Ternary complex associated domain 9; Novel uncharacterized protein domain found associated with the vWA-MoxR-VMAP ternary systems. This domain is likely a phosphotransferase enzyme.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200567  346 FSIQHGDLHGENILinITDNSSSLIDYGDIGEMVSIL-DPITLECSFLFHPAATKYDWPT 404
Cdd:pfam19974 296 TSSVHGDLNPRNIL--LDGDNVYLIDYARTRPGHPLLsDFAWLEVNLLRTVLADRLDLPE 353

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 490200567   9 LIVEDEADIAENISRIFNDvfDNIEITLVACRDEAYEILDDRRifFDYITLDLNFPIVkngfekdpqNGLAVLAKCVKNL 88
Cdd:cd00156    1 LIVDDDPAIRELLKSLLER--EGYEVDTAADGEEALELLREER--PDLVLLDLMMPGM---------DGLELLRKLRELP 67

                         90       100
                 ....*....|....*....|....*.
gi 490200567  89 KGTPILILTGTSTVEMIGQFLSSSVH 114
Cdd:cd00156   68 PDIPVIVLTAKADEEDAVRALELGAD 93

Ternary complex associated domain 9; Novel uncharacterized protein domain found associated with the vWA-MoxR-VMAP ternary systems. This domain is likely a phosphotransferase enzyme.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200567  346 FSIQHGDLHGENILinITDNSSSLIDYGDIGEMVSIL-DPITLECSFLFHPAATKYDWPT 404
Cdd:pfam19974 296 TSSVHGDLNPRNIL--LDGDNVYLIDYARTRPGHPLLsDFAWLEVNLLRTVLADRLDLPE 353

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490200567   4 RTFKLLIVEDEADIAENISRIFNDVFDNIEITLVACRDEAYEILDDRRIffDYITLDLNFPIvkngfekdpQNGLAVLAK 83
Cdd:COG4565    2 KMIRVLIVEDDPMVAELLRRYLERLPGFEVVGVASSGEEALALLAEHRP--DLILLDIYLPD---------GDGLELLRE 70

                         90       100       110
                 ....*....|....*....|....*....|
gi 490200567  84 CVKNLKGTPILILTGTSTVEMIGQFLSSSV 113
Cdd:COG4565   71 LRARGPDVDVIVITAARDPETVREALRAGV 100

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 490200567    9 LIVEDEADIAENISRIFNDvfDNIEITLVACRDEAYEILDDRRifFDYITLDLNFPIVkngfekdpqNGLAVLAKCVKNL 88
Cdd:pfam00072   2 LIVDDDPLIRELLRQLLEK--EGYVVAEADDGKEALELLKEER--PDLILLDINMPGM---------DGLELLKRIRRRD 68

                          90       100
                  ....*....|....*....|.
gi 490200567   89 KGTPILILTGTSTVEMIGQFL 109
Cdd:pfam00072  69 PTTPVIILTAHGDEDDAVEAL 89

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 490200567   7 KLLIVEDEADIAENISRIFNDvFDNIEITLVACR-DEAYEILDDRRIffDYITLDLNFPIVkngfekdpqNGLAVLAKCV 85
Cdd:COG4753    1 KVLIVDDEPLIREGLKRILEW-EAGFEVVGEAENgEEALELLEEHKP--DLVITDINMPGM---------DGLELLEAIR 68

                         90       100
                 ....*....|....*....|..
gi 490200567  86 KNLKGTPILILTGTSTVEMIGQ 107
Cdd:COG4753   69 ELDPDTKIIILSGYSDFEYAQE 90

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 490200567   1 MSNRTFKLLIVEDEADIAENISRIFNDVfdNIEITLVACRDEAYEILDDRRifFDYITLDLNFPiVKNGFEkdpqnglav 80
Cdd:COG0784    1 PPLGGKRILVVDDNPDNRELLRRLLERL--GYEVTTAEDGAEALELLRAGP--PDLILLDINMP-GMDGLE--------- 66

                         90       100       110
                 ....*....|....*....|....*....|....
gi 490200567  81 LAKCVK---NLKGTPILILTGTSTVEMIGQFLSS 111
Cdd:COG0784   67 LLRRIRalpRLPDIPIIALTAYADEEDRERALEA 100

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 490200567   2 SNRTFKLLIVEDEADIAENISRIFNDvfDNIEITLVACRDEAYEILDDRRifFDYITLDLNFPiVKNGFEkdpqngLAVL 81
Cdd:COG3437    3 TGQAPTVLIVDDDPENLELLRQLLRT--LGYDVVTAESGEEALELLLEAP--PDLILLDVRMP-GMDGFE------LLRL 71

                         90       100       110
                 ....*....|....*....|....*....|
gi 490200567  82 AKCVKNLKGTPILILTGTSTVEMIGQFLSS 111
Cdd:COG3437   72 LRADPSTRDIPVIFLTALADPEDRERALEA 101

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 490200567   7 KLLIVEDEADIAENISRIFNDvfDNIEITLVACRDEAYEILDDRRifFDYITLDLNFPivkNGfekdpqNGLAVLAKCVK 86
Cdd:COG4567    6 SLLLVDDDEAFARVLARALER--RGFEVTTAASVEEALALLEQAP--PDYAVLDLRLG---DG------SGLDLIEALRE 72

                         90
                 ....*....|....*....
gi 490200567  87 NLKGTPILILTGTSTVEMI 105
Cdd:COG4567   73 RDPDARIVVLTGYASIATA 91

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 490200567   9 LIVEDEADIAENISRIFNDvfDNIEITLVACRDEA-YEILDDRrifFDYITLDLNFPIVkngfekdpqNGLAVLAKCVKN 87
Cdd:cd17625    1 LVVEDEKDLSEAITKHLKK--EGYTVDVCFDGEEGlEYALSGI---YDLIILDIMLPGM---------DGLEVLKSLREE 66

                         90
                 ....*....|....*.
gi 490200567  88 LKGTPILILTGTSTVE 103
Cdd:cd17625   67 GIETPVLLLTALDAVE 82

phosphoacceptor receiver (REC) domain of CusR-like OmpR family response regulators; Escherichia coli CusR is part of the CusS/CusR two-component system (TCS) that is involved in response to copper and silver. Other members of this subfamily include Escherichia coli PcoR, Pseudomonas syringae CopR, and Streptomyces coelicolor CutR, which are all transcriptional regulatory proteins and components of TCSs that regulate genes involved in copper resistance and/or metabolism. member of the subfamily is Escherichia coli HprR (hydrogen peroxide response regulator), previously called YdeW, which is part of the HprSR (or YedVW) TCS involved in stress response to hydrogen peroxide, as well as Cupriavidus metallidurans CzcR, which is part of the CzcS/CzcR TCS involved in the control of cobalt, zinc, and cadmium homeostasis. Members of this subfamily 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 490200567   8 LLIVEDEADIAENISRIFN------DVFDNIEITLVACRDEAYeilddrriffDYITLDLNFPIVkngfekdpqNGLAVL 81
Cdd:cd19935    1 ILVVEDEKKLAEYLKKGLTeegyavDVAYDGEDGLHLALTNEY----------DLIILDVMLPGL---------DGLEVL 61

                         90       100
                 ....*....|....*....|..
gi 490200567  82 AKCVKNLKGTPILILTGTSTVE 103
Cdd:cd19935   62 RRLRAAGKQTPVLMLTARDSVE 83

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 490200567   8 LLIVEDEADIAENISRIFNDvfDNIEITLVACRDEAYEILDDRRifFDYITLDLNFPivkngfEKDpqnGLAVLAKCVKN 87
Cdd:cd17550    1 ILIVDDEEDIRESLSGILED--EGYEVDTAADGEEALKLIKERR--PDLVLLDIWLP------DMD---GLELLKEIKEK 67

                         90
                 ....*....|....*.
gi 490200567  88 LKGTPILILTGTSTVE 103
Cdd:cd17550   68 YPDLPVIMISGHGTIE 83

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 490200567   8 LLIVEDEADIAENISRIFNDVFDNIEITLVAcRD--EAYEILDDRRIffDYITLDLNFPIVkngfekdpqNGLAVLAKCV 85
Cdd:cd17536    1 VLIVDDEPLIREGLKKLIDWEELGFEVVGEA-ENgeEALELIEEHKP--DIVITDIRMPGM---------DGLELIEKIR 68

                         90
                 ....*....|...
gi 490200567  86 KNLKGTPILILTG 98
Cdd:cd17536   69 ELYPDIKIIILSG 81

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 490200567   8 LLIVEDEADIAENISRIFNDvfDNIEITLVACRDEAYEILDDRRifFDYITLDLNFPIVkngfekdpqNGLAVLAKCVKN 87
Cdd:cd17624    1 ILLVEDDALLGDGLKTGLRK--AGYAVDWVRTGAEAEAALASGP--YDLVILDLGLPDG---------DGLDLLRRWRRQ 67

                         90
                 ....*....|....*.
gi 490200567  88 LKGTPILILTGTSTVE 103
Cdd:cd17624   68 GQSLPVLILTARDGVD 83