GapMind for catabolism of small carbon sources

 

Protein Ga0059261_0516 in Sphingomonas koreensis DSMZ 15582

Annotation: Ga0059261_0516 vanillin dehydrogenase (EC 1.2.1.67)

Length: 478 amino acids

Source: Korea in FitnessBrowser

Candidate for 21 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 95% 297 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
L-arginine catabolism gabD lo NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 36% 95% 297 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 95% 297 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
L-citrulline catabolism gabD lo NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 36% 95% 297 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 95% 297 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 95% 297 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
putrescine catabolism gabD lo NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 36% 95% 297 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
L-arabinose catabolism xacF lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 36% 96% 262.3 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
D-galacturonate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 36% 96% 262.3 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
D-glucuronate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 36% 96% 262.3 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
D-xylose catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 36% 96% 262.3 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
4-hydroxybenzoate catabolism praB lo 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 35% 94% 259.2 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
L-tryptophan catabolism nbaE lo 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 35% 94% 259.2 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
L-tryptophan catabolism praB lo 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 35% 94% 259.2 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 36% 94% 258.8 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 36% 95% 231.5 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 36% 95% 231.5 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 36% 95% 231.5 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 32% 97% 226.1 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 32% 97% 226.1 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 32% 97% 226.1 vanillin dehydrogenase monomer (EC 1.2.1.67) 77% 719.9

Sequence Analysis Tools

View Ga0059261_0516 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

MATIAPPAPGKTFARLNPVTGEVATEAQAFTVDQANEAVEAAAAAFPAWSTLGPNARRAA
LNKAAEALAAKAEDFVEAMNGEIGATEGWARFNLMLAVSMVREAAALTTQIGGEVIPSDK
PGCIAMAIREPVGVMLGIAPWNAPIILGVRAVAAPLACGNTVVLKASEQCPRTHSLIAEA
FDEALPKGAVSIVTNAPEDAPEIVGALIDNPHIRRINFTGSTAVGRIIAKRAAEHLKPVL
LELGGKAPMLVLEDADLDEAVKAAAFGAFMNQGQICMSTERIIVVDAVADAFVEKFAAKV
GTMPVGDPREGKTPLGAVVDQKTVAHVKALIGDALAAGAVQVNGGGVLEGTGGVLMPAHV
IDHVTPDMKLFRDESFGPVVGVIRARDEAHAILLANDTEYGLSASVFTRDTARGLRVARQ
IKSGICHVNGPTVHDEAQMPFGGVKASGYGRFGGKAGIDAFTELRWITIETEPGHYPI

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