Potential Gaps in catabolism of small carbon sources in Pedobacter sp. GW460-11-11-14-LB5
Found 88 low-confidence and 44 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 | CA265_RS12370 | |
| acetate | deh: acetate/haloacid transporter | CA265_RS19920 | CA265_RS22390 |
| alanine | TRIC: TRIC-type L-alanine transporter | CA265_RS15435 | |
| arginine | rocD: ornithine aminotransferase | CA265_RS15205 | CA265_RS18530 |
| arginine | rocE: L-arginine permease | | |
| arginine | rocF: arginase | | |
| cellobiose | glk: glucokinase | CA265_RS15640 | CA265_RS11300 |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CA265_RS16020 | CA265_RS04175 |
| 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 | | |
| citrulline | rocD: ornithine aminotransferase | CA265_RS15205 | CA265_RS18530 |
| 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 | CA265_RS14425 | CA265_RS15860 |
| deoxyinosine | deoB: phosphopentomutase | CA265_RS09660 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | CA265_RS08355 | CA265_RS04230 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | CA265_RS04675 | CA265_RS08575 |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | CA265_RS12755 | CA265_RS12005 |
| fructose | glcP: fructose:H+ symporter GlcP | CA265_RS23325 | CA265_RS01275 |
| fructose | scrK: fructokinase | CA265_RS18205 | |
| fucose | fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase | CA265_RS08355 | CA265_RS13715 |
| fucose | fuconolactonase: L-fucono-1,5-lactonase | CA265_RS08340 | |
| glucose | glk: glucokinase | CA265_RS15640 | CA265_RS11300 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | CA265_RS07875 | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | LAT2: L-histidine transporter | CA265_RS14990 | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | CA265_RS22715 | CA265_RS02820 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | CA265_RS18405 | CA265_RS19580 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | CA265_RS09070 | CA265_RS19585 |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | CA265_RS20005 | CA265_RS17590 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | CA265_RS15450 | CA265_RS00760 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | CA265_RS02215 | CA265_RS18365 |
| L-lactate | L-LDH: L-lactate dehydrogenase | CA265_RS08335 | CA265_RS03080 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | glk: glucokinase | CA265_RS15640 | CA265_RS11300 |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | CA265_RS18405 | CA265_RS19580 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | CA265_RS09070 | CA265_RS19585 |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | CA265_RS02820 | CA265_RS22715 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | CA265_RS02215 | CA265_RS18365 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | CA265_RS10640 | CA265_RS16635 |
| lysine | davD: glutarate semialdehyde dehydrogenase | CA265_RS14635 | CA265_RS24850 |
| lysine | davT: 5-aminovalerate aminotransferase | CA265_RS18530 | CA265_RS15205 |
| lysine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | CA265_RS20005 | CA265_RS09125 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | CA265_RS08550 | |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | patD: 5-aminopentanal dehydrogenase | CA265_RS14635 | CA265_RS24850 |
| maltose | glk: glucokinase | CA265_RS15640 | CA265_RS11300 |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | gluP: mannose:Na+ symporter | CA265_RS04675 | CA265_RS08575 |
| mannose | man-isomerase: D-mannose isomerase | | |
| mannose | scrK: fructokinase | CA265_RS18205 | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | CA265_RS23295 | |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | CA265_RS12005 | |
| myoinositol | iolN: 2,4-diketo-inositol hydratase | | |
| myoinositol | iolO: 5-dehydro-L-gluconate epimerase | CA265_RS12255 | |
| myoinositol | iolT: myo-inositol:H+ symporter | CA265_RS01275 | CA265_RS23325 |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| myoinositol | uxuB: D-mannonate dehydrogenase | | |
| 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 | CA265_RS25075 | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | CA265_RS20005 | CA265_RS09125 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | | |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | CA265_RS17585 | CA265_RS06590 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | CA265_RS17585 | CA265_RS06590 |
| 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 | fahA: fumarylacetoacetate hydrolase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | CA265_RS02215 | CA265_RS18365 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | CA265_RS24850 | CA265_RS01080 |
| putrescine | gabT: gamma-aminobutyrate transaminase | CA265_RS14455 | CA265_RS18530 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | CA265_RS14635 | CA265_RS24850 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | CA265_RS02625 | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | serP: L-serine permease SerP | | |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | CA265_RS08605 | CA265_RS08355 |
| sucrose | ams: sucrose hydrolase (invertase) | CA265_RS18440 | |
| sucrose | glk: glucokinase | CA265_RS15640 | CA265_RS11300 |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| thymidine | deoB: phosphopentomutase | CA265_RS09660 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| trehalose | glk: glucokinase | CA265_RS15640 | CA265_RS11300 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | CA265_RS22715 | CA265_RS02820 |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | CA265_RS20005 | |
| valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | CA265_RS18405 | CA265_RS19580 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | CA265_RS09070 | CA265_RS19585 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | CA265_RS20005 | CA265_RS09125 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | CA265_RS14635 | CA265_RS19780 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | CA265_RS01080 | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | CA265_RS02215 | CA265_RS18365 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | CA265_RS23325 | CA265_RS01275 |
| xylitol | xdhA: xylitol dehydrogenase | CA265_RS08610 | CA265_RS12005 |
Confidence: high confidence medium confidence low confidence
This GapMind analysis is from Sep 17 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