Conserved Protein Domain Family
RepB_primase

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pfam16793: RepB_primase 
RepB DNA-primase from phage plasmid
RepB_primase is a DNA-primase produced by P4-like phages. It is a zinc-independent primase unlike Pri-type primases. It takes up a dumbbell shaped consisting of an N-terminal catalytic domain separated by a long alpha-helix plus tether and a C-terminal helical-bundle domain. Primases are necessary for phage replication. RepBprime primases such as in this family recognize both ssiA and ssiB, ie only 1 single-stranded primase initiation site on each strand, independently of each other and then synthesize primers that are elongated by DNA polymerase III. The phage is thus replicated exclusively in leading strand mode.
Statistics
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PSSM-Id: 318902
View PSSM: pfam16793
Aligned: 12 rows
Threshold Bit Score: 153.05
Threshold Setting Gi: 504008724
Created: 29-Jul-2016
Updated: 4-Aug-2016
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:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219523944  23 PEDERVMVGYAEEATVQTDENGRKLNAG--W------W----------P--------VPWKEG--KYI-------Ns--- 64
gi 504599440   5 ETVVRNMLQAIEAPLYDVGVLSDRGMLP--G------LdgitgdavlaR--------LPLLKY--RNA-------R---- 55
gi 295796762 410 aVQKQMTALGVERLLVGIRDARTGLMMH--R------K----------WsrselersVPWLKR--MNA-------R---- 458
gi 503346840  21 LLLRTESPAKTQQRVVTLEQAL-----G--P------R----------Y--------LSWLAH--ENH-------A---- 56
gi 503058513  23 DTRFDIGIGDANKALYFRRSGLSRLRSLdlQ------M----------R--------IPFFKA--ANIsgvgqvsR---- 72
gi 504008724   2 GVPEQVAALRVEKLLVRLADPFHPERRM--S------R----------R--------LPAAAL--TVGlvrewsdS---- 49
gi 502887194  41 EIAARITPGTRKGAFIQIAELRESAAAA--D------W----------L--------DALKKAgaLNR-------Rqppe 87
gi 502495717  22 DLFASVGAEAFDITHTNLQQEKRGFRPG--QslaqarQ----------S--------MPYLVP--SAA-------R---- 68
gi 503334242  21 ILLRRQDAAAPMQRVVRLERvle-------------------------------tryMAWLSY--ENQ-------H---- 56
gi 506378502  21 LLLRRENPRSVAQRVVRLETale-------------------------------pryRAWLAY--ENS-------T---- 56
gi 340558035 542 RYAEAVGAERYRVTSIKMYPDGKKQTfildkkdgvtr----------gftpeeiaqrMPEMLR--LQR-------R---- 598
gi 752730643 121 RYAQAVDAQRYRVTSVRLKPDGGRMTflldkragvsq----------gctpeevrqrMPRMQR--LSE-------R---- 177
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219523944  65 R-SNAYACisssiktpnpktgqmrywrgEa--------------sFGHGLALMVDDIGSGKGSKgdfnrdEFRERLEPTA 129
gi 504599440  56 G-SHIYIR--------------------P----------------SGEHRYTALDDLSEISLSR------LIADGFTPCA 92
gi 295796762 459 G-NDIYVR--------------------P----------------DGDHGLVLVDDLKAEALER------MQREGYAPAA 495
gi 503346840  57 G-ANVYVA--------------------AnplrcgsrrrtkesidSVRHLYLDIDEDGDARLAA------LRASDSVPPA 109
gi 503058513  73 P-LNIYVC--------------------Aa--------------vTEPQSWLMMDDLTLNQSRR------V--AGERTHM 109
gi 504008724  50 G-YDVSIA--------------------P----------------EAPDGLVVISRVTKPGLAK------LSAAGLEPAC 86
gi 502887194  88 G-ANIYIR--------------------Pl--------------hTASHPWILVDDIPAQRAQA------LAAQH-AGIA 125
gi 502495717  69 RqNNLIIR--------------------Pr--------------aGADVTLVQLDDLAPDTLAH-----------IAPAA 103
gi 503334242  57 GrNNIYVA--------------------AnplrpgsrkrtkeciaSVRHLYLDIDTDGDARLAVlr------tsDMVPPP 110
gi 506378502  57 G-ANVYVA--------------------AnplrsgsrkrtkeniaSVRHLYLDIDTDGDARLAAlr------asDLVPPP 109
gi 340558035 599 A-ENLYYT--------------------Pl---------------SDKKHHILIDDMDREKLERli------hdGYRPAV 636
gi 752730643 178 G-ERIDYT--------------------Pl---------------SADKHYLLIDAMSQAKLDQll------qdGYRPAV 215
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219523944 130 --IVETSPNNYQFWYFFK---EPMSHMLQ-----FKALLYSFvdqvlkkGGDNTVKDVSRYGRMPfGFNNKRgedgnfKY 199
gi 504599440  93 --VVETSAGNFQAWLKHP---AAFPKLLGtf--aAQHLAARY-------DADPSAADWRRFGRLP-GFTNCKp-----KY 152
gi 295796762 496 --LLETSPGNFQAWVKLSe--APLSVAVRtr--aAQELAQHY-------GGDLNSADGRHFGRLA-GFTNRKp-----QH 556
gi 503346840 110 taVLSTSPHKHQALWRVD----GFNFEQQea--aLKQLAIAF-------GGDPACTDCNRVLRIP-GFLNRKy-----SP 170
gi 503058513 110 --IIQTSPGLHHLWLATS---RLISIAERka--cQQVLQQRY-------GGDAASVSGDHFGRLP-GFKNIKr-----GK 169
gi 504008724  87 --VVRGSA-RYDAFVRLApkgDPLGTAPRvltaaARLVTAIA-------GQDPRA---VHWQRGG-MVVGTK-------- 144
gi 502887194 126 --VQTSDDGNGQFWLLLD---KSLPHTARtd--iAKALAERL-------DGDPGAANGSQFGRLA-GFQQRKg-----NK 185
gi 502495717 104 flILRTSPGGQQAWVAVTn--APRGFAAR--------LKEGT-------GADKEASGATRV---A-GTANFKp-----AY 157
gi 503334242 111 tsVLSTSPGKYQVLWRVE----DFHFSQQeq--tLKLLAIAF-------GGDPACTDCNRVLRIP-GFLNRKy-----YP 171
gi 506378502 110 tsILSTSPGKYQVLWRVE----GFDFERQeq--mLKLLAIAF-------GGDPACTDCNRVLRIP-GFLNQKy-----NP 170
gi 340558035 637 --VLESSPGNYQAIITVPklgTPHDRDVGnr--lSEALNREY--------GDRKLSGAIHPHRAP-GFENRKp-----KH 698
gi 752730643 216 --VLQSSPERFQALITVKkfgAFNDDEVGrq--lARQLNTEY-------GNPDLLGGCIQPHPAP-GYVDRQs-----TL 278
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219523944 200 A------DENGKPELVRLYHADYSKRYSPEEIAQAFgvriimpqmkK--VEINRDDWVYDQVWLKYAEHICTKYKMgEAA 271
gi 504599440 153 K------RPDGLFPFVRLKLHTGEQYPMAESFIEKIkkl-----yeA--REQERQARRLQAALSPQKGPRLTTLSL-ERF 218
gi 295796762 557 T------R-HNRQPYVLAQACPGTIARAAAAYLQQI----------A--QGLDKEAEELERRERRDA-----LQSArPGA 612
gi 503346840 171 --------------------------------AHCV----------T--VEYGSEAILSSADFRLPDVPAVTSLSLrSTA 206
gi 503058513 170 W--------------VNFVDSKIVDRRADVDVLLEL----------A-------------EKQGFILPPLGGVVSAqPQA 212
gi 504008724 145 -------RQLSGGPPVKLYADDGGLAPAGRMLLERA----------A--DVVEGVEDSRSMAYEGAVDPIGELDGIaGYN 205
gi 502887194 186 T-----------GWTNVLADTTRTLMPWPADRLLAL----------TgeAGVSRVARACPDVLSPCAAPA-ALPSL---- 239
gi 502495717 158 ApnfprvRIDAAQPGLNVTTQTLD----------------------A--MGVVAPARPIPVSLPPVASSSDSRTSKwPSY 213
gi 503334242 172 A--------------------------------YRV----------T--VEYPDDSIWTPNDFEIDTGAVDAMLFAqEIP 207
gi 506378502 171 A--------------------------------HRV----------T--VEYPDDSVWTPGDFRLEIAATDTTAYAlMNH 206
gi 340558035 699 Qre------dGSYPEVRLLKAERRECAKTLELARQI----------D--ADYQRQAQERAQKALERAQAV---GDReVQP 757
gi 752730643 279 Rqa------dGACWEVRLLQAERCECAKTLEIALRI----------S--AEKGQQAAPQGKEAVKAVTPS----GHtPQP 336
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219523944 272 GgqvqqnmsgkyrircpwgdehtnG-------D---------------PF-----------------------GAYFRGP 306
gi 504599440 219 R-----------------------T-------S---------------SK-----------------------YQDRPAA 230
gi 295796762 613 G-----------------------R-------DpiqeyqrqaqrllaqYG-----------------------ADADLSR 639
gi 503346840 207 R-----------------------S-------A---------------AS-----------------------HKDTRSE 218
gi 503058513 213 N------------------------------------------------L-----------------------HNAFASR 221
gi 504008724 206 Gplaeeqarq------vyeqqaaiS-------R---------------YY-----------------------GLTDPDA 234
gi 502887194 240 ------------------------------------------------SP-----------------------APARPPA 248
gi 502495717 214 A-----------------------RclegapiG---------------AG-----------------------GNPKRTS 232
gi 503334242 208 Shr--------------------------------------------------------------------slGKHSNSE 219
gi 506378502 207 Grk--------------------------------------------------------------------ppRKHSNSE 218
gi 340558035 758 D------------------------------------------------------------------------------- 758
gi 752730643 337 D-----------------------P-------A---------------LAlataaaldaywrhyrdvlsrhtaGRVNLSR 371
                        410
                 ....*....|....*.
gi 219523944 307 IPGAEHEYVFGCGHDT 322
gi 504599440 231 ADIAFCVAAYANGMDE 246
gi 295796762 640 VDWMIATDMAKSGRFT 655
gi 503346840 219 QDWAWISAQIAQGKDA 234
gi 503058513 222 VRSIAKPFIATGRNES 237
gi 504008724 235 VDRVVAVAALKAGADP 250
gi 502887194 249 ATGSRQRPAAGSGDQS 264
gi 502495717 233 ADFIWCKIALSWGHGI 248
gi 503334242 220 SDWAWVSHELANGKDA 235
gi 506378502 219 SDWAWVSSQLRQGKDA 234
gi 340558035 759 -------ALKIDSRAS 767
gi 752730643 372 VDSMIAVRLRVTGHAQ 387
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