GapMind for Amino acid biosynthesis


Protein H281DRAFT_04486 in Paraburkholderia bryophila 376MFSha3.1

Annotation: FitnessBrowser__Burk376:H281DRAFT_04486

Length: 465 amino acids

Source: Burk376 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 metY hi O-acetylhomoserine aminocarboxypropyltransferase (EC (characterized) 53% 97% 458.8 Sulfhydrylase FUB7; Fusaric acid biosynthesis protein 7; EC 2.5.1.- 50% 407.9
L-cysteine biosynthesis cysK med Homocysteine/cysteine synthase; O-acetylserine/O-acetylhomoserine sulfhydrylase; OAS-OAH SHLase; OAS-OAH sulfhydrylase; EC; EC (characterized) 43% 99% 345.5 O-acetylhomoserine aminocarboxypropyltransferase (EC 53% 458.8
L-methionine biosynthesis metZ lo O-acetylhomoserine sulfhydrylase protein; EC (characterized, see rationale) 37% 98% 261.5 Sulfhydrylase FUB7; Fusaric acid biosynthesis protein 7; EC 2.5.1.- 50% 407.9
L-cysteine biosynthesis CGL lo cystathionine gamma-lyase (EC (characterized) 36% 94% 233.8 O-acetylhomoserine aminocarboxypropyltransferase (EC 53% 458.8
L-methionine biosynthesis metC lo Cystathionine beta-lyase, chloroplastic; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC (characterized) 33% 81% 200.3 O-acetylhomoserine aminocarboxypropyltransferase (EC 53% 458.8
L-methionine biosynthesis metB lo Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized) 37% 56% 144.1 O-acetylhomoserine aminocarboxypropyltransferase (EC 53% 458.8

Sequence Analysis Tools

View H281DRAFT_04486 at FitnessBrowser

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

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



Related tools

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