GapMind for catabolism of small carbon sources

 

Protein WP_004107096.1 in Rhizobium freirei PRF 81

Annotation: NCBI__GCF_000359745.1:WP_004107096.1

Length: 323 amino acids

Source: GCF_000359745.1 in NCBI

Candidate for 11 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 hi Glyoxylate reductase; EC 1.1.1.26 (characterized) 45% 97% 254.2 hydroxypyruvate reductase subunit (EC 1.1.1.81) 39% 230.7
D-xylose catabolism gyaR hi Glyoxylate reductase; EC 1.1.1.26 (characterized) 45% 97% 254.2 hydroxypyruvate reductase subunit (EC 1.1.1.81) 39% 230.7
D-cellobiose catabolism kguD med 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized) 43% 95% 208.8 Glyoxylate reductase; EC 1.1.1.26 45% 254.2
D-gluconate catabolism kguD med 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized) 43% 95% 208.8 Glyoxylate reductase; EC 1.1.1.26 45% 254.2
D-glucose catabolism kguD med 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized) 43% 95% 208.8 Glyoxylate reductase; EC 1.1.1.26 45% 254.2
lactose catabolism kguD med 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized) 43% 95% 208.8 Glyoxylate reductase; EC 1.1.1.26 45% 254.2
D-maltose catabolism kguD med 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized) 43% 95% 208.8 Glyoxylate reductase; EC 1.1.1.26 45% 254.2
sucrose catabolism kguD med 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized) 43% 95% 208.8 Glyoxylate reductase; EC 1.1.1.26 45% 254.2
trehalose catabolism kguD med 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized) 43% 95% 208.8 Glyoxylate reductase; EC 1.1.1.26 45% 254.2
D-lactate catabolism D-LDH lo D-lactate dehydrogenase (EC 1.1.1.28) (characterized) 36% 98% 152.9 Glyoxylate reductase; EC 1.1.1.26 45% 254.2
L-threonine catabolism D-LDH lo D-lactate dehydrogenase (EC 1.1.1.28) (characterized) 36% 98% 152.9 Glyoxylate reductase; EC 1.1.1.26 45% 254.2

Sequence Analysis Tools

View WP_004107096.1 at NCBI

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

MSKPRVLVTRRWPVSVEAALSERFDATLSKDDAALDAAQLRDALLSYDAVLPTVSDRLPA
ALFEGDAVQSKIIGNFGVGFNHIDVAAARAKGIVVTNTPGVLTDCTADIAMLLLLSVARR
GGEGERELRAGAWTGWRPTHLVGTKVTGKTVGIIGFGRIGKAFAQRCHFGFGMDVVFYNR
SVVDPAEAARYGARQLQTVEDVLQVSDFVSLHCPGGAENRHLMNAARLAAMKPGAFLINT
ARGDVIDEAALIAALEQGTIRGAGLDVYEAEPHVPERLRVLDNVVLLPHLGSATEETRTA
MGMKVVDNVTAFFAGREPPDRVV

This GapMind analysis is from Sep 24 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