GapMind for catabolism of small carbon sources

 

Finding step hisM for L-lysine catabolism in Oceanisphaera arctica V1-41

5 candidates for hisM: L-lysine ABC transporter, permease component 1 (HisM)

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med UN63_RS03175 ABC transporter permease ABC transporter for L-Lysine, permease component 2 (characterized) 50% 97% 219.5 AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter 56% 258.1
med UN63_RS13370 arginine ABC transporter permease ArtM Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane 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) 42% 100% 181.4 Arginine ABC transporter permease protein ArtM 51% 225.3
lo UN63_RS12585 glutamine ABC transporter permease GlnP ABC transporter for L-Lysine, permease component 2 (characterized) 36% 97% 136.7 Glutamine transport system permease protein GlnP aka B0810, component of Three component ABC L-glutamine porter. The basal ATPase activity (ATP hydrolysis in the absence of substrate) is mainly caused by the docking of the closed-unliganded state of GlnH onto the transporter domain of GlnPQ. Unlike glutamine, arginine binds both GlnH domains, but does not trigger their closing. Comparison of the ATPase activity in nanodiscs with glutamine transport in proteoliposomes suggested that the stoichiometry of ATP per substrate is close to two 80% 353.2
lo UN63_RS04695 amino acid ABC transporter permease ABC transporter for L-Lysine, permease component 2 (characterized) 36% 96% 124.8 Probable amino-acid permease protein YxeN 49% 211.5
lo UN63_RS13375 arginine ABC transporter permease ArtQ Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane 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) 33% 93% 120.6 Arginine ABC transporter permease protein ArtQ 57% 241.5

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.

Definition of step hisM

Or cluster all characterized hisM proteins

This GapMind analysis is from Sep 24 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 (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:

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