Potential Gaps in catabolism of small carbon sources in Photobacterium gaetbulicola Gung47
Found 56 low-confidence and 42 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | Psest_0084: 2-oxoglutarate TRAP transporter, fused 4TM/12TM components | H744_RS02175 | |
| 2-oxoglutarate | Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component | H744_RS25950 | H744_RS07805 |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | H744_RS25800 | |
| 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 | H744_RS00100 | H744_RS03060 |
| citrate | cit1: citrate:H+ symporter Cit1 | H744_RS22650 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | H744_RS14465 | H744_RS04730 |
| citrulline | aruF: ornithine/arginine N-succinyltransferase subunit AruAI (AruF) | H744_RS11465 | |
| citrulline | aruG: ornithine/arginine N-succinyltransferase subunit AruAII (AruG) | H744_RS11465 | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | H744_RS06585 | H744_RS20715 |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | H744_RS20730 | H744_RS06570 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | H744_RS10180 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | H744_RS08145 | H744_RS07580 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | H744_RS05370 | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | | |
| fucose | fucO: L-lactaldehyde reductase | H744_RS22610 | H744_RS07660 |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | galP: galactose:H+ symporter GalP | H744_RS00100 | H744_RS03060 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | H744_RS05380 | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | H744_RS14955 | H744_RS21990 |
| glucuronate | dctP: D-glucuronate TRAP transporter, solute receptor component | H744_RS05590 | H744_RS03795 |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| histidine | hutV: L-histidine ABC transporter, ATPase component HutV | H744_RS02715 | H744_RS22590 |
| histidine | hutX: L-histidine ABC transporter, substrate-binding component HutX | H744_RS02725 | |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | H744_RS04245 | H744_RS26450 |
| isoleucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | H744_RS04250 | H744_RS26450 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | H744_RS04255 | H744_RS15065 |
| L-lactate | lutC: L-lactate dehydrogenase, LutC subunit | H744_RS16240 | |
| lactose | lacY: lactose:proton symporter LacY | H744_RS01475 | |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | H744_RS04245 | H744_RS26450 |
| leucine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | H744_RS04250 | H744_RS26450 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | H744_RS04255 | H744_RS15065 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | H744_RS09235 | |
| lysine | argT: L-lysine ABC transporter, substrate-binding component ArgT | H744_RS14470 | H744_RS20565 |
| lysine | davA: 5-aminovaleramidase | | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davT: 5-aminovalerate aminotransferase | H744_RS11460 | H744_RS16550 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | H744_RS02205 | |
| lysine | gcdH: glutaryl-CoA dehydrogenase | H744_RS04345 | H744_RS04325 |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | H744_RS14480 | H744_RS20575 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | H744_RS14465 | H744_RS06570 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | H744_RS14475 | H744_RS20570 |
| mannose | manP: mannose PTS system, EII-CBA components | H744_RS00870 | H744_RS20015 |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | H744_RS14955 | H744_RS17865 |
| 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 | H744_RS04320 | H744_RS10395 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | H744_RS00410 | H744_RS04320 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | H744_RS06715 | H744_RS10390 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | H744_RS06715 | H744_RS02875 |
| phenylacetate | paaK: phenylacetate-CoA ligase | H744_RS15175 | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | H744_RS04320 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | H744_RS07795 | H744_RS07770 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | H744_RS07795 | H744_RS07770 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | H744_RS01660 | H744_RS06160 |
| pyruvate | actP: large subunit of pyruvate transporter (actP-like) | H744_RS09195 | |
| pyruvate | yjcH: putative small subunit of pyruvate transporter (yjcH-like) | H744_RS09190 | |
| rhamnose | fucO: L-lactaldehyde reductase | H744_RS22610 | H744_RS07660 |
| 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 | H744_RS06405 | H744_RS03175 |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | H744_RS06415 | |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | H744_RS06410 | H744_RS03170 |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | H744_RS04305 | H744_RS22030 |
| valine | acdH: isobutyryl-CoA dehydrogenase | H744_RS04325 | H744_RS04345 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | H744_RS04315 | |
| valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | H744_RS04245 | H744_RS26450 |
| valine | bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | H744_RS04250 | H744_RS26450 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | H744_RS04255 | H744_RS15065 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | H744_RS00870 | H744_RS20015 |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | H744_RS19955 | |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | | |
| xylose | xylT: D-xylose transporter | H744_RS00100 | H744_RS03060 |
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