GapMind for catabolism of small carbon sources

 

Protein PfGW456L13_2122 in Pseudomonas fluorescens GW456-L13

Annotation: L-arabinose transport system permease protein (TC 3.A.1.2.2)

Length: 323 amino acids

Source: pseudo13_GW456_L13 in FitnessBrowser

Candidate for 25 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-galactose catabolism BPHYT_RS16925 hi Arabinose ABC transporter permease (characterized, see rationale) 98% 100% 609 L-arabinose ABC transporter, permease protein AraH 60% 385.2
L-arabinose catabolism araH hi L-arabinose ABC transporter, permease protein AraH (characterized) 60% 98% 385.2 Ribose import permease protein RbsC 36% 214.5
D-ribose catabolism rbsC lo Ribose import permease protein RbsC (characterized) 36% 100% 214.5 L-arabinose ABC transporter, permease protein AraH 60% 385.2
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) 35% 100% 203.4 L-arabinose ABC transporter, permease protein AraH 60% 385.2
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% 94% 196.8 L-arabinose ABC transporter, permease protein AraH 60% 385.2
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% 94% 196.8 L-arabinose ABC transporter, permease protein AraH 60% 385.2
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% 94% 196.8 L-arabinose ABC transporter, permease protein AraH 60% 385.2
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% 94% 196.8 L-arabinose ABC transporter, permease protein AraH 60% 385.2
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% 94% 196.8 L-arabinose ABC transporter, permease protein AraH 60% 385.2
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% 94% 196.8 L-arabinose ABC transporter, permease protein AraH 60% 385.2
D-xylose catabolism xylF_Tm lo ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized) 36% 94% 196.8 L-arabinose ABC transporter, permease protein AraH 60% 385.2
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% 94% 196.8 L-arabinose ABC transporter, permease protein AraH 60% 385.2
L-fucose catabolism HSERO_RS05255 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 35% 83% 183.3 L-arabinose ABC transporter, permease protein AraH 60% 385.2
myo-inositol catabolism PS417_11895 lo Inositol transport system permease protein (characterized) 33% 97% 180.3 L-arabinose ABC transporter, permease protein AraH 60% 385.2
D-fructose catabolism frcC lo Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 33% 88% 176.4 L-arabinose ABC transporter, permease protein AraH 60% 385.2
sucrose catabolism frcC lo Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 33% 88% 176.4 L-arabinose ABC transporter, permease protein AraH 60% 385.2
D-mannose catabolism HSERO_RS03645 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 33% 88% 175.3 L-arabinose ABC transporter, permease protein AraH 60% 385.2
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 35% 94% 170.2 L-arabinose ABC transporter, permease protein AraH 60% 385.2
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% 98% 168.3 L-arabinose ABC transporter, permease protein AraH 60% 385.2
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) 32% 93% 161 L-arabinose ABC transporter, permease protein AraH 60% 385.2
L-rhamnose catabolism rhaQ lo RhaQ (characterized, see rationale) 31% 92% 156.4 L-arabinose ABC transporter, permease protein AraH 60% 385.2
L-fucose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 31% 85% 155.6 L-arabinose ABC transporter, permease protein AraH 60% 385.2
L-rhamnose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 31% 85% 155.6 L-arabinose ABC transporter, permease protein AraH 60% 385.2
D-mannose catabolism frcC lo Fructose import permease protein FrcC (characterized) 31% 83% 140.6 L-arabinose ABC transporter, permease protein AraH 60% 385.2
D-ribose catabolism frcC lo Fructose import permease protein FrcC (characterized) 31% 83% 140.6 L-arabinose ABC transporter, permease protein AraH 60% 385.2

Sequence Analysis Tools

View PfGW456L13_2122 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MMTTQNNTLPTTRKPLDLRRFLDDWVMLLAAVGIFVACTLLIDNFLSPLNMRGLGLAIST
TGIAACTMLYCLASGHFDLSVGSVIACAGVVAAVVMRDTNSVFLGVCAALVMGLIVGLIN
GIVIAKLRVNALITTLATMQIVRGLAYIFANGKAVGVSQESFFVFGNGQMFGVPVPILIT
IVCFLFFGWLLNYTTYGRNTMAIGGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILA
SRMTSGQPMIGQGFELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDT
FYQYVIRGSILLLAVVIDRLKQR

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 paper from 2022 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