Table 3 B. cenocepacia J2315 genes identified using the second generation cep box motif
Motif namea | Positionb | bpc | gened | Gene/domain and predicted functione (Adjacent downstream genes possibly in operon) |
|---|---|---|---|---|
Cell Surface or Membrane | ||||
MST2008 (-) | 1:806161 | 45 | BCAL0738(-) | COG0793: Periplasmic protease; cell envelope biogenesis |
MST2009 (+) | 1:901874 | 295 | BCAL0831 (+) | phaP: phasin-like protein |
MST2031 (-) | 1:2662911 | 104 | BCAL2406(-) | COG0859, rfaF, LPS heptosyltransferase (rfa L,rfaG; LPS biosynthesis genes) |
MST2048 (-) | 2:211218 | 106 | BCAM0183 (+) | COG3468, autotransporter type V secretion, shdA homolog: adhesin |
MST2050 (+) | 2:1129604 | 172 | BCAM1015(-) | COG3203: Outer membrane protein |
MST2068 (-) | 3:174253 | 153 | BCAS0156(+) | COG1680: ampC, β-lactamase class C |
Hypothetical Protein | ||||
MST2014 (-) | 1:1228119 | 131 | BCAL1124 (+) | Conserved hypothetical protein |
MST2020 (+) MST028 f | 1:1484174 | 140 | BCAL1354(-) | COG4104: conserved hypothetical protein (vgrG: vgr related protein) |
MST2030 (-) | 1:2567308 | 41 | BCAL2313 (+) | hypothetical protein |
MST2052 (+) | 2:1249946 | 118 | BCAM1149 (+) | hypothetical protein |
MST2056 (-) | 2:1667312 | 57 | BCAM1502 (+) | hypothetical protein (Chemoreceptor mcpA) |
MST2063 (-) | 2:2720454 | -19 | BCAM2417 (+) | hypothetical protein |
MST2067 (+) | 2:3070180 | 254 | BCAM2713(-) | hypothetical protein |
MST2071 (+) | 3:836110 | 63 | BCAS0753(+) | hypothetical protein |
Metabolism | ||||
MST2002 (-) | 1:273243 | 21 | BCAL0232 (+) | Elongation factor Tu |
MST2005 (+) | 1:390962 | 47 | BCAL0358 (-) | COG0308: Aminopeptidase N |
MST2007 (+) MST011 | 1:778996 | 101 | BCAL0716 (+) | COG1250: fadB, 3-hydroxyacyl-CoA dehydrogenase; lipid metabolism |
MST2010 (-) | 1:963495 | 59 | BCAL0886 (+) | COG0183: paaJ, Probable beta-ketoadipyl CoA thiolase (caiD; lipid metabolism) |
MST2022 (-) | 1:1602043 | 50 | BCAL1448(-) | COG0525: valS, Valyl-tRNA synthetase |
MST2023 (-) | 1:1626201 | 104 | BCAL1468(-) | COG0644: fixC, electron transfer flavoprotein-ubiquinone oxidoreductase |
MST2027 (+) | 1:2465614 | 32 | BCAL2229(-) | Hypothetical signal peptide protein (COG3000: Sterol desaturase, lipid metabolism) |
MST2029 (-) | 1:2554533 | 153 | BCAL2302(-) | COG0556,uvrB: Helicase subunit of the DNA excision repair complex |
MST2029 (-) | 1:2554533 | 106 | BCAL2303 (+) | COG1448, tyrB: aspartate/tyrosine/aromatic aminotransferase |
MST2034 (+) | 1:2903040 | 55 | BCAL2638 (+) | COG0165,argH: Argininosuccinate lyase, arginine biosynthesis |
MST2035 (+) MST052 | 1:3009329 | 9 | BCAL2739 (+) | COG0480, fusA: Translation elongation factor |
MST2038 (+) | 1:3351536 | -15 | BCAL3058 (+) | COG0043, ubiD: 3-polyprenyl-4-hydroxybenzoate decarboxylase (rhtB, Putative threonine efflux or homoserine/homoserine lactone efflux) |
MST2039(+) MST059 f | 1:3488874 | 117 | BCAL3191(+) | COG1960: caiA, acyl CoA dehydrogenase |
MST2043 (+) | 1:3745369 | 60 | BCAL3419 (+) | COG0757: aroQ: 3-dehydroquinate dehydratase II |
MST2045 (+) | 2:11142 | 137 | BCAM0010(+) | kbl homolog, AKB ligase |
MST2046 (+) MST072 f | 2:84847 | 55 | BCAM0077(-) | COG0654: ubiH or mhpA, hydroxylase |
MST2055 (+) | 2:1564008 | 139 | BCAM1405(-) | sacB: Levansucrase (sacC: Levanase precursor) |
MST2059 (+) f | 2:2088113 | 71 | BCAM1870 (+) | cepI: homoserine lactone synthase |
MST2061(+) | 2:2134837 | 112 | BCAM1922(+) | repA: replication protein |
MST2064 (-) | 2:2839793 | 44 | BCAM2502(-) | COG0757: aroQ: 3-dehydroquinate dehydratase II (aroE: Shikimate 5-dehydrogenase) |
MST2064 (-) | 2:2839793 | 125 | BCAM2503(+) | COG3185: hppD, 4-hydroxyphenylpyruvate dioxygenase |
MST2065 (-) | 2:2938113 | 48 | BCAM2588(-) | menG: putative S-adenosylmethionine:2 demethylmenaquinone methyltransferase |
Phage genes | ||||
MST2024 (+) | 1:1735446 | 71 | BCAL1564 (-) | Hypothetical proteins Mup46, Mup47 and Mup48 [phage tail protein] |
MST2060 (+) | 2:2096677 | 28 | BCAM1879 (+) | Phage antirepressor |
Regulatory gene | ||||
MST2006 (-) | 1:616909 | 88 | BCAL0562(-) | COG2747, flgM: Negative regulator of flagellin synthesis (flgN; Flagellar biosynthesis/type III secretory pathway) |
MST2007 (+) MST011 f | 1:778996 | 59 | BCAL0715(-) | COG0583: LysR-type transcriptional regulator |
MST2013 (+) | 1:1085981 | 40 | BCAL0999 (+) | COG3073: RseA; Negative regulator of sigma E activity (RseB or MucB, negative regulator for alginate biosynthesis) |
MST2019 (-) | 1:1437591 | 385 | BCAL1318 (+) | COG3707, nasR: nitrate-and nitrite-responsive positive regulator |
MST2026 (+) | 1:2016418 | 259 | BCAL1826 (+) | gltF: regulator of gltBDF operon, glutamate synthaseenzymes |
MST2036 (-) | 1:3153030 | 18 | BCAL2871(-) | COG3073, rseA: Negative regulator of sigma E activity (mucB/rseB, mucD) |
MST2039 (+) MST059 | 1:3488874 | 102 | BCAL3190(-) | COG1414: Transcriptional regulator, IclR family |
MST2040 (-) | 1:3502381 | 36 | BCAL3205(-) | COG1396: hipB homolog, Putative transcription regulator |
MST2045 (+) MST068 f | 2:11142 | 22 | BCAM0009(-) | COG1396: hipB homolog, Predicted transcriptional regulator |
MST2046 (+) MST072 | 2:84847 | 58 | BCAM0076(-) | COG1309: ArcR domain: Bacterial regulatory proteins, tetR family |
MST2055(+) | 2:1564008 | 64 | BCAM1406(+) | COG: aglR, HTH-type transcriptional regulator |
MST2057 (+) | 2:1959876 | 36 | BCAM1750 (+) | COG1846: Transcriptional regulator, MarR family |
MST2058f (+) | 2:2087487 | 31 | BCAM1868(-) | cepR: Transcriptional regulator, LuxR family |
MST2071 (+) | 3:836110 | 40 | BCAS0752(-) | COG0583: LysR type Transcriptional regulator |
Secretion or secreted product | ||||
MST2003 (+) | 1:351306 | 25 | BCAL0321 (+) | COG3671: Predicted membrane protein (tatA, tatB, tatC secretion pathway) |
MST2004 (+) MST005 f | 1:366026 | 206 | BCAL0340 (+) | COG0457: TPR repeat, (evpA and evpB, evpC, evpE, evpF, and evpG virulence and possible secretion) |
MST2070(-) f | 3:478440 | 108 | BCAS0409 (+) | zmpA: extracellular zinc metalloprotease |
Transport | ||||
MST2001 (-) | 1:61816 | 272 | BCAL0051 (+) | COG0834: ABC-type amino acid transport/signal transduction systems |
MST2066 (+) f | 2:2974227 | 115 | BCAM2626 (+) | phuR: Haem/Haemoglobin uptake outer membrane receptor precursor (phuS, phuT, phuU phuV |
MST2072 (+) | P:55610 | 113 | PBCA053 (-) | COG1638,dctP homolog: TRAP-type C4-dicarboxylate transport system, |
Unknown | ||||
MST2004 (+) MST005 | 1:366026 | 181 | BCAL0339(-) | COG3521: Uncharacterized protein conserved in bacteria |
MST2025 (+) | 1:1979817 | 274 | BCAL1791 (-) | COG2606: Uncharacterized conserved protein |
MST2047 (-) | 2:169540 | 86 | BCAM0148 (+) | Putative vgr-related protein (pldA: Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthases) |
MST2051 (-) | 2:1150388 | -37 | BCAM1044(-) | no homology (COG1536: Flagellar motor switch protein) |
MST2053 (-) | 2:1467792 | 28 | BCAM1328-329 (+) | Unknown proteins |
MST2061 (+) | 2:2134837 | 59 | BCAM1921-919 (-) | no homologs |
MST2069 (+)f | 3:329197 | 160 | BCAS0293(-) | aidA, intracellular protein of unknown function involved in nematode virulence; (second aid A) |