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: 398566
Aligned: 439 rows
Threshold Bit Score: 95.2091
Threshold Setting Gi: 644970564
Created: 20-May-2020
Updated: 7-Aug-2020
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  147 DATELAR--SAESLTDHLHRQALSL-RLG-EVDRAALRFLIENLNDDGYLEDP-LDELAQGLagddleeceelvhRFT-- 219 Delftia acidov...
CCY78729       66 siientAsnSKESLFEHLKSQISI--VFNnKKDIELAELISTFINENGYLTIS-SEEIADIL-------------NISak 129 Brachyspira sp...
WP_002956175   78 rFEQNYI--SEQSLYEVLESQI-DSkLFPtSISQSIAFKILENINDEGYLDVA-VAELALEM-------------GVSeg 140 Helicobacter c...
Q7VH93         77 RFESIHI--SQQSLYEVLEEQI-DStLFPtEISRTIALKIVENLNDEGYLDTA-VGEIACEL-------------GLNee 139 Helicobacter h...
WP_006655072   78 GIEKFCI--QEESLEEVLKSQI-VPpLFPtKTSQAIAEKIIENLNEEGYFDGD-KEKIAKEC-------------QSNsl 140 Helicobacter c...
Q7M7T2         75 KIEALTI--QEDSLYDILYEQI-APpLFPtATSQKIALKIIENLNEEGYFEGE-IEKIALEC-------------ESSse 137 Wolinella succ...
jgi:Saut_1084  78 QIEALTI--QHKSLYDVLDEQI-GApLFPtPISQEIASFVIANLDEQGYYDGD-TEVFCQEH-------------DINiq 140 Sulfurimonas a...
Q30RF5         78 QIEALTF--VKKSLYDVLDEQI-EApLFPtPISQKIASFVVCNLDENGYYEGD-SEEFCKNN-------------AITie 140 Sulfurimonas d...
jgi:Sdel_1022  77 TIEALTL--DKKSLFQTLYEQV-NPpLFPtEKSQRIAYEIIENINAEGYFEADaLVEIAHTL-------------NVKet 140 Sulfurospirill...
WP_013133870   68 fieSLAI--YNESLNDVISEQI-CApNFStPNSQKVAMEILCDINEEGYFEGD-IEKIAITC-------------NVYke 130 Arcobacter nit...
WP_012202606  220 ---VALRLLQSLEPVGVGARDLAECLTLQLrdqladaeregsgsaededrqavlrtALDICAQPMD-LLARRD---LRKL 292 Delftia acidov...
CCY78729      130 kadEIIKILKTLEPIGIAAKNISECLSTQLknkenid-------------knikniAINIVENYLN-ELSKKD---YKYI 192 Brachyspira sp...
WP_002956175  141 efeRVRQRFAYLEPYGVGARDVLESFLFQL--------------------------------NNSD--LEGEGyelATKV 186 Helicobacter c...
Q7VH93        140 dveRVRQRFAYLEPYGVGAKDVIESFLFQL--------------------------------SNTE--LEGESydlAACV 185 Helicobacter h...
WP_006655072  141 eveKIRKRFAYLDPAGIAAENLIESFYFQL--------------------------------ENMD--IADSVysvCLKL 186 Helicobacter c...
Q7M7T2        138 sceKIRQRFSRLEPPGIGAKDVRESFLFQL--------------------------------DSSE--CDDELfslVREL 183 Wolinella succ...
jgi:Saut_1084 141 nfeKIRLRFLHVDPVGIGAKDLAESFLFQL--------------------------------DNAN--ISDKAyslAVEI 186 Sulfurimonas a...
Q30RF5        141 efeKVRLRFAHVEPVGVCAKNLLESFLFQL--------------------------------DSSD--ISDKVyplAIKV 186 Sulfurimonas d...
jgi:Sdel_1022 141 eveKIRQRFAYLEPLGVGAQDVKEAFLFQL--------------------------------QDLT--LENTLyemAEKL 186 Sulfurospirill...
WP_013133870  131 yveSIRQRFSLLEPSGIGSLNLSESFLFQL--------------------------------DACDkKIDDELynfIKKI 178 Arcobacter nit...
WP_012202606  293 ASLCGA----REE-RLREALVLITRLEPRPGRRFaDVQR-QIVVPDVIVRP---------VRSGagrmdFSVQLNPDVMP 357 Delftia acidov...
CCY78729      193 SSKMNI----SEK-NILEALKLIQTLEPYPAREF-DTTTiKYIVPELFIFK---------ENNK-----WQVKTNETFIL 252 Brachyspira sp...
WP_002956175  187 IKDLHNhskyKNHkDYNLVMKTIKSFKNPPAIEF-SPREaEII-PDIFIFErlksdslknTTYE-----LEVAINDAYYP 259 Helicobacter c...
Q7VH93        186 IRDLQNhskyKNHaAYNEVMKIIKSFRNPPAIEF-GAKEaEVI-PDIFIFErvktdalknTTYE-----LEVSINDVYYP 258 Helicobacter h...
WP_006655072  187 IGDLENhtkyKEDkNYTQAMRVISSFKNPPALDF-YQKEaAII-PDILVIQ---------ESNN-----IQVQINEKYYP 250 Helicobacter c...
Q7M7T2        184 IEELEYhtryKNHpRYVEAMRLIRSFKNPPAIDF-FEKEpDII-PDLFVHD---------SSGQ-----IEVRLNDAYYP 247 Wolinella succ...
jgi:Saut_1084 187 INDIQNihaySKEeSFSEVMHVIATFKNPPNIEY-QEDSaQIV-PDLMIYFn--------DEQQ-----IEVKLNDAYYP 251 Sulfurimonas a...
Q30RF5        187 IKDLENiydySNEaGFSEVMRVLTTFKNPPAIEY-LEESaQVI-PDLMIFFn--------DNDS-----IEVKLNDAFYP 251 Sulfurimonas d...
jgi:Sdel_1022 187 ILNFDViesfGKEpLFHEALNIIKRFHNPPAIDF-LEEEkEVV-PDIFIYT---------IEGA-----IEVRLNDTYYP 250 Sulfurospirill...
WP_013133870  179 IKDISHldkyAGHhRFDDAKEIIKYFNNPPAINY-MNDNvQII-PDFFVDIg--------ED-------INIKINHAYYP 241 Arcobacter nit...
WP_012202606  358 KLRVHDIY 365 Delftia acidovorans
CCY78729      253 PLKINKKY 260 Brachyspira sp. CAG:700
WP_002956175  260 KIVIEEnl 267 Helicobacter cinaedi
Q7VH93        259 KILIEEki 266 Helicobacter hepaticus
WP_006655072  251 SIEIETQk 258 Helicobacter canadensis
Q7M7T2        248 TIVLDTar 255 Wolinella succinogenes
jgi:Saut_1084 252 IINIDTSY 259 Sulfurimonas autotrophica DSM 16294
Q30RF5        252 IINIDTSY 259 Sulfurimonas denitrificans DSM 1251
jgi:Sdel_1022 251 EVIIDTeg 258 Sulfurospirillum deleyianum DSM 6946
WP_013133870  242 DLEVKDAf 249 Arcobacter nitrofigilis
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