GapMind for catabolism of small carbon sources

 

Protein H281DRAFT_03379 in Paraburkholderia bryophila 376MFSha3.1

Annotation: H281DRAFT_03379 monosaccharide ABC transporter membrane protein, CUT2 family

Length: 343 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 14 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-fucose catabolism HSERO_RS05255 hi ABC-type sugar transport system, permease component protein (characterized, see rationale) 43% 90% 252.7 Ribose import permease protein RbsC 47% 239.2
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) 42% 94% 235.3 Ribose import permease protein RbsC 47% 239.2
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) 42% 94% 235.3 Ribose import permease protein RbsC 47% 239.2
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) 42% 94% 235.3 Ribose import permease protein RbsC 47% 239.2
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) 42% 94% 235.3 Ribose import permease protein RbsC 47% 239.2
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) 42% 94% 235.3 Ribose import permease protein RbsC 47% 239.2
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) 42% 94% 235.3 Ribose import permease protein RbsC 47% 239.2
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) 42% 94% 235.3 Ribose import permease protein RbsC 47% 239.2
myo-inositol catabolism PS417_11895 med Inositol transport system permease protein (characterized) 40% 99% 230.3 Ribose import permease protein RbsC 47% 239.2
D-fructose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 43% 91% 214.2 Ribose import permease protein RbsC 47% 239.2
sucrose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 43% 91% 214.2 Ribose import permease protein RbsC 47% 239.2
D-mannose catabolism frcC lo Fructose import permease protein FrcC (characterized) 36% 90% 188 Ribose import permease protein RbsC 47% 239.2
D-ribose catabolism frcC lo Fructose import permease protein FrcC (characterized) 36% 90% 188 Ribose import permease protein RbsC 47% 239.2
myo-inositol catabolism PGA1_c07310 lo Inositol transport system permease protein (characterized) 32% 91% 149.1 Ribose import permease protein RbsC 47% 239.2

Sequence Analysis Tools

View H281DRAFT_03379 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

MLEITSGRTQALDKQARQRRRDLIQKFAALGSLVVLIVAFSLTSAAFFSVGNLMTVALQV
TSIAYLGVAATCVIITGGIDLSVGSVLALAGVAAALLVKAGVPVPVAMAGGMLVGAACGW
VNGICVTRMGLPPFIATLGMMLVARGLALQITGARPVSGLGDAFGELGNGALFKVSHIGA
DGFPDTVFPGIPYPVVIMVILFVAVSVLLSRTSLGRHIYAVGSNAEAARLSGVNVQGVKL
FTYVLSGLLAGATGCVLMSRLVTAQPNEGVMYELDAIASAVIGGTSLMGGVGTISGTAIG
AFVIGVLRNGLNMNGVSSFIQQIIIGVVILGTVWIDQLRNRKL

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