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Conserved domains on  [gi|1477047712|gb|RIH54613|]
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DNA-binding response regulator [Shigella boydii]

Protein Classification

transcriptional regulator RcsB( domain architecture ID 11484984)

transcriptional regulator RcsB is the response regulator, that binds to regulatory DNA regions, of the Rcs signaling system, which controls transcription of numerous genes including those involved in colanic acid capsule synthesis, biofilm formation, cell division, and outer membrane proteins synthesis

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 1-216 1.54e-158

transcriptional regulator RcsB; Provisional


:

Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 436.96  E-value: 1.54e-158
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   1 MNNMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKYGDGITLIKYIKRHFPS 80
Cdd:PRK10840    1 MNNMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKYGDGITLIKYIKRHFPS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712  81 LSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLEKISAGGYGDKRLSPKESEVLR 160
Cdd:PRK10840   81 LSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLEKISAGGYGDKRLSPKESEVLR 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1477047712 161 LFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLSSVTLSPADKD 216
Cdd:PRK10840  161 LFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLSSVTLSPADKD 216
 
Name Accession Description Interval E-value
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 1-216 1.54e-158

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 436.96  E-value: 1.54e-158
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   1 MNNMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKYGDGITLIKYIKRHFPS 80
Cdd:PRK10840    1 MNNMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKYGDGITLIKYIKRHFPS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712  81 LSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLEKISAGGYGDKRLSPKESEVLR 160
Cdd:PRK10840   81 LSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLEKISAGGYGDKRLSPKESEVLR 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1477047712 161 LFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLSSVTLSPADKD 216
Cdd:PRK10840  161 LFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLSSVTLSPADKD 216
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 6-122 1.20e-34

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: 119.15  E-value: 1.20e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   6 VIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHFPSLSIIV 85
Cdd:cd17535     1 VLIVDDHPLVREGLRRLLESEPDIEVVGEAADGEEALALLRELRPDVVLMDLSMPG---MDGIEALRRLRRRYPDLKVIV 77

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1477047712  86 LTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAA 122
Cdd:cd17535    78 LTAHDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRA 114
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 4-205 2.17e-23

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: 90.72  E-value: 2.17e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   4 MNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIkrhfpslsi 83
Cdd:COG2197     2 IRVLIVDDHPLVREGLRALLEAEPDIEVVGEAADGEEALELLEELRPDVVLLDIRMPG---MDGLEALRRL--------- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712  84 ivltmnnnpailsavldldiegivlkqgaptdlpkalaalqkgkkftpesvsrllekisaggygdkrLSPKESEVLRLFA 163
Cdd:COG2197    70 -------------------------------------------------------------------LTPREREVLRLLA 82

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1477047712 164 EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYL 205
Cdd:COG2197    83 EGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLA 124
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 6-121 2.22e-23

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: 89.90  E-value: 2.22e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   6 VIIADDHPIVLFGIRKSLEQieWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDkygDGITLIKYIKRHFPSLSIIV 85
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLEK--EGYVVAEADDGKEALELLKEERPDLILLDINMPGM---DGLELLKRIRRRDPTTPVII 75

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1477047712  86 LTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALA 121
Cdd:pfam00072  76 LTAHGDEDDAVEALEAGADDFLSKPFDPDELLAAIR 111
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 150-205 1.41e-15

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 68.32  E-value: 1.41e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1477047712  150 RLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYL 205
Cdd:smart00421   3 SLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 150-193 4.52e-05

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: 42.33  E-value: 4.52e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1477047712 150 RLSPKESEVLRLFA-EGFLVTEIAKKLNRSIKTISSQKKSAMMKL 193
Cdd:TIGR02937 110 KLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
 
Name Accession Description Interval E-value
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 1-216 1.54e-158

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 436.96  E-value: 1.54e-158
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   1 MNNMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKYGDGITLIKYIKRHFPS 80
Cdd:PRK10840    1 MNNMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKYGDGITLIKYIKRHFPS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712  81 LSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLEKISAGGYGDKRLSPKESEVLR 160
Cdd:PRK10840   81 LSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLEKISAGGYGDKRLSPKESEVLR 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1477047712 161 LFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLSSVTLSPADKD 216
Cdd:PRK10840  161 LFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLSSVTLSPADKD 216
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 6-122 1.20e-34

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: 119.15  E-value: 1.20e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   6 VIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHFPSLSIIV 85
Cdd:cd17535     1 VLIVDDHPLVREGLRRLLESEPDIEVVGEAADGEEALALLRELRPDVVLMDLSMPG---MDGIEALRRLRRRYPDLKVIV 77

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1477047712  86 LTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAA 122
Cdd:cd17535    78 LTAHDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRA 114
PRK15369 PRK15369
two component system response regulator;
1-204 1.95e-27

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 103.62  E-value: 1.95e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   1 MNNMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHFPS 80
Cdd:PRK15369    1 MKNYKILLVDDHELIINGIKNMLAPYPRYKIVGQVDNGLEVYNACRQLEPDIVILDLGLPG---MNGLDVIPQLHQRWPA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712  81 LSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLpkaLAALQ---KGKKFTPESVSR--LLEKISAGGYGDKRLSPKE 155
Cdd:PRK15369   78 MNILVLTARQEEHMASRTLAAGALGYVLKKSPQQIL---LAAIQtvaVGKRYIDPALNReaILALLNADDTNPPLLTPRE 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1477047712 156 SEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNY 204
Cdd:PRK15369  155 RQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNW 203
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 4-205 2.17e-23

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: 90.72  E-value: 2.17e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   4 MNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIkrhfpslsi 83
Cdd:COG2197     2 IRVLIVDDHPLVREGLRALLEAEPDIEVVGEAADGEEALELLEELRPDVVLLDIRMPG---MDGLEALRRL--------- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712  84 ivltmnnnpailsavldldiegivlkqgaptdlpkalaalqkgkkftpesvsrllekisaggygdkrLSPKESEVLRLFA 163
Cdd:COG2197    70 -------------------------------------------------------------------LTPREREVLRLLA 82

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1477047712 164 EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYL 205
Cdd:COG2197    83 EGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLA 124
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 6-121 2.22e-23

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: 89.90  E-value: 2.22e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   6 VIIADDHPIVLFGIRKSLEQieWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDkygDGITLIKYIKRHFPSLSIIV 85
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLEK--EGYVVAEADDGKEALELLKEERPDLILLDINMPGM---DGLELLKRIRRRDPTTPVII 75

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1477047712  86 LTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALA 121
Cdd:pfam00072  76 LTAHGDEDDAVEALEAGADDFLSKPFDPDELLAAIR 111
PRK10360 PRK10360
transcriptional regulator UhpA;
4-201 2.76e-20

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 84.64  E-value: 2.76e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   4 MNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKygdGITLIKYIKRhfpSLSI 83
Cdd:PRK10360    2 ITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDIS---GLELLSQLPK---GMAT 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712  84 IVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKF-TPESVSRLlekisAGGYGDKrLSPKESEVLRLF 162
Cdd:PRK10360   76 IMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYlTPDIAIKL-----ASGRQDP-LTKRERQVAEKL 149

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1477047712 163 AEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIAL 201
Cdd:PRK10360  150 AQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVEL 188
PRK09483 PRK09483
response regulator; Provisional
 4-201 4.16e-20

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 84.39  E-value: 4.16e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   4 MNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDkygDGITLIKYIKRHFPSLSI 83
Cdd:PRK09483    2 INVLLVDDHELVRAGIRRILEDIKGIKVVGEACCGEDAVKWCRTNAVDVVLMDMNMPGI---GGLEATRKILRYTPDVKI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712  84 IVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSR---LLEKISAGGYGDKRLSPKESEVLR 160
Cdd:PRK09483   79 IMLTVHTENPLPAKVMQAGAAGYLSKGAAPQEVVSAIRSVHSGQRYIASDIAQqmaLSQIEPATENPFASLSERELQIML 158

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1477047712 161 LFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIAL 201
Cdd:PRK09483  159 MITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVEL 199
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
4-204 9.09e-18

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 78.01  E-value: 9.09e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   4 MNVIIADDHPIVLFGIRKSLEQiEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDkygDGITLIKYIKRHFPSLSI 83
Cdd:PRK09958    1 MNAIIIDDHPLAIAAIRNLLIK-NDIEILAELTEGGSAVQRVETLKPDIVIIDVDIPGV---NGIQVLETLRKRQYSGII 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712  84 IVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESvsrlLEKISAGGYGDKR----LSPKESEVL 159
Cdd:PRK09958   77 IIVSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGYCYFPFS----LNRFVGSLTSDQQkldsLSKQEISVM 152

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1477047712 160 RLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNY 204
Cdd:PRK09958  153 RYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYTF 197
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
6-200 1.04e-17

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 77.97  E-value: 1.04e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   6 VIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHFPSLSIIV 85
Cdd:PRK10403    9 VLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLANRLDPDVILLDLNMKG---MSGLDTLNALRRDGVTAQIII 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712  86 LTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSR-LLEKISAGGYGD--KRLSPKESEVLRLF 162
Cdd:PRK10403   86 LTVSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKGSKVFSERVNQyLREREMFGAEEDpfSVLTERELDVLHEL 165

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1477047712 163 AEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIA 200
Cdd:PRK10403  166 AQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVA 203
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
1-210 4.35e-17

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 76.45  E-value: 4.35e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   1 MNNMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDkygDGITLIKYIKRHFPS 80
Cdd:PRK09935    1 MKPASVIIMDTHPIIRMSIEVLLQKNSELQIVLKTDDYRITIDYLRTRPVDLIIMDIDLPGT---DGFTFLKRIKQIQST 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712  81 LSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLE--KISAGGYGDKRLSPKESEV 158
Cdd:PRK09935   78 VKVLFLSSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMILSGYTFFPSETLNYIKsnKCSTNSSTDTVLSNREVTI 157

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1477047712 159 LRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLSSVTL 210
Cdd:PRK09935  158 LRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELIDYAKLHEL 209
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 151-204 1.20e-16

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: 71.03  E-value: 1.20e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1477047712 151 LSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNY 204
Cdd:cd06170     1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAY 54
PRK11475 PRK11475
DNA-binding transcriptional activator BglJ; Provisional
 35-203 7.19e-16

DNA-binding transcriptional activator BglJ; Provisional


Pssm-ID: 236915 [Multi-domain]  Cd Length: 207  Bit Score: 72.85  E-value: 7.19e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712  35 FEDSTALINNLPKLDAHVLITDLSMPGDKYGDGITLIKYIKRHFPSLSIIVLTMNNNPAIL-SAVLDLDIEGIVLKQGAP 113
Cdd:PRK11475   23 FSSQSSFQDAMSRISFSAVIFSLSAMRSERREGLSCLTELAIKFPRMRRLVIADDDIEARLiGSLSPSPLDGVLSKASTL 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712 114 TDLPKALAALQKGKKFTPESVSRLLEkisagGYGDKRLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKL 193
Cdd:PRK11475  103 EILQQELFLSLNGVRQATDRLNNQWY-----INQSRMLSPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKL 177

                         170
                  ....*....|
gi 1477047712 194 GVENDIALLN 203
Cdd:PRK11475  178 GVSSDAGLLD 187
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 6-194 9.18e-16

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 72.75  E-value: 9.18e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   6 VIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHFPSLSIIV 85
Cdd:PRK10651    9 ILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPG---MNGLETLDKLREKSLSGRIVV 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712  86 LTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGK-----KFTPESVSRLLEKISAGGYGDKRLSPKESEVLR 160
Cdd:PRK10651   86 FSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQAAAGEmvlseALTPVLAASLRANRATTERDVNQLTPRERDILK 165

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1477047712 161 LFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLG 194
Cdd:PRK10651  166 LIAQGLPNKMIARRLDITESTVKVHVKHMLKKMK 199
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 150-205 1.41e-15

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 68.32  E-value: 1.41e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1477047712  150 RLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYL 205
Cdd:smart00421   3 SLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
CitB COG4565
DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal ...
 1-125 2.07e-15

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


Pssm-ID: 443622 [Multi-domain]  Cd Length: 138  Bit Score: 70.00  E-value: 2.07e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   1 MNNMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHFPS 80
Cdd:COG4565     1 MKMIRVLIVEDDPMVAELLRRYLERLPGFEVVGVASSGEEALALLAEHRPDLILLDIYLPD---GDGLELLRELRARGPD 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1477047712  81 LSIIVLTMNNNPAILSAVLDLDIEGIVLKqgaPTDLPKALAALQK 125
Cdd:COG4565    78 VDVIVITAARDPETVREALRAGVVDYLIK---PFTFERLREALER 119
YesN COG4753
Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding ...
 5-109 5.88e-15

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: 67.88  E-value: 5.88e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   5 NVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHFPSLSII 84
Cdd:COG4753     1 KVLIVDDEPLIREGLKRILEWEAGFEVVGEAENGEEALELLEEHKPDLVITDINMPG---MDGLELLEAIRELDPDTKII 77

                          90       100
                  ....*....|....*....|....*
gi 1477047712  85 VLTMNNNPAILSAVLDLDIEGIVLK 109
Cdd:COG4753    78 ILSGYSDFEYAQEAIKLGADDYLLK 102
REC_YesN-like cd17536
phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response ...
 6-87 7.03e-15

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: 68.13  E-value: 7.03e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   6 VIIADDHPIVLFGIRKSLEQIEW-VNVVGEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHFPSLSII 84
Cdd:cd17536     1 VLIVDDEPLIREGLKKLIDWEELgFEVVGEAENGEEALELIEEHKPDIVITDIRMPG---MDGLELIEKIRELYPDIKII 77


                  ...
gi 1477047712  85 VLT 87
Cdd:cd17536    78 ILS 80
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
150-205 3.86e-13

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 65.16  E-value: 3.86e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1477047712 150 RLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYL 205
Cdd:COG2771   127 GLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVALA 182
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 6-202 1.12e-12

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: 63.97  E-value: 1.12e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   6 VIIADDHPIVLFGIRKSLEQIEWVnvVGEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHFPSLSIIV 85
Cdd:COG4566     2 VYIVDDDEAVRDSLAFLLESAGLR--VETFASAEAFLAALDPDRPGCLLLDVRMPG---MSGLELQEELAARGSPLPVIF 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712  86 LTmnNNPailsavldlDIEGIV--LKQGA---------PTDLPKAL-AALQKGKKFTPES--VSRLLEKISaggygdkRL 151
Cdd:COG4566    77 LT--GHG---------DVPMAVraMKAGAvdflekpfdDQALLDAVrRALARDRARRAERarRAELRARLA-------SL 138

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1477047712 152 SPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALL 202
Cdd:COG4566   139 TPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARSLAELV 189
LytT COG3279
DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction ...
 4-94 5.05e-11

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


Pssm-ID: 442510 [Multi-domain]  Cd Length: 235  Bit Score: 60.22  E-value: 5.05e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   4 MNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHFPSLSI 83
Cdd:COG3279     2 MKILIVDDEPLARERLERLLEKYPDLEVVGEASNGEEALELLEEHKPDLVFLDIQMPG---LDGFELARQLRELDPPPPI 78

                          90
                  ....*....|.
gi 1477047712  84 IVLTMNNNPAI 94
Cdd:COG3279    79 IFTTAYDEYAL 89
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 2-141 9.82e-10

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: 57.28  E-value: 9.82e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   2 NNMNVIIADDHPIVLFGIRKSLEQIEWvNVVgEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHFPSL 81
Cdd:COG2204     1 SMARILVVDDDPDIRRLLKELLERAGY-EVE-TAASGEEALALLREEPPDLVLLDLRMPG---MDGLELLRELRALDPDL 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1477047712  82 SIIVLTmnnnpailsavldldiegivlkqgAPTDLPKALAALQKG------KKFTPESVSRLLEKI 141
Cdd:COG2204    76 PVILLT------------------------GYGDVETAVEAIKAGafdyltKPFDLEELLAAVERA 117
GerE pfam00196
Bacterial regulatory proteins, luxR family;
151-201 1.42e-09

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 52.20  E-value: 1.42e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1477047712 151 LSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIAL 201
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVEL 53
CheY COG0784
CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator ...
 1-123 2.65e-09

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: 53.32  E-value: 2.65e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   1 MNNMNVIIADDHPIVLFGIRKSLEQIEwVNVVgEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRH--F 78
Cdd:COG0784     3 LGGKRILVVDDNPDNRELLRRLLERLG-YEVT-TAEDGAEALELLRAGPPDLILLDINMPG---MDGLELLRRIRALprL 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1477047712  79 PSLSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAAL 123
Cdd:COG0784    78 PDIPIIALTAYADEEDRERALEAGADDYLTKPVDPEELLEALRRL 122
AmiR COG3707
Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding ...
 1-116 7.35e-09

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: 53.42  E-value: 7.35e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   1 MNNMNVIIADDHPIVLFGIRKSLEQIeWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDkygDGITLIKYIKRHfPS 80
Cdd:COG3707     1 MRGLRVLVVDDEPLRRADLREGLREA-GYEVVAEAADGEDAVELVRELKPDLVIVDIDMPDR---DGLEAARQISEE-RP 75

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1477047712  81 LSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDL 116
Cdd:COG3707    76 APVILLTAYSDPELIERALEAGVSAYLVKPLDPEDL 111
REC_NarL cd19931
phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL); Nitrate ...
 6-120 8.27e-09

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: 51.96  E-value: 8.27e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   6 VIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHFPSLSIIV 85
Cdd:cd19931     1 VLLIDDHPLLRKGIKQLIELDPDFTVVGEASSGEEGIELAERLDPDLILLDLNMKG---MSGLDTLKALREEGVSARIVI 77

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1477047712  86 LTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKAL 120
Cdd:cd19931    78 LTVSDAEDDVVTALRAGADGYLLKDMEPEDLLEAL 112
REC cd00156
phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ...
 8-109 3.37e-08

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: 49.53  E-value: 3.37e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   8 IADDHPIVLFGIRKSLEQIEWVnvVGEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHFPSLSIIVLT 87
Cdd:cd00156     2 IVDDDPAIRELLKSLLEREGYE--VDTAADGEEALELLREERPDLVLLDLMMPG---MDGLELLRKLRELPPDIPVIVLT 76

                          90       100
                  ....*....|....*....|..
gi 1477047712  88 MNNNPAILSAVLDLDIEGIVLK 109
Cdd:cd00156    77 AKADEEDAVRALELGADDYLVK 98
REC_NtrC cd19919
phosphoacceptor receiver (REC) domain of DNA-binding transcriptional regulator NtrC; ...
 7-125 7.09e-08

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


Pssm-ID: 381146 [Multi-domain]  Cd Length: 116  Bit Score: 49.19  E-value: 7.09e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   7 IIADDHPI--VLfgiRKSLEQIEWVNVVgeFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHFPSLSII 84
Cdd:cd19919     5 IVDDDSSIrwVL---ERALAGAGLTVTS--FENAQEALAALASSQPDVLISDIRMPG---MDGLALLAQIKQRHPDLPVI 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1477047712  85 VLTmnnnpailsAVLDLDIEGIVLKQGA------PTDLPKALAALQK 125
Cdd:cd19919    77 IMT---------AHSDLDSAVSAYQGGAfeylpkPFDIDEAVALVER 114
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 149-197 1.32e-07

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: 47.26  E-value: 1.32e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1477047712 149 KRLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVEN 197
Cdd:COG5905    11 SLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRN 59
REC_DesR-like cd19930
phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of ...
 6-120 1.69e-07

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: 48.04  E-value: 1.69e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   6 VIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDkygDGITLIKYIKRHFPSLSIIV 85
Cdd:cd19930     1 VLIAEDQEMVRGALAALLELEDDLEVVAQASNGQEALRLVLKHSPDVAILDIEMPGR---TGLEVAAELREELPDTKVLI 77

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1477047712  86 LTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKAL 120
Cdd:cd19930    78 VTTFGRPGYFRRALAAGVDGYVLKDRPIEELADAI 112
REC_RpfG-like cd17551
phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator ...
 4-101 5.13e-07

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: 46.67  E-value: 5.13e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   4 MNVIIADDHPIVLFGIRKSLEQIEWVNVVGeFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHfPSLS- 82
Cdd:cd17551     1 MRILIVDDNPTNLLLLEALLRSAGYLEVVS-FTDPREALAWCRENPPDLILLDYMMPG---MDGLEFIRRLRAL-PGLEd 75

                          90       100
                  ....*....|....*....|.
gi 1477047712  83 --IIVLTMNNNPAILSAVLDL 101
Cdd:cd17551    76 vpIVMITADTDREVRLRALEA 96
RpfG COG3437
Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains ...
 3-109 1.19e-06

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: 47.47  E-value: 1.19e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   3 NMNVIIADDHPIVLFGIRKSLEQIEWvNVVgEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRH--FPS 80
Cdd:COG3437     6 APTVLIVDDDPENLELLRQLLRTLGY-DVV-TAESGEEALELLLEAPPDLILLDVRMPG---MDGFELLRLLRADpsTRD 80

                          90       100
                  ....*....|....*....|....*....
gi 1477047712  81 LSIIVLTMNNNPAILSAVLDLDIEGIVLK 109
Cdd:COG3437    81 IPVIFLTALADPEDRERALEAGADDYLTK 109
REC_DctD-like cd17549
phosphoacceptor receiver (REC) domain of C4-dicarboxylic acid transport protein D (DctD) and ...
 6-140 2.79e-06

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: 45.17  E-value: 2.79e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   6 VIIADDHPIVLFGIRKSLEqIEWVNVVGeFEDSTALinnLPKLDAH---VLITDLSMPGdkyGDGITLIKYIKRHFPSLS 82
Cdd:cd17549     1 VLLVDDDADVREALQQTLE-LAGFRVRA-FADAEEA---LAALSPDfpgVVISDIRMPG---MDGLELLAQIRELDPDLP 72

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1477047712  83 IIVLTmnnnpailsavldldieGivlkQGaptDLPKALAALQKG------KKFTPE----SVSRLLEK 140
Cdd:cd17549    73 VILIT-----------------G----HG---DVPMAVEAMRAGaydfleKPFDPErlldVVRRALEK 116
OmpR COG0745
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...
 6-164 5.97e-06

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: 45.33  E-value: 5.97e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   6 VIIADDHPIVLFGIRKSLEQIEW-VNVVGEFEDSTALINNLPkldAHVLITDLSMPGdkyGDGITLIKYIKRHFPSLSII 84
Cdd:COG0745     4 ILVVEDDPDIRELLADALEREGYeVDTAADGEEALELLEEER---PDLILLDLMLPG---MDGLEVCRRLRARPSDIPII 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712  85 VLTMNNNPAILSAVLDLDIEGIVLKqgaPTDLP------KALAALQKGKKFTPESVSRLLEKISAGGYGDKRLSPKESEV 158
Cdd:COG0745    78 MLTARDDEEDRVRGLEAGADDYLTK---PFDPEellariRALLRRRAAEVLRVGDLLDLAAREVTRDGEPVELTPKEFRL 154


                  ....*.
gi 1477047712 159 LRLFAE 164
Cdd:COG0745   155 LELLMR 160
REC smart00448
cheY-homologous receiver domain; CheY regulates the clockwise rotation of E. coli flagellar ...
 4-60 7.03e-06

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


Pssm-ID: 214668 [Multi-domain]  Cd Length: 55  Bit Score: 42.17  E-value: 7.03e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1477047712    4 MNVIIADDHPIVLFGIRKSLEQIEWVnvVGEFEDSTALINNLPKLDAHVLITDLSMP 60
Cdd:smart00448   1 MRILVVDDDPLLRELLKALLEKEGYE--VDEATDGEEALELLKEEKPDLILLDIMMP 55
glnG PRK10923
nitrogen regulation protein NR(I); Provisional
 35-118 8.01e-06

nitrogen regulation protein NR(I); Provisional


Pssm-ID: 182842 [Multi-domain]  Cd Length: 469  Bit Score: 45.63  E-value: 8.01e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712  35 FEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHFPSLSIIVLTMNNnpailsavlDLDIEGIVLKQGAPT 114
Cdd:PRK10923   33 FENGNEVLEALASKTPDVLLSDIRMPG---MDGLALLKQIKQRHPMLPVIIMTAHS---------DLDAAVSAYQQGAFD 100


                  ....
gi 1477047712 115 DLPK 118
Cdd:PRK10923  101 YLPK 104
PleD COG3706
Two-component response regulator, PleD family, consists of two REC domains and a diguanylate ...
 3-109 2.12e-05

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: 43.36  E-value: 2.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   3 NMNVIIADDHPIVLFGIRKSLEQIEWvNVVgEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRH--FPS 80
Cdd:COG3706     1 PARILVVDDDPTNRKLLRRLLEAAGY-EVV-EAADGEEALELLQEHRPDLILLDLEMPD---MDGLELCRRLRADprTAD 75

                          90       100
                  ....*....|....*....|....*....
gi 1477047712  81 LSIIVLTMNNNPAILSAVLDLDIEGIVLK 109
Cdd:COG3706    76 IPIIFLTALDDEEDRARALEAGADDYLTK 104
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 150-193 4.52e-05

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: 42.33  E-value: 4.52e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1477047712 150 RLSPKESEVLRLFA-EGFLVTEIAKKLNRSIKTISSQKKSAMMKL 193
Cdd:TIGR02937 110 KLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 150-193 1.46e-04

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


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 41.13  E-value: 1.46e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1477047712 150 RLSPKESEVLRL-FAEGFLVTEIAKKLNRSIKTISSQKKSAMMKL 193
Cdd:COG1595   127 RLPPRQREVLVLrYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171
REC_RegA-like cd17563
phosphoacceptor receiver (REC) domain of photosynthetic apparatus regulatory protein RegA; ...
 4-87 2.96e-04

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: 38.96  E-value: 2.96e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   4 MNVIIADDHPIVLFGIRKSLEQIEW-VNVVGEFEDSTALINNLPKldAHVLItDLSMPGDkygDGITLIKYIKRHFPSLS 82
Cdd:cd17563     1 KSLLLVDDDEVFAERLARALERRGFeVETAHSVEEALALAREEKP--DYAVL-DLRLGGD---SGLDLIPPLRALQPDAR 74


                  ....*
gi 1477047712  83 IIVLT 87
Cdd:cd17563    75 IVVLT 79
REC_WspR-like cd17575
phosphoacceptor receiver (REC) domain of WspR response regulator and similar proteins; The ...
 6-101 3.13e-04

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


Pssm-ID: 381117 [Multi-domain]  Cd Length: 128  Bit Score: 39.31  E-value: 3.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   6 VIIADDHPIVLFGIRKSLEQIEwvNVVGEF-EDSTALINNLPKLDAHVLITDLSMPGDkygDGITLIKYIKRHfPS---L 81
Cdd:cd17575     3 VLLVDDQAIIGEAVRRALADEE--DIDFHYcSDPTEAIEVASQIKPTVILQDLVMPGV---DGLTLVRFFRAN-PAtrdI 76

                          90       100
                  ....*....|....*....|
gi 1477047712  82 SIIVLTMNNNPAILSAVLDL 101
Cdd:cd17575    77 PIIVLSTKEEPEVKSEAFAL 96
REC_CheY_CheY3 cd19923
phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY ...
 4-141 3.50e-04

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: 38.86  E-value: 3.50e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   4 MNVIIADDHPIVLFGIRKSLEQIEWVNVVgEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKR--HFPSL 81
Cdd:cd19923     1 MKVLVVDDFSTMRRIIKNLLKELGFNNVE-EAEDGVDALEKLKAGGFDFVITDWNMPN---MDGLELLKTIRAdgALSHL 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712  82 SIIVLTMNNNPAILSAVLDLDIEGIVlkqgaptdlpkalaalqkGKKFTPESVSRLLEKI 141
Cdd:cd19923    77 PVLMVTAEAKKENVIAAAQAGVNNYI------------------VKPFTAATLKEKLEKI 118
REC_DC-like cd17534
phosphoacceptor receiver (REC) domain of modulated diguanylate cyclase and similar domains; ...
 4-109 4.70e-04

phosphoacceptor receiver (REC) domain of modulated diguanylate cyclase and similar domains; This groups includes a modulated diguanylate cyclase containing a PAS sensor domain from Desulfovibrio desulfuricans G20. Members of this group contain N-terminal REC domains and various output domains including the GGDEF, histidine kinase, and helix-turn-helix (HTH) DNA binding domains. Also included in this family is Mycobacterium tuberculosis PdtaR, a transcriptional antiterminator that contains a REC domain and an ANTAR RNA-binding output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381089 [Multi-domain]  Cd Length: 117  Bit Score: 38.54  E-value: 4.70e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   4 MNVIIADDHPIVLFGIRKSLEQIEWvNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKygDGITLIKYIKRHFPsLSI 83
Cdd:cd17534     1 KKILIVEDEAIIALDLKEILESLGY-EVVGIADSGEEAIELAEENKPDLILMDINLKGDM--DGIEAAREIREKFD-IPV 76

                          90       100
                  ....*....|....*....|....*.
gi 1477047712  84 IVLTMNNNPAILSAVLDLDIEGIVLK 109
Cdd:cd17534    77 IFLTAYSDEETLERAKETNPYGYLVK 102
fixJ PRK09390
response regulator FixJ; Provisional
 35-197 8.03e-04

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 39.22  E-value: 8.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712  35 FEDSTALINNLPKLDAHVLITDLSMPGDkygDGITLIKYIKRHFPSLSIIVLTMNNNPAilsavldLDIEGIvlKQGA-- 112
Cdd:PRK09390   33 FESAQAFLDALPGLRFGCVVTDVRMPGI---DGIELLRRLKARGSPLPVIVMTGHGDVP-------LAVEAM--KLGAvd 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712 113 ----PTD-------LPKALAALQKGKKFTPESvSRLLEKISAggygdkrLSPKESEVLRLFAEGFLVTEIAKKLNRSIKT 181
Cdd:PRK09390  101 fiekPFEderligaIERALAQAPEAAKSEAVA-ADIRARIAS-------LSERERQVMDGLVAGLSNKVIARDLDISPRT 172

                         170
                  ....*....|....*.
gi 1477047712 182 ISSQKKSAMMKLGVEN 197
Cdd:PRK09390  173 VEVYRANVMTKMQAGS 188
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 149-193 9.89e-04

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


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 36.31  E-value: 9.89e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1477047712 149 KRLSPKESEVLRL-FAEGFLVTEIAKKLNRSIKTISSQKKSAMMKL 193
Cdd:cd06171     9 DKLPEREREVILLrFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
REC_OmpR cd17574
phosphoacceptor receiver (REC) domain of OmpR family response regulators; OmpR-like proteins ...
 8-87 1.24e-03

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: 37.00  E-value: 1.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   8 IADDHPIVLFGIRKSLEQIEWVnvVGEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHFPSLSIIVLT 87
Cdd:cd17574     2 VVEDDEEIAELLSDYLEKEGYE--VDTAADGEEALELAREEQPDLIILDVMLPG---MDGFEVCRRLREKGSDIPIIMLT 76
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
115-197 1.27e-03

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 38.15  E-value: 1.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712 115 DLPKALAALQKGKKFTPESVSRLLEKISAGGYGDKRLSPKESEvLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLG 194
Cdd:COG2909    88 DPEEALALLERLLALAEAAGRLLLRALALRALGDREEALAALR-RRLLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLG 166


                  ...
gi 1477047712 195 VEN 197
Cdd:COG2909   167 VRS 169
PRK15201 PRK15201
fimbriae biosynthesis transcriptional regulator FimW;
149-205 1.38e-03

fimbriae biosynthesis transcriptional regulator FimW;


Pssm-ID: 185123  Cd Length: 198  Bit Score: 38.49  E-value: 1.38e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1477047712 149 KRLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYL 205
Cdd:PRK15201  132 RHFSVTERHLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLHVKTEQQFLKYI 188
HTH_38 pfam13936
Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is ...
 149-183 1.39e-03

Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.


Pssm-ID: 433591 [Multi-domain]  Cd Length: 44  Bit Score: 35.57  E-value: 1.39e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1477047712 149 KRLSPKESEVL-RLFAEGFLVTEIAKKLNRSIKTIS 183
Cdd:pfam13936   3 KHLSLEEREEIaRLLAEGLSLREIARRLGRSPSTIS 38
REC_LytTR_AlgR-like cd17532
phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AlgR; ...
 6-87 1.65e-03

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: 37.13  E-value: 1.65e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   6 VIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDkygDGITLIKYIkRHFPSLSIIV 85
Cdd:cd17532     1 ALIVDDEPLAREELRYLLEEHPDIEIVGEAENGEEALEAIEELKPDVVFLDIQMPGL---DGLELAKKL-SKLAKPPLIV 76


                  ..
gi 1477047712  86 LT 87
Cdd:cd17532    77 FV 78
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
149-183 2.08e-03

Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 38.32  E-value: 2.08e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1477047712 149 KRLSPKE-SEVLRLFAEGFLVTEIAKKLNRSIKTIS 183
Cdd:COG2826     5 KHLTLEErEEIEALLKAGLSVREIARRLGRSPSTIS 40
REC_PdtaR-like cd19932
phosphoacceptor receiver (REC) domain of PdtaR and similar proteins; This subfamily includes ...
 4-87 4.30e-03

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: 35.85  E-value: 4.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   4 MNVIIADDHPIVLFGIRKSLEQiEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPgdkYGDGITLIKYIKRHFPSlSI 83
Cdd:cd19932     1 VRVLIAEDEALIRMDLREMLEE-AGYEVVGEASDGEEAVELAKKHKPDLVIMDVKMP---RLDGIEAAKIITSENIA-PI 75


                  ....
gi 1477047712  84 IVLT 87
Cdd:cd19932    76 VLLT 79
REC_citrate_TCS cd19925
phosphoacceptor receiver (REC) domain of citrate family two-component system response ...
 5-109 5.28e-03

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: 35.68  E-value: 5.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   5 NVIIADDHPIVLFGIRKSLEQIEWVNVVGE---FEDSTALINnLPKLDahVLITDLSMPGdkyGDGITLIKYIKRHFPSL 81
Cdd:cd19925     2 NVLIVEDDPMVAEIHRAYVEQVPGFTVIGTagtGEEALKLLK-ERQPD--LILLDIYLPD---GNGLDLLRELRAAGHDV 75

                          90       100
                  ....*....|....*....|....*...
gi 1477047712  82 SIIVLTMNNNPAILSAVLDLDIEGIVLK 109
Cdd:cd19925    76 DVIVVTAANDVETVREALRLGVVDYLIK 103
COG4567 COG4567
DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains ...
 50-137 6.39e-03

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: 36.05  E-value: 6.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712  50 AHVLItDLSMPGdkyGDGITLIKYIKRHFPSLSIIVLTmnNNPAILSAVldldiEGIvlKQGA------PTDLPKALAAL 123
Cdd:COG4567    50 DYAVL-DLRLGD---GSGLDLIEALRERDPDARIVVLT--GYASIATAV-----EAI--KLGAddylakPADADDLLAAL 116

                          90       100
                  ....*....|....*....|
gi 1477047712 124 QKGK------KFTPESVSRL 137
Cdd:COG4567   117 ERAEgdapapPENPMSLDRL 136
REC_NtrX-like cd17550
phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and ...
 6-87 7.62e-03

phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and similar proteins; NtrX is part of the two-component regulatory system NtrY/NtrX that is involved in the activation of nitrogen assimilatory genes such as Gln. It is phosphorylated by the histidine kinase NtrY and interacts with sigma-54. NtrX is a member of the NtrC family, characterized by a domain architecture containing an N-terminal REC domain, followed by a central sigma-54 interaction/ATPase domain, and a C-terminal DNA binding domain. NtrC family response regulators are sigma54-dependent transcriptional activators. Also included in this subfamily is Aquifex aeolicus NtrC4. The ability of the central domain to hydrolyze ATP and thus to interact effectively with a complex of RNA polymerase, sigma54, and promoter, is controlled by the phosphorylation status of the REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381102 [Multi-domain]  Cd Length: 115  Bit Score: 35.17  E-value: 7.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1477047712   6 VIIADDHPivlfGIRKSLEQI---E--WVNVVGEFEDSTALINNLPkldAHVLITDLSMPGdkyGDGITLIKYIKRHFPS 80
Cdd:cd17550     1 ILIVDDEE----DIRESLSGIledEgyEVDTAADGEEALKLIKERR---PDLVLLDIWLPD---MDGLELLKEIKEKYPD 70


                  ....*..
gi 1477047712  81 LSIIVLT 87
Cdd:cd17550    71 LPVIMIS 77
 
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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