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Conserved domains on  [gi|1942334314|ref|WP_197388122|]
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MULTISPECIES: response regulator transcription factor [Ralstonia solanacearum species complex]

Protein Classification

response regulator transcription factor( domain architecture ID 1013612)

two-component system response regulator transcription factor binds DNA upon phosphorylation and functions as transcriptional regulator

CATH:  3.40.50.2300
Gene Ontology:  GO:0000156|GO:0000160|GO:0003677|GO:0006355
PubMed:  31100988|10966457
SCOP:  4003632

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK15369 super family cl33127
two component system response regulator;
4-207 7.66e-47

two component system response regulator;


The actual alignment was detected with superfamily member PRK15369:

Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 153.31  E-value: 7.66e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   4 PVKLLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLV 83
Cdd:PRK15369    3 NYKILLVDDHELIINGIKNMLAPYPRYKIVGQVDNGLEVYNACRQLEPDIVILDLGLPGMNGLDVIPQLHQRWPAMNILV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  84 LSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAGRPFYSAQLAMRMAEQA--VAPIPAEALTPRERDILDGVA 161
Cdd:PRK15369   83 LTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGKRYIDPALNREAILALlnADDTNPPLLTPRERQILKLIT 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1942334314 162 QGWSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKFAVEAG 207
Cdd:PRK15369  163 EGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNWARRLG 208
 
Name Accession Description Interval E-value
PRK15369 PRK15369
two component system response regulator;
4-207 7.66e-47

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 153.31  E-value: 7.66e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   4 PVKLLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLV 83
Cdd:PRK15369    3 NYKILLVDDHELIINGIKNMLAPYPRYKIVGQVDNGLEVYNACRQLEPDIVILDLGLPGMNGLDVIPQLHQRWPAMNILV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  84 LSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAGRPFYSAQLAMRMAEQA--VAPIPAEALTPRERDILDGVA 161
Cdd:PRK15369   83 LTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGKRYIDPALNREAILALlnADDTNPPLLTPRERQILKLIT 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1942334314 162 QGWSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKFAVEAG 207
Cdd:PRK15369  163 EGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNWARRLG 208
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 8-123 2.05e-37

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: 126.09  E-value: 2.05e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   8 LLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMH 87
Cdd:cd17535     2 LIVDDHPLVREGLRRLLESEPDIEVVGEAADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRRYPDLKVIVLTAH 81

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1942334314  88 DNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLA 123
Cdd:cd17535    82 DDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAVAA 117
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 9-207 1.42e-35

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: 124.06  E-value: 1.42e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   9 LVDDHPLVRDGVRVRLEAV----------PHFAVVGeageaagaleaaRTLSPDLVLMDIGMRGMNGIALTEQFGERFPE 78
Cdd:COG4566     4 IVDDDEAVRDSLAFLLESAglrvetfasaEAFLAAL------------DPDRPGCLLLDVRMPGMSGLELQEELAARGSP 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  79 IAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAgrpFYSAQLAMRMAEQAVAPIpAEALTPRERDILD 158
Cdd:COG4566    72 LPVIFLTGHGDVPMAVRAMKAGAVDFLEKPFDDQALLDAVRRALA---RDRARRAERARRAELRAR-LASLTPREREVLD 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1942334314 159 GVAQGWSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKFAVEAG 207
Cdd:COG4566   148 LVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARSLAELVRLALALG 196
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 8-119 5.88e-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: 81.04  E-value: 5.88e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   8 LLVDDHPLVRDGVRVRLEaVPHFAVVGEAGEAAGALEAaRTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMH 87
Cdd:pfam00072   2 LIVDDDPLIRELLRQLLE-KEGYVVAEADDGKEALELL-KEERPDLILLDINMPGMDGLELLKRIRRRDPTTPVIILTAH 79

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1942334314  88 DNLEYVRQVMRAGARGYVLKDAPASELVEAID 119
Cdd:pfam00072  80 GDEDDAVEALEAGADDFLSKPFDPDELLAAIR 111
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 146-203 6.11e-19

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 76.80  E-value: 6.11e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1942334314  146 AEALTPRERDILDGVAQGWSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKFA 203
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 147-191 7.47e-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: 41.56  E-value: 7.47e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1942334314 147 EALTPRERDILDGVA-QGWSNKRIADELGLSVRTVESHRLSLKRKL 191
Cdd:TIGR02937 109 EKLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
 
Name Accession Description Interval E-value
PRK15369 PRK15369
two component system response regulator;
4-207 7.66e-47

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 153.31  E-value: 7.66e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   4 PVKLLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLV 83
Cdd:PRK15369    3 NYKILLVDDHELIINGIKNMLAPYPRYKIVGQVDNGLEVYNACRQLEPDIVILDLGLPGMNGLDVIPQLHQRWPAMNILV 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  84 LSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAGRPFYSAQLAMRMAEQA--VAPIPAEALTPRERDILDGVA 161
Cdd:PRK15369   83 LTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGKRYIDPALNREAILALlnADDTNPPLLTPRERQILKLIT 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1942334314 162 QGWSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKFAVEAG 207
Cdd:PRK15369  163 EGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNWARRLG 208
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 8-123 2.05e-37

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: 126.09  E-value: 2.05e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   8 LLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMH 87
Cdd:cd17535     2 LIVDDHPLVREGLRRLLESEPDIEVVGEAADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRRYPDLKVIVLTAH 81

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1942334314  88 DNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLA 123
Cdd:cd17535    82 DDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAVAA 117
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 1-205 2.94e-37

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 128.99  E-value: 2.94e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   1 MNTPVKLLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIA 80
Cdd:PRK10651    3 NQEPATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLSGR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  81 VLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAGRPFYSAQLAMRMAEQAVAPIPA-----EALTPRERD 155
Cdd:PRK10651   83 IVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQAAAGEMVLSEALTPVLAASLRANRATterdvNQLTPRERD 162

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1942334314 156 ILDGVAQGWSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKFAVE 205
Cdd:PRK10651  163 ILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQ 212
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 9-207 1.42e-35

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: 124.06  E-value: 1.42e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   9 LVDDHPLVRDGVRVRLEAV----------PHFAVVGeageaagaleaaRTLSPDLVLMDIGMRGMNGIALTEQFGERFPE 78
Cdd:COG4566     4 IVDDDEAVRDSLAFLLESAglrvetfasaEAFLAAL------------DPDRPGCLLLDVRMPGMSGLELQEELAARGSP 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  79 IAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAgrpFYSAQLAMRMAEQAVAPIpAEALTPRERDILD 158
Cdd:COG4566    72 LPVIFLTGHGDVPMAVRAMKAGAVDFLEKPFDDQALLDAVRRALA---RDRARRAERARRAELRAR-LASLTPREREVLD 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1942334314 159 GVAQGWSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKFAVEAG 207
Cdd:COG4566   148 LVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARSLAELVRLALALG 196
PRK09483 PRK09483
response regulator; Provisional
 5-207 2.59e-35

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 124.06  E-value: 2.59e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   5 VKLLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVL 84
Cdd:PRK09483    2 INVLLVDDHELVRAGIRRILEDIKGIKVVGEACCGEDAVKWCRTNAVDVVLMDMNMPGIGGLEATRKILRYTPDVKIIML 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  85 SMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAGRPFYSAQLAMRMAEQAVAPI---PAEALTPRERDILDGVA 161
Cdd:PRK09483   82 TVHTENPLPAKVMQAGAAGYLSKGAAPQEVVSAIRSVHSGQRYIASDIAQQMALSQIEPAtenPFASLSERELQIMLMIT 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1942334314 162 QGWSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKFAVEAG 207
Cdd:PRK09483  162 KGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRHG 207
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
3-193 6.07e-30

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 109.94  E-value: 6.07e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   3 TPVKLLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVL 82
Cdd:PRK10403    5 TPFQVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLANRLDPDVILLDLNMKGMSGLDTLNALRRDGVTAQII 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  83 VLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAGRPFYSAQLAMRMAEQAV---APIPAEALTPRERDILDG 159
Cdd:PRK10403   85 ILTVSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKGSKVFSERVNQYLREREMfgaEEDPFSVLTERELDVLHE 164

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1942334314 160 VAQGWSNKRIADELGLSVRTVESHRLSLKRKLGI 193
Cdd:PRK10403  165 LAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNV 198
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 4-207 4.53e-29

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: 105.36  E-value: 4.53e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   4 PVKLLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFgerfpeiavlv 83
Cdd:COG2197     1 MIRVLIVDDHPLVREGLRALLEAEPDIEVVGEAADGEEALELLEELRPDVVLLDIRMPGMDGLEALRRL----------- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  84 lsmhdnleyvrqvmragargyvlkdapaselveaidavlagrpfysaqlamrmaeqavapipaeaLTPRERDILDGVAQG 163
Cdd:COG2197    70 -----------------------------------------------------------------LTPREREVLRLLAEG 84

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1942334314 164 WSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKFAVEAG 207
Cdd:COG2197    85 LSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLG 128
PRK10360 PRK10360
transcriptional regulator UhpA;
5-201 2.43e-26

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 100.05  E-value: 2.43e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   5 VKLLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFgerfPE-IAVLV 83
Cdd:PRK10360    2 ITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQL----PKgMATIM 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  84 LSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAGRPFYSAQLAMRMAEQAVAPipaeaLTPRERDILDGVAQG 163
Cdd:PRK10360   78 LSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASGRQDP-----LTKRERQVAEKLAQG 152

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1942334314 164 WSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVK 201
Cdd:PRK10360  153 MAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELAR 190
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
4-203 1.45e-23

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 93.40  E-value: 1.45e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   4 PVKLLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLV 83
Cdd:PRK09935    3 PASVIIMDTHPIIRMSIEVLLQKNSELQIVLKTDDYRITIDYLRTRPVDLIIMDIDLPGTDGFTFLKRIKQIQSTVKVLF 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  84 LSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAGRPFYSAQ-------LAMRMAEQAVAPipaeaLTPRERDI 156
Cdd:PRK09935   83 LSSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMILSGYTFFPSEtlnyiksNKCSTNSSTDTV-----LSNREVTI 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1942334314 157 LDGVAQGWSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKFA 203
Cdd:PRK09935  158 LRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELIDYA 204
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 8-119 5.88e-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: 81.04  E-value: 5.88e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   8 LLVDDHPLVRDGVRVRLEaVPHFAVVGEAGEAAGALEAaRTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMH 87
Cdd:pfam00072   2 LIVDDDPLIRELLRQLLE-KEGYVVAEADDGKEALELL-KEERPDLILLDINMPGMDGLELLKRIRRRDPTTPVIILTAH 79

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1942334314  88 DNLEYVRQVMRAGARGYVLKDAPASELVEAID 119
Cdd:pfam00072  80 GDEDDAVEALEAGADDFLSKPFDPDELLAAIR 111
REC_YesN-like cd17536
phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response ...
 7-118 1.51e-19

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: 80.07  E-value: 1.51e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   7 LLLVDDHPLVRDGVRVRL-----------------EAVphfavvgeageaagalEAARTLSPDLVLMDIGMRGMNGIALT 69
Cdd:cd17536     1 VLIVDDEPLIREGLKKLIdweelgfevvgeaengeEAL----------------ELIEEHKPDIVITDIRMPGMDGLELI 64

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1942334314  70 EQFGERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAI 118
Cdd:cd17536    65 EKIRELYPDIKIIILSGYDDFEYAQKAIRLGVVDYLLKPVDEEELEEAL 113
fixJ PRK09390
response regulator FixJ; Provisional
 48-207 2.83e-19

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 81.59  E-value: 2.83e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  48 TLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAGRPf 127
Cdd:PRK09390   45 GLRFGCVVTDVRMPGIDGIELLRRLKARGSPLPVIVMTGHGDVPLAVEAMKLGAVDFIEKPFEDERLIGAIERALAQAP- 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314 128 ysaQLAMRMAEQAVAPIPAEALTPRERDILDGVAQGWSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKFAVEAG 207
Cdd:PRK09390  124 ---EAAKSEAVAADIRARIASLSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSLSELVRMALRAG 200
YesN COG4753
Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding ...
 6-107 3.58e-19

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: 78.66  E-value: 3.58e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   6 KLLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLS 85
Cdd:COG4753     1 KVLIVDDEPLIREGLKRILEWEAGFEVVGEAENGEEALELLEEHKPDLVITDINMPGMDGLELLEAIRELDPDTKIIILS 80

                          90       100
                  ....*....|....*....|..
gi 1942334314  86 MHDNLEYVRQVMRAGARGYVLK 107
Cdd:COG4753    81 GYSDFEYAQEAIKLGADDYLLK 102
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 146-203 6.11e-19

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 76.80  E-value: 6.11e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1942334314  146 AEALTPRERDILDGVAQGWSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKFA 203
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
REC_NarL cd19931
phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL); Nitrate ...
 7-118 8.68e-18

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: 75.46  E-value: 8.68e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   7 LLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSM 86
Cdd:cd19931     1 VLLIDDHPLLRKGIKQLIELDPDFTVVGEASSGEEGIELAERLDPDLILLDLNMKGMSGLDTLKALREEGVSARIVILTV 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1942334314  87 HDNLEYVRQVMRAGARGYVLKDAPASELVEAI 118
Cdd:cd19931    81 SDAEDDVVTALRAGADGYLLKDMEPEDLLEAL 112
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
8-203 1.71e-17

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 77.24  E-value: 1.71e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   8 LLVDDHPLVRDGVRVRLEAvPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMH 87
Cdd:PRK09958    4 IIIDDHPLAIAAIRNLLIK-NDIEILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVSAK 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  88 DNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAGR---PFYSAQLAMRMAEQAVApipAEALTPRERDILDGVAQGW 164
Cdd:PRK09958   83 NDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGYcyfPFSLNRFVGSLTSDQQK---LDSLSKQEISVMRYILDGK 159

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1942334314 165 SNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKFA 203
Cdd:PRK09958  160 DNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYTFA 198
REC_DesR-like cd19930
phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of ...
 7-123 8.90e-17

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: 73.08  E-value: 8.90e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   7 LLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSM 86
Cdd:cd19930     1 VLIAEDQEMVRGALAALLELEDDLEVVAQASNGQEALRLVLKHSPDVAILDIEMPGRTGLEVAAELREELPDTKVLIVTT 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1942334314  87 HDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLA 123
Cdd:cd19930    81 FGRPGYFRRALAAGVDGYVLKDRPIEELADAIRTVHA 117
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 1-202 2.32e-16

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 74.48  E-value: 2.32e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   1 MNTpVKLLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRG---MNGIALTEQFGERFP 77
Cdd:PRK10840    1 MNN-MNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHFP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  78 EIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAGRPFYSAQLAMRMAEQAVAPIPAEALTPRERDIL 157
Cdd:PRK10840   80 SLSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLEKISAGGYGDKRLSPKESEVL 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1942334314 158 DGVAQGWSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKF 202
Cdd:PRK10840  160 RLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNY 204
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 149-205 3.36e-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: 69.49  E-value: 3.36e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1942334314 149 LTPRERDILDGVAQGWSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKFAVE 205
Cdd:cd06170     1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 134-208 3.92e-16

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


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 69.99  E-value: 3.92e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1942334314 134 MRMAEQAVAPipaEALTPRERDILDGVAQGWSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKFAVEAGK 208
Cdd:COG5905     1 MMPSSSTSHP---SLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWALRLGL 72
CitB COG4565
DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal ...
 6-125 5.19e-16

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


Pssm-ID: 443622 [Multi-domain]  Cd Length: 138  Bit Score: 71.54  E-value: 5.19e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   6 KLLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLS 85
Cdd:COG4565     5 RVLIVEDDPMVAELLRRYLERLPGFEVVGVASSGEEALALLAEHRPDLILLDIYLPDGDGLELLRELRARGPDVDVIVIT 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1942334314  86 MHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAGR 125
Cdd:COG4565    85 AARDPETVREALRAGVVDYLIKPFTFERLREALERYLEYR 124
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
23-207 2.35e-15

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 71.33  E-value: 2.35e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  23 RLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMHDNLEYVRQVMRAGAR 102
Cdd:COG2771     2 LLLALALLLLALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314 103 GYVLKDAPASELVEAIDAVLAGRPFYSAQLAMRMAEQAVAPIPAEALTPRERDILDGVAQGWSNKRIADELGLSVRTVES 182
Cdd:COG2771    82 LALLLLLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRT 161

                         170       180
                  ....*....|....*....|....*
gi 1942334314 183 HRLSLKRKLGIEGQAELVKFAVEAG 207
Cdd:COG2771   162 HLKRIYRKLGVSSRAELVALALRLG 186
GerE pfam00196
Bacterial regulatory proteins, luxR family;
149-203 7.85e-15

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 66.07  E-value: 7.85e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1942334314 149 LTPRERDILDGVAQGWSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKFA 203
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 6-125 1.44e-14

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: 71.15  E-value: 1.44e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   6 KLLLVDDHPLVRDGVRVRLEAVPHfaVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLS 85
Cdd:COG2204     4 RILVVDDDPDIRRLLKELLERAGY--EVETAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRALDPDLPVILLT 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1942334314  86 MHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAGR 125
Cdd:COG2204    82 GYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERALERR 121
OmpR COG0745
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...
 6-194 2.19e-14

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: 68.83  E-value: 2.19e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   6 KLLLVDDHPLVRDGVRVRLEAVPHfaVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLS 85
Cdd:COG0745     3 RILVVEDDPDIRELLADALEREGY--EVDTAADGEEALELLEEERPDLILLDLMLPGMDGLEVCRRLRARPSDIPIIMLT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  86 MHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVL---------AGRPFYSAQLAMRMAEQAVapipaeALTPRERDI 156
Cdd:COG0745    81 ARDDEEDRVRGLEAGADDYLTKPFDPEELLARIRALLrrraaevlrVGDLLDLAAREVTRDGEPV------ELTPKEFRL 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1942334314 157 LDGVA----QGWSNKRIADEL----GLSVRTVESHRLSLKRKLGIE 194
Cdd:COG0745   155 LELLMrnpgRVVSREQLLEEVwgydYGDDRTVDVHISRLRKKLEDD 200
REC cd00156
phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ...
 8-107 3.08e-14

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: 65.71  E-value: 3.08e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   8 LLVDDHPLVRDGVRVRLEAvpHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMH 87
Cdd:cd00156     1 LIVDDDPAIRELLKSLLER--EGYEVDTAADGEEALELLREERPDLVLLDLMMPGMDGLELLRKLRELPPDIPVIVLTAK 78

                          90       100
                  ....*....|....*....|
gi 1942334314  88 DNLEYVRQVMRAGARGYVLK 107
Cdd:cd00156    79 ADEEDAVRALELGADDYLVK 98
PleD COG3706
Two-component response regulator, PleD family, consists of two REC domains and a diguanylate ...
 4-150 2.34e-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: 65.32  E-value: 2.34e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   4 PVKLLLVDDHPLVRDGVRVRLEAVPHfaVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQF--GERFPEIAV 81
Cdd:COG3706     1 PARILVVDDDPTNRKLLRRLLEAAGY--EVVEAADGEEALELLQEHRPDLILLDLEMPDMDGLELCRRLraDPRTADIPI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  82 LVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDavLAGR----------PFYSAQLAMRMAE---QAVAPIPAEA 148
Cdd:COG3706    79 IFLTALDDEEDRARALEAGADDYLTKPFDPEELLARVD--LVARyggeefaillPGTDLEGALAVAErirEAVAELPSLR 156


                  ..
gi 1942334314 149 LT 150
Cdd:COG3706   157 VT 158
CheY COG0784
CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator ...
 4-125 6.81e-13

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: 62.95  E-value: 6.81e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   4 PVKLLLVDDHPLVRD---------GVRVRL-----EAVPHFavvgeageaagaleaaRTLSPDLVLMDIGMRGMNGIALT 69
Cdd:COG0784     5 GKRILVVDDNPDNREllrrllerlGYEVTTaedgaEALELL----------------RAGPPDLILLDINMPGMDGLELL 68

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1942334314  70 EQF--GERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAGR 125
Cdd:COG0784    69 RRIraLPRLPDIPIIALTAYADEEDRERALEAGADDYLTKPVDPEELLEALRRLLARA 126
REC_CheY cd17542
phosphoacceptor receiver (REC) domain of chemotaxis protein CheY; The chemotaxis response ...
 49-122 3.26e-11

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: 58.06  E-value: 3.26e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1942334314  49 LSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVL 122
Cdd:cd17542    44 LKPDLVTMDITMPEMDGIEALKEIKKIDPNAKVIMCSAMGQEEMVKEAIKAGAKDFIVKPFQPERVLEAVEKVL 117
LytT COG3279
DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction ...
 6-123 1.20e-10

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


Pssm-ID: 442510 [Multi-domain]  Cd Length: 235  Bit Score: 59.06  E-value: 1.20e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   6 KLLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLS 85
Cdd:COG3279     3 KILIVDDEPLARERLERLLEKYPDLEVVGEASNGEEALELLEEHKPDLVFLDIQMPGLDGFELARQLRELDPPPPIIFTT 82

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1942334314  86 MHDnlEYVRQVMRAGARGYVLKDAPASELVEAIDAVLA 123
Cdd:COG3279    83 AYD--EYALEAFEVNAVDYLLKPIDEERLAKALEKAKE 118
RpfG COG3437
Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains ...
 1-125 1.40e-10

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: 58.64  E-value: 1.40e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   1 MNT--PVKLLLVDDHPLVRDGVRVRLEavPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFG--ERF 76
Cdd:COG3437     1 MRTgqAPTVLIVDDDPENLELLRQLLR--TLGYDVVTAESGEEALELLLEAPPDLILLDVRMPGMDGFELLRLLRadPST 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1942334314  77 PEIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAGR 125
Cdd:COG3437    79 RDIPVIFLTALADPEDRERALEAGADDYLTKPFDPEELLARVRNALELR 127
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
120-207 8.24e-10

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 55.87  E-value: 8.24e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314 120 AVLAGRPFYSAQLAMRMAEQAVApipAEALTPRErdildgVAQGWSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAEL 199
Cdd:COG2909   103 AEAAGRLLLRALALRALGDREEA---LAALRRRL------LAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEA 173


                  ....*...
gi 1942334314 200 VKFAVEAG 207
Cdd:COG2909   174 VARARELG 181
AmiR COG3707
Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding ...
 4-123 1.12e-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: 55.73  E-value: 1.12e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   4 PVKLLLVDDHPLVRDGVRVRLEAVPHfAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERfPEIAVLV 83
Cdd:COG3707     3 GLRVLVVDDEPLRRADLREGLREAGY-EVVAEAADGEDAVELVRELKPDLVIVDIDMPDRDGLEAARQISEE-RPAPVIL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1942334314  84 LSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLA 123
Cdd:COG3707    81 LTAYSDPELIERALEAGVSAYLVKPLDPEDLLPALELALA 120
REC_PdtaR-like cd19932
phosphoacceptor receiver (REC) domain of PdtaR and similar proteins; This subfamily includes ...
 5-123 1.53e-09

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: 53.57  E-value: 1.53e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   5 VKLLLVDDHPLVRDGVRVRLEAVPHfAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPeIAVLVL 84
Cdd:cd19932     1 VRVLIAEDEALIRMDLREMLEEAGY-EVVGEASDGEEAVELAKKHKPDLVIMDVKMPRLDGIEAAKIITSENI-APIVLL 78

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1942334314  85 SMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLA 123
Cdd:cd19932    79 TAYSQQDLVERAKEAGAMAYLVKPFSESDLIPAIEMAIA 117
REC_DC-like cd17534
phosphoacceptor receiver (REC) domain of modulated diguanylate cyclase and similar domains; ...
 47-122 5.24e-09

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: 52.02  E-value: 5.24e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1942334314  47 RTLSPDLVLMDIGMRG-MNGIALTEQFGERFPeIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVL 122
Cdd:cd17534    42 EENKPDLILMDINLKGdMDGIEAAREIREKFD-IPVIFLTAYSDEETLERAKETNPYGYLVKPFNERELKAAIELAL 117
REC_citrate_TCS cd19925
phosphoacceptor receiver (REC) domain of citrate family two-component system response ...
 5-120 5.71e-08

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: 49.55  E-value: 5.71e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   5 VKLLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVL 84
Cdd:cd19925     1 INVLIVEDDPMVAEIHRAYVEQVPGFTVIGTAGTGEEALKLLKERQPDLILLDIYLPDGNGLDLLRELRAAGHDVDVIVV 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1942334314  85 SMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDA 120
Cdd:cd19925    81 TAANDVETVREALRLGVVDYLIKPFTFERLRQRLER 116
Spo0F COG5803
Stage 0 sporulation initiation response regulator Spo0F [Cell cycle control, cell division, ...
 49-123 6.11e-08

Stage 0 sporulation initiation response regulator Spo0F [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 444505 [Multi-domain]  Cd Length: 119  Bit Score: 49.41  E-value: 6.11e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1942334314  49 LSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLA 123
Cdd:COG5803    45 LKPDLVLLDMKMPGMDGIEILKEIKEIDPDIPVIMMTAYGELDMVEEAKELGAKGYFTKPFDIDELREAVNKLLK 119
PRK10100 PRK10100
transcriptional regulator CsgD;
79-203 1.85e-07

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 49.87  E-value: 1.85e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  79 IAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAGRPFYSAQLA----MRMAEQAVAPIPAEALTPRER 154
Cdd:PRK10100   82 IKILLLNTPEDYPYREIENWPHINGVFYAMEDQERVVNGLQGVLRGECYFTQKLAsyliTHSGNYRYNSTESALLTHREK 161

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1942334314 155 DILDGVAQGWSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKFA 203
Cdd:PRK10100  162 EILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQAVSWA 210
REC_RssB-like cd17555
phosphoacceptor receiver (REC) domain of Pseudomonas aeruginosa RssB and similar domains; ...
 5-107 1.94e-07

phosphoacceptor receiver (REC) domain of Pseudomonas aeruginosa RssB and similar domains; Pseudomonas aeruginosa RssB is an orphan atypical response regulator containing a REC domain and a PP2C-type protein phosphatase output domain. Its function is still unknown. Escherichia RssB, which is not included in this subfamily, is a ClpX adaptor protein which alters ClpX specificity by mediating a specific interaction between ClpX and the substrates such as RpoS, an RNA polymerase sigma factor. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381107 [Multi-domain]  Cd Length: 116  Bit Score: 47.97  E-value: 1.94e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   5 VKLLLVDDHPLVRDGVRVRLE--------------AVPHFavvgeageaagaleaaRTLSPDLVLMDIGMRGMNGIALTE 70
Cdd:cd17555     1 ATILVIDDDEVVRESIAAYLEdsgfqvlqaadgrqGLELF----------------RSEQPDLVLCDLRMPEMDGLEVLK 64

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1942334314  71 QFGERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLK 107
Cdd:cd17555    65 QITKESPDTPVIVVSGAGVMSDAVEALRLGAWDYLTK 101
REC_TrrA-like cd17554
phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator TrrA and ...
 51-119 2.67e-07

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: 47.60  E-value: 2.67e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1942334314  51 PDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMHDnlEYVRQVMRAGARGYVLKDAPASELVEAID 119
Cdd:cd17554    45 PDLVILDIKMPGMDGLETLRKIREKKPDLPVIICTAYS--EYKSDFSSWAADAYVVKSSDLTELKETIK 111
PRK10693 PRK10693
two-component system response regulator RssB;
49-123 5.63e-07

two-component system response regulator RssB;


Pssm-ID: 182652 [Multi-domain]  Cd Length: 303  Bit Score: 48.83  E-value: 5.63e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1942334314  49 LSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLKdaPASELVEAIDAVLA 123
Cdd:PRK10693   16 FTPDLIICDLAMPRMNGIEFVEHLRNRGDQTPVLVISATENMADIAKALRLGVQDVLLK--PVKDLNRLREMVFA 88
REC_CheB-like cd17541
phosphoacceptor receiver (REC) domain of chemotaxis response regulator protein-glutamate ...
 5-118 6.02e-07

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: 46.62  E-value: 6.02e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   5 VKLLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPeIAVLVL 84
Cdd:cd17541     1 IRVLIVDDSAVMRKLLSRILESDPDIEVVGTARDGEEALEKIKELKPDVITLDIEMPVMDGLEALRRIMAERP-TPVVMV 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1942334314  85 S--MHDNLEYVRQVMRAGARGYVLK---------DAPASELVEAI 118
Cdd:cd17541    80 SslTEEGAEITLEALELGAVDFIAKpsggisldlEEIAEELIEKI 124
REC_NtrX-like cd17550
phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and ...
 50-101 2.45e-06

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: 44.80  E-value: 2.45e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1942334314  50 SPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMHDNLEYVRQVMRAGA 101
Cdd:cd17550    42 RPDLVLLDIWLPDMDGLELLKEIKEKYPDLPVIMISGHGTIETAVKATKLGA 93
REC_NtrC cd19919
phosphoacceptor receiver (REC) domain of DNA-binding transcriptional regulator NtrC; ...
 51-107 2.81e-06

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: 44.57  E-value: 2.81e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1942334314  51 PDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLK 107
Cdd:cd19919    45 PDVLISDIRMPGMDGLALLAQIKQRHPDLPVIIMTAHSDLDSAVSAYQGGAFEYLPK 101
PRK12555 PRK12555
chemotaxis-specific protein-glutamate methyltransferase CheB;
5-165 7.39e-06

chemotaxis-specific protein-glutamate methyltransferase CheB;


Pssm-ID: 237135 [Multi-domain]  Cd Length: 337  Bit Score: 45.64  E-value: 7.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   5 VKLLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPeIAVLVL 84
Cdd:PRK12555    1 MRIGIVNDSPLAVEALRRALARDPDHEVVWVATDGAQAVERCAAQPPDVILMDLEMPRMDGVEATRRIMAERP-CPILIV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  85 SM--HDNLEYVRQVMRAGARGYVLK---------DAPASELVEAIDAVlagrpfysAQLAMRMAEQAVAPIPAEALTPRE 153
Cdd:PRK12555   80 TSltERNASRVFEAMGAGALDAVDTptlgigaglEEYAAELLAKIDQI--------GRLLGRRLAPAAAPAAASAAPFRT 151

                         170
                  ....*....|..
gi 1942334314 154 RDILdgVAQGWS 165
Cdd:PRK12555  152 TPRL--VAIGAS 161
REC_DivK-like cd17548
phosphoacceptor receiver (REC) domain of DivK and similar proteins; Caulobacter crescentus ...
 51-107 1.09e-05

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: 42.91  E-value: 1.09e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1942334314  51 PDLVLMDIGMRGMNGIALTEQFGE-----RFPEIAVLVLSMHDNLEyvrQVMRAGARGYVLK 107
Cdd:cd17548    44 PDLILMDIQLPGMDGLEATRLLKEdpatrDIPVIALTAYAMKGDRE---KILEAGCDGYISK 102
glnG PRK10923
nitrogen regulation protein NR(I); Provisional
 50-123 1.55e-05

nitrogen regulation protein NR(I); Provisional


Pssm-ID: 182842 [Multi-domain]  Cd Length: 469  Bit Score: 44.86  E-value: 1.55e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1942334314  50 SPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLA 123
Cdd:PRK10923   47 TPDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAIS 120
REC_hyHK_CKI1_RcsC-like cd17546
phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinases/response regulators ...
 7-118 1.60e-05

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: 42.46  E-value: 1.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   7 LLLVDDHP---------LVRDGVRVR-----LEAVPHFavvgeageaagaleaaRTLSPDLVLMDIGMRGMNGIALTE-- 70
Cdd:cd17546     1 VLVVDDNPvnrkvlkklLEKLGYEVDvaengQEALELL----------------KEEPFDLVLMDLQMPVMDGLEATRri 64

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1942334314  71 -QFGERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAI 118
Cdd:cd17546    65 rELEGGGRRTPIIALTANALEEDREKCLEAGMDDYLSKPVKLDQLKEVL 113
REC_CheY_CheY3 cd19923
phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY ...
 5-122 2.04e-05

phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY family proteins; CheY family chemotaxis response regulators (RRs) comprise about 17% of bacterial RRs and almost half of all RRs in archaea. This subfamily contains Vibrio cholerae CheY3, Escherichia coli CheY, and similar CheY family RRs. CheY proteins control bacterial motility and participate in signaling phosphorelays and in protein-protein interactions. CheY RRs contain only the REC domain with no output/effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381150 [Multi-domain]  Cd Length: 119  Bit Score: 42.33  E-value: 2.04e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   5 VKLLLVDDHPLVRDGVRVRLEAVpHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQF--GERFPEIAVL 82
Cdd:cd19923     1 MKVLVVDDFSTMRRIIKNLLKEL-GFNNVEEAEDGVDALEKLKAGGFDFVITDWNMPNMDGLELLKTIraDGALSHLPVL 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1942334314  83 VLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVL 122
Cdd:cd19923    80 MVTAEAKKENVIAAAQAGVNNYIVKPFTAATLKEKLEKIF 119
REC_Rcp-like cd17557
phosphoacceptor receiver (REC) domain of cyanobacterial phytochrome response regulator Rcp and ...
 51-121 2.50e-05

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: 42.40  E-value: 2.50e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1942334314  51 PDLVLMDIGMRGMNGI----ALTEQfgERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAV 121
Cdd:cd17557    53 PDLILLDLNMPRMDGFevlrEIKAD--PDLRRIPVVVLTTSDAEEDIERAYELGANSYIVKPVDFEEFVEAIRSL 125
COG4567 COG4567
DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains ...
 47-123 2.56e-05

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: 42.98  E-value: 2.56e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1942334314  47 RTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLA 123
Cdd:COG4567    45 EQAPPDYAVLDLRLGDGSGLDLIEALRERDPDARIVVLTGYASIATAVEAIKLGADDYLAKPADADDLLAALERAEG 121
REC_OmpR cd17574
phosphoacceptor receiver (REC) domain of OmpR family response regulators; OmpR-like proteins ...
 8-107 3.33e-05

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: 41.24  E-value: 3.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   8 LLVDDHPLVRDGVRVRL--------------EAVPHFavvgeageaagaleaaRTLSPDLVLMDIGMRGMNGIALTEQFG 73
Cdd:cd17574     1 LVVEDDEEIAELLSDYLekegyevdtaadgeEALELA----------------REEQPDLIILDVMLPGMDGFEVCRRLR 64

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1942334314  74 ERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLK 107
Cdd:cd17574    65 EKGSDIPIIMLTAKDEEEDKVLGLELGADDYITK 98
PRK11361 PRK11361
acetoacetate metabolism transcriptional regulator AtoC;
1-114 4.13e-05

acetoacetate metabolism transcriptional regulator AtoC;


Pssm-ID: 183099 [Multi-domain]  Cd Length: 457  Bit Score: 43.68  E-value: 4.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   1 MNTPVKLLLVDDHPLVR---------DGVRVR-----LEAVPHFavvgeageaagaleaaRTLSPDLVLMDIGMRGMNGI 66
Cdd:PRK11361    1 MTAINRILIVDDEDNVRrmlstafalQGFETHcanngRTALHLF----------------ADIHPDVVLMDIRMPEMDGI 64

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1942334314  67 ALTEQFGERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASEL 114
Cdd:PRK11361   65 KALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDEL 112
PRK10365 PRK10365
sigma-54-dependent response regulator transcription factor ZraR;
52-139 7.12e-05

sigma-54-dependent response regulator transcription factor ZraR;


Pssm-ID: 182412 [Multi-domain]  Cd Length: 441  Bit Score: 42.71  E-value: 7.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  52 DLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAGRPFYSAQ 131
Cdd:PRK10365   51 DLVLCDVRMAEMDGIATLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAHTHSIDAE 130


                  ....*...
gi 1942334314 132 LAMRMAEQ 139
Cdd:PRK10365  131 TPAVTASQ 138
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 147-191 7.47e-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: 41.56  E-value: 7.47e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1942334314 147 EALTPRERDILDGVA-QGWSNKRIADELGLSVRTVESHRLSLKRKL 191
Cdd:TIGR02937 109 EKLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
REC_RpfG-like cd17551
phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator ...
 51-107 1.04e-04

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: 40.50  E-value: 1.04e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1942334314  51 PDLVLMDIGMRGMNGIALTEQFGERFP--EIAVLVLSMHDNLEYVRQVMRAGARGYVLK 107
Cdd:cd17551    46 PDLILLDYMMPGMDGLEFIRRLRALPGleDVPIVMITADTDREVRLRALEAGATDFLTK 104
REC_LytTR_AlgR-like cd17532
phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AlgR; ...
 8-118 1.07e-04

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: 40.21  E-value: 1.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   8 LLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMH 87
Cdd:cd17532     2 LIVDDEPLAREELRYLLEEHPDIEIVGEAENGEEALEAIEELKPDVVFLDIQMPGLDGLELAKKLSKLAKPPLIVFVTAY 81

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1942334314  88 DnlEYVRQVMRAGARGYVLKDAPASELVEAI 118
Cdd:cd17532    82 D--EYAVEAFELNAVDYLLKPFSEERLAEAL 110
REC_hyHK_blue-like cd18161
phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinase/response regulators ...
 8-85 1.08e-04

phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinase/response regulators similar to Pseudomonas savastanoi blue-light-activated histidine kinase; Typically, two-component regulatory systems (TCSs) consist of a sensor (histidine kinase) that responds to specific input(s) by modifying the output of a cognate response regulator (RR). TCSs allow organisms to sense and respond to changes in environmental conditions. Hybrid sensor histidine kinase (HK)/response regulators contain all the elements of a classical TCS in a single polypeptide chain. Pseudomonas savastanoi blue-light-activated histidine kinase is a photosensitive HK and RR that is involved in increased bacterial virulence upon exposure to light. RRs share the common phosphoacceptor REC domain and different effector/output domains such as DNA, RNA, ligand-binding, protein-binding, or enzymatic domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381145 [Multi-domain]  Cd Length: 102  Bit Score: 40.02  E-value: 1.08e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1942334314   8 LLVDDHPLVRDGVRVRLEAVpHFAVVGEAGEAAGALEAARTLSPDLVLMDIGM-RGMNGIALTEQFGERFPEIAVLVLS 85
Cdd:cd18161     2 LVVEDDPDVRRLTAEVLEDL-GYTVLEAASGDEALDLLESGPDIDLLVTDVIMpGGMNGSQLAEEARRRRPDLKVLLTS 79
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
144-203 1.22e-04

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 42.24  E-value: 1.22e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314 144 IPAEALTPRERDILDGVAQGWSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKFA 203
Cdd:PRK04841  834 IRTSPLTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQHA 893
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 162-188 1.40e-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: 40.62  E-value: 1.40e-04
                          10        20
                  ....*....|....*....|....*...
gi 1942334314 162 QGWSNKRIADELGLSVRTVESH-RLSLK 188
Cdd:TIGR02985 128 EGLSNKEIAEELGISVKTVEYHiTKALK 155
REC_DctD-like cd17549
phosphoacceptor receiver (REC) domain of C4-dicarboxylic acid transport protein D (DctD) and ...
 8-118 1.49e-04

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: 40.17  E-value: 1.49e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   8 LLVDDHPLVRD---------GVRVRLEAVPHfavvgeageaagalEAARTLSPD---LVLMDIGMRGMNGIALTEQFGER 75
Cdd:cd17549     2 LLVDDDADVREalqqtlelaGFRVRAFADAE--------------EALAALSPDfpgVVISDIRMPGMDGLELLAQIREL 67

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1942334314  76 FPEIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAI 118
Cdd:cd17549    68 DPDLPVILITGHGDVPMAVEAMRAGAYDFLEKPFDPERLLDVV 110
PRK15115 PRK15115
response regulator GlrR; Provisional
 3-126 1.84e-04

response regulator GlrR; Provisional


Pssm-ID: 185070 [Multi-domain]  Cd Length: 444  Bit Score: 41.75  E-value: 1.84e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   3 TPVKLLLVDDHP--LVRDGVRVRLEAvphFAVVGEAGEAAGALEAARTlSPDLVLMDIGMRGMNGIALTEQFGERFPEIA 80
Cdd:PRK15115    4 KPAHLLLVDDDPglLKLLGMRLTSEG---YSVVTAESGQEALRVLNRE-KVDLVISDLRMDEMDGMQLFAEIQKVQPGMP 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1942334314  81 VLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAGRP 126
Cdd:PRK15115   80 VIILTAHGSIPDAVAATQQGVFSFLTKPVDRDALYKAIDDALEQSA 125
REC_PA4781-like cd19920
phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase PA4781 and similar ...
 47-107 2.33e-04

phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase PA4781 and similar domains; Pseudomonas aeruginosa cyclic di-GMP phosphodiesterase PA4781 contains an N-terminal REC domain and a C-terminal catalytic HD-GYP domain, characteristics of RpfG family response regulators. PA4781 is involved in cyclic di-3',5'-GMP (c-di-GMP) hydrolysis/degradation in a two-step reaction via the linear intermediate pGpG to produce GMP. Its unphosphorylated REC domain prevents accessibility of c-di-GMP to the active site. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381147 [Multi-domain]  Cd Length: 103  Bit Score: 39.03  E-value: 2.33e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1942334314  47 RTLSPDLVLMDIGMRGMNGIALTEQF--GERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLK 107
Cdd:cd19920    39 QAEPPDLILLDVMMPGMDGFEVCRRLkaDPATRHIPVIFLTALTDTEDKVKGFELGAVDYITK 101
PRK11475 PRK11475
DNA-binding transcriptional activator BglJ; Provisional
 64-203 2.49e-04

DNA-binding transcriptional activator BglJ; Provisional


Pssm-ID: 236915 [Multi-domain]  Cd Length: 207  Bit Score: 40.50  E-value: 2.49e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  64 NGIALTEQFGERFPEIAVLVLSMHDN-LEYVRQVMRAGARGYVLKDAPASELVEAIDAVLAGrpfySAQLAMRMAEQAVA 142
Cdd:PRK11475   54 EGLSCLTELAIKFPRMRRLVIADDDIeARLIGSLSPSPLDGVLSKASTLEILQQELFLSLNG----VRQATDRLNNQWYI 129

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1942334314 143 PiPAEALTPRERDILDGVAQGWSNKRIADELGLSVRTVESHRLSLKRKLGIEGQAELVKFA 203
Cdd:PRK11475  130 N-QSRMLSPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVSSDAGLLDAA 189
REC_OmpR_MtPhoP-like cd17615
phosphoacceptor receiver (REC) domain of MtPhoP-like OmpR family response regulators; ...
 6-122 4.95e-04

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: 38.49  E-value: 4.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   6 KLLLVDDHPLVRDGVRVRLeavpHFA--VVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLV 83
Cdd:cd17615     1 RVLVVDDEPNITELLSMAL----RYEgwDVETAADGAEALAAAREFRPDAVVLDIMLPDMDGLEVLRRLRADGPDVPVLF 76

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1942334314  84 LSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVL 122
Cdd:cd17615    77 LTAKDSVEDRIAGLTAGGDDYVTKPFSLEEVVARLRALL 115
PRK06930 PRK06930
positive control sigma-like factor; Validated
 148-198 6.74e-04

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 38.94  E-value: 6.74e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1942334314 148 ALTPRERDI-LDGVAQGWSNKRIADELGLSVRTVESHrlsLKR-KLGIEGQAE 198
Cdd:PRK06930  114 VLTEREKEVyLMHRGYGLSYSEIADYLNIKKSTVQSM---IERaEKKIARQIN 163
REC_NtrC1-like cd17572
phosphoacceptor receiver (REC) domain of nitrogen regulatory protein C 1 (NtrC1) from Aquifex ...
 50-115 6.89e-04

phosphoacceptor receiver (REC) domain of nitrogen regulatory protein C 1 (NtrC1) from Aquifex aeolicus and similar NtrC family response regulators; NtrC family proteins are transcriptional regulators that have REC, AAA+ ATPase/sigma-54 interaction, and DNA-binding output domains. This subfamily of NtrC proteins include Aquifex aeolicus NtrC1 and Vibrio quorum-sensing signal integrator LuxO. The N-terminal REC domain of NtrC proteins regulate the activity of the protein and its phosphorylation controls the AAA+ domain oligomerization, while the central AAA+ domain participates in nucleotide binding, hydrolysis, oligomerization, and sigma54 interaction. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381114 [Multi-domain]  Cd Length: 121  Bit Score: 37.95  E-value: 6.89e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1942334314  50 SPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELV 115
Cdd:cd17572    42 PPDVVLLDLKLPDMSGMEILKWIQERSLPTSVIVITAHGSVDIAVEAMRLGAYDFLEKPFDADRLR 107
REC_2_DhkD-like cd17580
second phosphoacceptor receiver (REC) domain of Dictyostelium discoideum hybrid signal ...
 8-118 1.62e-03

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: 37.05  E-value: 1.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   8 LLVDDHPLVRDGVRVRLEAVPHfaVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIAL-----TEQFGERFPEIAvl 82
Cdd:cd17580     2 LVVDDNEDAAEMLALLLELEGA--EVTTAHSGEEALEAAQRFRPDVILSDIGMPGMDGYELarrlrELPWLANTPAIA-- 77

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1942334314  83 vLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAI 118
Cdd:cd17580    78 -LTGYGQPEDRERALEAGFDAHLVKPVDPDELIELI 112
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 147-195 1.62e-03

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: 38.05  E-value: 1.62e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1942334314 147 EALTPRERDILD-GVAQGWSNKRIADELGLSVRTVESH----RLSLKRKLGIEG 195
Cdd:COG1595   126 ERLPPRQREVLVlRYLEGLSYAEIAEILGISEGTVKSRlsraRKKLREALEEEG 179
REC_Spo0F-like cd17553
phosphoacceptor receiver (REC) domain of Spo0F and similar domains; Spo0F, a stand-alone ...
 51-118 1.95e-03

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


Pssm-ID: 381105 [Multi-domain]  Cd Length: 117  Bit Score: 36.76  E-value: 1.95e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1942334314  51 PDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAI 118
Cdd:cd17553    45 PDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAV 112
REC_HP-RR-like cd17573
phosphoacceptor receiver (REC) domain of orphan response regulator HP-RR and similar proteins; ...
 52-107 2.31e-03

phosphoacceptor receiver (REC) domain of orphan response regulator HP-RR and similar proteins; Helicobacter pylori response regulator hp1043 (HP-RR) is an orphan response regulator which is phosphorylation-independent and is essential for growth. HP-RR functions as a cell growth-associated regulator in the absence of post-translational modification. Members of this subfamily contain REC and DNA-binding output domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381115 [Multi-domain]  Cd Length: 110  Bit Score: 36.25  E-value: 2.31e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1942334314  52 DLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLK 107
Cdd:cd17573    44 DLVLVSDKLPDGNGLSIVSRIKEKHPSIVVIVLSDNPKTEQEIEAFKEGADDYIAK 99
REC_FixJ cd17537
phosphoacceptor receiver (REC) domain of FixJ family response regulators; FixJ family response ...
 54-122 2.56e-03

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


Pssm-ID: 381092 [Multi-domain]  Cd Length: 116  Bit Score: 36.42  E-value: 2.56e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1942334314  54 VLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVL 122
Cdd:cd17537    48 LVLDVRMPGMSGLELQDELLARGSNIPIIFITGHGDVPMAVEAMKAGAVDFLEKPFRDQVLLDAIEQAL 116
dpiA PRK10046
two-component response regulator DpiA; Provisional
 1-107 2.64e-03

two-component response regulator DpiA; Provisional


Pssm-ID: 182208 [Multi-domain]  Cd Length: 225  Bit Score: 37.69  E-value: 2.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   1 MNTPVKLLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGE-RFPEI 79
Cdd:PRK10046    1 MTAPLTLLIVEDETPLAEMHAEYIRHIPGFSQILLAGNLAQARMMIERFKPGLILLDNYLPDGRGINLLHELVQaHYPGD 80

                          90       100
                  ....*....|....*....|....*...
gi 1942334314  80 AVLVLSMHDnLEYVRQVMRAGARGYVLK 107
Cdd:PRK10046   81 VVFTTAASD-METVSEAVRCGVFDYLIK 107
REC_OmpR_PmrA-like cd17624
phosphoacceptor receiver (REC) domain of PmrA-like OmpR family response regulators; This ...
 7-122 2.72e-03

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: 36.31  E-value: 2.72e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   7 LLLVDDHPLVRDGVRVRLE----AVPHFAVVGEAGEAAGALeaartlSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVL 82
Cdd:cd17624     1 ILLVEDDALLGDGLKTGLRkagyAVDWVRTGAEAEAALASG------PYDLVILDLGLPDGDGLDLLRRWRRQGQSLPVL 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1942334314  83 VLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVL 122
Cdd:cd17624    75 ILTARDGVDDRVAGLDAGADDYLVKPFALEELLARLRALL 114
PRK00742 PRK00742
chemotaxis-specific protein-glutamate methyltransferase CheB;
4-151 2.87e-03

chemotaxis-specific protein-glutamate methyltransferase CheB;


Pssm-ID: 234828 [Multi-domain]  Cd Length: 354  Bit Score: 37.82  E-value: 2.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   4 PVKLLLVDDHPLVRDGVRVRLEAVPHFAVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLV 83
Cdd:PRK00742    3 KIRVLVVDDSAFMRRLISEILNSDPDIEVVGTAPDGLEAREKIKKLNPDVITLDVEMPVMDGLDALEKIMRLRPTPVVMV 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1942334314  84 LSM-HDNLEYVRQVMRAGARGYVLK---------DAPASELVEAIDAVLAGRPFYSAQLAMRMAEQAVAPIPAEALTP 151
Cdd:PRK00742   83 SSLtERGAEITLRALELGAVDFVTKpflgislgmDEYKEELAEKVRAAARARVRALPPRAAAAARAAAAAPAALAAAP 160
PRK10430 PRK10430
two-component system response regulator DcuR;
5-129 3.02e-03

two-component system response regulator DcuR;


Pssm-ID: 182454 [Multi-domain]  Cd Length: 239  Bit Score: 37.40  E-value: 3.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   5 VKLLLVDDHPLVRDGVRVRLEAVPHFA--VVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVL 82
Cdd:PRK10430    2 INVLIVDDDAMVAELNRRYVAQIPGFQccGTASTLEQAKEIIFNSDTPIDLILLDIYMQQENGLDLLPVLHEAGCKSDVI 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1942334314  83 VLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDA------VLAGRPFYS 129
Cdd:PRK10430   82 VISSAADAATIKDSLHYGVVDYLIKPFQASRFEEALTGwrqkkmALEKHQYYD 134
REC_OmpR_MtrA-like cd17626
phosphoacceptor receiver (REC) domain of MtrA-like OmpR family response regulators; MtrA is ...
 47-122 3.08e-03

phosphoacceptor receiver (REC) domain of MtrA-like OmpR family response regulators; MtrA is part of MtrA/MtrB (or MtrAB), a highly conserved two-component system (TCS) implicated in the regulation of cell division in the actinobacteria. In unicellular Mycobacterium tuberculosis, MtrAB coordinates DNA replication with cell division and regulates the transcription of resuscitation-promoting factor B. In filamentous Streptomyces venezuelae, it links antibiotic production to sporulation. MtrA belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381141 [Multi-domain]  Cd Length: 115  Bit Score: 36.29  E-value: 3.08e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1942334314  47 RTLSPDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMHDNLEYVRQvMRAGARGYVLKDAPASELVEAIDAVL 122
Cdd:cd17626    41 REVRPDLVLLDLMLPGIDGIEVCRQIRAESGVPIVMLTAKSDTVDVVLG-LESGADDYVAKPFKPKELVARIRARL 115
REC_typeB_ARR-like cd17584
phosphoacceptor receiver (REC) domain of type B Arabidopsis response regulators (ARRs) and ...
 52-107 3.24e-03

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


Pssm-ID: 381121 [Multi-domain]  Cd Length: 115  Bit Score: 36.07  E-value: 3.24e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1942334314  52 DLVLMDIGMRGMNGIALTEQFGERFpEIAVLVLSMHDNLEYVRQVMRAGARGYVLK 107
Cdd:cd17584    46 DLVITDVHMPDMDGFEFLELIRLEM-DLPVIMMSADGSTSTVMKGLAHGACDYLLK 100
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 147-183 3.34e-03

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 34.74  E-value: 3.34e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1942334314 147 EALTPRERDILDG-VAQGWSNKRIADELGLSVRTVESH 183
Cdd:pfam08281   9 EELPPRQREVFLLrYLEGLSYAEIAELLGISEGTVKSR 46
REC_OmpR_PhoB cd17618
phosphoacceptor receiver (REC) domain of PhoB response regulator from the OmpR family; The ...
 6-122 4.71e-03

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


Pssm-ID: 381133 [Multi-domain]  Cd Length: 118  Bit Score: 35.69  E-value: 4.71e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314   6 KLLLVDDHPLVRDGVRVRLEAVPHfaVVGEAGEAAGALEAARTLSPDLVLMDIGMRGMNGIALTEQF--GERFPEIAVLV 83
Cdd:cd17618     2 TILIVEDEPAIREMIAFNLERAGF--DVVEAEDAESAVNLIVEPRPDLILLDWMLPGGSGIQFIRRLkrDEMTRDIPIIM 79

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1942334314  84 LSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVL 122
Cdd:cd17618    80 LTARGEEEDKVRGLEAGADDYITKPFSPRELVARIKAVL 118
PRK15347 PRK15347
two component system sensor kinase;
52-205 5.29e-03

two component system sensor kinase;


Pssm-ID: 237951 [Multi-domain]  Cd Length: 921  Bit Score: 37.31  E-value: 5.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  52 DLVLMDIGMRGMNGIALTEQFGE----RFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDavlagrpf 127
Cdd:PRK15347  736 DLVLMDIRMPGLDGLETTQLWRDdpnnLDPDCMIVALTANAAPEEIHRCKKAGMNHYLTKPVTLAQLARALE-------- 807

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314 128 YSA--QLAMRMAEQAVAPIPAEALTPRERDILDGVAQgwSNKRIADELGLSVRTVE--SHRL-SLKRKLGIEGQAELVKF 202
Cdd:PRK15347  808 LAAeyQLLRGIELSPQDSSCSPLLDTDDMALNSKLYQ--SLLLLLAQIEQAVENQEvlSQLLhTLKGCAGQAGLTELQCA 885


                  ...
gi 1942334314 203 AVE 205
Cdd:PRK15347  886 VID 888
REC_OmpR_DrrD-like cd17625
phosphoacceptor receiver (REC) domain of DrrD-like OmpR family response regulators; DrrD is a ...
 52-122 5.63e-03

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: 35.27  E-value: 5.63e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1942334314  52 DLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMHDNLEYVRQVMRAGARGYVLKDAPASELVEAIDAVL 122
Cdd:cd17625    43 DLIILDIMLPGMDGLEVLKSLREEGIETPVLLLTALDAVEDRVKGLDLGADDYLPKPFSLAELLARIRALL 113
PRK10701 PRK10701
DNA-binding transcriptional regulator RstA; Provisional
 51-151 7.46e-03

DNA-binding transcriptional regulator RstA; Provisional


Pssm-ID: 236738 [Multi-domain]  Cd Length: 240  Bit Score: 36.15  E-value: 7.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942334314  51 PDLVLMDIGMRGMNGIALTEQFGERFPEIAVLVLSMHDNLEYVRQvMRAGARGYVLKDAPAselveaidAVLAGRpfYSA 130
Cdd:PRK10701   46 PDLVLLDIMLPGKDGMTICRDLRPKWQGPIVLLTSLDSDMNHILA-LEMGACDYILKTTPP--------AVLLAR--LRL 114

                          90       100
                  ....*....|....*....|.
gi 1942334314 131 QLAMRMAEQAVAPIPAEALTP 151
Cdd:PRK10701  115 HLRQNEQATQTKGLQETSLTP 135
 
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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