GapMind for catabolism of small carbon sources

 

Protein WP_066604618.1 in Sphingobium czechense LL01

Annotation: NCBI__GCF_001046645.1:WP_066604618.1

Length: 259 amino acids

Source: GCF_001046645.1 in NCBI

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
citrate catabolism fecE med iron(III) dicitrate transport ATP-binding protein FecE (characterized) 41% 96% 179.9 CchE, component of Ferric iron-coelichelin uptake porter, CchCDEF 42% 201.8
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 94% 97.1 CchE, component of Ferric iron-coelichelin uptake porter, CchCDEF 42% 201.8
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 94% 97.1 CchE, component of Ferric iron-coelichelin uptake porter, CchCDEF 42% 201.8
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 94% 97.1 CchE, component of Ferric iron-coelichelin uptake porter, CchCDEF 42% 201.8
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 94% 97.1 CchE, component of Ferric iron-coelichelin uptake porter, CchCDEF 42% 201.8
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 32% 87% 95.9 CchE, component of Ferric iron-coelichelin uptake porter, CchCDEF 42% 201.8
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 33% 84% 93.2 CchE, component of Ferric iron-coelichelin uptake porter, CchCDEF 42% 201.8
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 33% 84% 93.2 CchE, component of Ferric iron-coelichelin uptake porter, CchCDEF 42% 201.8
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 33% 84% 93.2 CchE, component of Ferric iron-coelichelin uptake porter, CchCDEF 42% 201.8
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 33% 84% 93.2 CchE, component of Ferric iron-coelichelin uptake porter, CchCDEF 42% 201.8
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 33% 84% 93.2 CchE, component of Ferric iron-coelichelin uptake porter, CchCDEF 42% 201.8
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 33% 84% 93.2 CchE, component of Ferric iron-coelichelin uptake porter, CchCDEF 42% 201.8

Sequence Analysis Tools

View WP_066604618.1 at NCBI

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

MVTISAQGLTVRLGRHAAVRDVDVRLEPGALVGVIGPNGAGKSTLIRALLGLVKPQAGRV
LIDGQNVTRLDRRAMARAVAYLPQGQTLHWPLSVERLVALGRLPHLGPLSRMSADDEAVI
EAAMVRADVQHLKGRTATELSGGERARVLLARALAVGAHGLIADEPLAALDPGHQIDVMD
LLRGEARGGALVVTVLHDLGMAARYCDRLLLMDGGALVADGAPMDVLTAGALARVYGVTA
RIERDGDVPLIVPMARVNE

This GapMind analysis is from Sep 24 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:

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