Potential Gaps in catabolism of small carbon sources in Hafnia paralvei ATCC 29927
Found 41 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 | M988_RS04780 | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | M988_RS03505 | |
| 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 | M988_RS09040 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | M988_RS06580 | M988_RS14700 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | M988_RS06575 | M988_RS12735 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | M988_RS06570 | M988_RS12730 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | M988_RS06565 | M988_RS12725 |
| citrulline | odc: L-ornithine decarboxylase | M988_RS18910 | M988_RS18205 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | M988_RS18840 | M988_RS09575 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | M988_RS01850 | M988_RS04770 |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | M988_RS18430 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | M988_RS02060 | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | M988_RS02475 | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | M988_RS07890 | M988_RS04450 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| isoleucine | prpC: 2-methylcitrate synthase | M988_RS14005 | |
| isoleucine | prpD: 2-methylcitrate dehydratase | | |
| lactose | lacY: lactose:proton symporter LacY | M988_RS18245 | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | M988_RS01915 | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | M988_RS14765 | M988_RS02490 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | M988_RS05220 | |
| 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 | M988_RS00400 | M988_RS15820 |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| phenylacetate | ppa: phenylacetate permease ppa | M988_RS19280 | |
| phenylalanine | ARO10: phenylpyruvate decarboxylase | M988_RS13395 | |
| propionate | prpC: 2-methylcitrate synthase | M988_RS14005 | |
| propionate | prpD: 2-methylcitrate dehydratase | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | M988_RS18840 | M988_RS08735 |
| sucrose | ams: sucrose hydrolase (invertase) | M988_RS04655 | M988_RS02105 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | M988_RS04805 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | M988_RS02045 | |
| valine | acdH: isobutyryl-CoA dehydrogenase | M988_RS02475 | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | M988_RS14765 | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | M988_RS14765 | M988_RS06370 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | M988_RS02510 | M988_RS13220 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | M988_RS18370 | M988_RS20435 |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| valine | prpC: 2-methylcitrate synthase | M988_RS14005 | |
| valine | prpD: 2-methylcitrate dehydratase | | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | M988_RS07300 | M988_RS15595 |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | M988_RS20300 | |
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