-- dump date 20140620_041902 -- class Genbank::Feature -- table feature -- table main -- field 1 id -- field 2 type -- field 3 name -- field 4 contig -- field 5 start_pos -- field 6 end_pos -- field 7 strand -- field 8 description -- field 9 chrom_position -- field 10 organism -- field 11 GeneID -- header -- id type name contig start_pos end_pos strand description chrom_position organism GeneID 292414000001 SEQ_END SEQ_END NC_008042.1 130973 130973 DR NC_008042.1; contig end 130973..130973 Ruegeria sp. TM1040 292414000002 SEQ_END SEQ_END NC_008043.1 821788 821788 DR NC_008043.1; contig end 821788..821788 Ruegeria sp. TM1040 292414000003 SEQ_END SEQ_END NC_008044.1 3200938 3200938 DR NC_008044.1; contig end 3200938..3200938 Ruegeria sp. TM1040 YP_611162.1 CDS TM1040_3767 NC_008042.1 27 5300 D 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 27..5300 Ruegeria sp. TM1040 4074939 YP_611163.1 CDS TM1040_3768 NC_008042.1 6566 7546 D KEGG: xcb:XC_2789 hypothetical protein, ev=6e-14, 47% identity; hypothetical protein 6566..7546 Ruegeria sp. TM1040 4074940 YP_611164.1 CDS TM1040_3769 NC_008042.1 7780 8247 D hypothetical protein 7780..8247 Ruegeria sp. TM1040 4074941 YP_611165.1 CDS TM1040_3770 NC_008042.1 14155 14565 D hypothetical protein 14155..14565 Ruegeria sp. TM1040 4074942 YP_611166.1 CDS TM1040_3771 NC_008042.1 15000 16031 R KEGG: rsp:RSP_3991 hypothetical protein, ev=1e-99, 57% identity; hypothetical protein complement(15000..16031) Ruegeria sp. TM1040 4074943 YP_611167.1 CDS TM1040_3772 NC_008042.1 16148 17152 R KEGG: jan:Jann_4266 RepA, ev=1e-126, 68% identity; hypothetical protein complement(16148..17152) Ruegeria sp. TM1040 4074944 YP_611168.1 CDS TM1040_3773 NC_008042.1 17636 19045 D 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 17636..19045 Ruegeria sp. TM1040 4074945 YP_611169.1 CDS TM1040_3774 NC_008042.1 19119 20249 D PFAM: ParB-like nuclease: (6e-05); KEGG: jan:Jann_4264 ParB-like nuclease, ev=1e-48, 36% identity; ParB-like nuclease 19119..20249 Ruegeria sp. TM1040 4074946 YP_611170.1 CDS TM1040_3775 NC_008042.1 20354 21658 R 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 complement(20354..21658) Ruegeria sp. TM1040 4074870 YP_611171.1 CDS TM1040_3776 NC_008042.1 22480 23481 R 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 complement(22480..23481) Ruegeria sp. TM1040 4074871 YP_611172.1 CDS TM1040_3777 NC_008042.1 24265 24642 R PFAM: helix-turn-helix motif: (2e-07); KEGG: jan:Jann_1232 transcriptional regulator, XRE family, ev=2e-29, 54% identity; XRE family transcriptional regulator complement(24265..24642) Ruegeria sp. TM1040 4074872 YP_611173.1 CDS TM1040_3778 NC_008042.1 25175 26596 R 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) complement(25175..26596) Ruegeria sp. TM1040 4074873 YP_611174.1 CDS TM1040_3779 NC_008042.1 27852 28736 D PFAM: Domain of unknown function DUF1738: (4.4e-59); KEGG: jan:Jann_3213 antirestriction protein-like, ev=1e-116, 90% identity; hypothetical protein 27852..28736 Ruegeria sp. TM1040 4074874 YP_611175.1 CDS TM1040_3780 NC_008042.1 29156 30001 R KEGG: jan:Jann_0647 hypothetical protein, ev=7e-82, 56% identity; hypothetical protein complement(29156..30001) Ruegeria sp. TM1040 4074875 YP_611176.1 CDS TM1040_3781 NC_008042.1 30047 30502 R PFAM: Methionine sulfoxide reductase B: (4.5e-58); KEGG: sme:SMc01724 hypothetical protein, ev=8e-54, 61% identity; protein-methionine-S-oxide reductase complement(30047..30502) Ruegeria sp. TM1040 4074876 YP_611177.1 CDS TM1040_3782 NC_008042.1 30573 31124 R 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 complement(30573..31124) Ruegeria sp. TM1040 4074877 YP_611178.1 CDS TM1040_3783 NC_008042.1 31246 31932 R KEGG: jan:Jann_0649 hypothetical protein, ev=2e-42, 45% identity; hypothetical protein complement(31246..31932) Ruegeria sp. TM1040 4074878 YP_611179.1 CDS TM1040_3784 NC_008042.1 31929 32483 R 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 complement(31929..32483) Ruegeria sp. TM1040 4074879 YP_611180.1 CDS TM1040_3785 NC_008042.1 33104 35482 D 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 33104..35482 Ruegeria sp. TM1040 4074880 YP_611181.1 CDS TM1040_3786 NC_008042.1 35844 36596 D hypothetical protein 35844..36596 Ruegeria sp. TM1040 4074881 YP_611182.1 CDS TM1040_3787 NC_008042.1 37024 37380 R PFAM: nucleic acid binding, OB-fold, tRNA/helicase-type: (0.092); nucleic acid binding, OB-fold, tRNA/helicase-type complement(37024..37380) Ruegeria sp. TM1040 4074882 YP_611183.1 CDS TM1040_3788 NC_008042.1 37746 38255 D KEGG: rsp:RSP_7254 hypothetical protein, ev=2e-23, 45% identity; hypothetical protein 37746..38255 Ruegeria sp. TM1040 4074883 YP_611184.1 CDS TM1040_3789 NC_008042.1 38357 38752 D SMART: Staphylococcus nuclease (SNase-like): (3.9e-06); KEGG: jan:Jann_3714 nuclease (SNase-like), ev=3e-21, 46% identity; SNase-like nuclease 38357..38752 Ruegeria sp. TM1040 4074884 YP_611185.1 CDS TM1040_3791 NC_008042.1 39882 40088 D hypothetical protein 39882..40088 Ruegeria sp. TM1040 4074885 YP_611186.1 CDS TM1040_3792 NC_008042.1 40650 41243 D hypothetical protein 40650..41243 Ruegeria sp. TM1040 4074886 YP_611187.1 CDS TM1040_3793 NC_008042.1 41230 43440 D 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 41230..43440 Ruegeria sp. TM1040 4074887 YP_611188.1 CDS TM1040_3794 NC_008042.1 43437 45443 D PFAM: TRAG protein: (3.6e-71); KEGG: ret:RHE_PA00070 transport secretion system IV, VirD4 protein, ev=2e-77, 34% identity; TRAG protein 43437..45443 Ruegeria sp. TM1040 4074888 YP_611189.1 CDS TM1040_3795 NC_008042.1 45670 47667 R 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 complement(45670..47667) Ruegeria sp. TM1040 4074889 YP_611190.1 CDS TM1040_3796 NC_008042.1 47907 48452 R hypothetical protein complement(47907..48452) Ruegeria sp. TM1040 4074947 YP_611191.1 CDS TM1040_3797 NC_008042.1 49911 51461 D hypothetical protein 49911..51461 Ruegeria sp. TM1040 4074948 YP_611192.1 CDS TM1040_3798 NC_008042.1 52027 52281 D hypothetical protein 52027..52281 Ruegeria sp. TM1040 4074949 YP_611193.1 CDS TM1040_3799 NC_008042.1 52469 53038 D hypothetical protein 52469..53038 Ruegeria sp. TM1040 4074950 YP_611194.1 CDS TM1040_3800 NC_008042.1 53072 54244 D PFAM: protein of unknown function DUF1625: (2.9e-40); KEGG: mlo:mll2895 hypothetical protein, ev=3e-77, 40% identity; hypothetical protein 53072..54244 Ruegeria sp. TM1040 4074951 YP_611195.1 CDS TM1040_3801 NC_008042.1 54278 54745 D hypothetical protein 54278..54745 Ruegeria sp. TM1040 4074952 YP_611196.1 CDS TM1040_3802 NC_008042.1 54757 55578 D hypothetical protein 54757..55578 Ruegeria sp. TM1040 4074953 YP_611197.1 CDS TM1040_3803 NC_008042.1 55589 56197 D KEGG: sil:SPO3001 hypothetical protein, ev=4e-19, 34% identity; hypothetical protein 55589..56197 Ruegeria sp. TM1040 4074954 YP_611198.1 CDS TM1040_3804 NC_008042.1 56206 56622 D hypothetical protein 56206..56622 Ruegeria sp. TM1040 4074955 YP_611199.1 CDS TM1040_3805 NC_008042.1 56625 57533 D hypothetical protein 56625..57533 Ruegeria sp. TM1040 4074956 YP_611200.1 CDS TM1040_3806 NC_008042.1 57539 58570 D hypothetical protein 57539..58570 Ruegeria sp. TM1040 4074957 YP_611201.1 CDS TM1040_3807 NC_008042.1 58658 59440 D hypothetical protein 58658..59440 Ruegeria sp. TM1040 4074958 YP_611202.1 CDS TM1040_3808 NC_008042.1 59718 60518 D PFAM: regulatory protein, LuxR: (5.9e-05); LuxR family transcriptional regulator 59718..60518 Ruegeria sp. TM1040 4074959 YP_611203.1 CDS TM1040_3809 NC_008042.1 60669 61748 R 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 complement(60669..61748) Ruegeria sp. TM1040 4074960 YP_611204.1 CDS TM1040_3810 NC_008042.1 61761 62174 R hypothetical protein complement(61761..62174) Ruegeria sp. TM1040 4074961 YP_611205.1 CDS TM1040_3811 NC_008042.1 62171 62365 R hypothetical protein complement(62171..62365) Ruegeria sp. TM1040 4074962 YP_611206.1 CDS TM1040_3812 NC_008042.1 62362 63348 R 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 complement(62362..63348) Ruegeria sp. TM1040 4074963 YP_611207.1 CDS TM1040_3813 NC_008042.1 63353 64732 R PFAM: conjugation TrbI-like protein: (1.2e-61); KEGG: mlo:mlr9259 conjugal transfer protein, ev=3e-38, 36% identity; conjugation TrbI-like protein complement(63353..64732) Ruegeria sp. TM1040 4074964 YP_611208.1 CDS TM1040_3814 NC_008042.1 64729 65424 R 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 complement(64729..65424) Ruegeria sp. TM1040 4074965 YP_611209.1 CDS TM1040_3815 NC_008042.1 65427 66080 R PFAM: VirB8: (7.9e-10); KEGG: atc:AGR_pAT_228 virB8 type IV secretion protein, ev=7e-11, 26% identity; VirB8 complement(65427..66080) Ruegeria sp. TM1040 4074966 YP_611210.1 CDS TM1040_3816 NC_008042.1 66097 66906 R KEGG: xoo:XOO0603 TraF protein, ev=7e-07, 24% identity; hypothetical protein complement(66097..66906) Ruegeria sp. TM1040 4074967 YP_611211.1 CDS TM1040_3817 NC_008042.1 66906 68060 R PFAM: Lytic transglycosylase, catalytic: (7.1e-19); KEGG: bsu:BG13596 similar to lytic transglycosylase, ev=1e-26, 57% identity; lytic transglycosylase, catalytic complement(66906..68060) Ruegeria sp. TM1040 4074968 YP_611212.1 CDS TM1040_3818 NC_008042.1 68050 68217 R hypothetical protein complement(68050..68217) Ruegeria sp. TM1040 4074969 YP_611213.1 CDS TM1040_3819 NC_008042.1 68214 70589 R 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 complement(68214..70589) Ruegeria sp. TM1040 4074970 YP_611214.1 CDS TM1040_3820 NC_008042.1 70579 70824 R PFAM: type IV secretory pathway, VirB3-like: (2.2e-09); type IV secretory pathway, VirB3-like complement(70579..70824) Ruegeria sp. TM1040 4074971 YP_611215.1 CDS TM1040_3821 NC_008042.1 70850 71143 R 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 complement(70850..71143) Ruegeria sp. TM1040 4074972 YP_611216.1 CDS TM1040_3822 NC_008042.1 71140 71754 R PFAM: Lytic transglycosylase, catalytic: (2.9e-17); KEGG: mta:Moth_1608 lytic transglycosylase, catalytic, ev=1e-24, 41% identity; lytic transglycosylase, catalytic complement(71140..71754) Ruegeria sp. TM1040 4074973 YP_611217.1 CDS TM1040_3823 NC_008042.1 71798 72151 R hypothetical protein complement(71798..72151) Ruegeria sp. TM1040 4074974 YP_611218.1 CDS TM1040_3824 NC_008042.1 72319 72615 D hypothetical protein 72319..72615 Ruegeria sp. TM1040 4074975 YP_611219.1 CDS TM1040_3825 NC_008042.1 72863 73168 D hypothetical protein 72863..73168 Ruegeria sp. TM1040 4074976 YP_611220.1 CDS TM1040_3826 NC_008042.1 73161 73388 D hypothetical protein 73161..73388 Ruegeria sp. TM1040 4074977 YP_611221.1 CDS TM1040_3827 NC_008042.1 73530 73781 R hypothetical protein complement(73530..73781) Ruegeria sp. TM1040 4074978 YP_611222.1 CDS TM1040_3828 NC_008042.1 73771 74475 R 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 complement(73771..74475) Ruegeria sp. TM1040 4074979 YP_611223.1 CDS TM1040_3829 NC_008042.1 74574 75452 D 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 74574..75452 Ruegeria sp. TM1040 4074980 YP_611224.1 CDS TM1040_3830 NC_008042.1 75610 76341 R hypothetical protein complement(75610..76341) Ruegeria sp. TM1040 4074981 YP_611225.1 CDS TM1040_3832 NC_008042.1 76954 78234 D PFAM: glycosyl transferase, group 1: (5.6e-23); KEGG: ctc:CTC00268 mannosyltransferase, ev=2e-21, 26% identity; glycosyl transferase, group 1 76954..78234 Ruegeria sp. TM1040 4074982 YP_611226.1 CDS TM1040_3833 NC_008042.1 78296 79729 R PFAM: glycosyl transferase, group 1: (0.00036); KEGG: jan:Jann_2029 glycosyl transferase, group 1, ev=7e-59, 47% identity; glycosyl transferase, group 1 complement(78296..79729) Ruegeria sp. TM1040 4074983 YP_611227.1 CDS TM1040_3834 NC_008042.1 79812 81131 R 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 complement(79812..81131) Ruegeria sp. TM1040 4074984 YP_611228.1 CDS TM1040_3835 NC_008042.1 81194 82906 R 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 complement(81194..82906) Ruegeria sp. TM1040 4074985 YP_611229.1 CDS TM1040_3836 NC_008042.1 83259 83615 D hypothetical protein 83259..83615 Ruegeria sp. TM1040 4074900 YP_611230.1 CDS TM1040_3838 NC_008042.1 84226 84423 R KEGG: rru:Rru_B0036 hypothetical protein, ev=1e-06, 45% identity; hypothetical protein complement(84226..84423) Ruegeria sp. TM1040 4074901 YP_611231.1 CDS TM1040_3839 NC_008042.1 84443 85978 R PFAM: Methyltransferase type 11: (0.00031); KEGG: ccr:CC1017 hypothetical protein, ev=1e-152, 51% identity; methyltransferase type 11 complement(84443..85978) Ruegeria sp. TM1040 4074902 YP_611232.1 CDS TM1040_3840 NC_008042.1 86070 89351 R 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 complement(86070..89351) Ruegeria sp. TM1040 4074903 YP_611233.1 CDS TM1040_3841 NC_008042.1 89417 89767 D hypothetical protein 89417..89767 Ruegeria sp. TM1040 4074904 YP_611234.1 CDS TM1040_3842 NC_008042.1 90028 90330 D 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 90028..90330 Ruegeria sp. TM1040 4074905 YP_611235.1 CDS TM1040_3843 NC_008042.1 90406 92100 D KEGG: ccr:CC1005 hypothetical protein, ev=8e-14, 22% identity; hypothetical protein 90406..92100 Ruegeria sp. TM1040 4074906 YP_611236.1 CDS TM1040_3844 NC_008042.1 92309 93592 R KEGG: ccr:CC1003 glyscosyl transferase, group 1 family protein, ev=6e-23, 27% identity; hypothetical protein complement(92309..93592) Ruegeria sp. TM1040 4074907 YP_611237.1 CDS TM1040_3845 NC_008042.1 93592 96000 R 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 complement(93592..96000) Ruegeria sp. TM1040 4074908 YP_611238.1 CDS TM1040_3846 NC_008042.1 96000 97055 R 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 complement(96000..97055) Ruegeria sp. TM1040 4074909 YP_611239.1 CDS TM1040_3847 NC_008042.1 97529 100117 R 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 complement(97529..100117) Ruegeria sp. TM1040 4074910 YP_611240.1 CDS TM1040_3848 NC_008042.1 100442 102199 R 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 complement(100442..102199) Ruegeria sp. TM1040 4074911 YP_611241.1 CDS TM1040_3849 NC_008042.1 102308 102607 R hypothetical protein complement(102308..102607) Ruegeria sp. TM1040 4074912 YP_611242.1 CDS TM1040_3850 NC_008042.1 102774 103088 R hypothetical protein complement(102774..103088) Ruegeria sp. TM1040 4074913 YP_611243.1 CDS TM1040_3851 NC_008042.1 103394 103981 D KEGG: sil:SPO0081 hypothetical protein, ev=2e-27, 34% identity; hypothetical protein 103394..103981 Ruegeria sp. TM1040 4074914 YP_611244.1 CDS TM1040_3852 NC_008042.1 104093 104719 R hypothetical protein complement(104093..104719) Ruegeria sp. TM1040 4074915 YP_611245.1 CDS TM1040_3853 NC_008042.1 105732 105923 R KEGG: rru:Rru_B0036 hypothetical protein, ev=2e-10, 55% identity; hypothetical protein complement(105732..105923) Ruegeria sp. TM1040 4074916 YP_611246.1 CDS TM1040_3854 NC_008042.1 106169 107140 R 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 complement(106169..107140) Ruegeria sp. TM1040 4074917 YP_611247.1 CDS TM1040_3855 NC_008042.1 107450 107809 D PFAM: DGPFAETKE: (2.2e-37); KEGG: rba:RB560 hypothetical protein, ev=2e-21, 46% identity; hypothetical protein 107450..107809 Ruegeria sp. TM1040 4074918 YP_611248.1 CDS TM1040_3856 NC_008042.1 107815 109062 D 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 107815..109062 Ruegeria sp. TM1040 4074919 YP_611249.1 CDS TM1040_3857 NC_008042.1 109117 109884 D KEGG: cvi:CV0374 hypothetical protein, ev=4e-36, 35% identity; hypothetical protein 109117..109884 Ruegeria sp. TM1040 4074920 YP_611250.1 CDS TM1040_3858 NC_008042.1 109942 111195 R 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 complement(109942..111195) Ruegeria sp. TM1040 4074921 YP_611251.1 CDS TM1040_3859 NC_008042.1 111206 112078 R 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 complement(111206..112078) Ruegeria sp. TM1040 4074922 YP_611252.1 CDS TM1040_3860 NC_008042.1 112075 112974 R 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 complement(112075..112974) Ruegeria sp. TM1040 4074923 YP_611253.1 CDS TM1040_3861 NC_008042.1 112986 114038 R 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 complement(112986..114038) Ruegeria sp. TM1040 4074924 YP_611254.1 CDS TM1040_3862 NC_008042.1 114096 115220 R PFAM: acyltransferase 3: (7.7e-36); KEGG: ade:Adeh_1161 acyltransferase 3, ev=2e-46, 36% identity; acyltransferase 3 complement(114096..115220) Ruegeria sp. TM1040 4074925 YP_611255.1 CDS TM1040_3863 NC_008042.1 115225 115773 R 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 complement(115225..115773) Ruegeria sp. TM1040 4074926 YP_611256.1 CDS TM1040_3864 NC_008042.1 116076 116963 R PFAM: PfkB: (4e-38); KEGG: jan:Jann_2574 PfkB, ev=3e-69, 51% identity; 2-keto-3-deoxygluconate kinase complement(116076..116963) Ruegeria sp. TM1040 4074927 YP_611257.1 CDS TM1040_3865 NC_008042.1 116963 118360 R catalyzes the interconversion of D-glucuronate to D-fructuronate or D-galacturonate to D-tagaturonate; functions in glucuronic and galacturonic metabolism; glucuronate isomerase complement(116963..118360) Ruegeria sp. TM1040 4074928 YP_611258.1 CDS TM1040_3866 NC_008042.1 118357 119772 R 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 complement(118357..119772) Ruegeria sp. TM1040 4074929 YP_611259.1 CDS TM1040_3867 NC_008042.1 119769 122123 R PFAM: glycoside hydrolase, family 31: (1.1e-156); KEGG: ypm:YP3545 putative glucosidase, ev=0.0, 55% identity; Alpha-glucosidase complement(119769..122123) Ruegeria sp. TM1040 4074930 YP_611260.1 CDS TM1040_3868 NC_008042.1 122123 123424 R 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 complement(122123..123424) Ruegeria sp. TM1040 4074931 YP_611261.1 CDS TM1040_3869 NC_008042.1 123436 123951 R 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 complement(123436..123951) Ruegeria sp. TM1040 4074932 YP_611262.1 CDS TM1040_3870 NC_008042.1 124211 125185 D 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 124211..125185 Ruegeria sp. TM1040 4074933 YP_611263.1 CDS TM1040_3871 NC_008042.1 125204 127015 D 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 125204..127015 Ruegeria sp. TM1040 4074934 YP_611264.1 CDS TM1040_3872 NC_008042.1 127012 127743 D 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 127012..127743 Ruegeria sp. TM1040 4074935 YP_611265.1 CDS TM1040_3873 NC_008042.1 127810 128979 D catalyzes the formation of 2-dehydro-3-deoxy-D-gluconate from mannonate; mannonate dehydratase 127810..128979 Ruegeria sp. TM1040 4074936 YP_611266.1 CDS TM1040_3874 NC_008042.1 129842 130435 R hypothetical protein complement(129842..130435) Ruegeria sp. TM1040 4074937 YP_611267.1 CDS TM1040_3875 NC_008042.1 130436 130963 R hypothetical protein complement(130436..130963) Ruegeria sp. TM1040 4074938 YP_611268.1 CDS TM1040_3032 NC_008043.1 6 827 D 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 6..827 Ruegeria sp. TM1040 4075737 YP_611269.1 CDS TM1040_3033 NC_008043.1 855 1769 D 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 855..1769 Ruegeria sp. TM1040 4075738 YP_611270.1 CDS TM1040_3034 NC_008043.1 1785 2594 R 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 complement(1785..2594) Ruegeria sp. TM1040 4075739 YP_611271.1 CDS TM1040_3035 NC_008043.1 2587 3354 R 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 complement(2587..3354) Ruegeria sp. TM1040 4075740 YP_611272.1 CDS TM1040_3036 NC_008043.1 3409 4425 R KEGG: sil:SPO3620 sulfonate ABC transporter, periplamic sulfonate-binding protein, ev=1e-119, 66% identity; sulfonate ABC transporter, periplamic sulfonate-binding protein complement(3409..4425) Ruegeria sp. TM1040 4075741 YP_611273.1 CDS TM1040_3037 NC_008043.1 4480 5145 R 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 complement(4480..5145) Ruegeria sp. TM1040 4075742 YP_611274.1 CDS TM1040_3038 NC_008043.1 5407 6159 D 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 5407..6159 Ruegeria sp. TM1040 4075743 YP_611275.1 CDS TM1040_3039 NC_008043.1 6188 6838 D 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 6188..6838 Ruegeria sp. TM1040 4075133 YP_611276.1 CDS TM1040_3040 NC_008043.1 6835 7581 D 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 6835..7581 Ruegeria sp. TM1040 4075134 YP_611277.1 CDS TM1040_3041 NC_008043.1 8058 11189 D 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 8058..11189 Ruegeria sp. TM1040 4075135 YP_611278.1 CDS TM1040_3042 NC_008043.1 11228 12154 R PFAM: PfkB: (1.8e-27); KEGG: jan:Jann_2674 PfkB, ev=2e-95, 59% identity; PfkB protein complement(11228..12154) Ruegeria sp. TM1040 4075136 YP_611279.1 CDS TM1040_3043 NC_008043.1 12814 13383 D hypothetical protein 12814..13383 Ruegeria sp. TM1040 4075137 YP_611280.1 CDS TM1040_3044 NC_008043.1 13418 14599 D PFAM: protein of unknown function DUF1625: (2.9e-35); KEGG: mlo:mll2895 hypothetical protein, ev=2e-63, 35% identity; hypothetical protein 13418..14599 Ruegeria sp. TM1040 4075138 YP_611281.1 CDS TM1040_3045 NC_008043.1 14630 15097 D hypothetical protein 14630..15097 Ruegeria sp. TM1040 4075139 YP_611282.1 CDS TM1040_3046 NC_008043.1 15109 15927 D hypothetical protein 15109..15927 Ruegeria sp. TM1040 4075140 YP_611283.1 CDS TM1040_3047 NC_008043.1 15929 16912 D hypothetical protein 15929..16912 Ruegeria sp. TM1040 4075141 YP_611284.1 CDS TM1040_3048 NC_008043.1 16974 17483 R KEGG: ppu:PP2506 hypothetical protein, ev=1e-08, 30% identity; hypothetical protein complement(16974..17483) Ruegeria sp. TM1040 4075142 YP_611285.1 CDS TM1040_3049 NC_008043.1 17544 19208 R 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 complement(17544..19208) Ruegeria sp. TM1040 4075143 YP_611286.1 CDS TM1040_3050 NC_008043.1 19304 20188 R 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 complement(19304..20188) Ruegeria sp. TM1040 4075144 YP_611287.1 CDS TM1040_3051 NC_008043.1 20200 21609 R 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 complement(20200..21609) Ruegeria sp. TM1040 4075145 YP_611288.1 CDS TM1040_3052 NC_008043.1 21606 22877 R PFAM: amidohydrolase: (0.00015) Amidohydrolase 3: (0.00056); KEGG: jan:Jann_1474 amidohydrolase 3, ev=2e-43, 32% identity; amidohydrolase complement(21606..22877) Ruegeria sp. TM1040 4075146 YP_611289.1 CDS TM1040_3053 NC_008043.1 22874 23665 R PFAM: Creatininase: (4.9e-29); KEGG: mlo:mlr1298 creatinine amidohydrolase, , ev=6e-46, 39% identity; creatininase complement(22874..23665) Ruegeria sp. TM1040 4075147 YP_611290.1 CDS TM1040_3054 NC_008043.1 23662 24357 R KEGG: sme:SMc03236 glutamine amidotransferase, ev=4e-30, 34% identity; glutamine amidotransferase complement(23662..24357) Ruegeria sp. TM1040 4075148 YP_611291.1 CDS TM1040_3055 NC_008043.1 24485 24871 D PFAM: Endoribonuclease L-PSP: (3.1e-10); KEGG: jan:Jann_1470 endoribonuclease L-PSP, ev=7e-34, 56% identity; endoribonuclease L-PSP 24485..24871 Ruegeria sp. TM1040 4075149 YP_611292.1 CDS TM1040_3056 NC_008043.1 25025 25267 R hypothetical protein complement(25025..25267) Ruegeria sp. TM1040 4075150 YP_611293.1 CDS TM1040_3057 NC_008043.1 25251 25712 R KEGG: sil:SPO0300 hypothetical protein, ev=2e-50, 67% identity; hypothetical protein complement(25251..25712) Ruegeria sp. TM1040 4075151 YP_611294.1 CDS TM1040_3058 NC_008043.1 25759 26748 R PFAM: beta-lactamase-like: (1e-23); KEGG: sil:SPO0299 metallo-beta-lactamase family protein, ev=1e-166, 83% identity; beta-lactamase-like protein complement(25759..26748) Ruegeria sp. TM1040 4075152 YP_611295.1 CDS TM1040_3059 NC_008043.1 26802 28514 R 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 complement(26802..28514) Ruegeria sp. TM1040 4075153 YP_611296.1 CDS TM1040_3060 NC_008043.1 28710 29681 D 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 28710..29681 Ruegeria sp. TM1040 4075154 YP_611297.1 CDS TM1040_3061 NC_008043.1 29742 30509 D 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 29742..30509 Ruegeria sp. TM1040 4075155 YP_611298.1 CDS TM1040_3062 NC_008043.1 30534 31142 D PFAM: metallophosphoesterase: (6.1e-09); KEGG: sil:SPO0289 Ser/Thr protein phosphatase family protein, ev=6e-67, 63% identity; metallophosphoesterase 30534..31142 Ruegeria sp. TM1040 4075156 YP_611299.1 CDS TM1040_3063 NC_008043.1 31142 31765 D 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 31142..31765 Ruegeria sp. TM1040 4075157 YP_611300.1 CDS TM1040_3064 NC_008043.1 31771 32313 D 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 31771..32313 Ruegeria sp. TM1040 4075158 YP_611301.1 CDS TM1040_3065 NC_008043.1 32428 33891 D PFAM: secretion protein HlyD: (0.00049); KEGG: sil:SPO0292 efflux transporter, RND family, MFP subunit, ev=1e-147, 58% identity; secretion protein HlyD 32428..33891 Ruegeria sp. TM1040 4075159 YP_611302.1 CDS TM1040_3066 NC_008043.1 33952 37365 D PFAM: acriflavin resistance protein: (1.2e-39); KEGG: sil:SPO0293 transporter, AcrB/AcrD/AcrF family, ev=0.0, 74% identity; acriflavin resistance protein 33952..37365 Ruegeria sp. TM1040 4075160 YP_611303.1 CDS TM1040_3067 NC_008043.1 37311 37790 R PFAM: NUDIX hydrolase: (2.2e-22); KEGG: bur:Bcep18194_A5292 NUDIX hydrolase, ev=5e-24, 40% identity; NUDIX hydrolase complement(37311..37790) Ruegeria sp. TM1040 4075161 YP_611304.1 CDS TM1040_3068 NC_008043.1 37867 38652 R KEGG: sil:SPO0295 hypothetical protein, ev=4e-81, 56% identity; hypothetical protein complement(37867..38652) Ruegeria sp. TM1040 4075162 YP_611305.1 CDS TM1040_3069 NC_008043.1 38804 39424 D PFAM: protein of unknown function DUF179: (1.5e-86); KEGG: sil:SPO0296 transcriptional regulator, ev=2e-58, 63% identity; hypothetical protein 38804..39424 Ruegeria sp. TM1040 4075163 YP_611306.1 CDS pyrB NC_008043.1 39746 40705 D catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis; aspartate carbamoyltransferase catalytic subunit 39746..40705 Ruegeria sp. TM1040 4075164 YP_611307.1 CDS TM1040_3071 NC_008043.1 40711 41244 D KEGG: sil:SPO0286 hypothetical protein, ev=2e-28, 45% identity; hypothetical protein 40711..41244 Ruegeria sp. TM1040 4075165 YP_611308.1 CDS TM1040_3072 NC_008043.1 41351 42661 D 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 41351..42661 Ruegeria sp. TM1040 4075166 YP_611309.1 CDS TM1040_3073 NC_008043.1 42661 43269 D 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 42661..43269 Ruegeria sp. TM1040 4075167 YP_611310.1 CDS TM1040_3074 NC_008043.1 43540 44025 D KEGG: sil:SPO0281 hypothetical protein, ev=9e-60, 70% identity; hypothetical protein 43540..44025 Ruegeria sp. TM1040 4075168 YP_611311.1 CDS TM1040_3075 NC_008043.1 44125 44379 R hypothetical protein complement(44125..44379) Ruegeria sp. TM1040 4075169 YP_611312.1 CDS TM1040_3076 NC_008043.1 44581 45951 R 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 complement(44581..45951) Ruegeria sp. TM1040 4075170 YP_611313.1 CDS TM1040_3077 NC_008043.1 46057 46584 R KEGG: sil:SPO3627 hypothetical protein, ev=4e-51, 57% identity; hypothetical protein complement(46057..46584) Ruegeria sp. TM1040 4075171 YP_611314.1 CDS TM1040_3078 NC_008043.1 46581 47450 R PFAM: GCN5-related N-acetyltransferase: (0.0033); KEGG: sil:SPO3628 acetyltransferase, GNAT family, ev=3e-45, 38% identity; N-acetyltransferase GCN5 complement(46581..47450) Ruegeria sp. TM1040 4075524 YP_611315.1 CDS TM1040_3079 NC_008043.1 47450 48190 R 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 complement(47450..48190) Ruegeria sp. TM1040 4075525 YP_611316.1 CDS ubiA NC_008043.1 48203 49165 D 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 48203..49165 Ruegeria sp. TM1040 4075526 YP_611317.1 CDS TM1040_3081 NC_008043.1 49247 51208 D PFAM: OmpA/MotB: (3e-26); KEGG: sil:SPO3631 OmpA domain protein, ev=0.0, 58% identity; OmpA/MotB 49247..51208 Ruegeria sp. TM1040 4075527 YP_611318.1 CDS TM1040_3082 NC_008043.1 51205 51525 D KEGG: sil:SPO3632 hypothetical protein, ev=6e-45, 90% identity; hypothetical protein 51205..51525 Ruegeria sp. TM1040 4075528 YP_611319.1 CDS TM1040_3083 NC_008043.1 51515 51922 D KEGG: sil:SPO1334 hypothetical protein, ev=1e-23, 47% identity; hypothetical protein 51515..51922 Ruegeria sp. TM1040 4075529 YP_611320.1 CDS TM1040_3084 NC_008043.1 52129 52830 D catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine; phosphatidylserine decarboxylase 52129..52830 Ruegeria sp. TM1040 4075530 YP_611321.1 CDS TM1040_3085 NC_008043.1 52823 53590 D 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 52823..53590 Ruegeria sp. TM1040 4075531 YP_611322.1 CDS TM1040_3086 NC_008043.1 53571 54212 D 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 53571..54212 Ruegeria sp. TM1040 4075532 YP_611323.1 CDS TM1040_3087 NC_008043.1 54543 55976 D KEGG: sil:SPO3333 hypothetical protein, ev=1e-61, 41% identity; hypothetical protein 54543..55976 Ruegeria sp. TM1040 4075533 YP_611324.1 CDS lipB NC_008043.1 56519 57196 D lipoyl-[acyl-carrier protein]-protein-N-lipoyltransferse; lipoate-protein ligase B; transfers lipoate to apolipoproteins; involved in lipoate metabolism; lipoyltransferase 56519..57196 Ruegeria sp. TM1040 4075535 YP_611325.1 CDS TM1040_3089 NC_008043.1 57652 59874 D 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 57652..59874 Ruegeria sp. TM1040 4075536 YP_611326.1 CDS TM1040_3090 NC_008043.1 59876 60520 D PFAM: Haem oxygenase: (0.00097); heme oxygenase 59876..60520 Ruegeria sp. TM1040 4075537 YP_611327.1 CDS TM1040_3091 NC_008043.1 60682 61245 D PFAM: nitrogen-fixing NifU-like: (4.2e-31); KEGG: sil:SPO0382 NifU domain protein, ev=2e-93, 89% identity; nitrogen-fixing NifU-like 60682..61245 Ruegeria sp. TM1040 4075538 YP_611328.1 CDS TM1040_3092 NC_008043.1 61469 62116 D PFAM: peptidase M22, glycoprotease: (1.6e-33); KEGG: rsp:RSP_2213 hypothetical protein, ev=2e-55, 58% identity; peptidase M22, glycoprotease 61469..62116 Ruegeria sp. TM1040 4075539 YP_611329.1 CDS TM1040_3093 NC_008043.1 62120 62554 D PFAM: GCN5-related N-acetyltransferase: (2.9e-11); KEGG: sil:SPO0380 ribosomal-protein-alanine acetyltransferase, , ev=2e-36, 55% identity; N-acetyltransferase GCN5 62120..62554 Ruegeria sp. TM1040 4075540 YP_611330.1 CDS TM1040_3094 NC_008043.1 62691 63686 D 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 62691..63686 Ruegeria sp. TM1040 4075541 YP_611331.1 CDS TM1040_3095 NC_008043.1 63876 65405 D 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 63876..65405 Ruegeria sp. TM1040 4075542 YP_611332.1 CDS TM1040_3096 NC_008043.1 65406 66500 D PFAM: inner-membrane translocator: (3.3e-43); KEGG: sil:SPO0377 sugar ABC transporter, permease protein, ev=1e-167, 78% identity; inner-membrane translocator 65406..66500 Ruegeria sp. TM1040 4075543 YP_611333.1 CDS TM1040_3097 NC_008043.1 66500 67507 D PFAM: inner-membrane translocator: (2.6e-34); KEGG: sil:SPO0376 sugar ABC transporter, permease protein, ev=1e-141, 76% identity; inner-membrane translocator 66500..67507 Ruegeria sp. TM1040 4075544 YP_611334.1 CDS TM1040_3098 NC_008043.1 67629 68621 D PFAM: protein of unknown function DUF81: (9.7e-36); KEGG: sil:SPO0375 membrane protein, ev=1e-135, 80% identity; hypothetical protein 67629..68621 Ruegeria sp. TM1040 4075545 YP_611335.1 CDS TM1040_3099 NC_008043.1 68621 69388 D KEGG: sil:SPO0374 hypothetical protein, ev=4e-89, 65% identity; hypothetical protein 68621..69388 Ruegeria sp. TM1040 4075546 YP_611336.1 CDS TM1040_3100 NC_008043.1 69504 70241 R 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 complement(69504..70241) Ruegeria sp. TM1040 4075547 YP_611337.1 CDS TM1040_3101 NC_008043.1 70238 71791 R SMART: ATPase: (9.9e-06); KEGG: sil:SPO0373 helicase, ATP-dependent, , ev=0.0, 89% identity; ATPase complement(70238..71791) Ruegeria sp. TM1040 4075548 YP_611338.1 CDS TM1040_3102 NC_008043.1 71833 72552 R 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 complement(71833..72552) Ruegeria sp. TM1040 4075549 YP_611339.1 CDS TM1040_3103 NC_008043.1 72590 73012 D hypothetical protein 72590..73012 Ruegeria sp. TM1040 4075550 YP_611340.1 CDS TM1040_3104 NC_008043.1 73015 74295 R 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 complement(73015..74295) Ruegeria sp. TM1040 4075551 YP_611341.1 CDS TM1040_3105 NC_008043.1 74421 75851 R PFAM: phospholipid/glycerol acyltransferase: (3.4e-12); KEGG: sil:SPO0369 acyltransferase family protein, ev=1e-166, 64% identity; glycerol-3-phosphate acyltransferase complement(74421..75851) Ruegeria sp. TM1040 4075552 YP_611342.1 CDS TM1040_3106 NC_008043.1 76029 78014 D 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 76029..78014 Ruegeria sp. TM1040 4075553 YP_611343.1 CDS TM1040_3107 NC_008043.1 78144 78464 D 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 78144..78464 Ruegeria sp. TM1040 4075554 YP_611344.1 CDS deoD NC_008043.1 78483 79187 D catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate; purine nucleoside phosphorylase 78483..79187 Ruegeria sp. TM1040 4075555 YP_611345.1 CDS TM1040_3109 NC_008043.1 79360 80217 R KEGG: sil:SPO0365 hypothetical protein, ev=1e-137, 80% identity; hypothetical protein complement(79360..80217) Ruegeria sp. TM1040 4075556 YP_611346.1 CDS TM1040_3110 NC_008043.1 80347 81519 R PFAM: Orn/DAP/Arg decarboxylase 2: (3.5e-28); KEGG: sil:SPO0364 decarboxylase, pyridoxal-dependent, ev=1e-157, 70% identity; ornithine decarboxylase complement(80347..81519) Ruegeria sp. TM1040 4075557 YP_611347.1 CDS TM1040_3111 NC_008043.1 82004 82963 R 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 complement(82004..82963) Ruegeria sp. TM1040 4075558 YP_611348.1 CDS TM1040_3112 NC_008043.1 83029 84546 D 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 83029..84546 Ruegeria sp. TM1040 4075559 YP_611349.1 CDS TM1040_3113 NC_008043.1 84619 85536 D 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 84619..85536 Ruegeria sp. TM1040 4075560 YP_611350.1 CDS TM1040_3114 NC_008043.1 85541 86449 D 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 85541..86449 Ruegeria sp. TM1040 4075561 YP_611351.1 CDS TM1040_3115 NC_008043.1 86470 88485 D 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 86470..88485 Ruegeria sp. TM1040 4074986 YP_611352.1 CDS TM1040_3116 NC_008043.1 88482 89669 D 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 88482..89669 Ruegeria sp. TM1040 4074987 YP_611353.1 CDS TM1040_3117 NC_008043.1 89666 90961 D KEGG: sme:SMb21041 conserved protein, possibly related to processing of cell wall amino acids, ev=2e-33, 29% identity; poly-gamma-glutamate biosynthesis protein 89666..90961 Ruegeria sp. TM1040 4074988 YP_611354.1 CDS TM1040_3118 NC_008043.1 91339 91971 D PFAM: phage integrase: (7e-05); KEGG: bps:BPSL0587 phage integrase family protein, ev=2e-64, 54% identity; phage integrase 91339..91971 Ruegeria sp. TM1040 4074989 YP_611355.1 CDS TM1040_3119 NC_008043.1 92141 92704 D hypothetical protein 92141..92704 Ruegeria sp. TM1040 4074990 YP_611356.1 CDS TM1040_3120 NC_008043.1 93112 93603 D hypothetical protein 93112..93603 Ruegeria sp. TM1040 4074991 YP_611357.1 CDS TM1040_3121 NC_008043.1 93987 94586 R hypothetical protein complement(93987..94586) Ruegeria sp. TM1040 4074992 YP_611358.1 CDS TM1040_3122 NC_008043.1 95143 96261 R KEGG: bja:blr2115 hypothetical protein, ev=2e-58, 34% identity; hypothetical protein complement(95143..96261) Ruegeria sp. TM1040 4074993 YP_611359.1 CDS TM1040_3123 NC_008043.1 96406 97101 R hypothetical protein complement(96406..97101) Ruegeria sp. TM1040 4074994 YP_611360.1 CDS TM1040_3124 NC_008043.1 98105 99355 R KEGG: spn:SP1145 hypothetical protein, ev=3e-18, 30% identity; hypothetical protein complement(98105..99355) Ruegeria sp. TM1040 4074995 YP_611361.1 CDS TM1040_3125 NC_008043.1 99835 100098 D hypothetical protein 99835..100098 Ruegeria sp. TM1040 4074996 YP_611362.1 CDS TM1040_3126 NC_008043.1 100360 101157 R PFAM: Integrase, catalytic region: (4.6e-37); KEGG: mlo:mll6088 transposase, ev=1e-117, 75% identity; integrase catalytic subunit complement(100360..101157) Ruegeria sp. TM1040 4074997 YP_611363.1 CDS TM1040_3127 NC_008043.1 101190 101456 R 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 complement(101190..101456) Ruegeria sp. TM1040 4074998 YP_611364.1 CDS TM1040_3128 NC_008043.1 101920 102945 D 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 101920..102945 Ruegeria sp. TM1040 4075000 YP_611365.1 CDS TM1040_3129 NC_008043.1 103016 104521 R 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 complement(103016..104521) Ruegeria sp. TM1040 4075001 YP_611366.1 CDS TM1040_3130 NC_008043.1 104518 105138 R KEGG: sil:SPO3694 hypothetical protein, ev=3e-67, 63% identity; hypothetical protein complement(104518..105138) Ruegeria sp. TM1040 4075002 YP_611367.1 CDS TM1040_3131 NC_008043.1 105191 106237 R 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 complement(105191..106237) Ruegeria sp. TM1040 4075003 YP_611368.1 CDS TM1040_3132 NC_008043.1 106447 108480 R 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 complement(106447..108480) Ruegeria sp. TM1040 4075004 YP_611369.1 CDS TM1040_3133 NC_008043.1 108763 110277 D PFAM: sulfatase: (2.6e-20) type I phosphodiesterase/nucleotide pyrophosphatase: (7.2e-05); KEGG: sil:SPO1083 choline sulfatase, ev=0.0, 80% identity; sulfatase 108763..110277 Ruegeria sp. TM1040 4075005 YP_611370.1 CDS TM1040_3134 NC_008043.1 110420 111265 R PFAM: flagellin-like: (2.7e-06); KEGG: bmb:BruAb2_1084 flagellin family protein, ev=6e-47, 41% identity; flagellin-like protein complement(110420..111265) Ruegeria sp. TM1040 4075006 YP_611371.1 CDS TM1040_3135 NC_008043.1 111923 112831 D PFAM: Di-haem cytochrome c peroxidase: (1.5e-48); KEGG: bja:blr1552 methylamine utilization protein precursor, ev=2e-64, 43% identity; cytochrome-c peroxidase 111923..112831 Ruegeria sp. TM1040 4075007 YP_611372.1 CDS TM1040_3136 NC_008043.1 112844 114946 D 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 112844..114946 Ruegeria sp. TM1040 4075008 YP_611373.1 CDS TM1040_3137 NC_008043.1 114961 117006 R 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 complement(114961..117006) Ruegeria sp. TM1040 4075009 YP_611374.1 CDS TM1040_3138 NC_008043.1 117100 117723 D PFAM: regulatory protein, TetR: (0.00091); KEGG: sil:SPO0168 transcriptional regulator, TetR family, ev=4e-63, 59% identity; TetR family transcriptional regulator 117100..117723 Ruegeria sp. TM1040 4075010 YP_611375.1 CDS TM1040_3139 NC_008043.1 117760 118725 R 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 complement(117760..118725) Ruegeria sp. TM1040 4075011 YP_611376.1 CDS TM1040_3140 NC_008043.1 118725 119699 R 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 complement(118725..119699) Ruegeria sp. TM1040 4075012 YP_611377.1 CDS TM1040_3141 NC_008043.1 119699 120640 R 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 complement(119699..120640) Ruegeria sp. TM1040 4075013 YP_611378.1 CDS TM1040_3142 NC_008043.1 120640 121620 R 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 complement(120640..121620) Ruegeria sp. TM1040 4075014 YP_611379.1 CDS TM1040_3143 NC_008043.1 121684 123258 R 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 complement(121684..123258) Ruegeria sp. TM1040 4075015 YP_611380.1 CDS TM1040_3144 NC_008043.1 123368 124948 R 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 complement(123368..124948) Ruegeria sp. TM1040 4075016 YP_611381.1 CDS TM1040_3145 NC_008043.1 125313 125930 R KEGG: jan:Jann_4169 hypothetical protein, ev=9e-66, 59% identity; hypothetical protein complement(125313..125930) Ruegeria sp. TM1040 4075017 YP_611382.1 CDS TM1040_3146 NC_008043.1 125943 128207 R 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 complement(125943..128207) Ruegeria sp. TM1040 4075018 YP_611383.1 CDS TM1040_3147 NC_008043.1 128211 128669 R 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 complement(128211..128669) Ruegeria sp. TM1040 4075019 YP_611384.1 CDS TM1040_3148 NC_008043.1 128830 129972 R 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 complement(128830..129972) Ruegeria sp. TM1040 4075020 YP_611385.1 CDS TM1040_3149 NC_008043.1 129969 130997 R 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) complement(129969..130997) Ruegeria sp. TM1040 4075021 YP_611386.1 CDS TM1040_3150 NC_008043.1 131072 131827 R 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 complement(131072..131827) Ruegeria sp. TM1040 4075022 YP_611387.1 CDS TM1040_3151 NC_008043.1 131814 132701 R 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 complement(131814..132701) Ruegeria sp. TM1040 4075023 YP_611388.1 CDS murQ NC_008043.1 132916 133797 D 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 132916..133797 Ruegeria sp. TM1040 4075322 YP_611389.1 CDS TM1040_3153 NC_008043.1 133822 135075 D 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 133822..135075 Ruegeria sp. TM1040 4075323 YP_611390.1 CDS TM1040_3154 NC_008043.1 135160 136074 D 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 135160..136074 Ruegeria sp. TM1040 4075324 YP_611391.1 CDS TM1040_3155 NC_008043.1 136087 136926 D 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 136087..136926 Ruegeria sp. TM1040 4075325 YP_611392.1 CDS TM1040_3156 NC_008043.1 137006 138040 D 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 137006..138040 Ruegeria sp. TM1040 4075326 YP_611393.1 CDS TM1040_3157 NC_008043.1 138037 139032 D 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 138037..139032 Ruegeria sp. TM1040 4075327 YP_611394.1 CDS TM1040_3158 NC_008043.1 139146 139754 D PFAM: regulatory protein, TetR: (2.4e-07); KEGG: sil:SPO1082 HTH-type transcriptional regulator BetI, ev=1e-44, 49% identity; TetR family transcriptional regulator 139146..139754 Ruegeria sp. TM1040 4075328 YP_611395.1 CDS TM1040_3159 NC_008043.1 139953 140921 D KEGG: sil:SPO2161 hypothetical protein, ev=2e-35, 35% identity; hypothetical protein 139953..140921 Ruegeria sp. TM1040 4075329 YP_611396.1 CDS TM1040_3160 NC_008043.1 140996 141958 R 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 complement(140996..141958) Ruegeria sp. TM1040 4075330 YP_611397.1 CDS TM1040_3161 NC_008043.1 142179 143012 D 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 142179..143012 Ruegeria sp. TM1040 4075331 YP_611398.1 CDS TM1040_3162 NC_008043.1 143129 143734 R PFAM: Lysine exporter protein (LYSE/YGGA): (0.00023); KEGG: sil:SPO3613 transporter, LysE family, ev=1e-86, 78% identity; lysine exporter protein LysE/YggA complement(143129..143734) Ruegeria sp. TM1040 4075332 YP_611399.1 CDS TM1040_3163 NC_008043.1 143808 144260 D PFAM: regulatory proteins, AsnC/Lrp: (1.7e-22); KEGG: sil:SPO3612 transcriptional regulator, AsnC family, ev=6e-63, 79% identity; AsnC family transcriptional regulator 143808..144260 Ruegeria sp. TM1040 4075333 YP_611400.1 CDS TM1040_3164 NC_008043.1 144824 145243 D PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase: (0.00019); KEGG: sil:SPO0917 glyoxalase family protein, ev=2e-33, 57% identity; glyoxalase/bleomycin resistance protein/dioxygenase 144824..145243 Ruegeria sp. TM1040 4075334 YP_611401.1 CDS TM1040_3165 NC_008043.1 145368 146330 R PFAM: HpcH/HpaI aldolase: (7.3e-36); KEGG: sil:SPO3608 malyl-CoA lyase, ev=1e-164, 90% identity; citryl-CoA lyase complement(145368..146330) Ruegeria sp. TM1040 4075335 YP_611402.1 CDS TM1040_3166 NC_008043.1 146638 147639 D PFAM: protein of unknown function DUF1611: (1.9e-125); KEGG: sil:SPO3607 hypothetical protein, ev=1e-158, 81% identity; hypothetical protein 146638..147639 Ruegeria sp. TM1040 4075336 YP_611403.1 CDS TM1040_3167 NC_008043.1 147745 148710 D 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 147745..148710 Ruegeria sp. TM1040 4075337 YP_611404.1 CDS TM1040_3168 NC_008043.1 148721 149581 D PFAM: aminotransferase, class IV: (1.3e-66); KEGG: sil:SPO3604 D-amino acid aminotransferase, , ev=1e-140, 86% identity; aminotransferase, class IV 148721..149581 Ruegeria sp. TM1040 4075338 YP_611405.1 CDS TM1040_3169 NC_008043.1 149646 150440 R 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 complement(149646..150440) Ruegeria sp. TM1040 4075339 YP_611406.1 CDS TM1040_3170 NC_008043.1 150625 150957 R PFAM: protein of unknown function DUF1244: (1e-44); KEGG: sil:SPO3602 hypothetical protein, ev=1e-41, 77% identity; hypothetical protein complement(150625..150957) Ruegeria sp. TM1040 4075340 YP_611407.1 CDS TM1040_3171 NC_008043.1 151141 152124 D 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 151141..152124 Ruegeria sp. TM1040 4075341 YP_611408.1 CDS TM1040_3172 NC_008043.1 152144 153709 R PFAM: ASPIC/UnbV: (2.9e-15); KEGG: sil:SPO0859 FG-GAP repeat domain protein, ev=0.0, 63% identity; ASPIC/UnbV complement(152144..153709) Ruegeria sp. TM1040 4075342 YP_611409.1 CDS TM1040_3173 NC_008043.1 153696 155003 R PFAM: ROK: (9.8e-29); KEGG: sil:SPO0860 xylose repressor, , ev=1e-115, 55% identity; ROK domain-containing protein complement(153696..155003) Ruegeria sp. TM1040 4075343 YP_611410.1 CDS TM1040_3174 NC_008043.1 155096 156124 D 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 155096..156124 Ruegeria sp. TM1040 4075344 YP_611411.1 CDS TM1040_3175 NC_008043.1 156210 157508 D PFAM: inner-membrane translocator: (1.2e-50); KEGG: sil:SPO0862 xylose ABC transporter, permease protein, ev=0.0, 76% identity; inner-membrane translocator 156210..157508 Ruegeria sp. TM1040 4075345 YP_611412.1 CDS TM1040_3176 NC_008043.1 157508 158299 D 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 157508..158299 Ruegeria sp. TM1040 4075346 YP_611413.1 CDS TM1040_3177 NC_008043.1 158482 160731 D 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 158482..160731 Ruegeria sp. TM1040 4075347 YP_611414.1 CDS TM1040_3178 NC_008043.1 161441 162601 D 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 161441..162601 Ruegeria sp. TM1040 4075348 YP_611415.1 CDS TM1040_3179 NC_008043.1 162710 165367 D 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 162710..165367 Ruegeria sp. TM1040 4075349 YP_611416.1 CDS TM1040_3180 NC_008043.1 165490 165984 R KEGG: sil:SPO1053 hypothetical protein, ev=1e-45, 58% identity; hypothetical protein complement(165490..165984) Ruegeria sp. TM1040 4075350 YP_611417.1 CDS TM1040_3181 NC_008043.1 166163 166966 R PFAM: regulatory protein, LuxR: (2.4e-05); KEGG: sil:SPO2286 autoinducer-binding transcriptional regulator LuxR, ev=5e-07, 23% identity; LuxR family transcriptional regulator complement(166163..166966) Ruegeria sp. TM1040 4075351 YP_611418.1 CDS TM1040_3182 NC_008043.1 167108 168082 R KEGG: rsp:RSP_3350 lipocalin-related protein, ev=2e-10, 23% identity; hypothetical protein complement(167108..168082) Ruegeria sp. TM1040 4075352 YP_611419.1 CDS TM1040_3183 NC_008043.1 168159 169166 R hypothetical protein complement(168159..169166) Ruegeria sp. TM1040 4075353 YP_611420.1 CDS TM1040_3184 NC_008043.1 169278 170225 R 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 complement(169278..170225) Ruegeria sp. TM1040 4075354 YP_611421.1 CDS TM1040_3185 NC_008043.1 170270 171157 D 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 170270..171157 Ruegeria sp. TM1040 4075355 YP_611422.1 CDS TM1040_3186 NC_008043.1 171207 172082 R PFAM: regulatory protein, LysR: (2.3e-23); KEGG: sil:SPO0639 transcriptional regulator, LysR family, ev=2e-59, 45% identity; LysR family transcriptional regulator complement(171207..172082) Ruegeria sp. TM1040 4075356 YP_611423.1 CDS TM1040_3187 NC_008043.1 172197 172787 D PFAM: metal-dependent phosphohydrolase, HD subdomain: (3.9e-05); KEGG: sil:SPO0638 hypothetical protein, ev=5e-80, 68% identity; metal dependent phosphohydrolase 172197..172787 Ruegeria sp. TM1040 4075357 YP_611424.1 CDS TM1040_3188 NC_008043.1 179563 180438 R 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 complement(179563..180438) Ruegeria sp. TM1040 4075292 YP_611425.1 CDS TM1040_3189 NC_008043.1 180535 180816 D KEGG: sil:SPO3302 hypothetical protein, ev=7e-18, 47% identity; hypothetical protein 180535..180816 Ruegeria sp. TM1040 4075293 YP_611426.1 CDS TM1040_3190 NC_008043.1 181083 183857 R 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 complement(181083..183857) Ruegeria sp. TM1040 4075294 YP_611427.1 CDS TM1040_3191 NC_008043.1 183861 185549 R 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) complement(183861..185549) Ruegeria sp. TM1040 4075295 YP_611428.1 CDS TM1040_3192 NC_008043.1 185663 186469 R PFAM: LysR, substrate-binding: (1.3e-27); KEGG: sil:SPO0832 transcriptional regulator, LysR family, ev=3e-81, 57% identity; LysR family transcriptional regulator complement(185663..186469) Ruegeria sp. TM1040 4075296 YP_611429.1 CDS TM1040_3193 NC_008043.1 186865 187434 D KEGG: vch:VCA0032 hypothetical protein, ev=6e-40, 44% identity; hypothetical protein 186865..187434 Ruegeria sp. TM1040 4075297 YP_611430.1 CDS TM1040_3194 NC_008043.1 187476 189320 D 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 187476..189320 Ruegeria sp. TM1040 4075298 YP_611431.1 CDS TM1040_3195 NC_008043.1 190067 191065 D 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 190067..191065 Ruegeria sp. TM1040 4075299 YP_611432.1 CDS TM1040_3196 NC_008043.1 191222 191779 D hypothetical protein 191222..191779 Ruegeria sp. TM1040 4075300 YP_611433.1 CDS TM1040_3197 NC_008043.1 191776 193065 D 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 191776..193065 Ruegeria sp. TM1040 4075301 YP_611434.1 CDS TM1040_3198 NC_008043.1 193350 194309 D PFAM: dihydrodipicolinate synthetase: (1.2e-09); KEGG: sil:SPOA0267 dihydroxydipicolinate synthase family protein, ev=1e-158, 84% identity; dihydrodipicolinate synthetase 193350..194309 Ruegeria sp. TM1040 4075302 YP_611435.1 CDS TM1040_3199 NC_008043.1 194300 195226 D PFAM: proline racemase: (2.1e-89); KEGG: sil:SPOA0266 proline racemase, , ev=1e-113, 65% identity; proline racemase 194300..195226 Ruegeria sp. TM1040 4075303 YP_611436.1 CDS TM1040_3200 NC_008043.1 195244 196530 D PFAM: FAD dependent oxidoreductase: (1.1e-74); KEGG: sil:SPOA0262 oxidoreductase, FAD-binding, ev=1e-158, 66% identity; D-amino acid dehydrogenase small subunit 195244..196530 Ruegeria sp. TM1040 4075304 YP_611437.1 CDS TM1040_3201 NC_008043.1 196546 197571 D PFAM: proline racemase: (1.5e-190); KEGG: atc:AGR_L_395 hypothetical protein PA1255, ev=1e-155, 77% identity; proline racemase 196546..197571 Ruegeria sp. TM1040 4075305 YP_611438.1 CDS TM1040_3202 NC_008043.1 197964 198293 R hypothetical protein complement(197964..198293) Ruegeria sp. TM1040 4075306 YP_611439.1 CDS TM1040_3203 NC_008043.1 198295 198681 R PFAM: response regulator receiver: (9.1e-15); KEGG: rsp:RSP_2433 chemotaxis response regulator, CheY2, ev=8e-40, 60% identity; response regulator receiver protein complement(198295..198681) Ruegeria sp. TM1040 4075307 YP_611440.1 CDS TM1040_3204 NC_008043.1 198725 199582 R PFAM: MCP methyltransferase, CheR-type: (1.6e-78); KEGG: rsp:RSP_2434 MCP methyltransferase, CheR1, ev=4e-66, 46% identity; chemotaxis protein CheR complement(198725..199582) Ruegeria sp. TM1040 4075308 YP_611441.1 CDS TM1040_3205 NC_008043.1 199579 200067 R PFAM: CheW-like protein: (3e-29); KEGG: ret:RHE_CH02831 chemotaxis signal transduction protein, ev=1e-30, 48% identity; CheW protein complement(199579..200067) Ruegeria sp. TM1040 4075309 YP_611442.1 CDS TM1040_3206 NC_008043.1 200051 202186 R 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 complement(200051..202186) Ruegeria sp. TM1040 4075310 YP_611443.1 CDS TM1040_3207 NC_008043.1 202188 202562 R 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 complement(202188..202562) Ruegeria sp. TM1040 4075311 YP_611444.1 CDS TM1040_3208 NC_008043.1 202559 202861 R hypothetical protein complement(202559..202861) Ruegeria sp. TM1040 4075312 YP_611445.1 CDS TM1040_3209 NC_008043.1 203191 205539 D 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 203191..205539 Ruegeria sp. TM1040 4075313 YP_611446.1 CDS TM1040_3210 NC_008043.1 205699 206634 D PFAM: CheB methylesterase: (1.7e-61); KEGG: jan:Jann_2844 CheB methylesterase, ev=4e-48, 40% identity; CheB methylesterase 205699..206634 Ruegeria sp. TM1040 4075314 YP_611447.1 CDS TM1040_3211 NC_008043.1 206661 207224 D PFAM: CheD: (2.5e-30); KEGG: atc:AGR_C_918 chemotaxis protein cheD, ev=1e-43, 51% identity; MCP proteins methylation stimulator CheD 206661..207224 Ruegeria sp. TM1040 4075315 YP_611448.1 CDS TM1040_3212 NC_008043.1 207380 208021 D PFAM: regulatory protein, TetR: (1.7e-10); KEGG: sil:SPOA0067 transcriptional regulator, TetR family, ev=4e-44, 42% identity; TetR family transcriptional regulator 207380..208021 Ruegeria sp. TM1040 4075316 YP_611449.1 CDS TM1040_3213 NC_008043.1 208049 209620 D 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 208049..209620 Ruegeria sp. TM1040 4075317 YP_611450.1 CDS TM1040_3214 NC_008043.1 209629 210435 R 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 complement(209629..210435) Ruegeria sp. TM1040 4075318 YP_611451.1 CDS TM1040_3215 NC_008043.1 210432 211307 R 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 complement(210432..211307) Ruegeria sp. TM1040 4075319 YP_611452.1 CDS TM1040_3216 NC_008043.1 211368 212645 R 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 complement(211368..212645) Ruegeria sp. TM1040 4075320 YP_611453.1 CDS TM1040_3217 NC_008043.1 212764 213834 R 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 complement(212764..213834) Ruegeria sp. TM1040 4075321 YP_611454.1 CDS TM1040_3218 NC_008043.1 214064 215131 R 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 complement(214064..215131) Ruegeria sp. TM1040 4075360 YP_611455.1 CDS TM1040_3219 NC_008043.1 215137 216363 R 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 complement(215137..216363) Ruegeria sp. TM1040 4075361 YP_611456.1 CDS TM1040_3220 NC_008043.1 216964 217980 D 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 216964..217980 Ruegeria sp. TM1040 4075362 YP_611457.1 CDS TM1040_3221 NC_008043.1 218070 218747 D 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 218070..218747 Ruegeria sp. TM1040 4075363 YP_611458.1 CDS TM1040_3222 NC_008043.1 218740 220140 D 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 218740..220140 Ruegeria sp. TM1040 4075364 YP_611459.1 CDS TM1040_3223 NC_008043.1 220725 221492 R KEGG: cvi:CV0102 probable ABC transporter, periplasmic substrate-binding, ev=6e-37, 36% identity; ABC transporter, periplasmic substrate-binding complement(220725..221492) Ruegeria sp. TM1040 4075365 YP_611460.1 CDS TM1040_3224 NC_008043.1 221636 222574 R hypothetical protein complement(221636..222574) Ruegeria sp. TM1040 4075366 YP_611461.1 CDS TM1040_3225 NC_008043.1 222584 224017 R 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 complement(222584..224017) Ruegeria sp. TM1040 4075367 YP_611462.1 CDS TM1040_3226 NC_008043.1 224021 224833 R hypothetical protein complement(224021..224833) Ruegeria sp. TM1040 4075368 YP_611463.1 CDS TM1040_3227 NC_008043.1 224962 226599 D 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 224962..226599 Ruegeria sp. TM1040 4075369 YP_611464.1 CDS TM1040_3228 NC_008043.1 226645 227544 R 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 complement(226645..227544) Ruegeria sp. TM1040 4075370 YP_611465.1 CDS TM1040_3229 NC_008043.1 227859 228323 D 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 227859..228323 Ruegeria sp. TM1040 4075371 YP_611466.1 CDS TM1040_3230 NC_008043.1 228329 230506 D 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 228329..230506 Ruegeria sp. TM1040 4075372 YP_611467.1 CDS TM1040_3231 NC_008043.1 230751 233225 R 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 complement(230751..233225) Ruegeria sp. TM1040 4075373 YP_611468.1 CDS TM1040_3232 NC_008043.1 233222 233956 R 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 complement(233222..233956) Ruegeria sp. TM1040 4075374 YP_611469.1 CDS TM1040_3233 NC_008043.1 234200 235180 D 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 234200..235180 Ruegeria sp. TM1040 4075375 YP_611470.1 CDS TM1040_3234 NC_008043.1 235287 236060 D 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 235287..236060 Ruegeria sp. TM1040 4075376 YP_611471.1 CDS TM1040_3235 NC_008043.1 236057 236863 D 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 236057..236863 Ruegeria sp. TM1040 4075377 YP_611472.1 CDS TM1040_3236 NC_008043.1 236860 237690 D 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 236860..237690 Ruegeria sp. TM1040 4075378 YP_611473.1 CDS TM1040_3237 NC_008043.1 237883 238554 R PFAM: DSBA oxidoreductase: (1.5e-07); KEGG: efa:EF1088 hypothetical protein, ev=5e-24, 31% identity; DSBA oxidoreductase complement(237883..238554) Ruegeria sp. TM1040 4075379 YP_611474.1 CDS TM1040_3238 NC_008043.1 238624 239436 R KEGG: xft:PD0713 hypothetical protein, ev=9e-58, 45% identity; hypothetical protein complement(238624..239436) Ruegeria sp. TM1040 4075380 YP_611475.1 CDS TM1040_3239 NC_008043.1 239499 240455 R KEGG: sme:SMc02708 glutathione S-transferase, ev=5e-95, 57% identity; glutathione S-transferase complement(239499..240455) Ruegeria sp. TM1040 4075381 YP_611476.1 CDS TM1040_3240 NC_008043.1 240577 241494 D 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 240577..241494 Ruegeria sp. TM1040 4075382 YP_611477.1 CDS TM1040_3241 NC_008043.1 242356 242763 D hypothetical protein 242356..242763 Ruegeria sp. TM1040 4075383 YP_611478.1 CDS TM1040_3242 NC_008043.1 243791 246433 D 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 243791..246433 Ruegeria sp. TM1040 4075384 YP_611479.1 CDS TM1040_3243 NC_008043.1 246458 247288 D PFAM: MCP methyltransferase, CheR-type: (9.6e-50); KEGG: bba:Bd2830 chemotaxis protein methyltransferase, ev=9e-56, 40% identity; chemotaxis protein CheR 246458..247288 Ruegeria sp. TM1040 4075385 YP_611480.1 CDS TM1040_3244 NC_008043.1 247293 247832 D KEGG: bba:Bd2829 chemotaxis protein, ev=6e-14, 30% identity; MCP proteins methylation stimulator CheD 247293..247832 Ruegeria sp. TM1040 4075386 YP_611481.1 CDS TM1040_3245 NC_008043.1 247832 249418 D PFAM: CheW-like protein: (5.2e-16); KEGG: bba:Bd2828 purine-binding chemotaxis protein CheW, ev=6e-67, 29% identity; CheW protein 247832..249418 Ruegeria sp. TM1040 4075387 YP_611482.1 CDS TM1040_3246 NC_008043.1 249743 250009 D 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 249743..250009 Ruegeria sp. TM1040 4075388 YP_611483.1 CDS TM1040_3247 NC_008043.1 250042 250839 D PFAM: Integrase, catalytic region: (4.6e-37); KEGG: mlo:mll6088 transposase, ev=1e-117, 75% identity; integrase catalytic subunit 250042..250839 Ruegeria sp. TM1040 4075389 YP_611484.1 CDS TM1040_3248 NC_008043.1 250950 251117 D KEGG: mag:amb0914 transposase and inactivated derivative, ev=1e-09, 53% identity; transposase and inactivated derivative 250950..251117 Ruegeria sp. TM1040 4075390 YP_611485.1 CDS TM1040_3249 NC_008043.1 251153 251410 D KEGG: deh:cbdb_A1487 transposase orfB, ev=1e-20, 59% identity; transposase orfB 251153..251410 Ruegeria sp. TM1040 4075391 YP_611486.1 CDS TM1040_3250 NC_008043.1 251761 252285 R PFAM: CBS: (3.4e-30); KEGG: sil:SPOA0034 CBS domain protein, ev=7e-46, 53% identity; signal-transduction protein complement(251761..252285) Ruegeria sp. TM1040 4075392 YP_611487.1 CDS TM1040_3251 NC_008043.1 252364 252546 D KEGG: sil:SPOA0035 hypothetical protein, ev=6e-08, 50% identity; hypothetical protein 252364..252546 Ruegeria sp. TM1040 4075393 YP_611488.1 CDS TM1040_3252 NC_008043.1 252601 253611 R PFAM: inner-membrane translocator: (2.2e-60); KEGG: ppr:PBPRB0472 sugar ABC transporter (permease), ev=6e-58, 37% identity; inner-membrane translocator complement(252601..253611) Ruegeria sp. TM1040 4075394 YP_611489.1 CDS TM1040_3253 NC_008043.1 253608 255110 R 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 complement(253608..255110) Ruegeria sp. TM1040 4075395 YP_611490.1 CDS TM1040_3254 NC_008043.1 255172 256242 R periplasmic sensory protein associated with the TorRS two-component regulatory system; TMAO reductase system periplasmic protein TorT complement(255172..256242) Ruegeria sp. TM1040 4075396 YP_611491.1 CDS TM1040_3255 NC_008043.1 256334 257305 R PFAM: Allophanate hydrolase subunit 2: (1.2e-69); KEGG: bps:BPSS0194 hypothetical protein, ev=1e-105, 57% identity; Urea carboxylase complement(256334..257305) Ruegeria sp. TM1040 4075397 YP_611492.1 CDS TM1040_3256 NC_008043.1 257295 258170 R PFAM: Allophanate hydrolase subunit 1: (5.3e-09); KEGG: allophanate hydrolase, subunit 1, ev=1e-113, 64% identity; allophanate hydrolase subunit 1 complement(257295..258170) Ruegeria sp. TM1040 4075398 YP_611493.1 CDS TM1040_3257 NC_008043.1 258167 259543 R 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 complement(258167..259543) Ruegeria sp. TM1040 4075399 YP_611494.1 CDS TM1040_3258 NC_008043.1 259547 259780 R PFAM: biotin/lipoyl attachment: (3e-14); KEGG: pae:PA0493 acetyl-CoA carboxylase, ev=4e-13, 48% identity; hypothetical protein complement(259547..259780) Ruegeria sp. TM1040 4075400 YP_611495.1 CDS TM1040_3259 NC_008043.1 259817 260596 R PFAM: LamB/YcsF: (4.5e-111); KEGG: LamB/YcsF family protein, ev=1e-89, 63% identity; hypothetical protein complement(259817..260596) Ruegeria sp. TM1040 4075401 YP_611496.1 CDS TM1040_3260 NC_008043.1 260876 261793 D 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 260876..261793 Ruegeria sp. TM1040 4075402 YP_611497.1 CDS TM1040_3261 NC_008043.1 261790 262362 R 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 complement(261790..262362) Ruegeria sp. TM1040 4075403 YP_611498.1 CDS TM1040_3262 NC_008043.1 262509 263786 D catalyzes the formation of succinate semialdehyde and glutamate from 4-aminobutanoate and 2-oxoglutarate; 4-aminobutyrate aminotransferase 262509..263786 Ruegeria sp. TM1040 4075404 YP_611499.1 CDS TM1040_3263 NC_008043.1 263788 265257 D 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 263788..265257 Ruegeria sp. TM1040 4075405 YP_611500.1 CDS TM1040_3264 NC_008043.1 265413 266627 D PFAM: ROK: (3.6e-30); KEGG: jan:Jann_0880 ROK, ev=1e-107, 51% identity; ROK domain-containing protein 265413..266627 Ruegeria sp. TM1040 4075406 YP_611501.1 CDS TM1040_3265 NC_008043.1 266624 267874 D PFAM: peptidase M20: (2.6e-23) peptidase dimerisation: (1.4e-05); KEGG: jan:Jann_0881 peptidase M20, ev=1e-138, 57% identity; acetylornithine deacetylase 266624..267874 Ruegeria sp. TM1040 4075407 YP_611502.1 CDS TM1040_3266 NC_008043.1 267890 268942 D KEGG: jan:Jann_0882 periplasmic binding protein/LacI transcriptional regulator, ev=1e-145, 74% identity; periplasmic binding protein/LacI transcriptional regulator 267890..268942 Ruegeria sp. TM1040 4075408 YP_611503.1 CDS TM1040_3267 NC_008043.1 269124 270077 D PFAM: inner-membrane translocator: (1e-57); KEGG: jan:Jann_0883 inner-membrane translocator, ev=1e-130, 77% identity; inner-membrane translocator 269124..270077 Ruegeria sp. TM1040 4075409 YP_611504.1 CDS TM1040_3268 NC_008043.1 270091 271302 D KEGG: jan:Jann_0884 hypothetical protein, ev=1e-163, 71% identity; hypothetical protein 270091..271302 Ruegeria sp. TM1040 4075410 YP_611505.1 CDS TM1040_3269 NC_008043.1 271299 272042 D 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 271299..272042 Ruegeria sp. TM1040 4075411 YP_611506.1 CDS TM1040_3270 NC_008043.1 272076 272879 R 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 complement(272076..272879) Ruegeria sp. TM1040 4075412 YP_611507.1 CDS TM1040_3271 NC_008043.1 272876 274402 R 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 complement(272876..274402) Ruegeria sp. TM1040 4075413 YP_611508.1 CDS TM1040_3272 NC_008043.1 274399 275559 R 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 complement(274399..275559) Ruegeria sp. TM1040 4075414 YP_611509.1 CDS TM1040_3273 NC_008043.1 275643 276200 D 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 275643..276200 Ruegeria sp. TM1040 4075415 YP_611510.1 CDS TM1040_3274 NC_008043.1 276579 276818 R hypothetical protein complement(276579..276818) Ruegeria sp. TM1040 4075416 YP_611511.1 CDS TM1040_3275 NC_008043.1 276840 277046 D KEGG: eli:ELI_14900 transposase orfB, ev=3e-15, 62% identity; transposase orfB 276840..277046 Ruegeria sp. TM1040 4075417 YP_611512.1 CDS TM1040_3276 NC_008043.1 277180 277410 D KEGG: deh:cbdb_A1487 transposase orfB, ev=2e-11, 48% identity; transposase orfB 277180..277410 Ruegeria sp. TM1040 4075680 YP_611513.1 CDS TM1040_3277 NC_008043.1 277819 280044 R 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 complement(277819..280044) Ruegeria sp. TM1040 4075681 YP_611514.1 CDS TM1040_3278 NC_008043.1 280321 281094 R hypothetical protein complement(280321..281094) Ruegeria sp. TM1040 4075682 YP_611515.1 CDS TM1040_3279 NC_008043.1 281477 281905 D KEGG: sil:SPO2951 hypothetical protein, ev=1e-17, 45% identity; hypothetical protein 281477..281905 Ruegeria sp. TM1040 4075683 YP_611516.1 CDS TM1040_3280 NC_008043.1 282061 282978 R PFAM: protein of unknown function DUF6, transmembrane: (8.3e-09); KEGG: vpa:VPA1215 hypothetical protein, ev=1e-35, 31% identity; hypothetical protein complement(282061..282978) Ruegeria sp. TM1040 4075684 YP_611517.1 CDS TM1040_3281 NC_008043.1 283051 283272 R 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 complement(283051..283272) Ruegeria sp. TM1040 4075685 YP_611518.1 CDS TM1040_3282 NC_008043.1 283277 283657 R KEGG: ccr:CC2974 hypothetical protein, ev=3e-19, 37% identity; hypothetical protein complement(283277..283657) Ruegeria sp. TM1040 4075686 YP_611519.1 CDS TM1040_3283 NC_008043.1 284032 284922 R 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 complement(284032..284922) Ruegeria sp. TM1040 4075687 YP_611520.1 CDS TM1040_3284 NC_008043.1 285111 285689 D PFAM: NADPH-dependent FMN reductase: (0.0023); KEGG: reu:Reut_B4867 flavodoxin/nitric oxide synthase, ev=6e-58, 60% identity; NADPH-dependent FMN reductase 285111..285689 Ruegeria sp. TM1040 4075688 YP_611521.1 CDS TM1040_3285 NC_008043.1 286135 291822 R 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 complement(286135..291822) Ruegeria sp. TM1040 4075689 YP_611522.1 CDS TM1040_3286 NC_008043.1 292367 292873 D PFAM: phage Tail Collar: (3.5e-20); KEGG: mlo:mll4443 microcystin dependent protein MdpB, ev=4e-50, 55% identity; phage tail Collar 292367..292873 Ruegeria sp. TM1040 4075690 YP_611523.1 CDS TM1040_3287 NC_008043.1 292891 293409 D PFAM: phage Tail Collar: (4.3e-26); KEGG: hch:HCH_06045 microcystin-dependent protein, ev=2e-47, 51% identity; phage tail Collar 292891..293409 Ruegeria sp. TM1040 4075691 YP_611524.1 CDS TM1040_3288 NC_008043.1 293419 293946 D PFAM: phage Tail Collar: (4.4e-20); KEGG: mlo:mll4441 microcystin dependent protein MdpB, ev=2e-48, 53% identity; phage tail Collar 293419..293946 Ruegeria sp. TM1040 4075692 YP_611525.1 CDS TM1040_3289 NC_008043.1 294016 295233 D KEGG: cac:CAC3395 predicted membrane protein, ev=3e-09, 22% identity; hypothetical protein 294016..295233 Ruegeria sp. TM1040 4075693 YP_611526.1 CDS TM1040_3290 NC_008043.1 295230 295811 D PFAM: GCN5-related N-acetyltransferase: (1.7e-08); KEGG: mlo:mll4440 contains weak similarity to acetyltransferase, ev=8e-45, 62% identity; N-acetyltransferase GCN5 295230..295811 Ruegeria sp. TM1040 4075694 YP_611527.1 CDS TM1040_3291 NC_008043.1 295787 296080 R KEGG: mlo:mlr4438 hypothetical protein, ev=1e-08, 39% identity; hypothetical protein complement(295787..296080) Ruegeria sp. TM1040 4075695 YP_611528.1 CDS TM1040_3292 NC_008043.1 296382 297275 R hypothetical protein complement(296382..297275) Ruegeria sp. TM1040 4075696 YP_611529.1 CDS TM1040_3293 NC_008043.1 297512 298483 R 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 complement(297512..298483) Ruegeria sp. TM1040 4075697 YP_611530.1 CDS TM1040_3294 NC_008043.1 298528 300558 D AcsA; in Sinorhizobium meliloti this enzyme is required for acetoacetate activation; similar to acetyl-CoA synthase; acetoacetyl-CoA synthetase 298528..300558 Ruegeria sp. TM1040 4075698 YP_611531.1 CDS TM1040_3295 NC_008043.1 300578 301495 D PFAM: protein of unknown function DUF849: (8e-195); KEGG: jan:Jann_3825 protein of unknown function DUF849, ev=1e-148, 82% identity; hypothetical protein 300578..301495 Ruegeria sp. TM1040 4075699 YP_611532.1 CDS TM1040_3298 NC_008043.1 303158 304633 D PFAM: BCCT transporter: (2.3e-102); KEGG: cps:CPS_4027 transporter, BCCT family, ev=1e-122, 48% identity; BCCT transporter 303158..304633 Ruegeria sp. TM1040 4075701 YP_611533.1 CDS TM1040_3299 NC_008043.1 304724 306997 D 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 304724..306997 Ruegeria sp. TM1040 4075702 YP_611534.1 CDS TM1040_3300 NC_008043.1 307142 308299 D 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 307142..308299 Ruegeria sp. TM1040 4075703 YP_611535.1 CDS TM1040_3301 NC_008043.1 308585 308794 R PFAM: Endoribonuclease L-PSP: (0.0046); KEGG: jan:Jann_2297 endoribonuclease L-PSP, ev=4e-24, 81% identity; endoribonuclease L-PSP complement(308585..308794) Ruegeria sp. TM1040 4075704 YP_611536.1 CDS TM1040_3302 NC_008043.1 308814 309152 R KEGG: neu:NE2446 transposase IS4 family, ev=2e-11, 51% identity; hypothetical protein complement(308814..309152) Ruegeria sp. TM1040 4075705 YP_611537.1 CDS TM1040_3303 NC_008043.1 310065 311162 R 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 complement(310065..311162) Ruegeria sp. TM1040 4075707 YP_611538.1 CDS TM1040_3304 NC_008043.1 311182 312834 R 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 complement(311182..312834) Ruegeria sp. TM1040 4075708 YP_611539.1 CDS TM1040_3305 NC_008043.1 312880 314028 R 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 complement(312880..314028) Ruegeria sp. TM1040 4075709 YP_611540.1 CDS TM1040_3306 NC_008043.1 314042 315049 R 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 complement(314042..315049) Ruegeria sp. TM1040 4075710 YP_611541.1 CDS TM1040_3307 NC_008043.1 315194 316543 R 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 complement(315194..316543) Ruegeria sp. TM1040 4075711 YP_611542.1 CDS TM1040_3308 NC_008043.1 316810 317850 D 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 316810..317850 Ruegeria sp. TM1040 4075712 YP_611543.1 CDS TM1040_3309 NC_008043.1 317847 319181 D PFAM: glycoside hydrolase, family 1: (5.3e-161); KEGG: jan:Jann_1944 beta-glucosidase, ev=0.0, 69% identity; Beta-glucosidase 317847..319181 Ruegeria sp. TM1040 4075713 YP_611544.1 CDS TM1040_3310 NC_008043.1 319232 319723 R 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 complement(319232..319723) Ruegeria sp. TM1040 4075714 YP_611545.1 CDS TM1040_3311 NC_008043.1 320075 321163 D 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 320075..321163 Ruegeria sp. TM1040 4075716 YP_611546.1 CDS TM1040_3312 NC_008043.1 321168 322187 D KEGG: bbr:BB4927 probable periplasmic solute-binding protein, ev=1e-126, 62% identity; periplasmic solute-binding protein 321168..322187 Ruegeria sp. TM1040 4075717 YP_611547.1 CDS TM1040_3313 NC_008043.1 322245 323048 D 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 322245..323048 Ruegeria sp. TM1040 4075718 YP_611548.1 CDS TM1040_3314 NC_008043.1 323052 323840 D 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 323052..323840 Ruegeria sp. TM1040 4075719 YP_611549.1 CDS TM1040_3315 NC_008043.1 323837 324865 D 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 323837..324865 Ruegeria sp. TM1040 4075720 YP_611550.1 CDS TM1040_3316 NC_008043.1 324875 325687 D PFAM: metallophosphoesterase: (9.7e-16); KEGG: rpb:RPB_4042 metallophosphoesterase, ev=8e-46, 41% identity; metallophosphoesterase 324875..325687 Ruegeria sp. TM1040 4075721 YP_611551.1 CDS TM1040_3317 NC_008043.1 325731 327014 R 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 complement(325731..327014) Ruegeria sp. TM1040 4075722 YP_611552.1 CDS TM1040_3318 NC_008043.1 327007 327534 R 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 complement(327007..327534) Ruegeria sp. TM1040 4075723 YP_611553.1 CDS TM1040_3319 NC_008043.1 327591 328571 R 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 complement(327591..328571) Ruegeria sp. TM1040 4075724 YP_611554.1 CDS TM1040_3320 NC_008043.1 328688 329566 R 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 complement(328688..329566) Ruegeria sp. TM1040 4075725 YP_611555.1 CDS TM1040_3321 NC_008043.1 329654 331141 R PFAM: aldehyde dehydrogenase: (3.9e-234); KEGG: mlo:mll2319 aldehyde dehydrogenase, ev=0.0, 75% identity; aldehyde dehydrogenase (acceptor) complement(329654..331141) Ruegeria sp. TM1040 4075726 YP_611556.1 CDS TM1040_3322 NC_008043.1 331411 332034 D hypothetical protein 331411..332034 Ruegeria sp. TM1040 4075727 YP_611557.1 CDS TM1040_3323 NC_008043.1 332127 333173 R 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 complement(332127..333173) Ruegeria sp. TM1040 4075728 YP_611558.1 CDS TM1040_3324 NC_008043.1 333330 334019 D 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 333330..334019 Ruegeria sp. TM1040 4075729 YP_611559.1 CDS TM1040_3325 NC_008043.1 334135 335655 D PFAM: aldehyde dehydrogenase: (1.8e-16); KEGG: sil:SPOA0260 aldehyde dehydrogenase family protein, ev=0.0, 76% identity; aldehyde dehydrogenase 334135..335655 Ruegeria sp. TM1040 4075730 YP_611560.1 CDS TM1040_3326 NC_008043.1 336360 336977 D 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 336360..336977 Ruegeria sp. TM1040 4075731 YP_611561.1 CDS TM1040_3327 NC_008043.1 336974 337579 D 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 336974..337579 Ruegeria sp. TM1040 4075732 YP_611562.1 CDS TM1040_3328 NC_008043.1 337576 339660 D PFAM: Mammalian cell entry related: (5e-08); KEGG: sil:SPO1249 paraquat-inducible protein, , ev=1e-120, 36% identity; hypothetical protein 337576..339660 Ruegeria sp. TM1040 4075733 YP_611563.1 CDS TM1040_3329 NC_008043.1 339662 340219 D 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 339662..340219 Ruegeria sp. TM1040 4075734 YP_611564.1 CDS TM1040_3330 NC_008043.1 340248 340973 R 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 complement(340248..340973) Ruegeria sp. TM1040 4075735 YP_611565.1 CDS TM1040_3331 NC_008043.1 340970 341773 R 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 complement(340970..341773) Ruegeria sp. TM1040 4075736 YP_611566.1 CDS TM1040_3332 NC_008043.1 341777 342667 R 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 complement(341777..342667) Ruegeria sp. TM1040 4075231 YP_611567.1 CDS TM1040_3333 NC_008043.1 342686 343723 R 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 complement(342686..343723) Ruegeria sp. TM1040 4075232 YP_611568.1 CDS TM1040_3334 NC_008043.1 344066 345592 D KEGG: bja:blr7618 hypothetical protein, ev=1e-62, 36% identity; hypothetical protein 344066..345592 Ruegeria sp. TM1040 4075233 YP_611569.1 CDS TM1040_3335 NC_008043.1 345607 346299 D 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 345607..346299 Ruegeria sp. TM1040 4075234 YP_611570.1 CDS TM1040_3336 NC_008043.1 346296 347858 D 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 346296..347858 Ruegeria sp. TM1040 4075235 YP_611571.1 CDS TM1040_3337 NC_008043.1 347840 348940 R PFAM: NADH:flavin oxidoreductase/NADH oxidase: (2.6e-90); KEGG: cvi:CV2245 flavoprotein NADH-dependent oxidoreductase, ev=1e-133, 65% identity; NADH:flavin oxidoreductase complement(347840..348940) Ruegeria sp. TM1040 4075236 YP_611572.1 CDS TM1040_3338 NC_008043.1 349061 349960 D 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 349061..349960 Ruegeria sp. TM1040 4075237 YP_611573.1 CDS TM1040_3339 NC_008043.1 350035 350931 R 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 complement(350035..350931) Ruegeria sp. TM1040 4075238 YP_611574.1 CDS TM1040_3340 NC_008043.1 351039 351881 D KEGG: bur:Bcep18194_C7720 hypothetical protein, ev=2e-86, 56% identity; hypothetical protein 351039..351881 Ruegeria sp. TM1040 4075239 YP_611575.1 CDS TM1040_3341 NC_008043.1 352034 352822 R 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 complement(352034..352822) Ruegeria sp. TM1040 4075240 YP_611576.1 CDS TM1040_3342 NC_008043.1 352824 353945 R PFAM: inner-membrane translocator: (1.9e-72); KEGG: jan:Jann_1426 inner-membrane translocator, ev=1e-157, 74% identity; inner-membrane translocator complement(352824..353945) Ruegeria sp. TM1040 4075241 YP_611577.1 CDS TM1040_3343 NC_008043.1 354019 354969 R 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 complement(354019..354969) Ruegeria sp. TM1040 4075242 YP_611578.1 CDS TM1040_3344 NC_008043.1 355156 356160 D 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 355156..356160 Ruegeria sp. TM1040 4075243 YP_611579.1 CDS TM1040_3345 NC_008043.1 356157 357290 R PFAM: oxidoreductase-like: (6.4e-40) Oxidoreductase-like: (3.2e-10); KEGG: jan:Jann_1423 oxidoreductase-like, ev=1e-179, 80% identity; oxidoreductase-like complement(356157..357290) Ruegeria sp. TM1040 4075244 YP_611580.1 CDS TM1040_3346 NC_008043.1 357303 358196 R 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 complement(357303..358196) Ruegeria sp. TM1040 4075245 YP_611581.1 CDS TM1040_3347 NC_008043.1 358216 359319 R PFAM: oxidoreductase-like: (1.3e-26) Oxidoreductase-like: (0.0011); KEGG: jan:Jann_1421 oxidoreductase-like, ev=1e-154, 71% identity; oxidoreductase-like complement(358216..359319) Ruegeria sp. TM1040 4075246 YP_611582.1 CDS TM1040_3348 NC_008043.1 359443 361311 D 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 359443..361311 Ruegeria sp. TM1040 4075247 YP_611583.1 CDS TM1040_3349 NC_008043.1 361412 362386 D PFAM: PfkB: (1e-55); KEGG: jan:Jann_1419 PfkB, ev=1e-112, 62% identity; PfkB protein 361412..362386 Ruegeria sp. TM1040 4075248 YP_611584.1 CDS TM1040_3350 NC_008043.1 362399 363241 D KEGG: jan:Jann_1418 myo-inositol catabolism IolB protein, ev=1e-128, 76% identity; myo-inositol catabolism IolB protein 362399..363241 Ruegeria sp. TM1040 4075249 YP_611585.1 CDS TM1040_3351 NC_008043.1 363238 364068 D PFAM: ketose-bisphosphate aldolase, class-II: (6.2e-38); KEGG: jan:Jann_1417 fructose-bisphosphate aldolase, ev=1e-115, 73% identity; fructose-bisphosphate aldolase 363238..364068 Ruegeria sp. TM1040 4075250 YP_611586.1 CDS TM1040_3352 NC_008043.1 364070 365059 D 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 364070..365059 Ruegeria sp. TM1040 4075251 YP_611587.1 CDS TM1040_3353 NC_008043.1 365203 366228 R PFAM: conserved hypothetical protein 698: (8.6e-58); KEGG: rsp:RSP_4010 conserved hypothetical protein 698, ev=5e-94, 55% identity; hypothetical protein complement(365203..366228) Ruegeria sp. TM1040 4075252 YP_611588.1 CDS TM1040_3354 NC_008043.1 366235 367584 R 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 complement(366235..367584) Ruegeria sp. TM1040 4075253 YP_611589.1 CDS TM1040_3355 NC_008043.1 367612 368055 D PFAM: Sel1-like repeat: (0.0001); KEGG: mca:MCA0405 hypothetical protein, ev=7e-15, 35% identity; Sel1 repeat-containing protein 367612..368055 Ruegeria sp. TM1040 4075254 YP_611590.1 CDS TM1040_3356 NC_008043.1 368123 368437 R 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 complement(368123..368437) Ruegeria sp. TM1040 4075255 YP_611591.1 CDS TM1040_3357 NC_008043.1 368526 369584 R 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 complement(368526..369584) Ruegeria sp. TM1040 4075256 YP_611592.1 CDS TM1040_3358 NC_008043.1 369621 371096 R 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 complement(369621..371096) Ruegeria sp. TM1040 4075257 YP_611593.1 CDS TM1040_3359 NC_008043.1 371096 371686 R 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 complement(371096..371686) Ruegeria sp. TM1040 4075258 YP_611594.1 CDS TM1040_3360 NC_008043.1 371744 372262 R 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 complement(371744..372262) Ruegeria sp. TM1040 4075259 YP_611595.1 CDS TM1040_3361 NC_008043.1 372262 373152 R PFAM: aldo/keto reductase: (1.3e-38); KEGG: jan:Jann_1942 aldo/keto reductase, ev=1e-107, 65% identity; aldo/keto reductase complement(372262..373152) Ruegeria sp. TM1040 4075260 YP_611596.1 CDS TM1040_3362 NC_008043.1 373152 374306 R PFAM: luciferase-like: (1.2e-05); KEGG: jan:Jann_1941 alkanesulfonate monooxygenase, ev=0.0, 83% identity; alkanesulfonate monooxygenase complement(373152..374306) Ruegeria sp. TM1040 4075261 YP_611597.1 CDS TM1040_3363 NC_008043.1 374370 375119 D 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 374370..375119 Ruegeria sp. TM1040 4075262 YP_611598.1 CDS TM1040_3364 NC_008043.1 375128 376234 D PFAM: oxidoreductase-like: (1.4e-19) Oxidoreductase-like: (1.1e-06); KEGG: jan:Jann_1939 oxidoreductase-like, ev=1e-126, 62% identity; oxidoreductase-like 375128..376234 Ruegeria sp. TM1040 4075263 YP_611599.1 CDS TM1040_3365 NC_008043.1 376336 377040 R PFAM: protein of unknown function DUF125, transmembrane: (1.7e-76); KEGG: mlo:mlr6622 similar to nodulin 21, ev=1e-64, 58% identity; hypothetical protein complement(376336..377040) Ruegeria sp. TM1040 4075264 YP_611600.1 CDS TM1040_3366 NC_008043.1 377231 378076 R PFAM: LytTr DNA-binding region: (4.1e-15); KEGG: rsp:RSP_0660 hypothetical protein, ev=4e-11, 32% identity; response regulator receiver protein complement(377231..378076) Ruegeria sp. TM1040 4075265 YP_611601.1 CDS TM1040_3367 NC_008043.1 378322 379098 D PFAM: MltA-interacting MipA: (9.4e-33); KEGG: atc:AGR_C_1796 outer membrane protein, ev=9e-17, 27% identity; MltA-interacting MipA 378322..379098 Ruegeria sp. TM1040 4075266 YP_611602.1 CDS TM1040_3368 NC_008043.1 379109 380320 D 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 379109..380320 Ruegeria sp. TM1040 4075267 YP_611603.1 CDS TM1040_3369 NC_008043.1 380407 381780 R PFAM: ABC-1: (1.9e-36); KEGG: rsp:RSP_3305 ubiquinol-cytochrome-c reductase assembly protein, ev=1e-128, 55% identity; hypothetical protein complement(380407..381780) Ruegeria sp. TM1040 4075268 YP_611604.1 CDS TM1040_3370 NC_008043.1 381777 383009 R KEGG: jan:Jann_2809 DNA photolyase-like protein, ev=1e-89, 47% identity; deoxyribodipyrimidine photo-lyase family protein complement(381777..383009) Ruegeria sp. TM1040 4075269 YP_611605.1 CDS TM1040_3371 NC_008043.1 383222 385885 D 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 383222..385885 Ruegeria sp. TM1040 4075270 YP_611606.1 CDS TM1040_3372 NC_008043.1 385946 386266 D PFAM: response regulator receiver: (0.00047); KEGG: eba:ebA6722 histidine kinase, ev=1e-11, 37% identity; response regulator receiver protein 385946..386266 Ruegeria sp. TM1040 4075271 YP_611607.1 CDS TM1040_3373 NC_008043.1 386263 386979 D 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 386263..386979 Ruegeria sp. TM1040 4075272 YP_611608.1 CDS TM1040_3374 NC_008043.1 387083 388558 R PFAM: Hemolysin-type calcium-binding region: (0.014); KEGG: bja:bll7673 hypothetical protein, ev=5e-68, 40% identity; hemolysin-type calcium-binding region complement(387083..388558) Ruegeria sp. TM1040 4075273 YP_611609.1 CDS TM1040_3375 NC_008043.1 389009 390259 D 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 389009..390259 Ruegeria sp. TM1040 4075274 YP_611610.1 CDS TM1040_3376 NC_008043.1 390288 390584 D 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 390288..390584 Ruegeria sp. TM1040 4075275 YP_611611.1 CDS TM1040_3377 NC_008043.1 390581 393535 D 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 390581..393535 Ruegeria sp. TM1040 4075276 YP_611612.1 CDS TM1040_3378 NC_008043.1 393528 394079 D KEGG: sil:SPO1585 sarcosine oxidase, gamma subunit family, ev=2e-35, 42% identity; sarcosine oxidase subunit gamma 393528..394079 Ruegeria sp. TM1040 4075277 YP_611613.1 CDS TM1040_3379 NC_008043.1 394091 395104 R 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 complement(394091..395104) Ruegeria sp. TM1040 4075278 YP_611614.1 CDS TM1040_3380 NC_008043.1 395104 396009 R 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 complement(395104..396009) Ruegeria sp. TM1040 4075279 YP_611615.1 CDS TM1040_3381 NC_008043.1 396121 397569 D PFAM: aldehyde dehydrogenase: (2.1e-186); KEGG: sil:SPO3191 aldehyde dehydrogenase family protein, ev=0.0, 89% identity; aldehyde dehydrogenase 396121..397569 Ruegeria sp. TM1040 4075280 YP_611616.1 CDS TM1040_3382 NC_008043.1 397569 398549 D PFAM: peptidase M19, renal dipeptidase: (7.8e-102); KEGG: sil:SPO3190 renal dipeptidase family protein, ev=1e-168, 85% identity; peptidase M19, renal dipeptidase 397569..398549 Ruegeria sp. TM1040 4075281 YP_611617.1 CDS TM1040_3383 NC_008043.1 398618 400162 D PFAM: BCCT transporter: (1.4e-60); KEGG: pha:PSHAa1072 glycine betaine transporter, ev=0.0, 61% identity; BCCT transporter 398618..400162 Ruegeria sp. TM1040 4075282 YP_611618.1 CDS TM1040_3384 NC_008043.1 400275 401978 D KEGG: sil:SPO3189 hypothetical protein, ev=0.0, 66% identity; hypothetical protein 400275..401978 Ruegeria sp. TM1040 4075283 YP_611619.1 CDS TM1040_3385 NC_008043.1 401975 402625 D KEGG: sil:SPO3188 hypothetical protein, ev=2e-39, 46% identity; hypothetical protein 401975..402625 Ruegeria sp. TM1040 4075284 YP_611620.1 CDS TM1040_3386 NC_008043.1 402659 403693 D 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 402659..403693 Ruegeria sp. TM1040 4075285 YP_611621.1 CDS TM1040_3387 NC_008043.1 404374 407385 D 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 404374..407385 Ruegeria sp. TM1040 4075287 YP_611622.1 CDS TM1040_3388 NC_008043.1 407476 408393 R 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 complement(407476..408393) Ruegeria sp. TM1040 4075562 YP_611623.1 CDS TM1040_3389 NC_008043.1 408474 410201 D 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 408474..410201 Ruegeria sp. TM1040 4075563 YP_611624.1 CDS TM1040_3390 NC_008043.1 410234 411202 R 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 complement(410234..411202) Ruegeria sp. TM1040 4075564 YP_611625.1 CDS TM1040_3391 NC_008043.1 411219 412496 R 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 complement(411219..412496) Ruegeria sp. TM1040 4075565 YP_611626.1 CDS TM1040_3392 NC_008043.1 412493 413338 R 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 complement(412493..413338) Ruegeria sp. TM1040 4075566 YP_611627.1 CDS TM1040_3393 NC_008043.1 413357 414115 R 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 complement(413357..414115) Ruegeria sp. TM1040 4075567 YP_611628.1 CDS TM1040_3394 NC_008043.1 414112 414441 R PFAM: protein of unknown function DUF718: (1e-64); KEGG: atc:AGR_C_5099 hypothetical protein Cj0488, ev=6e-48, 77% identity; hypothetical protein complement(414112..414441) Ruegeria sp. TM1040 4075568 YP_611629.1 CDS TM1040_3395 NC_008043.1 414441 415550 R 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 complement(414441..415550) Ruegeria sp. TM1040 4075569 YP_611630.1 CDS TM1040_3396 NC_008043.1 415555 416649 R 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 complement(415555..416649) Ruegeria sp. TM1040 4075570 YP_611631.1 CDS TM1040_3397 NC_008043.1 416653 417516 R 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 complement(416653..417516) Ruegeria sp. TM1040 4075571 YP_611632.1 CDS TM1040_3398 NC_008043.1 417522 418418 R 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 complement(417522..418418) Ruegeria sp. TM1040 4075572 YP_611633.1 CDS TM1040_3399 NC_008043.1 418497 419819 R 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 complement(418497..419819) Ruegeria sp. TM1040 4075573 YP_611634.1 CDS TM1040_3400 NC_008043.1 419964 420770 D PFAM: regulatory proteins, IclR: (9.9e-05); KEGG: bur:Bcep18194_B0136 transcriptional regulator, IclR family, ev=4e-58, 45% identity; IclR family transcriptional regulator 419964..420770 Ruegeria sp. TM1040 4075574 YP_611635.1 CDS TM1040_3401 NC_008043.1 420767 421627 D PFAM: amidohydrolase 2: (5.2e-29); KEGG: amidohydrolase family superfamily, ev=4e-63, 50% identity; amidohydrolase 2 420767..421627 Ruegeria sp. TM1040 4075575 YP_611636.1 CDS TM1040_3402 NC_008043.1 421630 422220 R PFAM: chromosome segregation and condensation protein ScpB: (1.6e-46); KEGG: mlo:mlr9362 hypothetical protein, ev=1e-52, 55% identity; transcriptional regulator complement(421630..422220) Ruegeria sp. TM1040 4075576 YP_611637.1 CDS TM1040_3403 NC_008043.1 422223 423107 R PFAM: protein of unknown function DUF1403: (9.8e-77); KEGG: mlo:mlr6196 hypothetical protein, ev=7e-27, 34% identity; hypothetical protein complement(422223..423107) Ruegeria sp. TM1040 4075577 YP_611638.1 CDS TM1040_3404 NC_008043.1 423285 424160 D KEGG: mlo:mll9356 integrase, ev=3e-53, 40% identity; integrase 423285..424160 Ruegeria sp. TM1040 4075578 YP_611639.1 CDS TM1040_3405 NC_008043.1 424166 425248 R PFAM: ParB-like nuclease: (2.9e-15); KEGG: rsp:RSP_1422 ParB-like nuclease, ev=1e-74, 46% identity; ParB-like nuclease complement(424166..425248) Ruegeria sp. TM1040 4075579 YP_611640.1 CDS TM1040_3406 NC_008043.1 425250 426713 R 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 complement(425250..426713) Ruegeria sp. TM1040 4075580 YP_611641.1 CDS TM1040_3407 NC_008043.1 427302 428594 D PFAM: initiator RepB protein: (0.0063); KEGG: rsp:RSP_1425 plasmid replication initiation protein, ev=1e-153, 64% identity; initiator RepB protein 427302..428594 Ruegeria sp. TM1040 4075581 YP_611642.1 CDS TM1040_3408 NC_008043.1 428668 430182 R catalyzes the formation of malonyl-CoA from malonate and CoA; malonyl-CoA synthase complement(428668..430182) Ruegeria sp. TM1040 4075582 YP_611643.1 CDS TM1040_3409 NC_008043.1 430821 431840 D 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 430821..431840 Ruegeria sp. TM1040 4075583 YP_611644.1 CDS TM1040_3410 NC_008043.1 431965 432822 D PFAM: NmrA-like: (0.00044); KEGG: sil:SPO1056 hypothetical protein, ev=2e-95, 60% identity; NmrA-like 431965..432822 Ruegeria sp. TM1040 4075584 YP_611645.1 CDS TM1040_3411 NC_008043.1 432819 433247 D KEGG: sil:SPO1055 membrane protein, , ev=8e-35, 56% identity; hypothetical protein 432819..433247 Ruegeria sp. TM1040 4075585 YP_611646.1 CDS TM1040_3412 NC_008043.1 433541 434764 R 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 complement(433541..434764) Ruegeria sp. TM1040 4075586 YP_611647.1 CDS TM1040_3413 NC_008043.1 434778 435386 R 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 complement(434778..435386) Ruegeria sp. TM1040 4075587 YP_611648.1 CDS TM1040_3414 NC_008043.1 435386 436039 R 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 complement(435386..436039) Ruegeria sp. TM1040 4075588 YP_611649.1 CDS TM1040_3415 NC_008043.1 436039 436851 R 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 complement(436039..436851) Ruegeria sp. TM1040 4075589 YP_611650.1 CDS TM1040_3416 NC_008043.1 436844 438043 R 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 complement(436844..438043) Ruegeria sp. TM1040 4075590 YP_611651.1 CDS TM1040_3417 NC_008043.1 438048 439391 R 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 complement(438048..439391) Ruegeria sp. TM1040 4075591 YP_611652.1 CDS TM1040_3418 NC_008043.1 439560 440591 D PFAM: ApbE-like lipoprotein: (4.8e-87); KEGG: sil:SPOA0036 thiamin biosynthesis lipoprotein ApbE, ev=5e-79, 48% identity; ApbE-like lipoprotein 439560..440591 Ruegeria sp. TM1040 4075592 YP_611653.1 CDS TM1040_3419 NC_008043.1 440622 440861 D KEGG: sil:SPOA0037 hypothetical protein, ev=1e-24, 68% identity; hypothetical protein 440622..440861 Ruegeria sp. TM1040 4075593 YP_611654.1 CDS TM1040_3420 NC_008043.1 440986 444114 R 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 complement(440986..444114) Ruegeria sp. TM1040 4075594 YP_611655.1 CDS TM1040_3421 NC_008043.1 444126 445271 R PFAM: secretion protein HlyD: (2.1e-22); KEGG: bms:BRA0335 HlyD family secretion protein, ev=3e-62, 39% identity; secretion protein HlyD complement(444126..445271) Ruegeria sp. TM1040 4075595 YP_611656.1 CDS TM1040_3422 NC_008043.1 445506 445916 D PFAM: WxcM-like: (3.7e-74); KEGG: tel:tlr1343 hypothetical protein, ev=1e-52, 73% identity; hypothetical protein 445506..445916 Ruegeria sp. TM1040 4075596 YP_611657.1 CDS TM1040_3423 NC_008043.1 445913 447013 D 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 445913..447013 Ruegeria sp. TM1040 4075597 YP_611658.1 CDS TM1040_3424 NC_008043.1 447010 447975 D 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 447010..447975 Ruegeria sp. TM1040 4075598 YP_611659.1 CDS TM1040_3425 NC_008043.1 448036 448977 R KEGG: xac:XAC1690 hypothetical protein, ev=7e-69, 44% identity; hypothetical protein complement(448036..448977) Ruegeria sp. TM1040 4075599 YP_611660.1 CDS TM1040_3426 NC_008043.1 448974 449903 R KEGG: xac:XAC1689 hypothetical protein, ev=1e-58, 41% identity; hypothetical protein complement(448974..449903) Ruegeria sp. TM1040 4075600 YP_611661.1 CDS TM1040_3427 NC_008043.1 449905 450579 R KEGG: xac:XAC1688 hypothetical protein, ev=4e-48, 46% identity; hypothetical protein complement(449905..450579) Ruegeria sp. TM1040 4075601 YP_611662.1 CDS TM1040_3428 NC_008043.1 450816 452498 D PFAM: Tetratricopeptide TPR_2: (0.00021); KEGG: ccr:CC3718 TPR domain protein, ev=2e-85, 38% identity; tetratricopeptide TPR_2 450816..452498 Ruegeria sp. TM1040 4075602 YP_611663.1 CDS TM1040_3429 NC_008043.1 452503 453402 R PFAM: Rhodanese-like: (2.5e-13); KEGG: sil:SPO0091 rhodanese-like domain protein, ev=1e-153, 86% identity; rhodanese-like protein complement(452503..453402) Ruegeria sp. TM1040 4075603 YP_611664.1 CDS TM1040_3430 NC_008043.1 453595 454200 D PFAM: isochorismatase hydrolase: (2.3e-14); KEGG: sil:SPO0093 pyrazinamidase/nicotinamidase, ev=2e-82, 74% identity; nicotinamidase 453595..454200 Ruegeria sp. TM1040 4075604 YP_611665.1 CDS TM1040_3431 NC_008043.1 454284 456554 D 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 454284..456554 Ruegeria sp. TM1040 4075605 YP_611666.1 CDS TM1040_3432 NC_008043.1 456618 457907 D catalyzes the formation of nictonate and 5-phospho-alpha-D-ribose 1-diphosphate from nicotinate D-ribonucleotide and diphosphate; nicotinate phosphoribosyltransferase 456618..457907 Ruegeria sp. TM1040 4075606 YP_611667.1 CDS TM1040_3433 NC_008043.1 457908 458381 R hypothetical protein complement(457908..458381) Ruegeria sp. TM1040 4075607 YP_611668.1 CDS TM1040_3434 NC_008043.1 458378 459988 R 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 complement(458378..459988) Ruegeria sp. TM1040 4075608 YP_611669.1 CDS TM1040_3435 NC_008043.1 459985 460800 R 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 complement(459985..460800) Ruegeria sp. TM1040 4075609 YP_611670.1 CDS TM1040_3436 NC_008043.1 460797 461744 R 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 complement(460797..461744) Ruegeria sp. TM1040 4075610 YP_611671.1 CDS TM1040_3437 NC_008043.1 461879 463357 R 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 complement(461879..463357) Ruegeria sp. TM1040 4075611 YP_611672.1 CDS panB NC_008043.1 463587 464429 D catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate; 3-methyl-2-oxobutanoate hydroxymethyltransferase 463587..464429 Ruegeria sp. TM1040 4075612 YP_611673.1 CDS panC NC_008043.1 464443 465285 D catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine; pantoate--beta-alanine ligase 464443..465285 Ruegeria sp. TM1040 4075613 YP_611674.1 CDS TM1040_3440 NC_008043.1 465392 466876 D TIGRFAM: glycerol kinase: (6.1e-293); PFAM: carbohydrate kinase, FGGY: (2e-102); KEGG: sil:SPO0104 glycerol kinase, ev=0.0, 75% identity; glycerol kinase 465392..466876 Ruegeria sp. TM1040 4075614 YP_611675.1 CDS TM1040_3441 NC_008043.1 466970 468223 R PFAM: monooxygenase, FAD-binding: (4e-06); KEGG: sil:SPO0105 monooxygenase family protein, ev=0.0, 73% identity; hypothetical protein complement(466970..468223) Ruegeria sp. TM1040 4075615 YP_611676.1 CDS TM1040_3442 NC_008043.1 468295 468849 R 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 complement(468295..468849) Ruegeria sp. TM1040 4075616 YP_611677.1 CDS TM1040_3443 NC_008043.1 468998 469465 R PFAM: cytochrome c, class I: (7.9e-27); KEGG: sil:SPO0130 cytochrome c family protein, ev=1e-41, 62% identity; cytochrome c, class I complement(468998..469465) Ruegeria sp. TM1040 4075617 YP_611678.1 CDS TM1040_3444 NC_008043.1 469717 470052 D hypothetical protein 469717..470052 Ruegeria sp. TM1040 4075618 YP_611679.1 CDS TM1040_3445 NC_008043.1 470059 470502 D hypothetical protein 470059..470502 Ruegeria sp. TM1040 4075619 YP_611680.1 CDS TM1040_3446 NC_008043.1 470506 470958 R PFAM: protein of unknown function DUF188: (2e-34); KEGG: sil:SPO3827 YaiI/YqxD family protein, ev=3e-65, 83% identity; hypothetical protein complement(470506..470958) Ruegeria sp. TM1040 4075620 YP_611681.1 CDS TM1040_3447 NC_008043.1 470955 472460 R catalyzes the conversion of NADPH to NADH; soluble pyridine nucleotide transhydrogenase complement(470955..472460) Ruegeria sp. TM1040 4075081 YP_611682.1 CDS TM1040_3448 NC_008043.1 472465 473310 R PFAM: esterase: (1.2e-74); KEGG: sil:SPO3829 S-formylglutathione hydrolase, , ev=1e-133, 80% identity; carboxylesterase complement(472465..473310) Ruegeria sp. TM1040 4075082 YP_611683.1 CDS TM1040_3449 NC_008043.1 473527 473868 D PFAM: protein of unknown function DUF861, cupin_3: (2.1e-32); KEGG: sil:SPO3326 hypothetical protein, ev=7e-45, 75% identity; hypothetical protein 473527..473868 Ruegeria sp. TM1040 4075083 YP_611684.1 CDS TM1040_3450 NC_008043.1 473885 474808 R PFAM: Auxin Efflux Carrier: (2.3e-15); KEGG: sil:SPO3843 malonate transporter, , ev=1e-126, 73% identity; auxin efflux carrier complement(473885..474808) Ruegeria sp. TM1040 4075084 YP_611685.1 CDS TM1040_3451 NC_008043.1 475100 475750 D PFAM: regulatory protein, TetR: (7.5e-18); KEGG: rsp:RSP_6137 transcriptional regulator, TetR family, ev=2e-58, 58% identity; TetR family transcriptional regulator 475100..475750 Ruegeria sp. TM1040 4075085 YP_611686.1 CDS TM1040_3452 NC_008043.1 475895 476599 D PFAM: regulatory protein, ArsR: (0.0022); KEGG: sil:SPO3809 transcriptional regulator, ArsR family, ev=3e-67, 58% identity; ArsR family transcriptional regulator 475895..476599 Ruegeria sp. TM1040 4075086 YP_611687.1 CDS TM1040_3453 NC_008043.1 476650 476988 D KEGG: jan:Jann_0104 hypothetical protein, ev=6e-41, 79% identity; hypothetical protein 476650..476988 Ruegeria sp. TM1040 4075087 YP_611688.1 CDS TM1040_3454 NC_008043.1 477138 477878 R PFAM: NLP/P60: (2.4e-06); KEGG: sil:SPO3718 NLP/P60 family protein, ev=3e-82, 59% identity; NLP/P60 complement(477138..477878) Ruegeria sp. TM1040 4075088 YP_611689.1 CDS TM1040_3455 NC_008043.1 477875 479293 R PFAM: peptidase M17, leucyl aminopeptidase-like: (4e-101); KEGG: sil:SPO3717 cytosol aminopeptidase family protein, ev=1e-167, 67% identity; leucyl aminopeptidase complement(477875..479293) Ruegeria sp. TM1040 4075089 YP_611690.1 CDS TM1040_3456 NC_008043.1 479425 479805 R KEGG: sil:SPO3716 hypothetical protein, ev=4e-39, 65% identity; hypothetical protein complement(479425..479805) Ruegeria sp. TM1040 4075090 YP_611691.1 CDS TM1040_3457 NC_008043.1 479959 480609 D PFAM: carbonic anhydrase: (3.6e-32); KEGG: sil:SPO3715 carbonic anhydrase, , ev=1e-102, 80% identity; carbonate dehydratase 479959..480609 Ruegeria sp. TM1040 4075091 YP_611692.1 CDS TM1040_3458 NC_008043.1 480673 481824 R KEGG: sil:SPO3710 hypothetical protein, ev=1e-112, 52% identity; hypothetical protein complement(480673..481824) Ruegeria sp. TM1040 4075092 YP_611693.1 CDS TM1040_3459 NC_008043.1 482089 483111 D catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde; aspartate-semialdehyde dehydrogenase 482089..483111 Ruegeria sp. TM1040 4075093 YP_611694.1 CDS TM1040_3460 NC_008043.1 483277 484920 D TIGRFAM: conserved hypothetical protein: (5.3e-26); KEGG: sil:SPO3713 hypothetical protein, ev=2e-98, 39% identity; hypothetical protein 483277..484920 Ruegeria sp. TM1040 4075094 YP_611695.1 CDS TM1040_3461 NC_008043.1 485089 485412 D hypothetical protein 485089..485412 Ruegeria sp. TM1040 4075095 YP_611696.1 CDS TM1040_3462 NC_008043.1 485556 487508 D PFAM: amidohydrolase: (0.0044) Amidohydrolase 3: (1e-100); KEGG: pfl:PFL_2413 conserved hypothetical protein, ev=1e-160, 51% identity; amidohydrolase 3 485556..487508 Ruegeria sp. TM1040 4075096 YP_611697.1 CDS TM1040_3463 NC_008043.1 487552 488316 R 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 complement(487552..488316) Ruegeria sp. TM1040 4075097 YP_611698.1 CDS TM1040_3464 NC_008043.1 488329 489129 R 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 complement(488329..489129) Ruegeria sp. TM1040 4075098 YP_611699.1 CDS TM1040_3465 NC_008043.1 489126 489983 R 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 complement(489126..489983) Ruegeria sp. TM1040 4075099 YP_611700.1 CDS TM1040_3466 NC_008043.1 489983 491395 R PFAM: Pyridoxal-dependent decarboxylase: (7.4e-117); KEGG: sil:SPO3687 decarboxylase, pyridoxal-dependent, ev=0.0, 82% identity; aromatic-L-amino-acid decarboxylase complement(489983..491395) Ruegeria sp. TM1040 4075100 YP_611701.1 CDS TM1040_3467 NC_008043.1 491473 492453 R 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 complement(491473..492453) Ruegeria sp. TM1040 4075101 YP_611702.1 CDS TM1040_3468 NC_008043.1 492552 494063 R 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 complement(492552..494063) Ruegeria sp. TM1040 4075102 YP_611703.1 CDS TM1040_3469 NC_008043.1 494060 494455 R 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 complement(494060..494455) Ruegeria sp. TM1040 4075103 YP_611704.1 CDS TM1040_3470 NC_008043.1 494584 495018 D 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 494584..495018 Ruegeria sp. TM1040 4075104 YP_611705.1 CDS TM1040_3471 NC_008043.1 495015 496277 R PFAM: MOFRL: (1.3e-46); KEGG: sil:SPO1564 MOFRL domain protein, ev=3e-96, 49% identity; hydroxypyruvate reductase complement(495015..496277) Ruegeria sp. TM1040 4075105 YP_611706.1 CDS TM1040_3472 NC_008043.1 496475 497305 D 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 496475..497305 Ruegeria sp. TM1040 4075106 YP_611707.1 CDS TM1040_3473 NC_008043.1 497379 498818 R 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 complement(497379..498818) Ruegeria sp. TM1040 4075107 YP_611708.1 CDS TM1040_3474 NC_008043.1 498896 499402 R catalyzes the formation of glyoxylate from (S)-ureidoglycolate; ureidoglycolate hydrolase complement(498896..499402) Ruegeria sp. TM1040 4075108 YP_611709.1 CDS TM1040_3475 NC_008043.1 499399 500814 R PFAM: polysaccharide deacetylase: (2.9e-06); KEGG: rsp:RSP_1554 possible polysaccharide deacetylase, ev=0.0, 74% identity; polysaccharide deacetylase complement(499399..500814) Ruegeria sp. TM1040 4075109 YP_611710.1 CDS TM1040_3476 NC_008043.1 501014 501370 D PFAM: Transthyretin: (3.6e-59); KEGG: jan:Jann_2609 transthyretin, ev=6e-46, 69% identity; transthyretin 501014..501370 Ruegeria sp. TM1040 4075110 YP_611711.1 CDS TM1040_3477 NC_008043.1 501443 502357 R 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 complement(501443..502357) Ruegeria sp. TM1040 4075111 YP_611712.1 CDS TM1040_3478 NC_008043.1 502467 503726 D PFAM: protein of unknown function DUF989: (2e-260); KEGG: sil:SPO0869 membrane protein, , ev=1e-179, 74% identity; hypothetical protein 502467..503726 Ruegeria sp. TM1040 4075112 YP_611713.1 CDS TM1040_3479 NC_008043.1 503802 505187 D Catalyzes the deamination of guanine; guanine deaminase 503802..505187 Ruegeria sp. TM1040 4075113 YP_611714.1 CDS TM1040_3480 NC_008043.1 511757 512116 R PFAM: response regulator receiver: (0.00015); KEGG: lic:LIC12088 response regulator, ev=1e-10, 44% identity; response regulator receiver protein complement(511757..512116) Ruegeria sp. TM1040 4075120 YP_611715.1 CDS TM1040_3481 NC_008043.1 512374 513432 R 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 complement(512374..513432) Ruegeria sp. TM1040 4075121 YP_611716.1 CDS TM1040_3482 NC_008043.1 513488 514279 R PFAM: regulatory proteins, IclR: (1.8e-32); KEGG: jan:Jann_3839 transcriptional regulator, IclR family, ev=8e-86, 64% identity; IclR family transcriptional regulator complement(513488..514279) Ruegeria sp. TM1040 4075122 YP_611717.1 CDS TM1040_3483 NC_008043.1 514420 515673 D 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 514420..515673 Ruegeria sp. TM1040 4075123 YP_611718.1 CDS TM1040_3484 NC_008043.1 515908 516735 D 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 515908..516735 Ruegeria sp. TM1040 4075124 YP_611719.1 CDS TM1040_3485 NC_008043.1 516735 517583 D 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 516735..517583 Ruegeria sp. TM1040 4075125 YP_611720.1 CDS TM1040_3486 NC_008043.1 517580 519646 D 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 517580..519646 Ruegeria sp. TM1040 4075126 YP_611721.1 CDS TM1040_3487 NC_008043.1 519643 521358 D catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate; dihydroxy-acid dehydratase 519643..521358 Ruegeria sp. TM1040 4075127 YP_611722.1 CDS TM1040_3488 NC_008043.1 521360 522130 D 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 521360..522130 Ruegeria sp. TM1040 4075128 YP_611723.1 CDS TM1040_3489 NC_008043.1 522127 523041 D 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 522127..523041 Ruegeria sp. TM1040 4075129 YP_611724.1 CDS TM1040_3490 NC_008043.1 523050 523655 D 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 523050..523655 Ruegeria sp. TM1040 4075130 YP_611725.1 CDS TM1040_3491 NC_008043.1 523652 524497 D 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 523652..524497 Ruegeria sp. TM1040 4075131 YP_611726.1 CDS TM1040_3492 NC_008043.1 524505 526412 D 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 524505..526412 Ruegeria sp. TM1040 4075132 YP_611727.1 CDS TM1040_3493 NC_008043.1 526566 527798 D PFAM: metallophosphoesterase: (1.1e-15); KEGG: sme:SMc01909 hypothetical protein, ev=5e-91, 43% identity; metallophosphoesterase 526566..527798 Ruegeria sp. TM1040 4075172 YP_611728.1 CDS TM1040_3494 NC_008043.1 527798 531232 D KEGG: rsp:RSP_3215 hypothetical protein, ev=1e-127, 32% identity; hypothetical protein 527798..531232 Ruegeria sp. TM1040 4075173 YP_611729.1 CDS TM1040_3495 NC_008043.1 531293 532558 D 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 531293..532558 Ruegeria sp. TM1040 4075174 YP_611730.1 CDS TM1040_3496 NC_008043.1 532652 535303 D TIGRFAM: conserved hypothetical protein: (1.7e-77); KEGG: sil:SPO0335 hypothetical protein, ev=0.0, 58% identity; hypothetical protein 532652..535303 Ruegeria sp. TM1040 4075175 YP_611731.1 CDS TM1040_3497 NC_008043.1 535485 536399 R TIGRFAM: Zinc finger/thioredoxin : (8.4e-12); KEGG: sil:SPO0336 MJ0042 family finger-like domain protein, ev=2e-57, 43% identity; Zinc finger/thioredoxin complement(535485..536399) Ruegeria sp. TM1040 4075176 YP_611732.1 CDS TM1040_3498 NC_008043.1 536625 537302 D 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 536625..537302 Ruegeria sp. TM1040 4075177 YP_611733.1 CDS TM1040_3499 NC_008043.1 537299 538192 D PFAM: protein of unknown function DUF214: (0.0015); KEGG: sil:SPO0338 cell division permease protein FtsX, , ev=1e-122, 78% identity; hypothetical protein 537299..538192 Ruegeria sp. TM1040 4075178 YP_611734.1 CDS TM1040_3500 NC_008043.1 538189 538938 D PFAM: phospholipid/glycerol acyltransferase: (2.6e-15); KEGG: sil:SPO0339 acyltransferase family protein, ev=1e-97, 70% identity; phospholipid/glycerol acyltransferase 538189..538938 Ruegeria sp. TM1040 4075179 YP_611735.1 CDS TM1040_3501 NC_008043.1 538916 539521 D 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 538916..539521 Ruegeria sp. TM1040 4075180 YP_611736.1 CDS TM1040_3502 NC_008043.1 539572 540084 R hypothetical protein complement(539572..540084) Ruegeria sp. TM1040 4075181 YP_611737.1 CDS TM1040_3503 NC_008043.1 540098 540412 R 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 complement(540098..540412) Ruegeria sp. TM1040 4075182 YP_611738.1 CDS TM1040_3504 NC_008043.1 540502 541899 R 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 complement(540502..541899) Ruegeria sp. TM1040 4075183 YP_611739.1 CDS TM1040_3505 NC_008043.1 542040 542600 R KEGG: mlo:mlr7497 hypothetical protein, ev=3e-45, 60% identity; hypothetical protein complement(542040..542600) Ruegeria sp. TM1040 4075184 YP_611740.1 CDS TM1040_3506 NC_008043.1 542597 543007 R KEGG: jan:Jann_0835 inner membrane protein, ev=3e-49, 69% identity; inner membrane protein complement(542597..543007) Ruegeria sp. TM1040 4075185 YP_611741.1 CDS TM1040_3507 NC_008043.1 543009 543401 R KEGG: jan:Jann_0835 inner membrane protein, ev=1e-26, 44% identity; inner membrane protein complement(543009..543401) Ruegeria sp. TM1040 4075186 YP_611742.1 CDS TM1040_3508 NC_008043.1 543398 543925 R hypothetical protein complement(543398..543925) Ruegeria sp. TM1040 4075187 YP_611743.1 CDS TM1040_3509 NC_008043.1 543942 544376 R hypothetical protein complement(543942..544376) Ruegeria sp. TM1040 4075188 YP_611744.1 CDS TM1040_3510 NC_008043.1 544384 545889 R 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 complement(544384..545889) Ruegeria sp. TM1040 4075189 YP_611745.1 CDS sucA NC_008043.1 545904 548855 R 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 complement(545904..548855) Ruegeria sp. TM1040 4075190 YP_611746.1 CDS TM1040_3512 NC_008043.1 549097 549984 R 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 complement(549097..549984) Ruegeria sp. TM1040 4075191 YP_611747.1 CDS TM1040_3513 NC_008043.1 550003 550842 R 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 complement(550003..550842) Ruegeria sp. TM1040 4075192 YP_611748.1 CDS sucC NC_008043.1 550901 552094 R catalyzes the interconversion of succinyl-CoA and succinate; succinyl-CoA synthetase subunit beta complement(550901..552094) Ruegeria sp. TM1040 4075193 YP_611749.1 CDS TM1040_3515 NC_008043.1 552295 552765 D hypothetical protein 552295..552765 Ruegeria sp. TM1040 4075194 YP_611750.1 CDS TM1040_3516 NC_008043.1 552904 553734 R hypothetical protein complement(552904..553734) Ruegeria sp. TM1040 4075195 YP_611751.1 CDS TM1040_3517 NC_008043.1 553904 554866 R Catalyzes the reversible oxidation of malate to oxaloacetate; malate dehydrogenase complement(553904..554866) Ruegeria sp. TM1040 4075196 YP_611752.1 CDS TM1040_3518 NC_008043.1 555160 555711 D hypothetical protein 555160..555711 Ruegeria sp. TM1040 4075197 YP_611753.1 CDS TM1040_3519 NC_008043.1 555736 556047 R KEGG: sil:SPO0351 hypothetical protein, ev=5e-29, 61% identity; hypothetical protein complement(555736..556047) Ruegeria sp. TM1040 4075198 YP_611754.1 CDS TM1040_3520 NC_008043.1 556410 557264 D PFAM: HpcH/HpaI aldolase: (1.9e-43); KEGG: sil:SPO0352 citrate lyase, beta subunit, ev=1e-127, 80% identity; citryl-CoA lyase 556410..557264 Ruegeria sp. TM1040 4075199 YP_611755.1 CDS TM1040_3521 NC_008043.1 557330 557878 D PFAM: NnrU: (1.5e-16); KEGG: sil:SPO0353 NnrU family protein, ev=2e-69, 67% identity; protein NnrU 557330..557878 Ruegeria sp. TM1040 4075200 YP_611756.1 CDS TM1040_3522 NC_008043.1 557883 558086 D KEGG: rsp:RSP_0972 hypothetical protein, ev=1e-24, 71% identity; hypothetical protein 557883..558086 Ruegeria sp. TM1040 4075201 YP_611757.1 CDS TM1040_3523 NC_008043.1 558088 559128 D KEGG: sil:SPO0355 hypothetical protein, ev=1e-165, 82% identity; hypothetical protein 558088..559128 Ruegeria sp. TM1040 4075202 YP_611758.1 CDS TM1040_3524 NC_008043.1 559224 559799 D PFAM: Phosphoglycerate mutase: (2.1e-05); KEGG: jan:Jann_3544 phosphoglycerate mutase, ev=5e-45, 54% identity; phosphoglycerate mutase 559224..559799 Ruegeria sp. TM1040 4075203 YP_611759.1 CDS TM1040_3525 NC_008043.1 560022 560405 D 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 560022..560405 Ruegeria sp. TM1040 4075204 YP_611760.1 CDS TM1040_3526 NC_008043.1 560420 560791 D KEGG: sil:SPO0359 succinate dehydrogenase, hydrophobic membrane anchor protein, ev=8e-32, 53% identity; succinate dehydrogenase subunit D 560420..560791 Ruegeria sp. TM1040 4075205 YP_611761.1 CDS sdhA NC_008043.1 560816 562624 D 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 560816..562624 Ruegeria sp. TM1040 4075206 YP_611762.1 CDS TM1040_3528 NC_008043.1 562688 563497 D hypothetical protein 562688..563497 Ruegeria sp. TM1040 4075207 YP_611763.1 CDS TM1040_3529 NC_008043.1 563494 564360 D hypothetical protein 563494..564360 Ruegeria sp. TM1040 4075208 YP_611764.1 CDS sdhB NC_008043.1 564490 565269 D 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 564490..565269 Ruegeria sp. TM1040 4075209 YP_611765.1 CDS TM1040_3531 NC_008043.1 566500 567681 R PFAM: Phytanoyl-CoA dioxygenase: (2.4e-27); KEGG: ret:RHE_CH03702 hypothetical protein, ev=1e-118, 58% identity; phytanoyl-CoA dioxygenase complement(566500..567681) Ruegeria sp. TM1040 4075210 YP_611766.1 CDS TM1040_3532 NC_008043.1 567761 568780 D PFAM: regulatory protein, LacI: (0.00039); KEGG: sco:SCO6986 DNA-binding protein, ev=9e-71, 44% identity; LacI family transcriptional regulator 567761..568780 Ruegeria sp. TM1040 4075211 YP_611767.1 CDS TM1040_3533 NC_008043.1 569523 570311 R PFAM: phage integrase: (0.001); phage integrase complement(569523..570311) Ruegeria sp. TM1040 4075212 YP_611768.1 CDS TM1040_3534 NC_008043.1 570525 570791 D 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 570525..570791 Ruegeria sp. TM1040 4075213 YP_611769.1 CDS TM1040_3535 NC_008043.1 570824 571621 D PFAM: Integrase, catalytic region: (4.6e-37); KEGG: mlo:mll6088 transposase, ev=1e-117, 75% identity; integrase catalytic subunit 570824..571621 Ruegeria sp. TM1040 4075214 YP_611770.1 CDS TM1040_3537 NC_008043.1 572581 575973 R 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 complement(572581..575973) Ruegeria sp. TM1040 4075215 YP_611771.1 CDS TM1040_3538 NC_008043.1 575970 578069 R 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 complement(575970..578069) Ruegeria sp. TM1040 4075216 YP_611772.1 CDS TM1040_3539 NC_008043.1 578094 579023 R KEGG: mac:MA2416 hypothetical protein, ev=5e-53, 36% identity; hypothetical protein complement(578094..579023) Ruegeria sp. TM1040 4075217 YP_611773.1 CDS TM1040_3540 NC_008043.1 579025 580188 R 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 complement(579025..580188) Ruegeria sp. TM1040 4075218 YP_611774.1 CDS TM1040_3541 NC_008043.1 580185 581759 R 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 complement(580185..581759) Ruegeria sp. TM1040 4075219 YP_611775.1 CDS TM1040_3542 NC_008043.1 582228 583346 R PFAM: phage integrase: (0.001); KEGG: aci:ACIAD2657 site-specific tyrosine recombinase, ev=2e-06, 23% identity; phage integrase complement(582228..583346) Ruegeria sp. TM1040 4075220 YP_611776.1 CDS TM1040_3544 NC_008043.1 583832 584236 R transcriptional regulator complement(583832..584236) Ruegeria sp. TM1040 4075221 YP_611777.1 CDS TM1040_3546 NC_008043.1 586363 586938 R PFAM: BRO-like: (0.002); KEGG: bme:BMEI0899 phage-related DNA binding protein, ev=6e-10, 32% identity; BRO family protein complement(586363..586938) Ruegeria sp. TM1040 4075222 YP_611778.1 CDS TM1040_3547 NC_008043.1 587243 589153 R hypothetical protein complement(587243..589153) Ruegeria sp. TM1040 4075223 YP_611779.1 CDS TM1040_3548 NC_008043.1 589306 590034 R PFAM: protein of unknown function DUF45: (4.2e-63); KEGG: dvu:DVU1702 hypothetical protein, ev=4e-63, 49% identity; hypothetical protein complement(589306..590034) Ruegeria sp. TM1040 4075224 YP_611780.1 CDS TM1040_3549 NC_008043.1 590038 593316 R 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 complement(590038..593316) Ruegeria sp. TM1040 4075225 YP_611781.1 CDS TM1040_3550 NC_008043.1 593428 594681 R 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 complement(593428..594681) Ruegeria sp. TM1040 4075226 YP_611782.1 CDS TM1040_3551 NC_008043.1 594681 596180 R 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 complement(594681..596180) Ruegeria sp. TM1040 4075227 YP_611783.1 CDS TM1040_3552 NC_008043.1 596707 597282 D PFAM: BRO-like: (0.002); KEGG: bme:BMEI0899 phage-related DNA binding protein, ev=6e-10, 32% identity; BRO family protein 596707..597282 Ruegeria sp. TM1040 4075228 YP_611784.1 CDS TM1040_3553 NC_008043.1 597614 598792 R PFAM: phage integrase: (0.00022); KEGG: dar:Daro_0788 phage integrase, ev=2e-42, 31% identity; phage integrase complement(597614..598792) Ruegeria sp. TM1040 4075229 YP_611785.1 CDS TM1040_3554 NC_008043.1 599009 599191 R 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 complement(599009..599191) Ruegeria sp. TM1040 4075475 YP_611786.1 CDS TM1040_3555 NC_008043.1 599188 600210 R KEGG: sil:SPOA0079 ribonuclease, Rne/Rng family, ev=1e-137, 73% identity; ribonuclease complement(599188..600210) Ruegeria sp. TM1040 4075476 YP_611787.1 CDS TM1040_3556 NC_008043.1 600207 600788 R 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 complement(600207..600788) Ruegeria sp. TM1040 4075477 YP_611788.1 CDS infA NC_008043.1 600920 601138 R stimulates the activities of the other two initiation factors, IF-2 and IF-3; translation initiation factor IF-1 complement(600920..601138) Ruegeria sp. TM1040 4075478 YP_611789.1 CDS TM1040_3558 NC_008043.1 601223 602101 R 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 complement(601223..602101) Ruegeria sp. TM1040 4075479 YP_611790.1 CDS TM1040_3559 NC_008043.1 602195 602782 R KEGG: sil:SPOA0075 hypothetical protein, ev=8e-80, 72% identity; hypothetical protein complement(602195..602782) Ruegeria sp. TM1040 4075480 YP_611791.1 CDS TM1040_3560 NC_008043.1 602782 603177 R TIGRFAM: conserved hypothetical protein: (8.1e-41); KEGG: sil:SPOA0074 hypothetical protein, ev=4e-52, 73% identity; hypothetical protein complement(602782..603177) Ruegeria sp. TM1040 4075481 YP_611792.1 CDS TM1040_3561 NC_008043.1 603178 603633 R PFAM: low molecular weight phosphotyrosine protein phosphatase: (3.3e-12); KEGG: sil:SPOA0073 arsenate reductase, ev=2e-71, 84% identity; protein tyrosine phosphatase complement(603178..603633) Ruegeria sp. TM1040 4075482 YP_611793.1 CDS TM1040_3562 NC_008043.1 603637 604116 R PFAM: Uncharacterised conserved protein UCP032146: (8.4e-77); KEGG: sil:SPOA0072 hypothetical protein, ev=2e-76, 86% identity; hypothetical protein complement(603637..604116) Ruegeria sp. TM1040 4075483 YP_611794.1 CDS hisD NC_008043.1 604396 605700 R catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase complement(604396..605700) Ruegeria sp. TM1040 4075484 YP_611795.1 CDS TM1040_3564 NC_008043.1 606074 606229 D KEGG: sil:SPOA0136 hypothetical protein, ev=5e-08, 71% identity; hypothetical protein 606074..606229 Ruegeria sp. TM1040 4075486 YP_611796.1 CDS TM1040_3565 NC_008043.1 606235 607506 D 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 606235..607506 Ruegeria sp. TM1040 4075487 YP_611797.1 CDS TM1040_3566 NC_008043.1 607506 607982 D KEGG: sil:SPOA0138 hypothetical protein, ev=6e-62, 74% identity; hypothetical protein 607506..607982 Ruegeria sp. TM1040 4075488 YP_611798.1 CDS TM1040_3567 NC_008043.1 608024 608818 R 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 complement(608024..608818) Ruegeria sp. TM1040 4075489 YP_611799.1 CDS TM1040_3568 NC_008043.1 608968 609945 R 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 complement(608968..609945) Ruegeria sp. TM1040 4075490 YP_611800.1 CDS TM1040_3569 NC_008043.1 609942 610790 R PFAM: alpha/beta hydrolase fold: (3.6e-13); KEGG: sil:SPOA0436 hydrolase, alpha/beta fold family, ev=4e-70, 50% identity; alpha/beta hydrolase complement(609942..610790) Ruegeria sp. TM1040 4075491 YP_611801.1 CDS TM1040_3570 NC_008043.1 610813 611502 R 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 complement(610813..611502) Ruegeria sp. TM1040 4075492 YP_611802.1 CDS TM1040_3571 NC_008043.1 611669 612097 D 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 611669..612097 Ruegeria sp. TM1040 4075493 YP_611803.1 CDS TM1040_3572 NC_008043.1 612350 613423 D KEGG: pca:Pcar_0492 spermidine/putrescine-binding periplasmic protein-like, ev=3e-16, 23% identity; spermidine/putrescine-binding periplasmic protein-like 612350..613423 Ruegeria sp. TM1040 4075494 YP_611804.1 CDS TM1040_3573 NC_008043.1 613580 614725 D 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 613580..614725 Ruegeria sp. TM1040 4075495 YP_611805.1 CDS TM1040_3574 NC_008043.1 614751 615059 R KEGG: jan:Jann_1588 hypothetical protein, ev=3e-16, 45% identity; hypothetical protein complement(614751..615059) Ruegeria sp. TM1040 4075496 YP_611806.1 CDS TM1040_3575 NC_008043.1 615049 616101 R KEGG: sil:SPOA0095 hypothetical protein, ev=1e-140, 68% identity; hypothetical protein complement(615049..616101) Ruegeria sp. TM1040 4075497 YP_611807.1 CDS TM1040_3576 NC_008043.1 616098 616508 R KEGG: sil:SPOA0094 hypothetical protein, ev=6e-62, 85% identity; hypothetical protein complement(616098..616508) Ruegeria sp. TM1040 4075498 YP_611808.1 CDS TM1040_3577 NC_008043.1 616505 617992 R PFAM: FAD linked oxidase-like: (1e-10); KEGG: sil:SPOA0093 FAD binding domain protein, ev=0.0, 80% identity; FAD linked oxidase-like protein complement(616505..617992) Ruegeria sp. TM1040 4075499 YP_611809.1 CDS TM1040_3578 NC_008043.1 618302 621514 D 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 618302..621514 Ruegeria sp. TM1040 4075500 YP_611810.1 CDS TM1040_3579 NC_008043.1 628194 629282 R hypothetical protein complement(628194..629282) Ruegeria sp. TM1040 4075507 YP_611811.1 CDS TM1040_3580 NC_008043.1 629292 630824 R KEGG: sil:SPO1693 hypothetical protein, ev=1e-107, 42% identity; hypothetical protein complement(629292..630824) Ruegeria sp. TM1040 4075508 YP_611812.1 CDS TM1040_3581 NC_008043.1 631198 632346 R hypothetical protein complement(631198..632346) Ruegeria sp. TM1040 4075509 YP_611813.1 CDS TM1040_3582 NC_008043.1 632527 632745 R hypothetical protein complement(632527..632745) Ruegeria sp. TM1040 4075510 YP_611814.1 CDS TM1040_3583 NC_008043.1 632864 633151 R KEGG: rso:RSc2607 hypothetical protein, ev=7e-09, 53% identity; hypothetical protein complement(632864..633151) Ruegeria sp. TM1040 4075511 YP_611815.1 CDS TM1040_3584 NC_008043.1 633225 633935 R hypothetical protein complement(633225..633935) Ruegeria sp. TM1040 4075512 YP_611816.1 CDS TM1040_3585 NC_008043.1 634104 635339 R PFAM: phage integrase: (7e-22); KEGG: rso:RSc2622 probable integrase protein, ev=5e-76, 41% identity; phage integrase complement(634104..635339) Ruegeria sp. TM1040 4075513 YP_611817.1 CDS TM1040_3588 NC_008043.1 636897 637490 D PFAM: phage integrase: (3.5e-13); KEGG: gox:GOX2485 phage related integrase, ev=2e-21, 41% identity; phage integrase 636897..637490 Ruegeria sp. TM1040 4075514 YP_611818.1 CDS TM1040_3589 NC_008043.1 637924 638838 D PFAM: Sporulation related: (3e-15); KEGG: sil:SPO2738 lipoprotein, , ev=8e-99, 66% identity; sporulation related protein 637924..638838 Ruegeria sp. TM1040 4075516 YP_611819.1 CDS TM1040_3590 NC_008043.1 638899 640080 D 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 638899..640080 Ruegeria sp. TM1040 4075517 YP_611820.1 CDS TM1040_3591 NC_008043.1 640077 640721 D PFAM: thymidylate kinase: (2.9e-57); KEGG: sil:SPO2740 thymidylate kinase, ev=1e-91, 81% identity; thymidylate kinase 640077..640721 Ruegeria sp. TM1040 4075518 YP_611821.1 CDS TM1040_3592 NC_008043.1 640718 641839 D 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' 640718..641839 Ruegeria sp. TM1040 4075519 YP_611822.1 CDS TM1040_3593 NC_008043.1 641900 642703 D PFAM: TatD-related deoxyribonuclease: (4.1e-93); KEGG: sil:SPO2742 hydrolase, TatD family, ev=1e-127, 82% identity; TatD-related deoxyribonuclease 641900..642703 Ruegeria sp. TM1040 4075520 YP_611823.1 CDS TM1040_3594 NC_008043.1 642703 643500 D PFAM: beta-lactamase-like: (3.1e-05); KEGG: jan:Jann_1274 beta-lactamase-like, ev=1e-110, 70% identity; beta-lactamase-like protein 642703..643500 Ruegeria sp. TM1040 4075521 YP_611824.1 CDS TM1040_3595 NC_008043.1 643537 644469 D PFAM: Auxin Efflux Carrier: (4.7e-24); KEGG: sil:SPO2744 malonate transporter, , ev=1e-118, 68% identity; auxin efflux carrier 643537..644469 Ruegeria sp. TM1040 4075522 YP_611825.1 CDS TM1040_3596 NC_008043.1 644593 645138 D 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 644593..645138 Ruegeria sp. TM1040 4075523 YP_611826.1 CDS TM1040_3597 NC_008043.1 645205 646596 R PFAM: peptidase M20: (5e-17); KEGG: bur:Bcep18194_A4728 peptidase M20, ev=1e-135, 54% identity; hypothetical protein complement(645205..646596) Ruegeria sp. TM1040 4075024 YP_611827.1 CDS TM1040_3598 NC_008043.1 646593 648158 R PFAM: gamma-glutamyltranspeptidase: (1e-69); KEGG: rpa:RPA0776 possible gamma-glutamyltranspeptidase precursor, ev=1e-142, 51% identity; gamma-glutamyltransferase 1 complement(646593..648158) Ruegeria sp. TM1040 4075025 YP_611828.1 CDS TM1040_3599 NC_008043.1 648155 649138 R 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 complement(648155..649138) Ruegeria sp. TM1040 4075026 YP_611829.1 CDS TM1040_3600 NC_008043.1 649135 650130 R 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 complement(649135..650130) Ruegeria sp. TM1040 4075027 YP_611830.1 CDS TM1040_3601 NC_008043.1 650134 651030 R 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 complement(650134..651030) Ruegeria sp. TM1040 4075028 YP_611831.1 CDS TM1040_3602 NC_008043.1 651032 651949 R 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 complement(651032..651949) Ruegeria sp. TM1040 4075029 YP_611832.1 CDS TM1040_3603 NC_008043.1 652050 653573 R 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 complement(652050..653573) Ruegeria sp. TM1040 4075030 YP_611833.1 CDS TM1040_3604 NC_008043.1 653725 654486 D PFAM: regulatory proteins, IclR: (9.3e-16); KEGG: rru:Rru_A1344 transcriptional regulator, IclR family, ev=3e-56, 45% identity; IclR family transcriptional regulator 653725..654486 Ruegeria sp. TM1040 4075031 YP_611834.1 CDS TM1040_3605 NC_008043.1 654670 655857 D 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 654670..655857 Ruegeria sp. TM1040 4075032 YP_611835.1 CDS TM1040_3606 NC_008043.1 655964 657247 D 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 655964..657247 Ruegeria sp. TM1040 4075033 YP_611836.1 CDS TM1040_3607 NC_008043.1 657267 658217 D PFAM: Asparaginase/glutaminase: (6.5e-73); KEGG: eca:ECA2340 cytoplasmic asparaginase I, ev=3e-50, 38% identity; asparaginase 657267..658217 Ruegeria sp. TM1040 4075034 YP_611837.1 CDS TM1040_3608 NC_008043.1 658318 659745 D 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 658318..659745 Ruegeria sp. TM1040 4075035 YP_611838.1 CDS TM1040_3609 NC_008043.1 659788 660702 R PFAM: sugar isomerase (SIS): (0.0046); KEGG: sil:SPO1591 SIS domain protein, ev=3e-33, 30% identity; RpiR family transcriptional regulator complement(659788..660702) Ruegeria sp. TM1040 4075036 YP_611839.1 CDS TM1040_3610 NC_008043.1 660766 664488 R 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 complement(660766..664488) Ruegeria sp. TM1040 4075037 YP_611840.1 CDS TM1040_3611 NC_008043.1 664980 665789 D TIGRFAM: Phosphonate-binding periplasmic protein: (5.5e-11); KEGG: ppr:PBPRB1010 hypothetical protein, ev=1e-66, 54% identity; phosphonate-binding periplasmic protein 664980..665789 Ruegeria sp. TM1040 4075038 YP_611841.1 CDS TM1040_3612 NC_008043.1 665882 668194 D 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 665882..668194 Ruegeria sp. TM1040 4075039 YP_611842.1 CDS TM1040_3613 NC_008043.1 668225 669037 R PFAM: ABC-3: (1.5e-75); KEGG: jan:Jann_0315 ABC-3, ev=2e-95, 70% identity; hypothetical protein complement(668225..669037) Ruegeria sp. TM1040 4075040 YP_611843.1 CDS TM1040_3614 NC_008043.1 669034 669783 R 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 complement(669034..669783) Ruegeria sp. TM1040 4075041 YP_611844.1 CDS TM1040_3615 NC_008043.1 669789 670259 R KEGG: jan:Jann_0313 ferric uptake regulator, FUR family, ev=5e-57, 67% identity; ferric uptake regulator family protein complement(669789..670259) Ruegeria sp. TM1040 4075042 YP_611845.1 CDS TM1040_3616 NC_008043.1 670359 671495 D 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 670359..671495 Ruegeria sp. TM1040 4075043 YP_611846.1 CDS TM1040_3617 NC_008043.1 671764 672813 D PFAM: homocysteine S-methyltransferase: (1.5e-124); KEGG: rsp:RSP_3347 methionine synthase, 5-methyltetrahydrofolate--homocysteine methyltransferase, ev=1e-152, 77% identity; methionine synthase 671764..672813 Ruegeria sp. TM1040 4075044 YP_611847.1 CDS TM1040_3618 NC_008043.1 672806 675547 D 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 672806..675547 Ruegeria sp. TM1040 4075045 YP_611848.1 CDS TM1040_3619 NC_008043.1 675641 676090 D PFAM: thiol-disulphide oxidoreductase DCC: (9.6e-22); KEGG: ret:RHE_CH01012 hypothetical protein, ev=6e-23, 40% identity; thiol-disulfide oxidoreductase DCC 675641..676090 Ruegeria sp. TM1040 4075046 YP_611849.1 CDS TM1040_3620 NC_008043.1 676087 677670 D PFAM: Saccharopine dehydrogenase: (5.7e-09); KEGG: ret:RHE_CH01011 hypothetical protein, ev=7e-60, 34% identity; saccharopine dehydrogenase 676087..677670 Ruegeria sp. TM1040 4075047 YP_611850.1 CDS TM1040_3621 NC_008043.1 677733 679253 R PFAM: aldehyde dehydrogenase: (4.8e-221); KEGG: bha:BH0681 aldehyde dehydrogenase, ev=0.0, 76% identity; aldehyde dehydrogenase complement(677733..679253) Ruegeria sp. TM1040 4075048 YP_611851.1 CDS TM1040_3622 NC_008043.1 679401 680360 R 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 complement(679401..680360) Ruegeria sp. TM1040 4075049 YP_611852.1 CDS pheT NC_008043.1 680579 682975 D 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 680579..682975 Ruegeria sp. TM1040 4075050 YP_611853.1 CDS TM1040_3624 NC_008043.1 683214 683663 D KEGG: jan:Jann_0455 hypothetical protein, ev=1e-66, 81% identity; hypothetical protein 683214..683663 Ruegeria sp. TM1040 4075051 YP_611854.1 CDS TM1040_3625 NC_008043.1 683660 684190 D KEGG: mlo:mll3172 hypothetical protein, ev=2e-46, 50% identity; hypothetical protein 683660..684190 Ruegeria sp. TM1040 4075052 YP_611855.1 CDS TM1040_3626 NC_008043.1 684353 684931 D hypothetical protein 684353..684931 Ruegeria sp. TM1040 4075053 YP_611856.1 CDS TM1040_3627 NC_008043.1 684940 685746 R 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 complement(684940..685746) Ruegeria sp. TM1040 4075054 YP_611857.1 CDS TM1040_3628 NC_008043.1 685988 687112 R 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 complement(685988..687112) Ruegeria sp. TM1040 4075055 YP_611858.1 CDS TM1040_3629 NC_008043.1 687251 687712 D PFAM: regulatory proteins, AsnC/Lrp: (3.5e-31); KEGG: sil:SPO0223 transcriptional regulator, AsnC family, ev=1e-68, 85% identity; AsnC family transcriptional regulator 687251..687712 Ruegeria sp. TM1040 4075056 YP_611859.1 CDS TM1040_3630 NC_008043.1 687919 688836 D PFAM: protein of unknown function DUF344: (4.5e-164); KEGG: sil:SPO0224 polyphosphate kinase, , ev=1e-156, 85% identity; hypothetical protein 687919..688836 Ruegeria sp. TM1040 4075057 YP_611860.1 CDS TM1040_3631 NC_008043.1 689022 689693 D 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 689022..689693 Ruegeria sp. TM1040 4075058 YP_611861.1 CDS TM1040_3632 NC_008043.1 689693 689938 D 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 689693..689938 Ruegeria sp. TM1040 4075059 YP_611862.1 CDS TM1040_3633 NC_008043.1 689943 690389 D PFAM: molybdopterin biosynthesis MoaE: (5.7e-46); KEGG: sil:SPO3633 molybdopterin converting factor, subunit 2, ev=1e-53, 72% identity; molybdopterin synthase subunit MoaE 689943..690389 Ruegeria sp. TM1040 4075060 YP_611863.1 CDS TM1040_3634 NC_008043.1 690768 691682 R 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 complement(690768..691682) Ruegeria sp. TM1040 4075062 YP_611864.1 CDS TM1040_3635 NC_008043.1 691965 693041 D 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 691965..693041 Ruegeria sp. TM1040 4075063 YP_611865.1 CDS TM1040_3636 NC_008043.1 693110 694219 D 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 693110..694219 Ruegeria sp. TM1040 4075064 YP_611866.1 CDS TM1040_3637 NC_008043.1 694216 695085 D 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 694216..695085 Ruegeria sp. TM1040 4075065 YP_611867.1 CDS TM1040_3638 NC_008043.1 695082 695942 D 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 695082..695942 Ruegeria sp. TM1040 4075066 YP_611868.1 CDS TM1040_3639 NC_008043.1 696015 697565 R 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 complement(696015..697565) Ruegeria sp. TM1040 4075067 YP_611869.1 CDS TM1040_3640 NC_008043.1 697562 698059 R 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 complement(697562..698059) Ruegeria sp. TM1040 4075068 YP_611870.1 CDS TM1040_3641 NC_008043.1 698127 699212 R 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 complement(698127..699212) Ruegeria sp. TM1040 4075069 YP_611871.1 CDS TM1040_3642 NC_008043.1 699414 700115 D 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 699414..700115 Ruegeria sp. TM1040 4075070 YP_611872.1 CDS TM1040_3643 NC_008043.1 700125 700790 D 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 700125..700790 Ruegeria sp. TM1040 4075071 YP_611873.1 CDS TM1040_3644 NC_008043.1 700886 701098 D hypothetical protein 700886..701098 Ruegeria sp. TM1040 4075072 YP_611874.1 CDS TM1040_3645 NC_008043.1 701101 701532 D 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 701101..701532 Ruegeria sp. TM1040 4075073 YP_611875.1 CDS TM1040_3646 NC_008043.1 701537 701965 D 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 701537..701965 Ruegeria sp. TM1040 4075074 YP_611876.1 CDS TM1040_3647 NC_008043.1 701992 702876 D PFAM: beta-lactamase-like: (3.2e-19); KEGG: jan:Jann_2816 beta-lactamase-like, ev=1e-122, 71% identity; beta-lactamase-like protein 701992..702876 Ruegeria sp. TM1040 4075075 YP_611877.1 CDS TM1040_3648 NC_008043.1 702946 704712 D 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 702946..704712 Ruegeria sp. TM1040 4075076 YP_611878.1 CDS TM1040_3649 NC_008043.1 704949 705752 D 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 704949..705752 Ruegeria sp. TM1040 4075078 YP_611879.1 CDS TM1040_3650 NC_008043.1 705749 706723 D 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 705749..706723 Ruegeria sp. TM1040 4075079 YP_611880.1 CDS TM1040_3651 NC_008043.1 706707 706901 D 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 706707..706901 Ruegeria sp. TM1040 4075080 YP_611881.1 CDS thiG NC_008043.1 706904 707674 D 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 706904..707674 Ruegeria sp. TM1040 4075621 YP_611882.1 CDS thiE NC_008043.1 707671 708267 D Condenses 4-methyl-5-(beta-hydroxyethyl)-thiazole monophosphate and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate to form thiamine monophosphate; thiamine-phosphate pyrophosphorylase 707671..708267 Ruegeria sp. TM1040 4075622 YP_611883.1 CDS TM1040_3654 NC_008043.1 708264 709220 D 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 708264..709220 Ruegeria sp. TM1040 4075623 YP_611884.1 CDS TM1040_3655 NC_008043.1 709241 710176 D PFAM: NLPA lipoprotein: (0.0025); KEGG: sil:SPO0050 ABC transporter, periplasmic substrate-binding protein, ev=1e-148, 82% identity; NLPA lipoprotein 709241..710176 Ruegeria sp. TM1040 4075624 YP_611885.1 CDS TM1040_3656 NC_008043.1 710173 710850 D 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 710173..710850 Ruegeria sp. TM1040 4075625 YP_611886.1 CDS TM1040_3657 NC_008043.1 710847 711575 D 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 710847..711575 Ruegeria sp. TM1040 4075626 YP_611887.1 CDS TM1040_3658 NC_008043.1 711572 712309 D 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 711572..712309 Ruegeria sp. TM1040 4075627 YP_611888.1 CDS TM1040_3659 NC_008043.1 712417 712956 R PFAM: BioY protein: (2.7e-35); KEGG: plu:plu3847 unnamed protein product; similar to biotin synthase, ev=5e-53, 55% identity; BioY protein complement(712417..712956) Ruegeria sp. TM1040 4075628 YP_611889.1 CDS TM1040_3660 NC_008043.1 712996 713586 R 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 complement(712996..713586) Ruegeria sp. TM1040 4075629 YP_611890.1 CDS TM1040_3661 NC_008043.1 713579 714259 R 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 complement(713579..714259) Ruegeria sp. TM1040 4075630 YP_611891.1 CDS TM1040_3662 NC_008043.1 714370 715461 R 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 complement(714370..715461) Ruegeria sp. TM1040 4075631 YP_611892.1 CDS modB NC_008043.1 715458 716150 R part of ModCBA molybdate transporter; member of ABC superfamily; inner membrane component; regulated by repressor protein ModE; molybdate ABC transporter permease complement(715458..716150) Ruegeria sp. TM1040 4075632 YP_611893.1 CDS TM1040_3664 NC_008043.1 716162 716986 R 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 complement(716162..716986) Ruegeria sp. TM1040 4075633 YP_611894.1 CDS TM1040_3665 NC_008043.1 717409 717669 D KEGG: sil:SPO1811 hypothetical protein, ev=4e-35, 83% identity; hypothetical protein 717409..717669 Ruegeria sp. TM1040 4075634 YP_611895.1 CDS TM1040_3666 NC_008043.1 717675 719459 D PFAM: Na+/solute symporter: (3.8e-16); KEGG: sil:SPO1810 sodium/solute symporter family protein, ev=0.0, 85% identity; Na+/solute symporter 717675..719459 Ruegeria sp. TM1040 4075635 YP_611896.1 CDS TM1040_3667 NC_008043.1 719557 721377 D 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 719557..721377 Ruegeria sp. TM1040 4075636 YP_611897.1 CDS TM1040_3668 NC_008043.1 721382 721900 D KEGG: sil:SPO1808 hypothetical protein, ev=1e-52, 56% identity; hypothetical protein 721382..721900 Ruegeria sp. TM1040 4075637 YP_611898.1 CDS TM1040_3669 NC_008043.1 721903 723342 D 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 721903..723342 Ruegeria sp. TM1040 4075638 YP_611899.1 CDS TM1040_3670 NC_008043.1 723351 724298 R 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 complement(723351..724298) Ruegeria sp. TM1040 4075639 YP_611900.1 CDS TM1040_3671 NC_008043.1 724386 725099 D 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 724386..725099 Ruegeria sp. TM1040 4075640 YP_611901.1 CDS TM1040_3672 NC_008043.1 725233 726333 D 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 725233..726333 Ruegeria sp. TM1040 4075641 YP_611902.1 CDS TM1040_3673 NC_008043.1 726497 727729 D 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 726497..727729 Ruegeria sp. TM1040 4075642 YP_611903.1 CDS TM1040_3674 NC_008043.1 727968 728249 D PFAM: regulatory protein, ArsR: (4.1e-10); KEGG: sil:SPOA0427 transcriptional regulator, ArsR family, ev=5e-23, 61% identity; ArsR family transcriptional regulator 727968..728249 Ruegeria sp. TM1040 4075643 YP_611904.1 CDS TM1040_3675 NC_008043.1 728286 729134 R 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 complement(728286..729134) Ruegeria sp. TM1040 4075644 YP_611905.1 CDS TM1040_3676 NC_008043.1 729194 732325 R 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 complement(729194..732325) Ruegeria sp. TM1040 4075645 YP_611906.1 CDS TM1040_3677 NC_008043.1 732480 732869 D KEGG: sil:SPO0573 hypothetical protein, ev=2e-38, 56% identity; hypothetical protein 732480..732869 Ruegeria sp. TM1040 4075646 YP_611907.1 CDS TM1040_3678 NC_008043.1 732994 733584 R PFAM: ThiJ/PfpI: (5.3e-07); KEGG: cvi:CV2336 probable ThiJ/PfpI family protein, ev=9e-39, 46% identity; ThiJ/PfpI complement(732994..733584) Ruegeria sp. TM1040 4075647 YP_611908.1 CDS TM1040_3679 NC_008043.1 733684 734142 R 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 complement(733684..734142) Ruegeria sp. TM1040 4075648 YP_611909.1 CDS TM1040_3680 NC_008043.1 734296 737715 D catalyzes the ferredoxin-dependent oxidative decarboxylation of arylpyruvates; 2-oxoacid ferredoxin oxidoreductase 734296..737715 Ruegeria sp. TM1040 4075649 YP_611910.1 CDS TM1040_3681 NC_008043.1 737812 738486 R PFAM: regulatory protein, TetR: (1.1e-09); KEGG: sil:SPO0566 transcriptional regulator, TetR family, ev=1e-64, 58% identity; TetR family transcriptional regulator complement(737812..738486) Ruegeria sp. TM1040 4075650 YP_611911.1 CDS TM1040_3682 NC_008043.1 738877 740649 D 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 738877..740649 Ruegeria sp. TM1040 4075651 YP_611912.1 CDS TM1040_3683 NC_008043.1 740642 742561 D 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 740642..742561 Ruegeria sp. TM1040 4075652 YP_611913.1 CDS TM1040_3684 NC_008043.1 742561 743589 D 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 742561..743589 Ruegeria sp. TM1040 4075653 YP_611914.1 CDS TM1040_3685 NC_008043.1 743586 744743 D 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 743586..744743 Ruegeria sp. TM1040 4075654 YP_611915.1 CDS TM1040_3686 NC_008043.1 744740 746095 D 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 744740..746095 Ruegeria sp. TM1040 4075655 YP_611916.1 CDS TM1040_3687 NC_008043.1 746168 748522 R 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 complement(746168..748522) Ruegeria sp. TM1040 4075656 YP_611917.1 CDS TM1040_3688 NC_008043.1 748946 750166 D KEGG: sil:SPO0555 hypothetical protein, ev=1e-176, 77% identity; hypothetical protein 748946..750166 Ruegeria sp. TM1040 4075657 YP_611918.1 CDS TM1040_3689 NC_008043.1 750163 751407 D 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 750163..751407 Ruegeria sp. TM1040 4075658 YP_611919.1 CDS TM1040_3690 NC_008043.1 751404 752513 D PFAM: glycosyl transferase, group 1: (4.1e-17); KEGG: sil:SPO0553 glycosyltransferase, group 1, ev=1e-112, 61% identity; group 1 glycosyl transferase 751404..752513 Ruegeria sp. TM1040 4075659 YP_611920.1 CDS TM1040_3691 NC_008043.1 752510 753094 D PFAM: Phosphoglycerate mutase: (3e-31); KEGG: sil:SPO0552 phosphoglycerate mutase family protein, ev=1e-74, 71% identity; phosphoglycerate mutase 752510..753094 Ruegeria sp. TM1040 4075660 YP_611921.1 CDS TM1040_3692 NC_008043.1 753091 754230 D KEGG: sil:SPO0551 hypothetical protein, ev=1e-130, 64% identity; hypothetical protein 753091..754230 Ruegeria sp. TM1040 4075661 YP_611922.1 CDS TM1040_3693 NC_008043.1 754251 755009 D KEGG: sil:SPO0550 hypothetical protein, ev=6e-79, 57% identity; hypothetical protein 754251..755009 Ruegeria sp. TM1040 4075662 YP_611923.1 CDS TM1040_3694 NC_008043.1 755010 755489 D KEGG: sil:SPO0549 hypothetical protein, ev=2e-62, 72% identity; hypothetical protein 755010..755489 Ruegeria sp. TM1040 4075663 YP_611924.1 CDS TM1040_3695 NC_008043.1 755884 757026 R 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 complement(755884..757026) Ruegeria sp. TM1040 4075664 YP_611925.1 CDS TM1040_3696 NC_008043.1 757079 757762 D PFAM: protein of unknown function DUF1045: (3e-47); KEGG: sil:SPO0475 hypothetical protein, ev=2e-81, 65% identity; hypothetical protein 757079..757762 Ruegeria sp. TM1040 4075665 YP_611926.1 CDS TM1040_3697 NC_008043.1 757744 758316 R 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 complement(757744..758316) Ruegeria sp. TM1040 4075666 YP_611927.1 CDS TM1040_3698 NC_008043.1 758313 759017 R 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 complement(758313..759017) Ruegeria sp. TM1040 4075667 YP_611928.1 CDS phnK NC_008043.1 759088 759858 R 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 complement(759088..759858) Ruegeria sp. TM1040 4075668 YP_611929.1 CDS TM1040_3700 NC_008043.1 759858 760739 R PFAM: phosphonate metabolism PhnJ: (1e-209); KEGG: sil:SPO0471 alkylphosphonate utilization protein PhnJ, ev=1e-146, 91% identity; phosphonate metabolism PhnJ complement(759858..760739) Ruegeria sp. TM1040 4075669 YP_611930.1 CDS TM1040_3701 NC_008043.1 760854 761957 R PFAM: phosphonate metabolism: (8.1e-225); KEGG: sil:SPO0470 alkylphosphonate utilization protein PhnI, ev=1e-176, 85% identity; phosphonate metabolism protein complement(760854..761957) Ruegeria sp. TM1040 4075670 YP_611931.1 CDS phnH NC_008043.1 761962 762537 R KEGG: sil:SPO0469 alkylphosphonate utilization protein PhnH, ev=5e-59, 60% identity; carbon-phosphorus lyase complex subunit complement(761962..762537) Ruegeria sp. TM1040 4075671 YP_611932.1 CDS TM1040_3703 NC_008043.1 762537 762989 R PFAM: phosphonate metabolism PhnG: (2.3e-68); KEGG: sil:SPO0468 alkylphosphonate utilization protein PhnG, ev=1e-42, 59% identity; phosphonate metabolism PhnG complement(762537..762989) Ruegeria sp. TM1040 4075672 YP_611933.1 CDS TM1040_3704 NC_008043.1 763112 763834 D 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 763112..763834 Ruegeria sp. TM1040 4075673 YP_611934.1 CDS TM1040_3705 NC_008043.1 763884 764498 R PFAM: transferase hexapeptide repeat: (0.031); KEGG: sil:SPO0784 chloramphenicol acetyltransferase, , ev=7e-95, 79% identity; hexapaptide repeat-containing transferase complement(763884..764498) Ruegeria sp. TM1040 4075674 YP_611935.1 CDS TM1040_3706 NC_008043.1 764648 765967 R 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 complement(764648..765967) Ruegeria sp. TM1040 4075675 YP_611936.1 CDS TM1040_3707 NC_008043.1 765971 766849 R 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 complement(765971..766849) Ruegeria sp. TM1040 4075676 YP_611937.1 CDS TM1040_3708 NC_008043.1 766961 767863 R 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 complement(766961..767863) Ruegeria sp. TM1040 4075677 YP_611938.1 CDS TM1040_3709 NC_008043.1 767931 768749 R 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 complement(767931..768749) Ruegeria sp. TM1040 4075678 YP_611939.1 CDS TM1040_3710 NC_008043.1 769037 769717 D 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 769037..769717 Ruegeria sp. TM1040 4075679 YP_611940.1 CDS TM1040_3711 NC_008043.1 769944 770234 R KEGG: sil:SPO0776 conserved hypothetical protein TIGR00369, ev=5e-16, 49% identity; hypothetical protein complement(769944..770234) Ruegeria sp. TM1040 4075418 YP_611941.1 CDS TM1040_3712 NC_008043.1 770332 771564 R PFAM: protein of unknown function UPF0261: (3e-144); KEGG: sil:SPOA0356 hypothetical protein, ev=1e-175, 74% identity; hypothetical protein complement(770332..771564) Ruegeria sp. TM1040 4075419 YP_611942.1 CDS TM1040_3713 NC_008043.1 771666 773009 R PFAM: aldehyde dehydrogenase: (3e-218); KEGG: jan:Jann_3507 aldehyde dehydrogenase, ev=0.0, 68% identity; betaine-aldehyde dehydrogenase complement(771666..773009) Ruegeria sp. TM1040 4075420 YP_611943.1 CDS TM1040_3714 NC_008043.1 773015 774634 R PFAM: protein of unknown function DUF112, transmembrane: (3.1e-111); KEGG: sil:SPO0771 membrane protein, ev=0.0, 83% identity; hypothetical protein complement(773015..774634) Ruegeria sp. TM1040 4075421 YP_611944.1 CDS TM1040_3715 NC_008043.1 774662 775264 R KEGG: sil:SPO0770 hypothetical protein, ev=3e-62, 59% identity; hypothetical protein complement(774662..775264) Ruegeria sp. TM1040 4075422 YP_611945.1 CDS TM1040_3716 NC_008043.1 775296 776240 R PFAM: Uncharacterized protein UPF0065: (6.2e-09); KEGG: sil:SPO0769 hypothetical protein, ev=1e-155, 85% identity; hypothetical protein complement(775296..776240) Ruegeria sp. TM1040 4075423 YP_611946.1 CDS TM1040_3717 NC_008043.1 776456 777235 D PFAM: regulatory proteins, IclR: (1.2e-15); KEGG: sil:SPO0768 transcriptional regulator, IclR family, ev=4e-89, 63% identity; IclR family transcriptional regulator 776456..777235 Ruegeria sp. TM1040 4075424 YP_611947.1 CDS TM1040_3718 NC_008043.1 777265 778632 D PFAM: aminotransferase class-III: (1.2e-110); KEGG: jan:Jann_3512 aminotransferase class-III, ev=0.0, 78% identity; hypothetical protein 777265..778632 Ruegeria sp. TM1040 4075425 YP_611948.1 CDS TM1040_3719 NC_008043.1 778782 779498 R TIGRFAM: Methyltransferase FkbM: (1.7e-15); KEGG: sil:SPO0767 methyltransferase, FkbM family, ev=2e-82, 68% identity; methyltransferase FkbM complement(778782..779498) Ruegeria sp. TM1040 4075426 YP_611949.1 CDS TM1040_3720 NC_008043.1 779668 780957 R PFAM: glutamine synthetase, catalytic region: (3.5e-56); KEGG: sil:SPO0765 glutamine synthetase family protein, ev=0.0, 84% identity; glutamate--ammonia ligase complement(779668..780957) Ruegeria sp. TM1040 4075427 YP_611950.1 CDS TM1040_3721 NC_008043.1 781124 782383 R PFAM: cytochrome P450: (2.1e-06); KEGG: sil:SPO0764 cytochrome P450 family protein, ev=0.0, 84% identity; cytochrome P450 complement(781124..782383) Ruegeria sp. TM1040 4075428 YP_611951.1 CDS TM1040_3722 NC_008043.1 782475 783194 D PFAM: glutamine amidotransferase class-I: (0.00033); KEGG: sil:SPO0763 glutamine amidotransferase, class I, ev=5e-75, 58% identity; glutamine amidotransferase 782475..783194 Ruegeria sp. TM1040 4075429 YP_611952.1 CDS TM1040_3723 NC_008043.1 783160 783810 R 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 complement(783160..783810) Ruegeria sp. TM1040 4075430 YP_611953.1 CDS paaA NC_008043.1 784063 785055 D with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA; phenylacetate-CoA oxygenase subunit PaaA 784063..785055 Ruegeria sp. TM1040 4075431 YP_611954.1 CDS paaB NC_008043.1 785128 785412 D with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA; involved in phenylacetate degradation; phenylacetate-CoA oxygenase subunit PaaB 785128..785412 Ruegeria sp. TM1040 4075432 YP_611955.1 CDS TM1040_3726 NC_008043.1 785412 786173 D 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 785412..786173 Ruegeria sp. TM1040 4075433 YP_611956.1 CDS TM1040_3727 NC_008043.1 786301 786777 D 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 786301..786777 Ruegeria sp. TM1040 4075434 YP_611957.1 CDS TM1040_3728 NC_008043.1 786791 787861 D 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 786791..787861 Ruegeria sp. TM1040 4075435 YP_611958.1 CDS TM1040_3729 NC_008043.1 788006 788869 D PFAM: aminotransferase, class IV: (4.4e-26); KEGG: sil:SPO0388 aminotransferase, class IV, ev=1e-125, 74% identity; aminotransferase 788006..788869 Ruegeria sp. TM1040 4075436 YP_611959.1 CDS TM1040_3730 NC_008043.1 789027 789482 D PFAM: UspA: (2.3e-16); KEGG: sil:SPO0386 universal stress family protein, ev=7e-72, 83% identity; hypothetical protein 789027..789482 Ruegeria sp. TM1040 4075437 YP_611960.1 CDS TM1040_3731 NC_008043.1 789799 789975 R KEGG: sil:SPO0333 lipoprotein, , ev=8e-11, 49% identity; lipoprotein complement(789799..789975) Ruegeria sp. TM1040 4075438 YP_611961.1 CDS TM1040_3732 NC_008043.1 790000 791391 R catalyzes the formation of arginine from (N-L-arginino)succinate; argininosuccinate lyase complement(790000..791391) Ruegeria sp. TM1040 4075439 YP_611962.1 CDS TM1040_3733 NC_008043.1 791412 791975 D PFAM: Redoxin: (3.4e-15); KEGG: sil:SPO0331 thiol:disulfide interchange protein, , ev=5e-63, 64% identity; redoxin 791412..791975 Ruegeria sp. TM1040 4075440 YP_611963.1 CDS TM1040_3734 NC_008043.1 792143 792982 D PFAM: EAL: (6.5e-41); KEGG: sil:SPO0327 EAL domain protein, ev=4e-97, 63% identity; diguanylate phosphodiesterase 792143..792982 Ruegeria sp. TM1040 4075441 YP_611964.1 CDS TM1040_3735 NC_008043.1 793512 794687 D 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 793512..794687 Ruegeria sp. TM1040 4075442 YP_611965.1 CDS TM1040_3736 NC_008043.1 794909 795631 D 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 794909..795631 Ruegeria sp. TM1040 4075443 YP_611966.1 CDS TM1040_3737 NC_008043.1 795993 796931 D 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 795993..796931 Ruegeria sp. TM1040 4075444 YP_611967.1 CDS TM1040_3738 NC_008043.1 796938 797849 D PFAM: protein of unknown function DUF6, transmembrane: (4.2e-07); KEGG: sil:SPO0323 membrane protein, , ev=1e-124, 76% identity; hypothetical protein 796938..797849 Ruegeria sp. TM1040 4075445 YP_611968.1 CDS TM1040_3739 NC_008043.1 797974 798141 R PFAM: protein of unknown function DUF465: (5.8e-05); KEGG: sil:SPO0322 hypothetical protein, ev=1e-12, 64% identity; hypothetical protein complement(797974..798141) Ruegeria sp. TM1040 4075446 YP_611969.1 CDS TM1040_3740 NC_008043.1 798374 799162 R PFAM: methyltransferase small: (3.3e-05); KEGG: sil:SPO0321 hypothetical protein, ev=1e-89, 64% identity; methyltransferase small complement(798374..799162) Ruegeria sp. TM1040 4075447 YP_611970.1 CDS TM1040_3741 NC_008043.1 799155 799382 R KEGG: sil:SPO0320 hypothetical protein, ev=4e-22, 71% identity; hypothetical protein complement(799155..799382) Ruegeria sp. TM1040 4075448 YP_611971.1 CDS TM1040_3742 NC_008043.1 799434 800444 D PFAM: Polyprenyl synthetase: (1.2e-82); KEGG: sil:SPO0319 decaprenyl diphosphate synthase, ev=1e-151, 84% identity; farnesyltranstransferase 799434..800444 Ruegeria sp. TM1040 4075449 YP_611972.1 CDS TM1040_3743 NC_008043.1 800506 801330 R 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 complement(800506..801330) Ruegeria sp. TM1040 4075450 YP_611973.1 CDS TM1040_3744 NC_008043.1 801317 803035 R 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 complement(801317..803035) Ruegeria sp. TM1040 4075451 YP_611974.1 CDS TM1040_3745 NC_008043.1 803160 804809 R 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 complement(803160..804809) Ruegeria sp. TM1040 4075452 YP_611975.1 CDS TM1040_3746 NC_008043.1 805045 805500 R 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 complement(805045..805500) Ruegeria sp. TM1040 4075453 YP_611976.1 CDS TM1040_3747 NC_008043.1 805646 806026 D 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 805646..806026 Ruegeria sp. TM1040 4075454 YP_611977.1 CDS greA NC_008043.1 806339 806809 D 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 806339..806809 Ruegeria sp. TM1040 4075455 YP_611978.1 CDS TM1040_3749 NC_008043.1 806846 807877 D KEGG: sil:SPO0311 hypothetical protein, ev=1e-101, 62% identity; hypothetical protein 806846..807877 Ruegeria sp. TM1040 4075456 YP_611979.1 CDS TM1040_3750 NC_008043.1 807896 808414 D PFAM: GCN5-related N-acetyltransferase: (6.4e-16); KEGG: rsp:RSP_0613 hypothetical protein, ev=1e-51, 57% identity; N-acetyltransferase GCN5 807896..808414 Ruegeria sp. TM1040 4075457 YP_611980.1 CDS TM1040_3751 NC_008043.1 808645 809904 R is involved in the formation of active molybdenum cofactor and the chelation of molybdenum; molybdopterin biosynthesis protein MoeA complement(808645..809904) Ruegeria sp. TM1040 4075458 YP_611981.1 CDS TM1040_3752 NC_008043.1 809901 810713 R KEGG: sil:SPO0309 hypothetical protein, ev=1e-100, 66% identity; hypothetical protein complement(809901..810713) Ruegeria sp. TM1040 4075459 YP_611982.1 CDS TM1040_3753 NC_008043.1 810734 811225 R 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 complement(810734..811225) Ruegeria sp. TM1040 4075460 YP_611983.1 CDS mobA NC_008043.1 811225 811860 R 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 complement(811225..811860) Ruegeria sp. TM1040 4075461 YP_611984.1 CDS TM1040_3755 NC_008043.1 811857 812315 R hypothetical protein complement(811857..812315) Ruegeria sp. TM1040 4075462 YP_611985.1 CDS TM1040_3756 NC_008043.1 812413 813294 R 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 complement(812413..813294) Ruegeria sp. TM1040 4075463 YP_611986.1 CDS TM1040_3757 NC_008043.1 813350 814078 D PFAM: AzlC-like: (5.6e-48); KEGG: sil:SPO0305 AzlC family protein, ev=1e-82, 64% identity; AzlC-like 813350..814078 Ruegeria sp. TM1040 4075464 YP_611987.1 CDS TM1040_3758 NC_008043.1 814075 814419 D 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 814075..814419 Ruegeria sp. TM1040 4075465 YP_611988.1 CDS TM1040_3759 NC_008043.1 814548 815171 R KEGG: sil:SPO0304 lipoprotein, , ev=4e-61, 56% identity; lipoprotein complement(814548..815171) Ruegeria sp. TM1040 4075466 YP_611989.1 CDS TM1040_3760 NC_008043.1 815201 815335 R hypothetical protein complement(815201..815335) Ruegeria sp. TM1040 4075467 YP_611990.1 CDS TM1040_3761 NC_008043.1 815638 816594 R 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 complement(815638..816594) Ruegeria sp. TM1040 4075469 YP_611991.1 CDS TM1040_3762 NC_008043.1 816768 817871 R catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis; 3-isopropylmalate dehydrogenase complement(816768..817871) Ruegeria sp. TM1040 4075470 YP_611992.1 CDS TM1040_3763 NC_008043.1 817967 818992 R PFAM: Endonuclease/exonuclease/phosphatase: (9.5e-05); KEGG: sil:SPO0213 hypothetical protein, ev=2e-79, 47% identity; endonuclease/exonuclease/phosphatase complement(817967..818992) Ruegeria sp. TM1040 4075471 YP_611993.1 CDS TM1040_3764 NC_008043.1 818989 819819 R KEGG: sil:SPO0214 membrane protein, , ev=3e-76, 52% identity; hypothetical protein complement(818989..819819) Ruegeria sp. TM1040 4075472 YP_611994.1 CDS TM1040_3765 NC_008043.1 820294 821019 D 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 820294..821019 Ruegeria sp. TM1040 4075473 YP_611995.1 CDS TM1040_3766 NC_008043.1 821012 821770 D 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 821012..821770 Ruegeria sp. TM1040 4075474 YP_611996.1 CDS dnaA NC_008044.1 45 1457 D 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 45..1457 Ruegeria sp. TM1040 4078745 YP_611997.1 CDS TM1040_0002 NC_008044.1 1739 2860 D binds the polymerase to DNA and acts as a sliding clamp; DNA polymerase III subunit beta 1739..2860 Ruegeria sp. TM1040 4078746 YP_611998.1 CDS recF NC_008044.1 2950 4023 D Required for DNA replication; binds preferentially to single-stranded, linear DNA; recombination protein F 2950..4023 Ruegeria sp. TM1040 4078666 YP_611999.1 CDS TM1040_0004 NC_008044.1 4020 4640 D PFAM: Lysine exporter protein (LYSE/YGGA): (3e-09); KEGG: sil:SPO0152 transporter, LysE family, ev=2e-76, 67% identity; lysine exporter protein LysE/YggA 4020..4640 Ruegeria sp. TM1040 4078667 YP_612000.1 CDS TM1040_0005 NC_008044.1 4633 5220 R PFAM: regulatory protein, TetR: (5.9e-13); KEGG: sil:SPO0153 transcriptional regulator, TetR family, ev=2e-57, 58% identity; TetR family transcriptional regulator complement(4633..5220) Ruegeria sp. TM1040 4078668 YP_612001.1 CDS TM1040_0006 NC_008044.1 5336 5929 D 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) 5336..5929 Ruegeria sp. TM1040 4078669 YP_612002.1 CDS gyrB NC_008044.1 6015 8432 D negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit B 6015..8432 Ruegeria sp. TM1040 4078670 YP_612003.1 CDS radC NC_008044.1 8429 9205 R 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 complement(8429..9205) Ruegeria sp. TM1040 4078671 YP_612004.1 CDS TM1040_0009 NC_008044.1 9343 10500 R 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 complement(9343..10500) Ruegeria sp. TM1040 4078672 YP_612005.1 CDS dnaK NC_008044.1 10577 12505 R 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 complement(10577..12505) Ruegeria sp. TM1040 4078673 YP_612006.1 CDS TM1040_0011 NC_008044.1 12713 13315 D PFAM: 2OG-Fe(II) oxygenase: (2.2e-08); KEGG: sil:SPO0042 alkylated DNA repair protein, , ev=8e-75, 68% identity; DNA-N1-methyladenine dioxygenase 12713..13315 Ruegeria sp. TM1040 4078674 YP_612007.1 CDS TM1040_0012 NC_008044.1 13332 14210 R KEGG: sil:SPO0040 ABC transporter, permease protein, ev=1e-103, 63% identity; ABC transporter permease complement(13332..14210) Ruegeria sp. TM1040 4078675 YP_612008.1 CDS TM1040_0013 NC_008044.1 14274 15071 D 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 14274..15071 Ruegeria sp. TM1040 4078676 YP_612009.1 CDS TM1040_0014 NC_008044.1 15072 15872 D 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 15072..15872 Ruegeria sp. TM1040 4078677 YP_612010.1 CDS TM1040_0015 NC_008044.1 16023 16916 D 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 16023..16916 Ruegeria sp. TM1040 4078678 YP_612011.1 CDS TM1040_0016 NC_008044.1 17017 18000 D 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 17017..18000 Ruegeria sp. TM1040 4078679 YP_612012.1 CDS TM1040_0017 NC_008044.1 18017 19078 D KEGG: sil:SPO0037 hypothetical protein, ev=1e-109, 57% identity; hypothetical protein 18017..19078 Ruegeria sp. TM1040 4078680 YP_612013.1 CDS TM1040_0018 NC_008044.1 19217 20203 D KEGG: sil:SPO0036 hypothetical protein, ev=1e-147, 73% identity; hypothetical protein 19217..20203 Ruegeria sp. TM1040 4078681 YP_612014.1 CDS TM1040_0019 NC_008044.1 20200 21900 D 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 20200..21900 Ruegeria sp. TM1040 4078682 YP_612015.1 CDS TM1040_0020 NC_008044.1 21907 23346 D KEGG: sil:SPO0034 hypothetical protein, ev=0.0, 65% identity; hypothetical protein 21907..23346 Ruegeria sp. TM1040 4078683 YP_612016.1 CDS TM1040_0021 NC_008044.1 23420 23884 R 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 complement(23420..23884) Ruegeria sp. TM1040 4078684 YP_612017.1 CDS TM1040_0022 NC_008044.1 23940 24503 R 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 complement(23940..24503) Ruegeria sp. TM1040 4078685 YP_612018.1 CDS TM1040_0023 NC_008044.1 24596 24820 D hypothetical protein 24596..24820 Ruegeria sp. TM1040 4076290 YP_612019.1 CDS TM1040_0024 NC_008044.1 24823 25581 R 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 complement(24823..25581) Ruegeria sp. TM1040 4076291 YP_612020.1 CDS TM1040_0025 NC_008044.1 25581 26015 R PFAM: OstA-like protein: (2.9e-26); KEGG: sil:SPO0080 hypothetical protein, ev=5e-37, 56% identity; OstA-like protein complement(25581..26015) Ruegeria sp. TM1040 4076292 YP_612021.1 CDS TM1040_0026 NC_008044.1 26085 26684 R KEGG: sil:SPO0081 hypothetical protein, ev=2e-50, 51% identity; hypothetical protein complement(26085..26684) Ruegeria sp. TM1040 4076293 YP_612022.1 CDS TM1040_0027 NC_008044.1 26757 27371 R PFAM: 3'-5' exonuclease: (4.8e-36); KEGG: sil:SPO0083 exonuclease, , ev=1e-98, 83% identity; 3'-5' exonuclease complement(26757..27371) Ruegeria sp. TM1040 4076294 YP_612023.1 CDS TM1040_0028 NC_008044.1 27635 29086 D TIGRFAM: xylulokinase: (4.1e-214); PFAM: carbohydrate kinase, FGGY: (2.2e-90); KEGG: sil:SPO0855 xylulokinase, ev=1e-173, 62% identity; xylulokinase 27635..29086 Ruegeria sp. TM1040 4076295 YP_612024.1 CDS TM1040_0029 NC_008044.1 29083 30393 D catalyzes the interconversion of D-xylose to D-xylulose; xylose isomerase 29083..30393 Ruegeria sp. TM1040 4076296 YP_612025.1 CDS TM1040_0030 NC_008044.1 30394 31401 D PFAM: Aldose 1-epimerase: (1.6e-57); KEGG: sil:SPO0857 aldose 1-epimerase, ev=3e-63, 42% identity; aldose 1-epimerase 30394..31401 Ruegeria sp. TM1040 4076297 YP_612026.1 CDS TM1040_0031 NC_008044.1 31401 32708 D KEGG: sil:SPO0858 methylamine utilization protein MauG, , ev=1e-152, 65% identity; methylamine utilization protein MauG 31401..32708 Ruegeria sp. TM1040 4076298 YP_612027.1 CDS TM1040_0032 NC_008044.1 32737 34287 R PFAM: phospholipase D/Transphosphatidylase: (1.5e-05); KEGG: bbr:BB0822 phospholipase D protein, ev=1e-112, 46% identity; phospholipase D/transphosphatidylase complement(32737..34287) Ruegeria sp. TM1040 4076299 YP_612028.1 CDS TM1040_0033 NC_008044.1 34629 35831 D 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 34629..35831 Ruegeria sp. TM1040 4076300 YP_612029.1 CDS TM1040_0034 NC_008044.1 35895 36665 R 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 complement(35895..36665) Ruegeria sp. TM1040 4076301 YP_612030.1 CDS TM1040_0035 NC_008044.1 36662 37519 R 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 complement(36662..37519) Ruegeria sp. TM1040 4076302 YP_612031.1 CDS TM1040_0036 NC_008044.1 37516 38433 R 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 complement(37516..38433) Ruegeria sp. TM1040 4076303 YP_612032.1 CDS TM1040_0037 NC_008044.1 38430 39488 R 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 complement(38430..39488) Ruegeria sp. TM1040 4076304 YP_612033.1 CDS TM1040_0038 NC_008044.1 39490 41088 R 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 complement(39490..41088) Ruegeria sp. TM1040 4076305 YP_612034.1 CDS TM1040_0039 NC_008044.1 41146 42195 R PFAM: peptidase M19, renal dipeptidase: (2.4e-119); KEGG: sil:SPO1542 renal dipeptidase family protein, ev=1e-118, 61% identity; dipeptidase AC complement(41146..42195) Ruegeria sp. TM1040 4076306 YP_612035.1 CDS TM1040_0040 NC_008044.1 42535 43575 D 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 42535..43575 Ruegeria sp. TM1040 4076307 YP_612036.1 CDS TM1040_0041 NC_008044.1 43680 44879 D 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 43680..44879 Ruegeria sp. TM1040 4076308 YP_612037.1 CDS TM1040_0042 NC_008044.1 44852 45442 R PFAM: glutathione S-transferase-like: (1.3e-08); KEGG: jan:Jann_0408 glutathione S-transferase-like, ev=3e-60, 59% identity; glutathione S-transferase complement(44852..45442) Ruegeria sp. TM1040 4078705 YP_612038.1 CDS TM1040_0043 NC_008044.1 45518 46546 R 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 complement(45518..46546) Ruegeria sp. TM1040 4078706 YP_612039.1 CDS TM1040_0044 NC_008044.1 46543 47076 R KEGG: sil:SPO3433 lipoprotein, , ev=8e-35, 50% identity; lipoprotein complement(46543..47076) Ruegeria sp. TM1040 4078707 YP_612040.1 CDS leuS NC_008044.1 47063 49636 R 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 complement(47063..49636) Ruegeria sp. TM1040 4078708 YP_612041.1 CDS TM1040_0046 NC_008044.1 49724 50212 R KEGG: sil:SPO3431 hypothetical protein, ev=3e-48, 61% identity; hypothetical protein complement(49724..50212) Ruegeria sp. TM1040 4078709 YP_612042.1 CDS TM1040_0047 NC_008044.1 50494 51438 D KEGG: sil:SPO3430 outer membrane porin, ev=6e-30, 34% identity; outer membrane porin 50494..51438 Ruegeria sp. TM1040 4078710 YP_612043.1 CDS TM1040_0048 NC_008044.1 51557 52213 D 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 51557..52213 Ruegeria sp. TM1040 4078711 YP_612044.1 CDS TM1040_0049 NC_008044.1 52205 52660 R KEGG: sil:SPO3428 hypothetical protein, ev=6e-62, 72% identity; hypothetical protein complement(52205..52660) Ruegeria sp. TM1040 4078712 YP_612045.1 CDS TM1040_0050 NC_008044.1 52702 53790 R 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 complement(52702..53790) Ruegeria sp. TM1040 4078713 YP_612046.1 CDS TM1040_0051 NC_008044.1 53960 54646 D 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 53960..54646 Ruegeria sp. TM1040 4078714 YP_612047.1 CDS TM1040_0052 NC_008044.1 54785 55993 R 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 complement(54785..55993) Ruegeria sp. TM1040 4078715 YP_612048.1 CDS TM1040_0053 NC_008044.1 56222 57010 D 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 56222..57010 Ruegeria sp. TM1040 4078716 YP_612049.1 CDS TM1040_0054 NC_008044.1 57235 58170 D PFAM: Tetratricopeptide TPR_4: (0.016) Thioredoxin domain: (9e-22); KEGG: sil:SPO3423 thioredoxin, ev=1e-125, 75% identity; thioredoxin domain-containing protein 57235..58170 Ruegeria sp. TM1040 4078717 YP_612050.1 CDS TM1040_0055 NC_008044.1 58198 58842 D 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 58198..58842 Ruegeria sp. TM1040 4078718 YP_612051.1 CDS TM1040_0056 NC_008044.1 58839 59024 D PFAM: protein of unknown function DUF343: (2e-16); KEGG: sil:SPO3421 hypothetical protein, ev=5e-20, 78% identity; hypothetical protein 58839..59024 Ruegeria sp. TM1040 4078719 YP_612052.1 CDS TM1040_0057 NC_008044.1 59044 60270 R 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 complement(59044..60270) Ruegeria sp. TM1040 4078720 YP_612053.1 CDS TM1040_0058 NC_008044.1 60494 61825 D PFAM: Amidase: (1.7e-76); KEGG: sil:SPO3418 amidase family protein, ev=1e-180, 73% identity; amidase 60494..61825 Ruegeria sp. TM1040 4078721 YP_612054.1 CDS TM1040_0059 NC_008044.1 61934 63112 D PFAM: aminotransferase, class I and II: (7e-33); KEGG: sil:SPO3417 aminotransferase, classes I and II, ev=0.0, 78% identity; aminotransferase 61934..63112 Ruegeria sp. TM1040 4078722 YP_612055.1 CDS TM1040_0060 NC_008044.1 63232 66279 D PFAM: cell divisionFtsK/SpoIIIE: (1.4e-78); KEGG: sil:SPO3416 FtsK/SpoIIIE family protein, ev=0.0, 68% identity; DNA translocase FtsK 63232..66279 Ruegeria sp. TM1040 4078723 YP_612056.1 CDS TM1040_0061 NC_008044.1 66347 66943 D 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 66347..66943 Ruegeria sp. TM1040 4078724 YP_612057.1 CDS TM1040_0062 NC_008044.1 67002 67589 R KEGG: sil:SPO3414 lipoprotein, , ev=9e-76, 65% identity; hypothetical protein complement(67002..67589) Ruegeria sp. TM1040 4075959 YP_612058.1 CDS TM1040_0063 NC_008044.1 67820 68146 D TIGRFAM: Hemimethylated DNA-binding region: (1.9e-50); KEGG: sil:SPO3412 hypothetical protein, ev=1e-48, 79% identity; hemimethylated DNA-binding region 67820..68146 Ruegeria sp. TM1040 4075960 YP_612059.1 CDS TM1040_0064 NC_008044.1 68184 69761 R PFAM: gamma-glutamyltranspeptidase: (1.2e-171); KEGG: sil:SPO3411 gamma-glutamyltranspeptidase, , ev=0.0, 74% identity; gamma-glutamyltransferase 2 complement(68184..69761) Ruegeria sp. TM1040 4075961 YP_612060.1 CDS TM1040_0065 NC_008044.1 70069 70509 R 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 complement(70069..70509) Ruegeria sp. TM1040 4075962 YP_612061.1 CDS TM1040_0066 NC_008044.1 70543 70887 R 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 complement(70543..70887) Ruegeria sp. TM1040 4075963 YP_612062.1 CDS TM1040_0067 NC_008044.1 70985 72157 D PFAM: Thiolase: (1.6e-116); KEGG: sil:SPO3408 acetyl-CoA C-acetyltransferase, ev=0.0, 87% identity; Acetyl-CoA C-acetyltransferase 70985..72157 Ruegeria sp. TM1040 4075964 YP_612063.1 CDS TM1040_0068 NC_008044.1 72257 72724 D SMART: GAF: (3.9e-06); KEGG: jan:Jann_4049 GAF sensor protein, ev=3e-61, 73% identity; GAF sensor protein 72257..72724 Ruegeria sp. TM1040 4075965 YP_612064.1 CDS TM1040_0069 NC_008044.1 72740 73369 D 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 72740..73369 Ruegeria sp. TM1040 4075966 YP_612065.1 CDS TM1040_0070 NC_008044.1 73397 73768 D PFAM: glutathione-dependent formaldehyde-activating, GFA: (1.5e-22); KEGG: sil:SPO3401 hypothetical protein, ev=4e-47, 72% identity; glutathione-dependent formaldehyde-activating protein 73397..73768 Ruegeria sp. TM1040 4075967 YP_612066.1 CDS TM1040_0071 NC_008044.1 73920 74855 D 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 73920..74855 Ruegeria sp. TM1040 4075968 YP_612067.1 CDS TM1040_0072 NC_008044.1 74929 75582 D 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 74929..75582 Ruegeria sp. TM1040 4075969 YP_612068.1 CDS TM1040_0073 NC_008044.1 75566 76279 R 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 complement(75566..76279) Ruegeria sp. TM1040 4075970 YP_612069.1 CDS TM1040_0074 NC_008044.1 76421 77863 R PFAM: aldehyde dehydrogenase: (3.7e-208); KEGG: sil:SPO3382 aldehyde dehydrogenase family protein, ev=0.0, 86% identity; aldehyde dehydrogenase complement(76421..77863) Ruegeria sp. TM1040 4075971 YP_612070.1 CDS TM1040_0075 NC_008044.1 78109 78759 D 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 78109..78759 Ruegeria sp. TM1040 4075972 YP_612071.1 CDS TM1040_0076 NC_008044.1 78842 79999 R KEGG: jan:Jann_4277 lipopolysaccharide biosynthesis protein-like, ev=3e-32, 35% identity; lipopolysaccharide biosynthesis protein-like complement(78842..79999) Ruegeria sp. TM1040 4075973 YP_612072.1 CDS TM1040_0077 NC_008044.1 80070 80933 R 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 complement(80070..80933) Ruegeria sp. TM1040 4075974 YP_612073.1 CDS TM1040_0078 NC_008044.1 81035 83170 R 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 complement(81035..83170) Ruegeria sp. TM1040 4075975 YP_612074.1 CDS TM1040_0079 NC_008044.1 83364 83552 R KEGG: jan:Jann_2252 hypothetical protein, ev=6e-11, 55% identity; hypothetical protein complement(83364..83552) Ruegeria sp. TM1040 4075976 YP_612075.1 CDS TM1040_0080 NC_008044.1 83627 84841 R 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 complement(83627..84841) Ruegeria sp. TM1040 4075977 YP_612076.1 CDS rpsO NC_008044.1 85005 85274 R 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 complement(85005..85274) Ruegeria sp. TM1040 4078747 YP_612077.1 CDS TM1040_0082 NC_008044.1 85539 86606 R KEGG: sil:SPO3839 type I secretion target repeat protein, ev=6e-63, 40% identity; type I secretion target repeat-containing protein complement(85539..86606) Ruegeria sp. TM1040 4078748 YP_612078.1 CDS TM1040_0083 NC_008044.1 86710 87231 R PFAM: protein of unknown function DUF1643: (4.2e-41); KEGG: sil:SPO3838 hypothetical protein, ev=3e-68, 71% identity; hypothetical protein complement(86710..87231) Ruegeria sp. TM1040 4078749 YP_612079.1 CDS truB NC_008044.1 87460 88368 R catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs; tRNA pseudouridine synthase B complement(87460..88368) Ruegeria sp. TM1040 4078750 YP_612080.1 CDS TM1040_0085 NC_008044.1 88426 89199 R KEGG: sil:SPO3836 hypothetical protein, ev=1e-88, 68% identity; hypothetical protein complement(88426..89199) Ruegeria sp. TM1040 4078751 YP_612081.1 CDS rbfA NC_008044.1 89204 89599 R 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 complement(89204..89599) Ruegeria sp. TM1040 4078752 YP_612082.1 CDS TM1040_0087 NC_008044.1 89693 90502 D catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate reductase 89693..90502 Ruegeria sp. TM1040 4078753 YP_612083.1 CDS TM1040_0088 NC_008044.1 90697 90891 R PFAM: protein of unknown function DUF1674: (2.5e-22); KEGG: sil:SPO3377 hypothetical protein, ev=1e-19, 87% identity; hypothetical protein complement(90697..90891) Ruegeria sp. TM1040 4078754 YP_612084.1 CDS TM1040_0089 NC_008044.1 90990 92264 D 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 90990..92264 Ruegeria sp. TM1040 4078755 YP_612085.1 CDS TM1040_0090 NC_008044.1 92456 94201 D PFAM: Heparinase II/III-like: (1.7e-14); KEGG: sil:SPO3375 hypothetical protein, ev=0.0, 72% identity; heparinase II/III-like 92456..94201 Ruegeria sp. TM1040 4078756 YP_612086.1 CDS purH NC_008044.1 94226 95815 D involved in de novo purine biosynthesis; bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase 94226..95815 Ruegeria sp. TM1040 4078757 YP_612087.1 CDS TM1040_0092 NC_008044.1 95835 96317 D lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis; lipoprotein signal peptidase 95835..96317 Ruegeria sp. TM1040 4078758 YP_612088.1 CDS TM1040_0093 NC_008044.1 96470 96976 D KEGG: sil:SPO3372 hypothetical protein, ev=3e-39, 46% identity; hypothetical protein 96470..96976 Ruegeria sp. TM1040 4078759 YP_612089.1 CDS TM1040_0094 NC_008044.1 97110 98543 D PFAM: peptidase M16-like: (7.5e-35); KEGG: sil:SPO3371 peptidase, M16 family, ev=0.0, 74% identity; peptidase M16-like protein 97110..98543 Ruegeria sp. TM1040 4078760 YP_612090.1 CDS TM1040_0095 NC_008044.1 98540 99913 D PFAM: peptidase M16-like: (1.8e-39); KEGG: sil:SPO3370 peptidase, M16 family, ev=1e-157, 63% identity; peptidase M16-like protein 98540..99913 Ruegeria sp. TM1040 4078761 YP_612091.1 CDS TM1040_0096 NC_008044.1 100018 102360 R PFAM: aldehyde dehydrogenase: (1.2e-201); KEGG: sil:SPO3368 aldehyde dehydrogenase family protein, ev=0.0, 78% identity; aldehyde dehydrogenase complement(100018..102360) Ruegeria sp. TM1040 4078762 YP_612092.1 CDS TM1040_0097 NC_008044.1 102371 103426 R 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 complement(102371..103426) Ruegeria sp. TM1040 4078763 YP_612093.1 CDS TM1040_0098 NC_008044.1 103637 104599 D 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 103637..104599 Ruegeria sp. TM1040 4078764 YP_612094.1 CDS TM1040_0099 NC_008044.1 104599 105405 D 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 104599..105405 Ruegeria sp. TM1040 4078765 YP_612095.1 CDS TM1040_0100 NC_008044.1 105437 106639 D PFAM: ABC-3: (2.2e-59); KEGG: sil:SPO3364 zinc/manganese/iron ABC transporter, permease protein, ev=1e-178, 81% identity; hypothetical protein 105437..106639 Ruegeria sp. TM1040 4078766 YP_612096.1 CDS TM1040_0101 NC_008044.1 106640 107566 D PFAM: ABC-3: (5.6e-26); KEGG: sil:SPO3363 zinc/manganese/iron ABC transporter, permease protein, ev=1e-143, 84% identity; hypothetical protein 106640..107566 Ruegeria sp. TM1040 4078686 YP_612097.1 CDS mutL NC_008044.1 107657 109591 D 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 107657..109591 Ruegeria sp. TM1040 4078687 YP_612098.1 CDS TM1040_0103 NC_008044.1 109602 110837 D PFAM: protein of unknown function DUF195: (7.5e-73); KEGG: sil:SPO3361 RmuC domain protein, ev=1e-166, 73% identity; hypothetical protein 109602..110837 Ruegeria sp. TM1040 4078688 YP_612099.1 CDS TM1040_0104 NC_008044.1 110834 112147 D PFAM: adenylyl cyclase class-3/4/guanylyl cyclase: (2.1e-14); KEGG: sme:SMa1103 probable adenylate cyclase, ev=2e-64, 36% identity; guanylate cyclase 110834..112147 Ruegeria sp. TM1040 4078689 YP_612100.1 CDS TM1040_0105 NC_008044.1 112226 112549 D KEGG: sil:SPO3310 hypothetical protein, ev=2e-27, 58% identity; hypothetical protein 112226..112549 Ruegeria sp. TM1040 4078690 YP_612101.1 CDS TM1040_0106 NC_008044.1 112632 113774 R 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) complement(112632..113774) Ruegeria sp. TM1040 4078691 YP_612102.1 CDS TM1040_0107 NC_008044.1 113804 114856 R PFAM: alanine dehydrogenase/PNT-like: (0.00018); KEGG: sil:SPO3307 saccharopine dehydrogenase, , ev=1e-171, 84% identity; saccharopine dehydrogenase complement(113804..114856) Ruegeria sp. TM1040 4078692 YP_612103.1 CDS TM1040_0108 NC_008044.1 114868 115482 R PFAM: glutathione S-transferase-like: (7.7e-07); KEGG: sil:SPO3306 glutathione S-transferase, , ev=5e-73, 67% identity; glutathione S-transferase complement(114868..115482) Ruegeria sp. TM1040 4078693 YP_612104.1 CDS TM1040_0109 NC_008044.1 115503 116159 R PFAM: Phosphoglycerate mutase: (1.4e-20); KEGG: sil:SPO3305 phosphoglycerate mutase family protein, ev=6e-82, 66% identity; phosphoglycerate mutase complement(115503..116159) Ruegeria sp. TM1040 4078694 YP_612105.1 CDS TM1040_0110 NC_008044.1 116273 116500 R KEGG: rsp:RSP_1085 hypothetical protein, ev=5e-10, 54% identity; hypothetical protein complement(116273..116500) Ruegeria sp. TM1040 4078695 YP_612106.1 CDS TM1040_0111 NC_008044.1 116589 117308 R 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 complement(116589..117308) Ruegeria sp. TM1040 4078696 YP_612107.1 CDS TM1040_0112 NC_008044.1 117301 119205 R 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 complement(117301..119205) Ruegeria sp. TM1040 4078697 YP_612108.1 CDS TM1040_0113 NC_008044.1 119466 121451 D PFAM: AMP-dependent synthetase and ligase: (7.4e-70); KEGG: sil:SPO3296 AMP-binding enzyme, ev=0.0, 79% identity; AMP-dependent synthetase/ligase 119466..121451 Ruegeria sp. TM1040 4078698 YP_612109.1 CDS TM1040_0114 NC_008044.1 121536 122354 D 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 121536..122354 Ruegeria sp. TM1040 4078699 YP_612110.1 CDS TM1040_0115 NC_008044.1 122393 123379 D 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 122393..123379 Ruegeria sp. TM1040 4078700 YP_612111.1 CDS TM1040_0116 NC_008044.1 123416 123841 R hypothetical protein complement(123416..123841) Ruegeria sp. TM1040 4078701 YP_612112.1 CDS TM1040_0117 NC_008044.1 123944 124204 D KEGG: sil:SPO3293 hypothetical protein, ev=6e-19, 53% identity; hypothetical protein 123944..124204 Ruegeria sp. TM1040 4078702 YP_612113.1 CDS TM1040_0118 NC_008044.1 124243 125319 D 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 124243..125319 Ruegeria sp. TM1040 4078703 YP_612114.1 CDS TM1040_0119 NC_008044.1 125411 126694 D 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 125411..126694 Ruegeria sp. TM1040 4078704 YP_612115.1 CDS TM1040_0120 NC_008044.1 126813 127649 D 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 126813..127649 Ruegeria sp. TM1040 4078725 YP_612116.1 CDS TM1040_0121 NC_008044.1 127666 128883 D KEGG: sil:SPO3289 phenylacetate-CoA ligase, , ev=0.0, 84% identity; phenylacetate-CoA ligase 127666..128883 Ruegeria sp. TM1040 4078726 YP_612117.1 CDS TM1040_0122 NC_008044.1 129006 130685 D 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 129006..130685 Ruegeria sp. TM1040 4078727 YP_612118.1 CDS TM1040_0123 NC_008044.1 130689 131552 R 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 complement(130689..131552) Ruegeria sp. TM1040 4078728 YP_612119.1 CDS TM1040_0124 NC_008044.1 131939 132949 R 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 complement(131939..132949) Ruegeria sp. TM1040 4078729 YP_612120.1 CDS rpmJ NC_008044.1 133310 133435 R 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 complement(133310..133435) Ruegeria sp. TM1040 4078730 YP_612121.1 CDS TM1040_0126 NC_008044.1 133740 134600 D PFAM: N-formylglutamate amidohydrolase: (2.6e-59); KEGG: rsp:RSP_1399 hypothetical protein, ev=2e-92, 57% identity; N-formylglutamate amidohydrolase 133740..134600 Ruegeria sp. TM1040 4078731 YP_612122.1 CDS TM1040_0127 NC_008044.1 134637 135908 R 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 complement(134637..135908) Ruegeria sp. TM1040 4078732 YP_612123.1 CDS TM1040_0128 NC_008044.1 136011 136430 D PFAM: NUDIX hydrolase: (1.9e-16); KEGG: sil:SPO3279 NUDIX domain protein, ev=2e-38, 58% identity; NUDIX hydrolase 136011..136430 Ruegeria sp. TM1040 4078733 YP_612124.1 CDS TM1040_0129 NC_008044.1 136844 137569 R 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 complement(136844..137569) Ruegeria sp. TM1040 4078734 YP_612125.1 CDS TM1040_0130 NC_008044.1 137814 140432 D 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 137814..140432 Ruegeria sp. TM1040 4078735 YP_612126.1 CDS TM1040_0131 NC_008044.1 140622 142115 D PFAM: ferredoxin-dependent glutamate synthase: (1.7e-82); KEGG: sil:SPO3272 glutamate synthase family protein, ev=0.0, 68% identity; ferredoxin-dependent glutamate synthase 140622..142115 Ruegeria sp. TM1040 4078736 YP_612127.1 CDS TM1040_0132 NC_008044.1 142088 142489 R hypothetical protein complement(142088..142489) Ruegeria sp. TM1040 4078737 YP_612128.1 CDS TM1040_0133 NC_008044.1 142784 143686 D 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 142784..143686 Ruegeria sp. TM1040 4078738 YP_612129.1 CDS TM1040_0134 NC_008044.1 143686 144285 D 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 143686..144285 Ruegeria sp. TM1040 4078739 YP_612130.1 CDS TM1040_0135 NC_008044.1 144346 144612 D hypothetical protein 144346..144612 Ruegeria sp. TM1040 4078740 YP_612131.1 CDS TM1040_0136 NC_008044.1 150726 151112 R PFAM: response regulator receiver: (5.3e-09); KEGG: lic:LIC13330 response regulator, ev=4e-13, 32% identity; response regulator receiver protein complement(150726..151112) Ruegeria sp. TM1040 4078741 YP_612132.1 CDS TM1040_0137 NC_008044.1 151103 152278 R 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 complement(151103..152278) Ruegeria sp. TM1040 4078742 YP_612133.1 CDS TM1040_0138 NC_008044.1 152275 152919 R KEGG: nfa:nfa32140 sigma activity regulating serine phosphatase, ev=9e-11, 25% identity; hypothetical protein complement(152275..152919) Ruegeria sp. TM1040 4078743 YP_612134.1 CDS TM1040_0139 NC_008044.1 152904 153326 R 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 complement(152904..153326) Ruegeria sp. TM1040 4078744 YP_612135.1 CDS TM1040_0140 NC_008044.1 153323 153679 R PFAM: Sulfate transporter/antisigma-factor antagonist STAS: (3.6e-10); KEGG: mpa:MAP0378c hypothetical protein, ev=1e-24, 54% identity; anti-sigma-factor antagonist complement(153323..153679) Ruegeria sp. TM1040 4078807 YP_612136.1 CDS TM1040_0141 NC_008044.1 153682 154578 R 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 complement(153682..154578) Ruegeria sp. TM1040 4078808 YP_612137.1 CDS TM1040_0142 NC_008044.1 154810 156234 R KEGG: rru:Rru_A0400 hypothetical protein, ev=2e-79, 38% identity; hypothetical protein complement(154810..156234) Ruegeria sp. TM1040 4078809 YP_612138.1 CDS TM1040_0143 NC_008044.1 156335 156646 R 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 complement(156335..156646) Ruegeria sp. TM1040 4078810 YP_612139.1 CDS TM1040_0144 NC_008044.1 156843 159035 D 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 156843..159035 Ruegeria sp. TM1040 4078811 YP_612140.1 CDS TM1040_0145 NC_008044.1 159057 160424 R 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 complement(159057..160424) Ruegeria sp. TM1040 4078812 YP_612141.1 CDS TM1040_0146 NC_008044.1 160500 161540 R PFAM: FAD dependent oxidoreductase: (1.2e-31); KEGG: sil:SPO3552 oxidoreductase, FAD-binding, ev=1e-136, 69% identity; FAD dependent oxidoreductase complement(160500..161540) Ruegeria sp. TM1040 4078813 YP_612142.1 CDS TM1040_0147 NC_008044.1 161599 162282 D PFAM: protein of unknown function DUF752: (2e-97); KEGG: sil:SPO3553 hypothetical protein, ev=7e-95, 73% identity; hypothetical protein 161599..162282 Ruegeria sp. TM1040 4078814 YP_612143.1 CDS TM1040_0148 NC_008044.1 162286 163173 D PFAM: protein of unknown function DUF6, transmembrane: (6.6e-06); KEGG: sil:SPO3554 membrane protein, , ev=1e-118, 69% identity; hypothetical protein 162286..163173 Ruegeria sp. TM1040 4078815 YP_612144.1 CDS TM1040_0149 NC_008044.1 163129 165096 R 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 complement(163129..165096) Ruegeria sp. TM1040 4078816 YP_612145.1 CDS TM1040_0150 NC_008044.1 165208 166107 D catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate synthase 165208..166107 Ruegeria sp. TM1040 4078817 YP_612146.1 CDS TM1040_0151 NC_008044.1 166208 167086 R 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 complement(166208..167086) Ruegeria sp. TM1040 4078818 YP_612147.1 CDS TM1040_0152 NC_008044.1 167083 167544 R TIGRFAM: Alkylhydroperoxidase AhpD core: (6.2e-15); PFAM: Carboxymuconolactone decarboxylase: (4.3e-22); KEGG: rpb:RPB_1807 alkylhydroperoxidase, ev=7e-48, 66% identity; alkylhydroperoxidase complement(167083..167544) Ruegeria sp. TM1040 4078819 YP_612148.1 CDS TM1040_0153 NC_008044.1 167639 168676 R PFAM: conserved hypothetical protein 698: (2.7e-71); KEGG: rsp:RSP_4010 conserved hypothetical protein 698, ev=1e-112, 65% identity; hypothetical protein complement(167639..168676) Ruegeria sp. TM1040 4078820 YP_612149.1 CDS TM1040_0154 NC_008044.1 168851 169603 R KEGG: pub:SAR11_1347 hypothetical protein, ev=5e-25, 27% identity; hypothetical protein complement(168851..169603) Ruegeria sp. TM1040 4078821 YP_612150.1 CDS TM1040_0155 NC_008044.1 169615 171393 R catalyzes the formation of acetyl phosphate and sulfite from 2-sulfoacetaldehyde; is active when grown on taurine as a sole carbon source; sulfoacetaldehyde acetyltransferase complement(169615..171393) Ruegeria sp. TM1040 4078822 YP_612151.1 CDS TM1040_0156 NC_008044.1 171551 173017 R 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 complement(171551..173017) Ruegeria sp. TM1040 4078823 YP_612152.1 CDS TM1040_0157 NC_008044.1 173159 173482 D PFAM: regulatory protein, ArsR: (9.8e-07); KEGG: sil:SPO3563 transcriptional regulator, ArsR family, ev=7e-26, 60% identity; ArsR family transcriptional regulator 173159..173482 Ruegeria sp. TM1040 4078824 YP_612153.1 CDS TM1040_0158 NC_008044.1 173475 174506 D PFAM: permease: (4e-14); KEGG: sil:SPO3564 permease, , ev=1e-132, 72% identity; permease 173475..174506 Ruegeria sp. TM1040 4078825 YP_612154.1 CDS TM1040_0159 NC_008044.1 174832 176232 R PFAM: aminotransferase class-III: (4.8e-89); KEGG: sil:SPO0673 taurine--pyruvate aminotransferase, ev=0.0, 87% identity; aminotransferase complement(174832..176232) Ruegeria sp. TM1040 4078767 YP_612155.1 CDS TM1040_0160 NC_008044.1 176517 177329 D PFAM: protein of unknown function DUF849: (4.3e-13); KEGG: sil:SPO1400 hypothetical protein, ev=2e-58, 51% identity; hypothetical protein 176517..177329 Ruegeria sp. TM1040 4078768 YP_612156.1 CDS TM1040_0161 NC_008044.1 177326 178654 D PFAM: aminotransferase class-III: (1.8e-106); KEGG: sil:SPO1401 aminotransferase, class III, ev=0.0, 75% identity; hypothetical protein 177326..178654 Ruegeria sp. TM1040 4078769 YP_612157.1 CDS TM1040_0162 NC_008044.1 178748 179851 D 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 178748..179851 Ruegeria sp. TM1040 4078770 YP_612158.1 CDS TM1040_0163 NC_008044.1 179945 180706 R KEGG: ret:RHE_CH00424 carboxyphosphonoenolpyruvate phosphonomutase protein, ev=5e-68, 51% identity; carboxyphosphonoenolpyruvate phosphonomutase protein complement(179945..180706) Ruegeria sp. TM1040 4078771 YP_612159.1 CDS recR NC_008044.1 180902 181501 R involved in a recombinational process of DNA repair, independent of the recBC complex; recombination protein RecR complement(180902..181501) Ruegeria sp. TM1040 4078772 YP_612160.1 CDS TM1040_0165 NC_008044.1 181645 181989 R PFAM: conserved hypothetical protein 103: (2.4e-36); KEGG: sil:SPO3570 conserved hypothetical protein TIGR00103, ev=2e-45, 77% identity; hypothetical protein complement(181645..181989) Ruegeria sp. TM1040 4078773 YP_612161.1 CDS TM1040_0166 NC_008044.1 182088 183914 R 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 complement(182088..183914) Ruegeria sp. TM1040 4078774 YP_612162.1 CDS TM1040_0167 NC_008044.1 184138 184677 D 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 184138..184677 Ruegeria sp. TM1040 4078775 YP_612163.1 CDS TM1040_0168 NC_008044.1 184688 185185 R KEGG: sil:SPO3547 hypothetical protein, ev=4e-21, 42% identity; hypothetical protein complement(184688..185185) Ruegeria sp. TM1040 4078776 YP_612164.1 CDS TM1040_0169 NC_008044.1 185822 187720 R 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 complement(185822..187720) Ruegeria sp. TM1040 4078777 YP_612165.1 CDS TM1040_0170 NC_008044.1 187981 188964 D PFAM: NUDIX hydrolase: (5e-25); KEGG: sil:SPO3541 hydrolase, NUDIX family, ev=1e-112, 62% identity; NUDIX hydrolase 187981..188964 Ruegeria sp. TM1040 4078778 YP_612166.1 CDS TM1040_0171 NC_008044.1 189050 189517 D KEGG: rsp:RSP_0707 hypothetical protein, ev=1e-16, 33% identity; hypothetical protein 189050..189517 Ruegeria sp. TM1040 4078779 YP_612167.1 CDS TM1040_0172 NC_008044.1 189692 191749 D 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 189692..191749 Ruegeria sp. TM1040 4078780 YP_612168.1 CDS TM1040_0173 NC_008044.1 191860 192174 D KEGG: nar:Saro_2759 transposase orfA IS5 family element, ev=5e-43, 79% identity; IS5 family transposase 191860..192174 Ruegeria sp. TM1040 4078781 YP_612169.1 CDS TM1040_0174 NC_008044.1 192195 192584 D PFAM: transposase, IS4: (2.1e-13); KEGG: sil:SPOA0134 ISSpo7, transposase, ev=6e-74, 70% identity; IS4 family transposase 192195..192584 Ruegeria sp. TM1040 4078782 YP_612170.1 CDS TM1040_0175 NC_008044.1 192594 195974 R 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 complement(192594..195974) Ruegeria sp. TM1040 4078783 YP_612171.1 CDS TM1040_0176 NC_008044.1 195974 197275 R KEGG: sil:SPO0671 hypothetical protein, ev=0.0, 68% identity; hypothetical protein complement(195974..197275) Ruegeria sp. TM1040 4078784 YP_612172.1 CDS TM1040_0177 NC_008044.1 197394 197981 R KEGG: sil:SPO0672 hypothetical protein, ev=9e-57, 58% identity; hypothetical protein complement(197394..197981) Ruegeria sp. TM1040 4078785 YP_612173.1 CDS TM1040_0178 NC_008044.1 198056 198667 R 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 complement(198056..198667) Ruegeria sp. TM1040 4078786 YP_612174.1 CDS TM1040_0179 NC_008044.1 198664 199296 R PFAM: metal-dependent phosphohydrolase, HD subdomain: (7.9e-08); KEGG: bja:blr7676 hypothetical protein, ev=2e-34, 36% identity; metal dependent phosphohydrolase complement(198664..199296) Ruegeria sp. TM1040 4078411 YP_612175.1 CDS TM1040_0180 NC_008044.1 199436 200230 R KEGG: sil:SPOA0439 enoyl-(acyl-carrier-protein) reductase, ev=1e-129, 88% identity; enoyl-ACP reductase complement(199436..200230) Ruegeria sp. TM1040 4078412 YP_612176.1 CDS TM1040_0181 NC_008044.1 200236 201465 R 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 complement(200236..201465) Ruegeria sp. TM1040 4078413 YP_612177.1 CDS TM1040_0182 NC_008044.1 201548 202057 R catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to 2,3-decenoyl-ACP or 3,4-decenoyl-ACP; 3-hydroxydecanoyl-ACP dehydratase complement(201548..202057) Ruegeria sp. TM1040 4078414 YP_612178.1 CDS TM1040_0183 NC_008044.1 202285 202713 D PFAM: ferric-uptake regulator: (8.2e-15); KEGG: sil:SPOA0445 transcriptional regulator, Fur family, ev=5e-61, 81% identity; ferric uptake regulator 202285..202713 Ruegeria sp. TM1040 4078415 YP_612179.1 CDS TM1040_0184 NC_008044.1 202858 203727 R KEGG: sil:SPOA0001 hypothetical protein, ev=1e-131, 73% identity; hypothetical protein complement(202858..203727) Ruegeria sp. TM1040 4078416 YP_612180.1 CDS TM1040_0185 NC_008044.1 203892 205214 D 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 203892..205214 Ruegeria sp. TM1040 4078417 YP_612181.1 CDS TM1040_0186 NC_008044.1 205559 206137 D PFAM: OmpA/MotB: (1.3e-14); KEGG: sil:SPOA0004 OmpA family protein, ev=7e-59, 58% identity; OmpA/MotB protein 205559..206137 Ruegeria sp. TM1040 4078418 YP_612182.1 CDS TM1040_0187 NC_008044.1 206149 206454 D KEGG: sil:SPOA0005 lipoprotein, , ev=1e-22, 53% identity; lipoprotein 206149..206454 Ruegeria sp. TM1040 4078419 YP_612183.1 CDS TM1040_0188 NC_008044.1 206670 207686 D PFAM: PhoH-like protein: (8.6e-116); KEGG: sil:SPOA0006 PhoH family protein, ev=1e-141, 76% identity; PhoH-like protein 206670..207686 Ruegeria sp. TM1040 4078420 YP_612184.1 CDS TM1040_0189 NC_008044.1 207790 208269 R PFAM: GCN5-related N-acetyltransferase: (9.9e-16); KEGG: vvu:VV20941 histone acetyltransferase HPA2, ev=4e-25, 44% identity; N-acetyltransferase GCN5 complement(207790..208269) Ruegeria sp. TM1040 4078421 YP_612185.1 CDS TM1040_0190 NC_008044.1 208272 208856 D PFAM: protein of unknown function UPF0054: (7.6e-31); KEGG: sil:SPOA0008 conserved hypothetical protein TIGR00043, ev=2e-52, 62% identity; hypothetical protein 208272..208856 Ruegeria sp. TM1040 4078422 YP_612186.1 CDS TM1040_0191 NC_008044.1 208879 209781 D PFAM: CBS: (1.3e-22) transporter-associated region: (1.4e-18); KEGG: sil:SPOA0009 hemolysin, , ev=1e-115, 70% identity; hypothetical protein 208879..209781 Ruegeria sp. TM1040 4078423 YP_612187.1 CDS TM1040_0192 NC_008044.1 209778 211304 D 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 209778..211304 Ruegeria sp. TM1040 4078424 YP_612188.1 CDS TM1040_0193 NC_008044.1 211416 212597 D catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase; S-adenosylmethionine synthetase 211416..212597 Ruegeria sp. TM1040 4078425 YP_612189.1 CDS TM1040_0194 NC_008044.1 212764 213438 D KEGG: sil:SPOA0013 hypothetical protein, ev=2e-50, 48% identity; hypothetical protein 212764..213438 Ruegeria sp. TM1040 4078426 YP_612190.1 CDS trmB NC_008044.1 213570 214337 D 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 213570..214337 Ruegeria sp. TM1040 4078427 YP_612191.1 CDS TM1040_0196 NC_008044.1 214406 215035 R PFAM: nitroreductase: (9.4e-38); KEGG: ccr:CC1449 nitroreductase family protein, ev=8e-63, 59% identity; nitroreductase complement(214406..215035) Ruegeria sp. TM1040 4078428 YP_612192.1 CDS cmk NC_008044.1 215228 215839 R Catalyzes the formation of (d)CDP from ATP and (d)CMP; cytidylate kinase complement(215228..215839) Ruegeria sp. TM1040 4078429 YP_612193.1 CDS TM1040_0198 NC_008044.1 215899 216381 R PFAM: GCN5-related N-acetyltransferase: (1.4e-11); KEGG: bur:Bcep18194_C7224 GCN5-related N-acetyltransferase, ev=5e-19, 44% identity; N-acetyltransferase GCN5 complement(215899..216381) Ruegeria sp. TM1040 4078646 YP_612194.1 CDS TM1040_0199 NC_008044.1 216374 217726 R catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis; 3-phosphoshikimate 1-carboxyvinyltransferase complement(216374..217726) Ruegeria sp. TM1040 4078647 YP_612195.1 CDS rpsA NC_008044.1 218325 220001 D 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 218325..220001 Ruegeria sp. TM1040 4078648 YP_612196.1 CDS TM1040_0201 NC_008044.1 220102 220743 R KEGG: ret:RHE_PF00158 hypothetical protein, ev=2e-72, 59% identity; hypothetical protein complement(220102..220743) Ruegeria sp. TM1040 4078649 YP_612197.1 CDS ihfB NC_008044.1 221101 221388 D 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 221101..221388 Ruegeria sp. TM1040 4078650 YP_612198.1 CDS TM1040_0203 NC_008044.1 221389 221739 D KEGG: sil:SPO0805 hypothetical protein, ev=6e-37, 66% identity; hypothetical protein 221389..221739 Ruegeria sp. TM1040 4078651 YP_612199.1 CDS TM1040_0204 NC_008044.1 221741 222388 D 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 221741..222388 Ruegeria sp. TM1040 4078652 YP_612200.1 CDS TM1040_0205 NC_008044.1 222662 223507 D PFAM: regulatory protein, LysR: (5e-17); KEGG: jan:Jann_2521 transcriptional regulator, LysR family, ev=3e-58, 45% identity; LysR family transcriptional regulator 222662..223507 Ruegeria sp. TM1040 4078653 YP_612201.1 CDS TM1040_0206 NC_008044.1 223721 224980 D catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate; tryptophan synthase subunit beta 223721..224980 Ruegeria sp. TM1040 4078654 YP_612202.1 CDS TM1040_0207 NC_008044.1 225112 225483 R PFAM: helix-turn-helix, HxlR type: (9.1e-25); KEGG: ppr:PBPRB1657 hypothetical transcriptional regulator, ev=3e-36, 55% identity; HxlR family transcriptional regulator complement(225112..225483) Ruegeria sp. TM1040 4078655 YP_612203.1 CDS TM1040_0208 NC_008044.1 225625 226233 D 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) 225625..226233 Ruegeria sp. TM1040 4078656 YP_612204.1 CDS TM1040_0209 NC_008044.1 226220 226921 D PFAM: glutathione S-transferase-like: (2.6e-15); KEGG: ppr:PBPRB0681 glutathione S-transferase, ev=8e-52, 49% identity; glutathione S-transferase 226220..226921 Ruegeria sp. TM1040 4078657 YP_612205.1 CDS TM1040_0210 NC_008044.1 226926 227567 D PFAM: DSBA oxidoreductase: (2.6e-37); KEGG: sil:SPO1390 thioredoxin domain protein, DsbA family, ev=3e-69, 59% identity; DSBA oxidoreductase 226926..227567 Ruegeria sp. TM1040 4078658 YP_612206.1 CDS TM1040_0211 NC_008044.1 227730 228554 D PFAM: penicillin-binding protein, transpeptidase: (5.5e-13); KEGG: mca:MCA2220 beta-lactamase, ev=5e-24, 33% identity; beta-lactamase 227730..228554 Ruegeria sp. TM1040 4078659 YP_612207.1 CDS TM1040_0212 NC_008044.1 228609 229106 R 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 complement(228609..229106) Ruegeria sp. TM1040 4078660 YP_612208.1 CDS TM1040_0213 NC_008044.1 229195 230097 D 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 229195..230097 Ruegeria sp. TM1040 4078661 YP_612209.1 CDS TM1040_0214 NC_008044.1 230182 230928 R Enables the recycling of peptidyl-tRNAs produced at termination of translation; peptidyl-tRNA hydrolase complement(230182..230928) Ruegeria sp. TM1040 4078662 YP_612210.1 CDS TM1040_0215 NC_008044.1 231109 231594 D hypothetical protein 231109..231594 Ruegeria sp. TM1040 4078663 YP_612211.1 CDS TM1040_0216 NC_008044.1 231708 232337 R 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 complement(231708..232337) Ruegeria sp. TM1040 4078664 YP_612212.1 CDS TM1040_0217 NC_008044.1 232430 233146 R KEGG: jan:Jann_1985 hypothetical protein, ev=2e-32, 40% identity; hypothetical protein complement(232430..233146) Ruegeria sp. TM1040 4078665 YP_612213.1 CDS TM1040_0218 NC_008044.1 233213 234322 D 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 233213..234322 Ruegeria sp. TM1040 4076251 YP_612214.1 CDS TM1040_0219 NC_008044.1 234369 235532 R 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) complement(234369..235532) Ruegeria sp. TM1040 4076252 YP_612215.1 CDS TM1040_0220 NC_008044.1 235564 235827 D hypothetical protein 235564..235827 Ruegeria sp. TM1040 4076253 YP_612216.1 CDS TM1040_0221 NC_008044.1 236023 237453 D 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 236023..237453 Ruegeria sp. TM1040 4076254 YP_612217.2 CDS trpA NC_008044.1 237554 238357 R catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis; tryptophan synthase subunit alpha complement(237554..238357) Ruegeria sp. TM1040 4076255 YP_612218.1 CDS TM1040_0223 NC_008044.1 238456 238968 R KEGG: sil:SPO0816 hypothetical protein, ev=6e-28, 40% identity; hypothetical protein complement(238456..238968) Ruegeria sp. TM1040 4076256 YP_612219.1 CDS TM1040_0224 NC_008044.1 239155 240252 D 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 239155..240252 Ruegeria sp. TM1040 4076257 YP_612220.1 CDS TM1040_0225 NC_008044.1 240406 241329 D 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 240406..241329 Ruegeria sp. TM1040 4076258 YP_612221.1 CDS secE NC_008044.1 241515 241712 D 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 241515..241712 Ruegeria sp. TM1040 4076259 YP_612222.1 CDS TM1040_0227 NC_008044.1 241908 242441 D 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 241908..242441 Ruegeria sp. TM1040 4076260 YP_612223.1 CDS TM1040_0228 NC_008044.1 242545 243768 D 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 242545..243768 Ruegeria sp. TM1040 4076261 YP_612224.1 CDS rplK NC_008044.1 243929 244354 D binds directly to 23S ribosomal RNA; 50S ribosomal protein L11 243929..244354 Ruegeria sp. TM1040 4076262 YP_612225.1 CDS rplA NC_008044.1 244356 245054 D 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 244356..245054 Ruegeria sp. TM1040 4076263 YP_612226.1 CDS TM1040_0231 NC_008044.1 245198 246118 D KEGG: sil:SPO3511 hypothetical protein, ev=3e-83, 52% identity; hypothetical protein 245198..246118 Ruegeria sp. TM1040 4076264 YP_612227.1 CDS rplJ NC_008044.1 246441 246959 D binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit; 50S ribosomal protein L10 246441..246959 Ruegeria sp. TM1040 4076265 YP_612228.1 CDS rplL NC_008044.1 247040 247417 D 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 247040..247417 Ruegeria sp. TM1040 4076266 YP_612229.1 CDS rpoB NC_008044.1 247712 251851 D 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 247712..251851 Ruegeria sp. TM1040 4076267 YP_612230.1 CDS TM1040_0235 NC_008044.1 251905 256137 D 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' 251905..256137 Ruegeria sp. TM1040 4076268 YP_612231.1 CDS TM1040_0236 NC_008044.1 256298 257110 D KEGG: jan:Jann_0572 hypothetical protein, ev=3e-27, 34% identity; hypothetical protein 256298..257110 Ruegeria sp. TM1040 4076269 YP_612232.1 CDS TM1040_0237 NC_008044.1 257154 257993 D PFAM: protein of unknown function DUF6, transmembrane: (1.8e-05); KEGG: sil:SPO3504 membrane protein, , ev=1e-78, 58% identity; hypothetical protein 257154..257993 Ruegeria sp. TM1040 4075997 YP_612233.1 CDS TM1040_0238 NC_008044.1 257972 258856 R KEGG: sil:SPO3502 hypothetical protein, ev=3e-96, 64% identity; hypothetical protein complement(257972..258856) Ruegeria sp. TM1040 4075998 YP_612234.1 CDS rpsL NC_008044.1 259113 259484 D 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 259113..259484 Ruegeria sp. TM1040 4075999 YP_612235.1 CDS TM1040_0240 NC_008044.1 259503 259973 D binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit; 30S ribosomal protein S7 259503..259973 Ruegeria sp. TM1040 4076000 YP_612236.1 CDS TM1040_0241 NC_008044.1 259995 262115 D EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene; elongation factor G 259995..262115 Ruegeria sp. TM1040 4076001 YP_612237.1 CDS TM1040_0242 NC_008044.1 262178 263353 D 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 262178..263353 Ruegeria sp. TM1040 4076002 YP_612238.1 CDS TM1040_0243 NC_008044.1 263547 264038 D KEGG: jan:Jann_3603 hypothetical protein, ev=1e-23, 45% identity; hypothetical protein 263547..264038 Ruegeria sp. TM1040 4076003 YP_612239.1 CDS TM1040_0244 NC_008044.1 264476 264727 D hypothetical protein 264476..264727 Ruegeria sp. TM1040 4076004 YP_612240.1 CDS rpsJ NC_008044.1 264947 265261 D 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 264947..265261 Ruegeria sp. TM1040 4076005 YP_612241.1 CDS rplC NC_008044.1 265280 265999 D 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 265280..265999 Ruegeria sp. TM1040 4076006 YP_612242.1 CDS rplD NC_008044.1 265996 266613 D 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 265996..266613 Ruegeria sp. TM1040 4076007 YP_612243.1 CDS rplW NC_008044.1 266610 266906 D binds third domain of 23S rRNA and protein L29; part of exit tunnel; 50S ribosomal protein L23 266610..266906 Ruegeria sp. TM1040 4076008 YP_612244.1 CDS TM1040_0249 NC_008044.1 267190 267591 D hypothetical protein 267190..267591 Ruegeria sp. TM1040 4076009 YP_612245.1 CDS TM1040_0250 NC_008044.1 267658 268230 D KEGG: mlo:mll6838 hypothetical protein, ev=1e-06, 65% identity; hypothetical protein 267658..268230 Ruegeria sp. TM1040 4076010 YP_612246.1 CDS TM1040_0251 NC_008044.1 268431 268688 D hypothetical protein 268431..268688 Ruegeria sp. TM1040 4076011 YP_612247.1 CDS rplB NC_008044.1 268935 269777 D 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 268935..269777 Ruegeria sp. TM1040 4076012 YP_612248.1 CDS rpsS NC_008044.1 269781 270059 D protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA; 30S ribosomal protein S19 269781..270059 Ruegeria sp. TM1040 4076013 YP_612249.1 CDS rplV NC_008044.1 270063 270443 D 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 270063..270443 Ruegeria sp. TM1040 4076014 YP_612250.1 CDS rpsC NC_008044.1 270443 271162 D 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 270443..271162 Ruegeria sp. TM1040 4076015 YP_612251.1 CDS rplP NC_008044.1 271175 271588 D located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e; 50S ribosomal protein L16 271175..271588 Ruegeria sp. TM1040 4076016 YP_612252.1 CDS TM1040_0257 NC_008044.1 271848 272147 D hypothetical protein 271848..272147 Ruegeria sp. TM1040 4077665 YP_612253.1 CDS TM1040_0258 NC_008044.1 272252 272962 D 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 272252..272962 Ruegeria sp. TM1040 4077666 YP_612254.1 CDS TM1040_0259 NC_008044.1 273110 273730 D TIGRFAM: conserved hypothetical protein: (2.2e-119); KEGG: sil:SPO0491 hypothetical protein, ev=4e-97, 81% identity; hypothetical protein 273110..273730 Ruegeria sp. TM1040 4077667 YP_612255.1 CDS TM1040_0260 NC_008044.1 273804 274844 D PFAM: Succinylglutamate desuccinylase/aspartoacylase: (2.1e-71); KEGG: tcx:Tcr_2062 succinylglutamate desuccinylase/aspartoacylase, ev=2e-91, 53% identity; succinylglutamate desuccinylase/aspartoacylase 273804..274844 Ruegeria sp. TM1040 4077668 YP_612256.1 CDS TM1040_0261 NC_008044.1 274857 275486 R KEGG: sil:SPO2022 hypothetical protein, ev=7e-42, 46% identity; hypothetical protein complement(274857..275486) Ruegeria sp. TM1040 4077669 YP_612257.1 CDS TM1040_0262 NC_008044.1 275778 275978 D one of the stabilizing components for the large ribosomal subunit; 50S ribosomal protein L29 275778..275978 Ruegeria sp. TM1040 4077670 YP_612258.1 CDS rpsQ NC_008044.1 275991 276221 D primary binding protein; helps mediate assembly; involved in translation fidelity; 30S ribosomal protein S17 275991..276221 Ruegeria sp. TM1040 4077671 YP_612259.1 CDS rplN NC_008044.1 276322 276690 D binds to the 23S rRNA between the centers for peptidyl transferase and GTPase; 50S ribosomal protein L14 276322..276690 Ruegeria sp. TM1040 4077672 YP_612260.1 CDS rplX NC_008044.1 276690 276995 D assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel; 50S ribosomal protein L24 276690..276995 Ruegeria sp. TM1040 4077673 YP_612261.1 CDS rplE NC_008044.1 276995 277558 D 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 276995..277558 Ruegeria sp. TM1040 4077674 YP_612262.1 CDS rpsN NC_008044.1 277577 277882 D 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 277577..277882 Ruegeria sp. TM1040 4077675 YP_612263.1 CDS rpsH NC_008044.1 277895 278287 D binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit; 30S ribosomal protein S8 277895..278287 Ruegeria sp. TM1040 4077676 YP_612264.1 CDS rplF NC_008044.1 278303 278836 D 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 278303..278836 Ruegeria sp. TM1040 4077677 YP_612265.1 CDS rplR NC_008044.1 278848 279207 D binds 5S rRNA along with protein L5 and L25; 50S ribosomal protein L18 278848..279207 Ruegeria sp. TM1040 4077678 YP_612266.1 CDS rpsE NC_008044.1 279375 279938 D 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 279375..279938 Ruegeria sp. TM1040 4077679 YP_612267.1 CDS rpmD NC_008044.1 279951 280139 D L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7; 50S ribosomal protein L30 279951..280139 Ruegeria sp. TM1040 4077680 YP_612268.1 CDS TM1040_0273 NC_008044.1 280364 280579 D PFAM: protein of unknown function DUF1127: (2.1e-05); hypothetical protein 280364..280579 Ruegeria sp. TM1040 4077681 YP_612269.1 CDS rplO NC_008044.1 281136 281606 D late assembly protein; 50S ribosomal protein L15 281136..281606 Ruegeria sp. TM1040 4077682 YP_612270.1 CDS secY NC_008044.1 281717 283081 D 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 281717..283081 Ruegeria sp. TM1040 4077683 YP_612271.1 CDS adk NC_008044.1 283078 283659 D essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP; adenylate kinase 283078..283659 Ruegeria sp. TM1040 4077411 YP_612272.1 CDS rpsM NC_008044.1 284068 284436 D 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 284068..284436 Ruegeria sp. TM1040 4077412 YP_612273.1 CDS TM1040_0278 NC_008044.1 284453 284842 D 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 284453..284842 Ruegeria sp. TM1040 4077413 YP_612274.1 CDS TM1040_0279 NC_008044.1 284956 285972 D 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 284956..285972 Ruegeria sp. TM1040 4077414 YP_612275.1 CDS rplQ NC_008044.1 286119 286544 D is a component of the macrolide binding site in the peptidyl transferase center; 50S ribosomal protein L17 286119..286544 Ruegeria sp. TM1040 4077415 YP_612276.1 CDS TM1040_0281 NC_008044.1 286665 287573 D hypothetical protein 286665..287573 Ruegeria sp. TM1040 4077416 YP_612277.1 CDS TM1040_0282 NC_008044.1 287589 287927 R 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 complement(287589..287927) Ruegeria sp. TM1040 4077417 YP_612278.1 CDS TM1040_0283 NC_008044.1 288006 288905 R 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 complement(288006..288905) Ruegeria sp. TM1040 4077418 YP_612279.1 CDS TM1040_0284 NC_008044.1 289070 289723 D PFAM: protein of unknown function DUF161: (2.1e-17); KEGG: rsp:RSP_0447 hypothetical protein, ev=5e-38, 45% identity; hypothetical protein 289070..289723 Ruegeria sp. TM1040 4077419 YP_612280.1 CDS TM1040_0285 NC_008044.1 289710 291107 R 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 complement(289710..291107) Ruegeria sp. TM1040 4077420 YP_612281.1 CDS TM1040_0286 NC_008044.1 291466 292560 D 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 291466..292560 Ruegeria sp. TM1040 4077421 YP_612282.1 CDS TM1040_0287 NC_008044.1 292758 294155 D 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 292758..294155 Ruegeria sp. TM1040 4077422 YP_612283.1 CDS TM1040_0288 NC_008044.1 294157 295488 D 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 294157..295488 Ruegeria sp. TM1040 4077423 YP_612284.1 CDS TM1040_0289 NC_008044.1 295557 296987 R 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 complement(295557..296987) Ruegeria sp. TM1040 4077424 YP_612285.1 CDS TM1040_0290 NC_008044.1 297078 297542 D PFAM: Camphor resistance CrcB protein: (2.7e-23); KEGG: rsp:RSP_1744 CrcB-like protein, ev=7e-35, 62% identity; camphor resistance protein CrcB 297078..297542 Ruegeria sp. TM1040 4077425 YP_612286.1 CDS TM1040_0291 NC_008044.1 297539 298585 D 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 297539..298585 Ruegeria sp. TM1040 4077426 YP_612287.1 CDS TM1040_0292 NC_008044.1 298582 299250 D 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 298582..299250 Ruegeria sp. TM1040 4077427 YP_612288.1 CDS TM1040_0293 NC_008044.1 299318 300022 D PFAM: ATP12 ATPase: (9.3e-53); KEGG: sil:SPO0518 hypothetical protein, ev=1e-87, 66% identity; ATP12 ATPase 299318..300022 Ruegeria sp. TM1040 4077428 YP_612289.1 CDS TM1040_0294 NC_008044.1 300335 301351 D 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 300335..301351 Ruegeria sp. TM1040 4077429 YP_612290.1 CDS TM1040_0295 NC_008044.1 301493 302761 D 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 301493..302761 Ruegeria sp. TM1040 4077430 YP_612291.1 CDS TM1040_0296 NC_008044.1 302763 304091 D 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 302763..304091 Ruegeria sp. TM1040 4077119 YP_612292.1 CDS TM1040_0297 NC_008044.1 304104 304895 D 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 304104..304895 Ruegeria sp. TM1040 4077120 YP_612293.1 CDS TM1040_0298 NC_008044.1 305059 305484 R 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 complement(305059..305484) Ruegeria sp. TM1040 4077121 YP_612294.1 CDS TM1040_0299 NC_008044.1 305689 306186 R PFAM: Phosphoglycerate mutase: (1e-10); KEGG: sil:SPO0523 phosphoglycerate mutase family protein, ev=2e-38, 51% identity; phosphohistidine phosphatase, SixA complement(305689..306186) Ruegeria sp. TM1040 4077122 YP_612295.1 CDS TM1040_0300 NC_008044.1 306183 306878 R KEGG: sil:SPO0524 hypothetical protein, ev=3e-49, 49% identity; hypothetical protein complement(306183..306878) Ruegeria sp. TM1040 4077123 YP_612296.1 CDS TM1040_0301 NC_008044.1 307007 307867 R catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate; acetylglutamate kinase complement(307007..307867) Ruegeria sp. TM1040 4077124 YP_612297.1 CDS TM1040_0302 NC_008044.1 308089 308820 D 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 308089..308820 Ruegeria sp. TM1040 4077125 YP_612298.1 CDS TM1040_0303 NC_008044.1 308867 310279 R 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 complement(308867..310279) Ruegeria sp. TM1040 4077126 YP_612299.1 CDS TM1040_0304 NC_008044.1 310348 310680 R KEGG: sil:SPO0529 hypothetical protein, ev=5e-18, 40% identity; hypothetical protein complement(310348..310680) Ruegeria sp. TM1040 4077127 YP_612300.1 CDS engB NC_008044.1 310715 311365 R 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 complement(310715..311365) Ruegeria sp. TM1040 4077128 YP_612301.1 CDS TM1040_0306 NC_008044.1 311365 312102 R PFAM: MOSC: (2.2e-17); KEGG: jan:Jann_0636 MOSC, ev=4e-72, 53% identity; MOSC domain-containing protein complement(311365..312102) Ruegeria sp. TM1040 4077129 YP_612302.1 CDS TM1040_0307 NC_008044.1 312099 313925 R 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 complement(312099..313925) Ruegeria sp. TM1040 4077130 YP_612303.1 CDS TM1040_0308 NC_008044.1 314351 315850 R 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 complement(314351..315850) Ruegeria sp. TM1040 4077131 YP_612304.1 CDS TM1040_0309 NC_008044.1 315963 316850 R TtcA; YdaO; catalyzes the thiolation of cytosine 32 in specific tRNAs; C32 tRNA thiolase complement(315963..316850) Ruegeria sp. TM1040 4077132 YP_612305.1 CDS TM1040_0310 NC_008044.1 316985 317530 D KEGG: jan:Jann_0639 hypothetical protein, ev=2e-56, 63% identity; hypothetical protein 316985..317530 Ruegeria sp. TM1040 4077133 YP_612306.1 CDS TM1040_0311 NC_008044.1 317527 317787 R PFAM: protein of unknown function DUF37: (4e-26); KEGG: rsp:RSP_1061 hypothetical protein, ev=9e-31, 75% identity; hypothetical protein complement(317527..317787) Ruegeria sp. TM1040 4077134 YP_612307.1 CDS TM1040_0312 NC_008044.1 317986 318423 R 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 complement(317986..318423) Ruegeria sp. TM1040 4077135 YP_612308.1 CDS rpmH NC_008044.1 318476 318610 R in Escherichia coli transcription of this gene is enhanced by polyamines; 50S ribosomal protein L34 complement(318476..318610) Ruegeria sp. TM1040 4077136 YP_612309.1 CDS TM1040_0314 NC_008044.1 319077 319814 D KEGG: sil:SPO0539 membrane protein, , ev=2e-85, 68% identity; hypothetical protein 319077..319814 Ruegeria sp. TM1040 4077137 YP_612310.1 CDS TM1040_0315 NC_008044.1 319818 321233 D 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 319818..321233 Ruegeria sp. TM1040 4076211 YP_612311.1 CDS TM1040_0316 NC_008044.1 321251 322636 D 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 321251..322636 Ruegeria sp. TM1040 4076212 YP_612312.1 CDS TM1040_0317 NC_008044.1 323531 324073 D hypothetical protein 323531..324073 Ruegeria sp. TM1040 4076213 YP_612313.1 CDS TM1040_0318 NC_008044.1 324245 324664 D hypothetical protein 324245..324664 Ruegeria sp. TM1040 4076214 YP_612314.1 CDS TM1040_0319 NC_008044.1 324863 325447 D PFAM: regulatory protein, TetR: (0.0011); KEGG: rba:RB13253 probable TetR-family transcriptional regulator, ev=3e-27, 34% identity; TetR family transcriptional regulator 324863..325447 Ruegeria sp. TM1040 4076215 YP_612315.1 CDS TM1040_0320 NC_008044.1 325584 326150 D PFAM: Carboxymuconolactone decarboxylase: (3.5e-05); KEGG: par:Psyc_1394 hypothetical protein, ev=3e-53, 53% identity; carboxymuconolactone decarboxylase 325584..326150 Ruegeria sp. TM1040 4076216 YP_612316.1 CDS TM1040_0321 NC_008044.1 326224 326781 D PFAM: Redoxin: (4e-05); KEGG: mca:MCA2020 hypothetical protein, ev=3e-51, 56% identity; redoxin 326224..326781 Ruegeria sp. TM1040 4076217 YP_612317.1 CDS TM1040_0322 NC_008044.1 326868 327740 R 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 complement(326868..327740) Ruegeria sp. TM1040 4076218 YP_612318.1 CDS TM1040_0323 NC_008044.1 327846 328961 D 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 327846..328961 Ruegeria sp. TM1040 4076219 YP_612319.1 CDS TM1040_0324 NC_008044.1 329049 329936 D 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 329049..329936 Ruegeria sp. TM1040 4076220 YP_612320.1 CDS TM1040_0325 NC_008044.1 329940 330761 D 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 329940..330761 Ruegeria sp. TM1040 4076221 YP_612321.1 CDS TM1040_0326 NC_008044.1 330758 331876 D 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 330758..331876 Ruegeria sp. TM1040 4076222 YP_612322.1 CDS TM1040_0327 NC_008044.1 331873 333141 D PFAM: Amidase: (4e-65); KEGG: pst:PSPTO4204 amidase family protein, ev=2e-73, 41% identity; amidase 331873..333141 Ruegeria sp. TM1040 4076223 YP_612323.1 CDS TM1040_0328 NC_008044.1 333138 334046 D PFAM: polysaccharide deacetylase: (5.1e-14); KEGG: sme:SMb21100 saccharide deacetylase, slightly similar to NodB protein, ev=4e-40, 35% identity; polysaccharide deacetylase 333138..334046 Ruegeria sp. TM1040 4076224 YP_612324.1 CDS TM1040_0329 NC_008044.1 334033 334734 D KEGG: rsp:RSP_3746 hypothetical protein, ev=7e-37, 39% identity; hypothetical protein 334033..334734 Ruegeria sp. TM1040 4076225 YP_612325.1 CDS TM1040_0330 NC_008044.1 334809 335477 R PFAM: NAD(P)H dehydrogenase (quinone): (7.2e-20); KEGG: ilo:IL1610 acyl carrier protein phosphodiesterase, ev=7e-46, 44% identity; ACP phosphodiesterase complement(334809..335477) Ruegeria sp. TM1040 4076226 YP_612326.1 CDS TM1040_0331 NC_008044.1 335647 336549 D 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 335647..336549 Ruegeria sp. TM1040 4076227 YP_612327.1 CDS TM1040_0332 NC_008044.1 336588 337442 R 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 complement(336588..337442) Ruegeria sp. TM1040 4076228 YP_612328.1 CDS TM1040_0333 NC_008044.1 337542 338690 D 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 337542..338690 Ruegeria sp. TM1040 4076229 YP_612329.1 CDS TM1040_0334 NC_008044.1 338687 339277 D KEGG: sil:SPO3381 hypothetical protein, ev=3e-81, 76% identity; hypothetical protein 338687..339277 Ruegeria sp. TM1040 4076230 YP_612330.1 CDS TM1040_0335 NC_008044.1 339509 339937 R KEGG: ppu:PP2202 hypothetical protein, ev=1e-45, 63% identity; hypothetical protein complement(339509..339937) Ruegeria sp. TM1040 4076036 YP_612331.1 CDS TM1040_0336 NC_008044.1 339939 341264 R PFAM: major facilitator superfamily MFS_1: (4.3e-24); KEGG: sme:SMa1641 probable NreB protein, ev=1e-153, 62% identity; major facilitator superfamily transporter complement(339939..341264) Ruegeria sp. TM1040 4076037 YP_612332.1 CDS TM1040_0337 NC_008044.1 341517 341957 D catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis; 3-dehydroquinate dehydratase 341517..341957 Ruegeria sp. TM1040 4076038 YP_612333.1 CDS TM1040_0338 NC_008044.1 342242 343732 D 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 342242..343732 Ruegeria sp. TM1040 4076039 YP_612334.1 CDS TM1040_0339 NC_008044.1 343924 344769 D KEGG: sco:SCO5273 hypothetical protein, ev=2e-06, 26% identity; hypothetical protein 343924..344769 Ruegeria sp. TM1040 4076040 YP_612335.1 CDS TM1040_0340 NC_008044.1 344893 345972 D PFAM: Peptidoglycan-binding LysM: (0.0037); KEGG: sil:SPO1062 LysM domain protein, ev=3e-38, 32% identity; peptidoglycan-binding LysM 344893..345972 Ruegeria sp. TM1040 4076041 YP_612336.1 CDS TM1040_0341 NC_008044.1 345984 347057 D KEGG: sil:SPO1060 hypothetical protein, ev=2e-31, 33% identity; hypothetical protein 345984..347057 Ruegeria sp. TM1040 4076042 YP_612337.1 CDS TM1040_0342 NC_008044.1 347255 349738 D 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 347255..349738 Ruegeria sp. TM1040 4076043 YP_612338.1 CDS hmuV NC_008044.1 349883 350665 R with HmuTU is involved in the transport of hemin; hemin importer ATP-binding subunit complement(349883..350665) Ruegeria sp. TM1040 4076044 YP_612339.1 CDS TM1040_0344 NC_008044.1 350662 351750 R PFAM: transport system permease protein: (3.1e-108); KEGG: jan:Jann_2135 transport system permease protein, ev=1e-122, 66% identity; transport system permease complement(350662..351750) Ruegeria sp. TM1040 4076045 YP_612340.1 CDS TM1040_0345 NC_008044.1 351754 352602 R PFAM: periplasmic binding protein: (1.4e-24); KEGG: jan:Jann_2134 periplasmic binding protein, ev=3e-79, 58% identity; periplasmic binding protein complement(351754..352602) Ruegeria sp. TM1040 4076046 YP_612341.1 CDS TM1040_0346 NC_008044.1 352602 353681 R PFAM: Haemin-degrading: (1.8e-106); KEGG: jan:Jann_2133 Haemin-degrading, ev=2e-99, 54% identity; hemin-degrading protein complement(352602..353681) Ruegeria sp. TM1040 4076047 YP_612342.1 CDS TM1040_0347 NC_008044.1 353932 355944 D 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 353932..355944 Ruegeria sp. TM1040 4076048 YP_612343.1 CDS TM1040_0348 NC_008044.1 355964 356425 D KEGG: jan:Jann_2131 hypothetical protein, ev=2e-23, 47% identity; hypothetical protein 355964..356425 Ruegeria sp. TM1040 4076049 YP_612344.1 CDS TM1040_0349 NC_008044.1 356422 357102 D 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 356422..357102 Ruegeria sp. TM1040 4076050 YP_612345.1 CDS TM1040_0350 NC_008044.1 357102 357494 D KEGG: jan:Jann_2129 biopolymer transport protein ExbD/TolR, ev=2e-25, 51% identity; biopolymer transport protein ExbD/TolR 357102..357494 Ruegeria sp. TM1040 4076051 YP_612346.1 CDS TM1040_0351 NC_008044.1 357498 357893 D KEGG: jan:Jann_2128 hypothetical protein, ev=1e-26, 50% identity; hypothetical protein 357498..357893 Ruegeria sp. TM1040 4076052 YP_612347.1 CDS TM1040_0352 NC_008044.1 357890 358804 D TIGRFAM: TonB-like: (7e-10); KEGG: jan:Jann_2127 TonB-like, ev=3e-40, 37% identity; TonB-like protein 357890..358804 Ruegeria sp. TM1040 4076053 YP_612348.1 CDS TM1040_0353 NC_008044.1 358801 359538 R KEGG: sil:SPOA0416 hypothetical protein, ev=5e-90, 66% identity; hypothetical protein complement(358801..359538) Ruegeria sp. TM1040 4076054 YP_612349.1 CDS TM1040_0354 NC_008044.1 359541 360473 R 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 complement(359541..360473) Ruegeria sp. TM1040 4077684 YP_612350.1 CDS TM1040_0355 NC_008044.1 360576 361823 D PFAM: FAD dependent oxidoreductase: (2.1e-63); KEGG: jan:Jann_1410 D-amino-acid dehydrogenase, ev=1e-151, 61% identity; D-amino-acid dehydrogenase 360576..361823 Ruegeria sp. TM1040 4077685 YP_612351.1 CDS TM1040_0356 NC_008044.1 361863 362840 D 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 361863..362840 Ruegeria sp. TM1040 4077686 YP_612352.1 CDS TM1040_0357 NC_008044.1 363053 363667 D KEGG: sil:SPO3664 hypothetical protein, ev=8e-25, 38% identity; hypothetical protein 363053..363667 Ruegeria sp. TM1040 4077687 YP_612353.1 CDS TM1040_0358 NC_008044.1 363664 364962 D 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 363664..364962 Ruegeria sp. TM1040 4077688 YP_612354.1 CDS TM1040_0359 NC_008044.1 365386 368169 D 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 365386..368169 Ruegeria sp. TM1040 4077689 YP_612355.1 CDS TM1040_0360 NC_008044.1 368350 370440 D 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 368350..370440 Ruegeria sp. TM1040 4077690 YP_612356.1 CDS TM1040_0361 NC_008044.1 370462 371640 D PFAM: Thiolase: (2.8e-72); KEGG: sil:SPO0773 acetyl-CoA acyltransferase/thiolase family protein, ev=1e-157, 72% identity; Acetyl-CoA C-acyltransferase 370462..371640 Ruegeria sp. TM1040 4077691 YP_612357.1 CDS TM1040_0362 NC_008044.1 371829 372626 D SMART: regulatory proteins, IclR: (6.6e-20); KEGG: mag:amb2598 transcriptional regulator, ev=5e-35, 36% identity; IclR family transcriptional regulator 371829..372626 Ruegeria sp. TM1040 4077692 YP_612358.1 CDS TM1040_0363 NC_008044.1 372959 373921 D PFAM: ROK: (0.00052) Glucokinase: (3.4e-65); KEGG: sme:SMc02835 probable glucokinase transmembrane protein, ev=2e-42, 37% identity; glucokinase 372959..373921 Ruegeria sp. TM1040 4077693 YP_612359.1 CDS TM1040_0364 NC_008044.1 374058 374852 D KEGG: ccr:CC3356 hypothetical protein, ev=8e-62, 53% identity; hypothetical protein 374058..374852 Ruegeria sp. TM1040 4077694 YP_612360.1 CDS TM1040_0365 NC_008044.1 374933 375625 R 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 complement(374933..375625) Ruegeria sp. TM1040 4077695 YP_612361.1 CDS TM1040_0366 NC_008044.1 375616 376452 R 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 complement(375616..376452) Ruegeria sp. TM1040 4077696 YP_612362.1 CDS TM1040_0367 NC_008044.1 376581 377822 R 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 complement(376581..377822) Ruegeria sp. TM1040 4077697 YP_612363.1 CDS TM1040_0368 NC_008044.1 377973 378989 D 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 377973..378989 Ruegeria sp. TM1040 4077698 YP_612364.1 CDS TM1040_0369 NC_008044.1 379177 380241 D PFAM: inner-membrane translocator: (1.8e-62); KEGG: jan:Jann_1374 inner-membrane translocator, ev=1e-150, 77% identity; inner-membrane translocator 379177..380241 Ruegeria sp. TM1040 4077699 YP_612365.1 CDS TM1040_0370 NC_008044.1 380238 381017 D 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 380238..381017 Ruegeria sp. TM1040 4077700 YP_612366.1 CDS frcK NC_008044.1 381014 381637 D KEGG: sme:SMc02167 hypothetical protein, ev=5e-46, 47% identity; fructose transport system kinase 381014..381637 Ruegeria sp. TM1040 4077701 YP_612367.1 CDS TM1040_0372 NC_008044.1 381666 382331 D PFAM: protein of unknown function DUF1498: (1.3e-127); KEGG: mlo:mlr8329 hypothetical protein, ev=7e-84, 67% identity; hypothetical protein 381666..382331 Ruegeria sp. TM1040 4077702 YP_612368.1 CDS TM1040_0373 NC_008044.1 382535 383410 R PFAM: NAD-dependent epimerase/dehydratase: (1.7e-08); KEGG: sil:SPO2846 hypothetical protein, ev=2e-53, 42% identity; NAD-dependent epimerase/dehydratase complement(382535..383410) Ruegeria sp. TM1040 4077703 YP_612369.1 CDS TM1040_0374 NC_008044.1 383481 383897 R 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 complement(383481..383897) Ruegeria sp. TM1040 4078607 YP_612370.1 CDS TM1040_0375 NC_008044.1 384038 384685 R 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 complement(384038..384685) Ruegeria sp. TM1040 4078608 YP_612371.1 CDS TM1040_0376 NC_008044.1 384690 386501 R catalyzes the formation of 2-dehydro-3-deoxy-6-phospho-D-gluconate from 6-phospho-D-gluconate; phosphogluconate dehydratase complement(384690..386501) Ruegeria sp. TM1040 4078609 YP_612372.1 CDS TM1040_0377 NC_008044.1 386534 387985 R catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate; glucose-6-phosphate 1-dehydrogenase complement(386534..387985) Ruegeria sp. TM1040 4078610 YP_612373.1 CDS TM1040_0378 NC_008044.1 388010 389620 R PFAM: phosphoglucose isomerase (PGI): (4.9e-230); KEGG: mlo:mlr5411 glucose-6-phosphate isomerase, ev=0.0, 64% identity; glucose-6-phosphate isomerase complement(388010..389620) Ruegeria sp. TM1040 4078611 YP_612374.1 CDS TM1040_0379 NC_008044.1 389724 390131 R hypothetical protein complement(389724..390131) Ruegeria sp. TM1040 4078612 YP_612375.1 CDS TM1040_0380 NC_008044.1 390218 390859 R 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 complement(390218..390859) Ruegeria sp. TM1040 4078613 YP_612376.1 CDS TM1040_0381 NC_008044.1 390856 391500 R PFAM: Urease accessory protein UreF: (4.6e-07); KEGG: sil:SPO1716 urease accessory protein UreF, ev=3e-53, 50% identity; urease accessory protein UreF complement(390856..391500) Ruegeria sp. TM1040 4078614 YP_612377.1 CDS ureE NC_008044.1 391490 392020 R involved in the assembly of the urease metallocenter; possible nickel donor; urease accessory protein UreE complement(391490..392020) Ruegeria sp. TM1040 4078615 YP_612378.1 CDS TM1040_0383 NC_008044.1 392070 392297 R hypothetical protein complement(392070..392297) Ruegeria sp. TM1040 4078616 YP_612379.1 CDS TM1040_0384 NC_008044.1 392436 393050 R hypothetical protein complement(392436..393050) Ruegeria sp. TM1040 4078617 YP_612380.1 CDS ureC NC_008044.1 393082 394794 R 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 complement(393082..394794) Ruegeria sp. TM1040 4078618 YP_612381.1 CDS TM1040_0386 NC_008044.1 394907 395212 R 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 complement(394907..395212) Ruegeria sp. TM1040 4078619 YP_612382.1 CDS ureA NC_008044.1 395402 395704 R 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 complement(395402..395704) Ruegeria sp. TM1040 4078620 YP_612383.1 CDS TM1040_0388 NC_008044.1 395726 396619 R PFAM: Urease accessory protein UreD: (2.5e-39); KEGG: sil:SPO1711 urease accessory protein UreD, ev=1e-58, 51% identity; urease accessory protein UreD complement(395726..396619) Ruegeria sp. TM1040 4078621 YP_612384.1 CDS TM1040_0389 NC_008044.1 396997 398121 D 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 396997..398121 Ruegeria sp. TM1040 4078622 YP_612385.1 CDS TM1040_0390 NC_008044.1 398118 398918 R KEGG: mlo:mll6996 hypothetical protein, ev=8e-40, 37% identity; hypothetical protein complement(398118..398918) Ruegeria sp. TM1040 4078623 YP_612386.1 CDS TM1040_0391 NC_008044.1 399046 401052 D 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 399046..401052 Ruegeria sp. TM1040 4078624 YP_612387.1 CDS TM1040_0392 NC_008044.1 401118 401666 R hypothetical protein complement(401118..401666) Ruegeria sp. TM1040 4078625 YP_612388.1 CDS TM1040_0393 NC_008044.1 401790 402266 R KEGG: sil:SPO1805 hypothetical protein, ev=6e-59, 70% identity; hypothetical protein complement(401790..402266) Ruegeria sp. TM1040 4078787 YP_612389.1 CDS TM1040_0394 NC_008044.1 402282 402986 R KEGG: sil:SPO1804 hypothetical protein, ev=8e-78, 64% identity; hypothetical protein complement(402282..402986) Ruegeria sp. TM1040 4078788 YP_612390.1 CDS TM1040_0395 NC_008044.1 402983 404047 R KEGG: sil:SPO1803 Mrp/NBP35 family protein, ev=1e-155, 78% identity; Mrp/NBP35 family protein complement(402983..404047) Ruegeria sp. TM1040 4078789 YP_612391.1 CDS TM1040_0396 NC_008044.1 404143 406101 R 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 complement(404143..406101) Ruegeria sp. TM1040 4078790 YP_612392.1 CDS TM1040_0397 NC_008044.1 406357 407001 D KEGG: mag:amb2667 molybdopterin-guanine dinucleotide biosynthesis protein A, ev=6e-18, 35% identity; hypothetical protein 406357..407001 Ruegeria sp. TM1040 4078791 YP_612393.1 CDS TM1040_0398 NC_008044.1 406998 407654 D KEGG: sil:SPO1799 hypothetical protein, ev=4e-48, 53% identity; hypothetical protein 406998..407654 Ruegeria sp. TM1040 4078792 YP_612394.1 CDS TM1040_0399 NC_008044.1 407651 408277 D PFAM: cytoplasmic chaperone TorD: (9.9e-24); KEGG: sil:SPO1798 chaperone, TorD family, ev=3e-81, 73% identity; cytoplasmic chaperone TorD 407651..408277 Ruegeria sp. TM1040 4078793 YP_612395.1 CDS TM1040_0400 NC_008044.1 408384 408572 D 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 408384..408572 Ruegeria sp. TM1040 4078794 YP_612396.1 CDS TM1040_0401 NC_008044.1 408686 411580 D 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 408686..411580 Ruegeria sp. TM1040 4078795 YP_612397.1 CDS TM1040_0402 NC_008044.1 411594 412187 D 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 411594..412187 Ruegeria sp. TM1040 4078796 YP_612398.1 CDS TM1040_0403 NC_008044.1 412303 413517 D TIGRFAM: Formate dehydrogenase, gamma subunit: (1.6e-36); KEGG: sil:SPO1794 formate dehydrogenase, gamma subunit, ev=1e-131, 59% identity; formate dehydrogenase subunit gamma 412303..413517 Ruegeria sp. TM1040 4078797 YP_612399.1 CDS TM1040_0404 NC_008044.1 413522 414805 D 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 413522..414805 Ruegeria sp. TM1040 4078798 YP_612400.1 CDS TM1040_0405 NC_008044.1 414942 416294 D 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 414942..416294 Ruegeria sp. TM1040 4078799 YP_612401.1 CDS TM1040_0406 NC_008044.1 416325 418301 R 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 complement(416325..418301) Ruegeria sp. TM1040 4078800 YP_612402.1 CDS TM1040_0407 NC_008044.1 418401 419141 R 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 complement(418401..419141) Ruegeria sp. TM1040 4078801 YP_612403.1 CDS TM1040_0408 NC_008044.1 419138 419860 R 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 complement(419138..419860) Ruegeria sp. TM1040 4078802 YP_612404.1 CDS TM1040_0409 NC_008044.1 419857 420426 R KEGG: sil:SPO1486 hypothetical protein, ev=5e-59, 59% identity; hypothetical protein complement(419857..420426) Ruegeria sp. TM1040 4078803 YP_612405.1 CDS TM1040_0410 NC_008044.1 420423 421640 R KEGG: sil:SPO1485 sodium:galactoside symporter family protein, ev=1e-118, 56% identity; sodium:galactoside symporter family protein complement(420423..421640) Ruegeria sp. TM1040 4078804 YP_612406.1 CDS TM1040_0411 NC_008044.1 421643 422185 R KEGG: sil:SPO1484 hypothetical protein, ev=6e-23, 35% identity; hypothetical protein complement(421643..422185) Ruegeria sp. TM1040 4078805 YP_612407.1 CDS TM1040_0412 NC_008044.1 422175 423335 R 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 complement(422175..423335) Ruegeria sp. TM1040 4078806 YP_612408.1 CDS TM1040_0413 NC_008044.1 423335 424114 R 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 complement(423335..424114) Ruegeria sp. TM1040 4076173 YP_612409.1 CDS TM1040_0414 NC_008044.1 424111 425442 R PFAM: amine oxidase: (0.00038) FAD dependent oxidoreductase: (3e-06); KEGG: sil:SPO1482 hypothetical protein, ev=1e-151, 60% identity; FAD dependent oxidoreductase complement(424111..425442) Ruegeria sp. TM1040 4076174 YP_612410.1 CDS TM1040_0415 NC_008044.1 425629 426225 D 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 425629..426225 Ruegeria sp. TM1040 4076175 YP_612411.1 CDS TM1040_0416 NC_008044.1 426222 426857 D TIGRFAM: Anti-sigma factor ChrR , : (6.8e-79); KEGG: sil:SPO1479 transcriptional activator, , ev=1e-71, 61% identity; anti-ECF sigma factor ChrR 426222..426857 Ruegeria sp. TM1040 4076176 YP_612412.1 CDS TM1040_0417 NC_008044.1 427011 428015 R 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 complement(427011..428015) Ruegeria sp. TM1040 4076177 YP_612413.1 CDS TM1040_0418 NC_008044.1 428354 430087 D 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 428354..430087 Ruegeria sp. TM1040 4076178 YP_612414.1 CDS TM1040_0419 NC_008044.1 430269 430526 D KEGG: hch:HCH_03746 hypothetical protein, ev=4e-24, 62% identity; hypothetical protein 430269..430526 Ruegeria sp. TM1040 4076179 YP_612415.1 CDS TM1040_0420 NC_008044.1 430753 431982 R KEGG: hch:HCH_00270 glycosyltransferase involved in cell wall biogenesis, ev=1e-140, 58% identity; cell wall biosynthesis glycosyltransferase complement(430753..431982) Ruegeria sp. TM1040 4076180 YP_612416.1 CDS TM1040_0421 NC_008044.1 431975 432754 R catalyzes the hydrolysis of mannosyl-3-phosphoglycerate to form the osmolyte mannosylglycerate; mannosyl-3-phosphoglycerate phosphatase complement(431975..432754) Ruegeria sp. TM1040 4076181 YP_612417.1 CDS TM1040_0422 NC_008044.1 432884 434839 D PFAM: BCCT transporter: (1.3e-131); KEGG: jan:Jann_1593 BCCT transporter, ev=0.0, 65% identity; BCCT transporter 432884..434839 Ruegeria sp. TM1040 4076182 YP_612418.1 CDS TM1040_0423 NC_008044.1 434944 435714 D PFAM: fumarylacetoacetate (FAA) hydrolase: (9.3e-59); KEGG: rsp:RSP_1562 fumarylacetoacetate hydrolase family protein, ev=4e-91, 71% identity; fumarylacetoacetate (FAA) hydrolase 434944..435714 Ruegeria sp. TM1040 4076183 YP_612419.1 CDS TM1040_0424 NC_008044.1 435852 437273 D KEGG: jan:Jann_2999 hypothetical protein, ev=1e-134, 53% identity; hypothetical protein 435852..437273 Ruegeria sp. TM1040 4076184 YP_612420.1 CDS TM1040_0425 NC_008044.1 437482 437877 D hypothetical protein 437482..437877 Ruegeria sp. TM1040 4076185 YP_612421.1 CDS TM1040_0426 NC_008044.1 437908 439386 R 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 complement(437908..439386) Ruegeria sp. TM1040 4076186 YP_612422.1 CDS TM1040_0427 NC_008044.1 439386 440156 R Converts D-sorbitol to L-sorbose; sorbitol dehydrogenase complement(439386..440156) Ruegeria sp. TM1040 4076187 YP_612423.1 CDS TM1040_0428 NC_008044.1 440156 441160 R 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 complement(440156..441160) Ruegeria sp. TM1040 4076188 YP_612424.1 CDS TM1040_0429 NC_008044.1 441173 442003 R 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 complement(441173..442003) Ruegeria sp. TM1040 4076189 YP_612425.1 CDS TM1040_0430 NC_008044.1 442019 442885 R 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 complement(442019..442885) Ruegeria sp. TM1040 4076190 YP_612426.1 CDS TM1040_0431 NC_008044.1 442988 444295 R 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 complement(442988..444295) Ruegeria sp. TM1040 4076191 YP_612427.1 CDS TM1040_0432 NC_008044.1 444427 445458 R 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 complement(444427..445458) Ruegeria sp. TM1040 4076075 YP_612428.1 CDS TM1040_0433 NC_008044.1 445657 447987 R 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 complement(445657..447987) Ruegeria sp. TM1040 4076076 YP_612429.1 CDS TM1040_0434 NC_008044.1 448712 451171 R 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 complement(448712..451171) Ruegeria sp. TM1040 4076077 YP_612430.1 CDS TM1040_0435 NC_008044.1 451273 451926 D PFAM: regulatory protein, TetR: (6.3e-11); KEGG: mlo:mll3671 transcriptional regulator, ev=5e-33, 37% identity; TetR family transcriptional regulator 451273..451926 Ruegeria sp. TM1040 4076078 YP_612431.1 CDS TM1040_0436 NC_008044.1 452191 453096 R PFAM: PaaX-like: (1.1e-10); KEGG: sil:SPO0734 PaaX domain protein, ev=2e-66, 50% identity; PaaX-like protein complement(452191..453096) Ruegeria sp. TM1040 4076079 YP_612432.1 CDS TM1040_0437 NC_008044.1 453126 455156 R catalyzes the ring cleavage reaction in phenylacetate degradation and the formation of 3-hydroxyacyl-CoA from crotonyl-CoA; bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase complement(453126..455156) Ruegeria sp. TM1040 4076080 YP_612433.1 CDS TM1040_0438 NC_008044.1 455317 456102 D Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 455317..456102 Ruegeria sp. TM1040 4076081 YP_612434.1 CDS TM1040_0439 NC_008044.1 456106 456537 D 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 456106..456537 Ruegeria sp. TM1040 4076082 YP_612435.1 CDS TM1040_0440 NC_008044.1 456593 457903 D TIGRFAM: Phenylacetate-CoA ligase: (3.5e-299); KEGG: sil:SPO0742 phenylacetate-CoA ligase, ev=0.0, 83% identity; phenylacetate-CoA ligase 456593..457903 Ruegeria sp. TM1040 4076083 YP_612436.1 CDS TM1040_0441 NC_008044.1 457910 458506 D PFAM: regulatory protein, TetR: (1.7e-18); KEGG: sil:SPO0743 transcriptional regulator, TetR family, ev=3e-69, 61% identity; TetR family transcriptional regulator 457910..458506 Ruegeria sp. TM1040 4076084 YP_612437.1 CDS TM1040_0442 NC_008044.1 458711 458974 D PFAM: 17 kDa surface antigen: (3e-05); KEGG: vpa:VPA0312 hypothetical protein, ev=8e-06, 59% identity; 17 kDa surface antigen 458711..458974 Ruegeria sp. TM1040 4076085 YP_612438.1 CDS TM1040_0443 NC_008044.1 459119 460147 R 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 complement(459119..460147) Ruegeria sp. TM1040 4076086 YP_612439.1 CDS TM1040_0444 NC_008044.1 460262 460948 D PFAM: Rhomboid-like protein: (2.3e-06); KEGG: sil:SPO0393 rhomboid family protein, ev=3e-79, 62% identity; rhomboid-like protein 460262..460948 Ruegeria sp. TM1040 4076087 YP_612440.1 CDS TM1040_0445 NC_008044.1 460965 462512 R 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 complement(460965..462512) Ruegeria sp. TM1040 4076088 YP_612441.1 CDS TM1040_0446 NC_008044.1 462509 465190 R catalyzes the uridylylation or deuridylylation of the PII nitrogen regulatory protein; PII uridylyl-transferase complement(462509..465190) Ruegeria sp. TM1040 4076089 YP_612442.1 CDS TM1040_0447 NC_008044.1 465297 466481 R PFAM: Extracellular ligand-binding receptor: (4.4e-05); KEGG: sil:SPO0398 hypothetical protein, ev=1e-157, 72% identity; extracellular ligand-binding receptor complement(465297..466481) Ruegeria sp. TM1040 4076090 YP_612443.1 CDS TM1040_0448 NC_008044.1 466570 467433 D 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 466570..467433 Ruegeria sp. TM1040 4076091 YP_612444.1 CDS TM1040_0449 NC_008044.1 467439 467813 D PFAM: protein of unknown function UPF0102: (3.6e-07); KEGG: sil:SPO0400 endonuclease, ev=3e-26, 52% identity; hypothetical protein 467439..467813 Ruegeria sp. TM1040 4076092 YP_612445.1 CDS TM1040_0450 NC_008044.1 467874 468809 D catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione; glutathione synthetase 467874..468809 Ruegeria sp. TM1040 4076093 YP_612446.1 CDS TM1040_0451 NC_008044.1 468806 469702 D PFAM: Alpha/beta hydrolase fold-3: (3e-51); KEGG: bpm:BURPS1710b_0827 esterase, , ev=2e-46, 38% identity; alpha/beta hydrolase 468806..469702 Ruegeria sp. TM1040 4076094 YP_612447.1 CDS TM1040_0452 NC_008044.1 469699 471201 R 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 complement(469699..471201) Ruegeria sp. TM1040 4078334 YP_612448.1 CDS TM1040_0453 NC_008044.1 471312 471992 R KEGG: sil:SPO0403 hypothetical protein, ev=2e-83, 66% identity; hypothetical protein complement(471312..471992) Ruegeria sp. TM1040 4078335 YP_612449.1 CDS TM1040_0454 NC_008044.1 472051 472632 R PFAM: Phosphoglycerate mutase: (5.3e-24); KEGG: sil:SPO0404 phosphoglycerate mutase family protein, ev=2e-68, 63% identity; phosphoglycerate mutase complement(472051..472632) Ruegeria sp. TM1040 4078336 YP_612450.1 CDS TM1040_0455 NC_008044.1 472629 473249 R PFAM: cobalbumin biosynthesis enzyme: (7e-53); KEGG: sil:SPO0405 cobinamide kinase/cobinamide phosphate guanyltransferase, ev=5e-60, 68% identity; adenosylcobinamide kinase complement(472629..473249) Ruegeria sp. TM1040 4078337 YP_612451.1 CDS rpoH2 NC_008044.1 473334 474212 D 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 473334..474212 Ruegeria sp. TM1040 4078338 YP_612452.1 CDS TM1040_0457 NC_008044.1 474209 475072 D KEGG: sil:SPO0407 hypothetical protein, ev=2e-69, 52% identity; hypothetical protein 474209..475072 Ruegeria sp. TM1040 4078339 YP_612453.1 CDS TM1040_0458 NC_008044.1 475190 476401 D 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 475190..476401 Ruegeria sp. TM1040 4078340 YP_612454.1 CDS TM1040_0459 NC_008044.1 476638 477012 D hypothetical protein 476638..477012 Ruegeria sp. TM1040 4078341 YP_612455.1 CDS TM1040_0460 NC_008044.1 477198 479711 D 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 477198..479711 Ruegeria sp. TM1040 4078342 YP_612456.1 CDS TM1040_0461 NC_008044.1 479863 480354 D 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 479863..480354 Ruegeria sp. TM1040 4078343 YP_612457.1 CDS TM1040_0462 NC_008044.1 480351 481427 D 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 480351..481427 Ruegeria sp. TM1040 4078344 YP_612458.1 CDS TM1040_0463 NC_008044.1 481430 482221 D 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 481430..482221 Ruegeria sp. TM1040 4078345 YP_612459.1 CDS TM1040_0464 NC_008044.1 482295 483101 D 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 482295..483101 Ruegeria sp. TM1040 4078346 YP_612460.1 CDS TM1040_0465 NC_008044.1 483198 485213 D PFAM: peptidase M3A and M3B, thimet/oligopeptidase F: (8.4e-115); KEGG: sil:SPO0414 peptidyl-dipeptidase, , ev=0.0, 79% identity; peptidyl-dipeptidase Dcp 483198..485213 Ruegeria sp. TM1040 4078347 YP_612461.1 CDS TM1040_0466 NC_008044.1 485294 486220 R 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 complement(485294..486220) Ruegeria sp. TM1040 4078348 YP_612462.1 CDS TM1040_0467 NC_008044.1 486217 486627 R 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 complement(486217..486627) Ruegeria sp. TM1040 4078349 YP_612463.1 CDS TM1040_0468 NC_008044.1 486728 487573 D 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 486728..487573 Ruegeria sp. TM1040 4078350 YP_612464.1 CDS TM1040_0469 NC_008044.1 487570 488709 R 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 complement(487570..488709) Ruegeria sp. TM1040 4078351 YP_612465.1 CDS TM1040_0470 NC_008044.1 488706 490652 R 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 complement(488706..490652) Ruegeria sp. TM1040 4078352 YP_612466.1 CDS TM1040_0471 NC_008044.1 490649 491188 R KEGG: sil:SPO0418 rod shape-determining protein MreD, ev=2e-56, 60% identity; rod shape-determining protein MreD complement(490649..491188) Ruegeria sp. TM1040 4078509 YP_612467.1 CDS TM1040_0472 NC_008044.1 491181 492128 R 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 complement(491181..492128) Ruegeria sp. TM1040 4078510 YP_612468.1 CDS TM1040_0473 NC_008044.1 492184 493230 R functions in MreBCD complex in some organisms; rod shape-determining protein MreB complement(492184..493230) Ruegeria sp. TM1040 4078511 YP_612469.1 CDS TM1040_0474 NC_008044.1 493430 494182 R KEGG: jan:Jann_0595 hypothetical protein, ev=1e-44, 47% identity; hypothetical protein complement(493430..494182) Ruegeria sp. TM1040 4078512 YP_612470.1 CDS TM1040_0475 NC_008044.1 494301 495080 D PFAM: protein of unknown function DUF519: (3.8e-54); KEGG: sil:SPO0421 hypothetical protein, ev=1e-103, 70% identity; hypothetical protein 494301..495080 Ruegeria sp. TM1040 4078513 YP_612471.1 CDS TM1040_0476 NC_008044.1 495160 496929 R 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 complement(495160..496929) Ruegeria sp. TM1040 4078514 YP_612472.1 CDS TM1040_0477 NC_008044.1 497149 499365 R 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 complement(497149..499365) Ruegeria sp. TM1040 4078515 YP_612473.1 CDS TM1040_0478 NC_008044.1 499866 501158 D 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 499866..501158 Ruegeria sp. TM1040 4078516 YP_612474.1 CDS TM1040_0479 NC_008044.1 501173 501775 R PFAM: protein of unknown function DUF1058: (2.6e-16); KEGG: sil:SPO0631 hypothetical protein, ev=1e-58, 65% identity; hypothetical protein complement(501173..501775) Ruegeria sp. TM1040 4078517 YP_612475.1 CDS TM1040_0480 NC_008044.1 501938 502924 D 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 501938..502924 Ruegeria sp. TM1040 4078518 YP_612476.1 CDS TM1040_0481 NC_008044.1 502866 503246 R KEGG: lma:LmjF35.0550 proteophosphoglycan ppg1, ev=4e-07, 26% identity; hypothetical protein complement(502866..503246) Ruegeria sp. TM1040 4078519 YP_612477.1 CDS TM1040_0482 NC_008044.1 503457 504770 D PFAM: gamma-glutamyltranspeptidase: (7.5e-127); KEGG: sil:SPO0633 gamma-glutamyltranspeptidase, ev=0.0, 76% identity; gamma-glutamyltransferase 1 503457..504770 Ruegeria sp. TM1040 4078520 YP_612478.1 CDS TM1040_0483 NC_008044.1 505027 506433 D PFAM: FAD linked oxidase-like: (9.6e-76); KEGG: sil:SPO0634 oxidoreductase, FAD-binding, ev=0.0, 72% identity; FAD linked oxidase-like protein 505027..506433 Ruegeria sp. TM1040 4078521 YP_612479.1 CDS TM1040_0484 NC_008044.1 506534 506977 D hypothetical protein 506534..506977 Ruegeria sp. TM1040 4078522 YP_612480.1 CDS TM1040_0485 NC_008044.1 506989 507420 R 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 complement(506989..507420) Ruegeria sp. TM1040 4078523 YP_612481.1 CDS TM1040_0486 NC_008044.1 507703 510210 D 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 507703..510210 Ruegeria sp. TM1040 4078524 YP_612482.1 CDS TM1040_0487 NC_008044.1 510374 511339 D KEGG: vvy:VV2684 GGDEF family protein, ev=5e-08, 20% identity; hypothetical protein 510374..511339 Ruegeria sp. TM1040 4078525 YP_612483.1 CDS TM1040_0488 NC_008044.1 511342 511809 R PFAM: Calcium-binding EF-hand: (0.0024); KEGG: rpb:RPB_3148 hypothetical protein, ev=4e-13, 30% identity; calcium-binding EF-hand complement(511342..511809) Ruegeria sp. TM1040 4078526 YP_612484.1 CDS TM1040_0489 NC_008044.1 511915 512568 R 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 complement(511915..512568) Ruegeria sp. TM1040 4078527 YP_612485.1 CDS TM1040_0490 NC_008044.1 512568 513653 R PFAM: FAD dependent oxidoreductase: (5.5e-58); KEGG: sil:SPO0642 oxidoreductase, FAD-binding, ev=1e-119, 60% identity; FAD dependent oxidoreductase complement(512568..513653) Ruegeria sp. TM1040 4078528 YP_612486.1 CDS TM1040_0491 NC_008044.1 513650 514654 R PFAM: aldo/keto reductase: (1.7e-59); KEGG: sil:SPO0643 oxidoreductase, aldo/keto reductase family, ev=1e-115, 66% identity; aldo/keto reductase complement(513650..514654) Ruegeria sp. TM1040 4078237 YP_612487.1 CDS TM1040_0492 NC_008044.1 514715 515323 D PFAM: CDP-alcohol phosphatidyltransferase: (3.6e-10); KEGG: rsp:RSP_0198 phosphatidylglycerophosphate synthase, ev=2e-64, 64% identity; CDP-alcohol phosphatidyltransferase 514715..515323 Ruegeria sp. TM1040 4078238 YP_612488.1 CDS TM1040_0493 NC_008044.1 515592 516668 R PFAM: basic membrane lipoprotein: (1.2e-47); KEGG: sil:SPO0648 bmp family protein, ev=0.0, 88% identity; basic membrane lipoprotein complement(515592..516668) Ruegeria sp. TM1040 4078239 YP_612489.1 CDS TM1040_0494 NC_008044.1 516786 517706 R PFAM: inner-membrane translocator: (5.7e-44); KEGG: sil:SPO0649 sugar ABC transporter, permease protein, ev=1e-150, 88% identity; inner-membrane translocator complement(516786..517706) Ruegeria sp. TM1040 4078240 YP_612490.1 CDS TM1040_0495 NC_008044.1 517706 518788 R PFAM: inner-membrane translocator: (3e-51); KEGG: sil:SPO0650 sugar ABC transporter, permease protein, ev=0.0, 87% identity; inner-membrane translocator complement(517706..518788) Ruegeria sp. TM1040 4078241 YP_612491.1 CDS TM1040_0496 NC_008044.1 518906 520426 R 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 complement(518906..520426) Ruegeria sp. TM1040 4078242 YP_612492.1 CDS TM1040_0497 NC_008044.1 520423 521358 R PFAM: protein of unknown function DUF182: (8.2e-12); KEGG: sil:SPO0652 xanthine dehydrogenase accessory factor, ev=1e-107, 61% identity; molybdenum cofactor sulfurylase complement(520423..521358) Ruegeria sp. TM1040 4078243 YP_612493.1 CDS TM1040_0498 NC_008044.1 521348 523696 R 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 complement(521348..523696) Ruegeria sp. TM1040 4078244 YP_612494.1 CDS TM1040_0499 NC_008044.1 523693 525096 R 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 complement(523693..525096) Ruegeria sp. TM1040 4078245 YP_612495.1 CDS dnaE NC_008044.1 525502 529002 D 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 525502..529002 Ruegeria sp. TM1040 4078246 YP_612496.1 CDS TM1040_0501 NC_008044.1 529337 529831 R KEGG: sme:SMb20463 hypothetical protein, ev=4e-08, 27% identity; hypothetical protein complement(529337..529831) Ruegeria sp. TM1040 4078247 YP_612497.1 CDS TM1040_0502 NC_008044.1 529955 530149 R KEGG: sil:SPO0665 SlyX protein, , ev=9e-18, 65% identity; SlyX protein complement(529955..530149) Ruegeria sp. TM1040 4078248 YP_612498.1 CDS hisS NC_008044.1 530303 531805 D 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 530303..531805 Ruegeria sp. TM1040 4078249 YP_612499.1 CDS hisZ NC_008044.1 531808 532899 D May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine; ATP phosphoribosyltransferase 531808..532899 Ruegeria sp. TM1040 4078250 YP_612500.1 CDS hisG NC_008044.1 532896 533588 D 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 532896..533588 Ruegeria sp. TM1040 4078251 YP_612501.1 CDS TM1040_0506 NC_008044.1 533746 534213 R PFAM: Uncharacterised conserved protein UCP032025: (1.4e-56); KEGG: sil:SPO3193 hypothetical protein, ev=8e-58, 69% identity; hypothetical protein complement(533746..534213) Ruegeria sp. TM1040 4078252 YP_612502.1 CDS TM1040_0507 NC_008044.1 534367 534696 R TIGRFAM: conserved hypothetical protein: (7.9e-10); KEGG: sil:SPO3623 hypothetical protein, ev=1e-41, 71% identity; hypothetical protein complement(534367..534696) Ruegeria sp. TM1040 4078253 YP_612503.1 CDS TM1040_0508 NC_008044.1 534809 535510 D PFAM: protein of unknown function DUF45: (4.9e-65); KEGG: sil:SPO3622 hypothetical protein, ev=7e-69, 59% identity; hypothetical protein 534809..535510 Ruegeria sp. TM1040 4078254 YP_612504.1 CDS TM1040_0509 NC_008044.1 535543 536205 D 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 535543..536205 Ruegeria sp. TM1040 4078255 YP_612505.1 CDS TM1040_0510 NC_008044.1 536336 537115 D KEGG: vch:VC2649 serine acetyltransferase, ev=5e-34, 38% identity; Serine O-acetyltransferase 536336..537115 Ruegeria sp. TM1040 4077216 YP_612506.1 CDS TM1040_0511 NC_008044.1 537112 538005 D KEGG: psp:PSPPH_1713 hypothetical protein, ev=1e-36, 34% identity; hypothetical protein 537112..538005 Ruegeria sp. TM1040 4077217 YP_612507.1 CDS TM1040_0512 NC_008044.1 538014 539153 D 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 538014..539153 Ruegeria sp. TM1040 4077218 YP_612508.1 CDS TM1040_0513 NC_008044.1 539153 540061 D 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 539153..540061 Ruegeria sp. TM1040 4077219 YP_612509.1 CDS TM1040_0514 NC_008044.1 540185 541099 D 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 540185..541099 Ruegeria sp. TM1040 4077220 YP_612510.1 CDS TM1040_0515 NC_008044.1 541096 542631 D PFAM: aldehyde dehydrogenase: (2.5e-214); KEGG: psb:Psyr_3524 aldehyde dehydrogenase (NAD+), ev=1e-156, 55% identity; aldehyde dehydrogenase 541096..542631 Ruegeria sp. TM1040 4077221 YP_612511.1 CDS TM1040_0516 NC_008044.1 542752 543573 D KEGG: cvi:CV1885 hypothetical protein, ev=2e-73, 52% identity; hypothetical protein 542752..543573 Ruegeria sp. TM1040 4077222 YP_612512.1 CDS TM1040_0517 NC_008044.1 543576 544052 D KEGG: dde:Dde_3032 hypothetical protein, ev=3e-24, 43% identity; hypothetical protein 543576..544052 Ruegeria sp. TM1040 4077223 YP_612513.1 CDS nrdF NC_008044.1 544203 545219 R 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 complement(544203..545219) Ruegeria sp. TM1040 4077224 YP_612514.1 CDS TM1040_0519 NC_008044.1 545281 547413 R Catalyzes the rate-limiting step in dNTP synthesis; ribonucleotide-diphosphate reductase subunit alpha complement(545281..547413) Ruegeria sp. TM1040 4077225 YP_612515.1 CDS nrdI NC_008044.1 547395 547817 R in Salmonella NrdI has a stimulatory effect on the ribonucleotide reductase activity of NrdH with NrdEF; ribonucleotide reductase stimulatory protein complement(547395..547817) Ruegeria sp. TM1040 4077226 YP_612516.1 CDS TM1040_0521 NC_008044.1 547839 548060 R 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 complement(547839..548060) Ruegeria sp. TM1040 4077227 YP_612517.1 CDS TM1040_0522 NC_008044.1 548599 548973 R 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 complement(548599..548973) Ruegeria sp. TM1040 4077228 YP_612518.1 CDS TM1040_0523 NC_008044.1 549000 550034 R 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 complement(549000..550034) Ruegeria sp. TM1040 4077229 YP_612519.1 CDS TM1040_0524 NC_008044.1 550031 551305 R PFAM: major facilitator superfamily MFS_1: (0.00025); KEGG: sil:SPO3879 membrane protein, , ev=0.0, 83% identity; major facilitator superfamily transporter complement(550031..551305) Ruegeria sp. TM1040 4077230 YP_612520.1 CDS TM1040_0525 NC_008044.1 551302 552300 R 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 complement(551302..552300) Ruegeria sp. TM1040 4077231 YP_612521.1 CDS TM1040_0526 NC_008044.1 552342 553172 R 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 complement(552342..553172) Ruegeria sp. TM1040 4077232 YP_612522.1 CDS TM1040_0527 NC_008044.1 553735 554442 D 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 553735..554442 Ruegeria sp. TM1040 4077233 YP_612523.1 CDS TM1040_0528 NC_008044.1 554564 555736 R 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 complement(554564..555736) Ruegeria sp. TM1040 4077234 YP_612524.1 CDS TM1040_0529 NC_008044.1 555733 558348 R 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 complement(555733..558348) Ruegeria sp. TM1040 4077235 YP_612525.1 CDS TM1040_0530 NC_008044.1 558345 559640 R PFAM: outer membrane efflux protein: (4.7e-06); KEGG: pae:PA1875 hypothetical protein, ev=3e-13, 21% identity; outer membrane efflux protein complement(558345..559640) Ruegeria sp. TM1040 4077177 YP_612526.1 CDS TM1040_0531 NC_008044.1 559749 562301 R KEGG: ecs:ECs0541 hypothetical protein, ev=1e-61, 27% identity; hypothetical protein complement(559749..562301) Ruegeria sp. TM1040 4077178 YP_612527.1 CDS TM1040_0532 NC_008044.1 563004 564938 D 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 563004..564938 Ruegeria sp. TM1040 4077179 YP_612528.1 CDS TM1040_0533 NC_008044.1 564957 565316 D KEGG: cvi:CV1790 hypothetical protein, ev=2e-26, 52% identity; hypothetical protein 564957..565316 Ruegeria sp. TM1040 4077180 YP_612529.1 CDS TM1040_0534 NC_008044.1 565370 566272 D PFAM: protein of unknown function DUF444: (1e-58); KEGG: mlo:mll9637 hypothetical protein, ev=3e-85, 54% identity; hypothetical protein 565370..566272 Ruegeria sp. TM1040 4077181 YP_612530.1 CDS TM1040_0535 NC_008044.1 566278 567795 D PFAM: SpoVR: (5.1e-261); KEGG: sme:SMc01265 hypothetical protein, ev=0.0, 63% identity; SpoVR family protein 566278..567795 Ruegeria sp. TM1040 4077182 YP_612531.1 CDS TM1040_0536 NC_008044.1 567866 568981 R 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 complement(567866..568981) Ruegeria sp. TM1040 4077183 YP_612532.1 CDS TM1040_0537 NC_008044.1 569385 569786 D 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 569385..569786 Ruegeria sp. TM1040 4077184 YP_612533.1 CDS TM1040_0538 NC_008044.1 570587 571387 D KEGG: rpb:RPB_0861 TPR repeat protein, ev=6e-19, 31% identity; SARP family transcriptional regulator 570587..571387 Ruegeria sp. TM1040 4077185 YP_612534.1 CDS TM1040_0539 NC_008044.1 571387 572250 D KEGG: rsp:RSP_1299 binding domain, ev=3e-16, 27% identity; hypothetical protein 571387..572250 Ruegeria sp. TM1040 4077186 YP_612535.1 CDS TM1040_0540 NC_008044.1 573038 573619 R PFAM: Phosphoglycerate mutase: (1.3e-29); KEGG: rru:Rru_A2210 phosphoglycerate/bisphosphoglycerate mutase, ev=2e-17, 35% identity; phosphoglycerate mutase complement(573038..573619) Ruegeria sp. TM1040 4077187 YP_612536.1 CDS TM1040_0541 NC_008044.1 573619 574689 R PFAM: beta-lactamase-like: (3.3e-07); KEGG: bca:BCE1814 metallo-beta-lactamase family protein, ev=1e-15, 24% identity; beta-lactamase-like protein complement(573619..574689) Ruegeria sp. TM1040 4077188 YP_612537.1 CDS TM1040_0542 NC_008044.1 574699 575739 R 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 complement(574699..575739) Ruegeria sp. TM1040 4077189 YP_612538.1 CDS TM1040_0543 NC_008044.1 575727 577433 R 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 complement(575727..577433) Ruegeria sp. TM1040 4077190 YP_612539.1 CDS TM1040_0544 NC_008044.1 577430 578398 R 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 complement(577430..578398) Ruegeria sp. TM1040 4077191 YP_612540.1 CDS TM1040_0545 NC_008044.1 578562 579359 D 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 578562..579359 Ruegeria sp. TM1040 4077192 YP_612541.1 CDS TM1040_0546 NC_008044.1 579549 580178 D KEGG: ddi:DDB0168118 hypothetical protein, ev=4e-06, 28% identity; hypothetical protein 579549..580178 Ruegeria sp. TM1040 4077193 YP_612542.1 CDS TM1040_0547 NC_008044.1 580200 582749 R TIGRFAM: Twin-arginine translocation pathway signal: (0.13); KEGG: ava:Ava_1569 hypothetical protein, ev=7e-20, 25% identity; twin-arginine translocation pathway signal complement(580200..582749) Ruegeria sp. TM1040 4077194 YP_612543.1 CDS TM1040_0548 NC_008044.1 582746 585754 R 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 complement(582746..585754) Ruegeria sp. TM1040 4077195 YP_612544.1 CDS TM1040_0549 NC_008044.1 586629 587639 D KEGG: rsp:RSP_3343 glycosyl transferase, ev=1e-06, 27% identity; hypothetical protein 586629..587639 Ruegeria sp. TM1040 4077900 YP_612545.1 CDS TM1040_0550 NC_008044.1 587652 588155 R PFAM: regulatory protein, MarR: (1.3e-15); KEGG: pha:PSHAa2967 transcriptional regulator, ev=6e-29, 39% identity; MarR family transcriptional regulator complement(587652..588155) Ruegeria sp. TM1040 4077901 YP_612546.1 CDS TM1040_0551 NC_008044.1 588383 588934 D 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 588383..588934 Ruegeria sp. TM1040 4077902 YP_612547.1 CDS TM1040_0552 NC_008044.1 588982 590268 D catalyzes the reversible formation of diaminobutyrate and 2-oxoglutarate from glutamate and L-aspartic beta-semialdehyde; diaminobutyrate--2-oxoglutarate aminotransferase 588982..590268 Ruegeria sp. TM1040 4077903 YP_612548.1 CDS ectC NC_008044.1 590293 590685 D N-acetyldiaminobutyrate dehydratase; catalyzes the formation of the osmoprotectant ecotoine from gamma-N-acetyl-alpha,gamma-diaminobutyric acid; L-ectoine synthase 590293..590685 Ruegeria sp. TM1040 4077904 YP_612549.1 CDS TM1040_0554 NC_008044.1 590711 592147 D catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP; aspartate kinase 590711..592147 Ruegeria sp. TM1040 4077905 YP_612550.1 CDS TM1040_0555 NC_008044.1 592559 593632 R Catalyzes the cycloisomerization of cis,cis-muconate; 3-carboxy-cis,cis-muconate cycloisomerase complement(592559..593632) Ruegeria sp. TM1040 4077906 YP_612551.1 CDS TM1040_0556 NC_008044.1 593672 594505 R PFAM: protein of unknown function DUF849: (1e-49); KEGG: sil:SPOA0042 hypothetical protein, ev=1e-130, 79% identity; hypothetical protein complement(593672..594505) Ruegeria sp. TM1040 4077907 YP_612552.1 CDS TM1040_0557 NC_008044.1 594515 595132 R 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 complement(594515..595132) Ruegeria sp. TM1040 4077908 YP_612553.1 CDS TM1040_0558 NC_008044.1 595135 595857 R 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 complement(595135..595857) Ruegeria sp. TM1040 4077909 YP_612554.1 CDS TM1040_0559 NC_008044.1 595854 596258 R 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 complement(595854..596258) Ruegeria sp. TM1040 4077910 YP_612555.1 CDS TM1040_0560 NC_008044.1 596251 597039 R 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 complement(596251..597039) Ruegeria sp. TM1040 4077911 YP_612556.1 CDS TM1040_0561 NC_008044.1 597039 598208 R catalyzes the formation of protocatechuate from 4-hydroxybenzoate; 4-hydroxybenzoate 3-monooxygenase complement(597039..598208) Ruegeria sp. TM1040 4077912 YP_612557.1 CDS TM1040_0562 NC_008044.1 598290 599228 D 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 598290..599228 Ruegeria sp. TM1040 4077913 YP_612558.1 CDS TM1040_0563 NC_008044.1 599575 600474 D 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 599575..600474 Ruegeria sp. TM1040 4077914 YP_612559.1 CDS TM1040_0564 NC_008044.1 600959 602131 R PFAM: peptidase M19, renal dipeptidase: (1.6e-57); KEGG: sil:SPO1410 renal dipeptidase family protein, ev=1e-141, 64% identity; peptidase M19 complement(600959..602131) Ruegeria sp. TM1040 4077915 YP_612560.1 CDS TM1040_0565 NC_008044.1 602298 603287 D PFAM: oxidoreductase-like: (3.4e-35) Oxidoreductase-like: (0.00051); KEGG: jan:Jann_3398 oxidoreductase-like, ev=6e-79, 51% identity; oxidoreductase-like 602298..603287 Ruegeria sp. TM1040 4077916 YP_612561.1 CDS TM1040_0566 NC_008044.1 603420 603689 D 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 603420..603689 Ruegeria sp. TM1040 4077917 YP_612562.1 CDS TM1040_0567 NC_008044.1 603693 604196 R PFAM: GCN5-related N-acetyltransferase: (0.00014); KEGG: hch:HCH_03525 histone acetyltransferase HPA2/related acetyltransferase, ev=7e-21, 39% identity; N-acetyltransferase GCN5 complement(603693..604196) Ruegeria sp. TM1040 4077918 YP_612563.1 CDS TM1040_0568 NC_008044.1 604197 605432 R 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 complement(604197..605432) Ruegeria sp. TM1040 4077919 YP_612564.1 CDS TM1040_0569 NC_008044.1 605508 607328 R 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 complement(605508..607328) Ruegeria sp. TM1040 4076134 YP_612565.1 CDS TM1040_0570 NC_008044.1 607521 608468 R PFAM: alpha/beta hydrolase fold: (6.4e-06); KEGG: sil:SPO1414 hydrolase, alpha/beta fold family, ev=5e-98, 58% identity; alpha/beta hydrolase complement(607521..608468) Ruegeria sp. TM1040 4076135 YP_612566.1 CDS TM1040_0571 NC_008044.1 608489 608803 R PFAM: Sterol-binding: (3e-09); KEGG: sil:SPO1415 sterol carrier family protein, ev=1e-33, 73% identity; sterol-binding complement(608489..608803) Ruegeria sp. TM1040 4076136 YP_612567.1 CDS TM1040_0572 NC_008044.1 608877 609461 D 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 608877..609461 Ruegeria sp. TM1040 4076137 YP_612568.1 CDS TM1040_0573 NC_008044.1 609547 612501 D PFAM: helicase-like: (9e-12); KEGG: sil:SPO1417 helicase, , ev=0.0, 76% identity; helicase-like protein 609547..612501 Ruegeria sp. TM1040 4076138 YP_612569.1 CDS TM1040_0574 NC_008044.1 612509 612883 D PFAM: RNA-binding S4: (1.2e-14); KEGG: jan:Jann_3310 RNA-binding S4, ev=8e-30, 62% identity; RNA-binding protein S4 612509..612883 Ruegeria sp. TM1040 4076139 YP_612570.1 CDS TM1040_0575 NC_008044.1 612951 613289 D 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 612951..613289 Ruegeria sp. TM1040 4076140 YP_612571.1 CDS TM1040_0576 NC_008044.1 613567 614076 D PFAM: transcription factor CarD: (6.8e-33); KEGG: sil:SPO1420 transcriptional regulator, CarD family, ev=9e-83, 92% identity; CarD family transcriptional regulator 613567..614076 Ruegeria sp. TM1040 4076141 YP_612572.1 CDS TM1040_0577 NC_008044.1 614143 614895 R 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 complement(614143..614895) Ruegeria sp. TM1040 4076142 YP_612573.1 CDS cobT NC_008044.1 614997 616007 D catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide and 5,6-dimethylbenzimidazole; nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase 614997..616007 Ruegeria sp. TM1040 4076143 YP_612574.1 CDS TM1040_0579 NC_008044.1 616034 617911 R 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 complement(616034..617911) Ruegeria sp. TM1040 4076144 YP_612575.1 CDS TM1040_0580 NC_008044.1 618069 619292 R KEGG: bba:Bd1322 sensory protein, ev=2e-41, 29% identity; hypothetical protein complement(618069..619292) Ruegeria sp. TM1040 4076145 YP_612576.1 CDS TM1040_0581 NC_008044.1 619356 619811 R PFAM: regulatory proteins, AsnC/Lrp: (1e-25); KEGG: sil:SPO1425 transcriptional regulator, AsnC family, ev=5e-56, 70% identity; AsnC family transcriptional regulator complement(619356..619811) Ruegeria sp. TM1040 4076146 YP_612577.1 CDS TM1040_0582 NC_008044.1 619950 621050 D 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 619950..621050 Ruegeria sp. TM1040 4076147 YP_612578.1 CDS TM1040_0583 NC_008044.1 621175 623808 R KEGG: sil:SPO1427 hypothetical protein, ev=1e-132, 39% identity; hypothetical protein complement(621175..623808) Ruegeria sp. TM1040 4076148 YP_612579.1 CDS TM1040_0584 NC_008044.1 624063 624779 D PFAM: protein of unknown function DUF541: (7.6e-53); KEGG: sil:SPO1429 outer membrane protein, 28Kda, ev=5e-35, 40% identity; hypothetical protein 624063..624779 Ruegeria sp. TM1040 4076149 YP_612580.1 CDS TM1040_0585 NC_008044.1 624873 626165 R 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 complement(624873..626165) Ruegeria sp. TM1040 4076150 YP_612581.1 CDS TM1040_0586 NC_008044.1 626316 627305 R KEGG: sil:SPO1769 hypothetical protein, ev=1e-138, 70% identity; hypothetical protein complement(626316..627305) Ruegeria sp. TM1040 4076151 YP_612582.1 CDS TM1040_0587 NC_008044.1 627404 628279 R KEGG: sil:SPO1034 hypothetical protein, ev=9e-73, 45% identity; hypothetical protein complement(627404..628279) Ruegeria sp. TM1040 4076152 YP_612583.1 CDS TM1040_0588 NC_008044.1 628389 628832 R PFAM: MaoC-like dehydratase: (2.4e-37); KEGG: sil:SPO3152 MaoC domain protein, ev=2e-69, 85% identity; MaoC-like dehydratase complement(628389..628832) Ruegeria sp. TM1040 4078626 YP_612584.1 CDS TM1040_0589 NC_008044.1 629035 629910 R 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 complement(629035..629910) Ruegeria sp. TM1040 4078627 YP_612585.1 CDS TM1040_0590 NC_008044.1 630062 632194 R 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 complement(630062..632194) Ruegeria sp. TM1040 4078628 YP_612586.1 CDS TM1040_0591 NC_008044.1 632483 633289 D PFAM: peptidase M48, Ste24p: (2.3e-07); KEGG: sil:SPO0939 peptidase, M48 family, ev=8e-32, 36% identity; peptidase M48, Ste24p 632483..633289 Ruegeria sp. TM1040 4078629 YP_612587.1 CDS TM1040_0592 NC_008044.1 633408 634328 R catalyzes the hydrolysis of pyrophosphate to phosphate; manganese-dependent inorganic pyrophosphatase complement(633408..634328) Ruegeria sp. TM1040 4078630 YP_612588.1 CDS TM1040_0593 NC_008044.1 634464 635525 R PFAM: GumN: (1.1e-10); KEGG: sil:SPO3145 GumN family protein, ev=3e-80, 49% identity; GumN protein complement(634464..635525) Ruegeria sp. TM1040 4078631 YP_612589.1 CDS TM1040_0594 NC_008044.1 635522 636592 R PFAM: GumN: (2.4e-29); KEGG: sil:SPO3146 GumN family protein, ev=7e-55, 39% identity; GumN protein complement(635522..636592) Ruegeria sp. TM1040 4078632 YP_612590.1 CDS TM1040_0595 NC_008044.1 636662 637360 D KEGG: sil:SPO3144 hypothetical protein, ev=4e-84, 68% identity; hypothetical protein 636662..637360 Ruegeria sp. TM1040 4078633 YP_612591.1 CDS groES NC_008044.1 637635 637922 D 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 637635..637922 Ruegeria sp. TM1040 4078634 YP_612592.1 CDS groEL NC_008044.1 637983 639626 D 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 637983..639626 Ruegeria sp. TM1040 4078635 YP_612593.1 CDS TM1040_0598 NC_008044.1 639694 639996 D hypothetical protein 639694..639996 Ruegeria sp. TM1040 4078636 YP_612594.1 CDS TM1040_0599 NC_008044.1 640194 640463 D hypothetical protein 640194..640463 Ruegeria sp. TM1040 4078637 YP_612595.1 CDS TM1040_0600 NC_008044.1 640633 641526 D PFAM: protein of unknown function DUF6, transmembrane: (7.8e-13); KEGG: sil:SPO0889 membrane protein, , ev=2e-70, 54% identity; hypothetical protein 640633..641526 Ruegeria sp. TM1040 4078638 YP_612596.1 CDS TM1040_0601 NC_008044.1 641536 642342 D KEGG: sil:SPO0890 lipase, , ev=4e-78, 63% identity; lipase 641536..642342 Ruegeria sp. TM1040 4078639 YP_612597.1 CDS TM1040_0602 NC_008044.1 642346 643503 D PFAM: amidohydrolase: (0.0053) Amidohydrolase 3: (0.00054); KEGG: sil:SPO0891 alkylphosphonate utilization protein PhnM, , ev=1e-144, 68% identity; amidohydrolase 642346..643503 Ruegeria sp. TM1040 4078640 YP_612598.1 CDS TM1040_0603 NC_008044.1 643704 644801 R With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway; phosphoribosylaminoimidazole carboxylase ATPase subunit complement(643704..644801) Ruegeria sp. TM1040 4078641 YP_612599.1 CDS TM1040_0604 NC_008044.1 644794 645282 R 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 complement(644794..645282) Ruegeria sp. TM1040 4078642 YP_612600.1 CDS TM1040_0605 NC_008044.1 645532 646422 D 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 645532..646422 Ruegeria sp. TM1040 4078643 YP_612601.1 CDS TM1040_0606 NC_008044.1 646512 646958 D PFAM: glutathione-dependent formaldehyde-activating, GFA: (4.9e-13); KEGG: ccr:CC1514 hypothetical protein, ev=9e-20, 44% identity; glutathione-dependent formaldehyde-activating protein 646512..646958 Ruegeria sp. TM1040 4078644 YP_612602.1 CDS TM1040_0607 NC_008044.1 646940 647470 R KEGG: mth:MTH293 hypothetical protein, ev=8e-40, 49% identity; hypothetical protein complement(646940..647470) Ruegeria sp. TM1040 4078645 YP_612603.1 CDS TM1040_0608 NC_008044.1 647574 649058 R PFAM: phosphate transporter: (2.3e-127); KEGG: sil:SPO0967 phosphate transporter family protein, ev=0.0, 72% identity; phosphate transporter complement(647574..649058) Ruegeria sp. TM1040 4078121 YP_612604.1 CDS TM1040_0609 NC_008044.1 649309 649533 R KEGG: sil:SPO0896 hypothetical protein, ev=7e-20, 66% identity; hypothetical protein complement(649309..649533) Ruegeria sp. TM1040 4078122 YP_612605.1 CDS TM1040_0610 NC_008044.1 649537 649950 R 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 complement(649537..649950) Ruegeria sp. TM1040 4078123 YP_612606.1 CDS TM1040_0611 NC_008044.1 650146 650370 D PFAM: protein of unknown function DUF465: (5.9e-08); KEGG: sil:SPO0894 hypothetical protein, ev=3e-24, 75% identity; hypothetical protein 650146..650370 Ruegeria sp. TM1040 4078124 YP_612607.1 CDS TM1040_0612 NC_008044.1 650528 652246 R 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 complement(650528..652246) Ruegeria sp. TM1040 4078125 YP_612608.1 CDS TM1040_0613 NC_008044.1 652460 654220 R 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 complement(652460..654220) Ruegeria sp. TM1040 4078126 YP_612609.1 CDS TM1040_0614 NC_008044.1 654406 655347 R 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 complement(654406..655347) Ruegeria sp. TM1040 4078127 YP_612610.1 CDS TM1040_0615 NC_008044.1 655592 656092 D PFAM: regulatory proteins, AsnC/Lrp: (5.6e-22); KEGG: sil:SPO0904 leucine-responsive regulatory protein, , ev=7e-80, 89% identity; AsnC family transcriptional regulator 655592..656092 Ruegeria sp. TM1040 4078128 YP_612611.1 CDS TM1040_0616 NC_008044.1 656123 656890 R KEGG: sil:SPO0905 hypothetical protein, ev=7e-86, 60% identity; hypothetical protein complement(656123..656890) Ruegeria sp. TM1040 4078129 YP_612612.1 CDS TM1040_0617 NC_008044.1 657064 657369 D hypothetical protein 657064..657369 Ruegeria sp. TM1040 4078130 YP_612613.1 CDS TM1040_0618 NC_008044.1 657574 658341 R PFAM: protein of unknown function DUF152: (2e-55); KEGG: sil:SPO0906 conserved hypothetical protein TIGR00726, ev=8e-98, 70% identity; hypothetical protein complement(657574..658341) Ruegeria sp. TM1040 4078131 YP_612614.1 CDS TM1040_0619 NC_008044.1 658338 659411 R PFAM: protein of unknown function DUF185: (5.6e-45); KEGG: sil:SPO0907 hypothetical protein, ev=1e-136, 68% identity; hypothetical protein complement(658338..659411) Ruegeria sp. TM1040 4078132 YP_612615.1 CDS TM1040_0620 NC_008044.1 659408 660316 R transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein; prolipoprotein diacylglyceryl transferase complement(659408..660316) Ruegeria sp. TM1040 4078133 YP_612616.1 CDS TM1040_0621 NC_008044.1 660413 660676 D PFAM: protein of unknown function DUF526: (8.4e-17); KEGG: sil:SPO0909 hypothetical protein, ev=2e-33, 89% identity; hypothetical protein 660413..660676 Ruegeria sp. TM1040 4078134 YP_612617.1 CDS TM1040_0622 NC_008044.1 661243 661743 D KEGG: sil:SPO0910 hypothetical protein, ev=8e-73, 75% identity; hypothetical protein 661243..661743 Ruegeria sp. TM1040 4078135 YP_612618.1 CDS TM1040_0623 NC_008044.1 661804 662619 D catalyzes the formation of L-proline from pyrroline-5-carboxylate; pyrroline-5-carboxylate reductase 661804..662619 Ruegeria sp. TM1040 4078136 YP_612619.1 CDS TM1040_0624 NC_008044.1 662612 662962 D 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 662612..662962 Ruegeria sp. TM1040 4078137 YP_612620.1 CDS TM1040_0625 NC_008044.1 662962 663930 D 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 662962..663930 Ruegeria sp. TM1040 4078138 YP_612621.1 CDS TM1040_0626 NC_008044.1 664038 664640 R catalyzes the formation of thymidine 5'-phosphate from thymidine; thymidine kinase complement(664038..664640) Ruegeria sp. TM1040 4078139 YP_612622.1 CDS TM1040_0627 NC_008044.1 665179 665640 D KEGG: sil:SPO0915 hypothetical protein, ev=4e-65, 82% identity; hypothetical protein 665179..665640 Ruegeria sp. TM1040 4076114 YP_612623.1 CDS TM1040_0628 NC_008044.1 665754 666878 R 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 complement(665754..666878) Ruegeria sp. TM1040 4076115 YP_612624.1 CDS TM1040_0629 NC_008044.1 667095 667577 D PFAM: regulatory protein, MarR: (6.5e-10); KEGG: sil:SPO0919 transcriptional regulator, MarR family, ev=2e-27, 46% identity; MarR family transcriptional regulator 667095..667577 Ruegeria sp. TM1040 4076116 YP_612625.1 CDS TM1040_0630 NC_008044.1 667574 668647 D TIGRFAM: Secretion protein HlyD: (1.3e-48); KEGG: sil:SPO0920 efflux transporter, RND family, MFP subunit, ev=1e-98, 57% identity; secretion protein HlyD 667574..668647 Ruegeria sp. TM1040 4076117 YP_612626.1 CDS TM1040_0631 NC_008044.1 668659 671709 D PFAM: acriflavin resistance protein: (9.5e-69); KEGG: sil:SPO0921 transporter, AcrB/AcrD/AcrF family, ev=0.0, 72% identity; acriflavin resistance protein 668659..671709 Ruegeria sp. TM1040 4076118 YP_612627.1 CDS carB NC_008044.1 672273 675635 R 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 complement(672273..675635) Ruegeria sp. TM1040 4076119 YP_612628.1 CDS TM1040_0633 NC_008044.1 675784 676980 D catalyzes the formation of 4-amino-4-deoxychorismate from chorismate and glutamine; aminodeoxychorismate synthase 675784..676980 Ruegeria sp. TM1040 4076120 YP_612629.1 CDS TM1040_0634 NC_008044.1 676977 677582 D KEGG: sil:SPO0925 4-amino-4-deoxychorismate lyase, ev=7e-56, 53% identity; hypothetical protein 676977..677582 Ruegeria sp. TM1040 4076121 YP_612630.1 CDS aspS NC_008044.1 677748 679532 D 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 677748..679532 Ruegeria sp. TM1040 4076122 YP_612631.1 CDS TM1040_0636 NC_008044.1 680127 680846 R PFAM: response regulator receiver: (7e-21); KEGG: sil:SPO0931 response regulator, ev=6e-82, 66% identity; response regulator receiver protein complement(680127..680846) Ruegeria sp. TM1040 4076123 YP_612632.1 CDS TM1040_0637 NC_008044.1 681032 681436 D 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 681032..681436 Ruegeria sp. TM1040 4076124 YP_612633.1 CDS TM1040_0638 NC_008044.1 681506 681781 D KEGG: sil:SPO0933 hypothetical protein, ev=2e-29, 67% identity; hypothetical protein 681506..681781 Ruegeria sp. TM1040 4076125 YP_612634.1 CDS TM1040_0639 NC_008044.1 681912 682865 R 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 complement(681912..682865) Ruegeria sp. TM1040 4076126 YP_612635.1 CDS TM1040_0640 NC_008044.1 683422 683763 R PFAM: protein of unknown function DUF427: (5.6e-28); KEGG: sil:SPO2858 hypothetical protein, ev=3e-41, 72% identity; hypothetical protein complement(683422..683763) Ruegeria sp. TM1040 4076127 YP_612636.1 CDS TM1040_0641 NC_008044.1 683825 685609 R PFAM: peptidase M24: (3.3e-09); KEGG: sil:SPO2857 metallopeptidase, family M24, ev=0.0, 70% identity; peptidase M24 complement(683825..685609) Ruegeria sp. TM1040 4076128 YP_612637.1 CDS TM1040_0642 NC_008044.1 686000 687877 R 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 complement(686000..687877) Ruegeria sp. TM1040 4076129 YP_612638.1 CDS TM1040_0643 NC_008044.1 688037 689023 R 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 complement(688037..689023) Ruegeria sp. TM1040 4076130 YP_612639.1 CDS TM1040_0644 NC_008044.1 689252 689851 R KEGG: sil:SPO2852 CzcN domain protein, ev=2e-77, 68% identity; CzcN domain-containing protein complement(689252..689851) Ruegeria sp. TM1040 4076131 YP_612640.1 CDS TM1040_0645 NC_008044.1 690169 690795 R PFAM: heat shock protein DnaJ-like: (8.6e-06); KEGG: sil:SPO2850 DnaJ domain protein, ev=1e-106, 86% identity; molecular chaperone DnaJ complement(690169..690795) Ruegeria sp. TM1040 4076132 YP_612641.1 CDS TM1040_0646 NC_008044.1 690913 691167 D PFAM: BolA-like protein: (5.9e-13); KEGG: sil:SPO2849 BolA protein, truncation, ev=1e-24, 65% identity; BolA-like protein 690913..691167 Ruegeria sp. TM1040 4076133 YP_612642.1 CDS TM1040_0647 NC_008044.1 691219 691788 R KEGG: sil:SPO2848 hypothetical protein, ev=4e-30, 53% identity; hypothetical protein complement(691219..691788) Ruegeria sp. TM1040 4078160 YP_612643.1 CDS TM1040_0648 NC_008044.1 691865 693112 R catalyzes the release of the N-terminal amino acid from a tripeptide; peptidase T complement(691865..693112) Ruegeria sp. TM1040 4078161 YP_612644.1 CDS rimO NC_008044.1 693219 694622 R catalyzes the methylthiolation of an aspartic acid residue of the S12 protein of the 30S ribosomal subunit; 30S ribosomal protein S12 methylthiotransferase complement(693219..694622) Ruegeria sp. TM1040 4078162 YP_612645.1 CDS TM1040_0650 NC_008044.1 694800 696089 D KEGG: mba:Mbar_A0126 hypothetical protein, ev=6e-07, 30% identity; hypothetical protein 694800..696089 Ruegeria sp. TM1040 4078163 YP_612646.1 CDS TM1040_0651 NC_008044.1 696203 698143 D PFAM: AsmA: (2.4e-07); KEGG: sil:SPO0945 AsmA family protein, ev=1e-138, 41% identity; AsmA protein 696203..698143 Ruegeria sp. TM1040 4078164 YP_612647.1 CDS TM1040_0652 NC_008044.1 698293 699789 R 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 complement(698293..699789) Ruegeria sp. TM1040 4078165 YP_612648.1 CDS TM1040_0653 NC_008044.1 699813 700646 R 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 complement(699813..700646) Ruegeria sp. TM1040 4078166 YP_612649.1 CDS TM1040_0654 NC_008044.1 700651 702408 R KEGG: sil:SPO0948 capsular polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family, ev=1e-136, 65% identity; capsule polysaccharide export protein complement(700651..702408) Ruegeria sp. TM1040 4078167 YP_612650.1 CDS TM1040_0655 NC_008044.1 702386 703045 R 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 complement(702386..703045) Ruegeria sp. TM1040 4078168 YP_612651.1 CDS TM1040_0656 NC_008044.1 703380 703982 D PFAM: Uracil-DNA glycosylase superfamily: (5.3e-05); KEGG: sil:SPO0950 uracil-DNA glycosylase, , ev=1e-80, 72% identity; uracil-DNA glycosylase 703380..703982 Ruegeria sp. TM1040 4078169 YP_612652.1 CDS TM1040_0657 NC_008044.1 703975 704766 D KEGG: sil:SPO0951 hypothetical protein, ev=2e-89, 66% identity; hypothetical protein 703975..704766 Ruegeria sp. TM1040 4078170 YP_612653.1 CDS TM1040_0658 NC_008044.1 704912 705784 R YghU; B2989; one of eight glutathione transferase proteins from E. coli; glutathione S-transferase complement(704912..705784) Ruegeria sp. TM1040 4078171 YP_612654.1 CDS TM1040_0659 NC_008044.1 706043 706831 D PFAM: protein of unknown function DUF88: (0.0004); KEGG: jan:Jann_0048 protein of unknown function DUF88, ev=3e-85, 64% identity; hypothetical protein 706043..706831 Ruegeria sp. TM1040 4078172 YP_612655.1 CDS TM1040_0660 NC_008044.1 706831 707241 D KEGG: bja:blr5357 hypothetical protein, ev=3e-22, 50% identity; hypothetical protein 706831..707241 Ruegeria sp. TM1040 4078173 YP_612656.1 CDS TM1040_0661 NC_008044.1 707349 707921 D KEGG: sil:SPO0954 hypothetical protein, ev=6e-69, 72% identity; hypothetical protein 707349..707921 Ruegeria sp. TM1040 4078174 YP_612657.1 CDS TM1040_0662 NC_008044.1 708098 708688 R PFAM: GcrA cell cycle regulator: (2.2e-57); KEGG: sil:SPO0956 hypothetical protein, ev=3e-86, 81% identity; GcrA cell cycle regulator complement(708098..708688) Ruegeria sp. TM1040 4078175 YP_612658.1 CDS TM1040_0663 NC_008044.1 708878 709702 D PFAM: ABC-2 type transporter: (4.4e-32); KEGG: sil:SPO0957 ABC transporter, permease protein, ev=1e-111, 74% identity; ABC transporter 708878..709702 Ruegeria sp. TM1040 4078176 YP_612659.1 CDS TM1040_0664 NC_008044.1 709699 710691 R PFAM: protein of unknown function DUF6, transmembrane: (2.7e-15); KEGG: sil:SPO0959 membrane protein, , ev=1e-108, 69% identity; hypothetical protein complement(709699..710691) Ruegeria sp. TM1040 4078177 YP_612660.1 CDS argD NC_008044.1 710999 712174 D 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 710999..712174 Ruegeria sp. TM1040 4078178 YP_612661.1 CDS TM1040_0666 NC_008044.1 712251 713177 D catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation; ornithine carbamoyltransferase 712251..713177 Ruegeria sp. TM1040 4077274 YP_612662.1 CDS TM1040_0667 NC_008044.1 713370 714860 R PFAM: phosphate transporter: (1e-105); KEGG: sil:SPO0967 phosphate transporter family protein, ev=1e-143, 53% identity; phosphate transporter complement(713370..714860) Ruegeria sp. TM1040 4077275 YP_612663.1 CDS TM1040_0668 NC_008044.1 714982 715449 R PFAM: NUDIX hydrolase: (3.6e-17); KEGG: sil:SPO0968 hydrolase, NUDIX family, ev=2e-45, 58% identity; NUDIX hydrolase complement(714982..715449) Ruegeria sp. TM1040 4077276 YP_612664.1 CDS TM1040_0669 NC_008044.1 715629 718154 R 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 complement(715629..718154) Ruegeria sp. TM1040 4077277 YP_612665.1 CDS TM1040_0670 NC_008044.1 718401 719402 D 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 718401..719402 Ruegeria sp. TM1040 4077278 YP_612666.1 CDS rpmB NC_008044.1 719704 719994 D required for 70S ribosome assembly; 50S ribosomal protein L28 719704..719994 Ruegeria sp. TM1040 4077279 YP_612667.1 CDS TM1040_0672 NC_008044.1 720156 720500 D KEGG: sil:SPO0975 hypothetical protein, ev=9e-12, 39% identity; hypothetical protein 720156..720500 Ruegeria sp. TM1040 4077280 YP_612668.1 CDS TM1040_0673 NC_008044.1 720577 721068 D PFAM: protein of unknown function DUF461: (4e-38); KEGG: sil:SPO0976 hypothetical protein, ev=4e-38, 57% identity; hypothetical protein 720577..721068 Ruegeria sp. TM1040 4077281 YP_612669.1 CDS TM1040_0674 NC_008044.1 721127 721825 R Modulates the activities of several enzymes which are inactive in their acetylated form; NAD-dependent deacetylase complement(721127..721825) Ruegeria sp. TM1040 4077282 YP_612670.1 CDS TM1040_0675 NC_008044.1 721940 722389 D 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 721940..722389 Ruegeria sp. TM1040 4077283 YP_612671.1 CDS TM1040_0676 NC_008044.1 722497 723462 R 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 complement(722497..723462) Ruegeria sp. TM1040 4077284 YP_612672.1 CDS TM1040_0677 NC_008044.1 723729 724040 R KEGG: rsp:RSP_2018 hypothetical protein, ev=7e-18, 50% identity; hypothetical protein complement(723729..724040) Ruegeria sp. TM1040 4077285 YP_612673.1 CDS TM1040_0678 NC_008044.1 724251 726050 D binds to the ribosome on the universally-conserved alpha-sarcin loop; GTP-binding protein LepA 724251..726050 Ruegeria sp. TM1040 4077286 YP_612674.1 CDS murD NC_008044.1 726193 727596 D 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 726193..727596 Ruegeria sp. TM1040 4077287 YP_612675.1 CDS TM1040_0680 NC_008044.1 727602 728786 R 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 complement(727602..728786) Ruegeria sp. TM1040 4077288 YP_612676.1 CDS TM1040_0681 NC_008044.1 729001 730170 D 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 729001..730170 Ruegeria sp. TM1040 4077289 YP_612677.1 CDS murG NC_008044.1 730217 731314 D 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 730217..731314 Ruegeria sp. TM1040 4077290 YP_612678.1 CDS murC NC_008044.1 731311 732720 D 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 731311..732720 Ruegeria sp. TM1040 4077291 YP_612679.1 CDS TM1040_0684 NC_008044.1 732884 733126 D KEGG: sil:SPO1198 hypothetical protein, ev=2e-30, 73% identity; hypothetical protein 732884..733126 Ruegeria sp. TM1040 4077292 YP_612680.1 CDS murB NC_008044.1 733268 734194 D catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis; UDP-N-acetylenolpyruvoylglucosamine reductase 733268..734194 Ruegeria sp. TM1040 4077293 YP_612681.1 CDS ddl NC_008044.1 734517 735437 D 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 734517..735437 Ruegeria sp. TM1040 4077353 YP_612682.1 CDS TM1040_0687 NC_008044.1 735425 736324 D PFAM: cell division protein FtsQ: (3.2e-10); KEGG: sil:SPO1202 cell division protein FtsQ, ev=1e-102, 64% identity; cell division protein FtsQ 735425..736324 Ruegeria sp. TM1040 4077354 YP_612683.1 CDS TM1040_0688 NC_008044.1 736308 737660 D PFAM: cell division protein FtsA: (2e-53); KEGG: sil:SPO1203 cell division protein FtsA, ev=0.0, 84% identity; cell division protein FtsA 736308..737660 Ruegeria sp. TM1040 4077355 YP_612684.1 CDS TM1040_0689 NC_008044.1 738085 739758 D 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 738085..739758 Ruegeria sp. TM1040 4077356 YP_612685.1 CDS lpxC NC_008044.1 739957 740904 D 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 739957..740904 Ruegeria sp. TM1040 4077357 YP_612686.1 CDS TM1040_0691 NC_008044.1 741250 742101 D KEGG: sil:SPO1206 competence lipoprotein ComL, , ev=1e-123, 76% identity; competence lipoprotein ComL 741250..742101 Ruegeria sp. TM1040 4077358 YP_612687.1 CDS TM1040_0692 NC_008044.1 742178 743827 D 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 742178..743827 Ruegeria sp. TM1040 4077359 YP_612688.1 CDS TM1040_0693 NC_008044.1 743914 745608 D 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 743914..745608 Ruegeria sp. TM1040 4077360 YP_612689.1 CDS TM1040_0694 NC_008044.1 745727 746419 R KEGG: sil:SPO0934 membrane protein, , ev=2e-85, 72% identity; hypothetical protein complement(745727..746419) Ruegeria sp. TM1040 4077361 YP_612690.1 CDS TM1040_0695 NC_008044.1 746416 746994 R PFAM: nitroreductase: (2.2e-06); KEGG: sil:SPO0935 nitroreductase family protein, ev=9e-78, 73% identity; nitroreductase complement(746416..746994) Ruegeria sp. TM1040 4077362 YP_612691.1 CDS TM1040_0696 NC_008044.1 747262 747540 D PFAM: protein of unknown function DUF167: (2.6e-18); KEGG: sil:SPO0937 hypothetical protein, ev=2e-20, 56% identity; hypothetical protein 747262..747540 Ruegeria sp. TM1040 4077363 YP_612692.1 CDS TM1040_0697 NC_008044.1 747648 747890 R KEGG: sil:SPO0938 hypothetical protein, ev=9e-29, 81% identity; hypothetical protein complement(747648..747890) Ruegeria sp. TM1040 4077364 YP_612693.1 CDS TM1040_0698 NC_008044.1 748019 748678 D PFAM: peptidase M48, Ste24p: (2.8e-08); KEGG: sil:SPO0939 peptidase, M48 family, ev=7e-57, 49% identity; peptidase M48, Ste24p 748019..748678 Ruegeria sp. TM1040 4077365 YP_612694.1 CDS TM1040_0699 NC_008044.1 748689 749069 D PFAM: protein of unknown function UPF0029: (4.7e-17); KEGG: sil:SPO0940 hypothetical protein, ev=1e-49, 84% identity; hypothetical protein 748689..749069 Ruegeria sp. TM1040 4077366 YP_612695.1 CDS TM1040_0700 NC_008044.1 749165 749440 D KEGG: sil:SPO0941 hypothetical protein, ev=1e-12, 46% identity; hypothetical protein 749165..749440 Ruegeria sp. TM1040 4077367 YP_612696.1 CDS gatB NC_008044.1 749516 751024 R 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 complement(749516..751024) Ruegeria sp. TM1040 4077368 YP_612697.1 CDS TM1040_0702 NC_008044.1 751184 751918 R 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 complement(751184..751918) Ruegeria sp. TM1040 4077369 YP_612698.1 CDS TM1040_0703 NC_008044.1 752089 754533 D 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 752089..754533 Ruegeria sp. TM1040 4077370 YP_612699.1 CDS TM1040_0704 NC_008044.1 754656 756002 R KEGG: sil:SPO2845 hypothetical protein, ev=2e-89, 45% identity; hypothetical protein complement(754656..756002) Ruegeria sp. TM1040 4077371 YP_612700.1 CDS TM1040_0705 NC_008044.1 756188 756643 R KEGG: sil:SPO2843 hypothetical protein, ev=3e-18, 40% identity; hypothetical protein complement(756188..756643) Ruegeria sp. TM1040 4076982 YP_612701.1 CDS pepN NC_008044.1 756633 759197 R 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 complement(756633..759197) Ruegeria sp. TM1040 4076983 YP_612702.1 CDS TM1040_0707 NC_008044.1 759629 761062 R 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 complement(759629..761062) Ruegeria sp. TM1040 4076984 YP_612703.1 CDS pntA NC_008044.1 761076 762650 R 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 complement(761076..762650) Ruegeria sp. TM1040 4076985 YP_612704.1 CDS TM1040_0709 NC_008044.1 762745 762972 D hypothetical protein 762745..762972 Ruegeria sp. TM1040 4076986 YP_612705.1 CDS TM1040_0710 NC_008044.1 762988 763779 R PFAM: peptidase C26: (1.1e-79); KEGG: sil:SPO2837 hypothetical protein, ev=1e-117, 81% identity; peptidase C26 complement(762988..763779) Ruegeria sp. TM1040 4076987 YP_612706.1 CDS TM1040_0711 NC_008044.1 763923 766052 R catalyzes the formation of malate from glyoxylate and acetyl-CoA; malate synthase G complement(763923..766052) Ruegeria sp. TM1040 4076988 YP_612707.1 CDS TM1040_0712 NC_008044.1 766372 767652 D KEGG: sil:SPO2818 hypothetical protein, ev=1e-158, 66% identity; hypothetical protein 766372..767652 Ruegeria sp. TM1040 4076989 YP_612708.1 CDS TM1040_0713 NC_008044.1 767742 768734 R 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 complement(767742..768734) Ruegeria sp. TM1040 4076990 YP_612709.1 CDS TM1040_0714 NC_008044.1 768727 769734 R 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 complement(768727..769734) Ruegeria sp. TM1040 4076991 YP_612710.1 CDS TM1040_0715 NC_008044.1 769931 771628 R 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 complement(769931..771628) Ruegeria sp. TM1040 4076992 YP_612711.1 CDS TM1040_0716 NC_008044.1 771989 773809 D 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 771989..773809 Ruegeria sp. TM1040 4076993 YP_612712.1 CDS TM1040_0717 NC_008044.1 773813 774979 D catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine; acetylornithine deacetylase 773813..774979 Ruegeria sp. TM1040 4076994 YP_612713.1 CDS TM1040_0718 NC_008044.1 775182 776354 D 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 775182..776354 Ruegeria sp. TM1040 4076995 YP_612714.1 CDS TM1040_0719 NC_008044.1 776435 777598 D 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 776435..777598 Ruegeria sp. TM1040 4076996 YP_612715.1 CDS TM1040_0720 NC_008044.1 777706 778089 R hypothetical protein complement(777706..778089) Ruegeria sp. TM1040 4076997 YP_612716.1 CDS TM1040_0721 NC_008044.1 778374 778766 R hypothetical protein complement(778374..778766) Ruegeria sp. TM1040 4076998 YP_612717.1 CDS TM1040_0722 NC_008044.1 779020 780093 R 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 complement(779020..780093) Ruegeria sp. TM1040 4076999 YP_612718.1 CDS TM1040_0723 NC_008044.1 780104 781408 R 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 complement(780104..781408) Ruegeria sp. TM1040 4077000 YP_612719.1 CDS moaA NC_008044.1 781420 782427 R together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z; molybdenum cofactor biosynthesis protein A complement(781420..782427) Ruegeria sp. TM1040 4077001 YP_612720.1 CDS TM1040_0725 NC_008044.1 782613 783122 D KEGG: jan:Jann_3286 hypothetical protein, ev=3e-17, 45% identity; hypothetical protein 782613..783122 Ruegeria sp. TM1040 4076095 YP_612721.1 CDS TM1040_0726 NC_008044.1 783149 783826 R KEGG: sil:SPO2798 hypothetical protein, ev=4e-90, 71% identity; hypothetical protein complement(783149..783826) Ruegeria sp. TM1040 4076096 YP_612722.1 CDS TM1040_0727 NC_008044.1 783823 785631 R Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source; glucosamine--fructose-6-phosphate aminotransferase complement(783823..785631) Ruegeria sp. TM1040 4076097 YP_612723.1 CDS glmU NC_008044.1 785636 786985 R 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 complement(785636..786985) Ruegeria sp. TM1040 4076098 YP_612724.1 CDS TM1040_0729 NC_008044.1 787121 787798 D 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 787121..787798 Ruegeria sp. TM1040 4076099 YP_612725.1 CDS TM1040_0730 NC_008044.1 787842 788300 R KEGG: sil:SPO1770 hypothetical protein, ev=1e-41, 60% identity; hypothetical protein complement(787842..788300) Ruegeria sp. TM1040 4076100 YP_612726.1 CDS TM1040_0731 NC_008044.1 788430 789647 D 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 788430..789647 Ruegeria sp. TM1040 4076101 YP_612727.1 CDS TM1040_0732 NC_008044.1 789814 790977 D 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 789814..790977 Ruegeria sp. TM1040 4076102 YP_612728.1 CDS TM1040_0733 NC_008044.1 790985 791335 D hypothetical protein 790985..791335 Ruegeria sp. TM1040 4076103 YP_612729.1 CDS TM1040_0734 NC_008044.1 791464 792066 R PFAM: OmpW: (6.3e-45); KEGG: sil:SPO2792 outer membrane protein OmpW, ev=2e-67, 61% identity; OmpW protein complement(791464..792066) Ruegeria sp. TM1040 4076104 YP_612730.1 CDS TM1040_0735 NC_008044.1 792161 793741 D 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 792161..793741 Ruegeria sp. TM1040 4076105 YP_612731.1 CDS TM1040_0736 NC_008044.1 793741 794145 D hypothetical protein 793741..794145 Ruegeria sp. TM1040 4076106 YP_612732.1 CDS TM1040_0737 NC_008044.1 794142 795746 D PFAM: carboxyl transferase: (1.3e-204); KEGG: sil:SPO2790 methylcrotonyl-CoA carboxylase, beta subunit, ev=0.0, 91% identity; propionyl-CoA carboxylase 794142..795746 Ruegeria sp. TM1040 4076107 YP_612733.1 CDS TM1040_0738 NC_008044.1 795827 797764 D 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 795827..797764 Ruegeria sp. TM1040 4076108 YP_612734.1 CDS TM1040_0739 NC_008044.1 797797 798663 D catalyzes the formation of acetoacetate and acetyl-CoA from 3-hydroxy-3-methylglutaryl-CoA; hydroxymethylglutaryl-CoA lyase 797797..798663 Ruegeria sp. TM1040 4076109 YP_612735.1 CDS TM1040_0740 NC_008044.1 798693 799478 D Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase 798693..799478 Ruegeria sp. TM1040 4076110 YP_612736.1 CDS TM1040_0741 NC_008044.1 799720 800085 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit A 799720..800085 Ruegeria sp. TM1040 4076111 YP_612737.1 CDS TM1040_0742 NC_008044.1 800085 800609 D 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 800085..800609 Ruegeria sp. TM1040 4076112 YP_612738.1 CDS TM1040_0743 NC_008044.1 800625 801230 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit C 800625..801230 Ruegeria sp. TM1040 4076113 YP_612739.1 CDS TM1040_0744 NC_008044.1 801379 802590 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit D 801379..802590 Ruegeria sp. TM1040 4076153 YP_612740.1 CDS TM1040_0745 NC_008044.1 802587 803081 D hypothetical protein 802587..803081 Ruegeria sp. TM1040 4076154 YP_612741.1 CDS TM1040_0746 NC_008044.1 803081 804277 D catalyzes the transfer of electrons from NADH to ubiquinone; NADH dehydrogenase subunit E 803081..804277 Ruegeria sp. TM1040 4076155 YP_612742.1 CDS TM1040_0747 NC_008044.1 804336 804566 D KEGG: sil:SPO2778 hypothetical protein, ev=7e-23, 68% identity; hypothetical protein 804336..804566 Ruegeria sp. TM1040 4076156 YP_612743.1 CDS TM1040_0748 NC_008044.1 804573 805871 D 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 804573..805871 Ruegeria sp. TM1040 4076157 YP_612744.1 CDS TM1040_0749 NC_008044.1 805880 806239 D KEGG: sil:SPO2776 hypothetical protein, ev=3e-14, 38% identity; hypothetical protein 805880..806239 Ruegeria sp. TM1040 4076158 YP_612745.1 CDS TM1040_0750 NC_008044.1 806338 806802 D KEGG: sil:SPO2775 hypothetical protein, ev=4e-27, 44% identity; hypothetical protein 806338..806802 Ruegeria sp. TM1040 4076159 YP_612746.1 CDS TM1040_0751 NC_008044.1 806806 808788 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit G 806806..808788 Ruegeria sp. TM1040 4076160 YP_612747.1 CDS TM1040_0752 NC_008044.1 808785 809177 D KEGG: sil:SPO2773 lipoprotein, , ev=6e-41, 64% identity; lipoprotein 808785..809177 Ruegeria sp. TM1040 4076161 YP_612748.1 CDS TM1040_0753 NC_008044.1 809184 810221 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit H 809184..810221 Ruegeria sp. TM1040 4076162 YP_612749.1 CDS TM1040_0754 NC_008044.1 810223 810717 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit I 810223..810717 Ruegeria sp. TM1040 4076163 YP_612750.1 CDS TM1040_0755 NC_008044.1 810750 811124 D PFAM: Carboxymuconolactone decarboxylase: (1.9e-13); KEGG: sil:SPO2768 4-carboxymuconolactone decarboxylase, , ev=5e-53, 84% identity; carboxymuconolactone decarboxylase 810750..811124 Ruegeria sp. TM1040 4076164 YP_612751.1 CDS TM1040_0756 NC_008044.1 811121 811723 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit J 811121..811723 Ruegeria sp. TM1040 4076165 YP_612752.1 CDS TM1040_0757 NC_008044.1 811738 812043 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit K 811738..812043 Ruegeria sp. TM1040 4076166 YP_612753.1 CDS TM1040_0758 NC_008044.1 812049 814169 D Catalyzes the transfer of electrons from NADH to ubiquinone; NADH dehydrogenase subunit L 812049..814169 Ruegeria sp. TM1040 4076167 YP_612754.1 CDS TM1040_0759 NC_008044.1 814169 815734 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit M 814169..815734 Ruegeria sp. TM1040 4076168 YP_612755.1 CDS TM1040_0760 NC_008044.1 815747 817183 D Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit N 815747..817183 Ruegeria sp. TM1040 4076169 YP_612756.1 CDS TM1040_0761 NC_008044.1 817272 818021 D 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 817272..818021 Ruegeria sp. TM1040 4076170 YP_612757.1 CDS TM1040_0762 NC_008044.1 818036 818818 D 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 818036..818818 Ruegeria sp. TM1040 4076171 YP_612758.1 CDS TM1040_0763 NC_008044.1 818815 820482 D 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 818815..820482 Ruegeria sp. TM1040 4076172 YP_612759.1 CDS TM1040_0764 NC_008044.1 820756 821496 R PFAM: triosephosphate isomerase: (9.1e-116); KEGG: jan:Jann_1733 triosephosphate isomerase, ev=2e-88, 66% identity; triosephosphate isomerase complement(820756..821496) Ruegeria sp. TM1040 4078076 YP_612760.1 CDS TM1040_0765 NC_008044.1 821644 821997 R PFAM: HesB/YadR/YfhF: (1.1e-33); KEGG: sil:SPO2620 iron-sulfur cluster assembly accessory protein, ev=6e-51, 83% identity; HesB/YadR/YfhF complement(821644..821997) Ruegeria sp. TM1040 4078077 YP_612761.1 CDS TM1040_0766 NC_008044.1 822118 822480 R PFAM: protein of unknown function DUF59: (5.3e-26); KEGG: sil:SPO2619 hypothetical protein, ev=3e-55, 80% identity; hypothetical protein complement(822118..822480) Ruegeria sp. TM1040 4078078 YP_612762.1 CDS TM1040_0767 NC_008044.1 822656 822928 R KEGG: sil:SPO2618 hypothetical protein, ev=5e-26, 67% identity; hypothetical protein complement(822656..822928) Ruegeria sp. TM1040 4078079 YP_612763.1 CDS TM1040_0768 NC_008044.1 822928 823815 R PFAM: band 7 protein: (6.5e-61); KEGG: sil:SPO2617 SPFH domain/band 7 family protein, ev=1e-135, 85% identity; hypothetical protein complement(822928..823815) Ruegeria sp. TM1040 4078080 YP_612764.1 CDS TM1040_0769 NC_008044.1 823906 825321 R 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 complement(823906..825321) Ruegeria sp. TM1040 4078081 YP_612765.1 CDS tgt NC_008044.1 825392 826522 D Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr); queuine tRNA-ribosyltransferase 825392..826522 Ruegeria sp. TM1040 4078082 YP_612766.1 CDS TM1040_0771 NC_008044.1 826781 827053 R hypothetical protein complement(826781..827053) Ruegeria sp. TM1040 4078083 YP_612767.1 CDS TM1040_0772 NC_008044.1 827050 827559 R hypothetical protein complement(827050..827559) Ruegeria sp. TM1040 4078084 YP_612768.1 CDS TM1040_0773 NC_008044.1 827885 828559 D 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 827885..828559 Ruegeria sp. TM1040 4078085 YP_612769.1 CDS TM1040_0774 NC_008044.1 828617 828880 D KEGG: sil:SPO2615 NADH-dependent flavin oxidoreductase, Oye family, ev=3e-20, 60% identity; Oye family NADH-dependent flavin oxidoreductase 828617..828880 Ruegeria sp. TM1040 4078086 YP_612770.1 CDS TM1040_0775 NC_008044.1 829194 831602 D 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 829194..831602 Ruegeria sp. TM1040 4078087 YP_612771.1 CDS TM1040_0776 NC_008044.1 832173 833177 R PFAM: phage integrase: (3.2e-24); KEGG: rsp:RSP_3805 possible integrase, ev=9e-93, 54% identity; phage integrase complement(832173..833177) Ruegeria sp. TM1040 4078088 YP_612772.1 CDS TM1040_0777 NC_008044.1 833487 833819 R hypothetical protein complement(833487..833819) Ruegeria sp. TM1040 4078089 YP_612773.1 CDS TM1040_0778 NC_008044.1 833924 834868 R hypothetical protein complement(833924..834868) Ruegeria sp. TM1040 4078090 YP_612774.1 CDS TM1040_0779 NC_008044.1 834865 835524 R KEGG: rsp:RSP_3792 hypothetical protein, ev=2e-76, 59% identity; hypothetical protein complement(834865..835524) Ruegeria sp. TM1040 4078091 YP_612775.1 CDS TM1040_0780 NC_008044.1 835670 836443 R KEGG: bpm:BURPS1710b_1662 gp47, ev=2e-17, 26% identity; hypothetical protein complement(835670..836443) Ruegeria sp. TM1040 4078092 YP_612776.1 CDS TM1040_0781 NC_008044.1 836465 836770 R PFAM: protein of unknown function DUF1364: (2.1e-18); KEGG: ecj:JW0537 hypothetical protein, ev=2e-13, 54% identity; hypothetical protein complement(836465..836770) Ruegeria sp. TM1040 4078093 YP_612777.1 CDS TM1040_0782 NC_008044.1 836839 837342 R hypothetical protein complement(836839..837342) Ruegeria sp. TM1040 4078094 YP_612778.1 CDS TM1040_0783 NC_008044.1 837342 837950 R KEGG: bhe:BH06850 exonuclease, ev=2e-41, 43% identity; exonuclease complement(837342..837950) Ruegeria sp. TM1040 4076055 YP_612779.1 CDS TM1040_0784 NC_008044.1 837950 838672 R PFAM: ERF: (2.6e-12); KEGG: bhe:BH06860 phage related protein, ev=4e-16, 28% identity; hypothetical protein complement(837950..838672) Ruegeria sp. TM1040 4076056 YP_612780.1 CDS TM1040_0785 NC_008044.1 838781 839026 R hypothetical protein complement(838781..839026) Ruegeria sp. TM1040 4076057 YP_612781.1 CDS TM1040_0786 NC_008044.1 839240 839599 R hypothetical protein complement(839240..839599) Ruegeria sp. TM1040 4076058 YP_612782.1 CDS TM1040_0787 NC_008044.1 839907 840665 R hypothetical protein complement(839907..840665) Ruegeria sp. TM1040 4076059 YP_612783.1 CDS TM1040_0788 NC_008044.1 840662 841195 R hypothetical protein complement(840662..841195) Ruegeria sp. TM1040 4076060 YP_612784.1 CDS TM1040_0789 NC_008044.1 841219 841935 R 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 complement(841219..841935) Ruegeria sp. TM1040 4076061 YP_612785.1 CDS TM1040_0790 NC_008044.1 842213 842701 D hypothetical protein 842213..842701 Ruegeria sp. TM1040 4076062 YP_612786.1 CDS TM1040_0791 NC_008044.1 842939 843241 D hypothetical protein 842939..843241 Ruegeria sp. TM1040 4076063 YP_612787.1 CDS TM1040_0792 NC_008044.1 843244 843765 D KEGG: ava:Ava_B0325 hypothetical protein, ev=9e-07, 33% identity; hypothetical protein 843244..843765 Ruegeria sp. TM1040 4076064 YP_612788.1 CDS TM1040_0793 NC_008044.1 843762 844118 D PFAM: endodeoxyribonuclease RusA: (0.008); KEGG: nfa:nfa39720 hypothetical protein, ev=3e-06, 39% identity; endodeoxyribonuclease RusA 843762..844118 Ruegeria sp. TM1040 4076065 YP_612789.1 CDS TM1040_0794 NC_008044.1 844130 844861 D KEGG: bbr:BB1683 phage-related hypothetical protein, ev=1e-15, 38% identity; hypothetical protein 844130..844861 Ruegeria sp. TM1040 4076066 YP_612790.1 CDS TM1040_0795 NC_008044.1 844851 845414 D hypothetical protein 844851..845414 Ruegeria sp. TM1040 4076067 YP_612791.1 CDS TM1040_0796 NC_008044.1 845629 846108 D 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 845629..846108 Ruegeria sp. TM1040 4076068 YP_612792.1 CDS TM1040_0797 NC_008044.1 846108 846362 D hypothetical protein 846108..846362 Ruegeria sp. TM1040 4076069 YP_612793.1 CDS TM1040_0798 NC_008044.1 846385 846966 D hypothetical protein 846385..846966 Ruegeria sp. TM1040 4076070 YP_612794.1 CDS TM1040_0799 NC_008044.1 847447 847725 R hypothetical protein complement(847447..847725) Ruegeria sp. TM1040 4076071 YP_612795.1 CDS TM1040_0800 NC_008044.1 847787 848365 D PFAM: Terminase small subunit: (4.2e-30); KEGG: gox:GOX2458 phage terminase small subunit, ev=3e-25, 45% identity; terminase small subunit 847787..848365 Ruegeria sp. TM1040 4076072 YP_612796.1 CDS TM1040_0801 NC_008044.1 848343 849593 D PFAM: protein of unknown function DUF264: (1.3e-31); KEGG: pfl:PFL_3766 hypothetical protein, ev=1e-117, 52% identity; hypothetical protein 848343..849593 Ruegeria sp. TM1040 4076073 YP_612797.1 CDS TM1040_0802 NC_008044.1 849590 850969 D KEGG: rru:Rru_A2589 hypothetical protein, ev=1e-42, 33% identity; hypothetical protein 849590..850969 Ruegeria sp. TM1040 4076074 YP_612798.1 CDS TM1040_0803 NC_008044.1 850956 852005 D 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 850956..852005 Ruegeria sp. TM1040 4076192 YP_612799.1 CDS TM1040_0804 NC_008044.1 852235 852918 D KEGG: ypk:y2206 hypothetical protein, ev=7e-07, 25% identity; hypothetical protein 852235..852918 Ruegeria sp. TM1040 4076193 YP_612800.1 CDS TM1040_0805 NC_008044.1 852931 853899 D KEGG: bbr:BB3501 hypothetical protein, ev=1e-120, 67% identity; hypothetical protein 852931..853899 Ruegeria sp. TM1040 4076194 YP_612801.1 CDS TM1040_0806 NC_008044.1 853963 854214 D hypothetical protein 853963..854214 Ruegeria sp. TM1040 4076195 YP_612802.1 CDS TM1040_0807 NC_008044.1 854216 854683 D KEGG: bpe:BP3375 hypothetical protein, ev=1e-17, 37% identity; hypothetical protein 854216..854683 Ruegeria sp. TM1040 4076196 YP_612803.1 CDS TM1040_0808 NC_008044.1 854680 855129 D hypothetical protein 854680..855129 Ruegeria sp. TM1040 4076197 YP_612804.1 CDS TM1040_0809 NC_008044.1 855126 855500 D hypothetical protein 855126..855500 Ruegeria sp. TM1040 4076198 YP_612805.1 CDS TM1040_0810 NC_008044.1 855500 855901 D KEGG: bbr:BB3496 hypothetical protein, ev=9e-21, 43% identity; hypothetical protein 855500..855901 Ruegeria sp. TM1040 4076199 YP_612806.1 CDS TM1040_0811 NC_008044.1 855898 856296 D KEGG: mlo:mlr8015 hypothetical protein, ev=5e-07, 28% identity; hypothetical protein 855898..856296 Ruegeria sp. TM1040 4076200 YP_612807.1 CDS TM1040_0812 NC_008044.1 856572 857060 D hypothetical protein 856572..857060 Ruegeria sp. TM1040 4076201 YP_612808.1 CDS TM1040_0813 NC_008044.1 857163 857633 D hypothetical protein 857163..857633 Ruegeria sp. TM1040 4076202 YP_612809.1 CDS TM1040_0814 NC_008044.1 857759 858004 D hypothetical protein 857759..858004 Ruegeria sp. TM1040 4076203 YP_612810.1 CDS TM1040_0815 NC_008044.1 858001 858372 R KEGG: rpa:RPA3130 transcriptional regulator, XRE family, ev=3e-30, 53% identity; XRE family transcriptional regulator complement(858001..858372) Ruegeria sp. TM1040 4076204 YP_612811.1 CDS TM1040_0816 NC_008044.1 858386 858688 R KEGG: rpa:RPA3131 hypothetical protein, ev=1e-30, 60% identity; hypothetical protein complement(858386..858688) Ruegeria sp. TM1040 4076205 YP_612812.1 CDS TM1040_0817 NC_008044.1 858798 859124 R hypothetical protein complement(858798..859124) Ruegeria sp. TM1040 4076206 YP_612813.1 CDS TM1040_0818 NC_008044.1 859121 859564 R KEGG: sil:SPO3110 TonB domain protein, , ev=9e-10, 40% identity; hypothetical protein complement(859121..859564) Ruegeria sp. TM1040 4076207 YP_612814.1 CDS TM1040_0819 NC_008044.1 859581 863936 D 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 859581..863936 Ruegeria sp. TM1040 4076208 YP_612815.1 CDS TM1040_0820 NC_008044.1 863936 864880 D KEGG: nar:Saro_0661 hypothetical protein, ev=2e-26, 25% identity; hypothetical protein 863936..864880 Ruegeria sp. TM1040 4076209 YP_612816.1 CDS TM1040_0821 NC_008044.1 864877 866394 D KEGG: pub:SAR11_0932 hypothetical protein, ev=2e-31, 28% identity; hypothetical protein 864877..866394 Ruegeria sp. TM1040 4076210 YP_612817.1 CDS TM1040_0822 NC_008044.1 866391 866936 D hypothetical protein 866391..866936 Ruegeria sp. TM1040 4077528 YP_612818.1 CDS TM1040_0823 NC_008044.1 866908 867261 D hypothetical protein 866908..867261 Ruegeria sp. TM1040 4077529 YP_612819.1 CDS TM1040_0824 NC_008044.1 867268 867564 D hypothetical protein 867268..867564 Ruegeria sp. TM1040 4077530 YP_612820.1 CDS TM1040_0825 NC_008044.1 867561 867995 D hypothetical protein 867561..867995 Ruegeria sp. TM1040 4077531 YP_612821.1 CDS TM1040_0826 NC_008044.1 867997 868806 D PFAM: protein of unknown function DUF847: (8.8e-67); KEGG: bmb:BruAb1_0990 secretion activator protein, hypothetical, ev=2e-43, 39% identity; hypothetical protein 867997..868806 Ruegeria sp. TM1040 4077532 YP_612822.1 CDS TM1040_0827 NC_008044.1 868803 869201 D hypothetical protein 868803..869201 Ruegeria sp. TM1040 4077533 YP_612823.1 CDS TM1040_0828 NC_008044.1 869373 869987 R 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 complement(869373..869987) Ruegeria sp. TM1040 4077534 YP_612824.1 CDS TM1040_0829 NC_008044.1 870157 870582 R PFAM: response regulator receiver: (2.6e-05); KEGG: lic:LIC13330 response regulator, ev=8e-14, 35% identity; response regulator receiver protein complement(870157..870582) Ruegeria sp. TM1040 4077535 YP_612825.1 CDS TM1040_0830 NC_008044.1 870579 871763 R 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 complement(870579..871763) Ruegeria sp. TM1040 4077536 YP_612826.1 CDS TM1040_0831 NC_008044.1 872933 873844 R 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 complement(872933..873844) Ruegeria sp. TM1040 4077537 YP_612827.1 CDS TM1040_0832 NC_008044.1 873956 875506 D 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) 873956..875506 Ruegeria sp. TM1040 4077538 YP_612828.1 CDS TM1040_0833 NC_008044.1 875521 877938 D KEGG: jan:Jann_1258 hypothetical protein, ev=0.0, 58% identity; hypothetical protein 875521..877938 Ruegeria sp. TM1040 4077539 YP_612829.1 CDS TM1040_0834 NC_008044.1 878016 879683 R PFAM: Amidohydrolase 3: (9.2e-81); KEGG: sil:SPO1605 hypothetical protein, ev=0.0, 62% identity; amidohydrolase complement(878016..879683) Ruegeria sp. TM1040 4077540 YP_612830.1 CDS TM1040_0835 NC_008044.1 879761 880786 R 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 complement(879761..880786) Ruegeria sp. TM1040 4077541 YP_612831.1 CDS TM1040_0836 NC_008044.1 880854 881654 R 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 complement(880854..881654) Ruegeria sp. TM1040 4077542 YP_612832.1 CDS TM1040_0837 NC_008044.1 881647 882579 R 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 complement(881647..882579) Ruegeria sp. TM1040 4077543 YP_612833.1 CDS TM1040_0838 NC_008044.1 882584 883696 R 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 complement(882584..883696) Ruegeria sp. TM1040 4077544 YP_612834.1 CDS TM1040_0839 NC_008044.1 884254 887037 D 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 884254..887037 Ruegeria sp. TM1040 4077545 YP_612835.1 CDS TM1040_0840 NC_008044.1 887215 887457 R hypothetical protein complement(887215..887457) Ruegeria sp. TM1040 4077546 YP_612836.1 CDS TM1040_0841 NC_008044.1 887959 888321 D hypothetical protein 887959..888321 Ruegeria sp. TM1040 4077547 YP_612837.1 CDS TM1040_0842 NC_008044.1 888359 889966 D PFAM: peptidase C1A, papain: (2.9e-08); KEGG: lic:LIC20197 cysteine protease, ev=3e-24, 30% identity; peptidase C1A, papain 888359..889966 Ruegeria sp. TM1040 4076017 YP_612838.1 CDS TM1040_0843 NC_008044.1 889986 894845 D 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 889986..894845 Ruegeria sp. TM1040 4076018 YP_612839.1 CDS TM1040_0844 NC_008044.1 894888 895775 R 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 complement(894888..895775) Ruegeria sp. TM1040 4076019 YP_612840.1 CDS TM1040_0845 NC_008044.1 895892 897502 D 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 895892..897502 Ruegeria sp. TM1040 4076020 YP_612841.1 CDS TM1040_0846 NC_008044.1 897499 898674 D 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 897499..898674 Ruegeria sp. TM1040 4076021 YP_612842.1 CDS TM1040_0847 NC_008044.1 898671 900155 D PFAM: aldehyde dehydrogenase: (6.4e-209); KEGG: bbr:BB4965 probable aldehyde dehydrogenase, ev=1e-103, 43% identity; betaine aldehyde dehydrogenase 898671..900155 Ruegeria sp. TM1040 4076022 YP_612843.1 CDS TM1040_0848 NC_008044.1 900379 901287 R 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 complement(900379..901287) Ruegeria sp. TM1040 4076023 YP_612844.1 CDS TM1040_0849 NC_008044.1 901433 902737 D 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 901433..902737 Ruegeria sp. TM1040 4076024 YP_612845.1 CDS TM1040_0850 NC_008044.1 902829 903710 D 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 902829..903710 Ruegeria sp. TM1040 4076025 YP_612846.1 CDS TM1040_0851 NC_008044.1 903710 904561 D 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 903710..904561 Ruegeria sp. TM1040 4076026 YP_612847.1 CDS ugpC NC_008044.1 904570 905625 D part of the UgpABCE glycerol-3-phosphate uptake system; glycerol-3-phosphate transporter ATP-binding subunit 904570..905625 Ruegeria sp. TM1040 4076027 YP_612848.1 CDS TM1040_0853 NC_008044.1 905622 906569 D PFAM: glycerophosphoryl diester phosphodiesterase: (1.4e-38); KEGG: sil:SPO0236 glycerophosphoryl diester phosphodiesterase, , ev=5e-90, 56% identity; glycerophosphoryl diester phosphodiesterase 905622..906569 Ruegeria sp. TM1040 4076028 YP_612849.1 CDS TM1040_0854 NC_008044.1 906573 907493 D PFAM: Haloacid dehalogenase-like hydrolase: (1.2e-07); KEGG: rru:Rru_A1795 HAD-superfamily hydrolase, subfamily IIA, ev=7e-39, 39% identity; haloacid dehalogenase 906573..907493 Ruegeria sp. TM1040 4076029 YP_612850.1 CDS TM1040_0855 NC_008044.1 907552 909198 D PFAM: Na+/Pi-cotransporter: (3.3e-33); KEGG: sme:SMb21536 hypothetical protein, ev=1e-106, 41% identity; Na+/Pi-cotransporter 907552..909198 Ruegeria sp. TM1040 4076030 YP_612851.1 CDS TM1040_0856 NC_008044.1 909271 909846 D PFAM: Phosphoglycerate mutase: (5.1e-35); KEGG: jan:Jann_2515 phosphoglycerate mutase, ev=3e-31, 42% identity; phosphoglycerate mutase 909271..909846 Ruegeria sp. TM1040 4076031 YP_612852.1 CDS TM1040_0857 NC_008044.1 910004 910333 R hypothetical protein complement(910004..910333) Ruegeria sp. TM1040 4076032 YP_612853.1 CDS TM1040_0858 NC_008044.1 910897 911307 D PFAM: thioesterase superfamily: (2.8e-19); KEGG: ccr:CC0190 acyl-CoA thioester hydrolase, ev=9e-34, 53% identity; thioesterase superfamily protein 910897..911307 Ruegeria sp. TM1040 4076033 YP_612854.1 CDS TM1040_0859 NC_008044.1 911391 912782 R 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 complement(911391..912782) Ruegeria sp. TM1040 4076034 YP_612855.2 CDS TM1040_0860 NC_008044.1 913262 914491 D catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine; 5-aminolevulinate synthase 913262..914491 Ruegeria sp. TM1040 4076035 YP_612856.1 CDS TM1040_0861 NC_008044.1 914620 915837 D KEGG: rsp:RSP_2983 hypothetical protein, ev=2e-95, 50% identity; hypothetical protein 914620..915837 Ruegeria sp. TM1040 4076231 YP_612857.1 CDS ispG NC_008044.1 915958 917091 D 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 915958..917091 Ruegeria sp. TM1040 4076232 YP_612858.1 CDS TM1040_0863 NC_008044.1 917168 917932 R PFAM: DSBA oxidoreductase: (1.4e-24); KEGG: sil:SPO2591 27 kDa outer membrane protein, , ev=5e-85, 63% identity; DSBA oxidoreductase complement(917168..917932) Ruegeria sp. TM1040 4076233 YP_612859.1 CDS TM1040_0864 NC_008044.1 917929 919350 R 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 complement(917929..919350) Ruegeria sp. TM1040 4076234 YP_612860.1 CDS TM1040_0865 NC_008044.1 919373 920518 D PFAM: aminotransferase, class I and II: (3.3e-50); KEGG: sil:SPO2589 aminotransferase, classes I and II, ev=1e-179, 82% identity; aminotransferase 919373..920518 Ruegeria sp. TM1040 4076235 YP_612861.1 CDS TM1040_0866 NC_008044.1 920518 921756 D 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 920518..921756 Ruegeria sp. TM1040 4076236 YP_612862.1 CDS TM1040_0867 NC_008044.1 922143 924650 D 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 922143..924650 Ruegeria sp. TM1040 4076237 YP_612863.1 CDS prfB NC_008044.1 924764 925888 D 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 924764..925888 Ruegeria sp. TM1040 4076238 YP_612864.1 CDS TM1040_0869 NC_008044.1 926009 927346 R PFAM: major facilitator superfamily MFS_1: (6.7e-21); KEGG: sco:SCO1457 transport protein, ev=8e-16, 27% identity; major facilitator superfamily transporter complement(926009..927346) Ruegeria sp. TM1040 4076239 YP_612865.1 CDS TM1040_0870 NC_008044.1 927480 928859 D catalyzes the hydrolysis of a monocarboxylic acid amid to form a monocarboxylate and ammonia; amidase 927480..928859 Ruegeria sp. TM1040 4076240 YP_612866.1 CDS TM1040_0871 NC_008044.1 928914 929723 D KEGG: sil:SPO2582 membrane protein, , ev=8e-97, 66% identity; hypothetical protein 928914..929723 Ruegeria sp. TM1040 4076241 YP_612867.1 CDS TM1040_0872 NC_008044.1 929716 930516 R SMART: Helix-turn-helix type 3: (1.5e-07); KEGG: sil:SPO2581 DNA-binding protein, , ev=2e-86, 59% identity; XRE family transcriptional regulator complement(929716..930516) Ruegeria sp. TM1040 4076242 YP_612868.1 CDS TM1040_0873 NC_008044.1 930711 931130 D KEGG: sil:SPO2580 hypothetical protein, ev=4e-07, 38% identity; hypothetical protein 930711..931130 Ruegeria sp. TM1040 4076243 YP_612869.1 CDS ilvH NC_008044.1 931317 931877 R 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 complement(931317..931877) Ruegeria sp. TM1040 4076244 YP_612870.1 CDS TM1040_0875 NC_008044.1 931943 933694 R 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 complement(931943..933694) Ruegeria sp. TM1040 4076245 YP_612871.1 CDS TM1040_0876 NC_008044.1 934294 934995 R 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 complement(934294..934995) Ruegeria sp. TM1040 4076246 YP_612872.1 CDS TM1040_0877 NC_008044.1 935016 936440 R 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 complement(935016..936440) Ruegeria sp. TM1040 4076247 YP_612873.1 CDS TM1040_0878 NC_008044.1 936737 937822 D 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 936737..937822 Ruegeria sp. TM1040 4076248 YP_612874.1 CDS TM1040_0879 NC_008044.1 937960 938907 D KEGG: sil:SPO2572 hypothetical protein, ev=1e-114, 83% identity; TRAP-type mannitol/chloroaromatic compound transport system small permease-like 937960..938907 Ruegeria sp. TM1040 4076249 YP_612875.1 CDS TM1040_0880 NC_008044.1 938924 941278 D 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 938924..941278 Ruegeria sp. TM1040 4076250 YP_612876.1 CDS TM1040_0881 NC_008044.1 941492 941875 R 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 complement(941492..941875) Ruegeria sp. TM1040 4075978 YP_612877.1 CDS TM1040_0882 NC_008044.1 941881 942705 R Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate; arginyl-tRNA-protein transferase complement(941881..942705) Ruegeria sp. TM1040 4075979 YP_612878.1 CDS TM1040_0883 NC_008044.1 942879 943310 R PFAM: RDD: (1.4e-10); KEGG: sil:SPO2568 RDD family protein, ev=4e-46, 63% identity; RDD domain-containing protein complement(942879..943310) Ruegeria sp. TM1040 4075980 YP_612879.1 CDS TM1040_0884 NC_008044.1 943379 943834 R KEGG: sil:SPO2567 hypothetical protein, ev=1e-49, 66% identity; hypothetical protein complement(943379..943834) Ruegeria sp. TM1040 4075981 YP_612880.1 CDS TM1040_0885 NC_008044.1 944459 947317 D PFAM: glutamate-ammonia ligase adenylyltransferase: (3.4e-65); KEGG: sil:SPO2523 glutamate-ammonia ligase adenylyltransferase, ev=0.0, 68% identity; glutamate-ammonia-ligase adenylyltransferase 944459..947317 Ruegeria sp. TM1040 4075982 YP_612881.1 CDS TM1040_0886 NC_008044.1 947364 947594 D KEGG: sil:SPO2522 hypothetical protein, ev=9e-23, 58% identity; hypothetical protein 947364..947594 Ruegeria sp. TM1040 4075983 YP_612882.1 CDS TM1040_0887 NC_008044.1 948037 949254 D KEGG: sil:SPO2520 hypothetical protein, ev=1e-175, 77% identity; SAM-dependent methyltransferase 948037..949254 Ruegeria sp. TM1040 4075984 YP_612883.1 CDS TM1040_0888 NC_008044.1 949266 949805 D KEGG: sil:SPO2519 hypothetical protein, ev=1e-65, 70% identity; hypothetical protein 949266..949805 Ruegeria sp. TM1040 4075985 YP_612884.1 CDS TM1040_0889 NC_008044.1 949911 950897 R PFAM: luciferase-like: (4.3e-16); KEGG: sil:SPO2518 bacterial luciferase family protein, ev=1e-136, 75% identity; luciferase-like protein complement(949911..950897) Ruegeria sp. TM1040 4075986 YP_612885.1 CDS TM1040_0890 NC_008044.1 950986 951672 R PFAM: peptidase M48, Ste24p: (3.3e-22); KEGG: sil:SPO2517 peptidase, M48 family, ev=3e-97, 77% identity; peptidase M48, Ste24p complement(950986..951672) Ruegeria sp. TM1040 4075987 YP_612886.1 CDS TM1040_0891 NC_008044.1 952013 953197 R KEGG: sil:SPO2515 hypothetical protein, ev=0.0, 87% identity; hypothetical protein complement(952013..953197) Ruegeria sp. TM1040 4075988 YP_612887.1 CDS TM1040_0892 NC_008044.1 953229 953396 R KEGG: sil:SPO2514 hypothetical protein, ev=1e-08, 50% identity; hypothetical protein complement(953229..953396) Ruegeria sp. TM1040 4075989 YP_612888.1 CDS TM1040_0893 NC_008044.1 953503 954951 R KEGG: sil:SPO2513 hypothetical protein, ev=1e-119, 50% identity; hypothetical protein complement(953503..954951) Ruegeria sp. TM1040 4075990 YP_612889.1 CDS TM1040_0894 NC_008044.1 955075 955914 R 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 complement(955075..955914) Ruegeria sp. TM1040 4075991 YP_612890.1 CDS TM1040_0895 NC_008044.1 956048 956524 D 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 956048..956524 Ruegeria sp. TM1040 4075992 YP_612891.1 CDS TM1040_0896 NC_008044.1 956617 957786 D 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 956617..957786 Ruegeria sp. TM1040 4075993 YP_612892.1 CDS TM1040_0897 NC_008044.1 958089 958895 R 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 complement(958089..958895) Ruegeria sp. TM1040 4075994 YP_612893.1 CDS TM1040_0898 NC_008044.1 959238 959534 R hypothetical protein complement(959238..959534) Ruegeria sp. TM1040 4075995 YP_612894.1 CDS TM1040_0899 NC_008044.1 959653 960717 D hypothetical protein 959653..960717 Ruegeria sp. TM1040 4075996 YP_612895.1 CDS TM1040_0900 NC_008044.1 960714 961715 D PFAM: protein of unknown function DUF6, transmembrane: (7.4e-07); KEGG: sil:SPO2507 membrane protein, , ev=2e-78, 54% identity; hypothetical protein 960714..961715 Ruegeria sp. TM1040 4076270 YP_612896.1 CDS TM1040_0901 NC_008044.1 961909 962232 R PFAM: HesB/YadR/YfhF: (1.2e-25); KEGG: sil:SPO2506 iron-sulfur cluster assembly family protein, ev=1e-49, 87% identity; HesB/YadR/YfhF complement(961909..962232) Ruegeria sp. TM1040 4076271 YP_612897.1 CDS TM1040_0902 NC_008044.1 962323 963465 D 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 962323..963465 Ruegeria sp. TM1040 4076272 YP_612898.1 CDS argS NC_008044.1 963640 965382 D 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 963640..965382 Ruegeria sp. TM1040 4076273 YP_612899.1 CDS TM1040_0904 NC_008044.1 965892 966827 D PFAM: Sporulation related: (1.6e-05); KEGG: sil:SPO2503 hypothetical protein, ev=4e-79, 48% identity; sporulation-like protein 965892..966827 Ruegeria sp. TM1040 4076274 YP_612900.1 CDS TM1040_0905 NC_008044.1 966827 967888 D PFAM: glycoside hydrolase, family 3-like: (7.8e-11); KEGG: sil:SPO2502 beta-N-acetylhexosaminidase, , ev=1e-123, 64% identity; beta-N-acetylhexosaminidase 966827..967888 Ruegeria sp. TM1040 4076275 YP_612901.1 CDS TM1040_0906 NC_008044.1 967881 968678 D 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 967881..968678 Ruegeria sp. TM1040 4076276 YP_612902.1 CDS TM1040_0907 NC_008044.1 968678 969358 D 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 968678..969358 Ruegeria sp. TM1040 4076277 YP_612903.1 CDS TM1040_0908 NC_008044.1 969526 969846 D hypothetical protein 969526..969846 Ruegeria sp. TM1040 4076278 YP_612904.1 CDS TM1040_0909 NC_008044.1 969800 970999 R 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 complement(969800..970999) Ruegeria sp. TM1040 4076279 YP_612905.1 CDS TM1040_0910 NC_008044.1 971071 971610 D PFAM: regulatory proteins, AsnC/Lrp: (6.5e-18); KEGG: mlo:mlr7283 transcriptional regulator, ev=6e-46, 55% identity; AsnC family transcriptional regulator 971071..971610 Ruegeria sp. TM1040 4076280 YP_612906.1 CDS TM1040_0911 NC_008044.1 971618 972697 R Catalyzes the deamination of dCTP to form dUTP; 2'-deoxycytidine 5'-triphosphate deaminase complement(971618..972697) Ruegeria sp. TM1040 4076281 YP_612907.1 CDS TM1040_0912 NC_008044.1 973041 975563 R PFAM: regulatory protein, MerR: (1.2e-08); KEGG: lma:LmjF35.0550 proteophosphoglycan ppg1, ev=2e-48, 23% identity; MerR family transcriptional regulator complement(973041..975563) Ruegeria sp. TM1040 4076282 YP_612908.1 CDS ihfA NC_008044.1 975623 975925 R 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 complement(975623..975925) Ruegeria sp. TM1040 4076283 YP_612909.1 CDS TM1040_0914 NC_008044.1 976013 976984 R 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 complement(976013..976984) Ruegeria sp. TM1040 4076284 YP_612910.1 CDS TM1040_0915 NC_008044.1 977000 978127 R 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 complement(977000..978127) Ruegeria sp. TM1040 4076285 YP_612911.1 CDS rpmF NC_008044.1 978169 978375 R some L32 proteins have zinc finger motifs consisting of CXXC while others do not; 50S ribosomal protein L32 complement(978169..978375) Ruegeria sp. TM1040 4076286 YP_612912.1 CDS TM1040_0917 NC_008044.1 978666 979214 R KEGG: sil:SPO2491 hypothetical protein, ev=1e-49, 59% identity; hypothetical protein complement(978666..979214) Ruegeria sp. TM1040 4076287 YP_612913.1 CDS TM1040_0918 NC_008044.1 979301 979768 D KEGG: sil:SPO2490 lipoprotein, SmpA/OmlA family, ev=4e-42, 56% identity; SmpA/OmlA family lipoprotein 979301..979768 Ruegeria sp. TM1040 4076288 YP_612914.1 CDS TM1040_0919 NC_008044.1 979926 980702 D KEGG: sil:SPO2489 hypothetical protein, ev=1e-109, 81% identity; ornithine-acyl-ACP N-acyltransferase 979926..980702 Ruegeria sp. TM1040 4076289 YP_612915.1 CDS TM1040_0920 NC_008044.1 980789 982579 D 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 980789..982579 Ruegeria sp. TM1040 4077548 YP_612916.1 CDS TM1040_0921 NC_008044.1 982763 983518 R 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 complement(982763..983518) Ruegeria sp. TM1040 4077549 YP_612917.1 CDS TM1040_0922 NC_008044.1 983670 984593 R KEGG: sil:SPO2486 hypothetical protein, ev=1e-79, 55% identity; hypothetical protein complement(983670..984593) Ruegeria sp. TM1040 4077550 YP_612918.1 CDS TM1040_0923 NC_008044.1 984889 986142 R 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 complement(984889..986142) Ruegeria sp. TM1040 4077551 YP_612919.1 CDS anmK NC_008044.1 986286 987413 D 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 986286..987413 Ruegeria sp. TM1040 4077552 YP_612920.1 CDS TM1040_0925 NC_008044.1 987585 988055 R PFAM: protein of unknown function DUF985: (1.7e-63); KEGG: sil:SPO2479 hypothetical protein, ev=6e-56, 66% identity; hypothetical protein complement(987585..988055) Ruegeria sp. TM1040 4077553 YP_612921.1 CDS TM1040_0926 NC_008044.1 988123 989541 D PFAM: protein of unknown function UPF0061: (3.7e-80); KEGG: sil:SPO2480 hypothetical protein, ev=0.0, 71% identity; hypothetical protein 988123..989541 Ruegeria sp. TM1040 4077554 YP_612922.1 CDS TM1040_0927 NC_008044.1 989796 991133 R 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 complement(989796..991133) Ruegeria sp. TM1040 4077555 YP_612923.1 CDS TM1040_0928 NC_008044.1 991564 991980 D PFAM: ferric-uptake regulator: (4.4e-58); KEGG: sil:SPO2477 transcriptional regulator, Fur family, ev=5e-62, 82% identity; FUR family manganese uptake regulator 991564..991980 Ruegeria sp. TM1040 4077556 YP_612924.1 CDS TM1040_0929 NC_008044.1 992140 993033 D PFAM: protein of unknown function DUF6, transmembrane: (0.00011); KEGG: sil:SPO2475 membrane protein, , ev=2e-88, 56% identity; hypothetical protein 992140..993033 Ruegeria sp. TM1040 4077557 YP_612925.1 CDS TM1040_0930 NC_008044.1 993036 994274 R 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 complement(993036..994274) Ruegeria sp. TM1040 4077558 YP_612926.1 CDS eno NC_008044.1 994521 995798 D enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis; phosphopyruvate hydratase 994521..995798 Ruegeria sp. TM1040 4077559 YP_612927.1 CDS TM1040_0932 NC_008044.1 995924 996535 D PFAM: GCN5-related N-acetyltransferase: (3.3e-05); KEGG: bja:blr1411 hypothetical protein, ev=7e-50, 51% identity; N-acetyltransferase GCN5 995924..996535 Ruegeria sp. TM1040 4077560 YP_612928.1 CDS TM1040_0933 NC_008044.1 996615 997064 R PFAM: GCN5-related N-acetyltransferase: (1.6e-10); KEGG: sil:SPO2471 acetyltransferase, GNAT family, ev=4e-54, 69% identity; N-acetyltransferase GCN5 complement(996615..997064) Ruegeria sp. TM1040 4077561 YP_612929.1 CDS TM1040_0934 NC_008044.1 997061 998002 R 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 complement(997061..998002) Ruegeria sp. TM1040 4077562 YP_612930.1 CDS TM1040_0935 NC_008044.1 998101 999015 D KEGG: sil:SPO1104 hypothetical protein, ev=2e-09, 27% identity; hypothetical protein 998101..999015 Ruegeria sp. TM1040 4077563 YP_612931.1 CDS mazG NC_008044.1 999002 999844 R 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 complement(999002..999844) Ruegeria sp. TM1040 4077564 YP_612932.1 CDS TM1040_0937 NC_008044.1 999907 1001070 D 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 999907..1001070 Ruegeria sp. TM1040 4077565 YP_612933.1 CDS TM1040_0938 NC_008044.1 1001097 1002125 D catalyzes the formation of putrescine from agmatine; agmatinase 1001097..1002125 Ruegeria sp. TM1040 4077566 YP_612934.1 CDS TM1040_0939 NC_008044.1 1002122 1003069 D TIGRFAM: agmatinase, : (1.3e-70); PFAM: Arginase/agmatinase/formiminoglutamase: (1.6e-59); KEGG: sil:SPO2464 agmatinase, ev=1e-148, 80% identity; agmatinase 1002122..1003069 Ruegeria sp. TM1040 4077333 YP_612935.1 CDS TM1040_0940 NC_008044.1 1003342 1003671 R KEGG: sil:SPO2462 hypothetical protein, ev=1e-27, 66% identity; hypothetical protein complement(1003342..1003671) Ruegeria sp. TM1040 4077334 YP_612936.1 CDS prfA NC_008044.1 1003744 1004796 D 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 1003744..1004796 Ruegeria sp. TM1040 4077335 YP_612937.1 CDS TM1040_0942 NC_008044.1 1004793 1005629 D 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 1004793..1005629 Ruegeria sp. TM1040 4077336 YP_612938.1 CDS TM1040_0943 NC_008044.1 1005791 1006501 D KEGG: sil:SPO2459 hypothetical protein, ev=2e-67, 59% identity; hypothetical protein 1005791..1006501 Ruegeria sp. TM1040 4077337 YP_612939.1 CDS ksgA NC_008044.1 1006604 1007446 R 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 complement(1006604..1007446) Ruegeria sp. TM1040 4077338 YP_612940.1 CDS pdxA NC_008044.1 1007596 1008576 R 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 complement(1007596..1008576) Ruegeria sp. TM1040 4077339 YP_612941.1 CDS TM1040_0946 NC_008044.1 1008573 1009847 R 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 complement(1008573..1009847) Ruegeria sp. TM1040 4077340 YP_612942.1 CDS TM1040_0947 NC_008044.1 1009832 1012027 R 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 complement(1009832..1012027) Ruegeria sp. TM1040 4077341 YP_612943.1 CDS TM1040_0948 NC_008044.1 1012011 1013117 R PFAM: permease YjgP/YjgQ: (4.3e-38); KEGG: sil:SPO2454 permease, YjgP/YjgQ family, ev=1e-138, 68% identity; permease YjgP/YjgQ complement(1012011..1013117) Ruegeria sp. TM1040 4077342 YP_612944.1 CDS TM1040_0949 NC_008044.1 1013114 1014253 R PFAM: permease YjgP/YjgQ: (7e-30); KEGG: sil:SPO3780 membrane protein, , ev=1e-90, 46% identity; permease YjgP/YjgQ complement(1013114..1014253) Ruegeria sp. TM1040 4077343 YP_612945.1 CDS TM1040_0950 NC_008044.1 1014475 1015950 D catalyzes the removal of N-terminal amino acids preferably leucine from various peptides; leucyl aminopeptidase 1014475..1015950 Ruegeria sp. TM1040 4077344 YP_612946.1 CDS TM1040_0951 NC_008044.1 1015957 1016421 D 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 1015957..1016421 Ruegeria sp. TM1040 4077345 YP_612947.1 CDS TM1040_0952 NC_008044.1 1016672 1017253 R TIGRFAM: conserved hypothetical protein: (7.7e-53); KEGG: sil:SPO2449 hypothetical protein, ev=2e-53, 54% identity; hypothetical protein complement(1016672..1017253) Ruegeria sp. TM1040 4077346 YP_612948.1 CDS TM1040_0953 NC_008044.1 1017303 1017926 R 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 complement(1017303..1017926) Ruegeria sp. TM1040 4077347 YP_612949.1 CDS TM1040_0954 NC_008044.1 1017923 1019824 R 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 complement(1017923..1019824) Ruegeria sp. TM1040 4077348 YP_612950.1 CDS TM1040_0955 NC_008044.1 1020018 1021610 D KEGG: ret:RHE_CH01984 hypothetical protein, ev=4e-65, 38% identity; hypothetical protein 1020018..1021610 Ruegeria sp. TM1040 4077349 YP_612951.1 CDS TM1040_0956 NC_008044.1 1021740 1022948 D 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 1021740..1022948 Ruegeria sp. TM1040 4077350 YP_612952.1 CDS ndk NC_008044.1 1023097 1023519 D catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate; nucleoside diphosphate kinase 1023097..1023519 Ruegeria sp. TM1040 4077351 YP_612953.1 CDS TM1040_0958 NC_008044.1 1023637 1023972 R KEGG: sil:SPO1621 TfoX domain protein, ev=4e-36, 67% identity; TfoX domain-containing protein complement(1023637..1023972) Ruegeria sp. TM1040 4077352 YP_612954.1 CDS TM1040_0959 NC_008044.1 1024317 1025639 D 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 1024317..1025639 Ruegeria sp. TM1040 4077255 YP_612955.1 CDS TM1040_0960 NC_008044.1 1026394 1027038 R 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 complement(1026394..1027038) Ruegeria sp. TM1040 4077256 YP_612956.1 CDS TM1040_0961 NC_008044.1 1027361 1027828 D PFAM: oxidoreductase, molybdopterin binding: (0.00091); KEGG: sil:SPO0162 hypothetical protein, ev=8e-34, 51% identity; oxidoreductase, molybdopterin binding 1027361..1027828 Ruegeria sp. TM1040 4077257 YP_612957.1 CDS TM1040_0962 NC_008044.1 1027874 1030345 D 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 1027874..1030345 Ruegeria sp. TM1040 4077258 YP_612958.1 CDS TM1040_0963 NC_008044.1 1030665 1031591 D 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 1030665..1031591 Ruegeria sp. TM1040 4077259 YP_612959.1 CDS TM1040_0964 NC_008044.1 1031901 1032911 D 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 1031901..1032911 Ruegeria sp. TM1040 4077260 YP_612960.1 CDS TM1040_0965 NC_008044.1 1032917 1033714 D KEGG: sil:SPO2353 hypothetical protein, ev=4e-88, 59% identity; hypothetical protein 1032917..1033714 Ruegeria sp. TM1040 4077261 YP_612961.1 CDS TM1040_0966 NC_008044.1 1033845 1034081 R 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 complement(1033845..1034081) Ruegeria sp. TM1040 4077262 YP_612962.1 CDS TM1040_0967 NC_008044.1 1034085 1034558 R similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function; Holliday junction resolvase-like protein complement(1034085..1034558) Ruegeria sp. TM1040 4077263 YP_612963.1 CDS TM1040_0968 NC_008044.1 1034555 1035793 R KEGG: sil:SPO2349 cytochrome c-type biogenesis protein CycH, ev=1e-105, 52% identity; cytochrome c-type biogenesis protein CycH complement(1034555..1035793) Ruegeria sp. TM1040 4077264 YP_612964.1 CDS TM1040_0969 NC_008044.1 1035985 1037280 D 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 1035985..1037280 Ruegeria sp. TM1040 4077265 YP_612965.1 CDS TM1040_0970 NC_008044.1 1037333 1037665 D 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 1037333..1037665 Ruegeria sp. TM1040 4077266 YP_612966.1 CDS TM1040_0971 NC_008044.1 1037740 1040775 D 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 1037740..1040775 Ruegeria sp. TM1040 4077267 YP_612967.1 CDS TM1040_0972 NC_008044.1 1040768 1041337 D 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 1040768..1041337 Ruegeria sp. TM1040 4077268 YP_612968.1 CDS TM1040_0973 NC_008044.1 1041451 1041861 D hypothetical protein 1041451..1041861 Ruegeria sp. TM1040 4077269 YP_612969.1 CDS TM1040_0974 NC_008044.1 1042009 1042398 D hypothetical protein 1042009..1042398 Ruegeria sp. TM1040 4077270 YP_612970.1 CDS TM1040_0975 NC_008044.1 1042474 1042935 D hypothetical protein 1042474..1042935 Ruegeria sp. TM1040 4077271 YP_612971.1 CDS TM1040_0976 NC_008044.1 1043026 1043625 D PFAM: manganese and iron superoxide dismutase: (8.6e-34); KEGG: sil:SPO2340 superoxide dismutase, Fe, ev=1e-107, 90% identity; superoxide dismutase 1043026..1043625 Ruegeria sp. TM1040 4077272 YP_612972.1 CDS TM1040_0977 NC_008044.1 1043784 1044398 D PFAM: GCN5-related N-acetyltransferase: (7.5e-09); KEGG: dde:Dde_3171 acetyltransferase, ev=1e-34, 44% identity; N-acetyltransferase GCN5 1043784..1044398 Ruegeria sp. TM1040 4077273 YP_612973.1 CDS TM1040_0978 NC_008044.1 1044530 1045072 R PFAM: conserved hypothetical protein 730: (7e-51); KEGG: sil:SPO2337 decarboxylase family protein, ev=2e-73, 73% identity; hypothetical protein complement(1044530..1045072) Ruegeria sp. TM1040 4078140 YP_612974.1 CDS TM1040_0979 NC_008044.1 1045222 1047177 D PFAM: Peptidoglycan-binding LysM: (2.1e-06); KEGG: sil:SPO2336 LysM domain protein, ev=3e-79, 35% identity; peptidoglycan-binding LysM 1045222..1047177 Ruegeria sp. TM1040 4078141 YP_612975.1 CDS TM1040_0980 NC_008044.1 1047285 1049105 D 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 1047285..1049105 Ruegeria sp. TM1040 4078142 YP_612976.1 CDS TM1040_0981 NC_008044.1 1049409 1049657 D PFAM: Calcium-binding EF-hand: (0.0064); KEGG: jan:Jann_1891 hypothetical protein, ev=3e-07, 41% identity; calcium-binding EF-hand 1049409..1049657 Ruegeria sp. TM1040 4078143 YP_612977.1 CDS TM1040_0982 NC_008044.1 1050017 1050601 R PFAM: regulatory protein, TetR: (7.3e-17); KEGG: sma:SAV4715 TetR-family transcriptional regulator, ev=9e-17, 35% identity; TetR family transcriptional regulator complement(1050017..1050601) Ruegeria sp. TM1040 4078144 YP_612978.1 CDS TM1040_0983 NC_008044.1 1050757 1051590 D 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 1050757..1051590 Ruegeria sp. TM1040 4078145 YP_612979.1 CDS TM1040_0984 NC_008044.1 1052015 1053841 D 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 1052015..1053841 Ruegeria sp. TM1040 4078146 YP_612980.1 CDS TM1040_0985 NC_008044.1 1054046 1054285 R hypothetical protein complement(1054046..1054285) Ruegeria sp. TM1040 4078147 YP_612981.1 CDS TM1040_0986 NC_008044.1 1054261 1054578 R hypothetical protein complement(1054261..1054578) Ruegeria sp. TM1040 4078148 YP_612982.1 CDS TM1040_0987 NC_008044.1 1054875 1058678 R PFAM: acriflavin resistance protein: (2.8e-24); KEGG: sil:SPO2332 transporter, AcrB/AcrD/AcrF family, ev=0.0, 73% identity; acriflavin resistance protein complement(1054875..1058678) Ruegeria sp. TM1040 4078149 YP_612983.1 CDS TM1040_0988 NC_008044.1 1058675 1059922 R PFAM: secretion protein HlyD: (0.00012); KEGG: sil:SPO2331 efflux transporter, RND family, MFP subunit, ev=1e-141, 64% identity; secretion protein HlyD complement(1058675..1059922) Ruegeria sp. TM1040 4078150 YP_612984.1 CDS TM1040_0989 NC_008044.1 1060287 1060955 D KEGG: sil:SPO2330 hypothetical protein, ev=5e-57, 56% identity; hypothetical protein 1060287..1060955 Ruegeria sp. TM1040 4078151 YP_612985.1 CDS TM1040_0990 NC_008044.1 1061024 1062349 D SMART: Pyrrolo-quinoline quinone: (0.057); KEGG: sil:SPO2329 PQQ enzyme repeat family protein, ev=1e-149, 61% identity; Pyrrolo-quinoline quinone 1061024..1062349 Ruegeria sp. TM1040 4078152 YP_612986.1 CDS engA NC_008044.1 1062663 1064141 D 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 1062663..1064141 Ruegeria sp. TM1040 4078153 YP_612987.1 CDS TM1040_0992 NC_008044.1 1064391 1065344 D PFAM: fatty acid desaturase: (1.4e-18); KEGG: sil:SPO2327 fatty acid desaturase, ev=1e-146, 75% identity; fatty acid desaturase 1064391..1065344 Ruegeria sp. TM1040 4078154 YP_612988.1 CDS TM1040_0993 NC_008044.1 1065465 1066124 D 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 1065465..1066124 Ruegeria sp. TM1040 4078155 YP_612989.1 CDS TM1040_0994 NC_008044.1 1066244 1067536 R 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 complement(1066244..1067536) Ruegeria sp. TM1040 4078156 YP_612990.1 CDS TM1040_0995 NC_008044.1 1067792 1068076 D 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 1067792..1068076 Ruegeria sp. TM1040 4078157 YP_612991.1 CDS secD NC_008044.1 1068111 1069775 D 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 1068111..1069775 Ruegeria sp. TM1040 4078158 YP_612992.1 CDS secF NC_008044.1 1069779 1070747 D 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 1069779..1070747 Ruegeria sp. TM1040 4078159 YP_612993.1 CDS TM1040_0998 NC_008044.1 1070995 1071348 D PFAM: protein of unknown function DUF498: (4.1e-35); KEGG: sil:SPO2318 hypothetical protein, ev=1e-45, 75% identity; hypothetical protein 1070995..1071348 Ruegeria sp. TM1040 4078218 YP_612994.1 CDS TM1040_0999 NC_008044.1 1071433 1072047 D ATP-binding protein; required for proper cytochrome c maturation; cytochrome c biogenesis protein CcmA 1071433..1072047 Ruegeria sp. TM1040 4078219 YP_612995.1 CDS TM1040_1000 NC_008044.1 1072044 1072700 D 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 1072044..1072700 Ruegeria sp. TM1040 4078220 YP_612996.1 CDS TM1040_1001 NC_008044.1 1072745 1073479 D 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 1072745..1073479 Ruegeria sp. TM1040 4078221 YP_612997.1 CDS TM1040_1002 NC_008044.1 1073472 1073627 D 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 1073472..1073627 Ruegeria sp. TM1040 4078222 YP_612998.1 CDS TM1040_1003 NC_008044.1 1073620 1074156 D 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 1073620..1074156 Ruegeria sp. TM1040 4078223 YP_612999.1 CDS TM1040_1004 NC_008044.1 1074159 1074863 R 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 complement(1074159..1074863) Ruegeria sp. TM1040 4078224 YP_613000.1 CDS TM1040_1005 NC_008044.1 1075048 1075395 R hypothetical protein complement(1075048..1075395) Ruegeria sp. TM1040 4078225 YP_613001.1 CDS TM1040_1006 NC_008044.1 1075536 1078283 R Catalyzes the conversion of citrate to isocitrate; aconitate hydratase complement(1075536..1078283) Ruegeria sp. TM1040 4078226 YP_613002.1 CDS TM1040_1007 NC_008044.1 1078584 1079210 D PFAM: protein of unknown function DUF1223: (1.9e-58); KEGG: sil:SPO2311 hypothetical protein, ev=3e-59, 48% identity; hypothetical protein 1078584..1079210 Ruegeria sp. TM1040 4078227 YP_613003.1 CDS TM1040_1008 NC_008044.1 1079214 1080134 R 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 complement(1079214..1080134) Ruegeria sp. TM1040 4078228 YP_613004.1 CDS TM1040_1009 NC_008044.1 1080288 1081391 R 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 complement(1080288..1081391) Ruegeria sp. TM1040 4078229 YP_613005.1 CDS TM1040_1010 NC_008044.1 1081470 1082015 R PFAM: TPR repeat: (7.2e-05) Tetratricopeptide TPR_2: (6.9e-05); KEGG: sil:SPO2307 hypothetical protein, ev=4e-55, 59% identity; hypothetical protein complement(1081470..1082015) Ruegeria sp. TM1040 4078230 YP_613006.1 CDS TM1040_1011 NC_008044.1 1082157 1083461 R Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide; adenylosuccinate lyase complement(1082157..1083461) Ruegeria sp. TM1040 4078231 YP_613007.1 CDS TM1040_1012 NC_008044.1 1083576 1083908 R hypothetical protein complement(1083576..1083908) Ruegeria sp. TM1040 4078232 YP_613008.1 CDS TM1040_1013 NC_008044.1 1083921 1085192 R PFAM: OsmC-like protein: (1.4e-33); KEGG: sil:SPO2301 osmC-like family protein, ev=1e-179, 77% identity; OsmC-like protein complement(1083921..1085192) Ruegeria sp. TM1040 4078233 YP_613009.1 CDS TM1040_1014 NC_008044.1 1085321 1085908 D PFAM: NUDIX hydrolase: (0.00022); KEGG: xac:XAC1843 hypothetical protein, ev=4e-27, 44% identity; NUDIX hydrolase 1085321..1085908 Ruegeria sp. TM1040 4078234 YP_613010.1 CDS TM1040_1015 NC_008044.1 1085908 1086813 D PFAM: Endonuclease/exonuclease/phosphatase: (3.9e-06); KEGG: jan:Jann_1778 endonuclease/exonuclease/phosphatase, ev=6e-41, 35% identity; endonuclease/exonuclease/phosphatase 1085908..1086813 Ruegeria sp. TM1040 4078235 YP_613011.1 CDS TM1040_1016 NC_008044.1 1086832 1088175 R PFAM: peptidase M24: (2.7e-06); KEGG: sil:SPO2299 metallopeptidase, family M24, ev=0.0, 88% identity; peptidase M24 complement(1086832..1088175) Ruegeria sp. TM1040 4078236 YP_613012.1 CDS TM1040_1017 NC_008044.1 1088369 1089136 D KEGG: sil:SPO2298 hypothetical protein, ev=9e-79, 62% identity; hypothetical protein 1088369..1089136 Ruegeria sp. TM1040 4078529 YP_613013.1 CDS TM1040_1018 NC_008044.1 1089174 1090373 R KEGG: sil:SPO2297 hypothetical protein, ev=2e-12, 24% identity; hypothetical protein complement(1089174..1090373) Ruegeria sp. TM1040 4078530 YP_613014.1 CDS TM1040_1019 NC_008044.1 1090440 1091252 R KEGG: sil:SPO2296 hypothetical protein, ev=1e-108, 73% identity; hypothetical protein complement(1090440..1091252) Ruegeria sp. TM1040 4078531 YP_613015.1 CDS TM1040_1020 NC_008044.1 1091340 1092602 R KEGG: rsp:RSP_3200 molecular chaperone, DnaK, ev=1e-111, 54% identity; molecular chaperone DnaK complement(1091340..1092602) Ruegeria sp. TM1040 4078532 YP_613016.1 CDS TM1040_1021 NC_008044.1 1092602 1093228 D hypothetical protein 1092602..1093228 Ruegeria sp. TM1040 4078533 YP_613017.1 CDS TM1040_1022 NC_008044.1 1093375 1094781 R 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 complement(1093375..1094781) Ruegeria sp. TM1040 4078534 YP_613018.1 CDS TM1040_1023 NC_008044.1 1094869 1095207 R 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 complement(1094869..1095207) Ruegeria sp. TM1040 4078535 YP_613019.1 CDS TM1040_1024 NC_008044.1 1095376 1096962 D 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 1095376..1096962 Ruegeria sp. TM1040 4078536 YP_613020.1 CDS TM1040_1025 NC_008044.1 1096959 1097507 R KEGG: sil:SPO2292 hypothetical protein, ev=6e-25, 42% identity; hypothetical protein complement(1096959..1097507) Ruegeria sp. TM1040 4078537 YP_613021.1 CDS TM1040_1026 NC_008044.1 1097776 1100565 D catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase 1097776..1100565 Ruegeria sp. TM1040 4078538 YP_613022.1 CDS TM1040_1027 NC_008044.1 1100965 1103352 D 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 1100965..1103352 Ruegeria sp. TM1040 4078539 YP_613023.1 CDS TM1040_1028 NC_008044.1 1103990 1107736 D 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 1103990..1107736 Ruegeria sp. TM1040 4078540 YP_613024.1 CDS TM1040_1029 NC_008044.1 1107741 1108124 D PFAM: response regulator receiver: (0.00011); KEGG: lic:LIC12088 response regulator, ev=2e-08, 31% identity; response regulator receiver protein 1107741..1108124 Ruegeria sp. TM1040 4078541 YP_613025.1 CDS TM1040_1030 NC_008044.1 1108141 1110486 D 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 1108141..1110486 Ruegeria sp. TM1040 4078542 YP_613026.1 CDS TM1040_1031 NC_008044.1 1110483 1110878 D 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 1110483..1110878 Ruegeria sp. TM1040 4078543 YP_613027.1 CDS TM1040_1032 NC_008044.1 1111339 1112463 D KEGG: sil:SPO2289 hypothetical protein, ev=4e-79, 46% identity; hypothetical protein 1111339..1112463 Ruegeria sp. TM1040 4078544 YP_613028.1 CDS tig NC_008044.1 1112761 1114092 D Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer; trigger factor 1112761..1114092 Ruegeria sp. TM1040 4078545 YP_613029.1 CDS TM1040_1034 NC_008044.1 1114264 1114497 D hypothetical protein 1114264..1114497 Ruegeria sp. TM1040 4078546 YP_613030.1 CDS TM1040_1035 NC_008044.1 1114531 1115472 D 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 1114531..1115472 Ruegeria sp. TM1040 4078547 YP_613031.1 CDS cpdB NC_008044.1 1115617 1117575 R 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 complement(1115617..1117575) Ruegeria sp. TM1040 4078548 YP_613032.1 CDS TM1040_1037 NC_008044.1 1117856 1118326 R PFAM: Lytic transglycosylase, catalytic: (9.6e-05); KEGG: sil:SPO2284 transglycosylase SLT domain protein, ev=1e-59, 72% identity; lytic transglycosylase, catalytic complement(1117856..1118326) Ruegeria sp. TM1040 4078095 YP_613033.1 CDS TM1040_1038 NC_008044.1 1118812 1119660 D PFAM: flagellin-like: (1.4e-06); KEGG: bmb:BruAb2_1084 flagellin family protein, ev=2e-48, 40% identity; flagellin-like protein 1118812..1119660 Ruegeria sp. TM1040 4078096 YP_613034.1 CDS TM1040_1039 NC_008044.1 1119990 1120835 D PFAM: flagellin-like: (5.7e-06); KEGG: jan:Jann_4203 flagellin-like, ev=5e-48, 45% identity; flagellin-like protein 1119990..1120835 Ruegeria sp. TM1040 4078097 YP_613035.1 CDS TM1040_1040 NC_008044.1 1121099 1121977 D PFAM: flagellin-like: (1.2e-06); KEGG: ret:RHE_PE00392 flagellin C protein, ev=4e-46, 39% identity; flagellin-like protein 1121099..1121977 Ruegeria sp. TM1040 4078098 YP_613036.1 CDS TM1040_1041 NC_008044.1 1122288 1122662 D KEGG: ppr:PBPRB1724 hypothetical protein, ev=4e-09, 36% identity; hypothetical protein 1122288..1122662 Ruegeria sp. TM1040 4078099 YP_613037.1 CDS TM1040_1042 NC_008044.1 1123134 1123481 R hypothetical protein complement(1123134..1123481) Ruegeria sp. TM1040 4078100 YP_613038.1 CDS rplI NC_008044.1 1123604 1124218 R in Escherichia coli this protein is wrapped around the base of the L1 stalk; 50S ribosomal protein L9 complement(1123604..1124218) Ruegeria sp. TM1040 4078101 YP_613039.1 CDS rpsR NC_008044.1 1124232 1124459 R 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 complement(1124232..1124459) Ruegeria sp. TM1040 4078102 YP_613040.1 CDS rpsF NC_008044.1 1124490 1124843 R binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21; 30S ribosomal protein S6 complement(1124490..1124843) Ruegeria sp. TM1040 4078103 YP_613041.1 CDS TM1040_1046 NC_008044.1 1125241 1125774 D KEGG: sil:SPO2280 hypothetical protein, ev=4e-24, 36% identity; hypothetical protein 1125241..1125774 Ruegeria sp. TM1040 4078104 YP_613042.1 CDS TM1040_1047 NC_008044.1 1126045 1126620 D PFAM: YceI: (4e-49); KEGG: sil:SPO2279 hypothetical protein, ev=6e-77, 74% identity; YceI protein 1126045..1126620 Ruegeria sp. TM1040 4078105 YP_613043.1 CDS TM1040_1048 NC_008044.1 1126856 1127638 D KEGG: mag:amb0186 ABC-type amino acid transport/signal transduction systems, ev=4e-20, 32% identity; amino acid ABC transporter/signal transduction system protein 1126856..1127638 Ruegeria sp. TM1040 4078106 YP_613044.1 CDS TM1040_1049 NC_008044.1 1127786 1129018 R PFAM: YceI: (2.8e-11) cytochrome B561: (8.9e-33); KEGG: sil:SPO2277 cytochrome, , ev=1e-118, 54% identity; cytochrome B561 complement(1127786..1129018) Ruegeria sp. TM1040 4078107 YP_613045.1 CDS TM1040_1050 NC_008044.1 1129265 1130200 D 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 1129265..1130200 Ruegeria sp. TM1040 4078108 YP_613046.1 CDS TM1040_1051 NC_008044.1 1130221 1130958 D 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 1130221..1130958 Ruegeria sp. TM1040 4078109 YP_613047.1 CDS acpP NC_008044.1 1131343 1131576 D carries the fatty acid chain in fatty acid biosynthesis; acyl carrier protein 1131343..1131576 Ruegeria sp. TM1040 4078110 YP_613048.1 CDS TM1040_1053 NC_008044.1 1131760 1132503 D PFAM: histidine biosynthesis: (1.5e-53); KEGG: sil:SPO2272 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase, , ev=4e-92, 65% identity; histidine biosynthesis protein 1131760..1132503 Ruegeria sp. TM1040 4078111 YP_613049.1 CDS TM1040_1054 NC_008044.1 1133065 1134333 D 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 1133065..1134333 Ruegeria sp. TM1040 4078112 YP_613050.1 CDS TM1040_1055 NC_008044.1 1134335 1135489 D PFAM: aminodeoxychorismate lyase: (1e-112); KEGG: sil:SPO2270 conserved hypothetical protein TIGR00247, ev=1e-161, 74% identity; aminodeoxychorismate lyase 1134335..1135489 Ruegeria sp. TM1040 4078113 YP_613051.1 CDS TM1040_1056 NC_008044.1 1135720 1136163 D KEGG: sil:SPO2267 hypothetical protein, ev=2e-08, 39% identity; hypothetical protein 1135720..1136163 Ruegeria sp. TM1040 4077196 YP_613052.1 CDS TM1040_1057 NC_008044.1 1136156 1137433 D PFAM: protein of unknown function DUF264: (9.5e-52); KEGG: sil:SPO2266 terminase, large subunit, , ev=1e-174, 73% identity; hypothetical protein 1136156..1137433 Ruegeria sp. TM1040 4077197 YP_613053.1 CDS TM1040_1058 NC_008044.1 1137683 1138888 D 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 1137683..1138888 Ruegeria sp. TM1040 4077198 YP_613054.1 CDS TM1040_1059 NC_008044.1 1138881 1139105 D KEGG: sil:SPO2263 hypothetical protein, ev=4e-17, 60% identity; hypothetical protein 1138881..1139105 Ruegeria sp. TM1040 4077199 YP_613055.1 CDS TM1040_1060 NC_008044.1 1139140 1139712 D 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 1139140..1139712 Ruegeria sp. TM1040 4077200 YP_613056.1 CDS TM1040_1061 NC_008044.1 1139733 1140929 D 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 1139733..1140929 Ruegeria sp. TM1040 4077201 YP_613057.1 CDS TM1040_1062 NC_008044.1 1141108 1141710 D TIGRFAM: Phage conserved hypothetical protein, phiE125 gp8: (9.4e-50); KEGG: sil:SPO2260 hypothetical protein, ev=9e-50, 53% identity; hypothetical protein 1141108..1141710 Ruegeria sp. TM1040 4077202 YP_613058.1 CDS TM1040_1063 NC_008044.1 1141707 1142045 D TIGRFAM: conserved hypothetical protein: (0.0012); KEGG: sil:SPO2259 head-tail adaptor, , ev=5e-29, 55% identity; hypothetical protein 1141707..1142045 Ruegeria sp. TM1040 4077203 YP_613059.1 CDS TM1040_1064 NC_008044.1 1142042 1142449 D KEGG: sil:SPO2258 hypothetical protein, ev=3e-41, 64% identity; hypothetical protein 1142042..1142449 Ruegeria sp. TM1040 4077204 YP_613060.1 CDS TM1040_1065 NC_008044.1 1142485 1142898 D 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 1142485..1142898 Ruegeria sp. TM1040 4077205 YP_613061.1 CDS TM1040_1066 NC_008044.1 1142902 1143225 D KEGG: sil:SPO2256 hypothetical protein, ev=3e-30, 63% identity; hypothetical protein 1142902..1143225 Ruegeria sp. TM1040 4077206 YP_613062.1 CDS TM1040_1067 NC_008044.1 1143222 1143437 D TIGRFAM: conserved hypothetical protein: (7e-19); KEGG: sil:SPO2255 hypothetical protein, ev=6e-14, 67% identity; hypothetical protein 1143222..1143437 Ruegeria sp. TM1040 4077207 YP_613063.1 CDS TM1040_1068 NC_008044.1 1143441 1144100 D KEGG: jan:Jann_1642 phage-related minor tail protein-like, ev=1e-60, 56% identity; phage-related minor tail protein-like 1143441..1144100 Ruegeria sp. TM1040 4077208 YP_613064.1 CDS TM1040_1069 NC_008044.1 1144114 1144746 D TIGRFAM: conserved hypothetical protein: (9.6e-99); KEGG: sil:SPO2253 hypothetical protein, ev=2e-84, 70% identity; hypothetical protein 1144114..1144746 Ruegeria sp. TM1040 4077209 YP_613065.1 CDS TM1040_1070 NC_008044.1 1144746 1145624 D TIGRFAM: Phage conserved hypothetical protein BR0599: (5.4e-129); KEGG: sil:SPO2252 hypothetical protein, ev=1e-113, 66% identity; phage protein 1144746..1145624 Ruegeria sp. TM1040 4077210 YP_613066.1 CDS TM1040_1071 NC_008044.1 1145621 1146058 D 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 1145621..1146058 Ruegeria sp. TM1040 4077211 YP_613067.1 CDS TM1040_1072 NC_008044.1 1146071 1149991 D KEGG: sil:SPO2250 hypothetical protein, ev=0.0, 63% identity; hypothetical protein 1146071..1149991 Ruegeria sp. TM1040 4077212 YP_613068.1 CDS TM1040_1073 NC_008044.1 1149988 1150299 D KEGG: sil:SPO2249 hypothetical protein, ev=1e-12, 43% identity; hypothetical protein 1149988..1150299 Ruegeria sp. TM1040 4077213 YP_613069.1 CDS TM1040_1074 NC_008044.1 1150412 1150618 R 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 complement(1150412..1150618) Ruegeria sp. TM1040 4077214 YP_613070.1 CDS TM1040_1075 NC_008044.1 1150977 1151783 D 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 1150977..1151783 Ruegeria sp. TM1040 4077215 YP_613071.1 CDS TM1040_1076 NC_008044.1 1151953 1152252 D PFAM: protein of unknown function DUF1330: (8.2e-30); KEGG: mlo:mll3541 hypothetical protein, ev=2e-11, 41% identity; hypothetical protein 1151953..1152252 Ruegeria sp. TM1040 4076309 YP_613072.1 CDS TM1040_1077 NC_008044.1 1152399 1153739 R 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 complement(1152399..1153739) Ruegeria sp. TM1040 4076310 YP_613073.1 CDS TM1040_1078 NC_008044.1 1153751 1155127 R 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 complement(1153751..1155127) Ruegeria sp. TM1040 4076311 YP_613074.1 CDS TM1040_1079 NC_008044.1 1155145 1156158 R PFAM: dehydrogenase, E1 component: (1.4e-135); KEGG: jan:Jann_1691 pyruvate dehydrogenase (lipoamide), ev=1e-169, 84% identity; pyruvate dehydrogenase (lipoamide) complement(1155145..1156158) Ruegeria sp. TM1040 4076312 YP_613075.1 CDS TM1040_1080 NC_008044.1 1156201 1156446 R hypothetical protein complement(1156201..1156446) Ruegeria sp. TM1040 4076313 YP_613076.1 CDS TM1040_1081 NC_008044.1 1156589 1156888 R PFAM: Septum formation initiator: (3.1e-10); KEGG: sil:SPO2239 hypothetical protein, ev=4e-33, 69% identity; septum formation initiator complement(1156589..1156888) Ruegeria sp. TM1040 4076314 YP_613077.1 CDS TM1040_1082 NC_008044.1 1157120 1157569 R KEGG: rso:RSc0006 hypothetical protein, ev=5e-19, 50% identity; hypothetical protein complement(1157120..1157569) Ruegeria sp. TM1040 4076315 YP_613078.1 CDS TM1040_1083 NC_008044.1 1157674 1159446 R 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 complement(1157674..1159446) Ruegeria sp. TM1040 4076316 YP_613079.1 CDS pgk NC_008044.1 1159751 1160941 R Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway; phosphoglycerate kinase complement(1159751..1160941) Ruegeria sp. TM1040 4076317 YP_613080.1 CDS TM1040_1085 NC_008044.1 1161321 1161827 D 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 1161321..1161827 Ruegeria sp. TM1040 4076318 YP_613081.1 CDS TM1040_1086 NC_008044.1 1161820 1162368 D 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 1161820..1162368 Ruegeria sp. TM1040 4076319 YP_613082.1 CDS TM1040_1087 NC_008044.1 1162460 1163047 R 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 complement(1162460..1163047) Ruegeria sp. TM1040 4076320 YP_613083.1 CDS TM1040_1088 NC_008044.1 1163480 1164001 R PFAM: protein of unknown function DUF583: (2.4e-30); KEGG: sil:SPO2231 hypothetical protein, ev=3e-67, 79% identity; hypothetical protein complement(1163480..1164001) Ruegeria sp. TM1040 4076321 YP_613084.1 CDS TM1040_1089 NC_008044.1 1163991 1165322 R PFAM: peptidase M23B: (6e-51); KEGG: sil:SPO2230 peptidase, M23/M37 family, ev=1e-179, 70% identity; peptidase M23B complement(1163991..1165322) Ruegeria sp. TM1040 4076322 YP_613085.1 CDS TM1040_1090 NC_008044.1 1165550 1166392 R PFAM: protein of unknown function DUF455: (8e-83); KEGG: sil:SPO2229 hypothetical protein, ev=1e-124, 78% identity; hypothetical protein complement(1165550..1166392) Ruegeria sp. TM1040 4076323 YP_613086.1 CDS TM1040_1091 NC_008044.1 1166917 1167378 R 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 complement(1166917..1167378) Ruegeria sp. TM1040 4076324 YP_613087.1 CDS TM1040_1092 NC_008044.1 1167440 1170907 D KEGG: sil:SPO2227 hypothetical protein, ev=0.0, 45% identity; hypothetical protein 1167440..1170907 Ruegeria sp. TM1040 4076325 YP_613088.1 CDS queA NC_008044.1 1171133 1172182 D Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step; S-adenosylmethionine--tRNA ribosyltransferase-isomerase 1171133..1172182 Ruegeria sp. TM1040 4076326 YP_613089.1 CDS TM1040_1094 NC_008044.1 1172453 1173727 D PFAM: major facilitator superfamily MFS_1: (1e-28); KEGG: sil:SPO2225 membrane protein, , ev=1e-166, 70% identity; major facilitator superfamily transporter 1172453..1173727 Ruegeria sp. TM1040 4076327 YP_613090.1 CDS TM1040_1095 NC_008044.1 1173877 1174455 D PFAM: protein of unknown function DUF924: (1.9e-68); KEGG: sil:SPO2224 hypothetical protein, ev=1e-78, 71% identity; hypothetical protein 1173877..1174455 Ruegeria sp. TM1040 4077802 YP_613091.1 CDS TM1040_1096 NC_008044.1 1174730 1176124 D E3 component of pyruvate complex; catalyzes the oxidation of dihydrolipoamide to lipoamide; dihydrolipoamide dehydrogenase 1174730..1176124 Ruegeria sp. TM1040 4077803 YP_613092.1 CDS TM1040_1097 NC_008044.1 1176282 1177466 D PFAM: major facilitator superfamily MFS_1: (3.5e-19); KEGG: sil:SPO3505 membrane protein, , ev=3e-85, 45% identity; major facilitator superfamily transporter 1176282..1177466 Ruegeria sp. TM1040 4077804 YP_613093.1 CDS uvrA NC_008044.1 1177570 1180461 D 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 1177570..1180461 Ruegeria sp. TM1040 4077805 YP_613094.1 CDS TM1040_1099 NC_008044.1 1180567 1181016 R hypothetical protein complement(1180567..1181016) Ruegeria sp. TM1040 4077806 YP_613095.1 CDS TM1040_1100 NC_008044.1 1181139 1181903 D PFAM: helix-turn-helix motif: (2.4e-07); KEGG: sil:SPO2216 DNA-binding protein, , ev=8e-71, 58% identity; XRE family transcriptional regulator 1181139..1181903 Ruegeria sp. TM1040 4077807 YP_613096.1 CDS TM1040_1101 NC_008044.1 1181900 1182772 R 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 complement(1181900..1182772) Ruegeria sp. TM1040 4077808 YP_613097.1 CDS TM1040_1102 NC_008044.1 1182774 1183817 R 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 complement(1182774..1183817) Ruegeria sp. TM1040 4077809 YP_613098.1 CDS TM1040_1103 NC_008044.1 1183842 1184987 R 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 complement(1183842..1184987) Ruegeria sp. TM1040 4077810 YP_613099.1 CDS TM1040_1104 NC_008044.1 1185278 1187128 D 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 1185278..1187128 Ruegeria sp. TM1040 4077811 YP_613100.1 CDS TM1040_1105 NC_008044.1 1187238 1187855 R 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 complement(1187238..1187855) Ruegeria sp. TM1040 4077812 YP_613101.1 CDS TM1040_1106 NC_008044.1 1188053 1189552 R 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 complement(1188053..1189552) Ruegeria sp. TM1040 4077813 YP_613102.1 CDS TM1040_1107 NC_008044.1 1189708 1190604 D 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 1189708..1190604 Ruegeria sp. TM1040 4077814 YP_613103.1 CDS TM1040_1108 NC_008044.1 1190660 1191094 D PFAM: CBS: (1.5e-31); KEGG: sil:SPO2201 CBS domain protein, ev=5e-43, 62% identity; signal-transduction protein 1190660..1191094 Ruegeria sp. TM1040 4077815 YP_613104.1 CDS coaD NC_008044.1 1191220 1191717 D Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA; phosphopantetheine adenylyltransferase 1191220..1191717 Ruegeria sp. TM1040 4077816 YP_613105.1 CDS TM1040_1110 NC_008044.1 1191785 1191928 R KEGG: sil:SPO2199 hypothetical protein, ev=5e-11, 63% identity; hypothetical protein complement(1191785..1191928) Ruegeria sp. TM1040 4077817 YP_613106.1 CDS TM1040_1111 NC_008044.1 1192007 1193008 R 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 complement(1192007..1193008) Ruegeria sp. TM1040 4077818 YP_613107.1 CDS TM1040_1112 NC_008044.1 1193263 1194213 D PFAM: protein of unknown function DUF808: (1.9e-153); KEGG: sil:SPO2197 hypothetical protein, ev=1e-107, 65% identity; hypothetical protein 1193263..1194213 Ruegeria sp. TM1040 4077819 YP_613108.1 CDS TM1040_1113 NC_008044.1 1194349 1196370 R 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 complement(1194349..1196370) Ruegeria sp. TM1040 4077820 YP_613109.1 CDS TM1040_1114 NC_008044.1 1196728 1197648 D KEGG: sil:SPO1866 hypothetical protein, ev=3e-37, 39% identity; hypothetical protein 1196728..1197648 Ruegeria sp. TM1040 4077821 YP_613110.1 CDS TM1040_1115 NC_008044.1 1197648 1198193 D KEGG: sil:SPO1867 hypothetical protein, ev=6e-49, 76% identity; hypothetical protein 1197648..1198193 Ruegeria sp. TM1040 4077236 YP_613111.1 CDS TM1040_1116 NC_008044.1 1198356 1198718 R 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 complement(1198356..1198718) Ruegeria sp. TM1040 4077237 YP_613112.1 CDS TM1040_1117 NC_008044.1 1199086 1199322 R PFAM: BolA-like protein: (5.2e-09); KEGG: jan:Jann_2172 BolA-like protein, ev=4e-33, 87% identity; BolA-like protein complement(1199086..1199322) Ruegeria sp. TM1040 4077238 YP_613113.1 CDS TM1040_1118 NC_008044.1 1199601 1201766 R 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 complement(1199601..1201766) Ruegeria sp. TM1040 4077239 YP_613114.1 CDS TM1040_1119 NC_008044.1 1202216 1203121 R 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 complement(1202216..1203121) Ruegeria sp. TM1040 4077240 YP_613115.1 CDS TM1040_1120 NC_008044.1 1203290 1206709 D Catalyzes the ferredoxin-dependent oxidative decarboxylation of arylpyruvates; indolepyruvate ferredoxin oxidoreductase 1203290..1206709 Ruegeria sp. TM1040 4077241 YP_613116.1 CDS TM1040_1121 NC_008044.1 1206847 1207725 D PFAM: phospholipid/glycerol acyltransferase: (0.00044); KEGG: sil:SPO1874 acyltransferase domain protein, ev=1e-136, 78% identity; phospholipid/glycerol acyltransferase 1206847..1207725 Ruegeria sp. TM1040 4077242 YP_613117.1 CDS TM1040_1122 NC_008044.1 1207757 1208566 D 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 1207757..1208566 Ruegeria sp. TM1040 4077243 YP_613118.1 CDS argC NC_008044.1 1208651 1209679 D 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 1208651..1209679 Ruegeria sp. TM1040 4077244 YP_613119.1 CDS TM1040_1124 NC_008044.1 1209696 1210139 D 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 1209696..1210139 Ruegeria sp. TM1040 4077245 YP_613120.1 CDS TM1040_1125 NC_008044.1 1210282 1210890 D PFAM: protein of unknown function DUF847: (6.3e-72); KEGG: sil:SPO1878 hypothetical protein, ev=3e-74, 68% identity; hypothetical protein 1210282..1210890 Ruegeria sp. TM1040 4077246 YP_613121.1 CDS TM1040_1126 NC_008044.1 1210900 1211436 D KEGG: rsp:RSP_6081 hypothetical protein, ev=3e-26, 47% identity; hypothetical protein 1210900..1211436 Ruegeria sp. TM1040 4077247 YP_613122.1 CDS TM1040_1127 NC_008044.1 1211514 1213478 D 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 1211514..1213478 Ruegeria sp. TM1040 4077248 YP_613123.1 CDS TM1040_1128 NC_008044.1 1213475 1213960 D 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 1213475..1213960 Ruegeria sp. TM1040 4077249 YP_613124.1 CDS TM1040_1129 NC_008044.1 1214188 1214706 D KEGG: rpa:RPA2489 hypothetical protein, ev=3e-30, 42% identity; hypothetical protein 1214188..1214706 Ruegeria sp. TM1040 4077250 YP_613125.1 CDS TM1040_1130 NC_008044.1 1214788 1215567 D 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 1214788..1215567 Ruegeria sp. TM1040 4077251 YP_613126.1 CDS TM1040_1131 NC_008044.1 1215643 1216653 R PFAM: Hemolysin-type calcium-binding region: (0.66); KEGG: bja:bll7673 hypothetical protein, ev=5e-47, 44% identity; hemolysin-type calcium-binding protein complement(1215643..1216653) Ruegeria sp. TM1040 4077252 YP_613127.1 CDS TM1040_1132 NC_008044.1 1216941 1218236 R 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 complement(1216941..1218236) Ruegeria sp. TM1040 4077253 YP_613128.1 CDS gltX NC_008044.1 1218376 1219776 R Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase complement(1218376..1219776) Ruegeria sp. TM1040 4077254 YP_613129.1 CDS TM1040_1134 NC_008044.1 1219862 1221880 D PFAM: ComEC/Rec2-related protein: (5.2e-62); KEGG: sil:SPO2155 competence protein, ev=0.0, 53% identity; ComEC/Rec2-like protein 1219862..1221880 Ruegeria sp. TM1040 4078430 YP_613130.1 CDS TM1040_1135 NC_008044.1 1221954 1222679 R Represses a number of genes involved in the response to DNA damage; LexA repressor complement(1221954..1222679) Ruegeria sp. TM1040 4078431 YP_613131.1 CDS TM1040_1136 NC_008044.1 1222806 1223978 R 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 complement(1222806..1223978) Ruegeria sp. TM1040 4078432 YP_613132.1 CDS moaC NC_008044.1 1223982 1224452 R 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 complement(1223982..1224452) Ruegeria sp. TM1040 4078433 YP_613133.1 CDS trpC NC_008044.1 1224499 1225308 R 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 complement(1224499..1225308) Ruegeria sp. TM1040 4078434 YP_613134.1 CDS TM1040_1139 NC_008044.1 1225301 1226005 R 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 complement(1225301..1226005) Ruegeria sp. TM1040 4078435 YP_613135.1 CDS trpD NC_008044.1 1226005 1227027 R Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate; anthranilate phosphoribosyltransferase complement(1226005..1227027) Ruegeria sp. TM1040 4078436 YP_613136.1 CDS TM1040_1141 NC_008044.1 1227024 1227605 R TrpG; with TrpE catalyzes the formation of anthranilate and glutamate from chorismate and glutamine; TrpG provides the glutamine amidotransferase activity; anthranilate synthase component II complement(1227024..1227605) Ruegeria sp. TM1040 4078437 YP_613137.1 CDS TM1040_1142 NC_008044.1 1227757 1229316 D KEGG: sil:SPO2148 hypothetical protein, ev=1e-106, 47% identity; hypothetical protein 1227757..1229316 Ruegeria sp. TM1040 4078438 YP_613138.1 CDS TM1040_1143 NC_008044.1 1229411 1230922 R with component II, the glutamine amidotransferase, catalyzes the formation of anthranilate from chorismate and glutamine; anthranilate synthase component I complement(1229411..1230922) Ruegeria sp. TM1040 4078439 YP_613139.1 CDS TM1040_1144 NC_008044.1 1230946 1232781 R KEGG: sil:SPO2145 peptidyl-prolyl cis-trans isomerse D, ev=1e-178, 52% identity; peptidyl-prolyl cis-trans isomerse D complement(1230946..1232781) Ruegeria sp. TM1040 4078440 YP_613140.1 CDS TM1040_1145 NC_008044.1 1232945 1234120 R PFAM: aminotransferase, class I and II: (1.4e-35); KEGG: sil:SPO2144 aminotransferase, classes I and II, ev=1e-150, 67% identity; hypothetical protein complement(1232945..1234120) Ruegeria sp. TM1040 4078441 YP_613141.1 CDS TM1040_1146 NC_008044.1 1234272 1234802 R catalyzes the conversion of guanine, xanthine and, to a lesser extent, hypoxanthine to GMP, XMP and IMP, respectively; xanthine-guanine phosphoribosyltransferase complement(1234272..1234802) Ruegeria sp. TM1040 4078442 YP_613142.1 CDS TM1040_1147 NC_008044.1 1234809 1235615 R Catalyzes a key regulatory step in fatty acid biosynthesis; enoyl-ACP reductase complement(1234809..1235615) Ruegeria sp. TM1040 4078443 YP_613143.1 CDS TM1040_1148 NC_008044.1 1235783 1236388 D 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 1235783..1236388 Ruegeria sp. TM1040 4078444 YP_613144.1 CDS TM1040_1149 NC_008044.1 1236516 1237055 D 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 1236516..1237055 Ruegeria sp. TM1040 4078445 YP_613145.1 CDS TM1040_1150 NC_008044.1 1237055 1237534 D PFAM: protein of unknown function DUF192: (1.7e-38); KEGG: sil:SPO2139 hypothetical protein, ev=1e-44, 52% identity; hypothetical protein 1237055..1237534 Ruegeria sp. TM1040 4078446 YP_613146.1 CDS TM1040_1151 NC_008044.1 1238449 1242102 D Catalyzes the rate-limiting step in dNTP synthesis; ribonucleotide-diphosphate reductase subunit alpha 1238449..1242102 Ruegeria sp. TM1040 4078447 YP_613147.1 CDS TM1040_1152 NC_008044.1 1242589 1243077 D hypothetical protein 1242589..1243077 Ruegeria sp. TM1040 4078448 YP_613148.1 CDS cysS NC_008044.1 1243613 1244986 D 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 1243613..1244986 Ruegeria sp. TM1040 4078449 YP_613149.1 CDS TM1040_1154 NC_008044.1 1244983 1246611 D 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 1244983..1246611 Ruegeria sp. TM1040 4075940 YP_613150.1 CDS TM1040_1155 NC_008044.1 1246601 1247377 D KEGG: sil:SPO2129 hypothetical protein, ev=5e-82, 59% identity; hypothetical protein 1246601..1247377 Ruegeria sp. TM1040 4075941 YP_613151.1 CDS TM1040_1156 NC_008044.1 1247435 1248664 R PFAM: major facilitator superfamily MFS_1: (3.9e-19); KEGG: sil:SPO2128 transporter, , ev=0.0, 80% identity; major facilitator superfamily transporter complement(1247435..1248664) Ruegeria sp. TM1040 4075942 YP_613152.1 CDS TM1040_1157 NC_008044.1 1248737 1249369 D PFAM: HhH-GPD: (2.8e-14); KEGG: sil:SPO2127 DNA-3-methyladenine glycosylase II, , ev=1e-93, 81% identity; HhH-GPD 1248737..1249369 Ruegeria sp. TM1040 4075943 YP_613153.1 CDS TM1040_1158 NC_008044.1 1249366 1250031 D PFAM: phospholipase/Carboxylesterase: (4.4e-35); KEGG: sil:SPO2126 phospholipase/carboxylesterase family protein, ev=1e-105, 85% identity; phospholipase/carboxylesterase 1249366..1250031 Ruegeria sp. TM1040 4075944 YP_613154.1 CDS TM1040_1159 NC_008044.1 1250051 1250512 R PFAM: regulatory proteins, AsnC/Lrp: (1.7e-06); KEGG: sme:SMc02504 transcription regulator protein, ev=6e-13, 34% identity; AsnC family transcriptional regulator complement(1250051..1250512) Ruegeria sp. TM1040 4075945 YP_613155.1 CDS TM1040_1160 NC_008044.1 1250605 1250919 D PFAM: Cupin 2, conserved barrel: (0.0012); KEGG: nma:NMA0001 hypothetical protein, ev=1e-30, 62% identity; cupin 1250605..1250919 Ruegeria sp. TM1040 4075946 YP_613156.1 CDS TM1040_1161 NC_008044.1 1250925 1251590 R 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 complement(1250925..1251590) Ruegeria sp. TM1040 4075947 YP_613157.1 CDS TM1040_1162 NC_008044.1 1251838 1252422 D 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 1251838..1252422 Ruegeria sp. TM1040 4075948 YP_613158.1 CDS TM1040_1163 NC_008044.1 1252474 1253520 R catalyzes the formation of L-proline from L-ornithine; ornithine cyclodeaminase complement(1252474..1253520) Ruegeria sp. TM1040 4075949 YP_613159.1 CDS TM1040_1164 NC_008044.1 1253517 1254446 R KEGG: sil:SPO2120 amidinotransferase family protein, ev=1e-124, 75% identity; amidinotransferase complement(1253517..1254446) Ruegeria sp. TM1040 4075950 YP_613160.1 CDS TM1040_1165 NC_008044.1 1254443 1255372 R TIGRFAM: arginase: (7.6e-114); PFAM: Arginase/agmatinase/formiminoglutamase: (8.7e-97); KEGG: sil:SPO2119 arginase, ev=1e-126, 70% identity; arginase complement(1254443..1255372) Ruegeria sp. TM1040 4075951 YP_613161.1 CDS TM1040_1166 NC_008044.1 1255482 1255913 D 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 1255482..1255913 Ruegeria sp. TM1040 4075952 YP_613162.1 CDS TM1040_1167 NC_008044.1 1255924 1256397 R 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 complement(1255924..1256397) Ruegeria sp. TM1040 4075953 YP_613163.1 CDS TM1040_1168 NC_008044.1 1256394 1256972 R KEGG: sil:SPO2116 DedA family protein, ev=3e-85, 81% identity; DedA family protein complement(1256394..1256972) Ruegeria sp. TM1040 4075954 YP_613164.1 CDS TM1040_1169 NC_008044.1 1257343 1259133 R 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 complement(1257343..1259133) Ruegeria sp. TM1040 4075955 YP_613165.1 CDS TM1040_1170 NC_008044.1 1259585 1261216 R activates fatty acids by binding to coenzyme A; acyl-CoA synthetase complement(1259585..1261216) Ruegeria sp. TM1040 4075956 YP_613166.1 CDS TM1040_1171 NC_008044.1 1261221 1262021 R Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase complement(1261221..1262021) Ruegeria sp. TM1040 4075957 YP_613167.1 CDS TM1040_1172 NC_008044.1 1262032 1262481 R PFAM: OsmC-like protein: (1.7e-22); KEGG: son:SO3409 OsmC/Ohr family protein, ev=1e-26, 41% identity; OsmC-like protein complement(1262032..1262481) Ruegeria sp. TM1040 4075958 YP_613168.1 CDS TM1040_1173 NC_008044.1 1262504 1263646 R 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) complement(1262504..1263646) Ruegeria sp. TM1040 4077782 YP_613169.1 CDS TM1040_1174 NC_008044.1 1263806 1264339 R PFAM: regulatory proteins, AsnC/Lrp: (4.9e-17); KEGG: sme:SMb20425 transcriptional regulator protein, ev=7e-36, 47% identity; AsnC family transcriptional regulator complement(1263806..1264339) Ruegeria sp. TM1040 4077783 YP_613170.1 CDS TM1040_1175 NC_008044.1 1264744 1265736 D 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 1264744..1265736 Ruegeria sp. TM1040 4077784 YP_613171.1 CDS TM1040_1176 NC_008044.1 1265730 1266737 R KEGG: sil:SPO2183 hypothetical protein, ev=1e-124, 62% identity; hypothetical protein complement(1265730..1266737) Ruegeria sp. TM1040 4077785 YP_613172.1 CDS TM1040_1177 NC_008044.1 1266814 1269228 R PFAM: protein of unknown function DUF214: (7.3e-09); KEGG: sil:SPO2182 permease, , ev=0.0, 49% identity; hypothetical protein complement(1266814..1269228) Ruegeria sp. TM1040 4077786 YP_613173.1 CDS TM1040_1178 NC_008044.1 1269225 1269887 R 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 complement(1269225..1269887) Ruegeria sp. TM1040 4077787 YP_613174.1 CDS TM1040_1179 NC_008044.1 1270013 1270456 D PFAM: Ion transport 2: (2e-08); KEGG: sil:SPO2179 hypothetical protein, ev=2e-35, 51% identity; Ion transport 2 1270013..1270456 Ruegeria sp. TM1040 4077788 YP_613175.1 CDS TM1040_1180 NC_008044.1 1270487 1271353 D TIGRFAM: ribonuclease BN, : (1.1e-22); PFAM: ribonuclease BN: (1.6e-41); KEGG: sil:SPO1856 ribonuclease BN, , ev=1e-71, 54% identity; ribonuclease BN 1270487..1271353 Ruegeria sp. TM1040 4077789 YP_613176.1 CDS TM1040_1181 NC_008044.1 1271442 1271687 D hypothetical protein 1271442..1271687 Ruegeria sp. TM1040 4077790 YP_613177.1 CDS TM1040_1182 NC_008044.1 1271718 1272434 R 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 complement(1271718..1272434) Ruegeria sp. TM1040 4077791 YP_613178.1 CDS TM1040_1183 NC_008044.1 1272519 1273631 R PFAM: Ppx/GppA phosphatase: (1.7e-28); KEGG: sil:SPO1859 phosphatase, Ppx/GppA family, ev=0.0, 89% identity; Ppx/GppA phosphatase complement(1272519..1273631) Ruegeria sp. TM1040 4077792 YP_613179.1 CDS TM1040_1184 NC_008044.1 1273898 1274194 D KEGG: sil:SPO1861 hypothetical protein, ev=3e-43, 84% identity; hypothetical protein 1273898..1274194 Ruegeria sp. TM1040 4077793 YP_613180.1 CDS TM1040_1185 NC_008044.1 1274224 1275156 D KEGG: sil:SPO1862 metFprotein, homolog, ev=1e-144, 83% identity; metF protein-like 1274224..1275156 Ruegeria sp. TM1040 4077794 YP_613181.1 CDS TM1040_1186 NC_008044.1 1275160 1276218 D 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 1275160..1276218 Ruegeria sp. TM1040 4077795 YP_613182.1 CDS TM1040_1187 NC_008044.1 1276546 1277559 D KEGG: atc:AGR_L_1930 sugar ABC transporter (sugar-binding protein), ev=1e-135, 70% identity; sugar ABC transporter (sugar-binding protein) 1276546..1277559 Ruegeria sp. TM1040 4077796 YP_613183.1 CDS TM1040_1188 NC_008044.1 1277641 1279176 D 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 1277641..1279176 Ruegeria sp. TM1040 4077797 YP_613184.1 CDS TM1040_1189 NC_008044.1 1279188 1280183 D PFAM: inner-membrane translocator: (3.7e-55); KEGG: atc:AGR_L_1933 ribose ABC transporter (permease), ev=1e-132, 74% identity; inner-membrane translocator 1279188..1280183 Ruegeria sp. TM1040 4077798 YP_613185.1 CDS TM1040_1190 NC_008044.1 1280191 1281171 D PFAM: sugar-binding region: (8.9e-68); KEGG: atc:AGR_L_1935 transcriptional regulator, ev=1e-101, 58% identity; DeoR family transcriptional regulator 1280191..1281171 Ruegeria sp. TM1040 4077799 YP_613186.1 CDS TM1040_1191 NC_008044.1 1281161 1282156 D PFAM: aldo/keto reductase: (2.9e-52); KEGG: ret:RHE_PB00074 probable aldoketo reductase protein, ev=1e-133, 69% identity; aldo/keto reductase 1281161..1282156 Ruegeria sp. TM1040 4077800 YP_613187.1 CDS TM1040_1192 NC_008044.1 1282229 1283944 D PFAM: FAD dependent oxidoreductase: (1.8e-47); KEGG: atc:AGR_L_1938 glycerol-3-phosphate dehydrogenase, ev=1e-166, 54% identity; FAD dependent oxidoreductase 1282229..1283944 Ruegeria sp. TM1040 4077801 YP_613188.1 CDS TM1040_1193 NC_008044.1 1283941 1284777 D 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 1283941..1284777 Ruegeria sp. TM1040 4076328 YP_613189.1 CDS TM1040_1194 NC_008044.1 1284794 1286305 D PFAM: carbohydrate kinase, FGGY: (9.5e-59); KEGG: atc:AGR_L_1942 L-xylulokinase, ev=1e-171, 58% identity; carbohydrate kinase 1284794..1286305 Ruegeria sp. TM1040 4076329 YP_613190.1 CDS TM1040_1195 NC_008044.1 1286318 1286605 D PFAM: Antibiotic biosynthesis monooxygenase: (1.9e-17); KEGG: bld:BLi00471 YcnE, ev=1e-09, 41% identity; antibiotic biosynthesis monooxygenase 1286318..1286605 Ruegeria sp. TM1040 4076330 YP_613191.1 CDS TM1040_1196 NC_008044.1 1286849 1287859 D 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 1286849..1287859 Ruegeria sp. TM1040 4076331 YP_613192.1 CDS TM1040_1197 NC_008044.1 1288124 1288369 D hypothetical protein 1288124..1288369 Ruegeria sp. TM1040 4076332 YP_613193.1 CDS TM1040_1198 NC_008044.1 1288731 1289417 D KEGG: reu:Reut_A3273 (acyl-carrier protein) phosphodiesterase, ev=5e-08, 32% identity; hypothetical protein 1288731..1289417 Ruegeria sp. TM1040 4076333 YP_613194.1 CDS TM1040_1199 NC_008044.1 1289858 1290730 D KEGG: sil:SPO1992 hypothetical protein, ev=1e-76, 57% identity; hypothetical protein 1289858..1290730 Ruegeria sp. TM1040 4076334 YP_613195.1 CDS TM1040_1200 NC_008044.1 1290983 1291579 D fusion of ribosomal protein L21 and COG3743; 50S ribosomal protein L21 1290983..1291579 Ruegeria sp. TM1040 4076335 YP_613196.1 CDS rpmA NC_008044.1 1291592 1291861 D involved in the peptidyltransferase reaction during translation; 50S ribosomal protein L27 1291592..1291861 Ruegeria sp. TM1040 4076336 YP_613197.1 CDS TM1040_1202 NC_008044.1 1292084 1292620 D PFAM: GCN5-related N-acetyltransferase: (5.1e-06); KEGG: sil:SPO1987 acetyltransferase, GNAT family, ev=2e-73, 73% identity; N-acetyltransferase GCN5 1292084..1292620 Ruegeria sp. TM1040 4076337 YP_613198.1 CDS obgE NC_008044.1 1292795 1293841 D essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication; GTPase ObgE 1292795..1293841 Ruegeria sp. TM1040 4076338 YP_613199.1 CDS TM1040_1204 NC_008044.1 1293829 1294935 D catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis; gamma-glutamyl kinase 1293829..1294935 Ruegeria sp. TM1040 4076339 YP_613200.1 CDS proA NC_008044.1 1294988 1296292 D Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway; gamma-glutamyl phosphate reductase 1294988..1296292 Ruegeria sp. TM1040 4076340 YP_613201.1 CDS TM1040_1206 NC_008044.1 1296378 1296974 R KEGG: sil:SPO1983 hypothetical protein, ev=4e-54, 51% identity; hypothetical protein complement(1296378..1296974) Ruegeria sp. TM1040 4076341 YP_613202.1 CDS TM1040_1207 NC_008044.1 1297004 1297186 D KEGG: sil:SPO1982 hypothetical protein, ev=8e-24, 83% identity; hypothetical protein 1297004..1297186 Ruegeria sp. TM1040 4076342 YP_613203.1 CDS TM1040_1208 NC_008044.1 1297294 1298055 D KEGG: sil:SPO1980 hypothetical protein, ev=1e-100, 70% identity; ornithine-acyl-ACP N-acyltransferase 1297294..1298055 Ruegeria sp. TM1040 4076343 YP_613204.1 CDS TM1040_1209 NC_008044.1 1298052 1298912 D PFAM: phospholipid/glycerol acyltransferase: (3.2e-21); KEGG: sil:SPO1979 acyltransferase, , ev=1e-104, 68% identity; lyso-ornithine lipid acyltransferase 1298052..1298912 Ruegeria sp. TM1040 4076344 YP_613205.1 CDS rpsB NC_008044.1 1299082 1299852 D 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 1299082..1299852 Ruegeria sp. TM1040 4076345 YP_613206.1 CDS tsf NC_008044.1 1299933 1300808 D 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 1299933..1300808 Ruegeria sp. TM1040 4076346 YP_613207.1 CDS TM1040_1212 NC_008044.1 1301262 1302017 R 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 complement(1301262..1302017) Ruegeria sp. TM1040 4075920 YP_613208.1 CDS TM1040_1213 NC_008044.1 1302014 1302514 R hypothetical protein complement(1302014..1302514) Ruegeria sp. TM1040 4075921 YP_613209.1 CDS TM1040_1214 NC_008044.1 1302602 1303312 D 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 1302602..1303312 Ruegeria sp. TM1040 4075922 YP_613210.1 CDS TM1040_1215 NC_008044.1 1304000 1304461 R PFAM: response regulator receiver: (1.3e-13); KEGG: cps:CPS_3951 response regulator, ev=1e-25, 42% identity; response regulator receiver protein complement(1304000..1304461) Ruegeria sp. TM1040 4075923 YP_613211.1 CDS TM1040_1216 NC_008044.1 1304451 1306760 R 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 complement(1304451..1306760) Ruegeria sp. TM1040 4075924 YP_613212.1 CDS TM1040_1217 NC_008044.1 1307375 1307941 R 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 complement(1307375..1307941) Ruegeria sp. TM1040 4075925 YP_613213.1 CDS TM1040_1218 NC_008044.1 1308297 1309919 D PFAM: Peptidoglycan-binding domain 1: (1.7e-17); KEGG: sil:SPO1929 peptidoglycan binding protein, , ev=1e-180, 59% identity; peptidoglycan binding domain-containing protein 1308297..1309919 Ruegeria sp. TM1040 4075926 YP_613214.1 CDS TM1040_1219 NC_008044.1 1309957 1311030 D 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 1309957..1311030 Ruegeria sp. TM1040 4075927 YP_613215.1 CDS TM1040_1220 NC_008044.1 1311082 1311339 D PFAM: phosphopantetheine-binding: (4.8e-09); KEGG: sil:SPO1931 acyl carrier protein, , ev=1e-33, 86% identity; phosphopantetheine-binding protein 1311082..1311339 Ruegeria sp. TM1040 4075928 YP_613216.1 CDS TM1040_1221 NC_008044.1 1311374 1312582 D PFAM: beta-ketoacyl synthase: (1.2e-52); KEGG: sil:SPO1932 beta-ketoacyl synthase family protein, ev=0.0, 90% identity; 3-oxoacyl-ACP synthase 1311374..1312582 Ruegeria sp. TM1040 4075929 YP_613217.1 CDS TM1040_1222 NC_008044.1 1312723 1313358 R PFAM: Invasion associated locus B: (1.3e-19); KEGG: sil:SPO1933 invasion associated family protein, ev=1e-67, 62% identity; invasion associated locus B complement(1312723..1313358) Ruegeria sp. TM1040 4075930 YP_613218.1 CDS TM1040_1223 NC_008044.1 1313953 1315497 D PFAM: protein of unknown function DUF853, NPT hydrolase : (1.2e-295); KEGG: sil:SPO1934 hypothetical protein, ev=0.0, 76% identity; hypothetical protein 1313953..1315497 Ruegeria sp. TM1040 4075931 YP_613219.1 CDS TM1040_1224 NC_008044.1 1315559 1317007 R 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 complement(1315559..1317007) Ruegeria sp. TM1040 4075932 YP_613220.1 CDS TM1040_1225 NC_008044.1 1317194 1318342 D 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 1317194..1318342 Ruegeria sp. TM1040 4075933 YP_613221.1 CDS TM1040_1226 NC_008044.1 1318425 1320509 D PFAM: ferredoxin: (0.0056); KEGG: sil:SPO2041 iron-sulfur cluster-binding protein, ev=0.0, 84% identity; ferredoxin 1318425..1320509 Ruegeria sp. TM1040 4075934 YP_613222.1 CDS TM1040_1227 NC_008044.1 1320632 1321807 D PFAM: Fmu (Sun): (8.2e-13); KEGG: sil:SPO2037 NOL1/NOP2/sun family protein, ev=1e-121, 58% identity; hypothetical protein 1320632..1321807 Ruegeria sp. TM1040 4075935 YP_613223.1 CDS TM1040_1228 NC_008044.1 1321904 1324213 D 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 1321904..1324213 Ruegeria sp. TM1040 4075936 YP_613224.1 CDS TM1040_1229 NC_008044.1 1324244 1324903 R KEGG: sil:SPO2035 hypothetical protein, ev=1e-62, 58% identity; hypothetical protein complement(1324244..1324903) Ruegeria sp. TM1040 4075937 YP_613225.1 CDS recA NC_008044.1 1325036 1326109 D 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 1325036..1326109 Ruegeria sp. TM1040 4075938 YP_613226.1 CDS TM1040_1231 NC_008044.1 1326112 1326660 D KEGG: rsp:RSP_3140 hypothetical protein, ev=5e-56, 59% identity; hypothetical protein 1326112..1326660 Ruegeria sp. TM1040 4075939 YP_613227.1 CDS alaS NC_008044.1 1326722 1329430 D 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 1326722..1329430 Ruegeria sp. TM1040 4076347 YP_613228.1 CDS TM1040_1233 NC_008044.1 1329437 1329724 D PFAM: protein of unknown function DUF1330: (8.8e-41); KEGG: sil:SPO2032 hypothetical protein, ev=2e-43, 91% identity; hypothetical protein 1329437..1329724 Ruegeria sp. TM1040 4076348 YP_613229.1 CDS TM1040_1234 NC_008044.1 1329844 1330620 D PFAM: glutamine amidotransferase, class-II: (0.00099); KEGG: rsp:RSP_0449 glutamine amidotransferase, ev=2e-94, 66% identity; glutamine amidotransferase, class-II 1329844..1330620 Ruegeria sp. TM1040 4076349 YP_613230.1 CDS TM1040_1235 NC_008044.1 1330689 1332509 R 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 complement(1330689..1332509) Ruegeria sp. TM1040 4076350 YP_613231.1 CDS TM1040_1236 NC_008044.1 1332636 1332965 R 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 complement(1332636..1332965) Ruegeria sp. TM1040 4076351 YP_613232.1 CDS TM1040_1237 NC_008044.1 1333106 1334272 R KEGG: sil:SPO2028 HD domain protein, ev=1e-123, 58% identity; HD domain-containing protein complement(1333106..1334272) Ruegeria sp. TM1040 4076352 YP_613233.1 CDS TM1040_1238 NC_008044.1 1334269 1334517 R KEGG: sil:SPO2027 hypothetical protein, ev=9e-18, 62% identity; hypothetical protein complement(1334269..1334517) Ruegeria sp. TM1040 4076353 YP_613234.1 CDS TM1040_1239 NC_008044.1 1334517 1335170 R KEGG: sil:SPO2026 hypothetical protein, ev=1e-120, 94% identity; hypothetical protein complement(1334517..1335170) Ruegeria sp. TM1040 4076354 YP_613235.1 CDS TM1040_1240 NC_008044.1 1335357 1335815 D 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 1335357..1335815 Ruegeria sp. TM1040 4076355 YP_613236.1 CDS TM1040_1241 NC_008044.1 1335882 1336925 D PFAM: aminotransferase, class V: (8.6e-29); KEGG: rsp:RSP_0442 aminotransferase, ev=1e-131, 67% identity; class V aminotransferase 1335882..1336925 Ruegeria sp. TM1040 4076356 YP_613237.1 CDS TM1040_1242 NC_008044.1 1336941 1338461 D with SufCD activates cysteine desulfurase SufS; cysteine desulfurase activator complex subunit SufB 1336941..1338461 Ruegeria sp. TM1040 4076357 YP_613238.1 CDS TM1040_1243 NC_008044.1 1338500 1338814 D PFAM: protein of unknown function DUF74: (5.9e-61); KEGG: sil:SPO2021 hypothetical protein, ev=5e-43, 90% identity; hypothetical protein 1338500..1338814 Ruegeria sp. TM1040 4076358 YP_613239.1 CDS TM1040_1244 NC_008044.1 1338827 1339591 D TIGRFAM: Methyltransferase FkbM: (1.9e-26); KEGG: jan:Jann_2362 methyltransferase FkbM, ev=6e-56, 49% identity; methyltransferase FkbM 1338827..1339591 Ruegeria sp. TM1040 4076359 YP_613240.1 CDS TM1040_1245 NC_008044.1 1339654 1340409 D 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 1339654..1340409 Ruegeria sp. TM1040 4076360 YP_613241.1 CDS TM1040_1246 NC_008044.1 1340409 1341689 D PFAM: SufBD: (6.7e-27); KEGG: sil:SPO2017 FeS assembly protein SufD, ev=0.0, 79% identity; SufBD protein 1340409..1341689 Ruegeria sp. TM1040 4076361 YP_613242.1 CDS TM1040_1247 NC_008044.1 1341698 1342183 D KEGG: sil:SPO2016 hypothetical protein, ev=4e-56, 66% identity; hypothetical protein 1341698..1342183 Ruegeria sp. TM1040 4076362 YP_613243.1 CDS TM1040_1248 NC_008044.1 1342183 1342761 D KEGG: sil:SPO2015 hypothetical protein, ev=6e-19, 31% identity; hypothetical protein 1342183..1342761 Ruegeria sp. TM1040 4076363 YP_613244.1 CDS TM1040_1249 NC_008044.1 1342754 1343974 D 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 1342754..1343974 Ruegeria sp. TM1040 4076364 YP_613245.1 CDS TM1040_1250 NC_008044.1 1344152 1344583 R PFAM: UspA: (5.5e-19); KEGG: sil:SPO2185 universal stress protein family protein, ev=1e-26, 45% identity; hypothetical protein complement(1344152..1344583) Ruegeria sp. TM1040 4076365 YP_613246.1 CDS TM1040_1251 NC_008044.1 1344583 1347180 R 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 complement(1344583..1347180) Ruegeria sp. TM1040 4077645 YP_613247.1 CDS TM1040_1252 NC_008044.1 1347286 1348257 R 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 complement(1347286..1348257) Ruegeria sp. TM1040 4077646 YP_613248.1 CDS TM1040_1253 NC_008044.1 1348352 1349239 R PFAM: sugar isomerase (SIS): (5.7e-06); KEGG: sil:SPO1591 SIS domain protein, ev=1e-36, 29% identity; RpiR family transcriptional regulator complement(1348352..1349239) Ruegeria sp. TM1040 4077647 YP_613249.1 CDS TM1040_1254 NC_008044.1 1349387 1351786 D 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 1349387..1351786 Ruegeria sp. TM1040 4077648 YP_613250.1 CDS TM1040_1255 NC_008044.1 1352244 1353467 R 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 complement(1352244..1353467) Ruegeria sp. TM1040 4077649 YP_613251.1 CDS TM1040_1256 NC_008044.1 1353542 1354474 D 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 1353542..1354474 Ruegeria sp. TM1040 4077650 YP_613252.1 CDS TM1040_1257 NC_008044.1 1354554 1355243 R 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 complement(1354554..1355243) Ruegeria sp. TM1040 4077651 YP_613253.1 CDS TM1040_1258 NC_008044.1 1355247 1355957 R PFAM: PhoU: (1.2e-29); KEGG: sil:SPO1952 phosphate transport system regulatory protein PhoU, ev=1e-93, 74% identity; phosphate uptake regulator PhoU complement(1355247..1355957) Ruegeria sp. TM1040 4077652 YP_613254.1 CDS TM1040_1259 NC_008044.1 1355974 1356771 R 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 complement(1355974..1356771) Ruegeria sp. TM1040 4077653 YP_613255.1 CDS TM1040_1260 NC_008044.1 1356784 1358151 R 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 complement(1356784..1358151) Ruegeria sp. TM1040 4077654 YP_613256.1 CDS TM1040_1261 NC_008044.1 1358151 1359629 R 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 complement(1358151..1359629) Ruegeria sp. TM1040 4077655 YP_613257.1 CDS TM1040_1262 NC_008044.1 1359739 1360779 R KEGG: sil:SPO1948 phosphate ABC transporter, periplasmic phosphate-binding protein, ev=1e-179, 90% identity; phosphate ABC transporter substrate-binding protein complement(1359739..1360779) Ruegeria sp. TM1040 4077656 YP_613258.1 CDS TM1040_1263 NC_008044.1 1361081 1362121 R 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 complement(1361081..1362121) Ruegeria sp. TM1040 4077657 YP_613259.1 CDS TM1040_1264 NC_008044.1 1362175 1363356 R 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 complement(1362175..1363356) Ruegeria sp. TM1040 4077658 YP_613260.1 CDS TM1040_1265 NC_008044.1 1363359 1363880 R PFAM: transferase hexapeptide repeat: (0.044); KEGG: sil:SPO1946 bacterial transferase family protein, ev=5e-82, 84% identity; hexapaptide repeat-containing transferase complement(1363359..1363880) Ruegeria sp. TM1040 4077659 YP_613261.1 CDS gmk NC_008044.1 1363877 1364530 R Essential for recycling GMP and indirectly, cGMP; guanylate kinase complement(1363877..1364530) Ruegeria sp. TM1040 4077660 YP_613262.1 CDS TM1040_1267 NC_008044.1 1364546 1365442 R 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 complement(1364546..1365442) Ruegeria sp. TM1040 4077661 YP_613263.1 CDS TM1040_1268 NC_008044.1 1365684 1366631 D KEGG: sil:SPO1943 hypothetical protein, ev=1e-55, 48% identity; hypothetical protein 1365684..1366631 Ruegeria sp. TM1040 4077662 YP_613264.1 CDS TM1040_1269 NC_008044.1 1366861 1368231 R 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 complement(1366861..1368231) Ruegeria sp. TM1040 4077663 YP_613265.1 CDS TM1040_1270 NC_008044.1 1368432 1369436 D 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 1368432..1369436 Ruegeria sp. TM1040 4077664 YP_613266.1 CDS TM1040_1271 NC_008044.1 1369443 1370549 R PFAM: glucose sorbosone dehydrogenase: (4e-53); KEGG: sil:SPO1940 hypothetical protein, ev=1e-128, 61% identity; glucose sorbosone dehydrogenase complement(1369443..1370549) Ruegeria sp. TM1040 4077431 YP_613267.1 CDS TM1040_1272 NC_008044.1 1370689 1371888 D 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 1370689..1371888 Ruegeria sp. TM1040 4077432 YP_613268.1 CDS TM1040_1273 NC_008044.1 1371995 1372786 D 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 1371995..1372786 Ruegeria sp. TM1040 4077433 YP_613269.1 CDS TM1040_1274 NC_008044.1 1372783 1373496 D 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 1372783..1373496 Ruegeria sp. TM1040 4077434 YP_613270.1 CDS TM1040_1275 NC_008044.1 1373500 1374510 D 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 1373500..1374510 Ruegeria sp. TM1040 4077435 YP_613271.1 CDS TM1040_1276 NC_008044.1 1374507 1375832 D 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 1374507..1375832 Ruegeria sp. TM1040 4077436 YP_613272.1 CDS TM1040_1277 NC_008044.1 1375914 1376249 R KEGG: rpb:RPB_3781 hypothetical protein, ev=5e-10, 33% identity; hypothetical protein complement(1375914..1376249) Ruegeria sp. TM1040 4077437 YP_613273.1 CDS TM1040_1278 NC_008044.1 1376648 1377646 R PFAM: phage late control D: (6.8e-98); KEGG: xfa:XF2479 hypothetical protein, ev=5e-64, 38% identity; phage late control D complement(1376648..1377646) Ruegeria sp. TM1040 4077438 YP_613274.1 CDS TM1040_1279 NC_008044.1 1377646 1377864 R PFAM: phage tail X: (3.5e-15); KEGG: sbo:SBO_0763 probable phage tail protein, ev=1e-08, 45% identity; phage tail X complement(1377646..1377864) Ruegeria sp. TM1040 4077439 YP_613275.1 CDS TM1040_1280 NC_008044.1 1377836 1378246 R PFAM: phage P2 GpU: (6.3e-49); KEGG: syf:Synpcc7942_0751 hypothetical protein, ev=2e-28, 51% identity; phage P2 GpU complement(1377836..1378246) Ruegeria sp. TM1040 4077440 YP_613276.1 CDS TM1040_1281 NC_008044.1 1378246 1380720 R KEGG: nar:Saro_2736 hypothetical protein, ev=9e-28, 38% identity; hypothetical protein complement(1378246..1380720) Ruegeria sp. TM1040 4077441 YP_613277.1 CDS TM1040_1282 NC_008044.1 1380844 1381143 R KEGG: xft:PD1092 hypothetical protein, ev=1e-07, 37% identity; hypothetical protein complement(1380844..1381143) Ruegeria sp. TM1040 4077442 YP_613278.1 CDS TM1040_1283 NC_008044.1 1381153 1381659 R PFAM: phage major tail tube protein: (6.2e-47); KEGG: xfa:XF2484 hypothetical protein, ev=3e-36, 45% identity; phage major tail tube protein complement(1381153..1381659) Ruegeria sp. TM1040 4077443 YP_613279.1 CDS TM1040_1284 NC_008044.1 1381659 1382876 R 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 complement(1381659..1382876) Ruegeria sp. TM1040 4077444 YP_613280.1 CDS TM1040_1285 NC_008044.1 1382990 1383349 R hypothetical protein complement(1382990..1383349) Ruegeria sp. TM1040 4077445 YP_613281.1 CDS TM1040_1286 NC_008044.1 1383350 1383850 R hypothetical protein complement(1383350..1383850) Ruegeria sp. TM1040 4077446 YP_613282.1 CDS TM1040_1287 NC_008044.1 1383852 1384859 R KEGG: rba:RB7745 serine protease homologue- secreted serine protease, ev=1e-29, 36% identity; secreted serine protease complement(1383852..1384859) Ruegeria sp. TM1040 4077447 YP_613283.1 CDS TM1040_1288 NC_008044.1 1384859 1385146 R hypothetical protein complement(1384859..1385146) Ruegeria sp. TM1040 4077448 YP_613284.1 CDS TM1040_1289 NC_008044.1 1385181 1385909 R KEGG: ecc:c0968 probable variable tail fibre protein, ev=8e-31, 37% identity; variable tail fiber protein complement(1385181..1385909) Ruegeria sp. TM1040 4077449 YP_613285.1 CDS TM1040_1290 NC_008044.1 1385920 1386465 R TIGRFAM: Phage tail protein I: (4.5e-37); KEGG: pfl:PFL_2006 tail protein I, ev=3e-31, 43% identity; Phage tail protein I complement(1385920..1386465) Ruegeria sp. TM1040 4078489 YP_613286.1 CDS TM1040_1291 NC_008044.1 1386446 1387345 R PFAM: Baseplate J-like protein: (2.3e-74); KEGG: pae:PA0618 probable bacteriophage protein, ev=9e-73, 48% identity; baseplate J-like protein complement(1386446..1387345) Ruegeria sp. TM1040 4078490 YP_613287.1 CDS TM1040_1292 NC_008044.1 1387345 1387683 R PFAM: GPW/gp25: (1.3e-45); KEGG: syf:Synpcc7942_0739 hypothetical protein, ev=2e-25, 51% identity; hypothetical protein complement(1387345..1387683) Ruegeria sp. TM1040 4078491 YP_613288.1 CDS TM1040_1293 NC_008044.1 1387732 1388022 R PFAM: PAAR: (0.003); KEGG: eca:ECA3426 phospholipase, ev=2e-19, 47% identity; hypothetical protein complement(1387732..1388022) Ruegeria sp. TM1040 4078492 YP_613289.1 CDS TM1040_1294 NC_008044.1 1388022 1388399 R 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 complement(1388022..1388399) Ruegeria sp. TM1040 4078493 YP_613290.1 CDS TM1040_1295 NC_008044.1 1388396 1388932 R KEGG: xfa:XF2493 hypothetical protein, ev=1e-28, 39% identity; hypothetical protein complement(1388396..1388932) Ruegeria sp. TM1040 4078494 YP_613291.1 CDS TM1040_1296 NC_008044.1 1388932 1389480 R KEGG: wol:WD0644 prophage LambdaW5, minor tail protein Z, , ev=3e-12, 32% identity; prophage LambdaW5, minor tail protein Z complement(1388932..1389480) Ruegeria sp. TM1040 4078495 YP_613292.1 CDS TM1040_1297 NC_008044.1 1389485 1389796 R KEGG: xft:PD1104 hypothetical protein, ev=3e-17, 44% identity; hypothetical protein complement(1389485..1389796) Ruegeria sp. TM1040 4078496 YP_613293.1 CDS TM1040_1298 NC_008044.1 1389796 1390053 R hypothetical protein complement(1389796..1390053) Ruegeria sp. TM1040 4078497 YP_613294.1 CDS TM1040_1299 NC_008044.1 1390120 1392111 R 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 complement(1390120..1392111) Ruegeria sp. TM1040 4078498 YP_613295.1 CDS TM1040_1300 NC_008044.1 1392128 1393741 R PFAM: phage portal protein, lambda: (1.8e-62); KEGG: xft:PD1107 phage-related portal protein, ev=7e-99, 38% identity; phage portal protein, lambda complement(1392128..1393741) Ruegeria sp. TM1040 4078499 YP_613296.1 CDS TM1040_1301 NC_008044.1 1393738 1394232 R KEGG: xfa:XF2499 hypothetical protein, ev=3e-27, 40% identity; hypothetical protein complement(1393738..1394232) Ruegeria sp. TM1040 4078500 YP_613297.1 CDS TM1040_1302 NC_008044.1 1394279 1396231 R PFAM: phage terminase GpA: (2.5e-216); KEGG: xft:PD1109 phage-related terminase large subunit, ev=0.0, 56% identity; phage terminase GpA complement(1394279..1396231) Ruegeria sp. TM1040 4078501 YP_613298.1 CDS TM1040_1303 NC_008044.1 1396228 1396782 R PFAM: phage DNA packaging Nu1: (2.7e-27); KEGG: xfa:XF2501 hypothetical protein, ev=6e-42, 49% identity; phage DNA packaging Nu1 complement(1396228..1396782) Ruegeria sp. TM1040 4078502 YP_613299.1 CDS TM1040_1304 NC_008044.1 1396955 1397338 R hypothetical protein complement(1396955..1397338) Ruegeria sp. TM1040 4078503 YP_613300.1 CDS TM1040_1305 NC_008044.1 1397338 1397748 R PFAM: glycoside hydrolase, family 24: (3.9e-18); KEGG: xfa:XF0513 phage-related endolysin, ev=2e-27, 46% identity; glycoside hydrolase complement(1397338..1397748) Ruegeria sp. TM1040 4078504 YP_613301.1 CDS TM1040_1306 NC_008044.1 1398109 1398345 R hypothetical protein complement(1398109..1398345) Ruegeria sp. TM1040 4078505 YP_613302.1 CDS TM1040_1307 NC_008044.1 1398593 1399195 D hypothetical protein 1398593..1399195 Ruegeria sp. TM1040 4078506 YP_613303.1 CDS TM1040_1308 NC_008044.1 1399240 1399593 D KEGG: psb:Psyr_0103 hypothetical protein, ev=5e-10, 34% identity; hypothetical protein 1399240..1399593 Ruegeria sp. TM1040 4078507 YP_613304.1 CDS TM1040_1309 NC_008044.1 1399675 1400223 R hypothetical protein complement(1399675..1400223) Ruegeria sp. TM1040 4078508 YP_613305.1 CDS TM1040_1310 NC_008044.1 1400406 1400966 R KEGG: xft:PD1114 hypothetical protein, ev=5e-07, 39% identity; hypothetical protein complement(1400406..1400966) Ruegeria sp. TM1040 4078353 YP_613306.1 CDS TM1040_1311 NC_008044.1 1400970 1401371 R KEGG: bte:BTH_II1034 GP72, ev=5e-08, 42% identity; hypothetical protein complement(1400970..1401371) Ruegeria sp. TM1040 4078354 YP_613307.1 CDS TM1040_1312 NC_008044.1 1401380 1401808 R hypothetical protein complement(1401380..1401808) Ruegeria sp. TM1040 4078355 YP_613308.1 CDS TM1040_1313 NC_008044.1 1401814 1402140 R KEGG: jan:Jann_2635 hypothetical protein, ev=1e-28, 72% identity; hypothetical protein complement(1401814..1402140) Ruegeria sp. TM1040 4078356 YP_613309.1 CDS TM1040_1314 NC_008044.1 1402391 1402690 R hypothetical protein complement(1402391..1402690) Ruegeria sp. TM1040 4078357 YP_613310.1 CDS TM1040_1315 NC_008044.1 1402687 1403685 R hypothetical protein complement(1402687..1403685) Ruegeria sp. TM1040 4078358 YP_613311.1 CDS TM1040_1316 NC_008044.1 1403888 1404421 R hypothetical protein complement(1403888..1404421) Ruegeria sp. TM1040 4078359 YP_613312.1 CDS TM1040_1317 NC_008044.1 1404414 1404701 R hypothetical protein complement(1404414..1404701) Ruegeria sp. TM1040 4078360 YP_613313.1 CDS TM1040_1318 NC_008044.1 1404882 1405148 D hypothetical protein 1404882..1405148 Ruegeria sp. TM1040 4078361 YP_613314.1 CDS TM1040_1319 NC_008044.1 1405184 1405507 R hypothetical protein complement(1405184..1405507) Ruegeria sp. TM1040 4078362 YP_613315.1 CDS TM1040_1320 NC_008044.1 1405803 1406438 D PFAM: peptidase S24, S26A and S26B: (0.018); KEGG: rsp:RSP_3771 hypothetical protein, ev=1e-35, 40% identity; phage repressor 1405803..1406438 Ruegeria sp. TM1040 4078363 YP_613316.1 CDS TM1040_1321 NC_008044.1 1406799 1407716 R KEGG: lma:LmjF34.0690 hypothetical protein, conserved, ev=4e-08, 33% identity; hypothetical protein complement(1406799..1407716) Ruegeria sp. TM1040 4078364 YP_613317.1 CDS TM1040_1322 NC_008044.1 1407723 1408715 R 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 complement(1407723..1408715) Ruegeria sp. TM1040 4078365 YP_613318.1 CDS TM1040_1323 NC_008044.1 1409154 1409492 R hypothetical protein complement(1409154..1409492) Ruegeria sp. TM1040 4078366 YP_613319.1 CDS TM1040_1324 NC_008044.1 1409890 1412040 R KEGG: psp:PSPPH_A0091 hypothetical protein, ev=1e-102, 45% identity; hypothetical protein complement(1409890..1412040) Ruegeria sp. TM1040 4078367 YP_613320.1 CDS TM1040_1325 NC_008044.1 1412750 1413019 D hypothetical protein 1412750..1413019 Ruegeria sp. TM1040 4078368 YP_613321.1 CDS TM1040_1326 NC_008044.1 1413107 1413550 D hypothetical protein 1413107..1413550 Ruegeria sp. TM1040 4078369 YP_613322.1 CDS TM1040_1327 NC_008044.1 1413693 1414379 D KEGG: rsp:RSP_3624 hypothetical protein, ev=5e-64, 51% identity; hypothetical protein 1413693..1414379 Ruegeria sp. TM1040 4078370 YP_613323.1 CDS TM1040_1328 NC_008044.1 1414830 1415831 D PFAM: phage integrase: (3e-06); KEGG: mag:amb2709 integrase, ev=5e-35, 33% identity; phage integrase 1414830..1415831 Ruegeria sp. TM1040 4078371 YP_613324.1 CDS TM1040_1329 NC_008044.1 1416383 1416856 D PFAM: thioesterase superfamily: (0.00047); KEGG: jan:Jann_1972 thioesterase superfamily, ev=2e-24, 38% identity; thioesterase superfamily protein 1416383..1416856 Ruegeria sp. TM1040 4075900 YP_613325.1 CDS TM1040_1330 NC_008044.1 1416887 1417558 R TIGRFAM: 6-phosphogluconolactonase: (7.2e-34); KEGG: sil:SPO2047 6-phosphogluconolactonase, ev=7e-68, 59% identity; 6-phosphogluconolactonase complement(1416887..1417558) Ruegeria sp. TM1040 4075901 YP_613326.1 CDS TM1040_1331 NC_008044.1 1417659 1417928 R PFAM: Usg-like: (5.9e-50); KEGG: sil:SPO2050 Usg, , ev=2e-37, 78% identity; Usg-like protein complement(1417659..1417928) Ruegeria sp. TM1040 4075902 YP_613327.1 CDS TM1040_1332 NC_008044.1 1418119 1420857 D negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit A 1418119..1420857 Ruegeria sp. TM1040 4075903 YP_613328.1 CDS TM1040_1333 NC_008044.1 1420988 1421338 D KEGG: sil:SPO2052 hypothetical protein, ev=2e-49, 77% identity; hypothetical protein 1420988..1421338 Ruegeria sp. TM1040 4075904 YP_613329.1 CDS TM1040_1334 NC_008044.1 1421393 1422862 R PFAM: peptidase M32, carboxypeptidase Taq metallopeptidase: (2.1e-114); KEGG: sil:SPO2053 thermostable carboxypeptidase, ev=0.0, 71% identity; carboxypeptidase complement(1421393..1422862) Ruegeria sp. TM1040 4075905 YP_613330.1 CDS TM1040_1335 NC_008044.1 1422867 1424012 R PFAM: cytochrome oxidase assembly: (4.2e-46); KEGG: sil:SPO2054 cytochrome c oxidase assembly protein, ev=1e-167, 78% identity; cytochrome oxidase assembly complement(1422867..1424012) Ruegeria sp. TM1040 4075906 YP_613331.1 CDS TM1040_1336 NC_008044.1 1424076 1424825 R 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 complement(1424076..1424825) Ruegeria sp. TM1040 4075907 YP_613332.1 CDS TM1040_1337 NC_008044.1 1424982 1425614 D PFAM: thiamine monophosphate synthase: (1e-13); KEGG: sil:SPO2056 thiamine-phosphate pyrophosphorylase, , ev=3e-82, 70% identity; thiamine monophosphate synthase 1424982..1425614 Ruegeria sp. TM1040 4075908 YP_613333.1 CDS TM1040_1338 NC_008044.1 1425754 1426662 D PFAM: PfkB: (3.5e-09); KEGG: sil:SPO2060 kinase, PfkB family, ev=1e-125, 77% identity; PfkB protein 1425754..1426662 Ruegeria sp. TM1040 4075909 YP_613334.1 CDS TM1040_1339 NC_008044.1 1426659 1427567 D 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 1426659..1427567 Ruegeria sp. TM1040 4075910 YP_613335.1 CDS TM1040_1340 NC_008044.1 1427655 1428362 D PFAM: protein of unknown function DUF502: (1.1e-55); KEGG: sil:SPO2062 hypothetical protein, ev=1e-100, 80% identity; hypothetical protein 1427655..1428362 Ruegeria sp. TM1040 4075911 YP_613336.1 CDS TM1040_1341 NC_008044.1 1428363 1429391 R PFAM: Patatin: (3.1e-08); KEGG: sil:SPO2064 phospholipase, patatin-like family, ev=1e-136, 68% identity; patatin complement(1428363..1429391) Ruegeria sp. TM1040 4075912 YP_613337.1 CDS TM1040_1342 NC_008044.1 1429486 1430259 R 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 complement(1429486..1430259) Ruegeria sp. TM1040 4075913 YP_613338.1 CDS TM1040_1343 NC_008044.1 1430594 1432423 D 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 1430594..1432423 Ruegeria sp. TM1040 4075914 YP_613339.1 CDS TM1040_1344 NC_008044.1 1432587 1432883 D hypothetical protein 1432587..1432883 Ruegeria sp. TM1040 4075915 YP_613340.1 CDS TM1040_1345 NC_008044.1 1432942 1433571 R 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 complement(1432942..1433571) Ruegeria sp. TM1040 4075916 YP_613341.1 CDS TM1040_1346 NC_008044.1 1433650 1435158 D 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 1433650..1435158 Ruegeria sp. TM1040 4075917 YP_613342.1 CDS TM1040_1347 NC_008044.1 1435162 1435863 D PFAM: DSBA oxidoreductase: (7.5e-43); KEGG: sil:SPO2070 DSBA-like thioredoxin family protein, ev=1e-88, 70% identity; DSBA oxidoreductase 1435162..1435863 Ruegeria sp. TM1040 4075918 YP_613343.1 CDS TM1040_1348 NC_008044.1 1436054 1437277 D 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 1436054..1437277 Ruegeria sp. TM1040 4075919 YP_613344.1 CDS TM1040_1349 NC_008044.1 1437358 1440807 R 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 complement(1437358..1440807) Ruegeria sp. TM1040 4076366 YP_613345.1 CDS TM1040_1350 NC_008044.1 1440838 1441377 R KEGG: sil:SPO2075 hypothetical protein, ev=6e-54, 58% identity; hypothetical protein complement(1440838..1441377) Ruegeria sp. TM1040 4076367 YP_613346.1 CDS TM1040_1351 NC_008044.1 1441498 1442535 D catalyzes the formation of porphobilinogen from 5-aminolevulinate; delta-aminolevulinic acid dehydratase 1441498..1442535 Ruegeria sp. TM1040 4076368 YP_613347.1 CDS TM1040_1352 NC_008044.1 1442665 1443237 D 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 1442665..1443237 Ruegeria sp. TM1040 4076369 YP_613348.1 CDS TM1040_1353 NC_008044.1 1443294 1444166 R 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 complement(1443294..1444166) Ruegeria sp. TM1040 4076370 YP_613349.1 CDS TM1040_1354 NC_008044.1 1444280 1446769 D PFAM: peptidase S45, penicillin amidase: (1e-122); KEGG: sil:SPO2078 penicillin amidase family protein, ev=0.0, 75% identity; penicillin amidase 1444280..1446769 Ruegeria sp. TM1040 4076371 YP_613350.1 CDS TM1040_1355 NC_008044.1 1446786 1448057 R 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 complement(1446786..1448057) Ruegeria sp. TM1040 4076372 YP_613351.1 CDS hfq NC_008044.1 1448057 1448296 R Stimulates the elongation of poly(A) tails; RNA-binding protein Hfq complement(1448057..1448296) Ruegeria sp. TM1040 4076373 YP_613352.1 CDS TM1040_1357 NC_008044.1 1448429 1449967 R PFAM: cation transporter: (2.5e-09); KEGG: sil:SPO2082 trk system potassium uptake protein TrkH, ev=0.0, 61% identity; cation transporter complement(1448429..1449967) Ruegeria sp. TM1040 4076374 YP_613353.1 CDS trkA NC_008044.1 1449969 1451345 R 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 complement(1449969..1451345) Ruegeria sp. TM1040 4076375 YP_613354.1 CDS TM1040_1359 NC_008044.1 1451445 1452863 R 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 complement(1451445..1452863) Ruegeria sp. TM1040 4076376 YP_613355.1 CDS TM1040_1360 NC_008044.1 1452860 1455139 R 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 complement(1452860..1455139) Ruegeria sp. TM1040 4076377 YP_613356.1 CDS TM1040_1361 NC_008044.1 1455239 1456618 R 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 complement(1455239..1456618) Ruegeria sp. TM1040 4076378 YP_613357.1 CDS TM1040_1362 NC_008044.1 1456636 1457724 R 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 complement(1456636..1457724) Ruegeria sp. TM1040 4076379 YP_613358.1 CDS TM1040_1363 NC_008044.1 1457721 1458707 R 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 complement(1457721..1458707) Ruegeria sp. TM1040 4076380 YP_613359.1 CDS TM1040_1364 NC_008044.1 1458902 1460050 D 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 1458902..1460050 Ruegeria sp. TM1040 4076381 YP_613360.1 CDS TM1040_1365 NC_008044.1 1460047 1460544 D PFAM: phosphatidylglycerophosphatase A: (5.1e-30); KEGG: sil:SPO2091 phosphatidylglycerophosphatase, , ev=3e-65, 68% identity; phosphatidylglycerophosphatase 1460047..1460544 Ruegeria sp. TM1040 4076382 YP_613361.1 CDS TM1040_1366 NC_008044.1 1460541 1461020 D PFAM: CinA-like: (1.2e-63); KEGG: sil:SPO2092 competence/damage-inducible protein CinA domain protein, ev=5e-51, 65% identity; CinA-like protein 1460541..1461020 Ruegeria sp. TM1040 4076383 YP_613362.1 CDS TM1040_1367 NC_008044.1 1461054 1461500 R PFAM: cyclase/dehydrase: (5e-38); KEGG: sil:SPO2096 aromatic-rich family protein, ev=2e-66, 80% identity; cyclase/dehydrase complement(1461054..1461500) Ruegeria sp. TM1040 4076384 YP_613363.1 CDS TM1040_1368 NC_008044.1 1461575 1462117 D KEGG: sil:SPO2097 hypoxanthine phosphoribosyltransferase, ev=6e-83, 88% identity; TIGRFAM: hypoxanthine phosphoribosyltransferase: (1.3e-90); PFAM: phosphoribosyltransferase: (1.1e-33); hypoxanthine phosphoribosyltransferase 1461575..1462117 Ruegeria sp. TM1040 4075861 YP_613364.1 CDS TM1040_1369 NC_008044.1 1462243 1462569 D hypothetical protein 1462243..1462569 Ruegeria sp. TM1040 4075862 YP_613365.1 CDS TM1040_1370 NC_008044.1 1462602 1463744 R 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 complement(1462602..1463744) Ruegeria sp. TM1040 4075863 YP_613366.1 CDS TM1040_1371 NC_008044.1 1463741 1464733 R 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 complement(1463741..1464733) Ruegeria sp. TM1040 4075864 YP_613367.1 CDS TM1040_1372 NC_008044.1 1464883 1465929 R KEGG: sil:SPO2106 hypothetical protein, ev=3e-69, 43% identity; hypothetical protein complement(1464883..1465929) Ruegeria sp. TM1040 4075865 YP_613368.1 CDS TM1040_1373 NC_008044.1 1466164 1466496 D KEGG: sil:SPO2107 hypothetical protein, ev=7e-12, 41% identity; hypothetical protein 1466164..1466496 Ruegeria sp. TM1040 4075866 YP_613369.1 CDS TM1040_1374 NC_008044.1 1466516 1468060 R PFAM: trimethylamine methyltransferase: (2e-275); KEGG: sil:SPO2108 trimethylamine methyltransferase family protein, ev=0.0, 84% identity; trimethylamine methyltransferase complement(1466516..1468060) Ruegeria sp. TM1040 4075867 YP_613370.1 CDS guaA NC_008044.1 1468257 1469819 D contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway; GMP synthase 1468257..1469819 Ruegeria sp. TM1040 4075868 YP_613371.1 CDS TM1040_1376 NC_008044.1 1469995 1470888 D PFAM: protein of unknown function DUF6, transmembrane: (1.2e-08); KEGG: sil:SPO2110 membrane protein, , ev=2e-97, 62% identity; hypothetical protein 1469995..1470888 Ruegeria sp. TM1040 4075869 YP_613372.1 CDS TM1040_1377 NC_008044.1 1471021 1472160 D 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 1471021..1472160 Ruegeria sp. TM1040 4075870 YP_613373.1 CDS TM1040_1378 NC_008044.1 1472383 1473192 D KEGG: sil:SPO2113 hypothetical protein, ev=1e-114, 71% identity; hypothetical protein 1472383..1473192 Ruegeria sp. TM1040 4075871 YP_613374.1 CDS TM1040_1379 NC_008044.1 1473238 1474176 D catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis; homoserine O-succinyltransferase 1473238..1474176 Ruegeria sp. TM1040 4075872 YP_613375.1 CDS TM1040_1380 NC_008044.1 1474186 1475151 D PFAM: alpha/beta hydrolase fold: (1.9e-12); KEGG: sil:SPO1728 esterase, , ev=9e-87, 52% identity; alpha/beta hydrolase 1474186..1475151 Ruegeria sp. TM1040 4075873 YP_613376.1 CDS TM1040_1381 NC_008044.1 1475213 1476082 D PFAM: protein of unknown function DUF344: (2.7e-137); KEGG: sil:SPO1727 polyphosphate kinase 2, , ev=1e-115, 69% identity; hypothetical protein 1475213..1476082 Ruegeria sp. TM1040 4075874 YP_613377.1 CDS TM1040_1382 NC_008044.1 1476075 1476692 D PFAM: regulatory protein, TetR: (5e-13); KEGG: sil:SPO3896 transcriptional regulator, TetR family, ev=3e-89, 79% identity; TetR family transcriptional regulator 1476075..1476692 Ruegeria sp. TM1040 4075875 YP_613378.1 CDS TM1040_1383 NC_008044.1 1476848 1478965 D 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 1476848..1478965 Ruegeria sp. TM1040 4075876 YP_613379.1 CDS rpsI NC_008044.1 1479063 1479548 R forms a direct contact with the tRNA during translation; 30S ribosomal protein S9 complement(1479063..1479548) Ruegeria sp. TM1040 4075877 YP_613380.1 CDS rplM NC_008044.1 1479554 1480012 R in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit; 50S ribosomal protein L13 complement(1479554..1480012) Ruegeria sp. TM1040 4075878 YP_613381.1 CDS TM1040_1386 NC_008044.1 1480196 1481611 R 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 complement(1480196..1481611) Ruegeria sp. TM1040 4075879 YP_613382.1 CDS TM1040_1387 NC_008044.1 1481680 1481946 R hypothetical protein complement(1481680..1481946) Ruegeria sp. TM1040 4075880 YP_613383.1 CDS TM1040_1388 NC_008044.1 1482166 1482672 D 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 1482166..1482672 Ruegeria sp. TM1040 4075881 YP_613384.1 CDS TM1040_1389 NC_008044.1 1482669 1483523 D catalyzes the formation of spermidine from putrescine and S-adenosylmethioninamine; spermidine synthase 1482669..1483523 Ruegeria sp. TM1040 4075882 YP_613385.1 CDS TM1040_1390 NC_008044.1 1483581 1484003 R 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 complement(1483581..1484003) Ruegeria sp. TM1040 4075883 YP_613386.1 CDS TM1040_1391 NC_008044.1 1484388 1485740 D 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 1484388..1485740 Ruegeria sp. TM1040 4075884 YP_613387.1 CDS TM1040_1392 NC_008044.1 1485777 1486391 D 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 1485777..1486391 Ruegeria sp. TM1040 4075885 YP_613388.1 CDS TM1040_1393 NC_008044.1 1486388 1487236 D 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 1486388..1487236 Ruegeria sp. TM1040 4075886 YP_613389.1 CDS TM1040_1394 NC_008044.1 1487246 1487635 R PFAM: phosphoribosyl-AMP cyclohydrolase: (9.7e-52); KEGG: sil:SPO1684 phosphoribosyl-AMP cyclohydrolase, ev=3e-51, 77% identity; phosphoribosyl-AMP cyclohydrolase complement(1487246..1487635) Ruegeria sp. TM1040 4075887 YP_613390.1 CDS TM1040_1395 NC_008044.1 1487653 1488147 D KEGG: sil:SPO1683 hypothetical protein, ev=4e-62, 78% identity; hypothetical protein 1487653..1488147 Ruegeria sp. TM1040 4075888 YP_613391.1 CDS TM1040_1396 NC_008044.1 1488276 1488533 D hypothetical protein 1488276..1488533 Ruegeria sp. TM1040 4075889 YP_613392.1 CDS TM1040_1397 NC_008044.1 1488653 1490743 R catalyzes branch migration in Holliday junction intermediates; ATP-dependent DNA helicase RecG complement(1488653..1490743) Ruegeria sp. TM1040 4075890 YP_613393.1 CDS TM1040_1398 NC_008044.1 1490751 1492970 R 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 complement(1490751..1492970) Ruegeria sp. TM1040 4075891 YP_613394.1 CDS TM1040_1399 NC_008044.1 1493148 1493867 R 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 complement(1493148..1493867) Ruegeria sp. TM1040 4075892 YP_613395.1 CDS TM1040_1400 NC_008044.1 1493993 1494271 R KEGG: sil:SPO1678 hypothetical protein, ev=6e-32, 70% identity; hypothetical protein complement(1493993..1494271) Ruegeria sp. TM1040 4075893 YP_613396.1 CDS mnmA NC_008044.1 1494429 1495574 D catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs; tRNA-specific 2-thiouridylase MnmA 1494429..1495574 Ruegeria sp. TM1040 4075894 YP_613397.1 CDS TM1040_1402 NC_008044.1 1495642 1496802 R 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 complement(1495642..1496802) Ruegeria sp. TM1040 4075895 YP_613398.1 CDS TM1040_1403 NC_008044.1 1496806 1497594 R PFAM: protein of unknown function DUF1009: (1.9e-50); KEGG: sil:SPO1674 hypothetical protein, ev=3e-89, 61% identity; hypothetical protein complement(1496806..1497594) Ruegeria sp. TM1040 4075896 YP_613399.1 CDS TM1040_1404 NC_008044.1 1497608 1498393 R catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis; UDP-N-acetylglucosamine acyltransferase complement(1497608..1498393) Ruegeria sp. TM1040 4075897 YP_613400.1 CDS fabZ NC_008044.1 1498393 1498875 R 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 complement(1498393..1498875) Ruegeria sp. TM1040 4075898 YP_613401.1 CDS TM1040_1406 NC_008044.1 1498939 1499484 R PFAM: outer membrane chaperone Skp (OmpH): (4.6e-14); KEGG: sil:SPO1671 hypothetical protein, ev=3e-34, 46% identity; outer membrane chaperone Skp complement(1498939..1499484) Ruegeria sp. TM1040 4075899 YP_613402.1 CDS TM1040_1407 NC_008044.1 1499580 1501970 R 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) complement(1499580..1501970) Ruegeria sp. TM1040 4078037 YP_613403.1 CDS TM1040_1408 NC_008044.1 1502126 1502254 R KEGG: sil:SPO1669 hypothetical protein, ev=9e-07, 60% identity; hypothetical protein complement(1502126..1502254) Ruegeria sp. TM1040 4078038 YP_613404.1 CDS TM1040_1409 NC_008044.1 1502394 1503746 R 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 complement(1502394..1503746) Ruegeria sp. TM1040 4078039 YP_613405.1 CDS TM1040_1410 NC_008044.1 1503751 1504938 R 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 complement(1503751..1504938) Ruegeria sp. TM1040 4078040 YP_613406.1 CDS TM1040_1411 NC_008044.1 1504970 1505767 R PFAM: phosphatidate cytidylyltransferase: (2.5e-51); KEGG: sil:SPO1666 phosphatidate cytidylyltransferase, ev=2e-64, 50% identity; phosphatidate cytidylyltransferase complement(1504970..1505767) Ruegeria sp. TM1040 4078041 YP_613407.1 CDS TM1040_1412 NC_008044.1 1505764 1506534 R 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 complement(1505764..1506534) Ruegeria sp. TM1040 4078042 YP_613408.1 CDS frr NC_008044.1 1506544 1507107 R 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 complement(1506544..1507107) Ruegeria sp. TM1040 4078043 YP_613409.1 CDS pyrH NC_008044.1 1507284 1508033 R Catalyzes the phosphorylation of UMP to UDP; uridylate kinase complement(1507284..1508033) Ruegeria sp. TM1040 4078044 YP_613410.1 CDS miaA NC_008044.1 1508184 1509050 D 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 1508184..1509050 Ruegeria sp. TM1040 4078045 YP_613411.1 CDS TM1040_1416 NC_008044.1 1509244 1510074 D 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 1509244..1510074 Ruegeria sp. TM1040 4078046 YP_613412.1 CDS TM1040_1417 NC_008044.1 1510334 1512001 D 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 1510334..1512001 Ruegeria sp. TM1040 4078047 YP_613413.1 CDS TM1040_1418 NC_008044.1 1512170 1513222 D 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 1512170..1513222 Ruegeria sp. TM1040 4078048 YP_613414.1 CDS TM1040_1419 NC_008044.1 1513238 1514674 D 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 1513238..1514674 Ruegeria sp. TM1040 4078049 YP_613415.1 CDS TM1040_1420 NC_008044.1 1514770 1516857 D 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 1514770..1516857 Ruegeria sp. TM1040 4078050 YP_613416.1 CDS TM1040_1421 NC_008044.1 1516976 1518391 R PFAM: Tetratricopeptide TPR_2: (0.00025); KEGG: ccr:CC3128 TPR domain protein, ev=1e-19, 23% identity; hypothetical protein complement(1516976..1518391) Ruegeria sp. TM1040 4078051 YP_613417.1 CDS TM1040_1422 NC_008044.1 1518520 1519656 R 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 complement(1518520..1519656) Ruegeria sp. TM1040 4078052 YP_613418.1 CDS TM1040_1423 NC_008044.1 1519788 1520162 R hypothetical protein complement(1519788..1520162) Ruegeria sp. TM1040 4078053 YP_613419.1 CDS TM1040_1424 NC_008044.1 1520328 1520903 R PFAM: Lytic transglycosylase, catalytic: (1.7e-29); KEGG: sil:SPO1638 transglycosylase SLT domain protein, ev=1e-60, 60% identity; lytic transglycosylase, catalytic complement(1520328..1520903) Ruegeria sp. TM1040 4078054 YP_613420.1 CDS TM1040_1425 NC_008044.1 1521186 1521710 D 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 1521186..1521710 Ruegeria sp. TM1040 4078055 YP_613421.1 CDS TM1040_1426 NC_008044.1 1521820 1524237 R 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 complement(1521820..1524237) Ruegeria sp. TM1040 4078056 YP_613422.1 CDS TM1040_1427 NC_008044.1 1524444 1525757 R 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 complement(1524444..1525757) Ruegeria sp. TM1040 4078057 YP_613423.1 CDS TM1040_1428 NC_008044.1 1525837 1526790 R 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 complement(1525837..1526790) Ruegeria sp. TM1040 4078058 YP_613424.1 CDS TM1040_1429 NC_008044.1 1526794 1528326 R KEGG: rsp:RSP_2816 hypothetical protein, ev=1e-111, 46% identity; hypothetical protein complement(1526794..1528326) Ruegeria sp. TM1040 4078059 YP_613425.1 CDS TM1040_1430 NC_008044.1 1528316 1528465 R hypothetical protein complement(1528316..1528465) Ruegeria sp. TM1040 4078060 YP_613426.1 CDS TM1040_1431 NC_008044.1 1528549 1529139 D catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis; shikimate kinase 1528549..1529139 Ruegeria sp. TM1040 4078061 YP_613427.1 CDS aroB NC_008044.1 1529139 1530260 D catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis; 3-dehydroquinate synthase 1529139..1530260 Ruegeria sp. TM1040 4078062 YP_613428.1 CDS TM1040_1433 NC_008044.1 1530278 1530904 D KEGG: rsp:RSP_2928 hypothetical protein, ev=1e-35, 47% identity; hypothetical protein 1530278..1530904 Ruegeria sp. TM1040 4078063 YP_613429.1 CDS TM1040_1434 NC_008044.1 1530905 1531567 R KEGG: sil:SPO1626 type I secretion target repeat protein, ev=8e-80, 69% identity; type I secretion target repeat-containing protein complement(1530905..1531567) Ruegeria sp. TM1040 4078064 YP_613430.1 CDS TM1040_1435 NC_008044.1 1531769 1532020 R hypothetical protein complement(1531769..1532020) Ruegeria sp. TM1040 4078065 YP_613431.1 CDS TM1040_1436 NC_008044.1 1532091 1532918 R 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 complement(1532091..1532918) Ruegeria sp. TM1040 4078066 YP_613432.1 CDS TM1040_1437 NC_008044.1 1532982 1533809 R PFAM: inositol monophosphatase: (7.9e-31); KEGG: sme:SMc00535 hypothetical protein, ev=8e-54, 41% identity; inositol monophosphatase complement(1532982..1533809) Ruegeria sp. TM1040 4078067 YP_613433.1 CDS TM1040_1438 NC_008044.1 1534364 1536886 R 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 complement(1534364..1536886) Ruegeria sp. TM1040 4078068 YP_613434.1 CDS TM1040_1439 NC_008044.1 1536892 1538076 R CysK; forms a complex with serine acetyltransferase CysE; functions in cysteine biosynthesis; cysteine synthase A complement(1536892..1538076) Ruegeria sp. TM1040 4078069 YP_613435.1 CDS TM1040_1440 NC_008044.1 1538196 1538750 R KEGG: sil:SPO1919 tellurite resistance protein, ev=6e-44, 56% identity; tellurite resistance protein complement(1538196..1538750) Ruegeria sp. TM1040 4078070 YP_613436.1 CDS TM1040_1441 NC_008044.1 1538768 1540192 R 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 complement(1538768..1540192) Ruegeria sp. TM1040 4078071 YP_613437.1 CDS TM1040_1442 NC_008044.1 1540223 1541452 R PFAM: aminotransferase, class V: (3.3e-28); KEGG: sil:SPO1916 aminotransferase, class V, ev=0.0, 77% identity; class V aminotransferase complement(1540223..1541452) Ruegeria sp. TM1040 4078072 YP_613438.1 CDS TM1040_1443 NC_008044.1 1541561 1542556 R 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 complement(1541561..1542556) Ruegeria sp. TM1040 4078073 YP_613439.1 CDS dmdA NC_008044.1 1542571 1543728 R 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 complement(1542571..1543728) Ruegeria sp. TM1040 4078074 YP_613440.1 CDS TM1040_1445 NC_008044.1 1543768 1544442 R 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 complement(1543768..1544442) Ruegeria sp. TM1040 4078075 YP_613441.1 CDS TM1040_1446 NC_008044.1 1544461 1545234 R KEGG: jan:Jann_2384 hypothetical protein, ev=9e-89, 62% identity; hypothetical protein complement(1544461..1545234) Ruegeria sp. TM1040 4077743 YP_613442.1 CDS TM1040_1447 NC_008044.1 1545359 1546090 D 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 1545359..1546090 Ruegeria sp. TM1040 4077744 YP_613443.1 CDS TM1040_1448 NC_008044.1 1546769 1547203 D PFAM: protein of unknown function DUF1486: (2.1e-05); KEGG: sil:SPO1909 hypothetical protein, ev=6e-22, 33% identity; hypothetical protein 1546769..1547203 Ruegeria sp. TM1040 4077745 YP_613444.1 CDS TM1040_1449 NC_008044.1 1547314 1548600 D PFAM: Chromate transporter: (1.2e-38); KEGG: sil:SPO1908 chromate transporter, ev=1e-132, 60% identity; chromate transporter 1547314..1548600 Ruegeria sp. TM1040 4077746 YP_613445.1 CDS TM1040_1450 NC_008044.1 1548715 1549194 D PFAM: protein of unknown function DUF1321: (5.5e-58); KEGG: sil:SPO1907 hypothetical protein, ev=3e-61, 70% identity; hypothetical protein 1548715..1549194 Ruegeria sp. TM1040 4077747 YP_613446.1 CDS TM1040_1451 NC_008044.1 1549340 1549924 R KEGG: sil:SPO1906 hypothetical protein, ev=1e-52, 59% identity; hypothetical protein complement(1549340..1549924) Ruegeria sp. TM1040 4077748 YP_613447.1 CDS fumC NC_008044.1 1550169 1551566 D 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 1550169..1551566 Ruegeria sp. TM1040 4077749 YP_613448.1 CDS TM1040_1453 NC_008044.1 1551847 1553010 D KEGG: sil:SPO1626 type I secretion target repeat protein, ev=5e-39, 41% identity; hypothetical protein 1551847..1553010 Ruegeria sp. TM1040 4077750 YP_613449.1 CDS TM1040_1454 NC_008044.1 1553015 1553245 D KEGG: jan:Jann_2395 uncharacterized arylsulfate sulfotransferase-like protein, ev=4e-17, 61% identity; arylsulfate sulfotransferase-like protein 1553015..1553245 Ruegeria sp. TM1040 4077751 YP_613450.1 CDS TM1040_1455 NC_008044.1 1553254 1554612 R PFAM: cytochrome P450: (2.8e-56); KEGG: sil:SPO1898 cytochrome P450 family protein, ev=0.0, 75% identity; cytochrome P450 complement(1553254..1554612) Ruegeria sp. TM1040 4077752 YP_613451.1 CDS TM1040_1456 NC_008044.1 1554609 1555856 R KEGG: sil:SPO1897 hypothetical protein, ev=1e-142, 63% identity; hypothetical protein complement(1554609..1555856) Ruegeria sp. TM1040 4077753 YP_613452.1 CDS TM1040_1457 NC_008044.1 1555970 1556722 R 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 complement(1555970..1556722) Ruegeria sp. TM1040 4077754 YP_613453.1 CDS TM1040_1458 NC_008044.1 1556817 1557053 D PFAM: SirA-like: (8.6e-22); KEGG: sil:SPO1895 SirA family protein, ev=2e-25, 70% identity; SirA-like protein 1556817..1557053 Ruegeria sp. TM1040 4077755 YP_613454.1 CDS TM1040_1459 NC_008044.1 1557176 1560106 R TIGRFAM: ribonuclease, Rne/Rng family: (5.3e-203); KEGG: sil:SPO1893 ribonuclease, Rne/Rng family, ev=0.0, 69% identity; RNAse E complement(1557176..1560106) Ruegeria sp. TM1040 4077756 YP_613455.1 CDS TM1040_1460 NC_008044.1 1560700 1561389 R 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 complement(1560700..1561389) Ruegeria sp. TM1040 4077757 YP_613456.1 CDS TM1040_1461 NC_008044.1 1561389 1562726 R 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 complement(1561389..1562726) Ruegeria sp. TM1040 4077758 YP_613457.1 CDS TM1040_1462 NC_008044.1 1562751 1564553 R 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 complement(1562751..1564553) Ruegeria sp. TM1040 4077759 YP_613458.1 CDS TM1040_1463 NC_008044.1 1564590 1565258 R 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 complement(1564590..1565258) Ruegeria sp. TM1040 4077760 YP_613459.1 CDS TM1040_1464 NC_008044.1 1565258 1565488 R PFAM: phosphoribosylformylglycinamidine synthetase PurS: (5.4e-32); KEGG: sil:SPO1888 phosphoribosylformylglycinamidine synthase, PurS protein, ev=2e-31, 88% identity; phosphoribosylformylglycinamidine synthase subunit PurS complement(1565258..1565488) Ruegeria sp. TM1040 4077761 YP_613460.2 CDS TM1040_1465 NC_008044.1 1565595 1566356 R 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 complement(1565595..1566356) Ruegeria sp. TM1040 4077762 YP_613461.1 CDS TM1040_1466 NC_008044.1 1566817 1567134 D PFAM: protein of unknown function DUF1476: (7.2e-47); KEGG: rsp:RSP_2125 hypothetical protein, ev=9e-26, 57% identity; hypothetical protein 1566817..1567134 Ruegeria sp. TM1040 4077763 YP_613462.1 CDS TM1040_1467 NC_008044.1 1567246 1569153 D KEGG: sil:SPO1885 membrane protein, , ev=1e-131, 45% identity; hypothetical protein 1567246..1569153 Ruegeria sp. TM1040 4077764 YP_613463.1 CDS TM1040_1468 NC_008044.1 1569216 1570238 D catalyzes the formation of methionine from L-homocysteine and S-adenosyl-L-methionine; methionine synthase I 1569216..1570238 Ruegeria sp. TM1040 4077765 YP_613464.1 CDS TM1040_1469 NC_008044.1 1570319 1571401 R 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 complement(1570319..1571401) Ruegeria sp. TM1040 4077766 YP_613465.1 CDS TM1040_1470 NC_008044.1 1571618 1572316 D 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 1571618..1572316 Ruegeria sp. TM1040 4077767 YP_613466.1 CDS TM1040_1471 NC_008044.1 1572318 1573064 D KEGG: sil:SPO2162 hypothetical protein, ev=3e-72, 63% identity; hypothetical protein 1572318..1573064 Ruegeria sp. TM1040 4077768 YP_613467.1 CDS TM1040_1472 NC_008044.1 1573147 1573569 R 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 complement(1573147..1573569) Ruegeria sp. TM1040 4077769 YP_613468.1 CDS TM1040_1473 NC_008044.1 1573688 1574203 D KEGG: sil:SPO2166 lipoprotein, , ev=4e-36, 51% identity; lipoprotein 1573688..1574203 Ruegeria sp. TM1040 4077770 YP_613469.1 CDS TM1040_1474 NC_008044.1 1574347 1575504 R 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 complement(1574347..1575504) Ruegeria sp. TM1040 4077771 YP_613470.1 CDS TM1040_1475 NC_008044.1 1575595 1576149 R 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 complement(1575595..1576149) Ruegeria sp. TM1040 4077772 YP_613471.1 CDS TM1040_1476 NC_008044.1 1576197 1577243 R catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis; phosphoribosylaminoimidazole synthetase complement(1576197..1577243) Ruegeria sp. TM1040 4077773 YP_613472.1 CDS TM1040_1477 NC_008044.1 1577426 1578394 R 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 complement(1577426..1578394) Ruegeria sp. TM1040 4077774 YP_613473.1 CDS TM1040_1478 NC_008044.1 1578515 1579444 D 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 1578515..1579444 Ruegeria sp. TM1040 4077775 YP_613474.1 CDS TM1040_1479 NC_008044.1 1579845 1581173 R 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 complement(1579845..1581173) Ruegeria sp. TM1040 4077776 YP_613475.1 CDS TM1040_1480 NC_008044.1 1581224 1582147 D PFAM: beta-lactamase-like: (3.6e-24); KEGG: sil:SPO2174 metallo-beta-lactamase family protein, ev=1e-104, 62% identity; beta-lactamase-like protein 1581224..1582147 Ruegeria sp. TM1040 4077777 YP_613476.1 CDS TM1040_1481 NC_008044.1 1582635 1583594 R 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 complement(1582635..1583594) Ruegeria sp. TM1040 4077778 YP_613477.1 CDS TM1040_1482 NC_008044.1 1583603 1584724 R 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 complement(1583603..1584724) Ruegeria sp. TM1040 4077779 YP_613478.1 CDS TM1040_1483 NC_008044.1 1584788 1585987 R 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 complement(1584788..1585987) Ruegeria sp. TM1040 4077780 YP_613479.1 CDS TM1040_1484 NC_008044.1 1585984 1586757 R PFAM: glycosyl transferase, family 2: (4.4e-26); KEGG: bfs:BF2599 LPS biosynthesis related glycosyltransferase, ev=7e-23, 32% identity; glycosyl transferase family protein complement(1585984..1586757) Ruegeria sp. TM1040 4077781 YP_613480.1 CDS TM1040_1485 NC_008044.1 1586750 1587571 R 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 complement(1586750..1587571) Ruegeria sp. TM1040 4077041 YP_613481.1 CDS TM1040_1486 NC_008044.1 1587568 1588521 R hypothetical protein complement(1587568..1588521) Ruegeria sp. TM1040 4077042 YP_613482.1 CDS TM1040_1487 NC_008044.1 1588830 1590218 D 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 1588830..1590218 Ruegeria sp. TM1040 4077043 YP_613483.1 CDS TM1040_1488 NC_008044.1 1591016 1593580 D 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 1591016..1593580 Ruegeria sp. TM1040 4077044 YP_613484.1 CDS TM1040_1489 NC_008044.1 1593933 1595891 D 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 1593933..1595891 Ruegeria sp. TM1040 4077045 YP_613485.1 CDS TM1040_1490 NC_008044.1 1595898 1596581 D 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 1595898..1596581 Ruegeria sp. TM1040 4077046 YP_613486.1 CDS TM1040_1491 NC_008044.1 1596744 1597244 D 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 1596744..1597244 Ruegeria sp. TM1040 4077047 YP_613487.1 CDS TM1040_1492 NC_008044.1 1597298 1598041 R PFAM: 4Fe-4S ferredoxin, iron-sulfur binding: (6.7e-06); KEGG: vvy:VV1703 ferredoxin, ev=2e-10, 41% identity; 4Fe-4S ferredoxin complement(1597298..1598041) Ruegeria sp. TM1040 4077048 YP_613488.1 CDS TM1040_1493 NC_008044.1 1598143 1599129 R KEGG: sil:SPO1788 ABC transporter, periplasmic substrate-binding protein, ev=1e-150, 80% identity; ABC transporter substrate-binding protein complement(1598143..1599129) Ruegeria sp. TM1040 4077049 YP_613489.1 CDS TM1040_1494 NC_008044.1 1599332 1600177 R 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 complement(1599332..1600177) Ruegeria sp. TM1040 4077050 YP_613490.1 CDS TM1040_1495 NC_008044.1 1600230 1601147 R 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 complement(1600230..1601147) Ruegeria sp. TM1040 4077051 YP_613491.1 CDS TM1040_1496 NC_008044.1 1601172 1601939 R 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 complement(1601172..1601939) Ruegeria sp. TM1040 4077052 YP_613492.1 CDS TM1040_1497 NC_008044.1 1602053 1603507 R catalyzes the hydrolytic cleavage of hydantoin with aromatic side chains at the 5'position; phenylhydantoinase complement(1602053..1603507) Ruegeria sp. TM1040 4077053 YP_613493.1 CDS TM1040_1498 NC_008044.1 1603637 1604887 R 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 complement(1603637..1604887) Ruegeria sp. TM1040 4077054 YP_613494.1 CDS TM1040_1499 NC_008044.1 1605177 1605788 D 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 1605177..1605788 Ruegeria sp. TM1040 4077055 YP_613495.1 CDS TM1040_1500 NC_008044.1 1606078 1607382 R catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines; dihydropyrimidine dehydrogenase complement(1606078..1607382) Ruegeria sp. TM1040 4077056 YP_613496.1 CDS TM1040_1501 NC_008044.1 1607447 1608781 R function undetermined; similar to glutamate synthase beta subunit and related oxidoreductases which transfer electrons from NADPH to an acceptor protein or protein domain; oxidoreductase complement(1607447..1608781) Ruegeria sp. TM1040 4077057 YP_613497.1 CDS TM1040_1502 NC_008044.1 1609074 1609340 R KEGG: jan:Jann_2635 hypothetical protein, ev=2e-29, 79% identity; hypothetical protein complement(1609074..1609340) Ruegeria sp. TM1040 4077058 YP_613498.1 CDS TM1040_1503 NC_008044.1 1609548 1609763 D KEGG: sil:SPO1032 hypothetical protein, ev=3e-18, 60% identity; hypothetical protein 1609548..1609763 Ruegeria sp. TM1040 4077059 YP_613499.1 CDS TM1040_1504 NC_008044.1 1609805 1610020 R KEGG: sil:SPO1031 hypothetical protein, ev=4e-08, 40% identity; hypothetical protein complement(1609805..1610020) Ruegeria sp. TM1040 4077060 YP_613500.1 CDS TM1040_1505 NC_008044.1 1610302 1610730 D PFAM: protein of unknown function DUF442: (3.1e-44); KEGG: sil:SPO1027 conserved hypothetical protein TIGR01244, ev=6e-48, 67% identity; hypothetical protein 1610302..1610730 Ruegeria sp. TM1040 4077061 YP_613501.1 CDS TM1040_1506 NC_008044.1 1610887 1612149 R 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 complement(1610887..1612149) Ruegeria sp. TM1040 4077062 YP_613502.1 CDS TM1040_1507 NC_008044.1 1612226 1614916 R 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 complement(1612226..1614916) Ruegeria sp. TM1040 4077063 YP_613503.1 CDS TM1040_1508 NC_008044.1 1614913 1615326 R KEGG: sil:SPO1024 hypothetical protein, ev=8e-13, 52% identity; hypothetical protein complement(1614913..1615326) Ruegeria sp. TM1040 4077064 YP_613504.1 CDS TM1040_1509 NC_008044.1 1615337 1615750 R PFAM: response regulator receiver: (5.6e-31); KEGG: sil:SPO1023 response regulator, ev=2e-47, 77% identity; response regulator receiver protein complement(1615337..1615750) Ruegeria sp. TM1040 4077065 YP_613505.1 CDS TM1040_1510 NC_008044.1 1615849 1617180 R PFAM: helix-turn-helix motif: (5e-13); KEGG: sil:SPO1022 transcriptional regulator, , ev=1e-145, 62% identity; XRE family transcriptional regulator complement(1615849..1617180) Ruegeria sp. TM1040 4077066 YP_613506.1 CDS TM1040_1511 NC_008044.1 1617419 1618765 D 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 1617419..1618765 Ruegeria sp. TM1040 4077067 YP_613507.1 CDS TM1040_1512 NC_008044.1 1618965 1619996 D 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 1618965..1619996 Ruegeria sp. TM1040 4077068 YP_613508.1 CDS TM1040_1513 NC_008044.1 1620001 1621200 D 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 1620001..1621200 Ruegeria sp. TM1040 4077069 YP_613509.1 CDS TM1040_1514 NC_008044.1 1621211 1621966 D 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 1621211..1621966 Ruegeria sp. TM1040 4077070 YP_613510.1 CDS TM1040_1515 NC_008044.1 1621985 1622740 D 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 1621985..1622740 Ruegeria sp. TM1040 4077071 YP_613511.1 CDS TM1040_1516 NC_008044.1 1622952 1623500 D PFAM: regulatory protein, LuxR: (1.7e-17); KEGG: sil:SPO1012 transcriptional regulator, LuxR family, ev=2e-59, 63% identity; LuxR family transcriptional regulator 1622952..1623500 Ruegeria sp. TM1040 4077072 YP_613512.1 CDS TM1040_1517 NC_008044.1 1623674 1624165 D 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 1623674..1624165 Ruegeria sp. TM1040 4077073 YP_613513.1 CDS TM1040_1518 NC_008044.1 1624175 1625524 D 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 1624175..1625524 Ruegeria sp. TM1040 4077074 YP_613514.1 CDS aat NC_008044.1 1625590 1626222 D 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 1625590..1626222 Ruegeria sp. TM1040 4077075 YP_613515.1 CDS TM1040_1520 NC_008044.1 1626186 1626623 R KEGG: sil:SPO1008 hypothetical protein, ev=3e-32, 69% identity; hypothetical protein complement(1626186..1626623) Ruegeria sp. TM1040 4077076 YP_613516.1 CDS TM1040_1521 NC_008044.1 1626623 1627075 R PFAM: Mammalian cell entry related: (8.4e-22); KEGG: sil:SPO1007 ABC transport system substrate-binding protein, ev=4e-51, 71% identity; hypothetical protein complement(1626623..1627075) Ruegeria sp. TM1040 4077077 YP_613517.1 CDS TM1040_1522 NC_008044.1 1627146 1627532 R 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 complement(1627146..1627532) Ruegeria sp. TM1040 4077078 YP_613518.1 CDS TM1040_1523 NC_008044.1 1627653 1628045 R PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase: (2e-08); KEGG: ppu:PP3509 glyoxalase family protein, ev=5e-37, 59% identity; glyoxalase/bleomycin resistance protein/dioxygenase complement(1627653..1628045) Ruegeria sp. TM1040 4077079 YP_613519.1 CDS TM1040_1524 NC_008044.1 1628057 1628422 R PFAM: Endoribonuclease L-PSP: (2.8e-20); KEGG: sil:SPO1005 endoribonuclease L-PSP family protein, ev=7e-52, 84% identity; endoribonuclease L-PSP complement(1628057..1628422) Ruegeria sp. TM1040 4075822 YP_613520.1 CDS TM1040_1525 NC_008044.1 1628514 1629239 R PFAM: dienelactone hydrolase: (3.5e-35); KEGG: mca:MCA1803 dienelactone hydrolase family protein, ev=2e-55, 48% identity; dienelactone hydrolase complement(1628514..1629239) Ruegeria sp. TM1040 4075823 YP_613521.1 CDS clpX NC_008044.1 1629344 1630609 R binds and unfolds substrates as part of the ClpXP protease; ATP-dependent protease ATP-binding subunit ClpX complement(1629344..1630609) Ruegeria sp. TM1040 4075824 YP_613522.1 CDS clpP NC_008044.1 1630761 1631417 R hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates; ATP-dependent Clp protease proteolytic subunit complement(1630761..1631417) Ruegeria sp. TM1040 4075825 YP_613523.1 CDS TM1040_1528 NC_008044.1 1631689 1632696 D 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 1631689..1632696 Ruegeria sp. TM1040 4075826 YP_613524.1 CDS TM1040_1529 NC_008044.1 1632820 1633362 D KEGG: sil:SPO2884 hypothetical protein, ev=1e-45, 63% identity; hypothetical protein 1632820..1633362 Ruegeria sp. TM1040 4075827 YP_613525.1 CDS TM1040_1530 NC_008044.1 1633394 1635007 D 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 1633394..1635007 Ruegeria sp. TM1040 4075828 YP_613526.1 CDS TM1040_1531 NC_008044.1 1634991 1636193 D 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 1634991..1636193 Ruegeria sp. TM1040 4075829 YP_613527.1 CDS TM1040_1532 NC_008044.1 1636457 1637821 D KEGG: sil:SPO2887 hypothetical protein, ev=1e-167, 63% identity; hypothetical protein 1636457..1637821 Ruegeria sp. TM1040 4075830 YP_613528.1 CDS TM1040_1533 NC_008044.1 1637844 1639151 D KEGG: sil:SPO2888 membrane protein, , ev=1e-151, 61% identity; hypothetical protein 1637844..1639151 Ruegeria sp. TM1040 4075831 YP_613529.1 CDS mdoG NC_008044.1 1639148 1640674 D involved in the biosynthesis of osmoregulated periplasmic glucans; required for the assembly of the polyglucose structure of glucan; glucan biosynthesis protein G 1639148..1640674 Ruegeria sp. TM1040 4075832 YP_613530.1 CDS TM1040_1535 NC_008044.1 1640675 1642567 D necessary for biosynthesis of osmoregulated periplasmic glucans possibly involved in the transfer to the periplasmic space; glucosyltransferase MdoH 1640675..1642567 Ruegeria sp. TM1040 4075833 YP_613531.1 CDS TM1040_1536 NC_008044.1 1642659 1643489 R KEGG: sil:SPO2891 polyhydroxybutyrate depolymerase, ev=2e-74, 51% identity; polyhydroxybutyrate depolymerase complement(1642659..1643489) Ruegeria sp. TM1040 4075834 YP_613532.1 CDS TM1040_1537 NC_008044.1 1643486 1644013 R SMART: Rhodanese-like: (6.8e-12); KEGG: sil:SPO2892 hypothetical protein, ev=4e-32, 54% identity; rhodanese-like protein complement(1643486..1644013) Ruegeria sp. TM1040 4075835 YP_613533.1 CDS TM1040_1538 NC_008044.1 1644301 1647162 D 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 1644301..1647162 Ruegeria sp. TM1040 4075836 YP_613534.1 CDS TM1040_1539 NC_008044.1 1647167 1647520 D subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; monovalent cation/H+ antiporter subunit C 1647167..1647520 Ruegeria sp. TM1040 4075837 YP_613535.1 CDS TM1040_1540 NC_008044.1 1647517 1649139 D 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 1647517..1649139 Ruegeria sp. TM1040 4075838 YP_613536.1 CDS TM1040_1541 NC_008044.1 1649139 1649636 D 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 1649139..1649636 Ruegeria sp. TM1040 4075839 YP_613537.1 CDS TM1040_1542 NC_008044.1 1649633 1649902 D 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 1649633..1649902 Ruegeria sp. TM1040 4075840 YP_613538.1 CDS TM1040_1543 NC_008044.1 1649913 1650290 D 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 1649913..1650290 Ruegeria sp. TM1040 4075841 YP_613539.1 CDS TM1040_1544 NC_008044.1 1650329 1652491 D 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 1650329..1652491 Ruegeria sp. TM1040 4075842 YP_613540.1 CDS TM1040_1545 NC_008044.1 1652518 1653561 R 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 complement(1652518..1653561) Ruegeria sp. TM1040 4075843 YP_613541.1 CDS TM1040_1546 NC_008044.1 1653637 1654122 D PFAM: regulatory protein, MarR: (1.6e-14); KEGG: bja:bll4221 transcriptional regulatory protein, ev=5e-27, 48% identity; MarR family transcriptional regulator 1653637..1654122 Ruegeria sp. TM1040 4075844 YP_613542.1 CDS TM1040_1547 NC_008044.1 1654155 1654457 R KEGG: bte:BTH_I2061 hypothetical protein, ev=8e-11, 45% identity; hypothetical protein complement(1654155..1654457) Ruegeria sp. TM1040 4075845 YP_613543.1 CDS TM1040_1548 NC_008044.1 1654635 1656215 R 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 complement(1654635..1656215) Ruegeria sp. TM1040 4075846 YP_613544.1 CDS TM1040_1549 NC_008044.1 1656405 1656743 D PFAM: protein of unknown function DUF952: (7.4e-46); KEGG: sil:SPO2905 hypothetical protein, ev=9e-45, 77% identity; hypothetical protein 1656405..1656743 Ruegeria sp. TM1040 4075847 YP_613545.1 CDS TM1040_1550 NC_008044.1 1656807 1657865 D 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 1656807..1657865 Ruegeria sp. TM1040 4075848 YP_613546.1 CDS TM1040_1551 NC_008044.1 1658100 1659422 R 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 complement(1658100..1659422) Ruegeria sp. TM1040 4075849 YP_613547.1 CDS TM1040_1552 NC_008044.1 1659441 1659959 R KEGG: rsp:RSP_2203 hypothetical protein, ev=1e-63, 72% identity; hypothetical protein complement(1659441..1659959) Ruegeria sp. TM1040 4075850 YP_613548.1 CDS TM1040_1553 NC_008044.1 1659956 1660378 R 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 complement(1659956..1660378) Ruegeria sp. TM1040 4075851 YP_613549.1 CDS TM1040_1554 NC_008044.1 1660504 1660872 D PFAM: regulatory protein, MerR: (3e-05); KEGG: sil:SPO2912 transcriptional regulator, MerR family, ev=3e-46, 75% identity; MerR family transcriptional regulator 1660504..1660872 Ruegeria sp. TM1040 4075852 YP_613550.1 CDS TM1040_1555 NC_008044.1 1660885 1661163 D hypothetical protein 1660885..1661163 Ruegeria sp. TM1040 4075853 YP_613551.1 CDS TM1040_1556 NC_008044.1 1661412 1661813 D PFAM: regulatory protein, MerR: (2.3e-10); KEGG: sil:SPO2914 transcriptional regulator, MerR family, ev=1e-57, 81% identity; MerR family transcriptional regulator 1661412..1661813 Ruegeria sp. TM1040 4075854 YP_613552.1 CDS TM1040_1557 NC_008044.1 1661878 1663659 D PFAM: acyl-CoA dehydrogenase-like: (3.9e-22); KEGG: sil:SPO2915 acyl-CoA dehydrogenase family protein, ev=0.0, 87% identity; acyl-CoA dehydrogenase 1661878..1663659 Ruegeria sp. TM1040 4075855 YP_613553.1 CDS TM1040_1558 NC_008044.1 1663752 1663964 D KEGG: sil:SPO2916 hypothetical protein, ev=8e-29, 87% identity; hypothetical protein 1663752..1663964 Ruegeria sp. TM1040 4075856 YP_613554.1 CDS TM1040_1559 NC_008044.1 1664004 1665167 D 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 1664004..1665167 Ruegeria sp. TM1040 4075857 YP_613555.1 CDS TM1040_1560 NC_008044.1 1665453 1666085 D PFAM: glutathione S-transferase-like: (1.3e-10); KEGG: sil:SPO2917 glutathione S-transferase family protein, ev=1e-94, 76% identity; glutathione S-transferase 1665453..1666085 Ruegeria sp. TM1040 4075858 YP_613556.1 CDS TM1040_1561 NC_008044.1 1666096 1667307 D 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 1666096..1667307 Ruegeria sp. TM1040 4075859 YP_613557.1 CDS TM1040_1562 NC_008044.1 1667347 1669548 D 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 1667347..1669548 Ruegeria sp. TM1040 4075860 YP_613558.1 CDS TM1040_1563 NC_008044.1 1669877 1670569 R KEGG: sil:SPO2921 hypothetical protein, ev=2e-35, 41% identity; hypothetical protein complement(1669877..1670569) Ruegeria sp. TM1040 4078372 YP_613559.1 CDS TM1040_1564 NC_008044.1 1670697 1671362 R KEGG: sil:SPO2922 hypothetical protein, ev=1e-70, 59% identity; hypothetical protein complement(1670697..1671362) Ruegeria sp. TM1040 4078373 YP_613560.1 CDS TM1040_1565 NC_008044.1 1671523 1673154 D 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 1671523..1673154 Ruegeria sp. TM1040 4078374 YP_613561.1 CDS TM1040_1566 NC_008044.1 1673331 1673972 R KEGG: vvy:VV1861 hypothetical protein, ev=5e-27, 41% identity; hypothetical protein complement(1673331..1673972) Ruegeria sp. TM1040 4078375 YP_613562.1 CDS TM1040_1567 NC_008044.1 1674284 1675339 D KEGG: sil:SPO2924 hypothetical protein, ev=1e-107, 56% identity; hypothetical protein 1674284..1675339 Ruegeria sp. TM1040 4078376 YP_613563.1 CDS TM1040_1568 NC_008044.1 1675407 1676660 R PFAM: Sporulation related: (3e-05); KEGG: jan:Jann_2982 hypothetical protein, ev=3e-32, 30% identity; sporulation related protein complement(1675407..1676660) Ruegeria sp. TM1040 4078377 YP_613564.1 CDS upp NC_008044.1 1676842 1677474 R Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate; uracil phosphoribosyltransferase complement(1676842..1677474) Ruegeria sp. TM1040 4078378 YP_613565.1 CDS TM1040_1570 NC_008044.1 1677559 1678773 R catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose; phosphopentomutase complement(1677559..1678773) Ruegeria sp. TM1040 4078379 YP_613566.1 CDS deoA NC_008044.1 1678773 1680077 R Catalyzes the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate; thymidine phosphorylase complement(1678773..1680077) Ruegeria sp. TM1040 4078380 YP_613567.1 CDS TM1040_1572 NC_008044.1 1680082 1680576 R 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 complement(1680082..1680576) Ruegeria sp. TM1040 4078381 YP_613568.1 CDS TM1040_1573 NC_008044.1 1680851 1683130 D NAD-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; does not decarboxylate oxaloacetate; malic enzyme 1680851..1683130 Ruegeria sp. TM1040 4078382 YP_613569.1 CDS TM1040_1574 NC_008044.1 1683467 1685359 D PFAM: AMP-dependent synthetase and ligase: (2.7e-112); KEGG: sil:SPO2934 propionate--CoA ligase, ev=0.0, 85% identity; AMP-dependent synthetase/ligase 1683467..1685359 Ruegeria sp. TM1040 4078383 YP_613570.1 CDS TM1040_1575 NC_008044.1 1685432 1685641 R PFAM: CsbD-like: (3.4e-09); KEGG: noc:Noc_0274 CsbD-like protein, ev=6e-19, 60% identity; CsbD-like protein complement(1685432..1685641) Ruegeria sp. TM1040 4078384 YP_613571.1 CDS TM1040_1576 NC_008044.1 1685763 1686308 R hypothetical protein complement(1685763..1686308) Ruegeria sp. TM1040 4078385 YP_613572.1 CDS TM1040_1577 NC_008044.1 1686460 1687896 D catalyzes the hydrolysis of a monocarboxylic acid amid to form a monocarboxylate and ammonia; amidase 1686460..1687896 Ruegeria sp. TM1040 4078386 YP_613573.1 CDS ppnK NC_008044.1 1688007 1688762 R catalyzes the phosphorylation of NAD to NADP; inorganic polyphosphate/ATP-NAD kinase complement(1688007..1688762) Ruegeria sp. TM1040 4078387 YP_613574.1 CDS glyA NC_008044.1 1688939 1690234 D catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate; serine hydroxymethyltransferase 1688939..1690234 Ruegeria sp. TM1040 4078388 YP_613575.1 CDS TM1040_1580 NC_008044.1 1690351 1691043 D PFAM: protein of unknown function DUF159: (2e-25); KEGG: rsp:RSP_2605 hypothetical protein, ev=4e-30, 35% identity; hypothetical protein 1690351..1691043 Ruegeria sp. TM1040 4078389 YP_613576.1 CDS TM1040_1581 NC_008044.1 1691081 1691368 R KEGG: jan:Jann_2992 hypothetical protein, ev=6e-30, 69% identity; hypothetical protein complement(1691081..1691368) Ruegeria sp. TM1040 4078390 YP_613577.1 CDS TM1040_1582 NC_008044.1 1691455 1692153 R KEGG: jan:Jann_2993 phage shock protein A, PspA, ev=3e-54, 53% identity; phage shock protein A, PspA complement(1691455..1692153) Ruegeria sp. TM1040 4078391 YP_613578.1 CDS TM1040_1583 NC_008044.1 1692230 1692826 R PFAM: regulatory protein, TetR: (0.0022); KEGG: jan:Jann_2994 transcriptional regulator, TetR family, ev=4e-54, 55% identity; TetR family transcriptional regulator complement(1692230..1692826) Ruegeria sp. TM1040 4078392 YP_613579.1 CDS TM1040_1584 NC_008044.1 1692970 1693896 D PFAM: protein of unknown function DUF817: (1.2e-94); KEGG: sil:SPO2941 membrane protein, , ev=1e-115, 78% identity; hypothetical protein 1692970..1693896 Ruegeria sp. TM1040 4078393 YP_613580.1 CDS TM1040_1585 NC_008044.1 1693850 1694215 R KEGG: sil:SPO2942 hypothetical protein, ev=1e-12, 34% identity; hypothetical protein complement(1693850..1694215) Ruegeria sp. TM1040 4078394 YP_613581.1 CDS TM1040_1586 NC_008044.1 1694338 1695096 D 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 1694338..1695096 Ruegeria sp. TM1040 4078395 YP_613582.1 CDS TM1040_1587 NC_008044.1 1695177 1696058 R 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 complement(1695177..1696058) Ruegeria sp. TM1040 4078396 YP_613583.1 CDS TM1040_1588 NC_008044.1 1696199 1699753 R 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 complement(1696199..1699753) Ruegeria sp. TM1040 4078397 YP_613584.1 CDS TM1040_1589 NC_008044.1 1700175 1701434 R 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 complement(1700175..1701434) Ruegeria sp. TM1040 4078398 YP_613585.1 CDS TM1040_1590 NC_008044.1 1701431 1701970 R 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 complement(1701431..1701970) Ruegeria sp. TM1040 4078399 YP_613586.1 CDS TM1040_1591 NC_008044.1 1702034 1703014 R 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 complement(1702034..1703014) Ruegeria sp. TM1040 4078400 YP_613587.1 CDS TM1040_1592 NC_008044.1 1703050 1703613 R 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 complement(1703050..1703613) Ruegeria sp. TM1040 4078401 YP_613588.1 CDS TM1040_1593 NC_008044.1 1703743 1704630 R PFAM: protein of unknown function DUF6, transmembrane: (0.00071); KEGG: eba:p2A115 hypothetical protein, potential permease subunit, ev=8e-21, 27% identity; hypothetical protein complement(1703743..1704630) Ruegeria sp. TM1040 4078402 YP_613589.1 CDS TM1040_1594 NC_008044.1 1704640 1705593 R PFAM: dihydrodipicolinate synthetase: (1e-11); KEGG: sil:SPO2882 dihydrodipicolinate synthase family protein, ev=1e-132, 72% identity; dihydrodipicolinate synthetase complement(1704640..1705593) Ruegeria sp. TM1040 4078403 YP_613590.1 CDS TM1040_1595 NC_008044.1 1705772 1706560 D catalyzes the formation of L-aspartate to iminoaspartate in NAD(+) biosynthesis; L-aspartate dehydrogenase 1705772..1706560 Ruegeria sp. TM1040 4078404 YP_613591.1 CDS TM1040_1596 NC_008044.1 1706570 1707535 D 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 1706570..1707535 Ruegeria sp. TM1040 4078405 YP_613592.1 CDS TM1040_1597 NC_008044.1 1707581 1709071 D PFAM: aldehyde dehydrogenase: (7.2e-185); KEGG: atc:AGR_L_2660 aldehyde dehydrogenase, ev=1e-135, 49% identity; succinate semialdehyde dehydrogenase 1707581..1709071 Ruegeria sp. TM1040 4078406 YP_613593.1 CDS TM1040_1598 NC_008044.1 1709078 1710358 R 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 complement(1709078..1710358) Ruegeria sp. TM1040 4078407 YP_613594.1 CDS TM1040_1599 NC_008044.1 1710889 1711800 R PFAM: Hemolysin-type calcium-binding region: (0.00015); KEGG: rpb:RPB_0803 5'-nucleotidase, ev=4e-36, 40% identity; hemolysin-type calcium-binding protein complement(1710889..1711800) Ruegeria sp. TM1040 4078408 YP_613595.1 CDS TM1040_1600 NC_008044.1 1712411 1712728 D hypothetical protein 1712411..1712728 Ruegeria sp. TM1040 4078409 YP_613596.1 CDS TM1040_1601 NC_008044.1 1712755 1713351 R hypothetical protein complement(1712755..1713351) Ruegeria sp. TM1040 4078410 YP_613597.1 CDS TM1040_1602 NC_008044.1 1713369 1714235 R hypothetical protein complement(1713369..1714235) Ruegeria sp. TM1040 4077704 YP_613598.1 CDS TM1040_1603 NC_008044.1 1714470 1714868 R hypothetical protein complement(1714470..1714868) Ruegeria sp. TM1040 4077705 YP_613599.1 CDS TM1040_1604 NC_008044.1 1714865 1715674 R PFAM: protein of unknown function DUF847: (8.8e-67); KEGG: bmb:BruAb1_0990 secretion activator protein, hypothetical, ev=2e-43, 39% identity; hypothetical protein complement(1714865..1715674) Ruegeria sp. TM1040 4077706 YP_613600.1 CDS TM1040_1605 NC_008044.1 1715676 1716110 R hypothetical protein complement(1715676..1716110) Ruegeria sp. TM1040 4077707 YP_613601.1 CDS TM1040_1606 NC_008044.1 1716107 1716403 R hypothetical protein complement(1716107..1716403) Ruegeria sp. TM1040 4077708 YP_613602.1 CDS TM1040_1607 NC_008044.1 1716410 1716757 R hypothetical protein complement(1716410..1716757) Ruegeria sp. TM1040 4077709 YP_613603.1 CDS TM1040_1608 NC_008044.1 1716735 1717235 R hypothetical protein complement(1716735..1717235) Ruegeria sp. TM1040 4077710 YP_613604.1 CDS TM1040_1609 NC_008044.1 1717238 1718308 R KEGG: nar:Saro_2740 PE-PGRS family protein, ev=2e-34, 37% identity; hypothetical protein complement(1717238..1718308) Ruegeria sp. TM1040 4077711 YP_613605.1 CDS TM1040_1610 NC_008044.1 1718305 1719249 R KEGG: rsp:RSP_1635 hypothetical protein, ev=2e-27, 27% identity; hypothetical protein complement(1718305..1719249) Ruegeria sp. TM1040 4077712 YP_613606.1 CDS TM1040_1611 NC_008044.1 1719249 1723772 R KEGG: rsp:RSP_3791 hypothetical protein, ev=2e-86, 23% identity; hypothetical protein complement(1719249..1723772) Ruegeria sp. TM1040 4077713 YP_613607.1 CDS TM1040_1612 NC_008044.1 1724207 1724542 R hypothetical protein complement(1724207..1724542) Ruegeria sp. TM1040 4077714 YP_613608.1 CDS TM1040_1613 NC_008044.1 1724641 1725090 R KEGG: rsp:RSP_3788 hypothetical protein, ev=2e-29, 46% identity; hypothetical protein complement(1724641..1725090) Ruegeria sp. TM1040 4077715 YP_613609.1 CDS TM1040_1614 NC_008044.1 1725189 1725638 R KEGG: nar:Saro_0657 hypothetical protein, ev=2e-32, 50% identity; hypothetical protein complement(1725189..1725638) Ruegeria sp. TM1040 4077716 YP_613610.1 CDS TM1040_1615 NC_008044.1 1725699 1725983 R hypothetical protein complement(1725699..1725983) Ruegeria sp. TM1040 4077717 YP_613611.1 CDS TM1040_1616 NC_008044.1 1726025 1726378 R KEGG: rsp:RSP_6012 hypothetical protein, ev=1e-08, 36% identity; hypothetical protein complement(1726025..1726378) Ruegeria sp. TM1040 4077718 YP_613612.1 CDS TM1040_1617 NC_008044.1 1726378 1726833 R KEGG: rsp:RSP_1640 hypothetical protein, ev=5e-14, 35% identity; hypothetical protein complement(1726378..1726833) Ruegeria sp. TM1040 4077719 YP_613613.1 CDS TM1040_1618 NC_008044.1 1726834 1727211 D hypothetical protein 1726834..1727211 Ruegeria sp. TM1040 4077720 YP_613614.1 CDS TM1040_1619 NC_008044.1 1727252 1727833 R 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 complement(1727252..1727833) Ruegeria sp. TM1040 4077721 YP_613615.1 CDS TM1040_1620 NC_008044.1 1727837 1728298 R hypothetical protein complement(1727837..1728298) Ruegeria sp. TM1040 4077722 YP_613616.1 CDS TM1040_1621 NC_008044.1 1728295 1728756 R hypothetical protein complement(1728295..1728756) Ruegeria sp. TM1040 4077723 YP_613617.1 CDS TM1040_1622 NC_008044.1 1728820 1730139 R KEGG: ppu:PP3877 hypothetical protein, ev=3e-77, 41% identity; hypothetical protein complement(1728820..1730139) Ruegeria sp. TM1040 4077724 YP_613618.1 CDS TM1040_1623 NC_008044.1 1730142 1731089 R PFAM: peptidase S49: (1.8e-23); KEGG: nmu:Nmul_A0057 peptidase S49, ev=1e-42, 41% identity; serine peptidase complement(1730142..1731089) Ruegeria sp. TM1040 4077725 YP_613619.1 CDS TM1040_1624 NC_008044.1 1731086 1732372 R 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 complement(1731086..1732372) Ruegeria sp. TM1040 4077726 YP_613620.1 CDS TM1040_1625 NC_008044.1 1732375 1734075 R PFAM: phage Terminase: (6.4e-10); KEGG: rsp:RSP_2070 phage-related terminase, ev=1e-156, 52% identity; phage terminase complement(1732375..1734075) Ruegeria sp. TM1040 4077727 YP_613621.1 CDS TM1040_1626 NC_008044.1 1734086 1734631 R hypothetical protein complement(1734086..1734631) Ruegeria sp. TM1040 4077728 YP_613622.1 CDS TM1040_1627 NC_008044.1 1734735 1735055 D hypothetical protein 1734735..1735055 Ruegeria sp. TM1040 4077729 YP_613623.1 CDS TM1040_1628 NC_008044.1 1735346 1735738 D hypothetical protein 1735346..1735738 Ruegeria sp. TM1040 4077730 YP_613624.1 CDS TM1040_1629 NC_008044.1 1736144 1738018 R KEGG: pca:Pcar_1822 conserved hypothetical protein, ev=2e-23, 25% identity; hypothetical protein complement(1736144..1738018) Ruegeria sp. TM1040 4077731 YP_613625.1 CDS TM1040_1630 NC_008044.1 1738048 1738329 R hypothetical protein complement(1738048..1738329) Ruegeria sp. TM1040 4077732 YP_613626.1 CDS TM1040_1631 NC_008044.1 1738333 1739175 R hypothetical protein complement(1738333..1739175) Ruegeria sp. TM1040 4077733 YP_613627.1 CDS TM1040_1632 NC_008044.1 1739172 1739651 R KEGG: rsp:RSP_0134 hypothetical protein, ev=6e-11, 47% identity; hypothetical protein complement(1739172..1739651) Ruegeria sp. TM1040 4077734 YP_613628.1 CDS TM1040_1633 NC_008044.1 1739641 1740522 R KEGG: mag:amb1747 hypothetical protein, ev=1e-12, 31% identity; hypothetical protein complement(1739641..1740522) Ruegeria sp. TM1040 4077735 YP_613629.1 CDS TM1040_1634 NC_008044.1 1740519 1740797 R hypothetical protein complement(1740519..1740797) Ruegeria sp. TM1040 4077736 YP_613630.1 CDS TM1040_1635 NC_008044.1 1740964 1741440 R hypothetical protein complement(1740964..1741440) Ruegeria sp. TM1040 4077737 YP_613631.1 CDS TM1040_1636 NC_008044.1 1741814 1742167 D SMART: Helix-turn-helix type 3: (1.5e-09); XRE family transcriptional regulator 1741814..1742167 Ruegeria sp. TM1040 4077738 YP_613632.1 CDS TM1040_1637 NC_008044.1 1742333 1743016 D hypothetical protein 1742333..1743016 Ruegeria sp. TM1040 4077739 YP_613633.1 CDS TM1040_1638 NC_008044.1 1742974 1743864 R hypothetical protein complement(1742974..1743864) Ruegeria sp. TM1040 4077740 YP_613634.1 CDS TM1040_1639 NC_008044.1 1744087 1744389 D hypothetical protein 1744087..1744389 Ruegeria sp. TM1040 4077741 YP_613635.1 CDS TM1040_1640 NC_008044.1 1744698 1745402 D hypothetical protein 1744698..1745402 Ruegeria sp. TM1040 4077742 YP_613636.1 CDS TM1040_1641 NC_008044.1 1745594 1745950 D hypothetical protein 1745594..1745950 Ruegeria sp. TM1040 4075744 YP_613637.1 CDS TM1040_1642 NC_008044.1 1745947 1747818 D KEGG: rsp:RSP_3609 ParB-like nuclease, ev=1e-100, 38% identity; ParB-like nuclease 1745947..1747818 Ruegeria sp. TM1040 4075745 YP_613638.1 CDS TM1040_1643 NC_008044.1 1748176 1748427 D hypothetical protein 1748176..1748427 Ruegeria sp. TM1040 4075746 YP_613639.1 CDS TM1040_1644 NC_008044.1 1748417 1749649 D KEGG: nwi:Nwi_1140 phage integrase, ev=1e-24, 29% identity; hypothetical protein 1748417..1749649 Ruegeria sp. TM1040 4075747 YP_613640.1 CDS TM1040_1645 NC_008044.1 1750371 1751012 R PFAM: Resolvase-like: (8.9e-52); KEGG: ece:Z0318 DNA invertase from prophage CP-933H, ev=1e-33, 49% identity; resolvase-like protein complement(1750371..1751012) Ruegeria sp. TM1040 4075748 YP_613641.1 CDS TM1040_1646 NC_008044.1 1751144 1751659 D hypothetical protein 1751144..1751659 Ruegeria sp. TM1040 4075749 YP_613642.1 CDS TM1040_1647 NC_008044.1 1751638 1752096 R hypothetical protein complement(1751638..1752096) Ruegeria sp. TM1040 4075750 YP_613643.1 CDS TM1040_1648 NC_008044.1 1752165 1752485 R hypothetical protein complement(1752165..1752485) Ruegeria sp. TM1040 4075751 YP_613644.1 CDS TM1040_1649 NC_008044.1 1752567 1752965 R hypothetical protein complement(1752567..1752965) Ruegeria sp. TM1040 4075752 YP_613645.1 CDS TM1040_1650 NC_008044.1 1752962 1753771 R PFAM: protein of unknown function DUF847: (8.8e-67); KEGG: bmb:BruAb1_0990 secretion activator protein, hypothetical, ev=1e-43, 39% identity; hypothetical protein complement(1752962..1753771) Ruegeria sp. TM1040 4075753 YP_613646.1 CDS TM1040_1651 NC_008044.1 1753773 1754207 R hypothetical protein complement(1753773..1754207) Ruegeria sp. TM1040 4075754 YP_613647.1 CDS TM1040_1652 NC_008044.1 1754204 1754461 R hypothetical protein complement(1754204..1754461) Ruegeria sp. TM1040 4075755 YP_613648.1 CDS TM1040_1653 NC_008044.1 1754507 1754854 R hypothetical protein complement(1754507..1754854) Ruegeria sp. TM1040 4075756 YP_613649.1 CDS TM1040_1654 NC_008044.1 1754832 1755464 R hypothetical protein complement(1754832..1755464) Ruegeria sp. TM1040 4075757 YP_613650.1 CDS TM1040_1655 NC_008044.1 1755461 1756456 R KEGG: pub:SAR11_0932 hypothetical protein, ev=2e-20, 32% identity; hypothetical protein complement(1755461..1756456) Ruegeria sp. TM1040 4075758 YP_613651.1 CDS TM1040_1656 NC_008044.1 1756975 1757919 R KEGG: nar:Saro_0661 hypothetical protein, ev=7e-28, 26% identity; hypothetical protein complement(1756975..1757919) Ruegeria sp. TM1040 4075759 YP_613652.1 CDS TM1040_1657 NC_008044.1 1757916 1762442 R KEGG: rsp:RSP_3791 hypothetical protein, ev=5e-91, 24% identity; hypothetical protein complement(1757916..1762442) Ruegeria sp. TM1040 4075760 YP_613653.1 CDS TM1040_1658 NC_008044.1 1762471 1762809 D hypothetical protein 1762471..1762809 Ruegeria sp. TM1040 4075761 YP_613654.1 CDS TM1040_1659 NC_008044.1 1762850 1763731 R hypothetical protein complement(1762850..1763731) Ruegeria sp. TM1040 4075762 YP_613655.1 CDS TM1040_1660 NC_008044.1 1763994 1764332 R hypothetical protein complement(1763994..1764332) Ruegeria sp. TM1040 4075763 YP_613656.1 CDS TM1040_1661 NC_008044.1 1764431 1764880 R KEGG: rsp:RSP_3788 hypothetical protein, ev=2e-29, 46% identity; hypothetical protein complement(1764431..1764880) Ruegeria sp. TM1040 4075764 YP_613657.1 CDS TM1040_1662 NC_008044.1 1764979 1765428 R KEGG: nar:Saro_0657 hypothetical protein, ev=2e-32, 50% identity; hypothetical protein complement(1764979..1765428) Ruegeria sp. TM1040 4075765 YP_613658.1 CDS TM1040_1663 NC_008044.1 1765489 1765773 R hypothetical protein complement(1765489..1765773) Ruegeria sp. TM1040 4075766 YP_613659.1 CDS TM1040_1664 NC_008044.1 1765815 1766120 R KEGG: rsp:RSP_6012 hypothetical protein, ev=3e-07, 35% identity; hypothetical protein complement(1765815..1766120) Ruegeria sp. TM1040 4075767 YP_613660.1 CDS TM1040_1665 NC_008044.1 1766168 1766623 R KEGG: rsp:RSP_1640 hypothetical protein, ev=2e-14, 35% identity; hypothetical protein complement(1766168..1766623) Ruegeria sp. TM1040 4075768 YP_613661.1 CDS TM1040_1666 NC_008044.1 1766620 1766958 R TIGRFAM: conserved hypothetical protein: (0.13); hypothetical protein complement(1766620..1766958) Ruegeria sp. TM1040 4075769 YP_613662.1 CDS TM1040_1667 NC_008044.1 1766958 1767530 R 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 complement(1766958..1767530) Ruegeria sp. TM1040 4075770 YP_613663.1 CDS TM1040_1668 NC_008044.1 1767772 1768983 R KEGG: nar:Saro_0649 phage major capsid protein, HK97, ev=1e-103, 52% identity; phage major capsid protein, HK97 complement(1767772..1768983) Ruegeria sp. TM1040 4075771 YP_613664.1 CDS TM1040_1669 NC_008044.1 1769008 1769694 R 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 complement(1769008..1769694) Ruegeria sp. TM1040 4075772 YP_613665.1 CDS TM1040_1670 NC_008044.1 1769678 1770901 R 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 complement(1769678..1770901) Ruegeria sp. TM1040 4075773 YP_613666.1 CDS TM1040_1671 NC_008044.1 1770902 1772683 R PFAM: phage Terminase: (9.1e-37); KEGG: sgl:SG0724 phage terminase large subunit, ev=1e-100, 37% identity; phage terminase complement(1770902..1772683) Ruegeria sp. TM1040 4075774 YP_613667.1 CDS TM1040_1672 NC_008044.1 1772661 1773068 R hypothetical protein complement(1772661..1773068) Ruegeria sp. TM1040 4075775 YP_613668.1 CDS TM1040_1673 NC_008044.1 1773573 1773896 D hypothetical protein 1773573..1773896 Ruegeria sp. TM1040 4075776 YP_613669.1 CDS TM1040_1674 NC_008044.1 1774102 1774671 R hypothetical protein complement(1774102..1774671) Ruegeria sp. TM1040 4075777 YP_613670.1 CDS TM1040_1675 NC_008044.1 1774694 1774942 R hypothetical protein complement(1774694..1774942) Ruegeria sp. TM1040 4075778 YP_613671.1 CDS TM1040_1676 NC_008044.1 1774948 1775424 R 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 complement(1774948..1775424) Ruegeria sp. TM1040 4075779 YP_613672.1 CDS TM1040_1677 NC_008044.1 1775642 1776403 R hypothetical protein complement(1775642..1776403) Ruegeria sp. TM1040 4075780 YP_613673.1 CDS TM1040_1678 NC_008044.1 1776938 1777294 R PFAM: endodeoxyribonuclease RusA: (0.0097); endodeoxyribonuclease RusA complement(1776938..1777294) Ruegeria sp. TM1040 4075781 YP_613674.1 CDS TM1040_1679 NC_008044.1 1777291 1777863 R PFAM: MT-A70: (1.7e-36); KEGG: ana:all7280 adenine-specific DNA methyltransferase, ev=1e-25, 35% identity; hypothetical protein complement(1777291..1777863) Ruegeria sp. TM1040 4075782 YP_613675.1 CDS TM1040_1680 NC_008044.1 1777863 1778165 R hypothetical protein complement(1777863..1778165) Ruegeria sp. TM1040 4078256 YP_613676.1 CDS TM1040_1681 NC_008044.1 1778403 1778846 R hypothetical protein complement(1778403..1778846) Ruegeria sp. TM1040 4078257 YP_613677.1 CDS TM1040_1682 NC_008044.1 1779272 1779922 D KEGG: rsp:RSP_3771 hypothetical protein, ev=4e-17, 47% identity; hypothetical protein 1779272..1779922 Ruegeria sp. TM1040 4078258 YP_613678.1 CDS TM1040_1683 NC_008044.1 1779945 1780214 D KEGG: noc:Noc_2744 hypothetical protein, ev=2e-08, 38% identity; hypothetical protein 1779945..1780214 Ruegeria sp. TM1040 4078259 YP_613679.1 CDS TM1040_1684 NC_008044.1 1780207 1780608 D PFAM: protein of unknown function UPF0150: (1.1e-18); KEGG: noc:Noc_2743 hypothetical protein, ev=4e-18, 58% identity; hypothetical protein 1780207..1780608 Ruegeria sp. TM1040 4078260 YP_613680.1 CDS TM1040_1685 NC_008044.1 1780907 1781299 D hypothetical protein 1780907..1781299 Ruegeria sp. TM1040 4078261 YP_613681.1 CDS TM1040_1686 NC_008044.1 1781513 1781776 D hypothetical protein 1781513..1781776 Ruegeria sp. TM1040 4078262 YP_613682.1 CDS TM1040_1687 NC_008044.1 1781885 1782862 D KEGG: sgl:SG1827 hypothetical protein, ev=4e-58, 41% identity; hypothetical protein 1781885..1782862 Ruegeria sp. TM1040 4078263 YP_613683.1 CDS TM1040_1688 NC_008044.1 1782883 1783587 D KEGG: lpf:lpl1360 hypothetical protein, ev=1e-10, 30% identity; hypothetical protein 1782883..1783587 Ruegeria sp. TM1040 4078264 YP_613684.1 CDS TM1040_1689 NC_008044.1 1783760 1784104 D hypothetical protein 1783760..1784104 Ruegeria sp. TM1040 4078265 YP_613685.1 CDS TM1040_1690 NC_008044.1 1784101 1784478 D SMART: HNH nuclease: (2.4e-06); KEGG: mlo:mll7975 hypothetical protein, ev=1e-10, 40% identity; HNH nuclease 1784101..1784478 Ruegeria sp. TM1040 4078266 YP_613686.1 CDS TM1040_1691 NC_008044.1 1784602 1786695 D 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 1784602..1786695 Ruegeria sp. TM1040 4078267 YP_613687.1 CDS TM1040_1692 NC_008044.1 1787053 1788099 D PFAM: phage integrase: (0.0014); KEGG: mag:amb2709 integrase, ev=4e-15, 25% identity; phage integrase 1787053..1788099 Ruegeria sp. TM1040 4078268 YP_613688.1 CDS TM1040_1693 NC_008044.1 1788393 1789004 R 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 complement(1788393..1789004) Ruegeria sp. TM1040 4078269 YP_613689.1 CDS TM1040_1694 NC_008044.1 1789014 1789490 R PFAM: regulatory proteins, AsnC/Lrp: (1.2e-20); KEGG: sil:SPO3009 proline dehydrogenase transcriptional activator, ev=2e-56, 67% identity; AsnC family transcriptional regulator complement(1789014..1789490) Ruegeria sp. TM1040 4078270 YP_613690.1 CDS TM1040_1695 NC_008044.1 1789603 1793010 D 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 1789603..1793010 Ruegeria sp. TM1040 4078271 YP_613691.1 CDS TM1040_1696 NC_008044.1 1793112 1793882 D PFAM: Rhomboid-like protein: (1.1e-40); KEGG: sil:SPO3011 rhomboid family protein, ev=6e-91, 65% identity; rhomboid-like protein 1793112..1793882 Ruegeria sp. TM1040 4078272 YP_613692.1 CDS TM1040_1697 NC_008044.1 1793908 1794294 D 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 1793908..1794294 Ruegeria sp. TM1040 4078273 YP_613693.1 CDS TM1040_1698 NC_008044.1 1794466 1795251 R PFAM: inositol monophosphatase: (6.5e-71); KEGG: sil:SPO3012 inositol-1-monophosphatase, , ev=1e-130, 86% identity; inositol monophosphatase complement(1794466..1795251) Ruegeria sp. TM1040 4078274 YP_613694.1 CDS TM1040_1699 NC_008044.1 1795432 1796337 R 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 complement(1795432..1796337) Ruegeria sp. TM1040 4078275 YP_613695.1 CDS TM1040_1700 NC_008044.1 1796495 1797364 D 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 1796495..1797364 Ruegeria sp. TM1040 4078276 YP_613696.1 CDS TM1040_1701 NC_008044.1 1797423 1797905 D 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 1797423..1797905 Ruegeria sp. TM1040 4078277 YP_613697.1 CDS TM1040_1702 NC_008044.1 1797922 1798926 R KEGG: eca:ECA3200 hypothetical protein, ev=7e-59, 39% identity; hypothetical protein complement(1797922..1798926) Ruegeria sp. TM1040 4078278 YP_613698.1 CDS TM1040_1703 NC_008044.1 1798978 1799601 D PFAM: GCN5-related N-acetyltransferase: (8.5e-15); KEGG: jan:Jann_3325 GCN5-related N-acetyltransferase, ev=3e-47, 52% identity; N-acetyltransferase GCN5 1798978..1799601 Ruegeria sp. TM1040 4078279 YP_613699.1 CDS TM1040_1704 NC_008044.1 1799623 1800708 R KEGG: sil:SPO3018 hypothetical protein, ev=1e-137, 68% identity; hypothetical protein complement(1799623..1800708) Ruegeria sp. TM1040 4078280 YP_613700.1 CDS TM1040_1705 NC_008044.1 1800686 1802995 R 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 complement(1800686..1802995) Ruegeria sp. TM1040 4078281 YP_613701.1 CDS valS NC_008044.1 1803784 1806879 D 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 1803784..1806879 Ruegeria sp. TM1040 4078282 YP_613702.1 CDS TM1040_1707 NC_008044.1 1807090 1807383 D PFAM: protein of unknown function DUF1330: (7.9e-40); KEGG: rpa:RPA0338 hypothetical protein, ev=2e-24, 55% identity; hypothetical protein 1807090..1807383 Ruegeria sp. TM1040 4078283 YP_613703.1 CDS TM1040_1708 NC_008044.1 1807406 1807864 D KEGG: sil:SPO1310 hypothetical protein, ev=6e-57, 77% identity; hypothetical protein 1807406..1807864 Ruegeria sp. TM1040 4078284 YP_613704.1 CDS TM1040_1709 NC_008044.1 1807873 1808316 D PFAM: protein of unknown function DUF1332: (3.5e-18); KEGG: sil:SPO1309 hypothetical protein, ev=2e-44, 66% identity; hypothetical protein 1807873..1808316 Ruegeria sp. TM1040 4078285 YP_613705.1 CDS TM1040_1710 NC_008044.1 1808313 1809083 D KEGG: sil:SPO1308 hypothetical protein, ev=2e-72, 54% identity; hypothetical protein 1808313..1809083 Ruegeria sp. TM1040 4078286 YP_613706.1 CDS TM1040_1711 NC_008044.1 1809264 1810043 D 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 1809264..1810043 Ruegeria sp. TM1040 4078287 YP_613707.1 CDS TM1040_1712 NC_008044.1 1810083 1810790 D 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 1810083..1810790 Ruegeria sp. TM1040 4078288 YP_613708.1 CDS TM1040_1713 NC_008044.1 1810884 1811792 D 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 1810884..1811792 Ruegeria sp. TM1040 4078289 YP_613709.1 CDS TM1040_1714 NC_008044.1 1811789 1812595 D 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 1811789..1812595 Ruegeria sp. TM1040 4078290 YP_613710.1 CDS TM1040_1715 NC_008044.1 1812653 1814482 R 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 complement(1812653..1814482) Ruegeria sp. TM1040 4078291 YP_613711.1 CDS TM1040_1716 NC_008044.1 1814631 1815902 D 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 1814631..1815902 Ruegeria sp. TM1040 4078292 YP_613712.1 CDS TM1040_1717 NC_008044.1 1815914 1816507 D KEGG: sil:SPO1290 hypothetical protein, ev=1e-52, 50% identity; hypothetical protein 1815914..1816507 Ruegeria sp. TM1040 4078293 YP_613713.1 CDS TM1040_1718 NC_008044.1 1816511 1817314 R KEGG: sil:SPO1289 hydrolase, alpha/beta fold family, ev=3e-44, 44% identity; alpha/beta hydrolase complement(1816511..1817314) Ruegeria sp. TM1040 4078294 YP_613714.1 CDS TM1040_1719 NC_008044.1 1817526 1817951 R 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 complement(1817526..1817951) Ruegeria sp. TM1040 4075783 YP_613715.1 CDS TM1040_1720 NC_008044.1 1818044 1818787 R KEGG: sil:SPO1285 hypothetical protein, ev=3e-98, 72% identity; hypothetical protein complement(1818044..1818787) Ruegeria sp. TM1040 4075784 YP_613716.1 CDS thrS NC_008044.1 1819028 1820974 D 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 1819028..1820974 Ruegeria sp. TM1040 4075785 YP_613717.1 CDS TM1040_1722 NC_008044.1 1821195 1821500 D KEGG: sil:SPO1281 hypothetical protein, ev=6e-41, 82% identity; hypothetical protein 1821195..1821500 Ruegeria sp. TM1040 4075786 YP_613718.1 CDS TM1040_1723 NC_008044.1 1821631 1822482 D PFAM: protein of unknown function DUF692: (4.8e-111); KEGG: sil:SPO1280 hypothetical protein, ev=1e-131, 81% identity; hypothetical protein 1821631..1822482 Ruegeria sp. TM1040 4075787 YP_613719.1 CDS TM1040_1724 NC_008044.1 1822482 1823228 D KEGG: sil:SPO1279 hypothetical protein, ev=2e-88, 66% identity; hypothetical protein 1822482..1823228 Ruegeria sp. TM1040 4075788 YP_613720.1 CDS TM1040_1725 NC_008044.1 1823237 1823800 D PFAM: DoxX: (0.00021); KEGG: sil:SPO1278 hypothetical protein, ev=1e-81, 81% identity; DoxX protein 1823237..1823800 Ruegeria sp. TM1040 4075789 YP_613721.1 CDS TM1040_1726 NC_008044.1 1823880 1824197 R PFAM: arsenate reductase and related: (6.6e-12); KEGG: sil:SPO1276 ArsC family protein, ev=2e-31, 62% identity; arsenate reductase complement(1823880..1824197) Ruegeria sp. TM1040 4075790 YP_613722.1 CDS TM1040_1727 NC_008044.1 1824418 1824624 D 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 1824418..1824624 Ruegeria sp. TM1040 4075791 YP_613723.1 CDS TM1040_1728 NC_008044.1 1824709 1825200 R PFAM: dihydrofolate reductase region: (5.1e-44); KEGG: rsp:RSP_0389 dihydrofolate reductase, ev=3e-49, 59% identity; dihydrofolate reductase complement(1824709..1825200) Ruegeria sp. TM1040 4075792 YP_613724.1 CDS thyA NC_008044.1 1825228 1826061 R 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 complement(1825228..1826061) Ruegeria sp. TM1040 4075793 YP_613725.1 CDS TM1040_1730 NC_008044.1 1826199 1826627 D 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 1826199..1826627 Ruegeria sp. TM1040 4075794 YP_613726.1 CDS TM1040_1731 NC_008044.1 1827197 1827694 R PFAM: regulatory protein, MarR: (1.1e-09); KEGG: jan:Jann_2651 transcriptional regulator, MarR family, ev=6e-70, 76% identity; MarR family transcriptional regulator complement(1827197..1827694) Ruegeria sp. TM1040 4075795 YP_613727.1 CDS TM1040_1732 NC_008044.1 1827774 1828052 R PFAM: protein of unknown function DUF339: (5.5e-20); KEGG: sil:SPO1266 TPR repeat family protein, ev=9e-26, 65% identity; hypothetical protein complement(1827774..1828052) Ruegeria sp. TM1040 4075796 YP_613728.1 CDS TM1040_1733 NC_008044.1 1828049 1828450 R PFAM: helix-turn-helix motif: (1.7e-13); KEGG: sil:SPO1265 DNA-binding protein, , ev=2e-39, 64% identity; XRE family transcriptional regulator complement(1828049..1828450) Ruegeria sp. TM1040 4075797 YP_613729.1 CDS TM1040_1734 NC_008044.1 1828535 1829737 D catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate; aspartate aminotransferase 1828535..1829737 Ruegeria sp. TM1040 4075798 YP_613730.1 CDS TM1040_1735 NC_008044.1 1830011 1830427 D KEGG: jan:Jann_2660 hypothetical protein, ev=6e-49, 69% identity; hypothetical protein 1830011..1830427 Ruegeria sp. TM1040 4075799 YP_613731.1 CDS TM1040_1736 NC_008044.1 1830497 1831915 R 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 complement(1830497..1831915) Ruegeria sp. TM1040 4075800 YP_613732.1 CDS TM1040_1737 NC_008044.1 1832077 1833159 R 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 complement(1832077..1833159) Ruegeria sp. TM1040 4075801 YP_613733.1 CDS TM1040_1738 NC_008044.1 1833164 1833802 R KEGG: jan:Jann_1928 hypothetical protein, ev=6e-37, 42% identity; hypothetical protein complement(1833164..1833802) Ruegeria sp. TM1040 4075802 YP_613734.1 CDS TM1040_1739 NC_008044.1 1833899 1834507 R 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 complement(1833899..1834507) Ruegeria sp. TM1040 4075803 YP_613735.1 CDS TM1040_1740 NC_008044.1 1834669 1836678 D decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit B 1834669..1836678 Ruegeria sp. TM1040 4075804 YP_613736.1 CDS TM1040_1741 NC_008044.1 1836784 1837215 R PFAM: cytochrome c, class I: (0.0041); KEGG: sil:SPOA0361 cytochrome c family protein, ev=2e-35, 60% identity; cytochrome c, class I complement(1836784..1837215) Ruegeria sp. TM1040 4075805 YP_613737.1 CDS TM1040_1742 NC_008044.1 1837357 1838223 R PFAM: copper resistance D: (8.5e-07); KEGG: pha:PSHAb0008 copper export protein, ev=1e-22, 29% identity; copper resistance D complement(1837357..1838223) Ruegeria sp. TM1040 4075806 YP_613738.1 CDS TM1040_1743 NC_008044.1 1838226 1838576 R PFAM: copper resistance protein CopC: (5e-14); KEGG: bur:Bcep18194_A5818 copper resistance protein CopC, ev=2e-09, 27% identity; copper resistance protein CopC complement(1838226..1838576) Ruegeria sp. TM1040 4075807 YP_613739.1 CDS TM1040_1744 NC_008044.1 1838579 1839010 R PFAM: cytochrome c, class I: (0.0091); KEGG: sil:SPOA0359 cytochrome c family protein, ev=2e-28, 51% identity; cytochrome c, class I complement(1838579..1839010) Ruegeria sp. TM1040 4075808 YP_613740.1 CDS TM1040_1745 NC_008044.1 1839068 1839442 R hypothetical protein complement(1839068..1839442) Ruegeria sp. TM1040 4075809 YP_613741.1 CDS TM1040_1746 NC_008044.1 1839580 1840134 R KEGG: ddi:DDB0168118 hypothetical protein, ev=5e-09, 30% identity; hypothetical protein complement(1839580..1840134) Ruegeria sp. TM1040 4075810 YP_613742.1 CDS TM1040_1747 NC_008044.1 1840384 1841259 D PFAM: EAL: (2.8e-43); KEGG: ccr:CC3148 hypothetical protein, ev=2e-75, 56% identity; diguanylate phosphodiesterase 1840384..1841259 Ruegeria sp. TM1040 4075811 YP_613743.1 CDS TM1040_1748 NC_008044.1 1841365 1842276 R 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 complement(1841365..1842276) Ruegeria sp. TM1040 4075812 YP_613744.1 CDS TM1040_1749 NC_008044.1 1842361 1843008 D 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 1842361..1843008 Ruegeria sp. TM1040 4075813 YP_613745.1 CDS TM1040_1750 NC_008044.1 1843111 1843791 R PFAM: ThiJ/PfpI: (1.5e-21); KEGG: sme:SMb20212 hypothetical protein, ev=3e-57, 52% identity; ThiJ/PfpI complement(1843111..1843791) Ruegeria sp. TM1040 4075814 YP_613746.1 CDS TM1040_1751 NC_008044.1 1843922 1844821 D 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 1843922..1844821 Ruegeria sp. TM1040 4075815 YP_613747.1 CDS TM1040_1752 NC_008044.1 1845256 1845462 D 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 1845256..1845462 Ruegeria sp. TM1040 4075816 YP_613748.1 CDS TM1040_1753 NC_008044.1 1845455 1845703 D hypothetical protein 1845455..1845703 Ruegeria sp. TM1040 4075817 YP_613749.1 CDS TM1040_1754 NC_008044.1 1846069 1846413 D KEGG: rsp:RSP_3622 hypothetical protein, ev=6e-14, 45% identity; hypothetical protein 1846069..1846413 Ruegeria sp. TM1040 4075818 YP_613750.1 CDS TM1040_1755 NC_008044.1 1846962 1847441 R PFAM: regulatory proteins, AsnC/Lrp: (1.5e-21); KEGG: sil:SPO2631 transcriptional regulator, AsnC family, ev=9e-71, 88% identity; AsnC family transcriptional regulator complement(1846962..1847441) Ruegeria sp. TM1040 4075819 YP_613751.1 CDS TM1040_1756 NC_008044.1 1847652 1848404 D 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 1847652..1848404 Ruegeria sp. TM1040 4075820 YP_613752.1 CDS TM1040_1757 NC_008044.1 1848404 1848724 D KEGG: sil:SPO2633 hypothetical protein, ev=2e-37, 78% identity; hypothetical protein 1848404..1848724 Ruegeria sp. TM1040 4075821 YP_613753.1 CDS TM1040_1758 NC_008044.1 1848717 1850384 D 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 1848717..1850384 Ruegeria sp. TM1040 4076787 YP_613754.1 CDS TM1040_1759 NC_008044.1 1850388 1851149 D catalyzes the reduction of 3'-phosphoadenylyl sulfate into sulfite; phosphoadenosine phosphosulfate reductase 1850388..1851149 Ruegeria sp. TM1040 4076788 YP_613755.1 CDS TM1040_1760 NC_008044.1 1851155 1851559 D KEGG: sil:SPO2636 hypothetical protein, ev=2e-44, 67% identity; hypothetical protein 1851155..1851559 Ruegeria sp. TM1040 4076789 YP_613756.1 CDS TM1040_1761 NC_008044.1 1851726 1852598 D PFAM: Oxidoreductase FAD-binding region: (0.00066); KEGG: jan:Jann_1770 ferredoxin--NADP(+) reductase, ev=1e-143, 85% identity; ferredoxin--NADP(+) reductase 1851726..1852598 Ruegeria sp. TM1040 4076790 YP_613757.1 CDS TM1040_1762 NC_008044.1 1852751 1853548 R KEGG: jan:Jann_1769 mucin-associated surface protein, ev=6e-27, 37% identity; mucin-associated surface protein complement(1852751..1853548) Ruegeria sp. TM1040 4076791 YP_613758.1 CDS TM1040_1763 NC_008044.1 1853932 1854345 D 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 1853932..1854345 Ruegeria sp. TM1040 4076792 YP_613759.1 CDS TM1040_1764 NC_008044.1 1854464 1855252 R PFAM: molybdopterin dehydrogenase, FAD-binding: (1e-60); KEGG: sil:SPO1520 carbon monoxide dehydrogenase, medium subunit, , ev=1e-107, 76% identity; molybdopterin dehydrogenase complement(1854464..1855252) Ruegeria sp. TM1040 4076793 YP_613760.1 CDS TM1040_1765 NC_008044.1 1855343 1857721 R 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 complement(1855343..1857721) Ruegeria sp. TM1040 4076794 YP_613761.1 CDS TM1040_1766 NC_008044.1 1857876 1858361 R 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 complement(1857876..1858361) Ruegeria sp. TM1040 4076795 YP_613762.1 CDS TM1040_1767 NC_008044.1 1858406 1859479 R PFAM: molybdopterin binding domain: (0.00035); KEGG: sil:SPO2639 molybdopterin biosynthesis protein, ev=1e-104, 57% identity; molybdopterin binding domain-containing protein complement(1858406..1859479) Ruegeria sp. TM1040 4076796 YP_613763.1 CDS TM1040_1768 NC_008044.1 1859476 1860504 R PFAM: protein of unknown function DUF182: (7.8e-27); KEGG: sil:SPO2640 XdhC/CoxI family protein, ev=1e-131, 73% identity; hypothetical protein complement(1859476..1860504) Ruegeria sp. TM1040 4076797 YP_613764.1 CDS TM1040_1769 NC_008044.1 1860620 1861903 R 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 complement(1860620..1861903) Ruegeria sp. TM1040 4076798 YP_613765.1 CDS TM1040_1770 NC_008044.1 1861967 1862881 R 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 complement(1861967..1862881) Ruegeria sp. TM1040 4076799 YP_613766.1 CDS TM1040_1771 NC_008044.1 1863225 1864166 D KEGG: sil:SPO2647 hypothetical protein, ev=1e-144, 72% identity; hypothetical protein 1863225..1864166 Ruegeria sp. TM1040 4076800 YP_613767.1 CDS TM1040_1772 NC_008044.1 1864177 1864836 D KEGG: sil:SPO2648 hypothetical protein, ev=2e-44, 44% identity; hypothetical protein 1864177..1864836 Ruegeria sp. TM1040 4076801 YP_613768.1 CDS TM1040_1773 NC_008044.1 1864836 1867199 D KEGG: sil:SPO2649 hypothetical protein, ev=0.0, 60% identity; hypothetical protein 1864836..1867199 Ruegeria sp. TM1040 4076802 YP_613769.1 CDS TM1040_1774 NC_008044.1 1867202 1868335 D KEGG: sil:SPO2651 glycosyl transferase, group 2 family protein, ev=1e-131, 64% identity; glycosyl transferase family protein 1867202..1868335 Ruegeria sp. TM1040 4076803 YP_613770.1 CDS TM1040_1775 NC_008044.1 1868485 1869480 D KEGG: sil:SPO2652 hypothetical protein, ev=1e-120, 65% identity; hypothetical protein 1868485..1869480 Ruegeria sp. TM1040 4076804 YP_613771.1 CDS TM1040_1776 NC_008044.1 1869523 1870563 D catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis; dihydroorotase 1869523..1870563 Ruegeria sp. TM1040 4076805 YP_613772.1 CDS pyrE NC_008044.1 1870640 1871320 D 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 1870640..1871320 Ruegeria sp. TM1040 4076806 YP_613773.1 CDS TM1040_1778 NC_008044.1 1871573 1873090 D unwinds double stranded DNA; replicative DNA helicase 1871573..1873090 Ruegeria sp. TM1040 4076807 YP_613774.1 CDS TM1040_1779 NC_008044.1 1873275 1874312 D 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 1873275..1874312 Ruegeria sp. TM1040 4076808 YP_613775.1 CDS TM1040_1780 NC_008044.1 1874309 1875091 D PFAM: protein of unknown function DUF140: (1.4e-87); KEGG: sil:SPO2671 membrane protein, ev=1e-117, 83% identity; hypothetical protein 1874309..1875091 Ruegeria sp. TM1040 4076809 YP_613776.1 CDS TM1040_1781 NC_008044.1 1875088 1875846 D 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 1875088..1875846 Ruegeria sp. TM1040 4076810 YP_613777.1 CDS TM1040_1782 NC_008044.1 1875910 1876587 D hypothetical protein 1875910..1876587 Ruegeria sp. TM1040 4076811 YP_613778.1 CDS TM1040_1783 NC_008044.1 1876584 1877072 D PFAM: Paraquat-inducible protein A: (5.2e-07); KEGG: sil:SPO2673 paraquat-inducible protein A, , ev=2e-60, 78% identity; paraquat-inducible protein A 1876584..1877072 Ruegeria sp. TM1040 4076812 YP_613779.1 CDS TM1040_1784 NC_008044.1 1877394 1878758 D 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 1877394..1878758 Ruegeria sp. TM1040 4076813 YP_613780.1 CDS TM1040_1785 NC_008044.1 1878733 1879356 D PFAM: Colicin V production protein: (2e-21); KEGG: sil:SPO2675 CvpA family protein, ev=2e-73, 73% identity; colicin V production protein 1878733..1879356 Ruegeria sp. TM1040 4076814 YP_613781.1 CDS TM1040_1786 NC_008044.1 1879765 1880475 D KEGG: sil:SPO2676 hypothetical protein, ev=7e-18, 35% identity; hypothetical protein 1879765..1880475 Ruegeria sp. TM1040 4076815 YP_613782.1 CDS TM1040_1787 NC_008044.1 1880937 1882457 D Catalyzes first step of the de novo purine nucleotide biosynthetic pathway; amidophosphoribosyltransferase 1880937..1882457 Ruegeria sp. TM1040 4076816 YP_613783.1 CDS TM1040_1788 NC_008044.1 1882654 1883196 D KEGG: bca:BCE1117 hypothetical protein, ev=2e-07, 27% identity; hypothetical protein 1882654..1883196 Ruegeria sp. TM1040 4076817 YP_613784.1 CDS TM1040_1789 NC_008044.1 1883451 1883705 D KEGG: sil:SPO2678 hypothetical protein, ev=2e-07, 35% identity; hypothetical protein 1883451..1883705 Ruegeria sp. TM1040 4076818 YP_613785.1 CDS TM1040_1790 NC_008044.1 1883789 1884436 D 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 1883789..1884436 Ruegeria sp. TM1040 4076819 YP_613786.1 CDS TM1040_1791 NC_008044.1 1884712 1885494 D catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate; stationary phase survival protein SurE 1884712..1885494 Ruegeria sp. TM1040 4076820 YP_613787.1 CDS TM1040_1792 NC_008044.1 1885491 1886138 D 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 1885491..1886138 Ruegeria sp. TM1040 4076821 YP_613788.1 CDS TM1040_1793 NC_008044.1 1886267 1887547 D 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 1886267..1887547 Ruegeria sp. TM1040 4076822 YP_613789.1 CDS TM1040_1794 NC_008044.1 1887686 1888561 R PFAM: protein of unknown function DUF815: (1.1e-60); KEGG: sil:SPO2680 hypothetical protein, ev=1e-139, 85% identity; hypothetical protein complement(1887686..1888561) Ruegeria sp. TM1040 4076823 YP_613790.1 CDS TM1040_1795 NC_008044.1 1888716 1889606 R 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 complement(1888716..1889606) Ruegeria sp. TM1040 4076824 YP_613791.1 CDS TM1040_1796 NC_008044.1 1889603 1890091 R 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 complement(1889603..1890091) Ruegeria sp. TM1040 4076825 YP_613792.1 CDS TM1040_1797 NC_008044.1 1890099 1890314 R 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 complement(1890099..1890314) Ruegeria sp. TM1040 4076943 YP_613793.1 CDS TM1040_1798 NC_008044.1 1890558 1890881 D KEGG: sil:SPO2684 hypothetical protein, ev=1e-23, 53% identity; hypothetical protein 1890558..1890881 Ruegeria sp. TM1040 4076944 YP_613794.1 CDS TM1040_1799 NC_008044.1 1890915 1891604 D 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 1890915..1891604 Ruegeria sp. TM1040 4076945 YP_613795.1 CDS TM1040_1800 NC_008044.1 1891610 1892491 R PFAM: GCN5-related N-acetyltransferase: (6.7e-12); KEGG: syn:sll1469 hypothetical protein, ev=5e-70, 47% identity; N-acetyltransferase GCN5 complement(1891610..1892491) Ruegeria sp. TM1040 4076946 YP_613796.1 CDS TM1040_1801 NC_008044.1 1892504 1893631 R 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 complement(1892504..1893631) Ruegeria sp. TM1040 4076947 YP_613797.1 CDS TM1040_1802 NC_008044.1 1893699 1894817 R KEGG: sil:SPO2691 hypothetical protein, ev=1e-125, 61% identity; hypothetical protein complement(1893699..1894817) Ruegeria sp. TM1040 4076948 YP_613798.1 CDS TM1040_1803 NC_008044.1 1894822 1895601 R 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 complement(1894822..1895601) Ruegeria sp. TM1040 4076949 YP_613799.1 CDS TM1040_1804 NC_008044.1 1895802 1896818 D KEGG: sil:SPO2693 hypothetical protein, ev=2e-97, 53% identity; hypothetical protein 1895802..1896818 Ruegeria sp. TM1040 4076950 YP_613800.1 CDS TM1040_1805 NC_008044.1 1896897 1897289 R hypothetical protein complement(1896897..1897289) Ruegeria sp. TM1040 4076951 YP_613801.1 CDS TM1040_1806 NC_008044.1 1897294 1897587 R PFAM: protein of unknown function DUF883, ElaB: (1.3e-05); KEGG: bmb:BruAb1_1648 hypothetical protein, ev=9e-07, 32% identity; hypothetical protein complement(1897294..1897587) Ruegeria sp. TM1040 4076952 YP_613802.1 CDS TM1040_1807 NC_008044.1 1897799 1899487 D 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 1897799..1899487 Ruegeria sp. TM1040 4076953 YP_613803.1 CDS TM1040_1808 NC_008044.1 1899560 1900498 D KEGG: sil:SPO1444 hypothetical protein, ev=1e-92, 54% identity; hypothetical protein 1899560..1900498 Ruegeria sp. TM1040 4076954 YP_613804.1 CDS TM1040_1809 NC_008044.1 1900693 1902174 D 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 1900693..1902174 Ruegeria sp. TM1040 4076955 YP_613805.1 CDS TM1040_1810 NC_008044.1 1902340 1902666 R hypothetical protein complement(1902340..1902666) Ruegeria sp. TM1040 4076956 YP_613806.1 CDS TM1040_1811 NC_008044.1 1902842 1904218 R 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 complement(1902842..1904218) Ruegeria sp. TM1040 4076957 YP_613807.1 CDS TM1040_1812 NC_008044.1 1904218 1904895 R 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 complement(1904218..1904895) Ruegeria sp. TM1040 4076958 YP_613808.1 CDS TM1040_1813 NC_008044.1 1905025 1906029 R 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 complement(1905025..1906029) Ruegeria sp. TM1040 4076959 YP_613809.1 CDS TM1040_1814 NC_008044.1 1906276 1907505 R 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 complement(1906276..1907505) Ruegeria sp. TM1040 4076960 YP_613810.1 CDS TM1040_1815 NC_008044.1 1907502 1909253 R 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 complement(1907502..1909253) Ruegeria sp. TM1040 4076961 YP_613811.1 CDS TM1040_1816 NC_008044.1 1909253 1910500 D PFAM: cytochrome P450: (3.7e-09); KEGG: jan:Jann_1726 cytochrome P450, ev=1e-130, 61% identity; cytochrome P450 1909253..1910500 Ruegeria sp. TM1040 4076962 YP_613812.1 CDS TM1040_1817 NC_008044.1 1910678 1911868 D KEGG: sil:SPO2988 hypothetical protein, ev=1e-176, 77% identity; hypothetical protein 1910678..1911868 Ruegeria sp. TM1040 4076963 YP_613813.1 CDS TM1040_1818 NC_008044.1 1912042 1913139 D KEGG: sil:SPO2990 hypothetical protein, ev=1e-145, 67% identity; hypothetical protein 1912042..1913139 Ruegeria sp. TM1040 4076964 YP_613814.1 CDS TM1040_1819 NC_008044.1 1913416 1913886 D 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 1913416..1913886 Ruegeria sp. TM1040 4076965 YP_613815.1 CDS TM1040_1820 NC_008044.1 1914075 1915658 D 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 1914075..1915658 Ruegeria sp. TM1040 4076966 YP_613816.1 CDS TM1040_1821 NC_008044.1 1915660 1916616 D 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 1915660..1916616 Ruegeria sp. TM1040 4076967 YP_613817.1 CDS TM1040_1822 NC_008044.1 1916613 1917428 D 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 1916613..1917428 Ruegeria sp. TM1040 4076968 YP_613818.1 CDS TM1040_1823 NC_008044.1 1917425 1919062 D 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 1917425..1919062 Ruegeria sp. TM1040 4076969 YP_613819.1 CDS TM1040_1824 NC_008044.1 1919245 1920081 D KEGG: sil:SPO3000 hypothetical protein, ev=1e-146, 87% identity; hypothetical protein 1919245..1920081 Ruegeria sp. TM1040 4076970 YP_613820.1 CDS TM1040_1825 NC_008044.1 1920125 1920685 D KEGG: sil:SPO3001 hypothetical protein, ev=2e-51, 52% identity; hypothetical protein 1920125..1920685 Ruegeria sp. TM1040 4076971 YP_613821.1 CDS TM1040_1826 NC_008044.1 1920735 1921682 R PFAM: Alpha/beta hydrolase fold-3: (2.2e-72); KEGG: sil:SPO3002 lipase, , ev=6e-99, 58% identity; alpha/beta hydrolase complement(1920735..1921682) Ruegeria sp. TM1040 4076972 YP_613822.1 CDS TM1040_1827 NC_008044.1 1921801 1923687 R activates fatty acids by binding to coenzyme A; AMP-binding protein complement(1921801..1923687) Ruegeria sp. TM1040 4076973 YP_613823.1 CDS TM1040_1828 NC_008044.1 1923997 1925799 R 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 complement(1923997..1925799) Ruegeria sp. TM1040 4076974 YP_613824.1 CDS TM1040_1829 NC_008044.1 1926225 1927085 D KEGG: hch:HCH_01550 hypothetical protein, ev=2e-50, 37% identity; hypothetical protein 1926225..1927085 Ruegeria sp. TM1040 4076975 YP_613825.1 CDS TM1040_1830 NC_008044.1 1927315 1927812 D hypothetical protein 1927315..1927812 Ruegeria sp. TM1040 4076976 YP_613826.1 CDS TM1040_1831 NC_008044.1 1927865 1928956 R PFAM: protein of unknown function DUF900, hydrolase-like: (8.7e-23); KEGG: rso:RSc0827 hypothetical protein, ev=6e-27, 32% identity; hypothetical protein complement(1927865..1928956) Ruegeria sp. TM1040 4076977 YP_613827.1 CDS TM1040_1832 NC_008044.1 1929196 1930872 D KEGG: bja:bll3105 hypothetical protein, ev=1e-128, 45% identity; hypothetical protein 1929196..1930872 Ruegeria sp. TM1040 4076978 YP_613828.1 CDS TM1040_1833 NC_008044.1 1931108 1931575 R hypothetical protein complement(1931108..1931575) Ruegeria sp. TM1040 4076979 YP_613829.1 CDS TM1040_1834 NC_008044.1 1931935 1934538 D KEGG: bja:bll7673 hypothetical protein, ev=1e-33, 34% identity; RTX toxin-like protein 1931935..1934538 Ruegeria sp. TM1040 4076980 YP_613830.1 CDS TM1040_1835 NC_008044.1 1935253 1935987 D 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 1935253..1935987 Ruegeria sp. TM1040 4076981 YP_613831.1 CDS TM1040_1836 NC_008044.1 1936107 1937426 D PFAM: glutamine synthetase, catalytic region: (2.3e-96); KEGG: rsp:RSP_0375 probable glutamine synthetase, ev=1e-153, 61% identity; L-glutamine synthetase 1936107..1937426 Ruegeria sp. TM1040 4077861 YP_613832.1 CDS TM1040_1837 NC_008044.1 1937482 1938162 D KEGG: sil:SPO1301 glutamine amidotransferase, class I, ev=1e-82, 63% identity; glutamine amidotransferase 1937482..1938162 Ruegeria sp. TM1040 4077862 YP_613833.1 CDS TM1040_1838 NC_008044.1 1938162 1939529 D PFAM: glutamine synthetase, catalytic region: (5.5e-94); KEGG: sil:SPO1300 glutamine synthetase family protein, ev=0.0, 88% identity; L-glutamine synthetase 1938162..1939529 Ruegeria sp. TM1040 4077863 YP_613834.1 CDS TM1040_1839 NC_008044.1 1939640 1940950 D PFAM: FAD dependent oxidoreductase: (3.7e-96); KEGG: rsp:RSP_0378 hypothetical protein, ev=1e-150, 62% identity; FAD dependent oxidoreductase 1939640..1940950 Ruegeria sp. TM1040 4077864 YP_613835.1 CDS TM1040_1840 NC_008044.1 1941291 1942529 D 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 1941291..1942529 Ruegeria sp. TM1040 4077865 YP_613836.1 CDS TM1040_1841 NC_008044.1 1942779 1943336 R 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 complement(1942779..1943336) Ruegeria sp. TM1040 4077866 YP_613837.1 CDS TM1040_1842 NC_008044.1 1943664 1944110 R KEGG: sil:SPO1293 phasin, PhaP, ev=2e-60, 81% identity; phasin, PhaP complement(1943664..1944110) Ruegeria sp. TM1040 4077867 YP_613838.1 CDS TM1040_1843 NC_008044.1 1944522 1944884 D hypothetical protein 1944522..1944884 Ruegeria sp. TM1040 4077868 YP_613839.1 CDS TM1040_1844 NC_008044.1 1944980 1945750 D KEGG: sil:SPO1128 hypothetical protein, ev=3e-84, 67% identity; hypothetical protein 1944980..1945750 Ruegeria sp. TM1040 4077869 YP_613840.1 CDS TM1040_1845 NC_008044.1 1945917 1946600 R 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 complement(1945917..1946600) Ruegeria sp. TM1040 4077870 YP_613841.1 CDS TM1040_1846 NC_008044.1 1946593 1947876 R 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 complement(1946593..1947876) Ruegeria sp. TM1040 4077871 YP_613842.1 CDS TM1040_1847 NC_008044.1 1947965 1948477 R KEGG: ret:RHE_CH03836 hypothetical protein, ev=4e-18, 39% identity; hypothetical protein complement(1947965..1948477) Ruegeria sp. TM1040 4077872 YP_613843.1 CDS TM1040_1848 NC_008044.1 1948766 1949188 R PFAM: thioesterase superfamily: (9.8e-06); KEGG: bja:blr1345 hypothetical protein, ev=2e-11, 31% identity; thioesterase superfamily protein complement(1948766..1949188) Ruegeria sp. TM1040 4077873 YP_613844.1 CDS TM1040_1849 NC_008044.1 1949215 1950009 R hypothetical protein complement(1949215..1950009) Ruegeria sp. TM1040 4077874 YP_613845.1 CDS TM1040_1850 NC_008044.1 1950214 1950744 R 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 complement(1950214..1950744) Ruegeria sp. TM1040 4077875 YP_613846.1 CDS TM1040_1851 NC_008044.1 1951398 1952174 R hypothetical protein complement(1951398..1952174) Ruegeria sp. TM1040 4077876 YP_613847.1 CDS TM1040_1852 NC_008044.1 1952289 1953644 R catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro); prolyl-tRNA synthetase complement(1952289..1953644) Ruegeria sp. TM1040 4077877 YP_613848.1 CDS TM1040_1853 NC_008044.1 1953837 1954169 R hypothetical protein complement(1953837..1954169) Ruegeria sp. TM1040 4077878 YP_613849.1 CDS TM1040_1854 NC_008044.1 1954506 1956245 D 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 1954506..1956245 Ruegeria sp. TM1040 4077879 YP_613850.1 CDS TM1040_1855 NC_008044.1 1956344 1957486 D PFAM: protein of unknown function UPF0118: (2.7e-50); KEGG: sil:SPO1119 membrane protein, ev=1e-136, 65% identity; hypothetical protein 1956344..1957486 Ruegeria sp. TM1040 4077880 YP_613851.1 CDS TM1040_1856 NC_008044.1 1957540 1958217 D PFAM: Chromosomal replication initiator, DnaA: (0.0011); KEGG: sil:SPO1118 hypothetical protein, ev=1e-77, 66% identity; chromosomal replication initiator DnaA 1957540..1958217 Ruegeria sp. TM1040 4077881 YP_613852.1 CDS TM1040_1857 NC_008044.1 1958393 1960039 D PFAM: Ppx/GppA phosphatase: (9.9e-28); KEGG: sil:SPO1117 phosphatase, Ppx/GppA family, ev=0.0, 73% identity; Ppx/GppA phosphatase 1958393..1960039 Ruegeria sp. TM1040 4077882 YP_613853.1 CDS TM1040_1858 NC_008044.1 1960107 1960547 R KEGG: rsp:RSP_6229 hypothetical protein, ev=1e-15, 39% identity; hypothetical protein complement(1960107..1960547) Ruegeria sp. TM1040 4077883 YP_613854.1 CDS TM1040_1859 NC_008044.1 1960571 1961605 R PFAM: Endonuclease/exonuclease/phosphatase: (8e-05); KEGG: sil:SPO1109 endonuclease/exonuclease/phosphatase family protein, ev=1e-106, 59% identity; endonuclease/exonuclease/phosphatase complement(1960571..1961605) Ruegeria sp. TM1040 4077884 YP_613855.1 CDS TM1040_1860 NC_008044.1 1961586 1962293 R PFAM: heat shock protein DnaJ-like: (9.2e-06); KEGG: sil:SPO1108 DnaJ-like protein DjlA, , ev=1e-94, 73% identity; molecular chaperone DnaJ complement(1961586..1962293) Ruegeria sp. TM1040 4077885 YP_613856.1 CDS TM1040_1861 NC_008044.1 1962303 1962836 R PFAM: GCN5-related N-acetyltransferase: (2e-17); KEGG: sil:SPO1107 phosphinothricin N-acetyltransferase, , ev=5e-37, 54% identity; N-acetyltransferase GCN5 complement(1962303..1962836) Ruegeria sp. TM1040 4077886 YP_613857.1 CDS TM1040_1862 NC_008044.1 1962836 1963474 R KEGG: sil:SPO1106 hypothetical protein, ev=3e-68, 66% identity; hypothetical protein complement(1962836..1963474) Ruegeria sp. TM1040 4077887 YP_613858.1 CDS TM1040_1863 NC_008044.1 1963667 1964164 D 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 1963667..1964164 Ruegeria sp. TM1040 4077888 YP_613859.1 CDS TM1040_1864 NC_008044.1 1964494 1964646 R KEGG: atc:AGR_L_680 hypothetical protein, ev=1e-08, 65% identity; hypothetical protein complement(1964494..1964646) Ruegeria sp. TM1040 4077889 YP_613860.1 CDS TM1040_1865 NC_008044.1 1964662 1966647 R MDM; functions in conversion of succinate to propionate; methylmalonyl-CoA mutase complement(1964662..1966647) Ruegeria sp. TM1040 4077890 YP_613861.1 CDS TM1040_1866 NC_008044.1 1966754 1967707 R KEGG: sil:SPO1104 hypothetical protein, ev=3e-87, 53% identity; hypothetical protein complement(1966754..1967707) Ruegeria sp. TM1040 4077891 YP_613862.1 CDS TM1040_1867 NC_008044.1 1967864 1968388 D KEGG: sil:SPO1103 hypothetical protein, ev=1e-34, 61% identity; hypothetical protein 1967864..1968388 Ruegeria sp. TM1040 4077892 YP_613863.1 CDS TM1040_1868 NC_008044.1 1968507 1969112 R KEGG: sil:SPO1102 lipoprotein, , ev=2e-30, 40% identity; hypothetical protein complement(1968507..1969112) Ruegeria sp. TM1040 4077893 YP_613864.1 CDS TM1040_1869 NC_008044.1 1969271 1971301 R 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 complement(1969271..1971301) Ruegeria sp. TM1040 4077894 YP_613865.1 CDS TM1040_1870 NC_008044.1 1971445 1971648 R KEGG: sil:SPO1100 lipoprotein, , ev=1e-11, 55% identity; lipoprotein complement(1971445..1971648) Ruegeria sp. TM1040 4077895 YP_613866.1 CDS TM1040_1871 NC_008044.1 1971641 1971898 R hypothetical protein complement(1971641..1971898) Ruegeria sp. TM1040 4077896 YP_613867.1 CDS TM1040_1872 NC_008044.1 1972185 1972532 R KEGG: sil:SPO1097 hypothetical protein, ev=3e-52, 82% identity; hypothetical protein complement(1972185..1972532) Ruegeria sp. TM1040 4077897 YP_613868.1 CDS TM1040_1873 NC_008044.1 1972602 1972745 R KEGG: sil:SPO1096 lipoprotein, , ev=8e-08, 59% identity; lipoprotein complement(1972602..1972745) Ruegeria sp. TM1040 4077898 YP_613869.1 CDS TM1040_1874 NC_008044.1 1972960 1973274 R KEGG: rsp:RSP_6040 hypothetical protein, ev=2e-15, 41% identity; hypothetical protein complement(1972960..1973274) Ruegeria sp. TM1040 4077899 YP_613870.1 CDS TM1040_1875 NC_008044.1 1973883 1974230 R KEGG: sil:SPO1095 hypothetical protein, ev=2e-23, 65% identity; hypothetical protein complement(1973883..1974230) Ruegeria sp. TM1040 4077372 YP_613871.1 CDS TM1040_1876 NC_008044.1 1974319 1974792 R hypothetical protein complement(1974319..1974792) Ruegeria sp. TM1040 4077373 YP_613872.1 CDS TM1040_1877 NC_008044.1 1974839 1976371 R PFAM: carboxyl transferase: (2.3e-287); KEGG: sil:SPO1094 propionyl-CoA carboxylase, beta subunit, ev=0.0, 91% identity; propionyl-CoA carboxylase complement(1974839..1976371) Ruegeria sp. TM1040 4077374 YP_613873.1 CDS TM1040_1878 NC_008044.1 1976745 1977938 D 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 1976745..1977938 Ruegeria sp. TM1040 4077375 YP_613874.1 CDS TM1040_1879 NC_008044.1 1978118 1979593 D 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 1978118..1979593 Ruegeria sp. TM1040 4077376 YP_613875.1 CDS TM1040_1880 NC_008044.1 1979648 1979887 R PFAM: protein of unknown function DUF465: (2.7e-05); KEGG: sil:SPO1089 hypothetical protein, ev=1e-32, 84% identity; hypothetical protein complement(1979648..1979887) Ruegeria sp. TM1040 4077377 YP_613876.1 CDS TM1040_1881 NC_008044.1 1980254 1980664 D hypothetical protein 1980254..1980664 Ruegeria sp. TM1040 4077378 YP_613877.1 CDS TM1040_1882 NC_008044.1 1980763 1982418 R catalyzes the oxidation of choline to betaine aldehyde and betain aldehyde to glycine betaine; choline dehydrogenase complement(1980763..1982418) Ruegeria sp. TM1040 4077379 YP_613878.1 CDS TM1040_1883 NC_008044.1 1982575 1984032 R catalyzes the formation of betaine from betaine aldehyde; betaine aldehyde dehydrogenase complement(1982575..1984032) Ruegeria sp. TM1040 4077380 YP_613879.1 CDS TM1040_1884 NC_008044.1 1984236 1985444 R KEGG: sil:SPO1087 membrane protein, , ev=1e-165, 70% identity; hypothetical protein complement(1984236..1985444) Ruegeria sp. TM1040 4077381 YP_613880.1 CDS TM1040_1885 NC_008044.1 1985642 1986232 D PFAM: regulatory protein, TetR: (1e-13); KEGG: sil:SPO1086 transcriptional regulator, TetR family, ev=4e-54, 54% identity; TetR family transcriptional regulator 1985642..1986232 Ruegeria sp. TM1040 4077382 YP_613881.1 CDS TM1040_1886 NC_008044.1 1986308 1987381 R KEGG: sil:SPO1081 hypothetical protein, ev=2e-17, 37% identity; integral membrane protein-like protein complement(1986308..1987381) Ruegeria sp. TM1040 4077383 YP_613882.1 CDS TM1040_1887 NC_008044.1 1987499 1988431 R PFAM: protein of unknown function DUF6, transmembrane: (0.00035); KEGG: sil:SPO1080 membrane protein, , ev=1e-106, 64% identity; hypothetical protein complement(1987499..1988431) Ruegeria sp. TM1040 4077384 YP_613883.1 CDS TM1040_1888 NC_008044.1 1988725 1990362 D 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 1988725..1990362 Ruegeria sp. TM1040 4077385 YP_613884.1 CDS TM1040_1889 NC_008044.1 1990311 1991252 R PFAM: Pirin-like: (3e-57); KEGG: sil:SPO2601 pirin domain protein, ev=1e-126, 69% identity; pirin complement(1990311..1991252) Ruegeria sp. TM1040 4077386 YP_613885.1 CDS TM1040_1890 NC_008044.1 1991345 1991974 R 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 complement(1991345..1991974) Ruegeria sp. TM1040 4077387 YP_613886.1 CDS TM1040_1891 NC_008044.1 1992084 1993004 D 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 1992084..1993004 Ruegeria sp. TM1040 4077388 YP_613887.1 CDS TM1040_1892 NC_008044.1 1993025 1993882 D KEGG: rso:RS03125 probable transmembrane protein, ev=6e-13, 25% identity; hypothetical protein 1993025..1993882 Ruegeria sp. TM1040 4077389 YP_613888.2 CDS TM1040_1893 NC_008044.1 1994121 1994861 R PFAM: protein of unknown function DUF28: (4.3e-147); KEGG: sil:SPO1072 conserved hypothetical protein TIGR01033, ev=1e-123, 89% identity; hypothetical protein complement(1994121..1994861) Ruegeria sp. TM1040 4077390 YP_613889.1 CDS TM1040_1894 NC_008044.1 1994821 1995183 R hypothetical protein complement(1994821..1995183) Ruegeria sp. TM1040 4077391 YP_613890.1 CDS TM1040_1895 NC_008044.1 1995323 1997098 D 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 1995323..1997098 Ruegeria sp. TM1040 4077392 YP_613891.1 CDS TM1040_1896 NC_008044.1 1997303 1998976 D proposed role in polysaccahride synthesis; FAD-binding dehydrogenase 1997303..1998976 Ruegeria sp. TM1040 4077393 YP_613892.1 CDS TM1040_1897 NC_008044.1 1999008 1999481 D TIGRFAM: conserved hypothetical protein: (1.7e-48); KEGG: jan:Jann_2797 hypothetical protein, ev=3e-59, 73% identity; hypothetical protein 1999008..1999481 Ruegeria sp. TM1040 4077394 YP_613893.1 CDS TM1040_1898 NC_008044.1 1999575 2000039 R 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 complement(1999575..2000039) Ruegeria sp. TM1040 4077395 YP_613894.1 CDS TM1040_1899 NC_008044.1 2000157 2001935 R PFAM: Citrate transporter: (7.1e-07) TrkA-C: (1.9e-11); KEGG: sil:SPO2952 TrkA domain protein, ev=0.0, 84% identity; hypothetical protein complement(2000157..2001935) Ruegeria sp. TM1040 4077396 YP_613895.1 CDS TM1040_1900 NC_008044.1 2002217 2003110 D PFAM: beta-lactamase: (1.6e-37); KEGG: jan:Jann_2001 beta-lactamase, ev=2e-84, 56% identity; beta-lactamase 2002217..2003110 Ruegeria sp. TM1040 4077397 YP_613896.1 CDS TM1040_1901 NC_008044.1 2003515 2004327 R 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 complement(2003515..2004327) Ruegeria sp. TM1040 4077398 YP_613897.1 CDS TM1040_1902 NC_008044.1 2004704 2005543 D KEGG: ana:alr5242 hypothetical protein, ev=1e-16, 30% identity; hypothetical protein 2004704..2005543 Ruegeria sp. TM1040 4077399 YP_613898.1 CDS TM1040_1903 NC_008044.1 2005708 2006295 R 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 complement(2005708..2006295) Ruegeria sp. TM1040 4077400 YP_613899.1 CDS TM1040_1904 NC_008044.1 2006318 2007706 R 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 complement(2006318..2007706) Ruegeria sp. TM1040 4077401 YP_613900.1 CDS TM1040_1905 NC_008044.1 2007845 2009134 D Catalyzes the deamination of guanine; guanine deaminase 2007845..2009134 Ruegeria sp. TM1040 4077402 YP_613901.1 CDS TM1040_1906 NC_008044.1 2009233 2010573 R catalyzes the transformation of hydroxyatrazine to N-isopropylammelide and ethylamine in the atrazine degradation pathway.; hydroxydechloroatrazine ethylaminohydrolase complement(2009233..2010573) Ruegeria sp. TM1040 4077403 YP_613902.1 CDS TM1040_1907 NC_008044.1 2010784 2011578 R 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 complement(2010784..2011578) Ruegeria sp. TM1040 4077404 YP_613903.1 CDS TM1040_1908 NC_008044.1 2011553 2011843 R hypothetical protein complement(2011553..2011843) Ruegeria sp. TM1040 4077405 YP_613904.1 CDS TM1040_1909 NC_008044.1 2011866 2012237 R PFAM: helix-turn-helix motif: (4e-13); KEGG: sil:SPO2959 DNA-binding protein, , ev=4e-56, 86% identity; XRE family transcriptional regulator complement(2011866..2012237) Ruegeria sp. TM1040 4077406 YP_613905.1 CDS TM1040_1910 NC_008044.1 2012602 2013576 D 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 2012602..2013576 Ruegeria sp. TM1040 4077407 YP_613906.1 CDS TM1040_1911 NC_008044.1 2013545 2014462 R 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 complement(2013545..2014462) Ruegeria sp. TM1040 4077408 YP_613907.1 CDS TM1040_1912 NC_008044.1 2014585 2014797 D PFAM: protein of unknown function DUF1127: (2.6e-07); KEGG: sil:SPO2962 hypothetical protein, ev=6e-09, 51% identity; hypothetical protein 2014585..2014797 Ruegeria sp. TM1040 4077409 YP_613908.1 CDS TM1040_1913 NC_008044.1 2015026 2015805 D PFAM: protein of unknown function UPF0005: (9.6e-13); KEGG: sil:SPO2963 membrane protein, , ev=1e-116, 82% identity; hypothetical protein 2015026..2015805 Ruegeria sp. TM1040 4077410 YP_613909.1 CDS TM1040_1914 NC_008044.1 2015909 2016448 D PFAM: GCN5-related N-acetyltransferase: (6.5e-09); N-acetyltransferase GCN5 2015909..2016448 Ruegeria sp. TM1040 4076865 YP_613910.1 CDS rpmG NC_008044.1 2016984 2017151 R 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 complement(2016984..2017151) Ruegeria sp. TM1040 4076866 YP_613911.1 CDS TM1040_1916 NC_008044.1 2017873 2018532 R 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 complement(2017873..2018532) Ruegeria sp. TM1040 4076867 YP_613912.1 CDS TM1040_1917 NC_008044.1 2018542 2019306 R KEGG: sil:SPO2968 hypothetical protein, ev=6e-74, 56% identity; hypothetical protein complement(2018542..2019306) Ruegeria sp. TM1040 4076868 YP_613913.1 CDS gatA NC_008044.1 2019347 2020834 R 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 complement(2019347..2020834) Ruegeria sp. TM1040 4076869 YP_613914.1 CDS gatC NC_008044.1 2020838 2021125 R 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 complement(2020838..2021125) Ruegeria sp. TM1040 4076870 YP_613915.1 CDS TM1040_1920 NC_008044.1 2021537 2022229 D PFAM: beta-lactamase-like: (3.5e-11); KEGG: sil:SPO2976 metallo-beta-lactamase family protein, ev=1e-104, 76% identity; beta-lactamase-like protein 2021537..2022229 Ruegeria sp. TM1040 4076871 YP_613916.1 CDS TM1040_1921 NC_008044.1 2022229 2023398 D PFAM: peptidase M24: (3.8e-06); KEGG: ret:RHE_PF00180 probable peptidase protein, ev=1e-116, 52% identity; peptidase M24 2022229..2023398 Ruegeria sp. TM1040 4076872 YP_613917.1 CDS TM1040_1922 NC_008044.1 2023619 2024221 R PFAM: methyladenine glycosylase: (1.9e-78); KEGG: sil:SPO1900 DNA-3-methyladenine glycosylase I, ev=3e-74, 69% identity; DNA-3-methyladenine glycosylase I complement(2023619..2024221) Ruegeria sp. TM1040 4076873 YP_613918.1 CDS TM1040_1923 NC_008044.1 2024218 2024511 R PFAM: YCII-related: (6.8e-09); KEGG: hch:HCH_03235 hypothetical protein, ev=4e-16, 43% identity; hypothetical protein complement(2024218..2024511) Ruegeria sp. TM1040 4076874 YP_613919.1 CDS TM1040_1924 NC_008044.1 2024543 2025112 R PFAM: regulatory protein, TetR: (1.3e-17); KEGG: sil:SPO1902 transcription regulator, TetR family, ev=6e-52, 58% identity; TetR family transcriptional regulator complement(2024543..2025112) Ruegeria sp. TM1040 4076875 YP_613920.1 CDS TM1040_1925 NC_008044.1 2025310 2025552 R hypothetical protein complement(2025310..2025552) Ruegeria sp. TM1040 4076876 YP_613921.1 CDS TM1040_1926 NC_008044.1 2025549 2025983 R 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 complement(2025549..2025983) Ruegeria sp. TM1040 4076877 YP_613922.1 CDS TM1040_1927 NC_008044.1 2026097 2027365 D 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 2026097..2027365 Ruegeria sp. TM1040 4076878 YP_613923.1 CDS TM1040_1928 NC_008044.1 2027532 2028440 D KEGG: sil:SPO2985 hypothetical protein, ev=5e-93, 59% identity; hypothetical protein 2027532..2028440 Ruegeria sp. TM1040 4076879 YP_613924.1 CDS TM1040_1929 NC_008044.1 2028463 2029653 D PFAM: toxic anion resistance: (4.7e-146); KEGG: sil:SPO2986 tellurite resistance protein, ev=1e-177, 82% identity; toxic anion resistance 2028463..2029653 Ruegeria sp. TM1040 4076880 YP_613925.1 CDS TM1040_1930 NC_008044.1 2029664 2030617 D KEGG: sil:SPO2987 lipoprotein, , ev=2e-78, 53% identity; lipoprotein 2029664..2030617 Ruegeria sp. TM1040 4076881 YP_613926.1 CDS TM1040_1931 NC_008044.1 2030640 2031323 R PFAM: glutathione S-transferase-like: (9.1e-06); KEGG: eba:ebA3377 glutathione-S-transferase-related protein, ev=2e-62, 58% identity; glutathione S-transferase complement(2030640..2031323) Ruegeria sp. TM1040 4076882 YP_613927.1 CDS TM1040_1932 NC_008044.1 2031373 2033085 R 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 complement(2031373..2033085) Ruegeria sp. TM1040 4076883 YP_613928.1 CDS TM1040_1933 NC_008044.1 2033657 2035897 R 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 complement(2033657..2035897) Ruegeria sp. TM1040 4076884 YP_613929.1 CDS TM1040_1934 NC_008044.1 2036243 2037481 R 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 complement(2036243..2037481) Ruegeria sp. TM1040 4076885 YP_613930.1 CDS TM1040_1935 NC_008044.1 2037616 2039064 R PFAM: cation transporter: (3.3e-39); KEGG: sil:SPO1353 trk system potassium uptake protein TrkH, ev=0.0, 76% identity; cation transporter complement(2037616..2039064) Ruegeria sp. TM1040 4076886 YP_613931.1 CDS TM1040_1936 NC_008044.1 2039112 2039879 R KEGG: lma:LmjF35.0290 hypothetical protein, conserved, ev=2e-18, 37% identity; hypothetical protein complement(2039112..2039879) Ruegeria sp. TM1040 4076887 YP_613932.1 CDS TM1040_1937 NC_008044.1 2040105 2041208 R 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 complement(2040105..2041208) Ruegeria sp. TM1040 4076888 YP_613933.1 CDS TM1040_1938 NC_008044.1 2041410 2042597 R 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 complement(2041410..2042597) Ruegeria sp. TM1040 4076889 YP_613934.1 CDS TM1040_1939 NC_008044.1 2043063 2044004 D hypothetical protein 2043063..2044004 Ruegeria sp. TM1040 4076890 YP_613935.1 CDS TM1040_1940 NC_008044.1 2044201 2044836 R 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 complement(2044201..2044836) Ruegeria sp. TM1040 4076891 YP_613936.1 CDS TM1040_1941 NC_008044.1 2044881 2045789 R PFAM: protein of unknown function DUF6, transmembrane: (1.5e-09); KEGG: sil:SPO1337 membrane protein, , ev=1e-140, 83% identity; hypothetical protein complement(2044881..2045789) Ruegeria sp. TM1040 4076892 YP_613937.1 CDS TM1040_1942 NC_008044.1 2045848 2047008 R 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 complement(2045848..2047008) Ruegeria sp. TM1040 4076893 YP_613938.1 CDS TM1040_1943 NC_008044.1 2047082 2047735 R PFAM: YhhN-like: (7.7e-29); KEGG: sil:SPO1340 membrane protein, , ev=1e-42, 51% identity; YhhN-like protein complement(2047082..2047735) Ruegeria sp. TM1040 4076894 YP_613939.1 CDS TM1040_1944 NC_008044.1 2047873 2048283 D KEGG: sil:SPO1342 hypothetical protein, ev=9e-31, 50% identity; hypothetical protein 2047873..2048283 Ruegeria sp. TM1040 4076895 YP_613940.1 CDS xseA NC_008044.1 2048352 2049860 R bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides; exodeoxyribonuclease VII large subunit complement(2048352..2049860) Ruegeria sp. TM1040 4076896 YP_613941.1 CDS TM1040_1946 NC_008044.1 2050013 2051275 D catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis; phosphoribosylamine--glycine ligase 2050013..2051275 Ruegeria sp. TM1040 4076897 YP_613942.1 CDS TM1040_1948 NC_008044.1 2051746 2052543 R KEGG: jan:Jann_3167 integrins alpha chain, ev=6e-54, 50% identity; integrins alpha chain complement(2051746..2052543) Ruegeria sp. TM1040 4076898 YP_613943.1 CDS TM1040_1949 NC_008044.1 2052543 2052935 R PFAM: ferredoxin: (6e-14); KEGG: sil:SPO1348 iron-sulfur cluster-binding protein, ev=1e-54, 92% identity; ferredoxin complement(2052543..2052935) Ruegeria sp. TM1040 4076899 YP_613944.1 CDS TM1040_1950 NC_008044.1 2053273 2053719 D PFAM: Peptidoglycan-binding domain 1: (0.00064); KEGG: sil:SPO1349 lipoprotein, , ev=5e-37, 51% identity; peptidoglycan binding domain-containing protein 2053273..2053719 Ruegeria sp. TM1040 4076900 YP_613945.1 CDS TM1040_1951 NC_008044.1 2053848 2054516 D 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 2053848..2054516 Ruegeria sp. TM1040 4076901 YP_613946.1 CDS TM1040_1952 NC_008044.1 2055091 2056218 D PFAM: Tetratricopeptide TPR_2: (0.0012); KEGG: sme:SMc03099 adenylate cyclase protein, ev=4e-45, 30% identity; hypothetical protein 2055091..2056218 Ruegeria sp. TM1040 4076902 YP_613947.1 CDS TM1040_1953 NC_008044.1 2056616 2058115 R 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 complement(2056616..2058115) Ruegeria sp. TM1040 4076903 YP_613948.1 CDS TM1040_1954 NC_008044.1 2058558 2059079 D hypothetical protein 2058558..2059079 Ruegeria sp. TM1040 4077138 YP_613949.1 CDS TM1040_1955 NC_008044.1 2059189 2060073 R 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 complement(2059189..2060073) Ruegeria sp. TM1040 4077139 YP_613950.1 CDS TM1040_1956 NC_008044.1 2060073 2061236 R 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 complement(2060073..2061236) Ruegeria sp. TM1040 4077140 YP_613951.1 CDS TM1040_1957 NC_008044.1 2061345 2062700 R 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 complement(2061345..2062700) Ruegeria sp. TM1040 4077141 YP_613952.1 CDS TM1040_1958 NC_008044.1 2062849 2063478 R hypothetical protein complement(2062849..2063478) Ruegeria sp. TM1040 4077142 YP_613953.1 CDS TM1040_1959 NC_008044.1 2063653 2064093 D PFAM: transmembrane pair: (1.2e-30); KEGG: atc:AGR_C_3030 hypothetical protein PA2880, ev=6e-52, 66% identity; transmembrane pair 2063653..2064093 Ruegeria sp. TM1040 4077143 YP_613954.1 CDS TM1040_1960 NC_008044.1 2064158 2064946 R Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway; ribose-5-phosphate isomerase A complement(2064158..2064946) Ruegeria sp. TM1040 4077144 YP_613955.1 CDS TM1040_1961 NC_008044.1 2065279 2065986 D PFAM: glutathione S-transferase-like: (1.5e-12); KEGG: sil:SPO1324 glutathione S-transferase family protein, ev=1e-67, 55% identity; glutathione S-transferase 2065279..2065986 Ruegeria sp. TM1040 4077145 YP_613956.1 CDS TM1040_1962 NC_008044.1 2065987 2067360 D 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 2065987..2067360 Ruegeria sp. TM1040 4077146 YP_613957.1 CDS TM1040_1963 NC_008044.1 2067414 2067986 R PFAM: regulatory protein, TetR: (2.4e-13); KEGG: sil:SPO3545 transcriptional regulator, TetR family, ev=2e-29, 40% identity; TetR family transcriptional regulator complement(2067414..2067986) Ruegeria sp. TM1040 4077147 YP_613958.1 CDS TM1040_1964 NC_008044.1 2068068 2068943 D KEGG: sil:SPO3544 hypothetical protein, ev=6e-61, 42% identity; hypothetical protein 2068068..2068943 Ruegeria sp. TM1040 4077148 YP_613959.1 CDS TM1040_1965 NC_008044.1 2069025 2069999 D PFAM: protein of unknown function DUF6, transmembrane: (6.5e-10); KEGG: sil:SPO1322 membrane protein, , ev=3e-95, 62% identity; hypothetical protein 2069025..2069999 Ruegeria sp. TM1040 4077149 YP_613960.1 CDS TM1040_1966 NC_008044.1 2069965 2070636 R 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 complement(2069965..2070636) Ruegeria sp. TM1040 4077150 YP_613961.1 CDS TM1040_1967 NC_008044.1 2070774 2072972 D KEGG: sil:SPO1320 lipoprotein, , ev=1e-125, 42% identity; CheA signal transduction histidine kinase 2070774..2072972 Ruegeria sp. TM1040 4077151 YP_613962.1 CDS TM1040_1968 NC_008044.1 2073325 2073570 R KEGG: rsp:RSP_6113 hypothetical protein, ev=3e-19, 60% identity; hypothetical protein complement(2073325..2073570) Ruegeria sp. TM1040 4077152 YP_613963.1 CDS TM1040_1969 NC_008044.1 2073570 2074883 R catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis; adenylosuccinate synthetase complement(2073570..2074883) Ruegeria sp. TM1040 4077153 YP_613964.1 CDS TM1040_1970 NC_008044.1 2075153 2075515 R KEGG: sil:SPO1316 hypothetical protein, ev=6e-35, 65% identity; hypothetical protein complement(2075153..2075515) Ruegeria sp. TM1040 4077154 YP_613965.1 CDS TM1040_1971 NC_008044.1 2075512 2076216 R KEGG: sil:SPO1315 nitrile hydratase beta subunit, ev=1e-77, 64% identity; nitrile hydratase complement(2075512..2076216) Ruegeria sp. TM1040 4077155 YP_613966.1 CDS TM1040_1972 NC_008044.1 2076213 2076839 R 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 complement(2076213..2076839) Ruegeria sp. TM1040 4077156 YP_613967.1 CDS pyrG NC_008044.1 2077611 2079254 D 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 2077611..2079254 Ruegeria sp. TM1040 4077157 YP_613968.1 CDS TM1040_1974 NC_008044.1 2079396 2079827 D hypothetical protein 2079396..2079827 Ruegeria sp. TM1040 4077158 YP_613969.1 CDS TM1040_1975 NC_008044.1 2079901 2080233 D KEGG: sil:SPO3023 hypothetical protein, ev=1e-37, 70% identity; hypothetical protein 2079901..2080233 Ruegeria sp. TM1040 4077159 YP_613970.1 CDS TM1040_1976 NC_008044.1 2080346 2081248 D catalyzes the formation of glycerone phosphate and D-glyceraldehyde 3-phosphate from D-fructose 1,6-bisphosphate in glycolysis; fructose-1,6-bisphosphate aldolase 2080346..2081248 Ruegeria sp. TM1040 4077160 YP_613971.1 CDS TM1040_1977 NC_008044.1 2081321 2082778 R 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 complement(2081321..2082778) Ruegeria sp. TM1040 4077161 YP_613972.1 CDS TM1040_1978 NC_008044.1 2082931 2083242 D hypothetical protein 2082931..2083242 Ruegeria sp. TM1040 4077162 YP_613973.1 CDS TM1040_1979 NC_008044.1 2083197 2083919 R PFAM: fatty acid hydroxylase: (3.1e-07); KEGG: bce:BC1607 fatty acid hydroxylase FAH1P, ev=8e-20, 30% identity; fatty acid hydroxylase complement(2083197..2083919) Ruegeria sp. TM1040 4077163 YP_613974.1 CDS TM1040_1980 NC_008044.1 2083971 2084768 R Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase complement(2083971..2084768) Ruegeria sp. TM1040 4077164 YP_613975.1 CDS TM1040_1981 NC_008044.1 2084941 2086053 D catalyzes the formation of histidinol phosphate and 2-oxoglutarate from glutamate and imidazole acetol-phosphate; histidinol-phosphate aminotransferase 2084941..2086053 Ruegeria sp. TM1040 4077165 YP_613976.1 CDS TM1040_1982 NC_008044.1 2086159 2086395 D hypothetical protein 2086159..2086395 Ruegeria sp. TM1040 4077166 YP_613977.1 CDS TM1040_1983 NC_008044.1 2086629 2087843 R PFAM: aminotransferase, class V: (9.1e-10); KEGG: sil:SPO3029 serine--glyoxylate transaminase, , ev=1e-169, 71% identity; class V aminotransferase complement(2086629..2087843) Ruegeria sp. TM1040 4077167 YP_613978.1 CDS TM1040_1984 NC_008044.1 2088076 2089935 D 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 2088076..2089935 Ruegeria sp. TM1040 4077168 YP_613979.1 CDS TM1040_1985 NC_008044.1 2090043 2090789 D 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) 2090043..2090789 Ruegeria sp. TM1040 4077169 YP_613980.1 CDS TM1040_1986 NC_008044.1 2090902 2091483 D hypothetical protein 2090902..2091483 Ruegeria sp. TM1040 4077170 YP_613981.1 CDS TM1040_1987 NC_008044.1 2091657 2092220 R Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA; elongation factor P complement(2091657..2092220) Ruegeria sp. TM1040 4077171 YP_613982.1 CDS TM1040_1988 NC_008044.1 2092447 2092764 D KEGG: sil:SPO1243 hypothetical protein, ev=1e-51, 96% identity; hypothetical protein 2092447..2092764 Ruegeria sp. TM1040 4077172 YP_613983.1 CDS TM1040_1989 NC_008044.1 2092984 2094432 D 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 2092984..2094432 Ruegeria sp. TM1040 4077173 YP_613984.1 CDS TM1040_1990 NC_008044.1 2094770 2096077 R KEGG: sil:SPO1241 hypothetical protein, ev=2e-28, 32% identity; hypothetical protein complement(2094770..2096077) Ruegeria sp. TM1040 4077174 YP_613985.1 CDS TM1040_1991 NC_008044.1 2096154 2097575 R 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 complement(2096154..2097575) Ruegeria sp. TM1040 4077175 YP_613986.1 CDS TM1040_1992 NC_008044.1 2097720 2098373 R 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 complement(2097720..2098373) Ruegeria sp. TM1040 4077176 YP_613987.1 CDS TM1040_1993 NC_008044.1 2098899 2099207 R KEGG: rsp:RSP_0166 DnaK suppressor protein, ev=8e-06, 45% identity; TraR/DksA family transcriptional regulator complement(2098899..2099207) Ruegeria sp. TM1040 4077450 YP_613988.1 CDS TM1040_1994 NC_008044.1 2099466 2099696 D PFAM: Entericidin EcnAB: (1e-08); entericidin EcnAB 2099466..2099696 Ruegeria sp. TM1040 4077451 YP_613989.1 CDS TM1040_1995 NC_008044.1 2099764 2100681 R 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 complement(2099764..2100681) Ruegeria sp. TM1040 4077452 YP_613990.1 CDS TM1040_1996 NC_008044.1 2100825 2101094 R hypothetical protein complement(2100825..2101094) Ruegeria sp. TM1040 4077453 YP_613991.1 CDS TM1040_1997 NC_008044.1 2101188 2102966 D 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 2101188..2102966 Ruegeria sp. TM1040 4077454 YP_613992.1 CDS TM1040_1998 NC_008044.1 2102968 2103390 D PFAM: response regulator receiver: (4.5e-19); KEGG: cps:CPS_3951 response regulator, ev=1e-26, 45% identity; response regulator receiver protein 2102968..2103390 Ruegeria sp. TM1040 4077455 YP_613993.1 CDS TM1040_1999 NC_008044.1 2103528 2103923 D hypothetical protein 2103528..2103923 Ruegeria sp. TM1040 4077456 YP_613994.1 CDS TM1040_2000 NC_008044.1 2103846 2105762 R 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 complement(2103846..2105762) Ruegeria sp. TM1040 4077457 YP_613995.1 CDS TM1040_2001 NC_008044.1 2106141 2106440 D KEGG: jan:Jann_2370 hypothetical protein, ev=3e-11, 41% identity; hypothetical protein 2106141..2106440 Ruegeria sp. TM1040 4077458 YP_613996.1 CDS TM1040_2002 NC_008044.1 2106428 2108020 D 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 2106428..2108020 Ruegeria sp. TM1040 4077459 YP_613997.1 CDS TM1040_2003 NC_008044.1 2108344 2109321 D 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 2108344..2109321 Ruegeria sp. TM1040 4077460 YP_613998.1 CDS TM1040_2004 NC_008044.1 2109545 2110426 D 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 2109545..2110426 Ruegeria sp. TM1040 4077461 YP_613999.1 CDS TM1040_2005 NC_008044.1 2110423 2111313 R 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 complement(2110423..2111313) Ruegeria sp. TM1040 4077462 YP_614000.1 CDS TM1040_2006 NC_008044.1 2111425 2112573 D 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 2111425..2112573 Ruegeria sp. TM1040 4077463 YP_614001.1 CDS TM1040_2007 NC_008044.1 2112570 2113298 D PFAM: class II aldolase/adducin-like: (4.5e-34); KEGG: aci:ACIAD3485 hypothetical protein, ev=2e-56, 46% identity; hypothetical protein 2112570..2113298 Ruegeria sp. TM1040 4077464 YP_614002.1 CDS TM1040_2008 NC_008044.1 2113464 2113961 R PFAM: helix-turn-helix, HxlR type: (1.2e-13); KEGG: eli:ELI_10910 hypothetical protein, ev=1e-19, 37% identity; HxlR family transcriptional regulator complement(2113464..2113961) Ruegeria sp. TM1040 4077465 YP_614003.1 CDS TM1040_2009 NC_008044.1 2114021 2114866 D KEGG: ccr:CC0038 dienelactone hydrolase family protein, ev=8e-49, 42% identity; dienelactone hydrolase family protein 2114021..2114866 Ruegeria sp. TM1040 4077466 YP_614004.1 CDS TM1040_2010 NC_008044.1 2114985 2116049 R 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 complement(2114985..2116049) Ruegeria sp. TM1040 4077467 YP_614005.1 CDS TM1040_2011 NC_008044.1 2116316 2116756 D KEGG: mag:amb1751 site-specific DNA methylase, ev=5e-07, 46% identity; hypothetical protein 2116316..2116756 Ruegeria sp. TM1040 4077468 YP_614006.1 CDS TM1040_2012 NC_008044.1 2116783 2117112 D hypothetical protein 2116783..2117112 Ruegeria sp. TM1040 4077469 YP_614007.1 CDS TM1040_2013 NC_008044.1 2117215 2117454 R hypothetical protein complement(2117215..2117454) Ruegeria sp. TM1040 4077470 YP_614008.1 CDS TM1040_2014 NC_008044.1 2117561 2118064 D MraZ; UPF0040; crystal structure shows similarity to AbrB; cell division protein MraZ 2117561..2118064 Ruegeria sp. TM1040 4077471 YP_614009.1 CDS mraW NC_008044.1 2118068 2119057 D PFAM: methyltransferase: (5.6e-97); KEGG: sil:SPO1179 S-adenosyl-methyltransferase MraW, ev=1e-137, 76% identity; S-adenosyl-methyltransferase MraW 2118068..2119057 Ruegeria sp. TM1040 4077472 YP_614010.1 CDS TM1040_2016 NC_008044.1 2119057 2119404 D KEGG: sil:SPO1180 hypothetical protein, ev=5e-34, 63% identity; hypothetical protein 2119057..2119404 Ruegeria sp. TM1040 4077473 YP_614011.1 CDS TM1040_2017 NC_008044.1 2119401 2121182 D 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 2119401..2121182 Ruegeria sp. TM1040 4077474 YP_614012.1 CDS murE NC_008044.1 2121197 2122681 D 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 2121197..2122681 Ruegeria sp. TM1040 4077475 YP_614013.1 CDS TM1040_2019 NC_008044.1 2122678 2124069 D 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 2122678..2124069 Ruegeria sp. TM1040 4077476 YP_614014.1 CDS mraY NC_008044.1 2124111 2125193 D First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan; phospho-N-acetylmuramoyl-pentapeptide- transferase 2124111..2125193 Ruegeria sp. TM1040 4077477 YP_614015.1 CDS TM1040_2021 NC_008044.1 2125506 2126579 R hypothetical protein complement(2125506..2126579) Ruegeria sp. TM1040 4077478 YP_614016.1 CDS TM1040_2022 NC_008044.1 2126599 2127684 R KEGG: rsp:RSP_2093 Mrp (multidrug resistance-associated proteins) family protein, ev=1e-138, 69% identity; Mrp (multidrug resistance-associated proteins) family protein complement(2126599..2127684) Ruegeria sp. TM1040 4077479 YP_614017.1 CDS TM1040_2023 NC_008044.1 2128003 2128224 D PFAM: protein of unknown function DUF1127: (1.1e-06); KEGG: sil:SPO1177 hypothetical protein, ev=3e-12, 69% identity; hypothetical protein 2128003..2128224 Ruegeria sp. TM1040 4077480 YP_614018.1 CDS TM1040_2024 NC_008044.1 2128764 2131208 R PFAM: UvrD/REP helicase: (7.9e-183); KEGG: sil:SPO1174 DNA helicase II, , ev=0.0, 78% identity; ATP-dependent DNA helicase Rep complement(2128764..2131208) Ruegeria sp. TM1040 4077481 YP_614019.1 CDS TM1040_2025 NC_008044.1 2131376 2131885 D PFAM: BLUF: (7.6e-22); KEGG: cef:CE2367 hypothetical protein, ev=1e-13, 38% identity; BLUF domain-containing protein 2131376..2131885 Ruegeria sp. TM1040 4077482 YP_614020.1 CDS TM1040_2026 NC_008044.1 2132061 2133230 D 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) 2132061..2133230 Ruegeria sp. TM1040 4077483 YP_614021.1 CDS TM1040_2027 NC_008044.1 2133373 2133807 R PFAM: BLUF: (2.8e-13); KEGG: jan:Jann_2780 BLUF, ev=2e-17, 35% identity; BLUF domain-containing protein complement(2133373..2133807) Ruegeria sp. TM1040 4077484 YP_614022.1 CDS TM1040_2028 NC_008044.1 2134246 2137686 D biotin-containing enzyme that catalyzes a two step carboxylation of pyruvate to oxaloacetate; pyruvate carboxylase 2134246..2137686 Ruegeria sp. TM1040 4077485 YP_614023.1 CDS TM1040_2029 NC_008044.1 2137758 2138666 D hypothetical protein 2137758..2138666 Ruegeria sp. TM1040 4077486 YP_614024.1 CDS TM1040_2030 NC_008044.1 2138667 2139152 R KEGG: sil:SPO3765 hypothetical protein, ev=1e-50, 62% identity; hypothetical protein complement(2138667..2139152) Ruegeria sp. TM1040 4077487 YP_614025.1 CDS TM1040_2031 NC_008044.1 2140200 2141552 D PFAM: aminotransferase class-III: (6.9e-87); KEGG: sil:SPO1166 aminotransferase, class III family, ev=0.0, 82% identity; aminotransferase 2140200..2141552 Ruegeria sp. TM1040 4077488 YP_614026.1 CDS TM1040_2032 NC_008044.1 2141699 2141938 R PFAM: regulatory proteins, AsnC/Lrp: (8.2e-12); KEGG: sil:SPO1164 hypothetical protein, ev=7e-36, 91% identity; AsnC family transcriptional regulator complement(2141699..2141938) Ruegeria sp. TM1040 4077959 YP_614027.1 CDS hisB NC_008044.1 2142137 2142724 D 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 2142137..2142724 Ruegeria sp. TM1040 4077960 YP_614028.1 CDS hisH NC_008044.1 2142831 2143469 D 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 2142831..2143469 Ruegeria sp. TM1040 4077961 YP_614029.1 CDS TM1040_2035 NC_008044.1 2143723 2144454 R PFAM: helix-turn-helix, AraC type: (0.00031); KEGG: sil:SPO1161 transcriptional regulator, AraC family, ev=4e-70, 61% identity; AraC family transcriptional regulator complement(2143723..2144454) Ruegeria sp. TM1040 4077962 YP_614030.1 CDS TM1040_2036 NC_008044.1 2144634 2145170 D 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 2144634..2145170 Ruegeria sp. TM1040 4077963 YP_614031.1 CDS TM1040_2037 NC_008044.1 2145288 2145539 D hypothetical protein 2145288..2145539 Ruegeria sp. TM1040 4077964 YP_614032.1 CDS TM1040_2038 NC_008044.1 2145590 2145979 R KEGG: jan:Jann_2791 hypothetical protein, ev=8e-40, 56% identity; hypothetical protein complement(2145590..2145979) Ruegeria sp. TM1040 4077965 YP_614033.1 CDS TM1040_2039 NC_008044.1 2146291 2147013 D 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 2146291..2147013 Ruegeria sp. TM1040 4077966 YP_614034.1 CDS TM1040_2040 NC_008044.1 2147329 2147820 D KEGG: sil:SPO1157 hypothetical protein, ev=5e-55, 70% identity; hypothetical protein 2147329..2147820 Ruegeria sp. TM1040 4077967 YP_614035.1 CDS TM1040_2041 NC_008044.1 2147963 2148724 D 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 2147963..2148724 Ruegeria sp. TM1040 4077968 YP_614036.1 CDS hisE NC_008044.1 2148721 2149038 D catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribolsyl)-ATP in histidine biosynthesis; phosphoribosyl-ATP pyrophosphatase 2148721..2149038 Ruegeria sp. TM1040 4077969 YP_614037.1 CDS TM1040_2043 NC_008044.1 2149095 2150258 R PFAM: protein of unknown function DUF1006: (4.5e-85); KEGG: sil:SPO3685 hypothetical protein, ev=4e-83, 44% identity; hypothetical protein complement(2149095..2150258) Ruegeria sp. TM1040 4077970 YP_614038.1 CDS TM1040_2044 NC_008044.1 2150402 2150866 R NADPH-dependent; catalyzes the reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine in queuosine biosynthesis; 7-cyano-7-deazaguanine reductase complement(2150402..2150866) Ruegeria sp. TM1040 4077971 YP_614039.1 CDS TM1040_2045 NC_008044.1 2150883 2151590 R PFAM: Radical SAM: (0.0075); KEGG: sil:SPO3752 radical SAM domain protein, ev=8e-91, 68% identity; radical SAM family protein complement(2150883..2151590) Ruegeria sp. TM1040 4077972 YP_614040.1 CDS TM1040_2046 NC_008044.1 2151587 2151940 R 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 complement(2151587..2151940) Ruegeria sp. TM1040 4077973 YP_614041.1 CDS TM1040_2047 NC_008044.1 2151940 2152641 R PFAM: ExsB: (5.9e-74); KEGG: sil:SPO3751 ExsB, ev=1e-104, 78% identity; ExsB protein complement(2151940..2152641) Ruegeria sp. TM1040 4077974 YP_614042.1 CDS TM1040_2048 NC_008044.1 2152684 2152923 D hypothetical protein 2152684..2152923 Ruegeria sp. TM1040 4077975 YP_614043.1 CDS TM1040_2049 NC_008044.1 2153152 2153940 D 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 2153152..2153940 Ruegeria sp. TM1040 4077976 YP_614044.1 CDS TM1040_2050 NC_008044.1 2154013 2154354 D hypothetical protein 2154013..2154354 Ruegeria sp. TM1040 4077977 YP_614045.1 CDS TM1040_2051 NC_008044.1 2154527 2155009 D KEGG: sil:SPO1152 twin-arginine translocation pathway signal sequence domain protein, , ev=2e-29, 44% identity; hypothetical protein 2154527..2155009 Ruegeria sp. TM1040 4077978 YP_614046.1 CDS TM1040_2052 NC_008044.1 2155337 2155801 D PFAM: CoA-binding: (8.3e-13); KEGG: sil:SPO1153 CoA-binding domain protein, ev=2e-66, 81% identity; CoA-binding protein 2155337..2155801 Ruegeria sp. TM1040 4077979 YP_614047.1 CDS TM1040_2053 NC_008044.1 2155876 2156439 R KEGG: sil:SPO1135 hypothetical protein, ev=2e-54, 60% identity; 3-dehydroquinate dehydratase complement(2155876..2156439) Ruegeria sp. TM1040 4077980 YP_614048.1 CDS TM1040_2054 NC_008044.1 2156958 2158784 D required for the synthesis of the hydromethylpyrimidine moiety of thiamine; thiamine biosynthesis protein ThiC 2156958..2158784 Ruegeria sp. TM1040 4077981 YP_614049.1 CDS TM1040_2055 NC_008044.1 2158951 2159724 R PFAM: LamB/YcsF: (1.9e-100); KEGG: sil:SPO3659 LamB/YcsF family protein, ev=5e-89, 64% identity; LamB/YcsF family protein complement(2158951..2159724) Ruegeria sp. TM1040 4077982 YP_614050.1 CDS TM1040_2056 NC_008044.1 2159766 2160791 R PFAM: Allophanate hydrolase subunit 2: (1.1e-27); KEGG: sil:SPO3660 urea amidolyase, homolog, ev=1e-100, 58% identity; allophanate hydrolase subunit 2 complement(2159766..2160791) Ruegeria sp. TM1040 4077983 YP_614051.1 CDS TM1040_2057 NC_008044.1 2160788 2161558 R PFAM: Allophanate hydrolase subunit 1: (9.4e-09); KEGG: sil:SPO3661 allophanate hydrolase family protein, ev=6e-78, 60% identity; allophanate hydrolase subunit 1 complement(2160788..2161558) Ruegeria sp. TM1040 4077984 YP_614052.1 CDS TM1040_2058 NC_008044.1 2161695 2162609 D 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 2161695..2162609 Ruegeria sp. TM1040 4077985 YP_614053.1 CDS TM1040_2059 NC_008044.1 2162703 2163857 D 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 2162703..2163857 Ruegeria sp. TM1040 4077986 YP_614054.1 CDS TM1040_2060 NC_008044.1 2163854 2164123 D hypothetical protein 2163854..2164123 Ruegeria sp. TM1040 4077987 YP_614055.1 CDS TM1040_2061 NC_008044.1 2164175 2165095 R 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 complement(2164175..2165095) Ruegeria sp. TM1040 4077988 YP_614056.1 CDS TM1040_2062 NC_008044.1 2165213 2165494 D PFAM: protein of unknown function DUF465: (1.7e-05); KEGG: sil:SPO2237 hypothetical protein, ev=8e-11, 43% identity; hypothetical protein 2165213..2165494 Ruegeria sp. TM1040 4077989 YP_614057.1 CDS TM1040_2063 NC_008044.1 2165626 2168046 D 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 2165626..2168046 Ruegeria sp. TM1040 4077990 YP_614058.1 CDS TM1040_2064 NC_008044.1 2168043 2169287 R PFAM: FAD dependent oxidoreductase: (7.7e-55); KEGG: reu:Reut_A1655 D-amino-acid dehydrogenase, ev=5e-94, 44% identity; FAD dependent oxidoreductase complement(2168043..2169287) Ruegeria sp. TM1040 4077991 YP_614059.1 CDS TM1040_2065 NC_008044.1 2169390 2169740 R PFAM: Endoribonuclease L-PSP: (1.8e-34); KEGG: sil:SPO2000 endoribonuclease L-PSP family protein, ev=2e-46, 75% identity; endoribonuclease L-PSP complement(2169390..2169740) Ruegeria sp. TM1040 4077992 YP_614060.1 CDS TM1040_2066 NC_008044.1 2169776 2170804 R PFAM: histone deacetylase superfamily: (5.8e-61); KEGG: sil:SPO2002 acetylpolyamine aminohydrolase, ev=1e-145, 72% identity; histone deacetylase superfamily protein complement(2169776..2170804) Ruegeria sp. TM1040 4077993 YP_614061.1 CDS TM1040_2067 NC_008044.1 2170824 2172110 R 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 complement(2170824..2172110) Ruegeria sp. TM1040 4077994 YP_614062.1 CDS TM1040_2068 NC_008044.1 2172115 2172678 R KEGG: dps:DP3053 DctMQ fusion protein (C4-dicarboxylate transporter), ev=1e-06, 30% identity; hypothetical protein complement(2172115..2172678) Ruegeria sp. TM1040 4077995 YP_614063.1 CDS TM1040_2069 NC_008044.1 2172766 2173767 R 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 complement(2172766..2173767) Ruegeria sp. TM1040 4077996 YP_614064.1 CDS TM1040_2070 NC_008044.1 2174017 2175000 D 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 2174017..2175000 Ruegeria sp. TM1040 4077997 YP_614065.1 CDS TM1040_2071 NC_008044.1 2175116 2176048 D 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 2175116..2176048 Ruegeria sp. TM1040 4077822 YP_614066.1 CDS TM1040_2072 NC_008044.1 2176058 2176528 D PFAM: Uncharacterised conserved protein UCP006173: (2.9e-82); KEGG: sil:SPO3155 hypothetical protein, ev=8e-74, 75% identity; hypothetical protein 2176058..2176528 Ruegeria sp. TM1040 4077823 YP_614067.1 CDS TM1040_2073 NC_008044.1 2176578 2177414 R PFAM: alpha/beta hydrolase fold: (3.2e-05); KEGG: sil:SPO3157 hydrolase, alpha/beta fold family, ev=6e-70, 50% identity; alpha/beta hydrolase complement(2176578..2177414) Ruegeria sp. TM1040 4077824 YP_614068.1 CDS TM1040_2074 NC_008044.1 2177411 2178025 R PFAM: DSBA oxidoreductase: (1.6e-27); KEGG: sil:SPO3158 2-hydroxychromene-2-carboxylate isomerase, ev=2e-83, 75% identity; DSBA oxidoreductase complement(2177411..2178025) Ruegeria sp. TM1040 4077825 YP_614069.1 CDS TM1040_2075 NC_008044.1 2178130 2179152 D 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 2178130..2179152 Ruegeria sp. TM1040 4077826 YP_614070.1 CDS TM1040_2076 NC_008044.1 2179542 2180870 D 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 2179542..2180870 Ruegeria sp. TM1040 4077827 YP_614071.1 CDS TM1040_2077 NC_008044.1 2180867 2181340 D KEGG: ret:RHE_CH02786 hypothetical conserved membrane protein, ev=5e-47, 61% identity; hypothetical protein 2180867..2181340 Ruegeria sp. TM1040 4077828 YP_614072.1 CDS TM1040_2078 NC_008044.1 2181427 2182290 D 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 2181427..2182290 Ruegeria sp. TM1040 4077829 YP_614073.1 CDS TM1040_2079 NC_008044.1 2182353 2183846 R hypothetical protein complement(2182353..2183846) Ruegeria sp. TM1040 4077830 YP_614074.1 CDS TM1040_2080 NC_008044.1 2183985 2186429 R 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 complement(2183985..2186429) Ruegeria sp. TM1040 4077831 YP_614075.1 CDS TM1040_2081 NC_008044.1 2186594 2186947 R 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 complement(2186594..2186947) Ruegeria sp. TM1040 4077832 YP_614076.1 CDS TM1040_2082 NC_008044.1 2187014 2187454 D KEGG: pfo:Pfl_0678 hypothetical protein, ev=8e-11, 32% identity; hypothetical protein 2187014..2187454 Ruegeria sp. TM1040 4077833 YP_614077.1 CDS TM1040_2083 NC_008044.1 2187810 2188334 R hypothetical protein complement(2187810..2188334) Ruegeria sp. TM1040 4077834 YP_614078.1 CDS TM1040_2084 NC_008044.1 2188344 2188700 R KEGG: sil:SPO3160 hypothetical protein, ev=2e-30, 54% identity; hypothetical protein complement(2188344..2188700) Ruegeria sp. TM1040 4077835 YP_614079.1 CDS atpC NC_008044.1 2188825 2189238 R 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 complement(2188825..2189238) Ruegeria sp. TM1040 4077836 YP_614080.1 CDS TM1040_2086 NC_008044.1 2189250 2190674 R 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 complement(2189250..2190674) Ruegeria sp. TM1040 4077837 YP_614081.1 CDS TM1040_2087 NC_008044.1 2190695 2191570 R 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 complement(2190695..2191570) Ruegeria sp. TM1040 4077838 YP_614082.1 CDS TM1040_2088 NC_008044.1 2191586 2193127 R 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 complement(2191586..2193127) Ruegeria sp. TM1040 4077839 YP_614083.1 CDS TM1040_2089 NC_008044.1 2193128 2193781 R 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 complement(2193128..2193781) Ruegeria sp. TM1040 4077840 YP_614084.1 CDS TM1040_2090 NC_008044.1 2194104 2194850 R KEGG: sil:SPO3167 hypothetical protein, ev=1e-111, 75% identity; hypothetical protein complement(2194104..2194850) Ruegeria sp. TM1040 4077841 YP_614085.1 CDS TM1040_2091 NC_008044.1 2194905 2195720 D PFAM: beta-lactamase-like: (1.6e-33); KEGG: sil:SPO3168 hydroxyacylglutathione hydrolase, , ev=1e-76, 55% identity; hydroxyacylglutathione hydrolase 2194905..2195720 Ruegeria sp. TM1040 4077842 YP_614086.1 CDS TM1040_2092 NC_008044.1 2195880 2198258 D 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 2195880..2198258 Ruegeria sp. TM1040 4077843 YP_614087.1 CDS TM1040_2093 NC_008044.1 2198470 2199066 R KEGG: sil:SPO0694 hypothetical protein, ev=6e-16, 30% identity; hypothetical protein complement(2198470..2199066) Ruegeria sp. TM1040 4077844 YP_614088.1 CDS TM1040_2094 NC_008044.1 2199187 2199534 R KEGG: rsp:RSP_0427 hypothetical protein, ev=7e-12, 41% identity; hypothetical protein complement(2199187..2199534) Ruegeria sp. TM1040 4077845 YP_614089.1 CDS TM1040_2095 NC_008044.1 2199768 2202122 R PFAM: OmpA/MotB: (2.9e-19); KEGG: sil:SPO3171 OmpA domain protein, ev=0.0, 67% identity; hypothetical protein complement(2199768..2202122) Ruegeria sp. TM1040 4077846 YP_614090.1 CDS TM1040_2096 NC_008044.1 2202126 2203304 R KEGG: sil:SPO3172 hypothetical protein, ev=1e-154, 72% identity; hypothetical protein complement(2202126..2203304) Ruegeria sp. TM1040 4077847 YP_614091.1 CDS TM1040_2097 NC_008044.1 2203383 2203910 R PFAM: ChaC-like protein: (1.1e-58); KEGG: sil:SPO3173 cation transport protein ChaC, , ev=3e-69, 72% identity; ChaC-like protein complement(2203383..2203910) Ruegeria sp. TM1040 4077848 YP_614092.1 CDS TM1040_2098 NC_008044.1 2203979 2204992 D KEGG: sil:SPO3174 hypothetical protein, ev=2e-99, 52% identity; hypothetical protein 2203979..2204992 Ruegeria sp. TM1040 4077849 YP_614093.1 CDS TM1040_2099 NC_008044.1 2205061 2205927 R PFAM: Extensin-like-like: (9.2e-43); KEGG: sil:SPO3175 hypothetical protein, ev=6e-74, 52% identity; extensin-like protein complement(2205061..2205927) Ruegeria sp. TM1040 4077850 YP_614094.1 CDS TM1040_2100 NC_008044.1 2205924 2206856 R dual function enzyme catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate and the formation of tyrosine from arogenate; cyclohexadienyl dehydrogenase complement(2205924..2206856) Ruegeria sp. TM1040 4077851 YP_614095.1 CDS TM1040_2101 NC_008044.1 2206853 2207941 R catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis; histidinol-phosphate aminotransferase complement(2206853..2207941) Ruegeria sp. TM1040 4077852 YP_614096.1 CDS TM1040_2102 NC_008044.1 2207938 2208177 R hypothetical protein complement(2207938..2208177) Ruegeria sp. TM1040 4077853 YP_614097.1 CDS TM1040_2103 NC_008044.1 2208354 2209778 R PFAM: aminotransferase, class V: (2.3e-18); KEGG: sil:SPO3178 hypothetical protein, ev=0.0, 70% identity; class V aminotransferase complement(2208354..2209778) Ruegeria sp. TM1040 4077854 YP_614098.1 CDS TM1040_2104 NC_008044.1 2209885 2210346 D PFAM: regulatory proteins, AsnC/Lrp: (1.3e-24); KEGG: sil:SPO3179 transcriptional regulator, AsnC family, ev=3e-64, 80% identity; AsnC family transcriptional regulator 2209885..2210346 Ruegeria sp. TM1040 4077855 YP_614099.1 CDS TM1040_2105 NC_008044.1 2210392 2210859 R PFAM: GCN5-related N-acetyltransferase: (5.2e-07); KEGG: sil:SPO2447 acetyltransferase, GNAT family, ev=4e-31, 48% identity; N-acetyltransferase GCN5 complement(2210392..2210859) Ruegeria sp. TM1040 4077856 YP_614100.1 CDS TM1040_2106 NC_008044.1 2210931 2211518 R KEGG: sil:SPO3611 hypothetical protein, ev=2e-50, 52% identity; hypothetical protein complement(2210931..2211518) Ruegeria sp. TM1040 4077857 YP_614101.1 CDS rpsD NC_008044.1 2211714 2212334 R 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 complement(2211714..2212334) Ruegeria sp. TM1040 4077858 YP_614102.1 CDS TM1040_2108 NC_008044.1 2212779 2213840 R KEGG: sil:SPO3182 hypothetical protein, ev=1e-144, 69% identity; hypothetical protein complement(2212779..2213840) Ruegeria sp. TM1040 4077859 YP_614103.1 CDS TM1040_2109 NC_008044.1 2213973 2214914 R KEGG: jan:Jann_0952 hypothetical protein, ev=4e-50, 43% identity; hypothetical protein complement(2213973..2214914) Ruegeria sp. TM1040 4077860 YP_614104.1 CDS TM1040_2110 NC_008044.1 2215089 2215490 R SMART: Rhodanese-like: (3.1e-14); KEGG: jan:Jann_2299 rhodanese-like, ev=1e-41, 64% identity; rhodanese-like protein complement(2215089..2215490) Ruegeria sp. TM1040 4076424 YP_614105.1 CDS TM1040_2111 NC_008044.1 2215682 2216980 D PFAM: FAD dependent oxidoreductase: (3.4e-86); KEGG: ppu:PP5257 oxidoreductase, FAD-binding, ev=1e-98, 45% identity; L-pipecolate dehydrogenase 2215682..2216980 Ruegeria sp. TM1040 4076425 YP_614106.1 CDS TM1040_2112 NC_008044.1 2217033 2217839 R SMART: regulatory proteins, IclR: (7.6e-09); KEGG: pfo:Pfl_1294 transcriptional regulator, IclR family, ev=1e-19, 27% identity; IclR family transcriptional regulator complement(2217033..2217839) Ruegeria sp. TM1040 4076426 YP_614107.1 CDS TM1040_2113 NC_008044.1 2217848 2219566 D PFAM: sulfatase: (3.1e-28); KEGG: sil:SPO3593 sulfatase family protein, ev=0.0, 65% identity; sulfatase 2217848..2219566 Ruegeria sp. TM1040 4076427 YP_614108.1 CDS TM1040_2114 NC_008044.1 2219895 2221355 D 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 2219895..2221355 Ruegeria sp. TM1040 4076428 YP_614109.1 CDS TM1040_2115 NC_008044.1 2221360 2222301 D 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 2221360..2222301 Ruegeria sp. TM1040 4076429 YP_614110.1 CDS TM1040_2116 NC_008044.1 2222305 2223102 D PFAM: transglutaminase-like: (1.1e-15) transglutaminase-like-like: (8.1e-26); KEGG: jan:Jann_2678 transglutaminase-like, ev=7e-77, 55% identity; transglutaminase 2222305..2223102 Ruegeria sp. TM1040 4076430 YP_614111.1 CDS TM1040_2117 NC_008044.1 2223110 2223844 D 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 2223110..2223844 Ruegeria sp. TM1040 4076431 YP_614112.1 CDS TM1040_2118 NC_008044.1 2223999 2225012 R 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 complement(2223999..2225012) Ruegeria sp. TM1040 4076432 YP_614113.1 CDS TM1040_2119 NC_008044.1 2225035 2225343 D KEGG: sil:SPO1407 hypothetical protein, ev=1e-23, 56% identity; hypothetical protein 2225035..2225343 Ruegeria sp. TM1040 4076433 YP_614114.1 CDS TM1040_2120 NC_008044.1 2225676 2226056 D KEGG: jan:Jann_3405 hypothetical protein, ev=3e-17, 68% identity; hypothetical protein 2225676..2226056 Ruegeria sp. TM1040 4076434 YP_614115.1 CDS TM1040_2121 NC_008044.1 2226311 2227423 D KEGG: lma:LmjF35.0290 hypothetical protein, conserved, ev=2e-09, 29% identity; CheA signal transduction histidine kinase 2226311..2227423 Ruegeria sp. TM1040 4076435 YP_614116.1 CDS TM1040_2122 NC_008044.1 2227506 2227973 R PFAM: protein of unknown function DUF1052: (9.5e-44); KEGG: sil:SPO1766 hypothetical protein, ev=9e-61, 78% identity; hypothetical protein complement(2227506..2227973) Ruegeria sp. TM1040 4076436 YP_614117.1 CDS TM1040_2123 NC_008044.1 2228459 2228779 R KEGG: sil:SPO1765 hypothetical protein, ev=4e-20, 48% identity; hypothetical protein complement(2228459..2228779) Ruegeria sp. TM1040 4076437 YP_614118.1 CDS TM1040_2124 NC_008044.1 2228973 2230523 D PFAM: adenylyl cyclase class-3/4/guanylyl cyclase: (8.9e-27); KEGG: bja:bll7624 probable adenylate cyclase, ev=1e-145, 57% identity; guanylate cyclase 2228973..2230523 Ruegeria sp. TM1040 4076438 YP_614119.1 CDS TM1040_2125 NC_008044.1 2230638 2232287 R 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 complement(2230638..2232287) Ruegeria sp. TM1040 4076439 YP_614120.1 CDS TM1040_2126 NC_008044.1 2232329 2232745 R KEGG: rpb:RPB_3824 UspA, ev=2e-10, 30% identity; hypothetical protein complement(2232329..2232745) Ruegeria sp. TM1040 4076440 YP_614121.1 CDS TM1040_2127 NC_008044.1 2232999 2233481 R 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 complement(2232999..2233481) Ruegeria sp. TM1040 4076441 YP_614122.1 CDS ribH NC_008044.1 2233505 2234029 R 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 complement(2233505..2234029) Ruegeria sp. TM1040 4076442 YP_614123.1 CDS TM1040_2129 NC_008044.1 2234044 2235168 R 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 complement(2234044..2235168) Ruegeria sp. TM1040 4076443 YP_614124.1 CDS TM1040_2130 NC_008044.1 2235462 2236064 R KEGG: sil:SPO1760 hypothetical protein, ev=2e-56, 57% identity; hypothetical protein complement(2235462..2236064) Ruegeria sp. TM1040 4076444 YP_614125.1 CDS TM1040_2131 NC_008044.1 2236064 2236669 R catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine; riboflavin synthase subunit alpha complement(2236064..2236669) Ruegeria sp. TM1040 4076445 YP_614126.1 CDS TM1040_2132 NC_008044.1 2236933 2238237 D PFAM: Capsule polysaccharide biosynthesis: (3.1e-30); KEGG: sil:SPO1757 capsular polysaccharide export protein KpsS, ev=0.0, 75% identity; capsule polysaccharide biosynthesis 2236933..2238237 Ruegeria sp. TM1040 4076446 YP_614127.1 CDS TM1040_2133 NC_008044.1 2238343 2239470 D PFAM: polysaccharide export protein: (3.9e-14); KEGG: sil:SPO1756 polysaccharide biosynthesis/export protein, ev=1e-165, 76% identity; polysaccharide export protein 2238343..2239470 Ruegeria sp. TM1040 4076447 YP_614128.1 CDS TM1040_2134 NC_008044.1 2239477 2241516 D PFAM: Capsule polysaccharide biosynthesis: (2.5e-72); KEGG: sil:SPO1755 capsular polysaccharide export protein KpsC, ev=0.0, 66% identity; capsule polysaccharide biosynthesis 2239477..2241516 Ruegeria sp. TM1040 4076448 YP_614129.1 CDS TM1040_2135 NC_008044.1 2241583 2242659 R 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 complement(2241583..2242659) Ruegeria sp. TM1040 4076449 YP_614130.1 CDS nrdR NC_008044.1 2242735 2243202 R 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 complement(2242735..2243202) Ruegeria sp. TM1040 4076450 YP_614131.1 CDS TM1040_2137 NC_008044.1 2243348 2243776 R 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 complement(2243348..2243776) Ruegeria sp. TM1040 4076451 YP_614132.1 CDS TM1040_2138 NC_008044.1 2243781 2244239 R KEGG: sil:SPO1751 hypothetical protein, ev=1e-18, 44% identity; hypothetical protein complement(2243781..2244239) Ruegeria sp. TM1040 4076452 YP_614133.1 CDS TM1040_2139 NC_008044.1 2244370 2244678 R hypothetical protein complement(2244370..2244678) Ruegeria sp. TM1040 4076453 YP_614134.1 CDS TM1040_2140 NC_008044.1 2244894 2245364 R hypothetical protein complement(2244894..2245364) Ruegeria sp. TM1040 4076454 YP_614135.1 CDS TM1040_2141 NC_008044.1 2245649 2247643 R 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 complement(2245649..2247643) Ruegeria sp. TM1040 4076455 YP_614136.1 CDS dnaG NC_008044.1 2247809 2249818 R synthesizes RNA primers at the replication forks; DNA primase complement(2247809..2249818) Ruegeria sp. TM1040 4076456 YP_614137.1 CDS TM1040_2143 NC_008044.1 2249884 2250240 R KEGG: sil:SPO1748 hypothetical protein, ev=4e-15, 40% identity; hypothetical protein complement(2249884..2250240) Ruegeria sp. TM1040 4076457 YP_614138.1 CDS TM1040_2144 NC_008044.1 2250279 2250836 R 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 complement(2250279..2250836) Ruegeria sp. TM1040 4076458 YP_614139.1 CDS TM1040_2145 NC_008044.1 2250829 2253774 R 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 complement(2250829..2253774) Ruegeria sp. TM1040 4076459 YP_614140.1 CDS TM1040_2146 NC_008044.1 2253771 2254049 R 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 complement(2253771..2254049) Ruegeria sp. TM1040 4076460 YP_614141.1 CDS TM1040_2147 NC_008044.1 2254116 2255420 R 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 complement(2254116..2255420) Ruegeria sp. TM1040 4076461 YP_614142.1 CDS TM1040_2148 NC_008044.1 2255558 2256244 D PFAM: regulatory protein, TetR: (4.9e-12); KEGG: bat:BAS2304 transcriptional regulator, TetR family, ev=1e-10, 29% identity; TetR family transcriptional regulator 2255558..2256244 Ruegeria sp. TM1040 4076462 YP_614143.1 CDS TM1040_2149 NC_008044.1 2256244 2257008 D PFAM: Abortive infection protein: (1.4e-08); KEGG: hma:rrnB0071 hypothetical protein, ev=2e-15, 29% identity; abortive infection protein 2256244..2257008 Ruegeria sp. TM1040 4076748 YP_614144.1 CDS TM1040_2150 NC_008044.1 2257115 2258545 R 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 complement(2257115..2258545) Ruegeria sp. TM1040 4076749 YP_614145.1 CDS TM1040_2151 NC_008044.1 2258932 2260680 D KEGG: sil:SPO1742 hypothetical protein, ev=1e-125, 44% identity; hypothetical protein 2258932..2260680 Ruegeria sp. TM1040 4076750 YP_614146.1 CDS TM1040_2152 NC_008044.1 2260677 2261225 D PFAM: TadE-like: (1.9e-07); KEGG: sil:SPO1741 hypothetical protein, ev=9e-40, 48% identity; TadE-like protein 2260677..2261225 Ruegeria sp. TM1040 4076751 YP_614147.1 CDS TM1040_2153 NC_008044.1 2261229 2261834 D KEGG: sil:SPO1740 hypothetical protein, ev=7e-34, 41% identity; hypothetical protein 2261229..2261834 Ruegeria sp. TM1040 4076752 YP_614148.1 CDS TM1040_2154 NC_008044.1 2261944 2262378 R KEGG: ret:RHE_CH01338 hypothetical protein, ev=3e-24, 43% identity; hypothetical protein complement(2261944..2262378) Ruegeria sp. TM1040 4076753 YP_614149.1 CDS TM1040_2155 NC_008044.1 2262375 2263757 R 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 complement(2262375..2263757) Ruegeria sp. TM1040 4076754 YP_614150.1 CDS TM1040_2156 NC_008044.1 2264063 2266777 D 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 2264063..2266777 Ruegeria sp. TM1040 4076755 YP_614151.1 CDS TM1040_2157 NC_008044.1 2266835 2267326 R KEGG: sil:SPO1739 hypothetical protein, ev=2e-48, 60% identity; hypothetical protein complement(2266835..2267326) Ruegeria sp. TM1040 4076756 YP_614152.1 CDS TM1040_2158 NC_008044.1 2267409 2268128 R 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 complement(2267409..2268128) Ruegeria sp. TM1040 4076757 YP_614153.1 CDS TM1040_2159 NC_008044.1 2268651 2270105 D 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 2268651..2270105 Ruegeria sp. TM1040 4076758 YP_614154.1 CDS TM1040_2160 NC_008044.1 2270248 2271159 D PFAM: Pirin-like: (6.2e-45); KEGG: sil:SPO1737 pirin domain protein, ev=1e-154, 84% identity; pirin 2270248..2271159 Ruegeria sp. TM1040 4076759 YP_614155.1 CDS TM1040_2161 NC_008044.1 2271476 2271964 R PFAM: GCN5-related N-acetyltransferase: (8e-07); KEGG: vfi:VF1328 ferrichrome-binding protein, ev=2e-09, 33% identity; N-acetyltransferase GCN5 complement(2271476..2271964) Ruegeria sp. TM1040 4076760 YP_614156.1 CDS TM1040_2162 NC_008044.1 2271969 2272598 R PFAM: regulatory protein, TetR: (7.5e-12); KEGG: sil:SPO1736 transcriptional regulator, TetR family, ev=1e-70, 72% identity; TetR family transcriptional regulator complement(2271969..2272598) Ruegeria sp. TM1040 4076761 YP_614157.1 CDS TM1040_2163 NC_008044.1 2272682 2272984 D KEGG: sil:SPO1735 hypothetical protein, ev=1e-09, 45% identity; hypothetical protein 2272682..2272984 Ruegeria sp. TM1040 4076762 YP_614158.1 CDS TM1040_2164 NC_008044.1 2273080 2274366 D catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine; homoserine dehydrogenase 2273080..2274366 Ruegeria sp. TM1040 4076763 YP_614159.1 CDS glpX NC_008044.1 2274543 2275526 D type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese; fructose 1,6-bisphosphatase II 2274543..2275526 Ruegeria sp. TM1040 4076764 YP_614160.1 CDS TM1040_2166 NC_008044.1 2275574 2277385 D 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 2275574..2277385 Ruegeria sp. TM1040 4076765 YP_614161.1 CDS TM1040_2167 NC_008044.1 2277923 2279320 R 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 complement(2277923..2279320) Ruegeria sp. TM1040 4076766 YP_614162.1 CDS TM1040_2168 NC_008044.1 2279428 2281509 R 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 complement(2279428..2281509) Ruegeria sp. TM1040 4076767 YP_614163.1 CDS TM1040_2169 NC_008044.1 2281704 2282726 R TIGRFAM: GGDEF domain: (5.1e-30); PFAM: GGDEF: (1.7e-46); KEGG: sil:SPO2747 diguanylate cyclase, , ev=1e-112, 65% identity; diguanylate cyclase complement(2281704..2282726) Ruegeria sp. TM1040 4076768 YP_614164.1 CDS TM1040_2170 NC_008044.1 2282723 2283310 R KEGG: sil:SPO2748 hypothetical protein, ev=3e-67, 65% identity; hypothetical protein complement(2282723..2283310) Ruegeria sp. TM1040 4076769 YP_614165.1 CDS TM1040_2171 NC_008044.1 2283726 2285285 R PFAM: trimethylamine methyltransferase: (1.9e-247); KEGG: sil:SPO2750 trimethylamine methyltransferase family protein, ev=0.0, 82% identity; trimethylamine methyltransferase complement(2283726..2285285) Ruegeria sp. TM1040 4076770 YP_614166.1 CDS TM1040_2172 NC_008044.1 2285415 2286107 R 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 complement(2285415..2286107) Ruegeria sp. TM1040 4076771 YP_614167.1 CDS TM1040_2173 NC_008044.1 2286144 2286428 R KEGG: sil:SPO2752 hypothetical protein, ev=6e-27, 59% identity; hypothetical protein complement(2286144..2286428) Ruegeria sp. TM1040 4076772 YP_614168.1 CDS TM1040_2174 NC_008044.1 2286545 2287948 D 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 2286545..2287948 Ruegeria sp. TM1040 4076773 YP_614169.1 CDS TM1040_2175 NC_008044.1 2287994 2288503 R KEGG: rsp:RSP_0414 hypothetical protein, ev=5e-10, 30% identity; hypothetical protein complement(2287994..2288503) Ruegeria sp. TM1040 4076774 YP_614170.1 CDS TM1040_2176 NC_008044.1 2288500 2288895 R KEGG: sil:SPO2755 hypothetical protein, ev=3e-11, 33% identity; hypothetical protein complement(2288500..2288895) Ruegeria sp. TM1040 4076775 YP_614171.1 CDS TM1040_2177 NC_008044.1 2288888 2289514 R 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 complement(2288888..2289514) Ruegeria sp. TM1040 4076776 YP_614172.1 CDS TM1040_2178 NC_008044.1 2289585 2290088 R KEGG: jan:Jann_3135 calcium-binding EF-hand, ev=6e-20, 44% identity; hypothetical protein complement(2289585..2290088) Ruegeria sp. TM1040 4076777 YP_614173.1 CDS TM1040_2179 NC_008044.1 2290354 2290785 D PFAM: protein of unknown function DUF983: (5.5e-31); KEGG: sil:SPO2758 hypothetical protein, ev=5e-50, 68% identity; hypothetical protein 2290354..2290785 Ruegeria sp. TM1040 4076778 YP_614174.1 CDS TM1040_2180 NC_008044.1 2290874 2291602 D PFAM: NUDIX hydrolase: (1.3e-11); KEGG: sil:SPO2759 hydrolase, NUDIX family, ev=1e-82, 66% identity; NUDIX hydrolase 2290874..2291602 Ruegeria sp. TM1040 4076779 YP_614175.1 CDS TM1040_2181 NC_008044.1 2291629 2292531 R PFAM: protein of unknown function DUF6, transmembrane: (0.0017); KEGG: sil:SPO1442 membrane protein, , ev=1e-100, 67% identity; hypothetical protein complement(2291629..2292531) Ruegeria sp. TM1040 4076780 YP_614176.1 CDS TM1040_2182 NC_008044.1 2292577 2293533 R PFAM: fatty acid desaturase: (5.2e-08); KEGG: sil:SPO1441 fatty acid desaturase family protein, ev=2e-99, 58% identity; fatty acid desaturase complement(2292577..2293533) Ruegeria sp. TM1040 4076781 YP_614177.1 CDS TM1040_2183 NC_008044.1 2293595 2293801 R KEGG: sil:SPO1440 hypothetical protein, ev=2e-21, 68% identity; hypothetical protein complement(2293595..2293801) Ruegeria sp. TM1040 4076782 YP_614178.1 CDS TM1040_2184 NC_008044.1 2293906 2294775 D PFAM: helix-turn-helix motif: (9.7e-12); KEGG: sil:SPO1439 DNA binding protein, , ev=1e-121, 75% identity; XRE family transcriptional regulator 2293906..2294775 Ruegeria sp. TM1040 4076783 YP_614179.1 CDS fabG NC_008044.1 2294846 2295598 R Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis; 3-ketoacyl-ACP reductase complement(2294846..2295598) Ruegeria sp. TM1040 4076784 YP_614180.1 CDS TM1040_2186 NC_008044.1 2295598 2297073 R Converts (S)-3-hydroxyacyl-CoA to 3-oxyacyl-CoA; may also act as a thioesterase; bifunctional 3-hydroxyacyl-CoA dehydrogenase/thioesterase complement(2295598..2297073) Ruegeria sp. TM1040 4076785 YP_614181.1 CDS TM1040_2187 NC_008044.1 2297086 2297646 R PFAM: Lipocalin-like: (4.6e-66); KEGG: rsp:RSP_0595 outer membrane lipoprotein Blc, ev=1e-26, 45% identity; Lipocalin-like protein complement(2297086..2297646) Ruegeria sp. TM1040 4076786 YP_614182.1 CDS TM1040_2188 NC_008044.1 2297712 2298629 R PFAM: protein of unknown function DUF849: (7.1e-195); KEGG: sil:SPO1435 hypothetical protein, ev=1e-151, 86% identity; hypothetical protein complement(2297712..2298629) Ruegeria sp. TM1040 4078179 YP_614183.1 CDS TM1040_2189 NC_008044.1 2298764 2299795 D 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 2298764..2299795 Ruegeria sp. TM1040 4078180 YP_614184.1 CDS TM1040_2190 NC_008044.1 2299874 2300920 R PFAM: aldo/keto reductase: (1.1e-18); KEGG: sil:SPO1433 oxidoreductase, aldo/keto reductase family, ev=1e-139, 70% identity; aldo/keto reductase complement(2299874..2300920) Ruegeria sp. TM1040 4078181 YP_614185.1 CDS TM1040_2191 NC_008044.1 2301194 2302420 D PFAM: major facilitator superfamily MFS_1: (3.8e-24); KEGG: sil:SPO1404 membrane protein, , ev=1e-180, 75% identity; major facilitator superfamily transporter 2301194..2302420 Ruegeria sp. TM1040 4078182 YP_614186.1 CDS TM1040_2192 NC_008044.1 2302522 2303400 R 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 complement(2302522..2303400) Ruegeria sp. TM1040 4078183 YP_614187.1 CDS TM1040_2193 NC_008044.1 2303499 2304203 D PFAM: short-chain dehydrogenase/reductase SDR: (1.8e-07); KEGG: sme:SMc00136 oxidoreductase protein, ev=1e-95, 69% identity; short-chain dehydrogenase/reductase SDR 2303499..2304203 Ruegeria sp. TM1040 4078184 YP_614188.1 CDS TM1040_2194 NC_008044.1 2304193 2304444 D hypothetical protein 2304193..2304444 Ruegeria sp. TM1040 4078185 YP_614189.1 CDS TM1040_2195 NC_008044.1 2304591 2306279 R PFAM: band 7 protein: (1.4e-14); KEGG: jan:Jann_1794 band 7 protein, ev=0.0, 76% identity; hypothetical protein complement(2304591..2306279) Ruegeria sp. TM1040 4078186 YP_614190.1 CDS TM1040_2196 NC_008044.1 2306335 2307012 R PFAM: protein of unknown function DUF1449: (6.7e-09); KEGG: jan:Jann_1795 hypothetical protein, ev=4e-56, 49% identity; hypothetical protein complement(2306335..2307012) Ruegeria sp. TM1040 4078187 YP_614191.2 CDS TM1040_2197 NC_008044.1 2307335 2309056 D 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 2307335..2309056 Ruegeria sp. TM1040 4078188 YP_614192.1 CDS TM1040_2198 NC_008044.1 2309443 2309622 D KEGG: rsp:RSP_6006 hypothetical protein, ev=4e-08, 76% identity; hypothetical protein 2309443..2309622 Ruegeria sp. TM1040 4078189 YP_614193.1 CDS TM1040_2199 NC_008044.1 2309674 2310942 D KEGG: sil:SPO0086 lipoprotein, , ev=1e-172, 71% identity; imelysin 2309674..2310942 Ruegeria sp. TM1040 4078190 YP_614194.1 CDS TM1040_2200 NC_008044.1 2311172 2311459 D KEGG: rsp:RSP_1547 probable bacterioferritin-associated ferredoxin, ev=6e-25, 65% identity; bacterioferritin-associated ferredoxin 2311172..2311459 Ruegeria sp. TM1040 4078191 YP_614195.1 CDS TM1040_2201 NC_008044.1 2311530 2311898 D PFAM: Ferritin and Dps: (2.4e-18); KEGG: bmb:BruAb2_0659 Bfr, bacterioferritin, ev=2e-42, 70% identity; ferritin 2311530..2311898 Ruegeria sp. TM1040 4078192 YP_614196.1 CDS TM1040_2202 NC_008044.1 2311933 2313438 D 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 2311933..2313438 Ruegeria sp. TM1040 4078193 YP_614197.1 CDS TM1040_2203 NC_008044.1 2313438 2314466 D KEGG: jan:Jann_1370 hypothetical protein, ev=6e-88, 50% identity; hypothetical protein 2313438..2314466 Ruegeria sp. TM1040 4078194 YP_614198.1 CDS TM1040_2204 NC_008044.1 2314503 2315603 D PFAM: Uncharacterised conserved protein UCP028101: (9e-104); KEGG: sil:SPO0090 hypothetical protein, ev=1e-110, 53% identity; hypothetical protein 2314503..2315603 Ruegeria sp. TM1040 4078195 YP_614199.1 CDS TM1040_2205 NC_008044.1 2315748 2316542 D 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 2315748..2316542 Ruegeria sp. TM1040 4078196 YP_614200.1 CDS glpD NC_008044.1 2316535 2318115 D 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 2316535..2318115 Ruegeria sp. TM1040 4078197 YP_614201.1 CDS TM1040_2207 NC_008044.1 2318230 2318916 R 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 complement(2318230..2318916) Ruegeria sp. TM1040 4078198 YP_614202.1 CDS TM1040_2208 NC_008044.1 2319278 2319781 D PFAM: protein of unknown function DUF1636: (4.7e-41); KEGG: rsp:RSP_2829 hypothetical protein, ev=1e-27, 59% identity; hypothetical protein 2319278..2319781 Ruegeria sp. TM1040 4078199 YP_614203.1 CDS TM1040_2209 NC_008044.1 2319801 2320835 D 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 2319801..2320835 Ruegeria sp. TM1040 4078200 YP_614204.1 CDS cobN NC_008044.1 2320961 2324206 D 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 2320961..2324206 Ruegeria sp. TM1040 4078201 YP_614205.1 CDS TM1040_2211 NC_008044.1 2324203 2325363 D 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 2324203..2325363 Ruegeria sp. TM1040 4078202 YP_614206.1 CDS cobH NC_008044.1 2325365 2325994 D catalyzes the interconversion of precorrin-8X and hydrogenobyrinate; precorrin-8X methylmutase 2325365..2325994 Ruegeria sp. TM1040 4078203 YP_614207.1 CDS TM1040_2213 NC_008044.1 2326011 2326742 D 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 2326011..2326742 Ruegeria sp. TM1040 4078204 YP_614208.1 CDS TM1040_2214 NC_008044.1 2326739 2327560 D 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 2326739..2327560 Ruegeria sp. TM1040 4078205 YP_614209.1 CDS TM1040_2215 NC_008044.1 2327557 2328318 R 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 complement(2327557..2328318) Ruegeria sp. TM1040 4078206 YP_614210.1 CDS TM1040_2216 NC_008044.1 2328500 2329525 D 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 2328500..2329525 Ruegeria sp. TM1040 4078207 YP_614211.1 CDS TM1040_2217 NC_008044.1 2329522 2329884 D KEGG: rsp:RSP_2822 precorrin methylase, ev=1e-16, 45% identity; precorrin methylase 2329522..2329884 Ruegeria sp. TM1040 4078208 YP_614212.1 CDS TM1040_2218 NC_008044.1 2329881 2330675 D 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 2329881..2330675 Ruegeria sp. TM1040 4078209 YP_614213.1 CDS TM1040_2219 NC_008044.1 2330775 2332091 D responsible for the amidation of carboxylic groups at position A and C of cobyrinic acid or hydrogenobrynic acid; cobyrinic acid a,c-diamide synthase 2330775..2332091 Ruegeria sp. TM1040 4078210 YP_614214.1 CDS TM1040_2220 NC_008044.1 2332088 2332825 D 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 2332088..2332825 Ruegeria sp. TM1040 4078211 YP_614215.1 CDS TM1040_2221 NC_008044.1 2332822 2333205 D PFAM: protein of unknown function DUF1636: (3.8e-11); KEGG: mlo:mlr8225 hypothetical protein, ev=7e-12, 37% identity; hypothetical protein 2332822..2333205 Ruegeria sp. TM1040 4078212 YP_614216.1 CDS TM1040_2222 NC_008044.1 2333650 2334423 D TIGRFAM: Cobalt transporter subunit CbtA, : (5.3e-104); KEGG: sil:SPO2876 membrane protein, , ev=2e-97, 74% identity; cobalt transporter subunit CbtA 2333650..2334423 Ruegeria sp. TM1040 4078213 YP_614217.1 CDS TM1040_2223 NC_008044.1 2334529 2335020 D KEGG: sil:SPO2877 hypothetical protein, ev=2e-56, 64% identity; hypothetical protein 2334529..2335020 Ruegeria sp. TM1040 4078214 YP_614218.1 CDS TM1040_2224 NC_008044.1 2335093 2335857 D catalyzes the formation of precorrin 6x from precorrin 5; precorrin 6A synthase 2335093..2335857 Ruegeria sp. TM1040 4078215 YP_614219.1 CDS TM1040_2225 NC_008044.1 2336081 2337271 R TIGRFAM: kynureninase: (3.7e-85); PFAM: aminotransferase, class V: (6.1e-08); KEGG: jan:Jann_2085 kynureninase, ev=1e-154, 66% identity; kynureninase complement(2336081..2337271) Ruegeria sp. TM1040 4078216 YP_614220.1 CDS TM1040_2226 NC_008044.1 2337273 2338112 R PFAM: tryptophan 2,3-dioxygenase: (7e-101); KEGG: jan:Jann_2084 tryptophan 2,3-dioxygenase, ev=1e-104, 68% identity; tryptophan 2,3-dioxygenase complement(2337273..2338112) Ruegeria sp. TM1040 4078217 YP_614221.1 CDS TM1040_2227 NC_008044.1 2338410 2340884 D 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 2338410..2340884 Ruegeria sp. TM1040 4077294 YP_614222.1 CDS TM1040_2228 NC_008044.1 2341200 2341916 D KEGG: jan:Jann_2565 hypothetical protein, ev=8e-06, 22% identity; hypothetical protein 2341200..2341916 Ruegeria sp. TM1040 4077295 YP_614223.1 CDS TM1040_2229 NC_008044.1 2342347 2344095 R 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 complement(2342347..2344095) Ruegeria sp. TM1040 4077296 YP_614224.1 CDS TM1040_2230 NC_008044.1 2344893 2345891 D 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 2344893..2345891 Ruegeria sp. TM1040 4077297 YP_614225.1 CDS TM1040_2231 NC_008044.1 2345962 2346357 R PFAM: Endoribonuclease L-PSP: (7.7e-24); KEGG: sil:SPOA0400 endoribonuclease L-PSP family protein, ev=1e-48, 66% identity; endoribonuclease L-PSP complement(2345962..2346357) Ruegeria sp. TM1040 4077298 YP_614226.1 CDS TM1040_2232 NC_008044.1 2346354 2346758 R PFAM: thioesterase superfamily: (3.1e-10); KEGG: sil:SPO0786 thioesterase family protein, ev=2e-38, 60% identity; thioesterase superfamily protein complement(2346354..2346758) Ruegeria sp. TM1040 4077299 YP_614227.1 CDS TM1040_2233 NC_008044.1 2346762 2347448 R 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 complement(2346762..2347448) Ruegeria sp. TM1040 4077300 YP_614228.1 CDS TM1040_2234 NC_008044.1 2347445 2348194 R 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 complement(2347445..2348194) Ruegeria sp. TM1040 4077301 YP_614229.1 CDS TM1040_2235 NC_008044.1 2348187 2349170 R PFAM: inner-membrane translocator: (2e-33); KEGG: bja:blr1065 ABC transporter permease protein, ev=1e-75, 49% identity; inner-membrane translocator complement(2348187..2349170) Ruegeria sp. TM1040 4077302 YP_614230.1 CDS TM1040_2236 NC_008044.1 2349167 2350087 R PFAM: inner-membrane translocator: (3.3e-32); KEGG: bja:blr1064 ABC transporter permease protein, ev=1e-89, 57% identity; inner-membrane translocator complement(2349167..2350087) Ruegeria sp. TM1040 4077303 YP_614231.1 CDS TM1040_2237 NC_008044.1 2350145 2351275 R KEGG: dar:Daro_4043 extracellular ligand-binding receptor, ev=1e-104, 50% identity; extracellular ligand-binding receptor complement(2350145..2351275) Ruegeria sp. TM1040 4077304 YP_614232.1 CDS TM1040_2238 NC_008044.1 2351314 2352930 R 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 complement(2351314..2352930) Ruegeria sp. TM1040 4077305 YP_614233.1 CDS TM1040_2239 NC_008044.1 2352927 2354081 R 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 complement(2352927..2354081) Ruegeria sp. TM1040 4077306 YP_614234.1 CDS TM1040_2240 NC_008044.1 2354147 2354950 R Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA; enoyl-CoA hydratase complement(2354147..2354950) Ruegeria sp. TM1040 4077307 YP_614235.1 CDS TM1040_2241 NC_008044.1 2354957 2355442 R PFAM: regulatory protein, MarR: (1.2e-10); KEGG: jan:Jann_1325 transcriptional regulator, MarR family, ev=1e-40, 60% identity; MarR family transcriptional regulator complement(2354957..2355442) Ruegeria sp. TM1040 4077308 YP_614236.1 CDS TM1040_2242 NC_008044.1 2355439 2356188 R 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 complement(2355439..2356188) Ruegeria sp. TM1040 4077309 YP_614237.1 CDS TM1040_2243 NC_008044.1 2356185 2358479 R catalyzes the conversion of salicylyl-CoA to gentisyl-CoA; salicylyl-CoA 5-hydroxylase complement(2356185..2358479) Ruegeria sp. TM1040 4077310 YP_614238.1 CDS TM1040_2244 NC_008044.1 2358787 2359728 R 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 complement(2358787..2359728) Ruegeria sp. TM1040 4077311 YP_614239.1 CDS TM1040_2245 NC_008044.1 2359730 2360392 R PFAM: glutathione S-transferase-like: (6.6e-18); KEGG: hch:HCH_03323 glutathione S-transferase, ev=3e-64, 53% identity; glutathione S-transferase complement(2359730..2360392) Ruegeria sp. TM1040 4077312 YP_614240.1 CDS TM1040_2246 NC_008044.1 2360446 2360919 R PFAM: protein of unknown function DUF1348: (4e-93); KEGG: nar:Saro_2764 protein of unknown function DUF1348, ev=6e-71, 80% identity; hypothetical protein complement(2360446..2360919) Ruegeria sp. TM1040 4077313 YP_614241.1 CDS TM1040_2247 NC_008044.1 2361048 2361980 D 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 2361048..2361980 Ruegeria sp. TM1040 4077314 YP_614242.1 CDS TM1040_2248 NC_008044.1 2361977 2362825 R 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 complement(2361977..2362825) Ruegeria sp. TM1040 4077315 YP_614243.1 CDS TM1040_2249 NC_008044.1 2362822 2364417 R catalyzes the formation of oxaloacetate from L-aspartate; L-aspartate oxidase complement(2362822..2364417) Ruegeria sp. TM1040 4077316 YP_614244.1 CDS TM1040_2250 NC_008044.1 2364425 2365480 R 3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate; quinolinate synthetase complement(2364425..2365480) Ruegeria sp. TM1040 4077317 YP_614245.1 CDS TM1040_2251 NC_008044.1 2365793 2366992 D KEGG: rsp:RSP_0200 ABC transporter, periplasmic binding protein, ev=1e-121, 56% identity; ABC transporter substrate-binding protein 2365793..2366992 Ruegeria sp. TM1040 4077318 YP_614246.1 CDS TM1040_2252 NC_008044.1 2367010 2368707 D KEGG: rsp:RSP_0201 ABC transporter, fused inner membrane subunits, ev=1e-169, 57% identity; ABC transporter inner membrane protein 2367010..2368707 Ruegeria sp. TM1040 4077319 YP_614247.1 CDS TM1040_2253 NC_008044.1 2368700 2369335 D 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 2368700..2369335 Ruegeria sp. TM1040 4077320 YP_614248.1 CDS TM1040_2254 NC_008044.1 2369508 2369942 R hypothetical protein complement(2369508..2369942) Ruegeria sp. TM1040 4077321 YP_614249.1 CDS TM1040_2255 NC_008044.1 2370043 2371710 R ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence; ABC transporter ATP-binding protein complement(2370043..2371710) Ruegeria sp. TM1040 4077322 YP_614250.1 CDS TM1040_2256 NC_008044.1 2371759 2372181 D hypothetical protein 2371759..2372181 Ruegeria sp. TM1040 4077323 YP_614251.1 CDS TM1040_2257 NC_008044.1 2372457 2372696 D hypothetical protein 2372457..2372696 Ruegeria sp. TM1040 4077324 YP_614252.1 CDS nadD NC_008044.1 2372850 2373452 D 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 2372850..2373452 Ruegeria sp. TM1040 4077325 YP_614253.1 CDS TM1040_2259 NC_008044.1 2373550 2375034 D 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 2373550..2375034 Ruegeria sp. TM1040 4077326 YP_614254.1 CDS TM1040_2260 NC_008044.1 2375180 2375602 R KEGG: sil:SPO0452 hypothetical protein, ev=3e-57, 79% identity; hypothetical protein complement(2375180..2375602) Ruegeria sp. TM1040 4077327 YP_614255.1 CDS lysK NC_008044.1 2375821 2377464 D 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 2375821..2377464 Ruegeria sp. TM1040 4077328 YP_614256.1 CDS TM1040_2262 NC_008044.1 2377716 2378129 D KEGG: sil:SPO0457 hypothetical protein, ev=1e-34, 57% identity; hypothetical protein 2377716..2378129 Ruegeria sp. TM1040 4077329 YP_614257.1 CDS TM1040_2263 NC_008044.1 2378251 2380536 D KEGG: sil:SPO0459 hypothetical protein, ev=0.0, 64% identity; hypothetical protein 2378251..2380536 Ruegeria sp. TM1040 4077330 YP_614258.1 CDS TM1040_2264 NC_008044.1 2380533 2381048 R 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 complement(2380533..2381048) Ruegeria sp. TM1040 4077331 YP_614259.1 CDS TM1040_2265 NC_008044.1 2381126 2381788 R KEGG: sil:SPO0460 hypothetical protein, ev=4e-17, 29% identity; hypothetical protein complement(2381126..2381788) Ruegeria sp. TM1040 4077332 YP_614260.1 CDS TM1040_2266 NC_008044.1 2381892 2382212 D PFAM: Antibiotic biosynthesis monooxygenase: (8.5e-05); KEGG: sil:SPO0462 antibiotic biosynthesis monooxygenase domain protein, ev=7e-41, 74% identity; antibiotic biosynthesis monooxygenase 2381892..2382212 Ruegeria sp. TM1040 4078450 YP_614261.1 CDS TM1040_2267 NC_008044.1 2382231 2382629 R KEGG: rsp:RSP_0683 hypothetical protein, ev=3e-14, 39% identity; hypothetical protein complement(2382231..2382629) Ruegeria sp. TM1040 4078451 YP_614262.1 CDS TM1040_2268 NC_008044.1 2382783 2383712 R PFAM: metal-dependent protein hydrolase: (1.5e-26); KEGG: atc:AGR_L_2056 MYG1 protein, ev=1e-110, 65% identity; metal-dependent protein hydrolase complement(2382783..2383712) Ruegeria sp. TM1040 4078452 YP_614263.1 CDS TM1040_2269 NC_008044.1 2383855 2384532 R 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 complement(2383855..2384532) Ruegeria sp. TM1040 4078453 YP_614264.1 CDS TM1040_2270 NC_008044.1 2384585 2385289 D 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 2384585..2385289 Ruegeria sp. TM1040 4078454 YP_614265.1 CDS TM1040_2271 NC_008044.1 2385286 2387814 D PFAM: protein of unknown function DUF214: (9.5e-14); KEGG: sil:SPO0433 ABC transporter, permease protein, ev=0.0, 69% identity; hypothetical protein 2385286..2387814 Ruegeria sp. TM1040 4078455 YP_614266.1 CDS TM1040_2272 NC_008044.1 2387829 2388293 R 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 complement(2387829..2388293) Ruegeria sp. TM1040 4078456 YP_614267.1 CDS TM1040_2273 NC_008044.1 2388397 2388966 D KEGG: sil:SPO0431 hypothetical protein, ev=5e-45, 48% identity; hypothetical protein 2388397..2388966 Ruegeria sp. TM1040 4078457 YP_614268.1 CDS TM1040_2274 NC_008044.1 2388963 2390147 D KEGG: jan:Jann_2342 hypothetical protein, ev=9e-64, 38% identity; hypothetical protein 2388963..2390147 Ruegeria sp. TM1040 4078458 YP_614269.1 CDS gltX NC_008044.1 2390226 2391551 R Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase complement(2390226..2391551) Ruegeria sp. TM1040 4078459 YP_614270.1 CDS TM1040_2276 NC_008044.1 2391780 2392718 D 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 2391780..2392718 Ruegeria sp. TM1040 4078460 YP_614271.1 CDS TM1040_2277 NC_008044.1 2392715 2394016 R 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 complement(2392715..2394016) Ruegeria sp. TM1040 4078461 YP_614272.1 CDS nadE NC_008044.1 2394154 2395815 R 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 complement(2394154..2395815) Ruegeria sp. TM1040 4078462 YP_614273.1 CDS TM1040_2279 NC_008044.1 2395984 2397486 D PFAM: MORN motif: (0.00013); KEGG: sil:SPO0425 MORN repeat protein, ev=0.0, 71% identity; hypothetical protein 2395984..2397486 Ruegeria sp. TM1040 4078463 YP_614274.1 CDS TM1040_2280 NC_008044.1 2397495 2398535 D hypothetical protein 2397495..2398535 Ruegeria sp. TM1040 4078464 YP_614275.1 CDS TM1040_2281 NC_008044.1 2398532 2400055 R PFAM: deoxyribodipyrimidine photolyase-related protein: (3.6e-63); KEGG: rsp:RSP_3077 hypothetical protein, ev=0.0, 68% identity; deoxyribodipyrimidine photolyase-like protein complement(2398532..2400055) Ruegeria sp. TM1040 4078465 YP_614276.1 CDS TM1040_2282 NC_008044.1 2400415 2401998 D catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis; 2-isopropylmalate synthase 2400415..2401998 Ruegeria sp. TM1040 4078466 YP_614277.1 CDS TM1040_2283 NC_008044.1 2402080 2403336 R KEGG: atc:AGR_C_231 transport protein, ev=2e-95, 46% identity; transporter complement(2402080..2403336) Ruegeria sp. TM1040 4078467 YP_614278.1 CDS TM1040_2284 NC_008044.1 2403547 2404638 D 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 2403547..2404638 Ruegeria sp. TM1040 4078468 YP_614279.1 CDS TM1040_2285 NC_008044.1 2404642 2406678 D 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 2404642..2406678 Ruegeria sp. TM1040 4078469 YP_614280.1 CDS TM1040_2286 NC_008044.1 2406682 2407326 D 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 2406682..2407326 Ruegeria sp. TM1040 4078470 YP_614281.1 CDS TM1040_2287 NC_008044.1 2407323 2407670 D 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 2407323..2407670 Ruegeria sp. TM1040 4078471 YP_614282.1 CDS TM1040_2288 NC_008044.1 2407667 2408398 D PFAM: Surfeit locus 1: (1e-06); KEGG: bja:blr0153 probable surfeit locus protein 1, ev=1e-41, 39% identity; Surfeit locus 1 2407667..2408398 Ruegeria sp. TM1040 4078472 YP_614283.1 CDS TM1040_2289 NC_008044.1 2408455 2408850 R 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 complement(2408455..2408850) Ruegeria sp. TM1040 4078473 YP_614284.1 CDS TM1040_2290 NC_008044.1 2408933 2409352 R PFAM: histidine triad (HIT) protein: (3.8e-42); KEGG: sil:SPO1386 HIT family protein, ev=2e-58, 83% identity; histidine triad (HIT) protein complement(2408933..2409352) Ruegeria sp. TM1040 4078474 YP_614285.1 CDS TM1040_2291 NC_008044.1 2409675 2411333 D 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 2409675..2411333 Ruegeria sp. TM1040 4078475 YP_614286.1 CDS TM1040_2292 NC_008044.1 2411475 2411969 D KEGG: sil:SPO1381 hypothetical protein, ev=2e-45, 55% identity; hypothetical protein 2411475..2411969 Ruegeria sp. TM1040 4078476 YP_614287.1 CDS TM1040_2293 NC_008044.1 2412068 2412541 R PFAM: GatB/Yqey: (6.9e-37); KEGG: sil:SPO1378 GatB/YqeY domain protein, ev=3e-63, 77% identity; hypothetical protein complement(2412068..2412541) Ruegeria sp. TM1040 4078477 YP_614288.1 CDS TM1040_2294 NC_008044.1 2412716 2413876 D 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 2412716..2413876 Ruegeria sp. TM1040 4078478 YP_614289.1 CDS TM1040_2295 NC_008044.1 2414270 2415799 D 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 2414270..2415799 Ruegeria sp. TM1040 4078479 YP_614290.1 CDS TM1040_2296 NC_008044.1 2415802 2416452 R 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 complement(2415802..2416452) Ruegeria sp. TM1040 4078480 YP_614291.1 CDS TM1040_2297 NC_008044.1 2416579 2417223 D 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 2416579..2417223 Ruegeria sp. TM1040 4078481 YP_614292.1 CDS TM1040_2298 NC_008044.1 2417308 2417556 D KEGG: sil:SPO1372 hypothetical protein, ev=3e-26, 68% identity; hypothetical protein 2417308..2417556 Ruegeria sp. TM1040 4078482 YP_614293.1 CDS TM1040_2299 NC_008044.1 2417642 2418838 D 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 2417642..2418838 Ruegeria sp. TM1040 4078483 YP_614294.1 CDS TM1040_2300 NC_008044.1 2418908 2420032 R PFAM: aminotransferase, class V: (0.00029); KEGG: sil:SPO1370 aminotransferase family protein, ev=1e-169, 79% identity; class V aminotransferase complement(2418908..2420032) Ruegeria sp. TM1040 4078484 YP_614295.1 CDS TM1040_2301 NC_008044.1 2420155 2420613 R 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 complement(2420155..2420613) Ruegeria sp. TM1040 4078485 YP_614296.1 CDS TM1040_2302 NC_008044.1 2420610 2421065 R PFAM: regulatory proteins, AsnC/Lrp: (7.6e-14); KEGG: sil:SPO1367 transcriptional regulator, AsnC family, ev=6e-52, 67% identity; AsnC family transcriptional regulator complement(2420610..2421065) Ruegeria sp. TM1040 4078486 YP_614297.1 CDS TM1040_2303 NC_008044.1 2421204 2422226 D 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 2421204..2422226 Ruegeria sp. TM1040 4078487 YP_614298.1 CDS TM1040_2304 NC_008044.1 2422378 2423277 D 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 2422378..2423277 Ruegeria sp. TM1040 4078488 YP_614299.1 CDS glmM NC_008044.1 2423398 2424741 R catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate; phosphoglucosamine mutase complement(2423398..2424741) Ruegeria sp. TM1040 4078295 YP_614300.1 CDS TM1040_2306 NC_008044.1 2424802 2425797 R 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 complement(2424802..2425797) Ruegeria sp. TM1040 4078296 YP_614301.1 CDS TM1040_2307 NC_008044.1 2425794 2426714 R TIGRFAM: Dihydroneopterin aldolase: (5.4e-07); KEGG: sil:SPO1362 dihydroneopterin aldolase, , ev=1e-130, 78% identity; dihydroneopterin aldolase complement(2425794..2426714) Ruegeria sp. TM1040 4078297 YP_614302.1 CDS TM1040_2308 NC_008044.1 2426867 2427511 R PFAM: cell wall hydrolase, SleB: (7.4e-36); KEGG: sil:SPO1360 hypothetical protein, ev=1e-62, 59% identity; cell wall hydrolase SleB complement(2426867..2427511) Ruegeria sp. TM1040 4078298 YP_614303.1 CDS TM1040_2309 NC_008044.1 2427681 2430245 R catalyzes the formation of phosphoenolpyruvate from pyruvate; pyruvate phosphate dikinase complement(2427681..2430245) Ruegeria sp. TM1040 4078299 YP_614304.1 CDS glyS NC_008044.1 2430406 2432469 R 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 complement(2430406..2432469) Ruegeria sp. TM1040 4078300 YP_614305.1 CDS TM1040_2311 NC_008044.1 2432547 2433074 R KEGG: rsp:RSP_1857 hypothetical protein, ev=2e-36, 48% identity; hypothetical protein complement(2432547..2433074) Ruegeria sp. TM1040 4078301 YP_614306.1 CDS glyQ NC_008044.1 2433097 2434047 R 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 complement(2433097..2434047) Ruegeria sp. TM1040 4078302 YP_614307.1 CDS TM1040_2313 NC_008044.1 2434344 2436134 D 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 2434344..2436134 Ruegeria sp. TM1040 4078303 YP_614308.1 CDS TM1040_2314 NC_008044.1 2436241 2436690 R 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 complement(2436241..2436690) Ruegeria sp. TM1040 4078304 YP_614309.1 CDS TM1040_2315 NC_008044.1 2436816 2437457 R 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 complement(2436816..2437457) Ruegeria sp. TM1040 4078305 YP_614310.1 CDS TM1040_2316 NC_008044.1 2437528 2438043 R PFAM: protein of unknown function DUF1178: (1.7e-53); KEGG: rsp:RSP_2387 hypothetical protein, ev=8e-45, 53% identity; hypothetical protein complement(2437528..2438043) Ruegeria sp. TM1040 4078306 YP_614311.1 CDS TM1040_2317 NC_008044.1 2438318 2439094 R KEGG: sil:SPO3054 hypothetical protein, ev=4e-74, 60% identity; hypothetical protein complement(2438318..2439094) Ruegeria sp. TM1040 4078307 YP_614312.1 CDS TM1040_2318 NC_008044.1 2439184 2439684 R PFAM: GCN5-related N-acetyltransferase: (7.4e-08); KEGG: sil:SPO3055 acetyltransferase, GNAT family, ev=9e-67, 75% identity; N-acetyltransferase GCN5 complement(2439184..2439684) Ruegeria sp. TM1040 4078308 YP_614313.1 CDS TM1040_2319 NC_008044.1 2439794 2440399 D KEGG: sil:SPO3056 hypothetical protein, ev=2e-89, 74% identity; hypothetical protein 2439794..2440399 Ruegeria sp. TM1040 4078309 YP_614314.1 CDS TM1040_2320 NC_008044.1 2440401 2441042 D PFAM: transferase hexapeptide repeat: (0.031); KEGG: sil:SPO3057 streptogramin acetyltransferase, , ev=4e-87, 68% identity; chloramphenicol O-acetyltransferase 2440401..2441042 Ruegeria sp. TM1040 4078310 YP_614315.1 CDS TM1040_2321 NC_008044.1 2441144 2442754 R 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 complement(2441144..2442754) Ruegeria sp. TM1040 4078311 YP_614316.1 CDS TM1040_2322 NC_008044.1 2443037 2443366 D hypothetical protein 2443037..2443366 Ruegeria sp. TM1040 4078312 YP_614317.1 CDS TM1040_2323 NC_008044.1 2443610 2444542 D KEGG: sma:SAV6152 hypothetical protein, ev=4e-13, 25% identity; hypothetical protein 2443610..2444542 Ruegeria sp. TM1040 4078313 YP_614318.1 CDS TM1040_2324 NC_008044.1 2444645 2445517 D Catalyzes the reversible phosphorolysis of 5'-deoxy-5'- methylthioadenosine (MTA) to adenine and 5-methylthio-D-ribose-1- phosphate; 5'-methylthioadenosine phosphorylase 2444645..2445517 Ruegeria sp. TM1040 4078314 YP_614319.1 CDS TM1040_2325 NC_008044.1 2445634 2446173 D catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis; adenine phosphoribosyltransferase 2445634..2446173 Ruegeria sp. TM1040 4078315 YP_614320.1 CDS TM1040_2326 NC_008044.1 2446388 2446870 D 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 2446388..2446870 Ruegeria sp. TM1040 4078316 YP_614321.1 CDS TM1040_2327 NC_008044.1 2446978 2448393 R PFAM: FAD linked oxidase-like: (1.1e-52); KEGG: sil:SPO3067 oxidoreductase, FAD-binding, ev=0.0, 70% identity; FAD linked oxidase-like protein complement(2446978..2448393) Ruegeria sp. TM1040 4078317 YP_614322.1 CDS TM1040_2328 NC_008044.1 2448461 2449051 R PFAM: GCN5-related N-acetyltransferase: (8.2e-11); KEGG: sil:SPO3069 ribosomal-protein-alanine acetyltransferase, , ev=2e-87, 78% identity; N-acetyltransferase GCN5 complement(2448461..2449051) Ruegeria sp. TM1040 4078318 YP_614323.1 CDS TM1040_2329 NC_008044.1 2449051 2450313 R PFAM: peptidase M16-like: (1.3e-48); KEGG: sil:SPO3070 peptidase, M16 family, ev=0.0, 78% identity; peptidase complement(2449051..2450313) Ruegeria sp. TM1040 4078319 YP_614324.1 CDS TM1040_2330 NC_008044.1 2450310 2451701 R catalyzes the formation of L-threonine from O-phospho-L-homoserine; threonine synthase complement(2450310..2451701) Ruegeria sp. TM1040 4078320 YP_614325.1 CDS TM1040_2331 NC_008044.1 2451716 2452378 R KEGG: sil:SPO3072 SURF1 family protein, ev=3e-65, 57% identity; SURF1 family protein complement(2451716..2452378) Ruegeria sp. TM1040 4078321 YP_614326.1 CDS TM1040_2332 NC_008044.1 2452530 2453345 R 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 complement(2452530..2453345) Ruegeria sp. TM1040 4078322 YP_614327.1 CDS TM1040_2333 NC_008044.1 2453371 2453958 R involved in the insertion of copper into subunit I of cytochrome C oxidase; cytochrome C oxidase assembly protein complement(2453371..2453958) Ruegeria sp. TM1040 4078323 YP_614328.1 CDS TM1040_2334 NC_008044.1 2453963 2454124 R KEGG: rsp:RSP_6021 hypothetical protein, ev=3e-07, 55% identity; hypothetical protein complement(2453963..2454124) Ruegeria sp. TM1040 4078324 YP_614329.1 CDS TM1040_2335 NC_008044.1 2454126 2455067 R converts protoheme IX and farnesyl diphosphate to heme O; protoheme IX farnesyltransferase complement(2454126..2455067) Ruegeria sp. TM1040 4078325 YP_614330.1 CDS TM1040_2336 NC_008044.1 2455186 2456100 R 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 complement(2455186..2456100) Ruegeria sp. TM1040 4078326 YP_614331.1 CDS TM1040_2337 NC_008044.1 2456281 2457702 D 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 2456281..2457702 Ruegeria sp. TM1040 4078327 YP_614332.1 CDS TM1040_2338 NC_008044.1 2458080 2459228 D 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 2458080..2459228 Ruegeria sp. TM1040 4078328 YP_614333.1 CDS TM1040_2339 NC_008044.1 2459369 2462050 D catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity; DNA topoisomerase I 2459369..2462050 Ruegeria sp. TM1040 4078329 YP_614334.1 CDS TM1040_2340 NC_008044.1 2462335 2463039 D 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 2462335..2463039 Ruegeria sp. TM1040 4078330 YP_614335.1 CDS TM1040_2341 NC_008044.1 2463043 2463669 D 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 2463043..2463669 Ruegeria sp. TM1040 4078331 YP_614336.1 CDS TM1040_2342 NC_008044.1 2463866 2464684 R PFAM: Lytic transglycosylase, catalytic: (1.4e-24); KEGG: sil:SPO3084 transglycosylase, Slt family, ev=4e-75, 55% identity; lytic transglycosylase, catalytic complement(2463866..2464684) Ruegeria sp. TM1040 4078332 YP_614337.1 CDS TM1040_2343 NC_008044.1 2465040 2465225 D KEGG: sil:SPO3085 hypothetical protein, ev=4e-11, 64% identity; hypothetical protein 2465040..2465225 Ruegeria sp. TM1040 4078333 YP_614338.1 CDS TM1040_2344 NC_008044.1 2465332 2465526 D KEGG: rsp:RSP_6025 hypothetical protein, ev=2e-07, 49% identity; hypothetical protein 2465332..2465526 Ruegeria sp. TM1040 4076463 YP_614339.1 CDS TM1040_2345 NC_008044.1 2465660 2466523 D PFAM: Flp pilus assembly CpaB: (6.2e-29); KEGG: sil:SPO3086 CpaB family protein, ev=1e-103, 66% identity; Flp pilus assembly CpaB 2465660..2466523 Ruegeria sp. TM1040 4076464 YP_614340.1 CDS TM1040_2346 NC_008044.1 2466653 2468146 D 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 2466653..2468146 Ruegeria sp. TM1040 4076465 YP_614341.1 CDS TM1040_2347 NC_008044.1 2468168 2468791 D PFAM: OmpA/MotB: (4.5e-19); KEGG: sil:SPO3088 OmpA family protein, ev=3e-63, 61% identity; OmpA/MotB protein 2468168..2468791 Ruegeria sp. TM1040 4076466 YP_614342.1 CDS TM1040_2348 NC_008044.1 2469041 2470285 D KEGG: sil:SPO3089 ATPase, , ev=1e-174, 72% identity; response regulator receiver protein 2469041..2470285 Ruegeria sp. TM1040 4076467 YP_614343.1 CDS TM1040_2349 NC_008044.1 2470318 2471775 D 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 2470318..2471775 Ruegeria sp. TM1040 4076468 YP_614344.1 CDS TM1040_2350 NC_008044.1 2471775 2472743 D 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 2471775..2472743 Ruegeria sp. TM1040 4076469 YP_614345.1 CDS TM1040_2351 NC_008044.1 2472754 2473725 D 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 2472754..2473725 Ruegeria sp. TM1040 4076470 YP_614346.1 CDS TM1040_2352 NC_008044.1 2473735 2474340 D 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 2473735..2474340 Ruegeria sp. TM1040 4076471 YP_614347.1 CDS TM1040_2353 NC_008044.1 2474374 2475225 D SMART: Tetratricopeptide region: (0.15); KEGG: sil:SPO3094 lipoprotein, , ev=1e-111, 70% identity; hypothetical protein 2474374..2475225 Ruegeria sp. TM1040 4076472 YP_614348.1 CDS TM1040_2354 NC_008044.1 2475241 2475738 D KEGG: sil:SPO3095 membrane protein, , ev=3e-39, 47% identity; hypothetical protein 2475241..2475738 Ruegeria sp. TM1040 4076473 YP_614349.1 CDS TM1040_2355 NC_008044.1 2475902 2477209 D KEGG: sil:SPO3096 hypothetical protein, ev=0.0, 86% identity; hypothetical protein 2475902..2477209 Ruegeria sp. TM1040 4076474 YP_614350.1 CDS TM1040_2356 NC_008044.1 2477322 2478224 R 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 complement(2477322..2478224) Ruegeria sp. TM1040 4076475 YP_614351.1 CDS TM1040_2357 NC_008044.1 2478269 2478574 R PFAM: Chorismate mutase: (2e-18); KEGG: sil:SPO3102 chorismate mutase family protein, ev=3e-29, 64% identity; chorismate mutase complement(2478269..2478574) Ruegeria sp. TM1040 4076476 YP_614352.1 CDS TM1040_2358 NC_008044.1 2478640 2480316 R catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate; formate--tetrahydrofolate ligase complement(2478640..2480316) Ruegeria sp. TM1040 4076477 YP_614353.1 CDS TM1040_2359 NC_008044.1 2480493 2481074 R PFAM: MOSC: (2.6e-07); KEGG: sil:SPO3104 MOSC domain protein, ev=4e-66, 62% identity; MOSC domain-containing protein complement(2480493..2481074) Ruegeria sp. TM1040 4076478 YP_614354.1 CDS TM1040_2360 NC_008044.1 2481123 2481845 R KEGG: rsp:RSP_0664 hypothetical protein, ev=1e-17, 35% identity; hypothetical protein complement(2481123..2481845) Ruegeria sp. TM1040 4076479 YP_614355.1 CDS TM1040_2361 NC_008044.1 2482013 2483926 R 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 complement(2482013..2483926) Ruegeria sp. TM1040 4076480 YP_614356.1 CDS TM1040_2362 NC_008044.1 2484016 2485308 R 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 complement(2484016..2485308) Ruegeria sp. TM1040 4076481 YP_614357.1 CDS TM1040_2363 NC_008044.1 2485299 2486150 R PFAM: Tetratricopeptide TPR_2: (0.0047); KEGG: sil:SPO3107 hypothetical protein, ev=2e-74, 56% identity; hypothetical protein complement(2485299..2486150) Ruegeria sp. TM1040 4076482 YP_614358.1 CDS TM1040_2364 NC_008044.1 2486156 2486659 R PFAM: OmpA/MotB: (1.3e-31); KEGG: jan:Jann_0976 OmpA/MotB, ev=1e-48, 59% identity; OmpA/MotB protein complement(2486156..2486659) Ruegeria sp. TM1040 4076483 YP_614359.1 CDS tolB NC_008044.1 2486763 2488088 R 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 complement(2486763..2488088) Ruegeria sp. TM1040 4076484 YP_614360.1 CDS TM1040_2366 NC_008044.1 2488085 2489236 R KEGG: sil:SPO3110 TonB domain protein, , ev=2e-95, 50% identity; TonB domain-containing protein complement(2488085..2489236) Ruegeria sp. TM1040 4076485 YP_614361.1 CDS TM1040_2367 NC_008044.1 2489250 2489738 R 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 complement(2489250..2489738) Ruegeria sp. TM1040 4076486 YP_614362.1 CDS TM1040_2368 NC_008044.1 2489742 2490437 R 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 complement(2489742..2490437) Ruegeria sp. TM1040 4076487 YP_614363.1 CDS TM1040_2369 NC_008044.1 2490552 2490938 R 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 complement(2490552..2490938) Ruegeria sp. TM1040 4076488 YP_614364.1 CDS TM1040_2370 NC_008044.1 2490935 2491600 R KEGG: sil:SPO3114 hypothetical protein, ev=4e-78, 70% identity; hypothetical protein complement(2490935..2491600) Ruegeria sp. TM1040 4076489 YP_614365.1 CDS ruvB NC_008044.1 2491837 2492856 R 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 complement(2491837..2492856) Ruegeria sp. TM1040 4076490 YP_614366.1 CDS ruvA NC_008044.1 2492868 2493557 R plays an essential role in ATP-dependent branch migration of the Holliday junction; Holliday junction DNA helicase RuvA complement(2492868..2493557) Ruegeria sp. TM1040 4076491 YP_614367.1 CDS ruvC NC_008044.1 2493554 2494120 R 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 complement(2493554..2494120) Ruegeria sp. TM1040 4076492 YP_614368.1 CDS TM1040_2374 NC_008044.1 2494425 2494643 D PFAM: protein of unknown function DUF1127: (3.1e-06); KEGG: sil:SPO3118 hypothetical protein, ev=1e-14, 59% identity; hypothetical protein 2494425..2494643 Ruegeria sp. TM1040 4076493 YP_614369.1 CDS TM1040_2375 NC_008044.1 2494796 2495056 R KEGG: sil:SPO3119 hypothetical protein, ev=5e-13, 46% identity; hypothetical protein complement(2494796..2495056) Ruegeria sp. TM1040 4076494 YP_614370.1 CDS TM1040_2376 NC_008044.1 2495256 2496125 R 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 complement(2495256..2496125) Ruegeria sp. TM1040 4076495 YP_614371.1 CDS TM1040_2377 NC_008044.1 2496237 2497472 R PFAM: major facilitator superfamily MFS_1: (3.5e-09); KEGG: sil:SPO3122 membrane protein, , ev=0.0, 79% identity; major facilitator superfamily transporter complement(2496237..2497472) Ruegeria sp. TM1040 4076496 YP_614372.1 CDS TM1040_2378 NC_008044.1 2497575 2499782 R binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity; primosome assembly protein PriA complement(2497575..2499782) Ruegeria sp. TM1040 4076497 YP_614373.1 CDS TM1040_2379 NC_008044.1 2499963 2500616 D similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity; translaldolase 2499963..2500616 Ruegeria sp. TM1040 4076498 YP_614374.1 CDS TM1040_2380 NC_008044.1 2500799 2501512 D KEGG: sil:SPO3129 hypothetical protein, ev=7e-80, 65% identity; hypothetical protein 2500799..2501512 Ruegeria sp. TM1040 4076499 YP_614375.1 CDS xerC NC_008044.1 2501509 2502444 D 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 2501509..2502444 Ruegeria sp. TM1040 4076500 YP_614376.1 CDS TM1040_2382 NC_008044.1 2502569 2503261 D PFAM: CDP-alcohol phosphatidyltransferase: (0.0088); KEGG: sil:SPO3131 phosphatidylcholine synthase, ev=1e-102, 76% identity; CDP-diacylglycerol-choline O-phosphatidyltransferase 2502569..2503261 Ruegeria sp. TM1040 4076501 YP_614377.1 CDS TM1040_2383 NC_008044.1 2503459 2503764 D hypothetical protein 2503459..2503764 Ruegeria sp. TM1040 4076709 YP_614378.1 CDS truA NC_008044.1 2503881 2504660 R mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability; tRNA pseudouridine synthase A complement(2503881..2504660) Ruegeria sp. TM1040 4076710 YP_614379.1 CDS TM1040_2385 NC_008044.1 2504863 2506260 D PFAM: protein of unknown function DUF463, YcjX-like protein: (3.7e-130); KEGG: sil:SPO3142 hypothetical protein, ev=0.0, 72% identity; hypothetical protein 2504863..2506260 Ruegeria sp. TM1040 4076711 YP_614380.1 CDS TM1040_2386 NC_008044.1 2506257 2506721 D PFAM: GCN5-related N-acetyltransferase: (6.6e-13); KEGG: sil:SPO3141 acetyltransferase, GNAT family, ev=3e-38, 53% identity; N-acetyltransferase GCN5 2506257..2506721 Ruegeria sp. TM1040 4076712 YP_614381.1 CDS TM1040_2387 NC_008044.1 2506718 2507698 D KEGG: sil:SPO3140 conserved hypothetical protein TIGR01620, ev=5e-94, 55% identity; hypothetical protein 2506718..2507698 Ruegeria sp. TM1040 4076713 YP_614382.1 CDS TM1040_2388 NC_008044.1 2507721 2508134 R KEGG: sil:SPO3139 hypothetical protein, ev=2e-41, 60% identity; hypothetical protein complement(2507721..2508134) Ruegeria sp. TM1040 4076714 YP_614383.1 CDS ileS NC_008044.1 2508425 2511349 D 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 2508425..2511349 Ruegeria sp. TM1040 4076715 YP_614384.1 CDS TM1040_2390 NC_008044.1 2511432 2511881 R hypothetical protein complement(2511432..2511881) Ruegeria sp. TM1040 4076716 YP_614385.1 CDS TM1040_2391 NC_008044.1 2512654 2515503 R acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine; glycine dehydrogenase complement(2512654..2515503) Ruegeria sp. TM1040 4076717 YP_614386.1 CDS TM1040_2392 NC_008044.1 2515630 2515989 R 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 complement(2515630..2515989) Ruegeria sp. TM1040 4076718 YP_614387.1 CDS TM1040_2393 NC_008044.1 2516031 2517155 R 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 complement(2516031..2517155) Ruegeria sp. TM1040 4076719 YP_614388.1 CDS TM1040_2394 NC_008044.1 2517618 2518607 D 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 2517618..2518607 Ruegeria sp. TM1040 4076720 YP_614389.1 CDS TM1040_2395 NC_008044.1 2518778 2520610 D PFAM: surface antigen (D15): (4.1e-35); KEGG: sil:SPO0868 outer membrane protein, OMP85 family, ev=1e-170, 51% identity; surface antigen (D15) 2518778..2520610 Ruegeria sp. TM1040 4076721 YP_614390.1 CDS TM1040_2396 NC_008044.1 2520607 2524614 D PFAM: protein of unknown function DUF490: (3e-39); KEGG: sil:SPO0867 hypothetical protein, ev=0.0, 43% identity; hypothetical protein 2520607..2524614 Ruegeria sp. TM1040 4076722 YP_614391.1 CDS TM1040_2397 NC_008044.1 2524618 2525616 D 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 2524618..2525616 Ruegeria sp. TM1040 4076723 YP_614392.1 CDS TM1040_2398 NC_008044.1 2525684 2526406 R 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 complement(2525684..2526406) Ruegeria sp. TM1040 4076724 YP_614393.1 CDS TM1040_2399 NC_008044.1 2526578 2528044 D KEGG: sil:SPO0850 membrane protein, , ev=1e-137, 50% identity; hypothetical protein 2526578..2528044 Ruegeria sp. TM1040 4076725 YP_614394.1 CDS TM1040_2400 NC_008044.1 2528233 2534685 D 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 2528233..2534685 Ruegeria sp. TM1040 4076726 YP_614395.1 CDS TM1040_2401 NC_008044.1 2534689 2535711 D 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 2534689..2535711 Ruegeria sp. TM1040 4076727 YP_614396.1 CDS TM1040_2402 NC_008044.1 2535708 2540267 D 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 2535708..2540267 Ruegeria sp. TM1040 4076728 YP_614397.1 CDS TM1040_2403 NC_008044.1 2540264 2540974 D PFAM: 4'-phosphopantetheinyl transferase: (2.9e-07); KEGG: sil:SPO0846 phosphopantetheinyl transferase PptA, , ev=1e-44, 46% identity; 4'-phosphopantetheinyl transferase 2540264..2540974 Ruegeria sp. TM1040 4076729 YP_614398.1 CDS TM1040_2404 NC_008044.1 2540971 2541936 D KEGG: sil:SPO0845 hypothetical protein, ev=6e-76, 50% identity; hypothetical protein 2540971..2541936 Ruegeria sp. TM1040 4076730 YP_614399.1 CDS TM1040_2405 NC_008044.1 2541933 2544470 D KEGG: sil:SPO0844 hypothetical protein, ev=0.0, 53% identity; hypothetical protein 2541933..2544470 Ruegeria sp. TM1040 4076731 YP_614400.1 CDS TM1040_2406 NC_008044.1 2544467 2545309 D 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 2544467..2545309 Ruegeria sp. TM1040 4076732 YP_614401.1 CDS TM1040_2407 NC_008044.1 2545320 2546534 R 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 complement(2545320..2546534) Ruegeria sp. TM1040 4076733 YP_614402.1 CDS TM1040_2408 NC_008044.1 2546676 2548091 D PFAM: polysaccharide biosynthesis protein: (4e-16); KEGG: sil:SPO0841 polysaccharide biosynthesis protein, ev=1e-121, 48% identity; polysaccharide biosynthesis protein 2546676..2548091 Ruegeria sp. TM1040 4076734 YP_614403.1 CDS TM1040_2409 NC_008044.1 2548100 2549374 R PFAM: lipopolysaccharide biosynthesis: (0.013); KEGG: sil:SPO0840 chain length determinant protein, , ev=1e-104, 49% identity; lipopolysaccharide biosynthesis protein complement(2548100..2549374) Ruegeria sp. TM1040 4076735 YP_614404.1 CDS TM1040_2410 NC_008044.1 2549408 2550409 R KEGG: sil:SPO0839 exopolysaccharide biosynthesis domain protein, ev=2e-63, 44% identity; exopolysaccharide biosynthesis domain-containing protein complement(2549408..2550409) Ruegeria sp. TM1040 4076736 YP_614405.1 CDS TM1040_2411 NC_008044.1 2550750 2551463 R PFAM: sugar transferase: (3.1e-66); KEGG: sil:SPO0838 bacterial sugar transferase, ev=2e-63, 58% identity; UDP-phosphate galactosephosphotransferase complement(2550750..2551463) Ruegeria sp. TM1040 4076737 YP_614406.1 CDS TM1040_2412 NC_008044.1 2551834 2552994 R 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 complement(2551834..2552994) Ruegeria sp. TM1040 4076738 YP_614407.1 CDS TM1040_2413 NC_008044.1 2553324 2554130 D KEGG: sil:SPO0785 2-dehydro-3-deoxygalactonokinase, , ev=8e-27, 31% identity; 2-dehydro-3-deoxygalactonokinase 2553324..2554130 Ruegeria sp. TM1040 4076739 YP_614408.1 CDS TM1040_2414 NC_008044.1 2554164 2554964 R KEGG: sil:SPO0581 hypothetical protein, ev=6e-64, 50% identity; hypothetical protein complement(2554164..2554964) Ruegeria sp. TM1040 4076740 YP_614409.1 CDS TM1040_2415 NC_008044.1 2555077 2556198 R PFAM: RNA methylase: (6.3e-33); KEGG: sil:SPOA0322 hypothetical protein, ev=1e-127, 62% identity; RNA methylase complement(2555077..2556198) Ruegeria sp. TM1040 4076741 YP_614410.1 CDS TM1040_2416 NC_008044.1 2556474 2558207 D 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 2556474..2558207 Ruegeria sp. TM1040 4076742 YP_614411.1 CDS TM1040_2417 NC_008044.1 2558405 2559481 D 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 2558405..2559481 Ruegeria sp. TM1040 4076743 YP_614412.1 CDS TM1040_2418 NC_008044.1 2559491 2560564 D 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 2559491..2560564 Ruegeria sp. TM1040 4076744 YP_614413.1 CDS TM1040_2419 NC_008044.1 2560570 2561433 D 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 2560570..2561433 Ruegeria sp. TM1040 4076745 YP_614414.1 CDS TM1040_2420 NC_008044.1 2561445 2562242 D 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 2561445..2562242 Ruegeria sp. TM1040 4076746 YP_614415.1 CDS TM1040_2421 NC_008044.1 2562244 2562522 D KEGG: sil:SPO0613 hypothetical protein, ev=2e-45, 89% identity; hypothetical protein 2562244..2562522 Ruegeria sp. TM1040 4076747 YP_614416.1 CDS TM1040_2422 NC_008044.1 2562766 2563215 D PFAM: Penicillinase repressor: (1.4e-28); KEGG: sil:SPO0614 transcriptional regulator, , ev=6e-52, 80% identity; CopY family transcriptional regulator 2562766..2563215 Ruegeria sp. TM1040 4076904 YP_614417.1 CDS TM1040_2423 NC_008044.1 2563205 2564347 D PFAM: peptidase M56, BlaR1: (5.2e-08); KEGG: sil:SPO0615 hypothetical protein, ev=1e-104, 52% identity; peptidase M56, BlaR1 2563205..2564347 Ruegeria sp. TM1040 4076905 YP_614418.1 CDS TM1040_2424 NC_008044.1 2564427 2565302 R converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA; 3-hydroxybutyryl-CoA dehydrogenase complement(2564427..2565302) Ruegeria sp. TM1040 4076906 YP_614419.1 CDS TM1040_2425 NC_008044.1 2565459 2566295 D KEGG: sil:SPO0718 hypothetical protein, ev=1e-64, 49% identity; hypothetical protein 2565459..2566295 Ruegeria sp. TM1040 4076907 YP_614420.1 CDS TM1040_2426 NC_008044.1 2566366 2567295 R 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 complement(2566366..2567295) Ruegeria sp. TM1040 4076908 YP_614421.1 CDS TM1040_2427 NC_008044.1 2567295 2568053 R 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 complement(2567295..2568053) Ruegeria sp. TM1040 4076909 YP_614422.1 CDS TM1040_2428 NC_008044.1 2568362 2568934 R 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 complement(2568362..2568934) Ruegeria sp. TM1040 4076910 YP_614423.1 CDS TM1040_2429 NC_008044.1 2568936 2569139 R KEGG: sil:SPO0723 hypothetical protein, ev=2e-13, 57% identity; hypothetical protein complement(2568936..2569139) Ruegeria sp. TM1040 4076911 YP_614424.1 CDS TM1040_2430 NC_008044.1 2569211 2570041 R 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 complement(2569211..2570041) Ruegeria sp. TM1040 4076912 YP_614425.1 CDS TM1040_2431 NC_008044.1 2570072 2570755 R 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 complement(2570072..2570755) Ruegeria sp. TM1040 4076913 YP_614426.1 CDS TM1040_2432 NC_008044.1 2571061 2573409 D decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling; DNA topoisomerase IV subunit A 2571061..2573409 Ruegeria sp. TM1040 4076914 YP_614427.1 CDS TM1040_2433 NC_008044.1 2573544 2574128 D KEGG: sil:SPO0727 hypothetical protein, ev=6e-59, 61% identity; hypothetical protein 2573544..2574128 Ruegeria sp. TM1040 4076915 YP_614428.1 CDS TM1040_2434 NC_008044.1 2574242 2575417 D 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 2574242..2575417 Ruegeria sp. TM1040 4076916 YP_614429.1 CDS TM1040_2435 NC_008044.1 2576659 2577612 R KEGG: sil:SPO0716 hypothetical protein, ev=1e-131, 76% identity; hypothetical protein complement(2576659..2577612) Ruegeria sp. TM1040 4076917 YP_614430.1 CDS TM1040_2436 NC_008044.1 2577596 2577865 R 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 complement(2577596..2577865) Ruegeria sp. TM1040 4076918 YP_614431.1 CDS TM1040_2437 NC_008044.1 2577869 2578273 R 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 complement(2577869..2578273) Ruegeria sp. TM1040 4076919 YP_614432.1 CDS TM1040_2438 NC_008044.1 2578283 2579185 R PFAM: Uncharacterised P-loop ATPase protein UPF0042: (6e-80); KEGG: sil:SPO0713 ATPase, , ev=1e-94, 63% identity; hypothetical protein complement(2578283..2579185) Ruegeria sp. TM1040 4076920 YP_614433.1 CDS TM1040_2439 NC_008044.1 2579157 2579645 R KEGG: rsp:RSP_1683 kinase/phosphatase, ev=3e-33, 56% identity; Hpr(Ser) kinase/phosphatase complement(2579157..2579645) Ruegeria sp. TM1040 4076921 YP_614434.1 CDS TM1040_2440 NC_008044.1 2579623 2581356 R 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 complement(2579623..2581356) Ruegeria sp. TM1040 4076922 YP_614435.1 CDS TM1040_2441 NC_008044.1 2581396 2582097 R 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 complement(2581396..2582097) Ruegeria sp. TM1040 4076923 YP_614436.1 CDS TM1040_2442 NC_008044.1 2582496 2584094 D PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP; phosphoenolpyruvate carboxykinase 2582496..2584094 Ruegeria sp. TM1040 4076924 YP_614437.1 CDS TM1040_2443 NC_008044.1 2584215 2584895 R 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 complement(2584215..2584895) Ruegeria sp. TM1040 4076925 YP_614438.1 CDS TM1040_2444 NC_008044.1 2584992 2586695 R 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 complement(2584992..2586695) Ruegeria sp. TM1040 4076926 YP_614439.1 CDS TM1040_2445 NC_008044.1 2586837 2587604 D 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 2586837..2587604 Ruegeria sp. TM1040 4076927 YP_614440.1 CDS TM1040_2446 NC_008044.1 2587609 2588523 D 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 2587609..2588523 Ruegeria sp. TM1040 4076928 YP_614441.1 CDS TM1040_2447 NC_008044.1 2588565 2589110 R 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 complement(2588565..2589110) Ruegeria sp. TM1040 4076929 YP_614442.1 CDS TM1040_2448 NC_008044.1 2589284 2589949 R PFAM: OmpA/MotB: (2e-26); KEGG: sil:SPO3576 OmpA domain protein, ev=2e-67, 60% identity; OmpA/MotB protein complement(2589284..2589949) Ruegeria sp. TM1040 4076930 YP_614443.1 CDS TM1040_2449 NC_008044.1 2590138 2590827 R 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 complement(2590138..2590827) Ruegeria sp. TM1040 4076931 YP_614444.1 CDS TM1040_2450 NC_008044.1 2591174 2592025 R 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 complement(2591174..2592025) Ruegeria sp. TM1040 4076932 YP_614445.1 CDS TM1040_2451 NC_008044.1 2592128 2592871 D 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 2592128..2592871 Ruegeria sp. TM1040 4076933 YP_614446.1 CDS TM1040_2452 NC_008044.1 2592868 2593860 D PFAM: PfkB: (7.2e-41); KEGG: sil:SPO3582 kinase, PfkB family, ev=1e-142, 79% identity; PfkB protein 2592868..2593860 Ruegeria sp. TM1040 4076934 YP_614447.1 CDS TM1040_2453 NC_008044.1 2594208 2596574 D 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 2594208..2596574 Ruegeria sp. TM1040 4076935 YP_614448.1 CDS TM1040_2454 NC_008044.1 2596656 2597144 R PFAM: regulatory protein, MarR: (5.6e-17); KEGG: sil:SPO3583 transcriptional regulator PecS, ev=1e-49, 62% identity; MarR family transcriptional regulator complement(2596656..2597144) Ruegeria sp. TM1040 4076936 YP_614449.1 CDS TM1040_2455 NC_008044.1 2597317 2598135 D 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 2597317..2598135 Ruegeria sp. TM1040 4076937 YP_614450.1 CDS TM1040_2456 NC_008044.1 2598178 2598633 R hypothetical protein complement(2598178..2598633) Ruegeria sp. TM1040 4076938 YP_614451.1 CDS TM1040_2457 NC_008044.1 2598701 2599207 R PFAM: NUDIX hydrolase: (1.6e-27); KEGG: sil:SPO3585 hydrolase, NUDIX family, NudH subfamily, ev=9e-62, 67% identity; NUDIX hydrolase complement(2598701..2599207) Ruegeria sp. TM1040 4076939 YP_614452.1 CDS TM1040_2458 NC_008044.1 2599378 2601405 D 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 2599378..2601405 Ruegeria sp. TM1040 4076940 YP_614453.1 CDS TM1040_2459 NC_008044.1 2601478 2602539 R PFAM: 2-nitropropane dioxygenase, NPD: (1.8e-68); KEGG: nar:Saro_1176 2-nitropropane dioxygenase, NPD, ev=2e-96, 56% identity; 2-nitropropane dioxygenase complement(2601478..2602539) Ruegeria sp. TM1040 4076941 YP_614454.1 CDS TM1040_2460 NC_008044.1 2602719 2603624 R 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 complement(2602719..2603624) Ruegeria sp. TM1040 4076942 YP_614455.1 CDS TM1040_2461 NC_008044.1 2603833 2604165 D PFAM: NIPSNAP: (2.3e-29); KEGG: sil:SPO3589 hypothetical protein, ev=7e-44, 78% identity; NIPSNAP domain-containing protein 2603833..2604165 Ruegeria sp. TM1040 4076826 YP_614456.1 CDS TM1040_2462 NC_008044.1 2604162 2604518 D PFAM: Antibiotic biosynthesis monooxygenase: (5.8e-14); KEGG: sil:SPO3588 hypothetical protein, ev=1e-39, 71% identity; antibiotic biosynthesis monooxygenase 2604162..2604518 Ruegeria sp. TM1040 4076827 YP_614457.1 CDS TM1040_2463 NC_008044.1 2604785 2605372 D 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 2604785..2605372 Ruegeria sp. TM1040 4076828 YP_614458.1 CDS TM1040_2464 NC_008044.1 2605380 2606438 R PFAM: OmpA/MotB: (1.8e-24); KEGG: sil:SPO3756 OmpA domain protein, ev=5e-53, 39% identity; OmpA/MotB protein complement(2605380..2606438) Ruegeria sp. TM1040 4076829 YP_614459.1 CDS TM1040_2465 NC_008044.1 2606459 2607031 R 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 complement(2606459..2607031) Ruegeria sp. TM1040 4076830 YP_614460.1 CDS TM1040_2466 NC_008044.1 2607061 2607786 R PFAM: GCN5-related N-acetyltransferase: (1.3e-12); KEGG: sil:SPO3758 acetyltransferase, GNAT family, ev=1e-73, 57% identity; N-acetyltransferase GCN5 complement(2607061..2607786) Ruegeria sp. TM1040 4076831 YP_614461.1 CDS TM1040_2467 NC_008044.1 2607783 2608505 R 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 complement(2607783..2608505) Ruegeria sp. TM1040 4076832 YP_614462.1 CDS TM1040_2468 NC_008044.1 2608608 2609324 D Regulatory factor involved in maltose metabolism; sugar fermentation stimulation protein A 2608608..2609324 Ruegeria sp. TM1040 4076833 YP_614463.1 CDS TM1040_2469 NC_008044.1 2609508 2610323 D 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 2609508..2610323 Ruegeria sp. TM1040 4076834 YP_614464.1 CDS TM1040_2470 NC_008044.1 2610478 2611035 R PFAM: conserved hypothetical protein 95: (9.1e-67); KEGG: sil:SPO3738 methyltransferase, , ev=7e-67, 69% identity; hypothetical protein complement(2610478..2611035) Ruegeria sp. TM1040 4076835 YP_614465.1 CDS TM1040_2471 NC_008044.1 2611032 2612243 R 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 complement(2611032..2612243) Ruegeria sp. TM1040 4076836 YP_614466.1 CDS TM1040_2472 NC_008044.1 2612366 2612851 D PFAM: Redoxin: (1.7e-46); KEGG: rsp:RSP_0899 AhpC/TSA family protein, ev=1e-65, 73% identity; thiol peroxidase 2612366..2612851 Ruegeria sp. TM1040 4076837 YP_614467.1 CDS TM1040_2473 NC_008044.1 2612901 2613770 D KEGG: mag:amb1972 hypothetical protein, ev=8e-13, 23% identity; hypothetical protein 2612901..2613770 Ruegeria sp. TM1040 4076838 YP_614468.1 CDS phhB NC_008044.1 2613915 2614211 R 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 complement(2613915..2614211) Ruegeria sp. TM1040 4076839 YP_614469.1 CDS TM1040_2475 NC_008044.1 2614208 2615395 R PFAM: protein of unknown function DUF482: (6.7e-195); KEGG: sil:SPO3732 hypothetical protein, ev=0.0, 77% identity; hypothetical protein complement(2614208..2615395) Ruegeria sp. TM1040 4076840 YP_614470.1 CDS TM1040_2476 NC_008044.1 2615443 2616219 R PFAM: glycerophosphoryl diester phosphodiesterase: (1.4e-17); KEGG: sil:SPO3731 glycerophosphoryl diester phosphodiesterase, , ev=5e-80, 60% identity; glycerophosphoryl diester phosphodiesterase complement(2615443..2616219) Ruegeria sp. TM1040 4076841 YP_614471.1 CDS TM1040_2477 NC_008044.1 2616228 2616689 R PFAM: Endoribonuclease L-PSP: (4.2e-17); KEGG: sil:SPO3730 endoribonuclease L-PSP family protein, ev=4e-59, 75% identity; endoribonuclease L-PSP complement(2616228..2616689) Ruegeria sp. TM1040 4076842 YP_614472.1 CDS TM1040_2478 NC_008044.1 2616801 2618123 R 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 complement(2616801..2618123) Ruegeria sp. TM1040 4076843 YP_614473.1 CDS TM1040_2479 NC_008044.1 2618120 2619883 R 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 complement(2618120..2619883) Ruegeria sp. TM1040 4076844 YP_614474.1 CDS TM1040_2480 NC_008044.1 2620035 2620835 D PFAM: VacJ-like lipoprotein: (3.9e-54); KEGG: sil:SPO3727 VacJ lipoprotein, , ev=1e-76, 57% identity; VacJ-like lipoprotein 2620035..2620835 Ruegeria sp. TM1040 4076845 YP_614475.1 CDS TM1040_2481 NC_008044.1 2620839 2621429 D PFAM: toluene tolerance: (6.8e-14); KEGG: sil:SPO3726 toluene tolerance family protein, ev=9e-57, 58% identity; toluene tolerance 2620839..2621429 Ruegeria sp. TM1040 4076846 YP_614476.1 CDS smpB NC_008044.1 2621561 2622037 R 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 complement(2621561..2622037) Ruegeria sp. TM1040 4076847 YP_614477.1 CDS TM1040_2483 NC_008044.1 2622133 2622999 R PFAM: protein of unknown function DUF6, transmembrane: (1.5e-05); KEGG: sil:SPO0261 membrane protein, , ev=4e-86, 58% identity; hypothetical protein complement(2622133..2622999) Ruegeria sp. TM1040 4076848 YP_614478.1 CDS TM1040_2484 NC_008044.1 2623072 2623635 R 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 complement(2623072..2623635) Ruegeria sp. TM1040 4076849 YP_614479.1 CDS TM1040_2485 NC_008044.1 2623777 2624955 D 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 2623777..2624955 Ruegeria sp. TM1040 4076850 YP_614480.1 CDS TM1040_2486 NC_008044.1 2625094 2626938 D catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis; dihydroxy-acid dehydratase 2625094..2626938 Ruegeria sp. TM1040 4076851 YP_614481.1 CDS TM1040_2487 NC_008044.1 2627160 2627978 R KEGG: sil:SPO3318 hypothetical protein, ev=1e-138, 83% identity; hypothetical protein complement(2627160..2627978) Ruegeria sp. TM1040 4076852 YP_614482.1 CDS TM1040_2488 NC_008044.1 2628115 2629692 D PFAM: glycosyl transferase, family 14: (1.1e-05); KEGG: sil:SPO3319 EpsK domain protein, ev=0.0, 75% identity; glycosyl transferase family protein 2628115..2629692 Ruegeria sp. TM1040 4076853 YP_614483.1 CDS TM1040_2489 NC_008044.1 2629773 2630507 R KEGG: mag:amb2748 hypothetical protein, ev=2e-45, 41% identity; hypothetical protein complement(2629773..2630507) Ruegeria sp. TM1040 4076854 YP_614484.1 CDS TM1040_2490 NC_008044.1 2630666 2631304 R PFAM: protein of unknown function DUF1523: (1.1e-18); KEGG: sil:SPO3320 hypothetical protein, ev=1e-84, 68% identity; hypothetical protein complement(2630666..2631304) Ruegeria sp. TM1040 4076855 YP_614485.1 CDS TM1040_2491 NC_008044.1 2631472 2632680 R PFAM: creatinase: (1.9e-60) peptidase M24: (1.3e-53); KEGG: sil:SPO3327 creatinase, ev=0.0, 83% identity; creatinase complement(2631472..2632680) Ruegeria sp. TM1040 4076856 YP_614486.1 CDS TM1040_2492 NC_008044.1 2632860 2633645 R KEGG: rsp:RSP_1010 possible esterase/lipase/thioesterase, ev=4e-74, 56% identity; esterase/lipase/thioesterase complement(2632860..2633645) Ruegeria sp. TM1040 4076857 YP_614487.1 CDS TM1040_2493 NC_008044.1 2633749 2635221 D 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 2633749..2635221 Ruegeria sp. TM1040 4076858 YP_614488.1 CDS TM1040_2494 NC_008044.1 2635245 2635676 R PFAM: globin: (0.00031); KEGG: sil:SPO3329 globin domain protein, ev=3e-18, 40% identity; globin complement(2635245..2635676) Ruegeria sp. TM1040 4076859 YP_614489.1 CDS TM1040_2495 NC_008044.1 2635844 2638015 D KEGG: rsp:RSP_1753 hypothetical protein, ev=0.0, 59% identity; hypothetical protein 2635844..2638015 Ruegeria sp. TM1040 4076860 YP_614490.1 CDS TM1040_2496 NC_008044.1 2638410 2639303 D PFAM: protein of unknown function DUF6, transmembrane: (1.2e-07); KEGG: vch:VCA1010 hypothetical protein, ev=8e-66, 46% identity; hypothetical protein 2638410..2639303 Ruegeria sp. TM1040 4076861 YP_614491.1 CDS TM1040_2497 NC_008044.1 2639283 2639888 R PFAM: regulatory protein, TetR: (1.5e-15); KEGG: mtc:MT1047 transcriptional regulator, TetR family, ev=7e-10, 43% identity; TetR family transcriptional regulator complement(2639283..2639888) Ruegeria sp. TM1040 4076862 YP_614492.1 CDS TM1040_2498 NC_008044.1 2640025 2640492 R 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 complement(2640025..2640492) Ruegeria sp. TM1040 4076863 YP_614493.1 CDS TM1040_2499 NC_008044.1 2640633 2641487 R 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 complement(2640633..2641487) Ruegeria sp. TM1040 4076864 YP_614494.1 CDS TM1040_2500 NC_008044.1 2641580 2642899 R 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 complement(2641580..2642899) Ruegeria sp. TM1040 4076502 YP_614495.1 CDS TM1040_2501 NC_008044.1 2642904 2643995 R 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 complement(2642904..2643995) Ruegeria sp. TM1040 4076503 YP_614496.1 CDS TM1040_2502 NC_008044.1 2644053 2645501 R PFAM: FAD linked oxidase-like: (2.7e-68); KEGG: sil:SPO3478 glycolate oxidase, GlcD subunit, ev=0.0, 86% identity; D-lactate dehydrogenase complement(2644053..2645501) Ruegeria sp. TM1040 4076504 YP_614497.1 CDS TM1040_2503 NC_008044.1 2645583 2646305 D PFAM: protein of unknown function DUF599: (7.3e-28); KEGG: sil:SPO3477 hypothetical protein, ev=4e-84, 64% identity; hypothetical protein 2645583..2646305 Ruegeria sp. TM1040 4076505 YP_614498.1 CDS TM1040_2504 NC_008044.1 2646341 2646700 D KEGG: sil:SPO3476 hypothetical protein, ev=3e-39, 67% identity; hypothetical protein 2646341..2646700 Ruegeria sp. TM1040 4076506 YP_614499.1 CDS TM1040_2505 NC_008044.1 2646706 2647176 R 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 complement(2646706..2647176) Ruegeria sp. TM1040 4076507 YP_614500.1 CDS TM1040_2506 NC_008044.1 2647306 2647665 R PFAM: Iojap-related protein: (5.9e-34); KEGG: sil:SPO0219 iojap-related protein, ev=1e-45, 73% identity; Iojap-related protein complement(2647306..2647665) Ruegeria sp. TM1040 4076508 YP_614501.1 CDS TM1040_2507 NC_008044.1 2647796 2649223 R 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 complement(2647796..2649223) Ruegeria sp. TM1040 4076509 YP_614502.1 CDS TM1040_2508 NC_008044.1 2649508 2650911 D dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; isopropylmalate isomerase large subunit 2649508..2650911 Ruegeria sp. TM1040 4076510 YP_614503.1 CDS leuD NC_008044.1 2650924 2651529 D catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D; isopropylmalate isomerase small subunit 2650924..2651529 Ruegeria sp. TM1040 4076511 YP_614504.1 CDS TM1040_2510 NC_008044.1 2651628 2651927 R hypothetical protein complement(2651628..2651927) Ruegeria sp. TM1040 4076512 YP_614505.1 CDS pheS NC_008044.1 2651928 2653001 R 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 complement(2651928..2653001) Ruegeria sp. TM1040 4076513 YP_614506.1 CDS TM1040_2512 NC_008044.1 2653223 2654206 D KEGG: ret:RHE_CH02814 adenylate cyclase protein, ev=2e-53, 38% identity; guanylate cyclase 2653223..2654206 Ruegeria sp. TM1040 4076514 YP_614507.1 CDS rplT NC_008044.1 2654320 2654685 R binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit; 50S ribosomal protein L20 complement(2654320..2654685) Ruegeria sp. TM1040 4076515 YP_614508.1 CDS rpmI NC_008044.1 2654701 2654901 R PFAM: ribosomal protein L35: (2e-14); KEGG: sil:SPO3599 ribosomal protein L35, ev=4e-29, 95% identity; 50S ribosomal protein L35 complement(2654701..2654901) Ruegeria sp. TM1040 4076516 YP_614509.1 CDS TM1040_2515 NC_008044.1 2655018 2655239 R hypothetical protein complement(2655018..2655239) Ruegeria sp. TM1040 4076517 YP_614510.1 CDS TM1040_2516 NC_008044.1 2655276 2656721 R PFAM: pyruvate kinase: (1.1e-141); KEGG: sil:SPO3600 pyruvate kinase, ev=0.0, 86% identity; pyruvate kinase complement(2655276..2656721) Ruegeria sp. TM1040 4076518 YP_614511.1 CDS TM1040_2517 NC_008044.1 2657069 2658073 R 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 complement(2657069..2658073) Ruegeria sp. TM1040 4076519 YP_614512.1 CDS TM1040_2518 NC_008044.1 2658190 2658900 R TIGRFAM: RpsU-divergently transcribed: (2.1e-62); PFAM: COQ9: (2e-39); KEGG: sil:SPO0230 hypothetical protein, ev=2e-85, 69% identity; hypothetical protein complement(2658190..2658900) Ruegeria sp. TM1040 4076520 YP_614513.1 CDS rpsU NC_008044.1 2659018 2659224 D 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 2659018..2659224 Ruegeria sp. TM1040 4076521 YP_614514.1 CDS uvrC NC_008044.1 2659370 2661277 R 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 complement(2659370..2661277) Ruegeria sp. TM1040 4076522 YP_614515.1 CDS TM1040_2521 NC_008044.1 2661587 2662363 R 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 complement(2661587..2662363) Ruegeria sp. TM1040 4076523 YP_614516.1 CDS TM1040_2522 NC_008044.1 2662400 2663344 R 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 complement(2662400..2663344) Ruegeria sp. TM1040 4076524 YP_614517.1 CDS TM1040_2523 NC_008044.1 2663516 2664313 R PFAM: peptidase S49: (2.1e-33); KEGG: sil:SPO3640 peptidase, family S49, ev=1e-115, 77% identity; peptidase S49 complement(2663516..2664313) Ruegeria sp. TM1040 4076525 YP_614518.1 CDS TM1040_2524 NC_008044.1 2664552 2665313 R PFAM: ABC-2 type transporter: (4.8e-39); KEGG: sil:SPO3641 ABC transporter, permease protein, ev=1e-122, 83% identity; ABC transporter complement(2664552..2665313) Ruegeria sp. TM1040 4076526 YP_614519.1 CDS TM1040_2525 NC_008044.1 2665310 2666239 R 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 complement(2665310..2666239) Ruegeria sp. TM1040 4076527 YP_614520.1 CDS TM1040_2526 NC_008044.1 2666437 2666982 R 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 complement(2666437..2666982) Ruegeria sp. TM1040 4076528 YP_614521.1 CDS TM1040_2527 NC_008044.1 2667184 2668305 D 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 2667184..2668305 Ruegeria sp. TM1040 4076529 YP_614522.1 CDS hemE NC_008044.1 2668364 2669401 R catalyzes the formation of coproporphyrinogen from uroporphyrinogen III; uroporphyrinogen decarboxylase complement(2668364..2669401) Ruegeria sp. TM1040 4076530 YP_614523.1 CDS hemC NC_008044.1 2669522 2670478 D transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis; porphobilinogen deaminase 2669522..2670478 Ruegeria sp. TM1040 4076531 YP_614524.1 CDS TM1040_2530 NC_008044.1 2670697 2671575 R PFAM: glycoside hydrolase, family 25: (1.1e-81); KEGG: sil:SPO3258 glycosyl hydrolase, family 25, ev=2e-90, 57% identity; glycoside hydrolase complement(2670697..2671575) Ruegeria sp. TM1040 4076532 YP_614525.1 CDS TM1040_2531 NC_008044.1 2671697 2672599 R catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis; coproporphyrinogen III oxidase complement(2671697..2672599) Ruegeria sp. TM1040 4076533 YP_614526.1 CDS TM1040_2532 NC_008044.1 2672639 2673442 R 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 complement(2672639..2673442) Ruegeria sp. TM1040 4076534 YP_614527.1 CDS TM1040_2533 NC_008044.1 2673606 2674592 R PFAM: methyltransferase small: (1.5e-65) Methyltransferase type 11: (0.0022); KEGG: sil:SPO3655 methyltransferase, , ev=4e-95, 57% identity; methyltransferase small complement(2673606..2674592) Ruegeria sp. TM1040 4076535 YP_614528.1 CDS TM1040_2534 NC_008044.1 2674632 2674973 R 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 complement(2674632..2674973) Ruegeria sp. TM1040 4076536 YP_614529.1 CDS TM1040_2535 NC_008044.1 2675064 2675777 D PFAM: Haloacid dehalogenase-like hydrolase: (2.6e-09); KEGG: sil:SPO3657 hydrolase, haloacid delahogenase-like family, ev=2e-86, 67% identity; haloacid dehalogenase 2675064..2675777 Ruegeria sp. TM1040 4076537 YP_614530.1 CDS TM1040_2536 NC_008044.1 2676295 2677785 D 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 2676295..2677785 Ruegeria sp. TM1040 4076538 YP_614531.1 CDS TM1040_2537 NC_008044.1 2677985 2678143 R 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 complement(2677985..2678143) Ruegeria sp. TM1040 4076539 YP_614532.1 CDS TM1040_2538 NC_008044.1 2678162 2680345 R 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 complement(2678162..2680345) Ruegeria sp. TM1040 4076540 YP_614533.1 CDS TM1040_2539 NC_008044.1 2680424 2680900 R PFAM: FixH: (1.5e-52); KEGG: sil:SPO3521 FixH protein, , ev=3e-55, 71% identity; FixH protein complement(2680424..2680900) Ruegeria sp. TM1040 4076670 YP_614534.1 CDS TM1040_2540 NC_008044.1 2680904 2682334 R 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 complement(2680904..2682334) Ruegeria sp. TM1040 4076671 YP_614535.1 CDS TM1040_2541 NC_008044.1 2682482 2683366 R 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 complement(2682482..2683366) Ruegeria sp. TM1040 4076672 YP_614536.1 CDS TM1040_2542 NC_008044.1 2684043 2684927 R 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 complement(2684043..2684927) Ruegeria sp. TM1040 4076673 YP_614537.1 CDS TM1040_2543 NC_008044.1 2684924 2685121 R 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 complement(2684924..2685121) Ruegeria sp. TM1040 4076674 YP_614538.1 CDS TM1040_2544 NC_008044.1 2685136 2685864 R CcoO; FixO; cbb3-type cytochrome c oxidase subunit II complement(2685136..2685864) Ruegeria sp. TM1040 4076675 YP_614539.1 CDS TM1040_2545 NC_008044.1 2685879 2687483 R CcoN; FixN; cbb3-type cytochrome c oxidase subunit I complement(2685879..2687483) Ruegeria sp. TM1040 4076676 YP_614540.1 CDS TM1040_2546 NC_008044.1 2687707 2688546 D PFAM: UspA: (2.9e-19); KEGG: sil:SPO3527 universal stress protein family protein, ev=4e-83, 54% identity; hypothetical protein 2687707..2688546 Ruegeria sp. TM1040 4076677 YP_614541.1 CDS TM1040_2547 NC_008044.1 2688724 2689464 R 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 complement(2688724..2689464) Ruegeria sp. TM1040 4076678 YP_614542.1 CDS TM1040_2548 NC_008044.1 2689525 2690880 D catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase 2689525..2690880 Ruegeria sp. TM1040 4076679 YP_614543.1 CDS TM1040_2549 NC_008044.1 2690971 2692563 R 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 complement(2690971..2692563) Ruegeria sp. TM1040 4076680 YP_614544.1 CDS TM1040_2550 NC_008044.1 2692619 2693725 R 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 complement(2692619..2693725) Ruegeria sp. TM1040 4076681 YP_614545.1 CDS TM1040_2551 NC_008044.1 2693730 2694818 R 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 complement(2693730..2694818) Ruegeria sp. TM1040 4076682 YP_614546.1 CDS TM1040_2552 NC_008044.1 2694826 2696676 R 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 complement(2694826..2696676) Ruegeria sp. TM1040 4076683 YP_614547.1 CDS TM1040_2553 NC_008044.1 2697020 2697520 R PFAM: cytochrome c, class I: (2.6e-18); KEGG: sil:SPO3538 cytochrome c552, ev=2e-54, 65% identity; cytochrome c, class I complement(2697020..2697520) Ruegeria sp. TM1040 4076684 YP_614548.1 CDS TM1040_2554 NC_008044.1 2697641 2698471 D catalyzes the formation of phenylpyruvate from prephenate in phenylalanine biosynthesis; prephenate dehydratase 2697641..2698471 Ruegeria sp. TM1040 4076685 YP_614549.1 CDS TM1040_2555 NC_008044.1 2698525 2700408 R 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 complement(2698525..2700408) Ruegeria sp. TM1040 4076686 YP_614550.1 CDS recO NC_008044.1 2700556 2701281 R 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 complement(2700556..2701281) Ruegeria sp. TM1040 4076687 YP_614551.1 CDS TM1040_2557 NC_008044.1 2701285 2701614 R PFAM: protein of unknown function DUF1491: (3.4e-17); KEGG: rsp:RSP_1677 hypothetical protein, ev=1e-39, 75% identity; hypothetical protein complement(2701285..2701614) Ruegeria sp. TM1040 4076688 YP_614552.1 CDS era NC_008044.1 2701779 2702684 R 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 complement(2701779..2702684) Ruegeria sp. TM1040 4076689 YP_614553.1 CDS TM1040_2559 NC_008044.1 2702681 2703409 R 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 complement(2702681..2703409) Ruegeria sp. TM1040 4076690 YP_614554.1 CDS TM1040_2560 NC_008044.1 2703577 2704413 R 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 complement(2703577..2704413) Ruegeria sp. TM1040 4076691 YP_614555.1 CDS acpS NC_008044.1 2704558 2704986 R 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 complement(2704558..2704986) Ruegeria sp. TM1040 4076692 YP_614556.1 CDS TM1040_2562 NC_008044.1 2705013 2705438 R KEGG: jan:Jann_0517 hypothetical protein, ev=6e-06, 28% identity; hypothetical protein complement(2705013..2705438) Ruegeria sp. TM1040 4076693 YP_614557.1 CDS TM1040_2563 NC_008044.1 2705435 2706193 R involved in the de novo synthesis of pyridoxine (Vitamin B6); pyridoxine 5'-phosphate synthase complement(2705435..2706193) Ruegeria sp. TM1040 4076694 YP_614558.1 CDS TM1040_2564 NC_008044.1 2706314 2707018 R KEGG: sil:SPO3202 hypothetical protein, ev=5e-75, 62% identity; hypothetical protein complement(2706314..2707018) Ruegeria sp. TM1040 4076695 YP_614559.1 CDS TM1040_2565 NC_008044.1 2707049 2709181 R 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 complement(2707049..2709181) Ruegeria sp. TM1040 4076696 YP_614560.1 CDS TM1040_2566 NC_008044.1 2709220 2709573 R 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 complement(2709220..2709573) Ruegeria sp. TM1040 4076697 YP_614561.1 CDS TM1040_2567 NC_008044.1 2709688 2710257 R 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 complement(2709688..2710257) Ruegeria sp. TM1040 4076698 YP_614562.1 CDS TM1040_2568 NC_008044.1 2710393 2710962 D PFAM: protein of unknown function DUF88: (6e-81); KEGG: sil:SPO3206 hypothetical protein, ev=9e-99, 94% identity; hypothetical protein 2710393..2710962 Ruegeria sp. TM1040 4076699 YP_614563.1 CDS ispH NC_008044.1 2711132 2712082 D 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 2711132..2712082 Ruegeria sp. TM1040 4076700 YP_614564.1 CDS TM1040_2570 NC_008044.1 2712248 2712865 D 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 2712248..2712865 Ruegeria sp. TM1040 4076701 YP_614565.1 CDS TM1040_2571 NC_008044.1 2712865 2713323 D KEGG: sil:SPO3210 membrane protein, , ev=7e-56, 67% identity; hypothetical protein 2712865..2713323 Ruegeria sp. TM1040 4076702 YP_614566.1 CDS TM1040_2572 NC_008044.1 2713320 2713919 D PFAM: Methyltransferase type 11: (7e-20) Methyltransferase type 12: (2e-18); KEGG: sil:SPO3211 hypothetical protein, ev=3e-49, 52% identity; type 11 methyltransferase 2713320..2713919 Ruegeria sp. TM1040 4076703 YP_614567.1 CDS rnhA NC_008044.1 2713912 2714385 D An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids; ribonuclease H 2713912..2714385 Ruegeria sp. TM1040 4076704 YP_614568.1 CDS TM1040_2574 NC_008044.1 2714499 2715122 D PFAM: protein of unknown function UPF0126: (3.3e-12); KEGG: sil:SPO3213 membrane protein, , ev=2e-80, 73% identity; hypothetical protein 2714499..2715122 Ruegeria sp. TM1040 4076705 YP_614569.1 CDS TM1040_2575 NC_008044.1 2715176 2715412 R KEGG: sil:SPO3214 hypothetical protein, ev=1e-21, 62% identity; hypothetical protein complement(2715176..2715412) Ruegeria sp. TM1040 4076706 YP_614570.1 CDS TM1040_2576 NC_008044.1 2715494 2715730 R KEGG: sil:SPO3215 hypothetical protein, ev=9e-29, 73% identity; hypothetical protein complement(2715494..2715730) Ruegeria sp. TM1040 4076707 YP_614571.1 CDS TM1040_2577 NC_008044.1 2715727 2716653 R 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 complement(2715727..2716653) Ruegeria sp. TM1040 4076708 YP_614572.1 CDS TM1040_2578 NC_008044.1 2716810 2717307 R PFAM: formylmethionine deformylase: (2.1e-35); KEGG: sil:SPO3217 peptide deformylase, ev=6e-81, 90% identity; formylmethionine deformylase complement(2716810..2717307) Ruegeria sp. TM1040 4077489 YP_614573.1 CDS TM1040_2579 NC_008044.1 2717304 2717813 R PFAM: formylmethionine deformylase: (2e-45); KEGG: sil:SPO3218 peptide deformylase, ev=3e-40, 51% identity; peptide deformylase complement(2717304..2717813) Ruegeria sp. TM1040 4077490 YP_614574.1 CDS TM1040_2580 NC_008044.1 2717810 2718334 R PFAM: formylmethionine deformylase: (2.5e-71); KEGG: sil:SPO3219 peptide deformylase, ev=6e-85, 88% identity; peptide deformylase complement(2717810..2718334) Ruegeria sp. TM1040 4077491 YP_614575.1 CDS TM1040_2581 NC_008044.1 2718493 2719665 D 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 2718493..2719665 Ruegeria sp. TM1040 4077492 YP_614576.1 CDS TM1040_2582 NC_008044.1 2719778 2720146 R KEGG: sil:SPO3221 hypothetical protein, ev=6e-32, 63% identity; hypothetical protein complement(2719778..2720146) Ruegeria sp. TM1040 4077493 YP_614577.1 CDS TM1040_2583 NC_008044.1 2720387 2721361 D KEGG: sil:SPO3222 glutathione S-transferase, ev=1e-150, 73% identity; glutathione S-transferase 2720387..2721361 Ruegeria sp. TM1040 4077494 YP_614578.1 CDS TM1040_2584 NC_008044.1 2721455 2722450 D PFAM: aminotransferase, class I and II: (1.1e-08); KEGG: sil:SPO3224 cobalamin biosynthetic protein CobC, ev=1e-117, 66% identity; aminotransferase 2721455..2722450 Ruegeria sp. TM1040 4077495 YP_614579.1 CDS cobD NC_008044.1 2722447 2723358 D CobD; CbiD in Salmonella; converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group; cobalamin biosynthesis protein 2722447..2723358 Ruegeria sp. TM1040 4077496 YP_614580.1 CDS TM1040_2586 NC_008044.1 2723401 2724597 D 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 2723401..2724597 Ruegeria sp. TM1040 4077497 YP_614581.1 CDS TM1040_2587 NC_008044.1 2724658 2728113 R 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 complement(2724658..2728113) Ruegeria sp. TM1040 4077498 YP_614582.1 CDS TM1040_2588 NC_008044.1 2728243 2729457 R 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 complement(2728243..2729457) Ruegeria sp. TM1040 4077499 YP_614583.1 CDS TM1040_2589 NC_008044.1 2729612 2730379 D 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 2729612..2730379 Ruegeria sp. TM1040 4077500 YP_614584.1 CDS TM1040_2590 NC_008044.1 2730376 2731197 R 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 complement(2730376..2731197) Ruegeria sp. TM1040 4077501 YP_614585.1 CDS TM1040_2591 NC_008044.1 2731437 2731994 R 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 complement(2731437..2731994) Ruegeria sp. TM1040 4077502 YP_614586.1 CDS TM1040_2592 NC_008044.1 2731997 2732542 R 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' complement(2731997..2732542) Ruegeria sp. TM1040 4077503 YP_614587.1 CDS TM1040_2593 NC_008044.1 2732629 2732853 R 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 complement(2732629..2732853) Ruegeria sp. TM1040 4077504 YP_614588.1 CDS TM1040_2594 NC_008044.1 2732910 2733713 R 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 complement(2732910..2733713) Ruegeria sp. TM1040 4077505 YP_614589.1 CDS TM1040_2595 NC_008044.1 2733753 2734094 R KEGG: sil:SPO3237 ATP synthase F0, subunit I, ev=2e-30, 63% identity; ATP synthase F0 subunit I complement(2733753..2734094) Ruegeria sp. TM1040 4077506 YP_614590.1 CDS TM1040_2596 NC_008044.1 2734304 2735191 R PFAM: protein of unknown function DUF6, transmembrane: (1.3e-17); KEGG: mlo:mlr1585 hypothetical protein, ev=1e-42, 33% identity; hypothetical protein complement(2734304..2735191) Ruegeria sp. TM1040 4077507 YP_614591.1 CDS TM1040_2597 NC_008044.1 2735291 2735620 D PFAM: regulatory protein, ArsR: (1.8e-11); KEGG: sil:SPO3238 transcriptional regulator, ArsR family, ev=5e-46, 87% identity; ArsR family transcriptional regulator 2735291..2735620 Ruegeria sp. TM1040 4077508 YP_614592.1 CDS TM1040_2598 NC_008044.1 2735663 2736574 R PFAM: protein of unknown function DUF6, transmembrane: (5.2e-11); KEGG: sil:SPO3239 integral membrane protein, ev=1e-113, 70% identity; hypothetical protein complement(2735663..2736574) Ruegeria sp. TM1040 4077509 YP_614593.1 CDS TM1040_2599 NC_008044.1 2736583 2737461 R 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 complement(2736583..2737461) Ruegeria sp. TM1040 4077510 YP_614594.1 CDS TM1040_2600 NC_008044.1 2737602 2738183 D 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 2737602..2738183 Ruegeria sp. TM1040 4077511 YP_614595.1 CDS TM1040_2601 NC_008044.1 2738369 2738899 R 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 complement(2738369..2738899) Ruegeria sp. TM1040 4077512 YP_614596.1 CDS TM1040_2602 NC_008044.1 2738987 2739772 R hypothetical protein complement(2738987..2739772) Ruegeria sp. TM1040 4077513 YP_614597.1 CDS TM1040_2603 NC_008044.1 2740131 2741675 D 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) 2740131..2741675 Ruegeria sp. TM1040 4077514 YP_614598.1 CDS TM1040_2604 NC_008044.1 2741685 2742215 D PFAM: GCN5-related N-acetyltransferase: (1.3e-07); KEGG: jan:Jann_3667 GCN5-related N-acetyltransferase, ev=9e-34, 46% identity; N-acetyltransferase GCN5 2741685..2742215 Ruegeria sp. TM1040 4077515 YP_614599.1 CDS TM1040_2605 NC_008044.1 2742212 2742817 D KEGG: sil:SPO3251 hypothetical protein, ev=1e-100, 83% identity; hypothetical protein 2742212..2742817 Ruegeria sp. TM1040 4077516 YP_614600.1 CDS TM1040_2606 NC_008044.1 2742810 2743118 D catalyzes the interconversion of chorismate to prephenate; chorismate mutase 2742810..2743118 Ruegeria sp. TM1040 4077517 YP_614601.1 CDS rpsP NC_008044.1 2743178 2743543 D 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 2743178..2743543 Ruegeria sp. TM1040 4077518 YP_614602.1 CDS TM1040_2608 NC_008044.1 2743548 2744201 D 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 2743548..2744201 Ruegeria sp. TM1040 4077519 YP_614603.1 CDS rimM NC_008044.1 2744391 2744906 D Essential for efficient processing of 16S rRNA; 16S rRNA-processing protein RimM 2744391..2744906 Ruegeria sp. TM1040 4077520 YP_614604.1 CDS TM1040_2610 NC_008044.1 2744907 2745917 R hypothetical protein complement(2744907..2745917) Ruegeria sp. TM1040 4077521 YP_614605.1 CDS trmD NC_008044.1 2745980 2746780 D methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA; tRNA (guanine-N(1)-)-methyltransferase 2745980..2746780 Ruegeria sp. TM1040 4077522 YP_614606.1 CDS TM1040_2612 NC_008044.1 2746781 2747173 R hypothetical protein complement(2746781..2747173) Ruegeria sp. TM1040 4077523 YP_614607.1 CDS TM1040_2613 NC_008044.1 2747330 2747662 D 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 2747330..2747662 Ruegeria sp. TM1040 4077524 YP_614608.1 CDS TM1040_2614 NC_008044.1 2747739 2748164 R PFAM: regulatory protein, MerR: (1.8e-10); KEGG: sil:SPO3734 transcriptional regulator, MerR family, ev=3e-39, 56% identity; MerR family transcriptional regulator complement(2747739..2748164) Ruegeria sp. TM1040 4077525 YP_614609.1 CDS TM1040_2615 NC_008044.1 2748232 2749446 D 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 2748232..2749446 Ruegeria sp. TM1040 4077526 YP_614610.1 CDS rplS NC_008044.1 2749710 2750081 D 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 2749710..2750081 Ruegeria sp. TM1040 4077527 YP_614611.1 CDS rpmE NC_008044.1 2750093 2750314 D 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 2750093..2750314 Ruegeria sp. TM1040 4077920 YP_614612.1 CDS TM1040_2618 NC_008044.1 2750599 2751408 D KEGG: sil:SPO0689 chromosome partitioning protein, ev=1e-124, 84% identity; chromosome partitioning protein 2750599..2751408 Ruegeria sp. TM1040 4077921 YP_614613.1 CDS TM1040_2619 NC_008044.1 2751599 2752744 R PFAM: adenylyl cyclase class-3/4/guanylyl cyclase: (1.8e-09); KEGG: sil:SPO0688 adenylate/guanylate cyclase, ev=1e-108, 51% identity; guanylate cyclase complement(2751599..2752744) Ruegeria sp. TM1040 4077922 YP_614614.1 CDS TM1040_2620 NC_008044.1 2752842 2753300 R PFAM: regulatory protein, MarR: (1.5e-10); KEGG: sil:SPO0687 transcriptional regulator, MarR family, ev=1e-45, 64% identity; MarR family transcriptional regulator complement(2752842..2753300) Ruegeria sp. TM1040 4077923 YP_614615.1 CDS TM1040_2621 NC_008044.1 2753377 2754732 D 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 2753377..2754732 Ruegeria sp. TM1040 4077924 YP_614616.1 CDS TM1040_2622 NC_008044.1 2754850 2756106 D KEGG: sil:SPO0685 fumarylacetoacetase, ev=1e-169, 70% identity; TIGRFAM: fumarylacetoacetase: (3.8e-197); PFAM: fumarylacetoacetate (FAA) hydrolase: (1.7e-69); fumarylacetoacetate hydrolase 2754850..2756106 Ruegeria sp. TM1040 4077925 YP_614617.1 CDS TM1040_2623 NC_008044.1 2756189 2757139 D PFAM: beta-lactamase-like: (3.9e-08); KEGG: sil:SPO0683 metallo-beta-lactamase family protein, ev=1e-173, 93% identity; beta-lactamase-like protein 2756189..2757139 Ruegeria sp. TM1040 4077926 YP_614618.1 CDS TM1040_2624 NC_008044.1 2757262 2758869 D 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 2757262..2758869 Ruegeria sp. TM1040 4077927 YP_614619.1 CDS TM1040_2625 NC_008044.1 2758875 2759081 D KEGG: sil:SPO0681 hypothetical protein, ev=2e-15, 70% identity; hypothetical protein 2758875..2759081 Ruegeria sp. TM1040 4077928 YP_614620.1 CDS TM1040_2626 NC_008044.1 2759074 2759721 D 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 2759074..2759721 Ruegeria sp. TM1040 4077929 YP_614621.1 CDS TM1040_2627 NC_008044.1 2759858 2761072 D PFAM: protein of unknown function UPF0052 and CofD: (3.6e-22); KEGG: dde:Dde_3600 hypothetical protein, ev=2e-84, 45% identity; hypothetical protein 2759858..2761072 Ruegeria sp. TM1040 4077930 YP_614622.1 CDS TM1040_2628 NC_008044.1 2761148 2763355 R 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 complement(2761148..2763355) Ruegeria sp. TM1040 4077931 YP_614623.1 CDS TM1040_2629 NC_008044.1 2763645 2763983 D 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 2763645..2763983 Ruegeria sp. TM1040 4077932 YP_614624.1 CDS TM1040_2630 NC_008044.1 2764013 2765335 D 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 2764013..2765335 Ruegeria sp. TM1040 4077933 YP_614625.1 CDS TM1040_2631 NC_008044.1 2765408 2766052 R PFAM: ribonuclease T2: (3.3e-08); KEGG: sil:SPO3567 ribonuclease T2 family protein, ev=2e-90, 72% identity; ribonuclease T2 complement(2765408..2766052) Ruegeria sp. TM1040 4077934 YP_614626.1 CDS TM1040_2632 NC_008044.1 2766222 2766989 D PFAM: protein of unknown function DUF1013: (4.5e-87); KEGG: sil:SPO3566 hypothetical protein, ev=1e-119, 83% identity; hypothetical protein 2766222..2766989 Ruegeria sp. TM1040 4077935 YP_614627.1 CDS TM1040_2633 NC_008044.1 2767201 2767701 D hypothetical protein 2767201..2767701 Ruegeria sp. TM1040 4077936 YP_614628.1 CDS TM1040_2634 NC_008044.1 2767830 2768681 D PFAM: Rhodanese-like: (7.5e-26); KEGG: sil:SPO3719 thiosulfate sulfurtransferase, , ev=1e-138, 81% identity; 3-mercaptopyruvate sulfurtransferase 2767830..2768681 Ruegeria sp. TM1040 4077937 YP_614629.1 CDS TM1040_2635 NC_008044.1 2768685 2769869 D catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate; aromatic amino acid aminotransferase 2768685..2769869 Ruegeria sp. TM1040 4077938 YP_614630.1 CDS TM1040_2636 NC_008044.1 2769971 2770585 R 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 complement(2769971..2770585) Ruegeria sp. TM1040 4077939 YP_614631.1 CDS TM1040_2637 NC_008044.1 2770582 2771331 R 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 complement(2770582..2771331) Ruegeria sp. TM1040 4077940 YP_614632.1 CDS TM1040_2638 NC_008044.1 2771466 2772980 D KEGG: sil:SPO3441 hypothetical protein, ev=1e-119, 41% identity; hypothetical protein 2771466..2772980 Ruegeria sp. TM1040 4077941 YP_614633.1 CDS TM1040_2639 NC_008044.1 2773042 2774463 D PFAM: peptidase U62, modulator of DNA gyrase: (3.6e-40); KEGG: sil:SPO3442 PmbA, ev=0.0, 73% identity; microcin-processing peptidase 1 2773042..2774463 Ruegeria sp. TM1040 4077942 YP_614634.1 CDS TM1040_2640 NC_008044.1 2774450 2775250 D PFAM: inositol monophosphatase: (9.2e-54); KEGG: sil:SPO3443 inositol monophosphatase family protein, ev=3e-86, 59% identity; inositol monophosphatase 2774450..2775250 Ruegeria sp. TM1040 4077943 YP_614635.1 CDS TM1040_2641 NC_008044.1 2775250 2776446 D KEGG: sil:SPO3444 3-deoxy-D-manno-octulosonic-acid transferase, , ev=5e-81, 42% identity; 3-deoxy-D-manno-octulosonic-acid transferase 2775250..2776446 Ruegeria sp. TM1040 4077944 YP_614636.1 CDS lpxK NC_008044.1 2776433 2777434 D 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 2776433..2777434 Ruegeria sp. TM1040 4077945 YP_614637.1 CDS TM1040_2643 NC_008044.1 2777471 2778172 R KEGG: sil:SPO3446 thiol:disulfide interchange protein, DsbA family, ev=3e-80, 64% identity; DsbA family thiol:disulfide interchange protein complement(2777471..2778172) Ruegeria sp. TM1040 4077946 YP_614638.1 CDS TM1040_2644 NC_008044.1 2778169 2778696 R PFAM: protein of unknown function DUF1159: (7.1e-21); KEGG: sil:SPO3447 hypothetical protein, ev=2e-59, 68% identity; hypothetical protein complement(2778169..2778696) Ruegeria sp. TM1040 4077947 YP_614639.1 CDS TM1040_2645 NC_008044.1 2778782 2779843 D 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 2778782..2779843 Ruegeria sp. TM1040 4077948 YP_614640.1 CDS TM1040_2646 NC_008044.1 2779924 2781066 D PFAM: fatty acid desaturase: (2e-06); KEGG: sil:SPO3449 fatty acid desaturase family protein, ev=1e-172, 73% identity; alkane 1-monooxygenase 2779924..2781066 Ruegeria sp. TM1040 4077949 YP_614641.1 CDS TM1040_2647 NC_008044.1 2781272 2782768 R 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 complement(2781272..2782768) Ruegeria sp. TM1040 4077950 YP_614642.1 CDS TM1040_2648 NC_008044.1 2782796 2784190 R PFAM: adenylyl cyclase class-3/4/guanylyl cyclase: (9.6e-33); KEGG: sil:SPO3450 adenylate/guanylate cyclase, ev=1e-134, 57% identity; guanylate cyclase complement(2782796..2784190) Ruegeria sp. TM1040 4077951 YP_614643.1 CDS TM1040_2649 NC_008044.1 2784374 2785543 R 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 complement(2784374..2785543) Ruegeria sp. TM1040 4077952 YP_614644.1 CDS rnhB NC_008044.1 2785589 2786278 R RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids; ribonuclease HII complement(2785589..2786278) Ruegeria sp. TM1040 4077953 YP_614645.1 CDS TM1040_2651 NC_008044.1 2786322 2786789 R hypothetical protein complement(2786322..2786789) Ruegeria sp. TM1040 4077954 YP_614646.1 CDS TM1040_2652 NC_008044.1 2786968 2787261 D KEGG: sil:SPO3453 hypothetical protein, ev=2e-26, 64% identity; hypothetical protein 2786968..2787261 Ruegeria sp. TM1040 4077955 YP_614647.1 CDS TM1040_2653 NC_008044.1 2787233 2787934 D KEGG: sil:SPO3454 hypothetical protein, ev=2e-98, 80% identity; transcriptional regulator CadC 2787233..2787934 Ruegeria sp. TM1040 4077956 YP_614648.1 CDS TM1040_2654 NC_008044.1 2788187 2789740 D 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 2788187..2789740 Ruegeria sp. TM1040 4077957 YP_614649.1 CDS TM1040_2655 NC_008044.1 2789859 2791367 R PFAM: aldehyde dehydrogenase: (5e-136); KEGG: sil:SPO0235 aldehyde dehydrogenase family protein, ev=0.0, 84% identity; aldehyde dehydrogenase complement(2789859..2791367) Ruegeria sp. TM1040 4077958 YP_614650.1 CDS TM1040_2656 NC_008044.1 2791376 2792497 R PFAM: TrkA-N: (0.00012) Saccharopine dehydrogenase: (3.4e-81); KEGG: sil:SPO0234 hypothetical protein, ev=1e-170, 81% identity; saccharopine dehydrogenase complement(2791376..2792497) Ruegeria sp. TM1040 4077567 YP_614651.1 CDS TM1040_2657 NC_008044.1 2792625 2793053 R PFAM: regulatory proteins, AsnC/Lrp: (6.9e-19); KEGG: sil:SPO0233 transcriptional regulator, AsnC family, ev=2e-60, 81% identity; AsnC family transcriptional regulator complement(2792625..2793053) Ruegeria sp. TM1040 4077568 YP_614652.1 CDS TM1040_2658 NC_008044.1 2793057 2793812 R PFAM: protein of unknown function DUF328: (2.1e-61); KEGG: sil:SPO0106 hypothetical protein, ev=5e-54, 44% identity; hypothetical protein complement(2793057..2793812) Ruegeria sp. TM1040 4077569 YP_614653.1 CDS TM1040_2659 NC_008044.1 2793914 2795953 R 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 complement(2793914..2795953) Ruegeria sp. TM1040 4077570 YP_614654.1 CDS TM1040_2660 NC_008044.1 2796082 2796411 R KEGG: sil:SPO0122 YGGT family protein, ev=1e-24, 57% identity; hypothetical protein complement(2796082..2796411) Ruegeria sp. TM1040 4077571 YP_614655.1 CDS TM1040_2661 NC_008044.1 2796504 2797082 D KEGG: rsp:RSP_1361 hypothetical protein, ev=3e-50, 54% identity; hypothetical protein 2796504..2797082 Ruegeria sp. TM1040 4077572 YP_614656.1 CDS TM1040_2662 NC_008044.1 2797133 2798515 D PFAM: major facilitator superfamily MFS_1: (3.4e-13); KEGG: sil:SPO0123 membrane protein, , ev=0.0, 73% identity; major facilitator superfamily transporter 2797133..2798515 Ruegeria sp. TM1040 4077573 YP_614657.1 CDS mepA NC_008044.1 2798512 2799435 D D-alanyl-D-alanine endopeptidase; functions in hydrolyzing cell wall peptidoglycan; similar to LAS metallopeptidases; forms a dimer in periplasm; penicillin-insensitive murein endopeptidase 2798512..2799435 Ruegeria sp. TM1040 4077574 YP_614658.1 CDS TM1040_2664 NC_008044.1 2799408 2800334 D KEGG: sil:SPO0125 hypothetical protein, ev=6e-56, 42% identity; hypothetical protein 2799408..2800334 Ruegeria sp. TM1040 4077575 YP_614659.1 CDS TM1040_2665 NC_008044.1 2800489 2801121 D PFAM: protein of unknown function DUF165: (4e-28); KEGG: rsp:RSP_1365 hypothetical protein, ev=9e-83, 73% identity; hypothetical protein 2800489..2801121 Ruegeria sp. TM1040 4077576 YP_614660.1 CDS TM1040_2666 NC_008044.1 2801738 2802157 D 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 2801738..2802157 Ruegeria sp. TM1040 4077577 YP_614661.1 CDS TM1040_2667 NC_008044.1 2802298 2803320 D PFAM: peptidase S58, DmpA: (6e-38); KEGG: sil:SPO0129 peptidase, T4 family, ev=1e-135, 71% identity; peptidase S58, DmpA 2802298..2803320 Ruegeria sp. TM1040 4077578 YP_614662.1 CDS TM1040_2668 NC_008044.1 2803833 2804795 D PFAM: protein of unknown function DUF6, transmembrane: (1.2e-15); KEGG: sil:SPO3643 integral membrane protein, ev=9e-63, 44% identity; hypothetical protein 2803833..2804795 Ruegeria sp. TM1040 4077579 YP_614663.1 CDS TM1040_2669 NC_008044.1 2804811 2805431 D 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 2804811..2805431 Ruegeria sp. TM1040 4077580 YP_614664.1 CDS TM1040_2670 NC_008044.1 2805428 2806345 D 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 2805428..2806345 Ruegeria sp. TM1040 4077581 YP_614665.1 CDS TM1040_2671 NC_008044.1 2806342 2807274 D PFAM: alpha/beta hydrolase fold: (4.8e-18); KEGG: sma:SAV297 alpha/beta hydrolase, ev=4e-20, 29% identity; alpha/beta hydrolase 2806342..2807274 Ruegeria sp. TM1040 4077582 YP_614666.1 CDS TM1040_2672 NC_008044.1 2807277 2808515 R 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 complement(2807277..2808515) Ruegeria sp. TM1040 4077583 YP_614667.1 CDS TM1040_2673 NC_008044.1 2808684 2809748 D PFAM: AFG1-like ATPase: (2.8e-136); KEGG: sil:SPO3819 ATPase, AFG1 family, ev=1e-148, 76% identity; AFG1-like ATPase 2808684..2809748 Ruegeria sp. TM1040 4077584 YP_614668.1 CDS TM1040_2674 NC_008044.1 2809876 2810637 D 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 2809876..2810637 Ruegeria sp. TM1040 4077585 YP_614669.1 CDS TM1040_2675 NC_008044.1 2810634 2811905 R 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 complement(2810634..2811905) Ruegeria sp. TM1040 4077586 YP_614670.1 CDS TM1040_2676 NC_008044.1 2812060 2813022 R 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 complement(2812060..2813022) Ruegeria sp. TM1040 4077587 YP_614671.1 CDS TM1040_2677 NC_008044.1 2813085 2813969 R PFAM: Abortive infection protein: (2.8e-14); KEGG: sil:SPO3816 CAAX amino terminal protease family protein, ev=3e-74, 50% identity; abortive infection protein complement(2813085..2813969) Ruegeria sp. TM1040 4077588 YP_614672.1 CDS TM1040_2678 NC_008044.1 2814095 2817148 R PFAM: cyclic nucleotide-binding: (1.2e-15); KEGG: sil:SPO3815 ABC transporter, permease protein, ev=0.0, 61% identity; cyclic nucleotide-binding protein complement(2814095..2817148) Ruegeria sp. TM1040 4077589 YP_614673.1 CDS TM1040_2679 NC_008044.1 2817505 2818284 D hypothetical protein 2817505..2818284 Ruegeria sp. TM1040 4077590 YP_614674.1 CDS TM1040_2680 NC_008044.1 2818500 2819261 D KEGG: sil:SPO3814 hypothetical protein, ev=1e-103, 72% identity; hypothetical protein 2818500..2819261 Ruegeria sp. TM1040 4077591 YP_614675.1 CDS TM1040_2681 NC_008044.1 2819297 2819674 D KEGG: sil:SPO3813 hypothetical protein, ev=7e-39, 64% identity; hypothetical protein 2819297..2819674 Ruegeria sp. TM1040 4077592 YP_614676.1 CDS TM1040_2682 NC_008044.1 2819870 2820934 R 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 complement(2819870..2820934) Ruegeria sp. TM1040 4077593 YP_614677.1 CDS TM1040_2683 NC_008044.1 2821249 2822205 R 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 complement(2821249..2822205) Ruegeria sp. TM1040 4077594 YP_614678.1 CDS TM1040_2684 NC_008044.1 2822202 2824085 R 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 complement(2822202..2824085) Ruegeria sp. TM1040 4077595 YP_614679.1 CDS TM1040_2685 NC_008044.1 2824082 2825029 R 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 complement(2824082..2825029) Ruegeria sp. TM1040 4077596 YP_614680.1 CDS TM1040_2686 NC_008044.1 2825147 2826733 R 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 complement(2825147..2826733) Ruegeria sp. TM1040 4077597 YP_614681.1 CDS TM1040_2687 NC_008044.1 2826841 2827515 D KEGG: sil:SPO2555 hypothetical protein, ev=4e-53, 51% identity; hypothetical protein 2826841..2827515 Ruegeria sp. TM1040 4077598 YP_614682.1 CDS TM1040_2688 NC_008044.1 2827522 2828361 R 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 complement(2827522..2828361) Ruegeria sp. TM1040 4077599 YP_614683.1 CDS TM1040_2689 NC_008044.1 2828383 2829603 D 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 2828383..2829603 Ruegeria sp. TM1040 4077600 YP_614684.1 CDS TM1040_2690 NC_008044.1 2829620 2831923 R 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 complement(2829620..2831923) Ruegeria sp. TM1040 4077601 YP_614685.1 CDS TM1040_2691 NC_008044.1 2832091 2833464 R PFAM: aminotransferase class-III: (7.1e-80); KEGG: sil:SPO1136 aminotransferase, class III, ev=0.0, 91% identity; hypothetical protein complement(2832091..2833464) Ruegeria sp. TM1040 4077602 YP_614686.1 CDS TM1040_2692 NC_008044.1 2833528 2835003 R PFAM: aldehyde dehydrogenase: (1e-212); KEGG: sil:SPO1137 succinate-semialdehyde dehydrogenase, ev=0.0, 82% identity; succinate semialdehyde dehydrogenase complement(2833528..2835003) Ruegeria sp. TM1040 4077603 YP_614687.1 CDS TM1040_2693 NC_008044.1 2835087 2835566 R PFAM: regulatory proteins, AsnC/Lrp: (8.7e-19); KEGG: sil:SPO1138 transcriptional regulator, AsnC family, ev=1e-73, 85% identity; AsnC family transcriptional regulator complement(2835087..2835566) Ruegeria sp. TM1040 4077604 YP_614688.1 CDS TM1040_2694 NC_008044.1 2835568 2836560 R PFAM: Succinylglutamate desuccinylase/aspartoacylase: (3.8e-92); KEGG: sil:SPO1139 succinylglutamate desuccinylase/aspartoacylase family protein, ev=1e-161, 84% identity; succinylglutamate desuccinylase/aspartoacylase complement(2835568..2836560) Ruegeria sp. TM1040 4077605 YP_614689.1 CDS TM1040_2695 NC_008044.1 2836696 2837706 R 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 complement(2836696..2837706) Ruegeria sp. TM1040 4077002 YP_614690.1 CDS TM1040_2696 NC_008044.1 2837919 2838587 D PFAM: CHAP: (4.9e-07); KEGG: eli:ELI_01090 hypothetical protein, ev=3e-29, 44% identity; hypothetical protein 2837919..2838587 Ruegeria sp. TM1040 4077003 YP_614691.1 CDS TM1040_2697 NC_008044.1 2838703 2839605 R PFAM: PRC-barrel: (0.0002); KEGG: jan:Jann_2065 PRC protein, ev=1e-41, 34% identity; PRC-barrel protein complement(2838703..2839605) Ruegeria sp. TM1040 4077004 YP_614692.1 CDS TM1040_2698 NC_008044.1 2839728 2840570 R PFAM: regulatory proteins, IclR: (6.2e-41); KEGG: jan:Jann_3261 transcriptional regulator, IclR family, ev=1e-102, 68% identity; IclR family transcriptional regulator complement(2839728..2840570) Ruegeria sp. TM1040 4077005 YP_614693.1 CDS TM1040_2699 NC_008044.1 2840738 2841928 D PFAM: aminotransferase, class V: (3.4e-14); KEGG: sil:SPOA0144 serine--glyoxylate transaminase, , ev=0.0, 87% identity; serine-glyoxylate aminotransferase 2840738..2841928 Ruegeria sp. TM1040 4077006 YP_614694.1 CDS TM1040_2700 NC_008044.1 2841928 2842893 D 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 2841928..2842893 Ruegeria sp. TM1040 4077007 YP_614695.1 CDS TM1040_2701 NC_008044.1 2842959 2844122 D PFAM: alanine racemase-like: (1.7e-08); KEGG: sil:SPOA0146 threonine aldolase, low-specificity, ev=0.0, 83% identity; D-3-hydroxyaspartate aldolase 2842959..2844122 Ruegeria sp. TM1040 4077008 YP_614696.1 CDS TM1040_2702 NC_008044.1 2844218 2845183 D PFAM: ornithine cyclodeaminase/mu-crystallin: (1.3e-43); KEGG: jan:Jann_2605 ornithine cyclodeaminase, ev=1e-153, 85% identity; ornithine cyclodeaminase 2844218..2845183 Ruegeria sp. TM1040 4077009 YP_614697.1 CDS TM1040_2703 NC_008044.1 2845236 2846147 R 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 complement(2845236..2846147) Ruegeria sp. TM1040 4077010 YP_614698.1 CDS TM1040_2704 NC_008044.1 2846327 2847790 D 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 2846327..2847790 Ruegeria sp. TM1040 4077011 YP_614699.1 CDS TM1040_2705 NC_008044.1 2847805 2850138 D 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 2847805..2850138 Ruegeria sp. TM1040 4077012 YP_614700.1 CDS TM1040_2706 NC_008044.1 2850143 2850994 D PFAM: protein of unknown function DUF182: (5.2e-12); KEGG: mlo:mlr5136 xanthine dehydrogenase accessory factor, ev=4e-64, 46% identity; hypothetical protein 2850143..2850994 Ruegeria sp. TM1040 4077013 YP_614701.1 CDS TM1040_2707 NC_008044.1 2851063 2852646 D PFAM: Xanthine/uracil/vitamin C permease: (0.00031); KEGG: bha:BH1513 hypothetical protein, ev=1e-100, 41% identity; xanthine/uracil/vitamin C permease 2851063..2852646 Ruegeria sp. TM1040 4077014 YP_614702.1 CDS TM1040_2708 NC_008044.1 2852734 2853201 R 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 complement(2852734..2853201) Ruegeria sp. TM1040 4077015 YP_614703.1 CDS TM1040_2709 NC_008044.1 2853377 2854435 D 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 2853377..2854435 Ruegeria sp. TM1040 4077016 YP_614704.1 CDS TM1040_2710 NC_008044.1 2854428 2855591 D PFAM: peptidase M24: (3.3e-12); KEGG: jan:Jann_1829 peptidase M24, ev=1e-107, 53% identity; peptidase M24 2854428..2855591 Ruegeria sp. TM1040 4077017 YP_614705.1 CDS TM1040_2711 NC_008044.1 2855588 2856346 D PFAM: Asp/Glu racemase: (1.6e-07); KEGG: sil:SPO2450 Asp/Glu/Hydantoin racemase family protein, ev=2e-67, 54% identity; Asp/Glu racemase 2855588..2856346 Ruegeria sp. TM1040 4077018 YP_614706.1 CDS TM1040_2712 NC_008044.1 2856397 2857500 R PFAM: peptidase M24: (1.1e-46); KEGG: jan:Jann_2048 peptidase M24, ev=1e-122, 61% identity; peptidase M24 complement(2856397..2857500) Ruegeria sp. TM1040 4077019 YP_614707.1 CDS TM1040_2713 NC_008044.1 2857581 2859170 R 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 complement(2857581..2859170) Ruegeria sp. TM1040 4077020 YP_614708.1 CDS TM1040_2714 NC_008044.1 2859216 2859830 R 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 complement(2859216..2859830) Ruegeria sp. TM1040 4077021 YP_614709.1 CDS TM1040_2715 NC_008044.1 2859969 2861120 D 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 2859969..2861120 Ruegeria sp. TM1040 4077022 YP_614710.1 CDS TM1040_2716 NC_008044.1 2861130 2862035 D 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 2861130..2862035 Ruegeria sp. TM1040 4077023 YP_614711.1 CDS TM1040_2717 NC_008044.1 2862032 2862871 D 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 2862032..2862871 Ruegeria sp. TM1040 4077024 YP_614712.1 CDS TM1040_2718 NC_008044.1 2862868 2863617 D 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 2862868..2863617 Ruegeria sp. TM1040 4077025 YP_614713.1 CDS TM1040_2719 NC_008044.1 2863621 2864109 D KEGG: jan:Jann_2041 hypothetical protein, ev=3e-35, 46% identity; hypothetical protein 2863621..2864109 Ruegeria sp. TM1040 4077026 YP_614714.1 CDS TM1040_2720 NC_008044.1 2864282 2864500 D 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 2864282..2864500 Ruegeria sp. TM1040 4077027 YP_614715.1 CDS TM1040_2721 NC_008044.1 2864555 2865052 D PFAM: Ferritin and Dps: (1.2e-17); KEGG: rru:Rru_A0333 ferritin and Dps, ev=8e-31, 44% identity; ferritin 2864555..2865052 Ruegeria sp. TM1040 4077028 YP_614716.1 CDS TM1040_2722 NC_008044.1 2865208 2866029 R in Caulobacter crescentus, CC3477 is differentially expressed in minimal salts media with glucose as compared to complex media; two-component response regulator complement(2865208..2866029) Ruegeria sp. TM1040 4077029 YP_614717.1 CDS TM1040_2723 NC_008044.1 2866340 2866897 D 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 2866340..2866897 Ruegeria sp. TM1040 4077030 YP_614718.1 CDS TM1040_2724 NC_008044.1 2866903 2868744 D 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 2866903..2868744 Ruegeria sp. TM1040 4077031 YP_614719.1 CDS TM1040_2725 NC_008044.1 2868869 2869456 R PFAM: Exopolysaccharide synthesis, ExoD: (6.6e-19); KEGG: jan:Jann_0449 exopolysaccharide synthesis, ExoD, ev=1e-29, 40% identity; exopolysaccharide synthesis, ExoD complement(2868869..2869456) Ruegeria sp. TM1040 4077032 YP_614720.1 CDS TM1040_2726 NC_008044.1 2869670 2870158 D KEGG: rsp:RSP_1276 hypothetical protein, ev=2e-18, 37% identity; hypothetical protein 2869670..2870158 Ruegeria sp. TM1040 4077033 YP_614721.1 CDS TM1040_2727 NC_008044.1 2870342 2871370 R PFAM: ammonia monooxygenase: (6.8e-17); KEGG: atc:AGR_C_342 hypothetical protein YhjN, ev=6e-49, 34% identity; ammonia monooxygenase complement(2870342..2871370) Ruegeria sp. TM1040 4077034 YP_614722.1 CDS TM1040_2728 NC_008044.1 2871357 2872124 R PFAM: Citrate synthase: (1.8e-07); KEGG: reu:Reut_B4959 citrate synthase, ev=3e-90, 65% identity; citrate synthase complement(2871357..2872124) Ruegeria sp. TM1040 4077035 YP_614723.1 CDS TM1040_2729 NC_008044.1 2872121 2873308 R 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 complement(2872121..2873308) Ruegeria sp. TM1040 4077036 YP_614724.1 CDS TM1040_2730 NC_008044.1 2873298 2874818 R PFAM: protein of unknown function DUF112, transmembrane: (1.9e-152); KEGG: sil:SPO0184 membrane protein, , ev=0.0, 85% identity; hypothetical protein complement(2873298..2874818) Ruegeria sp. TM1040 4077037 YP_614725.1 CDS TM1040_2731 NC_008044.1 2874831 2875316 R KEGG: jan:Jann_3488 hypothetical protein, ev=2e-58, 70% identity; hypothetical protein complement(2874831..2875316) Ruegeria sp. TM1040 4077038 YP_614726.1 CDS TM1040_2732 NC_008044.1 2875403 2876383 R PFAM: Uncharacterized protein UPF0065: (1.4e-09); KEGG: sil:SPO0186 bordetella uptake gene family protein, ev=1e-145, 78% identity; hypothetical protein complement(2875403..2876383) Ruegeria sp. TM1040 4077039 YP_614727.1 CDS TM1040_2733 NC_008044.1 2876423 2877151 D 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 2876423..2877151 Ruegeria sp. TM1040 4077040 YP_614728.1 CDS TM1040_2734 NC_008044.1 2877148 2878533 D 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 2877148..2878533 Ruegeria sp. TM1040 4077606 YP_614729.1 CDS TM1040_2735 NC_008044.1 2878629 2879540 D KEGG: sil:SPO0189 iron(III) transport system substrate-binding protein, ev=3e-84, 49% identity; iron(III) transport system substrate-binding protein 2878629..2879540 Ruegeria sp. TM1040 4077607 YP_614730.1 CDS TM1040_2736 NC_008044.1 2879545 2881929 R KEGG: sil:SPOA0319 transketolase, , ev=0.0, 80% identity; transketolase complement(2879545..2881929) Ruegeria sp. TM1040 4077608 YP_614731.1 CDS TM1040_2737 NC_008044.1 2881941 2883143 R catalyzes the formation of methanethiol and 2-ocobutanoate from L-methionine; methionine gamma-lyase complement(2881941..2883143) Ruegeria sp. TM1040 4077609 YP_614732.1 CDS TM1040_2738 NC_008044.1 2883257 2883715 D PFAM: regulatory proteins, AsnC/Lrp: (1.9e-30); KEGG: sil:SPOA0317 transcriptional regulator, AsnC family, ev=3e-66, 81% identity; AsnC family transcriptional regulator 2883257..2883715 Ruegeria sp. TM1040 4077610 YP_614733.1 CDS TM1040_2739 NC_008044.1 2883772 2885655 R PFAM: glycoside hydrolase, family 20: (6.8e-138); KEGG: atc:AGR_C_4704 beta-N-acetylhexosaminidase, ev=1e-159, 47% identity; beta-N-acetylhexosaminidase complement(2883772..2885655) Ruegeria sp. TM1040 4077611 YP_614734.1 CDS TM1040_2740 NC_008044.1 2885691 2886146 R PFAM: GCN5-related N-acetyltransferase: (5.2e-06); KEGG: bcl:ABC0535 hypothetical protein, ev=8e-41, 52% identity; N-acetyltransferase GCN5 complement(2885691..2886146) Ruegeria sp. TM1040 4077612 YP_614735.1 CDS TM1040_2741 NC_008044.1 2886139 2887068 R 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 complement(2886139..2887068) Ruegeria sp. TM1040 4077613 YP_614736.1 CDS TM1040_2742 NC_008044.1 2887058 2887870 R 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 complement(2887058..2887870) Ruegeria sp. TM1040 4077614 YP_614737.1 CDS TM1040_2743 NC_008044.1 2887867 2888775 R 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 complement(2887867..2888775) Ruegeria sp. TM1040 4077615 YP_614738.1 CDS TM1040_2744 NC_008044.1 2888775 2889809 R 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 complement(2888775..2889809) Ruegeria sp. TM1040 4077616 YP_614739.1 CDS TM1040_2745 NC_008044.1 2889841 2891496 R 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 complement(2889841..2891496) Ruegeria sp. TM1040 4077617 YP_614740.1 CDS TM1040_2746 NC_008044.1 2891848 2895138 D 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 2891848..2895138 Ruegeria sp. TM1040 4077618 YP_614741.1 CDS TM1040_2747 NC_008044.1 2895144 2896046 R 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 complement(2895144..2896046) Ruegeria sp. TM1040 4077619 YP_614742.1 CDS TM1040_2748 NC_008044.1 2896222 2896743 D 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 2896222..2896743 Ruegeria sp. TM1040 4077620 YP_614743.1 CDS TM1040_2749 NC_008044.1 2896740 2898026 D 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 2896740..2898026 Ruegeria sp. TM1040 4077621 YP_614744.1 CDS TM1040_2750 NC_008044.1 2898076 2899119 D 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 2898076..2899119 Ruegeria sp. TM1040 4077622 YP_614745.1 CDS TM1040_2751 NC_008044.1 2899183 2900649 D 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 2899183..2900649 Ruegeria sp. TM1040 4077623 YP_614746.1 CDS TM1040_2752 NC_008044.1 2900649 2901704 D 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 2900649..2901704 Ruegeria sp. TM1040 4077624 YP_614747.1 CDS TM1040_2753 NC_008044.1 2901701 2902627 D PFAM: PfkB: (3e-47); KEGG: bur:Bcep18194_A5081 sugar kinase, ribokinase family, ev=3e-75, 50% identity; PfkB protein 2901701..2902627 Ruegeria sp. TM1040 4077625 YP_614748.1 CDS TM1040_2754 NC_008044.1 2902654 2903043 D PFAM: Endoribonuclease L-PSP: (4.9e-36); KEGG: sme:SMb21139 protein, similar to translation initiation inhibitors, ev=4e-35, 56% identity; endoribonuclease L-PSP 2902654..2903043 Ruegeria sp. TM1040 4077626 YP_614749.1 CDS TM1040_2755 NC_008044.1 2903128 2904465 R 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 complement(2903128..2904465) Ruegeria sp. TM1040 4077627 YP_614750.1 CDS TM1040_2756 NC_008044.1 2904473 2905576 R PFAM: peptidase M23B: (0.00023); KEGG: sil:SPO3811 hypothetical protein, ev=1e-132, 70% identity; peptidase M23B complement(2904473..2905576) Ruegeria sp. TM1040 4077628 YP_614751.1 CDS TM1040_2757 NC_008044.1 2905615 2907135 R catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate; phosphoglyceromutase complement(2905615..2907135) Ruegeria sp. TM1040 4077629 YP_614752.1 CDS TM1040_2758 NC_008044.1 2907361 2907822 D PFAM: protein of unknown function DUF1203: (1.3e-72); KEGG: sil:SPO3849 hypothetical protein, ev=3e-55, 66% identity; hypothetical protein 2907361..2907822 Ruegeria sp. TM1040 4077630 YP_614753.1 CDS TM1040_2759 NC_008044.1 2907826 2908299 R PFAM: GCN5-related N-acetyltransferase: (8.4e-09); KEGG: gvi:glr3142 acetyltransferase, ev=6e-24, 39% identity; acetyltransferase complement(2907826..2908299) Ruegeria sp. TM1040 4077631 YP_614754.1 CDS TM1040_2760 NC_008044.1 2908299 2909255 R 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 complement(2908299..2909255) Ruegeria sp. TM1040 4077632 YP_614755.1 CDS TM1040_2761 NC_008044.1 2909299 2909481 D KEGG: sil:SPO3846 hypothetical protein, ev=2e-21, 86% identity; hypothetical protein 2909299..2909481 Ruegeria sp. TM1040 4077633 YP_614756.1 CDS TM1040_2762 NC_008044.1 2909535 2910020 D KEGG: sil:SPO0221 hypothetical protein, ev=5e-67, 78% identity; hypothetical protein 2909535..2910020 Ruegeria sp. TM1040 4077634 YP_614757.1 CDS TM1040_2763 NC_008044.1 2910088 2910621 R KEGG: jan:Jann_1682 hypothetical protein, ev=1e-08, 26% identity; hypothetical protein complement(2910088..2910621) Ruegeria sp. TM1040 4077635 YP_614758.1 CDS TM1040_2764 NC_008044.1 2910652 2913459 D 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 2910652..2913459 Ruegeria sp. TM1040 4077636 YP_614759.1 CDS TM1040_2765 NC_008044.1 2913628 2914395 R PFAM: Xylose isomerase-like TIM barrel: (6.4e-35); KEGG: reu:Reut_A1423 hydroxypyruvate isomerase, ev=2e-52, 44% identity; hydroxypyruvate isomerase complement(2913628..2914395) Ruegeria sp. TM1040 4077637 YP_614760.1 CDS TM1040_2766 NC_008044.1 2914614 2915207 R PFAM: protein of unknown function DUF1285: (3.1e-89); KEGG: sil:SPO0140 hypothetical protein, ev=1e-70, 67% identity; hypothetical protein complement(2914614..2915207) Ruegeria sp. TM1040 4077638 YP_614761.1 CDS TM1040_2767 NC_008044.1 2915260 2916267 D 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 2915260..2916267 Ruegeria sp. TM1040 4077639 YP_614762.1 CDS TM1040_2768 NC_008044.1 2916264 2917172 D KEGG: sil:SPO0138 hypothetical protein, ev=1e-114, 72% identity; hypothetical protein 2916264..2917172 Ruegeria sp. TM1040 4077640 YP_614763.1 CDS TM1040_2769 NC_008044.1 2917169 2919958 D TIGRFAM: Double-transmembrane region-like: (7.7e-15); KEGG: sil:SPO0137 hypothetical protein, ev=0.0, 62% identity; double-transmembrane region-like protein 2917169..2919958 Ruegeria sp. TM1040 4077641 YP_614764.1 CDS TM1040_2770 NC_008044.1 2920004 2922046 D KEGG: sil:SPO0136 hypothetical protein, ev=0.0, 69% identity; hypothetical protein 2920004..2922046 Ruegeria sp. TM1040 4077642 YP_614765.1 CDS TM1040_2771 NC_008044.1 2922245 2923147 R KEGG: dar:Daro_4183 hydratase/decarboxylase, ev=6e-48, 41% identity; hydratase/decarboxylase complement(2922245..2923147) Ruegeria sp. TM1040 4077643 YP_614766.1 CDS TM1040_2772 NC_008044.1 2923147 2925219 R 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 complement(2923147..2925219) Ruegeria sp. TM1040 4077644 YP_614767.1 CDS TM1040_2773 NC_008044.1 2925324 2930771 R 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 complement(2925324..2930771) Ruegeria sp. TM1040 4076541 YP_614768.1 CDS TM1040_2774 NC_008044.1 2930923 2933208 D 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 2930923..2933208 Ruegeria sp. TM1040 4076542 YP_614769.1 CDS TM1040_2775 NC_008044.1 2933253 2934611 R 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 complement(2933253..2934611) Ruegeria sp. TM1040 4076543 YP_614770.1 CDS TM1040_2776 NC_008044.1 2934612 2935877 R 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 complement(2934612..2935877) Ruegeria sp. TM1040 4076544 YP_614771.1 CDS TM1040_2777 NC_008044.1 2935882 2936895 R 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 complement(2935882..2936895) Ruegeria sp. TM1040 4076545 YP_614772.1 CDS TM1040_2778 NC_008044.1 2936897 2938138 R 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 complement(2936897..2938138) Ruegeria sp. TM1040 4076546 YP_614773.1 CDS TM1040_2779 NC_008044.1 2938135 2939205 R 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 complement(2938135..2939205) Ruegeria sp. TM1040 4076547 YP_614774.1 CDS TM1040_2780 NC_008044.1 2939325 2939792 D PFAM: regulatory proteins, AsnC/Lrp: (1.8e-20); KEGG: sil:SPO0389 transcriptional regulator, AsnC family, ev=2e-33, 46% identity; AsnC family transcriptional regulator 2939325..2939792 Ruegeria sp. TM1040 4076548 YP_614775.1 CDS TM1040_2781 NC_008044.1 2939877 2941073 R PFAM: iron-containing alcohol dehydrogenase: (3.2e-79); KEGG: sil:SPO2609 alcohol dehydrogenase, iron-containing, ev=1e-168, 74% identity; iron-containing alcohol dehydrogenase complement(2939877..2941073) Ruegeria sp. TM1040 4076549 YP_614776.1 CDS TM1040_2782 NC_008044.1 2941116 2942498 R PFAM: aldehyde dehydrogenase: (5.7e-120); KEGG: sil:SPO2608 aldehyde dehydrogenase, , ev=0.0, 71% identity; aldehyde dehydrogenase complement(2941116..2942498) Ruegeria sp. TM1040 4076550 YP_614777.1 CDS TM1040_2783 NC_008044.1 2942601 2943953 R PFAM: glutamine synthetase, catalytic region: (3.4e-92); KEGG: sil:SPO2607 gamma-glutamylisopropylamide synthetase, , ev=0.0, 71% identity; L-glutamine synthetase complement(2942601..2943953) Ruegeria sp. TM1040 4076551 YP_614778.1 CDS TM1040_2784 NC_008044.1 2944029 2945063 R 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 complement(2944029..2945063) Ruegeria sp. TM1040 4076552 YP_614779.1 CDS TM1040_2785 NC_008044.1 2945118 2946437 R 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 complement(2945118..2946437) Ruegeria sp. TM1040 4076553 YP_614780.1 CDS TM1040_2786 NC_008044.1 2946434 2947021 R KEGG: sil:SPO2604 hypothetical protein, ev=1e-54, 57% identity; hypothetical protein complement(2946434..2947021) Ruegeria sp. TM1040 4076554 YP_614781.1 CDS TM1040_2787 NC_008044.1 2947018 2947791 R 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 complement(2947018..2947791) Ruegeria sp. TM1040 4076555 YP_614782.1 CDS TM1040_2788 NC_008044.1 2947896 2948753 D 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 2947896..2948753 Ruegeria sp. TM1040 4076556 YP_614783.1 CDS TM1040_2789 NC_008044.1 2948817 2949971 D 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 2948817..2949971 Ruegeria sp. TM1040 4076557 YP_614784.1 CDS TM1040_2790 NC_008044.1 2949971 2951074 D PFAM: Thiolase: (1e-21); KEGG: ret:RHE_PF00014 acetyl-CoA acetyltransferase (beta-ketothiolase) protein, ev=1e-60, 41% identity; Acetyl-CoA C-acetyltransferase 2949971..2951074 Ruegeria sp. TM1040 4076558 YP_614785.1 CDS TM1040_2791 NC_008044.1 2951135 2953351 R 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 complement(2951135..2953351) Ruegeria sp. TM1040 4076559 YP_614786.1 CDS TM1040_2792 NC_008044.1 2953530 2954453 D 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 2953530..2954453 Ruegeria sp. TM1040 4076560 YP_614787.1 CDS TM1040_2793 NC_008044.1 2954463 2955251 R catalyzes the dehydration of L-carnitinyl-CoA to crotonobetainyl-CoA; carnitinyl-CoA dehydratase complement(2954463..2955251) Ruegeria sp. TM1040 4076561 YP_614788.1 CDS TM1040_2794 NC_008044.1 2955248 2957287 R PFAM: CoA-binding: (1e-08); KEGG: sil:SPOA0287 acyl-CoA synthetase, , ev=0.0, 60% identity; CoA-binding protein complement(2955248..2957287) Ruegeria sp. TM1040 4076562 YP_614789.1 CDS TM1040_2795 NC_008044.1 2957294 2957608 R 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 complement(2957294..2957608) Ruegeria sp. TM1040 4076563 YP_614790.1 CDS TM1040_2796 NC_008044.1 2957611 2958810 R 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 complement(2957611..2958810) Ruegeria sp. TM1040 4076564 YP_614791.1 CDS TM1040_2797 NC_008044.1 2958859 2959806 D 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 2958859..2959806 Ruegeria sp. TM1040 4076565 YP_614792.1 CDS TM1040_2798 NC_008044.1 2959852 2960235 R PFAM: arsenate reductase and related: (8.2e-28); KEGG: jan:Jann_2102 arsenate reductase, ev=7e-33, 56% identity; arsenate reductase complement(2959852..2960235) Ruegeria sp. TM1040 4076566 YP_614793.1 CDS TM1040_2799 NC_008044.1 2960323 2962128 D KEGG: sil:SPO3746 adenine deaminase, ev=0.0, 84% identity; TIGRFAM: adenine deaminase: (4.6e-140); PFAM: amidohydrolase: (4.9e-23); adenine deaminase 2960323..2962128 Ruegeria sp. TM1040 4076567 YP_614794.1 CDS TM1040_2800 NC_008044.1 2962121 2963587 D Catalyzes the hydrolysis of AMP to form adenine and ribose 5-phosphate using water as the nucleophile; AMP nucleosidase 2962121..2963587 Ruegeria sp. TM1040 4076568 YP_614795.1 CDS TM1040_2801 NC_008044.1 2963731 2964024 D 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 2963731..2964024 Ruegeria sp. TM1040 4076569 YP_614796.1 CDS TM1040_2802 NC_008044.1 2964165 2965082 D PFAM: protein of unknown function DUF6, transmembrane: (2.8e-11); KEGG: sil:SPO3743 membrane protein, , ev=1e-120, 77% identity; hypothetical protein 2964165..2965082 Ruegeria sp. TM1040 4076570 YP_614797.1 CDS TM1040_2803 NC_008044.1 2965204 2965653 D 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 2965204..2965653 Ruegeria sp. TM1040 4076571 YP_614798.1 CDS TM1040_2804 NC_008044.1 2965650 2966165 D 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 2965650..2966165 Ruegeria sp. TM1040 4076572 YP_614799.1 CDS TM1040_2805 NC_008044.1 2966243 2968249 R 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 complement(2966243..2968249) Ruegeria sp. TM1040 4076573 YP_614800.1 CDS TM1040_2806 NC_008044.1 2968323 2969366 R 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 complement(2968323..2969366) Ruegeria sp. TM1040 4076574 YP_614801.1 CDS TM1040_2807 NC_008044.1 2969475 2970821 R PFAM: beta-lactamase: (8.8e-24); KEGG: atc:AGR_C_1692 6-aminohexanoate-dimer hydrolase, ev=1e-147, 55% identity; 6-aminohexanoate-dimer hydrolase complement(2969475..2970821) Ruegeria sp. TM1040 4076575 YP_614802.1 CDS TM1040_2808 NC_008044.1 2970802 2972226 R KEGG: atc:AGR_C_1694 hypothetical protein, ev=1e-152, 56% identity; hypothetical protein complement(2970802..2972226) Ruegeria sp. TM1040 4076576 YP_614803.1 CDS TM1040_2809 NC_008044.1 2972936 2973763 D PFAM: diaminopimelate epimerase: (4.4e-36); KEGG: sil:SPO0278 diaminopimelate epimerase, ev=1e-121, 76% identity; diaminopimelate epimerase 2972936..2973763 Ruegeria sp. TM1040 4076577 YP_614804.1 CDS TM1040_2810 NC_008044.1 2973760 2975025 D 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 2973760..2975025 Ruegeria sp. TM1040 4076578 YP_614805.1 CDS TM1040_2811 NC_008044.1 2975043 2975564 D KEGG: ppr:PBPRA2780 hypothetical protein, ev=1e-25, 38% identity; hypothetical protein 2975043..2975564 Ruegeria sp. TM1040 4076579 YP_614806.1 CDS TM1040_2812 NC_008044.1 2975706 2976497 R PFAM: cytochrome c1: (9.4e-109); KEGG: sil:SPO0273 ubiquinol--cytochrome c reductase, cytochrome c1, ev=1e-104, 66% identity; cytochrome c1 complement(2975706..2976497) Ruegeria sp. TM1040 4076631 YP_614807.1 CDS TM1040_2813 NC_008044.1 2976516 2977844 R 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 complement(2976516..2977844) Ruegeria sp. TM1040 4076632 YP_614808.1 CDS TM1040_2814 NC_008044.1 2977860 2978420 R 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 complement(2977860..2978420) Ruegeria sp. TM1040 4076633 YP_614809.1 CDS TM1040_2815 NC_008044.1 2978645 2979247 R PFAM: glutathione S-transferase-like: (0.0074); KEGG: sil:SPO0270 glutathione S-transferase family protein, ev=1e-60, 55% identity; glutathione S-transferase complement(2978645..2979247) Ruegeria sp. TM1040 4076634 YP_614810.1 CDS TM1040_2816 NC_008044.1 2979365 2980060 R 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 complement(2979365..2980060) Ruegeria sp. TM1040 4076635 YP_614811.1 CDS thiP NC_008044.1 2980047 2981618 R 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 complement(2980047..2981618) Ruegeria sp. TM1040 4076636 YP_614812.1 CDS tbpA NC_008044.1 2981594 2982574 R part of the thiamine and TPP transport system tbpA-thiPQ; thiamine transporter substrate binding subunit complement(2981594..2982574) Ruegeria sp. TM1040 4076637 YP_614813.1 CDS TM1040_2819 NC_008044.1 2983051 2984163 D catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis; chorismate synthase 2983051..2984163 Ruegeria sp. TM1040 4076638 YP_614814.1 CDS TM1040_2820 NC_008044.1 2984942 2985931 D 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 2984942..2985931 Ruegeria sp. TM1040 4076639 YP_614815.1 CDS TM1040_2821 NC_008044.1 2985990 2986793 R 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 complement(2985990..2986793) Ruegeria sp. TM1040 4076640 YP_614816.1 CDS TM1040_2822 NC_008044.1 2987026 2988468 D function undetermined; similar to glutamate synthase beta subunit and related oxidoreductases which transfer electrons from NADPH to an acceptor protein or protein domain; oxidoreductase 2987026..2988468 Ruegeria sp. TM1040 4076641 YP_614817.1 CDS TM1040_2823 NC_008044.1 2988543 2993075 D 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 2988543..2993075 Ruegeria sp. TM1040 4076642 YP_614818.1 CDS TM1040_2824 NC_008044.1 2993220 2993963 D 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 2993220..2993963 Ruegeria sp. TM1040 4076643 YP_614819.1 CDS TM1040_2825 NC_008044.1 2994033 2994698 D PFAM: glutathione S-transferase-like: (4.1e-10); KEGG: sil:SPO3764 glutathione S-transferase family protein, ev=1e-110, 85% identity; glutathione S-transferase 2994033..2994698 Ruegeria sp. TM1040 4076644 YP_614820.1 CDS TM1040_2826 NC_008044.1 2994998 2996482 R PFAM: HemY-like: (2.7e-22); KEGG: sil:SPO3851 HemY domain protein, ev=0.0, 69% identity; HemY-like protein complement(2994998..2996482) Ruegeria sp. TM1040 4076645 YP_614821.1 CDS TM1040_2827 NC_008044.1 2996493 2997812 R KEGG: sil:SPO3852 hypothetical protein, ev=1e-87, 44% identity; hypothetical protein complement(2996493..2997812) Ruegeria sp. TM1040 4076646 YP_614822.1 CDS TM1040_2828 NC_008044.1 2997862 2998599 R PFAM: Uroporphyrinogen III synthase HEM4: (1.6e-07); KEGG: sil:SPO3853 uroporphyrinogen-III synthase, , ev=2e-39, 41% identity; uroporphyrinogen III synthase HEM4 complement(2997862..2998599) Ruegeria sp. TM1040 4076647 YP_614823.1 CDS TM1040_2829 NC_008044.1 2998674 2999771 D 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 2998674..2999771 Ruegeria sp. TM1040 4076648 YP_614824.1 CDS gpsA NC_008044.1 2999768 3000730 D catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate; NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 2999768..3000730 Ruegeria sp. TM1040 4076649 YP_614825.1 CDS TM1040_2831 NC_008044.1 3000732 3001004 D 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 3000732..3001004 Ruegeria sp. TM1040 4076650 YP_614826.1 CDS TM1040_2832 NC_008044.1 3001004 3001426 D PFAM: protein of unknown function DUF589: (3.7e-77); KEGG: sil:SPO3857 hypothetical protein, ev=2e-63, 77% identity; hypothetical protein 3001004..3001426 Ruegeria sp. TM1040 4076651 YP_614827.1 CDS TM1040_2833 NC_008044.1 3001480 3001875 D KEGG: sil:SPO3858 hypothetical protein, ev=2e-43, 60% identity; hypothetical protein 3001480..3001875 Ruegeria sp. TM1040 4076652 YP_614828.1 CDS TM1040_2834 NC_008044.1 3002076 3002417 R KEGG: sil:SPO3859 hypothetical protein, ev=2e-51, 88% identity; hypothetical protein complement(3002076..3002417) Ruegeria sp. TM1040 4076653 YP_614829.1 CDS TM1040_2835 NC_008044.1 3002642 3004027 R catalyzes the formation of L-homocysteine from S-adenosyl-L-homocysteine; S-adenosyl-L-homocysteine hydrolase complement(3002642..3004027) Ruegeria sp. TM1040 4076654 YP_614830.1 CDS TM1040_2836 NC_008044.1 3004294 3004902 D PFAM: metal-dependent phosphohydrolase, HD subdomain: (4.7e-07); KEGG: jan:Jann_4073 metal dependent phosphohydrolase, ev=7e-87, 75% identity; metal dependent phosphohydrolase 3004294..3004902 Ruegeria sp. TM1040 4076655 YP_614831.1 CDS TM1040_2837 NC_008044.1 3004905 3006122 R KEGG: sil:SPO3864 hypothetical protein, ev=1e-142, 63% identity; hypothetical protein complement(3004905..3006122) Ruegeria sp. TM1040 4076656 YP_614832.1 CDS TM1040_2838 NC_008044.1 3006131 3006685 R PFAM: response regulator receiver: (4e-23); KEGG: sil:SPO3865 photosynthetic apparatus regulatory protein RegA, ev=8e-89, 89% identity; response regulator receiver protein complement(3006131..3006685) Ruegeria sp. TM1040 4076657 YP_614833.1 CDS TM1040_2839 NC_008044.1 3006766 3007389 R 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 complement(3006766..3007389) Ruegeria sp. TM1040 4076658 YP_614834.1 CDS TM1040_2840 NC_008044.1 3007508 3008905 D 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 3007508..3008905 Ruegeria sp. TM1040 4076659 YP_614835.1 CDS TM1040_2841 NC_008044.1 3008991 3010541 D KEGG: sil:SPO3868 hypothetical protein, ev=1e-149, 53% identity; hypothetical protein 3008991..3010541 Ruegeria sp. TM1040 4076660 YP_614836.1 CDS TM1040_2842 NC_008044.1 3010583 3011059 D PFAM: protein of unknown function UPF0079: (6.3e-37); KEGG: sil:SPO3869 conserved hypothetical protein TIGR00150, ev=4e-41, 52% identity; hypothetical protein 3010583..3011059 Ruegeria sp. TM1040 4076661 YP_614837.1 CDS TM1040_2843 NC_008044.1 3011056 3012054 D PFAM: aminoglycoside phosphotransferase: (5.2e-27); KEGG: sil:SPO3870 hypothetical protein, ev=4e-89, 53% identity; aminoglycoside phosphotransferase 3011056..3012054 Ruegeria sp. TM1040 4076662 YP_614838.1 CDS TM1040_2844 NC_008044.1 3012051 3012731 D PFAM: Nucleotidyl transferase: (9.7e-07); KEGG: sil:SPO3871 nucleotidyltransferase family protein, ev=7e-66, 53% identity; nucleotidyl transferase 3012051..3012731 Ruegeria sp. TM1040 4076663 YP_614839.1 CDS TM1040_2845 NC_008044.1 3012733 3015666 D KEGG: sil:SPO3872 hypothetical protein, ev=0.0, 65% identity; hypothetical protein 3012733..3015666 Ruegeria sp. TM1040 4076664 YP_614840.1 CDS TM1040_2846 NC_008044.1 3015663 3019028 D 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 3015663..3019028 Ruegeria sp. TM1040 4076665 YP_614841.1 CDS TM1040_2847 NC_008044.1 3019090 3019410 D TIGRFAM: thioredoxin: (9.2e-52); PFAM: glutaredoxin: (0.0003) Thioredoxin domain: (2.8e-47); KEGG: sil:SPO3874 thioredoxin, ev=7e-52, 92% identity; thioredoxin 3019090..3019410 Ruegeria sp. TM1040 4076666 YP_614842.1 CDS TM1040_2848 NC_008044.1 3019551 3019745 R 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 complement(3019551..3019745) Ruegeria sp. TM1040 4076667 YP_614843.1 CDS TM1040_2849 NC_008044.1 3019981 3020538 D heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease peptidase subunit 3019981..3020538 Ruegeria sp. TM1040 4076668 YP_614844.1 CDS TM1040_2850 NC_008044.1 3020535 3021590 D KEGG: jan:Jann_0186 hypothetical protein, ev=2e-82, 50% identity; hypothetical protein 3020535..3021590 Ruegeria sp. TM1040 4076669 YP_614845.1 CDS hslU NC_008044.1 3021606 3022916 D heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease ATP-binding subunit HslU 3021606..3022916 Ruegeria sp. TM1040 4076385 YP_614846.1 CDS TM1040_2852 NC_008044.1 3022996 3024117 D PFAM: protein of unknown function DUF900, hydrolase-like: (3.4e-45); KEGG: sil:SPO3883 lipoprotein, , ev=3e-95, 53% identity; hypothetical protein 3022996..3024117 Ruegeria sp. TM1040 4076386 YP_614847.1 CDS TM1040_2853 NC_008044.1 3024125 3024727 R PFAM: Smr protein/MutS2: (4.1e-17); KEGG: sil:SPO3884 smr domain protein, ev=4e-73, 69% identity; Smr protein/MutS2 complement(3024125..3024727) Ruegeria sp. TM1040 4076387 YP_614848.1 CDS TM1040_2854 NC_008044.1 3024727 3025785 R PFAM: MltA: (2e-74) 3D: (3.7e-32); KEGG: sil:SPO3885 MltA/3D domain protein, ev=1e-138, 69% identity; MltA protein complement(3024727..3025785) Ruegeria sp. TM1040 4076388 YP_614849.1 CDS TM1040_2855 NC_008044.1 3025782 3026438 R 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 complement(3025782..3026438) Ruegeria sp. TM1040 4076389 YP_614850.1 CDS TM1040_2856 NC_008044.1 3026553 3027050 D PFAM: FxsA cytoplasmic membrane protein: (7e-33); KEGG: sil:SPO3887 FxsA, ev=8e-60, 72% identity; FxsA cytoplasmic membrane protein 3026553..3027050 Ruegeria sp. TM1040 4076390 YP_614851.1 CDS TM1040_2857 NC_008044.1 3027115 3027609 D 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 3027115..3027609 Ruegeria sp. TM1040 4076391 YP_614852.1 CDS TM1040_2858 NC_008044.1 3027669 3028400 R 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 complement(3027669..3028400) Ruegeria sp. TM1040 4076392 YP_614853.1 CDS coaE NC_008044.1 3028393 3028986 R catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis; dephospho-CoA kinase complement(3028393..3028986) Ruegeria sp. TM1040 4076393 YP_614854.1 CDS aroE NC_008044.1 3028986 3029816 R AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate; shikimate 5-dehydrogenase complement(3028986..3029816) Ruegeria sp. TM1040 4076394 YP_614855.1 CDS TM1040_2861 NC_008044.1 3029813 3030412 R PFAM: Maf-like protein: (1.3e-25); KEGG: sil:SPO3892 Maf, ev=6e-70, 66% identity; Maf-like protein complement(3029813..3030412) Ruegeria sp. TM1040 4076395 YP_614856.1 CDS TM1040_2862 NC_008044.1 3030831 3031286 D PFAM: conserved hypothetical protein 701: (6.3e-64); KEGG: sil:SPO3893 membrane protein, , ev=2e-62, 74% identity; hypothetical protein 3030831..3031286 Ruegeria sp. TM1040 4076396 YP_614857.1 CDS rho NC_008044.1 3031417 3032688 D An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes; transcription termination factor Rho 3031417..3032688 Ruegeria sp. TM1040 4076397 YP_614858.1 CDS trmE NC_008044.1 3032719 3034005 D 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 3032719..3034005 Ruegeria sp. TM1040 4076398 YP_614859.1 CDS TM1040_2865 NC_008044.1 3034009 3035892 D 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 3034009..3035892 Ruegeria sp. TM1040 4076399 YP_614860.1 CDS TM1040_2866 NC_008044.1 3035889 3036506 D 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 3035889..3036506 Ruegeria sp. TM1040 4076400 YP_614861.1 CDS TM1040_2867 NC_008044.1 3036499 3037311 D 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 3036499..3037311 Ruegeria sp. TM1040 4076401 YP_614862.1 CDS TM1040_2868 NC_008044.1 3037330 3038229 D 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 3037330..3038229 Ruegeria sp. TM1040 4076402 YP_614863.1 CDS TM1040_2869 NC_008044.1 3038219 3038572 R PFAM: protein of unknown function DUF454: (6.8e-12); KEGG: sil:SPO0005 hypothetical protein, ev=6e-43, 70% identity; hypothetical protein complement(3038219..3038572) Ruegeria sp. TM1040 4076403 YP_614864.1 CDS TM1040_2870 NC_008044.1 3038576 3039730 R catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase complement(3038576..3039730) Ruegeria sp. TM1040 4076404 YP_614865.1 CDS TM1040_2871 NC_008044.1 3039723 3040337 R 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 complement(3039723..3040337) Ruegeria sp. TM1040 4076405 YP_614866.1 CDS rph NC_008044.1 3040334 3041047 R 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 complement(3040334..3041047) Ruegeria sp. TM1040 4076406 YP_614867.1 CDS hrcA NC_008044.1 3041186 3042250 D 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 3041186..3042250 Ruegeria sp. TM1040 4076407 YP_614868.1 CDS TM1040_2874 NC_008044.1 3042260 3042823 D PFAM: GrpE protein: (2e-50); KEGG: sil:SPO0010 co-chaperone GrpE, ev=6e-84, 82% identity; heat shock protein GrpE 3042260..3042823 Ruegeria sp. TM1040 4076408 YP_614869.1 CDS TM1040_2875 NC_008044.1 3042910 3045549 R This protein performs the mismatch recognition step during the DNA repair process; DNA mismatch repair protein MutS complement(3042910..3045549) Ruegeria sp. TM1040 4076409 YP_614870.1 CDS TM1040_2876 NC_008044.1 3045670 3046518 R PFAM: flagellin-like: (7.4e-07); KEGG: ccr:CC0793 flagellin FljN, ev=5e-33, 32% identity; flagellin-like protein complement(3045670..3046518) Ruegeria sp. TM1040 4076410 YP_614871.1 CDS TM1040_2877 NC_008044.1 3046844 3049099 D NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate; malic enzyme 3046844..3049099 Ruegeria sp. TM1040 4076411 YP_614872.1 CDS TM1040_2878 NC_008044.1 3049119 3049991 D PFAM: PfkB: (2.6e-32); KEGG: sil:SPO0013 ribokinase, ev=1e-105, 65% identity; PfkB protein 3049119..3049991 Ruegeria sp. TM1040 4076412 YP_614873.1 CDS TM1040_2879 NC_008044.1 3050052 3050723 R 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 complement(3050052..3050723) Ruegeria sp. TM1040 4076413 YP_614874.1 CDS TM1040_2880 NC_008044.1 3050862 3051143 R PFAM: Sterol-binding: (1.4e-08); KEGG: sil:SPO0016 sterol carrier family protein, ev=9e-29, 66% identity; sterol-binding complement(3050862..3051143) Ruegeria sp. TM1040 4076414 YP_614875.1 CDS TM1040_2881 NC_008044.1 3051234 3051620 R PFAM: protein of unknown function DUF1036: (2.3e-41); KEGG: bja:blr7137 hypothetical protein, ev=2e-26, 44% identity; hypothetical protein complement(3051234..3051620) Ruegeria sp. TM1040 4076415 YP_614876.1 CDS TM1040_2882 NC_008044.1 3051722 3052183 R KEGG: sil:SPO0017 hypothetical protein, ev=3e-47, 63% identity; hypothetical protein complement(3051722..3052183) Ruegeria sp. TM1040 4076416 YP_614877.1 CDS TM1040_2883 NC_008044.1 3052183 3053406 R catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming; argininosuccinate synthase complement(3052183..3053406) Ruegeria sp. TM1040 4076417 YP_614878.1 CDS TM1040_2884 NC_008044.1 3053537 3054292 D KEGG: jan:Jann_0068 hypothetical protein, ev=2e-27, 30% identity; hypothetical protein 3053537..3054292 Ruegeria sp. TM1040 4076418 YP_614879.1 CDS TM1040_2885 NC_008044.1 3054365 3055591 D catalyzes the formation of 2-oxobutanoate from L-threonine; biosynthetic; threonine dehydratase 3054365..3055591 Ruegeria sp. TM1040 4076419 YP_614880.1 CDS TM1040_2886 NC_008044.1 3055623 3055979 R PFAM: Hpt: (6.2e-11); KEGG: sil:SPO0021 Hpt domain protein, ev=8e-29, 63% identity; Hpt protein complement(3055623..3055979) Ruegeria sp. TM1040 4076420 YP_614881.1 CDS TM1040_2887 NC_008044.1 3056120 3057391 D 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 3056120..3057391 Ruegeria sp. TM1040 4076421 YP_614882.1 CDS TM1040_2888 NC_008044.1 3057398 3057841 R PFAM: NUDIX hydrolase: (1e-18); KEGG: sil:SPO0023 hydrolase, NUDIX family, ev=3e-54, 70% identity; NUDIX hydrolase complement(3057398..3057841) Ruegeria sp. TM1040 4076422 YP_614883.1 CDS TM1040_2889 NC_008044.1 3057918 3058895 D PFAM: Hsp33 protein: (7.3e-53); KEGG: sil:SPO0024 chaperonin, 33 kDa, ev=1e-158, 84% identity; Hsp33 protein 3057918..3058895 Ruegeria sp. TM1040 4076423 YP_614884.1 CDS TM1040_2890 NC_008044.1 3058901 3059500 D PFAM: NUDIX hydrolase: (2.6e-12); KEGG: sil:SPO0025 hydrolase, NUDIX family, ev=4e-66, 66% identity; NUDIX hydrolase 3058901..3059500 Ruegeria sp. TM1040 4078568 YP_614885.1 CDS TM1040_2891 NC_008044.1 3059497 3060657 D PFAM: Polynucleotide adenylyltransferase region: (3.3e-38); KEGG: sil:SPO0026 polyA polymerase family protein, ev=1e-127, 62% identity; polynucleotide adenylyltransferase 3059497..3060657 Ruegeria sp. TM1040 4078569 YP_614886.1 CDS TM1040_2892 NC_008044.1 3060885 3062723 D 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 3060885..3062723 Ruegeria sp. TM1040 4078570 YP_614887.1 CDS TM1040_2893 NC_008044.1 3062720 3064564 D 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 3062720..3064564 Ruegeria sp. TM1040 4078571 YP_614888.1 CDS TM1040_2894 NC_008044.1 3064623 3065867 D 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 3064623..3065867 Ruegeria sp. TM1040 4078572 YP_614889.1 CDS TM1040_2895 NC_008044.1 3065895 3066680 D PFAM: Ion transport protein: (2.1e-34); KEGG: sil:SPO0030 voltage-gated sodium channel, ev=1e-106, 74% identity; Ion transport protein 3065895..3066680 Ruegeria sp. TM1040 4078573 YP_614890.1 CDS TM1040_2896 NC_008044.1 3066782 3067270 D 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 3066782..3067270 Ruegeria sp. TM1040 4078574 YP_614891.1 CDS TM1040_2897 NC_008044.1 3067377 3067907 R PFAM: Allergen V5/Tpx-1 related: (1.4e-10); KEGG: sil:SPO0076 lipoprotein, , ev=9e-52, 63% identity; Allergen V5/Tpx-1 related complement(3067377..3067907) Ruegeria sp. TM1040 4078575 YP_614892.1 CDS TM1040_2898 NC_008044.1 3068040 3068657 D 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 3068040..3068657 Ruegeria sp. TM1040 4078576 YP_614893.1 CDS TM1040_2899 NC_008044.1 3068800 3068982 D KEGG: sil:SPO0074 hypothetical protein, ev=1e-16, 73% identity; hypothetical protein 3068800..3068982 Ruegeria sp. TM1040 4078577 YP_614894.1 CDS hemH NC_008044.1 3069070 3070134 R 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 complement(3069070..3070134) Ruegeria sp. TM1040 4078578 YP_614895.1 CDS TM1040_2901 NC_008044.1 3070236 3071075 R KEGG: sil:SPO0072 hypothetical protein, ev=1e-90, 62% identity; hypothetical protein complement(3070236..3071075) Ruegeria sp. TM1040 4078579 YP_614896.1 CDS TM1040_2902 NC_008044.1 3071087 3071818 D KEGG: sil:SPO0071 competence protein F, , ev=1e-80, 61% identity; competence protein F 3071087..3071818 Ruegeria sp. TM1040 4078580 YP_614897.1 CDS TM1040_2903 NC_008044.1 3071890 3072147 D TIGRFAM: Glutaredoxin, GrxC: (2.4e-49); PFAM: glutaredoxin: (3e-25); KEGG: sil:SPO0070 glutaredoxin, ev=4e-32, 74% identity; glutaredoxin GrxC 3071890..3072147 Ruegeria sp. TM1040 4078581 YP_614898.1 CDS TM1040_2904 NC_008044.1 3072152 3072985 D 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 3072152..3072985 Ruegeria sp. TM1040 4078582 YP_614899.1 CDS TM1040_2905 NC_008044.1 3072985 3073425 D PFAM: regulatory protein, MarR: (3.4e-08); KEGG: sil:SPO0068 transcriptional regulator, , ev=2e-54, 72% identity; MarR family transcriptional regulator 3072985..3073425 Ruegeria sp. TM1040 4078583 YP_614900.1 CDS TM1040_2906 NC_008044.1 3073732 3074475 R Involved in ubiquinone biosynthesis; 3-demethylubiquinone-9 3-methyltransferase complement(3073732..3074475) Ruegeria sp. TM1040 4078584 YP_614901.1 CDS TM1040_2907 NC_008044.1 3074527 3075507 D 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 3074527..3075507 Ruegeria sp. TM1040 4078585 YP_614902.1 CDS TM1040_2908 NC_008044.1 3075504 3076355 D 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 3075504..3076355 Ruegeria sp. TM1040 4078586 YP_614903.1 CDS TM1040_2909 NC_008044.1 3076592 3077203 D 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 3076592..3077203 Ruegeria sp. TM1040 4078587 YP_614904.1 CDS nusA NC_008044.1 3077203 3078819 D modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination; transcription elongation factor NusA 3077203..3078819 Ruegeria sp. TM1040 4078588 YP_614905.1 CDS TM1040_2911 NC_008044.1 3078849 3079466 D PFAM: protein of unknown function DUF448: (1.6e-28); KEGG: sil:SPO0062 hypothetical protein, ev=3e-84, 74% identity; hypothetical protein 3078849..3079466 Ruegeria sp. TM1040 4078589 YP_614906.1 CDS infB NC_008044.1 3079475 3081982 D 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 3079475..3081982 Ruegeria sp. TM1040 4078590 YP_614907.1 CDS TM1040_2913 NC_008044.1 3082087 3082383 R hypothetical protein complement(3082087..3082383) Ruegeria sp. TM1040 4078591 YP_614908.1 CDS TM1040_2914 NC_008044.1 3082512 3082922 R 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 complement(3082512..3082922) Ruegeria sp. TM1040 4078592 YP_614909.1 CDS argJ NC_008044.1 3082919 3084145 R 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 complement(3082919..3084145) Ruegeria sp. TM1040 4078593 YP_614910.1 CDS TM1040_2916 NC_008044.1 3084178 3085029 R 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 complement(3084178..3085029) Ruegeria sp. TM1040 4078594 YP_614911.1 CDS TM1040_2917 NC_008044.1 3085207 3087894 D 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 3085207..3087894 Ruegeria sp. TM1040 4078595 YP_614912.1 CDS TM1040_2918 NC_008044.1 3088030 3088926 D KEGG: jan:Jann_0288 hypothetical protein, ev=3e-32, 35% identity; hypothetical protein 3088030..3088926 Ruegeria sp. TM1040 4078596 YP_614913.1 CDS TM1040_2919 NC_008044.1 3088950 3090503 D PFAM: OmpA/MotB: (0.00021); KEGG: sil:SPO0055 OmpA domain protein, ev=0.0, 67% identity; OmpA/MotB protein 3088950..3090503 Ruegeria sp. TM1040 4078597 YP_614914.1 CDS TM1040_2920 NC_008044.1 3090662 3092599 R catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate; 1-deoxy-D-xylulose-5-phosphate synthase complement(3090662..3092599) Ruegeria sp. TM1040 4078598 YP_614915.1 CDS TM1040_2921 NC_008044.1 3092630 3093493 R PFAM: Polyprenyl synthetase: (3.4e-68); KEGG: rsp:RSP_1135 geranylgeranyl pyrophosphate synthetase, ev=2e-93, 65% identity; farnesyl-diphosphate synthase complement(3092630..3093493) Ruegeria sp. TM1040 4078599 YP_614916.1 CDS TM1040_2922 NC_008044.1 3093500 3093745 R 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 complement(3093500..3093745) Ruegeria sp. TM1040 4078600 YP_614917.1 CDS TM1040_2923 NC_008044.1 3093742 3094668 R PFAM: histone deacetylase superfamily: (1.9e-82); KEGG: sil:SPO0250 histone deacetylase family protein, ev=1e-139, 77% identity; histone deacetylase superfamily protein complement(3093742..3094668) Ruegeria sp. TM1040 4078601 YP_614918.1 CDS TM1040_2924 NC_008044.1 3094788 3095492 R 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 complement(3094788..3095492) Ruegeria sp. TM1040 4078602 YP_614919.1 CDS TM1040_2925 NC_008044.1 3095489 3096001 R PFAM: regulatory protein, MarR: (1.2e-07); KEGG: sil:SPO0252 transcriptional regulator PetP, ev=5e-71, 79% identity; MarR family transcriptional regulator complement(3095489..3096001) Ruegeria sp. TM1040 4078603 YP_614920.1 CDS TM1040_2926 NC_008044.1 3096162 3097028 D catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids; branched-chain amino acid aminotransferase 3096162..3097028 Ruegeria sp. TM1040 4078604 YP_614921.1 CDS TM1040_2927 NC_008044.1 3097197 3097625 R PFAM: OsmC-like protein: (1.1e-32); KEGG: sil:SPO0254 organic hydroperoxide resistance protein, ev=1e-50, 67% identity; OsmC-like protein complement(3097197..3097625) Ruegeria sp. TM1040 4078605 YP_614922.1 CDS TM1040_2928 NC_008044.1 3097733 3098164 D PFAM: regulatory protein, MarR: (8.1e-20); KEGG: sil:SPO0255 transcriptional regulator, MarR family, ev=3e-44, 61% identity; MarR family transcriptional regulator 3097733..3098164 Ruegeria sp. TM1040 4078606 YP_614923.1 CDS TM1040_2929 NC_008044.1 3098183 3099124 R 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 complement(3098183..3099124) Ruegeria sp. TM1040 4077080 YP_614924.1 CDS TM1040_2930 NC_008044.1 3099209 3099859 R PFAM: cation efflux protein: (0.00014); KEGG: bja:bll4927 hypothetical protein, ev=7e-72, 66% identity; cation efflux protein complement(3099209..3099859) Ruegeria sp. TM1040 4077081 YP_614925.1 CDS TM1040_2931 NC_008044.1 3099944 3100360 D PFAM: regulatory protein, MerR: (3e-11); KEGG: sil:SPOA0389 transcriptional regulator, MerR family, ev=5e-39, 56% identity; MerR family transcriptional regulator 3099944..3100360 Ruegeria sp. TM1040 4077082 YP_614926.1 CDS TM1040_2932 NC_008044.1 3100370 3101275 R 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 complement(3100370..3101275) Ruegeria sp. TM1040 4077083 YP_614927.1 CDS TM1040_2933 NC_008044.1 3101671 3102390 D KEGG: jan:Jann_2250 hypothetical protein, ev=2e-64, 50% identity; hypothetical protein 3101671..3102390 Ruegeria sp. TM1040 4077084 YP_614928.1 CDS TM1040_2934 NC_008044.1 3102377 3103309 D PFAM: periplasmic binding protein: (3.5e-10); KEGG: jan:Jann_2249 periplasmic binding protein, ev=1e-106, 63% identity; periplasmic binding protein 3102377..3103309 Ruegeria sp. TM1040 4077085 YP_614929.1 CDS TM1040_2935 NC_008044.1 3103310 3104317 D PFAM: transport system permease protein: (6e-92); KEGG: jan:Jann_2248 transport system permease protein, ev=1e-114, 62% identity; transport system permease 3103310..3104317 Ruegeria sp. TM1040 4077086 YP_614930.1 CDS TM1040_2936 NC_008044.1 3104307 3105140 D 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 3104307..3105140 Ruegeria sp. TM1040 4077087 YP_614931.1 CDS TM1040_2937 NC_008044.1 3105098 3107272 R 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 complement(3105098..3107272) Ruegeria sp. TM1040 4077088 YP_614932.1 CDS TM1040_2938 NC_008044.1 3107839 3108678 D PFAM: OmpA/MotB: (2.3e-05); KEGG: sil:SPO0191 chemotaxis protein MotB, ev=3e-91, 60% identity; OmpA/MotB protein 3107839..3108678 Ruegeria sp. TM1040 4077089 YP_614933.1 CDS TM1040_2939 NC_008044.1 3108809 3110077 D 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 3108809..3110077 Ruegeria sp. TM1040 4077090 YP_614934.1 CDS flgK NC_008044.1 3110129 3111577 D with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook; flagellar hook-associated protein FlgK 3110129..3111577 Ruegeria sp. TM1040 4077091 YP_614935.1 CDS TM1040_2941 NC_008044.1 3111581 3112588 D KEGG: sil:SPO0194 flagellar hook-associated protein FlgL family protein, ev=4e-58, 37% identity; flagellar hook-associated protein FlgL family protein 3111581..3112588 Ruegeria sp. TM1040 4077092 YP_614936.1 CDS flgI NC_008044.1 3112588 3113691 D 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 3112588..3113691 Ruegeria sp. TM1040 4077093 YP_614937.1 CDS TM1040_2943 NC_008044.1 3113864 3114184 R hypothetical protein complement(3113864..3114184) Ruegeria sp. TM1040 4077094 YP_614938.1 CDS fliP NC_008044.1 3114200 3114946 R FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus; flagellar biosynthesis protein FliP complement(3114200..3114946) Ruegeria sp. TM1040 4077095 YP_614939.1 CDS TM1040_2945 NC_008044.1 3114943 3115239 R 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 complement(3114943..3115239) Ruegeria sp. TM1040 4077096 YP_614940.1 CDS TM1040_2946 NC_008044.1 3115232 3115828 R KEGG: sil:SPO0198 ABC transporter, ATP-binding protein, flagellar, , ev=2e-45, 46% identity; flagellar ABC transporter ATP-binding protein complement(3115232..3115828) Ruegeria sp. TM1040 4077097 YP_614941.1 CDS fliF NC_008044.1 3115828 3117543 R 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 complement(3115828..3117543) Ruegeria sp. TM1040 4077098 YP_614942.1 CDS TM1040_2948 NC_008044.1 3117624 3118148 D 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 3117624..3118148 Ruegeria sp. TM1040 4077099 YP_614943.1 CDS TM1040_2949 NC_008044.1 3118158 3118616 D KEGG: sil:SPO0201 hypothetical protein, ev=9e-40, 59% identity; hypothetical protein 3118158..3118616 Ruegeria sp. TM1040 4077100 YP_614944.1 CDS TM1040_2950 NC_008044.1 3118616 3119233 D KEGG: sil:SPO0202 hypothetical protein, ev=2e-51, 57% identity; hypothetical protein 3118616..3119233 Ruegeria sp. TM1040 4077101 YP_614945.1 CDS TM1040_2951 NC_008044.1 3119308 3120177 D 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 3119308..3120177 Ruegeria sp. TM1040 4077102 YP_614946.1 CDS TM1040_2952 NC_008044.1 3120174 3122588 D KEGG: sil:SPO0204 hypothetical protein, ev=1e-77, 28% identity; hypothetical protein 3120174..3122588 Ruegeria sp. TM1040 4077103 YP_614947.1 CDS flhA NC_008044.1 3122923 3125013 D membrane protein involved in the flagellar export apparatus; flagellar biosynthesis protein FlhA 3122923..3125013 Ruegeria sp. TM1040 4077104 YP_614948.1 CDS TM1040_2954 NC_008044.1 3125010 3125789 D KEGG: sil:SPO0171 flagellar biosynthetic protein FliR, ev=1e-70, 51% identity; flagellar biosynthetic protein FliR 3125010..3125789 Ruegeria sp. TM1040 4077105 YP_614949.1 CDS flhB NC_008044.1 3125786 3126877 D membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export; flagellar biosynthesis protein FlhB 3125786..3126877 Ruegeria sp. TM1040 4077106 YP_614950.1 CDS TM1040_2956 NC_008044.1 3126889 3127278 D KEGG: sil:SPO0173 hypothetical protein, ev=2e-19, 38% identity; hypothetical protein 3126889..3127278 Ruegeria sp. TM1040 4077107 YP_614951.1 CDS TM1040_2957 NC_008044.1 3127555 3128064 R KEGG: sil:SPO0174 hypothetical protein, ev=2e-38, 45% identity; hypothetical protein complement(3127555..3128064) Ruegeria sp. TM1040 4077108 YP_614952.1 CDS flgH NC_008044.1 3128076 3128813 R 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 complement(3128076..3128813) Ruegeria sp. TM1040 4077109 YP_614953.1 CDS flgA NC_008044.1 3128813 3129229 R required for the assembly of the flagellar basal body P-ring; flagellar basal body P-ring biosynthesis protein FlgA complement(3128813..3129229) Ruegeria sp. TM1040 4077110 YP_614954.1 CDS flgG NC_008044.1 3129230 3130015 R 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 complement(3129230..3130015) Ruegeria sp. TM1040 4077111 YP_614955.1 CDS flgF NC_008044.1 3130025 3130741 R 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 complement(3130025..3130741) Ruegeria sp. TM1040 4077112 YP_614956.1 CDS TM1040_2962 NC_008044.1 3130741 3131019 R PFAM: export protein FliQ, family 3: (3.9e-14); KEGG: sil:SPO0179 flagellar biosynthetic protein FliQ, ev=5e-27, 65% identity; export protein FliQ complement(3130741..3131019) Ruegeria sp. TM1040 4077113 YP_614957.1 CDS fliE NC_008044.1 3131023 3131319 R 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 complement(3131023..3131319) Ruegeria sp. TM1040 4077114 YP_614958.1 CDS flgC NC_008044.1 3131343 3131735 R with FlgF and B makes up the proximal portion of the flagellar basal body rod; flagellar basal body rod protein FlgC complement(3131343..3131735) Ruegeria sp. TM1040 4077115 YP_614959.1 CDS flgB NC_008044.1 3131752 3132141 R with FlgF and C makes up the proximal portion of the flagellar basal body rod; flagellar basal-body rod protein FlgB complement(3131752..3132141) Ruegeria sp. TM1040 4077116 YP_614960.1 CDS TM1040_2966 NC_008044.1 3132230 3133558 D 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 3132230..3133558 Ruegeria sp. TM1040 4077117 YP_614961.1 CDS TM1040_2967 NC_008044.1 3133720 3134007 D 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 3133720..3134007 Ruegeria sp. TM1040 4077118 YP_614962.1 CDS TM1040_2968 NC_008044.1 3134061 3134855 D PFAM: Integrase, catalytic region: (3.3e-31); KEGG: jan:Jann_3728 integrase protein, ev=1e-100, 76% identity; integrase catalytic subunit 3134061..3134855 Ruegeria sp. TM1040 4077998 YP_614963.1 CDS TM1040_2969 NC_008044.1 3134929 3135195 D 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 3134929..3135195 Ruegeria sp. TM1040 4077999 YP_614964.1 CDS TM1040_2970 NC_008044.1 3135228 3136025 D PFAM: Integrase, catalytic region: (4.6e-37); KEGG: mlo:mll6088 transposase, ev=1e-117, 75% identity; integrase catalytic subunit 3135228..3136025 Ruegeria sp. TM1040 4078000 YP_614965.1 CDS TM1040_2971 NC_008044.1 3136295 3138247 R KEGG: sil:SPO3456 flagellar protein, , ev=4e-43, 33% identity; hypothetical protein complement(3136295..3138247) Ruegeria sp. TM1040 4078001 YP_614966.1 CDS flbT NC_008044.1 3138244 3138648 R 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 complement(3138244..3138648) Ruegeria sp. TM1040 4078002 YP_614967.1 CDS flaF NC_008044.1 3138651 3139022 R 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 complement(3138651..3139022) Ruegeria sp. TM1040 4078003 YP_614968.1 CDS TM1040_2974 NC_008044.1 3139109 3139957 R PFAM: flagellin-like: (1.6e-06); KEGG: sil:SPO3459 flagellin protein, ev=5e-47, 55% identity; flagellin-like protein complement(3139109..3139957) Ruegeria sp. TM1040 4078004 YP_614969.1 CDS TM1040_2975 NC_008044.1 3140173 3140541 R KEGG: sil:SPO3460 hypothetical protein, ev=3e-24, 51% identity; hypothetical protein complement(3140173..3140541) Ruegeria sp. TM1040 4078005 YP_614970.1 CDS TM1040_2976 NC_008044.1 3140538 3140828 R KEGG: sil:SPO3461 flagellar protein FlgJ, , ev=8e-22, 55% identity; flagellar protein FlgJ complement(3140538..3140828) Ruegeria sp. TM1040 4078006 YP_614971.1 CDS TM1040_2977 NC_008044.1 3140954 3142540 D KEGG: sil:SPO3462 flagellar hook-length control protein, ev=7e-20, 24% identity; hypothetical protein 3140954..3142540 Ruegeria sp. TM1040 4078007 YP_614972.1 CDS flgD NC_008044.1 3142545 3143240 D 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 3142545..3143240 Ruegeria sp. TM1040 4078008 YP_614973.1 CDS TM1040_2979 NC_008044.1 3143290 3144138 D PFAM: aminoglycoside phosphotransferase: (1.4e-19); KEGG: sil:SPO3464 hypothetical protein, ev=1e-61, 50% identity; aminoglycoside phosphotransferase 3143290..3144138 Ruegeria sp. TM1040 4078009 YP_614974.1 CDS TM1040_2980 NC_008044.1 3144135 3145442 R PFAM: FAD dependent oxidoreductase: (5.5e-71); KEGG: sil:SPO3465 hypothetical protein, ev=1e-150, 60% identity; FAD dependent oxidoreductase complement(3144135..3145442) Ruegeria sp. TM1040 4078010 YP_614975.1 CDS TM1040_2981 NC_008044.1 3145439 3146257 R 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 complement(3145439..3146257) Ruegeria sp. TM1040 4078011 YP_614976.1 CDS TM1040_2982 NC_008044.1 3146254 3147135 R 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 complement(3146254..3147135) Ruegeria sp. TM1040 4078012 YP_614977.1 CDS TM1040_2983 NC_008044.1 3147135 3148331 R 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 complement(3147135..3148331) Ruegeria sp. TM1040 4078013 YP_614978.1 CDS TM1040_2984 NC_008044.1 3148365 3149453 R 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 complement(3148365..3149453) Ruegeria sp. TM1040 4078014 YP_614979.1 CDS TM1040_2985 NC_008044.1 3149540 3150286 D 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 3149540..3150286 Ruegeria sp. TM1040 4078015 YP_614980.1 CDS TM1040_2986 NC_008044.1 3150350 3151747 D PFAM: aminotransferase class-III: (4.2e-109); KEGG: sil:SPO3471 aminotransferase, class III, ev=0.0, 82% identity; aminotransferase 3150350..3151747 Ruegeria sp. TM1040 4078016 YP_614981.1 CDS TM1040_2987 NC_008044.1 3152051 3153151 D 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 3152051..3153151 Ruegeria sp. TM1040 4078017 YP_614982.1 CDS TM1040_2988 NC_008044.1 3153256 3154362 D KEGG: jan:Jann_1267 polyamine ABC trasnporter, periplasmic polyamine-binding protein, ev=1e-153, 68% identity; polyamine ABC transporter substrate-binding protein 3153256..3154362 Ruegeria sp. TM1040 4078018 YP_614983.1 CDS TM1040_2989 NC_008044.1 3154473 3156098 D 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 3154473..3156098 Ruegeria sp. TM1040 4078019 YP_614984.1 CDS TM1040_2990 NC_008044.1 3156106 3157281 D 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 3156106..3157281 Ruegeria sp. TM1040 4078020 YP_614985.1 CDS TM1040_2991 NC_008044.1 3157346 3158713 R 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 complement(3157346..3158713) Ruegeria sp. TM1040 4078021 YP_614986.1 CDS TM1040_2992 NC_008044.1 3158821 3159579 R 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 complement(3158821..3159579) Ruegeria sp. TM1040 4078022 YP_614987.1 CDS TM1040_2993 NC_008044.1 3159600 3160313 D KEGG: sil:SPO3486 hypothetical protein, ev=4e-40, 42% identity; hypothetical protein 3159600..3160313 Ruegeria sp. TM1040 4078023 YP_614988.1 CDS TM1040_2994 NC_008044.1 3160462 3162747 R 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 complement(3160462..3162747) Ruegeria sp. TM1040 4078024 YP_614989.1 CDS TM1040_2995 NC_008044.1 3162863 3163285 R PFAM: GCN5-related N-acetyltransferase: (2.8e-17); KEGG: rsp:RSP_1127 acetyltransferase, GNAT family, ev=2e-33, 54% identity; N-acetyltransferase GCN5 complement(3162863..3163285) Ruegeria sp. TM1040 4078025 YP_614990.1 CDS TM1040_2996 NC_008044.1 3163282 3164427 R 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 complement(3163282..3164427) Ruegeria sp. TM1040 4078026 YP_614991.1 CDS TM1040_2997 NC_008044.1 3164896 3165993 D KEGG: sil:SPO3334 hypothetical protein, ev=7e-92, 48% identity; hypothetical protein 3164896..3165993 Ruegeria sp. TM1040 4078027 YP_614992.1 CDS TM1040_2998 NC_008044.1 3166064 3167128 D 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 3166064..3167128 Ruegeria sp. TM1040 4078028 YP_614993.1 CDS TM1040_2999 NC_008044.1 3167180 3167545 R KEGG: sil:SPO3336 hypothetical protein, ev=2e-45, 83% identity; hypothetical protein complement(3167180..3167545) Ruegeria sp. TM1040 4078029 YP_614994.1 CDS TM1040_3000 NC_008044.1 3167703 3169283 D KEGG: sil:SPO3333 hypothetical protein, ev=1e-127, 47% identity; hypothetical protein 3167703..3169283 Ruegeria sp. TM1040 4078030 YP_614995.1 CDS TM1040_3001 NC_008044.1 3169277 3169930 R 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 complement(3169277..3169930) Ruegeria sp. TM1040 4078031 YP_614996.1 CDS TM1040_3002 NC_008044.1 3170058 3170588 D PFAM: protein of unknown function DUF886: (4.4e-11); KEGG: sil:SPO2147 hypothetical protein, ev=7e-20, 43% identity; hypothetical protein 3170058..3170588 Ruegeria sp. TM1040 4078032 YP_614997.1 CDS TM1040_3003 NC_008044.1 3170563 3171927 R catalyzes the deimination of N-formimino-L-glutamate to ammonia and N-formyl-L-glutamate; N-formimino-L-glutamate deiminase complement(3170563..3171927) Ruegeria sp. TM1040 4078033 YP_614998.1 CDS TM1040_3004 NC_008044.1 3172003 3173220 D catalyzing the hydrolysis of 4-imidazolone-5-propionate to N-formimidoyl-L-glutamate, the third step in the histidine degradation pathway; imidazolonepropionase 3172003..3173220 Ruegeria sp. TM1040 4078034 YP_614999.1 CDS TM1040_3005 NC_008044.1 3173217 3174740 D catalyzes the degradation of histidine to urocanate and ammmonia; histidine ammonia-lyase 3173217..3174740 Ruegeria sp. TM1040 4078035 YP_615000.1 CDS TM1040_3006 NC_008044.1 3174737 3175513 D PFAM: N-formylglutamate amidohydrolase: (1.7e-88); KEGG: atc:AGR_L_1827 N-formylglutamate amidohydrolase, ev=2e-94, 64% identity; N-formylglutamate amidohydrolase 3174737..3175513 Ruegeria sp. TM1040 4078036 YP_615001.1 CDS TM1040_3007 NC_008044.1 3175510 3177198 D catalyzes the formation of 4-imidazolone-5-propanoate from urocanate during histidine metabolism; urocanate hydratase 3175510..3177198 Ruegeria sp. TM1040 4076580 YP_615002.1 CDS TM1040_3008 NC_008044.1 3177254 3177643 R PFAM: Glyoxalase/bleomycin resistance protein/dioxygenase: (2.9e-05); KEGG: mca:MCA2808 hypothetical protein, ev=8e-16, 34% identity; glyoxalase/bleomycin resistance protein/dioxygenase complement(3177254..3177643) Ruegeria sp. TM1040 4076581 YP_615003.2 CDS dapD NC_008044.1 3177816 3178643 R 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 complement(3177816..3178643) Ruegeria sp. TM1040 4076582 YP_615004.1 CDS TM1040_3010 NC_008044.1 3178764 3179393 R 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 complement(3178764..3179393) Ruegeria sp. TM1040 4076583 YP_615005.1 CDS TM1040_3011 NC_008044.1 3179412 3180365 R catalyzes the formation of 2-oxobutanoate from L-threonine; threonine dehydratase complement(3179412..3180365) Ruegeria sp. TM1040 4076584 YP_615006.1 CDS TM1040_3012 NC_008044.1 3180522 3181370 D PFAM: conserved hypothetical protein 730: (3e-58); KEGG: sil:SPO3342 decarboxylase family protein, ev=1e-119, 74% identity; hypothetical protein 3180522..3181370 Ruegeria sp. TM1040 4076585 YP_615007.1 CDS TM1040_3013 NC_008044.1 3181566 3181769 R KEGG: sil:SPO3343 hypothetical protein, ev=1e-12, 55% identity; hypothetical protein complement(3181566..3181769) Ruegeria sp. TM1040 4076586 YP_615008.1 CDS TM1040_3014 NC_008044.1 3181937 3183130 R 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 complement(3181937..3183130) Ruegeria sp. TM1040 4076587 YP_615009.1 CDS TM1040_3015 NC_008044.1 3183354 3183902 R KEGG: sil:SPO3348 hypothetical protein, ev=3e-65, 69% identity; hypothetical protein complement(3183354..3183902) Ruegeria sp. TM1040 4076588 YP_615010.1 CDS TM1040_3016 NC_008044.1 3184117 3185124 D PFAM: L-asparaginase II: (2.3e-103); KEGG: sil:SPO3349 L-asparaginase, thermolabile family, ev=1e-122, 65% identity; L-asparaginase II 3184117..3185124 Ruegeria sp. TM1040 4076589 YP_615011.1 CDS TM1040_3017 NC_008044.1 3185138 3185458 R PFAM: DGPFAETKE: (4.8e-06); KEGG: sil:SPO3350 hypothetical protein, ev=8e-37, 70% identity; hypothetical protein complement(3185138..3185458) Ruegeria sp. TM1040 4076590 YP_615012.1 CDS TM1040_3018 NC_008044.1 3185545 3186303 R PFAM: protein of unknown function DUF81: (1.4e-31); KEGG: mlo:mlr1193 hypothetical protein, ev=1e-78, 58% identity; hypothetical protein complement(3185545..3186303) Ruegeria sp. TM1040 4076591 YP_615013.1 CDS TM1040_3019 NC_008044.1 3186312 3187187 R 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 complement(3186312..3187187) Ruegeria sp. TM1040 4076592 YP_615014.1 CDS TM1040_3020 NC_008044.1 3187424 3188569 D catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate; phosphoserine aminotransferase 3187424..3188569 Ruegeria sp. TM1040 4076593 YP_615015.1 CDS TM1040_3021 NC_008044.1 3188663 3190258 D 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 3188663..3190258 Ruegeria sp. TM1040 4076594 YP_615016.1 CDS TM1040_3022 NC_008044.1 3190437 3191171 D PFAM: metallophosphoesterase: (4.5e-13); KEGG: sil:SPO3358 serine/threonine protein phosphatase family protein, ev=8e-81, 58% identity; bis(5'-nucleosyl)-tetraphosphatase 3190437..3191171 Ruegeria sp. TM1040 4076595 YP_615017.1 CDS tdh NC_008044.1 3191378 3192424 R converts threonine and NAD to 1,2-amino-3-oxobutanoate and NADH; functions in threonine catabolism; L-threonine 3-dehydrogenase complement(3191378..3192424) Ruegeria sp. TM1040 4076596 YP_615018.1 CDS TM1040_3024 NC_008044.1 3192426 3193610 R catalyzes the formation of 2-amino-3-oxobutanoate from acetyl-CoA and glycine; 2-amino-3-ketobutyrate CoA ligase complement(3192426..3193610) Ruegeria sp. TM1040 4076597 YP_615019.1 CDS TM1040_3025 NC_008044.1 3193775 3194341 R 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 complement(3193775..3194341) Ruegeria sp. TM1040 4076598 YP_615020.1 CDS TM1040_3026 NC_008044.1 3194450 3195625 D catalyzes the formation of beta-ketovaleryl-CoA from acetyl-CoA and propionyl-CoA; beta-ketothiolase 3194450..3195625 Ruegeria sp. TM1040 4076599 YP_615021.1 CDS TM1040_3027 NC_008044.1 3195735 3197261 R 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 complement(3195735..3197261) Ruegeria sp. TM1040 4076600 YP_615022.1 CDS TM1040_3028 NC_008044.1 3197265 3198017 R 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 complement(3197265..3198017) Ruegeria sp. TM1040 4076601 YP_615023.1 CDS TM1040_3029 NC_008044.1 3198104 3198955 D 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 3198104..3198955 Ruegeria sp. TM1040 4076602 YP_615024.1 CDS TM1040_3030 NC_008044.1 3199021 3199797 D PFAM: Enoyl-CoA hydratase/isomerase: (4.1e-74); KEGG: sil:SPO0147 enoyl-CoA hydratase, ev=1e-116, 80% identity; short chain enoyl-CoA hydratase 3199021..3199797 Ruegeria sp. TM1040 4076603 YP_615025.1 CDS rpsT NC_008044.1 3200122 3200385 D binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase; 30S ribosomal protein S20 3200122..3200385 Ruegeria sp. TM1040 4076604 TM1040_R0081 tRNA TM1040_R0081 NC_008042.1 8272 8348 R tRNA-Met complement(8272..8348) Ruegeria sp. TM1040 4074890 TM1040_R0084 tRNA TM1040_R0084 NC_008042.1 12084 12159 R tRNA-Ala complement(12084..12159) Ruegeria sp. TM1040 4074893 TM1040_R0085 tRNA TM1040_R0085 NC_008042.1 12225 12301 R tRNA-Ile complement(12225..12301) Ruegeria sp. TM1040 4074894 TM1040_R0087 tRNA TM1040_R0087 NC_008042.1 23609 23684 R tRNA-Thr complement(23609..23684) Ruegeria sp. TM1040 4074896 TM1040_R0052 tRNA TM1040_R0052 NC_008043.1 56033 56119 R tRNA-Leu complement(56033..56119) Ruegeria sp. TM1040 4075534 TM1040_R0053 tRNA TM1040_R0053 NC_008043.1 101719 101795 R tRNA-Arg complement(101719..101795) Ruegeria sp. TM1040 4074999 TM1040_R0054 tRNA TM1040_R0054 NC_008043.1 173064 173140 R tRNA-Met complement(173064..173140) Ruegeria sp. TM1040 4075358 TM1040_R0057 tRNA TM1040_R0057 NC_008043.1 176932 177007 R tRNA-Ala complement(176932..177007) Ruegeria sp. TM1040 4075289 TM1040_R0058 tRNA TM1040_R0058 NC_008043.1 177073 177149 R tRNA-Ile complement(177073..177149) Ruegeria sp. TM1040 4075290 TM1040_R0060 tRNA TM1040_R0060 NC_008043.1 309837 309913 R tRNA-Arg complement(309837..309913) Ruegeria sp. TM1040 4075706 TM1040_R0062 tRNA TM1040_R0062 NC_008043.1 403923 403998 R tRNA-Ala complement(403923..403998) Ruegeria sp. TM1040 4075286 TM1040_R0064 tRNA TM1040_R0064 NC_008043.1 507587 507663 D tRNA-Ile 507587..507663 Ruegeria sp. TM1040 4075115 TM1040_R0065 tRNA TM1040_R0065 NC_008043.1 507729 507804 D tRNA-Ala 507729..507804 Ruegeria sp. TM1040 4075116 TM1040_R0068 tRNA TM1040_R0068 NC_008043.1 511596 511672 D tRNA-Met 511596..511672 Ruegeria sp. TM1040 4075119 TM1040_R0069 tRNA TM1040_R0069 NC_008043.1 598854 598928 R tRNA-Phe complement(598854..598928) Ruegeria sp. TM1040 4075230 TM1040_R0070 tRNA TM1040_R0070 NC_008043.1 605916 605990 R tRNA-Thr complement(605916..605990) Ruegeria sp. TM1040 4075485 TM1040_R0072 tRNA TM1040_R0072 NC_008043.1 623839 623915 D tRNA-Ile 623839..623915 Ruegeria sp. TM1040 4075502 TM1040_R0073 tRNA TM1040_R0073 NC_008043.1 623981 624056 D tRNA-Ala 623981..624056 Ruegeria sp. TM1040 4075503 TM1040_R0076 tRNA TM1040_R0076 NC_008043.1 627848 627924 D tRNA-Met 627848..627924 Ruegeria sp. TM1040 4075506 TM1040_R0077 tRNA TM1040_R0077 NC_008043.1 637570 637659 R tRNA-Ser complement(637570..637659) Ruegeria sp. TM1040 4075515 TM1040_R0078 tRNA TM1040_R0078 NC_008043.1 690461 690536 R tRNA-Thr complement(690461..690536) Ruegeria sp. TM1040 4075061 TM1040_R0080 tRNA TM1040_R0080 NC_008043.1 815517 815593 R tRNA-Pro complement(815517..815593) Ruegeria sp. TM1040 4075468 TM1040_R0001 tRNA TM1040_R0001 NC_008044.1 133517 133591 R tRNA-Val complement(133517..133591) Ruegeria sp. TM1040 4076605 TM1040_R0003 tRNA TM1040_R0003 NC_008044.1 146556 146632 D tRNA-Ile 146556..146632 Ruegeria sp. TM1040 4076607 TM1040_R0004 tRNA TM1040_R0004 NC_008044.1 146698 146773 D tRNA-Ala 146698..146773 Ruegeria sp. TM1040 4076608 TM1040_R0007 tRNA TM1040_R0007 NC_008044.1 150565 150641 D tRNA-Met 150565..150641 Ruegeria sp. TM1040 4076611 TM1040_R0009 tRNA TM1040_R0009 NC_008044.1 322763 322839 D tRNA-Arg 322763..322839 Ruegeria sp. TM1040 4076613 TM1040_R0010 tRNA TM1040_R0010 NC_008044.1 452000 452076 R tRNA-Met complement(452000..452076) Ruegeria sp. TM1040 4076614 TM1040_R0011 tRNA TM1040_R0011 NC_008044.1 572500 572574 D tRNA-Gln 572500..572574 Ruegeria sp. TM1040 4076615 TM1040_R0012 tRNA TM1040_R0012 NC_008044.1 832030 832104 D tRNA-Val 832030..832104 Ruegeria sp. TM1040 4076616 TM1040_R0013 tRNA TM1040_R0013 NC_008044.1 909925 910000 D tRNA-Val 909925..910000 Ruegeria sp. TM1040 4076617 TM1040_R0014 tRNA TM1040_R0014 NC_008044.1 910354 910430 D tRNA-Asp 910354..910430 Ruegeria sp. TM1040 4076618 TM1040_R0015 tRNA TM1040_R0015 NC_008044.1 910513 910589 D tRNA-Asp 910513..910589 Ruegeria sp. TM1040 4076619 TM1040_R0016 tRNA TM1040_R0016 NC_008044.1 910673 910749 D tRNA-Asp 910673..910749 Ruegeria sp. TM1040 4076620 TM1040_R0017 tRNA TM1040_R0017 NC_008044.1 972863 972939 R tRNA-Pro complement(972863..972939) Ruegeria sp. TM1040 4076621 TM1040_R0018 tRNA TM1040_R0018 NC_008044.1 1051685 1051759 R tRNA-Asn complement(1051685..1051759) Ruegeria sp. TM1040 4076622 TM1040_R0019 tRNA TM1040_R0019 NC_008044.1 1237578 1237654 D tRNA-Pro 1237578..1237654 Ruegeria sp. TM1040 4076623 TM1040_R0020 tRNA TM1040_R0020 NC_008044.1 1257137 1257222 D tRNA-Leu 1257137..1257222 Ruegeria sp. TM1040 4076624 TM1040_R0021 tRNA TM1040_R0021 NC_008044.1 1289648 1289737 R tRNA-Ser complement(1289648..1289737) Ruegeria sp. TM1040 4076625 TM1040_R0022 tRNA TM1040_R0022 NC_008044.1 1307059 1307135 R tRNA-Arg complement(1307059..1307135) Ruegeria sp. TM1040 4076626 TM1040_R0023 tRNA TM1040_R0023 NC_008044.1 1415927 1416011 R tRNA-Leu complement(1415927..1416011) Ruegeria sp. TM1040 4076627 TM1040_R0024 tRNA TM1040_R0024 NC_008044.1 1416226 1416299 D tRNA-Gly 1416226..1416299 Ruegeria sp. TM1040 4076628 TM1040_R0025 tRNA TM1040_R0025 NC_008044.1 1534030 1534119 R tRNA-Ser complement(1534030..1534119) Ruegeria sp. TM1040 4076629 TM1040_R0027 tRNA TM1040_R0027 NC_008044.1 1579604 1579679 D tRNA-Met 1579604..1579679 Ruegeria sp. TM1040 4078549 TM1040_R0028 tRNA TM1040_R0028 NC_008044.1 1582218 1582292 D tRNA-Asn 1582218..1582292 Ruegeria sp. TM1040 4078550 TM1040_R0029 tRNA TM1040_R0029 NC_008044.1 1788222 1788305 R tRNA-Leu complement(1788222..1788305) Ruegeria sp. TM1040 4078551 TM1040_R0030 tRNA TM1040_R0030 NC_008044.1 1846712 1846785 R tRNA-Cys complement(1846712..1846785) Ruegeria sp. TM1040 4078552 TM1040_R0031 tRNA TM1040_R0031 NC_008044.1 1934839 1934912 R tRNA-Gly complement(1934839..1934912) Ruegeria sp. TM1040 4078553 TM1040_R0033 tRNA TM1040_R0033 NC_008044.1 2139444 2139518 D tRNA-Gly 2139444..2139518 Ruegeria sp. TM1040 4078555 TM1040_R0034 tRNA TM1040_R0034 NC_008044.1 2139710 2139784 D tRNA-Gly 2139710..2139784 Ruegeria sp. TM1040 4078556 TM1040_R0035 tRNA TM1040_R0035 NC_008044.1 2139963 2140037 D tRNA-Gly 2139963..2140037 Ruegeria sp. TM1040 4078557 TM1040_R0036 tRNA TM1040_R0036 NC_008044.1 2152949 2153032 R tRNA-OTHER complement(2152949..2153032) Ruegeria sp. TM1040 4078558 TM1040_R0038 tRNA TM1040_R0038 NC_008044.1 2225464 2225540 R tRNA-His complement(2225464..2225540) Ruegeria sp. TM1040 4078560 TM1040_R0039 tRNA TM1040_R0039 NC_008044.1 2277500 2277574 D tRNA-Glu 2277500..2277574 Ruegeria sp. TM1040 4078561 TM1040_R0040 tRNA TM1040_R0040 NC_008044.1 2277789 2277863 D tRNA-Glu 2277789..2277863 Ruegeria sp. TM1040 4078562 TM1040_R0043 tRNA TM1040_R0043 NC_008044.1 2575693 2575768 D tRNA-Trp 2575693..2575768 Ruegeria sp. TM1040 4078565 TM1040_R0044 tRNA TM1040_R0044 NC_008044.1 2576175 2576264 D tRNA-Ser 2576175..2576264 Ruegeria sp. TM1040 4078566 TM1040_R0046 tRNA TM1040_R0046 NC_008044.1 2821104 2821181 R tRNA-Arg complement(2821104..2821181) Ruegeria sp. TM1040 4078114 TM1040_R0047 tRNA TM1040_R0047 NC_008044.1 2972614 2972689 R tRNA-Lys complement(2972614..2972689) Ruegeria sp. TM1040 4078115 TM1040_R0049 tRNA TM1040_R0049 NC_008044.1 2984411 2984497 R tRNA-Leu complement(2984411..2984497) Ruegeria sp. TM1040 4078117 TM1040_R0050 tRNA TM1040_R0050 NC_008044.1 2984654 2984740 R tRNA-Leu complement(2984654..2984740) Ruegeria sp. TM1040 4078118 TM1040_R0051 tRNA TM1040_R0051 NC_008044.1 2994766 2994841 D tRNA-Thr 2994766..2994841 Ruegeria sp. TM1040 4078119 TM1040_R0082 rRNA TM1040_R0082 NC_008042.1 8400 8514 R 5S ribosomal RNA complement(8400..8514) Ruegeria sp. TM1040 4074891 TM1040_R0083 rRNA TM1040_R0083 NC_008042.1 8752 11595 R 23S ribosomal RNA complement(8752..11595) Ruegeria sp. TM1040 4074892 TM1040_R0086 rRNA TM1040_R0086 NC_008042.1 12441 13895 R 16S ribosomal RNA complement(12441..13895) Ruegeria sp. TM1040 4074895 TM1040_R0055 rRNA TM1040_R0055 NC_008043.1 173192 173306 R 5S ribosomal RNA complement(173192..173306) Ruegeria sp. TM1040 4075359 TM1040_R0056 rRNA TM1040_R0056 NC_008043.1 173544 176387 R 23S ribosomal RNA complement(173544..176387) Ruegeria sp. TM1040 4075288 TM1040_R0059 rRNA TM1040_R0059 NC_008043.1 177290 178744 R 16S ribosomal RNA complement(177290..178744) Ruegeria sp. TM1040 4075291 TM1040_R0063 rRNA TM1040_R0063 NC_008043.1 505993 507447 D 16S ribosomal RNA 505993..507447 Ruegeria sp. TM1040 4075114 TM1040_R0066 rRNA TM1040_R0066 NC_008043.1 508349 511192 D 23S ribosomal RNA 508349..511192 Ruegeria sp. TM1040 4075117 TM1040_R0067 rRNA TM1040_R0067 NC_008043.1 511430 511544 D 5S ribosomal RNA 511430..511544 Ruegeria sp. TM1040 4075118 TM1040_R0071 rRNA TM1040_R0071 NC_008043.1 622244 623698 D 16S ribosomal RNA 622244..623698 Ruegeria sp. TM1040 4075501 TM1040_R0074 rRNA TM1040_R0074 NC_008043.1 624601 627444 D 23S ribosomal RNA 624601..627444 Ruegeria sp. TM1040 4075504 TM1040_R0075 rRNA TM1040_R0075 NC_008043.1 627682 627796 D 5S ribosomal RNA 627682..627796 Ruegeria sp. TM1040 4075505 TM1040_R0002 rRNA TM1040_R0002 NC_008044.1 144962 146416 D 16S ribosomal RNA 144962..146416 Ruegeria sp. TM1040 4076606 TM1040_R0005 rRNA TM1040_R0005 NC_008044.1 147318 150161 D 23S ribosomal RNA 147318..150161 Ruegeria sp. TM1040 4076609 TM1040_R0006 rRNA TM1040_R0006 NC_008044.1 150399 150513 D 5S ribosomal RNA 150399..150513 Ruegeria sp. TM1040 4076610