GapMind for catabolism of small carbon sources

 

Protein CA265_RS19780 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: CA265_RS19780 aldehyde dehydrogenase family protein

Length: 513 amino acids

Source: Pedo557 in FitnessBrowser

Candidate for 27 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-lysine catabolism amaB hi L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale) 61% 100% 600.9 Aldehyde dehydrogenase family 7 member B4; Antiquitin-1; Turgor-responsive ALDH; EC 1.2.1.3 49% 499.2
4-hydroxybenzoate catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 55% 92% 528.1 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
2'-deoxyinosine catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 55% 92% 528.1 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
2-deoxy-D-ribose catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 55% 92% 528.1 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
ethanol catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 55% 92% 528.1 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
L-threonine catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 55% 92% 528.1 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
thymidine catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 55% 92% 528.1 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
L-tryptophan catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 55% 92% 528.1 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
L-arabinose catabolism xacF lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 256.5 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 256.5 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
D-galacturonate catabolism dopDH lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 256.5 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
D-glucuronate catabolism dopDH lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 256.5 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 256.5 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 256.5 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
D-xylose catabolism dopDH lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 33% 95% 256.5 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-arginine catabolism gabD lo aldehyde dehydrogenase-like protein yneI (characterized) 30% 97% 211.5 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
L-citrulline catabolism gabD lo aldehyde dehydrogenase-like protein yneI (characterized) 30% 97% 211.5 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
putrescine catabolism gabD lo aldehyde dehydrogenase-like protein yneI (characterized) 30% 97% 211.5 Δ1-piperideine-6-carboxylate dehydrogenase 47% 403.3
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% 97% 209.9 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-arginine catabolism kauB lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 30% 97% 201.1 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-arginine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 30% 97% 201.1 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-citrulline catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 30% 97% 201.1 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
putrescine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 30% 97% 201.1 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 31% 90% 195.3 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 31% 90% 195.3 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconic semialdehyde dehydrogenase; HMSD; EC 1.2.1.85 (characterized) 33% 70% 177.2 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1
L-tryptophan catabolism praB lo 2-hydroxymuconic semialdehyde dehydrogenase; HMSD; EC 1.2.1.85 (characterized) 33% 70% 177.2 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 528.1

Sequence Analysis Tools

View CA265_RS19780 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

MTTDIQSILNKLGINASNAAYSTGSNWGGELNVNTLESFSPVDGKLIASAKIATADDYDA
VVLKAQEAFTAWRSVPAPKRGEIVRQFGDALRENKDALGTLVSYEMGKSLQEGFGEVQEM
IDICDFAVGLSRQLYGLTMHSERPSHRMYEQWHPLGIVGIISAFNFPVAVWSWNTALALV
CGNVCIWKPSEKTPLTAIACQHIIAKVFKDNDIAEGVCNLILGDREVGERMTNDGRIPLI
SATGSTRMGKAVGAAVGARLGKSLLELGGNNAIIISEHADLDMSLIGAVFGAVGTAGQRC
TSTRRLIIHESVYDAFTAKLVKAYGQLRIGDPLDQNNHVGPLIDTDAVAAYLDSIAKCKA
EGGNFVVEGGVLSGDAYTSGCYVKPCIAEVQNDFKIVQHETFAPILYLIKYKTLDEAIAL
QNGVPQGLSSAIMTLNLREAEQFLSAKGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRE
SGSDAWRAYMRRQTNTINYSNTLPLAQGIKFDL

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