GapMind for catabolism of small carbon sources


Finding step Ac3H11_2560 for L-histidine catabolism in Acidovorax sp. GW101-3H11

4 candidates for Ac3H11_2560: L-histidine ABC transporter, ATPase component

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi Ac3H11_2560 Urea carboxylase-related ABC transporter, ATPase protein ABC transporter for L-Histidine, ATPase component (characterized) 100% 100% 511.9 Putative taurin uptake ABC transporter ATP-binding protein, component of The taurine uptake system, TauABC 41% 220.3
hi Ac3H11_3725 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component ABC transporter for L-Histidine, ATPase component (characterized) 44% 99% 210.3 Bicarbonate transport ATP-binding protein CmpC; EC 7.6.2.- 44% 184.9
hi Ac3H11_1076 Hydroxymethylpyrimidine ABC transporter, ATPase component ABC transporter for L-Histidine, ATPase component (characterized) 44% 91% 195.3 CynD, component of Bispecific cyanate/nitrite transporter 41% 184.5
med Ac3H11_3222 Nitrate ABC transporter, ATP-binding protein ABC transporter for L-Histidine, ATPase component (characterized) 41% 94% 186.4 Nitrate import ATP-binding protein NrtD; EC 53% 287.3

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 Ac3H11_2560

Or cluster all characterized Ac3H11_2560 proteins

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.



Related tools

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