GapMind for catabolism of small carbon sources

 

Protein 7025539 in Shewanella sp. ANA-3

Annotation: Shewana3_2690 short chain dehydrogenase (RefSeq)

Length: 255 amino acids

Source: ANA3 in FitnessBrowser

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-rhamnose catabolism LRA1 lo NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized) 37% 98% 146.7 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase LinX; 2,5-DDOL dehydrogenase; EC 1.1.1.- 40% 174.9
D-sorbitol (glucitol) catabolism sdh lo L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized) 39% 94% 144.8 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase LinX; 2,5-DDOL dehydrogenase; EC 1.1.1.- 40% 174.9
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% 92% 142.5 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase LinX; 2,5-DDOL dehydrogenase; EC 1.1.1.- 40% 174.9
D-galactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 34% 92% 142.5 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase LinX; 2,5-DDOL dehydrogenase; EC 1.1.1.- 40% 174.9
lactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 34% 92% 142.5 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase LinX; 2,5-DDOL dehydrogenase; EC 1.1.1.- 40% 174.9
L-fucose catabolism fucDH lo Short-chain dehydrogenase/reductase SDR (characterized, see rationale) 38% 98% 135.6 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase LinX; 2,5-DDOL dehydrogenase; EC 1.1.1.- 40% 174.9
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) 36% 88% 127.5 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase LinX; 2,5-DDOL dehydrogenase; EC 1.1.1.- 40% 174.9
2-deoxy-D-ribonate catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 34% 99% 123.2 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase LinX; 2,5-DDOL dehydrogenase; EC 1.1.1.- 40% 174.9
2-deoxy-D-ribose catabolism deoxyribonate-dehyd lo 2-deoxy-D-ribonate dehydrogenase (characterized) 34% 99% 123.2 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase LinX; 2,5-DDOL dehydrogenase; EC 1.1.1.- 40% 174.9
D-xylose catabolism xdh lo NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale) 31% 92% 116.3 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase LinX; 2,5-DDOL dehydrogenase; EC 1.1.1.- 40% 174.9
L-fucose catabolism fdh lo Short-chain dehydrogenase (characterized, see rationale) 35% 96% 115.2 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase LinX; 2,5-DDOL dehydrogenase; EC 1.1.1.- 40% 174.9

Sequence Analysis Tools

View 7025539 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

MAVLQGKVAIITGASSGIGYATAKRFAREGAKLVLGARRGAILASLVDEIITQGGEAIYL
AGDVTDEVYASDLVALAVEQYGGLDIAFNNVGINGELGVDSDALSRAEWENTLTTNLTSA
FLAAKYQLPQMLKRGAGSIIFTSSFVGYTIGFPQTAAYAASKAGMIGLTQSLAVEYGARG
IRVNALLPGGTDTPMGREFANTPEAMAFVKNLHALKRLADPAEIAQSALYLASDAASFTT
GIALLVDGGVSICKT

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