GapMind for catabolism of small carbon sources

 

Protein GFF4092 in Marinobacter adhaerens HP15

Annotation: HP15_4032 betaine aldehyde dehydrogenase

Length: 486 amino acids

Source: Marino 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
4-hydroxybenzoate catabolism praB hi 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 85% 100% 869.4 retinal dehydrogenase (EC 1.2.1.36) 45% 434.5
L-tryptophan catabolism praB hi 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 85% 100% 869.4 retinal dehydrogenase (EC 1.2.1.36) 45% 434.5
L-tryptophan catabolism nbaE med aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 74% 96% 726.9 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 96% 347.1 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 96% 347.1 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 96% 347.1 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 40% 96% 347.1 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 95% 344 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 95% 344 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 41% 95% 344 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
L-arginine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 95% 343.2 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
L-arginine catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 95% 343.2 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
L-citrulline catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 95% 343.2 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
L-citrulline catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 95% 343.2 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
putrescine catabolism gabD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 95% 343.2 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
putrescine catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 39% 95% 343.2 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 39% 99% 318.2 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 36% 99% 300.1 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 36% 99% 300.1 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 36% 99% 300.1 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 36% 99% 300.1 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized) 33% 96% 237.3 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
L-arginine catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 33% 95% 199.5 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4
L-citrulline catabolism astD lo Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized) 33% 95% 199.5 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) 85% 869.4

Sequence Analysis Tools

View GFF4092 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MKDIKHYINGQYVGSASGRLFDNVNPANGKVISKVHEAGREEVDAAVKAARAALRGPWGK
MTLEQRTAILHKVADGINARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADMIKN
VPTESFEMPTPDGTGALNYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPS
EETPTTTALLGEVMKEAGVPDGVYNVVHGFGGDSAGAYLTEHPQVDGFTFTGETGTGEVI
MKAAAKGIRDISLELGGKNAGLVFADCDMEKAIEGTMRSAFANCGQVCLGTERVYVERSI
FDEFVGRLKEAAEGLKIGPPDDADANLGPLVSLKHREKVLSYYQKAVDDGATVVTGGGVP
DMPAELAGGAWVEPTIWTGLPDDSAVVTDEIFGPCCHIRPFDTEEEAIELANSLPYGLAS
AIWSENITRAHRVAGQIEAGIIWVNSWFLRDLRTPFGGSKQSGVGREGGVHSLEFYTEMK
NICVKL

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, the preprint on GapMind for carbon sources, 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