GapMind for catabolism of small carbon sources

 

Protein WP_085635685.1 in Marivita geojedonensis DPG-138

Annotation: NCBI__GCF_002115805.1:WP_085635685.1

Length: 358 amino acids

Source: GCF_002115805.1 in NCBI

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-fructose catabolism frcC hi Fructose import permease protein FrcC (characterized) 67% 98% 474.2 Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR 33% 176.8
D-mannose catabolism frcC hi Fructose import permease protein FrcC (characterized) 67% 98% 474.2 Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR 33% 176.8
D-ribose catabolism frcC hi Fructose import permease protein FrcC (characterized) 67% 98% 474.2 Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR 33% 176.8
sucrose catabolism frcC hi Fructose import permease protein FrcC (characterized) 67% 98% 474.2 Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR 33% 176.8
L-fucose catabolism HSERO_RS05255 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 34% 97% 183.3 Fructose import permease protein FrcC 67% 474.2
D-cellobiose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 32% 99% 150.2 Fructose import permease protein FrcC 67% 474.2
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 32% 99% 150.2 Fructose import permease protein FrcC 67% 474.2
D-glucose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 32% 99% 150.2 Fructose import permease protein FrcC 67% 474.2
lactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 32% 99% 150.2 Fructose import permease protein FrcC 67% 474.2
D-maltose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 32% 99% 150.2 Fructose import permease protein FrcC 67% 474.2
sucrose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 32% 99% 150.2 Fructose import permease protein FrcC 67% 474.2
trehalose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 32% 99% 150.2 Fructose import permease protein FrcC 67% 474.2
D-ribose catabolism rbsC lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 30% 90% 148.3 Fructose import permease protein FrcC 67% 474.2
L-arabinose catabolism araZsh lo Inner-membrane translocator (characterized, see rationale) 31% 93% 140.2 Fructose import permease protein FrcC 67% 474.2
L-fucose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 31% 95% 140.2 Fructose import permease protein FrcC 67% 474.2
L-rhamnose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 31% 95% 140.2 Fructose import permease protein FrcC 67% 474.2
D-fructose catabolism fruF lo Fructose import permease protein FruF (characterized) 33% 79% 129.8 Fructose import permease protein FrcC 67% 474.2
sucrose catabolism fruF lo Fructose import permease protein FruF (characterized) 33% 79% 129.8 Fructose import permease protein FrcC 67% 474.2

Sequence Analysis Tools

View WP_085635685.1 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

MASDRTNDNYESALSGASTDVASFEYHKKGFVGRLHDLLHTNPALVPLIVLVAAIIIFGI
ALGSKFFSPFALTLILQQVQIVGVLAAAQSLIILTAGIDLSVGAMAVISSVIMGQFTFRY
GLPAPMAVAAGLAIGTAIGALNGWLVSRVKLPPFIVTLGMWQIVLAANYLFSRNETIRAQ
DIEANAPFLHFMGYKFQIGGATFTLGVLVMILLVLLLAYVLRNTAWGRHVYAVGDDPEAA
QLAGVDVHKTLMSVYMLVGFICALAGWVMIGRFGSVSPSASTGMMGNIQSITAVVIGGIS
LFGGRGSILGAFFGALIVGVFELGLRMAGADPQWTFLLIGALIIAAVSVDQWIRKVSA

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