-- dump date 20140620_084512 -- class Genbank::Gene -- table gene_note -- id note 4442211 equivalent gene in S.pneumoniae TIGR4 = SP0299; equivalent gene in S.pneumoniae R6 = spr0014; truncated IS630-Spn1, transposase Orf1 identified by match to protein family HMM PF01710; authentic frameshift mutation that leads to truncation after amino acid 109 4442199 equivalent gene in S.pneumoniae R6 = spr0019; IS1167, transposase, degenerate 4442436 equivalent gene in S.pneumoniae TIGR4 = SP0028; equivalent gene in S.pneumoniae R6 = spr0029; IS1167, transposase, truncation 4442523 equivalent gene in S.pneumoniae TIGR4 = SP0039; equivalent gene in S.pneumoniae R6 = spr0039; IS1381, transposase OrfB, truncation 4442090 equivalent gene in S.pneumoniae TIGR4 = SP1262; equivalent gene in S.pneumoniae R6 = spr0042; IS1167, transposase, interruption 4442849 conserved hypothetical protein, FRAMESHIFT 4442005 equivalent gene in S.pneumoniae R6 = spr0105; ABC transporter permease, authentic truncation 4442716 equivalent gene in S.pneumoniae R6 = spr0132; IS1167, transposase, degenerate 4441200 equivalent gene in S.pneumoniae TIGR4 = SP0239; equivalent gene in S.pneumoniae R6 = spr0218; conserved hypothetical protein, FRAMESHIFT; identified by match to protein family HMM PF05167 4442361 IS200S, transposase, interruption 4441612 equivalent gene in S.pneumoniae TIGR4 = SP0016; equivalent gene in S.pneumoniae R6 = spr0312; IS630-Spn1, transposase Orf2, FRAMESHIFT 4441418 equivalent gene in S.pneumoniae TIGR4 = SP0299; equivalent gene in S.pneumoniae R6 = spr0313. In TIGR4 this gene is annotated as a truncation; however in R6 there are numerous near perfect copies as well as copies with a slightly longer version with a different end that is not present in either R6 or TIGR4 This indicates it may still function as a transposase; IS630-Spn1, transposase Orf1; identified by match to protein family HMM PF01710 4442156 equivalent gene in S.pneumoniae R6 = spr0324; IS66 family element, Orf3, degenerate 4442221 equivalent gene in S.pneumoniae R6 = spr0347. The R6 and D39 versions are also frameshifted relative to orthologs; DNA alkylation repair enzyme, , authentic frameshift 4441439 equivalent gene in S.pneumoniae TIGR4 = SP0390; equivalent gene in S.pneumoniae R6 = spr0349. The R6 gene has the same frameshift; choline binding protein G, authentic frameshift 4441598 equivalent gene in S.pneumoniae R6 = spr0353; transposase, , degenerate 4441107 equivalent gene in S.pneumoniae TIGR4 = SP0917; equivalent gene in S.pneumoniae R6 = spr0412; transposase IS116/IS110/IS902 family protein , degenerate; identified by match to protein family HMM PF02371 4442306 transposase, IS116-IS110-IS902 family protein, degenerate 4442851 equivalent gene in S.pneumoniae TIGR4 = SP0529; equivalent gene in S.pneumoniae R6 = spr0467. The R6 version has the same stop mutation; BlpC ABC transporter authentic truncation 4442028 equivalent gene in S.pneumoniae R6 = spr0469; BlpC ABC transporter ATP-binding protein, authentic frameshift; identified by match to protein family HMM PF03412 4441919 equivalent gene in S.pneumoniae TIGR4 = SP1485; equivalent gene in S.pneumoniae R6 = spr0496; IS3-Spn1, transposase, degenerate; identified by match to protein family HMM PF00665 4441457 equivalent gene in S.pneumoniae TIGR4 = SP1485; equivalent gene in S.pneumoniae R6 = spr0497; truncated IS3-Spn1, transposase; authentic frameshift mutation that leads to truncation after amino acid 85 4442905 equivalent gene in S.pneumoniae TIGR4 = SP0574; equivalent gene in S.pneumoniae R6 = spr0499. The R6 version has the same mutations relative to TIGR4 and orthologs; conserved hypothetical protein, degenerate 4442222 equivalent gene in S.pneumoniae TIGR4 = SP0915; equivalent gene in S.pneumoniae R6 = spr0511; IS1239, transposase, , degenerate 4442778 equivalent gene in S.pneumoniae TIGR4 = SP0610; equivalent gene in S.pneumoniae R6 = spr0536; amino acid ABC transporter ATP-binding protein, degenerate 4442734 equivalent gene in S.pneumoniae TIGR4 = SP0639. In R6 and D39 this gene is frameshifted relative to orthologs; conserved hypothetical protein, authentic frameshift 4441131 equivalent gene in S.pneumoniae R6 = spr0567. The R6 gene is similarly degenerate to orthologs; transposase , degenerate 4442055 equivalent gene in S.pneumoniae R6 = spr0610. The R6 gene has a point mutation in the same spot causing the truncation; ABC transporter ATP-binding protein, authentic truncation 4443046 equivalent gene in S.pneumoniae R6 = spr0612; transposase, IS30 family protein, degenerate 4442453 equivalent gene in S.pneumoniae R6 = spr0621; ABC transporter substrate-binding protein, authentic truncation 4441406 equivalent gene in S.pneumoniae TIGR4 = SP0735; equivalent gene in S.pneumoniae R6 = spr0646; phospho-beta-gluco or galactosidase, truncation 4442101 equivalent gene in S.pneumoniae TIGR4 = SP0739; equivalent gene in S.pneumoniae R6 = spr0649. R6 has the same frame shift. TIGR4 and orthologs do not; transcriptional regulator, MerR family protein, authentic frameshift; identified by match to protein family HMM PF07739 4442071 equivalent gene in S.pneumoniae R6 = spr0719; IS66 family element, Orf2, interruption 4442947 equivalent gene in S.pneumoniae TIGR4 = SP0830; equivalent gene in S.pneumoniae R6 = spr0733. The TIGR4 protein is 44 amino acids longer than the D39 and R6 genes. Similar genes in other species are the same length as the TIGR4 gene; conserved hypothetical protein, truncation; identified by match to protein family HMM PF08002 4441195 equivalent gene in S.pneumoniae TIGR4 = SP1596; equivalent gene in S.pneumoniae R6 = spr0751; IS3-Spn1, transposase, authentic frameshift 4442865 equivalent gene in S.pneumoniae TIGR4 = SP1485; equivalent gene in S.pneumoniae R6 = spr0753; IS3-Spn1, transposase, authentic frameshift 4442103 equivalent gene in S.pneumoniae TIGR4 = SP1582; equivalent gene in S.pneumoniae R6 = spr0767; IS1167, transposase, degenerate 4443039 equivalent gene in S.pneumoniae TIGR4 = SP1310; equivalent gene in S.pneumoniae R6 = spr0801; IS1381, transposase OrfA, truncation 4441108 equivalent gene in S.pneumoniae TIGR4 = SP0917; equivalent gene in S.pneumoniae R6 = spr0818; pilin inverting-related protein; authentic frameshift mutation that leads to divergence after amino acid 141 4442152 equivalent gene in S.pneumoniae R6 = spr0854; alanine dehydrogenase, authentic frameshift 4442255 equivalent gene in S.pneumoniae R6 = spr0898; IS630-Spn1, transposase Orf1, degenerate; identified by match to protein family HMM PF01710 4441434 equivalent gene in S.pneumoniae R6 = spr0909; pneumococcal histidine triad protein, authentic frameshift 4441383 equivalent gene in S.pneumoniae R6 = spr0910; pneumococcal histidine triad protein E precursor, truncation; identified by match to protein family HMM PF04270 4442107 equivalent gene in S.pneumoniae R6 = spr0958; Tn5252, relaxase, degenerate 4442314 equivalent gene in S.pneumoniae TIGR4 = SP1582; equivalent gene in S.pneumoniae R6 = spr0988; IS1167 transposase, degenerate 4442039 equivalent gene in S.pneumoniae TIGR4 = SP1262; equivalent gene in S.pneumoniae R6 = spr1009; IS1167, transposase, degenerate 4441203 equivalent gene in S.pneumoniae R6 = spr1033. The R6 and D39 versions of this gene are both frameshifted relative to orthologs; phosphoserine phosphatase SerB, degenerate 4442823 equivalent gene in S.pneumoniae TIGR4 = SP0538; equivalent gene in S.pneumoniae R6 = spr1078; IS1381, transposase OrfB, degenerate 4441149 equivalent gene in S.pneumoniae TIGR4 = SP1927; equivalent gene in S.pneumoniae R6 = spr1079; IS1381, transposase OrfA, truncation 4442446 equivalent gene in S.pneumoniae TIGR4 = SP1198; equivalent gene in S.pneumoniae R6 = spr1081. The R6 version is identically degenerate while The TIGR4 version and orthologs are not; PTS system IIA component, , degenerate 4442529 equivalent gene in S.pneumoniae TIGR4 = SP1258; equivalent gene in S.pneumoniae R6 = spr1136 & spr1137. The R6 gene has on ortholog in the same position; 2-isopropylmalate synthase, authentic truncation 4441331 equivalent gene in S.pneumoniae TIGR4 = SP1086; equivalent gene in S.pneumoniae R6 = spr1197; IS1381, transposase OrfB, truncation 4442041 Possibly an isoschizomer of XbaI. equivalent gene in S.pneumoniae R6 = spr1286; type II restriction endonuclease, , authentic point mutation 4443017 equivalent gene in S.pneumoniae TIGR4 = SP1485; equivalent gene in S.pneumoniae R6 = spr1339; IS3-Spn1, transposase, authentic truncation; identified by match to protein family HMM PF00665 4441859 equivalent gene in S.pneumoniae TIGR4 = SP1485; equivalent gene in S.pneumoniae R6 = spr0753; IS3-Spn1, transposase, authentic frameshift 4441197 equivalent gene in S.pneumoniae TIGR4 = SP1596; equivalent gene in S.pneumoniae R6 = spr1448; IS3-Spn1, hypothetical protein, interruption 4442023 equivalent gene in S.pneumoniae R6 = spr1350; IS630-Spn1, transposase Orf1, degenerate 4442414 The equivalent genes in S.pneumoniae R6 spr138o and spr1381 were merged here; ABC transporter permease, authentic truncation 4442140 equivalent gene in S.pneumoniae R6 = spr1387; conserved hypothetical protein, authentic frameshift 4441172 equivalent gene in S.pneumoniae TIGR4 = SP1485; equivalent gene in S.pneumoniae R6 = spr1447; IS3-Spn1, transposase, authentic frameshift 4442391 equivalent gene in S.pneumoniae TIGR4 = SP1596; equivalent gene in S.pneumoniae R6 = spr1448; IS3-Spn1, hypothetical protein, interruption 4442893 equivalent gene in S.pneumoniae TIGR4 = SP1640. This gene is not predicted in R6; however the R6 sequence is similar to the D39 gene; conserved hypothetical protein, authentic frameshift 4442634 equivalent gene in S.pneumoniae R6 = spr1545. The R6 version has the same mutation; conserved hypothetical protein, authentic frameshift 4441036 equivalent gene in S.pneumoniae R6 = spr1563; IS1239, transposase, , degenerate 4442044 equivalent gene in S.pneumoniae TIGR4 = SP2079; equivalent gene in S.pneumoniae R6 = spr1573; IS1381, transposase OrfA/OrfB, truncation; identified by match to protein family HMM PF01609 4441848 equivalent gene in S.pneumoniae R6 = spr1661. The R6 and D39 genes are also degenerate relative to orthologs; conserved hypothetical protein, degenerate 4441127 equivalent gene in S.pneumoniae TIGR4 = SP1262; equivalent gene in S.pneumoniae R6 = spr0042; IS1167, transposase, degenerate 4441540 equivalent gene in S.pneumoniae TIGR4 = SP1262; equivalent gene in S.pneumoniae R6 = spr1701; IS1167, transposase, degenerate; identified by match to protein family HMM PF01610 4441047 equivalent gene in S.pneumoniae TIGR4 = SP0836; equivalent gene in S.pneumoniae R6 = spr1716. The gene is identicle in R6, but not TIGR4; IS1167, transposase, internal deletion 4442035 equivalent gene in S.pneumoniae TIGR4 = SP1919; equivalent gene in S.pneumoniae R6 = spr1736. This gene and the R6 version have a point mutation relative to the TIGR4 version; ABC transporter permease, point mutation 4441983 equivalent gene in S.pneumoniae TIGR4 = SP1920; equivalent gene in S.pneumoniae R6 = spr1737.The gene is identically degenerate in R6; transcriptional regulator, MarR family protein, degenerate; identified by match to protein family HMM PF01047 4441499 equivalent gene in S.pneumoniae TIGR4 = SP1086; equivalent gene in S.pneumoniae R6 = spr1745; IS1381, transposase OrfB, degenerate 4441587 equivalent gene in S.pneumoniae TIGR4 = SP0299; equivalent gene in S.pneumoniae R6 = spr0014; IS630-Spn1, transposase Orf1, truncation; identified by match to protein family HMM PF01710 4441453 equivalent gene in S.pneumoniae TIGR4 = SP2060; equivalent gene in S.pneumoniae R6 = spr1872; pyrrolidone-carboxylate peptidase, degenerate 4442570 equivalent gene in S.pneumoniae TIGR4 = SP2062; equivalent gene in S.pneumoniae R6 = spr1874. The gene is identically degenerate in R6; transcriptional regulator, MarR family protein, degenerate; identified by match to protein family HMM PF01022; match to protein family HMM PF01047 4441592 equivalent gene in S.pneumoniae TIGR4 = SP2089; equivalent gene in S.pneumoniae R6 = spr1900; IS1380-Spn1, transposase, truncation 4441226 equivalent gene in S.pneumoniae TIGR4 = SP2148; equivalent gene in S.pneumoniae R6 = spr1955. This gene has the same framshit mutation at about amino acid 245 as does R6 relative to TIGR4; arginine deiminase, authentic framshift 4441028 equivalent gene in S.pneumoniae TIGR4 SP2154; IS3-Spn1, hypothetical protein, interruption 4442062 equivalent gene in S.pneumoniae R6 = spr1985; group II intron, maturase, degenerate 4442824 equivalent gene in S.pneumoniae TIGR4 SP2212; transposase family protein, degenerate 4441179 equivalent gene in S.pneumoniae R6 = spr2018; IS66 family element, Orf2, interruption; identified by match to protein family HMM PF05717 4441978 equivalent gene in S.pneumoniae TIGR4 = SP2233; equivalent gene in S.pneumoniae R6 = spr2039. The R6 version is similarly mutated relative to orthologs; conserved hypothetical protein, degenerate