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 489305951   4 VSVLVVDDASFIRDLVKKCLRNYFPGiKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREQPHLKAMPFV 83
Cdd:cd19923    1 MKVLVVDDFSTMRRIIKNLLKELGFN-NVEEAEDGVDALEKLKAGGFDFVITDWNMPNMDGLELLKTIRADGALSHLPVL 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 489305951  84 MVTSRGDKENVVQAIQAGVSGYVSKPFTNEQLLNKVKQAL 123
Cdd:cd19923   80 MVTAEAKKENVIAAAQAGVNNYIVKPFTAATLKEKLEKIF 119

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 489305951   4 VSVLVVDDASFIRDLVKKCLRNYFPGiKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREQPHLKAMPFV 83
Cdd:cd19923    1 MKVLVVDDFSTMRRIIKNLLKELGFN-NVEEAEDGVDALEKLKAGGFDFVITDWNMPNMDGLELLKTIRADGALSHLPVL 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 489305951  84 MVTSRGDKENVVQAIQAGVSGYVSKPFTNEQLLNKVKQAL 123
Cdd:cd19923   80 MVTAEAKKENVIAAAQAGVNNYIVKPFTAATLKEKLEKIF 119

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 489305951    6 VLVVDDASFIRDLVKKCLRNYfpGIKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREQPHlkAMPFVMV 85
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLEKE--GYVVAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIRRRDP--TTPVIIL 76

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 489305951   86 TSRGDKENVVQAIQAGVSGYVSKPFTNEQLLNKVK 120
Cdd:pfam00072  77 TAHGDEDDAVEALEAGADDFLSKPFDPDELLAAIR 111

response regulator YycF;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489305951   6 VLVVDDASFIRDLVKKCLRNyfPGIKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELltwCREQPHLKAMPFVMV 85
Cdd:NF040534   3 ILVVDDEKPIADILEFNLKK--EGYEVFCAYDGNEALELVEEEVPDLVLLDIMLPGRDGMEV---CREVRKKYDMPIIML 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 489305951  86 TSRGDKENVVQAIQAGVSGYVSKPFTNEQLLNKVKQALNK 125
Cdd:NF040534  78 TAKDSEIDKVLGLELGADDYVTKPFSTRELIARVKANLRR 117

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 489305951   4 VSVLVVDDASFIRDLVKKCLRNYFPGiKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREQPHLKAMPFV 83
Cdd:cd19923    1 MKVLVVDDFSTMRRIIKNLLKELGFN-NVEEAEDGVDALEKLKAGGFDFVITDWNMPNMDGLELLKTIRADGALSHLPVL 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 489305951  84 MVTSRGDKENVVQAIQAGVSGYVSKPFTNEQLLNKVKQAL 123
Cdd:cd19923   80 MVTAEAKKENVIAAAQAGVNNYIVKPFTAATLKEKLEKIF 119

Two-component response regulator, PleD family, consists of two REC domains and a diguanylate cyclase (GGDEF) domain [Signal transduction mechanisms, Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489305951   3 KVSVLVVDDASFIRDLVKKCLRNYfpGIKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREQPHLKAMPF 82
Cdd:COG3706    1 PARILVVDDDPTNRKLLRRLLEAA--GYEVVEAADGEEALELLQEHRPDLILLDLEMPDMDGLELCRRLRADPRTADIPI 78

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 489305951  83 VMVTSRGDKENVVQAIQAGVSGYVSKPFTNEQLLNKV 119
Cdd:COG3706   79 IFLTALDDEEDRARALEAGADDYLTKPFDPEELLARV 115

DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, and a Fis-type DNA-binding domains [Signal transduction mechanisms];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489305951   2 SKVSVLVVDDASFIRDLVKKCLRnyFPGIKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREQPHlkAMP 81
Cdd:COG2204    1 SMARILVVDDDPDIRRLLKELLE--RAGYEVETAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRALDP--DLP 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 489305951  82 FVMVTSRGDKENVVQAIQAGVSGYVSKPFTNEQLLNKVKQALNK 125
Cdd:COG2204   77 VILLTGYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERALER 120

DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain [Signal transduction mechanisms, Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489305951   3 KVSVLVVDDASFIRDLVKKCLRNYfpGIKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREQPhlKAMPF 82
Cdd:COG0745    1 MPRILVVEDDPDIRELLADALERE--GYEVDTAADGEEALELLEEERPDLILLDLMLPGMDGLEVCRRLRARP--SDIPI 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 489305951  83 VMVTSRGDKENVVQAIQAGVSGYVSKPFTNEQLLNKVKQAL 123
Cdd:COG0745   77 IMLTARDDEEDRVRGLEAGADDYLTKPFDPEELLARIRALL 117

chemotaxis protein CheY;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489305951   7 LVVDDASFIRDLVKKCLRNYfpGI-KIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREQPHLKAMPFVMV 85
Cdd:PRK10610   9 LVVDDFSTMRRIVRNLLKEL--GFnNVEEAEDGVDALNKLQAGGFGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMV 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 489305951  86 TSRGDKENVVQAIQAGVSGYVSKPFTNEQLLNKVKQALNKIG 127
Cdd:PRK10610  87 TAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKLG 128

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 489305951   7 LVVDDASFIRDLVKKCLRNYfpGIKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREQPhlKAMPFVMVT 86
Cdd:cd00156    1 LIVDDDPAIRELLKSLLERE--GYEVDTAADGEEALELLREERPDLVLLDLMMPGMDGLELLRKLRELP--PDIPVIVLT 76

                         90       100
                 ....*....|....*....|...
gi 489305951  87 SRGDKENVVQAIQAGVSGYVSKP 109
Cdd:cd00156   77 AKADEEDAVRALELGADDYLVKP 99

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 489305951   6 VLVVDDASFIRDLVKKCLRNYfpGIKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREQPH-LKAMPFVM 84
Cdd:cd17546    1 VLVVDDNPVNRKVLKKLLEKL--GYEVDVAENGQEALELLKEEPFDLVLMDLQMPVMDGLEATRRIRELEGgGRRTPIIA 78

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 489305951  85 VTSRGDKENVVQAIQAGVSGYVSKPFTNEQLLNKV 119
Cdd:cd17546   79 LTANALEEDREKCLEAGMDDYLSKPVKLDQLKEVL 113

phosphoacceptor receiver (REC) domain of OmpR family response regulators; OmpR-like proteins are one of the most widespread transcriptional regulators. OmpR family members contain REC and winged helix-turn-helix (wHTH) DNA-binding output effector domain. They are involved in the control of environmental stress tolerance (such as the oxidative, osmotic and acid stress response), motility, virulence, outer membrane biogenesis and other processes. 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 489305951   7 LVVDDASFIRDLVKKCLRNYfpGIKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREQPHlkAMPFVMVT 86
Cdd:cd17574    1 LVVEDDEEIAELLSDYLEKE--GYEVDTAADGEEALELAREEQPDLIILDVMLPGMDGFEVCRRLREKGS--DIPIIMLT 76

                         90       100
                 ....*....|....*....|...
gi 489305951  87 SRGDKENVVQAIQAGVSGYVSKP 109
Cdd:cd17574   77 AKDEEEDKVLGLELGADDYITKP 99

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 489305951   5 SVLVVDDASFIRDLVKKCLRNYfpGIKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREQ-PHLKAMpfv 83
Cdd:cd17569    2 TILLVDDEPNILKALKRLLRRE--GYEVLTATSGEEALEILKQEPVDVVISDQRMPGMDGAELLKRVRERyPDTVRI--- 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 489305951  84 MVTSRGDKENVVQAI-QAGVSGYVSKPFTNEQLLNKVKQAL 123
Cdd:cd17569   77 LLTGYADLDAAIEAInEGEIYRFLTKPWDDEELKETIRQAL 117

phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator RpfG and similar proteins; Cyclic di-GMP phosphodiesterase response regulator RpfG, together with sensory/regulatory protein RpfC, constitute a two-component system implicated in sensing and responding to the diffusible signal factor (DSF) that is essential for cell-cell signaling. RpfC is a hybrid sensor/histidine kinase that phosphorylates and activates RpfG, which degrades cyclic di-GMP to GMP, leading to the activation of Clp, a global transcriptional regulator that regulates a large set of genes in the DSF pathway. RpfG contains a CheY-like receiver domain attached to a histidine-aspartic acid-glycine-tyrosine-proline (HD-GYP) cyclic di-GMP phosphodiesterase 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 489305951   6 VLVVDDASFIRDLVKKCLRNyFPGIKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREQPHLKAMPFVMV 85
Cdd:cd17551    3 ILIVDDNPTNLLLLEALLRS-AGYLEVVSFTDPREALAWCRENPPDLILLDYMMPGMDGLEFIRRLRALPGLEDVPIVMI 81

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 489305951  86 TSRGDKENVVQAIQAGVSGYVSKPFTNEQLLNKVK 120
Cdd:cd17551   82 TADTDREVRLRALEAGATDFLTKPFDPVELLARVR 116

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 489305951   6 VLVVDDASFIRDLVKKCLRNYfpGIKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREQPHLKAMPFVMV 85
Cdd:cd17580    1 ILVVDDNEDAAEMLALLLELE--GAEVTTAHSGEEALEAAQRFRPDVILSDIGMPGMDGYELARRLRELPWLANTPAIAL 78

                         90       100       110
                 ....*....|....*....|....*....|....
gi 489305951  86 TSRGDKENVVQAIQAGVSGYVSKPFTNEQLLNKV 119
Cdd:cd17580   79 TGYGQPEDRERALEAGFDAHLVKPVDPDELIELI 112

phosphoacceptor receiver (REC) domain of chemotaxis protein CheV and similar proteins; This subfamily includes the REC domains of Bacillus subtilis chemotaxis protein CheV, Myxococcus xanthus gliding motility regulatory protein FrzE, and similar proteins. CheV is a hybrid protein with an N-terminal CheW-like domain and a C-terminal CheY-like REC domain. The CheV pathway is one of three systems employed by B. subtilis for sensory adaptation that contribute to chemotaxis. It is involved in the transmission of sensory signals from chemoreceptors to flagellar motors. Together with CheW, it is involved in the coupling of methyl-accepting chemoreceptors to the central two-component histidine kinase CheA. FrzE is a hybrid sensor histidine kinase/response regulator that is part of the Frz pathway that controls cell reversal frequency to support directional motility during swarming and fruiting body formation. 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 489305951   6 VLVVDDASFIRDLVKKCLRNYfpGIKIEDAVNGKKAQAILM---------RETFDMVLCDWEMPEMSGLELLTWCREQPH 76
Cdd:cd19924    1 ILVVDDSPTARKQLRDLLKNL--GFEIAEAVDGEEALNKLEnlakegndlSKELDLIITDIEMPKMDGYELTFELRDDPR 78

                         90       100       110
                 ....*....|....*....|....*....|...
gi 489305951  77 LKAMPFVMVTSRGDKENVVQAIQAGVSGYVSKP 109
Cdd:cd19924   79 LANIPVILNSSLSGEFSRARGKKVGADAYLAKF 111

phosphoacceptor receiver (REC) domain of C4-dicarboxylic acid transport protein D (DctD) and similar proteins; C4-dicarboxylic acid transport protein D (DctD) is part of the two-component regulatory system DctB/DctD, which regulates C4-dicarboxylate transport via regulation of expression of the dctPQM operon and dctA. It is an activator of sigma(54)-RNA polymerase holoenzyme that uses the energy released from ATP hydrolysis to stimulate the isomerization of a closed promoter complex to an open complex capable of initiating transcription. DctD 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. 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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489305951   6 VLVVDDASFIRDLVKKCLRnyFPGIKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTwcreqpHLKAM----P 81
Cdd:cd17549    1 VLLVDDDADVREALQQTLE--LAGFRVRAFADAEEALAALSPDFPGVVISDIRMPGMDGLELLA------QIRELdpdlP 72

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 489305951  82 FVMVTSRGDKENVVQAIQAGVSGYVSKPFTNEQLLNKVKQALNK 125
Cdd:cd17549   73 VILITGHGDVPMAVEAMRAGAYDFLEKPFDPERLLDVVRRALEK 116

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489305951   6 VLVVDDASFIRDLVKKCLRNyfPGIKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREQPHLkaMPFVMV 85
Cdd:cd17550    1 ILIVDDEEDIRESLSGILED--EGYEVDTAADGEEALKLIKERRPDLVLLDIWLPDMDGLELLKEIKEKYPD--LPVIMI 76

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 489305951  86 TSRGDKENVVQAIQAGVSGYVSKPFTNEQLLNKVKQAL 123
Cdd:cd17550   77 SGHGTIETAVKATKLGAYDFIEKPLSLDRLLLTIERAL 114

phosphoacceptor receiver (REC) domain of uncharacterized hybrid sensor histidine kinase/response regulators; Typically, two-component regulatory systems (TCSs) consist of a sensor (histidine kinase) that responds to specific input(s) by modifying the output of a cognate response regulator (RR). TCSs allow organisms to sense and respond to changes in environmental conditions. Hybrid sensor histidine kinase/response regulators contain all the elements of a classical TCS in a single polypeptide chain. RRs share the common phosphoacceptor REC domain and different effector/output domains such as DNA, RNA, ligand-binding, protein-binding, or enzymatic 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 489305951   6 VLVVDDASFIRDLVKKCLRNYfpGIKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREQPHLKAMPFVMV 85
Cdd:cd17598    1 ILIVEDSPTQAEQLKHILEEQ--GYKVQVARNGREALAMLAEHRPTLVISDIVMPEMDGYELCRKIKSDPDLKDIPVILL 78

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 489305951  86 TSRGDKENVVQAIQAGVSGYVSKPFTNEQLLNKVKQAL 123
Cdd:cd17598   79 TTLSDPRDVIRGLECGADNFITKPYDEKYLLSRIKYIL 116

phosphoacceptor receiver (REC) domain of chemotaxis response regulator protein-glutamate methylesterase CheB and similar chemotaxis proteins; Methylesterase CheB is a chemotaxis response regulator with an N-terminal REC domain and a C-terminal methylesterase domain. Chemotaxis is a behavior known in motile bacteria that directs their movement in response to chemical gradients. CheB is a phosphorylation-activated response regulator involved in the reversible modification of bacterial chemotaxis receptors. It catalyzes the demethylation of specific methylglutamate residues introduced into the chemoreceptors (methyl-accepting chemotaxis proteins) by CheR. The CheB REC domain packs against the active site of the C-terminal domain and inhibits methylesterase activity by directly restricting access to the active site. Also included in this family is chemotaxis response regulator CheY, which contains a stand-alone REC domain, and an uncharacterized subfamily composed of proteins containing an N-terminal REC domain and a C-terminal CheY-P phosphatase (CheC) 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 489305951   4 VSVLVVDDASFIRDLVKKCLRNyFPGIK-IEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREQphlKAMPF 82
Cdd:cd17541    1 IRVLIVDDSAVMRKLLSRILES-DPDIEvVGTARDGEEALEKIKELKPDVITLDIEMPVMDGLEALRRIMAE---RPTPV 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 489305951  83 VMVTSRGDK--ENVVQAIQAGVSGYVSKPFTN---------EQLLNKVK 120
Cdd:cd17541   77 VMVSSLTEEgaEITLEALELGAVDFIAKPSGGisldleeiaEELIEKIK 125

first (D1) phosphoacceptor receiver (REC) domain of response regulator PleD and similar domains; PleD contains a REC domain (D1) with the phosphorylatable aspartate, a REC-like adaptor domain (D2), and the enzymatic diguanylate cyclase (DGC) domain, also called the GGDEF domain according to a conserved sequence motif, as its output domain. The GGDEF-containing PleD response regulators are global regulators of cell metabolism in some important human pathogens. This model describes D1 of PleD and similar 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 489305951   6 VLVVDDASFIRDLVKKCLRNYfpGIKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREQPHLKAMPFVMV 85
Cdd:cd17538    2 ILVVDDEPANRELLEALLSAE--GYEVLTADSGQEALALAEEELPDLILLDVMMPGMDGFEVCRRLKEDPETRHIPVIMI 79

                         90       100
                 ....*....|....*....|....*
gi 489305951  86 TSRGDKENVVQAIQAGVSGYVSKPF 110
Cdd:cd17538   80 TALDDREDRIRGLEAGADDFLSKPI 104

phosphate response regulator transcription factor PhoB;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489305951   6 VLVVDDASFIRDLVKKCL-RNYFPGIKIED---AVNGkkaqailMRETF-DMVLCDWEMPEMSGLELLTWCREQPHLKAM 80
Cdd:PRK10161   5 ILVVEDEAPIREMVCFVLeQNGFQPVEAEDydsAVNQ-------LNEPWpDLILLDWMLPGGSGIQFIKHLKRESMTRDI 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 489305951  81 PFVMVTSRGDKENVVQAIQAGVSGYVSKPFTNEQLLNKVKQALNKI 126
Cdd:PRK10161  78 PVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRRI 123

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 489305951   6 VLVVDDASFIRDLVKKCLRNyFPGIKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREQPHLKAMPFVMV 85
Cdd:cd17552    4 ILVIDDEEDIREVVQACLEK-LAGWEVLTASSGQEGLEKAATEQPDAILLDVMMPDMDGLATLKKLQANPETQSIPVILL 82

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 489305951  86 TSRGDKENVVQAIQAGVSGYVSKPFTNEQLLNKVKQALN 124
Cdd:cd17552   83 TAKAQPSDRQRFASLGVAGVIAKPFDPLTLAEQIAKLLG 121

phosphoacceptor receiver (REC) domain of MtPhoP-like OmpR family response regulators; Mycobacterium tuberculosis PhoP (MtPhoP) is part of the PhoP/PhoR two-component system that is involved in phosphate control by stimulating expression of genes involved in scavenging, transport and mobilization of phosphate, and repressing the utilization of nitrogen sources. Also included in this subfamily is Mycobacterium tuberculosis transcriptional regulatory protein TcrX, part of the two-component regulatory system TcrY/TcrX that may be involved in virulence. 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 489305951   6 VLVVDDASFIRDLVKKCLRnyFPGIKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCREqpHLKAMPFVMV 85
Cdd:cd17615    2 VLVVDDEPNITELLSMALR--YEGWDVETAADGAEALAAAREFRPDAVVLDIMLPDMDGLEVLRRLRA--DGPDVPVLFL 77

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 489305951  86 TSRGDKENVVQAIQAGVSGYVSKPFTNEQLLNKVKQAL 123
Cdd:cd17615   78 TAKDSVEDRIAGLTAGGDDYVTKPFSLEEVVARLRALL 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 489305951   6 VLVVDDASFIRDLVKKCLRNYfpGIKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELltwCR---EQPHLKAMPF 82
Cdd:cd19920    1 ILIVDDVPDNLRLLSELLRAA--GYRVLVATDGQQALQRAQAEPPDLILLDVMMPGMDGFEV---CRrlkADPATRHIPV 75

                         90       100
                 ....*....|....*....|....*...
gi 489305951  83 VMVTSRGDKENVVQAIQAGVSGYVSKPF 110
Cdd:cd19920   76 IFLTALTDTEDKVKGFELGAVDYITKPF 103

phosphoacceptor receiver (REC) domain of type 4 fimbriae expression regulatory protein PilR and similar proteins; Pseudomonas aeruginosa PilR is the response regulator of the PilS/PilR two-component regulatory system (PilSR TCS) that acts in conjunction with sigma-54 to regulate the expression of type 4 pilus (T4P) major subunit PilA. In addition, the PilSR TCS regulates flagellum-dependent swimming motility and pilus-dependent twitching motility. PilR contains an N-terminal REC domain, a central sigma-54 interaction domain, and a C-terminal Fis-type helix-turn-helix DNA-binding 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 489305951   6 VLVVDDASFIRDLVKKCLRNYfpGIKIEDAVNGKKAQAILMRETFDMVLCDWEMPEMSGLELLTWCreQPHLKAMPFVMV 85
Cdd:cd19926    1 VLVVDDEPDIRELLEITLGRM--GLDVRSARNVKEARELLASEPYDLCLTDMRLPDGSGLELVQHI--QQRLPQTPVAVI 76