Conserved Protein Domain Family
Sigma54_CBD

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pfam04963: Sigma54_CBD 
Sigma-54 factor, core binding domain
This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme. The centre of this domain contains a very weak similarity to a helix-turn-helix motif which may represent the other DNA binding domain.
Statistics
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PSSM-Id: 461501
Aligned: 412 rows
Threshold Bit Score: 116.396
Created: 22-Mar-2022
Updated: 17-Oct-2022
Structure
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Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
WP_012202606  148 ATELARSAESLTDHLHRQAlSl-RLG-EVDRAALRFLIENLNDDGYLEdpl-deLAQGLagddleeceelvhRFT----- 219 Delftia acidov...
WP_013133870   69 ieSLAIYNESLNDVISEQI-CapNFStPNSQKVAMEILCDINEEGYFEgdi-ekIAITC-------------NVYkeyve 133 Arcobacter nit...
WP_006655072   79 IEKFCIQEESLEEVLKSQI-VppLFPtKTSQAIAEKIIENLNEEGYFDgdk-ekIAKEC-------------QSNsleve 143 Helicobacter c...
Q7M7T2         76 IEALTIQEDSLYDILYEQI-AppLFPtATSQKIALKIIENLNEEGYFEgei-ekIALEC-------------ESSsesce 140 Wolinella succ...
jgi:Sdel_1022  78 IEALTLDKKSLFQTLYEQV-NppLFPtEKSQRIAYEIIENINAEGYFEadalveIAHTL-------------NVKeteve 143
WP_013890258   72 IEALSVYEKSLYESLHEQI-IppLFPtPLSMQIAHDILDNLNSEGYFEgdl-tqQAQSL-------------GVSpqeye 136 Helicobacter b...
P56143         69 LENFATASKSLFETLEAQI-IppLFPtETSQKIAMDIISGLNNEGYFEeni-eeRARIL-------------GVEsevye 133 Helicobacter p...
WP_002956175   79 FEQNYISEQSLYEVLESQI-DskLFPtSISQSIAFKILENINDEGYLDvav-aeLALEM-------------GVSegefe 143 Helicobacter c...
Q7VH93         78 FESIHISQQSLYEVLEEQI-DstLFPtEISRTIALKIVENLNDEGYLDtav-geIACEL-------------GLNeedve 142 Helicobacter h...
jgi:Saut_1084  79 IEALTIQHKSLYDVLDEQI-GapLFPtPISQEIASFVIANLDEQGYYDgdt-evFCQEH-------------DINiqnfe 143
WP_012202606  220 VALRLLQSLEPVGVGARDLAECLTLQLrdqladaeregsgsaededrqavlrtaldicaQPMD-LLARRD---LRKLASL 295 Delftia acidov...
WP_013133870  134 SIRQRFSLLEPSGIGSLNLSESFLFQL--------------------------------DACDkKIDDELynfIKKIIKD 181 Arcobacter nit...
WP_006655072  144 KIRKRFAYLDPAGIAAENLIESFYFQL--------------------------------ENMD--IADSVysvCLKLIGD 189 Helicobacter c...
Q7M7T2        141 KIRQRFSRLEPPGIGAKDVRESFLFQL--------------------------------DSSE--CDDELfslVRELIEE 186 Wolinella succ...
jgi:Sdel_1022 144 KIRQRFAYLEPLGVGAQDVKEAFLFQL--------------------------------QDLT--LENTLyemAEKLILN 189
WP_013890258  137 KVRQRFAYLDPPGIGACTLQESFLFQL--------------------------------NHHD-ELDTPTydlCAQIIQN 183 Helicobacter b...
P56143        134 KVRKRFSYLNPAGIGAKDVKESFLFQL--------------------------------ESRE-LDDNELyeeTRKIILN 180 Helicobacter p...
WP_002956175  144 RVRQRFAYLEPYGVGARDVLESFLFQL--------------------------------NNSD--LEGEGyelATKVIKD 189 Helicobacter c...
Q7VH93        143 RVRQRFAYLEPYGVGAKDVIESFLFQL--------------------------------SNTE--LEGESydlAACVIRD 188 Helicobacter h...
jgi:Saut_1084 144 KIRLRFLHVDPVGIGAKDLAESFLFQL--------------------------------DNAN--ISDKAyslAVEIIND 189
WP_012202606  296 CGA----REE-RLREALVLITRLEPRPGRRFaDVQR-QIVvPDVIVRP---------VRSGagrmdFSVQLNPDVMPKLR 360 Delftia acidov...
WP_013133870  182 ISHldkyAGHhRFDDAKEIIKYFNNPPAINY-MNDNvQII-PDFFVDIg--------ED-------INIKINHAYYPDLE 244 Arcobacter nit...
WP_006655072  190 LENhtkyKEDkNYTQAMRVISSFKNPPALDF-YQKEaAII-PDILVIQ---------ESNN-----IQVQINEKYYPSIE 253 Helicobacter c...
Q7M7T2        187 LEYhtryKNHpRYVEAMRLIRSFKNPPAIDF-FEKEpDII-PDLFVHD---------SSGQ-----IEVRLNDAYYPTIV 250 Wolinella succ...
jgi:Sdel_1022 190 FDViesfGKEpLFHEALNIIKRFHNPPAIDF-LEEEkEVV-PDIFIYT---------IEGA-----IEVRLNDTYYPEVI 253
WP_013890258  184 LEChkefSHLpSYAKAMQTITSFKNPPALDF-ADKIpPII-PDLLVLE---------EEGN-----IFVQLNEGYYPKVV 247 Helicobacter b...
P56143        181 LEKhhefSKDfYYEKALKILKSFKNPPAIEF-LEKEiEVI-PELFIVE---------VDNG-----IIVRLNDESYPTIS 244 Helicobacter p...
WP_002956175  190 LHNhskyKNHkDYNLVMKTIKSFKNPPAIEF-SPREaEII-PDIFIFErlksdslknTTYE-----LEVAINDAYYPKIV 262 Helicobacter c...
Q7VH93        189 LQNhskyKNHaAYNEVMKIIKSFRNPPAIEF-GAKEaEVI-PDIFIFErvktdalknTTYE-----LEVSINDVYYPKIL 261 Helicobacter h...
jgi:Saut_1084 190 IQNihaySKEeSFSEVMHVIATFKNPPNIEY-QEDSaQIV-PDLMIYFn--------DEQQ-----IEVKLNDAYYPIIN 254
WP_012202606  361 VHDIY 365 Delftia acidovorans
WP_013133870  245 VKDAf 249 Arcobacter nitrofigilis
WP_006655072  254 IETQk 258 Helicobacter canadensis
Q7M7T2        251 LDTar 255 Wolinella succinogenes
jgi:Sdel_1022 254 IDTeg 258
WP_013890258  248 IEEik 252 Helicobacter bizzozeronii
P56143        245 LEENR 249 Helicobacter pylori 26695
WP_002956175  263 IEEnl 267 Helicobacter cinaedi
Q7VH93        262 IEEki 266 Helicobacter hepaticus
jgi:Saut_1084 255 IDTSY 259
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