GapMind for Amino acid biosynthesis

 

Protein Synpcc7942_2265 in Synechococcus elongatus PCC 7942

Annotation: Synpcc7942_2265 glutamate-5-semialdehyde dehydrogenase

Length: 431 amino acids

Source: SynE in FitnessBrowser

Candidate for 2 steps in Amino acid biosynthesis

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline biosynthesis proA hi Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; GSA dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; EC 1.2.1.41 (characterized) 45% 97% 356.7
L-proline biosynthesis proA hi proA: glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (TIGR00407) 100% 544.1
L-proline biosynthesis proB lo δ1-pyrroline-5-carboxylate synthetase (EC 1.2.1.41; EC 2.7.2.11) (characterized) 45% 58% 342.4 Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; GSA dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; EC 1.2.1.41 45% 356.7

Sequence Analysis Tools

View Synpcc7942_2265 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

VATLSVDLEVQAQATRAAARQLAQWSGADRQRLLSAIATTLEQEAPRILAANQADCEAAT
TEGIAPALYARLKLDADKLAAAIAGVRDLAQLPDPLGQIQIDRELDEGLILQRLTCPVGV
LGVIFEARPDAVIQIASLAIKSGNGAILKGGREAICSCQAIVAAIAQALAEQQAPVEAIR
LLTSREETLALLKLDRYVDLIIPRGSNSFVRFVQDNTHIPVLGHADGICHLYVDQAAAIE
KTVTITVDAKTQYPAACNAIETLLIHEAIAPQFLPVVAAALHEKGVSLRGDAAAQTIVPM
EAATEEDWRTEYSDLVLAVRLVPSLDAAIAHINEYGSGHTDAIATEDAAAAAQFFSQVDS
AGVYHNCSTRFADGFRYGFGAEVGISTQKLPPRGPVGLEGLVTYKYVLSGDGQIAATYSG
AQAKPFLHRDR

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

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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