GapMind for Amino acid biosynthesis

 

Protein WP_086510266.1 in Halomonas desiderata SP1

Annotation: NCBI__GCF_002151265.1:WP_086510266.1

Length: 298 amino acids

Source: GCF_002151265.1 in NCBI

Candidate for 4 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-cysteine biosynthesis cysK hi Cysteine synthase B; CSase B; O-acetylserine (thiol)-lyase B; OAS-TL B; O-acetylserine sulfhydrylase B; EC 2.5.1.47 (characterized) 68% 97% 395.6
L-cysteine biosynthesis cysK hi cysM: cysteine synthase B (EC 2.5.1.47) (TIGR01138) 100% 481.9
L-cysteine biosynthesis PSSH med O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized) 45% 100% 266.5 Cysteine synthase B; CSase B; O-acetylserine (thiol)-lyase B; OAS-TL B; O-acetylserine sulfhydrylase B; EC 2.5.1.47 68% 395.6
L-cysteine biosynthesis Mt_cysM med [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase (EC 2.5.1.113); O-phosphoserine sulfhydrylase (EC 2.5.1.65) (characterized) 42% 94% 229.9 Cysteine synthase B; CSase B; O-acetylserine (thiol)-lyase B; OAS-TL B; O-acetylserine sulfhydrylase B; EC 2.5.1.47 68% 395.6
L-cysteine biosynthesis CBS lo Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized) 40% 64% 213.8 Cysteine synthase B; CSase B; O-acetylserine (thiol)-lyase B; OAS-TL B; O-acetylserine sulfhydrylase B; EC 2.5.1.47 68% 395.6

Sequence Analysis Tools

View WP_086510266.1 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

MQFPTIEDVVGHTPLVRLKRITAGRNNTLLAKLEGNNPAGSVKDRPALSMLEQAEARGDI
TPGDTLIEATSGNTGIALAMAAAIKGYRMVLIMPDSASSERKQAMAAYGARLITVSKEGG
MEEARDLAEAMVSRGEGKPLNQFANPDNPLAHYRGTGPELWEQTGGTITHFVSSMGTTGT
IMGVSRYLKERNPEVQIVGLQPEDGASIAGIRRWPKEYLPSIFDATRVDRVLDIGQHEAE
EHMRRLAREEGILAGVSSGGALAGALRVAEEVENAVIVFIVCDRGDRYLSTGLFAPEV

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