Protein Ga0059261_0516 in Sphingomonas koreensis DSMZ 15582

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

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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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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Protein sequences (fasta format)
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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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources