GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_4287 in Pseudomonas fluorescens FW300-N1B4

Annotation: FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4287

Length: 340 amino acids

Source: pseudo1_N1B4 in FitnessBrowser

Candidate for 31 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
myo-inositol catabolism PS417_11895 hi m-Inositol ABC transporter, permease component (iatP) (characterized) 98% 100% 632.1 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 40% 228.0
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) 45% 100% 267.3 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
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) 40% 97% 228 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
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) 40% 97% 228 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
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) 40% 97% 228 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
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) 40% 97% 228 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
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) 40% 97% 228 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
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) 40% 97% 228 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
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) 40% 97% 228 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
D-fructose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 43% 87% 216.9 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
sucrose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 43% 87% 216.9 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
D-mannose catabolism HSERO_RS03645 med ABC-type sugar transport system, permease component protein (characterized, see rationale) 41% 95% 215.3 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
D-ribose catabolism rbsC med ABC transporter permease (characterized, see rationale) 40% 84% 179.9 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
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) 38% 97% 217.6 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 35% 99% 208.4 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
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) 38% 99% 202.6 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
L-fucose catabolism HSERO_RS05255 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 33% 97% 192.2 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
L-arabinose catabolism araH lo L-arabinose ABC transporter, permease protein AraH (characterized) 36% 82% 180.3 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
D-galactose catabolism BPHYT_RS16925 lo Arabinose ABC transporter permease (characterized, see rationale) 33% 98% 179.1 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
D-mannose catabolism frcC lo Fructose import permease protein FrcC (characterized) 33% 89% 176.8 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
D-ribose catabolism frcC lo Fructose import permease protein FrcC (characterized) 33% 89% 176.8 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
D-galactose catabolism ytfT lo Galactofuranose transporter permease protein YtfT (characterized) 33% 95% 174.9 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
L-arabinose catabolism araZsh lo Inner-membrane translocator (characterized, see rationale) 34% 99% 166.8 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
L-arabinose catabolism araWsh lo Inner-membrane translocator (characterized, see rationale) 34% 77% 164.9 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
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% 93% 163.7 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
D-fructose catabolism fruG lo Fructose import permease protein FruG (characterized) 32% 97% 156.8 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
sucrose catabolism fruG lo Fructose import permease protein FruG (characterized) 32% 97% 156.8 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
D-fructose catabolism fruF lo Fructose import permease protein FruF (characterized) 32% 82% 150.2 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
sucrose catabolism fruF lo Fructose import permease protein FruF (characterized) 32% 82% 150.2 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
L-arabinose catabolism xylHsa lo Xylose/arabinose import permease protein XylH (characterized, see rationale) 30% 88% 139 m-Inositol ABC transporter, permease component (iatP) 98% 632.1
D-galactose catabolism yjtF lo Inner membrane ABC transporter permease protein YjfF (characterized) 31% 93% 137.9 m-Inositol ABC transporter, permease component (iatP) 98% 632.1

Sequence Analysis Tools

View Pf1N1B4_4287 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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Sequence

MNAILENKPAAVPVKSRRRFPTELSIFLVLIGIGLVFEMFGWIVRDQSFLMNSQRLVLMI
LQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVW
IPVIVGLGVGLLAGAINGSIIAITGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYT
AIGHGAMPVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIA
GLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGV
MASGFTFVGVDAYIQDIIKGLIIVVAVVIDQYRNKRKLKR

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:

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