GapMind for Amino acid biosynthesis


Protein 5209311 in Shewanella loihica PV-4

Annotation: FitnessBrowser__PV4:5209311

Length: 395 amino acids

Source: PV4 in FitnessBrowser

Candidate for 5 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-methionine biosynthesis metC hi cystathionine beta-lyase (EC (characterized) 52% 98% 424.1 cystathionine gamma-synthase (EC 35% 226.1
L-methionine biosynthesis metB lo Cystathionine gamma-synthase; CGS; EC; O-succinylhomoserine (thiol)-lyase (uncharacterized) 36% 100% 228.4 cystathionine beta-lyase (EC 52% 424.1
L-cysteine biosynthesis CGL lo cystathionine gamma-lyase (EC; cystathionine beta-lyase (EC (characterized) 34% 99% 206.5 cystathionine beta-lyase (EC 52% 424.1
L-methionine biosynthesis metZ lo O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized) 30% 95% 155.6 cystathionine beta-lyase (EC 52% 424.1
L-methionine biosynthesis metY lo O-acetylhomoserine aminocarboxypropyltransferase (EC (characterized) 33% 51% 115.9 cystathionine beta-lyase (EC 52% 424.1

Sequence Analysis Tools

View 5209311 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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:

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:

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