GapMind for catabolism of small carbon sources

 

Protein GFF5097 in Pseudomonas simiae WCS417

Annotation: FitnessBrowser__WCS417:GFF5097

Length: 241 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
L-lysine catabolism hisP hi Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 72% 93% 341.7 ABC transporter for D-Alanine, ATPase component 64% 312.8
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 64% 95% 312.8 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 63% 306.6
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) 64% 93% 305.1 ABC transporter for D-Alanine, ATPase component 64% 312.8
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) 64% 93% 305.1 ABC transporter for D-Alanine, ATPase component 64% 312.8
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) 64% 93% 305.1 ABC transporter for D-Alanine, ATPase component 64% 312.8
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) 64% 93% 305.1 ABC transporter for D-Alanine, ATPase component 64% 312.8
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) 64% 93% 305.1 ABC transporter for D-Alanine, ATPase component 64% 312.8
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) 64% 93% 305.1 ABC transporter for D-Alanine, ATPase component 64% 312.8
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 62% 90% 293.1 ABC transporter for D-Alanine, ATPase component 64% 312.8
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 62% 90% 293.1 ABC transporter for D-Alanine, ATPase component 64% 312.8
L-glutamate catabolism gltL med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 62% 90% 293.1 ABC transporter for D-Alanine, ATPase component 64% 312.8
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 59% 92% 272.3 ABC transporter for D-Alanine, ATPase component 64% 312.8
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 59% 92% 272.3 ABC transporter for D-Alanine, ATPase component 64% 312.8
L-asparagine catabolism aatP med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 56% 99% 267.7 ABC transporter for D-Alanine, ATPase component 64% 312.8
L-aspartate catabolism aatP med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 56% 99% 267.7 ABC transporter for D-Alanine, ATPase component 64% 312.8
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 51% 99% 240.4 ABC transporter for D-Alanine, ATPase component 64% 312.8
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 51% 99% 240.4 ABC transporter for D-Alanine, ATPase component 64% 312.8

Sequence Analysis Tools

View GFF5097 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

Fitness BLAST: loading...

Sequence

MVQISGLNKWYGNFQVLHAIDLTVSQGERIVLCGPSGSGKSTLIRCISRLEVADSGVIRA
LDADLGKPSPARHKALREIGMVFQNFNLFPHMTVLQNCTLAPMSVRGFSRKRAEAHARHF
LDKVGIENQANKYPSQLSGGQQQRVAIARALCMEPKIMLFDEPTSALDPEMVKEVLDVIV
TLADTGMTMLCVTHEMGFARQVAERVLFLDAGRIVEDLPPEQFFTAPKSDRAQAFLAQIH
H

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