GapMind for catabolism of small carbon sources

 

Protein 5211158 in Shewanella loihica PV-4

Annotation: Shew_3574 aldehyde dehydrogenase (RefSeq)

Length: 506 amino acids

Source: PV4 in FitnessBrowser

Candidate for 41 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) 74% 100% 793.5 NAD+-dependent secondary alcohol dehydrogenase III monomer 69% 724.2
2'-deoxyinosine catabolism adh hi Aldehyde dehydrogenase (EC 1.2.1.3) (characterized) 74% 100% 793.5 NAD+-dependent secondary alcohol dehydrogenase III monomer 69% 724.2
2-deoxy-D-ribose catabolism adh hi Aldehyde dehydrogenase (EC 1.2.1.3) (characterized) 74% 100% 793.5 NAD+-dependent secondary alcohol dehydrogenase III monomer 69% 724.2
ethanol catabolism adh hi Aldehyde dehydrogenase (EC 1.2.1.3) (characterized) 74% 100% 793.5 NAD+-dependent secondary alcohol dehydrogenase III monomer 69% 724.2
L-threonine catabolism adh hi Aldehyde dehydrogenase (EC 1.2.1.3) (characterized) 74% 100% 793.5 NAD+-dependent secondary alcohol dehydrogenase III monomer 69% 724.2
thymidine catabolism adh hi Aldehyde dehydrogenase (EC 1.2.1.3) (characterized) 74% 100% 793.5 NAD+-dependent secondary alcohol dehydrogenase III monomer 69% 724.2
L-tryptophan catabolism adh hi Aldehyde dehydrogenase (EC 1.2.1.3) (characterized) 74% 100% 793.5 NAD+-dependent secondary alcohol dehydrogenase III monomer 69% 724.2
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 43% 91% 378.6 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 42% 94% 364 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 42% 94% 364 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 42% 94% 364 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 42% 94% 364 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 95% 344 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 95% 344 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 95% 344 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
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) 74% 793.5
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) 74% 793.5
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) 74% 793.5
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 96% 332 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 96% 332 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 96% 332 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-arginine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 38% 96% 323.2 NAD+-dependent secondary alcohol dehydrogenase III monomer 69% 724.2
L-citrulline catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 38% 96% 323.2 NAD+-dependent secondary alcohol dehydrogenase III monomer 69% 724.2
putrescine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 38% 96% 323.2 NAD+-dependent secondary alcohol dehydrogenase III monomer 69% 724.2
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 37% 99% 316.6 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 36% 100% 290 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 36% 100% 290 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 36% 100% 290 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 36% 100% 290 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 98% 274.2 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 98% 274.2 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 98% 274.2 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 98% 274.2 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 89% 232.3 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 89% 232.3 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 89% 232.3 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 89% 232.3 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 89% 232.3 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-valine catabolism mmsA lo Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized) 31% 94% 220.7 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 93% 164.1 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 32% 93% 164.1 Aldehyde dehydrogenase (EC 1.2.1.3) 74% 793.5

Sequence Analysis Tools

View 5211158 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MIYSKPGTTDAIVNFNSRYDNFIGGQWVAPVGGEYFDNRSPVDGQVFCQVARSDERDIEL
ALDAAHAAKDAWGKTSVTERSNLLLKIADRVEQNLEFLAVAETWENGKAVRETLNADLPL
FVDHFRYFAGCIRAQEGSAADIDNNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALA
AGNCIVLKPAEQTPVSILVMVELIQDLLPAGVLNIVNGFGTEAGQALAVSKRIAKLAFTG
STQIGHHILKCAAESLIPSTVELGGKSPNIYFADVMEQEDEYLDKAVEGMLLAFFNQGEV
CTCPSRVLIAESIYDKFIDKVIARAKTIKQGNPLDTDTQVGAQASQEQFDKILSYLEIGR
NEGAEVLIGGTSCQLSGDQSSGFYIEPTILKGHNKMRVFQEEIFGPVISVTTFKDEAEAL
AIANDTEYGLGAGVWTRDMNRAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRET
HKMMLSHYQNTKNLLVSYDVNPLGFF

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, the preprint on GapMind for carbon sources, 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