GapMind for Amino acid biosynthesis

 

Protein Pf6N2E2_5721 in Pseudomonas fluorescens FW300-N2E2

Annotation: FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5721

Length: 300 amino acids

Source: pseudo6_N2E2 in FitnessBrowser

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 S-sulfo-L-cysteine synthase (O-acetyl-L-serine-dependent) (EC 2.5.1.144); cysteine synthase (EC 2.5.1.47) (characterized) 70% 96% 408.3
L-cysteine biosynthesis cysK hi cysM: cysteine synthase B (EC 2.5.1.47) (TIGR01138) 100% 534.1
L-cysteine biosynthesis PSSH med O-phosphoserine sulfhydrylase monomer (EC 2.5.1.47; EC 2.5.1.65) (characterized) 46% 99% 267.7 S-sulfo-L-cysteine synthase (O-acetyl-L-serine-dependent) (EC 2.5.1.144); cysteine synthase (EC 2.5.1.47) 70% 408.3
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) 41% 95% 223.8 S-sulfo-L-cysteine synthase (O-acetyl-L-serine-dependent) (EC 2.5.1.144); cysteine synthase (EC 2.5.1.47) 70% 408.3
L-cysteine biosynthesis CBS lo Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized) 41% 65% 212.2 S-sulfo-L-cysteine synthase (O-acetyl-L-serine-dependent) (EC 2.5.1.144); cysteine synthase (EC 2.5.1.47) 70% 408.3

Sequence Analysis Tools

View Pf6N2E2_5721 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

MTLQYPTIADCVGNTPLVRLQRLPGVTTNTLLLKLEGNNPAGSVKDRPALSMITRGELRG
QIRPGDTLIEATSGNTGIALAMAAAIKGYKMILIMPDNSSAERKAAMTAYGAELILVTQE
QGMEGARDLAERMQAEGRGKVLDQFANGDNPEAHYTSTGPEIWRQTDGTITHFVSSMGTT
GTIMGTSRYLKEQNPNVQIIGLQPMEGSAIPGIRRWPEEYLPKIYQADRVDRIIDMAQSE
AEDTTRRLAREEGIFCGVSSGGAVAGMLRLSKEVENAVIVAIICDRGDRYLSTGIFDAPN

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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