Potential Gaps in catabolism of small carbon sources in Epibacterium ulvae U95
Found 62 low-confidence and 66 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaB: 3-carboxymuconate cycloisomerase | | |
| 4-hydroxybenzoate | pcaC: 4-carboxymuconolactone decarboxylase | CV091_RS09720 | CV091_RS07930 |
| 4-hydroxybenzoate | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | CV091_RS12260 | CV091_RS08390 |
| 4-hydroxybenzoate | pcaG: protocatechuate 3,4-dioxygenase, beta subunit | CV091_RS11145 | CV091_RS11140 |
| 4-hydroxybenzoate | pcaH: protocatechuate 3,4-dioxygenase, alpha subunit | CV091_RS11140 | CV091_RS11145 |
| 4-hydroxybenzoate | pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI) | CV091_RS14305 | |
| 4-hydroxybenzoate | pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ) | CV091_RS14310 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arabinose | xacB: L-arabinose 1-dehydrogenase | CV091_RS08700 | CV091_RS14860 |
| cellobiose | glk: glucokinase | CV091_RS16870 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | CV091_RS09960 | CV091_RS05370 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | CV091_RS19365 | CV091_RS00375 |
| D-alanine | Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 | CV091_RS19370 | CV091_RS00370 |
| D-alanine | Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1 | CV091_RS19375 | CV091_RS00365 |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | CV091_RS19380 | CV091_RS00300 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | CV091_RS07925 | CV091_RS19215 |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | CV091_RS08125 | |
| deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | CV091_RS08140 | |
| deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | CV091_RS07300 | CV091_RS08145 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | CV091_RS11090 | CV091_RS12690 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | CV091_RS11965 | |
| deoxyribose | deoK: deoxyribokinase | CV091_RS17900 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | CV091_RS17200 | CV091_RS05710 |
| fructose | Slc2a5: fructose:H+ symporter | | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | | |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| galactose | dgoD: D-galactonate dehydratase | CV091_RS08705 | CV091_RS09555 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaA: D-altronate dehydratase | CV091_RS03785 | |
| galacturonate | uxaB: tagaturonate reductase | | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | CV091_RS01040 | |
| glucose | glk: glucokinase | CV091_RS16870 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | CV091_RS09940 | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| histidine | hutV: L-histidine ABC transporter, ATPase component HutV | CV091_RS07040 | CV091_RS09745 |
| histidine | hutX: L-histidine ABC transporter, substrate-binding component HutX | CV091_RS14885 | CV091_RS09735 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | CV091_RS04145 | CV091_RS00315 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | dgoD: D-galactonate dehydratase | CV091_RS08705 | CV091_RS09555 |
| lactose | glk: glucokinase | CV091_RS16870 | |
| lactose | lacP: lactose permease LacP | | |
| leucine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | CV091_RS19375 | CV091_RS00365 |
| leucine | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | CV091_RS19380 | CV091_RS00300 |
| leucine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | CV091_RS19370 | CV091_RS00370 |
| lysine | argT: L-lysine ABC transporter, substrate-binding component ArgT | CV091_RS09955 | CV091_RS05365 |
| lysine | cadA: lysine decarboxylase | CV091_RS15520 | |
| lysine | davT: 5-aminovalerate aminotransferase | CV091_RS09670 | CV091_RS06535 |
| lysine | fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase | CV091_RS05225 | CV091_RS16190 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | CV091_RS05080 | CV091_RS11120 |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | CV091_RS09965 | CV091_RS05375 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | CV091_RS09960 | CV091_RS00365 |
| lysine | patA: cadaverine aminotransferase | CV091_RS06535 | CV091_RS07085 |
| maltose | glk: glucokinase | CV091_RS16870 | |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | CV091_RS13450 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | CV091_RS13445 | CV091_RS15925 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | CV091_RS13440 | CV091_RS17305 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | CV091_RS13435 | CV091_RS15940 |
| mannose | manA: mannose-6-phosphate isomerase | CV091_RS15225 | |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | CV091_RS01040 | |
| 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 | CV091_RS16630 | CV091_RS11440 |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | CV091_RS05225 | CV091_RS16190 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | CV091_RS08390 | CV091_RS12260 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | CV091_RS12260 | CV091_RS08390 |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | CV091_RS03570 | CV091_RS11440 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | CV091_RS07260 | |
| proline | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | CV091_RS19375 | CV091_RS00365 |
| proline | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | CV091_RS19380 | CV091_RS00300 |
| proline | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | CV091_RS19370 | CV091_RS00370 |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | CV091_RS16515 | |
| pyruvate | dctQ: pyruvate TRAP transporter, small permease component | CV091_RS17460 | |
| 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 | CV091_RS09525 | CV091_RS04390 |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | CV091_RS09530 | |
| ribose | rbsK: ribokinase | CV091_RS17900 | |
| serine | snatA: L-serine transporter | CV091_RS02025 | |
| sorbitol | sdh: sorbitol dehydrogenase | CV091_RS09500 | CV091_RS04145 |
| sucrose | glk: glucokinase | CV091_RS16870 | |
| threonine | snatA: L-threonine transporter snatA | CV091_RS02025 | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | glk: glucokinase | CV091_RS16870 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | CV091_RS01060 | CV091_RS03710 |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | CV091_RS03700 | CV091_RS05715 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | CV091_RS03720 | CV091_RS02805 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | CV091_RS09505 | |
| xylose | aldA: (glycol)aldehyde dehydrogenase | CV091_RS11005 | CV091_RS09535 |
| xylose | DKDP-aldolase: 2-dehydro-3-deoxy-D-arabinonate aldolase | | |
| xylose | gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA | CV091_RS17350 | CV091_RS09860 |
| xylose | gtsB: xylose ABC transporter, permease component 1 GtsB | CV091_RS17355 | CV091_RS09865 |
| xylose | gtsC: xylose ABC transporter, permease component 2 GtsC | CV091_RS17360 | CV091_RS09870 |
| xylose | gtsD: xylose ABC transporter, ATPase component GtsD | CV091_RS17365 | CV091_RS17310 |
| xylose | xad: D-xylonate dehydratase | CV091_RS08705 | CV091_RS15655 |
| xylose | xdh: D-xylose dehydrogenase | CV091_RS08700 | CV091_RS11090 |
| xylose | xylC: xylonolactonase | CV091_RS17150 | CV091_RS08685 |
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