GapMind for catabolism of small carbon sources

 

Protein PP_3597 in Pseudomonas putida KT2440

Annotation: PP_3597 Amino-acid ABC transporter, ATP-binding protein

Length: 260 amino acids

Source: Putida 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
L-lysine catabolism hisP hi Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 100% 100% 512.7 ABC transporter for D-Alanine, ATPase component 65% 329.3
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 65% 95% 329.3 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 63% 324.3
L-asparagine catabolism aapP med AapP, 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) 65% 94% 321.2 ABC transporter for D-Alanine, ATPase component 65% 329.3
L-aspartate catabolism aapP med AapP, 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) 65% 94% 321.2 ABC transporter for D-Alanine, ATPase component 65% 329.3
L-glutamate catabolism aapP med AapP, 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) 65% 94% 321.2 ABC transporter for D-Alanine, ATPase component 65% 329.3
L-histidine catabolism aapP med AapP, 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) 65% 94% 321.2 ABC transporter for D-Alanine, ATPase component 65% 329.3
L-leucine catabolism aapP med AapP, 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) 65% 94% 321.2 ABC transporter for D-Alanine, ATPase component 65% 329.3
L-proline catabolism aapP med AapP, 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) 65% 94% 321.2 ABC transporter for D-Alanine, ATPase component 65% 329.3
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 65% 92% 320.5 ABC transporter for D-Alanine, ATPase component 65% 329.3
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 65% 92% 320.5 ABC transporter for D-Alanine, ATPase component 65% 329.3
L-glutamate catabolism gltL med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 65% 92% 320.5 ABC transporter for D-Alanine, ATPase component 65% 329.3
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 58% 100% 287 ABC transporter for D-Alanine, ATPase component 65% 329.3
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 58% 100% 287 ABC transporter for D-Alanine, ATPase component 65% 329.3
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 56% 97% 274.2 ABC transporter for D-Alanine, ATPase component 65% 329.3
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 56% 97% 274.2 ABC transporter for D-Alanine, ATPase component 65% 329.3
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 53% 100% 258.5 ABC transporter for D-Alanine, ATPase component 65% 329.3
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 53% 99% 255.4 ABC transporter for D-Alanine, ATPase component 65% 329.3
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 53% 99% 255.4 ABC transporter for D-Alanine, ATPase component 65% 329.3
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 52% 98% 252.7 ABC transporter for D-Alanine, ATPase component 65% 329.3
L-citrulline catabolism PS417_17605 med ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 52% 95% 245 ABC transporter for D-Alanine, ATPase component 65% 329.3
L-histidine catabolism hisP med Histidine transport ATP-binding protein HisP (characterized) 51% 96% 235.7 ABC transporter for D-Alanine, ATPase component 65% 329.3

Sequence Analysis Tools

View PP_3597 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

MTAPLSLATLAPEPDPRPVLIRIEGLNKHYGAFHVLRDIDLQVREGERIVLCGPSGSGKS
TLIRCINRLEVAQQGSIQVDGIDLAATTREAAQVRSDIGMVFQHFNLFPHMSVLDNCLLA
PTSVRGLSRKDAEERARMYLSKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFD
EPTSALDPEMVAEVLDVLVQLAGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIEDSPPQ
VFFNQPRTERAKAFLAQILH

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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