Conserved Protein Domain Family
POLBc_alpha

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cd05532: POLBc_alpha 
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. In most organisms no specific repair role, other than check point control, has been assigned to this enzyme. Pol alpha contains both polymerase and exonuclease domains, but lacks exonuclease activity suggesting that the exonuclease domain may be for structural purposes only.
Statistics
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PSSM-Id: 99915
View PSSM: cd05532
Aligned: 35 rows
Threshold Bit Score: 467.826
Threshold Setting Gi: 123425608
Created: 23-May-2007
Updated: 17-Jan-2013
Structure
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Aligned Rows:
 
active sitemetal-binding
Feature 1:active site [active site]
Evidence:
  • Comment:Based on similarity to bacteriophage RB69 POLBc (1Q9Y)

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                     #  ###                                              
gi 45644974   852 QTKKKAAYAGGLVLEPMRGLYEKYVLLMDFNSLYPSIIQEYNICFTTVQQPVdadelp---------------------- 909
gi 156086442  790 SDSKKKNYEGGLVLEPETGLYDNFVLLLDFNSLYPSIIQEFNVCFTTVKLLEdgsv------------------------ 845
gi 85000361   620 QLDDMKSYEGGLVFEPISGLYDNFILLLDFNSLYPSIIQEYNICFTTTVAKDednv------------------------ 675
gi 66359588   832 NSKKEETYSGGLVLEPITGLYDSFILLLDFNSLYPSIIQEFNICFTTREPTDlgpdatetfess---------------- 895
gi 410720    1019 KNKNTAKYLGGLVLDPLCGYYDTFVLYLDFNSLYPSIIIEYNVCFSTLKLKNcdvsiednklntkkngninndyeknihs 1098
gi 146164643  787 PKKKENKYKGGQVFEPEKGLYNEYIVLLDFNSLYPSIIQEFNVCFTTCVRDPiplemqmapflgnkkaaiqysknqntke 866
gi 145521204  684 EQESKKTYGGGLVFEPKADIYTQYVLLLDFNSLYPSIIMEYNICFTTVQRDKinfevdktqleeeptqtkpqksnknk-- 761
gi 19173639   396 VSRREVKYSGGLVLPPQTGFYEDLVLLLDFNSLYPSIIQEFNVCFSTIGMFDrsisgnmsseq----------------- 458
gi 66812196   882 DKDNHAAYSGGLVLDPKIDFYDRYVVLLDFNSLYPSIIQEYNVCFTTINRVKrddgkwee-------------------- 941
gi 154418827  695 PKSKLGKYRGATVLQPKKGFYDTIIVLLDFTSLYPSIISEYNLCFTTVDKRNpnsee----------------------- 751
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                           #             
gi 45644974   910 ------------------------------------------tlpdskTEPG--ILPLQLKRLVESRKEVKKLMAAPdls 945
gi 156086442  846 --------------------------------------------qvltETTG--MLPQILKRLVELRASVKAAIAVEk-n 878
gi 85000361   676 ---------------------------------------------viqDNVG--VLPSILKRLVELRLNIKNIIKGEk-n 707
gi 66359588   896 -------------------------------------slidrnsssnqFDST--VLPGILESLVKRRRHIKEILKNMp-s 935
gi 410720    1099 daeknihsdddknihsddeknydndksynkleddnllennveidefdrSKPG--ILPCILKSLVEKRSVIKKLISNEk-n 1175
gi 146164643  867 ---------------------nkmqdedeedneneqivqthdvlptieVIKGiaPLPSILQYLVEQRKVVKNQIKGQk-d 924
gi 145521204  762 ----------------------kkkdqtqdendtkekikdfigsvdpdAGSG--ILPQIIEKLVNMRKQAKKEMSRSt-- 815
gi 19173639   459 --------------------------------------lvrltedaknSERG--FLPRILEGFVRRRKAVKDLLKQGg-t 497
gi 66812196   942 -----------------------------------------ampppssIEKG--ILPKVLHGLVSKRREIKKRMEQEk-n 977
gi 154418827  752 --------------------------------------------avncGRKG--ILPEIMENLTKMRIELKNKMNTLqdd 785
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                       #   #                                                  #          
gi 45644974   946 PELQMQYHIRQMALKLTANSMYGCLGFAHSRFFAQHLAALVTHKGREILTNTQQLVQkm-nyDVVYGDTDSLMINTNI-- 1022
gi 156086442  879 DSRKAQLGVRQLALKLVANSLYGCLGSVYSRFHARHMAAYITQQGRLVLQSTRERVEnqyslHVIYGDTDSLMIDTNIrd 958
gi 85000361   708 EVRRVQLSTRQLALKLIANSIYGCLGSNFSRFHCKYIASYITKLGRELLRSTKEKVEnvfnlQVIYGDTDSLMINTNIrd 787
gi 66359588   936 GTRKSQLEIRQLALKLTANSLYGCLGYKNSRFYAKDLASIITFYGRQILQKTKLKVEdetklQVIYGDTDSIMVNTNIld 1015
gi 410720    1176 KEKKELLLIQSLSIKLISNSIYGCLGNTNNRFYAKHLASYITSKGRNLLQHTKFKVEkefnlKVIYGDTDSIMIDTGIka 1255
gi 146164643  925 PQVIETLDIKQKAFKLVANSMYGCLGFSSSRFYAMPLASFITAKGRHILFDSKKIVEdm-gySVIYGDTDSLMIKPGT-- 1001
gi 145521204  816 GLMKQIYNIKQLAVKLVANSIYGCLGFSSSRFYAVGIASLITQKGRSILMDSKNTVErs--nDVIYGDTDSMMICARQe- 892
gi 19173639   498 PEETKALDIRQKALKLTANSIYGCLGFVGSRFCNYTMAAYITSKGRDLLLEAKRIAEgecgvRIIYGDTDSVMVHTGLag 577
gi 66812196   978 KIIKAQYDIQQQAVKLIANSMYGCLGFSHSRFYALPLAELVTRKGRENLQKGASIVNkm-cyDVIYGDTDSLMIYTGV-- 1054
gi 154418827  786 KFNFDRFLIKQQAIKSLSNSIYGYLGFSLSRFASNEIAALITERGRFVLQKTVETVEslgkfSVIYGDTDSVMVNTGT-- 863
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 45644974  1023 ----TDYDQVYKIGHNIKQSVNKLYK--QLELDIDGVFGCLLLLKKKKYAAIKLSkdsk------gnlrREQEHKGLDIV 1090
gi 156086442  959 dgseTSYEAAKQIANTLMSSINKSHK--KLEIGMDAMFNRLLLLKKKKYAALKVVdyk--------sriFAREIKGLDFI 1028
gi 85000361   788 dgnlANYNAANQLANNLVTFINKSHK--KLEIGIDAVFTRLLLLKKKKYASLKVIeye--------tgqFAREIKGLDFI 857
gi 66359588  1016 dgngEGYYHVLKLASQIKQIVNKDYT--KLELDLDGVLQRLLLLKKKKYACIQIVdfh--------rkqLKLECKGLDLV 1085
gi 410720    1256 n-niNNYKESFKLAHLIKNSINKNYK--KLELDLECIFSKLLLLKKKKYACAKVIdnn--------lekYEYEMKGINFI 1324
gi 146164643 1002 ----NEFLEAVKTGLSIKIKVNSKYK--KLQLDIDGVFKNMLLLKKKKYATLKVAnweevkn-tnapekLEKEIKGIDVV 1074
gi 145521204  893 ----KNLSEILVLGTQIAKEINKKYK--KLVLAIDGVFDTLLLMKKKKYAGIKIDnledlmtgqteqpkFKMEVKGIDIV 966
gi 19173639   578 --kkSNYTKALELSRRLQDAINSRYK--KIEIEVDKVFKKLLLYKKKRYAGLYMTdd----------gkGRIEYKGLDLV 643
gi 66812196  1055 ----GTFNEAETIGKEIQKKINDQYRgsVMEIGLDGIFKRLLLFKKKKYACLKEFrids------tttkCERENKGIDIV 1124
gi 154418827  864 ----KSVEEAKKIANDISEKVTKQYK--FLKLTVSGLFTKMLLVAKKKYAVTVYDdd----------nkCHREVKGLDMV 927
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 45644974  1091 RRDWSQLAVMVGKAVLDEVLSekpl--------------------eekLDAVHAQLEKIKTqiae--------------- 1135
gi 156086442 1029 RRDWSILTKEVGNALLAIILNdkvndpe-------------elgventVEKIHETLRDVNNkiae--------------- 1080
gi 85000361   858 RRDWSLLTKEIGNKLLDIILNsnyyn-----------------gvdgiVQEIHSTLINLNDqlnn--------------- 905
gi 66359588  1086 RRDWSILTRNVSTQLLNLLFSnepi--------------------dtvITNILNTLESLNEalns--------------- 1130
gi 410720    1325 KRDFSKISKLIGNEVLRIIFTnrdvdskni----------pvplendlSEQIHEYLRTINQriqn--------------- 1379
gi 146164643 1075 RRDWCQLSRDAGNKILEIILEskss--------------------enmLDDIKKYLIQLNDdinq--------------- 1119
gi 145521204  967 RREFCDISKKMQSHVLDILLKtk------------------------nRDDIHGDLITLMQeirsmfdalsgnsnad--- 1019
gi 19173639   644 RKDFCEVSRKICRIVLELLLAdcedpetyrrfyegepkmvlndgsikiREAVYDELRKVSSdle---------------- 707
gi 66812196  1125 RRDYCDLTKDIGQWVLNLILGgeek--------------------ialFSLIKEYLESVQQqikd--------------- 1169
gi 154418827  928 RRDWCQLTKYLSSFVLDQMMNnddrslt-------------vrnclseFHNVAKLLRKSNNdeqnslfyydenfslhnks 994
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 45644974       --------------------------------------------------------------------------------
gi 156086442      --------------------------------------------------------------------------------
gi 85000361       --------------------------------------------------------------------------------
gi 66359588       --------------------------------------------------------------------------------
gi 410720         --------------------------------------------------------------------------------
gi 146164643      --------------------------------------------------------------------------------
gi 145521204      --------------------------------------------------------------------------------
gi 19173639       --------------------------------------------------------------------------------
gi 66812196       --------------------------------------------------------------------------------
gi 154418827  995 nkndvdkkndkinsnenekqnsknelksdkinskendkensknsvnenesksetkdkinsnenddeqksvnflsksdtes 1074
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 45644974  1136 --------------------------------------gvvPLPLFVITKQLTRTPQEYANsaSLPHVQVALRMnrern- 1176
gi 156086442 1081 --------------------------------------gniPPKAWIITRQLAKNPQEYGQnnNLPHVTVALRMnesg-- 1120
gi 85000361   906 --------------------------------------nsiELSKFLITKQLTKNPKEYSDvqNLPHVSVALRLnekgh- 946
gi 66359588  1131 --------------------------------------nsiPLESFIITKTLTKLPQFYSDpyLLPHVIVAKRMissg-- 1170
gi 410720    1380 --------------------------------------defDLDYYIITKKLTKNVHEYQDknSLGHVLVAERMikdg-- 1419
gi 146164643 1120 --------------------------------------kniKNSNYYITKRLTKRVDQYGEk-NLPHVAVAQRSiqekgi 1160
gi 145521204 1020 --------------------------pkqliaqnrfityeiPTSDFIIVKQLNKAPHEYSDtiSAPHVQVALRMvneygr 1073
gi 19173639   708 ---------------------------------------giPAREFVIHNTLSKAPESYDAcaALPHVSLALRLkerg-- 746
gi 66812196  1170 --------------------------------------ntlAVEKFIITKTLSKQPEEYNDadIQPHVQVALQMrakg-- 1209
gi 154418827 1075 ssipnyqevksyssslksdksdtksdgeesnssksfhlkkiTKEMLIIYRQLNKKISEYSDkrNNPHVSIALRMmkrg-- 1152
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                         
gi 45644974  1177 -rrykKGDMVDYVICLDgttn----------------------aamqRAYHLDElkts-----------edkKLQLDTNY 1222
gi 156086442 1121 -asfsAGHEVPFIICSKesieklvlqdnaesnekkteldvklrslcnRAYSLTEfq--------------qkGLEPDIQY 1185
gi 85000361   947 -anysTGHEISYIICTKssaskfhtnsdnsae-ntsssgntgsslssRAFSYNEvt--------------enGLEVDISY 1010
gi 66359588  1171 -lpvsSGTEIPYIICKEvnsqssdev------------apkssmlskRAYSPEEvk--------------snGLNIDIEW 1223
gi 410720    1420 -ynicVNKEIQYCVCTSed--------------------------asRFYKKTSeklnnsqccfsineikkyNLKIDKEY 1472
gi 146164643 1161 dpqtyVNQIISYIICKNeqsklffvdscmv----niqrekwwlllvdKAYSPQEfit------------qskSLEIDLQY 1224
gi 145521204 1074 saqslVNHFIRYVICEDptqk----------------------nlsfRAYTVDEli--------------nkNLTIDYYY 1117
gi 19173639   747 -mkfeQGDVVCYVIGKGdpgq----------------------aihkRAYHPDE------------------DFAIDYGY 785
gi 66812196  1210 -lhvqPGEQVPYIITHGnsssdi------------------keewhhRARAPSDve---------------sIQDVDIDW 1255
gi 154418827 1153 -ekvpQHATIPMIVTSPdvre-----------------------lcdKVKLPDEvk---------------dMSEIDSQW 1193
                         650       660       670
                  ....*....|....*....|....*....|..
Feature 1                                         
gi 45644974  1223 YLGHQIHPVVTRMVEVLEGTDASRIAECLGMD 1254
gi 156086442 1186 YKTQQLLPPILRLCGVIEGTDPQKLASCLQIQ 1217
gi 85000361  1011 YKQQQLLPPILRLCSIIEGTDIQRLSRCLQIE 1042
gi 66359588  1224 YKTQQLLPPLSRLCAPIPGLEISRIGQCLGLE 1255
gi 410720    1473 YIRNQILSPINRLCQYIEGTSAEKLSSCFNIY 1504
gi 146164643 1225 YKRFQLFEPIKRMLEVIEGINLQEIASILEVH 1256
gi 145521204 1118 YLSTQIFDPIVRLCKNVQVISISELAQILGLK 1149
gi 19173639   786 YISSQILPPLLRVVGIVKGFHAGKIGKIFGVE 817
gi 66812196  1256 YLSQQILPSIQRNTGPIGMEPHELAQWLGMTG 1287
gi 154418827 1194 YLVNQILPPIIRLFAPYEHVGSSTIGRSLGLT 1225

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