Groups of bacterial histidine kinases according to the domain architectures of their sensing domains

Histidine kinase groupTransmembrane region (N terminal)Cytoplasmic region (C terminal)No. of kinaseseBacterial groupfReference(s)
ArchitectureaLength (aa)bArchitecturecHK classd
Periplasmic sensing∼2,500
    Prototypical sensorsTMR-(50-300 aa)-TMR100-350(HAMP)- HK-(REC-HPt)NAg<1,000NA 18, 40, 139, 284
    NarX/Q-likehTMR-P-60 aa-P′-TMR∼180HAMP-Y(Cys)Q-HKHPK730Proteobacteria 35, 242
    CitA/DcuS-likeTMR-“PAS”-TMR∼200PAS-HKHPK520Proteobacteria 144, 201, 219
    VirA-likeTMR-200 aa-TMR∼300HK-RECHPK420 Agrobacterium 36, 234, 235
    VanS-likeTMR-(25-30 aa)-TMR∼90HKHPK1a10-20Actinobacteria 104, 106
    PrmB-likeTMR-(30-40 aa)-TMR∼90HAMP-HKHPK2a10-20Proteobacteria 281
    PBPb sensors (BvgS-like)TMR-PBPb1-3-TMR300-600(PAS-PAC)-HK-(REC-HPt)HPK1b50Proteobacteria 26, 148, 252
    CACHE sensorsTMR-100-CACHE-50-TMR∼300HKNAi3NAi 6
    CHASE-CHASE6 sensorsTMR-CHASE-TMR1/3∼380(HAMP)-(PAS-PAC)-HKHPK1a/b100jNAj 7, 288
    Reg-prop sensorsTMR-2βprop-(YYY)-TMR∼1,000HK-REC-AraC-HTHHPK1a40 Bacteroides 63
TMR associated∼800
    LiaS-likeTMR-(5-25 aa)-TMR∼70(HAMP)-HKHPK720 Firmicutes 120, 151, 166, 167
    BceS-likeTMR-(5-10 aa)-TMR∼60HKHPK3i70 Firmicutes 166, 167, 194
    DesK-like4/5 TMR∼150HKHPK720 Firmicutes 3
    RegB-like3TMR-RB-3TMR∼200HKcysHPK3e30Proteobacteria 55
    ComD/AgrC-like6/7 TMR∼210HKHPK1030 Firmicutes 98, 119, 160-162
    ComP-like8/10 TMR300-350HKHPK710 Firmicutes 208
    LuxN-like8/10 TMR∼300HK-RECHPK410 Vibrio 62
    PutP/CbrA-like (SSSF containing)12-20 TMR400-600(PAS)-HKHPK3d30Proteobacteria 124, 125
    MHYT sensors6 TMR∼300HK-(REC-Hpt)NAi3NAi 67
    UhpB-likeMASE1∼300HKHPK720Proteobacteria 130
    MASE sensorsMASE1250-400(PAS-PAC)-HK-RECHPK1b10Proteobacteria 5, 186
    7TMR-DISM-likeTMR-(DISMED2)-7TMR∼200/400HK-(REC)HPK1b30Proteobacteria/ spirochetes 5
    LytS-like6TMR (TMR-5TMR-LYT)∼200GAF-HKHPK840 Firmicutes/ proteobacteria 5
Cytoplasmic sensingk∼1,600 65, 88
    KdpD-like (membrane-anchored, N-terminal input)KdpD-Usp-4TMR∼500GAF-HKHPK1a100 Firmicutes/ proteobacteria 267
    ArcB-like (membrane anchored, C-terminal input)TMR-(10-20 aa)-TMR∼80Leucine zipper-PAS-HK-REC-HptHPK1b20Proteobacteria 163
    FixL-like (membrane-anchored, C-terminal input)2/3 TMRm∼100mPAS-PAC-(PAS-PAC)-HKHPK430Proteobacteria 77, 79
    CheA-like (soluble)HPT-HK-CheWHPK9150Proteobacteria 243, 244, 250, 278
    Phytochrome sensorsl (soluble)PAS-GAF- phytochrome-HKHPK3h20 133, 135, 265
  • a Conserved domains were identified using the SMART tool (229). Sizes are averages and can vary greatly. TMR are putative. RB, RegB box; P/P′, boxes defined by Stewart (242); 2β-prop, two seven-bladed sensor-specific β-propellers, based on the presence of 14 Reg_prop domains (Pfam entry), arranged in tandem repeats. All other domains are as defined in the original publications or the SMART, Interpro, or Pfam database entries (see the text and references therein).

  • b Average size of the input domain, including all (flanking) transmembrane regions.

  • c Conserved domains were identified using the SMART tool (229). HK, histidine kinase (consisting of the SMART HisKA and HATPase_c domains); HKcys, histidine kinase domain bearing additional conserved (redox-active) cysteine residues; REC, receiver domain. All other domains are according to database entries or previous publications (see the text and references).

  • d Assignment is derived from multiple-sequence alignments of each group, based on the histidine kinase classification system of Grebe and Stock (87).

  • e Due to the dynamics in the availability of sequence information in the databases, the numbers given should be viewed as rough estimates, indicative only of the distribution and general importance of each group of sensor kinases.

  • f Predominant bacterial groups are given only if <70% of the corresponding sequences are derived from one phylum.

  • g NA, not applicable.

  • h According to Stewart (242), NarX- and NarQ-like sensors differ in the absence or presence of the cysteine-rich central domain, respectively.

  • i NA due to the small number of HKs containing these domains.

  • j CHASE to CHASE6 domain-containing sensors form six independent subgroups, belonging to different HK classes from different groups of organisms. Therefore, no details can be given for these kinases as a whole.

  • k Of the extremely diverse group of cytoplasmic-sensing HKs, only individual prominent examples are represented in this table. See the text for details. There are ∼1,200 soluble kinases.

  • l There are 110 additional phytochrome sensors in plants.

  • m A number of FixL-like kinases are soluble proteins, lacking the TMR.