Potential Gaps in catabolism of small carbon sources in Flammeovirga pacifica WPAGA1
Found 90 low-confidence and 48 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 | NH26_RS16960 | |
| 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 | | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | NH26_RS15385 | NH26_RS15330 |
| arginine | rocE: L-arginine permease | | |
| cellobiose | SSS-glucose: Sodium/glucose cotransporter | NH26_RS16735 | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | NH26_RS12760 | NH26_RS01185 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | NH26_RS13165 | NH26_RS18095 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | NH26_RS09860 | NH26_RS10445 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | NH26_RS04155 | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | NH26_RS19815 | NH26_RS09710 |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | NH26_RS15790 | NH26_RS24450 |
| fructose | scrK: fructokinase | NH26_RS04570 | NH26_RS15080 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | NH26_RS23035 | |
| galactose | galP: galactose:H+ symporter GalP | NH26_RS15385 | NH26_RS15330 |
| galacturonate | exuT: D-galacturonate transporter ExuT | NH26_RS23465 | NH26_RS10080 |
| gluconate | edd: phosphogluconate dehydratase | NH26_RS18075 | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| glucosamine | nagP: N-acetylglucosamine transporter NagP | | |
| glucose | SSS-glucose: Sodium/glucose cotransporter | NH26_RS16735 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | NH26_RS10080 | NH26_RS23465 |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | NH26_RS07095 | NH26_RS09395 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | NH26_RS04460 | |
| glycerol | glpF: glycerol facilitator glpF | NH26_RS20160 | |
| histidine | permease: L-histidine permease | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | NH26_RS05485 | NH26_RS11310 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | NH26_RS14285 | |
| isoleucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | NH26_RS16575 | NH26_RS04255 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | NH26_RS10650 | NH26_RS18295 |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | NH26_RS03310 | NH26_RS11755 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | NH26_RS23460 | NH26_RS10445 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | NH26_RS03725 | NH26_RS18360 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-lactate | lldG: L-lactate dehydrogenase, LldG subunit | NH26_RS23020 | NH26_RS20045 |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
| lactose | lacP: lactose permease LacP | | |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | NH26_RS14285 | |
| leucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | NH26_RS16575 | NH26_RS04255 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | NH26_RS10650 | NH26_RS18295 |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | NH26_RS05485 | NH26_RS11310 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | NH26_RS18360 | NH26_RS03725 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | NH26_RS04345 | NH26_RS04540 |
| lysine | davT: 5-aminovalerate aminotransferase | NH26_RS10640 | NH26_RS00235 |
| lysine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | NH26_RS03310 | NH26_RS17105 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | NH26_RS09125 | NH26_RS09210 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | patA: cadaverine aminotransferase | NH26_RS10640 | NH26_RS00235 |
| lysine | patD: 5-aminopentanal dehydrogenase | NH26_RS05385 | NH26_RS23040 |
| maltose | malI: maltose transporter | NH26_RS11355 | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | STP6: mannose:H+ symporter | NH26_RS15385 | NH26_RS15330 |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | | |
| myoinositol | iolN: 2,4-diketo-inositol hydratase | | |
| myoinositol | iolO: 5-dehydro-L-gluconate epimerase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | NH26_RS15385 | NH26_RS15330 |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| myoinositol | uxuB: D-mannonate dehydrogenase | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagP: N-acetylglucosamine transporter NagP | | |
| 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 | NH26_RS12415 | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | NH26_RS03310 | NH26_RS17105 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | NH26_RS03310 | |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | NH26_RS11750 | NH26_RS05840 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | NH26_RS11750 | NH26_RS05840 |
| phenylacetate | paaK: phenylacetate-CoA ligase | NH26_RS07725 | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | NH26_RS03310 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | NH26_RS13340 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | NH26_RS14495 | NH26_RS00175 |
| proline | ectP: proline transporter EctP | NH26_RS01465 | NH26_RS13570 |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | NH26_RS03725 | NH26_RS18360 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | NH26_RS08030 | NH26_RS10640 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | NH26_RS10640 | NH26_RS00235 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | NH26_RS05385 | NH26_RS23040 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | dctM: pyruvate TRAP transporter, large permease component | NH26_RS05505 | |
| pyruvate | dctQ: pyruvate TRAP transporter, small permease component | NH26_RS05500 | |
| rhamnose | rhaB: L-rhamnulokinase | NH26_RS20075 | |
| rhamnose | rhaD: rhamnulose 1-phosphate aldolase | | |
| ribose | rbsK: ribokinase | | |
| serine | snatA: L-serine transporter | NH26_RS14335 | NH26_RS05030 |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | NH26_RS10445 | NH26_RS10075 |
| succinate | satP: succinate:H+ symporter SatP | NH26_RS01475 | NH26_RS24715 |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| sucrose | SSS-glucose: Sodium/glucose cotransporter | NH26_RS16735 | |
| threonine | snatA: L-threonine transporter snatA | NH26_RS14335 | NH26_RS05030 |
| trehalose | SSS-glucose: Sodium/glucose cotransporter | NH26_RS16735 | |
| trehalose | treF: trehalase | NH26_RS13265 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | NH26_RS05485 | NH26_RS11310 |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | NH26_RS03310 | |
| valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | NH26_RS14285 | |
| valine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | NH26_RS16575 | NH26_RS04255 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | NH26_RS10650 | NH26_RS18295 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | NH26_RS03310 | NH26_RS17105 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | NH26_RS05385 | NH26_RS24650 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | NH26_RS03725 | NH26_RS18360 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | NH26_RS15330 | |
| xylitol | xdhA: xylitol dehydrogenase | NH26_RS24450 | NH26_RS24640 |
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