GapMind for catabolism of small carbon sources

 

Protein PP_5023 in Pseudomonas putida KT2440

Annotation: PP_5023 Amino acid ABC transporter, permease protein

Length: 320 amino acids

Source: Putida in FitnessBrowser

Candidate for 24 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) 43% 93% 158.7 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-asparagine catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 38% 58% 136.7 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-aspartate catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 38% 58% 136.7 Basic amino acid uptake transporter, BgtAB 49% 175.6
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% 87% 132.1 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-asparagine catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 36% 73% 131.7 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-aspartate catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 36% 73% 131.7 Basic amino acid uptake transporter, BgtAB 49% 175.6
D-glucosamine (chitosamine) catabolism AO353_21720 lo ABC transporter for D-Glucosamine, permease component 1 (characterized) 35% 94% 129 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-asparagine catabolism aatQ lo ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 1 (characterized) 33% 87% 127.1 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-aspartate catabolism aatQ lo ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 1 (characterized) 33% 87% 127.1 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-histidine catabolism aapM lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized) 35% 58% 124 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-asparagine catabolism aatM lo PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized) 38% 95% 123.2 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-aspartate catabolism aatM lo PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized) 38% 95% 123.2 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-glutamate catabolism gltK lo PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized) 38% 95% 123.2 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 36% 73% 117.1 Basic amino acid uptake transporter, BgtAB 49% 175.6
D-alanine catabolism Pf6N2E2_5404 lo ABC transporter for D-Alanine, permease component 1 (characterized) 35% 58% 115.9 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-glutamate catabolism gluC lo GluC aka CGL1952, component of Glutamate porter (characterized) 32% 97% 107.5 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-asparagine catabolism peb1D lo Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) 31% 93% 106.7 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-aspartate catabolism peb1D lo Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) 31% 93% 106.7 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-asparagine catabolism aapQ lo 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) 30% 52% 87.8 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-aspartate catabolism aapQ lo 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) 30% 52% 87.8 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-glutamate catabolism aapQ lo 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) 30% 52% 87.8 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-histidine catabolism aapQ lo 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) 30% 52% 87.8 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-leucine catabolism aapQ lo 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) 30% 52% 87.8 Basic amino acid uptake transporter, BgtAB 49% 175.6
L-proline catabolism aapQ lo 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) 30% 52% 87.8 Basic amino acid uptake transporter, BgtAB 49% 175.6

Sequence Analysis Tools

View PP_5023 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

MIKHKKAQWPWHGLTALVLVGLALSLYMATSMISYEWRWNRVPQYFAYKAEETQRAAGYG
TVQEIVISGDNARVTLKDESGAEQVLDVDKDSLQLSRGDDVAEGDQIGVTRHWAAGPLAW
GLWTTLWISVVSGALGLVIGLFAGLCRLSNNPTLRDLSTVYVELVRGTPLLVQIFIFYFF
IGTVLNLSREFAGVAALALFTGAYVAEIVRAGVQSIAKGQNEAARSLGLNAGQSMRHVIL
PQAFKRVLPPLAGQFISLVKDTSLVSVIAITELTKSGREAITTSFSTFEIWFCVAGLYLL
INLPLSHIASRLERRLAQSD

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