GapMind for catabolism of small carbon sources

 

Protein CCNA_01892 in Caulobacter crescentus NA1000

Annotation: CCNA_01892 short chain dehydrogenase

Length: 546 amino acids

Source: Caulo in FitnessBrowser

Candidate for 12 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% 100% 174.9 D-threitol dehydrogenase; EC 1.1.1.403 40% 175.6
glycerol catabolism dhaD lo NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized) 36% 97% 154.8 D-threitol dehydrogenase; EC 1.1.1.403 40% 175.6
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) 33% 88% 134.8 D-threitol dehydrogenase; EC 1.1.1.403 40% 175.6
xylitol catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 33% 100% 134.4 D-threitol dehydrogenase; EC 1.1.1.403 40% 175.6
D-xylose catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 33% 100% 134.4 D-threitol dehydrogenase; EC 1.1.1.403 40% 175.6
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 34% 96% 128.6 galactitol 2-dehydrogenase (L-tagatose-forming) (EC 1.1.1.406) 41% 159.1
D-galactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 34% 96% 128.6 galactitol 2-dehydrogenase (L-tagatose-forming) (EC 1.1.1.406) 41% 159.1
lactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 34% 96% 128.6 galactitol 2-dehydrogenase (L-tagatose-forming) (EC 1.1.1.406) 41% 159.1
2-deoxy-D-ribonate catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 37% 93% 124.4 D-threitol dehydrogenase; EC 1.1.1.403 40% 175.6
2-deoxy-D-ribose catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 37% 93% 124.4 D-threitol dehydrogenase; EC 1.1.1.403 40% 175.6
L-fucose catabolism fdh lo Short-chain dehydrogenase (characterized, see rationale) 37% 97% 121.7 D-threitol dehydrogenase; EC 1.1.1.403 40% 175.6
D-sorbitol (glucitol) catabolism srlD lo Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized) 31% 97% 119 D-threitol dehydrogenase; EC 1.1.1.403 40% 175.6

Sequence Analysis Tools

View CCNA_01892 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MARGGALLGFREGRHPRRPHETEYAMTSKAQSRVVLVTGGADGIGWAACQRFARAGDQVL
VADRNVERARERADSLGPDHHAIAMDVSSEAQIREGFEQLHREFGRLDVLVNNAGVTDPQ
PTATLDQTAEEVARLQAINVTGAFLAAREAGRLMIEQGHGAIINLASGAGLVALAKRTSY
SASKAAVISLTRTLACEWAAKGVRVNAVLPGYTRTQMVQDQIDAGLLDPSIVLSRIPLGR
MGEPEEMAEGAFFLASDAASYVVGATLVVDGGYTVYGGSGPASTTPAPSPLAPSPRVSAI
TGGGRGIGRCVVDLFHAAGDRLLVIERDAEGAKALAEALGDEHIVVQADITDVAAVEAAF
AQAQARWGRLDVLINNAGAADVFKPSLEQTAQDFTSVYDLNFSGPLATAKAAARLMSQGG
VIVNLGSIAGLGALPQRNAYCAAKAAVTMMSRSLACEWASAGIRVNTVAPGYIETPAVLA
LKSAGRAQFDKIRRRAPIGRLGDPMEVARTIAFLASPAASYVAGATLTVDGGWTAFGDAG
DASDIL

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, the preprint 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