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 489534369   3 NKILIVDDAIFMRMIIKEALSKSGYNNLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAKVVMCS 82
Cdd:cd17542    1 KKVLIVDDAAFMRMMLKDILTKAGYEVVGEAANGEEAVEKYKELKPDLVTMDITMPEMDGIEALKEIKKIDPNAKVIMCS 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 489534369  83 AIGQENMIVEAIKLGALDFIVKPFKTETLVKVVDNAL 119
Cdd:cd17542   81 AMGQEEMVKEAIKAGAKDFIVKPFQPERVLEAVEKVL 117

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 489534369   3 NKILIVDDAIFMRMIIKEALSKSGYNNLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAKVVMCS 82
Cdd:cd17542    1 KKVLIVDDAAFMRMMLKDILTKAGYEVVGEAANGEEAVEKYKELKPDLVTMDITMPEMDGIEALKEIKKIDPNAKVIMCS 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 489534369  83 AIGQENMIVEAIKLGALDFIVKPFKTETLVKVVDNAL 119
Cdd:cd17542   81 AMGQEEMVKEAIKAGAKDFIVKPFQPERVLEAVEKVL 117

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 489534369    5 ILIVDDAIFMRMIIKEALSKSGYNnLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAKVVMCSAI 84
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLEKEGYV-VAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIRRRDPTTPVIILTAH 79

                          90       100       110
                  ....*....|....*....|....*....|..
gi 489534369   85 GQENMIVEAIKLGALDFIVKPFKTETLVKVVD 116
Cdd:pfam00072  80 GDEDDAVEALEAGADDFLSKPFDPDELLAAIR 111

sporulation transcription factor Spo0A; Spo0A, the stage 0 sporulation protein A, is a transcription factor critical for the initiation of sporulation. It contains a response regulator receiver domain (pfam00072). In Bacillus subtilis, it works together with response regulator Spo0F and the phosphotransferase Spo0B, both of which are missing from at least some sporulating species and thus not part of the endospore forming bacteria minimal gene set. Spo0A, however, is universal among endospore-forming species. [Cellular processes, Sporulation and germination]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489534369    4 KILIVDDAIFMRMIIKEALSKSGYNNLIE-ANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIK--KLDSSAKVVM 80
Cdd:TIGR02875   4 RIVIADDNKEFCNLLKEYLAAQPDMEVVGvAHNGVDALELIKEQQPDVVVLDIIMPHLDGIGVLEKLNeiELSARPRVIM 83

                          90       100       110
                  ....*....|....*....|....*....|...
gi 489534369   81 CSAIGQENMIVEAIKLGALDFIVKPFKTETLVK 113
Cdd:TIGR02875  84 LSAFGQEKITQRAVALGADYYVLKPFDLEILAA 116

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 489534369   3 NKILIVDDAIFMRMIIKEALSKSGYNNLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAKVVMCS 82
Cdd:cd17542    1 KKVLIVDDAAFMRMMLKDILTKAGYEVVGEAANGEEAVEKYKELKPDLVTMDITMPEMDGIEALKEIKKIDPNAKVIMCS 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 489534369  83 AIGQENMIVEAIKLGALDFIVKPFKTETLVKVVDNAL 119
Cdd:cd17542   81 AMGQEEMVKEAIKAGAKDFIVKPFQPERVLEAVEKVL 117

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 489534369   4 KILIVDDAIFMRMIIKEALSKSGYNnLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAKVVMCSA 83
Cdd:COG2204    4 RILVVDDDPDIRRLLKELLERAGYE-VETAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRALDPDLPVILLTG 82

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 489534369  84 IGQENMIVEAIKLGALDFIVKPFKTETLVKVVDNALK 120
Cdd:COG2204   83 YGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERALE 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 489534369   4 KILIVDDAIFMRMIIKEALSKSGYNnLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAK--VVMC 81
Cdd:COG3706    3 RILVVDDDPTNRKLLRRLLEAAGYE-VVEAADGEEALELLQEHRPDLILLDLEMPDMDGLELCRRLRADPRTADipIIFL 81

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 489534369  82 SAIGQENMIVEAIKLGALDFIVKPFKTETLVKVVD 116
Cdd:COG3706   82 TALDDEEDRARALEAGADDYLTKPFDPEELLARVD 116

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 489534369   4 KILIVDDAIFMRMIIKEALSKSGYNnLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLD--SSAKVVMC 81
Cdd:COG0784    7 RILVVDDNPDNRELLRRLLERLGYE-VTTAEDGAEALELLRAGPPDLILLDINMPGMDGLELLRRIRALPrlPDIPIIAL 85

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 489534369  82 SAIGQENMIVEAIKLGALDFIVKPFKTETLVKVVDNALK 120
Cdd:COG0784   86 TAYADEEDRERALEAGADDYLTKPVDPEELLEALRRLLA 124

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 489534369   5 ILIVDDAIFMRMIIKEALSKSGYNnLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAKVVMCSAI 84
Cdd:cd17550    1 ILIVDDEEDIRESLSGILEDEGYE-VDTAADGEEALKLIKERRPDLVLLDIWLPDMDGLELLKEIKEKYPDLPVIMISGH 79

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489534369  85 GQENMIVEAIKLGALDFIVKPFKTETLVKVVDNALK 120
Cdd:cd17550   80 GTIETAVKATKLGAYDFIEKPLSLDRLLLTIERALE 115

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 489534369   6 LIVDDAIFMRMIIKEALSKSGYNnLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAKVVMCSAIG 85
Cdd:cd00156    1 LIVDDDPAIRELLKSLLEREGYE-VDTAADGEEALELLREERPDLVLLDLMMPGMDGLELLRKLRELPPDIPVIVLTAKA 79

                         90       100
                 ....*....|....*....|
gi 489534369  86 QENMIVEAIKLGALDFIVKP 105
Cdd:cd00156   80 DEEDAVRALELGADDYLVKP 99

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 489534369   4 KILIVDDAIFMRMIIKEALSKSGYNNLI-EANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLdSSAKVVMCS 82
Cdd:cd17541    2 RVLIVDDSAVMRKLLSRILESDPDIEVVgTARDGEEALEKIKELKPDVITLDIEMPVMDGLEALRRIMAE-RPTPVVMVS 80

                         90       100
                 ....*....|....*....|....*
gi 489534369  83 AIGQENMIV--EAIKLGALDFIVKP 105
Cdd:cd17541   81 SLTEEGAEItlEALELGAVDFIAKP 105

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 489534369   6 LIVDDAIFMRMIIKEALSKSGYNnLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAKVVMCSAIG 85
Cdd:cd17574    1 LVVEDDEEIAELLSDYLEKEGYE-VDTAADGEEALELAREEQPDLIILDVMLPGMDGFEVCRRLREKGSDIPIIMLTAKD 79

                         90       100
                 ....*....|....*....|
gi 489534369  86 QENMIVEAIKLGALDFIVKP 105
Cdd:cd17574   80 EEEDKVLGLELGADDYITKP 99

DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction mechanisms];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489534369   4 KILIVDDAIFMRMIIKEALSKSGYNNLI-EANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAKVVMCS 82
Cdd:COG3279    3 KILIVDDEPLARERLERLLEKYPDLEVVgEASNGEEALELLEEHKPDLVFLDIQMPGLDGFELARQLRELDPPPPIIFTT 82

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 489534369  83 AigQENMIVEAIKLGALDFIVKPFKTETLVKVVDNALK 120
Cdd:COG3279   83 A--YDEYALEAFEVNAVDYLLKPIDEERLAKALEKAKE 118

Stage 0 sporulation initiation regulator Spo0A (response regulator, REC-HTH domains) [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489534369   1 MENKI--LIVDDAIFMRMIIKEALSKSGYNNLI-EANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSA- 76
Cdd:COG5801    1 MMEKIkvLIADDNREFCELLEEYLSSQPDMEVVgVAYNGLEALELIEEKKPDVVILDIIMPHLDGLGVLEKLREMNLEKr 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 489534369  77 -KVVMCSAIGQENMIVEAIKLGALDFIVKPFKTETLVK 113
Cdd:COG5801   81 pKVIMLTAFGQEDITQRAVELGADYYILKPFDLDVLAE 118

phosphoacceptor receiver (REC) domain of cyanobacterial phytochrome response regulator Rcp and similar domains; This family is composed of response regulators (RRs) that are members of phytochrome-associated, light-sensing two-component signal transduction pathways such as Synechocystis sp. Rcp1, Tolypothrix sp. RcpA, and Agrobacterium tumefaciens bacteriophytochrome response regulator AtBRR. They are stand-alone RRs containing only a REC domain with no output/effector domain. The REC domain itself functions as an effector domain. Also included in this family us Methanosaeta harundinacea methanogenesis regulatory protein FilR2, also a stand-alone RR. 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 489534369   4 KILIVDDAIFMRMIIKEALSKSGY-NNLIEANDGEEACNIF-------KYEKPDLMLLDITMPKKDGLEVLREIKKlDSS 75
Cdd:cd17557    1 TILLVEDNPGDAELIQEAFKEAGVpNELHVVRDGEEALDFLrgegeyaDAPRPDLILLDLNMPRMDGFEVLREIKA-DPD 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 489534369  76 AK---VVMCSAIGQENMIVEAIKLGALDFIVKPFKTETLVKVV 115
Cdd:cd17557   80 LRripVVVLTTSDAEEDIERAYELGANSYIVKPVDFEEFVEAI 122

phosphoacceptor receiver (REC) domain of uncharacterized response regulators containing a CheC domain; This subfamily is composed of uncharacterized proteins containing an N-terminal REC domain and a C-terminal CheC domain that may function as the output/effector domain of a response regulator. CheC is a CheY-P phosphatase, affecting the level of phosphorylated CheY which controls the sense of flagella rotation and determine swimming behavior of chemotactic bacteria. 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 489534369   4 KILIVDDAIFMRMIIKEALSKSGYNNLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAKVVMCSA 83
Cdd:cd17593    2 KVLICDDSSMARKQLARALPADWDVEITFAENGEEALEILREGRIDVLFLDLTMPVMDGYEVLEALPVEQLETKVIVVSG 81

                         90       100       110
                 ....*....|....*....|....*....|.
gi 489534369  84 IGQENMIVEAIKLGALDFIVKPFKTETLVKV 114
Cdd:cd17593   82 DVQPEAKERVLELGALAFLKKPFDPEKLAQL 112

phosphoacceptor receiver (REC) domain of nitrogen regulatory protein C 1 (NtrC1) from Aquifex aeolicus 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 Aquifex aeolicus NtrC1 and Vibrio quorum-sensing signal integrator LuxO. 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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489534369   5 ILIVDDAIFMRMIIKEALSKSGYNnLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAKVVMCSAI 84
Cdd:cd17572    1 VLLVEDSPSLAALYQEYLSDEGYK-VTHVETGKEALAFLSDQPPDVVLLDLKLPDMSGMEILKWIQERSLPTSVIVITAH 79

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489534369  85 GQENMIVEAIKLGALDFIVKPFKTETLVKVVDNALK 120
Cdd:cd17572   80 GSVDIAVEAMRLGAYDFLEKPFDADRLRVTVRNALK 115

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 489534369   4 KILIVDDAIFMRMIIKEALSKSGYNNLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAKV--VMC 81
Cdd:cd17551    2 RILIVDDNPTNLLLLEALLRSAGYLEVVSFTDPREALAWCRENPPDLILLDYMMPGMDGLEFIRRLRALPGLEDVpiVMI 81

                         90       100       110
                 ....*....|....*....|....*....|....
gi 489534369  82 SAIGQENMIVEAIKLGALDFIVKPF-KTETLVKV 114
Cdd:cd17551   82 TADTDREVRLRALEAGATDFLTKPFdPVELLARV 115

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 489534369   5 ILIVDDAIFMRMIIKEALSKSGYNnLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAKVVMCSAI 84
Cdd:cd17549    1 VLLVDDDADVREALQQTLELAGFR-VRAFADAEEALAALSPDFPGVVISDIRMPGMDGLELLAQIRELDPDLPVILITGH 79

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489534369  85 GQENMIVEAIKLGALDFIVKPFKTETLVKVVDNALK 120
Cdd:cd17549   80 GDVPMAVEAMRAGAYDFLEKPFDPERLLDVVRRALE 115

phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family response regulators; The NarL family is one of the more abundant families of DNA-binding response regulators (RRs). Members of the NarL family contain a REC domain and a helix-turn-helix (HTH) DNA-binding output domain, with a majority of members containing a LuxR-type HTH domain. They function as transcriptional regulators. 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 489534369   5 ILIVDDAIFMRMIIKEALSK-SGYNNLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAKVVMCSA 83
Cdd:cd17535    1 VLIVDDHPLVREGLRRLLESePDIEVVGEAADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRRYPDLKVIVLTA 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 489534369  84 IGQENMIVEAIKLGALDFIVKPFKTETLVKVV 115
Cdd:cd17535   81 HDDPEYVLRALKAGAAGYLLKDSSPEELIEAI 112

phosphoacceptor receiver (REC) domain of PdtaR and similar proteins; This subfamily includes Mycobacterium tuberculosis PdtaR, also called Rv1626, and similar proteins containing a REC domain and an ANTAR (AmiR and NasR transcription antitermination regulators) RNA-binding output domain. PdtaR is a response regulator that acts at the level of transcriptional antitermination and is a member of the PdtaR/PdtaS two-component regulatory system. 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 489534369   4 KILIVDDAIFMRMIIKEALSKSGYNNLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKlDSSAKVVMCSA 83
Cdd:cd19932    2 RVLIAEDEALIRMDLREMLEEAGYEVVGEASDGEEAVELAKKHKPDLVIMDVKMPRLDGIEAAKIITS-ENIAPIVLLTA 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489534369  84 IGQENMIVEAIKLGALDFIVKPFKTETLVKVVDNAL 119
Cdd:cd19932   81 YSQQDLVERAKEAGAMAYLVKPFSESDLIPAIEMAI 116

phosphoacceptor receiver (REC) domain of YrcF-like OmpR family response regulators; YycF appears to play an important role in cell wall integrity in a wide range of gram-positive bacteria, and may also modulate cell membrane integrity. It functions as part of a phosphotransfer system that ultimately controls the levels of competence within the bacteria. YycF belongs to the OmpR family of response regulators, which are characterized by a REC domain and a winged helix-turn-helix effector domain involved in DNA binding. 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 489534369   5 ILIVDDAIFMRMIIKEALSKSGYNnLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLdSSAKVVMCSAI 84
Cdd:cd17614    1 ILVVDDEKPISDILKFNLTKEGYE-VVTAYDGREALEKVEEEQPDLILLDLMLPEKDGLEVCREVRKT-SNVPIIMLTAK 78

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489534369  85 GQENMIVEAIKLGALDFIVKPFKTETLVKVVDNALK 120
Cdd:cd17614   79 DSEVDKVLGLELGADDYVTKPFSNRELLARVKANLR 114

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 489534369   4 KILIVDDAIFMRMIIKEALSKSGYNnLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAKVVMCSA 83
Cdd:cd17554    2 KILVVDDEENIRELYKEELEDEGYE-VVTAGNGEEALEKLESEDPDLVILDIKMPGMDGLETLRKIREKKPDLPVIICTA 80

DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains [Signal transduction mechanisms, Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489534369   2 ENKILIVDDAIFMRMIIKEALSKSGYNnLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAKVVMC 81
Cdd:COG4567    4 DRSLLLVDDDEAFARVLARALERRGFE-VTTAASVEEALALLEQAPPDYAVLDLRLGDGSGLDLIEALRERDPDARIVVL 82

                         90       100       110
                 ....*....|....*....|....*....|.
gi 489534369  82 SAIGQENMIVEAIKLGALDFIVKPFKTETLV 112
Cdd:COG4567   83 TGYASIATAVEAIKLGADDYLAKPADADDLL 113

sporulation transcription factor Spo0A; Spo0A, the stage 0 sporulation protein A, is a transcription factor critical for the initiation of sporulation. It contains a response regulator receiver domain (pfam00072). In Bacillus subtilis, it works together with response regulator Spo0F and the phosphotransferase Spo0B, both of which are missing from at least some sporulating species and thus not part of the endospore forming bacteria minimal gene set. Spo0A, however, is universal among endospore-forming species. [Cellular processes, Sporulation and germination]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489534369    4 KILIVDDAIFMRMIIKEALSKSGYNNLIE-ANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIK--KLDSSAKVVM 80
Cdd:TIGR02875   4 RIVIADDNKEFCNLLKEYLAAQPDMEVVGvAHNGVDALELIKEQQPDVVVLDIIMPHLDGIGVLEKLNeiELSARPRVIM 83

                          90       100       110
                  ....*....|....*....|....*....|...
gi 489534369   81 CSAIGQENMIVEAIKLGALDFIVKPFKTETLVK 113
Cdd:TIGR02875  84 LSAFGQEKITQRAVALGADYYVLKPFDLEILAA 116

phosphoacceptor receiver (REC) domain of DrrD-like OmpR family response regulators; DrrD is a OmpR/PhoB homolog from Thermotoga maritima whose function is not yet known. This subfamily also includes Streptococcus agalactiae transcriptional regulatory protein DltR, part of the DltS/DltR two-component system (TCS), and Pseudomonas aeruginosa transcriptional activator protein PfeR, part of the PfeR/PfeS TCS, which activates expression of the ferric enterobactin receptor. The DltS/DltR TCS regulates the expression of the dlt operon, which comprises four genes (dltA, dltB, dltC, and dltD) that catalyze the incorporation of D-alanine residues into the lipoteichoic acids. Members of this subfamily belong to the OmpR/PhoB family, which comprises of two domains, an N-terminal receiver domain and a C-terminal DNA-binding winged helix-turn-helix 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 489534369   6 LIVDDAIFMRMIIKEALSKSGYNnLIEANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAKVVMCSAIG 85
Cdd:cd17625    1 LVVEDEKDLSEAITKHLKKEGYT-VDVCFDGEEGLEYALSGIYDLIILDIMLPGMDGLEVLKSLREEGIETPVLLLTALD 79

                         90       100
                 ....*....|....*....|....*.
gi 489534369  86 QENMIVEAIKLGALDFIVKPFKTETL 111
Cdd:cd17625   80 AVEDRVKGLDLGADDYLPKPFSLAEL 105

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 489534369   5 ILIVDDAIFMRMIIKEALSKSGYNNLIeANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAK--VVMCS 82
Cdd:cd19920    1 ILIVDDVPDNLRLLSELLRAAGYRVLV-ATDGQQALQRAQAEPPDLILLDVMMPGMDGFEVCRRLKADPATRHipVIFLT 79

                         90       100
                 ....*....|....*....|....
gi 489534369  83 AIGQENMIVEAIKLGALDFIVKPF 106
Cdd:cd19920   80 ALTDTEDKVKGFELGAVDYITKPF 103

sigma-54-dependent response regulator transcription factor ZraR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489534369   5 ILIVDDAIFMRMIIKEALSKSGYNNLIeANDGEEACNIFKYEKPDLMLLDITMPKKDGLEVLREIKKLDSSAKVVMCSAI 84
Cdd:PRK10365   8 ILVVDDDISHCTILQALLRGWGYNVAL-ANSGRQALEQVREQVFDLVLCDVRMAEMDGIATLKEIKALNPAIPVLIMTAY 86

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 489534369  85 GQENMIVEAIKLGALDFIVKPFKTETLVKVVDNAL 119
Cdd:PRK10365  87 SSVETAVEALKTGALDYLIKPLDFDNLQATLEKAL 121