GapMind for catabolism of small carbon sources

 

Protein 7023382 in Shewanella sp. ANA-3

Annotation: Shewana3_0612 succinylglutamic semialdehyde dehydrogenase (RefSeq)

Length: 487 amino acids

Source: ANA3 in FitnessBrowser

Candidate for 16 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism astD hi Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 96% 100% 935.3 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 36% 229.2
L-arginine catabolism astD hi astD: succinylglutamate-semialdehyde dehydrogenase (EC 1.2.1.71) (TIGR03240) 100% 811.7 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 36% 229.2
L-citrulline catabolism astD hi Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 96% 100% 935.3 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 36% 229.2
L-citrulline catabolism astD hi astD: succinylglutamate-semialdehyde dehydrogenase (EC 1.2.1.71) (TIGR03240) 100% 811.7 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) 36% 229.2
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 57% 99% 573.5 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 96% 935.3
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 57% 99% 573.5 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 96% 935.3
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 57% 99% 573.5 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 96% 935.3
ethanol catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 57% 99% 573.5 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 96% 935.3
L-threonine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 57% 99% 573.5 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 96% 935.3
thymidine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 57% 99% 573.5 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 96% 935.3
L-tryptophan catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 57% 99% 573.5 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 96% 935.3
L-lysine catabolism amaB lo Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale) 31% 94% 186 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 96% 935.3
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 91% 177.9 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 96% 935.3
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 91% 177.9 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 96% 935.3
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 91% 177.9 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 96% 935.3
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 91% 177.9 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 96% 935.3
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 32% 91% 177.9 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 96% 935.3
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized) 31% 91% 174.9 Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) 96% 935.3

Sequence Analysis Tools

View 7023382 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

MTHFIKGQWQAGKGHDVTSSNPANSEIIWRGQTATAEQVNAAVDAAREAQFDWFMLGFDG
RLKIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSATAYNKRTGTEA
NDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELM
VSLWEKAGLPAGVINLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL
ALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKLVE
AVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQANLQNLGGVSLVELSHLQAGTGLVSP
GLIDVTAVGELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSAGILADSRDDYEYFLA
RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASVEADAVSLPASL
SPGLSLE

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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.

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