Protein WP_011912550.1 in Pseudomonas stutzeri A1501
Annotation: NCBI__GCF_000013785.1:WP_011912550.1
Length: 594 amino acids
Source: GCF_000013785.1 in NCBI
Candidate for 4 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-isoleucine catabolism | pccA2 | lo | acyl CoA carboxylase biotin carboxyl carrier protein subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized) | 33% | 71% | 48.5 | DCOA aka OADA1 aka OADA aka STM0055 aka OADA2 aka STM3352, component of Na+-transporting oxalo-acetate decarboxylase. Subunit stoichiometries have been described (Balsera et al., 2011). The crystal structure of the carboxyltransferase at 1.7 A resolution shows a dimer of alpha(8)beta(8) barrels with an active site metal ion, identified spectroscopically as Zn2+ | 68% | 796.6 |
| propionate catabolism | pccA2 | lo | acyl CoA carboxylase biotin carboxyl carrier protein subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized) | 33% | 71% | 48.5 | DCOA aka OADA1 aka OADA aka STM0055 aka OADA2 aka STM3352, component of Na+-transporting oxalo-acetate decarboxylase. Subunit stoichiometries have been described (Balsera et al., 2011). The crystal structure of the carboxyltransferase at 1.7 A resolution shows a dimer of alpha(8)beta(8) barrels with an active site metal ion, identified spectroscopically as Zn2+ | 68% | 796.6 |
| L-threonine catabolism | pccA2 | lo | acyl CoA carboxylase biotin carboxyl carrier protein subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized) | 33% | 71% | 48.5 | DCOA aka OADA1 aka OADA aka STM0055 aka OADA2 aka STM3352, component of Na+-transporting oxalo-acetate decarboxylase. Subunit stoichiometries have been described (Balsera et al., 2011). The crystal structure of the carboxyltransferase at 1.7 A resolution shows a dimer of alpha(8)beta(8) barrels with an active site metal ion, identified spectroscopically as Zn2+ | 68% | 796.6 |
| L-valine catabolism | pccA2 | lo | acyl CoA carboxylase biotin carboxyl carrier protein subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized) | 33% | 71% | 48.5 | DCOA aka OADA1 aka OADA aka STM0055 aka OADA2 aka STM3352, component of Na+-transporting oxalo-acetate decarboxylase. Subunit stoichiometries have been described (Balsera et al., 2011). The crystal structure of the carboxyltransferase at 1.7 A resolution shows a dimer of alpha(8)beta(8) barrels with an active site metal ion, identified spectroscopically as Zn2+ | 68% | 796.6 |
Sequence Analysis Tools
View WP_011912550.1 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
MTVAKKPLGITDVVLRDAHQSILATRVRLEDMLPIAAKLDQVGFWSVESWGGATFDACIR
YLGEDPWERIRELKKAMPNTRQQMLLRGQNLLGYRHYADDVVEKFVERAAVNGVDVFRVF
DAMNDPRNLETALRAVKRLGKHAQGTISYTTSPVHTLEMWVELAKRIEDMGADSVAIKDM
AGILTPYMAFELVSRLKASLDIPIHMQCHATAGLSTAAILKAVEAGIDNVDTAISSLSMT
YGHSPTESVVAIFQGTARDTGLNLELLEEIAAYFREVRKKYAKFEGTLRGVDSRILVAQV
PGGMLTNMEGQLKEQGALDKFDEVLAEIPRVRQDLGFIPLVTPTSQIVGTQAVINVLTGE
RYKSITKETAGVLKGEYGAAPAPFDAELQERVLDGTEVITCRPADLLQPEMDRLAAELEG
LAQEKGITLATDSIDDVLTYALFPQIGLKFLENRGNPAAFEPAPTGSEQPPREVGKPQVY
TVEVNGRAFVVQVSDGGDIEGIKPLGGAGTPVAAPAGAAVAPGAGEPQTAPLAGNIFKVL
VQPGQLVQEGDLVVILEAMKMETEIRAFRAGTVAAVNVKVGDAVSVGDSLLSIA
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