GapMind for catabolism of small carbon sources

 

Protein GFF2316 in Phaeobacter inhibens BS107

Annotation: PGA1_c23480 putative D-beta-hydroxybutyrate dehydrogenase

Length: 257 amino acids

Source: Phaeo in FitnessBrowser

Candidate for 8 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-galactose catabolism galdh lo Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized) 37% 96% 143.3 3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) 40% 175.6
lactose catabolism galdh lo Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized) 37% 96% 143.3 3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) 40% 175.6
2-deoxy-D-ribonate catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 30% 94% 126.3 3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) 40% 175.6
2-deoxy-D-ribose catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 30% 94% 126.3 3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) 40% 175.6
D-xylose catabolism xdh lo NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale) 35% 93% 125.6 3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) 40% 175.6
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 31% 89% 107.8 3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) 40% 175.6
D-sorbitol (glucitol) catabolism srlD lo sorbitol-6-phosphate dehydrogenase; EC 1.1.1.140 (characterized) 31% 98% 106.3 3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) 40% 175.6
L-fucose catabolism fdh lo Short-chain dehydrogenase (characterized, see rationale) 32% 95% 102.4 3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) 40% 175.6

Sequence Analysis Tools

View GFF2316 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSNLAGKDLAGRHVVVTGGGSGVGAALARSFAGGGARLTLLGRRIEPLQEVAAETGALPL
ACDVTEAEAVRAALDTARQQHGPVSVAIANAGAAPSKPFAKMDLADFEAALAVNLSGVFN
LWQAALPDMKSAGWGRMIAVASTAGLKGYPYVSGYCAAKHGVVGLTRSLAQELARSGITV
NAICPGFIETPLLERSIATIVSTTGMSEEEAAKSLRAGNPQGRFIQPEEVADAALFLASS
SAASINGSALPITGGEI

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 (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 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