GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_0465 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_0465 aldehyde dehydrogenase (NAD+)

Length: 511 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 24 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) 57% 99% 534.3 Aldehyde dehydrogenase family 7 member B4; Antiquitin-1; Turgor-responsive ALDH; EC 1.2.1.3 50% 496.5
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% 532.7 Δ1-piperideine-6-carboxylate dehydrogenase 48% 375.9
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% 532.7 Δ1-piperideine-6-carboxylate dehydrogenase 48% 375.9
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% 532.7 Δ1-piperideine-6-carboxylate dehydrogenase 48% 375.9
ethanol catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 55% 92% 532.7 Δ1-piperideine-6-carboxylate dehydrogenase 48% 375.9
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% 532.7 Δ1-piperideine-6-carboxylate dehydrogenase 48% 375.9
thymidine catabolism adh hi aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized) 55% 92% 532.7 Δ1-piperideine-6-carboxylate dehydrogenase 48% 375.9
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% 532.7 Δ1-piperideine-6-carboxylate dehydrogenase 48% 375.9
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 31% 96% 242.7 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 532.7
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 31% 96% 242.7 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 532.7
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 31% 96% 242.7 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 532.7
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 31% 96% 242.7 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 532.7
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 32% 99% 236.5 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 532.7
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 32% 99% 236.5 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 532.7
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 32% 99% 236.5 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 532.7
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) 32% 97% 219.9 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 532.7
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 97% 201.1 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 532.7
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 97% 201.1 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 532.7
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 97% 201.1 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 532.7
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 97% 201.1 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 532.7
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 97% 201.1 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 532.7
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 30% 96% 199.9 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 532.7
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 30% 96% 199.9 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 532.7
L-tryptophan catabolism nbaE lo aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 31% 93% 171.4 aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) 55% 532.7

Sequence Analysis Tools

View N515DRAFT_0465 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

MSHEILKALGIGAEHSGTYLGQGEWSRTSDAGALQPVNPATGEVIGTVHASSAADYETIV
KRAQEAFKTWRTTPAPRRGEAVRLCGEALRKHKDALGSLVALEMGKIKPEGDGEVQEMID
IADFAVGQSRMLYGYTMHSERPGHRMYEQYHPLGLVGIISAFNFPVAVWAWNAFLAAICG
DICIWKPSPKTPLSAIATMKICNEALKAGGFPDIFFLFNDAGTDLSQGFVDDKRIPLISF
TGSTKVGRMVGERVARRMGRSLLELGGNNAIILDASADLKLAIPAIVFGAVGTAGQRCTT
TRRLFVHESIVGEVTDKLVAAYKQVEGKIGDPTLATTLMGPLNSQDAVQAYLGAVEKAKA
SGGKVLTGGAALSDRKGNFVLPTIVTGVKNSDEVVQTETFAPILYIMPFKSLDEAIELQN
DVPQGLSSAIFTRDLKAAEQYLSSAGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESG
SDAWKVYMRRQTNTSNYSDSLPLAQGIKFDL

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