Potential Gaps in catabolism of small carbon sources in Bacillus safensis FO-36b
Found 63 low-confidence and 52 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 | BA81_RS04205 | BA81_RS18805 |
| 4-hydroxybenzoate | praD: 2-oxohex-3-enedioate decarboxylase | | |
| acetate | actP: cation/acetate symporter ActP | BA81_RS07060 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | BA81_RS01665 | BA81_RS02855 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | BA81_RS07110 | BA81_RS06220 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | BA81_RS07110 | BA81_RS01830 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | BA81_RS02845 | BA81_RS16565 |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | BA81_RS17670 | BA81_RS13045 |
| D-serine | dsdA: D-serine ammonia-lyase | BA81_RS03945 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | BA81_RS07990 | BA81_RS09485 |
| 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 | BA81_RS04205 | BA81_RS18805 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| 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 | BA81_RS06010 | BA81_RS01930 |
| galacturonate | PS417_04205: D-galacturonate transporter | BA81_RS11615 | BA81_RS14805 |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | BA81_RS08455 | BA81_RS16085 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | BA81_RS18385 | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glucuronate | uxuL: D-glucaro-1,5-lactonase UxuL or UxuF | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | BA81_RS06580 | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | BA81_RS06505 | BA81_RS17640 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | BA81_RS02825 | BA81_RS08825 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | BA81_RS09485 | BA81_RS06750 |
| lactose | lacP: lactose permease LacP | | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | BA81_RS02825 | BA81_RS08825 |
| leucine | liuA: isovaleryl-CoA dehydrogenase | BA81_RS17640 | BA81_RS06505 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | BA81_RS08925 | BA81_RS02705 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | BA81_RS17615 | BA81_RS01055 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | BA81_RS17610 | BA81_RS02875 |
| lysine | cadA: lysine decarboxylase | BA81_RS05335 | BA81_RS10970 |
| lysine | davD: glutarate semialdehyde dehydrogenase | BA81_RS16630 | BA81_RS04205 |
| lysine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | BA81_RS17615 | BA81_RS01055 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | BA81_RS14800 | |
| lysine | gcdH: glutaryl-CoA dehydrogenase | BA81_RS06505 | BA81_RS17640 |
| lysine | lysP: L-lysine:H+ symporter LysP | BA81_RS05130 | BA81_RS14410 |
| lysine | patA: cadaverine aminotransferase | BA81_RS05135 | BA81_RS10845 |
| lysine | patD: 5-aminopentanal dehydrogenase | BA81_RS04205 | BA81_RS18805 |
| mannose | manP: mannose PTS system, EII-CBA components | BA81_RS08730 | BA81_RS17550 |
| 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 | BA81_RS01055 | BA81_RS17615 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | BA81_RS11410 | BA81_RS17615 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | BA81_RS04605 | BA81_RS06520 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | BA81_RS04605 | BA81_RS06520 |
| phenylacetate | paaK: phenylacetate-CoA ligase | BA81_RS01045 | BA81_RS11245 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | BA81_RS11410 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | BA81_RS07060 | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | BA81_RS18395 | BA81_RS13735 |
| 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 | BA81_RS01055 | BA81_RS17615 |
| phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | BA81_RS11410 | BA81_RS17615 |
| phenylalanine | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | BA81_RS04605 | BA81_RS06520 |
| phenylalanine | paaJ2: 3-oxoadipyl-CoA thiolase | BA81_RS04605 | BA81_RS06520 |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | BA81_RS11410 | |
| phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | BA81_RS13475 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | BA81_RS16620 | BA81_RS11700 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | BA81_RS11700 | BA81_RS13555 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | BA81_RS18805 | BA81_RS04205 |
| pyruvate | mctC: pyruvate symporter MctC | BA81_RS07060 | |
| rhamnose | aldA: lactaldehyde dehydrogenase | BA81_RS04205 | BA81_RS18805 |
| 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 | | |
| ribose | rbsA: D-ribose ABC transporter, ATPase component RbsA | BA81_RS06075 | BA81_RS07135 |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | BA81_RS06085 | |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | BA81_RS06080 | BA81_RS07130 |
| serine | serP: L-serine permease SerP | BA81_RS07805 | BA81_RS18395 |
| sorbitol | sdh: sorbitol dehydrogenase | BA81_RS07960 | BA81_RS10240 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | BA81_RS06010 | BA81_RS15400 |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | BA81_RS02600 | BA81_RS02595 |
| threonine | ltaE: L-threonine aldolase | BA81_RS06375 | |
| threonine | serP1: L-threonine uptake transporter SerP1 | BA81_RS07805 | BA81_RS18395 |
| trehalose | treC: trehalose-6-phosphate hydrolase | BA81_RS16135 | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | BA81_RS13735 | BA81_RS07805 |
| tyrosine | fahA: fumarylacetoacetate hydrolase | BA81_RS11035 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | BA81_RS06505 | BA81_RS17640 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | BA81_RS17615 | BA81_RS00035 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | BA81_RS02825 | BA81_RS08825 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | BA81_RS17615 | BA81_RS01055 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | BA81_RS07440 | BA81_RS08490 |
| xylitol | EIIA-Axl: xylitol PTS, enzyme IIA (EIIA-Axl) | BA81_RS07940 | |
| xylitol | EIIB-Axl: xylitol PTS, enzyme IIB (EIIB-Axl) | BA81_RS07950 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | BA81_RS01820 | BA81_RS07960 |
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