Potential Gaps in catabolism of small carbon sources in Psychromonas ingrahamii 37
Found 75 low-confidence and 52 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 | | |
| alanine | alsT: L-alanine symporter AlsT/DagA | PING_RS10770 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | gabT: gamma-aminobutyrate transaminase | PING_RS09840 | PING_RS00300 |
| arginine | patA: putrescine aminotransferase (PatA/SpuC) | PING_RS14175 | PING_RS00300 |
| arginine | patD: gamma-aminobutyraldehyde dehydrogenase | PING_RS10720 | PING_RS13070 |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | PING_RS14615 | PING_RS12535 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | PING_RS14605 | PING_RS09975 |
| citrulline | arcC: carbamate kinase | | |
| citrulline | gabT: gamma-aminobutyrate transaminase | PING_RS09840 | PING_RS00300 |
| citrulline | odc: L-ornithine decarboxylase | PING_RS07470 | |
| citrulline | patA: putrescine aminotransferase (PatA/SpuC) | PING_RS14175 | PING_RS00300 |
| citrulline | patD: gamma-aminobutyraldehyde dehydrogenase | PING_RS10720 | PING_RS13070 |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | PING_RS14535 | PING_RS14555 |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | PING_RS14570 | PING_RS14550 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | PING_RS15615 | PING_RS17230 |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | PING_RS13080 | |
| 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 | PING_RS13070 | PING_RS10720 |
| 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 | | |
| galactose | galE: UDP-glucose 4-epimerase | PING_RS10450 | PING_RS17970 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | PING_RS02565 | PING_RS14065 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctP: D-glucuronate TRAP transporter, solute receptor component | PING_RS00745 | |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| histidine | hisJ: L-histidine ABC transporter, substrate-binding component HisJ | PING_RS14610 | PING_RS01600 |
| histidine | hisM: L-histidine ABC transporter, permease component 1 (HisM) | PING_RS14600 | PING_RS09975 |
| histidine | hisP: L-histidine ABC transporter, ATPase component HisP | PING_RS14615 | PING_RS02195 |
| histidine | hisQ: L-histidine ABC transporter, permease component 2 (HisQ) | PING_RS14605 | PING_RS02205 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | PING_RS13440 | |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | PING_RS05770 | PING_RS05265 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lactose | galE: UDP-glucose 4-epimerase | PING_RS10450 | PING_RS17970 |
| lactose | lacP: lactose permease LacP | | |
| leucine | aacS: acetoacetyl-CoA synthetase | | |
| leucine | aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ | PING_RS14555 | PING_RS14535 |
| leucine | aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) | PING_RS14545 | PING_RS14565 |
| leucine | aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | PING_RS14570 | PING_RS14550 |
| leucine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | PING_RS14560 | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | PING_RS13440 | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | PING_RS14630 | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | PING_RS03450 | PING_RS03455 |
| 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 | PING_RS14610 | PING_RS01600 |
| lysine | davA: 5-aminovaleramidase | | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | PING_RS09835 | PING_RS14365 |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | PING_RS14600 | PING_RS09975 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | PING_RS14615 | PING_RS14550 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | PING_RS14605 | PING_RS02205 |
| mannose | manA: mannose-6-phosphate isomerase | PING_RS04045 | |
| mannose | manP: mannose PTS system, EII-CBA components | PING_RS18350 | |
| 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 | PS417_11885: myo-inositol ABC transporter, substrate-binding component | PING_RS14480 | |
| myoinositol | PS417_11890: myo-inositol ABC transporter, ATPase component | PING_RS01830 | PING_RS14490 |
| myoinositol | PS417_11895: myo-inositol ABC transporter, permease component | PING_RS01835 | PING_RS14485 |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | PING_RS02565 | PING_RS14065 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | ARO10: phenylpyruvate decarboxylase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | PING_RS13070 | PING_RS10720 |
| putrescine | gabT: gamma-aminobutyrate transaminase | PING_RS09840 | PING_RS00300 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | PING_RS14175 | PING_RS00300 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | PING_RS10720 | PING_RS13070 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | dctQ: pyruvate TRAP transporter, small permease component | PING_RS16220 | |
| rhamnose | aldA: lactaldehyde dehydrogenase | PING_RS13070 | PING_RS10720 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | PING_RS05770 | PING_RS13080 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsA: D-ribose ABC transporter, ATPase component RbsA | PING_RS01830 | PING_RS14385 |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | PING_RS01840 | PING_RS05885 |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | PING_RS01835 | PING_RS14485 |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | PING_RS05770 | |
| trehalose | treC: trehalose-6-phosphate hydrolase | PING_RS02750 | PING_RS12270 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | PING_RS14800 | |
| valine | acdH: isobutyryl-CoA dehydrogenase | PING_RS13440 | |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | PING_RS03450 | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | PING_RS13445 | PING_RS03450 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | PING_RS14185 | PING_RS17315 |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| xylitol | PS417_12055: xylitol ABC transporter, substrate-binding component | | |
| xylitol | PS417_12065: xylitol ABC transporter, ATPase component | PING_RS01830 | PING_RS14490 |
| xylitol | xdhA: xylitol dehydrogenase | PING_RS09660 | PING_RS13080 |
| xylose | gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA | PING_RS10150 | PING_RS11775 |
| xylose | gtsB: xylose ABC transporter, permease component 1 GtsB | PING_RS10155 | PING_RS10425 |
| xylose | gtsC: xylose ABC transporter, permease component 2 GtsC | PING_RS10160 | PING_RS10420 |
| xylose | xylA: xylose isomerase | | |
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