Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes
Fig 4
Relationship between Cache (red), PAS (blue) and GAF (green) superfamilies.
(A) HMM-to-HMM comparisons. The nodes represent domain families. Links represent reciprocal hits in hhsearch. Hits with an E-value <1e-3 are shown as thick lines, those with E-value <1e-1 are shown as thin lines and dotted lines represent hits with >90 probability score. Filled circles represent PAS and GAF domain families that were identified in HHpred search using new Cache models. Families that were not identified in these searches are depicted by empty circles (B) Sequence-to-sequence comparisons. The outer circle represents domain families. Links between individual sequences represent reciprocal BLAST hits with an E-value threshold of 1e-8, the lowest E-value at which no links between superfamilies were found. However, the overall relationships shown here remain at less stringent E-values.