chemotaxis protein CheY;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446686521   1 MADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSA 80
Cdd:PRK10610   1 MADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGFGFVISDWNMPNMDGLELLKTIRADGAMSA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 446686521  81 LPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKLGM 129
Cdd:PRK10610  81 LPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKLGM 129

chemotaxis protein CheY;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446686521   1 MADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSA 80
Cdd:PRK10610   1 MADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGFGFVISDWNMPNMDGLELLKTIRADGAMSA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 446686521  81 LPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKLGM 129
Cdd:PRK10610  81 LPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKLGM 129

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 446686521   1 MADKELKFLVVDDFSTMRRIVRNLLKELGFNnVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSA 80
Cdd:COG0784    1 PPLGGKRILVVDDNPDNRELLRRLLERLGYE-VTTAEDGAEALELLRAGPPDLILLDINMPGMDGLELLRRIRALPRLPD 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 446686521  81 LPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 126
Cdd:COG0784   80 IPIIALTAYADEEDRERALEAGADDYLTKPVDPEELLEALRRLLAR 125

chemotaxis protein CheY;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446686521   1 MADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSA 80
Cdd:PRK10610   1 MADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGFGFVISDWNMPNMDGLELLKTIRADGAMSA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 446686521  81 LPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKLGM 129
Cdd:PRK10610  81 LPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKLGM 129

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 446686521   1 MADKELKFLVVDDFSTMRRIVRNLLKELGFNnVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSA 80
Cdd:COG0784    1 PPLGGKRILVVDDNPDNRELLRRLLERLGYE-VTTAEDGAEALELLRAGPPDLILLDINMPGMDGLELLRRIRALPRLPD 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 446686521  81 LPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 126
Cdd:COG0784   80 IPIIALTAYADEEDRERALEAGADDYLTKPVDPEELLEALRRLLAR 125

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 446686521   6 LKFLVVDDFSTMRRIVRNLLKELGFNnVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGamSALPVLM 85
Cdd:COG0745    2 PRILVVEDDPDIRELLADALEREGYE-VDTAADGEEALELLEEERPDLILLDLMLPGMDGLEVCRRLRARP--SDIPIIM 78

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 446686521  86 VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKI 123
Cdd:COG0745   79 LTARDDEEDRVRGLEAGADDYLTKPFDPEELLARIRAL 116

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446686521   7 KFLVVDDFSTMRRIVRNLLKELGFNnVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMV 86
Cdd:cd17562    2 KILAVDDSASIRQMVSFTLRGAGYE-VVEAADGRDALSKAQSKKFDLIITDQNMPNMDGIELIKELRKLPAYKFTPILML 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 446686521  87 TAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKI 123
Cdd:cd17562   81 TTESSDEKKQEGKAAGATGWLVKPFDPEQLLEVVKKV 117

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 446686521   9 LVVDDFSTMRRIVRNLLKELGFNnVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGamSALPVLMVTA 88
Cdd:cd00156    1 LIVDDDPAIRELLKSLLEREGYE-VDTAADGEEALELLREERPDLVLLDLMMPGMDGLELLRKLRELP--PDIPVIVLTA 77

                         90       100
                 ....*....|....*....|..
gi 446686521  89 EAKKENIIAAAQAGASGYVVKP 110
Cdd:cd00156   78 KADEEDAVRALELGADDYLVKP 99

Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding domains [Signal transduction mechanisms, Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446686521   7 KFLVVDDFSTMRRIVRNLLKEL-GFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGamSALPVLM 85
Cdd:COG4753    1 KVLIVDDEPLIREGLKRILEWEaGFEVVGEAENGEEALELLEEHKPDLVITDINMPGMDGLELLEAIRELD--PDTKIII 78

                         90       100
                 ....*....|....*....|....*
gi 446686521  86 VTAEAKKENIIAAAQAGASGYVVKP 110
Cdd:COG4753   79 LSGYSDFEYAQEAIKLGADDYLLKP 103

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 446686521   9 LVVDDFSTMRRIVRNLLKELGFNnVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGamSALPVLMVTA 88
Cdd:cd17574    1 LVVEDDEEIAELLSDYLEKEGYE-VDTAADGEEALELAREEQPDLIILDVMLPGMDGFEVCRRLREKG--SDIPIIMLTA 77

                         90       100
                 ....*....|....*....|..
gi 446686521  89 EAKKENIIAAAQAGASGYVVKP 110
Cdd:cd17574   78 KDEEEDKVLGLELGADDYITKP 99

DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal transduction mechanisms];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446686521   6 LKFLVVDDFSTMRRIVRNLLKEL-GFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAmsALPVL 84
Cdd:COG4565    4 IRVLIVEDDPMVAELLRRYLERLpGFEVVGVASSGEEALALLAEHRPDLILLDIYLPDGDGLELLRELRARGP--DVDVI 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 446686521  85 MVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 126
Cdd:COG4565   82 VITAARDPETVREALRAGVVDYLIKPFTFERLREALERYLEY 123

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 446686521   9 LVVDDFSTMRRIVRNLL-KELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADgaMSALPVLMVT 87
Cdd:cd17535    2 LIVDDHPLVREGLRRLLeSEPDIEVVGEAADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRR--YPDLKVIVLT 79

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 446686521  88 AEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFE 125
Cdd:cd17535   80 AHDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAVAA 117

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 446686521   9 LVVDDFSTMRRIVRNLLKELGFNnVEEAEDGVDALNKLQAGG---------YGFVISDWNMPNMDGLELLKTIRADGAMS 79
Cdd:cd19924    2 LVVDDSPTARKQLRDLLKNLGFE-IAEAVDGEEALNKLENLAkegndlskeLDLIITDIEMPKMDGYELTFELRDDPRLA 80

                         90       100       110
                 ....*....|....*....|....*....|.
gi 446686521  80 ALPVLMVTAEAKKENIIAAAQAGASGYVVKP 110
Cdd:cd19924   81 NIPVILNSSLSGEFSRARGKKVGADAYLAKF 111

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 446686521   4 KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMsalPV 83
Cdd:COG3707    2 RGLRVLVVDDEPLRRADLREGLREAGYEVVAEAADGEDAVELVRELKPDLVIVDIDMPDRDGLEAARQISEERPA---PV 78

                         90       100       110
                 ....*....|....*....|....*....|...
gi 446686521  84 LMVTAEAKKENIIAAAQAGASGYVVKPFTAATL 116
Cdd:COG3707   79 ILLTAYSDPELIERALEAGVSAYLVKPLDPEDL 111

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446686521   7 KFLVVDDFSTMRRIVRNLLKELGFNnVEEAEDGVDALNKLQA-GGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 85
Cdd:cd17544    2 KVLVVDDSATSRNHLRALLRRHNFQ-VLEAANGQEALEVLEQhPDIKLVITDYNMPEMDGFELVREIRKKYSRDQLAIIG 80

                         90       100
                 ....*....|....*....|....*...
gi 446686521  86 VTAEAKkeNIIAAA--QAGASGYVVKPF 111
Cdd:cd17544   81 ISASGD--NALSARfiKAGANDFLTKPF 106

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446686521   8 FLVVDDFSTMRRIVRNLLKELGFNnVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGamSALPVLMVT 87
Cdd:cd17624    1 ILLVEDDALLGDGLKTGLRKAGYA-VDWVRTGAEAEAALASGPYDLVILDLGLPDGDGLDLLRRWRRQG--QSLPVLILT 77

                         90       100
                 ....*....|....*....|....
gi 446686521  88 AEAKKENIIAAAQAGASGYVVKPF 111
Cdd:cd17624   78 ARDGVDDRVAGLDAGADDYLVKPF 101

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446686521   9 LVVDDFSTMRRIVRNLL--KELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGamSALPVLMV 86
Cdd:cd17536    2 LIVDDEPLIREGLKKLIdwEELGFEVVGEAENGEEALELIEEHKPDIVITDIRMPGMDGLELIEKIRELY--PDIKIIIL 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 446686521  87 TAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKL 127
Cdd:cd17536   80 SGYDDFEYAQKAIRLGVVDYLLKPVDEEELEEALEKAKEEL 120

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 446686521   9 LVVDDFSTMRRIVRNLLKELGFNnVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTA 88
Cdd:cd17598    2 LIVEDSPTQAEQLKHILEEQGYK-VQVARNGREALAMLAEHRPTLVISDIVMPEMDGYELCRKIKSDPDLKDIPVILLTT 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 446686521  89 EAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKI 123
Cdd:cd17598   81 LSDPRDVIRGLECGADNFITKPYDEKYLLSRIKYI 115

phosphoacceptor receiver (REC) domain of uncharacterized tetratricopeptide repeat (TPR)-containing response regulators; Response regulators share the common phosphoacceptor REC domain and different output domains. This subfamily contains uncharacterized response regulators with TPR repeats as the effector or output domain, which might contain between 3 to 16 TPR repeats (each about 34 amino acids). TPR-containing proteins occur in all domains of life and the abundance of TPR-containing proteins in a bacterial proteome is not indicative of virulence. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Some members in this subfamily may contain inactive REC domains lacking canonical metal-binding and active site residues.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446686521   8 FLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPN-MDGLELLKTIRADG--AMSALpVL 84
Cdd:cd17589    1 FLIVDDQPTFRSMLKSMLRSLGVTRIDTASSGEEALRMCENKTYDIVLCDYNLGKgKNGQQLLEELRHKKliSPSTV-FI 79

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 446686521  85 MVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKL 120
Cdd:cd17589   80 MVTGESSRAMVLSALELEPDDYLLKPFTVSELRERL 115

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446686521   7 KFLVVDDFSTMRRIVRNLLKELGFNnVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMV 86
Cdd:cd17548    1 KILIVEDNPLNMKLARDLLESAGYE-VLEAADGEEALEIARKEKPDLILMDIQLPGMDGLEATRLLKEDPATRDIPVIAL 79

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 446686521  87 TAEAKK---ENIIAaaqAGASGYVVKPFTAATLEEKLNK 122
Cdd:cd17548   80 TAYAMKgdrEKILE---AGCDGYISKPIDTREFLETVAK 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 446686521   9 LVVDDFSTMRRIVRNLLKELGFNnVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTA 88
Cdd:cd19920    2 LIVDDVPDNLRLLSELLRAAGYR-VLVATDGQQALQRAQAEPPDLILLDVMMPGMDGFEVCRRLKADPATRHIPVIFLTA 80

                         90       100
                 ....*....|....*....|...
gi 446686521  89 EAKKENIIAAAQAGASGYVVKPF 111
Cdd:cd19920   81 LTDTEDKVKGFELGAVDYITKPF 103

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 446686521   9 LVVDDFSTMRRIVRNLLKELGFNnVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGamSALPVLMVTA 88
Cdd:cd17625    1 LVVEDEKDLSEAITKHLKKEGYT-VDVCFDGEEGLEYALSGIYDLIILDIMLPGMDGLEVLKSLREEG--IETPVLLLTA 77

                         90       100
                 ....*....|....*....|....*...
gi 446686521  89 EAKKENIIAAAQAGASGYVVKPFTAATL 116
Cdd:cd17625   78 LDAVEDRVKGLDLGADDYLPKPFSLAEL 105

phosphoacceptor receiver (REC) domain of probable transcriptional regulator Ycf29; Ycf29 is a probable response regulator of a two-component system (TCS), typically consisting a sensor and a response regulator, that functions in adaptation to changing environments. Processes regulated by TCSs in bacteria include sporulation, pathogenicity, virulence, chemotaxis, and membrane transport. Ycf29 contains an N-terminal REC domain and a LuxR-type helix-turn-helix DNA-binding output domain. 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 446686521   9 LVVDDFSTMRRIVRNLLKELGFNnVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTA 88
Cdd:cd19927    2 LLVDDDPGIRLAVKDYLEDQGFT-VIAASNGLEALDLLNQYIPDLIISDIIMPGVDGYSLLGKLRKNADFDTIPVIFLTA 80

                         90       100
                 ....*....|....*....|..
gi 446686521  89 EAKKENIIAAAQAGASGYVVKP 110
Cdd:cd19927   81 KGMTSDRIKGYNAGCDGYLSKP 102

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 446686521   7 KFLVVDDFSTMRRIVRNLLKELGFNnVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMV 86
Cdd:cd17538    1 KILVVDDEPANRELLEALLSAEGYE-VLTADSGQEALALAEEELPDLILLDVMMPGMDGFEVCRRLKEDPETRHIPVIMI 79

                         90       100
                 ....*....|....*....|....*
gi 446686521  87 TAEAKKENIIAAAQAGASGYVVKPF 111
Cdd:cd17538   80 TALDDREDRIRGLEAGADDFLSKPI 104

phosphoacceptor receiver (REC) domain of CpxR-like OmpR family response regulators; CpxR is part of the CpxA/CpxR two-component regulatory system that mediates envelope stress responses that is key for virulence and antibiotic resistance in several Gram negative pathogens. CpxR is a transcription factor/response regulator that controls the expression of numerous genes, including those of the classical porins OmpF and OmpC. It belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446686521   9 LVVDDFSTMRRIVRNLLKELGFNnVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADgamSALPVLMVTA 88
Cdd:cd17623    2 LLIDDDRELTELLTEYLEMEGFN-VRAAHDGEQGLAALLEGSPDLVVLDVMLPKMNGLDVLKELRKT---SQVPVLMLTA 77

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 446686521  89 EAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKI 123
Cdd:cd17623   78 RGDDIDRILGLELGADDYLPKPFNPRELVARIRAI 112

sigma-54-dependent response regulator transcription factor ZraR;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446686521   1 MADKELKFLVVDDFSTMRRIVRNLLKELGFNnVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRAdgAMSA 80
Cdd:PRK10365   1 MTHDNIDILVVDDDISHCTILQALLRGWGYN-VALANSGRQALEQVREQVFDLVLCDVRMAEMDGIATLKEIKA--LNPA 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 446686521  81 LPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNK 122
Cdd:PRK10365  78 IPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEK 119

phosphoacceptor receiver (REC) domain of PrrA-like OmpR family response regulators; The Mycobacterium tuberculosis PrrA is part of the PrrA/PrrB two-component system (TCS) that has been implicated in early intracellular multiplication and is essential for viability. Also included in this subfamily is Mycobacterium tuberculosis MprA, part of the MprAB TCS that regulates EspR, a key regulator of the ESX-1 secretion system, and is required for establishment and maintenance of persistent infection in a tissue- and stage-specific fashion. PrrA and MprA belong to the OmpR family of DNA-binding response regulators, which contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446686521   9 LVVDDFSTMRRIVRNLLKELGFNnVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGamSALPVLMVTA 88
Cdd:cd17627    2 LVVDDDRAVRESLRRSLRFEGYE-VETAVDGAEALRVISGNRPDAVVLDVMMPRLDGLEVCRRLRAAG--NDLPILVLTA 78

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 446686521  89 EAKKENIIAAAQAGASGYVVKPFtaaTLEEKLNKI 123
Cdd:cd17627   79 RDSVSDRVAGLDAGADDYLVKPF---ALEELLARV 110

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 446686521   6 LKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADgamSALPVLM 85
Cdd:cd19932    1 VRVLIAEDEALIRMDLREMLEEAGYEVVGEASDGEEAVELAKKHKPDLVIMDVKMPRLDGIEAAKIITSE---NIAPIVL 77

                         90       100       110
                 ....*....|....*....|....*....|.
gi 446686521  86 VTAEAKKENIIAAAQAGASGYVVKPFTAATL 116
Cdd:cd19932   78 LTAYSQQDLVERAKEAGAMAYLVKPFSESDL 108

phosphoacceptor receiver (REC) domain of type B Arabidopsis response regulators (ARRs) and similar domains; Type-B ARRs (Arabidopsis response regulators) are a class of MYB-type transcription factors that act as major players in the transcriptional activation of cytokinin-responsive genes. They directly regulate the expression of type-A ARR genes and other downstream target genes. Cytokinin is a plant hormone implicated in many growth and development processes including shoot organogenesis, leaf senescence, sink/source relationships, vascular development, lateral bud release, and photomorphogenic development. Cytokinin signaling involves a phosphorelay cascade by histidine kinase receptors (AHKs), histidine phosphotransfer proteins (AHPs) and downstream ARRs. ARRs are divided into two groups, type-A and -B, according to their sequence and domain structure. Type-B ARRs contain a receiver (REC) domain and a large C-terminal extension that has characteristics of an effector or output domain, with a Myb-like DNA binding domain referred to as the GARP domain. The GARP domain is a motif specific to plant transcription factors. 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 446686521   9 LVVDDFSTMRRIVRNLLKELGFNnVEEAEDGVDALNKL--QAGGYGFVISDWNMPNMDGLELLKTIRadGAMSaLPVLMV 86
Cdd:cd17584    2 LVVDDDPTCLAILKRMLLRCGYQ-VTTCTDAEEALSMLreNKDEFDLVITDVHMPDMDGFEFLELIR--LEMD-LPVIMM 77

                         90       100       110
                 ....*....|....*....|....*....|
gi 446686521  87 TAEAKKENIIAAAQAGASGYVVKPFTAATL 116
Cdd:cd17584   78 SADGSTSTVMKGLAHGACDYLLKPVSIEDL 107