GapMind for catabolism of small carbon sources

 

Protein CCNA_00457 in Caulobacter crescentus NA1000

Annotation: FitnessBrowser__Caulo:CCNA_00457

Length: 852 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% 692.2 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% 692.2 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% 692.2
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% 692.2
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% 692.2
N-acetyl-D-glucosamine catabolism nagEIIA med Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 44% 77% 127.5 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 692.2
D-glucosamine (chitosamine) catabolism nagEIIA med Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 44% 77% 127.5 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 692.2
D-maltose catabolism malEIIA med Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 44% 77% 127.5 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 692.2
D-cellobiose catabolism crr med glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 41% 85% 124 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 692.2
D-glucose catabolism crr med glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 41% 85% 124 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 692.2
lactose catabolism crr med glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 41% 85% 124 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 692.2
D-maltose catabolism crr med glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 41% 85% 124 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 692.2
sucrose catabolism crr med glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 41% 85% 124 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 692.2
trehalose catabolism crr med glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 41% 85% 124 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 48% 692.2
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% 692.2
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% 692.2

Sequence Analysis Tools

View CCNA_00457 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

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Sequence

MIVSNLVLTAPLQGWVSALEEAPDAVFAERMLGDGLAIDPLGSTLHAPCDGSVVSVHRAR
HAVTLRATNGAEILMHVGLETVALNGEGFEVFVEEGQTVKAGDRLIGLDLDLLAQRARSL
ITPVVITNGEAFQIVRRDQDRQIGVGQFLMELSPIAGASRAAASGAADQITRQIIVPLAH
GIHARPAARIAQMAKTFASDLTLATGPRRANARSPVGLMSLAIRHGDTIQLLASGPDAQA
AVTALAELIEGGMGEGAPVAAKTSSTKTAPTKTEPSEPPPPAPLPRDGVLKGVPAAPGLA
IGKAVRLSTAEIVVREAGEGVAHEEAALAVALETVRARIGKAAETGDKARKAILAAHQAF
LDDPELYAGAHRLIAEGKSAGFAWRRAVGGYVQALQALGDRRMAERVDDLIDLERQVLRA
LSGEEETGAALAPGSILLADELLPSQLMGADPAALAGFATARGGPTSHVAILAAAMGVPA
LVAVGGALSKVKDGATLILDADAGTLRVAPDAKALEAAQTALAQRQQRKAAAKAAAHEPA
VTRDGVRIEVFANTGSVADAQAAVANGAEGSGLLRTEFLFLDRETPPDEDEQARQYQAIA
EALDGRPLIIRTLDVGGDKAAPYLPIPAEENPALGLRGVRVSLWRPHLLKAQLRAILRVE
PRGQCKIMVPMVASLDELRAVRAVLEEAKRELGITDRVQLGVMIETPAAAVTADLLAAEA
DFLSIGTNDLTQYVLAMDRGNPELAAGIDALHPAVLRMIDQTCQGAARHHRWVGVCGGLA
SDLDATPILLGLGVAELSTTASIAPDVKARVRALSLEACRALAAQALEQTSPQAVRALVQ
GQTNTPLGGLNP

This GapMind analysis is from Apr 09 2024. 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