS YP_612283.1 99080129 4077423 294157..295488 1 NC_008044.1 PFAM: AAA ATPase, central region: (8.4e-17) ATPase associated with various cellular activities, AAA_5: (0.00031); SMART: ATPase: (5.1e-14); KEGG: sil:SPO0515 ATPase, AAA family, ev=0.0, 82% identity; recombination factor protein RarA 295488 4077423 TM1040_0288 Ruegeria sp. TM1040 recombination factor protein RarA YP_612283.1 294157 D 292414 CDS YP_612284.1 99080130 4077424 complement(295557..296987) 1 NC_008044.1 PFAM: multicopper oxidase, type 1: (0.0033) multicopper oxidase, type 2: (5.9e-22) multicopper oxidase, type 3: (1.5e-47); KEGG: sil:SPOA0360 multicopper oxidase, , ev=1e-134, 52% identity; multicopper oxidase, type 3 296987 4077424 TM1040_0289 Ruegeria sp. TM1040 multicopper oxidase, type 3 YP_612284.1 295557 R 292414 CDS YP_612285.1 99080131 4077425 297078..297542 1 NC_008044.1 PFAM: Camphor resistance CrcB protein: (2.7e-23); KEGG: rsp:RSP_1744 CrcB-like protein, ev=7e-35, 62% identity; camphor resistance protein CrcB 297542 4077425 TM1040_0290 Ruegeria sp. TM1040 camphor resistance protein CrcB YP_612285.1 297078 D 292414 CDS YP_612286.1 99080132 4077426 297539..298585 1 NC_008044.1 TIGRFAM: Pseudouridine synthase, RluD: (1.8e-70); PFAM: RNA-binding S4: (2.3e-06) pseudouridine synthase: (3e-41); KEGG: sil:SPO0516 ribosomal large subunit pseudouridine synthase C, ev=1e-159, 77% identity; ribosomal large subunit pseudouridine synthase C 298585 4077426 TM1040_0291 Ruegeria sp. TM1040 ribosomal large subunit pseudouridine synthase C YP_612286.1 297539 D 292414 CDS YP_612287.1 99080133 4077427 298582..299250 1 NC_008044.1 TIGRFAM: HAD-superfamily hydrolase subfamily IA, variant 3: (1.5e-05) HAD-superfamily hydrolase, subfamily IA, variant 1: (3e-06); PFAM: Haloacid dehalogenase-like hydrolase: (1.2e-27); KEGG: sil:SPO0517 HAD-superfamily hydrolase, subfamily IA, variant 1, ev=2e-71, 63% identity; HAD family hydrolase 299250 4077427 TM1040_0292 Ruegeria sp. TM1040 HAD family hydrolase YP_612287.1 298582 D 292414 CDS YP_612288.1 99080134 4077428 299318..300022 1 NC_008044.1 PFAM: ATP12 ATPase: (9.3e-53); KEGG: sil:SPO0518 hypothetical protein, ev=1e-87, 66% identity; ATP12 ATPase 300022 4077428 TM1040_0293 Ruegeria sp. TM1040 ATP12 ATPase YP_612288.1 299318 D 292414 CDS YP_612289.1 99080135 4077429 300335..301351 1 NC_008044.1 TIGRFAM: Lysine-arginine-ornithine-binding periplasmic protein: (1.7e-107); SMART: extracellular solute-binding protein, family 3: (1e-59); KEGG: sil:SPO0519 glutamate/glutamine/aspartate/asparagine ABC transporter, periplasmic substrate-binding protein, ev=1e-170, 84% identity; lysine-arginine-ornithine-binding periplasmic protein 301351 4077429 TM1040_0294 Ruegeria sp. TM1040 lysine-arginine-ornithine-binding periplasmic protein YP_612289.1 300335 D 292414 CDS YP_612290.1 99080136 4077430 301493..302761 1 NC_008044.1 TIGRFAM: Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine: (5.5e-07); PFAM: binding-protein-dependent transport systems inner membrane component: (1.3e-13); KEGG: sil:SPO0520 glutamate/glutamine/aspartate/asparagine ABC transporter, permease protein, ev=0.0, 77% identity; amino acid ABC transporter permease 302761 4077430 TM1040_0295 Ruegeria sp. TM1040 amino acid ABC transporter permease YP_612290.1 301493 D 292414 CDS YP_612291.1 99080137 4077119 302763..304091 1 NC_008044.1 TIGRFAM: Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine: (9.1e-09); PFAM: binding-protein-dependent transport systems inner membrane component: (1.7e-12); KEGG: sil:SPO0521 glutamate/glutamine/aspartate/asparagine ABC transporter, permease protein, ev=0.0, 73% identity; amino acid ABC transporter permease 304091 4077119 TM1040_0296 Ruegeria sp. TM1040 amino acid ABC transporter permease YP_612291.1 302763 D 292414 CDS YP_612292.1 99080138 4077120 304104..304895 1 NC_008044.1 PFAM: ABC transporter related: (2e-65); SMART: ATPase: (3.2e-16); KEGG: sil:SPO0522 glutamate/glutamine/aspartate/asparagine ABC transporter, ATP-binding protein, ev=1e-142, 96% identity; ABC transporter 304895 4077120 TM1040_0297 Ruegeria sp. TM1040 ABC transporter YP_612292.1 304104 D 292414 CDS YP_612293.1 99080139 4077121 complement(305059..305484) 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (3.5e-16) FR47-like: (0.00023); KEGG: rba:RB9493 probable acetyltransferase, ev=1e-27, 46% identity; N-acetyltransferase GCN5 305484 4077121 TM1040_0298 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_612293.1 305059 R 292414 CDS YP_612294.1 99080140 4077122 complement(305689..306186) 1 NC_008044.1 PFAM: Phosphoglycerate mutase: (1e-10); KEGG: sil:SPO0523 phosphoglycerate mutase family protein, ev=2e-38, 51% identity; phosphohistidine phosphatase, SixA 306186 4077122 TM1040_0299 Ruegeria sp. TM1040 phosphohistidine phosphatase, SixA YP_612294.1 305689 R 292414 CDS YP_612295.1 99080141 4077123 complement(306183..306878) 1 NC_008044.1 KEGG: sil:SPO0524 hypothetical protein, ev=3e-49, 49% identity; hypothetical protein 306878 4077123 TM1040_0300 Ruegeria sp. TM1040 hypothetical protein YP_612295.1 306183 R 292414 CDS YP_612296.1 99080142 4077124 complement(307007..307867) 1 NC_008044.1 catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate; acetylglutamate kinase 307867 4077124 TM1040_0301 Ruegeria sp. TM1040 acetylglutamate kinase YP_612296.1 307007 R 292414 CDS YP_612297.1 99080143 4077125 308089..308820 1 NC_008044.1 PFAM: NAD-dependent epimerase/dehydratase: (4.3e-05) short-chain dehydrogenase/reductase SDR: (4.7e-18); KEGG: sil:SPO0527 oxidoreductase, short chain dehydrogenase/reductase family, ev=1e-113, 84% identity; short-chain dehydrogenase/reductase SDR 308820 4077125 TM1040_0302 Ruegeria sp. TM1040 short-chain dehydrogenase/reductase SDR YP_612297.1 308089 D 292414 CDS YP_612298.1 99080144 4077126 complement(308867..310279) 1 NC_008044.1 PFAM: Propeptide, PepSY amd peptidase M4: (0.024) PepSY-associated TM helix: (0.003); KEGG: sil:SPO0528 membrane protein, , ev=0.0, 69% identity; PepSY-associated TM helix family protein 310279 4077126 TM1040_0303 Ruegeria sp. TM1040 PepSY-associated TM helix family protein YP_612298.1 308867 R 292414 CDS YP_612299.1 99080145 4077127 complement(310348..310680) 1 NC_008044.1 KEGG: sil:SPO0529 hypothetical protein, ev=5e-18, 40% identity; hypothetical protein 310680 4077127 TM1040_0304 Ruegeria sp. TM1040 hypothetical protein YP_612299.1 310348 R 292414 CDS YP_612300.1 99080146 4077128 complement(310715..311365) 1 NC_008044.1 binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential; ribosome biogenesis GTP-binding protein YsxC 311365 engB 4077128 engB Ruegeria sp. TM1040 ribosome biogenesis GTP-binding protein YsxC YP_612300.1 310715 R 292414 CDS YP_612301.1 99080147 4077129 complement(311365..312102) 1 NC_008044.1 PFAM: MOSC: (2.2e-17); KEGG: jan:Jann_0636 MOSC, ev=4e-72, 53% identity; MOSC domain-containing protein 312102 4077129 TM1040_0306 Ruegeria sp. TM1040 MOSC domain-containing protein YP_612301.1 311365 R 292414 CDS YP_612302.1 99080148 4077130 complement(312099..313925) 1 NC_008044.1 functions to insert inner membrane proteins into the IM in Escherichia coli; interacts with transmembrane segments; functions in both Sec-dependent and -independent membrane insertion; similar to Oxa1p in mitochondria; inner membrane protein translocase component YidC 313925 4077130 TM1040_0307 Ruegeria sp. TM1040 inner membrane protein translocase component YidC YP_612302.1 312099 R 292414 CDS YP_612303.1 99080149 4077131 complement(314351..315850) 1 NC_008044.1 TIGRFAM: GGDEF domain: (4.3e-12); PFAM: GGDEF: (7.8e-09) EAL: (5e-80); KEGG: sil:SPO0533 diguanylate cyclase, , ev=1e-179, 61% identity; diguanylate cyclase/phosphodiesterase 315850 4077131 TM1040_0308 Ruegeria sp. TM1040 diguanylate cyclase/phosphodiesterase YP_612303.1 314351 R 292414 CDS YP_612304.1 99080150 4077132 complement(315963..316850) 1 NC_008044.1 TtcA; YdaO; catalyzes the thiolation of cytosine 32 in specific tRNAs; C32 tRNA thiolase 316850 4077132 TM1040_0309 Ruegeria sp. TM1040 C32 tRNA thiolase YP_612304.1 315963 R 292414 CDS YP_612305.1 99080151 4077133 316985..317530 1 NC_008044.1 KEGG: jan:Jann_0639 hypothetical protein, ev=2e-56, 63% identity; hypothetical protein 317530 4077133 TM1040_0310 Ruegeria sp. TM1040 hypothetical protein YP_612305.1 316985 D 292414 CDS YP_612306.1 99080152 4077134 complement(317527..317787) 1 NC_008044.1 PFAM: protein of unknown function DUF37: (4e-26); KEGG: rsp:RSP_1061 hypothetical protein, ev=9e-31, 75% identity; hypothetical protein 317787 4077134 TM1040_0311 Ruegeria sp. TM1040 hypothetical protein YP_612306.1 317527 R 292414 CDS YP_612307.1 99080153 4077135 complement(317986..318423) 1 NC_008044.1 TIGRFAM: ribonuclease P protein component: (4.9e-12); PFAM: ribonuclease P protein: (7.3e-13); KEGG: sil:SPO0537 ribonuclease P protein component, ev=1e-36, 59% identity; ribonuclease P protein component 318423 4077135 TM1040_0312 Ruegeria sp. TM1040 ribonuclease P protein component YP_612307.1 317986 R 292414 CDS YP_612308.1 99080154 4077136 complement(318476..318610) 1 NC_008044.1 in Escherichia coli transcription of this gene is enhanced by polyamines; 50S ribosomal protein L34 318610 rpmH 4077136 rpmH Ruegeria sp. TM1040 50S ribosomal protein L34 YP_612308.1 318476 R 292414 CDS YP_612309.1 99080155 4077137 319077..319814 1 NC_008044.1 KEGG: sil:SPO0539 membrane protein, , ev=2e-85, 68% identity; hypothetical protein 319814 4077137 TM1040_0314 Ruegeria sp. TM1040 hypothetical protein YP_612309.1 319077 D 292414 CDS YP_612310.1 99080156 4076211 319818..321233 1 NC_008044.1 PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase: (3.2e-22) glucose-inhibited division protein A: (0.0015) pyridine nucleotide-disulphide oxidoreductase dimerisation region: (1.6e-33) HI0933-like protein: (0.0018) FAD dependent oxidoreductase: (0.00026); KEGG: sil:SPO0540 mercuric reductase, , ev=0.0, 68% identity; pyridine nucleotide-disulfide oxidoreductase dimerisation region 321233 4076211 TM1040_0315 Ruegeria sp. TM1040 pyridine nucleotide-disulfide oxidoreductase dimerisation region YP_612310.1 319818 D 292414 CDS YP_612311.1 99080157 4076212 321251..322636 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (1e-30) histidine kinase, HAMP region: (0.00066) histidine kinase A-like: (2.3e-07); KEGG: sil:SPO0541 sensor histidine kinase, ev=1e-177, 71% identity; sensor signal transduction histidine kinase 322636 4076212 TM1040_0316 Ruegeria sp. TM1040 sensor signal transduction histidine kinase YP_612311.1 321251 D 292414 CDS YP_612312.1 99080158 4076213 323531..324073 1 NC_008044.1 hypothetical protein 324073 4076213 TM1040_0317 Ruegeria sp. TM1040 hypothetical protein YP_612312.1 323531 D 292414 CDS YP_612313.1 99080159 4076214 324245..324664 1 NC_008044.1 hypothetical protein 324664 4076214 TM1040_0318 Ruegeria sp. TM1040 hypothetical protein YP_612313.1 324245 D 292414 CDS YP_612314.1 99080160 4076215 324863..325447 1 NC_008044.1 PFAM: regulatory protein, TetR: (0.0011); KEGG: rba:RB13253 probable TetR-family transcriptional regulator, ev=3e-27, 34% identity; TetR family transcriptional regulator 325447 4076215 TM1040_0319 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_612314.1 324863 D 292414 CDS YP_612315.1 99080161 4076216 325584..326150 1 NC_008044.1 PFAM: Carboxymuconolactone decarboxylase: (3.5e-05); KEGG: par:Psyc_1394 hypothetical protein, ev=3e-53, 53% identity; carboxymuconolactone decarboxylase 326150 4076216 TM1040_0320 Ruegeria sp. TM1040 carboxymuconolactone decarboxylase YP_612315.1 325584 D 292414 CDS YP_612316.1 99080162 4076217 326224..326781 1 NC_008044.1 PFAM: Redoxin: (4e-05); KEGG: mca:MCA2020 hypothetical protein, ev=3e-51, 56% identity; redoxin 326781 4076217 TM1040_0321 Ruegeria sp. TM1040 redoxin YP_612316.1 326224 D 292414 CDS YP_612317.1 99080163 4076218 complement(326868..327740) 1 NC_008044.1 PFAM: regulatory protein, LysR: (3.9e-16) LysR, substrate-binding: (7.6e-29); KEGG: sme:SMa2287 LysR-family transcriptional regulator, ev=5e-46, 41% identity; LysR family transcriptional regulator 327740 4076218 TM1040_0322 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_612317.1 326868 R 292414 CDS YP_612318.1 99080164 4076219 327846..328961 1 NC_008044.1 TIGRFAM: Twin-arginine translocation pathway signal: (0.12); KEGG: mlo:mll0236 probable binding protein component of ABC transporter, ev=1e-39, 30% identity; twin-arginine translocation pathway signal 328961 4076219 TM1040_0323 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_612318.1 327846 D 292414 CDS YP_612319.1 99080165 4076220 329049..329936 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (0.0052); KEGG: sme:SMc01633 permease ABC transporter protein, ev=9e-30, 29% identity; binding-protein-dependent transport system inner membrane protein 329936 4076220 TM1040_0324 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_612319.1 329049 D 292414 CDS YP_612320.1 99080166 4076221 329940..330761 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (2.5e-06); KEGG: mlo:mll1739 permease protein of polyamine ABC transporter, ev=6e-38, 35% identity; binding-protein-dependent transport system inner membrane protein 330761 4076221 TM1040_0325 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_612320.1 329940 D 292414 CDS YP_612321.1 99080167 4076222 330758..331876 1 NC_008044.1 PFAM: ABC transporter related: (7.6e-62) TOBE: (9.3e-05) Transport-associated OB: (2.2e-12); SMART: ATPase: (8.6e-20); KEGG: mlo:mll8445 ABC-transporter ATP-binding protein, ev=2e-72, 41% identity; ABC transporter 331876 4076222 TM1040_0326 Ruegeria sp. TM1040 ABC transporter YP_612321.1 330758 D 292414 CDS YP_612322.1 99080168 4076223 331873..333141 1 NC_008044.1 PFAM: Amidase: (4e-65); KEGG: pst:PSPTO4204 amidase family protein, ev=2e-73, 41% identity; amidase 333141 4076223 TM1040_0327 Ruegeria sp. TM1040 amidase YP_612322.1 331873 D 292414 CDS YP_612323.1 99080169 4076224 333138..334046 1 NC_008044.1 PFAM: polysaccharide deacetylase: (5.1e-14); KEGG: sme:SMb21100 saccharide deacetylase, slightly similar to NodB protein, ev=4e-40, 35% identity; polysaccharide deacetylase 334046 4076224 TM1040_0328 Ruegeria sp. TM1040 polysaccharide deacetylase YP_612323.1 333138 D 292414 CDS YP_612324.1 99080170 4076225 334033..334734 1 NC_008044.1 KEGG: rsp:RSP_3746 hypothetical protein, ev=7e-37, 39% identity; hypothetical protein 334734 4076225 TM1040_0329 Ruegeria sp. TM1040 hypothetical protein YP_612324.1 334033 D 292414 CDS YP_612325.1 99080171 4076226 complement(334809..335477) 1 NC_008044.1 PFAM: NAD(P)H dehydrogenase (quinone): (7.2e-20); KEGG: ilo:IL1610 acyl carrier protein phosphodiesterase, ev=7e-46, 44% identity; ACP phosphodiesterase 335477 4076226 TM1040_0330 Ruegeria sp. TM1040 ACP phosphodiesterase YP_612325.1 334809 R 292414 CDS YP_612326.1 99080172 4076227 335647..336549 1 NC_008044.1 PFAM: regulatory protein, LysR: (1e-15) LysR, substrate-binding: (2.9e-26); KEGG: sme:SMa0179 transcriptional activator, ev=2e-40, 38% identity; LysR family transcriptional regulator 336549 4076227 TM1040_0331 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_612326.1 335647 D 292414 CDS YP_612327.1 99080173 4076228 complement(336588..337442) 1 NC_008044.1 PFAM: regulatory protein, LysR: (1.6e-20) LysR, substrate-binding: (0.00013); KEGG: mlo:mlr1441 transcriptional activator protein AmpR, ev=8e-42, 42% identity; LysR family transcriptional regulator 337442 4076228 TM1040_0332 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_612327.1 336588 R 292414 CDS YP_612328.1 99080174 4076229 337542..338690 1 NC_008044.1 PFAM: Taurine catabolism dioxygenase TauD/TfdA: (1.3e-32); KEGG: sil:SPO3380 gamma-butyrobetaine hydroxylase, , ev=1e-132, 63% identity; gamma-butyrobetaine,2-oxoglutarate dioxygenase 338690 4076229 TM1040_0333 Ruegeria sp. TM1040 gamma-butyrobetaine,2-oxoglutarate dioxygenase YP_612328.1 337542 D 292414 CDS YP_612329.1 99080175 4076230 338687..339277 1 NC_008044.1 KEGG: sil:SPO3381 hypothetical protein, ev=3e-81, 76% identity; hypothetical protein 339277 4076230 TM1040_0334 Ruegeria sp. TM1040 hypothetical protein YP_612329.1 338687 D 292414 CDS YP_612330.1 99080176 4076036 complement(339509..339937) 1 NC_008044.1 KEGG: ppu:PP2202 hypothetical protein, ev=1e-45, 63% identity; hypothetical protein 339937 4076036 TM1040_0335 Ruegeria sp. TM1040 hypothetical protein YP_612330.1 339509 R 292414 CDS YP_612331.1 99080177 4076037 complement(339939..341264) 1 NC_008044.1 PFAM: major facilitator superfamily MFS_1: (4.3e-24); KEGG: sme:SMa1641 probable NreB protein, ev=1e-153, 62% identity; major facilitator superfamily transporter 341264 4076037 TM1040_0336 Ruegeria sp. TM1040 major facilitator superfamily transporter YP_612331.1 339939 R 292414 CDS YP_612332.1 99080178 4076038 341517..341957 1 NC_008044.1 catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis; 3-dehydroquinate dehydratase 341957 4076038 TM1040_0337 Ruegeria sp. TM1040 3-dehydroquinate dehydratase YP_612332.1 341517 D 292414 CDS YP_612333.1 99080179 4076039 342242..343732 1 NC_008044.1 TIGRFAM: NCS1 nucleoside transporter family: (3.3e-126); PFAM: permease for cytosine/purines, uracil, thiamine, allantoin: (2e-121); KEGG: rso:RSc1233 probable transporter transmembrane protein, ev=1e-152, 56% identity; NCS1 nucleoside transporter 343732 4076039 TM1040_0338 Ruegeria sp. TM1040 NCS1 nucleoside transporter YP_612333.1 342242 D 292414 CDS YP_612334.1 99080180 4076040 343924..344769 1 NC_008044.1 KEGG: sco:SCO5273 hypothetical protein, ev=2e-06, 26% identity; hypothetical protein 344769 4076040 TM1040_0339 Ruegeria sp. TM1040 hypothetical protein YP_612334.1 343924 D 292414 CDS YP_612335.1 99080181 4076041 344893..345972 1 NC_008044.1 PFAM: Peptidoglycan-binding LysM: (0.0037); KEGG: sil:SPO1062 LysM domain protein, ev=3e-38, 32% identity; peptidoglycan-binding LysM 345972 4076041 TM1040_0340 Ruegeria sp. TM1040 peptidoglycan-binding LysM YP_612335.1 344893 D 292414 CDS YP_612336.1 99080182 4076042 345984..347057 1 NC_008044.1 KEGG: sil:SPO1060 hypothetical protein, ev=2e-31, 33% identity; hypothetical protein 347057 4076042 TM1040_0341 Ruegeria sp. TM1040 hypothetical protein YP_612336.1 345984 D 292414 CDS YP_612337.1 99080183 4076043 347255..349738 1 NC_008044.1 PFAM: response regulator receiver: (1.3e-33) ATP-binding region, ATPase-like: (3.5e-39) histidine kinase A-like: (2e-27) CHASE: (3.1e-27) PAS fold-3: (4.2e-11) PAS fold-4: (2.1e-13) PAS fold: (2.8e-14); SMART: PAS: (6.5e-09) PAC motif: (3.9e-10); KEGG: sil:SPO0094 sensory box sensor histidine kinase/response regulator, ev=1e-146, 48% identity; multi-sensor hybrid histidine kinase 349738 4076043 TM1040_0342 Ruegeria sp. TM1040 multi-sensor hybrid histidine kinase YP_612337.1 347255 D 292414 CDS YP_612338.1 99080184 4076044 complement(349883..350665) 1 NC_008044.1 with HmuTU is involved in the transport of hemin; hemin importer ATP-binding subunit 350665 hmuV 4076044 hmuV Ruegeria sp. TM1040 hemin importer ATP-binding subunit YP_612338.1 349883 R 292414 CDS YP_612339.1 99080185 4076045 complement(350662..351750) 1 NC_008044.1 PFAM: transport system permease protein: (3.1e-108); KEGG: jan:Jann_2135 transport system permease protein, ev=1e-122, 66% identity; transport system permease 351750 4076045 TM1040_0344 Ruegeria sp. TM1040 transport system permease YP_612339.1 350662 R 292414 CDS YP_612340.1 99080186 4076046 complement(351754..352602) 1 NC_008044.1 PFAM: periplasmic binding protein: (1.4e-24); KEGG: jan:Jann_2134 periplasmic binding protein, ev=3e-79, 58% identity; periplasmic binding protein 352602 4076046 TM1040_0345 Ruegeria sp. TM1040 periplasmic binding protein YP_612340.1 351754 R 292414 CDS YP_612341.1 99080187 4076047 complement(352602..353681) 1 NC_008044.1 PFAM: Haemin-degrading: (1.8e-106); KEGG: jan:Jann_2133 Haemin-degrading, ev=2e-99, 54% identity; hemin-degrading protein 353681 4076047 TM1040_0346 Ruegeria sp. TM1040 hemin-degrading protein YP_612341.1 352602 R 292414 CDS YP_612342.1 99080188 4076048 353932..355944 1 NC_008044.1 PFAM: TonB-dependent receptor: (4.9e-14) TonB-dependent receptor, plug: (1.8e-18); KEGG: jan:Jann_2132 TonB-dependent haem/haemoglobin receptor, ev=4e-66, 31% identity; TonB-dependent receptor, plug 355944 4076048 TM1040_0347 Ruegeria sp. TM1040 TonB-dependent receptor, plug YP_612342.1 353932 D 292414 CDS YP_612343.1 99080189 4076049 355964..356425 1 NC_008044.1 KEGG: jan:Jann_2131 hypothetical protein, ev=2e-23, 47% identity; hypothetical protein 356425 4076049 TM1040_0348 Ruegeria sp. TM1040 hypothetical protein YP_612343.1 355964 D 292414 CDS YP_612344.1 99080190 4076050 356422..357102 1 NC_008044.1 PFAM: MotA/TolQ/ExbB proton channel: (8.3e-16); KEGG: jan:Jann_2130 MotA/TolQ/ExbB proton channel, ev=5e-43, 45% identity; MotA/TolQ/ExbB proton channel 357102 4076050 TM1040_0349 Ruegeria sp. TM1040 MotA/TolQ/ExbB proton channel YP_612344.1 356422 D 292414 CDS YP_612345.1 99080191 4076051 357102..357494 1 NC_008044.1 KEGG: jan:Jann_2129 biopolymer transport protein ExbD/TolR, ev=2e-25, 51% identity; biopolymer transport protein ExbD/TolR 357494 4076051 TM1040_0350 Ruegeria sp. TM1040 biopolymer transport protein ExbD/TolR YP_612345.1 357102 D 292414 CDS YP_612346.1 99080192 4076052 357498..357893 1 NC_008044.1 KEGG: jan:Jann_2128 hypothetical protein, ev=1e-26, 50% identity; hypothetical protein 357893 4076052 TM1040_0351 Ruegeria sp. TM1040 hypothetical protein YP_612346.1 357498 D 292414 CDS YP_612347.1 99080193 4076053 357890..358804 1 NC_008044.1 TIGRFAM: TonB-like: (7e-10); KEGG: jan:Jann_2127 TonB-like, ev=3e-40, 37% identity; TonB-like protein 358804 4076053 TM1040_0352 Ruegeria sp. TM1040 TonB-like protein YP_612347.1 357890 D 292414 CDS YP_612348.1 99080194 4076054 complement(358801..359538) 1 NC_008044.1 KEGG: sil:SPOA0416 hypothetical protein, ev=5e-90, 66% identity; hypothetical protein 359538 4076054 TM1040_0353 Ruegeria sp. TM1040 hypothetical protein YP_612348.1 358801 R 292414 CDS YP_612349.1 99080195 4077684 complement(359541..360473) 1 NC_008044.1 PFAM: regulatory protein, LysR: (1e-18) LysR, substrate-binding: (2.1e-37); KEGG: jan:Jann_1407 transcriptional regulator, LysR family, ev=1e-113, 66% identity; LysR family transcriptional regulator 360473 4077684 TM1040_0354 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_612349.1 359541 R 292414 CDS YP_612350.1 99080196 4077685 360576..361823 1 NC_008044.1 PFAM: FAD dependent oxidoreductase: (2.1e-63); KEGG: jan:Jann_1410 D-amino-acid dehydrogenase, ev=1e-151, 61% identity; D-amino-acid dehydrogenase 361823 4077685 TM1040_0355 Ruegeria sp. TM1040 D-amino-acid dehydrogenase YP_612350.1 360576 D 292414 CDS YP_612351.1 99080197 4077686 361863..362840 1 NC_008044.1 PFAM: TRAP dicarboxylate transporter- DctP subunit: (1.7e-22); KEGG: sil:SPO3665 bacterial extracellular solute-binding protein, family 7, ev=5e-97, 54% identity; TRAP dicarboxylate transporter- DctP subunit 362840 4077686 TM1040_0356 Ruegeria sp. TM1040 TRAP dicarboxylate transporter- DctP subunit YP_612351.1 361863 D 292414 CDS YP_612352.1 99080198 4077687 363053..363667 1 NC_008044.1 KEGG: sil:SPO3664 hypothetical protein, ev=8e-25, 38% identity; hypothetical protein 363667 4077687 TM1040_0357 Ruegeria sp. TM1040 hypothetical protein YP_612352.1 363053 D 292414 CDS YP_612353.1 99080199 4077688 363664..364962 1 NC_008044.1 TIGRFAM: TRAP dicarboxylate transporter- DctM subunit: (4.2e-116); PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit: (2.7e-66); KEGG: sil:SPO3663 TRAP dicarboxylate family transporter, DctM subunit, ev=0.0, 73% identity; TRAP dicarboxylate transporter- DctM subunit 364962 4077688 TM1040_0358 Ruegeria sp. TM1040 TRAP dicarboxylate transporter- DctM subunit YP_612353.1 363664 D 292414 CDS YP_612354.1 99080200 4077689 365386..368169 1 NC_008044.1 PFAM: histidine kinase, HAMP region: (1.5e-08) chemotaxis sensory transducer: (1.2e-84); KEGG: sme:SMc01104 probable chemoreceptor (methyl-accepting chemotaxis) transmembrane protein, ev=3e-93, 47% identity; methyl-accepting chemotaxis sensory transducer 368169 4077689 TM1040_0359 Ruegeria sp. TM1040 methyl-accepting chemotaxis sensory transducer YP_612354.1 365386 D 292414 CDS YP_612355.1 99080201 4077690 368350..370440 1 NC_008044.1 PFAM: Enoyl-CoA hydratase/isomerase: (4.3e-58) 3-hydroxyacyl-CoA dehydrogenase-like: (5.1e-06) 3-hydroxyacyl-CoA dehydrogenase, NAD-binding: (1e-76); KEGG: sil:SPO0772 enoyl-CoA hydratase/isomerase/3-hydroxyacyl-CoA dehydrogenase, ev=0.0, 63% identity; short chain enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase 370440 4077690 TM1040_0360 Ruegeria sp. TM1040 short chain enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase YP_612355.1 368350 D 292414 CDS YP_612356.1 99080202 4077691 370462..371640 1 NC_008044.1 PFAM: Thiolase: (2.8e-72); KEGG: sil:SPO0773 acetyl-CoA acyltransferase/thiolase family protein, ev=1e-157, 72% identity; Acetyl-CoA C-acyltransferase 371640 4077691 TM1040_0361 Ruegeria sp. TM1040 Acetyl-CoA C-acyltransferase YP_612356.1 370462 D 292414 CDS YP_612357.1 99080203 4077692 371829..372626 1 NC_008044.1 SMART: regulatory proteins, IclR: (6.6e-20); KEGG: mag:amb2598 transcriptional regulator, ev=5e-35, 36% identity; IclR family transcriptional regulator 372626 4077692 TM1040_0362 Ruegeria sp. TM1040 IclR family transcriptional regulator YP_612357.1 371829 D 292414 CDS YP_612358.1 99080204 4077693 372959..373921 1 NC_008044.1 PFAM: ROK: (0.00052) Glucokinase: (3.4e-65); KEGG: sme:SMc02835 probable glucokinase transmembrane protein, ev=2e-42, 37% identity; glucokinase 373921 4077693 TM1040_0363 Ruegeria sp. TM1040 glucokinase YP_612358.1 372959 D 292414 CDS YP_612359.1 99080205 4077694 374058..374852 1 NC_008044.1 KEGG: ccr:CC3356 hypothetical protein, ev=8e-62, 53% identity; hypothetical protein 374852 4077694 TM1040_0364 Ruegeria sp. TM1040 hypothetical protein YP_612359.1 374058 D 292414 CDS YP_612360.1 99080206 4077695 complement(374933..375625) 1 NC_008044.1 PFAM: regulatory protein GntR, HTH: (3.2e-07) GntR-like: (2.2e-23); KEGG: psb:Psyr_2675 regulatory protein, GntR:bacterial regulatory protein, GntR, ev=9e-26, 36% identity; GntR family transcriptional regulator 375625 4077695 TM1040_0365 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_612360.1 374933 R 292414 CDS YP_612361.1 99080207 4077696 complement(375616..376452) 1 NC_008044.1 PFAM: protein of unknown function DUF81: (4.8e-33); KEGG: rru:Rru_A1348 protein of unknown function DUF81, ev=1e-50, 41% identity; hypothetical protein 376452 4077696 TM1040_0366 Ruegeria sp. TM1040 hypothetical protein YP_612361.1 375616 R 292414 CDS YP_612362.1 99080208 4077697 complement(376581..377822) 1 NC_008044.1 PFAM: ROK: (2.8e-06) Helix-turn-helix, type 11: (0.0016); KEGG: ret:RHE_CH00464 sugar transcriptional regulator protein, ROK family, ev=1e-105, 45% identity; ROK domain-containing protein 377822 4077697 TM1040_0367 Ruegeria sp. TM1040 ROK domain-containing protein YP_612362.1 376581 R 292414 CDS YP_612363.1 99080209 4077698 377973..378989 1 NC_008044.1 PFAM: periplasmic binding protein/LacI transcriptional regulator: (4.9e-08); KEGG: jan:Jann_1373 periplasmic binding protein/LacI transcriptional regulator, ev=1e-146, 76% identity; periplasmic binding protein/LacI transcriptional regulator 378989 4077698 TM1040_0368 Ruegeria sp. TM1040 periplasmic binding protein/LacI transcriptional regulator YP_612363.1 377973 D 292414 CDS YP_612364.1 99080210 4077699 379177..380241 1 NC_008044.1 PFAM: inner-membrane translocator: (1.8e-62); KEGG: jan:Jann_1374 inner-membrane translocator, ev=1e-150, 77% identity; inner-membrane translocator 380241 4077699 TM1040_0369 Ruegeria sp. TM1040 inner-membrane translocator YP_612364.1 379177 D 292414 CDS YP_612365.1 99080211 4077700 380238..381017 1 NC_008044.1 PFAM: ABC transporter related: (1.7e-44); SMART: ATPase: (2.3e-18); KEGG: jan:Jann_1375 ABC transporter related, ev=1e-116, 82% identity; ABC transporter 381017 4077700 TM1040_0370 Ruegeria sp. TM1040 ABC transporter YP_612365.1 380238 D 292414 CDS YP_612366.1 99080212 4077701 381014..381637 1 NC_008044.1 KEGG: sme:SMc02167 hypothetical protein, ev=5e-46, 47% identity; fructose transport system kinase 381637 frcK 4077701 frcK Ruegeria sp. TM1040 fructose transport system kinase YP_612366.1 381014 D 292414 CDS YP_612367.1 99080213 4077702 381666..382331 1 NC_008044.1 PFAM: protein of unknown function DUF1498: (1.3e-127); KEGG: mlo:mlr8329 hypothetical protein, ev=7e-84, 67% identity; hypothetical protein 382331 4077702 TM1040_0372 Ruegeria sp. TM1040 hypothetical protein YP_612367.1 381666 D 292414 CDS YP_612368.1 99080214 4077703 complement(382535..383410) 1 NC_008044.1 PFAM: NAD-dependent epimerase/dehydratase: (1.7e-08); KEGG: sil:SPO2846 hypothetical protein, ev=2e-53, 42% identity; NAD-dependent epimerase/dehydratase 383410 4077703 TM1040_0373 Ruegeria sp. TM1040 NAD-dependent epimerase/dehydratase YP_612368.1 382535 R 292414 CDS YP_612369.1 99080215 4078607 complement(383481..383897) 1 NC_008044.1 PFAM: glutathione-dependent formaldehyde-activating, GFA: (5.6e-07); KEGG: dde:Dde_3339 hypothetical protein, ev=1e-25, 41% identity; glutathione-dependent formaldehyde-activating protein 383897 4078607 TM1040_0374 Ruegeria sp. TM1040 glutathione-dependent formaldehyde-activating protein YP_612369.1 383481 R 292414 CDS YP_612370.1 99080216 4078608 complement(384038..384685) 1 NC_008044.1 KEGG: sil:SPO3031 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase, ev=2e-84, 77% identity; TIGRFAM: 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase: (8.5e-91); PFAM: KDPG and KHG aldolase: (1.1e-81); 2-keto-3-deoxy-phosphogluconate aldolase 384685 4078608 TM1040_0375 Ruegeria sp. TM1040 2-keto-3-deoxy-phosphogluconate aldolase YP_612370.1 384038 R 292414 CDS YP_612371.1 99080217 4078609 complement(384690..386501) 1 NC_008044.1 catalyzes the formation of 2-dehydro-3-deoxy-6-phospho-D-gluconate from 6-phospho-D-gluconate; phosphogluconate dehydratase 386501 4078609 TM1040_0376 Ruegeria sp. TM1040 phosphogluconate dehydratase YP_612371.1 384690 R 292414 CDS YP_612372.1 99080218 4078610 complement(386534..387985) 1 NC_008044.1 catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate; glucose-6-phosphate 1-dehydrogenase 387985 4078610 TM1040_0377 Ruegeria sp. TM1040 glucose-6-phosphate 1-dehydrogenase YP_612372.1 386534 R 292414 CDS YP_612373.1 99080219 4078611 complement(388010..389620) 1 NC_008044.1 PFAM: phosphoglucose isomerase (PGI): (4.9e-230); KEGG: mlo:mlr5411 glucose-6-phosphate isomerase, ev=0.0, 64% identity; glucose-6-phosphate isomerase 389620 4078611 TM1040_0378 Ruegeria sp. TM1040 glucose-6-phosphate isomerase YP_612373.1 388010 R 292414 CDS YP_612374.1 99080220 4078612 complement(389724..390131) 1 NC_008044.1 hypothetical protein 390131 4078612 TM1040_0379 Ruegeria sp. TM1040 hypothetical protein YP_612374.1 389724 R 292414 CDS YP_612375.1 99080221 4078613 complement(390218..390859) 1 NC_008044.1 TIGRFAM: urease accessory protein UreG: (1.9e-114); PFAM: cobalamin synthesis protein, P47K: (5.1e-68); KEGG: sil:SPO1717 urease accessory protein UreG, ev=1e-88, 81% identity; urease accessory protein UreG 390859 4078613 TM1040_0380 Ruegeria sp. TM1040 urease accessory protein UreG YP_612375.1 390218 R 292414 CDS YP_612376.1 99080222 4078614 complement(390856..391500) 1 NC_008044.1 PFAM: Urease accessory protein UreF: (4.6e-07); KEGG: sil:SPO1716 urease accessory protein UreF, ev=3e-53, 50% identity; urease accessory protein UreF 391500 4078614 TM1040_0381 Ruegeria sp. TM1040 urease accessory protein UreF YP_612376.1 390856 R 292414 CDS YP_612377.1 99080223 4078615 complement(391490..392020) 1 NC_008044.1 involved in the assembly of the urease metallocenter; possible nickel donor; urease accessory protein UreE 392020 ureE 4078615 ureE Ruegeria sp. TM1040 urease accessory protein UreE YP_612377.1 391490 R 292414 CDS YP_612378.1 99080224 4078616 complement(392070..392297) 1 NC_008044.1 hypothetical protein 392297 4078616 TM1040_0383 Ruegeria sp. TM1040 hypothetical protein YP_612378.1 392070 R 292414 CDS YP_612379.1 99080225 4078617 complement(392436..393050) 1 NC_008044.1 hypothetical protein 393050 4078617 TM1040_0384 Ruegeria sp. TM1040 hypothetical protein YP_612379.1 392436 R 292414 CDS YP_612380.1 99080226 4078618 complement(393082..394794) 1 NC_008044.1 ureases catalyze the hydrolysis of urea into ammonia and carbon dioxide; in Helicobacter pylori the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa; the holoenzyme is composed of 3 ureC (alpha) and 3 ureAB (gamma/beta) subunits; urease subunit alpha 394794 ureC 4078618 ureC Ruegeria sp. TM1040 urease subunit alpha YP_612380.1 393082 R 292414 CDS YP_612381.1 99080227 4078619 complement(394907..395212) 1 NC_008044.1 KEGG: sil:SPO1713 urease, beta subunit, ev=2e-41, 80% identity; TIGRFAM: urease, beta subunit: (1.1e-42); PFAM: Urease, beta subunit: (2e-63); urease subunit beta 395212 4078619 TM1040_0386 Ruegeria sp. TM1040 urease subunit beta YP_612381.1 394907 R 292414 CDS YP_612382.1 99080228 4078620 complement(395402..395704) 1 NC_008044.1 UreA, with UreB and UreC catalyzes the hydrolysis of urea into ammonia and carbon dioxide; nickel metalloenzyme; accessory proteins UreD, UreE, UreF, and UreG are necessary for assembly of the metallocenter; urease subunit gamma 395704 ureA 4078620 ureA Ruegeria sp. TM1040 urease subunit gamma YP_612382.1 395402 R 292414 CDS YP_612383.1 99080229 4078621 complement(395726..396619) 1 NC_008044.1 PFAM: Urease accessory protein UreD: (2.5e-39); KEGG: sil:SPO1711 urease accessory protein UreD, ev=1e-58, 51% identity; urease accessory protein UreD 396619 4078621 TM1040_0388 Ruegeria sp. TM1040 urease accessory protein UreD YP_612383.1 395726 R 292414 CDS YP_612384.1 99080230 4078622 396997..398121 1 NC_008044.1 PFAM: L-carnitine dehydratase/bile acid-inducible protein F: (2.4e-82); KEGG: sil:SPO0820 CAIB/BAIF family protein, ev=1e-141, 64% identity; L-carnitine dehydratase/bile acid-inducible protein F 398121 4078622 TM1040_0389 Ruegeria sp. TM1040 L-carnitine dehydratase/bile acid-inducible protein F YP_612384.1 396997 D 292414 CDS YP_612385.1 99080231 4078623 complement(398118..398918) 1 NC_008044.1 KEGG: mlo:mll6996 hypothetical protein, ev=8e-40, 37% identity; hypothetical protein 398918 4078623 TM1040_0390 Ruegeria sp. TM1040 hypothetical protein YP_612385.1 398118 R 292414 CDS YP_612386.1 99080232 4078624 399046..401052 1 NC_008044.1 PFAM: peptidase S15: (5.3e-82) X-Pro dipeptidyl-peptidase-like: (1.2e-54); KEGG: mlo:mll5128 similar to glutaryl 7-ACA acylase, ev=1e-159, 44% identity; peptidase S15 401052 4078624 TM1040_0391 Ruegeria sp. TM1040 peptidase S15 YP_612386.1 399046 D 292414 CDS YP_612387.1 99080233 4078625 complement(401118..401666) 1 NC_008044.1 hypothetical protein 401666 4078625 TM1040_0392 Ruegeria sp. TM1040 hypothetical protein YP_612387.1 401118 R 292414 CDS YP_612388.1 99080234 4078787 complement(401790..402266) 1 NC_008044.1 KEGG: sil:SPO1805 hypothetical protein, ev=6e-59, 70% identity; hypothetical protein 402266 4078787 TM1040_0393 Ruegeria sp. TM1040 hypothetical protein YP_612388.1 401790 R 292414 CDS YP_612389.1 99080235 4078788 complement(402282..402986) 1 NC_008044.1 KEGG: sil:SPO1804 hypothetical protein, ev=8e-78, 64% identity; hypothetical protein 402986 4078788 TM1040_0394 Ruegeria sp. TM1040 hypothetical protein YP_612389.1 402282 R 292414 CDS YP_612390.1 99080236 4078789 complement(402983..404047) 1 NC_008044.1 KEGG: sil:SPO1803 Mrp/NBP35 family protein, ev=1e-155, 78% identity; Mrp/NBP35 family protein 404047 4078789 TM1040_0395 Ruegeria sp. TM1040 Mrp/NBP35 family protein YP_612390.1 402983 R 292414 CDS YP_612391.1 99080237 4078790 complement(404143..406101) 1 NC_008044.1 PFAM: 4Fe-4S ferredoxin, iron-sulfur binding: (3.8e-07); KEGG: sil:SPO1800 iron-sulfur cluster-binding protein, ev=0.0, 60% identity; 4Fe-4S ferredoxin 406101 4078790 TM1040_0396 Ruegeria sp. TM1040 4Fe-4S ferredoxin YP_612391.1 404143 R 292414 CDS YP_612392.1 99080238 4078791 406357..407001 1 NC_008044.1 KEGG: mag:amb2667 molybdopterin-guanine dinucleotide biosynthesis protein A, ev=6e-18, 35% identity; hypothetical protein 407001 4078791 TM1040_0397 Ruegeria sp. TM1040 hypothetical protein YP_612392.1 406357 D 292414 CDS YP_612393.1 99080239 4078792 406998..407654 1 NC_008044.1 KEGG: sil:SPO1799 hypothetical protein, ev=4e-48, 53% identity; hypothetical protein 407654 4078792 TM1040_0398 Ruegeria sp. TM1040 hypothetical protein YP_612393.1 406998 D 292414 CDS YP_612394.1 99080240 4078793 407651..408277 1 NC_008044.1 PFAM: cytoplasmic chaperone TorD: (9.9e-24); KEGG: sil:SPO1798 chaperone, TorD family, ev=3e-81, 73% identity; cytoplasmic chaperone TorD 408277 4078793 TM1040_0399 Ruegeria sp. TM1040 cytoplasmic chaperone TorD YP_612394.1 407651 D 292414 CDS YP_612395.1 99080241 4078794 408384..408572 1 NC_008044.1 TIGRFAM: Twin-arginine translocation pathway signal: (0.0019); KEGG: sil:SPO1797 twin-arginine translocation pathway signal sequence domain protein, ev=3e-13, 65% identity; twin-arginine translocation pathway signal 408572 4078794 TM1040_0400 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_612395.1 408384 D 292414 CDS YP_612396.1 99080242 4078795 408686..411580 1 NC_008044.1 TIGRFAM: Twin-arginine translocation pathway signal: (0.019); PFAM: molybdopterin oxidoreductase: (1.4e-55) molydopterin dinucleotide-binding region: (1.3e-26) molybdopterin oxidoreductase Fe4S4 region: (1.3e-15); KEGG: sil:SPO1796 formate dehydrogenase, alpha subunit, , ev=0.0, 91% identity; formate dehydrogenase alpha subunit 411580 4078795 TM1040_0401 Ruegeria sp. TM1040 formate dehydrogenase alpha subunit YP_612396.1 408686 D 292414 CDS YP_612397.1 99080243 4078796 411594..412187 1 NC_008044.1 PFAM: 4Fe-4S ferredoxin, iron-sulfur binding: (6.5e-07); KEGG: sil:SPO1795 formate dehydrogenase, iron-sulfur subunit, , ev=1e-115, 95% identity; 4Fe-4S ferredoxin 412187 4078796 TM1040_0402 Ruegeria sp. TM1040 4Fe-4S ferredoxin YP_612397.1 411594 D 292414 CDS YP_612398.1 99080244 4078797 412303..413517 1 NC_008044.1 TIGRFAM: Formate dehydrogenase, gamma subunit: (1.6e-36); KEGG: sil:SPO1794 formate dehydrogenase, gamma subunit, ev=1e-131, 59% identity; formate dehydrogenase subunit gamma 413517 4078797 TM1040_0403 Ruegeria sp. TM1040 formate dehydrogenase subunit gamma YP_612398.1 412303 D 292414 CDS YP_612399.1 99080245 4078798 413522..414805 1 NC_008044.1 PFAM: WD-40 repeat: (0.00053) cytochrome c, class I: (7e-05); KEGG: sil:SPO1793 WD domain/cytochrome c family protein, ev=1e-125, 56% identity; cytochrome c, class I 414805 4078798 TM1040_0404 Ruegeria sp. TM1040 cytochrome c, class I YP_612399.1 413522 D 292414 CDS YP_612400.1 99080246 4078799 414942..416294 1 NC_008044.1 PFAM: response regulator receiver: (9.2e-27) sigma-54 factor, interaction region: (5.2e-95) helix-turn-helix, Fis-type: (1.8e-07) ATPase associated with various cellular activities, AAA_5: (0.00012); SMART: ATPase: (2.2e-10); KEGG: eba:ebA2951 sigma-54 dependent response regulator, ev=1e-116, 49% identity; two component, sigma54 specific, Fis family transcriptional regulator 416294 4078799 TM1040_0405 Ruegeria sp. TM1040 two component, sigma54 specific, Fis family transcriptional regulator YP_612400.1 414942 D 292414 CDS YP_612401.1 99080247 4078800 complement(416325..418301) 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (8.8e-32) histidine kinase, HAMP region: (1.9e-14) histidine kinase A-like: (2e-12); KEGG: dar:Daro_1828 ATP-binding region, ATPase-like:histidine kinase, HAMP region:histidine kinase A, N-terminal, ev=1e-154, 45% identity; sensor signal transduction histidine kinase 418301 4078800 TM1040_0406 Ruegeria sp. TM1040 sensor signal transduction histidine kinase YP_612401.1 416325 R 292414 CDS YP_612402.1 99080248 4078801 complement(418401..419141) 1 NC_008044.1 PFAM: short-chain dehydrogenase/reductase SDR: (5.4e-06); KEGG: nar:Saro_2960 short-chain dehydrogenase/reductase SDR, ev=2e-57, 51% identity; short-chain dehydrogenase/reductase SDR 419141 4078801 TM1040_0407 Ruegeria sp. TM1040 short-chain dehydrogenase/reductase SDR YP_612402.1 418401 R 292414 CDS YP_612403.1 99080249 4078802 complement(419138..419860) 1 NC_008044.1 PFAM: NAD-dependent epimerase/dehydratase: (0.0033) short-chain dehydrogenase/reductase SDR: (1.4e-15); KEGG: sil:SPO1480 oxidoreductase, short-chain dehydrogenase/reductase family, ev=2e-72, 57% identity; short-chain dehydrogenase/reductase SDR 419860 4078802 TM1040_0408 Ruegeria sp. TM1040 short-chain dehydrogenase/reductase SDR YP_612403.1 419138 R 292414 CDS YP_612404.1 99080250 4078803 complement(419857..420426) 1 NC_008044.1 KEGG: sil:SPO1486 hypothetical protein, ev=5e-59, 59% identity; hypothetical protein 420426 4078803 TM1040_0409 Ruegeria sp. TM1040 hypothetical protein YP_612404.1 419857 R 292414 CDS YP_612405.1 99080251 4078804 complement(420423..421640) 1 NC_008044.1 KEGG: sil:SPO1485 sodium:galactoside symporter family protein, ev=1e-118, 56% identity; sodium:galactoside symporter family protein 421640 4078804 TM1040_0410 Ruegeria sp. TM1040 sodium:galactoside symporter family protein YP_612405.1 420423 R 292414 CDS YP_612406.1 99080252 4078805 complement(421643..422185) 1 NC_008044.1 KEGG: sil:SPO1484 hypothetical protein, ev=6e-23, 35% identity; hypothetical protein 422185 4078805 TM1040_0411 Ruegeria sp. TM1040 hypothetical protein YP_612406.1 421643 R 292414 CDS YP_612407.1 99080253 4078806 complement(422175..423335) 1 NC_008044.1 PFAM: Cyclopropane-fatty-acyl-phospholipid synthase: (5e-80) Methyltransferase type 11: (2.4e-09) Methyltransferase type 12: (9.5e-12); KEGG: sil:SPO1483 cyclopropane-fatty-acyl-phospholipid synthase, , ev=1e-135, 60% identity; cyclopropane-fatty-acyl-phospholipid synthase 423335 4078806 TM1040_0412 Ruegeria sp. TM1040 cyclopropane-fatty-acyl-phospholipid synthase YP_612407.1 422175 R 292414 CDS YP_612408.1 99080254 4076173 complement(423335..424114) 1 NC_008044.1 PFAM: protein of unknown function DUF1365: (2.3e-29); KEGG: rsp:RSP_1090 cyclopropane/cyclopropene fatty acid synthesis protein, ev=3e-74, 57% identity; hypothetical protein 424114 4076173 TM1040_0413 Ruegeria sp. TM1040 hypothetical protein YP_612408.1 423335 R 292414 CDS YP_612409.1 99080255 4076174 complement(424111..425442) 1 NC_008044.1 PFAM: amine oxidase: (0.00038) FAD dependent oxidoreductase: (3e-06); KEGG: sil:SPO1482 hypothetical protein, ev=1e-151, 60% identity; FAD dependent oxidoreductase 425442 4076174 TM1040_0414 Ruegeria sp. TM1040 FAD dependent oxidoreductase YP_612409.1 424111 R 292414 CDS YP_612410.1 99080256 4076175 425629..426225 1 NC_008044.1 Member of the extracytoplasmic function sigma factors which are active under specific conditions; binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; this sigma factor is involved in heat shock and oxidative stress response; RNA polymerase sigma factor RpoE 426225 4076175 TM1040_0415 Ruegeria sp. TM1040 RNA polymerase sigma factor RpoE YP_612410.1 425629 D 292414 CDS YP_612411.1 99080257 4076176 426222..426857 1 NC_008044.1 TIGRFAM: Anti-sigma factor ChrR , : (6.8e-79); KEGG: sil:SPO1479 transcriptional activator, , ev=1e-71, 61% identity; anti-ECF sigma factor ChrR 426857 4076176 TM1040_0416 Ruegeria sp. TM1040 anti-ECF sigma factor ChrR YP_612411.1 426222 D 292414 CDS YP_612412.1 99080258 4076177 complement(427011..428015) 1 NC_008044.1 KEGG: sil:SPO0701 glyceraldehyde-3-phosphate dehydrogenase, type I, ev=1e-149, 79% identity; TIGRFAM: glyceraldehyde-3-phosphate dehydrogenase, type I: (3.1e-179); PFAM: glyceraldehyde 3-phosphate dehydrogenase: (1.8e-82); glyceraldehyde-3-phosphate dehydrogenase 428015 4076177 TM1040_0417 Ruegeria sp. TM1040 glyceraldehyde-3-phosphate dehydrogenase YP_612412.1 427011 R 292414 CDS YP_612413.1 99080259 4076178 428354..430087 1 NC_008044.1 PFAM: alpha amylase, catalytic region: (8.7e-07); SMART: Alpha amylase, catalytic subdomain: (3.3e-09); KEGG: hch:HCH_00269 glycosidase, ev=1e-160, 48% identity; alpha amylase 430087 4076178 TM1040_0418 Ruegeria sp. TM1040 alpha amylase YP_612413.1 428354 D 292414 CDS YP_612414.1 99080260 4076179 430269..430526 1 NC_008044.1 KEGG: hch:HCH_03746 hypothetical protein, ev=4e-24, 62% identity; hypothetical protein 430526 4076179 TM1040_0419 Ruegeria sp. TM1040 hypothetical protein YP_612414.1 430269 D 292414 CDS YP_612415.1 99080261 4076180 complement(430753..431982) 1 NC_008044.1 KEGG: hch:HCH_00270 glycosyltransferase involved in cell wall biogenesis, ev=1e-140, 58% identity; cell wall biosynthesis glycosyltransferase 431982 4076180 TM1040_0420 Ruegeria sp. TM1040 cell wall biosynthesis glycosyltransferase YP_612415.1 430753 R 292414 CDS YP_612416.1 99080262 4076181 complement(431975..432754) 1 NC_008044.1 catalyzes the hydrolysis of mannosyl-3-phosphoglycerate to form the osmolyte mannosylglycerate; mannosyl-3-phosphoglycerate phosphatase 432754 4076181 TM1040_0421 Ruegeria sp. TM1040 mannosyl-3-phosphoglycerate phosphatase YP_612416.1 431975 R 292414 CDS YP_612417.1 99080263 4076182 432884..434839 1 NC_008044.1 PFAM: BCCT transporter: (1.3e-131); KEGG: jan:Jann_1593 BCCT transporter, ev=0.0, 65% identity; BCCT transporter 434839 4076182 TM1040_0422 Ruegeria sp. TM1040 BCCT transporter YP_612417.1 432884 D 292414 CDS YP_612418.1 99080264 4076183 434944..435714 1 NC_008044.1 PFAM: fumarylacetoacetate (FAA) hydrolase: (9.3e-59); KEGG: rsp:RSP_1562 fumarylacetoacetate hydrolase family protein, ev=4e-91, 71% identity; fumarylacetoacetate (FAA) hydrolase 435714 4076183 TM1040_0423 Ruegeria sp. TM1040 fumarylacetoacetate (FAA) hydrolase YP_612418.1 434944 D 292414 CDS YP_612419.1 99080265 4076184 435852..437273 1 NC_008044.1 KEGG: jan:Jann_2999 hypothetical protein, ev=1e-134, 53% identity; hypothetical protein 437273 4076184 TM1040_0424 Ruegeria sp. TM1040 hypothetical protein YP_612419.1 435852 D 292414 CDS YP_612420.1 99080266 4076185 437482..437877 1 NC_008044.1 hypothetical protein 437877 4076185 TM1040_0425 Ruegeria sp. TM1040 hypothetical protein YP_612420.1 437482 D 292414 CDS YP_612421.1 99080267 4076186 complement(437908..439386) 1 NC_008044.1 PFAM: Mannitol dehydrogenase-like: (2.5e-85) Mannitol dehydrogenase rossman-like: (1.7e-77); KEGG: jan:Jann_2907 mannitol dehydrogenase-like, ev=0.0, 68% identity; mannitol dehydrogenase 439386 4076186 TM1040_0426 Ruegeria sp. TM1040 mannitol dehydrogenase YP_612421.1 437908 R 292414 CDS YP_612422.1 99080268 4076187 complement(439386..440156) 1 NC_008044.1 Converts D-sorbitol to L-sorbose; sorbitol dehydrogenase 440156 4076187 TM1040_0427 Ruegeria sp. TM1040 sorbitol dehydrogenase YP_612422.1 439386 R 292414 CDS YP_612423.1 99080269 4076188 complement(440156..441160) 1 NC_008044.1 PFAM: ABC transporter related: (1.2e-61) TOBE: (0.00066) Transport-associated OB: (3.2e-09); SMART: ATPase: (4.3e-17); KEGG: jan:Jann_2905 ABC transporter related, ev=1e-149, 79% identity; ABC transporter 441160 4076188 TM1040_0428 Ruegeria sp. TM1040 ABC transporter YP_612423.1 440156 R 292414 CDS YP_612424.1 99080270 4076189 complement(441173..442003) 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (4.7e-12); KEGG: jan:Jann_2904 binding-protein-dependent transport systems inner membrane component, ev=1e-131, 84% identity; binding-protein-dependent transport system inner membrane protein 442003 4076189 TM1040_0429 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_612424.1 441173 R 292414 CDS YP_612425.1 99080271 4076190 complement(442019..442885) 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (9.7e-11); KEGG: jan:Jann_2903 binding-protein-dependent transport systems inner membrane component, ev=1e-132, 79% identity; binding-protein-dependent transport system inner membrane protein 442885 4076190 TM1040_0430 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_612425.1 442019 R 292414 CDS YP_612426.1 99080272 4076191 complement(442988..444295) 1 NC_008044.1 PFAM: extracellular solute-binding protein, family 1: (5e-49); KEGG: rsp:RSP_0091 ABC sorbitol/mannitol transporter, periplasmic binding protein, ev=0.0, 72% identity; extracellular solute-binding protein 444295 4076191 TM1040_0431 Ruegeria sp. TM1040 extracellular solute-binding protein YP_612426.1 442988 R 292414 CDS YP_612427.1 99080273 4076075 complement(444427..445458) 1 NC_008044.1 PFAM: periplasmic binding protein/LacI transcriptional regulator: (2.6e-05); SMART: regulatory protein, LacI: (6.1e-14); KEGG: jan:Jann_2901 transcriptional regulator, LacI family, ev=1e-122, 62% identity; LacI family transcriptional regulator 445458 4076075 TM1040_0432 Ruegeria sp. TM1040 LacI family transcriptional regulator YP_612427.1 444427 R 292414 CDS YP_612428.1 99080274 4076076 complement(445657..447987) 1 NC_008044.1 PFAM: histidine kinase, HAMP region: (7.9e-16) chemotaxis sensory transducer: (4.5e-59); KEGG: ret:RHE_CH03477 probable methyl-accepting chemotaxis protein, ev=5e-84, 32% identity; methyl-accepting chemotaxis sensory transducer 447987 4076076 TM1040_0433 Ruegeria sp. TM1040 methyl-accepting chemotaxis sensory transducer YP_612428.1 445657 R 292414 CDS YP_612429.1 99080275 4076077 complement(448712..451171) 1 NC_008044.1 PFAM: FAD dependent oxidoreductase: (1.4e-87) glycine cleavage T protein (aminomethyl transferase): (6.4e-60); KEGG: sme:SMb21534 dehydrogenase protein, ev=0.0, 47% identity; FAD dependent oxidoreductase 451171 4076077 TM1040_0434 Ruegeria sp. TM1040 FAD dependent oxidoreductase YP_612429.1 448712 R 292414 CDS YP_612430.1 99080276 4076078 451273..451926 1 NC_008044.1 PFAM: regulatory protein, TetR: (6.3e-11); KEGG: mlo:mll3671 transcriptional regulator, ev=5e-33, 37% identity; TetR family transcriptional regulator 451926 4076078 TM1040_0435 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_612430.1 451273 D 292414 CDS YP_612431.1 99080277 4076079 complement(452191..453096) 1 NC_008044.1 PFAM: PaaX-like: (1.1e-10); KEGG: sil:SPO0734 PaaX domain protein, ev=2e-66, 50% identity; PaaX-like protein 453096 4076079 TM1040_0436 Ruegeria sp. TM1040 PaaX-like protein YP_612431.1 452191 R 292414 CDS YP_612432.1 99080278 4076080 complement(453126..455156) 1 NC_008044.1 catalyzes the ring cleavage reaction in phenylacetate degradation and the formation of 3-hydroxyacyl-CoA from crotonyl-CoA; bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase 455156 4076080 TM1040_0437 Ruegeria sp. TM1040 bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase YP_612432.1 453126 R 292414 CDS YP_612433.1 99080279 4076081 455317..456102 1 NC_008044.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 456102 4076081 TM1040_0438 Ruegeria sp. TM1040 enoyl-CoA hydratase YP_612433.1 455317 D 292414 CDS YP_612434.1 99080280 4076082 456106..456537 1 NC_008044.1 TIGRFAM: Phenylacetic acid degradation-related protein: (1e-24) Phenylacetic acid degradation protein PaaD: (1.7e-58); PFAM: thioesterase superfamily: (1.8e-18); KEGG: sil:SPO0741 phenylacetic acid degradation protein PaaD, ev=1e-59, 78% identity; phenylacetic acid degradation protein PaaD 456537 4076082 TM1040_0439 Ruegeria sp. TM1040 phenylacetic acid degradation protein PaaD YP_612434.1 456106 D 292414 CDS YP_612435.1 99080281 4076083 456593..457903 1 NC_008044.1 TIGRFAM: Phenylacetate-CoA ligase: (3.5e-299); KEGG: sil:SPO0742 phenylacetate-CoA ligase, ev=0.0, 83% identity; phenylacetate-CoA ligase 457903 4076083 TM1040_0440 Ruegeria sp. TM1040 phenylacetate-CoA ligase YP_612435.1 456593 D 292414 CDS YP_612436.1 99080282 4076084 457910..458506 1 NC_008044.1 PFAM: regulatory protein, TetR: (1.7e-18); KEGG: sil:SPO0743 transcriptional regulator, TetR family, ev=3e-69, 61% identity; TetR family transcriptional regulator 458506 4076084 TM1040_0441 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_612436.1 457910 D 292414 CDS YP_612437.1 99080283 4076085 458711..458974 1 NC_008044.1 PFAM: 17 kDa surface antigen: (3e-05); KEGG: vpa:VPA0312 hypothetical protein, ev=8e-06, 59% identity; 17 kDa surface antigen 458974 4076085 TM1040_0442 Ruegeria sp. TM1040 17 kDa surface antigen YP_612437.1 458711 D 292414 CDS YP_612438.1 99080284 4076086 complement(459119..460147) 1 NC_008044.1 catalyzes a two-step reaction, first charging a tryptophan molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; tryptophanyl-tRNA synthetase 460147 4076086 TM1040_0443 Ruegeria sp. TM1040 tryptophanyl-tRNA synthetase YP_612438.1 459119 R 292414 CDS YP_612439.1 99080285 4076087 460262..460948 1 NC_008044.1 PFAM: Rhomboid-like protein: (2.3e-06); KEGG: sil:SPO0393 rhomboid family protein, ev=3e-79, 62% identity; rhomboid-like protein 460948 4076087 TM1040_0444 Ruegeria sp. TM1040 rhomboid-like protein YP_612439.1 460262 D 292414 CDS YP_612440.1 99080286 4076088 complement(460965..462512) 1 NC_008044.1 TIGRFAM: integral membrane protein MviN: (6.6e-117); PFAM: virulence factor MVIN-like: (3e-113); KEGG: sil:SPO0396 integral membrane protein MviN, ev=0.0, 74% identity; integral membrane protein MviN 462512 4076088 TM1040_0445 Ruegeria sp. TM1040 integral membrane protein MviN YP_612440.1 460965 R 292414 CDS YP_612441.1 99080287 4076089 complement(462509..465190) 1 NC_008044.1 catalyzes the uridylylation or deuridylylation of the PII nitrogen regulatory protein; PII uridylyl-transferase 465190 4076089 TM1040_0446 Ruegeria sp. TM1040 PII uridylyl-transferase YP_612441.1 462509 R 292414 CDS YP_612442.1 99080288 4076090 complement(465297..466481) 1 NC_008044.1 PFAM: Extracellular ligand-binding receptor: (4.4e-05); KEGG: sil:SPO0398 hypothetical protein, ev=1e-157, 72% identity; extracellular ligand-binding receptor 466481 4076090 TM1040_0447 Ruegeria sp. TM1040 extracellular ligand-binding receptor YP_612442.1 465297 R 292414 CDS YP_612443.1 99080289 4076091 466570..467433 1 NC_008044.1 TIGRFAM: Protein of unknown function UPF0011: (1.4e-60); PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase: (6.4e-35); KEGG: sil:SPO0399 tetrapyrrole methylase family protein, ev=1e-106, 70% identity; hypothetical protein 467433 4076091 TM1040_0448 Ruegeria sp. TM1040 hypothetical protein YP_612443.1 466570 D 292414 CDS YP_612444.1 99080290 4076092 467439..467813 1 NC_008044.1 PFAM: protein of unknown function UPF0102: (3.6e-07); KEGG: sil:SPO0400 endonuclease, ev=3e-26, 52% identity; hypothetical protein 467813 4076092 TM1040_0449 Ruegeria sp. TM1040 hypothetical protein YP_612444.1 467439 D 292414 CDS YP_612445.1 99080291 4076093 467874..468809 1 NC_008044.1 catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione; glutathione synthetase 468809 4076093 TM1040_0450 Ruegeria sp. TM1040 glutathione synthetase YP_612445.1 467874 D 292414 CDS YP_612446.1 99080292 4076094 468806..469702 1 NC_008044.1 PFAM: Alpha/beta hydrolase fold-3: (3e-51); KEGG: bpm:BURPS1710b_0827 esterase, , ev=2e-46, 38% identity; alpha/beta hydrolase 469702 4076094 TM1040_0451 Ruegeria sp. TM1040 alpha/beta hydrolase YP_612446.1 468806 D 292414 CDS YP_612447.1 99080293 4078334 complement(469699..471201) 1 NC_008044.1 KEGG: sil:SPO0402 competence protein ComM, ev=0.0, 73% identity; TIGRFAM: Mg chelatase-related protein: (1.4e-184); PFAM: magnesium chelatase, ChlI subunit: (3.3e-141); SMART: ATPase: (5.9e-09); Mg chelatase-like protein 471201 4078334 TM1040_0452 Ruegeria sp. TM1040 Mg chelatase-like protein YP_612447.1 469699 R 292414 CDS YP_612448.1 99080294 4078335 complement(471312..471992) 1 NC_008044.1 KEGG: sil:SPO0403 hypothetical protein, ev=2e-83, 66% identity; hypothetical protein 471992 4078335 TM1040_0453 Ruegeria sp. TM1040 hypothetical protein YP_612448.1 471312 R 292414 CDS YP_612449.1 99080295 4078336 complement(472051..472632) 1 NC_008044.1 PFAM: Phosphoglycerate mutase: (5.3e-24); KEGG: sil:SPO0404 phosphoglycerate mutase family protein, ev=2e-68, 63% identity; phosphoglycerate mutase 472632 4078336 TM1040_0454 Ruegeria sp. TM1040 phosphoglycerate mutase YP_612449.1 472051 R 292414 CDS YP_612450.1 99080296 4078337 complement(472629..473249) 1 NC_008044.1 PFAM: cobalbumin biosynthesis enzyme: (7e-53); KEGG: sil:SPO0405 cobinamide kinase/cobinamide phosphate guanyltransferase, ev=5e-60, 68% identity; adenosylcobinamide kinase 473249 4078337 TM1040_0455 Ruegeria sp. TM1040 adenosylcobinamide kinase YP_612450.1 472629 R 292414 CDS YP_612451.1 99080297 4078338 473334..474212 1 NC_008044.1 binds with the catalytic core of RNA polymerase to produce the holoenzyme; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; sigma-32 is responsible for the expression of heat shock promoters; there are paralogs in Rhizobium and Sinorhizobium; the proteins in this cluster act as secondary heat shock sigma factors; the Rhizobium sigma-32 factor may also be involved in exopolysaccharide production; RNA polymerase factor sigma-32 474212 rpoH2 4078338 rpoH2 Ruegeria sp. TM1040 RNA polymerase factor sigma-32 YP_612451.1 473334 D 292414 CDS YP_612452.1 99080298 4078339 474209..475072 1 NC_008044.1 KEGG: sil:SPO0407 hypothetical protein, ev=2e-69, 52% identity; hypothetical protein 475072 4078339 TM1040_0457 Ruegeria sp. TM1040 hypothetical protein YP_612452.1 474209 D 292414 CDS YP_612453.1 99080299 4078340 475190..476401 1 NC_008044.1 catalyzes the conjugation of cysteine to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, which is then decarboxylated to form 4'-phosphopantotheine; bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase 476401 4078340 TM1040_0458 Ruegeria sp. TM1040 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase YP_612453.1 475190 D 292414 CDS YP_612454.1 99080300 4078341 476638..477012 1 NC_008044.1 hypothetical protein 477012 4078341 TM1040_0459 Ruegeria sp. TM1040 hypothetical protein YP_612454.1 476638 D 292414 CDS YP_612455.1 99080301 4078342 477198..479711 1 NC_008044.1 PFAM: CheB methylesterase: (1.8e-14) MCP methyltransferase, CheR-type: (2.1e-60); KEGG: jan:Jann_2564 MCP methyltransferase/methylesterase, CheR/CheB with PAS/PAC sensor, ev=0.0, 51% identity; chemotaxis protein CheR 479711 4078342 TM1040_0460 Ruegeria sp. TM1040 chemotaxis protein CheR YP_612455.1 477198 D 292414 CDS YP_612456.1 99080302 4078343 479863..480354 1 NC_008044.1 KEGG: reu:Reut_A2749 DeoxyUTP pyrophosphatase subfamily 1, ev=2e-52, 61% identity; TIGRFAM: deoxyuridine 5'-triphosphate nucleotidohydrolase (dut): (1.8e-42); PFAM: deoxyUTP pyrophosphatase: (4.7e-31); deoxyuridine 5'-triphosphate nucleotidohydrolase 480354 4078343 TM1040_0461 Ruegeria sp. TM1040 deoxyuridine 5'-triphosphate nucleotidohydrolase YP_612456.1 479863 D 292414 CDS YP_612457.1 99080303 4078344 480351..481427 1 NC_008044.1 PFAM: UBA/THIF-type NAD/FAD binding fold: (7.8e-62) MoeZ/MoeB: (7.5e-39); KEGG: sil:SPO0410 molybdopterin biosynthesis protein MoeB, , ev=1e-133, 70% identity; UBA/THIF-type NAD/FAD binding fold 481427 4078344 TM1040_0462 Ruegeria sp. TM1040 UBA/THIF-type NAD/FAD binding fold YP_612457.1 480351 D 292414 CDS YP_612458.1 99080304 4078345 481430..482221 1 NC_008044.1 PFAM: extracellular solute-binding protein, family 3: (5.2e-58); SMART: Ionotropic glutamate receptor: (4.1e-06); KEGG: sme:SMc03864 amino acid-binding periplasmic (signal peptide) ABC transporter protein, ev=1e-98, 67% identity; extracellular solute-binding protein 482221 4078345 TM1040_0463 Ruegeria sp. TM1040 extracellular solute-binding protein YP_612458.1 481430 D 292414 CDS YP_612459.1 99080305 4078346 482295..483101 1 NC_008044.1 TIGRFAM: Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine: (1.4e-12); PFAM: binding-protein-dependent transport systems inner membrane component: (1.3e-29); KEGG: jan:Jann_0911 amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine, ev=9e-95, 68% identity; amino acid ABC transporter permease 483101 4078346 TM1040_0464 Ruegeria sp. TM1040 amino acid ABC transporter permease YP_612459.1 482295 D 292414 CDS YP_612460.1 99080306 4078347 483198..485213 1 NC_008044.1 PFAM: peptidase M3A and M3B, thimet/oligopeptidase F: (8.4e-115); KEGG: sil:SPO0414 peptidyl-dipeptidase, , ev=0.0, 79% identity; peptidyl-dipeptidase Dcp 485213 4078347 TM1040_0465 Ruegeria sp. TM1040 peptidyl-dipeptidase Dcp YP_612460.1 483198 D 292414 CDS YP_612461.1 99080307 4078348 complement(485294..486220) 1 NC_008044.1 PFAM: D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding: (5e-48); KEGG: sil:SPO0415 D-isomer specific 2-hydroxyacid dehydrogenase family protein, ev=1e-117, 65% identity; D-isomer specific 2-hydroxyacid dehydrogenase 486220 4078348 TM1040_0466 Ruegeria sp. TM1040 D-isomer specific 2-hydroxyacid dehydrogenase YP_612461.1 485294 R 292414 CDS YP_612462.1 99080308 4078349 complement(486217..486627) 1 NC_008044.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase: (1.6e-10); KEGG: atc:AGR_pAT_700 probable ring-cleaving dioxygenase PA0817, ev=2e-55, 70% identity; glyoxalase/bleomycin resistance protein/dioxygenase 486627 4078349 TM1040_0467 Ruegeria sp. TM1040 glyoxalase/bleomycin resistance protein/dioxygenase YP_612462.1 486217 R 292414 CDS YP_612463.1 99080309 4078350 486728..487573 1 NC_008044.1 PFAM: regulatory protein, LysR: (1.6e-15) LysR, substrate-binding: (1.2e-17); KEGG: bpa:BPP1605 probable LysR-family transcriptional regulator, ev=4e-36, 38% identity; LysR family transcriptional regulator 487573 4078350 TM1040_0468 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_612463.1 486728 D 292414 CDS YP_612464.1 99080310 4078351 complement(487570..488709) 1 NC_008044.1 TIGRFAM: Rod shape-determining protein RodA: (6.5e-183); PFAM: cell cycle protein: (4.8e-107); KEGG: sil:SPO0416 rod shape-determining protein MreD, ev=0.0, 82% identity; rod shape-determining protein RodA 488709 4078351 TM1040_0469 Ruegeria sp. TM1040 rod shape-determining protein RodA YP_612464.1 487570 R 292414 CDS YP_612465.1 99080311 4078352 complement(488706..490652) 1 NC_008044.1 PFAM: penicillin-binding protein, transpeptidase: (6.7e-70) Penicillin-binding protein, dimerisation domain: (5.1e-35); KEGG: sil:SPO0417 penicillin-binding protein 2, ev=0.0, 76% identity; peptidoglycan glycosyltransferase 490652 4078352 TM1040_0470 Ruegeria sp. TM1040 peptidoglycan glycosyltransferase YP_612465.1 488706 R 292414 CDS YP_612466.1 99080312 4078509 complement(490649..491188) 1 NC_008044.1 KEGG: sil:SPO0418 rod shape-determining protein MreD, ev=2e-56, 60% identity; rod shape-determining protein MreD 491188 4078509 TM1040_0471 Ruegeria sp. TM1040 rod shape-determining protein MreD YP_612466.1 490649 R 292414 CDS YP_612467.1 99080313 4078510 complement(491181..492128) 1 NC_008044.1 in some organisms this protein is a transmembrane protein while in others it is periplasmic; involved in some organisms with other components of the MreBCD complex and with penicillin binding proteins in the periplasm or cell wall; rod shape-determining protein MreC 492128 4078510 TM1040_0472 Ruegeria sp. TM1040 rod shape-determining protein MreC YP_612467.1 491181 R 292414 CDS YP_612468.1 99080314 4078511 complement(492184..493230) 1 NC_008044.1 functions in MreBCD complex in some organisms; rod shape-determining protein MreB 493230 4078511 TM1040_0473 Ruegeria sp. TM1040 rod shape-determining protein MreB YP_612468.1 492184 R 292414 CDS YP_612469.1 99080315 4078512 complement(493430..494182) 1 NC_008044.1 KEGG: jan:Jann_0595 hypothetical protein, ev=1e-44, 47% identity; hypothetical protein 494182 4078512 TM1040_0474 Ruegeria sp. TM1040 hypothetical protein YP_612469.1 493430 R 292414 CDS YP_612470.1 99080316 4078513 494301..495080 1 NC_008044.1 PFAM: protein of unknown function DUF519: (3.8e-54); KEGG: sil:SPO0421 hypothetical protein, ev=1e-103, 70% identity; hypothetical protein 495080 4078513 TM1040_0475 Ruegeria sp. TM1040 hypothetical protein YP_612470.1 494301 D 292414 CDS YP_612471.1 99080317 4078514 complement(495160..496929) 1 NC_008044.1 PFAM: histidine kinase, HAMP region: (3e-12) chemotaxis sensory transducer: (6.9e-68) Cache, type 2: (6.7e-24); KEGG: sme:SMc04227 probable chemoreceptor (methyl-accepting chemotaxis) transmembrane protein, ev=1e-103, 38% identity; methyl-accepting chemotaxis sensory transducer 496929 4078514 TM1040_0476 Ruegeria sp. TM1040 methyl-accepting chemotaxis sensory transducer YP_612471.1 495160 R 292414 CDS YP_612472.1 99080318 4078515 complement(497149..499365) 1 NC_008044.1 KEGG: sil:SPOA0315 isocitrate dehydrogenase, NADP-dependent, ev=0.0, 83% identity; TIGRFAM: isocitrate dehydrogenase, NADP-dependent: (0); PFAM: Isocitrate dehydrogenase NADP-dependent, monomeric type: (0); isocitrate dehydrogenase 499365 4078515 TM1040_0477 Ruegeria sp. TM1040 isocitrate dehydrogenase YP_612472.1 497149 R 292414 CDS YP_612473.1 99080319 4078516 499866..501158 1 NC_008044.1 PFAM: glycosyl transferase, group 1: (2.7e-05); KEGG: fra:Francci3_3362 glycosyl transferase, group 1, ev=7e-12, 29% identity; group 1 glycosyl transferase 501158 4078516 TM1040_0478 Ruegeria sp. TM1040 group 1 glycosyl transferase YP_612473.1 499866 D 292414 CDS YP_612474.1 99080320 4078517 complement(501173..501775) 1 NC_008044.1 PFAM: protein of unknown function DUF1058: (2.6e-16); KEGG: sil:SPO0631 hypothetical protein, ev=1e-58, 65% identity; hypothetical protein 501775 4078517 TM1040_0479 Ruegeria sp. TM1040 hypothetical protein YP_612474.1 501173 R 292414 CDS YP_612475.1 99080321 4078518 501938..502924 1 NC_008044.1 PFAM: D-isomer specific 2-hydroxyacid dehydrogenase, catalytic region: (8.5e-38) D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding: (2.4e-81); KEGG: sil:SPO0632 D-isomer specific 2-hydroxyacid dehydrogenase family protein, ev=1e-162, 85% identity; glycolate reductase 502924 4078518 TM1040_0480 Ruegeria sp. TM1040 glycolate reductase YP_612475.1 501938 D 292414 CDS YP_612476.1 99080322 4078519 complement(502866..503246) 1 NC_008044.1 KEGG: lma:LmjF35.0550 proteophosphoglycan ppg1, ev=4e-07, 26% identity; hypothetical protein 503246 4078519 TM1040_0481 Ruegeria sp. TM1040 hypothetical protein YP_612476.1 502866 R 292414 CDS YP_612477.1 99080323 4078520 503457..504770 1 NC_008044.1 PFAM: gamma-glutamyltranspeptidase: (7.5e-127); KEGG: sil:SPO0633 gamma-glutamyltranspeptidase, ev=0.0, 76% identity; gamma-glutamyltransferase 1 504770 4078520 TM1040_0482 Ruegeria sp. TM1040 gamma-glutamyltransferase 1 YP_612477.1 503457 D 292414 CDS YP_612478.1 99080324 4078521 505027..506433 1 NC_008044.1 PFAM: FAD linked oxidase-like: (9.6e-76); KEGG: sil:SPO0634 oxidoreductase, FAD-binding, ev=0.0, 72% identity; FAD linked oxidase-like protein 506433 4078521 TM1040_0483 Ruegeria sp. TM1040 FAD linked oxidase-like protein YP_612478.1 505027 D 292414 CDS YP_612479.1 99080325 4078522 506534..506977 1 NC_008044.1 hypothetical protein 506977 4078522 TM1040_0484 Ruegeria sp. TM1040 hypothetical protein YP_612479.1 506534 D 292414 CDS YP_612480.1 99080326 4078523 complement(506989..507420) 1 NC_008044.1 PFAM: glutathione-dependent formaldehyde-activating, GFA: (2.7e-11); KEGG: atc:AGR_C_2344 hypothetical protein SPAC29B12.13, ev=3e-19, 37% identity; glutathione-dependent formaldehyde-activating protein 507420 4078523 TM1040_0485 Ruegeria sp. TM1040 glutathione-dependent formaldehyde-activating protein YP_612480.1 506989 R 292414 CDS YP_612481.1 99080327 4078524 507703..510210 1 NC_008044.1 PFAM: FAD dependent oxidoreductase: (4e-80) glycine cleavage T protein (aminomethyl transferase): (1e-45); KEGG: sil:SPO0635 aminomethyl transferase family protein, ev=0.0, 92% identity; FAD dependent oxidoreductase 510210 4078524 TM1040_0486 Ruegeria sp. TM1040 FAD dependent oxidoreductase YP_612481.1 507703 D 292414 CDS YP_612482.1 99080328 4078525 510374..511339 1 NC_008044.1 KEGG: vvy:VV2684 GGDEF family protein, ev=5e-08, 20% identity; hypothetical protein 511339 4078525 TM1040_0487 Ruegeria sp. TM1040 hypothetical protein YP_612482.1 510374 D 292414 CDS YP_612483.1 99080329 4078526 complement(511342..511809) 1 NC_008044.1 PFAM: Calcium-binding EF-hand: (0.0024); KEGG: rpb:RPB_3148 hypothetical protein, ev=4e-13, 30% identity; calcium-binding EF-hand 511809 4078526 TM1040_0488 Ruegeria sp. TM1040 calcium-binding EF-hand YP_612483.1 511342 R 292414 CDS YP_612484.1 99080330 4078527 complement(511915..512568) 1 NC_008044.1 PFAM: protein of unknown function DUF938: (6.9e-36) Methyltransferase type 11: (3.7e-07) Methyltransferase type 12: (9.1e-06); KEGG: sil:SPO0641 hypothetical protein, ev=2e-53, 52% identity; hypothetical protein 512568 4078527 TM1040_0489 Ruegeria sp. TM1040 hypothetical protein YP_612484.1 511915 R 292414 CDS YP_612485.1 99080331 4078528 complement(512568..513653) 1 NC_008044.1 PFAM: FAD dependent oxidoreductase: (5.5e-58); KEGG: sil:SPO0642 oxidoreductase, FAD-binding, ev=1e-119, 60% identity; FAD dependent oxidoreductase 513653 4078528 TM1040_0490 Ruegeria sp. TM1040 FAD dependent oxidoreductase YP_612485.1 512568 R 292414 CDS YP_612486.1 99080332 4078237 complement(513650..514654) 1 NC_008044.1 PFAM: aldo/keto reductase: (1.7e-59); KEGG: sil:SPO0643 oxidoreductase, aldo/keto reductase family, ev=1e-115, 66% identity; aldo/keto reductase 514654 4078237 TM1040_0491 Ruegeria sp. TM1040 aldo/keto reductase YP_612486.1 513650 R 292414 CDS YP_612487.1 99080333 4078238 514715..515323 1 NC_008044.1 PFAM: CDP-alcohol phosphatidyltransferase: (3.6e-10); KEGG: rsp:RSP_0198 phosphatidylglycerophosphate synthase, ev=2e-64, 64% identity; CDP-alcohol phosphatidyltransferase 515323 4078238 TM1040_0492 Ruegeria sp. TM1040 CDP-alcohol phosphatidyltransferase YP_612487.1 514715 D 292414 CDS YP_612488.1 99080334 4078239 complement(515592..516668) 1 NC_008044.1 PFAM: basic membrane lipoprotein: (1.2e-47); KEGG: sil:SPO0648 bmp family protein, ev=0.0, 88% identity; basic membrane lipoprotein 516668 4078239 TM1040_0493 Ruegeria sp. TM1040 basic membrane lipoprotein YP_612488.1 515592 R 292414 CDS YP_612489.1 99080335 4078240 complement(516786..517706) 1 NC_008044.1 PFAM: inner-membrane translocator: (5.7e-44); KEGG: sil:SPO0649 sugar ABC transporter, permease protein, ev=1e-150, 88% identity; inner-membrane translocator 517706 4078240 TM1040_0494 Ruegeria sp. TM1040 inner-membrane translocator YP_612489.1 516786 R 292414 CDS YP_612490.1 99080336 4078241 complement(517706..518788) 1 NC_008044.1 PFAM: inner-membrane translocator: (3e-51); KEGG: sil:SPO0650 sugar ABC transporter, permease protein, ev=0.0, 87% identity; inner-membrane translocator 518788 4078241 TM1040_0495 Ruegeria sp. TM1040 inner-membrane translocator YP_612490.1 517706 R 292414 CDS YP_612491.1 99080337 4078242 complement(518906..520426) 1 NC_008044.1 PFAM: ABC transporter related: (2.2e-09); SMART: ATPase: (5e-11); KEGG: sil:SPO0651 sugar ABC transporter, ATP-binding protein, ev=0.0, 86% identity; ABC transporter 520426 4078242 TM1040_0496 Ruegeria sp. TM1040 ABC transporter YP_612491.1 518906 R 292414 CDS YP_612492.1 99080338 4078243 complement(520423..521358) 1 NC_008044.1 PFAM: protein of unknown function DUF182: (8.2e-12); KEGG: sil:SPO0652 xanthine dehydrogenase accessory factor, ev=1e-107, 61% identity; molybdenum cofactor sulfurylase 521358 4078243 TM1040_0497 Ruegeria sp. TM1040 molybdenum cofactor sulfurylase YP_612492.1 520423 R 292414 CDS YP_612493.1 99080339 4078244 complement(521348..523696) 1 NC_008044.1 PFAM: aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead: (8.9e-38) aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding: (3.2e-203); KEGG: sil:SPO0653 xanthine dehydrogenase, B subunit, ev=0.0, 77% identity; xanthine dehydrogenase, molybdenum binding subunit apoprotein / xanthine oxidase 523696 4078244 TM1040_0498 Ruegeria sp. TM1040 xanthine dehydrogenase, molybdenum binding subunit apoprotein / xanthine oxidase YP_612493.1 521348 R 292414 CDS YP_612494.1 99080340 4078245 complement(523693..525096) 1 NC_008044.1 PFAM: ferredoxin: (1.3e-09) molybdopterin dehydrogenase, FAD-binding: (2.5e-50) [2Fe-2S]-binding: (7e-37) CO dehydrogenase flavoprotein-like: (2.1e-26); KEGG: sil:SPO0654 xanthine dehydrogenase, A subunit, ev=0.0, 71% identity; molybdopterin dehydrogenase 525096 4078245 TM1040_0499 Ruegeria sp. TM1040 molybdopterin dehydrogenase YP_612494.1 523693 R 292414 CDS YP_612495.1 99080341 4078246 525502..529002 1 NC_008044.1 catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase; DNA polymerase III subunit alpha 529002 dnaE 4078246 dnaE Ruegeria sp. TM1040 DNA polymerase III subunit alpha YP_612495.1 525502 D 292414 CDS YP_612496.1 99080342 4078247 complement(529337..529831) 1 NC_008044.1 KEGG: sme:SMb20463 hypothetical protein, ev=4e-08, 27% identity; hypothetical protein 529831 4078247 TM1040_0501 Ruegeria sp. TM1040 hypothetical protein YP_612496.1 529337 R 292414 CDS YP_612497.1 99080343 4078248 complement(529955..530149) 1 NC_008044.1 KEGG: sil:SPO0665 SlyX protein, , ev=9e-18, 65% identity; SlyX protein 530149 4078248 TM1040_0502 Ruegeria sp. TM1040 SlyX protein YP_612497.1 529955 R 292414 CDS YP_612498.1 99080344 4078249 530303..531805 1 NC_008044.1 catalyzes a two-step reaction, first charging a histidine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class II aminoacyl-tRNA synthetase; forms homodimers; some organisms have a paralogous gene, hisZ, that is similar to hisS and produces a protein that performs the first step in histidine biosynthesis along with HisG; histidyl-tRNA synthetase 531805 hisS 4078249 hisS Ruegeria sp. TM1040 histidyl-tRNA synthetase YP_612498.1 530303 D 292414 CDS YP_612499.1 99080345 4078250 531808..532899 1 NC_008044.1 May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine; ATP phosphoribosyltransferase 532899 hisZ 4078250 hisZ Ruegeria sp. TM1040 ATP phosphoribosyltransferase YP_612499.1 531808 D 292414 CDS YP_612500.1 99080346 4078251 532896..533588 1 NC_008044.1 short form of enzyme; requires HisZ for function; catalyzes the formation of N'-5'-phosphoribosyl-ATP from phosphoribosyl pyrophosphate; crucial role in histidine biosynthesis; forms heteromultimer of HisG and HisZ; ATP phosphoribosyltransferase 533588 hisG 4078251 hisG Ruegeria sp. TM1040 ATP phosphoribosyltransferase YP_612500.1 532896 D 292414 CDS YP_612501.1 99080347 4078252 complement(533746..534213) 1 NC_008044.1 PFAM: Uncharacterised conserved protein UCP032025: (1.4e-56); KEGG: sil:SPO3193 hypothetical protein, ev=8e-58, 69% identity; hypothetical protein 534213 4078252 TM1040_0506 Ruegeria sp. TM1040 hypothetical protein YP_612501.1 533746 R 292414 CDS YP_612502.1 99080348 4078253 complement(534367..534696) 1 NC_008044.1 TIGRFAM: conserved hypothetical protein: (7.9e-10); KEGG: sil:SPO3623 hypothetical protein, ev=1e-41, 71% identity; hypothetical protein 534696 4078253 TM1040_0507 Ruegeria sp. TM1040 hypothetical protein YP_612502.1 534367 R 292414 CDS YP_612503.1 99080349 4078254 534809..535510 1 NC_008044.1 PFAM: protein of unknown function DUF45: (4.9e-65); KEGG: sil:SPO3622 hypothetical protein, ev=7e-69, 59% identity; hypothetical protein 535510 4078254 TM1040_0508 Ruegeria sp. TM1040 hypothetical protein YP_612503.1 534809 D 292414 CDS YP_612504.1 99080350 4078255 535543..536205 1 NC_008044.1 PFAM: regulatory protein GntR, HTH: (6.2e-11) GntR-like: (6.2e-05); KEGG: sil:SPO3621 transcriptional regulator, GntR family, ev=4e-99, 90% identity; GntR family transcriptional regulator 536205 4078255 TM1040_0509 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_612504.1 535543 D 292414 CDS YP_612505.1 99080351 4077216 536336..537115 1 NC_008044.1 KEGG: vch:VC2649 serine acetyltransferase, ev=5e-34, 38% identity; Serine O-acetyltransferase 537115 4077216 TM1040_0510 Ruegeria sp. TM1040 Serine O-acetyltransferase YP_612505.1 536336 D 292414 CDS YP_612506.1 99080352 4077217 537112..538005 1 NC_008044.1 KEGG: psp:PSPPH_1713 hypothetical protein, ev=1e-36, 34% identity; hypothetical protein 538005 4077217 TM1040_0511 Ruegeria sp. TM1040 hypothetical protein YP_612506.1 537112 D 292414 CDS YP_612507.1 99080353 4077218 538014..539153 1 NC_008044.1 KEGG: cvi:CV1884 hippurate hydrolase, ev=1e-103, 51% identity; TIGRFAM: Peptidase M20D, amidohydrolase: (1.2e-119); PFAM: peptidase M20: (3.5e-59) peptidase dimerisation: (2.2e-05); peptidase M20D, amidohydrolase 539153 4077218 TM1040_0512 Ruegeria sp. TM1040 peptidase M20D, amidohydrolase YP_612507.1 538014 D 292414 CDS YP_612508.1 99080354 4077219 539153..540061 1 NC_008044.1 PFAM: regulatory protein, LysR: (6.6e-19) LysR, substrate-binding: (2.6e-37); KEGG: bbr:BB0654 LysR-family transcriptional regulator, ev=1e-37, 34% identity; LysR family transcriptional regulator 540061 4077219 TM1040_0513 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_612508.1 539153 D 292414 CDS YP_612509.1 99080355 4077220 540185..541099 1 NC_008044.1 PFAM: 6-phosphogluconate dehydrogenase, NAD-binding: (9.9e-48) 3-hydroxyacyl-CoA dehydrogenase, NAD-binding: (0.00031); KEGG: psb:Psyr_3525 3-hydroxyisobutyrate dehydrogenase, ev=2e-61, 44% identity; 6-phosphogluconate dehydrogenase 541099 4077220 TM1040_0514 Ruegeria sp. TM1040 6-phosphogluconate dehydrogenase YP_612509.1 540185 D 292414 CDS YP_612510.1 99080356 4077221 541096..542631 1 NC_008044.1 PFAM: aldehyde dehydrogenase: (2.5e-214); KEGG: psb:Psyr_3524 aldehyde dehydrogenase (NAD+), ev=1e-156, 55% identity; aldehyde dehydrogenase 542631 4077221 TM1040_0515 Ruegeria sp. TM1040 aldehyde dehydrogenase YP_612510.1 541096 D 292414 CDS YP_612511.1 99080357 4077222 542752..543573 1 NC_008044.1 KEGG: cvi:CV1885 hypothetical protein, ev=2e-73, 52% identity; hypothetical protein 543573 4077222 TM1040_0516 Ruegeria sp. TM1040 hypothetical protein YP_612511.1 542752 D 292414 CDS YP_612512.1 99080358 4077223 543576..544052 1 NC_008044.1 KEGG: dde:Dde_3032 hypothetical protein, ev=3e-24, 43% identity; hypothetical protein 544052 4077223 TM1040_0517 Ruegeria sp. TM1040 hypothetical protein YP_612512.1 543576 D 292414 CDS YP_612513.1 99080359 4077224 complement(544203..545219) 1 NC_008044.1 B2 or R2 protein; type 1b enzyme; catalyzes the rate-limiting step in dNTP synthesis; converts nucleotides to deoxynucleotides; forms a homodimer and then a multimeric complex with NrdE; ribonucleotide-diphosphate reductase subunit beta 545219 nrdF 4077224 nrdF Ruegeria sp. TM1040 ribonucleotide-diphosphate reductase subunit beta YP_612513.1 544203 R 292414 CDS YP_612514.1 99080360 4077225 complement(545281..547413) 1 NC_008044.1 Catalyzes the rate-limiting step in dNTP synthesis; ribonucleotide-diphosphate reductase subunit alpha 547413 4077225 TM1040_0519 Ruegeria sp. TM1040 ribonucleotide-diphosphate reductase subunit alpha YP_612514.1 545281 R 292414 CDS YP_612515.1 99080361 4077226 complement(547395..547817) 1 NC_008044.1 in Salmonella NrdI has a stimulatory effect on the ribonucleotide reductase activity of NrdH with NrdEF; ribonucleotide reductase stimulatory protein 547817 nrdI 4077226 nrdI Ruegeria sp. TM1040 ribonucleotide reductase stimulatory protein YP_612515.1 547395 R 292414 CDS YP_612516.1 99080362 4077227 complement(547839..548060) 1 NC_008044.1 TIGRFAM: Glutaredoxin-like protein NrdH: (9.8e-37); PFAM: glutaredoxin: (8.8e-16); KEGG: bmb:BruAb2_0867 NrdH, glutaredoxin-like protein NrdH, ev=3e-25, 68% identity; ribonucleoside-diphosphate reductase class Ib glutaredoxin subunit 548060 4077227 TM1040_0521 Ruegeria sp. TM1040 ribonucleoside-diphosphate reductase class Ib glutaredoxin subunit YP_612516.1 547839 R 292414 CDS YP_612517.1 99080363 4077228 complement(548599..548973) 1 NC_008044.1 PFAM: glutathione-dependent formaldehyde-activating, GFA: (1.7e-13); KEGG: pfo:Pfl_2171 glutathione-dependent formaldehyde-activating, GFA, ev=2e-40, 58% identity; glutathione-dependent formaldehyde-activating protein 548973 4077228 TM1040_0522 Ruegeria sp. TM1040 glutathione-dependent formaldehyde-activating protein YP_612517.1 548599 R 292414 CDS YP_612518.1 99080364 4077229 complement(549000..550034) 1 NC_008044.1 PFAM: Bile acid:sodium symporter: (3.9e-39); KEGG: rsp:RSP_3126 arsenite efflux pump, ACR3 family, ev=1e-137, 74% identity; bile acid:sodium symporter 550034 4077229 TM1040_0523 Ruegeria sp. TM1040 bile acid:sodium symporter YP_612518.1 549000 R 292414 CDS YP_612519.1 99080365 4077230 complement(550031..551305) 1 NC_008044.1 PFAM: major facilitator superfamily MFS_1: (0.00025); KEGG: sil:SPO3879 membrane protein, , ev=0.0, 83% identity; major facilitator superfamily transporter 551305 4077230 TM1040_0524 Ruegeria sp. TM1040 major facilitator superfamily transporter YP_612519.1 550031 R 292414 CDS YP_612520.1 99080366 4077231 complement(551302..552300) 1 NC_008044.1 KEGG: sil:SPO3878 glyceraldehyde-3-phosphate dehydrogenase, type I, ev=1e-166, 87% identity; TIGRFAM: glyceraldehyde-3-phosphate dehydrogenase, type I: (5.9e-160); PFAM: glyceraldehyde 3-phosphate dehydrogenase: (2e-61); glyceraldehyde-3-phosphate dehydrogenase 552300 4077231 TM1040_0525 Ruegeria sp. TM1040 glyceraldehyde-3-phosphate dehydrogenase YP_612520.1 551302 R 292414 CDS YP_612521.1 99080367 4077232 complement(552342..553172) 1 NC_008044.1 PFAM: low molecular weight phosphotyrosine protein phosphatase: (2.4e-35) regulatory protein, ArsR: (0.00029); KEGG: sil:SPO3877 transcriptional regulator/arsenate reductase, ev=1e-124, 77% identity; ArsR family transcriptional regulator 553172 4077232 TM1040_0526 Ruegeria sp. TM1040 ArsR family transcriptional regulator YP_612521.1 552342 R 292414 CDS YP_612522.1 99080368 4077233 553735..554442 1 NC_008044.1 PFAM: peptidase S1 and S6, chymotrypsin/Hap: (8.2e-07); KEGG: sil:SPO3482 trypsin domain protein, ev=5e-43, 44% identity; peptidase S1 and S6, chymotrypsin/Hap 554442 4077233 TM1040_0527 Ruegeria sp. TM1040 peptidase S1 and S6, chymotrypsin/Hap YP_612522.1 553735 D 292414 CDS YP_612523.1 99080369 4077234 complement(554564..555736) 1 NC_008044.1 TIGRFAM: Type I secretion membrane fusion protein, HlyD: (3.3e-94); PFAM: secretion protein HlyD: (9.8e-15); KEGG: bja:blr5469 probable HlyD family secretion protein, ev=1e-67, 37% identity; Type I secretion membrane fusion protein, HlyD 555736 4077234 TM1040_0528 Ruegeria sp. TM1040 Type I secretion membrane fusion protein, HlyD YP_612523.1 554564 R 292414 CDS YP_612524.1 99080370 4077235 complement(555733..558348) 1 NC_008044.1 PFAM: ABC transporter, transmembrane region: (5.1e-08) ABC transporter related: (4.1e-55); SMART: ATPase: (5.2e-20); KEGG: pae:PA1876 probable ATP-binding/permease fusion ABC transporter, ev=1e-132, 39% identity; ABC transporter 558348 4077235 TM1040_0529 Ruegeria sp. TM1040 ABC transporter YP_612524.1 555733 R 292414 CDS YP_612525.1 99080371 4077177 complement(558345..559640) 1 NC_008044.1 PFAM: outer membrane efflux protein: (4.7e-06); KEGG: pae:PA1875 hypothetical protein, ev=3e-13, 21% identity; outer membrane efflux protein 559640 4077177 TM1040_0530 Ruegeria sp. TM1040 outer membrane efflux protein YP_612525.1 558345 R 292414 CDS YP_612526.1 99080372 4077178 complement(559749..562301) 1 NC_008044.1 KEGG: ecs:ECs0541 hypothetical protein, ev=1e-61, 27% identity; hypothetical protein 562301 4077178 TM1040_0531 Ruegeria sp. TM1040 hypothetical protein YP_612526.1 559749 R 292414 CDS YP_612527.1 99080373 4077179 563004..564938 1 NC_008044.1 PFAM: PrkA serine kinase: (8.1e-165) PrkA AAA: (7.4e-250); KEGG: mag:amb2153 Ser protein kinase, ev=0.0, 75% identity; serine protein kinase PrkA 564938 4077179 TM1040_0532 Ruegeria sp. TM1040 serine protein kinase PrkA YP_612527.1 563004 D 292414 CDS YP_612528.1 99080374 4077180 564957..565316 1 NC_008044.1 KEGG: cvi:CV1790 hypothetical protein, ev=2e-26, 52% identity; hypothetical protein 565316 4077180 TM1040_0533 Ruegeria sp. TM1040 hypothetical protein YP_612528.1 564957 D 292414 CDS YP_612529.1 99080375 4077181 565370..566272 1 NC_008044.1 PFAM: protein of unknown function DUF444: (1e-58); KEGG: mlo:mll9637 hypothetical protein, ev=3e-85, 54% identity; hypothetical protein 566272 4077181 TM1040_0534 Ruegeria sp. TM1040 hypothetical protein YP_612529.1 565370 D 292414 CDS YP_612530.1 99080376 4077182 566278..567795 1 NC_008044.1 PFAM: SpoVR: (5.1e-261); KEGG: sme:SMc01265 hypothetical protein, ev=0.0, 63% identity; SpoVR family protein 567795 4077182 TM1040_0535 Ruegeria sp. TM1040 SpoVR family protein YP_612530.1 566278 D 292414 CDS YP_612531.1 99080377 4077183 complement(567866..568981) 1 NC_008044.1 PFAM: Alcohol dehydrogenase, zinc-binding: (3.4e-30) Alcohol dehydrogenase GroES-like: (5.4e-35); KEGG: jan:Jann_0044 alcohol dehydrogenase GroES-like, ev=0.0, 87% identity; molecular chaperone GroES 568981 4077183 TM1040_0536 Ruegeria sp. TM1040 molecular chaperone GroES YP_612531.1 567866 R 292414 CDS YP_612532.1 99080378 4077184 569385..569786 1 NC_008044.1 TIGRFAM: Cu(I)-responsive transcriptional regulator: (2.3e-57); PFAM: regulatory protein, MerR: (9.4e-12); KEGG: sil:SPO0793 Cu(I)-responsive transcriptional regulator, ev=2e-50, 74% identity; MerR family transcriptional regulator 569786 4077184 TM1040_0537 Ruegeria sp. TM1040 MerR family transcriptional regulator YP_612532.1 569385 D 292414 CDS YP_612533.1 99080379 4077185 570587..571387 1 NC_008044.1 KEGG: rpb:RPB_0861 TPR repeat protein, ev=6e-19, 31% identity; SARP family transcriptional regulator 571387 4077185 TM1040_0538 Ruegeria sp. TM1040 SARP family transcriptional regulator YP_612533.1 570587 D 292414 CDS YP_612534.1 99080380 4077186 571387..572250 1 NC_008044.1 KEGG: rsp:RSP_1299 binding domain, ev=3e-16, 27% identity; hypothetical protein 572250 4077186 TM1040_0539 Ruegeria sp. TM1040 hypothetical protein YP_612534.1 571387 D 292414 CDS YP_612535.1 99080381 4077187 complement(573038..573619) 1 NC_008044.1 PFAM: Phosphoglycerate mutase: (1.3e-29); KEGG: rru:Rru_A2210 phosphoglycerate/bisphosphoglycerate mutase, ev=2e-17, 35% identity; phosphoglycerate mutase 573619 4077187 TM1040_0540 Ruegeria sp. TM1040 phosphoglycerate mutase YP_612535.1 573038 R 292414 CDS YP_612536.1 99080382 4077188 complement(573619..574689) 1 NC_008044.1 PFAM: beta-lactamase-like: (3.3e-07); KEGG: bca:BCE1814 metallo-beta-lactamase family protein, ev=1e-15, 24% identity; beta-lactamase-like protein 574689 4077188 TM1040_0541 Ruegeria sp. TM1040 beta-lactamase-like protein YP_612536.1 573619 R 292414 CDS YP_612537.1 99080383 4077189 complement(574699..575739) 1 NC_008044.1 PFAM: ABC transporter related: (9.1e-60) Transport-associated OB: (2.3e-11); SMART: ATPase: (7.2e-18); KEGG: atc:AGR_C_3650 AgtA, ev=9e-81, 48% identity; ABC transporter 575739 4077189 TM1040_0542 Ruegeria sp. TM1040 ABC transporter YP_612537.1 574699 R 292414 CDS YP_612538.1 99080384 4077190 complement(575727..577433) 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1.4e-19); KEGG: sme:SMc04316 probable ferric iron transport system permease protein, ev=1e-155, 51% identity; binding-protein-dependent transport system inner membrane protein 577433 4077190 TM1040_0543 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_612538.1 575727 R 292414 CDS YP_612539.1 99080385 4077191 complement(577430..578398) 1 NC_008044.1 PFAM: extracellular solute-binding protein, family 1: (7.4e-08); KEGG: sme:SMc04317 iron-binding periplasmic protein, ev=1e-109, 61% identity; extracellular solute-binding protein 578398 4077191 TM1040_0544 Ruegeria sp. TM1040 extracellular solute-binding protein YP_612539.1 577430 R 292414 CDS YP_612540.1 99080386 4077192 578562..579359 1 NC_008044.1 PFAM: regulatory protein, DeoR: (5.8e-26) Helix-turn-helix, type 11: (6.4e-07); KEGG: vch:VCA0940 transcriptional regulator, DeoR family, ev=1e-34, 36% identity; DeoR family transcriptional regulator 579359 4077192 TM1040_0545 Ruegeria sp. TM1040 DeoR family transcriptional regulator YP_612540.1 578562 D 292414 CDS YP_612541.1 99080387 4077193 579549..580178 1 NC_008044.1 KEGG: ddi:DDB0168118 hypothetical protein, ev=4e-06, 28% identity; hypothetical protein 580178 4077193 TM1040_0546 Ruegeria sp. TM1040 hypothetical protein YP_612541.1 579549 D 292414 CDS YP_612542.1 99080388 4077194 complement(580200..582749) 1 NC_008044.1 TIGRFAM: Twin-arginine translocation pathway signal: (0.13); KEGG: ava:Ava_1569 hypothetical protein, ev=7e-20, 25% identity; twin-arginine translocation pathway signal 582749 4077194 TM1040_0547 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_612542.1 580200 R 292414 CDS YP_612543.1 99080389 4077195 complement(582746..585754) 1 NC_008044.1 PFAM: glycosyl transferase, family 2: (1.3e-33) polysaccharide deacetylase: (2.3e-31); KEGG: btk:BT9727_3202 glycosyl transferase and polysaccharide deacetylase fusion, ev=1e-153, 31% identity; glycosyl transferase family protein 585754 4077195 TM1040_0548 Ruegeria sp. TM1040 glycosyl transferase family protein YP_612543.1 582746 R 292414 CDS YP_612544.1 99080390 4077900 586629..587639 1 NC_008044.1 KEGG: rsp:RSP_3343 glycosyl transferase, ev=1e-06, 27% identity; hypothetical protein 587639 4077900 TM1040_0549 Ruegeria sp. TM1040 hypothetical protein YP_612544.1 586629 D 292414 CDS YP_612545.1 99080391 4077901 complement(587652..588155) 1 NC_008044.1 PFAM: regulatory protein, MarR: (1.3e-15); KEGG: pha:PSHAa2967 transcriptional regulator, ev=6e-29, 39% identity; MarR family transcriptional regulator 588155 4077901 TM1040_0550 Ruegeria sp. TM1040 MarR family transcriptional regulator YP_612545.1 587652 R 292414 CDS YP_612546.1 99080392 4077902 588383..588934 1 NC_008044.1 TIGRFAM: L-2,4-diaminobutyric acid acetyltransferase: (3.8e-63); PFAM: GCN5-related N-acetyltransferase: (3.3e-12); KEGG: vfi:VFA1122 L-2,4-diaminobutyric acid acetyltransferase, ev=7e-34, 43% identity; L-2,4-diaminobutyric acid acetyltransferase 588934 4077902 TM1040_0551 Ruegeria sp. TM1040 L-2,4-diaminobutyric acid acetyltransferase YP_612546.1 588383 D 292414 CDS YP_612547.1 99080393 4077903 588982..590268 1 NC_008044.1 catalyzes the reversible formation of diaminobutyrate and 2-oxoglutarate from glutamate and L-aspartic beta-semialdehyde; diaminobutyrate--2-oxoglutarate aminotransferase 590268 4077903 TM1040_0552 Ruegeria sp. TM1040 diaminobutyrate--2-oxoglutarate aminotransferase YP_612547.1 588982 D 292414 CDS YP_612548.1 99080394 4077904 590293..590685 1 NC_008044.1 N-acetyldiaminobutyrate dehydratase; catalyzes the formation of the osmoprotectant ecotoine from gamma-N-acetyl-alpha,gamma-diaminobutyric acid; L-ectoine synthase 590685 ectC 4077904 ectC Ruegeria sp. TM1040 L-ectoine synthase YP_612548.1 590293 D 292414 CDS YP_612549.1 99080395 4077905 590711..592147 1 NC_008044.1 catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP; aspartate kinase 592147 4077905 TM1040_0554 Ruegeria sp. TM1040 aspartate kinase YP_612549.1 590711 D 292414 CDS YP_612550.1 99080396 4077906 complement(592559..593632) 1 NC_008044.1 Catalyzes the cycloisomerization of cis,cis-muconate; 3-carboxy-cis,cis-muconate cycloisomerase 593632 4077906 TM1040_0555 Ruegeria sp. TM1040 3-carboxy-cis,cis-muconate cycloisomerase YP_612550.1 592559 R 292414 CDS YP_612551.1 99080397 4077907 complement(593672..594505) 1 NC_008044.1 PFAM: protein of unknown function DUF849: (1e-49); KEGG: sil:SPOA0042 hypothetical protein, ev=1e-130, 79% identity; hypothetical protein 594505 4077907 TM1040_0556 Ruegeria sp. TM1040 hypothetical protein YP_612551.1 593672 R 292414 CDS YP_612552.1 99080398 4077908 complement(594515..595132) 1 NC_008044.1 KEGG: bmb:BruAb2_0580 protocatechuate 3,4-dioxygenase, alpha subunit, ev=4e-77, 68% identity; TIGRFAM: Protocatechuate 3,4-dioxygenase, alpha subunit: (1.8e-107); PFAM: intradiol ring-cleavage dioxygenase: (1.6e-09); protocatechuate 3,4-dioxygenase subunit alpha 595132 4077908 TM1040_0557 Ruegeria sp. TM1040 protocatechuate 3,4-dioxygenase subunit alpha YP_612552.1 594515 R 292414 CDS YP_612553.1 99080399 4077909 complement(595135..595857) 1 NC_008044.1 TIGRFAM: Protocatechuate 3,4-dioxygenase, beta subunit: (5.9e-168); PFAM: intradiol ring-cleavage dioxygenase: (8.2e-70); KEGG: ret:RHE_PE00057 protocatechuate 3,4-dioxygenase beta chain protein, ev=3e-98, 68% identity; protocatechuate 3,4-dioxygenase subunit beta 595857 4077909 TM1040_0558 Ruegeria sp. TM1040 protocatechuate 3,4-dioxygenase subunit beta YP_612553.1 595135 R 292414 CDS YP_612554.1 99080400 4077910 complement(595854..596258) 1 NC_008044.1 TIGRFAM: 4-carboxymuconolactone decarboxylase: (8.3e-84); PFAM: Carboxymuconolactone decarboxylase: (4.7e-24); KEGG: sil:SPOA0045 4-carboxymuconolactone decarboxylase, ev=3e-53, 81% identity; 4-carboxymuconolactone decarboxylase 596258 4077910 TM1040_0559 Ruegeria sp. TM1040 4-carboxymuconolactone decarboxylase YP_612554.1 595854 R 292414 CDS YP_612555.1 99080401 4077911 complement(596251..597039) 1 NC_008044.1 TIGRFAM: 3-oxoadipate enol-lactonase: (1.7e-123); PFAM: alpha/beta hydrolase fold: (1.4e-21); KEGG: sil:SPOA0434 3-oxoadipate enol-lactone hydrolase, ev=7e-76, 54% identity; 3-oxoadipate enol-lactonase 597039 4077911 TM1040_0560 Ruegeria sp. TM1040 3-oxoadipate enol-lactonase YP_612555.1 596251 R 292414 CDS YP_612556.1 99080402 4077912 complement(597039..598208) 1 NC_008044.1 catalyzes the formation of protocatechuate from 4-hydroxybenzoate; 4-hydroxybenzoate 3-monooxygenase 598208 4077912 TM1040_0561 Ruegeria sp. TM1040 4-hydroxybenzoate 3-monooxygenase YP_612556.1 597039 R 292414 CDS YP_612557.1 99080403 4077913 598290..599228 1 NC_008044.1 TIGRFAM: Pca transcription factor PcaQ: (6e-133); PFAM: regulatory protein, LysR: (5.9e-20) LysR, substrate-binding: (1.1e-35); KEGG: sil:SPOA0047 pca operon transcriptional activator PcaQ, ev=4e-98, 60% identity; LysR family transcriptional regulator 599228 4077913 TM1040_0562 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_612557.1 598290 D 292414 CDS YP_612558.1 99080404 4077914 599575..600474 1 NC_008044.1 binds with the catalytic core of RNA polymerase to produce the holoenzyme; this sigma factor is responsible for the expression of heat shock promoters; RNA polymerase factor sigma-32 600474 4077914 TM1040_0563 Ruegeria sp. TM1040 RNA polymerase factor sigma-32 YP_612558.1 599575 D 292414 CDS YP_612559.1 99080405 4077915 complement(600959..602131) 1 NC_008044.1 PFAM: peptidase M19, renal dipeptidase: (1.6e-57); KEGG: sil:SPO1410 renal dipeptidase family protein, ev=1e-141, 64% identity; peptidase M19 602131 4077915 TM1040_0564 Ruegeria sp. TM1040 peptidase M19 YP_612559.1 600959 R 292414 CDS YP_612560.1 99080406 4077916 602298..603287 1 NC_008044.1 PFAM: oxidoreductase-like: (3.4e-35) Oxidoreductase-like: (0.00051); KEGG: jan:Jann_3398 oxidoreductase-like, ev=6e-79, 51% identity; oxidoreductase-like 603287 4077916 TM1040_0565 Ruegeria sp. TM1040 oxidoreductase-like YP_612560.1 602298 D 292414 CDS YP_612561.1 99080407 4077917 603420..603689 1 NC_008044.1 PFAM: zinc finger, DksA/TraR C4-type: (4.2e-13); KEGG: sil:SPO1411 C4-type zinc finger protein, DksA/TraR family, ev=1e-37, 82% identity; hypothetical protein 603689 4077917 TM1040_0566 Ruegeria sp. TM1040 hypothetical protein YP_612561.1 603420 D 292414 CDS YP_612562.1 99080408 4077918 complement(603693..604196) 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (0.00014); KEGG: hch:HCH_03525 histone acetyltransferase HPA2/related acetyltransferase, ev=7e-21, 39% identity; N-acetyltransferase GCN5 604196 4077918 TM1040_0567 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_612562.1 603693 R 292414 CDS YP_612563.1 99080409 4077919 complement(604197..605432) 1 NC_008044.1 PFAM: Hemolysin-type calcium-binding region: (0.036); KEGG: ppu:PP2561 secreted hemolysin-type calcium-binding bacteriocin, , ev=4e-24, 36% identity; hemolysin-type calcium-binding protein 605432 4077919 TM1040_0568 Ruegeria sp. TM1040 hemolysin-type calcium-binding protein YP_612563.1 604197 R 292414 CDS YP_612564.1 99080410 4076134 complement(605508..607328) 1 NC_008044.1 TIGRFAM: Peptidase M3B, oligoendopeptidase-related clade 3: (1.2e-230); PFAM: peptidase M3A and M3B, thimet/oligopeptidase F: (5.1e-32) Oligopeptidase F: (3.2e-20); KEGG: sil:SPO1413 oligoendopeptidase F, ev=0.0, 86% identity; peptidase M3B, oligoendopeptidase-related clade 3 607328 4076134 TM1040_0569 Ruegeria sp. TM1040 peptidase M3B, oligoendopeptidase-related clade 3 YP_612564.1 605508 R 292414 CDS YP_612565.1 99080411 4076135 complement(607521..608468) 1 NC_008044.1 PFAM: alpha/beta hydrolase fold: (6.4e-06); KEGG: sil:SPO1414 hydrolase, alpha/beta fold family, ev=5e-98, 58% identity; alpha/beta hydrolase 608468 4076135 TM1040_0570 Ruegeria sp. TM1040 alpha/beta hydrolase YP_612565.1 607521 R 292414 CDS YP_612566.1 99080412 4076136 complement(608489..608803) 1 NC_008044.1 PFAM: Sterol-binding: (3e-09); KEGG: sil:SPO1415 sterol carrier family protein, ev=1e-33, 73% identity; sterol-binding 608803 4076136 TM1040_0571 Ruegeria sp. TM1040 sterol-binding YP_612566.1 608489 R 292414 CDS YP_612567.1 99080413 4076137 608877..609461 1 NC_008044.1 PFAM: TPR repeat: (0.014) Tetratricopeptide TPR_2: (5.1e-05); SMART: Tetratricopeptide region: (0.00062); KEGG: sil:SPO1416 TPR domain protein, ev=4e-53, 60% identity; hypothetical protein 609461 4076137 TM1040_0572 Ruegeria sp. TM1040 hypothetical protein YP_612567.1 608877 D 292414 CDS YP_612568.1 99080414 4076138 609547..612501 1 NC_008044.1 PFAM: helicase-like: (9e-12); KEGG: sil:SPO1417 helicase, , ev=0.0, 76% identity; helicase-like protein 612501 4076138 TM1040_0573 Ruegeria sp. TM1040 helicase-like protein YP_612568.1 609547 D 292414 CDS YP_612569.1 99080415 4076139 612509..612883 1 NC_008044.1 PFAM: RNA-binding S4: (1.2e-14); KEGG: jan:Jann_3310 RNA-binding S4, ev=8e-30, 62% identity; RNA-binding protein S4 612883 4076139 TM1040_0574 Ruegeria sp. TM1040 RNA-binding protein S4 YP_612569.1 612509 D 292414 CDS YP_612570.1 99080416 4076140 612951..613289 1 NC_008044.1 PFAM: 4Fe-4S ferredoxin, iron-sulfur binding: (4.5e-07); KEGG: sil:SPO1419 iron-sulfur cluster-binding protein, ev=3e-60, 89% identity; 4Fe-4S ferredoxin 613289 4076140 TM1040_0575 Ruegeria sp. TM1040 4Fe-4S ferredoxin YP_612570.1 612951 D 292414 CDS YP_612571.1 99080417 4076141 613567..614076 1 NC_008044.1 PFAM: transcription factor CarD: (6.8e-33); KEGG: sil:SPO1420 transcriptional regulator, CarD family, ev=9e-83, 92% identity; CarD family transcriptional regulator 614076 4076141 TM1040_0576 Ruegeria sp. TM1040 CarD family transcriptional regulator YP_612571.1 613567 D 292414 CDS YP_612572.1 99080418 4076142 complement(614143..614895) 1 NC_008044.1 TIGRFAM: cobalamin 5'-phosphate synthase: (3.7e-15); PFAM: cobalamin-5-phosphate synthase CobS: (4.8e-21); KEGG: sil:SPO1422 cobalamin 5'-phosphate synthase, ev=2e-68, 57% identity; cobalamin-5'-phosphate synthase 614895 4076142 TM1040_0577 Ruegeria sp. TM1040 cobalamin-5'-phosphate synthase YP_612572.1 614143 R 292414 CDS YP_612573.1 99080419 4076143 614997..616007 1 NC_008044.1 catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide and 5,6-dimethylbenzimidazole; nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase 616007 cobT 4076143 cobT Ruegeria sp. TM1040 nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase YP_612573.1 614997 D 292414 CDS YP_612574.1 99080420 4076144 complement(616034..617911) 1 NC_008044.1 TIGRFAM: Potassium efflux system protein: (9.4e-95); PFAM: TrkA-N: (4.1e-30) sodium/hydrogen exchanger: (1.7e-60); KEGG: sil:SPO1424 glutathione-regulated potassium-efflux system protein, ev=0.0, 75% identity; potassium efflux system protein 617911 4076144 TM1040_0579 Ruegeria sp. TM1040 potassium efflux system protein YP_612574.1 616034 R 292414 CDS YP_612575.1 99080421 4076145 complement(618069..619292) 1 NC_008044.1 KEGG: bba:Bd1322 sensory protein, ev=2e-41, 29% identity; hypothetical protein 619292 4076145 TM1040_0580 Ruegeria sp. TM1040 hypothetical protein YP_612575.1 618069 R 292414 CDS YP_612576.1 99080422 4076146 complement(619356..619811) 1 NC_008044.1 PFAM: regulatory proteins, AsnC/Lrp: (1e-25); KEGG: sil:SPO1425 transcriptional regulator, AsnC family, ev=5e-56, 70% identity; AsnC family transcriptional regulator 619811 4076146 TM1040_0581 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_612576.1 619356 R 292414 CDS YP_612577.1 99080423 4076147 619950..621050 1 NC_008044.1 KEGG: sil:SPO1426 4-hydroxyphenylpyruvate dioxygenase, ev=0.0, 85% identity; TIGRFAM: 4-hydroxyphenylpyruvate dioxygenase: (1.6e-164); PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase: (9.9e-13); 4-hydroxyphenylpyruvate dioxygenase 621050 4076147 TM1040_0582 Ruegeria sp. TM1040 4-hydroxyphenylpyruvate dioxygenase YP_612577.1 619950 D 292414 CDS YP_612578.1 99080424 4076148 complement(621175..623808) 1 NC_008044.1 KEGG: sil:SPO1427 hypothetical protein, ev=1e-132, 39% identity; hypothetical protein 623808 4076148 TM1040_0583 Ruegeria sp. TM1040 hypothetical protein YP_612578.1 621175 R 292414 CDS YP_612579.1 99080425 4076149 624063..624779 1 NC_008044.1 PFAM: protein of unknown function DUF541: (7.6e-53); KEGG: sil:SPO1429 outer membrane protein, 28Kda, ev=5e-35, 40% identity; hypothetical protein 624779 4076149 TM1040_0584 Ruegeria sp. TM1040 hypothetical protein YP_612579.1 624063 D 292414 CDS YP_612580.1 99080426 4076150 complement(624873..626165) 1 NC_008044.1 KEGG: sil:SPO1431 O-acetylhomoserine aminocarboxypropyltransferase, ev=0.0, 92% identity; TIGRFAM: O-acetylhomoserine/O-acetylserine sulfhydrylase: (8e-236); PFAM: Cys/Met metabolism pyridoxal-phosphate-dependent enzymes: (1.2e-171); O-acetylhomoserine/O-acetylserine sulfhydrylase 626165 4076150 TM1040_0585 Ruegeria sp. TM1040 O-acetylhomoserine/O-acetylserine sulfhydrylase YP_612580.1 624873 R 292414 CDS YP_612581.1 99080427 4076151 complement(626316..627305) 1 NC_008044.1 KEGG: sil:SPO1769 hypothetical protein, ev=1e-138, 70% identity; hypothetical protein 627305 4076151 TM1040_0586 Ruegeria sp. TM1040 hypothetical protein YP_612581.1 626316 R 292414 CDS YP_612582.1 99080428 4076152 complement(627404..628279) 1 NC_008044.1 KEGG: sil:SPO1034 hypothetical protein, ev=9e-73, 45% identity; hypothetical protein 628279 4076152 TM1040_0587 Ruegeria sp. TM1040 hypothetical protein YP_612582.1 627404 R 292414 CDS YP_612583.1 99080429 4078626 complement(628389..628832) 1 NC_008044.1 PFAM: MaoC-like dehydratase: (2.4e-37); KEGG: sil:SPO3152 MaoC domain protein, ev=2e-69, 85% identity; MaoC-like dehydratase 628832 4078626 TM1040_0588 Ruegeria sp. TM1040 MaoC-like dehydratase YP_612583.1 628389 R 292414 CDS YP_612584.1 99080430 4078627 complement(629035..629910) 1 NC_008044.1 TIGRFAM: HAD-superfamily subfamily IIA hydrolase, hypothetical 3: (9.6e-27) HAD-superfamily hydrolase, subfamily IIA: (6.4e-25); PFAM: Haloacid dehalogenase-like hydrolase: (0.00081); KEGG: sil:SPO3151 HAD-superfamily subfamily IIA hydrolase, TIGR01459, ev=1e-137, 78% identity; HAD family hydrolase 629910 4078627 TM1040_0589 Ruegeria sp. TM1040 HAD family hydrolase YP_612584.1 629035 R 292414 CDS YP_612585.1 99080431 4078628 complement(630062..632194) 1 NC_008044.1 PFAM: helicase-like: (6.3e-30) DbpA, RNA-binding: (1e-10) DEAD/DEAH box helicase-like: (5.7e-61); KEGG: jan:Jann_1574 DEAD/DEAH box helicase-like, ev=0.0, 56% identity; DEAD/DEAH box helicase 632194 4078628 TM1040_0590 Ruegeria sp. TM1040 DEAD/DEAH box helicase YP_612585.1 630062 R 292414 CDS YP_612586.1 99080432 4078629 632483..633289 1 NC_008044.1 PFAM: peptidase M48, Ste24p: (2.3e-07); KEGG: sil:SPO0939 peptidase, M48 family, ev=8e-32, 36% identity; peptidase M48, Ste24p 633289 4078629 TM1040_0591 Ruegeria sp. TM1040 peptidase M48, Ste24p YP_612586.1 632483 D 292414 CDS YP_612587.1 99080433 4078630 complement(633408..634328) 1 NC_008044.1 catalyzes the hydrolysis of pyrophosphate to phosphate; manganese-dependent inorganic pyrophosphatase 634328 4078630 TM1040_0592 Ruegeria sp. TM1040 manganese-dependent inorganic pyrophosphatase YP_612587.1 633408 R 292414 CDS YP_612588.1 99080434 4078631 complement(634464..635525) 1 NC_008044.1 PFAM: GumN: (1.1e-10); KEGG: sil:SPO3145 GumN family protein, ev=3e-80, 49% identity; GumN protein 635525 4078631 TM1040_0593 Ruegeria sp. TM1040 GumN protein YP_612588.1 634464 R 292414 CDS YP_612589.1 99080435 4078632 complement(635522..636592) 1 NC_008044.1 PFAM: GumN: (2.4e-29); KEGG: sil:SPO3146 GumN family protein, ev=7e-55, 39% identity; GumN protein 636592 4078632 TM1040_0594 Ruegeria sp. TM1040 GumN protein YP_612589.1 635522 R 292414 CDS YP_612590.1 99080436 4078633 636662..637360 1 NC_008044.1 KEGG: sil:SPO3144 hypothetical protein, ev=4e-84, 68% identity; hypothetical protein 637360 4078633 TM1040_0595 Ruegeria sp. TM1040 hypothetical protein YP_612590.1 636662 D 292414 CDS YP_612591.1 99080437 4078634 637635..637922 1 NC_008044.1 10 kDa chaperonin; Cpn10; GroES; forms homoheptameric ring; binds to one or both ends of the GroEL double barrel in the presence of adenine nucleotides capping it; folding of unfolded substrates initiates in a GroEL-substrate bound and capped by GroES; release of the folded substrate is dependent on ATP binding and hydrolysis in the trans ring; co-chaperonin GroES 637922 groES 4078634 groES Ruegeria sp. TM1040 co-chaperonin GroES YP_612591.1 637635 D 292414 CDS YP_612592.1 99080438 4078635 637983..639626 1 NC_008044.1 60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; many bacteria have multiple copies of the groEL gene which are active under different environmental conditions; the B.japonicum protein in this cluster is expressed constitutively; in Rhodobacter, Corynebacterium and Rhizobium this protein is not essential for growth; molecular chaperone GroEL 639626 groEL 4078635 groEL Ruegeria sp. TM1040 molecular chaperone GroEL YP_612592.1 637983 D 292414 CDS YP_612593.1 99080439 4078636 639694..639996 1 NC_008044.1 hypothetical protein 639996 4078636 TM1040_0598 Ruegeria sp. TM1040 hypothetical protein YP_612593.1 639694 D 292414 CDS YP_612594.1 99080440 4078637 640194..640463 1 NC_008044.1 hypothetical protein 640463 4078637 TM1040_0599 Ruegeria sp. TM1040 hypothetical protein YP_612594.1 640194 D 292414 CDS YP_612595.1 99080441 4078638 640633..641526 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (7.8e-13); KEGG: sil:SPO0889 membrane protein, , ev=2e-70, 54% identity; hypothetical protein 641526 4078638 TM1040_0600 Ruegeria sp. TM1040 hypothetical protein YP_612595.1 640633 D 292414 CDS YP_612596.1 99080442 4078639 641536..642342 1 NC_008044.1 KEGG: sil:SPO0890 lipase, , ev=4e-78, 63% identity; lipase 642342 4078639 TM1040_0601 Ruegeria sp. TM1040 lipase YP_612596.1 641536 D 292414 CDS YP_612597.1 99080443 4078640 642346..643503 1 NC_008044.1 PFAM: amidohydrolase: (0.0053) Amidohydrolase 3: (0.00054); KEGG: sil:SPO0891 alkylphosphonate utilization protein PhnM, , ev=1e-144, 68% identity; amidohydrolase 643503 4078640 TM1040_0602 Ruegeria sp. TM1040 amidohydrolase YP_612597.1 642346 D 292414 CDS YP_612598.1 99080444 4078641 complement(643704..644801) 1 NC_008044.1 With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway; phosphoribosylaminoimidazole carboxylase ATPase subunit 644801 4078641 TM1040_0603 Ruegeria sp. TM1040 phosphoribosylaminoimidazole carboxylase ATPase subunit YP_612598.1 643704 R 292414 CDS YP_612599.1 99080445 4078642 complement(644794..645282) 1 NC_008044.1 KEGG: sil:SPO0893 phosphoribosylaminoimidazole carboxylase, catalytic subunit, ev=4e-76, 88% identity; TIGRFAM: phosphoribosylaminoimidazole carboxylase, catalytic subunit: (1.1e-91); PFAM: 1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate (AIR) carboxylase: (4.1e-86); phosphoribosylaminoimidazole carboxylase catalytic subunit 645282 4078642 TM1040_0604 Ruegeria sp. TM1040 phosphoribosylaminoimidazole carboxylase catalytic subunit YP_612599.1 644794 R 292414 CDS YP_612600.1 99080446 4078643 645532..646422 1 NC_008044.1 PFAM: Phenazine biosynthesis PhzC/PhzF protein: (1.8e-21); KEGG: sil:SPO0897 phenazine biosynthesis protein, PhzF family, ev=1e-109, 67% identity; phenazine biosynthesis PhzC/PhzF protein 646422 4078643 TM1040_0605 Ruegeria sp. TM1040 phenazine biosynthesis PhzC/PhzF protein YP_612600.1 645532 D 292414 CDS YP_612601.1 99080447 4078644 646512..646958 1 NC_008044.1 PFAM: glutathione-dependent formaldehyde-activating, GFA: (4.9e-13); KEGG: ccr:CC1514 hypothetical protein, ev=9e-20, 44% identity; glutathione-dependent formaldehyde-activating protein 646958 4078644 TM1040_0606 Ruegeria sp. TM1040 glutathione-dependent formaldehyde-activating protein YP_612601.1 646512 D 292414 CDS YP_612602.1 99080448 4078645 complement(646940..647470) 1 NC_008044.1 KEGG: mth:MTH293 hypothetical protein, ev=8e-40, 49% identity; hypothetical protein 647470 4078645 TM1040_0607 Ruegeria sp. TM1040 hypothetical protein YP_612602.1 646940 R 292414 CDS YP_612603.1 99080449 4078121 complement(647574..649058) 1 NC_008044.1 PFAM: phosphate transporter: (2.3e-127); KEGG: sil:SPO0967 phosphate transporter family protein, ev=0.0, 72% identity; phosphate transporter 649058 4078121 TM1040_0608 Ruegeria sp. TM1040 phosphate transporter YP_612603.1 647574 R 292414 CDS YP_612604.1 99080450 4078122 complement(649309..649533) 1 NC_008044.1 KEGG: sil:SPO0896 hypothetical protein, ev=7e-20, 66% identity; hypothetical protein 649533 4078122 TM1040_0609 Ruegeria sp. TM1040 hypothetical protein YP_612604.1 649309 R 292414 CDS YP_612605.1 99080451 4078123 complement(649537..649950) 1 NC_008044.1 PFAM: heat shock protein Hsp20: (2.5e-17); KEGG: sil:SPO0895 heat shock protein, Hsp20 family, ev=1e-64, 89% identity; heat shock protein Hsp20 649950 4078123 TM1040_0610 Ruegeria sp. TM1040 heat shock protein Hsp20 YP_612605.1 649537 R 292414 CDS YP_612606.1 99080452 4078124 650146..650370 1 NC_008044.1 PFAM: protein of unknown function DUF465: (5.9e-08); KEGG: sil:SPO0894 hypothetical protein, ev=3e-24, 75% identity; hypothetical protein 650370 4078124 TM1040_0611 Ruegeria sp. TM1040 hypothetical protein YP_612606.1 650146 D 292414 CDS YP_612607.1 99080453 4078125 complement(650528..652246) 1 NC_008044.1 in Rhizobium meliloti this protein is involved in the synthesis of nodulation factors that are active on the roots of alfalfa; catalyzes formation of activated sulfate intermediate; converts ATP and sulfate to diphosphate and adenylylsulfate and then ATP and adenylyl sulfate to ADP and 3'-phosphoadenylyl sulfate; the activated intermediate is transferred to the nodulation factors by NodH; may interact with NodP and NodQ; similar to the CysD and CysN proteins from Escherichia coli involved in cysteine biosynthesis; bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase 652246 4078125 TM1040_0612 Ruegeria sp. TM1040 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase YP_612607.1 650528 R 292414 CDS YP_612608.1 99080454 4078126 complement(652460..654220) 1 NC_008044.1 PFAM: ferredoxin: (2.5e-09) adenylyl cyclase class-3/4/guanylyl cyclase: (2.1e-09); KEGG: sil:SPO0901 adenylate/guanylate cyclase, ev=0.0, 58% identity; guanylate cyclase 654220 4078126 TM1040_0613 Ruegeria sp. TM1040 guanylate cyclase YP_612608.1 652460 R 292414 CDS YP_612609.1 99080455 4078127 complement(654406..655347) 1 NC_008044.1 TIGRFAM: thioredoxin reductase: (4.8e-176); PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase: (4.6e-28); KEGG: sil:SPO0903 thioredoxin-disulfide reductase, ev=1e-162, 90% identity; thioredoxin reductase 655347 4078127 TM1040_0614 Ruegeria sp. TM1040 thioredoxin reductase YP_612609.1 654406 R 292414 CDS YP_612610.1 99080456 4078128 655592..656092 1 NC_008044.1 PFAM: regulatory proteins, AsnC/Lrp: (5.6e-22); KEGG: sil:SPO0904 leucine-responsive regulatory protein, , ev=7e-80, 89% identity; AsnC family transcriptional regulator 656092 4078128 TM1040_0615 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_612610.1 655592 D 292414 CDS YP_612611.1 99080457 4078129 complement(656123..656890) 1 NC_008044.1 KEGG: sil:SPO0905 hypothetical protein, ev=7e-86, 60% identity; hypothetical protein 656890 4078129 TM1040_0616 Ruegeria sp. TM1040 hypothetical protein YP_612611.1 656123 R 292414 CDS YP_612612.1 99080458 4078130 657064..657369 1 NC_008044.1 hypothetical protein 657369 4078130 TM1040_0617 Ruegeria sp. TM1040 hypothetical protein YP_612612.1 657064 D 292414 CDS YP_612613.1 99080459 4078131 complement(657574..658341) 1 NC_008044.1 PFAM: protein of unknown function DUF152: (2e-55); KEGG: sil:SPO0906 conserved hypothetical protein TIGR00726, ev=8e-98, 70% identity; hypothetical protein 658341 4078131 TM1040_0618 Ruegeria sp. TM1040 hypothetical protein YP_612613.1 657574 R 292414 CDS YP_612614.1 99080460 4078132 complement(658338..659411) 1 NC_008044.1 PFAM: protein of unknown function DUF185: (5.6e-45); KEGG: sil:SPO0907 hypothetical protein, ev=1e-136, 68% identity; hypothetical protein 659411 4078132 TM1040_0619 Ruegeria sp. TM1040 hypothetical protein YP_612614.1 658338 R 292414 CDS YP_612615.1 99080461 4078133 complement(659408..660316) 1 NC_008044.1 transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein; prolipoprotein diacylglyceryl transferase 660316 4078133 TM1040_0620 Ruegeria sp. TM1040 prolipoprotein diacylglyceryl transferase YP_612615.1 659408 R 292414 CDS YP_612616.1 99080462 4078134 660413..660676 1 NC_008044.1 PFAM: protein of unknown function DUF526: (8.4e-17); KEGG: sil:SPO0909 hypothetical protein, ev=2e-33, 89% identity; hypothetical protein 660676 4078134 TM1040_0621 Ruegeria sp. TM1040 hypothetical protein YP_612616.1 660413 D 292414 CDS YP_612617.1 99080463 4078135 661243..661743 1 NC_008044.1 KEGG: sil:SPO0910 hypothetical protein, ev=8e-73, 75% identity; hypothetical protein 661743 4078135 TM1040_0622 Ruegeria sp. TM1040 hypothetical protein YP_612617.1 661243 D 292414 CDS YP_612618.1 99080464 4078136 661804..662619 1 NC_008044.1 catalyzes the formation of L-proline from pyrroline-5-carboxylate; pyrroline-5-carboxylate reductase 662619 4078136 TM1040_0623 Ruegeria sp. TM1040 pyrroline-5-carboxylate reductase YP_612618.1 661804 D 292414 CDS YP_612619.1 99080465 4078137 662612..662962 1 NC_008044.1 TIGRFAM: Secretion chaperone CsaA: (4.8e-61); PFAM: t-RNA-binding region: (4.2e-16); KEGG: sil:SPO0912 chaperonin CsaA, ev=3e-49, 81% identity; secretion chaperone CsaA 662962 4078137 TM1040_0624 Ruegeria sp. TM1040 secretion chaperone CsaA YP_612619.1 662612 D 292414 CDS YP_612620.1 99080466 4078138 662962..663930 1 NC_008044.1 PFAM: D-isomer specific 2-hydroxyacid dehydrogenase, catalytic region: (1.3e-29) D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding: (4.7e-73); KEGG: sil:SPO0913 D-isomer specific 2-hydroxyacid dehydrogenase family protein, ev=1e-133, 75% identity; D-isomer specific 2-hydroxyacid dehydrogenase 663930 4078138 TM1040_0625 Ruegeria sp. TM1040 D-isomer specific 2-hydroxyacid dehydrogenase YP_612620.1 662962 D 292414 CDS YP_612621.1 99080467 4078139 complement(664038..664640) 1 NC_008044.1 catalyzes the formation of thymidine 5'-phosphate from thymidine; thymidine kinase 664640 4078139 TM1040_0626 Ruegeria sp. TM1040 thymidine kinase YP_612621.1 664038 R 292414 CDS YP_612622.1 99080468 4076114 665179..665640 1 NC_008044.1 KEGG: sil:SPO0915 hypothetical protein, ev=4e-65, 82% identity; hypothetical protein 665640 4076114 TM1040_0627 Ruegeria sp. TM1040 hypothetical protein YP_612622.1 665179 D 292414 CDS YP_612623.1 99080469 4076115 complement(665754..666878) 1 NC_008044.1 catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation; differs from 3-oxoacyl-(acyl carrier protein) synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs; 3-oxoacyl-ACP synthase 666878 4076115 TM1040_0628 Ruegeria sp. TM1040 3-oxoacyl-ACP synthase YP_612623.1 665754 R 292414 CDS YP_612624.1 99080470 4076116 667095..667577 1 NC_008044.1 PFAM: regulatory protein, MarR: (6.5e-10); KEGG: sil:SPO0919 transcriptional regulator, MarR family, ev=2e-27, 46% identity; MarR family transcriptional regulator 667577 4076116 TM1040_0629 Ruegeria sp. TM1040 MarR family transcriptional regulator YP_612624.1 667095 D 292414 CDS YP_612625.1 99080471 4076117 667574..668647 1 NC_008044.1 TIGRFAM: Secretion protein HlyD: (1.3e-48); KEGG: sil:SPO0920 efflux transporter, RND family, MFP subunit, ev=1e-98, 57% identity; secretion protein HlyD 668647 4076117 TM1040_0630 Ruegeria sp. TM1040 secretion protein HlyD YP_612625.1 667574 D 292414 CDS YP_612626.1 99080472 4076118 668659..671709 1 NC_008044.1 PFAM: acriflavin resistance protein: (9.5e-69); KEGG: sil:SPO0921 transporter, AcrB/AcrD/AcrF family, ev=0.0, 72% identity; acriflavin resistance protein 671709 4076118 TM1040_0631 Ruegeria sp. TM1040 acriflavin resistance protein YP_612626.1 668659 D 292414 CDS YP_612627.1 99080473 4076119 complement(672273..675635) 1 NC_008044.1 four CarB-CarA dimers form the carbamoyl phosphate synthetase holoenzyme that catalyzes the production of carbamoyl phosphate; CarB is responsible for the amidotransferase activity; carbamoyl phosphate synthase large subunit 675635 carB 4076119 carB Ruegeria sp. TM1040 carbamoyl phosphate synthase large subunit YP_612627.1 672273 R 292414 CDS YP_612628.1 99080474 4076120 675784..676980 1 NC_008044.1 catalyzes the formation of 4-amino-4-deoxychorismate from chorismate and glutamine; aminodeoxychorismate synthase 676980 4076120 TM1040_0633 Ruegeria sp. TM1040 aminodeoxychorismate synthase YP_612628.1 675784 D 292414 CDS YP_612629.1 99080475 4076121 676977..677582 1 NC_008044.1 KEGG: sil:SPO0925 4-amino-4-deoxychorismate lyase, ev=7e-56, 53% identity; hypothetical protein 677582 4076121 TM1040_0634 Ruegeria sp. TM1040 hypothetical protein YP_612629.1 676977 D 292414 CDS YP_612630.1 99080476 4076122 677748..679532 1 NC_008044.1 catalyzes a two-step reaction, first charging an aspartate molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; contains discriminating and non-discriminating subtypes; aspartyl-tRNA synthetase 679532 aspS 4076122 aspS Ruegeria sp. TM1040 aspartyl-tRNA synthetase YP_612630.1 677748 D 292414 CDS YP_612631.1 99080477 4076123 complement(680127..680846) 1 NC_008044.1 PFAM: response regulator receiver: (7e-21); KEGG: sil:SPO0931 response regulator, ev=6e-82, 66% identity; response regulator receiver protein 680846 4076123 TM1040_0636 Ruegeria sp. TM1040 response regulator receiver protein YP_612631.1 680127 R 292414 CDS YP_612632.1 99080478 4076124 681032..681436 1 NC_008044.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase: (3.4e-20); KEGG: rsp:RSP_0812 glyoxalase I (lactoylglutathione lyase), ev=4e-67, 91% identity; methylmalonyl-CoA epimerase 681436 4076124 TM1040_0637 Ruegeria sp. TM1040 methylmalonyl-CoA epimerase YP_612632.1 681032 D 292414 CDS YP_612633.1 99080479 4076125 681506..681781 1 NC_008044.1 KEGG: sil:SPO0933 hypothetical protein, ev=2e-29, 67% identity; hypothetical protein 681781 4076125 TM1040_0638 Ruegeria sp. TM1040 hypothetical protein YP_612633.1 681506 D 292414 CDS YP_612634.1 99080480 4076126 complement(681912..682865) 1 NC_008044.1 PFAM: regulatory protein, LysR: (1.4e-14) LysR, substrate-binding: (2.1e-05); KEGG: sil:SPO0588 transcriptional regulator, LysR family, ev=7e-32, 31% identity; LysR family transcriptional regulator 682865 4076126 TM1040_0639 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_612634.1 681912 R 292414 CDS YP_612635.1 99080481 4076127 complement(683422..683763) 1 NC_008044.1 PFAM: protein of unknown function DUF427: (5.6e-28); KEGG: sil:SPO2858 hypothetical protein, ev=3e-41, 72% identity; hypothetical protein 683763 4076127 TM1040_0640 Ruegeria sp. TM1040 hypothetical protein YP_612635.1 683422 R 292414 CDS YP_612636.1 99080482 4076128 complement(683825..685609) 1 NC_008044.1 PFAM: peptidase M24: (3.3e-09); KEGG: sil:SPO2857 metallopeptidase, family M24, ev=0.0, 70% identity; peptidase M24 685609 4076128 TM1040_0641 Ruegeria sp. TM1040 peptidase M24 YP_612636.1 683825 R 292414 CDS YP_612637.1 99080483 4076129 complement(686000..687877) 1 NC_008044.1 PFAM: Cobalt chelatase, CobT subunit: (3.5e-268); SMART: von Willebrand factor, type A: (2.1e-10); KEGG: sil:SPO2855 cobalt chelatase, pCobT subunit, ev=0.0, 84% identity; cobalt chelatase subunit CobT 687877 4076129 TM1040_0642 Ruegeria sp. TM1040 cobalt chelatase subunit CobT YP_612637.1 686000 R 292414 CDS YP_612638.1 99080484 4076130 complement(688037..689023) 1 NC_008044.1 TIGRFAM: cobalt chelatase, pCobS small subunit: (4.1e-215); PFAM: ATPase associated with various cellular activities, AAA_5: (1.5e-08); KEGG: sil:SPO2853 cobalt chelatase, CobS subunit, ev=1e-176, 92% identity; hydrogenobyrinic acid a,c-diamide cobaltochelatase 689023 4076130 TM1040_0643 Ruegeria sp. TM1040 hydrogenobyrinic acid a,c-diamide cobaltochelatase YP_612638.1 688037 R 292414 CDS YP_612639.1 99080485 4076131 complement(689252..689851) 1 NC_008044.1 KEGG: sil:SPO2852 CzcN domain protein, ev=2e-77, 68% identity; CzcN domain-containing protein 689851 4076131 TM1040_0644 Ruegeria sp. TM1040 CzcN domain-containing protein YP_612639.1 689252 R 292414 CDS YP_612640.1 99080486 4076132 complement(690169..690795) 1 NC_008044.1 PFAM: heat shock protein DnaJ-like: (8.6e-06); KEGG: sil:SPO2850 DnaJ domain protein, ev=1e-106, 86% identity; molecular chaperone DnaJ 690795 4076132 TM1040_0645 Ruegeria sp. TM1040 molecular chaperone DnaJ YP_612640.1 690169 R 292414 CDS YP_612641.1 99080487 4076133 690913..691167 1 NC_008044.1 PFAM: BolA-like protein: (5.9e-13); KEGG: sil:SPO2849 BolA protein, truncation, ev=1e-24, 65% identity; BolA-like protein 691167 4076133 TM1040_0646 Ruegeria sp. TM1040 BolA-like protein YP_612641.1 690913 D 292414 CDS YP_612642.1 99080488 4078160 complement(691219..691788) 1 NC_008044.1 KEGG: sil:SPO2848 hypothetical protein, ev=4e-30, 53% identity; hypothetical protein 691788 4078160 TM1040_0647 Ruegeria sp. TM1040 hypothetical protein YP_612642.1 691219 R 292414 CDS YP_612643.1 99080489 4078161 complement(691865..693112) 1 NC_008044.1 catalyzes the release of the N-terminal amino acid from a tripeptide; peptidase T 693112 4078161 TM1040_0648 Ruegeria sp. TM1040 peptidase T YP_612643.1 691865 R 292414 CDS YP_612644.1 99080490 4078162 complement(693219..694622) 1 NC_008044.1 catalyzes the methylthiolation of an aspartic acid residue of the S12 protein of the 30S ribosomal subunit; 30S ribosomal protein S12 methylthiotransferase 694622 rimO 4078162 rimO Ruegeria sp. TM1040 30S ribosomal protein S12 methylthiotransferase YP_612644.1 693219 R 292414 CDS YP_612645.1 99080491 4078163 694800..696089 1 NC_008044.1 KEGG: mba:Mbar_A0126 hypothetical protein, ev=6e-07, 30% identity; hypothetical protein 696089 4078163 TM1040_0650 Ruegeria sp. TM1040 hypothetical protein YP_612645.1 694800 D 292414 CDS YP_612646.1 99080492 4078164 696203..698143 1 NC_008044.1 PFAM: AsmA: (2.4e-07); KEGG: sil:SPO0945 AsmA family protein, ev=1e-138, 41% identity; AsmA protein 698143 4078164 TM1040_0651 Ruegeria sp. TM1040 AsmA protein YP_612646.1 696203 D 292414 CDS YP_612647.1 99080493 4078165 complement(698293..699789) 1 NC_008044.1 PFAM: phosphoglucomutase/phosphomannomutase C terminal: (0.00053) phosphoglucomutase/phosphomannomutase alpha/beta/alpha domain I: (2e-28) phosphoglucomutase/phosphomannomutase alpha/beta/alpha domain II: (1e-25) phosphoglucomutase/phosphomannomutase alpha/beta/alpha domain III: (0.0012); KEGG: sil:SPO0946 phosphomannomutase/phosphoglucomutase, ev=0.0, 90% identity; phosphoglucomutase/phosphomannomutase alpha/beta/subunit 699789 4078165 TM1040_0652 Ruegeria sp. TM1040 phosphoglucomutase/phosphomannomutase alpha/beta/subunit YP_612647.1 698293 R 292414 CDS YP_612648.1 99080494 4078166 complement(699813..700646) 1 NC_008044.1 catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis; 2-dehydro-3-deoxyphosphooctonate aldolase 700646 4078166 TM1040_0653 Ruegeria sp. TM1040 2-dehydro-3-deoxyphosphooctonate aldolase YP_612648.1 699813 R 292414 CDS YP_612649.1 99080495 4078167 complement(700651..702408) 1 NC_008044.1 KEGG: sil:SPO0948 capsular polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family, ev=1e-136, 65% identity; capsule polysaccharide export protein 702408 4078167 TM1040_0654 Ruegeria sp. TM1040 capsule polysaccharide export protein YP_612649.1 700651 R 292414 CDS YP_612650.1 99080496 4078168 complement(702386..703045) 1 NC_008044.1 PFAM: ABC transporter related: (3.7e-10); SMART: ATPase: (9.6e-07); KEGG: sil:SPO0949 capsular polysaccharide export ATP-binding protein, ev=1e-107, 84% identity; ABC transporter 703045 4078168 TM1040_0655 Ruegeria sp. TM1040 ABC transporter YP_612650.1 702386 R 292414 CDS YP_612651.1 99080497 4078169 703380..703982 1 NC_008044.1 PFAM: Uracil-DNA glycosylase superfamily: (5.3e-05); KEGG: sil:SPO0950 uracil-DNA glycosylase, , ev=1e-80, 72% identity; uracil-DNA glycosylase 703982 4078169 TM1040_0656 Ruegeria sp. TM1040 uracil-DNA glycosylase YP_612651.1 703380 D 292414 CDS YP_612652.1 99080498 4078170 703975..704766 1 NC_008044.1 KEGG: sil:SPO0951 hypothetical protein, ev=2e-89, 66% identity; hypothetical protein 704766 4078170 TM1040_0657 Ruegeria sp. TM1040 hypothetical protein YP_612652.1 703975 D 292414 CDS YP_612653.1 99080499 4078171 complement(704912..705784) 1 NC_008044.1 YghU; B2989; one of eight glutathione transferase proteins from E. coli; glutathione S-transferase 705784 4078171 TM1040_0658 Ruegeria sp. TM1040 glutathione S-transferase YP_612653.1 704912 R 292414 CDS YP_612654.1 99080500 4078172 706043..706831 1 NC_008044.1 PFAM: protein of unknown function DUF88: (0.0004); KEGG: jan:Jann_0048 protein of unknown function DUF88, ev=3e-85, 64% identity; hypothetical protein 706831 4078172 TM1040_0659 Ruegeria sp. TM1040 hypothetical protein YP_612654.1 706043 D 292414 CDS YP_612655.1 99080501 4078173 706831..707241 1 NC_008044.1 KEGG: bja:blr5357 hypothetical protein, ev=3e-22, 50% identity; hypothetical protein 707241 4078173 TM1040_0660 Ruegeria sp. TM1040 hypothetical protein YP_612655.1 706831 D 292414 CDS YP_612656.1 99080502 4078174 707349..707921 1 NC_008044.1 KEGG: sil:SPO0954 hypothetical protein, ev=6e-69, 72% identity; hypothetical protein 707921 4078174 TM1040_0661 Ruegeria sp. TM1040 hypothetical protein YP_612656.1 707349 D 292414 CDS YP_612657.1 99080503 4078175 complement(708098..708688) 1 NC_008044.1 PFAM: GcrA cell cycle regulator: (2.2e-57); KEGG: sil:SPO0956 hypothetical protein, ev=3e-86, 81% identity; GcrA cell cycle regulator 708688 4078175 TM1040_0662 Ruegeria sp. TM1040 GcrA cell cycle regulator YP_612657.1 708098 R 292414 CDS YP_612658.1 99080504 4078176 708878..709702 1 NC_008044.1 PFAM: ABC-2 type transporter: (4.4e-32); KEGG: sil:SPO0957 ABC transporter, permease protein, ev=1e-111, 74% identity; ABC transporter 709702 4078176 TM1040_0663 Ruegeria sp. TM1040 ABC transporter YP_612658.1 708878 D 292414 CDS YP_612659.1 99080505 4078177 complement(709699..710691) 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (2.7e-15); KEGG: sil:SPO0959 membrane protein, , ev=1e-108, 69% identity; hypothetical protein 710691 4078177 TM1040_0664 Ruegeria sp. TM1040 hypothetical protein YP_612659.1 709699 R 292414 CDS YP_612660.1 99080506 4078178 710999..712174 1 NC_008044.1 DapATase; functions in arginine biosynthetic pathway; catalyzes the formation of N-acetyl-L-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine; acetylornithine transaminase protein 712174 argD 4078178 argD Ruegeria sp. TM1040 acetylornithine transaminase protein YP_612660.1 710999 D 292414 CDS YP_612661.1 99080507 4077274 712251..713177 1 NC_008044.1 catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation; ornithine carbamoyltransferase 713177 4077274 TM1040_0666 Ruegeria sp. TM1040 ornithine carbamoyltransferase YP_612661.1 712251 D 292414 CDS YP_612662.1 99080508 4077275 complement(713370..714860) 1 NC_008044.1 PFAM: phosphate transporter: (1e-105); KEGG: sil:SPO0967 phosphate transporter family protein, ev=1e-143, 53% identity; phosphate transporter 714860 4077275 TM1040_0667 Ruegeria sp. TM1040 phosphate transporter YP_612662.1 713370 R 292414 CDS YP_612663.1 99080509 4077276 complement(714982..715449) 1 NC_008044.1 PFAM: NUDIX hydrolase: (3.6e-17); KEGG: sil:SPO0968 hydrolase, NUDIX family, ev=2e-45, 58% identity; NUDIX hydrolase 715449 4077276 TM1040_0668 Ruegeria sp. TM1040 NUDIX hydrolase YP_612663.1 714982 R 292414 CDS YP_612664.1 99080510 4077277 complement(715629..718154) 1 NC_008044.1 TIGRFAM: ATP-dependent helicase HrpB: (0); PFAM: helicase-like: (9.2e-10) helicase-associated region: (2.8e-09) DEAD/DEAH box helicase-like: (6.1e-05) Helicase ATP-dependent-like: (3.7e-75); KEGG: sil:SPO0972 ATP-dependent helicase HrpB, ev=0.0, 71% identity; ATP-dependent helicase HrpB 718154 4077277 TM1040_0669 Ruegeria sp. TM1040 ATP-dependent helicase HrpB YP_612664.1 715629 R 292414 CDS YP_612665.1 99080511 4077278 718401..719402 1 NC_008044.1 functions in transport of arginine/ornithine; inner membrane ATPase that cleaves ATP and phosphorylates two periplasmic proteins that function as two distinct transport systems, the AO (arginine and ornithine) and LAO (lysine, arginine, and ornithine) periplasmic binding proteins; arginine/ornithine transport system ATPase 719402 4077278 TM1040_0670 Ruegeria sp. TM1040 arginine/ornithine transport system ATPase YP_612665.1 718401 D 292414 CDS YP_612666.1 99080512 4077279 719704..719994 1 NC_008044.1 required for 70S ribosome assembly; 50S ribosomal protein L28 719994 rpmB 4077279 rpmB Ruegeria sp. TM1040 50S ribosomal protein L28 YP_612666.1 719704 D 292414 CDS YP_612667.1 99080513 4077280 720156..720500 1 NC_008044.1 KEGG: sil:SPO0975 hypothetical protein, ev=9e-12, 39% identity; hypothetical protein 720500 4077280 TM1040_0672 Ruegeria sp. TM1040 hypothetical protein YP_612667.1 720156 D 292414 CDS YP_612668.1 99080514 4077281 720577..721068 1 NC_008044.1 PFAM: protein of unknown function DUF461: (4e-38); KEGG: sil:SPO0976 hypothetical protein, ev=4e-38, 57% identity; hypothetical protein 721068 4077281 TM1040_0673 Ruegeria sp. TM1040 hypothetical protein YP_612668.1 720577 D 292414 CDS YP_612669.1 99080515 4077282 complement(721127..721825) 1 NC_008044.1 Modulates the activities of several enzymes which are inactive in their acetylated form; NAD-dependent deacetylase 721825 4077282 TM1040_0674 Ruegeria sp. TM1040 NAD-dependent deacetylase YP_612669.1 721127 R 292414 CDS YP_612670.1 99080516 4077283 721940..722389 1 NC_008044.1 PFAM: low molecular weight phosphotyrosine protein phosphatase: (1.2e-45); KEGG: sil:SPO0979 low molecular weight phosphotyrosine protein phosphatase, ev=1e-43, 58% identity; protein tyrosine phosphatase 722389 4077283 TM1040_0675 Ruegeria sp. TM1040 protein tyrosine phosphatase YP_612670.1 721940 D 292414 CDS YP_612671.1 99080517 4077284 complement(722497..723462) 1 NC_008044.1 PFAM: regulatory protein, LysR: (1.6e-17) LysR, substrate-binding: (1.4e-05); KEGG: sil:SPO0980 transcriptional regulator, LysR family, ev=1e-130, 72% identity; LysR family transcriptional regulator 723462 4077284 TM1040_0676 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_612671.1 722497 R 292414 CDS YP_612672.1 99080518 4077285 complement(723729..724040) 1 NC_008044.1 KEGG: rsp:RSP_2018 hypothetical protein, ev=7e-18, 50% identity; hypothetical protein 724040 4077285 TM1040_0677 Ruegeria sp. TM1040 hypothetical protein YP_612672.1 723729 R 292414 CDS YP_612673.1 99080519 4077286 724251..726050 1 NC_008044.1 binds to the ribosome on the universally-conserved alpha-sarcin loop; GTP-binding protein LepA 726050 4077286 TM1040_0678 Ruegeria sp. TM1040 GTP-binding protein LepA YP_612673.1 724251 D 292414 CDS YP_612674.1 99080520 4077287 726193..727596 1 NC_008044.1 UDP-N-acetylmuramoylalanine--D-glutamate ligase; involved in peptidoglycan biosynthesis; cytoplasmic; catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine during cell wall formation; UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase 727596 murD 4077287 murD Ruegeria sp. TM1040 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase YP_612674.1 726193 D 292414 CDS YP_612675.1 99080521 4077288 complement(727602..728786) 1 NC_008044.1 PFAM: fumarate reductase/succinate dehydrogenase flavoprotein-like: (5.1e-05) HI0933-like protein: (4.4e-194) FAD dependent oxidoreductase: (0.00012) FAD-dependent pyridine nucleotide-disulphide oxidoreductase: (0.00042); KEGG: sil:SPO1188 conserved hypothetical protein TIGR00275, ev=1e-170, 74% identity; hypothetical protein 728786 4077288 TM1040_0680 Ruegeria sp. TM1040 hypothetical protein YP_612675.1 727602 R 292414 CDS YP_612676.1 99080522 4077289 729001..730170 1 NC_008044.1 TIGRFAM: Cell division protein FtsW: (5.8e-141); PFAM: cell cycle protein: (7.6e-63); KEGG: sil:SPO1194 cell division protein FtsW, ev=0.0, 85% identity; cell division protein FtsW 730170 4077289 TM1040_0681 Ruegeria sp. TM1040 cell division protein FtsW YP_612676.1 729001 D 292414 CDS YP_612677.1 99080523 4077290 730217..731314 1 NC_008044.1 UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase; involved in cell wall formation; inner membrane-associated; last step of peptidoglycan synthesis; UDPdiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase 731314 murG 4077290 murG Ruegeria sp. TM1040 UDPdiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase YP_612677.1 730217 D 292414 CDS YP_612678.1 99080524 4077291 731311..732720 1 NC_008044.1 Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis; UDP-N-acetylmuramate--L-alanine ligase 732720 murC 4077291 murC Ruegeria sp. TM1040 UDP-N-acetylmuramate--L-alanine ligase YP_612678.1 731311 D 292414 CDS YP_612679.1 99080525 4077292 732884..733126 1 NC_008044.1 KEGG: sil:SPO1198 hypothetical protein, ev=2e-30, 73% identity; hypothetical protein 733126 4077292 TM1040_0684 Ruegeria sp. TM1040 hypothetical protein YP_612679.1 732884 D 292414 CDS YP_612680.1 99080526 4077293 733268..734194 1 NC_008044.1 catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis; UDP-N-acetylenolpyruvoylglucosamine reductase 734194 murB 4077293 murB Ruegeria sp. TM1040 UDP-N-acetylenolpyruvoylglucosamine reductase YP_612680.1 733268 D 292414 CDS YP_612681.1 99080527 4077353 734517..735437 1 NC_008044.1 D-alanine--D-alanine ligase; DdlA; DdlB; cytoplasmic; catalyzes the formation of D-alanyl-D-alanine from two D-alanines in peptidoglycan synthesis; there are two forms of this enzyme in Escherichia coli; D-alanine--D-alanine ligase 735437 ddl 4077353 ddl Ruegeria sp. TM1040 D-alanine--D-alanine ligase YP_612681.1 734517 D 292414 CDS YP_612682.1 99080528 4077354 735425..736324 1 NC_008044.1 PFAM: cell division protein FtsQ: (3.2e-10); KEGG: sil:SPO1202 cell division protein FtsQ, ev=1e-102, 64% identity; cell division protein FtsQ 736324 4077354 TM1040_0687 Ruegeria sp. TM1040 cell division protein FtsQ YP_612682.1 735425 D 292414 CDS YP_612683.1 99080529 4077355 736308..737660 1 NC_008044.1 PFAM: cell division protein FtsA: (2e-53); KEGG: sil:SPO1203 cell division protein FtsA, ev=0.0, 84% identity; cell division protein FtsA 737660 4077355 TM1040_0688 Ruegeria sp. TM1040 cell division protein FtsA YP_612683.1 736308 D 292414 CDS YP_612684.1 99080530 4077356 738085..739758 1 NC_008044.1 GTPase; similar structure to tubulin; forms ring-shaped polymers at the site of cell division; other proteins such as FtsA, ZipA, and ZapA, interact with and regulate FtsZ function; cell division protein FtsZ 739758 4077356 TM1040_0689 Ruegeria sp. TM1040 cell division protein FtsZ YP_612684.1 738085 D 292414 CDS YP_612685.1 99080531 4077357 739957..740904 1 NC_008044.1 zinc-dependent; catalyzes the deacetylation of UDP-(3-O-acyl)-N-acetylglucosamine to UDP-3-O-(3-hydroxytetradecanoyl)-glucosamine in the second step of lipid A biosynthesis; UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase 740904 lpxC 4077357 lpxC Ruegeria sp. TM1040 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase YP_612685.1 739957 D 292414 CDS YP_612686.1 99080532 4077358 741250..742101 1 NC_008044.1 KEGG: sil:SPO1206 competence lipoprotein ComL, , ev=1e-123, 76% identity; competence lipoprotein ComL 742101 4077358 TM1040_0691 Ruegeria sp. TM1040 competence lipoprotein ComL YP_612686.1 741250 D 292414 CDS YP_612687.1 99080533 4077359 742178..743827 1 NC_008044.1 TIGRFAM: DNA repair protein RecN: (1.6e-139); PFAM: SMC protein-like: (3.6e-08); KEGG: sil:SPO1207 DNA repair protein RecN, ev=0.0, 74% identity; DNA repair protein RecN 743827 4077359 TM1040_0692 Ruegeria sp. TM1040 DNA repair protein RecN YP_612687.1 742178 D 292414 CDS YP_612688.1 99080534 4077360 743914..745608 1 NC_008044.1 PFAM: Cl- channel, voltage gated: (3.8e-25); KEGG: sil:SPO1208 voltage-gated chloride channel family protein, ev=0.0, 71% identity; VWA containing CoxE-like protein 745608 4077360 TM1040_0693 Ruegeria sp. TM1040 VWA containing CoxE-like protein YP_612688.1 743914 D 292414 CDS YP_612689.1 99080535 4077361 complement(745727..746419) 1 NC_008044.1 KEGG: sil:SPO0934 membrane protein, , ev=2e-85, 72% identity; hypothetical protein 746419 4077361 TM1040_0694 Ruegeria sp. TM1040 hypothetical protein YP_612689.1 745727 R 292414 CDS YP_612690.1 99080536 4077362 complement(746416..746994) 1 NC_008044.1 PFAM: nitroreductase: (2.2e-06); KEGG: sil:SPO0935 nitroreductase family protein, ev=9e-78, 73% identity; nitroreductase 746994 4077362 TM1040_0695 Ruegeria sp. TM1040 nitroreductase YP_612690.1 746416 R 292414 CDS YP_612691.1 99080537 4077363 747262..747540 1 NC_008044.1 PFAM: protein of unknown function DUF167: (2.6e-18); KEGG: sil:SPO0937 hypothetical protein, ev=2e-20, 56% identity; hypothetical protein 747540 4077363 TM1040_0696 Ruegeria sp. TM1040 hypothetical protein YP_612691.1 747262 D 292414 CDS YP_612692.1 99080538 4077364 complement(747648..747890) 1 NC_008044.1 KEGG: sil:SPO0938 hypothetical protein, ev=9e-29, 81% identity; hypothetical protein 747890 4077364 TM1040_0697 Ruegeria sp. TM1040 hypothetical protein YP_612692.1 747648 R 292414 CDS YP_612693.1 99080539 4077365 748019..748678 1 NC_008044.1 PFAM: peptidase M48, Ste24p: (2.8e-08); KEGG: sil:SPO0939 peptidase, M48 family, ev=7e-57, 49% identity; peptidase M48, Ste24p 748678 4077365 TM1040_0698 Ruegeria sp. TM1040 peptidase M48, Ste24p YP_612693.1 748019 D 292414 CDS YP_612694.1 99080540 4077366 748689..749069 1 NC_008044.1 PFAM: protein of unknown function UPF0029: (4.7e-17); KEGG: sil:SPO0940 hypothetical protein, ev=1e-49, 84% identity; hypothetical protein 749069 4077366 TM1040_0699 Ruegeria sp. TM1040 hypothetical protein YP_612694.1 748689 D 292414 CDS YP_612695.1 99080541 4077367 749165..749440 1 NC_008044.1 KEGG: sil:SPO0941 hypothetical protein, ev=1e-12, 46% identity; hypothetical protein 749440 4077367 TM1040_0700 Ruegeria sp. TM1040 hypothetical protein YP_612695.1 749165 D 292414 CDS YP_612696.1 99080542 4077368 complement(749516..751024) 1 NC_008044.1 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; aspartyl/glutamyl-tRNA amidotransferase subunit B 751024 gatB 4077368 gatB Ruegeria sp. TM1040 aspartyl/glutamyl-tRNA amidotransferase subunit B YP_612696.1 749516 R 292414 CDS YP_612697.1 99080543 4077369 complement(751184..751918) 1 NC_008044.1 SMART: extracellular solute-binding protein, family 3: (7e-06); KEGG: hch:HCH_01375 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain, ev=3e-21, 27% identity; extracellular solute-binding protein 751918 4077369 TM1040_0702 Ruegeria sp. TM1040 extracellular solute-binding protein YP_612697.1 751184 R 292414 CDS YP_612698.1 99080544 4077370 752089..754533 1 NC_008044.1 PFAM: RNA binding S1: (4.1e-24); SMART: Resolvase, RNase H-like fold: (8.8e-34); KEGG: sil:SPOA0306 S1 RNA binding domain protein, ev=0.0, 78% identity; RNA binding S1 754533 4077370 TM1040_0703 Ruegeria sp. TM1040 RNA binding S1 YP_612698.1 752089 D 292414 CDS YP_612699.1 99080545 4077371 complement(754656..756002) 1 NC_008044.1 KEGG: sil:SPO2845 hypothetical protein, ev=2e-89, 45% identity; hypothetical protein 756002 4077371 TM1040_0704 Ruegeria sp. TM1040 hypothetical protein YP_612699.1 754656 R 292414 CDS YP_612700.1 99080546 4076982 complement(756188..756643) 1 NC_008044.1 KEGG: sil:SPO2843 hypothetical protein, ev=3e-18, 40% identity; hypothetical protein 756643 4076982 TM1040_0705 Ruegeria sp. TM1040 hypothetical protein YP_612700.1 756188 R 292414 CDS YP_612701.1 99080547 4076983 complement(756633..759197) 1 NC_008044.1 TIGRFAM: Peptidase M1, alanyl aminopeptidase: (0); PFAM: peptidase M1, membrane alanine aminopeptidase: (5.2e-51); KEGG: sil:SPO2841 aminopeptidase N, ev=0.0, 71% identity; aminopeptidase 759197 pepN 4076983 pepN Ruegeria sp. TM1040 aminopeptidase YP_612701.1 756633 R 292414 CDS YP_612702.1 99080548 4076984 complement(759629..761062) 1 NC_008044.1 PFAM: NAD(P) transhydrogenase, beta subunit: (1.3e-251); KEGG: sil:SPO2819 NAD(P)+ transhydrogenase, beta subunit, ev=0.0, 86% identity; NAD(P) transhydrogenase subunit beta 761062 4076984 TM1040_0707 Ruegeria sp. TM1040 NAD(P) transhydrogenase subunit beta YP_612702.1 759629 R 292414 CDS YP_612703.1 99080549 4076985 complement(761076..762650) 1 NC_008044.1 forms a tetramer composed of 2 alpha subunits and 2 beta subunits in the inner membrane; involved in catalyzing transfer of hydride ion equivalents between NAD and NADP; stereospecific (AB-specific); functions as a proton pump by translocating protons from cytoplasm to periplasm; NAD(P) transhydrogenase subunit alpha 762650 pntA 4076985 pntA Ruegeria sp. TM1040 NAD(P) transhydrogenase subunit alpha YP_612703.1 761076 R 292414 CDS YP_612704.1 99080550 4076986 762745..762972 1 NC_008044.1 hypothetical protein 762972 4076986 TM1040_0709 Ruegeria sp. TM1040 hypothetical protein YP_612704.1 762745 D 292414 CDS YP_612705.1 99080551 4076987 complement(762988..763779) 1 NC_008044.1 PFAM: peptidase C26: (1.1e-79); KEGG: sil:SPO2837 hypothetical protein, ev=1e-117, 81% identity; peptidase C26 763779 4076987 TM1040_0710 Ruegeria sp. TM1040 peptidase C26 YP_612705.1 762988 R 292414 CDS YP_612706.1 99080552 4076988 complement(763923..766052) 1 NC_008044.1 catalyzes the formation of malate from glyoxylate and acetyl-CoA; malate synthase G 766052 4076988 TM1040_0711 Ruegeria sp. TM1040 malate synthase G YP_612706.1 763923 R 292414 CDS YP_612707.1 99080553 4076989 766372..767652 1 NC_008044.1 KEGG: sil:SPO2818 hypothetical protein, ev=1e-158, 66% identity; hypothetical protein 767652 4076989 TM1040_0712 Ruegeria sp. TM1040 hypothetical protein YP_612707.1 766372 D 292414 CDS YP_612708.1 99080554 4076990 complement(767742..768734) 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1.2e-39); KEGG: sil:SPO2816 peptide/nickel/opine uptake family ABC transporter, permease protein, ev=1e-110, 65% identity; binding-protein-dependent transport system inner membrane protein 768734 4076990 TM1040_0713 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_612708.1 767742 R 292414 CDS YP_612709.1 99080555 4076991 complement(768727..769734) 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (3.7e-49); KEGG: sil:SPO2815 peptide/nickel/opine uptake family ABC transporter, permease protein, ev=1e-177, 92% identity; binding-protein-dependent transport system inner membrane protein 769734 4076991 TM1040_0714 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_612709.1 768727 R 292414 CDS YP_612710.1 99080556 4076992 complement(769931..771628) 1 NC_008044.1 PFAM: extracellular solute-binding protein, family 5: (4.8e-54); KEGG: sil:SPO2814 peptide/opine/nickel uptake family ABC transporter, periplasmic substrate-binding protein, ev=0.0, 79% identity; extracellular solute-binding protein 771628 4076992 TM1040_0715 Ruegeria sp. TM1040 extracellular solute-binding protein YP_612710.1 769931 R 292414 CDS YP_612711.1 99080557 4076993 771989..773809 1 NC_008044.1 PFAM: ABC transporter related: (3.6e-53) Oligopeptide/dipeptide ABC transporter-like: (1.4e-09); SMART: ATPase: (9.6e-17); KEGG: sil:SPO2813 peptide/nickel/opine uptake family ABC transporter, ATP-binding protein, , ev=0.0, 82% identity; ABC transporter 773809 4076993 TM1040_0716 Ruegeria sp. TM1040 ABC transporter YP_612711.1 771989 D 292414 CDS YP_612712.1 99080558 4076994 773813..774979 1 NC_008044.1 catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine; acetylornithine deacetylase 774979 4076994 TM1040_0717 Ruegeria sp. TM1040 acetylornithine deacetylase YP_612712.1 773813 D 292414 CDS YP_612713.1 99080559 4076995 775182..776354 1 NC_008044.1 KEGG: sil:SPO2811 amidohydrolase family protein, ev=1e-168, 74% identity; TIGRFAM: Peptidase M20D, amidohydrolase: (6.8e-130); PFAM: peptidase M20: (2.1e-65) peptidase dimerisation: (1.8e-10); peptidase M20D, amidohydrolase 776354 4076995 TM1040_0718 Ruegeria sp. TM1040 peptidase M20D, amidohydrolase YP_612713.1 775182 D 292414 CDS YP_612714.1 99080560 4076996 776435..777598 1 NC_008044.1 KEGG: sil:SPO2808 amidohydrolase family protein, ev=0.0, 87% identity; TIGRFAM: Peptidase M20D, amidohydrolase: (2.2e-133); PFAM: peptidase M20: (3.8e-64) peptidase dimerisation: (0.00021); peptidase M20D, amidohydrolase 777598 4076996 TM1040_0719 Ruegeria sp. TM1040 peptidase M20D, amidohydrolase YP_612714.1 776435 D 292414 CDS YP_612715.1 99080561 4076997 complement(777706..778089) 1 NC_008044.1 hypothetical protein 778089 4076997 TM1040_0720 Ruegeria sp. TM1040 hypothetical protein YP_612715.1 777706 R 292414 CDS YP_612716.1 99080562 4076998 complement(778374..778766) 1 NC_008044.1 hypothetical protein 778766 4076998 TM1040_0721 Ruegeria sp. TM1040 hypothetical protein YP_612716.1 778374 R 292414 CDS YP_612717.1 99080563 4076999 complement(779020..780093) 1 NC_008044.1 PFAM: glycosyl transferase, group 1: (2.1e-40); KEGG: jan:Jann_3847 glycosyl transferase, group 1, ev=1e-105, 57% identity; group 1 glycosyl transferase 780093 4076999 TM1040_0722 Ruegeria sp. TM1040 group 1 glycosyl transferase YP_612717.1 779020 R 292414 CDS YP_612718.1 99080564 4077000 complement(780104..781408) 1 NC_008044.1 PFAM: glycosyl transferase, group 1: (0.0014) Three-deoxy-D-manno-octulosonic-acid transferase-like: (5.2e-59); KEGG: sil:SPO2800 3-deoxy-D-manno-octulosonic acid transferase, ev=1e-147, 62% identity; three-deoxy-D-manno-octulosonic-acid transferase-like protein 781408 4077000 TM1040_0723 Ruegeria sp. TM1040 three-deoxy-D-manno-octulosonic-acid transferase-like protein YP_612718.1 780104 R 292414 CDS YP_612719.1 99080565 4077001 complement(781420..782427) 1 NC_008044.1 together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z; molybdenum cofactor biosynthesis protein A 782427 moaA 4077001 moaA Ruegeria sp. TM1040 molybdenum cofactor biosynthesis protein A YP_612719.1 781420 R 292414 CDS YP_612720.1 99080566 4076095 782613..783122 1 NC_008044.1 KEGG: jan:Jann_3286 hypothetical protein, ev=3e-17, 45% identity; hypothetical protein 783122 4076095 TM1040_0725 Ruegeria sp. TM1040 hypothetical protein YP_612720.1 782613 D 292414 CDS YP_612721.1 99080567 4076096 complement(783149..783826) 1 NC_008044.1 KEGG: sil:SPO2798 hypothetical protein, ev=4e-90, 71% identity; hypothetical protein 783826 4076096 TM1040_0726 Ruegeria sp. TM1040 hypothetical protein YP_612721.1 783149 R 292414 CDS YP_612722.1 99080568 4076097 complement(783823..785631) 1 NC_008044.1 Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source; glucosamine--fructose-6-phosphate aminotransferase 785631 4076097 TM1040_0727 Ruegeria sp. TM1040 glucosamine--fructose-6-phosphate aminotransferase YP_612722.1 783823 R 292414 CDS YP_612723.1 99080569 4076098 complement(785636..786985) 1 NC_008044.1 forms a homotrimer; catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc; function in cell wall synthesis; bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase 786985 glmU 4076098 glmU Ruegeria sp. TM1040 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase YP_612723.1 785636 R 292414 CDS YP_612724.1 99080570 4076099 787121..787798 1 NC_008044.1 KEGG: sil:SPO2796 phosphoglycolate phosphatase, ev=3e-88, 74% identity; TIGRFAM: HAD-superfamily hydrolase subfamily IA, variant 3: (2.7e-05) HAD-superfamily hydrolase, subfamily IA, variant 1: (4e-05); PFAM: Haloacid dehalogenase-like hydrolase: (5.6e-28); HAD family hydrolase 787798 4076099 TM1040_0729 Ruegeria sp. TM1040 HAD family hydrolase YP_612724.1 787121 D 292414 CDS YP_612725.1 99080571 4076100 complement(787842..788300) 1 NC_008044.1 KEGG: sil:SPO1770 hypothetical protein, ev=1e-41, 60% identity; hypothetical protein 788300 4076100 TM1040_0730 Ruegeria sp. TM1040 hypothetical protein YP_612725.1 787842 R 292414 CDS YP_612726.1 99080572 4076101 788430..789647 1 NC_008044.1 PFAM: DegT/DnrJ/EryC1/StrS aminotransferase: (4.2e-48); KEGG: sil:SPO2795 aminotransferase, DegT/DnrJ/EryC1/StrS family, ev=0.0, 79% identity; DegT/DnrJ/EryC1/StrS aminotransferase 789647 4076101 TM1040_0731 Ruegeria sp. TM1040 DegT/DnrJ/EryC1/StrS aminotransferase YP_612726.1 788430 D 292414 CDS YP_612727.1 99080573 4076102 789814..790977 1 NC_008044.1 PFAM: acyl-CoA dehydrogenase-like: (3.6e-55) Acyl-CoA dehydrogenase, type 2-like: (3.8e-13); KEGG: sil:SPO2793 isovaleryl-CoA dehydrogenase, ev=0.0, 89% identity; isovaleryl-CoA dehydrogenase 790977 4076102 TM1040_0732 Ruegeria sp. TM1040 isovaleryl-CoA dehydrogenase YP_612727.1 789814 D 292414 CDS YP_612728.1 99080574 4076103 790985..791335 1 NC_008044.1 hypothetical protein 791335 4076103 TM1040_0733 Ruegeria sp. TM1040 hypothetical protein YP_612728.1 790985 D 292414 CDS YP_612729.1 99080575 4076104 complement(791464..792066) 1 NC_008044.1 PFAM: OmpW: (6.3e-45); KEGG: sil:SPO2792 outer membrane protein OmpW, ev=2e-67, 61% identity; OmpW protein 792066 4076104 TM1040_0734 Ruegeria sp. TM1040 OmpW protein YP_612729.1 791464 R 292414 CDS YP_612730.1 99080576 4076105 792161..793741 1 NC_008044.1 PFAM: AMP-dependent synthetase and ligase: (3.3e-94); KEGG: sil:SPO2791 acetyl-coenzyme A synthetase, ev=0.0, 78% identity; AMP-dependent synthetase/ligase 793741 4076105 TM1040_0735 Ruegeria sp. TM1040 AMP-dependent synthetase/ligase YP_612730.1 792161 D 292414 CDS YP_612731.1 99080577 4076106 793741..794145 1 NC_008044.1 hypothetical protein 794145 4076106 TM1040_0736 Ruegeria sp. TM1040 hypothetical protein YP_612731.1 793741 D 292414 CDS YP_612732.1 99080578 4076107 794142..795746 1 NC_008044.1 PFAM: carboxyl transferase: (1.3e-204); KEGG: sil:SPO2790 methylcrotonyl-CoA carboxylase, beta subunit, ev=0.0, 91% identity; propionyl-CoA carboxylase 795746 4076107 TM1040_0737 Ruegeria sp. TM1040 propionyl-CoA carboxylase YP_612732.1 794142 D 292414 CDS YP_612733.1 99080579 4076108 795827..797764 1 NC_008044.1 PFAM: biotin/lipoyl attachment: (2.9e-21) ATP-dependent carboxylate-amine ligase-like, ATP-grasp: (0.0042) Carbamoyl-phosphate synthase L chain, ATP-binding: (1.7e-93) Carbamoyl-phosphate synthetase large chain-like: (2.4e-43) biotin carboxylase-like: (2.9e-41); KEGG: sil:SPO2789 methylcrotonyl-CoA carboxylase, alpha subunit, ev=0.0, 77% identity; 3-methylcrotonoyl-CoA carboxylase subunit alpha 797764 4076108 TM1040_0738 Ruegeria sp. TM1040 3-methylcrotonoyl-CoA carboxylase subunit alpha YP_612733.1 795827 D 292414 CDS YP_612734.1 99080580 4076109 797797..798663 1 NC_008044.1 catalyzes the formation of acetoacetate and acetyl-CoA from 3-hydroxy-3-methylglutaryl-CoA; hydroxymethylglutaryl-CoA lyase 798663 4076109 TM1040_0739 Ruegeria sp. TM1040 hydroxymethylglutaryl-CoA lyase YP_612734.1 797797 D 292414 CDS YP_612735.1 99080581 4076110 798693..799478 1 NC_008044.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 799478 4076110 TM1040_0740 Ruegeria sp. TM1040 enoyl-CoA hydratase YP_612735.1 798693 D 292414 CDS YP_612736.1 99080582 4076111 799720..800085 1 NC_008044.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit A 800085 4076111 TM1040_0741 Ruegeria sp. TM1040 NADH dehydrogenase subunit A YP_612736.1 799720 D 292414 CDS YP_612737.1 99080583 4076112 800085..800609 1 NC_008044.1 The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen; NADH dehydrogenase subunit B 800609 4076112 TM1040_0742 Ruegeria sp. TM1040 NADH dehydrogenase subunit B YP_612737.1 800085 D 292414 CDS YP_612738.1 99080584 4076113 800625..801230 1 NC_008044.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit C 801230 4076113 TM1040_0743 Ruegeria sp. TM1040 NADH dehydrogenase subunit C YP_612738.1 800625 D 292414 CDS YP_612739.1 99080585 4076153 801379..802590 1 NC_008044.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit D 802590 4076153 TM1040_0744 Ruegeria sp. TM1040 NADH dehydrogenase subunit D YP_612739.1 801379 D 292414 CDS YP_612740.1 99080586 4076154 802587..803081 1 NC_008044.1 hypothetical protein 803081 4076154 TM1040_0745 Ruegeria sp. TM1040 hypothetical protein YP_612740.1 802587 D 292414 CDS YP_612741.1 99080587 4076155 803081..804277 1 NC_008044.1 catalyzes the transfer of electrons from NADH to ubiquinone; NADH dehydrogenase subunit E 804277 4076155 TM1040_0746 Ruegeria sp. TM1040 NADH dehydrogenase subunit E YP_612741.1 803081 D 292414 CDS YP_612742.1 99080588 4076156 804336..804566 1 NC_008044.1 KEGG: sil:SPO2778 hypothetical protein, ev=7e-23, 68% identity; hypothetical protein 804566 4076156 TM1040_0747 Ruegeria sp. TM1040 hypothetical protein YP_612742.1 804336 D 292414 CDS YP_612743.1 99080589 4076157 804573..805871 1 NC_008044.1 part of NADH-ubiquinone oxidoreductase complex I; shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain; NuoF is part of the soluble NADH dehydrogenase fragment, which represents the electron input part of NADH dehydrogenase; NADH dehydrogenase I subunit F 805871 4076157 TM1040_0748 Ruegeria sp. TM1040 NADH dehydrogenase I subunit F YP_612743.1 804573 D 292414 CDS YP_612744.1 99080590 4076158 805880..806239 1 NC_008044.1 KEGG: sil:SPO2776 hypothetical protein, ev=3e-14, 38% identity; hypothetical protein 806239 4076158 TM1040_0749 Ruegeria sp. TM1040 hypothetical protein YP_612744.1 805880 D 292414 CDS YP_612745.1 99080591 4076159 806338..806802 1 NC_008044.1 KEGG: sil:SPO2775 hypothetical protein, ev=4e-27, 44% identity; hypothetical protein 806802 4076159 TM1040_0750 Ruegeria sp. TM1040 hypothetical protein YP_612745.1 806338 D 292414 CDS YP_612746.1 99080592 4076160 806806..808788 1 NC_008044.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit G 808788 4076160 TM1040_0751 Ruegeria sp. TM1040 NADH dehydrogenase subunit G YP_612746.1 806806 D 292414 CDS YP_612747.1 99080593 4076161 808785..809177 1 NC_008044.1 KEGG: sil:SPO2773 lipoprotein, , ev=6e-41, 64% identity; lipoprotein 809177 4076161 TM1040_0752 Ruegeria sp. TM1040 lipoprotein YP_612747.1 808785 D 292414 CDS YP_612748.1 99080594 4076162 809184..810221 1 NC_008044.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit H 810221 4076162 TM1040_0753 Ruegeria sp. TM1040 NADH dehydrogenase subunit H YP_612748.1 809184 D 292414 CDS YP_612749.1 99080595 4076163 810223..810717 1 NC_008044.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit I 810717 4076163 TM1040_0754 Ruegeria sp. TM1040 NADH dehydrogenase subunit I YP_612749.1 810223 D 292414 CDS YP_612750.1 99080596 4076164 810750..811124 1 NC_008044.1 PFAM: Carboxymuconolactone decarboxylase: (1.9e-13); KEGG: sil:SPO2768 4-carboxymuconolactone decarboxylase, , ev=5e-53, 84% identity; carboxymuconolactone decarboxylase 811124 4076164 TM1040_0755 Ruegeria sp. TM1040 carboxymuconolactone decarboxylase YP_612750.1 810750 D 292414 CDS YP_612751.1 99080597 4076165 811121..811723 1 NC_008044.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit J 811723 4076165 TM1040_0756 Ruegeria sp. TM1040 NADH dehydrogenase subunit J YP_612751.1 811121 D 292414 CDS YP_612752.1 99080598 4076166 811738..812043 1 NC_008044.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit K 812043 4076166 TM1040_0757 Ruegeria sp. TM1040 NADH dehydrogenase subunit K YP_612752.1 811738 D 292414 CDS YP_612753.1 99080599 4076167 812049..814169 1 NC_008044.1 Catalyzes the transfer of electrons from NADH to ubiquinone; NADH dehydrogenase subunit L 814169 4076167 TM1040_0758 Ruegeria sp. TM1040 NADH dehydrogenase subunit L YP_612753.1 812049 D 292414 CDS YP_612754.1 99080600 4076168 814169..815734 1 NC_008044.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit M 815734 4076168 TM1040_0759 Ruegeria sp. TM1040 NADH dehydrogenase subunit M YP_612754.1 814169 D 292414 CDS YP_612755.1 99080601 4076169 815747..817183 1 NC_008044.1 Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit N 817183 4076169 TM1040_0760 Ruegeria sp. TM1040 NADH dehydrogenase subunit N YP_612755.1 815747 D 292414 CDS YP_612756.1 99080602 4076170 817272..818021 1 NC_008044.1 KEGG: sil:SPO2762 biotin--acetyl-CoA-carboxylase ligase, ev=5e-97, 72% identity; TIGRFAM: Biotin--acetyl-CoA-carboxylase ligase: (6.6e-33); PFAM: biotin protein ligase-like: (6.5e-07) biotin/lipoate A/B protein ligase: (6.1e-16); biotin--acetyl-CoA-carboxylase ligase 818021 4076170 TM1040_0761 Ruegeria sp. TM1040 biotin--acetyl-CoA-carboxylase ligase YP_612756.1 817272 D 292414 CDS YP_612757.1 99080603 4076171 818036..818818 1 NC_008044.1 type III; catalyzes the formation of (R)-4'-phosphopantothenate from (R)-pantothenate in coenzyme A biosynthesis; type III pantothenate kinases are not subject to feedback inhibition from coenzyme A and have a high Km for ATP; pantothenate kinase 818818 4076171 TM1040_0762 Ruegeria sp. TM1040 pantothenate kinase YP_612757.1 818036 D 292414 CDS YP_612758.1 99080604 4076172 818815..820482 1 NC_008044.1 PFAM: beta-lactamase-like: (1.8e-24) RNA-metabolising metallo-beta-lactamase: (2.8e-07); KEGG: sil:SPO2760 metallo-beta-lactamase family protein, ev=0.0, 74% identity; beta-lactamase-like protein 820482 4076172 TM1040_0763 Ruegeria sp. TM1040 beta-lactamase-like protein YP_612758.1 818815 D 292414 CDS YP_612759.1 99080605 4078076 complement(820756..821496) 1 NC_008044.1 PFAM: triosephosphate isomerase: (9.1e-116); KEGG: jan:Jann_1733 triosephosphate isomerase, ev=2e-88, 66% identity; triosephosphate isomerase 821496 4078076 TM1040_0764 Ruegeria sp. TM1040 triosephosphate isomerase YP_612759.1 820756 R 292414 CDS YP_612760.1 99080606 4078077 complement(821644..821997) 1 NC_008044.1 PFAM: HesB/YadR/YfhF: (1.1e-33); KEGG: sil:SPO2620 iron-sulfur cluster assembly accessory protein, ev=6e-51, 83% identity; HesB/YadR/YfhF 821997 4078077 TM1040_0765 Ruegeria sp. TM1040 HesB/YadR/YfhF YP_612760.1 821644 R 292414 CDS YP_612761.1 99080607 4078078 complement(822118..822480) 1 NC_008044.1 PFAM: protein of unknown function DUF59: (5.3e-26); KEGG: sil:SPO2619 hypothetical protein, ev=3e-55, 80% identity; hypothetical protein 822480 4078078 TM1040_0766 Ruegeria sp. TM1040 hypothetical protein YP_612761.1 822118 R 292414 CDS YP_612762.1 99080608 4078079 complement(822656..822928) 1 NC_008044.1 KEGG: sil:SPO2618 hypothetical protein, ev=5e-26, 67% identity; hypothetical protein 822928 4078079 TM1040_0767 Ruegeria sp. TM1040 hypothetical protein YP_612762.1 822656 R 292414 CDS YP_612763.1 99080609 4078080 complement(822928..823815) 1 NC_008044.1 PFAM: band 7 protein: (6.5e-61); KEGG: sil:SPO2617 SPFH domain/band 7 family protein, ev=1e-135, 85% identity; hypothetical protein 823815 4078080 TM1040_0768 Ruegeria sp. TM1040 hypothetical protein YP_612763.1 822928 R 292414 CDS YP_612764.1 99080610 4078081 complement(823906..825321) 1 NC_008044.1 TIGRFAM: S6 modification enzyme RimK: (6.5e-102); PFAM: protein of unknown function DUF201: (7.9e-06) protein of unknown function DUF785: (2.5e-29) RimK-like ATP-grasp: (8.3e-79); KEGG: syw:SYNW1384 possible ribosomal protein S6 modification protein, ev=1e-116, 50% identity; 30S ribosomal protein S6 modification protein RimK 825321 4078081 TM1040_0769 Ruegeria sp. TM1040 30S ribosomal protein S6 modification protein RimK YP_612764.1 823906 R 292414 CDS YP_612765.1 99080611 4078082 825392..826522 1 NC_008044.1 Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr); queuine tRNA-ribosyltransferase 826522 tgt 4078082 tgt Ruegeria sp. TM1040 queuine tRNA-ribosyltransferase YP_612765.1 825392 D 292414 CDS YP_612766.1 99080612 4078083 complement(826781..827053) 1 NC_008044.1 hypothetical protein 827053 4078083 TM1040_0771 Ruegeria sp. TM1040 hypothetical protein YP_612766.1 826781 R 292414 CDS YP_612767.1 99080613 4078084 complement(827050..827559) 1 NC_008044.1 hypothetical protein 827559 4078084 TM1040_0772 Ruegeria sp. TM1040 hypothetical protein YP_612767.1 827050 R 292414 CDS YP_612768.1 99080614 4078085 827885..828559 1 NC_008044.1 PFAM: NADH:flavin oxidoreductase/NADH oxidase: (5.2e-17); KEGG: sil:SPO2615 NADH-dependent flavin oxidoreductase, Oye family, ev=2e-70, 56% identity; NADH:flavin oxidoreductase 828559 4078085 TM1040_0773 Ruegeria sp. TM1040 NADH:flavin oxidoreductase YP_612768.1 827885 D 292414 CDS YP_612769.1 99080615 4078086 828617..828880 1 NC_008044.1 KEGG: sil:SPO2615 NADH-dependent flavin oxidoreductase, Oye family, ev=3e-20, 60% identity; Oye family NADH-dependent flavin oxidoreductase 828880 4078086 TM1040_0774 Ruegeria sp. TM1040 Oye family NADH-dependent flavin oxidoreductase YP_612769.1 828617 D 292414 CDS YP_612770.1 99080616 4078087 829194..831602 1 NC_008044.1 KEGG: sil:SPO2613 ATP-dependent protease La, ev=0.0, 86% identity; TIGRFAM: ATP-dependent protease La: (0); PFAM: peptidase S16, lon-like: (1.1e-34) AAA ATPase, central region: (4.1e-48) ATPase associated with various cellular activities, AAA_5: (0.00026); SMART: ATPase: (6e-14); Lon-A peptidase 831602 4078087 TM1040_0775 Ruegeria sp. TM1040 Lon-A peptidase YP_612770.1 829194 D 292414 CDS YP_612771.1 99080617 4078088 complement(832173..833177) 1 NC_008044.1 PFAM: phage integrase: (3.2e-24); KEGG: rsp:RSP_3805 possible integrase, ev=9e-93, 54% identity; phage integrase 833177 4078088 TM1040_0776 Ruegeria sp. TM1040 phage integrase YP_612771.1 832173 R 292414 CDS YP_612772.1 99080618 4078089 complement(833487..833819) 1 NC_008044.1 hypothetical protein 833819 4078089 TM1040_0777 Ruegeria sp. TM1040 hypothetical protein YP_612772.1 833487 R 292414 CDS YP_612773.1 99080619 4078090 complement(833924..834868) 1 NC_008044.1 hypothetical protein 834868 4078090 TM1040_0778 Ruegeria sp. TM1040 hypothetical protein YP_612773.1 833924 R 292414 CDS YP_612774.1 99080620 4078091 complement(834865..835524) 1 NC_008044.1 KEGG: rsp:RSP_3792 hypothetical protein, ev=2e-76, 59% identity; hypothetical protein 835524 4078091 TM1040_0779 Ruegeria sp. TM1040 hypothetical protein YP_612774.1 834865 R 292414 CDS YP_612775.1 99080621 4078092 complement(835670..836443) 1 NC_008044.1 KEGG: bpm:BURPS1710b_1662 gp47, ev=2e-17, 26% identity; hypothetical protein 836443 4078092 TM1040_0780 Ruegeria sp. TM1040 hypothetical protein YP_612775.1 835670 R 292414 CDS YP_612776.1 99080622 4078093 complement(836465..836770) 1 NC_008044.1 PFAM: protein of unknown function DUF1364: (2.1e-18); KEGG: ecj:JW0537 hypothetical protein, ev=2e-13, 54% identity; hypothetical protein 836770 4078093 TM1040_0781 Ruegeria sp. TM1040 hypothetical protein YP_612776.1 836465 R 292414 CDS YP_612777.1 99080623 4078094 complement(836839..837342) 1 NC_008044.1 hypothetical protein 837342 4078094 TM1040_0782 Ruegeria sp. TM1040 hypothetical protein YP_612777.1 836839 R 292414 CDS YP_612778.1 99080624 4076055 complement(837342..837950) 1 NC_008044.1 KEGG: bhe:BH06850 exonuclease, ev=2e-41, 43% identity; exonuclease 837950 4076055 TM1040_0783 Ruegeria sp. TM1040 exonuclease YP_612778.1 837342 R 292414 CDS YP_612779.1 99080625 4076056 complement(837950..838672) 1 NC_008044.1 PFAM: ERF: (2.6e-12); KEGG: bhe:BH06860 phage related protein, ev=4e-16, 28% identity; hypothetical protein 838672 4076056 TM1040_0784 Ruegeria sp. TM1040 hypothetical protein YP_612779.1 837950 R 292414 CDS YP_612780.1 99080626 4076057 complement(838781..839026) 1 NC_008044.1 hypothetical protein 839026 4076057 TM1040_0785 Ruegeria sp. TM1040 hypothetical protein YP_612780.1 838781 R 292414 CDS YP_612781.1 99080627 4076058 complement(839240..839599) 1 NC_008044.1 hypothetical protein 839599 4076058 TM1040_0786 Ruegeria sp. TM1040 hypothetical protein YP_612781.1 839240 R 292414 CDS YP_612782.1 99080628 4076059 complement(839907..840665) 1 NC_008044.1 hypothetical protein 840665 4076059 TM1040_0787 Ruegeria sp. TM1040 hypothetical protein YP_612782.1 839907 R 292414 CDS YP_612783.1 99080629 4076060 complement(840662..841195) 1 NC_008044.1 hypothetical protein 841195 4076060 TM1040_0788 Ruegeria sp. TM1040 hypothetical protein YP_612783.1 840662 R 292414 CDS YP_612784.1 99080630 4076061 complement(841219..841935) 1 NC_008044.1 PFAM: peptidase S24, S26A and S26B: (0.022); SMART: Helix-turn-helix type 3: (2.6e-07); KEGG: rsp:RSP_3771 hypothetical protein, ev=8e-38, 41% identity; phage repressor 841935 4076061 TM1040_0789 Ruegeria sp. TM1040 phage repressor YP_612784.1 841219 R 292414 CDS YP_612785.1 99080631 4076062 842213..842701 1 NC_008044.1 hypothetical protein 842701 4076062 TM1040_0790 Ruegeria sp. TM1040 hypothetical protein YP_612785.1 842213 D 292414 CDS YP_612786.1 99080632 4076063 842939..843241 1 NC_008044.1 hypothetical protein 843241 4076063 TM1040_0791 Ruegeria sp. TM1040 hypothetical protein YP_612786.1 842939 D 292414 CDS YP_612787.1 99080633 4076064 843244..843765 1 NC_008044.1 KEGG: ava:Ava_B0325 hypothetical protein, ev=9e-07, 33% identity; hypothetical protein 843765 4076064 TM1040_0792 Ruegeria sp. TM1040 hypothetical protein YP_612787.1 843244 D 292414 CDS YP_612788.1 99080634 4076065 843762..844118 1 NC_008044.1 PFAM: endodeoxyribonuclease RusA: (0.008); KEGG: nfa:nfa39720 hypothetical protein, ev=3e-06, 39% identity; endodeoxyribonuclease RusA 844118 4076065 TM1040_0793 Ruegeria sp. TM1040 endodeoxyribonuclease RusA YP_612788.1 843762 D 292414 CDS YP_612789.1 99080635 4076066 844130..844861 1 NC_008044.1 KEGG: bbr:BB1683 phage-related hypothetical protein, ev=1e-15, 38% identity; hypothetical protein 844861 4076066 TM1040_0794 Ruegeria sp. TM1040 hypothetical protein YP_612789.1 844130 D 292414 CDS YP_612790.1 99080636 4076067 844851..845414 1 NC_008044.1 hypothetical protein 845414 4076067 TM1040_0795 Ruegeria sp. TM1040 hypothetical protein YP_612790.1 844851 D 292414 CDS YP_612791.1 99080637 4076068 845629..846108 1 NC_008044.1 TIGRFAM: single-strand binding protein: (4.7e-55); PFAM: single-strand binding protein/Primosomal replication protein n: (9.2e-33); KEGG: sil:SPO1637 single-strand binding protein, ev=7e-66, 72% identity; single-strand binding protein 846108 4076068 TM1040_0796 Ruegeria sp. TM1040 single-strand binding protein YP_612791.1 845629 D 292414 CDS YP_612792.1 99080638 4076069 846108..846362 1 NC_008044.1 hypothetical protein 846362 4076069 TM1040_0797 Ruegeria sp. TM1040 hypothetical protein YP_612792.1 846108 D 292414 CDS YP_612793.1 99080639 4076070 846385..846966 1 NC_008044.1 hypothetical protein 846966 4076070 TM1040_0798 Ruegeria sp. TM1040 hypothetical protein YP_612793.1 846385 D 292414 CDS YP_612794.1 99080640 4076071 complement(847447..847725) 1 NC_008044.1 hypothetical protein 847725 4076071 TM1040_0799 Ruegeria sp. TM1040 hypothetical protein YP_612794.1 847447 R 292414 CDS YP_612795.1 99080641 4076072 847787..848365 1 NC_008044.1 PFAM: Terminase small subunit: (4.2e-30); KEGG: gox:GOX2458 phage terminase small subunit, ev=3e-25, 45% identity; terminase small subunit 848365 4076072 TM1040_0800 Ruegeria sp. TM1040 terminase small subunit YP_612795.1 847787 D 292414 CDS YP_612796.1 99080642 4076073 848343..849593 1 NC_008044.1 PFAM: protein of unknown function DUF264: (1.3e-31); KEGG: pfl:PFL_3766 hypothetical protein, ev=1e-117, 52% identity; hypothetical protein 849593 4076073 TM1040_0801 Ruegeria sp. TM1040 hypothetical protein YP_612796.1 848343 D 292414 CDS YP_612797.1 99080643 4076074 849590..850969 1 NC_008044.1 KEGG: rru:Rru_A2589 hypothetical protein, ev=1e-42, 33% identity; hypothetical protein 850969 4076074 TM1040_0802 Ruegeria sp. TM1040 hypothetical protein YP_612797.1 849590 D 292414 CDS YP_612798.1 99080644 4076192 850956..852005 1 NC_008044.1 PFAM: phage head morphogenesis protein, SPP1 gp7: (3.9e-07); KEGG: ypk:y2207 hypothetical protein, ev=4e-57, 36% identity; phage head morphogenesis protein, SPP1 gp7 852005 4076192 TM1040_0803 Ruegeria sp. TM1040 phage head morphogenesis protein, SPP1 gp7 YP_612798.1 850956 D 292414 CDS YP_612799.1 99080645 4076193 852235..852918 1 NC_008044.1 KEGG: ypk:y2206 hypothetical protein, ev=7e-07, 25% identity; hypothetical protein 852918 4076193 TM1040_0804 Ruegeria sp. TM1040 hypothetical protein YP_612799.1 852235 D 292414 CDS YP_612800.1 99080646 4076194 852931..853899 1 NC_008044.1 KEGG: bbr:BB3501 hypothetical protein, ev=1e-120, 67% identity; hypothetical protein 853899 4076194 TM1040_0805 Ruegeria sp. TM1040 hypothetical protein YP_612800.1 852931 D 292414 CDS YP_612801.1 99080647 4076195 853963..854214 1 NC_008044.1 hypothetical protein 854214 4076195 TM1040_0806 Ruegeria sp. TM1040 hypothetical protein YP_612801.1 853963 D 292414 CDS YP_612802.1 99080648 4076196 854216..854683 1 NC_008044.1 KEGG: bpe:BP3375 hypothetical protein, ev=1e-17, 37% identity; hypothetical protein 854683 4076196 TM1040_0807 Ruegeria sp. TM1040 hypothetical protein YP_612802.1 854216 D 292414 CDS YP_612803.1 99080649 4076197 854680..855129 1 NC_008044.1 hypothetical protein 855129 4076197 TM1040_0808 Ruegeria sp. TM1040 hypothetical protein YP_612803.1 854680 D 292414 CDS YP_612804.1 99080650 4076198 855126..855500 1 NC_008044.1 hypothetical protein 855500 4076198 TM1040_0809 Ruegeria sp. TM1040 hypothetical protein YP_612804.1 855126 D 292414 CDS YP_612805.1 99080651 4076199 855500..855901 1 NC_008044.1 KEGG: bbr:BB3496 hypothetical protein, ev=9e-21, 43% identity; hypothetical protein 855901 4076199 TM1040_0810 Ruegeria sp. TM1040 hypothetical protein YP_612805.1 855500 D 292414 CDS YP_612806.1 99080652 4076200 855898..856296 1 NC_008044.1 KEGG: mlo:mlr8015 hypothetical protein, ev=5e-07, 28% identity; hypothetical protein 856296 4076200 TM1040_0811 Ruegeria sp. TM1040 hypothetical protein YP_612806.1 855898 D 292414 CDS YP_612807.1 99080653 4076201 856572..857060 1 NC_008044.1 hypothetical protein 857060 4076201 TM1040_0812 Ruegeria sp. TM1040 hypothetical protein YP_612807.1 856572 D 292414 CDS YP_612808.1 99080654 4076202 857163..857633 1 NC_008044.1 hypothetical protein 857633 4076202 TM1040_0813 Ruegeria sp. TM1040 hypothetical protein YP_612808.1 857163 D 292414 CDS YP_612809.1 99080655 4076203 857759..858004 1 NC_008044.1 hypothetical protein 858004 4076203 TM1040_0814 Ruegeria sp. TM1040 hypothetical protein YP_612809.1 857759 D 292414 CDS YP_612810.1 99080656 4076204 complement(858001..858372) 1 NC_008044.1 KEGG: rpa:RPA3130 transcriptional regulator, XRE family, ev=3e-30, 53% identity; XRE family transcriptional regulator 858372 4076204 TM1040_0815 Ruegeria sp. TM1040 XRE family transcriptional regulator YP_612810.1 858001 R 292414 CDS YP_612811.1 99080657 4076205 complement(858386..858688) 1 NC_008044.1 KEGG: rpa:RPA3131 hypothetical protein, ev=1e-30, 60% identity; hypothetical protein 858688 4076205 TM1040_0816 Ruegeria sp. TM1040 hypothetical protein YP_612811.1 858386 R 292414 CDS YP_612812.1 99080658 4076206 complement(858798..859124) 1 NC_008044.1 hypothetical protein 859124 4076206 TM1040_0817 Ruegeria sp. TM1040 hypothetical protein YP_612812.1 858798 R 292414 CDS YP_612813.1 99080659 4076207 complement(859121..859564) 1 NC_008044.1 KEGG: sil:SPO3110 TonB domain protein, , ev=9e-10, 40% identity; hypothetical protein 859564 4076207 TM1040_0818 Ruegeria sp. TM1040 hypothetical protein YP_612813.1 859121 R 292414 CDS YP_612814.1 99080660 4076208 859581..863936 1 NC_008044.1 TIGRFAM: Tape measure domain: (6.6e-14); KEGG: rsp:RSP_2059 potential phage tail tape measure protein, ev=1e-117, 28% identity; tape measure domain-containing protein 863936 4076208 TM1040_0819 Ruegeria sp. TM1040 tape measure domain-containing protein YP_612814.1 859581 D 292414 CDS YP_612815.1 99080661 4076209 863936..864880 1 NC_008044.1 KEGG: nar:Saro_0661 hypothetical protein, ev=2e-26, 25% identity; hypothetical protein 864880 4076209 TM1040_0820 Ruegeria sp. TM1040 hypothetical protein YP_612815.1 863936 D 292414 CDS YP_612816.1 99080662 4076210 864877..866394 1 NC_008044.1 KEGG: pub:SAR11_0932 hypothetical protein, ev=2e-31, 28% identity; hypothetical protein 866394 4076210 TM1040_0821 Ruegeria sp. TM1040 hypothetical protein YP_612816.1 864877 D 292414 CDS YP_612817.1 99080663 4077528 866391..866936 1 NC_008044.1 hypothetical protein 866936 4077528 TM1040_0822 Ruegeria sp. TM1040 hypothetical protein YP_612817.1 866391 D 292414 CDS YP_612818.1 99080664 4077529 866908..867261 1 NC_008044.1 hypothetical protein 867261 4077529 TM1040_0823 Ruegeria sp. TM1040 hypothetical protein YP_612818.1 866908 D 292414 CDS YP_612819.1 99080665 4077530 867268..867564 1 NC_008044.1 hypothetical protein 867564 4077530 TM1040_0824 Ruegeria sp. TM1040 hypothetical protein YP_612819.1 867268 D 292414 CDS YP_612820.1 99080666 4077531 867561..867995 1 NC_008044.1 hypothetical protein 867995 4077531 TM1040_0825 Ruegeria sp. TM1040 hypothetical protein YP_612820.1 867561 D 292414 CDS YP_612821.1 99080667 4077532 867997..868806 1 NC_008044.1 PFAM: protein of unknown function DUF847: (8.8e-67); KEGG: bmb:BruAb1_0990 secretion activator protein, hypothetical, ev=2e-43, 39% identity; hypothetical protein 868806 4077532 TM1040_0826 Ruegeria sp. TM1040 hypothetical protein YP_612821.1 867997 D 292414 CDS YP_612822.1 99080668 4077533 868803..869201 1 NC_008044.1 hypothetical protein 869201 4077533 TM1040_0827 Ruegeria sp. TM1040 hypothetical protein YP_612822.1 868803 D 292414 CDS YP_612823.1 99080669 4077534 complement(869373..869987) 1 NC_008044.1 PFAM: regulatory protein, LuxR: (3.4e-17) response regulator receiver: (1e-22); KEGG: sil:SPO0161 DNA-binding response regulator, LuxR family, ev=1e-50, 51% identity; two component LuxR family transcriptional regulator 869987 4077534 TM1040_0828 Ruegeria sp. TM1040 two component LuxR family transcriptional regulator YP_612823.1 869373 R 292414 CDS YP_612824.1 99080670 4077535 complement(870157..870582) 1 NC_008044.1 PFAM: response regulator receiver: (2.6e-05); KEGG: lic:LIC13330 response regulator, ev=8e-14, 35% identity; response regulator receiver protein 870582 4077535 TM1040_0829 Ruegeria sp. TM1040 response regulator receiver protein YP_612824.1 870157 R 292414 CDS YP_612825.1 99080671 4077536 complement(870579..871763) 1 NC_008044.1 KEGG: rru:Rru_A1875 multi-sensor signal transduction histidine kinase, ev=1e-46, 32% identity; TIGRFAM: PAS: (8.4e-07); PFAM: ATP-binding region, ATPase-like: (2.3e-31) histidine kinase A-like: (2.2e-11) PAS fold-3: (3.7e-21); SMART: PAC motif: (1.7e-08); PAS/PAC sensor signal transduction histidine kinase 871763 4077536 TM1040_0830 Ruegeria sp. TM1040 PAS/PAC sensor signal transduction histidine kinase YP_612825.1 870579 R 292414 CDS YP_612826.1 99080672 4077537 complement(872933..873844) 1 NC_008044.1 PFAM: regulatory protein, LysR: (2.7e-20) LysR, substrate-binding: (2.2e-21); KEGG: xcv:XCV2178 transcriptional regulator, LysR family, ev=1e-102, 66% identity; LysR family transcriptional regulator 873844 4077537 TM1040_0831 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_612826.1 872933 R 292414 CDS YP_612827.1 99080673 4077538 873956..875506 1 NC_008044.1 PFAM: NADH/Ubiquinone/plastoquinone (complex I): (3e-26); KEGG: jan:Jann_1259 NADH dehydrogenase (quinone), ev=0.0, 65% identity; NADH/ubiquinone/plastoquinone (complex I) 875506 4077538 TM1040_0832 Ruegeria sp. TM1040 NADH/ubiquinone/plastoquinone (complex I) YP_612827.1 873956 D 292414 CDS YP_612828.1 99080674 4077539 875521..877938 1 NC_008044.1 KEGG: jan:Jann_1258 hypothetical protein, ev=0.0, 58% identity; hypothetical protein 877938 4077539 TM1040_0833 Ruegeria sp. TM1040 hypothetical protein YP_612828.1 875521 D 292414 CDS YP_612829.1 99080675 4077540 complement(878016..879683) 1 NC_008044.1 PFAM: Amidohydrolase 3: (9.2e-81); KEGG: sil:SPO1605 hypothetical protein, ev=0.0, 62% identity; amidohydrolase 879683 4077540 TM1040_0834 Ruegeria sp. TM1040 amidohydrolase YP_612829.1 878016 R 292414 CDS YP_612830.1 99080676 4077541 complement(879761..880786) 1 NC_008044.1 PFAM: extracellular solute-binding protein, family 1: (0.00028); KEGG: sil:SPO1606 spermidine/putrescine ABC transporter, periplasmic substrate-binding protein, ev=1e-152, 76% identity; extracellular solute-binding protein 880786 4077541 TM1040_0835 Ruegeria sp. TM1040 extracellular solute-binding protein YP_612830.1 879761 R 292414 CDS YP_612831.1 99080677 4077542 complement(880854..881654) 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (0.00096); KEGG: sil:SPO1607 spermidine/putrescine ABC transporter, permease protein, ev=1e-119, 80% identity; binding-protein-dependent transport system inner membrane protein 881654 4077542 TM1040_0836 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_612831.1 880854 R 292414 CDS YP_612832.1 99080678 4077543 complement(881647..882579) 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (2e-09); KEGG: sil:SPO1608 spermidine/putrescine ABC transporter, permease protein, ev=1e-127, 74% identity; binding-protein-dependent transport system inner membrane protein 882579 4077543 TM1040_0837 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_612832.1 881647 R 292414 CDS YP_612833.1 99080679 4077544 complement(882584..883696) 1 NC_008044.1 KEGG: sil:SPO1609 spermidine/putrescine ABC transporter, ATP-binding component, ev=1e-122, 63% identity; TIGRFAM: spermidine/putrescine ABC transporter ATP-binding subunit: (1.6e-148); PFAM: ABC transporter related: (1.7e-61) TOBE: (0.0011) Transport-associated OB: (1.8e-18); SMART: ATPase: (4.1e-23); spermidine/putrescine ABC transporter ATP-binding subunit 883696 4077544 TM1040_0838 Ruegeria sp. TM1040 spermidine/putrescine ABC transporter ATP-binding subunit YP_612833.1 882584 R 292414 CDS YP_612834.1 99080680 4077545 884254..887037 1 NC_008044.1 PFAM: histidine kinase, HAMP region: (1.8e-09) chemotaxis sensory transducer: (1.2e-84); KEGG: sme:SMc01104 probable chemoreceptor (methyl-accepting chemotaxis) transmembrane protein, ev=4e-93, 47% identity; methyl-accepting chemotaxis sensory transducer 887037 4077545 TM1040_0839 Ruegeria sp. TM1040 methyl-accepting chemotaxis sensory transducer YP_612834.1 884254 D 292414 CDS YP_612835.1 99080681 4077546 complement(887215..887457) 1 NC_008044.1 hypothetical protein 887457 4077546 TM1040_0840 Ruegeria sp. TM1040 hypothetical protein YP_612835.1 887215 R 292414 CDS YP_612836.1 99080682 4077547 887959..888321 1 NC_008044.1 hypothetical protein 888321 4077547 TM1040_0841 Ruegeria sp. TM1040 hypothetical protein YP_612836.1 887959 D 292414 CDS YP_612837.1 99080683 4076017 888359..889966 1 NC_008044.1 PFAM: peptidase C1A, papain: (2.9e-08); KEGG: lic:LIC20197 cysteine protease, ev=3e-24, 30% identity; peptidase C1A, papain 889966 4076017 TM1040_0842 Ruegeria sp. TM1040 peptidase C1A, papain YP_612837.1 888359 D 292414 CDS YP_612838.1 99080684 4076018 889986..894845 1 NC_008044.1 PFAM: OmpA/MotB: (1.1e-28) peptidase C14, caspase catalytic subunit p20: (4.8e-11); KEGG: pca:Pcar_2377 OmpA domain protein, ev=1e-16, 46% identity; OmpA/MotB protein 894845 4076018 TM1040_0843 Ruegeria sp. TM1040 OmpA/MotB protein YP_612838.1 889986 D 292414 CDS YP_612839.1 99080685 4076019 complement(894888..895775) 1 NC_008044.1 PFAM: regulatory protein, LysR: (9.2e-18) LysR, substrate-binding: (3.4e-25); KEGG: sil:SPO1640 transcriptional regulator, LysR family, ev=1e-50, 39% identity; LysR family transcriptional regulator 895775 4076019 TM1040_0844 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_612839.1 894888 R 292414 CDS YP_612840.1 99080686 4076020 895892..897502 1 NC_008044.1 PFAM: glucose-methanol-choline oxidoreductase: (8.2e-97) FAD dependent oxidoreductase: (0.00062) GMC oxidoreductase: (7.6e-30) FAD-dependent pyridine nucleotide-disulphide oxidoreductase: (0.0024); KEGG: sil:SPOA0386 oxidoreductase, GMC family, ev=1e-159, 51% identity; glucose-methanol-choline oxidoreductase 897502 4076020 TM1040_0845 Ruegeria sp. TM1040 glucose-methanol-choline oxidoreductase YP_612840.1 895892 D 292414 CDS YP_612841.1 99080687 4076021 897499..898674 1 NC_008044.1 PFAM: Mandelate racemase/muconate lactonizing enzyme-like: (8.4e-08); KEGG: sil:SPOA0378 mandelate racemase/muconate lactonizing enzyme family protein, ev=1e-142, 63% identity; mandelate racemase/muconate lactonizing-like protein 898674 4076021 TM1040_0846 Ruegeria sp. TM1040 mandelate racemase/muconate lactonizing-like protein YP_612841.1 897499 D 292414 CDS YP_612842.1 99080688 4076022 898671..900155 1 NC_008044.1 PFAM: aldehyde dehydrogenase: (6.4e-209); KEGG: bbr:BB4965 probable aldehyde dehydrogenase, ev=1e-103, 43% identity; betaine aldehyde dehydrogenase 900155 4076022 TM1040_0847 Ruegeria sp. TM1040 betaine aldehyde dehydrogenase YP_612842.1 898671 D 292414 CDS YP_612843.1 99080689 4076023 complement(900379..901287) 1 NC_008044.1 PFAM: regulatory protein, LysR: (1.7e-17) LysR, substrate-binding: (7.2e-38); KEGG: sil:SPO0241 transcriptional regulator, LysR family, ev=1e-110, 64% identity; LysR family transcriptional regulator 901287 4076023 TM1040_0848 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_612843.1 900379 R 292414 CDS YP_612844.1 99080690 4076024 901433..902737 1 NC_008044.1 PFAM: extracellular solute-binding protein, family 1: (7.9e-17); KEGG: sil:SPO0240 SN-glycerol-3-phophate ABC transporter, periplasmic SN-glycerol-3-phosphate-binding protein, ev=0.0, 87% identity; extracellular solute-binding protein 902737 4076024 TM1040_0849 Ruegeria sp. TM1040 extracellular solute-binding protein YP_612844.1 901433 D 292414 CDS YP_612845.1 99080691 4076025 902829..903710 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1.8e-09); KEGG: sil:SPO0239 SN-glycerol-3-phosphate ABC transporter, permease protein, ev=1e-149, 88% identity; binding-protein-dependent transport system inner membrane protein 903710 4076025 TM1040_0850 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_612845.1 902829 D 292414 CDS YP_612846.1 99080692 4076026 903710..904561 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1.9e-23); KEGG: sil:SPO0238 SN-glycerol-3-phosphate ABC transporter, permease protein, ev=1e-152, 93% identity; binding-protein-dependent transport system inner membrane protein 904561 4076026 TM1040_0851 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_612846.1 903710 D 292414 CDS YP_612847.1 99080693 4076027 904570..905625 1 NC_008044.1 part of the UgpABCE glycerol-3-phosphate uptake system; glycerol-3-phosphate transporter ATP-binding subunit 905625 ugpC 4076027 ugpC Ruegeria sp. TM1040 glycerol-3-phosphate transporter ATP-binding subunit YP_612847.1 904570 D 292414 CDS YP_612848.1 99080694 4076028 905622..906569 1 NC_008044.1 PFAM: glycerophosphoryl diester phosphodiesterase: (1.4e-38); KEGG: sil:SPO0236 glycerophosphoryl diester phosphodiesterase, , ev=5e-90, 56% identity; glycerophosphoryl diester phosphodiesterase 906569 4076028 TM1040_0853 Ruegeria sp. TM1040 glycerophosphoryl diester phosphodiesterase YP_612848.1 905622 D 292414 CDS YP_612849.1 99080695 4076029 906573..907493 1 NC_008044.1 PFAM: Haloacid dehalogenase-like hydrolase: (1.2e-07); KEGG: rru:Rru_A1795 HAD-superfamily hydrolase, subfamily IIA, ev=7e-39, 39% identity; haloacid dehalogenase 907493 4076029 TM1040_0854 Ruegeria sp. TM1040 haloacid dehalogenase YP_612849.1 906573 D 292414 CDS YP_612850.1 99080696 4076030 907552..909198 1 NC_008044.1 PFAM: Na+/Pi-cotransporter: (3.3e-33); KEGG: sme:SMb21536 hypothetical protein, ev=1e-106, 41% identity; Na+/Pi-cotransporter 909198 4076030 TM1040_0855 Ruegeria sp. TM1040 Na+/Pi-cotransporter YP_612850.1 907552 D 292414 CDS YP_612851.1 99080697 4076031 909271..909846 1 NC_008044.1 PFAM: Phosphoglycerate mutase: (5.1e-35); KEGG: jan:Jann_2515 phosphoglycerate mutase, ev=3e-31, 42% identity; phosphoglycerate mutase 909846 4076031 TM1040_0856 Ruegeria sp. TM1040 phosphoglycerate mutase YP_612851.1 909271 D 292414 CDS YP_612852.1 99080698 4076032 complement(910004..910333) 1 NC_008044.1 hypothetical protein 910333 4076032 TM1040_0857 Ruegeria sp. TM1040 hypothetical protein YP_612852.1 910004 R 292414 CDS YP_612853.1 99080699 4076033 910897..911307 1 NC_008044.1 PFAM: thioesterase superfamily: (2.8e-19); KEGG: ccr:CC0190 acyl-CoA thioester hydrolase, ev=9e-34, 53% identity; thioesterase superfamily protein 911307 4076033 TM1040_0858 Ruegeria sp. TM1040 thioesterase superfamily protein YP_612853.1 910897 D 292414 CDS YP_612854.1 99080700 4076034 complement(911391..912782) 1 NC_008044.1 PFAM: peptidase M20: (1.7e-34) peptidase dimerisation: (2.4e-22); KEGG: sil:SPO2597 peptidase, M20/M25/M40 family, ev=0.0, 75% identity; hypothetical protein 912782 4076034 TM1040_0859 Ruegeria sp. TM1040 hypothetical protein YP_612854.1 911391 R 292414 CDS YP_612855.2 161899030 4076035 913262..914491 1 NC_008044.1 catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine; 5-aminolevulinate synthase 914491 4076035 TM1040_0860 Ruegeria sp. TM1040 5-aminolevulinate synthase YP_612855.2 913262 D 292414 CDS YP_612856.1 99080702 4076231 914620..915837 1 NC_008044.1 KEGG: rsp:RSP_2983 hypothetical protein, ev=2e-95, 50% identity; hypothetical protein 915837 4076231 TM1040_0861 Ruegeria sp. TM1040 hypothetical protein YP_612856.1 914620 D 292414 CDS YP_612857.1 99080703 4076232 915958..917091 1 NC_008044.1 catalyzes the conversion of 2C-methyl-D-erythritol 2,4-cyclodiphosphate into 4-hydroxy-3-methyl-2-en-1-yl diphosphate; involved in isoprenoid synthesis; 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase 917091 ispG 4076232 ispG Ruegeria sp. TM1040 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase YP_612857.1 915958 D 292414 CDS YP_612858.1 99080704 4076233 complement(917168..917932) 1 NC_008044.1 PFAM: DSBA oxidoreductase: (1.4e-24); KEGG: sil:SPO2591 27 kDa outer membrane protein, , ev=5e-85, 63% identity; DSBA oxidoreductase 917932 4076233 TM1040_0863 Ruegeria sp. TM1040 DSBA oxidoreductase YP_612858.1 917168 R 292414 CDS YP_612859.1 99080705 4076234 complement(917929..919350) 1 NC_008044.1 PFAM: peptidase M48, Ste24p: (2.5e-18) Tetratricopeptide TPR_2: (0.0011); KEGG: sil:SPO2590 peptidase, M48 family, ev=1e-132, 54% identity; peptidase M48, Ste24p 919350 4076234 TM1040_0864 Ruegeria sp. TM1040 peptidase M48, Ste24p YP_612859.1 917929 R 292414 CDS YP_612860.1 99080706 4076235 919373..920518 1 NC_008044.1 PFAM: aminotransferase, class I and II: (3.3e-50); KEGG: sil:SPO2589 aminotransferase, classes I and II, ev=1e-179, 82% identity; aminotransferase 920518 4076235 TM1040_0865 Ruegeria sp. TM1040 aminotransferase YP_612860.1 919373 D 292414 CDS YP_612861.1 99080707 4076236 920518..921756 1 NC_008044.1 PFAM: cell wall hydrolase/autolysin: (1.2e-58); KEGG: sil:SPO2588 N-acetylmuramoyl-L-alanine amidase, family 3, ev=1e-136, 61% identity; N-acetylmuramoyl-L-alanine amidase 921756 4076236 TM1040_0866 Ruegeria sp. TM1040 N-acetylmuramoyl-L-alanine amidase YP_612861.1 920518 D 292414 CDS YP_612862.1 99080708 4076237 922143..924650 1 NC_008044.1 KEGG: sil:SPO2587 penicillin-binding protein 1A, ev=0.0, 77% identity; TIGRFAM: Penicillin-binding protein 1A: (2.1e-205); PFAM: glycosyl transferase, family 51: (1.2e-73) penicillin-binding protein, transpeptidase: (1.3e-32); penicillin-binding protein 1A 924650 4076237 TM1040_0867 Ruegeria sp. TM1040 penicillin-binding protein 1A YP_612862.1 922143 D 292414 CDS YP_612863.1 99080709 4076238 924764..925888 1 NC_008044.1 recognizes the termination signals UGA and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF2; in some organisms control of PrfB protein levels is maintained through a +1 ribosomal frameshifting mechanism; this protein is similar to release factor 1; peptide chain release factor 2 925888 prfB 4076238 prfB Ruegeria sp. TM1040 peptide chain release factor 2 YP_612863.1 924764 D 292414 CDS YP_612864.1 99080710 4076239 complement(926009..927346) 1 NC_008044.1 PFAM: major facilitator superfamily MFS_1: (6.7e-21); KEGG: sco:SCO1457 transport protein, ev=8e-16, 27% identity; major facilitator superfamily transporter 927346 4076239 TM1040_0869 Ruegeria sp. TM1040 major facilitator superfamily transporter YP_612864.1 926009 R 292414 CDS YP_612865.1 99080711 4076240 927480..928859 1 NC_008044.1 catalyzes the hydrolysis of a monocarboxylic acid amid to form a monocarboxylate and ammonia; amidase 928859 4076240 TM1040_0870 Ruegeria sp. TM1040 amidase YP_612865.1 927480 D 292414 CDS YP_612866.1 99080712 4076241 928914..929723 1 NC_008044.1 KEGG: sil:SPO2582 membrane protein, , ev=8e-97, 66% identity; hypothetical protein 929723 4076241 TM1040_0871 Ruegeria sp. TM1040 hypothetical protein YP_612866.1 928914 D 292414 CDS YP_612867.1 99080713 4076242 complement(929716..930516) 1 NC_008044.1 SMART: Helix-turn-helix type 3: (1.5e-07); KEGG: sil:SPO2581 DNA-binding protein, , ev=2e-86, 59% identity; XRE family transcriptional regulator 930516 4076242 TM1040_0872 Ruegeria sp. TM1040 XRE family transcriptional regulator YP_612867.1 929716 R 292414 CDS YP_612868.1 99080714 4076243 930711..931130 1 NC_008044.1 KEGG: sil:SPO2580 hypothetical protein, ev=4e-07, 38% identity; hypothetical protein 931130 4076243 TM1040_0873 Ruegeria sp. TM1040 hypothetical protein YP_612868.1 930711 D 292414 CDS YP_612869.1 99080715 4076244 complement(931317..931877) 1 NC_008044.1 with IlvI catalyzes the formation of 2-acetolactate from pyruvate, the small subunit is required for full activity and valine sensitivity; E.coli produces 3 isoenzymes of acetolactate synthase which differ in specificity to substrates, valine sensitivity and affinity for cofactors; also known as acetolactate synthase 3 small subunit; acetolactate synthase 3 regulatory subunit 931877 ilvH 4076244 ilvH Ruegeria sp. TM1040 acetolactate synthase 3 regulatory subunit YP_612869.1 931317 R 292414 CDS YP_612870.1 99080716 4076245 complement(931943..933694) 1 NC_008044.1 TIGRFAM: acetolactate synthase, large subunit, biosynthetic type: (1.1e-304); PFAM: thiamine pyrophosphate enzyme-like TPP-binding: (6.9e-67) thiamine pyrophosphate enzyme, central region: (3.1e-53) thiamine pyrophosphate enzyme-like TPP binding region: (2.1e-100); KEGG: sil:SPO2578 acetolactate synthase, large subunit, biosynthetic type, ev=0.0, 92% identity; acetolactate synthase 3 catalytic subunit 933694 4076245 TM1040_0875 Ruegeria sp. TM1040 acetolactate synthase 3 catalytic subunit YP_612870.1 931943 R 292414 CDS YP_612871.1 99080717 4076246 complement(934294..934995) 1 NC_008044.1 PFAM: regulatory protein, LuxR: (4.1e-23) response regulator receiver: (1.5e-38) Sigma-70, region 4 type 2: (0.00038); KEGG: sil:SPO2575 DNA-binding response regulator, LuxR family, ev=7e-92, 81% identity; two component LuxR family transcriptional regulator 934995 4076246 TM1040_0876 Ruegeria sp. TM1040 two component LuxR family transcriptional regulator YP_612871.1 934294 R 292414 CDS YP_612872.1 99080718 4076247 complement(935016..936440) 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (5.1e-17) histidine kinase, dimerisation and phosphoacceptor region: (4.4e-16) Cache, type 2: (4e-21); KEGG: sil:SPO2574 sensor histidine kinase, ev=0.0, 77% identity; sensor signal transduction histidine kinase 936440 4076247 TM1040_0877 Ruegeria sp. TM1040 sensor signal transduction histidine kinase YP_612872.1 935016 R 292414 CDS YP_612873.1 99080719 4076248 936737..937822 1 NC_008044.1 TIGRFAM: Twin-arginine translocation pathway signal: (0.00058); PFAM: TRAP dicarboxylate transporter- DctP subunit: (4.5e-49); KEGG: sil:SPO2573 bacterial extracellular solute-binding protein, family 7, ev=0.0, 88% identity; twin-arginine translocation pathway signal 937822 4076248 TM1040_0878 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_612873.1 936737 D 292414 CDS YP_612874.1 99080720 4076249 937960..938907 1 NC_008044.1 KEGG: sil:SPO2572 hypothetical protein, ev=1e-114, 83% identity; TRAP-type mannitol/chloroaromatic compound transport system small permease-like 938907 4076249 TM1040_0879 Ruegeria sp. TM1040 TRAP-type mannitol/chloroaromatic compound transport system small permease-like YP_612874.1 937960 D 292414 CDS YP_612875.1 99080721 4076250 938924..941278 1 NC_008044.1 PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit: (1.1e-27); KEGG: sil:SPO2571 TRAP transporter, DctM subunit, , ev=0.0, 83% identity; TRAP dicarboxylate transporter subunit DctM 941278 4076250 TM1040_0880 Ruegeria sp. TM1040 TRAP dicarboxylate transporter subunit DctM YP_612875.1 938924 D 292414 CDS YP_612876.1 99080722 4075978 complement(941492..941875) 1 NC_008044.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase: (1.8e-20); KEGG: sil:SPO2570 glyoxalase family protein, ev=6e-45, 75% identity; glyoxalase/bleomycin resistance protein/dioxygenase 941875 4075978 TM1040_0881 Ruegeria sp. TM1040 glyoxalase/bleomycin resistance protein/dioxygenase YP_612876.1 941492 R 292414 CDS YP_612877.1 99080723 4075979 complement(941881..942705) 1 NC_008044.1 Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate; arginyl-tRNA-protein transferase 942705 4075979 TM1040_0882 Ruegeria sp. TM1040 arginyl-tRNA-protein transferase YP_612877.1 941881 R 292414 CDS YP_612878.1 99080724 4075980 complement(942879..943310) 1 NC_008044.1 PFAM: RDD: (1.4e-10); KEGG: sil:SPO2568 RDD family protein, ev=4e-46, 63% identity; RDD domain-containing protein 943310 4075980 TM1040_0883 Ruegeria sp. TM1040 RDD domain-containing protein YP_612878.1 942879 R 292414 CDS YP_612879.1 99080725 4075981 complement(943379..943834) 1 NC_008044.1 KEGG: sil:SPO2567 hypothetical protein, ev=1e-49, 66% identity; hypothetical protein 943834 4075981 TM1040_0884 Ruegeria sp. TM1040 hypothetical protein YP_612879.1 943379 R 292414 CDS YP_612880.1 99080726 4075982 944459..947317 1 NC_008044.1 PFAM: glutamate-ammonia ligase adenylyltransferase: (3.4e-65); KEGG: sil:SPO2523 glutamate-ammonia ligase adenylyltransferase, ev=0.0, 68% identity; glutamate-ammonia-ligase adenylyltransferase 947317 4075982 TM1040_0885 Ruegeria sp. TM1040 glutamate-ammonia-ligase adenylyltransferase YP_612880.1 944459 D 292414 CDS YP_612881.1 99080727 4075983 947364..947594 1 NC_008044.1 KEGG: sil:SPO2522 hypothetical protein, ev=9e-23, 58% identity; hypothetical protein 947594 4075983 TM1040_0886 Ruegeria sp. TM1040 hypothetical protein YP_612881.1 947364 D 292414 CDS YP_612882.1 99080728 4075984 948037..949254 1 NC_008044.1 KEGG: sil:SPO2520 hypothetical protein, ev=1e-175, 77% identity; SAM-dependent methyltransferase 949254 4075984 TM1040_0887 Ruegeria sp. TM1040 SAM-dependent methyltransferase YP_612882.1 948037 D 292414 CDS YP_612883.1 99080729 4075985 949266..949805 1 NC_008044.1 KEGG: sil:SPO2519 hypothetical protein, ev=1e-65, 70% identity; hypothetical protein 949805 4075985 TM1040_0888 Ruegeria sp. TM1040 hypothetical protein YP_612883.1 949266 D 292414 CDS YP_612884.1 99080730 4075986 complement(949911..950897) 1 NC_008044.1 PFAM: luciferase-like: (4.3e-16); KEGG: sil:SPO2518 bacterial luciferase family protein, ev=1e-136, 75% identity; luciferase-like protein 950897 4075986 TM1040_0889 Ruegeria sp. TM1040 luciferase-like protein YP_612884.1 949911 R 292414 CDS YP_612885.1 99080731 4075987 complement(950986..951672) 1 NC_008044.1 PFAM: peptidase M48, Ste24p: (3.3e-22); KEGG: sil:SPO2517 peptidase, M48 family, ev=3e-97, 77% identity; peptidase M48, Ste24p 951672 4075987 TM1040_0890 Ruegeria sp. TM1040 peptidase M48, Ste24p YP_612885.1 950986 R 292414 CDS YP_612886.1 99080732 4075988 complement(952013..953197) 1 NC_008044.1 KEGG: sil:SPO2515 hypothetical protein, ev=0.0, 87% identity; hypothetical protein 953197 4075988 TM1040_0891 Ruegeria sp. TM1040 hypothetical protein YP_612886.1 952013 R 292414 CDS YP_612887.1 99080733 4075989 complement(953229..953396) 1 NC_008044.1 KEGG: sil:SPO2514 hypothetical protein, ev=1e-08, 50% identity; hypothetical protein 953396 4075989 TM1040_0892 Ruegeria sp. TM1040 hypothetical protein YP_612887.1 953229 R 292414 CDS YP_612888.1 99080734 4075990 complement(953503..954951) 1 NC_008044.1 KEGG: sil:SPO2513 hypothetical protein, ev=1e-119, 50% identity; hypothetical protein 954951 4075990 TM1040_0893 Ruegeria sp. TM1040 hypothetical protein YP_612888.1 953503 R 292414 CDS YP_612889.1 99080735 4075991 complement(955075..955914) 1 NC_008044.1 PFAM: AAA ATPase, central region: (7.3e-06) ATPase associated with various cellular activities, AAA_5: (7.7e-09); SMART: ATPase: (4.2e-11); KEGG: sil:SPO2512 ATPase, AAA family, ev=1e-141, 89% identity; ATPase 955914 4075991 TM1040_0894 Ruegeria sp. TM1040 ATPase YP_612889.1 955075 R 292414 CDS YP_612890.1 99080736 4075992 956048..956524 1 NC_008044.1 TIGRFAM: RNA polymerase-binding, DksA: (1.1e-65); PFAM: zinc finger, DksA/TraR C4-type: (1e-08); KEGG: sil:SPO2511 DnaK suppressor protein, , ev=5e-72, 86% identity; TraR/DksA family transcriptional regulator 956524 4075992 TM1040_0895 Ruegeria sp. TM1040 TraR/DksA family transcriptional regulator YP_612890.1 956048 D 292414 CDS YP_612891.1 99080737 4075993 956617..957786 1 NC_008044.1 PFAM: monooxygenase, FAD-binding: (1.7e-11) FAD dependent oxidoreductase: (1.7e-06); KEGG: sil:SPO2510 salicylate hydroxylase, ev=1e-135, 65% identity; FAD-binding monooxygenase 957786 4075993 TM1040_0896 Ruegeria sp. TM1040 FAD-binding monooxygenase YP_612891.1 956617 D 292414 CDS YP_612892.1 99080738 4075994 complement(958089..958895) 1 NC_008044.1 TIGRFAM: exodeoxyribonuclease III: (1.6e-75) exodeoxyribonuclease III (xth): (5.2e-73); PFAM: Endonuclease/exonuclease/phosphatase: (1.3e-33); KEGG: sil:SPO2509 exodeoxyribonuclease III, ev=1e-135, 85% identity; exodeoxyribonuclease III 958895 4075994 TM1040_0897 Ruegeria sp. TM1040 exodeoxyribonuclease III YP_612892.1 958089 R 292414 CDS YP_612893.1 99080739 4075995 complement(959238..959534) 1 NC_008044.1 hypothetical protein 959534 4075995 TM1040_0898 Ruegeria sp. TM1040 hypothetical protein YP_612893.1 959238 R 292414 CDS YP_612894.1 99080740 4075996 959653..960717 1 NC_008044.1 hypothetical protein 960717 4075996 TM1040_0899 Ruegeria sp. TM1040 hypothetical protein YP_612894.1 959653 D 292414 CDS YP_612895.1 99080741 4076270 960714..961715 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (7.4e-07); KEGG: sil:SPO2507 membrane protein, , ev=2e-78, 54% identity; hypothetical protein 961715 4076270 TM1040_0900 Ruegeria sp. TM1040 hypothetical protein YP_612895.1 960714 D 292414 CDS YP_612896.1 99080742 4076271 complement(961909..962232) 1 NC_008044.1 PFAM: HesB/YadR/YfhF: (1.2e-25); KEGG: sil:SPO2506 iron-sulfur cluster assembly family protein, ev=1e-49, 87% identity; HesB/YadR/YfhF 962232 4076271 TM1040_0901 Ruegeria sp. TM1040 HesB/YadR/YfhF YP_612896.1 961909 R 292414 CDS YP_612897.1 99080743 4076272 962323..963465 1 NC_008044.1 KEGG: sil:SPO2505 deoxyguanosinetriphosphate triphosphohydrolase, , ev=1e-162, 76% identity; TIGRFAM: Deoxyguanosinetriphosphate triphosphohydrolase: (3.7e-107); PFAM: metal-dependent phosphohydrolase, HD subdomain: (1.6e-17); SMART: Metal-dependent phosphohydrolase, HD region: (3.1e-12); deoxyguanosinetriphosphate triphosphohydrolase 963465 4076272 TM1040_0902 Ruegeria sp. TM1040 deoxyguanosinetriphosphate triphosphohydrolase YP_612897.1 962323 D 292414 CDS YP_612898.1 99080744 4076273 963640..965382 1 NC_008044.1 catalyzes a two-step reaction, first charging an arginine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class-I aminoacyl-tRNA synthetase; arginyl-tRNA synthetase 965382 argS 4076273 argS Ruegeria sp. TM1040 arginyl-tRNA synthetase YP_612898.1 963640 D 292414 CDS YP_612899.1 99080745 4076274 965892..966827 1 NC_008044.1 PFAM: Sporulation related: (1.6e-05); KEGG: sil:SPO2503 hypothetical protein, ev=4e-79, 48% identity; sporulation-like protein 966827 4076274 TM1040_0904 Ruegeria sp. TM1040 sporulation-like protein YP_612899.1 965892 D 292414 CDS YP_612900.1 99080746 4076275 966827..967888 1 NC_008044.1 PFAM: glycoside hydrolase, family 3-like: (7.8e-11); KEGG: sil:SPO2502 beta-N-acetylhexosaminidase, , ev=1e-123, 64% identity; beta-N-acetylhexosaminidase 967888 4076275 TM1040_0905 Ruegeria sp. TM1040 beta-N-acetylhexosaminidase YP_612900.1 966827 D 292414 CDS YP_612901.1 99080747 4076276 967881..968678 1 NC_008044.1 PFAM: chromosome segregation and condensation protein ScpA: (7.1e-07); KEGG: sil:SPO2501 segregation and condensation protein A, ev=1e-116, 80% identity; condensin subunit ScpA 968678 4076276 TM1040_0906 Ruegeria sp. TM1040 condensin subunit ScpA YP_612901.1 967881 D 292414 CDS YP_612902.1 99080748 4076277 968678..969358 1 NC_008044.1 PFAM: chromosome segregation and condensation protein ScpB: (6.8e-69); KEGG: sil:SPO2500 segregation and condensation protein B, ev=1e-95, 84% identity; condensin subunit ScpB 969358 4076277 TM1040_0907 Ruegeria sp. TM1040 condensin subunit ScpB YP_612902.1 968678 D 292414 CDS YP_612903.1 99080749 4076278 969526..969846 1 NC_008044.1 hypothetical protein 969846 4076278 TM1040_0908 Ruegeria sp. TM1040 hypothetical protein YP_612903.1 969526 D 292414 CDS YP_612904.1 99080750 4076279 complement(969800..970999) 1 NC_008044.1 PFAM: major facilitator superfamily MFS_1: (1.1e-39); KEGG: mlo:mll7282 similar to multidrug-efflux transporter, ev=1e-76, 42% identity; major facilitator superfamily transporter 970999 4076279 TM1040_0909 Ruegeria sp. TM1040 major facilitator superfamily transporter YP_612904.1 969800 R 292414 CDS YP_612905.1 99080751 4076280 971071..971610 1 NC_008044.1 PFAM: regulatory proteins, AsnC/Lrp: (6.5e-18); KEGG: mlo:mlr7283 transcriptional regulator, ev=6e-46, 55% identity; AsnC family transcriptional regulator 971610 4076280 TM1040_0910 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_612905.1 971071 D 292414 CDS YP_612906.1 99080752 4076281 complement(971618..972697) 1 NC_008044.1 Catalyzes the deamination of dCTP to form dUTP; 2'-deoxycytidine 5'-triphosphate deaminase 972697 4076281 TM1040_0911 Ruegeria sp. TM1040 2'-deoxycytidine 5'-triphosphate deaminase YP_612906.1 971618 R 292414 CDS YP_612907.1 99080753 4076282 complement(973041..975563) 1 NC_008044.1 PFAM: regulatory protein, MerR: (1.2e-08); KEGG: lma:LmjF35.0550 proteophosphoglycan ppg1, ev=2e-48, 23% identity; MerR family transcriptional regulator 975563 4076282 TM1040_0912 Ruegeria sp. TM1040 MerR family transcriptional regulator YP_612907.1 973041 R 292414 CDS YP_612908.1 99080754 4076283 complement(975623..975925) 1 NC_008044.1 This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control; integration host factor subunit alpha 975925 ihfA 4076283 ihfA Ruegeria sp. TM1040 integration host factor subunit alpha YP_612908.1 975623 R 292414 CDS YP_612909.1 99080755 4076284 complement(976013..976984) 1 NC_008044.1 KEGG: sil:SPO2494 3-oxoacyl-(acyl-carrier-protein) synthase III, ev=1e-155, 86% identity; TIGRFAM: 3-oxoacyl-(acyl-carrier-protein) synthase III: (2.3e-156); PFAM: 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal: (1.1e-53) 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III: (1.5e-46); 3-oxoacyl-ACP synthase 976984 4076284 TM1040_0914 Ruegeria sp. TM1040 3-oxoacyl-ACP synthase YP_612909.1 976013 R 292414 CDS YP_612910.1 99080756 4076285 complement(977000..978127) 1 NC_008044.1 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY; glycerol-3-phosphate acyltransferase PlsX 978127 4076285 TM1040_0915 Ruegeria sp. TM1040 glycerol-3-phosphate acyltransferase PlsX YP_612910.1 977000 R 292414 CDS YP_612911.1 99080757 4076286 complement(978169..978375) 1 NC_008044.1 some L32 proteins have zinc finger motifs consisting of CXXC while others do not; 50S ribosomal protein L32 978375 rpmF 4076286 rpmF Ruegeria sp. TM1040 50S ribosomal protein L32 YP_612911.1 978169 R 292414 CDS YP_612912.1 99080758 4076287 complement(978666..979214) 1 NC_008044.1 KEGG: sil:SPO2491 hypothetical protein, ev=1e-49, 59% identity; hypothetical protein 979214 4076287 TM1040_0917 Ruegeria sp. TM1040 hypothetical protein YP_612912.1 978666 R 292414 CDS YP_612913.1 99080759 4076288 979301..979768 1 NC_008044.1 KEGG: sil:SPO2490 lipoprotein, SmpA/OmlA family, ev=4e-42, 56% identity; SmpA/OmlA family lipoprotein 979768 4076288 TM1040_0918 Ruegeria sp. TM1040 SmpA/OmlA family lipoprotein YP_612913.1 979301 D 292414 CDS YP_612914.1 99080760 4076289 979926..980702 1 NC_008044.1 KEGG: sil:SPO2489 hypothetical protein, ev=1e-109, 81% identity; ornithine-acyl-ACP N-acyltransferase 980702 4076289 TM1040_0919 Ruegeria sp. TM1040 ornithine-acyl-ACP N-acyltransferase YP_612914.1 979926 D 292414 CDS YP_612915.1 99080761 4077548 980789..982579 1 NC_008044.1 PFAM: ABC transporter related: (6.5e-50); SMART: ATPase: (7.3e-17); KEGG: sil:SPO2488 ABC transporter, ATP-binding protein, ev=0.0, 82% identity; ABC transporter 982579 4077548 TM1040_0920 Ruegeria sp. TM1040 ABC transporter YP_612915.1 980789 D 292414 CDS YP_612916.1 99080762 4077549 complement(982763..983518) 1 NC_008044.1 PFAM: short-chain dehydrogenase/reductase SDR: (2.9e-13); KEGG: sil:SPO2487 3-hydroxyacyl-CoA dehydrogenase, type II, ev=1e-108, 78% identity; short-chain dehydrogenase/reductase SDR 983518 4077549 TM1040_0921 Ruegeria sp. TM1040 short-chain dehydrogenase/reductase SDR YP_612916.1 982763 R 292414 CDS YP_612917.1 99080763 4077550 complement(983670..984593) 1 NC_008044.1 KEGG: sil:SPO2486 hypothetical protein, ev=1e-79, 55% identity; hypothetical protein 984593 4077550 TM1040_0922 Ruegeria sp. TM1040 hypothetical protein YP_612917.1 983670 R 292414 CDS YP_612918.1 99080764 4077551 complement(984889..986142) 1 NC_008044.1 KEGG: sil:SPO2484 tyrosyl-tRNA synthetase, ev=0.0, 83% identity; TIGRFAM: tyrosyl-tRNA synthetase: (1.5e-109); PFAM: aminoacyl-tRNA synthetase, class Ib: (1.2e-96); tyrosyl-tRNA synthetase 986142 4077551 TM1040_0923 Ruegeria sp. TM1040 tyrosyl-tRNA synthetase YP_612918.1 984889 R 292414 CDS YP_612919.1 99080765 4077552 986286..987413 1 NC_008044.1 catalyzes hydrolysis of 1,6-anhydro bond of anyhydro-N-acetylmuramic acid (anhMurNAc) and phosphorylates anhMurNAc to produce N-acetyl-muramate-6-phosphate; involved in murein recycling; anhydro-N-acetylmuramic acid kinase 987413 anmK 4077552 anmK Ruegeria sp. TM1040 anhydro-N-acetylmuramic acid kinase YP_612919.1 986286 D 292414 CDS YP_612920.1 99080766 4077553 complement(987585..988055) 1 NC_008044.1 PFAM: protein of unknown function DUF985: (1.7e-63); KEGG: sil:SPO2479 hypothetical protein, ev=6e-56, 66% identity; hypothetical protein 988055 4077553 TM1040_0925 Ruegeria sp. TM1040 hypothetical protein YP_612920.1 987585 R 292414 CDS YP_612921.1 99080767 4077554 988123..989541 1 NC_008044.1 PFAM: protein of unknown function UPF0061: (3.7e-80); KEGG: sil:SPO2480 hypothetical protein, ev=0.0, 71% identity; hypothetical protein 989541 4077554 TM1040_0926 Ruegeria sp. TM1040 hypothetical protein YP_612921.1 988123 D 292414 CDS YP_612922.1 99080768 4077555 complement(989796..991133) 1 NC_008044.1 PFAM: helicase-like: (4.8e-35) DEAD/DEAH box helicase-like: (4.9e-67); KEGG: sme:SMb20880 ATP-dependent RNA helicase protein, ev=1e-139, 60% identity; DEAD/DEAH box helicase 991133 4077555 TM1040_0927 Ruegeria sp. TM1040 DEAD/DEAH box helicase YP_612922.1 989796 R 292414 CDS YP_612923.1 99080769 4077556 991564..991980 1 NC_008044.1 PFAM: ferric-uptake regulator: (4.4e-58); KEGG: sil:SPO2477 transcriptional regulator, Fur family, ev=5e-62, 82% identity; FUR family manganese uptake regulator 991980 4077556 TM1040_0928 Ruegeria sp. TM1040 FUR family manganese uptake regulator YP_612923.1 991564 D 292414 CDS YP_612924.1 99080770 4077557 992140..993033 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (0.00011); KEGG: sil:SPO2475 membrane protein, , ev=2e-88, 56% identity; hypothetical protein 993033 4077557 TM1040_0929 Ruegeria sp. TM1040 hypothetical protein YP_612924.1 992140 D 292414 CDS YP_612925.1 99080771 4077558 complement(993036..994274) 1 NC_008044.1 PFAM: major facilitator superfamily MFS_1: (3.6e-37); KEGG: jan:Jann_0119 major facilitator superfamily MFS_1, ev=4e-87, 41% identity; major facilitator superfamily transporter 994274 4077558 TM1040_0930 Ruegeria sp. TM1040 major facilitator superfamily transporter YP_612925.1 993036 R 292414 CDS YP_612926.1 99080772 4077559 994521..995798 1 NC_008044.1 enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis; phosphopyruvate hydratase 995798 eno 4077559 eno Ruegeria sp. TM1040 phosphopyruvate hydratase YP_612926.1 994521 D 292414 CDS YP_612927.1 99080773 4077560 995924..996535 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (3.3e-05); KEGG: bja:blr1411 hypothetical protein, ev=7e-50, 51% identity; N-acetyltransferase GCN5 996535 4077560 TM1040_0932 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_612927.1 995924 D 292414 CDS YP_612928.1 99080774 4077561 complement(996615..997064) 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (1.6e-10); KEGG: sil:SPO2471 acetyltransferase, GNAT family, ev=4e-54, 69% identity; N-acetyltransferase GCN5 997064 4077561 TM1040_0933 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_612928.1 996615 R 292414 CDS YP_612929.1 99080775 4077562 complement(997061..998002) 1 NC_008044.1 PFAM: Inosine/uridine-preferring nucleoside hydrolase: (2.4e-121); KEGG: sil:SPO2470 inosine-uridine preferring nucleoside hydrolase, ev=1e-133, 76% identity; inosine/uridine-preferring nucleoside hydrolase 998002 4077562 TM1040_0934 Ruegeria sp. TM1040 inosine/uridine-preferring nucleoside hydrolase YP_612929.1 997061 R 292414 CDS YP_612930.1 99080776 4077563 998101..999015 1 NC_008044.1 KEGG: sil:SPO1104 hypothetical protein, ev=2e-09, 27% identity; hypothetical protein 999015 4077563 TM1040_0935 Ruegeria sp. TM1040 hypothetical protein YP_612930.1 998101 D 292414 CDS YP_612931.1 99080777 4077564 complement(999002..999844) 1 NC_008044.1 functions in degradation of stringent response intracellular messenger ppGpp; in Escherichia coli this gene is co-transcribed with the toxin/antitoxin genes mazEF; activity of MazG is inhibited by MazEF in vitro; ppGpp inhibits mazEF expression; MazG thus works in limiting the toxic activity of the MazF toxin induced during starvation; MazG also interacts with the GTPase protein Era; nucleoside triphosphate pyrophosphohydrolase 999844 mazG 4077564 mazG Ruegeria sp. TM1040 nucleoside triphosphate pyrophosphohydrolase YP_612931.1 999002 R 292414 CDS YP_612932.1 99080778 4077565 999907..1001070 1 NC_008044.1 KEGG: sil:SPO2468 amidohydrolase family protein, ev=1e-169, 75% identity; TIGRFAM: Peptidase M20D, amidohydrolase: (2.4e-142); PFAM: peptidase M20: (1.2e-59) peptidase dimerisation: (9.4e-07); peptidase M20D, amidohydrolase 1001070 4077565 TM1040_0937 Ruegeria sp. TM1040 peptidase M20D, amidohydrolase YP_612932.1 999907 D 292414 CDS YP_612933.1 99080779 4077566 1001097..1002125 1 NC_008044.1 catalyzes the formation of putrescine from agmatine; agmatinase 1002125 4077566 TM1040_0938 Ruegeria sp. TM1040 agmatinase YP_612933.1 1001097 D 292414 CDS YP_612934.1 99080780 4077333 1002122..1003069 1 NC_008044.1 TIGRFAM: agmatinase, : (1.3e-70); PFAM: Arginase/agmatinase/formiminoglutamase: (1.6e-59); KEGG: sil:SPO2464 agmatinase, ev=1e-148, 80% identity; agmatinase 1003069 4077333 TM1040_0939 Ruegeria sp. TM1040 agmatinase YP_612934.1 1002122 D 292414 CDS YP_612935.1 99080781 4077334 complement(1003342..1003671) 1 NC_008044.1 KEGG: sil:SPO2462 hypothetical protein, ev=1e-27, 66% identity; hypothetical protein 1003671 4077334 TM1040_0940 Ruegeria sp. TM1040 hypothetical protein YP_612935.1 1003342 R 292414 CDS YP_612936.1 99080782 4077335 1003744..1004796 1 NC_008044.1 recognizes the termination signals UAG and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF1; this protein is similar to release factor 2; peptide chain release factor 1 1004796 prfA 4077335 prfA Ruegeria sp. TM1040 peptide chain release factor 1 YP_612936.1 1003744 D 292414 CDS YP_612937.1 99080783 4077336 1004793..1005629 1 NC_008044.1 TIGRFAM: modification methylase, HemK family: (7.6e-52); PFAM: methyltransferase small: (9.1e-08); KEGG: sil:SPO2460 modification methylase, HemK family, ev=1e-113, 78% identity; HemK family modification methylase 1005629 4077336 TM1040_0942 Ruegeria sp. TM1040 HemK family modification methylase YP_612937.1 1004793 D 292414 CDS YP_612938.1 99080784 4077337 1005791..1006501 1 NC_008044.1 KEGG: sil:SPO2459 hypothetical protein, ev=2e-67, 59% identity; hypothetical protein 1006501 4077337 TM1040_0943 Ruegeria sp. TM1040 hypothetical protein YP_612938.1 1005791 D 292414 CDS YP_612939.1 99080785 4077338 complement(1006604..1007446) 1 NC_008044.1 catalyzes the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases A1518 and A1519 in 16S rRNA; mutations in ksgA causes resistance to the translation initiation inhibitor kasugamycin; dimethyladenosine transferase 1007446 ksgA 4077338 ksgA Ruegeria sp. TM1040 dimethyladenosine transferase YP_612939.1 1006604 R 292414 CDS YP_612940.1 99080786 4077339 complement(1007596..1008576) 1 NC_008044.1 catalyzes oxidation of 4-(phosphohydroxy)-L-threonine into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which decarboxylates to form 1-amino-3-(phosphohydroxy)propan-2-one (3-amino-2-oxopropyl phosphate); 4-hydroxythreonine-4-phosphate dehydrogenase 1008576 pdxA 4077339 pdxA Ruegeria sp. TM1040 4-hydroxythreonine-4-phosphate dehydrogenase YP_612940.1 1007596 R 292414 CDS YP_612941.1 99080787 4077340 complement(1008573..1009847) 1 NC_008044.1 PFAM: PpiC-type peptidyl-prolyl cis-trans isomerase: (0.00034); KEGG: sil:SPO2456 PPIC-type PPIASE domain, ev=1e-110, 52% identity; PpiC-type peptidyl-prolyl cis-trans isomerase 1009847 4077340 TM1040_0946 Ruegeria sp. TM1040 PpiC-type peptidyl-prolyl cis-trans isomerase YP_612941.1 1008573 R 292414 CDS YP_612942.1 99080788 4077341 complement(1009832..1012027) 1 NC_008044.1 PFAM: OstA-like protein: (0.0024) Organic solvent tolerance protein: (3.5e-17); KEGG: sil:SPO2455 organic solvent tolerance protein, , ev=0.0, 56% identity; organic solvent tolerance protein 1012027 4077341 TM1040_0947 Ruegeria sp. TM1040 organic solvent tolerance protein YP_612942.1 1009832 R 292414 CDS YP_612943.1 99080789 4077342 complement(1012011..1013117) 1 NC_008044.1 PFAM: permease YjgP/YjgQ: (4.3e-38); KEGG: sil:SPO2454 permease, YjgP/YjgQ family, ev=1e-138, 68% identity; permease YjgP/YjgQ 1013117 4077342 TM1040_0948 Ruegeria sp. TM1040 permease YjgP/YjgQ YP_612943.1 1012011 R 292414 CDS YP_612944.1 99080790 4077343 complement(1013114..1014253) 1 NC_008044.1 PFAM: permease YjgP/YjgQ: (7e-30); KEGG: sil:SPO3780 membrane protein, , ev=1e-90, 46% identity; permease YjgP/YjgQ 1014253 4077343 TM1040_0949 Ruegeria sp. TM1040 permease YjgP/YjgQ YP_612944.1 1013114 R 292414 CDS YP_612945.1 99080791 4077344 1014475..1015950 1 NC_008044.1 catalyzes the removal of N-terminal amino acids preferably leucine from various peptides; leucyl aminopeptidase 1015950 4077344 TM1040_0950 Ruegeria sp. TM1040 leucyl aminopeptidase YP_612945.1 1014475 D 292414 CDS YP_612946.1 99080792 4077345 1015957..1016421 1 NC_008044.1 binds to single-strand binding (SSB) protein and acts as a bridge between the DnaX clamp loader complex and the SSB; DNA polymerase III subunit chi 1016421 4077345 TM1040_0951 Ruegeria sp. TM1040 DNA polymerase III subunit chi YP_612946.1 1015957 D 292414 CDS YP_612947.1 99080793 4077346 complement(1016672..1017253) 1 NC_008044.1 TIGRFAM: conserved hypothetical protein: (7.7e-53); KEGG: sil:SPO2449 hypothetical protein, ev=2e-53, 54% identity; hypothetical protein 1017253 4077346 TM1040_0952 Ruegeria sp. TM1040 hypothetical protein YP_612947.1 1016672 R 292414 CDS YP_612948.1 99080794 4077347 complement(1017303..1017926) 1 NC_008044.1 PFAM: multiple antibiotic resistance (MarC)-related proteins: (1e-65); KEGG: sil:SPO2448 membrane protein, MarC family, ev=5e-77, 71% identity; multiple antibiotic resistance (MarC)-like proteins 1017926 4077347 TM1040_0953 Ruegeria sp. TM1040 multiple antibiotic resistance (MarC)-like proteins YP_612948.1 1017303 R 292414 CDS YP_612949.1 99080795 4077348 complement(1017923..1019824) 1 NC_008044.1 PFAM: ABC transporter related: (2.2e-34); SMART: ATPase: (7.7e-08); KEGG: sil:SPO2446 ABC transporter, ATP-binding protein, ev=0.0, 78% identity; ABC transporter 1019824 4077348 TM1040_0954 Ruegeria sp. TM1040 ABC transporter YP_612949.1 1017923 R 292414 CDS YP_612950.1 99080796 4077349 1020018..1021610 1 NC_008044.1 KEGG: ret:RHE_CH01984 hypothetical protein, ev=4e-65, 38% identity; hypothetical protein 1021610 4077349 TM1040_0955 Ruegeria sp. TM1040 hypothetical protein YP_612950.1 1020018 D 292414 CDS YP_612951.1 99080797 4077350 1021740..1022948 1 NC_008044.1 TIGRFAM: Drug resistance transporter Bcr/CflA subfamily: (1.3e-31); PFAM: major facilitator superfamily MFS_1: (5.4e-48); KEGG: sil:SPO2445 drug resistance transporter, Bcr/CflA subfamily, ev=1e-153, 68% identity; Bcr/CflA subfamily drug resistance transporter 1022948 4077350 TM1040_0956 Ruegeria sp. TM1040 Bcr/CflA subfamily drug resistance transporter YP_612951.1 1021740 D 292414 CDS YP_612952.1 99080798 4077351 1023097..1023519 1 NC_008044.1 catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate; nucleoside diphosphate kinase 1023519 ndk 4077351 ndk Ruegeria sp. TM1040 nucleoside diphosphate kinase YP_612952.1 1023097 D 292414 CDS YP_612953.1 99080799 4077352 complement(1023637..1023972) 1 NC_008044.1 KEGG: sil:SPO1621 TfoX domain protein, ev=4e-36, 67% identity; TfoX domain-containing protein 1023972 4077352 TM1040_0958 Ruegeria sp. TM1040 TfoX domain-containing protein YP_612953.1 1023637 R 292414 CDS YP_612954.1 99080800 4077255 1024317..1025639 1 NC_008044.1 PFAM: mannose-6-phosphate isomerase, type II: (6.8e-07) Nucleotidyl transferase: (0.00095) Cupin 2, conserved barrel: (0.0021); KEGG: rsp:RSP_0834 mannose-6-phosphate isomerase / mannose-1-phosphate guanylyltransferase, ev=5e-45, 30% identity; mannose-6-phosphate isomerase 1025639 4077255 TM1040_0959 Ruegeria sp. TM1040 mannose-6-phosphate isomerase YP_612954.1 1024317 D 292414 CDS YP_612955.1 99080801 4077256 complement(1026394..1027038) 1 NC_008044.1 PFAM: regulatory protein, LuxR: (6e-19) response regulator receiver: (1.4e-23); KEGG: sil:SPO0161 DNA-binding response regulator, LuxR family, ev=4e-67, 63% identity; two component LuxR family transcriptional regulator 1027038 4077256 TM1040_0960 Ruegeria sp. TM1040 two component LuxR family transcriptional regulator YP_612955.1 1026394 R 292414 CDS YP_612956.1 99080802 4077257 1027361..1027828 1 NC_008044.1 PFAM: oxidoreductase, molybdopterin binding: (0.00091); KEGG: sil:SPO0162 hypothetical protein, ev=8e-34, 51% identity; oxidoreductase, molybdopterin binding 1027828 4077257 TM1040_0961 Ruegeria sp. TM1040 oxidoreductase, molybdopterin binding YP_612956.1 1027361 D 292414 CDS YP_612957.1 99080803 4077258 1027874..1030345 1 NC_008044.1 PFAM: response regulator receiver: (7e-31) ATP-binding region, ATPase-like: (2.3e-39) histidine kinase A-like: (1e-21) Hpt: (6.2e-05) PAS fold-3: (0.00049) PAS fold-4: (0.00011) PAS fold: (4.3e-07); SMART: PAS: (2.2e-10); KEGG: sil:SPO0163 sensory box histidine kinase/response regulator, ev=1e-145, 41% identity; PAS/PAC sensor hybrid histidine kinase 1030345 4077258 TM1040_0962 Ruegeria sp. TM1040 PAS/PAC sensor hybrid histidine kinase YP_612957.1 1027874 D 292414 CDS YP_612958.1 99080804 4077259 1030665..1031591 1 NC_008044.1 PFAM: Sulfate transporter/antisigma-factor antagonist STAS: (1e-16); KEGG: vvy:VVA0580 anti-anti-sigma regulatory factor, ev=4e-33, 26% identity; anti-sigma-factor antagonist 1031591 4077259 TM1040_0963 Ruegeria sp. TM1040 anti-sigma-factor antagonist YP_612958.1 1030665 D 292414 CDS YP_612959.1 99080805 4077260 1031901..1032911 1 NC_008044.1 TIGRFAM: TIM-barrel protein, yjbN family: (6e-160); PFAM: dihydrouridine synthase, DuS: (2.1e-102); KEGG: sil:SPO2374 tRNA-dihydrouridine synthase A, ev=1e-143, 78% identity; tRNA-dihydrouridine synthase A 1032911 4077260 TM1040_0964 Ruegeria sp. TM1040 tRNA-dihydrouridine synthase A YP_612959.1 1031901 D 292414 CDS YP_612960.1 99080806 4077261 1032917..1033714 1 NC_008044.1 KEGG: sil:SPO2353 hypothetical protein, ev=4e-88, 59% identity; hypothetical protein 1033714 4077261 TM1040_0965 Ruegeria sp. TM1040 hypothetical protein YP_612960.1 1032917 D 292414 CDS YP_612961.1 99080807 4077262 complement(1033845..1034081) 1 NC_008044.1 PFAM: protein of unknown function DUF1289: (8.4e-21); KEGG: jan:Jann_2180 protein of unknown function DUF1289, ev=3e-23, 63% identity; hypothetical protein 1034081 4077262 TM1040_0966 Ruegeria sp. TM1040 hypothetical protein YP_612961.1 1033845 R 292414 CDS YP_612962.1 99080808 4077263 complement(1034085..1034558) 1 NC_008044.1 similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function; Holliday junction resolvase-like protein 1034558 4077263 TM1040_0967 Ruegeria sp. TM1040 Holliday junction resolvase-like protein YP_612962.1 1034085 R 292414 CDS YP_612963.1 99080809 4077264 complement(1034555..1035793) 1 NC_008044.1 KEGG: sil:SPO2349 cytochrome c-type biogenesis protein CycH, ev=1e-105, 52% identity; cytochrome c-type biogenesis protein CycH 1035793 4077264 TM1040_0968 Ruegeria sp. TM1040 cytochrome c-type biogenesis protein CycH YP_612963.1 1034555 R 292414 CDS YP_612964.1 99080810 4077265 1035985..1037280 1 NC_008044.1 TIGRFAM: sarcosine oxidase, beta subunit family: (1.4e-259); PFAM: FAD dependent oxidoreductase: (7.8e-79); KEGG: sil:SPO2348 sarcosine oxidase, beta subunit family, ev=0.0, 86% identity; sarcosine oxidase subunit beta 1037280 4077265 TM1040_0969 Ruegeria sp. TM1040 sarcosine oxidase subunit beta YP_612964.1 1035985 D 292414 CDS YP_612965.1 99080811 4077266 1037333..1037665 1 NC_008044.1 PFAM: Sarcosine oxidase, delta subunit, heterotetrameric: (1.5e-22); KEGG: sil:SPO2346 sarcosine oxidase, delta subunit family, ev=2e-51, 81% identity; sarcosine oxidase, delta subunit, heterotetrameric 1037665 4077266 TM1040_0970 Ruegeria sp. TM1040 sarcosine oxidase, delta subunit, heterotetrameric YP_612965.1 1037333 D 292414 CDS YP_612966.1 99080812 4077267 1037740..1040775 1 NC_008044.1 KEGG: sil:SPO2345 sarcosine oxidase, alpha subunit family, ev=0.0, 80% identity; TIGRFAM: sarcosine oxidase, alpha subunit family: (0); PFAM: glycine cleavage T protein (aminomethyl transferase): (5.5e-69); sarcosine oxidase subunit alpha 1040775 4077267 TM1040_0971 Ruegeria sp. TM1040 sarcosine oxidase subunit alpha YP_612966.1 1037740 D 292414 CDS YP_612967.1 99080813 4077268 1040768..1041337 1 NC_008044.1 PFAM: Sarcosine oxidase, gamma subunit: (1.6e-18); KEGG: sil:SPO2344 sarcosine oxidase, gamma subunit family, ev=1e-47, 54% identity; sarcosine oxidase, gamma subunit 1041337 4077268 TM1040_0972 Ruegeria sp. TM1040 sarcosine oxidase, gamma subunit YP_612967.1 1040768 D 292414 CDS YP_612968.1 99080814 4077269 1041451..1041861 1 NC_008044.1 hypothetical protein 1041861 4077269 TM1040_0973 Ruegeria sp. TM1040 hypothetical protein YP_612968.1 1041451 D 292414 CDS YP_612969.1 99080815 4077270 1042009..1042398 1 NC_008044.1 hypothetical protein 1042398 4077270 TM1040_0974 Ruegeria sp. TM1040 hypothetical protein YP_612969.1 1042009 D 292414 CDS YP_612970.1 99080816 4077271 1042474..1042935 1 NC_008044.1 hypothetical protein 1042935 4077271 TM1040_0975 Ruegeria sp. TM1040 hypothetical protein YP_612970.1 1042474 D 292414 CDS YP_612971.1 99080817 4077272 1043026..1043625 1 NC_008044.1 PFAM: manganese and iron superoxide dismutase: (8.6e-34); KEGG: sil:SPO2340 superoxide dismutase, Fe, ev=1e-107, 90% identity; superoxide dismutase 1043625 4077272 TM1040_0976 Ruegeria sp. TM1040 superoxide dismutase YP_612971.1 1043026 D 292414 CDS YP_612972.1 99080818 4077273 1043784..1044398 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (7.5e-09); KEGG: dde:Dde_3171 acetyltransferase, ev=1e-34, 44% identity; N-acetyltransferase GCN5 1044398 4077273 TM1040_0977 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_612972.1 1043784 D 292414 CDS YP_612973.1 99080819 4078140 complement(1044530..1045072) 1 NC_008044.1 PFAM: conserved hypothetical protein 730: (7e-51); KEGG: sil:SPO2337 decarboxylase family protein, ev=2e-73, 73% identity; hypothetical protein 1045072 4078140 TM1040_0978 Ruegeria sp. TM1040 hypothetical protein YP_612973.1 1044530 R 292414 CDS YP_612974.1 99080820 4078141 1045222..1047177 1 NC_008044.1 PFAM: Peptidoglycan-binding LysM: (2.1e-06); KEGG: sil:SPO2336 LysM domain protein, ev=3e-79, 35% identity; peptidoglycan-binding LysM 1047177 4078141 TM1040_0979 Ruegeria sp. TM1040 peptidoglycan-binding LysM YP_612974.1 1045222 D 292414 CDS YP_612975.1 99080821 4078142 1047285..1049105 1 NC_008044.1 PFAM: ABC transporter, transmembrane region: (6e-27) ABC transporter related: (5.6e-66); SMART: ATPase: (4e-20); KEGG: sil:SPO2335 ABC transporter, ATP-binding/permease protein, ev=0.0, 77% identity; ABC transporter 1049105 4078142 TM1040_0980 Ruegeria sp. TM1040 ABC transporter YP_612975.1 1047285 D 292414 CDS YP_612976.1 99080822 4078143 1049409..1049657 1 NC_008044.1 PFAM: Calcium-binding EF-hand: (0.0064); KEGG: jan:Jann_1891 hypothetical protein, ev=3e-07, 41% identity; calcium-binding EF-hand 1049657 4078143 TM1040_0981 Ruegeria sp. TM1040 calcium-binding EF-hand YP_612976.1 1049409 D 292414 CDS YP_612977.1 99080823 4078144 complement(1050017..1050601) 1 NC_008044.1 PFAM: regulatory protein, TetR: (7.3e-17); KEGG: sma:SAV4715 TetR-family transcriptional regulator, ev=9e-17, 35% identity; TetR family transcriptional regulator 1050601 4078144 TM1040_0982 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_612977.1 1050017 R 292414 CDS YP_612978.1 99080824 4078145 1050757..1051590 1 NC_008044.1 PFAM: NAD-dependent epimerase/dehydratase: (0.0014) short-chain dehydrogenase/reductase SDR: (5.7e-16); KEGG: rso:RS03890 short chain dehydrogenase, ev=3e-65, 47% identity; short chain dehydrogenase 1051590 4078145 TM1040_0983 Ruegeria sp. TM1040 short chain dehydrogenase YP_612978.1 1050757 D 292414 CDS YP_612979.1 99080825 4078146 1052015..1053841 1 NC_008044.1 PFAM: histidine kinase, HAMP region: (4.5e-11) chemotaxis sensory transducer: (3.1e-88); KEGG: ccr:CC0430 methyl-accepting chemotaxis protein McpA, ev=1e-100, 48% identity; methyl-accepting chemotaxis sensory transducer 1053841 4078146 TM1040_0984 Ruegeria sp. TM1040 methyl-accepting chemotaxis sensory transducer YP_612979.1 1052015 D 292414 CDS YP_612980.1 99080826 4078147 complement(1054046..1054285) 1 NC_008044.1 hypothetical protein 1054285 4078147 TM1040_0985 Ruegeria sp. TM1040 hypothetical protein YP_612980.1 1054046 R 292414 CDS YP_612981.1 99080827 4078148 complement(1054261..1054578) 1 NC_008044.1 hypothetical protein 1054578 4078148 TM1040_0986 Ruegeria sp. TM1040 hypothetical protein YP_612981.1 1054261 R 292414 CDS YP_612982.1 99080828 4078149 complement(1054875..1058678) 1 NC_008044.1 PFAM: acriflavin resistance protein: (2.8e-24); KEGG: sil:SPO2332 transporter, AcrB/AcrD/AcrF family, ev=0.0, 73% identity; acriflavin resistance protein 1058678 4078149 TM1040_0987 Ruegeria sp. TM1040 acriflavin resistance protein YP_612982.1 1054875 R 292414 CDS YP_612983.1 99080829 4078150 complement(1058675..1059922) 1 NC_008044.1 PFAM: secretion protein HlyD: (0.00012); KEGG: sil:SPO2331 efflux transporter, RND family, MFP subunit, ev=1e-141, 64% identity; secretion protein HlyD 1059922 4078150 TM1040_0988 Ruegeria sp. TM1040 secretion protein HlyD YP_612983.1 1058675 R 292414 CDS YP_612984.1 99080830 4078151 1060287..1060955 1 NC_008044.1 KEGG: sil:SPO2330 hypothetical protein, ev=5e-57, 56% identity; hypothetical protein 1060955 4078151 TM1040_0989 Ruegeria sp. TM1040 hypothetical protein YP_612984.1 1060287 D 292414 CDS YP_612985.1 99080831 4078152 1061024..1062349 1 NC_008044.1 SMART: Pyrrolo-quinoline quinone: (0.057); KEGG: sil:SPO2329 PQQ enzyme repeat family protein, ev=1e-149, 61% identity; Pyrrolo-quinoline quinone 1062349 4078152 TM1040_0990 Ruegeria sp. TM1040 Pyrrolo-quinoline quinone YP_612985.1 1061024 D 292414 CDS YP_612986.1 99080832 4078153 1062663..1064141 1 NC_008044.1 EngA; essential Neisserial GTPase; synchronizes cellular events by interacting with multiple targets with tandem G-domains; overexpression in Escherichia coli suppresses rrmJ mutation; structural analysis of the Thermotoga maritima ortholog shows different nucleotide binding affinities in the two binding domains; GTP-binding protein EngA 1064141 engA 4078153 engA Ruegeria sp. TM1040 GTP-binding protein EngA YP_612986.1 1062663 D 292414 CDS YP_612987.1 99080833 4078154 1064391..1065344 1 NC_008044.1 PFAM: fatty acid desaturase: (1.4e-18); KEGG: sil:SPO2327 fatty acid desaturase, ev=1e-146, 75% identity; fatty acid desaturase 1065344 4078154 TM1040_0992 Ruegeria sp. TM1040 fatty acid desaturase YP_612987.1 1064391 D 292414 CDS YP_612988.1 99080834 4078155 1065465..1066124 1 NC_008044.1 SMART: Helix-hairpin-helix DNA-binding, class 1: (0.017); KEGG: sil:SPO2326 hypothetical protein, ev=8e-26, 42% identity; helix-hairpin-helix DNA-binding protein 1066124 4078155 TM1040_0993 Ruegeria sp. TM1040 helix-hairpin-helix DNA-binding protein YP_612988.1 1065465 D 292414 CDS YP_612989.1 99080835 4078156 complement(1066244..1067536) 1 NC_008044.1 catalyzes a two-step reaction, first charging a serine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; seryl-tRNA synthetase 1067536 4078156 TM1040_0994 Ruegeria sp. TM1040 seryl-tRNA synthetase YP_612989.1 1066244 R 292414 CDS YP_612990.1 99080836 4078157 1067792..1068076 1 NC_008044.1 TIGRFAM: preprotein translocase, YajC subunit: (5.6e-30); PFAM: YajC: (4.8e-31); KEGG: sil:SPO2322 preprotein translocase, YajC subunit, ev=5e-40, 86% identity; protein translocase subunit yajC 1068076 4078157 TM1040_0995 Ruegeria sp. TM1040 protein translocase subunit yajC YP_612990.1 1067792 D 292414 CDS YP_612991.1 99080837 4078158 1068111..1069775 1 NC_008044.1 part of the preprotein secretory system; when complexed with proteins SecF and YajC, SecDFyajC stimulates the proton motive force-driven protein translocation, and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane; preprotein translocase subunit SecD 1069775 secD 4078158 secD Ruegeria sp. TM1040 preprotein translocase subunit SecD YP_612991.1 1068111 D 292414 CDS YP_612992.1 99080838 4078159 1069779..1070747 1 NC_008044.1 forms a complex with SecD and YajC; SecDFyajC stimulates the proton motive force-driven protein translocation; seems to modulate the cycling of SecA by stabilizing its membrane-inserted state and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane; in some organisms, such as Bacillus subtilis, SecD is fused to SecF; preprotein translocase subunit SecF 1070747 secF 4078159 secF Ruegeria sp. TM1040 preprotein translocase subunit SecF YP_612992.1 1069779 D 292414 CDS YP_612993.1 99080839 4078218 1070995..1071348 1 NC_008044.1 PFAM: protein of unknown function DUF498: (4.1e-35); KEGG: sil:SPO2318 hypothetical protein, ev=1e-45, 75% identity; hypothetical protein 1071348 4078218 TM1040_0998 Ruegeria sp. TM1040 hypothetical protein YP_612993.1 1070995 D 292414 CDS YP_612994.1 99080840 4078219 1071433..1072047 1 NC_008044.1 ATP-binding protein; required for proper cytochrome c maturation; cytochrome c biogenesis protein CcmA 1072047 4078219 TM1040_0999 Ruegeria sp. TM1040 cytochrome c biogenesis protein CcmA YP_612994.1 1071433 D 292414 CDS YP_612995.1 99080841 4078220 1072044..1072700 1 NC_008044.1 TIGRFAM: heme exporter protein CcmB: (2.8e-116); PFAM: cytochrome c-type biogenesis protein CcmB: (2.5e-107); KEGG: sil:SPO2316 heme exporter protein CcmB, ev=3e-99, 84% identity; heme exporter protein CcmB 1072700 4078220 TM1040_1000 Ruegeria sp. TM1040 heme exporter protein CcmB YP_612995.1 1072044 D 292414 CDS YP_612996.1 99080842 4078221 1072745..1073479 1 NC_008044.1 TIGRFAM: heme exporter protein CcmC: (2.6e-113); PFAM: cytochrome c assembly protein: (9.3e-48); KEGG: rsp:RSP_1803 ABC heme exporter, inner membrane subunit CcmC, ev=1e-111, 78% identity; heme exporter protein CcmC 1073479 4078221 TM1040_1001 Ruegeria sp. TM1040 heme exporter protein CcmC YP_612996.1 1072745 D 292414 CDS YP_612997.1 99080843 4078222 1073472..1073627 1 NC_008044.1 PFAM: Heme exporter protein D (CcmD): (3.6e-10); KEGG: rsp:RSP_1804 heme exporter protein D, ev=9e-07, 51% identity; Heme exporter protein CcmD 1073627 4078222 TM1040_1002 Ruegeria sp. TM1040 Heme exporter protein CcmD YP_612997.1 1073472 D 292414 CDS YP_612998.1 99080844 4078223 1073620..1074156 1 NC_008044.1 TIGRFAM: periplasmic protein thiol: (1.2e-69); PFAM: Redoxin: (1.3e-15); KEGG: sil:SPO2314 periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily, ev=4e-73, 71% identity; periplasmic protein thiol-disulfide oxidoreductase DsbE 1074156 4078223 TM1040_1003 Ruegeria sp. TM1040 periplasmic protein thiol-disulfide oxidoreductase DsbE YP_612998.1 1073620 D 292414 CDS YP_612999.1 99080845 4078224 complement(1074159..1074863) 1 NC_008044.1 PFAM: NAD-dependent epimerase/dehydratase: (8e-05) short-chain dehydrogenase/reductase SDR: (2e-19); KEGG: bur:Bcep18194_C7123 short-chain dehydrogenase/reductase SDR, ev=2e-33, 35% identity; short-chain dehydrogenase/reductase SDR 1074863 4078224 TM1040_1004 Ruegeria sp. TM1040 short-chain dehydrogenase/reductase SDR YP_612999.1 1074159 R 292414 CDS YP_613000.1 99080846 4078225 complement(1075048..1075395) 1 NC_008044.1 hypothetical protein 1075395 4078225 TM1040_1005 Ruegeria sp. TM1040 hypothetical protein YP_613000.1 1075048 R 292414 CDS YP_613001.1 99080847 4078226 complement(1075536..1078283) 1 NC_008044.1 Catalyzes the conversion of citrate to isocitrate; aconitate hydratase 1078283 4078226 TM1040_1006 Ruegeria sp. TM1040 aconitate hydratase YP_613001.1 1075536 R 292414 CDS YP_613002.1 99080848 4078227 1078584..1079210 1 NC_008044.1 PFAM: protein of unknown function DUF1223: (1.9e-58); KEGG: sil:SPO2311 hypothetical protein, ev=3e-59, 48% identity; hypothetical protein 1079210 4078227 TM1040_1007 Ruegeria sp. TM1040 hypothetical protein YP_613002.1 1078584 D 292414 CDS YP_613003.1 99080849 4078228 complement(1079214..1080134) 1 NC_008044.1 PFAM: lipid A biosynthesis acyltransferase: (2.1e-25); KEGG: sil:SPO2310 lipid A biosynthesis lauroyl acyltransferase, , ev=1e-94, 56% identity; lipid A biosynthesis acyltransferase 1080134 4078228 TM1040_1008 Ruegeria sp. TM1040 lipid A biosynthesis acyltransferase YP_613003.1 1079214 R 292414 CDS YP_613004.1 99080850 4078229 complement(1080288..1081391) 1 NC_008044.1 PFAM: flagellar motor switch protein FliG: (2.8e-06); KEGG: sil:SPO2308 flagellar motor switch protein FliG, ev=1e-106, 60% identity; flagellar motor switch protein FliG 1081391 4078229 TM1040_1009 Ruegeria sp. TM1040 flagellar motor switch protein FliG YP_613004.1 1080288 R 292414 CDS YP_613005.1 99080851 4078230 complement(1081470..1082015) 1 NC_008044.1 PFAM: TPR repeat: (7.2e-05) Tetratricopeptide TPR_2: (6.9e-05); KEGG: sil:SPO2307 hypothetical protein, ev=4e-55, 59% identity; hypothetical protein 1082015 4078230 TM1040_1010 Ruegeria sp. TM1040 hypothetical protein YP_613005.1 1081470 R 292414 CDS YP_613006.1 99080852 4078231 complement(1082157..1083461) 1 NC_008044.1 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide; adenylosuccinate lyase 1083461 4078231 TM1040_1011 Ruegeria sp. TM1040 adenylosuccinate lyase YP_613006.1 1082157 R 292414 CDS YP_613007.1 99080853 4078232 complement(1083576..1083908) 1 NC_008044.1 hypothetical protein 1083908 4078232 TM1040_1012 Ruegeria sp. TM1040 hypothetical protein YP_613007.1 1083576 R 292414 CDS YP_613008.1 99080854 4078233 complement(1083921..1085192) 1 NC_008044.1 PFAM: OsmC-like protein: (1.4e-33); KEGG: sil:SPO2301 osmC-like family protein, ev=1e-179, 77% identity; OsmC-like protein 1085192 4078233 TM1040_1013 Ruegeria sp. TM1040 OsmC-like protein YP_613008.1 1083921 R 292414 CDS YP_613009.1 99080855 4078234 1085321..1085908 1 NC_008044.1 PFAM: NUDIX hydrolase: (0.00022); KEGG: xac:XAC1843 hypothetical protein, ev=4e-27, 44% identity; NUDIX hydrolase 1085908 4078234 TM1040_1014 Ruegeria sp. TM1040 NUDIX hydrolase YP_613009.1 1085321 D 292414 CDS YP_613010.1 99080856 4078235 1085908..1086813 1 NC_008044.1 PFAM: Endonuclease/exonuclease/phosphatase: (3.9e-06); KEGG: jan:Jann_1778 endonuclease/exonuclease/phosphatase, ev=6e-41, 35% identity; endonuclease/exonuclease/phosphatase 1086813 4078235 TM1040_1015 Ruegeria sp. TM1040 endonuclease/exonuclease/phosphatase YP_613010.1 1085908 D 292414 CDS YP_613011.1 99080857 4078236 complement(1086832..1088175) 1 NC_008044.1 PFAM: peptidase M24: (2.7e-06); KEGG: sil:SPO2299 metallopeptidase, family M24, ev=0.0, 88% identity; peptidase M24 1088175 4078236 TM1040_1016 Ruegeria sp. TM1040 peptidase M24 YP_613011.1 1086832 R 292414 CDS YP_613012.1 99080858 4078529 1088369..1089136 1 NC_008044.1 KEGG: sil:SPO2298 hypothetical protein, ev=9e-79, 62% identity; hypothetical protein 1089136 4078529 TM1040_1017 Ruegeria sp. TM1040 hypothetical protein YP_613012.1 1088369 D 292414 CDS YP_613013.1 99080859 4078530 complement(1089174..1090373) 1 NC_008044.1 KEGG: sil:SPO2297 hypothetical protein, ev=2e-12, 24% identity; hypothetical protein 1090373 4078530 TM1040_1018 Ruegeria sp. TM1040 hypothetical protein YP_613013.1 1089174 R 292414 CDS YP_613014.1 99080860 4078531 complement(1090440..1091252) 1 NC_008044.1 KEGG: sil:SPO2296 hypothetical protein, ev=1e-108, 73% identity; hypothetical protein 1091252 4078531 TM1040_1019 Ruegeria sp. TM1040 hypothetical protein YP_613014.1 1090440 R 292414 CDS YP_613015.1 99080861 4078532 complement(1091340..1092602) 1 NC_008044.1 KEGG: rsp:RSP_3200 molecular chaperone, DnaK, ev=1e-111, 54% identity; molecular chaperone DnaK 1092602 4078532 TM1040_1020 Ruegeria sp. TM1040 molecular chaperone DnaK YP_613015.1 1091340 R 292414 CDS YP_613016.1 99080862 4078533 1092602..1093228 1 NC_008044.1 hypothetical protein 1093228 4078533 TM1040_1021 Ruegeria sp. TM1040 hypothetical protein YP_613016.1 1092602 D 292414 CDS YP_613017.1 99080863 4078534 complement(1093375..1094781) 1 NC_008044.1 KEGG: sil:SPO2295 glutamine synthetase, type I, ev=0.0, 93% identity; TIGRFAM: glutamine synthetase, type I: (1.1e-280); PFAM: glutamine synthetase, catalytic region: (2.5e-166) glutamine synthetase, beta-Grasp: (6.6e-40); L-glutamine synthetase 1094781 4078534 TM1040_1022 Ruegeria sp. TM1040 L-glutamine synthetase YP_613017.1 1093375 R 292414 CDS YP_613018.1 99080864 4078535 complement(1094869..1095207) 1 NC_008044.1 PFAM: nitrogen regulatory protein P-II: (3.9e-69); KEGG: sil:SPO2294 nitrogen regulatory protein P-II, ev=1e-53, 94% identity; nitrogen regulatory protein P-II 1095207 4078535 TM1040_1023 Ruegeria sp. TM1040 nitrogen regulatory protein P-II YP_613018.1 1094869 R 292414 CDS YP_613019.1 99080865 4078536 1095376..1096962 1 NC_008044.1 PFAM: protein of unknown function UPF0031: (2.4e-39) YjeF-related protein-like: (4.1e-45); KEGG: sil:SPO2293 YjeF family protein, ev=1e-172, 60% identity; hypothetical protein 1096962 4078536 TM1040_1024 Ruegeria sp. TM1040 hypothetical protein YP_613019.1 1095376 D 292414 CDS YP_613020.1 99080866 4078537 complement(1096959..1097507) 1 NC_008044.1 KEGG: sil:SPO2292 hypothetical protein, ev=6e-25, 42% identity; hypothetical protein 1097507 4078537 TM1040_1025 Ruegeria sp. TM1040 hypothetical protein YP_613020.1 1096959 R 292414 CDS YP_613021.1 99080867 4078538 1097776..1100565 1 NC_008044.1 catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase 1100565 4078538 TM1040_1026 Ruegeria sp. TM1040 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase YP_613021.1 1097776 D 292414 CDS YP_613022.1 99080868 4078539 1100965..1103352 1 NC_008044.1 PFAM: histidine kinase, HAMP region: (6e-08) chemotaxis sensory transducer: (1.7e-79); KEGG: ret:RHE_CH03477 probable methyl-accepting chemotaxis protein, ev=3e-88, 32% identity; methyl-accepting chemotaxis sensory transducer 1103352 4078539 TM1040_1027 Ruegeria sp. TM1040 methyl-accepting chemotaxis sensory transducer YP_613022.1 1100965 D 292414 CDS YP_613023.1 99080869 4078540 1103990..1107736 1 NC_008044.1 PFAM: CheB methylesterase: (1.2e-20) MCP methyltransferase, CheR-type: (8.2e-58) ATP-binding region, ATPase-like: (1e-30) histidine kinase A-like: (1.1e-11) PAS fold-3: (5.2e-26); SMART: PAS: (0.0017) PAC motif: (3.1e-09); KEGG: ava:Ava_0314 signal transduction histidine kinase (STHK) with CheB and CheR activity, ev=1e-134, 29% identity; signal transduction histidine kinase with CheB and CheR activity 1107736 4078540 TM1040_1028 Ruegeria sp. TM1040 signal transduction histidine kinase with CheB and CheR activity YP_613023.1 1103990 D 292414 CDS YP_613024.1 99080870 4078541 1107741..1108124 1 NC_008044.1 PFAM: response regulator receiver: (0.00011); KEGG: lic:LIC12088 response regulator, ev=2e-08, 31% identity; response regulator receiver protein 1108124 4078541 TM1040_1029 Ruegeria sp. TM1040 response regulator receiver protein YP_613024.1 1107741 D 292414 CDS YP_613025.1 99080871 4078542 1108141..1110486 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (5.8e-21) histidine kinase A-like: (0.00038); SMART: extracellular solute-binding protein, family 3: (2.3e-16); KEGG: ana:all2899 phytochrome-like protein, two-component sensor, ev=9e-33, 38% identity; histidine kinase 1110486 4078542 TM1040_1030 Ruegeria sp. TM1040 histidine kinase YP_613025.1 1108141 D 292414 CDS YP_613026.1 99080872 4078543 1110483..1110878 1 NC_008044.1 PFAM: response regulator receiver: (4.1e-23); KEGG: ret:RHE_CH00624 probable two-component sensor histidine kinase/response regulator hybrid protein, ev=5e-18, 41% identity; response regulator receiver protein 1110878 4078543 TM1040_1031 Ruegeria sp. TM1040 response regulator receiver protein YP_613026.1 1110483 D 292414 CDS YP_613027.1 99080873 4078544 1111339..1112463 1 NC_008044.1 KEGG: sil:SPO2289 hypothetical protein, ev=4e-79, 46% identity; hypothetical protein 1112463 4078544 TM1040_1032 Ruegeria sp. TM1040 hypothetical protein YP_613027.1 1111339 D 292414 CDS YP_613028.1 99080874 4078545 1112761..1114092 1 NC_008044.1 Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer; trigger factor 1114092 tig 4078545 tig Ruegeria sp. TM1040 trigger factor YP_613028.1 1112761 D 292414 CDS YP_613029.1 99080875 4078546 1114264..1114497 1 NC_008044.1 hypothetical protein 1114497 4078546 TM1040_1034 Ruegeria sp. TM1040 hypothetical protein YP_613029.1 1114264 D 292414 CDS YP_613030.1 99080876 4078547 1114531..1115472 1 NC_008044.1 TIGRFAM: GGDEF domain: (3.3e-26); PFAM: GGDEF: (1.5e-35); KEGG: rru:Rru_A3391 diguanylate cyclase (GGDEF domain), ev=8e-25, 34% identity; diguanylate cyclase 1115472 4078547 TM1040_1035 Ruegeria sp. TM1040 diguanylate cyclase YP_613030.1 1114531 D 292414 CDS YP_613031.1 99080877 4078548 complement(1115617..1117575) 1 NC_008044.1 periplasmic enzyme; functions during ribonucleic acid degradation; 2',3'-cyclic nucleotides are first converted to 3'-nucleotide and then cleaved to yield a ribonucleotide and a phosphate; bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic protein 1117575 cpdB 4078548 cpdB Ruegeria sp. TM1040 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase periplasmic protein YP_613031.1 1115617 R 292414 CDS YP_613032.1 99080878 4078095 complement(1117856..1118326) 1 NC_008044.1 PFAM: Lytic transglycosylase, catalytic: (9.6e-05); KEGG: sil:SPO2284 transglycosylase SLT domain protein, ev=1e-59, 72% identity; lytic transglycosylase, catalytic 1118326 4078095 TM1040_1037 Ruegeria sp. TM1040 lytic transglycosylase, catalytic YP_613032.1 1117856 R 292414 CDS YP_613033.1 99080879 4078096 1118812..1119660 1 NC_008044.1 PFAM: flagellin-like: (1.4e-06); KEGG: bmb:BruAb2_1084 flagellin family protein, ev=2e-48, 40% identity; flagellin-like protein 1119660 4078096 TM1040_1038 Ruegeria sp. TM1040 flagellin-like protein YP_613033.1 1118812 D 292414 CDS YP_613034.1 99080880 4078097 1119990..1120835 1 NC_008044.1 PFAM: flagellin-like: (5.7e-06); KEGG: jan:Jann_4203 flagellin-like, ev=5e-48, 45% identity; flagellin-like protein 1120835 4078097 TM1040_1039 Ruegeria sp. TM1040 flagellin-like protein YP_613034.1 1119990 D 292414 CDS YP_613035.1 99080881 4078098 1121099..1121977 1 NC_008044.1 PFAM: flagellin-like: (1.2e-06); KEGG: ret:RHE_PE00392 flagellin C protein, ev=4e-46, 39% identity; flagellin-like protein 1121977 4078098 TM1040_1040 Ruegeria sp. TM1040 flagellin-like protein YP_613035.1 1121099 D 292414 CDS YP_613036.1 99080882 4078099 1122288..1122662 1 NC_008044.1 KEGG: ppr:PBPRB1724 hypothetical protein, ev=4e-09, 36% identity; hypothetical protein 1122662 4078099 TM1040_1041 Ruegeria sp. TM1040 hypothetical protein YP_613036.1 1122288 D 292414 CDS YP_613037.1 99080883 4078100 complement(1123134..1123481) 1 NC_008044.1 hypothetical protein 1123481 4078100 TM1040_1042 Ruegeria sp. TM1040 hypothetical protein YP_613037.1 1123134 R 292414 CDS YP_613038.1 99080884 4078101 complement(1123604..1124218) 1 NC_008044.1 in Escherichia coli this protein is wrapped around the base of the L1 stalk; 50S ribosomal protein L9 1124218 rplI 4078101 rplI Ruegeria sp. TM1040 50S ribosomal protein L9 YP_613038.1 1123604 R 292414 CDS YP_613039.1 99080885 4078102 complement(1124232..1124459) 1 NC_008044.1 binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit; 30S ribosomal protein S18 1124459 rpsR 4078102 rpsR Ruegeria sp. TM1040 30S ribosomal protein S18 YP_613039.1 1124232 R 292414 CDS YP_613040.1 99080886 4078103 complement(1124490..1124843) 1 NC_008044.1 binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21; 30S ribosomal protein S6 1124843 rpsF 4078103 rpsF Ruegeria sp. TM1040 30S ribosomal protein S6 YP_613040.1 1124490 R 292414 CDS YP_613041.1 99080887 4078104 1125241..1125774 1 NC_008044.1 KEGG: sil:SPO2280 hypothetical protein, ev=4e-24, 36% identity; hypothetical protein 1125774 4078104 TM1040_1046 Ruegeria sp. TM1040 hypothetical protein YP_613041.1 1125241 D 292414 CDS YP_613042.1 99080888 4078105 1126045..1126620 1 NC_008044.1 PFAM: YceI: (4e-49); KEGG: sil:SPO2279 hypothetical protein, ev=6e-77, 74% identity; YceI protein 1126620 4078105 TM1040_1047 Ruegeria sp. TM1040 YceI protein YP_613042.1 1126045 D 292414 CDS YP_613043.1 99080889 4078106 1126856..1127638 1 NC_008044.1 KEGG: mag:amb0186 ABC-type amino acid transport/signal transduction systems, ev=4e-20, 32% identity; amino acid ABC transporter/signal transduction system protein 1127638 4078106 TM1040_1048 Ruegeria sp. TM1040 amino acid ABC transporter/signal transduction system protein YP_613043.1 1126856 D 292414 CDS YP_613044.1 99080890 4078107 complement(1127786..1129018) 1 NC_008044.1 PFAM: YceI: (2.8e-11) cytochrome B561: (8.9e-33); KEGG: sil:SPO2277 cytochrome, , ev=1e-118, 54% identity; cytochrome B561 1129018 4078107 TM1040_1049 Ruegeria sp. TM1040 cytochrome B561 YP_613044.1 1127786 R 292414 CDS YP_613045.1 99080891 4078108 1129265..1130200 1 NC_008044.1 TIGRFAM: malonyl CoA-acyl carrier protein transacylase: (5.7e-130); PFAM: acyl transferase region: (8.5e-16); KEGG: sil:SPO2276 malonyl CoA-acyl carrier protein transacylase, ev=1e-138, 84% identity; ACP S-malonyltransferase 1130200 4078108 TM1040_1050 Ruegeria sp. TM1040 ACP S-malonyltransferase YP_613045.1 1129265 D 292414 CDS YP_613046.1 99080892 4078109 1130221..1130958 1 NC_008044.1 TIGRFAM: 3-oxoacyl-(acyl-carrier-protein) reductase: (1.1e-146); PFAM: NAD-dependent epimerase/dehydratase: (0.0009) short-chain dehydrogenase/reductase SDR: (6.3e-46) Male sterility-like: (0.0027); KEGG: sil:SPO2275 3-oxoacyl-(acyl-carrier-protein) reductase, ev=1e-115, 84% identity; 3-oxoacyl-ACP reductase 1130958 4078109 TM1040_1051 Ruegeria sp. TM1040 3-oxoacyl-ACP reductase YP_613046.1 1130221 D 292414 CDS YP_613047.1 99080893 4078110 1131343..1131576 1 NC_008044.1 carries the fatty acid chain in fatty acid biosynthesis; acyl carrier protein 1131576 acpP 4078110 acpP Ruegeria sp. TM1040 acyl carrier protein YP_613047.1 1131343 D 292414 CDS YP_613048.1 99080894 4078111 1131760..1132503 1 NC_008044.1 PFAM: histidine biosynthesis: (1.5e-53); KEGG: sil:SPO2272 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase, , ev=4e-92, 65% identity; histidine biosynthesis protein 1132503 4078111 TM1040_1053 Ruegeria sp. TM1040 histidine biosynthesis protein YP_613048.1 1131760 D 292414 CDS YP_613049.1 99080895 4078112 1133065..1134333 1 NC_008044.1 FabF; beta-ketoacyl-ACP synthase II, KASII; catalyzes a condensation reaction in fatty acid biosynthesis: addition of an acyl acceptor of two carbons from malonyl-ACP; required for the elongation of short-chain unsaturated acyl-ACP; 3-oxoacyl-ACP synthase 1134333 4078112 TM1040_1054 Ruegeria sp. TM1040 3-oxoacyl-ACP synthase YP_613049.1 1133065 D 292414 CDS YP_613050.1 99080896 4078113 1134335..1135489 1 NC_008044.1 PFAM: aminodeoxychorismate lyase: (1e-112); KEGG: sil:SPO2270 conserved hypothetical protein TIGR00247, ev=1e-161, 74% identity; aminodeoxychorismate lyase 1135489 4078113 TM1040_1055 Ruegeria sp. TM1040 aminodeoxychorismate lyase YP_613050.1 1134335 D 292414 CDS YP_613051.1 99080897 4077196 1135720..1136163 1 NC_008044.1 KEGG: sil:SPO2267 hypothetical protein, ev=2e-08, 39% identity; hypothetical protein 1136163 4077196 TM1040_1056 Ruegeria sp. TM1040 hypothetical protein YP_613051.1 1135720 D 292414 CDS YP_613052.1 99080898 4077197 1136156..1137433 1 NC_008044.1 PFAM: protein of unknown function DUF264: (9.5e-52); KEGG: sil:SPO2266 terminase, large subunit, , ev=1e-174, 73% identity; hypothetical protein 1137433 4077197 TM1040_1057 Ruegeria sp. TM1040 hypothetical protein YP_613052.1 1136156 D 292414 CDS YP_613053.1 99080899 4077198 1137683..1138888 1 NC_008044.1 TIGRFAM: Phage portal protein, HK97: (1.2e-64); PFAM: phage portal protein: (2e-89); KEGG: sil:SPO2264 portal protein, HK97 family, ev=1e-157, 70% identity; Phage portal protein, HK97 1138888 4077198 TM1040_1058 Ruegeria sp. TM1040 Phage portal protein, HK97 YP_613053.1 1137683 D 292414 CDS YP_613054.1 99080900 4077199 1138881..1139105 1 NC_008044.1 KEGG: sil:SPO2263 hypothetical protein, ev=4e-17, 60% identity; hypothetical protein 1139105 4077199 TM1040_1059 Ruegeria sp. TM1040 hypothetical protein YP_613054.1 1138881 D 292414 CDS YP_613055.1 99080901 4077200 1139140..1139712 1 NC_008044.1 PFAM: peptidase U35, phage prohead HK97: (2e-52); KEGG: sil:SPO2262 phage prohead protease, HK97 family, ev=5e-54, 62% identity; peptidase U35, phage prohead HK97 1139712 4077200 TM1040_1060 Ruegeria sp. TM1040 peptidase U35, phage prohead HK97 YP_613055.1 1139140 D 292414 CDS YP_613056.1 99080902 4077201 1139733..1140929 1 NC_008044.1 PFAM: phage major capsid protein, HK97: (1.4e-92); KEGG: sil:SPO2261 major capsid protein, HK97 family, ev=1e-170, 80% identity; phage major capsid protein, HK97 1140929 4077201 TM1040_1061 Ruegeria sp. TM1040 phage major capsid protein, HK97 YP_613056.1 1139733 D 292414 CDS YP_613057.1 99080903 4077202 1141108..1141710 1 NC_008044.1 TIGRFAM: Phage conserved hypothetical protein, phiE125 gp8: (9.4e-50); KEGG: sil:SPO2260 hypothetical protein, ev=9e-50, 53% identity; hypothetical protein 1141710 4077202 TM1040_1062 Ruegeria sp. TM1040 hypothetical protein YP_613057.1 1141108 D 292414 CDS YP_613058.1 99080904 4077203 1141707..1142045 1 NC_008044.1 TIGRFAM: conserved hypothetical protein: (0.0012); KEGG: sil:SPO2259 head-tail adaptor, , ev=5e-29, 55% identity; hypothetical protein 1142045 4077203 TM1040_1063 Ruegeria sp. TM1040 hypothetical protein YP_613058.1 1141707 D 292414 CDS YP_613059.1 99080905 4077204 1142042..1142449 1 NC_008044.1 KEGG: sil:SPO2258 hypothetical protein, ev=3e-41, 64% identity; hypothetical protein 1142449 4077204 TM1040_1064 Ruegeria sp. TM1040 hypothetical protein YP_613059.1 1142042 D 292414 CDS YP_613060.1 99080906 4077205 1142485..1142898 1 NC_008044.1 TIGRFAM: Phage major tail protein, TP901-1: (9.2e-36); KEGG: sil:SPO2257 major tail protein, TP901-1 family, ev=3e-61, 83% identity; Phage major tail protein, TP901-1 1142898 4077205 TM1040_1065 Ruegeria sp. TM1040 Phage major tail protein, TP901-1 YP_613060.1 1142485 D 292414 CDS YP_613061.1 99080907 4077206 1142902..1143225 1 NC_008044.1 KEGG: sil:SPO2256 hypothetical protein, ev=3e-30, 63% identity; hypothetical protein 1143225 4077206 TM1040_1066 Ruegeria sp. TM1040 hypothetical protein YP_613061.1 1142902 D 292414 CDS YP_613062.1 99080908 4077207 1143222..1143437 1 NC_008044.1 TIGRFAM: conserved hypothetical protein: (7e-19); KEGG: sil:SPO2255 hypothetical protein, ev=6e-14, 67% identity; hypothetical protein 1143437 4077207 TM1040_1067 Ruegeria sp. TM1040 hypothetical protein YP_613062.1 1143222 D 292414 CDS YP_613063.1 99080909 4077208 1143441..1144100 1 NC_008044.1 KEGG: jan:Jann_1642 phage-related minor tail protein-like, ev=1e-60, 56% identity; phage-related minor tail protein-like 1144100 4077208 TM1040_1068 Ruegeria sp. TM1040 phage-related minor tail protein-like YP_613063.1 1143441 D 292414 CDS YP_613064.1 99080910 4077209 1144114..1144746 1 NC_008044.1 TIGRFAM: conserved hypothetical protein: (9.6e-99); KEGG: sil:SPO2253 hypothetical protein, ev=2e-84, 70% identity; hypothetical protein 1144746 4077209 TM1040_1069 Ruegeria sp. TM1040 hypothetical protein YP_613064.1 1144114 D 292414 CDS YP_613065.1 99080911 4077210 1144746..1145624 1 NC_008044.1 TIGRFAM: Phage conserved hypothetical protein BR0599: (5.4e-129); KEGG: sil:SPO2252 hypothetical protein, ev=1e-113, 66% identity; phage protein 1145624 4077210 TM1040_1070 Ruegeria sp. TM1040 phage protein YP_613065.1 1144746 D 292414 CDS YP_613066.1 99080912 4077211 1145621..1146058 1 NC_008044.1 TIGRFAM: phage cell wall peptidase, NlpC/P60: (5.4e-71); PFAM: NLP/P60: (3.3e-06); KEGG: sil:SPO2251 hypothetical protein, ev=3e-46, 65% identity; phage cell wall peptidase, NlpC/P60 1146058 4077211 TM1040_1071 Ruegeria sp. TM1040 phage cell wall peptidase, NlpC/P60 YP_613066.1 1145621 D 292414 CDS YP_613067.1 99080913 4077212 1146071..1149991 1 NC_008044.1 KEGG: sil:SPO2250 hypothetical protein, ev=0.0, 63% identity; hypothetical protein 1149991 4077212 TM1040_1072 Ruegeria sp. TM1040 hypothetical protein YP_613067.1 1146071 D 292414 CDS YP_613068.1 99080914 4077213 1149988..1150299 1 NC_008044.1 KEGG: sil:SPO2249 hypothetical protein, ev=1e-12, 43% identity; hypothetical protein 1150299 4077213 TM1040_1073 Ruegeria sp. TM1040 hypothetical protein YP_613068.1 1149988 D 292414 CDS YP_613069.1 99080915 4077214 complement(1150412..1150618) 1 NC_008044.1 PFAM: Cold-shock protein, DNA-binding: (2.5e-28); SMART: Cold shock protein: (2.4e-25); KEGG: rsp:RSP_0591 cold-shock protein, ev=9e-23, 72% identity; cold-shock DNA-binding protein family protein 1150618 4077214 TM1040_1074 Ruegeria sp. TM1040 cold-shock DNA-binding protein family protein YP_613069.1 1150412 R 292414 CDS YP_613070.1 99080916 4077215 1150977..1151783 1 NC_008044.1 KEGG: sil:SPO2247 serine O-acetyltransferase, ev=1e-129, 83% identity; TIGRFAM: serine O-acetyltransferase: (1.3e-96); PFAM: transferase hexapeptide repeat: (0.081) serine acetyltransferase-like: (2.5e-43); serine O-acetyltransferase 1151783 4077215 TM1040_1075 Ruegeria sp. TM1040 serine O-acetyltransferase YP_613070.1 1150977 D 292414 CDS YP_613071.1 99080917 4076309 1151953..1152252 1 NC_008044.1 PFAM: protein of unknown function DUF1330: (8.2e-30); KEGG: mlo:mll3541 hypothetical protein, ev=2e-11, 41% identity; hypothetical protein 1152252 4076309 TM1040_1076 Ruegeria sp. TM1040 hypothetical protein YP_613071.1 1151953 D 292414 CDS YP_613072.1 99080918 4076310 complement(1152399..1153739) 1 NC_008044.1 KEGG: sil:SPO2242 pyruvate dehydrogenase complex, E2 component, dihydrolipoamide acetyltransferase, ev=0.0, 83% identity; TIGRFAM: Dihydrolipoamide acetyltransferase, long form: (2.2e-209); PFAM: biotin/lipoyl attachment: (1.8e-23) catalytic domain of components of various dehydrogenase complexes: (5.8e-114) E3 binding: (6e-18); branched-chain alpha-keto acid dehydrogenase subunit E2 1153739 4076310 TM1040_1077 Ruegeria sp. TM1040 branched-chain alpha-keto acid dehydrogenase subunit E2 YP_613072.1 1152399 R 292414 CDS YP_613073.1 99080919 4076311 complement(1153751..1155127) 1 NC_008044.1 catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of a lipoic acid-containing dihydrolipoamide acetyltransferase within the complex. The E1 component of the pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase(E2) and lipoamide dehydrogenase; pyruvate dehydrogenase subunit beta 1155127 4076311 TM1040_1078 Ruegeria sp. TM1040 pyruvate dehydrogenase subunit beta YP_613073.1 1153751 R 292414 CDS YP_613074.1 99080920 4076312 complement(1155145..1156158) 1 NC_008044.1 PFAM: dehydrogenase, E1 component: (1.4e-135); KEGG: jan:Jann_1691 pyruvate dehydrogenase (lipoamide), ev=1e-169, 84% identity; pyruvate dehydrogenase (lipoamide) 1156158 4076312 TM1040_1079 Ruegeria sp. TM1040 pyruvate dehydrogenase (lipoamide) YP_613074.1 1155145 R 292414 CDS YP_613075.1 99080921 4076313 complement(1156201..1156446) 1 NC_008044.1 hypothetical protein 1156446 4076313 TM1040_1080 Ruegeria sp. TM1040 hypothetical protein YP_613075.1 1156201 R 292414 CDS YP_613076.1 99080922 4076314 complement(1156589..1156888) 1 NC_008044.1 PFAM: Septum formation initiator: (3.1e-10); KEGG: sil:SPO2239 hypothetical protein, ev=4e-33, 69% identity; septum formation initiator 1156888 4076314 TM1040_1081 Ruegeria sp. TM1040 septum formation initiator YP_613076.1 1156589 R 292414 CDS YP_613077.1 99080923 4076315 complement(1157120..1157569) 1 NC_008044.1 KEGG: rso:RSc0006 hypothetical protein, ev=5e-19, 50% identity; hypothetical protein 1157569 4076315 TM1040_1082 Ruegeria sp. TM1040 hypothetical protein YP_613077.1 1157120 R 292414 CDS YP_613078.1 99080924 4076316 complement(1157674..1159446) 1 NC_008044.1 PFAM: histidine kinase, HAMP region: (1.5e-10) chemotaxis sensory transducer: (3.2e-66); KEGG: sme:SMc01104 probable chemoreceptor (methyl-accepting chemotaxis) transmembrane protein, ev=9e-72, 40% identity; methyl-accepting chemotaxis sensory transducer 1159446 4076316 TM1040_1083 Ruegeria sp. TM1040 methyl-accepting chemotaxis sensory transducer YP_613078.1 1157674 R 292414 CDS YP_613079.1 99080925 4076317 complement(1159751..1160941) 1 NC_008044.1 Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway; phosphoglycerate kinase 1160941 pgk 4076317 pgk Ruegeria sp. TM1040 phosphoglycerate kinase YP_613079.1 1159751 R 292414 CDS YP_613080.1 99080926 4076318 1161321..1161827 1 NC_008044.1 PFAM: peptidyl-prolyl cis-trans isomerase, cyclophilin type: (2e-21); KEGG: sil:SPO2234 peptidyl-prolyl cis-trans isomerase, cyclophilin-type, ev=3e-79, 86% identity; cyclophilin type peptidyl-prolyl cis-trans isomerase 1161827 4076318 TM1040_1085 Ruegeria sp. TM1040 cyclophilin type peptidyl-prolyl cis-trans isomerase YP_613080.1 1161321 D 292414 CDS YP_613081.1 99080927 4076319 1161820..1162368 1 NC_008044.1 PFAM: peptidyl-prolyl cis-trans isomerase, cyclophilin type: (4.8e-21); KEGG: sil:SPO2233 peptidyl-prolyl cis-trans isomerase, cyclophilin-type, ev=2e-68, 72% identity; cyclophilin type peptidyl-prolyl cis-trans isomerase 1162368 4076319 TM1040_1086 Ruegeria sp. TM1040 cyclophilin type peptidyl-prolyl cis-trans isomerase YP_613081.1 1161820 D 292414 CDS YP_613082.1 99080928 4076320 complement(1162460..1163047) 1 NC_008044.1 PFAM: Hemolysin-type calcium-binding region: (0.13); KEGG: sme:SMb21314 secreted calcium-binding protein, ev=6e-32, 39% identity; hemolysin-type calcium-binding protein 1163047 4076320 TM1040_1087 Ruegeria sp. TM1040 hemolysin-type calcium-binding protein YP_613082.1 1162460 R 292414 CDS YP_613083.1 99080929 4076321 complement(1163480..1164001) 1 NC_008044.1 PFAM: protein of unknown function DUF583: (2.4e-30); KEGG: sil:SPO2231 hypothetical protein, ev=3e-67, 79% identity; hypothetical protein 1164001 4076321 TM1040_1088 Ruegeria sp. TM1040 hypothetical protein YP_613083.1 1163480 R 292414 CDS YP_613084.1 99080930 4076322 complement(1163991..1165322) 1 NC_008044.1 PFAM: peptidase M23B: (6e-51); KEGG: sil:SPO2230 peptidase, M23/M37 family, ev=1e-179, 70% identity; peptidase M23B 1165322 4076322 TM1040_1089 Ruegeria sp. TM1040 peptidase M23B YP_613084.1 1163991 R 292414 CDS YP_613085.1 99080931 4076323 complement(1165550..1166392) 1 NC_008044.1 PFAM: protein of unknown function DUF455: (8e-83); KEGG: sil:SPO2229 hypothetical protein, ev=1e-124, 78% identity; hypothetical protein 1166392 4076323 TM1040_1090 Ruegeria sp. TM1040 hypothetical protein YP_613085.1 1165550 R 292414 CDS YP_613086.1 99080932 4076324 complement(1166917..1167378) 1 NC_008044.1 PFAM: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen: (5.3e-12) Redoxin: (9.3e-22); KEGG: sil:SPO2228 AhpC/TSA family protein, ev=2e-67, 79% identity; redoxin 1167378 4076324 TM1040_1091 Ruegeria sp. TM1040 redoxin YP_613086.1 1166917 R 292414 CDS YP_613087.1 99080933 4076325 1167440..1170907 1 NC_008044.1 KEGG: sil:SPO2227 hypothetical protein, ev=0.0, 45% identity; hypothetical protein 1170907 4076325 TM1040_1092 Ruegeria sp. TM1040 hypothetical protein YP_613087.1 1167440 D 292414 CDS YP_613088.1 99080934 4076326 1171133..1172182 1 NC_008044.1 Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step; S-adenosylmethionine--tRNA ribosyltransferase-isomerase 1172182 queA 4076326 queA Ruegeria sp. TM1040 S-adenosylmethionine--tRNA ribosyltransferase-isomerase YP_613088.1 1171133 D 292414 CDS YP_613089.1 99080935 4076327 1172453..1173727 1 NC_008044.1 PFAM: major facilitator superfamily MFS_1: (1e-28); KEGG: sil:SPO2225 membrane protein, , ev=1e-166, 70% identity; major facilitator superfamily transporter 1173727 4076327 TM1040_1094 Ruegeria sp. TM1040 major facilitator superfamily transporter YP_613089.1 1172453 D 292414 CDS YP_613090.1 99080936 4077802 1173877..1174455 1 NC_008044.1 PFAM: protein of unknown function DUF924: (1.9e-68); KEGG: sil:SPO2224 hypothetical protein, ev=1e-78, 71% identity; hypothetical protein 1174455 4077802 TM1040_1095 Ruegeria sp. TM1040 hypothetical protein YP_613090.1 1173877 D 292414 CDS YP_613091.1 99080937 4077803 1174730..1176124 1 NC_008044.1 E3 component of pyruvate complex; catalyzes the oxidation of dihydrolipoamide to lipoamide; dihydrolipoamide dehydrogenase 1176124 4077803 TM1040_1096 Ruegeria sp. TM1040 dihydrolipoamide dehydrogenase YP_613091.1 1174730 D 292414 CDS YP_613092.1 99080938 4077804 1176282..1177466 1 NC_008044.1 PFAM: major facilitator superfamily MFS_1: (3.5e-19); KEGG: sil:SPO3505 membrane protein, , ev=3e-85, 45% identity; major facilitator superfamily transporter 1177466 4077804 TM1040_1097 Ruegeria sp. TM1040 major facilitator superfamily transporter YP_613092.1 1176282 D 292414 CDS YP_613093.1 99080939 4077805 1177570..1180461 1 NC_008044.1 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 uvrA and 2 uvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by uvrB, the uvrA molecules dissociate; excinuclease ABC subunit A 1180461 uvrA 4077805 uvrA Ruegeria sp. TM1040 excinuclease ABC subunit A YP_613093.1 1177570 D 292414 CDS YP_613094.1 99080940 4077806 complement(1180567..1181016) 1 NC_008044.1 hypothetical protein 1181016 4077806 TM1040_1099 Ruegeria sp. TM1040 hypothetical protein YP_613094.1 1180567 R 292414 CDS YP_613095.1 99080941 4077807 1181139..1181903 1 NC_008044.1 PFAM: helix-turn-helix motif: (2.4e-07); KEGG: sil:SPO2216 DNA-binding protein, , ev=8e-71, 58% identity; XRE family transcriptional regulator 1181903 4077807 TM1040_1100 Ruegeria sp. TM1040 XRE family transcriptional regulator YP_613095.1 1181139 D 292414 CDS YP_613096.1 99080942 4077808 complement(1181900..1182772) 1 NC_008044.1 KEGG: sil:SPO2213 3-hydroxyisobutyrate dehydrogenase, ev=1e-138, 86% identity; TIGRFAM: 3-hydroxyisobutyrate dehydrogenase: (1.3e-142); PFAM: NADP oxidoreductase, coenzyme F420-dependent: (0.0011) 6-phosphogluconate dehydrogenase, NAD-binding: (2e-61); 3-hydroxyisobutyrate dehydrogenase 1182772 4077808 TM1040_1101 Ruegeria sp. TM1040 3-hydroxyisobutyrate dehydrogenase YP_613096.1 1181900 R 292414 CDS YP_613097.1 99080943 4077809 complement(1182774..1183817) 1 NC_008044.1 PFAM: Enoyl-CoA hydratase/isomerase: (2.8e-12); KEGG: sil:SPO2212 enoyl-CoA hydratase/isomerase family protein, ev=1e-144, 71% identity; enoyl-CoA hydratase/isomerase 1183817 4077809 TM1040_1102 Ruegeria sp. TM1040 enoyl-CoA hydratase/isomerase YP_613097.1 1182774 R 292414 CDS YP_613098.1 99080944 4077810 complement(1183842..1184987) 1 NC_008044.1 PFAM: acyl-CoA dehydrogenase-like: (2.7e-67) Acyl-CoA dehydrogenase, type 2-like: (2e-22); KEGG: sil:SPO2211 acyl-CoA dehydrogenase, ev=0.0, 90% identity; acyl-CoA dehydrogenase 1184987 4077810 TM1040_1103 Ruegeria sp. TM1040 acyl-CoA dehydrogenase YP_613098.1 1183842 R 292414 CDS YP_613099.1 99080945 4077811 1185278..1187128 1 NC_008044.1 PFAM: TPR repeat: (2.5e-05) Tetratricopeptide TPR_2: (0.0023); SMART: Tetratricopeptide region: (8.8e-07); KEGG: pmn:PMN2A_1232 TPR repeat, ev=1e-101, 38% identity; hypothetical protein 1187128 4077811 TM1040_1104 Ruegeria sp. TM1040 hypothetical protein YP_613099.1 1185278 D 292414 CDS YP_613100.1 99080946 4077812 complement(1187238..1187855) 1 NC_008044.1 PFAM: ErfK/YbiS/YcfS/YnhG: (1.7e-37); KEGG: sil:SPO2205 ErfK/YbiS/YcfS/YnhG family protein, ev=3e-88, 77% identity; ErfK/YbiS/YcfS/YnhG protein 1187855 4077812 TM1040_1105 Ruegeria sp. TM1040 ErfK/YbiS/YcfS/YnhG protein YP_613100.1 1187238 R 292414 CDS YP_613101.1 99080947 4077813 complement(1188053..1189552) 1 NC_008044.1 TIGRFAM: methylmalonate-semialdehyde dehydrogenase: (2e-255); PFAM: aldehyde dehydrogenase: (1.2e-176); KEGG: rsp:RSP_2962 methylmalonic acid semialdehyde dehydrogenase, ev=0.0, 76% identity; methylmalonate-semialdehyde dehydrogenase 1189552 4077813 TM1040_1106 Ruegeria sp. TM1040 methylmalonate-semialdehyde dehydrogenase YP_613101.1 1188053 R 292414 CDS YP_613102.1 99080948 4077814 1189708..1190604 1 NC_008044.1 PFAM: regulatory protein, LysR: (1.3e-14) LysR, substrate-binding: (2.4e-28); KEGG: sil:SPO2202 transcriptional regulator, LysR family, ev=1e-122, 74% identity; LysR family transcriptional regulator 1190604 4077814 TM1040_1107 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_613102.1 1189708 D 292414 CDS YP_613103.1 99080949 4077815 1190660..1191094 1 NC_008044.1 PFAM: CBS: (1.5e-31); KEGG: sil:SPO2201 CBS domain protein, ev=5e-43, 62% identity; signal-transduction protein 1191094 4077815 TM1040_1108 Ruegeria sp. TM1040 signal-transduction protein YP_613103.1 1190660 D 292414 CDS YP_613104.1 99080950 4077816 1191220..1191717 1 NC_008044.1 Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA; phosphopantetheine adenylyltransferase 1191717 coaD 4077816 coaD Ruegeria sp. TM1040 phosphopantetheine adenylyltransferase YP_613104.1 1191220 D 292414 CDS YP_613105.1 99080951 4077817 complement(1191785..1191928) 1 NC_008044.1 KEGG: sil:SPO2199 hypothetical protein, ev=5e-11, 63% identity; hypothetical protein 1191928 4077817 TM1040_1110 Ruegeria sp. TM1040 hypothetical protein YP_613105.1 1191785 R 292414 CDS YP_613106.1 99080952 4077818 complement(1192007..1193008) 1 NC_008044.1 KEGG: sil:SPO2198 glyceraldehyde-3-phosphate dehydrogenase, type I, ev=1e-167, 87% identity; TIGRFAM: glyceraldehyde-3-phosphate dehydrogenase, type I: (4.1e-169); PFAM: glyceraldehyde 3-phosphate dehydrogenase: (5.5e-59); glyceraldehyde-3-phosphate dehydrogenase 1193008 4077818 TM1040_1111 Ruegeria sp. TM1040 glyceraldehyde-3-phosphate dehydrogenase YP_613106.1 1192007 R 292414 CDS YP_613107.1 99080953 4077819 1193263..1194213 1 NC_008044.1 PFAM: protein of unknown function DUF808: (1.9e-153); KEGG: sil:SPO2197 hypothetical protein, ev=1e-107, 65% identity; hypothetical protein 1194213 4077819 TM1040_1112 Ruegeria sp. TM1040 hypothetical protein YP_613107.1 1193263 D 292414 CDS YP_613108.1 99080954 4077820 complement(1194349..1196370) 1 NC_008044.1 catalyzes the formation of ribose 5-phosphate and xylulose 5-phosphate from sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate; can transfer ketol groups between several groups; in Escherichia coli there are two tkt genes, tktA expressed during exponential growth and the tktB during stationary phase; transketolase 1196370 4077820 TM1040_1113 Ruegeria sp. TM1040 transketolase YP_613108.1 1194349 R 292414 CDS YP_613109.1 99080955 4077821 1196728..1197648 1 NC_008044.1 KEGG: sil:SPO1866 hypothetical protein, ev=3e-37, 39% identity; hypothetical protein 1197648 4077821 TM1040_1114 Ruegeria sp. TM1040 hypothetical protein YP_613109.1 1196728 D 292414 CDS YP_613110.1 99080956 4077236 1197648..1198193 1 NC_008044.1 KEGG: sil:SPO1867 hypothetical protein, ev=6e-49, 76% identity; hypothetical protein 1198193 4077236 TM1040_1115 Ruegeria sp. TM1040 hypothetical protein YP_613110.1 1197648 D 292414 CDS YP_613111.1 99080957 4077237 complement(1198356..1198718) 1 NC_008044.1 TIGRFAM: Glutaredoxin-related protein: (1.1e-54); PFAM: glutaredoxin: (1.4e-29); KEGG: sil:SPO1868 glutaredoxin-related protein, ev=2e-58, 88% identity; glutaredoxin-like protein 1198718 4077237 TM1040_1116 Ruegeria sp. TM1040 glutaredoxin-like protein YP_613111.1 1198356 R 292414 CDS YP_613112.1 99080958 4077238 complement(1199086..1199322) 1 NC_008044.1 PFAM: BolA-like protein: (5.2e-09); KEGG: jan:Jann_2172 BolA-like protein, ev=4e-33, 87% identity; BolA-like protein 1199322 4077238 TM1040_1117 Ruegeria sp. TM1040 BolA-like protein YP_613112.1 1199086 R 292414 CDS YP_613113.1 99080959 4077239 complement(1199601..1201766) 1 NC_008044.1 catalyzes the formation of 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide and L-glutamine in purine biosynthesis; phosphoribosylformylglycinamidine synthase II 1201766 4077239 TM1040_1118 Ruegeria sp. TM1040 phosphoribosylformylglycinamidine synthase II YP_613113.1 1199601 R 292414 CDS YP_613114.1 99080960 4077240 complement(1202216..1203121) 1 NC_008044.1 PFAM: regulatory protein, LysR: (1e-22) LysR, substrate-binding: (4.1e-33); KEGG: sil:SPO1872 transcriptional regulator, LysR family, ev=1e-136, 80% identity; LysR family transcriptional regulator 1203121 4077240 TM1040_1119 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_613114.1 1202216 R 292414 CDS YP_613115.1 99080961 4077241 1203290..1206709 1 NC_008044.1 Catalyzes the ferredoxin-dependent oxidative decarboxylation of arylpyruvates; indolepyruvate ferredoxin oxidoreductase 1206709 4077241 TM1040_1120 Ruegeria sp. TM1040 indolepyruvate ferredoxin oxidoreductase YP_613115.1 1203290 D 292414 CDS YP_613116.1 99080962 4077242 1206847..1207725 1 NC_008044.1 PFAM: phospholipid/glycerol acyltransferase: (0.00044); KEGG: sil:SPO1874 acyltransferase domain protein, ev=1e-136, 78% identity; phospholipid/glycerol acyltransferase 1207725 4077242 TM1040_1121 Ruegeria sp. TM1040 phospholipid/glycerol acyltransferase YP_613116.1 1206847 D 292414 CDS YP_613117.1 99080963 4077243 1207757..1208566 1 NC_008044.1 KEGG: sil:SPO1875 glutamate racemase, ev=1e-125, 83% identity; TIGRFAM: Glutamate racemase: (1.2e-32); PFAM: Asp/Glu racemase: (5.4e-54); glutamate racemase 1208566 4077243 TM1040_1122 Ruegeria sp. TM1040 glutamate racemase YP_613117.1 1207757 D 292414 CDS YP_613118.1 99080964 4077244 1208651..1209679 1 NC_008044.1 catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis and the reduction of N-acetyl-gamma-aminoadipyl-phosphate to N-acetyl-L-aminoadipate-semialdehyde in lysine biosynthesis; involved in both the arginine and lysine biosynthetic pathways; lysine is produced via the AAA pathway, lysine from alpha-aminoadipate; N-acetyl-gamma-glutamyl-phosphate reductase 1209679 argC 4077244 argC Ruegeria sp. TM1040 N-acetyl-gamma-glutamyl-phosphate reductase YP_613118.1 1208651 D 292414 CDS YP_613119.1 99080965 4077245 1209696..1210139 1 NC_008044.1 CycJ; periplasmic heme chaperone that binds heme transiently via a histidine residue and delivers it to newly synthesized and exported c-type cytochromes; requires the ATP hydrolysis activity of the CcmA protein in order to transfer the heme to the apocytochrome; part of the cytochrome c maturation system; periplasmic protein anchored to the inner membrane; cytochrome c-type biogenesis protein CcmE 1210139 4077245 TM1040_1124 Ruegeria sp. TM1040 cytochrome c-type biogenesis protein CcmE YP_613119.1 1209696 D 292414 CDS YP_613120.1 99080966 4077246 1210282..1210890 1 NC_008044.1 PFAM: protein of unknown function DUF847: (6.3e-72); KEGG: sil:SPO1878 hypothetical protein, ev=3e-74, 68% identity; hypothetical protein 1210890 4077246 TM1040_1125 Ruegeria sp. TM1040 hypothetical protein YP_613120.1 1210282 D 292414 CDS YP_613121.1 99080967 4077247 1210900..1211436 1 NC_008044.1 KEGG: rsp:RSP_6081 hypothetical protein, ev=3e-26, 47% identity; hypothetical protein 1211436 4077247 TM1040_1126 Ruegeria sp. TM1040 hypothetical protein YP_613121.1 1210900 D 292414 CDS YP_613122.1 99080968 4077248 1211514..1213478 1 NC_008044.1 TIGRFAM: cytochrome c-type biogenesis protein CcmF: (1.3e-213); PFAM: cytochrome c assembly protein: (3.6e-85); KEGG: sil:SPO1880 cytochrome c-type biogenesis protein CcmF, ev=0.0, 82% identity; cytochrome c-type biogenesis protein CcmF 1213478 4077248 TM1040_1127 Ruegeria sp. TM1040 cytochrome c-type biogenesis protein CcmF YP_613122.1 1211514 D 292414 CDS YP_613123.1 99080969 4077249 1213475..1213960 1 NC_008044.1 PFAM: cytochrome C biogenesis protein: (2.2e-55); KEGG: sil:SPO1881 cytochrome c biogenesis family protein, ev=5e-51, 71% identity; cytochrome C biogenesis protein 1213960 4077249 TM1040_1128 Ruegeria sp. TM1040 cytochrome C biogenesis protein YP_613123.1 1213475 D 292414 CDS YP_613124.1 99080970 4077250 1214188..1214706 1 NC_008044.1 KEGG: rpa:RPA2489 hypothetical protein, ev=3e-30, 42% identity; hypothetical protein 1214706 4077250 TM1040_1129 Ruegeria sp. TM1040 hypothetical protein YP_613124.1 1214188 D 292414 CDS YP_613125.1 99080971 4077251 1214788..1215567 1 NC_008044.1 PFAM: Enoyl-CoA hydratase/isomerase: (1.2e-60); KEGG: sil:SPO1882 enoyl-CoA hydratase/isomerase family protein, ev=1e-108, 76% identity; short chain enoyl-CoA hydratase / enoyl-CoA hydratase 1215567 4077251 TM1040_1130 Ruegeria sp. TM1040 short chain enoyl-CoA hydratase / enoyl-CoA hydratase YP_613125.1 1214788 D 292414 CDS YP_613126.1 99080972 4077252 complement(1215643..1216653) 1 NC_008044.1 PFAM: Hemolysin-type calcium-binding region: (0.66); KEGG: bja:bll7673 hypothetical protein, ev=5e-47, 44% identity; hemolysin-type calcium-binding protein 1216653 4077252 TM1040_1131 Ruegeria sp. TM1040 hemolysin-type calcium-binding protein YP_613126.1 1215643 R 292414 CDS YP_613127.1 99080973 4077253 complement(1216941..1218236) 1 NC_008044.1 KEGG: sil:SPO2157 citrate synthase I, ev=0.0, 86% identity; TIGRFAM: Citrate synthase I: (2.2e-277); PFAM: Citrate synthase: (2.1e-219); citrate synthase 1218236 4077253 TM1040_1132 Ruegeria sp. TM1040 citrate synthase YP_613127.1 1216941 R 292414 CDS YP_613128.1 99080974 4077254 complement(1218376..1219776) 1 NC_008044.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase 1219776 gltX 4077254 gltX Ruegeria sp. TM1040 glutamyl-tRNA synthetase YP_613128.1 1218376 R 292414 CDS YP_613129.1 99080975 4078430 1219862..1221880 1 NC_008044.1 PFAM: ComEC/Rec2-related protein: (5.2e-62); KEGG: sil:SPO2155 competence protein, ev=0.0, 53% identity; ComEC/Rec2-like protein 1221880 4078430 TM1040_1134 Ruegeria sp. TM1040 ComEC/Rec2-like protein YP_613129.1 1219862 D 292414 CDS YP_613130.1 99080976 4078431 complement(1221954..1222679) 1 NC_008044.1 Represses a number of genes involved in the response to DNA damage; LexA repressor 1222679 4078431 TM1040_1135 Ruegeria sp. TM1040 LexA repressor YP_613130.1 1221954 R 292414 CDS YP_613131.1 99080977 4078432 complement(1222806..1223978) 1 NC_008044.1 PFAM: molybdopterin binding domain: (8e-37) MoeA-like, domain I and II: (2.7e-56) MoeA-like, domain IV: (1.3e-15); KEGG: sil:SPO2153 molybdenum cofactor biosynthesis protein A, ev=1e-150, 70% identity; MoeA-like domain-containing protein 1223978 4078432 TM1040_1136 Ruegeria sp. TM1040 MoeA-like domain-containing protein YP_613131.1 1222806 R 292414 CDS YP_613132.1 99080978 4078433 complement(1223982..1224452) 1 NC_008044.1 MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis; molybdenum cofactor biosynthesis protein MoaC 1224452 moaC 4078433 moaC Ruegeria sp. TM1040 molybdenum cofactor biosynthesis protein MoaC YP_613132.1 1223982 R 292414 CDS YP_613133.1 99080979 4078434 complement(1224499..1225308) 1 NC_008044.1 involved in tryptophan biosynthesis; amino acid biosynthesis; converts 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate to C(1)-(3-indolyl)-glycerol 3-phosphate and carbon dioxide and water; indole-3-glycerol phosphate synthase 1225308 trpC 4078434 trpC Ruegeria sp. TM1040 indole-3-glycerol phosphate synthase YP_613133.1 1224499 R 292414 CDS YP_613134.1 99080980 4078435 complement(1225301..1226005) 1 NC_008044.1 TIGRFAM: uracil-DNA glycosylase: (1.3e-77); PFAM: Uracil-DNA glycosylase superfamily: (4.2e-56); KEGG: tcx:Tcr_0362 uracil-DNA glycosylase, ev=5e-49, 53% identity; uracil-DNA glycosylase 1226005 4078435 TM1040_1139 Ruegeria sp. TM1040 uracil-DNA glycosylase YP_613134.1 1225301 R 292414 CDS YP_613135.1 99080981 4078436 complement(1226005..1227027) 1 NC_008044.1 Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate; anthranilate phosphoribosyltransferase 1227027 trpD 4078436 trpD Ruegeria sp. TM1040 anthranilate phosphoribosyltransferase YP_613135.1 1226005 R 292414 CDS YP_613136.1 99080982 4078437 complement(1227024..1227605) 1 NC_008044.1 TrpG; with TrpE catalyzes the formation of anthranilate and glutamate from chorismate and glutamine; TrpG provides the glutamine amidotransferase activity; anthranilate synthase component II 1227605 4078437 TM1040_1141 Ruegeria sp. TM1040 anthranilate synthase component II YP_613136.1 1227024 R 292414 CDS YP_613137.1 99080983 4078438 1227757..1229316 1 NC_008044.1 KEGG: sil:SPO2148 hypothetical protein, ev=1e-106, 47% identity; hypothetical protein 1229316 4078438 TM1040_1142 Ruegeria sp. TM1040 hypothetical protein YP_613137.1 1227757 D 292414 CDS YP_613138.1 99080984 4078439 complement(1229411..1230922) 1 NC_008044.1 with component II, the glutamine amidotransferase, catalyzes the formation of anthranilate from chorismate and glutamine; anthranilate synthase component I 1230922 4078439 TM1040_1143 Ruegeria sp. TM1040 anthranilate synthase component I YP_613138.1 1229411 R 292414 CDS YP_613139.1 99080985 4078440 complement(1230946..1232781) 1 NC_008044.1 KEGG: sil:SPO2145 peptidyl-prolyl cis-trans isomerse D, ev=1e-178, 52% identity; peptidyl-prolyl cis-trans isomerse D 1232781 4078440 TM1040_1144 Ruegeria sp. TM1040 peptidyl-prolyl cis-trans isomerse D YP_613139.1 1230946 R 292414 CDS YP_613140.1 99080986 4078441 complement(1232945..1234120) 1 NC_008044.1 PFAM: aminotransferase, class I and II: (1.4e-35); KEGG: sil:SPO2144 aminotransferase, classes I and II, ev=1e-150, 67% identity; hypothetical protein 1234120 4078441 TM1040_1145 Ruegeria sp. TM1040 hypothetical protein YP_613140.1 1232945 R 292414 CDS YP_613141.1 99080987 4078442 complement(1234272..1234802) 1 NC_008044.1 catalyzes the conversion of guanine, xanthine and, to a lesser extent, hypoxanthine to GMP, XMP and IMP, respectively; xanthine-guanine phosphoribosyltransferase 1234802 4078442 TM1040_1146 Ruegeria sp. TM1040 xanthine-guanine phosphoribosyltransferase YP_613141.1 1234272 R 292414 CDS YP_613142.1 99080988 4078443 complement(1234809..1235615) 1 NC_008044.1 Catalyzes a key regulatory step in fatty acid biosynthesis; enoyl-ACP reductase 1235615 4078443 TM1040_1147 Ruegeria sp. TM1040 enoyl-ACP reductase YP_613142.1 1234809 R 292414 CDS YP_613143.1 99080989 4078444 1235783..1236388 1 NC_008044.1 KEGG: sil:SPO2141 pyridoxamine 5''-phosphate oxidase, , ev=5e-90, 77% identity; TIGRFAM: pyridoxamine 5'-phosphate oxidase: (4.9e-63); PFAM: pyridoxamine 5'-phosphate oxidase-related, FMN-binding: (1.8e-22); pyridoxamine 5'-phosphate oxidase 1236388 4078444 TM1040_1148 Ruegeria sp. TM1040 pyridoxamine 5'-phosphate oxidase YP_613143.1 1235783 D 292414 CDS YP_613144.1 99080990 4078445 1236516..1237055 1 NC_008044.1 PFAM: Cold-shock protein, DNA-binding: (9.3e-09); SMART: Cold shock protein: (1.2e-08); KEGG: sil:SPO2140 cold shock DNA-binding domain protein, ev=2e-73, 77% identity; cold-shock DNA-binding protein family protein 1237055 4078445 TM1040_1149 Ruegeria sp. TM1040 cold-shock DNA-binding protein family protein YP_613144.1 1236516 D 292414 CDS YP_613145.1 99080991 4078446 1237055..1237534 1 NC_008044.1 PFAM: protein of unknown function DUF192: (1.7e-38); KEGG: sil:SPO2139 hypothetical protein, ev=1e-44, 52% identity; hypothetical protein 1237534 4078446 TM1040_1150 Ruegeria sp. TM1040 hypothetical protein YP_613145.1 1237055 D 292414 CDS YP_613146.1 99080992 4078447 1238449..1242102 1 NC_008044.1 Catalyzes the rate-limiting step in dNTP synthesis; ribonucleotide-diphosphate reductase subunit alpha 1242102 4078447 TM1040_1151 Ruegeria sp. TM1040 ribonucleotide-diphosphate reductase subunit alpha YP_613146.1 1238449 D 292414 CDS YP_613147.1 99080993 4078448 1242589..1243077 1 NC_008044.1 hypothetical protein 1243077 4078448 TM1040_1152 Ruegeria sp. TM1040 hypothetical protein YP_613147.1 1242589 D 292414 CDS YP_613148.1 99080994 4078449 1243613..1244986 1 NC_008044.1 catalyzes a two-step reaction; charges a cysteine by linking its carboxyl group to the alpha-phosphate of ATP then transfers the aminoacyl-adenylate to its tRNA; cysteinyl-tRNA synthetase 1244986 cysS 4078449 cysS Ruegeria sp. TM1040 cysteinyl-tRNA synthetase YP_613148.1 1243613 D 292414 CDS YP_613149.1 99080995 4075940 1244983..1246611 1 NC_008044.1 TIGRFAM: 2-isopropylmalate synthase/homocitrate synthase: (1.5e-214); PFAM: pyruvate carboxyltransferase: (8.3e-27) LeuA allosteric (dimerisation) domain: (1.1e-26); KEGG: sil:SPO2130 2-isopropylmalate synthase/homocitrate synthase family protein, ev=0.0, 83% identity; alpha-isopropylmalate synthase 1246611 4075940 TM1040_1154 Ruegeria sp. TM1040 alpha-isopropylmalate synthase YP_613149.1 1244983 D 292414 CDS YP_613150.1 99080996 4075941 1246601..1247377 1 NC_008044.1 KEGG: sil:SPO2129 hypothetical protein, ev=5e-82, 59% identity; hypothetical protein 1247377 4075941 TM1040_1155 Ruegeria sp. TM1040 hypothetical protein YP_613150.1 1246601 D 292414 CDS YP_613151.1 99080997 4075942 complement(1247435..1248664) 1 NC_008044.1 PFAM: major facilitator superfamily MFS_1: (3.9e-19); KEGG: sil:SPO2128 transporter, , ev=0.0, 80% identity; major facilitator superfamily transporter 1248664 4075942 TM1040_1156 Ruegeria sp. TM1040 major facilitator superfamily transporter YP_613151.1 1247435 R 292414 CDS YP_613152.1 99080998 4075943 1248737..1249369 1 NC_008044.1 PFAM: HhH-GPD: (2.8e-14); KEGG: sil:SPO2127 DNA-3-methyladenine glycosylase II, , ev=1e-93, 81% identity; HhH-GPD 1249369 4075943 TM1040_1157 Ruegeria sp. TM1040 HhH-GPD YP_613152.1 1248737 D 292414 CDS YP_613153.1 99080999 4075944 1249366..1250031 1 NC_008044.1 PFAM: phospholipase/Carboxylesterase: (4.4e-35); KEGG: sil:SPO2126 phospholipase/carboxylesterase family protein, ev=1e-105, 85% identity; phospholipase/carboxylesterase 1250031 4075944 TM1040_1158 Ruegeria sp. TM1040 phospholipase/carboxylesterase YP_613153.1 1249366 D 292414 CDS YP_613154.1 99081000 4075945 complement(1250051..1250512) 1 NC_008044.1 PFAM: regulatory proteins, AsnC/Lrp: (1.7e-06); KEGG: sme:SMc02504 transcription regulator protein, ev=6e-13, 34% identity; AsnC family transcriptional regulator 1250512 4075945 TM1040_1159 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_613154.1 1250051 R 292414 CDS YP_613155.1 99081001 4075946 1250605..1250919 1 NC_008044.1 PFAM: Cupin 2, conserved barrel: (0.0012); KEGG: nma:NMA0001 hypothetical protein, ev=1e-30, 62% identity; cupin 1250919 4075946 TM1040_1160 Ruegeria sp. TM1040 cupin YP_613155.1 1250605 D 292414 CDS YP_613156.1 99081002 4075947 complement(1250925..1251590) 1 NC_008044.1 TIGRFAM: Pseudouridine synthase, Rsu: (4.4e-86); PFAM: pseudouridine synthase: (1e-23); KEGG: sil:SPO2124 RNA pseudouridylate synthase, ev=1e-75, 71% identity; ribosomal large subunit pseudouridine synthase E 1251590 4075947 TM1040_1161 Ruegeria sp. TM1040 ribosomal large subunit pseudouridine synthase E YP_613156.1 1250925 R 292414 CDS YP_613157.1 99081003 4075948 1251838..1252422 1 NC_008044.1 PFAM: HNH endonuclease: (8.6e-09); SMART: HNH nuclease: (1.6e-14); KEGG: sil:SPO2123 HNH endonuclease family protein, ev=3e-98, 84% identity; HNH endonuclease 1252422 4075948 TM1040_1162 Ruegeria sp. TM1040 HNH endonuclease YP_613157.1 1251838 D 292414 CDS YP_613158.1 99081004 4075949 complement(1252474..1253520) 1 NC_008044.1 catalyzes the formation of L-proline from L-ornithine; ornithine cyclodeaminase 1253520 4075949 TM1040_1163 Ruegeria sp. TM1040 ornithine cyclodeaminase YP_613158.1 1252474 R 292414 CDS YP_613159.1 99081005 4075950 complement(1253517..1254446) 1 NC_008044.1 KEGG: sil:SPO2120 amidinotransferase family protein, ev=1e-124, 75% identity; amidinotransferase 1254446 4075950 TM1040_1164 Ruegeria sp. TM1040 amidinotransferase YP_613159.1 1253517 R 292414 CDS YP_613160.1 99081006 4075951 complement(1254443..1255372) 1 NC_008044.1 TIGRFAM: arginase: (7.6e-114); PFAM: Arginase/agmatinase/formiminoglutamase: (8.7e-97); KEGG: sil:SPO2119 arginase, ev=1e-126, 70% identity; arginase 1255372 4075951 TM1040_1165 Ruegeria sp. TM1040 arginase YP_613160.1 1254443 R 292414 CDS YP_613161.1 99081007 4075952 1255482..1255913 1 NC_008044.1 PFAM: regulatory proteins, AsnC/Lrp: (1.7e-10) Helix-turn-helix, type 11: (0.0027); KEGG: sil:SPO2118 transcriptional regulator, AsnC family, ev=4e-60, 85% identity; AsnC family transcriptional regulator 1255913 4075952 TM1040_1166 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_613161.1 1255482 D 292414 CDS YP_613162.1 99081008 4075953 complement(1255924..1256397) 1 NC_008044.1 PFAM: Disulphide bond formation protein DsbB: (1.7e-05); KEGG: sil:SPO2117 disulfide bond formation protein, DsbB family, ev=2e-56, 68% identity; disulfide bond formation protein DsbB 1256397 4075953 TM1040_1167 Ruegeria sp. TM1040 disulfide bond formation protein DsbB YP_613162.1 1255924 R 292414 CDS YP_613163.1 99081009 4075954 complement(1256394..1256972) 1 NC_008044.1 KEGG: sil:SPO2116 DedA family protein, ev=3e-85, 81% identity; DedA family protein 1256972 4075954 TM1040_1168 Ruegeria sp. TM1040 DedA family protein YP_613163.1 1256394 R 292414 CDS YP_613164.1 99081010 4075955 complement(1257343..1259133) 1 NC_008044.1 KEGG: atc:AGR_L_3494 phototransducer; methyl-accepting chemotaxis protein; Ptr, ev=1e-152, 49% identity; TIGRFAM: GGDEF domain: (9.5e-38); PFAM: GGDEF: (1.1e-49) histidine kinase, HAMP region: (2.7e-12); SMART: GAF: (8.2e-06); GAF sensor-containing diguanylate cyclase 1259133 4075955 TM1040_1169 Ruegeria sp. TM1040 GAF sensor-containing diguanylate cyclase YP_613164.1 1257343 R 292414 CDS YP_613165.1 99081011 4075956 complement(1259585..1261216) 1 NC_008044.1 activates fatty acids by binding to coenzyme A; acyl-CoA synthetase 1261216 4075956 TM1040_1170 Ruegeria sp. TM1040 acyl-CoA synthetase YP_613165.1 1259585 R 292414 CDS YP_613166.1 99081012 4075957 complement(1261221..1262021) 1 NC_008044.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 1262021 4075957 TM1040_1171 Ruegeria sp. TM1040 enoyl-CoA hydratase YP_613166.1 1261221 R 292414 CDS YP_613167.1 99081013 4075958 complement(1262032..1262481) 1 NC_008044.1 PFAM: OsmC-like protein: (1.7e-22); KEGG: son:SO3409 OsmC/Ohr family protein, ev=1e-26, 41% identity; OsmC-like protein 1262481 4075958 TM1040_1172 Ruegeria sp. TM1040 OsmC-like protein YP_613167.1 1262032 R 292414 CDS YP_613168.1 99081014 4077782 complement(1262504..1263646) 1 NC_008044.1 PFAM: glycine cleavage T protein (aminomethyl transferase): (2.4e-45); KEGG: sil:SPO1648 aminomethyl transferase family protein, ev=2e-89, 44% identity; glycine cleavage T protein (aminomethyl transferase) 1263646 4077782 TM1040_1173 Ruegeria sp. TM1040 glycine cleavage T protein (aminomethyl transferase) YP_613168.1 1262504 R 292414 CDS YP_613169.1 99081015 4077783 complement(1263806..1264339) 1 NC_008044.1 PFAM: regulatory proteins, AsnC/Lrp: (4.9e-17); KEGG: sme:SMb20425 transcriptional regulator protein, ev=7e-36, 47% identity; AsnC family transcriptional regulator 1264339 4077783 TM1040_1174 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_613169.1 1263806 R 292414 CDS YP_613170.1 99081016 4077784 1264744..1265736 1 NC_008044.1 TIGRFAM: TRAP transporter solute receptor, TAXI family: (3.7e-67); KEGG: jan:Jann_2331 TRAP transporter solute receptor, TAXI family, ev=1e-83, 46% identity; TRAP transporter solute receptor TAXI family protein 1265736 4077784 TM1040_1175 Ruegeria sp. TM1040 TRAP transporter solute receptor TAXI family protein YP_613170.1 1264744 D 292414 CDS YP_613171.1 99081017 4077785 complement(1265730..1266737) 1 NC_008044.1 KEGG: sil:SPO2183 hypothetical protein, ev=1e-124, 62% identity; hypothetical protein 1266737 4077785 TM1040_1176 Ruegeria sp. TM1040 hypothetical protein YP_613171.1 1265730 R 292414 CDS YP_613172.1 99081018 4077786 complement(1266814..1269228) 1 NC_008044.1 PFAM: protein of unknown function DUF214: (7.3e-09); KEGG: sil:SPO2182 permease, , ev=0.0, 49% identity; hypothetical protein 1269228 4077786 TM1040_1177 Ruegeria sp. TM1040 hypothetical protein YP_613172.1 1266814 R 292414 CDS YP_613173.1 99081019 4077787 complement(1269225..1269887) 1 NC_008044.1 PFAM: ABC transporter related: (4.7e-58); SMART: ATPase: (4.5e-17); KEGG: sil:SPO2181 ABC transporter, ATP-binding protein, ev=2e-64, 61% identity; ABC transporter 1269887 4077787 TM1040_1178 Ruegeria sp. TM1040 ABC transporter YP_613173.1 1269225 R 292414 CDS YP_613174.1 99081020 4077788 1270013..1270456 1 NC_008044.1 PFAM: Ion transport 2: (2e-08); KEGG: sil:SPO2179 hypothetical protein, ev=2e-35, 51% identity; Ion transport 2 1270456 4077788 TM1040_1179 Ruegeria sp. TM1040 Ion transport 2 YP_613174.1 1270013 D 292414 CDS YP_613175.1 99081021 4077789 1270487..1271353 1 NC_008044.1 TIGRFAM: ribonuclease BN, : (1.1e-22); PFAM: ribonuclease BN: (1.6e-41); KEGG: sil:SPO1856 ribonuclease BN, , ev=1e-71, 54% identity; ribonuclease BN 1271353 4077789 TM1040_1180 Ruegeria sp. TM1040 ribonuclease BN YP_613175.1 1270487 D 292414 CDS YP_613176.1 99081022 4077790 1271442..1271687 1 NC_008044.1 hypothetical protein 1271687 4077790 TM1040_1181 Ruegeria sp. TM1040 hypothetical protein YP_613176.1 1271442 D 292414 CDS YP_613177.1 99081023 4077791 complement(1271718..1272434) 1 NC_008044.1 PFAM: ribosomal RNA methyltransferase RrmJ/FtsJ: (1.4e-61); KEGG: sil:SPO1858 ribosomal RNA large subunit methyltransferase J, ev=1e-115, 87% identity; ribosomal RNA methyltransferase RrmJ/FtsJ 1272434 4077791 TM1040_1182 Ruegeria sp. TM1040 ribosomal RNA methyltransferase RrmJ/FtsJ YP_613177.1 1271718 R 292414 CDS YP_613178.1 99081024 4077792 complement(1272519..1273631) 1 NC_008044.1 PFAM: Ppx/GppA phosphatase: (1.7e-28); KEGG: sil:SPO1859 phosphatase, Ppx/GppA family, ev=0.0, 89% identity; Ppx/GppA phosphatase 1273631 4077792 TM1040_1183 Ruegeria sp. TM1040 Ppx/GppA phosphatase YP_613178.1 1272519 R 292414 CDS YP_613179.1 99081025 4077793 1273898..1274194 1 NC_008044.1 KEGG: sil:SPO1861 hypothetical protein, ev=3e-43, 84% identity; hypothetical protein 1274194 4077793 TM1040_1184 Ruegeria sp. TM1040 hypothetical protein YP_613179.1 1273898 D 292414 CDS YP_613180.1 99081026 4077794 1274224..1275156 1 NC_008044.1 KEGG: sil:SPO1862 metFprotein, homolog, ev=1e-144, 83% identity; metF protein-like 1275156 4077794 TM1040_1185 Ruegeria sp. TM1040 metF protein-like YP_613180.1 1274224 D 292414 CDS YP_613181.1 99081027 4077795 1275160..1276218 1 NC_008044.1 catalyzes the transfer of the N5-methyl group from (6S)-methyl tetrahydrofolate to the cobalt center of a corrinoid iron-sulfur protein; methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase 1276218 4077795 TM1040_1186 Ruegeria sp. TM1040 methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase YP_613181.1 1275160 D 292414 CDS YP_613182.1 99081028 4077796 1276546..1277559 1 NC_008044.1 KEGG: atc:AGR_L_1930 sugar ABC transporter (sugar-binding protein), ev=1e-135, 70% identity; sugar ABC transporter (sugar-binding protein) 1277559 4077796 TM1040_1187 Ruegeria sp. TM1040 sugar ABC transporter (sugar-binding protein) YP_613182.1 1276546 D 292414 CDS YP_613183.1 99081029 4077797 1277641..1279176 1 NC_008044.1 PFAM: ABC transporter related: (2e-21); SMART: ATPase: (2.1e-09); KEGG: atc:AGR_L_1931 simple sugar transport system ATP-binding protein, ev=1e-179, 64% identity; ABC transporter 1279176 4077797 TM1040_1188 Ruegeria sp. TM1040 ABC transporter YP_613183.1 1277641 D 292414 CDS YP_613184.1 99081030 4077798 1279188..1280183 1 NC_008044.1 PFAM: inner-membrane translocator: (3.7e-55); KEGG: atc:AGR_L_1933 ribose ABC transporter (permease), ev=1e-132, 74% identity; inner-membrane translocator 1280183 4077798 TM1040_1189 Ruegeria sp. TM1040 inner-membrane translocator YP_613184.1 1279188 D 292414 CDS YP_613185.1 99081031 4077799 1280191..1281171 1 NC_008044.1 PFAM: sugar-binding region: (8.9e-68); KEGG: atc:AGR_L_1935 transcriptional regulator, ev=1e-101, 58% identity; DeoR family transcriptional regulator 1281171 4077799 TM1040_1190 Ruegeria sp. TM1040 DeoR family transcriptional regulator YP_613185.1 1280191 D 292414 CDS YP_613186.1 99081032 4077800 1281161..1282156 1 NC_008044.1 PFAM: aldo/keto reductase: (2.9e-52); KEGG: ret:RHE_PB00074 probable aldoketo reductase protein, ev=1e-133, 69% identity; aldo/keto reductase 1282156 4077800 TM1040_1191 Ruegeria sp. TM1040 aldo/keto reductase YP_613186.1 1281161 D 292414 CDS YP_613187.1 99081033 4077801 1282229..1283944 1 NC_008044.1 PFAM: FAD dependent oxidoreductase: (1.8e-47); KEGG: atc:AGR_L_1938 glycerol-3-phosphate dehydrogenase, ev=1e-166, 54% identity; FAD dependent oxidoreductase 1283944 4077801 TM1040_1192 Ruegeria sp. TM1040 FAD dependent oxidoreductase YP_613187.1 1282229 D 292414 CDS YP_613188.1 99081034 4076328 1283941..1284777 1 NC_008044.1 PFAM: deoxyribose-phosphate aldolase/phospho-2-dehydro-3-deoxyheptonate aldolase: (8.4e-69); KEGG: atc:AGR_L_1940 aldolase MTH579, ev=1e-131, 81% identity; deoxyribose-phosphate aldolase/phospho-2-dehydro-3-deoxyheptonate aldolase 1284777 4076328 TM1040_1193 Ruegeria sp. TM1040 deoxyribose-phosphate aldolase/phospho-2-dehydro-3-deoxyheptonate aldolase YP_613188.1 1283941 D 292414 CDS YP_613189.1 99081035 4076329 1284794..1286305 1 NC_008044.1 PFAM: carbohydrate kinase, FGGY: (9.5e-59); KEGG: atc:AGR_L_1942 L-xylulokinase, ev=1e-171, 58% identity; carbohydrate kinase 1286305 4076329 TM1040_1194 Ruegeria sp. TM1040 carbohydrate kinase YP_613189.1 1284794 D 292414 CDS YP_613190.1 99081036 4076330 1286318..1286605 1 NC_008044.1 PFAM: Antibiotic biosynthesis monooxygenase: (1.9e-17); KEGG: bld:BLi00471 YcnE, ev=1e-09, 41% identity; antibiotic biosynthesis monooxygenase 1286605 4076330 TM1040_1195 Ruegeria sp. TM1040 antibiotic biosynthesis monooxygenase YP_613190.1 1286318 D 292414 CDS YP_613191.1 99081037 4076331 1286849..1287859 1 NC_008044.1 PFAM: helix-turn-helix, AraC type: (1.3e-11); KEGG: sil:SPO1057 transcriptional regulator, AraC family, ev=1e-42, 32% identity; AraC family transcriptional regulator 1287859 4076331 TM1040_1196 Ruegeria sp. TM1040 AraC family transcriptional regulator YP_613191.1 1286849 D 292414 CDS YP_613192.1 99081038 4076332 1288124..1288369 1 NC_008044.1 hypothetical protein 1288369 4076332 TM1040_1197 Ruegeria sp. TM1040 hypothetical protein YP_613192.1 1288124 D 292414 CDS YP_613193.1 99081039 4076333 1288731..1289417 1 NC_008044.1 KEGG: reu:Reut_A3273 (acyl-carrier protein) phosphodiesterase, ev=5e-08, 32% identity; hypothetical protein 1289417 4076333 TM1040_1198 Ruegeria sp. TM1040 hypothetical protein YP_613193.1 1288731 D 292414 CDS YP_613194.1 99081040 4076334 1289858..1290730 1 NC_008044.1 KEGG: sil:SPO1992 hypothetical protein, ev=1e-76, 57% identity; hypothetical protein 1290730 4076334 TM1040_1199 Ruegeria sp. TM1040 hypothetical protein YP_613194.1 1289858 D 292414 CDS YP_613195.1 99081041 4076335 1290983..1291579 1 NC_008044.1 fusion of ribosomal protein L21 and COG3743; 50S ribosomal protein L21 1291579 4076335 TM1040_1200 Ruegeria sp. TM1040 50S ribosomal protein L21 YP_613195.1 1290983 D 292414 CDS YP_613196.1 99081042 4076336 1291592..1291861 1 NC_008044.1 involved in the peptidyltransferase reaction during translation; 50S ribosomal protein L27 1291861 rpmA 4076336 rpmA Ruegeria sp. TM1040 50S ribosomal protein L27 YP_613196.1 1291592 D 292414 CDS YP_613197.1 99081043 4076337 1292084..1292620 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (5.1e-06); KEGG: sil:SPO1987 acetyltransferase, GNAT family, ev=2e-73, 73% identity; N-acetyltransferase GCN5 1292620 4076337 TM1040_1202 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_613197.1 1292084 D 292414 CDS YP_613198.1 99081044 4076338 1292795..1293841 1 NC_008044.1 essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication; GTPase ObgE 1293841 obgE 4076338 obgE Ruegeria sp. TM1040 GTPase ObgE YP_613198.1 1292795 D 292414 CDS YP_613199.1 99081045 4076339 1293829..1294935 1 NC_008044.1 catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis; gamma-glutamyl kinase 1294935 4076339 TM1040_1204 Ruegeria sp. TM1040 gamma-glutamyl kinase YP_613199.1 1293829 D 292414 CDS YP_613200.1 99081046 4076340 1294988..1296292 1 NC_008044.1 Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway; gamma-glutamyl phosphate reductase 1296292 proA 4076340 proA Ruegeria sp. TM1040 gamma-glutamyl phosphate reductase YP_613200.1 1294988 D 292414 CDS YP_613201.1 99081047 4076341 complement(1296378..1296974) 1 NC_008044.1 KEGG: sil:SPO1983 hypothetical protein, ev=4e-54, 51% identity; hypothetical protein 1296974 4076341 TM1040_1206 Ruegeria sp. TM1040 hypothetical protein YP_613201.1 1296378 R 292414 CDS YP_613202.1 99081048 4076342 1297004..1297186 1 NC_008044.1 KEGG: sil:SPO1982 hypothetical protein, ev=8e-24, 83% identity; hypothetical protein 1297186 4076342 TM1040_1207 Ruegeria sp. TM1040 hypothetical protein YP_613202.1 1297004 D 292414 CDS YP_613203.1 99081049 4076343 1297294..1298055 1 NC_008044.1 KEGG: sil:SPO1980 hypothetical protein, ev=1e-100, 70% identity; ornithine-acyl-ACP N-acyltransferase 1298055 4076343 TM1040_1208 Ruegeria sp. TM1040 ornithine-acyl-ACP N-acyltransferase YP_613203.1 1297294 D 292414 CDS YP_613204.1 99081050 4076344 1298052..1298912 1 NC_008044.1 PFAM: phospholipid/glycerol acyltransferase: (3.2e-21); KEGG: sil:SPO1979 acyltransferase, , ev=1e-104, 68% identity; lyso-ornithine lipid acyltransferase 1298912 4076344 TM1040_1209 Ruegeria sp. TM1040 lyso-ornithine lipid acyltransferase YP_613204.1 1298052 D 292414 CDS YP_613205.1 99081051 4076345 1299082..1299852 1 NC_008044.1 one of the last subunits in the assembly of the 30S subunit; absence of S2 does not inhibit assembly but results in an inactive subunit; 30S ribosomal protein S2 1299852 rpsB 4076345 rpsB Ruegeria sp. TM1040 30S ribosomal protein S2 YP_613205.1 1299082 D 292414 CDS YP_613206.1 99081052 4076346 1299933..1300808 1 NC_008044.1 EF-Ts; functions during elongation stage of protein translation; forms a dimer; associates with EF-Tu-GDP complex and promotes exchange of GDP to GTP resulting in regeneration of the active form of EF-Tu; elongation factor Ts 1300808 tsf 4076346 tsf Ruegeria sp. TM1040 elongation factor Ts YP_613206.1 1299933 D 292414 CDS YP_613207.1 99081053 4075920 complement(1301262..1302017) 1 NC_008044.1 PFAM: regulatory protein, LuxR: (8.9e-09) Autoinducer-binding: (5.8e-07) Bacterio-opsin activator, HTH: (0.0031) Sigma-70, region 4 type 2: (6.3e-07); KEGG: sil:SPO1974 autoinducer-binding transcriptional regulator, LuxR family, ev=1e-91, 65% identity; LuxR family transcriptional regulator 1302017 4075920 TM1040_1212 Ruegeria sp. TM1040 LuxR family transcriptional regulator YP_613207.1 1301262 R 292414 CDS YP_613208.1 99081054 4075921 complement(1302014..1302514) 1 NC_008044.1 hypothetical protein 1302514 4075921 TM1040_1213 Ruegeria sp. TM1040 hypothetical protein YP_613208.1 1302014 R 292414 CDS YP_613209.1 99081055 4075922 1302602..1303312 1 NC_008044.1 PFAM: Enoyl-CoA hydratase/isomerase: (6.4e-08); KEGG: nfa:nfa21600 enoyl-CoA hydratase/isomerase family protein, ev=2e-11, 30% identity; enoyl-CoA hydratase/isomerase 1303312 4075922 TM1040_1214 Ruegeria sp. TM1040 enoyl-CoA hydratase/isomerase YP_613209.1 1302602 D 292414 CDS YP_613210.1 99081056 4075923 complement(1304000..1304461) 1 NC_008044.1 PFAM: response regulator receiver: (1.3e-13); KEGG: cps:CPS_3951 response regulator, ev=1e-25, 42% identity; response regulator receiver protein 1304461 4075923 TM1040_1215 Ruegeria sp. TM1040 response regulator receiver protein YP_613210.1 1304000 R 292414 CDS YP_613211.1 99081057 4075924 complement(1304451..1306760) 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (5.3e-26) histidine kinase, HAMP region: (8.7e-06) histidine kinase A-like: (4.9e-11) PAS fold-4: (4.5e-06) PAS fold: (3.9e-05); SMART: PAS: (2.4e-06); KEGG: rba:RB9418 signal-transducing histidine kinase, ev=1e-44, 37% identity; multi-sensor signal transduction histidine kinase 1306760 4075924 TM1040_1216 Ruegeria sp. TM1040 multi-sensor signal transduction histidine kinase YP_613211.1 1304451 R 292414 CDS YP_613212.1 99081058 4075925 complement(1307375..1307941) 1 NC_008044.1 TIGRFAM: Twin-arginine translocation pathway signal: (0.068); PFAM: protein of unknown function DUF882: (5.4e-48) Peptidase M15A: (8.3e-05); KEGG: sil:SPO1928 Tat (twin-arginine translocation) pathway signal sequence domain protein, ev=4e-86, 82% identity; twin-arginine translocation pathway signal 1307941 4075925 TM1040_1217 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_613212.1 1307375 R 292414 CDS YP_613213.1 99081059 4075926 1308297..1309919 1 NC_008044.1 PFAM: Peptidoglycan-binding domain 1: (1.7e-17); KEGG: sil:SPO1929 peptidoglycan binding protein, , ev=1e-180, 59% identity; peptidoglycan binding domain-containing protein 1309919 4075926 TM1040_1218 Ruegeria sp. TM1040 peptidoglycan binding domain-containing protein YP_613213.1 1308297 D 292414 CDS YP_613214.1 99081060 4075927 1309957..1311030 1 NC_008044.1 TIGRFAM: UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase: (3.9e-85); KEGG: sil:SPO1930 UDP-3-O-3-hydroxymyristoyl glucosamine N-acyltransferase, ev=1e-153, 74% identity; UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase 1311030 4075927 TM1040_1219 Ruegeria sp. TM1040 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase YP_613214.1 1309957 D 292414 CDS YP_613215.1 99081061 4075928 1311082..1311339 1 NC_008044.1 PFAM: phosphopantetheine-binding: (4.8e-09); KEGG: sil:SPO1931 acyl carrier protein, , ev=1e-33, 86% identity; phosphopantetheine-binding protein 1311339 4075928 TM1040_1220 Ruegeria sp. TM1040 phosphopantetheine-binding protein YP_613215.1 1311082 D 292414 CDS YP_613216.1 99081062 4075929 1311374..1312582 1 NC_008044.1 PFAM: beta-ketoacyl synthase: (1.2e-52); KEGG: sil:SPO1932 beta-ketoacyl synthase family protein, ev=0.0, 90% identity; 3-oxoacyl-ACP synthase 1312582 4075929 TM1040_1221 Ruegeria sp. TM1040 3-oxoacyl-ACP synthase YP_613216.1 1311374 D 292414 CDS YP_613217.1 99081063 4075930 complement(1312723..1313358) 1 NC_008044.1 PFAM: Invasion associated locus B: (1.3e-19); KEGG: sil:SPO1933 invasion associated family protein, ev=1e-67, 62% identity; invasion associated locus B 1313358 4075930 TM1040_1222 Ruegeria sp. TM1040 invasion associated locus B YP_613217.1 1312723 R 292414 CDS YP_613218.1 99081064 4075931 1313953..1315497 1 NC_008044.1 PFAM: protein of unknown function DUF853, NPT hydrolase : (1.2e-295); KEGG: sil:SPO1934 hypothetical protein, ev=0.0, 76% identity; hypothetical protein 1315497 4075931 TM1040_1223 Ruegeria sp. TM1040 hypothetical protein YP_613218.1 1313953 D 292414 CDS YP_613219.1 99081065 4075932 complement(1315559..1317007) 1 NC_008044.1 KEGG: sil:SPO2039 inosine-5'-monophosphate dehydrogenase, ev=0.0, 86% identity; TIGRFAM: inosine-5'-monophosphate dehydrogenase: (3e-254); PFAM: CBS: (1.7e-22) IMP dehydrogenase/GMP reductase: (1.1e-228); inosine-5'-monophosphate dehydrogenase 1317007 4075932 TM1040_1224 Ruegeria sp. TM1040 inosine-5'-monophosphate dehydrogenase YP_613219.1 1315559 R 292414 CDS YP_613220.1 99081066 4075933 1317194..1318342 1 NC_008044.1 PFAM: L-carnitine dehydratase/bile acid-inducible protein F: (6.6e-78); KEGG: sil:SPO2040 CaiB/BaiF family protein, ev=1e-176, 79% identity; L-carnitine dehydratase/bile acid-inducible protein F 1318342 4075933 TM1040_1225 Ruegeria sp. TM1040 L-carnitine dehydratase/bile acid-inducible protein F YP_613220.1 1317194 D 292414 CDS YP_613221.1 99081067 4075934 1318425..1320509 1 NC_008044.1 PFAM: ferredoxin: (0.0056); KEGG: sil:SPO2041 iron-sulfur cluster-binding protein, ev=0.0, 84% identity; ferredoxin 1320509 4075934 TM1040_1226 Ruegeria sp. TM1040 ferredoxin YP_613221.1 1318425 D 292414 CDS YP_613222.1 99081068 4075935 1320632..1321807 1 NC_008044.1 PFAM: Fmu (Sun): (8.2e-13); KEGG: sil:SPO2037 NOL1/NOP2/sun family protein, ev=1e-121, 58% identity; hypothetical protein 1321807 4075935 TM1040_1227 Ruegeria sp. TM1040 hypothetical protein YP_613222.1 1320632 D 292414 CDS YP_613223.1 99081069 4075936 1321904..1324213 1 NC_008044.1 TIGRFAM: PAS: (7.2e-06); PFAM: response regulator receiver: (5.7e-17) ATP-binding region, ATPase-like: (6e-36) histidine kinase A-like: (2.7e-11); KEGG: sil:SPO2036 sensory box sensor histidine kianse/response regulator, ev=0.0, 64% identity; multi-sensor hybrid histidine kinase 1324213 4075936 TM1040_1228 Ruegeria sp. TM1040 multi-sensor hybrid histidine kinase YP_613223.1 1321904 D 292414 CDS YP_613224.1 99081070 4075937 complement(1324244..1324903) 1 NC_008044.1 KEGG: sil:SPO2035 hypothetical protein, ev=1e-62, 58% identity; hypothetical protein 1324903 4075937 TM1040_1229 Ruegeria sp. TM1040 hypothetical protein YP_613224.1 1324244 R 292414 CDS YP_613225.1 99081071 4075938 1325036..1326109 1 NC_008044.1 catalyzes the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs; recombinase A 1326109 recA 4075938 recA Ruegeria sp. TM1040 recombinase A YP_613225.1 1325036 D 292414 CDS YP_613226.1 99081072 4075939 1326112..1326660 1 NC_008044.1 KEGG: rsp:RSP_3140 hypothetical protein, ev=5e-56, 59% identity; hypothetical protein 1326660 4075939 TM1040_1231 Ruegeria sp. TM1040 hypothetical protein YP_613226.1 1326112 D 292414 CDS YP_613227.1 99081073 4076347 1326722..1329430 1 NC_008044.1 Catalyzes a two-step reaction, first charging an alanyl molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; alanyl-tRNA synthetase 1329430 alaS 4076347 alaS Ruegeria sp. TM1040 alanyl-tRNA synthetase YP_613227.1 1326722 D 292414 CDS YP_613228.1 99081074 4076348 1329437..1329724 1 NC_008044.1 PFAM: protein of unknown function DUF1330: (8.8e-41); KEGG: sil:SPO2032 hypothetical protein, ev=2e-43, 91% identity; hypothetical protein 1329724 4076348 TM1040_1233 Ruegeria sp. TM1040 hypothetical protein YP_613228.1 1329437 D 292414 CDS YP_613229.1 99081075 4076349 1329844..1330620 1 NC_008044.1 PFAM: glutamine amidotransferase, class-II: (0.00099); KEGG: rsp:RSP_0449 glutamine amidotransferase, ev=2e-94, 66% identity; glutamine amidotransferase, class-II 1330620 4076349 TM1040_1234 Ruegeria sp. TM1040 glutamine amidotransferase, class-II YP_613229.1 1329844 D 292414 CDS YP_613230.1 99081076 4076350 complement(1330689..1332509) 1 NC_008044.1 TIGRFAM: Small GTP-binding protein domain: (1.5e-22) GTP-binding protein TypA: (0); PFAM: elongation factor G-like: (1.3e-23) protein synthesis factor, GTP-binding: (1.7e-72) elongation factor Tu, domain 2: (3e-08); KEGG: sil:SPO2031 GTP-binding protein TypA, ev=0.0, 90% identity; GTP-binding protein TypA 1332509 4076350 TM1040_1235 Ruegeria sp. TM1040 GTP-binding protein TypA YP_613230.1 1330689 R 292414 CDS YP_613231.1 99081077 4076351 complement(1332636..1332965) 1 NC_008044.1 PFAM: small multidrug resistance protein: (2.7e-36); KEGG: sil:SPO2030 multidrug resistance efflux protein, SMR family, ev=1e-40, 74% identity; small multidrug resistance protein 1332965 4076351 TM1040_1236 Ruegeria sp. TM1040 small multidrug resistance protein YP_613231.1 1332636 R 292414 CDS YP_613232.1 99081078 4076352 complement(1333106..1334272) 1 NC_008044.1 KEGG: sil:SPO2028 HD domain protein, ev=1e-123, 58% identity; HD domain-containing protein 1334272 4076352 TM1040_1237 Ruegeria sp. TM1040 HD domain-containing protein YP_613232.1 1333106 R 292414 CDS YP_613233.1 99081079 4076353 complement(1334269..1334517) 1 NC_008044.1 KEGG: sil:SPO2027 hypothetical protein, ev=9e-18, 62% identity; hypothetical protein 1334517 4076353 TM1040_1238 Ruegeria sp. TM1040 hypothetical protein YP_613233.1 1334269 R 292414 CDS YP_613234.1 99081080 4076354 complement(1334517..1335170) 1 NC_008044.1 KEGG: sil:SPO2026 hypothetical protein, ev=1e-120, 94% identity; hypothetical protein 1335170 4076354 TM1040_1239 Ruegeria sp. TM1040 hypothetical protein YP_613234.1 1334517 R 292414 CDS YP_613235.1 99081081 4076355 1335357..1335815 1 NC_008044.1 PFAM: protein of unknown function UPF0074: (1.8e-40); KEGG: sil:SPO2025 iron-sulfur cluster assembly transcription factor IscR, , ev=2e-71, 88% identity; BadM/Rrf2 family transcriptional regulator 1335815 4076355 TM1040_1240 Ruegeria sp. TM1040 BadM/Rrf2 family transcriptional regulator YP_613235.1 1335357 D 292414 CDS YP_613236.1 99081082 4076356 1335882..1336925 1 NC_008044.1 PFAM: aminotransferase, class V: (8.6e-29); KEGG: rsp:RSP_0442 aminotransferase, ev=1e-131, 67% identity; class V aminotransferase 1336925 4076356 TM1040_1241 Ruegeria sp. TM1040 class V aminotransferase YP_613236.1 1335882 D 292414 CDS YP_613237.1 99081083 4076357 1336941..1338461 1 NC_008044.1 with SufCD activates cysteine desulfurase SufS; cysteine desulfurase activator complex subunit SufB 1338461 4076357 TM1040_1242 Ruegeria sp. TM1040 cysteine desulfurase activator complex subunit SufB YP_613237.1 1336941 D 292414 CDS YP_613238.1 99081084 4076358 1338500..1338814 1 NC_008044.1 PFAM: protein of unknown function DUF74: (5.9e-61); KEGG: sil:SPO2021 hypothetical protein, ev=5e-43, 90% identity; hypothetical protein 1338814 4076358 TM1040_1243 Ruegeria sp. TM1040 hypothetical protein YP_613238.1 1338500 D 292414 CDS YP_613239.1 99081085 4076359 1338827..1339591 1 NC_008044.1 TIGRFAM: Methyltransferase FkbM: (1.9e-26); KEGG: jan:Jann_2362 methyltransferase FkbM, ev=6e-56, 49% identity; methyltransferase FkbM 1339591 4076359 TM1040_1244 Ruegeria sp. TM1040 methyltransferase FkbM YP_613239.1 1338827 D 292414 CDS YP_613240.1 99081086 4076360 1339654..1340409 1 NC_008044.1 KEGG: sil:SPO2018 FeS assembly ATPase SufC, ev=1e-127, 92% identity; TIGRFAM: FeS assembly ATPase SufC: (1.5e-163); PFAM: ABC transporter related: (9.6e-32); SMART: ATPase: (1.4e-06); FeS assembly ATPase SufC 1340409 4076360 TM1040_1245 Ruegeria sp. TM1040 FeS assembly ATPase SufC YP_613240.1 1339654 D 292414 CDS YP_613241.1 99081087 4076361 1340409..1341689 1 NC_008044.1 PFAM: SufBD: (6.7e-27); KEGG: sil:SPO2017 FeS assembly protein SufD, ev=0.0, 79% identity; SufBD protein 1341689 4076361 TM1040_1246 Ruegeria sp. TM1040 SufBD protein YP_613241.1 1340409 D 292414 CDS YP_613242.1 99081088 4076362 1341698..1342183 1 NC_008044.1 KEGG: sil:SPO2016 hypothetical protein, ev=4e-56, 66% identity; hypothetical protein 1342183 4076362 TM1040_1247 Ruegeria sp. TM1040 hypothetical protein YP_613242.1 1341698 D 292414 CDS YP_613243.1 99081089 4076363 1342183..1342761 1 NC_008044.1 KEGG: sil:SPO2015 hypothetical protein, ev=6e-19, 31% identity; hypothetical protein 1342761 4076363 TM1040_1248 Ruegeria sp. TM1040 hypothetical protein YP_613243.1 1342183 D 292414 CDS YP_613244.1 99081090 4076364 1342754..1343974 1 NC_008044.1 TIGRFAM: cysteine desulfurases, SufS subfamily: (6.6e-224); PFAM: aminotransferase, class V: (4.6e-167); KEGG: sil:SPO2014 cysteine desulfurase SufS, ev=0.0, 84% identity; cysteine desulfurase 1343974 4076364 TM1040_1249 Ruegeria sp. TM1040 cysteine desulfurase YP_613244.1 1342754 D 292414 CDS YP_613245.1 99081091 4076365 complement(1344152..1344583) 1 NC_008044.1 PFAM: UspA: (5.5e-19); KEGG: sil:SPO2185 universal stress protein family protein, ev=1e-26, 45% identity; hypothetical protein 1344583 4076365 TM1040_1250 Ruegeria sp. TM1040 hypothetical protein YP_613245.1 1344152 R 292414 CDS YP_613246.1 99081092 4077645 complement(1344583..1347180) 1 NC_008044.1 TIGRFAM: TRAP transporter, 4TM/12TM fusion protein: (5.1e-224); PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit: (1.7e-65); KEGG: dps:DP0744 hypothetical protein, ev=0.0, 53% identity; TRAP transporter, 4TM/12TM fusion protein 1347180 4077645 TM1040_1251 Ruegeria sp. TM1040 TRAP transporter, 4TM/12TM fusion protein YP_613246.1 1344583 R 292414 CDS YP_613247.1 99081093 4077646 complement(1347286..1348257) 1 NC_008044.1 TIGRFAM: TRAP transporter solute receptor, TAXI family: (7.5e-97); KEGG: sil:SPO2187 TRAP transporter solute receptor, TAXI family, ev=1e-110, 62% identity; TRAP transporter solute receptor TAXI family protein 1348257 4077646 TM1040_1252 Ruegeria sp. TM1040 TRAP transporter solute receptor TAXI family protein YP_613247.1 1347286 R 292414 CDS YP_613248.1 99081094 4077647 complement(1348352..1349239) 1 NC_008044.1 PFAM: sugar isomerase (SIS): (5.7e-06); KEGG: sil:SPO1591 SIS domain protein, ev=1e-36, 29% identity; RpiR family transcriptional regulator 1349239 4077647 TM1040_1253 Ruegeria sp. TM1040 RpiR family transcriptional regulator YP_613248.1 1348352 R 292414 CDS YP_613249.1 99081095 4077648 1349387..1351786 1 NC_008044.1 PFAM: FAD dependent oxidoreductase: (1.5e-93) glycine cleavage T protein (aminomethyl transferase): (7.6e-63); KEGG: sil:SPOA0311 FAD dependent oxidoreductase/aminomethyl transferase, ev=0.0, 48% identity; FAD dependent oxidoreductase 1351786 4077648 TM1040_1254 Ruegeria sp. TM1040 FAD dependent oxidoreductase YP_613249.1 1349387 D 292414 CDS YP_613250.1 99081096 4077649 complement(1352244..1353467) 1 NC_008044.1 PFAM: acyl-CoA dehydrogenase-like: (6e-24) Acyl-CoA dehydrogenase, type 2-like: (0.0012); KEGG: sil:SPO1955 glutaryl-CoA dehydrogenase, ev=0.0, 89% identity; acyl-CoA dehydrogenase 1353467 4077649 TM1040_1255 Ruegeria sp. TM1040 acyl-CoA dehydrogenase YP_613250.1 1352244 R 292414 CDS YP_613251.1 99081097 4077650 1353542..1354474 1 NC_008044.1 PFAM: regulatory protein, LysR: (5.5e-17) LysR, substrate-binding: (1.7e-38); KEGG: sil:SPO1954 transcriptional regulator, LysR family, ev=1e-111, 65% identity; LysR family transcriptional regulator 1354474 4077650 TM1040_1256 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_613251.1 1353542 D 292414 CDS YP_613252.1 99081098 4077651 complement(1354554..1355243) 1 NC_008044.1 TIGRFAM: Phosphate regulon transcriptional regulatory protein phoB: (1.6e-151); PFAM: response regulator receiver: (8.3e-39) transcriptional regulatory protein-like: (3.6e-26); KEGG: sil:SPO1953 phosphate regulon transcriptional regulatory protein PhoB, ev=1e-118, 90% identity; two component transcriptional regulator 1355243 4077651 TM1040_1257 Ruegeria sp. TM1040 two component transcriptional regulator YP_613252.1 1354554 R 292414 CDS YP_613253.1 99081099 4077652 complement(1355247..1355957) 1 NC_008044.1 PFAM: PhoU: (1.2e-29); KEGG: sil:SPO1952 phosphate transport system regulatory protein PhoU, ev=1e-93, 74% identity; phosphate uptake regulator PhoU 1355957 4077652 TM1040_1258 Ruegeria sp. TM1040 phosphate uptake regulator PhoU YP_613253.1 1355247 R 292414 CDS YP_613254.1 99081100 4077653 complement(1355974..1356771) 1 NC_008044.1 ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation; phosphate transporter ATP-binding protein 1356771 4077653 TM1040_1259 Ruegeria sp. TM1040 phosphate transporter ATP-binding protein YP_613254.1 1355974 R 292414 CDS YP_613255.1 99081101 4077654 complement(1356784..1358151) 1 NC_008044.1 TIGRFAM: Phosphate transport system permease protein 2: (9.5e-66); PFAM: binding-protein-dependent transport systems inner membrane component: (7.9e-16); KEGG: sil:SPO1950 phosphate ABC transporter, permease protein, ev=0.0, 80% identity; phosphate ABC transporter permease 1358151 4077654 TM1040_1260 Ruegeria sp. TM1040 phosphate ABC transporter permease YP_613255.1 1356784 R 292414 CDS YP_613256.1 99081102 4077655 complement(1358151..1359629) 1 NC_008044.1 TIGRFAM: Phosphate ABC transporter, permease protein PstC: (1.1e-103); PFAM: binding-protein-dependent transport systems inner membrane component: (1.2e-17); KEGG: sil:SPO1949 phosphate ABC transporter, permease protein, ev=0.0, 79% identity; phosphate ABC transporter permease 1359629 4077655 TM1040_1261 Ruegeria sp. TM1040 phosphate ABC transporter permease YP_613256.1 1358151 R 292414 CDS YP_613257.1 99081103 4077656 complement(1359739..1360779) 1 NC_008044.1 KEGG: sil:SPO1948 phosphate ABC transporter, periplasmic phosphate-binding protein, ev=1e-179, 90% identity; phosphate ABC transporter substrate-binding protein 1360779 4077656 TM1040_1262 Ruegeria sp. TM1040 phosphate ABC transporter substrate-binding protein YP_613257.1 1359739 R 292414 CDS YP_613258.1 99081104 4077657 complement(1361081..1362121) 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (9.3e-41) histidine kinase A-like: (2e-22); KEGG: sil:SPO1947 phosphate regulon sensor histidine kinase, , ev=1e-129, 68% identity; histidine kinase 1362121 4077657 TM1040_1263 Ruegeria sp. TM1040 histidine kinase YP_613258.1 1361081 R 292414 CDS YP_613259.1 99081105 4077658 complement(1362175..1363356) 1 NC_008044.1 PFAM: Cys/Met metabolism pyridoxal-phosphate-dependent enzymes: (4e-99) aromatic amino acid beta-eliminating lyase/threonine aldolase: (0.0045); KEGG: rsp:RSP_2917 cystathionine gamma-synthase beta-lyase, ev=1e-154, 69% identity; cystathionine gamma-synthase 1363356 4077658 TM1040_1264 Ruegeria sp. TM1040 cystathionine gamma-synthase YP_613259.1 1362175 R 292414 CDS YP_613260.1 99081106 4077659 complement(1363359..1363880) 1 NC_008044.1 PFAM: transferase hexapeptide repeat: (0.044); KEGG: sil:SPO1946 bacterial transferase family protein, ev=5e-82, 84% identity; hexapaptide repeat-containing transferase 1363880 4077659 TM1040_1265 Ruegeria sp. TM1040 hexapaptide repeat-containing transferase YP_613260.1 1363359 R 292414 CDS YP_613261.1 99081107 4077660 complement(1363877..1364530) 1 NC_008044.1 Essential for recycling GMP and indirectly, cGMP; guanylate kinase 1364530 gmk 4077660 gmk Ruegeria sp. TM1040 guanylate kinase YP_613261.1 1363877 R 292414 CDS YP_613262.1 99081108 4077661 complement(1364546..1365442) 1 NC_008044.1 TIGRFAM: conserved hypothetical protein: (9.1e-72); PFAM: YicC-like-like: (1.5e-31) Domain of unknown function DUF1732: (3.4e-55); KEGG: sil:SPO1944 YicC family protein, ev=9e-94, 61% identity; hypothetical protein 1365442 4077661 TM1040_1267 Ruegeria sp. TM1040 hypothetical protein YP_613262.1 1364546 R 292414 CDS YP_613263.1 99081109 4077662 1365684..1366631 1 NC_008044.1 KEGG: sil:SPO1943 hypothetical protein, ev=1e-55, 48% identity; hypothetical protein 1366631 4077662 TM1040_1268 Ruegeria sp. TM1040 hypothetical protein YP_613263.1 1365684 D 292414 CDS YP_613264.1 99081110 4077663 complement(1366861..1368231) 1 NC_008044.1 KEGG: sil:SPO1942 3-deoxy-7-phosphoheptulonate synthase, ev=0.0, 84% identity; TIGRFAM: phospho-2-dehydro-3-deoxyheptonate aldolase: (8e-294); PFAM: DAHP synthetase, class II: (8.2e-257); 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase 1368231 4077663 TM1040_1269 Ruegeria sp. TM1040 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase YP_613264.1 1366861 R 292414 CDS YP_613265.1 99081111 4077664 1368432..1369436 1 NC_008044.1 PFAM: helix-turn-helix, AraC type: (1.1e-06) ThiJ/PfpI: (1.4e-09); KEGG: sil:SPO1941 transcriptional regulator, AraC family, ev=1e-149, 81% identity; transcriptional regulator 1369436 4077664 TM1040_1270 Ruegeria sp. TM1040 transcriptional regulator YP_613265.1 1368432 D 292414 CDS YP_613266.1 99081112 4077431 complement(1369443..1370549) 1 NC_008044.1 PFAM: glucose sorbosone dehydrogenase: (4e-53); KEGG: sil:SPO1940 hypothetical protein, ev=1e-128, 61% identity; glucose sorbosone dehydrogenase 1370549 4077431 TM1040_1271 Ruegeria sp. TM1040 glucose sorbosone dehydrogenase YP_613266.1 1369443 R 292414 CDS YP_613267.1 99081113 4077432 1370689..1371888 1 NC_008044.1 PFAM: Extracellular ligand-binding receptor: (1.5e-22); KEGG: jan:Jann_2165 extracellular ligand-binding receptor, ev=1e-142, 63% identity; extracellular ligand-binding receptor 1371888 4077432 TM1040_1272 Ruegeria sp. TM1040 extracellular ligand-binding receptor YP_613267.1 1370689 D 292414 CDS YP_613268.1 99081114 4077433 1371995..1372786 1 NC_008044.1 PFAM: ABC transporter related: (3.9e-47); SMART: ATPase: (6.3e-10); KEGG: sil:SPO1938 branched-chain amino acid ABC transporter, ATP-binding protein, ev=1e-131, 88% identity; ABC transporter 1372786 4077433 TM1040_1273 Ruegeria sp. TM1040 ABC transporter YP_613268.1 1371995 D 292414 CDS YP_613269.1 99081115 4077434 1372783..1373496 1 NC_008044.1 PFAM: ABC transporter related: (8.2e-47); SMART: ATPase: (8.1e-12); KEGG: sil:SPO1937 branched-chain amino acid ABC transporter, ATP-binding protein, ev=1e-117, 90% identity; ABC transporter 1373496 4077434 TM1040_1274 Ruegeria sp. TM1040 ABC transporter YP_613269.1 1372783 D 292414 CDS YP_613270.1 99081116 4077435 1373500..1374510 1 NC_008044.1 PFAM: inner-membrane translocator: (2.9e-34); KEGG: sil:SPO1936 branched-chain amino acid ABC transporter, permease protein, ev=1e-155, 80% identity; inner-membrane translocator 1374510 4077435 TM1040_1275 Ruegeria sp. TM1040 inner-membrane translocator YP_613270.1 1373500 D 292414 CDS YP_613271.1 99081117 4077436 1374507..1375832 1 NC_008044.1 PFAM: inner-membrane translocator: (3.6e-08); KEGG: sil:SPO1935 branched-chain amino acid ABC transporter, permease protein, ev=0.0, 72% identity; inner-membrane translocator 1375832 4077436 TM1040_1276 Ruegeria sp. TM1040 inner-membrane translocator YP_613271.1 1374507 D 292414 CDS YP_613272.1 99081118 4077437 complement(1375914..1376249) 1 NC_008044.1 KEGG: rpb:RPB_3781 hypothetical protein, ev=5e-10, 33% identity; hypothetical protein 1376249 4077437 TM1040_1277 Ruegeria sp. TM1040 hypothetical protein YP_613272.1 1375914 R 292414 CDS YP_613273.1 99081119 4077438 complement(1376648..1377646) 1 NC_008044.1 PFAM: phage late control D: (6.8e-98); KEGG: xfa:XF2479 hypothetical protein, ev=5e-64, 38% identity; phage late control D 1377646 4077438 TM1040_1278 Ruegeria sp. TM1040 phage late control D YP_613273.1 1376648 R 292414 CDS YP_613274.1 99081120 4077439 complement(1377646..1377864) 1 NC_008044.1 PFAM: phage tail X: (3.5e-15); KEGG: sbo:SBO_0763 probable phage tail protein, ev=1e-08, 45% identity; phage tail X 1377864 4077439 TM1040_1279 Ruegeria sp. TM1040 phage tail X YP_613274.1 1377646 R 292414 CDS YP_613275.1 99081121 4077440 complement(1377836..1378246) 1 NC_008044.1 PFAM: phage P2 GpU: (6.3e-49); KEGG: syf:Synpcc7942_0751 hypothetical protein, ev=2e-28, 51% identity; phage P2 GpU 1378246 4077440 TM1040_1280 Ruegeria sp. TM1040 phage P2 GpU YP_613275.1 1377836 R 292414 CDS YP_613276.1 99081122 4077441 complement(1378246..1380720) 1 NC_008044.1 KEGG: nar:Saro_2736 hypothetical protein, ev=9e-28, 38% identity; hypothetical protein 1380720 4077441 TM1040_1281 Ruegeria sp. TM1040 hypothetical protein YP_613276.1 1378246 R 292414 CDS YP_613277.1 99081123 4077442 complement(1380844..1381143) 1 NC_008044.1 KEGG: xft:PD1092 hypothetical protein, ev=1e-07, 37% identity; hypothetical protein 1381143 4077442 TM1040_1282 Ruegeria sp. TM1040 hypothetical protein YP_613277.1 1380844 R 292414 CDS YP_613278.1 99081124 4077443 complement(1381153..1381659) 1 NC_008044.1 PFAM: phage major tail tube protein: (6.2e-47); KEGG: xfa:XF2484 hypothetical protein, ev=3e-36, 45% identity; phage major tail tube protein 1381659 4077443 TM1040_1283 Ruegeria sp. TM1040 phage major tail tube protein YP_613278.1 1381153 R 292414 CDS YP_613279.1 99081125 4077444 complement(1381659..1382876) 1 NC_008044.1 PFAM: phage tail sheath protein: (2.7e-129); KEGG: xft:PD1094 phage-related contractile tail sheath protein, ev=1e-132, 59% identity; phage tail sheath protein 1382876 4077444 TM1040_1284 Ruegeria sp. TM1040 phage tail sheath protein YP_613279.1 1381659 R 292414 CDS YP_613280.1 99081126 4077445 complement(1382990..1383349) 1 NC_008044.1 hypothetical protein 1383349 4077445 TM1040_1285 Ruegeria sp. TM1040 hypothetical protein YP_613280.1 1382990 R 292414 CDS YP_613281.1 99081127 4077446 complement(1383350..1383850) 1 NC_008044.1 hypothetical protein 1383850 4077446 TM1040_1286 Ruegeria sp. TM1040 hypothetical protein YP_613281.1 1383350 R 292414 CDS YP_613282.1 99081128 4077447 complement(1383852..1384859) 1 NC_008044.1 KEGG: rba:RB7745 serine protease homologue- secreted serine protease, ev=1e-29, 36% identity; secreted serine protease 1384859 4077447 TM1040_1287 Ruegeria sp. TM1040 secreted serine protease YP_613282.1 1383852 R 292414 CDS YP_613283.1 99081129 4077448 complement(1384859..1385146) 1 NC_008044.1 hypothetical protein 1385146 4077448 TM1040_1288 Ruegeria sp. TM1040 hypothetical protein YP_613283.1 1384859 R 292414 CDS YP_613284.1 99081130 4077449 complement(1385181..1385909) 1 NC_008044.1 KEGG: ecc:c0968 probable variable tail fibre protein, ev=8e-31, 37% identity; variable tail fiber protein 1385909 4077449 TM1040_1289 Ruegeria sp. TM1040 variable tail fiber protein YP_613284.1 1385181 R 292414 CDS YP_613285.1 99081131 4078489 complement(1385920..1386465) 1 NC_008044.1 TIGRFAM: Phage tail protein I: (4.5e-37); KEGG: pfl:PFL_2006 tail protein I, ev=3e-31, 43% identity; Phage tail protein I 1386465 4078489 TM1040_1290 Ruegeria sp. TM1040 Phage tail protein I YP_613285.1 1385920 R 292414 CDS YP_613286.1 99081132 4078490 complement(1386446..1387345) 1 NC_008044.1 PFAM: Baseplate J-like protein: (2.3e-74); KEGG: pae:PA0618 probable bacteriophage protein, ev=9e-73, 48% identity; baseplate J-like protein 1387345 4078490 TM1040_1291 Ruegeria sp. TM1040 baseplate J-like protein YP_613286.1 1386446 R 292414 CDS YP_613287.1 99081133 4078491 complement(1387345..1387683) 1 NC_008044.1 PFAM: GPW/gp25: (1.3e-45); KEGG: syf:Synpcc7942_0739 hypothetical protein, ev=2e-25, 51% identity; hypothetical protein 1387683 4078491 TM1040_1292 Ruegeria sp. TM1040 hypothetical protein YP_613287.1 1387345 R 292414 CDS YP_613288.1 99081134 4078492 complement(1387732..1388022) 1 NC_008044.1 PFAM: PAAR: (0.003); KEGG: eca:ECA3426 phospholipase, ev=2e-19, 47% identity; hypothetical protein 1388022 4078492 TM1040_1293 Ruegeria sp. TM1040 hypothetical protein YP_613288.1 1387732 R 292414 CDS YP_613289.1 99081135 4078493 complement(1388022..1388399) 1 NC_008044.1 PFAM: phage baseplate assembly protein V: (1.9e-13); KEGG: eca:ECA2612 baseplate assembly protein V, ev=5e-13, 41% identity; phage baseplate assembly protein V 1388399 4078493 TM1040_1294 Ruegeria sp. TM1040 phage baseplate assembly protein V YP_613289.1 1388022 R 292414 CDS YP_613290.1 99081136 4078494 complement(1388396..1388932) 1 NC_008044.1 KEGG: xfa:XF2493 hypothetical protein, ev=1e-28, 39% identity; hypothetical protein 1388932 4078494 TM1040_1295 Ruegeria sp. TM1040 hypothetical protein YP_613290.1 1388396 R 292414 CDS YP_613291.1 99081137 4078495 complement(1388932..1389480) 1 NC_008044.1 KEGG: wol:WD0644 prophage LambdaW5, minor tail protein Z, , ev=3e-12, 32% identity; prophage LambdaW5, minor tail protein Z 1389480 4078495 TM1040_1296 Ruegeria sp. TM1040 prophage LambdaW5, minor tail protein Z YP_613291.1 1388932 R 292414 CDS YP_613292.1 99081138 4078496 complement(1389485..1389796) 1 NC_008044.1 KEGG: xft:PD1104 hypothetical protein, ev=3e-17, 44% identity; hypothetical protein 1389796 4078496 TM1040_1297 Ruegeria sp. TM1040 hypothetical protein YP_613292.1 1389485 R 292414 CDS YP_613293.1 99081139 4078497 complement(1389796..1390053) 1 NC_008044.1 hypothetical protein 1390053 4078497 TM1040_1298 Ruegeria sp. TM1040 hypothetical protein YP_613293.1 1389796 R 292414 CDS YP_613294.1 99081140 4078498 complement(1390120..1392111) 1 NC_008044.1 PFAM: peptidase U35, phage prohead HK97: (6.5e-14) phage major capsid protein, HK97: (0.0041); KEGG: xfa:XF2497 hypothetical protein, ev=1e-128, 42% identity; peptidase U35, phage prohead HK97 1392111 4078498 TM1040_1299 Ruegeria sp. TM1040 peptidase U35, phage prohead HK97 YP_613294.1 1390120 R 292414 CDS YP_613295.1 99081141 4078499 complement(1392128..1393741) 1 NC_008044.1 PFAM: phage portal protein, lambda: (1.8e-62); KEGG: xft:PD1107 phage-related portal protein, ev=7e-99, 38% identity; phage portal protein, lambda 1393741 4078499 TM1040_1300 Ruegeria sp. TM1040 phage portal protein, lambda YP_613295.1 1392128 R 292414 CDS YP_613296.1 99081142 4078500 complement(1393738..1394232) 1 NC_008044.1 KEGG: xfa:XF2499 hypothetical protein, ev=3e-27, 40% identity; hypothetical protein 1394232 4078500 TM1040_1301 Ruegeria sp. TM1040 hypothetical protein YP_613296.1 1393738 R 292414 CDS YP_613297.1 99081143 4078501 complement(1394279..1396231) 1 NC_008044.1 PFAM: phage terminase GpA: (2.5e-216); KEGG: xft:PD1109 phage-related terminase large subunit, ev=0.0, 56% identity; phage terminase GpA 1396231 4078501 TM1040_1302 Ruegeria sp. TM1040 phage terminase GpA YP_613297.1 1394279 R 292414 CDS YP_613298.1 99081144 4078502 complement(1396228..1396782) 1 NC_008044.1 PFAM: phage DNA packaging Nu1: (2.7e-27); KEGG: xfa:XF2501 hypothetical protein, ev=6e-42, 49% identity; phage DNA packaging Nu1 1396782 4078502 TM1040_1303 Ruegeria sp. TM1040 phage DNA packaging Nu1 YP_613298.1 1396228 R 292414 CDS YP_613299.1 99081145 4078503 complement(1396955..1397338) 1 NC_008044.1 hypothetical protein 1397338 4078503 TM1040_1304 Ruegeria sp. TM1040 hypothetical protein YP_613299.1 1396955 R 292414 CDS YP_613300.1 99081146 4078504 complement(1397338..1397748) 1 NC_008044.1 PFAM: glycoside hydrolase, family 24: (3.9e-18); KEGG: xfa:XF0513 phage-related endolysin, ev=2e-27, 46% identity; glycoside hydrolase 1397748 4078504 TM1040_1305 Ruegeria sp. TM1040 glycoside hydrolase YP_613300.1 1397338 R 292414 CDS YP_613301.1 99081147 4078505 complement(1398109..1398345) 1 NC_008044.1 hypothetical protein 1398345 4078505 TM1040_1306 Ruegeria sp. TM1040 hypothetical protein YP_613301.1 1398109 R 292414 CDS YP_613302.1 99081148 4078506 1398593..1399195 1 NC_008044.1 hypothetical protein 1399195 4078506 TM1040_1307 Ruegeria sp. TM1040 hypothetical protein YP_613302.1 1398593 D 292414 CDS YP_613303.1 99081149 4078507 1399240..1399593 1 NC_008044.1 KEGG: psb:Psyr_0103 hypothetical protein, ev=5e-10, 34% identity; hypothetical protein 1399593 4078507 TM1040_1308 Ruegeria sp. TM1040 hypothetical protein YP_613303.1 1399240 D 292414 CDS YP_613304.1 99081150 4078508 complement(1399675..1400223) 1 NC_008044.1 hypothetical protein 1400223 4078508 TM1040_1309 Ruegeria sp. TM1040 hypothetical protein YP_613304.1 1399675 R 292414 CDS YP_613305.1 99081151 4078353 complement(1400406..1400966) 1 NC_008044.1 KEGG: xft:PD1114 hypothetical protein, ev=5e-07, 39% identity; hypothetical protein 1400966 4078353 TM1040_1310 Ruegeria sp. TM1040 hypothetical protein YP_613305.1 1400406 R 292414 CDS YP_613306.1 99081152 4078354 complement(1400970..1401371) 1 NC_008044.1 KEGG: bte:BTH_II1034 GP72, ev=5e-08, 42% identity; hypothetical protein 1401371 4078354 TM1040_1311 Ruegeria sp. TM1040 hypothetical protein YP_613306.1 1400970 R 292414 CDS YP_613307.1 99081153 4078355 complement(1401380..1401808) 1 NC_008044.1 hypothetical protein 1401808 4078355 TM1040_1312 Ruegeria sp. TM1040 hypothetical protein YP_613307.1 1401380 R 292414 CDS YP_613308.1 99081154 4078356 complement(1401814..1402140) 1 NC_008044.1 KEGG: jan:Jann_2635 hypothetical protein, ev=1e-28, 72% identity; hypothetical protein 1402140 4078356 TM1040_1313 Ruegeria sp. TM1040 hypothetical protein YP_613308.1 1401814 R 292414 CDS YP_613309.1 99081155 4078357 complement(1402391..1402690) 1 NC_008044.1 hypothetical protein 1402690 4078357 TM1040_1314 Ruegeria sp. TM1040 hypothetical protein YP_613309.1 1402391 R 292414 CDS YP_613310.1 99081156 4078358 complement(1402687..1403685) 1 NC_008044.1 hypothetical protein 1403685 4078358 TM1040_1315 Ruegeria sp. TM1040 hypothetical protein YP_613310.1 1402687 R 292414 CDS YP_613311.1 99081157 4078359 complement(1403888..1404421) 1 NC_008044.1 hypothetical protein 1404421 4078359 TM1040_1316 Ruegeria sp. TM1040 hypothetical protein YP_613311.1 1403888 R 292414 CDS YP_613312.1 99081158 4078360 complement(1404414..1404701) 1 NC_008044.1 hypothetical protein 1404701 4078360 TM1040_1317 Ruegeria sp. TM1040 hypothetical protein YP_613312.1 1404414 R 292414 CDS YP_613313.1 99081159 4078361 1404882..1405148 1 NC_008044.1 hypothetical protein 1405148 4078361 TM1040_1318 Ruegeria sp. TM1040 hypothetical protein YP_613313.1 1404882 D 292414 CDS YP_613314.1 99081160 4078362 complement(1405184..1405507) 1 NC_008044.1 hypothetical protein 1405507 4078362 TM1040_1319 Ruegeria sp. TM1040 hypothetical protein YP_613314.1 1405184 R 292414 CDS YP_613315.1 99081161 4078363 1405803..1406438 1 NC_008044.1 PFAM: peptidase S24, S26A and S26B: (0.018); KEGG: rsp:RSP_3771 hypothetical protein, ev=1e-35, 40% identity; phage repressor 1406438 4078363 TM1040_1320 Ruegeria sp. TM1040 phage repressor YP_613315.1 1405803 D 292414 CDS YP_613316.1 99081162 4078364 complement(1406799..1407716) 1 NC_008044.1 KEGG: lma:LmjF34.0690 hypothetical protein, conserved, ev=4e-08, 33% identity; hypothetical protein 1407716 4078364 TM1040_1321 Ruegeria sp. TM1040 hypothetical protein YP_613316.1 1406799 R 292414 CDS YP_613317.1 99081163 4078365 complement(1407723..1408715) 1 NC_008044.1 PFAM: Ankyrin: (9.4e-05); KEGG: bta:528403 similar to ankyrin repeat and FYVE domain containing 1 isoform 1, ev=4e-13, 27% identity; ankyrin 1408715 4078365 TM1040_1322 Ruegeria sp. TM1040 ankyrin YP_613317.1 1407723 R 292414 CDS YP_613318.1 99081164 4078366 complement(1409154..1409492) 1 NC_008044.1 hypothetical protein 1409492 4078366 TM1040_1323 Ruegeria sp. TM1040 hypothetical protein YP_613318.1 1409154 R 292414 CDS YP_613319.1 99081165 4078367 complement(1409890..1412040) 1 NC_008044.1 KEGG: psp:PSPPH_A0091 hypothetical protein, ev=1e-102, 45% identity; hypothetical protein 1412040 4078367 TM1040_1324 Ruegeria sp. TM1040 hypothetical protein YP_613319.1 1409890 R 292414 CDS YP_613320.1 99081166 4078368 1412750..1413019 1 NC_008044.1 hypothetical protein 1413019 4078368 TM1040_1325 Ruegeria sp. TM1040 hypothetical protein YP_613320.1 1412750 D 292414 CDS YP_613321.1 99081167 4078369 1413107..1413550 1 NC_008044.1 hypothetical protein 1413550 4078369 TM1040_1326 Ruegeria sp. TM1040 hypothetical protein YP_613321.1 1413107 D 292414 CDS YP_613322.1 99081168 4078370 1413693..1414379 1 NC_008044.1 KEGG: rsp:RSP_3624 hypothetical protein, ev=5e-64, 51% identity; hypothetical protein 1414379 4078370 TM1040_1327 Ruegeria sp. TM1040 hypothetical protein YP_613322.1 1413693 D 292414 CDS YP_613323.1 99081169 4078371 1414830..1415831 1 NC_008044.1 PFAM: phage integrase: (3e-06); KEGG: mag:amb2709 integrase, ev=5e-35, 33% identity; phage integrase 1415831 4078371 TM1040_1328 Ruegeria sp. TM1040 phage integrase YP_613323.1 1414830 D 292414 CDS YP_613324.1 99081170 4075900 1416383..1416856 1 NC_008044.1 PFAM: thioesterase superfamily: (0.00047); KEGG: jan:Jann_1972 thioesterase superfamily, ev=2e-24, 38% identity; thioesterase superfamily protein 1416856 4075900 TM1040_1329 Ruegeria sp. TM1040 thioesterase superfamily protein YP_613324.1 1416383 D 292414 CDS YP_613325.1 99081171 4075901 complement(1416887..1417558) 1 NC_008044.1 TIGRFAM: 6-phosphogluconolactonase: (7.2e-34); KEGG: sil:SPO2047 6-phosphogluconolactonase, ev=7e-68, 59% identity; 6-phosphogluconolactonase 1417558 4075901 TM1040_1330 Ruegeria sp. TM1040 6-phosphogluconolactonase YP_613325.1 1416887 R 292414 CDS YP_613326.1 99081172 4075902 complement(1417659..1417928) 1 NC_008044.1 PFAM: Usg-like: (5.9e-50); KEGG: sil:SPO2050 Usg, , ev=2e-37, 78% identity; Usg-like protein 1417928 4075902 TM1040_1331 Ruegeria sp. TM1040 Usg-like protein YP_613326.1 1417659 R 292414 CDS YP_613327.1 99081173 4075903 1418119..1420857 1 NC_008044.1 negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit A 1420857 4075903 TM1040_1332 Ruegeria sp. TM1040 DNA gyrase subunit A YP_613327.1 1418119 D 292414 CDS YP_613328.1 99081174 4075904 1420988..1421338 1 NC_008044.1 KEGG: sil:SPO2052 hypothetical protein, ev=2e-49, 77% identity; hypothetical protein 1421338 4075904 TM1040_1333 Ruegeria sp. TM1040 hypothetical protein YP_613328.1 1420988 D 292414 CDS YP_613329.1 99081175 4075905 complement(1421393..1422862) 1 NC_008044.1 PFAM: peptidase M32, carboxypeptidase Taq metallopeptidase: (2.1e-114); KEGG: sil:SPO2053 thermostable carboxypeptidase, ev=0.0, 71% identity; carboxypeptidase 1422862 4075905 TM1040_1334 Ruegeria sp. TM1040 carboxypeptidase YP_613329.1 1421393 R 292414 CDS YP_613330.1 99081176 4075906 complement(1422867..1424012) 1 NC_008044.1 PFAM: cytochrome oxidase assembly: (4.2e-46); KEGG: sil:SPO2054 cytochrome c oxidase assembly protein, ev=1e-167, 78% identity; cytochrome oxidase assembly 1424012 4075906 TM1040_1335 Ruegeria sp. TM1040 cytochrome oxidase assembly YP_613330.1 1422867 R 292414 CDS YP_613331.1 99081177 4075907 complement(1424076..1424825) 1 NC_008044.1 TIGRFAM: RNA methyltransferase TrmH, group 1: (1.4e-42); PFAM: tRNA/rRNA methyltransferase (SpoU): (8.9e-28); KEGG: sil:SPO2055 RNA methyltransferase, TrmH family, group 1, ev=1e-107, 77% identity; RNA methyl transferase TrmH 1424825 4075907 TM1040_1336 Ruegeria sp. TM1040 RNA methyl transferase TrmH YP_613331.1 1424076 R 292414 CDS YP_613332.1 99081178 4075908 1424982..1425614 1 NC_008044.1 PFAM: thiamine monophosphate synthase: (1e-13); KEGG: sil:SPO2056 thiamine-phosphate pyrophosphorylase, , ev=3e-82, 70% identity; thiamine monophosphate synthase 1425614 4075908 TM1040_1337 Ruegeria sp. TM1040 thiamine monophosphate synthase YP_613332.1 1424982 D 292414 CDS YP_613333.1 99081179 4075909 1425754..1426662 1 NC_008044.1 PFAM: PfkB: (3.5e-09); KEGG: sil:SPO2060 kinase, PfkB family, ev=1e-125, 77% identity; PfkB protein 1426662 4075909 TM1040_1338 Ruegeria sp. TM1040 PfkB protein YP_613333.1 1425754 D 292414 CDS YP_613334.1 99081180 4075910 1426659..1427567 1 NC_008044.1 PFAM: Indigoidine synthase A like protein: (6.7e-172); KEGG: sil:SPO2061 indigoidine synthase A family protein, ev=1e-127, 79% identity; indigoidine synthase A like protein 1427567 4075910 TM1040_1339 Ruegeria sp. TM1040 indigoidine synthase A like protein YP_613334.1 1426659 D 292414 CDS YP_613335.1 99081181 4075911 1427655..1428362 1 NC_008044.1 PFAM: protein of unknown function DUF502: (1.1e-55); KEGG: sil:SPO2062 hypothetical protein, ev=1e-100, 80% identity; hypothetical protein 1428362 4075911 TM1040_1340 Ruegeria sp. TM1040 hypothetical protein YP_613335.1 1427655 D 292414 CDS YP_613336.1 99081182 4075912 complement(1428363..1429391) 1 NC_008044.1 PFAM: Patatin: (3.1e-08); KEGG: sil:SPO2064 phospholipase, patatin-like family, ev=1e-136, 68% identity; patatin 1429391 4075912 TM1040_1341 Ruegeria sp. TM1040 patatin YP_613336.1 1428363 R 292414 CDS YP_613337.1 99081183 4075913 complement(1429486..1430259) 1 NC_008044.1 TIGRFAM: 3-hydroxybutyrate dehydrogenase: (2.1e-160); PFAM: short-chain dehydrogenase/reductase SDR: (3.3e-33); KEGG: sil:SPO2065 D-beta-hydroxybutyrate dehydrogenase, ev=1e-125, 84% identity; 3-hydroxybutyrate dehydrogenase 1430259 4075913 TM1040_1342 Ruegeria sp. TM1040 3-hydroxybutyrate dehydrogenase YP_613337.1 1429486 R 292414 CDS YP_613338.1 99081184 4075914 1430594..1432423 1 NC_008044.1 PFAM: extracellular solute-binding protein, family 5: (7.3e-55); KEGG: sil:SPO2066 ABC transporter, periplasmic substrate-binding protein, ev=0.0, 66% identity; extracellular solute-binding protein 1432423 4075914 TM1040_1343 Ruegeria sp. TM1040 extracellular solute-binding protein YP_613338.1 1430594 D 292414 CDS YP_613339.1 99081185 4075915 1432587..1432883 1 NC_008044.1 hypothetical protein 1432883 4075915 TM1040_1344 Ruegeria sp. TM1040 hypothetical protein YP_613339.1 1432587 D 292414 CDS YP_613340.1 99081186 4075916 complement(1432942..1433571) 1 NC_008044.1 PFAM: helix-turn-helix motif: (6e-14) Cupin 2, conserved barrel: (2.1e-07); KEGG: sil:SPO2068 DNA-binding protein, , ev=4e-96, 83% identity; XRE family transcriptional regulator 1433571 4075916 TM1040_1345 Ruegeria sp. TM1040 XRE family transcriptional regulator YP_613340.1 1432942 R 292414 CDS YP_613341.1 99081187 4075917 1433650..1435158 1 NC_008044.1 PFAM: AMP-dependent synthetase and ligase: (2.9e-89); KEGG: sil:SPO2069 benzoate-coenzyme A ligase, , ev=1e-172, 58% identity; AMP-dependent synthetase/ligase 1435158 4075917 TM1040_1346 Ruegeria sp. TM1040 AMP-dependent synthetase/ligase YP_613341.1 1433650 D 292414 CDS YP_613342.1 99081188 4075918 1435162..1435863 1 NC_008044.1 PFAM: DSBA oxidoreductase: (7.5e-43); KEGG: sil:SPO2070 DSBA-like thioredoxin family protein, ev=1e-88, 70% identity; DSBA oxidoreductase 1435863 4075918 TM1040_1347 Ruegeria sp. TM1040 DSBA oxidoreductase YP_613342.1 1435162 D 292414 CDS YP_613343.1 99081189 4075919 1436054..1437277 1 NC_008044.1 PFAM: major facilitator superfamily MFS_1: (8e-40); KEGG: sil:SPO2071 drug resistance transporter, Bcr/CflA subfamily, ev=1e-150, 67% identity; major facilitator superfamily transporter 1437277 4075919 TM1040_1348 Ruegeria sp. TM1040 major facilitator superfamily transporter YP_613343.1 1436054 D 292414 CDS YP_613344.1 99081190 4076366 complement(1437358..1440807) 1 NC_008044.1 TIGRFAM: transcription-repair coupling factor: (0); PFAM: helicase-like: (1.8e-17) transcription factor CarD: (1.9e-42) TRCF: (1e-44) type III restriction enzyme, res subunit: (8.4e-07) DEAD/DEAH box helicase-like: (4.2e-34); KEGG: sil:SPO2074 transcription-repair coupling factor, ev=0.0, 86% identity; transcription-repair coupling factor 1440807 4076366 TM1040_1349 Ruegeria sp. TM1040 transcription-repair coupling factor YP_613344.1 1437358 R 292414 CDS YP_613345.1 99081191 4076367 complement(1440838..1441377) 1 NC_008044.1 KEGG: sil:SPO2075 hypothetical protein, ev=6e-54, 58% identity; hypothetical protein 1441377 4076367 TM1040_1350 Ruegeria sp. TM1040 hypothetical protein YP_613345.1 1440838 R 292414 CDS YP_613346.1 99081192 4076368 1441498..1442535 1 NC_008044.1 catalyzes the formation of porphobilinogen from 5-aminolevulinate; delta-aminolevulinic acid dehydratase 1442535 4076368 TM1040_1351 Ruegeria sp. TM1040 delta-aminolevulinic acid dehydratase YP_613346.1 1441498 D 292414 CDS YP_613347.1 99081193 4076369 1442665..1443237 1 NC_008044.1 KEGG: sil:SPO2077 twin-arginine translocation pathway signal sequence domain protein, , ev=9e-73, 70% identity; twin-arginine translocation pathway signal sequence domain-containing protein 1443237 4076369 TM1040_1352 Ruegeria sp. TM1040 twin-arginine translocation pathway signal sequence domain-containing protein YP_613347.1 1442665 D 292414 CDS YP_613348.1 99081194 4076370 complement(1443294..1444166) 1 NC_008044.1 PFAM: 6-phosphogluconate dehydrogenase, NAD-binding: (3.4e-77); KEGG: sil:SPO0792 6-phosphogluconate dehydrogenase domain protein, ev=1e-137, 82% identity; 3-hydroxyisobutyrate dehydrogenase 1444166 4076370 TM1040_1353 Ruegeria sp. TM1040 3-hydroxyisobutyrate dehydrogenase YP_613348.1 1443294 R 292414 CDS YP_613349.1 99081195 4076371 1444280..1446769 1 NC_008044.1 PFAM: peptidase S45, penicillin amidase: (1e-122); KEGG: sil:SPO2078 penicillin amidase family protein, ev=0.0, 75% identity; penicillin amidase 1446769 4076371 TM1040_1354 Ruegeria sp. TM1040 penicillin amidase YP_613349.1 1444280 D 292414 CDS YP_613350.1 99081196 4076372 complement(1446786..1448057) 1 NC_008044.1 PFAM: GTP-binding protein, HSR1-related: (5e-38); KEGG: sil:SPO2080 GTP-binding protein HflX, ev=0.0, 80% identity; HSR1-like GTP-binding protein 1448057 4076372 TM1040_1355 Ruegeria sp. TM1040 HSR1-like GTP-binding protein YP_613350.1 1446786 R 292414 CDS YP_613351.1 99081197 4076373 complement(1448057..1448296) 1 NC_008044.1 Stimulates the elongation of poly(A) tails; RNA-binding protein Hfq 1448296 hfq 4076373 hfq Ruegeria sp. TM1040 RNA-binding protein Hfq YP_613351.1 1448057 R 292414 CDS YP_613352.1 99081198 4076374 complement(1448429..1449967) 1 NC_008044.1 PFAM: cation transporter: (2.5e-09); KEGG: sil:SPO2082 trk system potassium uptake protein TrkH, ev=0.0, 61% identity; cation transporter 1449967 4076374 TM1040_1357 Ruegeria sp. TM1040 cation transporter YP_613352.1 1448429 R 292414 CDS YP_613353.1 99081199 4076375 complement(1449969..1451345) 1 NC_008044.1 involved in potassium uptake; found to be peripherally associated with the inner membrane in Escherichia coli; contains an NAD-binding domain; potassium transporter peripheral membrane protein 1451345 trkA 4076375 trkA Ruegeria sp. TM1040 potassium transporter peripheral membrane protein YP_613353.1 1449969 R 292414 CDS YP_613354.1 99081200 4076376 complement(1451445..1452863) 1 NC_008044.1 PFAM: response regulator receiver: (1.9e-35) sigma-54 factor, interaction region: (3.8e-92) helix-turn-helix, Fis-type: (1.3e-09); SMART: ATPase: (2.4e-12); KEGG: sil:SPO2085 nitrogen assimilation regulatory protein NtrX, ev=0.0, 81% identity; two component, sigma54 specific, Fis family transcriptional regulator 1452863 4076376 TM1040_1359 Ruegeria sp. TM1040 two component, sigma54 specific, Fis family transcriptional regulator YP_613354.1 1451445 R 292414 CDS YP_613355.1 99081201 4076377 complement(1452860..1455139) 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (1e-28) histidine kinase, HAMP region: (9.4e-19) histidine kinase A-like: (1.6e-12) PAS fold: (2.3e-06); KEGG: sil:SPO2086 nitrogen regulation protein NtrY, ev=0.0, 74% identity; multi-sensor signal transduction histidine kinase 1455139 4076377 TM1040_1360 Ruegeria sp. TM1040 multi-sensor signal transduction histidine kinase YP_613355.1 1452860 R 292414 CDS YP_613356.1 99081202 4076378 complement(1455239..1456618) 1 NC_008044.1 PFAM: response regulator receiver: (4.7e-39) sigma-54 factor, interaction region: (1.1e-40) helix-turn-helix, Fis-type: (1.6e-14); SMART: ATPase: (6.6e-08); KEGG: sil:SPO2087 nitrogen regulation protein NtrC, ev=0.0, 74% identity; two component, sigma54 specific, Fis family transcriptional regulator 1456618 4076378 TM1040_1361 Ruegeria sp. TM1040 two component, sigma54 specific, Fis family transcriptional regulator YP_613356.1 1455239 R 292414 CDS YP_613357.1 99081203 4076379 complement(1456636..1457724) 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (4.5e-32) histidine kinase A-like: (5.2e-12); KEGG: sil:SPO2088 nitrogen regulation protein NtrB, ev=1e-155, 77% identity; signal transduction histidine kinase, nitrogen specific, NtrB 1457724 4076379 TM1040_1362 Ruegeria sp. TM1040 signal transduction histidine kinase, nitrogen specific, NtrB YP_613357.1 1456636 R 292414 CDS YP_613358.1 99081204 4076380 complement(1457721..1458707) 1 NC_008044.1 TIGRFAM: Dihydrouridine synthase TIM-barrel protein nifR3: (1.4e-125); PFAM: dihydrouridine synthase, DuS: (7.1e-130); KEGG: sil:SPO2089 tRNA-dihydrouridine synthase, , ev=1e-141, 76% identity; dihydrouridine synthase TIM-barrel protein nifR3 1458707 4076380 TM1040_1363 Ruegeria sp. TM1040 dihydrouridine synthase TIM-barrel protein nifR3 YP_613358.1 1457721 R 292414 CDS YP_613359.1 99081205 4076381 1458902..1460050 1 NC_008044.1 TIGRFAM: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase: (4.5e-74); PFAM: 4-diphosphocytidyl-2C-methyl-D-erythritol synthase: (4.5e-76) MECDP-synthase: (4.1e-74); KEGG: sil:SPO2090 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/ 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, ev=1e-151, 69% identity; 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 1460050 4076381 TM1040_1364 Ruegeria sp. TM1040 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase YP_613359.1 1458902 D 292414 CDS YP_613360.1 99081206 4076382 1460047..1460544 1 NC_008044.1 PFAM: phosphatidylglycerophosphatase A: (5.1e-30); KEGG: sil:SPO2091 phosphatidylglycerophosphatase, , ev=3e-65, 68% identity; phosphatidylglycerophosphatase 1460544 4076382 TM1040_1365 Ruegeria sp. TM1040 phosphatidylglycerophosphatase YP_613360.1 1460047 D 292414 CDS YP_613361.1 99081207 4076383 1460541..1461020 1 NC_008044.1 PFAM: CinA-like: (1.2e-63); KEGG: sil:SPO2092 competence/damage-inducible protein CinA domain protein, ev=5e-51, 65% identity; CinA-like protein 1461020 4076383 TM1040_1366 Ruegeria sp. TM1040 CinA-like protein YP_613361.1 1460541 D 292414 CDS YP_613362.1 99081208 4076384 complement(1461054..1461500) 1 NC_008044.1 PFAM: cyclase/dehydrase: (5e-38); KEGG: sil:SPO2096 aromatic-rich family protein, ev=2e-66, 80% identity; cyclase/dehydrase 1461500 4076384 TM1040_1367 Ruegeria sp. TM1040 cyclase/dehydrase YP_613362.1 1461054 R 292414 CDS YP_613363.1 99081209 4075861 1461575..1462117 1 NC_008044.1 KEGG: sil:SPO2097 hypoxanthine phosphoribosyltransferase, ev=6e-83, 88% identity; TIGRFAM: hypoxanthine phosphoribosyltransferase: (1.3e-90); PFAM: phosphoribosyltransferase: (1.1e-33); hypoxanthine phosphoribosyltransferase 1462117 4075861 TM1040_1368 Ruegeria sp. TM1040 hypoxanthine phosphoribosyltransferase YP_613363.1 1461575 D 292414 CDS YP_613364.1 99081210 4075862 1462243..1462569 1 NC_008044.1 hypothetical protein 1462569 4075862 TM1040_1369 Ruegeria sp. TM1040 hypothetical protein YP_613364.1 1462243 D 292414 CDS YP_613365.1 99081211 4075863 complement(1462602..1463744) 1 NC_008044.1 TIGRFAM: Peptidase M20D, amidohydrolase: (2.2e-40); PFAM: peptidase M20: (5.7e-38) peptidase dimerisation: (0.0023); KEGG: sil:SPO2101 amidohydrolase family protein, ev=1e-137, 62% identity; peptidase M20D, amidohydrolase 1463744 4075863 TM1040_1370 Ruegeria sp. TM1040 peptidase M20D, amidohydrolase YP_613365.1 1462602 R 292414 CDS YP_613366.1 99081212 4075864 complement(1463741..1464733) 1 NC_008044.1 catalyzes the radical-mediated insertion of two sulfur atoms into an acyl carrier protein (ACP) bound to an octanoyl group to produce a lipoyl group; lipoyl synthase 1464733 4075864 TM1040_1371 Ruegeria sp. TM1040 lipoyl synthase YP_613366.1 1463741 R 292414 CDS YP_613367.1 99081213 4075865 complement(1464883..1465929) 1 NC_008044.1 KEGG: sil:SPO2106 hypothetical protein, ev=3e-69, 43% identity; hypothetical protein 1465929 4075865 TM1040_1372 Ruegeria sp. TM1040 hypothetical protein YP_613367.1 1464883 R 292414 CDS YP_613368.1 99081214 4075866 1466164..1466496 1 NC_008044.1 KEGG: sil:SPO2107 hypothetical protein, ev=7e-12, 41% identity; hypothetical protein 1466496 4075866 TM1040_1373 Ruegeria sp. TM1040 hypothetical protein YP_613368.1 1466164 D 292414 CDS YP_613369.1 99081215 4075867 complement(1466516..1468060) 1 NC_008044.1 PFAM: trimethylamine methyltransferase: (2e-275); KEGG: sil:SPO2108 trimethylamine methyltransferase family protein, ev=0.0, 84% identity; trimethylamine methyltransferase 1468060 4075867 TM1040_1374 Ruegeria sp. TM1040 trimethylamine methyltransferase YP_613369.1 1466516 R 292414 CDS YP_613370.1 99081216 4075868 1468257..1469819 1 NC_008044.1 contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway; GMP synthase 1469819 guaA 4075868 guaA Ruegeria sp. TM1040 GMP synthase YP_613370.1 1468257 D 292414 CDS YP_613371.1 99081217 4075869 1469995..1470888 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (1.2e-08); KEGG: sil:SPO2110 membrane protein, , ev=2e-97, 62% identity; hypothetical protein 1470888 4075869 TM1040_1376 Ruegeria sp. TM1040 hypothetical protein YP_613371.1 1469995 D 292414 CDS YP_613372.1 99081218 4075870 1471021..1472160 1 NC_008044.1 PFAM: membrane protein involved in aromatic hydrocarbon degradation: (4.1e-07); KEGG: rsp:RSP_0007 outer membrane protein, ev=1e-66, 39% identity; aromatic hydrocarbon degradation membrane protein 1472160 4075870 TM1040_1377 Ruegeria sp. TM1040 aromatic hydrocarbon degradation membrane protein YP_613372.1 1471021 D 292414 CDS YP_613373.1 99081219 4075871 1472383..1473192 1 NC_008044.1 KEGG: sil:SPO2113 hypothetical protein, ev=1e-114, 71% identity; hypothetical protein 1473192 4075871 TM1040_1378 Ruegeria sp. TM1040 hypothetical protein YP_613373.1 1472383 D 292414 CDS YP_613374.1 99081220 4075872 1473238..1474176 1 NC_008044.1 catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis; homoserine O-succinyltransferase 1474176 4075872 TM1040_1379 Ruegeria sp. TM1040 homoserine O-succinyltransferase YP_613374.1 1473238 D 292414 CDS YP_613375.1 99081221 4075873 1474186..1475151 1 NC_008044.1 PFAM: alpha/beta hydrolase fold: (1.9e-12); KEGG: sil:SPO1728 esterase, , ev=9e-87, 52% identity; alpha/beta hydrolase 1475151 4075873 TM1040_1380 Ruegeria sp. TM1040 alpha/beta hydrolase YP_613375.1 1474186 D 292414 CDS YP_613376.1 99081222 4075874 1475213..1476082 1 NC_008044.1 PFAM: protein of unknown function DUF344: (2.7e-137); KEGG: sil:SPO1727 polyphosphate kinase 2, , ev=1e-115, 69% identity; hypothetical protein 1476082 4075874 TM1040_1381 Ruegeria sp. TM1040 hypothetical protein YP_613376.1 1475213 D 292414 CDS YP_613377.1 99081223 4075875 1476075..1476692 1 NC_008044.1 PFAM: regulatory protein, TetR: (5e-13); KEGG: sil:SPO3896 transcriptional regulator, TetR family, ev=3e-89, 79% identity; TetR family transcriptional regulator 1476692 4075875 TM1040_1382 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_613377.1 1476075 D 292414 CDS YP_613378.1 99081224 4075876 1476848..1478965 1 NC_008044.1 PFAM: histidine kinase, HAMP region: (2.6e-06) chemotaxis sensory transducer: (4.9e-87) Nitrate and nitrite sensing: (7.3e-30); KEGG: ccr:CC0430 methyl-accepting chemotaxis protein McpA, ev=6e-92, 42% identity; methyl-accepting chemotaxis sensory transducer 1478965 4075876 TM1040_1383 Ruegeria sp. TM1040 methyl-accepting chemotaxis sensory transducer YP_613378.1 1476848 D 292414 CDS YP_613379.1 99081225 4075877 complement(1479063..1479548) 1 NC_008044.1 forms a direct contact with the tRNA during translation; 30S ribosomal protein S9 1479548 rpsI 4075877 rpsI Ruegeria sp. TM1040 30S ribosomal protein S9 YP_613379.1 1479063 R 292414 CDS YP_613380.1 99081226 4075878 complement(1479554..1480012) 1 NC_008044.1 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit; 50S ribosomal protein L13 1480012 rplM 4075878 rplM Ruegeria sp. TM1040 50S ribosomal protein L13 YP_613380.1 1479554 R 292414 CDS YP_613381.1 99081227 4075879 complement(1480196..1481611) 1 NC_008044.1 PFAM: regulatory protein GntR, HTH: (4.7e-18) aminotransferase, class I and II: (5.3e-07); KEGG: sil:SPO1690 transcriptional regulator, GntR family, ev=0.0, 67% identity; GntR family transcriptional regulator 1481611 4075879 TM1040_1386 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_613381.1 1480196 R 292414 CDS YP_613382.1 99081228 4075880 complement(1481680..1481946) 1 NC_008044.1 hypothetical protein 1481946 4075880 TM1040_1387 Ruegeria sp. TM1040 hypothetical protein YP_613382.1 1481680 R 292414 CDS YP_613383.1 99081229 4075881 1482166..1482672 1 NC_008044.1 PFAM: S-adenosylmethionine decarboxylase related: (1.2e-42); KEGG: tcx:Tcr_0272 S-adenosylmethionine decarboxylase related, ev=3e-35, 61% identity; S-adenosylmethionine decarboxylase-like protein 1482672 4075881 TM1040_1388 Ruegeria sp. TM1040 S-adenosylmethionine decarboxylase-like protein YP_613383.1 1482166 D 292414 CDS YP_613384.1 99081230 4075882 1482669..1483523 1 NC_008044.1 catalyzes the formation of spermidine from putrescine and S-adenosylmethioninamine; spermidine synthase 1483523 4075882 TM1040_1389 Ruegeria sp. TM1040 spermidine synthase YP_613384.1 1482669 D 292414 CDS YP_613385.1 99081231 4075883 complement(1483581..1484003) 1 NC_008044.1 TIGRFAM: Phenylacetic acid degradation-related protein: (1.1e-07); PFAM: thioesterase superfamily: (5.3e-11); KEGG: sil:SPO1688 thioesterase family protein, ev=2e-49, 69% identity; phenylacetic acid degradation-related protein 1484003 4075883 TM1040_1390 Ruegeria sp. TM1040 phenylacetic acid degradation-related protein YP_613385.1 1483581 R 292414 CDS YP_613386.1 99081232 4075884 1484388..1485740 1 NC_008044.1 TrmFO; Gid; glucose-inhibited division protein; similar to GidA; the gene from Bacillus subtilis encodes a tRNA-methyltransferase that utilizes folate as the carbon donor and bound flavin as reductant; modifies tRNA at position 54 (uridine) of the T-psi loop to form a C5-methyluridine; tRNA (uracil-5-)-methyltransferase Gid 1485740 4075884 TM1040_1391 Ruegeria sp. TM1040 tRNA (uracil-5-)-methyltransferase Gid YP_613386.1 1484388 D 292414 CDS YP_613387.1 99081233 4075885 1485777..1486391 1 NC_008044.1 PFAM: Methyltransferase type 11: (1.3e-07) Methyltransferase type 12: (2.3e-06); KEGG: jan:Jann_2499 methyltransferase type 12, ev=3e-36, 47% identity; type 11 methyltransferase 1486391 4075885 TM1040_1392 Ruegeria sp. TM1040 type 11 methyltransferase YP_613387.1 1485777 D 292414 CDS YP_613388.1 99081234 4075886 1486388..1487236 1 NC_008044.1 PFAM: glutamyl-tRNA synthetase, class Ic: (1.9e-24); KEGG: rsp:RSP_2628 glutamyl-/glutaminyl-tRNA synthetase, ev=9e-96, 64% identity; glutamyl-tRNA synthetase 1487236 4075886 TM1040_1393 Ruegeria sp. TM1040 glutamyl-tRNA synthetase YP_613388.1 1486388 D 292414 CDS YP_613389.1 99081235 4075887 complement(1487246..1487635) 1 NC_008044.1 PFAM: phosphoribosyl-AMP cyclohydrolase: (9.7e-52); KEGG: sil:SPO1684 phosphoribosyl-AMP cyclohydrolase, ev=3e-51, 77% identity; phosphoribosyl-AMP cyclohydrolase 1487635 4075887 TM1040_1394 Ruegeria sp. TM1040 phosphoribosyl-AMP cyclohydrolase YP_613389.1 1487246 R 292414 CDS YP_613390.1 99081236 4075888 1487653..1488147 1 NC_008044.1 KEGG: sil:SPO1683 hypothetical protein, ev=4e-62, 78% identity; hypothetical protein 1488147 4075888 TM1040_1395 Ruegeria sp. TM1040 hypothetical protein YP_613390.1 1487653 D 292414 CDS YP_613391.1 99081237 4075889 1488276..1488533 1 NC_008044.1 hypothetical protein 1488533 4075889 TM1040_1396 Ruegeria sp. TM1040 hypothetical protein YP_613391.1 1488276 D 292414 CDS YP_613392.1 99081238 4075890 complement(1488653..1490743) 1 NC_008044.1 catalyzes branch migration in Holliday junction intermediates; ATP-dependent DNA helicase RecG 1490743 4075890 TM1040_1397 Ruegeria sp. TM1040 ATP-dependent DNA helicase RecG YP_613392.1 1488653 R 292414 CDS YP_613393.1 99081239 4075891 complement(1490751..1492970) 1 NC_008044.1 KEGG: sil:SPO1680 DNA ligase, NAD-dependent, ev=0.0, 75% identity; TIGRFAM: DNA ligase, NAD-dependent: (4.1e-283); PFAM: BRCT: (1.9e-17) NAD-dependent DNA ligase: (2.1e-140) zinc-finger, NAD-dependent DNA ligase C4-type: (2.5e-10) NAD-dependent DNA ligase, OB-fold: (1.9e-38); NAD-dependent DNA ligase 1492970 4075891 TM1040_1398 Ruegeria sp. TM1040 NAD-dependent DNA ligase YP_613393.1 1490751 R 292414 CDS YP_613394.1 99081240 4075892 complement(1493148..1493867) 1 NC_008044.1 PFAM: response regulator receiver: (3e-37) transcriptional regulatory protein-like: (4e-21); KEGG: sil:SPO1679 DNA-binding response regulator CtrA, ev=1e-120, 90% identity; two component transcriptional regulator 1493867 4075892 TM1040_1399 Ruegeria sp. TM1040 two component transcriptional regulator YP_613394.1 1493148 R 292414 CDS YP_613395.1 99081241 4075893 complement(1493993..1494271) 1 NC_008044.1 KEGG: sil:SPO1678 hypothetical protein, ev=6e-32, 70% identity; hypothetical protein 1494271 4075893 TM1040_1400 Ruegeria sp. TM1040 hypothetical protein YP_613395.1 1493993 R 292414 CDS YP_613396.1 99081242 4075894 1494429..1495574 1 NC_008044.1 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs; tRNA-specific 2-thiouridylase MnmA 1495574 mnmA 4075894 mnmA Ruegeria sp. TM1040 tRNA-specific 2-thiouridylase MnmA YP_613396.1 1494429 D 292414 CDS YP_613397.1 99081243 4075895 complement(1495642..1496802) 1 NC_008044.1 KEGG: sil:SPO1675 lipid-A-disaccharide synthase, ev=1e-157, 74% identity; TIGRFAM: lipid-A-disaccharide synthase: (1.6e-61); PFAM: glycosyl transferase, family 19: (2e-88); lipid-A-disaccharide synthase 1496802 4075895 TM1040_1402 Ruegeria sp. TM1040 lipid-A-disaccharide synthase YP_613397.1 1495642 R 292414 CDS YP_613398.1 99081244 4075896 complement(1496806..1497594) 1 NC_008044.1 PFAM: protein of unknown function DUF1009: (1.9e-50); KEGG: sil:SPO1674 hypothetical protein, ev=3e-89, 61% identity; hypothetical protein 1497594 4075896 TM1040_1403 Ruegeria sp. TM1040 hypothetical protein YP_613398.1 1496806 R 292414 CDS YP_613399.1 99081245 4075897 complement(1497608..1498393) 1 NC_008044.1 catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis; UDP-N-acetylglucosamine acyltransferase 1498393 4075897 TM1040_1404 Ruegeria sp. TM1040 UDP-N-acetylglucosamine acyltransferase YP_613399.1 1497608 R 292414 CDS YP_613400.1 99081246 4075898 complement(1498393..1498875) 1 NC_008044.1 in Pseudomonas aeruginosa this enzyme is a trimer of dimers; essential for membrane formation; performs third step of type II fatty acid biosynthesis; catalyzes dehydration of (3R)-hydroxyacyl-ACP to trans-2-acyl-ACP; (3R)-hydroxymyristoyl-ACP dehydratase 1498875 fabZ 4075898 fabZ Ruegeria sp. TM1040 (3R)-hydroxymyristoyl-ACP dehydratase YP_613400.1 1498393 R 292414 CDS YP_613401.1 99081247 4075899 complement(1498939..1499484) 1 NC_008044.1 PFAM: outer membrane chaperone Skp (OmpH): (4.6e-14); KEGG: sil:SPO1671 hypothetical protein, ev=3e-34, 46% identity; outer membrane chaperone Skp 1499484 4075899 TM1040_1406 Ruegeria sp. TM1040 outer membrane chaperone Skp YP_613401.1 1498939 R 292414 CDS YP_613402.1 99081248 4078037 complement(1499580..1501970) 1 NC_008044.1 PFAM: surface antigen (D15): (4.4e-40) surface antigen variable number: (2.1e-14); KEGG: sil:SPO1670 outer membrane protein, OMP85 family, ev=0.0, 63% identity; surface antigen (D15) 1501970 4078037 TM1040_1407 Ruegeria sp. TM1040 surface antigen (D15) YP_613402.1 1499580 R 292414 CDS YP_613403.1 99081249 4078038 complement(1502126..1502254) 1 NC_008044.1 KEGG: sil:SPO1669 hypothetical protein, ev=9e-07, 60% identity; hypothetical protein 1502254 4078038 TM1040_1408 Ruegeria sp. TM1040 hypothetical protein YP_613403.1 1502126 R 292414 CDS YP_613404.1 99081250 4078039 complement(1502394..1503746) 1 NC_008044.1 TIGRFAM: Peptidase M50, membrane-associated zinc metallopeptidase: (4.7e-61); PFAM: PDZ/DHR/GLGF: (0.014) peptidase M50: (1e-65); KEGG: sil:SPO1668 membrane-associated zinc metalloprotease, , ev=1e-156, 59% identity; peptidase RseP 1503746 4078039 TM1040_1409 Ruegeria sp. TM1040 peptidase RseP YP_613404.1 1502394 R 292414 CDS YP_613405.1 99081251 4078040 complement(1503751..1504938) 1 NC_008044.1 catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate; 1-deoxy-D-xylulose 5-phosphate reductoisomerase 1504938 4078040 TM1040_1410 Ruegeria sp. TM1040 1-deoxy-D-xylulose 5-phosphate reductoisomerase YP_613405.1 1503751 R 292414 CDS YP_613406.1 99081252 4078041 complement(1504970..1505767) 1 NC_008044.1 PFAM: phosphatidate cytidylyltransferase: (2.5e-51); KEGG: sil:SPO1666 phosphatidate cytidylyltransferase, ev=2e-64, 50% identity; phosphatidate cytidylyltransferase 1505767 4078041 TM1040_1411 Ruegeria sp. TM1040 phosphatidate cytidylyltransferase YP_613406.1 1504970 R 292414 CDS YP_613407.1 99081253 4078042 complement(1505764..1506534) 1 NC_008044.1 KEGG: sil:SPO1665 UDP diphosphate synthase, ev=1e-115, 84% identity; TIGRFAM: UDP diphosphate synthase: (1.8e-103); PFAM: Di-trans-poly-cis-decaprenylcistransferase: (9.2e-107); UDP pyrophosphate synthetase 1506534 4078042 TM1040_1412 Ruegeria sp. TM1040 UDP pyrophosphate synthetase YP_613407.1 1505764 R 292414 CDS YP_613408.1 99081254 4078043 complement(1506544..1507107) 1 NC_008044.1 Rrf; Frr; ribosome-recycling factor; release factor 4; RF4; recycles ribosomes upon translation termination along with release factor RF-3 and elongation factor EF-G; A GTPase-dependent process results in release of 50S from 70S; inhibited by release factor RF-1; essential for viability; structurally similar to tRNAs; ribosome recycling factor 1507107 frr 4078043 frr Ruegeria sp. TM1040 ribosome recycling factor YP_613408.1 1506544 R 292414 CDS YP_613409.1 99081255 4078044 complement(1507284..1508033) 1 NC_008044.1 Catalyzes the phosphorylation of UMP to UDP; uridylate kinase 1508033 pyrH 4078044 pyrH Ruegeria sp. TM1040 uridylate kinase YP_613409.1 1507284 R 292414 CDS YP_613410.1 99081256 4078045 1508184..1509050 1 NC_008044.1 IPP transferase; isopentenyltransferase; involved in tRNA modification; in Escherichia coli this enzyme catalyzes the addition of a delta2-isopentenyl group from dimethylallyl diphosphate to the N6-nitrogen of adenosine adjacent to the anticodon of tRNA species that read codons starting with uracil; further tRNA modifications may occur; mutations in miaA result in defects in translation efficiency and fidelity; tRNA delta(2)-isopentenylpyrophosphate transferase 1509050 miaA 4078045 miaA Ruegeria sp. TM1040 tRNA delta(2)-isopentenylpyrophosphate transferase YP_613410.1 1508184 D 292414 CDS YP_613411.1 99081257 4078046 1509244..1510074 1 NC_008044.1 PFAM: helix-turn-helix, AraC type: (5.4e-08); KEGG: sil:SPO1660 transcriptional regulator, AraC family, ev=1e-50, 44% identity; AraC family transcriptional regulator 1510074 4078046 TM1040_1416 Ruegeria sp. TM1040 AraC family transcriptional regulator YP_613411.1 1509244 D 292414 CDS YP_613412.1 99081258 4078047 1510334..1512001 1 NC_008044.1 TIGRFAM: Twin-arginine translocation pathway signal: (0.0056); PFAM: extracellular solute-binding protein, family 5: (1.4e-47); KEGG: sil:SPO1659 oligopeptide/dipeptide ABC transporter, periplasmic substrate-binding protein, ev=0.0, 77% identity; twin-arginine translocation pathway signal 1512001 4078047 TM1040_1417 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_613412.1 1510334 D 292414 CDS YP_613413.1 99081259 4078048 1512170..1513222 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1.1e-26); KEGG: sil:SPO1658 oligopeptide/dipeptide ABC transporter, permease protein, ev=1e-161, 81% identity; binding-protein-dependent transport system inner membrane protein 1513222 4078048 TM1040_1418 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_613413.1 1512170 D 292414 CDS YP_613414.1 99081260 4078049 1513238..1514674 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (2.3e-32); KEGG: sil:SPO1657 oligopeptide/dipeptide ABC transporter, permease protein, ev=1e-176, 79% identity; binding-protein-dependent transport system inner membrane protein 1514674 4078049 TM1040_1419 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_613414.1 1513238 D 292414 CDS YP_613415.1 99081261 4078050 1514770..1516857 1 NC_008044.1 KEGG: sil:SPO1656 oligopeptide/dipeptide ABC transporter, ATP-binding protein, ev=0.0, 89% identity; TIGRFAM: Oligopeptide/dipeptide ABC transporter, ATP-binding protein-like: (3.3e-26); PFAM: ABC transporter related: (2.8e-59) Oligopeptide/dipeptide ABC transporter-like: (3.5e-26); SMART: ATPase: (5.7e-18); oligopeptide/dipeptide ABC transporter ATP-binding protein-like protein 1516857 4078050 TM1040_1420 Ruegeria sp. TM1040 oligopeptide/dipeptide ABC transporter ATP-binding protein-like protein YP_613415.1 1514770 D 292414 CDS YP_613416.1 99081262 4078051 complement(1516976..1518391) 1 NC_008044.1 PFAM: Tetratricopeptide TPR_2: (0.00025); KEGG: ccr:CC3128 TPR domain protein, ev=1e-19, 23% identity; hypothetical protein 1518391 4078051 TM1040_1421 Ruegeria sp. TM1040 hypothetical protein YP_613416.1 1516976 R 292414 CDS YP_613417.1 99081263 4078052 complement(1518520..1519656) 1 NC_008044.1 PFAM: Di-haem cytochrome c peroxidase: (1e-49); KEGG: atc:AGR_C_5068 methylamine utilization protein MauG precursor, ev=1e-112, 57% identity; di-heme cytochrome c peroxidase 1519656 4078052 TM1040_1422 Ruegeria sp. TM1040 di-heme cytochrome c peroxidase YP_613417.1 1518520 R 292414 CDS YP_613418.1 99081264 4078053 complement(1519788..1520162) 1 NC_008044.1 hypothetical protein 1520162 4078053 TM1040_1423 Ruegeria sp. TM1040 hypothetical protein YP_613418.1 1519788 R 292414 CDS YP_613419.1 99081265 4078054 complement(1520328..1520903) 1 NC_008044.1 PFAM: Lytic transglycosylase, catalytic: (1.7e-29); KEGG: sil:SPO1638 transglycosylase SLT domain protein, ev=1e-60, 60% identity; lytic transglycosylase, catalytic 1520903 4078054 TM1040_1424 Ruegeria sp. TM1040 lytic transglycosylase, catalytic YP_613419.1 1520328 R 292414 CDS YP_613420.1 99081266 4078055 1521186..1521710 1 NC_008044.1 TIGRFAM: single-strand binding protein: (4.6e-61); PFAM: single-strand binding protein/Primosomal replication protein n: (8e-33); KEGG: sil:SPO1637 single-strand binding protein, ev=1e-79, 82% identity; single-strand binding protein 1521710 4078055 TM1040_1425 Ruegeria sp. TM1040 single-strand binding protein YP_613420.1 1521186 D 292414 CDS YP_613421.1 99081267 4078056 complement(1521820..1524237) 1 NC_008044.1 PFAM: FAD dependent oxidoreductase: (9.9e-90) glycine cleavage T protein (aminomethyl transferase): (2.9e-46); KEGG: sil:SPO1628 aminomethyl transferase family protein, ev=0.0, 82% identity; FAD dependent oxidoreductase 1524237 4078056 TM1040_1426 Ruegeria sp. TM1040 FAD dependent oxidoreductase YP_613421.1 1521820 R 292414 CDS YP_613422.1 99081268 4078057 complement(1524444..1525757) 1 NC_008044.1 PFAM: CBS: (1.4e-28) protein of unknown function DUF21: (4e-56) transporter-associated region: (9.6e-28); KEGG: sil:SPO1631 CBS domain protein, ev=0.0, 79% identity; hypothetical protein 1525757 4078057 TM1040_1427 Ruegeria sp. TM1040 hypothetical protein YP_613422.1 1524444 R 292414 CDS YP_613423.1 99081269 4078058 complement(1525837..1526790) 1 NC_008044.1 PFAM: phage integrase: (5.1e-41) phage integrase-like SAM-like: (4.3e-13); KEGG: sil:SPO1632 tyrosine recombinase XerD, ev=1e-132, 75% identity; phage integrase 1526790 4078058 TM1040_1428 Ruegeria sp. TM1040 phage integrase YP_613423.1 1525837 R 292414 CDS YP_613424.1 99081270 4078059 complement(1526794..1528326) 1 NC_008044.1 KEGG: rsp:RSP_2816 hypothetical protein, ev=1e-111, 46% identity; hypothetical protein 1528326 4078059 TM1040_1429 Ruegeria sp. TM1040 hypothetical protein YP_613424.1 1526794 R 292414 CDS YP_613425.1 99081271 4078060 complement(1528316..1528465) 1 NC_008044.1 hypothetical protein 1528465 4078060 TM1040_1430 Ruegeria sp. TM1040 hypothetical protein YP_613425.1 1528316 R 292414 CDS YP_613426.1 99081272 4078061 1528549..1529139 1 NC_008044.1 catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis; shikimate kinase 1529139 4078061 TM1040_1431 Ruegeria sp. TM1040 shikimate kinase YP_613426.1 1528549 D 292414 CDS YP_613427.1 99081273 4078062 1529139..1530260 1 NC_008044.1 catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis; 3-dehydroquinate synthase 1530260 aroB 4078062 aroB Ruegeria sp. TM1040 3-dehydroquinate synthase YP_613427.1 1529139 D 292414 CDS YP_613428.1 99081274 4078063 1530278..1530904 1 NC_008044.1 KEGG: rsp:RSP_2928 hypothetical protein, ev=1e-35, 47% identity; hypothetical protein 1530904 4078063 TM1040_1433 Ruegeria sp. TM1040 hypothetical protein YP_613428.1 1530278 D 292414 CDS YP_613429.1 99081275 4078064 complement(1530905..1531567) 1 NC_008044.1 KEGG: sil:SPO1626 type I secretion target repeat protein, ev=8e-80, 69% identity; type I secretion target repeat-containing protein 1531567 4078064 TM1040_1434 Ruegeria sp. TM1040 type I secretion target repeat-containing protein YP_613429.1 1530905 R 292414 CDS YP_613430.1 99081276 4078065 complement(1531769..1532020) 1 NC_008044.1 hypothetical protein 1532020 4078065 TM1040_1435 Ruegeria sp. TM1040 hypothetical protein YP_613430.1 1531769 R 292414 CDS YP_613431.1 99081277 4078066 complement(1532091..1532918) 1 NC_008044.1 PFAM: Enoyl-CoA hydratase/isomerase: (7.7e-38); KEGG: sil:SPO1687 enoyl-CoA hydratase/isomerase family protein, ev=2e-83, 61% identity; enoyl-CoA hydratase/isomerase 1532918 4078066 TM1040_1436 Ruegeria sp. TM1040 enoyl-CoA hydratase/isomerase YP_613431.1 1532091 R 292414 CDS YP_613432.1 99081278 4078067 complement(1532982..1533809) 1 NC_008044.1 PFAM: inositol monophosphatase: (7.9e-31); KEGG: sme:SMc00535 hypothetical protein, ev=8e-54, 41% identity; inositol monophosphatase 1533809 4078067 TM1040_1437 Ruegeria sp. TM1040 inositol monophosphatase YP_613432.1 1532982 R 292414 CDS YP_613433.1 99081279 4078068 complement(1534364..1536886) 1 NC_008044.1 PFAM: MscS Mechanosensitive ion channel: (3.6e-74); KEGG: sil:SPO1922 mechanosensitive ion channel family protein, ev=0.0, 55% identity; mechanosensitive ion channel protein MscS 1536886 4078068 TM1040_1438 Ruegeria sp. TM1040 mechanosensitive ion channel protein MscS YP_613433.1 1534364 R 292414 CDS YP_613434.1 99081280 4078069 complement(1536892..1538076) 1 NC_008044.1 CysK; forms a complex with serine acetyltransferase CysE; functions in cysteine biosynthesis; cysteine synthase A 1538076 4078069 TM1040_1439 Ruegeria sp. TM1040 cysteine synthase A YP_613434.1 1536892 R 292414 CDS YP_613435.1 99081281 4078070 complement(1538196..1538750) 1 NC_008044.1 KEGG: sil:SPO1919 tellurite resistance protein, ev=6e-44, 56% identity; tellurite resistance protein 1538750 4078070 TM1040_1440 Ruegeria sp. TM1040 tellurite resistance protein YP_613435.1 1538196 R 292414 CDS YP_613436.1 99081282 4078071 complement(1538768..1540192) 1 NC_008044.1 PFAM: DNA photolyase, FAD-binding: (6.9e-79) DNA photolyase-like: (2.1e-40); KEGG: sil:SPO1917 deoxyribodipyrimidine photolyase, ev=1e-167, 58% identity; deoxyribodipyrimidine photo-lyase type I 1540192 4078071 TM1040_1441 Ruegeria sp. TM1040 deoxyribodipyrimidine photo-lyase type I YP_613436.1 1538768 R 292414 CDS YP_613437.1 99081283 4078072 complement(1540223..1541452) 1 NC_008044.1 PFAM: aminotransferase, class V: (3.3e-28); KEGG: sil:SPO1916 aminotransferase, class V, ev=0.0, 77% identity; class V aminotransferase 1541452 4078072 TM1040_1442 Ruegeria sp. TM1040 class V aminotransferase YP_613437.1 1540223 R 292414 CDS YP_613438.1 99081284 4078073 complement(1541561..1542556) 1 NC_008044.1 PFAM: Alcohol dehydrogenase, zinc-binding: (2.3e-16) Alcohol dehydrogenase GroES-like: (4.1e-09); KEGG: sil:SPO1914 oxidoreductase, zinc-binding dehydrogenase family, ev=1e-157, 84% identity; zinc-binding alcohol dehydrogenase 1542556 4078073 TM1040_1443 Ruegeria sp. TM1040 zinc-binding alcohol dehydrogenase YP_613438.1 1541561 R 292414 CDS YP_613439.1 99081285 4078074 complement(1542571..1543728) 1 NC_008044.1 DmdA; DMSP demethylase; in Silicibacter knockout of this gene results in an inability to convert DMSP to methanethiol which is restored with a cloned copy of the gene; dimethyl sulfoniopropionate demethylase 1543728 dmdA 4078074 dmdA Ruegeria sp. TM1040 dimethyl sulfoniopropionate demethylase YP_613439.1 1542571 R 292414 CDS YP_613440.1 99081286 4078075 complement(1543768..1544442) 1 NC_008044.1 PFAM: protein of unknown function DUF1326: (2.5e-77); KEGG: jan:Jann_2383 protein of unknown function DUF1326, ev=1e-103, 86% identity; hypothetical protein 1544442 4078075 TM1040_1445 Ruegeria sp. TM1040 hypothetical protein YP_613440.1 1543768 R 292414 CDS YP_613441.1 99081287 4077743 complement(1544461..1545234) 1 NC_008044.1 KEGG: jan:Jann_2384 hypothetical protein, ev=9e-89, 62% identity; hypothetical protein 1545234 4077743 TM1040_1446 Ruegeria sp. TM1040 hypothetical protein YP_613441.1 1544461 R 292414 CDS YP_613442.1 99081288 4077744 1545359..1546090 1 NC_008044.1 PFAM: regulatory protein GntR, HTH: (5.9e-17) GntR-like: (1.2e-14); KEGG: jan:Jann_2385 regulatory protein GntR, HTH, ev=3e-94, 75% identity; GntR family transcriptional regulator 1546090 4077744 TM1040_1447 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_613442.1 1545359 D 292414 CDS YP_613443.1 99081289 4077745 1546769..1547203 1 NC_008044.1 PFAM: protein of unknown function DUF1486: (2.1e-05); KEGG: sil:SPO1909 hypothetical protein, ev=6e-22, 33% identity; hypothetical protein 1547203 4077745 TM1040_1448 Ruegeria sp. TM1040 hypothetical protein YP_613443.1 1546769 D 292414 CDS YP_613444.1 99081290 4077746 1547314..1548600 1 NC_008044.1 PFAM: Chromate transporter: (1.2e-38); KEGG: sil:SPO1908 chromate transporter, ev=1e-132, 60% identity; chromate transporter 1548600 4077746 TM1040_1449 Ruegeria sp. TM1040 chromate transporter YP_613444.1 1547314 D 292414 CDS YP_613445.1 99081291 4077747 1548715..1549194 1 NC_008044.1 PFAM: protein of unknown function DUF1321: (5.5e-58); KEGG: sil:SPO1907 hypothetical protein, ev=3e-61, 70% identity; hypothetical protein 1549194 4077747 TM1040_1450 Ruegeria sp. TM1040 hypothetical protein YP_613445.1 1548715 D 292414 CDS YP_613446.1 99081292 4077748 complement(1549340..1549924) 1 NC_008044.1 KEGG: sil:SPO1906 hypothetical protein, ev=1e-52, 59% identity; hypothetical protein 1549924 4077748 TM1040_1451 Ruegeria sp. TM1040 hypothetical protein YP_613446.1 1549340 R 292414 CDS YP_613447.1 99081293 4077749 1550169..1551566 1 NC_008044.1 class II family (does not require metal); tetrameric enzyme; fumarase C; reversibly converts (S)-malate to fumarate and water; functions in the TCA cycle; fumarate hydratase 1551566 fumC 4077749 fumC Ruegeria sp. TM1040 fumarate hydratase YP_613447.1 1550169 D 292414 CDS YP_613448.1 99081294 4077750 1551847..1553010 1 NC_008044.1 KEGG: sil:SPO1626 type I secretion target repeat protein, ev=5e-39, 41% identity; hypothetical protein 1553010 4077750 TM1040_1453 Ruegeria sp. TM1040 hypothetical protein YP_613448.1 1551847 D 292414 CDS YP_613449.1 99081295 4077751 1553015..1553245 1 NC_008044.1 KEGG: jan:Jann_2395 uncharacterized arylsulfate sulfotransferase-like protein, ev=4e-17, 61% identity; arylsulfate sulfotransferase-like protein 1553245 4077751 TM1040_1454 Ruegeria sp. TM1040 arylsulfate sulfotransferase-like protein YP_613449.1 1553015 D 292414 CDS YP_613450.1 99081296 4077752 complement(1553254..1554612) 1 NC_008044.1 PFAM: cytochrome P450: (2.8e-56); KEGG: sil:SPO1898 cytochrome P450 family protein, ev=0.0, 75% identity; cytochrome P450 1554612 4077752 TM1040_1455 Ruegeria sp. TM1040 cytochrome P450 YP_613450.1 1553254 R 292414 CDS YP_613451.1 99081297 4077753 complement(1554609..1555856) 1 NC_008044.1 KEGG: sil:SPO1897 hypothetical protein, ev=1e-142, 63% identity; hypothetical protein 1555856 4077753 TM1040_1456 Ruegeria sp. TM1040 hypothetical protein YP_613451.1 1554609 R 292414 CDS YP_613452.1 99081298 4077754 complement(1555970..1556722) 1 NC_008044.1 PFAM: cytochrome c biogenesis protein, transmembrane region: (3e-59); KEGG: sil:SPO1896 cytochrome c-type biogenesis protein CcdA, ev=1e-118, 86% identity; cytochrome c biogenesis protein, transmembrane region 1556722 4077754 TM1040_1457 Ruegeria sp. TM1040 cytochrome c biogenesis protein, transmembrane region YP_613452.1 1555970 R 292414 CDS YP_613453.1 99081299 4077755 1556817..1557053 1 NC_008044.1 PFAM: SirA-like: (8.6e-22); KEGG: sil:SPO1895 SirA family protein, ev=2e-25, 70% identity; SirA-like protein 1557053 4077755 TM1040_1458 Ruegeria sp. TM1040 SirA-like protein YP_613453.1 1556817 D 292414 CDS YP_613454.1 99081300 4077756 complement(1557176..1560106) 1 NC_008044.1 TIGRFAM: ribonuclease, Rne/Rng family: (5.3e-203); KEGG: sil:SPO1893 ribonuclease, Rne/Rng family, ev=0.0, 69% identity; RNAse E 1560106 4077756 TM1040_1459 Ruegeria sp. TM1040 RNAse E YP_613454.1 1557176 R 292414 CDS YP_613455.1 99081301 4077757 complement(1560700..1561389) 1 NC_008044.1 TIGRFAM: HAD-superfamily hydrolase subfamily IA, variant 3: (7.8e-10); PFAM: Haloacid dehalogenase-like hydrolase: (2.5e-31); KEGG: bpm:BURPS1710b_1218 hydrolase, ev=1e-26, 35% identity; HAD family hydrolase 1561389 4077757 TM1040_1460 Ruegeria sp. TM1040 HAD family hydrolase YP_613455.1 1560700 R 292414 CDS YP_613456.1 99081302 4077758 complement(1561389..1562726) 1 NC_008044.1 PFAM: response regulator receiver: (5.5e-44) sigma-54 factor, interaction region: (1.6e-28) helix-turn-helix, Fis-type: (9.6e-07) ATPase associated with various cellular activities, AAA_5: (0.00016); SMART: ATPase: (9.8e-10); KEGG: sil:SPO1892 C4-dicarboxylate transport transcriptional regulatory protein DctD, ev=0.0, 92% identity; two component, sigma54 specific, Fis family transcriptional regulator 1562726 4077758 TM1040_1461 Ruegeria sp. TM1040 two component, sigma54 specific, Fis family transcriptional regulator YP_613456.1 1561389 R 292414 CDS YP_613457.1 99081303 4077759 complement(1562751..1564553) 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (3.7e-29) histidine kinase A-like: (9.4e-10); KEGG: sil:SPO1891 C4-dicarboxylate transport sensor protein DctB, , ev=0.0, 80% identity; sensor signal transduction histidine kinase 1564553 4077759 TM1040_1462 Ruegeria sp. TM1040 sensor signal transduction histidine kinase YP_613457.1 1562751 R 292414 CDS YP_613458.1 99081304 4077760 complement(1564590..1565258) 1 NC_008044.1 catalyzes the formation of 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide and L-glutamine in purine biosynthesis; phosphoribosylformylglycinamidine synthase I 1565258 4077760 TM1040_1463 Ruegeria sp. TM1040 phosphoribosylformylglycinamidine synthase I YP_613458.1 1564590 R 292414 CDS YP_613459.1 99081305 4077761 complement(1565258..1565488) 1 NC_008044.1 PFAM: phosphoribosylformylglycinamidine synthetase PurS: (5.4e-32); KEGG: sil:SPO1888 phosphoribosylformylglycinamidine synthase, PurS protein, ev=2e-31, 88% identity; phosphoribosylformylglycinamidine synthase subunit PurS 1565488 4077761 TM1040_1464 Ruegeria sp. TM1040 phosphoribosylformylglycinamidine synthase subunit PurS YP_613459.1 1565258 R 292414 CDS YP_613460.2 161899029 4077762 complement(1565595..1566356) 1 NC_008044.1 catalyzes the formation of (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamido)succinate from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate and L-aspartate in purine biosynthesis; SAICAR synthase; phosphoribosylaminoimidazolesuccinocarboxamide synthase 1566356 4077762 TM1040_1465 Ruegeria sp. TM1040 phosphoribosylaminoimidazolesuccinocarboxamide synthase YP_613460.2 1565595 R 292414 CDS YP_613461.1 99081307 4077763 1566817..1567134 1 NC_008044.1 PFAM: protein of unknown function DUF1476: (7.2e-47); KEGG: rsp:RSP_2125 hypothetical protein, ev=9e-26, 57% identity; hypothetical protein 1567134 4077763 TM1040_1466 Ruegeria sp. TM1040 hypothetical protein YP_613461.1 1566817 D 292414 CDS YP_613462.1 99081308 4077764 1567246..1569153 1 NC_008044.1 KEGG: sil:SPO1885 membrane protein, , ev=1e-131, 45% identity; hypothetical protein 1569153 4077764 TM1040_1467 Ruegeria sp. TM1040 hypothetical protein YP_613462.1 1567246 D 292414 CDS YP_613463.1 99081309 4077765 1569216..1570238 1 NC_008044.1 catalyzes the formation of methionine from L-homocysteine and S-adenosyl-L-methionine; methionine synthase I 1570238 4077765 TM1040_1468 Ruegeria sp. TM1040 methionine synthase I YP_613463.1 1569216 D 292414 CDS YP_613464.1 99081310 4077766 complement(1570319..1571401) 1 NC_008044.1 PFAM: Radical SAM: (2.1e-23); SMART: Elongator protein 3/MiaB/NifB: (1.7e-12); KEGG: sil:SPO2159 radical SAM domain protein, ev=1e-153, 78% identity; radical SAM family protein 1571401 4077766 TM1040_1469 Ruegeria sp. TM1040 radical SAM family protein YP_613464.1 1570319 R 292414 CDS YP_613465.1 99081311 4077767 1571618..1572316 1 NC_008044.1 PFAM: Methionine synthase, B12-binding module, cap: (3.2e-14) cobalamin B12-binding: (3.7e-36); KEGG: sil:SPO2160 corrinoid methyltransferase protein, , ev=1e-118, 92% identity; 5-methyltetrahydrofolate--homocysteine methyltransferase 1572316 4077767 TM1040_1470 Ruegeria sp. TM1040 5-methyltetrahydrofolate--homocysteine methyltransferase YP_613465.1 1571618 D 292414 CDS YP_613466.1 99081312 4077768 1572318..1573064 1 NC_008044.1 KEGG: sil:SPO2162 hypothetical protein, ev=3e-72, 63% identity; hypothetical protein 1573064 4077768 TM1040_1471 Ruegeria sp. TM1040 hypothetical protein YP_613466.1 1572318 D 292414 CDS YP_613467.1 99081313 4077769 complement(1573147..1573569) 1 NC_008044.1 PFAM: Fe-S metabolism associated SufE: (1.6e-41); KEGG: sil:SPO2165 Fe-S metabolism associated family protein, ev=3e-57, 80% identity; cysteine desulfuration protein SufE 1573569 4077769 TM1040_1472 Ruegeria sp. TM1040 cysteine desulfuration protein SufE YP_613467.1 1573147 R 292414 CDS YP_613468.1 99081314 4077770 1573688..1574203 1 NC_008044.1 KEGG: sil:SPO2166 lipoprotein, , ev=4e-36, 51% identity; lipoprotein 1574203 4077770 TM1040_1473 Ruegeria sp. TM1040 lipoprotein YP_613468.1 1573688 D 292414 CDS YP_613469.1 99081315 4077771 complement(1574347..1575504) 1 NC_008044.1 TIGRFAM: ribonuclease D: (2.6e-133); PFAM: 3'-5' exonuclease: (4.6e-48); KEGG: sil:SPO2167 ribonuclease D, ev=1e-178, 81% identity; ribonuclease D 1575504 4077771 TM1040_1474 Ruegeria sp. TM1040 ribonuclease D YP_613469.1 1574347 R 292414 CDS YP_613470.1 99081316 4077772 complement(1575595..1576149) 1 NC_008044.1 TIGRFAM: phosphoribosylglycinamide formyltransferase: (1.3e-58); PFAM: formyl transferase-like: (4.9e-47); KEGG: sil:SPO2168 phosphoribosylglycinamide formyltransferase, ev=5e-75, 78% identity; phosphoribosylglycinamide formyltransferase 1576149 4077772 TM1040_1475 Ruegeria sp. TM1040 phosphoribosylglycinamide formyltransferase YP_613470.1 1575595 R 292414 CDS YP_613471.1 99081317 4077773 complement(1576197..1577243) 1 NC_008044.1 catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis; phosphoribosylaminoimidazole synthetase 1577243 4077773 TM1040_1476 Ruegeria sp. TM1040 phosphoribosylaminoimidazole synthetase YP_613471.1 1576197 R 292414 CDS YP_613472.1 99081318 4077774 complement(1577426..1578394) 1 NC_008044.1 TIGRFAM: Twin-arginine translocation pathway signal: (0.013); PFAM: beta-lactamase-like: (7.8e-21); KEGG: sil:SPO2170 metallo-beta-lactamase family protein, ev=1e-108, 62% identity; twin-arginine translocation pathway signal 1578394 4077774 TM1040_1477 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_613472.1 1577426 R 292414 CDS YP_613473.1 99081319 4077775 1578515..1579444 1 NC_008044.1 PFAM: regulatory protein, LysR: (2.6e-16) LysR, substrate-binding: (4.7e-32); KEGG: sil:SPO2171 transcriptional regulator, LysR family, ev=1e-115, 67% identity; LysR family transcriptional regulator 1579444 4077775 TM1040_1478 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_613473.1 1578515 D 292414 CDS YP_613474.1 99081320 4077776 complement(1579845..1581173) 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (3.2e-23) histidine kinase, HAMP region: (7.9e-12) histidine kinase A-like: (7.7e-12); KEGG: sil:SPO2173 sensor histidine kinase, ev=1e-126, 56% identity; sensor signal transduction histidine kinase 1581173 4077776 TM1040_1479 Ruegeria sp. TM1040 sensor signal transduction histidine kinase YP_613474.1 1579845 R 292414 CDS YP_613475.1 99081321 4077777 1581224..1582147 1 NC_008044.1 PFAM: beta-lactamase-like: (3.6e-24); KEGG: sil:SPO2174 metallo-beta-lactamase family protein, ev=1e-104, 62% identity; beta-lactamase-like protein 1582147 4077777 TM1040_1480 Ruegeria sp. TM1040 beta-lactamase-like protein YP_613475.1 1581224 D 292414 CDS YP_613476.1 99081322 4077778 complement(1582635..1583594) 1 NC_008044.1 PFAM: NAD-dependent epimerase/dehydratase: (3.1e-87) dTDP-4-dehydrorhamnose reductase: (1e-05); KEGG: rru:Rru_A0254 NAD-dependent epimerase/dehydratase, ev=1e-115, 65% identity; NAD-dependent epimerase/dehydratase 1583594 4077778 TM1040_1481 Ruegeria sp. TM1040 NAD-dependent epimerase/dehydratase YP_613476.1 1582635 R 292414 CDS YP_613477.1 99081323 4077779 complement(1583603..1584724) 1 NC_008044.1 TIGRFAM: GDP-mannose 4,6-dehydratase: (4.2e-257); PFAM: NAD-dependent epimerase/dehydratase: (1.7e-107); KEGG: vvy:VV0349 GDP-mannose-4,6-dehydratase, ev=0.0, 82% identity; GDP-mannose 4,6-dehydratase 1584724 4077779 TM1040_1482 Ruegeria sp. TM1040 GDP-mannose 4,6-dehydratase YP_613477.1 1583603 R 292414 CDS YP_613478.1 99081324 4077780 complement(1584788..1585987) 1 NC_008044.1 PFAM: DegT/DnrJ/EryC1/StrS aminotransferase: (1.3e-76) aromatic amino acid beta-eliminating lyase/threonine aldolase: (0.0031); KEGG: cac:CAC2178 predicted CDP-4-keto-6-deoxy-D-glucose-3-dehydrase, ev=1e-61, 32% identity; DegT/DnrJ/EryC1/StrS aminotransferase 1585987 4077780 TM1040_1483 Ruegeria sp. TM1040 DegT/DnrJ/EryC1/StrS aminotransferase YP_613478.1 1584788 R 292414 CDS YP_613479.1 99081325 4077781 complement(1585984..1586757) 1 NC_008044.1 PFAM: glycosyl transferase, family 2: (4.4e-26); KEGG: bfs:BF2599 LPS biosynthesis related glycosyltransferase, ev=7e-23, 32% identity; glycosyl transferase family protein 1586757 4077781 TM1040_1484 Ruegeria sp. TM1040 glycosyl transferase family protein YP_613479.1 1585984 R 292414 CDS YP_613480.1 99081326 4077041 complement(1586750..1587571) 1 NC_008044.1 PFAM: NAD-dependent epimerase/dehydratase: (3e-28) 3-beta hydroxysteroid dehydrogenase/isomerase: (0.0046) dTDP-4-dehydrorhamnose reductase: (2.1e-10) Male sterility-like: (0.00022); KEGG: rru:Rru_A1486 UDP-glucose 4-epimerase, ev=3e-16, 29% identity; NAD-dependent epimerase/dehydratase 1587571 4077041 TM1040_1485 Ruegeria sp. TM1040 NAD-dependent epimerase/dehydratase YP_613480.1 1586750 R 292414 CDS YP_613481.1 99081327 4077042 complement(1587568..1588521) 1 NC_008044.1 hypothetical protein 1588521 4077042 TM1040_1486 Ruegeria sp. TM1040 hypothetical protein YP_613481.1 1587568 R 292414 CDS YP_613482.1 99081328 4077043 1588830..1590218 1 NC_008044.1 KEGG: jan:Jann_1379 methyl-accepting chemotaxis sensory transducer with PAS/Pac sensor, ev=1e-117, 52% identity; TIGRFAM: PAS: (6.3e-18); PFAM: chemotaxis sensory transducer: (3.8e-78) PAS fold-3: (5.1e-19) PAS fold-4: (4e-08) PAS fold: (0.00084); SMART: PAC motif: (6.7e-09); methyl-accepting chemotaxis sensory transducer with Pas/Pac sensor 1590218 4077043 TM1040_1487 Ruegeria sp. TM1040 methyl-accepting chemotaxis sensory transducer with Pas/Pac sensor YP_613482.1 1588830 D 292414 CDS YP_613483.1 99081329 4077044 1591016..1593580 1 NC_008044.1 PFAM: Hemolysin-type calcium-binding region: (0.08); KEGG: jan:Jann_1066 hemolysin-type calcium-binding protein, ev=2e-80, 38% identity; hemolysin-type calcium-binding protein 1593580 4077044 TM1040_1488 Ruegeria sp. TM1040 hemolysin-type calcium-binding protein YP_613483.1 1591016 D 292414 CDS YP_613484.1 99081330 4077045 1593933..1595891 1 NC_008044.1 TIGRFAM: Acetate--CoA ligase: (0); PFAM: AMP-dependent synthetase and ligase: (1.2e-135); KEGG: sil:SPO1813 acetyl-coenzyme A synthetase, ev=0.0, 89% identity; acetyl-coenzyme A synthetase 1595891 4077045 TM1040_1489 Ruegeria sp. TM1040 acetyl-coenzyme A synthetase YP_613484.1 1593933 D 292414 CDS YP_613485.1 99081331 4077046 1595898..1596581 1 NC_008044.1 TIGRFAM: adenylate kinases: (9.7e-102); PFAM: adenylate kinase: (3.6e-86) adenylate kinase, lid region: (1.1e-09); KEGG: sil:SPO1812 adenylate kinase, ev=5e-88, 75% identity; adenylate kinase 1596581 4077046 TM1040_1490 Ruegeria sp. TM1040 adenylate kinase YP_613485.1 1595898 D 292414 CDS YP_613486.1 99081332 4077047 1596744..1597244 1 NC_008044.1 PFAM: flavin reductase-like, FMN-binding: (3.4e-36); KEGG: sil:SPO1806 flavin reductase domain protein, ev=2e-37, 48% identity; flavin reductase-like, FMN-binding 1597244 4077047 TM1040_1491 Ruegeria sp. TM1040 flavin reductase-like, FMN-binding YP_613486.1 1596744 D 292414 CDS YP_613487.1 99081333 4077048 complement(1597298..1598041) 1 NC_008044.1 PFAM: 4Fe-4S ferredoxin, iron-sulfur binding: (6.7e-06); KEGG: vvy:VV1703 ferredoxin, ev=2e-10, 41% identity; 4Fe-4S ferredoxin 1598041 4077048 TM1040_1492 Ruegeria sp. TM1040 4Fe-4S ferredoxin YP_613487.1 1597298 R 292414 CDS YP_613488.1 99081334 4077049 complement(1598143..1599129) 1 NC_008044.1 KEGG: sil:SPO1788 ABC transporter, periplasmic substrate-binding protein, ev=1e-150, 80% identity; ABC transporter substrate-binding protein 1599129 4077049 TM1040_1493 Ruegeria sp. TM1040 ABC transporter substrate-binding protein YP_613488.1 1598143 R 292414 CDS YP_613489.1 99081335 4077050 complement(1599332..1600177) 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (4e-31); KEGG: sil:SPO1787 ABC transporter, permease protein, ev=1e-132, 83% identity; binding-protein-dependent transport system inner membrane protein 1600177 4077050 TM1040_1494 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_613489.1 1599332 R 292414 CDS YP_613490.1 99081336 4077051 complement(1600230..1601147) 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1.1e-33); KEGG: sil:SPO1786 ABC transporter, permease protein, ev=1e-136, 81% identity; binding-protein-dependent transport system inner membrane protein 1601147 4077051 TM1040_1495 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_613490.1 1600230 R 292414 CDS YP_613491.1 99081337 4077052 complement(1601172..1601939) 1 NC_008044.1 PFAM: ABC transporter related: (4.7e-47); SMART: ATPase: (1.6e-15); KEGG: sil:SPO1785 ABC transporter, ATP-binding protein, ev=1e-125, 85% identity; ABC transporter 1601939 4077052 TM1040_1496 Ruegeria sp. TM1040 ABC transporter YP_613491.1 1601172 R 292414 CDS YP_613492.1 99081338 4077053 complement(1602053..1603507) 1 NC_008044.1 catalyzes the hydrolytic cleavage of hydantoin with aromatic side chains at the 5'position; phenylhydantoinase 1603507 4077053 TM1040_1497 Ruegeria sp. TM1040 phenylhydantoinase YP_613492.1 1602053 R 292414 CDS YP_613493.1 99081339 4077054 complement(1603637..1604887) 1 NC_008044.1 allantoate amidohydrolase and N-carbamoyl-L-amino acid amidohydrolase are very similar; the allantoate amidohydrolase from Escherichia coli forms a dimer and binds zinc ions for catalytic activity and catalyzes the conversion of allantoate to (S)-ureidoglycolate and ammonia; carbamoyl amidohydrolase from Bacillus sp. converts N-carbamoyl amino acids to amino acids, ammonia, and carbon dioxide; allantoate amidohydrolase 1604887 4077054 TM1040_1498 Ruegeria sp. TM1040 allantoate amidohydrolase YP_613493.1 1603637 R 292414 CDS YP_613494.1 99081340 4077055 1605177..1605788 1 NC_008044.1 PFAM: regulatory protein, TetR: (1.6e-17) Tetracycline transcriptional regulator YcdC-like-like: (9.4e-60); KEGG: sil:SPO1780 transcriptional regulator, TetR family, ev=2e-74, 67% identity; TetR family transcriptional regulator 1605788 4077055 TM1040_1499 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_613494.1 1605177 D 292414 CDS YP_613495.1 99081341 4077056 complement(1606078..1607382) 1 NC_008044.1 catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines; dihydropyrimidine dehydrogenase 1607382 4077056 TM1040_1500 Ruegeria sp. TM1040 dihydropyrimidine dehydrogenase YP_613495.1 1606078 R 292414 CDS YP_613496.1 99081342 4077057 complement(1607447..1608781) 1 NC_008044.1 function undetermined; similar to glutamate synthase beta subunit and related oxidoreductases which transfer electrons from NADPH to an acceptor protein or protein domain; oxidoreductase 1608781 4077057 TM1040_1501 Ruegeria sp. TM1040 oxidoreductase YP_613496.1 1607447 R 292414 CDS YP_613497.1 99081343 4077058 complement(1609074..1609340) 1 NC_008044.1 KEGG: jan:Jann_2635 hypothetical protein, ev=2e-29, 79% identity; hypothetical protein 1609340 4077058 TM1040_1502 Ruegeria sp. TM1040 hypothetical protein YP_613497.1 1609074 R 292414 CDS YP_613498.1 99081344 4077059 1609548..1609763 1 NC_008044.1 KEGG: sil:SPO1032 hypothetical protein, ev=3e-18, 60% identity; hypothetical protein 1609763 4077059 TM1040_1503 Ruegeria sp. TM1040 hypothetical protein YP_613498.1 1609548 D 292414 CDS YP_613499.1 99081345 4077060 complement(1609805..1610020) 1 NC_008044.1 KEGG: sil:SPO1031 hypothetical protein, ev=4e-08, 40% identity; hypothetical protein 1610020 4077060 TM1040_1504 Ruegeria sp. TM1040 hypothetical protein YP_613499.1 1609805 R 292414 CDS YP_613500.1 99081346 4077061 1610302..1610730 1 NC_008044.1 PFAM: protein of unknown function DUF442: (3.1e-44); KEGG: sil:SPO1027 conserved hypothetical protein TIGR01244, ev=6e-48, 67% identity; hypothetical protein 1610730 4077061 TM1040_1505 Ruegeria sp. TM1040 hypothetical protein YP_613500.1 1610302 D 292414 CDS YP_613501.1 99081347 4077062 complement(1610887..1612149) 1 NC_008044.1 PFAM: surface presentation of antigens (SPOA) protein: (0.0028); KEGG: sil:SPO1026 hypothetical protein, ev=2e-49, 33% identity; surface presentation of antigens (SPOA) protein 1612149 4077062 TM1040_1506 Ruegeria sp. TM1040 surface presentation of antigens (SPOA) protein YP_613501.1 1610887 R 292414 CDS YP_613502.1 99081348 4077063 complement(1612226..1614916) 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (6.9e-31) histidine kinase A-like: (9.4e-22); KEGG: sil:SPO1025 sensor histidine kinase, ev=0.0, 74% identity; sensor signal transduction histidine kinase 1614916 4077063 TM1040_1507 Ruegeria sp. TM1040 sensor signal transduction histidine kinase YP_613502.1 1612226 R 292414 CDS YP_613503.1 99081349 4077064 complement(1614913..1615326) 1 NC_008044.1 KEGG: sil:SPO1024 hypothetical protein, ev=8e-13, 52% identity; hypothetical protein 1615326 4077064 TM1040_1508 Ruegeria sp. TM1040 hypothetical protein YP_613503.1 1614913 R 292414 CDS YP_613504.1 99081350 4077065 complement(1615337..1615750) 1 NC_008044.1 PFAM: response regulator receiver: (5.6e-31); KEGG: sil:SPO1023 response regulator, ev=2e-47, 77% identity; response regulator receiver protein 1615750 4077065 TM1040_1509 Ruegeria sp. TM1040 response regulator receiver protein YP_613504.1 1615337 R 292414 CDS YP_613505.1 99081351 4077066 complement(1615849..1617180) 1 NC_008044.1 PFAM: helix-turn-helix motif: (5e-13); KEGG: sil:SPO1022 transcriptional regulator, , ev=1e-145, 62% identity; XRE family transcriptional regulator 1617180 4077066 TM1040_1510 Ruegeria sp. TM1040 XRE family transcriptional regulator YP_613505.1 1615849 R 292414 CDS YP_613506.1 99081352 4077067 1617419..1618765 1 NC_008044.1 TIGRFAM: Twin-arginine translocation pathway signal: (0.015); KEGG: sil:SPO1021 branched-chain amino acid ABC transporter, periplasmic substrate-binding protein, ev=0.0, 77% identity; twin-arginine translocation pathway signal 1618765 4077067 TM1040_1511 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_613506.1 1617419 D 292414 CDS YP_613507.1 99081353 4077068 1618965..1619996 1 NC_008044.1 PFAM: inner-membrane translocator: (8.4e-24); KEGG: sil:SPO1020 branched-chain amino acid ABC transporter, permease protein, ev=1e-163, 84% identity; inner-membrane translocator 1619996 4077068 TM1040_1512 Ruegeria sp. TM1040 inner-membrane translocator YP_613507.1 1618965 D 292414 CDS YP_613508.1 99081354 4077069 1620001..1621200 1 NC_008044.1 PFAM: inner-membrane translocator: (3.8e-17); KEGG: sil:SPO1019 branched-chain amino acid ABC transporter, permease protein, ev=1e-179, 77% identity; inner-membrane translocator 1621200 4077069 TM1040_1513 Ruegeria sp. TM1040 inner-membrane translocator YP_613508.1 1620001 D 292414 CDS YP_613509.1 99081355 4077070 1621211..1621966 1 NC_008044.1 PFAM: ABC transporter related: (3.8e-45); SMART: ATPase: (8.6e-09); KEGG: sil:SPO1018 branched-chain amino acid ABC transporter, ATP-binding protein, ev=1e-123, 88% identity; ABC transporter 1621966 4077070 TM1040_1514 Ruegeria sp. TM1040 ABC transporter YP_613509.1 1621211 D 292414 CDS YP_613510.1 99081356 4077071 1621985..1622740 1 NC_008044.1 PFAM: ABC transporter related: (5.4e-43); SMART: ATPase: (1.4e-10); KEGG: sil:SPO1017 branched-chain amino acid ABC transporter, ATP-binding protein, ev=1e-126, 90% identity; ABC transporter 1622740 4077071 TM1040_1515 Ruegeria sp. TM1040 ABC transporter YP_613510.1 1621985 D 292414 CDS YP_613511.1 99081357 4077072 1622952..1623500 1 NC_008044.1 PFAM: regulatory protein, LuxR: (1.7e-17); KEGG: sil:SPO1012 transcriptional regulator, LuxR family, ev=2e-59, 63% identity; LuxR family transcriptional regulator 1623500 4077072 TM1040_1516 Ruegeria sp. TM1040 LuxR family transcriptional regulator YP_613511.1 1622952 D 292414 CDS YP_613512.1 99081358 4077073 1623674..1624165 1 NC_008044.1 TIGRFAM: acetyl-CoA carboxylase, biotin carboxyl carrier protein: (6.2e-38); PFAM: biotin/lipoyl attachment: (6e-29); KEGG: sil:SPO1011 acetyl-CoA carboxylase, biotin carboxyl carrier protein, ev=3e-60, 74% identity; biotin carboxyl carrier protein 1624165 4077073 TM1040_1517 Ruegeria sp. TM1040 biotin carboxyl carrier protein YP_613512.1 1623674 D 292414 CDS YP_613513.1 99081359 4077074 1624175..1625524 1 NC_008044.1 an AccC homodimer forms the biotin carboxylase subunit of the acetyl CoA carboxylase, an enzyme that catalyzes the formation of malonyl-CoA, which in turn controls the rate of fatty acid metabolism; acetyl-CoA carboxylase biotin carboxylase subunit 1625524 4077074 TM1040_1518 Ruegeria sp. TM1040 acetyl-CoA carboxylase biotin carboxylase subunit YP_613513.1 1624175 D 292414 CDS YP_613514.1 99081360 4077075 1625590..1626222 1 NC_008044.1 leucyltransferase; phenylalanyltransferse; functions in the N-end rule pathway; transfers Leu, Phe, Met, from aminoacyl-tRNAs to N-terminal of proteins with Arg or Lys; leucyl/phenylalanyl-tRNA--protein transferase 1626222 aat 4077075 aat Ruegeria sp. TM1040 leucyl/phenylalanyl-tRNA--protein transferase YP_613514.1 1625590 D 292414 CDS YP_613515.1 99081361 4077076 complement(1626186..1626623) 1 NC_008044.1 KEGG: sil:SPO1008 hypothetical protein, ev=3e-32, 69% identity; hypothetical protein 1626623 4077076 TM1040_1520 Ruegeria sp. TM1040 hypothetical protein YP_613515.1 1626186 R 292414 CDS YP_613516.1 99081362 4077077 complement(1626623..1627075) 1 NC_008044.1 PFAM: Mammalian cell entry related: (8.4e-22); KEGG: sil:SPO1007 ABC transport system substrate-binding protein, ev=4e-51, 71% identity; hypothetical protein 1627075 4077077 TM1040_1521 Ruegeria sp. TM1040 hypothetical protein YP_613516.1 1626623 R 292414 CDS YP_613517.1 99081363 4077078 complement(1627146..1627532) 1 NC_008044.1 Provides the input to the respiratory chain from the NAD-linked dehydrogenases of the citric acid cycle. The complex couples the oxidation of NADH and the reduction of ubiquinone, to the generation of a proton gradient which is then used for ATP synthesis; NADH dehydrogenase 1627532 4077078 TM1040_1522 Ruegeria sp. TM1040 NADH dehydrogenase YP_613517.1 1627146 R 292414 CDS YP_613518.1 99081364 4077079 complement(1627653..1628045) 1 NC_008044.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase: (2e-08); KEGG: ppu:PP3509 glyoxalase family protein, ev=5e-37, 59% identity; glyoxalase/bleomycin resistance protein/dioxygenase 1628045 4077079 TM1040_1523 Ruegeria sp. TM1040 glyoxalase/bleomycin resistance protein/dioxygenase YP_613518.1 1627653 R 292414 CDS YP_613519.1 99081365 4075822 complement(1628057..1628422) 1 NC_008044.1 PFAM: Endoribonuclease L-PSP: (2.8e-20); KEGG: sil:SPO1005 endoribonuclease L-PSP family protein, ev=7e-52, 84% identity; endoribonuclease L-PSP 1628422 4075822 TM1040_1524 Ruegeria sp. TM1040 endoribonuclease L-PSP YP_613519.1 1628057 R 292414 CDS YP_613520.1 99081366 4075823 complement(1628514..1629239) 1 NC_008044.1 PFAM: dienelactone hydrolase: (3.5e-35); KEGG: mca:MCA1803 dienelactone hydrolase family protein, ev=2e-55, 48% identity; dienelactone hydrolase 1629239 4075823 TM1040_1525 Ruegeria sp. TM1040 dienelactone hydrolase YP_613520.1 1628514 R 292414 CDS YP_613521.1 99081367 4075824 complement(1629344..1630609) 1 NC_008044.1 binds and unfolds substrates as part of the ClpXP protease; ATP-dependent protease ATP-binding subunit ClpX 1630609 clpX 4075824 clpX Ruegeria sp. TM1040 ATP-dependent protease ATP-binding subunit ClpX YP_613521.1 1629344 R 292414 CDS YP_613522.1 99081368 4075825 complement(1630761..1631417) 1 NC_008044.1 hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates; ATP-dependent Clp protease proteolytic subunit 1631417 clpP 4075825 clpP Ruegeria sp. TM1040 ATP-dependent Clp protease proteolytic subunit YP_613522.1 1630761 R 292414 CDS YP_613523.1 99081369 4075826 1631689..1632696 1 NC_008044.1 PFAM: helix-turn-helix, AraC type: (1.9e-09) ThiJ/PfpI: (0.0001); KEGG: sil:SPO1002 transcriptional regulator, AraC family, ev=1e-118, 60% identity; transcriptional regulator 1632696 4075826 TM1040_1528 Ruegeria sp. TM1040 transcriptional regulator YP_613523.1 1631689 D 292414 CDS YP_613524.1 99081370 4075827 1632820..1633362 1 NC_008044.1 KEGG: sil:SPO2884 hypothetical protein, ev=1e-45, 63% identity; hypothetical protein 1633362 4075827 TM1040_1529 Ruegeria sp. TM1040 hypothetical protein YP_613524.1 1632820 D 292414 CDS YP_613525.1 99081371 4075828 1633394..1635007 1 NC_008044.1 PFAM: thiamine pyrophosphate enzyme-like TPP-binding: (8.2e-35) thiamine pyrophosphate enzyme, central region: (2.8e-11) thiamine pyrophosphate enzyme-like TPP binding region: (4e-34); KEGG: sil:SPO2885 acetolactate synthase, catabolic, , ev=0.0, 70% identity; thiamine pyrophosphate enzyme-like protein 1635007 4075828 TM1040_1530 Ruegeria sp. TM1040 thiamine pyrophosphate enzyme-like protein YP_613525.1 1633394 D 292414 CDS YP_613526.1 99081372 4075829 1634991..1636193 1 NC_008044.1 PFAM: L-carnitine dehydratase/bile acid-inducible protein F: (2.5e-66); KEGG: sil:SPO2886 CAIB/BAIF family protein, ev=1e-155, 69% identity; L-carnitine dehydratase/bile acid-inducible protein F 1636193 4075829 TM1040_1531 Ruegeria sp. TM1040 L-carnitine dehydratase/bile acid-inducible protein F YP_613526.1 1634991 D 292414 CDS YP_613527.1 99081373 4075830 1636457..1637821 1 NC_008044.1 KEGG: sil:SPO2887 hypothetical protein, ev=1e-167, 63% identity; hypothetical protein 1637821 4075830 TM1040_1532 Ruegeria sp. TM1040 hypothetical protein YP_613527.1 1636457 D 292414 CDS YP_613528.1 99081374 4075831 1637844..1639151 1 NC_008044.1 KEGG: sil:SPO2888 membrane protein, , ev=1e-151, 61% identity; hypothetical protein 1639151 4075831 TM1040_1533 Ruegeria sp. TM1040 hypothetical protein YP_613528.1 1637844 D 292414 CDS YP_613529.1 99081375 4075832 1639148..1640674 1 NC_008044.1 involved in the biosynthesis of osmoregulated periplasmic glucans; required for the assembly of the polyglucose structure of glucan; glucan biosynthesis protein G 1640674 mdoG 4075832 mdoG Ruegeria sp. TM1040 glucan biosynthesis protein G YP_613529.1 1639148 D 292414 CDS YP_613530.1 99081376 4075833 1640675..1642567 1 NC_008044.1 necessary for biosynthesis of osmoregulated periplasmic glucans possibly involved in the transfer to the periplasmic space; glucosyltransferase MdoH 1642567 4075833 TM1040_1535 Ruegeria sp. TM1040 glucosyltransferase MdoH YP_613530.1 1640675 D 292414 CDS YP_613531.1 99081377 4075834 complement(1642659..1643489) 1 NC_008044.1 KEGG: sil:SPO2891 polyhydroxybutyrate depolymerase, ev=2e-74, 51% identity; polyhydroxybutyrate depolymerase 1643489 4075834 TM1040_1536 Ruegeria sp. TM1040 polyhydroxybutyrate depolymerase YP_613531.1 1642659 R 292414 CDS YP_613532.1 99081378 4075835 complement(1643486..1644013) 1 NC_008044.1 SMART: Rhodanese-like: (6.8e-12); KEGG: sil:SPO2892 hypothetical protein, ev=4e-32, 54% identity; rhodanese-like protein 1644013 4075835 TM1040_1537 Ruegeria sp. TM1040 rhodanese-like protein YP_613532.1 1643486 R 292414 CDS YP_613533.1 99081379 4075836 1644301..1647162 1 NC_008044.1 subunit A of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved with K+; monovalent cation/H+ antiporter subunit A 1647162 4075836 TM1040_1538 Ruegeria sp. TM1040 monovalent cation/H+ antiporter subunit A YP_613533.1 1644301 D 292414 CDS YP_613534.1 99081380 4075837 1647167..1647520 1 NC_008044.1 subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; monovalent cation/H+ antiporter subunit C 1647520 4075837 TM1040_1539 Ruegeria sp. TM1040 monovalent cation/H+ antiporter subunit C YP_613534.1 1647167 D 292414 CDS YP_613535.1 99081381 4075838 1647517..1649139 1 NC_008044.1 subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone; monovalent cation/H+ antiporter subunit D 1649139 4075838 TM1040_1540 Ruegeria sp. TM1040 monovalent cation/H+ antiporter subunit D YP_613535.1 1647517 D 292414 CDS YP_613536.1 99081382 4075839 1649139..1649636 1 NC_008044.1 subunit E of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport; monovalent cation/H+ antiporter subunit E 1649636 4075839 TM1040_1541 Ruegeria sp. TM1040 monovalent cation/H+ antiporter subunit E YP_613536.1 1649139 D 292414 CDS YP_613537.1 99081383 4075840 1649633..1649902 1 NC_008044.1 subunit F of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport; monovalent cation/H+ antiporter subunit F 1649902 4075840 TM1040_1542 Ruegeria sp. TM1040 monovalent cation/H+ antiporter subunit F YP_613537.1 1649633 D 292414 CDS YP_613538.1 99081384 4075841 1649913..1650290 1 NC_008044.1 subunit G of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport; monovalent cation/H+ antiporter subunit G 1650290 4075841 TM1040_1543 Ruegeria sp. TM1040 monovalent cation/H+ antiporter subunit G YP_613538.1 1649913 D 292414 CDS YP_613539.1 99081385 4075842 1650329..1652491 1 NC_008044.1 PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase: (0.00032) AIR synthase related protein-like: (1.6e-16); KEGG: sil:SPO2899 selenide,water dikinase, , ev=0.0, 63% identity; AIR synthase-like protein 1652491 4075842 TM1040_1544 Ruegeria sp. TM1040 AIR synthase-like protein YP_613539.1 1650329 D 292414 CDS YP_613540.1 99081386 4075843 complement(1652518..1653561) 1 NC_008044.1 catalyzes the selenophosphate-dependent transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA; tRNA 2-selenouridine synthase 1653561 4075843 TM1040_1545 Ruegeria sp. TM1040 tRNA 2-selenouridine synthase YP_613540.1 1652518 R 292414 CDS YP_613541.1 99081387 4075844 1653637..1654122 1 NC_008044.1 PFAM: regulatory protein, MarR: (1.6e-14); KEGG: bja:bll4221 transcriptional regulatory protein, ev=5e-27, 48% identity; MarR family transcriptional regulator 1654122 4075844 TM1040_1546 Ruegeria sp. TM1040 MarR family transcriptional regulator YP_613541.1 1653637 D 292414 CDS YP_613542.1 99081388 4075845 complement(1654155..1654457) 1 NC_008044.1 KEGG: bte:BTH_I2061 hypothetical protein, ev=8e-11, 45% identity; hypothetical protein 1654457 4075845 TM1040_1547 Ruegeria sp. TM1040 hypothetical protein YP_613542.1 1654155 R 292414 CDS YP_613543.1 99081389 4075846 complement(1654635..1656215) 1 NC_008044.1 PFAM: metallophosphoesterase: (3.6e-21) 5'-Nucleotidase-like: (3e-67); KEGG: sil:SPO2904 Ser/Thr protein phosphatase/nucleotidase, , ev=0.0, 62% identity; 5'-nucleotidase 1656215 4075846 TM1040_1548 Ruegeria sp. TM1040 5'-nucleotidase YP_613543.1 1654635 R 292414 CDS YP_613544.1 99081390 4075847 1656405..1656743 1 NC_008044.1 PFAM: protein of unknown function DUF952: (7.4e-46); KEGG: sil:SPO2905 hypothetical protein, ev=9e-45, 77% identity; hypothetical protein 1656743 4075847 TM1040_1549 Ruegeria sp. TM1040 hypothetical protein YP_613544.1 1656405 D 292414 CDS YP_613545.1 99081391 4075848 1656807..1657865 1 NC_008044.1 catalyzes the conversion of dihydroorotate to orotate in the pyrimidine biosynthesis pathway; uses a flavin nucleotide as an essential cofactor; class 2 enzymes are monomeric and compared to the class 1 class 2 possess an extended N terminus, which plays a role in the membrane association of the enzyme and provides the binding site for the respiratory quinones that serve as physiological electron acceptors; dihydroorotate dehydrogenase 2 1657865 4075848 TM1040_1550 Ruegeria sp. TM1040 dihydroorotate dehydrogenase 2 YP_613545.1 1656807 D 292414 CDS YP_613546.1 99081392 4075849 complement(1658100..1659422) 1 NC_008044.1 TIGRFAM: MATE efflux family protein: (4e-69); PFAM: multi antimicrobial extrusion protein MatE: (3.6e-17); KEGG: rsp:RSP_2204 multidrug efflux pump, MATE family, ev=1e-154, 63% identity; MATE efflux family protein 1659422 4075849 TM1040_1551 Ruegeria sp. TM1040 MATE efflux family protein YP_613546.1 1658100 R 292414 CDS YP_613547.1 99081393 4075850 complement(1659441..1659959) 1 NC_008044.1 KEGG: rsp:RSP_2203 hypothetical protein, ev=1e-63, 72% identity; hypothetical protein 1659959 4075850 TM1040_1552 Ruegeria sp. TM1040 hypothetical protein YP_613547.1 1659441 R 292414 CDS YP_613548.1 99081394 4075851 complement(1659956..1660378) 1 NC_008044.1 TIGRFAM: Phenylacetic acid degradation-related protein: (4.8e-17); PFAM: thioesterase superfamily: (2.1e-16); KEGG: sil:SPO2911 thioesterase family protein, ev=1e-58, 78% identity; phenylacetic acid degradation-related protein 1660378 4075851 TM1040_1553 Ruegeria sp. TM1040 phenylacetic acid degradation-related protein YP_613548.1 1659956 R 292414 CDS YP_613549.1 99081395 4075852 1660504..1660872 1 NC_008044.1 PFAM: regulatory protein, MerR: (3e-05); KEGG: sil:SPO2912 transcriptional regulator, MerR family, ev=3e-46, 75% identity; MerR family transcriptional regulator 1660872 4075852 TM1040_1554 Ruegeria sp. TM1040 MerR family transcriptional regulator YP_613549.1 1660504 D 292414 CDS YP_613550.1 99081396 4075853 1660885..1661163 1 NC_008044.1 hypothetical protein 1661163 4075853 TM1040_1555 Ruegeria sp. TM1040 hypothetical protein YP_613550.1 1660885 D 292414 CDS YP_613551.1 99081397 4075854 1661412..1661813 1 NC_008044.1 PFAM: regulatory protein, MerR: (2.3e-10); KEGG: sil:SPO2914 transcriptional regulator, MerR family, ev=1e-57, 81% identity; MerR family transcriptional regulator 1661813 4075854 TM1040_1556 Ruegeria sp. TM1040 MerR family transcriptional regulator YP_613551.1 1661412 D 292414 CDS YP_613552.1 99081398 4075855 1661878..1663659 1 NC_008044.1 PFAM: acyl-CoA dehydrogenase-like: (3.9e-22); KEGG: sil:SPO2915 acyl-CoA dehydrogenase family protein, ev=0.0, 87% identity; acyl-CoA dehydrogenase 1663659 4075855 TM1040_1557 Ruegeria sp. TM1040 acyl-CoA dehydrogenase YP_613552.1 1661878 D 292414 CDS YP_613553.1 99081399 4075856 1663752..1663964 1 NC_008044.1 KEGG: sil:SPO2916 hypothetical protein, ev=8e-29, 87% identity; hypothetical protein 1663964 4075856 TM1040_1558 Ruegeria sp. TM1040 hypothetical protein YP_613553.1 1663752 D 292414 CDS YP_613554.1 99081400 4075857 1664004..1665167 1 NC_008044.1 PFAM: acyl-CoA dehydrogenase-like: (3.6e-53) Acyl-CoA dehydrogenase, type 2-like: (1.5e-06); KEGG: bur:Bcep18194_C7184 acyl-CoA dehydrogenase, ev=1e-133, 58% identity; acyl-CoA dehydrogenase 1665167 4075857 TM1040_1559 Ruegeria sp. TM1040 acyl-CoA dehydrogenase YP_613554.1 1664004 D 292414 CDS YP_613555.1 99081401 4075858 1665453..1666085 1 NC_008044.1 PFAM: glutathione S-transferase-like: (1.3e-10); KEGG: sil:SPO2917 glutathione S-transferase family protein, ev=1e-94, 76% identity; glutathione S-transferase 1666085 4075858 TM1040_1560 Ruegeria sp. TM1040 glutathione S-transferase YP_613555.1 1665453 D 292414 CDS YP_613556.1 99081402 4075859 1666096..1667307 1 NC_008044.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation; acetyl-CoA acetyltransferase 1667307 4075859 TM1040_1561 Ruegeria sp. TM1040 acetyl-CoA acetyltransferase YP_613556.1 1666096 D 292414 CDS YP_613557.1 99081403 4075860 1667347..1669548 1 NC_008044.1 PFAM: Enoyl-CoA hydratase/isomerase: (3.8e-25) 3-hydroxyacyl-CoA dehydrogenase-like: (6.6e-24) 3-hydroxyacyl-CoA dehydrogenase, NAD-binding: (9.5e-85) NAD-dependent glycerol-3-phosphate dehydrogenase-like: (0.00045); KEGG: sil:SPO2920 fatty oxidation complex, alpha subunit, ev=0.0, 86% identity; 3-hydroxyacyl-CoA dehydrogenase 1669548 4075860 TM1040_1562 Ruegeria sp. TM1040 3-hydroxyacyl-CoA dehydrogenase YP_613557.1 1667347 D 292414 CDS YP_613558.1 99081404 4078372 complement(1669877..1670569) 1 NC_008044.1 KEGG: sil:SPO2921 hypothetical protein, ev=2e-35, 41% identity; hypothetical protein 1670569 4078372 TM1040_1563 Ruegeria sp. TM1040 hypothetical protein YP_613558.1 1669877 R 292414 CDS YP_613559.1 99081405 4078373 complement(1670697..1671362) 1 NC_008044.1 KEGG: sil:SPO2922 hypothetical protein, ev=1e-70, 59% identity; hypothetical protein 1671362 4078373 TM1040_1564 Ruegeria sp. TM1040 hypothetical protein YP_613559.1 1670697 R 292414 CDS YP_613560.1 99081406 4078374 1671523..1673154 1 NC_008044.1 PFAM: AMP-dependent synthetase and ligase: (5.5e-105); KEGG: jan:Jann_2979 AMP-dependent synthetase and ligase, ev=0.0, 72% identity; AMP-dependent synthetase/ligase 1673154 4078374 TM1040_1565 Ruegeria sp. TM1040 AMP-dependent synthetase/ligase YP_613560.1 1671523 D 292414 CDS YP_613561.1 99081407 4078375 complement(1673331..1673972) 1 NC_008044.1 KEGG: vvy:VV1861 hypothetical protein, ev=5e-27, 41% identity; hypothetical protein 1673972 4078375 TM1040_1566 Ruegeria sp. TM1040 hypothetical protein YP_613561.1 1673331 R 292414 CDS YP_613562.1 99081408 4078376 1674284..1675339 1 NC_008044.1 KEGG: sil:SPO2924 hypothetical protein, ev=1e-107, 56% identity; hypothetical protein 1675339 4078376 TM1040_1567 Ruegeria sp. TM1040 hypothetical protein YP_613562.1 1674284 D 292414 CDS YP_613563.1 99081409 4078377 complement(1675407..1676660) 1 NC_008044.1 PFAM: Sporulation related: (3e-05); KEGG: jan:Jann_2982 hypothetical protein, ev=3e-32, 30% identity; sporulation related protein 1676660 4078377 TM1040_1568 Ruegeria sp. TM1040 sporulation related protein YP_613563.1 1675407 R 292414 CDS YP_613564.1 99081410 4078378 complement(1676842..1677474) 1 NC_008044.1 Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate; uracil phosphoribosyltransferase 1677474 upp 4078378 upp Ruegeria sp. TM1040 uracil phosphoribosyltransferase YP_613564.1 1676842 R 292414 CDS YP_613565.1 99081411 4078379 complement(1677559..1678773) 1 NC_008044.1 catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose; phosphopentomutase 1678773 4078379 TM1040_1570 Ruegeria sp. TM1040 phosphopentomutase YP_613565.1 1677559 R 292414 CDS YP_613566.1 99081412 4078380 complement(1678773..1680077) 1 NC_008044.1 Catalyzes the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate; thymidine phosphorylase 1680077 deoA 4078380 deoA Ruegeria sp. TM1040 thymidine phosphorylase YP_613566.1 1678773 R 292414 CDS YP_613567.1 99081413 4078381 complement(1680082..1680576) 1 NC_008044.1 TIGRFAM: Cytidine deaminase, homotetrameric: (9.3e-42); PFAM: CMP/dCMP deaminase, zinc-binding: (3.8e-13); KEGG: sil:SPO2930 cytidine deaminase, ev=3e-50, 74% identity; cytidine deaminase 1680576 4078381 TM1040_1572 Ruegeria sp. TM1040 cytidine deaminase YP_613567.1 1680082 R 292414 CDS YP_613568.1 99081414 4078382 1680851..1683130 1 NC_008044.1 NAD-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; does not decarboxylate oxaloacetate; malic enzyme 1683130 4078382 TM1040_1573 Ruegeria sp. TM1040 malic enzyme YP_613568.1 1680851 D 292414 CDS YP_613569.1 99081415 4078383 1683467..1685359 1 NC_008044.1 PFAM: AMP-dependent synthetase and ligase: (2.7e-112); KEGG: sil:SPO2934 propionate--CoA ligase, ev=0.0, 85% identity; AMP-dependent synthetase/ligase 1685359 4078383 TM1040_1574 Ruegeria sp. TM1040 AMP-dependent synthetase/ligase YP_613569.1 1683467 D 292414 CDS YP_613570.1 99081416 4078384 complement(1685432..1685641) 1 NC_008044.1 PFAM: CsbD-like: (3.4e-09); KEGG: noc:Noc_0274 CsbD-like protein, ev=6e-19, 60% identity; CsbD-like protein 1685641 4078384 TM1040_1575 Ruegeria sp. TM1040 CsbD-like protein YP_613570.1 1685432 R 292414 CDS YP_613571.1 99081417 4078385 complement(1685763..1686308) 1 NC_008044.1 hypothetical protein 1686308 4078385 TM1040_1576 Ruegeria sp. TM1040 hypothetical protein YP_613571.1 1685763 R 292414 CDS YP_613572.1 99081418 4078386 1686460..1687896 1 NC_008044.1 catalyzes the hydrolysis of a monocarboxylic acid amid to form a monocarboxylate and ammonia; amidase 1687896 4078386 TM1040_1577 Ruegeria sp. TM1040 amidase YP_613572.1 1686460 D 292414 CDS YP_613573.1 99081419 4078387 complement(1688007..1688762) 1 NC_008044.1 catalyzes the phosphorylation of NAD to NADP; inorganic polyphosphate/ATP-NAD kinase 1688762 ppnK 4078387 ppnK Ruegeria sp. TM1040 inorganic polyphosphate/ATP-NAD kinase YP_613573.1 1688007 R 292414 CDS YP_613574.1 99081420 4078388 1688939..1690234 1 NC_008044.1 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate; serine hydroxymethyltransferase 1690234 glyA 4078388 glyA Ruegeria sp. TM1040 serine hydroxymethyltransferase YP_613574.1 1688939 D 292414 CDS YP_613575.1 99081421 4078389 1690351..1691043 1 NC_008044.1 PFAM: protein of unknown function DUF159: (2e-25); KEGG: rsp:RSP_2605 hypothetical protein, ev=4e-30, 35% identity; hypothetical protein 1691043 4078389 TM1040_1580 Ruegeria sp. TM1040 hypothetical protein YP_613575.1 1690351 D 292414 CDS YP_613576.1 99081422 4078390 complement(1691081..1691368) 1 NC_008044.1 KEGG: jan:Jann_2992 hypothetical protein, ev=6e-30, 69% identity; hypothetical protein 1691368 4078390 TM1040_1581 Ruegeria sp. TM1040 hypothetical protein YP_613576.1 1691081 R 292414 CDS YP_613577.1 99081423 4078391 complement(1691455..1692153) 1 NC_008044.1 KEGG: jan:Jann_2993 phage shock protein A, PspA, ev=3e-54, 53% identity; phage shock protein A, PspA 1692153 4078391 TM1040_1582 Ruegeria sp. TM1040 phage shock protein A, PspA YP_613577.1 1691455 R 292414 CDS YP_613578.1 99081424 4078392 complement(1692230..1692826) 1 NC_008044.1 PFAM: regulatory protein, TetR: (0.0022); KEGG: jan:Jann_2994 transcriptional regulator, TetR family, ev=4e-54, 55% identity; TetR family transcriptional regulator 1692826 4078392 TM1040_1583 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_613578.1 1692230 R 292414 CDS YP_613579.1 99081425 4078393 1692970..1693896 1 NC_008044.1 PFAM: protein of unknown function DUF817: (1.2e-94); KEGG: sil:SPO2941 membrane protein, , ev=1e-115, 78% identity; hypothetical protein 1693896 4078393 TM1040_1584 Ruegeria sp. TM1040 hypothetical protein YP_613579.1 1692970 D 292414 CDS YP_613580.1 99081426 4078394 complement(1693850..1694215) 1 NC_008044.1 KEGG: sil:SPO2942 hypothetical protein, ev=1e-12, 34% identity; hypothetical protein 1694215 4078394 TM1040_1585 Ruegeria sp. TM1040 hypothetical protein YP_613580.1 1693850 R 292414 CDS YP_613581.1 99081427 4078395 1694338..1695096 1 NC_008044.1 PFAM: alpha/beta hydrolase fold: (7.3e-21) PGAP1-like: (6.8e-05); KEGG: sil:SPO2943 hydrolase, alpha/beta fold family, ev=1e-104, 74% identity; alpha/beta hydrolase 1695096 4078395 TM1040_1586 Ruegeria sp. TM1040 alpha/beta hydrolase YP_613581.1 1694338 D 292414 CDS YP_613582.1 99081428 4078396 complement(1695177..1696058) 1 NC_008044.1 TIGRFAM: DNA adenine methylase: (2.5e-13); PFAM: D12 class N6 adenine-specific DNA methyltransferase: (8.1e-18); KEGG: vpa:VP2742 DNA adenine methylase, ev=3e-20, 30% identity; DNA adenine methylase Dam 1696058 4078396 TM1040_1587 Ruegeria sp. TM1040 DNA adenine methylase Dam YP_613582.1 1695177 R 292414 CDS YP_613583.1 99081429 4078397 complement(1696199..1699753) 1 NC_008044.1 TIGRFAM: Outer membrane autotransporter barrel: (4.1e-09); PFAM: Hyalin: (0.00045) Autotransporter beta-domain: (1.1e-08); KEGG: hch:HCH_03195 RTX toxins and related Ca2+-binding protein, ev=3e-47, 26% identity; Outer membrane autotransporter barrel 1699753 4078397 TM1040_1588 Ruegeria sp. TM1040 Outer membrane autotransporter barrel YP_613583.1 1696199 R 292414 CDS YP_613584.1 99081430 4078398 complement(1700175..1701434) 1 NC_008044.1 TIGRFAM: TRAP dicarboxylate transporter- DctM subunit: (3.7e-110); PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit: (4.1e-105); KEGG: jan:Jann_1450 TRAP dicarboxylate transporter-DctM subunit, ev=1e-180, 74% identity; TRAP dicarboxylate transporter- DctM subunit 1701434 4078398 TM1040_1589 Ruegeria sp. TM1040 TRAP dicarboxylate transporter- DctM subunit YP_613584.1 1700175 R 292414 CDS YP_613585.1 99081431 4078399 complement(1701431..1701970) 1 NC_008044.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component: (2.5e-07); KEGG: jan:Jann_1449 tripartite ATP-independent periplasmic transporter, DctQ component, ev=6e-57, 63% identity; tripartite ATP-independent periplasmic transporter DctQ 1701970 4078399 TM1040_1590 Ruegeria sp. TM1040 tripartite ATP-independent periplasmic transporter DctQ YP_613585.1 1701431 R 292414 CDS YP_613586.1 99081432 4078400 complement(1702034..1703014) 1 NC_008044.1 PFAM: TRAP dicarboxylate transporter- DctP subunit: (8.8e-43); KEGG: sil:SPO1773 TRAP dicarboxylate transporter, DctP subunit, , ev=1e-124, 70% identity; TRAP dicarboxylate transporter- DctP subunit 1703014 4078400 TM1040_1591 Ruegeria sp. TM1040 TRAP dicarboxylate transporter- DctP subunit YP_613586.1 1702034 R 292414 CDS YP_613587.1 99081433 4078401 complement(1703050..1703613) 1 NC_008044.1 catalyzes the oxidative ring opening of 3-hydroxyanthranilate to 2-amino-3-carboxymuconate semialdehyde in the final enzymatic step of quinolinate biosynthesis; 3-hydroxyanthranilate 3,4-dioxygenase 1703613 4078401 TM1040_1592 Ruegeria sp. TM1040 3-hydroxyanthranilate 3,4-dioxygenase YP_613587.1 1703050 R 292414 CDS YP_613588.1 99081434 4078402 complement(1703743..1704630) 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (0.00071); KEGG: eba:p2A115 hypothetical protein, potential permease subunit, ev=8e-21, 27% identity; hypothetical protein 1704630 4078402 TM1040_1593 Ruegeria sp. TM1040 hypothetical protein YP_613588.1 1703743 R 292414 CDS YP_613589.1 99081435 4078403 complement(1704640..1705593) 1 NC_008044.1 PFAM: dihydrodipicolinate synthetase: (1e-11); KEGG: sil:SPO2882 dihydrodipicolinate synthase family protein, ev=1e-132, 72% identity; dihydrodipicolinate synthetase 1705593 4078403 TM1040_1594 Ruegeria sp. TM1040 dihydrodipicolinate synthetase YP_613589.1 1704640 R 292414 CDS YP_613590.1 99081436 4078404 1705772..1706560 1 NC_008044.1 catalyzes the formation of L-aspartate to iminoaspartate in NAD(+) biosynthesis; L-aspartate dehydrogenase 1706560 4078404 TM1040_1595 Ruegeria sp. TM1040 L-aspartate dehydrogenase YP_613590.1 1705772 D 292414 CDS YP_613591.1 99081437 4078405 1706570..1707535 1 NC_008044.1 PFAM: regulatory protein, LysR: (5.4e-21) LysR, substrate-binding: (1.4e-36); KEGG: sil:SPO2879 transcriptional regulator, LysR family, ev=5e-97, 60% identity; LysR family transcriptional regulator 1707535 4078405 TM1040_1596 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_613591.1 1706570 D 292414 CDS YP_613592.1 99081438 4078406 1707581..1709071 1 NC_008044.1 PFAM: aldehyde dehydrogenase: (7.2e-185); KEGG: atc:AGR_L_2660 aldehyde dehydrogenase, ev=1e-135, 49% identity; succinate semialdehyde dehydrogenase 1709071 4078406 TM1040_1597 Ruegeria sp. TM1040 succinate semialdehyde dehydrogenase YP_613592.1 1707581 D 292414 CDS YP_613593.1 99081439 4078407 complement(1709078..1710358) 1 NC_008044.1 TIGRFAM: Twin-arginine translocation pathway signal: (0.068); PFAM: major facilitator superfamily MFS_1: (3.1e-26); KEGG: sil:SPO2225 membrane protein, , ev=1e-110, 49% identity; twin-arginine translocation pathway signal 1710358 4078407 TM1040_1598 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_613593.1 1709078 R 292414 CDS YP_613594.1 99081440 4078408 complement(1710889..1711800) 1 NC_008044.1 PFAM: Hemolysin-type calcium-binding region: (0.00015); KEGG: rpb:RPB_0803 5'-nucleotidase, ev=4e-36, 40% identity; hemolysin-type calcium-binding protein 1711800 4078408 TM1040_1599 Ruegeria sp. TM1040 hemolysin-type calcium-binding protein YP_613594.1 1710889 R 292414 CDS YP_613595.1 99081441 4078409 1712411..1712728 1 NC_008044.1 hypothetical protein 1712728 4078409 TM1040_1600 Ruegeria sp. TM1040 hypothetical protein YP_613595.1 1712411 D 292414 CDS YP_613596.1 99081442 4078410 complement(1712755..1713351) 1 NC_008044.1 hypothetical protein 1713351 4078410 TM1040_1601 Ruegeria sp. TM1040 hypothetical protein YP_613596.1 1712755 R 292414 CDS YP_613597.1 99081443 4077704 complement(1713369..1714235) 1 NC_008044.1 hypothetical protein 1714235 4077704 TM1040_1602 Ruegeria sp. TM1040 hypothetical protein YP_613597.1 1713369 R 292414 CDS YP_613598.1 99081444 4077705 complement(1714470..1714868) 1 NC_008044.1 hypothetical protein 1714868 4077705 TM1040_1603 Ruegeria sp. TM1040 hypothetical protein YP_613598.1 1714470 R 292414 CDS YP_613599.1 99081445 4077706 complement(1714865..1715674) 1 NC_008044.1 PFAM: protein of unknown function DUF847: (8.8e-67); KEGG: bmb:BruAb1_0990 secretion activator protein, hypothetical, ev=2e-43, 39% identity; hypothetical protein 1715674 4077706 TM1040_1604 Ruegeria sp. TM1040 hypothetical protein YP_613599.1 1714865 R 292414 CDS YP_613600.1 99081446 4077707 complement(1715676..1716110) 1 NC_008044.1 hypothetical protein 1716110 4077707 TM1040_1605 Ruegeria sp. TM1040 hypothetical protein YP_613600.1 1715676 R 292414 CDS YP_613601.1 99081447 4077708 complement(1716107..1716403) 1 NC_008044.1 hypothetical protein 1716403 4077708 TM1040_1606 Ruegeria sp. TM1040 hypothetical protein YP_613601.1 1716107 R 292414 CDS YP_613602.1 99081448 4077709 complement(1716410..1716757) 1 NC_008044.1 hypothetical protein 1716757 4077709 TM1040_1607 Ruegeria sp. TM1040 hypothetical protein YP_613602.1 1716410 R 292414 CDS YP_613603.1 99081449 4077710 complement(1716735..1717235) 1 NC_008044.1 hypothetical protein 1717235 4077710 TM1040_1608 Ruegeria sp. TM1040 hypothetical protein YP_613603.1 1716735 R 292414 CDS YP_613604.1 99081450 4077711 complement(1717238..1718308) 1 NC_008044.1 KEGG: nar:Saro_2740 PE-PGRS family protein, ev=2e-34, 37% identity; hypothetical protein 1718308 4077711 TM1040_1609 Ruegeria sp. TM1040 hypothetical protein YP_613604.1 1717238 R 292414 CDS YP_613605.1 99081451 4077712 complement(1718305..1719249) 1 NC_008044.1 KEGG: rsp:RSP_1635 hypothetical protein, ev=2e-27, 27% identity; hypothetical protein 1719249 4077712 TM1040_1610 Ruegeria sp. TM1040 hypothetical protein YP_613605.1 1718305 R 292414 CDS YP_613606.1 99081452 4077713 complement(1719249..1723772) 1 NC_008044.1 KEGG: rsp:RSP_3791 hypothetical protein, ev=2e-86, 23% identity; hypothetical protein 1723772 4077713 TM1040_1611 Ruegeria sp. TM1040 hypothetical protein YP_613606.1 1719249 R 292414 CDS YP_613607.1 99081453 4077714 complement(1724207..1724542) 1 NC_008044.1 hypothetical protein 1724542 4077714 TM1040_1612 Ruegeria sp. TM1040 hypothetical protein YP_613607.1 1724207 R 292414 CDS YP_613608.1 99081454 4077715 complement(1724641..1725090) 1 NC_008044.1 KEGG: rsp:RSP_3788 hypothetical protein, ev=2e-29, 46% identity; hypothetical protein 1725090 4077715 TM1040_1613 Ruegeria sp. TM1040 hypothetical protein YP_613608.1 1724641 R 292414 CDS YP_613609.1 99081455 4077716 complement(1725189..1725638) 1 NC_008044.1 KEGG: nar:Saro_0657 hypothetical protein, ev=2e-32, 50% identity; hypothetical protein 1725638 4077716 TM1040_1614 Ruegeria sp. TM1040 hypothetical protein YP_613609.1 1725189 R 292414 CDS YP_613610.1 99081456 4077717 complement(1725699..1725983) 1 NC_008044.1 hypothetical protein 1725983 4077717 TM1040_1615 Ruegeria sp. TM1040 hypothetical protein YP_613610.1 1725699 R 292414 CDS YP_613611.1 99081457 4077718 complement(1726025..1726378) 1 NC_008044.1 KEGG: rsp:RSP_6012 hypothetical protein, ev=1e-08, 36% identity; hypothetical protein 1726378 4077718 TM1040_1616 Ruegeria sp. TM1040 hypothetical protein YP_613611.1 1726025 R 292414 CDS YP_613612.1 99081458 4077719 complement(1726378..1726833) 1 NC_008044.1 KEGG: rsp:RSP_1640 hypothetical protein, ev=5e-14, 35% identity; hypothetical protein 1726833 4077719 TM1040_1617 Ruegeria sp. TM1040 hypothetical protein YP_613612.1 1726378 R 292414 CDS YP_613613.1 99081459 4077720 1726834..1727211 1 NC_008044.1 hypothetical protein 1727211 4077720 TM1040_1618 Ruegeria sp. TM1040 hypothetical protein YP_613613.1 1726834 D 292414 CDS YP_613614.1 99081460 4077721 complement(1727252..1727833) 1 NC_008044.1 TIGRFAM: Phage conserved hypothetical protein, phiE125 gp8: (7.5e-10); KEGG: nar:Saro_0652 phage conserved hypothetical protein, phiE125 gp8, ev=3e-15, 35% identity; hypothetical protein 1727833 4077721 TM1040_1619 Ruegeria sp. TM1040 hypothetical protein YP_613614.1 1727252 R 292414 CDS YP_613615.1 99081461 4077722 complement(1727837..1728298) 1 NC_008044.1 hypothetical protein 1728298 4077722 TM1040_1620 Ruegeria sp. TM1040 hypothetical protein YP_613615.1 1727837 R 292414 CDS YP_613616.1 99081462 4077723 complement(1728295..1728756) 1 NC_008044.1 hypothetical protein 1728756 4077723 TM1040_1621 Ruegeria sp. TM1040 hypothetical protein YP_613616.1 1728295 R 292414 CDS YP_613617.1 99081463 4077724 complement(1728820..1730139) 1 NC_008044.1 KEGG: ppu:PP3877 hypothetical protein, ev=3e-77, 41% identity; hypothetical protein 1730139 4077724 TM1040_1622 Ruegeria sp. TM1040 hypothetical protein YP_613617.1 1728820 R 292414 CDS YP_613618.1 99081464 4077725 complement(1730142..1731089) 1 NC_008044.1 PFAM: peptidase S49: (1.8e-23); KEGG: nmu:Nmul_A0057 peptidase S49, ev=1e-42, 41% identity; serine peptidase 1731089 4077725 TM1040_1623 Ruegeria sp. TM1040 serine peptidase YP_613618.1 1730142 R 292414 CDS YP_613619.1 99081465 4077726 complement(1731086..1732372) 1 NC_008044.1 TIGRFAM: Phage portal protein, HK97: (7.5e-44); PFAM: phage portal protein: (6.5e-40); KEGG: det:DET1087 portal protein, HK97 family, , ev=1e-51, 33% identity; Phage portal protein, HK97 1732372 4077726 TM1040_1624 Ruegeria sp. TM1040 Phage portal protein, HK97 YP_613619.1 1731086 R 292414 CDS YP_613620.1 99081466 4077727 complement(1732375..1734075) 1 NC_008044.1 PFAM: phage Terminase: (6.4e-10); KEGG: rsp:RSP_2070 phage-related terminase, ev=1e-156, 52% identity; phage terminase 1734075 4077727 TM1040_1625 Ruegeria sp. TM1040 phage terminase YP_613620.1 1732375 R 292414 CDS YP_613621.1 99081467 4077728 complement(1734086..1734631) 1 NC_008044.1 hypothetical protein 1734631 4077728 TM1040_1626 Ruegeria sp. TM1040 hypothetical protein YP_613621.1 1734086 R 292414 CDS YP_613622.1 99081468 4077729 1734735..1735055 1 NC_008044.1 hypothetical protein 1735055 4077729 TM1040_1627 Ruegeria sp. TM1040 hypothetical protein YP_613622.1 1734735 D 292414 CDS YP_613623.1 99081469 4077730 1735346..1735738 1 NC_008044.1 hypothetical protein 1735738 4077730 TM1040_1628 Ruegeria sp. TM1040 hypothetical protein YP_613623.1 1735346 D 292414 CDS YP_613624.1 99081470 4077731 complement(1736144..1738018) 1 NC_008044.1 KEGG: pca:Pcar_1822 conserved hypothetical protein, ev=2e-23, 25% identity; hypothetical protein 1738018 4077731 TM1040_1629 Ruegeria sp. TM1040 hypothetical protein YP_613624.1 1736144 R 292414 CDS YP_613625.1 99081471 4077732 complement(1738048..1738329) 1 NC_008044.1 hypothetical protein 1738329 4077732 TM1040_1630 Ruegeria sp. TM1040 hypothetical protein YP_613625.1 1738048 R 292414 CDS YP_613626.1 99081472 4077733 complement(1738333..1739175) 1 NC_008044.1 hypothetical protein 1739175 4077733 TM1040_1631 Ruegeria sp. TM1040 hypothetical protein YP_613626.1 1738333 R 292414 CDS YP_613627.1 99081473 4077734 complement(1739172..1739651) 1 NC_008044.1 KEGG: rsp:RSP_0134 hypothetical protein, ev=6e-11, 47% identity; hypothetical protein 1739651 4077734 TM1040_1632 Ruegeria sp. TM1040 hypothetical protein YP_613627.1 1739172 R 292414 CDS YP_613628.1 99081474 4077735 complement(1739641..1740522) 1 NC_008044.1 KEGG: mag:amb1747 hypothetical protein, ev=1e-12, 31% identity; hypothetical protein 1740522 4077735 TM1040_1633 Ruegeria sp. TM1040 hypothetical protein YP_613628.1 1739641 R 292414 CDS YP_613629.1 99081475 4077736 complement(1740519..1740797) 1 NC_008044.1 hypothetical protein 1740797 4077736 TM1040_1634 Ruegeria sp. TM1040 hypothetical protein YP_613629.1 1740519 R 292414 CDS YP_613630.1 99081476 4077737 complement(1740964..1741440) 1 NC_008044.1 hypothetical protein 1741440 4077737 TM1040_1635 Ruegeria sp. TM1040 hypothetical protein YP_613630.1 1740964 R 292414 CDS YP_613631.1 99081477 4077738 1741814..1742167 1 NC_008044.1 SMART: Helix-turn-helix type 3: (1.5e-09); XRE family transcriptional regulator 1742167 4077738 TM1040_1636 Ruegeria sp. TM1040 XRE family transcriptional regulator YP_613631.1 1741814 D 292414 CDS YP_613632.1 99081478 4077739 1742333..1743016 1 NC_008044.1 hypothetical protein 1743016 4077739 TM1040_1637 Ruegeria sp. TM1040 hypothetical protein YP_613632.1 1742333 D 292414 CDS YP_613633.1 99081479 4077740 complement(1742974..1743864) 1 NC_008044.1 hypothetical protein 1743864 4077740 TM1040_1638 Ruegeria sp. TM1040 hypothetical protein YP_613633.1 1742974 R 292414 CDS YP_613634.1 99081480 4077741 1744087..1744389 1 NC_008044.1 hypothetical protein 1744389 4077741 TM1040_1639 Ruegeria sp. TM1040 hypothetical protein YP_613634.1 1744087 D 292414 CDS YP_613635.1 99081481 4077742 1744698..1745402 1 NC_008044.1 hypothetical protein 1745402 4077742 TM1040_1640 Ruegeria sp. TM1040 hypothetical protein YP_613635.1 1744698 D 292414 CDS YP_613636.1 99081482 4075744 1745594..1745950 1 NC_008044.1 hypothetical protein 1745950 4075744 TM1040_1641 Ruegeria sp. TM1040 hypothetical protein YP_613636.1 1745594 D 292414 CDS YP_613637.1 99081483 4075745 1745947..1747818 1 NC_008044.1 KEGG: rsp:RSP_3609 ParB-like nuclease, ev=1e-100, 38% identity; ParB-like nuclease 1747818 4075745 TM1040_1642 Ruegeria sp. TM1040 ParB-like nuclease YP_613637.1 1745947 D 292414 CDS YP_613638.1 99081484 4075746 1748176..1748427 1 NC_008044.1 hypothetical protein 1748427 4075746 TM1040_1643 Ruegeria sp. TM1040 hypothetical protein YP_613638.1 1748176 D 292414 CDS YP_613639.1 99081485 4075747 1748417..1749649 1 NC_008044.1 KEGG: nwi:Nwi_1140 phage integrase, ev=1e-24, 29% identity; hypothetical protein 1749649 4075747 TM1040_1644 Ruegeria sp. TM1040 hypothetical protein YP_613639.1 1748417 D 292414 CDS YP_613640.1 99081486 4075748 complement(1750371..1751012) 1 NC_008044.1 PFAM: Resolvase-like: (8.9e-52); KEGG: ece:Z0318 DNA invertase from prophage CP-933H, ev=1e-33, 49% identity; resolvase-like protein 1751012 4075748 TM1040_1645 Ruegeria sp. TM1040 resolvase-like protein YP_613640.1 1750371 R 292414 CDS YP_613641.1 99081487 4075749 1751144..1751659 1 NC_008044.1 hypothetical protein 1751659 4075749 TM1040_1646 Ruegeria sp. TM1040 hypothetical protein YP_613641.1 1751144 D 292414 CDS YP_613642.1 99081488 4075750 complement(1751638..1752096) 1 NC_008044.1 hypothetical protein 1752096 4075750 TM1040_1647 Ruegeria sp. TM1040 hypothetical protein YP_613642.1 1751638 R 292414 CDS YP_613643.1 99081489 4075751 complement(1752165..1752485) 1 NC_008044.1 hypothetical protein 1752485 4075751 TM1040_1648 Ruegeria sp. TM1040 hypothetical protein YP_613643.1 1752165 R 292414 CDS YP_613644.1 99081490 4075752 complement(1752567..1752965) 1 NC_008044.1 hypothetical protein 1752965 4075752 TM1040_1649 Ruegeria sp. TM1040 hypothetical protein YP_613644.1 1752567 R 292414 CDS YP_613645.1 99081491 4075753 complement(1752962..1753771) 1 NC_008044.1 PFAM: protein of unknown function DUF847: (8.8e-67); KEGG: bmb:BruAb1_0990 secretion activator protein, hypothetical, ev=1e-43, 39% identity; hypothetical protein 1753771 4075753 TM1040_1650 Ruegeria sp. TM1040 hypothetical protein YP_613645.1 1752962 R 292414 CDS YP_613646.1 99081492 4075754 complement(1753773..1754207) 1 NC_008044.1 hypothetical protein 1754207 4075754 TM1040_1651 Ruegeria sp. TM1040 hypothetical protein YP_613646.1 1753773 R 292414 CDS YP_613647.1 99081493 4075755 complement(1754204..1754461) 1 NC_008044.1 hypothetical protein 1754461 4075755 TM1040_1652 Ruegeria sp. TM1040 hypothetical protein YP_613647.1 1754204 R 292414 CDS YP_613648.1 99081494 4075756 complement(1754507..1754854) 1 NC_008044.1 hypothetical protein 1754854 4075756 TM1040_1653 Ruegeria sp. TM1040 hypothetical protein YP_613648.1 1754507 R 292414 CDS YP_613649.1 99081495 4075757 complement(1754832..1755464) 1 NC_008044.1 hypothetical protein 1755464 4075757 TM1040_1654 Ruegeria sp. TM1040 hypothetical protein YP_613649.1 1754832 R 292414 CDS YP_613650.1 99081496 4075758 complement(1755461..1756456) 1 NC_008044.1 KEGG: pub:SAR11_0932 hypothetical protein, ev=2e-20, 32% identity; hypothetical protein 1756456 4075758 TM1040_1655 Ruegeria sp. TM1040 hypothetical protein YP_613650.1 1755461 R 292414 CDS YP_613651.1 99081497 4075759 complement(1756975..1757919) 1 NC_008044.1 KEGG: nar:Saro_0661 hypothetical protein, ev=7e-28, 26% identity; hypothetical protein 1757919 4075759 TM1040_1656 Ruegeria sp. TM1040 hypothetical protein YP_613651.1 1756975 R 292414 CDS YP_613652.1 99081498 4075760 complement(1757916..1762442) 1 NC_008044.1 KEGG: rsp:RSP_3791 hypothetical protein, ev=5e-91, 24% identity; hypothetical protein 1762442 4075760 TM1040_1657 Ruegeria sp. TM1040 hypothetical protein YP_613652.1 1757916 R 292414 CDS YP_613653.1 99081499 4075761 1762471..1762809 1 NC_008044.1 hypothetical protein 1762809 4075761 TM1040_1658 Ruegeria sp. TM1040 hypothetical protein YP_613653.1 1762471 D 292414 CDS YP_613654.1 99081500 4075762 complement(1762850..1763731) 1 NC_008044.1 hypothetical protein 1763731 4075762 TM1040_1659 Ruegeria sp. TM1040 hypothetical protein YP_613654.1 1762850 R 292414 CDS YP_613655.1 99081501 4075763 complement(1763994..1764332) 1 NC_008044.1 hypothetical protein 1764332 4075763 TM1040_1660 Ruegeria sp. TM1040 hypothetical protein YP_613655.1 1763994 R 292414 CDS YP_613656.1 99081502 4075764 complement(1764431..1764880) 1 NC_008044.1 KEGG: rsp:RSP_3788 hypothetical protein, ev=2e-29, 46% identity; hypothetical protein 1764880 4075764 TM1040_1661 Ruegeria sp. TM1040 hypothetical protein YP_613656.1 1764431 R 292414 CDS YP_613657.1 99081503 4075765 complement(1764979..1765428) 1 NC_008044.1 KEGG: nar:Saro_0657 hypothetical protein, ev=2e-32, 50% identity; hypothetical protein 1765428 4075765 TM1040_1662 Ruegeria sp. TM1040 hypothetical protein YP_613657.1 1764979 R 292414 CDS YP_613658.1 99081504 4075766 complement(1765489..1765773) 1 NC_008044.1 hypothetical protein 1765773 4075766 TM1040_1663 Ruegeria sp. TM1040 hypothetical protein YP_613658.1 1765489 R 292414 CDS YP_613659.1 99081505 4075767 complement(1765815..1766120) 1 NC_008044.1 KEGG: rsp:RSP_6012 hypothetical protein, ev=3e-07, 35% identity; hypothetical protein 1766120 4075767 TM1040_1664 Ruegeria sp. TM1040 hypothetical protein YP_613659.1 1765815 R 292414 CDS YP_613660.1 99081506 4075768 complement(1766168..1766623) 1 NC_008044.1 KEGG: rsp:RSP_1640 hypothetical protein, ev=2e-14, 35% identity; hypothetical protein 1766623 4075768 TM1040_1665 Ruegeria sp. TM1040 hypothetical protein YP_613660.1 1766168 R 292414 CDS YP_613661.1 99081507 4075769 complement(1766620..1766958) 1 NC_008044.1 TIGRFAM: conserved hypothetical protein: (0.13); hypothetical protein 1766958 4075769 TM1040_1666 Ruegeria sp. TM1040 hypothetical protein YP_613661.1 1766620 R 292414 CDS YP_613662.1 99081508 4075770 complement(1766958..1767530) 1 NC_008044.1 TIGRFAM: Phage conserved hypothetical protein, phiE125 gp8: (3.6e-09); KEGG: nar:Saro_0652 phage conserved hypothetical protein, phiE125 gp8, ev=3e-12, 30% identity; hypothetical protein 1767530 4075770 TM1040_1667 Ruegeria sp. TM1040 hypothetical protein YP_613662.1 1766958 R 292414 CDS YP_613663.1 99081509 4075771 complement(1767772..1768983) 1 NC_008044.1 KEGG: nar:Saro_0649 phage major capsid protein, HK97, ev=1e-103, 52% identity; phage major capsid protein, HK97 1768983 4075771 TM1040_1668 Ruegeria sp. TM1040 phage major capsid protein, HK97 YP_613663.1 1767772 R 292414 CDS YP_613664.1 99081510 4075772 complement(1769008..1769694) 1 NC_008044.1 PFAM: peptidase U35, phage prohead HK97: (2.4e-50); KEGG: hch:HCH_04554 phage prohead protease, HK97 family, ev=9e-29, 46% identity; prohead peptidase 1769694 4075772 TM1040_1669 Ruegeria sp. TM1040 prohead peptidase YP_613664.1 1769008 R 292414 CDS YP_613665.1 99081511 4075773 complement(1769678..1770901) 1 NC_008044.1 TIGRFAM: Phage portal protein, HK97: (1.7e-95); PFAM: phage portal protein: (3.6e-100); KEGG: nar:Saro_0647 phage portal protein, HK97, ev=1e-102, 52% identity; Phage portal protein, HK97 1770901 4075773 TM1040_1670 Ruegeria sp. TM1040 Phage portal protein, HK97 YP_613665.1 1769678 R 292414 CDS YP_613666.1 99081512 4075774 complement(1770902..1772683) 1 NC_008044.1 PFAM: phage Terminase: (9.1e-37); KEGG: sgl:SG0724 phage terminase large subunit, ev=1e-100, 37% identity; phage terminase 1772683 4075774 TM1040_1671 Ruegeria sp. TM1040 phage terminase YP_613666.1 1770902 R 292414 CDS YP_613667.1 99081513 4075775 complement(1772661..1773068) 1 NC_008044.1 hypothetical protein 1773068 4075775 TM1040_1672 Ruegeria sp. TM1040 hypothetical protein YP_613667.1 1772661 R 292414 CDS YP_613668.1 99081514 4075776 1773573..1773896 1 NC_008044.1 hypothetical protein 1773896 4075776 TM1040_1673 Ruegeria sp. TM1040 hypothetical protein YP_613668.1 1773573 D 292414 CDS YP_613669.1 99081515 4075777 complement(1774102..1774671) 1 NC_008044.1 hypothetical protein 1774671 4075777 TM1040_1674 Ruegeria sp. TM1040 hypothetical protein YP_613669.1 1774102 R 292414 CDS YP_613670.1 99081516 4075778 complement(1774694..1774942) 1 NC_008044.1 hypothetical protein 1774942 4075778 TM1040_1675 Ruegeria sp. TM1040 hypothetical protein YP_613670.1 1774694 R 292414 CDS YP_613671.1 99081517 4075779 complement(1774948..1775424) 1 NC_008044.1 TIGRFAM: single-strand binding protein: (7.4e-57); PFAM: single-strand binding protein/Primosomal replication protein n: (4e-32); KEGG: sil:SPO1637 single-strand binding protein, ev=5e-63, 68% identity; single-strand binding protein 1775424 4075779 TM1040_1676 Ruegeria sp. TM1040 single-strand binding protein YP_613671.1 1774948 R 292414 CDS YP_613672.1 99081518 4075780 complement(1775642..1776403) 1 NC_008044.1 hypothetical protein 1776403 4075780 TM1040_1677 Ruegeria sp. TM1040 hypothetical protein YP_613672.1 1775642 R 292414 CDS YP_613673.1 99081519 4075781 complement(1776938..1777294) 1 NC_008044.1 PFAM: endodeoxyribonuclease RusA: (0.0097); endodeoxyribonuclease RusA 1777294 4075781 TM1040_1678 Ruegeria sp. TM1040 endodeoxyribonuclease RusA YP_613673.1 1776938 R 292414 CDS YP_613674.1 99081520 4075782 complement(1777291..1777863) 1 NC_008044.1 PFAM: MT-A70: (1.7e-36); KEGG: ana:all7280 adenine-specific DNA methyltransferase, ev=1e-25, 35% identity; hypothetical protein 1777863 4075782 TM1040_1679 Ruegeria sp. TM1040 hypothetical protein YP_613674.1 1777291 R 292414 CDS YP_613675.1 99081521 4078256 complement(1777863..1778165) 1 NC_008044.1 hypothetical protein 1778165 4078256 TM1040_1680 Ruegeria sp. TM1040 hypothetical protein YP_613675.1 1777863 R 292414 CDS YP_613676.1 99081522 4078257 complement(1778403..1778846) 1 NC_008044.1 hypothetical protein 1778846 4078257 TM1040_1681 Ruegeria sp. TM1040 hypothetical protein YP_613676.1 1778403 R 292414 CDS YP_613677.1 99081523 4078258 1779272..1779922 1 NC_008044.1 KEGG: rsp:RSP_3771 hypothetical protein, ev=4e-17, 47% identity; hypothetical protein 1779922 4078258 TM1040_1682 Ruegeria sp. TM1040 hypothetical protein YP_613677.1 1779272 D 292414 CDS YP_613678.1 99081524 4078259 1779945..1780214 1 NC_008044.1 KEGG: noc:Noc_2744 hypothetical protein, ev=2e-08, 38% identity; hypothetical protein 1780214 4078259 TM1040_1683 Ruegeria sp. TM1040 hypothetical protein YP_613678.1 1779945 D 292414 CDS YP_613679.1 99081525 4078260 1780207..1780608 1 NC_008044.1 PFAM: protein of unknown function UPF0150: (1.1e-18); KEGG: noc:Noc_2743 hypothetical protein, ev=4e-18, 58% identity; hypothetical protein 1780608 4078260 TM1040_1684 Ruegeria sp. TM1040 hypothetical protein YP_613679.1 1780207 D 292414 CDS YP_613680.1 99081526 4078261 1780907..1781299 1 NC_008044.1 hypothetical protein 1781299 4078261 TM1040_1685 Ruegeria sp. TM1040 hypothetical protein YP_613680.1 1780907 D 292414 CDS YP_613681.1 99081527 4078262 1781513..1781776 1 NC_008044.1 hypothetical protein 1781776 4078262 TM1040_1686 Ruegeria sp. TM1040 hypothetical protein YP_613681.1 1781513 D 292414 CDS YP_613682.1 99081528 4078263 1781885..1782862 1 NC_008044.1 KEGG: sgl:SG1827 hypothetical protein, ev=4e-58, 41% identity; hypothetical protein 1782862 4078263 TM1040_1687 Ruegeria sp. TM1040 hypothetical protein YP_613682.1 1781885 D 292414 CDS YP_613683.1 99081529 4078264 1782883..1783587 1 NC_008044.1 KEGG: lpf:lpl1360 hypothetical protein, ev=1e-10, 30% identity; hypothetical protein 1783587 4078264 TM1040_1688 Ruegeria sp. TM1040 hypothetical protein YP_613683.1 1782883 D 292414 CDS YP_613684.1 99081530 4078265 1783760..1784104 1 NC_008044.1 hypothetical protein 1784104 4078265 TM1040_1689 Ruegeria sp. TM1040 hypothetical protein YP_613684.1 1783760 D 292414 CDS YP_613685.1 99081531 4078266 1784101..1784478 1 NC_008044.1 SMART: HNH nuclease: (2.4e-06); KEGG: mlo:mll7975 hypothetical protein, ev=1e-10, 40% identity; HNH nuclease 1784478 4078266 TM1040_1690 Ruegeria sp. TM1040 HNH nuclease YP_613685.1 1784101 D 292414 CDS YP_613686.1 99081532 4078267 1784602..1786695 1 NC_008044.1 PFAM: C-5 cytosine-specific DNA methylase: (4e-07); KEGG: yps:YPTB1799 modification methylase, ev=1e-106, 37% identity; C-5 cytosine-specific DNA methylase 1786695 4078267 TM1040_1691 Ruegeria sp. TM1040 C-5 cytosine-specific DNA methylase YP_613686.1 1784602 D 292414 CDS YP_613687.1 99081533 4078268 1787053..1788099 1 NC_008044.1 PFAM: phage integrase: (0.0014); KEGG: mag:amb2709 integrase, ev=4e-15, 25% identity; phage integrase 1788099 4078268 TM1040_1692 Ruegeria sp. TM1040 phage integrase YP_613687.1 1787053 D 292414 CDS YP_613688.1 99081534 4078269 complement(1788393..1789004) 1 NC_008044.1 PFAM: TPR repeat: (0.078) Tetratricopeptide TPR_2: (2.3e-06); SMART: Tetratricopeptide region: (0.059); KEGG: sil:SPO3008 TPR domain protein, ev=8e-62, 63% identity; hypothetical protein 1789004 4078269 TM1040_1693 Ruegeria sp. TM1040 hypothetical protein YP_613688.1 1788393 R 292414 CDS YP_613689.1 99081535 4078270 complement(1789014..1789490) 1 NC_008044.1 PFAM: regulatory proteins, AsnC/Lrp: (1.2e-20); KEGG: sil:SPO3009 proline dehydrogenase transcriptional activator, ev=2e-56, 67% identity; AsnC family transcriptional regulator 1789490 4078270 TM1040_1694 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_613689.1 1789014 R 292414 CDS YP_613690.1 99081536 4078271 1789603..1793010 1 NC_008044.1 proline utilization protein A; multifunctional protein that functions in proline catabolism in the first two enzymatic steps resulting in the conversion of proline to glutamate; in Escherichia coli this protein self regulates transcription via a DNA-binding domain at the N-terminus but the protein from Pseudomonas does not have this domain; bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase 1793010 4078271 TM1040_1695 Ruegeria sp. TM1040 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase YP_613690.1 1789603 D 292414 CDS YP_613691.1 99081537 4078272 1793112..1793882 1 NC_008044.1 PFAM: Rhomboid-like protein: (1.1e-40); KEGG: sil:SPO3011 rhomboid family protein, ev=6e-91, 65% identity; rhomboid-like protein 1793882 4078272 TM1040_1696 Ruegeria sp. TM1040 rhomboid-like protein YP_613691.1 1793112 D 292414 CDS YP_613692.1 99081538 4078273 1793908..1794294 1 NC_008044.1 PFAM: glutathione-dependent formaldehyde-activating, GFA: (2.5e-19); KEGG: rsp:RSP_2168 hypothetical protein, ev=4e-39, 61% identity; glutathione-dependent formaldehyde-activating protein 1794294 4078273 TM1040_1697 Ruegeria sp. TM1040 glutathione-dependent formaldehyde-activating protein YP_613692.1 1793908 D 292414 CDS YP_613693.1 99081539 4078274 complement(1794466..1795251) 1 NC_008044.1 PFAM: inositol monophosphatase: (6.5e-71); KEGG: sil:SPO3012 inositol-1-monophosphatase, , ev=1e-130, 86% identity; inositol monophosphatase 1795251 4078274 TM1040_1698 Ruegeria sp. TM1040 inositol monophosphatase YP_613693.1 1794466 R 292414 CDS YP_613694.1 99081540 4078275 complement(1795432..1796337) 1 NC_008044.1 PFAM: regulatory protein, LysR: (1.1e-18) LysR, substrate-binding: (5.8e-36); KEGG: sil:SPO3015 transcriptional regulator MetR, ev=1e-143, 84% identity; LysR family transcriptional regulator 1796337 4078275 TM1040_1699 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_613694.1 1795432 R 292414 CDS YP_613695.1 99081541 4078276 1796495..1797364 1 NC_008044.1 KEGG: sil:SPO3016 5,10-methylenetetrahydrofolate reductase, ev=1e-129, 78% identity; TIGRFAM: 5,10-methylenetetrahydrofolate reductase: (3.8e-128); PFAM: methylenetetrahydrofolate reductase: (9e-90); 5,10-methylenetetrahydrofolate reductase 1797364 4078276 TM1040_1700 Ruegeria sp. TM1040 5,10-methylenetetrahydrofolate reductase YP_613695.1 1796495 D 292414 CDS YP_613696.1 99081542 4078277 1797423..1797905 1 NC_008044.1 TIGRFAM: Phenylacetic acid degradation-related protein: (2.1e-16); PFAM: thioesterase superfamily: (1.1e-13); KEGG: sil:SPO3017 thioesterase family protein, ev=9e-57, 64% identity; phenylacetic acid degradation-related protein 1797905 4078277 TM1040_1701 Ruegeria sp. TM1040 phenylacetic acid degradation-related protein YP_613696.1 1797423 D 292414 CDS YP_613697.1 99081543 4078278 complement(1797922..1798926) 1 NC_008044.1 KEGG: eca:ECA3200 hypothetical protein, ev=7e-59, 39% identity; hypothetical protein 1798926 4078278 TM1040_1702 Ruegeria sp. TM1040 hypothetical protein YP_613697.1 1797922 R 292414 CDS YP_613698.1 99081544 4078279 1798978..1799601 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (8.5e-15); KEGG: jan:Jann_3325 GCN5-related N-acetyltransferase, ev=3e-47, 52% identity; N-acetyltransferase GCN5 1799601 4078279 TM1040_1703 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_613698.1 1798978 D 292414 CDS YP_613699.1 99081545 4078280 complement(1799623..1800708) 1 NC_008044.1 KEGG: sil:SPO3018 hypothetical protein, ev=1e-137, 68% identity; hypothetical protein 1800708 4078280 TM1040_1704 Ruegeria sp. TM1040 hypothetical protein YP_613699.1 1799623 R 292414 CDS YP_613700.1 99081546 4078281 complement(1800686..1802995) 1 NC_008044.1 PFAM: aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead: (4.1e-25) aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding: (1.8e-119); KEGG: sil:SPO3019 xanthine dehydrogenase family protein, large subunit, ev=0.0, 71% identity; xanthine dehydrogenase, molybdenum binding subunit apoprotein 1802995 4078281 TM1040_1705 Ruegeria sp. TM1040 xanthine dehydrogenase, molybdenum binding subunit apoprotein YP_613700.1 1800686 R 292414 CDS YP_613701.1 99081547 4078282 1803784..1806879 1 NC_008044.1 valine--tRNA ligase; ValRS; converts valine ATP and tRNA(Val) to AMP PPi and valyl-tRNA(Val); class-I aminoacyl-tRNA synthetase type 1 subfamily; has a posttransfer editing process to hydrolyze mischarged Thr-tRNA(Val) which is done by the editing domain; valyl-tRNA synthetase 1806879 valS 4078282 valS Ruegeria sp. TM1040 valyl-tRNA synthetase YP_613701.1 1803784 D 292414 CDS YP_613702.1 99081548 4078283 1807090..1807383 1 NC_008044.1 PFAM: protein of unknown function DUF1330: (7.9e-40); KEGG: rpa:RPA0338 hypothetical protein, ev=2e-24, 55% identity; hypothetical protein 1807383 4078283 TM1040_1707 Ruegeria sp. TM1040 hypothetical protein YP_613702.1 1807090 D 292414 CDS YP_613703.1 99081549 4078284 1807406..1807864 1 NC_008044.1 KEGG: sil:SPO1310 hypothetical protein, ev=6e-57, 77% identity; hypothetical protein 1807864 4078284 TM1040_1708 Ruegeria sp. TM1040 hypothetical protein YP_613703.1 1807406 D 292414 CDS YP_613704.1 99081550 4078285 1807873..1808316 1 NC_008044.1 PFAM: protein of unknown function DUF1332: (3.5e-18); KEGG: sil:SPO1309 hypothetical protein, ev=2e-44, 66% identity; hypothetical protein 1808316 4078285 TM1040_1709 Ruegeria sp. TM1040 hypothetical protein YP_613704.1 1807873 D 292414 CDS YP_613705.1 99081551 4078286 1808313..1809083 1 NC_008044.1 KEGG: sil:SPO1308 hypothetical protein, ev=2e-72, 54% identity; hypothetical protein 1809083 4078286 TM1040_1710 Ruegeria sp. TM1040 hypothetical protein YP_613705.1 1808313 D 292414 CDS YP_613706.1 99081552 4078287 1809264..1810043 1 NC_008044.1 PFAM: ABC transporter related: (7.4e-62); SMART: ATPase: (3.5e-15); KEGG: sil:SPO1307 His/Glu/Gln/Arg/opine family ABC transporter, ATP-binding protein, ev=1e-115, 77% identity; ABC transporter 1810043 4078287 TM1040_1711 Ruegeria sp. TM1040 ABC transporter YP_613706.1 1809264 D 292414 CDS YP_613707.1 99081553 4078288 1810083..1810790 1 NC_008044.1 PFAM: extracellular solute-binding protein, family 3: (7e-59); KEGG: sil:SPO1306 His/Glu/Gln/Arg/opine family ABC transporter, periplasmic His/Glu/Gln/Arg/opine family-binding protein, ev=4e-90, 70% identity; extracellular solute-binding protein 1810790 4078288 TM1040_1712 Ruegeria sp. TM1040 extracellular solute-binding protein YP_613707.1 1810083 D 292414 CDS YP_613708.1 99081554 4078289 1810884..1811792 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1.2e-11); KEGG: sil:SPO1305 ABC transporter, permease protein, HisMQ family, ev=1e-128, 72% identity; binding-protein-dependent transport system inner membrane protein 1811792 4078289 TM1040_1713 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_613708.1 1810884 D 292414 CDS YP_613709.1 99081555 4078290 1811789..1812595 1 NC_008044.1 TIGRFAM: Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine: (4.2e-08); PFAM: binding-protein-dependent transport systems inner membrane component: (1.7e-16); KEGG: sil:SPO1304 His/Glu/Gln/Arg/opine family ABC transporter, permease protein, ev=1e-120, 75% identity; amino acid ABC transporter permease 1812595 4078290 TM1040_1714 Ruegeria sp. TM1040 amino acid ABC transporter permease YP_613709.1 1811789 D 292414 CDS YP_613710.1 99081556 4078291 complement(1812653..1814482) 1 NC_008044.1 TIGRFAM: Poly(R)-hydroxyalkanoic acid synthase, class I: (5.1e-292); PFAM: Poly-beta-hydroxybutyrate polymerase-like: (2.4e-108); KEGG: sil:SPO1292 poly(3-hydroxyalkanoate) polymerase, ev=0.0, 69% identity; Poly(R)-hydroxyalkanoic acid synthase, class I 1814482 4078291 TM1040_1715 Ruegeria sp. TM1040 Poly(R)-hydroxyalkanoic acid synthase, class I YP_613710.1 1812653 R 292414 CDS YP_613711.1 99081557 4078292 1814631..1815902 1 NC_008044.1 TIGRFAM: polyhydroxyalkanoate depolymerase, intracellular: (1.5e-245); PFAM: PHB de-polymerase-like: (7.5e-129); KEGG: sil:SPO1291 polyhydroxyalkanoate depolymerase, intracellular, ev=0.0, 81% identity; polyhydroxyalkanoate depolymerase 1815902 4078292 TM1040_1716 Ruegeria sp. TM1040 polyhydroxyalkanoate depolymerase YP_613711.1 1814631 D 292414 CDS YP_613712.1 99081558 4078293 1815914..1816507 1 NC_008044.1 KEGG: sil:SPO1290 hypothetical protein, ev=1e-52, 50% identity; hypothetical protein 1816507 4078293 TM1040_1717 Ruegeria sp. TM1040 hypothetical protein YP_613712.1 1815914 D 292414 CDS YP_613713.1 99081559 4078294 complement(1816511..1817314) 1 NC_008044.1 KEGG: sil:SPO1289 hydrolase, alpha/beta fold family, ev=3e-44, 44% identity; alpha/beta hydrolase 1817314 4078294 TM1040_1718 Ruegeria sp. TM1040 alpha/beta hydrolase YP_613713.1 1816511 R 292414 CDS YP_613714.1 99081560 4075783 complement(1817526..1817951) 1 NC_008044.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase: (3.8e-17); KEGG: sil:SPO1287 glyoxalase family protein, ev=7e-52, 66% identity; glyoxalase/bleomycin resistance protein/dioxygenase 1817951 4075783 TM1040_1719 Ruegeria sp. TM1040 glyoxalase/bleomycin resistance protein/dioxygenase YP_613714.1 1817526 R 292414 CDS YP_613715.1 99081561 4075784 complement(1818044..1818787) 1 NC_008044.1 KEGG: sil:SPO1285 hypothetical protein, ev=3e-98, 72% identity; hypothetical protein 1818787 4075784 TM1040_1720 Ruegeria sp. TM1040 hypothetical protein YP_613715.1 1818044 R 292414 CDS YP_613716.1 99081562 4075785 1819028..1820974 1 NC_008044.1 catalyzes a two-step reaction, first charging a threonine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr); threonyl-tRNA synthetase 1820974 thrS 4075785 thrS Ruegeria sp. TM1040 threonyl-tRNA synthetase YP_613716.1 1819028 D 292414 CDS YP_613717.1 99081563 4075786 1821195..1821500 1 NC_008044.1 KEGG: sil:SPO1281 hypothetical protein, ev=6e-41, 82% identity; hypothetical protein 1821500 4075786 TM1040_1722 Ruegeria sp. TM1040 hypothetical protein YP_613717.1 1821195 D 292414 CDS YP_613718.1 99081564 4075787 1821631..1822482 1 NC_008044.1 PFAM: protein of unknown function DUF692: (4.8e-111); KEGG: sil:SPO1280 hypothetical protein, ev=1e-131, 81% identity; hypothetical protein 1822482 4075787 TM1040_1723 Ruegeria sp. TM1040 hypothetical protein YP_613718.1 1821631 D 292414 CDS YP_613719.1 99081565 4075788 1822482..1823228 1 NC_008044.1 KEGG: sil:SPO1279 hypothetical protein, ev=2e-88, 66% identity; hypothetical protein 1823228 4075788 TM1040_1724 Ruegeria sp. TM1040 hypothetical protein YP_613719.1 1822482 D 292414 CDS YP_613720.1 99081566 4075789 1823237..1823800 1 NC_008044.1 PFAM: DoxX: (0.00021); KEGG: sil:SPO1278 hypothetical protein, ev=1e-81, 81% identity; DoxX protein 1823800 4075789 TM1040_1725 Ruegeria sp. TM1040 DoxX protein YP_613720.1 1823237 D 292414 CDS YP_613721.1 99081567 4075790 complement(1823880..1824197) 1 NC_008044.1 PFAM: arsenate reductase and related: (6.6e-12); KEGG: sil:SPO1276 ArsC family protein, ev=2e-31, 62% identity; arsenate reductase 1824197 4075790 TM1040_1726 Ruegeria sp. TM1040 arsenate reductase YP_613721.1 1823880 R 292414 CDS YP_613722.1 99081568 4075791 1824418..1824624 1 NC_008044.1 PFAM: Cold-shock protein, DNA-binding: (2.4e-28); SMART: Cold shock protein: (1.4e-22); KEGG: sil:SPO1275 cold shock family protein, ev=9e-29, 83% identity; cold-shock DNA-binding protein family protein 1824624 4075791 TM1040_1727 Ruegeria sp. TM1040 cold-shock DNA-binding protein family protein YP_613722.1 1824418 D 292414 CDS YP_613723.1 99081569 4075792 complement(1824709..1825200) 1 NC_008044.1 PFAM: dihydrofolate reductase region: (5.1e-44); KEGG: rsp:RSP_0389 dihydrofolate reductase, ev=3e-49, 59% identity; dihydrofolate reductase 1825200 4075792 TM1040_1728 Ruegeria sp. TM1040 dihydrofolate reductase YP_613723.1 1824709 R 292414 CDS YP_613724.1 99081570 4075793 complement(1825228..1826061) 1 NC_008044.1 ThyA; catalyzes formation of dTMP and 7,8-dihydrofolate from 5,10-methylenetetrahydrofolate and dUMP; involved in deoxyribonucleotide biosynthesis; there are 2 copies in some Bacilli, one of which appears to be phage-derived; thymidylate synthase 1826061 thyA 4075793 thyA Ruegeria sp. TM1040 thymidylate synthase YP_613724.1 1825228 R 292414 CDS YP_613725.1 99081571 4075794 1826199..1826627 1 NC_008044.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase: (1.3e-20); KEGG: jan:Jann_1089 glyoxalase/bleomycin resistance protein/dioxygenase, ev=2e-64, 78% identity; glyoxalase/bleomycin resistance protein/dioxygenase 1826627 4075794 TM1040_1730 Ruegeria sp. TM1040 glyoxalase/bleomycin resistance protein/dioxygenase YP_613725.1 1826199 D 292414 CDS YP_613726.1 99081572 4075795 complement(1827197..1827694) 1 NC_008044.1 PFAM: regulatory protein, MarR: (1.1e-09); KEGG: jan:Jann_2651 transcriptional regulator, MarR family, ev=6e-70, 76% identity; MarR family transcriptional regulator 1827694 4075795 TM1040_1731 Ruegeria sp. TM1040 MarR family transcriptional regulator YP_613726.1 1827197 R 292414 CDS YP_613727.1 99081573 4075796 complement(1827774..1828052) 1 NC_008044.1 PFAM: protein of unknown function DUF339: (5.5e-20); KEGG: sil:SPO1266 TPR repeat family protein, ev=9e-26, 65% identity; hypothetical protein 1828052 4075796 TM1040_1732 Ruegeria sp. TM1040 hypothetical protein YP_613727.1 1827774 R 292414 CDS YP_613728.1 99081574 4075797 complement(1828049..1828450) 1 NC_008044.1 PFAM: helix-turn-helix motif: (1.7e-13); KEGG: sil:SPO1265 DNA-binding protein, , ev=2e-39, 64% identity; XRE family transcriptional regulator 1828450 4075797 TM1040_1733 Ruegeria sp. TM1040 XRE family transcriptional regulator YP_613728.1 1828049 R 292414 CDS YP_613729.1 99081575 4075798 1828535..1829737 1 NC_008044.1 catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate; aspartate aminotransferase 1829737 4075798 TM1040_1734 Ruegeria sp. TM1040 aspartate aminotransferase YP_613729.1 1828535 D 292414 CDS YP_613730.1 99081576 4075799 1830011..1830427 1 NC_008044.1 KEGG: jan:Jann_2660 hypothetical protein, ev=6e-49, 69% identity; hypothetical protein 1830427 4075799 TM1040_1735 Ruegeria sp. TM1040 hypothetical protein YP_613730.1 1830011 D 292414 CDS YP_613731.1 99081577 4075800 complement(1830497..1831915) 1 NC_008044.1 TIGRFAM: MATE efflux family protein: (4.8e-85); PFAM: multi antimicrobial extrusion protein MatE: (7.5e-40); KEGG: sil:SPO1260 MATE efflux family protein, ev=1e-163, 64% identity; MATE efflux family protein 1831915 4075800 TM1040_1736 Ruegeria sp. TM1040 MATE efflux family protein YP_613731.1 1830497 R 292414 CDS YP_613732.1 99081578 4075801 complement(1832077..1833159) 1 NC_008044.1 PFAM: high-affinity nickel-transporter: (9.5e-22); KEGG: jan:Jann_1929 high-affinity nickel-transporter, ev=8e-75, 46% identity; high-affinity nickel-transporter 1833159 4075801 TM1040_1737 Ruegeria sp. TM1040 high-affinity nickel-transporter YP_613732.1 1832077 R 292414 CDS YP_613733.1 99081579 4075802 complement(1833164..1833802) 1 NC_008044.1 KEGG: jan:Jann_1928 hypothetical protein, ev=6e-37, 42% identity; hypothetical protein 1833802 4075802 TM1040_1738 Ruegeria sp. TM1040 hypothetical protein YP_613733.1 1833164 R 292414 CDS YP_613734.1 99081580 4075803 complement(1833899..1834507) 1 NC_008044.1 TIGRFAM: Alkylhydroperoxidase AhpD core: (1e-06) Uncharacterised peroxidase-related: (1.2e-20); PFAM: Carboxymuconolactone decarboxylase: (0.0035); KEGG: sil:SPO1255 alkylhydroperoxidase AhpD family core domain protein, ev=5e-87, 75% identity; hypothetical protein 1834507 4075803 TM1040_1739 Ruegeria sp. TM1040 hypothetical protein YP_613734.1 1833899 R 292414 CDS YP_613735.1 99081581 4075804 1834669..1836678 1 NC_008044.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit B 1836678 4075804 TM1040_1740 Ruegeria sp. TM1040 DNA topoisomerase IV subunit B YP_613735.1 1834669 D 292414 CDS YP_613736.1 99081582 4075805 complement(1836784..1837215) 1 NC_008044.1 PFAM: cytochrome c, class I: (0.0041); KEGG: sil:SPOA0361 cytochrome c family protein, ev=2e-35, 60% identity; cytochrome c, class I 1837215 4075805 TM1040_1741 Ruegeria sp. TM1040 cytochrome c, class I YP_613736.1 1836784 R 292414 CDS YP_613737.1 99081583 4075806 complement(1837357..1838223) 1 NC_008044.1 PFAM: copper resistance D: (8.5e-07); KEGG: pha:PSHAb0008 copper export protein, ev=1e-22, 29% identity; copper resistance D 1838223 4075806 TM1040_1742 Ruegeria sp. TM1040 copper resistance D YP_613737.1 1837357 R 292414 CDS YP_613738.1 99081584 4075807 complement(1838226..1838576) 1 NC_008044.1 PFAM: copper resistance protein CopC: (5e-14); KEGG: bur:Bcep18194_A5818 copper resistance protein CopC, ev=2e-09, 27% identity; copper resistance protein CopC 1838576 4075807 TM1040_1743 Ruegeria sp. TM1040 copper resistance protein CopC YP_613738.1 1838226 R 292414 CDS YP_613739.1 99081585 4075808 complement(1838579..1839010) 1 NC_008044.1 PFAM: cytochrome c, class I: (0.0091); KEGG: sil:SPOA0359 cytochrome c family protein, ev=2e-28, 51% identity; cytochrome c, class I 1839010 4075808 TM1040_1744 Ruegeria sp. TM1040 cytochrome c, class I YP_613739.1 1838579 R 292414 CDS YP_613740.1 99081586 4075809 complement(1839068..1839442) 1 NC_008044.1 hypothetical protein 1839442 4075809 TM1040_1745 Ruegeria sp. TM1040 hypothetical protein YP_613740.1 1839068 R 292414 CDS YP_613741.1 99081587 4075810 complement(1839580..1840134) 1 NC_008044.1 KEGG: ddi:DDB0168118 hypothetical protein, ev=5e-09, 30% identity; hypothetical protein 1840134 4075810 TM1040_1746 Ruegeria sp. TM1040 hypothetical protein YP_613741.1 1839580 R 292414 CDS YP_613742.1 99081588 4075811 1840384..1841259 1 NC_008044.1 PFAM: EAL: (2.8e-43); KEGG: ccr:CC3148 hypothetical protein, ev=2e-75, 56% identity; diguanylate phosphodiesterase 1841259 4075811 TM1040_1747 Ruegeria sp. TM1040 diguanylate phosphodiesterase YP_613742.1 1840384 D 292414 CDS YP_613743.1 99081589 4075812 complement(1841365..1842276) 1 NC_008044.1 PFAM: regulatory protein, LysR: (1.3e-20) LysR, substrate-binding: (1.5e-35); KEGG: sil:SPO3490 transcriptional regulator, LysR family, ev=1e-103, 63% identity; LysR family transcriptional regulator 1842276 4075812 TM1040_1748 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_613743.1 1841365 R 292414 CDS YP_613744.1 99081590 4075813 1842361..1843008 1 NC_008044.1 PFAM: Methyltransferase type 11: (5.4e-22) Methyltransferase type 12: (4.2e-25); KEGG: sil:SPO3491 methyltransferase, UbiE/COQ5 family, ev=2e-44, 48% identity; type 12 methyltransferase 1843008 4075813 TM1040_1749 Ruegeria sp. TM1040 type 12 methyltransferase YP_613744.1 1842361 D 292414 CDS YP_613745.1 99081591 4075814 complement(1843111..1843791) 1 NC_008044.1 PFAM: ThiJ/PfpI: (1.5e-21); KEGG: sme:SMb20212 hypothetical protein, ev=3e-57, 52% identity; ThiJ/PfpI 1843791 4075814 TM1040_1750 Ruegeria sp. TM1040 ThiJ/PfpI YP_613745.1 1843111 R 292414 CDS YP_613746.1 99081592 4075815 1843922..1844821 1 NC_008044.1 PFAM: regulatory protein, LysR: (1.4e-21) LysR, substrate-binding: (1.3e-14); KEGG: bur:Bcep18194_B2495 transcriptional regulator, LysR family, ev=9e-39, 34% identity; LysR family transcriptional regulator 1844821 4075815 TM1040_1751 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_613746.1 1843922 D 292414 CDS YP_613747.1 99081593 4075816 1845256..1845462 1 NC_008044.1 PFAM: Cold-shock protein, DNA-binding: (2.7e-29); SMART: Cold shock protein: (5.7e-25); KEGG: sil:SPO3625 cold shock protein CspA, ev=2e-24, 75% identity; cold-shock DNA-binding protein family protein 1845462 4075816 TM1040_1752 Ruegeria sp. TM1040 cold-shock DNA-binding protein family protein YP_613747.1 1845256 D 292414 CDS YP_613748.1 99081594 4075817 1845455..1845703 1 NC_008044.1 hypothetical protein 1845703 4075817 TM1040_1753 Ruegeria sp. TM1040 hypothetical protein YP_613748.1 1845455 D 292414 CDS YP_613749.1 99081595 4075818 1846069..1846413 1 NC_008044.1 KEGG: rsp:RSP_3622 hypothetical protein, ev=6e-14, 45% identity; hypothetical protein 1846413 4075818 TM1040_1754 Ruegeria sp. TM1040 hypothetical protein YP_613749.1 1846069 D 292414 CDS YP_613750.1 99081596 4075819 complement(1846962..1847441) 1 NC_008044.1 PFAM: regulatory proteins, AsnC/Lrp: (1.5e-21); KEGG: sil:SPO2631 transcriptional regulator, AsnC family, ev=9e-71, 88% identity; AsnC family transcriptional regulator 1847441 4075819 TM1040_1755 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_613750.1 1846962 R 292414 CDS YP_613751.1 99081597 4075820 1847652..1848404 1 NC_008044.1 TIGRFAM: uroporphyrin-III C-methyltransferase: (1.4e-87); PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase: (2e-56); KEGG: sil:SPO2632 uroporphyrin-III C-methyltransferase, ev=8e-92, 70% identity; uroporphyrinogen-III C-methyltransferase 1848404 4075820 TM1040_1756 Ruegeria sp. TM1040 uroporphyrinogen-III C-methyltransferase YP_613751.1 1847652 D 292414 CDS YP_613752.1 99081598 4075821 1848404..1848724 1 NC_008044.1 KEGG: sil:SPO2633 hypothetical protein, ev=2e-37, 78% identity; hypothetical protein 1848724 4075821 TM1040_1757 Ruegeria sp. TM1040 hypothetical protein YP_613752.1 1848404 D 292414 CDS YP_613753.1 99081599 4076787 1848717..1850384 1 NC_008044.1 PFAM: nitrite/sulfite reductase, hemoprotein beta-component, ferrodoxin-like: (1e-11) nitrite and sulphite reductase 4Fe-4S region: (3.1e-05); KEGG: sil:SPO2634 sulfite reductase, , ev=0.0, 78% identity; nitrite/sulfite reductase, hemoprotein beta-component, ferrodoxin-like protein 1850384 4076787 TM1040_1758 Ruegeria sp. TM1040 nitrite/sulfite reductase, hemoprotein beta-component, ferrodoxin-like protein YP_613753.1 1848717 D 292414 CDS YP_613754.1 99081600 4076788 1850388..1851149 1 NC_008044.1 catalyzes the reduction of 3'-phosphoadenylyl sulfate into sulfite; phosphoadenosine phosphosulfate reductase 1851149 4076788 TM1040_1759 Ruegeria sp. TM1040 phosphoadenosine phosphosulfate reductase YP_613754.1 1850388 D 292414 CDS YP_613755.1 99081601 4076789 1851155..1851559 1 NC_008044.1 KEGG: sil:SPO2636 hypothetical protein, ev=2e-44, 67% identity; hypothetical protein 1851559 4076789 TM1040_1760 Ruegeria sp. TM1040 hypothetical protein YP_613755.1 1851155 D 292414 CDS YP_613756.1 99081602 4076790 1851726..1852598 1 NC_008044.1 PFAM: Oxidoreductase FAD-binding region: (0.00066); KEGG: jan:Jann_1770 ferredoxin--NADP(+) reductase, ev=1e-143, 85% identity; ferredoxin--NADP(+) reductase 1852598 4076790 TM1040_1761 Ruegeria sp. TM1040 ferredoxin--NADP(+) reductase YP_613756.1 1851726 D 292414 CDS YP_613757.1 99081603 4076791 complement(1852751..1853548) 1 NC_008044.1 KEGG: jan:Jann_1769 mucin-associated surface protein, ev=6e-27, 37% identity; mucin-associated surface protein 1853548 4076791 TM1040_1762 Ruegeria sp. TM1040 mucin-associated surface protein YP_613757.1 1852751 R 292414 CDS YP_613758.1 99081604 4076792 1853932..1854345 1 NC_008044.1 TIGRFAM: translation initiation factor IF-3: (1.6e-46); PFAM: initiation factor 3: (3.1e-54); KEGG: sil:SPO2638 translation initiation factor IF-3, ev=3e-70, 93% identity; translation initiation factor 3 1854345 4076792 TM1040_1763 Ruegeria sp. TM1040 translation initiation factor 3 YP_613758.1 1853932 D 292414 CDS YP_613759.1 99081605 4076793 complement(1854464..1855252) 1 NC_008044.1 PFAM: molybdopterin dehydrogenase, FAD-binding: (1e-60); KEGG: sil:SPO1520 carbon monoxide dehydrogenase, medium subunit, , ev=1e-107, 76% identity; molybdopterin dehydrogenase 1855252 4076793 TM1040_1764 Ruegeria sp. TM1040 molybdopterin dehydrogenase YP_613759.1 1854464 R 292414 CDS YP_613760.1 99081606 4076794 complement(1855343..1857721) 1 NC_008044.1 PFAM: aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead: (1.6e-34) aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding: (2.1e-157); KEGG: sil:SPO1519 carbon monoxide dehydrogenase, large subunit, ev=0.0, 88% identity; xanthine dehydrogenase, molybdenum binding subunit apoprotein 1857721 4076794 TM1040_1765 Ruegeria sp. TM1040 xanthine dehydrogenase, molybdenum binding subunit apoprotein YP_613760.1 1855343 R 292414 CDS YP_613761.1 99081607 4076795 complement(1857876..1858361) 1 NC_008044.1 PFAM: ferredoxin: (1.7e-05) [2Fe-2S]-binding: (9.8e-46); KEGG: jan:Jann_1763 (2Fe-2S)-binding, ev=6e-72, 80% identity; (2Fe-2S)-binding protein 1858361 4076795 TM1040_1766 Ruegeria sp. TM1040 (2Fe-2S)-binding protein YP_613761.1 1857876 R 292414 CDS YP_613762.1 99081608 4076796 complement(1858406..1859479) 1 NC_008044.1 PFAM: molybdopterin binding domain: (0.00035); KEGG: sil:SPO2639 molybdopterin biosynthesis protein, ev=1e-104, 57% identity; molybdopterin binding domain-containing protein 1859479 4076796 TM1040_1767 Ruegeria sp. TM1040 molybdopterin binding domain-containing protein YP_613762.1 1858406 R 292414 CDS YP_613763.1 99081609 4076797 complement(1859476..1860504) 1 NC_008044.1 PFAM: protein of unknown function DUF182: (7.8e-27); KEGG: sil:SPO2640 XdhC/CoxI family protein, ev=1e-131, 73% identity; hypothetical protein 1860504 4076797 TM1040_1768 Ruegeria sp. TM1040 hypothetical protein YP_613763.1 1859476 R 292414 CDS YP_613764.1 99081610 4076798 complement(1860620..1861903) 1 NC_008044.1 PFAM: VWA containing CoxE-like: (2.1e-89); KEGG: sil:SPO2644 VWA domain containing CoxE-like family protein, ev=1e-173, 71% identity; von Willebrand factor A 1861903 4076798 TM1040_1769 Ruegeria sp. TM1040 von Willebrand factor A YP_613764.1 1860620 R 292414 CDS YP_613765.1 99081611 4076799 complement(1861967..1862881) 1 NC_008044.1 PFAM: ATPase associated with various cellular activities, AAA_5: (6.6e-12); SMART: ATPase: (2e-06); KEGG: sil:SPO2646 hypothetical protein, ev=1e-137, 82% identity; ATPase 1862881 4076799 TM1040_1770 Ruegeria sp. TM1040 ATPase YP_613765.1 1861967 R 292414 CDS YP_613766.1 99081612 4076800 1863225..1864166 1 NC_008044.1 KEGG: sil:SPO2647 hypothetical protein, ev=1e-144, 72% identity; hypothetical protein 1864166 4076800 TM1040_1771 Ruegeria sp. TM1040 hypothetical protein YP_613766.1 1863225 D 292414 CDS YP_613767.1 99081613 4076801 1864177..1864836 1 NC_008044.1 KEGG: sil:SPO2648 hypothetical protein, ev=2e-44, 44% identity; hypothetical protein 1864836 4076801 TM1040_1772 Ruegeria sp. TM1040 hypothetical protein YP_613767.1 1864177 D 292414 CDS YP_613768.1 99081614 4076802 1864836..1867199 1 NC_008044.1 KEGG: sil:SPO2649 hypothetical protein, ev=0.0, 60% identity; hypothetical protein 1867199 4076802 TM1040_1773 Ruegeria sp. TM1040 hypothetical protein YP_613768.1 1864836 D 292414 CDS YP_613769.1 99081615 4076803 1867202..1868335 1 NC_008044.1 KEGG: sil:SPO2651 glycosyl transferase, group 2 family protein, ev=1e-131, 64% identity; glycosyl transferase family protein 1868335 4076803 TM1040_1774 Ruegeria sp. TM1040 glycosyl transferase family protein YP_613769.1 1867202 D 292414 CDS YP_613770.1 99081616 4076804 1868485..1869480 1 NC_008044.1 KEGG: sil:SPO2652 hypothetical protein, ev=1e-120, 65% identity; hypothetical protein 1869480 4076804 TM1040_1775 Ruegeria sp. TM1040 hypothetical protein YP_613770.1 1868485 D 292414 CDS YP_613771.1 99081617 4076805 1869523..1870563 1 NC_008044.1 catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis; dihydroorotase 1870563 4076805 TM1040_1776 Ruegeria sp. TM1040 dihydroorotase YP_613771.1 1869523 D 292414 CDS YP_613772.1 99081618 4076806 1870640..1871320 1 NC_008044.1 involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate; orotate phosphoribosyltransferase 1871320 pyrE 4076806 pyrE Ruegeria sp. TM1040 orotate phosphoribosyltransferase YP_613772.1 1870640 D 292414 CDS YP_613773.1 99081619 4076807 1871573..1873090 1 NC_008044.1 unwinds double stranded DNA; replicative DNA helicase 1873090 4076807 TM1040_1778 Ruegeria sp. TM1040 replicative DNA helicase YP_613773.1 1871573 D 292414 CDS YP_613774.1 99081620 4076808 1873275..1874312 1 NC_008044.1 KEGG: sil:SPO2670 alanine racemase, ev=1e-130, 67% identity; TIGRFAM: alanine racemase: (8.8e-50); PFAM: alanine racemase-like: (3.9e-55); alanine racemase 1874312 4076808 TM1040_1779 Ruegeria sp. TM1040 alanine racemase YP_613774.1 1873275 D 292414 CDS YP_613775.1 99081621 4076809 1874309..1875091 1 NC_008044.1 PFAM: protein of unknown function DUF140: (1.4e-87); KEGG: sil:SPO2671 membrane protein, ev=1e-117, 83% identity; hypothetical protein 1875091 4076809 TM1040_1780 Ruegeria sp. TM1040 hypothetical protein YP_613775.1 1874309 D 292414 CDS YP_613776.1 99081622 4076810 1875088..1875846 1 NC_008044.1 PFAM: ABC transporter related: (9.4e-51); SMART: ATPase: (2.8e-14); KEGG: sil:SPO2672 ABC transporter, ATP-binding protein, ev=1e-116, 85% identity; ABC transporter 1875846 4076810 TM1040_1781 Ruegeria sp. TM1040 ABC transporter YP_613776.1 1875088 D 292414 CDS YP_613777.1 99081623 4076811 1875910..1876587 1 NC_008044.1 hypothetical protein 1876587 4076811 TM1040_1782 Ruegeria sp. TM1040 hypothetical protein YP_613777.1 1875910 D 292414 CDS YP_613778.1 99081624 4076812 1876584..1877072 1 NC_008044.1 PFAM: Paraquat-inducible protein A: (5.2e-07); KEGG: sil:SPO2673 paraquat-inducible protein A, , ev=2e-60, 78% identity; paraquat-inducible protein A 1877072 4076812 TM1040_1783 Ruegeria sp. TM1040 paraquat-inducible protein A YP_613778.1 1876584 D 292414 CDS YP_613779.1 99081625 4076813 1877394..1878758 1 NC_008044.1 Sms; stabilizes the strand-invasion intermediate during the DNA repair; involved in recombination of donor DNA and plays an important role in DNA damage repair after exposure to mutagenic agents; DNA repair protein RadA 1878758 4076813 TM1040_1784 Ruegeria sp. TM1040 DNA repair protein RadA YP_613779.1 1877394 D 292414 CDS YP_613780.1 99081626 4076814 1878733..1879356 1 NC_008044.1 PFAM: Colicin V production protein: (2e-21); KEGG: sil:SPO2675 CvpA family protein, ev=2e-73, 73% identity; colicin V production protein 1879356 4076814 TM1040_1785 Ruegeria sp. TM1040 colicin V production protein YP_613780.1 1878733 D 292414 CDS YP_613781.1 99081627 4076815 1879765..1880475 1 NC_008044.1 KEGG: sil:SPO2676 hypothetical protein, ev=7e-18, 35% identity; hypothetical protein 1880475 4076815 TM1040_1786 Ruegeria sp. TM1040 hypothetical protein YP_613781.1 1879765 D 292414 CDS YP_613782.1 99081628 4076816 1880937..1882457 1 NC_008044.1 Catalyzes first step of the de novo purine nucleotide biosynthetic pathway; amidophosphoribosyltransferase 1882457 4076816 TM1040_1787 Ruegeria sp. TM1040 amidophosphoribosyltransferase YP_613782.1 1880937 D 292414 CDS YP_613783.1 99081629 4076817 1882654..1883196 1 NC_008044.1 KEGG: bca:BCE1117 hypothetical protein, ev=2e-07, 27% identity; hypothetical protein 1883196 4076817 TM1040_1788 Ruegeria sp. TM1040 hypothetical protein YP_613783.1 1882654 D 292414 CDS YP_613784.1 99081630 4076818 1883451..1883705 1 NC_008044.1 KEGG: sil:SPO2678 hypothetical protein, ev=2e-07, 35% identity; hypothetical protein 1883705 4076818 TM1040_1789 Ruegeria sp. TM1040 hypothetical protein YP_613784.1 1883451 D 292414 CDS YP_613785.1 99081631 4076819 1883789..1884436 1 NC_008044.1 PFAM: short-chain dehydrogenase/reductase SDR: (3.8e-09); KEGG: sil:SPO2679 oxidoreductase, short-chain dehydrogenase/reductase family, ev=2e-86, 76% identity; short-chain dehydrogenase/reductase SDR 1884436 4076819 TM1040_1790 Ruegeria sp. TM1040 short-chain dehydrogenase/reductase SDR YP_613785.1 1883789 D 292414 CDS YP_613786.1 99081632 4076820 1884712..1885494 1 NC_008044.1 catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate; stationary phase survival protein SurE 1885494 4076820 TM1040_1791 Ruegeria sp. TM1040 stationary phase survival protein SurE YP_613786.1 1884712 D 292414 CDS YP_613787.1 99081633 4076821 1885491..1886138 1 NC_008044.1 KEGG: sil:SPO2687 protein-L-isoaspartate O-methyltransferase, ev=8e-98, 83% identity; TIGRFAM: protein-L-isoaspartate O-methyltransferase: (6.2e-60); PFAM: protein-L-isoaspartate(D-aspartate) O-methyltransferase: (1.2e-59) Methyltransferase type 11: (0.0017); protein-L-isoaspartate O-methyltransferase 1886138 4076821 TM1040_1792 Ruegeria sp. TM1040 protein-L-isoaspartate O-methyltransferase YP_613787.1 1885491 D 292414 CDS YP_613788.1 99081634 4076822 1886267..1887547 1 NC_008044.1 PFAM: Peptidoglycan-binding LysM: (4.3e-14) peptidase M23B: (6e-21); KEGG: sil:SPO2686 LysM domain/M23/M37 peptidase, ev=1e-131, 64% identity; peptidase M23B 1887547 4076822 TM1040_1793 Ruegeria sp. TM1040 peptidase M23B YP_613788.1 1886267 D 292414 CDS YP_613789.1 99081635 4076823 complement(1887686..1888561) 1 NC_008044.1 PFAM: protein of unknown function DUF815: (1.1e-60); KEGG: sil:SPO2680 hypothetical protein, ev=1e-139, 85% identity; hypothetical protein 1888561 4076823 TM1040_1794 Ruegeria sp. TM1040 hypothetical protein YP_613789.1 1887686 R 292414 CDS YP_613790.1 99081636 4076824 complement(1888716..1889606) 1 NC_008044.1 TIGRFAM: Sec-independent protein translocase TatC: (7.5e-64); PFAM: Sec-independent periplasmic protein translocase: (2.9e-60); KEGG: sil:SPO2681 twin-arginine translocation protein TatC, ev=1e-144, 89% identity; Sec-independent protein translocase TatC 1889606 4076824 TM1040_1795 Ruegeria sp. TM1040 Sec-independent protein translocase TatC YP_613790.1 1888716 R 292414 CDS YP_613791.1 99081637 4076825 complement(1889603..1890091) 1 NC_008044.1 TIGRFAM: twin-arginine translocation protein TatB: (1.6e-23); PFAM: sec-independent translocation protein mttA/Hcf106: (8.7e-05); KEGG: sil:SPO2682 twin-arginine translocation protein TatB, ev=5e-54, 71% identity; twin-arginine translocation protein TatB 1890091 4076825 TM1040_1796 Ruegeria sp. TM1040 twin-arginine translocation protein TatB YP_613791.1 1889603 R 292414 CDS YP_613792.1 99081638 4076943 complement(1890099..1890314) 1 NC_008044.1 PFAM: sec-independent translocation protein mttA/Hcf106: (2.5e-06); KEGG: sil:SPO2683 twin-arginine translocation protein, TatA/E family, ev=1e-27, 84% identity; sec-independent translocation protein mttA/Hcf106 1890314 4076943 TM1040_1797 Ruegeria sp. TM1040 sec-independent translocation protein mttA/Hcf106 YP_613792.1 1890099 R 292414 CDS YP_613793.1 99081639 4076944 1890558..1890881 1 NC_008044.1 KEGG: sil:SPO2684 hypothetical protein, ev=1e-23, 53% identity; hypothetical protein 1890881 4076944 TM1040_1798 Ruegeria sp. TM1040 hypothetical protein YP_613793.1 1890558 D 292414 CDS YP_613794.1 99081640 4076945 1890915..1891604 1 NC_008044.1 PFAM: Helix-turn-helix, type 11: (3.8e-17); KEGG: sil:SPO2685 hypothetical protein, ev=1e-100, 83% identity; type 11 helix-turn-helix protein 1891604 4076945 TM1040_1799 Ruegeria sp. TM1040 type 11 helix-turn-helix protein YP_613794.1 1890915 D 292414 CDS YP_613795.1 99081641 4076946 complement(1891610..1892491) 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (6.7e-12); KEGG: syn:sll1469 hypothetical protein, ev=5e-70, 47% identity; N-acetyltransferase GCN5 1892491 4076946 TM1040_1800 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_613795.1 1891610 R 292414 CDS YP_613796.1 99081642 4076947 complement(1892504..1893631) 1 NC_008044.1 PFAM: ABC transporter related: (4.8e-60) Transport-associated OB: (8.4e-08); SMART: ATPase: (2.2e-22); KEGG: sil:SPO2689 iron ABC transporter, ATP-binding protein, , ev=1e-168, 81% identity; ABC transporter 1893631 4076947 TM1040_1801 Ruegeria sp. TM1040 ABC transporter YP_613796.1 1892504 R 292414 CDS YP_613797.1 99081643 4076948 complement(1893699..1894817) 1 NC_008044.1 KEGG: sil:SPO2691 hypothetical protein, ev=1e-125, 61% identity; hypothetical protein 1894817 4076948 TM1040_1802 Ruegeria sp. TM1040 hypothetical protein YP_613797.1 1893699 R 292414 CDS YP_613798.1 99081644 4076949 complement(1894822..1895601) 1 NC_008044.1 PFAM: short-chain dehydrogenase/reductase SDR: (2.9e-13); KEGG: sil:SPO2692 oxidoreductase, short chain dehydrogenase/reductase family, ev=1e-112, 77% identity; short-chain dehydrogenase/reductase SDR 1895601 4076949 TM1040_1803 Ruegeria sp. TM1040 short-chain dehydrogenase/reductase SDR YP_613798.1 1894822 R 292414 CDS YP_613799.1 99081645 4076950 1895802..1896818 1 NC_008044.1 KEGG: sil:SPO2693 hypothetical protein, ev=2e-97, 53% identity; hypothetical protein 1896818 4076950 TM1040_1804 Ruegeria sp. TM1040 hypothetical protein YP_613799.1 1895802 D 292414 CDS YP_613800.1 99081646 4076951 complement(1896897..1897289) 1 NC_008044.1 hypothetical protein 1897289 4076951 TM1040_1805 Ruegeria sp. TM1040 hypothetical protein YP_613800.1 1896897 R 292414 CDS YP_613801.1 99081647 4076952 complement(1897294..1897587) 1 NC_008044.1 PFAM: protein of unknown function DUF883, ElaB: (1.3e-05); KEGG: bmb:BruAb1_1648 hypothetical protein, ev=9e-07, 32% identity; hypothetical protein 1897587 4076952 TM1040_1806 Ruegeria sp. TM1040 hypothetical protein YP_613801.1 1897294 R 292414 CDS YP_613802.1 99081648 4076953 1897799..1899487 1 NC_008044.1 TIGRFAM: peptide chain release factor 3: (2.8e-226) Small GTP-binding protein domain: (3.3e-17); PFAM: protein synthesis factor, GTP-binding: (3.7e-54) elongation factor Tu, domain 2: (2.2e-07); KEGG: sil:SPO2695 peptide chain release factor 3, ev=0.0, 91% identity; peptide chain release factor 3 1899487 4076953 TM1040_1807 Ruegeria sp. TM1040 peptide chain release factor 3 YP_613802.1 1897799 D 292414 CDS YP_613803.1 99081649 4076954 1899560..1900498 1 NC_008044.1 KEGG: sil:SPO1444 hypothetical protein, ev=1e-92, 54% identity; hypothetical protein 1900498 4076954 TM1040_1808 Ruegeria sp. TM1040 hypothetical protein YP_613803.1 1899560 D 292414 CDS YP_613804.1 99081650 4076955 1900693..1902174 1 NC_008044.1 PFAM: helicase-like: (2.3e-36) DEAD/DEAH box helicase-like: (6.8e-68); KEGG: sil:SPO1443 ATP-dependent RNA helicase RhlE, ev=0.0, 75% identity; DEAD/DEAH box helicase 1902174 4076955 TM1040_1809 Ruegeria sp. TM1040 DEAD/DEAH box helicase YP_613804.1 1900693 D 292414 CDS YP_613805.1 99081651 4076956 complement(1902340..1902666) 1 NC_008044.1 hypothetical protein 1902666 4076956 TM1040_1810 Ruegeria sp. TM1040 hypothetical protein YP_613805.1 1902340 R 292414 CDS YP_613806.1 99081652 4076957 complement(1902842..1904218) 1 NC_008044.1 TIGRFAM: TRAP dicarboxylate transporter- DctM subunit: (8.4e-163); PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit: (2.1e-137); KEGG: sil:SPO2626 TRAP transporter, DctM subunit, ev=0.0, 81% identity; TRAP dicarboxylate transporter- DctM subunit 1904218 4076957 TM1040_1811 Ruegeria sp. TM1040 TRAP dicarboxylate transporter- DctM subunit YP_613806.1 1902842 R 292414 CDS YP_613807.1 99081653 4076958 complement(1904218..1904895) 1 NC_008044.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component: (1.4e-43); KEGG: sil:SPO2627 TRAP transporter, DctQ subunit, ev=1e-69, 58% identity; tripartite ATP-independent periplasmic transporter DctQ 1904895 4076958 TM1040_1812 Ruegeria sp. TM1040 tripartite ATP-independent periplasmic transporter DctQ YP_613807.1 1904218 R 292414 CDS YP_613808.1 99081654 4076959 complement(1905025..1906029) 1 NC_008044.1 TIGRFAM: TRAP dicarboxylate transporter, DctP subunit: (4.9e-85); PFAM: TRAP dicarboxylate transporter- DctP subunit: (3.4e-124); KEGG: sil:SPO2628 TRAP transporter solute receptor, DctP family, ev=1e-160, 84% identity; TRAP dicarboxylate transporter subunit DctP 1906029 4076959 TM1040_1813 Ruegeria sp. TM1040 TRAP dicarboxylate transporter subunit DctP YP_613808.1 1905025 R 292414 CDS YP_613809.1 99081655 4076960 complement(1906276..1907505) 1 NC_008044.1 PFAM: response regulator receiver: (1.8e-31) sigma-54 factor, interaction region: (6.1e-23) helix-turn-helix, Fis-type: (1.1e-08); KEGG: sil:SPO2629 C4-dicarboxylate transport transcriptional regulatory protein, ev=1e-161, 71% identity; two component, sigma54 specific, Fis family transcriptional regulator 1907505 4076960 TM1040_1814 Ruegeria sp. TM1040 two component, sigma54 specific, Fis family transcriptional regulator YP_613809.1 1906276 R 292414 CDS YP_613810.1 99081656 4076961 complement(1907502..1909253) 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (7.1e-25) histidine kinase A-like: (2.4e-14); KEGG: sil:SPO2630 C4-dicarboxylate transport sensor protein, ev=0.0, 65% identity; sensor signal transduction histidine kinase 1909253 4076961 TM1040_1815 Ruegeria sp. TM1040 sensor signal transduction histidine kinase YP_613810.1 1907502 R 292414 CDS YP_613811.1 99081657 4076962 1909253..1910500 1 NC_008044.1 PFAM: cytochrome P450: (3.7e-09); KEGG: jan:Jann_1726 cytochrome P450, ev=1e-130, 61% identity; cytochrome P450 1910500 4076962 TM1040_1816 Ruegeria sp. TM1040 cytochrome P450 YP_613811.1 1909253 D 292414 CDS YP_613812.1 99081658 4076963 1910678..1911868 1 NC_008044.1 KEGG: sil:SPO2988 hypothetical protein, ev=1e-176, 77% identity; hypothetical protein 1911868 4076963 TM1040_1817 Ruegeria sp. TM1040 hypothetical protein YP_613812.1 1910678 D 292414 CDS YP_613813.1 99081659 4076964 1912042..1913139 1 NC_008044.1 KEGG: sil:SPO2990 hypothetical protein, ev=1e-145, 67% identity; hypothetical protein 1913139 4076964 TM1040_1818 Ruegeria sp. TM1040 hypothetical protein YP_613813.1 1912042 D 292414 CDS YP_613814.1 99081660 4076965 1913416..1913886 1 NC_008044.1 hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine; D-tyrosyl-tRNA(Tyr) deacylase 1913886 4076965 TM1040_1819 Ruegeria sp. TM1040 D-tyrosyl-tRNA(Tyr) deacylase YP_613814.1 1913416 D 292414 CDS YP_613815.1 99081661 4076966 1914075..1915658 1 NC_008044.1 TIGRFAM: Twin-arginine translocation pathway signal: (0.0088); PFAM: extracellular solute-binding protein, family 5: (7.9e-79); KEGG: mlo:mll5127 ABC transporter, binding protein, ev=0.0, 62% identity; twin-arginine translocation pathway signal 1915658 4076966 TM1040_1820 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_613815.1 1914075 D 292414 CDS YP_613816.1 99081662 4076967 1915660..1916616 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (4.5e-45); KEGG: sil:SPO2996 peptide/nickel/opine uptake family ABC transporter, permease protein, ev=1e-138, 77% identity; binding-protein-dependent transport system inner membrane protein 1916616 4076967 TM1040_1821 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_613816.1 1915660 D 292414 CDS YP_613817.1 99081663 4076968 1916613..1917428 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (3.4e-35); KEGG: sil:SPO2997 peptide/nickel/opine uptake family ABC transporter, permease protein, ev=1e-127, 84% identity; binding-protein-dependent transport system inner membrane protein 1917428 4076968 TM1040_1822 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_613817.1 1916613 D 292414 CDS YP_613818.1 99081664 4076969 1917425..1919062 1 NC_008044.1 PFAM: ABC transporter related: (1e-55); SMART: ATPase: (1.5e-21); KEGG: sil:SPO2998 peptide/nickel/opine uptake family ABC transporter, ATP-binding protein, ev=0.0, 88% identity; ABC transporter 1919062 4076969 TM1040_1823 Ruegeria sp. TM1040 ABC transporter YP_613818.1 1917425 D 292414 CDS YP_613819.1 99081665 4076970 1919245..1920081 1 NC_008044.1 KEGG: sil:SPO3000 hypothetical protein, ev=1e-146, 87% identity; hypothetical protein 1920081 4076970 TM1040_1824 Ruegeria sp. TM1040 hypothetical protein YP_613819.1 1919245 D 292414 CDS YP_613820.1 99081666 4076971 1920125..1920685 1 NC_008044.1 KEGG: sil:SPO3001 hypothetical protein, ev=2e-51, 52% identity; hypothetical protein 1920685 4076971 TM1040_1825 Ruegeria sp. TM1040 hypothetical protein YP_613820.1 1920125 D 292414 CDS YP_613821.1 99081667 4076972 complement(1920735..1921682) 1 NC_008044.1 PFAM: Alpha/beta hydrolase fold-3: (2.2e-72); KEGG: sil:SPO3002 lipase, , ev=6e-99, 58% identity; alpha/beta hydrolase 1921682 4076972 TM1040_1826 Ruegeria sp. TM1040 alpha/beta hydrolase YP_613821.1 1920735 R 292414 CDS YP_613822.1 99081668 4076973 complement(1921801..1923687) 1 NC_008044.1 activates fatty acids by binding to coenzyme A; AMP-binding protein 1923687 4076973 TM1040_1827 Ruegeria sp. TM1040 AMP-binding protein YP_613822.1 1921801 R 292414 CDS YP_613823.1 99081669 4076974 complement(1923997..1925799) 1 NC_008044.1 KEGG: sil:SPO3005 ABC transporter, ATP binding/permease protein, ev=0.0, 77% identity; TIGRFAM: ABC transporter, ATP-binding/permease protein: (0); PFAM: ABC transporter, transmembrane region: (2.2e-35) ABC transporter related: (1.4e-70); SMART: ATPase: (2.1e-23); ABC transporter ATP-binding protein/permease 1925799 4076974 TM1040_1828 Ruegeria sp. TM1040 ABC transporter ATP-binding protein/permease YP_613823.1 1923997 R 292414 CDS YP_613824.1 99081670 4076975 1926225..1927085 1 NC_008044.1 KEGG: hch:HCH_01550 hypothetical protein, ev=2e-50, 37% identity; hypothetical protein 1927085 4076975 TM1040_1829 Ruegeria sp. TM1040 hypothetical protein YP_613824.1 1926225 D 292414 CDS YP_613825.1 99081671 4076976 1927315..1927812 1 NC_008044.1 hypothetical protein 1927812 4076976 TM1040_1830 Ruegeria sp. TM1040 hypothetical protein YP_613825.1 1927315 D 292414 CDS YP_613826.1 99081672 4076977 complement(1927865..1928956) 1 NC_008044.1 PFAM: protein of unknown function DUF900, hydrolase-like: (8.7e-23); KEGG: rso:RSc0827 hypothetical protein, ev=6e-27, 32% identity; hypothetical protein 1928956 4076977 TM1040_1831 Ruegeria sp. TM1040 hypothetical protein YP_613826.1 1927865 R 292414 CDS YP_613827.1 99081673 4076978 1929196..1930872 1 NC_008044.1 KEGG: bja:bll3105 hypothetical protein, ev=1e-128, 45% identity; hypothetical protein 1930872 4076978 TM1040_1832 Ruegeria sp. TM1040 hypothetical protein YP_613827.1 1929196 D 292414 CDS YP_613828.1 99081674 4076979 complement(1931108..1931575) 1 NC_008044.1 hypothetical protein 1931575 4076979 TM1040_1833 Ruegeria sp. TM1040 hypothetical protein YP_613828.1 1931108 R 292414 CDS YP_613829.1 99081675 4076980 1931935..1934538 1 NC_008044.1 KEGG: bja:bll7673 hypothetical protein, ev=1e-33, 34% identity; RTX toxin-like protein 1934538 4076980 TM1040_1834 Ruegeria sp. TM1040 RTX toxin-like protein YP_613829.1 1931935 D 292414 CDS YP_613830.1 99081676 4076981 1935253..1935987 1 NC_008044.1 PFAM: cobalamin (vitamin B12) biosynthesis CbiX protein: (3.4e-07); KEGG: sil:SPO2745 hypothetical protein, ev=6e-52, 47% identity; cobalamin (vitamin B12) biosynthesis CbiX protein 1935987 4076981 TM1040_1835 Ruegeria sp. TM1040 cobalamin (vitamin B12) biosynthesis CbiX protein YP_613830.1 1935253 D 292414 CDS YP_613831.1 99081677 4077861 1936107..1937426 1 NC_008044.1 PFAM: glutamine synthetase, catalytic region: (2.3e-96); KEGG: rsp:RSP_0375 probable glutamine synthetase, ev=1e-153, 61% identity; L-glutamine synthetase 1937426 4077861 TM1040_1836 Ruegeria sp. TM1040 L-glutamine synthetase YP_613831.1 1936107 D 292414 CDS YP_613832.1 99081678 4077862 1937482..1938162 1 NC_008044.1 KEGG: sil:SPO1301 glutamine amidotransferase, class I, ev=1e-82, 63% identity; glutamine amidotransferase 1938162 4077862 TM1040_1837 Ruegeria sp. TM1040 glutamine amidotransferase YP_613832.1 1937482 D 292414 CDS YP_613833.1 99081679 4077863 1938162..1939529 1 NC_008044.1 PFAM: glutamine synthetase, catalytic region: (5.5e-94); KEGG: sil:SPO1300 glutamine synthetase family protein, ev=0.0, 88% identity; L-glutamine synthetase 1939529 4077863 TM1040_1838 Ruegeria sp. TM1040 L-glutamine synthetase YP_613833.1 1938162 D 292414 CDS YP_613834.1 99081680 4077864 1939640..1940950 1 NC_008044.1 PFAM: FAD dependent oxidoreductase: (3.7e-96); KEGG: rsp:RSP_0378 hypothetical protein, ev=1e-150, 62% identity; FAD dependent oxidoreductase 1940950 4077864 TM1040_1839 Ruegeria sp. TM1040 FAD dependent oxidoreductase YP_613834.1 1939640 D 292414 CDS YP_613835.1 99081681 4077865 1941291..1942529 1 NC_008044.1 PFAM: DegT/DnrJ/EryC1/StrS aminotransferase: (1.1e-50) aminotransferase, class I and II: (5.8e-05); KEGG: sil:SPO1295 aminotransferase, DegT/DnrJ/EryC1/StrS family, ev=0.0, 80% identity; DegT/DnrJ/EryC1/StrS aminotransferase 1942529 4077865 TM1040_1840 Ruegeria sp. TM1040 DegT/DnrJ/EryC1/StrS aminotransferase YP_613835.1 1941291 D 292414 CDS YP_613836.1 99081682 4077866 complement(1942779..1943336) 1 NC_008044.1 TIGRFAM: Polyhydroxyalkanoate synthesis repressor PhaR: (7e-66); PFAM: PHB accumulation regulatory: (5.5e-09) PHA accumulation regulator DNA-binding-like: (1.1e-39); KEGG: sil:SPO1294 polyhydroxyalkanoate synthesis repressor PhaR, ev=1e-84, 84% identity; polyhydroxyalkonate synthesis repressor PhaR 1943336 4077866 TM1040_1841 Ruegeria sp. TM1040 polyhydroxyalkonate synthesis repressor PhaR YP_613836.1 1942779 R 292414 CDS YP_613837.1 99081683 4077867 complement(1943664..1944110) 1 NC_008044.1 KEGG: sil:SPO1293 phasin, PhaP, ev=2e-60, 81% identity; phasin, PhaP 1944110 4077867 TM1040_1842 Ruegeria sp. TM1040 phasin, PhaP YP_613837.1 1943664 R 292414 CDS YP_613838.1 99081684 4077868 1944522..1944884 1 NC_008044.1 hypothetical protein 1944884 4077868 TM1040_1843 Ruegeria sp. TM1040 hypothetical protein YP_613838.1 1944522 D 292414 CDS YP_613839.1 99081685 4077869 1944980..1945750 1 NC_008044.1 KEGG: sil:SPO1128 hypothetical protein, ev=3e-84, 67% identity; hypothetical protein 1945750 4077869 TM1040_1844 Ruegeria sp. TM1040 hypothetical protein YP_613839.1 1944980 D 292414 CDS YP_613840.1 99081686 4077870 complement(1945917..1946600) 1 NC_008044.1 PFAM: ABC transporter related: (8.3e-58); SMART: ATPase: (5.4e-16); KEGG: sil:SPO1124 lipoprotein releasing system ATP-binding protein, ev=1e-93, 78% identity; ABC transporter 1946600 4077870 TM1040_1845 Ruegeria sp. TM1040 ABC transporter YP_613840.1 1945917 R 292414 CDS YP_613841.1 99081687 4077871 complement(1946593..1947876) 1 NC_008044.1 TIGRFAM: Lipoprotein releasing system, transmembrane protein, LolC/E family: (9.8e-135); PFAM: protein of unknown function DUF214: (5.5e-40); KEGG: sil:SPO1123 lipoprotein releasing system transmembrane protein LolE, ev=0.0, 76% identity; LolC/E family lipoprotein releasing system, transmembrane protein 1947876 4077871 TM1040_1846 Ruegeria sp. TM1040 LolC/E family lipoprotein releasing system, transmembrane protein YP_613841.1 1946593 R 292414 CDS YP_613842.1 99081688 4077872 complement(1947965..1948477) 1 NC_008044.1 KEGG: ret:RHE_CH03836 hypothetical protein, ev=4e-18, 39% identity; hypothetical protein 1948477 4077872 TM1040_1847 Ruegeria sp. TM1040 hypothetical protein YP_613842.1 1947965 R 292414 CDS YP_613843.1 99081689 4077873 complement(1948766..1949188) 1 NC_008044.1 PFAM: thioesterase superfamily: (9.8e-06); KEGG: bja:blr1345 hypothetical protein, ev=2e-11, 31% identity; thioesterase superfamily protein 1949188 4077873 TM1040_1848 Ruegeria sp. TM1040 thioesterase superfamily protein YP_613843.1 1948766 R 292414 CDS YP_613844.1 99081690 4077874 complement(1949215..1950009) 1 NC_008044.1 hypothetical protein 1950009 4077874 TM1040_1849 Ruegeria sp. TM1040 hypothetical protein YP_613844.1 1949215 R 292414 CDS YP_613845.1 99081691 4077875 complement(1950214..1950744) 1 NC_008044.1 PFAM: bifunctional deaminase-reductase-like: (1.6e-07); KEGG: jan:Jann_2049 bifunctional deaminase-reductase-like, ev=4e-62, 62% identity; bifunctional deaminase/reductase-like protein 1950744 4077875 TM1040_1850 Ruegeria sp. TM1040 bifunctional deaminase/reductase-like protein YP_613845.1 1950214 R 292414 CDS YP_613846.1 99081692 4077876 complement(1951398..1952174) 1 NC_008044.1 hypothetical protein 1952174 4077876 TM1040_1851 Ruegeria sp. TM1040 hypothetical protein YP_613846.1 1951398 R 292414 CDS YP_613847.1 99081693 4077877 complement(1952289..1953644) 1 NC_008044.1 catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro); prolyl-tRNA synthetase 1953644 4077877 TM1040_1852 Ruegeria sp. TM1040 prolyl-tRNA synthetase YP_613847.1 1952289 R 292414 CDS YP_613848.1 99081694 4077878 complement(1953837..1954169) 1 NC_008044.1 hypothetical protein 1954169 4077878 TM1040_1853 Ruegeria sp. TM1040 hypothetical protein YP_613848.1 1953837 R 292414 CDS YP_613849.1 99081695 4077879 1954506..1956245 1 NC_008044.1 PFAM: response regulator receiver: (5.7e-18) GAF: (1.2e-16) ATP-binding region, ATPase-like: (2.8e-39) histidine kinase A-like: (2.1e-21); KEGG: ccr:CC2988 sensor histidine kinase/response regulator, ev=2e-61, 38% identity; GAF sensor hybrid histidine kinase 1956245 4077879 TM1040_1854 Ruegeria sp. TM1040 GAF sensor hybrid histidine kinase YP_613849.1 1954506 D 292414 CDS YP_613850.1 99081696 4077880 1956344..1957486 1 NC_008044.1 PFAM: protein of unknown function UPF0118: (2.7e-50); KEGG: sil:SPO1119 membrane protein, ev=1e-136, 65% identity; hypothetical protein 1957486 4077880 TM1040_1855 Ruegeria sp. TM1040 hypothetical protein YP_613850.1 1956344 D 292414 CDS YP_613851.1 99081697 4077881 1957540..1958217 1 NC_008044.1 PFAM: Chromosomal replication initiator, DnaA: (0.0011); KEGG: sil:SPO1118 hypothetical protein, ev=1e-77, 66% identity; chromosomal replication initiator DnaA 1958217 4077881 TM1040_1856 Ruegeria sp. TM1040 chromosomal replication initiator DnaA YP_613851.1 1957540 D 292414 CDS YP_613852.1 99081698 4077882 1958393..1960039 1 NC_008044.1 PFAM: Ppx/GppA phosphatase: (9.9e-28); KEGG: sil:SPO1117 phosphatase, Ppx/GppA family, ev=0.0, 73% identity; Ppx/GppA phosphatase 1960039 4077882 TM1040_1857 Ruegeria sp. TM1040 Ppx/GppA phosphatase YP_613852.1 1958393 D 292414 CDS YP_613853.1 99081699 4077883 complement(1960107..1960547) 1 NC_008044.1 KEGG: rsp:RSP_6229 hypothetical protein, ev=1e-15, 39% identity; hypothetical protein 1960547 4077883 TM1040_1858 Ruegeria sp. TM1040 hypothetical protein YP_613853.1 1960107 R 292414 CDS YP_613854.1 99081700 4077884 complement(1960571..1961605) 1 NC_008044.1 PFAM: Endonuclease/exonuclease/phosphatase: (8e-05); KEGG: sil:SPO1109 endonuclease/exonuclease/phosphatase family protein, ev=1e-106, 59% identity; endonuclease/exonuclease/phosphatase 1961605 4077884 TM1040_1859 Ruegeria sp. TM1040 endonuclease/exonuclease/phosphatase YP_613854.1 1960571 R 292414 CDS YP_613855.1 99081701 4077885 complement(1961586..1962293) 1 NC_008044.1 PFAM: heat shock protein DnaJ-like: (9.2e-06); KEGG: sil:SPO1108 DnaJ-like protein DjlA, , ev=1e-94, 73% identity; molecular chaperone DnaJ 1962293 4077885 TM1040_1860 Ruegeria sp. TM1040 molecular chaperone DnaJ YP_613855.1 1961586 R 292414 CDS YP_613856.1 99081702 4077886 complement(1962303..1962836) 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (2e-17); KEGG: sil:SPO1107 phosphinothricin N-acetyltransferase, , ev=5e-37, 54% identity; N-acetyltransferase GCN5 1962836 4077886 TM1040_1861 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_613856.1 1962303 R 292414 CDS YP_613857.1 99081703 4077887 complement(1962836..1963474) 1 NC_008044.1 KEGG: sil:SPO1106 hypothetical protein, ev=3e-68, 66% identity; hypothetical protein 1963474 4077887 TM1040_1862 Ruegeria sp. TM1040 hypothetical protein YP_613857.1 1962836 R 292414 CDS YP_613858.1 99081704 4077888 1963667..1964164 1 NC_008044.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase: (3.2e-11); KEGG: sil:SPOA0321 glyoxalase family protein, ev=9e-45, 59% identity; glyoxalase/bleomycin resistance protein/dioxygenase 1964164 4077888 TM1040_1863 Ruegeria sp. TM1040 glyoxalase/bleomycin resistance protein/dioxygenase YP_613858.1 1963667 D 292414 CDS YP_613859.1 99081705 4077889 complement(1964494..1964646) 1 NC_008044.1 KEGG: atc:AGR_L_680 hypothetical protein, ev=1e-08, 65% identity; hypothetical protein 1964646 4077889 TM1040_1864 Ruegeria sp. TM1040 hypothetical protein YP_613859.1 1964494 R 292414 CDS YP_613860.1 99081706 4077890 complement(1964662..1966647) 1 NC_008044.1 MDM; functions in conversion of succinate to propionate; methylmalonyl-CoA mutase 1966647 4077890 TM1040_1865 Ruegeria sp. TM1040 methylmalonyl-CoA mutase YP_613860.1 1964662 R 292414 CDS YP_613861.1 99081707 4077891 complement(1966754..1967707) 1 NC_008044.1 KEGG: sil:SPO1104 hypothetical protein, ev=3e-87, 53% identity; hypothetical protein 1967707 4077891 TM1040_1866 Ruegeria sp. TM1040 hypothetical protein YP_613861.1 1966754 R 292414 CDS YP_613862.1 99081708 4077892 1967864..1968388 1 NC_008044.1 KEGG: sil:SPO1103 hypothetical protein, ev=1e-34, 61% identity; hypothetical protein 1968388 4077892 TM1040_1867 Ruegeria sp. TM1040 hypothetical protein YP_613862.1 1967864 D 292414 CDS YP_613863.1 99081709 4077893 complement(1968507..1969112) 1 NC_008044.1 KEGG: sil:SPO1102 lipoprotein, , ev=2e-30, 40% identity; hypothetical protein 1969112 4077893 TM1040_1868 Ruegeria sp. TM1040 hypothetical protein YP_613863.1 1968507 R 292414 CDS YP_613864.1 99081710 4077894 complement(1969271..1971301) 1 NC_008044.1 PFAM: biotin/lipoyl attachment: (2.7e-18) ATP-dependent carboxylate-amine ligase-like, ATP-grasp: (0.00035) Carbamoyl-phosphate synthase L chain, ATP-binding: (5.6e-115) Carbamoyl-phosphate synthetase large chain-like: (1.6e-48) biotin carboxylase-like: (6e-56) RimK-like ATP-grasp: (0.00016); KEGG: sil:SPO1101 propionyl-CoA carboxylase, alpha subunit, ev=0.0, 86% identity; carbamoyl-phosphate synthase subunit L 1971301 4077894 TM1040_1869 Ruegeria sp. TM1040 carbamoyl-phosphate synthase subunit L YP_613864.1 1969271 R 292414 CDS YP_613865.1 99081711 4077895 complement(1971445..1971648) 1 NC_008044.1 KEGG: sil:SPO1100 lipoprotein, , ev=1e-11, 55% identity; lipoprotein 1971648 4077895 TM1040_1870 Ruegeria sp. TM1040 lipoprotein YP_613865.1 1971445 R 292414 CDS YP_613866.1 99081712 4077896 complement(1971641..1971898) 1 NC_008044.1 hypothetical protein 1971898 4077896 TM1040_1871 Ruegeria sp. TM1040 hypothetical protein YP_613866.1 1971641 R 292414 CDS YP_613867.1 99081713 4077897 complement(1972185..1972532) 1 NC_008044.1 KEGG: sil:SPO1097 hypothetical protein, ev=3e-52, 82% identity; hypothetical protein 1972532 4077897 TM1040_1872 Ruegeria sp. TM1040 hypothetical protein YP_613867.1 1972185 R 292414 CDS YP_613868.1 99081714 4077898 complement(1972602..1972745) 1 NC_008044.1 KEGG: sil:SPO1096 lipoprotein, , ev=8e-08, 59% identity; lipoprotein 1972745 4077898 TM1040_1873 Ruegeria sp. TM1040 lipoprotein YP_613868.1 1972602 R 292414 CDS YP_613869.1 99081715 4077899 complement(1972960..1973274) 1 NC_008044.1 KEGG: rsp:RSP_6040 hypothetical protein, ev=2e-15, 41% identity; hypothetical protein 1973274 4077899 TM1040_1874 Ruegeria sp. TM1040 hypothetical protein YP_613869.1 1972960 R 292414 CDS YP_613870.1 99081716 4077372 complement(1973883..1974230) 1 NC_008044.1 KEGG: sil:SPO1095 hypothetical protein, ev=2e-23, 65% identity; hypothetical protein 1974230 4077372 TM1040_1875 Ruegeria sp. TM1040 hypothetical protein YP_613870.1 1973883 R 292414 CDS YP_613871.1 99081717 4077373 complement(1974319..1974792) 1 NC_008044.1 hypothetical protein 1974792 4077373 TM1040_1876 Ruegeria sp. TM1040 hypothetical protein YP_613871.1 1974319 R 292414 CDS YP_613872.1 99081718 4077374 complement(1974839..1976371) 1 NC_008044.1 PFAM: carboxyl transferase: (2.3e-287); KEGG: sil:SPO1094 propionyl-CoA carboxylase, beta subunit, ev=0.0, 91% identity; propionyl-CoA carboxylase 1976371 4077374 TM1040_1877 Ruegeria sp. TM1040 propionyl-CoA carboxylase YP_613872.1 1974839 R 292414 CDS YP_613873.1 99081719 4077375 1976745..1977938 1 NC_008044.1 TIGRFAM: Drug resistance transporter Bcr/CflA subfamily: (9.4e-44); PFAM: major facilitator superfamily MFS_1: (1.5e-44); KEGG: sil:SPO1093 drug resistance transporter, Bcr/CflA family, ev=1e-143, 63% identity; Bcr/CflA subfamily drug resistance transporter 1977938 4077375 TM1040_1878 Ruegeria sp. TM1040 Bcr/CflA subfamily drug resistance transporter YP_613873.1 1976745 D 292414 CDS YP_613874.1 99081720 4077376 1978118..1979593 1 NC_008044.1 PFAM: helix-turn-helix motif: (1e-14) protein of unknown function DUF955: (3e-15); KEGG: sil:SPO1090 DNA-binding protein, , ev=0.0, 82% identity; XRE family transcriptional regulator 1979593 4077376 TM1040_1879 Ruegeria sp. TM1040 XRE family transcriptional regulator YP_613874.1 1978118 D 292414 CDS YP_613875.1 99081721 4077377 complement(1979648..1979887) 1 NC_008044.1 PFAM: protein of unknown function DUF465: (2.7e-05); KEGG: sil:SPO1089 hypothetical protein, ev=1e-32, 84% identity; hypothetical protein 1979887 4077377 TM1040_1880 Ruegeria sp. TM1040 hypothetical protein YP_613875.1 1979648 R 292414 CDS YP_613876.1 99081722 4077378 1980254..1980664 1 NC_008044.1 hypothetical protein 1980664 4077378 TM1040_1881 Ruegeria sp. TM1040 hypothetical protein YP_613876.1 1980254 D 292414 CDS YP_613877.1 99081723 4077379 complement(1980763..1982418) 1 NC_008044.1 catalyzes the oxidation of choline to betaine aldehyde and betain aldehyde to glycine betaine; choline dehydrogenase 1982418 4077379 TM1040_1882 Ruegeria sp. TM1040 choline dehydrogenase YP_613877.1 1980763 R 292414 CDS YP_613878.1 99081724 4077380 complement(1982575..1984032) 1 NC_008044.1 catalyzes the formation of betaine from betaine aldehyde; betaine aldehyde dehydrogenase 1984032 4077380 TM1040_1883 Ruegeria sp. TM1040 betaine aldehyde dehydrogenase YP_613878.1 1982575 R 292414 CDS YP_613879.1 99081725 4077381 complement(1984236..1985444) 1 NC_008044.1 KEGG: sil:SPO1087 membrane protein, , ev=1e-165, 70% identity; hypothetical protein 1985444 4077381 TM1040_1884 Ruegeria sp. TM1040 hypothetical protein YP_613879.1 1984236 R 292414 CDS YP_613880.1 99081726 4077382 1985642..1986232 1 NC_008044.1 PFAM: regulatory protein, TetR: (1e-13); KEGG: sil:SPO1086 transcriptional regulator, TetR family, ev=4e-54, 54% identity; TetR family transcriptional regulator 1986232 4077382 TM1040_1885 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_613880.1 1985642 D 292414 CDS YP_613881.1 99081727 4077383 complement(1986308..1987381) 1 NC_008044.1 KEGG: sil:SPO1081 hypothetical protein, ev=2e-17, 37% identity; integral membrane protein-like protein 1987381 4077383 TM1040_1886 Ruegeria sp. TM1040 integral membrane protein-like protein YP_613881.1 1986308 R 292414 CDS YP_613882.1 99081728 4077384 complement(1987499..1988431) 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (0.00035); KEGG: sil:SPO1080 membrane protein, , ev=1e-106, 64% identity; hypothetical protein 1988431 4077384 TM1040_1887 Ruegeria sp. TM1040 hypothetical protein YP_613882.1 1987499 R 292414 CDS YP_613883.1 99081729 4077385 1988725..1990362 1 NC_008044.1 PFAM: ABC transporter related: (1.1e-30); SMART: ATPase: (3.2e-17); KEGG: rru:Rru_A0047 ABC transporter component, ev=1e-162, 59% identity; ABC transporter 1990362 4077385 TM1040_1888 Ruegeria sp. TM1040 ABC transporter YP_613883.1 1988725 D 292414 CDS YP_613884.1 99081730 4077386 complement(1990311..1991252) 1 NC_008044.1 PFAM: Pirin-like: (3e-57); KEGG: sil:SPO2601 pirin domain protein, ev=1e-126, 69% identity; pirin 1991252 4077386 TM1040_1889 Ruegeria sp. TM1040 pirin YP_613884.1 1990311 R 292414 CDS YP_613885.1 99081731 4077387 complement(1991345..1991974) 1 NC_008044.1 PFAM: Lysine exporter protein (LYSE/YGGA): (3.4e-54); KEGG: sil:SPO1079 L-lysine exporter, , ev=6e-68, 66% identity; lysine exporter protein LysE/YggA 1991974 4077387 TM1040_1890 Ruegeria sp. TM1040 lysine exporter protein LysE/YggA YP_613885.1 1991345 R 292414 CDS YP_613886.1 99081732 4077388 1992084..1993004 1 NC_008044.1 specific inhibitor of chromosomal initiation of replication in vitro; binds the three 13-mers in the origin (oriC) to block initiation of replication; also controls genes involved in arginine transport; chromosome replication initiation inhibitor protein 1993004 4077388 TM1040_1891 Ruegeria sp. TM1040 chromosome replication initiation inhibitor protein YP_613886.1 1992084 D 292414 CDS YP_613887.1 99081733 4077389 1993025..1993882 1 NC_008044.1 KEGG: rso:RS03125 probable transmembrane protein, ev=6e-13, 25% identity; hypothetical protein 1993882 4077389 TM1040_1892 Ruegeria sp. TM1040 hypothetical protein YP_613887.1 1993025 D 292414 CDS YP_613888.2 161899028 4077390 complement(1994121..1994861) 1 NC_008044.1 PFAM: protein of unknown function DUF28: (4.3e-147); KEGG: sil:SPO1072 conserved hypothetical protein TIGR01033, ev=1e-123, 89% identity; hypothetical protein 1994861 4077390 TM1040_1893 Ruegeria sp. TM1040 hypothetical protein YP_613888.2 1994121 R 292414 CDS YP_613889.1 99081735 4077391 complement(1994821..1995183) 1 NC_008044.1 hypothetical protein 1995183 4077391 TM1040_1894 Ruegeria sp. TM1040 hypothetical protein YP_613889.1 1994821 R 292414 CDS YP_613890.1 99081736 4077392 1995323..1997098 1 NC_008044.1 PFAM: Citrate transporter: (3.1e-06) TrkA-C: (1.9e-06); KEGG: sil:SPO1076 trkA-C domain protein, ev=0.0, 79% identity; hypothetical protein 1997098 4077392 TM1040_1895 Ruegeria sp. TM1040 hypothetical protein YP_613890.1 1995323 D 292414 CDS YP_613891.1 99081737 4077393 1997303..1998976 1 NC_008044.1 proposed role in polysaccahride synthesis; FAD-binding dehydrogenase 1998976 4077393 TM1040_1896 Ruegeria sp. TM1040 FAD-binding dehydrogenase YP_613891.1 1997303 D 292414 CDS YP_613892.1 99081738 4077394 1999008..1999481 1 NC_008044.1 TIGRFAM: conserved hypothetical protein: (1.7e-48); KEGG: jan:Jann_2797 hypothetical protein, ev=3e-59, 73% identity; hypothetical protein 1999481 4077394 TM1040_1897 Ruegeria sp. TM1040 hypothetical protein YP_613892.1 1999008 D 292414 CDS YP_613893.1 99081739 4077395 complement(1999575..2000039) 1 NC_008044.1 TIGRFAM: Twin-arginine translocation pathway signal: (0.15); PFAM: protein of unknown function DUF306, Meta and HslJ: (9.4e-21); KEGG: sil:SPO2951 hypothetical protein, ev=9e-14, 41% identity; twin-arginine translocation pathway signal 2000039 4077395 TM1040_1898 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_613893.1 1999575 R 292414 CDS YP_613894.1 99081740 4077396 complement(2000157..2001935) 1 NC_008044.1 PFAM: Citrate transporter: (7.1e-07) TrkA-C: (1.9e-11); KEGG: sil:SPO2952 TrkA domain protein, ev=0.0, 84% identity; hypothetical protein 2001935 4077396 TM1040_1899 Ruegeria sp. TM1040 hypothetical protein YP_613894.1 2000157 R 292414 CDS YP_613895.1 99081741 4077397 2002217..2003110 1 NC_008044.1 PFAM: beta-lactamase: (1.6e-37); KEGG: jan:Jann_2001 beta-lactamase, ev=2e-84, 56% identity; beta-lactamase 2003110 4077397 TM1040_1900 Ruegeria sp. TM1040 beta-lactamase YP_613895.1 2002217 D 292414 CDS YP_613896.1 99081742 4077398 complement(2003515..2004327) 1 NC_008044.1 TIGRFAM: conserved hypothetical protein: (1.2e-74); PFAM: metallophosphoesterase: (4.8e-06); KEGG: sil:SPO2953 Ser/Thr protein phosphatase family protein, ev=1e-125, 80% identity; hypothetical protein 2004327 4077398 TM1040_1901 Ruegeria sp. TM1040 hypothetical protein YP_613896.1 2003515 R 292414 CDS YP_613897.1 99081743 4077399 2004704..2005543 1 NC_008044.1 KEGG: ana:alr5242 hypothetical protein, ev=1e-16, 30% identity; hypothetical protein 2005543 4077399 TM1040_1902 Ruegeria sp. TM1040 hypothetical protein YP_613897.1 2004704 D 292414 CDS YP_613898.1 99081744 4077400 complement(2005708..2006295) 1 NC_008044.1 PFAM: 5-formyltetrahydrofolate cyclo-ligase: (5.9e-26); KEGG: sil:SPO2954 5-formyltetrahydrofolate cyclo-ligase family protein, ev=2e-82, 83% identity; 5-formyltetrahydrofolate cyclo-ligase 2006295 4077400 TM1040_1903 Ruegeria sp. TM1040 5-formyltetrahydrofolate cyclo-ligase YP_613898.1 2005708 R 292414 CDS YP_613899.1 99081745 4077401 complement(2006318..2007706) 1 NC_008044.1 TIGRFAM: magnesium transporter: (7.8e-92); PFAM: CBS: (2.2e-18) MgtE integral membrane region: (8e-23) MgtE intracellular region: (3.4e-35); KEGG: sil:SPO2955 magnesium transporter, ev=0.0, 77% identity; magnesium transporter 2007706 4077401 TM1040_1904 Ruegeria sp. TM1040 magnesium transporter YP_613899.1 2006318 R 292414 CDS YP_613900.1 99081746 4077402 2007845..2009134 1 NC_008044.1 Catalyzes the deamination of guanine; guanine deaminase 2009134 4077402 TM1040_1905 Ruegeria sp. TM1040 guanine deaminase YP_613900.1 2007845 D 292414 CDS YP_613901.1 99081747 4077403 complement(2009233..2010573) 1 NC_008044.1 catalyzes the transformation of hydroxyatrazine to N-isopropylammelide and ethylamine in the atrazine degradation pathway.; hydroxydechloroatrazine ethylaminohydrolase 2010573 4077403 TM1040_1906 Ruegeria sp. TM1040 hydroxydechloroatrazine ethylaminohydrolase YP_613901.1 2009233 R 292414 CDS YP_613902.1 99081748 4077404 complement(2010784..2011578) 1 NC_008044.1 TIGRFAM: Histidinol-phosphate phosphatase, , inositol monophosphatase: (2e-108); PFAM: inositol monophosphatase: (3.9e-58); KEGG: sil:SPO2958 inositol monophosphatase family protein, ev=1e-99, 69% identity; histidinol-phosphate phosphatase 2011578 4077404 TM1040_1907 Ruegeria sp. TM1040 histidinol-phosphate phosphatase YP_613902.1 2010784 R 292414 CDS YP_613903.1 99081749 4077405 complement(2011553..2011843) 1 NC_008044.1 hypothetical protein 2011843 4077405 TM1040_1908 Ruegeria sp. TM1040 hypothetical protein YP_613903.1 2011553 R 292414 CDS YP_613904.1 99081750 4077406 complement(2011866..2012237) 1 NC_008044.1 PFAM: helix-turn-helix motif: (4e-13); KEGG: sil:SPO2959 DNA-binding protein, , ev=4e-56, 86% identity; XRE family transcriptional regulator 2012237 4077406 TM1040_1909 Ruegeria sp. TM1040 XRE family transcriptional regulator YP_613904.1 2011866 R 292414 CDS YP_613905.1 99081751 4077407 2012602..2013576 1 NC_008044.1 PFAM: Alcohol dehydrogenase, zinc-binding: (1e-38) Alcohol dehydrogenase GroES-like: (4.6e-19); KEGG: sil:SPO2960 oxidoreductase, zinc-binding dehydrogenase family, ev=1e-117, 65% identity; zinc-binding alcohol dehydrogenase 2013576 4077407 TM1040_1910 Ruegeria sp. TM1040 zinc-binding alcohol dehydrogenase YP_613905.1 2012602 D 292414 CDS YP_613906.1 99081752 4077408 complement(2013545..2014462) 1 NC_008044.1 PFAM: regulatory protein, LysR: (6.6e-20) LysR, substrate-binding: (8e-10); KEGG: sil:SPO2961 transcriptional regulator, LysR family, ev=4e-96, 60% identity; LysR family transcriptional regulator 2014462 4077408 TM1040_1911 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_613906.1 2013545 R 292414 CDS YP_613907.1 99081753 4077409 2014585..2014797 1 NC_008044.1 PFAM: protein of unknown function DUF1127: (2.6e-07); KEGG: sil:SPO2962 hypothetical protein, ev=6e-09, 51% identity; hypothetical protein 2014797 4077409 TM1040_1912 Ruegeria sp. TM1040 hypothetical protein YP_613907.1 2014585 D 292414 CDS YP_613908.1 99081754 4077410 2015026..2015805 1 NC_008044.1 PFAM: protein of unknown function UPF0005: (9.6e-13); KEGG: sil:SPO2963 membrane protein, , ev=1e-116, 82% identity; hypothetical protein 2015805 4077410 TM1040_1913 Ruegeria sp. TM1040 hypothetical protein YP_613908.1 2015026 D 292414 CDS YP_613909.1 99081755 4076865 2015909..2016448 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (6.5e-09); N-acetyltransferase GCN5 2016448 4076865 TM1040_1914 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_613909.1 2015909 D 292414 CDS YP_613910.1 99081756 4076866 complement(2016984..2017151) 1 NC_008044.1 in Escherichia coli BM108, a mutation that results in lack of L33 synthesis had no effect on ribosome synthesis or function; there are paralogous genes in several bacterial genomes, and a CXXC motif for zinc binding and an upstream regulation region of the paralog lacking this motif that are regulated by zinc similar to other ribosomal proteins like L31; the proteins in this group lack the CXXC motif; 50S ribosomal protein L33 2017151 rpmG 4076866 rpmG Ruegeria sp. TM1040 50S ribosomal protein L33 YP_613910.1 2016984 R 292414 CDS YP_613911.1 99081757 4076867 complement(2017873..2018532) 1 NC_008044.1 PFAM: N-acetylmuramoyl-L-alanine amidase, family 2: (9.5e-43); KEGG: sil:SPO2967 N-acetylmuramoyl-L-alanine amidase, , ev=2e-86, 72% identity; N-acetylmuramyl-L-alanine amidase, negative regulator of AmpC, AmpD 2018532 4076867 TM1040_1916 Ruegeria sp. TM1040 N-acetylmuramyl-L-alanine amidase, negative regulator of AmpC, AmpD YP_613911.1 2017873 R 292414 CDS YP_613912.1 99081758 4076868 complement(2018542..2019306) 1 NC_008044.1 KEGG: sil:SPO2968 hypothetical protein, ev=6e-74, 56% identity; hypothetical protein 2019306 4076868 TM1040_1917 Ruegeria sp. TM1040 hypothetical protein YP_613912.1 2018542 R 292414 CDS YP_613913.1 99081759 4076869 complement(2019347..2020834) 1 NC_008044.1 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; aspartyl/glutamyl-tRNA amidotransferase subunit A 2020834 gatA 4076869 gatA Ruegeria sp. TM1040 aspartyl/glutamyl-tRNA amidotransferase subunit A YP_613913.1 2019347 R 292414 CDS YP_613914.1 99081760 4076870 complement(2020838..2021125) 1 NC_008044.1 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; some Mycoplasma proteins contain an N-terminal fusion to an unknown domain; aspartyl/glutamyl-tRNA amidotransferase subunit C 2021125 gatC 4076870 gatC Ruegeria sp. TM1040 aspartyl/glutamyl-tRNA amidotransferase subunit C YP_613914.1 2020838 R 292414 CDS YP_613915.1 99081761 4076871 2021537..2022229 1 NC_008044.1 PFAM: beta-lactamase-like: (3.5e-11); KEGG: sil:SPO2976 metallo-beta-lactamase family protein, ev=1e-104, 76% identity; beta-lactamase-like protein 2022229 4076871 TM1040_1920 Ruegeria sp. TM1040 beta-lactamase-like protein YP_613915.1 2021537 D 292414 CDS YP_613916.1 99081762 4076872 2022229..2023398 1 NC_008044.1 PFAM: peptidase M24: (3.8e-06); KEGG: ret:RHE_PF00180 probable peptidase protein, ev=1e-116, 52% identity; peptidase M24 2023398 4076872 TM1040_1921 Ruegeria sp. TM1040 peptidase M24 YP_613916.1 2022229 D 292414 CDS YP_613917.1 99081763 4076873 complement(2023619..2024221) 1 NC_008044.1 PFAM: methyladenine glycosylase: (1.9e-78); KEGG: sil:SPO1900 DNA-3-methyladenine glycosylase I, ev=3e-74, 69% identity; DNA-3-methyladenine glycosylase I 2024221 4076873 TM1040_1922 Ruegeria sp. TM1040 DNA-3-methyladenine glycosylase I YP_613917.1 2023619 R 292414 CDS YP_613918.1 99081764 4076874 complement(2024218..2024511) 1 NC_008044.1 PFAM: YCII-related: (6.8e-09); KEGG: hch:HCH_03235 hypothetical protein, ev=4e-16, 43% identity; hypothetical protein 2024511 4076874 TM1040_1923 Ruegeria sp. TM1040 hypothetical protein YP_613918.1 2024218 R 292414 CDS YP_613919.1 99081765 4076875 complement(2024543..2025112) 1 NC_008044.1 PFAM: regulatory protein, TetR: (1.3e-17); KEGG: sil:SPO1902 transcription regulator, TetR family, ev=6e-52, 58% identity; TetR family transcriptional regulator 2025112 4076875 TM1040_1924 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_613919.1 2024543 R 292414 CDS YP_613920.1 99081766 4076876 complement(2025310..2025552) 1 NC_008044.1 hypothetical protein 2025552 4076876 TM1040_1925 Ruegeria sp. TM1040 hypothetical protein YP_613920.1 2025310 R 292414 CDS YP_613921.1 99081767 4076877 complement(2025549..2025983) 1 NC_008044.1 PFAM: CMP/dCMP deaminase, zinc-binding: (2.6e-33); KEGG: sil:SPO2983 cytidine and deoxycytidylate deaminase family protein, ev=1e-58, 76% identity; zinc-binding CMP/dCMP deaminase 2025983 4076877 TM1040_1926 Ruegeria sp. TM1040 zinc-binding CMP/dCMP deaminase YP_613921.1 2025549 R 292414 CDS YP_613922.1 99081768 4076878 2026097..2027365 1 NC_008044.1 TIGRFAM: Pseudouridine synthase, Rsu: (6e-43); PFAM: RNA-binding S4: (8.5e-13) pseudouridine synthase: (1.3e-09); KEGG: sil:SPO2984 RNA pseudouridylate synthase family protein, ev=1e-113, 63% identity; pseudouridine synthase 2027365 4076878 TM1040_1927 Ruegeria sp. TM1040 pseudouridine synthase YP_613922.1 2026097 D 292414 CDS YP_613923.1 99081769 4076879 2027532..2028440 1 NC_008044.1 KEGG: sil:SPO2985 hypothetical protein, ev=5e-93, 59% identity; hypothetical protein 2028440 4076879 TM1040_1928 Ruegeria sp. TM1040 hypothetical protein YP_613923.1 2027532 D 292414 CDS YP_613924.1 99081770 4076880 2028463..2029653 1 NC_008044.1 PFAM: toxic anion resistance: (4.7e-146); KEGG: sil:SPO2986 tellurite resistance protein, ev=1e-177, 82% identity; toxic anion resistance 2029653 4076880 TM1040_1929 Ruegeria sp. TM1040 toxic anion resistance YP_613924.1 2028463 D 292414 CDS YP_613925.1 99081771 4076881 2029664..2030617 1 NC_008044.1 KEGG: sil:SPO2987 lipoprotein, , ev=2e-78, 53% identity; lipoprotein 2030617 4076881 TM1040_1930 Ruegeria sp. TM1040 lipoprotein YP_613925.1 2029664 D 292414 CDS YP_613926.1 99081772 4076882 complement(2030640..2031323) 1 NC_008044.1 PFAM: glutathione S-transferase-like: (9.1e-06); KEGG: eba:ebA3377 glutathione-S-transferase-related protein, ev=2e-62, 58% identity; glutathione S-transferase 2031323 4076882 TM1040_1931 Ruegeria sp. TM1040 glutathione S-transferase YP_613926.1 2030640 R 292414 CDS YP_613927.1 99081773 4076883 complement(2031373..2033085) 1 NC_008044.1 PFAM: thiamine pyrophosphate enzyme-like TPP-binding: (4.4e-55) thiamine pyrophosphate enzyme, central region: (6.3e-07) thiamine pyrophosphate enzyme-like TPP binding region: (6.9e-54); KEGG: bms:BRA0945 acetolactate synthase large subunit, ev=1e-177, 55% identity; acetolactate synthase, large subunit 2033085 4076883 TM1040_1932 Ruegeria sp. TM1040 acetolactate synthase, large subunit YP_613927.1 2031373 R 292414 CDS YP_613928.1 99081774 4076884 complement(2033657..2035897) 1 NC_008044.1 TIGRFAM: Phosphoenolpyruvate-protein phosphotransferase: (1.1e-75); PFAM: PEP-utilizing enzyme: (1.2e-82) GAF: (6.5e-18) PEP-utilising enzyme, mobile region: (1.9e-10) PEP-utilising enzyme-like: (3e-19); KEGG: sil:SPO3034 phosphoenolpyruvate-protein phosphotransferase, ev=0.0, 84% identity; phosphoenolpyruvate-protein phosphotransferase PtsP 2035897 4076884 TM1040_1933 Ruegeria sp. TM1040 phosphoenolpyruvate-protein phosphotransferase PtsP YP_613928.1 2033657 R 292414 CDS YP_613929.1 99081775 4076885 complement(2036243..2037481) 1 NC_008044.1 KEGG: sil:SPO3035 aspartate kinase, monofunctional class, ev=0.0, 87% identity; TIGRFAM: aspartate kinase: (3.9e-173) aspartate kinase, monofunctional class: (1.3e-133); PFAM: aspartate/glutamate/uridylate kinase: (2.4e-62) amino acid-binding ACT: (2.2e-10); aspartate kinase 2037481 4076885 TM1040_1934 Ruegeria sp. TM1040 aspartate kinase YP_613929.1 2036243 R 292414 CDS YP_613930.1 99081776 4076886 complement(2037616..2039064) 1 NC_008044.1 PFAM: cation transporter: (3.3e-39); KEGG: sil:SPO1353 trk system potassium uptake protein TrkH, ev=0.0, 76% identity; cation transporter 2039064 4076886 TM1040_1935 Ruegeria sp. TM1040 cation transporter YP_613930.1 2037616 R 292414 CDS YP_613931.1 99081777 4076887 complement(2039112..2039879) 1 NC_008044.1 KEGG: lma:LmjF35.0290 hypothetical protein, conserved, ev=2e-18, 37% identity; hypothetical protein 2039879 4076887 TM1040_1936 Ruegeria sp. TM1040 hypothetical protein YP_613931.1 2039112 R 292414 CDS YP_613932.1 99081778 4076888 complement(2040105..2041208) 1 NC_008044.1 similar protein in Methanocaldococcus converts GTP to 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate as the first step in methanopterin biosynthesis; GTP cyclohydrolase 2041208 4076888 TM1040_1937 Ruegeria sp. TM1040 GTP cyclohydrolase YP_613932.1 2040105 R 292414 CDS YP_613933.1 99081779 4076889 complement(2041410..2042597) 1 NC_008044.1 KEGG: sil:SPO1351 O-succinylhomoserine sulfhydrylase, ev=0.0, 83% identity; TIGRFAM: O-succinylhomoserine sulfhydrylase: (6.7e-214); PFAM: aminotransferase, class V: (0.00042) Cys/Met metabolism pyridoxal-phosphate-dependent enzymes: (3.2e-172) aromatic amino acid beta-eliminating lyase/threonine aldolase: (0.00048); O-succinylhomoserine sulfhydrylase 2042597 4076889 TM1040_1938 Ruegeria sp. TM1040 O-succinylhomoserine sulfhydrylase YP_613933.1 2041410 R 292414 CDS YP_613934.1 99081780 4076890 2043063..2044004 1 NC_008044.1 hypothetical protein 2044004 4076890 TM1040_1939 Ruegeria sp. TM1040 hypothetical protein YP_613934.1 2043063 D 292414 CDS YP_613935.1 99081781 4076891 complement(2044201..2044836) 1 NC_008044.1 PFAM: Intracellular septation protein A: (1.4e-47); KEGG: rsp:RSP_1841 probable intracellular septation protein, ev=1e-76, 65% identity; intracellular septation protein A 2044836 4076891 TM1040_1940 Ruegeria sp. TM1040 intracellular septation protein A YP_613935.1 2044201 R 292414 CDS YP_613936.1 99081782 4076892 complement(2044881..2045789) 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (1.5e-09); KEGG: sil:SPO1337 membrane protein, , ev=1e-140, 83% identity; hypothetical protein 2045789 4076892 TM1040_1941 Ruegeria sp. TM1040 hypothetical protein YP_613936.1 2044881 R 292414 CDS YP_613937.1 99081783 4076893 complement(2045848..2047008) 1 NC_008044.1 KEGG: rsp:RSP_1843 signal recognition particle-docking protein FtsY, ev=1e-155, 74% identity; TIGRFAM: signal recognition particle-docking protein FtsY: (2.7e-132); PFAM: GTP-binding signal recognition particle SRP54, G-domain: (3e-105); SMART: ATPase: (7.7e-13); signal recognition particle-docking protein FtsY 2047008 4076893 TM1040_1942 Ruegeria sp. TM1040 signal recognition particle-docking protein FtsY YP_613937.1 2045848 R 292414 CDS YP_613938.1 99081784 4076894 complement(2047082..2047735) 1 NC_008044.1 PFAM: YhhN-like: (7.7e-29); KEGG: sil:SPO1340 membrane protein, , ev=1e-42, 51% identity; YhhN-like protein 2047735 4076894 TM1040_1943 Ruegeria sp. TM1040 YhhN-like protein YP_613938.1 2047082 R 292414 CDS YP_613939.1 99081785 4076895 2047873..2048283 1 NC_008044.1 KEGG: sil:SPO1342 hypothetical protein, ev=9e-31, 50% identity; hypothetical protein 2048283 4076895 TM1040_1944 Ruegeria sp. TM1040 hypothetical protein YP_613939.1 2047873 D 292414 CDS YP_613940.1 99081786 4076896 complement(2048352..2049860) 1 NC_008044.1 bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides; exodeoxyribonuclease VII large subunit 2049860 xseA 4076896 xseA Ruegeria sp. TM1040 exodeoxyribonuclease VII large subunit YP_613940.1 2048352 R 292414 CDS YP_613941.1 99081787 4076897 2050013..2051275 1 NC_008044.1 catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis; phosphoribosylamine--glycine ligase 2051275 4076897 TM1040_1946 Ruegeria sp. TM1040 phosphoribosylamine--glycine ligase YP_613941.1 2050013 D 292414 CDS YP_613942.1 99081788 4076898 complement(2051746..2052543) 1 NC_008044.1 KEGG: jan:Jann_3167 integrins alpha chain, ev=6e-54, 50% identity; integrins alpha chain 2052543 4076898 TM1040_1948 Ruegeria sp. TM1040 integrins alpha chain YP_613942.1 2051746 R 292414 CDS YP_613943.1 99081789 4076899 complement(2052543..2052935) 1 NC_008044.1 PFAM: ferredoxin: (6e-14); KEGG: sil:SPO1348 iron-sulfur cluster-binding protein, ev=1e-54, 92% identity; ferredoxin 2052935 4076899 TM1040_1949 Ruegeria sp. TM1040 ferredoxin YP_613943.1 2052543 R 292414 CDS YP_613944.1 99081790 4076900 2053273..2053719 1 NC_008044.1 PFAM: Peptidoglycan-binding domain 1: (0.00064); KEGG: sil:SPO1349 lipoprotein, , ev=5e-37, 51% identity; peptidoglycan binding domain-containing protein 2053719 4076900 TM1040_1950 Ruegeria sp. TM1040 peptidoglycan binding domain-containing protein YP_613944.1 2053273 D 292414 CDS YP_613945.1 99081791 4076901 2053848..2054516 1 NC_008044.1 PFAM: cyclic nucleotide-binding: (1.9e-24) regulatory protein, Crp: (4e-07); KEGG: sil:SPO1335 transcriptional regulator, Crp/Fnr family, ev=2e-70, 61% identity; Crp/FNR family transcriptional regulator 2054516 4076901 TM1040_1951 Ruegeria sp. TM1040 Crp/FNR family transcriptional regulator YP_613945.1 2053848 D 292414 CDS YP_613946.1 99081792 4076902 2055091..2056218 1 NC_008044.1 PFAM: Tetratricopeptide TPR_2: (0.0012); KEGG: sme:SMc03099 adenylate cyclase protein, ev=4e-45, 30% identity; hypothetical protein 2056218 4076902 TM1040_1952 Ruegeria sp. TM1040 hypothetical protein YP_613946.1 2055091 D 292414 CDS YP_613947.1 99081793 4076903 complement(2056616..2058115) 1 NC_008044.1 TIGRFAM: Peptidase S1C, Do: (4.1e-174); PFAM: peptidase S1 and S6, chymotrypsin/Hap: (3.8e-24) PDZ/DHR/GLGF: (1.9e-05); KEGG: sil:SPO1333 periplasmic serine protease, DO/DeqQ family, ev=0.0, 76% identity; peptidase S1C, Do 2058115 4076903 TM1040_1953 Ruegeria sp. TM1040 peptidase S1C, Do YP_613947.1 2056616 R 292414 CDS YP_613948.1 99081794 4077138 2058558..2059079 1 NC_008044.1 hypothetical protein 2059079 4077138 TM1040_1954 Ruegeria sp. TM1040 hypothetical protein YP_613948.1 2058558 D 292414 CDS YP_613949.1 99081795 4077139 complement(2059189..2060073) 1 NC_008044.1 TIGRFAM: HflC protein: (1.9e-47); PFAM: band 7 protein: (7.4e-34); KEGG: sil:SPO1330 HflC protein, ev=1e-125, 78% identity; HflC protein 2060073 4077139 TM1040_1955 Ruegeria sp. TM1040 HflC protein YP_613949.1 2059189 R 292414 CDS YP_613950.1 99081796 4077140 complement(2060073..2061236) 1 NC_008044.1 TIGRFAM: HflK protein: (2.4e-84); PFAM: band 7 protein: (3.4e-25); KEGG: sil:SPO1329 HflK protein, ev=1e-163, 75% identity; HflK protein 2061236 4077140 TM1040_1956 Ruegeria sp. TM1040 HflK protein YP_613950.1 2060073 R 292414 CDS YP_613951.1 99081797 4077141 complement(2061345..2062700) 1 NC_008044.1 TIGRFAM: Glutathione reductase, plant: (2.8e-243); PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase: (1.1e-21) pyridine nucleotide-disulphide oxidoreductase dimerisation region: (1.4e-44); KEGG: sil:SPO1328 glutathione-disulfide reductase, ev=0.0, 82% identity; NADPH-glutathione reductase 2062700 4077141 TM1040_1957 Ruegeria sp. TM1040 NADPH-glutathione reductase YP_613951.1 2061345 R 292414 CDS YP_613952.1 99081798 4077142 complement(2062849..2063478) 1 NC_008044.1 hypothetical protein 2063478 4077142 TM1040_1958 Ruegeria sp. TM1040 hypothetical protein YP_613952.1 2062849 R 292414 CDS YP_613953.1 99081799 4077143 2063653..2064093 1 NC_008044.1 PFAM: transmembrane pair: (1.2e-30); KEGG: atc:AGR_C_3030 hypothetical protein PA2880, ev=6e-52, 66% identity; transmembrane pair 2064093 4077143 TM1040_1959 Ruegeria sp. TM1040 transmembrane pair YP_613953.1 2063653 D 292414 CDS YP_613954.1 99081800 4077144 complement(2064158..2064946) 1 NC_008044.1 Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway; ribose-5-phosphate isomerase A 2064946 4077144 TM1040_1960 Ruegeria sp. TM1040 ribose-5-phosphate isomerase A YP_613954.1 2064158 R 292414 CDS YP_613955.1 99081801 4077145 2065279..2065986 1 NC_008044.1 PFAM: glutathione S-transferase-like: (1.5e-12); KEGG: sil:SPO1324 glutathione S-transferase family protein, ev=1e-67, 55% identity; glutathione S-transferase 2065986 4077145 TM1040_1961 Ruegeria sp. TM1040 glutathione S-transferase YP_613955.1 2065279 D 292414 CDS YP_613956.1 99081802 4077146 2065987..2067360 1 NC_008044.1 KEGG: sil:SPO1323 L-serine ammonia-lyase, ev=0.0, 88% identity; TIGRFAM: L-serine dehydratase 1: (1.8e-213); PFAM: serine dehydratase alpha chain: (3.3e-146) serine dehydratase beta chain: (7.8e-49); L-serine ammonia-lyase / 2-hydroxymethylglutarate dehydratase 2067360 4077146 TM1040_1962 Ruegeria sp. TM1040 L-serine ammonia-lyase / 2-hydroxymethylglutarate dehydratase YP_613956.1 2065987 D 292414 CDS YP_613957.1 99081803 4077147 complement(2067414..2067986) 1 NC_008044.1 PFAM: regulatory protein, TetR: (2.4e-13); KEGG: sil:SPO3545 transcriptional regulator, TetR family, ev=2e-29, 40% identity; TetR family transcriptional regulator 2067986 4077147 TM1040_1963 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_613957.1 2067414 R 292414 CDS YP_613958.1 99081804 4077148 2068068..2068943 1 NC_008044.1 KEGG: sil:SPO3544 hypothetical protein, ev=6e-61, 42% identity; hypothetical protein 2068943 4077148 TM1040_1964 Ruegeria sp. TM1040 hypothetical protein YP_613958.1 2068068 D 292414 CDS YP_613959.1 99081805 4077149 2069025..2069999 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (6.5e-10); KEGG: sil:SPO1322 membrane protein, , ev=3e-95, 62% identity; hypothetical protein 2069999 4077149 TM1040_1965 Ruegeria sp. TM1040 hypothetical protein YP_613959.1 2069025 D 292414 CDS YP_613960.1 99081806 4077150 complement(2069965..2070636) 1 NC_008044.1 TIGRFAM: thiamine pyrophosphokinase: (3e-22); PFAM: Thiamin pyrophosphokinase, catalytic region: (1.4e-20); KEGG: sil:SPO1321 thiamine pyrophosphokinase, ev=2e-55, 53% identity; thiamine pyrophosphokinase 2070636 4077150 TM1040_1966 Ruegeria sp. TM1040 thiamine pyrophosphokinase YP_613960.1 2069965 R 292414 CDS YP_613961.1 99081807 4077151 2070774..2072972 1 NC_008044.1 KEGG: sil:SPO1320 lipoprotein, , ev=1e-125, 42% identity; CheA signal transduction histidine kinase 2072972 4077151 TM1040_1967 Ruegeria sp. TM1040 CheA signal transduction histidine kinase YP_613961.1 2070774 D 292414 CDS YP_613962.1 99081808 4077152 complement(2073325..2073570) 1 NC_008044.1 KEGG: rsp:RSP_6113 hypothetical protein, ev=3e-19, 60% identity; hypothetical protein 2073570 4077152 TM1040_1968 Ruegeria sp. TM1040 hypothetical protein YP_613962.1 2073325 R 292414 CDS YP_613963.1 99081809 4077153 complement(2073570..2074883) 1 NC_008044.1 catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis; adenylosuccinate synthetase 2074883 4077153 TM1040_1969 Ruegeria sp. TM1040 adenylosuccinate synthetase YP_613963.1 2073570 R 292414 CDS YP_613964.1 99081810 4077154 complement(2075153..2075515) 1 NC_008044.1 KEGG: sil:SPO1316 hypothetical protein, ev=6e-35, 65% identity; hypothetical protein 2075515 4077154 TM1040_1970 Ruegeria sp. TM1040 hypothetical protein YP_613964.1 2075153 R 292414 CDS YP_613965.1 99081811 4077155 complement(2075512..2076216) 1 NC_008044.1 KEGG: sil:SPO1315 nitrile hydratase beta subunit, ev=1e-77, 64% identity; nitrile hydratase 2076216 4077155 TM1040_1971 Ruegeria sp. TM1040 nitrile hydratase YP_613965.1 2075512 R 292414 CDS YP_613966.1 99081812 4077156 complement(2076213..2076839) 1 NC_008044.1 KEGG: sil:SPO1314 nitrile hydratase subunit alpha, ev=1e-96, 84% identity; TIGRFAM: nitrile hydratase, alpha subunit: (3.2e-107); PFAM: Nitrile hydratase alpha chain: (3.5e-111); nitrile hydratase subunit alpha 2076839 4077156 TM1040_1972 Ruegeria sp. TM1040 nitrile hydratase subunit alpha YP_613966.1 2076213 R 292414 CDS YP_613967.1 99081813 4077157 2077611..2079254 1 NC_008044.1 CTP synthase; cytidine triphosphate synthetase; catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen; in Escherichia coli this enzyme forms a homotetramer; CTP synthetase 2079254 pyrG 4077157 pyrG Ruegeria sp. TM1040 CTP synthetase YP_613967.1 2077611 D 292414 CDS YP_613968.1 99081814 4077158 2079396..2079827 1 NC_008044.1 hypothetical protein 2079827 4077158 TM1040_1974 Ruegeria sp. TM1040 hypothetical protein YP_613968.1 2079396 D 292414 CDS YP_613969.1 99081815 4077159 2079901..2080233 1 NC_008044.1 KEGG: sil:SPO3023 hypothetical protein, ev=1e-37, 70% identity; hypothetical protein 2080233 4077159 TM1040_1975 Ruegeria sp. TM1040 hypothetical protein YP_613969.1 2079901 D 292414 CDS YP_613970.1 99081816 4077160 2080346..2081248 1 NC_008044.1 catalyzes the formation of glycerone phosphate and D-glyceraldehyde 3-phosphate from D-fructose 1,6-bisphosphate in glycolysis; fructose-1,6-bisphosphate aldolase 2081248 4077160 TM1040_1976 Ruegeria sp. TM1040 fructose-1,6-bisphosphate aldolase YP_613970.1 2080346 D 292414 CDS YP_613971.1 99081817 4077161 complement(2081321..2082778) 1 NC_008044.1 PFAM: chemotaxis sensory transducer: (6.5e-74); KEGG: nar:Saro_1430 methyl-accepting chemotaxis sensory transducer, ev=2e-86, 38% identity; methyl-accepting chemotaxis sensory transducer 2082778 4077161 TM1040_1977 Ruegeria sp. TM1040 methyl-accepting chemotaxis sensory transducer YP_613971.1 2081321 R 292414 CDS YP_613972.1 99081818 4077162 2082931..2083242 1 NC_008044.1 hypothetical protein 2083242 4077162 TM1040_1978 Ruegeria sp. TM1040 hypothetical protein YP_613972.1 2082931 D 292414 CDS YP_613973.1 99081819 4077163 complement(2083197..2083919) 1 NC_008044.1 PFAM: fatty acid hydroxylase: (3.1e-07); KEGG: bce:BC1607 fatty acid hydroxylase FAH1P, ev=8e-20, 30% identity; fatty acid hydroxylase 2083919 4077163 TM1040_1979 Ruegeria sp. TM1040 fatty acid hydroxylase YP_613973.1 2083197 R 292414 CDS YP_613974.1 99081820 4077164 complement(2083971..2084768) 1 NC_008044.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 2084768 4077164 TM1040_1980 Ruegeria sp. TM1040 enoyl-CoA hydratase YP_613974.1 2083971 R 292414 CDS YP_613975.1 99081821 4077165 2084941..2086053 1 NC_008044.1 catalyzes the formation of histidinol phosphate and 2-oxoglutarate from glutamate and imidazole acetol-phosphate; histidinol-phosphate aminotransferase 2086053 4077165 TM1040_1981 Ruegeria sp. TM1040 histidinol-phosphate aminotransferase YP_613975.1 2084941 D 292414 CDS YP_613976.1 99081822 4077166 2086159..2086395 1 NC_008044.1 hypothetical protein 2086395 4077166 TM1040_1982 Ruegeria sp. TM1040 hypothetical protein YP_613976.1 2086159 D 292414 CDS YP_613977.1 99081823 4077167 complement(2086629..2087843) 1 NC_008044.1 PFAM: aminotransferase, class V: (9.1e-10); KEGG: sil:SPO3029 serine--glyoxylate transaminase, , ev=1e-169, 71% identity; class V aminotransferase 2087843 4077167 TM1040_1983 Ruegeria sp. TM1040 class V aminotransferase YP_613977.1 2086629 R 292414 CDS YP_613978.1 99081824 4077168 2088076..2089935 1 NC_008044.1 PFAM: ABC transporter, transmembrane region: (1e-19) ABC transporter related: (1.4e-65); SMART: ATPase: (2.8e-20); KEGG: sil:SPO3030 efflux ABC transporter, transmembrane ATP-binding protein, ev=0.0, 67% identity; ABC transporter 2089935 4077168 TM1040_1984 Ruegeria sp. TM1040 ABC transporter YP_613978.1 2088076 D 292414 CDS YP_613979.1 99081825 4077169 2090043..2090789 1 NC_008044.1 PFAM: glycine cleavage T protein (aminomethyl transferase): (3.5e-12); KEGG: sil:SPO1246 aminomethyl transferase family protein, ev=1e-89, 69% identity; glycine cleavage T protein (aminomethyl transferase) 2090789 4077169 TM1040_1985 Ruegeria sp. TM1040 glycine cleavage T protein (aminomethyl transferase) YP_613979.1 2090043 D 292414 CDS YP_613980.1 99081826 4077170 2090902..2091483 1 NC_008044.1 hypothetical protein 2091483 4077170 TM1040_1986 Ruegeria sp. TM1040 hypothetical protein YP_613980.1 2090902 D 292414 CDS YP_613981.1 99081827 4077171 complement(2091657..2092220) 1 NC_008044.1 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA; elongation factor P 2092220 4077171 TM1040_1987 Ruegeria sp. TM1040 elongation factor P YP_613981.1 2091657 R 292414 CDS YP_613982.1 99081828 4077172 2092447..2092764 1 NC_008044.1 KEGG: sil:SPO1243 hypothetical protein, ev=1e-51, 96% identity; hypothetical protein 2092764 4077172 TM1040_1988 Ruegeria sp. TM1040 hypothetical protein YP_613982.1 2092447 D 292414 CDS YP_613983.1 99081829 4077173 2092984..2094432 1 NC_008044.1 catalyzes amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation; cobyric acid synthase 2094432 4077173 TM1040_1989 Ruegeria sp. TM1040 cobyric acid synthase YP_613983.1 2092984 D 292414 CDS YP_613984.1 99081830 4077174 complement(2094770..2096077) 1 NC_008044.1 KEGG: sil:SPO1241 hypothetical protein, ev=2e-28, 32% identity; hypothetical protein 2096077 4077174 TM1040_1990 Ruegeria sp. TM1040 hypothetical protein YP_613984.1 2094770 R 292414 CDS YP_613985.1 99081831 4077175 complement(2096154..2097575) 1 NC_008044.1 TIGRFAM: Type I secretion outer membrane protein, TolC: (3.5e-56); PFAM: outer membrane efflux protein: (4e-24); KEGG: sil:SPO1240 type I secretion outer membrane protein, TolC family, ev=1e-129, 55% identity; Type I secretion outer membrane protein, TolC 2097575 4077175 TM1040_1991 Ruegeria sp. TM1040 Type I secretion outer membrane protein, TolC YP_613985.1 2096154 R 292414 CDS YP_613986.1 99081832 4077176 complement(2097720..2098373) 1 NC_008044.1 PFAM: protein-L-isoaspartate(D-aspartate) O-methyltransferase: (5.5e-11) methyltransferase small: (0.00034) Methyltransferase type 11: (0.0012); KEGG: sil:SPO1239 protein-L-isoaspartate O-methyltransferase, ev=1e-75, 64% identity; protein-L-isoaspartate(D-aspartate) O-methyltransferase 2098373 4077176 TM1040_1992 Ruegeria sp. TM1040 protein-L-isoaspartate(D-aspartate) O-methyltransferase YP_613986.1 2097720 R 292414 CDS YP_613987.1 99081833 4077450 complement(2098899..2099207) 1 NC_008044.1 KEGG: rsp:RSP_0166 DnaK suppressor protein, ev=8e-06, 45% identity; TraR/DksA family transcriptional regulator 2099207 4077450 TM1040_1993 Ruegeria sp. TM1040 TraR/DksA family transcriptional regulator YP_613987.1 2098899 R 292414 CDS YP_613988.1 99081834 4077451 2099466..2099696 1 NC_008044.1 PFAM: Entericidin EcnAB: (1e-08); entericidin EcnAB 2099696 4077451 TM1040_1994 Ruegeria sp. TM1040 entericidin EcnAB YP_613988.1 2099466 D 292414 CDS YP_613989.1 99081835 4077452 complement(2099764..2100681) 1 NC_008044.1 PFAM: GAF: (9.7e-13) PAS fold-3: (4.1e-05) PAS fold-4: (5.2e-08) PAS fold: (5.1e-12); SMART: PAS: (1.3e-08) PAC motif: (5.5e-07); KEGG: ilo:IL2487 intracellular signaling protein (PAS,GAF,GGDEF domains), ev=3e-35, 33% identity; PAS/PAC sensor protein 2100681 4077452 TM1040_1995 Ruegeria sp. TM1040 PAS/PAC sensor protein YP_613989.1 2099764 R 292414 CDS YP_613990.1 99081836 4077453 complement(2100825..2101094) 1 NC_008044.1 hypothetical protein 2101094 4077453 TM1040_1996 Ruegeria sp. TM1040 hypothetical protein YP_613990.1 2100825 R 292414 CDS YP_613991.1 99081837 4077454 2101188..2102966 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (2.3e-31) histidine kinase A-like: (1.8e-07) CHASE: (7.2e-18); KEGG: cps:CPS_3952 sensor histidine kinase, ev=1e-108, 37% identity; sensor signal transduction histidine kinase 2102966 4077454 TM1040_1997 Ruegeria sp. TM1040 sensor signal transduction histidine kinase YP_613991.1 2101188 D 292414 CDS YP_613992.1 99081838 4077455 2102968..2103390 1 NC_008044.1 PFAM: response regulator receiver: (4.5e-19); KEGG: cps:CPS_3951 response regulator, ev=1e-26, 45% identity; response regulator receiver protein 2103390 4077455 TM1040_1998 Ruegeria sp. TM1040 response regulator receiver protein YP_613992.1 2102968 D 292414 CDS YP_613993.1 99081839 4077456 2103528..2103923 1 NC_008044.1 hypothetical protein 2103923 4077456 TM1040_1999 Ruegeria sp. TM1040 hypothetical protein YP_613993.1 2103528 D 292414 CDS YP_613994.1 99081840 4077457 complement(2103846..2105762) 1 NC_008044.1 TIGRFAM: Twin-arginine translocation pathway signal: (0.016); PFAM: Amidohydrolase 3: (2.2e-17); KEGG: sil:SPO0955 amidohydrolase domain protein, ev=0.0, 65% identity; twin-arginine translocation pathway signal 2105762 4077457 TM1040_2000 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_613994.1 2103846 R 292414 CDS YP_613995.1 99081841 4077458 2106141..2106440 1 NC_008044.1 KEGG: jan:Jann_2370 hypothetical protein, ev=3e-11, 41% identity; hypothetical protein 2106440 4077458 TM1040_2001 Ruegeria sp. TM1040 hypothetical protein YP_613995.1 2106141 D 292414 CDS YP_613996.1 99081842 4077459 2106428..2108020 1 NC_008044.1 PFAM: chemotaxis sensory transducer: (3e-80); SMART: Histidine kinase, HAMP region: (5.1e-08); KEGG: ccr:CC2847 methyl-accepting chemotaxis protein McpI, ev=1e-97, 42% identity; methyl-accepting chemotaxis sensory transducer 2108020 4077459 TM1040_2002 Ruegeria sp. TM1040 methyl-accepting chemotaxis sensory transducer YP_613996.1 2106428 D 292414 CDS YP_613997.1 99081843 4077460 2108344..2109321 1 NC_008044.1 PFAM: UDP-glucose/GDP-mannose dehydrogenase: (0.001) 6-phosphogluconate dehydrogenase, NAD-binding: (7.5e-42); KEGG: sil:SPO2859 3-hydroxyisobutyrate dehydrogenase family protein, ev=1e-143, 80% identity; 6-phosphogluconate dehydrogenase 2109321 4077460 TM1040_2003 Ruegeria sp. TM1040 6-phosphogluconate dehydrogenase YP_613997.1 2108344 D 292414 CDS YP_613998.1 99081844 4077461 2109545..2110426 1 NC_008044.1 PFAM: regulatory protein, LysR: (3.5e-19) LysR, substrate-binding: (1.3e-20); KEGG: sil:SPOA0284 transcriptional regulator, LysR family, ev=6e-64, 48% identity; LysR family transcriptional regulator 2110426 4077461 TM1040_2004 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_613998.1 2109545 D 292414 CDS YP_613999.1 99081845 4077462 complement(2110423..2111313) 1 NC_008044.1 PFAM: regulatory protein, LysR: (4.3e-21) LysR, substrate-binding: (5.4e-21); KEGG: bur:Bcep18194_C7696 transcriptional regulator, LysR family, ev=1e-39, 34% identity; LysR family transcriptional regulator 2111313 4077462 TM1040_2005 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_613999.1 2110423 R 292414 CDS YP_614000.1 99081846 4077463 2111425..2112573 1 NC_008044.1 PFAM: Taurine catabolism dioxygenase TauD/TfdA: (8.8e-25); KEGG: pfo:Pfl_5234 gamma-butyrobetaine hydroxylase, ev=8e-54, 34% identity; gamma-butyrobetaine,2-oxoglutarate dioxygenase 2112573 4077463 TM1040_2006 Ruegeria sp. TM1040 gamma-butyrobetaine,2-oxoglutarate dioxygenase YP_614000.1 2111425 D 292414 CDS YP_614001.1 99081847 4077464 2112570..2113298 1 NC_008044.1 PFAM: class II aldolase/adducin-like: (4.5e-34); KEGG: aci:ACIAD3485 hypothetical protein, ev=2e-56, 46% identity; hypothetical protein 2113298 4077464 TM1040_2007 Ruegeria sp. TM1040 hypothetical protein YP_614001.1 2112570 D 292414 CDS YP_614002.1 99081848 4077465 complement(2113464..2113961) 1 NC_008044.1 PFAM: helix-turn-helix, HxlR type: (1.2e-13); KEGG: eli:ELI_10910 hypothetical protein, ev=1e-19, 37% identity; HxlR family transcriptional regulator 2113961 4077465 TM1040_2008 Ruegeria sp. TM1040 HxlR family transcriptional regulator YP_614002.1 2113464 R 292414 CDS YP_614003.1 99081849 4077466 2114021..2114866 1 NC_008044.1 KEGG: ccr:CC0038 dienelactone hydrolase family protein, ev=8e-49, 42% identity; dienelactone hydrolase family protein 2114866 4077466 TM1040_2009 Ruegeria sp. TM1040 dienelactone hydrolase family protein YP_614003.1 2114021 D 292414 CDS YP_614004.1 99081850 4077467 complement(2114985..2116049) 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (6.9e-16) histidine kinase A-like: (4.1e-08) PAS fold-4: (7.4e-07); KEGG: jan:Jann_3638 histidine kinase, ev=3e-24, 28% identity; histidine kinase 2116049 4077467 TM1040_2010 Ruegeria sp. TM1040 histidine kinase YP_614004.1 2114985 R 292414 CDS YP_614005.1 99081851 4077468 2116316..2116756 1 NC_008044.1 KEGG: mag:amb1751 site-specific DNA methylase, ev=5e-07, 46% identity; hypothetical protein 2116756 4077468 TM1040_2011 Ruegeria sp. TM1040 hypothetical protein YP_614005.1 2116316 D 292414 CDS YP_614006.1 99081852 4077469 2116783..2117112 1 NC_008044.1 hypothetical protein 2117112 4077469 TM1040_2012 Ruegeria sp. TM1040 hypothetical protein YP_614006.1 2116783 D 292414 CDS YP_614007.1 99081853 4077470 complement(2117215..2117454) 1 NC_008044.1 hypothetical protein 2117454 4077470 TM1040_2013 Ruegeria sp. TM1040 hypothetical protein YP_614007.1 2117215 R 292414 CDS YP_614008.1 99081854 4077471 2117561..2118064 1 NC_008044.1 MraZ; UPF0040; crystal structure shows similarity to AbrB; cell division protein MraZ 2118064 4077471 TM1040_2014 Ruegeria sp. TM1040 cell division protein MraZ YP_614008.1 2117561 D 292414 CDS YP_614009.1 99081855 4077472 2118068..2119057 1 NC_008044.1 PFAM: methyltransferase: (5.6e-97); KEGG: sil:SPO1179 S-adenosyl-methyltransferase MraW, ev=1e-137, 76% identity; S-adenosyl-methyltransferase MraW 2119057 mraW 4077472 mraW Ruegeria sp. TM1040 S-adenosyl-methyltransferase MraW YP_614009.1 2118068 D 292414 CDS YP_614010.1 99081856 4077473 2119057..2119404 1 NC_008044.1 KEGG: sil:SPO1180 hypothetical protein, ev=5e-34, 63% identity; hypothetical protein 2119404 4077473 TM1040_2016 Ruegeria sp. TM1040 hypothetical protein YP_614010.1 2119057 D 292414 CDS YP_614011.1 99081857 4077474 2119401..2121182 1 NC_008044.1 PFAM: penicillin-binding protein, transpeptidase: (5.9e-58) Penicillin-binding protein, dimerisation domain: (1.8e-18); KEGG: sil:SPO1181 penicillin-binding protein, ev=0.0, 73% identity; peptidoglycan glycosyltransferase 2121182 4077474 TM1040_2017 Ruegeria sp. TM1040 peptidoglycan glycosyltransferase YP_614011.1 2119401 D 292414 CDS YP_614012.1 99081858 4077475 2121197..2122681 1 NC_008044.1 involved in cell wall formation; peptidoglycan synthesis; cytoplasmic enzyme; catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-aceylmuramoyl-l-alanyl-d-glutamate; UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase 2122681 murE 4077475 murE Ruegeria sp. TM1040 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase YP_614012.1 2121197 D 292414 CDS YP_614013.1 99081859 4077476 2122678..2124069 1 NC_008044.1 TIGRFAM: UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanyl ligase: (1.6e-125); PFAM: cytoplasmic peptidoglycan synthetase-like: (1.1e-18) cytoplasmic peptidoglycan synthetases-like: (0.0018) Mur ligase, middle region: (2e-49); KEGG: sil:SPO1183 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase, ev=1e-178, 70% identity; UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase 2124069 4077476 TM1040_2019 Ruegeria sp. TM1040 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase YP_614013.1 2122678 D 292414 CDS YP_614014.1 99081860 4077477 2124111..2125193 1 NC_008044.1 First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan; phospho-N-acetylmuramoyl-pentapeptide- transferase 2125193 mraY 4077477 mraY Ruegeria sp. TM1040 phospho-N-acetylmuramoyl-pentapeptide- transferase YP_614014.1 2124111 D 292414 CDS YP_614015.1 99081861 4077478 complement(2125506..2126579) 1 NC_008044.1 hypothetical protein 2126579 4077478 TM1040_2021 Ruegeria sp. TM1040 hypothetical protein YP_614015.1 2125506 R 292414 CDS YP_614016.1 99081862 4077479 complement(2126599..2127684) 1 NC_008044.1 KEGG: rsp:RSP_2093 Mrp (multidrug resistance-associated proteins) family protein, ev=1e-138, 69% identity; Mrp (multidrug resistance-associated proteins) family protein 2127684 4077479 TM1040_2022 Ruegeria sp. TM1040 Mrp (multidrug resistance-associated proteins) family protein YP_614016.1 2126599 R 292414 CDS YP_614017.1 99081863 4077480 2128003..2128224 1 NC_008044.1 PFAM: protein of unknown function DUF1127: (1.1e-06); KEGG: sil:SPO1177 hypothetical protein, ev=3e-12, 69% identity; hypothetical protein 2128224 4077480 TM1040_2023 Ruegeria sp. TM1040 hypothetical protein YP_614017.1 2128003 D 292414 CDS YP_614018.1 99081864 4077481 complement(2128764..2131208) 1 NC_008044.1 PFAM: UvrD/REP helicase: (7.9e-183); KEGG: sil:SPO1174 DNA helicase II, , ev=0.0, 78% identity; ATP-dependent DNA helicase Rep 2131208 4077481 TM1040_2024 Ruegeria sp. TM1040 ATP-dependent DNA helicase Rep YP_614018.1 2128764 R 292414 CDS YP_614019.1 99081865 4077482 2131376..2131885 1 NC_008044.1 PFAM: BLUF: (7.6e-22); KEGG: cef:CE2367 hypothetical protein, ev=1e-13, 38% identity; BLUF domain-containing protein 2131885 4077482 TM1040_2025 Ruegeria sp. TM1040 BLUF domain-containing protein YP_614019.1 2131376 D 292414 CDS YP_614020.1 99081866 4077483 2132061..2133230 1 NC_008044.1 PFAM: FMN-dependent alpha-hydroxy acid dehydrogenase: (7.6e-99); KEGG: sil:SPO1172 FMN-dependent alpha-hydroxy acid dehydrogenase family protein, ev=1e-145, 69% identity; L-lactate dehydrogenase (cytochrome) 2133230 4077483 TM1040_2026 Ruegeria sp. TM1040 L-lactate dehydrogenase (cytochrome) YP_614020.1 2132061 D 292414 CDS YP_614021.1 99081867 4077484 complement(2133373..2133807) 1 NC_008044.1 PFAM: BLUF: (2.8e-13); KEGG: jan:Jann_2780 BLUF, ev=2e-17, 35% identity; BLUF domain-containing protein 2133807 4077484 TM1040_2027 Ruegeria sp. TM1040 BLUF domain-containing protein YP_614021.1 2133373 R 292414 CDS YP_614022.1 99081868 4077485 2134246..2137686 1 NC_008044.1 biotin-containing enzyme that catalyzes a two step carboxylation of pyruvate to oxaloacetate; pyruvate carboxylase 2137686 4077485 TM1040_2028 Ruegeria sp. TM1040 pyruvate carboxylase YP_614022.1 2134246 D 292414 CDS YP_614023.1 99081869 4077486 2137758..2138666 1 NC_008044.1 hypothetical protein 2138666 4077486 TM1040_2029 Ruegeria sp. TM1040 hypothetical protein YP_614023.1 2137758 D 292414 CDS YP_614024.1 99081870 4077487 complement(2138667..2139152) 1 NC_008044.1 KEGG: sil:SPO3765 hypothetical protein, ev=1e-50, 62% identity; hypothetical protein 2139152 4077487 TM1040_2030 Ruegeria sp. TM1040 hypothetical protein YP_614024.1 2138667 R 292414 CDS YP_614025.1 99081871 4077488 2140200..2141552 1 NC_008044.1 PFAM: aminotransferase class-III: (6.9e-87); KEGG: sil:SPO1166 aminotransferase, class III family, ev=0.0, 82% identity; aminotransferase 2141552 4077488 TM1040_2031 Ruegeria sp. TM1040 aminotransferase YP_614025.1 2140200 D 292414 CDS YP_614026.1 99081872 4077959 complement(2141699..2141938) 1 NC_008044.1 PFAM: regulatory proteins, AsnC/Lrp: (8.2e-12); KEGG: sil:SPO1164 hypothetical protein, ev=7e-36, 91% identity; AsnC family transcriptional regulator 2141938 4077959 TM1040_2032 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_614026.1 2141699 R 292414 CDS YP_614027.1 99081873 4077960 2142137..2142724 1 NC_008044.1 catalyzes the dehydration of D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate to 3-(imidazol-4-yl)-2-oxopropyl phosphate in histidine biosynthesis; imidazoleglycerol-phosphate dehydratase 2142724 hisB 4077960 hisB Ruegeria sp. TM1040 imidazoleglycerol-phosphate dehydratase YP_614027.1 2142137 D 292414 CDS YP_614028.1 99081874 4077961 2142831..2143469 1 NC_008044.1 with HisF IGPS catalyzes the conversion of phosphoribulosyl-formimino-5-aminoimidazole-4-carboxamide ribonucleotide phosphate and glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamide ribonucleotide, and glutamate in histidine biosynthesis; the HisH subunit provides the glutamine amidotransferase activity that produces the ammonia necessary to HisF for the synthesis of imidazole-glycerol phosphate and 5-aminoimidazol-4-carboxamide ribonucleotide; imidazole glycerol phosphate synthase subunit HisH 2143469 hisH 4077961 hisH Ruegeria sp. TM1040 imidazole glycerol phosphate synthase subunit HisH YP_614028.1 2142831 D 292414 CDS YP_614029.1 99081875 4077962 complement(2143723..2144454) 1 NC_008044.1 PFAM: helix-turn-helix, AraC type: (0.00031); KEGG: sil:SPO1161 transcriptional regulator, AraC family, ev=4e-70, 61% identity; AraC family transcriptional regulator 2144454 4077962 TM1040_2035 Ruegeria sp. TM1040 AraC family transcriptional regulator YP_614029.1 2143723 R 292414 CDS YP_614030.1 99081876 4077963 2144634..2145170 1 NC_008044.1 PFAM: alkyl hydroperoxide reductase/ Thiol specific antioxidant/ Mal allergen: (0.00026) Redoxin: (1.9e-10); KEGG: sil:SPO1160 hypothetical protein, ev=4e-80, 79% identity; redoxin 2145170 4077963 TM1040_2036 Ruegeria sp. TM1040 redoxin YP_614030.1 2144634 D 292414 CDS YP_614031.1 99081877 4077964 2145288..2145539 1 NC_008044.1 hypothetical protein 2145539 4077964 TM1040_2037 Ruegeria sp. TM1040 hypothetical protein YP_614031.1 2145288 D 292414 CDS YP_614032.1 99081878 4077965 complement(2145590..2145979) 1 NC_008044.1 KEGG: jan:Jann_2791 hypothetical protein, ev=8e-40, 56% identity; hypothetical protein 2145979 4077965 TM1040_2038 Ruegeria sp. TM1040 hypothetical protein YP_614032.1 2145590 R 292414 CDS YP_614033.1 99081879 4077966 2146291..2147013 1 NC_008044.1 catalyzes the formation of 5-(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino-l- (5-phosphoribosyl)imidazole-4-carboxamide from 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide; 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase 2147013 4077966 TM1040_2039 Ruegeria sp. TM1040 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase YP_614033.1 2146291 D 292414 CDS YP_614034.1 99081880 4077967 2147329..2147820 1 NC_008044.1 KEGG: sil:SPO1157 hypothetical protein, ev=5e-55, 70% identity; hypothetical protein 2147820 4077967 TM1040_2040 Ruegeria sp. TM1040 hypothetical protein YP_614034.1 2147329 D 292414 CDS YP_614035.1 99081881 4077968 2147963..2148724 1 NC_008044.1 catalyzes the conversion of 5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]- 1-(5-phosphoribosyl)imidazole-4-carboxamideand glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamideribonucleotide and glutamate; the HisF subunit acts as a cyclase; imidazole glycerol phosphate synthase subunit HisF 2148724 4077968 TM1040_2041 Ruegeria sp. TM1040 imidazole glycerol phosphate synthase subunit HisF YP_614035.1 2147963 D 292414 CDS YP_614036.1 99081882 4077969 2148721..2149038 1 NC_008044.1 catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribolsyl)-ATP in histidine biosynthesis; phosphoribosyl-ATP pyrophosphatase 2149038 hisE 4077969 hisE Ruegeria sp. TM1040 phosphoribosyl-ATP pyrophosphatase YP_614036.1 2148721 D 292414 CDS YP_614037.1 99081883 4077970 complement(2149095..2150258) 1 NC_008044.1 PFAM: protein of unknown function DUF1006: (4.5e-85); KEGG: sil:SPO3685 hypothetical protein, ev=4e-83, 44% identity; hypothetical protein 2150258 4077970 TM1040_2043 Ruegeria sp. TM1040 hypothetical protein YP_614037.1 2149095 R 292414 CDS YP_614038.1 99081884 4077971 complement(2150402..2150866) 1 NC_008044.1 NADPH-dependent; catalyzes the reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine in queuosine biosynthesis; 7-cyano-7-deazaguanine reductase 2150866 4077971 TM1040_2044 Ruegeria sp. TM1040 7-cyano-7-deazaguanine reductase YP_614038.1 2150402 R 292414 CDS YP_614039.1 99081885 4077972 complement(2150883..2151590) 1 NC_008044.1 PFAM: Radical SAM: (0.0075); KEGG: sil:SPO3752 radical SAM domain protein, ev=8e-91, 68% identity; radical SAM family protein 2151590 4077972 TM1040_2045 Ruegeria sp. TM1040 radical SAM family protein YP_614039.1 2150883 R 292414 CDS YP_614040.1 99081886 4077973 complement(2151587..2151940) 1 NC_008044.1 PFAM: 6-pyruvoyl tetrahydropterin synthase and hypothetical protein: (2.7e-09); KEGG: ret:RHE_CH03712 6-pyruvoyl tetrahydropterin synthase protein, ev=1e-48, 74% identity; 6-pyruvoyl tetrahydrobiopterin synthase 2151940 4077973 TM1040_2046 Ruegeria sp. TM1040 6-pyruvoyl tetrahydrobiopterin synthase YP_614040.1 2151587 R 292414 CDS YP_614041.1 99081887 4077974 complement(2151940..2152641) 1 NC_008044.1 PFAM: ExsB: (5.9e-74); KEGG: sil:SPO3751 ExsB, ev=1e-104, 78% identity; ExsB protein 2152641 4077974 TM1040_2047 Ruegeria sp. TM1040 ExsB protein YP_614041.1 2151940 R 292414 CDS YP_614042.1 99081888 4077975 2152684..2152923 1 NC_008044.1 hypothetical protein 2152923 4077975 TM1040_2048 Ruegeria sp. TM1040 hypothetical protein YP_614042.1 2152684 D 292414 CDS YP_614043.1 99081889 4077976 2153152..2153940 1 NC_008044.1 TIGRFAM: RNA methyltransferase TrmH, group 3: (6.2e-46); PFAM: tRNA/rRNA methyltransferase (SpoU): (7.5e-42) RNA 2-O ribose methyltransferase, substrate binding: (1.6e-07); KEGG: sil:SPO1150 RNA methyltransferase, TrmH family, group 3, ev=1e-116, 84% identity; RNA methyltransferase TrmH, group 3 2153940 4077976 TM1040_2049 Ruegeria sp. TM1040 RNA methyltransferase TrmH, group 3 YP_614043.1 2153152 D 292414 CDS YP_614044.1 99081890 4077977 2154013..2154354 1 NC_008044.1 hypothetical protein 2154354 4077977 TM1040_2050 Ruegeria sp. TM1040 hypothetical protein YP_614044.1 2154013 D 292414 CDS YP_614045.1 99081891 4077978 2154527..2155009 1 NC_008044.1 KEGG: sil:SPO1152 twin-arginine translocation pathway signal sequence domain protein, , ev=2e-29, 44% identity; hypothetical protein 2155009 4077978 TM1040_2051 Ruegeria sp. TM1040 hypothetical protein YP_614045.1 2154527 D 292414 CDS YP_614046.1 99081892 4077979 2155337..2155801 1 NC_008044.1 PFAM: CoA-binding: (8.3e-13); KEGG: sil:SPO1153 CoA-binding domain protein, ev=2e-66, 81% identity; CoA-binding protein 2155801 4077979 TM1040_2052 Ruegeria sp. TM1040 CoA-binding protein YP_614046.1 2155337 D 292414 CDS YP_614047.1 99081893 4077980 complement(2155876..2156439) 1 NC_008044.1 KEGG: sil:SPO1135 hypothetical protein, ev=2e-54, 60% identity; 3-dehydroquinate dehydratase 2156439 4077980 TM1040_2053 Ruegeria sp. TM1040 3-dehydroquinate dehydratase YP_614047.1 2155876 R 292414 CDS YP_614048.1 99081894 4077981 2156958..2158784 1 NC_008044.1 required for the synthesis of the hydromethylpyrimidine moiety of thiamine; thiamine biosynthesis protein ThiC 2158784 4077981 TM1040_2054 Ruegeria sp. TM1040 thiamine biosynthesis protein ThiC YP_614048.1 2156958 D 292414 CDS YP_614049.1 99081895 4077982 complement(2158951..2159724) 1 NC_008044.1 PFAM: LamB/YcsF: (1.9e-100); KEGG: sil:SPO3659 LamB/YcsF family protein, ev=5e-89, 64% identity; LamB/YcsF family protein 2159724 4077982 TM1040_2055 Ruegeria sp. TM1040 LamB/YcsF family protein YP_614049.1 2158951 R 292414 CDS YP_614050.1 99081896 4077983 complement(2159766..2160791) 1 NC_008044.1 PFAM: Allophanate hydrolase subunit 2: (1.1e-27); KEGG: sil:SPO3660 urea amidolyase, homolog, ev=1e-100, 58% identity; allophanate hydrolase subunit 2 2160791 4077983 TM1040_2056 Ruegeria sp. TM1040 allophanate hydrolase subunit 2 YP_614050.1 2159766 R 292414 CDS YP_614051.1 99081897 4077984 complement(2160788..2161558) 1 NC_008044.1 PFAM: Allophanate hydrolase subunit 1: (9.4e-09); KEGG: sil:SPO3661 allophanate hydrolase family protein, ev=6e-78, 60% identity; allophanate hydrolase subunit 1 2161558 4077984 TM1040_2057 Ruegeria sp. TM1040 allophanate hydrolase subunit 1 YP_614051.1 2160788 R 292414 CDS YP_614052.1 99081898 4077985 2161695..2162609 1 NC_008044.1 PFAM: regulatory protein, LysR: (1.3e-16) LysR, substrate-binding: (4.8e-32); KEGG: sme:SMa0750 probable LysR-family transcriptional activator, ev=2e-57, 40% identity; LysR family transcriptional regulator 2162609 4077985 TM1040_2058 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_614052.1 2161695 D 292414 CDS YP_614053.1 99081899 4077986 2162703..2163857 1 NC_008044.1 PFAM: Rieske [2Fe-2S] region: (1.2e-23); KEGG: jan:Jann_1889 Rieske (2Fe-2S) protein, ev=1e-145, 61% identity; Rieske (2Fe-2S) protein 2163857 4077986 TM1040_2059 Ruegeria sp. TM1040 Rieske (2Fe-2S) protein YP_614053.1 2162703 D 292414 CDS YP_614054.1 99081900 4077987 2163854..2164123 1 NC_008044.1 hypothetical protein 2164123 4077987 TM1040_2060 Ruegeria sp. TM1040 hypothetical protein YP_614054.1 2163854 D 292414 CDS YP_614055.1 99081901 4077988 complement(2164175..2165095) 1 NC_008044.1 PFAM: regulatory protein, LysR: (1.7e-19) LysR, substrate-binding: (1.6e-46); KEGG: sil:SPO2238 transcriptional regulator, LysR family, ev=3e-85, 56% identity; LysR family transcriptional regulator 2165095 4077988 TM1040_2061 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_614055.1 2164175 R 292414 CDS YP_614056.1 99081902 4077989 2165213..2165494 1 NC_008044.1 PFAM: protein of unknown function DUF465: (1.7e-05); KEGG: sil:SPO2237 hypothetical protein, ev=8e-11, 43% identity; hypothetical protein 2165494 4077989 TM1040_2062 Ruegeria sp. TM1040 hypothetical protein YP_614056.1 2165213 D 292414 CDS YP_614057.1 99081903 4077990 2165626..2168046 1 NC_008044.1 PFAM: FAD dependent oxidoreductase: (2.9e-95) glycine cleavage T protein (aminomethyl transferase): (3.7e-40); KEGG: sme:SMa1483 dimethylglycine dehydrogenase, ev=0.0, 74% identity; FAD dependent oxidoreductase 2168046 4077990 TM1040_2063 Ruegeria sp. TM1040 FAD dependent oxidoreductase YP_614057.1 2165626 D 292414 CDS YP_614058.1 99081904 4077991 complement(2168043..2169287) 1 NC_008044.1 PFAM: FAD dependent oxidoreductase: (7.7e-55); KEGG: reu:Reut_A1655 D-amino-acid dehydrogenase, ev=5e-94, 44% identity; FAD dependent oxidoreductase 2169287 4077991 TM1040_2064 Ruegeria sp. TM1040 FAD dependent oxidoreductase YP_614058.1 2168043 R 292414 CDS YP_614059.1 99081905 4077992 complement(2169390..2169740) 1 NC_008044.1 PFAM: Endoribonuclease L-PSP: (1.8e-34); KEGG: sil:SPO2000 endoribonuclease L-PSP family protein, ev=2e-46, 75% identity; endoribonuclease L-PSP 2169740 4077992 TM1040_2065 Ruegeria sp. TM1040 endoribonuclease L-PSP YP_614059.1 2169390 R 292414 CDS YP_614060.1 99081906 4077993 complement(2169776..2170804) 1 NC_008044.1 PFAM: histone deacetylase superfamily: (5.8e-61); KEGG: sil:SPO2002 acetylpolyamine aminohydrolase, ev=1e-145, 72% identity; histone deacetylase superfamily protein 2170804 4077993 TM1040_2066 Ruegeria sp. TM1040 histone deacetylase superfamily protein YP_614060.1 2169776 R 292414 CDS YP_614061.1 99081907 4077994 complement(2170824..2172110) 1 NC_008044.1 TIGRFAM: TRAP dicarboxylate transporter- DctM subunit: (8.1e-81); PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit: (2.3e-73); KEGG: dps:DP0487 DctM (C4-dicarboxylate permease, large subunit), ev=4e-99, 42% identity; TRAP dicarboxylate transporter- DctM subunit 2172110 4077994 TM1040_2067 Ruegeria sp. TM1040 TRAP dicarboxylate transporter- DctM subunit YP_614061.1 2170824 R 292414 CDS YP_614062.1 99081908 4077995 complement(2172115..2172678) 1 NC_008044.1 KEGG: dps:DP3053 DctMQ fusion protein (C4-dicarboxylate transporter), ev=1e-06, 30% identity; hypothetical protein 2172678 4077995 TM1040_2068 Ruegeria sp. TM1040 hypothetical protein YP_614062.1 2172115 R 292414 CDS YP_614063.1 99081909 4077996 complement(2172766..2173767) 1 NC_008044.1 PFAM: TRAP dicarboxylate transporter- DctP subunit: (1.1e-09); KEGG: bbr:BB3954 periplasmic solute-binding transport protein, ev=3e-25, 28% identity; TRAP dicarboxylate transporter- DctP subunit 2173767 4077996 TM1040_2069 Ruegeria sp. TM1040 TRAP dicarboxylate transporter- DctP subunit YP_614063.1 2172766 R 292414 CDS YP_614064.1 99081910 4077997 2174017..2175000 1 NC_008044.1 PFAM: regulatory protein, MarR: (0.0018) regulatory protein, LysR: (2.5e-21) LysR, substrate-binding: (7.1e-34); KEGG: sil:SPO2010 transcriptional regulator, LysR family, ev=1e-114, 61% identity; LysR family transcriptional regulator 2175000 4077997 TM1040_2070 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_614064.1 2174017 D 292414 CDS YP_614065.1 99081911 4077822 2175116..2176048 1 NC_008044.1 TIGRFAM: riboflavin biosynthesis protein RibF: (1.7e-78); PFAM: Riboflavin kinase / FAD synthetase: (2.6e-52); KEGG: sil:SPO3154 riboflavin biosynthesis protein RibF, ev=1e-143, 79% identity; FMN adenylyltransferase / riboflavin kinase 2176048 4077822 TM1040_2071 Ruegeria sp. TM1040 FMN adenylyltransferase / riboflavin kinase YP_614065.1 2175116 D 292414 CDS YP_614066.1 99081912 4077823 2176058..2176528 1 NC_008044.1 PFAM: Uncharacterised conserved protein UCP006173: (2.9e-82); KEGG: sil:SPO3155 hypothetical protein, ev=8e-74, 75% identity; hypothetical protein 2176528 4077823 TM1040_2072 Ruegeria sp. TM1040 hypothetical protein YP_614066.1 2176058 D 292414 CDS YP_614067.1 99081913 4077824 complement(2176578..2177414) 1 NC_008044.1 PFAM: alpha/beta hydrolase fold: (3.2e-05); KEGG: sil:SPO3157 hydrolase, alpha/beta fold family, ev=6e-70, 50% identity; alpha/beta hydrolase 2177414 4077824 TM1040_2073 Ruegeria sp. TM1040 alpha/beta hydrolase YP_614067.1 2176578 R 292414 CDS YP_614068.1 99081914 4077825 complement(2177411..2178025) 1 NC_008044.1 PFAM: DSBA oxidoreductase: (1.6e-27); KEGG: sil:SPO3158 2-hydroxychromene-2-carboxylate isomerase, ev=2e-83, 75% identity; DSBA oxidoreductase 2178025 4077825 TM1040_2074 Ruegeria sp. TM1040 DSBA oxidoreductase YP_614068.1 2177411 R 292414 CDS YP_614069.1 99081915 4077826 2178130..2179152 1 NC_008044.1 KEGG: sil:SPO3159 ribose-phosphate pyrophosphokinase, ev=1e-171, 90% identity; TIGRFAM: ribose-phosphate pyrophosphokinase: (3.4e-112); PFAM: phosphoribosyltransferase: (7.4e-30); ribose-phosphate pyrophosphokinase 2179152 4077826 TM1040_2075 Ruegeria sp. TM1040 ribose-phosphate pyrophosphokinase YP_614069.1 2178130 D 292414 CDS YP_614070.1 99081916 4077827 2179542..2180870 1 NC_008044.1 PFAM: NAD-dependent epimerase/dehydratase: (5.7e-05) dTDP-4-dehydrorhamnose reductase: (1.4e-05) Male sterility-like: (0.0011); KEGG: ccr:CC2899 hypothetical protein, ev=1e-79, 41% identity; dTDP-4-dehydrorhamnose reductase 2180870 4077827 TM1040_2076 Ruegeria sp. TM1040 dTDP-4-dehydrorhamnose reductase YP_614070.1 2179542 D 292414 CDS YP_614071.1 99081917 4077828 2180867..2181340 1 NC_008044.1 KEGG: ret:RHE_CH02786 hypothetical conserved membrane protein, ev=5e-47, 61% identity; hypothetical protein 2181340 4077828 TM1040_2077 Ruegeria sp. TM1040 hypothetical protein YP_614071.1 2180867 D 292414 CDS YP_614072.1 99081918 4077829 2181427..2182290 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (4.4e-08); KEGG: jan:Jann_3630 protein of unknown function DUF6, transmembrane, ev=2e-67, 50% identity; hypothetical protein 2182290 4077829 TM1040_2078 Ruegeria sp. TM1040 hypothetical protein YP_614072.1 2181427 D 292414 CDS YP_614073.1 99081919 4077830 complement(2182353..2183846) 1 NC_008044.1 hypothetical protein 2183846 4077830 TM1040_2079 Ruegeria sp. TM1040 hypothetical protein YP_614073.1 2182353 R 292414 CDS YP_614074.1 99081920 4077831 complement(2183985..2186429) 1 NC_008044.1 TIGRFAM: ATPase, P-type, K/Mg/Cd/Cu/Zn/Na/Ca/Na/H-transporter: (1.5e-39) ATPase, P type cation/copper-transporter: (3.5e-231) Heavy metal translocating P-type ATPase: (8.1e-243); PFAM: Haloacid dehalogenase-like hydrolase: (1.5e-34) Heavy metal transport/detoxification protein: (1.4e-13) E1-E2 ATPase-associated region: (6.5e-98); KEGG: sil:SPO0794 copper-translocating P-type ATPase, ev=0.0, 61% identity; heavy metal translocating P-type ATPase 2186429 4077831 TM1040_2080 Ruegeria sp. TM1040 heavy metal translocating P-type ATPase YP_614074.1 2183985 R 292414 CDS YP_614075.1 99081921 4077832 complement(2186594..2186947) 1 NC_008044.1 PFAM: regulatory protein, MerR: (5.7e-11); KEGG: pfo:Pfl_0677 possible transcriptional regulator, MerR family, ev=8e-19, 43% identity; MerR family transcriptional regulator 2186947 4077832 TM1040_2081 Ruegeria sp. TM1040 MerR family transcriptional regulator YP_614075.1 2186594 R 292414 CDS YP_614076.1 99081922 4077833 2187014..2187454 1 NC_008044.1 KEGG: pfo:Pfl_0678 hypothetical protein, ev=8e-11, 32% identity; hypothetical protein 2187454 4077833 TM1040_2082 Ruegeria sp. TM1040 hypothetical protein YP_614076.1 2187014 D 292414 CDS YP_614077.1 99081923 4077834 complement(2187810..2188334) 1 NC_008044.1 hypothetical protein 2188334 4077834 TM1040_2083 Ruegeria sp. TM1040 hypothetical protein YP_614077.1 2187810 R 292414 CDS YP_614078.1 99081924 4077835 complement(2188344..2188700) 1 NC_008044.1 KEGG: sil:SPO3160 hypothetical protein, ev=2e-30, 54% identity; hypothetical protein 2188700 4077835 TM1040_2084 Ruegeria sp. TM1040 hypothetical protein YP_614078.1 2188344 R 292414 CDS YP_614079.1 99081925 4077836 complement(2188825..2189238) 1 NC_008044.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the epsilon subunit is part of the catalytic core of the ATP synthase complex; ATP synthase F0F1 subunit epsilon 2189238 atpC 4077836 atpC Ruegeria sp. TM1040 ATP synthase F0F1 subunit epsilon YP_614079.1 2188825 R 292414 CDS YP_614080.1 99081926 4077837 complement(2189250..2190674) 1 NC_008044.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit; ATP synthase F0F1 subunit beta 2190674 4077837 TM1040_2086 Ruegeria sp. TM1040 ATP synthase F0F1 subunit beta YP_614080.1 2189250 R 292414 CDS YP_614081.1 99081927 4077838 complement(2190695..2191570) 1 NC_008044.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit; ATP synthase F0F1 subunit gamma 2191570 4077838 TM1040_2087 Ruegeria sp. TM1040 ATP synthase F0F1 subunit gamma YP_614081.1 2190695 R 292414 CDS YP_614082.1 99081928 4077839 complement(2191586..2193127) 1 NC_008044.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit; ATP synthase F0F1 subunit alpha 2193127 4077839 TM1040_2088 Ruegeria sp. TM1040 ATP synthase F0F1 subunit alpha YP_614082.1 2191586 R 292414 CDS YP_614083.1 99081929 4077840 complement(2193128..2193781) 1 NC_008044.1 TIGRFAM: ATP synthase F1, delta subunit: (2e-35); PFAM: H+-transporting two-sector ATPase, delta (OSCP) subunit: (1e-64); KEGG: sil:SPO3165 ATP synthase delta chain, ev=3e-68, 76% identity; ATP synthase F1 subunit delta 2193781 4077840 TM1040_2089 Ruegeria sp. TM1040 ATP synthase F1 subunit delta YP_614083.1 2193128 R 292414 CDS YP_614084.1 99081930 4077841 complement(2194104..2194850) 1 NC_008044.1 KEGG: sil:SPO3167 hypothetical protein, ev=1e-111, 75% identity; hypothetical protein 2194850 4077841 TM1040_2090 Ruegeria sp. TM1040 hypothetical protein YP_614084.1 2194104 R 292414 CDS YP_614085.1 99081931 4077842 2194905..2195720 1 NC_008044.1 PFAM: beta-lactamase-like: (1.6e-33); KEGG: sil:SPO3168 hydroxyacylglutathione hydrolase, , ev=1e-76, 55% identity; hydroxyacylglutathione hydrolase 2195720 4077842 TM1040_2091 Ruegeria sp. TM1040 hydroxyacylglutathione hydrolase YP_614085.1 2194905 D 292414 CDS YP_614086.1 99081932 4077843 2195880..2198258 1 NC_008044.1 KEGG: sil:SPO3169 ATP-dependent Clp protease, ATP-binding subunit ClpA, ev=0.0, 90% identity; TIGRFAM: ATP-dependent Clp protease ATP-binding subunit clpA: (0); PFAM: AAA ATPase, central region: (7.6e-09) Clp, N terminal: (7.3e-14) ATPase associated with various cellular activities, AAA_5: (1.4e-07) ATPase AAA-2: (1.5e-91); SMART: ATPase: (4.6e-12); ATP-dependent Clp protease ATP-binding subunit clpA 2198258 4077843 TM1040_2092 Ruegeria sp. TM1040 ATP-dependent Clp protease ATP-binding subunit clpA YP_614086.1 2195880 D 292414 CDS YP_614087.1 99081933 4077844 complement(2198470..2199066) 1 NC_008044.1 KEGG: sil:SPO0694 hypothetical protein, ev=6e-16, 30% identity; hypothetical protein 2199066 4077844 TM1040_2093 Ruegeria sp. TM1040 hypothetical protein YP_614087.1 2198470 R 292414 CDS YP_614088.1 99081934 4077845 complement(2199187..2199534) 1 NC_008044.1 KEGG: rsp:RSP_0427 hypothetical protein, ev=7e-12, 41% identity; hypothetical protein 2199534 4077845 TM1040_2094 Ruegeria sp. TM1040 hypothetical protein YP_614088.1 2199187 R 292414 CDS YP_614089.1 99081935 4077846 complement(2199768..2202122) 1 NC_008044.1 PFAM: OmpA/MotB: (2.9e-19); KEGG: sil:SPO3171 OmpA domain protein, ev=0.0, 67% identity; hypothetical protein 2202122 4077846 TM1040_2095 Ruegeria sp. TM1040 hypothetical protein YP_614089.1 2199768 R 292414 CDS YP_614090.1 99081936 4077847 complement(2202126..2203304) 1 NC_008044.1 KEGG: sil:SPO3172 hypothetical protein, ev=1e-154, 72% identity; hypothetical protein 2203304 4077847 TM1040_2096 Ruegeria sp. TM1040 hypothetical protein YP_614090.1 2202126 R 292414 CDS YP_614091.1 99081937 4077848 complement(2203383..2203910) 1 NC_008044.1 PFAM: ChaC-like protein: (1.1e-58); KEGG: sil:SPO3173 cation transport protein ChaC, , ev=3e-69, 72% identity; ChaC-like protein 2203910 4077848 TM1040_2097 Ruegeria sp. TM1040 ChaC-like protein YP_614091.1 2203383 R 292414 CDS YP_614092.1 99081938 4077849 2203979..2204992 1 NC_008044.1 KEGG: sil:SPO3174 hypothetical protein, ev=2e-99, 52% identity; hypothetical protein 2204992 4077849 TM1040_2098 Ruegeria sp. TM1040 hypothetical protein YP_614092.1 2203979 D 292414 CDS YP_614093.1 99081939 4077850 complement(2205061..2205927) 1 NC_008044.1 PFAM: Extensin-like-like: (9.2e-43); KEGG: sil:SPO3175 hypothetical protein, ev=6e-74, 52% identity; extensin-like protein 2205927 4077850 TM1040_2099 Ruegeria sp. TM1040 extensin-like protein YP_614093.1 2205061 R 292414 CDS YP_614094.1 99081940 4077851 complement(2205924..2206856) 1 NC_008044.1 dual function enzyme catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate and the formation of tyrosine from arogenate; cyclohexadienyl dehydrogenase 2206856 4077851 TM1040_2100 Ruegeria sp. TM1040 cyclohexadienyl dehydrogenase YP_614094.1 2205924 R 292414 CDS YP_614095.1 99081941 4077852 complement(2206853..2207941) 1 NC_008044.1 catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis; histidinol-phosphate aminotransferase 2207941 4077852 TM1040_2101 Ruegeria sp. TM1040 histidinol-phosphate aminotransferase YP_614095.1 2206853 R 292414 CDS YP_614096.1 99081942 4077853 complement(2207938..2208177) 1 NC_008044.1 hypothetical protein 2208177 4077853 TM1040_2102 Ruegeria sp. TM1040 hypothetical protein YP_614096.1 2207938 R 292414 CDS YP_614097.1 99081943 4077854 complement(2208354..2209778) 1 NC_008044.1 PFAM: aminotransferase, class V: (2.3e-18); KEGG: sil:SPO3178 hypothetical protein, ev=0.0, 70% identity; class V aminotransferase 2209778 4077854 TM1040_2103 Ruegeria sp. TM1040 class V aminotransferase YP_614097.1 2208354 R 292414 CDS YP_614098.1 99081944 4077855 2209885..2210346 1 NC_008044.1 PFAM: regulatory proteins, AsnC/Lrp: (1.3e-24); KEGG: sil:SPO3179 transcriptional regulator, AsnC family, ev=3e-64, 80% identity; AsnC family transcriptional regulator 2210346 4077855 TM1040_2104 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_614098.1 2209885 D 292414 CDS YP_614099.1 99081945 4077856 complement(2210392..2210859) 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (5.2e-07); KEGG: sil:SPO2447 acetyltransferase, GNAT family, ev=4e-31, 48% identity; N-acetyltransferase GCN5 2210859 4077856 TM1040_2105 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_614099.1 2210392 R 292414 CDS YP_614100.1 99081946 4077857 complement(2210931..2211518) 1 NC_008044.1 KEGG: sil:SPO3611 hypothetical protein, ev=2e-50, 52% identity; hypothetical protein 2211518 4077857 TM1040_2106 Ruegeria sp. TM1040 hypothetical protein YP_614100.1 2210931 R 292414 CDS YP_614101.1 99081947 4077858 complement(2211714..2212334) 1 NC_008044.1 primary rRNA binding protein; nucleates 30S assembly; involved in translational accuracy with proteins S5 and S12; interacts with protein S5; involved in autogeneously regulating ribosomal proteins by binding to pseudoknot structures in the polycistronic mRNA; interacts with transcription complex and functions similar to protein NusA in antitermination; 30S ribosomal protein S4 2212334 rpsD 4077858 rpsD Ruegeria sp. TM1040 30S ribosomal protein S4 YP_614101.1 2211714 R 292414 CDS YP_614102.1 99081948 4077859 complement(2212779..2213840) 1 NC_008044.1 KEGG: sil:SPO3182 hypothetical protein, ev=1e-144, 69% identity; hypothetical protein 2213840 4077859 TM1040_2108 Ruegeria sp. TM1040 hypothetical protein YP_614102.1 2212779 R 292414 CDS YP_614103.1 99081949 4077860 complement(2213973..2214914) 1 NC_008044.1 KEGG: jan:Jann_0952 hypothetical protein, ev=4e-50, 43% identity; hypothetical protein 2214914 4077860 TM1040_2109 Ruegeria sp. TM1040 hypothetical protein YP_614103.1 2213973 R 292414 CDS YP_614104.1 99081950 4076424 complement(2215089..2215490) 1 NC_008044.1 SMART: Rhodanese-like: (3.1e-14); KEGG: jan:Jann_2299 rhodanese-like, ev=1e-41, 64% identity; rhodanese-like protein 2215490 4076424 TM1040_2110 Ruegeria sp. TM1040 rhodanese-like protein YP_614104.1 2215089 R 292414 CDS YP_614105.1 99081951 4076425 2215682..2216980 1 NC_008044.1 PFAM: FAD dependent oxidoreductase: (3.4e-86); KEGG: ppu:PP5257 oxidoreductase, FAD-binding, ev=1e-98, 45% identity; L-pipecolate dehydrogenase 2216980 4076425 TM1040_2111 Ruegeria sp. TM1040 L-pipecolate dehydrogenase YP_614105.1 2215682 D 292414 CDS YP_614106.1 99081952 4076426 complement(2217033..2217839) 1 NC_008044.1 SMART: regulatory proteins, IclR: (7.6e-09); KEGG: pfo:Pfl_1294 transcriptional regulator, IclR family, ev=1e-19, 27% identity; IclR family transcriptional regulator 2217839 4076426 TM1040_2112 Ruegeria sp. TM1040 IclR family transcriptional regulator YP_614106.1 2217033 R 292414 CDS YP_614107.1 99081953 4076427 2217848..2219566 1 NC_008044.1 PFAM: sulfatase: (3.1e-28); KEGG: sil:SPO3593 sulfatase family protein, ev=0.0, 65% identity; sulfatase 2219566 4076427 TM1040_2113 Ruegeria sp. TM1040 sulfatase YP_614107.1 2217848 D 292414 CDS YP_614108.1 99081954 4076428 2219895..2221355 1 NC_008044.1 PFAM: protein of unknown function DUF404: (4.5e-180) protein of unknown function DUF407: (1.3e-84); KEGG: jan:Jann_2676 protein of unknown function DUF404, ev=0.0, 76% identity; hypothetical protein 2221355 4076428 TM1040_2114 Ruegeria sp. TM1040 hypothetical protein YP_614108.1 2219895 D 292414 CDS YP_614109.1 99081955 4076429 2221360..2222301 1 NC_008044.1 PFAM: protein of unknown function DUF403: (5.9e-110); KEGG: jan:Jann_2677 protein of unknown function DUF403, ev=2e-91, 58% identity; hypothetical protein 2222301 4076429 TM1040_2115 Ruegeria sp. TM1040 hypothetical protein YP_614109.1 2221360 D 292414 CDS YP_614110.1 99081956 4076430 2222305..2223102 1 NC_008044.1 PFAM: transglutaminase-like: (1.1e-15) transglutaminase-like-like: (8.1e-26); KEGG: jan:Jann_2678 transglutaminase-like, ev=7e-77, 55% identity; transglutaminase 2223102 4076430 TM1040_2116 Ruegeria sp. TM1040 transglutaminase YP_614110.1 2222305 D 292414 CDS YP_614111.1 99081957 4076431 2223110..2223844 1 NC_008044.1 PFAM: 20S proteasome, A and B subunits: (0.0046); KEGG: mlo:mll0713 proteasome-type protease, ev=4e-85, 64% identity; 20S proteasome subunits A/B 2223844 4076431 TM1040_2117 Ruegeria sp. TM1040 20S proteasome subunits A/B YP_614111.1 2223110 D 292414 CDS YP_614112.1 99081958 4076432 complement(2223999..2225012) 1 NC_008044.1 KEGG: sil:SPO1408 ribosomal large subunit pseudouridine synthase D, ev=1e-146, 74% identity; TIGRFAM: Pseudouridine synthase, RluD: (6.2e-111); PFAM: RNA-binding S4: (8e-05) pseudouridine synthase: (5.9e-68); ribosomal large subunit pseudouridine synthase D 2225012 4076432 TM1040_2118 Ruegeria sp. TM1040 ribosomal large subunit pseudouridine synthase D YP_614112.1 2223999 R 292414 CDS YP_614113.1 99081959 4076433 2225035..2225343 1 NC_008044.1 KEGG: sil:SPO1407 hypothetical protein, ev=1e-23, 56% identity; hypothetical protein 2225343 4076433 TM1040_2119 Ruegeria sp. TM1040 hypothetical protein YP_614113.1 2225035 D 292414 CDS YP_614114.1 99081960 4076434 2225676..2226056 1 NC_008044.1 KEGG: jan:Jann_3405 hypothetical protein, ev=3e-17, 68% identity; hypothetical protein 2226056 4076434 TM1040_2120 Ruegeria sp. TM1040 hypothetical protein YP_614114.1 2225676 D 292414 CDS YP_614115.1 99081961 4076435 2226311..2227423 1 NC_008044.1 KEGG: lma:LmjF35.0290 hypothetical protein, conserved, ev=2e-09, 29% identity; CheA signal transduction histidine kinase 2227423 4076435 TM1040_2121 Ruegeria sp. TM1040 CheA signal transduction histidine kinase YP_614115.1 2226311 D 292414 CDS YP_614116.1 99081962 4076436 complement(2227506..2227973) 1 NC_008044.1 PFAM: protein of unknown function DUF1052: (9.5e-44); KEGG: sil:SPO1766 hypothetical protein, ev=9e-61, 78% identity; hypothetical protein 2227973 4076436 TM1040_2122 Ruegeria sp. TM1040 hypothetical protein YP_614116.1 2227506 R 292414 CDS YP_614117.1 99081963 4076437 complement(2228459..2228779) 1 NC_008044.1 KEGG: sil:SPO1765 hypothetical protein, ev=4e-20, 48% identity; hypothetical protein 2228779 4076437 TM1040_2123 Ruegeria sp. TM1040 hypothetical protein YP_614117.1 2228459 R 292414 CDS YP_614118.1 99081964 4076438 2228973..2230523 1 NC_008044.1 PFAM: adenylyl cyclase class-3/4/guanylyl cyclase: (8.9e-27); KEGG: bja:bll7624 probable adenylate cyclase, ev=1e-145, 57% identity; guanylate cyclase 2230523 4076438 TM1040_2124 Ruegeria sp. TM1040 guanylate cyclase YP_614118.1 2228973 D 292414 CDS YP_614119.1 99081965 4076439 complement(2230638..2232287) 1 NC_008044.1 TIGRFAM: choline/carnitine/betaine transport: (1.3e-180); PFAM: BCCT transporter: (8.8e-196); KEGG: vpa:VP1723 transporter, BCCT family, ev=0.0, 66% identity; choline/carnitine/betaine transport 2232287 4076439 TM1040_2125 Ruegeria sp. TM1040 choline/carnitine/betaine transport YP_614119.1 2230638 R 292414 CDS YP_614120.1 99081966 4076440 complement(2232329..2232745) 1 NC_008044.1 KEGG: rpb:RPB_3824 UspA, ev=2e-10, 30% identity; hypothetical protein 2232745 4076440 TM1040_2126 Ruegeria sp. TM1040 hypothetical protein YP_614120.1 2232329 R 292414 CDS YP_614121.1 99081967 4076441 complement(2232999..2233481) 1 NC_008044.1 TIGRFAM: transcription antitermination factor NusB: (4.4e-28); PFAM: NusB/RsmB/TIM44: (2.2e-22); KEGG: sil:SPO1763 transcription antitermination factor NusB, ev=2e-64, 76% identity; NusB antitermination factor 2233481 4076441 TM1040_2127 Ruegeria sp. TM1040 NusB antitermination factor YP_614121.1 2232999 R 292414 CDS YP_614122.1 99081968 4076442 complement(2233505..2234029) 1 NC_008044.1 RibE; 6,7-diimethyl-8-ribityllumazine synthase; DMRL synthase; lumazine synthase; beta subunit of riboflavin synthase; condenses 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate to generate 6,6-dimethyl-8-lumazine (DMRL); riboflavin synthase then uses 2 molecules of DMRL to produce riboflavin (vitamin B12); involved in the last steps of riboflavin biosynthesis; forms a 60mer (icosahedral shell) in both Bacillus subtilis and Escherichia coli; in Bacillus subtilis this 60mer is associated with the riboflavin synthase subunit (alpha) while in Escherichia coli it is not; 6,7-dimethyl-8-ribityllumazine synthase 2234029 ribH 4076442 ribH Ruegeria sp. TM1040 6,7-dimethyl-8-ribityllumazine synthase YP_614122.1 2233505 R 292414 CDS YP_614123.1 99081969 4076443 complement(2234044..2235168) 1 NC_008044.1 PFAM: 3,4-dihydroxy-2-butanone 4-phosphate synthase: (1.8e-106) GTP cyclohydrolase II: (9.5e-08); KEGG: sil:SPO1761 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II, , ev=0.0, 87% identity; GTP cyclohydrolase II 2235168 4076443 TM1040_2129 Ruegeria sp. TM1040 GTP cyclohydrolase II YP_614123.1 2234044 R 292414 CDS YP_614124.1 99081970 4076444 complement(2235462..2236064) 1 NC_008044.1 KEGG: sil:SPO1760 hypothetical protein, ev=2e-56, 57% identity; hypothetical protein 2236064 4076444 TM1040_2130 Ruegeria sp. TM1040 hypothetical protein YP_614124.1 2235462 R 292414 CDS YP_614125.1 99081971 4076445 complement(2236064..2236669) 1 NC_008044.1 catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine; riboflavin synthase subunit alpha 2236669 4076445 TM1040_2131 Ruegeria sp. TM1040 riboflavin synthase subunit alpha YP_614125.1 2236064 R 292414 CDS YP_614126.1 99081972 4076446 2236933..2238237 1 NC_008044.1 PFAM: Capsule polysaccharide biosynthesis: (3.1e-30); KEGG: sil:SPO1757 capsular polysaccharide export protein KpsS, ev=0.0, 75% identity; capsule polysaccharide biosynthesis 2238237 4076446 TM1040_2132 Ruegeria sp. TM1040 capsule polysaccharide biosynthesis YP_614126.1 2236933 D 292414 CDS YP_614127.1 99081973 4076447 2238343..2239470 1 NC_008044.1 PFAM: polysaccharide export protein: (3.9e-14); KEGG: sil:SPO1756 polysaccharide biosynthesis/export protein, ev=1e-165, 76% identity; polysaccharide export protein 2239470 4076447 TM1040_2133 Ruegeria sp. TM1040 polysaccharide export protein YP_614127.1 2238343 D 292414 CDS YP_614128.1 99081974 4076448 2239477..2241516 1 NC_008044.1 PFAM: Capsule polysaccharide biosynthesis: (2.5e-72); KEGG: sil:SPO1755 capsular polysaccharide export protein KpsC, ev=0.0, 66% identity; capsule polysaccharide biosynthesis 2241516 4076448 TM1040_2134 Ruegeria sp. TM1040 capsule polysaccharide biosynthesis YP_614128.1 2239477 D 292414 CDS YP_614129.1 99081975 4076449 complement(2241583..2242659) 1 NC_008044.1 KEGG: sil:SPO1754 riboflavin biosynthesis protein RibD, ev=1e-155, 75% identity; TIGRFAM: riboflavin biosynthesis protein RibD: (1e-118) Riboflavin-specific deaminase-like: (6.1e-54); PFAM: CMP/dCMP deaminase, zinc-binding: (4.5e-27) bifunctional deaminase-reductase-like: (8.7e-51); 5-amino-6-(5-phosphoribosylamino)uracil reductase 2242659 4076449 TM1040_2135 Ruegeria sp. TM1040 5-amino-6-(5-phosphoribosylamino)uracil reductase YP_614129.1 2241583 R 292414 CDS YP_614130.1 99081976 4076450 complement(2242735..2243202) 1 NC_008044.1 TIGRFAM: Ribonucleotide reductase regulator NrdR-like: (5.4e-49); PFAM: ATP-cone: (2.1e-29); KEGG: sil:SPO1753 riboflavin biosynthesis protein RibX, ev=2e-83, 97% identity; transcriptional regulator NrdR 2243202 nrdR 4076450 nrdR Ruegeria sp. TM1040 transcriptional regulator NrdR YP_614130.1 2242735 R 292414 CDS YP_614131.1 99081977 4076451 complement(2243348..2243776) 1 NC_008044.1 PFAM: protein of unknown function UPF0047: (3.9e-36); KEGG: atc:AGR_C_3925 It is a member of an uncharacterized protein family PF|01894. ESTs gb|T43915, gb|AA395185 and gb|AI997079 come from this gene., ev=2e-49, 60% identity; hypothetical protein 2243776 4076451 TM1040_2137 Ruegeria sp. TM1040 hypothetical protein YP_614131.1 2243348 R 292414 CDS YP_614132.1 99081978 4076452 complement(2243781..2244239) 1 NC_008044.1 KEGG: sil:SPO1751 hypothetical protein, ev=1e-18, 44% identity; hypothetical protein 2244239 4076452 TM1040_2138 Ruegeria sp. TM1040 hypothetical protein YP_614132.1 2243781 R 292414 CDS YP_614133.1 99081979 4076453 complement(2244370..2244678) 1 NC_008044.1 hypothetical protein 2244678 4076453 TM1040_2139 Ruegeria sp. TM1040 hypothetical protein YP_614133.1 2244370 R 292414 CDS YP_614134.1 99081980 4076454 complement(2244894..2245364) 1 NC_008044.1 hypothetical protein 2245364 4076454 TM1040_2140 Ruegeria sp. TM1040 hypothetical protein YP_614134.1 2244894 R 292414 CDS YP_614135.1 99081981 4076455 complement(2245649..2247643) 1 NC_008044.1 sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this is the primary sigma factor of bacteria; RNA polymerase sigma factor RpoD 2247643 4076455 TM1040_2141 Ruegeria sp. TM1040 RNA polymerase sigma factor RpoD YP_614135.1 2245649 R 292414 CDS YP_614136.1 99081982 4076456 complement(2247809..2249818) 1 NC_008044.1 synthesizes RNA primers at the replication forks; DNA primase 2249818 dnaG 4076456 dnaG Ruegeria sp. TM1040 DNA primase YP_614136.1 2247809 R 292414 CDS YP_614137.1 99081983 4076457 complement(2249884..2250240) 1 NC_008044.1 KEGG: sil:SPO1748 hypothetical protein, ev=4e-15, 40% identity; hypothetical protein 2250240 4076457 TM1040_2143 Ruegeria sp. TM1040 hypothetical protein YP_614137.1 2249884 R 292414 CDS YP_614138.1 99081984 4076458 complement(2250279..2250836) 1 NC_008044.1 PFAM: Sarcosine oxidase, gamma subunit: (2.2e-12); KEGG: sil:SPO1747 sarcosine oxidase, gamma subunit family, ev=9e-46, 54% identity; sarcosine oxidase, gamma subunit 2250836 4076458 TM1040_2144 Ruegeria sp. TM1040 sarcosine oxidase, gamma subunit YP_614138.1 2250279 R 292414 CDS YP_614139.1 99081985 4076459 complement(2250829..2253774) 1 NC_008044.1 TIGRFAM: sarcosine oxidase, alpha subunit family: (0); PFAM: glycine cleavage T protein (aminomethyl transferase): (1.3e-41); KEGG: sil:SPO1746 sarcosine oxidase, alpha subunit family, ev=0.0, 70% identity; sarcosine oxidase subunit alpha 2253774 4076459 TM1040_2145 Ruegeria sp. TM1040 sarcosine oxidase subunit alpha YP_614139.1 2250829 R 292414 CDS YP_614140.1 99081986 4076460 complement(2253771..2254049) 1 NC_008044.1 PFAM: Sarcosine oxidase, delta subunit, heterotetrameric: (1.3e-33); KEGG: sil:SPO1745 sarcosine oxidase, delta subunit family, ev=2e-24, 62% identity; sarcosine oxidase, delta subunit, heterotetrameric 2254049 4076460 TM1040_2146 Ruegeria sp. TM1040 sarcosine oxidase, delta subunit, heterotetrameric YP_614140.1 2253771 R 292414 CDS YP_614141.1 99081987 4076461 complement(2254116..2255420) 1 NC_008044.1 TIGRFAM: sarcosine oxidase, beta subunit family: (1.9e-270); PFAM: FAD dependent oxidoreductase: (5.7e-89); KEGG: sil:SPO1744 sarcosine oxidase, beta subunit family, ev=0.0, 76% identity; sarcosine oxidase subunit beta 2255420 4076461 TM1040_2147 Ruegeria sp. TM1040 sarcosine oxidase subunit beta YP_614141.1 2254116 R 292414 CDS YP_614142.1 99081988 4076462 2255558..2256244 1 NC_008044.1 PFAM: regulatory protein, TetR: (4.9e-12); KEGG: bat:BAS2304 transcriptional regulator, TetR family, ev=1e-10, 29% identity; TetR family transcriptional regulator 2256244 4076462 TM1040_2148 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_614142.1 2255558 D 292414 CDS YP_614143.1 99081989 4076748 2256244..2257008 1 NC_008044.1 PFAM: Abortive infection protein: (1.4e-08); KEGG: hma:rrnB0071 hypothetical protein, ev=2e-15, 29% identity; abortive infection protein 2257008 4076748 TM1040_2149 Ruegeria sp. TM1040 abortive infection protein YP_614143.1 2256244 D 292414 CDS YP_614144.1 99081990 4076749 complement(2257115..2258545) 1 NC_008044.1 PFAM: Glu/Leu/Phe/Val dehydrogenase, C terminal: (1e-73) Glu/Leu/Phe/Val dehydrogenase, dimerisation region: (6.2e-52); KEGG: sil:SPO1743 glutamate dehydrogenase, ev=0.0, 84% identity; Glu/Leu/Phe/Val dehydrogenase 2258545 4076749 TM1040_2150 Ruegeria sp. TM1040 Glu/Leu/Phe/Val dehydrogenase YP_614144.1 2257115 R 292414 CDS YP_614145.1 99081991 4076750 2258932..2260680 1 NC_008044.1 KEGG: sil:SPO1742 hypothetical protein, ev=1e-125, 44% identity; hypothetical protein 2260680 4076750 TM1040_2151 Ruegeria sp. TM1040 hypothetical protein YP_614145.1 2258932 D 292414 CDS YP_614146.1 99081992 4076751 2260677..2261225 1 NC_008044.1 PFAM: TadE-like: (1.9e-07); KEGG: sil:SPO1741 hypothetical protein, ev=9e-40, 48% identity; TadE-like protein 2261225 4076751 TM1040_2152 Ruegeria sp. TM1040 TadE-like protein YP_614146.1 2260677 D 292414 CDS YP_614147.1 99081993 4076752 2261229..2261834 1 NC_008044.1 KEGG: sil:SPO1740 hypothetical protein, ev=7e-34, 41% identity; hypothetical protein 2261834 4076752 TM1040_2153 Ruegeria sp. TM1040 hypothetical protein YP_614147.1 2261229 D 292414 CDS YP_614148.1 99081994 4076753 complement(2261944..2262378) 1 NC_008044.1 KEGG: ret:RHE_CH01338 hypothetical protein, ev=3e-24, 43% identity; hypothetical protein 2262378 4076753 TM1040_2154 Ruegeria sp. TM1040 hypothetical protein YP_614148.1 2261944 R 292414 CDS YP_614149.1 99081995 4076754 complement(2262375..2263757) 1 NC_008044.1 PFAM: multi antimicrobial extrusion protein MatE: (1.4e-18); KEGG: rru:Rru_A0678 multi antimicrobial extrusion protein MatE, ev=2e-89, 41% identity; multi anti extrusion protein MatE 2263757 4076754 TM1040_2155 Ruegeria sp. TM1040 multi anti extrusion protein MatE YP_614149.1 2262375 R 292414 CDS YP_614150.1 99081996 4076755 2264063..2266777 1 NC_008044.1 TIGRFAM: GGDEF domain: (1e-30); PFAM: GGDEF: (3.7e-39) EAL: (1.2e-69) Rh-like protein/ammonium transporter: (4.9e-99); KEGG: tcx:Tcr_2151 ammonium transporter, ev=1e-103, 35% identity; diguanylate cyclase/phosphodiesterase 2266777 4076755 TM1040_2156 Ruegeria sp. TM1040 diguanylate cyclase/phosphodiesterase YP_614150.1 2264063 D 292414 CDS YP_614151.1 99081997 4076756 complement(2266835..2267326) 1 NC_008044.1 KEGG: sil:SPO1739 hypothetical protein, ev=2e-48, 60% identity; hypothetical protein 2267326 4076756 TM1040_2157 Ruegeria sp. TM1040 hypothetical protein YP_614151.1 2266835 R 292414 CDS YP_614152.1 99081998 4076757 complement(2267409..2268128) 1 NC_008044.1 PFAM: helix-turn-helix motif: (4.1e-14) Cupin 2, conserved barrel: (4.7e-12); KEGG: ppr:PBPRB1321 transcriptional regulator, HTH_3family, ev=7e-34, 40% identity; XRE family transcriptional regulator 2268128 4076757 TM1040_2158 Ruegeria sp. TM1040 XRE family transcriptional regulator YP_614152.1 2267409 R 292414 CDS YP_614153.1 99081999 4076758 2268651..2270105 1 NC_008044.1 PFAM: Na+/H+ antiporter NhaC: (2.3e-75); KEGG: rsp:RSP_0133 Na+/H+ antiporter, NhaC family, ev=0.0, 70% identity; Na+/H+ antiporter NhaC 2270105 4076758 TM1040_2159 Ruegeria sp. TM1040 Na+/H+ antiporter NhaC YP_614153.1 2268651 D 292414 CDS YP_614154.1 99082000 4076759 2270248..2271159 1 NC_008044.1 PFAM: Pirin-like: (6.2e-45); KEGG: sil:SPO1737 pirin domain protein, ev=1e-154, 84% identity; pirin 2271159 4076759 TM1040_2160 Ruegeria sp. TM1040 pirin YP_614154.1 2270248 D 292414 CDS YP_614155.1 99082001 4076760 complement(2271476..2271964) 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (8e-07); KEGG: vfi:VF1328 ferrichrome-binding protein, ev=2e-09, 33% identity; N-acetyltransferase GCN5 2271964 4076760 TM1040_2161 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_614155.1 2271476 R 292414 CDS YP_614156.1 99082002 4076761 complement(2271969..2272598) 1 NC_008044.1 PFAM: regulatory protein, TetR: (7.5e-12); KEGG: sil:SPO1736 transcriptional regulator, TetR family, ev=1e-70, 72% identity; TetR family transcriptional regulator 2272598 4076761 TM1040_2162 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_614156.1 2271969 R 292414 CDS YP_614157.1 99082003 4076762 2272682..2272984 1 NC_008044.1 KEGG: sil:SPO1735 hypothetical protein, ev=1e-09, 45% identity; hypothetical protein 2272984 4076762 TM1040_2163 Ruegeria sp. TM1040 hypothetical protein YP_614157.1 2272682 D 292414 CDS YP_614158.1 99082004 4076763 2273080..2274366 1 NC_008044.1 catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine; homoserine dehydrogenase 2274366 4076763 TM1040_2164 Ruegeria sp. TM1040 homoserine dehydrogenase YP_614158.1 2273080 D 292414 CDS YP_614159.1 99082005 4076764 2274543..2275526 1 NC_008044.1 type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese; fructose 1,6-bisphosphatase II 2275526 glpX 4076764 glpX Ruegeria sp. TM1040 fructose 1,6-bisphosphatase II YP_614159.1 2274543 D 292414 CDS YP_614160.1 99082006 4076765 2275574..2277385 1 NC_008044.1 TIGRFAM: single-stranded-DNA-specific exonuclease RecJ: (1.3e-187); PFAM: phosphoesterase, RecJ-like: (1.6e-37) phosphoesterase, DHHA1: (6.2e-09); KEGG: sil:SPO1732 single-stranded-DNA-specific exonuclease RecJ, ev=0.0, 78% identity; single-stranded-DNA-specific exonuclease RecJ 2277385 4076765 TM1040_2166 Ruegeria sp. TM1040 single-stranded-DNA-specific exonuclease RecJ YP_614160.1 2275574 D 292414 CDS YP_614161.1 99082007 4076766 complement(2277923..2279320) 1 NC_008044.1 PFAM: regulatory protein GntR, HTH: (9.8e-13) aminotransferase, class I and II: (5e-08); KEGG: sil:SPO3185 transcriptional regulator, GntR family, ev=1e-139, 55% identity; GntR family transcriptional regulator 2279320 4076766 TM1040_2167 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_614161.1 2277923 R 292414 CDS YP_614162.1 99082008 4076767 complement(2279428..2281509) 1 NC_008044.1 PFAM: molybdopterin oxidoreductase: (5e-27) molydopterin dinucleotide-binding region: (6.5e-29) molybdopterin oxidoreductase Fe4S4 region: (8.3e-10); KEGG: sil:SPO3183 oxidoreductase, molybdopterin-binding, ev=0.0, 67% identity; molydopterin dinucleotide-binding region 2281509 4076767 TM1040_2168 Ruegeria sp. TM1040 molydopterin dinucleotide-binding region YP_614162.1 2279428 R 292414 CDS YP_614163.1 99082009 4076768 complement(2281704..2282726) 1 NC_008044.1 TIGRFAM: GGDEF domain: (5.1e-30); PFAM: GGDEF: (1.7e-46); KEGG: sil:SPO2747 diguanylate cyclase, , ev=1e-112, 65% identity; diguanylate cyclase 2282726 4076768 TM1040_2169 Ruegeria sp. TM1040 diguanylate cyclase YP_614163.1 2281704 R 292414 CDS YP_614164.1 99082010 4076769 complement(2282723..2283310) 1 NC_008044.1 KEGG: sil:SPO2748 hypothetical protein, ev=3e-67, 65% identity; hypothetical protein 2283310 4076769 TM1040_2170 Ruegeria sp. TM1040 hypothetical protein YP_614164.1 2282723 R 292414 CDS YP_614165.1 99082011 4076770 complement(2283726..2285285) 1 NC_008044.1 PFAM: trimethylamine methyltransferase: (1.9e-247); KEGG: sil:SPO2750 trimethylamine methyltransferase family protein, ev=0.0, 82% identity; trimethylamine methyltransferase 2285285 4076770 TM1040_2171 Ruegeria sp. TM1040 trimethylamine methyltransferase YP_614165.1 2283726 R 292414 CDS YP_614166.1 99082012 4076771 complement(2285415..2286107) 1 NC_008044.1 TIGRFAM: HAD-superfamily hydrolase subfamily IA, variant 3: (5.6e-06) HAD-superfamily hydrolase, subfamily IA, variant 1: (1.4e-05); PFAM: Haloacid dehalogenase-like hydrolase: (8.3e-28); KEGG: rsp:RSP_0412 phosphatase, ev=5e-59, 52% identity; HAD family hydrolase 2286107 4076771 TM1040_2172 Ruegeria sp. TM1040 HAD family hydrolase YP_614166.1 2285415 R 292414 CDS YP_614167.1 99082013 4076772 complement(2286144..2286428) 1 NC_008044.1 KEGG: sil:SPO2752 hypothetical protein, ev=6e-27, 59% identity; hypothetical protein 2286428 4076772 TM1040_2173 Ruegeria sp. TM1040 hypothetical protein YP_614167.1 2286144 R 292414 CDS YP_614168.1 99082014 4076773 2286545..2287948 1 NC_008044.1 TIGRFAM: GGDEF domain: (1.1e-44); PFAM: GGDEF: (3.4e-58) response regulator receiver: (6.8e-11); KEGG: sil:SPO2753 diguanylate cyclase, /response regulator, ev=1e-115, 50% identity; response regulator receiver modulated diguanylate cyclase 2287948 4076773 TM1040_2174 Ruegeria sp. TM1040 response regulator receiver modulated diguanylate cyclase YP_614168.1 2286545 D 292414 CDS YP_614169.1 99082015 4076774 complement(2287994..2288503) 1 NC_008044.1 KEGG: rsp:RSP_0414 hypothetical protein, ev=5e-10, 30% identity; hypothetical protein 2288503 4076774 TM1040_2175 Ruegeria sp. TM1040 hypothetical protein YP_614169.1 2287994 R 292414 CDS YP_614170.1 99082016 4076775 complement(2288500..2288895) 1 NC_008044.1 KEGG: sil:SPO2755 hypothetical protein, ev=3e-11, 33% identity; hypothetical protein 2288895 4076775 TM1040_2176 Ruegeria sp. TM1040 hypothetical protein YP_614170.1 2288500 R 292414 CDS YP_614171.1 99082017 4076776 complement(2288888..2289514) 1 NC_008044.1 Bacteria have multiple sigma factors which are active under specific conditions; the sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; RNA polymerase sigma factor 2289514 4076776 TM1040_2177 Ruegeria sp. TM1040 RNA polymerase sigma factor YP_614171.1 2288888 R 292414 CDS YP_614172.1 99082018 4076777 complement(2289585..2290088) 1 NC_008044.1 KEGG: jan:Jann_3135 calcium-binding EF-hand, ev=6e-20, 44% identity; hypothetical protein 2290088 4076777 TM1040_2178 Ruegeria sp. TM1040 hypothetical protein YP_614172.1 2289585 R 292414 CDS YP_614173.1 99082019 4076778 2290354..2290785 1 NC_008044.1 PFAM: protein of unknown function DUF983: (5.5e-31); KEGG: sil:SPO2758 hypothetical protein, ev=5e-50, 68% identity; hypothetical protein 2290785 4076778 TM1040_2179 Ruegeria sp. TM1040 hypothetical protein YP_614173.1 2290354 D 292414 CDS YP_614174.1 99082020 4076779 2290874..2291602 1 NC_008044.1 PFAM: NUDIX hydrolase: (1.3e-11); KEGG: sil:SPO2759 hydrolase, NUDIX family, ev=1e-82, 66% identity; NUDIX hydrolase 2291602 4076779 TM1040_2180 Ruegeria sp. TM1040 NUDIX hydrolase YP_614174.1 2290874 D 292414 CDS YP_614175.1 99082021 4076780 complement(2291629..2292531) 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (0.0017); KEGG: sil:SPO1442 membrane protein, , ev=1e-100, 67% identity; hypothetical protein 2292531 4076780 TM1040_2181 Ruegeria sp. TM1040 hypothetical protein YP_614175.1 2291629 R 292414 CDS YP_614176.1 99082022 4076781 complement(2292577..2293533) 1 NC_008044.1 PFAM: fatty acid desaturase: (5.2e-08); KEGG: sil:SPO1441 fatty acid desaturase family protein, ev=2e-99, 58% identity; fatty acid desaturase 2293533 4076781 TM1040_2182 Ruegeria sp. TM1040 fatty acid desaturase YP_614176.1 2292577 R 292414 CDS YP_614177.1 99082023 4076782 complement(2293595..2293801) 1 NC_008044.1 KEGG: sil:SPO1440 hypothetical protein, ev=2e-21, 68% identity; hypothetical protein 2293801 4076782 TM1040_2183 Ruegeria sp. TM1040 hypothetical protein YP_614177.1 2293595 R 292414 CDS YP_614178.1 99082024 4076783 2293906..2294775 1 NC_008044.1 PFAM: helix-turn-helix motif: (9.7e-12); KEGG: sil:SPO1439 DNA binding protein, , ev=1e-121, 75% identity; XRE family transcriptional regulator 2294775 4076783 TM1040_2184 Ruegeria sp. TM1040 XRE family transcriptional regulator YP_614178.1 2293906 D 292414 CDS YP_614179.1 99082025 4076784 complement(2294846..2295598) 1 NC_008044.1 Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis; 3-ketoacyl-ACP reductase 2295598 fabG 4076784 fabG Ruegeria sp. TM1040 3-ketoacyl-ACP reductase YP_614179.1 2294846 R 292414 CDS YP_614180.1 99082026 4076785 complement(2295598..2297073) 1 NC_008044.1 Converts (S)-3-hydroxyacyl-CoA to 3-oxyacyl-CoA; may also act as a thioesterase; bifunctional 3-hydroxyacyl-CoA dehydrogenase/thioesterase 2297073 4076785 TM1040_2186 Ruegeria sp. TM1040 bifunctional 3-hydroxyacyl-CoA dehydrogenase/thioesterase YP_614180.1 2295598 R 292414 CDS YP_614181.1 99082027 4076786 complement(2297086..2297646) 1 NC_008044.1 PFAM: Lipocalin-like: (4.6e-66); KEGG: rsp:RSP_0595 outer membrane lipoprotein Blc, ev=1e-26, 45% identity; Lipocalin-like protein 2297646 4076786 TM1040_2187 Ruegeria sp. TM1040 Lipocalin-like protein YP_614181.1 2297086 R 292414 CDS YP_614182.1 99082028 4078179 complement(2297712..2298629) 1 NC_008044.1 PFAM: protein of unknown function DUF849: (7.1e-195); KEGG: sil:SPO1435 hypothetical protein, ev=1e-151, 86% identity; hypothetical protein 2298629 4078179 TM1040_2188 Ruegeria sp. TM1040 hypothetical protein YP_614182.1 2297712 R 292414 CDS YP_614183.1 99082029 4078180 2298764..2299795 1 NC_008044.1 PFAM: helix-turn-helix, AraC type: (5.6e-07) ThiJ/PfpI: (2.2e-05); KEGG: sil:SPO1434 transcriptional regulator, AraC family, ev=1e-138, 76% identity; transcriptional regulator 2299795 4078180 TM1040_2189 Ruegeria sp. TM1040 transcriptional regulator YP_614183.1 2298764 D 292414 CDS YP_614184.1 99082030 4078181 complement(2299874..2300920) 1 NC_008044.1 PFAM: aldo/keto reductase: (1.1e-18); KEGG: sil:SPO1433 oxidoreductase, aldo/keto reductase family, ev=1e-139, 70% identity; aldo/keto reductase 2300920 4078181 TM1040_2190 Ruegeria sp. TM1040 aldo/keto reductase YP_614184.1 2299874 R 292414 CDS YP_614185.1 99082031 4078182 2301194..2302420 1 NC_008044.1 PFAM: major facilitator superfamily MFS_1: (3.8e-24); KEGG: sil:SPO1404 membrane protein, , ev=1e-180, 75% identity; major facilitator superfamily transporter 2302420 4078182 TM1040_2191 Ruegeria sp. TM1040 major facilitator superfamily transporter YP_614185.1 2301194 D 292414 CDS YP_614186.1 99082032 4078183 complement(2302522..2303400) 1 NC_008044.1 PFAM: regulatory protein, LysR: (3e-16) LysR, substrate-binding: (1e-25); KEGG: mlo:mlr1832 probable transcriptional regulator, ev=7e-75, 51% identity; LysR family transcriptional regulator 2303400 4078183 TM1040_2192 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_614186.1 2302522 R 292414 CDS YP_614187.1 99082033 4078184 2303499..2304203 1 NC_008044.1 PFAM: short-chain dehydrogenase/reductase SDR: (1.8e-07); KEGG: sme:SMc00136 oxidoreductase protein, ev=1e-95, 69% identity; short-chain dehydrogenase/reductase SDR 2304203 4078184 TM1040_2193 Ruegeria sp. TM1040 short-chain dehydrogenase/reductase SDR YP_614187.1 2303499 D 292414 CDS YP_614188.1 99082034 4078185 2304193..2304444 1 NC_008044.1 hypothetical protein 2304444 4078185 TM1040_2194 Ruegeria sp. TM1040 hypothetical protein YP_614188.1 2304193 D 292414 CDS YP_614189.1 99082035 4078186 complement(2304591..2306279) 1 NC_008044.1 PFAM: band 7 protein: (1.4e-14); KEGG: jan:Jann_1794 band 7 protein, ev=0.0, 76% identity; hypothetical protein 2306279 4078186 TM1040_2195 Ruegeria sp. TM1040 hypothetical protein YP_614189.1 2304591 R 292414 CDS YP_614190.1 99082036 4078187 complement(2306335..2307012) 1 NC_008044.1 PFAM: protein of unknown function DUF1449: (6.7e-09); KEGG: jan:Jann_1795 hypothetical protein, ev=4e-56, 49% identity; hypothetical protein 2307012 4078187 TM1040_2196 Ruegeria sp. TM1040 hypothetical protein YP_614190.1 2306335 R 292414 CDS YP_614191.2 161899027 4078188 2307335..2309056 1 NC_008044.1 methionine--tRNA ligase; MetRS; adds methionine to tRNA(Met) with cleavage of ATP to AMP and diphosphate; some MetRS enzymes form dimers depending on a C-terminal domain that is also found in other proteins such as Trbp111 in Aquifex aeolicus and the cold-shock protein CsaA from Bacillus subtilis while others do not; four subfamilies exist based on sequence motifs and zinc content; methionyl-tRNA synthetase 2309056 4078188 TM1040_2197 Ruegeria sp. TM1040 methionyl-tRNA synthetase YP_614191.2 2307335 D 292414 CDS YP_614192.1 99082038 4078189 2309443..2309622 1 NC_008044.1 KEGG: rsp:RSP_6006 hypothetical protein, ev=4e-08, 76% identity; hypothetical protein 2309622 4078189 TM1040_2198 Ruegeria sp. TM1040 hypothetical protein YP_614192.1 2309443 D 292414 CDS YP_614193.1 99082039 4078190 2309674..2310942 1 NC_008044.1 KEGG: sil:SPO0086 lipoprotein, , ev=1e-172, 71% identity; imelysin 2310942 4078190 TM1040_2199 Ruegeria sp. TM1040 imelysin YP_614193.1 2309674 D 292414 CDS YP_614194.1 99082040 4078191 2311172..2311459 1 NC_008044.1 KEGG: rsp:RSP_1547 probable bacterioferritin-associated ferredoxin, ev=6e-25, 65% identity; bacterioferritin-associated ferredoxin 2311459 4078191 TM1040_2200 Ruegeria sp. TM1040 bacterioferritin-associated ferredoxin YP_614194.1 2311172 D 292414 CDS YP_614195.1 99082041 4078192 2311530..2311898 1 NC_008044.1 PFAM: Ferritin and Dps: (2.4e-18); KEGG: bmb:BruAb2_0659 Bfr, bacterioferritin, ev=2e-42, 70% identity; ferritin 2311898 4078192 TM1040_2201 Ruegeria sp. TM1040 ferritin YP_614195.1 2311530 D 292414 CDS YP_614196.1 99082042 4078193 2311933..2313438 1 NC_008044.1 PFAM: protein of unknown function DUF1111: (2.8e-258); KEGG: jan:Jann_1369 protein of unknown function DUF1111, ev=0.0, 64% identity; hypothetical protein 2313438 4078193 TM1040_2202 Ruegeria sp. TM1040 hypothetical protein YP_614196.1 2311933 D 292414 CDS YP_614197.1 99082043 4078194 2313438..2314466 1 NC_008044.1 KEGG: jan:Jann_1370 hypothetical protein, ev=6e-88, 50% identity; hypothetical protein 2314466 4078194 TM1040_2203 Ruegeria sp. TM1040 hypothetical protein YP_614197.1 2313438 D 292414 CDS YP_614198.1 99082044 4078195 2314503..2315603 1 NC_008044.1 PFAM: Uncharacterised conserved protein UCP028101: (9e-104); KEGG: sil:SPO0090 hypothetical protein, ev=1e-110, 53% identity; hypothetical protein 2315603 4078195 TM1040_2204 Ruegeria sp. TM1040 hypothetical protein YP_614198.1 2314503 D 292414 CDS YP_614199.1 99082045 4078196 2315748..2316542 1 NC_008044.1 PFAM: regulatory protein, DeoR: (1.3e-52) Helix-turn-helix, type 11: (5.4e-08); KEGG: sil:SPO0731 glycerol-3-phosphate regulon repressor, ev=7e-92, 69% identity; DeoR family transcriptional regulator 2316542 4078196 TM1040_2205 Ruegeria sp. TM1040 DeoR family transcriptional regulator YP_614199.1 2315748 D 292414 CDS YP_614200.1 99082046 4078197 2316535..2318115 1 NC_008044.1 in Escherichia coli this homodimeric enzyme is expressed under aerobic conditions; anaerobic expression is repressed by the arcAB system; converts sn-glycerol-3-phosphate and ubiquinone-8 to dihydroxy acetone phosphate and ubiquinol-8; associates with the cytoplasmic membrane; glycerol-3-phosphate dehydrogenase 2318115 glpD 4078197 glpD Ruegeria sp. TM1040 glycerol-3-phosphate dehydrogenase YP_614200.1 2316535 D 292414 CDS YP_614201.1 99082047 4078198 complement(2318230..2318916) 1 NC_008044.1 KEGG: bja:bll3260 cob(I)yrinic acid a,c-diamide adenosyltransferase, ev=1e-89, 79% identity; TIGRFAM: cob(I)alamin adenosyltransferase: (4.2e-82); PFAM: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP: (3.2e-81); cob(I)yrinic acid a,c-diamide adenosyltransferase 2318916 4078198 TM1040_2207 Ruegeria sp. TM1040 cob(I)yrinic acid a,c-diamide adenosyltransferase YP_614201.1 2318230 R 292414 CDS YP_614202.1 99082048 4078199 2319278..2319781 1 NC_008044.1 PFAM: protein of unknown function DUF1636: (4.7e-41); KEGG: rsp:RSP_2829 hypothetical protein, ev=1e-27, 59% identity; hypothetical protein 2319781 4078199 TM1040_2208 Ruegeria sp. TM1040 hypothetical protein YP_614202.1 2319278 D 292414 CDS YP_614203.1 99082049 4078200 2319801..2320835 1 NC_008044.1 TIGRFAM: Cobalamin (vitamin B12) biosynthesis CobW: (1.8e-229); PFAM: cobalamin synthesis protein, P47K: (1.5e-86) cobalamin synthesis CobW-like: (7.2e-19); KEGG: jan:Jann_2933 cobalamin (vitamin B12) biosynthesis CobW, ev=1e-146, 75% identity; cobalamin (vitamin B12) biosynthesis CobW 2320835 4078200 TM1040_2209 Ruegeria sp. TM1040 cobalamin (vitamin B12) biosynthesis CobW YP_614203.1 2319801 D 292414 CDS YP_614204.1 99082050 4078201 2320961..2324206 1 NC_008044.1 with CobST catalyzes the formation of cobyrinic acid a,c-diamide from hydrogenobyrinic acid a,c-diamide in an ATP-dependent manner; involved in porphyrin and chlorophyll metabolism; vitamin B12 metabolism; cobaltochelatase subunit CobN 2324206 cobN 4078201 cobN Ruegeria sp. TM1040 cobaltochelatase subunit CobN YP_614204.1 2320961 D 292414 CDS YP_614205.1 99082051 4078202 2324203..2325363 1 NC_008044.1 TIGRFAM: Precorrin-3B synthase: (8.7e-77); PFAM: nitrite/sulfite reductase, hemoprotein beta-component, ferrodoxin-like: (2.4e-10); KEGG: bja:blr3264 hypothetical protein, ev=1e-87, 48% identity; precorrin-3B synthase 2325363 4078202 TM1040_2211 Ruegeria sp. TM1040 precorrin-3B synthase YP_614205.1 2324203 D 292414 CDS YP_614206.1 99082052 4078203 2325365..2325994 1 NC_008044.1 catalyzes the interconversion of precorrin-8X and hydrogenobyrinate; precorrin-8X methylmutase 2325994 cobH 4078203 cobH Ruegeria sp. TM1040 precorrin-8X methylmutase YP_614206.1 2325365 D 292414 CDS YP_614207.1 99082053 4078204 2326011..2326742 1 NC_008044.1 TIGRFAM: precorrin-2 C20-methyltransferase: (2.8e-92); PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase: (2.8e-25); KEGG: rsp:RSP_2826 precorrin-2 C20-methyltransferase, ev=9e-94, 68% identity; precorrin-2 C(20)-methyltransferase 2326742 4078204 TM1040_2213 Ruegeria sp. TM1040 precorrin-2 C(20)-methyltransferase YP_614207.1 2326011 D 292414 CDS YP_614208.1 99082054 4078205 2326739..2327560 1 NC_008044.1 TIGRFAM: precorrin-3B C17-methyltransferase: (2.8e-115); PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase: (4.2e-24); KEGG: rsp:RSP_2824 precorrin-3B C17-methyltransferase, ev=2e-94, 73% identity; precorrin-3 methyltransferase 2327560 4078205 TM1040_2214 Ruegeria sp. TM1040 precorrin-3 methyltransferase YP_614208.1 2326739 D 292414 CDS YP_614209.1 99082055 4078206 complement(2327557..2328318) 1 NC_008044.1 KEGG: sil:SPO2868 precorrin-6x reductase, ev=1e-76, 56% identity; TIGRFAM: precorrin-6x reductase: (1.3e-35); PFAM: Precorrin-6x reductase CbiJ/CobK: (2.1e-35); precorrin-6A reductase 2328318 4078206 TM1040_2215 Ruegeria sp. TM1040 precorrin-6A reductase YP_614209.1 2327557 R 292414 CDS YP_614210.1 99082056 4078207 2328500..2329525 1 NC_008044.1 KEGG: bja:blr3269 precorrin-6Y C5,15-methyltransferase / precorrin-8W decarboxylase, ev=1e-125, 59% identity; TIGRFAM: Precorrin-6y C5,15-methyltransferase, subunit CbiE: (1.6e-27); PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase: (4.2e-10); precorrin-6y C5,15-methyltransferase subunit CbiE 2329525 4078207 TM1040_2216 Ruegeria sp. TM1040 precorrin-6y C5,15-methyltransferase subunit CbiE YP_614210.1 2328500 D 292414 CDS YP_614211.1 99082057 4078208 2329522..2329884 1 NC_008044.1 KEGG: rsp:RSP_2822 precorrin methylase, ev=1e-16, 45% identity; precorrin methylase 2329884 4078208 TM1040_2217 Ruegeria sp. TM1040 precorrin methylase YP_614211.1 2329522 D 292414 CDS YP_614212.1 99082058 4078209 2329881..2330675 1 NC_008044.1 TIGRFAM: precorrin-4 C11-methyltransferase: (1.3e-136); PFAM: Uroporphyrin-III C/tetrapyrrole (Corrin/Porphyrin) methyltransferase: (7.9e-58); KEGG: sil:SPO2871 precorrin-4 C11-methyltransferase, ev=1e-114, 75% identity; precorrin-4 C(11)-methyltransferase 2330675 4078209 TM1040_2218 Ruegeria sp. TM1040 precorrin-4 C(11)-methyltransferase YP_614212.1 2329881 D 292414 CDS YP_614213.1 99082059 4078210 2330775..2332091 1 NC_008044.1 responsible for the amidation of carboxylic groups at position A and C of cobyrinic acid or hydrogenobrynic acid; cobyrinic acid a,c-diamide synthase 2332091 4078210 TM1040_2219 Ruegeria sp. TM1040 cobyrinic acid a,c-diamide synthase YP_614213.1 2330775 D 292414 CDS YP_614214.1 99082060 4078211 2332088..2332825 1 NC_008044.1 catalyzes 2 sequential methylations, the formation of precorrin-1 and S-adenosyl-L-homocysteine from S-adenosyl-L-methionine and uroporphyrin III, and the formation of precorrin-2 and S-adenosyl-L-homocysteine from S-adenosyl-L-methionine and precorrin-1; uroporphyrin-III C-methyltransferase 2332825 4078211 TM1040_2220 Ruegeria sp. TM1040 uroporphyrin-III C-methyltransferase YP_614214.1 2332088 D 292414 CDS YP_614215.1 99082061 4078212 2332822..2333205 1 NC_008044.1 PFAM: protein of unknown function DUF1636: (3.8e-11); KEGG: mlo:mlr8225 hypothetical protein, ev=7e-12, 37% identity; hypothetical protein 2333205 4078212 TM1040_2221 Ruegeria sp. TM1040 hypothetical protein YP_614215.1 2332822 D 292414 CDS YP_614216.1 99082062 4078213 2333650..2334423 1 NC_008044.1 TIGRFAM: Cobalt transporter subunit CbtA, : (5.3e-104); KEGG: sil:SPO2876 membrane protein, , ev=2e-97, 74% identity; cobalt transporter subunit CbtA 2334423 4078213 TM1040_2222 Ruegeria sp. TM1040 cobalt transporter subunit CbtA YP_614216.1 2333650 D 292414 CDS YP_614217.1 99082063 4078214 2334529..2335020 1 NC_008044.1 KEGG: sil:SPO2877 hypothetical protein, ev=2e-56, 64% identity; hypothetical protein 2335020 4078214 TM1040_2223 Ruegeria sp. TM1040 hypothetical protein YP_614217.1 2334529 D 292414 CDS YP_614218.1 99082064 4078215 2335093..2335857 1 NC_008044.1 catalyzes the formation of precorrin 6x from precorrin 5; precorrin 6A synthase 2335857 4078215 TM1040_2224 Ruegeria sp. TM1040 precorrin 6A synthase YP_614218.1 2335093 D 292414 CDS YP_614219.1 99082065 4078216 complement(2336081..2337271) 1 NC_008044.1 TIGRFAM: kynureninase: (3.7e-85); PFAM: aminotransferase, class V: (6.1e-08); KEGG: jan:Jann_2085 kynureninase, ev=1e-154, 66% identity; kynureninase 2337271 4078216 TM1040_2225 Ruegeria sp. TM1040 kynureninase YP_614219.1 2336081 R 292414 CDS YP_614220.1 99082066 4078217 complement(2337273..2338112) 1 NC_008044.1 PFAM: tryptophan 2,3-dioxygenase: (7e-101); KEGG: jan:Jann_2084 tryptophan 2,3-dioxygenase, ev=1e-104, 68% identity; tryptophan 2,3-dioxygenase 2338112 4078217 TM1040_2226 Ruegeria sp. TM1040 tryptophan 2,3-dioxygenase YP_614220.1 2337273 R 292414 CDS YP_614221.1 99082067 4077294 2338410..2340884 1 NC_008044.1 PFAM: CheB methylesterase: (2.7e-16) MCP methyltransferase, CheR-type: (6.4e-66); SMART: PAS: (9.7e-06); KEGG: jan:Jann_2564 MCP methyltransferase/methylesterase, CheR/CheB with PAS/PAC sensor, ev=0.0, 53% identity; chemotaxis protein CheR 2340884 4077294 TM1040_2227 Ruegeria sp. TM1040 chemotaxis protein CheR YP_614221.1 2338410 D 292414 CDS YP_614222.1 99082068 4077295 2341200..2341916 1 NC_008044.1 KEGG: jan:Jann_2565 hypothetical protein, ev=8e-06, 22% identity; hypothetical protein 2341916 4077295 TM1040_2228 Ruegeria sp. TM1040 hypothetical protein YP_614222.1 2341200 D 292414 CDS YP_614223.1 99082069 4077296 complement(2342347..2344095) 1 NC_008044.1 TIGRFAM: GGDEF domain: (1.4e-36); PFAM: GGDEF: (4.5e-47) EAL: (5.6e-58); KEGG: jan:Jann_2600 diguanylate cyclase/phosphodiesterase with PAS/PAC sensor(s), ev=7e-96, 36% identity; diguanylate cyclase/phosphodiesterase 2344095 4077296 TM1040_2229 Ruegeria sp. TM1040 diguanylate cyclase/phosphodiesterase YP_614223.1 2342347 R 292414 CDS YP_614224.1 99082070 4077297 2344893..2345891 1 NC_008044.1 PFAM: Alcohol dehydrogenase, zinc-binding: (1.6e-30) Alcohol dehydrogenase GroES-like: (2.4e-12); KEGG: sil:SPO0616 oxidoreductase, zinc-binding dehydrogenase family, ev=1e-70, 44% identity; zinc-binding alcohol dehydrogenase 2345891 4077297 TM1040_2230 Ruegeria sp. TM1040 zinc-binding alcohol dehydrogenase YP_614224.1 2344893 D 292414 CDS YP_614225.1 99082071 4077298 complement(2345962..2346357) 1 NC_008044.1 PFAM: Endoribonuclease L-PSP: (7.7e-24); KEGG: sil:SPOA0400 endoribonuclease L-PSP family protein, ev=1e-48, 66% identity; endoribonuclease L-PSP 2346357 4077298 TM1040_2231 Ruegeria sp. TM1040 endoribonuclease L-PSP YP_614225.1 2345962 R 292414 CDS YP_614226.1 99082072 4077299 complement(2346354..2346758) 1 NC_008044.1 PFAM: thioesterase superfamily: (3.1e-10); KEGG: sil:SPO0786 thioesterase family protein, ev=2e-38, 60% identity; thioesterase superfamily protein 2346758 4077299 TM1040_2232 Ruegeria sp. TM1040 thioesterase superfamily protein YP_614226.1 2346354 R 292414 CDS YP_614227.1 99082073 4077300 complement(2346762..2347448) 1 NC_008044.1 PFAM: ABC transporter related: (2.2e-47); SMART: ATPase: (2.3e-12); KEGG: bja:blr1067 ABC transporter ATP-binding protein, ev=1e-62, 52% identity; ABC transporter 2347448 4077300 TM1040_2233 Ruegeria sp. TM1040 ABC transporter YP_614227.1 2346762 R 292414 CDS YP_614228.1 99082074 4077301 complement(2347445..2348194) 1 NC_008044.1 PFAM: ABC transporter related: (1.4e-39); SMART: ATPase: (2e-10); KEGG: bja:blr1066 ABC transporter ATP-binding protein, ev=1e-59, 49% identity; ABC transporter 2348194 4077301 TM1040_2234 Ruegeria sp. TM1040 ABC transporter YP_614228.1 2347445 R 292414 CDS YP_614229.1 99082075 4077302 complement(2348187..2349170) 1 NC_008044.1 PFAM: inner-membrane translocator: (2e-33); KEGG: bja:blr1065 ABC transporter permease protein, ev=1e-75, 49% identity; inner-membrane translocator 2349170 4077302 TM1040_2235 Ruegeria sp. TM1040 inner-membrane translocator YP_614229.1 2348187 R 292414 CDS YP_614230.1 99082076 4077303 complement(2349167..2350087) 1 NC_008044.1 PFAM: inner-membrane translocator: (3.3e-32); KEGG: bja:blr1064 ABC transporter permease protein, ev=1e-89, 57% identity; inner-membrane translocator 2350087 4077303 TM1040_2236 Ruegeria sp. TM1040 inner-membrane translocator YP_614230.1 2349167 R 292414 CDS YP_614231.1 99082077 4077304 complement(2350145..2351275) 1 NC_008044.1 KEGG: dar:Daro_4043 extracellular ligand-binding receptor, ev=1e-104, 50% identity; extracellular ligand-binding receptor 2351275 4077304 TM1040_2237 Ruegeria sp. TM1040 extracellular ligand-binding receptor YP_614231.1 2350145 R 292414 CDS YP_614232.1 99082078 4077305 complement(2351314..2352930) 1 NC_008044.1 PFAM: AMP-dependent synthetase and ligase: (2.2e-101); KEGG: sil:SPOA0401 benzoate-coenzyme A ligase, ev=0.0, 81% identity; AMP-dependent synthetase/ligase 2352930 4077305 TM1040_2238 Ruegeria sp. TM1040 AMP-dependent synthetase/ligase YP_614232.1 2351314 R 292414 CDS YP_614233.1 99082079 4077306 complement(2352927..2354081) 1 NC_008044.1 PFAM: acyl-CoA dehydrogenase-like: (2.8e-50) Acyl-CoA dehydrogenase, type 2-like: (1.6e-22); KEGG: sil:SPOA0403 acyl-CoA dehydrogenase family protein, ev=1e-166, 79% identity; acyl-CoA dehydrogenase 2354081 4077306 TM1040_2239 Ruegeria sp. TM1040 acyl-CoA dehydrogenase YP_614233.1 2352927 R 292414 CDS YP_614234.1 99082080 4077307 complement(2354147..2354950) 1 NC_008044.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 2354950 4077307 TM1040_2240 Ruegeria sp. TM1040 enoyl-CoA hydratase YP_614234.1 2354147 R 292414 CDS YP_614235.1 99082081 4077308 complement(2354957..2355442) 1 NC_008044.1 PFAM: regulatory protein, MarR: (1.2e-10); KEGG: jan:Jann_1325 transcriptional regulator, MarR family, ev=1e-40, 60% identity; MarR family transcriptional regulator 2355442 4077308 TM1040_2241 Ruegeria sp. TM1040 MarR family transcriptional regulator YP_614235.1 2354957 R 292414 CDS YP_614236.1 99082082 4077309 complement(2355439..2356188) 1 NC_008044.1 PFAM: short-chain dehydrogenase/reductase SDR: (4.8e-30); KEGG: jan:Jann_1324 short-chain dehydrogenase/reductase SDR, ev=2e-82, 65% identity; short-chain dehydrogenase/reductase SDR 2356188 4077309 TM1040_2242 Ruegeria sp. TM1040 short-chain dehydrogenase/reductase SDR YP_614236.1 2355439 R 292414 CDS YP_614237.1 99082083 4077310 complement(2356185..2358479) 1 NC_008044.1 catalyzes the conversion of salicylyl-CoA to gentisyl-CoA; salicylyl-CoA 5-hydroxylase 2358479 4077310 TM1040_2243 Ruegeria sp. TM1040 salicylyl-CoA 5-hydroxylase YP_614237.1 2356185 R 292414 CDS YP_614238.1 99082084 4077311 complement(2358787..2359728) 1 NC_008044.1 PFAM: pyridoxamine 5'-phosphate oxidase-related, FMN-binding: (1.1e-09); KEGG: hch:HCH_03324 predicted flavin-nucleotide-binding protein structurally related to pyridoxine 5'-phosphate oxidase, ev=1e-72, 46% identity; pyridoxamine 5'-phosphate oxidase-like FMN-binding protein 2359728 4077311 TM1040_2244 Ruegeria sp. TM1040 pyridoxamine 5'-phosphate oxidase-like FMN-binding protein YP_614238.1 2358787 R 292414 CDS YP_614239.1 99082085 4077312 complement(2359730..2360392) 1 NC_008044.1 PFAM: glutathione S-transferase-like: (6.6e-18); KEGG: hch:HCH_03323 glutathione S-transferase, ev=3e-64, 53% identity; glutathione S-transferase 2360392 4077312 TM1040_2245 Ruegeria sp. TM1040 glutathione S-transferase YP_614239.1 2359730 R 292414 CDS YP_614240.1 99082086 4077313 complement(2360446..2360919) 1 NC_008044.1 PFAM: protein of unknown function DUF1348: (4e-93); KEGG: nar:Saro_2764 protein of unknown function DUF1348, ev=6e-71, 80% identity; hypothetical protein 2360919 4077313 TM1040_2246 Ruegeria sp. TM1040 hypothetical protein YP_614240.1 2360446 R 292414 CDS YP_614241.1 99082087 4077314 2361048..2361980 1 NC_008044.1 PFAM: regulatory protein, LysR: (5.7e-19) LysR, substrate-binding: (2.9e-40); KEGG: cvi:CV1773 GstR-like transcriptional regulator protein, ev=1e-81, 51% identity; LysR family transcriptional regulator 2361980 4077314 TM1040_2247 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_614241.1 2361048 D 292414 CDS YP_614242.1 99082088 4077315 complement(2361977..2362825) 1 NC_008044.1 KEGG: sil:SPO3245 nicotinate-nucleotide pyrophosphorylase, ev=1e-110, 75% identity; TIGRFAM: nicotinate-nucleotide pyrophosphorylase: (3.2e-126); PFAM: Quinolinate phosphoribosyl transferase: (4.9e-84); nicotinate-nucleotide pyrophosphorylase 2362825 4077315 TM1040_2248 Ruegeria sp. TM1040 nicotinate-nucleotide pyrophosphorylase YP_614242.1 2361977 R 292414 CDS YP_614243.1 99082089 4077316 complement(2362822..2364417) 1 NC_008044.1 catalyzes the formation of oxaloacetate from L-aspartate; L-aspartate oxidase 2364417 4077316 TM1040_2249 Ruegeria sp. TM1040 L-aspartate oxidase YP_614243.1 2362822 R 292414 CDS YP_614244.1 99082090 4077317 complement(2364425..2365480) 1 NC_008044.1 3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate; quinolinate synthetase 2365480 4077317 TM1040_2250 Ruegeria sp. TM1040 quinolinate synthetase YP_614244.1 2364425 R 292414 CDS YP_614245.1 99082091 4077318 2365793..2366992 1 NC_008044.1 KEGG: rsp:RSP_0200 ABC transporter, periplasmic binding protein, ev=1e-121, 56% identity; ABC transporter substrate-binding protein 2366992 4077318 TM1040_2251 Ruegeria sp. TM1040 ABC transporter substrate-binding protein YP_614245.1 2365793 D 292414 CDS YP_614246.1 99082092 4077319 2367010..2368707 1 NC_008044.1 KEGG: rsp:RSP_0201 ABC transporter, fused inner membrane subunits, ev=1e-169, 57% identity; ABC transporter inner membrane protein 2368707 4077319 TM1040_2252 Ruegeria sp. TM1040 ABC transporter inner membrane protein YP_614246.1 2367010 D 292414 CDS YP_614247.1 99082093 4077320 2368700..2369335 1 NC_008044.1 PFAM: ABC transporter related: (2.4e-48); SMART: ATPase: (1.1e-13); KEGG: rsp:RSP_6101 ABC transporter, ATPase subunit, ev=2e-64, 60% identity; ABC transporter 2369335 4077320 TM1040_2253 Ruegeria sp. TM1040 ABC transporter YP_614247.1 2368700 D 292414 CDS YP_614248.1 99082094 4077321 complement(2369508..2369942) 1 NC_008044.1 hypothetical protein 2369942 4077321 TM1040_2254 Ruegeria sp. TM1040 hypothetical protein YP_614248.1 2369508 R 292414 CDS YP_614249.1 99082095 4077322 complement(2370043..2371710) 1 NC_008044.1 ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence; ABC transporter ATP-binding protein 2371710 4077322 TM1040_2255 Ruegeria sp. TM1040 ABC transporter ATP-binding protein YP_614249.1 2370043 R 292414 CDS YP_614250.1 99082096 4077323 2371759..2372181 1 NC_008044.1 hypothetical protein 2372181 4077323 TM1040_2256 Ruegeria sp. TM1040 hypothetical protein YP_614250.1 2371759 D 292414 CDS YP_614251.1 99082097 4077324 2372457..2372696 1 NC_008044.1 hypothetical protein 2372696 4077324 TM1040_2257 Ruegeria sp. TM1040 hypothetical protein YP_614251.1 2372457 D 292414 CDS YP_614252.1 99082098 4077325 2372850..2373452 1 NC_008044.1 transfers an adenyl group from ATP to NaMN to form nicotinic acid adenine dinucleotide (NaAD) which is then converted to the ubiquitous compound NAD by NAD synthetase; essential enzyme in bacteria; nicotinic acid mononucleotide adenylyltransferase 2373452 nadD 4077325 nadD Ruegeria sp. TM1040 nicotinic acid mononucleotide adenylyltransferase YP_614252.1 2372850 D 292414 CDS YP_614253.1 99082099 4077326 2373550..2375034 1 NC_008044.1 TIGRFAM: D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase: (1.8e-25) Twin-arginine translocation pathway signal: (0.016); PFAM: peptidase S13, D-Ala-D-Ala carboxypeptidase C: (2.4e-24); KEGG: sil:SPO0451 D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase, ev=1e-150, 54% identity; D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase 2375034 4077326 TM1040_2259 Ruegeria sp. TM1040 D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase YP_614253.1 2373550 D 292414 CDS YP_614254.1 99082100 4077327 complement(2375180..2375602) 1 NC_008044.1 KEGG: sil:SPO0452 hypothetical protein, ev=3e-57, 79% identity; hypothetical protein 2375602 4077327 TM1040_2260 Ruegeria sp. TM1040 hypothetical protein YP_614254.1 2375180 R 292414 CDS YP_614255.1 99082101 4077328 2375821..2377464 1 NC_008044.1 class I; LysRS1; catalyzes a two-step reaction, first charging a lysine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; in Methanosarcina barkeri this enzyme charges both tRNA molecules for lysine that exist in this organism (but the tRNALysUUU very poorly) and in the presence of LysRS2 can charge tRNAPyl with lysine; lysyl-tRNA synthetase 2377464 lysK 4077328 lysK Ruegeria sp. TM1040 lysyl-tRNA synthetase YP_614255.1 2375821 D 292414 CDS YP_614256.1 99082102 4077329 2377716..2378129 1 NC_008044.1 KEGG: sil:SPO0457 hypothetical protein, ev=1e-34, 57% identity; hypothetical protein 2378129 4077329 TM1040_2262 Ruegeria sp. TM1040 hypothetical protein YP_614256.1 2377716 D 292414 CDS YP_614257.1 99082103 4077330 2378251..2380536 1 NC_008044.1 KEGG: sil:SPO0459 hypothetical protein, ev=0.0, 64% identity; hypothetical protein 2380536 4077330 TM1040_2263 Ruegeria sp. TM1040 hypothetical protein YP_614257.1 2378251 D 292414 CDS YP_614258.1 99082104 4077331 complement(2380533..2381048) 1 NC_008044.1 PFAM: pyridoxamine 5'-phosphate oxidase-related, FMN-binding: (1.2e-12); KEGG: jan:Jann_3613 pyridoxamine 5'-phosphate oxidase-related, FMN-binding, ev=7e-38, 53% identity; pyridoxamine 5'-phosphate oxidase-like FMN-binding protein 2381048 4077331 TM1040_2264 Ruegeria sp. TM1040 pyridoxamine 5'-phosphate oxidase-like FMN-binding protein YP_614258.1 2380533 R 292414 CDS YP_614259.1 99082105 4077332 complement(2381126..2381788) 1 NC_008044.1 KEGG: sil:SPO0460 hypothetical protein, ev=4e-17, 29% identity; hypothetical protein 2381788 4077332 TM1040_2265 Ruegeria sp. TM1040 hypothetical protein YP_614259.1 2381126 R 292414 CDS YP_614260.1 99082106 4078450 2381892..2382212 1 NC_008044.1 PFAM: Antibiotic biosynthesis monooxygenase: (8.5e-05); KEGG: sil:SPO0462 antibiotic biosynthesis monooxygenase domain protein, ev=7e-41, 74% identity; antibiotic biosynthesis monooxygenase 2382212 4078450 TM1040_2266 Ruegeria sp. TM1040 antibiotic biosynthesis monooxygenase YP_614260.1 2381892 D 292414 CDS YP_614261.1 99082107 4078451 complement(2382231..2382629) 1 NC_008044.1 KEGG: rsp:RSP_0683 hypothetical protein, ev=3e-14, 39% identity; hypothetical protein 2382629 4078451 TM1040_2267 Ruegeria sp. TM1040 hypothetical protein YP_614261.1 2382231 R 292414 CDS YP_614262.1 99082108 4078452 complement(2382783..2383712) 1 NC_008044.1 PFAM: metal-dependent protein hydrolase: (1.5e-26); KEGG: atc:AGR_L_2056 MYG1 protein, ev=1e-110, 65% identity; metal-dependent protein hydrolase 2383712 4078452 TM1040_2268 Ruegeria sp. TM1040 metal-dependent protein hydrolase YP_614262.1 2382783 R 292414 CDS YP_614263.1 99082109 4078453 complement(2383855..2384532) 1 NC_008044.1 PFAM: lipolytic enzyme, G-D-S-L: (2.4e-20); KEGG: sil:SPO0435 acyl-CoA thioesterase, , ev=3e-57, 61% identity; lipolytic protein G-D-S-L 2384532 4078453 TM1040_2269 Ruegeria sp. TM1040 lipolytic protein G-D-S-L YP_614263.1 2383855 R 292414 CDS YP_614264.1 99082110 4078454 2384585..2385289 1 NC_008044.1 PFAM: ABC transporter related: (4.5e-64); SMART: ATPase: (3.4e-16); KEGG: rsp:RSP_3602 ABC efflux transporter, ATPase subunit, ev=9e-90, 75% identity; ABC transporter 2385289 4078454 TM1040_2270 Ruegeria sp. TM1040 ABC transporter YP_614264.1 2384585 D 292414 CDS YP_614265.1 99082111 4078455 2385286..2387814 1 NC_008044.1 PFAM: protein of unknown function DUF214: (9.5e-14); KEGG: sil:SPO0433 ABC transporter, permease protein, ev=0.0, 69% identity; hypothetical protein 2387814 4078455 TM1040_2271 Ruegeria sp. TM1040 hypothetical protein YP_614265.1 2385286 D 292414 CDS YP_614266.1 99082112 4078456 complement(2387829..2388293) 1 NC_008044.1 PFAM: protein of unknown function UPF0074: (5.9e-45); KEGG: sil:SPO0432 rrf2 family protein, ev=2e-55, 72% identity; BadM/Rrf2 family transcriptional regulator 2388293 4078456 TM1040_2272 Ruegeria sp. TM1040 BadM/Rrf2 family transcriptional regulator YP_614266.1 2387829 R 292414 CDS YP_614267.1 99082113 4078457 2388397..2388966 1 NC_008044.1 KEGG: sil:SPO0431 hypothetical protein, ev=5e-45, 48% identity; hypothetical protein 2388966 4078457 TM1040_2273 Ruegeria sp. TM1040 hypothetical protein YP_614267.1 2388397 D 292414 CDS YP_614268.1 99082114 4078458 2388963..2390147 1 NC_008044.1 KEGG: jan:Jann_2342 hypothetical protein, ev=9e-64, 38% identity; hypothetical protein 2390147 4078458 TM1040_2274 Ruegeria sp. TM1040 hypothetical protein YP_614268.1 2388963 D 292414 CDS YP_614269.1 99082115 4078459 complement(2390226..2391551) 1 NC_008044.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase 2391551 gltX 4078459 gltX Ruegeria sp. TM1040 glutamyl-tRNA synthetase YP_614269.1 2390226 R 292414 CDS YP_614270.1 99082116 4078460 2391780..2392718 1 NC_008044.1 TIGRFAM: Twin-arginine translocation pathway signal: (0.027); PFAM: beta-lactamase-like: (5.1e-14); KEGG: sil:SPO0429 metallo-beta-lactamase family protein, ev=1e-113, 66% identity; twin-arginine translocation pathway signal 2392718 4078460 TM1040_2276 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_614270.1 2391780 D 292414 CDS YP_614271.1 99082117 4078461 complement(2392715..2394016) 1 NC_008044.1 PFAM: FAD dependent oxidoreductase: (3.1e-94) FAD-dependent pyridine nucleotide-disulphide oxidoreductase: (0.0014); KEGG: sil:SPO0428 amino acid deaminase, , ev=1e-144, 56% identity; FAD dependent oxidoreductase 2394016 4078461 TM1040_2277 Ruegeria sp. TM1040 FAD dependent oxidoreductase YP_614271.1 2392715 R 292414 CDS YP_614272.1 99082118 4078462 complement(2394154..2395815) 1 NC_008044.1 NH(3)-dependent; catalyzes the formation of nicotinamide adenine dinucleotide (NAD) from nicotinic acid adenine dinucleotide (NAAD) using either ammonia or glutamine as the amide donor and ATP; ammonia-utilizing enzymes include the ones from Bacillus and Escherichia coli while glutamine-utilizing enzymes include the Mycobacterial one; forms homodimers; NAD synthetase 2395815 nadE 4078462 nadE Ruegeria sp. TM1040 NAD synthetase YP_614272.1 2394154 R 292414 CDS YP_614273.1 99082119 4078463 2395984..2397486 1 NC_008044.1 PFAM: MORN motif: (0.00013); KEGG: sil:SPO0425 MORN repeat protein, ev=0.0, 71% identity; hypothetical protein 2397486 4078463 TM1040_2279 Ruegeria sp. TM1040 hypothetical protein YP_614273.1 2395984 D 292414 CDS YP_614274.1 99082120 4078464 2397495..2398535 1 NC_008044.1 hypothetical protein 2398535 4078464 TM1040_2280 Ruegeria sp. TM1040 hypothetical protein YP_614274.1 2397495 D 292414 CDS YP_614275.1 99082121 4078465 complement(2398532..2400055) 1 NC_008044.1 PFAM: deoxyribodipyrimidine photolyase-related protein: (3.6e-63); KEGG: rsp:RSP_3077 hypothetical protein, ev=0.0, 68% identity; deoxyribodipyrimidine photolyase-like protein 2400055 4078465 TM1040_2281 Ruegeria sp. TM1040 deoxyribodipyrimidine photolyase-like protein YP_614275.1 2398532 R 292414 CDS YP_614276.1 99082122 4078466 2400415..2401998 1 NC_008044.1 catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis; 2-isopropylmalate synthase 2401998 4078466 TM1040_2282 Ruegeria sp. TM1040 2-isopropylmalate synthase YP_614276.1 2400415 D 292414 CDS YP_614277.1 99082123 4078467 complement(2402080..2403336) 1 NC_008044.1 KEGG: atc:AGR_C_231 transport protein, ev=2e-95, 46% identity; transporter 2403336 4078467 TM1040_2283 Ruegeria sp. TM1040 transporter YP_614277.1 2402080 R 292414 CDS YP_614278.1 99082124 4078468 2403547..2404638 1 NC_008044.1 TIGRFAM: ubiquinol oxidase, subunit II: (5.3e-133); PFAM: COX aromatic rich: (6.2e-13); KEGG: rpb:RPB_0242 ubiquinol oxidase, subunit II, ev=1e-104, 57% identity; ubiquinol oxidase subunit II 2404638 4078468 TM1040_2284 Ruegeria sp. TM1040 ubiquinol oxidase subunit II YP_614278.1 2403547 D 292414 CDS YP_614279.1 99082125 4078469 2404642..2406678 1 NC_008044.1 PFAM: cytochrome c oxidase, subunit I: (3e-242); KEGG: atc:AGR_C_227 ba-type ubiquinol oxidase chain I, ev=0.0, 69% identity; cytochrome-c oxidase 2406678 4078469 TM1040_2285 Ruegeria sp. TM1040 cytochrome-c oxidase YP_614279.1 2404642 D 292414 CDS YP_614280.1 99082126 4078470 2406682..2407326 1 NC_008044.1 PFAM: cytochrome c oxidase, subunit III: (0.0015); KEGG: atc:AGR_C_225 bo-type ubiquinol oxidase chain III, ev=4e-70, 60% identity; cytochrome c oxidase subunit III 2407326 4078470 TM1040_2286 Ruegeria sp. TM1040 cytochrome c oxidase subunit III YP_614280.1 2406682 D 292414 CDS YP_614281.1 99082127 4078471 2407323..2407670 1 NC_008044.1 PFAM: cytochrome C oxidase subunit IV: (4.3e-35); KEGG: rpb:RPB_0239 cytochrome c oxidase subunit IV, ev=1e-30, 56% identity; cytochrome C oxidase subunit IV 2407670 4078471 TM1040_2287 Ruegeria sp. TM1040 cytochrome C oxidase subunit IV YP_614281.1 2407323 D 292414 CDS YP_614282.1 99082128 4078472 2407667..2408398 1 NC_008044.1 PFAM: Surfeit locus 1: (1e-06); KEGG: bja:blr0153 probable surfeit locus protein 1, ev=1e-41, 39% identity; Surfeit locus 1 2408398 4078472 TM1040_2288 Ruegeria sp. TM1040 Surfeit locus 1 YP_614282.1 2407667 D 292414 CDS YP_614283.1 99082129 4078473 complement(2408455..2408850) 1 NC_008044.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase: (5.8e-15); KEGG: rsp:RSP_3237 lactoylglutathione lyase, ev=3e-42, 62% identity; glyoxalase/bleomycin resistance protein/dioxygenase 2408850 4078473 TM1040_2289 Ruegeria sp. TM1040 glyoxalase/bleomycin resistance protein/dioxygenase YP_614283.1 2408455 R 292414 CDS YP_614284.1 99082130 4078474 complement(2408933..2409352) 1 NC_008044.1 PFAM: histidine triad (HIT) protein: (3.8e-42); KEGG: sil:SPO1386 HIT family protein, ev=2e-58, 83% identity; histidine triad (HIT) protein 2409352 4078474 TM1040_2290 Ruegeria sp. TM1040 histidine triad (HIT) protein YP_614284.1 2408933 R 292414 CDS YP_614285.1 99082131 4078475 2409675..2411333 1 NC_008044.1 PFAM: cytochrome c oxidase, subunit I: (8e-288); KEGG: sil:SPO1383 cytochrome c oxidase, aa3-type, subunit I, ev=0.0, 90% identity; cytochrome-c oxidase 2411333 4078475 TM1040_2291 Ruegeria sp. TM1040 cytochrome-c oxidase YP_614285.1 2409675 D 292414 CDS YP_614286.1 99082132 4078476 2411475..2411969 1 NC_008044.1 KEGG: sil:SPO1381 hypothetical protein, ev=2e-45, 55% identity; hypothetical protein 2411969 4078476 TM1040_2292 Ruegeria sp. TM1040 hypothetical protein YP_614286.1 2411475 D 292414 CDS YP_614287.1 99082133 4078477 complement(2412068..2412541) 1 NC_008044.1 PFAM: GatB/Yqey: (6.9e-37); KEGG: sil:SPO1378 GatB/YqeY domain protein, ev=3e-63, 77% identity; hypothetical protein 2412541 4078477 TM1040_2293 Ruegeria sp. TM1040 hypothetical protein YP_614287.1 2412068 R 292414 CDS YP_614288.1 99082134 4078478 2412716..2413876 1 NC_008044.1 catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers; carbamoyl phosphate synthase small subunit 2413876 4078478 TM1040_2294 Ruegeria sp. TM1040 carbamoyl phosphate synthase small subunit YP_614288.1 2412716 D 292414 CDS YP_614289.1 99082135 4078479 2414270..2415799 1 NC_008044.1 PFAM: glycosyl transferase, family 2: (1.6e-06); KEGG: sil:SPO1376 glycosyl transferase, group 2 family protein, ev=1e-142, 52% identity; glycosyl transferase family protein 2415799 4078479 TM1040_2295 Ruegeria sp. TM1040 glycosyl transferase family protein YP_614289.1 2414270 D 292414 CDS YP_614290.1 99082136 4078480 complement(2415802..2416452) 1 NC_008044.1 PFAM: regulatory protein GntR, HTH: (4e-17) GntR-like: (5.5e-30); KEGG: sil:SPO1375 transcriptional regulator, GntR family, ev=7e-88, 81% identity; GntR family transcriptional regulator 2416452 4078480 TM1040_2296 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_614290.1 2415802 R 292414 CDS YP_614291.1 99082137 4078481 2416579..2417223 1 NC_008044.1 TIGRFAM: HAD-superfamily hydrolase subfamily IA, variant 3: (2.4e-07) Pyrimidine 5-nucleotidase: (3.4e-74); PFAM: Haloacid dehalogenase-like hydrolase: (3.3e-12); KEGG: sil:SPO1374 pyrimidine 5'-nucleotidase, ev=3e-91, 72% identity; pyrimidine 5-nucleotidase 2417223 4078481 TM1040_2297 Ruegeria sp. TM1040 pyrimidine 5-nucleotidase YP_614291.1 2416579 D 292414 CDS YP_614292.1 99082138 4078482 2417308..2417556 1 NC_008044.1 KEGG: sil:SPO1372 hypothetical protein, ev=3e-26, 68% identity; hypothetical protein 2417556 4078482 TM1040_2298 Ruegeria sp. TM1040 hypothetical protein YP_614292.1 2417308 D 292414 CDS YP_614293.1 99082139 4078483 2417642..2418838 1 NC_008044.1 TIGRFAM: Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family: (4.9e-85); PFAM: monooxygenase, FAD-binding: (5.8e-10) FAD dependent oxidoreductase: (0.0017); KEGG: sil:SPO1371 2-octaprenyl-6-methoxyphenol hydroxylase, , ev=1e-166, 74% identity; 2-octaprenyl-6-methoxyphenyl hydroxylase 2418838 4078483 TM1040_2299 Ruegeria sp. TM1040 2-octaprenyl-6-methoxyphenyl hydroxylase YP_614293.1 2417642 D 292414 CDS YP_614294.1 99082140 4078484 complement(2418908..2420032) 1 NC_008044.1 PFAM: aminotransferase, class V: (0.00029); KEGG: sil:SPO1370 aminotransferase family protein, ev=1e-169, 79% identity; class V aminotransferase 2420032 4078484 TM1040_2300 Ruegeria sp. TM1040 class V aminotransferase YP_614294.1 2418908 R 292414 CDS YP_614295.1 99082141 4078485 complement(2420155..2420613) 1 NC_008044.1 PFAM: regulatory proteins, AsnC/Lrp: (9.1e-24) regulatory protein, ArsR: (0.0044); KEGG: sil:SPO1368 transcriptional regulator, AsnC family, ev=1e-62, 79% identity; AsnC family transcriptional regulator 2420613 4078485 TM1040_2301 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_614295.1 2420155 R 292414 CDS YP_614296.1 99082142 4078486 complement(2420610..2421065) 1 NC_008044.1 PFAM: regulatory proteins, AsnC/Lrp: (7.6e-14); KEGG: sil:SPO1367 transcriptional regulator, AsnC family, ev=6e-52, 67% identity; AsnC family transcriptional regulator 2421065 4078486 TM1040_2302 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_614296.1 2420610 R 292414 CDS YP_614297.1 99082143 4078487 2421204..2422226 1 NC_008044.1 catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis; ketol-acid reductoisomerase 2422226 4078487 TM1040_2303 Ruegeria sp. TM1040 ketol-acid reductoisomerase YP_614297.1 2421204 D 292414 CDS YP_614298.1 99082144 4078488 2422378..2423277 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (2e-14) Protein of unknown function DUF250: (0.0036); KEGG: sil:SPO1365 membrane protein, , ev=6e-98, 61% identity; hypothetical protein 2423277 4078488 TM1040_2304 Ruegeria sp. TM1040 hypothetical protein YP_614298.1 2422378 D 292414 CDS YP_614299.1 99082145 4078295 complement(2423398..2424741) 1 NC_008044.1 catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate; phosphoglucosamine mutase 2424741 glmM 4078295 glmM Ruegeria sp. TM1040 phosphoglucosamine mutase YP_614299.1 2423398 R 292414 CDS YP_614300.1 99082146 4078296 complement(2424802..2425797) 1 NC_008044.1 KEGG: sil:SPO1363 dihydropteroate synthase, ev=1e-104, 73% identity; TIGRFAM: dihydropteroate synthase: (1.3e-138); PFAM: dihydropteroate synthase, DHPS: (2.7e-100); dihydropteroate synthase 2425797 4078296 TM1040_2306 Ruegeria sp. TM1040 dihydropteroate synthase YP_614300.1 2424802 R 292414 CDS YP_614301.1 99082147 4078297 complement(2425794..2426714) 1 NC_008044.1 TIGRFAM: Dihydroneopterin aldolase: (5.4e-07); KEGG: sil:SPO1362 dihydroneopterin aldolase, , ev=1e-130, 78% identity; dihydroneopterin aldolase 2426714 4078297 TM1040_2307 Ruegeria sp. TM1040 dihydroneopterin aldolase YP_614301.1 2425794 R 292414 CDS YP_614302.1 99082148 4078298 complement(2426867..2427511) 1 NC_008044.1 PFAM: cell wall hydrolase, SleB: (7.4e-36); KEGG: sil:SPO1360 hypothetical protein, ev=1e-62, 59% identity; cell wall hydrolase SleB 2427511 4078298 TM1040_2308 Ruegeria sp. TM1040 cell wall hydrolase SleB YP_614302.1 2426867 R 292414 CDS YP_614303.1 99082149 4078299 complement(2427681..2430245) 1 NC_008044.1 catalyzes the formation of phosphoenolpyruvate from pyruvate; pyruvate phosphate dikinase 2430245 4078299 TM1040_2309 Ruegeria sp. TM1040 pyruvate phosphate dikinase YP_614303.1 2427681 R 292414 CDS YP_614304.1 99082150 4078300 complement(2430406..2432469) 1 NC_008044.1 glycine--tRNA ligase beta chain; glyS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking the carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA; glycyl-tRNA synthetase subunit beta 2432469 glyS 4078300 glyS Ruegeria sp. TM1040 glycyl-tRNA synthetase subunit beta YP_614304.1 2430406 R 292414 CDS YP_614305.1 99082151 4078301 complement(2432547..2433074) 1 NC_008044.1 KEGG: rsp:RSP_1857 hypothetical protein, ev=2e-36, 48% identity; hypothetical protein 2433074 4078301 TM1040_2311 Ruegeria sp. TM1040 hypothetical protein YP_614305.1 2432547 R 292414 CDS YP_614306.1 99082152 4078302 complement(2433097..2434047) 1 NC_008044.1 glycine--tRNA ligase alpha chain; GlyRS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA; glycyl-tRNA synthetase subunit alpha 2434047 glyQ 4078302 glyQ Ruegeria sp. TM1040 glycyl-tRNA synthetase subunit alpha YP_614306.1 2433097 R 292414 CDS YP_614307.1 99082153 4078303 2434344..2436134 1 NC_008044.1 PFAM: Peptidoglycan-binding domain 1: (3.8e-11) Sporulation related: (4.6e-05); KEGG: sil:SPO1354 peptidoglycan binding domain protein, ev=0.0, 61% identity; peptidoglycan binding domain-containing protein 2436134 4078303 TM1040_2313 Ruegeria sp. TM1040 peptidoglycan binding domain-containing protein YP_614307.1 2434344 D 292414 CDS YP_614308.1 99082154 4078304 complement(2436241..2436690) 1 NC_008044.1 TIGRFAM: sugar-phosphate isomerases, RpiB/LacA/LacB family: (5.1e-65) ribose 5-phosphate isomerase B: (1.7e-56); PFAM: Ribose/galactose isomerase: (6e-46); KEGG: sil:SPO3180 ribose 5-phosphate isomerase B, ev=1e-61, 78% identity; ribose-5-phosphate isomerase 2436690 4078304 TM1040_2314 Ruegeria sp. TM1040 ribose-5-phosphate isomerase YP_614308.1 2436241 R 292414 CDS YP_614309.1 99082155 4078305 complement(2436816..2437457) 1 NC_008044.1 PFAM: short-chain dehydrogenase/reductase SDR: (7.2e-07); KEGG: sil:SPO3051 oxidoreductase, short-chain dehydrogenase/reductase family, ev=5e-81, 70% identity; short-chain dehydrogenase/reductase SDR 2437457 4078305 TM1040_2315 Ruegeria sp. TM1040 short-chain dehydrogenase/reductase SDR YP_614309.1 2436816 R 292414 CDS YP_614310.1 99082156 4078306 complement(2437528..2438043) 1 NC_008044.1 PFAM: protein of unknown function DUF1178: (1.7e-53); KEGG: rsp:RSP_2387 hypothetical protein, ev=8e-45, 53% identity; hypothetical protein 2438043 4078306 TM1040_2316 Ruegeria sp. TM1040 hypothetical protein YP_614310.1 2437528 R 292414 CDS YP_614311.1 99082157 4078307 complement(2438318..2439094) 1 NC_008044.1 KEGG: sil:SPO3054 hypothetical protein, ev=4e-74, 60% identity; hypothetical protein 2439094 4078307 TM1040_2317 Ruegeria sp. TM1040 hypothetical protein YP_614311.1 2438318 R 292414 CDS YP_614312.1 99082158 4078308 complement(2439184..2439684) 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (7.4e-08); KEGG: sil:SPO3055 acetyltransferase, GNAT family, ev=9e-67, 75% identity; N-acetyltransferase GCN5 2439684 4078308 TM1040_2318 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_614312.1 2439184 R 292414 CDS YP_614313.1 99082159 4078309 2439794..2440399 1 NC_008044.1 KEGG: sil:SPO3056 hypothetical protein, ev=2e-89, 74% identity; hypothetical protein 2440399 4078309 TM1040_2319 Ruegeria sp. TM1040 hypothetical protein YP_614313.1 2439794 D 292414 CDS YP_614314.1 99082160 4078310 2440401..2441042 1 NC_008044.1 PFAM: transferase hexapeptide repeat: (0.031); KEGG: sil:SPO3057 streptogramin acetyltransferase, , ev=4e-87, 68% identity; chloramphenicol O-acetyltransferase 2441042 4078310 TM1040_2320 Ruegeria sp. TM1040 chloramphenicol O-acetyltransferase YP_614314.1 2440401 D 292414 CDS YP_614315.1 99082161 4078311 complement(2441144..2442754) 1 NC_008044.1 PFAM: Sulfate transporter/antisigma-factor antagonist STAS: (0.00075) Xanthine/uracil/vitamin C permease: (8.4e-05) sulphate transporter: (1.3e-68); KEGG: sil:SPO3058 sulfate transporter family protein, ev=0.0, 80% identity; sulfate transporter 2442754 4078311 TM1040_2321 Ruegeria sp. TM1040 sulfate transporter YP_614315.1 2441144 R 292414 CDS YP_614316.1 99082162 4078312 2443037..2443366 1 NC_008044.1 hypothetical protein 2443366 4078312 TM1040_2322 Ruegeria sp. TM1040 hypothetical protein YP_614316.1 2443037 D 292414 CDS YP_614317.1 99082163 4078313 2443610..2444542 1 NC_008044.1 KEGG: sma:SAV6152 hypothetical protein, ev=4e-13, 25% identity; hypothetical protein 2444542 4078313 TM1040_2323 Ruegeria sp. TM1040 hypothetical protein YP_614317.1 2443610 D 292414 CDS YP_614318.1 99082164 4078314 2444645..2445517 1 NC_008044.1 Catalyzes the reversible phosphorolysis of 5'-deoxy-5'- methylthioadenosine (MTA) to adenine and 5-methylthio-D-ribose-1- phosphate; 5'-methylthioadenosine phosphorylase 2445517 4078314 TM1040_2324 Ruegeria sp. TM1040 5'-methylthioadenosine phosphorylase YP_614318.1 2444645 D 292414 CDS YP_614319.1 99082165 4078315 2445634..2446173 1 NC_008044.1 catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis; adenine phosphoribosyltransferase 2446173 4078315 TM1040_2325 Ruegeria sp. TM1040 adenine phosphoribosyltransferase YP_614319.1 2445634 D 292414 CDS YP_614320.1 99082166 4078316 2446388..2446870 1 NC_008044.1 PFAM: beta-Ig-H3/fasciclin: (1.1e-55); KEGG: rsp:RSP_1409 beta-Ig-H3/fasciclin, ev=3e-45, 60% identity; beta-Ig-H3/fasciclin 2446870 4078316 TM1040_2326 Ruegeria sp. TM1040 beta-Ig-H3/fasciclin YP_614320.1 2446388 D 292414 CDS YP_614321.1 99082167 4078317 complement(2446978..2448393) 1 NC_008044.1 PFAM: FAD linked oxidase-like: (1.1e-52); KEGG: sil:SPO3067 oxidoreductase, FAD-binding, ev=0.0, 70% identity; FAD linked oxidase-like protein 2448393 4078317 TM1040_2327 Ruegeria sp. TM1040 FAD linked oxidase-like protein YP_614321.1 2446978 R 292414 CDS YP_614322.1 99082168 4078318 complement(2448461..2449051) 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (8.2e-11); KEGG: sil:SPO3069 ribosomal-protein-alanine acetyltransferase, , ev=2e-87, 78% identity; N-acetyltransferase GCN5 2449051 4078318 TM1040_2328 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_614322.1 2448461 R 292414 CDS YP_614323.1 99082169 4078319 complement(2449051..2450313) 1 NC_008044.1 PFAM: peptidase M16-like: (1.3e-48); KEGG: sil:SPO3070 peptidase, M16 family, ev=0.0, 78% identity; peptidase 2450313 4078319 TM1040_2329 Ruegeria sp. TM1040 peptidase YP_614323.1 2449051 R 292414 CDS YP_614324.1 99082170 4078320 complement(2450310..2451701) 1 NC_008044.1 catalyzes the formation of L-threonine from O-phospho-L-homoserine; threonine synthase 2451701 4078320 TM1040_2330 Ruegeria sp. TM1040 threonine synthase YP_614324.1 2450310 R 292414 CDS YP_614325.1 99082171 4078321 complement(2451716..2452378) 1 NC_008044.1 KEGG: sil:SPO3072 SURF1 family protein, ev=3e-65, 57% identity; SURF1 family protein 2452378 4078321 TM1040_2331 Ruegeria sp. TM1040 SURF1 family protein YP_614325.1 2451716 R 292414 CDS YP_614326.1 99082172 4078322 complement(2452530..2453345) 1 NC_008044.1 PFAM: cytochrome c oxidase, subunit III: (5e-88); KEGG: sil:SPO3073 cytochrome c oxidase, subunit III, ev=1e-129, 77% identity; cytochrome c oxidase subunit III 2453345 4078322 TM1040_2332 Ruegeria sp. TM1040 cytochrome c oxidase subunit III YP_614326.1 2452530 R 292414 CDS YP_614327.1 99082173 4078323 complement(2453371..2453958) 1 NC_008044.1 involved in the insertion of copper into subunit I of cytochrome C oxidase; cytochrome C oxidase assembly protein 2453958 4078323 TM1040_2333 Ruegeria sp. TM1040 cytochrome C oxidase assembly protein YP_614327.1 2453371 R 292414 CDS YP_614328.1 99082174 4078324 complement(2453963..2454124) 1 NC_008044.1 KEGG: rsp:RSP_6021 hypothetical protein, ev=3e-07, 55% identity; hypothetical protein 2454124 4078324 TM1040_2334 Ruegeria sp. TM1040 hypothetical protein YP_614328.1 2453963 R 292414 CDS YP_614329.1 99082175 4078325 complement(2454126..2455067) 1 NC_008044.1 converts protoheme IX and farnesyl diphosphate to heme O; protoheme IX farnesyltransferase 2455067 4078325 TM1040_2335 Ruegeria sp. TM1040 protoheme IX farnesyltransferase YP_614329.1 2454126 R 292414 CDS YP_614330.1 99082176 4078326 complement(2455186..2456100) 1 NC_008044.1 PFAM: cytochrome c oxidase, subunit II: (2.5e-50) cytochrome C oxidase subunit II, transmembrane region: (8.7e-26); KEGG: sil:SPO3076 cytochrome c oxidase, subunit II, ev=1e-108, 64% identity; cytochrome c oxidase subunit II 2456100 4078326 TM1040_2336 Ruegeria sp. TM1040 cytochrome c oxidase subunit II YP_614330.1 2455186 R 292414 CDS YP_614331.1 99082177 4078327 2456281..2457702 1 NC_008044.1 PFAM: peptidase U62, modulator of DNA gyrase: (3.4e-74); KEGG: sil:SPO3077 TldD/PmbA family protein, ev=0.0, 82% identity; microcin-processing peptidase 2 2457702 4078327 TM1040_2337 Ruegeria sp. TM1040 microcin-processing peptidase 2 YP_614331.1 2456281 D 292414 CDS YP_614332.1 99082178 4078328 2458080..2459228 1 NC_008044.1 TIGRFAM: DNA processing protein DprA, : (1.9e-73); PFAM: SMF protein: (1.2e-75); KEGG: sil:SPO3078 DNA processing protein DprA, , ev=1e-127, 63% identity; DNA processing protein DprA 2459228 4078328 TM1040_2338 Ruegeria sp. TM1040 DNA processing protein DprA YP_614332.1 2458080 D 292414 CDS YP_614333.1 99082179 4078329 2459369..2462050 1 NC_008044.1 catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity; DNA topoisomerase I 2462050 4078329 TM1040_2339 Ruegeria sp. TM1040 DNA topoisomerase I YP_614333.1 2459369 D 292414 CDS YP_614334.1 99082180 4078330 2462335..2463039 1 NC_008044.1 KEGG: sil:SPO3082 3-oxoadipate CoA-succinyl transferase, alpha subunit, ev=1e-113, 85% identity; TIGRFAM: 3-oxoacid CoA-transferase, subunit A: (1.3e-82); PFAM: coenzyme A transferase: (1.5e-95); 3-oxoacid CoA-transferase subunit A 2463039 4078330 TM1040_2340 Ruegeria sp. TM1040 3-oxoacid CoA-transferase subunit A YP_614334.1 2462335 D 292414 CDS YP_614335.1 99082181 4078331 2463043..2463669 1 NC_008044.1 KEGG: sil:SPO3083 3-oxoadipate CoA-succinyl transferase, beta subunit, ev=1e-106, 91% identity; TIGRFAM: 3-oxoacid CoA-transferase, subunit B: (1.1e-146); PFAM: coenzyme A transferase: (9.2e-54); butyryl-CoA:acetate CoA transferase 2463669 4078331 TM1040_2341 Ruegeria sp. TM1040 butyryl-CoA:acetate CoA transferase YP_614335.1 2463043 D 292414 CDS YP_614336.1 99082182 4078332 complement(2463866..2464684) 1 NC_008044.1 PFAM: Lytic transglycosylase, catalytic: (1.4e-24); KEGG: sil:SPO3084 transglycosylase, Slt family, ev=4e-75, 55% identity; lytic transglycosylase, catalytic 2464684 4078332 TM1040_2342 Ruegeria sp. TM1040 lytic transglycosylase, catalytic YP_614336.1 2463866 R 292414 CDS YP_614337.1 99082183 4078333 2465040..2465225 1 NC_008044.1 KEGG: sil:SPO3085 hypothetical protein, ev=4e-11, 64% identity; hypothetical protein 2465225 4078333 TM1040_2343 Ruegeria sp. TM1040 hypothetical protein YP_614337.1 2465040 D 292414 CDS YP_614338.1 99082184 4076463 2465332..2465526 1 NC_008044.1 KEGG: rsp:RSP_6025 hypothetical protein, ev=2e-07, 49% identity; hypothetical protein 2465526 4076463 TM1040_2344 Ruegeria sp. TM1040 hypothetical protein YP_614338.1 2465332 D 292414 CDS YP_614339.1 99082185 4076464 2465660..2466523 1 NC_008044.1 PFAM: Flp pilus assembly CpaB: (6.2e-29); KEGG: sil:SPO3086 CpaB family protein, ev=1e-103, 66% identity; Flp pilus assembly CpaB 2466523 4076464 TM1040_2345 Ruegeria sp. TM1040 Flp pilus assembly CpaB YP_614339.1 2465660 D 292414 CDS YP_614340.1 99082186 4076465 2466653..2468146 1 NC_008044.1 PFAM: type II and III secretion system protein: (6.1e-57) transport-associated: (1e-08); KEGG: sil:SPO3087 bacterial type II/III secretion system protein, ev=1e-179, 69% identity; type II and III secretion system protein 2468146 4076465 TM1040_2346 Ruegeria sp. TM1040 type II and III secretion system protein YP_614340.1 2466653 D 292414 CDS YP_614341.1 99082187 4076466 2468168..2468791 1 NC_008044.1 PFAM: OmpA/MotB: (4.5e-19); KEGG: sil:SPO3088 OmpA family protein, ev=3e-63, 61% identity; OmpA/MotB protein 2468791 4076466 TM1040_2347 Ruegeria sp. TM1040 OmpA/MotB protein YP_614341.1 2468168 D 292414 CDS YP_614342.1 99082188 4076467 2469041..2470285 1 NC_008044.1 KEGG: sil:SPO3089 ATPase, , ev=1e-174, 72% identity; response regulator receiver protein 2470285 4076467 TM1040_2348 Ruegeria sp. TM1040 response regulator receiver protein YP_614342.1 2469041 D 292414 CDS YP_614343.1 99082189 4076468 2470318..2471775 1 NC_008044.1 PFAM: type II secretion system protein E: (1.7e-119); KEGG: sil:SPO3090 type II/IV secretion system protein, TadA subfamily, ev=0.0, 85% identity; type II secretion system protein E 2471775 4076468 TM1040_2349 Ruegeria sp. TM1040 type II secretion system protein E YP_614343.1 2470318 D 292414 CDS YP_614344.1 99082190 4076469 2471775..2472743 1 NC_008044.1 PFAM: type II secretion system protein: (4.1e-09); KEGG: sil:SPO3091 type II/IV secretion system protein, TadC subfamily, ev=1e-140, 79% identity; type II secretion system protein 2472743 4076469 TM1040_2350 Ruegeria sp. TM1040 type II secretion system protein YP_614344.1 2471775 D 292414 CDS YP_614345.1 99082191 4076470 2472754..2473725 1 NC_008044.1 PFAM: type II secretion system protein: (9e-17); KEGG: sil:SPO3092 type II/IV secretion system protein, TadC subfamily, ev=1e-131, 73% identity; type II secretion system protein 2473725 4076470 TM1040_2351 Ruegeria sp. TM1040 type II secretion system protein YP_614345.1 2472754 D 292414 CDS YP_614346.1 99082192 4076471 2473735..2474340 1 NC_008044.1 PFAM: TPR repeat: (0.00041) Tetratricopeptide TPR_4: (0.0013) Tetratricopeptide TPR_2: (1.9e-05); SMART: Tetratricopeptide region: (2.7e-06); KEGG: sil:SPO3093 TPR domain protein, ev=2e-47, 51% identity; hypothetical protein 2474340 4076471 TM1040_2352 Ruegeria sp. TM1040 hypothetical protein YP_614346.1 2473735 D 292414 CDS YP_614347.1 99082193 4076472 2474374..2475225 1 NC_008044.1 SMART: Tetratricopeptide region: (0.15); KEGG: sil:SPO3094 lipoprotein, , ev=1e-111, 70% identity; hypothetical protein 2475225 4076472 TM1040_2353 Ruegeria sp. TM1040 hypothetical protein YP_614347.1 2474374 D 292414 CDS YP_614348.1 99082194 4076473 2475241..2475738 1 NC_008044.1 KEGG: sil:SPO3095 membrane protein, , ev=3e-39, 47% identity; hypothetical protein 2475738 4076473 TM1040_2354 Ruegeria sp. TM1040 hypothetical protein YP_614348.1 2475241 D 292414 CDS YP_614349.1 99082195 4076474 2475902..2477209 1 NC_008044.1 KEGG: sil:SPO3096 hypothetical protein, ev=0.0, 86% identity; hypothetical protein 2477209 4076474 TM1040_2355 Ruegeria sp. TM1040 hypothetical protein YP_614349.1 2475902 D 292414 CDS YP_614350.1 99082196 4076475 complement(2477322..2478224) 1 NC_008044.1 catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate; bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase 2478224 4076475 TM1040_2356 Ruegeria sp. TM1040 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase YP_614350.1 2477322 R 292414 CDS YP_614351.1 99082197 4076476 complement(2478269..2478574) 1 NC_008044.1 PFAM: Chorismate mutase: (2e-18); KEGG: sil:SPO3102 chorismate mutase family protein, ev=3e-29, 64% identity; chorismate mutase 2478574 4076476 TM1040_2357 Ruegeria sp. TM1040 chorismate mutase YP_614351.1 2478269 R 292414 CDS YP_614352.1 99082198 4076477 complement(2478640..2480316) 1 NC_008044.1 catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate; formate--tetrahydrofolate ligase 2480316 4076477 TM1040_2358 Ruegeria sp. TM1040 formate--tetrahydrofolate ligase YP_614352.1 2478640 R 292414 CDS YP_614353.1 99082199 4076478 complement(2480493..2481074) 1 NC_008044.1 PFAM: MOSC: (2.6e-07); KEGG: sil:SPO3104 MOSC domain protein, ev=4e-66, 62% identity; MOSC domain-containing protein 2481074 4076478 TM1040_2359 Ruegeria sp. TM1040 MOSC domain-containing protein YP_614353.1 2480493 R 292414 CDS YP_614354.1 99082200 4076479 complement(2481123..2481845) 1 NC_008044.1 KEGG: rsp:RSP_0664 hypothetical protein, ev=1e-17, 35% identity; hypothetical protein 2481845 4076479 TM1040_2360 Ruegeria sp. TM1040 hypothetical protein YP_614354.1 2481123 R 292414 CDS YP_614355.1 99082201 4076480 complement(2482013..2483926) 1 NC_008044.1 KEGG: sil:SPO3105 ATP-dependent metalloprotease FtsH, ev=0.0, 89% identity; TIGRFAM: ATP-dependent metalloprotease FtsH: (0); PFAM: peptidase M41: (3.6e-96) AAA ATPase, central region: (6.3e-98) peptidase M41, FtsH extracellular: (4.1e-41) ATPase associated with various cellular activities, AAA_5: (0.0005); SMART: ATPase: (2.2e-26); ATP-dependent metalloprotease FtsH 2483926 4076480 TM1040_2361 Ruegeria sp. TM1040 ATP-dependent metalloprotease FtsH YP_614355.1 2482013 R 292414 CDS YP_614356.1 99082202 4076481 complement(2484016..2485308) 1 NC_008044.1 TIGRFAM: tRNA(Ile)-lysidine synthetase-like: (5.9e-62); PFAM: PP-loop: (2.2e-55); KEGG: sil:SPO3106 PP-loop family protein, ev=1e-87, 45% identity; tRNA(Ile)-lysidine synthetase-like protein 2485308 4076481 TM1040_2362 Ruegeria sp. TM1040 tRNA(Ile)-lysidine synthetase-like protein YP_614356.1 2484016 R 292414 CDS YP_614357.1 99082203 4076482 complement(2485299..2486150) 1 NC_008044.1 PFAM: Tetratricopeptide TPR_2: (0.0047); KEGG: sil:SPO3107 hypothetical protein, ev=2e-74, 56% identity; hypothetical protein 2486150 4076482 TM1040_2363 Ruegeria sp. TM1040 hypothetical protein YP_614357.1 2485299 R 292414 CDS YP_614358.1 99082204 4076483 complement(2486156..2486659) 1 NC_008044.1 PFAM: OmpA/MotB: (1.3e-31); KEGG: jan:Jann_0976 OmpA/MotB, ev=1e-48, 59% identity; OmpA/MotB protein 2486659 4076483 TM1040_2364 Ruegeria sp. TM1040 OmpA/MotB protein YP_614358.1 2486156 R 292414 CDS YP_614359.1 99082205 4076484 complement(2486763..2488088) 1 NC_008044.1 forms dimers; may be involved in cell envelope integrity; interacts with outer membrane proteins and with the C-terminal domain of inner membrane protein TolA; translocation protein TolB 2488088 tolB 4076484 tolB Ruegeria sp. TM1040 translocation protein TolB YP_614359.1 2486763 R 292414 CDS YP_614360.1 99082206 4076485 complement(2488085..2489236) 1 NC_008044.1 KEGG: sil:SPO3110 TonB domain protein, , ev=2e-95, 50% identity; TonB domain-containing protein 2489236 4076485 TM1040_2366 Ruegeria sp. TM1040 TonB domain-containing protein YP_614360.1 2488085 R 292414 CDS YP_614361.1 99082207 4076486 complement(2489250..2489738) 1 NC_008044.1 PFAM: Biopolymer transport protein ExbD/TolR: (4.7e-21); KEGG: sil:SPO3111 biopolymer transport protein, ExbD/TolR family, ev=8e-65, 81% identity; biopolymer transport protein ExbD/TolR 2489738 4076486 TM1040_2367 Ruegeria sp. TM1040 biopolymer transport protein ExbD/TolR YP_614361.1 2489250 R 292414 CDS YP_614362.1 99082208 4076487 complement(2489742..2490437) 1 NC_008044.1 PFAM: MotA/TolQ/ExbB proton channel: (1.8e-46); KEGG: sil:SPO3112 proton transporter TolQ, ev=1e-107, 83% identity; MotA/TolQ/ExbB proton channel 2490437 4076487 TM1040_2368 Ruegeria sp. TM1040 MotA/TolQ/ExbB proton channel YP_614362.1 2489742 R 292414 CDS YP_614363.1 99082209 4076488 complement(2490552..2490938) 1 NC_008044.1 TIGRFAM: 4-hydroxybenzoyl-CoA thioesterase: (1.5e-37); PFAM: thioesterase superfamily: (6.7e-17); KEGG: sil:SPO3113 conserved hypothetical protein TIGR00051, ev=2e-44, 69% identity; 4-hydroxybenzoyl-CoA thioesterase 2490938 4076488 TM1040_2369 Ruegeria sp. TM1040 4-hydroxybenzoyl-CoA thioesterase YP_614363.1 2490552 R 292414 CDS YP_614364.1 99082210 4076489 complement(2490935..2491600) 1 NC_008044.1 KEGG: sil:SPO3114 hypothetical protein, ev=4e-78, 70% identity; hypothetical protein 2491600 4076489 TM1040_2370 Ruegeria sp. TM1040 hypothetical protein YP_614364.1 2490935 R 292414 CDS YP_614365.1 99082211 4076490 complement(2491837..2492856) 1 NC_008044.1 promotes strand exchange during homologous recombination; RuvAB complex promotes branch migration; RuvABC complex scans the DNA during branch migration and resolves Holliday junctions at consensus sequences; forms hexameric rings around opposite DNA arms; requires ATP for branch migration and orientation of RuvAB complex determines direction of migration; Holliday junction DNA helicase RuvB 2492856 ruvB 4076490 ruvB Ruegeria sp. TM1040 Holliday junction DNA helicase RuvB YP_614365.1 2491837 R 292414 CDS YP_614366.1 99082212 4076491 complement(2492868..2493557) 1 NC_008044.1 plays an essential role in ATP-dependent branch migration of the Holliday junction; Holliday junction DNA helicase RuvA 2493557 ruvA 4076491 ruvA Ruegeria sp. TM1040 Holliday junction DNA helicase RuvA YP_614366.1 2492868 R 292414 CDS YP_614367.1 99082213 4076492 complement(2493554..2494120) 1 NC_008044.1 endonuclease; resolves Holliday structures; forms a complex of RuvABC; the junction binding protein RuvA forms a hexameric ring along with the RuvB helicase and catalyzes branch migration; RuvC then interacts with RuvAB to resolve the Holliday junction by nicking DNA strands of like polarity; Holliday junction resolvase 2494120 ruvC 4076492 ruvC Ruegeria sp. TM1040 Holliday junction resolvase YP_614367.1 2493554 R 292414 CDS YP_614368.1 99082214 4076493 2494425..2494643 1 NC_008044.1 PFAM: protein of unknown function DUF1127: (3.1e-06); KEGG: sil:SPO3118 hypothetical protein, ev=1e-14, 59% identity; hypothetical protein 2494643 4076493 TM1040_2374 Ruegeria sp. TM1040 hypothetical protein YP_614368.1 2494425 D 292414 CDS YP_614369.1 99082215 4076494 complement(2494796..2495056) 1 NC_008044.1 KEGG: sil:SPO3119 hypothetical protein, ev=5e-13, 46% identity; hypothetical protein 2495056 4076494 TM1040_2375 Ruegeria sp. TM1040 hypothetical protein YP_614369.1 2494796 R 292414 CDS YP_614370.1 99082216 4076495 complement(2495256..2496125) 1 NC_008044.1 PFAM: methyltransferase small: (2e-05) ribosomal L11 methyltransferase: (2.3e-47) Methyltransferase type 12: (0.00024); KEGG: sil:SPO3120 ribosomal protein L11 methyltransferase, , ev=1e-130, 81% identity; 50S ribosomal protein L20 2496125 4076495 TM1040_2376 Ruegeria sp. TM1040 50S ribosomal protein L20 YP_614370.1 2495256 R 292414 CDS YP_614371.1 99082217 4076496 complement(2496237..2497472) 1 NC_008044.1 PFAM: major facilitator superfamily MFS_1: (3.5e-09); KEGG: sil:SPO3122 membrane protein, , ev=0.0, 79% identity; major facilitator superfamily transporter 2497472 4076496 TM1040_2377 Ruegeria sp. TM1040 major facilitator superfamily transporter YP_614371.1 2496237 R 292414 CDS YP_614372.1 99082218 4076497 complement(2497575..2499782) 1 NC_008044.1 binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity; primosome assembly protein PriA 2499782 4076497 TM1040_2378 Ruegeria sp. TM1040 primosome assembly protein PriA YP_614372.1 2497575 R 292414 CDS YP_614373.1 99082219 4076498 2499963..2500616 1 NC_008044.1 similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity; translaldolase 2500616 4076498 TM1040_2379 Ruegeria sp. TM1040 translaldolase YP_614373.1 2499963 D 292414 CDS YP_614374.1 99082220 4076499 2500799..2501512 1 NC_008044.1 KEGG: sil:SPO3129 hypothetical protein, ev=7e-80, 65% identity; hypothetical protein 2501512 4076499 TM1040_2380 Ruegeria sp. TM1040 hypothetical protein YP_614374.1 2500799 D 292414 CDS YP_614375.1 99082221 4076500 2501509..2502444 1 NC_008044.1 site-specific tyrosine recombinase which cuts and rejoins DNA molecules; binds cooperatively to specific DNA consensus sites; forms a heterotetrameric complex with XerC; XerCD exhibit similar sequences; essential to convert chromosome dimers to monomers during cell division and functions during plasmid segregation; cell division protein FtsK may regulate the XerCD complex; enzyme from Streptococcus group has unusual active site motifs; site-specific tyrosine recombinase XerC 2502444 xerC 4076500 xerC Ruegeria sp. TM1040 site-specific tyrosine recombinase XerC YP_614375.1 2501509 D 292414 CDS YP_614376.1 99082222 4076501 2502569..2503261 1 NC_008044.1 PFAM: CDP-alcohol phosphatidyltransferase: (0.0088); KEGG: sil:SPO3131 phosphatidylcholine synthase, ev=1e-102, 76% identity; CDP-diacylglycerol-choline O-phosphatidyltransferase 2503261 4076501 TM1040_2382 Ruegeria sp. TM1040 CDP-diacylglycerol-choline O-phosphatidyltransferase YP_614376.1 2502569 D 292414 CDS YP_614377.1 99082223 4076709 2503459..2503764 1 NC_008044.1 hypothetical protein 2503764 4076709 TM1040_2383 Ruegeria sp. TM1040 hypothetical protein YP_614377.1 2503459 D 292414 CDS YP_614378.1 99082224 4076710 complement(2503881..2504660) 1 NC_008044.1 mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability; tRNA pseudouridine synthase A 2504660 truA 4076710 truA Ruegeria sp. TM1040 tRNA pseudouridine synthase A YP_614378.1 2503881 R 292414 CDS YP_614379.1 99082225 4076711 2504863..2506260 1 NC_008044.1 PFAM: protein of unknown function DUF463, YcjX-like protein: (3.7e-130); KEGG: sil:SPO3142 hypothetical protein, ev=0.0, 72% identity; hypothetical protein 2506260 4076711 TM1040_2385 Ruegeria sp. TM1040 hypothetical protein YP_614379.1 2504863 D 292414 CDS YP_614380.1 99082226 4076712 2506257..2506721 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (6.6e-13); KEGG: sil:SPO3141 acetyltransferase, GNAT family, ev=3e-38, 53% identity; N-acetyltransferase GCN5 2506721 4076712 TM1040_2386 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_614380.1 2506257 D 292414 CDS YP_614381.1 99082227 4076713 2506718..2507698 1 NC_008044.1 KEGG: sil:SPO3140 conserved hypothetical protein TIGR01620, ev=5e-94, 55% identity; hypothetical protein 2507698 4076713 TM1040_2387 Ruegeria sp. TM1040 hypothetical protein YP_614381.1 2506718 D 292414 CDS YP_614382.1 99082228 4076714 complement(2507721..2508134) 1 NC_008044.1 KEGG: sil:SPO3139 hypothetical protein, ev=2e-41, 60% identity; hypothetical protein 2508134 4076714 TM1040_2388 Ruegeria sp. TM1040 hypothetical protein YP_614382.1 2507721 R 292414 CDS YP_614383.1 99082229 4076715 2508425..2511349 1 NC_008044.1 IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase family type 1 subfamily; some organisms carry two different copies of this enzyme; isoleucyl-tRNA synthetase 2511349 ileS 4076715 ileS Ruegeria sp. TM1040 isoleucyl-tRNA synthetase YP_614383.1 2508425 D 292414 CDS YP_614384.1 99082230 4076716 complement(2511432..2511881) 1 NC_008044.1 hypothetical protein 2511881 4076716 TM1040_2390 Ruegeria sp. TM1040 hypothetical protein YP_614384.1 2511432 R 292414 CDS YP_614385.1 99082231 4076717 complement(2512654..2515503) 1 NC_008044.1 acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine; glycine dehydrogenase 2515503 4076717 TM1040_2391 Ruegeria sp. TM1040 glycine dehydrogenase YP_614385.1 2512654 R 292414 CDS YP_614386.1 99082232 4076718 complement(2515630..2515989) 1 NC_008044.1 TIGRFAM: glycine cleavage system H protein: (3.1e-42); PFAM: glycine cleavage H-protein: (4.6e-51); KEGG: sil:SPO0878 glycine cleavage system H protein, ev=3e-51, 81% identity; glycine cleavage system H protein 2515989 4076718 TM1040_2392 Ruegeria sp. TM1040 glycine cleavage system H protein YP_614386.1 2515630 R 292414 CDS YP_614387.1 99082233 4076719 complement(2516031..2517155) 1 NC_008044.1 TIGRFAM: glycine cleavage system T protein: (4.4e-95); PFAM: glycine cleavage T protein (aminomethyl transferase): (1.7e-88); KEGG: rsp:RSP_2193 predicted aminomethyltransferase, tetrahydrofolate dependent, ev=1e-132, 64% identity; glycine cleavage system T protein 2517155 4076719 TM1040_2393 Ruegeria sp. TM1040 glycine cleavage system T protein YP_614387.1 2516031 R 292414 CDS YP_614388.1 99082234 4076720 2517618..2518607 1 NC_008044.1 PFAM: glyceraldehyde 3-phosphate dehydrogenase: (2.6e-68); KEGG: sil:SPO0875 glyceraldehyde-3-phosphate dehydrogenase, type I, ev=1e-123, 67% identity; glyceraldehyde 3-phosphate dehydrogenase 2518607 4076720 TM1040_2394 Ruegeria sp. TM1040 glyceraldehyde 3-phosphate dehydrogenase YP_614388.1 2517618 D 292414 CDS YP_614389.1 99082235 4076721 2518778..2520610 1 NC_008044.1 PFAM: surface antigen (D15): (4.1e-35); KEGG: sil:SPO0868 outer membrane protein, OMP85 family, ev=1e-170, 51% identity; surface antigen (D15) 2520610 4076721 TM1040_2395 Ruegeria sp. TM1040 surface antigen (D15) YP_614389.1 2518778 D 292414 CDS YP_614390.1 99082236 4076722 2520607..2524614 1 NC_008044.1 PFAM: protein of unknown function DUF490: (3e-39); KEGG: sil:SPO0867 hypothetical protein, ev=0.0, 43% identity; hypothetical protein 2524614 4076722 TM1040_2396 Ruegeria sp. TM1040 hypothetical protein YP_614390.1 2520607 D 292414 CDS YP_614391.1 99082237 4076723 2524618..2525616 1 NC_008044.1 PFAM: glycosyl transferase, family 2: (1.6e-14); KEGG: jan:Jann_4255 glycosyl transferase, family 2, ev=1e-103, 59% identity; glycosyl transferase family protein 2525616 4076723 TM1040_2397 Ruegeria sp. TM1040 glycosyl transferase family protein YP_614391.1 2524618 D 292414 CDS YP_614392.1 99082238 4076724 complement(2525684..2526406) 1 NC_008044.1 TIGRFAM: glycosyl transferase, WecB/TagA/CpsF family: (8.8e-28); PFAM: glycosyl transferase WecB/TagA/CpsF: (2.4e-28); KEGG: sil:SPO0851 glycosyl transferase, WecB/TagA/CpsF family, ev=5e-72, 60% identity; WecB/TagA/CpsF family glycosyl transferase 2526406 4076724 TM1040_2398 Ruegeria sp. TM1040 WecB/TagA/CpsF family glycosyl transferase YP_614392.1 2525684 R 292414 CDS YP_614393.1 99082239 4076725 2526578..2528044 1 NC_008044.1 KEGG: sil:SPO0850 membrane protein, , ev=1e-137, 50% identity; hypothetical protein 2528044 4076725 TM1040_2399 Ruegeria sp. TM1040 hypothetical protein YP_614393.1 2526578 D 292414 CDS YP_614394.1 99082240 4076726 2528233..2534685 1 NC_008044.1 PFAM: beta-ketoacyl synthase: (4.6e-76) Thioesterase: (4.9e-08) acyl transferase region: (4.2e-49) short-chain dehydrogenase/reductase SDR: (3e-38) phosphopantetheine-binding: (6e-21); KEGG: sil:SPO0849 non-ribosomal peptide synthase, ev=0.0, 63% identity; beta-ketoacyl synthase 2534685 4076726 TM1040_2400 Ruegeria sp. TM1040 beta-ketoacyl synthase YP_614394.1 2528233 D 292414 CDS YP_614395.1 99082241 4076727 2534689..2535711 1 NC_008044.1 PFAM: glycosyl transferase, family 2: (5.5e-08); KEGG: sil:SPO0848 glycosyl transferase, group 2 family protein, ev=1e-108, 57% identity; glycosyl transferase family protein 2535711 4076727 TM1040_2401 Ruegeria sp. TM1040 glycosyl transferase family protein YP_614395.1 2534689 D 292414 CDS YP_614396.1 99082242 4076728 2535708..2540267 1 NC_008044.1 TIGRFAM: Amino acid adenylation: (2.6e-117); PFAM: AMP-dependent synthetase and ligase: (8.5e-132) formyl transferase-like: (4.7e-09) phosphopantetheine-binding: (9.3e-14) luciferase-like: (2.1e-13); KEGG: sil:SPO0847 non-ribosomal peptide synthetase, ev=0.0, 62% identity; amino acid adenylation protein 2540267 4076728 TM1040_2402 Ruegeria sp. TM1040 amino acid adenylation protein YP_614396.1 2535708 D 292414 CDS YP_614397.1 99082243 4076729 2540264..2540974 1 NC_008044.1 PFAM: 4'-phosphopantetheinyl transferase: (2.9e-07); KEGG: sil:SPO0846 phosphopantetheinyl transferase PptA, , ev=1e-44, 46% identity; 4'-phosphopantetheinyl transferase 2540974 4076729 TM1040_2403 Ruegeria sp. TM1040 4'-phosphopantetheinyl transferase YP_614397.1 2540264 D 292414 CDS YP_614398.1 99082244 4076730 2540971..2541936 1 NC_008044.1 KEGG: sil:SPO0845 hypothetical protein, ev=6e-76, 50% identity; hypothetical protein 2541936 4076730 TM1040_2404 Ruegeria sp. TM1040 hypothetical protein YP_614398.1 2540971 D 292414 CDS YP_614399.1 99082245 4076731 2541933..2544470 1 NC_008044.1 KEGG: sil:SPO0844 hypothetical protein, ev=0.0, 53% identity; hypothetical protein 2544470 4076731 TM1040_2405 Ruegeria sp. TM1040 hypothetical protein YP_614399.1 2541933 D 292414 CDS YP_614400.1 99082246 4076732 2544467..2545309 1 NC_008044.1 PFAM: glycosyl transferase, family 2: (1.4e-19); KEGG: sil:SPO0843 glycosyl transferase, group 2 family protein, ev=5e-75, 53% identity; glycosyl transferase family protein 2545309 4076732 TM1040_2406 Ruegeria sp. TM1040 glycosyl transferase family protein YP_614400.1 2544467 D 292414 CDS YP_614401.1 99082247 4076733 complement(2545320..2546534) 1 NC_008044.1 PFAM: glycosyl transferase, group 1: (1.1e-37); KEGG: sil:SPO0842 glycosyl transferase, group 1 family protein, ev=1e-134, 64% identity; group 1 glycosyl transferase 2546534 4076733 TM1040_2407 Ruegeria sp. TM1040 group 1 glycosyl transferase YP_614401.1 2545320 R 292414 CDS YP_614402.1 99082248 4076734 2546676..2548091 1 NC_008044.1 PFAM: polysaccharide biosynthesis protein: (4e-16); KEGG: sil:SPO0841 polysaccharide biosynthesis protein, ev=1e-121, 48% identity; polysaccharide biosynthesis protein 2548091 4076734 TM1040_2408 Ruegeria sp. TM1040 polysaccharide biosynthesis protein YP_614402.1 2546676 D 292414 CDS YP_614403.1 99082249 4076735 complement(2548100..2549374) 1 NC_008044.1 PFAM: lipopolysaccharide biosynthesis: (0.013); KEGG: sil:SPO0840 chain length determinant protein, , ev=1e-104, 49% identity; lipopolysaccharide biosynthesis protein 2549374 4076735 TM1040_2409 Ruegeria sp. TM1040 lipopolysaccharide biosynthesis protein YP_614403.1 2548100 R 292414 CDS YP_614404.1 99082250 4076736 complement(2549408..2550409) 1 NC_008044.1 KEGG: sil:SPO0839 exopolysaccharide biosynthesis domain protein, ev=2e-63, 44% identity; exopolysaccharide biosynthesis domain-containing protein 2550409 4076736 TM1040_2410 Ruegeria sp. TM1040 exopolysaccharide biosynthesis domain-containing protein YP_614404.1 2549408 R 292414 CDS YP_614405.1 99082251 4076737 complement(2550750..2551463) 1 NC_008044.1 PFAM: sugar transferase: (3.1e-66); KEGG: sil:SPO0838 bacterial sugar transferase, ev=2e-63, 58% identity; UDP-phosphate galactosephosphotransferase 2551463 4076737 TM1040_2411 Ruegeria sp. TM1040 UDP-phosphate galactosephosphotransferase YP_614405.1 2550750 R 292414 CDS YP_614406.1 99082252 4076738 complement(2551834..2552994) 1 NC_008044.1 PFAM: helix-turn-helix, AraC type: (2.2e-09); KEGG: bur:Bcep18194_B2989 transcriptional regulator, AraC family, ev=1e-26, 28% identity; AraC family transcriptional regulator 2552994 4076738 TM1040_2412 Ruegeria sp. TM1040 AraC family transcriptional regulator YP_614406.1 2551834 R 292414 CDS YP_614407.1 99082253 4076739 2553324..2554130 1 NC_008044.1 KEGG: sil:SPO0785 2-dehydro-3-deoxygalactonokinase, , ev=8e-27, 31% identity; 2-dehydro-3-deoxygalactonokinase 2554130 4076739 TM1040_2413 Ruegeria sp. TM1040 2-dehydro-3-deoxygalactonokinase YP_614407.1 2553324 D 292414 CDS YP_614408.1 99082254 4076740 complement(2554164..2554964) 1 NC_008044.1 KEGG: sil:SPO0581 hypothetical protein, ev=6e-64, 50% identity; hypothetical protein 2554964 4076740 TM1040_2414 Ruegeria sp. TM1040 hypothetical protein YP_614408.1 2554164 R 292414 CDS YP_614409.1 99082255 4076741 complement(2555077..2556198) 1 NC_008044.1 PFAM: RNA methylase: (6.3e-33); KEGG: sil:SPOA0322 hypothetical protein, ev=1e-127, 62% identity; RNA methylase 2556198 4076741 TM1040_2415 Ruegeria sp. TM1040 RNA methylase YP_614409.1 2555077 R 292414 CDS YP_614410.1 99082256 4076742 2556474..2558207 1 NC_008044.1 PFAM: extracellular solute-binding protein, family 1: (4.2e-07); KEGG: sil:SPO0608 sugar ABC transporter, periplasmic sugar-binding protein, ev=0.0, 92% identity; extracellular solute-binding protein 2558207 4076742 TM1040_2416 Ruegeria sp. TM1040 extracellular solute-binding protein YP_614410.1 2556474 D 292414 CDS YP_614411.1 99082257 4076743 2558405..2559481 1 NC_008044.1 PFAM: ABC transporter related: (4.7e-46) Transport-associated OB: (4.9e-06); SMART: ATPase: (7.4e-11); KEGG: sil:SPO0609 sugar ABC transporter, ATP-binding protein, ev=1e-166, 83% identity; ABC transporter 2559481 4076743 TM1040_2417 Ruegeria sp. TM1040 ABC transporter YP_614411.1 2558405 D 292414 CDS YP_614412.1 99082258 4076744 2559491..2560564 1 NC_008044.1 PFAM: ABC transporter related: (7.4e-41) TOBE: (0.00016) Transport-associated OB: (1.6e-06); SMART: ATPase: (3e-13); KEGG: sil:SPO0610 sugar ABC transporter, ATP-binding protein, ev=1e-166, 82% identity; ABC transporter 2560564 4076744 TM1040_2418 Ruegeria sp. TM1040 ABC transporter YP_614412.1 2559491 D 292414 CDS YP_614413.1 99082259 4076745 2560570..2561433 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (0.0001); KEGG: sil:SPO0611 sugar ABC transporter, permease protein, ev=1e-161, 96% identity; binding-protein-dependent transport system inner membrane protein 2561433 4076745 TM1040_2419 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_614413.1 2560570 D 292414 CDS YP_614414.1 99082260 4076746 2561445..2562242 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (5.8e-09); KEGG: sil:SPO0612 sugar ABC transporter, permease protein, ev=1e-142, 93% identity; binding-protein-dependent transport system inner membrane protein 2562242 4076746 TM1040_2420 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_614414.1 2561445 D 292414 CDS YP_614415.1 99082261 4076747 2562244..2562522 1 NC_008044.1 KEGG: sil:SPO0613 hypothetical protein, ev=2e-45, 89% identity; hypothetical protein 2562522 4076747 TM1040_2421 Ruegeria sp. TM1040 hypothetical protein YP_614415.1 2562244 D 292414 CDS YP_614416.1 99082262 4076904 2562766..2563215 1 NC_008044.1 PFAM: Penicillinase repressor: (1.4e-28); KEGG: sil:SPO0614 transcriptional regulator, , ev=6e-52, 80% identity; CopY family transcriptional regulator 2563215 4076904 TM1040_2422 Ruegeria sp. TM1040 CopY family transcriptional regulator YP_614416.1 2562766 D 292414 CDS YP_614417.1 99082263 4076905 2563205..2564347 1 NC_008044.1 PFAM: peptidase M56, BlaR1: (5.2e-08); KEGG: sil:SPO0615 hypothetical protein, ev=1e-104, 52% identity; peptidase M56, BlaR1 2564347 4076905 TM1040_2423 Ruegeria sp. TM1040 peptidase M56, BlaR1 YP_614417.1 2563205 D 292414 CDS YP_614418.1 99082264 4076906 complement(2564427..2565302) 1 NC_008044.1 converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA; 3-hydroxybutyryl-CoA dehydrogenase 2565302 4076906 TM1040_2424 Ruegeria sp. TM1040 3-hydroxybutyryl-CoA dehydrogenase YP_614418.1 2564427 R 292414 CDS YP_614419.1 99082265 4076907 2565459..2566295 1 NC_008044.1 KEGG: sil:SPO0718 hypothetical protein, ev=1e-64, 49% identity; hypothetical protein 2566295 4076907 TM1040_2425 Ruegeria sp. TM1040 hypothetical protein YP_614419.1 2565459 D 292414 CDS YP_614420.1 99082266 4076908 complement(2566366..2567295) 1 NC_008044.1 PFAM: electron transfer flavoprotein beta-subunit: (3e-40) electron transfer flavoprotein, alpha subunit: (4.9e-58); KEGG: sil:SPO0719 electron transfer flavoprotein, alpha subunit, ev=1e-148, 88% identity; electron transfer flavoprotein subunit alpha 2567295 4076908 TM1040_2426 Ruegeria sp. TM1040 electron transfer flavoprotein subunit alpha YP_614420.1 2566366 R 292414 CDS YP_614421.1 99082267 4076909 complement(2567295..2568053) 1 NC_008044.1 PFAM: electron transfer flavoprotein beta-subunit: (2.5e-77); KEGG: sil:SPO0720 electron transfer flavoprotein, beta subunit, ev=1e-124, 90% identity; electron transfer flavoprotein subunit beta 2568053 4076909 TM1040_2427 Ruegeria sp. TM1040 electron transfer flavoprotein subunit beta YP_614421.1 2567295 R 292414 CDS YP_614422.1 99082268 4076910 complement(2568362..2568934) 1 NC_008044.1 TIGRFAM: ATP: (7.6e-78); PFAM: cobalamin adenosyltransferase: (2.5e-92); KEGG: sil:SPO0722 ATP:cob(I)alamin adenosyltransferase, , ev=1e-79, 77% identity; ATP:cob(I)alamin adenosyltransferase 2568934 4076910 TM1040_2428 Ruegeria sp. TM1040 ATP:cob(I)alamin adenosyltransferase YP_614422.1 2568362 R 292414 CDS YP_614423.1 99082269 4076911 complement(2568936..2569139) 1 NC_008044.1 KEGG: sil:SPO0723 hypothetical protein, ev=2e-13, 57% identity; hypothetical protein 2569139 4076911 TM1040_2429 Ruegeria sp. TM1040 hypothetical protein YP_614423.1 2568936 R 292414 CDS YP_614424.1 99082270 4076912 complement(2569211..2570041) 1 NC_008044.1 PFAM: short-chain dehydrogenase/reductase SDR: (5.4e-18); KEGG: sil:SPO0724 oxidoreductase, short-chain dehydrogenase/reductase family, ev=1e-124, 78% identity; short-chain dehydrogenase/reductase SDR 2570041 4076912 TM1040_2430 Ruegeria sp. TM1040 short-chain dehydrogenase/reductase SDR YP_614424.1 2569211 R 292414 CDS YP_614425.1 99082271 4076913 complement(2570072..2570755) 1 NC_008044.1 PFAM: SH3: (0.13) SH3, type 3: (2.2e-06); SMART: SH3-like region: (2e-10); KEGG: rsp:RSP_1695 hypothetical protein, ev=6e-08, 30% identity; hypothetical protein 2570755 4076913 TM1040_2431 Ruegeria sp. TM1040 hypothetical protein YP_614425.1 2570072 R 292414 CDS YP_614426.1 99082272 4076914 2571061..2573409 1 NC_008044.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit A 2573409 4076914 TM1040_2432 Ruegeria sp. TM1040 DNA topoisomerase IV subunit A YP_614426.1 2571061 D 292414 CDS YP_614427.1 99082273 4076915 2573544..2574128 1 NC_008044.1 KEGG: sil:SPO0727 hypothetical protein, ev=6e-59, 61% identity; hypothetical protein 2574128 4076915 TM1040_2433 Ruegeria sp. TM1040 hypothetical protein YP_614427.1 2573544 D 292414 CDS YP_614428.1 99082274 4076916 2574242..2575417 1 NC_008044.1 EF-Tu; promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis; when the tRNA anticodon matches the mRNA codon, GTP hydrolysis results; the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts; many prokaryotes have two copies of the gene encoding EF-Tu; elongation factor Tu 2575417 4076916 TM1040_2434 Ruegeria sp. TM1040 elongation factor Tu YP_614428.1 2574242 D 292414 CDS YP_614429.1 99082275 4076917 complement(2576659..2577612) 1 NC_008044.1 KEGG: sil:SPO0716 hypothetical protein, ev=1e-131, 76% identity; hypothetical protein 2577612 4076917 TM1040_2435 Ruegeria sp. TM1040 hypothetical protein YP_614429.1 2576659 R 292414 CDS YP_614430.1 99082276 4076918 complement(2577596..2577865) 1 NC_008044.1 TIGRFAM: Phosphotransferase system, HPr: (1.3e-28); PFAM: phosphocarrier HPr protein: (2.9e-23); KEGG: sil:SPO0715 phosphocarrier protein HPr, ev=3e-36, 85% identity; phosphotransferase system, HPr 2577865 4076918 TM1040_2436 Ruegeria sp. TM1040 phosphotransferase system, HPr YP_614430.1 2577596 R 292414 CDS YP_614431.1 99082277 4076919 complement(2577869..2578273) 1 NC_008044.1 PFAM: PTS system fructose subfamily IIA component: (1e-21); KEGG: sil:SPO0714 PTS system IIA component, Man family, ev=1e-53, 84% identity; PTS system fructose subfamily transporter subunit IIA 2578273 4076919 TM1040_2437 Ruegeria sp. TM1040 PTS system fructose subfamily transporter subunit IIA YP_614431.1 2577869 R 292414 CDS YP_614432.1 99082278 4076920 complement(2578283..2579185) 1 NC_008044.1 PFAM: Uncharacterised P-loop ATPase protein UPF0042: (6e-80); KEGG: sil:SPO0713 ATPase, , ev=1e-94, 63% identity; hypothetical protein 2579185 4076920 TM1040_2438 Ruegeria sp. TM1040 hypothetical protein YP_614432.1 2578283 R 292414 CDS YP_614433.1 99082279 4076921 complement(2579157..2579645) 1 NC_008044.1 KEGG: rsp:RSP_1683 kinase/phosphatase, ev=3e-33, 56% identity; Hpr(Ser) kinase/phosphatase 2579645 4076921 TM1040_2439 Ruegeria sp. TM1040 Hpr(Ser) kinase/phosphatase YP_614433.1 2579157 R 292414 CDS YP_614434.1 99082280 4076922 complement(2579623..2581356) 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (5.3e-35) histidine kinase, HAMP region: (7.5e-10) histidine kinase A-like: (2.9e-16); KEGG: sil:SPO0711 sensor histidine kinase ChvG, ev=0.0, 70% identity; sensor signal transduction histidine kinase 2581356 4076922 TM1040_2440 Ruegeria sp. TM1040 sensor signal transduction histidine kinase YP_614434.1 2579623 R 292414 CDS YP_614435.1 99082281 4076923 complement(2581396..2582097) 1 NC_008044.1 PFAM: response regulator receiver: (8.4e-34) transcriptional regulatory protein-like: (2.5e-18); KEGG: sil:SPO0710 DNA-binding response regulator ChvI, ev=1e-121, 96% identity; two component transcriptional regulator 2582097 4076923 TM1040_2441 Ruegeria sp. TM1040 two component transcriptional regulator YP_614435.1 2581396 R 292414 CDS YP_614436.1 99082282 4076924 2582496..2584094 1 NC_008044.1 PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP; phosphoenolpyruvate carboxykinase 2584094 4076924 TM1040_2442 Ruegeria sp. TM1040 phosphoenolpyruvate carboxykinase YP_614436.1 2582496 D 292414 CDS YP_614437.1 99082283 4076925 complement(2584215..2584895) 1 NC_008044.1 PFAM: lipolytic enzyme, G-D-S-L: (1.2e-05); KEGG: sil:SPO3303 GDSL-like lipase/acylhydrolase, , ev=9e-60, 51% identity; lipolytic protein G-D-S-L 2584895 4076925 TM1040_2443 Ruegeria sp. TM1040 lipolytic protein G-D-S-L YP_614437.1 2584215 R 292414 CDS YP_614438.1 99082284 4076926 complement(2584992..2586695) 1 NC_008044.1 PFAM: acyl-CoA dehydrogenase-like: (1.1e-51) Acyl-CoA dehydrogenase, type 2-like: (1.5e-06); KEGG: sil:SPO0693 isobutyryl-CoA dehydrogenase, ev=0.0, 86% identity; isovaleryl-CoA dehydrogenase 2586695 4076926 TM1040_2444 Ruegeria sp. TM1040 isovaleryl-CoA dehydrogenase YP_614438.1 2584992 R 292414 CDS YP_614439.1 99082285 4076927 2586837..2587604 1 NC_008044.1 PFAM: protein of unknown function DUF81: (1.3e-08); KEGG: jan:Jann_0531 protein of unknown function DUF81, ev=1e-50, 39% identity; hypothetical protein 2587604 4076927 TM1040_2445 Ruegeria sp. TM1040 hypothetical protein YP_614439.1 2586837 D 292414 CDS YP_614440.1 99082286 4076928 2587609..2588523 1 NC_008044.1 TIGRFAM: cation diffusion facilitator family transporter: (8.2e-67); PFAM: cation efflux protein: (5.9e-83); KEGG: ret:RHE_CH03072 probable cation efflux protein, ev=4e-84, 54% identity; cation diffusion facilitator family transporter 2588523 4076928 TM1040_2446 Ruegeria sp. TM1040 cation diffusion facilitator family transporter YP_614440.1 2587609 D 292414 CDS YP_614441.1 99082287 4076929 complement(2588565..2589110) 1 NC_008044.1 PFAM: NADPH-dependent FMN reductase: (9.3e-25); KEGG: sil:SPO3573 NADPH-dependent FMN reductase domain protein, ev=1e-63, 70% identity; NADPH-dependent FMN reductase 2589110 4076929 TM1040_2447 Ruegeria sp. TM1040 NADPH-dependent FMN reductase YP_614441.1 2588565 R 292414 CDS YP_614442.1 99082288 4076930 complement(2589284..2589949) 1 NC_008044.1 PFAM: OmpA/MotB: (2e-26); KEGG: sil:SPO3576 OmpA domain protein, ev=2e-67, 60% identity; OmpA/MotB protein 2589949 4076930 TM1040_2448 Ruegeria sp. TM1040 OmpA/MotB protein YP_614442.1 2589284 R 292414 CDS YP_614443.1 99082289 4076931 complement(2590138..2590827) 1 NC_008044.1 PFAM: Helix-turn-helix, type 11: (2.8e-16); KEGG: sil:SPO3577 hypothetical protein, ev=6e-78, 63% identity; type 11 helix-turn-helix protein 2590827 4076931 TM1040_2449 Ruegeria sp. TM1040 type 11 helix-turn-helix protein YP_614443.1 2590138 R 292414 CDS YP_614444.1 99082290 4076932 complement(2591174..2592025) 1 NC_008044.1 TIGRFAM: methylated-DNA--protein-cysteine methyltransferase: (2.3e-36); PFAM: helix-turn-helix, AraC type: (9.3e-08) methylated-DNA-[protein]-cysteine S-methyltransferase: (2.5e-35); KEGG: sil:SPO3578 ADA regulatory protein, ev=1e-115, 70% identity; AraC family transcriptional regulator 2592025 4076932 TM1040_2450 Ruegeria sp. TM1040 AraC family transcriptional regulator YP_614444.1 2591174 R 292414 CDS YP_614445.1 99082291 4076933 2592128..2592871 1 NC_008044.1 KEGG: sil:SPO3581 endonuclease III, ev=1e-106, 85% identity; TIGRFAM: endonuclease III: (1.3e-104); PFAM: helix-hairpin-helix motif: (8e-07) HhH-GPD: (3.4e-13); SMART: Iron-sulfur cluster loop: (3.9e-06); DNA-(apurinic or apyrimidinic site) lyase / endonuclease III 2592871 4076933 TM1040_2451 Ruegeria sp. TM1040 DNA-(apurinic or apyrimidinic site) lyase / endonuclease III YP_614445.1 2592128 D 292414 CDS YP_614446.1 99082292 4076934 2592868..2593860 1 NC_008044.1 PFAM: PfkB: (7.2e-41); KEGG: sil:SPO3582 kinase, PfkB family, ev=1e-142, 79% identity; PfkB protein 2593860 4076934 TM1040_2452 Ruegeria sp. TM1040 PfkB protein YP_614446.1 2592868 D 292414 CDS YP_614447.1 99082293 4076935 2594208..2596574 1 NC_008044.1 PFAM: histidine kinase, HAMP region: (1.9e-13) chemotaxis sensory transducer: (6.8e-88); KEGG: atc:AGR_L_2218 hypothetical chemoreceptor gene similar to orf2 gene in pTi15955, ev=2e-93, 32% identity; methyl-accepting chemotaxis sensory transducer 2596574 4076935 TM1040_2453 Ruegeria sp. TM1040 methyl-accepting chemotaxis sensory transducer YP_614447.1 2594208 D 292414 CDS YP_614448.1 99082294 4076936 complement(2596656..2597144) 1 NC_008044.1 PFAM: regulatory protein, MarR: (5.6e-17); KEGG: sil:SPO3583 transcriptional regulator PecS, ev=1e-49, 62% identity; MarR family transcriptional regulator 2597144 4076936 TM1040_2454 Ruegeria sp. TM1040 MarR family transcriptional regulator YP_614448.1 2596656 R 292414 CDS YP_614449.1 99082295 4076937 2597317..2598135 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (8.4e-22); KEGG: sil:SPO3584 membrane protein, drug/metabolite transporter (DMT) family, ev=1e-105, 65% identity; hypothetical protein 2598135 4076937 TM1040_2455 Ruegeria sp. TM1040 hypothetical protein YP_614449.1 2597317 D 292414 CDS YP_614450.1 99082296 4076938 complement(2598178..2598633) 1 NC_008044.1 hypothetical protein 2598633 4076938 TM1040_2456 Ruegeria sp. TM1040 hypothetical protein YP_614450.1 2598178 R 292414 CDS YP_614451.1 99082297 4076939 complement(2598701..2599207) 1 NC_008044.1 PFAM: NUDIX hydrolase: (1.6e-27); KEGG: sil:SPO3585 hydrolase, NUDIX family, NudH subfamily, ev=9e-62, 67% identity; NUDIX hydrolase 2599207 4076939 TM1040_2457 Ruegeria sp. TM1040 NUDIX hydrolase YP_614451.1 2598701 R 292414 CDS YP_614452.1 99082298 4076940 2599378..2601405 1 NC_008044.1 PFAM: NADH:flavin oxidoreductase/NADH oxidase: (1.6e-113) FAD-dependent pyridine nucleotide-disulphide oxidoreductase: (0.0034); KEGG: sil:SPO3586 2,4-dienoyl-CoA reductase, ev=0.0, 84% identity; 2,4-dienoyl-CoA reductase 2601405 4076940 TM1040_2458 Ruegeria sp. TM1040 2,4-dienoyl-CoA reductase YP_614452.1 2599378 D 292414 CDS YP_614453.1 99082299 4076941 complement(2601478..2602539) 1 NC_008044.1 PFAM: 2-nitropropane dioxygenase, NPD: (1.8e-68); KEGG: nar:Saro_1176 2-nitropropane dioxygenase, NPD, ev=2e-96, 56% identity; 2-nitropropane dioxygenase 2602539 4076941 TM1040_2459 Ruegeria sp. TM1040 2-nitropropane dioxygenase YP_614453.1 2601478 R 292414 CDS YP_614454.1 99082300 4076942 complement(2602719..2603624) 1 NC_008044.1 PFAM: regulatory protein, LysR: (2.6e-18) LysR, substrate-binding: (2.9e-51); KEGG: sil:SPO3592 transcriptional regulator, LysR family, ev=1e-154, 90% identity; LysR family transcriptional regulator 2603624 4076942 TM1040_2460 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_614454.1 2602719 R 292414 CDS YP_614455.1 99082301 4076826 2603833..2604165 1 NC_008044.1 PFAM: NIPSNAP: (2.3e-29); KEGG: sil:SPO3589 hypothetical protein, ev=7e-44, 78% identity; NIPSNAP domain-containing protein 2604165 4076826 TM1040_2461 Ruegeria sp. TM1040 NIPSNAP domain-containing protein YP_614455.1 2603833 D 292414 CDS YP_614456.1 99082302 4076827 2604162..2604518 1 NC_008044.1 PFAM: Antibiotic biosynthesis monooxygenase: (5.8e-14); KEGG: sil:SPO3588 hypothetical protein, ev=1e-39, 71% identity; antibiotic biosynthesis monooxygenase 2604518 4076827 TM1040_2462 Ruegeria sp. TM1040 antibiotic biosynthesis monooxygenase YP_614456.1 2604162 D 292414 CDS YP_614457.1 99082303 4076828 2604785..2605372 1 NC_008044.1 PFAM: Lysine exporter protein (LYSE/YGGA): (9.3e-06); KEGG: jan:Jann_0017 lysine exporter protein (LysE/YggA), ev=1e-49, 52% identity; lysine exporter protein LysE/YggA 2605372 4076828 TM1040_2463 Ruegeria sp. TM1040 lysine exporter protein LysE/YggA YP_614457.1 2604785 D 292414 CDS YP_614458.1 99082304 4076829 complement(2605380..2606438) 1 NC_008044.1 PFAM: OmpA/MotB: (1.8e-24); KEGG: sil:SPO3756 OmpA domain protein, ev=5e-53, 39% identity; OmpA/MotB protein 2606438 4076829 TM1040_2464 Ruegeria sp. TM1040 OmpA/MotB protein YP_614458.1 2605380 R 292414 CDS YP_614459.1 99082305 4076830 complement(2606459..2607031) 1 NC_008044.1 TIGRFAM: Alkylhydroperoxidase AhpD core: (6.5e-11) Uncharacterised peroxidase-related: (2.6e-83); PFAM: Carboxymuconolactone decarboxylase: (0.0017); KEGG: sil:SPO3757 alkylhydroperoxidase AhpD family core domain protein, ev=3e-86, 83% identity; hypothetical protein 2607031 4076830 TM1040_2465 Ruegeria sp. TM1040 hypothetical protein YP_614459.1 2606459 R 292414 CDS YP_614460.1 99082306 4076831 complement(2607061..2607786) 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (1.3e-12); KEGG: sil:SPO3758 acetyltransferase, GNAT family, ev=1e-73, 57% identity; N-acetyltransferase GCN5 2607786 4076831 TM1040_2466 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_614460.1 2607061 R 292414 CDS YP_614461.1 99082307 4076832 complement(2607783..2608505) 1 NC_008044.1 PFAM: molybdopterin binding domain: (3.9e-42); KEGG: sil:SPO3759 molybdenum cofactor biosynthesis domain protein, ev=1e-112, 84% identity; molybdopterin binding domain-containing protein 2608505 4076832 TM1040_2467 Ruegeria sp. TM1040 molybdopterin binding domain-containing protein YP_614461.1 2607783 R 292414 CDS YP_614462.1 99082308 4076833 2608608..2609324 1 NC_008044.1 Regulatory factor involved in maltose metabolism; sugar fermentation stimulation protein A 2609324 4076833 TM1040_2468 Ruegeria sp. TM1040 sugar fermentation stimulation protein A YP_614462.1 2608608 D 292414 CDS YP_614463.1 99082309 4076834 2609508..2610323 1 NC_008044.1 KEGG: sil:SPO3761 methionine aminopeptidase, type I, ev=1e-135, 85% identity; TIGRFAM: methionine aminopeptidase, type I: (4.2e-113); PFAM: peptidase M24: (1.1e-71); methionine aminopeptidase 2610323 4076834 TM1040_2469 Ruegeria sp. TM1040 methionine aminopeptidase YP_614463.1 2609508 D 292414 CDS YP_614464.1 99082310 4076835 complement(2610478..2611035) 1 NC_008044.1 PFAM: conserved hypothetical protein 95: (9.1e-67); KEGG: sil:SPO3738 methyltransferase, , ev=7e-67, 69% identity; hypothetical protein 2611035 4076835 TM1040_2470 Ruegeria sp. TM1040 hypothetical protein YP_614464.1 2610478 R 292414 CDS YP_614465.1 99082311 4076836 complement(2611032..2612243) 1 NC_008044.1 PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase: (9.2e-27); KEGG: sil:SPO3737 pyridine nucleotide-disulphide oxidoreductase family protein, ev=0.0, 80% identity; FAD-dependent pyridine nucleotide-disulfide oxidoreductase 2612243 4076836 TM1040_2471 Ruegeria sp. TM1040 FAD-dependent pyridine nucleotide-disulfide oxidoreductase YP_614465.1 2611032 R 292414 CDS YP_614466.1 99082312 4076837 2612366..2612851 1 NC_008044.1 PFAM: Redoxin: (1.7e-46); KEGG: rsp:RSP_0899 AhpC/TSA family protein, ev=1e-65, 73% identity; thiol peroxidase 2612851 4076837 TM1040_2472 Ruegeria sp. TM1040 thiol peroxidase YP_614466.1 2612366 D 292414 CDS YP_614467.1 99082313 4076838 2612901..2613770 1 NC_008044.1 KEGG: mag:amb1972 hypothetical protein, ev=8e-13, 23% identity; hypothetical protein 2613770 4076838 TM1040_2473 Ruegeria sp. TM1040 hypothetical protein YP_614467.1 2612901 D 292414 CDS YP_614468.1 99082314 4076839 complement(2613915..2614211) 1 NC_008044.1 4-alpha-hydroxytetrahydrobiopterin dehydratase activity; catalyzes the formation of (6R)-6-(L-erythro-1,2-dihydroxypropyl)-7, 8-dihydro-6H-pterin from (6R)-6-(L-erythro-1,2-dihydroxypropyl)-5,6,7, 8-tetrahydro-4a-hydroxypterin; functions in recycling tetrahydrobiopterin (BH4) in phenylalanine hydroxylase reaction; pterin-4-alpha-carbinolamine dehydratase 2614211 phhB 4076839 phhB Ruegeria sp. TM1040 pterin-4-alpha-carbinolamine dehydratase YP_614468.1 2613915 R 292414 CDS YP_614469.1 99082315 4076840 complement(2614208..2615395) 1 NC_008044.1 PFAM: protein of unknown function DUF482: (6.7e-195); KEGG: sil:SPO3732 hypothetical protein, ev=0.0, 77% identity; hypothetical protein 2615395 4076840 TM1040_2475 Ruegeria sp. TM1040 hypothetical protein YP_614469.1 2614208 R 292414 CDS YP_614470.1 99082316 4076841 complement(2615443..2616219) 1 NC_008044.1 PFAM: glycerophosphoryl diester phosphodiesterase: (1.4e-17); KEGG: sil:SPO3731 glycerophosphoryl diester phosphodiesterase, , ev=5e-80, 60% identity; glycerophosphoryl diester phosphodiesterase 2616219 4076841 TM1040_2476 Ruegeria sp. TM1040 glycerophosphoryl diester phosphodiesterase YP_614470.1 2615443 R 292414 CDS YP_614471.1 99082317 4076842 complement(2616228..2616689) 1 NC_008044.1 PFAM: Endoribonuclease L-PSP: (4.2e-17); KEGG: sil:SPO3730 endoribonuclease L-PSP family protein, ev=4e-59, 75% identity; endoribonuclease L-PSP 2616689 4076842 TM1040_2477 Ruegeria sp. TM1040 endoribonuclease L-PSP YP_614471.1 2616228 R 292414 CDS YP_614472.1 99082318 4076843 complement(2616801..2618123) 1 NC_008044.1 TIGRFAM: Type I secretion membrane fusion protein, HlyD: (6.2e-108); PFAM: secretion protein HlyD: (5.2e-33); KEGG: sil:SPO3729 type I secretion membrane fusion protein, HlyD family, ev=1e-160, 68% identity; Type I secretion membrane fusion protein, HlyD 2618123 4076843 TM1040_2478 Ruegeria sp. TM1040 Type I secretion membrane fusion protein, HlyD YP_614472.1 2616801 R 292414 CDS YP_614473.1 99082319 4076844 complement(2618120..2619883) 1 NC_008044.1 KEGG: sil:SPO3728 type I secretion system ATPase, ev=0.0, 69% identity; TIGRFAM: Type I secretion system ATPase, PrtD: (1.9e-250); PFAM: ABC transporter related: (6e-59); SMART: ATPase: (2.2e-15); Type I secretion system ATPase, PrtD 2619883 4076844 TM1040_2479 Ruegeria sp. TM1040 Type I secretion system ATPase, PrtD YP_614473.1 2618120 R 292414 CDS YP_614474.1 99082320 4076845 2620035..2620835 1 NC_008044.1 PFAM: VacJ-like lipoprotein: (3.9e-54); KEGG: sil:SPO3727 VacJ lipoprotein, , ev=1e-76, 57% identity; VacJ-like lipoprotein 2620835 4076845 TM1040_2480 Ruegeria sp. TM1040 VacJ-like lipoprotein YP_614474.1 2620035 D 292414 CDS YP_614475.1 99082321 4076846 2620839..2621429 1 NC_008044.1 PFAM: toluene tolerance: (6.8e-14); KEGG: sil:SPO3726 toluene tolerance family protein, ev=9e-57, 58% identity; toluene tolerance 2621429 4076846 TM1040_2481 Ruegeria sp. TM1040 toluene tolerance YP_614475.1 2620839 D 292414 CDS YP_614476.1 99082322 4076847 complement(2621561..2622037) 1 NC_008044.1 binds to ssrA RNA (tmRNA) and is required for its successful binding to ribosomes; also appears to function in the trans-translation step by promoting accommodation of tmRNA into the ribosomal A site; SmpB protects the tmRNA from RNase R degradation in Caulobacter crescentus; both the tmRNA and SmpB are regulated in cell cycle-dependent manner; functions in release of stalled ribosomes from damaged mRNAs and targeting proteins for degradation; SsrA-binding protein 2622037 smpB 4076847 smpB Ruegeria sp. TM1040 SsrA-binding protein YP_614476.1 2621561 R 292414 CDS YP_614477.1 99082323 4076848 complement(2622133..2622999) 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (1.5e-05); KEGG: sil:SPO0261 membrane protein, , ev=4e-86, 58% identity; hypothetical protein 2622999 4076848 TM1040_2483 Ruegeria sp. TM1040 hypothetical protein YP_614477.1 2622133 R 292414 CDS YP_614478.1 99082324 4076849 complement(2623072..2623635) 1 NC_008044.1 PFAM: helix-turn-helix motif: (7.3e-16) Cupin 2, conserved barrel: (6e-13); KEGG: sil:SPO3313 DNA-binding protein, , ev=1e-67, 68% identity; XRE family transcriptional regulator 2623635 4076849 TM1040_2484 Ruegeria sp. TM1040 XRE family transcriptional regulator YP_614478.1 2623072 R 292414 CDS YP_614479.1 99082325 4076850 2623777..2624955 1 NC_008044.1 TIGRFAM: benzoate transporter: (2.4e-116); PFAM: Benzoate membrane transport protein: (9e-168) Xanthine/uracil/vitamin C permease: (0.0057); KEGG: plu:plu0511 unnamed protein product; highly similar to benzoate membrane transport protein, ev=1e-103, 51% identity; benzoate transporter 2624955 4076850 TM1040_2485 Ruegeria sp. TM1040 benzoate transporter YP_614479.1 2623777 D 292414 CDS YP_614480.1 99082326 4076851 2625094..2626938 1 NC_008044.1 catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis; dihydroxy-acid dehydratase 2626938 4076851 TM1040_2486 Ruegeria sp. TM1040 dihydroxy-acid dehydratase YP_614480.1 2625094 D 292414 CDS YP_614481.1 99082327 4076852 complement(2627160..2627978) 1 NC_008044.1 KEGG: sil:SPO3318 hypothetical protein, ev=1e-138, 83% identity; hypothetical protein 2627978 4076852 TM1040_2487 Ruegeria sp. TM1040 hypothetical protein YP_614481.1 2627160 R 292414 CDS YP_614482.1 99082328 4076853 2628115..2629692 1 NC_008044.1 PFAM: glycosyl transferase, family 14: (1.1e-05); KEGG: sil:SPO3319 EpsK domain protein, ev=0.0, 75% identity; glycosyl transferase family protein 2629692 4076853 TM1040_2488 Ruegeria sp. TM1040 glycosyl transferase family protein YP_614482.1 2628115 D 292414 CDS YP_614483.1 99082329 4076854 complement(2629773..2630507) 1 NC_008044.1 KEGG: mag:amb2748 hypothetical protein, ev=2e-45, 41% identity; hypothetical protein 2630507 4076854 TM1040_2489 Ruegeria sp. TM1040 hypothetical protein YP_614483.1 2629773 R 292414 CDS YP_614484.1 99082330 4076855 complement(2630666..2631304) 1 NC_008044.1 PFAM: protein of unknown function DUF1523: (1.1e-18); KEGG: sil:SPO3320 hypothetical protein, ev=1e-84, 68% identity; hypothetical protein 2631304 4076855 TM1040_2490 Ruegeria sp. TM1040 hypothetical protein YP_614484.1 2630666 R 292414 CDS YP_614485.1 99082331 4076856 complement(2631472..2632680) 1 NC_008044.1 PFAM: creatinase: (1.9e-60) peptidase M24: (1.3e-53); KEGG: sil:SPO3327 creatinase, ev=0.0, 83% identity; creatinase 2632680 4076856 TM1040_2491 Ruegeria sp. TM1040 creatinase YP_614485.1 2631472 R 292414 CDS YP_614486.1 99082332 4076857 complement(2632860..2633645) 1 NC_008044.1 KEGG: rsp:RSP_1010 possible esterase/lipase/thioesterase, ev=4e-74, 56% identity; esterase/lipase/thioesterase 2633645 4076857 TM1040_2492 Ruegeria sp. TM1040 esterase/lipase/thioesterase YP_614486.1 2632860 R 292414 CDS YP_614487.1 99082333 4076858 2633749..2635221 1 NC_008044.1 KEGG: sil:SPO3328 succinate-semialdehyde dehydrogenase, ev=0.0, 79% identity; TIGRFAM: succinic semialdehyde dehydrogenase: (2.6e-302); PFAM: aldehyde dehydrogenase: (1.4e-222); succinate semialdehyde dehydrogenase 2635221 4076858 TM1040_2493 Ruegeria sp. TM1040 succinate semialdehyde dehydrogenase YP_614487.1 2633749 D 292414 CDS YP_614488.1 99082334 4076859 complement(2635245..2635676) 1 NC_008044.1 PFAM: globin: (0.00031); KEGG: sil:SPO3329 globin domain protein, ev=3e-18, 40% identity; globin 2635676 4076859 TM1040_2494 Ruegeria sp. TM1040 globin YP_614488.1 2635245 R 292414 CDS YP_614489.1 99082335 4076860 2635844..2638015 1 NC_008044.1 KEGG: rsp:RSP_1753 hypothetical protein, ev=0.0, 59% identity; hypothetical protein 2638015 4076860 TM1040_2495 Ruegeria sp. TM1040 hypothetical protein YP_614489.1 2635844 D 292414 CDS YP_614490.1 99082336 4076861 2638410..2639303 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (1.2e-07); KEGG: vch:VCA1010 hypothetical protein, ev=8e-66, 46% identity; hypothetical protein 2639303 4076861 TM1040_2496 Ruegeria sp. TM1040 hypothetical protein YP_614490.1 2638410 D 292414 CDS YP_614491.1 99082337 4076862 complement(2639283..2639888) 1 NC_008044.1 PFAM: regulatory protein, TetR: (1.5e-15); KEGG: mtc:MT1047 transcriptional regulator, TetR family, ev=7e-10, 43% identity; TetR family transcriptional regulator 2639888 4076862 TM1040_2497 Ruegeria sp. TM1040 TetR family transcriptional regulator YP_614491.1 2639283 R 292414 CDS YP_614492.1 99082338 4076863 complement(2640025..2640492) 1 NC_008044.1 PFAM: heat shock protein Hsp20: (7.2e-18); KEGG: sil:SPO3484 heat shock protein, Hsp20 family, ev=5e-63, 76% identity; heat shock protein Hsp20 2640492 4076863 TM1040_2498 Ruegeria sp. TM1040 heat shock protein Hsp20 YP_614492.1 2640025 R 292414 CDS YP_614493.1 99082339 4076864 complement(2640633..2641487) 1 NC_008044.1 PFAM: peptidase S1 and S6, chymotrypsin/Hap: (3.1e-06); KEGG: sil:SPO3482 trypsin domain protein, ev=6e-82, 62% identity; peptidase S1 and S6, chymotrypsin/Hap 2641487 4076864 TM1040_2499 Ruegeria sp. TM1040 peptidase S1 and S6, chymotrypsin/Hap YP_614493.1 2640633 R 292414 CDS YP_614494.1 99082340 4076502 complement(2641580..2642899) 1 NC_008044.1 PFAM: 4Fe-4S ferredoxin, iron-sulfur binding: (0.0022) protein of unknown function DUF224, cysteine-rich region: (3.7e-17); KEGG: sil:SPO3480 glycolate oxidase, iron-sulfur subunit, ev=0.0, 85% identity; hypothetical protein 2642899 4076502 TM1040_2500 Ruegeria sp. TM1040 hypothetical protein YP_614494.1 2641580 R 292414 CDS YP_614495.1 99082341 4076503 complement(2642904..2643995) 1 NC_008044.1 PFAM: FAD linked oxidase-like: (2.1e-09); KEGG: sil:SPO3479 glycolate oxidase, GlcE subunit, ev=1e-125, 66% identity; FAD linked oxidase-like protein 2643995 4076503 TM1040_2501 Ruegeria sp. TM1040 FAD linked oxidase-like protein YP_614495.1 2642904 R 292414 CDS YP_614496.1 99082342 4076504 complement(2644053..2645501) 1 NC_008044.1 PFAM: FAD linked oxidase-like: (2.7e-68); KEGG: sil:SPO3478 glycolate oxidase, GlcD subunit, ev=0.0, 86% identity; D-lactate dehydrogenase 2645501 4076504 TM1040_2502 Ruegeria sp. TM1040 D-lactate dehydrogenase YP_614496.1 2644053 R 292414 CDS YP_614497.1 99082343 4076505 2645583..2646305 1 NC_008044.1 PFAM: protein of unknown function DUF599: (7.3e-28); KEGG: sil:SPO3477 hypothetical protein, ev=4e-84, 64% identity; hypothetical protein 2646305 4076505 TM1040_2503 Ruegeria sp. TM1040 hypothetical protein YP_614497.1 2645583 D 292414 CDS YP_614498.1 99082344 4076506 2646341..2646700 1 NC_008044.1 KEGG: sil:SPO3476 hypothetical protein, ev=3e-39, 67% identity; hypothetical protein 2646700 4076506 TM1040_2504 Ruegeria sp. TM1040 hypothetical protein YP_614498.1 2646341 D 292414 CDS YP_614499.1 99082345 4076507 complement(2646706..2647176) 1 NC_008044.1 SPOUT methyltransferase family protein; crystal structure shows homodimer; in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA; rRNA large subunit methyltransferase 2647176 4076507 TM1040_2505 Ruegeria sp. TM1040 rRNA large subunit methyltransferase YP_614499.1 2646706 R 292414 CDS YP_614500.1 99082346 4076508 complement(2647306..2647665) 1 NC_008044.1 PFAM: Iojap-related protein: (5.9e-34); KEGG: sil:SPO0219 iojap-related protein, ev=1e-45, 73% identity; Iojap-related protein 2647665 4076508 TM1040_2506 Ruegeria sp. TM1040 Iojap-related protein YP_614500.1 2647306 R 292414 CDS YP_614501.1 99082347 4076509 complement(2647796..2649223) 1 NC_008044.1 PFAM: MscS Mechanosensitive ion channel: (5.2e-49); KEGG: sil:SPO0218 mechanosensitive ion channel family protein, ev=1e-172, 66% identity; mechanosensitive ion channel protein MscS 2649223 4076509 TM1040_2507 Ruegeria sp. TM1040 mechanosensitive ion channel protein MscS YP_614501.1 2647796 R 292414 CDS YP_614502.1 99082348 4076510 2649508..2650911 1 NC_008044.1 dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; isopropylmalate isomerase large subunit 2650911 4076510 TM1040_2508 Ruegeria sp. TM1040 isopropylmalate isomerase large subunit YP_614502.1 2649508 D 292414 CDS YP_614503.1 99082349 4076511 2650924..2651529 1 NC_008044.1 catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D; isopropylmalate isomerase small subunit 2651529 leuD 4076511 leuD Ruegeria sp. TM1040 isopropylmalate isomerase small subunit YP_614503.1 2650924 D 292414 CDS YP_614504.1 99082350 4076512 complement(2651628..2651927) 1 NC_008044.1 hypothetical protein 2651927 4076512 TM1040_2510 Ruegeria sp. TM1040 hypothetical protein YP_614504.1 2651628 R 292414 CDS YP_614505.1 99082351 4076513 complement(2651928..2653001) 1 NC_008044.1 catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a heterotetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 1 subfamily; phenylalanyl-tRNA synthetase subunit alpha 2653001 pheS 4076513 pheS Ruegeria sp. TM1040 phenylalanyl-tRNA synthetase subunit alpha YP_614505.1 2651928 R 292414 CDS YP_614506.1 99082352 4076514 2653223..2654206 1 NC_008044.1 KEGG: ret:RHE_CH02814 adenylate cyclase protein, ev=2e-53, 38% identity; guanylate cyclase 2654206 4076514 TM1040_2512 Ruegeria sp. TM1040 guanylate cyclase YP_614506.1 2653223 D 292414 CDS YP_614507.1 99082353 4076515 complement(2654320..2654685) 1 NC_008044.1 binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit; 50S ribosomal protein L20 2654685 rplT 4076515 rplT Ruegeria sp. TM1040 50S ribosomal protein L20 YP_614507.1 2654320 R 292414 CDS YP_614508.1 99082354 4076516 complement(2654701..2654901) 1 NC_008044.1 PFAM: ribosomal protein L35: (2e-14); KEGG: sil:SPO3599 ribosomal protein L35, ev=4e-29, 95% identity; 50S ribosomal protein L35 2654901 rpmI 4076516 rpmI Ruegeria sp. TM1040 50S ribosomal protein L35 YP_614508.1 2654701 R 292414 CDS YP_614509.1 99082355 4076517 complement(2655018..2655239) 1 NC_008044.1 hypothetical protein 2655239 4076517 TM1040_2515 Ruegeria sp. TM1040 hypothetical protein YP_614509.1 2655018 R 292414 CDS YP_614510.1 99082356 4076518 complement(2655276..2656721) 1 NC_008044.1 PFAM: pyruvate kinase: (1.1e-141); KEGG: sil:SPO3600 pyruvate kinase, ev=0.0, 86% identity; pyruvate kinase 2656721 4076518 TM1040_2516 Ruegeria sp. TM1040 pyruvate kinase YP_614510.1 2655276 R 292414 CDS YP_614511.1 99082357 4076519 complement(2657069..2658073) 1 NC_008044.1 PFAM: Alcohol dehydrogenase, zinc-binding: (6.2e-33) Alcohol dehydrogenase GroES-like: (2.2e-16); KEGG: sil:SPO0231 alcohol dehydrogenase, zinc-containing, ev=1e-142, 76% identity; zinc-binding alcohol dehydrogenase 2658073 4076519 TM1040_2517 Ruegeria sp. TM1040 zinc-binding alcohol dehydrogenase YP_614511.1 2657069 R 292414 CDS YP_614512.1 99082358 4076520 complement(2658190..2658900) 1 NC_008044.1 TIGRFAM: RpsU-divergently transcribed: (2.1e-62); PFAM: COQ9: (2e-39); KEGG: sil:SPO0230 hypothetical protein, ev=2e-85, 69% identity; hypothetical protein 2658900 4076520 TM1040_2518 Ruegeria sp. TM1040 hypothetical protein YP_614512.1 2658190 R 292414 CDS YP_614513.1 99082359 4076521 2659018..2659224 1 NC_008044.1 a small basic protein that is one of the last in the subunit assembly; omission does not prevent assembly but the subunit is inactive; binds central domain of 16S rRNA; 30S ribosomal protein S21 2659224 rpsU 4076521 rpsU Ruegeria sp. TM1040 30S ribosomal protein S21 YP_614513.1 2659018 D 292414 CDS YP_614514.1 99082360 4076522 complement(2659370..2661277) 1 NC_008044.1 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision; excinuclease ABC subunit C 2661277 uvrC 4076522 uvrC Ruegeria sp. TM1040 excinuclease ABC subunit C YP_614514.1 2659370 R 292414 CDS YP_614515.1 99082361 4076523 complement(2661587..2662363) 1 NC_008044.1 PFAM: short-chain dehydrogenase/reductase SDR: (1.4e-05); KEGG: sil:SPO3638 oxidoreductase, short chain dehydrogenase/reductase family, ev=8e-90, 66% identity; short chain dehydrogenase 2662363 4076523 TM1040_2521 Ruegeria sp. TM1040 short chain dehydrogenase YP_614515.1 2661587 R 292414 CDS YP_614516.1 99082362 4076524 complement(2662400..2663344) 1 NC_008044.1 TIGRFAM: K+-dependent Na+/Ca+ exchanger related-protein: (2.9e-56); PFAM: sodium/calcium exchanger membrane region: (1.8e-43); KEGG: sil:SPO3639 K+-dependent Na+/Ca+ exchanger related-protein, ev=1e-134, 78% identity; K+-dependent Na+/Ca+ exchanger-like protein 2663344 4076524 TM1040_2522 Ruegeria sp. TM1040 K+-dependent Na+/Ca+ exchanger-like protein YP_614516.1 2662400 R 292414 CDS YP_614517.1 99082363 4076525 complement(2663516..2664313) 1 NC_008044.1 PFAM: peptidase S49: (2.1e-33); KEGG: sil:SPO3640 peptidase, family S49, ev=1e-115, 77% identity; peptidase S49 2664313 4076525 TM1040_2523 Ruegeria sp. TM1040 peptidase S49 YP_614517.1 2663516 R 292414 CDS YP_614518.1 99082364 4076526 complement(2664552..2665313) 1 NC_008044.1 PFAM: ABC-2 type transporter: (4.8e-39); KEGG: sil:SPO3641 ABC transporter, permease protein, ev=1e-122, 83% identity; ABC transporter 2665313 4076526 TM1040_2524 Ruegeria sp. TM1040 ABC transporter YP_614518.1 2664552 R 292414 CDS YP_614519.1 99082365 4076527 complement(2665310..2666239) 1 NC_008044.1 PFAM: ABC transporter related: (2.3e-60); SMART: ATPase: (4.9e-19); KEGG: sil:SPO3642 ABC transporter, ATP-binding protein, ev=1e-129, 76% identity; ABC transporter 2666239 4076527 TM1040_2525 Ruegeria sp. TM1040 ABC transporter YP_614519.1 2665310 R 292414 CDS YP_614520.1 99082366 4076528 complement(2666437..2666982) 1 NC_008044.1 PFAM: carbon monoxide dehydrogenase subunit G: (2.3e-47); KEGG: sil:SPO1517 carbon monoxide dehydrogenase operon G protein, ev=2e-58, 68% identity; carbon monoxide dehydrogenase subunit G 2666982 4076528 TM1040_2526 Ruegeria sp. TM1040 carbon monoxide dehydrogenase subunit G YP_614520.1 2666437 R 292414 CDS YP_614521.1 99082367 4076529 2667184..2668305 1 NC_008044.1 PFAM: L-carnitine dehydratase/bile acid-inducible protein F: (3.8e-51); KEGG: sil:SPO3647 CAIB/BAIF family protein, ev=1e-136, 67% identity; L-carnitine dehydratase/bile acid-inducible protein F 2668305 4076529 TM1040_2527 Ruegeria sp. TM1040 L-carnitine dehydratase/bile acid-inducible protein F YP_614521.1 2667184 D 292414 CDS YP_614522.1 99082368 4076530 complement(2668364..2669401) 1 NC_008044.1 catalyzes the formation of coproporphyrinogen from uroporphyrinogen III; uroporphyrinogen decarboxylase 2669401 hemE 4076530 hemE Ruegeria sp. TM1040 uroporphyrinogen decarboxylase YP_614522.1 2668364 R 292414 CDS YP_614523.1 99082369 4076531 2669522..2670478 1 NC_008044.1 transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis; porphobilinogen deaminase 2670478 hemC 4076531 hemC Ruegeria sp. TM1040 porphobilinogen deaminase YP_614523.1 2669522 D 292414 CDS YP_614524.1 99082370 4076532 complement(2670697..2671575) 1 NC_008044.1 PFAM: glycoside hydrolase, family 25: (1.1e-81); KEGG: sil:SPO3258 glycosyl hydrolase, family 25, ev=2e-90, 57% identity; glycoside hydrolase 2671575 4076532 TM1040_2530 Ruegeria sp. TM1040 glycoside hydrolase YP_614524.1 2670697 R 292414 CDS YP_614525.1 99082371 4076533 complement(2671697..2672599) 1 NC_008044.1 catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis; coproporphyrinogen III oxidase 2672599 4076533 TM1040_2531 Ruegeria sp. TM1040 coproporphyrinogen III oxidase YP_614525.1 2671697 R 292414 CDS YP_614526.1 99082372 4076534 complement(2672639..2673442) 1 NC_008044.1 PFAM: short-chain dehydrogenase/reductase SDR: (4.6e-08); KEGG: sil:SPO3654 7-alpha-hydroxysteroid dehydrogenase, , ev=1e-103, 72% identity; short-chain dehydrogenase/reductase SDR 2673442 4076534 TM1040_2532 Ruegeria sp. TM1040 short-chain dehydrogenase/reductase SDR YP_614526.1 2672639 R 292414 CDS YP_614527.1 99082373 4076535 complement(2673606..2674592) 1 NC_008044.1 PFAM: methyltransferase small: (1.5e-65) Methyltransferase type 11: (0.0022); KEGG: sil:SPO3655 methyltransferase, , ev=4e-95, 57% identity; methyltransferase small 2674592 4076535 TM1040_2533 Ruegeria sp. TM1040 methyltransferase small YP_614527.1 2673606 R 292414 CDS YP_614528.1 99082374 4076536 complement(2674632..2674973) 1 NC_008044.1 PFAM: ATP-dependent Clp protease adaptor protein ClpS: (4.2e-49); KEGG: sil:SPO3656 ATP-dependent Clp protease, adaptor protein ClpS, ev=2e-46, 78% identity; ATP-dependent Clp protease adaptor protein ClpS 2674973 4076536 TM1040_2534 Ruegeria sp. TM1040 ATP-dependent Clp protease adaptor protein ClpS YP_614528.1 2674632 R 292414 CDS YP_614529.1 99082375 4076537 2675064..2675777 1 NC_008044.1 PFAM: Haloacid dehalogenase-like hydrolase: (2.6e-09); KEGG: sil:SPO3657 hydrolase, haloacid delahogenase-like family, ev=2e-86, 67% identity; haloacid dehalogenase 2675777 4076537 TM1040_2535 Ruegeria sp. TM1040 haloacid dehalogenase YP_614529.1 2675064 D 292414 CDS YP_614530.1 99082376 4076538 2676295..2677785 1 NC_008044.1 PFAM: beta-lactamase: (0.0012) peptidase S11, D-alanyl-D-alanine carboxypeptidase 1: (1.8e-70); KEGG: sil:SPO3658 D-alanyl-D-alanine carboxypeptidase family protein, ev=1e-158, 60% identity; serine-type D-Ala-D-Ala carboxypeptidase 2677785 4076538 TM1040_2536 Ruegeria sp. TM1040 serine-type D-Ala-D-Ala carboxypeptidase YP_614530.1 2676295 D 292414 CDS YP_614531.1 99082377 4076539 complement(2677985..2678143) 1 NC_008044.1 TIGRFAM: cytochrome oxidase maturation protein, cbb3-type: (2.7e-21); PFAM: cytochrome oxidase maturation protein cbb3-type: (1.8e-22); KEGG: sil:SPO3519 cytochrome oxidase maturation protein, cbb3-type, ev=3e-17, 76% identity; cbb3-type cytochrome oxidase maturation protein 2678143 4076539 TM1040_2537 Ruegeria sp. TM1040 cbb3-type cytochrome oxidase maturation protein YP_614531.1 2677985 R 292414 CDS YP_614532.1 99082378 4076540 complement(2678162..2680345) 1 NC_008044.1 TIGRFAM: ATPase, P-type, K/Mg/Cd/Cu/Zn/Na/Ca/Na/H-transporter: (7.2e-21) ATPase, P type cation/copper-transporter: (5.4e-172) Heavy metal translocating P-type ATPase: (6.7e-182); PFAM: Haloacid dehalogenase-like hydrolase: (1.3e-22) Heavy metal transport/detoxification protein: (1.3e-11) E1-E2 ATPase-associated region: (2.7e-68); KEGG: sil:SPO3520 copper-translocating P-type ATPase, ev=0.0, 76% identity; heavy metal translocating P-type ATPase 2680345 4076540 TM1040_2538 Ruegeria sp. TM1040 heavy metal translocating P-type ATPase YP_614532.1 2678162 R 292414 CDS YP_614533.1 99082379 4076670 complement(2680424..2680900) 1 NC_008044.1 PFAM: FixH: (1.5e-52); KEGG: sil:SPO3521 FixH protein, , ev=3e-55, 71% identity; FixH protein 2680900 4076670 TM1040_2539 Ruegeria sp. TM1040 FixH protein YP_614533.1 2680424 R 292414 CDS YP_614534.1 99082380 4076671 complement(2680904..2682334) 1 NC_008044.1 PFAM: 4Fe-4S ferredoxin, iron-sulfur binding: (0.0038); KEGG: sil:SPO3522 iron-sulfur-binding protein, RdxA/RdxB/FixG family, ev=0.0, 80% identity; 4Fe-4S ferredoxin 2682334 4076671 TM1040_2540 Ruegeria sp. TM1040 4Fe-4S ferredoxin YP_614534.1 2680904 R 292414 CDS YP_614535.1 99082381 4076672 complement(2682482..2683366) 1 NC_008044.1 PFAM: regulatory protein, LysR: (2.6e-17) LysR, substrate-binding: (5.5e-31); KEGG: jan:Jann_4071 transcriptional regulator, LysR family, ev=3e-52, 43% identity; LysR family transcriptional regulator 2683366 4076672 TM1040_2541 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_614535.1 2682482 R 292414 CDS YP_614536.1 99082382 4076673 complement(2684043..2684927) 1 NC_008044.1 TIGRFAM: cytochrome c oxidase, cbb3-type, subunit III: (1.3e-149); PFAM: cytochrome c, class I: (8.3e-09); KEGG: sil:SPO3523 cytochrome c oxidase, cbb3-type, subunit III, ev=1e-125, 71% identity; cytochrome c oxidase, cbb3-type subunit III 2684927 4076673 TM1040_2542 Ruegeria sp. TM1040 cytochrome c oxidase, cbb3-type subunit III YP_614536.1 2684043 R 292414 CDS YP_614537.1 99082383 4076674 complement(2684924..2685121) 1 NC_008044.1 PFAM: Cbb3-type cytochrome oxidase component: (1.8e-23); KEGG: sil:SPO3524 cytochrome c oxidase, cbb3-type, subunit IV, ev=6e-20, 81% identity; cbb3-type cytochrome oxidase subunit 2685121 4076674 TM1040_2543 Ruegeria sp. TM1040 cbb3-type cytochrome oxidase subunit YP_614537.1 2684924 R 292414 CDS YP_614538.1 99082384 4076675 complement(2685136..2685864) 1 NC_008044.1 CcoO; FixO; cbb3-type cytochrome c oxidase subunit II 2685864 4076675 TM1040_2544 Ruegeria sp. TM1040 cbb3-type cytochrome c oxidase subunit II YP_614538.1 2685136 R 292414 CDS YP_614539.1 99082385 4076676 complement(2685879..2687483) 1 NC_008044.1 CcoN; FixN; cbb3-type cytochrome c oxidase subunit I 2687483 4076676 TM1040_2545 Ruegeria sp. TM1040 cbb3-type cytochrome c oxidase subunit I YP_614539.1 2685879 R 292414 CDS YP_614540.1 99082386 4076677 2687707..2688546 1 NC_008044.1 PFAM: UspA: (2.9e-19); KEGG: sil:SPO3527 universal stress protein family protein, ev=4e-83, 54% identity; hypothetical protein 2688546 4076677 TM1040_2546 Ruegeria sp. TM1040 hypothetical protein YP_614540.1 2687707 D 292414 CDS YP_614541.1 99082387 4076678 complement(2688724..2689464) 1 NC_008044.1 PFAM: cyclic nucleotide-binding: (5.5e-15) regulatory protein, Crp: (3.1e-11); KEGG: sil:SPO3531 transcriptional activator protein FnrL, ev=1e-113, 84% identity; Crp/FNR family transcriptional regulator 2689464 4076678 TM1040_2547 Ruegeria sp. TM1040 Crp/FNR family transcriptional regulator YP_614541.1 2688724 R 292414 CDS YP_614542.1 99082388 4076679 2689525..2690880 1 NC_008044.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase 2690880 4076679 TM1040_2548 Ruegeria sp. TM1040 coproporphyrinogen III oxidase YP_614542.1 2689525 D 292414 CDS YP_614543.1 99082389 4076680 complement(2690971..2692563) 1 NC_008044.1 PFAM: ABC transporter related: (1.1e-61) Oligopeptide/dipeptide ABC transporter-like: (2e-06); SMART: ATPase: (6.9e-20); KEGG: sil:SPO3534 oligopeptide/dipeptide uptake family ABC transporter, ATP-binding protein, ev=0.0, 78% identity; ABC transporter 2692563 4076680 TM1040_2549 Ruegeria sp. TM1040 ABC transporter YP_614543.1 2690971 R 292414 CDS YP_614544.1 99082390 4076681 complement(2692619..2693725) 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1.2e-48); KEGG: sil:SPO3535 oligopeptide/dipeptide uptake family ABC transporter, permease protein, ev=1e-174, 80% identity; binding-protein-dependent transport system inner membrane protein 2693725 4076681 TM1040_2550 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_614544.1 2692619 R 292414 CDS YP_614545.1 99082391 4076682 complement(2693730..2694818) 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1.4e-47); KEGG: rsp:RSP_0703 ABC peptide transporter, inner membrane subunit, ev=1e-165, 79% identity; binding-protein-dependent transport system inner membrane protein 2694818 4076682 TM1040_2551 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_614545.1 2693730 R 292414 CDS YP_614546.1 99082392 4076683 complement(2694826..2696676) 1 NC_008044.1 PFAM: extracellular solute-binding protein, family 5: (1.9e-48); KEGG: sil:SPO3537 oligopeptide/dipeptide uptake family ABC transporter, periplasmic substrate-binding protein, ev=1e-179, 51% identity; extracellular solute-binding protein 2696676 4076683 TM1040_2552 Ruegeria sp. TM1040 extracellular solute-binding protein YP_614546.1 2694826 R 292414 CDS YP_614547.1 99082393 4076684 complement(2697020..2697520) 1 NC_008044.1 PFAM: cytochrome c, class I: (2.6e-18); KEGG: sil:SPO3538 cytochrome c552, ev=2e-54, 65% identity; cytochrome c, class I 2697520 4076684 TM1040_2553 Ruegeria sp. TM1040 cytochrome c, class I YP_614547.1 2697020 R 292414 CDS YP_614548.1 99082394 4076685 2697641..2698471 1 NC_008044.1 catalyzes the formation of phenylpyruvate from prephenate in phenylalanine biosynthesis; prephenate dehydratase 2698471 4076685 TM1040_2554 Ruegeria sp. TM1040 prephenate dehydratase YP_614548.1 2697641 D 292414 CDS YP_614549.1 99082395 4076686 complement(2698525..2700408) 1 NC_008044.1 TIGRFAM: Twin-arginine translocation pathway signal: (0.096); PFAM: protein of unknown function DUF839: (5.7e-240); KEGG: jan:Jann_1898 protein of unknown function DUF839, ev=0.0, 63% identity; twin-arginine translocation pathway signal 2700408 4076686 TM1040_2555 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_614549.1 2698525 R 292414 CDS YP_614550.1 99082396 4076687 complement(2700556..2701281) 1 NC_008044.1 involved in DNA repair and RecFOR pathway recombination; RecFOR proteins displace ssDNA-binding protein and facilitate the production of RecA-coated ssDNA; DNA repair protein RecO 2701281 recO 4076687 recO Ruegeria sp. TM1040 DNA repair protein RecO YP_614550.1 2700556 R 292414 CDS YP_614551.1 99082397 4076688 complement(2701285..2701614) 1 NC_008044.1 PFAM: protein of unknown function DUF1491: (3.4e-17); KEGG: rsp:RSP_1677 hypothetical protein, ev=1e-39, 75% identity; hypothetical protein 2701614 4076688 TM1040_2557 Ruegeria sp. TM1040 hypothetical protein YP_614551.1 2701285 R 292414 CDS YP_614552.1 99082398 4076689 complement(2701779..2702684) 1 NC_008044.1 Era; Escherichia coli Ras-like protein; Bex; Bacillus Era-complementing segment; essential protein in Escherichia coli that is involved in many cellular processes; GTPase; binds the cell membrane through apparent C-terminal domain; mutants are arrested during the cell cycle; Streptococcus pneumoniae Era binds to RNA and Escherichia coli Era binds 16S rRNA and 30S ribosome; GTP-binding protein Era 2702684 era 4076689 era Ruegeria sp. TM1040 GTP-binding protein Era YP_614552.1 2701779 R 292414 CDS YP_614553.1 99082399 4076690 complement(2702681..2703409) 1 NC_008044.1 KEGG: sil:SPO3198 ribonuclease III, ev=3e-89, 76% identity; TIGRFAM: Ribonuclease III: (1.5e-100); PFAM: ribonuclease III: (2e-34) double-stranded RNA binding: (3.1e-16); RNAse III 2703409 4076690 TM1040_2559 Ruegeria sp. TM1040 RNAse III YP_614553.1 2702681 R 292414 CDS YP_614554.1 99082400 4076691 complement(2703577..2704413) 1 NC_008044.1 KEGG: sil:SPO3199 signal peptidase I, ev=1e-127, 77% identity; TIGRFAM: Peptidase S26A, signal peptidase I: (9e-54); PFAM: peptidase S24, S26A and S26B: (2e-22); signal peptidase I 2704413 4076691 TM1040_2560 Ruegeria sp. TM1040 signal peptidase I YP_614554.1 2703577 R 292414 CDS YP_614555.1 99082401 4076692 complement(2704558..2704986) 1 NC_008044.1 Catalyzes the formation of holo-ACP, which mediates the essential transfer of acyl fatty acid intermediates during the biosynthesis of fatty acids and lipids; 4'-phosphopantetheinyl transferase 2704986 acpS 4076692 acpS Ruegeria sp. TM1040 4'-phosphopantetheinyl transferase YP_614555.1 2704558 R 292414 CDS YP_614556.1 99082402 4076693 complement(2705013..2705438) 1 NC_008044.1 KEGG: jan:Jann_0517 hypothetical protein, ev=6e-06, 28% identity; hypothetical protein 2705438 4076693 TM1040_2562 Ruegeria sp. TM1040 hypothetical protein YP_614556.1 2705013 R 292414 CDS YP_614557.1 99082403 4076694 complement(2705435..2706193) 1 NC_008044.1 involved in the de novo synthesis of pyridoxine (Vitamin B6); pyridoxine 5'-phosphate synthase 2706193 4076694 TM1040_2563 Ruegeria sp. TM1040 pyridoxine 5'-phosphate synthase YP_614557.1 2705435 R 292414 CDS YP_614558.1 99082404 4076695 complement(2706314..2707018) 1 NC_008044.1 KEGG: sil:SPO3202 hypothetical protein, ev=5e-75, 62% identity; hypothetical protein 2707018 4076695 TM1040_2564 Ruegeria sp. TM1040 hypothetical protein YP_614558.1 2706314 R 292414 CDS YP_614559.1 99082405 4076696 complement(2707049..2709181) 1 NC_008044.1 KEGG: sil:SPO3203 guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase, , ev=0.0, 87% identity; TIGRFAM: RelA/SpoT family protein: (6.2e-237); PFAM: TGS: (1.5e-26) metal-dependent phosphohydrolase, HD subdomain: (7.3e-12) RelA/SpoT: (3.7e-48); SMART: Metal-dependent phosphohydrolase, HD region: (7.5e-14); metal dependent phosphohydrolase 2709181 4076696 TM1040_2565 Ruegeria sp. TM1040 metal dependent phosphohydrolase YP_614559.1 2707049 R 292414 CDS YP_614560.1 99082406 4076697 complement(2709220..2709573) 1 NC_008044.1 Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits; DNA-directed RNA polymerase subunit omega 2709573 4076697 TM1040_2566 Ruegeria sp. TM1040 DNA-directed RNA polymerase subunit omega YP_614560.1 2709220 R 292414 CDS YP_614561.1 99082407 4076698 complement(2709688..2710257) 1 NC_008044.1 TIGRFAM: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase: (9.6e-30); PFAM: 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK: (6.2e-24); KEGG: sil:SPO3205 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase, ev=2e-46, 50% identity; 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase 2710257 4076698 TM1040_2567 Ruegeria sp. TM1040 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase YP_614561.1 2709688 R 292414 CDS YP_614562.1 99082408 4076699 2710393..2710962 1 NC_008044.1 PFAM: protein of unknown function DUF88: (6e-81); KEGG: sil:SPO3206 hypothetical protein, ev=9e-99, 94% identity; hypothetical protein 2710962 4076699 TM1040_2568 Ruegeria sp. TM1040 hypothetical protein YP_614562.1 2710393 D 292414 CDS YP_614563.1 99082409 4076700 2711132..2712082 1 NC_008044.1 catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP); functions in the nonmevalonate isoprenoid biosynthesis pathway; 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 2712082 ispH 4076700 ispH Ruegeria sp. TM1040 4-hydroxy-3-methylbut-2-enyl diphosphate reductase YP_614563.1 2711132 D 292414 CDS YP_614564.1 99082410 4076701 2712248..2712865 1 NC_008044.1 PFAM: Lysine exporter protein (LYSE/YGGA): (2.5e-27); KEGG: jan:Jann_0505 lysine exporter protein (LysE/YggA), ev=9e-80, 73% identity; lysine exporter protein LysE/YggA 2712865 4076701 TM1040_2570 Ruegeria sp. TM1040 lysine exporter protein LysE/YggA YP_614564.1 2712248 D 292414 CDS YP_614565.1 99082411 4076702 2712865..2713323 1 NC_008044.1 KEGG: sil:SPO3210 membrane protein, , ev=7e-56, 67% identity; hypothetical protein 2713323 4076702 TM1040_2571 Ruegeria sp. TM1040 hypothetical protein YP_614565.1 2712865 D 292414 CDS YP_614566.1 99082412 4076703 2713320..2713919 1 NC_008044.1 PFAM: Methyltransferase type 11: (7e-20) Methyltransferase type 12: (2e-18); KEGG: sil:SPO3211 hypothetical protein, ev=3e-49, 52% identity; type 11 methyltransferase 2713919 4076703 TM1040_2572 Ruegeria sp. TM1040 type 11 methyltransferase YP_614566.1 2713320 D 292414 CDS YP_614567.1 99082413 4076704 2713912..2714385 1 NC_008044.1 An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids; ribonuclease H 2714385 rnhA 4076704 rnhA Ruegeria sp. TM1040 ribonuclease H YP_614567.1 2713912 D 292414 CDS YP_614568.1 99082414 4076705 2714499..2715122 1 NC_008044.1 PFAM: protein of unknown function UPF0126: (3.3e-12); KEGG: sil:SPO3213 membrane protein, , ev=2e-80, 73% identity; hypothetical protein 2715122 4076705 TM1040_2574 Ruegeria sp. TM1040 hypothetical protein YP_614568.1 2714499 D 292414 CDS YP_614569.1 99082415 4076706 complement(2715176..2715412) 1 NC_008044.1 KEGG: sil:SPO3214 hypothetical protein, ev=1e-21, 62% identity; hypothetical protein 2715412 4076706 TM1040_2575 Ruegeria sp. TM1040 hypothetical protein YP_614569.1 2715176 R 292414 CDS YP_614570.1 99082416 4076707 complement(2715494..2715730) 1 NC_008044.1 KEGG: sil:SPO3215 hypothetical protein, ev=9e-29, 73% identity; hypothetical protein 2715730 4076707 TM1040_2576 Ruegeria sp. TM1040 hypothetical protein YP_614570.1 2715494 R 292414 CDS YP_614571.1 99082417 4076708 complement(2715727..2716653) 1 NC_008044.1 TIGRFAM: methionyl-tRNA formyltransferase: (2.5e-102); PFAM: formyl transferase-like: (4.3e-52); KEGG: sil:SPO3216 methionyl-tRNA formyltransferase, ev=1e-133, 78% identity; methionyl-tRNA formyltransferase 2716653 4076708 TM1040_2577 Ruegeria sp. TM1040 methionyl-tRNA formyltransferase YP_614571.1 2715727 R 292414 CDS YP_614572.1 99082418 4077489 complement(2716810..2717307) 1 NC_008044.1 PFAM: formylmethionine deformylase: (2.1e-35); KEGG: sil:SPO3217 peptide deformylase, ev=6e-81, 90% identity; formylmethionine deformylase 2717307 4077489 TM1040_2578 Ruegeria sp. TM1040 formylmethionine deformylase YP_614572.1 2716810 R 292414 CDS YP_614573.1 99082419 4077490 complement(2717304..2717813) 1 NC_008044.1 PFAM: formylmethionine deformylase: (2e-45); KEGG: sil:SPO3218 peptide deformylase, ev=3e-40, 51% identity; peptide deformylase 2717813 4077490 TM1040_2579 Ruegeria sp. TM1040 peptide deformylase YP_614573.1 2717304 R 292414 CDS YP_614574.1 99082420 4077491 complement(2717810..2718334) 1 NC_008044.1 PFAM: formylmethionine deformylase: (2.5e-71); KEGG: sil:SPO3219 peptide deformylase, ev=6e-85, 88% identity; peptide deformylase 2718334 4077491 TM1040_2580 Ruegeria sp. TM1040 peptide deformylase YP_614574.1 2717810 R 292414 CDS YP_614575.1 99082421 4077492 2718493..2719665 1 NC_008044.1 PFAM: aminotransferase, class I and II: (1.2e-40); KEGG: sil:SPO3220 aminotransferase, classes I and II, ev=1e-167, 71% identity; class I and II aminotransferase 2719665 4077492 TM1040_2581 Ruegeria sp. TM1040 class I and II aminotransferase YP_614575.1 2718493 D 292414 CDS YP_614576.1 99082422 4077493 complement(2719778..2720146) 1 NC_008044.1 KEGG: sil:SPO3221 hypothetical protein, ev=6e-32, 63% identity; hypothetical protein 2720146 4077493 TM1040_2582 Ruegeria sp. TM1040 hypothetical protein YP_614576.1 2719778 R 292414 CDS YP_614577.1 99082423 4077494 2720387..2721361 1 NC_008044.1 KEGG: sil:SPO3222 glutathione S-transferase, ev=1e-150, 73% identity; glutathione S-transferase 2721361 4077494 TM1040_2583 Ruegeria sp. TM1040 glutathione S-transferase YP_614577.1 2720387 D 292414 CDS YP_614578.1 99082424 4077495 2721455..2722450 1 NC_008044.1 PFAM: aminotransferase, class I and II: (1.1e-08); KEGG: sil:SPO3224 cobalamin biosynthetic protein CobC, ev=1e-117, 66% identity; aminotransferase 2722450 4077495 TM1040_2584 Ruegeria sp. TM1040 aminotransferase YP_614578.1 2721455 D 292414 CDS YP_614579.1 99082425 4077496 2722447..2723358 1 NC_008044.1 CobD; CbiD in Salmonella; converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group; cobalamin biosynthesis protein 2723358 cobD 4077496 cobD Ruegeria sp. TM1040 cobalamin biosynthesis protein YP_614579.1 2722447 D 292414 CDS YP_614580.1 99082426 4077497 2723401..2724597 1 NC_008044.1 TIGRFAM: Lytic murein transglycosylase: (6.1e-120); PFAM: Peptidoglycan-binding domain 1: (2.5e-08); KEGG: sil:SPO3226 hypothetical protein, ev=1e-163, 71% identity; lytic murein transglycosylase 2724597 4077497 TM1040_2586 Ruegeria sp. TM1040 lytic murein transglycosylase YP_614580.1 2723401 D 292414 CDS YP_614581.1 99082427 4077498 complement(2724658..2728113) 1 NC_008044.1 TIGRFAM: Chromosome segregation protein SMC: (4.6e-247); PFAM: SMC protein-like: (6.6e-85) SMCs flexible hinge: (2e-10); KEGG: sil:SPO3228 SMC protein, ev=0.0, 75% identity; chromosome segregation protein SMC 2728113 4077498 TM1040_2587 Ruegeria sp. TM1040 chromosome segregation protein SMC YP_614581.1 2724658 R 292414 CDS YP_614582.1 99082428 4077499 complement(2728243..2729457) 1 NC_008044.1 PFAM: aminotransferase, class I and II: (3.2e-14); KEGG: sil:SPO3230 aminotransferase, classes I and II, ev=1e-162, 72% identity; class I and II aminotransferase 2729457 4077499 TM1040_2588 Ruegeria sp. TM1040 class I and II aminotransferase YP_614582.1 2728243 R 292414 CDS YP_614583.1 99082429 4077500 2729612..2730379 1 NC_008044.1 PFAM: regulatory protein GntR, HTH: (3.8e-24) GntR-like: (1.1e-37); KEGG: sil:SPO3231 pyruvate dehydrogenase complex repressor, ev=2e-98, 70% identity; GntR family transcriptional regulator 2730379 4077500 TM1040_2589 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_614583.1 2729612 D 292414 CDS YP_614584.1 99082430 4077501 complement(2730376..2731197) 1 NC_008044.1 PFAM: ABC transporter related: (7e-31); SMART: ATPase: (2.2e-09); KEGG: chy:CHY_2116 phosphate ABC transporter, ATP-binding protein PstB, ev=5e-38, 34% identity; ABC transporter 2731197 4077501 TM1040_2590 Ruegeria sp. TM1040 ABC transporter YP_614584.1 2730376 R 292414 CDS YP_614585.1 99082431 4077502 complement(2731437..2731994) 1 NC_008044.1 produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B is part of the membrane proton channel.; F0F1 ATP synthase subunit B 2731994 4077502 TM1040_2591 Ruegeria sp. TM1040 F0F1 ATP synthase subunit B YP_614585.1 2731437 R 292414 CDS YP_614586.1 99082432 4077503 complement(2731997..2732542) 1 NC_008044.1 produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B' is part of the membrane proton channel.; ATP synthase F0F1 subunit B' 2732542 4077503 TM1040_2592 Ruegeria sp. TM1040 ATP synthase F0F1 subunit B' YP_614586.1 2731997 R 292414 CDS YP_614587.1 99082433 4077504 complement(2732629..2732853) 1 NC_008044.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit C is part of the membrane proton channel F0; ATP synthase F0F1 subunit C 2732853 4077504 TM1040_2593 Ruegeria sp. TM1040 ATP synthase F0F1 subunit C YP_614587.1 2732629 R 292414 CDS YP_614588.1 99082434 4077505 complement(2732910..2733713) 1 NC_008044.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit A is part of the membrane proton channel F0; ATP synthase F0F1 subunit A 2733713 4077505 TM1040_2594 Ruegeria sp. TM1040 ATP synthase F0F1 subunit A YP_614588.1 2732910 R 292414 CDS YP_614589.1 99082435 4077506 complement(2733753..2734094) 1 NC_008044.1 KEGG: sil:SPO3237 ATP synthase F0, subunit I, ev=2e-30, 63% identity; ATP synthase F0 subunit I 2734094 4077506 TM1040_2595 Ruegeria sp. TM1040 ATP synthase F0 subunit I YP_614589.1 2733753 R 292414 CDS YP_614590.1 99082436 4077507 complement(2734304..2735191) 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (1.3e-17); KEGG: mlo:mlr1585 hypothetical protein, ev=1e-42, 33% identity; hypothetical protein 2735191 4077507 TM1040_2596 Ruegeria sp. TM1040 hypothetical protein YP_614590.1 2734304 R 292414 CDS YP_614591.1 99082437 4077508 2735291..2735620 1 NC_008044.1 PFAM: regulatory protein, ArsR: (1.8e-11); KEGG: sil:SPO3238 transcriptional regulator, ArsR family, ev=5e-46, 87% identity; ArsR family transcriptional regulator 2735620 4077508 TM1040_2597 Ruegeria sp. TM1040 ArsR family transcriptional regulator YP_614591.1 2735291 D 292414 CDS YP_614592.1 99082438 4077509 complement(2735663..2736574) 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (5.2e-11); KEGG: sil:SPO3239 integral membrane protein, ev=1e-113, 70% identity; hypothetical protein 2736574 4077509 TM1040_2598 Ruegeria sp. TM1040 hypothetical protein YP_614592.1 2735663 R 292414 CDS YP_614593.1 99082439 4077510 complement(2736583..2737461) 1 NC_008044.1 PFAM: regulatory protein, LysR: (5.8e-14) LysR, substrate-binding: (6.3e-32); KEGG: sil:SPO3240 transcriptional regulator, LysR family, ev=1e-123, 73% identity; LysR family transcriptional regulator 2737461 4077510 TM1040_2599 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_614593.1 2736583 R 292414 CDS YP_614594.1 99082440 4077511 2737602..2738183 1 NC_008044.1 PFAM: NAD(P)H dehydrogenase (quinone): (5.5e-35) NADPH-dependent FMN reductase: (0.0045); KEGG: jan:Jann_0760 (acyl-carrier protein) phosphodiesterase, ev=2e-62, 61% identity; ACP phosphodiesterase 2738183 4077511 TM1040_2600 Ruegeria sp. TM1040 ACP phosphodiesterase YP_614594.1 2737602 D 292414 CDS YP_614595.1 99082441 4077512 complement(2738369..2738899) 1 NC_008044.1 PFAM: YbaK/prolyl-tRNA synthetase associated region: (6.4e-05); KEGG: sil:SPO3242 YbaK/prolyl-tRNA synthetase domain protein, ev=1e-60, 65% identity; Ala-tRNA(Pro) hydrolase 2738899 4077512 TM1040_2601 Ruegeria sp. TM1040 Ala-tRNA(Pro) hydrolase YP_614595.1 2738369 R 292414 CDS YP_614596.1 99082442 4077513 complement(2738987..2739772) 1 NC_008044.1 hypothetical protein 2739772 4077513 TM1040_2602 Ruegeria sp. TM1040 hypothetical protein YP_614596.1 2738987 R 292414 CDS YP_614597.1 99082443 4077514 2740131..2741675 1 NC_008044.1 KEGG: sil:SPO3246 signal recognition particle protein, ev=0.0, 87% identity; TIGRFAM: signal recognition particle protein: (9.9e-247); PFAM: GTP-binding signal recognition particle SRP54, G-domain: (1.4e-98) Signal peptide binding (SRP54) M-domain: (6.5e-40); SMART: ATPase: (1.1e-09); signal recognition particle subunit FFH/SRP54 (srp54) 2741675 4077514 TM1040_2603 Ruegeria sp. TM1040 signal recognition particle subunit FFH/SRP54 (srp54) YP_614597.1 2740131 D 292414 CDS YP_614598.1 99082444 4077515 2741685..2742215 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (1.3e-07); KEGG: jan:Jann_3667 GCN5-related N-acetyltransferase, ev=9e-34, 46% identity; N-acetyltransferase GCN5 2742215 4077515 TM1040_2604 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_614598.1 2741685 D 292414 CDS YP_614599.1 99082445 4077516 2742212..2742817 1 NC_008044.1 KEGG: sil:SPO3251 hypothetical protein, ev=1e-100, 83% identity; hypothetical protein 2742817 4077516 TM1040_2605 Ruegeria sp. TM1040 hypothetical protein YP_614599.1 2742212 D 292414 CDS YP_614600.1 99082446 4077517 2742810..2743118 1 NC_008044.1 catalyzes the interconversion of chorismate to prephenate; chorismate mutase 2743118 4077517 TM1040_2606 Ruegeria sp. TM1040 chorismate mutase YP_614600.1 2742810 D 292414 CDS YP_614601.1 99082447 4077518 2743178..2743543 1 NC_008044.1 binds to lower part of 30S body where it stabilizes two domains; required for efficient assembly of 30S; in Escherichia coli this protein has nuclease activity; 30S ribosomal protein S16 2743543 rpsP 4077518 rpsP Ruegeria sp. TM1040 30S ribosomal protein S16 YP_614601.1 2743178 D 292414 CDS YP_614602.1 99082448 4077519 2743548..2744201 1 NC_008044.1 TIGRFAM: Cob(II)yrinic acid a,c-diamide reductase: (2.1e-116); PFAM: nitroreductase: (1.7e-20); KEGG: sil:SPO3254 cobalamin biosynthesis protein BluB, ev=5e-82, 70% identity; Cob(II)yrinic acid a,c-diamide reductase 2744201 4077519 TM1040_2608 Ruegeria sp. TM1040 Cob(II)yrinic acid a,c-diamide reductase YP_614602.1 2743548 D 292414 CDS YP_614603.1 99082449 4077520 2744391..2744906 1 NC_008044.1 Essential for efficient processing of 16S rRNA; 16S rRNA-processing protein RimM 2744906 rimM 4077520 rimM Ruegeria sp. TM1040 16S rRNA-processing protein RimM YP_614603.1 2744391 D 292414 CDS YP_614604.1 99082450 4077521 complement(2744907..2745917) 1 NC_008044.1 hypothetical protein 2745917 4077521 TM1040_2610 Ruegeria sp. TM1040 hypothetical protein YP_614604.1 2744907 R 292414 CDS YP_614605.1 99082451 4077522 2745980..2746780 1 NC_008044.1 methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA; tRNA (guanine-N(1)-)-methyltransferase 2746780 trmD 4077522 trmD Ruegeria sp. TM1040 tRNA (guanine-N(1)-)-methyltransferase YP_614605.1 2745980 D 292414 CDS YP_614606.1 99082452 4077523 complement(2746781..2747173) 1 NC_008044.1 hypothetical protein 2747173 4077523 TM1040_2612 Ruegeria sp. TM1040 hypothetical protein YP_614606.1 2746781 R 292414 CDS YP_614607.1 99082453 4077524 2747330..2747662 1 NC_008044.1 PFAM: protein of unknown function DUF1508: (4.9e-23); KEGG: nmu:Nmul_A2168 protein of unknown function DUF1508, ev=1e-36, 67% identity; hypothetical protein 2747662 4077524 TM1040_2613 Ruegeria sp. TM1040 hypothetical protein YP_614607.1 2747330 D 292414 CDS YP_614608.1 99082454 4077525 complement(2747739..2748164) 1 NC_008044.1 PFAM: regulatory protein, MerR: (1.8e-10); KEGG: sil:SPO3734 transcriptional regulator, MerR family, ev=3e-39, 56% identity; MerR family transcriptional regulator 2748164 4077525 TM1040_2614 Ruegeria sp. TM1040 MerR family transcriptional regulator YP_614608.1 2747739 R 292414 CDS YP_614609.1 99082455 4077526 2748232..2749446 1 NC_008044.1 PFAM: major facilitator superfamily MFS_1: (2.9e-36); KEGG: sil:SPO3735 major facilitator family protein, ev=2e-98, 52% identity; major facilitator superfamily transporter 2749446 4077526 TM1040_2615 Ruegeria sp. TM1040 major facilitator superfamily transporter YP_614609.1 2748232 D 292414 CDS YP_614610.1 99082456 4077527 2749710..2750081 1 NC_008044.1 this protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site; 50S ribosomal protein L19 2750081 rplS 4077527 rplS Ruegeria sp. TM1040 50S ribosomal protein L19 YP_614610.1 2749710 D 292414 CDS YP_614611.1 99082457 4077920 2750093..2750314 1 NC_008044.1 RpmE; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster do not have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome; 50S ribosomal protein L31 2750314 rpmE 4077920 rpmE Ruegeria sp. TM1040 50S ribosomal protein L31 YP_614611.1 2750093 D 292414 CDS YP_614612.1 99082458 4077921 2750599..2751408 1 NC_008044.1 KEGG: sil:SPO0689 chromosome partitioning protein, ev=1e-124, 84% identity; chromosome partitioning protein 2751408 4077921 TM1040_2618 Ruegeria sp. TM1040 chromosome partitioning protein YP_614612.1 2750599 D 292414 CDS YP_614613.1 99082459 4077922 complement(2751599..2752744) 1 NC_008044.1 PFAM: adenylyl cyclase class-3/4/guanylyl cyclase: (1.8e-09); KEGG: sil:SPO0688 adenylate/guanylate cyclase, ev=1e-108, 51% identity; guanylate cyclase 2752744 4077922 TM1040_2619 Ruegeria sp. TM1040 guanylate cyclase YP_614613.1 2751599 R 292414 CDS YP_614614.1 99082460 4077923 complement(2752842..2753300) 1 NC_008044.1 PFAM: regulatory protein, MarR: (1.5e-10); KEGG: sil:SPO0687 transcriptional regulator, MarR family, ev=1e-45, 64% identity; MarR family transcriptional regulator 2753300 4077923 TM1040_2620 Ruegeria sp. TM1040 MarR family transcriptional regulator YP_614614.1 2752842 R 292414 CDS YP_614615.1 99082461 4077924 2753377..2754732 1 NC_008044.1 An oxygenase that acts to open the ring of homogentisate formingmaleylacetoacetate as part of the catabolism of L-tyrosine and L-phenylalanine; homogentisate 1,2-dioxygenase 2754732 4077924 TM1040_2621 Ruegeria sp. TM1040 homogentisate 1,2-dioxygenase YP_614615.1 2753377 D 292414 CDS YP_614616.1 99082462 4077925 2754850..2756106 1 NC_008044.1 KEGG: sil:SPO0685 fumarylacetoacetase, ev=1e-169, 70% identity; TIGRFAM: fumarylacetoacetase: (3.8e-197); PFAM: fumarylacetoacetate (FAA) hydrolase: (1.7e-69); fumarylacetoacetate hydrolase 2756106 4077925 TM1040_2622 Ruegeria sp. TM1040 fumarylacetoacetate hydrolase YP_614616.1 2754850 D 292414 CDS YP_614617.1 99082463 4077926 2756189..2757139 1 NC_008044.1 PFAM: beta-lactamase-like: (3.9e-08); KEGG: sil:SPO0683 metallo-beta-lactamase family protein, ev=1e-173, 93% identity; beta-lactamase-like protein 2757139 4077926 TM1040_2623 Ruegeria sp. TM1040 beta-lactamase-like protein YP_614617.1 2756189 D 292414 CDS YP_614618.1 99082464 4077927 2757262..2758869 1 NC_008044.1 PFAM: monooxygenase, FAD-binding: (5.2e-47) FAD dependent oxidoreductase: (0.00024); KEGG: sil:SPO0682 monooxygenase family protein, ev=0.0, 75% identity; FAD-dependent oxidoreductase 2758869 4077927 TM1040_2624 Ruegeria sp. TM1040 FAD-dependent oxidoreductase YP_614618.1 2757262 D 292414 CDS YP_614619.1 99082465 4077928 2758875..2759081 1 NC_008044.1 KEGG: sil:SPO0681 hypothetical protein, ev=2e-15, 70% identity; hypothetical protein 2759081 4077928 TM1040_2625 Ruegeria sp. TM1040 hypothetical protein YP_614619.1 2758875 D 292414 CDS YP_614620.1 99082466 4077929 2759074..2759721 1 NC_008044.1 TIGRFAM: maleylacetoacetate isomerase: (6.9e-93); PFAM: glutathione S-transferase-like: (3e-16); KEGG: sil:SPO0679 maleylacetoacetate isomerase, ev=5e-76, 65% identity; maleylacetoacetate isomerase 2759721 4077929 TM1040_2626 Ruegeria sp. TM1040 maleylacetoacetate isomerase YP_614620.1 2759074 D 292414 CDS YP_614621.1 99082467 4077930 2759858..2761072 1 NC_008044.1 PFAM: protein of unknown function UPF0052 and CofD: (3.6e-22); KEGG: dde:Dde_3600 hypothetical protein, ev=2e-84, 45% identity; hypothetical protein 2761072 4077930 TM1040_2627 Ruegeria sp. TM1040 hypothetical protein YP_614621.1 2759858 D 292414 CDS YP_614622.1 99082468 4077931 complement(2761148..2763355) 1 NC_008044.1 KEGG: sil:SPO3725 penicillin-binding protein, 1A family, ev=0.0, 64% identity; TIGRFAM: Penicillin-binding protein 1A: (1.9e-182); PFAM: glycosyl transferase, family 51: (2.8e-67) penicillin-binding protein, transpeptidase: (1.1e-29); penicillin-binding protein 1A 2763355 4077931 TM1040_2628 Ruegeria sp. TM1040 penicillin-binding protein 1A YP_614622.1 2761148 R 292414 CDS YP_614623.1 99082469 4077932 2763645..2763983 1 NC_008044.1 PFAM: nitrogen regulatory protein P-II: (2.7e-63); KEGG: jan:Jann_4056 nitrogen regulatory protein P-II (GlnB, GlnK), ev=4e-45, 82% identity; nitrogen regulatory protein P-II 2763983 4077932 TM1040_2629 Ruegeria sp. TM1040 nitrogen regulatory protein P-II YP_614623.1 2763645 D 292414 CDS YP_614624.1 99082470 4077933 2764013..2765335 1 NC_008044.1 TIGRFAM: ammonium transporter: (6.3e-135); PFAM: Rh-like protein/ammonium transporter: (2.2e-128); KEGG: jan:Jann_4057 ammonium transporter, ev=0.0, 78% identity; ammonium transporter 2765335 4077933 TM1040_2630 Ruegeria sp. TM1040 ammonium transporter YP_614624.1 2764013 D 292414 CDS YP_614625.1 99082471 4077934 complement(2765408..2766052) 1 NC_008044.1 PFAM: ribonuclease T2: (3.3e-08); KEGG: sil:SPO3567 ribonuclease T2 family protein, ev=2e-90, 72% identity; ribonuclease T2 2766052 4077934 TM1040_2631 Ruegeria sp. TM1040 ribonuclease T2 YP_614625.1 2765408 R 292414 CDS YP_614626.1 99082472 4077935 2766222..2766989 1 NC_008044.1 PFAM: protein of unknown function DUF1013: (4.5e-87); KEGG: sil:SPO3566 hypothetical protein, ev=1e-119, 83% identity; hypothetical protein 2766989 4077935 TM1040_2632 Ruegeria sp. TM1040 hypothetical protein YP_614626.1 2766222 D 292414 CDS YP_614627.1 99082473 4077936 2767201..2767701 1 NC_008044.1 hypothetical protein 2767701 4077936 TM1040_2633 Ruegeria sp. TM1040 hypothetical protein YP_614627.1 2767201 D 292414 CDS YP_614628.1 99082474 4077937 2767830..2768681 1 NC_008044.1 PFAM: Rhodanese-like: (7.5e-26); KEGG: sil:SPO3719 thiosulfate sulfurtransferase, , ev=1e-138, 81% identity; 3-mercaptopyruvate sulfurtransferase 2768681 4077937 TM1040_2634 Ruegeria sp. TM1040 3-mercaptopyruvate sulfurtransferase YP_614628.1 2767830 D 292414 CDS YP_614629.1 99082475 4077938 2768685..2769869 1 NC_008044.1 catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate; aromatic amino acid aminotransferase 2769869 4077938 TM1040_2635 Ruegeria sp. TM1040 aromatic amino acid aminotransferase YP_614629.1 2768685 D 292414 CDS YP_614630.1 99082476 4077939 complement(2769971..2770585) 1 NC_008044.1 PFAM: Enoyl-CoA hydratase/isomerase: (2.2e-22); KEGG: sil:SPO3439 enoyl-CoA hydratase/isomerase family protein, ev=3e-73, 73% identity; enoyl-CoA hydratase/isomerase 2770585 4077939 TM1040_2636 Ruegeria sp. TM1040 enoyl-CoA hydratase/isomerase YP_614630.1 2769971 R 292414 CDS YP_614631.1 99082477 4077940 complement(2770582..2771331) 1 NC_008044.1 PFAM: short-chain dehydrogenase/reductase SDR: (1.4e-33); KEGG: sil:SPO3440 20-beta-hydroxysteroid dehydrogenase, , ev=9e-89, 67% identity; short-chain dehydrogenase/reductase SDR 2771331 4077940 TM1040_2637 Ruegeria sp. TM1040 short-chain dehydrogenase/reductase SDR YP_614631.1 2770582 R 292414 CDS YP_614632.1 99082478 4077941 2771466..2772980 1 NC_008044.1 KEGG: sil:SPO3441 hypothetical protein, ev=1e-119, 41% identity; hypothetical protein 2772980 4077941 TM1040_2638 Ruegeria sp. TM1040 hypothetical protein YP_614632.1 2771466 D 292414 CDS YP_614633.1 99082479 4077942 2773042..2774463 1 NC_008044.1 PFAM: peptidase U62, modulator of DNA gyrase: (3.6e-40); KEGG: sil:SPO3442 PmbA, ev=0.0, 73% identity; microcin-processing peptidase 1 2774463 4077942 TM1040_2639 Ruegeria sp. TM1040 microcin-processing peptidase 1 YP_614633.1 2773042 D 292414 CDS YP_614634.1 99082480 4077943 2774450..2775250 1 NC_008044.1 PFAM: inositol monophosphatase: (9.2e-54); KEGG: sil:SPO3443 inositol monophosphatase family protein, ev=3e-86, 59% identity; inositol monophosphatase 2775250 4077943 TM1040_2640 Ruegeria sp. TM1040 inositol monophosphatase YP_614634.1 2774450 D 292414 CDS YP_614635.1 99082481 4077944 2775250..2776446 1 NC_008044.1 KEGG: sil:SPO3444 3-deoxy-D-manno-octulosonic-acid transferase, , ev=5e-81, 42% identity; 3-deoxy-D-manno-octulosonic-acid transferase 2776446 4077944 TM1040_2641 Ruegeria sp. TM1040 3-deoxy-D-manno-octulosonic-acid transferase YP_614635.1 2775250 D 292414 CDS YP_614636.1 99082482 4077945 2776433..2777434 1 NC_008044.1 transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate; tetraacyldisaccharide 4'-kinase 2777434 lpxK 4077945 lpxK Ruegeria sp. TM1040 tetraacyldisaccharide 4'-kinase YP_614636.1 2776433 D 292414 CDS YP_614637.1 99082483 4077946 complement(2777471..2778172) 1 NC_008044.1 KEGG: sil:SPO3446 thiol:disulfide interchange protein, DsbA family, ev=3e-80, 64% identity; DsbA family thiol:disulfide interchange protein 2778172 4077946 TM1040_2643 Ruegeria sp. TM1040 DsbA family thiol:disulfide interchange protein YP_614637.1 2777471 R 292414 CDS YP_614638.1 99082484 4077947 complement(2778169..2778696) 1 NC_008044.1 PFAM: protein of unknown function DUF1159: (7.1e-21); KEGG: sil:SPO3447 hypothetical protein, ev=2e-59, 68% identity; hypothetical protein 2778696 4077947 TM1040_2644 Ruegeria sp. TM1040 hypothetical protein YP_614638.1 2778169 R 292414 CDS YP_614639.1 99082485 4077948 2778782..2779843 1 NC_008044.1 TIGRFAM: A/G-specific adenine glycosylase: (6.4e-105); PFAM: helix-hairpin-helix motif: (1.5e-06) HhH-GPD: (2.4e-11); KEGG: sil:SPO3448 A/G-specific adenine glycosylase, ev=1e-154, 76% identity; A/G-specific adenine glycosylase 2779843 4077948 TM1040_2645 Ruegeria sp. TM1040 A/G-specific adenine glycosylase YP_614639.1 2778782 D 292414 CDS YP_614640.1 99082486 4077949 2779924..2781066 1 NC_008044.1 PFAM: fatty acid desaturase: (2e-06); KEGG: sil:SPO3449 fatty acid desaturase family protein, ev=1e-172, 73% identity; alkane 1-monooxygenase 2781066 4077949 TM1040_2646 Ruegeria sp. TM1040 alkane 1-monooxygenase YP_614640.1 2779924 D 292414 CDS YP_614641.1 99082487 4077950 complement(2781272..2782768) 1 NC_008044.1 PFAM: chemotaxis sensory transducer: (9e-46); KEGG: atc:AGR_C_1888 methyl-accepting chemotaxis protein McpV, ev=6e-71, 34% identity; methyl-accepting chemotaxis sensory transducer 2782768 4077950 TM1040_2647 Ruegeria sp. TM1040 methyl-accepting chemotaxis sensory transducer YP_614641.1 2781272 R 292414 CDS YP_614642.1 99082488 4077951 complement(2782796..2784190) 1 NC_008044.1 PFAM: adenylyl cyclase class-3/4/guanylyl cyclase: (9.6e-33); KEGG: sil:SPO3450 adenylate/guanylate cyclase, ev=1e-134, 57% identity; guanylate cyclase 2784190 4077951 TM1040_2648 Ruegeria sp. TM1040 guanylate cyclase YP_614642.1 2782796 R 292414 CDS YP_614643.1 99082489 4077952 complement(2784374..2785543) 1 NC_008044.1 PFAM: DNA methylase N-4/N-6: (4.2e-91); KEGG: sil:SPO3451 modification methylase, ev=0.0, 88% identity; DNA methylase N-4/N-6 2785543 4077952 TM1040_2649 Ruegeria sp. TM1040 DNA methylase N-4/N-6 YP_614643.1 2784374 R 292414 CDS YP_614644.1 99082490 4077953 complement(2785589..2786278) 1 NC_008044.1 RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids; ribonuclease HII 2786278 rnhB 4077953 rnhB Ruegeria sp. TM1040 ribonuclease HII YP_614644.1 2785589 R 292414 CDS YP_614645.1 99082491 4077954 complement(2786322..2786789) 1 NC_008044.1 hypothetical protein 2786789 4077954 TM1040_2651 Ruegeria sp. TM1040 hypothetical protein YP_614645.1 2786322 R 292414 CDS YP_614646.1 99082492 4077955 2786968..2787261 1 NC_008044.1 KEGG: sil:SPO3453 hypothetical protein, ev=2e-26, 64% identity; hypothetical protein 2787261 4077955 TM1040_2652 Ruegeria sp. TM1040 hypothetical protein YP_614646.1 2786968 D 292414 CDS YP_614647.1 99082493 4077956 2787233..2787934 1 NC_008044.1 KEGG: sil:SPO3454 hypothetical protein, ev=2e-98, 80% identity; transcriptional regulator CadC 2787934 4077956 TM1040_2653 Ruegeria sp. TM1040 transcriptional regulator CadC YP_614647.1 2787233 D 292414 CDS YP_614648.1 99082494 4077957 2788187..2789740 1 NC_008044.1 PFAM: adenylyl cyclase class-3/4/guanylyl cyclase: (4.1e-08) protein of unknown function DUF427: (1.3e-17); KEGG: sil:SPO3455 adenylate/guanylate cyclase, ev=0.0, 62% identity; guanylate cyclase 2789740 4077957 TM1040_2654 Ruegeria sp. TM1040 guanylate cyclase YP_614648.1 2788187 D 292414 CDS YP_614649.1 99082495 4077958 complement(2789859..2791367) 1 NC_008044.1 PFAM: aldehyde dehydrogenase: (5e-136); KEGG: sil:SPO0235 aldehyde dehydrogenase family protein, ev=0.0, 84% identity; aldehyde dehydrogenase 2791367 4077958 TM1040_2655 Ruegeria sp. TM1040 aldehyde dehydrogenase YP_614649.1 2789859 R 292414 CDS YP_614650.1 99082496 4077567 complement(2791376..2792497) 1 NC_008044.1 PFAM: TrkA-N: (0.00012) Saccharopine dehydrogenase: (3.4e-81); KEGG: sil:SPO0234 hypothetical protein, ev=1e-170, 81% identity; saccharopine dehydrogenase 2792497 4077567 TM1040_2656 Ruegeria sp. TM1040 saccharopine dehydrogenase YP_614650.1 2791376 R 292414 CDS YP_614651.1 99082497 4077568 complement(2792625..2793053) 1 NC_008044.1 PFAM: regulatory proteins, AsnC/Lrp: (6.9e-19); KEGG: sil:SPO0233 transcriptional regulator, AsnC family, ev=2e-60, 81% identity; AsnC family transcriptional regulator 2793053 4077568 TM1040_2657 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_614651.1 2792625 R 292414 CDS YP_614652.1 99082498 4077569 complement(2793057..2793812) 1 NC_008044.1 PFAM: protein of unknown function DUF328: (2.1e-61); KEGG: sil:SPO0106 hypothetical protein, ev=5e-54, 44% identity; hypothetical protein 2793812 4077569 TM1040_2658 Ruegeria sp. TM1040 hypothetical protein YP_614652.1 2793057 R 292414 CDS YP_614653.1 99082499 4077570 complement(2793914..2795953) 1 NC_008044.1 TIGRFAM: ATP-dependent DNA helicase, RecQ family: (5.5e-169) ATP-dependent DNA helicase RecQ: (2.7e-264); PFAM: helicase-like: (7.3e-27) HRDC: (8.7e-22) DEAD/DEAH box helicase-like: (6e-34); KEGG: sil:SPO0107 ATP-dependent DNA helicase RecQ, ev=0.0, 81% identity; ATP-dependent DNA helicase RecQ 2795953 4077570 TM1040_2659 Ruegeria sp. TM1040 ATP-dependent DNA helicase RecQ YP_614653.1 2793914 R 292414 CDS YP_614654.1 99082500 4077571 complement(2796082..2796411) 1 NC_008044.1 KEGG: sil:SPO0122 YGGT family protein, ev=1e-24, 57% identity; hypothetical protein 2796411 4077571 TM1040_2660 Ruegeria sp. TM1040 hypothetical protein YP_614654.1 2796082 R 292414 CDS YP_614655.1 99082501 4077572 2796504..2797082 1 NC_008044.1 KEGG: rsp:RSP_1361 hypothetical protein, ev=3e-50, 54% identity; hypothetical protein 2797082 4077572 TM1040_2661 Ruegeria sp. TM1040 hypothetical protein YP_614655.1 2796504 D 292414 CDS YP_614656.1 99082502 4077573 2797133..2798515 1 NC_008044.1 PFAM: major facilitator superfamily MFS_1: (3.4e-13); KEGG: sil:SPO0123 membrane protein, , ev=0.0, 73% identity; major facilitator superfamily transporter 2798515 4077573 TM1040_2662 Ruegeria sp. TM1040 major facilitator superfamily transporter YP_614656.1 2797133 D 292414 CDS YP_614657.1 99082503 4077574 2798512..2799435 1 NC_008044.1 D-alanyl-D-alanine endopeptidase; functions in hydrolyzing cell wall peptidoglycan; similar to LAS metallopeptidases; forms a dimer in periplasm; penicillin-insensitive murein endopeptidase 2799435 mepA 4077574 mepA Ruegeria sp. TM1040 penicillin-insensitive murein endopeptidase YP_614657.1 2798512 D 292414 CDS YP_614658.1 99082504 4077575 2799408..2800334 1 NC_008044.1 KEGG: sil:SPO0125 hypothetical protein, ev=6e-56, 42% identity; hypothetical protein 2800334 4077575 TM1040_2664 Ruegeria sp. TM1040 hypothetical protein YP_614658.1 2799408 D 292414 CDS YP_614659.1 99082505 4077576 2800489..2801121 1 NC_008044.1 PFAM: protein of unknown function DUF165: (4e-28); KEGG: rsp:RSP_1365 hypothetical protein, ev=9e-83, 73% identity; hypothetical protein 2801121 4077576 TM1040_2665 Ruegeria sp. TM1040 hypothetical protein YP_614659.1 2800489 D 292414 CDS YP_614660.1 99082506 4077577 2801738..2802157 1 NC_008044.1 PFAM: Class I peptide chain release factor: (4.9e-17); KEGG: sil:SPO0127 peptidyl-tRNA hydrolase domain protein, ev=2e-56, 77% identity; peptidyl-tRNA hydrolase domain-containing protein 2802157 4077577 TM1040_2666 Ruegeria sp. TM1040 peptidyl-tRNA hydrolase domain-containing protein YP_614660.1 2801738 D 292414 CDS YP_614661.1 99082507 4077578 2802298..2803320 1 NC_008044.1 PFAM: peptidase S58, DmpA: (6e-38); KEGG: sil:SPO0129 peptidase, T4 family, ev=1e-135, 71% identity; peptidase S58, DmpA 2803320 4077578 TM1040_2667 Ruegeria sp. TM1040 peptidase S58, DmpA YP_614661.1 2802298 D 292414 CDS YP_614662.1 99082508 4077579 2803833..2804795 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (1.2e-15); KEGG: sil:SPO3643 integral membrane protein, ev=9e-63, 44% identity; hypothetical protein 2804795 4077579 TM1040_2668 Ruegeria sp. TM1040 hypothetical protein YP_614662.1 2803833 D 292414 CDS YP_614663.1 99082509 4077580 2804811..2805431 1 NC_008044.1 TIGRFAM: HAD-superfamily hydrolase subfamily IA, variant 3: (2.6e-06); PFAM: Haloacid dehalogenase-like hydrolase: (4.7e-06); KEGG: sil:SPO3822 HAD-superfamily hydrolase, subfamily IA, variant 1 family protein, ev=3e-71, 62% identity; HAD family hydrolase 2805431 4077580 TM1040_2669 Ruegeria sp. TM1040 HAD family hydrolase YP_614663.1 2804811 D 292414 CDS YP_614664.1 99082510 4077581 2805428..2806345 1 NC_008044.1 PFAM: ornithine cyclodeaminase/mu-crystallin: (5.8e-26) Shikimate/quinate 5-dehydrogenase: (2.3e-05); KEGG: sil:SPO3821 ornithine cyclodeaminase/mu-crystallin family protein, ev=1e-111, 66% identity; ornithine cyclodeaminase 2806345 4077581 TM1040_2670 Ruegeria sp. TM1040 ornithine cyclodeaminase YP_614664.1 2805428 D 292414 CDS YP_614665.1 99082511 4077582 2806342..2807274 1 NC_008044.1 PFAM: alpha/beta hydrolase fold: (4.8e-18); KEGG: sma:SAV297 alpha/beta hydrolase, ev=4e-20, 29% identity; alpha/beta hydrolase 2807274 4077582 TM1040_2671 Ruegeria sp. TM1040 alpha/beta hydrolase YP_614665.1 2806342 D 292414 CDS YP_614666.1 99082512 4077583 complement(2807277..2808515) 1 NC_008044.1 PFAM: major facilitator superfamily MFS_1: (4.2e-34); KEGG: sil:SPO3820 transmembrane transporter, major facilitator family, ev=0.0, 80% identity; major facilitator superfamily transporter 2808515 4077583 TM1040_2672 Ruegeria sp. TM1040 major facilitator superfamily transporter YP_614666.1 2807277 R 292414 CDS YP_614667.1 99082513 4077584 2808684..2809748 1 NC_008044.1 PFAM: AFG1-like ATPase: (2.8e-136); KEGG: sil:SPO3819 ATPase, AFG1 family, ev=1e-148, 76% identity; AFG1-like ATPase 2809748 4077584 TM1040_2673 Ruegeria sp. TM1040 AFG1-like ATPase YP_614667.1 2808684 D 292414 CDS YP_614668.1 99082514 4077585 2809876..2810637 1 NC_008044.1 PFAM: regulatory protein, DeoR: (2.7e-32) Helix-turn-helix, type 11: (1.5e-08); KEGG: pae:PA3583 glycerol-3-phosphate regulon repressor, ev=2e-39, 39% identity; DeoR family transcriptional regulator 2810637 4077585 TM1040_2674 Ruegeria sp. TM1040 DeoR family transcriptional regulator YP_614668.1 2809876 D 292414 CDS YP_614669.1 99082515 4077586 complement(2810634..2811905) 1 NC_008044.1 TIGRFAM: FolC bifunctional protein: (8.5e-134); PFAM: Mur ligase, middle region: (6.8e-06); KEGG: sil:SPO3818 FolC bifunctional protein, ev=0.0, 78% identity; bifunctional folylpolyglutamate synthase/dihydrofolate synthase 2811905 4077586 TM1040_2675 Ruegeria sp. TM1040 bifunctional folylpolyglutamate synthase/dihydrofolate synthase YP_614669.1 2810634 R 292414 CDS YP_614670.1 99082516 4077587 complement(2812060..2813022) 1 NC_008044.1 TIGRFAM: acetyl-CoA carboxylase, carboxyl transferase, beta subunit: (5.9e-129); KEGG: sil:SPO3817 acetyl-CoA carboxylase, carboxyl transferase, beta subunit, ev=1e-149, 83% identity; acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha 2813022 4077587 TM1040_2676 Ruegeria sp. TM1040 acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha YP_614670.1 2812060 R 292414 CDS YP_614671.1 99082517 4077588 complement(2813085..2813969) 1 NC_008044.1 PFAM: Abortive infection protein: (2.8e-14); KEGG: sil:SPO3816 CAAX amino terminal protease family protein, ev=3e-74, 50% identity; abortive infection protein 2813969 4077588 TM1040_2677 Ruegeria sp. TM1040 abortive infection protein YP_614671.1 2813085 R 292414 CDS YP_614672.1 99082518 4077589 complement(2814095..2817148) 1 NC_008044.1 PFAM: cyclic nucleotide-binding: (1.2e-15); KEGG: sil:SPO3815 ABC transporter, permease protein, ev=0.0, 61% identity; cyclic nucleotide-binding protein 2817148 4077589 TM1040_2678 Ruegeria sp. TM1040 cyclic nucleotide-binding protein YP_614672.1 2814095 R 292414 CDS YP_614673.1 99082519 4077590 2817505..2818284 1 NC_008044.1 hypothetical protein 2818284 4077590 TM1040_2679 Ruegeria sp. TM1040 hypothetical protein YP_614673.1 2817505 D 292414 CDS YP_614674.1 99082520 4077591 2818500..2819261 1 NC_008044.1 KEGG: sil:SPO3814 hypothetical protein, ev=1e-103, 72% identity; hypothetical protein 2819261 4077591 TM1040_2680 Ruegeria sp. TM1040 hypothetical protein YP_614674.1 2818500 D 292414 CDS YP_614675.1 99082521 4077592 2819297..2819674 1 NC_008044.1 KEGG: sil:SPO3813 hypothetical protein, ev=7e-39, 64% identity; hypothetical protein 2819674 4077592 TM1040_2681 Ruegeria sp. TM1040 hypothetical protein YP_614675.1 2819297 D 292414 CDS YP_614676.1 99082522 4077593 complement(2819870..2820934) 1 NC_008044.1 KEGG: sil:SPO3311 ADA regulatory protein, , ev=1e-126, 65% identity; TIGRFAM: methylated-DNA--protein-cysteine methyltransferase: (4.4e-40); PFAM: methylated-DNA-[protein]-cysteine S-methyltransferase: (5e-36) Ada, metal-binding: (2.3e-37); SMART: Helix-turn-helix, AraC type: (1.2e-12); DNA-O6-methylguanine--protein-cysteine S-methyltransferase/transcriptional regulator Ada 2820934 4077593 TM1040_2682 Ruegeria sp. TM1040 DNA-O6-methylguanine--protein-cysteine S-methyltransferase/transcriptional regulator Ada YP_614676.1 2819870 R 292414 CDS YP_614677.1 99082523 4077594 complement(2821249..2822205) 1 NC_008044.1 KEGG: sil:SPO2551 peptide/opine/nickel uptake family ABC transporter, ATP-binding protein, ev=1e-129, 73% identity; TIGRFAM: Oligopeptide/dipeptide ABC transporter, ATP-binding protein-like: (9.2e-24); PFAM: ABC transporter related: (6.2e-68) Oligopeptide/dipeptide ABC transporter-like: (1.5e-22); SMART: ATPase: (3.5e-21); oligopeptide/dipeptide ABC transporter ATP-binding protein-like protein 2822205 4077594 TM1040_2683 Ruegeria sp. TM1040 oligopeptide/dipeptide ABC transporter ATP-binding protein-like protein YP_614677.1 2821249 R 292414 CDS YP_614678.1 99082524 4077595 complement(2822202..2824085) 1 NC_008044.1 KEGG: sil:SPO2552 peptide/opine/nickel uptake family ABC transporter, permease/ATP-binding protein, ev=0.0, 79% identity; TIGRFAM: Oligopeptide/dipeptide ABC transporter, ATP-binding protein-like: (6.6e-24); PFAM: binding-protein-dependent transport systems inner membrane component: (7.1e-44) ABC transporter related: (1.1e-60) Oligopeptide/dipeptide ABC transporter-like: (7.1e-25); SMART: ATPase: (2.7e-19); oligopeptide/dipeptide ABC transporter ATP-binding protein-like protein 2824085 4077595 TM1040_2684 Ruegeria sp. TM1040 oligopeptide/dipeptide ABC transporter ATP-binding protein-like protein YP_614678.1 2822202 R 292414 CDS YP_614679.1 99082525 4077596 complement(2824082..2825029) 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (7.7e-47); KEGG: sil:SPO2553 peptide/opine/nickel uptake family ABC transporter, permease protein, ev=1e-149, 84% identity; binding-protein-dependent transport system inner membrane protein 2825029 4077596 TM1040_2685 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_614679.1 2824082 R 292414 CDS YP_614680.1 99082526 4077597 complement(2825147..2826733) 1 NC_008044.1 PFAM: extracellular solute-binding protein, family 5: (1.4e-89); KEGG: sil:SPO2554 peptide/opine/nickel uptake family ABC transporter, periplasmic substrate-binding protein, ev=0.0, 82% identity; extracellular solute-binding protein 2826733 4077597 TM1040_2686 Ruegeria sp. TM1040 extracellular solute-binding protein YP_614680.1 2825147 R 292414 CDS YP_614681.1 99082527 4077598 2826841..2827515 1 NC_008044.1 KEGG: sil:SPO2555 hypothetical protein, ev=4e-53, 51% identity; hypothetical protein 2827515 4077598 TM1040_2687 Ruegeria sp. TM1040 hypothetical protein YP_614681.1 2826841 D 292414 CDS YP_614682.1 99082528 4077599 complement(2827522..2828361) 1 NC_008044.1 PFAM: regulatory protein GntR, HTH: (3.8e-15) GntR-like: (8.8e-20); KEGG: sil:SPO2550 transcriptional regulator, GntR family, ev=4e-80, 61% identity; GntR family transcriptional regulator 2828361 4077599 TM1040_2688 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_614682.1 2827522 R 292414 CDS YP_614683.1 99082529 4077600 2828383..2829603 1 NC_008044.1 allantoate amidohydrolase and N-carbamoyl-L-amino acid amidohydrolase are very similar; the allantoate amidohydrolase from Escherichia coli forms a dimer and binds zinc ions for catalytic activity and catalyzes the conversion of allantoate to (S)-ureidoglycolate and ammonia; carbamoyl amidohydrolase from Bacillus sp. converts N-carbamoyl amino acids to amino acids, ammonia, and carbon dioxide; allantoate amidohydrolase 2829603 4077600 TM1040_2689 Ruegeria sp. TM1040 allantoate amidohydrolase YP_614683.1 2828383 D 292414 CDS YP_614684.1 99082530 4077601 complement(2829620..2831923) 1 NC_008044.1 PFAM: Hemolysin-type calcium-binding region: (0.0016); KEGG: sil:SPO1626 type I secretion target repeat protein, ev=1e-67, 29% identity; hemolysin-type calcium-binding protein 2831923 4077601 TM1040_2690 Ruegeria sp. TM1040 hemolysin-type calcium-binding protein YP_614684.1 2829620 R 292414 CDS YP_614685.1 99082531 4077602 complement(2832091..2833464) 1 NC_008044.1 PFAM: aminotransferase class-III: (7.1e-80); KEGG: sil:SPO1136 aminotransferase, class III, ev=0.0, 91% identity; hypothetical protein 2833464 4077602 TM1040_2691 Ruegeria sp. TM1040 hypothetical protein YP_614685.1 2832091 R 292414 CDS YP_614686.1 99082532 4077603 complement(2833528..2835003) 1 NC_008044.1 PFAM: aldehyde dehydrogenase: (1e-212); KEGG: sil:SPO1137 succinate-semialdehyde dehydrogenase, ev=0.0, 82% identity; succinate semialdehyde dehydrogenase 2835003 4077603 TM1040_2692 Ruegeria sp. TM1040 succinate semialdehyde dehydrogenase YP_614686.1 2833528 R 292414 CDS YP_614687.1 99082533 4077604 complement(2835087..2835566) 1 NC_008044.1 PFAM: regulatory proteins, AsnC/Lrp: (8.7e-19); KEGG: sil:SPO1138 transcriptional regulator, AsnC family, ev=1e-73, 85% identity; AsnC family transcriptional regulator 2835566 4077604 TM1040_2693 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_614687.1 2835087 R 292414 CDS YP_614688.1 99082534 4077605 complement(2835568..2836560) 1 NC_008044.1 PFAM: Succinylglutamate desuccinylase/aspartoacylase: (3.8e-92); KEGG: sil:SPO1139 succinylglutamate desuccinylase/aspartoacylase family protein, ev=1e-161, 84% identity; succinylglutamate desuccinylase/aspartoacylase 2836560 4077605 TM1040_2694 Ruegeria sp. TM1040 succinylglutamate desuccinylase/aspartoacylase YP_614688.1 2835568 R 292414 CDS YP_614689.1 99082535 4077002 complement(2836696..2837706) 1 NC_008044.1 PFAM: helix-turn-helix, AraC type: (2.4e-08); KEGG: sil:SPO3397 transcriptional regulator, AraC family, ev=4e-29, 28% identity; AraC family transcriptional regulator 2837706 4077002 TM1040_2695 Ruegeria sp. TM1040 AraC family transcriptional regulator YP_614689.1 2836696 R 292414 CDS YP_614690.1 99082536 4077003 2837919..2838587 1 NC_008044.1 PFAM: CHAP: (4.9e-07); KEGG: eli:ELI_01090 hypothetical protein, ev=3e-29, 44% identity; hypothetical protein 2838587 4077003 TM1040_2696 Ruegeria sp. TM1040 hypothetical protein YP_614690.1 2837919 D 292414 CDS YP_614691.1 99082537 4077004 complement(2838703..2839605) 1 NC_008044.1 PFAM: PRC-barrel: (0.0002); KEGG: jan:Jann_2065 PRC protein, ev=1e-41, 34% identity; PRC-barrel protein 2839605 4077004 TM1040_2697 Ruegeria sp. TM1040 PRC-barrel protein YP_614691.1 2838703 R 292414 CDS YP_614692.1 99082538 4077005 complement(2839728..2840570) 1 NC_008044.1 PFAM: regulatory proteins, IclR: (6.2e-41); KEGG: jan:Jann_3261 transcriptional regulator, IclR family, ev=1e-102, 68% identity; IclR family transcriptional regulator 2840570 4077005 TM1040_2698 Ruegeria sp. TM1040 IclR family transcriptional regulator YP_614692.1 2839728 R 292414 CDS YP_614693.1 99082539 4077006 2840738..2841928 1 NC_008044.1 PFAM: aminotransferase, class V: (3.4e-14); KEGG: sil:SPOA0144 serine--glyoxylate transaminase, , ev=0.0, 87% identity; serine-glyoxylate aminotransferase 2841928 4077006 TM1040_2699 Ruegeria sp. TM1040 serine-glyoxylate aminotransferase YP_614693.1 2840738 D 292414 CDS YP_614694.1 99082540 4077007 2841928..2842893 1 NC_008044.1 PFAM: Pyridoxal-5'-phosphate-dependent enzyme, beta subunit: (2.6e-56); KEGG: sil:SPOA0145 pyridoxal-phosphate dependent enzyme, ev=1e-162, 88% identity; pyridoxal-5'-phosphate-dependent protein subunit beta 2842893 4077007 TM1040_2700 Ruegeria sp. TM1040 pyridoxal-5'-phosphate-dependent protein subunit beta YP_614694.1 2841928 D 292414 CDS YP_614695.1 99082541 4077008 2842959..2844122 1 NC_008044.1 PFAM: alanine racemase-like: (1.7e-08); KEGG: sil:SPOA0146 threonine aldolase, low-specificity, ev=0.0, 83% identity; D-3-hydroxyaspartate aldolase 2844122 4077008 TM1040_2701 Ruegeria sp. TM1040 D-3-hydroxyaspartate aldolase YP_614695.1 2842959 D 292414 CDS YP_614696.1 99082542 4077009 2844218..2845183 1 NC_008044.1 PFAM: ornithine cyclodeaminase/mu-crystallin: (1.3e-43); KEGG: jan:Jann_2605 ornithine cyclodeaminase, ev=1e-153, 85% identity; ornithine cyclodeaminase 2845183 4077009 TM1040_2702 Ruegeria sp. TM1040 ornithine cyclodeaminase YP_614696.1 2844218 D 292414 CDS YP_614697.1 99082543 4077010 complement(2845236..2846147) 1 NC_008044.1 PFAM: regulatory protein, LysR: (1.2e-20) LysR, substrate-binding: (9e-45); KEGG: sme:SMb21291 transcriptional regulator, LysR family protein, ev=1e-104, 59% identity; LysR family transcriptional regulator 2846147 4077010 TM1040_2703 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_614697.1 2845236 R 292414 CDS YP_614698.1 99082544 4077011 2846327..2847790 1 NC_008044.1 PFAM: ferredoxin: (2e-05) molybdopterin dehydrogenase, FAD-binding: (3.5e-70) [2Fe-2S]-binding: (1.4e-44) CO dehydrogenase flavoprotein-like: (4.6e-28); KEGG: sme:SMb21286 probable xanthine dehydrogenase protein, ev=1e-164, 59% identity; molybdopterin dehydrogenase 2847790 4077011 TM1040_2704 Ruegeria sp. TM1040 molybdopterin dehydrogenase YP_614698.1 2846327 D 292414 CDS YP_614699.1 99082545 4077012 2847805..2850138 1 NC_008044.1 PFAM: aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead: (3.4e-39) aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding: (4.9e-203); KEGG: sme:SMb21287 xanthine dehydrogenase protein, ev=0.0, 73% identity; xanthine oxidase/xanthine dehydrogenase, molybdenum binding subunit apoprotein 2850138 4077012 TM1040_2705 Ruegeria sp. TM1040 xanthine oxidase/xanthine dehydrogenase, molybdenum binding subunit apoprotein YP_614699.1 2847805 D 292414 CDS YP_614700.1 99082546 4077013 2850143..2850994 1 NC_008044.1 PFAM: protein of unknown function DUF182: (5.2e-12); KEGG: mlo:mlr5136 xanthine dehydrogenase accessory factor, ev=4e-64, 46% identity; hypothetical protein 2850994 4077013 TM1040_2706 Ruegeria sp. TM1040 hypothetical protein YP_614700.1 2850143 D 292414 CDS YP_614701.1 99082547 4077014 2851063..2852646 1 NC_008044.1 PFAM: Xanthine/uracil/vitamin C permease: (0.00031); KEGG: bha:BH1513 hypothetical protein, ev=1e-100, 41% identity; xanthine/uracil/vitamin C permease 2852646 4077014 TM1040_2707 Ruegeria sp. TM1040 xanthine/uracil/vitamin C permease YP_614701.1 2851063 D 292414 CDS YP_614702.1 99082548 4077015 complement(2852734..2853201) 1 NC_008044.1 PFAM: regulatory proteins, AsnC/Lrp: (4.2e-24); KEGG: atc:AGR_L_238 hypothetical transcriptional regulator Y4TD, ev=6e-39, 49% identity; AsnC family transcriptional regulator 2853201 4077015 TM1040_2708 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_614702.1 2852734 R 292414 CDS YP_614703.1 99082549 4077016 2853377..2854435 1 NC_008044.1 PFAM: Pyridoxal-5'-phosphate-dependent enzyme, beta subunit: (3.4e-26); KEGG: jan:Jann_1828 pyridoxal-5'-phosphate-dependent enzyme, beta subunit, ev=1e-97, 57% identity; pyridoxal-5'-phosphate-dependent protein subunit beta 2854435 4077016 TM1040_2709 Ruegeria sp. TM1040 pyridoxal-5'-phosphate-dependent protein subunit beta YP_614703.1 2853377 D 292414 CDS YP_614704.1 99082550 4077017 2854428..2855591 1 NC_008044.1 PFAM: peptidase M24: (3.3e-12); KEGG: jan:Jann_1829 peptidase M24, ev=1e-107, 53% identity; peptidase M24 2855591 4077017 TM1040_2710 Ruegeria sp. TM1040 peptidase M24 YP_614704.1 2854428 D 292414 CDS YP_614705.1 99082551 4077018 2855588..2856346 1 NC_008044.1 PFAM: Asp/Glu racemase: (1.6e-07); KEGG: sil:SPO2450 Asp/Glu/Hydantoin racemase family protein, ev=2e-67, 54% identity; Asp/Glu racemase 2856346 4077018 TM1040_2711 Ruegeria sp. TM1040 Asp/Glu racemase YP_614705.1 2855588 D 292414 CDS YP_614706.1 99082552 4077019 complement(2856397..2857500) 1 NC_008044.1 PFAM: peptidase M24: (1.1e-46); KEGG: jan:Jann_2048 peptidase M24, ev=1e-122, 61% identity; peptidase M24 2857500 4077019 TM1040_2712 Ruegeria sp. TM1040 peptidase M24 YP_614706.1 2856397 R 292414 CDS YP_614707.1 99082553 4077020 complement(2857581..2859170) 1 NC_008044.1 PFAM: extracellular solute-binding protein, family 5: (9.9e-62); KEGG: jan:Jann_2047 extracellular solute-binding protein, family 5, ev=0.0, 75% identity; extracellular solute-binding protein 2859170 4077020 TM1040_2713 Ruegeria sp. TM1040 extracellular solute-binding protein YP_614707.1 2857581 R 292414 CDS YP_614708.1 99082554 4077021 complement(2859216..2859830) 1 NC_008044.1 PFAM: helix-turn-helix motif: (8.6e-16) Cupin 2, conserved barrel: (1.6e-17); KEGG: jan:Jann_2046 transcriptional regulator, XRE family with cupin sensor domain, ev=1e-74, 66% identity; XRE family transcriptional regulator 2859830 4077021 TM1040_2714 Ruegeria sp. TM1040 XRE family transcriptional regulator YP_614708.1 2859216 R 292414 CDS YP_614709.1 99082555 4077022 2859969..2861120 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (4.4e-47); KEGG: jan:Jann_2045 binding-protein-dependent transport systems inner membrane component, ev=1e-151, 80% identity; binding-protein-dependent transport system inner membrane protein 2861120 4077022 TM1040_2715 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_614709.1 2859969 D 292414 CDS YP_614710.1 99082556 4077023 2861130..2862035 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1e-46); KEGG: jan:Jann_2044 binding-protein-dependent transport systems inner membrane component, ev=1e-132, 78% identity; binding-protein-dependent transport system inner membrane protein 2862035 4077023 TM1040_2716 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_614710.1 2861130 D 292414 CDS YP_614711.1 99082557 4077024 2862032..2862871 1 NC_008044.1 PFAM: ABC transporter related: (2e-52); SMART: ATPase: (9.8e-16); KEGG: jan:Jann_2043 ABC transporter related, ev=1e-107, 72% identity; ABC transporter 2862871 4077024 TM1040_2717 Ruegeria sp. TM1040 ABC transporter YP_614711.1 2862032 D 292414 CDS YP_614712.1 99082558 4077025 2862868..2863617 1 NC_008044.1 PFAM: ABC transporter related: (8.3e-61); SMART: ATPase: (1.5e-16); KEGG: jan:Jann_2042 ABC transporter related, ev=1e-103, 77% identity; ABC transporter 2863617 4077025 TM1040_2718 Ruegeria sp. TM1040 ABC transporter YP_614712.1 2862868 D 292414 CDS YP_614713.1 99082559 4077026 2863621..2864109 1 NC_008044.1 KEGG: jan:Jann_2041 hypothetical protein, ev=3e-35, 46% identity; hypothetical protein 2864109 4077026 TM1040_2719 Ruegeria sp. TM1040 hypothetical protein YP_614713.1 2863621 D 292414 CDS YP_614714.1 99082560 4077027 2864282..2864500 1 NC_008044.1 PFAM: protein of unknown function DUF1328: (7.8e-20); KEGG: jan:Jann_3570 protein of unknown function DUF1328, ev=3e-14, 66% identity; hypothetical protein 2864500 4077027 TM1040_2720 Ruegeria sp. TM1040 hypothetical protein YP_614714.1 2864282 D 292414 CDS YP_614715.1 99082561 4077028 2864555..2865052 1 NC_008044.1 PFAM: Ferritin and Dps: (1.2e-17); KEGG: rru:Rru_A0333 ferritin and Dps, ev=8e-31, 44% identity; ferritin 2865052 4077028 TM1040_2721 Ruegeria sp. TM1040 ferritin YP_614715.1 2864555 D 292414 CDS YP_614716.1 99082562 4077029 complement(2865208..2866029) 1 NC_008044.1 in Caulobacter crescentus, CC3477 is differentially expressed in minimal salts media with glucose as compared to complex media; two-component response regulator 2866029 4077029 TM1040_2722 Ruegeria sp. TM1040 two-component response regulator YP_614716.1 2865208 R 292414 CDS YP_614717.1 99082563 4077030 2866340..2866897 1 NC_008044.1 Bacteria have multiple sigma factors which are active under specific conditions; the sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; RNA polymerase sigma factor 2866897 4077030 TM1040_2723 Ruegeria sp. TM1040 RNA polymerase sigma factor YP_614717.1 2866340 D 292414 CDS YP_614718.1 99082564 4077031 2866903..2868744 1 NC_008044.1 PFAM: histidine kinase, dimerisation/phosphoacceptor: (1.1e-21); KEGG: jan:Jann_3564 signal transduction histidine kinase, ev=4e-82, 33% identity; signal transduction histidine kinase 2868744 4077031 TM1040_2724 Ruegeria sp. TM1040 signal transduction histidine kinase YP_614718.1 2866903 D 292414 CDS YP_614719.1 99082565 4077032 complement(2868869..2869456) 1 NC_008044.1 PFAM: Exopolysaccharide synthesis, ExoD: (6.6e-19); KEGG: jan:Jann_0449 exopolysaccharide synthesis, ExoD, ev=1e-29, 40% identity; exopolysaccharide synthesis, ExoD 2869456 4077032 TM1040_2725 Ruegeria sp. TM1040 exopolysaccharide synthesis, ExoD YP_614719.1 2868869 R 292414 CDS YP_614720.1 99082566 4077033 2869670..2870158 1 NC_008044.1 KEGG: rsp:RSP_1276 hypothetical protein, ev=2e-18, 37% identity; hypothetical protein 2870158 4077033 TM1040_2726 Ruegeria sp. TM1040 hypothetical protein YP_614720.1 2869670 D 292414 CDS YP_614721.1 99082567 4077034 complement(2870342..2871370) 1 NC_008044.1 PFAM: ammonia monooxygenase: (6.8e-17); KEGG: atc:AGR_C_342 hypothetical protein YhjN, ev=6e-49, 34% identity; ammonia monooxygenase 2871370 4077034 TM1040_2727 Ruegeria sp. TM1040 ammonia monooxygenase YP_614721.1 2870342 R 292414 CDS YP_614722.1 99082568 4077035 complement(2871357..2872124) 1 NC_008044.1 PFAM: Citrate synthase: (1.8e-07); KEGG: reu:Reut_B4959 citrate synthase, ev=3e-90, 65% identity; citrate synthase 2872124 4077035 TM1040_2728 Ruegeria sp. TM1040 citrate synthase YP_614722.1 2871357 R 292414 CDS YP_614723.1 99082569 4077036 complement(2872121..2873308) 1 NC_008044.1 PFAM: L-carnitine dehydratase/bile acid-inducible protein F: (2.3e-57); KEGG: jan:Jann_3486 L-carnitine dehydratase/bile acid-inducible protein F, ev=1e-134, 62% identity; L-carnitine dehydratase/bile acid-inducible protein F 2873308 4077036 TM1040_2729 Ruegeria sp. TM1040 L-carnitine dehydratase/bile acid-inducible protein F YP_614723.1 2872121 R 292414 CDS YP_614724.1 99082570 4077037 complement(2873298..2874818) 1 NC_008044.1 PFAM: protein of unknown function DUF112, transmembrane: (1.9e-152); KEGG: sil:SPO0184 membrane protein, , ev=0.0, 85% identity; hypothetical protein 2874818 4077037 TM1040_2730 Ruegeria sp. TM1040 hypothetical protein YP_614724.1 2873298 R 292414 CDS YP_614725.1 99082571 4077038 complement(2874831..2875316) 1 NC_008044.1 KEGG: jan:Jann_3488 hypothetical protein, ev=2e-58, 70% identity; hypothetical protein 2875316 4077038 TM1040_2731 Ruegeria sp. TM1040 hypothetical protein YP_614725.1 2874831 R 292414 CDS YP_614726.1 99082572 4077039 complement(2875403..2876383) 1 NC_008044.1 PFAM: Uncharacterized protein UPF0065: (1.4e-09); KEGG: sil:SPO0186 bordetella uptake gene family protein, ev=1e-145, 78% identity; hypothetical protein 2876383 4077039 TM1040_2732 Ruegeria sp. TM1040 hypothetical protein YP_614726.1 2875403 R 292414 CDS YP_614727.1 99082573 4077040 2876423..2877151 1 NC_008044.1 PFAM: response regulator receiver: (1e-22) transcriptional regulatory protein-like: (7.6e-17); KEGG: sil:SPO0187 DNA-binding response regulator, ev=2e-81, 69% identity; two component transcriptional regulator 2877151 4077040 TM1040_2733 Ruegeria sp. TM1040 two component transcriptional regulator YP_614727.1 2876423 D 292414 CDS YP_614728.1 99082574 4077606 2877148..2878533 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (7.6e-33) histidine kinase, HAMP region: (4.3e-07) histidine kinase A-like: (5.8e-06) Two-component sensor kinase-like: (1.6e-31); KEGG: sil:SPO0188 sensor histidine kinase, ev=1e-132, 55% identity; sensor signal transduction histidine kinase 2878533 4077606 TM1040_2734 Ruegeria sp. TM1040 sensor signal transduction histidine kinase YP_614728.1 2877148 D 292414 CDS YP_614729.1 99082575 4077607 2878629..2879540 1 NC_008044.1 KEGG: sil:SPO0189 iron(III) transport system substrate-binding protein, ev=3e-84, 49% identity; iron(III) transport system substrate-binding protein 2879540 4077607 TM1040_2735 Ruegeria sp. TM1040 iron(III) transport system substrate-binding protein YP_614729.1 2878629 D 292414 CDS YP_614730.1 99082576 4077608 complement(2879545..2881929) 1 NC_008044.1 KEGG: sil:SPOA0319 transketolase, , ev=0.0, 80% identity; transketolase 2881929 4077608 TM1040_2736 Ruegeria sp. TM1040 transketolase YP_614730.1 2879545 R 292414 CDS YP_614731.1 99082577 4077609 complement(2881941..2883143) 1 NC_008044.1 catalyzes the formation of methanethiol and 2-ocobutanoate from L-methionine; methionine gamma-lyase 2883143 4077609 TM1040_2737 Ruegeria sp. TM1040 methionine gamma-lyase YP_614731.1 2881941 R 292414 CDS YP_614732.1 99082578 4077610 2883257..2883715 1 NC_008044.1 PFAM: regulatory proteins, AsnC/Lrp: (1.9e-30); KEGG: sil:SPOA0317 transcriptional regulator, AsnC family, ev=3e-66, 81% identity; AsnC family transcriptional regulator 2883715 4077610 TM1040_2738 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_614732.1 2883257 D 292414 CDS YP_614733.1 99082579 4077611 complement(2883772..2885655) 1 NC_008044.1 PFAM: glycoside hydrolase, family 20: (6.8e-138); KEGG: atc:AGR_C_4704 beta-N-acetylhexosaminidase, ev=1e-159, 47% identity; beta-N-acetylhexosaminidase 2885655 4077611 TM1040_2739 Ruegeria sp. TM1040 beta-N-acetylhexosaminidase YP_614733.1 2883772 R 292414 CDS YP_614734.1 99082580 4077612 complement(2885691..2886146) 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (5.2e-06); KEGG: bcl:ABC0535 hypothetical protein, ev=8e-41, 52% identity; N-acetyltransferase GCN5 2886146 4077612 TM1040_2740 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_614734.1 2885691 R 292414 CDS YP_614735.1 99082581 4077613 complement(2886139..2887068) 1 NC_008044.1 PFAM: ABC transporter related: (1.9e-48) Oligopeptide/dipeptide ABC transporter-like: (0.00011); SMART: ATPase: (1e-15); KEGG: vvy:VVA0003 ABC-type oligopeptide transport system, ATPase component, ev=2e-80, 52% identity; ABC transporter 2887068 4077613 TM1040_2741 Ruegeria sp. TM1040 ABC transporter YP_614735.1 2886139 R 292414 CDS YP_614736.1 99082582 4077614 complement(2887058..2887870) 1 NC_008044.1 PFAM: ABC transporter related: (5.5e-52); SMART: ATPase: (1.7e-18); KEGG: vfi:VFA0200 oligosaccharide transport ATP-binding protein, ev=1e-84, 59% identity; ABC transporter 2887870 4077614 TM1040_2742 Ruegeria sp. TM1040 ABC transporter YP_614736.1 2887058 R 292414 CDS YP_614737.1 99082583 4077615 complement(2887867..2888775) 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (8.9e-28); KEGG: ret:RHE_PE00330 peptide ABC transporter, permease protein, ev=1e-106, 63% identity; binding-protein-dependent transport system inner membrane protein 2888775 4077615 TM1040_2743 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_614737.1 2887867 R 292414 CDS YP_614738.1 99082584 4077616 complement(2888775..2889809) 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (2.9e-46); KEGG: ret:RHE_PE00331 peptide ABC transporter, permease protein, ev=1e-107, 58% identity; binding-protein-dependent transport system inner membrane protein 2889809 4077616 TM1040_2744 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_614738.1 2888775 R 292414 CDS YP_614739.1 99082585 4077617 complement(2889841..2891496) 1 NC_008044.1 PFAM: extracellular solute-binding protein, family 5: (5.9e-63); KEGG: ret:RHE_PE00332 peptide ABC transporter, substrate-binding protein, ev=1e-166, 51% identity; extracellular solute-binding protein 2891496 4077617 TM1040_2745 Ruegeria sp. TM1040 extracellular solute-binding protein YP_614739.1 2889841 R 292414 CDS YP_614740.1 99082586 4077618 2891848..2895138 1 NC_008044.1 PFAM: response regulator receiver: (1.7e-37) ATP-binding region, ATPase-like: (4.4e-36) histidine kinase, HAMP region: (1.8e-16) histidine kinase A-like: (6.4e-20); KEGG: vpa:VP2478 sensory box sensor histidine kinase/response regulator, ev=1e-157, 32% identity; multi-sensor hybrid histidine kinase 2895138 4077618 TM1040_2746 Ruegeria sp. TM1040 multi-sensor hybrid histidine kinase YP_614740.1 2891848 D 292414 CDS YP_614741.1 99082587 4077619 complement(2895144..2896046) 1 NC_008044.1 PFAM: helix-turn-helix protein RpiR: (1e-13) sugar isomerase (SIS): (1.2e-12); KEGG: bja:bll0307 transcriptional regulatory protein, ev=3e-48, 41% identity; RpiR family transcriptional regulator 2896046 4077619 TM1040_2747 Ruegeria sp. TM1040 RpiR family transcriptional regulator YP_614741.1 2895144 R 292414 CDS YP_614742.1 99082588 4077620 2896222..2896743 1 NC_008044.1 PFAM: Tripartite ATP-independent periplasmic transporter, DctQ component: (5.3e-12); KEGG: sme:SMb20296 permease protein, ev=4e-12, 27% identity; tripartite ATP-independent periplasmic transporter DctQ 2896743 4077620 TM1040_2748 Ruegeria sp. TM1040 tripartite ATP-independent periplasmic transporter DctQ YP_614742.1 2896222 D 292414 CDS YP_614743.1 99082589 4077621 2896740..2898026 1 NC_008044.1 TIGRFAM: TRAP dicarboxylate transporter- DctM subunit: (1.1e-133); PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit: (3.6e-131); KEGG: bcl:ABC4044 TRAP-type transport system permease large protein, ev=3e-91, 42% identity; TRAP dicarboxylate transporter- DctM subunit 2898026 4077621 TM1040_2749 Ruegeria sp. TM1040 TRAP dicarboxylate transporter- DctM subunit YP_614743.1 2896740 D 292414 CDS YP_614744.1 99082590 4077622 2898076..2899119 1 NC_008044.1 TIGRFAM: TRAP dicarboxylate transporter, DctP subunit: (9e-51); PFAM: TRAP dicarboxylate transporter- DctP subunit: (3.4e-69); KEGG: mag:amb1225 TRAP-type C4-dicarboxylate transport system, ev=4e-52, 36% identity; TRAP dicarboxylate transporter subunit DctP 2899119 4077622 TM1040_2750 Ruegeria sp. TM1040 TRAP dicarboxylate transporter subunit DctP YP_614744.1 2898076 D 292414 CDS YP_614745.1 99082591 4077623 2899183..2900649 1 NC_008044.1 PFAM: Uncharacterised conserved protein UCP012702: (9.8e-157) MlrC-like: (1.5e-89); KEGG: bms:BRA0752 hypothetical protein, ev=1e-159, 56% identity; hypothetical protein 2900649 4077623 TM1040_2751 Ruegeria sp. TM1040 hypothetical protein YP_614745.1 2899183 D 292414 CDS YP_614746.1 99082592 4077624 2900649..2901704 1 NC_008044.1 PFAM: alanine racemase-like: (5.8e-19); KEGG: sme:SMb21134 amino acid processing enzyme, similar to low specificity D-threonine aldolase protein, ev=1e-128, 66% identity; alanine racemase 2901704 4077624 TM1040_2752 Ruegeria sp. TM1040 alanine racemase YP_614746.1 2900649 D 292414 CDS YP_614747.1 99082593 4077625 2901701..2902627 1 NC_008044.1 PFAM: PfkB: (3e-47); KEGG: bur:Bcep18194_A5081 sugar kinase, ribokinase family, ev=3e-75, 50% identity; PfkB protein 2902627 4077625 TM1040_2753 Ruegeria sp. TM1040 PfkB protein YP_614747.1 2901701 D 292414 CDS YP_614748.1 99082594 4077626 2902654..2903043 1 NC_008044.1 PFAM: Endoribonuclease L-PSP: (4.9e-36); KEGG: sme:SMb21139 protein, similar to translation initiation inhibitors, ev=4e-35, 56% identity; endoribonuclease L-PSP 2903043 4077626 TM1040_2754 Ruegeria sp. TM1040 endoribonuclease L-PSP YP_614748.1 2902654 D 292414 CDS YP_614749.1 99082595 4077627 complement(2903128..2904465) 1 NC_008044.1 KEGG: sil:SPO3812 carboxyl-terminal protease family protein, ev=0.0, 83% identity; TIGRFAM: carboxyl-terminal protease: (5.8e-93); PFAM: PDZ/DHR/GLGF: (1.7e-10) peptidase S41: (1e-73); carboxyl-terminal protease 2904465 4077627 TM1040_2755 Ruegeria sp. TM1040 carboxyl-terminal protease YP_614749.1 2903128 R 292414 CDS YP_614750.1 99082596 4077628 complement(2904473..2905576) 1 NC_008044.1 PFAM: peptidase M23B: (0.00023); KEGG: sil:SPO3811 hypothetical protein, ev=1e-132, 70% identity; peptidase M23B 2905576 4077628 TM1040_2756 Ruegeria sp. TM1040 peptidase M23B YP_614750.1 2904473 R 292414 CDS YP_614751.1 99082597 4077629 complement(2905615..2907135) 1 NC_008044.1 catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate; phosphoglyceromutase 2907135 4077629 TM1040_2757 Ruegeria sp. TM1040 phosphoglyceromutase YP_614751.1 2905615 R 292414 CDS YP_614752.1 99082598 4077630 2907361..2907822 1 NC_008044.1 PFAM: protein of unknown function DUF1203: (1.3e-72); KEGG: sil:SPO3849 hypothetical protein, ev=3e-55, 66% identity; hypothetical protein 2907822 4077630 TM1040_2758 Ruegeria sp. TM1040 hypothetical protein YP_614752.1 2907361 D 292414 CDS YP_614753.1 99082599 4077631 complement(2907826..2908299) 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (8.4e-09); KEGG: gvi:glr3142 acetyltransferase, ev=6e-24, 39% identity; acetyltransferase 2908299 4077631 TM1040_2759 Ruegeria sp. TM1040 acetyltransferase YP_614753.1 2907826 R 292414 CDS YP_614754.1 99082600 4077632 complement(2908299..2909255) 1 NC_008044.1 PFAM: ABC transporter related: (1.8e-54); SMART: ATPase: (7e-14); KEGG: sil:SPO3847 ABC transporter, ATP-binding protein, ev=1e-146, 84% identity; ABC transporter 2909255 4077632 TM1040_2760 Ruegeria sp. TM1040 ABC transporter YP_614754.1 2908299 R 292414 CDS YP_614755.1 99082601 4077633 2909299..2909481 1 NC_008044.1 KEGG: sil:SPO3846 hypothetical protein, ev=2e-21, 86% identity; hypothetical protein 2909481 4077633 TM1040_2761 Ruegeria sp. TM1040 hypothetical protein YP_614755.1 2909299 D 292414 CDS YP_614756.1 99082602 4077634 2909535..2910020 1 NC_008044.1 KEGG: sil:SPO0221 hypothetical protein, ev=5e-67, 78% identity; hypothetical protein 2910020 4077634 TM1040_2762 Ruegeria sp. TM1040 hypothetical protein YP_614756.1 2909535 D 292414 CDS YP_614757.1 99082603 4077635 complement(2910088..2910621) 1 NC_008044.1 KEGG: jan:Jann_1682 hypothetical protein, ev=1e-08, 26% identity; hypothetical protein 2910621 4077635 TM1040_2763 Ruegeria sp. TM1040 hypothetical protein YP_614757.1 2910088 R 292414 CDS YP_614758.1 99082604 4077636 2910652..2913459 1 NC_008044.1 has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair; DNA polymerase I 2913459 4077636 TM1040_2764 Ruegeria sp. TM1040 DNA polymerase I YP_614758.1 2910652 D 292414 CDS YP_614759.1 99082605 4077637 complement(2913628..2914395) 1 NC_008044.1 PFAM: Xylose isomerase-like TIM barrel: (6.4e-35); KEGG: reu:Reut_A1423 hydroxypyruvate isomerase, ev=2e-52, 44% identity; hydroxypyruvate isomerase 2914395 4077637 TM1040_2765 Ruegeria sp. TM1040 hydroxypyruvate isomerase YP_614759.1 2913628 R 292414 CDS YP_614760.1 99082606 4077638 complement(2914614..2915207) 1 NC_008044.1 PFAM: protein of unknown function DUF1285: (3.1e-89); KEGG: sil:SPO0140 hypothetical protein, ev=1e-70, 67% identity; hypothetical protein 2915207 4077638 TM1040_2766 Ruegeria sp. TM1040 hypothetical protein YP_614760.1 2914614 R 292414 CDS YP_614761.1 99082607 4077639 2915260..2916267 1 NC_008044.1 PFAM: ATPase associated with various cellular activities, AAA_3: (1.6e-74) ATPase associated with various cellular activities, AAA_5: (1.1e-08); KEGG: sil:SPO0139 ATPase, MoxR family, ev=1e-152, 81% identity; ATPase 2916267 4077639 TM1040_2767 Ruegeria sp. TM1040 ATPase YP_614761.1 2915260 D 292414 CDS YP_614762.1 99082608 4077640 2916264..2917172 1 NC_008044.1 KEGG: sil:SPO0138 hypothetical protein, ev=1e-114, 72% identity; hypothetical protein 2917172 4077640 TM1040_2768 Ruegeria sp. TM1040 hypothetical protein YP_614762.1 2916264 D 292414 CDS YP_614763.1 99082609 4077641 2917169..2919958 1 NC_008044.1 TIGRFAM: Double-transmembrane region-like: (7.7e-15); KEGG: sil:SPO0137 hypothetical protein, ev=0.0, 62% identity; double-transmembrane region-like protein 2919958 4077641 TM1040_2769 Ruegeria sp. TM1040 double-transmembrane region-like protein YP_614763.1 2917169 D 292414 CDS YP_614764.1 99082610 4077642 2920004..2922046 1 NC_008044.1 KEGG: sil:SPO0136 hypothetical protein, ev=0.0, 69% identity; hypothetical protein 2922046 4077642 TM1040_2770 Ruegeria sp. TM1040 hypothetical protein YP_614764.1 2920004 D 292414 CDS YP_614765.1 99082611 4077643 complement(2922245..2923147) 1 NC_008044.1 KEGG: dar:Daro_4183 hydratase/decarboxylase, ev=6e-48, 41% identity; hydratase/decarboxylase 2923147 4077643 TM1040_2771 Ruegeria sp. TM1040 hydratase/decarboxylase YP_614765.1 2922245 R 292414 CDS YP_614766.1 99082612 4077644 complement(2923147..2925219) 1 NC_008044.1 KEGG: sil:SPO0135 penicillin-binding protein 1C, ev=0.0, 61% identity; TIGRFAM: Penicillin-binding protein 1C: (4.6e-220); PFAM: glycosyl transferase, family 51: (1.1e-62) penicillin-binding protein, transpeptidase: (4.7e-14) Penicillin-binding-like: (5.8e-10); penicillin-binding protein 1C 2925219 4077644 TM1040_2772 Ruegeria sp. TM1040 penicillin-binding protein 1C YP_614766.1 2923147 R 292414 CDS YP_614767.1 99082613 4076541 complement(2925324..2930771) 1 NC_008044.1 PFAM: alpha-2-macroglobulin-like: (1.4e-45) N/apple PAN: (0.0056) alpha-2-macroglobulin-like 2: (6.9e-19); KEGG: sil:SPO0133 PAN domain protein, ev=0.0, 61% identity; alpha-2-macroglobulin-like protein 2930771 4076541 TM1040_2773 Ruegeria sp. TM1040 alpha-2-macroglobulin-like protein YP_614767.1 2925324 R 292414 CDS YP_614768.1 99082614 4076542 2930923..2933208 1 NC_008044.1 PFAM: response regulator receiver: (2.7e-27) ATP-binding region, ATPase-like: (4.6e-40) histidine kinase A-like: (1.3e-25); KEGG: sil:SPO0132 sensor histidine kinase/response regulator, ev=0.0, 65% identity; histidine kinase 2933208 4076542 TM1040_2774 Ruegeria sp. TM1040 histidine kinase YP_614768.1 2930923 D 292414 CDS YP_614769.1 99082615 4076543 complement(2933253..2934611) 1 NC_008044.1 TIGRFAM: Dihydrolipoamide dehydrogenase: (6.2e-170); PFAM: FAD-dependent pyridine nucleotide-disulphide oxidoreductase: (1.5e-29) pyridine nucleotide-disulphide oxidoreductase dimerisation region: (1.7e-30); KEGG: sme:SMc03204 dihydrolipoamide dehydrogenase, ev=1e-166, 66% identity; dihydrolipoamide dehydrogenase 2934611 4076543 TM1040_2775 Ruegeria sp. TM1040 dihydrolipoamide dehydrogenase YP_614769.1 2933253 R 292414 CDS YP_614770.1 99082616 4076544 complement(2934612..2935877) 1 NC_008044.1 PFAM: biotin/lipoyl attachment: (3.1e-22) catalytic domain of components of various dehydrogenase complexes: (8.5e-110) E3 binding: (1.7e-13); KEGG: mlo:mll4471 dihydrolipoamide S-(2-methylpropanoyl)transferase, ev=1e-147, 60% identity; branched-chain alpha-keto acid dehydrogenase E2 component 2935877 4076544 TM1040_2776 Ruegeria sp. TM1040 branched-chain alpha-keto acid dehydrogenase E2 component YP_614770.1 2934612 R 292414 CDS YP_614771.1 99082617 4076545 complement(2935882..2936895) 1 NC_008044.1 PFAM: Transketolase, central region: (7.2e-78) Transketolase-like: (4.4e-57); KEGG: mlo:mll4472 2-oxoisovalerate dehydrogenase (beta subunit), ev=1e-162, 80% identity; branched-chain alpha-keto acid dehydrogenase E1 component 2936895 4076545 TM1040_2777 Ruegeria sp. TM1040 branched-chain alpha-keto acid dehydrogenase E1 component YP_614771.1 2935882 R 292414 CDS YP_614772.1 99082618 4076546 complement(2936897..2938138) 1 NC_008044.1 PFAM: dehydrogenase, E1 component: (6.3e-114); KEGG: bme:BMEII0748 2-oxoisovalerate dehydrogenase alpha subunit, ev=0.0, 78% identity; branched-chain alpha-keto acid dehydrogenase E1 component 2938138 4076546 TM1040_2778 Ruegeria sp. TM1040 branched-chain alpha-keto acid dehydrogenase E1 component YP_614772.1 2936897 R 292414 CDS YP_614773.1 99082619 4076547 complement(2938135..2939205) 1 NC_008044.1 PFAM: Glu/Leu/Phe/Val dehydrogenase, C terminal: (1.2e-22) Glu/Leu/Phe/Val dehydrogenase, dimerisation region: (2.8e-42); KEGG: bca:BCE4237 leucine dehydrogenase, ev=8e-85, 45% identity; Glu/Leu/Phe/Val dehydrogenase 2939205 4076547 TM1040_2779 Ruegeria sp. TM1040 Glu/Leu/Phe/Val dehydrogenase YP_614773.1 2938135 R 292414 CDS YP_614774.1 99082620 4076548 2939325..2939792 1 NC_008044.1 PFAM: regulatory proteins, AsnC/Lrp: (1.8e-20); KEGG: sil:SPO0389 transcriptional regulator, AsnC family, ev=2e-33, 46% identity; AsnC family transcriptional regulator 2939792 4076548 TM1040_2780 Ruegeria sp. TM1040 AsnC family transcriptional regulator YP_614774.1 2939325 D 292414 CDS YP_614775.1 99082621 4076549 complement(2939877..2941073) 1 NC_008044.1 PFAM: iron-containing alcohol dehydrogenase: (3.2e-79); KEGG: sil:SPO2609 alcohol dehydrogenase, iron-containing, ev=1e-168, 74% identity; iron-containing alcohol dehydrogenase 2941073 4076549 TM1040_2781 Ruegeria sp. TM1040 iron-containing alcohol dehydrogenase YP_614775.1 2939877 R 292414 CDS YP_614776.1 99082622 4076550 complement(2941116..2942498) 1 NC_008044.1 PFAM: aldehyde dehydrogenase: (5.7e-120); KEGG: sil:SPO2608 aldehyde dehydrogenase, , ev=0.0, 71% identity; aldehyde dehydrogenase 2942498 4076550 TM1040_2782 Ruegeria sp. TM1040 aldehyde dehydrogenase YP_614776.1 2941116 R 292414 CDS YP_614777.1 99082623 4076551 complement(2942601..2943953) 1 NC_008044.1 PFAM: glutamine synthetase, catalytic region: (3.4e-92); KEGG: sil:SPO2607 gamma-glutamylisopropylamide synthetase, , ev=0.0, 71% identity; L-glutamine synthetase 2943953 4076551 TM1040_2783 Ruegeria sp. TM1040 L-glutamine synthetase YP_614777.1 2942601 R 292414 CDS YP_614778.1 99082624 4076552 complement(2944029..2945063) 1 NC_008044.1 TIGRFAM: Twin-arginine translocation pathway signal: (1.3e-05); PFAM: TRAP dicarboxylate transporter- DctP subunit: (4.3e-08); KEGG: sil:SPO2606 bacterial extracellular solute-binding protein, family 7, ev=0.0, 93% identity; twin-arginine translocation pathway signal 2945063 4076552 TM1040_2784 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_614778.1 2944029 R 292414 CDS YP_614779.1 99082625 4076553 complement(2945118..2946437) 1 NC_008044.1 PFAM: TRAP C4-dicarboxylate transport system permease DctM subunit: (3.2e-49); KEGG: sil:SPO2605 TRAP dicarboxylate transporter, DctM subunit, ev=0.0, 82% identity; TRAP dicarboxylate transporter subunit DctM 2946437 4076553 TM1040_2785 Ruegeria sp. TM1040 TRAP dicarboxylate transporter subunit DctM YP_614779.1 2945118 R 292414 CDS YP_614780.1 99082626 4076554 complement(2946434..2947021) 1 NC_008044.1 KEGG: sil:SPO2604 hypothetical protein, ev=1e-54, 57% identity; hypothetical protein 2947021 4076554 TM1040_2786 Ruegeria sp. TM1040 hypothetical protein YP_614780.1 2946434 R 292414 CDS YP_614781.1 99082627 4076555 complement(2947018..2947791) 1 NC_008044.1 PFAM: N-formylglutamate amidohydrolase: (1.8e-60); KEGG: atc:AGR_C_3887 similar to orf3 gene in Methylobacterium extorquens, ev=1e-57, 54% identity; N-formylglutamate amidohydrolase 2947791 4076555 TM1040_2787 Ruegeria sp. TM1040 N-formylglutamate amidohydrolase YP_614781.1 2947018 R 292414 CDS YP_614782.1 99082628 4076556 2947896..2948753 1 NC_008044.1 PFAM: helix-turn-helix protein RpiR: (3.6e-06) sugar isomerase (SIS): (1.5e-13); KEGG: sme:SMc01602 hypothetical protein, ev=4e-76, 51% identity; RpiR family transcriptional regulator 2948753 4076556 TM1040_2788 Ruegeria sp. TM1040 RpiR family transcriptional regulator YP_614782.1 2947896 D 292414 CDS YP_614783.1 99082629 4076557 2948817..2949971 1 NC_008044.1 PFAM: AMP-dependent synthetase and ligase: (1.1e-17); KEGG: rru:Rru_A2517 AMP-dependent synthetase and ligase, ev=3e-39, 36% identity; AMP-dependent synthetase/ligase 2949971 4076557 TM1040_2789 Ruegeria sp. TM1040 AMP-dependent synthetase/ligase YP_614783.1 2948817 D 292414 CDS YP_614784.1 99082630 4076558 2949971..2951074 1 NC_008044.1 PFAM: Thiolase: (1e-21); KEGG: ret:RHE_PF00014 acetyl-CoA acetyltransferase (beta-ketothiolase) protein, ev=1e-60, 41% identity; Acetyl-CoA C-acetyltransferase 2951074 4076558 TM1040_2790 Ruegeria sp. TM1040 Acetyl-CoA C-acetyltransferase YP_614784.1 2949971 D 292414 CDS YP_614785.1 99082631 4076559 complement(2951135..2953351) 1 NC_008044.1 KEGG: dar:Daro_3836 fungal/archaeal/bacterial haem catalase/peroxidase, ev=0.0, 72% identity; TIGRFAM: catalase/peroxidase HPI: (0); PFAM: Haem peroxidase: (1.5e-110); catalase/peroxidase HPI 2953351 4076559 TM1040_2791 Ruegeria sp. TM1040 catalase/peroxidase HPI YP_614785.1 2951135 R 292414 CDS YP_614786.1 99082632 4076560 2953530..2954453 1 NC_008044.1 PFAM: regulatory protein, LysR: (2.6e-20) LysR, substrate-binding: (4.9e-45); KEGG: bja:bll0777 transcriptional regulatory protein, ev=1e-111, 70% identity; LysR family transcriptional regulator 2954453 4076560 TM1040_2792 Ruegeria sp. TM1040 LysR family transcriptional regulator YP_614786.1 2953530 D 292414 CDS YP_614787.1 99082633 4076561 complement(2954463..2955251) 1 NC_008044.1 catalyzes the dehydration of L-carnitinyl-CoA to crotonobetainyl-CoA; carnitinyl-CoA dehydratase 2955251 4076561 TM1040_2793 Ruegeria sp. TM1040 carnitinyl-CoA dehydratase YP_614787.1 2954463 R 292414 CDS YP_614788.1 99082634 4076562 complement(2955248..2957287) 1 NC_008044.1 PFAM: CoA-binding: (1e-08); KEGG: sil:SPOA0287 acyl-CoA synthetase, , ev=0.0, 60% identity; CoA-binding protein 2957287 4076562 TM1040_2794 Ruegeria sp. TM1040 CoA-binding protein YP_614788.1 2955248 R 292414 CDS YP_614789.1 99082635 4076563 complement(2957294..2957608) 1 NC_008044.1 TIGRFAM: SelT/selW/selH selenoprotein: (2e-23); PFAM: Selenoprotein W-related: (2.7e-46); KEGG: sme:SMc00345 selenoprotein W-related protein, ev=2e-29, 65% identity; SelT/selW/selH selenoprotein 2957608 4076563 TM1040_2795 Ruegeria sp. TM1040 SelT/selW/selH selenoprotein YP_614789.1 2957294 R 292414 CDS YP_614790.1 99082636 4076564 complement(2957611..2958810) 1 NC_008044.1 PFAM: acyl-CoA dehydrogenase-like: (2.7e-63) Acyl-CoA dehydrogenase, type 2-like: (5.3e-26); KEGG: mlo:mlr5042 acyl-CoA dehydrogenase, ev=0.0, 84% identity; butyryl-CoA dehydrogenase 2958810 4076564 TM1040_2796 Ruegeria sp. TM1040 butyryl-CoA dehydrogenase YP_614790.1 2957611 R 292414 CDS YP_614791.1 99082637 4076565 2958859..2959806 1 NC_008044.1 PFAM: helix-turn-helix, AraC type: (8.6e-09) ThiJ/PfpI: (2.7e-05); KEGG: sil:SPOA0289 transcriptional regulator, AraC family, ev=5e-91, 60% identity; transcriptional regulator 2959806 4076565 TM1040_2797 Ruegeria sp. TM1040 transcriptional regulator YP_614791.1 2958859 D 292414 CDS YP_614792.1 99082638 4076566 complement(2959852..2960235) 1 NC_008044.1 PFAM: arsenate reductase and related: (8.2e-28); KEGG: jan:Jann_2102 arsenate reductase, ev=7e-33, 56% identity; arsenate reductase 2960235 4076566 TM1040_2798 Ruegeria sp. TM1040 arsenate reductase YP_614792.1 2959852 R 292414 CDS YP_614793.1 99082639 4076567 2960323..2962128 1 NC_008044.1 KEGG: sil:SPO3746 adenine deaminase, ev=0.0, 84% identity; TIGRFAM: adenine deaminase: (4.6e-140); PFAM: amidohydrolase: (4.9e-23); adenine deaminase 2962128 4076567 TM1040_2799 Ruegeria sp. TM1040 adenine deaminase YP_614793.1 2960323 D 292414 CDS YP_614794.1 99082640 4076568 2962121..2963587 1 NC_008044.1 Catalyzes the hydrolysis of AMP to form adenine and ribose 5-phosphate using water as the nucleophile; AMP nucleosidase 2963587 4076568 TM1040_2800 Ruegeria sp. TM1040 AMP nucleosidase YP_614794.1 2962121 D 292414 CDS YP_614795.1 99082641 4076569 2963731..2964024 1 NC_008044.1 PFAM: histone-like DNA-binding protein: (2.6e-25); KEGG: sil:SPO3744 DNA-binding protein HU, ev=1e-39, 91% identity; histone-like DNA-binding protein 2964024 4076569 TM1040_2801 Ruegeria sp. TM1040 histone-like DNA-binding protein YP_614795.1 2963731 D 292414 CDS YP_614796.1 99082642 4076570 2964165..2965082 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (2.8e-11); KEGG: sil:SPO3743 membrane protein, , ev=1e-120, 77% identity; hypothetical protein 2965082 4076570 TM1040_2802 Ruegeria sp. TM1040 hypothetical protein YP_614796.1 2964165 D 292414 CDS YP_614797.1 99082643 4076571 2965204..2965653 1 NC_008044.1 this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form; provides protection against oxidative stress; methionine sulfoxide reductase B 2965653 4076571 TM1040_2803 Ruegeria sp. TM1040 methionine sulfoxide reductase B YP_614797.1 2965204 D 292414 CDS YP_614798.1 99082644 4076572 2965650..2966165 1 NC_008044.1 this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; provides protection against oxidative stress; methionine sulfoxide reductase A 2966165 4076572 TM1040_2804 Ruegeria sp. TM1040 methionine sulfoxide reductase A YP_614798.1 2965650 D 292414 CDS YP_614799.1 99082645 4076573 complement(2966243..2968249) 1 NC_008044.1 PFAM: Hydantoinase/oxoprolinase: (4.2e-58) Hydantoinaseoxoprolinase-like: (1.4e-46); KEGG: sil:SPO3739 hydantoinase/oxoprolinase family protein, ev=0.0, 69% identity; hydantoinase/oxoprolinase 2968249 4076573 TM1040_2805 Ruegeria sp. TM1040 hydantoinase/oxoprolinase YP_614799.1 2966243 R 292414 CDS YP_614800.1 99082646 4076574 complement(2968323..2969366) 1 NC_008044.1 PFAM: 4Fe-4S ferredoxin, iron-sulfur binding: (0.0006) Domain of unknown function DUF1730: (3.2e-37); KEGG: sil:SPO3763 iron-sulfur cluster-binding protein, ev=1e-160, 80% identity; hypothetical protein 2969366 4076574 TM1040_2806 Ruegeria sp. TM1040 hypothetical protein YP_614800.1 2968323 R 292414 CDS YP_614801.1 99082647 4076575 complement(2969475..2970821) 1 NC_008044.1 PFAM: beta-lactamase: (8.8e-24); KEGG: atc:AGR_C_1692 6-aminohexanoate-dimer hydrolase, ev=1e-147, 55% identity; 6-aminohexanoate-dimer hydrolase 2970821 4076575 TM1040_2807 Ruegeria sp. TM1040 6-aminohexanoate-dimer hydrolase YP_614801.1 2969475 R 292414 CDS YP_614802.1 99082648 4076576 complement(2970802..2972226) 1 NC_008044.1 KEGG: atc:AGR_C_1694 hypothetical protein, ev=1e-152, 56% identity; hypothetical protein 2972226 4076576 TM1040_2808 Ruegeria sp. TM1040 hypothetical protein YP_614802.1 2970802 R 292414 CDS YP_614803.1 99082649 4076577 2972936..2973763 1 NC_008044.1 PFAM: diaminopimelate epimerase: (4.4e-36); KEGG: sil:SPO0278 diaminopimelate epimerase, ev=1e-121, 76% identity; diaminopimelate epimerase 2973763 4076577 TM1040_2809 Ruegeria sp. TM1040 diaminopimelate epimerase YP_614803.1 2972936 D 292414 CDS YP_614804.1 99082650 4076578 2973760..2975025 1 NC_008044.1 KEGG: sil:SPO0277 MiaB-like tRNA modifying enzyme, ev=0.0, 84% identity; TIGRFAM: MiaB-like tRNA modifying enzyme: (7.2e-170); PFAM: protein of unknown function UPF0004: (8.9e-21) Radical SAM: (1.1e-29); SMART: Elongator protein 3/MiaB/NifB: (1.7e-54); MiaB-like tRNA modifying enzyme 2975025 4076578 TM1040_2810 Ruegeria sp. TM1040 MiaB-like tRNA modifying enzyme YP_614804.1 2973760 D 292414 CDS YP_614805.1 99082651 4076579 2975043..2975564 1 NC_008044.1 KEGG: ppr:PBPRA2780 hypothetical protein, ev=1e-25, 38% identity; hypothetical protein 2975564 4076579 TM1040_2811 Ruegeria sp. TM1040 hypothetical protein YP_614805.1 2975043 D 292414 CDS YP_614806.1 99082652 4076631 complement(2975706..2976497) 1 NC_008044.1 PFAM: cytochrome c1: (9.4e-109); KEGG: sil:SPO0273 ubiquinol--cytochrome c reductase, cytochrome c1, ev=1e-104, 66% identity; cytochrome c1 2976497 4076631 TM1040_2812 Ruegeria sp. TM1040 cytochrome c1 YP_614806.1 2975706 R 292414 CDS YP_614807.1 99082653 4076632 complement(2976516..2977844) 1 NC_008044.1 PFAM: cytochrome b/b6-like: (7.8e-94); KEGG: sil:SPO0272 ubiquinol--cytochrome c reductase, cytochrome B, ev=0.0, 92% identity; cytochrome b/b6-like protein 2977844 4076632 TM1040_2813 Ruegeria sp. TM1040 cytochrome b/b6-like protein YP_614807.1 2976516 R 292414 CDS YP_614808.1 99082654 4076633 complement(2977860..2978420) 1 NC_008044.1 TIGRFAM: Twin-arginine translocation pathway signal: (3.3e-05) Ubiquinol-cytochrome c reductase, iron-sulfur subunit: (1.4e-97); PFAM: Rieske [2Fe-2S] region: (4e-18); KEGG: sil:SPO0271 ubiquinol-cytochrome c reductase, iron-sulfur subunit, ev=4e-92, 86% identity; ubiquinol-cytochrome c reductase, iron-sulfur subunit 2978420 4076633 TM1040_2814 Ruegeria sp. TM1040 ubiquinol-cytochrome c reductase, iron-sulfur subunit YP_614808.1 2977860 R 292414 CDS YP_614809.1 99082655 4076634 complement(2978645..2979247) 1 NC_008044.1 PFAM: glutathione S-transferase-like: (0.0074); KEGG: sil:SPO0270 glutathione S-transferase family protein, ev=1e-60, 55% identity; glutathione S-transferase 2979247 4076634 TM1040_2815 Ruegeria sp. TM1040 glutathione S-transferase YP_614809.1 2978645 R 292414 CDS YP_614810.1 99082656 4076635 complement(2979365..2980060) 1 NC_008044.1 PFAM: ABC transporter related: (1.9e-59); SMART: ATPase: (7.2e-18); KEGG: rsp:RSP_1393 ABC thiamine transporter, ATPase subunit, ev=3e-71, 60% identity; ABC transporter 2980060 4076635 TM1040_2816 Ruegeria sp. TM1040 ABC transporter YP_614810.1 2979365 R 292414 CDS YP_614811.1 99082657 4076636 complement(2980047..2981618) 1 NC_008044.1 permease; with TbpA and ThiQ functions in transport of thiamine and thiamine pyrophosphate into the cell; repressed in presence of exogenous thiamine; thiamine transporter membrane protein 2981618 thiP 4076636 thiP Ruegeria sp. TM1040 thiamine transporter membrane protein YP_614811.1 2980047 R 292414 CDS YP_614812.1 99082658 4076637 complement(2981594..2982574) 1 NC_008044.1 part of the thiamine and TPP transport system tbpA-thiPQ; thiamine transporter substrate binding subunit 2982574 tbpA 4076637 tbpA Ruegeria sp. TM1040 thiamine transporter substrate binding subunit YP_614812.1 2981594 R 292414 CDS YP_614813.1 99082659 4076638 2983051..2984163 1 NC_008044.1 catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis; chorismate synthase 2984163 4076638 TM1040_2819 Ruegeria sp. TM1040 chorismate synthase YP_614813.1 2983051 D 292414 CDS YP_614814.1 99082660 4076639 2984942..2985931 1 NC_008044.1 PFAM: NAD-dependent epimerase/dehydratase: (2.1e-11) 3-beta hydroxysteroid dehydrogenase/isomerase: (7e-12) dTDP-4-dehydrorhamnose reductase: (5.1e-07) NmrA-like: (0.00092) Male sterility-like: (3e-07); KEGG: sil:SPO3772 NADH ubiquinone oxidoreductase, , ev=1e-137, 74% identity; 3-beta hydroxysteroid dehydrogenase/isomerase 2985931 4076639 TM1040_2820 Ruegeria sp. TM1040 3-beta hydroxysteroid dehydrogenase/isomerase YP_614814.1 2984942 D 292414 CDS YP_614815.1 99082661 4076640 complement(2985990..2986793) 1 NC_008044.1 BacA; phosphatase activity in Escherichia coli not kinase; involved in bacitracin resistance as bacitracin supposedly sequesters UDP disphosphate which reduces the pool of lipid carrier available to the cell; UDP pyrophosphate phosphatase 2986793 4076640 TM1040_2821 Ruegeria sp. TM1040 UDP pyrophosphate phosphatase YP_614815.1 2985990 R 292414 CDS YP_614816.1 99082662 4076641 2987026..2988468 1 NC_008044.1 function undetermined; similar to glutamate synthase beta subunit and related oxidoreductases which transfer electrons from NADPH to an acceptor protein or protein domain; oxidoreductase 2988468 4076641 TM1040_2822 Ruegeria sp. TM1040 oxidoreductase YP_614816.1 2987026 D 292414 CDS YP_614817.1 99082663 4076642 2988543..2993075 1 NC_008044.1 PFAM: glutamine amidotransferase, class-II: (4.8e-211) glutamate synthase, alpha subunit-like: (6.6e-94) ferredoxin-dependent glutamate synthase: (1.2e-219) glutamate synthase: (4.5e-158); KEGG: sil:SPO3768 glutamate synthase, large subunit, ev=0.0, 88% identity; glutamate synthase (NADPH) large subunit 2993075 4076642 TM1040_2823 Ruegeria sp. TM1040 glutamate synthase (NADPH) large subunit YP_614817.1 2988543 D 292414 CDS YP_614818.1 99082664 4076643 2993220..2993963 1 NC_008044.1 TIGRFAM: Monofunctional biosynthetic peptidoglycan transglycosylase: (2.2e-78); PFAM: glycosyl transferase, family 51: (2.8e-66); KEGG: sil:SPO3766 monofunctional biosynthetic peptidoglycan transglycosylase, ev=3e-84, 70% identity; monofunctional biosynthetic peptidoglycan transglycosylase 2993963 4076643 TM1040_2824 Ruegeria sp. TM1040 monofunctional biosynthetic peptidoglycan transglycosylase YP_614818.1 2993220 D 292414 CDS YP_614819.1 99082665 4076644 2994033..2994698 1 NC_008044.1 PFAM: glutathione S-transferase-like: (4.1e-10); KEGG: sil:SPO3764 glutathione S-transferase family protein, ev=1e-110, 85% identity; glutathione S-transferase 2994698 4076644 TM1040_2825 Ruegeria sp. TM1040 glutathione S-transferase YP_614819.1 2994033 D 292414 CDS YP_614820.1 99082666 4076645 complement(2994998..2996482) 1 NC_008044.1 PFAM: HemY-like: (2.7e-22); KEGG: sil:SPO3851 HemY domain protein, ev=0.0, 69% identity; HemY-like protein 2996482 4076645 TM1040_2826 Ruegeria sp. TM1040 HemY-like protein YP_614820.1 2994998 R 292414 CDS YP_614821.1 99082667 4076646 complement(2996493..2997812) 1 NC_008044.1 KEGG: sil:SPO3852 hypothetical protein, ev=1e-87, 44% identity; hypothetical protein 2997812 4076646 TM1040_2827 Ruegeria sp. TM1040 hypothetical protein YP_614821.1 2996493 R 292414 CDS YP_614822.1 99082668 4076647 complement(2997862..2998599) 1 NC_008044.1 PFAM: Uroporphyrinogen III synthase HEM4: (1.6e-07); KEGG: sil:SPO3853 uroporphyrinogen-III synthase, , ev=2e-39, 41% identity; uroporphyrinogen III synthase HEM4 2998599 4076647 TM1040_2828 Ruegeria sp. TM1040 uroporphyrinogen III synthase HEM4 YP_614822.1 2997862 R 292414 CDS YP_614823.1 99082669 4076648 2998674..2999771 1 NC_008044.1 in most organisms, only the N-terminal domain is present in a single polypeptide; in some archaea this domain is fused to a kinase domain; this gene is essential for growth in Escherichia coli and Bacillus subtilis; the secreted glycoprotease from Pasteurella haemolytica showed specificity for O-sialoglycosylated proteins; the Pyrococcus structure shows DNA-binding properties, iron-binding, ATP-binding, and AP endonuclease activity; DNA-binding/iron metalloprotein/AP endonuclease 2999771 4076648 TM1040_2829 Ruegeria sp. TM1040 DNA-binding/iron metalloprotein/AP endonuclease YP_614823.1 2998674 D 292414 CDS YP_614824.1 99082670 4076649 2999768..3000730 1 NC_008044.1 catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate; NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 3000730 gpsA 4076649 gpsA Ruegeria sp. TM1040 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase YP_614824.1 2999768 D 292414 CDS YP_614825.1 99082671 4076650 3000732..3001004 1 NC_008044.1 unknown function; YciI from Haemophilus influenzae presents crystal structure similarity to a muconolactone isomerase, but does not seem to catalyze any of the predicted reactions based on sequence and structure similarity; hypothetical protein 3001004 4076650 TM1040_2831 Ruegeria sp. TM1040 hypothetical protein YP_614825.1 3000732 D 292414 CDS YP_614826.1 99082672 4076651 3001004..3001426 1 NC_008044.1 PFAM: protein of unknown function DUF589: (3.7e-77); KEGG: sil:SPO3857 hypothetical protein, ev=2e-63, 77% identity; hypothetical protein 3001426 4076651 TM1040_2832 Ruegeria sp. TM1040 hypothetical protein YP_614826.1 3001004 D 292414 CDS YP_614827.1 99082673 4076652 3001480..3001875 1 NC_008044.1 KEGG: sil:SPO3858 hypothetical protein, ev=2e-43, 60% identity; hypothetical protein 3001875 4076652 TM1040_2833 Ruegeria sp. TM1040 hypothetical protein YP_614827.1 3001480 D 292414 CDS YP_614828.1 99082674 4076653 complement(3002076..3002417) 1 NC_008044.1 KEGG: sil:SPO3859 hypothetical protein, ev=2e-51, 88% identity; hypothetical protein 3002417 4076653 TM1040_2834 Ruegeria sp. TM1040 hypothetical protein YP_614828.1 3002076 R 292414 CDS YP_614829.1 99082675 4076654 complement(3002642..3004027) 1 NC_008044.1 catalyzes the formation of L-homocysteine from S-adenosyl-L-homocysteine; S-adenosyl-L-homocysteine hydrolase 3004027 4076654 TM1040_2835 Ruegeria sp. TM1040 S-adenosyl-L-homocysteine hydrolase YP_614829.1 3002642 R 292414 CDS YP_614830.1 99082676 4076655 3004294..3004902 1 NC_008044.1 PFAM: metal-dependent phosphohydrolase, HD subdomain: (4.7e-07); KEGG: jan:Jann_4073 metal dependent phosphohydrolase, ev=7e-87, 75% identity; metal dependent phosphohydrolase 3004902 4076655 TM1040_2836 Ruegeria sp. TM1040 metal dependent phosphohydrolase YP_614830.1 3004294 D 292414 CDS YP_614831.1 99082677 4076656 complement(3004905..3006122) 1 NC_008044.1 KEGG: sil:SPO3864 hypothetical protein, ev=1e-142, 63% identity; hypothetical protein 3006122 4076656 TM1040_2837 Ruegeria sp. TM1040 hypothetical protein YP_614831.1 3004905 R 292414 CDS YP_614832.1 99082678 4076657 complement(3006131..3006685) 1 NC_008044.1 PFAM: response regulator receiver: (4e-23); KEGG: sil:SPO3865 photosynthetic apparatus regulatory protein RegA, ev=8e-89, 89% identity; response regulator receiver protein 3006685 4076657 TM1040_2838 Ruegeria sp. TM1040 response regulator receiver protein YP_614832.1 3006131 R 292414 CDS YP_614833.1 99082679 4076658 complement(3006766..3007389) 1 NC_008044.1 PFAM: electron transport protein SCO1/SenC: (5.6e-30); KEGG: sil:SPO3866 regulatory protein SenC, ev=5e-85, 74% identity; electron transport protein SCO1/SenC 3007389 4076658 TM1040_2839 Ruegeria sp. TM1040 electron transport protein SCO1/SenC YP_614833.1 3006766 R 292414 CDS YP_614834.1 99082680 4076659 3007508..3008905 1 NC_008044.1 PFAM: ATP-binding region, ATPase-like: (2.8e-21) histidine kinase A-like: (9.9e-10); KEGG: sil:SPO3867 sensor histidine kinase RegB, ev=0.0, 67% identity; sensor signal transduction histidine kinase 3008905 4076659 TM1040_2840 Ruegeria sp. TM1040 sensor signal transduction histidine kinase YP_614834.1 3007508 D 292414 CDS YP_614835.1 99082681 4076660 3008991..3010541 1 NC_008044.1 KEGG: sil:SPO3868 hypothetical protein, ev=1e-149, 53% identity; hypothetical protein 3010541 4076660 TM1040_2841 Ruegeria sp. TM1040 hypothetical protein YP_614835.1 3008991 D 292414 CDS YP_614836.1 99082682 4076661 3010583..3011059 1 NC_008044.1 PFAM: protein of unknown function UPF0079: (6.3e-37); KEGG: sil:SPO3869 conserved hypothetical protein TIGR00150, ev=4e-41, 52% identity; hypothetical protein 3011059 4076661 TM1040_2842 Ruegeria sp. TM1040 hypothetical protein YP_614836.1 3010583 D 292414 CDS YP_614837.1 99082683 4076662 3011056..3012054 1 NC_008044.1 PFAM: aminoglycoside phosphotransferase: (5.2e-27); KEGG: sil:SPO3870 hypothetical protein, ev=4e-89, 53% identity; aminoglycoside phosphotransferase 3012054 4076662 TM1040_2843 Ruegeria sp. TM1040 aminoglycoside phosphotransferase YP_614837.1 3011056 D 292414 CDS YP_614838.1 99082684 4076663 3012051..3012731 1 NC_008044.1 PFAM: Nucleotidyl transferase: (9.7e-07); KEGG: sil:SPO3871 nucleotidyltransferase family protein, ev=7e-66, 53% identity; nucleotidyl transferase 3012731 4076663 TM1040_2844 Ruegeria sp. TM1040 nucleotidyl transferase YP_614838.1 3012051 D 292414 CDS YP_614839.1 99082685 4076664 3012733..3015666 1 NC_008044.1 KEGG: sil:SPO3872 hypothetical protein, ev=0.0, 65% identity; hypothetical protein 3015666 4076664 TM1040_2845 Ruegeria sp. TM1040 hypothetical protein YP_614839.1 3012733 D 292414 CDS YP_614840.1 99082686 4076665 3015663..3019028 1 NC_008044.1 PFAM: UvrD/REP helicase: (7.6e-49); KEGG: sil:SPO3873 ATP-dependent DNA helicase, UvrD/Rep family, ev=0.0, 68% identity; UvrD/REP helicase 3019028 4076665 TM1040_2846 Ruegeria sp. TM1040 UvrD/REP helicase YP_614840.1 3015663 D 292414 CDS YP_614841.1 99082687 4076666 3019090..3019410 1 NC_008044.1 TIGRFAM: thioredoxin: (9.2e-52); PFAM: glutaredoxin: (0.0003) Thioredoxin domain: (2.8e-47); KEGG: sil:SPO3874 thioredoxin, ev=7e-52, 92% identity; thioredoxin 3019410 4076666 TM1040_2847 Ruegeria sp. TM1040 thioredoxin YP_614841.1 3019090 D 292414 CDS YP_614842.1 99082688 4076667 complement(3019551..3019745) 1 NC_008044.1 PFAM: protein of unknown function DUF1127: (3.6e-11); KEGG: jan:Jann_0963 protein of unknown function DUF1127, ev=3e-06, 64% identity; hypothetical protein 3019745 4076667 TM1040_2848 Ruegeria sp. TM1040 hypothetical protein YP_614842.1 3019551 R 292414 CDS YP_614843.1 99082689 4076668 3019981..3020538 1 NC_008044.1 heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease peptidase subunit 3020538 4076668 TM1040_2849 Ruegeria sp. TM1040 ATP-dependent protease peptidase subunit YP_614843.1 3019981 D 292414 CDS YP_614844.1 99082690 4076669 3020535..3021590 1 NC_008044.1 KEGG: jan:Jann_0186 hypothetical protein, ev=2e-82, 50% identity; hypothetical protein 3021590 4076669 TM1040_2850 Ruegeria sp. TM1040 hypothetical protein YP_614844.1 3020535 D 292414 CDS YP_614845.1 99082691 4076385 3021606..3022916 1 NC_008044.1 heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease ATP-binding subunit HslU 3022916 hslU 4076385 hslU Ruegeria sp. TM1040 ATP-dependent protease ATP-binding subunit HslU YP_614845.1 3021606 D 292414 CDS YP_614846.1 99082692 4076386 3022996..3024117 1 NC_008044.1 PFAM: protein of unknown function DUF900, hydrolase-like: (3.4e-45); KEGG: sil:SPO3883 lipoprotein, , ev=3e-95, 53% identity; hypothetical protein 3024117 4076386 TM1040_2852 Ruegeria sp. TM1040 hypothetical protein YP_614846.1 3022996 D 292414 CDS YP_614847.1 99082693 4076387 complement(3024125..3024727) 1 NC_008044.1 PFAM: Smr protein/MutS2: (4.1e-17); KEGG: sil:SPO3884 smr domain protein, ev=4e-73, 69% identity; Smr protein/MutS2 3024727 4076387 TM1040_2853 Ruegeria sp. TM1040 Smr protein/MutS2 YP_614847.1 3024125 R 292414 CDS YP_614848.1 99082694 4076388 complement(3024727..3025785) 1 NC_008044.1 PFAM: MltA: (2e-74) 3D: (3.7e-32); KEGG: sil:SPO3885 MltA/3D domain protein, ev=1e-138, 69% identity; MltA protein 3025785 4076388 TM1040_2854 Ruegeria sp. TM1040 MltA protein YP_614848.1 3024727 R 292414 CDS YP_614849.1 99082695 4076389 complement(3025782..3026438) 1 NC_008044.1 PFAM: import inner membrane translocase, subunit Tim44: (1.9e-44); KEGG: sil:SPO3886 transporter, Tim44 family, ev=2e-81, 68% identity; import inner membrane translocase subunit Tim44 3026438 4076389 TM1040_2855 Ruegeria sp. TM1040 import inner membrane translocase subunit Tim44 YP_614849.1 3025782 R 292414 CDS YP_614850.1 99082696 4076390 3026553..3027050 1 NC_008044.1 PFAM: FxsA cytoplasmic membrane protein: (7e-33); KEGG: sil:SPO3887 FxsA, ev=8e-60, 72% identity; FxsA cytoplasmic membrane protein 3027050 4076390 TM1040_2856 Ruegeria sp. TM1040 FxsA cytoplasmic membrane protein YP_614850.1 3026553 D 292414 CDS YP_614851.1 99082697 4076391 3027115..3027609 1 NC_008044.1 molecular chaperone that is required for the normal export of envelope proteins out of the cell cytoplasm; in Escherichia coli this proteins forms a homotetramer in the cytoplasm and delivers proteins to be exported to SecA; preprotein translocase subunit SecB 3027609 4076391 TM1040_2857 Ruegeria sp. TM1040 preprotein translocase subunit SecB YP_614851.1 3027115 D 292414 CDS YP_614852.1 99082698 4076392 complement(3027669..3028400) 1 NC_008044.1 KEGG: sil:SPO3889 DNA polymerase III, epsilon subunit, ev=1e-103, 75% identity; TIGRFAM: DNA polymerase III, epsilon subunit: (5.6e-44); PFAM: Exonuclease, RNase T and DNA polymerase III: (6.1e-36); SMART: Exonuclease: (4e-41); DNA polymerase III subunit epsilon 3028400 4076392 TM1040_2858 Ruegeria sp. TM1040 DNA polymerase III subunit epsilon YP_614852.1 3027669 R 292414 CDS YP_614853.1 99082699 4076393 complement(3028393..3028986) 1 NC_008044.1 catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis; dephospho-CoA kinase 3028986 coaE 4076393 coaE Ruegeria sp. TM1040 dephospho-CoA kinase YP_614853.1 3028393 R 292414 CDS YP_614854.1 99082700 4076394 complement(3028986..3029816) 1 NC_008044.1 AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate; shikimate 5-dehydrogenase 3029816 aroE 4076394 aroE Ruegeria sp. TM1040 shikimate 5-dehydrogenase YP_614854.1 3028986 R 292414 CDS YP_614855.1 99082701 4076395 complement(3029813..3030412) 1 NC_008044.1 PFAM: Maf-like protein: (1.3e-25); KEGG: sil:SPO3892 Maf, ev=6e-70, 66% identity; Maf-like protein 3030412 4076395 TM1040_2861 Ruegeria sp. TM1040 Maf-like protein YP_614855.1 3029813 R 292414 CDS YP_614856.1 99082702 4076396 3030831..3031286 1 NC_008044.1 PFAM: conserved hypothetical protein 701: (6.3e-64); KEGG: sil:SPO3893 membrane protein, , ev=2e-62, 74% identity; hypothetical protein 3031286 4076396 TM1040_2862 Ruegeria sp. TM1040 hypothetical protein YP_614856.1 3030831 D 292414 CDS YP_614857.1 99082703 4076397 3031417..3032688 1 NC_008044.1 An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes; transcription termination factor Rho 3032688 rho 4076397 rho Ruegeria sp. TM1040 transcription termination factor Rho YP_614857.1 3031417 D 292414 CDS YP_614858.1 99082704 4076398 3032719..3034005 1 NC_008044.1 in Escherichia coli this protein is involved in the biosynthesis of the hypermodified nucleoside 5-methylaminomethyl-2-thiouridine, which is found in the wobble position of some tRNAs and affects ribosomal frameshifting; shows potassium-dependent dimerization and GTP hydrolysis; also involved in regulation of glutamate-dependent acid resistance and activation of gadE; tRNA modification GTPase TrmE 3034005 trmE 4076398 trmE Ruegeria sp. TM1040 tRNA modification GTPase TrmE YP_614858.1 3032719 D 292414 CDS YP_614859.1 99082705 4076399 3034009..3035892 1 NC_008044.1 GidA; glucose-inhibited cell division protein A; involved in the 5-carboxymethylaminomethyl modification (mnm(5)s(2)U) of the wobble uridine base in some tRNAs; tRNA uridine 5-carboxymethylaminomethyl modification protein GidA 3035892 4076399 TM1040_2865 Ruegeria sp. TM1040 tRNA uridine 5-carboxymethylaminomethyl modification protein GidA YP_614859.1 3034009 D 292414 CDS YP_614860.1 99082706 4076400 3035889..3036506 1 NC_008044.1 TIGRFAM: methyltransferase GidB: (2.2e-38); PFAM: glucose inhibited division protein: (3e-38); KEGG: sil:SPO0002 glucose-inhibited division protein B, ev=1e-67, 62% identity; methyltransferase GidB 3036506 4076400 TM1040_2866 Ruegeria sp. TM1040 methyltransferase GidB YP_614860.1 3035889 D 292414 CDS YP_614861.1 99082707 4076401 3036499..3037311 1 NC_008044.1 PFAM: Cobyrinic acid a,c-diamide synthase: (2.3e-57); KEGG: sil:SPO0003 chromosome partitioning protein ParA, ev=1e-118, 81% identity; chromosome segregation ATPase 3037311 4076401 TM1040_2867 Ruegeria sp. TM1040 chromosome segregation ATPase YP_614861.1 3036499 D 292414 CDS YP_614862.1 99082708 4076402 3037330..3038229 1 NC_008044.1 TIGRFAM: parB-like partition proteins: (9.4e-55); PFAM: ParB-like nuclease: (8.4e-37); KEGG: sil:SPO0004 chromosome partitioning protein ParB, ev=1e-110, 70% identity; chromosome segregation DNA-binding protein 3038229 4076402 TM1040_2868 Ruegeria sp. TM1040 chromosome segregation DNA-binding protein YP_614862.1 3037330 D 292414 CDS YP_614863.1 99082709 4076403 complement(3038219..3038572) 1 NC_008044.1 PFAM: protein of unknown function DUF454: (6.8e-12); KEGG: sil:SPO0005 hypothetical protein, ev=6e-43, 70% identity; hypothetical protein 3038572 4076403 TM1040_2869 Ruegeria sp. TM1040 hypothetical protein YP_614863.1 3038219 R 292414 CDS YP_614864.1 99082710 4076404 complement(3038576..3039730) 1 NC_008044.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase 3039730 4076404 TM1040_2870 Ruegeria sp. TM1040 coproporphyrinogen III oxidase YP_614864.1 3038576 R 292414 CDS YP_614865.1 99082711 4076405 complement(3039723..3040337) 1 NC_008044.1 HAM1-like protein; Rec-dependent growth; RgdB; yggV; it is suspected that this protein functions to remove misincorporated bases such as xanthine or hypoxanthine; deoxyribonucleotide triphosphate pyrophosphatase 3040337 4076405 TM1040_2871 Ruegeria sp. TM1040 deoxyribonucleotide triphosphate pyrophosphatase YP_614865.1 3039723 R 292414 CDS YP_614866.1 99082712 4076406 complement(3040334..3041047) 1 NC_008044.1 RNase PH; tRNA nucleotidyltransferase; forms hexamers in Bacillus subtilis; phosphoroltic 3'-5' exoribonuclease; involved in maturation of tRNA precursors and removes terminal nucleotides near CCA acceptor arms of mature tRNAs; ribonuclease PH 3041047 rph 4076406 rph Ruegeria sp. TM1040 ribonuclease PH YP_614866.1 3040334 R 292414 CDS YP_614867.1 99082713 4076407 3041186..3042250 1 NC_008044.1 Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons; heat-inducible transcription repressor 3042250 hrcA 4076407 hrcA Ruegeria sp. TM1040 heat-inducible transcription repressor YP_614867.1 3041186 D 292414 CDS YP_614868.1 99082714 4076408 3042260..3042823 1 NC_008044.1 PFAM: GrpE protein: (2e-50); KEGG: sil:SPO0010 co-chaperone GrpE, ev=6e-84, 82% identity; heat shock protein GrpE 3042823 4076408 TM1040_2874 Ruegeria sp. TM1040 heat shock protein GrpE YP_614868.1 3042260 D 292414 CDS YP_614869.1 99082715 4076409 complement(3042910..3045549) 1 NC_008044.1 This protein performs the mismatch recognition step during the DNA repair process; DNA mismatch repair protein MutS 3045549 4076409 TM1040_2875 Ruegeria sp. TM1040 DNA mismatch repair protein MutS YP_614869.1 3042910 R 292414 CDS YP_614870.1 99082716 4076410 complement(3045670..3046518) 1 NC_008044.1 PFAM: flagellin-like: (7.4e-07); KEGG: ccr:CC0793 flagellin FljN, ev=5e-33, 32% identity; flagellin-like protein 3046518 4076410 TM1040_2876 Ruegeria sp. TM1040 flagellin-like protein YP_614870.1 3045670 R 292414 CDS YP_614871.1 99082717 4076411 3046844..3049099 1 NC_008044.1 NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate; malic enzyme 3049099 4076411 TM1040_2877 Ruegeria sp. TM1040 malic enzyme YP_614871.1 3046844 D 292414 CDS YP_614872.1 99082718 4076412 3049119..3049991 1 NC_008044.1 PFAM: PfkB: (2.6e-32); KEGG: sil:SPO0013 ribokinase, ev=1e-105, 65% identity; PfkB protein 3049991 4076412 TM1040_2878 Ruegeria sp. TM1040 PfkB protein YP_614872.1 3049119 D 292414 CDS YP_614873.1 99082719 4076413 complement(3050052..3050723) 1 NC_008044.1 KEGG: sil:SPO0014 methionine-S-sulfoxide reductase, ev=7e-78, 66% identity; TIGRFAM: peptide methionine sulfoxide reductase: (4.7e-55); PFAM: Methionine sulfoxide reductase A: (1.5e-60); peptide methionine sulfoxide reductase 3050723 4076413 TM1040_2879 Ruegeria sp. TM1040 peptide methionine sulfoxide reductase YP_614873.1 3050052 R 292414 CDS YP_614874.1 99082720 4076414 complement(3050862..3051143) 1 NC_008044.1 PFAM: Sterol-binding: (1.4e-08); KEGG: sil:SPO0016 sterol carrier family protein, ev=9e-29, 66% identity; sterol-binding 3051143 4076414 TM1040_2880 Ruegeria sp. TM1040 sterol-binding YP_614874.1 3050862 R 292414 CDS YP_614875.1 99082721 4076415 complement(3051234..3051620) 1 NC_008044.1 PFAM: protein of unknown function DUF1036: (2.3e-41); KEGG: bja:blr7137 hypothetical protein, ev=2e-26, 44% identity; hypothetical protein 3051620 4076415 TM1040_2881 Ruegeria sp. TM1040 hypothetical protein YP_614875.1 3051234 R 292414 CDS YP_614876.1 99082722 4076416 complement(3051722..3052183) 1 NC_008044.1 KEGG: sil:SPO0017 hypothetical protein, ev=3e-47, 63% identity; hypothetical protein 3052183 4076416 TM1040_2882 Ruegeria sp. TM1040 hypothetical protein YP_614876.1 3051722 R 292414 CDS YP_614877.1 99082723 4076417 complement(3052183..3053406) 1 NC_008044.1 catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming; argininosuccinate synthase 3053406 4076417 TM1040_2883 Ruegeria sp. TM1040 argininosuccinate synthase YP_614877.1 3052183 R 292414 CDS YP_614878.1 99082724 4076418 3053537..3054292 1 NC_008044.1 KEGG: jan:Jann_0068 hypothetical protein, ev=2e-27, 30% identity; hypothetical protein 3054292 4076418 TM1040_2884 Ruegeria sp. TM1040 hypothetical protein YP_614878.1 3053537 D 292414 CDS YP_614879.1 99082725 4076419 3054365..3055591 1 NC_008044.1 catalyzes the formation of 2-oxobutanoate from L-threonine; biosynthetic; threonine dehydratase 3055591 4076419 TM1040_2885 Ruegeria sp. TM1040 threonine dehydratase YP_614879.1 3054365 D 292414 CDS YP_614880.1 99082726 4076420 complement(3055623..3055979) 1 NC_008044.1 PFAM: Hpt: (6.2e-11); KEGG: sil:SPO0021 Hpt domain protein, ev=8e-29, 63% identity; Hpt protein 3055979 4076420 TM1040_2886 Ruegeria sp. TM1040 Hpt protein YP_614880.1 3055623 R 292414 CDS YP_614881.1 99082727 4076421 3056120..3057391 1 NC_008044.1 PFAM: response regulator receiver: (3.3e-38) Stage II sporulation E: (1.8e-34); SMART: Protein phosphatase 2C-like: (1.8e-14); KEGG: sil:SPO0022 response regulator, ev=1e-177, 71% identity; response regulator receiver modulated serine phosphatase 3057391 4076421 TM1040_2887 Ruegeria sp. TM1040 response regulator receiver modulated serine phosphatase YP_614881.1 3056120 D 292414 CDS YP_614882.1 99082728 4076422 complement(3057398..3057841) 1 NC_008044.1 PFAM: NUDIX hydrolase: (1e-18); KEGG: sil:SPO0023 hydrolase, NUDIX family, ev=3e-54, 70% identity; NUDIX hydrolase 3057841 4076422 TM1040_2888 Ruegeria sp. TM1040 NUDIX hydrolase YP_614882.1 3057398 R 292414 CDS YP_614883.1 99082729 4076423 3057918..3058895 1 NC_008044.1 PFAM: Hsp33 protein: (7.3e-53); KEGG: sil:SPO0024 chaperonin, 33 kDa, ev=1e-158, 84% identity; Hsp33 protein 3058895 4076423 TM1040_2889 Ruegeria sp. TM1040 Hsp33 protein YP_614883.1 3057918 D 292414 CDS YP_614884.1 99082730 4078568 3058901..3059500 1 NC_008044.1 PFAM: NUDIX hydrolase: (2.6e-12); KEGG: sil:SPO0025 hydrolase, NUDIX family, ev=4e-66, 66% identity; NUDIX hydrolase 3059500 4078568 TM1040_2890 Ruegeria sp. TM1040 NUDIX hydrolase YP_614884.1 3058901 D 292414 CDS YP_614885.1 99082731 4078569 3059497..3060657 1 NC_008044.1 PFAM: Polynucleotide adenylyltransferase region: (3.3e-38); KEGG: sil:SPO0026 polyA polymerase family protein, ev=1e-127, 62% identity; polynucleotide adenylyltransferase 3060657 4078569 TM1040_2891 Ruegeria sp. TM1040 polynucleotide adenylyltransferase YP_614885.1 3059497 D 292414 CDS YP_614886.1 99082732 4078570 3060885..3062723 1 NC_008044.1 PFAM: ABC transporter, transmembrane region: (4.1e-07) ABC transporter related: (6.1e-60); SMART: ATPase: (8.2e-22); KEGG: sil:SPO0027 ABC transporter, transmembrane ATP-binding protein, ev=0.0, 82% identity; ABC transporter 3062723 4078570 TM1040_2892 Ruegeria sp. TM1040 ABC transporter YP_614886.1 3060885 D 292414 CDS YP_614887.1 99082733 4078571 3062720..3064564 1 NC_008044.1 PFAM: ABC transporter, transmembrane region: (6.9e-06) ABC transporter related: (7e-54); SMART: ATPase: (2.3e-20); KEGG: sil:SPO0028 ABC transporter, transmembrane ATP-binding protein, ev=0.0, 70% identity; ABC transporter 3064564 4078571 TM1040_2893 Ruegeria sp. TM1040 ABC transporter YP_614887.1 3062720 D 292414 CDS YP_614888.1 99082734 4078572 3064623..3065867 1 NC_008044.1 PFAM: (Uracil-5)-methyltransferase: (0.0026); KEGG: sil:SPO0029 23S rRNA (uracil-5-)-methyltransferase RumA, ev=1e-160, 68% identity; 23S rRNA (uracil-5-)-methyltransferase RumA 3065867 4078572 TM1040_2894 Ruegeria sp. TM1040 23S rRNA (uracil-5-)-methyltransferase RumA YP_614888.1 3064623 D 292414 CDS YP_614889.1 99082735 4078573 3065895..3066680 1 NC_008044.1 PFAM: Ion transport protein: (2.1e-34); KEGG: sil:SPO0030 voltage-gated sodium channel, ev=1e-106, 74% identity; Ion transport protein 3066680 4078573 TM1040_2895 Ruegeria sp. TM1040 Ion transport protein YP_614889.1 3065895 D 292414 CDS YP_614890.1 99082736 4078574 3066782..3067270 1 NC_008044.1 PFAM: ErfK/YbiS/YcfS/YnhG: (4e-05); KEGG: sil:SPO0031 ErfK/YbiS/YcfS/YnhG family protein, ev=1e-60, 70% identity; ErfK/YbiS/YcfS/YnhG protein 3067270 4078574 TM1040_2896 Ruegeria sp. TM1040 ErfK/YbiS/YcfS/YnhG protein YP_614890.1 3066782 D 292414 CDS YP_614891.1 99082737 4078575 complement(3067377..3067907) 1 NC_008044.1 PFAM: Allergen V5/Tpx-1 related: (1.4e-10); KEGG: sil:SPO0076 lipoprotein, , ev=9e-52, 63% identity; Allergen V5/Tpx-1 related 3067907 4078575 TM1040_2897 Ruegeria sp. TM1040 Allergen V5/Tpx-1 related YP_614891.1 3067377 R 292414 CDS YP_614892.1 99082738 4078576 3068040..3068657 1 NC_008044.1 TIGRFAM: Twin-arginine translocation pathway signal: (0.15); PFAM: ErfK/YbiS/YcfS/YnhG: (3e-47); KEGG: sil:SPO0075 ErfK/YbiS/YcfS/YnhG family protein/Tat domain protein, ev=6e-86, 72% identity; twin-arginine translocation pathway signal 3068657 4078576 TM1040_2898 Ruegeria sp. TM1040 twin-arginine translocation pathway signal YP_614892.1 3068040 D 292414 CDS YP_614893.1 99082739 4078577 3068800..3068982 1 NC_008044.1 KEGG: sil:SPO0074 hypothetical protein, ev=1e-16, 73% identity; hypothetical protein 3068982 4078577 TM1040_2899 Ruegeria sp. TM1040 hypothetical protein YP_614893.1 3068800 D 292414 CDS YP_614894.1 99082740 4078578 complement(3069070..3070134) 1 NC_008044.1 protoheme ferro-lyase; catalyzes the insertion of a ferrous ion into protoporphyrin IX to form protoheme; involved in protoheme biosynthesis; in some organisms this protein is membrane-associated while in others it is cytosolic; ferrochelatase 3070134 hemH 4078578 hemH Ruegeria sp. TM1040 ferrochelatase YP_614894.1 3069070 R 292414 CDS YP_614895.1 99082741 4078579 complement(3070236..3071075) 1 NC_008044.1 KEGG: sil:SPO0072 hypothetical protein, ev=1e-90, 62% identity; hypothetical protein 3071075 4078579 TM1040_2901 Ruegeria sp. TM1040 hypothetical protein YP_614895.1 3070236 R 292414 CDS YP_614896.1 99082742 4078580 3071087..3071818 1 NC_008044.1 KEGG: sil:SPO0071 competence protein F, , ev=1e-80, 61% identity; competence protein F 3071818 4078580 TM1040_2902 Ruegeria sp. TM1040 competence protein F YP_614896.1 3071087 D 292414 CDS YP_614897.1 99082743 4078581 3071890..3072147 1 NC_008044.1 TIGRFAM: Glutaredoxin, GrxC: (2.4e-49); PFAM: glutaredoxin: (3e-25); KEGG: sil:SPO0070 glutaredoxin, ev=4e-32, 74% identity; glutaredoxin GrxC 3072147 4078581 TM1040_2903 Ruegeria sp. TM1040 glutaredoxin GrxC YP_614897.1 3071890 D 292414 CDS YP_614898.1 99082744 4078582 3072152..3072985 1 NC_008044.1 PFAM: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase: (4.1e-40); KEGG: sil:SPO0069 hydrolase, carbon-nitrogen family, ev=1e-101, 67% identity; nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase 3072985 4078582 TM1040_2904 Ruegeria sp. TM1040 nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase YP_614898.1 3072152 D 292414 CDS YP_614899.1 99082745 4078583 3072985..3073425 1 NC_008044.1 PFAM: regulatory protein, MarR: (3.4e-08); KEGG: sil:SPO0068 transcriptional regulator, , ev=2e-54, 72% identity; MarR family transcriptional regulator 3073425 4078583 TM1040_2905 Ruegeria sp. TM1040 MarR family transcriptional regulator YP_614899.1 3072985 D 292414 CDS YP_614900.1 99082746 4078584 complement(3073732..3074475) 1 NC_008044.1 Involved in ubiquinone biosynthesis; 3-demethylubiquinone-9 3-methyltransferase 3074475 4078584 TM1040_2906 Ruegeria sp. TM1040 3-demethylubiquinone-9 3-methyltransferase YP_614900.1 3073732 R 292414 CDS YP_614901.1 99082747 4078585 3074527..3075507 1 NC_008044.1 KEGG: sil:SPO0066 proline iminopeptidase, ev=1e-153, 78% identity; TIGRFAM: proline iminopeptidase: (9.6e-155); PFAM: alpha/beta hydrolase fold: (4.6e-23); prolyl aminopeptidase 3075507 4078585 TM1040_2907 Ruegeria sp. TM1040 prolyl aminopeptidase YP_614901.1 3074527 D 292414 CDS YP_614902.1 99082748 4078586 3075504..3076355 1 NC_008044.1 KEGG: sil:SPO0065 peptide/opine/nickel uptake family ABC transporter, periplasmic substrate-binding protein, ev=8e-76, 53% identity; peptide/opine/nickel uptake ABC transporter substrate-binding protein 3076355 4078586 TM1040_2908 Ruegeria sp. TM1040 peptide/opine/nickel uptake ABC transporter substrate-binding protein YP_614902.1 3075504 D 292414 CDS YP_614903.1 99082749 4078587 3076592..3077203 1 NC_008044.1 in Streptococcus pneumoniae this gene was found to be essential; structure determination of the Streptococcus protein shows that it is similar to a number of other proteins; hypothetical protein 3077203 4078587 TM1040_2909 Ruegeria sp. TM1040 hypothetical protein YP_614903.1 3076592 D 292414 CDS YP_614904.1 99082750 4078588 3077203..3078819 1 NC_008044.1 modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination; transcription elongation factor NusA 3078819 nusA 4078588 nusA Ruegeria sp. TM1040 transcription elongation factor NusA YP_614904.1 3077203 D 292414 CDS YP_614905.1 99082751 4078589 3078849..3079466 1 NC_008044.1 PFAM: protein of unknown function DUF448: (1.6e-28); KEGG: sil:SPO0062 hypothetical protein, ev=3e-84, 74% identity; hypothetical protein 3079466 4078589 TM1040_2911 Ruegeria sp. TM1040 hypothetical protein YP_614905.1 3078849 D 292414 CDS YP_614906.1 99082752 4078590 3079475..3081982 1 NC_008044.1 Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits during initiation of protein synthesis. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex; translation initiation factor IF-2 3081982 infB 4078590 infB Ruegeria sp. TM1040 translation initiation factor IF-2 YP_614906.1 3079475 D 292414 CDS YP_614907.1 99082753 4078591 complement(3082087..3082383) 1 NC_008044.1 hypothetical protein 3082383 4078591 TM1040_2913 Ruegeria sp. TM1040 hypothetical protein YP_614907.1 3082087 R 292414 CDS YP_614908.1 99082754 4078592 complement(3082512..3082922) 1 NC_008044.1 TIGRFAM: mutator mutT protein: (1.9e-31); PFAM: NUDIX hydrolase: (1.4e-23); KEGG: sil:SPO0060 mutator MutT protein, ev=2e-64, 87% identity; mutator mutT protein 3082922 4078592 TM1040_2914 Ruegeria sp. TM1040 mutator mutT protein YP_614908.1 3082512 R 292414 CDS YP_614909.1 99082755 4078593 complement(3082919..3084145) 1 NC_008044.1 bifunctional arginine biosynthesis protein ArgJ; functions at the 1st and 5th steps in arginine biosynthesis; involved in synthesis of acetylglutamate from glutamate and acetyl-CoA and ornithine by transacetylation between acetylornithine and glutmate; bifunctional ornithine acetyltransferase/N-acetylglutamate synthase 3084145 argJ 4078593 argJ Ruegeria sp. TM1040 bifunctional ornithine acetyltransferase/N-acetylglutamate synthase YP_614909.1 3082919 R 292414 CDS YP_614910.1 99082756 4078594 complement(3084178..3085029) 1 NC_008044.1 PFAM: PpiC-type peptidyl-prolyl cis-trans isomerase: (6.9e-33); KEGG: sil:SPO0058 PPIC-type PPIASE domain protein, ev=1e-85, 56% identity; PpiC-type peptidyl-prolyl cis-trans isomerase 3085029 4078594 TM1040_2916 Ruegeria sp. TM1040 PpiC-type peptidyl-prolyl cis-trans isomerase YP_614910.1 3084178 R 292414 CDS YP_614911.1 99082757 4078595 3085207..3087894 1 NC_008044.1 functions in protein export; can interact with acidic membrane phospholipids and the SecYEG protein complex; binds to preproteins; binds to ATP and undergoes a conformational change to promote membrane insertion of SecA/bound preprotein; ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane; additional proteins SecD/F/YajC aid SecA recycling; exists in an equilibrium between monomers and dimers; may possibly form higher order oligomers; proteins in this cluster correspond SecA1; SecA2 is not essential and seems to play a role in secretion of a subset of proteins; preprotein translocase subunit SecA 3087894 4078595 TM1040_2917 Ruegeria sp. TM1040 preprotein translocase subunit SecA YP_614911.1 3085207 D 292414 CDS YP_614912.1 99082758 4078596 3088030..3088926 1 NC_008044.1 KEGG: jan:Jann_0288 hypothetical protein, ev=3e-32, 35% identity; hypothetical protein 3088926 4078596 TM1040_2918 Ruegeria sp. TM1040 hypothetical protein YP_614912.1 3088030 D 292414 CDS YP_614913.1 99082759 4078597 3088950..3090503 1 NC_008044.1 PFAM: OmpA/MotB: (0.00021); KEGG: sil:SPO0055 OmpA domain protein, ev=0.0, 67% identity; OmpA/MotB protein 3090503 4078597 TM1040_2919 Ruegeria sp. TM1040 OmpA/MotB protein YP_614913.1 3088950 D 292414 CDS YP_614914.1 99082760 4078598 complement(3090662..3092599) 1 NC_008044.1 catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate; 1-deoxy-D-xylulose-5-phosphate synthase 3092599 4078598 TM1040_2920 Ruegeria sp. TM1040 1-deoxy-D-xylulose-5-phosphate synthase YP_614914.1 3090662 R 292414 CDS YP_614915.1 99082761 4078599 complement(3092630..3093493) 1 NC_008044.1 PFAM: Polyprenyl synthetase: (3.4e-68); KEGG: rsp:RSP_1135 geranylgeranyl pyrophosphate synthetase, ev=2e-93, 65% identity; farnesyl-diphosphate synthase 3093493 4078599 TM1040_2921 Ruegeria sp. TM1040 farnesyl-diphosphate synthase YP_614915.1 3092630 R 292414 CDS YP_614916.1 99082762 4078600 complement(3093500..3093745) 1 NC_008044.1 TIGRFAM: exodeoxyribonuclease VII, small subunit: (3.1e-25); PFAM: Exonuclease VII, small subunit: (1.3e-27); KEGG: sil:SPO0249 exodeoxyribonuclease VII, small subunit, ev=6e-27, 85% identity; exodeoxyribonuclease VII small subunit 3093745 4078600 TM1040_2922 Ruegeria sp. TM1040 exodeoxyribonuclease VII small subunit YP_614916.1 3093500 R 292414 CDS YP_614917.1 99082763 4078601 complement(3093742..3094668) 1 NC_008044.1 PFAM: histone deacetylase superfamily: (1.9e-82); KEGG: sil:SPO0250 histone deacetylase family protein, ev=1e-139, 77% identity; histone deacetylase superfamily protein 3094668 4078601 TM1040_2923 Ruegeria sp. TM1040 histone deacetylase superfamily protein YP_614917.1 3093742 R 292414 CDS YP_614918.1 99082764 4078602 complement(3094788..3095492) 1 NC_008044.1 PFAM: response regulator receiver: (6.4e-37) transcriptional regulatory protein-like: (4e-21); KEGG: sil:SPO0251 DNA-binding response regulator PetR, ev=1e-108, 84% identity; two component transcriptional regulator 3095492 4078602 TM1040_2924 Ruegeria sp. TM1040 two component transcriptional regulator YP_614918.1 3094788 R 292414 CDS YP_614919.1 99082765 4078603 complement(3095489..3096001) 1 NC_008044.1 PFAM: regulatory protein, MarR: (1.2e-07); KEGG: sil:SPO0252 transcriptional regulator PetP, ev=5e-71, 79% identity; MarR family transcriptional regulator 3096001 4078603 TM1040_2925 Ruegeria sp. TM1040 MarR family transcriptional regulator YP_614919.1 3095489 R 292414 CDS YP_614920.1 99082766 4078604 3096162..3097028 1 NC_008044.1 catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids; branched-chain amino acid aminotransferase 3097028 4078604 TM1040_2926 Ruegeria sp. TM1040 branched-chain amino acid aminotransferase YP_614920.1 3096162 D 292414 CDS YP_614921.1 99082767 4078605 complement(3097197..3097625) 1 NC_008044.1 PFAM: OsmC-like protein: (1.1e-32); KEGG: sil:SPO0254 organic hydroperoxide resistance protein, ev=1e-50, 67% identity; OsmC-like protein 3097625 4078605 TM1040_2927 Ruegeria sp. TM1040 OsmC-like protein YP_614921.1 3097197 R 292414 CDS YP_614922.1 99082768 4078606 3097733..3098164 1 NC_008044.1 PFAM: regulatory protein, MarR: (8.1e-20); KEGG: sil:SPO0255 transcriptional regulator, MarR family, ev=3e-44, 61% identity; MarR family transcriptional regulator 3098164 4078606 TM1040_2928 Ruegeria sp. TM1040 MarR family transcriptional regulator YP_614922.1 3097733 D 292414 CDS YP_614923.1 99082769 4077080 complement(3098183..3099124) 1 NC_008044.1 PFAM: protein of unknown function DUF6, transmembrane: (4e-07) UAA transporter: (0.0036); KEGG: sil:SPO0263 membrane protein, ev=1e-113, 65% identity; hypothetical protein 3099124 4077080 TM1040_2929 Ruegeria sp. TM1040 hypothetical protein YP_614923.1 3098183 R 292414 CDS YP_614924.1 99082770 4077081 complement(3099209..3099859) 1 NC_008044.1 PFAM: cation efflux protein: (0.00014); KEGG: bja:bll4927 hypothetical protein, ev=7e-72, 66% identity; cation efflux protein 3099859 4077081 TM1040_2930 Ruegeria sp. TM1040 cation efflux protein YP_614924.1 3099209 R 292414 CDS YP_614925.1 99082771 4077082 3099944..3100360 1 NC_008044.1 PFAM: regulatory protein, MerR: (3e-11); KEGG: sil:SPOA0389 transcriptional regulator, MerR family, ev=5e-39, 56% identity; MerR family transcriptional regulator 3100360 4077082 TM1040_2931 Ruegeria sp. TM1040 MerR family transcriptional regulator YP_614925.1 3099944 D 292414 CDS YP_614926.1 99082772 4077083 complement(3100370..3101275) 1 NC_008044.1 PFAM: NAD-dependent epimerase/dehydratase: (0.0014) dTDP-4-dehydrorhamnose reductase: (0.0033); KEGG: sil:SPO3755 hypothetical protein, ev=1e-102, 64% identity; NAD-dependent epimerase/dehydratase 3101275 4077083 TM1040_2932 Ruegeria sp. TM1040 NAD-dependent epimerase/dehydratase YP_614926.1 3100370 R 292414 CDS YP_614927.1 99082773 4077084 3101671..3102390 1 NC_008044.1 KEGG: jan:Jann_2250 hypothetical protein, ev=2e-64, 50% identity; hypothetical protein 3102390 4077084 TM1040_2933 Ruegeria sp. TM1040 hypothetical protein YP_614927.1 3101671 D 292414 CDS YP_614928.1 99082774 4077085 3102377..3103309 1 NC_008044.1 PFAM: periplasmic binding protein: (3.5e-10); KEGG: jan:Jann_2249 periplasmic binding protein, ev=1e-106, 63% identity; periplasmic binding protein 3103309 4077085 TM1040_2934 Ruegeria sp. TM1040 periplasmic binding protein YP_614928.1 3102377 D 292414 CDS YP_614929.1 99082775 4077086 3103310..3104317 1 NC_008044.1 PFAM: transport system permease protein: (6e-92); KEGG: jan:Jann_2248 transport system permease protein, ev=1e-114, 62% identity; transport system permease 3104317 4077086 TM1040_2935 Ruegeria sp. TM1040 transport system permease YP_614929.1 3103310 D 292414 CDS YP_614930.1 99082776 4077087 3104307..3105140 1 NC_008044.1 PFAM: ABC transporter related: (3.4e-51); SMART: ATPase: (4.8e-09); KEGG: jan:Jann_2247 ABC transporter related, ev=1e-69, 55% identity; ABC transporter 3105140 4077087 TM1040_2936 Ruegeria sp. TM1040 ABC transporter YP_614930.1 3104307 D 292414 CDS YP_614931.1 99082777 4077088 complement(3105098..3107272) 1 NC_008044.1 PFAM: histidine kinase, HAMP region: (1.5e-06) chemotaxis sensory transducer: (1.2e-62); KEGG: atc:AGR_C_678 methyl-accepting chemotaxis protein McpT, ev=4e-75, 34% identity; methyl-accepting chemotaxis sensory transducer 3107272 4077088 TM1040_2937 Ruegeria sp. TM1040 methyl-accepting chemotaxis sensory transducer YP_614931.1 3105098 R 292414 CDS YP_614932.1 99082778 4077089 3107839..3108678 1 NC_008044.1 PFAM: OmpA/MotB: (2.3e-05); KEGG: sil:SPO0191 chemotaxis protein MotB, ev=3e-91, 60% identity; OmpA/MotB protein 3108678 4077089 TM1040_2938 Ruegeria sp. TM1040 OmpA/MotB protein YP_614932.1 3107839 D 292414 CDS YP_614933.1 99082779 4077090 3108809..3110077 1 NC_008044.1 PFAM: flagellar basal body rod protein: (6.7e-09) protein of unknown function DUF1078-like: (9.9e-17); KEGG: sil:SPO0192 flagellar hook protein FlgE, , ev=1e-133, 56% identity; hypothetical protein 3110077 4077090 TM1040_2939 Ruegeria sp. TM1040 hypothetical protein YP_614933.1 3108809 D 292414 CDS YP_614934.1 99082780 4077091 3110129..3111577 1 NC_008044.1 with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook; flagellar hook-associated protein FlgK 3111577 flgK 4077091 flgK Ruegeria sp. TM1040 flagellar hook-associated protein FlgK YP_614934.1 3110129 D 292414 CDS YP_614935.1 99082781 4077092 3111581..3112588 1 NC_008044.1 KEGG: sil:SPO0194 flagellar hook-associated protein FlgL family protein, ev=4e-58, 37% identity; flagellar hook-associated protein FlgL family protein 3112588 4077092 TM1040_2941 Ruegeria sp. TM1040 flagellar hook-associated protein FlgL family protein YP_614935.1 3111581 D 292414 CDS YP_614936.1 99082782 4077093 3112588..3113691 1 NC_008044.1 part of the basal body which consists of four rings L, P, S, and M mounted on a central rod; Vibrio parahaemolyticus, Yersinia, Bradyrhizobium and other bacteria have two copies of this and other flagellar genes; the V. parahaemolyticus protein is associated with the polar flagella and the Bradyrhizobium protein is associated with the thick flagellum; flagellar basal body P-ring protein 3113691 flgI 4077093 flgI Ruegeria sp. TM1040 flagellar basal body P-ring protein YP_614936.1 3112588 D 292414 CDS YP_614937.1 99082783 4077094 complement(3113864..3114184) 1 NC_008044.1 hypothetical protein 3114184 4077094 TM1040_2943 Ruegeria sp. TM1040 hypothetical protein YP_614937.1 3113864 R 292414 CDS YP_614938.1 99082784 4077095 complement(3114200..3114946) 1 NC_008044.1 FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus; flagellar biosynthesis protein FliP 3114946 fliP 4077095 fliP Ruegeria sp. TM1040 flagellar biosynthesis protein FliP YP_614938.1 3114200 R 292414 CDS YP_614939.1 99082785 4077096 complement(3114943..3115239) 1 NC_008044.1 PFAM: surface presentation of antigens (SPOA) protein: (3.4e-10); KEGG: sil:SPO0197 flagellar motor switch protein FliN, ev=5e-34, 79% identity; surface presentation of antigens (SPOA) protein 3115239 4077096 TM1040_2945 Ruegeria sp. TM1040 surface presentation of antigens (SPOA) protein YP_614939.1 3114943 R 292414 CDS YP_614940.1 99082786 4077097 complement(3115232..3115828) 1 NC_008044.1 KEGG: sil:SPO0198 ABC transporter, ATP-binding protein, flagellar, , ev=2e-45, 46% identity; flagellar ABC transporter ATP-binding protein 3115828 4077097 TM1040_2946 Ruegeria sp. TM1040 flagellar ABC transporter ATP-binding protein YP_614940.1 3115232 R 292414 CDS YP_614941.1 99082787 4077098 complement(3115828..3117543) 1 NC_008044.1 the MS-ring anchors the flagellum to the cytoplasmic membrane; part of the flagellar basal body which consists of four rings L, P, S, and M mounted on a central rod; flagellar MS-ring protein 3117543 fliF 4077098 fliF Ruegeria sp. TM1040 flagellar MS-ring protein YP_614941.1 3115828 R 292414 CDS YP_614942.1 99082788 4077099 3117624..3118148 1 NC_008044.1 PFAM: flagellar basal body-associated protein FliL: (1.2e-13); KEGG: sil:SPO0200 flagellar basal body-associated protein FliL, ev=1e-40, 50% identity; flagellar basal body-associated protein FliL 3118148 4077099 TM1040_2948 Ruegeria sp. TM1040 flagellar basal body-associated protein FliL YP_614942.1 3117624 D 292414 CDS YP_614943.1 99082789 4077100 3118158..3118616 1 NC_008044.1 KEGG: sil:SPO0201 hypothetical protein, ev=9e-40, 59% identity; hypothetical protein 3118616 4077100 TM1040_2949 Ruegeria sp. TM1040 hypothetical protein YP_614943.1 3118158 D 292414 CDS YP_614944.1 99082790 4077101 3118616..3119233 1 NC_008044.1 KEGG: sil:SPO0202 hypothetical protein, ev=2e-51, 57% identity; hypothetical protein 3119233 4077101 TM1040_2950 Ruegeria sp. TM1040 hypothetical protein YP_614944.1 3118616 D 292414 CDS YP_614945.1 99082791 4077102 3119308..3120177 1 NC_008044.1 With MotB forms the ion channels that couple flagellar rotation to proton/sodium motive force across the membrane and forms the stator elements of the rotary flagellar machine; flagellar motor protein MotA 3120177 4077102 TM1040_2951 Ruegeria sp. TM1040 flagellar motor protein MotA YP_614945.1 3119308 D 292414 CDS YP_614946.1 99082792 4077103 3120174..3122588 1 NC_008044.1 KEGG: sil:SPO0204 hypothetical protein, ev=1e-77, 28% identity; hypothetical protein 3122588 4077103 TM1040_2952 Ruegeria sp. TM1040 hypothetical protein YP_614946.1 3120174 D 292414 CDS YP_614947.1 99082793 4077104 3122923..3125013 1 NC_008044.1 membrane protein involved in the flagellar export apparatus; flagellar biosynthesis protein FlhA 3125013 flhA 4077104 flhA Ruegeria sp. TM1040 flagellar biosynthesis protein FlhA YP_614947.1 3122923 D 292414 CDS YP_614948.1 99082794 4077105 3125010..3125789 1 NC_008044.1 KEGG: sil:SPO0171 flagellar biosynthetic protein FliR, ev=1e-70, 51% identity; flagellar biosynthetic protein FliR 3125789 4077105 TM1040_2954 Ruegeria sp. TM1040 flagellar biosynthetic protein FliR YP_614948.1 3125010 D 292414 CDS YP_614949.1 99082795 4077106 3125786..3126877 1 NC_008044.1 membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export; flagellar biosynthesis protein FlhB 3126877 flhB 4077106 flhB Ruegeria sp. TM1040 flagellar biosynthesis protein FlhB YP_614949.1 3125786 D 292414 CDS YP_614950.1 99082796 4077107 3126889..3127278 1 NC_008044.1 KEGG: sil:SPO0173 hypothetical protein, ev=2e-19, 38% identity; hypothetical protein 3127278 4077107 TM1040_2956 Ruegeria sp. TM1040 hypothetical protein YP_614950.1 3126889 D 292414 CDS YP_614951.1 99082797 4077108 complement(3127555..3128064) 1 NC_008044.1 KEGG: sil:SPO0174 hypothetical protein, ev=2e-38, 45% identity; hypothetical protein 3128064 4077108 TM1040_2957 Ruegeria sp. TM1040 hypothetical protein YP_614951.1 3127555 R 292414 CDS YP_614952.1 99082798 4077109 complement(3128076..3128813) 1 NC_008044.1 part of the flagellar basal body which consists of four rings L,P, S and M mounted on a central rod; flagellar basal body L-ring protein 3128813 flgH 4077109 flgH Ruegeria sp. TM1040 flagellar basal body L-ring protein YP_614952.1 3128076 R 292414 CDS YP_614953.1 99082799 4077110 complement(3128813..3129229) 1 NC_008044.1 required for the assembly of the flagellar basal body P-ring; flagellar basal body P-ring biosynthesis protein FlgA 3129229 flgA 4077110 flgA Ruegeria sp. TM1040 flagellar basal body P-ring biosynthesis protein FlgA YP_614953.1 3128813 R 292414 CDS YP_614954.1 99082800 4077111 complement(3129230..3130015) 1 NC_008044.1 makes up the distal portion of the flagellar basal body rod; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thick flagella; flagellar basal body rod protein FlgG 3130015 flgG 4077111 flgG Ruegeria sp. TM1040 flagellar basal body rod protein FlgG YP_614954.1 3129230 R 292414 CDS YP_614955.1 99082801 4077112 complement(3130025..3130741) 1 NC_008044.1 FlgF, with FlgB and C, makes up the proximal portion of the flagellar basal body rod; Rhodobacter sphaeroides has 2 copies of this and other flagella genes; flagellar basal body rod protein FlgF 3130741 flgF 4077112 flgF Ruegeria sp. TM1040 flagellar basal body rod protein FlgF YP_614955.1 3130025 R 292414 CDS YP_614956.1 99082802 4077113 complement(3130741..3131019) 1 NC_008044.1 PFAM: export protein FliQ, family 3: (3.9e-14); KEGG: sil:SPO0179 flagellar biosynthetic protein FliQ, ev=5e-27, 65% identity; export protein FliQ 3131019 4077113 TM1040_2962 Ruegeria sp. TM1040 export protein FliQ YP_614956.1 3130741 R 292414 CDS YP_614957.1 99082803 4077114 complement(3131023..3131319) 1 NC_008044.1 forms a junction between the M-ring and FlgB during flagella biosynthesis; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella; flagellar hook-basal body protein FliE 3131319 fliE 4077114 fliE Ruegeria sp. TM1040 flagellar hook-basal body protein FliE YP_614957.1 3131023 R 292414 CDS YP_614958.1 99082804 4077115 complement(3131343..3131735) 1 NC_008044.1 with FlgF and B makes up the proximal portion of the flagellar basal body rod; flagellar basal body rod protein FlgC 3131735 flgC 4077115 flgC Ruegeria sp. TM1040 flagellar basal body rod protein FlgC YP_614958.1 3131343 R 292414 CDS YP_614959.1 99082805 4077116 complement(3131752..3132141) 1 NC_008044.1 with FlgF and C makes up the proximal portion of the flagellar basal body rod; flagellar basal-body rod protein FlgB 3132141 flgB 4077116 flgB Ruegeria sp. TM1040 flagellar basal-body rod protein FlgB YP_614959.1 3131752 R 292414 CDS YP_614960.1 99082806 4077117 3132230..3133558 1 NC_008044.1 KEGG: sil:SPO0183 H+-transporting two-sector ATPase, flagellum-specific, ev=1e-169, 68% identity; TIGRFAM: ATP synthase FliI/YscN: (6.8e-133); PFAM: H+-transporting two-sector ATPase, alpha/beta subunit, central region: (9.4e-97); SMART: ATPase: (2.1e-08); ATP synthase FliI/YscN 3133558 4077117 TM1040_2966 Ruegeria sp. TM1040 ATP synthase FliI/YscN YP_614960.1 3132230 D 292414 CDS YP_614961.1 99082807 4077118 3133720..3134007 1 NC_008044.1 PFAM: transposase IS3/IS911: (1.6e-20); KEGG: atc:AGR_L_545 insertion element ISR1 hypothetical 10 KD protein A3, ev=3e-25, 67% identity; transposase IS3/IS911 3134007 4077118 TM1040_2967 Ruegeria sp. TM1040 transposase IS3/IS911 YP_614961.1 3133720 D 292414 CDS YP_614962.1 99082808 4077998 3134061..3134855 1 NC_008044.1 PFAM: Integrase, catalytic region: (3.3e-31); KEGG: jan:Jann_3728 integrase protein, ev=1e-100, 76% identity; integrase catalytic subunit 3134855 4077998 TM1040_2968 Ruegeria sp. TM1040 integrase catalytic subunit YP_614962.1 3134061 D 292414 CDS YP_614963.1 99082809 4077999 3134929..3135195 1 NC_008044.1 PFAM: transposase IS3/IS911: (2.9e-19); KEGG: ret:RHE_PA00090 probable insertion sequence transposase protein, IS3/IS911 family, ev=2e-34, 77% identity; transposase IS3/IS911 3135195 4077999 TM1040_2969 Ruegeria sp. TM1040 transposase IS3/IS911 YP_614963.1 3134929 D 292414 CDS YP_614964.1 99082810 4078000 3135228..3136025 1 NC_008044.1 PFAM: Integrase, catalytic region: (4.6e-37); KEGG: mlo:mll6088 transposase, ev=1e-117, 75% identity; integrase catalytic subunit 3136025 4078000 TM1040_2970 Ruegeria sp. TM1040 integrase catalytic subunit YP_614964.1 3135228 D 292414 CDS YP_614965.1 99082811 4078001 complement(3136295..3138247) 1 NC_008044.1 KEGG: sil:SPO3456 flagellar protein, , ev=4e-43, 33% identity; hypothetical protein 3138247 4078001 TM1040_2971 Ruegeria sp. TM1040 hypothetical protein YP_614965.1 3136295 R 292414 CDS YP_614966.1 99082812 4078002 complement(3138244..3138648) 1 NC_008044.1 post-transcriptional repressor of flagellum biosynthesis; promotes degradation of fljK mRNA: Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella; flagellar biosynthesis repressor FlbT 3138648 flbT 4078002 flbT Ruegeria sp. TM1040 flagellar biosynthesis repressor FlbT YP_614966.1 3138244 R 292414 CDS YP_614967.1 99082813 4078003 complement(3138651..3139022) 1 NC_008044.1 acts as an activator of flagellin translation and may be required for filament secretion or assembly; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thick flagellum; flagellar biosynthesis regulatory protein FlaF 3139022 flaF 4078003 flaF Ruegeria sp. TM1040 flagellar biosynthesis regulatory protein FlaF YP_614967.1 3138651 R 292414 CDS YP_614968.1 99082814 4078004 complement(3139109..3139957) 1 NC_008044.1 PFAM: flagellin-like: (1.6e-06); KEGG: sil:SPO3459 flagellin protein, ev=5e-47, 55% identity; flagellin-like protein 3139957 4078004 TM1040_2974 Ruegeria sp. TM1040 flagellin-like protein YP_614968.1 3139109 R 292414 CDS YP_614969.1 99082815 4078005 complement(3140173..3140541) 1 NC_008044.1 KEGG: sil:SPO3460 hypothetical protein, ev=3e-24, 51% identity; hypothetical protein 3140541 4078005 TM1040_2975 Ruegeria sp. TM1040 hypothetical protein YP_614969.1 3140173 R 292414 CDS YP_614970.1 99082816 4078006 complement(3140538..3140828) 1 NC_008044.1 KEGG: sil:SPO3461 flagellar protein FlgJ, , ev=8e-22, 55% identity; flagellar protein FlgJ 3140828 4078006 TM1040_2976 Ruegeria sp. TM1040 flagellar protein FlgJ YP_614970.1 3140538 R 292414 CDS YP_614971.1 99082817 4078007 3140954..3142540 1 NC_008044.1 KEGG: sil:SPO3462 flagellar hook-length control protein, ev=7e-20, 24% identity; hypothetical protein 3142540 4078007 TM1040_2977 Ruegeria sp. TM1040 hypothetical protein YP_614971.1 3140954 D 292414 CDS YP_614972.1 99082818 4078008 3142545..3143240 1 NC_008044.1 acts as a scaffold for the assembly of hook proteins onto the flagellar basal body rod; Rhodobacter sphaeroides has 2 copies of many flagellar genes; the Rhodobacter protein in this cluster is associated with a set of flagellar genes acquired by lateral gene transfer; these genes are not normally expressed; flagellar basal body rod modification protein 3143240 flgD 4078008 flgD Ruegeria sp. TM1040 flagellar basal body rod modification protein YP_614972.1 3142545 D 292414 CDS YP_614973.1 99082819 4078009 3143290..3144138 1 NC_008044.1 PFAM: aminoglycoside phosphotransferase: (1.4e-19); KEGG: sil:SPO3464 hypothetical protein, ev=1e-61, 50% identity; aminoglycoside phosphotransferase 3144138 4078009 TM1040_2979 Ruegeria sp. TM1040 aminoglycoside phosphotransferase YP_614973.1 3143290 D 292414 CDS YP_614974.1 99082820 4078010 complement(3144135..3145442) 1 NC_008044.1 PFAM: FAD dependent oxidoreductase: (5.5e-71); KEGG: sil:SPO3465 hypothetical protein, ev=1e-150, 60% identity; FAD dependent oxidoreductase 3145442 4078010 TM1040_2980 Ruegeria sp. TM1040 FAD dependent oxidoreductase YP_614974.1 3144135 R 292414 CDS YP_614975.1 99082821 4078011 complement(3145439..3146257) 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (1.3e-11); KEGG: sil:SPO3466 putrescine ABC transporter, permease protein, ev=1e-129, 87% identity; binding-protein-dependent transport system inner membrane protein 3146257 4078011 TM1040_2981 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_614975.1 3145439 R 292414 CDS YP_614976.1 99082822 4078012 complement(3146254..3147135) 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (8.5e-21); KEGG: sil:SPO3467 putrescine ABC transporter, permease protein, ev=1e-145, 85% identity; binding-protein-dependent transport system inner membrane protein 3147135 4078012 TM1040_2982 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_614976.1 3146254 R 292414 CDS YP_614977.1 99082823 4078013 complement(3147135..3148331) 1 NC_008044.1 KEGG: sil:SPO3468 putrescine ABC transporter, ATP-binding protein, ev=1e-170, 80% identity; TIGRFAM: spermidine/putrescine ABC transporter ATP-binding subunit: (3e-149); PFAM: ABC transporter related: (1.6e-58) Transport-associated OB: (4.4e-21); SMART: ATPase: (7.7e-19); spermidine/putrescine ABC transporter ATP-binding subunit 3148331 4078013 TM1040_2983 Ruegeria sp. TM1040 spermidine/putrescine ABC transporter ATP-binding subunit YP_614977.1 3147135 R 292414 CDS YP_614978.1 99082824 4078014 complement(3148365..3149453) 1 NC_008044.1 PFAM: extracellular solute-binding protein, family 1: (2.3e-06); KEGG: sil:SPO3469 putrescine ABC transporter, periplasmic putrescine-binding protein, ev=1e-153, 72% identity; extracellular solute-binding protein 3149453 4078014 TM1040_2984 Ruegeria sp. TM1040 extracellular solute-binding protein YP_614978.1 3148365 R 292414 CDS YP_614979.1 99082825 4078015 3149540..3150286 1 NC_008044.1 PFAM: regulatory protein GntR, HTH: (3.1e-13) GntR-like: (1.2e-09); KEGG: sil:SPO3470 transcriptional regulator, GntR family, ev=9e-71, 65% identity; GntR family transcriptional regulator 3150286 4078015 TM1040_2985 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_614979.1 3149540 D 292414 CDS YP_614980.1 99082826 4078016 3150350..3151747 1 NC_008044.1 PFAM: aminotransferase class-III: (4.2e-109); KEGG: sil:SPO3471 aminotransferase, class III, ev=0.0, 82% identity; aminotransferase 3151747 4078016 TM1040_2986 Ruegeria sp. TM1040 aminotransferase YP_614980.1 3150350 D 292414 CDS YP_614981.1 99082827 4078017 3152051..3153151 1 NC_008044.1 KEGG: sil:SPO3472 polyamine ABC transporter, ATP-binding protein, ev=0.0, 87% identity; TIGRFAM: spermidine/putrescine ABC transporter ATP-binding subunit: (1.2e-140); PFAM: ABC transporter related: (7.6e-59) Transport-associated OB: (6.3e-19); SMART: ATPase: (3.7e-16); spermidine/putrescine ABC transporter ATP-binding subunit 3153151 4078017 TM1040_2987 Ruegeria sp. TM1040 spermidine/putrescine ABC transporter ATP-binding subunit YP_614981.1 3152051 D 292414 CDS YP_614982.1 99082828 4078018 3153256..3154362 1 NC_008044.1 KEGG: jan:Jann_1267 polyamine ABC trasnporter, periplasmic polyamine-binding protein, ev=1e-153, 68% identity; polyamine ABC transporter substrate-binding protein 3154362 4078018 TM1040_2988 Ruegeria sp. TM1040 polyamine ABC transporter substrate-binding protein YP_614982.1 3153256 D 292414 CDS YP_614983.1 99082829 4078019 3154473..3156098 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (3.2e-18); KEGG: jan:Jann_1269 binding-protein-dependent transport systems inner membrane component, ev=0.0, 63% identity; binding-protein-dependent transport system inner membrane protein 3156098 4078019 TM1040_2989 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_614983.1 3154473 D 292414 CDS YP_614984.1 99082830 4078020 3156106..3157281 1 NC_008044.1 PFAM: binding-protein-dependent transport systems inner membrane component: (2e-11); KEGG: jan:Jann_1271 binding-protein-dependent transport systems inner membrane component, ev=1e-120, 70% identity; binding-protein-dependent transport system inner membrane protein 3157281 4078020 TM1040_2990 Ruegeria sp. TM1040 binding-protein-dependent transport system inner membrane protein YP_614984.1 3156106 D 292414 CDS YP_614985.1 99082831 4078021 complement(3157346..3158713) 1 NC_008044.1 TIGRFAM: Lytic murein transglycosylase: (2.9e-148); PFAM: Peptidoglycan-binding domain 1: (1e-07); KEGG: sil:SPO3488 peptidoglycan binding domain protein, ev=1e-146, 62% identity; lytic murein transglycosylase 3158713 4078021 TM1040_2991 Ruegeria sp. TM1040 lytic murein transglycosylase YP_614985.1 3157346 R 292414 CDS YP_614986.1 99082832 4078022 complement(3158821..3159579) 1 NC_008044.1 PFAM: Helix-turn-helix, type 11: (6.8e-17); KEGG: sil:SPO3487 hypothetical protein, ev=1e-74, 65% identity; type 11 helix-turn-helix protein 3159579 4078022 TM1040_2992 Ruegeria sp. TM1040 type 11 helix-turn-helix protein YP_614986.1 3158821 R 292414 CDS YP_614987.1 99082833 4078023 3159600..3160313 1 NC_008044.1 KEGG: sil:SPO3486 hypothetical protein, ev=4e-40, 42% identity; hypothetical protein 3160313 4078023 TM1040_2993 Ruegeria sp. TM1040 hypothetical protein YP_614987.1 3159600 D 292414 CDS YP_614988.1 99082834 4078024 complement(3160462..3162747) 1 NC_008044.1 KEGG: sil:SPO3330 ribonuclease R, ev=0.0, 79% identity; TIGRFAM: VacB and RNase II family 3'-5' exoribonucleases: (1.2e-145) Ribonuclease R: (6.3e-259); PFAM: ribonuclease II: (3.2e-79) RNA binding S1: (1.7e-10); RNAse R 3162747 4078024 TM1040_2994 Ruegeria sp. TM1040 RNAse R YP_614988.1 3160462 R 292414 CDS YP_614989.1 99082835 4078025 complement(3162863..3163285) 1 NC_008044.1 PFAM: GCN5-related N-acetyltransferase: (2.8e-17); KEGG: rsp:RSP_1127 acetyltransferase, GNAT family, ev=2e-33, 54% identity; N-acetyltransferase GCN5 3163285 4078025 TM1040_2995 Ruegeria sp. TM1040 N-acetyltransferase GCN5 YP_614989.1 3162863 R 292414 CDS YP_614990.1 99082836 4078026 complement(3163282..3164427) 1 NC_008044.1 dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE), catalyzes the hydrolysis of N-succinyl-L,Ldiaminopimelate L,L-SDAP to L,L-diaminopimelate and succinate. It is a metalloprotease containing dinuclear active sites. Its structure is similar to the carboxypeptidase G2 from Pseudomonas sp. strain RS-16 and the aminopeptidase from Aeromonas proteolytica.; succinyl-diaminopimelate desuccinylase 3164427 4078026 TM1040_2996 Ruegeria sp. TM1040 succinyl-diaminopimelate desuccinylase YP_614990.1 3163282 R 292414 CDS YP_614991.1 99082837 4078027 3164896..3165993 1 NC_008044.1 KEGG: sil:SPO3334 hypothetical protein, ev=7e-92, 48% identity; hypothetical protein 3165993 4078027 TM1040_2997 Ruegeria sp. TM1040 hypothetical protein YP_614991.1 3164896 D 292414 CDS YP_614992.1 99082838 4078028 3166064..3167128 1 NC_008044.1 PFAM: extracellular solute-binding protein, family 3: (1.1e-20); SMART: Ionotropic glutamate receptor: (7.4e-09); KEGG: sil:SPO3335 glutamine ABC transporter, periplasmic glutamine-binding protein, ev=1e-114, 62% identity; extracellular solute-binding protein 3167128 4078028 TM1040_2998 Ruegeria sp. TM1040 extracellular solute-binding protein YP_614992.1 3166064 D 292414 CDS YP_614993.1 99082839 4078029 complement(3167180..3167545) 1 NC_008044.1 KEGG: sil:SPO3336 hypothetical protein, ev=2e-45, 83% identity; hypothetical protein 3167545 4078029 TM1040_2999 Ruegeria sp. TM1040 hypothetical protein YP_614993.1 3167180 R 292414 CDS YP_614994.1 99082840 4078030 3167703..3169283 1 NC_008044.1 KEGG: sil:SPO3333 hypothetical protein, ev=1e-127, 47% identity; hypothetical protein 3169283 4078030 TM1040_3000 Ruegeria sp. TM1040 hypothetical protein YP_614994.1 3167703 D 292414 CDS YP_614995.1 99082841 4078031 complement(3169277..3169930) 1 NC_008044.1 PFAM: regulatory protein GntR, HTH: (1.4e-07) UbiC transcription regulator-associated: (2.2e-27); KEGG: sil:SPO1369 transcriptional regulator, GntR family, ev=6e-74, 59% identity; GntR family transcriptional regulator 3169930 4078031 TM1040_3001 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_614995.1 3169277 R 292414 CDS YP_614996.1 99082842 4078032 3170058..3170588 1 NC_008044.1 PFAM: protein of unknown function DUF886: (4.4e-11); KEGG: sil:SPO2147 hypothetical protein, ev=7e-20, 43% identity; hypothetical protein 3170588 4078032 TM1040_3002 Ruegeria sp. TM1040 hypothetical protein YP_614996.1 3170058 D 292414 CDS YP_614997.1 99082843 4078033 complement(3170563..3171927) 1 NC_008044.1 catalyzes the deimination of N-formimino-L-glutamate to ammonia and N-formyl-L-glutamate; N-formimino-L-glutamate deiminase 3171927 4078033 TM1040_3003 Ruegeria sp. TM1040 N-formimino-L-glutamate deiminase YP_614997.1 3170563 R 292414 CDS YP_614998.1 99082844 4078034 3172003..3173220 1 NC_008044.1 catalyzing the hydrolysis of 4-imidazolone-5-propionate to N-formimidoyl-L-glutamate, the third step in the histidine degradation pathway; imidazolonepropionase 3173220 4078034 TM1040_3004 Ruegeria sp. TM1040 imidazolonepropionase YP_614998.1 3172003 D 292414 CDS YP_614999.1 99082845 4078035 3173217..3174740 1 NC_008044.1 catalyzes the degradation of histidine to urocanate and ammmonia; histidine ammonia-lyase 3174740 4078035 TM1040_3005 Ruegeria sp. TM1040 histidine ammonia-lyase YP_614999.1 3173217 D 292414 CDS YP_615000.1 99082846 4078036 3174737..3175513 1 NC_008044.1 PFAM: N-formylglutamate amidohydrolase: (1.7e-88); KEGG: atc:AGR_L_1827 N-formylglutamate amidohydrolase, ev=2e-94, 64% identity; N-formylglutamate amidohydrolase 3175513 4078036 TM1040_3006 Ruegeria sp. TM1040 N-formylglutamate amidohydrolase YP_615000.1 3174737 D 292414 CDS YP_615001.1 99082847 4076580 3175510..3177198 1 NC_008044.1 catalyzes the formation of 4-imidazolone-5-propanoate from urocanate during histidine metabolism; urocanate hydratase 3177198 4076580 TM1040_3007 Ruegeria sp. TM1040 urocanate hydratase YP_615001.1 3175510 D 292414 CDS YP_615002.1 99082848 4076581 complement(3177254..3177643) 1 NC_008044.1 PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase: (2.9e-05); KEGG: mca:MCA2808 hypothetical protein, ev=8e-16, 34% identity; glyoxalase/bleomycin resistance protein/dioxygenase 3177643 4076581 TM1040_3008 Ruegeria sp. TM1040 glyoxalase/bleomycin resistance protein/dioxygenase YP_615002.1 3177254 R 292414 CDS YP_615003.2 161899026 4076582 complement(3177816..3178643) 1 NC_008044.1 catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate in the lysine biosynthetic pathway; 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase 3178643 dapD 4076582 dapD Ruegeria sp. TM1040 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase YP_615003.2 3177816 R 292414 CDS YP_615004.1 99082850 4076583 complement(3178764..3179393) 1 NC_008044.1 PFAM: regulatory protein GntR, HTH: (1.2e-14) GntR-like: (1.5e-05); KEGG: sil:SPO3340 transcriptional regulator, GntR family, ev=6e-65, 61% identity; GntR family transcriptional regulator 3179393 4076583 TM1040_3010 Ruegeria sp. TM1040 GntR family transcriptional regulator YP_615004.1 3178764 R 292414 CDS YP_615005.1 99082851 4076584 complement(3179412..3180365) 1 NC_008044.1 catalyzes the formation of 2-oxobutanoate from L-threonine; threonine dehydratase 3180365 4076584 TM1040_3011 Ruegeria sp. TM1040 threonine dehydratase YP_615005.1 3179412 R 292414 CDS YP_615006.1 99082852 4076585 3180522..3181370 1 NC_008044.1 PFAM: conserved hypothetical protein 730: (3e-58); KEGG: sil:SPO3342 decarboxylase family protein, ev=1e-119, 74% identity; hypothetical protein 3181370 4076585 TM1040_3012 Ruegeria sp. TM1040 hypothetical protein YP_615006.1 3180522 D 292414 CDS YP_615007.1 99082853 4076586 complement(3181566..3181769) 1 NC_008044.1 KEGG: sil:SPO3343 hypothetical protein, ev=1e-12, 55% identity; hypothetical protein 3181769 4076586 TM1040_3013 Ruegeria sp. TM1040 hypothetical protein YP_615007.1 3181566 R 292414 CDS YP_615008.1 99082854 4076587 complement(3181937..3183130) 1 NC_008044.1 TIGRFAM: conserved hypothetical protein: (1.2e-137); PFAM: Radical SAM: (3.2e-20); KEGG: sil:SPO3346 radical SAM enzyme, Cfr family, ev=0.0, 89% identity; hypothetical protein 3183130 4076587 TM1040_3014 Ruegeria sp. TM1040 hypothetical protein YP_615008.1 3181937 R 292414 CDS YP_615009.1 99082855 4076588 complement(3183354..3183902) 1 NC_008044.1 KEGG: sil:SPO3348 hypothetical protein, ev=3e-65, 69% identity; hypothetical protein 3183902 4076588 TM1040_3015 Ruegeria sp. TM1040 hypothetical protein YP_615009.1 3183354 R 292414 CDS YP_615010.1 99082856 4076589 3184117..3185124 1 NC_008044.1 PFAM: L-asparaginase II: (2.3e-103); KEGG: sil:SPO3349 L-asparaginase, thermolabile family, ev=1e-122, 65% identity; L-asparaginase II 3185124 4076589 TM1040_3016 Ruegeria sp. TM1040 L-asparaginase II YP_615010.1 3184117 D 292414 CDS YP_615011.1 99082857 4076590 complement(3185138..3185458) 1 NC_008044.1 PFAM: DGPFAETKE: (4.8e-06); KEGG: sil:SPO3350 hypothetical protein, ev=8e-37, 70% identity; hypothetical protein 3185458 4076590 TM1040_3017 Ruegeria sp. TM1040 hypothetical protein YP_615011.1 3185138 R 292414 CDS YP_615012.1 99082858 4076591 complement(3185545..3186303) 1 NC_008044.1 PFAM: protein of unknown function DUF81: (1.4e-31); KEGG: mlo:mlr1193 hypothetical protein, ev=1e-78, 58% identity; hypothetical protein 3186303 4076591 TM1040_3018 Ruegeria sp. TM1040 hypothetical protein YP_615012.1 3185545 R 292414 CDS YP_615013.1 99082859 4076592 complement(3186312..3187187) 1 NC_008044.1 KEGG: sil:SPO3353 phosphoserine phosphatase, ev=1e-131, 80% identity; TIGRFAM: phosphoserine phosphatase SerB: (4.2e-73) HAD-superfamily hydrolase subfamily IB, PSPase-like: (2.2e-39); PFAM: Haloacid dehalogenase-like hydrolase: (2.4e-15); phosphoserine phosphatase 3187187 4076592 TM1040_3019 Ruegeria sp. TM1040 phosphoserine phosphatase YP_615013.1 3186312 R 292414 CDS YP_615014.1 99082860 4076593 3187424..3188569 1 NC_008044.1 catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate; phosphoserine aminotransferase 3188569 4076593 TM1040_3020 Ruegeria sp. TM1040 phosphoserine aminotransferase YP_615014.1 3187424 D 292414 CDS YP_615015.1 99082861 4076594 3188663..3190258 1 NC_008044.1 catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate; D-3-phosphoglycerate dehydrogenase 3190258 4076594 TM1040_3021 Ruegeria sp. TM1040 D-3-phosphoglycerate dehydrogenase YP_615015.1 3188663 D 292414 CDS YP_615016.1 99082862 4076595 3190437..3191171 1 NC_008044.1 PFAM: metallophosphoesterase: (4.5e-13); KEGG: sil:SPO3358 serine/threonine protein phosphatase family protein, ev=8e-81, 58% identity; bis(5'-nucleosyl)-tetraphosphatase 3191171 4076595 TM1040_3022 Ruegeria sp. TM1040 bis(5'-nucleosyl)-tetraphosphatase YP_615016.1 3190437 D 292414 CDS YP_615017.1 99082863 4076596 complement(3191378..3192424) 1 NC_008044.1 converts threonine and NAD to 1,2-amino-3-oxobutanoate and NADH; functions in threonine catabolism; L-threonine 3-dehydrogenase 3192424 tdh 4076596 tdh Ruegeria sp. TM1040 L-threonine 3-dehydrogenase YP_615017.1 3191378 R 292414 CDS YP_615018.1 99082864 4076597 complement(3192426..3193610) 1 NC_008044.1 catalyzes the formation of 2-amino-3-oxobutanoate from acetyl-CoA and glycine; 2-amino-3-ketobutyrate CoA ligase 3193610 4076597 TM1040_3024 Ruegeria sp. TM1040 2-amino-3-ketobutyrate CoA ligase YP_615018.1 3192426 R 292414 CDS YP_615019.1 99082865 4076598 complement(3193775..3194341) 1 NC_008044.1 PFAM: helix-turn-helix motif: (2.6e-17) Cupin 2, conserved barrel: (0.0048); KEGG: sil:SPO0141 DNA binding protein, , ev=2e-73, 79% identity; XRE family transcriptional regulator 3194341 4076598 TM1040_3025 Ruegeria sp. TM1040 XRE family transcriptional regulator YP_615019.1 3193775 R 292414 CDS YP_615020.1 99082866 4076599 3194450..3195625 1 NC_008044.1 catalyzes the formation of beta-ketovaleryl-CoA from acetyl-CoA and propionyl-CoA; beta-ketothiolase 3195625 4076599 TM1040_3026 Ruegeria sp. TM1040 beta-ketothiolase YP_615020.1 3194450 D 292414 CDS YP_615021.1 99082867 4076600 complement(3195735..3197261) 1 NC_008044.1 TIGRFAM: 2-polyprenylphenol 6-hydroxylase: (2.9e-202); PFAM: ABC-1: (5.1e-44); KEGG: sil:SPO0144 2-polyprenylphenol 6-hydroxylase, ev=0.0, 82% identity; 2-octaprenylphenol hydroxylase 3197261 4076600 TM1040_3027 Ruegeria sp. TM1040 2-octaprenylphenol hydroxylase YP_615021.1 3195735 R 292414 CDS YP_615022.1 99082868 4076601 complement(3197265..3198017) 1 NC_008044.1 TIGRFAM: ubiquinone/menaquinone biosynthesis methyltransferases: (3.1e-122); PFAM: UbiE/COQ5 methyltransferase: (6e-119) Methyltransferase type 11: (4.7e-25) Methyltransferase type 12: (4.4e-13); KEGG: sil:SPO0145 ubiquinone/menaquinone biosynthesis methyltransferase UbiE, ev=1e-130, 89% identity; demethylmenaquinone methyltransferase / 2-octaprenyl-6-methoxy-1,4-benzoquinone methylase 3198017 4076601 TM1040_3028 Ruegeria sp. TM1040 demethylmenaquinone methyltransferase / 2-octaprenyl-6-methoxy-1,4-benzoquinone methylase YP_615022.1 3197265 R 292414 CDS YP_615023.1 99082869 4076602 3198104..3198955 1 NC_008044.1 Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases; formamidopyrimidine-DNA glycosylase 3198955 4076602 TM1040_3029 Ruegeria sp. TM1040 formamidopyrimidine-DNA glycosylase YP_615023.1 3198104 D 292414 CDS YP_615024.1 99082870 4076603 3199021..3199797 1 NC_008044.1 PFAM: Enoyl-CoA hydratase/isomerase: (4.1e-74); KEGG: sil:SPO0147 enoyl-CoA hydratase, ev=1e-116, 80% identity; short chain enoyl-CoA hydratase 3199797 4076603 TM1040_3030 Ruegeria sp. TM1040 short chain enoyl-CoA hydratase YP_615024.1 3199021 D 292414 CDS YP_615025.1 99082871 4076604 3200122..3200385 1 NC_008044.1 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase; 30S ribosomal protein S20 3200385 rpsT 4076604 rpsT Ruegeria sp. TM1040 30S ribosomal protein S20 YP_615025.1 3200122 D 292414 CDS