GapMind for catabolism of small carbon sources

 

Protein CA265_RS12005 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: CA265_RS12005 glutathione-dependent formaldehyde dehydrogenase

Length: 385 amino acids

Source: Pedo557 in FitnessBrowser

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
ethanol catabolism etoh-dh-nad lo alcohol dehydrogenase (EC 1.1.1.1) (characterized) 36% 99% 233.8 Uncharacterized zinc-type alcohol dehydrogenase-like protein AdhB; EC 1.-.-.- 45% 343.6
4-hydroxybenzoate catabolism adh lo Alcohol dehydrogenase; EC 1.1.1.1; EC 1.1.1.4; EC 1.2.1.3 (characterized) 34% 99% 203 Uncharacterized zinc-type alcohol dehydrogenase-like protein AdhB; EC 1.-.-.- 45% 343.6
2'-deoxyinosine catabolism adh lo Alcohol dehydrogenase; EC 1.1.1.1; EC 1.1.1.4; EC 1.2.1.3 (characterized) 34% 99% 203 Uncharacterized zinc-type alcohol dehydrogenase-like protein AdhB; EC 1.-.-.- 45% 343.6
2-deoxy-D-ribose catabolism adh lo Alcohol dehydrogenase; EC 1.1.1.1; EC 1.1.1.4; EC 1.2.1.3 (characterized) 34% 99% 203 Uncharacterized zinc-type alcohol dehydrogenase-like protein AdhB; EC 1.-.-.- 45% 343.6
ethanol catabolism adh lo Alcohol dehydrogenase; EC 1.1.1.1; EC 1.1.1.4; EC 1.2.1.3 (characterized) 34% 99% 203 Uncharacterized zinc-type alcohol dehydrogenase-like protein AdhB; EC 1.-.-.- 45% 343.6
L-threonine catabolism adh lo Alcohol dehydrogenase; EC 1.1.1.1; EC 1.1.1.4; EC 1.2.1.3 (characterized) 34% 99% 203 Uncharacterized zinc-type alcohol dehydrogenase-like protein AdhB; EC 1.-.-.- 45% 343.6
thymidine catabolism adh lo Alcohol dehydrogenase; EC 1.1.1.1; EC 1.1.1.4; EC 1.2.1.3 (characterized) 34% 99% 203 Uncharacterized zinc-type alcohol dehydrogenase-like protein AdhB; EC 1.-.-.- 45% 343.6
L-tryptophan catabolism adh lo Alcohol dehydrogenase; EC 1.1.1.1; EC 1.1.1.4; EC 1.2.1.3 (characterized) 34% 99% 203 Uncharacterized zinc-type alcohol dehydrogenase-like protein AdhB; EC 1.-.-.- 45% 343.6
D-sorbitol (glucitol) catabolism sdh lo L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized) 30% 97% 139.4 Uncharacterized zinc-type alcohol dehydrogenase-like protein AdhB; EC 1.-.-.- 45% 343.6
xylitol catabolism xdhA lo L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized) 30% 97% 139.4 Uncharacterized zinc-type alcohol dehydrogenase-like protein AdhB; EC 1.-.-.- 45% 343.6
D-xylose catabolism xdhA lo L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized) 30% 97% 139.4 Uncharacterized zinc-type alcohol dehydrogenase-like protein AdhB; EC 1.-.-.- 45% 343.6
L-threonine catabolism tdh lo L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized) 31% 94% 138.7 Uncharacterized zinc-type alcohol dehydrogenase-like protein AdhB; EC 1.-.-.- 45% 343.6
myo-inositol catabolism iolM lo scyllo-inosose 3-dehydrogenase; 2-keto-myo-inositol dehydrogenase; EC 1.1.1.- (characterized) 31% 66% 108.2 Uncharacterized zinc-type alcohol dehydrogenase-like protein AdhB; EC 1.-.-.- 45% 343.6

Sequence Analysis Tools

View CA265_RS12005 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

MKAAVFHKPGDIRVDYVPDPKILDPRDVILKVTSTAICGSDLHILSGAVPQKDPLIMGHE
FMGIVEEVGASITNLKRGDRVVVPFPISCGKCFFCTHEASPACETSNFKNYGPNGDMMSQ
KGAALFGYTDLYGGYSGGQAQYVRVPYADISPRIVPEHLSDEQALFLTDIFPTGWSAIDW
AQLKGGEVVAIFGSGPVGLMAQKAAWINGASRVIAIDPLDYRLEKAKAVNNVDILNPHKV
DVVEAIREMTGGRGADLCVDAVGFEPERSFFDKVKATVHFEKGSIKVLEMCFEAVRRMGT
VSIMGVYGSPYDNFPLFRIFDKGITIKQGQAPVLNYIDKLIGLVNEGKVVLDDIITHTLP
LEDAAHGYKIFDNKEEDCVKVVLKP

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