Protein WP_012991725.1 in Thermocrinis albus DSM 14484
Annotation: NCBI__GCF_000025605.1:WP_012991725.1
Length: 658 amino acids
Source: GCF_000025605.1 in NCBI
Candidate for 9 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| citrate catabolism | acn | med | aconitate hydratase; EC 4.2.1.3 (characterized) | 37% | 92% | 394 | | | |
| citrate catabolism | acn | hi | putative aconitate hydratase (EC 4.2.1.3) (TIGR01342) | | 99% | 1224.4 | | | |
| L-isoleucine catabolism | acnD | lo | 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) | 32% | 66% | 203.8 | aconitate hydratase; EC 4.2.1.3 | 37% | 394.0 |
| propionate catabolism | acnD | lo | 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) | 32% | 66% | 203.8 | aconitate hydratase; EC 4.2.1.3 | 37% | 394.0 |
| L-threonine catabolism | acnD | lo | 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) | 32% | 66% | 203.8 | aconitate hydratase; EC 4.2.1.3 | 37% | 394.0 |
| L-valine catabolism | acnD | lo | 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized) | 32% | 66% | 203.8 | aconitate hydratase; EC 4.2.1.3 | 37% | 394.0 |
| L-isoleucine catabolism | acn | lo | Aconitate hydratase A; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) | 33% | 62% | 199.1 | | | |
| propionate catabolism | acn | lo | Aconitate hydratase A; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) | 33% | 62% | 199.1 | | | |
| L-threonine catabolism | acn | lo | Aconitate hydratase A; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) | 33% | 62% | 199.1 | | | |
| L-valine catabolism | acn | lo | Aconitate hydratase A; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized) | 33% | 62% | 199.1 | | | |
Sequence Analysis Tools
View WP_012991725.1 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
MAKGTVAYKILQQHLVSGRLVPGEEIAIKIDQTLTQDATGTMAYLQLEAMGIDRVKTELS
VSYIDHNMLQTDYKNPDDHKYLMTVAKRYGIYLSKPGNGICHQVHLERFAKPGKTLLGSD
SHTPTAGGIGMLAIGAGGLDVAAAMAGEPFYMKMPKIVGVHLKGKLPPWVTAKDIILELL
RRLTVKGGLGKIFEYFGEGIRELSVPERATITNMGAELGATTSIFPSDDITRAYLRAQGR
EEDWIELLPDPDAQYDEVIELDLSSLEPLIACPHSPDNVVPVREVEGIKVDQVVIGSCTN
SSFVDLTRAAKLLEGRKVHPDVVFAVAPGSKQALELITQNGALLSFLKAGARILETACGP
CIGMGFAPPSGGVSVRSFNRNFEGRSGTPDAKVYLASPEVCVACAIAGEIIDPRKLAQKE
KITWVKVEMPERFPYGDEAIIEPLPEEEAKKVEIYRGPNIKPLPQFDPLPETLEAEVSLI
VGDNITTDHIMPAGAKILPLRSNIYAISEYVYHYVDPEFVARAKKIRDEKKKFSVIIGGE
NYGQGSSREHAALAPRFLGVRVVIAKSFARIHHANLVNFGILPLEFVDKEDYNKFSLGDE
IYIPELYESLNSGKELVVINKTTGHEILCRYNLTPKQVSVLMAGGLLNWIKNKQGVKV
This GapMind analysis is from Apr 09 2024. 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