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Conserved domains on  [gi|446541897|ref|WP_000619243|]
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MULTISPECIES: response regulator transcription factor [Bacillus]

Protein Classification

response regulator transcription factor( domain architecture ID 14448143)

response regulator transcription factor with a signal receiver (REC) domain and a LuxR family helix-turn-helix (HTH) domain that may be part of a two-component regulatory system

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
REC_DesR-like cd19930
phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of ...
 4-120 9.30e-62

phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of Bacillus subtilis DesR, Streptococcus pneumoniae response regulator spr1814, and similar proteins, all containing an N-terminal REC domain and a C-terminal LuxR family helix-turn-helix (HTH) DNA-binding output domain. DesR is a response regulator that, together with its cognate sensor kinase DesK, comprises a two-component regulatory system that controls membrane fluidity. Phosphorylation of the REC domain of DesR is allosterically coupled to two distinct exposed surfaces of the protein, controlling noncanonical dimerization/tetramerization, cooperative activation, and DesK binding. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


:

Pssm-ID: 381157 [Multi-domain]  Cd Length: 117  Bit Score: 187.48  E-value: 9.30e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTT 83
Cdd:cd19930    1 VLIAEDQEMVRGALAALLELEDDLEVVAQASNGQEALRLVLKHSPDVAILDIEMPGRTGLEVAAELREELPDTKVLIVTT 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 446541897  84 FARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMK 120
Cdd:cd19930   81 FGRPGYFRRALAAGVDGYVLKDRPIEELADAIRTVHA 117
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 139-194 4.25e-19

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


:

Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 76.80  E-value: 4.25e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 446541897   139 PLSDREKEVLLLAKEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEAITIA 194
Cdd:smart00421   3 SLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
 
Name Accession Description Interval E-value
REC_DesR-like cd19930
phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of ...
 4-120 9.30e-62

phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of Bacillus subtilis DesR, Streptococcus pneumoniae response regulator spr1814, and similar proteins, all containing an N-terminal REC domain and a C-terminal LuxR family helix-turn-helix (HTH) DNA-binding output domain. DesR is a response regulator that, together with its cognate sensor kinase DesK, comprises a two-component regulatory system that controls membrane fluidity. Phosphorylation of the REC domain of DesR is allosterically coupled to two distinct exposed surfaces of the protein, controlling noncanonical dimerization/tetramerization, cooperative activation, and DesK binding. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381157 [Multi-domain]  Cd Length: 117  Bit Score: 187.48  E-value: 9.30e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTT 83
Cdd:cd19930    1 VLIAEDQEMVRGALAALLELEDDLEVVAQASNGQEALRLVLKHSPDVAILDIEMPGRTGLEVAAELREELPDTKVLIVTT 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 446541897  84 FARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMK 120
Cdd:cd19930   81 FGRPGYFRRALAAGVDGYVLKDRPIEELADAIRTVHA 117
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 1-200 3.24e-40

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 133.48  E-value: 3.24e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   1 MIRIIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALkkekspckvmi 80
Cdd:COG2197    1 MIRVLIVDDHPLVREGLRALLEAEPDIEVVGEAADGEEALELLEELRPDVVLLDIRMPGMDGLEALRRL----------- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  81 lttfarpgyferamkagvhgyllkdspsedlaaairnvmkgkrevsqelmfglwqeqnpLSDREKEVLLLAKEGKTANEI 160
Cdd:COG2197   70 -----------------------------------------------------------LTPREREVLRLLAEGLSNKEI 90

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 446541897 161 AKALYLSPGTVRNYISEVLTKLDAKNRIEAITIAEEKGWI 200
Cdd:COG2197   91 AERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 3-190 8.01e-32

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 114.36  E-value: 8.01e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILT 82
Cdd:PRK10651   8 TILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLSGRIVVFS 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  83 TFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMKGKREVS----QELMFGLWQEQNP-------LSDREKEVLLLA 151
Cdd:PRK10651  88 VSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQAAAGEMVLSealtPVLAASLRANRATterdvnqLTPRERDILKLI 167

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 446541897 152 KEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEA 190
Cdd:PRK10651 168 AQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEA 206
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 4-116 2.72e-24

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.


Pssm-ID: 395025 [Multi-domain]  Cd Length: 111  Bit Score: 91.83  E-value: 2.72e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897    4 IIIAEDQRMLRGALGALLDLEDdiEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTT 83
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLEKEG--YVVAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIRRRDPTTPVIILTA 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 446541897   84 FARPGYFERAMKAGVHGYLLKDSPSEDLAAAIR 116
Cdd:pfam00072  79 HGDEDDAVEALEAGADDFLSKPFDPDELLAAIR 111
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 139-194 4.25e-19

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 76.80  E-value: 4.25e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 446541897   139 PLSDREKEVLLLAKEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEAITIA 194
Cdd:smart00421   3 SLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 139-200 1.25e-16

Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 71.14  E-value: 1.25e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446541897 139 PLSDREKEVLLLAKEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEAITIAEEKGWI 200
Cdd:COG5905   12 LLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWALRLGLL 73
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 140-196 3.79e-15

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 66.79  E-value: 3.79e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446541897 140 LSDREKEVLLLAKEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEAITIAEE 196
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
GerE pfam00196
Bacterial regulatory proteins, luxR family;
139-194 2.44e-14

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 64.53  E-value: 2.44e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 446541897  139 PLSDREKEVLLLAKEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEAITIA 194
Cdd:pfam00196   2 SLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
REC smart00448
cheY-homologous receiver domain; CheY regulates the clockwise rotation of E. coli flagellar ...
 2-58 8.53e-10

cheY-homologous receiver domain; CheY regulates the clockwise rotation of E. coli flagellar motors. This domain contains a phosphoacceptor site that is phosphorylated by histidine kinase homologues.


Pssm-ID: 214668 [Multi-domain]  Cd Length: 55  Bit Score: 52.57  E-value: 8.53e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 446541897     2 IRIIIAEDQRMLRGALGALLdlEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMP 58
Cdd:smart00448   1 MRILVVDDDPLLRELLKALL--EKEGYEVDEATDGEEALELLKEEKPDLILLDIMMP 55
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
139-196 2.49e-04

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 41.08  E-value: 2.49e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446541897 139 PLSDREKEVLLLAKEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEAITIAEE 196
Cdd:PRK04841 838 PLTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQHAQD 895
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 140-182 3.64e-04

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 39.25  E-value: 3.64e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 446541897  140 LSDREKEVLLLAK-EGKTANEIAKALYLSPGTVRNYISEVLTKL 182
Cdd:TIGR02937 111 LPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
 
Name Accession Description Interval E-value
REC_DesR-like cd19930
phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of ...
 4-120 9.30e-62

phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of Bacillus subtilis DesR, Streptococcus pneumoniae response regulator spr1814, and similar proteins, all containing an N-terminal REC domain and a C-terminal LuxR family helix-turn-helix (HTH) DNA-binding output domain. DesR is a response regulator that, together with its cognate sensor kinase DesK, comprises a two-component regulatory system that controls membrane fluidity. Phosphorylation of the REC domain of DesR is allosterically coupled to two distinct exposed surfaces of the protein, controlling noncanonical dimerization/tetramerization, cooperative activation, and DesK binding. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381157 [Multi-domain]  Cd Length: 117  Bit Score: 187.48  E-value: 9.30e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTT 83
Cdd:cd19930    1 VLIAEDQEMVRGALAALLELEDDLEVVAQASNGQEALRLVLKHSPDVAILDIEMPGRTGLEVAAELREELPDTKVLIVTT 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 446541897  84 FARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMK 120
Cdd:cd19930   81 FGRPGYFRRALAAGVDGYVLKDRPIEELADAIRTVHA 117
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 4-119 1.09e-42

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.


Pssm-ID: 381090 [Multi-domain]  Cd Length: 117  Bit Score: 139.18  E-value: 1.09e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTT 83
Cdd:cd17535    1 VLIVDDHPLVREGLRRLLESEPDIEVVGEAADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRRYPDLKVIVLTA 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 446541897  84 FARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVM 119
Cdd:cd17535   81 HDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAVA 116
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 1-200 3.24e-40

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 133.48  E-value: 3.24e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   1 MIRIIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALkkekspckvmi 80
Cdd:COG2197    1 MIRVLIVDDHPLVREGLRALLEAEPDIEVVGEAADGEEALELLEELRPDVVLLDIRMPGMDGLEALRRL----------- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  81 lttfarpgyferamkagvhgyllkdspsedlaaairnvmkgkrevsqelmfglwqeqnpLSDREKEVLLLAKEGKTANEI 160
Cdd:COG2197   70 -----------------------------------------------------------LTPREREVLRLLAEGLSNKEI 90

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 446541897 161 AKALYLSPGTVRNYISEVLTKLDAKNRIEAITIAEEKGWI 200
Cdd:COG2197   91 AERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLL 130
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 3-190 8.01e-32

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 114.36  E-value: 8.01e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILT 82
Cdd:PRK10651   8 TILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLSGRIVVFS 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  83 TFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMKGKREVS----QELMFGLWQEQNP-------LSDREKEVLLLA 151
Cdd:PRK10651  88 VSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQAAAGEMVLSealtPVLAASLRANRATterdvnqLTPRERDILKLI 167

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 446541897 152 KEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEA 190
Cdd:PRK10651 168 AQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEA 206
YesN COG4753
Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding ...
 3-104 1.37e-31

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


Pssm-ID: 443786 [Multi-domain]  Cd Length: 103  Bit Score: 110.25  E-value: 1.37e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILT 82
Cdd:COG4753    1 KVLIVDDEPLIREGLKRILEWEAGFEVVGEAENGEEALELLEEHKPDLVITDINMPGMDGLELLEAIRELDPDTKIIILS 80

                         90       100
                 ....*....|....*....|..
gi 446541897  83 TFARPGYFERAMKAGVHGYLLK 104
Cdd:COG4753   81 GYSDFEYAQEAIKLGADDYLLK 102
REC_YesN-like cd17536
phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response ...
 4-120 6.58e-30

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.


Pssm-ID: 381091 [Multi-domain]  Cd Length: 121  Bit Score: 106.65  E-value: 6.58e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDLED-DIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILT 82
Cdd:cd17536    1 VLIVDDEPLIREGLKKLIDWEElGFEVVGEAENGEEALELIEEHKPDIVITDIRMPGMDGLELIEKIRELYPDIKIIILS 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 446541897  83 tfarpGY--FE---RAMKAGVHGYLLKDSPSEDLAAAIRNVMK 120
Cdd:cd17536   81 -----GYddFEyaqKAIRLGVVDYLLKPVDEEELEEALEKAKE 118
PRK09483 PRK09483
response regulator; Provisional
 1-189 1.93e-29

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 108.27  E-value: 1.93e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   1 MIRIIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMI 80
Cdd:PRK09483   1 MINVLLVDDHELVRAGIRRILEDIKGIKVVGEACCGEDAVKWCRTNAVDVVLMDMNMPGIGGLEATRKILRYTPDVKIIM 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  81 LTTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMKGKR----EVSQELMFGLW--QEQNP---LSDREKEVLLLA 151
Cdd:PRK09483  81 LTVHTENPLPAKVMQAGAAGYLSKGAAPQEVVSAIRSVHSGQRyiasDIAQQMALSQIepATENPfasLSERELQIMLMI 160

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 446541897 152 KEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIE 189
Cdd:PRK09483 161 TKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVE 198
PRK10360 PRK10360
transcriptional regulator UhpA;
1-189 1.08e-28

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 105.83  E-value: 1.08e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   1 MIRIIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSpckVMI 80
Cdd:PRK10360   1 MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMA---TIM 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  81 LTTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMKGKREVSQELMFGLWQ-EQNPLSDREKEVLLLAKEGKTANE 159
Cdd:PRK10360  78 LSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASgRQDPLTKRERQVAEKLAQGMAVKE 157

                        170       180       190
                 ....*....|....*....|....*....|
gi 446541897 160 IAKALYLSPGTVRNYISEVLTKLDAKNRIE 189
Cdd:PRK10360 158 IAAELGLSPKTVHVHRANLMEKLGVSNDVE 187
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
3-190 7.34e-28

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 104.16  E-value: 7.34e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILT 82
Cdd:PRK10403   8 QVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLANRLDPDVILLDLNMKGMSGLDTLNALRRDGVTAQIIILT 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  83 TFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMKGKREVSQEL--------MFGlwQEQNP---LSDREKEVLLLA 151
Cdd:PRK10403  88 VSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKGSKVFSERVnqylrereMFG--AEEDPfsvLTERELDVLHEL 165

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 446541897 152 KEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEA 190
Cdd:PRK10403 166 AQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAA 204
LytT COG3279
DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction ...
 1-120 4.90e-27

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


Pssm-ID: 442510 [Multi-domain]  Cd Length: 235  Bit Score: 102.59  E-value: 4.90e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   1 MIRIIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVmI 80
Cdd:COG3279    1 MMKILIVDDEPLARERLERLLEKYPDLEVVGEASNGEEALELLEEHKPDLVFLDIQMPGLDGFELARQLRELDPPPPI-I 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446541897  81 LTTfARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMK 120
Cdd:COG3279   80 FTT-AYDEYALEAFEVNAVDYLLKPIDEERLAKALEKAKE 118
CitB COG4565
DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal ...
 1-128 3.13e-26

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


Pssm-ID: 443622 [Multi-domain]  Cd Length: 138  Bit Score: 97.73  E-value: 3.13e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   1 MIRIIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMI 80
Cdd:COG4565    3 MIRVLIVEDDPMVAELLRRYLERLPGFEVVGVASSGEEALALLAEHRPDLILLDIYLPDGDGLELLRELRARGPDVDVIV 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 446541897  81 LTTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMKGKREVSQE 128
Cdd:COG4565   83 ITAARDPETVREALRAGVVDYLIKPFTFERLREALERYLEYRRLLRED 130
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 4-116 2.72e-24

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.


Pssm-ID: 395025 [Multi-domain]  Cd Length: 111  Bit Score: 91.83  E-value: 2.72e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897    4 IIIAEDQRMLRGALGALLDLEDdiEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTT 83
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLEKEG--YVVAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIRRRDPTTPVIILTA 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 446541897   84 FARPGYFERAMKAGVHGYLLKDSPSEDLAAAIR 116
Cdd:pfam00072  79 HGDEDDAVEALEAGADDFLSKPFDPDELLAAIR 111
REC_NarL cd19931
phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL); Nitrate ...
 4-120 8.74e-24

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.


Pssm-ID: 381158 [Multi-domain]  Cd Length: 117  Bit Score: 90.87  E-value: 8.74e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTT 83
Cdd:cd19931    1 VLLIDDHPLLRKGIKQLIELDPDFTVVGEASSGEEGIELAERLDPDLILLDLNMKGMSGLDTLKALREEGVSARIVILTV 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 446541897  84 FARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMK 120
Cdd:cd19931   81 SDAEDDVVTALRAGADGYLLKDMEPEDLLEALKQAAS 117
PRK15369 PRK15369
two component system response regulator;
2-191 1.33e-23

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 93.22  E-value: 1.33e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   2 IRIIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMIL 81
Cdd:PRK15369   4 YKILLVDDHELIINGIKNMLAPYPRYKIVGQVDNGLEVYNACRQLEPDIVILDLGLPGMNGLDVIPQLHQRWPAMNILVL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  82 TTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMKGKREV----SQELMFGLWQ--EQNP--LSDREKEVLLLAKE 153
Cdd:PRK15369  84 TARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGKRYIdpalNREAILALLNadDTNPplLTPRERQILKLITE 163

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 446541897 154 GKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEAI 191
Cdd:PRK15369 164 GYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELL 201
REC_CheB-like cd17541
phosphoacceptor receiver (REC) domain of chemotaxis response regulator protein-glutamate ...
 2-96 1.86e-23

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.


Pssm-ID: 381096 [Multi-domain]  Cd Length: 125  Bit Score: 90.14  E-value: 1.86e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   2 IRIIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLdvaEALKK--EKSPCKVM 79
Cdd:cd17541    1 IRVLIVDDSAVMRKLLSRILESDPDIEVVGTARDGEEALEKIKELKPDVITLDIEMPVMDGL---EALRRimAERPTPVV 77

                         90
                 ....*....|....*..
gi 446541897  80 ILTTFARPGyFERAMKA 96
Cdd:cd17541   78 MVSSLTEEG-AEITLEA 93
OmpR COG0745
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...
 1-185 1.45e-22

DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain [Signal transduction mechanisms, Transcription];


Pssm-ID: 440508 [Multi-domain]  Cd Length: 204  Bit Score: 90.02  E-value: 1.45e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   1 MIRIIIAEDQRMLRGALGALLDLEDdIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMI 80
Cdd:COG0745    1 MPRILVVEDDPDIRELLADALEREG-YEVD-TAADGEEALELLEEERPDLILLDLMLPGMDGLEVCRRLRARPSDIPIIM 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  81 LTTFARPGYFERAMKAGVHGYLLKD-SPSEdLAAAIRNVMkgKREVSQELMFGLW-----------QEQNPLSDREKEVL 148
Cdd:COG0745   79 LTARDDEEDRVRGLEAGADDYLTKPfDPEE-LLARIRALL--RRRAAEVLRVGDLldlaarevtrdGEPVELTPKEFRLL 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 446541897 149 --LLAKEGK--TANEIAKAL----YLSPGTVRNYISEVLTKLDAK 185
Cdd:COG0745  156 elLMRNPGRvvSREQLLEEVwgydYGDDRTVDVHISRLRKKLEDD 200
CheY COG0784
CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator ...
 1-124 3.93e-22

CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator Spo0F [Signal transduction mechanisms];


Pssm-ID: 440547 [Multi-domain]  Cd Length: 128  Bit Score: 86.83  E-value: 3.93e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   1 MIRIIIAEDQRMLRGALGALLDlEDDIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEK--SPCKV 78
Cdd:COG0784    5 GKRILVVDDNPDNRELLRRLLE-RLGYEVT-TAEDGAEALELLRAGPPDLILLDINMPGMDGLELLRRIRALPrlPDIPI 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 446541897  79 MILTTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMKGKRE 124
Cdd:COG0784   83 IALTAYADEEDRERALEAGADDYLTKPVDPEELLEALRRLLARASA 128
REC_PdtaR-like cd19932
phosphoacceptor receiver (REC) domain of PdtaR and similar proteins; This subfamily includes ...
 2-115 1.62e-21

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.


Pssm-ID: 381159 [Multi-domain]  Cd Length: 118  Bit Score: 85.16  E-value: 1.62e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   2 IRIIIAEDQRMLRGALGALLDlEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKsPCKVMIL 81
Cdd:cd19932    1 VRVLIAEDEALIRMDLREMLE-EAGYEVVGEASDGEEAVELAKKHKPDLVIMDVKMPRLDGIEAAKIITSEN-IAPIVLL 78

                         90       100       110
                 ....*....|....*....|....*....|....
gi 446541897  82 TTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAI 115
Cdd:cd19932   79 TAYSQQDLVERAKEAGAMAYLVKPFSESDLIPAI 112
REC_LytTR_AlgR-like cd17532
phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AlgR; ...
 4-120 4.16e-21

phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AlgR; Members of the LytTR/AlgR family of response regulators contain a REC domain and a unique LytTR DNA-binding output domain that lacks the helix-turn-helix motif and consists mostly of beta-strands. Transcriptional regulators with the LytTR-type output domains are involved in biosynthesis of extracellular polysaccharides, fimbriation, expression of exoproteins, including toxins, and quorum sensing. Included in this AlgR-like group of LytTR/AlgR family response regulators are Streptococcus agalactiae sensory transduction protein LytR, Pseudomonas aeruginosa positive alginate biosynthesis regulatory protein AlgR, Bacillus subtilis sensory transduction protein LytT, and Escherichia coli transcriptional regulatory protein BtsR, which are members of two-component regulatory systems. LytR and LytT are components of regulatory systems that regulate genes involved in cell wall metabolism. AlgR positively regulates the algD gene, which codes for a GDP-mannose dehydrogenase, a key enzyme in the alginate biosynthesis pathway. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381087 [Multi-domain]  Cd Length: 118  Bit Score: 83.74  E-value: 4.16e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTt 83
Cdd:cd17532    1 ALIVDDEPLAREELRYLLEEHPDIEIVGEAENGEEALEAIEELKPDVVFLDIQMPGLDGLELAKKLSKLAKPPLIVFVT- 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446541897  84 farpGYFERAMKA---GVHGYLLKDSPSEDLAAAIRNVMK 120
Cdd:cd17532   80 ----AYDEYAVEAfelNAVDYLLKPFSEERLAEALAKLRK 115
AmiR COG3707
Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding ...
 1-116 6.82e-21

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


Pssm-ID: 442921 [Multi-domain]  Cd Length: 194  Bit Score: 85.39  E-value: 6.82e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   1 MIRIIIAEDQRMLRGALGALLdLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKsPCKVMI 80
Cdd:COG3707    3 GLRVLVVDDEPLRRADLREGL-REAGYEVVAEAADGEDAVELVRELKPDLVIVDIDMPDRDGLEAARQISEER-PAPVIL 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 446541897  81 LTTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIR 116
Cdd:COG3707   81 LTAYSDPELIERALEAGVSAYLVKPLDPEDLLPALE 116
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 1-127 7.53e-21

DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, and a Fis-type DNA-binding domains [Signal transduction mechanisms];


Pssm-ID: 441806 [Multi-domain]  Cd Length: 418  Bit Score: 88.87  E-value: 7.53e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   1 MIRIIIAEDQRMLRGALGALLDlEDDIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMI 80
Cdd:COG2204    2 MARILVVDDDPDIRRLLKELLE-RAGYEVE-TAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRALDPDLPVIL 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 446541897  81 LTTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMKGKREVSQ 127
Cdd:COG2204   80 LTGYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERALERRRLRRE 126
REC cd00156
phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ...
 6-104 7.95e-21

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.


Pssm-ID: 381085 [Multi-domain]  Cd Length: 99  Bit Score: 82.66  E-value: 7.95e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   6 IAEDQRMLRGALGALLdlEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTTFA 85
Cdd:cd00156    2 IVDDDPAIRELLKSLL--EREGYEVDTAADGEEALELLREERPDLVLLDLMMPGMDGLELLRKLRELPPDIPVIVLTAKA 79

                         90
                 ....*....|....*....
gi 446541897  86 RPGYFERAMKAGVHGYLLK 104
Cdd:cd00156   80 DEEDAVRALELGADDYLVK 98
PRK00742 PRK00742
chemotaxis-specific protein-glutamate methyltransferase CheB;
1-129 2.93e-20

chemotaxis-specific protein-glutamate methyltransferase CheB;


Pssm-ID: 234828 [Multi-domain]  Cd Length: 354  Bit Score: 86.74  E-value: 2.93e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   1 MIRIIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDvaeALKK--EKSPCKV 78
Cdd:PRK00742   3 KIRVLVVDDSAFMRRLISEILNSDPDIEVVGTAPDGLEAREKIKKLNPDVITLDVEMPVMDGLD---ALEKimRLRPTPV 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446541897  79 MILTTFARPGYFE--RAMKAGVHGYLLKdsPSEDLAAairnvmkGKREVSQEL 129
Cdd:PRK00742  80 VMVSSLTERGAEItlRALELGAVDFVTK--PFLGISL-------GMDEYKEEL 123
PleD COG3706
Two-component response regulator, PleD family, consists of two REC domains and a diguanylate ...
 1-115 1.09e-19

Two-component response regulator, PleD family, consists of two REC domains and a diguanylate cyclase (GGDEF) domain [Signal transduction mechanisms, Transcription];


Pssm-ID: 442920 [Multi-domain]  Cd Length: 179  Bit Score: 81.88  E-value: 1.09e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   1 MIRIIIAEDQRMLRGALGALLDlEDDIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCK--V 78
Cdd:COG3706    1 PARILVVDDDPTNRKLLRRLLE-AAGYEVV-EAADGEEALELLQEHRPDLILLDLEMPDMDGLELCRRLRADPRTADipI 78

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 446541897  79 MILTTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAI 115
Cdd:COG3706   79 IFLTALDDEEDRARALEAGADDYLTKPFDPEELLARV 115
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 4-198 1.14e-19

DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 82.46  E-value: 1.14e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDLEDdIEVIGqAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTT 83
Cdd:COG4566    2 VYIVDDDEAVRDSLAFLLESAG-LRVET-FASAEAFLAALDPDRPGCLLLDVRMPGMSGLELQEELAARGSPLPVIFLTG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  84 F-----ARpgyfeRAMKAGVHGYLLKDSPSEDLAAAIRNVMK------GKREVSQELMFGLWQeqnpLSDREKEVLLLAK 152
Cdd:COG4566   80 HgdvpmAV-----RAMKAGAVDFLEKPFDDQALLDAVRRALArdrarrAERARRAELRARLAS----LTPREREVLDLVV 150

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 446541897 153 EGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEAITIAEEKG 198
Cdd:COG4566  151 AGLSNKQIARELGISPRTVEVHRANVMEKLGARSLAELVRLALALG 196
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 139-194 4.25e-19

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 76.80  E-value: 4.25e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 446541897   139 PLSDREKEVLLLAKEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEAITIA 194
Cdd:smart00421   3 SLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
REC_Spo0A cd17561
phosphoacceptor receiver (REC) domain of Spo0A; Spo0A is a response regulator of the ...
 2-104 8.74e-19

phosphoacceptor receiver (REC) domain of Spo0A; Spo0A is a response regulator of the phosphorelay system in the early stage of spore formation. It may be an element of the effector pathway responsible for the activation of sporulation genes in response to nutritional stress and may act in the with sigma factor spo0H to control the expression of some genes that are critical to the sporulation process. Spo0A contains a regulatory N-terminal REC domain and a C-terminal DNA-binding transcription activation domain as its effector/output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381109 [Multi-domain]  Cd Length: 108  Bit Score: 77.65  E-value: 8.74e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   2 IRIIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEAL---KKEKSPcKV 78
Cdd:cd17561    2 IKVLIADDNREFVQLLEEYLNSQPDMEVVGVAHNGQEALELIEEKEPDVLLLDIIMPHLDGIGVLEKLrrmRLEKRP-KI 80

                         90       100
                 ....*....|....*....|....*.
gi 446541897  79 MILTTFARPGYFERAMKAGVHGYLLK 104
Cdd:cd17561   81 IMLTAFGQEDITQRAVELGASYYILK 106
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
5-196 2.54e-18

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 79.17  E-value: 2.54e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   5 IIAEDQRMLRGALGALLDlEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTTF 84
Cdd:PRK09958   4 IIIDDHPLAIAAIRNLLI-KNDIEILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVSAK 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  85 ARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMKGKR------EVSQELMFGLWQEQNPLSDREKEVLLLAKEGKTAN 158
Cdd:PRK09958  83 NDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGYCyfpfslNRFVGSLTSDQQKLDSLSKQEISVMRYILDGKDNN 162

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 446541897 159 EIAKALYLSPGTVRNYISEVLTKLDAKNRIEAITIAEE 196
Cdd:PRK09958 163 DIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYTFAQR 200
RpfG COG3437
Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains ...
 3-155 6.29e-18

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


Pssm-ID: 442663 [Multi-domain]  Cd Length: 224  Bit Score: 78.28  E-value: 6.29e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRGALGALLDlEDDIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSP--CKVMI 80
Cdd:COG3437    8 TVLIVDDDPENLELLRQLLR-TLGYDVV-TAESGEEALELLLEAPPDLILLDVRMPGMDGFELLRLLRADPSTrdIPVIF 85

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446541897  81 LTTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMKGKREVSQELMFGLWQEQN-PLSDREKEVL---LLAKEGK 155
Cdd:COG3437   86 LTALADPEDRERALEAGADDYLTKPFDPEELLARVRNALELRRLQRELDDLVLYLKLAaPLHDIGKIGIpdaILLKPGK 164
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 139-200 1.25e-16

Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 71.14  E-value: 1.25e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446541897 139 PLSDREKEVLLLAKEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEAITIAEEKGWI 200
Cdd:COG5905   12 LLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWALRLGLL 73
REC_DC-like cd17534
phosphoacceptor receiver (REC) domain of modulated diguanylate cyclase and similar domains; ...
 2-115 3.32e-16

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.


Pssm-ID: 381089 [Multi-domain]  Cd Length: 117  Bit Score: 71.28  E-value: 3.32e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   2 IRIIIAEDQRMLRgalgalLDLEDDIE-----VIGQAANGEEALKLIESLKPDISIMDIEMP-IQSGLDVAEALKKeKSP 75
Cdd:cd17534    1 KKILIVEDEAIIA------LDLKEILEslgyeVVGIADSGEEAIELAEENKPDLILMDINLKgDMDGIEAAREIRE-KFD 73

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 446541897  76 CKVMILTTFARPGYFERAMKAGVHGYLLKdsP--SEDLAAAI 115
Cdd:cd17534   74 IPVIFLTAYSDEETLERAKETNPYGYLVK--PfnERELKAAI 113
PRK11697 PRK11697
two-component system response regulator BtsR;
1-104 6.75e-16

two-component system response regulator BtsR;


Pssm-ID: 236956 [Multi-domain]  Cd Length: 238  Bit Score: 72.96  E-value: 6.75e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   1 MIRIIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPcKVMI 80
Cdd:PRK11697   1 MIKVLIVDDEPLAREELRELLQEEGDIEIVGECSNAIEAIGAIHRLKPDVVFLDIQMPRISGLELVGMLDPEHMP-YIVF 79

                         90       100
                 ....*....|....*....|....*..
gi 446541897  81 LTTFArpgyfERAMKA---GVHGYLLK 104
Cdd:PRK11697  80 VTAFD-----EYAIKAfeeHAFDYLLK 101
COG4567 COG4567
DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains ...
 3-130 1.08e-15

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


Pssm-ID: 443624 [Multi-domain]  Cd Length: 177  Bit Score: 71.49  E-value: 1.08e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRGALGALLDlEDDIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILT 82
Cdd:COG4567    6 SLLLVDDDEAFARVLARALE-RRGFEVT-TAASVEEALALLEQAPPDYAVLDLRLGDGSGLDLIEALRERDPDARIVVLT 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 446541897  83 TFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMKGKREVSQELM 130
Cdd:COG4567   84 GYASIATAVEAIKLGADDYLAKPADADDLLAALERAEGDAPAPPENPM 131
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
4-195 1.66e-15

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 71.45  E-value: 1.66e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTT 83
Cdd:PRK09935   6 VIIMDTHPIIRMSIEVLLQKNSELQIVLKTDDYRITIDYLRTRPVDLIIMDIDLPGTDGFTFLKRIKQIQSTVKVLFLSS 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  84 FARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMKGKREVSQELMFGLWQEQN--------PLSDREKEVLLLAKEGK 155
Cdd:PRK09935  86 KSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMILSGYTFFPSETLNYIKSNKCstnsstdtVLSNREVTILRYLVSGL 165

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 446541897 156 TANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEAITIAE 195
Cdd:PRK09935 166 SNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELIDYAK 205
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 140-196 3.79e-15

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 66.79  E-value: 3.79e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446541897 140 LSDREKEVLLLAKEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEAITIAEE 196
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
123-200 4.28e-15

DNA-binding transcriptional regulator, CsgD family [Transcription];


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 70.17  E-value: 4.28e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446541897 123 REVSQELMFGLWQEQNPLSDREKEVLLLAKEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEAITIAEEKGWI 200
Cdd:COG2771  111 AALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVALALRLGLI 188
REC_CheY cd17542
phosphoacceptor receiver (REC) domain of chemotaxis protein CheY; The chemotaxis response ...
 2-119 1.32e-14

phosphoacceptor receiver (REC) domain of chemotaxis protein CheY; The chemotaxis response regulator CheY contains a stand-alone REC domain. Chemotaxis is a behavior known for motile bacteria that directs their movement in response to chemical gradients. CheY is involved in transmitting sensory signals from chemoreceptors to the flagellar motors. Phosphorylated CheY interacts with the flagella switch components FliM and FliY, which causes counterclockwise rotation of the flagella, resulting in smooth swimming. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381097 [Multi-domain]  Cd Length: 117  Bit Score: 66.92  E-value: 1.32e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   2 IRIIIAEDQRMLRGALGALLDlEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMIL 81
Cdd:cd17542    1 KKVLIVDDAAFMRMMLKDILT-KAGYEVVGEAANGEEAVEKYKELKPDLVTMDITMPEMDGIEALKEIKKIDPNAKVIMC 79

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 446541897  82 TTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVM 119
Cdd:cd17542   80 SAMGQEEMVKEAIKAGAKDFIVKPFQPERVLEAVEKVL 117
REC_citrate_TCS cd19925
phosphoacceptor receiver (REC) domain of citrate family two-component system response ...
 2-115 2.35e-14

phosphoacceptor receiver (REC) domain of citrate family two-component system response regulators; This family includes Lactobacillus paracasei MaeR, Escherichia coli DcuR and DpiA, Klebsiella pneumoniae CitB, as well as Bacillus DctR, MalR, and CitT. These are all response regulators of two-component systems (TCSs) from the citrate family, and are involved in the transcriptional regulation of genes associated with L-malate catabolism (MaeRK), citrate-specific fermentation (DpiAB, CitAB), plasmid inheritance (DpiAB), anaerobic fumarate respiratory system (DcuRS), and malate transport/utilization (MalKR). REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381152 [Multi-domain]  Cd Length: 118  Bit Score: 66.50  E-value: 2.35e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   2 IRIIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMIL 81
Cdd:cd19925    1 INVLIVEDDPMVAEIHRAYVEQVPGFTVIGTAGTGEEALKLLKERQPDLILLDIYLPDGNGLDLLRELRAAGHDVDVIVV 80

                         90       100       110
                 ....*....|....*....|....*....|....
gi 446541897  82 TTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAI 115
Cdd:cd19925   81 TAANDVETVREALRLGVVDYLIKPFTFERLRQRL 114
GerE pfam00196
Bacterial regulatory proteins, luxR family;
139-194 2.44e-14

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 64.53  E-value: 2.44e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 446541897  139 PLSDREKEVLLLAKEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEAITIA 194
Cdd:pfam00196   2 SLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
PRK12555 PRK12555
chemotaxis-specific protein-glutamate methyltransferase CheB;
2-83 2.62e-14

chemotaxis-specific protein-glutamate methyltransferase CheB;


Pssm-ID: 237135 [Multi-domain]  Cd Length: 337  Bit Score: 69.91  E-value: 2.62e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   2 IRIIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIqsgLDVAEALKK--EKSPCKVM 79
Cdd:PRK12555   1 MRIGIVNDSPLAVEALRRALARDPDHEVVWVATDGAQAVERCAAQPPDVILMDLEMPR---MDGVEATRRimAERPCPIL 77


                 ....
gi 446541897  80 ILTT 83
Cdd:PRK12555  78 IVTS 81
REC_TrrA-like cd17554
phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator TrrA and ...
 3-116 1.02e-13

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.


Pssm-ID: 381106 [Multi-domain]  Cd Length: 113  Bit Score: 64.55  E-value: 1.02e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRgalgALLD--LEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMI 80
Cdd:cd17554    2 KILVVDDEENIR----ELYKeeLEDEGYEVVTAGNGEEALEKLESEDPDLVILDIKMPGMDGLETLRKIREKKPDLPVII 77

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 446541897  81 LTtfARPGYFERAMKAGVHGYLLKDSPSEDLAAAIR 116
Cdd:cd17554   78 CT--AYSEYKSDFSSWAADAYVVKSSDLTELKETIK 111
REC_DivK-like cd17548
phosphoacceptor receiver (REC) domain of DivK and similar proteins; Caulobacter crescentus ...
 3-104 6.21e-13

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.


Pssm-ID: 381100 [Multi-domain]  Cd Length: 115  Bit Score: 62.56  E-value: 6.21e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRGALGALLDLEDdIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKK--EKSPCKVMI 80
Cdd:cd17548    1 KILIVEDNPLNMKLARDLLESAG-YEVL-EAADGEEALEIARKEKPDLILMDIQLPGMDGLEATRLLKEdpATRDIPVIA 78

                         90       100
                 ....*....|....*....|....
gi 446541897  81 LTTFARPGYFERAMKAGVHGYLLK 104
Cdd:cd17548   79 LTAYAMKGDREKILEAGCDGYISK 102
PRK11361 PRK11361
acetoacetate metabolism transcriptional regulator AtoC;
3-164 2.34e-12

acetoacetate metabolism transcriptional regulator AtoC;


Pssm-ID: 183099 [Multi-domain]  Cd Length: 457  Bit Score: 64.87  E-value: 2.34e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRGALGALLDLEDdIEVIGqAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILT 82
Cdd:PRK11361   6 RILIVDDEDNVRRMLSTAFALQG-FETHC-ANNGRTALHLFADIHPDVVLMDIRMPEMDGIKALKEMRSHETRTPVILMT 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  83 TFARPGYFERAMKAGVHGYLLKDSPSEDL------AAAIRNVMKGKREVSQELMfGLWQEQNPLSDREKEVLLLAKEGKT 156
Cdd:PRK11361  84 AYAEVETAVEALRCGAFDYVIKPFDLDELnlivqrALQLQSMKKEIRHLHQALS-TSWQWGHILTNSPAMMDICKDTAKI 162


                 ....*...
gi 446541897 157 ANEIAKAL 164
Cdd:PRK11361 163 ALSQASVL 170
REC_hyHK_CKI1_RcsC-like cd17546
phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinases/response regulators ...
 4-104 3.49e-12

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.


Pssm-ID: 381099 [Multi-domain]  Cd Length: 113  Bit Score: 60.56  E-value: 3.49e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAED----QRMLRGALGALldledDIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKK-EKSPCKV 78
Cdd:cd17546    1 VLVVDDnpvnRKVLKKLLEKL-----GYEVD-VAENGQEALELLKEEPFDLVLMDLQMPVMDGLEATRRIRElEGGGRRT 74

                         90       100
                 ....*....|....*....|....*...
gi 446541897  79 MI--LTTFARPGYFERAMKAGVHGYLLK 104
Cdd:cd17546   75 PIiaLTANALEEDREKCLEAGMDDYLSK 102
REC_CheC-like cd17593
phosphoacceptor receiver (REC) domain of uncharacterized response regulators containing a CheC ...
 2-118 8.96e-12

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.


Pssm-ID: 381124 [Multi-domain]  Cd Length: 117  Bit Score: 59.47  E-value: 8.96e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   2 IRIIIAEDQRMLRGALGALLDLEDDIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMIL 81
Cdd:cd17593    1 MKVLICDDSSMARKQLARALPADWDVEIT-FAENGEEALEILREGRIDVLFLDLTMPVMDGYEVLEALPVEQLETKVIVV 79

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 446541897  82 TTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNV 118
Cdd:cd17593   80 SGDVQPEAKERVLELGALAFLKKPFDPEKLAQLLEEL 116
REC_NtrC1-like cd17572
phosphoacceptor receiver (REC) domain of nitrogen regulatory protein C 1 (NtrC1) from Aquifex ...
 4-123 9.50e-12

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.


Pssm-ID: 381114 [Multi-domain]  Cd Length: 121  Bit Score: 59.52  E-value: 9.50e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDLED-DIEVigqAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILT 82
Cdd:cd17572    1 VLLVEDSPSLAALYQEYLSDEGyKVTH---VETGKEALAFLSDQPPDVVLLDLKLPDMSGMEILKWIQERSLPTSVIVIT 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 446541897  83 TFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMKGKR 123
Cdd:cd17572   78 AHGSVDIAVEAMRLGAYDFLEKPFDADRLRVTVRNALKHRK 118
REC_OmpR cd17574
phosphoacceptor receiver (REC) domain of OmpR family response regulators; OmpR-like proteins ...
 6-82 3.64e-11

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.


Pssm-ID: 381116 [Multi-domain]  Cd Length: 99  Bit Score: 57.42  E-value: 3.64e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446541897   6 IAEDQRMLRGALGALLDLEDdIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILT 82
Cdd:cd17574    2 VVEDDEEIAELLSDYLEKEG-YEVD-TAADGEEALELAREEQPDLIILDVMLPGMDGFEVCRRLREKGSDIPIIMLT 76
REC_OmpR_PrrA-like cd17627
phosphoacceptor receiver (REC) domain of PrrA-like OmpR family response regulators; The ...
 4-116 4.06e-11

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.


Pssm-ID: 381142 [Multi-domain]  Cd Length: 116  Bit Score: 57.78  E-value: 4.06e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDLED-DIEVigqAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILT 82
Cdd:cd17627    1 ILVVDDDRAVRESLRRSLRFEGyEVET---AVDGAEALRVISGNRPDAVVLDVMMPRLDGLEVCRRLRAAGNDLPILVLT 77

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 446541897  83 tfARPGYFER--AMKAGVHGYLLKDSPSEDLAAAIR 116
Cdd:cd17627   78 --ARDSVSDRvaGLDAGADDYLVKPFALEELLARVR 111
REC_2_DhkD-like cd17580
second phosphoacceptor receiver (REC) domain of Dictyostelium discoideum hybrid signal ...
 4-115 2.92e-10

second phosphoacceptor receiver (REC) domain of Dictyostelium discoideum hybrid signal transduction histidine kinase D and similar domains; Dictyostelium discoideum hybrid signal transduction histidine kinase D (DhkD) is a large protein that contains two histidine kinase (HK) and two REC domains on the intracellular side of a single pass transmembrane domain, and extracellular PAS and PAC domains that likely are involved in ligand binding. This model represents the second REC domain and similar domains. DhkD activates the cAMP phosphodiesterase RegA to ensure proper prestalk and prespore patterning, tip formation, and the vertical elongation of the mound into a finger, in Dictyostelium discoideum. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381118 [Multi-domain]  Cd Length: 112  Bit Score: 55.16  E-value: 2.92e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDLED-DIEVigqAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMI-- 80
Cdd:cd17580    1 ILVVDDNEDAAEMLALLLELEGaEVTT---AHSGEEALEAAQRFRPDVILSDIGMPGMDGYELARRLRELPWLANTPAia 77

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 446541897  81 LTTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAI 115
Cdd:cd17580   78 LTGYGQPEDRERALEAGFDAHLVKPVDPDELIELI 112
REC smart00448
cheY-homologous receiver domain; CheY regulates the clockwise rotation of E. coli flagellar ...
 2-58 8.53e-10

cheY-homologous receiver domain; CheY regulates the clockwise rotation of E. coli flagellar motors. This domain contains a phosphoacceptor site that is phosphorylated by histidine kinase homologues.


Pssm-ID: 214668 [Multi-domain]  Cd Length: 55  Bit Score: 52.57  E-value: 8.53e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 446541897     2 IRIIIAEDQRMLRGALGALLdlEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMP 58
Cdd:smart00448   1 MRILVVDDDPLLRELLKALL--EKEGYEVDEATDGEEALELLKEEKPDLILLDIMMP 55
PRK10100 PRK10100
transcriptional regulator CsgD;
63-196 9.55e-10

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 56.03  E-value: 9.55e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  63 LDVAEALKK-----------EKSPCKVMILTTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMKGKREVSQELMF 131
Cdd:PRK10100  58 LDMMEADKKlihywqdtlsrKNNNIKILLLNTPEDYPYREIENWPHINGVFYAMEDQERVVNGLQGVLRGECYFTQKLAS 137

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446541897 132 GLWQ----------EQNPLSDREKEVLLLAKEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEAITIAEE 196
Cdd:PRK10100 138 YLIThsgnyrynstESALLTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWAND 212
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
150-200 1.36e-09

ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 55.10  E-value: 1.36e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446541897 150 LAKEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEAITIAEEKGWI 200
Cdd:COG2909  133 LLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARARELGLL 183
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 2-188 1.44e-09

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 55.61  E-value: 1.44e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   2 IRIIIAEDQRMLRGALGALLDLEDDIEVIGQAangEEALKLIESL---KPDISIMDIEMP---IQSGLDVAEALKKEKSP 75
Cdd:PRK10840   4 MNVIIADDHPIVLFGIRKSLEQIEWVNVVGEF---EDSTALINNLpklDAHVLITDLSMPgdkYGDGITLIKYIKRHFPS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  76 CKVMILTTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMKGKREVSQELMFGLWQ------EQNPLSDREKEVLL 149
Cdd:PRK10840  81 LSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLEKisaggyGDKRLSPKESEVLR 160

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 446541897 150 LAKEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRI 188
Cdd:PRK10840 161 LFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDI 199
REC_RssB-like cd17555
phosphoacceptor receiver (REC) domain of Pseudomonas aeruginosa RssB and similar domains; ...
 3-117 2.78e-09

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.


Pssm-ID: 381107 [Multi-domain]  Cd Length: 116  Bit Score: 52.59  E-value: 2.78e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRGALGALLdlED-DIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMIL 81
Cdd:cd17555    2 TILVIDDDEVVRESIAAYL--EDsGFQVL-QAADGRQGLELFRSEQPDLVLCDLRMPEMDGLEVLKQITKESPDTPVIVV 78

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 446541897  82 TTFARPGYFERAMKAGVHGYLLKdsPSEDLAA---AIRN 117
Cdd:cd17555   79 SGAGVMSDAVEALRLGAWDYLTK--PIEDLAVlehAVRR 115
REC_RegA-like cd17563
phosphoacceptor receiver (REC) domain of photosynthetic apparatus regulatory protein RegA; ...
 32-114 4.92e-09

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.


Pssm-ID: 381111 [Multi-domain]  Cd Length: 112  Bit Score: 52.06  E-value: 4.92e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  32 QAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTtfarpGY------FErAMKAGVHGYLLKD 105
Cdd:cd17563   29 TAHSVEEALALAREEKPDYAVLDLRLGGDSGLDLIPPLRALQPDARIVVLT-----GYasiataVE-AIKLGADDYLAKP 102


                 ....*....
gi 446541897 106 SPSEDLAAA 114
Cdd:cd17563  103 ADADEILAA 111
REC_DctD-like cd17549
phosphoacceptor receiver (REC) domain of C4-dicarboxylic acid transport protein D (DctD) and ...
 4-125 6.60e-09

phosphoacceptor receiver (REC) domain of C4-dicarboxylic acid transport protein D (DctD) and similar proteins; C4-dicarboxylic acid transport protein D (DctD) is part of the two-component regulatory system DctB/DctD, which regulates C4-dicarboxylate transport via regulation of expression of the dctPQM operon and dctA. It is an activator of sigma(54)-RNA polymerase holoenzyme that uses the energy released from ATP hydrolysis to stimulate the isomerization of a closed promoter complex to an open complex capable of initiating transcription. DctD is a member of the NtrC family, characterized by a domain architecture containing an N-terminal REC domain, followed by a central sigma-54 interaction/ATPase domain, and a C-terminal DNA binding domain. The ability of the central domain to hydrolyze ATP and thus to interact effectively with a complex of RNA polymerase, sigma54, and promoter, is controlled by the phosphorylation status of the REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381101 [Multi-domain]  Cd Length: 130  Bit Score: 52.11  E-value: 6.60e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDLEDdIEVIGqAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTt 83
Cdd:cd17549    1 VLLVDDDADVREALQQTLELAG-FRVRA-FADAEEALAALSPDFPGVVISDIRMPGMDGLELLAQIRELDPDLPVILIT- 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 446541897  84 farpGYFE-----RAMKAGVHGYLLKDSPSEDLAAAIRNVMKGKREV 125
Cdd:cd17549   78 ----GHGDvpmavEAMRAGAYDFLEKPFDPERLLDVVRRALEKRRLV 120
PRK14084 PRK14084
DNA-binding response regulator;
2-148 9.43e-09

DNA-binding response regulator;


Pssm-ID: 184495 [Multi-domain]  Cd Length: 246  Bit Score: 53.60  E-value: 9.43e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   2 IRIIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMIL 81
Cdd:PRK14084   1 MKALIVDDEPLARNELTYLLNEIGGFEEINEAENVKETLEALLINQYDIIFLDINLMDESGIELAAKIQKMKEPPAIIFA 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446541897  82 TtfARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMKGKREVSQELMfglwQEQNPLSDREKEVL 148
Cdd:PRK14084  81 T--AHDQFAVKAFELNATDYILKPFEQKRIEQAVNKVRATKAKDDNNAS----AIANDMSANFDQSL 141
REC_D1_PleD-like cd17538
first (D1) phosphoacceptor receiver (REC) domain of response regulator PleD and similar ...
 3-70 9.44e-09

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.


Pssm-ID: 381093 [Multi-domain]  Cd Length: 104  Bit Score: 50.96  E-value: 9.44e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446541897   3 RIIIAEDQRMLRGALGALLDLEDdIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALK 70
Cdd:cd17538    1 KILVVDDEPANRELLEALLSAEG-YEVL-TADSGQEALALAEEELPDLILLDVMMPGMDGFEVCRRLK 66
fixJ PRK09390
response regulator FixJ; Provisional
 5-194 1.27e-08

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 52.70  E-value: 1.27e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   5 IIAEDQRMlRGALGALLDlEDDIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTTF 84
Cdd:PRK09390   8 VVDDDEAM-RDSLAFLLD-SAGFEVR-LFESAQAFLDALPGLRFGCVVTDVRMPGIDGIELLRRLKARGSPLPVIVMTGH 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  85 ARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMKGKRE------VSQELMFGLWQeqnpLSDREKEVL--LLAkeGKT 156
Cdd:PRK09390  85 GDVPLAVEAMKLGAVDFIEKPFEDERLIGAIERALAQAPEaakseaVAADIRARIAS----LSERERQVMdgLVA--GLS 158

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 446541897 157 ANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEAITIA 194
Cdd:PRK09390 159 NKVIARDLDISPRTVEVYRANVMTKMQAGSLSELVRMA 196
REC_CheY4-like cd17562
phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY4 and similar CheY ...
 3-119 3.26e-08

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.


Pssm-ID: 381110 [Multi-domain]  Cd Length: 118  Bit Score: 49.99  E-value: 3.26e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRGALGALLDlEDDIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKK----EKSPckV 78
Cdd:cd17562    2 KILAVDDSASIRQMVSFTLR-GAGYEVV-EAADGRDALSKAQSKKFDLIITDQNMPNMDGIELIKELRKlpayKFTP--I 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 446541897  79 MILTTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVM 119
Cdd:cd17562   78 LMLTTESSDEKKQEGKAAGATGWLVKPFDPEQLLEVVKKVL 118
REC_GlnL-like cd17565
phosphoacceptor receiver (REC) domain of transcriptional regulatory protein GlnL and similar ...
 4-104 7.25e-08

phosphoacceptor receiver (REC) domain of transcriptional regulatory protein GlnL and similar proteins; Bacillus subtilis GlnL is part of the GlnK-GlnL (formerly YcbA-YcbB) two-component system that positively regulates the expression of the glsA-glnT (formerly ybgJ-ybgH) operon in response to glutamine. It contains a REC domain and a DNA-binding output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381112 [Multi-domain]  Cd Length: 103  Bit Score: 48.42  E-value: 7.25e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTT 83
Cdd:cd17565    1 FYIVDDDKNIIKILSDIIEDDDLGEVVGEADNGAQAYDEILFLQPDIVLIDLLMPGMDGIQLVRKLKDTGSNGKFIMISQ 80

                         90       100
                 ....*....|....*....|.
gi 446541897  84 FARPGYFERAMKAGVHGYLLK 104
Cdd:cd17565   81 VSDKEMIGKAYQAGIEFFINK 101
REC_Spo0F-like cd17553
phosphoacceptor receiver (REC) domain of Spo0F and similar domains; Spo0F, a stand-alone ...
 3-119 9.95e-08

phosphoacceptor receiver (REC) domain of Spo0F and similar domains; Spo0F, a stand-alone response regulator containing only a REC domain with no output/effector domain, controls sporulation in Bacillus subtilis through the exchange of a phosphoryl group. Bacillus subtilis forms spores when conditions for growth become unfavorable. The initiation of sporulation is controlled by a phosphorelay (an expanded version of the two-component system) that consists of four main components: a histidine kinase (KinA), a secondary messenger (Spo0F), a phosphotransferase (Spo0B), and a transcription factor (Spo0A). REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381105 [Multi-domain]  Cd Length: 117  Bit Score: 48.70  E-value: 9.95e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRGALGALLDLEDDIEVigQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILT 82
Cdd:cd17553    2 KILIVDDQYGIRILLNEVFNKEGYQTF--QAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMT 79

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 446541897  83 TFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVM 119
Cdd:cd17553   80 AYGELDMIQESKELGALTHFAKPFDIDEIRDAVKKYL 116
REC_OmpR_DrrD-like cd17625
phosphoacceptor receiver (REC) domain of DrrD-like OmpR family response regulators; DrrD is a ...
 6-116 1.02e-07

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.


Pssm-ID: 381140 [Multi-domain]  Cd Length: 115  Bit Score: 48.37  E-value: 1.02e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   6 IAEDQRMLRGALGALLdlEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTtfA 85
Cdd:cd17625    2 VVEDEKDLSEAITKHL--KKEGYTVDVCFDGEEGLEYALSGIYDLIILDIMLPGMDGLEVLKSLREEGIETPVLLLT--A 77

                         90       100       110
                 ....*....|....*....|....*....|...
gi 446541897  86 RPGYFER--AMKAGVHGYLLKDSPSEDLAAAIR 116
Cdd:cd17625   78 LDAVEDRvkGLDLGADDYLPKPFSLAELLARIR 110
PRK10693 PRK10693
two-component system response regulator RssB;
32-112 1.39e-07

two-component system response regulator RssB;


Pssm-ID: 182652 [Multi-domain]  Cd Length: 303  Bit Score: 50.37  E-value: 1.39e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  32 QAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTTFARPGYFERAMKAGVHGYLLKdsPSEDL 111
Cdd:PRK10693   2 LAANGVDALELLGGFTPDLIICDLAMPRMNGIEFVEHLRNRGDQTPVLVISATENMADIAKALRLGVQDVLLK--PVKDL 79


                 .
gi 446541897 112 A 112
Cdd:PRK10693  80 N 80
REC_NtrX-like cd17550
phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and ...
 4-80 1.75e-07

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.


Pssm-ID: 381102 [Multi-domain]  Cd Length: 115  Bit Score: 47.88  E-value: 1.75e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446541897   4 IIIAEDQRMLRGALGALLdlEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKV-MI 80
Cdd:cd17550    1 ILIVDDEEDIRESLSGIL--EDEGYEVDTAADGEEALKLIKERRPDLVLLDIWLPDMDGLELLKEIKEKYPDLPViMI 76
REC_Rcp-like cd17557
phosphoacceptor receiver (REC) domain of cyanobacterial phytochrome response regulator Rcp and ...
 3-118 2.61e-07

phosphoacceptor receiver (REC) domain of cyanobacterial phytochrome response regulator Rcp and similar domains; This family is composed of response regulators (RRs) that are members of phytochrome-associated, light-sensing two-component signal transduction pathways such as Synechocystis sp. Rcp1, Tolypothrix sp. RcpA, and Agrobacterium tumefaciens bacteriophytochrome response regulator AtBRR. They are stand-alone RRs containing only a REC domain with no output/effector domain. The REC domain itself functions as an effector domain. Also included in this family us Methanosaeta harundinacea methanogenesis regulatory protein FilR2, also a stand-alone RR. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381108 [Multi-domain]  Cd Length: 129  Bit Score: 47.80  E-value: 2.61e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAED----QRMLRGALGALlDLEDDIEVigqAANGEEAL-------KLIESLKPDISIMDIEMPIQSGLDVAEALKK 71
Cdd:cd17557    1 TILLVEDnpgdAELIQEAFKEA-GVPNELHV---VRDGEEALdflrgegEYADAPRPDLILLDLNMPRMDGFEVLREIKA 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 446541897  72 EKSPCK--VMILTTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNV 118
Cdd:cd17557   77 DPDLRRipVVVLTTSDAEEDIERAYELGANSYIVKPVDFEEFVEAIRSL 125
PRK10955 PRK10955
envelope stress response regulator transcription factor CpxR;
1-120 4.28e-07

envelope stress response regulator transcription factor CpxR;


Pssm-ID: 182864 [Multi-domain]  Cd Length: 232  Bit Score: 48.65  E-value: 4.28e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   1 MIRIIIAEDQRMLRGALGALLDLEDDIEVIgqAANGEEALKLIESlKPDISIMDIEMPIQSGLDVAEALKKEKSpCKVMI 80
Cdd:PRK10955   1 MNKILLVDDDRELTSLLKELLEMEGFNVIV--AHDGEQALDLLDD-SIDLLLLDVMMPKKNGIDTLKELRQTHQ-TPVIM 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 446541897  81 LTtfARPGYFER--AMKAGVHGYLLKDSPSEDLAAAIRNVMK 120
Cdd:PRK10955  77 LT--ARGSELDRvlGLELGADDYLPKPFNDRELVARIRAILR 116
REC_OmpR_EcPhoP-like cd19934
phosphoacceptor receiver (REC) domain of EcPhoP-like OmpR family response regulators; ...
 4-116 4.92e-07

phosphoacceptor receiver (REC) domain of EcPhoP-like OmpR family response regulators; Escherichia coli PhoP (EcPhoP) is part of the PhoQ/PhoP two-component system (TCS) that regulates virulence genes and plays an essential role in the response of the bacteria to the environment of their mammalian hosts, sensing several stimuli such as extracellular magnesium limitation, low pH, the presence of cationic antimicrobial peptides, and osmotic upshift. This subfamily also includes Brucella suis FeuP, part of the FeuPQ TCS that is involved in the regulation of iron uptake, and Microchaete diplosiphon RcaC, which is required for chromatic adaptation. 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.


Pssm-ID: 381161 [Multi-domain]  Cd Length: 117  Bit Score: 46.51  E-value: 4.92e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGAllDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTt 83
Cdd:cd19934    1 LLLVEDDALLAAQLKE--QLSDAGYVVDVAEDGEEALFQGEEEPYDLVVLDLGLPGMDGLSVLRRWRSEGRATPVLILT- 77

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 446541897  84 fARPGYFER--AMKAGVHGYLLKDSPSEDLAAAIR 116
Cdd:cd19934   78 -ARDSWQDKveGLDAGADDYLTKPFHIEELLARLR 111
REC_OmpR_CpxR cd17623
phosphoacceptor receiver (REC) domain of CpxR-like OmpR family response regulators; CpxR is ...
 4-120 5.59e-07

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.


Pssm-ID: 381138 [Multi-domain]  Cd Length: 115  Bit Score: 46.53  E-value: 5.59e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDLED-DIEVigqAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEkSPCKVMILT 82
Cdd:cd17623    1 ILLIDDDRELTELLTEYLEMEGfNVRA---AHDGEQGLAALLEGSPDLVVLDVMLPKMNGLDVLKELRKT-SQVPVLMLT 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446541897  83 tfARPGYFER--AMKAGVHGYLLKDSPSEDLAAAIRNVMK 120
Cdd:cd17623   77 --ARGDDIDRilGLELGADDYLPKPFNPRELVARIRAILR 114
REC_Ycf29 cd19927
phosphoacceptor receiver (REC) domain of probable transcriptional regulator Ycf29; Ycf29 is a ...
 4-104 6.46e-07

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.


Pssm-ID: 381154 [Multi-domain]  Cd Length: 102  Bit Score: 45.83  E-value: 6.46e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDlEDDIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCK--VMIL 81
Cdd:cd19927    1 ILLVDDDPGIRLAVKDYLE-DQGFTVI-AASNGLEALDLLNQYIPDLIISDIIMPGVDGYSLLGKLRKNADFDTipVIFL 78

                         90       100
                 ....*....|....*....|...
gi 446541897  82 TTFARPGYFERAMKAGVHGYLLK 104
Cdd:cd19927   79 TAKGMTSDRIKGYNAGCDGYLSK 101
PRK15347 PRK15347
two component system sensor kinase;
33-115 1.13e-06

two component system sensor kinase;


Pssm-ID: 237951 [Multi-domain]  Cd Length: 921  Bit Score: 48.10  E-value: 1.13e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  33 AANGEEALKLIESLKPDISIMDIEMPIQSGLDVA----EALKKEKSPCKVMILTTFARPGYFERAMKAGVHGYLLKDSPS 108
Cdd:PRK15347 720 AASGTEALELGRQHRFDLVLMDIRMPGLDGLETTqlwrDDPNNLDPDCMIVALTANAAPEEIHRCKKAGMNHYLTKPVTL 799


                 ....*..
gi 446541897 109 EDLAAAI 115
Cdd:PRK15347 800 AQLARAL 806
REC_OmpR_MtPhoP-like cd17615
phosphoacceptor receiver (REC) domain of MtPhoP-like OmpR family response regulators; ...
 3-120 1.17e-06

phosphoacceptor receiver (REC) domain of MtPhoP-like OmpR family response regulators; Mycobacterium tuberculosis PhoP (MtPhoP) is part of the PhoP/PhoR two-component system that is involved in phosphate control by stimulating expression of genes involved in scavenging, transport and mobilization of phosphate, and repressing the utilization of nitrogen sources. Also included in this subfamily is Mycobacterium tuberculosis transcriptional regulatory protein TcrX, part of the two-component regulatory system TcrY/TcrX that may be involved in virulence. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381131 [Multi-domain]  Cd Length: 118  Bit Score: 45.81  E-value: 1.17e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRGALGALLDLED-DIEVigqAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMIL 81
Cdd:cd17615    1 RVLVVDDEPNITELLSMALRYEGwDVET---AADGAEALAAAREFRPDAVVLDIMLPDMDGLEVLRRLRADGPDVPVLFL 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 446541897  82 TtfARPGYFER--AMKAGVHGYLLKDSPSEDLAAAIRNVMK 120
Cdd:cd17615   78 T--AKDSVEDRiaGLTAGGDDYVTKPFSLEEVVARLRALLR 116
REC_2_GGDEF cd17544
second phosphoacceptor receiver (REC) domain of uncharacterized GGDEF domain proteins; This ...
 2-74 2.66e-06

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.


Pssm-ID: 381098 [Multi-domain]  Cd Length: 122  Bit Score: 44.82  E-value: 2.66e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446541897   2 IRIIIAEDQRMLRGALGALLDLEDdIEVIgQAANGEEALKLIESlKPDIS--IMDIEMPIQSGLDVAEALKKEKS 74
Cdd:cd17544    1 IKVLVVDDSATSRNHLRALLRRHN-FQVL-EAANGQEALEVLEQ-HPDIKlvITDYNMPEMDGFELVREIRKKYS 72
REC_RpfG-like cd17551
phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator ...
 3-117 4.05e-06

phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator RpfG and similar proteins; Cyclic di-GMP phosphodiesterase response regulator RpfG, together with sensory/regulatory protein RpfC, constitute a two-component system implicated in sensing and responding to the diffusible signal factor (DSF) that is essential for cell-cell signaling. RpfC is a hybrid sensor/histidine kinase that phosphorylates and activates RpfG, which degrades cyclic di-GMP to GMP, leading to the activation of Clp, a global transcriptional regulator that regulates a large set of genes in the DSF pathway. RpfG contains a CheY-like receiver domain attached to a histidine-aspartic acid-glycine-tyrosine-proline (HD-GYP) cyclic di-GMP phosphodiesterase domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381103 [Multi-domain]  Cd Length: 118  Bit Score: 43.97  E-value: 4.05e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRGALGALLDLEDDIEVIGqAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKS----PckV 78
Cdd:cd17551    2 RILIVDDNPTNLLLLEALLRSAGYLEVVS-FTDPREALAWCRENPPDLILLDYMMPGMDGLEFIRRLRALPGledvP--I 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 446541897  79 MILTTFARPGYFERAMKAGVHGYLLK--DsPSEdLAAAIRN 117
Cdd:cd17551   79 VMITADTDREVRLRALEAGATDFLTKpfD-PVE-LLARVRN 117
REC_OmpR_PmrA-like cd17624
phosphoacceptor receiver (REC) domain of PmrA-like OmpR family response regulators; This ...
 4-116 4.07e-06

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.


Pssm-ID: 381139 [Multi-domain]  Cd Length: 115  Bit Score: 44.01  E-value: 4.07e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDLEDDIevIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTt 83
Cdd:cd17624    1 ILLVEDDALLGDGLKTGLRKAGYA--VDWVRTGAEAEAALASGPYDLVILDLGLPDGDGLDLLRRWRRQGQSLPVLILT- 77

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 446541897  84 fARPGYFER--AMKAGVHGYLLKDSPSEDLAAAIR 116
Cdd:cd17624   78 -ARDGVDDRvaGLDAGADDYLVKPFALEELLARLR 111
REC_CheV-like cd19924
phosphoacceptor receiver (REC) domain of chemotaxis protein CheV and similar proteins; This ...
 4-104 4.34e-06

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.


Pssm-ID: 381151 [Multi-domain]  Cd Length: 111  Bit Score: 43.91  E-value: 4.34e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDlEDDIEVIgQAANGEEALKLIESLKP---------DISIMDIEMPIQSGLDVAEALKKEK- 73
Cdd:cd19924    1 ILVVDDSPTARKQLRDLLK-NLGFEIA-EAVDGEEALNKLENLAKegndlskelDLIITDIEMPKMDGYELTFELRDDPr 78

                         90       100       110
                 ....*....|....*....|....*....|..
gi 446541897  74 -SPCKVMILTTFARPGYFERAMKAGVHGYLLK 104
Cdd:cd19924   79 lANIPVILNSSLSGEFSRARGKKVGADAYLAK 110
REC_PFxFATGY cd17586
phosphoacceptor receiver (REC) domain of PFxFATGY motif single-domain (stand-alone) response ...
 4-75 1.09e-05

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.


Pssm-ID: 381122 [Multi-domain]  Cd Length: 111  Bit Score: 42.84  E-value: 1.09e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446541897   4 IIIAEDQRMLrgALGALLDLED-DIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSP 75
Cdd:cd17586    1 VLVLEDEPLI--AMNLEDALEDlGGKEVVTAATCAEALRSLADGPIDIAILDVNLGGETSIPVADALKRRAIP 71
REC_hyHK cd17598
phosphoacceptor receiver (REC) domain of uncharacterized hybrid sensor histidine kinase ...
 4-119 1.29e-05

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.


Pssm-ID: 381128 [Multi-domain]  Cd Length: 118  Bit Score: 42.70  E-value: 1.29e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDlEDDIEViGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKS----PckVM 79
Cdd:cd17598    1 ILIVEDSPTQAEQLKHILE-EQGYKV-QVARNGREALAMLAEHRPTLVISDIVMPEMDGYELCRKIKSDPDlkdiP--VI 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446541897  80 ILTTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVM 119
Cdd:cd17598   77 LLTTLSDPRDVIRGLECGADNFITKPYDEKYLLSRIKYIL 116
REC_CheY_CheY3 cd19923
phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY ...
 2-104 1.68e-05

phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 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 CheY3, Escherichia coli CheY, 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.


Pssm-ID: 381150 [Multi-domain]  Cd Length: 119  Bit Score: 42.33  E-value: 1.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   2 IRIIIAEDQRMLRGALGALLDlEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMIL 81
Cdd:cd19923    1 MKVLVVDDFSTMRRIIKNLLK-ELGFNNVEEAEDGVDALEKLKAGGFDFVITDWNMPNMDGLELLKTIRADGALSHLPVL 79

                         90       100
                 ....*....|....*....|....*
gi 446541897  82 --TTFARPGYFERAMKAGVHGYLLK 104
Cdd:cd19923   80 mvTAEAKKENVIAAAQAGVNNYIVK 104
REC_RR468-like cd17552
phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator RR468 and ...
 3-119 1.85e-05

phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator RR468 and similar domains; Thermotoga maritima RR468 (encoded by gene TM0468) is the cognate response regulator (RR) of the class I histidine kinase HK853 (product of gene TM0853). HK853/RR468 comprise a two-component system (TCS) that couples environmental stimuli to adaptive responses. This subfamily also includes Fremyella diplosiphon complementary adaptation response regulator homolog RcaF, a small RR that is involved in four-step phosphorelays of the complementary chromatic adaptation (CCA) system that occurs in many cyanobacteria. Both RR468 and RcaF are stand-alone RRs 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.


Pssm-ID: 381104 [Multi-domain]  Cd Length: 121  Bit Score: 42.54  E-value: 1.85e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRGALGALLDLEDDIEVIGqAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKK--EKSPCKVMI 80
Cdd:cd17552    3 RILVIDDEEDIREVVQACLEKLAGWEVLT-ASSGQEGLEKAATEQPDAILLDVMMPDMDGLATLKKLQAnpETQSIPVIL 81

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 446541897  81 LTTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVM 119
Cdd:cd17552   82 LTAKAQPSDRQRFASLGVAGVIAKPFDPLTLAEQIAKLL 120
PRK11107 PRK11107
hybrid sensory histidine kinase BarA; Provisional
 18-104 2.16e-05

hybrid sensory histidine kinase BarA; Provisional


Pssm-ID: 236848 [Multi-domain]  Cd Length: 919  Bit Score: 44.45  E-value: 2.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  18 GALLdlEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKK----EKSPckVMILTTFARPGYFERA 93
Cdd:PRK11107 684 GALL--EEQVEHVVLCDSGHQAVEQAKQRPFDLILMDIQMPGMDGIRACELIRQlphnQNTP--IIAVTAHAMAGERERL 759

                         90
                 ....*....|.
gi 446541897  94 MKAGVHGYLLK 104
Cdd:PRK11107 760 LSAGMDDYLAK 770
REC_hyHK_blue-like cd18161
phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinase/response regulators ...
 4-88 3.36e-05

phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinase/response regulators similar to Pseudomonas savastanoi blue-light-activated histidine kinase; 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 (HK)/response regulators contain all the elements of a classical TCS in a single polypeptide chain. Pseudomonas savastanoi blue-light-activated histidine kinase is a photosensitive HK and RR that is involved in increased bacterial virulence upon exposure to light. 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.


Pssm-ID: 381145 [Multi-domain]  Cd Length: 102  Bit Score: 41.18  E-value: 3.36e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDleDDIEVIGQAANGEEALKLIES-LKPDISIMDIEMP-IQSGLDVAEALKKEKSPCKVMIL 81
Cdd:cd18161    1 VLVVEDDPDVRRLTAEVLE--DLGYTVLEAASGDEALDLLESgPDIDLLVTDVIMPgGMNGSQLAEEARRRRPDLKVLLT 78


                 ....*..
gi 446541897  82 TTFARPG 88
Cdd:cd18161   79 SGYAENA 85
dpiA PRK10046
two-component response regulator DpiA; Provisional
 2-175 4.31e-05

two-component response regulator DpiA; Provisional


Pssm-ID: 182208 [Multi-domain]  Cd Length: 225  Bit Score: 42.70  E-value: 4.31e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   2 IRIIIAEDQRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMIL 81
Cdd:PRK10046   5 LTLLIVEDETPLAEMHAEYIRHIPGFSQILLAGNLAQARMMIERFKPGLILLDNYLPDGRGINLLHELVQAHYPGDVVFT 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  82 TTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAI------RNVMKGKREVSQ---ELMFGLWQEQNPLSDRE-------- 144
Cdd:PRK10046  85 TAASDMETVSEAVRCGVFDYLIKPIAYERLGQTLtrfrqrKHMLESIDSASQkqiDEMFNAYARGEPKDELPtgidpltl 164

                        170       180       190
                 ....*....|....*....|....*....|....
gi 446541897 145 KEVLLLAKEGK---TANEIAKALYLSPGTVRNYI 175
Cdd:PRK10046 165 NAVRKLFKEPGvqhTAETVAQALTISRTTARRYL 198
PRK10643 PRK10643
two-component system response regulator PmrA;
2-130 4.84e-05

two-component system response regulator PmrA;


Pssm-ID: 182612 [Multi-domain]  Cd Length: 222  Bit Score: 42.72  E-value: 4.84e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   2 IRIIIAEDQRMLRGALgaLLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMIL 81
Cdd:PRK10643   1 MKILIVEDDTLLLQGL--ILALQTEGYACDCASTAREAEALLESGHYSLVVLDLGLPDEDGLHLLRRWRQKKYTLPVLIL 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446541897  82 TtfARPGYFER--AMKAGVHGYLLKDSPSEDLAAAIRNVMKGKREVSQELM 130
Cdd:PRK10643  79 T--ARDTLEDRvaGLDVGADDYLVKPFALEELHARIRALIRRHQGQGENEL 127
REC_OmpR_BsPhoP-like cd19937
phosphoacceptor receiver (REC) domain of BsPhoP-like OmpR family response regulators; Bacillus ...
 33-112 5.25e-05

phosphoacceptor receiver (REC) domain of BsPhoP-like OmpR family response regulators; Bacillus subtilis PhoP (BsPhoP) is part of the PhoPR two-component system that participates in a signal transduction network that controls adaptation of the bacteria to phosphate deficiency by regulating (activating or repressing) genes of the Pho regulon upon phosphorylation by PhoR. When activated, PhoPR directs expression of phosphate scavenging enzymes, lowers synthesis of the phosphate-rich wall teichoic acid (WTA) and initiates synthesis of teichuronic acid, a non-phosphate containing replacement anionic polymer. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381164 [Multi-domain]  Cd Length: 116  Bit Score: 41.10  E-value: 5.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  33 AANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTTFARPGYFER--AMKAGVHGYLLKD-SPSE 109
Cdd:cd19937   27 AYDGEEALKRAKDEKPDLIILDLMLPGIDGLEVCRILRSDPKTSSIPIIMLTAKGEEFDKvlGLELGADDYITKPfSPRE 106


                 ...
gi 446541897 110 DLA 112
Cdd:cd19937  107 LLA 109
orf27 CHL00148
Ycf27; Reviewed
 3-120 5.90e-05

Ycf27; Reviewed


Pssm-ID: 214376 [Multi-domain]  Cd Length: 240  Bit Score: 42.40  E-value: 5.90e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRGALGALLDLEDdIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEkSPCKVMILT 82
Cdd:CHL00148   8 KILVVDDEAYIRKILETRLSIIG-YEVI-TASDGEEALKLFRKEQPDLVILDVMMPKLDGYGVCQEIRKE-SDVPIIMLT 84

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 446541897  83 TFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMK 120
Cdd:CHL00148  85 ALGDVSDRITGLELGADDYVVKPFSPKELEARIRSVLR 122
REC_OmpR_CusR-like cd19935
phosphoacceptor receiver (REC) domain of CusR-like OmpR family response regulators; ...
 4-82 6.09e-05

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.


Pssm-ID: 381162 [Multi-domain]  Cd Length: 100  Bit Score: 40.50  E-value: 6.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGAL--GalldLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMIL 81
Cdd:cd19935    1 ILVVEDEKKLAEYLkkG----LTEEGYAVDVAYDGEDGLHLALTNEYDLIILDVMLPGLDGLEVLRRLRAAGKQTPVLML 76


                 .
gi 446541897  82 T 82
Cdd:cd19935   77 T 77
REC_HupR-like cd17569
phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR) and similar ...
 2-117 7.03e-05

phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR) and similar domains; This family is composed of mostly uncharacterized response regulators with similarity to the REC domains of response regulator components of two-component systems that regulates hydrogenase activity, including HupR and HoxA. HupR is part of the HupT/HupR system that controls the synthesis of the membrane-bound [NiFe]hydrogenase, HupSL, of the photosynthetic bacterium Rhodobacter capsulatus. It contains an N-terminal REC domain, a central sigma-54 interaction domain that lacks ATPase activity, and a C-terminal DNA-binding domain. Members of this family contain a REC domain and various output domains including the cyclase homology domain (CHD) and the c-di-GMP phosphodiesterase domains, HD-GYP and EAL. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381113 [Multi-domain]  Cd Length: 118  Bit Score: 40.85  E-value: 7.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   2 IRIIIAEDQRMLRGALGALLDLEDdIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALkKEKSPCKVMIL 81
Cdd:cd17569    1 PTILLVDDEPNILKALKRLLRREG-YEVL-TATSGEEALEILKQEPVDVVISDQRMPGMDGAELLKRV-RERYPDTVRIL 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 446541897  82 TTfarpGY--FERAMKA----GVHGYLLKDSPSEDLAAAIRN 117
Cdd:cd17569   78 LT----GYadLDAAIEAinegEIYRFLTKPWDDEELKETIRQ 115
PRK10816 PRK10816
two-component system response regulator PhoP;
2-120 9.66e-05

two-component system response regulator PhoP;


Pssm-ID: 182755 [Multi-domain]  Cd Length: 223  Bit Score: 41.65  E-value: 9.66e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   2 IRIIIAEDQRMLRGALGalLDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMIL 81
Cdd:PRK10816   1 MRVLVVEDNALLRHHLK--VQLQDAGHQVDAAEDAKEADYYLNEHLPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVL 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 446541897  82 TtfARPGYFER--AMKAGVHGYLLKDSPSEDLAAAIRNVMK 120
Cdd:PRK10816  79 T--ARESWQDKveVLSAGADDYVTKPFHIEEVMARMQALMR 117
REC_PA4781-like cd19920
phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase PA4781 and similar ...
 33-71 1.04e-04

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.


Pssm-ID: 381147 [Multi-domain]  Cd Length: 103  Bit Score: 39.80  E-value: 1.04e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 446541897  33 AANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKK 71
Cdd:cd19920   28 ATDGQQALQRAQAEPPDLILLDVMMPGMDGFEVCRRLKA 66
REC_OmpR_kpRstA-like cd17622
phosphoacceptor receiver (REC) domain of kpRstA-like OmpR family response regulators; ...
 3-120 1.05e-04

phosphoacceptor receiver (REC) domain of kpRstA-like OmpR family response regulators; Klebsiella pneumoniae RstA (kpRstA) is part of the RstA/RstB two-component regulatory system that may play a regulatory role in virulence. 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.


Pssm-ID: 381137 [Multi-domain]  Cd Length: 116  Bit Score: 40.05  E-value: 1.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRGALGALLDlEDDIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKeKSPCKVMILT 82
Cdd:cd17622    2 RILLVEDDPKLARLIADFLE-SHGFNVV-VEHRGDRALEVIAREKPDAVLLDIMLPGIDGLTLCRDLRP-KYQGPILLLT 78

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 446541897  83 TFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIRNVMK 120
Cdd:cd17622   79 ALDSDIDHILGLELGADDYVVKPVEPAVLLARLRALLR 116
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 140-182 1.46e-04

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 40.75  E-value: 1.46e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 446541897 140 LSDREKEVLLLAK-EGKTANEIAKALYLSPGTVRNYISEVLTKL 182
Cdd:COG1595  128 LPPRQREVLVLRYlEGLSYAEIAEILGISEGTVKSRLSRARKKL 171
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
139-196 2.49e-04

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 41.08  E-value: 2.49e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446541897 139 PLSDREKEVLLLAKEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEAITIAEE 196
Cdd:PRK04841 838 PLTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQHAQD 895
REC_OmpR_YycF-like cd17614
phosphoacceptor receiver (REC) domain of YrcF-like OmpR family response regulators; YycF ...
 4-80 2.75e-04

phosphoacceptor receiver (REC) domain of YrcF-like OmpR family response regulators; YycF appears to play an important role in cell wall integrity in a wide range of gram-positive bacteria, and may also modulate cell membrane integrity. It functions as part of a phosphotransfer system that ultimately controls the levels of competence within the bacteria. YycF belongs to the OmpR family of response regulators, which are characterized by a REC domain and a winged helix-turn-helix effector domain involved in DNA binding. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381130 [Multi-domain]  Cd Length: 115  Bit Score: 38.94  E-value: 2.75e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446541897   4 IIIAEDQRMLRGALGALLDLED-DIEVigqAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMI 80
Cdd:cd17614    1 ILVVDDEKPISDILKFNLTKEGyEVVT---AYDGREALEKVEEEQPDLILLDLMLPEKDGLEVCREVRKTSNVPIIML 75
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 140-182 3.64e-04

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 39.25  E-value: 3.64e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 446541897  140 LSDREKEVLLLAK-EGKTANEIAKALYLSPGTVRNYISEVLTKL 182
Cdd:TIGR02937 111 LPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
REC_NtrC cd19919
phosphoacceptor receiver (REC) domain of DNA-binding transcriptional regulator NtrC; ...
 34-82 4.05e-04

phosphoacceptor receiver (REC) domain of DNA-binding transcriptional regulator NtrC; DNA-binding transcriptional regulator NtrC is also called nitrogen regulation protein NR(I) or nitrogen regulator I (NRI). It contains an N-terminal receiver (REC) domain, followed by a sigma-54 interaction domain, and a C-terminal helix-turn-helix DNA-binding domain. It is part of the two-component regulatory system NtrB/NtrC, which controls expression of the nitrogen-regulated (ntr) genes in response to nitrogen limitation. DNA-binding response regulator NtrC is phosphorylated by NtrB; phosphorylation of the N-terminal REC domain activates the central sigma-54 interaction domain and leads to the transcriptional activation from promoters that require sigma(54)-containing RNA polymerase. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381146 [Multi-domain]  Cd Length: 116  Bit Score: 38.41  E-value: 4.05e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 446541897  34 ANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILT 82
Cdd:cd19919   31 ENAQEALAALASSQPDVLISDIRMPGMDGLALLAQIKQRHPDLPVIIMT 79
PRK11083 PRK11083
DNA-binding response regulator CreB; Provisional
 36-120 4.17e-04

DNA-binding response regulator CreB; Provisional


Pssm-ID: 236838 [Multi-domain]  Cd Length: 228  Bit Score: 39.95  E-value: 4.17e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  36 GEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTtfARPGYFER--AMKAGVHGYLLKD-SPSEdLA 112
Cdd:PRK11083  36 GLPALDKLRQQPPDLVILDVGLPDISGFELCRQLLAFHPALPVIFLT--ARSDEVDRlvGLEIGADDYVAKPfSPRE-VA 112


                 ....*...
gi 446541897 113 AAIRNVMK 120
Cdd:PRK11083 113 ARVRTILR 120
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 123-175 4.59e-04

CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein Csa3, CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 442641 [Multi-domain]  Cd Length: 325  Bit Score: 40.22  E-value: 4.59e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446541897 123 REVSQELMFGLWQEQNPLSDREKEVLLLAKEGKTANEIAKALYLSPGTVRNYI 175
Cdd:COG3415    7 EEERRDLEKLLRKTKDAREARRLRAVLLLAEGLSVREIAERLGVSRSTVYRWL 59
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 140-182 5.02e-04

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 36.70  E-value: 5.02e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 446541897 140 LSDREKEVLLLAK-EGKTANEIAKALYLSPGTVRNYISEVLTKL 182
Cdd:cd06171   11 LPEREREVILLRFgEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
REC_LytTR_AgrA-like cd17533
phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AgrA; ...
 2-117 6.85e-04

phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AgrA; Members of the LytTR/AlgR family of response regulators contain a REC domain and a unique LytTR DNA-binding output domain that lacks the helix-turn-helix motif and consists mostly of beta-strands. Transcriptional regulators with the LytTR-type output domains are involved in biosynthesis of extracellular polysaccharides, fimbriation, expression of exoproteins, including toxins, and quorum sensing. Included in this AgrA-like group of LytTR/AlgR family response regulators are Staphylococcus aureus accessory gene regulator protein A (AgrA) and Streptococcus pneumoniae response regulator ComE, which are members of two-component regulatory systems. AgrA is a global regulator that controls the synthesis of virulence factors and other exoproteins. ComE is part of the ComD-ComE system that is part of a quorum-sensing signaling pathway that controls the development of competence, a physiological state required for genetic transformation. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381088 [Multi-domain]  Cd Length: 131  Bit Score: 38.37  E-value: 6.85e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   2 IRIIIAED----QRMLRGALGALLDLEDDIEVIGQAANGEEALKLIESLKP---DISIMDIEMPIQSGLDVAEALKKEKS 74
Cdd:cd17533    1 MNIFILEDdkiqRVRLEEIIENILKIENIEYVIELTGKTEELLEKIKERGKngiYFLDIDIKMEEKNGLEVAQKIRKYDP 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 446541897  75 PCKVMILTTFAR--PGYFERamKAGVHGYLLKDSPSEDLAAAIRN 117
Cdd:cd17533   81 YAIIIFVTTHSEfaPLTFEY--KVAALDFILKPLKLEEFKKRIEE 123
REC_OmpR_PhoB cd17618
phosphoacceptor receiver (REC) domain of PhoB response regulator from the OmpR family; The ...
 3-119 7.52e-04

phosphoacceptor receiver (REC) domain of PhoB response regulator from the OmpR family; The transcription factor PhoB is a component of the PhoR/PhoB two-component system, a key regulatory protein network that facilitates response to inorganic phosphate (Pi) starvation conditions by turning on the phosphate (pho) regulon whose products are involved in phosphorus uptake and metabolism. PhoB is a member of the OmpR family of DNA-binding response regulators that contains REC and winged helix-turn-helix (wHTH) DNA-binding output effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381133 [Multi-domain]  Cd Length: 118  Bit Score: 38.00  E-value: 7.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRGALGALLDLEDdIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILT 82
Cdd:cd17618    2 TILIVEDEPAIREMIAFNLERAG-FDVV-EAEDAESAVNLIVEPRPDLILLDWMLPGGSGIQFIRRLKRDEMTRDIPIIM 79

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 446541897  83 TFARPGYFER--AMKAGVHGYLLKDSPSEDLAAAIRNVM 119
Cdd:cd17618   80 LTARGEEEDKvrGLEAGADDYITKPFSPRELVARIKAVL 118
REC_CpdR_CckA-like cd18160
phosphoacceptor receiver (REC) domain of Brucella abortus CpdR and CckA, and similar domains; ...
 3-96 7.89e-04

phosphoacceptor receiver (REC) domain of Brucella abortus CpdR and CckA, and similar domains; Two-component systems (TCSs), consisting of a sensor and a response regulator, are used by bacteria to adapt to changing environments. Processes regulated by TCSs in bacteria include sporulation, pathogenicity, virulence, chemotaxis and membrane transport. Response regulators share the common phosphoacceptor REC domain and differ output domains such as DNA, RNA, ligand, and protein-binding, or enzymatic domain. CpdR is a stand-alone REC protein. CckA is a sensor histidine kinase containing N-terminal PAS domains and a C-terminal REC domain. CpdR and CckA are components of a regulatory phosphorelay system (composed of CckA, ChpT, CtrA and CpdR) that controls Brucella abortus cell growth, division, and intracellular survival inside mammalian host cells. CckA autophosphorylates in the presence of ATP and transfers a phosphoryl group to the conserved aspartic acid residue on its C-terminal REC domain, which is relayed to the ChpT phosphotransferase. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381144 [Multi-domain]  Cd Length: 103  Bit Score: 37.48  E-value: 7.89e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRgaLGALLDLEDDIEVIGQAANGEEALKLIESLKP-DISIMDIEMPIQSGLDVAEALKKEKSPCKVMIL 81
Cdd:cd18160    1 TILLADDEPSVR--KFIVTTLKKAGYAVTEAESGAEALEKLQQGKDiDIVVTDIVMPEMDGIELAREARKIDPDVKILFI 78

                         90
                 ....*....|....*
gi 446541897  82 TTFARPGyFERAMKA 96
Cdd:cd18160   79 SGGAAAA-PELLSDA 92
PRK15479 PRK15479
transcriptional regulator TctD;
2-148 8.05e-04

transcriptional regulator TctD;


Pssm-ID: 185376 [Multi-domain]  Cd Length: 221  Bit Score: 38.93  E-value: 8.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   2 IRIIIAEDQR----MLRGAL---GALLDLeddievigqAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKS 74
Cdd:PRK15479   1 MRLLLAEDNRelahWLEKALvqnGFAVDC---------VFDGLAADHLLQSEMYALAVLDINMPGMDGLEVLQRLRKRGQ 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  75 PCKVMILTtfARPGYFER--AMKAGVHGYLLKDSPSEDLAAAIRNVMKGKREVSQELM------------FGLWQEQNPL 140
Cdd:PRK15479  72 TLPVLLLT--ARSAVADRvkGLNVGADDYLPKPFELEELDARLRALLRRSAGQVQEVQqlgelifhdegyFLLQGQPLAL 149


                 ....*...
gi 446541897 141 SDREKEVL 148
Cdd:PRK15479 150 TPREQALL 157
PRK10188 PRK10188
transcriptional regulator SdiA;
140-200 9.36e-04

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 39.00  E-value: 9.36e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446541897 140 LSDREKEVLLLAKEGKTANEIAKALYLSPGTVRNYISEVLTKLDAKNRIEAITIAEEKGWI 200
Cdd:PRK10188 180 FSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATGLI 240
REC_OmpR_KdpE-like cd17620
phosphoacceptor receiver (REC) domain of KdpE-like OmpR family response regulators; KdpE is a ...
 4-104 9.46e-04

phosphoacceptor receiver (REC) domain of KdpE-like OmpR family response regulators; KdpE is a component of the KdpD/KdpE two-component system (TCS) and is activated when histidine kinase KdpD senses a drop in external K+ concentration or upshift in ionic osmolarity, resulting in the expression of a heterooligomeric transporter KdpFABC. In addition, the KdpD/KdpE TCS is also an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. KdpE is a member of the OmpR family of DNA-binding response regulators that contain REC and winged helix-turn-helix (wHTH) DNA-binding output effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381135 [Multi-domain]  Cd Length: 99  Bit Score: 37.14  E-value: 9.46e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGAllDLEDDIEVIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVaeaLKKEKSPCKVMILTT 83
Cdd:cd17620    1 ILVIEDEPQIRRFLRT--ALEAHGYRVFEAETGQEGLLEAATRKPDLIILDLGLPDMDGLEV---IRRLREWSAVPVIVL 75

                         90       100
                 ....*....|....*....|...
gi 446541897  84 FARPGYFE--RAMKAGVHGYLLK 104
Cdd:cd17620   76 SARDEESDkiAALDAGADDYLTK 98
PRK10365 PRK10365
sigma-54-dependent response regulator transcription factor ZraR;
33-129 9.98e-04

sigma-54-dependent response regulator transcription factor ZraR;


Pssm-ID: 182412 [Multi-domain]  Cd Length: 441  Bit Score: 39.24  E-value: 9.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  33 AANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTTFARPGYFERAMKAGVHGYLLKDSPSEDLA 112
Cdd:PRK10365  35 ANSGRQALEQVREQVFDLVLCDVRMAEMDGIATLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQ 114

                         90
                 ....*....|....*..
gi 446541897 113 AAIRNVMKGKREVSQEL 129
Cdd:PRK10365 115 ATLEKALAHTHSIDAET 131
pleD PRK09581
response regulator PleD; Reviewed
 33-70 1.03e-03

response regulator PleD; Reviewed


Pssm-ID: 236577 [Multi-domain]  Cd Length: 457  Bit Score: 39.11  E-value: 1.03e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 446541897  33 AANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALK 70
Cdd:PRK09581  32 ASSGAEAIAICEREQPDIILLDVMMPGMDGFEVCRRLK 69
REC_HupR cd17596
phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR); Members of ...
 23-117 1.27e-03

phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR); Members of this subfamily are response regulator components of two-component systems that regulates hydrogenase activity, including HupR and HoxA. HupR is part of the HupT/HupR system that controls the synthesis of the membrane-bound [NiFe]hydrogenase, HupSL, of the photosynthetic bacterium Rhodobacter capsulatus. It belongs to the nitrogen regulatory protein C (NtrC) family of response regulators, which activate transcription by RNA polymerase (RNAP) in response to a change in the environment. HupR is an unusual member of this family as it activates transcription when unphosphorylated, and transcription is inhibited by phosphorylation. Proteins in this subfamily contain an N-terminal REC domain, a central sigma-54 interaction domain that lacks ATPase activity, and a C-terminal DNA-binding domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381127 [Multi-domain]  Cd Length: 133  Bit Score: 37.35  E-value: 1.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  23 LEDDIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLD-VAEAlkKEKSPCKV-MILTTFARPGYFERAM-KAGVH 99
Cdd:cd17596   20 LEEDFDVL-TAASAEEALAILEEEWVQVILCDQRMPGTTGVEfLKEV--RERWPEVVrIIISGYTDSEDIIAGInEAGIY 96

                         90
                 ....*....|....*...
gi 446541897 100 GYLLKDSPSEDLAAAIRN 117
Cdd:cd17596   97 QYLTKPWHPDQLLLTVRN 114
PRK13435 PRK13435
response regulator; Provisional
 1-72 1.37e-03

response regulator; Provisional


Pssm-ID: 184052 [Multi-domain]  Cd Length: 145  Bit Score: 37.72  E-value: 1.37e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446541897   1 MIRIIIAEDQrmlrgALGALlDLEDDIE-----VIGQAANGEEALKLIESLKPDISIMDIE-MPIQSGLDVAEALKKE 72
Cdd:PRK13435   5 QLKVLIVEDE-----ALIAL-ELEKLVEeagheVVGIAMSSEQAIALGRRRQPDVALVDVHlADGPTGVEVARRLSAD 76
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 140-182 1.56e-03

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 35.51  E-value: 1.56e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 446541897  140 LSDREKEVLLLAK-EGKTANEIAKALYLSPGTVRNYISEVLTKL 182
Cdd:pfam08281  11 LPPRQREVFLLRYlEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
REC_OmpR_MtrA-like cd17626
phosphoacceptor receiver (REC) domain of MtrA-like OmpR family response regulators; MtrA is ...
 3-116 1.58e-03

phosphoacceptor receiver (REC) domain of MtrA-like OmpR family response regulators; MtrA is part of MtrA/MtrB (or MtrAB), a highly conserved two-component system (TCS) implicated in the regulation of cell division in the actinobacteria. In unicellular Mycobacterium tuberculosis, MtrAB coordinates DNA replication with cell division and regulates the transcription of resuscitation-promoting factor B. In filamentous Streptomyces venezuelae, it links antibiotic production to sporulation. MtrA 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.


Pssm-ID: 381141 [Multi-domain]  Cd Length: 115  Bit Score: 37.06  E-value: 1.58e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRGALGALLDLED-DIEVIGqaaNGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMiL 81
Cdd:cd17626    2 RILVVDDDAALAEMIGIVLRGEGfDPAFCG---DGTQALAAFREVRPDLVLLDLMLPGIDGIEVCRQIRAESGVPIVM-L 77

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 446541897  82 TTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIR 116
Cdd:cd17626   78 TAKSDTVDVVLGLESGADDYVAKPFKPKELVARIR 112
PRK10161 PRK10161
phosphate response regulator transcription factor PhoB;
3-120 2.00e-03

phosphate response regulator transcription factor PhoB;


Pssm-ID: 182277 [Multi-domain]  Cd Length: 229  Bit Score: 37.78  E-value: 2.00e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   3 RIIIAEDQRMLRGALGALLDlEDDIEVIgQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILT 82
Cdd:PRK10161   4 RILVVEDEAPIREMVCFVLE-QNGFQPV-EAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVM 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 446541897  83 TFARpGYFE---RAMKAGVHGYLLKDSPSEDLAAAIRNVMK 120
Cdd:PRK10161  82 LTAR-GEEEdrvRGLETGADDYITKPFSPKELVARIKAVMR 121
PRK15115 PRK15115
response regulator GlrR; Provisional
 33-137 2.32e-03

response regulator GlrR; Provisional


Pssm-ID: 185070 [Multi-domain]  Cd Length: 444  Bit Score: 38.28  E-value: 2.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  33 AANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTTFARPGYFERAMKAGVHGYLLKDSPSEDLA 112
Cdd:PRK15115  35 AESGQEALRVLNREKVDLVISDLRMDEMDGMQLFAEIQKVQPGMPVIILTAHGSIPDAVAATQQGVFSFLTKPVDRDALY 114

                         90       100
                 ....*....|....*....|....*
gi 446541897 113 AAIRNVMKGKREVSQElmfgLWQEQ 137
Cdd:PRK15115 115 KAIDDALEQSAPATDE----RWREA 135
REC_OmpR_CtrA cd17616
phosphoacceptor receiver (REC) domain of CtrA-like OmpR family response regulators; CtrA is ...
 36-119 2.53e-03

phosphoacceptor receiver (REC) domain of CtrA-like OmpR family response regulators; CtrA is part of the CckA-ChpT-CtrA phosphorelay that is conserved in alphaproteobacteria and is important in orchestrating the cell cycle, polar development, and flagellar biogenesis. CtrA is the master regulator of flagella synthesis genes and also regulates genes involved in the cell cycle, exopolysaccharide synthesis, and cyclic-di-GMP signaling. CtrA is active as a transcription factor when phosphorylated. It is a member of the OmpR family of DNA-binding response regulators, characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381132 [Multi-domain]  Cd Length: 114  Bit Score: 36.23  E-value: 2.53e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  36 GEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAI 115
Cdd:cd17616   31 GEEGLDLGKLYDYDIILLDLNLPDMSGYEVLRTLRLAKVKTPILILSGLADIEDKVKGLGFGADDYMTKPFHKDELVARI 110


                 ....
gi 446541897 116 RNVM 119
Cdd:cd17616  111 HAIV 114
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 140-182 2.87e-03

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 34.71  E-value: 2.87e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 446541897  140 LSDREKEVLLLAK-EGKTANEIAKALYLSPGTVRNYISEVLTKL 182
Cdd:pfam04545   5 LPPRERQVLVLRYgEGLTLEEIGERLGISRERVRQIEKRALRKL 48
PRK06930 PRK06930
positive control sigma-like factor; Validated
 140-191 4.21e-03

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 36.63  E-value: 4.21e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446541897 140 LSDREKEVLLLAK-EGKTANEIAKALYLSPGTVRNYISEVLTKLdaKNRIEAI 191
Cdd:PRK06930 115 LTEREKEVYLMHRgYGLSYSEIADYLNIKKSTVQSMIERAEKKI--ARQINES 165
REC_RcNtrC-like cd19928
phosphoacceptor receiver (REC) domain of Rhodobacter capsulatus nitrogen regulatory protein C ...
 4-104 6.95e-03

phosphoacceptor receiver (REC) domain of Rhodobacter capsulatus nitrogen regulatory protein C (NtrC) 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 NtrC, also called nitrogen regulator I (NRI), from Rhodobacter capsulatus, Azospirillum brasilense, and Azorhizobium caulinodans. NtrC is part of the NtrB/NtrC two-component system that controls the expression of the nitrogen-regulated (ntr) genes in response to nitrogen limitation. 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.


Pssm-ID: 381155 [Multi-domain]  Cd Length: 100  Bit Score: 34.79  E-value: 6.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALG-ALLDLEDDIEVIGQAANgeeALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILT 82
Cdd:cd19928    1 ILVADDDRAIRTVLTqALGRAGYEVRTTGNAAT---LWRWVEEGEGDLVITDVVMPDENGLDLIPRIKKARPDLPIIVMS 77

                         90       100
                 ....*....|....*....|..
gi 446541897  83 TFARPGYFERAMKAGVHGYLLK 104
Cdd:cd19928   78 AQNTLMTAVKAAERGAFEYLPK 99
PRK11475 PRK11475
DNA-binding transcriptional activator BglJ; Provisional
 94-182 7.31e-03

DNA-binding transcriptional activator BglJ; Provisional


Pssm-ID: 236915 [Multi-domain]  Cd Length: 207  Bit Score: 35.88  E-value: 7.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897  94 MKAGVHGYLLKDSPSEDLAAAIRNVMKGKREVSqELMFGLWQ-EQN-PLSDREKEVLLLAKEGKTANEIAKALYLSPGTV 171
Cdd:PRK11475  88 SPSPLDGVLSKASTLEILQQELFLSLNGVRQAT-DRLNNQWYiNQSrMLSPTEREILRFMSRGYSMPQIAEQLERNIKTI 166

                         90
                 ....*....|.
gi 446541897 172 RNYISEVLTKL 182
Cdd:PRK11475 167 RAHKFNVMSKL 177
REC_FixJ cd17537
phosphoacceptor receiver (REC) domain of FixJ family response regulators; FixJ family response ...
 4-116 9.04e-03

phosphoacceptor receiver (REC) domain of FixJ family response regulators; FixJ family response regulators contain an N-terminal receiver domain (REC) and a C-terminal LuxR family helix-turn-helix (HTH) DNA-binding output domain. The Sinorhizobium meliloti two-component system FixL/FixJ regulates nitrogen fixation in response to oxygen during symbiosis. Under microaerobic conditions, the kinase FixL phosphorylates the response regulator FixJ resulting in the regulation of nitrogen fixation genes such as nifA and fixK. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381092 [Multi-domain]  Cd Length: 116  Bit Score: 34.88  E-value: 9.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   4 IIIAEDQRMLRGALGALLDlEDDIEVIGQAAnGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALKKEKSPCKVMILTt 83
Cdd:cd17537    3 VYVVDDDEAVRDSLAFLLR-SVGLAVKTFTS-ASAFLAAAPPDQPGCLVLDVRMPGMSGLELQDELLARGSNIPIIFIT- 79

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 446541897  84 farpGYFE-----RAMKAGVHGYLLKDSPSEDLAAAIR 116
Cdd:cd17537   80 ----GHGDvpmavEAMKAGAVDFLEKPFRDQVLLDAIE 113
REC_WspR-like cd17575
phosphoacceptor receiver (REC) domain of WspR response regulator and similar proteins; The ...
 2-116 9.93e-03

phosphoacceptor receiver (REC) domain of WspR response regulator and similar proteins; The GGDEF response regulator WspR is part of the Wsp system that is homologous to chemotaxis systems and also includes the membrane-bound receptor protein WspA. In response to growth on surfaces, WspR is phosphorylated by the Wsp signal transduction complex and is activated, functioning as a diguanylate cyclase (DGC) that catalyzes c-di-GMP synthesis. WspR is a hybrid response regulator-diguanylate cyclase, containing an N-terminal REC domain and a C-terminal GGDEF domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381117 [Multi-domain]  Cd Length: 128  Bit Score: 34.69  E-value: 9.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446541897   2 IRIIIAEDQRMLRGALGALLDLEDDIEvIGQAANGEEALKLIESLKPDISIMDIEMPIQSGLDVAEALK--KEKSPCKVM 79
Cdd:cd17575    1 IMVLLVDDQAIIGEAVRRALADEEDID-FHYCSDPTEAIEVASQIKPTVILQDLVMPGVDGLTLVRFFRanPATRDIPII 79

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 446541897  80 ILTTFARPGYFERAMKAGVHGYLLKDSPSEDLAAAIR 116
Cdd:cd17575   80 VLSTKEEPEVKSEAFALGANDYLVKLPDKIELVARIR 116
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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