GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Vagococcus penaei CD276

Found 117 low-confidence and 42 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate praB: 2-hydroxymuconate 6-semialdehyde dehydrogenase BW732_RS08950 BW732_RS08430
4-hydroxybenzoate praD: 2-oxohex-3-enedioate decarboxylase
acetate ybhL: acetate uptake transporter YbhL BW732_RS00770
alanine cycA: L-alanine symporter CycA
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase BW732_RS06860
arabinose araE: L-arabinose:H+ symporter
arginine artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA BW732_RS08200 BW732_RS10010
arginine bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) BW732_RS08205 BW732_RS10015
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase BW732_RS08950 BW732_RS08430
arginine rocD: ornithine aminotransferase
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component BW732_RS10010 BW732_RS08200
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 BW732_RS08205 BW732_RS00340
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 BW732_RS10015
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component BW732_RS00350
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase BW732_RS08950 BW732_RS08430
citrulline rocD: ornithine aminotransferase
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate larD: D,L-lactic acid transporter BW732_RS05000
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase
deoxyribonate atoA: acetoacetyl-CoA transferase, A subunit BW732_RS04645
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BW732_RS04765 BW732_RS08225
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter
fucose aldA: lactaldehyde dehydrogenase BW732_RS08950 BW732_RS08430
fucose fucA: L-fuculose-phosphate aldolase FucA BW732_RS06860
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
galactose galP: galactose:H+ symporter GalP
galacturonate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
gluconate gntK: D-gluconate kinase BW732_RS02815
gluconate gntT: gluconate:H+ symporter GntT
glucosamine manX: glucosamine PTS system, EII-AB component ManX BW732_RS08265 BW732_RS08260
glucosamine manY: glucosamine PTS system, EII-C component ManY BW732_RS08270
glucosamine manZ: glucosamine PTS system, EII-D component ManZ BW732_RS08275 BW732_RS00695
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate garL: 5-dehydro-4-deoxy-D-glucarate aldolase
glucuronate garR: tartronate semialdehyde reductase BW732_RS01305
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent BW732_RS00810
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase BW732_RS10870
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BW732_RS10930 BW732_RS01640
isoleucine dddA: 3-hydroxypropionate dehydrogenase
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase BW732_RS07075 BW732_RS04650
isoleucine hpcD: 3-hydroxypropionyl-CoA dehydratase BW732_RS07075 BW732_RS10880
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase BW732_RS11280 BW732_RS01515
L-lactate larD: D,L-lactic acid transporter LarD BW732_RS05000
lactose lacE: lactose ABC transporter, substrate-binding component BW732_RS04900
lactose lacK: lactose ABC transporter, ATPase component BW732_RS04310 BW732_RS08200
leucine atoA: acetoacetyl-CoA transferase, A subunit BW732_RS04645
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BW732_RS10930 BW732_RS01640
leucine liuA: isovaleryl-CoA dehydrogenase BW732_RS10855 BW732_RS10870
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BW732_RS00005 BW732_RS02630
leucine liuC: 3-methylglutaconyl-CoA hydratase BW732_RS10880 BW732_RS07075
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
lysine bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) BW732_RS08205 BW732_RS10015
lysine davA: 5-aminovaleramidase
lysine davB: L-lysine 2-monooxygenase
lysine davD: glutarate semialdehyde dehydrogenase BW732_RS08950 BW732_RS08430
lysine davT: 5-aminovalerate aminotransferase
lysine gcdG: succinyl-CoA:glutarate CoA-transferase
lysine gcdH: glutaryl-CoA dehydrogenase BW732_RS10855 BW732_RS07055
lysine hisP: L-lysine ABC transporter, ATPase component HisP BW732_RS10010 BW732_RS09835
mannitol mt2d: mannitol 2-dehydrogenase BW732_RS03595 BW732_RS11280
mannitol PLT5: polyol transporter PLT5
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase BW732_RS08955 BW732_RS08440
myoinositol iolT: myo-inositol:H+ symporter
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components BW732_RS09200 BW732_RS08155
phenylacetate paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A
phenylacetate paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B
phenylacetate paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C
phenylacetate paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase BW732_RS04650 BW732_RS10880
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase BW732_RS04650 BW732_RS07075
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase BW732_RS04660 BW732_RS10865
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase BW732_RS04660 BW732_RS10865
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine atoA: acetoacetyl-CoA transferase, A subunit BW732_RS04645
phenylalanine fahA: fumarylacetoacetate hydrolase
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase BW732_RS08950 BW732_RS08430
propionate dddA: 3-hydroxypropionate dehydrogenase
propionate hpcD: 3-hydroxypropionyl-CoA dehydratase BW732_RS07075 BW732_RS10880
propionate prpE: propionyl-CoA synthetase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase BW732_RS07110 BW732_RS11030
putrescine gabT: gamma-aminobutyrate transaminase
putrescine patA: putrescine aminotransferase (PatA/SpuC)
putrescine patD: gamma-aminobutyraldehyde dehydrogenase BW732_RS08950 BW732_RS08430
putrescine potA: putrescine ABC transporter, ATPase component (PotA/PotG) BW732_RS04310 BW732_RS10820
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase BW732_RS08950 BW732_RS08430
rhamnose rhaA: L-rhamnose isomerase
rhamnose rhaB: L-rhamnulokinase
rhamnose rhaD: rhamnulose 1-phosphate aldolase
rhamnose rhaM: L-rhamnose mutarotase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
sorbitol sdh: sorbitol dehydrogenase BW732_RS01410 BW732_RS04765
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
succinate sdc: succinate:Na+ symporter Sdc
threonine dddA: 3-hydroxypropionate dehydrogenase
threonine hpcD: 3-hydroxypropionyl-CoA dehydratase BW732_RS07075 BW732_RS10880
threonine tdcB: L-threonine dehydratase
thymidine nupG: thymidine permease NupG/XapB
trehalose treB: trehalose PTS system, EII-BC components TreB BW732_RS03570 BW732_RS03850
trehalose treC: trehalose-6-phosphate hydrolase BW732_RS03115 BW732_RS03855
trehalose treEIIA: N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) BW732_RS09200 BW732_RS03425
tryptophan tnaA: tryptophanase
tryptophan trpP: energy-coupling factor transporter, tryptophan-specific (S) component TrpP
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine atoA: acetoacetyl-CoA transferase, A subunit BW732_RS04645
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase BW732_RS07055 BW732_RS10870
valine bch: 3-hydroxyisobutyryl-CoA hydrolase BW732_RS04650 BW732_RS10880
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BW732_RS10930 BW732_RS01640
valine dddA: 3-hydroxypropionate dehydrogenase
valine hpcD: 3-hydroxypropionyl-CoA dehydratase BW732_RS07075 BW732_RS10880
valine mmsB: 3-hydroxyisobutyrate dehydrogenase BW732_RS01305
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase BW732_RS03595
xylose xylA: xylose isomerase
xylose xylB: xylulokinase
xylose xylT: D-xylose transporter

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory