phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response regulators (PRRs); Two-component systems (TCSs) involving a sensor and a response regulator are used by bacteria to adapt to changing environments. Processes regulated by two-component systems in bacteria include sporulation, pathogenicity, virulence, chemotaxis, and membrane transport. Response regulators (RRs) share the common phosphoacceptor REC domain and different effector/output domains such as DNA, RNA, ligand-binding, protein-binding, or enzymatic domains. Response regulators regulate transcription, post-transcription or post-translation, or have functions such as methylesterases, adenylate or diguanylate cyclase, c-di-GMP-specific phosphodiesterases, histidine kinases, serine/threonine protein kinases, and protein phosphatases, depending on their output domains. The function of some output domains are still unknown. TCSs are found in all three domains of life - bacteria, archaea, and eukaryotes, however, the presence and abundance of particular RRs vary between the lineages. Archaea encode very few RRs with DNA-binding output domains; most are stand-alone REC domains. Among eukaryotes, TCSs are found primarily in protozoa, fungi, algae, and green plants. REC domains function as phosphorylation-mediated switches within RRs, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   4 KILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLR-EEPFSLLLTDIVMPEMDGIELARRATELDPDLKVMFITG 82
Cdd:cd18160    1 TILLADDEPSVRKFIVTTLKKAGYAVTEAESGAEALEKLQqGKDIDIVVTDIVMPEMDGIELAREARKIDPDVKILFISG 80

                         90       100
                 ....*....|....*....|...
gi 489626708  83 FAAVALNPDSKAPKDAKVLSKPF 105
Cdd:cd18160   81 GAAAAPELLSDAVGDNATLKKPF 103

phosphoacceptor receiver (REC) domain of Brucella abortus CpdR and CckA, and similar domains; Two-component systems (TCSs), consisting of a sensor and a response regulator, are used by bacteria to adapt to changing environments. Processes regulated by TCSs in bacteria include sporulation, pathogenicity, virulence, chemotaxis and membrane transport. Response regulators share the common phosphoacceptor REC domain and differ output domains such as DNA, RNA, ligand, and protein-binding, or enzymatic domain. CpdR is a stand-alone REC protein. CckA is a sensor histidine kinase containing N-terminal PAS domains and a C-terminal REC domain. CpdR and CckA are components of a regulatory phosphorelay system (composed of CckA, ChpT, CtrA and CpdR) that controls Brucella abortus cell growth, division, and intracellular survival inside mammalian host cells. CckA autophosphorylates in the presence of ATP and transfers a phosphoryl group to the conserved aspartic acid residue on its C-terminal REC domain, which is relayed to the ChpT phosphotransferase. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   4 KILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLR-EEPFSLLLTDIVMPEMDGIELARRATELDPDLKVMFITG 82
Cdd:cd18160    1 TILLADDEPSVRKFIVTTLKKAGYAVTEAESGAEALEKLQqGKDIDIVVTDIVMPEMDGIELAREARKIDPDVKILFISG 80

                         90       100
                 ....*....|....*....|...
gi 489626708  83 FAAVALNPDSKAPKDAKVLSKPF 105
Cdd:cd18160   81 GAAAAPELLSDAVGDNATLKKPF 103

Response regulator receiver domain; This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708    5 ILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELARRATELDPDLKVMFITGFA 84
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLEKEGYVVAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIRRRDPTTPVIILTAHG 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 489626708   85 AValnPDSKAPKDA---KVLSKPFHLRDLVNEVN 115
Cdd:pfam00072  81 DE---DDAVEALEAgadDFLSKPFDPDELLAAIR 111

cheY-homologous receiver domain; CheY regulates the clockwise rotation of E. coli flagellar motors. This domain contains a phosphoacceptor site that is phosphorylated by histidine kinase homologues.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 489626708     4 KILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMP 57
Cdd:smart00448   2 RILVVDDDPLLRELLKALLEKEGYEVDEATDGEEALELLKEEKPDLILLDIMMP 55

phosphoacceptor receiver (REC) domain of Brucella abortus CpdR and CckA, and similar domains; Two-component systems (TCSs), consisting of a sensor and a response regulator, are used by bacteria to adapt to changing environments. Processes regulated by TCSs in bacteria include sporulation, pathogenicity, virulence, chemotaxis and membrane transport. Response regulators share the common phosphoacceptor REC domain and differ output domains such as DNA, RNA, ligand, and protein-binding, or enzymatic domain. CpdR is a stand-alone REC protein. CckA is a sensor histidine kinase containing N-terminal PAS domains and a C-terminal REC domain. CpdR and CckA are components of a regulatory phosphorelay system (composed of CckA, ChpT, CtrA and CpdR) that controls Brucella abortus cell growth, division, and intracellular survival inside mammalian host cells. CckA autophosphorylates in the presence of ATP and transfers a phosphoryl group to the conserved aspartic acid residue on its C-terminal REC domain, which is relayed to the ChpT phosphotransferase. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   4 KILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLR-EEPFSLLLTDIVMPEMDGIELARRATELDPDLKVMFITG 82
Cdd:cd18160    1 TILLADDEPSVRKFIVTTLKKAGYAVTEAESGAEALEKLQqGKDIDIVVTDIVMPEMDGIELAREARKIDPDVKILFISG 80

                         90       100
                 ....*....|....*....|...
gi 489626708  83 FAAVALNPDSKAPKDAKVLSKPF 105
Cdd:cd18160   81 GAAAAPELLSDAVGDNATLKKPF 103

CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator Spo0F [Signal transduction mechanisms];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   1 MTAKILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELAR--RATELDPDLKVM 78
Cdd:COG0784    4 GGKRILVVDDNPDNRELLRRLLERLGYEVTTAEDGAEALELLRAGPPDLILLDINMPGMDGLELLRriRALPRLPDIPII 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 489626708  79 FITGFAAVALNPDSKAPKDAKVLSKPFHLRDLVNEVNKMLAA 120
Cdd:COG0784   84 ALTAYADEEDRERALEAGADDYLTKPVDPEELLEALRRLLAR 125

Response regulator receiver domain; This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708    5 ILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELARRATELDPDLKVMFITGFA 84
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLEKEGYVVAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIRRRDPTTPVIILTAHG 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 489626708   85 AValnPDSKAPKDA---KVLSKPFHLRDLVNEVN 115
Cdd:pfam00072  81 DE---DDAVEALEAgadDFLSKPFDPDELLAAIR 111

Stage 0 sporulation initiation response regulator Spo0F [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   1 MTAKILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELARRATELDPDLKVMFI 80
Cdd:COG5803    1 MMKKILIVDDQAGIRMLLKEVLKKEGYEVFQAANGKEALEKVKELKPDLVLLDMKMPGMDGIEILKEIKEIDPDIPVIMM 80

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 489626708  81 TGFAAVALNPDSKAPKDAKVLSKPFHLRDLVNEVNKMLA 119
Cdd:COG5803   81 TAYGELDMVEEAKELGAKGYFTKPFDIDELREAVNKLLK 119

phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response regulators (PRRs); Two-component systems (TCSs) involving a sensor and a response regulator are used by bacteria to adapt to changing environments. Processes regulated by two-component systems in bacteria include sporulation, pathogenicity, virulence, chemotaxis, and membrane transport. Response regulators (RRs) share the common phosphoacceptor REC domain and different effector/output domains such as DNA, RNA, ligand-binding, protein-binding, or enzymatic domains. Response regulators regulate transcription, post-transcription or post-translation, or have functions such as methylesterases, adenylate or diguanylate cyclase, c-di-GMP-specific phosphodiesterases, histidine kinases, serine/threonine protein kinases, and protein phosphatases, depending on their output domains. The function of some output domains are still unknown. TCSs are found in all three domains of life - bacteria, archaea, and eukaryotes, however, the presence and abundance of particular RRs vary between the lineages. Archaea encode very few RRs with DNA-binding output domains; most are stand-alone REC domains. Among eukaryotes, TCSs are found primarily in protozoa, fungi, algae, and green plants. REC domains function as phosphorylation-mediated switches within RRs, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   6 LLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELARRATELDPDLKVMFITGFAA 85
Cdd:cd00156    1 LIVDDDPAIRELLKSLLEREGYEVDTAADGEEALELLREERPDLVLLDLMMPGMDGLELLRKLRELPPDIPVIVLTAKAD 80

                         90
                 ....*....|....*....
gi 489626708  86 VALNPDSKAPKDAKVLSKP 104
Cdd:cd00156   81 EEDAVRALELGADDYLVKP 99

Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains [Signal transduction mechanisms];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   1 MTAKILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELAR--RATELDPDLKVM 78
Cdd:COG3437    5 QAPTVLIVDDDPENLELLRQLLRTLGYDVVTAESGEEALELLLEAPPDLILLDVRMPGMDGFELLRllRADPSTRDIPVI 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 489626708  79 FITGFAAVALNPDSKAPKDAKVLSKPFHLRDLVNEVNKMLA 119
Cdd:COG3437   85 FLTALADPEDRERALEAGADDYLTKPFDPEELLARVRNALE 125

phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinases/response regulators similar to Arabidopsis thaliana CKI1 and Escherichia coli RcsC; This family is composed of hybrid sensor histidine kinases/response regulators that are sensor histidine kinases (HKs) fused with a REC domain, similar to the sensor histidine kinase CKI1 from Arabidopsis thaliana, which is involved in multi-step phosphorelay (MSP) signaling that mediates responses to a variety of important stimuli in plants. MSP involves a signal being transferred from HKs via histidine phosphotransfer proteins (AHP1-AHP5) to nuclear response regulators. The CKI1 REC domain specifically interacts with the downstream signaling protein AHP2, AHP3 and AHP5. The plant MSP system has evolved from the prokaryotic two-component system (TCS), which allows organisms to sense and respond to changes in environmental conditions. This family also includes bacterial hybrid sensor HKs such as Escherichia coli RcsC, which is a component of the Rcs signalling pathway that controls a variety of physiological functions like capsule synthesis, cell division, and motility. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   5 ILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELARRATELDPDLKVMFITGFA 84
Cdd:cd17546    1 VLVVDDNPVNRKVLKKLLEKLGYEVDVAENGQEALELLKEEPFDLVLMDLQMPVMDGLEATRRIRELEGGGRRTPIIALT 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 489626708  85 AVALNPDSKAPKDA---KVLSKPFHLRDLVNEV 114
Cdd:cd17546   81 ANALEEDREKCLEAgmdDYLSKPVKLDQLKEVL 113

phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator TrrA and similar domains; Thermotoga maritima contains a two-component signal transduction system (TCS) composed of the ThkA sensory histidine kinase (HK) and its cognate response regulator (RR) TrrA; the specific function of the system is unknown. TCSs couple environmental stimuli to adaptive responses. TrrA is a stand-alone RR containing only a REC domain with no output/effector domain. The REC domain itself functions as an effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   3 AKILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELARRATELDPDLKVMFITG 82
Cdd:cd17554    1 KKILVVDDEENIRELYKEELEDEGYEVVTAGNGEEALEKLESEDPDLVILDIKMPGMDGLETLRKIREKKPDLPVIICTA 80

                 .
gi 489626708  83 F 83
Cdd:cd17554   81 Y 81

histidine kinase; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   2 TAKILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEP-FSLLLTDIVMP-EMDGIELARRATELDPDLKVMF 79
Cdd:PRK13557 415 TETILIVDDRPDVAELARMILEDFGYRTLVASNGREALEILDSHPeVDLLFTDLIMPgGMNGVMLAREARRRQPKIKVLL 494

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 489626708  80 ITGFAAVALNPDSKAPKDAKVLSKPFHLRDLVNEVNKML 118
Cdd:PRK13557 495 TTGYAEASIERTDAGGSEFDILNKPYRRAELARRVRMVL 533

phosphoacceptor receiver (REC) domain of DNA-binding transcriptional regulator NtrC; DNA-binding transcriptional regulator NtrC is also called nitrogen regulation protein NR(I) or nitrogen regulator I (NRI). It contains an N-terminal receiver (REC) domain, followed by a sigma-54 interaction domain, and a C-terminal helix-turn-helix DNA-binding domain. It is part of the two-component regulatory system NtrB/NtrC, which controls expression of the nitrogen-regulated (ntr) genes in response to nitrogen limitation. DNA-binding response regulator NtrC is phosphorylated by NtrB; phosphorylation of the N-terminal REC domain activates the central sigma-54 interaction domain and leads to the transcriptional activation from promoters that require sigma(54)-containing RNA polymerase. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489626708   4 KILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELARRATELDPDLKVMFIT 81
Cdd:cd19919    2 TVWIVDDDSSIRWVLERALAGAGLTVTSFENAQEALAALASSQPDVLISDIRMPGMDGLALLAQIKQRHPDLPVIIMT 79

phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR) and similar domains; This family is composed of mostly uncharacterized response regulators with similarity to the REC domains of response regulator components of two-component systems that regulates hydrogenase activity, including HupR and HoxA. HupR is part of the HupT/HupR system that controls the synthesis of the membrane-bound [NiFe]hydrogenase, HupSL, of the photosynthetic bacterium Rhodobacter capsulatus. It contains an N-terminal REC domain, a central sigma-54 interaction domain that lacks ATPase activity, and a C-terminal DNA-binding domain. Members of this family contain a REC domain and various output domains including the cyclase homology domain (CHD) and the c-di-GMP phosphodiesterase domains, HD-GYP and EAL. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   4 KILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELARRATELDPDLKVMFITGF 83
Cdd:cd17569    2 TILLVDDEPNILKALKRLLRREGYEVLTATSGEEALEILKQEPVDVVISDQRMPGMDGAELLKRVRERYPDTVRILLTGY 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 489626708  84 AavalnpDSKAPKDA-------KVLSKPFHLRDLVNEVNKMLA 119
Cdd:cd17569   82 A------DLDAAIEAinegeiyRFLTKPWDDEELKETIRQALE 118

phosphoacceptor receiver (REC) domain of DivK and similar proteins; Caulobacter crescentus DivK is an essential response regulator that is involved in the complex phosphorelay pathways controlling both cell division and motility. It localizes cell cycle regulators to specific poles of the cell during division. DivK contains a stand-alone REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   4 KILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELARRATElDPDLKVMFITGF 83
Cdd:cd17548    1 KILIVEDNPLNMKLARDLLESAGYEVLEAADGEEALEIARKEKPDLILMDIQLPGMDGLEATRLLKE-DPATRDIPVIAL 79

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 489626708  84 AAVALNPDS----KAPKDAkVLSKPFHLRDLVNEVNK 116
Cdd:cd17548   80 TAYAMKGDRekilEAGCDG-YISKPIDTREFLETVAK 115

phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase PA4781 and similar domains; Pseudomonas aeruginosa cyclic di-GMP phosphodiesterase PA4781 contains an N-terminal REC domain and a C-terminal catalytic HD-GYP domain, characteristics of RpfG family response regulators. PA4781 is involved in cyclic di-3',5'-GMP (c-di-GMP) hydrolysis/degradation in a two-step reaction via the linear intermediate pGpG to produce GMP. Its unphosphorylated REC domain prevents accessibility of c-di-GMP to the active site. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   5 ILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELARR--ATELDPDLKVMFITG 82
Cdd:cd19920    1 ILIVDDVPDNLRLLSELLRAAGYRVLVATDGQQALQRAQAEPPDLILLDVMMPGMDGFEVCRRlkADPATRHIPVIFLTA 80

                 ....
gi 489626708  83 FAAV 86
Cdd:cd19920   81 LTDT 84

phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and similar proteins; NtrX is part of the two-component regulatory system NtrY/NtrX that is involved in the activation of nitrogen assimilatory genes such as Gln. It is phosphorylated by the histidine kinase NtrY and interacts with sigma-54. NtrX is a member of the NtrC family, characterized by a domain architecture containing an N-terminal REC domain, followed by a central sigma-54 interaction/ATPase domain, and a C-terminal DNA binding domain. NtrC family response regulators are sigma54-dependent transcriptional activators. Also included in this subfamily is Aquifex aeolicus NtrC4. The ability of the central domain to hydrolyze ATP and thus to interact effectively with a complex of RNA polymerase, sigma54, and promoter, is controlled by the phosphorylation status of the REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489626708   5 ILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELARRATELDPDLKVMFITG 82
Cdd:cd17550    1 ILIVDDEEDIRESLSGILEDEGYEVDTAADGEEALKLIKERRPDLVLLDIWLPDMDGLELLKEIKEKYPDLPVIMISG 78

DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   5 ILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELARRATELDPDLKVMFITGFA 84
Cdd:COG4566    2 VYIVDDDEAVRDSLAFLLESAGLRVETFASAEAFLAALDPDRPGCLLLDVRMPGMSGLELQEELAARGSPLPVIFLTGHG 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 489626708  85 AV----------ALNpdskapkdakVLSKPFHLRDLVNEVNKMLAA 120
Cdd:COG4566   82 DVpmavramkagAVD----------FLEKPFDDQALLDAVRRALAR 117

second phosphoacceptor receiver (REC) domain of Dictyostelium discoideum hybrid signal transduction histidine kinase D and similar domains; Dictyostelium discoideum hybrid signal transduction histidine kinase D (DhkD) is a large protein that contains two histidine kinase (HK) and two REC domains on the intracellular side of a single pass transmembrane domain, and extracellular PAS and PAC domains that likely are involved in ligand binding. This model represents the second REC domain and similar domains. DhkD activates the cAMP phosphodiesterase RegA to ensure proper prestalk and prespore patterning, tip formation, and the vertical elongation of the mound into a finger, in Dictyostelium discoideum. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   5 ILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELARRATELDPDLKVMFI--TG 82
Cdd:cd17580    1 ILVVDDNEDAAEMLALLLELEGAEVTTAHSGEEALEAAQRFRPDVILSDIGMPGMDGYELARRLRELPWLANTPAIalTG 80

                 ..
gi 489626708  83 FA 84
Cdd:cd17580   81 YG 82

phosphoacceptor receiver (REC) domain of PmrA-like OmpR family response regulators; This subfamily contains various OmpR family response regulators including PmrA, BasR, QseB, tctD, and RssB, which are components of two-component regulatory systems (TCSs). The PmrA/PmrB TCS controls transcription of genes that are involved in lipopolysaccharide modification in the outer membrane of bacteria, increasing bacterial resistance to host-derived antimicrobial peptides. The BasS/BasR TCS functions as an iron- and zinc-sensing transcription regulator. The QseB/QseC TCS activates the flagella regulon by activating transcription of FlhDC. The RssA/RssB TCS regulates swarming behavior in Serratia marcescens. OmpR family DNA-binding response regulators contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   5 ILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELARRATELDPDLKVMFITGFA 84
Cdd:cd17624    1 ILLVEDDALLGDGLKTGLRKAGYAVDWVRTGAEAEAALASGPYDLVILDLGLPDGDGLDLLRRWRRQGQSLPVLILTARD 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 489626708  85 AValnPDSKAPKDA---KVLSKPFHLRDLV 111
Cdd:cd17624   81 GV---DDRVAGLDAgadDYLVKPFALEELL 107

phosphoacceptor receiver (REC) domain of modulated diguanylate cyclase and similar domains; This groups includes a modulated diguanylate cyclase containing a PAS sensor domain from Desulfovibrio desulfuricans G20. Members of this group contain N-terminal REC domains and various output domains including the GGDEF, histidine kinase, and helix-turn-helix (HTH) DNA binding domains. Also included in this family is Mycobacterium tuberculosis PdtaR, a transcriptional antiterminator that contains a REC domain and an ANTAR RNA-binding output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   3 AKILLAEDDNDMRRFLVKALEKAGYKVLSY-DNGASAYDRLREEPFSLLLTDIVMP-EMDGIELARRATELdPDLKVMFI 80
Cdd:cd17534    1 KKILIVEDEAIIALDLKEILESLGYEVVGIaDSGEEAIELAEENKPDLILMDINLKgDMDGIEAAREIREK-FDIPVIFL 79

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489626708  81 TGFAavalnpDSKAPKDAKV------LSKPFHLRDL 110
Cdd:cd17534   80 TAYS------DEETLERAKEtnpygyLVKPFNEREL 109

second phosphoacceptor receiver (REC) domain of uncharacterized GGDEF domain proteins; This family is composed of uncharacterized PleD-like response regulators that contain two N-terminal REC domains and a C-terminal diguanylate cyclase output domain with the characteristic GGDEF motif at the active site. Unlike PleD which contains a REC-like adaptor domain, the second REC domain of these uncharacterized GGDEF domain proteins, described in this model, contains characteristic metal-binding and active site residues. PleD response regulators are global regulators of cell metabolism in some important human pathogens. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489626708   4 KILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEP-FSLLLTDIVMPEMDGIELARR 67
Cdd:cd17544    2 KVLVVDDSATSRNHLRALLRRHNFQVLEAANGQEALEVLEQHPdIKLVITDYNMPEMDGFELVRE 66

phosphoacceptor receiver (REC) domain of BsPhoP-like OmpR family response regulators; Bacillus subtilis PhoP (BsPhoP) is part of the PhoPR two-component system that participates in a signal transduction network that controls adaptation of the bacteria to phosphate deficiency by regulating (activating or repressing) genes of the Pho regulon upon phosphorylation by PhoR. When activated, PhoPR directs expression of phosphate scavenging enzymes, lowers synthesis of the phosphate-rich wall teichoic acid (WTA) and initiates synthesis of teichuronic acid, a non-phosphate containing replacement anionic polymer. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   6 LLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELAR--RATELDPDLKVMFITgf 83
Cdd:cd19937    1 LVVDDEEDIVELLKYNLEKEGYEVVTAYDGEEALKRAKDEKPDLIILDLMLPGIDGLEVCRilRSDPKTSSIPIIMLT-- 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 489626708  84 aavalnpdSKAPKDAKVL----------SKPFHLRDLVNEVNKML 118
Cdd:cd19937   79 --------AKGEEFDKVLglelgaddyiTKPFSPRELLARVKAVL 115

phosphoacceptor receiver (REC) domain of Rhodobacter capsulatus nitrogen regulatory protein C (NtrC) and similar NtrC family response regulators; NtrC family proteins are transcriptional regulators that have REC, AAA+ ATPase/sigma-54 interaction, and DNA-binding output domains. This subfamily of NtrC proteins include NtrC, also called nitrogen regulator I (NRI), from Rhodobacter capsulatus, Azospirillum brasilense, and Azorhizobium caulinodans. NtrC is part of the NtrB/NtrC two-component system that controls the expression of the nitrogen-regulated (ntr) genes in response to nitrogen limitation. The N-terminal REC domain of NtrC proteins regulate the activity of the protein and its phosphorylation controls the AAA+ domain oligomerization, while the central AAA+ domain participates in nucleotide binding, hydrolysis, oligomerization, and sigma54 interaction. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489626708   5 ILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELARRATELDPDLKVMFIT 81
Cdd:cd19928    1 ILVADDDRAIRTVLTQALGRAGYEVRTTGNAATLWRWVEEGEGDLVITDVVMPDENGLDLIPRIKKARPDLPIIVMS 77

phosphoacceptor receiver (REC) domain of KdpE-like OmpR family response regulators; KdpE is a component of the KdpD/KdpE two-component system (TCS) and is activated when histidine kinase KdpD senses a drop in external K+ concentration or upshift in ionic osmolarity, resulting in the expression of a heterooligomeric transporter KdpFABC. In addition, the KdpD/KdpE TCS is also an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. KdpE is a member of the OmpR family of DNA-binding response regulators that contain REC and winged helix-turn-helix (wHTH) DNA-binding output effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489626708   5 ILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELARR 67
Cdd:cd17620    1 ILVIEDEPQIRRFLRTALEAHGYRVFEAETGQEGLLEAATRKPDLIILDLGLPDMDGLEVIRR 63

phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator RR468 and similar domains; Thermotoga maritima RR468 (encoded by gene TM0468) is the cognate response regulator (RR) of the class I histidine kinase HK853 (product of gene TM0853). HK853/RR468 comprise a two-component system (TCS) that couples environmental stimuli to adaptive responses. This subfamily also includes Fremyella diplosiphon complementary adaptation response regulator homolog RcaF, a small RR that is involved in four-step phosphorelays of the complementary chromatic adaptation (CCA) system that occurs in many cyanobacteria. Both RR468 and RcaF are stand-alone RRs containing only a REC domain with no output/effector domain. The REC domain itself functions as an effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   2 TAKILLAEDDNDMRRFLVKALEK-AGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELARR-----ATELDPdl 75
Cdd:cd17552    1 SKRILVIDDEEDIREVVQACLEKlAGWEVLTASSGQEGLEKAATEQPDAILLDVMMPDMDGLATLKKlqanpETQSIP-- 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 489626708  76 kVMFITgfaAVALNPDSKAPKD---AKVLSKPFHLRDLVNEVNKML 118
Cdd:cd17552   79 -VILLT---AKAQPSDRQRFASlgvAGVIAKPFDPLTLAEQIAKLL 120

phosphoacceptor receiver (REC) domain of ChvI-like OmpR family response regulators; Sinorhizobium meliloti ChvI is part of the ExoS/ChvI two-component regulatory system (TCS) that is required for nitrogen-fixing symbiosis and exopolysaccharide synthesis. ExoS/ChvI also play important roles in regulating biofilm formation, motility, nutrient utilization, and the viability of free-living bacteria. ChvI belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489626708   5 ILLAEDDNDMRRFLVKALEKAGYKVLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELARRATELDpDLKVMFIT 81
Cdd:cd19936    1 IALVDDDRNILTSVSMALEAEGFSVETYTDGASALDGLNARPPDLAILDIKMPRMDGMELLQRLRQKS-TLPVIFLT 76

phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY family proteins; CheY family chemotaxis response regulators (RRs) comprise about 17% of bacterial RRs and almost half of all RRs in archaea. This subfamily contains Vibrio cholerae CheY3, Escherichia coli CheY, and similar CheY family RRs. CheY proteins control bacterial motility and participate in signaling phosphorelays and in protein-protein interactions. CheY RRs contain only the REC domain with no output/effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   4 KILLAEDDNDMRRFLVKALEKAGYK-VLSYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELAR--RATELDPDLKVMFI 80
Cdd:cd19923    2 KVLVVDDFSTMRRIIKNLLKELGFNnVEEAEDGVDALEKLKAGGFDFVITDWNMPNMDGLELLKtiRADGALSHLPVLMV 81

                 .
gi 489626708  81 T 81
Cdd:cd19923   82 T 82

phosphoacceptor receiver (REC) domain of chemotaxis protein CheY; The chemotaxis response regulator CheY contains a stand-alone REC domain. Chemotaxis is a behavior known for motile bacteria that directs their movement in response to chemical gradients. CheY is involved in transmitting sensory signals from chemoreceptors to the flagellar motors. Phosphorylated CheY interacts with the flagella switch components FliM and FliY, which causes counterclockwise rotation of the flagella, resulting in smooth swimming. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489626708   4 KILLAEDDNDMRRFLVKALEKAGYKVL-SYDNGASAYDRLREEPFSLLLTDIVMPEMDGIELARRATELDPDLKVMFITG 82
Cdd:cd17542    2 KVLIVDDAAFMRMMLKDILTKAGYEVVgEAANGEEAVEKYKELKPDLVTMDITMPEMDGIEALKEIKKIDPNAKVIMCSA 81

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489626708  83 FAAVALNPDSKAPKDAKVLSKPFHLRDLVNEVNKML 118
Cdd:cd17542   82 MGQEEMVKEAIKAGAKDFIVKPFQPERVLEAVEKVL 117