GapMind for catabolism of small carbon sources

 

Finding step AO353_03055 for L-citrulline catabolism in Pseudomonas putida KT2440

3 candidates for AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi PP_4486 lysine / arginine / ornithine ABC transporter - periplasmic binding protein ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized) 86% 100% 436 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 43% 232.3
med PP_0282 L-arginine ABC transporter - periplasmic binding subunit ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized) 46% 98% 209.1 ABC transporter for L-Lysine, periplasmic substrate-binding component 82% 414.5
med PP_3593 Amino acid ABC transporter, periplasmic binding protein ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized) 40% 99% 181.4 Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter periplasmic binding protein, 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 45% 207.2

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 AO353_03055

Or cluster all characterized AO353_03055 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