GapMind for Amino acid biosynthesis

 

Protein WP_012385734.1 in Beijerinckia indica subsp. indica ATCC 9039

Annotation: NCBI__GCF_000019845.1:WP_012385734.1

Length: 412 amino acids

Source: GCF_000019845.1 in NCBI

Candidate for 9 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline biosynthesis OAT hi Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 (characterized) 52% 98% 417.5
L-proline biosynthesis OAT hi rocD: ornithine--oxo-acid transaminase (EC 2.6.1.13) (TIGR01885) 99% 488.3
L-arginine biosynthesis argD med Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized) 41% 95% 287.3 Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 52% 417.5
L-proline biosynthesis argD med Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized) 41% 95% 287.3 Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 52% 417.5
L-lysine biosynthesis dapC lo acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized) 37% 98% 245.4 Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 52% 417.5
L-lysine biosynthesis lysJ lo [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized) 39% 94% 244.2 Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 52% 417.5
L-arginine biosynthesis argD'B lo succinylornithine transaminase (EC 2.6.1.81) (characterized) 36% 97% 236.1 Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 52% 417.5
L-arginine biosynthesis lysJ lo Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized) 34% 98% 216.1 Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 52% 417.5
L-proline biosynthesis lysJ lo Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized) 34% 98% 216.1 Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 52% 417.5
L-lysine biosynthesis lysN lo 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized) 34% 97% 187.6 Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 52% 417.5

Sequence Analysis Tools

View WP_012385734.1 at NCBI

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

MRHDFIDQEERFGAHNYAPLPVVLSHGQGAFLFDCDGRRYLDMMSAYSAASFGHLHPRLV
GALKRQLERLDLVSRAYHTDTLGPFCEDLARLTGLDACLPMNTGAEAVETAIKAARRYGY
DRLSIPEDQAEIIVAAGNFHGRTTTIIGFSSDAATRRGFGPFAPGFVLVPFGDAGALEAA
VGPRTAAVLIEPIQGEAGIILPPPGYLAALRRLCDRHGILLIFDEVQSGFGRTGRTFAFE
HEGAKPDGLILGKALGGGLLPVSAFAAKRSLMDVFDPGSHGSTFGGNPLAMAVAREAMHV
LQEEHLVERSEKLGGVLLDALRAIDHPAVLAVRGKGLWAGVDLDPALADAKKVCLKMMER
GVLTKETHATTIRFAPPLVITEADLLEAVGIFRAVLESLSLPTAVSTLSFAK

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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