GapMind for catabolism of small carbon sources

 

Finding step aatQ for L-aspartate catabolism in Mesorhizobium ciceri WSM1271

5 candidates for aatQ: aspartate/asparagine ABC transporter, permease component 1 (AatQ)

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
lo Mesci_2739 polar amino acid ABC transporter inner membrane subunit PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 35% 86% 126.7 Glutamine ABC transporter permease and substrate binding protein protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity 37% 142.5
lo Mesci_1006 polar amino acid ABC transporter inner membrane subunit PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 32% 89% 119 Basic amino acid uptake transporter, BgtAB 41% 152.9
lo Mesci_5750 polar amino acid ABC transporter inner membrane subunit ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 (characterized) 31% 92% 114.4 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 33% 119.4
lo Mesci_0568 polar amino acid ABC transporter inner membrane subunit ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 1 (characterized) 36% 82% 105.5 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 36% 124.4
lo Mesci_3925 polar amino acid ABC transporter inner membrane subunit Glutamate/aspartate import permease protein GltJ (characterized) 31% 96% 98.6 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 41% 174.5

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 aatQ

Or cluster all characterized aatQ 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