GapMind for catabolism of small carbon sources

 

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

4 candidates for argT: L-lysine ABC transporter, substrate-binding component ArgT

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi PP_3593 Amino acid ABC transporter, periplasmic binding protein Amino acid ABC transporter, periplasmic binding protein (characterized, see rationale) 100% 100% 501.1 AotJ aka PA0888, component of Arginine/ornithine (but not lysine) porter 41% 186.8
hi PP_0282 L-arginine ABC transporter - periplasmic binding subunit ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized) 82% 100% 414.5 ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component 46% 209.1
med PP_4486 lysine / arginine / ornithine ABC transporter - periplasmic binding protein ArgT aka B2310, component of Histidine/Arginine/Lysine (basic amino acid) uptake porter, HisJ/ArgT/HisP/HisM/HisQ [R, R, C, M, M, respectively] (Gilson et al. 1982). HisJ binds L-His (preferred), but 1-methyl-L-His and 3-methyl-L-His also bind, while the dipeptide carnosine binds weakly; D-histidine and the histidine degradation products, histamine, urocanic acid and imidazole do not bind. L-Arg, homo-L-Arg, and post-translationally modified methylated Arg-analogs also bind with the exception of symmetric dimethylated-L-Arg. L-Lys and L-Orn show weaker interactions with HisJ and methylated and acetylated Lys variants show poor binding.The carboxylate groups of these amino acids and their variants are essential (characterized) 43% 100% 232.3 ABC transporter for L-Arginine, substrate-binding component 87% 453.4
lo PP_0227 periplasmic cystine-binding protein ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized) 32% 100% 144.1 L-cystine-binding protein FliY; CBP; Protein FliY; Sulfate starvation-induced protein 7; SSI7 62% 324.3

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 argT

Or cluster all characterized argT 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