GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_1220 in Pseudomonas fluorescens FW300-N1B4

Annotation: FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1220

Length: 291 amino acids

Source: pseudo1_N1B4 in FitnessBrowser

Candidate for 5 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism gyaR lo glyoxylate reductase (EC 1.1.1.26); 4-hydroxybutyrate dehydrogenase (EC 1.1.1.61); glyoxylate reductase (NADP+) (EC 1.1.1.79) (characterized) 33% 98% 147.5 NAD-dependent succinate semialdehyde dehydrogenase (EC 1.2.1.24) 33% 153.3
D-xylose catabolism gyaR lo glyoxylate reductase (EC 1.1.1.26); 4-hydroxybutyrate dehydrogenase (EC 1.1.1.61); glyoxylate reductase (NADP+) (EC 1.1.1.79) (characterized) 33% 98% 147.5 NAD-dependent succinate semialdehyde dehydrogenase (EC 1.2.1.24) 33% 153.3
L-valine catabolism mmsB lo 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized) 32% 97% 129.8 NAD-dependent succinate semialdehyde dehydrogenase (EC 1.2.1.24) 33% 153.3
D-glucuronate catabolism garR lo 2-hydroxy-3-oxopropionate reductase; EC 1.1.1.60; Tartronate semialdehyde reductase; TSAR (uncharacterized) 30% 97% 122.9 NAD-dependent succinate semialdehyde dehydrogenase (EC 1.2.1.24) 33% 153.3
D-gluconate catabolism gnd lo phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating) (EC 1.1.1.343) (characterized) 30% 52% 57.4 NAD-dependent succinate semialdehyde dehydrogenase (EC 1.2.1.24) 33% 153.3

Sequence Analysis Tools

View Pf1N1B4_1220 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

MELGFIGLGTMGVPMVLNLLKAGHRVKVWNRSSAPLDELARAGAQPVDSPALAAQAEVLI
SMLGDDVAIRSVFIDGKGLDGLAAGSVHVNMSTVSVALAKEFAALHTERDVAYVSAPVLG
RVDVAAAGNLNILASGPAQALARVQPLFDVLGRKTWPFGECAELACVAKLSANLMIASAI
ESMAQASTLASSYGISRATFIEMITSTLFPVPVYQGYGQLMIDKHFEPAGFKLSLGLKDI
RLALEAGEAAQVPLPFASVLKDNLLDGMAHGQGDQDWASLSEVSARRAGSR

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