GapMind for Amino acid biosynthesis

 

Protein WP_012049112.1 in Rhizorhabdus wittichii RW1

Annotation: NCBI__GCF_000016765.1:WP_012049112.1

Length: 301 amino acids

Source: GCF_000016765.1 in NCBI

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) 51% 95% 302.8
L-arginine biosynthesis argB hi argB: acetylglutamate kinase (EC 2.7.2.8) (TIGR00761) 100% 258.4
L-proline biosynthesis argB hi acetylglutamate kinase (EC 2.7.2.8) (characterized) 51% 95% 302.8
L-proline biosynthesis argB hi argB: acetylglutamate kinase (EC 2.7.2.8) (TIGR00761) 100% 258.4
L-lysine biosynthesis lysZ lo [LysW]-L-2-aminoadipate 6-kinase monomer (EC 2.7.2.17) (characterized) 32% 99% 128.6 acetylglutamate kinase (EC 2.7.2.8) 51% 302.8
L-arginine biosynthesis lysZ lo Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized) 31% 92% 126.3 acetylglutamate kinase (EC 2.7.2.8) 51% 302.8
L-proline biosynthesis lysZ lo Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized) 31% 92% 126.3 acetylglutamate kinase (EC 2.7.2.8) 51% 302.8
L-arginine biosynthesis argA lo amino-acid N-acetyltransferase (EC 2.3.1.1); acetylglutamate kinase (EC 2.7.2.8) (characterized) 31% 63% 114 acetylglutamate kinase (EC 2.7.2.8) 51% 302.8
L-proline biosynthesis argA lo amino-acid N-acetyltransferase (EC 2.3.1.1); acetylglutamate kinase (EC 2.7.2.8) (characterized) 31% 63% 114 acetylglutamate kinase (EC 2.7.2.8) 51% 302.8

Sequence Analysis Tools

View WP_012049112.1 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

MSTDHSPDPLLLTKAETLVEALPYMQRYAGETFVVKYGGHAMGDPEAARDFAEDIVLLKA
VGINPVVVHGGGPQIGKMLKTLGVESRFVDGLRVTDAETARVAEMVLCGSINKEIVSWIA
QAGGRAVGLSGKDGRMVVAEKVRRTQRDPDSNIEKAVDLGFVGEPADIDRRVIDTISKAG
MIPVVAPIAIGEDGHTYNVNADTMAGAIAIALGAARLFLLTDVAGVLDKEKKLIRDLTPR
QINALREDGTIQGGMIPKLETCVHAVEGGVDAAVILDGRVPHAMLIEAFTRRGAGTLIGM
G

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