GapMind for catabolism of small carbon sources

 

Protein WP_068008969.1 in Pseudovibrio axinellae Ad2

Annotation: NCBI__GCF_001623255.1:WP_068008969.1

Length: 850 amino acids

Source: GCF_001623255.1 in NCBI

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 D-trehalose PTS system, I, HPr, and IIA components (characterized) 43% 97% 626.7 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 38% 562.8
D-fructose catabolism fruI med Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized) 41% 70% 480.3 D-trehalose PTS system, I, HPr, and IIA components 43% 626.7
sucrose catabolism fruI med Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized) 41% 70% 480.3 D-trehalose PTS system, I, HPr, and IIA components 43% 626.7
N-acetyl-D-glucosamine catabolism nagEIIA med Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 40% 79% 116.3 D-trehalose PTS system, I, HPr, and IIA components 43% 626.7
D-glucosamine (chitosamine) catabolism nagEIIA med Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 40% 79% 116.3 D-trehalose PTS system, I, HPr, and IIA components 43% 626.7
D-maltose catabolism malEIIA med Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 40% 79% 116.3 D-trehalose PTS system, I, HPr, and IIA components 43% 626.7
N-acetyl-D-glucosamine catabolism nagF lo N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized) 38% 99% 562.8 D-trehalose PTS system, I, HPr, and IIA components 43% 626.7
D-glucosamine (chitosamine) catabolism nagF lo N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized) 38% 99% 562.8 D-trehalose PTS system, I, HPr, and IIA components 43% 626.7
D-cellobiose catabolism crr lo PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 38% 90% 108.2 D-trehalose PTS system, I, HPr, and IIA components 43% 626.7
D-glucose catabolism crr lo PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 38% 90% 108.2 D-trehalose PTS system, I, HPr, and IIA components 43% 626.7
lactose catabolism crr lo PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 38% 90% 108.2 D-trehalose PTS system, I, HPr, and IIA components 43% 626.7
D-maltose catabolism crr lo PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 38% 90% 108.2 D-trehalose PTS system, I, HPr, and IIA components 43% 626.7
sucrose catabolism crr lo PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 38% 90% 108.2 D-trehalose PTS system, I, HPr, and IIA components 43% 626.7
trehalose catabolism crr lo PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized) 38% 90% 108.2 D-trehalose PTS system, I, HPr, and IIA components 43% 626.7
N-acetyl-D-glucosamine catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 38% 72% 75.9 D-trehalose PTS system, I, HPr, and IIA components 43% 626.7
D-glucosamine (chitosamine) catabolism crr lo Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 38% 72% 75.9 D-trehalose PTS system, I, HPr, and IIA components 43% 626.7

Sequence Analysis Tools

View WP_068008969.1 at NCBI

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

MKDPKNNFSIQLPLKGIVQAVTDLPDPVFAEKMMGDGVAIDPTDNVLYAPFSGQITQIHN
SHHAVTLQQGDVELLMHIGLDTVALKGRGFELHVAEGDQVEQGQPLITFDADVIARECVS
VQSAIVITSGQEITTVAPLGAVQTDLNQVVFTVPSSNDPQGTTAPAQETAAEPTGPAITG
SIKIPNATGLHARPAARLAVEVRKADAKVTFTVNGKTCSGSSVTGIMSLKTKLGDELEIE
AVGPDAQQVVADVIAAVKAGLGEEITSFSEAPHIKVEEEAPLLQVKSGEDGVLIGFTASP
GRAIGKLVKHNQTLPEVTRESIGAAEERAAFKASVKSSIADLQSIIDRLTKNDQQDLAEV
FNAHIELLSDPELSEKPLADIAKGQGAAWSWKLAYEAQAETLAKMDDPLLAGRAVDVRDI
GLRVIKKLLGVDDGGEILEEGTILLQEDVTPSEIVALDLTKIVGLCTTHGGSSSHAAIIA
RSNDLPYLVNVEDGMKDLKDGTVLLLDAKRGKIKVSPTDEEQAAFTKKIENAAKQAEEYQ
RDAHKPAITTDGFQIEIAANIGSVEDAEKAVVAGAEAVGLLRSEFLYMERLNEPTEEEQA
EKIGAILEVMGKERPVIIRTLDVGGDKPLPYLPMPHEENPFLGVRGVRIGIERPSILRRQ
VRAILSQAHKGHARIMYPMISALDELRAVNALVREEQKNLGVEHVEVGIMIEVPSAALMA
DKLAQEVDFFSIGTNDLTQYVMAIDRGHPGLASRADALHPAVLRMIELTVRAANDAGKWV
GVCGGLASQIEAVPVLIGLGIKELSVSVPALPEVKHKVRTVSMEESCKLAQAALDCADTS
DVKDLLKSQS

This GapMind analysis is from Sep 24 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