254780834

254780834

DNA primase

GeneID in NCBI database:8209845Locus tag:CLIBASIA_03645
Protein GI in NCBI database:254780834Protein Accession:YP_003065247.1
Gene range:+(801416, 803362)Protein Length:648aa
Gene description:DNA primase
COG prediction:[L] DNA primase (bacterial type)
KEGG prediction:dnaG; DNA primase (EC:2.7.7.-); K02316 DNA primase [EC:2.7.7.-]
SEED prediction:DNA primase (EC 2.7.7.-)
Pathway involved in KEGG:DNA replication [PATH:las03030]
Subsystem involved in SEED:DNA-replication
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPRED2 TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------65
MNYPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQLFQKYITEHSGYGRYWKKNARHRDQKGPSQRLMQSSLVKGKLSKKPSLREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKRFRLLSRQKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQIESQEAMIEGFGKMSGRL
ccccHHHHHHHHHHccHHHHHHHHccccccccccccccEEEEccccccccccEEEEccccEEEEccccccccHHHHHHHHccccHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHccccHHHHHHcccccccccHHHHHHHHHHccccHHHHHHcccEEEcccccccccEEccEEEEEEEcccccEEEEEEEEccccccccEEccccccccccHHHHHcHHHHHHHHHHHcccccccccccEEEEEccHHHHHHHHHccccccEEcccccccHHHHHHHHHHcccEEEEEcccHHHHHHHHHHHHHHHHHHccccEEEEEEccccccHHHHHHHccHHHHHHHHHccccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHcccccccccHHHHHHHHHHHHHcHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccc
ccccHHHHHHHHHcccHHHHHccccccccccccccccEEEEcccccccccccEEEEccccEEEEcccccEEcHHHHHHHHHcccHHHHHHHHHHHHccccHHHcccccccccHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHccccHHHHHHHccccccccHHHHHHHHccccccHHHHHHcccEEEccccccEcccccccEEEEccccccEEEEEccEEccccccccccccccccHHccccHHccHHHHHHHHHcccHccccccccccEEEEEcHHHHHHHHHHcccEEEEcccccccHHHHHHHHHHcccEEEEEccccHHHHHHHHHHHHHHHHcccccEEEEEEcccccccHHHHHHHcHHHHHHHHHHcccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHccccHHHHHHHHHHHcccccccccccccccccHHHccccccccccccccHHHHHHHHHHHHcHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHccccccHHHHHHHHHHccHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccc
MNYPRDFIKDLLIHIpisnligqyvdwdrrktnavkgdywaccpfhdektpsfhcndskgfyycfschvkgdHLSFLSALLGCSFIESVQRLAAIagvplpvvdpkiekkEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFklgyapdsrySLREHLRQKGFSEEKIIEAgllidgdnsatsydRFRNRlifpirssrgqviafggrtlskgesvkylnspetilfhkgknlyNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKlsprivlcfdgddpglRAAYKAIDLVLChlipgnrvNFVLlsrgedpdsfirCYGKTAFEKLIVESLPLVDMLWKRetenrsfntpdERAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQLFQKYITEHsgygrywkknarhrdqkgpsqrlmqsslvkgklskkpsLREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFveqkyflpeEIHQRLCERGFGELLKQLDRQVRDAGlwsatteaNIVDVRQGYQQALALYKRFRLLSRQKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQIESQEAMIEGFGKMSGRL
MNYPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAgvplpvvdpkiekKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEagllidgdnsatSYDRFRNRLifpirssrgqvIAFGgrtlskgesvKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETenrsfntpdERAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQLFQKYITEHSgygrywkknarhrdqkgpsqrlmqsslvkgklskkPSLREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWsatteanivdvRQGYQQALALYKRFRLLSRQKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQIESQEAMIEGFGKMSGRL
MNYPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQLFQKYITEHSGYGRYWKKNARHRDQKGPSQRLMQSSLVKGKLSKKPSLREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKRFRLLSRQKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQIESQEAMIEGFGKMSGRL
MNYPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGV*********************LIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQ********RNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRET***********AELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQ*************************************************EAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKRFR***************************LISILHEVH**********AMIEGFGKMSG**
MNYPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQLFQKYITEHSGYGRYWKK*************LMQSSL*********SLREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKRFRLLSRQKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQIESQEAMIEGFGKMSGRL
MNYPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQLFQKYITEHSGYGR*******************QSSLVKGKLSKKPSLREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKRFRLLSRQKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQIESQEAMIEGFGK*****
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MNYPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQLFQKYITEHSGYGRYWKKNARHRDQKGPSQRLMQSSLVKGKLSKKPSLREAALLLTLINHPAIxxxxxxxxxxxxxxxxxxxxxWSFLFSDFVEQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKRxxxxxxxxxxxxxxxxxxxxxGEAEKTAILISILHEVHIQIHQIESQEAMIEGFGKMSGRL
MNYPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQLFQKYITEHSGYGRYWKKNARHRDQKGPSQRLMQSSLVKGKLSKKPSLREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKRFRLLSRQKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQIESQEAMIEGFGKMSGRL
MNYPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQLFQKYITEHSGYGRYWKKNARHRDQKGPSQRLMQSSLVKGKLSKKPSLREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIHQRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKRFRLLSRQKEEIEKQIAQVTAKGEAEKTAILISILHEVHIQIHQIESQEAMIEGFGKMSGRL

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target648 DNA primase [Candidatus Liberibacter asiaticus str. psy
315122784650 DNA primase [Candidatus Liberibacter solanacearum CLso- 1 0.0
86358556665 DNA primase [Rhizobium etli CFN 42] Length = 665 1 1e-180
209550283666 DNA primase [Rhizobium leguminosarum bv. trifolii WSM23 1 1e-178
190892704666 DNA primase [Rhizobium etli CIAT 652] Length = 666 1 1e-177
222086545664 DNA primase protein [Agrobacterium radiobacter K84] Len 1 1e-177
327192723666 DNA primase protein [Rhizobium etli CNPAF512] Length = 1 1e-177
116253150669 DNA primase [Rhizobium leguminosarum bv. viciae 3841] L 1 1e-175
241205664669 DNA primase [Rhizobium leguminosarum bv. trifolii WSM13 1 1e-175
325293529661 DNA primase [Agrobacterium sp. H13-3] Length = 661 1 1e-172
222149283678 DNA primase [Agrobacterium vitis S4] Length = 678 1 1e-171
>gi|315122784|ref|YP_004063273.1| DNA primase [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 650 Back     alignment and organism information
 Score = 1020 bits (2637), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 488/650 (75%), Positives = 566/650 (87%), Gaps = 2/650 (0%)

Query: 1   MNYPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKG 60
           M+YP DFI DLLI  PIS+LIGQ+V+WDR+KTNAVKGDYW+CCPFH+EK PSFHC+D KG
Sbjct: 1   MHYPHDFIDDLLIRTPISHLIGQHVNWDRKKTNAVKGDYWSCCPFHNEKNPSFHCDDRKG 60

Query: 61  FYYCFSCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRL 120
            YYCFSCH  G+HL+FLS LLGCSFIESVQ+LA IAGV LP  DP ++KK+K QT LI+L
Sbjct: 61  VYYCFSCHATGNHLTFLSTLLGCSFIESVQKLAVIAGVSLPTFDPILDKKQKKQTSLIQL 120

Query: 121 IEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSE 180
           I++A DFFH SLKN  +KRL YYLD+RGI+SH+IE FKLGYAPDSR+SL E+L  KGF++
Sbjct: 121 IDIAADFFHQSLKNNDNKRLRYYLDKRGINSHSIETFKLGYAPDSRHSLEEYLHTKGFTQ 180

Query: 181 EKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETI 240
           EKIIEAGLLI GDN  T YDRFR+RLIFPI SSRGQ IAFGGR+LSKG+++KYLNSPETI
Sbjct: 181 EKIIEAGLLIHGDNITTPYDRFRDRLIFPILSSRGQGIAFGGRSLSKGDNIKYLNSPETI 240

Query: 241 LFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGT 300
           LFHKGKNLYNFFGALNY Q+SIR+DV++ SSSFI+LVEGYMDV+SL QAG+QNVVSSLGT
Sbjct: 241 LFHKGKNLYNFFGALNYRQRSIRQDVQKQSSSFIVLVEGYMDVVSLHQAGIQNVVSSLGT 300

Query: 301 ALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPD 360
           +LTE QLRLLWKLSPR+VLCFDGDDPGLRAAYKA+DLVL HL  GN VNF+LLS GEDPD
Sbjct: 301 SLTEDQLRLLWKLSPRVVLCFDGDDPGLRAAYKAVDLVLSHLSIGNSVNFILLSEGEDPD 360

Query: 361 SFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKDQKL 420
           SF++ YGK AFEKLI+ES+PLVD+LWKRETE  SF TPD RAELE  LKNC++ I DQKL
Sbjct: 361 SFVQRYGKIAFEKLILESVPLVDVLWKRETEYHSFETPDARAELEGRLKNCLDRITDQKL 420

Query: 421 RYYYSQAIRDRLQQLFQKYITEHS--GYGRYWKKNARHRDQKGPSQRLMQSSLVKGKLSK 478
           RYYY ++I++RL  LFQ     HS  G+G+YW K  ++RD+ GPSQRLMQSSLVKGK SK
Sbjct: 421 RYYYFKSIQERLHHLFQTNPRPHSSYGHGQYWGKKVKYRDKAGPSQRLMQSSLVKGKNSK 480

Query: 479 KPSLREAALLLTLINHPAILQEQYQELADIRYDNNELQKLWSFLFSDFVEQKYFLPEEIH 538
           KPSLREAALLLTLINHP ILQEQ  EL DI YDN+ELQK+WSFLFS+FV QK F  EEI+
Sbjct: 481 KPSLREAALLLTLINHPKILQEQCYELTDISYDNSELQKMWSFLFSEFVVQKDFSREEIN 540

Query: 539 QRLCERGFGELLKQLDRQVRDAGLWSATTEANIVDVRQGYQQALALYKRFRLLSRQKEEI 598
           Q+LC RGFGELL++LD+QVRDAGLWSAT EA+IVDVRQGYQQA+ALYKRFRLLSRQK ++
Sbjct: 541 QKLCTRGFGELLQRLDKQVRDAGLWSATAEADIVDVRQGYQQAVALYKRFRLLSRQKADL 600

Query: 599 EKQIAQVTAKGEAEKTAILISILHEVHIQIHQIESQEAMIEGFGKMSGRL 648
           EKQIAQ+T +GE +KT  LISIL+++HIQI+ IE QEA+IEGFGKMSGR+
Sbjct: 601 EKQIAQMTEQGEEKKTTTLISILNDIHIQINTIECQEAIIEGFGKMSGRV 650


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|86358556|ref|YP_470448.1| DNA primase [Rhizobium etli CFN 42] Length = 665 Back     alignment and organism information
>gi|209550283|ref|YP_002282200.1| DNA primase [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 666 Back     alignment and organism information
>gi|190892704|ref|YP_001979246.1| DNA primase [Rhizobium etli CIAT 652] Length = 666 Back     alignment and organism information
>gi|222086545|ref|YP_002545079.1| DNA primase protein [Agrobacterium radiobacter K84] Length = 664 Back     alignment and organism information
>gi|327192723|gb|EGE59660.1| DNA primase protein [Rhizobium etli CNPAF512] Length = 666 Back     alignment and organism information
>gi|116253150|ref|YP_768988.1| DNA primase [Rhizobium leguminosarum bv. viciae 3841] Length = 669 Back     alignment and organism information
>gi|241205664|ref|YP_002976760.1| DNA primase [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 669 Back     alignment and organism information
>gi|325293529|ref|YP_004279393.1| DNA primase [Agrobacterium sp. H13-3] Length = 661 Back     alignment and organism information
>gi|222149283|ref|YP_002550240.1| DNA primase [Agrobacterium vitis S4] Length = 678 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target648 DNA primase [Candidatus Liberibacter asiaticus str. psy
PRK05667580 PRK05667, dnaG, DNA primase; Validated 1e-161
COG0358568 COG0358, DnaG, DNA primase (bacterial type) [DNA replic 3e-99
TIGR01391415 TIGR01391, dnaG, DNA primase, catalytic core 1e-121
pfam08275128 pfam08275, Toprim_N, DNA primase catalytic core, N-term 6e-41
pfam0180798 pfam01807, zf-CHC2, CHC2 zinc finger 5e-26
cd0336479 cd03364, TOPRIM_DnaG_primases, TOPRIM_DnaG_primases: Th 2e-25
cd0102979 cd01029, TOPRIM_primases, TOPRIM_primases: The topoisom 1e-21
smart0049376 smart00493, TOPRIM, topoisomerases, DnaG-type primases, 2e-11
cd0018883 cd00188, TOPRIM, Topoisomerase-primase domain 5e-11
pfam0175189 pfam01751, Toprim, Toprim domain 2e-08
smart0040055 smart00400, ZnF_CHCC, zinc finger 4e-17
>gnl|CDD|180189 PRK05667, dnaG, DNA primase; Validated Back     alignment and domain information
>gnl|CDD|30707 COG0358, DnaG, DNA primase (bacterial type) [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|162334 TIGR01391, dnaG, DNA primase, catalytic core Back     alignment and domain information
>gnl|CDD|149368 pfam08275, Toprim_N, DNA primase catalytic core, N-terminal domain Back     alignment and domain information
>gnl|CDD|110780 pfam01807, zf-CHC2, CHC2 zinc finger Back     alignment and domain information
>gnl|CDD|173784 cd03364, TOPRIM_DnaG_primases, TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG Back     alignment and domain information
>gnl|CDD|173779 cd01029, TOPRIM_primases, TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs Back     alignment and domain information
>gnl|CDD|128769 smart00493, TOPRIM, topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins Back     alignment and domain information
>gnl|CDD|173773 cd00188, TOPRIM, Topoisomerase-primase domain Back     alignment and domain information
>gnl|CDD|145089 pfam01751, Toprim, Toprim domain Back     alignment and domain information
>gnl|CDD|128681 smart00400, ZnF_CHCC, zinc finger Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 648 DNA primase [Candidatus Liberibacter asiaticus str. psy
PRK05667600 dnaG DNA primase; Validated 100.0
COG0358568 DnaG DNA primase (bacterial type) [DNA replication, rec 100.0
TIGR01391424 dnaG DNA primase; InterPro: IPR006295 DNA primase synth 100.0
pfam08275128 Toprim_N DNA primase catalytic core, N-terminal domain. 99.97
PRK08624373 hypothetical protein; Provisional 99.97
pfam0180798 zf-CHC2 CHC2 zinc finger. This domain is principally in 99.96
smart0040055 ZnF_CHCC zinc finger. 99.75
PRK09165484 replicative DNA helicase; Provisional 96.23
COG0305435 DnaB Replicative DNA helicase [DNA replication, recombi 95.99
cd0336479 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisom 99.7
cd0102979 TOPRIM_primases TOPRIM_primases: The topoisomerase-prim 99.31
pfam0175189 Toprim Toprim domain. This is a conserved region from D 98.83
smart0049376 TOPRIM topoisomerases, DnaG-type primases, OLD family n 98.75
cd0018883 TOPRIM Topoisomerase-primase domain. This is a nucleoti 97.94
cd0102781 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoiso 97.84
LOAD_Toprim98 consensus 97.43
COG1658127 Small primase-like proteins (Toprim domain) [DNA replic 96.87
PRK04017132 hypothetical protein; Provisional 96.82
TIGR00334176 primaseG_like primase homolog; InterPro: IPR004466 This 90.81
PRK05301375 pyrroloquinoline quinone biosynthesis protein PqqE; Pro 90.56
PHA02415 930 DNA primase domain-containing protein 99.68
PHA02031274 putative DnaG-like primase 99.13
TIGR027602193 TraI_TIGR conjugative transfer relaxase protein TraI; I 98.88
COG4643366 Uncharacterized protein conserved in bacteria [Function 98.32
PRK04031420 DNA primase; Provisional 98.43
TIGR00646218 MG010 DNA primase homolog; InterPro: IPR004611 The DNA 98.43
pfam1041059 DnaB_bind DnaB-helicase binding domain of primase. This 97.83
PRK06904472 replicative DNA helicase; Validated 97.47
PRK08760476 replicative DNA helicase; Provisional 97.31
TIGR03600421 phage_DnaB phage replicative helicase, DnaB family, HK0 97.28
PRK08006471 replicative DNA helicase; Provisional 97.15
PRK07004460 replicative DNA helicase; Provisional 97.11
PRK05748448 replicative DNA helicase; Provisional 96.98
PRK08082453 consensus 96.93
PRK08694468 consensus 96.92
PRK08840464 replicative DNA helicase; Provisional 96.84
PRK07263453 consensus 96.73
PRK06321472 replicative DNA helicase; Provisional 96.7
PRK08506473 replicative DNA helicase; Provisional 96.58
PRK05595444 replicative DNA helicase; Provisional 96.52
PRK06749428 replicative DNA helicase; Provisional 95.37
smart00766125 DnaG_DnaB_bind DNA primase DnaG DnaB-binding. DnaG_DnaB 96.9
pfam08278126 DnaG_DnaB_bind DNA primase DnaG DnaB-binding. Eubacteri 96.36
PRK07773868 replicative DNA helicase; Validated 96.73
PRK05636507 replicative DNA helicase; Provisional 96.64
COG3593581 Predicted ATP-dependent endonuclease of the OLD family 96.12
pfam00772103 DnaB DnaB-like helicase N terminal domain. The hexameri 95.95
>PRK05667 dnaG DNA primase; Validated Back     alignment and domain information
>COG0358 DnaG DNA primase (bacterial type) [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR01391 dnaG DNA primase; InterPro: IPR006295 DNA primase synthesizes the RNA primers for the Okazaki fragments in lagging strand DNA synthesis Back     alignment and domain information
>pfam08275 Toprim_N DNA primase catalytic core, N-terminal domain Back     alignment and domain information
>PRK08624 hypothetical protein; Provisional Back     alignment and domain information
>pfam01807 zf-CHC2 CHC2 zinc finger Back     alignment and domain information
>smart00400 ZnF_CHCC zinc finger Back     alignment and domain information
>PRK09165 replicative DNA helicase; Provisional Back     alignment and domain information
>COG0305 DnaB Replicative DNA helicase [DNA replication, recombination, and repair] Back     alignment and domain information
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG Back     alignment and domain information
>cd01029 TOPRIM_primases TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs Back     alignment and domain information
>pfam01751 Toprim Toprim domain Back     alignment and domain information
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins Back     alignment and domain information
>cd00188 TOPRIM Topoisomerase-primase domain Back     alignment and domain information
>cd01027 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea Back     alignment and domain information
>LOAD_Toprim consensus Back     alignment and domain information
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK04017 hypothetical protein; Provisional Back     alignment and domain information
>TIGR00334 primaseG_like primase homolog; InterPro: IPR004466 This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase Back     alignment and domain information
>PRK05301 pyrroloquinoline quinone biosynthesis protein PqqE; Provisional Back     alignment and domain information
>PHA02415 DNA primase domain-containing protein Back     alignment and domain information
>PHA02031 putative DnaG-like primase Back     alignment and domain information
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI; InterPro: IPR014129 This entry represents TraI, which is a component of the relaxosome complex Back     alignment and domain information
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>PRK04031 DNA primase; Provisional Back     alignment and domain information
>TIGR00646 MG010 DNA primase homolog; InterPro: IPR004611 The DNA primase DnaG of Escherichia coli and its apparent orthologs in other bacterial species are approximately 600 residues in length Back     alignment and domain information
>pfam10410 DnaB_bind DnaB-helicase binding domain of primase Back     alignment and domain information
>PRK06904 replicative DNA helicase; Validated Back     alignment and domain information
>PRK08760 replicative DNA helicase; Provisional Back     alignment and domain information
>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily Back     alignment and domain information
>PRK08006 replicative DNA helicase; Provisional Back     alignment and domain information
>PRK07004 replicative DNA helicase; Provisional Back     alignment and domain information
>PRK05748 replicative DNA helicase; Provisional Back     alignment and domain information
>PRK08082 consensus Back     alignment and domain information
>PRK08694 consensus Back     alignment and domain information
>PRK08840 replicative DNA helicase; Provisional Back     alignment and domain information
>PRK07263 consensus Back     alignment and domain information
>PRK06321 replicative DNA helicase; Provisional Back     alignment and domain information
>PRK08506 replicative DNA helicase; Provisional Back     alignment and domain information
>PRK05595 replicative DNA helicase; Provisional Back     alignment and domain information
>PRK06749 replicative DNA helicase; Provisional Back     alignment and domain information
>smart00766 DnaG_DnaB_bind DNA primase DnaG DnaB-binding Back     alignment and domain information
>pfam08278 DnaG_DnaB_bind DNA primase DnaG DnaB-binding Back     alignment and domain information
>PRK07773 replicative DNA helicase; Validated Back     alignment and domain information
>PRK05636 replicative DNA helicase; Provisional Back     alignment and domain information
>COG3593 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair] Back     alignment and domain information
>pfam00772 DnaB DnaB-like helicase N terminal domain Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target648 DNA primase [Candidatus Liberibacter asiaticus str. psy
2au3_A407 Crystal Structure Of The Aquifex Aeolicus Primase ( 8e-64
1d0q_A103 Structure Of The Zinc-Binding Domain Of Bacillus St 2e-47
3b39_A322 Structure Of The Dnag Primase Catalytic Domain Boun 1e-43
1dd9_A338 Structure Of The Dnag Catalytic Core Length = 338 4e-43
1eqn_A321 E.Coli Primase Catalytic Core Length = 321 6e-41
1z8s_A146 Dnab Binding Domain Of Dnag (P16) From Bacillus Ste 4e-07
2r6a_C143 Crystal Form Bh1 Length = 143 2e-05
2r5u_A200 Crystal Structure Of The N-Terminal Domain Of Dnab 1e-04
>gi|83754038|pdb|2AU3|A Chain A, Crystal Structure Of The Aquifex Aeolicus Primase (Zinc Binding And Rna Polymerase Domains) Length = 407 Back     alignment and structure
 Score =  249 bits (636), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 133/440 (30%), Positives = 202/440 (45%), Gaps = 37/440 (8%)

Query: 6   DFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCF 65
             I +L   I I ++I +Y++ ++  +N     Y   CPFH + TPSF+ + SK  + CF
Sbjct: 5   SDIDELRREIDIVDVISEYLNLEKVGSN-----YRTNCPFHPDDTPSFYVSPSKQIFKCF 59

Query: 66  SCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVAT 125
            C V GD + F+S     S+ E+   LA   G  L        +K      +   ++   
Sbjct: 60  GCGVGGDAIKFVSLYEDISYFEAALELAKRYGKKL------DLEKISKDEKVYVALDRVC 113

Query: 126 DFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIE 185
           DF+  SL   R+     Y+  RGID      F LGYAP S   ++     K     +   
Sbjct: 114 DFYRESLLKNREASE--YVKSRGIDPKVARKFDLGYAPSSEALVKVL---KENDLLEAYL 168

Query: 186 AGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKG 245
               +         D F  R++ PI+  RG+VI FGGR + + +S KY+NSP++ +F KG
Sbjct: 169 ETKNLLSPTKGVYRDLFLRRVVIPIKDPRGRVIGFGGRRIVEDKSPKYINSPDSRVFKKG 228

Query: 246 KNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEY 305
           +NL+  + A  Y++             F ILVEGY D+L L   G++NVV+ LGTALT+ 
Sbjct: 229 ENLFGLYEAKEYIK----------EEGFAILVEGYFDLLRLFSEGIRNVVAPLGTALTQN 278

Query: 306 QLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRC 365
           Q  LL K + ++ + +DGDD G +A   AI L    L  G  V  V L  G DPD FI+ 
Sbjct: 279 QANLLSKFTKKVYILYDGDDAGRKAMKSAIPL---LLSAGVEVYPVYLPEGYDPDEFIKE 335

Query: 366 YGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYS 425
           +GK    +LI  S  L + L K           +   E     +  +  I D   R+  +
Sbjct: 336 FGKEELRRLINSSGELFETLIKTAR--------ENLEEKTREFRYYLGFISDGVRRFALA 387

Query: 426 QAIRDRLQQLFQKYITEHSG 445
                + +   +  + +   
Sbjct: 388 SEFHTKYKVPMEILLMKIEK 407


>gi|7546338|pdb|1D0Q|A Chain A, Structure Of The Zinc-Binding Domain Of Bacillus Stearothermophilus Dna Primase Length = 103 Back     alignment and structure
>gi|165761277|pdb|3B39|A Chain A, Structure Of The Dnag Primase Catalytic Domain Bound To Ssdna Length = 322 Back     alignment and structure
>gi|7767196|pdb|1DD9|A Chain A, Structure Of The Dnag Catalytic Core Length = 338 Back     alignment and structure
>gi|9256898|pdb|1EQN|A Chain A, E.Coli Primase Catalytic Core Length = 321 Back     alignment and structure
>gi|78101045|pdb|1Z8S|A Chain A, Dnab Binding Domain Of Dnag (P16) From Bacillus Stearothermophilus (Residues 452-597) Length = 146 Back     alignment and structure
>gi|160286059|pdb|2R6A|C Chain C, Crystal Form Bh1 Length = 143 Back     alignment and structure
>gi|189095961|pdb|2R5U|A Chain A, Crystal Structure Of The N-Terminal Domain Of Dnab Helicase From Mycobacterium Tuberculosis Length = 200 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target648 DNA primase [Candidatus Liberibacter asiaticus str. psy
2au3_A407 DNA primase; zinc ribbon, toprim, RNA polymerase, DNA r 1e-57
1dd9_A338 DNA primase, DNAG; toprim, 3-helix bundle, DNA-binding 6e-55
1d0q_A103 DNA primase; zinc-binding motif, protein; HET: DNA; 1.7 2e-19
1q57_A503 DNA primase/helicase; dntpase, DNA replication, transfe 7e-17
1t6t_1118 Putative protein; structural genomics, PSI, protein str 1e-15
2fcj_A119 Small toprim domain protein; structural genomics, PSI, 2e-11
1nui_A255 DNA primase/helicase; zinc-biding domain, toprim fold, 8e-11
>2au3_A DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication, transferase; HET: DNA; 2.00A {Aquifex aeolicus} Length = 407 Back     alignment and structure
 Score =  219 bits (559), Expect = 1e-57
 Identities = 138/428 (32%), Positives = 204/428 (47%), Gaps = 37/428 (8%)

Query: 6   DFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCF 65
             I +L   I I ++I +Y++ ++  +N     Y   CPFH + TPSF+ + SK  + CF
Sbjct: 5   SDIDELRREIDIVDVISEYLNLEKVGSN-----YRTNCPFHPDDTPSFYVSPSKQIFKCF 59

Query: 66  SCHVKGDHLSFLSALLGCSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVAT 125
            C V GD + F+S     S+ E+   LA   G  L +     ++K  +       ++   
Sbjct: 60  GCGVGGDAIKFVSLYEDISYFEAALELAKRYGKKLDLEKISKDEKVYV------ALDRVC 113

Query: 126 DFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIE 185
           DF+  SL   R+     Y+  RGID      F LGYAP S   ++  L++    E  +  
Sbjct: 114 DFYRESLLKNREAS--EYVKSRGIDPKVARKFDLGYAPSSEALVK-VLKENDLLEAYLET 170

Query: 186 AGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKG 245
             LL          D F  R++ PI+  RG+VI FGGR + + +S KY+NSP++ +F KG
Sbjct: 171 KNLLSPTKGV--YRDLFLRRVVIPIKDPRGRVIGFGGRRIVEDKSPKYINSPDSRVFKKG 228

Query: 246 KNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEY 305
           +NL+  + A  Y               F ILVEGY D+L L   G++NVV+ LGTALT+ 
Sbjct: 229 ENLFGLYEAKEY----------IKEEGFAILVEGYFDLLRLFSEGIRNVVAPLGTALTQN 278

Query: 306 QLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRC 365
           Q  LL K + ++ + +DGDD G +A   AI      L  G  V  V L  G DPD FI+ 
Sbjct: 279 QANLLSKFTKKVYILYDGDDAGRKAMKSAIP---LLLSAGVEVYPVYLPEGYDPDEFIKE 335

Query: 366 YGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYS 425
           +GK    +LI  S  L + L K   EN    T + R          +  I D   R+  +
Sbjct: 336 FGKEELRRLINSSGELFETLIKTARENLEEKTREFRYY--------LGFISDGVRRFALA 387

Query: 426 QAIRDRLQ 433
                + +
Sbjct: 388 SEFHTKYK 395


>1dd9_A DNA primase, DNAG; toprim, 3-helix bundle, DNA-binding protein, RNA polymerase, replication protein; HET: DNA; 1.60A {Escherichia coli} SCOP: e.13.1.1 PDB: 1dde_A* 1eqn_A* 3b39_A* Length = 338 Back     alignment and structure
>1d0q_A DNA primase; zinc-binding motif, protein; HET: DNA; 1.71A {Bacillus stearothermophilus} SCOP: g.41.3.2 Length = 103 Back     alignment and structure
>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2 Length = 503 Back     alignment and structure
>1t6t_1 Putative protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG, unknown function; 1.80A {Aquifex aeolicus VF5} SCOP: c.136.1.1 Length = 118 Back     alignment and structure
>2fcj_A Small toprim domain protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: MES; 1.30A {Geobacillus stearothermophilus} SCOP: c.136.1.1 PDB: 2i5r_A* Length = 119 Back     alignment and structure
>1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA- directed RNA polymerase, primosome, late protein; HET: DNA; 2.90A {Enterobacteria phage T7} SCOP: e.13.1.2 g.41.3.2 Length = 255 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target648 DNA primase [Candidatus Liberibacter asiaticus str. psy
2au3_A407 DNA primase; zinc ribbon, toprim, RNA polymerase, DNA r 100.0
1dd9_A338 DNA primase, DNAG; toprim, 3-helix bundle, DNA-binding 100.0
1d0q_A103 DNA primase; zinc-binding motif, protein, transferase; 99.91
1nui_A255 DNA primase/helicase; zinc-biding domain, toprim fold, 99.91
1q57_A503 DNA primase/helicase; dntpase, DNA replication, transfe 99.77
1t6t_1118 Putative protein; structural genomics, PSI, protein str 99.68
2fcj_A119 Small toprim domain protein; structural genomics, PSI, 99.22
2r6a_C143 DNAG primase, helicase binding domain, replicative heli 98.57
2r5u_A200 Replicative DNA helicase; DNAB, primase, replication, A 97.38
3gxv_A123 Replicative DNA helicase; hexameric helicase, primase, 96.62
1b79_A119 DNAB helicase; hexamer, DNA replication, hydrolase; 2.3 96.43
2r6a_A454 DNAB helicase, replicative helicase; replication, DNAB; 96.57
2q6t_A444 DNAB replication FORK helicase; hydrolase; 2.90A {Therm 96.33
3bgw_A444 DNAB-like replicative helicase; ATPase, replication; 3. 96.0
1t3w_A148 DNA primase; DNAG, DNA-directed RNA polymerase, E. coli 96.43
>2au3_A DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication, transferase; HET: DNA; 2.00A {Aquifex aeolicus} Back     alignment and structure
Probab=100.00  E-value=0  Score=761.12  Aligned_cols=399  Identities=34%  Similarity=0.590  Sum_probs=354.9

Q ss_pred             CCHHHHHHHHHHCCHHHHHHHHCCCEECCCCCCCCCEEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHCC
Q ss_conf             78889999987488888754122210158877777557534588885878798178974671368888789899898859
Q gi|254780834|r    3 YPRDFIKDLLIHIPISNLIGQYVDWDRRKTNAVKGDYWACCPFHDEKTPSFHCNDSKGFYYCFSCHVKGDHLSFLSALLG   82 (648)
Q Consensus         3 i~~~~i~~i~~~~~i~~vv~~~v~l~~~g~n~~~~~~~~~cPfh~ektpsf~v~~~~~~~~cf~c~~~gd~~~f~~~~~~   82 (648)
                      +| +.||+|++++||||||++||+|+|+|+|     |+|+||||+||||||+|||+||+|||||||+|||+|+|||+++|
T Consensus         3 ~~-~~i~~ik~~~~I~~v~~~~~~l~~~G~~-----~~~~CPfH~dktPSf~V~~~k~~~~CF~Cg~~Gd~i~fv~~~~~   76 (407)
T 2au3_A            3 MS-SDIDELRREIDIVDVISEYLNLEKVGSN-----YRTNCPFHPDDTPSFYVSPSKQIFKCFGCGVGGDAIKFVSLYED   76 (407)
T ss_dssp             CC-CHHHHHHHHCCHHHHHHHHSCCEEETTE-----EEECCSSSCCSSCCEEEETTTTEEEETTTCCEECHHHHHHHHHT
T ss_pred             CC-HHHHHHHHHCCHHHHHHHCCEEEECCCE-----EEEECCCCCCCCCCEEEECCCCEEEECCCCCCCCHHHHHHHHHC
T ss_conf             71-7999999849999998506228986984-----79879498998998599889998996789999789999999819


Q ss_pred             CCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHCCCCCCCC
Q ss_conf             99799999999981885877682036777889999999999999999973267775789999850688535101244225
Q gi|254780834|r   83 CSFIESVQRLAAIAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYA  162 (648)
Q Consensus        83 ~~f~ea~~~la~~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a~~yl~~Rg~~~~~~~~f~lG~a  162 (648)
                      ++|+||+++||+++||+++.......      .....+++.+..+|+..+..  +..+++|+..||++++++++|.+||+
T Consensus        77 ~sf~eA~~~l~~~~gi~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~--~~~~~~yl~~r~l~~~~i~~f~~g~~  148 (407)
T 2au3_A           77 ISYFEAALELAKRYGKKLDLEKISKD------EKVYVALDRVCDFYRESLLK--NREASEYVKSRGIDPKVARKFDLGYA  148 (407)
T ss_dssp             CCHHHHHHHHHHHHTCCCCTTSCCHH------HHHHHHHHHHHHHHHHHHHH--CHHHHHHHHHTTCCHHHHHHTTCEEC
T ss_pred             CCHHHHHHHHHHHHCCCCHHCCCHHH------HHHHHHHHHHHHHHHHHHHC--CHHHHHHHHHCCCCHHHHHHHCCCCC
T ss_conf             98899999999981976300111016------78999999999999997513--89999999867999999986223577


Q ss_pred             CCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCCCCC
Q ss_conf             67741034554205997345232012100346541000016716888970778588850100146553001038767653
Q gi|254780834|r  163 PDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILF  242 (648)
Q Consensus       163 p~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~if  242 (648)
                      |..|..+.... ..+...+ ....++......|. +||+|++||||||+|.+|++|||+||.+.++..|||+|||+|++|
T Consensus       149 ~~~~~~~~~~~-~~~~~~~-~~~~~~~~~~~~~~-~~d~f~~ri~fPi~~~~G~~v~f~~R~~~~~~~~Kylns~~~~~f  225 (407)
T 2au3_A          149 PSSEALVKVLK-ENDLLEA-YLETKNLLSPTKGV-YRDLFLRRVVIPIKDPRGRVIGFGGRRIVEDKSPKYINSPDSRVF  225 (407)
T ss_dssp             CCHHHHHHHHH-HHTCHHH-HHTTTCEECSSTTC-CEETTTTEEEEEEECTTSCEEEEEEEECSCCSSCSEEECCCCSSC
T ss_pred             CCCHHHHHHHH-HCCHHHH-HHHHCCCCCCCCCC-CEECCCCCEEEEEEECCCCEEEEEEEECCCCCCCCCCCCCCCCCC
T ss_conf             86247788875-0010688-87750661037895-112256734500450079389998666478887654467653001


Q ss_pred             CCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEEC
Q ss_conf             52101108178888643310000235678708997143889998743554211343213662678988512681899617
Q gi|254780834|r  243 HKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFD  322 (648)
Q Consensus       243 ~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fD  322 (648)
                      +|+..|||++.+++.+++.          +.+||||||||||++|++|++|+||++||++|.+|+..|+|++++||+|||
T Consensus       226 ~K~~~l~~~~~~~~~~~~~----------~~viivEG~~D~l~l~~~Gi~n~va~~Gt~lt~~~~~~L~~~~~~vvl~~D  295 (407)
T 2au3_A          226 KKGENLFGLYEAKEYIKEE----------GFAILVEGYFDLLRLFSEGIRNVVAPLGTALTQNQANLLSKFTKKVYILYD  295 (407)
T ss_dssp             CGGGCEETHHHHHHHHHHH----------TCEEECSSHHHHHHHHHTTCCSEEEESSSSCCHHHHHHHHTTCSEEEEECC
T ss_pred             CCCCCCHHHHHHHHHHCCC----------CCCEEECCCCHHHHHHHCCCCCEEECCCCCCCHHHHHHHHCCCCEEEEECC
T ss_conf             5530000069999863025----------432530363039999866976457415776838999998611671588458


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCHHHHH
Q ss_conf             88662257778888887775369730675257888888997203668899886414992799999998530233145799
Q gi|254780834|r  323 GDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRGEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERA  402 (648)
Q Consensus       323 gD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl~~~l~~~~dl~spe~ka  402 (648)
                      +|+||++|+.|+++.+   ++.|++++|+.||+|+|||||++++|.++|.+++++|.+++||+|+.+.++.+..+++.+ 
T Consensus       296 ~D~AG~~A~~k~~~~l---~~~g~~v~vv~lP~gkDpdd~l~~~g~~~~~~~i~~a~~~~~~~~~~~~~~~~~~~~~~~-  371 (407)
T 2au3_A          296 GDDAGRKAMKSAIPLL---LSAGVEVYPVYLPEGYDPDEFIKEFGKEELRRLINSSGELFETLIKTARENLEEKTREFR-  371 (407)
T ss_dssp             SSHHHHHHHHHHHHHH---HHTTCEEEEECCCTTCCHHHHHHHHCHHHHHHHHHHCCCHHHHHHHHGGGCHHHHHHHHH-
T ss_pred             CCHHHHHHHHHHHHHH---HHCCCEEEEEECCCCCCHHHHHHHCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHH-
T ss_conf             8699999999999998---751760489979899895999987399999999956885899999998736886789999-


Q ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999885417998999999999999988765776
Q gi|254780834|r  403 ELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQLFQKY  439 (648)
Q Consensus       403 ~~~~~l~~~I~~I~d~~~R~~yl~~la~~L~~~~~~~  439 (648)
                             ..++.|+|++.|..|+++++++++.....+
T Consensus       372 -------~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l  401 (407)
T 2au3_A          372 -------YYLGFISDGVRRFALASEFHTKYKVPMEIL  401 (407)
T ss_dssp             -------HHHTTCCCHHHHHHHHHHHHHHHCCCHHHH
T ss_pred             -------HHHHHCCCHHHHHHHHHHHHHHHCCCHHHH
T ss_conf             -------999868999999999999999969899999



>1dd9_A DNA primase, DNAG; toprim, 3-helix bundle, DNA-binding protein, RNA polymerase, replication protein, transferase; HET: DNA; 1.60A {Escherichia coli} SCOP: e.13.1.1 PDB: 1dde_A* 1eqn_A* 3b39_A* Back     alignment and structure
>1d0q_A DNA primase; zinc-binding motif, protein, transferase; HET: DNA; 1.71A {Geobacillus stearothermophilus} SCOP: g.41.3.2 Back     alignment and structure
>1nui_A DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA- directed RNA polymerase, primosome, late protein; HET: DNA; 2.90A {Enterobacteria phage T7} SCOP: e.13.1.2 g.41.3.2 Back     alignment and structure
>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2 Back     alignment and structure
>1t6t_1 Putative protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG, unknown function; 1.80A {Aquifex aeolicus VF5} SCOP: c.136.1.1 Back     alignment and structure
>2fcj_A Small toprim domain protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: MES; 1.30A {Geobacillus stearothermophilus} SCOP: c.136.1.1 PDB: 2i5r_A* Back     alignment and structure
>2r6a_C DNAG primase, helicase binding domain, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_G 1z8s_A* Back     alignment and structure
>2r5u_A Replicative DNA helicase; DNAB, primase, replication, ATP-binding, autocatalytic cleavage, DNA replication, DNA-binding, endonuclease; 1.90A {Mycobacterium tuberculosis} Back     alignment and structure
>3gxv_A Replicative DNA helicase; hexameric helicase, primase, replication, ATP-binding, autocatalytic cleavage, DNA replication; 2.20A {Helicobacter pylori} PDB: 3gxv_D 3gxv_C Back     alignment and structure
>1b79_A DNAB helicase; hexamer, DNA replication, hydrolase; 2.30A {Escherichia coli} SCOP: a.81.1.1 PDB: 1jwe_A Back     alignment and structure
>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A Back     alignment and structure
>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus} Back     alignment and structure
>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1} Back     alignment and structure
>1t3w_A DNA primase; DNAG, DNA-directed RNA polymerase, E. coli, DNA replication; HET: DNA MSE; 2.80A {Escherichia coli} SCOP: a.236.1.1 PDB: 2haj_A* Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 648 DNA primase [Candidatus Liberibacter asiaticus str. psy
d1dd9a_314 e.13.1.1 (A:) DNA primase DnaG catalytic core {Escheric 1e-50
d1t6t1_108 c.136.1.1 (1:) Hypothetical protein aq_2086 {Aquifex ae 1e-20
d1d0qa_102 g.41.3.2 (A:) Zinc-binding domain of DNA primase {Bacil 2e-20
d1nuia1192 e.13.1.2 (A:64-255) Primase fragment of primase-helicas 3e-16
d2fcja1114 c.136.1.1 (A:1-114) Hypothetical protein RBSTP2199 {Bac 4e-12
>d1dd9a_ e.13.1.1 (A:) DNA primase DnaG catalytic core {Escherichia coli [TaxId: 562]} Length = 314 Back     information, alignment and structure

class: Multi-domain proteins (alpha and beta)
fold: DNA primase core
superfamily: DNA primase core
family: DNA primase DnaG catalytic core
domain: DNA primase DnaG catalytic core
species: Escherichia coli [TaxId: 562]
 Score =  194 bits (494), Expect = 1e-50
 Identities = 110/316 (34%), Positives = 175/316 (55%), Gaps = 12/316 (3%)

Query: 117 LIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQK 176
           L +L++    F+  SL+         YL++RG+    I  F +G+AP    ++ +     
Sbjct: 2   LYQLMDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGN 61

Query: 177 GFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNS 236
             + + +I+AG+L+  D    SYDRFR R++FPIR  RG+VI FGGR L      KYLNS
Sbjct: 62  PENRQSLIDAGMLVTNDQG-RSYDRFRERVMFPIRDKRGRVIGFGGRVLGNDT-PKYLNS 119

Query: 237 PETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFIILVEGYMDVLSLCQAGVQNVVS 296
           PET +FHKG+ LY  + A                 + +++VEGYMDV++L Q G+   V+
Sbjct: 120 PETDIFHKGRQLYGLYEAQQD----------NAEPNRLLVVEGYMDVVALAQYGINYAVA 169

Query: 297 SLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSRG 356
           SLGT+ T   ++LL++ +  ++ C+DGD  G  AA++A++  L ++  G ++ F+ L  G
Sbjct: 170 SLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDG 229

Query: 357 EDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIK 416
           EDPD+ +R  GK AFE  + +++PL   L+         +TPD RA L       I+ + 
Sbjct: 230 EDPDTLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVP 289

Query: 417 DQKLRYYYSQAIRDRL 432
            + LR Y  Q + ++L
Sbjct: 290 GETLRIYLRQELGNKL 305


>d1t6t1_ c.136.1.1 (1:) Hypothetical protein aq_2086 {Aquifex aeolicus [TaxId: 63363]} Length = 108 Back     information, alignment and structure
>d1d0qa_ g.41.3.2 (A:) Zinc-binding domain of DNA primase {Bacillus stearothermophilus [TaxId: 1422]} Length = 102 Back     information, alignment and structure
>d1nuia1 e.13.1.2 (A:64-255) Primase fragment of primase-helicase protein {Bacteriophage T7 [TaxId: 10760]} Length = 192 Back     information, alignment and structure
>d2fcja1 c.136.1.1 (A:1-114) Hypothetical protein RBSTP2199 {Bacillus stearothermophilus [TaxId: 1422]} Length = 114 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target648 DNA primase [Candidatus Liberibacter asiaticus str. psy
d1dd9a_314 DNA primase DnaG catalytic core {Escherichia coli [TaxI 100.0
d1d0qa_102 Zinc-binding domain of DNA primase {Bacillus stearother 99.93
d1nuia1192 Primase fragment of primase-helicase protein {Bacteriop 99.81
d1t6t1_108 Hypothetical protein aq_2086 {Aquifex aeolicus [TaxId: 99.71
d2fcja1114 Hypothetical protein RBSTP2199 {Bacillus stearothermoph 99.04
d1t3wa_134 DNA primase DnaG, C-terminal domain {Escherichia coli [ 96.58
d1b79a_102 N-terminal domain of DnaB helicase {Escherichia coli [T 96.37
>d1dd9a_ e.13.1.1 (A:) DNA primase DnaG catalytic core {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Multi-domain proteins (alpha and beta)
fold: DNA primase core
superfamily: DNA primase core
family: DNA primase DnaG catalytic core
domain: DNA primase DnaG catalytic core
species: Escherichia coli [TaxId: 562]
Probab=100.00  E-value=0  Score=663.80  Aligned_cols=311  Identities=36%  Similarity=0.673  Sum_probs=299.4

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHCCCEECCCC
Q ss_conf             99999999999999973267775789999850688535101244225677410345542059973452320121003465
Q gi|254780834|r  116 DLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNS  195 (648)
Q Consensus       116 ~~~~~~~~~~~~~~~~l~~~~~~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~~~~~~~~~~~~~gl~~~~~~~  195 (648)
                      +||++++.|++|||.+|+++.+++|++||++||+++++|++|+|||||.+|+.|+++|.++|++.+.+.++||+..+++|
T Consensus         1 ~L~~i~~~a~~~y~~~L~~~~~~~a~~YL~~Rgl~~~~i~~f~lGyap~~~~~l~~~l~~~~~~~~~l~~~gl~~~~~~g   80 (314)
T d1dd9a_           1 TLYQLMDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQG   80 (314)
T ss_dssp             CHHHHHHHHHHHHHHHHTSGGGHHHHHHHHHTTCCHHHHHHHTCEEECSSSCHHHHHHCSSHHHHHHHHHTTSEEEC---
T ss_pred             CHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHEEECCCC
T ss_conf             97999999999999995898408999999977989999987452547665799999986578751566653311211444


Q ss_pred             CCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCCCCCCCCHHCCCHHHHHHHHHHHHCCCCCCCCCCEEE
Q ss_conf             41000016716888970778588850100146553001038767653521011081788886433100002356787089
Q gi|254780834|r  196 ATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFHKGKNLYNFFGALNYLQKSIRKDVRRNSSSFII  275 (648)
Q Consensus       196 ~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~K~~~Ly~l~~a~~~~~~~~~~~~~~~~~~~~i  275 (648)
                      . +||+|+|||||||+|.+|+|||||||++++ ..|||+|||||++|+|+++|||++.|++.|++          .+++|
T Consensus        81 ~-~~d~F~~ri~fPI~d~~g~~i~f~gR~~~~-~~~KY~ns~et~~f~k~~~ly~~~~a~~~~~~----------~~~~i  148 (314)
T d1dd9a_          81 R-SYDRFRERVMFPIRDKRGRVIGFGGRVLGN-DTPKYLNSPETDIFHKGRQLYGLYEAQQDNAE----------PNRLL  148 (314)
T ss_dssp             C-EEESCCSEEEEEEECTTSCEEEEEEEESSS-CSCSEEECCCCSSCCTTTCCBTHHHHHHTCSS----------CSCEE
T ss_pred             C-CCHHCCCEEEEEEECCCCEEEEEEEEECCC-CCCCCCCCCCCCCCCCHHHCCCHHHHHHHHCC----------CCCEE
T ss_conf             3-100104406888850650389994023155-43235578763233311210219998764135----------66359


Q ss_pred             EECCHHHHHHHHHCCCCCCHHHHHCCCCHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             97143889998743554211343213662678988512681899617886622577788888877753697306752578
Q gi|254780834|r  276 LVEGYMDVLSLCQAGVQNVVSSLGTALTEYQLRLLWKLSPRIVLCFDGDDPGLRAAYKAIDLVLCHLIPGNRVNFVLLSR  355 (648)
Q Consensus       276 ~vEGy~Dvi~l~~~G~~n~va~~Gtalt~~~~~~l~r~~~~vvl~fDgD~AG~kAa~Ra~e~~l~~l~~g~~v~vv~LP~  355 (648)
                      |||||||||+|||+||+||||+||||+|++|+++|+|++++|++|||||+||++|+.|++++++++...|.+|+|+.+|+
T Consensus       149 ivEG~~Dvi~l~q~Gi~n~Va~~Gta~t~~~~~~l~~~~~~i~l~~D~D~AG~~A~~r~~~~~~~~~~~g~~v~v~~lp~  228 (314)
T d1dd9a_         149 VVEGYMDVVALAQYGINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPD  228 (314)
T ss_dssp             EESSHHHHHHHHHTTCCCEEECCC-CCCHHHHHHHHHHCSEEEEEEESSHHHHHHHHHHHHHHGGGCCTTCEEEEEEECT
T ss_pred             EEECHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCC
T ss_conf             99456989999970421115677640015889998741786589850675222688868988668735997289996467


Q ss_pred             CCCHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             88888997203668899886414992799999998530233145799999999988541799899999999999998876
Q gi|254780834|r  356 GEDPDSFIRCYGKTAFEKLIVESLPLVDMLWKRETENRSFNTPDERAELEIHLKNCINHIKDQKLRYYYSQAIRDRLQQL  435 (648)
Q Consensus       356 G~DPDe~ir~~G~eaf~~ll~~A~~l~dFl~~~l~~~~dl~spe~ka~~~~~l~~~I~~I~d~~~R~~yl~~la~~L~~~  435 (648)
                      |+|||||++++|+++|.+++++|.++++|+|+.+..+.++++|++++.+++++.++++.|+|+++|++|+++++++++..
T Consensus       229 g~DPDe~l~k~G~e~~~~ll~~a~~~~eFli~~~~~~~d~~s~e~k~~~~~~l~~~i~~i~d~~~r~~y~~~la~~lgis  308 (314)
T d1dd9a_         229 GEDPDTLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLRIYLRQELGNKLGIL  308 (314)
T ss_dssp             TCCHHHHHHHHHHHHHHHHHTTCEEHHHHHHHHHGGGCCTTSHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHTCS
T ss_pred             CCCHHHHHHHCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCC
T ss_conf             67889998732799999887558989999999998558999999999999999999996899999999999999881998


Q ss_pred             HHH
Q ss_conf             577
Q gi|254780834|r  436 FQK  438 (648)
Q Consensus       436 ~~~  438 (648)
                      ...
T Consensus       309 e~a  311 (314)
T d1dd9a_         309 DDS  311 (314)
T ss_dssp             CGG
T ss_pred             HHH
T ss_conf             077



>d1d0qa_ g.41.3.2 (A:) Zinc-binding domain of DNA primase {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1nuia1 e.13.1.2 (A:64-255) Primase fragment of primase-helicase protein {Bacteriophage T7 [TaxId: 10760]} Back     information, alignment and structure
>d1t6t1_ c.136.1.1 (1:) Hypothetical protein aq_2086 {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d2fcja1 c.136.1.1 (A:1-114) Hypothetical protein RBSTP2199 {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1t3wa_ a.236.1.1 (A:) DNA primase DnaG, C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1b79a_ a.81.1.1 (A:) N-terminal domain of DnaB helicase {Escherichia coli [TaxId: 562]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 648 DNA primase [Candidatus Liberibacter asiaticus str
1dd9_A_1-145145 (A:1-145) DNA primase, DNAG; toprim, 3-helix bundl 1e-37
2au3_A_96-224129 (A:96-224) DNA primase; zinc ribbon, toprim, RNA p 4e-32
1dd9_A_146-285140 (A:146-285) DNA primase, DNAG; toprim, 3-helix bun 7e-30
2au3_A_225-349125 (A:225-349) DNA primase; zinc ribbon, toprim, RNA 3e-27
1t6t_1_118 (1:) Putative protein; structural genomics, PSI, p 7e-25
2fcj_A_119 (A:) Small toprim domain protein; structural genom 3e-21
1q57_A_75-203129 (A:75-203) DNA primase/helicase; dntpase, DNA repl 2e-20
1nui_A_138-255118 (A:138-255) DNA primase/helicase; zinc-biding doma 6e-19
1d0q_A_23-6947 (A:23-69) DNA primase; zinc-binding motif, protein 3e-17
2au3_A_20-6647 (A:20-66) DNA primase; zinc ribbon, toprim, RNA po 5e-17
>1dd9_A (A:1-145) DNA primase, DNAG; toprim, 3-helix bundle, DNA-binding protein, RNA polymerase, replication protein; HET: DNA; 1.60A {Escherichia coli}Length = 145 Back     alignment and structure
 Score =  152 bits (386), Expect = 1e-37
 Identities = 50/149 (33%), Positives = 75/149 (50%), Gaps = 4/149 (2%)

Query: 95  IAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAI 154
           + G                +  L +L++    F+  SL+         YL++RG+    I
Sbjct: 1   MRGSHHH--HHHGSGSMHQRQTLYQLMDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVI 58

Query: 155 EMFKLGYAPDSRYSLREHLRQKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSR 214
             F +G+AP    ++ +       + + +I+AG+L+  D    SYDRFR R++FPIR  R
Sbjct: 59  ARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQG-RSYDRFRERVMFPIRDKR 117

Query: 215 GQVIAFGGRTLSKGESVKYLNSPETILFH 243
           G+VI FGGR L      KYLNSPET +FH
Sbjct: 118 GRVIGFGGRVLGNDTP-KYLNSPETDIFH 145


>2au3_A (A:96-224) DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication, transferase; HET: DNA; 2.00A {Aquifex aeolicus}Length = 129 Back     alignment and structure
>1dd9_A (A:146-285) DNA primase, DNAG; toprim, 3-helix bundle, DNA-binding protein, RNA polymerase, replication protein; HET: DNA; 1.60A {Escherichia coli}Length = 140 Back     alignment and structure
>2au3_A (A:225-349) DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication, transferase; HET: DNA; 2.00A {Aquifex aeolicus}Length = 125 Back     alignment and structure
>1t6t_1 (1:) Putative protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG, unknown function; 1.80A {Aquifex aeolicus VF5}Length = 118 Back     alignment and structure
>2fcj_A (A:) Small toprim domain protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: MES; 1.30A {Geobacillus stearothermophilus}Length = 119 Back     alignment and structure
>1q57_A (A:75-203) DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7}Length = 129 Back     alignment and structure
>1nui_A (A:138-255) DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA- directed RNA polymerase, primosome, late protein; HET: DNA; 2.90A {Enterobacteria phage T7}Length = 118 Back     alignment and structure
>1d0q_A (A:23-69) DNA primase; zinc-binding motif, protein; HET: DNA; 1.71A {Bacillus stearothermophilus}Length = 47 Back     alignment and structure
>2au3_A (A:20-66) DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication, transferase; HET: DNA; 2.00A {Aquifex aeolicus}Length = 47 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target648 DNA primase [Candidatus Liberibacter asiaticus str. psy
1dd9_A_1-145145 DNA primase, DNAG; toprim, 3-helix bundle, DNA-bin 99.96
2au3_A_96-224129 DNA primase; zinc ribbon, toprim, RNA polymerase, 99.95
1dd9_A_146-285140 DNA primase, DNAG; toprim, 3-helix bundle, DNA-bin 99.82
2au3_A_225-349125 DNA primase; zinc ribbon, toprim, RNA polymerase, 99.79
1t6t_1_118 Putative protein; structural genomics, PSI, protei 99.7
1q57_A_75-203129 DNA primase/helicase; dntpase, DNA replication, tr 99.59
1nui_A_138-255118 DNA primase/helicase; zinc-biding domain, toprim f 99.57
2fcj_A_119 Small toprim domain protein; structural genomics, 99.75
1d0q_A_23-6947 DNA primase; zinc-binding motif, protein; HET: DNA 99.56
2au3_A_20-6647 DNA primase; zinc ribbon, toprim, RNA polymerase, 99.55
1d0q_A_1-22_70-10356 DNA primase; zinc-binding motif, protein; HET: DNA 97.86
2r5u_A_200 Replicative DNA helicase; DNAB, primase, replicati 97.63
2r6a_A_1-155155 DNAB helicase, replicative helicase; replication, 97.4
1b79_A_119 DNAB helicase; hexamer, DNA replication; 2.30A {Es 96.86
3gxv_A_123 Replicative DNA helicase; hexameric helicase, prim 96.82
2q6t_A_1-152152 DNAB replication FORK helicase; hydrolase; 2.90A { 96.71
3bgw_A_1-154154 DNAB-like replicative helicase; ATPase, replicatio 96.02
1t3w_A_1-109109 DNA primase; DNAG, DNA-directed RNA polymerase, E. 91.36
2r6a_C_1-100100 DNAG primase, helicase binding domain, replicative 97.11
2au3_A_1-19_67-9548 DNA primase; zinc ribbon, toprim, RNA polymerase, 90.85
>1dd9_A (A:1-145) DNA primase, DNAG; toprim, 3-helix bundle, DNA-binding protein, RNA polymerase, replication protein; HET: DNA; 1.60A {Escherichia coli} Back     alignment and structure
Probab=99.96  E-value=3.5e-30  Score=296.65  Aligned_cols=145  Identities=34%  Similarity=0.638  Sum_probs=133.9

Q ss_pred             HHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHCCCCCCCCCCCCCHHHHHHH
Q ss_conf             81885877682036777889999999999999999973267775789999850688535101244225677410345542
Q gi|254780834|r   95 IAGVPLPVVDPKIEKKEKIQTDLIRLIEVATDFFHHSLKNARDKRLHYYLDERGIDSHAIEMFKLGYAPDSRYSLREHLR  174 (648)
Q Consensus        95 ~~gi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~a~~yl~~Rg~~~~~~~~f~lG~ap~~~~~l~~~l~  174 (648)
                      .|||++|...  ..++..+++.++++++.|++|||.+|+++.+++|++||.+|||++++|+.|+|||||.+|+.|..++.
T Consensus         1 ~~gi~l~~~~--~~~~~~~~~~l~~~~~~a~~~y~~~L~~~~~~~a~~YL~~Rgl~~~~i~~F~lGyap~~~~~l~~~~~   78 (145)
T 1dd9_A            1 MRGSHHHHHH--GSGSMHQRQTLYQLMDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFG   78 (145)
T ss_dssp             ---------------------CHHHHHHHHHHHHHHHHTSGGGHHHHHHHHHTTCCHHHHHHHTCEEECSSSCHHHHHHC
T ss_pred             CCCCCCCCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHHHCCCCCCCCCHHHHHHHHH
T ss_conf             9875445667--88767799999999999999999996897408999999977989999986512547655799999987


Q ss_pred             CCCCCHHHHHHHCCCEECCCCCCCCCCCCCEEEEEEEECCCCEEEEECCCCCCCCCCEECCCCCCCCCC
Q ss_conf             059973452320121003465410000167168889707785888501001465530010387676535
Q gi|254780834|r  175 QKGFSEEKIIEAGLLIDGDNSATSYDRFRNRLIFPIRSSRGQVIAFGGRTLSKGESVKYLNSPETILFH  243 (648)
Q Consensus       175 ~~~~~~~~~~~~gl~~~~~~~~~~~d~Fr~Ri~fPi~~~~g~~i~f~gR~l~~~~~~KYlNSpeT~if~  243 (648)
                      ++|++.++|.++||+..+++|. +||+|+|||||||+|..|+|||||||+|+++ .|||||||||++|+
T Consensus        79 ~~~~~~~~l~~~GL~~~~~~g~-~~d~F~~RiifPI~d~~G~vvgF~gR~l~~~-~pKYlNspet~iF~  145 (145)
T 1dd9_A           79 GNPENRQSLIDAGMLVTNDQGR-SYDRFRERVMFPIRDKRGRVIGFGGRVLGND-TPKYLNSPETDIFH  145 (145)
T ss_dssp             SSHHHHHHHHHTTSEEEC---C-EEESCCSEEEEEEECTTSCEEEEEEEESSSC-SCSEEECCCCSSCC
T ss_pred             HCCCCHHHHHHCCCEEECCCCC-CHHHHCCEEEEEEECCCCEEEEEEEEECCCC-CCCCCCCCCCCCCC
T ss_conf             5798767787547734346533-0122223268888516621899931231666-43245788754544



>2au3_A (A:96-224) DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication, transferase; HET: DNA; 2.00A {Aquifex aeolicus} Back     alignment and structure
>1dd9_A (A:146-285) DNA primase, DNAG; toprim, 3-helix bundle, DNA-binding protein, RNA polymerase, replication protein; HET: DNA; 1.60A {Escherichia coli} Back     alignment and structure
>2au3_A (A:225-349) DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication, transferase; HET: DNA; 2.00A {Aquifex aeolicus} Back     alignment and structure
>1t6t_1 (1:) Putative protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG, unknown function; 1.80A {Aquifex aeolicus VF5} Back     alignment and structure
>1q57_A (A:75-203) DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} Back     alignment and structure
>1nui_A (A:138-255) DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA- directed RNA polymerase, primosome, late protein; HET: DNA; 2.90A {Enterobacteria phage T7} Back     alignment and structure
>2fcj_A (A:) Small toprim domain protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: MES; 1.30A {Geobacillus stearothermophilus} Back     alignment and structure
>1d0q_A (A:23-69) DNA primase; zinc-binding motif, protein; HET: DNA; 1.71A {Bacillus stearothermophilus} Back     alignment and structure
>2au3_A (A:20-66) DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication, transferase; HET: DNA; 2.00A {Aquifex aeolicus} Back     alignment and structure
>1d0q_A (A:1-22,A:70-103) DNA primase; zinc-binding motif, protein; HET: DNA; 1.71A {Bacillus stearothermophilus} Back     alignment and structure
>2r5u_A (A:) Replicative DNA helicase; DNAB, primase, replication, ATP-binding, autocatalytic cleavage, DNA replication, DNA-binding, endonuclease; 1.90A {Mycobacterium tuberculosis} Back     alignment and structure
>2r6a_A (A:1-155) DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A Back     alignment and structure
>1b79_A (A:) DNAB helicase; hexamer, DNA replication; 2.30A {Escherichia coli} Back     alignment and structure
>3gxv_A (A:) Replicative DNA helicase; hexameric helicase, primase, replication, ATP-binding, autocatalytic cleavage, DNA replication; 2.20A {Helicobacter pylori} PDB: 3gxv_D 3gxv_C Back     alignment and structure
>2q6t_A (A:1-152) DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus} Back     alignment and structure
>3bgw_A (A:1-154) DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1} Back     alignment and structure
>1t3w_A (A:1-109) DNA primase; DNAG, DNA-directed RNA polymerase, E. coli, DNA replication; HET: DNA MSE; 2.80A {Escherichia coli} Back     alignment and structure
>2r6a_C (C:1-100) DNAG primase, helicase binding domain, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_G 1z8s_A* Back     alignment and structure
>2au3_A (A:1-19,A:67-95) DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication, transferase; HET: DNA; 2.00A {Aquifex aeolicus} Back     alignment and structure