254780127

254780127

putative DNA polymerase from bacteriophage origin

GeneID in NCBI database:8209102Locus tag:CLIBASIA_00030
Protein GI in NCBI database:254780127Protein Accession:YP_003064540.1
Gene range:+(3745, 5772)Protein Length:675aa
Gene description:putative DNA polymerase from bacteriophage origin
COG prediction:[L] DNA polymerase I - 3'-5' exonuclease and polymerase domains
KEGG prediction:putative DNA polymerase from bacteriophage origin; K02334 DNA polymerase bacteriophage-type [EC:2.7.7.7]
SEED prediction:DNA polymerase I (EC 2.7.7.7)
Pathway involved in KEGG:not defined
Subsystem involved in SEED:DNA Repair Base Excision;
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
TOPPREDnone 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-------650-------660-------670-----
MSKLFIDIETRSPQPLPKVGVWAYAEQAVITLCAYAWDDEPVKLWDRTEQSAMPSDLLQYLRDETVMCVAHNSLFERILFKKTLGIDIPSKRWICTSVLARTNGLPSSLKNACLALNFSEHLTKMEEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFKRLIPLSDGERDLWLLDQTINDRGYRIDLDLVLKLQELIAQERKKLDEDIVKLTDGIIRSSRQTYALRMYLFLITGIDLVDMSEGTLKSILSHSNITQLAKDLILNRLASSGSAILKLNTLSEAVSSDGRLRGTLQFYGASRTGRWSGCVFQPQNLPRQERSEEILTQTIQALNRGETIADPLGLASDCVRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSKEQRAIGKVMELALGYQGGAKVFKTMASHCGLDLQQFSQNVKSTSTFEDWEQAESHHLWMQDQYPEFAVKDKLIGTACELVKKAWRAKHQGVLQLWKDLTEGFACVVQEGGSISARRVANVPRLVMRRHKRDVHIVLPSSRRLVYSDVKGDCSYLNTATSQLMRERTYGGKLTENIVQAISRDILCEGMKNATKNGYDIVLTVHDEIVSETPDTPYFSVGTLCSLMTKNPSWAKGLPLKAEGYEAKRYRK
ccEEEEEEcccccccccccccccccccccEEEEEEEcccccccEEcccccccccHHHHHHHHcccccEEEEcHHHHHHHHHHccccccccHHHHHHHHHHcccccccccHHHHHHHccccccccccccHHHHHHHccccccHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccEEEcHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEEEEEccccccccccccccccccccccHHHHcccccccccccccccccHHHHHHHHHHHccccccEEEEEccHHHHHHHHHHHHccHHHHHHHHccccHHHHHHHHHHcccHHHccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHccccEEEEEccccEEEEccccccHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEccEEEEEccccHHHHHHHHHHHHccccccccccccccccccHHcccc
ccEEEEEEcccccccHHHcccHHHHccccEEEEEEcccccccccccccccccHHHHHHHHHccHHHHHHHccccHHHHHHHHHcccccccHHHHHHHHHHHHHccccccccHHHHHHcHHHHHHHHccccEEEEEccccHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHcccccccccHHHHHHHHHcccccHHHHHHHHHHHHHHccccHHHHHHHccccccccEEEEEEEcccccccccccccccccccccccccHHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccccEEEEEcHHHHHHHHHHHHHcccHHHHHHHccccHHHHHHHHHHcccHHHccHHHHHHHHHHHHHHHccccHHHHHHHHHHHcccHHHHHHHHcccccHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHcccccccccccccccEEEEEEEccEEEEEcccccEEEEEccccEEEEEcccccHHHHEccccHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEccEEEEEccccccccHHHHHHHHcccccccccccccccccccccccc
MSKLFIDietrspqplpkvgvWAYAEQAVITLCAYawddepvklwdrteqsampsdlLQYLRDETVMCVAHNSLFERILFKktlgidipskrwICTSVLartnglpsslKNACLALNFSEHLTKMEEGKALIARFCkgsidsppydctraNHVQAWQLFGEYCKRDVEATRELFKRLiplsdgerdLWLLDqtindrgyrIDLDLVLKLQELIAQERKKLDEDIVKLTDGIIRSSRQTYALRMYLFLITGidlvdmsegTLKSILSHSNITQLAKDLILNRLASSGSAILKLNTLSeavssdgrlrgtlqfygasrtgrwsgcvfqpqnlprqerSEEILTQTIQALNrgetiadplglasdCVRSciiasngkKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSKEQRAIGKVMELALGYQGGAKVFKTMAshcgldlqqfsqnvkststfedWEQAESHHlwmqdqypefavkDKLIGTACELVKKAWRAKHQGVLQLWKDLTEGFACVVQeggsisarrvanvprlvmrrhkrdvhivlpssrrlvysdvkgdcsYLNTATSQLMrertyggkltENIVQAISRDILCEGMKNATKNGYDIVLTVHDeivsetpdtpyfsvGTLCSlmtknpswakglplkaegyeakryrk
msklfidietrspqplpkVGVWAYAEQAVITLCAYAWDDEPVKLWDRTEQSAMPSDLLQYLRDETVMCVAHNSLFERILFkktlgidipskRWICTSVLARTNGLPSSLKNACLALNFSEHLTKMEEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFKRliplsdgerdlWLLDQTINDRGYRIDLDLVLKLQELIAQErkkldedivkltdgiirssrqtyALRMYLFLITGIDLVDMSEGTLKSILSHSNITQLAKDLILNRLASSGSAILKLNTLseavssdgrlRGTLQFYgasrtgrwsgCVFQPQNLPRQERSEEILTQTIQALNRGETIADPLGLASDCVRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSKEQRAIGKVMELALGYQGGAKVFKTMASHCGLDLQQFSQNVKSTSTFEDWEQAESHHLWMQDQYPEFAVKDKLIGTACELVKKAWRAKHQGVLQLWKDLTEGFACVVqeggsisarrvanvprlvmrrhkrdvhivlpssrrlvysdvkGDCSYLNtatsqlmrertyggkltenIVQAISRDILCEGMKNATKNGYDIVLTVHDEIVSETPDTPYFSVGTLCSLMtknpswakglplkaegyeakryrk
MSKLFIDIETRSPQPLPKVGVWAYAEQAVITLCAYAWDDEPVKLWDRTEQSAMPSDLLQYLRDETVMCVAHNSLFERILFKKTLGIDIPSKRWICTSVLARTNGLPSSLKNACLALNFSEHLTKMEEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFKRLIPLSDGERDLWLLDQTINDRGYRIDLDLVLKLQELIAQERKKLDEDIVKLTDGIIRSSRQTYALRMYLFLITGIDLVDMSEGTLKSILSHSNITQLAKDLILNRLASSGSAILKLNTLSEAVSSDGRLRGTLQFYGASRTGRWSGCVFQPQNLPRQERSEEILTQTIQALNRGETIADPLGLASDCVRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSKEQRAIGKVMELALGYQGGAKVFKTMASHCGLDLQQFSQNVKSTSTFEDWEQAESHHLWMQDQYPEFAVKDKLIGTACELVKKAWRAKHQGVLQLWKDLTEGFACVVQEGGSISARRVANVPRLVMRRHKRDVHIVLPSSRRLVYSDVKGDCSYLNTATSQLMRERTYGGKLTENIVQAISRDILCEGMKNATKNGYDIVLTVHDEIVSETPDTPYFSVGTLCSLMTKNPSWAKGLPLKAEGYEAKRYRK
*SKLFIDIETRSPQPLPKVGVWAYAEQAVITLCAYAWDDEPVKLWDRTEQSAMPSDLLQYLRDETVMCVAHNSLFERILFKKTLGIDIPSKRWICTSVLARTNGLPSSLKNACLALNFSEHLTKMEEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFKRLIPLSDGERDLWLLDQTINDRGYRIDLDLVLKLQELIAQERKKLDEDIVKLTDGIIRSSRQTYALRMYLFLITG******************NITQLAKDLILNRLASSGSAILKLNTLSEAVSSDGRLRGTLQFYGASRTGRWSGCVFQPQNLPRQERSEEILTQTIQALNRGETIADPLGLASDCVRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDK*********KVMELALGYQGGAKVFKTMASHCGLDLQQFSQNVKSTSTFEDWEQAESHHLWMQDQYPEFAVKDKLIGTACELVKKAWRAKHQGVLQLWKDLTEGFACVVQEGGSISARRVANVPRLVMRRHKRDVHIVLPSSRRLVYSDVKGDCSYLNTATSQLMRERTYGGKLTENIVQAISRDILCEGMKNATKNGYDIVLTVHDEIVSETPDTPYFSVGTLCSLMTKNPSWAKGLPLKAEGYEAKRYRK
MSKLFIDIETRSPQPLPKVGVWAYAEQAVITLCAYAWDDEPVKLWDRTEQSAMPSDLLQYLRDETVMCVAHNSLFERILFKKTLGIDIPSKRWICTSVLARTNGLPSSLKNACLALNFSEHLTKMEEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFKRLIPLSDGERDLWLLDQTINDRGYRIDLDLVLKLQELIAQERKKLDEDIVKLTDGIIRSSRQTYALRMYLFLITGIDLVDMSEGTLKSILSHSNITQLAKDLILNRLASSGSAILKLNTLSEAVSSDGRLRGTLQFYGASRTGRWSGCVFQPQNLPRQERSEEILTQTIQALNRGETIADPLGLASDCVRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSKEQRAIGKVMELALGYQGGAKVFKTMASHCGLDLQQFSQNVKSTSTFEDWEQAESHHLWMQDQYPEFAVKDKLIGTACELVKKAWRAKHQGVLQLWKDLTEGFACVVQEGGSISARRVANVPRLVMRRHKRDVHIVLPSSRRLVYSDVKGDCSYLNTATSQLMRERTYGGKLTENIVQAISRDILCEGMKNATKNGYDIVLTVHDEIVSETPDTPYFSVGTLCSLMTKNPSWAKGLPLKAEGYEAKRYRK
MSKLFIDIETRSPQPLPKVGVWAYAEQAVITLCAYAWDDEPVKLWDRTEQSAMPSDLLQYLRDETVMCVAHNSLFERILFKKTLGIDIPSKRWICTSVLARTNGLPSSLKNACLALNFSEHLTKMEEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFKRLIPLSDGERDLWLLDQTINDRGYRIDLDLVLKLQELIAQERKKLDEDIVKLTDGIIRSSRQTYALRMYLFLITGIDLVDMSEGTLKSILSHSNITQLAKDLILNRLASSGSAILKLNTLSEAVSSDGRLRGTLQFYGASRTGRWSGCVFQPQNLPRQERSEEILTQTIQALNRGETIADPLGLASDCVRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSKEQRAIGKVMELALGYQGGAKVFKTMASHCGLDLQQFSQNVKSTSTFEDWEQAESHHLWMQDQYPEFAVKDKLIGTACELVKKAWRAKHQGVLQLWKDLTEGFACVVQEGGSISARRVANVPRLVMRRHKRDVHIVLPSSRRLVYSDVKGDCSYLNTATSQLMRERTYGGKLTENIVQAISRDILCEGMKNATKNGYDIVLTVHDEIVSETPDTPYFSVGTLCSLMTKNPSWAKGLPLKAEGYEAKRYRK
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MSKLFIDIETRSPQPLPKVGVWAYAEQAVITLCAYAWDDEPVKLWDRTEQSAMPSDLLQYLRDETVMCVAHNSLFERILFKKTLGIDIPSKRWICTSVLARTNGLPSSLKNACLALNFSEHLTKMEEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFKRLIPLSDGERDLWLLDQTINDRGYRIDLDLVLKLQELIAQERKKLDEDIVKLTDGIIRSSRQTYALRMYLFLITGIDLVDMSEGTLKSILSHSNITQLAKDLILNRLASSGSAILKLNTLSEAVSSDGRLRGTLQFYGASRTGRWSGCVFQPQNLPRQERSEEILTQTIQALNRGETIADPLGLASDCVRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSKEQRAIGKVMELALGYQGGAKVFKTMASHCGLDLQQFSQNVKSTSTFEDWEQAESHHLWMQDQYPEFAVKDKLIGTACELVKKAWRAKHQGVLQLWKDLTEGFACVVQEGGSISARRVANVPRLVMRRHKRDVHIVLPSSRRLVYSDVKGDCSYLNTATSQLMRERTYGGKLTENIVQAISRDILCEGMKNATKNGYDIVLTVHDEIVSETPDTPYFSVGTLCSLMTKNPSWAKGLPLKAEGYEAKRYRK
MSKLFIDIETRSPQPLPKVGVWAYAEQAVITLCAYAWDDEPVKLWDRTEQSAMPSDLLQYLRDETVMCVAHNSLFERILFKKTLGIDIPSKRWICTSVLARTNGLPSSLKNACLALNFSEHLTKMEEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFKRLIPLSDGERDLWLLDQTINDRGYRIDLDLVLKLQELIAQERKKLDEDIVKLTDGIIRSSRQTYALRMYLFLITGIDLVDMSEGTLKSILSHSNITQLAKDLILNRLASSGSAILKLNTLSEAVSSDGRLRGTLQFYGASRTGRWSGCVFQPQNLPRQERSEEILTQTIQALNRGETIADPLGLASDCVRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSKEQRAIGKVMELALGYQGGAKVFKTMASHCGLDLQQFSQNVKSTSTFEDWEQAESHHLWMQDQYPEFAVKDKLIGTACELVKKAWRAKHQGVLQLWKDLTEGFACVVQEGGSISARRVANVPRLVMRRHKRDVHIVLPSSRRLVYSDVKGDCSYLNTATSQLMRERTYGGKLTENIVQAISRDILCEGMKNATKNGYDIVLTVHDEIVSETPDTPYFSVGTLCSLMTKNPSWAKGLPLKAEGYEAKRYRK
MSKLFIDIETRSPQPLPKVGVWAYAEQAVITLCAYAWDDEPVKLWDRTEQSAMPSDLLQYLRDETVMCVAHNSLFERILFKKTLGIDIPSKRWICTSVLARTNGLPSSLKNACLALNFSEHLTKMEEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFKRLIPLSDGERDLWLLDQTINDRGYRIDLDLVLKLQELIAQERKKLDEDIVKLTDGIIRSSRQTYALRMYLFLITGIDLVDMSEGTLKSILSHSNITQLAKDLILNRLASSGSAILKLNTLSEAVSSDGRLRGTLQFYGASRTGRWSGCVFQPQNLPRQERSEEILTQTIQALNRGETIADPLGLASDCVRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSKEQRAIGKVMELALGYQGGAKVFKTMASHCGLDLQQFSQNVKSTSTFEDWEQAESHHLWMQDQYPEFAVKDKLIGTACELVKKAWRAKHQGVLQLWKDLTEGFACVVQEGGSISARRVANVPRLVMRRHKRDVHIVLPSSRRLVYSDVKGDCSYLNTATSQLMRERTYGGKLTENIVQAISRDILCEGMKNATKNGYDIVLTVHDEIVSETPDTPYFSVGTLCSLMTKNPSWAKGLPLKAEGYEAKRYRK

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target675 putative DNA polymerase from bacteriophage origin [Cand
254781193675 putative DNA polymerase from bacteriophage origin 0.0
254780277976 DNA polymerase I [Candidatus Liberibacter asiaticu 5e-07
>gi|254781193|ref|YP_003065606.1| putative DNA polymerase from bacteriophage origin [Candidatus Liberibacter asiaticus str. psy62] Length = 675 Back     alignment
 Score =  793 bits (2047), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 402/677 (59%), Positives = 484/677 (71%), Gaps = 4/677 (0%)

Query: 1   MSKLFIDIETRSPQPLPKVGVWAYAEQAVITLCAYAWDDEPVKLWDRTEQSAMPSDLLQY 60
           M+ LFID ETRSP  L K G+  YAE   + L A+ +DD PV+LWD      MP  L + 
Sbjct: 1   MATLFIDFETRSPIDLTKCGICKYAEDVCVILFAFGFDDHPVELWDCVHDPVMPQVLKEA 60

Query: 61  LRDETVMCVAHNSLFERILFKKTLGIDIPSKRWICTSVLARTNGLPSSLKNACLALNFSE 120
           L +  V  VAHNS FER + K    +DIP  RWICT VLAR+NGLPS+LK    AL  S 
Sbjct: 61  LENTDVTIVAHNSYFERTVLKACFNLDIPIHRWICTLVLARSNGLPSALKAVGEALKLSS 120

Query: 121 HLTKMEEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFKRLIPL 180
              KMEEGK LIARFCKG      YD  + NH +AW+LFGEYCK DV  TRE+FKRL PL
Sbjct: 121 Q--KMEEGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTREIFKRLEPL 178

Query: 181 SDGERDLWLLDQTINDRGYRIDLDLVLKLQELIAQERKKLDEDIVKLTDGIIRSSRQTYA 240
           S  E++LW LDQTINDRGY +D+ L   L +++  ER KLD+++  LT G++ SSR    
Sbjct: 179 SSKEQELWYLDQTINDRGYCVDVALAHTLNQIVDVERTKLDQELESLTYGLVSSSRCLEK 238

Query: 241 LRMYLFLITGIDLVDMSEGTLKSILS-HSNITQLAKDLILNRLASSGSAILKLNTLSEAV 299
           L+ +LFL TG+ L D++E T + +LS +  +T  A  +  NR+ +S SA+LKLNTL EA+
Sbjct: 239 LKTWLFLETGLHLEDLTETTCQRVLSSNKKLTPQAIQVFNNRMRASRSAVLKLNTLVEAM 298

Query: 300 SSDGRLRGTLQFYGASRTGRWSGCVFQPQNLPRQERSEEILTQTIQALNRGETI-ADPLG 358
           +SDGRLRGTLQF GASRTGRWSGCVF PQNLPR  RS E L Q I  L    T   DPL 
Sbjct: 299 NSDGRLRGTLQFLGASRTGRWSGCVFPPQNLPRPSRSHEELDQIITHLPTSITSDPDPLQ 358

Query: 359 LASDCVRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFN 418
           + SDCVRSC+IAS GKKLVVADLAGIEARVLAW+AGE WK+KAF  GED+YVTTYA++FN
Sbjct: 359 IISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFN 418

Query: 419 TPIDKVSKEQRAIGKVMELALGYQGGAKVFKTMASHCGLDLQQFSQNVKSTSTFEDWEQA 478
               +V+K+QRAIGKVMELALGYQGGAK F+ MAS  GL+L  F+  VK+ S  E+WE A
Sbjct: 419 VAPAQVTKDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNSAPEEWEDA 478

Query: 479 ESHHLWMQDQYPEFAVKDKLIGTACELVKKAWRAKHQGVLQLWKDLTEGFACVVQEGGSI 538
           E+   WMQ+ +PE A++D  IGTACE VKKAWR KH  V +LW +L + F   ++ G +I
Sbjct: 479 ENFCRWMQENHPEHAIEDLFIGTACERVKKAWRQKHSRVSELWNELHQAFEQTIENGKAI 538

Query: 539 SARRVANVPRLVMRRHKRDVHIVLPSSRRLVYSDVKGDCSYLNTATSQLMRERTYGGKLT 598
            AR+  +VP + M++ K ++ ++LPS R LVY DV  + SYLNT T QL RE TYGGKLT
Sbjct: 539 IARKRRDVPLVYMKKDKNNLILMLPSGRSLVYRDVGNNRSYLNTTTRQLTREYTYGGKLT 598

Query: 599 ENIVQAISRDILCEGMKNATKNGYDIVLTVHDEIVSETPDTPYFSVGTLCSLMTKNPSWA 658
           ENIVQA+SRDIL EGM NATK GYDIVLTVHDEIV ETPDT  F+   L  LMT NPSWA
Sbjct: 599 ENIVQAVSRDILAEGMMNATKAGYDIVLTVHDEIVCETPDTDEFNASMLYHLMTSNPSWA 658

Query: 659 KGLPLKAEGYEAKRYRK 675
           KGLPLKAEGYE+KRYRK
Sbjct: 659 KGLPLKAEGYESKRYRK 675

>gi|254780277|ref|YP_003064690.1| DNA polymerase I [Candidatus Liberibacter asiaticus str. psy62] Length = 976 Back     alignment
 Score = 48.1 bits (113), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 40/78 (51%)

Query: 364 VRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTPIDK 423
           +R   I+   KKL+ AD + IE R+LA IA      + F N  DI+    A+ F   I+K
Sbjct: 733 IRRAFISPPTKKLISADYSQIELRILAHIAKITPLYQVFENSLDIHRMVAAEIFGVNIEK 792

Query: 424 VSKEQRAIGKVMELALGY 441
           VS + R   K +  ++ Y
Sbjct: 793 VSPQMRRHAKTINFSIIY 810

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

IdentityAlignment graphLength Definition Round E-value
Target675 putative DNA polymerase from bacteriophage origin [Cand
255957611675 DNA-directed DNA polymerase [Candidatus Liberibacter as 1 0.0
255957621675 DNA-directed DNA polymerase [Candidatus Liberibacter as 1 0.0
255957561675 DNA-directed DNA polymerase [Candidatus Liberibacter as 1 0.0
255957596675 DNA-directed DNA polymerase [Candidatus Liberibacter as 1 0.0
255957556675 DNA-directed DNA polymerase [Candidatus Liberibacter as 1 0.0
315121967673 putative DNA polymerase from bacteriophage origin [Cand 1 0.0
315122935675 putative DNA polymerase from bacteriophage origin [Cand 1 0.0
254781193675 putative DNA polymerase from bacteriophage origin [Cand 1 0.0
212712317685 hypothetical protein PROVALCAL_03405 [Providencia alcal 1 1e-123
291283829687 DNA polymerase I - 3''''-5'''' exonuclease and polymera 1 1e-119
>gi|255957611|dbj|BAH96662.1| DNA-directed DNA polymerase [Candidatus Liberibacter asiaticus] Length = 675 Back     alignment and organism information
 Score = 1396 bits (3613), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 674/675 (99%), Positives = 674/675 (99%)

Query: 1   MSKLFIDIETRSPQPLPKVGVWAYAEQAVITLCAYAWDDEPVKLWDRTEQSAMPSDLLQY 60
           MSKLFIDIETRSPQPLPKVGVWAYAEQAVITLCAYAWDDEPVKLWDRTEQSAMPSDLLQY
Sbjct: 1   MSKLFIDIETRSPQPLPKVGVWAYAEQAVITLCAYAWDDEPVKLWDRTEQSAMPSDLLQY 60

Query: 61  LRDETVMCVAHNSLFERILFKKTLGIDIPSKRWICTSVLARTNGLPSSLKNACLALNFSE 120
           LRDETVMCVAHNSLFERILFKKTLGIDIPSKRWICTSVLARTNGLPSSLKNACLALNFSE
Sbjct: 61  LRDETVMCVAHNSLFERILFKKTLGIDIPSKRWICTSVLARTNGLPSSLKNACLALNFSE 120

Query: 121 HLTKMEEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFKRLIPL 180
           HLTKMEEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFKRLIPL
Sbjct: 121 HLTKMEEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFKRLIPL 180

Query: 181 SDGERDLWLLDQTINDRGYRIDLDLVLKLQELIAQERKKLDEDIVKLTDGIIRSSRQTYA 240
           SDGERDLWLLDQTINDRGYRIDLDLVLKLQELIAQERKKLDEDIVKLTDGIIRSSRQTY 
Sbjct: 181 SDGERDLWLLDQTINDRGYRIDLDLVLKLQELIAQERKKLDEDIVKLTDGIIRSSRQTYT 240

Query: 241 LRMYLFLITGIDLVDMSEGTLKSILSHSNITQLAKDLILNRLASSGSAILKLNTLSEAVS 300
           LRMYLFLITGIDLVDMSEGTLKSILSHSNITQLAKDLILNRLASSGSAILKLNTLSEAVS
Sbjct: 241 LRMYLFLITGIDLVDMSEGTLKSILSHSNITQLAKDLILNRLASSGSAILKLNTLSEAVS 300

Query: 301 SDGRLRGTLQFYGASRTGRWSGCVFQPQNLPRQERSEEILTQTIQALNRGETIADPLGLA 360
           SDGRLRGTLQFYGASRTGRWSGCVFQPQNLPRQERSEEILTQTIQALNRGETIADPLGLA
Sbjct: 301 SDGRLRGTLQFYGASRTGRWSGCVFQPQNLPRQERSEEILTQTIQALNRGETIADPLGLA 360

Query: 361 SDCVRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTP 420
           SDCVRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTP
Sbjct: 361 SDCVRSCIIASNGKKLVVADLAGIEARVLAWIAGEDWKIKAFANGEDIYVTTYAKAFNTP 420

Query: 421 IDKVSKEQRAIGKVMELALGYQGGAKVFKTMASHCGLDLQQFSQNVKSTSTFEDWEQAES 480
           IDKVSKEQRAIGKVMELALGYQGGAKVFKTMASHCGLDLQQFSQNVKSTSTFEDWEQAES
Sbjct: 421 IDKVSKEQRAIGKVMELALGYQGGAKVFKTMASHCGLDLQQFSQNVKSTSTFEDWEQAES 480

Query: 481 HHLWMQDQYPEFAVKDKLIGTACELVKKAWRAKHQGVLQLWKDLTEGFACVVQEGGSISA 540
           HHLWMQDQYPEFAVKDKLIGTACELVKKAWRAKHQGVLQLWKDLTEGFACVVQEGGSISA
Sbjct: 481 HHLWMQDQYPEFAVKDKLIGTACELVKKAWRAKHQGVLQLWKDLTEGFACVVQEGGSISA 540

Query: 541 RRVANVPRLVMRRHKRDVHIVLPSSRRLVYSDVKGDCSYLNTATSQLMRERTYGGKLTEN 600
           RRVANVPRLVMRRHKRDVHIVLPSSRRLVYSDVKGDCSYLNTATSQLMRERTYGGKLTEN
Sbjct: 541 RRVANVPRLVMRRHKRDVHIVLPSSRRLVYSDVKGDCSYLNTATSQLMRERTYGGKLTEN 600

Query: 601 IVQAISRDILCEGMKNATKNGYDIVLTVHDEIVSETPDTPYFSVGTLCSLMTKNPSWAKG 660
           IVQAISRDILCEGMKNATKNGYDIVLTVHDEIVSETPDTPYFSVGTLCSLMTKNPSWAKG
Sbjct: 601 IVQAISRDILCEGMKNATKNGYDIVLTVHDEIVSETPDTPYFSVGTLCSLMTKNPSWAKG 660

Query: 661 LPLKAEGYEAKRYRK 675
           LPLKAEGYEAKRYRK
Sbjct: 661 LPLKAEGYEAKRYRK 675


Species: Candidatus Liberibacter asiaticus
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|255957621|dbj|BAH96670.1| DNA-directed DNA polymerase [Candidatus Liberibacter asiaticus] Length = 675 Back     alignment and organism information
>gi|255957561|dbj|BAH96622.1| DNA-directed DNA polymerase [Candidatus Liberibacter asiaticus] Length = 675 Back     alignment and organism information
>gi|255957596|dbj|BAH96650.1| DNA-directed DNA polymerase [Candidatus Liberibacter asiaticus] Length = 675 Back     alignment and organism information
>gi|255957556|dbj|BAH96618.1| DNA-directed DNA polymerase [Candidatus Liberibacter asiaticus] Length = 675 Back     alignment and organism information
>gi|315121967|ref|YP_004062456.1| putative DNA polymerase from bacteriophage origin [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 673 Back     alignment and organism information
>gi|315122935|ref|YP_004063424.1| putative DNA polymerase from bacteriophage origin [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 675 Back     alignment and organism information
>gi|254781193|ref|YP_003065606.1| putative DNA polymerase from bacteriophage origin [Candidatus Liberibacter asiaticus str. psy62] Length = 675 Back     alignment and organism information
>gi|212712317|ref|ZP_03320445.1| hypothetical protein PROVALCAL_03405 [Providencia alcalifaciens DSM 30120] Length = 685 Back     alignment and organism information
>gi|291283829|ref|YP_003500647.1| DNA polymerase I - 3''''-5'''' exonuclease and polymerase domains [Escherichia coli O55:H7 str. CB9615] Length = 687 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
Target675 putative DNA polymerase from bacteriophage origin [Cand
cd08642378 cd08642, DNA_pol_A_pol_I_A, Polymerase I functions prim 1e-25
smart00482206 smart00482, POLAc, DNA polymerase A domain 9e-18
cd08637377 cd08637, DNA_pol_A_pol_I_C, Polymerase I functions prim 1e-13
PRK05755880 PRK05755, PRK05755, DNA polymerase I; Provisional 2e-12
PRK14975553 PRK14975, PRK14975, bifunctional 3'-5' exonuclease/DNA 8e-16
cd06444347 cd06444, DNA_pol_A, Family A polymerase primarily fills 2e-15
COG0749593 COG0749, PolA, DNA polymerase I - 3'-5' exonuclease and 2e-14
TIGR00593887 TIGR00593, pola, DNA polymerase I 4e-14
cd08639324 cd08639, DNA_pol_A_Aquificae_like, Phylum Aquificae Pol 8e-14
cd08638373 cd08638, DNA_pol_A_theta, DNA polymerase theta is a low 7e-09
cd08642378 cd08642, DNA_pol_A_pol_I_A, Polymerase I functions prim 3e-45
pfam00476383 pfam00476, DNA_pol_A, DNA polymerase family A 4e-11
cd08640371 cd08640, DNA_pol_A_plastid_like, DNA polymerase A type 1e-06
cd06130156 cd06130, DNA_pol_III_epsilon_like, an uncharacterized b 0.004
>gnl|CDD|176479 cd08642, DNA_pol_A_pol_I_A, Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication Back     alignment and domain information
>gnl|CDD|128758 smart00482, POLAc, DNA polymerase A domain Back     alignment and domain information
>gnl|CDD|176474 cd08637, DNA_pol_A_pol_I_C, Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication Back     alignment and domain information
>gnl|CDD|180237 PRK05755, PRK05755, DNA polymerase I; Provisional Back     alignment and domain information
>gnl|CDD|184938 PRK14975, PRK14975, bifunctional 3'-5' exonuclease/DNA polymerase; Provisional Back     alignment and domain information
>gnl|CDD|176473 cd06444, DNA_pol_A, Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication Back     alignment and domain information
>gnl|CDD|31092 COG0749, PolA, DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|161944 TIGR00593, pola, DNA polymerase I Back     alignment and domain information
>gnl|CDD|176476 cd08639, DNA_pol_A_Aquificae_like, Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences Back     alignment and domain information
>gnl|CDD|176475 cd08638, DNA_pol_A_theta, DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis and in somatic hypermutation Back     alignment and domain information
>gnl|CDD|176479 cd08642, DNA_pol_A_pol_I_A, Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication Back     alignment and domain information
>gnl|CDD|144170 pfam00476, DNA_pol_A, DNA polymerase family A Back     alignment and domain information
>gnl|CDD|176477 cd08640, DNA_pol_A_plastid_like, DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication Back     alignment and domain information
>gnl|CDD|99834 cd06130, DNA_pol_III_epsilon_like, an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 675 putative DNA polymerase from bacteriophage origin [Cand
PRK07556977 consensus 100.0
PRK06887954 consensus 100.0
PRK07997928 consensus 100.0
PRK05755889 DNA polymerase I; Provisional 100.0
PRK08786927 consensus 100.0
PRK07625922 consensus 100.0
PRK08835931 consensus 100.0
PRK05929870 consensus 100.0
PRK07456975 consensus 100.0
PRK07898902 consensus 100.0
PRK08928861 consensus 100.0
PRK08076877 consensus 100.0
PRK05797869 consensus 100.0
PRK08434887 consensus 100.0
PRK07300880 consensus 100.0
COG0749593 PolA DNA polymerase I - 3'-5' exonuclease and polymeras 100.0
TIGR005931005 pola DNA polymerase I; InterPro: IPR002298 DNA carries 100.0
cd06444379 DNA_pol_A DNA polymerase family A, 5'-3' polymerase dom 100.0
pfam00476383 DNA_pol_A DNA polymerase family A. 100.0
smart00482206 POLAc DNA polymerase A domain. 100.0
cd06128166 DNA_polA_exo The 3'-5' exonuclease domain of family-A D 99.92
cd06139193 DNA_polA_I_Ecoli_like_exo The 3'-5' exonuclease domain 99.92
cd06140178 DNA_polA_I_Bacillus_like_exo Bacillus stearothermophilu 99.81
cd00007155 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsi 99.8
cd06142178 RNaseD_exo Ribonuclease (RNase) D is a bacterial enzyme 99.77
pfam01612172 3_5_exonuc 3'-5' exonuclease. This domain is responsibl 99.75
smart00474172 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofread 99.74
cd06147192 Rrp6p_like_exo Yeast Rrp6p and its human homolog, the P 99.63
COG0349361 Rnd Ribonuclease D [Translation, ribosomal structure an 99.62
cd06148197 Egl_like_exo The Egalitarian (Egl) protein subfamily is 99.59
cd06129159 RNaseD_like The RNase D-like group is composed of RNase 99.47
cd06141168 WRN_exo WRN is a unique RecQ DNA helicase exhibiting an 99.44
PRK10829373 ribonuclease D; Provisional 99.31
cd06146191 mut-7_like_exo The mut-7 subfamily is composed of Caeno 99.3
TIGR01388374 rnd ribonuclease D; InterPro: IPR006292 These proteins 99.11
PRK07740240 hypothetical protein; Provisional 99.1
cd06126181 DEDDy DEDDy exonucleases, part of the DnaQ-like (or DED 99.09
cd05781188 DNA_polB_B3_exo The 3'-5' exonuclease domain of archaea 99.07
cd05785207 DNA_polB_like2_exo A subfamily of the 3'-5' exonuclease 98.94
PRK09145203 DNA polymerase III subunit epsilon; Validated 98.9
cd05780195 DNA_polB_Kod1_like_exo The 3'-5' exonuclease domain of 98.71
cd05784193 DNA_polB_II_exo The 3'-5' exonuclease domain of Escheri 98.61
PRK05762785 DNA polymerase II; Reviewed 98.51
cd05777230 DNA_polB_delta_exo The 3'-5' exonuclease domain of euka 98.4
cd05160200 DNA_polB_exo The 3'-5' exonuclease domain of family-B D 98.4
cd05779204 DNA_polB_epsilon_exo The 3'-5' exonuclease domain of eu 98.14
smart00486471 POLBc DNA polymerase type-B family. DNA polymerase alph 98.03
COG3359278 Predicted exonuclease [DNA replication, recombination, 98.02
cd05783204 DNA_polB_B1_exo The 3'-5' exonuclease domain of Sulfolo 97.92
KOG1798 2173 consensus 97.38
cd05778231 DNA_polB_zeta_exo The 3'-5' exonuclease domain of eukar 96.98
KOG36571075 consensus 99.77
PRK06631229 consensus 99.25
PRK06807313 DNA polymerase III subunit epsilon; Validated 99.18
PRK08517259 DNA polymerase III subunit epsilon; Provisional 99.08
PRK06310250 DNA polymerase III subunit epsilon; Validated 99.04
cd06131167 DNA_pol_III_epsilon_Ecoli_like This subfamily is compos 99.02
PRK06309232 DNA polymerase III subunit epsilon; Validated 99.01
PRK07942234 DNA polymerase III subunit epsilon; Provisional 98.98
cd06134189 RNaseT RNase T is a DEDDh-type DnaQ-like 3'-5' exoribon 98.92
PRK05168213 ribonuclease T; Provisional 98.78
PRK07983219 exodeoxyribonuclease X; Provisional 98.6
PRK07247195 DNA polymerase III subunit epsilon; Validated 98.52
smart00479169 EXOIII exonuclease domain in DNA-polymerase alpha and e 98.41
cd06133176 ERI-1_3'hExo_like This subfamily is composed of Caenorh 97.77
PTZ001661081 DNA polymerase delta catalytic subunit; Provisional 97.73
TIGR00573228 dnaq exonuclease, DNA polymerase III, epsilon subunit f 97.27
PRK05761777 DNA polymerase I; Reviewed 95.87
cd05776234 DNA_polB_alpha_exo The 3'-5' exonuclease domain of euka 95.6
KOG09691066 consensus 95.54
KOG2249280 consensus 94.94
pfam03175452 DNA_pol_B_2 DNA polymerase type B, organellar and viral 93.71
PRK05711240 DNA polymerase III subunit epsilon; Provisional 99.18
PRK07009241 consensus 99.18
PRK06022234 consensus 99.13
PRK07982243 consensus 99.12
PRK06859253 consensus 99.1
PRK06195309 DNA polymerase III subunit epsilon; Validated 99.08
TIGR01406246 dnaQ_proteo DNA polymerase III, epsilon subunit; InterP 99.07
PRK08858246 consensus 99.01
PRK07883575 hypothetical protein; Validated 99.0
cd06130156 DNA_pol_III_epsilon_like This subfamily is composed of 98.92
TIGR01405 1264 polC_Gram_pos DNA polymerase III, alpha subunit, Gram-p 98.92
PRK06063313 DNA polymerase III subunit epsilon; Provisional 98.9
PRK00448 1436 polC DNA polymerase III PolC; Validated 98.68
PRK09146239 DNA polymerase III subunit epsilon; Validated 98.63
cd06127159 DEDDh DEDDh exonucleases, part of the DnaQ-like (or DED 98.48
COG2176 1444 PolC DNA polymerase III, alpha subunit (gram-positive t 98.46
cd06136177 TREX1_2 Three prime repair exonuclease (TREX) 1 and 2 a 98.39
COG0847243 DnaQ DNA polymerase III, epsilon subunit and related 3' 98.23
cd06144152 REX4_like This subfamily is composed of RNA exonuclease 98.04
pfam00929162 Exonuc_X-T Exonuclease. This family includes a variety 98.01
cd06138183 ExoI_N This subfamily is composed of the N-terminal dom 97.58
PRK06722242 exonuclease; Provisional 96.9
cd06149157 ISG20 Interferon (IFN) Stimulated Gene product of 20 kD 96.78
cd06137161 DEDDh_RNase This group is composed of eukaryotic exorib 96.0
cd06145150 REX1_like This subfamily is composed of RNA exonuclease 94.75
pfam04857235 CAF1 CAF1 family ribonuclease. The major pathways of mR 93.65
cd06135173 Orn Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3 91.97
cd06143174 PAN2_exo PAN2 is the catalytic subunit of poly(A) nucle 91.11
PRK08074 932 bifunctional ATP-dependent DNA helicase/DNA polymerase 99.17
PRK08816244 consensus 99.17
PRK07246 820 bifunctional ATP-dependent DNA helicase/DNA polymerase 99.06
TIGR01407 944 dinG_rel DnaQ family exonuclease/DinG family helicase, 98.8
cd06125130 DnaQ_like_exo The DnaQ-like exonuclease superfamily is 98.62
PRK09182293 DNA polymerase III subunit epsilon; Validated 98.19
cd05782208 DNA_polB_like1_exo A subfamily of the 3'-5' exonuclease 98.78
pfam10108211 Exon_PolB Predicted 3'-5' exonuclease related to the ex 97.76
KOG2206687 consensus 97.75
TIGR005931005 pola DNA polymerase I; InterPro: IPR002298 DNA carries 98.27
COG0417792 PolB DNA polymerase elongation subunit (family B) [DNA 97.68
COG0749593 PolA DNA polymerase I - 3'-5' exonuclease and polymeras 97.62
PRK08928861 consensus 96.73
PRK07300880 consensus 96.6
PRK06887954 consensus 96.59
PRK07898902 consensus 96.55
PRK07625922 consensus 96.54
PRK08786927 consensus 96.53
PRK05755889 DNA polymerase I; Provisional 96.53
PRK08835931 consensus 96.47
PRK08076877 consensus 96.41
PRK05929870 consensus 96.36
PRK07997928 consensus 96.32
PRK05797869 consensus 96.15
pfam00476383 DNA_pol_A DNA polymerase family A. 93.35
cd06444379 DNA_pol_A DNA polymerase family A, 5'-3' polymerase dom 91.32
PRK05601377 DNA polymerase III subunit epsilon; Validated 97.01
PRK07556 977 consensus 96.53
pfam00940391 RNA_pol DNA-dependent RNA polymerase. This is a family 95.29
PRK08434887 consensus 95.23
PRK07456975 consensus 92.62
TIGR03491457 RecB family nuclease, putative, TM0106 family. Members 94.79
pfam03104254 DNA_pol_B_exo DNA polymerase family B, exonuclease doma 94.75
pfam11074127 DUF2779 Domain of unknown function(DUF2779). This domai 94.29
KOG09501008 consensus 91.34
>PRK07556 consensus Back     alignment and domain information
>PRK06887 consensus Back     alignment and domain information
>PRK07997 consensus Back     alignment and domain information
>PRK05755 DNA polymerase I; Provisional Back     alignment and domain information
>PRK08786 consensus Back     alignment and domain information
>PRK07625 consensus Back     alignment and domain information
>PRK08835 consensus Back     alignment and domain information
>PRK05929 consensus Back     alignment and domain information
>PRK07456 consensus Back     alignment and domain information
>PRK07898 consensus Back     alignment and domain information
>PRK08928 consensus Back     alignment and domain information
>PRK08076 consensus Back     alignment and domain information
>PRK05797 consensus Back     alignment and domain information
>PRK08434 consensus Back     alignment and domain information
>PRK07300 consensus Back     alignment and domain information
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00593 pola DNA polymerase I; InterPro: IPR002298 DNA carries the biological information that instructs cells how to exist in an ordered fashion Back     alignment and domain information
>cd06444 DNA_pol_A DNA polymerase family A, 5'-3' polymerase domain Back     alignment and domain information
>pfam00476 DNA_pol_A DNA polymerase family A Back     alignment and domain information
>smart00482 POLAc DNA polymerase A domain Back     alignment and domain information
>cd06128 DNA_polA_exo The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity Back     alignment and domain information
>cd06139 DNA_polA_I_Ecoli_like_exo The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity Back     alignment and domain information
>cd06140 DNA_polA_I_Bacillus_like_exo Bacillus stearothermophilus-like Polymerase I (pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region Back     alignment and domain information
>cd00007 35EXOc 3'-5' exonuclease Back     alignment and domain information
>cd06142 RNaseD_exo Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA Back     alignment and domain information
>pfam01612 3_5_exonuc 3'-5' exonuclease Back     alignment and domain information
>smart00474 35EXOc 3'-5' exonuclease Back     alignment and domain information
>cd06147 Rrp6p_like_exo Yeast Rrp6p and its human homolog, the Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs Back     alignment and domain information
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd06148 Egl_like_exo The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins Back     alignment and domain information
>cd06129 RNaseD_like The RNase D-like group is composed of RNase D, WRN, and similar proteins Back     alignment and domain information
>cd06141 WRN_exo WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity Back     alignment and domain information
>PRK10829 ribonuclease D; Provisional Back     alignment and domain information
>cd06146 mut-7_like_exo The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans Back     alignment and domain information
>TIGR01388 rnd ribonuclease D; InterPro: IPR006292 These proteins represent ribonuclease D, a 3-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo Back     alignment and domain information
>PRK07740 hypothetical protein; Provisional Back     alignment and domain information
>cd06126 DEDDy DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction Back     alignment and domain information
>cd05781 DNA_polB_B3_exo The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3 Back     alignment and domain information
>cd05785 DNA_polB_like2_exo A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases Back     alignment and domain information
>PRK09145 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>cd05780 DNA_polB_Kod1_like_exo The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D Back     alignment and domain information
>cd05784 DNA_polB_II_exo The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (PolII) and similar bacterial proteins Back     alignment and domain information
>PRK05762 DNA polymerase II; Reviewed Back     alignment and domain information
>cd05777 DNA_polB_delta_exo The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta Back     alignment and domain information
>cd05160 DNA_polB_exo The 3'-5' exonuclease domain of family-B DNA polymerases Back     alignment and domain information
>cd05779 DNA_polB_epsilon_exo The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon Back     alignment and domain information
>smart00486 POLBc DNA polymerase type-B family Back     alignment and domain information
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>cd05783 DNA_polB_B1_exo The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins Back     alignment and domain information
>KOG1798 consensus Back     alignment and domain information
>cd05778 DNA_polB_zeta_exo The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta Back     alignment and domain information
>KOG3657 consensus Back     alignment and domain information
>PRK06631 consensus Back     alignment and domain information
>PRK06807 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK08517 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK06310 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>cd06131 DNA_pol_III_epsilon_Ecoli_like This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (polIII) and similar proteins Back     alignment and domain information
>PRK06309 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK07942 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>cd06134 RNaseT RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA Back     alignment and domain information
>PRK05168 ribonuclease T; Provisional Back     alignment and domain information
>PRK07983 exodeoxyribonuclease X; Provisional Back     alignment and domain information
>PRK07247 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases Back     alignment and domain information
>cd06133 ERI-1_3'hExo_like This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria Back     alignment and domain information
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional Back     alignment and domain information
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family; InterPro: IPR006054 All proteins in this entry for which functions are known are components of the DNA polymerase III complex (epsilon subunit) Back     alignment and domain information
>PRK05761 DNA polymerase I; Reviewed Back     alignment and domain information
>cd05776 DNA_polB_alpha_exo The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha Back     alignment and domain information
>KOG0969 consensus Back     alignment and domain information
>KOG2249 consensus Back     alignment and domain information
>pfam03175 DNA_pol_B_2 DNA polymerase type B, organellar and viral Back     alignment and domain information
>PRK05711 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK07009 consensus Back     alignment and domain information
>PRK06022 consensus Back     alignment and domain information
>PRK07982 consensus Back     alignment and domain information
>PRK06859 consensus Back     alignment and domain information
>PRK06195 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit; InterPro: IPR006309 These represent DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria Back     alignment and domain information
>PRK08858 consensus Back     alignment and domain information
>PRK07883 hypothetical protein; Validated Back     alignment and domain information
>cd06130 DNA_pol_III_epsilon_like This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (polIII), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase Back     alignment and domain information
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha subunit, Gram-positive type; InterPro: IPR006308 These are the polypeptide chains of DNA polymerase III Back     alignment and domain information
>PRK06063 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK00448 polC DNA polymerase III PolC; Validated Back     alignment and domain information
>PRK09146 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>cd06127 DEDDh DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction Back     alignment and domain information
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair] Back     alignment and domain information
>cd06136 TREX1_2 Three prime repair exonuclease (TREX) 1 and 2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases Back     alignment and domain information
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair] Back     alignment and domain information
>cd06144 REX4_like This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins Back     alignment and domain information
>pfam00929 Exonuc_X-T Exonuclease Back     alignment and domain information
>cd06138 ExoI_N This subfamily is composed of the N-terminal domain of E Back     alignment and domain information
>PRK06722 exonuclease; Provisional Back     alignment and domain information
>cd06149 ISG20 Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA Back     alignment and domain information
>cd06137 DEDDh_RNase This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins Back     alignment and domain information
>cd06145 REX1_like This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins Back     alignment and domain information
>pfam04857 CAF1 CAF1 family ribonuclease Back     alignment and domain information
>cd06135 Orn Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides Back     alignment and domain information
>cd06143 PAN2_exo PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs Back     alignment and domain information
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK08816 consensus Back     alignment and domain information
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative; InterPro: IPR006310 These are a family of proteins in Gram-positive bacteria Back     alignment and domain information
>cd06125 DnaQ_like_exo The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction Back     alignment and domain information
>PRK09182 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>cd05782 DNA_polB_like1_exo A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases Back     alignment and domain information
>pfam10108 Exon_PolB Predicted 3'-5' exonuclease related to the exonuclease domain of PolB Back     alignment and domain information
>KOG2206 consensus Back     alignment and domain information
>TIGR00593 pola DNA polymerase I; InterPro: IPR002298 DNA carries the biological information that instructs cells how to exist in an ordered fashion Back     alignment and domain information
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair] Back     alignment and domain information
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK08928 consensus Back     alignment and domain information
>PRK07300 consensus Back     alignment and domain information
>PRK06887 consensus Back     alignment and domain information
>PRK07898 consensus Back     alignment and domain information
>PRK07625 consensus Back     alignment and domain information
>PRK08786 consensus Back     alignment and domain information
>PRK05755 DNA polymerase I; Provisional Back     alignment and domain information
>PRK08835 consensus Back     alignment and domain information
>PRK08076 consensus Back     alignment and domain information
>PRK05929 consensus Back     alignment and domain information
>PRK07997 consensus Back     alignment and domain information
>PRK05797 consensus Back     alignment and domain information
>pfam00476 DNA_pol_A DNA polymerase family A Back     alignment and domain information
>cd06444 DNA_pol_A DNA polymerase family A, 5'-3' polymerase domain Back     alignment and domain information
>PRK05601 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK07556 consensus Back     alignment and domain information
>pfam00940 RNA_pol DNA-dependent RNA polymerase Back     alignment and domain information
>PRK08434 consensus Back     alignment and domain information
>PRK07456 consensus Back     alignment and domain information
>TIGR03491 RecB family nuclease, putative, TM0106 family Back     alignment and domain information
>pfam03104 DNA_pol_B_exo DNA polymerase family B, exonuclease domain Back     alignment and domain information
>pfam11074 DUF2779 Domain of unknown function(DUF2779) Back     alignment and domain information
>KOG0950 consensus 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
Target675 putative DNA polymerase from bacteriophage origin [Cand
1dpi_A605 Structure Of Large Fragment Of Escherichia Coli Dna 1e-113
1kfs_A605 Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Muta 1e-113
1kln_A605 Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Muta 1e-111
1d8y_A605 Crystal Structure Of The Complex Of Dna Polymerase 1e-109
2xo7_A580 Crystal Structure Of A Da:o-Allylhydroxylamine-Dc B 2e-70
3hp6_A580 Crystal Structure Of Fragment Dna Polymerase I From 4e-69
1u45_A580 8oxoguanine At The Pre-Insertion Site Of The Polyme 3e-70
3bdp_A580 Dna Polymerase IDNA COMPLEX Length = 580 3e-70
1lv5_A580 Crystal Structure Of The Closed Conformation Of Bac 3e-70
1l3s_A580 Crystal Structure Of Bacillus Dna Polymerase I Frag 3e-70
2hhq_A580 O6-Methyl-Guanine:t Pair In The Polymerase-10 Basep 4e-70
3eyz_A580 Cocrystal Structure Of Bacillus Fragment Dna Polyme 6e-70
3hpo_A580 Crystal Structure Of Fragment Dna Polymerase I From 1e-69
3ht3_A579 Crystal Structure Of Fragment Dna Polymerase I From 2e-69
2hhw_A580 Ddttp:o6-Methyl-Guanine Pair In The Polymerase Acti 4e-69
2hvh_A580 Ddctp:o6meg Pair In The Polymerase Active Site (0 P 4e-69
5ktq_A543 Large Fragment Of Taq Dna Polymerase Bound To Dctp 3e-69
1qtm_A539 Ddttp-Trapped Closed Ternary Complex Of The Large F 4e-69
1qss_A539 Ddgtp-Trapped Closed Ternary Complex Of The Large F 4e-69
2ktq_A538 Open Ternary Complex Of The Large Fragment Of Dna P 4e-69
4ktq_A539 Binary Complex Of The Large Fragment Of Dna Polymer 4e-69
3ktq_A540 Crystal Structure Of An Active Ternary Complex Of T 4e-69
1bgx_T832 Taq Polymerase In Complex With Tp7, An Inhibitory F 4e-68
1taq_A832 Structure Of Taq Dna Polymerase Length = 832 7e-67
2ajq_A704 Structure Of Replicative Dna Polymerase Provides In 2e-11
1t7p_A698 T7 Dna Polymerase Complexed To Dna PrimerTEMPLATE,A 3e-11
1zyq_A698 T7 Dna Polymerase In Complex With 8og And Incoming 3e-11
2hbj_A410 Structure Of The Yeast Nuclear Exosome Component, R 1e-05
3ikm_A1172 Crystal Structure Of Human Mitochondrial Dna Polyme 0.001
>gi|157830862|pdb|1DPI|A Chain A, Structure Of Large Fragment Of Escherichia Coli Dna Polymerase I Complexed With DTMP Length = 605 Back     alignment and structure
 Score =  413 bits (1061), Expect = e-113,   Method: Composition-based stats.
 Identities = 106/707 (14%), Positives = 195/707 (27%), Gaps = 171/707 (24%)

Query: 4   LFIDIETRSPQPLPKVGVWAYAEQAVITLCAYAWDDEPVKLWDRTEQ----------SAM 53
              D ET S   +           A +   ++A +                         
Sbjct: 29  FAFDTETDSLDNI----------SANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERA 78

Query: 54  PSDLLQYLRDETVMCVAHNSLFERILFKKTLGIDIPSKRWICTSVLARTNGL---PSSLK 110
              L   L DE  + V  N  ++R +     GI++    +  T + +           + 
Sbjct: 79  LELLKPLLEDEKALKVGQNLKYDRGILANY-GIELRGIAF-DTMLESYILNSVAGRHDMD 136

Query: 111 NACLA-LNFSEHLTKMEEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEA 169
           +     L       +   GK                      +  A +  G Y   D + 
Sbjct: 137 SLAERWLKHKTITFEEIAGKGKNQL---------------TFNQIALEEAGRYAAEDADV 181

Query: 170 TRELFKRLIPLSDG-----------ERDLWLLDQTINDRGYRIDLDLVLKLQELIAQERK 218
           T +L  ++ P               E  L  +   I   G +ID  ++    E +     
Sbjct: 182 TLQLHLKMWPDLQKHKGPLNVFENIEMPLVPVLSRIERNGVKIDPKVLHNHSEELTLRLA 241

Query: 219 KLDEDIVKLTDGIIRSSRQTYALRMYLFLITGIDLVDMSE----GTLKSILSHSNITQLA 274
           +L++   ++      +   T  L+  LF   GI  +  +      T + +L    +    
Sbjct: 242 ELEKKAHEIAGEEF-NLSSTKQLQTILFEKQGIKPLKKTPGGAPSTSEEVLEELALDYPL 300

Query: 275 KDLILNRLASSGSAILKLNTLSEAVSS-DGRLRGTLQFYGASRTGRWSGCVFQPQNLPRQ 333
             +IL     +       + L   ++   GR+  +      + TGR S      QN+P  
Sbjct: 301 PKVILEYRGLAKLKSTYTDKLPLMINPKTGRVHTSYHQAV-TATGRLSSTDPNLQNIP-- 357

Query: 334 ERSEEILTQTIQALNRGETIADPLGLASDCVRSCIIASNGKKLVVADLAGIEARVLAWIA 393
                                         +R   IA     +V AD + IE R++A ++
Sbjct: 358 ----------------------VRNEEGRRIRQAFIAPEDYVIVSADYSQIELRIMAHLS 395

Query: 394 GEDWKIKAFANGEDIYVTTYAKAFNTPIDKVSKEQRAIGKVMELALGYQGGAKVFKTMAS 453
            +   + AFA G+DI+  T A+ F  P++ V+ EQR   K +                  
Sbjct: 396 RDKGLLTAFAEGKDIHRATAAEVFGLPLETVTSEQRRSAKAINF--------------GL 441

Query: 454 HCGLDLQQFSQNVKSTSTFEDWEQAESHHLWMQDQYPEFAVKDKLIGTACELVKKAWRAK 513
             G+                                   A +  +     +     +  +
Sbjct: 442 IYGMS------------------------------AFGLARQLNIPRKEAQKYMDLYFER 471

Query: 514 HQGVLQLWKDLTEGFACVVQEGGSISARRVANVPRLVMRRHKRDVHIVLPSSRRLVYSDV 573
           + GVL+  +                                     +     RRL   D+
Sbjct: 472 YPGVLEYMERTRAQAKEQGY--------------------------VETLDGRRLYLPDI 505

Query: 574 KGDCSYLNTATSQLMRERTYGGKLTENIVQAISRDILCEGMKNATK------NGYDIVLT 627
           K        A  +               +Q  + DI+   M               +++ 
Sbjct: 506 KSSNGARRAAAERAA---------INAPMQGTAADIIKRAMIAVDAWLQAEQPRVRMIMQ 556

Query: 628 VHDEIVSETPDTPYFSV-GTLCSLMTKNPSWAKGLPLKAEGYEAKRY 673
           VHDE+V E       +V   +  LM         +PL  E    + +
Sbjct: 557 VHDELVFEVHKDDVDAVAKQIHQLMENCTR--LDVPLLVEVGSGENW 601


gi|2982102|pdb|1KFS|A Chain A, Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) MutantDNA Complex Length = 605 Back     alignment and structure
>gi|809180|pdb|1KLN|A Chain A, Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) MutantDNA Complex Length = 605 Back     alignment and structure
>gi|6730276|pdb|1D8Y|A Chain A, Crystal Structure Of The Complex Of Dna Polymerase I Klenow Fragment With Dna Length = 605 Back     alignment and structure
>gi|306991581|pdb|2XO7|A Chain A, Crystal Structure Of A Da:o-Allylhydroxylamine-Dc Basepair In Complex With Fragment Dna Polymerase I From Bacillus Stearothermophilus Length = 580 Back     alignment and structure
>gi|299688922|pdb|3HP6|A Chain A, Crystal Structure Of Fragment Dna Polymerase I From Bacillus Stearothermophilus F710y Mutant Bound To G:t Mismatch Length = 580 Back     alignment and structure
>gi|55670162|pdb|1U45|A Chain A, 8oxoguanine At The Pre-Insertion Site Of The Polymerase Active Site Length = 580 Back     alignment and structure
>gi|4389065|pdb|3BDP|A Chain A, Dna Polymerase IDNA COMPLEX Length = 580 Back     alignment and structure