Protein WP_008483324.1 in Gallaecimonas xiamenensis 3-C-1
Annotation: NCBI__GCF_000299915.1:WP_008483324.1
Length: 717 amino acids
Source: GCF_000299915.1 in NCBI
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 | fadB | hi | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) | 56% | 99% | 780.8 | long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) | 42% | 532.7 |
| 4-hydroxybenzoate catabolism | paaH | hi | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) | 56% | 99% | 780.8 | long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) | 42% | 532.7 |
| L-arginine catabolism | fadB | hi | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) | 56% | 99% | 780.8 | long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) | 42% | 532.7 |
| L-citrulline catabolism | fadB | hi | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) | 56% | 99% | 780.8 | long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) | 42% | 532.7 |
| L-isoleucine catabolism | ech | hi | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) | 56% | 99% | 780.8 | | | |
| L-lysine catabolism | fadB | hi | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) | 56% | 99% | 780.8 | long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) | 42% | 532.7 |
| phenylacetate catabolism | fadB | hi | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) | 56% | 99% | 780.8 | long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) | 42% | 532.7 |
| phenylacetate catabolism | paaH | hi | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) | 56% | 99% | 780.8 | long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) | 42% | 532.7 |
| L-phenylalanine catabolism | fadB | hi | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) | 56% | 99% | 780.8 | long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) | 42% | 532.7 |
| L-phenylalanine catabolism | paaH | hi | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) | 56% | 99% | 780.8 | long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) | 42% | 532.7 |
| L-proline catabolism | fadB | hi | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized) | 56% | 99% | 780.8 | long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) | 42% | 532.7 |
| 4-hydroxybenzoate catabolism | ech | med | trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) | 42% | 70% | 131 | | | |
| 4-hydroxybenzoate catabolism | paaF | med | trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) | 42% | 70% | 131 | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 | 56% | 780.8 |
| L-arginine catabolism | ech | med | trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) | 42% | 70% | 131 | | | |
| L-citrulline catabolism | ech | med | trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) | 42% | 70% | 131 | | | |
| L-lysine catabolism | ech | med | trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) | 42% | 70% | 131 | | | |
| phenylacetate catabolism | ech | med | trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) | 42% | 70% | 131 | | | |
| phenylacetate catabolism | paaF | med | trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) | 42% | 70% | 131 | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 | 56% | 780.8 |
| L-phenylalanine catabolism | ech | med | trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) | 42% | 70% | 131 | | | |
| L-phenylalanine catabolism | paaF | med | trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) | 42% | 70% | 131 | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 | 56% | 780.8 |
| L-proline catabolism | ech | med | trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) | 42% | 70% | 131 | | | |
| L-valine catabolism | ech | med | trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized) | 42% | 70% | 131 | | | |
| 4-hydroxybenzoate catabolism | pimF | lo | 6-carboxyhex-2-enoyl-CoA hydratase (characterized) | 36% | 97% | 387.9 | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 | 56% | 780.8 |
| phenylacetate catabolism | pimF | lo | 6-carboxyhex-2-enoyl-CoA hydratase (characterized) | 36% | 97% | 387.9 | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 | 56% | 780.8 |
| L-phenylalanine catabolism | pimF | lo | 6-carboxyhex-2-enoyl-CoA hydratase (characterized) | 36% | 97% | 387.9 | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 | 56% | 780.8 |
| L-isoleucine catabolism | hpcD | lo | 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) | 37% | 91% | 137.1 | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 | 56% | 780.8 |
| propionate catabolism | hpcD | lo | 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) | 37% | 91% | 137.1 | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 | 56% | 780.8 |
| L-threonine catabolism | hpcD | lo | 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) | 37% | 91% | 137.1 | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 | 56% | 780.8 |
| L-valine catabolism | hpcD | lo | 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized) | 37% | 91% | 137.1 | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 | 56% | 780.8 |
| L-leucine catabolism | liuC | lo | methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized) | 38% | 72% | 111.7 | fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 | 56% | 780.8 |
Sequence Analysis Tools
View WP_008483324.1 at NCBI
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
Fitness BLAST: loading...
Sequence
MTDKTFSFALREDGIGIITMDVPGESMNTLKAAFAEEIRAILADIRHDPAVKGLVLVSGK
QGSFIAGADIGMLDKCESSQDAEALSKAGHAICAELESLKVPLIAAIHGPCLGGGLELAM
ACHGRVASDWDKTALGLPEVQLGLLPGSGGTQRLPRLVGIQKALDMMLTGKQLRPAQAKK
AGLVDEVVPQSILLDVAIGLAKKGKPLRDGVKLGFKDKLLEDNGVGRNIVFDQARKTVLK
KTGGHYPAPLKILECVRVGMTDGMDAGLAVEAKYFGELVKTPESKQLRGLFFATTQMKKE
TGAEGVTPRKVAKAAVLGGGLMGGGIANVTVTKAGVPVRIKDIGEQGISHAFKYSYDLLM
KKVKRRHLRKSQAQKQMMMLTGDTQYRGFHDVDIVVEAVFEDLALKHQMVKDIETHCGPE
TIFASNTSSLPIGQIAEAAQRPENVIGLHYFSPVDKMPLAEIIAHDKTSPQTIATTVAFA
RRQGKTPIVVKDGAGFYVNRILGLYMNEAAYLLMEGEPVEKLDKALTAFGMPVGPMTLLD
EVGIDVGAKIAPILEKELGERFQAPAAFDKLLADGRKGKKSQKGFYLYKDLPKSWNPLKK
LPKKPVDESVYRVLGISPAGRLDLDAIAERTLLQMLNEAARCLDEGIIQSARDGDIGAIF
GIGFPPFLGGPFRYMDKLGAKAVVAKLEALKAQHGERFAPSPLLVKMAEDGGHFYND
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