GapMind for catabolism of small carbon sources

 

Protein GFF3103 in Pseudomonas stutzeri RCH2

Annotation: FitnessBrowser__psRCH2:GFF3103

Length: 394 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 21 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-alanine catabolism Pf6N2E2_5403 hi ABC transporter for D-Alanine, permease component 2 (characterized) 69% 100% 528.1 AapQ, 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) 53% 409.5
L-asparagine catabolism aapQ med AapQ, 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) 53% 96% 409.5 ABC transporter for D-Alanine, permease component 2 69% 528.1
L-aspartate catabolism aapQ med AapQ, 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) 53% 96% 409.5 ABC transporter for D-Alanine, permease component 2 69% 528.1
L-glutamate catabolism aapQ med AapQ, 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) 53% 96% 409.5 ABC transporter for D-Alanine, permease component 2 69% 528.1
L-histidine catabolism aapQ med AapQ, 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) 53% 96% 409.5 ABC transporter for D-Alanine, permease component 2 69% 528.1
L-leucine catabolism aapQ med AapQ, 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) 53% 96% 409.5 ABC transporter for D-Alanine, permease component 2 69% 528.1
L-proline catabolism aapQ med AapQ, 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) 53% 96% 409.5 ABC transporter for D-Alanine, permease component 2 69% 528.1
L-asparagine catabolism bztB med glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) 43% 96% 300.1 ABC transporter for D-Alanine, permease component 2 69% 528.1
L-aspartate catabolism bztB med glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) 43% 96% 300.1 ABC transporter for D-Alanine, permease component 2 69% 528.1
L-glutamate catabolism bztB med glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) 43% 96% 300.1 ABC transporter for D-Alanine, permease component 2 69% 528.1
L-asparagine catabolism bgtB' lo ABC-type permease for basic amino acids and glutamine (characterized, see rationale) 39% 97% 247.7 ABC transporter for D-Alanine, permease component 2 69% 528.1
L-aspartate catabolism bgtB' lo ABC-type permease for basic amino acids and glutamine (characterized, see rationale) 39% 97% 247.7 ABC transporter for D-Alanine, permease component 2 69% 528.1
L-asparagine catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 37% 96% 164.9 ABC transporter for D-Alanine, permease component 2 69% 528.1
L-aspartate catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 37% 96% 164.9 ABC transporter for D-Alanine, permease component 2 69% 528.1
L-asparagine catabolism aatQ lo Glutamate/aspartate import permease protein GltJ (characterized) 32% 95% 102.4 ABC transporter for D-Alanine, permease component 2 69% 528.1
L-aspartate catabolism aatQ lo Glutamate/aspartate import permease protein GltJ (characterized) 32% 95% 102.4 ABC transporter for D-Alanine, permease component 2 69% 528.1
L-glutamate catabolism gltJ lo Glutamate/aspartate import permease protein GltJ (characterized) 32% 95% 102.4 ABC transporter for D-Alanine, permease component 2 69% 528.1
L-asparagine catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 32% 91% 94.7 ABC transporter for D-Alanine, permease component 2 69% 528.1
L-aspartate catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 32% 91% 94.7 ABC transporter for D-Alanine, permease component 2 69% 528.1
L-glutamate catabolism gltK lo Glutamate/aspartate import permease protein GltK (characterized) 32% 91% 94.7 ABC transporter for D-Alanine, permease component 2 69% 528.1
L-glutamate catabolism gluC lo GluC aka CGL1952, component of Glutamate porter (characterized) 33% 55% 79.3 ABC transporter for D-Alanine, permease component 2 69% 528.1

Sequence Analysis Tools

View GFF3103 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

MRSIARGAVPRRSPFTDPRIRAWVFQVLAVLAVVAFGWYLFHNTQTNLAHRGITSGFGFL
NNAAGFGISQHLIDYSESDTYGRVFWVGLLNTLLVSVIGIFLATVMGFILGVGRLSSNWL
IRQLATLYIEIFRNIPPLLLIFFVYFAVISPLPGPRNSLSLWDVVFVNNRGVQMPAPSAG
DGFWAFWLALLVALVAVVVLNRWARARRHATGRMFPVFWTSPGLFLAIPWLMTFIAGAPF
TWEVPELQRFNIRGGWVVIPELVSIVVALSVYTAAFIGETVRSGIQSVSHGQTEAAASLG
LRPGQVLRLVIVPQALRVIVPPLTSQYLNLAKNSSLAAAIGYPDMVSLFAGTVLNQTGQA
IETMAITMSVYLAISISISLLMNWYNKRIALIER

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