GapMind for catabolism of small carbon sources

 

Protein GFF2133 in Pseudomonas simiae WCS417

Annotation: FitnessBrowser__WCS417:GFF2133

Length: 447 amino acids

Source: WCS417 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 hi cytochrome c component of deoxyribose dehydrogenase (characterized) 100% 100% 926.4 D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) 51% 400.6
D-cellobiose catabolism gadh2 med D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized) 51% 94% 400.6 cytochrome c component of deoxyribose dehydrogenase 100% 926.4
D-gluconate catabolism gadh2 med D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized) 51% 94% 400.6 cytochrome c component of deoxyribose dehydrogenase 100% 926.4
D-glucose catabolism gadh2 med D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized) 51% 94% 400.6 cytochrome c component of deoxyribose dehydrogenase 100% 926.4
lactose catabolism gadh2 med D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized) 51% 94% 400.6 cytochrome c component of deoxyribose dehydrogenase 100% 926.4
D-maltose catabolism gadh2 med D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized) 51% 94% 400.6 cytochrome c component of deoxyribose dehydrogenase 100% 926.4
sucrose catabolism gadh2 med D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized) 51% 94% 400.6 cytochrome c component of deoxyribose dehydrogenase 100% 926.4
trehalose catabolism gadh2 med D-gluconate dehydrogenase cytochrome c subunit (EC 1.1.99.3) (characterized) 51% 94% 400.6 cytochrome c component of deoxyribose dehydrogenase 100% 926.4
ethanol catabolism adhBqn med 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) 48% 87% 387.5 cytochrome c component of deoxyribose dehydrogenase 100% 926.4
ethanol catabolism etoh-dh-c med alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized) 46% 88% 379.4 cytochrome c component of deoxyribose dehydrogenase 100% 926.4

Sequence Analysis Tools

View GFF2133 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MNNRRFARTAGWLALPCLVAAGLLAWYVTREPATPFEQEQAGATFEPALVSRGEYVARLS
DCVACHSLAGKAPFAGGLEMATPLGAIHATNITPDKSTGIGTYSLADFDRAVRHGVAPGG
RRLYPAMPYPSYVKLSDDDIKALYAFFMQGIKPANQPNIPSDIPWPLNMRWPIALWNGVF
APTATYAAKPDQDALWNRGAYIVQGPGHCGSCHTPRGLAFNEKALDEAGAPFLAGALLDG
WYAPSLRQDPNTGLGRWSEPQIVQFLKTGRNAHAVVYGSMTEAFNNSTQFMQDDDLAAIA
RYLKSLPGDPQRDGAPWQYQAVAAVQDAPGAHTYATRCASCHGLDGKGQPEWMPPLAGAT
SALAKESASAINITLNGSQRVVASGVPDAYRMPAFREQLSDTEIAEVLSYVRSTWGNNGG
AVDANAVGKLRGHTDPASSSPIILHMR

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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:

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