GapMind for catabolism of small carbon sources

 

Protein CA265_RS24850 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: CA265_RS24850 aldehyde dehydrogenase

Length: 454 amino acids

Source: Pedo557 in FitnessBrowser

Candidate for 33 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 med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 33% 92% 248.8 Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 32% 248.8
L-arginine catabolism gabD med Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 (characterized) 32% 93% 248.8 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 34% 245.0
L-citrulline catabolism gabD med Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 (characterized) 32% 93% 248.8 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 34% 245.0
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 33% 92% 248.8 Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 32% 248.8
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 33% 92% 248.8 Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 32% 248.8
ethanol catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 33% 92% 248.8 Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 32% 248.8
putrescine catabolism gabD med Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 (characterized) 32% 93% 248.8 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 34% 245.0
L-threonine catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 33% 92% 248.8 Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 32% 248.8
thymidine catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 33% 92% 248.8 Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 32% 248.8
L-tryptophan catabolism adh med aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized) 33% 92% 248.8 Succinate semialdehyde dehydrogenase; SSA dehydrogenase; EC 1.2.1.24 32% 248.8
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 93% 248.1 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 93% 248.1 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 93% 248.1 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 32% 93% 248.1 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 31% 95% 241.5 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 31% 95% 241.5 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 31% 95% 241.5 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 31% 95% 241.5 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 31% 95% 241.5 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 32% 94% 240.4 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 31% 91% 234.6 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 31% 91% 234.6 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 31% 91% 234.6 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 33% 91% 230.7 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 33% 91% 230.7 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 35% 85% 225.7 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 35% 85% 225.7 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 35% 85% 225.7 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 35% 85% 225.7 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-tryptophan catabolism nbaE lo 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 31% 93% 218.4 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 30% 94% 215.7 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-arginine catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 31% 90% 185.7 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8
L-citrulline catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 31% 90% 185.7 aldehyde dehydrogenase ALDH; EC 1.2.1.3 33% 248.8

Sequence Analysis Tools

View CA265_RS24850 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

MQIINPATAEIITSLEEDNLSTLQLKFDALQKAQPQWAGKTLQERIAVITHFSDLLEVEI
EKLASVLTSEVGKPLQQSRNEINGARARIKWMLANAEKYLADEVMTDEPGIKEIIKYEPL
GVVCNISAWNYPYLVGVNVFIPALLSGNTVMYKPSEYATLTGIEIEKLLKKAGVPDDVFH
IAIGAKETGSALLNMDFNGYFFTGSYKTGKLIYEKVAAKMVPCQLELGGKDPLYITDDVT
DVAAAAIGTADGAFYNNGQSCCAVERIYVQEKNYDDYCNAFVTEVKSWKTGIPTAEGVYI
GALTRKEQISVLENQVKDALNKGAKLLTGGKAVEGKGYYFEPTVLTDVTNDMLVMQEESF
GPIIGIMKVKDDAEALKMMKDTDYGLTASVYTASQERAEKILAQLDAGSGYWNCCDRVSA
ALPWSGRKYSGIGATLSHQGIRAFTKPKGYHLRR

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