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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        1 MGKRVLIVDDAAFMRMMLKDIITKAGYEVAgEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIV 80
Cdd:COG5803   1 MMKKILIVDDQAGIRMLLKEVLKKEGYEVF-QAANGKEALEKVKELKPDLVLLDMKMPGMDGIEILKEIKEIDPDIPVIM 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
1TMY_A       81 CSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKVSK 120
Cdd:COG5803  80 MTAYGELDMVEEAKELGAKGYFTKPFDIDELREAVNKLLK 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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A          5 VLIVDDAAFMRMMLKDIITKAGYEVAgEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAM 84
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLEKEGYVVA-EADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIRRRDPTTPVIILTAH 79

                          90       100       110
                  ....*....|....*....|....*....|..
1TMY_A         85 GQQAMVIEAIKAGAKDFIVKPFQPSRVVEALN 116
Cdd:pfam00072  80 GDEDDAVEALEAGADDFLSKPFDPDELLAAIR 111

PEP-CTERM-box response regulator transcription factor; Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC (see SP|Q06065). These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158). [Regulatory functions, DNA interactions]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A          5 VLIVDDAAFMRMMLKDIItkAGYEVAgEATNGREAVEKYKELKPDIVTMDITMPE-----MNGIDAIKEIMKIDPNAKII 79
Cdd:TIGR02915   1 LLIVEDDLGLQKQLKWSF--ADYELA-VAADRESAIALVRRHEPAVVTLDLGLPPdadgaSEGLAALQQILAIAPDTKVI 77

                          90       100
                  ....*....|....*....|....*....
1TMY_A         80 VCSAMGQQAMVIEAIKAGAKDFIVKPFQP 108
Cdd:TIGR02915  78 VITGNDDRENAVKAIGLGAYDFYQKPIDP 106

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        1 MGKRVLIVDDAAFMRMMLKDIITKAGYEVAgEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIV 80
Cdd:COG5803   1 MMKKILIVDDQAGIRMLLKEVLKKEGYEVF-QAANGKEALEKVKELKPDLVLLDMKMPGMDGIEILKEIKEIDPDIPVIM 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
1TMY_A       81 CSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKVSK 120
Cdd:COG5803  80 MTAYGELDMVEEAKELGAKGYFTKPFDIDELREAVNKLLK 119

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        4 RVLIVDDAAFMRMMLKDIITKA-GYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPnAKIIVCS 82
Cdd:cd17541   2 RVLIVDDSAVMRKLLSRILESDpDIEVVGTARDGEEALEKIKELKPDVITLDIEMPVMDGLEALRRIMAERP-TPVVMVS 80

                        90       100
                ....*....|....*....|....*
1TMY_A       83 AMGQQ--AMVIEAIKAGAKDFIVKP 105
Cdd:cd17541  81 SLTEEgaEITLEALELGAVDFIAKP 105

chemotaxis-specific protein-glutamate methyltransferase CheB;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A         4 RVLIVDDAAFMRMMLKDIITK-AGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPnAKIIVCS 82
Cdd:PRK00742   5 RVLVVDDSAFMRRLISEILNSdPDIEVVGTAPDGLEAREKIKKLNPDVITLDVEMPVMDGLDALEKIMRLRP-TPVVMVS 83

                         90       100
                 ....*....|....*....|....*.
1TMY_A        83 AMGQQ--AMVIEAIKAGAKDFIVKPF 106
Cdd:PRK00742  84 SLTERgaEITLRALELGAVDFVTKPF 109

phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response regulators; This family is composed of uncharacterized response regulators that contain a REC domain and a AraC family helix-turn-helix (HTH) DNA-binding output domain, including Bacillus subtilis uncharacterized transcriptional regulatory protein YesN and Staphylococcus aureus uncharacterized response regulatory protein SAR0214. YesN is a member of the two-component regulatory system YesM/YesN and SAR0214 is a member of the probable two-component regulatory system SAR0215/SAR0214. Also included in this family is the AlgR-like group of LytTR/AlgR family response, which includes Pseudomonas aeruginosa positive alginate biosynthesis regulatory protein AlgR and Bacillus subtilis sensory transduction protein LytT, among others. 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        5 VLIVDDAAFMRMMLKDII--TKAGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCS 82
Cdd:cd17536   1 VLIVDDEPLIREGLKKLIdwEELGFEVVGEAENGEEALELIEEHKPDIVITDIRMPGMDGLELIEKIRELYPDIKIIILS 80

                        90       100       110
                ....*....|....*....|....*....|....*.
1TMY_A       83 AMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKV 118
Cdd:cd17536  81 GYDDFEYAQKAIRLGVVDYLLKPVDEEELEEALEKA 116

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        5 VLIVDDAAFMRMMLKDIITKA-GYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSA 83
Cdd:cd17535   1 VLIVDDHPLVREGLRRLLESEpDIEVVGEAADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRRYPDLKVIVLTA 80

                        90       100       110
                ....*....|....*....|....*....|....*
1TMY_A       84 MGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKV 118
Cdd:cd17535  81 HDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAV 115

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        4 RVLIVDDAAFMRMMLKDIITKAGYEVAgEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEImKIDPNAK---IIV 80
Cdd:COG3706   3 RILVVDDDPTNRKLLRRLLEAAGYEVV-EAADGEEALELLQEHRPDLILLDLEMPDMDGLELCRRL-RADPRTAdipIIF 80

                        90       100       110
                ....*....|....*....|....*....|....*...
1TMY_A       81 CSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKV 118
Cdd:COG3706  81 LTALDDEEDRARALEAGADDYLTKPFDPEELLARVDLV 118

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        4 RVLIVDDAAFMRMMLKDIITK-AGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCS 82
Cdd:COG3279   3 KILIVDDEPLARERLERLLEKyPDLEVVGEASNGEEALELLEEHKPDLVFLDIQMPGLDGFELARQLRELDPPPPIIFTT 82

                        90       100       110
                ....*....|....*....|....*....|....*.
1TMY_A       83 AMGQQAmvIEAIKAGAKDFIVKPFQPSRVVEALNKV 118
Cdd:COG3279  83 AYDEYA--LEAFEVNAVDYLLKPIDEERLAKALEKA 116

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        6 LIVDDAAFMRMMLKDIITKAGYEVAgEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMG 85
Cdd:cd00156   1 LIVDDDPAIRELLKSLLEREGYEVD-TAADGEEALELLREERPDLVLLDLMMPGMDGLELLRKLRELPPDIPVIVLTAKA 79

                        90       100
                ....*....|....*....|
1TMY_A       86 QQAMVIEAIKAGAKDFIVKP 105
Cdd:cd00156  80 DEEDAVRALELGADDYLVKP 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        1 MGKRVLIVDDAAFMRMMLKDIITKAGYEVAgEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEImKIDPNAK--- 77
Cdd:COG3437   5 QAPTVLIVDDDPENLELLRQLLRTLGYDVV-TAESGEEALELLLEAPPDLILLDVRMPGMDGFELLRLL-RADPSTRdip 82

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
1TMY_A       78 IIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKV 118
Cdd:COG3437  83 VIFLTALADPEDRERALEAGADDYLTKPFDPEELLARVRNA 123

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        5 VLIVDDAAFMRMMLKDIITKAGYEVAgEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAK---IIVC 81
Cdd:cd17546   1 VLVVDDNPVNRKVLKKLLEKLGYEVD-VAENGQEALELLKEEPFDLVLMDLQMPVMDGLEATRRIRELEGGGRrtpIIAL 79

                        90       100       110
                ....*....|....*....|....*....|....
1TMY_A       82 SAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEAL 115
Cdd:cd17546  80 TANALEEDREKCLEAGMDDYLSKPVKLDQLKEVL 113

phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY4 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 CheY4 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        3 KRVLIVDDAAFMRMMLKDIITKAGYEVAgEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIdPNAK---II 79
Cdd:cd17562   1 KKILAVDDSASIRQMVSFTLRGAGYEVV-EAADGRDALSKAQSKKFDLIITDQNMPNMDGIELIKELRKL-PAYKftpIL 78

                        90       100       110
                ....*....|....*....|....*....|....*....
1TMY_A       80 VCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKV 118
Cdd:cd17562  79 MLTTESSDEKKQEGKAAGATGWLVKPFDPEQLLEVVKKV 117

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        5 VLIVDDAAFMRMMLKDIITKAGYEVAgEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAM 84
Cdd:cd17550   1 ILIVDDEEDIRESLSGILEDEGYEVD-TAADGEEALKLIKERRPDLVLLDIWLPDMDGLELLKEIKEKYPDLPVIMISGH 79

                        90       100       110
                ....*....|....*....|....*....|....*.
1TMY_A       85 GQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKVSK 120
Cdd:cd17550  80 GTIETAVKATKLGAYDFIEKPLSLDRLLLTIERALE 115

phosphoacceptor receiver (REC) domain of Pseudomonas aeruginosa RssB and similar domains; Pseudomonas aeruginosa RssB is an orphan atypical response regulator containing a REC domain and a PP2C-type protein phosphatase output domain. Its function is still unknown. Escherichia RssB, which is not included in this subfamily, is a ClpX adaptor protein which alters ClpX specificity by mediating a specific interaction between ClpX and the substrates such as RpoS, an RNA polymerase sigma factor. 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        3 KRVLIVDDAAFMRMMLKDIITKAGYEVAgEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCS 82
Cdd:cd17555   1 ATILVIDDDEVVRESIAAYLEDSGFQVL-QAADGRQGLELFRSEQPDLVLCDLRMPEMDGLEVLKQITKESPDTPVIVVS 79

                        90       100       110
                ....*....|....*....|....*....|.
1TMY_A       83 AMGQQAMVIEAIKAGAKDFIVKPFQPSRVVE 113
Cdd:cd17555  80 GAGVMSDAVEALRLGAWDYLTKPIEDLAVLE 110

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        3 KRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKELKPDIVTMDITMP-EMNGIDAIKEIMKIdPNAKIIVC 81
Cdd:cd17534   1 KKILIVEDEAIIALDLKEILESLGYEVVGIADSGEEAIELAEENKPDLILMDINLKgDMDGIEAAREIREK-FDIPVIFL 79

                        90       100
                ....*....|....*....|....*
1TMY_A       82 SAMGQQAMVIEAIKAGAKDFIVKPF 106
Cdd:cd17534  80 TAYSDEETLERAKETNPYGYLVKPF 104

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        3 KRVLIVDDAAFMRMMLKDIITKAGYEVAGeATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCS 82
Cdd:COG4567   5 RSLLLVDDDEAFARVLARALERRGFEVTT-AASVEEALALLEQAPPDYAVLDLRLGDGSGLDLIEALRERDPDARIVVLT 83

                        90       100       110
                ....*....|....*....|....*....|...
1TMY_A       83 AMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEAL 115
Cdd:COG4567  84 GYASIATAVEAIKLGADDYLAKPADADDLLAAL 116

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        4 RVLIVDDAAFMRMMLKDIITKAGYEVAgEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEImKIDPNAK---IIV 80
Cdd:cd17538   1 KILVVDDEPANRELLEALLSAEGYEVL-TADSGQEALALAEEELPDLILLDVMMPGMDGFEVCRRL-KEDPETRhipVIM 78

                        90       100
                ....*....|....*....|....*.
1TMY_A       81 CSAMGQQAMVIEAIKAGAKDFIVKPF 106
Cdd:cd17538  79 ITALDDREDRIRGLEAGADDFLSKPI 104

transcriptional regulator NarL; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A         4 RVLIVDDAAFMRMMLKDII-TKAGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCS 82
Cdd:PRK10651   8 TILLIDDHPMLRTGVKQLIsMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLSGRIVVFS 87

                         90       100       110
                 ....*....|....*....|....*....|....*.
1TMY_A        83 AMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKV 118
Cdd:PRK10651  88 VSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQA 123

phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL); Nitrate/nitrite response regulator protein NarL contains an N-terminal REC domain and a C-terminal LuxR family helix-turn-helix (HTH) DNA-binding output domain. Escherichia coli NarL activates the expression of the nitrate reductase (narGHJI) and formate dehydrogenase-N (fdnGHI) operons, and represses the transcription of the fumarate reductase (frdABCD) operon in response to a nitrate/nitrite induction signal. Phosphorylation of the NarL REC domain releases the C-terminal HTH output domain that subsequently binds specific DNA promoter sites to repress or activate gene expression. 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        5 VLIVDDAAFMRMMLKDIITKA-GYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSA 83
Cdd:cd19931   1 VLLIDDHPLLRKGIKQLIELDpDFTVVGEASSGEEGIELAERLDPDLILLDLNMKGMSGLDTLKALREEGVSARIVILTV 80

                        90       100       110
                ....*....|....*....|....*....|....
1TMY_A       84 MGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNK 117
Cdd:cd19931  81 SDAEDDVVTALRAGADGYLLKDMEPEDLLEALKQ 114

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        3 KRVLIVDDAAFMR-MMLKDIITKAGYEVAgEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVC 81
Cdd:cd17593   1 MKVLICDDSSMARkQLARALPADWDVEIT-FAENGEEALEILREGRIDVLFLDLTMPVMDGYEVLEALPVEQLETKVIVV 79

                        90       100       110
                ....*....|....*....|....*....|....*..
1TMY_A       82 SAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKV 118
Cdd:cd17593  80 SGDVQPEAKERVLELGALAFLKKPFDPEKLAQLLEEL 116

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        5 VLIVDDAAFMRMMLKDIITKAGYEVAgEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAM 84
Cdd:cd17572   1 VLLVEDSPSLAALYQEYLSDEGYKVT-HVETGKEALAFLSDQPPDVVLLDLKLPDMSGMEILKWIQERSLPTSVIVITAH 79

                        90       100       110
                ....*....|....*....|....*....|...
1TMY_A       85 GQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNK 117
Cdd:cd17572  80 GSVDIAVEAMRLGAYDFLEKPFDADRLRVTVRN 112

phosphoacceptor receiver (REC) domain of photosynthetic apparatus regulatory protein RegA; Rhodobacter sphaeroides RegA, also called response regulator PrrA, is the DNA binding regulatory protein of a redox-responsive two-component regulatory system RegB/RegA that is involved in transactivating anaerobic expression of the photosynthetic apparatus. It contains a REC domain and a DNA-binding helix-turn-helix 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        3 KRVLIVDDAAFMRMMLKDIITKAGYEVAgEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCS 82
Cdd:cd17563   1 KSLLLVDDDEVFAERLARALERRGFEVE-TAHSVEEALALAREEKPDYAVLDLRLGGDSGLDLIPPLRALQPDARIVVLT 79

                        90       100       110
                ....*....|....*....|....*....|...
1TMY_A       83 AMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEAL 115
Cdd:cd17563  80 GYASIATAVEAIKLGADDYLAKPADADEILAAL 112

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        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        4 RVLIVDDAAFMRMMLKDIITKAGYEVAgEATNGREAVEKYKElKPDI--VTMDITMPEMNGIDAIKEIMKIDP--NAKII 79
Cdd:cd17544   2 KVLVVDDSATSRNHLRALLRRHNFQVL-EAANGQEALEVLEQ-HPDIklVITDYNMPEMDGFELVREIRKKYSrdQLAII 79

                        90       100
                ....*....|....*....|....*....
1TMY_A       80 VCSAMGQQAMVIEAIKAGAKDFIVKPFQP 108
Cdd:cd17544  80 GISASGDNALSARFIKAGANDFLTKPFLP 108

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1TMY_A        5 VLIVDDAAFMRMMLKDIITKAGYEVAgEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEImKIDPNAK---IIVC 81
Cdd:cd17598   1 ILIVEDSPTQAEQLKHILEEQGYKVQ-VARNGREALAMLAEHRPTLVISDIVMPEMDGYELCRKI-KSDPDLKdipVILL 78

                        90       100
                ....*....|....*....|....*
1TMY_A       82 SAMGQQAMVIEAIKAGAKDFIVKPF 106
Cdd:cd17598  79 TTLSDPRDVIRGLECGADNFITKPY 103