TABLE 1.

Widespread types of bacterial response regulatorsa

Response regulator Output domain
TypebCOG no.Size (aa)No. in the set (% of total)NamePfam entryReference(s)
Stand-alone REC0784120659 (14.3%)RECPF00072125, 146
DNA-binding
    OmpR-like07452401526 (33.1%)wHTHPF0048688
    NarL-like2197240862 (18.7%)HTHPF0019612
    NtrC-like2204450393 (8.5%)AAA-FISPF00158 PF0295476, 95
    LytR-like3279c 250139 (3.0%)LytTRPF0439794
    PrrA-like456717048 (1.0%)FISPF0295473
    REC-AraC (YesN-like)475326048 (1.0%)HTH_AraCPF00165106
RNA-binding, AmiR/NasR-like370718040 (0.9%)ANTARPF03861119
Enzymatic
    Methylesterase (CheB-like)2201300107 (2.3%)CheBPF0133934
    Diguanylate cyclase (PleD-like)3706310154 (3.4%)d GGDEFPF0099028
    c-di-GMP phosphodiesterase (VieA-like)2200c 37083 (1.8%)d EALPF0056346
    c-di-GMP phosphodiesterase (RpfG-like)343736072 (1.6%)HD-GYP45, 111
    Protein phosphatase (RsbU-like)220835046 (1.0%)PP2C (SpoIIE)PF07228116
    Histidine kinase064235088 (1.9%)HisKA-HATPasePF00512 PF0251819
Protein-binding
    CheW-REC (CheV-like)0835c 30072 (1.6%)CheWPF01584110
  • a The table lists response regulators with at least 40 representatives in the analyzed set, found in at least two bacterial phyla.

  • b Description of the domain structure, if available, or sequence alignment.

  • c This COG contains only the output domain of this response regulator.

  • d Includes 50 response regulators that contain both GGDEF and EAL domains.