GapMind for catabolism of small carbon sources

 

Protein AO353_12325 in Pseudomonas fluorescens FW300-N2E3

Annotation: AO353_12325 ABC transporter permease

Length: 319 amino acids

Source: pseudo3_N2E3 in FitnessBrowser

Candidate for 20 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism Ac3H11_2554 med ABC transporter for L-Histidine, permease component 1 (characterized) 41% 93% 159.1 Basic amino acid uptake transporter, BgtAB 48% 176.4
L-asparagine catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 42% 54% 136 Basic amino acid uptake transporter, BgtAB 48% 176.4
L-aspartate catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 42% 54% 136 Basic amino acid uptake transporter, BgtAB 48% 176.4
D-glucosamine (chitosamine) catabolism AO353_21720 lo ABC transporter for D-Glucosamine, permease component 1 (characterized) 36% 94% 134.4 Basic amino acid uptake transporter, BgtAB 48% 176.4
L-glutamate catabolism gltJ lo Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized) 34% 85% 132.1 Basic amino acid uptake transporter, BgtAB 48% 176.4
L-histidine catabolism aapM lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized) 37% 58% 129.4 Basic amino acid uptake transporter, BgtAB 48% 176.4
L-asparagine catabolism aatQ lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 (characterized) 33% 86% 129 Basic amino acid uptake transporter, BgtAB 48% 176.4
L-aspartate catabolism aatQ lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 (characterized) 33% 86% 129 Basic amino acid uptake transporter, BgtAB 48% 176.4
L-asparagine catabolism aatM lo ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized) 38% 96% 125.9 Basic amino acid uptake transporter, BgtAB 48% 176.4
L-aspartate catabolism aatM lo ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized) 38% 96% 125.9 Basic amino acid uptake transporter, BgtAB 48% 176.4
L-asparagine catabolism aapM lo AapM, 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) 35% 54% 122.9 Basic amino acid uptake transporter, BgtAB 48% 176.4
L-aspartate catabolism aapM lo AapM, 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) 35% 54% 122.9 Basic amino acid uptake transporter, BgtAB 48% 176.4
L-glutamate catabolism aapM lo AapM, 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) 35% 54% 122.9 Basic amino acid uptake transporter, BgtAB 48% 176.4
L-leucine catabolism aapM lo AapM, 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) 35% 54% 122.9 Basic amino acid uptake transporter, BgtAB 48% 176.4
L-proline catabolism aapM lo AapM, 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) 35% 54% 122.9 Basic amino acid uptake transporter, BgtAB 48% 176.4
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 37% 74% 122.5 Basic amino acid uptake transporter, BgtAB 48% 176.4
D-alanine catabolism Pf6N2E2_5404 lo ABC transporter for D-Alanine, permease component 1 (characterized) 34% 61% 115.2 Basic amino acid uptake transporter, BgtAB 48% 176.4
L-glutamate catabolism gluC lo GluC aka CGL1952, component of Glutamate porter (characterized) 34% 97% 112.1 Basic amino acid uptake transporter, BgtAB 48% 176.4
L-asparagine catabolism peb1D lo Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) 30% 93% 106.7 Basic amino acid uptake transporter, BgtAB 48% 176.4
L-aspartate catabolism peb1D lo Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) 30% 93% 106.7 Basic amino acid uptake transporter, BgtAB 48% 176.4

Sequence Analysis Tools

View AO353_12325 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

MKQKKAQWPWHVLTVLVLIGMAGALYYATSLMSYEWRWNRVPQYFAYQAEETQRAADIST
VSELVRTGGKAEVTLRNDAGVEQLLSVDDNSLQVARGDDVAEGDVVGVTRHWAAGPLLWG
LWTTLWLSLVSGVLGLLIGLATGLCRLSNNPTLRDLSTVYIELVRGTPLLVQIFIFYFFI
GTVLNLSREFAGIAALSLFTGAYVAEIIRSGVQSIARGQNEAARSLGLSAGQSMRHVVLP
QAFKRVLPPLAGQFISLVKDTSLVSVIAITELLKSGREVITTSFSPFEILFCVAGLYLLI
NLPLSKIASRLERRLAQSD

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