GapMind for catabolism of small carbon sources

 

Protein Ac3H11_2257 in Acidovorax sp. GW101-3H11

Annotation: Short-chain dehydrogenase/reductase SDR

Length: 267 amino acids

Source: acidovorax_3H11 in FitnessBrowser

Candidate for 17 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) 43% 95% 163.3 dihydroanticapsin dehydrogenase (EC 1.1.1.385) 42% 185.3
L-rhamnose catabolism LRA1 med L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized) 41% 96% 151.8 dihydroanticapsin dehydrogenase (EC 1.1.1.385) 42% 185.3
glycerol catabolism dhaD lo NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized) 37% 96% 161 dihydroanticapsin dehydrogenase (EC 1.1.1.385) 42% 185.3
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized) 36% 97% 156.8 dihydroanticapsin dehydrogenase (EC 1.1.1.385) 42% 185.3
D-galactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 35% 97% 154.8 dihydroanticapsin dehydrogenase (EC 1.1.1.385) 42% 185.3
lactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 35% 97% 154.8 dihydroanticapsin dehydrogenase (EC 1.1.1.385) 42% 185.3
L-fucose catabolism fucDH lo Short-chain dehydrogenase/reductase SDR (characterized, see rationale) 35% 97% 148.3 dihydroanticapsin dehydrogenase (EC 1.1.1.385) 42% 185.3
xylitol catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 38% 98% 141.4 dihydroanticapsin dehydrogenase (EC 1.1.1.385) 42% 185.3
D-xylose catabolism xdh lo D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized) 35% 99% 141.4 dihydroanticapsin dehydrogenase (EC 1.1.1.385) 42% 185.3
D-xylose catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 38% 98% 141.4 dihydroanticapsin dehydrogenase (EC 1.1.1.385) 42% 185.3
4-hydroxybenzoate catabolism badH lo BadH (characterized) 34% 98% 138.7 dihydroanticapsin dehydrogenase (EC 1.1.1.385) 42% 185.3
phenylacetate catabolism badH lo BadH (characterized) 34% 98% 138.7 dihydroanticapsin dehydrogenase (EC 1.1.1.385) 42% 185.3
L-phenylalanine catabolism badH lo BadH (characterized) 34% 98% 138.7 dihydroanticapsin dehydrogenase (EC 1.1.1.385) 42% 185.3
D-xylose catabolism DKDP-dehydrog lo SDR family oxidoreductase (characterized, see rationale) 34% 96% 136 dihydroanticapsin dehydrogenase (EC 1.1.1.385) 42% 185.3
L-rhamnose catabolism LRA5 lo 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized) 35% 100% 132.1 dihydroanticapsin dehydrogenase (EC 1.1.1.385) 42% 185.3
D-sorbitol (glucitol) catabolism srlD lo Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized) 32% 96% 122.5 dihydroanticapsin dehydrogenase (EC 1.1.1.385) 42% 185.3
D-mannitol catabolism mt2d lo Probable NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Short chain dehydrogenase/reductase; YlSDR; EC 1.1.1.138 (characterized) 31% 93% 116.7 dihydroanticapsin dehydrogenase (EC 1.1.1.385) 42% 185.3

Sequence Analysis Tools

View Ac3H11_2257 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MNPSSPAPSLPSSIYFGHTGRVCIVTGGAQGIGEACVRRFAAEGAKPVIVDVDDARGQAL
AAELGALYVRCDVGDKAQVDALVAQVLAAHGRIDVLVNNAGIFRAADFLEVTEADFDAVL
RVNLKGSFLVGQAVARAMVTSGGGAIVNMSSVNGVLAIPNIASYNVSKGGVNQLTRVMAL
ALADKNIRVNAVAPGTIATELAAKAVLTSDEAKRKIMSRTPMKRLGQPSEIADVVAWLAS
DAASYVTGEIVTVDGGRMTLNYTVPVQ

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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