Potential Gaps in catabolism of small carbon sources in Psychromonas ossibalaenae JAMM 0738
Found 103 low-confidence and 37 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 | | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | G327_RS0109855 | |
| arginine | rocF: arginase | | |
| cellobiose | bgl: cellobiase | G327_RS0108850 | G327_RS24520 |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | G327_RS0101395 | G327_RS0101370 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | G327_RS0101385 | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | G327_RS0101355 | |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | G327_RS0101370 | G327_RS0101395 |
| 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 | G327_RS0117675 | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | | |
| deoxyribonate | atoB: acetyl-CoA C-acetyltransferase | G327_RS0105025 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | G327_RS0113160 | G327_RS0109255 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | G327_RS0111065 | G327_RS0113665 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | | |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| gluconate | edd: phosphogluconate dehydratase | G327_RS0109790 | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | G327_RS0123280 | G327_RS0120665 |
| glucuronate | dctP: D-glucuronate TRAP transporter, solute receptor component | G327_RS0121760 | |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| histidine | hutV: L-histidine ABC transporter, ATPase component HutV | G327_RS0122140 | G327_RS0112200 |
| histidine | hutX: L-histidine ABC transporter, substrate-binding component HutX | G327_RS0100195 | G327_RS0122130 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | G327_RS0105035 | |
| isoleucine | fadA: 2-methylacetoacetyl-CoA thiolase | G327_RS0105025 | G327_RS0105030 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | G327_RS0103380 | G327_RS0113160 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| isoleucine | prpB: 2-methylisocitrate lyase | | |
| isoleucine | prpC: 2-methylcitrate synthase | G327_RS0115340 | G327_RS0107575 |
| isoleucine | prpD: 2-methylcitrate dehydratase | | |
| L-lactate | lctO: L-lactate oxidase or 2-monooxygenase | | |
| lactose | lacP: lactose permease LacP | | |
| leucine | aacS: acetoacetyl-CoA synthetase | | |
| leucine | atoB: acetyl-CoA C-acetyltransferase | G327_RS0105025 | |
| leucine | ilvE: L-leucine transaminase | G327_RS0109230 | G327_RS0103850 |
| leucine | liuA: isovaleryl-CoA dehydrogenase | G327_RS0105035 | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | G327_RS0119860 | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | G327_RS0105030 | G327_RS0123040 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | argT: L-lysine ABC transporter, substrate-binding component ArgT | G327_RS0101390 | G327_RS0120805 |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | G327_RS0101380 | G327_RS0109395 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | G327_RS0101395 | G327_RS0101370 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | G327_RS0101385 | G327_RS0109395 |
| lysine | lysN: 2-aminoadipate transaminase | G327_RS0103850 | G327_RS0113345 |
| mannitol | mt2d: mannitol 2-dehydrogenase | G327_RS0121745 | G327_RS0103380 |
| mannitol | PLT5: polyol transporter PLT5 | G327_RS0109855 | |
| mannose | manP: mannose PTS system, EII-CBA components | G327_RS0110505 | G327_RS0110900 |
| 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 | G327_RS0109855 | |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | G327_RS0123280 | G327_RS0120665 |
| 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 | G327_RS0119485 | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | G327_RS0123040 | G327_RS0105030 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | | |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | G327_RS0105025 | |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | G327_RS0105025 | |
| 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 | aacS: acetoacetyl-CoA synthetase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | atoB: acetyl-CoA C-acetyltransferase | G327_RS0105025 | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | G327_RS0115985 | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | G327_RS0117755 | G327_RS0112765 |
| propionate | prpB: 2-methylisocitrate lyase | | |
| propionate | prpC: 2-methylcitrate synthase | G327_RS0115340 | G327_RS0107575 |
| propionate | prpD: 2-methylcitrate dehydratase | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | G327_RS0122610 | G327_RS0105250 |
| putrescine | gabD: succinate semialdehyde dehydrogenase | G327_RS0111065 | G327_RS0113665 |
| putrescine | gabT: gamma-aminobutyrate transaminase | G327_RS0113345 | G327_RS0109330 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | G327_RS0113345 | G327_RS0109330 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | G327_RS0113665 | G327_RS0111065 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | actP: large subunit of pyruvate transporter (actP-like) | G327_RS0120645 | |
| pyruvate | yjcH: putative small subunit of pyruvate transporter (yjcH-like) | G327_RS0120640 | |
| rhamnose | aldA: lactaldehyde dehydrogenase | G327_RS0111065 | G327_RS0113665 |
| 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 | G327_RS0109815 | |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | G327_RS0109805 | |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | G327_RS0109810 | |
| sorbitol | sdh: sorbitol dehydrogenase | G327_RS0121745 | G327_RS0108565 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | G327_RS0109855 | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | | |
| tyrosine | atoB: acetyl-CoA C-acetyltransferase | G327_RS0105025 | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | G327_RS0115985 | |
| valine | acdH: isobutyryl-CoA dehydrogenase | G327_RS0105035 | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | G327_RS0105030 | G327_RS0123040 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | G327_RS0111065 | G327_RS0113665 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| valine | prpB: 2-methylisocitrate lyase | | |
| valine | prpC: 2-methylcitrate synthase | G327_RS0115340 | G327_RS0107575 |
| valine | prpD: 2-methylcitrate dehydratase | | |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | G327_RS0109855 | |
| xylitol | xdhA: xylitol dehydrogenase | G327_RS0108565 | G327_RS0109255 |
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