GapMind for catabolism of small carbon sources

 

Protein PfGW456L13_5075 in Pseudomonas fluorescens GW456-L13

Annotation: Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)

Length: 953 amino acids

Source: pseudo13_GW456_L13 in FitnessBrowser

Candidate for 9 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-fructose catabolism fruI hi Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized) 93% 100% 1715.7 D-trehalose PTS system, I, HPr, and IIA components 45% 505.4
sucrose catabolism fruI hi Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized) 93% 100% 1715.7 D-trehalose PTS system, I, HPr, and IIA components 45% 505.4
trehalose catabolism treEIIA med D-trehalose PTS system, I, HPr, and IIA components (characterized) 45% 78% 505.4 Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) 93% 1715.7
N-acetyl-D-glucosamine catabolism nagF med N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized) 42% 80% 458.4 Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) 93% 1715.7
D-glucosamine (chitosamine) catabolism nagF med N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized) 42% 80% 458.4 Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) 93% 1715.7
D-fructose catabolism fruB lo Multiphosphoryl transfer protein; MTP; Diphosphoryl transfer protein; DTP; Phosphotransferase FPr protein; Pseudo-HPr (characterized) 40% 99% 242.3 Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) 93% 1715.7
sucrose catabolism fruB lo Multiphosphoryl transfer protein; MTP; Diphosphoryl transfer protein; DTP; Phosphotransferase FPr protein; Pseudo-HPr (characterized) 40% 99% 242.3 Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) 93% 1715.7
glycerol catabolism dhaM lo PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121 (characterized) 32% 68% 119.4 Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) 93% 1715.7
D-mannitol catabolism cmtB lo Mannitol-specific phosphotransferase enzyme IIA component (characterized, see rationale) 38% 94% 99 Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) 93% 1715.7

Sequence Analysis Tools

View PfGW456L13_5075 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

MLELTVEQISMGQSAVDKSAALQLLAGHLVADGLVAEGYLAGLQAREAQGSTFLGQGIAI
PHGTPETRDLVFTTGVRLMQFPDGVDWGDGHIVYLAIGIAAKSDEHLRLLQLLTRALGET
DLGQALRRAGSAEALLKLLQGAPQELALDAQMIGLGVAAEDFEELVWRGARLLRQADCVS
NGFSAVLQQVEALPLGDGLWWLHSEQTVKRPGLAFVTPDRPLRYLGQPLTGLFCLASLGE
AHQALLERLCALLIEGRGHELGRATSSRKVLEVLGGEVPADWPSARIALANAHGLHARPA
KILAQLAKSFEGDIRVRIVDGHDSAVSVKSLSKLLSLGARRGQVLEIIAEPGIAADALPA
LLAAIEEGLGEEVEPLPPVSQAREVVADMAEVVLAPSSGSVVQAIAAAPGFAIGPAHIQV
LQTIDYPLRGESAGIERERLQHALAQVRRDIQGLIERSKSKAIREIFITHQEMLDDPELT
DEVDTRLKQGESAEAAWMAVIEAAARQQETLQDALLAERAADLRDIGRRVLMQLSGIETP
SEPDQPYILVMDEVGPSDVARLDPARVAGILTARGGATAHSAIVARALGIPALVGAGPGV
LLLAPGTALLLDGQRGRLHVDADAATLQRATAERDTREQRLKAAAELRHQPALTIDGHAV
EVFANIGESAGVTSAVEQGAEGIGLLRTELIFMAHPQVPDEATQEVEYRRVLDGLAGRPL
VVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQIMEAQLRALLRAADNRPLRIM
FPMVGSVDEWRQARDMTERLRQEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTND
LTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVL
VGLGVDELSVGARSIAEVKARIRELGFTQTQTLARQALAVGSANEVRALVEAL

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