GapMind for catabolism of small carbon sources


Finding step hutV for L-histidine catabolism in Pseudomonas fluorescens GW456-L13

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

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi PfGW456L13_322 Histidine ABC transporter, ATP-binding protein (TC 3.A.1) ABC transporter for L-Histidine, ATPase component (characterized) 94% 100% 509.2 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 322.4
med PfGW456L13_3150 L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1) HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 54% 95% 280 BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport 45% 310.1
med PfGW456L13_1086 L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1) ABC transporter for L-Histidine, ATPase component (characterized) 50% 96% 248.8 ABC transporter for Carnitine, ATPase component 97% 758.1
med PfGW456L13_5065 L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1) ABC transporter for L-Histidine, ATPase component (characterized) 41% 95% 201.4 ABC-type quaternary amine transporter (EC 94% 716.8

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 hutV

Or cluster all characterized hutV 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