GapMind for Amino acid biosynthesis

 

Protein H281DRAFT_02214 in Paraburkholderia bryophila 376MFSha3.1

Annotation: FitnessBrowser__Burk376:H281DRAFT_02214

Length: 381 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 4 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-methionine biosynthesis metA hi Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized) 88% 100% 698
L-methionine biosynthesis metX med Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized) 49% 75% 361.7 Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 88% 698.0
L-methionine biosynthesis metX med metX: homoserine O-acetyltransferase (EC 2.3.1.31) (TIGR01392) 99% 462.5 Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 88% 698.0
L-cysteine biosynthesis SST med Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized) 43% 98% 276.2 Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 88% 698.0
L-cysteine biosynthesis cysE lo serine O-acetyltransferase (EC 2.3.1.30); homoserine O-acetyltransferase (EC 2.3.1.31) (characterized) 39% 95% 229.2 Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 88% 698.0

Sequence Analysis Tools

View H281DRAFT_02214 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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Sequence

MESIGIVAPQKMHFTEPLRLQNGSSLASYDLMVETYGTLNAARSNAVLVCHALNASHHVA
GVYADNLKDIGWWDNMVGPGKPLDTNKFFVIGVNNLGSCFGSTGPMSIDPATGNPYGATF
PVVTVEDWVNAQARVADQFGITRFAAVMGGSLGGMQALAWSMMYPERVGHCIVVASTPKL
SAQNIAFNEVARSAILSDPDFHGGNYYAHNVKPKRGLRVARMIGHITYLSDDDMAEKFGR
SLRRAEGALDAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAFEG
DLTAAVAHTTAKYLIASFTTDWRFAPARSRELVKALLDHKRTVTYAEIDAPHGHDAFLLD
DARYHNLMRAYYERIANEVNA

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