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Conserved domains on  [gi|491596075|ref|WP_005453637|]
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MULTISPECIES: response regulator [Vibrio]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10403 super family cl32510
nitrate/nitrite response regulator protein NarP;
5-207 3.24e-79

nitrate/nitrite response regulator protein NarP;


The actual alignment was detected with superfamily member PRK10403:

Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 235.90  E-value: 3.24e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILT 84
Cdd:PRK10403   8 QVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLANRLDPDVILLDLNMKGMSGLDTLNALRRDGVTAQIIILT 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  85 VSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQAHEGDKAYSQAVAKYLNERE---GQEDVFDSLTDRETQILQEVAR 161
Cdd:PRK10403  88 VSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKGSKVFSERVNQYLREREmfgAEEDPFSVLTERELDVLHELAQ 167

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 491596075 162 GFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVLYLERFG 207
Cdd:PRK10403 168 GLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATILFLQQRG 213
 
Name Accession Description Interval E-value
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
5-207 3.24e-79

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 235.90  E-value: 3.24e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILT 84
Cdd:PRK10403   8 QVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLANRLDPDVILLDLNMKGMSGLDTLNALRRDGVTAQIIILT 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  85 VSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQAHEGDKAYSQAVAKYLNERE---GQEDVFDSLTDRETQILQEVAR 161
Cdd:PRK10403  88 VSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKGSKVFSERVNQYLREREmfgAEEDPFSVLTERELDVLHELAQ 167

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 491596075 162 GFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVLYLERFG 207
Cdd:PRK10403 168 GLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATILFLQQRG 213
REC_NarL cd19931
phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL); Nitrate ...
 6-120 2.69e-48

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: 154.04  E-value: 2.69e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILTV 85
Cdd:cd19931    1 VLLIDDHPLLRKGIKQLIELDPDFTVVGEASSGEEGIELAERLDPDLILLDLNMKGMSGLDTLKALREEGVSARIVILTV 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 491596075  86 SDSPADIEAIVRSGADGYLLKDTEPDELVELLKQA 120
Cdd:cd19931   81 SDAEDDVVTALRAGADGYLLKDMEPEDLLEALKQA 115
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 5-205 1.62e-32

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: 114.22  E-value: 1.62e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALradgcearivilt 84
Cdd:COG2197    3 RVLIVDDHPLVREGLRALLEAEPDIEVVGEAADGEEALELLEELRPDVVLLDIRMPGMDGLEALRRL------------- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  85 vsdspadieaivrsgadgyllkdtepdelvellkqahegdkaysqavakylneregqedvfdsLTDRETQILQEVARGFR 164
Cdd:COG2197   70 ---------------------------------------------------------------LTPREREVLRLLAEGLS 86

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 491596075 165 NKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVLYLER 205
Cdd:COG2197   87 NKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRL 127
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 145-201 2.91e-20

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 80.26  E-value: 2.91e-20
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 491596075   145 FDSLTDRETQILQEVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVL 201
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 6-118 3.45e-20

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: 81.43  E-value: 3.45e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075    6 VMLVDDHPLMRRGIHQLLsfEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILTV 85
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLL--EKEGYVVAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIRRRDPTTPVIILTA 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 491596075   86 SDSPADIEAIVRSGADGYLLKDTEPDELVELLK 118
Cdd:pfam00072  79 HGDEDDAVEALEAGADDFLSKPFDPDELLAAIR 111
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 142-191 2.01e-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: 40.41  E-value: 2.01e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 491596075  142 EDVFDSLTDRETQILQEVA-RGFRNKQIADRLFISESTVKVHMKSLLKKLK 191
Cdd:TIGR02937 105 REALEKLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKLR 155
 
Name Accession Description Interval E-value
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
5-207 3.24e-79

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 235.90  E-value: 3.24e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILT 84
Cdd:PRK10403   8 QVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLANRLDPDVILLDLNMKGMSGLDTLNALRRDGVTAQIIILT 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  85 VSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQAHEGDKAYSQAVAKYLNERE---GQEDVFDSLTDRETQILQEVAR 161
Cdd:PRK10403  88 VSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKGSKVFSERVNQYLREREmfgAEEDPFSVLTERELDVLHELAQ 167

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 491596075 162 GFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVLYLERFG 207
Cdd:PRK10403 168 GLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATILFLQQRG 213
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 4-205 2.76e-70

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 213.35  E-value: 2.76e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   4 CKVMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVIL 83
Cdd:PRK10651   7 ATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLSGRIVVF 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  84 TVSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQAHEGDKAYSQAVAKYL------NEREGQEDVfDSLTDRETQILQ 157
Cdd:PRK10651  87 SVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQAAAGEMVLSEALTPVLaaslraNRATTERDV-NQLTPRERDILK 165

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 491596075 158 EVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVLYLER 205
Cdd:PRK10651 166 LIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQE 213
REC_NarL cd19931
phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL); Nitrate ...
 6-120 2.69e-48

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: 154.04  E-value: 2.69e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILTV 85
Cdd:cd19931    1 VLLIDDHPLLRKGIKQLIELDPDFTVVGEASSGEEGIELAERLDPDLILLDLNMKGMSGLDTLKALREEGVSARIVILTV 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 491596075  86 SDSPADIEAIVRSGADGYLLKDTEPDELVELLKQA 120
Cdd:cd19931   81 SDAEDDVVTALRAGADGYLLKDMEPEDLLEALKQA 115
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 6-122 3.98e-35

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: 120.31  E-value: 3.98e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILTV 85
Cdd:cd17535    1 VLIVDDHPLVREGLRRLLESEPDIEVVGEAADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRRYPDLKVIVLTA 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 491596075  86 SDSPADIEAIVRSGADGYLLKDTEPDELVELLKQAHE 122
Cdd:cd17535   81 HDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAVAA 117
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 5-205 1.62e-32

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: 114.22  E-value: 1.62e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALradgcearivilt 84
Cdd:COG2197    3 RVLIVDDHPLVREGLRALLEAEPDIEVVGEAADGEEALELLEELRPDVVLLDIRMPGMDGLEALRRL------------- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  85 vsdspadieaivrsgadgyllkdtepdelvellkqahegdkaysqavakylneregqedvfdsLTDRETQILQEVARGFR 164
Cdd:COG2197   70 ---------------------------------------------------------------LTPREREVLRLLAEGLS 86

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 491596075 165 NKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVLYLER 205
Cdd:COG2197   87 NKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRL 127
PRK10360 PRK10360
transcriptional regulator UhpA;
5-192 1.94e-32

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 115.84  E-value: 1.94e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADgceARIVILT 84
Cdd:PRK10360   3 TVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKG---MATIMLS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  85 VSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQAHEGDKAYSQAVAKYLneREGQEdvfDSLTDRETQILQEVARGFR 164
Cdd:PRK10360  80 VHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKL--ASGRQ---DPLTKRERQVAEKLAQGMA 154

                        170       180
                 ....*....|....*....|....*...
gi 491596075 165 NKQIADRLFISESTVKVHMKSLLKKLKV 192
Cdd:PRK10360 155 VKEIAAELGLSPKTVHVHRANLMEKLGV 182
PRK15369 PRK15369
two component system response regulator;
1-192 1.93e-27

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 103.23  E-value: 1.93e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   1 MTVCKVMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARI 80
Cdd:PRK15369   1 MKNYKILLVDDHELIINGIKNMLAPYPRYKIVGQVDNGLEVYNACRQLEPDIVILDLGLPGMNGLDVIPQLHQRWPAMNI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  81 VILTVSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQAHEGdKAY------SQAVAKYLNEREGQEDVfdsLTDRETQ 154
Cdd:PRK15369  81 LVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVG-KRYidpalnREAILALLNADDTNPPL---LTPRERQ 156

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 491596075 155 ILQEVARGFRNKQIADRLFISESTVKVHMKSLLKKLKV 192
Cdd:PRK15369 157 ILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDV 194
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 6-194 5.52e-27

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: 101.72  E-value: 5.52e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLLS---FEpefevVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVI 82
Cdd:COG4566    2 VYIVDDDEAVRDSLAFLLEsagLR-----VETFASAEAFLAALDPDRPGCLLLDVRMPGMSGLELQEELAARGSPLPVIF 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  83 LTvsdSPADIEAIVR---SGADGYLLKDTEPDELVELLKQAHEGDKAYSQAVAkylnEREGQEDVFDSLTDRETQILQEV 159
Cdd:COG4566   77 LT---GHGDVPMAVRamkAGAVDFLEKPFDDQALLDAVRRALARDRARRAERA----RRAELRARLASLTPREREVLDLV 149

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 491596075 160 ARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPS 194
Cdd:COG4566  150 VAGLSNKQIARELGISPRTVEVHRANVMEKLGARS 184
PRK09483 PRK09483
response regulator; Provisional
 6-192 1.15e-25

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 99.02  E-value: 1.15e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLD-TLKALRADGcEARIVILT 84
Cdd:PRK09483   4 VLLVDDHELVRAGIRRILEDIKGIKVVGEACCGEDAVKWCRTNAVDVVLMDMNMPGIGGLEaTRKILRYTP-DVKIIMLT 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  85 V-SDSPADIEaIVRSGADGYLLKDTEPDELVELLKQAHEGDKAYSQAVAKY--LNEREGQEDV-FDSLTDRETQILQEVA 160
Cdd:PRK09483  83 VhTENPLPAK-VMQAGAAGYLSKGAAPQEVVSAIRSVHSGQRYIASDIAQQmaLSQIEPATENpFASLSERELQIMLMIT 161

                        170       180       190
                 ....*....|....*....|....*....|..
gi 491596075 161 RGFRNKQIADRLFISESTVKVHMKSLLKKLKV 192
Cdd:PRK09483 162 KGQKVNEISEQLNLSPKTVNSYRYRMFSKLNI 193
OmpR COG0745
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...
 5-191 1.45e-23

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: 93.10  E-value: 1.45e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEpEFEVVaEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILT 84
Cdd:COG0745    3 RILVVEDDPDIRELLADALERE-GYEVD-TAADGEEALELLEEERPDLILLDLMLPGMDGLEVCRRLRARPSDIPIIMLT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  85 VSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQAHEGDKAYSQAVAKYLNEREGQ---EDVFDSLTDRETQILQEVA- 160
Cdd:COG0745   81 ARDDEEDRVRGLEAGADDYLTKPFDPEELLARIRALLRRRAAEVLRVGDLLDLAAREvtrDGEPVELTPKEFRLLELLMr 160

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 491596075 161 ---RGFRNKQIADRL----FISESTVKVHMKSLLKKLK 191
Cdd:COG0745  161 npgRVVSREQLLEEVwgydYGDDRTVDVHISRLRKKLE 198
REC_DesR-like cd19930
phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of ...
 6-122 1.68e-22

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: 87.71  E-value: 1.68e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILTV 85
Cdd:cd19930    1 VLIAEDQEMVRGALAALLELEDDLEVVAQASNGQEALRLVLKHSPDVAILDIEMPGRTGLEVAAELREELPDTKVLIVTT 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 491596075  86 SDSPADIEAIVRSGADGYLLKDTEPDELVELLKQAHE 122
Cdd:cd19930   81 FGRPGYFRRALAAGVDGYVLKDRPIEELADAIRTVHA 117
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 145-201 2.91e-20

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 80.26  E-value: 2.91e-20
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 491596075   145 FDSLTDRETQILQEVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVL 201
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 6-118 3.45e-20

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: 81.43  E-value: 3.45e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075    6 VMLVDDHPLMRRGIHQLLsfEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILTV 85
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLL--EKEGYVVAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIRRRDPTTPVIILTA 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 491596075   86 SDSPADIEAIVRSGADGYLLKDTEPDELVELLK 118
Cdd:pfam00072  79 HGDEDDAVEALEAGADDFLSKPFDPDELLAAIR 111
YesN COG4753
Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding ...
 5-106 5.26e-20

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: 80.97  E-value: 5.26e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILT 84
Cdd:COG4753    1 KVLIVDDEPLIREGLKRILEWEAGFEVVGEAENGEEALELLEEHKPDLVITDINMPGMDGLELLEAIRELDPDTKIIILS 80

                         90       100
                 ....*....|....*....|..
gi 491596075  85 VSDSPADIEAIVRSGADGYLLK 106
Cdd:COG4753   81 GYSDFEYAQEAIKLGADDYLLK 102
GerE pfam00196
Bacterial regulatory proteins, luxR family;
146-201 1.31e-19

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 78.40  E-value: 1.31e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 491596075  146 DSLTDRETQILQEVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVL 201
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRM 56
CitB COG4565
DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal ...
 1-120 1.46e-19

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


Pssm-ID: 443622 [Multi-domain]  Cd Length: 138  Bit Score: 80.78  E-value: 1.46e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   1 MTVCKVMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARI 80
Cdd:COG4565    1 MKMIRVLIVEDDPMVAELLRRYLERLPGFEVVGVASSGEEALALLAEHRPDLILLDIYLPDGDGLELLRELRARGPDVDV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 491596075  81 VILTVSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQA 120
Cdd:COG4565   81 IVITAARDPETVREALRAGVVDYLIKPFTFERLREALERY 120
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 138-210 4.74e-19

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: 77.69  E-value: 4.74e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491596075 138 REGQEDVFDSLTDRETQILQEVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVLYLeRFGEIK 210
Cdd:COG5905    3 PSSSTSHPSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWAL-RLGLLS 74
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 148-201 2.30e-18

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: 75.26  E-value: 2.30e-18
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 491596075 148 LTDRETQILQEVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVL 201
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAY 54
REC_YesN-like cd17536
phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response ...
 6-122 1.42e-16

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: 72.37  E-value: 1.42e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLLSFE-PEFEVVAEASSGADAVAKAheleldlvLLDL--------NMKGMSGLDTLKALRADGC 76
Cdd:cd17536    1 VLIVDDEPLIREGLKKLIDWEeLGFEVVGEAENGEEALELI--------EEHKpdivitdiRMPGMDGLELIEKIRELYP 72

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 491596075  77 EARIVILTvsdSPADIE----AIvRSGADGYLLKDTEPDELVELLKQAHE 122
Cdd:cd17536   73 DIKIIILS---GYDDFEyaqkAI-RLGVVDYLLKPVDEEELEEALEKAKE 118
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 5-122 1.43e-16

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: 76.93  E-value: 1.43e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEpEFEVVaEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILT 84
Cdd:COG2204    4 RILVVDDDPDIRRLLKELLERA-GYEVE-TAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRALDPDLPVILLT 81

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 491596075  85 VSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQAHE 122
Cdd:COG2204   82 GYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERALE 119
REC cd00156
phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ...
 7-106 4.05e-16

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: 70.72  E-value: 4.05e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   7 MLVDDHPLMRRGIHQLLsfEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILTVS 86
Cdd:cd00156    1 LIVDDDPAIRELLKSLL--EREGYEVDTAADGEEALELLREERPDLVLLDLMMPGMDGLELLRKLRELPPDIPVIVLTAK 78

                         90       100
                 ....*....|....*....|
gi 491596075  87 DSPADIEAIVRSGADGYLLK 106
Cdd:cd00156   79 ADEEDAVRALELGADDYLVK 98
CheY COG0784
CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator ...
 5-126 5.65e-16

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: 71.03  E-value: 5.65e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEpEFEVVaEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGC--EARIVI 82
Cdd:COG0784    7 RILVVDDNPDNRELLRRLLERL-GYEVT-TAEDGAEALELLRAGPPDLILLDINMPGMDGLELLRRIRALPRlpDIPIIA 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 491596075  83 LTVSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQAHEGDKA 126
Cdd:COG0784   85 LTAYADEEDRERALEAGADDYLTKPVDPEELLEALRRLLARASA 128
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
29-205 1.83e-15

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 71.33  E-value: 1.83e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  29 FEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILTVSDSPADIEAIVRSGADGYLLKDT 108
Cdd:COG2771    9 LLLALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLL 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075 109 EPDELVELLKQAHEGDKAYSQAVAKYLNEREGQEDVFDSLTDRETQILQEVARGFRNKQIADRLFISESTVKVHMKSLLK 188
Cdd:COG2771   89 ALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYR 168

                        170
                 ....*....|....*..
gi 491596075 189 KLKVPSRTAATVLYLER 205
Cdd:COG2771  169 KLGVSSRAELVALALRL 185
REC_CheY_CheY3 cd19923
phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY ...
 5-120 3.11e-15

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: 68.90  E-value: 3.11e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSfEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILT 84
Cdd:cd19923    2 KVLVVDDFSTMRRIIKNLLK-ELGFNNVEEAEDGVDALEKLKAGGFDFVITDWNMPNMDGLELLKTIRADGALSHLPVLM 80

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 491596075  85 VSdSPADIEAIV---RSGADGYLLKDTEPDELVELLKQA 120
Cdd:cd19923   81 VT-AEAKKENVIaaaQAGVNNYIVKPFTAATLKEKLEKI 118
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
7-194 1.27e-14

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 69.54  E-value: 1.27e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   7 MLVDDHPLMRRGIHQLLSfEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILTVS 86
Cdd:PRK09958   4 IIIDDHPLAIAAIRNLLI-KNDIEILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVSAK 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  87 DSPADIEAIVRSGADGYLLKDTEPDELVELLKQAHEGDKAYSQAVAKYLNEREGQEDVFDSLTDRETQILQEVARGFRNK 166
Cdd:PRK09958  83 NDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGYCYFPFSLNRFVGSLTSDQQKLDSLSKQEISVMRYILDGKDNN 162

                        170       180
                 ....*....|....*....|....*...
gi 491596075 167 QIADRLFISESTVKVHMKSLLKKLKVPS 194
Cdd:PRK09958 163 DIAEKMFISNKTVSTYKSRLMEKLECKS 190
REC_CheY cd17542
phosphoacceptor receiver (REC) domain of chemotaxis protein CheY; The chemotaxis response ...
 5-120 1.40e-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: 67.30  E-value: 1.40e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSfEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILT 84
Cdd:cd17542    2 KVLIVDDAAFMRMMLKDILT-KAGYEVVGEAANGEEAVEKYKELKPDLVTMDITMPEMDGIEALKEIKKIDPNAKVIMCS 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 491596075  85 -VSDSPADIEAIvRSGADGYLLKDTEPDELVELLKQA 120
Cdd:cd17542   81 aMGQEEMVKEAI-KAGAKDFIVKPFQPERVLEAVEKV 116
fixJ PRK09390
response regulator FixJ; Provisional
 6-194 5.16e-14

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 67.72  E-value: 5.16e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLLSfEPEFEVVAEASSGA--DAVAKAhelELDLVLLDLNMKGMSGLDTLKALRADGCEARIVIL 83
Cdd:PRK09390   6 VHVVDDDEAMRDSLAFLLD-SAGFEVRLFESAQAflDALPGL---RFGCVVTDVRMPGIDGIELLRRLKARGSPLPVIVM 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  84 T-VSDSPADIEAIvRSGADGYLLKDTEPDELVELLKQA--HEGDKAYSQAVAKYLNERegqedvFDSLTDRETQILQEVA 160
Cdd:PRK09390  82 TgHGDVPLAVEAM-KLGAVDFIEKPFEDERLIGAIERAlaQAPEAAKSEAVAADIRAR------IASLSERERQVMDGLV 154

                        170       180       190
                 ....*....|....*....|....*....|....
gi 491596075 161 RGFRNKQIADRLFISESTVKVHMKSLLKKLKVPS 194
Cdd:PRK09390 155 AGLSNKVIARDLDISPRTVEVYRANVMTKMQAGS 188
RpfG COG3437
Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains ...
 5-122 1.07e-13

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: 67.11  E-value: 1.07e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEPeFEVVaEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRAD--GCEARIVI 82
Cdd:COG3437    8 TVLIVDDDPENLELLRQLLRTLG-YDVV-TAESGEEALELLLEAPPDLILLDVRMPGMDGFELLRLLRADpsTRDIPVIF 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 491596075  83 LTVSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQAHE 122
Cdd:COG3437   86 LTALADPEDRERALEAGADDYLTKPFDPEELLARVRNALE 125
PleD COG3706
Two-component response regulator, PleD family, consists of two REC domains and a diguanylate ...
 5-114 1.18e-13

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: 66.09  E-value: 1.18e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSfEPEFEVVaEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEAR--IVI 82
Cdd:COG3706    3 RILVVDDDPTNRKLLRRLLE-AAGYEVV-EAADGEEALELLQEHRPDLILLDLEMPDMDGLELCRRLRADPRTADipIIF 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 491596075  83 LTVSDSPADIEAIVRSGADGYLLKDTEPDELV 114
Cdd:COG3706   81 LTALDDEEDRARALEAGADDYLTKPFDPEELL 112
LytT COG3279
DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction ...
 5-190 2.21e-13

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


Pssm-ID: 442510 [Multi-domain]  Cd Length: 235  Bit Score: 66.38  E-value: 2.21e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILT 84
Cdd:COG3279    3 KILIVDDEPLARERLERLLEKYPDLEVVGEASNGEEALELLEEHKPDLVFLDIQMPGLDGFELARQLRELDPPPPIIFTT 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  85 VSDSPAdIEAIvRSGADGYLLKDTEPDELvellkqahegdkaySQAVAKYLNEREGQEDVFDSLTDRETqILQEVARGFR 164
Cdd:COG3279   83 AYDEYA-LEAF-EVNAVDYLLKPIDEERL--------------AKALEKAKERLEAKAAAEASPEEKDR-IFVKSGGKLV 145

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 491596075 165 NKQIADRLFI--SESTVKVH-----------MKSLLKKL 190
Cdd:COG3279  146 KIPLDDILYIeaEGNYVKIHtkdkkylvrktLKELEEKL 184
PRK10100 PRK10100
transcriptional regulator CsgD;
84-198 2.16e-12

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 63.35  E-value: 2.16e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  84 TVSDSPADIEAIVRSGADGYLLKDTE------------PDE--LVELLKQAHEGDKAYSQAVAKYLNEREGQEDvFDS-- 147
Cdd:PRK10100  74 TLSRKNNNIKILLLNTPEDYPYREIEnwphingvfyamEDQerVVNGLQGVLRGECYFTQKLASYLITHSGNYR-YNSte 152

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 491596075 148 ---LTDRETQILQEVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAA 198
Cdd:PRK10100 153 salLTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQA 206
PRK10610 PRK10610
chemotaxis protein CheY;
5-122 2.77e-12

chemotaxis protein CheY;


Pssm-ID: 170568 [Multi-domain]  Cd Length: 129  Bit Score: 61.53  E-value: 2.77e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSfEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILT 84
Cdd:PRK10610   7 KFLVVDDFSTMRRIVRNLLK-ELGFNNVEEAEDGVDALNKLQAGGFGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 491596075  85 VSDSPA--DIEAIVRSGADGYLLKDTEPDELVELLKQAHE 122
Cdd:PRK10610  86 VTAEAKkeNIIAAAQAGASGYVVKPFTAATLEEKLNKIFE 125
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
71-198 3.23e-12

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 62.41  E-value: 3.23e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  71 LRADGCEARIVILTVSDSPADIEAIV-RSGADGYLLKDTEP--DELVELLKQAHEGDKAYSQAVAkyLNEREGQEDVFDS 147
Cdd:COG2909   51 LRREEAAALLRRRLLPLSEEDAARLAeRTEGWARLALDPEEalALLERLLALAEAAGRLLLRALA--LRALGDREEALAA 128

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 491596075 148 LTDREtqilqeVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAA 198
Cdd:COG2909  129 LRRRL------LAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEA 173
COG4567 COG4567
DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains ...
 5-126 6.88e-12

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: 61.47  E-value: 6.88e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHP---------LMRRGihqllsfepeFEVVAeASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADG 75
Cdd:COG4567    6 SLLLVDDDEafarvlaraLERRG----------FEVTT-AASVEEALALLEQAPPDYAVLDLRLGDGSGLDLIEALRERD 74

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 491596075  76 CEARIVILTVSDSPADIEAIVRSGADGYLLKDTEPDELVELLkQAHEGDKA 126
Cdd:COG4567   75 PDARIVVLTGYASIATAVEAIKLGADDYLAKPADADDLLAAL-ERAEGDAP 124
REC_CheB-like cd17541
phosphoacceptor receiver (REC) domain of chemotaxis response regulator protein-glutamate ...
 5-106 2.12e-11

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: 58.94  E-value: 2.12e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADgCEARIVI-- 82
Cdd:cd17541    2 RVLIVDDSAVMRKLLSRILESDPDIEVVGTARDGEEALEKIKELKPDVITLDIEMPVMDGLEALRRIMAE-RPTPVVMvs 80

                         90       100
                 ....*....|....*....|....*
gi 491596075  83 -LTVSDSPADIEAIvRSGADGYLLK 106
Cdd:cd17541   81 sLTEEGAEITLEAL-ELGAVDFIAK 104
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 1-192 2.42e-11

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 60.62  E-value: 2.42e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   1 MTVCKVMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKG---MSGLDTLKALRADGCE 77
Cdd:PRK10840   1 MNNMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHFPS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  78 ARIVILTVSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQAHEGDKAYSQAVAKYLNEREGQEDVFDSLTDRETQILQ 157
Cdd:PRK10840  81 LSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLEKISAGGYGDKRLSPKESEVLR 160

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 491596075 158 EVARGFRNKQIADRLFISESTVKVHMKSLLKKLKV 192
Cdd:PRK10840 161 LFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGV 195
AmiR COG3707
Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding ...
 1-120 4.40e-11

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: 59.59  E-value: 4.40e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   1 MTVCKVMLVDDHPLMRRGIHQLLSfEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGcEARI 80
Cdd:COG3707    1 MRGLRVLVVDDEPLRRADLREGLR-EAGYEVVAEAADGEDAVELVRELKPDLVIVDIDMPDRDGLEAARQISEER-PAPV 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 491596075  81 VILTVSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQA 120
Cdd:COG3707   79 ILLTAYSDPELIERALEAGVSAYLVKPLDPEDLLPALELA 118
REC_OmpR_PrrA-like cd17627
phosphoacceptor receiver (REC) domain of PrrA-like OmpR family response regulators; The ...
 6-118 6.64e-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: 57.39  E-value: 6.64e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLLSFEpEFEVvAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILTV 85
Cdd:cd17627    1 ILVVDDDRAVRESLRRSLRFE-GYEV-ETAVDGAEALRVISGNRPDAVVLDVMMPRLDGLEVCRRLRAAGNDLPILVLTA 78

                         90       100       110
                 ....*....|....*....|....*....|...
gi 491596075  86 SDSPADIEAIVRSGADGYLLKDTEPDELVELLK 118
Cdd:cd17627   79 RDSVSDRVAGLDAGADDYLVKPFALEELLARVR 111
REC_Rcp-like cd17557
phosphoacceptor receiver (REC) domain of cyanobacterial phytochrome response regulator Rcp and ...
 58-119 7.37e-11

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: 57.43  E-value: 7.37e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 491596075  58 NMKGMSGLDTLKALRADGCEARI--VILTVSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQ 119
Cdd:cd17557   61 NMPRMDGFEVLREIKADPDLRRIpvVVLTTSDAEEDIERAYELGANSYIVKPVDFEEFVEAIRS 124
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
1-194 2.45e-10

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 57.58  E-value: 2.45e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   1 MTVCKVMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARI 80
Cdd:PRK09935   1 MKPASVIIMDTHPIIRMSIEVLLQKNSELQIVLKTDDYRITIDYLRTRPVDLIIMDIDLPGTDGFTFLKRIKQIQSTVKV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  81 VILTVSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQAHEGDKAYSQAVAKYLNE---REGQEDVFdSLTDRETQILQ 157
Cdd:PRK09935  81 LFLSSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMILSGYTFFPSETLNYIKSnkcSTNSSTDT-VLSNREVTILR 159

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 491596075 158 EVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPS 194
Cdd:PRK09935 160 YLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHS 196
REC_hyHK_CKI1_RcsC-like cd17546
phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinases/response regulators ...
 6-117 2.74e-10

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: 55.55  E-value: 2.74e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLLsfEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEAR---IVI 82
Cdd:cd17546    1 VLVVDDNPVNRKVLKKLL--EKLGYEVDVAENGQEALELLKEEPFDLVLMDLQMPVMDGLEATRRIRELEGGGRrtpIIA 78

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 491596075  83 LTVSDSPADIEAIVRSGADGYLLKDTEPDELVELL 117
Cdd:cd17546   79 LTANALEEDREKCLEAGMDDYLSKPVKLDQLKEVL 113
REC_CheY4-like cd17562
phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY4 and similar CheY ...
 5-118 6.37e-10

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: 54.61  E-value: 6.37e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRrgihQLLSF---EPEFEVVaEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEAR-- 79
Cdd:cd17562    2 KILAVDDSASIR----QMVSFtlrGAGYEVV-EAADGRDALSKAQSKKFDLIITDQNMPNMDGIELIKELRKLPAYKFtp 76

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 491596075  80 IVILTVSDSPADIEAIVRSGADGYLLKDTEPDELVELLK 118
Cdd:cd17562   77 ILMLTTESSDEKKQEGKAAGATGWLVKPFDPEQLLEVVK 115
REC_LytTR_AlgR-like cd17532
phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AlgR; ...
 6-122 2.22e-09

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: 53.31  E-value: 2.22e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILTV 85
Cdd:cd17532    1 ALIVDDEPLAREELRYLLEEHPDIEIVGEAENGEEALEAIEELKPDVVFLDIQMPGLDGLELAKKLSKLAKPPLIVFVTA 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 491596075  86 SDSPAdIEAIvRSGADGYLLKDTEPDELVELLKQAHE 122
Cdd:cd17532   81 YDEYA-VEAF-ELNAVDYLLKPFSEERLAEALAKLRK 115
REC_OmpR_MtPhoP-like cd17615
phosphoacceptor receiver (REC) domain of MtPhoP-like OmpR family response regulators; ...
 5-118 8.42e-09

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: 51.58  E-value: 8.42e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEpEFEVVAeASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILT 84
Cdd:cd17615    1 RVLVVDDEPNITELLSMALRYE-GWDVET-AADGAEALAAAREFRPDAVVLDIMLPDMDGLEVLRRLRADGPDVPVLFLT 78

                         90       100       110
                 ....*....|....*....|....*....|....
gi 491596075  85 VSDSPADIEAIVRSGADGYLLKDTEPDELVELLK 118
Cdd:cd17615   79 AKDSVEDRIAGLTAGGDDYVTKPFSLEEVVARLR 112
REC_OmpR_PmrA-like cd17624
phosphoacceptor receiver (REC) domain of PmrA-like OmpR family response regulators; This ...
 6-114 1.63e-08

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: 50.95  E-value: 1.63e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLLSfePEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILTV 85
Cdd:cd17624    1 ILLVEDDALLGDGLKTGLR--KAGYAVDWVRTGAEAEAALASGPYDLVILDLGLPDGDGLDLLRRWRRQGQSLPVLILTA 78

                         90       100
                 ....*....|....*....|....*....
gi 491596075  86 SDSPADIEAIVRSGADGYLLKDTEPDELV 114
Cdd:cd17624   79 RDGVDDRVAGLDAGADDYLVKPFALEELL 107
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
131-198 2.37e-08

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 53.41  E-value: 2.37e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 491596075 131 VAKYLNEREGQEDVFDS-LTDRETQILQEVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAA 198
Cdd:PRK04841 821 VEKLLNHPDVPELIRTSpLTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEA 889
REC_DctD-like cd17549
phosphoacceptor receiver (REC) domain of C4-dicarboxylic acid transport protein D (DctD) and ...
 6-122 6.61e-08

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: 49.41  E-value: 6.61e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLLSFEpEFEVVAeASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILTV 85
Cdd:cd17549    1 VLLVDDDADVREALQQTLELA-GFRVRA-FADAEEALAALSPDFPGVVISDIRMPGMDGLELLAQIRELDPDLPVILITG 78

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 491596075  86 -SDSPADIEAIvRSGADGYLLKDTEPDELVELLKQAHE 122
Cdd:cd17549   79 hGDVPMAVEAM-RAGAYDFLEKPFDPERLLDVVRRALE 115
REC_D1_PleD-like cd17538
first (D1) phosphoacceptor receiver (REC) domain of response regulator PleD and similar ...
 5-106 7.77e-08

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: 48.65  E-value: 7.77e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEpEFEVVaEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARI--VI 82
Cdd:cd17538    1 KILVVDDEPANRELLEALLSAE-GYEVL-TADSGQEALALAEEELPDLILLDVMMPGMDGFEVCRRLKEDPETRHIpvIM 78

                         90       100
                 ....*....|....*....|....
gi 491596075  83 LTVSDSPADIEAIVRSGADGYLLK 106
Cdd:cd17538   79 ITALDDREDRIRGLEAGADDFLSK 102
REC_RegA-like cd17563
phosphoacceptor receiver (REC) domain of photosynthetic apparatus regulatory protein RegA; ...
 5-117 1.36e-07

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: 48.21  E-value: 1.36e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHP---------LMRRGIHqllsfepefevVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADG 75
Cdd:cd17563    2 SLLLVDDDEvfaerlaraLERRGFE-----------VETAHSVEEALALAREEKPDYAVLDLRLGGDSGLDLIPPLRALQ 70

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 491596075  76 CEARIVILTVSDS-PADIEAIvRSGADGYLLKDTEPDELVELL 117
Cdd:cd17563   71 PDARIVVLTGYASiATAVEAI-KLGADDYLAKPADADEILAAL 112
REC_OmpR cd17574
phosphoacceptor receiver (REC) domain of OmpR family response regulators; OmpR-like proteins ...
 7-106 1.54e-07

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: 47.79  E-value: 1.54e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   7 MLVDDHPLMRRGIHQLLSFEpEFEVVaEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILTVS 86
Cdd:cd17574    1 LVVEDDEEIAELLSDYLEKE-GYEVD-TAADGEEALELAREEQPDLIILDVMLPGMDGFEVCRRLREKGSDIPIIMLTAK 78

                         90       100
                 ....*....|....*....|
gi 491596075  87 DSPADIEAIVRSGADGYLLK 106
Cdd:cd17574   79 DEEEDKVLGLELGADDYITK 98
PRK00742 PRK00742
chemotaxis-specific protein-glutamate methyltransferase CheB;
5-71 1.90e-07

chemotaxis-specific protein-glutamate methyltransferase CheB;


Pssm-ID: 234828 [Multi-domain]  Cd Length: 354  Bit Score: 50.15  E-value: 1.90e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKAL 71
Cdd:PRK00742   5 RVLVVDDSAFMRRLISEILNSDPDIEVVGTAPDGLEAREKIKKLNPDVITLDVEMPVMDGLDALEKI 71
REC_HupR cd17596
phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR); Members of ...
 6-122 2.22e-07

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: 48.13  E-value: 2.22e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLLsfEPEFEVVAeASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEA-RIVILT 84
Cdd:cd17596    3 ILVVDDEVRSLEALRRTL--EEDFDVLT-AASAEEALAILEEEWVQVILCDQRMPGTTGVEFLKEVRERWPEVvRIIISG 79

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 491596075  85 VSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQAHE 122
Cdd:cd17596   80 YTDSEDIIAGINEAGIYQYLTKPWHPDQLLLTVRNAAR 117
REC_citrate_TCS cd19925
phosphoacceptor receiver (REC) domain of citrate family two-component system response ...
 5-106 6.62e-07

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: 46.47  E-value: 6.62e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILT 84
Cdd:cd19925    2 NVLIVEDDPMVAEIHRAYVEQVPGFTVIGTAGTGEEALKLLKERQPDLILLDIYLPDGNGLDLLRELRAAGHDVDVIVVT 81

                         90       100
                 ....*....|....*....|..
gi 491596075  85 VSDSPADIEAIVRSGADGYLLK 106
Cdd:cd19925   82 AANDVETVREALRLGVVDYLIK 103
PRK11361 PRK11361
acetoacetate metabolism transcriptional regulator AtoC;
5-161 3.36e-06

acetoacetate metabolism transcriptional regulator AtoC;


Pssm-ID: 183099 [Multi-domain]  Cd Length: 457  Bit Score: 46.77  E-value: 3.36e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEpEFEVVAeASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILT 84
Cdd:PRK11361   6 RILIVDDEDNVRRMLSTAFALQ-GFETHC-ANNGRTALHLFADIHPDVVLMDIRMPEMDGIKALKEMRSHETRTPVILMT 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  85 V-SDSPADIEAIvRSGADGYLLKDTEPDELVELLKQAHE--GDKAYSQAVAKYLNEREGQEDVfdsLTD--RETQILQEV 159
Cdd:PRK11361  84 AyAEVETAVEAL-RCGAFDYVIKPFDLDELNLIVQRALQlqSMKKEIRHLHQALSTSWQWGHI---LTNspAMMDICKDT 159


                 ..
gi 491596075 160 AR 161
Cdd:PRK11361 160 AK 161
REC_OmpR_CpxR cd17623
phosphoacceptor receiver (REC) domain of CpxR-like OmpR family response regulators; CpxR is ...
 6-118 3.50e-06

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: 44.60  E-value: 3.50e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLLSFEPeFEVVAeASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGcEARIVILTV 85
Cdd:cd17623    1 ILLIDDDRELTELLTEYLEMEG-FNVRA-AHDGEQGLAALLEGSPDLVVLDVMLPKMNGLDVLKELRKTS-QVPVLMLTA 77

                         90       100       110
                 ....*....|....*....|....*....|...
gi 491596075  86 SDSPADIEAIVRSGADGYLLKDTEPDELVELLK 118
Cdd:cd17623   78 RGDDIDRILGLELGADDYLPKPFNPRELVARIR 110
REC_PdtaR-like cd19932
phosphoacceptor receiver (REC) domain of PdtaR and similar proteins; This subfamily includes ...
 5-120 4.23e-06

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: 44.33  E-value: 4.23e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSfEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCeARIVILT 84
Cdd:cd19932    2 RVLIAEDEALIRMDLREMLE-EAGYEVVGEASDGEEAVELAKKHKPDLVIMDVKMPRLDGIEAAKIITSENI-APIVLLT 79

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 491596075  85 VSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQA 120
Cdd:cd19932   80 AYSQQDLVERAKEAGAMAYLVKPFSESDLIPAIEMA 115
REC_DivK-like cd17548
phosphoacceptor receiver (REC) domain of DivK and similar proteins; Caulobacter crescentus ...
 5-119 5.04e-06

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: 44.07  E-value: 5.04e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEpEFEVVaEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVI-- 82
Cdd:cd17548    1 KILIVEDNPLNMKLARDLLESA-GYEVL-EAADGEEALEIARKEKPDLILMDIQLPGMDGLEATRLLKEDPATRDIPVia 78

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 491596075  83 LTVSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQ 119
Cdd:cd17548   79 LTAYAMKGDREKILEAGCDGYISKPIDTREFLETVAK 115
REC_OmpR_EcPhoP-like cd19934
phosphoacceptor receiver (REC) domain of EcPhoP-like OmpR family response regulators; ...
 6-114 5.84e-06

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: 43.81  E-value: 5.84e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLLSfePEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILTV 85
Cdd:cd19934    1 LLLVEDDALLAAQLKEQLS--DAGYVVDVAEDGEEALFQGEEEPYDLVVLDLGLPGMDGLSVLRRWRSEGRATPVLILTA 78

                         90       100
                 ....*....|....*....|....*....
gi 491596075  86 SDSPADIEAIVRSGADGYLLKDTEPDELV 114
Cdd:cd19934   79 RDSWQDKVEGLDAGADDYLTKPFHIEELL 107
REC_RR468-like cd17552
phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator RR468 and ...
 5-120 9.17e-06

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: 43.31  E-value: 9.17e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEPEFEVVaEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARI--VI 82
Cdd:cd17552    3 RILVIDDEEDIREVVQACLEKLAGWEVL-TASSGQEGLEKAATEQPDAILLDVMMPDMDGLATLKKLQANPETQSIpvIL 81

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 491596075  83 LTVSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQA 120
Cdd:cd17552   82 LTAKAQPSDRQRFASLGVAGVIAKPFDPLTLAEQIAKL 119
PRK11697 PRK11697
two-component system response regulator BtsR;
5-113 1.05e-05

two-component system response regulator BtsR;


Pssm-ID: 236956 [Multi-domain]  Cd Length: 238  Bit Score: 44.84  E-value: 1.05e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGcEARIVILT 84
Cdd:PRK11697   3 KVLIVDDEPLAREELRELLQEEGDIEIVGECSNAIEAIGAIHRLKPDVVFLDIQMPRISGLELVGMLDPEH-MPYIVFVT 81

                         90       100
                 ....*....|....*....|....*....
gi 491596075  85 VSDSPAdIEAIVRSGADgYLLKDTEPDEL 113
Cdd:PRK11697  82 AFDEYA-IKAFEEHAFD-YLLKPIDPARL 108
REC_OmpR_ArcA_TorR-like cd17619
phosphoacceptor receiver (REC) domain of ArcA- and TorR-like OmpR family response regulators; ...
 6-114 3.34e-05

phosphoacceptor receiver (REC) domain of ArcA- and TorR-like OmpR family response regulators; This subfamily includes Escherichia coli TorR and ArcA, both OmpR family response regulators that mediate adaptation to changes in various respiratory growth conditions. The TorS-TorR two-component system (TCS) is responsible for the tight regulation of the torCAD operon, which encodes the trimethylamine N-oxide (TMAO) reductase respiratory system in response to anaerobic conditions and the presence of TMAO. The ArcA-ArcB TCS is involved in cell growth during anaerobiosis. ArcA is a global regulator that controls more than 30 operons involved in redox regulation (the Arc modulon). OmpR family DNA-binding response regulators 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: 381134 [Multi-domain]  Cd Length: 113  Bit Score: 41.60  E-value: 3.34e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRrgihQLLS--FEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRAdgcEARIVIL 83
Cdd:cd17619    3 ILIVEDEPVTR----ATLKsyFEQEGYDVSEAGDGEEMRQILARQDIDLVLLDINLPGKDGLSLTRELRE---QSEVGII 75

                         90       100       110
                 ....*....|....*....|....*....|...
gi 491596075  84 TVSDSPADIEAIV--RSGADGYLLKDTEPDELV 114
Cdd:cd17619   76 LVTGRDDEVDRIVglEIGADDYVTKPFNPRELL 108
REC_HupR-like cd17569
phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR) and similar ...
 5-120 3.37e-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: 41.62  E-value: 3.37e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEPeFEVVaEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEA-RIVIL 83
Cdd:cd17569    2 TILLVDDEPNILKALKRLLRREG-YEVL-TATSGEEALEILKQEPVDVVISDQRMPGMDGAELLKRVRERYPDTvRILLT 79

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 491596075  84 TVSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQA 120
Cdd:cd17569   80 GYADLDAAIEAINEGEIYRFLTKPWDDEELKETIRQA 116
REC_RpfG-like cd17551
phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator ...
 5-114 5.17e-05

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: 41.27  E-value: 5.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSgADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEAR--IVI 82
Cdd:cd17551    2 RILIVDDNPTNLLLLEALLRSAGYLEVVSFTDP-REALAWCRENPPDLILLDYMMPGMDGLEFIRRLRALPGLEDvpIVM 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 491596075  83 LTVSDSPA-DIEAIvRSGADGYLLKDTEPDELV 114
Cdd:cd17551   81 ITADTDREvRLRAL-EAGATDFLTKPFDPVELL 112
PRK10188 PRK10188
transcriptional regulator SdiA;
148-196 5.90e-05

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 42.47  E-value: 5.90e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 491596075 148 LTDRETQILQEVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRT 196
Cdd:PRK10188 180 FSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKT 228
REC_OmpR_CusR-like cd19935
phosphoacceptor receiver (REC) domain of CusR-like OmpR family response regulators; ...
 6-106 7.91e-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: 40.12  E-value: 7.91e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLLSfEPEFeVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILTV 85
Cdd:cd19935    1 ILVVEDEKKLAEYLKKGLT-EEGY-AVDVAYDGEDGLHLALTNEYDLIILDVMLPGLDGLEVLRRLRAAGKQTPVLMLTA 78

                         90       100
                 ....*....|....*....|.
gi 491596075  86 SDSPADIEAIVRSGADGYLLK 106
Cdd:cd19935   79 RDSVEDRVKGLDLGADDYLVK 99
REC_OmpR_CtrA cd17616
phosphoacceptor receiver (REC) domain of CtrA-like OmpR family response regulators; CtrA is ...
 6-114 1.09e-04

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: 40.09  E-value: 1.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLLSFEPEfeVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILTv 85
Cdd:cd17616    1 VLLIEDDSATAQSIELMLKSEGF--NVYTTDLGEEGLDLGKLYDYDIILLDLNLPDMSGYEVLRTLRLAKVKTPILILS- 77

                         90       100       110
                 ....*....|....*....|....*....|..
gi 491596075  86 sdSPADIEAIVRS---GADGYLLKDTEPDELV 114
Cdd:cd17616   78 --GLADIEDKVKGlgfGADDYMTKPFHKDELV 107
REC_FixJ cd17537
phosphoacceptor receiver (REC) domain of FixJ family response regulators; FixJ family response ...
 6-121 1.15e-04

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: 40.27  E-value: 1.15e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLL-SFEpeFEVVAeASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILT 84
Cdd:cd17537    3 VYVVDDDEAVRDSLAFLLrSVG--LAVKT-FTSASAFLAAAPPDQPGCLVLDVRMPGMSGLELQDELLARGSNIPIIFIT 79

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 491596075  85 V-SDSPADIEAIvRSGADGYLLKDTEPDELVELLKQAH 121
Cdd:cd17537   80 GhGDVPMAVEAM-KAGAVDFLEKPFRDQVLLDAIEQAL 116
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 142-191 2.01e-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: 40.41  E-value: 2.01e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 491596075  142 EDVFDSLTDRETQILQEVA-RGFRNKQIADRLFISESTVKVHMKSLLKKLK 191
Cdd:TIGR02937 105 REALEKLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKLR 155
REC_TrrA-like cd17554
phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator TrrA and ...
 5-113 2.34e-04

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: 39.13  E-value: 2.34e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSfEPEFEVVAeASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILT 84
Cdd:cd17554    2 KILVVDDEENIRELYKEELE-DEGYEVVT-AGNGEEALEKLESEDPDLVILDIKMPGMDGLETLRKIREKKPDLPVIICT 79

                         90       100       110
                 ....*....|....*....|....*....|
gi 491596075  85 -VSDSPADIEAIvrsGADGYLLKDTEPDEL 113
Cdd:cd17554   80 aYSEYKSDFSSW---AADAYVVKSSDLTEL 106
REC_OmpR_DrrD-like cd17625
phosphoacceptor receiver (REC) domain of DrrD-like OmpR family response regulators; DrrD is a ...
 58-117 2.89e-04

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: 39.13  E-value: 2.89e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  58 NMKGMSGLDTLKALRADGCEARIVILTVSDSPADIEAIVRSGADGYLLKdtePDELVELL 117
Cdd:cd17625   50 MLPGMDGLEVLKSLREEGIETPVLLLTALDAVEDRVKGLDLGADDYLPK---PFSLAELL 106
REC_2_DhkD-like cd17580
second phosphoacceptor receiver (REC) domain of Dictyostelium discoideum hybrid signal ...
 6-117 3.07e-04

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: 38.98  E-value: 3.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLLsfEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRA--DGCEARIVIL 83
Cdd:cd17580    1 ILVVDDNEDAAEMLALLL--ELEGAEVTTAHSGEEALEAAQRFRPDVILSDIGMPGMDGYELARRLRElpWLANTPAIAL 78

                         90       100       110
                 ....*....|....*....|....*....|....
gi 491596075  84 TVSDSPADIEAIVRSGADGYLLKDTEPDELVELL 117
Cdd:cd17580   79 TGYGQPEDRERALEAGFDAHLVKPVDPDELIELI 112
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 161-191 3.24e-04

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 39.85  E-value: 3.24e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 491596075  161 RGFRNKQIADRLFISESTVKVHMKSLLKKLK 191
Cdd:TIGR02985 128 EGLSNKEIAEELGISVKTVEYHITKALKFLR 158
PRK10365 PRK10365
sigma-54-dependent response regulator transcription factor ZraR;
32-120 3.37e-04

sigma-54-dependent response regulator transcription factor ZraR;


Pssm-ID: 182412 [Multi-domain]  Cd Length: 441  Bit Score: 40.78  E-value: 3.37e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  32 VAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILTVSDSPADIEAIVRSGADGYLLKDTEPD 111
Cdd:PRK10365  32 VALANSGRQALEQVREQVFDLVLCDVRMAEMDGIATLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFD 111


                 ....*....
gi 491596075 112 ELVELLKQA 120
Cdd:PRK10365 112 NLQATLEKA 120
REC_TrxB cd17595
phosphoacceptor receiver (REC) domain a fused response regulator with a thioredoxin reductase ...
 6-112 3.88e-04

phosphoacceptor receiver (REC) domain a fused response regulator with a thioredoxin reductase output domain; This family is composed of uncharacterized fusion proteins containing a REC domain and a thioredoxin reductase domain. Thioredoxin reductase catalyzes the reduction of thioredoxin and is thus a central component in the thioredoxin system. Fusion proteins containing REC and thioredoxin reductase domains could play an important role in the environmental regulation of the cellular dithiol-disulfide ratio. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381126 [Multi-domain]  Cd Length: 135  Bit Score: 39.24  E-value: 3.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHQLL--SFEPEFEVVAeASSGADAVA-----KAHELELDLVLLDLNMKGMSGLDTLKALRADGCEA 78
Cdd:cd17595    3 ILTVDDDPQVLRAVARDLrrQYGKDYRVLR-ADSGAEALDalkelKLRGEAVALFLVDQRMPEMDGVEFLEKAMELFPEA 81

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 491596075  79 RIVILTV-SDSPADIEAIVRSGADGYLLKDTEPDE 112
Cdd:cd17595   82 KRVLLTAyADTDAAIRAINDVQLDYYLLKPWDPPE 116
REC_CheC-like cd17593
phosphoacceptor receiver (REC) domain of uncharacterized response regulators containing a CheC ...
 5-119 5.71e-04

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: 38.29  E-value: 5.71e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRgihQLLSFEPEFE--VVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVI 82
Cdd:cd17593    2 KVLICDDSSMARK---QLARALPADWdvEITFAENGEEALEILREGRIDVLFLDLTMPVMDGYEVLEALPVEQLETKVIV 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 491596075  83 ltVSdspADI--EAIVRS---GADGYLLKDTEPDELVELLKQ 119
Cdd:cd17593   79 --VS---GDVqpEAKERVlelGALAFLKKPFDPEKLAQLLEE 115
PRK12555 PRK12555
chemotaxis-specific protein-glutamate methyltransferase CheB;
4-44 7.15e-04

chemotaxis-specific protein-glutamate methyltransferase CheB;


Pssm-ID: 237135 [Multi-domain]  Cd Length: 337  Bit Score: 39.48  E-value: 7.15e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 491596075   4 CKVMLVDDHPLMRRGIHQLLSFEPEFEVVAEASSGADAVAK 44
Cdd:PRK12555   1 MRIGIVNDSPLAVEALRRALARDPDHEVVWVATDGAQAVER 41
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 144-191 8.72e-04

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: 36.25  E-value: 8.72e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 491596075  144 VFDSLTDRETQILQevARGFRN---KQIADRLFISESTVKVHMKSLLKKLK 191
Cdd:pfam04545   1 ALASLPPRERQVLV--LRYGEGltlEEIGERLGISRERVRQIEKRALRKLR 49
REC_OmpR_MtrA-like cd17626
phosphoacceptor receiver (REC) domain of MtrA-like OmpR family response regulators; MtrA is ...
 5-114 9.16e-04

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: 37.83  E-value: 9.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLL---SFEPEFevvaeASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGcEARIV 81
Cdd:cd17626    2 RILVVDDDAALAEMIGIVLrgeGFDPAF-----CGDGTQALAAFREVRPDLVLLDLMLPGIDGIEVCRQIRAES-GVPIV 75

                         90       100       110
                 ....*....|....*....|....*....|...
gi 491596075  82 ILTVSDSPADIEAIVRSGADGYLLKDTEPDELV 114
Cdd:cd17626   76 MLTAKSDTVDVVLGLESGADDYVAKPFKPKELV 108
PRK15347 PRK15347
two component system sensor kinase;
5-162 2.11e-03

two component system sensor kinase;


Pssm-ID: 237951 [Multi-domain]  Cd Length: 921  Bit Score: 38.47  E-value: 2.11e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSfEPEFEVVAeASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRAD----GCEARI 80
Cdd:PRK15347 692 QILLVDDVETNRDIIGMMLV-ELGQQVTT-AASGTEALELGRQHRFDLVLMDIRMPGLDGLETTQLWRDDpnnlDPDCMI 769

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  81 VILTVSDSPADIEAIVRSGADGYLLKDTEPDEL---------------VELLKQAhEGDKAYSQAVAKYLNERegqedVF 145
Cdd:PRK15347 770 VALTANAAPEEIHRCKKAGMNHYLTKPVTLAQLaralelaaeyqllrgIELSPQD-SSCSPLLDTDDMALNSK-----LY 843

                        170
                 ....*....|....*..
gi 491596075 146 DSLTDRETQILQEVARG 162
Cdd:PRK15347 844 QSLLLLLAQIEQAVENQ 860
PRK09959 PRK09959
acid-sensing system histidine kinase EvgS;
6-170 2.25e-03

acid-sensing system histidine kinase EvgS;


Pssm-ID: 182169 [Multi-domain]  Cd Length: 1197  Bit Score: 38.56  E-value: 2.25e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075    6 VMLVDDHP----LMRRGIHqLLSFEpefevVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIV 81
Cdd:PRK09959  961 ILIADDHPtnrlLLKRQLN-LLGYD-----VDEATDGVQALHKVSMQHYDLLITDVNMPNMDGFELTRKLREQNSSLPIW 1034

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   82 ILTVSDSPADIEAIVRSGADGYLLKDTEPDELVELLKQAHEgdkaYSQAVAKYlneREGQEDVFDSLTDRETQILQEVAR 161
Cdd:PRK09959 1035 GLTANAQANEREKGLSCGMNLCLFKPLTLDVLKTHLSQLHQ----VAHIAPQY---RHLDIEALKNNTANDLQLMQEILM 1107


                  ....*....
gi 491596075  162 GFRNKQIAD 170
Cdd:PRK09959 1108 TFQHETHKD 1116
REC_2_GGDEF cd17544
second phosphoacceptor receiver (REC) domain of uncharacterized GGDEF domain proteins; This ...
 4-113 2.46e-03

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: 36.73  E-value: 2.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   4 CKVMLVDDHPLMRRGIHQLLSFEpEFEVVaEASSGADAVA--KAHELELDLVLLDlNMKGMSGLDTLKALRADGCEARIV 81
Cdd:cd17544    1 IKVLVVDDSATSRNHLRALLRRH-NFQVL-EAANGQEALEvlEQHPDIKLVITDY-NMPEMDGFELVREIRKKYSRDQLA 77

                         90       100       110
                 ....*....|....*....|....*....|....
gi 491596075  82 ILTVSDS-PADIEA-IVRSGADGYLLKDTEPDEL 113
Cdd:cd17544   78 IIGISASgDNALSArFIKAGANDFLTKPFLPEEF 111
PRK10643 PRK10643
two-component system response regulator PmrA;
5-117 2.54e-03

two-component system response regulator PmrA;


Pssm-ID: 182612 [Multi-domain]  Cd Length: 222  Bit Score: 37.71  E-value: 2.54e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIhqLLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILT 84
Cdd:PRK10643   2 KILIVEDDTLLLQGL--ILALQTEGYACDCASTAREAEALLESGHYSLVVLDLGLPDEDGLHLLRRWRQKKYTLPVLILT 79

                         90       100       110
                 ....*....|....*....|....*....|...
gi 491596075  85 VSDSPADIEAIVRSGADGYLLKdtePDELVELL 117
Cdd:PRK10643  80 ARDTLEDRVAGLDVGADDYLVK---PFALEELH 109
PRK10955 PRK10955
envelope stress response regulator transcription factor CpxR;
5-196 3.14e-03

envelope stress response regulator transcription factor CpxR;


Pssm-ID: 182864 [Multi-domain]  Cd Length: 232  Bit Score: 37.47  E-value: 3.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSFEpEFEVVAeASSGADAVAKAHELELDLVLLDLnMKGMSGLDTLKALRADGcEARIVILT 84
Cdd:PRK10955   3 KILLVDDDRELTSLLKELLEME-GFNVIV-AHDGEQALDLLDDSIDLLLLDVM-MPKKNGIDTLKELRQTH-QTPVIMLT 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075  85 VSDSPADIEAIVRSGADGYLLKDTEPDELVELLK----------QAHEGDKAYSQAVAKYLNEREG-QEDVFDS----LT 149
Cdd:PRK10955  79 ARGSELDRVLGLELGADDYLPKPFNDRELVARIRailrrshwseQQQNNDNGSPTLEVDALSLNPGrQEASFDGqtleLT 158

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 491596075 150 DRETQIL--------QEVARGFRNKQI-ADRLFISESTVKVHMKSLLKKLkvPSRT 196
Cdd:PRK10955 159 GTEFTLLyllaqhlgQVVSREHLSQEVlGKRLTPFDRAIDMHISNLRRKL--PDRK 212
PRK10336 PRK10336
two-component system response regulator QseB;
5-121 3.53e-03

two-component system response regulator QseB;


Pssm-ID: 182387 [Multi-domain]  Cd Length: 219  Bit Score: 37.18  E-value: 3.53e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSfEPEFEV--VAEASSGADAVAKAhelELDLVLLDLNMKGMSGLDTLKALRADGCEARIVI 82
Cdd:PRK10336   2 RILLIEDDMLIGDGIKTGLS-KMGFSVdwFTQGRQGKEALYSA---PYDAVILDLTLPGMDGRDILREWREKGQREPVLI 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 491596075  83 LTVSDSPADIEAIVRSGADGYLLKdtePDELVE-------LLKQAH 121
Cdd:PRK10336  78 LTARDALAERVEGLRLGADDYLCK---PFALIEvaarleaLMRRTN 120
COG4189 COG4189
Predicted transcriptional regulator, ArsR family [Transcription];
134-188 5.86e-03

Predicted transcriptional regulator, ArsR family [Transcription];


Pssm-ID: 443343 [Multi-domain]  Cd Length: 97  Bit Score: 34.94  E-value: 5.86e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 491596075 134 YLNEREGQEDVFDSLTDrET--QILQEVARGFRN-KQIADRLFISESTVKVHMKSLLK 188
Cdd:COG4189    2 VVLDDEESLEVLKALAS-ETrlRILRLLAEEPLNvNELAEALGLPKSTVSYHIRKLEE 58
REC_OmpR_KdpE-like cd17620
phosphoacceptor receiver (REC) domain of KdpE-like OmpR family response regulators; KdpE is a ...
 6-106 6.33e-03

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: 34.83  E-value: 6.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   6 VMLVDDHPLMRRGIHqlLSFEPEFEVVAEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRaDGCEARIVILTV 85
Cdd:cd17620    1 ILVIEDEPQIRRFLR--TALEAHGYRVFEAETGQEGLLEAATRKPDLIILDLGLPDMDGLEVIRRLR-EWSAVPVIVLSA 77

                         90       100
                 ....*....|....*....|.
gi 491596075  86 SDSPADIEAIVRSGADGYLLK 106
Cdd:cd17620   78 RDEESDKIAALDAGADDYLTK 98
PRK06930 PRK06930
positive control sigma-like factor; Validated
 136-191 7.33e-03

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 35.86  E-value: 7.33e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 491596075 136 NEREGQEDVFDSLTDRETQI-LQEVARGFRNKQIADRLFISESTVKVHMKSLLKKLK 191
Cdd:PRK06930 103 WDKIRIEDALSVLTEREKEVyLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIA 159
PRK10693 PRK10693
two-component system response regulator RssB;
33-106 9.45e-03

two-component system response regulator RssB;


Pssm-ID: 182652 [Multi-domain]  Cd Length: 303  Bit Score: 36.12  E-value: 9.45e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 491596075  33 AEASSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRADGCEARIVILTVSDSPADIEAIVRSGADGYLLK 106
Cdd:PRK10693   1 VLAANGVDALELLGGFTPDLIICDLAMPRMNGIEFVEHLRNRGDQTPVLVISATENMADIAKALRLGVQDVLLK 74
REC_OmpR_kpRstA-like cd17622
phosphoacceptor receiver (REC) domain of kpRstA-like OmpR family response regulators; ...
 5-118 9.84e-03

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: 34.66  E-value: 9.84e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491596075   5 KVMLVDDHPLMRRGIHQLLSfEPEFEVVAEaSSGADAVAKAHELELDLVLLDLNMKGMSGLDTLKALRaDGCEARIVILT 84
Cdd:cd17622    2 RILLVEDDPKLARLIADFLE-SHGFNVVVE-HRGDRALEVIAREKPDAVLLDIMLPGIDGLTLCRDLR-PKYQGPILLLT 78

                         90       100       110
                 ....*....|....*....|....*....|....
gi 491596075  85 VSDSPADIEAIVRSGADGYLLKDTEPDELVELLK 118
Cdd:cd17622   79 ALDSDIDHILGLELGADDYVVKPVEPAVLLARLR 112
 
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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