GapMind for catabolism of small carbon sources

 

Protein 208821 in Desulfovibrio vulgaris Hildenborough

Annotation: DVU3294 aldehyde dehydrogenase (NADP) family protein

Length: 464 amino acids

Source: 882 in MicrobesOnline

Candidate for 34 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism gabD med succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) (characterized) 33% 99% 250.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 34% 238.4
L-citrulline catabolism gabD med succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) (characterized) 33% 99% 250.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 34% 238.4
putrescine catabolism gabD med succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) (characterized) 33% 99% 250.4 lactaldehyde dehydrogenase (EC 1.2.1.22) 34% 238.4
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 34% 97% 238.4 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 34% 97% 238.4 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 34% 97% 238.4 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 91% 232.6 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 91% 232.6 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 91% 232.6 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 91% 232.6 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 35% 95% 204.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 35% 95% 204.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 35% 95% 204.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 35% 95% 204.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 33% 82% 196.4 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
4-hydroxybenzoate catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 32% 88% 196.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
2'-deoxyinosine catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 32% 88% 196.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
2-deoxy-D-ribose catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 32% 88% 196.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
ethanol catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 32% 88% 196.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-threonine catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 32% 88% 196.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
thymidine catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 32% 88% 196.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-tryptophan catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 32% 88% 196.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-arginine catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 31% 80% 183.7 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-citrulline catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 31% 80% 183.7 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
putrescine catabolism patD lo 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized) 31% 80% 183.7 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-arginine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 32% 84% 177.2 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-citrulline catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 32% 84% 177.2 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
putrescine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 32% 84% 177.2 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-lysine catabolism amaB lo Δ1-piperideine-6-carboxylate dehydrogenase (characterized) 33% 83% 169.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 87% 161.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 87% 161.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 87% 161.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 87% 161.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 30% 87% 161.8 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) 33% 250.4

Sequence Analysis Tools

View 208821 at MicrobesOnline

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

MSSITVRNPFDLSTVGEVPLMSEAEAFAALERAHALHGDPAHRIPAHERLAILERLATLM
RTHAEALVRDAVREGGKPWADSVVEVERAIDGVRWAARELAQLGGREVPMGLTPASAGRL
AFTVREPRGVVLAISAFNHPVNLIVHQAVPAFAAGCPVLVKPASATPLSCRNVLRLMHEA
GVPEAWATMLPCAAATAEKLVADPRVAFLSFIGSSRVGWHLRSKLAPGATCALEHGGAAP
VVLDASADLDAALPLLLKGGFYHAGQVCVSVQRVFAPHETARTFAERLAAAAAQLPTGDP
MRHDTAVGPLIDPREVSRVHEWVEEARAGGGTVLCGGAPLSETLYSPTVVYDPPQGCRLA
RNEVFGPVVAVFSTRDRDEAIARANDVPFIFQAAVFARDVDVALDTARRLNATGVMVNDH
TAFRVDWMPFGGRGESGMGTGGIGPAMHEMTTEKLIVLRSPAWA

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