GapMind for catabolism of small carbon sources

 

Protein RR42_RS21615 in Cupriavidus basilensis 4G11

Annotation: RR42_RS21615 alcohol dehydrogenase

Length: 1000 amino acids

Source: Cup4G11 in FitnessBrowser

Candidate for 10 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
2-deoxy-D-ribose catabolism drdehyd-cytc lo cytochrome c component of deoxyribose dehydrogenase (characterized) 35% 96% 244.2 nicotinate dehydrogenase (EC 1.17.1.5); nicotinate dehydrogenase (cytochrome) (EC 1.17.2.1) 45% 807.7
ethanol catabolism etoh-dh-c lo alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized) 36% 85% 244.2 nicotinate dehydrogenase (EC 1.17.1.5); nicotinate dehydrogenase (cytochrome) (EC 1.17.2.1) 45% 807.7
D-cellobiose catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c (characterized, see rationale) 38% 94% 240 nicotinate dehydrogenase (EC 1.17.1.5); nicotinate dehydrogenase (cytochrome) (EC 1.17.2.1) 45% 807.7
D-gluconate catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c (characterized, see rationale) 38% 94% 240 nicotinate dehydrogenase (EC 1.17.1.5); nicotinate dehydrogenase (cytochrome) (EC 1.17.2.1) 45% 807.7
D-glucose catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c (characterized, see rationale) 38% 94% 240 nicotinate dehydrogenase (EC 1.17.1.5); nicotinate dehydrogenase (cytochrome) (EC 1.17.2.1) 45% 807.7
lactose catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c (characterized, see rationale) 38% 94% 240 nicotinate dehydrogenase (EC 1.17.1.5); nicotinate dehydrogenase (cytochrome) (EC 1.17.2.1) 45% 807.7
D-maltose catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c (characterized, see rationale) 38% 94% 240 nicotinate dehydrogenase (EC 1.17.1.5); nicotinate dehydrogenase (cytochrome) (EC 1.17.2.1) 45% 807.7
sucrose catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c (characterized, see rationale) 38% 94% 240 nicotinate dehydrogenase (EC 1.17.1.5); nicotinate dehydrogenase (cytochrome) (EC 1.17.2.1) 45% 807.7
trehalose catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c (characterized, see rationale) 38% 94% 240 nicotinate dehydrogenase (EC 1.17.1.5); nicotinate dehydrogenase (cytochrome) (EC 1.17.2.1) 45% 807.7
ethanol catabolism adhBqn lo Alcohol dehydrogenase (quinone), cytochrome c subunit; ADH; Alcohol dehydrogenase (quinone), subunit II; Cytochrome c-553; Cytochrome c553; Ethanol:Q2 reductase; G3-ADH subunit II; Quinohemoprotein-cytochrome c complex; Ubiquinol oxidase; EC 1.1.5.5 (characterized) 35% 86% 227.6 nicotinate dehydrogenase (EC 1.17.1.5); nicotinate dehydrogenase (cytochrome) (EC 1.17.2.1) 45% 807.7

Sequence Analysis Tools

View RR42_RS21615 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

MAPASPGAWQPPPEREWLAGHVIRPPVLAWQTGTLLSARLIGCDETAARALPGVATVLRR
GDFLGIAADTAPQALQAAHALRARWQAPPKAAASGLPLARRIVAEHGDAAQAMADAAGRS
AQDYPWPLAGLQAAGCSAMAEWRDGALRVWLPSRRPGALRAELAALLGIGEDRITLICWQ
APGHDEDPLYAHHAAADAALLAHSAGRVVRVRVEAHELGATQAVVNTHIESAWTRDGEIA
AYAVNTAVDARGSAAVMHAPPLALWLTRTTAPVTEIEPQASAGGDTRDDAILPPYRFDSL
SVTQADLPGQPRVESTPAQAARAHVFAHESHLDEVAAASAQDPVALRLRHLDDTRGAGLV
RRVAAQANWQPRGERPQAQQNVRRGRGFAYASTIEAGLADGGQPVHSWSAWVAEVEVDAT
TGEVSVTGVTLGHDSDAGEQGGVDAVALQQEAARAAQQLTVDGSRSDSWPAANLPAVHDA
SLPALATAQLPEVRVGGALRPASATLGTSAAVTLPAAPAVANAIFDATGVRLREPPFSGE
RIRLALAAQANPESTPKRGAARKRNWLLAGATAAAGLFVTAMPWRAPIAPVAPPGAGFYS
AATIERGRLVAAAGDCAVCHTAPNGARNAGGLALDTPFGTIYSTNITPDVETGIGNWSYA
AFERAMRQGIHRDGRHLYPAFPYTAFAKTSDGDLQALYAYLMAAEPVRAKAPETALAFPY
NLRPLMAGWNLLFHSPKPFEADPARSAQWNRGAYLAEGLGHCSACHSPRNALGAEQGGRR
YLGGGEAEGWEAPALGKLSHAPVPWTEQALFSYLRTGYAPHHGAAAGPMAPVIEELALLP
EEDVRAIAHYVASFGDAQPDAALASAQARQLEQRSADAARTLGGPAARLYQNACAVCHQS
DQGIRQFGIKPSLALNTNLHGDKPDNLIRVLLDGIPTPGTSDLGYMPAFGESLDDRQLTQ
LVHYLRKRFAPDKPAWDNVDDTLARLRAAPAHRPNHQPNH

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