Annotation: NCBI__GCF_001298675.1:WP_054255928.1
Length: 315 amino acids
Source: GCF_001298675.1 in NCBI
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
---|---|---|---|---|---|---|---|---|---|
L-leucine catabolism | liuE | hi | hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4) (characterized) | 57% | 90% | 339.7 | |||
L-leucine catabolism | liuC | lo | 3-hydroxy-3-methylglutaryl-coenzyme A lyase/3-methylglutaconyl-coenzyme A hydratase; EC 4.1.3.4; EC 4.2.1.18 (characterized) | 45% | 52% | 255.4 | hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4) | 57% | 339.7 |
4-hydroxybenzoate catabolism | mhpE | lo | 4-hydroxy-2-oxovalerate aldolase; HOA; EC 4.1.3.39; 4-hydroxy-2-keto-pentanoic acid aldolase; 4-hydroxy-2-oxopentanoate aldolase (uncharacterized) | 31% | 77% | 84.7 | hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4) | 57% | 339.7 |
L-tryptophan catabolism | mhpE | lo | 4-hydroxy-2-oxovalerate aldolase; HOA; EC 4.1.3.39; 4-hydroxy-2-keto-pentanoic acid aldolase; 4-hydroxy-2-oxopentanoate aldolase (uncharacterized) | 31% | 77% | 84.7 | hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4) | 57% | 339.7 |
View WP_054255928.1 at NCBI
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Find functional residues: SitesBLAST
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
Fitness BLAST: loading...
MNIPTRVRIIDVGPRDGLQNEKQAVPSEVKIGLVQRLQDAGLREIEVTSYVSPKWVPQMA DNHAVMSGIARQAGVRYSVLTPNLKGWEAAVADRPDEIVVFGAASEAFSQKNINCSIAES IERFAPVVEAARAAGVAVRGAMSCTVGCPYEGEIAPERVAYLAGLMKGIGVQRVDVADTI GVGTPLKVQRAIAATLQHYELDAVSGHFHDTYGQALSNTLAALELGVWNFQSSVAGLGGC PYAKGATGNVATEDLVYLLHGMGIETGIDLDKLVDAGAYISDFLGRKSGSRVAVALLNKR AGQGTPDLIAASACL
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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:
Otherwise, a candidate is "medium confidence" if either:
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:
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