254781193

254781193

putative DNA polymerase from bacteriophage origin

GeneID in NCBI database:8210218Locus tag:CLIBASIA_05500
Protein GI in NCBI database:254781193Protein Accession:YP_003065606.1
Gene range:+(1191125, 1193152)Protein Length:675aa
Gene description:putative DNA polymerase from bacteriophage origin
COG prediction:[L] DNA polymerase III, epsilon subunit and related 3'-5' exonucleases
KEGG prediction:putative DNA polymerase from bacteriophage origin; K02334 DNA polymerase bacteriophage-type [EC:2.7.7.7]
SEED prediction:DNA polymerase, phage-associated
Pathway involved in KEGG:not defined
Subsystem involved in SEED:- none -
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-----
MATLFIDFETRSPIDLTKCGICKYAEDVCVILFAFGFDDHPVELWDCVHDPVMPQVLKEALENTDVTIVAHNSYFERTVLKACFNLDIPIHRWICTLVLARSNGLPSALKAVGEALKLSSQKMEEGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTREIFKRLEPLSSKEQELWYLDQTINDRGYCVDVALAHTLNQIVDVERTKLDQELESLTYGLVSSSRCLEKLKTWLFLETGLHLEDLTETTCQRVLSSNKKLTPQAIQVFNNRMRASRSAVLKLNTLVEAMNSDGRLRGTLQFLGASRTGRWSGCVFPPQNLPRPSRSHEELDQIITHLPTSITSDPDPLQIISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQVTKDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNSAPEEWEDAENFCRWMQENHPEHAIEDLFIGTACERVKKAWRQKHSRVSELWNELHQAFEQTIENGKAIIARKRRDVPLVYMKKDKNNLILMLPSGRSLVYRDVGNNRSYLNTTTRQLTREYTYGGKLTENIVQAVSRDILAEGMMNATKAGYDIVLTVHDEIVCETPDTDEFNASMLYHLMTSNPSWAKGLPLKAEGYESKRYRK
ccEEEEEccEEEccccccccHHHccccccEEEEEcccccccEEEEEccccccccHHHHHHHcccccEEEEEcHHHHHHHHHHHcccccccccccHHHHHHHHcccccccHHHHHHHcccccccccHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccHHHHcccHHHHHHHHHHHccEEEcHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHccccccccccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHccHHHHcccccccccccccccccHHHHHHcccccccccccHHccccHHHHHHcccccccEEEEEccHHHHHHHHHHHHccHHHHHHHHccccHHHHHHHHHHcccHHHccHHHHHHHHHHHHHHHHcccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHcccccHHHHHHHHHccHHHHHHccccHHcccccccEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEccEEEEEccHHHHHHHHHHHHHHcccccHHcccccEEEEEccccccc
ccEEEEEccccccccHHcccHHHHHHHHHHHHHHHHcccccEEEEEcccccccHHHHHHHHccccccEEcccccHHHHHHHHHcccccccHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHccccEEEEEEccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHcccEEcHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHccccccccHHHHHHHHHHccccccHHHHHHHHHHHHHHHcccccHHHccccccccccEEEEEEEcccccccccccccccccccccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHEccccccEEEEEcHHHHHHHHHHHHccccHHHHHHHccccHHHHHHHHHHcccHHHccHHHHHHHHHHHHHHcccccHHHHHHHHHHHHccccHHHHHHHHcHHHHHcHHHHHHHHHHHHHHHHcccEEEEEccEcccccHccccccHHHHHHHHHHHHHHHHcHHcccHHHHHHHHHHHHHHHHHHccccEEEcccccEEEEEcccccEEEEccccccEEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEccEEEEEccccccccHHHHHHHHcccccccccccccccccccccccc
matlfidfetrspidltkcgickYAEDVCVILFAfgfddhpvelwdcvhdpvmPQVLKEALENTDVTIVAHNSYFERTVLKacfnldipiHRWICTLVLARSNGLPSALKAVGEALKLSSQKMEEGKELIARFCkgetheclydrnkpnHREAWRLFGEYCKGDVTVTREIFKrleplsskeQELWYLDQTINDRGYCVDVALAHTLNQIVDVERTKLDQELESLTYGLVSSSRCLEKLKTWLFLetglhledltETTCQRVlssnkkltPQAIQVFNNRMRASRSAVLKLNTLVEAMNSDGRLRGTLQFlgasrtgrwsgcvfppqnlprpsrshEELDQIIThlptsitsdpdplqiISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARsfnvapaqvtkDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVktnsapeeweDAENFCRWMqenhpehaieDLFIGTACERVKKAWRQKHSRVSELWNELHQAFEQTIENGKAIIArkrrdvplvymkkdknnlilmlpsgrslvyrdvgnnrsylNTTTRQLtreytyggklTENIVQAVSRDILAEGMMNATKAGYDIVLTVHDeivcetpdtdefNASMLYHLMtsnpswakglplkaegyeskryrk
matlfidfetrspidlTKCGICKYAEDVCVILFAFGFDDHPVELWDCVHDPVMPQVLKEALENTDVTIVAHNSYFERTVLKACFNLDIPIHRWICTLVLARSNGLPSALKAVGEALKLSSQKMEEGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTREIFKrleplsskeqELWYLDQTINDRGYCVDVALAHTLNQIVDVERTKLDQELESLTyglvsssrCLEKLKTWLFLETGLHLEDLTETTCQRvlssnkkltpqAIQVFNNRMRASRSAVLKLNTLVEamnsdgrlrGTLQFLGASRTGRWSGCVFPPQNLPRPSRSHEELDQIITHLptsitsdpdPLQIISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARsfnvapaqvtkDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNSAPEEWEDAENFCRWMQENHPEHAIEDLFIGTACERVKKAWRQKHSRVSELWNELHQAFEQTIENGKAIIARKRRDVPLVYMKkdknnlilmlpsgrslvyrdvgnnrsylntttrqltreytyggkltenIVQAVSRDILAEGMMNATKAGYDIVLTVHDEIVCETPDTDEFNASMLYHLMTsnpswakglplkaegyeskryrk
MATLFIDFETRSPIDLTKCGICKYAEDVCVILFAFGFDDHPVELWDCVHDPVMPQVLKEALENTDVTIVAHNSYFERTVLKACFNLDIPIHRWICTLVLARSNGLPSALKAVGEALKLSSQKMEEGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTREIFKRLEPLSSKEQELWYLDQTINDRGYCVDVALAHTLNQIVDVERTKLDQELESLTYGLVSSSRCLEKLKTWLFLETGLHLEDLTETTCQRVLSSNKKLTPQAIQVFNNRMRASRSAVLKLNTLVEAMNSDGRLRGTLQFLGASRTGRWSGCVFPPQNLPRPSRSHEELDQIITHLPTSITSDPDPLQIISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQVTKDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNSAPEEWEDAENFCRWMQENHPEHAIEDLFIGTACERVKKAWRQKHSRVSELWNELHQAFEQTIENGKAIIARKRRDVPLVYMKKDKNNLILMLPSGRSLVYRDVGNNRSYLNTTTRQLTREYTYGGKLTENIVQAVSRDILAEGMMNATKAGYDIVLTVHDEIVCETPDTDEFNASMLYHLMTSNPSWAKGLPLKAEGYESKRYRK
*ATLFIDFETRSPIDLTKCGICKYAEDVCVILFAFGFDDHPVELWDCVHDPVMPQVLKEALENTDVTIVAHNSYFERTVLKACFNLDIPIHRWICTLVLARSNGLPSALKAVGEALKLSSQKMEEGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTREIFKRLEPLSSKEQELWYLDQTINDRGYCVDVALAHTLNQIVDVERTKLDQELESLTYGLVSSSRCLEKLKTWLFLETG**************LSSNKKLTPQAIQVFNNRMRASRSAVLKLNTLVEAMNSDGRLRGTLQFLGASRTGRWSGCVFPPQNLPRPSRSHEELDQIITHLPTSITSDPDPLQIISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPA**********KVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNSAPEEWEDAENFCRWMQENHPEHAIEDLFIGTACERVKKAWRQKHSRVSELWNELHQAFEQTIENGKAIIARKRRDVPLVYMKKDKNNLILMLPSGRSLVYRDVGNNRSYLNTTTRQLTREYTYGGKLTENIVQAVSRDILAEGMMNATKAGYDIVLTVHDEIVCETPDTDEFNASMLYHLMTSNPSWAKGLPLKAEGYESKRYRK
MATLFIDFETRSPIDLTKCGICKYAEDVCVILFAFGFDDHPVELWDCVHDPVMPQVLKEALENTDVTIVAHNSYFERTVLKACFNLDIPIHRWICTLVLARSNGLPSALKAVGEALKLSSQKMEEGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTREIFKRLEPLSSKEQELWYLDQTINDRGYCVDVALAHTLNQIVDVERTKLDQELESLTYGLVSSSRCLEKLKTWLFLETGLHLEDLTETTCQRVLSSNKKLTPQAIQVFNNRMRASRSAVLKLNTLVEAMNSDGRLRGTLQFLGASRTGRWSGCVFPPQNLPRPSRSHEELDQIITHLPTSITSDPDPLQIISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQVTKDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNSAPEEWEDAENFCRWMQENHPEHAIEDLFIGTACERVK********RVSELWNELHQAFEQTIENGKAIIARKRRDVPLVYMKKDKNNLILMLPSGRSLVYRDVGNNRSYLNTTTRQLTREYTYGGKLTENIVQAVSRDILAEGMMNATKAGYDIVLTVHDEIVCETPDTDEFNASMLYHLMTSNPSWAKGLPLKAEG********
MATLFIDFETRSPIDLTKCGICKYAEDVCVILFAFGFDDHPVELWDCVHDPVMPQVLKEALENTDVTIVAHNSYFERTVLKACFNLDIPIHRWICTLVLARSNGLPSALKAVGEALKLSSQKMEEGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTREIFKRLEPLSSKEQELWYLDQTINDRGYCVDVALAHTLNQIVDVERTKLDQELESLTYGLVSSSRCLEKLKTWLFLETGLHLEDLTETTCQRVLSSNKKLTPQAIQVFNNRMRASRSAVLKLNTLVEAMNSDGRLRGTLQFLGASRTGRWSGCVFPPQNLPRPSRSHEELDQIITHLPTSITSDPDPLQIISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQVTKDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNSAPEEWEDAENFCRWMQENHPEHAIEDLFIGTACERVKKAWRQKHSRVSELWNELHQAFEQTIENGKAIIARKRRDVPLVYMKKDKNNLILMLPSGRSLVYRDVGNNRSYLNTTTRQLTREYTYGGKLTENIVQAVSRDILAEGMMNATKAGYDIVLTVHDEIVCETPDTDEFNASMLYHLMTSNPSWAKGLPLKAEGYESKRYRK
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MATLFIDFETRSPIDLTKCGICKYAEDVCVILFAFGFDDHPVELWDCVHDPVMPQVLKEALENTDVTIVAHNSYFERTVLKACFNLDIPIHRWICTLVLARSNGLPSALKAVGEALKLSSQKMEEGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTREIFKRLEPLSSKEQELWYLDQTINDRGYCVDVALAHTLNQIVDVERTKLDQELESLTYGLVSSSRCLEKLKTWLFLETGLHLEDLTETTCQRVLSSNKKLTPQAIQVFNNRMRASRSAVLKLNTLVEAMNSDGRLRGTLQFLGASRTGRWSGCVFPPQNLPRPSRSHEELDQIITHLPTSITSDPDPLQIISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQVTKDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNSAPEEWEDAENFCRWMQENHPEHAIEDLFIGTACERVKKAWRQKHSRVSELWNELHQAFEQTIENGKAIIARKRRDVPLVYMKKDKNNLILMLPSGRSLVYRDVGNNRSYLNTTTRQLTREYTYGGKLTENIVQAVSRDILAEGMMNATKAGYDIVLTVHDEIVCETPDTDEFNASMLYHLMTSNPSWAKGLPLKAEGYESKRYRK
MATLFIDFETRSPIDLTKCGICKYAEDVCVILFAFGFDDHPVELWDCVHDPVMPQVLKEALENTDVTIVAHNSYFERTVLKACFNLDIPIHRWICTLVLARSNGLPSALKAVGEALKLSSQKMEEGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTREIFKRLEPLSSKEQELWYLDQTINDRGYCVDVALAHTLNQIVDVERTKLDQELESLTYGLVSSSRCLEKLKTWLFLETGLHLEDLTETTCQRVLSSNKKLTPQAIQVFNNRMRASRSAVLKLNTLVEAMNSDGRLRGTLQFLGASRTGRWSGCVFPPQNLPRPSRSHEELDQIITHLPTSITSDPDPLQIISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQVTKDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNSAPEEWEDAENFCRWMQENHPEHAIEDLFIGTACERVKKAWRQKHSRVSELWNELHQAFEQTIENGKAIIARKRRDVPLVYMKKDKNNLILMLPSGRSLVYRDVGNNRSYLNTTTRQLTREYTYGGKLTENIVQAVSRDILAEGMMNATKAGYDIVLTVHDEIVCETPDTDEFNASMLYHLMTSNPSWAKGLPLKAEGYESKRYRK
MATLFIDFETRSPIDLTKCGICKYAEDVCVILFAFGFDDHPVELWDCVHDPVMPQVLKEALENTDVTIVAHNSYFERTVLKACFNLDIPIHRWICTLVLARSNGLPSALKAVGEALKLSSQKMEEGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTREIFKRLEPLSSKEQELWYLDQTINDRGYCVDVALAHTLNQIVDVERTKLDQELESLTYGLVSSSRCLEKLKTWLFLETGLHLEDLTETTCQRVLSSNKKLTPQAIQVFNNRMRASRSAVLKLNTLVEAMNSDGRLRGTLQFLGASRTGRWSGCVFPPQNLPRPSRSHEELDQIITHLPTSITSDPDPLQIISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQVTKDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNSAPEEWEDAENFCRWMQENHPEHAIEDLFIGTACERVKKAWRQKHSRVSELWNELHQAFEQTIENGKAIIARKRRDVPLVYMKKDKNNLILMLPSGRSLVYRDVGNNRSYLNTTTRQLTREYTYGGKLTENIVQAVSRDILAEGMMNATKAGYDIVLTVHDEIVCETPDTDEFNASMLYHLMTSNPSWAKGLPLKAEGYESKRYRK

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
254780127675 putative DNA polymerase from bacteriophage origin 0.0
254780277976 DNA polymerase I [Candidatus Liberibacter asiaticu 1e-04
255764469361 putative permease protein [Candidatus Liberibacter 0.014
>gi|254780127|ref|YP_003064540.1| 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   MATLFIDFETRSPIDLTKCGICKYAEDVCVILFAFGFDDHPVELWDCVHDPVMPQVLKEA 60
           M+ LFID ETRSP  L K G+  YAE   + L A+ +DD PV+LWD      MP  L + 
Sbjct: 1   MSKLFIDIETRSPQPLPKVGVWAYAEQAVITLCAYAWDDEPVKLWDRTEQSAMPSDLLQY 60

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

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

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

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

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

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

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

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

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

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

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

>gi|254780277|ref|YP_003064690.1| DNA polymerase I [Candidatus Liberibacter asiaticus str. psy62] Length = 976 Back     alignment
 Score = 40.0 bits (92), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 37/78 (47%)

Query: 364 VRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFNVAPAQ 423
           +R   I+   KKL+ AD + IE R+LA +A      + FE   D++    A  F V   +
Sbjct: 733 IRRAFISPPTKKLISADYSQIELRILAHIAKITPLYQVFENSLDIHRMVAAEIFGVNIEK 792

Query: 424 VTKDQRAIGKVMELALGY 441
           V+   R   K +  ++ Y
Sbjct: 793 VSPQMRRHAKTINFSIIY 810

>gi|255764469|ref|YP_003064807.2| putative permease protein [Candidatus Liberibacter asiaticus str. psy62] Length = 361 Back     alignment
 Score = 33.1 bits (74), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 21/88 (23%)

Query: 473 EEWED-----AENFCRWMQENHPEHAIEDLFIGTACERVKKAWRQKHSRVSELWNELHQA 527
           ++W+D       +   WMQ ++P+   +D+FIG      KK   + H     +W +    
Sbjct: 136 QQWKDNGDKQKSDIIPWMQISNPQ---QDIFIGA-----KKILPENH-----IWEDFTSI 182

Query: 528 FEQTIENGKAIIARKRRDVPLVYMKKDK 555
              TI+    II RK  D+ ++Y  K K
Sbjct: 183 ---TIDKKNKIIHRKDADLAIIYNDKVK 207

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
315121967673 putative DNA polymerase from bacteriophage origin [Cand 1 0.0
315122935675 putative DNA polymerase from bacteriophage origin [Cand 1 0.0
255957611675 DNA-directed DNA polymerase [Candidatus Liberibacter as 1 0.0
254780127675 putative DNA polymerase from bacteriophage origin [Cand 1 0.0
255957561675 DNA-directed DNA polymerase [Candidatus Liberibacter as 1 0.0
255957621675 DNA-directed DNA polymerase [Candidatus Liberibacter as 1 0.0
255957556675 DNA-directed DNA polymerase [Candidatus Liberibacter as 1 0.0
255957596675 DNA-directed DNA polymerase [Candidatus Liberibacter as 1 0.0
291283829687 DNA polymerase I - 3''''-5'''' exonuclease and polymera 1 1e-125
191173996687 DNA polymerase [Escherichia coli F11] Length = 687 1 1e-125
>gi|315121967|ref|YP_004062456.1| putative DNA polymerase from bacteriophage origin [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 673 Back     alignment and organism information
 Score =  814 bits (2103), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 400/677 (59%), Positives = 491/677 (72%), Gaps = 6/677 (0%)

Query: 1   MATLFIDFETRSPIDLTKCGICKYAEDVCVILFAFGFDDHPVELWDCVHDPVMPQVLKEA 60
           M  LFID ETRSP  L K G+  YAE+  + L A+  +D  ++LWDC  +PVMP  L + 
Sbjct: 1   MPKLFIDIETRSPKPLPKVGVWAYAEEAKITLCAYAHNDETIKLWDCTANPVMPSDLLKH 60

Query: 61  LENTDVTIVAHNSYFERTVLKACFNLDIPIHRWICTLVLARSNGLPSALKAVGEALKLSS 120
           L++  V  VAHNS FER + K   N+ IP  RWICT  LAR NGLP++LK    ALK   
Sbjct: 61  LKDDTVVCVAHNSLFERILFKKSLNITIPPRRWICTSTLARINGLPASLKNACMALKFPE 120

Query: 121 Q--KMEEGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTREIFKRLEPL 178
              KMEEGK LIARFCKG   E  YD  + NH +AW+LFGEYCK DV  TRE++KRL PL
Sbjct: 121 TLTKMEEGKALIARFCKGSIEESPYDAKRANHVQAWQLFGEYCKRDVEATRELYKRLTPL 180

Query: 179 SSKEQELWYLDQTINDRGYCVDVALAHTLNQIVDVERTKLDQELESLTYGLVSSSRCLEK 238
           S  E+ LW LDQ INDRGY +D+ L   L +++  ER KLD+EL++LT+G++ SSR  + 
Sbjct: 181 SENERHLWLLDQEINDRGYAIDLNLVKKLQELIAFEREKLDEELKTLTFGVIGSSRKTDL 240

Query: 239 LKTWLFLETGLHLEDLTETTCQRVLSSNKKLTPQAIQVFNNRMRASRSAVLKLNTLVEAM 298
           L  +LFL  GL L D+ E+T    LS    +T +A  + NNR+ +S+SA+LKLNTL  A+
Sbjct: 241 LNKYLFLYMGLDLPDMAESTIATALS-QPNITQRAKDILNNRLSSSQSAILKLNTLSGAV 299

Query: 299 NSDGRLRGTLQFLGASRTGRWSGCVFPPQNLPRPSRSHEELDQIITHLPTSITSDPDPLQ 358
           + D RLRGTLQF GASRTGRWSGCVF PQNLPRP+ SHE +++ I    ++  SD DPL+
Sbjct: 300 SPDLRLRGTLQFYGASRTGRWSGCVFQPQNLPRPNTSHETIEEAIES--SNFPSD-DPLR 356

Query: 359 IISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQWKLKAFETGEDLYVTTYARSFN 418
             SDCVRSC+IAS GKKLVVADLAGIEARVLAW+AGEQWKL AF  GED+Y T Y+++FN
Sbjct: 357 FASDCVRSCIIASTGKKLVVADLAGIEARVLAWIAGEQWKLNAFANGEDIYKTAYSKAFN 416

Query: 419 VAPAQVTKDQRAIGKVMELALGYQGGAKAFQKMASTTGLNLNTFAHLVKTNSAPEEWEDA 478
           +  + VTKDQRAIGKVMELALGYQGGA+ FQ MAS  GL+L  F+  +K  +  ++WE A
Sbjct: 417 IPLSNVTKDQRAIGKVMELALGYQGGARVFQTMASNLGLDLKQFSKSIKQTATGDDWEQA 476

Query: 479 ENFCRWMQENHPEHAIEDLFIGTACERVKKAWRQKHSRVSELWNELHQAFEQTIENGKAI 538
           +  C WMQE +PE A+ D FIGTACE VK AWR KH  V +LW +  +AF+  I++G++I
Sbjct: 477 QRRCLWMQETYPEFAVHDPFIGTACELVKTAWRAKHKGVVQLWKDCEEAFDCVIKDGRSI 536

Query: 539 IARKRRDVPLVYMKKDKNNLILMLPSGRSLVYRDVGNNRSYLNTTTRQLTREYTYGGKLT 598
            AR+   VP + MKK   N+ + LPS R LVYRDV ++RSYLNT T Q+ RE TYGGKLT
Sbjct: 537 SARRVAGVPPLLMKKQHQNVFITLPSNRKLVYRDVKSDRSYLNTATAQIMRERTYGGKLT 596

Query: 599 ENIVQAVSRDILAEGMMNATKAGYDIVLTVHDEIVCETPDTDEFNASMLYHLMTSNPSWA 658
           ENIVQA+SRDILA GM+NAT+AGYDIVLTVHDEIVCETPDT EF++  L  LMT NP WA
Sbjct: 597 ENIVQAISRDILACGMINATRAGYDIVLTVHDEIVCETPDTPEFSSDELCFLMTQNPKWA 656

Query: 659 KGLPLKAEGYESKRYRK 675
           KGLPLKAEGYE+ RYRK
Sbjct: 657 KGLPLKAEGYEALRYRK 673


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>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|255957611|dbj|BAH96662.1| DNA-directed DNA polymerase [Candidatus Liberibacter asiaticus] Length = 675 Back     alignment and organism information
>gi|254780127|ref|YP_003064540.1| putative DNA polymerase from bacteriophage origin [Candidatus Liberibacter asiaticus str. psy62] 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|255957621|dbj|BAH96670.1| 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|255957596|dbj|BAH96650.1| DNA-directed DNA polymerase [Candidatus Liberibacter asiaticus] Length = 675 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
>gi|191173996|ref|ZP_03035513.1| DNA polymerase [Escherichia coli F11] 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 6e-25
smart00482206 smart00482, POLAc, DNA polymerase A domain 5e-20
cd06444347 cd06444, DNA_pol_A, Family A polymerase primarily fills 7e-19
PRK14975553 PRK14975, PRK14975, bifunctional 3'-5' exonuclease/DNA 3e-17
cd08639324 cd08639, DNA_pol_A_Aquificae_like, Phylum Aquificae Pol 4e-15
COG0749593 COG0749, PolA, DNA polymerase I - 3'-5' exonuclease and 1e-13
TIGR00593887 TIGR00593, pola, DNA polymerase I 9e-10
cd08638373 cd08638, DNA_pol_A_theta, DNA polymerase theta is a low 2e-09
pfam00476383 pfam00476, DNA_pol_A, DNA polymerase family A 3e-15
cd08637377 cd08637, DNA_pol_A_pol_I_C, Polymerase I functions prim 2e-12
PRK05755880 PRK05755, PRK05755, DNA polymerase I; Provisional 7e-11
cd08640371 cd08640, DNA_pol_A_plastid_like, DNA polymerase A type 5e-08
cd06130156 cd06130, DNA_pol_III_epsilon_like, an uncharacterized b 5e-07
cd06127159 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain family 3e-04
COG0847243 COG0847, DnaQ, DNA polymerase III, epsilon subunit and 0.004
pfam01612172 pfam01612, 3_5_exonuc, 3'-5' exonuclease 2e-04
cd00007155 cd00007, 35EXOc, 3'-5' exonuclease 0.002
cd08642378 cd08642, DNA_pol_A_pol_I_A, Polymerase I functions prim 2e-45
>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|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|184938 PRK14975, PRK14975, bifunctional 3'-5' exonuclease/DNA polymerase; Provisional 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|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|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|144170 pfam00476, DNA_pol_A, DNA polymerase family A 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|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
>gnl|CDD|176648 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain family Back     alignment and domain information
>gnl|CDD|31188 COG0847, DnaQ, DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|144991 pfam01612, 3_5_exonuc, 3'-5' exonuclease Back     alignment and domain information
>gnl|CDD|28891 cd00007, 35EXOc, 3'-5' exonuclease 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

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 675 putative DNA polymerase from bacteriophage origin [Cand
PRK06887954 consensus 100.0
PRK07556977 consensus 100.0
PRK05755889 DNA polymerase I; Provisional 100.0
PRK07997928 consensus 100.0
PRK07625922 consensus 100.0
PRK08786927 consensus 100.0
PRK05929870 consensus 100.0
PRK08835931 consensus 100.0
PRK07898902 consensus 100.0
PRK07456975 consensus 100.0
PRK08928861 consensus 100.0
PRK05797869 consensus 100.0
PRK08076877 consensus 100.0
PRK08434887 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
PRK07300880 consensus 100.0
pfam00476383 DNA_pol_A DNA polymerase family A. 100.0
cd06444379 DNA_pol_A DNA polymerase family A, 5'-3' polymerase dom 100.0
smart00482206 POLAc DNA polymerase A domain. 100.0
KOG36571075 consensus 99.79
PHA00452816 T3/T7-like RNA polymerase 96.3
cd06139193 DNA_polA_I_Ecoli_like_exo The 3'-5' exonuclease domain 99.94
cd06128166 DNA_polA_exo The 3'-5' exonuclease domain of family-A D 99.93
cd06140178 DNA_polA_I_Bacillus_like_exo Bacillus stearothermophilu 99.85
cd00007155 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsi 99.83
cd06142178 RNaseD_exo Ribonuclease (RNase) D is a bacterial enzyme 99.8
pfam01612172 3_5_exonuc 3'-5' exonuclease. This domain is responsibl 99.8
smart00474172 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofread 99.78
cd06147192 Rrp6p_like_exo Yeast Rrp6p and its human homolog, the P 99.68
cd06148197 Egl_like_exo The Egalitarian (Egl) protein subfamily is 99.67
COG0349361 Rnd Ribonuclease D [Translation, ribosomal structure an 99.67
cd06141168 WRN_exo WRN is a unique RecQ DNA helicase exhibiting an 99.54
TIGR01388374 rnd ribonuclease D; InterPro: IPR006292 These proteins 99.49
PRK10829373 ribonuclease D; Provisional 99.43
cd06146191 mut-7_like_exo The mut-7 subfamily is composed of Caeno 99.41
PRK07740240 hypothetical protein; Provisional 99.25
PRK07982243 consensus 99.23
PRK07009241 consensus 99.23
PRK08816244 consensus 99.22
cd05781188 DNA_polB_B3_exo The 3'-5' exonuclease domain of archaea 99.09
PRK09145203 DNA polymerase III subunit epsilon; Validated 99.06
cd05780195 DNA_polB_Kod1_like_exo The 3'-5' exonuclease domain of 98.88
PRK05762785 DNA polymerase II; Reviewed 98.57
cd05777230 DNA_polB_delta_exo The 3'-5' exonuclease domain of euka 98.52
smart00486471 POLBc DNA polymerase type-B family. DNA polymerase alph 98.25
COG3359278 Predicted exonuclease [DNA replication, recombination, 98.24
KOG1798 2173 consensus 97.82
COG0417792 PolB DNA polymerase elongation subunit (family B) [DNA 97.7
PRK07748205 sporulation inhibitor KapD; Provisional 91.69
cd06129159 RNaseD_like The RNase D-like group is composed of RNase 99.55
cd06126181 DEDDy DEDDy exonucleases, part of the DnaQ-like (or DED 99.26
cd05782208 DNA_polB_like1_exo A subfamily of the 3'-5' exonuclease 99.06
cd05785207 DNA_polB_like2_exo A subfamily of the 3'-5' exonuclease 99.03
cd05784193 DNA_polB_II_exo The 3'-5' exonuclease domain of Escheri 98.74
cd05160200 DNA_polB_exo The 3'-5' exonuclease domain of family-B D 98.59
cd05779204 DNA_polB_epsilon_exo The 3'-5' exonuclease domain of eu 98.51
cd05783204 DNA_polB_B1_exo The 3'-5' exonuclease domain of Sulfolo 98.31
cd05778231 DNA_polB_zeta_exo The 3'-5' exonuclease domain of eukar 97.34
PRK06807313 DNA polymerase III subunit epsilon; Validated 99.3
PRK06631229 consensus 99.29
PRK08517259 DNA polymerase III subunit epsilon; Provisional 99.27
TIGR01406246 dnaQ_proteo DNA polymerase III, epsilon subunit; InterP 99.22
PRK05711240 DNA polymerase III subunit epsilon; Provisional 99.21
PRK06310250 DNA polymerase III subunit epsilon; Validated 99.2
PRK06309232 DNA polymerase III subunit epsilon; Validated 99.18
PRK06022234 consensus 99.18
PRK07883575 hypothetical protein; Validated 99.15
PRK06859253 consensus 99.14
PRK08858246 consensus 99.12
cd06131167 DNA_pol_III_epsilon_Ecoli_like This subfamily is compos 99.1
PRK07942234 DNA polymerase III subunit epsilon; Provisional 99.08
cd06134189 RNaseT RNase T is a DEDDh-type DnaQ-like 3'-5' exoribon 99.0
PRK09146239 DNA polymerase III subunit epsilon; Validated 98.89
PRK05168213 ribonuclease T; Provisional 98.88
cd06136177 TREX1_2 Three prime repair exonuclease (TREX) 1 and 2 a 98.62
PRK07983219 exodeoxyribonuclease X; Provisional 98.59
smart00479169 EXOIII exonuclease domain in DNA-polymerase alpha and e 98.56
PRK07247195 DNA polymerase III subunit epsilon; Validated 98.54
COG0847243 DnaQ DNA polymerase III, epsilon subunit and related 3' 98.29
cd06144152 REX4_like This subfamily is composed of RNA exonuclease 98.13
PTZ001661081 DNA polymerase delta catalytic subunit; Provisional 98.02
cd06133176 ERI-1_3'hExo_like This subfamily is composed of Caenorh 97.96
TIGR00573228 dnaq exonuclease, DNA polymerase III, epsilon subunit f 97.83
cd05776234 DNA_polB_alpha_exo The 3'-5' exonuclease domain of euka 96.82
PRK05761777 DNA polymerase I; Reviewed 96.77
pfam03175452 DNA_pol_B_2 DNA polymerase type B, organellar and viral 95.39
KOG09691066 consensus 94.39
KOG2249280 consensus 93.46
PRK08074 932 bifunctional ATP-dependent DNA helicase/DNA polymerase 99.27
PRK07246 820 bifunctional ATP-dependent DNA helicase/DNA polymerase 99.24
TIGR01407 944 dinG_rel DnaQ family exonuclease/DinG family helicase, 98.99
cd06125130 DnaQ_like_exo The DnaQ-like exonuclease superfamily is 98.75
TIGR01405 1264 polC_Gram_pos DNA polymerase III, alpha subunit, Gram-p 99.2
PRK06195309 DNA polymerase III subunit epsilon; Validated 99.16
cd06130156 DNA_pol_III_epsilon_like This subfamily is composed of 98.98
PRK06063313 DNA polymerase III subunit epsilon; Provisional 98.96
PRK00448 1436 polC DNA polymerase III PolC; Validated 98.95
cd06127159 DEDDh DEDDh exonucleases, part of the DnaQ-like (or DED 98.72
COG2176 1444 PolC DNA polymerase III, alpha subunit (gram-positive t 98.67
pfam00929162 Exonuc_X-T Exonuclease. This family includes a variety 98.23
cd06138183 ExoI_N This subfamily is composed of the N-terminal dom 98.13
PRK09182293 DNA polymerase III subunit epsilon; Validated 98.02
cd06149157 ISG20 Interferon (IFN) Stimulated Gene product of 20 kD 97.42
PRK05601377 DNA polymerase III subunit epsilon; Validated 97.02
PRK06722242 exonuclease; Provisional 96.13
cd06137161 DEDDh_RNase This group is composed of eukaryotic exorib 95.56
cd06145150 REX1_like This subfamily is composed of RNA exonuclease 95.47
cd06143174 PAN2_exo PAN2 is the catalytic subunit of poly(A) nucle 94.18
pfam04857235 CAF1 CAF1 family ribonuclease. The major pathways of mR 93.47
cd06135173 Orn Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3 92.93
pfam10108211 Exon_PolB Predicted 3'-5' exonuclease related to the ex 98.26
KOG2206687 consensus 98.05
pfam00940391 RNA_pol DNA-dependent RNA polymerase. This is a family 97.44
TIGR03491457 RecB family nuclease, putative, TM0106 family. Members 96.84
pfam11074127 DUF2779 Domain of unknown function(DUF2779). This domai 95.22
pfam03104254 DNA_pol_B_exo DNA polymerase family B, exonuclease doma 94.95
TIGR005931005 pola DNA polymerase I; InterPro: IPR002298 DNA carries 93.96
PRK08928 861 consensus 92.85
PRK07556 977 consensus 90.79
PRK06887 954 consensus 90.32
PRK08076 877 consensus 90.18
PRK07625 922 consensus 90.01
PRK11779477 sbcB exonuclease I; Provisional 91.17
COG0749593 PolA DNA polymerase I - 3'-5' exonuclease and polymeras 90.39
>PRK06887 consensus Back     alignment and domain information
>PRK07556 consensus Back     alignment and domain information
>PRK05755 DNA polymerase I; Provisional Back     alignment and domain information
>PRK07997 consensus Back     alignment and domain information
>PRK07625 consensus Back     alignment and domain information
>PRK08786 consensus Back     alignment and domain information
>PRK05929 consensus Back     alignment and domain information
>PRK08835 consensus Back     alignment and domain information
>PRK07898 consensus Back     alignment and domain information
>PRK07456 consensus Back     alignment and domain information
>PRK08928 consensus Back     alignment and domain information
>PRK05797 consensus Back     alignment and domain information
>PRK08076 consensus Back     alignment and domain information
>PRK08434 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
>PRK07300 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
>smart00482 POLAc DNA polymerase A domain Back     alignment and domain information
>KOG3657 consensus Back     alignment and domain information
>PHA00452 T3/T7-like RNA polymerase 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
>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
>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
>cd06148 Egl_like_exo The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins Back     alignment and domain information
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>cd06141 WRN_exo WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity 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
>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
>PRK07740 hypothetical protein; Provisional Back     alignment and domain information
>PRK07982 consensus Back     alignment and domain information
>PRK07009 consensus Back     alignment and domain information
>PRK08816 consensus 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
>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
>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
>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
>KOG1798 consensus Back     alignment and domain information
>COG0417 PolB DNA polymerase elongation subunit (family B) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK07748 sporulation inhibitor KapD; Provisional 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
>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
>cd05782 DNA_polB_like1_exo A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases 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
>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
>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
>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
>cd05778 DNA_polB_zeta_exo The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta Back     alignment and domain information
>PRK06807 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06631 consensus Back     alignment and domain information
>PRK08517 DNA polymerase III subunit epsilon; Provisional 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
>PRK05711 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK06310 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06309 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06022 consensus Back     alignment and domain information
>PRK07883 hypothetical protein; Validated Back     alignment and domain information
>PRK06859 consensus Back     alignment and domain information
>PRK08858 consensus 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
>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
>PRK09146 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK05168 ribonuclease T; Provisional 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
>PRK07983 exodeoxyribonuclease X; Provisional 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
>PRK07247 DNA polymerase III subunit epsilon; Validated 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
>PTZ00166 DNA polymerase delta catalytic subunit; Provisional 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
>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
>cd05776 DNA_polB_alpha_exo The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha Back     alignment and domain information
>PRK05761 DNA polymerase I; Reviewed Back     alignment and domain information
>pfam03175 DNA_pol_B_2 DNA polymerase type B, organellar and viral Back     alignment and domain information
>KOG0969 consensus Back     alignment and domain information
>KOG2249 consensus Back     alignment and domain information
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated 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
>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
>PRK06195 DNA polymerase III subunit epsilon; 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
>PRK06063 DNA polymerase III subunit epsilon; Provisional Back     alignment and domain information
>PRK00448 polC DNA polymerase III PolC; 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
>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
>PRK09182 DNA polymerase III subunit epsilon; Validated 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
>PRK05601 DNA polymerase III subunit epsilon; Validated Back     alignment and domain information
>PRK06722 exonuclease; Provisional 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
>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
>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
>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
>pfam00940 RNA_pol DNA-dependent RNA polymerase Back     alignment and domain information
>TIGR03491 RecB family nuclease, putative, TM0106 family Back     alignment and domain information
>pfam11074 DUF2779 Domain of unknown function(DUF2779) Back     alignment and domain information
>pfam03104 DNA_pol_B_exo DNA polymerase family B, exonuclease domain 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
>PRK08928 consensus Back     alignment and domain information
>PRK07556 consensus Back     alignment and domain information
>PRK06887 consensus Back     alignment and domain information
>PRK08076 consensus Back     alignment and domain information
>PRK07625 consensus Back     alignment and domain information
>PRK11779 sbcB exonuclease I; Provisional 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

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-118
1kfs_A605 Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Muta 1e-118
1kln_A605 Dna Polymerase I Klenow Fragment (E.C.2.7.7.7) Muta 1e-116
1d8y_A605 Crystal Structure Of The Complex Of Dna Polymerase 1e-115
1u45_A580 8oxoguanine At The Pre-Insertion Site Of The Polyme 4e-81
1l3s_A580 Crystal Structure Of Bacillus Dna Polymerase I Frag 5e-81
2hhq_A580 O6-Methyl-Guanine:t Pair In The Polymerase-10 Basep 6e-81
3eyz_A580 Cocrystal Structure Of Bacillus Fragment Dna Polyme 9e-81
1lv5_A580 Crystal Structure Of The Closed Conformation Of Bac 1e-80
2xo7_A580 Crystal Structure Of A Da:o-Allylhydroxylamine-Dc B 1e-80
3bdp_A580 Dna Polymerase IDNA COMPLEX Length = 580 3e-80
3ht3_A579 Crystal Structure Of Fragment Dna Polymerase I From 4e-80
3hpo_A580 Crystal Structure Of Fragment Dna Polymerase I From 4e-80
2hhw_A580 Ddttp:o6-Methyl-Guanine Pair In The Polymerase Acti 5e-80
3hp6_A580 Crystal Structure Of Fragment Dna Polymerase I From 6e-80
2hvh_A580 Ddctp:o6meg Pair In The Polymerase Active Site (0 P 6e-80
5ktq_A543 Large Fragment Of Taq Dna Polymerase Bound To Dctp 3e-83
1qtm_A539 Ddttp-Trapped Closed Ternary Complex Of The Large F 3e-83
1qss_A539 Ddgtp-Trapped Closed Ternary Complex Of The Large F 3e-83
4ktq_A539 Binary Complex Of The Large Fragment Of Dna Polymer 3e-83
2ktq_A538 Open Ternary Complex Of The Large Fragment Of Dna P 3e-83
3ktq_A540 Crystal Structure Of An Active Ternary Complex Of T 3e-83
1bgx_T832 Taq Polymerase In Complex With Tp7, An Inhibitory F 6e-82
1taq_A832 Structure Of Taq Dna Polymerase Length = 832 1e-80
1t7p_A698 T7 Dna Polymerase Complexed To Dna PrimerTEMPLATE,A 2e-14
1zyq_A698 T7 Dna Polymerase In Complex With 8og And Incoming 2e-14
2ajq_A704 Structure Of Replicative Dna Polymerase Provides In 9e-14
2hbj_A410 Structure Of The Yeast Nuclear Exosome Component, R 9e-06
3ikm_A1172 Crystal Structure Of Human Mitochondrial Dna Polyme 2e-05
>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 =  431 bits (1107), Expect = e-118,   Method: Composition-based stats.
 Identities = 102/704 (14%), Positives = 205/704 (29%), Gaps = 167/704 (23%)

Query: 5   FIDFETRSPIDLTKCGICKYAEDVCVILFAFGFDDHPVELWDCVHD----------PVMP 54
             D ET S  +++            ++  +F  +          HD              
Sbjct: 30  AFDTETDSLDNIS----------ANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERAL 79

Query: 55  QVLKEALENTDVTIVAHNSYFERTVLKACFNLDIPIHRWICTLVLARSNGL---PSALKA 111
           ++LK  LE+     V  N  ++R +L     +++       T++ +           + +
Sbjct: 80  ELLKPLLEDEKALKVGQNLKYDRGILANY-GIELRGIA-FDTMLESYILNSVAGRHDMDS 137

Query: 112 VGEALKLSSQKMEEGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTREI 171
           + E              L  +    E            ++ A    G Y   D  VT ++
Sbjct: 138 LAER------------WLKHKTITFEEIAGKGKNQLTFNQIALEEAGRYAAEDADVTLQL 185

Query: 172 FKRLEPLSSKE-----------QELWYLDQTINDRGYCVDVALAHTLNQIVDVERTKLDQ 220
             ++ P   K              L  +   I   G  +D  + H  ++ + +   +L++
Sbjct: 186 HLKMWPDLQKHKGPLNVFENIEMPLVPVLSRIERNGVKIDPKVLHNHSEELTLRLAELEK 245

Query: 221 ELESLTYGLVSSSRCLEKLKTWLFLETGLHLEDLTE----TTCQRVLSSNKKLTPQAIQV 276
           +   +      +    ++L+T LF + G+     T     +T + VL       P    +
Sbjct: 246 KAHEIAG-EEFNLSSTKQLQTILFEKQGIKPLKKTPGGAPSTSEEVLEELALDYPLPKVI 304

Query: 277 FNNRMRASRSAVLKLNTLVEAMNSDGRLRGTLQFLGASRTGRWSGCVFPPQNLPRPSRSH 336
              R   ++      + L   +N       T      + TGR S      QN+P  +   
Sbjct: 305 LEYR-GLAKLKSTYTDKLPLMINPKTGRVHTSYHQAVTATGRLSSTDPNLQNIPVRNEEG 363

Query: 337 EELDQIITHLPTSITSDPDPLQIISDCVRSCVIASEGKKLVVADLAGIEARVLAWMAGEQ 396
                                      +R   IA E   +V AD + IE R++A ++ ++
Sbjct: 364 RR-------------------------IRQAFIAPEDYVIVSADYSQIELRIMAHLSRDK 398

Query: 397 WKLKAFETGEDLYVTTYARSFNVAPAQVTKDQRAIGKVMELALGYQGGAKAFQKMASTTG 456
             L AF  G+D++  T A  F +    VT +QR   K +                    G
Sbjct: 399 GLLTAFAEGKDIHRATAAEVFGLPLETVTSEQRRSAKAINF--------------GLIYG 444

Query: 457 LNLNTFAHLVKTNSAPEEWEDAENFCRWMQENHPEHAIEDLFIGTACERVKKAWRQKHSR 516
           ++                                  A +        ++    + +++  
Sbjct: 445 MS------------------------------AFGLARQLNIPRKEAQKYMDLYFERYPG 474

Query: 517 VSELWNELHQAFEQTIENGKAIIARKRRDVPLVYMKKDKNNLILMLPSGRSLVYRDVGNN 576
           V E         ++                             +    GR L   D+ ++
Sbjct: 475 VLEYMERTRAQAKE--------------------------QGYVETLDGRRLYLPDIKSS 508

Query: 577 RSYLNTTTRQLTREYTYGGKLTENIVQAVSRDILAEGMMNATKA------GYDIVLTVHD 630
                    +               +Q  + DI+   M+              +++ VHD
Sbjct: 509 NGARRAAAER---------AAINAPMQGTAADIIKRAMIAVDAWLQAEQPRVRMIMQVHD 559

Query: 631 EIVCETPDTDEFNASM-LYHLMTSNPSWAKGLPLKAEGYESKRY 673
           E+V E    D    +  ++ LM +       +PL  E    + +
Sbjct: 560 ELVFEVHKDDVDAVAKQIHQLMENCTR--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|55670162|pdb|1U45|A Chain A, 8oxoguanine At The Pre-Insertion Site Of The Polymerase Active Site Length = 580 Back     alignment and structure
>gi|29726371|pdb|1L3S|A Chain A, Crystal Structure Of Bacillus Dna Polymerase I Fragment Complexed To 9 Base Pairs Of Duplex Dna. Length = 580 Back     alignment and structure
>gi|122920392|pdb|2HHQ|A Chain A, O6-Methyl-Guanine:t Pair In The Polymerase-10 Basepair Position Length = 580 Back     alignment and structure
>gi|266618521|pdb|3EYZ|A Chain A, Cocrystal Structure Of Bacillus Fr