GapMind for catabolism of small carbon sources

 

Protein SMc00086 in Sinorhizobium meliloti 1021

Annotation: SMc00086 diheme cytochrome C-type signal peptide protein

Length: 304 amino acids

Source: Smeli 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
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% 63% 170.6 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 36% 186.4
ethanol catabolism etoh-dh-c lo alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized) 34% 63% 169.9 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 36% 186.4
2-deoxy-D-ribose catabolism drdehyd-cytc lo cytochrome c component of deoxyribose dehydrogenase (characterized) 34% 68% 157.9 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 36% 186.4
D-cellobiose catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized) 34% 60% 157.1 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 36% 186.4
D-gluconate catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized) 34% 60% 157.1 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 36% 186.4
D-glucose catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized) 34% 60% 157.1 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 36% 186.4
lactose catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized) 34% 60% 157.1 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 36% 186.4
D-maltose catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized) 34% 60% 157.1 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 36% 186.4
sucrose catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized) 34% 60% 157.1 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 36% 186.4
trehalose catabolism gadh2 lo Gluconate 2-dehydrogenase cytochrome c subunit; GA 2-DH cytochrome c subunit; GADH cytochrome c subunit; EC 1.1.99.3 (characterized) 34% 60% 157.1 Fructose dehydrogenase cytochrome subunit; Fructose dehydrogenase subunit II 36% 186.4

Sequence Analysis Tools

View SMc00086 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

MGRRARYLLSGLVLLVVAGASLAWWLTKPDRWDAAHWEGLGGPDLANGEQIFWAGGCVSC
HSAPGAKDDQRLVLTGGRTLKSPFGTFYPPNISPDETVGIGNWTLAEFGDAMTRGVGKDG
EHLYPSFPYGSYIRMTAKDVNDLWGFMQTLPKSSNATPPHDLAFPYNVRLALGAWKLLYL
SDEPRTQVNTADTKLARGQYLVEGPGHCGECHTPRDALGGFEEDRWLAGAPNPEGEGRIP
DITPSSKSIGDWSASDIASYLETGFTPDFDTVGGSMVEVQKNMAELPASDRDAIAAYLKA
LPAL

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 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