Potential Gaps in catabolism of small carbon sources in Cronobacter universalis NCTC 9529
Found 63 low-confidence and 18 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 | AFK65_RS03520 | |
| 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 | AFK65_RS13765 | AFK65_RS15280 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | AFK65_RS13770 | AFK65_RS06800 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | AFK65_RS13775 | AFK65_RS06805 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | AFK65_RS13785 | AFK65_RS13780 |
| D-serine | dsdA: D-serine ammonia-lyase | AFK65_RS12305 | AFK65_RS00865 |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | AFK65_RS11655 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | AFK65_RS14005 | AFK65_RS09920 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | AFK65_RS00060 | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | AFK65_RS00565 | |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | AFK65_RS13520 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | | |
| isoleucine | acnD: 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) | AFK65_RS11020 | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | AFK65_RS07725 | AFK65_RS05450 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| isoleucine | prpC: 2-methylcitrate synthase | AFK65_RS06090 | |
| isoleucine | prpF: methylaconitate isomerase | AFK65_RS19990 | |
| leucine | aacS: acetoacetyl-CoA synthetase | AFK65_RS11655 | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | AFK65_RS10290 | AFK65_RS01805 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | AFK65_RS13905 | AFK65_RS01475 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | AFK65_RS01895 | AFK65_RS10605 |
| lysine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | AFK65_RS01475 | AFK65_RS13905 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | | |
| lysine | gcdH: glutaryl-CoA dehydrogenase | | |
| 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 | AFK65_RS13570 | AFK65_RS01475 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | AFK65_RS13905 | |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | AFK65_RS15800 | AFK65_RS01470 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | AFK65_RS15800 | AFK65_RS01470 |
| phenylacetate | paaK: phenylacetate-CoA ligase | AFK65_RS11655 | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | AFK65_RS17425 | |
| phenylalanine | aacS: acetoacetyl-CoA synthetase | AFK65_RS11655 | |
| 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 | acnD: 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) | AFK65_RS11020 | |
| propionate | prpC: 2-methylcitrate synthase | AFK65_RS06090 | |
| propionate | prpF: methylaconitate isomerase | AFK65_RS19990 | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | AFK65_RS09920 | AFK65_RS04585 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | AFK65_RS11655 | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | | |
| valine | acnD: 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) | AFK65_RS11020 | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | AFK65_RS01475 | AFK65_RS13905 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | AFK65_RS19555 | AFK65_RS09755 |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| valine | prpC: 2-methylcitrate synthase | AFK65_RS06090 | |
| valine | prpF: methylaconitate isomerase | AFK65_RS19990 | |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | AFK65_RS04490 | |
| xylitol | xdhA: xylitol dehydrogenase | AFK65_RS02310 | AFK65_RS14005 |
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