GapMind for catabolism of small carbon sources

 

Protein GFF1678 in Pseudomonas stutzeri RCH2

Annotation: Psest_1716 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

Length: 253 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 14 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-fucose catabolism fucDH lo Short-chain dehydrogenase/reductase SDR (characterized, see rationale) 39% 99% 164.5 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 45% 203.8
xylitol catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 36% 100% 154.8 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 45% 203.8
D-xylose catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 36% 100% 154.8 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 45% 203.8
D-sorbitol (glucitol) catabolism sdh lo sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) (characterized) 36% 98% 153.7 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 45% 203.8
D-xylose catabolism DKDP-dehydrog lo SDR family oxidoreductase (characterized, see rationale) 38% 96% 152.1 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 45% 203.8
glycerol catabolism dhaD lo NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized) 36% 96% 149.8 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 45% 203.8
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized) 33% 91% 147.5 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 45% 203.8
D-galactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 33% 92% 147.1 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 45% 203.8
lactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 33% 92% 147.1 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 45% 203.8
2-deoxy-D-ribonate catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate 3-dehydrogenase (characterized) 34% 95% 126.7 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 45% 203.8
2-deoxy-D-ribose catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate 3-dehydrogenase (characterized) 34% 95% 126.7 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 45% 203.8
D-xylose catabolism xdh lo D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized) 34% 94% 124.8 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 45% 203.8
D-sorbitol (glucitol) catabolism srlD lo sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized) 32% 98% 113.6 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 45% 203.8
L-isoleucine catabolism ivdG lo 3-hydroxyacyl-CoA dehydrogenase type-2; 17-beta-hydroxysteroid dehydrogenase 10; 17-beta-HSD 10; 3-hydroxy-2-methylbutyryl-CoA dehydrogenase; 3-hydroxyacyl-CoA dehydrogenase type II; Mitochondrial ribonuclease P protein 2; Mitochondrial RNase P protein 2; Scully protein; Type II HADH; EC 1.1.1.35; EC 1.1.1.51; EC 1.1.1.178 (characterized) 32% 96% 105.9 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 45% 203.8

Sequence Analysis Tools

View GFF1678 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

MSMTFSGQVALVTGAAAGIGRATAQAFAEQGLKVVLADIDEAGIRDGAESIRAAGGEAIA
VRCDVTRDAEVKALIEQVLAQFGRLDYAFNNAGIEIEQGRLAEGSEAEFDAIMGVNVKGV
WLCMKHQLPVMLAQGGGAIVNTASVAGLGAAPKMSIYAASKHAVIGLTKSAAIEYAKKKI
RVNAVCPAVIDTDMFRRAYEADPRKAEFAAAMHPVGRIGKVEEIAAAVLYLCCDGAAFTT
GQALAVDGGATAI

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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:

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. 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:

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