GapMind for catabolism of small carbon sources

 

Protein 203555 in Shewanella oneidensis MR-1

Annotation: SO4480 aldehyde dehydrogenase (NCBI ptt file)

Length: 506 amino acids

Source: MR1 in FitnessBrowser

Candidate for 48 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism adh hi Aldehyde dehydrogenase (EC 1.2.1.3) (characterized) 75% 100% 805.1 Long-chain-aldehyde dehydrogenase; Aldehyde dehydrogenase 1; EC 1.2.1.48 69% 723.8
2'-deoxyinosine catabolism adh hi Aldehyde dehydrogenase (EC 1.2.1.3) (characterized) 75% 100% 805.1 Long-chain-aldehyde dehydrogenase; Aldehyde dehydrogenase 1; EC 1.2.1.48 69% 723.8
2-deoxy-D-ribose catabolism adh hi Aldehyde dehydrogenase (EC 1.2.1.3) (characterized) 75% 100% 805.1 Long-chain-aldehyde dehydrogenase; Aldehyde dehydrogenase 1; EC 1.2.1.48 69% 723.8
ethanol catabolism adh hi Aldehyde dehydrogenase (EC 1.2.1.3) (characterized) 75% 100% 805.1 Long-chain-aldehyde dehydrogenase; Aldehyde dehydrogenase 1; EC 1.2.1.48 69% 723.8
L-threonine catabolism adh hi Aldehyde dehydrogenase (EC 1.2.1.3) (characterized) 75% 100% 805.1 Long-chain-aldehyde dehydrogenase; Aldehyde dehydrogenase 1; EC 1.2.1.48 69% 723.8
thymidine catabolism adh hi Aldehyde dehydrogenase (EC 1.2.1.3) (characterized) 75% 100% 805.1 Long-chain-aldehyde dehydrogenase; Aldehyde dehydrogenase 1; EC 1.2.1.48 69% 723.8
L-tryptophan catabolism adh hi Aldehyde dehydrogenase (EC 1.2.1.3) (characterized) 75% 100% 805.1 Long-chain-aldehyde dehydrogenase; Aldehyde dehydrogenase 1; EC 1.2.1.48 69% 723.8
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 43% 93% 386 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 42% 94% 351.3 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 42% 94% 351.3 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 42% 94% 351.3 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 42% 94% 351.3 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 97% 350.9 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 97% 350.9 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 97% 350.9 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
4-hydroxybenzoate catabolism praB lo 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 39% 99% 357.1 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-tryptophan catabolism nbaE lo 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 39% 99% 357.1 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-tryptophan catabolism praB lo 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 39% 99% 357.1 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 96% 338.6 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 96% 338.6 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 96% 338.6 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-arginine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 95% 331.3 Long-chain-aldehyde dehydrogenase; Aldehyde dehydrogenase 1; EC 1.2.1.48 69% 723.8
L-citrulline catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 95% 331.3 Long-chain-aldehyde dehydrogenase; Aldehyde dehydrogenase 1; EC 1.2.1.48 69% 723.8
putrescine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 40% 95% 331.3 Long-chain-aldehyde dehydrogenase; Aldehyde dehydrogenase 1; EC 1.2.1.48 69% 723.8
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 95% 319.7 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 97% 278.5 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 97% 278.5 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 97% 278.5 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 97% 278.5 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-arabinose catabolism xacF lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 36% 99% 276.9 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
D-galacturonate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 36% 99% 276.9 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
D-glucuronate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 36% 99% 276.9 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
D-xylose catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 36% 99% 276.9 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 98% 255 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 32% 98% 255 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 35% 90% 229.6 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 35% 90% 229.6 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 35% 90% 229.6 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 35% 90% 229.6 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 35% 90% 229.6 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 99% 225.7 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 99% 225.7 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 99% 225.7 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 99% 225.7 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 99% 225.7 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 99% 225.7 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 33% 93% 168.7 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 33% 93% 168.7 Aldehyde dehydrogenase (EC 1.2.1.3) 75% 805.1

Sequence Analysis Tools

View 203555 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

MIYAQPGTAGALVNFKEKYANFIGGKWVAPVNGKYFDNRSPVNGQNFCKIPRSDAQDIEL
ALDAAHAAKDAWGKTSVTERSNILLRIADRVEQNLEYLAVAETWENGKAVRETLNADLPL
FVDHFRYFAGCIRAQEGSAADIDGNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALA
AGNCVVLKPAEQTPVSILVLLELIEDLLPPGVLNVVNGFGAEAGQALATSKRIAKLAFTG
STEVGFHILKCAAESLIPSTVELGGKSPNLYFADVMDQEDEYLDKAVEGMLLAFFNQGEV
CTCPSRVLIQESIYDRFIEKVLARAQTIKQGNPLDTATQVGAQASQEQFDKILSYLAIGK
DEGAQVLLGGSLCQLEGEQSKGYYISPTIMKGHNKMRIFQEEIFGPVISVTTFKDEAEAL
AIANDTEYGLGAGVWTRDMNRAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRET
HKMMLNHYQNTKNLLVSYDINPLGFF

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