Potential Gaps in catabolism of small carbon sources in Yersinia intermedia Y228
Found 55 low-confidence and 13 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 | CH53_RS06845 | |
| 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 | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CH53_RS01990 | CH53_RS04650 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | CH53_RS01995 | CH53_RS19700 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | CH53_RS02000 | CH53_RS19705 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | CH53_RS02005 | CH53_RS19710 |
| citrulline | rocD: ornithine aminotransferase | CH53_RS04790 | CH53_RS07545 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | CH53_RS04400 | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | CH53_RS11075 | CH53_RS01795 |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | CH53_RS08180 | CH53_RS16995 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | CH53_RS00030 | CH53_RS04400 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| isoleucine | prpC: 2-methylcitrate synthase | CH53_RS15475 | |
| isoleucine | prpD: 2-methylcitrate dehydratase | | |
| L-lactate | lctO: L-lactate oxidase or 2-monooxygenase | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | lacY: lactose:proton symporter LacY | CH53_RS12485 | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | CH53_RS10845 | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | CH53_RS10260 | CH53_RS02175 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | CH53_RS10940 | CH53_RS00970 |
| lysine | lat: L-lysine 6-aminotransferase | CH53_RS04790 | CH53_RS18415 |
| lysine | lysN: 2-aminoadipate transaminase | CH53_RS18150 | CH53_RS02075 |
| 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 | CH53_RS10260 | CH53_RS01760 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | CH53_RS10260 | |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | CH53_RS10520 | CH53_RS10255 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | CH53_RS10520 | CH53_RS10255 |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | CH53_RS07150 | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | | |
| propionate | prpC: 2-methylcitrate synthase | CH53_RS15475 | |
| propionate | prpD: 2-methylcitrate dehydratase | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | CH53_RS07545 | CH53_RS18415 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | CH53_RS18415 | CH53_RS07545 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | CH53_RS00970 | CH53_RS10940 |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | CH53_RS10260 | CH53_RS01760 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | CH53_RS06840 | CH53_RS00340 |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| valine | prpC: 2-methylcitrate synthase | CH53_RS15475 | |
| valine | prpD: 2-methylcitrate dehydratase | | |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | CH53_RS09270 | CH53_RS01810 |
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