GapMind for catabolism of small carbon sources


Finding step hisP for L-lysine catabolism in Pseudomonas putida KT2440

5 candidates for hisP: L-lysine ABC transporter, ATPase component HisP

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi PP_3597 Amino-acid ABC transporter, ATP-binding protein Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 100% 100% 512.7 ABC transporter for D-Alanine, ATPase component 65% 329.3
hi PP_0283 Arginine/ornithine transport ATP-binding protein AotP 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) 90% 100% 459.1 AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter 65% 324.3
med PP_4483 histidine lysine / arginine / ornithine ABC transporter - ATP binding subunit histidine transport ATP-binding protein hisP (characterized) 70% 98% 357.5 AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter 94% 473.0
med PP_1300 putative amino acid ABC transporter - ATP-binding subunit Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 67% 93% 336.3 ABC transporter for D-Alanine, ATPase component 96% 498.8
med PP_5022 Glutamine transport ATP-binding protein GlnQ Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 57% 92% 270 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 62% 288.1

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

Also see fitness data for the candidates

Definition of step hisP

Or cluster all characterized hisP proteins

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, 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