GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_833 in Pseudomonas fluorescens FW300-N1B4

Annotation: PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)

Length: 844 amino acids

Source: pseudo1_N1B4 in FitnessBrowser

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
trehalose catabolism treEIIA hi trehalose-specific PTS system, I, HPr, and IIA components (characterized) 80% 100% 1275 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 46% 663.7
N-acetyl-D-glucosamine catabolism nagF med N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized) 46% 99% 663.7 trehalose-specific PTS system, I, HPr, and IIA components 80% 1275.0
D-glucosamine (chitosamine) catabolism nagF med N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized) 46% 99% 663.7 trehalose-specific PTS system, I, HPr, and IIA components 80% 1275.0
D-fructose catabolism fruI med Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized) 41% 87% 525.4 trehalose-specific PTS system, I, HPr, and IIA components 80% 1275.0
sucrose catabolism fruI med Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized) 41% 87% 525.4 trehalose-specific PTS system, I, HPr, and IIA components 80% 1275.0
D-cellobiose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 39% 88% 121.3 trehalose-specific PTS system, I, HPr, and IIA components 80% 1275.0
D-glucose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 39% 88% 121.3 trehalose-specific PTS system, I, HPr, and IIA components 80% 1275.0
lactose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 39% 88% 121.3 trehalose-specific PTS system, I, HPr, and IIA components 80% 1275.0
D-maltose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 39% 88% 121.3 trehalose-specific PTS system, I, HPr, and IIA components 80% 1275.0
sucrose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 39% 88% 121.3 trehalose-specific PTS system, I, HPr, and IIA components 80% 1275.0
trehalose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 39% 88% 121.3 trehalose-specific PTS system, I, HPr, and IIA components 80% 1275.0
glycerol catabolism dhaM lo PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121 (characterized) 30% 65% 119.8 trehalose-specific PTS system, I, HPr, and IIA components 80% 1275.0
N-acetyl-D-glucosamine catabolism nagEIIA lo Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 37% 73% 99 trehalose-specific PTS system, I, HPr, and IIA components 80% 1275.0
D-glucosamine (chitosamine) catabolism nagEIIA lo Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 37% 73% 99 trehalose-specific PTS system, I, HPr, and IIA components 80% 1275.0
D-maltose catabolism malEIIA lo Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 37% 73% 99 trehalose-specific PTS system, I, HPr, and IIA components 80% 1275.0
N-acetyl-D-glucosamine catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 36% 95% 83.6 trehalose-specific PTS system, I, HPr, and IIA components 80% 1275.0
D-glucosamine (chitosamine) catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 36% 95% 83.6 trehalose-specific PTS system, I, HPr, and IIA components 80% 1275.0

Sequence Analysis Tools

View Pf1N1B4_833 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MATPQQLQLLAPLSGVLMPLDQVPDQVFSSRVIGDGLCIDPTSQTLCAPLTGVISNVQVS
GHAVSITDDNGVQVLMHIGLDTVNLAGKGFTRLVEEGQRVIVGQALIEFDADYIALHARS
LLTLMLVVSGEPFTWLAPETGVVESGQPLLSLNPSEGAADEGIAQEGEALFSKPVTLPNT
NGLHARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQTAHGDVLQVSAAGADAE
VAIKTLAELLAAGCGEAVTLMAEVETVAAQVSSLTVLRGVCASPGAAFGQVVQIAEQTLE
VSESGVSPQVEREHLSRALAKAVLALQQLRDKATGDAQADIFKAHQELLEDPGLLDQALA
LIDAGKSAGFAWRAATESTATLFKKLGNALLAERAADLADVGQRVLKLILGVEDRAMELP
DGAILIAEQLTPSQTAGLDTRKVLGFATVGGGATSHVAILARASGLPAICGLPVQVLTLI
NGTRVLLDADKGELQLDPELAAIEQLQANRQLQKQRQQYELANAGLAARTRDGHHVEITA
NIASLAEAEQAMALGGDGVGLLRSEFLYLDRNHAPSHDEQASTYGAIARALGPARNLVVR
TLDVGGDKPLAYVPMDRETNPFLGMRGIRLCLERPQLLRDQFKAILSSAGLARLHIMLPM
VTQLSELRLARQLLEEEALALGLTELPKLGIMIEVPAAALMADLFAPEVDFFSIGTNDLT
QYTLAMDRDHPRLASQADSFHPSVLRLIATTVKAAHAHGKWVGVCGALASEKLAVPLLLG
LGVDELSVSVPLIPAIKAAVREVDLLDCQAIAQQVLGLESAEQVREALRRHHEATVDTSL
VLEN

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, 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