GapMind for Amino acid biosynthesis

 

Protein SMc01726 in Sinorhizobium meliloti 1021

Annotation: FitnessBrowser__Smeli:SMc01726

Length: 295 amino acids

Source: Smeli in FitnessBrowser

Candidate for 7 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine biosynthesis argB hi acetylglutamate kinase (EC 2.7.2.8) (characterized) 48% 97% 291.2
L-arginine biosynthesis argB hi argB: acetylglutamate kinase (EC 2.7.2.8) (TIGR00761) 100% 256.7
L-proline biosynthesis argB hi acetylglutamate kinase (EC 2.7.2.8) (characterized) 48% 97% 291.2
L-proline biosynthesis argB hi argB: acetylglutamate kinase (EC 2.7.2.8) (TIGR00761) 100% 256.7
L-arginine biosynthesis lysZ lo Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.- (uncharacterized) 33% 97% 139 acetylglutamate kinase (EC 2.7.2.8) 48% 291.2
L-lysine biosynthesis lysZ lo Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.- (uncharacterized) 33% 97% 139 acetylglutamate kinase (EC 2.7.2.8) 48% 291.2
L-proline biosynthesis lysZ lo Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.- (uncharacterized) 33% 97% 139 acetylglutamate kinase (EC 2.7.2.8) 48% 291.2
L-arginine biosynthesis argA lo acetylglutamate kinase (EC 2.7.2.8) (characterized) 30% 61% 111.7 acetylglutamate kinase (EC 2.7.2.8) 48% 291.2
L-proline biosynthesis argA lo acetylglutamate kinase (EC 2.7.2.8) (characterized) 30% 61% 111.7 acetylglutamate kinase (EC 2.7.2.8) 48% 291.2

Sequence Analysis Tools

View SMc01726 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

MSASESEIQARLLAQALPYMQRYEHKTIVVKYGGHAMGNAELGRAFASDIALLKQSGVNP
IVVHGGGPQIGAMLNRMGIESKFEGGLRVTDEKTVEIVEMVLAGSINKEIVALINQTGEW
AIGLCGKDGNMVFAEKAKKTIRDPDSNIERVLDLGFVGDVVEVDRTLLDLLARSEMIPVI
APVAPGRDGHTYNINADTFAGAIAGALNATRLLFLTDVPGVLNKKGELIKQLSVAEARAL
IADGTISGGMIPKVETCIEAIKAGVQGVVILNGKTAHSVLLEIFTEHGAGTLIVP

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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