GapMind for catabolism of small carbon sources

 

Protein GFF4493 in Pseudomonas simiae WCS417

Annotation: FitnessBrowser__WCS417:GFF4493

Length: 836 amino acids

Source: WCS417 in FitnessBrowser

Candidate for 17 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-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized) 75% 100% 1216.1 D-trehalose PTS system, I, HPr, and IIA components 47% 672.2
D-glucosamine (chitosamine) catabolism nagF hi N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized) 75% 100% 1216.1 D-trehalose PTS system, I, HPr, and IIA components 47% 672.2
trehalose catabolism treEIIA med D-trehalose PTS system, I, HPr, and IIA components (characterized) 47% 98% 672.2 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 75% 1216.1
N-acetyl-D-glucosamine catabolism crr med Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 40% 97% 94.4 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 75% 1216.1
D-glucosamine (chitosamine) catabolism crr med Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale) 40% 97% 94.4 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 75% 1216.1
D-fructose catabolism fruI lo Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized) 42% 70% 469.5 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 75% 1216.1
sucrose catabolism fruI lo Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized) 42% 70% 469.5 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 75% 1216.1
glycerol catabolism dhaM lo PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121 (characterized) 31% 73% 125.2 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 75% 1216.1
D-cellobiose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 40% 89% 117.9 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 75% 1216.1
D-glucose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 40% 89% 117.9 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 75% 1216.1
lactose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 40% 89% 117.9 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 75% 1216.1
D-maltose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 40% 89% 117.9 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 75% 1216.1
sucrose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 40% 89% 117.9 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 75% 1216.1
trehalose catabolism crr lo glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized) 40% 89% 117.9 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 75% 1216.1
N-acetyl-D-glucosamine catabolism nagEIIA lo Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 39% 88% 112.5 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 75% 1216.1
D-glucosamine (chitosamine) catabolism nagEIIA lo Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 39% 88% 112.5 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 75% 1216.1
D-maltose catabolism malEIIA lo Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale) 39% 88% 112.5 N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) 75% 1216.1

Sequence Analysis Tools

View GFF4493 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

MSYNNNELTLSAPLSGPVLTLGNVPDEVFASGAMGDGIAIDPLNDCLYAPCDGVIIHVAR
TGHALTIRAENGAEVLMHVGIDTVELNGEGFALLVKDGARVSKGQALVQFDLDRIARQCK
SLVSLIILTNGERFELRAVAGQKVKVGEPLLQIVARSAAAVQTAVDNSEADVSASVRITH
RGGLHARPAALIRKTAQDFSSQAQLHFGDKSASCDSLIGLMGLGIGEGDEVRVTCRGKDA
EAALQALVAALSAVIKEEHHVPVVAPPRRAHTEAGVLQGVCAAPGLVCGPLFRLTGIELP
ADVGNHSADEQLQHLDTALEQVRSEIRSTLAHARQRKNVEEEDIFAAHLALLEDPNLLEA
ATRSIEQGSAATHAWRDAIQAQCAVLLALGKPLFAERANDLRDLQQRVLRALLGEAWHFE
LPAGSIVSAHELTPSDLLQLSAQHAVGICMAEGGATSHVAILARGKGLPCVVALGAEVLD
VPQGQRVVLDAVNGRLELEPTEARHAEVHQIRDAQKLRRQQQQAQAQEPARTTDGVSIEV
AANVASSAEAQVAFENGADGVGLLRTEFLFVDRRTAPDEQEQRHAYQAVLDAMGDKSVII
RTIDVGGDKQLDYLPLPVEANPVLGLRGIRMAQVRPELLDQQLRALLQVSPLERCRILLP
MVSEVDELLQIRQRLDELCVELELTQRPELGVMIEVPAAALMAEHLAKHADFLSIGTNDL
SQYTLAMDRDHAGLAARVDALHPALLRLIAQTCAGATKHGRWVGVCGALASDPLATPVLV
GLGVSELSVSPPQIAEIKDRVRHLDAAQCRQLSQGLLDLSSAKAVRQACQHHWPLS

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