GapMind for Amino acid biosynthesis

 

Protein 353284 in Bacteroides thetaiotaomicron VPI-5482

Annotation: FitnessBrowser__Btheta:353284

Length: 373 amino acids

Source: Btheta in FitnessBrowser

Candidate for 10 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine biosynthesis argD'B hi Acetylornithine aminotransferase (characterized, see rationale) 100% 100% 747.3 [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- 38% 251.1
L-arginine biosynthesis argD med Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized) 40% 97% 271.9 [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- 38% 251.1
L-proline biosynthesis argD med Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized) 40% 97% 271.9 [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- 38% 251.1
L-arginine biosynthesis lysJ med [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized) 38% 94% 251.9 acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] 36% 234.2
L-lysine biosynthesis lysJ med [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized) 38% 94% 251.9 acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] 36% 234.2
L-proline biosynthesis lysJ med [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized) 38% 94% 251.9 acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] 36% 234.2
L-lysine biosynthesis dapC lo acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized) 36% 97% 234.2 [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- 38% 251.1
L-proline biosynthesis OAT lo Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized) 33% 98% 209.5 [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- 38% 251.1
glycine biosynthesis agx1 lo Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized) 34% 83% 208.8 [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- 38% 251.1
L-lysine biosynthesis lysN lo 2-aminoadipate transaminase (2.6.1.39) (characterized) 32% 96% 177.2 [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- 38% 251.1

Sequence Analysis Tools

View 353284 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

Fitness BLAST: loading...

Sequence

MKLFDVYPLYDINIVKGQGCKVWDENGTEYLDLYGGHAVISIGHAHPHYVEMISNQVATL
GFYSNSVINKLQQQVAERLGKISGYEDYSLFLINSGAEANENALKLASFYNGRTKVISFS
KAFHGRTSLAVEATNNPTIIAPINNNGHVTYLPLNDIEAMKQELAKGDVCAVIIEGIQGV
GGIKIPTTEFMQELRKVCTETGTILILDEIQSGYGRSGKFFAHQYNHIQPDIITVAKGIG
NGFPMAGVLISPMFKPVYGQLGTTFGGNHLACSAALAVMDVIEQDNLVENAKAVGDYLLE
ELKKFPQIKEVRGRGLMIGLEFEEPIKELRSRLIYDEHVFTGASGTNVLRLLPPLCLSME
EADEFLARFKRVL

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