GapMind for catabolism of small carbon sources

 

Protein Ga0059261_1646 in Sphingomonas koreensis DSMZ 15582

Annotation: Ga0059261_1646 Phosphocarrier protein HPr/phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9)/PTS system IIA component, Glc family (TC 4.A.1)

Length: 830 amino acids

Source: Korea in FitnessBrowser

Candidate for 16 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
N-acetyl-D-glucosamine catabolism nagF hi N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized) 46% 98% 654.8 D-trehalose PTS system, I, HPr, and IIA components 42% 603.6
D-glucosamine (chitosamine) catabolism nagF hi N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized) 46% 98% 654.8 D-trehalose PTS system, I, HPr, and IIA components 42% 603.6
trehalose catabolism treEIIA med D-trehalose PTS system, I, HPr, and IIA components (characterized) 42% 98% 603.6 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 46% 654.8
D-fructose catabolism fruI med Multiphosphoryl transfer protein; MTP; Triphosphoryl transfer protein; TTP; EC 2.7.3.9 (characterized) 43% 80% 479.6 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 46% 654.8
sucrose catabolism fruI med Multiphosphoryl transfer protein; MTP; Triphosphoryl transfer protein; TTP; EC 2.7.3.9 (characterized) 43% 80% 479.6 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 46% 654.8
D-cellobiose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 42% 73% 113.6 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 46% 654.8
D-glucose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 42% 73% 113.6 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 46% 654.8
lactose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 42% 73% 113.6 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 46% 654.8
D-maltose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 42% 73% 113.6 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 46% 654.8
sucrose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 42% 73% 113.6 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 46% 654.8
trehalose catabolism crr med PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 42% 73% 113.6 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 46% 654.8
N-acetyl-D-glucosamine catabolism crr med Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 44% 83% 97.1 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 46% 654.8
D-glucosamine (chitosamine) catabolism crr med Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 44% 83% 97.1 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 46% 654.8
N-acetyl-D-glucosamine catabolism nagEIIA lo Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 39% 80% 118.2 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 46% 654.8
D-glucosamine (chitosamine) catabolism nagEIIA lo Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 39% 80% 118.2 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 46% 654.8
D-maltose catabolism malEIIA lo Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 39% 80% 118.2 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 46% 654.8

Sequence Analysis Tools

View Ga0059261_1646 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

MALIITSPLRGWAAPLDSVPDPVFAQRMMGDGVAIQPLADTVCAPFDGEVVTLHEAGHAV
SLRSDEGAEVLIHIGLDTVGLKGRGFTPLVAPGATVARGDPLIRFDMDAVALGATSLITP
VIVTNAEAFTITRRTMGRAIGAHEELMALAPARTQPRRWSDDGTVIEERVTLILPHGIHA
RPAARLGECARQFEAEIHLLHGDKRGDARSTVGLLALGTRLGDELVVQARGSDAEAALAA
IVALLGSDMGEGAPAHAPAIAVPAAPVLQPGQIGGVIASPGLAMGPAARLRQTAIAVERE
GKGVDAERTALDAARTEVRVRIGARADAAGGSVAAVMRAHLALLDDPELAAGAETRIAAG
NSAGYAWRGAVHDQIAALKATGNAHLIERTDDLVDIERQVLGVLTGIPAEADAIAAGAIL
VADDLLPSQLVSIAASKPAGICLVRGGPTSHVAILCAGMGLPALVAMGDAIEAIEDGTAL
LLDAEAGHVTPDPSQADADAFAARLAKREARRDAARAAAGNACQTADGVRIELFANLGTV
EDAKAAAAQGAEGSGLVRSEFLFLDREDAPSEDEQHAAYQGIADALPGKPVIVRLLDVGG
DKPAAYIPFDAEENPALGLRGIRVGLAHRDLLETQIRAILRVQPVGQCRIMLPMVASVSE
IRAVREVVERLRGEMGIETPIEVGVMVETPAAAITADLLAAEADFLSIGTNDLTQYVLAM
DRGNPAVASGVDAMHPAVLRMIAETCRRATAKGRWVGVCGGLASDPAAVPILIGLGATEL
STVPGFVPEAKAIVRSVTLADARDHAERALHCSSAAEVRALARAFEEKNA

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