GapMind for Amino acid biosynthesis

 

Protein GFF2323 in Phaeobacter inhibens BS107

Annotation: PGA1_c23540 O-succinylhomoserine sulfhydrylase MetZ

Length: 396 amino acids

Source: Phaeo in FitnessBrowser

Candidate for 6 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-methionine biosynthesis metZ hi O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized) 53% 96% 396.7 O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) 48% 370.2
L-methionine biosynthesis metY hi O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized) 48% 97% 370.2 methionine gamma-lyase (EC 4.4.1.11) 41% 318.9
L-cysteine biosynthesis CGL lo cystathionine gamma-lyase (EC 4.4.1.1) (characterized) 40% 95% 269.2 O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- 53% 396.7
L-methionine biosynthesis metB lo Cystathionine gamma-synthase 1, chloroplastic; AtCGS1; METHIONINE OVERACCUMULATION 1; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized) 36% 68% 248.1 O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- 53% 396.7
L-methionine biosynthesis metC lo Cystathionine beta-lyase; CBL; EC 4.4.1.13; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase (uncharacterized) 35% 98% 240.7 O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- 53% 396.7
L-cysteine biosynthesis cysK lo Homocysteine/cysteine synthase; O-acetylserine/O-acetylhomoserine sulfhydrylase; OAS-OAH SHLase; OAS-OAH sulfhydrylase; EC 2.5.1.47; EC 2.5.1.49 (characterized) 35% 50% 133.7 O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- 53% 396.7

Sequence Analysis Tools

View GFF2323 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSETWNKRTKLVHGGTRRSQYNEVSEAIYLTQGFVYDTAEQAEARFIETGPDEFIYARYG
NPTVAMFEERIAALEGAEDAFATASGMAAVNGALTSILKAGDHVVSAKALFGSCLYILEN
ILTRYGVEVTFVDGTDLDAWRAALRPDTKAVFFESMSNPTLEVIDIAAVAELAHAVGATV
VVDNVFSTPVFSNAIEQGADVVIYSATKHIDGQGRVLGGVILGTRDFIRGTVEPYMKHTG
GSLSPFNAWTLLKGLETISLRVNAQAETALELAQALSGHPALSRLMYPGLEDHAQHALVQ
RQLGGKGGTVLSLDLKGGKDAAFRFLNALTIPVISNNLGDAKSIATHPATTTHQRLSEEL
KSELGITPGLVRFSVGLEDAGDLIADLTQALAVAEG

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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