GapMind for catabolism of small carbon sources

 

Protein AZOBR_RS26825 in Azospirillum brasilense Sp245

Annotation: AZOBR_RS26825 aldehyde dehydrogenase

Length: 494 amino acids

Source: azobra in FitnessBrowser

Candidate for 18 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 (NAD+) (EC 1.2.1.3) (characterized) 43% 94% 377.1 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 41% 360.5
2'-deoxyinosine catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 43% 94% 377.1 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 41% 360.5
2-deoxy-D-ribose catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 43% 94% 377.1 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 41% 360.5
ethanol catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 43% 94% 377.1 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 41% 360.5
L-threonine catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 43% 94% 377.1 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 41% 360.5
thymidine catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 43% 94% 377.1 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 41% 360.5
L-tryptophan catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 43% 94% 377.1 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 41% 360.5
L-phenylalanine catabolism pad-dh med phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 41% 96% 341.7 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 43% 377.1
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 37% 99% 328.2 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 43% 377.1
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 37% 99% 328.2 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 43% 377.1
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 95% 306.2 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 43% 377.1
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 95% 306.2 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 43% 377.1
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 95% 306.2 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 43% 377.1
L-tryptophan catabolism nbaE lo aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 38% 95% 291.2 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 43% 377.1
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 33% 96% 278.1 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 43% 377.1
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 33% 96% 278.1 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 43% 377.1
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 33% 96% 278.1 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 43% 377.1
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 33% 96% 278.1 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) 43% 377.1

Sequence Analysis Tools

View AZOBR_RS26825 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

LVLNTTPHALARELSGLLLIGGELRPAATGKTFDVVNPATGDVIATAADGGERDVDAAVR
AAVAAQGAWARLSARERGRLLVECGRRLVGHAEEIGRLLALETGKAIRTESRVEASLVAD
TLTFYGGLASELKGETVPFHPKMLTFTQREPIGVVGAIIPWNVPLYLMALKIAPALVAGN
AVIVKSAEEAPLAALRVIQVMNQLLPPGVLNILSGDGPGCGAPLVTHPGVGKVTFTGSVE
TGKIISHLAADKLIPVTLELGGKSPMIVMGDADLDKAIDGAVAGMRFTRQGQSCTASSRI
FVHESLHDAFIDKLKAKVDAMTMGDPLDEATDIGTIISPQQFERVQSYIALGETTAGAIA
HRCSALPTDERLARGLFVQPVLFTGLANDHRLAREEIFGPVTCVIAFRDYEDALAMANDS
DFGLAATIWTRDLRTALDATRRLQAGFVQVNQNLVVQPGLSYGGFKQSGLGKEASLEAML
DHFTHKKTVIINMD

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