GapMind for catabolism of small carbon sources

 

Protein AO353_15995 in Pseudomonas fluorescens FW300-N2E3

Annotation: FitnessBrowser__pseudo3_N2E3:AO353_15995

Length: 844 amino acids

Source: pseudo3_N2E3 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
trehalose catabolism treEIIA hi trehalose-specific PTS system, I, HPr, and IIA components (characterized) 100% 100% 1612 N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA 45% 648.3
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) 45% 98% 648.3 trehalose-specific PTS system, I, HPr, and IIA components 100% 1612.0
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) 45% 98% 648.3 trehalose-specific PTS system, I, HPr, and IIA components 100% 1612.0
D-fructose catabolism fruI med Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized) 45% 71% 520 trehalose-specific PTS system, I, HPr, and IIA components 100% 1612.0
sucrose catabolism fruI med Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized) 45% 71% 520 trehalose-specific PTS system, I, HPr, and IIA components 100% 1612.0
D-cellobiose catabolism crr lo PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 40% 89% 127.9 trehalose-specific PTS system, I, HPr, and IIA components 100% 1612.0
D-glucose catabolism crr lo PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 40% 89% 127.9 trehalose-specific PTS system, I, HPr, and IIA components 100% 1612.0
lactose catabolism crr lo PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 40% 89% 127.9 trehalose-specific PTS system, I, HPr, and IIA components 100% 1612.0
D-maltose catabolism crr lo PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 40% 89% 127.9 trehalose-specific PTS system, I, HPr, and IIA components 100% 1612.0
sucrose catabolism crr lo PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 40% 89% 127.9 trehalose-specific PTS system, I, HPr, and IIA components 100% 1612.0
trehalose catabolism crr lo PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 40% 89% 127.9 trehalose-specific PTS system, I, HPr, and IIA components 100% 1612.0
N-acetyl-D-glucosamine catabolism nagEIIA lo Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 37% 73% 108.6 trehalose-specific PTS system, I, HPr, and IIA components 100% 1612.0
D-glucosamine (chitosamine) catabolism nagEIIA lo Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 37% 73% 108.6 trehalose-specific PTS system, I, HPr, and IIA components 100% 1612.0
D-maltose catabolism malEIIA lo Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 37% 73% 108.6 trehalose-specific PTS system, I, HPr, and IIA components 100% 1612.0
N-acetyl-D-glucosamine catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 36% 91% 83.2 trehalose-specific PTS system, I, HPr, and IIA components 100% 1612.0
D-glucosamine (chitosamine) catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 36% 91% 83.2 trehalose-specific PTS system, I, HPr, and IIA components 100% 1612.0

Sequence Analysis Tools

View AO353_15995 at FitnessBrowser

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MTLTQPLQLLAPLSGVLMPLDHVPDPVFASRVIGDGLCIDPTSQVLCAPLAGVVSNLQHS
GHAISITDDSGVQVLLHIGLDTVNLKGQGFSALVEQGQRVEAGQPLIEFDADYVALHARS
LLTLMLVVSGEPFSLLTPDSGLVACAQPVLRLSLGDPRTVVAQEEGEALFSKPVHLPNPN
GLHARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQTVHGDALQVSAVGEDAEL
AISTLAQLLADGCGEAVTPVAVVAPVVEAQEVSTKLLRGVCASAGSAFGYVVQVAERTLE
MPEFAADQQLERESLERALMHATQALQRLRDNAAGEAQADIFKAHQELLEDPSLLEQAQA
LIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLKLILGVPDGVWELP
DQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPAVCGLPLQVLSLA
SGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELENAARAAVTRDGHHFEVTA
NVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSAIARALGPQRNLVVR
TLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAILSSAGLARLHIMLPM
VSQLSELRLARLMLEEEALALGLRELPKLGIMIEVPAAALMADLFAPEVDFFSIGTNDLT
QYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLG
LGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQVLGLESAEQVREALSVQQQAMVETSQ
VLES

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