TABLE 5.

Strain-specific pseudogenes

ORF identifierGeneK-12 homologK-12 product
Strain 301
    SF4079 metA b4013Homoserine transsuccinylase
    SF0057 araA b0062 l-Arabinose isomerase
    SF3734 bglB b3721Phospho-β-glucosidase B, cryptic oxygen-insensitive NAD(P)H nitroreductase
    SF0485 nfnB b0578
    SF1862 zwf b1852Glucose-6-phosphate dehydrogenase
    SF2877 prfB b2891Peptide chain release factor RF-2
    SF1321 ycjS b1315Putative dehydrogenase
    SF3214 yhbX b3173Putative alkaline phosphatase I
    SF0275 yafL b0227Putative lipoprotein
    SF1338, SF1842 ycjZ b1328Putative transcriptional regulator, LysR type
    SF1534SF1534b1696Putative AraC-type regulator
    SF2163 yegW b2101Putative transcriptional regulator
    SF2448SF2448b2382Putative AraC-type regulator
    SF2490 yfeG b2437Putative AraC-type regulator
    SF3974 frvR b3897Putative frv operon regulator
    SF1368SF1368b1345Putative transposase
    SF1740SF1740b1485Putative transport protein
    SF1691 ydhE b1663Putative transport protein
    SF2477 cysW b2423Sulfate transport permease W
Strain 2457T
    S4407 bfr b3336Bacterioferrin, iron storage
    S1577 gdhA b1761NADP-specific glutamate dehydrogenase
    S2171 cobU b1993Cobinamide kinase/cobinamide phosphate guanylyltransferase
    S2637 hemF b2436Coproporphyrinogen III oxidase
    S3390 agaB b3138PTS N-acetylgalactosamine-specific IIB component EIIB-AGA
    S1776 hdhA b1619NAD-dependent 7α-hydroxysteroid dehydrogenase
    S4637 hsdR b4350Host restriction endonuclease R
    S3489 degQ b3234Serine endoprotease
    S4408 hofD b3335Leader peptidase
    S4636 hsdM b4349DNA methylase M
    S1063 torS b0993Sensor protein
    S1894 narY b1467Cryptic nitrate reductase 2 (β)
    S2680 hyfG b2487Hydrogenase 4 subunit
    S3606 fdhF b4079Selenopolypeptide subunit of formate dehydrogenase H
    S4516 cybC b4236Cytochrome b562
    S2957 rpoS b2741Sigma S (sigma38) factor
    S0832 dacC b0839 d-Alanyl-d-alanine-carboxypeptidase
    S4544 fklB b4207FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase)
    S4322 rtcA b3420RNA 3′-terminal phosphate cyclase
    S1606 celB b1737PEP-dependent phosphotransferase enzyme II
    S3990 glvC b3683PTS system, IIC component
    S1316 tpr b1229Protaminelike protein
    S2859 intA b2622Prophage CP4-57 integrase
    S0478 nfrB b0569Bacteriophage N4 receptor
    S0349 yajB b0404Putative glycoprotein
    S2352 yohG b2138Putative channel/filament protein
    S3355 yhaI b3104Putative cytochrome
    S0041 fixB b0042Probable flavoprotein subunit
    S0364 yajO b0419Putative NAD(P)H-dependent xylose reductase
    S0448 ybbP b0496Putative oxidoreductase
    S0459 ylbF b0520Putative carboxylase
    S0830 yliI b0837Putative dehydrogenase
    S1241S1241b1168Putative proteases
    S1864 pqqL b1494Putative peptidase
    S1858S1858b1498Putative sulfatase
    S1724S1724b1587Putative oxidoreductase, major subunit
    S1618S1618b1729Kinase (part)
    S2241 wcaE b2055Putative glycosyl transferase
    S2245 wcaC b2057Putative glycosyl transferase
    S2484 elaD b2269Putative sulfatase/phosphatase
    S2631S2631b2430Putative β-lactamase
    S2737 pbpC b2519Putative peptidoglycan enzyme
    S2869S2869b2657Putative enzyme
    S3119 yggC b2928Putative kinase
    S3321 ygjH b3074Putative tRNA synthetase
    S4149 yiaL b3576Putative lipase/PICK>
ORF identifierGeneK-12 homologK-12 product
    S4003 yidX b3696Putative replicase
    S3846 ysgA b3830Putative enzyme
    S3723 talC b3946Putative transaldolase
    S4609 aidB b4187Putative acyl coenzyme A dehydrogenase
    S2260S2260b2070Putative chaperonin
    S2576S2576b2372Putative receptor protein
    S3839S3839b3837Putative histone
    S1450S1450b1377Putative outer membrane protein
    S2264S2264b2074Putative membrane protein
    S2548S2548b2337Putative outer membrane protein
    S0954 ycaN b0900Putative transcriptional regulator
    S2312 yehI b2118Putative regulator
    S2684 hyfR b2491Putative 2-component regulator
    S4526 ytfQ b4227Putative transcriptional regulator
    S4668 yjjQ b4365Putative regulator
    S0473 fimZ b0535Fimbrial regulator, probable signal transducer
    S0641S0641b0663Putative RNA
    S0135 yadC b0135Putative fimbrial protein
    S1003 ycbQ b0938Putative fimbrial protein
    S1098 ycdV b1031Putative ribosomal protein
    S1657S1657b1502Putative adhesin, similar to FimH
    S1506 yebU b1835Putative nucleolar protein
    S2295 yehA b2108Putative type 1 fimbrial protein
    S2544S2544b2333Putative fimbrial-like protein
    S2546S2546b2335Putative fimbrial protein
    S4665 yjjP b4364Putative structural protein
    S2087 fliP b1948Flagellar export protein
    S2472 pmrD b2259Polymyxin resistance protein B
    S0801 ybiO b0808Putative transport protein
    S0955S0955b0899Putative transport protein
    S0998 ycbM b0934Putative transport system permease
    S1137 yceE b1053Putative transport protein
    S1242S1242b1169Putative ATP-binding component, transport system
    S1243S1243b1170Putative ATP-binding component, transport system (part)
    S1436 ydaH b1336Putative pump protein (transport)
    S1875S1875b1483Putative ATP-binding component, transport system
    S1677S1677b1543Putative transport protein
    S2059 fliY b1920Putative periplasmic binding transport protein
    S2895S2895b2681Putative transport protein
    S4170 yhiV b3514Putative transport permease
    S3797 yihP b3877Putative transport permease
    S4522 yjfF b4231Putative transport permease
    S2311 molR b2117Molybdate metabolism regulator
    S1092 phoH b1020PhoB-dependent, ATP-binding Pho regulon component
    S2672 gcvR b2479Transcriptional regulator
    S2276 gatR b2090Galactitol utilization operon repressor, fragment 2
    S3922 pssR b3763Regulator of pssA
    S1455 feaR b1384Regulator for 2-phenylethylamine catabolism
    S2032 flhD b1892Regulator of flagellar biosynthesis,
    S1158 flgC b1074Flagellar biosynthesis, cell-proximal portion of basal-body rod
    S2081 fliJ b1942Flagellar protein
    S2569 dsdX b2365Transport system permease
    S2038 araH b1899High-affinity l-arabinose transporter
    S3764 rhaT b3907Rhamnose transport