GapMind for Amino acid biosynthesis

 

Protein WP_011383255.1 in Magnetospirillum magneticum AMB-1

Annotation: NCBI__GCF_000009985.1:WP_011383255.1

Length: 388 amino acids

Source: GCF_000009985.1 in NCBI

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 hi acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized) 60% 97% 451.4
L-lysine biosynthesis dapC hi acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized) 60% 97% 451.4 Succinylornithine transaminase (EC 2.6.1.81) 46% 334.7
L-proline biosynthesis argD hi acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized) 60% 97% 451.4
L-arginine biosynthesis argD'B med Succinylornithine transaminase (EC 2.6.1.81) (characterized) 46% 96% 334.7 acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] 60% 451.4
L-proline biosynthesis OAT med ornithine aminotransferase; EC 2.6.1.13 (characterized) 40% 85% 245.4 acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] 60% 451.4
L-arginine biosynthesis lysJ lo [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized) 39% 94% 251.5 acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] 60% 451.4
L-lysine biosynthesis lysJ lo [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized) 39% 94% 251.5 acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] 60% 451.4
L-proline biosynthesis lysJ lo [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized) 39% 94% 251.5 acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] 60% 451.4
L-lysine biosynthesis lysN lo 2-aminoadipate transaminase (2.6.1.39) (characterized) 33% 95% 186.4 acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] 60% 451.4
glycine biosynthesis agx1 lo Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized) 32% 81% 170.6 acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] 60% 451.4

Sequence Analysis Tools

View WP_011383255.1 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

MFPDNLLPVFDRTDVIFEQGEGAWLTASDGRRFLDFGAGVAVNALGHAHPRLVAALEAQA
GKLWHCSNLYRVPGQERVAERLIKASFADTAFFCNTGAEAMELVIKIARRYHHCAGRPER
NRIVACTGSFHGRTIATLAAAGTPKYLEGFGPVAQGFDHVPYGDLEAARGAIGSNTAALL
VEPVQGEGGIRPADPAYLRGLRALADQFGLLLLMDEVQTGIGRTGKLFAHEWSGIAPDVM
GLAKGLGGGFPVGAVLATEKAASCMTPGTHGCTFGGNPLAMAVAEAVLDEVMAPGFLERV
QAVAALLRGRLDDLARRYPGAIAQVRGQGLMLGLKTVPVNTEFNAKLFAAGLLAVGAGDN
VVRLVPPLIIGEAEVERAVEIIDGVCRG

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