Potential Gaps in catabolism of small carbon sources in Domibacillus robiginosus WS 4628
Found 71 low-confidence and 56 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | csbX: 2-oxoglutarate permease csbX | VP97_RS08405 | |
| 4-hydroxybenzoate | adh: acetaldehyde dehydrogenase (not acylating) | VP97_RS18150 | VP97_RS15610 |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | VP97_RS07135 | VP97_RS02210 |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| 4-hydroxybenzoate | praB: 2-hydroxymuconate 6-semialdehyde dehydrogenase | VP97_RS22310 | VP97_RS18150 |
| 4-hydroxybenzoate | praD: 2-oxohex-3-enedioate decarboxylase | | |
| arabinose | araE: L-arabinose:H+ symporter | VP97_RS17620 | VP97_RS13930 |
| arginine | rocE: L-arginine permease | VP97_RS16255 | VP97_RS21640 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | VP97_RS09965 | VP97_RS20280 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | VP97_RS09970 | VP97_RS20285 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | VP97_RS20285 | VP97_RS20370 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | VP97_RS09975 | VP97_RS20435 |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | VP97_RS03555 | VP97_RS15930 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | VP97_RS18150 | VP97_RS15610 |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | VP97_RS15065 | VP97_RS07755 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | VP97_RS10115 | VP97_RS16815 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | VP97_RS18150 | VP97_RS15610 |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | VP97_RS18150 | VP97_RS15610 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | VP97_RS02120 | VP97_RS22530 |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | galP: galactose:H+ symporter GalP | VP97_RS17620 | VP97_RS13930 |
| galacturonate | PS417_04205: D-galacturonate transporter | VP97_RS22895 | VP97_RS22885 |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | VP97_RS11245 | VP97_RS11525 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | uxuA: D-mannonate dehydratase | | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | VP97_RS04250 | VP97_RS03495 |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| histidine | permease: L-histidine permease | VP97_RS16255 | VP97_RS21640 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | VP97_RS04280 | VP97_RS04275 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | VP97_RS09685 | VP97_RS06070 |
| isoleucine | brnQ: L-isoleucine:cation symporter BrnQ/BraZ/BraB | VP97_RS22755 | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | VP97_RS09170 | VP97_RS15675 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | VP97_RS10630 | VP97_RS06170 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | lacP: lactose permease LacP | | |
| leucine | aacS: acetoacetyl-CoA synthetase | VP97_RS15065 | VP97_RS07755 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | VP97_RS09685 | VP97_RS06070 |
| leucine | brnQ: L-leucine:Na+ symporter BrnQ/BraB | VP97_RS22755 | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | VP97_RS04280 | VP97_RS02945 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | VP97_RS16720 | VP97_RS09595 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | VP97_RS16685 | VP97_RS14280 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | VP97_RS06030 | |
| lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | VP97_RS15610 | VP97_RS03680 |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lat: L-lysine 6-aminotransferase | VP97_RS07910 | |
| lysine | lysN: 2-aminoadipate transaminase | VP97_RS05550 | VP97_RS21725 |
| lysine | lysP: L-lysine:H+ symporter LysP | VP97_RS16255 | VP97_RS21640 |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | | |
| mannose | STP6: mannose:H+ symporter | VP97_RS14730 | VP97_RS02705 |
| 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 | VP97_RS16685 | VP97_RS07200 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | VP97_RS14280 | VP97_RS16685 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | VP97_RS02940 | VP97_RS21790 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | VP97_RS02940 | VP97_RS21790 |
| phenylacetate | paaK: phenylacetate-CoA ligase | VP97_RS15065 | VP97_RS07755 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | VP97_RS14280 | VP97_RS16685 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | VP97_RS15225 | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | VP97_RS16255 | VP97_RS21640 |
| phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | | |
| phenylalanine | paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A | | |
| phenylalanine | paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B | | |
| phenylalanine | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | | |
| phenylalanine | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | VP97_RS16685 | VP97_RS07200 |
| phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | VP97_RS14280 | VP97_RS16685 |
| phenylalanine | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | VP97_RS02940 | VP97_RS21790 |
| phenylalanine | paaJ2: 3-oxoadipyl-CoA thiolase | VP97_RS02940 | VP97_RS21790 |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | VP97_RS14280 | VP97_RS16685 |
| phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | VP97_RS10630 | VP97_RS06170 |
| propionate | prpE: propionyl-CoA synthetase | VP97_RS19130 | VP97_RS07445 |
| putrescine | gabT: gamma-aminobutyrate transaminase | VP97_RS20440 | VP97_RS22300 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | VP97_RS20440 | VP97_RS22300 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | VP97_RS22310 | VP97_RS18150 |
| rhamnose | rhaP: L-rhamnose ABC transporter, permease component 1 (RhaP) | VP97_RS17870 | VP97_RS08510 |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | VP97_RS14020 | |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | VP97_RS14010 | VP97_RS17870 |
| serine | sdaB: L-serine ammonia-lyase | VP97_RS04145 | |
| sorbitol | mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK | VP97_RS02105 | VP97_RS04490 |
| sorbitol | sdh: sorbitol dehydrogenase | VP97_RS03575 | VP97_RS08490 |
| threonine | adh: acetaldehyde dehydrogenase (not acylating) | VP97_RS18150 | VP97_RS15610 |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | VP97_RS00955 | VP97_RS00950 |
| threonine | ltaE: L-threonine aldolase | VP97_RS17505 | |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | VP97_RS18150 | VP97_RS15610 |
| trehalose | treC: trehalose-6-phosphate hydrolase | VP97_RS09775 | VP97_RS19600 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | VP97_RS16255 | VP97_RS21640 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | VP97_RS15065 | VP97_RS07755 |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | VP97_RS16255 | VP97_RS19090 |
| tyrosine | fahA: fumarylacetoacetate hydrolase | VP97_RS20850 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | VP97_RS04280 | VP97_RS04275 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | | |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | VP97_RS09685 | VP97_RS06070 |
| valine | brnQ: L-valine:cation symporter BrnQ/BraZ/BraB | VP97_RS22755 | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | VP97_RS16685 | VP97_RS07200 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | VP97_RS11730 | VP97_RS03920 |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | VP97_RS10630 | VP97_RS06170 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | VP97_RS08140 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | VP97_RS08490 | |
| xylose | xdhA: xylitol dehydrogenase | VP97_RS08490 | VP97_RS22060 |
| xylose | xylB: xylulokinase | | |
| xylose | xylF: ABC transporter for xylose, substrate binding component xylF | VP97_RS14020 | |
| xylose | xyrA: xylitol reductase | VP97_RS13330 | VP97_RS21365 |
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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