GapMind for catabolism of small carbon sources

 

Protein PfGW456L13_376 in Pseudomonas fluorescens GW456-L13

Annotation: FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_376

Length: 257 amino acids

Source: pseudo13_GW456_L13 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-lysine catabolism hisP hi ABC transporter for L-Lysine, ATPase component (characterized) 97% 100% 487.6 AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter 67% 338.6
L-arginine catabolism artP hi Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 93% 100% 471.1 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 62% 319.3
L-histidine catabolism hisP hi Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 93% 100% 471.1 AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter 67% 338.6
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 65% 97% 332.8 ABC transporter for L-Lysine, ATPase component 97% 487.6
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-glucosamine, ATPase component (characterized) 53% 94% 260.4 ABC transporter for L-Lysine, ATPase component 97% 487.6
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 52% 90% 244.2 ABC transporter for L-Lysine, ATPase component 97% 487.6
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 52% 90% 244.2 ABC transporter for L-Lysine, ATPase component 97% 487.6
L-histidine catabolism aapP med ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 52% 92% 243.4 ABC transporter for L-Lysine, ATPase component 97% 487.6
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) 52% 93% 241.9 ABC transporter for L-Lysine, ATPase component 97% 487.6
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) 52% 93% 241.9 ABC transporter for L-Lysine, ATPase component 97% 487.6
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) 52% 93% 241.9 ABC transporter for L-Lysine, ATPase component 97% 487.6
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) 52% 93% 241.9 ABC transporter for L-Lysine, ATPase component 97% 487.6
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) 52% 93% 241.9 ABC transporter for L-Lysine, ATPase component 97% 487.6
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 50% 93% 238.8 ABC transporter for L-Lysine, ATPase component 97% 487.6

Sequence Analysis Tools

View PfGW456L13_376 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MAEATPALEIRNLHKRYGSLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPH
QGQILVAGEELKLKAAKNGELVAADGKQINRLRSEIGFVFQNFNLWPHMSVLDNIIEAPR
RVLGQSKAEAIEVAEALLAKVGIADKRHAYPAQLSGGQQQRAAIARTLAMQPKVILFDEP
TSALDPEMVQEVLNVIRALAEEGRTMLLVTHEMGFARQVSSEVVFLHQGLVEEQGSPQQV
FENPLSARCKQFMSSNR

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:

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