GapMind for catabolism of small carbon sources

 

Protein PP_1070 in Pseudomonas putida KT2440

Annotation: PP_1070 glutamate / aspartate ABC transporter - permease subunit

Length: 248 amino acids

Source: Putida in FitnessBrowser

Candidate for 14 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism aatQ hi PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 100% 100% 491.5 NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 37% 131.3
L-aspartate catabolism aatQ hi PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 100% 100% 491.5 NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 37% 131.3
L-glutamate catabolism gltJ hi PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 100% 100% 491.5 NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 37% 131.3
L-asparagine catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 37% 76% 131.3 PP1070, component of Acidic amino acid uptake porter, AatJMQP 100% 491.5
L-aspartate catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 37% 76% 131.3 PP1070, component of Acidic amino acid uptake porter, AatJMQP 100% 491.5
L-asparagine catabolism aatM lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) 32% 93% 130.2 PP1070, component of Acidic amino acid uptake porter, AatJMQP 100% 491.5
L-aspartate catabolism aatM lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) 32% 93% 130.2 PP1070, component of Acidic amino acid uptake porter, AatJMQP 100% 491.5
L-glutamate catabolism gltK lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) 32% 93% 130.2 PP1070, component of Acidic amino acid uptake porter, AatJMQP 100% 491.5
L-asparagine catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 33% 81% 123.2 PP1070, component of Acidic amino acid uptake porter, AatJMQP 100% 491.5
L-aspartate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 33% 81% 123.2 PP1070, component of Acidic amino acid uptake porter, AatJMQP 100% 491.5
L-glutamate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 33% 81% 123.2 PP1070, component of Acidic amino acid uptake porter, AatJMQP 100% 491.5
L-asparagine catabolism bztB lo glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) 31% 52% 94 PP1070, component of Acidic amino acid uptake porter, AatJMQP 100% 491.5
L-aspartate catabolism bztB lo glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) 31% 52% 94 PP1070, component of Acidic amino acid uptake porter, AatJMQP 100% 491.5
L-glutamate catabolism bztB lo glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) 31% 52% 94 PP1070, component of Acidic amino acid uptake porter, AatJMQP 100% 491.5

Sequence Analysis Tools

View PP_1070 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MNYNWDWGVFFKSTGVGSETYLDWYITGLGWTIAIAITAWIIALLLGSLLGVMRTVPNRL
VSGIATAYVELFRNVPLLVQLFIWYFLVPDLLPEGLQEWFKQDLNPTTSALISVVICLGL
FTAARVCEQVRTGIQALPKGQEAAARAMGFSLPQIYNNVLLPQAYRIIIPPLTSEFLNVF
KNSSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMGLMLLMRMVEKKVAVP
GLISVGGK

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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