GapMind for catabolism of small carbon sources

 

Protein GFF1093 in Pseudomonas simiae WCS417

Annotation: FitnessBrowser__WCS417:GFF1093

Length: 244 amino acids

Source: WCS417 in FitnessBrowser

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism aatP hi ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 96% 100% 470.7 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 60% 293.9
L-aspartate catabolism aatP hi ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 96% 100% 470.7 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 60% 293.9
L-glutamate catabolism gltL hi ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 96% 100% 470.7 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 60% 293.9
L-asparagine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 60% 93% 286.6 ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component 96% 470.7
L-aspartate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 60% 93% 286.6 ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component 96% 470.7
L-glutamate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 60% 93% 286.6 ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component 96% 470.7
L-histidine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 60% 93% 286.6 ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component 96% 470.7
L-leucine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 60% 93% 286.6 ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component 96% 470.7
L-proline catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 60% 93% 286.6 ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component 96% 470.7
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 59% 92% 285.4 ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component 96% 470.7
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 59% 92% 285.4 ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component 96% 470.7
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 58% 95% 283.5 ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component 96% 470.7
L-asparagine catabolism glnQ med Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 55% 98% 260.4 ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component 96% 470.7

Sequence Analysis Tools

View GFF1093 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

MISIKNINKWYGDFQVLTDCSTDVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDIVV
DGTSIADPKTNLPQLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATKKGLQL
LERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVMV
QLAQEGMTMMCVTHEMGFARKVADRVIFMDAGKIIEDCPKEEFFGDISARSERAQHFLEK
ILQH

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