GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_1146 in Pseudomonas fluorescens FW300-N1B4

Annotation: FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1146

Length: 953 amino acids

Source: pseudo1_N1B4 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) 100% 100% 1825.1 D-trehalose PTS system, I, HPr, and IIA components 44% 512.3
sucrose catabolism fruI hi Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized) 100% 100% 1825.1 D-trehalose PTS system, I, HPr, and IIA components 44% 512.3
trehalose catabolism treEIIA med D-trehalose PTS system, I, HPr, and IIA components (characterized) 44% 82% 512.3 Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) 100% 1825.1
N-acetyl-D-glucosamine catabolism nagF med N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized) 42% 80% 466.5 Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) 100% 1825.1
D-glucosamine (chitosamine) catabolism nagF med N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized) 42% 80% 466.5 Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) 100% 1825.1
D-fructose catabolism fruB lo Multiphosphoryl transfer protein; MTP; Diphosphoryl transfer protein; DTP; Phosphotransferase FPr protein; Pseudo-HPr (characterized) 40% 99% 244.2 Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) 100% 1825.1
sucrose catabolism fruB lo Multiphosphoryl transfer protein; MTP; Diphosphoryl transfer protein; DTP; Phosphotransferase FPr protein; Pseudo-HPr (characterized) 40% 99% 244.2 Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) 100% 1825.1
glycerol catabolism dhaM lo PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121 (characterized) 31% 68% 119.8 Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) 100% 1825.1
D-mannitol catabolism cmtB lo Mannitol-specific phosphotransferase enzyme IIA component (characterized, see rationale) 39% 94% 102.4 Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) 100% 1825.1

Sequence Analysis Tools

View Pf1N1B4_1146 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MLELTIEQISMGQSAVDKATALQLLADRLVTDGLVADGYLAGLQAREAQGSTFLGQGIAI
PHGTPQTRDLVFSTGVRLMQFPDGVDWGDGQIVYLAIGIAAKSDEHLRLLQLLTRALGET
DLGQALRRASTAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS
NGFAGVLQQVDALPLGDGLWWLHSEQTVKRPGLAFVTPDKPMRYLGQPLSGLFCLASLGE
AHQALLERLCALLIEGRGHELGRATSSRAVLEVLGGEVPADWPSARIALANTHGLHARPA
KILAQLAKSFEGEIRVRIVDGHDSAVSVKSLSKLLSLGARRGQVLEFIAEPTIAADALPA
LLAAIEEGLGEEVEPLPAVSQHREVIADVAEVLLAPASGSLIQAIAAAPGIAIGPAHIQV
QQVIDYPLRGESAAIERERLKQALADVRRDIEGLIERSKAKAIREIFITHQEMLDDPELT
DEVDTRLKQGESAEAAWMAVIEAAAKQQESLQDALLAERAADLRDIGRRVLAQLSGVETP
AEPEQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAV
LLLKPGTPLLIDGQRGRLHVDADAATLQRATEERDTRELRLKAAAEQRHQPALTTDGHAV
EVFANIGESAGVTSAVEQGAEGIGLLRTELIFMAHSQAPDEATQEVEYRRVLDGLAGRPL
VVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQVMEAQLRALLRAADNRPLRIM
FPMVGSVDEWRQARDMTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTND
LTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVL
VGLGVDELSVSGRSIAEVKARIRELSLTQTQTLAQQALAVGSANEVRALVEAL

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