GapMind for catabolism of small carbon sources

 

Protein AO353_04610 in Pseudomonas fluorescens FW300-N2E3

Annotation: AO353_04610 amino acid ABC transporter permease

Length: 393 amino acids

Source: pseudo3_N2E3 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
D-alanine catabolism Pf6N2E2_5403 hi ABC transporter for D-Alanine, permease component 2 (characterized) 91% 100% 684.5 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) 50% 384.0
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) 50% 96% 384 ABC transporter for D-Alanine, permease component 2 91% 684.5
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) 50% 96% 384 ABC transporter for D-Alanine, permease component 2 91% 684.5
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) 50% 96% 384 ABC transporter for D-Alanine, permease component 2 91% 684.5
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) 50% 96% 384 ABC transporter for D-Alanine, permease component 2 91% 684.5
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) 50% 96% 384 ABC transporter for D-Alanine, permease component 2 91% 684.5
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) 50% 96% 384 ABC transporter for D-Alanine, permease component 2 91% 684.5
L-asparagine catabolism bztB med glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) 44% 98% 310.1 ABC transporter for D-Alanine, permease component 2 91% 684.5
L-aspartate catabolism bztB med glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) 44% 98% 310.1 ABC transporter for D-Alanine, permease component 2 91% 684.5
L-glutamate catabolism bztB med glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) 44% 98% 310.1 ABC transporter for D-Alanine, permease component 2 91% 684.5
L-asparagine catabolism bgtB' med ABC-type permease for basic amino acids and glutamine (characterized, see rationale) 40% 98% 262.3 ABC transporter for D-Alanine, permease component 2 91% 684.5
L-aspartate catabolism bgtB' med ABC-type permease for basic amino acids and glutamine (characterized, see rationale) 40% 98% 262.3 ABC transporter for D-Alanine, permease component 2 91% 684.5
L-asparagine catabolism natG med NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 45% 71% 155.2 ABC transporter for D-Alanine, permease component 2 91% 684.5
L-aspartate catabolism natG med NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 45% 71% 155.2 ABC transporter for D-Alanine, permease component 2 91% 684.5

Sequence Analysis Tools

View AO353_04610 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MQNSIGAPKQRLSLSDPRVRAWLFQIITIVAVISMGWYLFNNTQTNLQHRGITSGFSFLE
RSAGFGIAQHLIDYTESDSYARVFVIGLLNTLLVTFIGVILATILGFIVGVARLSKNWII
NKLATVYVETFRNIPPLLQILFWYFAVFLTMPGPRNSHNFADTFFVSSRGLNMPAAQMAN
GFWAFVISIVVAIVAIVLMCRWANKRFEATGVPFHKFWVGLALFLLIPALCALIFGVPLH
WEMPKLQGFNFVGGWVLIPELLALTLALTVYTAAFIAEIVRSGINSVSHGQTEAARSLGL
RNGPTLRKVIIPQALRVIIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAI
EVIAITMSVYLAISISISLLMNWYNKRIALIER

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