GapMind for catabolism of small carbon sources


Finding step gltJ for L-glutamate catabolism in Herbaspirillum seropedicae SmR1

5 candidates for gltJ: L-glutamate ABC transporter, permease component 1 (gltJ/aatQ)

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi HSERO_RS17565 glutamate/aspartate ABC transporter permease GltJ Glutamate/aspartate import permease protein GltJ (characterized) 58% 100% 289.7 Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida 32% 121.7
hi HSERO_RS19250 glutamate ABC transporter permease ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized) 51% 100% 239.2 PEP1B, component of Uptake system for glutamate and aspartate 31% 114.4
lo HSERO_RS19245 glutamate/aspartate transporter permease GltK PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 34% 96% 132.5 ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 54% 226.5
lo HSERO_RS11445 ABC transporter permease Glutamate/aspartate import permease protein GltJ (characterized) 32% 88% 126.7 ABC transporter for L-Histidine, permease component 1 73% 328.6
lo HSERO_RS21620 amino acid ABC transporter permease Glutamate/aspartate import permease protein GltJ (characterized) 31% 97% 119 Basic amino acid uptake transporter, BgtAB 44% 180.6

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 gltJ

Or cluster all characterized gltJ 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 (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