Protein 354228 in Bacteroides thetaiotaomicron VPI-5482
Annotation: FitnessBrowser__Btheta:354228
Length: 274 amino acids
Source: Btheta in FitnessBrowser
Candidate for 30 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| 4-hydroxybenzoate catabolism | badI | med | BadI (characterized) | 49% | 100% | 250.8 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| phenylacetate catabolism | badI | med | BadI (characterized) | 49% | 100% | 250.8 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| L-phenylalanine catabolism | badI | med | BadI (characterized) | 49% | 100% | 250.8 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| 4-hydroxybenzoate catabolism | ech | lo | Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) | 38% | 98% | 152.9 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| L-arginine catabolism | ech | lo | Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) | 38% | 98% | 152.9 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| L-citrulline catabolism | ech | lo | Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) | 38% | 98% | 152.9 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| L-lysine catabolism | ech | lo | Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) | 38% | 98% | 152.9 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| phenylacetate catabolism | ech | lo | Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) | 38% | 98% | 152.9 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| L-phenylalanine catabolism | ech | lo | Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) | 38% | 98% | 152.9 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| L-proline catabolism | ech | lo | Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) | 38% | 98% | 152.9 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| L-valine catabolism | ech | lo | Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized) | 38% | 98% | 152.9 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| L-isoleucine catabolism | ech | lo | enoyl-CoA hydratase (EC 4.2.1.17); DELTA3,5-DELTA2,4-dienoyl-CoA isomerase (EC 5.3.3.21) (characterized) | 37% | 85% | 136.7 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| L-isoleucine catabolism | hpcD | lo | 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) | 34% | 99% | 134.8 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| propionate catabolism | hpcD | lo | 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) | 34% | 99% | 134.8 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| L-threonine catabolism | hpcD | lo | 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) | 34% | 99% | 134.8 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| L-valine catabolism | hpcD | lo | 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) | 34% | 99% | 134.8 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| 4-hydroxybenzoate catabolism | paaF | lo | trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) | 32% | 98% | 126.7 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| phenylacetate catabolism | paaF | lo | trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) | 32% | 98% | 126.7 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| L-phenylalanine catabolism | paaF | lo | trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) | 32% | 98% | 126.7 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| L-leucine catabolism | liuC | lo | methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) | 35% | 93% | 122.9 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| phenylacetate catabolism | paaG | lo | 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) | 32% | 99% | 107.1 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| L-phenylalanine catabolism | paaG | lo | 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized) | 32% | 99% | 107.1 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| phenylacetate catabolism | paaZ1 | lo | Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) | 33% | 93% | 106.3 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| L-phenylalanine catabolism | paaZ1 | lo | Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale) | 33% | 93% | 106.3 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| 4-hydroxybenzoate catabolism | badK | lo | BadK (characterized) | 32% | 97% | 105.1 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| phenylacetate catabolism | badK | lo | BadK (characterized) | 32% | 97% | 105.1 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| L-phenylalanine catabolism | badK | lo | BadK (characterized) | 32% | 97% | 105.1 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| 4-hydroxybenzoate catabolism | oah | lo | 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase; 6-OCH-CoA hydrolase; 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase; EC 3.7.1.21 (characterized) | 31% | 62% | 95.5 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| phenylacetate catabolism | oah | lo | 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase; 6-OCH-CoA hydrolase; 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase; EC 3.7.1.21 (characterized) | 31% | 62% | 95.5 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
| L-phenylalanine catabolism | oah | lo | 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase; 6-OCH-CoA hydrolase; 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase; EC 3.7.1.21 (characterized) | 31% | 62% | 95.5 | 1,4-dihydroxy-2-naphthoyl-CoA synthase; DHNA-CoA synthase; EC 4.1.3.36 | 68% | 394.8 |
Sequence Analysis Tools
View 354228 at FitnessBrowser
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
Compare to protein structures
Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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Sequence
MSTQREWTTIREYEDILFDYYNGIARITINRERYRNAFTPTTTAEMSDALRICREEADID
VIVITGAGDKAFCSGGDQNVKGRGGYIGKDGVPRLSVLDVQKQIRSIPKPVIAAVNGFAI
GGGHVLHVVCDLSIASENAIFGQTGPRVGSFDAGFGASYLARVVGQKKAREIWFLCRKYN
AQEALDMGLVNKVVPLEQLEDEYVQWAEEMMLLSPLALRMIKAGLNAELDGQAGIQELAG
DATLLYYLTDEAQEGKNAFLEKRKPNFKKYPKFP
This GapMind analysis is from Sep 17 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