GapMind for catabolism of small carbon sources


Finding step artJ for L-arginine catabolism in Desulfovibrio vulgaris Miyazaki F

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 DvMF_0860 extracellular solute-binding protein family 3 (RefSeq) Putative ABC transporter arginine-binding protein 2 (characterized) 34% 100% 132.1 Basic amino acid uptake transporter, BgtAB 34% 136.7
lo DvMF_1571 extracellular solute-binding protein family 3 (RefSeq) AotJ aka PA0888, component of Arginine/ornithine (but not lysine) porter (characterized) 35% 97% 128.3 L-cystine-binding protein FliY; CBP; Protein FliY; Sulfate starvation-induced protein 7; SSI7 35% 140.6
lo DvMF_1918 extracellular solute-binding protein family 3 (RefSeq) 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) 31% 99% 122.5 glutamine ABC transporter, periplasmic glutamine-binding protein GlnH 52% 248.4
lo DvMF_1344 extracellular solute-binding protein family 3 (RefSeq) arginine ABC transporter, periplasmic arginine-binding protein ArtJ (characterized) 32% 92% 108.6 ABC transporter glutamine-binding protein GlnH 32% 124.4
lo DvMF_3152 extracellular solute-binding protein family 3 (RefSeq) arginine ABC transporter, periplasmic arginine-binding protein ArtJ (characterized) 31% 99% 100.9 ABC transporter glutamine-binding protein GlnH 41% 181.0

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

GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.

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.



Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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