GapMind for catabolism of small carbon sources

 

Protein WP_104914316.1 in Pontimonas salivibrio CL-TW6

Annotation: NCBI__GCF_002950575.1:WP_104914316.1

Length: 239 amino acids

Source: GCF_002950575.1 in NCBI

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized) 37% 92% 153.3 cyclohexanol dehydrogenase (EC 1.1.1.245) 43% 199.9
L-fucose catabolism fucDH lo Short-chain alcohol dehydrogenase protein (characterized, see rationale) 39% 97% 151.8 cyclohexanol dehydrogenase (EC 1.1.1.245) 43% 199.9
D-xylose catabolism DKDP-dehydrog lo SDR family oxidoreductase (characterized, see rationale) 39% 97% 151 cyclohexanol dehydrogenase (EC 1.1.1.245) 43% 199.9
D-galactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 37% 92% 150.6 cyclohexanol dehydrogenase (EC 1.1.1.245) 43% 199.9
lactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 37% 92% 150.6 cyclohexanol dehydrogenase (EC 1.1.1.245) 43% 199.9
L-rhamnose catabolism LRA1 lo L-rhamnose-1-dehydrogenase; EC 1.1.1.173 (characterized) 34% 96% 142.5 cyclohexanol dehydrogenase (EC 1.1.1.245) 43% 199.9
D-sorbitol (glucitol) catabolism sdh lo L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized) 40% 93% 141.4 cyclohexanol dehydrogenase (EC 1.1.1.245) 43% 199.9
glycerol catabolism dhaD lo NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized) 35% 95% 133.3 cyclohexanol dehydrogenase (EC 1.1.1.245) 43% 199.9
D-mannitol catabolism mt2d lo NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Alt a 8; EC 1.1.1.138 (characterized) 35% 94% 123.2 cyclohexanol dehydrogenase (EC 1.1.1.245) 43% 199.9
xylitol catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 33% 99% 118.2 cyclohexanol dehydrogenase (EC 1.1.1.245) 43% 199.9
D-xylose catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 33% 99% 118.2 cyclohexanol dehydrogenase (EC 1.1.1.245) 43% 199.9
D-sorbitol (glucitol) catabolism srlD lo Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized) 31% 97% 107.5 cyclohexanol dehydrogenase (EC 1.1.1.245) 43% 199.9

Sequence Analysis Tools

View WP_104914316.1 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

MKRLEGKVAIVTGAGRGIGRAIAEIFHQEGATVVATSQSPNHEFAPGIDFIQQEVAEEKA
WELVVATTMQRHGRVDVLVNNAGIIAYEPLGDLTLADWDRVVAVNQTGVFLGMKAVLPHM
LQQKTGSIINISSIWGNAAVAGAHAYHATKGAVRNMSKNAAITYATTGVRVNSLHPGFIA
TPLTDAQDPDVNKFVVGMTPMGRAGQPEEIAWGAVFLASDESSFMTGSELVIDGGYLAQ

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