GapMind for catabolism of small carbon sources

 

Protein Pf6N2E2_5889 in Pseudomonas fluorescens FW300-N2E2

Annotation: FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5889

Length: 253 amino acids

Source: pseudo6_N2E2 in FitnessBrowser

Candidate for 9 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-sorbitol (glucitol) catabolism sdh med L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized) 41% 94% 152.9 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 43% 203.0
xylitol catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 36% 100% 156.4 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 43% 203.0
D-xylose catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 36% 100% 156.4 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 43% 203.0
L-fucose catabolism fucDH lo Short-chain dehydrogenase/reductase SDR (characterized, see rationale) 35% 99% 146.7 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 43% 203.0
glycerol catabolism dhaD lo NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized) 34% 99% 145.6 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 43% 203.0
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized) 32% 90% 142.5 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 43% 203.0
D-galactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 32% 91% 139.4 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 43% 203.0
lactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 32% 91% 139.4 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 43% 203.0
L-isoleucine catabolism ivdG lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 96% 107.5 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 43% 203.0

Sequence Analysis Tools

View Pf6N2E2_5889 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MSMTFSGQVAVVTGAAAGIGRATALAFAAEGLKVVVADLDVAGGEGTVQSIRDAGGEAVF
VRCNVTLENDVQQLMDEVIKTYGRLDYAFNNAGIEIEKGKLADGTLDEFDAIMGVNVKGV
WLCMKYQLPLLLAQGGGAIVNTASVAGLGAAPKMSIYAASKHAVIGLTKSAAIEYAKKKI
RVNAVCPAVIDTDMFRRAYEADPKKGEFANAMHPVGRIGKVEEIASAVLYLCSDGAAFTT
GHSLAVDGGVTAF

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:

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