GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_512 in Pseudomonas fluorescens FW300-N1B4

Annotation: Short-chain dehydrogenase/reductase SDR

Length: 253 amino acids

Source: pseudo1_N1B4 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
D-sorbitol (glucitol) catabolism sdh med L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized) 41% 94% 153.3 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 44% 204.1
xylitol catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 36% 100% 155.6 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 44% 204.1
D-xylose catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 36% 100% 155.6 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 44% 204.1
L-fucose catabolism fucDH lo Short-chain dehydrogenase/reductase SDR (characterized, see rationale) 36% 99% 149.8 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 44% 204.1
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized) 33% 90% 142.5 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 44% 204.1
glycerol catabolism dhaD lo NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized) 36% 99% 142.5 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 44% 204.1
4-hydroxybenzoate catabolism badH lo BadH (characterized) 36% 98% 141 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 44% 204.1
phenylacetate catabolism badH lo BadH (characterized) 36% 98% 141 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 44% 204.1
L-phenylalanine catabolism badH lo BadH (characterized) 36% 98% 141 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 44% 204.1
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% 139.8 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 44% 204.1
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% 139.8 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 44% 204.1
D-xylose catabolism DKDP-dehydrog lo SDR family oxidoreductase (characterized, see rationale) 36% 96% 137.5 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 44% 204.1
D-sorbitol (glucitol) catabolism srlD lo sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized) 32% 98% 114.4 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 44% 204.1
L-fucose catabolism fdh lo Short-chain dehydrogenase (characterized, see rationale) 32% 97% 99.8 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase; 2,5-DDOL dehydrogenase; EC 1.1.1.- 44% 204.1

Sequence Analysis Tools

View Pf1N1B4_512 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

MSMTFSGQVAVVTGAANGIGRATALAFAAEGLKVVVADLDAAGGEGTVALIRTAGGEATF
VRCNVTVESEVKNLMDEVVNTYGRLDYAFNNAGIEIEKGKLAEGTIDEFDAIMGVNVKGV
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 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