Potential Gaps in catabolism of small carbon sources in Halomonas stevensii S18214
Found 96 low-confidence and 34 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 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 | xylF: 2-hydroxymuconate semialdehyde hydrolase | | |
| acetate | actP: cation/acetate symporter ActP | HSS18214_RS0115435 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | Echvi_1880: L-arabinose:Na+ symporter | HSS18214_RS0109835 | |
| arginine | astE: succinylglutamate desuccinylase | HSS18214_RS0117305 | |
| cellobiose | bgl: cellobiase | | |
| citrate | cit1: citrate:H+ symporter Cit1 | HSS18214_RS0104730 | HSS18214_RS0110135 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | HSS18214_RS0117295 | HSS18214_RS0112275 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | HSS18214_RS0117290 | HSS18214_RS0112280 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | HSS18214_RS0117275 | HSS18214_RS0117280 |
| citrulline | arcC: carbamate kinase | | |
| citrulline | rocD: ornithine aminotransferase | HSS18214_RS0108505 | HSS18214_RS0110205 |
| D-alanine | dadA: D-alanine dehydrogenase | HSS18214_RS0110280 | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | HSS18214_RS0111285 | HSS18214_RS0111280 |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | HSS18214_RS0111300 | HSS18214_RS0112275 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | HSS18214_RS0112480 | HSS18214_RS0110470 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | HSS18214_RS0108140 | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | 1pfk: 1-phosphofructokinase | | |
| fucose | fdh: L-fucose 1-dehydrogenase | HSS18214_RS0115765 | HSS18214_RS0108190 |
| fucose | fucD: L-fuconate dehydratase | | |
| fucose | fuconolactonase: L-fucono-1,5-lactonase | | |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | | |
| galacturonate | uxaB: tagaturonate reductase | HSS18214_RS0108120 | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntA: gluconate TRAP transporter, small permease component | HSS18214_RS0107030 | HSS18214_RS0106425 |
| gluconate | gntB: gluconate TRAP transporter, large permease component | HSS18214_RS0107025 | HSS18214_RS0110310 |
| gluconate | gntC: gluconate TRAP transporter, periplasmic solute-binding component | HSS18214_RS0107035 | HSS18214_RS0110965 |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | HSS18214_RS0112175 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | HSS18214_RS0115335 | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | HSS18214_RS0102195 | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | aapM: L-histidine ABC transporter, permease component 2 (AapM) | HSS18214_RS0111295 | HSS18214_RS0112280 |
| histidine | aapP: L-histidine ABC transporter, ATPase component AapP | HSS18214_RS0111300 | HSS18214_RS0112275 |
| histidine | aapQ: L-histidine ABC transporter, permease component 1 (AapQ) | HSS18214_RS0111290 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | HSS18214_RS0110840 | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | HSS18214_RS0115380 | HSS18214_RS0106755 |
| lactose | klh: periplasmic 3'-ketolactose hydrolase | | |
| lactose | lacA': periplasmic lactose 3-dehydrogenase, LacA subunit | | |
| lactose | lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) | | |
| lactose | lacC': periplasmic lactose 3-dehydrogenase, LacC subunit | | |
| leucine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | HSS18214_RS0111295 | |
| leucine | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | HSS18214_RS0111300 | HSS18214_RS0112275 |
| leucine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | HSS18214_RS0111290 | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | HSS18214_RS0115380 | HSS18214_RS0106755 |
| lysine | davA: 5-aminovaleramidase | HSS18214_RS0109995 | HSS18214_RS0101390 |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | HSS18214_RS0101495 | HSS18214_RS0117090 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | manP: mannose PTS system, EII-CBA components | HSS18214_RS0105125 | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | HSS18214_RS0112175 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| 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 | HSS18214_RS0107095 | HSS18214_RS0102160 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | HSS18214_RS0103425 | HSS18214_RS0107095 |
| phenylacetate | paaK: phenylacetate-CoA ligase | HSS18214_RS0103455 | HSS18214_RS0105675 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | HSS18214_RS0107095 | HSS18214_RS0103425 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | HSS18214_RS0108135 | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | HSS18214_RS0110205 | HSS18214_RS0108505 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | HSS18214_RS0115935 | HSS18214_RS0110090 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | HSS18214_RS0102240 | HSS18214_RS0115760 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | HSS18214_RS0106125 | |
| rhamnose | Echvi_1617: L-rhamnose transporter | HSS18214_RS0110485 | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | HSS18214_RS0108190 | HSS18214_RS0101495 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | HSS18214_RS0114420 | HSS18214_RS0108140 |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| sorbitol | sdh: sorbitol dehydrogenase | HSS18214_RS0117000 | HSS18214_RS0104585 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | ams: sucrose hydrolase (invertase) | HSS18214_RS0105075 | HSS18214_RS0105045 |
| trehalose | treF: trehalase | HSS18214_RS0105075 | HSS18214_RS0105045 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | HSS18214_RS0108135 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | HSS18214_RS0101850 | HSS18214_RS0103460 |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | HSS18214_RS0115380 | HSS18214_RS0106755 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | HSS18214_RS0105125 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | HSS18214_RS0104585 | |
| xylose | gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA | HSS18214_RS0106710 | |
| xylose | gtsB: xylose ABC transporter, permease component 1 GtsB | HSS18214_RS0106705 | |
| xylose | gtsD: xylose ABC transporter, ATPase component GtsD | HSS18214_RS0106695 | HSS18214_RS0113695 |
| xylose | gyaR: glyoxylate reductase | HSS18214_RS0110980 | HSS18214_RS0111220 |
| xylose | xad: D-xylonate dehydratase | HSS18214_RS0117225 | HSS18214_RS0100210 |
| xylose | xdh: D-xylose dehydrogenase | HSS18214_RS0102785 | HSS18214_RS0101495 |
| xylose | xylC: xylonolactonase | | |
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