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 489061719   9 ILVVEDEVFVALDVAATVEDANGTVVGPVGTVRQAIDLINRQEVDAAILDVNLADGDVEPVLDRLKSRNIFVVIHTGGGL 88
Cdd:cd17586    1 VLVLEDEPLIAMNLEDALEDLGGKEVVTAATCAEALRSLADGPIDIAILDVNLGGETSIPVADALKRRAIPFIFATGYGD 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 489061719  89 PPRLAARYPEMPVFQKPIPPSVLTRTLATA 118
Cdd:cd17586   81 SHGIDSRLIDVPVLRKPFDADSALAALAML 110

phosphoacceptor receiver (REC) domain of PFxFATGY motif single-domain (stand-alone) response regulators; This subfamily is composed of stand-alone response regulators (RRs) containing the PFxFATG[G/Y] motif; RRs with such a motif are also called ''FAT GUY'' response regulators. Included in this subfamily are Sphingomonas melonis SdrG, Sinorhizobium meliloti Sma0114, and Erythrobacter litoralis EL_LovR. SdrG is involved in the control of the general stress response. Sma0114 is part of the Sma0113/Sma0114 two-component system (TCS) that is involved in catabolite repression and polyhydroxy butyrate synthesis. EL_LovR is involved in a light-regulated TCS. PFxFATG[G/Y] RRs are typically associated with histidine-tryptophan-glutamate (HWE) histidine kinases that constitute a subclass of the larger histidine kinase superfamily characterized by an altered ATP binding site, which lacks the F-box that is normally an integral component of the ATP lid. The PFxFATG[G/Y] motif is involved in conformational changes after phosphorylation that results in the activation of the 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 489061719   9 ILVVEDEVFVALDVAATVEDANGTVVGPVGTVRQAIDLINRQEVDAAILDVNLADGDVEPVLDRLKSRNIFVVIHTGGGL 88
Cdd:cd17586    1 VLVLEDEPLIAMNLEDALEDLGGKEVVTAATCAEALRSLADGPIDIAILDVNLGGETSIPVADALKRRAIPFIFATGYGD 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 489061719  89 PPRLAARYPEMPVFQKPIPPSVLTRTLATA 118
Cdd:cd17586   81 SHGIDSRLIDVPVLRKPFDADSALAALAML 110

response regulator; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489061719   8 RILVVEDEVFVALDVAATVEDANGTVVGPVGTVRQAIDLINRQEVDAAILDVNLADGDVEP-VLDRLKSRNIFVVIHTGG 86
Cdd:PRK13435   7 KVLIVEDEALIALELEKLVEEAGHEVVGIAMSSEQAIALGRRRQPDVALVDVHLADGPTGVeVARRLSADGGVEVVFMTG 86

                         90       100       110
                 ....*....|....*....|....*....|...
gi 489061719  87 G---LPPRLAaryPEMPVFQKPIPPSVLTRTLA 116
Cdd:PRK13435  87 NperVPHDFA---GALGVIAKPYSPRGVARALS 116

phosphoacceptor receiver (REC) domain of PFxFATGY motif single-domain (stand-alone) response regulators; This subfamily is composed of stand-alone response regulators (RRs) containing the PFxFATG[G/Y] motif; RRs with such a motif are also called ''FAT GUY'' response regulators. Included in this subfamily are Sphingomonas melonis SdrG, Sinorhizobium meliloti Sma0114, and Erythrobacter litoralis EL_LovR. SdrG is involved in the control of the general stress response. Sma0114 is part of the Sma0113/Sma0114 two-component system (TCS) that is involved in catabolite repression and polyhydroxy butyrate synthesis. EL_LovR is involved in a light-regulated TCS. PFxFATG[G/Y] RRs are typically associated with histidine-tryptophan-glutamate (HWE) histidine kinases that constitute a subclass of the larger histidine kinase superfamily characterized by an altered ATP binding site, which lacks the F-box that is normally an integral component of the ATP lid. The PFxFATG[G/Y] motif is involved in conformational changes after phosphorylation that results in the activation of the 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 489061719   9 ILVVEDEVFVALDVAATVEDANGTVVGPVGTVRQAIDLINRQEVDAAILDVNLADGDVEPVLDRLKSRNIFVVIHTGGGL 88
Cdd:cd17586    1 VLVLEDEPLIAMNLEDALEDLGGKEVVTAATCAEALRSLADGPIDIAILDVNLGGETSIPVADALKRRAIPFIFATGYGD 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 489061719  89 PPRLAARYPEMPVFQKPIPPSVLTRTLATA 118
Cdd:cd17586   81 SHGIDSRLIDVPVLRKPFDADSALAALAML 110

response regulator; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489061719   8 RILVVEDEVFVALDVAATVEDANGTVVGPVGTVRQAIDLINRQEVDAAILDVNLADGDVEP-VLDRLKSRNIFVVIHTGG 86
Cdd:PRK13435   7 KVLIVEDEALIALELEKLVEEAGHEVVGIAMSSEQAIALGRRRQPDVALVDVHLADGPTGVeVARRLSADGGVEVVFMTG 86

                         90       100       110
                 ....*....|....*....|....*....|...
gi 489061719  87 G---LPPRLAaryPEMPVFQKPIPPSVLTRTLA 116
Cdd:PRK13435  87 NperVPHDFA---GALGVIAKPYSPRGVARALS 116

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 489061719   7 RRILVVEDEVFVALDVAATVEDANGTVVGpVGTVRQAIDLINRQEVDAAILDVNLADGDVEPVLDRLKSR--NIFVVIHT 84
Cdd:COG2204    3 ARILVVDDDPDIRRLLKELLERAGYEVET-AASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRALdpDLPVILLT 81

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 489061719  85 GGGlPPRLAARYPEMPVF---QKPIPPSVLTRTLATAF 119
Cdd:COG2204   82 GYG-DVETAVEAIKAGAFdylTKPFDLEELLAAVERAL 118

phosphoacceptor receiver (REC) domain of response regulator PhyR and similar proteins; PhyR is a hybrid stress regulator that contains an N-terminal sigma-like (SL) domain and a C-terminal REC domain. Phosphorylation of the REC domain is known to promote binding of the SL domain to an anti-sigma factor. PhyR thus functions as an anti-anti-sigma factor in its phosphorylated state. It is involved in the general stress response. 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 489061719   8 RILVVEDEVFVALDVAATVEDANGTVVGPVGTVRQAIDLINRQEVDAAILDVNLADGD--VEPVLDRLKSRNIFVVIHTg 85
Cdd:cd17540    2 RVLIIEDEPLIAMDLEQIVEDLGHQVVGIARTRDEAVALARRERPDLILADIQLADGSsgIDAVNEILTTHDVPVIFVT- 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 489061719  86 gGLPPRLAARYPEMPVF--QKPIPPSVLTRTLATA 118
Cdd:cd17540   81 -AYPERLLTGERPEPTFliTKPFDPEMVKAAISQA 114

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489061719   1 MNDLEHRRILVVEDEVFVALDVAATVEDANGTVVgPVGTVRQAIDLINRQEVDAAILDVNLADGDVEPVLDRLKS----R 76
Cdd:COG3437    1 MRTGQAPTVLIVDDDPENLELLRQLLRTLGYDVV-TAESGEEALELLLEAPPDLILLDVRMPGMDGFELLRLLRAdpstR 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489061719  77 NIFVVIHTGGGLPPRL-------AARYpempvFQKPIPPSVLTRTLATAFS 120
Cdd:COG3437   80 DIPVIFLTALADPEDReraleagADDY-----LTKPFDPEELLARVRNALE 125

Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding antiterminator (ANTAR) domains [Signal transduction mechanisms, Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489061719   7 RRILVVEDEVFVALDVAATVEDANGTVVGPVGTVRQAIDLINRQEVDAAILDVNLADGDVEPVLDRLKSRNIF-VVIHTG 85
Cdd:COG3707    4 LRVLVVDDEPLRRADLREGLREAGYEVVAEAADGEDAVELVRELKPDLVIVDIDMPDRDGLEAARQISEERPApVILLTA 83

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 489061719  86 GGLPPRL--AARYPEMPVFQKPIPPSVLTRTLATAFS 120
Cdd:COG3707   84 YSDPELIerALEAGVSAYLVKPLDPEDLLPALELALA 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489061719   7 RRILVVEDEVFVALDVAATVEDANGTVVGpVGTVRQAIDLINRQEVDAAILDVNLADGDVEPVLDRLKSRNIFVVI 82
Cdd:COG0745    2 PRILVVEDDPDIRELLADALEREGYEVDT-AADGEEALELLEEERPDLILLDLMLPGMDGLEVCRRLRARPSDIPI 76

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 489061719   9 ILVVEDEVFVALDVAATVEDaNGTVVGPVGTVRQAIDLINRQEVDAAILDVNLADGDVEPVLDRLKsrnifvvihtgggl 88
Cdd:cd17550    1 ILIVDDEEDIRESLSGILED-EGYEVDTAADGEEALKLIKERRPDLVLLDIWLPDMDGLELLKEIK-------------- 65

                         90
                 ....*....|...
gi 489061719  89 pprlaARYPEMPV 101
Cdd:cd17550   66 -----EKYPDLPV 73

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 489061719   6 HRRILVVEDEVFVALDVAATVEDANGTVVgPVGTVRQAIDLINRQEVDAAILDVNLADGD-VEpVLDRLKS----RNIFV 80
Cdd:COG3706    1 PARILVVDDDPTNRKLLRRLLEAAGYEVV-EAADGEEALELLQEHRPDLILLDLEMPDMDgLE-LCRRLRAdprtADIPI 78

                 ....*
gi 489061719  81 VIHTG 85
Cdd:COG3706   79 IFLTA 83

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
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 489061719  10 LVVEDEVFVALDVAATVEDANGTVVgPVGTVRQAIDLINRQEVDAAILDVNLADGD 65
Cdd:cd17574    1 LVVEDDEEIAELLSDYLEKEGYEVD-TAADGEEALELAREEQPDLIILDVMLPGMD 55

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 489061719   7 RRILVVEDEVFVALDVAATVEDAnGTVVGPVGTVRQAIDLINRQEVDAAILDVNLADGDVEPVLDRLKSR--NIFVVIHT 84
Cdd:cd17554    1 KKILVVDDEENIRELYKEELEDE-GYEVVTAGNGEEALEKLESEDPDLVILDIKMPGMDGLETLRKIREKkpDLPVIICT 79

                 .
gi 489061719  85 G 85
Cdd:cd17554   80 A 80

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489061719   9 ILVVEDEVFVALDVAATVEDANG-TVVGPVGTVRQAIDLINRQEVDAAILDVNLADGDVEPVLDRLKSRN 77
Cdd:cd17535    1 VLIVDDHPLVREGLRRLLESEPDiEVVGEAADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRRY 70

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 489061719   9 ILVVEDEvfvaLDVAATVED---ANGTVVGPVGTVRQAIDLINRQEVDAAILDVNLADGDVEPVLDRLKSRNI--FVVIH 83
Cdd:cd17572    1 VLLVEDS----PSLAALYQEylsDEGYKVTHVETGKEALAFLSDQPPDVVLLDLKLPDMSGMEILKWIQERSLptSVIVI 76

                 ....
gi 489061719  84 TGGG 87
Cdd:cd17572   77 TAHG 80

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489061719   9 ILVVEDEVFVALDVAATVEDAnGTVVGPVGTVRQAIDLINRQEVDAAILDVNLADGDVEPVLDRLKSR 76
Cdd:cd17624    1 ILLVEDDALLGDGLKTGLRKA-GYAVDWVRTGAEAEAALASGPYDLVILDLGLPDGDGLDLLRRWRRQ 67