NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|763417343|ref|WP_044273267|]
View 

MULTISPECIES: response regulator transcription factor [Pseudomonas]

Protein Classification

response regulator transcription factor( domain architecture ID 11450879)

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

CATH:  1.10.10.10
Gene Ontology:  GO:0000160|GO:0006355|GO:0003677
PubMed:  10966457
SCOP:  3001179

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK10360 super family cl32505
transcriptional regulator UhpA;
4-211 1.10e-29

transcriptional regulator UhpA;


The actual alignment was detected with superfamily member PRK10360:

Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 109.30  E-value: 1.10e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   4 VRIALLDDHAVVRHGLANTLAAEANFDVVGIYEKSRDLLAGLvSAPADLLLLDFSLSPDeMDGVSLIRALrvkfPS-CQI 82
Cdd:PRK10360   2 ITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGL-PGRGVQVCICDISMPD-ISGLELLSQL----PKgMAT 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  83 LVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVVSGAVYLSTDMTYRLAetvtsETRKDPseasdalvqaeLT 162
Cdd:PRK10360  76 IMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLA-----SGRQDP-----------LT 139

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 763417343 163 SREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSNNEL 211
Cdd:PRK10360 140 KRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVEL 188
 
Name Accession Description Interval E-value
PRK10360 PRK10360
transcriptional regulator UhpA;
4-211 1.10e-29

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 109.30  E-value: 1.10e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   4 VRIALLDDHAVVRHGLANTLAAEANFDVVGIYEKSRDLLAGLvSAPADLLLLDFSLSPDeMDGVSLIRALrvkfPS-CQI 82
Cdd:PRK10360   2 ITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGL-PGRGVQVCICDISMPD-ISGLELLSQL----PKgMAT 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  83 LVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVVSGAVYLSTDMTYRLAetvtsETRKDPseasdalvqaeLT 162
Cdd:PRK10360  76 IMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLA-----SGRQDP-----------LT 139

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 763417343 163 SREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSNNEL 211
Cdd:PRK10360 140 KRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVEL 188
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 6-122 3.87e-22

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: 87.18  E-value: 3.87e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   6 IALLDDHAVVRHGLANTLAAEANFDVVGIYEKSRDLLAGLVSAPadlllldfslsPD---------EMDGVSLIRALRVK 76
Cdd:cd17535    1 VLIVDDHPLVREGLRRLLESEPDIEVVGEAADGEEALALLRELR-----------PDvvlmdlsmpGMDGIEALRRLRRR 69

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 763417343  77 FPSCQILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKV 122
Cdd:cd17535   70 YPDLKVIVLTAHDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAV 115
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 159-214 2.74e-14

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 64.86  E-value: 2.74e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 763417343   159 AELTSREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSNNELFKL 214
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 3-214 6.12e-14

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: 66.07  E-value: 6.12e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   3 PVRIALLDDHAVVRHGLANTLAAEANFDVVGIYEKSRDLLAGLVSAPadlllldfslsPD---------EMDGVSLIRAL 73
Cdd:COG2197    1 MIRVLIVDDHPLVREGLRALLEAEPDIEVVGEAADGEEALELLEELR-----------PDvvlldirmpGMDGLEALRRL 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  74 rvkfpscqilvlsahhdpatvalamrvgargfvgkgedmtqvvrairkvvsgavylstdmtyrlaetvtsetrkdpseas 153
Cdd:COG2197      --------------------------------------------------------------------------------

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 763417343 154 dalvqaeLTSREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSNNELFKL 214
Cdd:COG2197   70 -------LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLL 123
GerE pfam00196
Bacterial regulatory proteins, luxR family;
161-211 6.54e-09

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 50.66  E-value: 6.54e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 763417343  161 LTSREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSNNEL 211
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVEL 53
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 114-203 1.55e-07

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: 49.27  E-value: 1.55e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  114 QVVRAIRKVVSGAVYLSTDMTyRLAETVTSETRKDPSEASDALVQA--ELTSREQEVIR-CYLAGMTVSEIAEKFNRSIK 190
Cdd:TIGR02937  63 LILDYLRRKRRLRRELDLLEE-LLDSDPSPEEELEQEEEREALREAleKLPEREREVLVlRYLEGLSYKEIAEILGISVG 141

                          90
                  ....*....|...
gi 763417343  191 TISTQKTSAFRKL 203
Cdd:TIGR02937 142 TVKRRLKRARKKL 154
 
Name Accession Description Interval E-value
PRK10360 PRK10360
transcriptional regulator UhpA;
4-211 1.10e-29

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 109.30  E-value: 1.10e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   4 VRIALLDDHAVVRHGLANTLAAEANFDVVGIYEKSRDLLAGLvSAPADLLLLDFSLSPDeMDGVSLIRALrvkfPS-CQI 82
Cdd:PRK10360   2 ITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGL-PGRGVQVCICDISMPD-ISGLELLSQL----PKgMAT 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  83 LVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVVSGAVYLSTDMTYRLAetvtsETRKDPseasdalvqaeLT 162
Cdd:PRK10360  76 IMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLA-----SGRQDP-----------LT 139

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 763417343 163 SREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSNNEL 211
Cdd:PRK10360 140 KRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVEL 188
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 1-215 1.04e-25

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 99.52  E-value: 1.04e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   1 MKPVRIALLDDHAVVRHGLANTLAAEANFDVVGIYEKSRDLLAGLVSAPADLLLLDFSLSPDEM-DGVSLIRALRVKFPS 79
Cdd:PRK10840   1 MNNMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKYgDGITLIKYIKRHFPS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  80 CQILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVVSGAVYLSTDMTyRLAETVTSETRKDPSeasdalvqa 159
Cdd:PRK10840  81 LSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVS-RLLEKISAGGYGDKR--------- 150

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 763417343 160 eLTSREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVtsNNELFKLN 215
Cdd:PRK10840 151 -LSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGV--ENDIALLN 203
PRK15369 PRK15369
two component system response regulator;
1-211 1.90e-24

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 95.92  E-value: 1.90e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   1 MKPVRIALLDDHAVVRHGLANTLAAEANFDVVG-------IYEKSRDLLAGLV----SAPAdlllldfslspdeMDGVSL 69
Cdd:PRK15369   1 MKNYKILLVDDHELIINGIKNMLAPYPRYKIVGqvdngleVYNACRQLEPDIVildlGLPG-------------MNGLDV 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  70 IRALRVKFPSCQILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVVSGAVYLSTDMTYRLAETVTSETRKDP 149
Cdd:PRK15369  68 IPQLHQRWPAMNILVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGKRYIDPALNREAILALLNADDTNP 147

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 763417343 150 SeasdalvqaELTSREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSNNEL 211
Cdd:PRK15369 148 P---------LLTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAEL 200
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 6-122 3.87e-22

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: 87.18  E-value: 3.87e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   6 IALLDDHAVVRHGLANTLAAEANFDVVGIYEKSRDLLAGLVSAPadlllldfslsPD---------EMDGVSLIRALRVK 76
Cdd:cd17535    1 VLIVDDHPLVREGLRRLLESEPDIEVVGEAADGEEALALLRELR-----------PDvvlmdlsmpGMDGIEALRRLRRR 69

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 763417343  77 FPSCQILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKV 122
Cdd:cd17535   70 YPDLKVIVLTAHDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAV 115
PRK09483 PRK09483
response regulator; Provisional
 8-214 6.94e-17

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 75.91  E-value: 6.94e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   8 LLDDHAVVRHGLANTLAAEANFDVVGIYEKSRDLLAGLVSAPADLLLLDFslspdEMDGVSLIRALR--VKF-PSCQILV 84
Cdd:PRK09483   6 LVDDHELVRAGIRRILEDIKGIKVVGEACCGEDAVKWCRTNAVDVVLMDM-----NMPGIGGLEATRkiLRYtPDVKIIM 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  85 LSAHHD---PATValaMRVGARGFVGKGEDMTQVVRAIRKVVSGAVYLSTDMTYRLAETVTSETRKDPSEAsdalvqaeL 161
Cdd:PRK09483  81 LTVHTEnplPAKV---MQAGAAGYLSKGAAPQEVVSAIRSVHSGQRYIASDIAQQMALSQIEPATENPFAS--------L 149

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 763417343 162 TSREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSNNELFKL 214
Cdd:PRK09483 150 SERELQIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHL 202
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
1-216 1.01e-16

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 75.30  E-value: 1.01e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   1 MKPVRIALLDDHAVVRHGLANTLAAEANFDVVGIYEKSRDLLAGLVSAPADLLLLDFSLSpdEMDGVSLIRALRVKFPSC 80
Cdd:PRK09935   1 MKPASVIIMDTHPIIRMSIEVLLQKNSELQIVLKTDDYRITIDYLRTRPVDLIIMDIDLP--GTDGFTFLKRIKQIQSTV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  81 QILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVVSGAVYLSTdmtyrlaETVT--SETRKDPSEASDALvq 158
Cdd:PRK09935  79 KVLFLSSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMILSGYTFFPS-------ETLNyiKSNKCSTNSSTDTV-- 149

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 763417343 159 aeLTSREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSNNELFKLNK 216
Cdd:PRK09935 150 --LSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELIDYAK 205
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 2-210 5.03e-15

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 70.83  E-value: 5.03e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   2 KPVRIALLDDHAVVRHGLANTLAAEANFDVVGiyeKSRDLLAGLVSApadlllldFSLSPD---------EMDGVSLIRA 72
Cdd:PRK10651   5 EPATILLIDDHPMLRTGVKQLISMAPDITVVG---EASNGEQGIELA--------ESLDPDlilldlnmpGMNGLETLDK 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  73 LRVKFPSCQILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVVSGAVYLSTDMTYRLAETVTSETRkdPSEA 152
Cdd:PRK10651  74 LREKSLSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQAAAGEMVLSEALTPVLAASLRANRA--TTER 151

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 763417343 153 SDalvqAELTSREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSNNE 210
Cdd:PRK10651 152 DV----NQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVE 205
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 159-214 2.74e-14

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 64.86  E-value: 2.74e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 763417343   159 AELTSREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSNNELFKL 214
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 161-214 4.13e-14

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: 64.48  E-value: 4.13e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 763417343 161 LTSREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSNNELFKL 214
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAY 54
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 3-214 6.12e-14

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: 66.07  E-value: 6.12e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   3 PVRIALLDDHAVVRHGLANTLAAEANFDVVGIYEKSRDLLAGLVSAPadlllldfslsPD---------EMDGVSLIRAL 73
Cdd:COG2197    1 MIRVLIVDDHPLVREGLRALLEAEPDIEVVGEAADGEEALELLEELR-----------PDvvlldirmpGMDGLEALRRL 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  74 rvkfpscqilvlsahhdpatvalamrvgargfvgkgedmtqvvrairkvvsgavylstdmtyrlaetvtsetrkdpseas 153
Cdd:COG2197      --------------------------------------------------------------------------------

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 763417343 154 dalvqaeLTSREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSNNELFKL 214
Cdd:COG2197   70 -------LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLL 123
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
8-217 8.46e-14

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 67.23  E-value: 8.46e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   8 LLDDHAVVRHGLANTLaaeanfdvvgiyEKSRDLLAGLVSAPADLLLLDFSLSPD---------EMDGVSLIRALRVKFP 78
Cdd:PRK09958   5 IIDDHPLAIAAIRNLL------------IKNDIEILAELTEGGSAVQRVETLKPDiviidvdipGVNGIQVLETLRKRQY 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  79 SCQILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVVSGAVYLStdmtYRLAETVTSETrkdpseaSDALVQ 158
Cdd:PRK09958  73 SGIIIIVSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGYCYFP----FSLNRFVGSLT-------SDQQKL 141

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 763417343 159 AELTSREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSNNELFKL---NKI 217
Cdd:PRK09958 142 DSLSKQEISVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYTFaqrNKI 203
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 6-214 9.92e-12

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


Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 61.65  E-value: 9.92e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   6 IALLDDHAVVRHGLANTLAAeANFDVVGiYEKSRDLLAGLvsapadlllldFSLSP---------DEMDGVSLIRALRVK 76
Cdd:COG4566    2 VYIVDDDEAVRDSLAFLLES-AGLRVET-FASAEAFLAAL-----------DPDRPgcllldvrmPGMSGLELQEELAAR 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  77 FPSCQILVLSAHHD-PATVAlAMRVGARGFVGKGEDMTQVVRAIRKVvsgavyLSTDMTYRlaetvtsETRKDPSEASDA 155
Cdd:COG4566   69 GSPLPVIFLTGHGDvPMAVR-AMKAGAVDFLEKPFDDQALLDAVRRA------LARDRARR-------AERARRAELRAR 134

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 763417343 156 LvqAELTSREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSNNELFKL 214
Cdd:COG4566  135 L--ASLTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARSLAELVRL 191
YesN COG4753
Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding ...
 5-108 5.63e-11

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: 57.48  E-value: 5.63e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   5 RIALLDDHAVVRHGLANTLAAEANFDVVGIYEKSRDLLAglvsapadlllLDFSLSPD---------EMDGVSLIRALRV 75
Cdd:COG4753    1 KVLIVDDEPLIREGLKRILEWEAGFEVVGEAENGEEALE-----------LLEEHKPDlvitdinmpGMDGLELLEAIRE 69

                         90       100       110
                 ....*....|....*....|....*....|...
gi 763417343  76 KFPSCQILVLSAHHDPATVALAMRVGARGFVGK 108
Cdd:COG4753   70 LDPDTKIIILSGYSDFEYAQEAIKLGADDYLLK 102
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
69-214 9.48e-11

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 59.00  E-value: 9.48e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  69 LIRALRVKFPSCQILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVVSGAVYLSTDMTYRLAETVTSETRKD 148
Cdd:COG2771   36 LALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLALLALLAALLARLAALLLALALAALLL 115

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 763417343 149 PSEASDALVQAELTSREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSNNELFKL 214
Cdd:COG2771  116 AALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVAL 181
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
3-207 1.26e-10

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 58.71  E-value: 1.26e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   3 PVRIALLDDHAVVRHGLANTLAAEANFDVVGiyeksrdllagLVSAPADLLLLDFSLSPD---------EMDGVSLIRAL 73
Cdd:PRK10403   6 PFQVLIVDDHPLMRRGVRQLLELDPGFEVVA-----------EAGDGASAIDLANRLDPDvilldlnmkGMSGLDTLNAL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  74 RVKFPSCQILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVVSGAVYLSTDMTYRLAETVTSETRKDPSeas 153
Cdd:PRK10403  75 RRDGVTAQIIILTVSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKGSKVFSERVNQYLREREMFGAEEDPF--- 151

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 763417343 154 dalvqAELTSREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTS 207
Cdd:PRK10403 152 -----SVLTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRS 200
CitB COG4565
DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal ...
 1-121 4.88e-10

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


Pssm-ID: 443622 [Multi-domain]  Cd Length: 138  Bit Score: 55.75  E-value: 4.88e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   1 MKPVRIALLDDHAVVRHGLANTLAAEANFDVVGIYEKSRDLLAGLvsapadlllldFSLSPD---------EMDGVSLIR 71
Cdd:COG4565    1 MKMIRVLIVEDDPMVAELLRRYLERLPGFEVVGVASSGEEALALL-----------AEHRPDlilldiylpDGDGLELLR 69

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 763417343  72 ALRVKFPSCQILVLSAHHDPATVALAMRVGARGFVGK---GEDMTQVVRAIRK 121
Cdd:COG4565   70 ELRARGPDVDVIVITAARDPETVREALRAGVVDYLIKpftFERLREALERYLE 122
GerE pfam00196
Bacterial regulatory proteins, luxR family;
161-211 6.54e-09

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 50.66  E-value: 6.54e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 763417343  161 LTSREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSNNEL 211
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVEL 53
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 2-123 7.25e-09

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: 54.97  E-value: 7.25e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   2 KPVRIALLDDHAVVRHGLANTLAaEANFDVVgiyeksrdllagLVSAPADLLLLDFSLSPD---------EMDGVSLIRA 72
Cdd:COG2204    1 SMARILVVDDDPDIRRLLKELLE-RAGYEVE------------TAASGEEALALLREEPPDlvlldlrmpGMDGLELLRE 67

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 763417343  73 LRVKFPSCQILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVV 123
Cdd:COG2204   68 LRALDPDLPVILLTGYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERAL 118
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 6-120 1.81e-08

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: 50.61  E-value: 1.81e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343    6 IALLDDHAVVRHGLANTLAAEANfdVVGIYEKSRDLLAGLvsapadlllldFSLSPD---------EMDGVSLIRALRVK 76
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLEKEGY--VVAEADDGKEALELL-----------KEERPDlilldinmpGMDGLELLKRIRRR 67

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 763417343   77 FPSCQILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIR 120
Cdd:pfam00072  68 DPTTPVIILTAHGDEDDAVEALEAGADDFLSKPFDPDELLAAIR 111
CheY COG0784
CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator ...
 1-126 6.55e-08

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: 49.46  E-value: 6.55e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   1 MKPVRIALLDDHAVVRHGLANTLAaEANFDVVgIYEKSRDLLAGLVSAPadlllldfslsPD---------EMDGVSLIR 71
Cdd:COG0784    3 LGGKRILVVDDNPDNRELLRRLLE-RLGYEVT-TAEDGAEALELLRAGP-----------PDlilldinmpGMDGLELLR 69

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 763417343  72 ALR--VKFPSCQILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVVSGA 126
Cdd:COG0784   70 RIRalPRLPDIPIIALTAYADEEDRERALEAGADDYLTKPVDPEELLEALRRLLARA 126
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 114-203 1.55e-07

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: 49.27  E-value: 1.55e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  114 QVVRAIRKVVSGAVYLSTDMTyRLAETVTSETRKDPSEASDALVQA--ELTSREQEVIR-CYLAGMTVSEIAEKFNRSIK 190
Cdd:TIGR02937  63 LILDYLRRKRRLRRELDLLEE-LLDSDPSPEEELEQEEEREALREAleKLPEREREVLVlRYLEGLSYKEIAEILGISVG 141

                          90
                  ....*....|...
gi 763417343  191 TISTQKTSAFRKL 203
Cdd:TIGR02937 142 TVKRRLKRARKKL 154
REC_YesN-like cd17536
phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response ...
 10-123 1.76e-07

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: 48.10  E-value: 1.76e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  10 DDHAVVRHGLANTLA-AEANFDVVGIYEKSRDLLAGLvsapadlllldFSLSPD---------EMDGVSLIRALRVKFPS 79
Cdd:cd17536    5 DDEPLIREGLKKLIDwEELGFEVVGEAENGEEALELI-----------EEHKPDivitdirmpGMDGLELIEKIRELYPD 73

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 763417343  80 CQILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVV 123
Cdd:cd17536   74 IKIIILSGYDDFEYAQKAIRLGVVDYLLKPVDEEELEEALEKAK 117
fixJ PRK09390
response regulator FixJ; Provisional
 10-214 1.99e-07

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 49.62  E-value: 1.99e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  10 DDHAVVRHGLANTLAAeANFDVVgIYEKSRDLLAGLVSAPADLLLLDFSLsPDeMDGVSLIR---ALRVKFPscqILVLS 86
Cdd:PRK09390  10 DDDEAMRDSLAFLLDS-AGFEVR-LFESAQAFLDALPGLRFGCVVTDVRM-PG-IDGIELLRrlkARGSPLP---VIVMT 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  87 AHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVVSGAvylstdmtyrlaetvtSETRKDPSEASDALVQ-AELTSRE 165
Cdd:PRK09390  83 GHGDVPLAVEAMKLGAVDFIEKPFEDERLIGAIERALAQA----------------PEAAKSEAVAADIRARiASLSERE 146

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 763417343 166 QEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSNNELFKL 214
Cdd:PRK09390 147 RQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSLSELVRM 195
REC cd00156
phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ...
 8-108 2.36e-07

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: 47.22  E-value: 2.36e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   8 LLDDHAVVRHGLANTLaaEANFDVVGIYEKSRDLLAGLVSAPadlllldfslsPD---------EMDGVSLIRALRVKFP 78
Cdd:cd00156    2 IVDDDPAIRELLKSLL--EREGYEVDTAADGEEALELLREER-----------PDlvlldlmmpGMDGLELLRKLRELPP 68

                         90       100       110
                 ....*....|....*....|....*....|
gi 763417343  79 SCQILVLSAHHDPATVALAMRVGARGFVGK 108
Cdd:cd00156   69 DIPVIVLTAKADEEDAVRALELGADDYLVK 98
REC_CheY4-like cd17562
phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY4 and similar CheY ...
 5-123 5.42e-07

phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY4 and similar CheY family proteins; CheY family chemotaxis response regulators (RRs) comprise about 17% of bacterial RRs and almost half of all RRs in archaea. This subfamily contains Vibrio cholerae CheY4 and similar CheY family RRs. CheY proteins control bacterial motility and participate in signaling phosphorelays and in protein-protein interactions. CheY RRs contain only the REC domain with no output/effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381110 [Multi-domain]  Cd Length: 118  Bit Score: 46.91  E-value: 5.42e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   5 RIALLDDHAVVRHGLANTLAaEANFDVVgiyeKSRDLLAGL--VSAPADLLLLDFSLSPDeMDGVSLIRALR--VKFPSC 80
Cdd:cd17562    2 KILAVDDSASIRQMVSFTLR-GAGYEVV----EAADGRDALskAQSKKFDLIITDQNMPN-MDGIELIKELRklPAYKFT 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 763417343  81 QILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVV 123
Cdd:cd17562   76 PILMLTTESSDEKKQEGKAAGATGWLVKPFDPEQLLEVVKKVL 118
OmpR COG0745
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...
 5-171 1.43e-06

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


Pssm-ID: 440508 [Multi-domain]  Cd Length: 204  Bit Score: 47.26  E-value: 1.43e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   5 RIALLDDHAVVRHGLANTLAAEaNFDVVGiyekSRDLLAGLVSAPADLllldfslsPD---------EMDGVSLIRALRV 75
Cdd:COG0745    3 RILVVEDDPDIRELLADALERE-GYEVDT----AADGEEALELLEEER--------PDlilldlmlpGMDGLEVCRRLRA 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343  76 KFPSCQILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVVSgavyLSTDMTYRLAETVTSETRkdpsEASDA 155
Cdd:COG0745   70 RPSDIPIIMLTARDDEEDRVRGLEAGADDYLTKPFDPEELLARIRALLR----RRAAEVLRVGDLLDLAAR----EVTRD 141

                        170
                 ....*....|....*.
gi 763417343 156 LVQAELTSREQEVIRC 171
Cdd:COG0745  142 GEPVELTPKEFRLLEL 157
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 159-203 1.71e-06

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


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 43.57  E-value: 1.71e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 763417343  159 AELTSREQEVIR-CYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKL 203
Cdd:pfam04545   3 ASLPPRERQVLVlRYGEGLTLEEIGERLGISRERVRQIEKRALRKL 48
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 114-203 1.92e-06

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: 46.53  E-value: 1.92e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343 114 QVVRAIRKVVSGAVYLSTDMTYRLAETVTSETRKDPSEASDALVQA--ELTSREQEVIR-CYLAGMTVSEIAEKFNRSIK 190
Cdd:COG1595   79 LAIDHLRKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLAAleRLPPRQREVLVlRYLEGLSYAEIAEILGISEG 158

                         90
                 ....*....|...
gi 763417343 191 TISTQKTSAFRKL 203
Cdd:COG1595  159 TVKSRLSRARKKL 171
AmiR COG3707
Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding ...
 1-124 1.99e-06

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: 46.49  E-value: 1.99e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   1 MKPVRIALLDDHAVVRHGLANTLaAEANFDVVGIYEKSRDLLAgLVSAPADLLLLDFSLSPDeMDGVSLIRALRVKfPSC 80
Cdd:COG3707    1 MRGLRVLVVDDEPLRRADLREGL-REAGYEVVAEAADGEDAVE-LVRELKPDLVIVDIDMPD-RDGLEAARQISEE-RPA 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 763417343  81 QILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVVS 124
Cdd:COG3707   77 PVILLTAYSDPELIERALEAGVSAYLVKPLDPEDLLPALELALA 120
PRK11475 PRK11475
DNA-binding transcriptional activator BglJ; Provisional
 161-208 5.52e-06

DNA-binding transcriptional activator BglJ; Provisional


Pssm-ID: 236915 [Multi-domain]  Cd Length: 207  Bit Score: 45.51  E-value: 5.52e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 763417343 161 LTSREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSN 208
Cdd:PRK11475 135 LSPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVSSD 182
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 161-207 6.96e-06

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: 42.64  E-value: 6.96e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 763417343 161 LTSREQEVIRCYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTS 207
Cdd:COG5905   13 LTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRN 59
REC_CheY cd17542
phosphoacceptor receiver (REC) domain of chemotaxis protein CheY; The chemotaxis response ...
 63-123 1.41e-05

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: 43.04  E-value: 1.41e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 763417343  63 EMDGVSLIRALRVKFPSCQILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVV 123
Cdd:cd17542   57 EMDGIEALKEIKKIDPNAKVIMCSAMGQEEMVKEAIKAGAKDFIVKPFQPERVLEAVEKVL 117
PleD COG3706
Two-component response regulator, PleD family, consists of two REC domains and a diguanylate ...
 3-119 2.08e-05

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


Pssm-ID: 442920 [Multi-domain]  Cd Length: 179  Bit Score: 43.36  E-value: 2.08e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   3 PVRIALLDDHAVVRHGLANTLAaEANFDVVGIYeksrDLLAGLvsapadllLLDFSLSPD---------EMDGVSLIRAL 73
Cdd:COG3706    1 PARILVVDDDPTNRKLLRRLLE-AAGYEVVEAA----DGEEAL--------ELLQEHRPDlilldlempDMDGLELCRRL 67

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 763417343  74 RvKFPSCQ---ILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAI 119
Cdd:COG3706   68 R-ADPRTAdipIIFLTALDDEEDRARALEAGADDYLTKPFDPEELLARV 115
REC_RpfG-like cd17551
phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator ...
 63-108 5.11e-05

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


Pssm-ID: 381103 [Multi-domain]  Cd Length: 118  Bit Score: 41.27  E-value: 5.11e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 763417343  63 EMDGVSLIRALRvKFPSCQ---ILVLSAHHDPATVALAMRVGARGFVGK 108
Cdd:cd17551   57 GMDGLEFIRRLR-ALPGLEdvpIVMITADTDREVRLRALEAGATDFLTK 104
REC_DesR-like cd19930
phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of ...
 6-123 7.81e-05

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: 40.72  E-value: 7.81e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   6 IALLDDHAVVRHGLANTLAAEANFDVVGIYEKSRDLLAgLVSAPADLLLLDFSLSPdEMDGVSLIRALRVKFPSCQILVL 85
Cdd:cd19930    1 VLIAEDQEMVRGALAALLELEDDLEVVAQASNGQEALR-LVLKHSPDVAILDIEMP-GRTGLEVAAELREELPDTKVLIV 78

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 763417343  86 SAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVV 123
Cdd:cd19930   79 TTFGRPGYFRRALAAGVDGYVLKDRPIEELADAIRTVH 116
REC_NarL cd19931
phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL); Nitrate ...
 6-124 1.79e-04

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: 39.64  E-value: 1.79e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   6 IALLDDHAVVRHGLANTLAAEANFDVVgiyeksrdllaGLVSAPADLLLLDFSLSPD---------EMDGVSLIRALRVK 76
Cdd:cd19931    1 VLLIDDHPLLRKGIKQLIELDPDFTVV-----------GEASSGEEGIELAERLDPDlilldlnmkGMSGLDTLKALREE 69

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 763417343  77 FPSCQILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVVS 124
Cdd:cd19931   70 GVSARIVILTVSDAEDDVVTALRAGADGYLLKDMEPEDLLEALKQAAS 117
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
136-211 3.70e-04

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 40.07  E-value: 3.70e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 763417343 136 RLAETVTSETRKDPSEASDALVQAELtsreqevircyLAGMTVSEIAEKFNRSIKTISTQKTSAFRKLGVTSNNEL 211
Cdd:COG2909  109 LLLRALALRALGDREEALAALRRRLL-----------AEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEA 173
RpfG COG3437
Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains ...
 2-124 4.70e-04

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: 40.15  E-value: 4.70e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   2 KPVRIALLDDHAVVRHGLANTLAaEANFDVVGIyEKSRDLLAGLVSAPADLLLLdfslspD----EMDGVSLIRALRvKF 77
Cdd:COG3437    5 QAPTVLIVDDDPENLELLRQLLR-TLGYDVVTA-ESGEEALELLLEAPPDLILL------DvrmpGMDGFELLRLLR-AD 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 763417343  78 PSCQ---ILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVVS 124
Cdd:COG3437   76 PSTRdipVIFLTALADPEDRERALEAGADDYLTKPFDPEELLARVRNALE 125
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
161-192 7.79e-04

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 39.12  E-value: 7.79e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 763417343 161 LTSREQEVIRCYLAGMTVSEIAEKFNRSIKTI 192
Cdd:PRK08295 156 LSELEKEVLELYLDGKSYQEIAEELNRHVKSI 187
REC_CheB-like cd17541
phosphoacceptor receiver (REC) domain of chemotaxis response regulator protein-glutamate ...
 4-108 9.95e-04

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: 37.76  E-value: 9.95e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   4 VRIALLDDHAVVRHGLANTLAAEANFDVVGIY---EKSRDLLAGLvsapadlllldfslSPD---------EMDGVSLIR 71
Cdd:cd17541    1 IRVLIVDDSAVMRKLLSRILESDPDIEVVGTArdgEEALEKIKEL--------------KPDvitldiempVMDGLEALR 66

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 763417343  72 ALRVKFPsCQILVLSAH--HDPATVALAMRVGARGFVGK 108
Cdd:cd17541   67 RIMAERP-TPVVMVSSLteEGAEITLEALELGAVDFIAK 104
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 151-203 1.27e-03

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


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 38.65  E-value: 1.27e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 763417343 151 EASDALVQA--ELTSREQEVIRC-YLAGMTVSEIAEKFNRSIKTISTQKTSAFRKL 203
Cdd:COG1191  175 ELREALAEAieQLPERERLVLSLyYFEELTLKEIAEVLGVSESRVSRLHKKALARL 230
COG4567 COG4567
DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains ...
 62-134 1.34e-03

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


Pssm-ID: 443624 [Multi-domain]  Cd Length: 177  Bit Score: 38.36  E-value: 1.34e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 763417343  62 DEMDGVSLIRALRVKFPSCQILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVVSGAVYLSTDMT 134
Cdd:COG4567   59 GDGSGLDLIEALRERDPDARIVVLTGYASIATAVEAIKLGADDYLAKPADADDLLAALERAEGDAPAPPENPM 131
REC_citrate_TCS cd19925
phosphoacceptor receiver (REC) domain of citrate family two-component system response ...
 4-102 1.68e-03

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


Pssm-ID: 381152 [Multi-domain]  Cd Length: 118  Bit Score: 37.22  E-value: 1.68e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 763417343   4 VRIALLDDHAVVRHGLANTLAAEANFDVVGIYEKSRDLLAgLVSAPADLLLLDFSLSPDEmDGVSLIRALRVKFPSCQIL 83
Cdd:cd19925    1 INVLIVEDDPMVAEIHRAYVEQVPGFTVIGTAGTGEEALK-LLKERQPDLILLDIYLPDG-NGLDLLRELRAAGHDVDVI 78

                         90
                 ....*....|....*....
gi 763417343  84 VLSAHHDPATVALAMRVGA 102
Cdd:cd19925   79 VVTAANDVETVREALRLGV 97
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 159-203 1.92e-03

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 35.51  E-value: 1.92e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 763417343  159 AELTSREQEVIR-CYLAGMTVSEIAEKFNRSIKTISTQKTSAFRKL 203
Cdd:pfam08281   9 EELPPRQREVFLlRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 159-203 2.30e-03

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


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 35.16  E-value: 2.30e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 763417343 159 AELTSREQEVIRC-YLAGMTVSEIAEKFNRSIKTISTQKTSAFRKL 203
Cdd:cd06171    9 DKLPEREREVILLrFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
HTH_28 pfam13518
Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is ...
 167-193 2.42e-03

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


Pssm-ID: 463908 [Multi-domain]  Cd Length: 52  Bit Score: 34.88  E-value: 2.42e-03
                          10        20
                  ....*....|....*....|....*..
gi 763417343  167 EVIRCYLAGMTVSEIAEKFNRSIKTIS 193
Cdd:pfam13518   4 KIVLLALEGESIKEAARLFGISRSTVY 30
REC_RegA-like cd17563
phosphoacceptor receiver (REC) domain of photosynthetic apparatus regulatory protein RegA; ...
 62-118 3.99e-03

phosphoacceptor receiver (REC) domain of photosynthetic apparatus regulatory protein RegA; Rhodobacter sphaeroides RegA, also called response regulator PrrA, is the DNA binding regulatory protein of a redox-responsive two-component regulatory system RegB/RegA that is involved in transactivating anaerobic expression of the photosynthetic apparatus. It contains a REC domain and a DNA-binding helix-turn-helix output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381111 [Multi-domain]  Cd Length: 112  Bit Score: 35.88  E-value: 3.99e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 763417343  62 DEMDGVSLIRALRVKFPSCQILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRA 118
Cdd:cd17563   55 GGDSGLDLIPPLRALQPDARIVVLTGYASIATAVEAIKLGADDYLAKPADADEILAA 111
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
161-193 4.02e-03

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


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 37.55  E-value: 4.02e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 763417343 161 LTSREQEVIRCYL-AGMTVSEIAEKFNRSIKTIS 193
Cdd:COG2826    7 LTLEEREEIEALLkAGLSVREIARRLGRSPSTIS 40
REC_NtrX-like cd17550
phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and ...
 63-123 7.73e-03

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


Pssm-ID: 381102 [Multi-domain]  Cd Length: 115  Bit Score: 35.17  E-value: 7.73e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 763417343  63 EMDGVSLIRALRVKFPSCQILVLSAHHDPATVALAMRVGARGFVGKGEDMTQVVRAIRKVV 123
Cdd:cd17550   54 DMDGLELLKEIKEKYPDLPVIMISGHGTIETAVKATKLGAYDFIEKPLSLDRLLLTIERAL 114
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH