GapMind for catabolism of small carbon sources

 

Protein PfGW456L13_3499 in Pseudomonas fluorescens GW456-L13

Annotation: Short-chain dehydrogenase/reductase SDR

Length: 255 amino acids

Source: pseudo13_GW456_L13 in FitnessBrowser

Candidate for 3 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-rhamnose catabolism LRA1 lo NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized) 38% 98% 158.7 Dehydrogenase/reductase SDR family member 4; NADPH-dependent carbonyl reductase/NADP-retinol dehydrogenase; CR; PHCR; NADPH-dependent retinol dehydrogenase/reductase; NDRD; Peroxisomal short-chain alcohol dehydrogenase; PSCD; rabNRDR; EC 1.1.1.184 38% 170.6
D-mannitol catabolism mt2d lo Probable NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Short chain dehydrogenase/reductase; YlSDR; EC 1.1.1.138 (characterized) 34% 90% 141.7 Dehydrogenase/reductase SDR family member 4; NADPH-dependent carbonyl reductase/NADP-retinol dehydrogenase; CR; PHCR; NADPH-dependent retinol dehydrogenase/reductase; NDRD; Peroxisomal short-chain alcohol dehydrogenase; PSCD; rabNRDR; EC 1.1.1.184 38% 170.6
D-sorbitol (glucitol) catabolism srlD lo sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized) 31% 97% 108.6 Dehydrogenase/reductase SDR family member 4; NADPH-dependent carbonyl reductase/NADP-retinol dehydrogenase; CR; PHCR; NADPH-dependent retinol dehydrogenase/reductase; NDRD; Peroxisomal short-chain alcohol dehydrogenase; PSCD; rabNRDR; EC 1.1.1.184 38% 170.6

Sequence Analysis Tools

View PfGW456L13_3499 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

MSKTQLFDLDGKIAFVSGASRGIGEAIAKLLAQQGAHVIVSSRKLEGCQHVADAIIAAGG
KATAIACHIGEMEQISQVFAGIKEQFGRLDILVNNAATNPQFCNVLDTDLSAFQKTVDVN
IRGYFFMSVEAGKLMRENGGGSIINVASINGVSPGIFQGIYSVTKAAVINMTKVFAKECA
QFGIRCNALLPGLTDTKFASALVKNEAILNTALQQIPLKRVADPSEMAGAVLYLASDASS
YTTGVSLNVDGGFLS

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 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