GapMind for catabolism of small carbon sources

 

Protein Echvi_3822 in Echinicola vietnamensis KMM 6221, DSM 17526

Annotation: Echvi_3822 NAD-dependent aldehyde dehydrogenases

Length: 453 amino acids

Source: Cola in FitnessBrowser

Candidate for 31 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 hi succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 49% 99% 434.5
L-citrulline catabolism gabD hi succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 49% 99% 434.5
putrescine catabolism gabD hi succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized) 49% 99% 434.5
4-hydroxybenzoate catabolism adh med Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized) 46% 99% 396 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
2'-deoxyinosine catabolism adh med Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized) 46% 99% 396 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
2-deoxy-D-ribose catabolism adh med Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized) 46% 99% 396 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
ethanol catabolism adh med Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized) 46% 99% 396 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
L-threonine catabolism adh med Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized) 46% 99% 396 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
thymidine catabolism adh med Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized) 46% 99% 396 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
L-tryptophan catabolism adh med Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized) 46% 99% 396 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 34% 94% 273.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 34% 94% 273.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 34% 94% 273.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 34% 94% 273.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 31% 92% 252.3 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 31% 92% 252.3 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 31% 92% 252.3 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
L-arginine catabolism kauB lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 92% 236.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
L-arginine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 92% 236.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
L-citrulline catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 92% 236.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
putrescine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 92% 236.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
L-arabinose catabolism xacF lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 31% 94% 234.2 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
D-galacturonate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 31% 94% 234.2 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
D-glucuronate catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 31% 94% 234.2 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
D-xylose catabolism dopDH lo 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 31% 94% 234.2 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 32% 93% 233 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
L-fucose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 31% 92% 227.3 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
L-rhamnose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 31% 92% 227.3 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
L-threonine catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 31% 92% 227.3 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 31% 94% 221.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 31% 94% 221.1 succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) 49% 434.5

Sequence Analysis Tools

View Echvi_3822 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

MKSINPYTGELLEEFTDHTEQQVEAAIQKGQEAYLSWRELPISQRADLMKKAGQVLRDNT
DKYGKIISLEMGKVITESKSEVEKCAWVCEYYAENAEEMLADAPIALPDGKEAKVVYNPL
GIVLAVMPWNFPFWQVFRFAAPNLTAGNVGLLKHASNVPQCALAIEEVFTQAGFPEGVFQ
SLLIGSDKVANIIAHPDVKAATLTGSEKAGQKIAAQAGEQIKKTVLELGGSDPFIVLKDA
DVKEAAKTAAKGRMINFGQSCIAAKRFIIEQEVYDEFITHFKSAIESYVPGDPLDEKAGY
ACMARPDLAMELYEQVEASIQKGAEVILEGTKPEKGKAFIKPYILGKLTPDMPAYREELF
GPVASVFKANDVDEAIAIANDSAFGLGASLWTQDPQKADILSRKIESGAVFINSMVASNP
YLPFGGIKKSGYGRELAENGIKEFMNIKTVYLG

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