Skip to main content

Table 4 Updates and corrections to the genome sequence

From: An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3

Accession Gene locus CDS Gene Type of change
YP_166946 SPO1707a Branched-chain amino acid ABC transporter, ATP-binding protein, putative   Locus name
YP_167418 SPO2192a N-formylglutamate amidohydrolase hutG Locus name
YP_165298 SPO0025 Hydrolase, NUDIX family   ORF position
YP_165304 SPO0031 ErfK/YbiS/YcfS/YnhG family protein   ORF position
YP_165330 SPO0056 Hypothetical protein   ORF position
YP_165481 SPO0212 Hypothetical protein   ORF position
YP_165606 SPO0343 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase sucB ORF position
YP_165666 SPO0403 Conserved domain protein   ORF position
YP_165678 SPO0415 D-isomer specific 2-hydroxyacid dehydrogenase family protein   ORF position
YP_165703 SPO0440 Thioesterase family protein   ORF position
YP_165709 SPO0446 ABC transporter, ATP-binding protein   ORF position
YP_165719 SPO0456 Hypothetical protein   ORF position
YP_165753 SPO0491 Hypothetical protein   ORF position
YP_165766 SPO0504 Hypothetical protein   ORF position
YP_165767 SPO0505 Ribosomal protein L15 rplO ORF position
YP_165860 SPO0600 Carboxynorspermidine decarboxylase nspC ORF position
YP_165899 SPO0644 Hypothetical protein   ORF position
YP_165937 SPO0682 Monooxygenase family protein   ORF position
YP_165950 SPO0695 Hypothetical protein   ORF position
YP_008877643 SPO0876a Hypothetical protein   ORF position
YP_166130 SPO0877 Conserved domain protein   ORF position
YP_166199 SPO0946 Phosphomannomutase/phosphoglucomutase algC ORF position
YP_166255 SPO1003 ATP-dependent Clp protease, proteolytic subunit ClpP clpP ORF position
YP_166256 SPO1004 ATP-dependent Clp protease, ATP-binding subunit ClpX clpX ORF position
YP_166357 SPO1106 Hypothetical protein   ORF position
YP_166419 SPO1172 FMN-dependent alpha-hydroxy acid dehydrogenase family protein   ORF position
YP_166421 SPO1174 DNA helicase II, putative   ORF position
YP_166518 SPO1273 Thymidylate synthase, flavin-dependent thyX ORF position
YP_166577 SPO1334 Hypothetical protein   ORF position
YP_166601 SPO1359 Pyruvate, phosphate dikinase ppdK ORF position
YP_166628 SPO1386 HIT family protein   ORF position
YP_166803 SPO1562 Glycine cleavage system T protein, putative   ORF position
YP_166874 SPO1633 Hypothetical protein   ORF position
YP_167013 SPO1776 Pyridine nucleotide-disulphide oxidoreductase family protein   ORF position
YP_167049 SPO1812 Adenylate kinase adk-2 ORF position
YP_167155 SPO1920 Tellurite resistance protein trgB ORF position
YP_167190 SPO1955 Glutaryl-CoA dehydrogenase gcdH ORF position
YP_167207 SPO1972 Nodulation protein N   ORF position
YP_167208 SPO1973 3-dehydroquinte dehydratase, type II aroQ ORF position
YP_167281 SPO2051 DNA gyrase, A subunit gyrA ORF position
YP_167284 SPO2054 Cytochrome c oxidase assembly protein   ORF position
YP_167368 SPO2141 Pyridoxamine 5''-phosphate oxidase, putative   ORF position
YP_167443 SPO2217 Excinuclease   ORF position
YP_167514 SPO2290 Hypothetical protein   ORF position
YP_167549 SPO2326 Hypothetical protein   ORF position
YP_167562 SPO2339 Enoyl-CoA hydratase/isomerase family protein   ORF position
YP_167570 SPO2347 Hypothetical protein   ORF position
YP_167571 SPO2348 Sarcosine oxidase, beta subunit family   ORF position
YP_167714 SPO2499 Hypothetical protein   ORF position
YP_167808 SPO2595 Hypothetical protein   ORF position
YP_167819 SPO2608 Aldehyde dehydrogenase, putative   ORF position
YP_167822 SPO2612 DNA-binding protein HU, putative   ORF position
YP_008877659 SPO2723a Hypothetical protein   ORF position
YP_167934 SPO2724 Hypothetical protein   ORF position
YP_167992 SPO2785 NADH dehydrogense I, B subunit nuoB ORF position
YP_168024 SPO2816 Peptide/nickel/opine uptake family ABC transporter, permease protein   ORF position
YP_168061 SPO2853 Cobalt chelatase, CobS subunit   ORF position
YP_168080 SPO2872 Cobyrinic acid a,c-diamide synthase cobB ORF position
YP_168096 SPO2888 Membrane protein, putative   ORF position
YP_168125 SPO2917 Glutathione S-transferase family protein   ORF position
YP_168133 SPO2925 Sporulation related   ORF position
YP_168143 SPO2936 Hypothetical protein   ORF position
YP_168150 SPO2942 Hypothetical protein   ORF position
YP_168197 SPO2991 Nitroreductase family protein   ORF position
YP_168209 SPO3003 AMP-binding enzyme   ORF position
YP_168292 SPO3089 ATPase, putative   ORF position
YP_168317 SPO3114 Hypothetical protein   ORF position
YP_168354 SPO3151 HAD-superfamily subfamily IIA hydrolase, TIGR01459   ORF position
YP_168406 SPO3203 Guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase, putative   ORF position
YP_168423 SPO3220 Aminotransferase, classes I and II   ORF position
YP_168448 SPO3245 Nicotinate-nucleotide pyrophosphorylase nadC ORF position
YP_168475 SPO3278 Orotidine 5'-phosphate decarboxylase pyrF ORF position
YP_168540 SPO3344 Cys/Met metabolism PLP-dependent enzyme family protein   ORF position
YP_168563 SPO3367 Deoxyribose-phosphate aldolase deoC ORF position
YP_168618 SPO3422 ATP-dependent protease La domain protein   ORF position
YP_168712 SPO3517 Preprotein translocase, SecE subunit secE ORF position
YP_168722 SPO3527 Universal stress protein family protein   ORF position
YP_168735 SPO3540 Hypothetical protein   ORF position
YP_168802 SPO3607 Hypothetical protein   ORF position
YP_168911 SPO3717 Cytosol aminopeptidase family protein   ORF position
YP_168940 SPO3746 Adenine deaminse ade ORF position
YP_169017 SPO3829 S-formylglutathione hydrolase, putative   ORF position
YP_169021 SPO3833 ATP-dependent RNA helicase, DEAD/DEAH box family   ORF position
YP_164889 SPOA0058 Glycine cleavage system protein H gcvH-2 ORF position
YP_165979 SPO0725 Bacterial SH3 domain family protein   ORF position, Function
YP_167233 SPO1999 Collagen domain protein   ORF position, Function
YP_008877641 SPO0561 ABC transporter   Sequence
YP_008877654 SPO2024 Aminotransferase   Sequence
YP_008877662 SPO3316a Stress protein   Sequence
YP_008877661 SPO3904 Heat shock protein   Sequence
YP_167141 SPO1905 Fumarate hydratase, class II fumC Sequence, ORF position
YP_165491 SPO0222 Alanine dehydrogenase ald Function
YP_165503 SPO0234 Lysine dehydrogenase lysdh Function
YP_165504 SPO0235 α-aminoadipic-δ-semialdehyde dehydrogenase aasadh Function
YP_165716 SPO0453 DMSP lyase dddW Function
YP_165850 SPO0590 LacI family transcriptional regulator hpsR Function
YP_165851 SPO0591 Dihydroxypropanesulfonate (DHPS) TRAP transporter hpsK Function
YP_165852 SPO0592 Dihydroxypropanesulfonate (DHPS) TRAP transporter hpsL Function
YP_165853 SPO0593 Dihydroxypropanesulfonate (DHPS) TRAP transporter hpsM Function
YP_165854 SPO0594 Dihydroxypropanesulfonate-3-dehydrogenase hpsN Function
YP_165855 SPO0595 R or S-dihydroxypropanesulfonate-2-dehydrogenase hpsO Function
YP_165856 SPO0596 S or R-dihydroxypropanesulfonate-2-dehydrogenase hpsP Function
YP_165857 SPO0597 UspA stress protein hpsQ Function
YP_165858 SPO0598 Membrane-bound sulfolactate dehydrogenase slcD Function
YP_165912 SPO0657 Metallochaperone, putative naaT Function
YP_165913 SPO0658 N-acetyltaurine amidohydrolase naaS Function
YP_165914 SPO0659 LysR family transcriptional regulator naaR Function
YP_165915 SPO0660 N-acetyltaurine ABC transporter, periplasmic binding protein naaA Function
YP_165916 SPO0661 N-acetyltaurine ABC transporter, permease protein naaB Function
YP_165917 SPO0662 N-acetyltaurine ABC transporter, permease protein naaB' Function
YP_165918 SPO0663 N-acetyltaurine ABC transporter, ATP-binding protein naaC Function
YP_165919 SPO0664 N-acetyltaurine ABC transporter, ATP-binding protein naaC' Function
YP_165928 SPO0673 Taurine-pyruvate aminotransferase tpa Function
YP_165929 SPO0674 Taurine ABC transporter, periplasmic taurine-binding protein tauA Function
YP_165930 SPO0675 Taurine ABC transporter, ATP-binding protein tauB Function
YP_165931 SPO0676 Taurine ABC transporter, permease protein tauC Function
YP_166034 SPO0781 Phosphonate ABC transporter substrate-binding protein phnD Function
YP_166387 SPO1136 Diaminobutyric acid transaminase doeD Function
YP_166388 SPO1137 Aspartate-semialdehyde dehydrogenase doeC Function
YP_166389 SPO1138 AsnC/Lrp-like DNA-binding protein, transcriptional regulator doeX Function
YP_166390 SPO1139 Nα-acetyl-L-2,4-diaminobutyric acid deacetylase doeB Function
YP_166391 SPO1140 Ectoine hydrolase doeA Function
YP_166392 SPO1141 Ectoine utilization protein EutC eutC Function
YP_166394 SPO1143 Ectoine utilization protein EutA eutA Function
YP_166396 SPO1145 Ectoine/5-hydroxyectoine TRAP transporter, periplasmic binding protein uehC Function
YP_166397 SPO1146 Ectoine/5-hydroxyectoine TRAP transporter, small integral membrane protein uehB Function
YP_166398 SPO1147 Ectoine/5-hydroxyectoine TRAP transporter, large integral membrane protein uehA Function
YP_166399 SPO1148 Transcriptional regulator, GntR family gntR Function
YP_166792 SPO1551 Trimethylamine (TMA) monooxygenase tmm Function
YP_166837 SPO1596 DMSP lyase dddQ Function
YP_166942 SPO1703 DMSP lyase dddD Function
YP_167149 SPO1914 NADPH-dependent acrylyl-CoA reductase acuI Function
YP_167183 SPO1948 Phosphate ABC transporter substrate-binding protein pstS Function
YP_167275 SPO2045 3-methylmercaptopropionyl-CoA ligase dmdB Function
YP_167522 SPO2299 DMSP lyase dddP Function
YP_167578 SPO2355 Isethionate dissimilation regulator iseR Function
YP_167579 SPO2356 Isethionate TRAP transporter iseM Function
YP_167580 SPO2357 Isethionate TRAP transporter iseL Function
YP_167581 SPO2358 Isethionate TRAP transporter iseK Function
YP_167582 SPO2359 Isethionate dehydrogenase iseJ Function
YP_167694 SPO2477 Manganese uptake regulator mur Function
YP_168390 SPO3187 (2R)-3-sulfolactate dehydrogenase comC Function
YP_168503 SPO3307 Lysine-ketoglutarate reductase lkr Function
YP_168559 SPO3363 Manganese ABC transporter, permease protein sitD Function
YP_168560 SPO3364 Manganese ABC transporter, permease protein sitC Function
YP_168561 SPO3365 Manganese ABC transporter, ATP-binding protein sitB Function
YP_168562 SPO3366 Manganese ABC transporter, periplasmic protein sitA Function
YP_168752 SPO3557 Sulfite dehydrogenase subunit SoeC; transmembrane sulfate transporter soeC Function
YP_168753 SPO3558 Sulfite dehydrogenase iron-sulfur cluster-binding subunit SoeB; cytosolic protein soeB Function
YP_168754 SPO3559 Sulfite dehydrogenase molybdopterin cofactor-binding subunit SoeA; cytosolic protein soeA Function
YP_168755 SPO3560 Phosphate acetyltransferase pta Function
YP_168757 SPO3562 Taurine transcriptional regulator tauR Function
YP_168992 SPO3804 3-methylmercaptopropionyl-CoA dehydrogenase dmdC Function
YP_168993 SPO3805 Methylthioacryloyl-CoA hydratase dmdD Function
YP_164988 SPOA0157 Sulfite exporter cuyZ Function
YP_164989 SPOA0158 L-cysteate sulfo-lyase cuyA Function
YP_164990 SPOA0159 Transcriptional regulator cuyR cuyR Function
YP_165136 SPOA0309 Sulphoacetaldehyde acetyltransferase   Function
YP_008877636 SPO0344a Hypothetical protein   New ORF
YP_008877637 SPO0346a Hypothetical protein   New ORF
YP_008877638 SPO0360a Hypothetical protein   New ORF
YP_008877639 SPO0491a Hypothetical protein   New ORF
YP_008877640 SPO0504a Hypothetical protein   New ORF
YP_008877642 SPO0628a Hypothetical protein   New ORF
YP_008877644 SPO1044a Hypothetical protein   New ORF
YP_008877645 SPO1094a Hypothetical protein   New ORF
YP_008877646 SPO1226a Hypothetical protein   New ORF
YP_008877647 SPO1252a Transcriptional regulator   New ORF
YP_008877648 SPO1310a Hypothetical protein   New ORF
YP_008877649 SPO1337a Hypothetical protein   New ORF
YP_008877650 SPO1352a Hypothetical protein   New ORF
YP_008877651 SPO1356a Signal transduction   New ORF
YP_008877652 SPO1364a Hypothetical protein   New ORF
YP_008877653 SPO1412a Hypothetical protein   New ORF
YP_008877655 SPO2213a Hypothetical protein   New ORF
YP_008877656 SPO2341a Hypothetical protein   New ORF
YP_008877657 SPO2478 RNA helicase   New ORF
YP_008877658 SPO2652a Polyketide cyclase   New ORF
YP_008877660 SPO2973a Hypothetical protein   New ORF
YP_008877663 SPO3452a Hypothetical protein   New ORF
YP_008877664 SPO3498a Hypothetical protein   New ORF
YP_008877665 SPO3673a Hypothetical protein   New ORF
AHC32567 SPOA0087a Esterase-lipase   New ORF
AHC32568 SPOA0272a Hypothetical protein   New ORF
YP_165305 - Hypothetical protein   Removed ORF
YP_165605 - Hypothetical protein   Removed ORF
YP_166669 - Hypothetical protein   Removed ORF
YP_168865 - Hypothetical protein   Removed ORF
YP_165238 - Hypothetical protein   Removed ORF