GapMind for catabolism of small carbon sources


Finding step gltL for L-glutamate catabolism in Pseudomonas fluorescens FW300-N1B4

5 candidates for gltL: L-glutamate ABC transporter, ATPase component (GltL/GluA/BztD/GlnQ/AatP/PEB1C)

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi Pf1N1B4_774 Glutamate Aspartate transport ATP-binding protein GltL (TC 3.A.1.3.4) ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 100% 100% 485.7 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 58% 288.5
med Pf1N1B4_914 ABC-type polar amino acid transport system, ATPase component BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 80% 93% 402.9 ABC transporter for D-Alanine, ATPase component 100% 513.5
med Pf1N1B4_2210 Glutamate transport ATP-binding protein GluA aka CGL1950, component of Glutamate porter (characterized) 54% 100% 264.6 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 57% 267.7
med Pf1N1B4_1711 ABC-type polar amino acid transport system, ATPase component GluA aka CGL1950, component of Glutamate porter (characterized) 52% 99% 260 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 55% 268.9
med Pf1N1B4_3435 Arginine/ornithine ABC transporter, ATP-binding protein AotP Glutamine ABC transporter ATP-binding 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 (characterized) 54% 98% 255.8 ABC transporter for L-Arginine and L-Citrulline, ATPase component 100% 498.8

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 gltL

Or cluster all characterized gltL 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