GapMind for catabolism of small carbon sources

 

Protein CCNA_00571 in Caulobacter crescentus NA1000

Annotation: FitnessBrowser__Caulo:CCNA_00571

Length: 878 amino acids

Source: Caulo 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) 48% 98% 689.9 D-trehalose PTS system, I, HPr, and IIA components 44% 639.8
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) 48% 98% 689.9 D-trehalose PTS system, I, HPr, and IIA components 44% 639.8
trehalose catabolism treEIIA med D-trehalose PTS system, I, HPr, and IIA components (characterized) 44% 98% 639.8 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 689.9
D-fructose catabolism fruI med Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized) 45% 70% 512.7 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 689.9
sucrose catabolism fruI med Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized) 45% 70% 512.7 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 689.9
N-acetyl-D-glucosamine catabolism nagEIIA med Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 45% 74% 126.7 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 689.9
D-glucosamine (chitosamine) catabolism nagEIIA med Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 45% 74% 126.7 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 689.9
D-maltose catabolism malEIIA med Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 45% 74% 126.7 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 689.9
D-cellobiose catabolism crr med glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 41% 84% 124 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 689.9
D-glucose catabolism crr med glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 41% 84% 124 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 689.9
lactose catabolism crr med glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 41% 84% 124 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 689.9
D-maltose catabolism crr med glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 41% 84% 124 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 689.9
sucrose catabolism crr med glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 41% 84% 124 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 689.9
trehalose catabolism crr med glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 41% 84% 124 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 689.9
N-acetyl-D-glucosamine catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 38% 99% 91.3 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 689.9
D-glucosamine (chitosamine) catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 38% 99% 91.3 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 689.9

Sequence Analysis Tools

View CCNA_00571 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

MQKWPCQMVLKWNVVRSAGWTLAERGIQMSALVLTAPLQGWVSALEEAPDAVFAERMLGD
GLAIDPLGSTLHAPCDGSVVSVHRARHAVTLRATNGAEILMHVGLETVALNGEGFEVFVE
EGQTVKAGDRLIGLDLDLLAQRARSLITPVVITNGEAFQIVRRDQDRQIGVGQFLMELSP
IAGASRAAASGAADQITRQIIVPLAHGIHARPAARIAQMAKTFASDLTLATGPRRANARS
PVGLMSLAIRHGDTIQLLASGPDAQAAVTALAELIEGGMGEGAPVAAKTSSTKTAPTKTE
PSEPPPPAPLPRDGVLKGVPAAPGLAIGKAVRLSTAEIVVREAGEGVAHEEAALAVALET
VRARIGKAAETGDKARKAILAAHQAFLDDPELYAGAHRLIAEGKSAGFAWRRAVGGYVQA
LQALGDRRMAERVDDLIDLERQVLRALSGEEETGAALAPGSILLADELLPSQLMGADPAA
LAGFATARGGPTSHVAILAAAMGVPALVAVGGALSKVKDGATLILDADAGTLRVAPDAKA
LEAAQTALAQRQQRKAAAKAAAHEPAVTRDGVRIEVFANTGSVADAQAAVANGAEGSGLL
RTEFLFLDRETPPDEDEQARQYQAIAEALDGRPLIIRTLDVGGDKAAPYLPIPAEENPAL
GLRGVRVSLWRPHLLKAQLRAILRVEPRGQCKIMVPMVASLDELRAVRAVLEEAKRELGI
TDRVQLGVMIETPAAAVTADLLAAEADFLSIGTNDLTQYVLAMDRGNPELAAGIDALHPA
VLRMIDQTCQGAARHHRWVGVCGGLASDLDATPILLGLGVAELSTTASIAPDVKARVRAL
SLEACRALAAQALEQTSPQAVRALVQGQTNTPLGGLNP

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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