GapMind for Amino acid biosynthesis

 

Protein AO353_23295 in Pseudomonas fluorescens FW300-N2E3

Annotation: FitnessBrowser__pseudo3_N2E3:AO353_23295

Length: 392 amino acids

Source: pseudo3_N2E3 in FitnessBrowser

Candidate for 6 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-cysteine biosynthesis CGL hi cystathionine gamma-lyase (EC 4.4.1.1) (characterized) 65% 98% 530 Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 67% 511.5
L-methionine biosynthesis metC med Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized) 67% 97% 511.5 cystathionine gamma-lyase (EC 4.4.1.1) 65% 530.0
L-methionine biosynthesis metB med cystathionine gamma-synthase (EC 2.5.1.48) (characterized) 54% 99% 401.4 cystathionine gamma-lyase (EC 4.4.1.1) 65% 530.0
L-methionine biosynthesis metY med Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized) 42% 98% 310.8 cystathionine gamma-lyase (EC 4.4.1.1) 65% 530.0
L-methionine biosynthesis metZ med O-succinylhomoserine sulfhydrylase; OSH sulfhydrylase; OSHS sulfhydrylase; EC 2.5.1.- (characterized) 41% 98% 307.8 cystathionine gamma-lyase (EC 4.4.1.1) 65% 530.0
L-cysteine biosynthesis cysK lo Homocysteine/cysteine synthase; O-acetylserine/O-acetylhomoserine sulfhydrylase; OAS-OAH SHLase; OAS-OAH sulfhydrylase; EC 2.5.1.47; EC 2.5.1.49 (characterized) 37% 50% 125.2 cystathionine gamma-lyase (EC 4.4.1.1) 65% 530.0

Sequence Analysis Tools

View AO353_23295 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

MSQHDENATPRAFATRVIHAGQTPDPTTGALMPPIYANSTYLQQSPGVHKGFDYGRSHNP
TRFALERCVADLEGGTQAFAFASGLAAISTVLELLDTGSHIVSGNDLYGGTFRLFDKVRR
RSAGHRFSFVDLTDLTAFEAALQDDTRMVWVETPSNPLLRITDLAAVARTCRERGIICVA
DNTFASPRIQRPLELGFDIVLHSTTKYLNGHSDVIGGIAVVGQNAELRERLGFLQNAVGA
IAGPFDAFLTLRGVKTLALRMERHCSNALELARWLSHQPQVARVYYPGLPSHPQHELAQR
QMHGFGGMISLDLDTDLAGAKRFLESVQIFALAESLGGVESLIEHPAIMTHASIPAETRA
ELGIGDALIRLSVGIEDVEDLRADLAQALAQI

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