GapMind for catabolism of small carbon sources

 

Protein H281DRAFT_02703 in Paraburkholderia bryophila 376MFSha3.1

Annotation: H281DRAFT_02703 monosaccharide ABC transporter membrane protein, CUT2 family

Length: 333 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 23 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
xylitol catabolism PS417_12060 med ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) 43% 98% 253.4 Ribose import permease protein RbsC 46% 244.2
D-ribose catabolism rbsC med Ribose import permease protein RbsC (characterized) 46% 93% 244.2 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 41% 241.1
D-cellobiose catabolism mglC med 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 (characterized) 41% 99% 241.1 Ribose import permease protein RbsC 46% 244.2
D-glucose catabolism mglC med 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 (characterized) 41% 99% 241.1 Ribose import permease protein RbsC 46% 244.2
lactose catabolism mglC med 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 (characterized) 41% 99% 241.1 Ribose import permease protein RbsC 46% 244.2
D-maltose catabolism mglC med 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 (characterized) 41% 99% 241.1 Ribose import permease protein RbsC 46% 244.2
sucrose catabolism mglC med 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 (characterized) 41% 99% 241.1 Ribose import permease protein RbsC 46% 244.2
trehalose catabolism mglC med 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 (characterized) 41% 99% 241.1 Ribose import permease protein RbsC 46% 244.2
D-xylose catabolism xylH med 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 (characterized) 41% 99% 241.1 Ribose import permease protein RbsC 46% 244.2
myo-inositol catabolism iatP med Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) 41% 90% 222.6 Ribose import permease protein RbsC 46% 244.2
L-fucose catabolism HSERO_RS05255 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 39% 97% 224.9 Ribose import permease protein RbsC 46% 244.2
D-galactose catabolism BPHYT_RS16925 lo Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale) 35% 88% 203.8 Ribose import permease protein RbsC 46% 244.2
L-arabinose catabolism araH lo L-arabinose ABC transporter, permease protein AraH (characterized) 36% 98% 203.4 Ribose import permease protein RbsC 46% 244.2
D-mannose catabolism HSERO_RS03645 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 38% 90% 201.1 Ribose import permease protein RbsC 46% 244.2
L-fucose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 33% 93% 194.1 Ribose import permease protein RbsC 46% 244.2
L-rhamnose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 33% 93% 194.1 Ribose import permease protein RbsC 46% 244.2
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 36% 96% 193.4 Ribose import permease protein RbsC 46% 244.2
D-fructose catabolism frcC lo Fructose import permease protein FrcC (characterized) 33% 93% 183.7 Ribose import permease protein RbsC 46% 244.2
D-mannose catabolism frcC lo Fructose import permease protein FrcC (characterized) 33% 93% 183.7 Ribose import permease protein RbsC 46% 244.2
D-ribose catabolism frcC lo Fructose import permease protein FrcC (characterized) 33% 93% 183.7 Ribose import permease protein RbsC 46% 244.2
sucrose catabolism frcC lo Fructose import permease protein FrcC (characterized) 33% 93% 183.7 Ribose import permease protein RbsC 46% 244.2
D-galactose catabolism yjtF lo Inner membrane ABC transporter permease protein YjfF (characterized) 37% 85% 171 Ribose import permease protein RbsC 46% 244.2
L-arabinose catabolism araZsh lo Inner-membrane translocator (characterized, see rationale) 36% 90% 170.2 Ribose import permease protein RbsC 46% 244.2

Sequence Analysis Tools

View H281DRAFT_02703 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

MTSTAANRADTEALSRRVIRQLRSGIGPLFAALVIICIALSIASPEFLTTSTLTNIMVQV
SVVGIAAVGGTFVIITSGIDLSVGSLVALTGMVAATVMAGSSPGAIGLGIAGLCAALAVG
AAAGALNGLAVAWLRLVPFIVTLAMMAMARGLTLAISDGRTKFDFPNAFTAFGAKTVAGL
PMPMIVMLVIFVIGHVLLRKTTFGHQVFAVGGNQEAARLAGIPVHRVVFLTYMLAGVTAA
IAGIVLAGRLNSALPSAANGLELQVIAAVVIGGTSLAGGRGSIVGTFIGVVLIGVINVGL
SLLGVNPFWTQFIQGGVIFAAVLLDALSQRRKQ

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