GapMind for catabolism of small carbon sources

 

Finding step artJ for L-arginine catabolism in Herbaspirillum seropedicae SmR1

5 candidates for artJ: L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
lo HSERO_RS10775 cysteine ABC transporter substrate-binding protein 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 (characterized) 38% 99% 150.6 L-cystine-binding protein FliY; CBP; Protein FliY; Sulfate starvation-induced protein 7; SSI7 47% 218.0
lo HSERO_RS21615 ABC transporter substrate-binding protein ABC transporter for L-Arginine, substrate-binding component (characterized) 32% 90% 130.2 Basic amino acid uptake transporter, BgtAB 37% 135.2
lo HSERO_RS11440 ABC transporter permease arginine ABC transporter, periplasmic arginine-binding protein ArtJ (characterized) 32% 97% 129.4 ABC transporter for L-Histidine, periplasmic substrate-binding component 1 62% 300.1
lo HSERO_RS17550 amino acid ABC transporter substrate-binding protein Putative ABC transporter arginine-binding protein 2 (characterized) 35% 98% 128.6 glutamine ABC transporter, periplasmic glutamine-binding protein GlnH 62% 301.6
lo HSERO_RS00310 ABC transporter substrate-binding protein histidine ABC transporter, periplasmic histidine-binding protein HisJ (characterized) 31% 99% 116.7 Basic amino acid uptake transporter, BgtAB 36% 140.2

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 artJ

Or cluster all characterized artJ 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, 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