GapMind for catabolism of small carbon sources

 

Protein GFF2762 in Phaeobacter inhibens BS107

Annotation: PGA1_c28050 putative sugar transport system, permease protein

Length: 353 amino acids

Source: Phaeo in FitnessBrowser

Candidate for 24 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) 74% 97% 514.2 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 36% 193.7
D-mannose catabolism frcC hi Fructose import permease protein FrcC (characterized) 74% 97% 514.2 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 36% 193.7
D-ribose catabolism frcC hi Fructose import permease protein FrcC (characterized) 74% 97% 514.2 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 36% 193.7
sucrose catabolism frcC hi Fructose import permease protein FrcC (characterized) 74% 97% 514.2 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 36% 193.7
xylitol catabolism PS417_12060 lo ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) 38% 91% 202.2 Fructose import permease protein FrcC 74% 514.2
D-cellobiose catabolism mglC lo 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) 36% 96% 193.7 Fructose import permease protein FrcC 74% 514.2
D-glucose catabolism mglC lo 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) 36% 96% 193.7 Fructose import permease protein FrcC 74% 514.2
lactose catabolism mglC lo 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) 36% 96% 193.7 Fructose import permease protein FrcC 74% 514.2
D-maltose catabolism mglC lo 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) 36% 96% 193.7 Fructose import permease protein FrcC 74% 514.2
sucrose catabolism mglC lo 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) 36% 96% 193.7 Fructose import permease protein FrcC 74% 514.2
trehalose catabolism mglC lo 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) 36% 96% 193.7 Fructose import permease protein FrcC 74% 514.2
D-xylose catabolism xylH lo 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) 36% 96% 193.7 Fructose import permease protein FrcC 74% 514.2
L-fucose catabolism HSERO_RS05255 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 35% 86% 188.7 Fructose import permease protein FrcC 74% 514.2
D-mannose catabolism HSERO_RS03645 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 37% 91% 184.5 Fructose import permease protein FrcC 74% 514.2
D-ribose catabolism rbsC lo Ribose import permease protein RbsC (characterized) 36% 93% 176 Fructose import permease protein FrcC 74% 514.2
myo-inositol catabolism PS417_11895 lo Inositol transport system permease protein (characterized) 35% 91% 167.9 Fructose import permease protein FrcC 74% 514.2
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 33% 94% 157.1 Fructose import permease protein FrcC 74% 514.2
myo-inositol catabolism iatP lo 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) 32% 99% 155.6 Fructose import permease protein FrcC 74% 514.2
L-rhamnose catabolism rhaQ lo RhaQ (characterized, see rationale) 31% 90% 149.1 Fructose import permease protein FrcC 74% 514.2
myo-inositol catabolism PGA1_c07310 lo Inositol transport system permease protein (characterized) 30% 98% 144.4 Fructose import permease protein FrcC 74% 514.2
L-arabinose catabolism araZsh lo Inner-membrane translocator (characterized, see rationale) 31% 98% 143.7 Fructose import permease protein FrcC 74% 514.2
D-galactose catabolism yjtF lo Inner membrane ABC transporter permease protein YjfF (characterized) 30% 92% 141.4 Fructose import permease protein FrcC 74% 514.2
L-rhamnose catabolism rhaP lo RhaP, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized) 31% 89% 139.4 Fructose import permease protein FrcC 74% 514.2
D-galactose catabolism ytfT lo Galactofuranose transporter permease protein YtfT (characterized) 30% 90% 127.1 Fructose import permease protein FrcC 74% 514.2

Sequence Analysis Tools

View GFF2762 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

MTTPQSYEAAASGSPEAVADFDQGETSFISRFQHMLHVTPSLVPLIVLVLSVIVFGLLLG
SKFFSPFALTLILQQVGIVGIVACAQSLVILTAGIDLSVGAIMVLSSVVMGQFTFRYGLP
PEVAVACGLICGTICGFINGWLVARMKLPPFIVTLGMWQIVLASNFLYSANETIRSQTIA
AEAPLLQLFGEKIKIGGAVFTYGVIFMVILVVLLAYVLRHTAWGRHVYAVGDDPEAAELS
GVKVTRVLISVYMLSGLICAFAGWAMIGRIGSVSPTSGQLANIESITAVVIGGISLFGGR
GSILGTFFGALIVGVFTLGLRLLGADAQWTYLLIGLLIIAAVAVDQWIRKVSV

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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