GapMind for catabolism of small carbon sources


Finding step hisQ for L-lysine catabolism in Ochrobactrum thiophenivorans DSM 7216

4 candidates for hisQ: L-lysine ABC transporter, permease component 2 (HisQ)

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi CEV31_RS11195 ABC transporter permease Amino acid ABC transporter, membrane protein (characterized, see rationale) 50% 97% 223 NocQ aka ATU6026 aka AGR_PTI_66, component of Nopaline porter 38% 173.7
med CEV31_RS20085 ABC transporter permease subunit Histidine transport system permease protein HisQ (characterized) 40% 98% 182.2 Octopine transport system permease protein occQ, component of Octopine porter 54% 261.5
lo CEV31_RS19195 ABC transporter permease subunit ABC transporter for L-Lysine, permease component 1 (characterized) 39% 93% 166.8 ABC transporter for L-Arginine, permease component 2 40% 172.2
lo CEV31_RS19045 amino acid ABC transporter permease ABC transporter for L-Lysine, permease component 1 (characterized) 32% 95% 124 Arginine transport system permease protein ArtQ 38% 149.4

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 hisQ

Or cluster all characterized hisQ 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