GapMind for catabolism of small carbon sources

 

Protein PfGW456L13_5073 in Pseudomonas fluorescens GW456-L13

Annotation: PTS system, fructose-specific IIB component (EC 2.7.1.69) / PTS system, fructose-specific IIC component (EC 2.7.1.69)

Length: 579 amino acids

Source: pseudo13_GW456_L13 in FitnessBrowser

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-fructose catabolism fruA hi Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized) 74% 98% 811.2 The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system 46% 449.9
sucrose catabolism fruA hi Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized) 74% 98% 811.2 The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system 46% 449.9
D-fructose catabolism fruII-ABC med The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system (characterized) 46% 80% 449.9 Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 74% 811.2
sucrose catabolism fruII-ABC med The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system (characterized) 46% 80% 449.9 Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 74% 811.2
D-mannose catabolism manP med protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized) 45% 72% 392.9 Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 74% 811.2
D-fructose catabolism fruII-C med Sugar phosphotransferase system IIC component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized) 45% 93% 302.8 Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 74% 811.2
sucrose catabolism fruII-C med Sugar phosphotransferase system IIC component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized) 45% 93% 302.8 Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 74% 811.2
D-fructose catabolism fruII-B med PTS system, fructose-specific, IIB subunnit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized) 46% 76% 97.8 Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 74% 811.2
sucrose catabolism fruII-B med PTS system, fructose-specific, IIB subunnit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized) 46% 76% 97.8 Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 74% 811.2
D-ribose catabolism fru2-IIB med PTS system, fructose-specific, IIB component, component of D-allose/D-ribose transporting Enzyme II complex (Fru2; IIA/IIB/IIC) (Patron et al. 2017). This system is similar to Frz of E. coli (TC#4.A.2.1.9) which is involved in environmental sensing, host adaptation and virulence (characterized) 42% 94% 91.7 Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 74% 811.2
xylitol catabolism fruI lo The fructose inducible fructose/xylitol porter, FruI (characterized) 38% 90% 342.8 Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 74% 811.2
D-ribose catabolism fru2-IIC lo PTS system, fructose-specific, IIC component, component of D-allose/D-ribose transporting Enzyme II complex (Fru2; IIA/IIB/IIC) (Patron et al. 2017). This system is similar to Frz of E. coli (TC#4.A.2.1.9) which is involved in environmental sensing, host adaptation and virulence (characterized) 35% 95% 218 Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA 74% 811.2

Sequence Analysis Tools

View PfGW456L13_5073 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

MKLAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVTDAAHPEKQLSAATLDAAEWVL
LVTSAPVEMSRFVGKRVFQSTPAQALQDVEAVLRRGAQDAQVYAAEEAAVEPVAVVQNAP
RLVAVTACPTGVAHTFMAAEALQQAAKRLGYELQVETQGSVGARNPLSAQAIAEADVVLL
AADIEVATERFAGKKIYRCGTGIALKQAEATLKKALAEGQQESASSAAKTTAKQEKTGVY
KHLLTGVSFMLPMVVAGGLMIALSFVFGITAFKEEGTLAAALMQIGGDSAFKLMVPLLAG
YIAYSIADRPGLAPGMIGGLLASTLGAGFIGGIIAGFLAGYAARAINRYARLPQSLEALK
PILIIPLLASLFTGLVMIYVVGKPVAGMLAGLTNFLDSMGTTNAILLGVLLGGMMCVDLG
GPINKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGLGIATFIARRKFAQTEREAGKAAL
VLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLMAPHGGLFVLAIPNAI
NHALLYLLAIVAGSLLTAVAYALVKRPEVVELAVEPVTA

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