GapMind for Amino acid biosynthesis

 

Protein CA265_RS18530 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: CA265_RS18530 aspartate aminotransferase family protein

Length: 382 amino acids

Source: Pedo557 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) 58% 100% 453.4 [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- 36% 222.6
L-arginine biosynthesis argD med Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized) 41% 96% 257.7 [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- 36% 222.6
L-proline biosynthesis argD med Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized) 41% 96% 257.7 [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- 36% 222.6
L-arginine biosynthesis lysJ med [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (characterized) 36% 94% 222.6 5-aminovalerate transaminase (EC 2.6.1.48) 36% 212.6
L-lysine biosynthesis lysJ med [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (characterized) 36% 94% 222.6 5-aminovalerate transaminase (EC 2.6.1.48) 36% 212.6
L-proline biosynthesis lysJ med [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (characterized) 36% 94% 222.6 5-aminovalerate transaminase (EC 2.6.1.48) 36% 212.6
L-lysine biosynthesis dapC lo Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized) 34% 96% 215.7 [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- 36% 222.6
L-proline biosynthesis OAT lo Ornithine aminotransferase 1; OAT 1; EC 2.6.1.13; Ornithine--oxo-acid aminotransferase 1 (uncharacterized) 32% 99% 197.6 [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- 36% 222.6
glycine biosynthesis agx1 lo Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized) 32% 85% 179.1 [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- 36% 222.6
L-lysine biosynthesis lysN lo 2-aminoadipate transaminase (2.6.1.39) (characterized) 31% 96% 169.1 [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- 36% 222.6

Sequence Analysis Tools

View CA265_RS18530 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MQLFDVYPLNDIEITKAAGSNVWDANDQQYLDLYGGHAVISIGHTNPHYVNRLTDQLNKV
GFYSNSVKIPLQVQLAEKLGEVSGKKDFQLFLCNSGAEANENALKLASFYNGRKKVIAFT
GAFHGRTSLAVAVTDNPKIVAPVNQTENVIFLPFNNEIALEETFKAQGNEISAVIIEGIQ
GVGGIKEASKSFLQKIRSLCDEYNAVYIADSVQCGYGRTGSFYSHDYSGVEADVYTMAKG
MGNGFPVAGISIASKFKPWHGELGTTFGGNHLACAAALAVLEVMEKDNLIKNAEEVGNYL
IAELKKFEQVVEVRGRGLMIGIELPAELAHVKKELLFTHHIFTGEAKPNVIRLLPALNLT
KAHADEFLAAFEKAVKGVGQKA

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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