|
Name |
Accession |
Description |
Interval |
E-value |
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
1395-1872 |
0e+00 |
|
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen.
Pssm-ID: 99917 Cd Length: 451 Bit Score: 676.24 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1395 GSQYRVESMMLRLARLYNYVALSPTRKQVMEQAAIECLPLVMEPQSKLYTNPVIVLDFQSLYPSIIIAYNLCYSTCLGKM 1474
Cdd:cd05534 1 GSQFRVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1475 AYVDQK-KSKLGTLDGYEPNSELRKLLKHreegksieEDILITPNQCLFVKPNVRQGILPRMCTEILNTRVMVKQAMKET 1553
Cdd:cd05534 81 EELNGGgKFGFLGVKLYLPPPPLDLLLLK--------DDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKY 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1554 sKEDTETQRILNARQLGLKLIANVTYGYTSANFSGRMPLSDLADAIVQLARQTLENAIETVNQRFKGKCRVAYGDTDSLF 1633
Cdd:cd05534 153 -KDDKKLQRILDARQLALKLLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYGDTDSLF 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1634 VECIDSTKEEAFKLGKEIVKIVTNSNPKPITLQMERVFHPSFLVSKKRYVGLAFENPSQTKGTLFCKGIEAVRRDNCLMV 1713
Cdd:cd05534 232 VLLPGRTKEEAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAV 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1714 RSLMEKSLEILFETLDFSLVKSYLSRQFYRIISEKCSLQDFIFWKKVKLGYYKSEKNLPPSARVAIREMQRDPRAEPRFN 1793
Cdd:cd05534 312 QKILEKSLRILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLGTYKEGATLPAGAIVALRRMEKDPRAEPQYG 391
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2124384683 1794 ERVPYIVVFSplhPSKAKLSDMVIHPKYYIADRmgtstsnqvmihntrqKYRLHYNYYITRQLLPSLDRLFSLCFVNCN 1872
Cdd:cd05534 392 ERVPYVVVRG---EPGSRLIDLVVSPEEFLADP----------------SLRLDAEYYITKQIIPALDRLFNLVGVDVQ 451
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
1390-1864 |
1.10e-100 |
|
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.
Pssm-ID: 395085 Cd Length: 439 Bit Score: 331.50 E-value: 1.10e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1390 SVLNRGSQYRVESMMLRLARLYNYVALSPTRKQVME---QAAieclpLVMEPQSKLYTNPVIVLDFQSLYPSIIIAYNLC 1466
Cdd:pfam00136 5 RVLEGGQQIRVESCLLRLALEEGFILPDRPSAKGDEdgyQGA-----TVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLC 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1467 YSTCLGkmayvdqkksklgtldgyePNSELRKLlkhreEGKSIEEDILITPNQCLFVKPNVRQGILPRMCTEILNTRVMV 1546
Cdd:pfam00136 80 YTTLVR-------------------SVDEANNL-----PPEDNLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAI 135
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1547 KQAMKETSkeDTETQRILNARQLGLKLIANVTYGYTSANfSGRMPLSDLADAIVQLARQTLENAIETVNQRFKGKCRVAY 1626
Cdd:pfam00136 136 KKLLKEET--DPFERAILDKQQLALKITANSVYGFTGFA-NGRLPCLPIAASVTAIGREMLENTKDLVEGMYTYNFRVIY 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1627 GDTDSLFVECIDSTKEEAFKLGKEIVKIVTNSN-PKPITLQMERVFHPSFLVSKKRYVGLAFENPSQTkGTLFCKGIEAV 1705
Cdd:pfam00136 213 GDTDSVFIEFGGKDVEEAMKIGDELAEHVNQDLfKSPIKLEFEKVYKPLLLISKKKYAGLKYTAPSNF-NKLDMKGVDLV 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1706 RRDNCLMVRSLMEKSLEILFETLD----FSLVKSYLSRQFYRIISEKCSLQDFIFWKKVKLGYYKSEKNLPPSARVAIRE 1781
Cdd:pfam00136 292 RRDNCPLVKEVIKKVLDLLLSDRGlpvgLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNYKSKNLPHVEVALRM 371
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1782 MQRDPRAePRFNERVPYIVVFSPLHPSKAKLSDMVIHPKYYIADrmgtstsnqvmihntrqKYRLHYNYYITRQLLPSLD 1861
Cdd:pfam00136 372 NKRNGEA-PEVGDRIPYVIVKAAKGLKNLLIYERAEDPEYVLEN-----------------NLPIDYEYYFSNQLIPPVA 433
|
...
gi 2124384683 1862 RLF 1864
Cdd:pfam00136 434 RLL 436
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
1130-2007 |
6.93e-94 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 330.45 E-value: 6.93e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1130 IEChVTTRADFLPNPIYDPVQAIiicsqncadvanstESILLLNRDLEDN--DTIQHKLTCIPLNFDRFYEFKTEQDLLN 1207
Cdd:PTZ00166 271 IEC-IKLKGLGFPEAENDPVIQI--------------SSVVTNQGDEEEPltKFIFTLKECASIAGANVLSFETEKELLL 335
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1208 GFIDFICKEDPDILLGYEMQTEGLGYLIERGfTVLGKNICYDLSRAIfyqnenKANNTNKDKR-QDKIMKKAQeyarNKQ 1286
Cdd:PTZ00166 336 AWAEFVIAVDPDFLTGYNIINFDLPYLLNRA-KALKLNDFKYLGRIK------STRSVIKDSKfSSKQMGTRE----SKE 404
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1287 sgVMIKGRVVINVWRLMNGEMKLDMYTLHNVAFNILGKRIPYYSYQTLSELSNSCQHRKdsfeyRIILQYYYKKASITLE 1366
Cdd:PTZ00166 405 --INIEGRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETR-----RRIAVYCLKDAILPLR 477
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1367 LLNYLDFLNRTGELAKVFGIEFFSVLNRGSQYRVESMMLRLARLYNYVALSPTRKQVMEQAAIEClPLVMEPQSKLYTNP 1446
Cdd:PTZ00166 478 LLDKLLLIYNYVEMARVTGTPIGWLLTRGQQIKVTSQLLRKCKKLNYVIPTVKYSGGGSEEKYEG-ATVLEPKKGFYDEP 556
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1447 VIVLDFQSLYPSIIIAYNLCYSTCLgkmayvdqkksklgtldgyePNSELRKLlkhreegksiEEDILI-TPNQCLFVKP 1525
Cdd:PTZ00166 557 IATLDFASLYPSIMIAHNLCYSTLV--------------------PPNDANNY----------PEDTYVtTPTGDKFVKK 606
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1526 NVRQGILPRMCTEILNTRVMVKQAMKETSkeDTETQRILNARQLGLKLIANVTYGYTSANFSGRMPLSDLADAIVQLARQ 1605
Cdd:PTZ00166 607 EVRKGILPLIVEELIAARKKAKKEMKDEK--DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQLPCLEVSTSITSFGRQ 684
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1606 TLENAIETVNQRF------KGKCRVAYGDTDSLFVECIDSTKEEAFKLGKEIVKIVTNSNPKPITLQMERVFHPSFLVSK 1679
Cdd:PTZ00166 685 MIDKTKELVEKHYtkangyKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKFLKPIKLEFEKVYCPYLLMNK 764
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1680 KRYVGLAFENPsQTKGTLFCKGIEAVRRDNCLMVRSLMEKSLEILFETLDFSLVKSYLSRQFYRIISEKCSLQDFIFWKk 1759
Cdd:PTZ00166 765 KRYAGLLYTNP-EKYDKIDCKGIETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKGKISDLLQNRIDISLLVITK- 842
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1760 vKLGYYKSEKNLPPSArVAIREMQRDPRAEPRFNERVPYIVVfsplHPSK-AKLSDMVIHPKYyiadrmgtstsnqVMIH 1838
Cdd:PTZ00166 843 -SLGKDDYEGRLAHVE-LAKKLRQRDPGSAPNVGDRVSYVIV----KGAKgAPQYERAEDPLY-------------VLEN 903
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1839 NTrqkyRLHYNYYItRQLLPSLDRLFSLCFVNCNVWYMNLPKRDVYLMAdwrkqlfrKSKNFIERYFKpISLPCVSCGAI 1918
Cdd:PTZ00166 904 NI----PIDTQYYL-DQIKNPLLRIFEGVMDNPDSLFSGEHTRHITISS--------SSKGGLSKFVK-KQLQCLGCKSV 969
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1919 IdcktlnkvegaatdlsSQEPLCPKCKEYPLVLLLRLRSVERNK--NMLSEL---CRHCNHEL--DVTngllpyskvpsi 1991
Cdd:PTZ00166 970 I----------------KEGALCDNCNQNKEPSIYGKKLAKRRHkeAEYSQLwtqCQRCQGSLhqEVI------------ 1021
|
890
....*....|....*.
gi 2124384683 1992 eekCMSLECPILFSKV 2007
Cdd:PTZ00166 1022 ---CTNRDCPIFYRRK 1034
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
1124-1865 |
2.26e-78 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 277.86 E-value: 2.26e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1124 NINVMSIECHVTTRADFlPNPIYD-PVqaIIICSQNCADVanstESILLLNRDlEDNDTIQHkltciplnfdrfyeFKTE 1202
Cdd:COG0417 159 KLKVLSFDIEVSTPRGF-PDPERDgPI--ISIGLAGSDGE----KKVLMLGRE-GVDFEVEY--------------FDDE 216
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1203 QDLLNGFIDFICKEDPDILLGYEMQTEGLGYLIERgFTVLGKNIcyDLSRaifyqnenkanntnkDKRQDKIMKkaqeya 1282
Cdd:COG0417 217 KALLEAFFEIIREYDPDIIIGWNVDNFDLPYLQKR-AERLGIPL--DLGR---------------DGSEPSWRE------ 272
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1283 RNKQSGVMIKGRVVINVWR-LMNGEMKLDMYTLHNVAFNILGKRIPYYSYQTLSELSNscqHRKDSFeyriiLQYYYKKA 1361
Cdd:COG0417 273 HGGQGFASIPGRVVIDLYDaLKSATYKFKSYSLDAVAEELLGEGKLIVDGGEIERLWD---DDKPAL-----AEYNLRDA 344
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1362 SITLELLNYLDFLNRTGELAKVFGIEFFSVLNRGSQYRVESMMLRLARLYNYVAlsPTRKQVMEQA---AIeclplVMEP 1438
Cdd:COG0417 345 ELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGYLA--PNKGEIKGEAypgGY-----VLDP 417
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1439 QSKLYTNpVIVLDFQSLYPSIIIAYNLCYSTclgkmayvdqkksklgtLDgyepnselrkllkhrEEGKSIEEDILITPN 1518
Cdd:COG0417 418 KPGLYEN-VLVLDFKSLYPSIIRTFNISPET-----------------LV---------------EGGEEPCGDEDVAPG 464
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1519 Q-CLFVKPnvRQGILPRMCTEILNTRVMVKQAMKETSKEDTEtQRILNARQLGLKLIANVTYGYT-SANFsgrmPLSD-- 1594
Cdd:COG0417 465 FgHRFCRE--PKGILPSILEELWDERDEAKKKMKKAKPDSEE-YRLYDALQQALKILMNSFYGVLgSEGC----RFYDpe 537
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1595 LADAIVQLARQTLENAIETVNQRfkGKcRVAYGDTDSLFVECIDSTKEEAFKLGKEIVKIVTNSNPKPITLQMERVFHPS 1674
Cdd:COG0417 538 LAESITARGREIIKQTIEKAEEL--GY-KVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRRF 614
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1675 FLV-SKKRYVGLaFENpsqtkGTLFCKGIEAVRRDNCLMVRSLMEKSLEILFETLDFSLVKSYLSRQFYRIISEKCSLQD 1753
Cdd:COG0417 615 FFPgSKKRYAGL-TED-----GKIDIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDD 688
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1754 FIFWKKV--KLGYYksEKNLPPSARVAIREMQRDPRAEPRfnERVPYIVVfsplhpsKAKLSdmvihPKYYIADRMGTSt 1831
Cdd:COG0417 689 LVIRKRLrkPLSEY--EKNVPPHVRAARKLDERGRPYQRG--DKISYVIT-------KGGGR-----VEPVELAKERES- 751
|
730 740 750
....*....|....*....|....*....|....
gi 2124384683 1832 snqvmihntrqkyRLHYNYYITRQLLPSLDRLFS 1865
Cdd:COG0417 752 -------------EIDYDYYIEKQLKPTADRILE 772
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
1124-1636 |
5.99e-72 |
|
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Pssm-ID: 214691 [Multi-domain] Cd Length: 474 Bit Score: 249.76 E-value: 5.99e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1124 NINVMSIECHVTTRADFLPNPiYDPVQAIIicsQNCADVANSTESILLLNRDLEDNDTIQHKLTCIplnfdrfYEFKTEQ 1203
Cdd:smart00486 2 PLKILSFDIETYTDGGNFPDA-EIFDDEII---QISLVINDGDKKGANRRILFTLGTCKEIDGIEV-------YEFNNEK 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1204 DLLNGFIDFICKEDPDILLGYEMQTEGLGYLIERgFTVLGKNICYDLSRAIFYQNENKANNTNKDKRQDKIMKKaqeyar 1283
Cdd:smart00486 71 ELLLAFFEFIKKYDPDIIYGHNISNFDLPYIISR-LEKLKIDPLSKIGRLKIGLRIPNKKPLFGSKSFGLSDIK------ 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1284 nkqsgVMIKGRVVINVWRLMNGEMKLDMYTLHNVAFNILGKRIPYYSYQTLSELSNScqhrkDSFEYRIILQYYYKKASI 1363
Cdd:smart00486 144 -----VYIKGRLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNG-----NYEERDELLRYCIQDAVL 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1364 TLELLNYLDFLNRTGELAKVFGIEFFSVLNRGSQYRVESMMLRLARLYNYVAlsPTRKQVMEQAAIECL--------PLV 1435
Cdd:smart00486 214 TLKLFNKLNVIPLIIELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYIL--PSKELYDFKGSEPDLkkkvkyegGKV 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1436 MEPQSKLYTNPVIVLDFQSLYPSIIIAYNLCYSTCLGKmayvdqkksklgtldgyepNSELRKLLKHREEGKSIEEDIli 1515
Cdd:smart00486 292 LEPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGV-------------------GEVVIKGDLIIPEDLLTIKYE-- 350
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1516 TPNQCLFVKPNVRQGILPRMCTEILNTRVMVKQAMKETSKEDTETQRILNARQLGLKLIANVTYGYTSANFSgRMPLSDL 1595
Cdd:smart00486 351 KGNKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESEELKKLLDSRQLALKLTANSVYGYLGFTNS-RLPCKPL 429
|
490 500 510 520
....*....|....*....|....*....|....*....|...
gi 2124384683 1596 ADAIVQLARQTLENAIETVNQRFKGKC--RVAYGDTDSLFVEC 1636
Cdd:smart00486 430 AASVTALGREILEKTKELIEENGYPKPgfKVIYGDTDSIFVTK 472
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
1123-1369 |
4.22e-53 |
|
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Pssm-ID: 99821 [Multi-domain] Cd Length: 231 Bit Score: 186.29 E-value: 4.22e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1123 QNINVMSIECHVTTRADFLPNPIYDPVQAIIICSQN--CADVANSTESILLLNRDLEDNDTIQHKLTCIPlnFDRFYEFK 1200
Cdd:cd05778 2 QHLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDdvSPFILDANKVGVIIVDELKSNASNGRIRSGLS--GIPVEVVE 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1201 TEQDLLNGFIDFICKEDPDILLGYEMQTEGLGYLIERGFTVLGKNICYDLSRAIFYQNENKANNTNkdkrqdkimkkaqE 1280
Cdd:cd05778 80 SELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDD-------------E 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1281 YARNKQSGVMIKGRVVINVWRLMNGEMKLDMYTLHNVAFNILGKRIPYYSYQTLSEL--SNSCQHRKdsfeyrIILQYYY 1358
Cdd:cd05778 147 WGYTHTSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWykSGSASERW------RVLEYYL 220
|
250
....*....|.
gi 2124384683 1359 KKASITLELLN 1369
Cdd:cd05778 221 KRVRLNLEILD 231
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
1199-1864 |
4.77e-36 |
|
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA polymerases.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273159 [Multi-domain] Cd Length: 1172 Bit Score: 150.21 E-value: 4.77e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1199 FKTEQDLLNGFIDFICKEDPDILLGYEMQTEGLGYLIERgftvlgknicydlsraifyqnenkaNNTNKDKRQDKIMKKA 1278
Cdd:TIGR00592 581 LATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANR-------------------------INDLKIPTWSKIGRLR 635
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1279 QEYARNKQSGVMIKGRVVINVWRLMNGEMKLDMYTLHNVAFNILGK-RIPYYSYQTLSELSNSCQHRKdsfeyriILQYY 1357
Cdd:TIGR00592 636 RSPKFGRRFGERTCGRMICDVEISAKELIRCKSYDLSELVQQILKTeRKVIPIDNINNMYSESSSLTY-------LLEHT 708
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1358 YKKASITLELLNYLDFLNRTGELAKVFGIEFFSVLNRGSQYRVESMMLRLARLYNYVA--LSPTRKQ------------- 1422
Cdd:TIGR00592 709 WKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVpdKQIFRKQqklgdedeeidgy 788
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1423 VMEQAAIECLPLVMEPQSKLYTNPVIVLDFQSLYPSIIIAYNLCYSTclgkmayVDQKKSklgtldgyepnselrkllkh 1502
Cdd:TIGR00592 789 KKGKKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTT-------VQQKVD-------------------- 841
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1503 reegksiEEDILITPNqclfvkPNVRQGILPRMCTEILNTRVMVKQAMKETSKEDTETQriLNARQLGLKLIANVTYGYT 1582
Cdd:TIGR00592 842 -------EDELPELPD------SELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQ--YDIRQKALKLTANSMYGCL 906
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1583 SANFSgRMPLSDLADAIVQLARQTLENAIETVNQRFkgkCRVAYGDTDSLFVECIDSTKEEAFKLGKEIVKIVtNSNPKP 1662
Cdd:TIGR00592 907 GYSKS-RFYAKPLAALVTAKGREILEHTRQLVEEMN---LEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEV-NKLYKL 981
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1663 ITLQMERVFHPSFLVSKKRYVGLAFENPSQTKGT--LFCKGIEAVRRDNCLMVRSLMEKSLE-ILFE-TLDFSL--VKSY 1736
Cdd:TIGR00592 982 LELDIDGVFKRLLLLKKKKYAAIKVEGDSDGNYTtkQEVKGLDIVRRDWSPLAKETGKKVLDtILSDkDVEEAVeeVQEV 1061
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1737 LSRQFYRIISEKCSLQDFIFWKKVKLGY--YKSEKNLpPSARVAIREMQRDPRAEPRfNERVPYIVVfsplhPSKAKLSD 1814
Cdd:TIGR00592 1062 LEKIGKNVLNGEVPLEKFVINKQLTRDPkdYPDGASL-PHVHVALRINARGGRKVKA-GDVVSYVIC-----KDGGNLSA 1134
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1815 MvihPKYYIADRMGTSTSNqvMIHNTrqkyrlhyNYYITRQLLPSLDRLF 1864
Cdd:TIGR00592 1135 R---QRAYALEELQRKHNN--LIYDT--------QYYLEHQIHPVVLRIL 1171
|
|
| BAH |
smart00439 |
Bromo adjacent homology domain; |
558-688 |
2.38e-23 |
|
Bromo adjacent homology domain;
Pssm-ID: 214664 [Multi-domain] Cd Length: 121 Bit Score: 96.98 E-value: 2.38e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 558 DVSVGEFVYLRAP-KNCKPYIACVI-----DKNNQSKIVTVRWFYRPEETKGGVRDWNGENEVFLISHCDTNLIDTVIGK 631
Cdd:smart00439 1 TISVGDFVLVEPDdADEPYYIGRIEeifetKKNSESKMVRVRWFYRPEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGK 80
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 2124384683 632 CNVLFVDKYFkdlptnivvdnffieeKLPEEFVEQSKDTYFCRFEYSVKNNSFRKIS 688
Cdd:smart00439 81 CNVLYKSDYP----------------GLRPEGSIGEPDVFFCESAYDPEKGSFKKLP 121
|
|
| BAH |
pfam01426 |
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been ... |
557-688 |
1.77e-20 |
|
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction.
Pssm-ID: 460207 Cd Length: 120 Bit Score: 88.90 E-value: 1.77e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 557 EDVSVGEFVYLRAPKNCKPYIACVI-----DKNNQSKIVTVRWFYRPEETKGGVRDWNGENEVFLISHCDTNLIDTVIGK 631
Cdd:pfam01426 1 ETYSVGDFVLVEPDDADEPYYVARIeelfeDTKNGKKMVRVQWFYRPEETVHRAGKAFNKDELFLSDEEDDVPLSAIIGK 80
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 2124384683 632 CNVLFVDKYFKDLPTNIVVDnffieeklpeefveqskDTYFCRFEYSVKNNSFRKIS 688
Cdd:pfam01426 81 CSVLHKSDLESLDPYKIKEP-----------------DDFFCELLYDPKTKSFKKLP 120
|
|
| BAH_BAHCC1 |
cd04714 |
BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. ... |
557-677 |
4.87e-17 |
|
BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Pssm-ID: 240065 Cd Length: 121 Bit Score: 78.98 E-value: 4.87e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 557 EDVSVGEFVYLRAPKNCK-PYIACV----IDKNNQSKiVTVRWFYRPEETKGGVRDWNGENEVFLISHCDTNLIDTVIGK 631
Cdd:cd04714 2 EIIRVGDCVLFKSPGRPSlPYVARIeslwEDPEGNMV-VRVKWYYRPEETKGGRKPNHGEKELFASDHQDENSVQTIEHK 80
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 2124384683 632 CNVLFVDKYFKDLPTNIVVDNffieeklpeefveqSKDTYFCRFEY 677
Cdd:cd04714 81 CYVLTFAEYERLARVKKKPQD--------------GVDFYYCAGTY 112
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
1-280 |
5.56e-09 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 61.58 E-value: 5.56e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1 MLLQVLSLEYSLCLPQALfDDRKCSFFGGRSIDlVPIMHVYGtIQETKQKACLHIHQLYPYFMLSFPYELfleegEENDH 80
Cdd:PTZ00166 42 LVFFQLDADYTEKDDKSQ-GNPHNTVSGVRHVE-VPIIRLYG-VTKEGHSVLVNVHNFFPYFYIEAPPNF-----LPEDS 113
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 81 SNLKRTDNLLLKLnmrkvsdfihvlgntieqtfhrslygtslqqyqnmqqqnskqdQSVYKHQRQFIHDIVVVTGTPFYG 160
Cdd:PTZ00166 114 QKLKRELNAQLSE-------------------------------------------QSQFKKYQNTVLDIEIVKKESLMY 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 161 YWFNPQL-FLKVYVYNPSHVGKMAAMF--GNSSVMGH-----KFSVYEAHIPFSLQFMMDYNVYGMGDLSVEKvffrlpf 232
Cdd:PTZ00166 151 YKGNGEKdFLKITVQLPKMVPRLRSLIesGVVVCGGGwdgirLFQTYESNVPFVLRFLIDNNITGGSWLTLPK------- 223
|
250 260 270 280
....*....|....*....|....*....|....*....|....*...
gi 2124384683 233 haadndneNTQKISSQNatnygtilpenvKRLSKCEIEMDIFSRDVLN 280
Cdd:PTZ00166 224 --------GKYKIRPPK------------KKTSTCQIEVDCSYEDLIP 251
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
1197-1317 |
7.35e-05 |
|
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold.
Pssm-ID: 397292 Cd Length: 333 Bit Score: 47.03 E-value: 7.35e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1197 YEFKTEQDLLNGFIDFICKEDPDILLGYEMQteglgylierGFTvlgknICYDLSRAifyqNENKANNTNKDKRQDKIM- 1275
Cdd:pfam03104 229 FEFPSEKELLRRFFEFIRQYDPDIITGYNGD----------NFD-----WPYILNRA----KELYIVKLSSIGRLNRGGr 289
|
90 100 110 120
....*....|....*....|....*....|....*....|....
gi 2124384683 1276 KKAQE--YARNKQSGVMIKGRVVINVWRLMNGEMKLDMYTLHNV 1317
Cdd:pfam03104 290 SKVREigFGTRSYEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
147-224 |
8.95e-05 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 47.51 E-value: 8.95e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2124384683 147 IHDIVVVTGTPFYGywfNPQLFLKVYVYNPSHVGKMAamfgnSSVMGHKFSVYEAHIPFSLQFMMDYNVYGMGDLSVE 224
Cdd:COG0417 64 ITEVEPVKLKSFFG---EPVPVLKIYTRDPRDVRELR-----DRLKEGGIDVYEADIRFHDRYLIDRFLTPGVWYEGE 133
|
|
| zf-C4pol |
pfam14260 |
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ... |
1912-2006 |
1.36e-03 |
|
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1. Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1.
Pssm-ID: 464119 Cd Length: 68 Bit Score: 38.89 E-value: 1.36e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1912 CVSCGAiidcktlnkvegaatdlsSQEPLCPKCKEYPLVL----LLRLRSVERNKNMLSELCRHCNHELDvtngllpysk 1987
Cdd:pfam14260 1 CLGCGA------------------PEEPLCKNCRSDPQASylelLSRLRELERRFNRLWTICQRCQGSLH---------- 52
|
90
....*....|....*....
gi 2124384683 1988 vpsIEEKCMSLECPILFSK 2006
Cdd:pfam14260 53 ---EEVLCDSRDCPVFYMR 68
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| POLBc_zeta |
cd05534 |
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member ... |
1395-1872 |
0e+00 |
|
DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen.
Pssm-ID: 99917 Cd Length: 451 Bit Score: 676.24 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1395 GSQYRVESMMLRLARLYNYVALSPTRKQVMEQAAIECLPLVMEPQSKLYTNPVIVLDFQSLYPSIIIAYNLCYSTCLGKM 1474
Cdd:cd05534 1 GSQFRVESMLLRLAKPENYILPSPSRQQVAQQRALECLPLVMEPESGFYSDPVIVLDFQSLYPSIMIAYNYCYSTCLGRV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1475 AYVDQK-KSKLGTLDGYEPNSELRKLLKHreegksieEDILITPNQCLFVKPNVRQGILPRMCTEILNTRVMVKQAMKET 1553
Cdd:cd05534 81 EELNGGgKFGFLGVKLYLPPPPLDLLLLK--------DDVTISPNGVMFVKKSVRKGILPKMLEEILDTRIMVKKAMKKY 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1554 sKEDTETQRILNARQLGLKLIANVTYGYTSANFSGRMPLSDLADAIVQLARQTLENAIETVNQRFKGKCRVAYGDTDSLF 1633
Cdd:cd05534 153 -KDDKKLQRILDARQLALKLLANVTYGYTAASFSGRMPCVEIADSIVQTGRETLERAIELIESTPKWGAKVVYGDTDSLF 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1634 VECIDSTKEEAFKLGKEIVKIVTNSNPKPITLQMERVFHPSFLVSKKRYVGLAFENPSQTKGTLFCKGIEAVRRDNCLMV 1713
Cdd:cd05534 232 VLLPGRTKEEAFKIGKEIAEAVTAANPSPIKLKFEKVYHPCVLVTKKRYVGYKYESPDQTEPTFDAKGIETVRRDGCPAV 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1714 RSLMEKSLEILFETLDFSLVKSYLSRQFYRIISEKCSLQDFIFWKKVKLGYYKSEKNLPPSARVAIREMQRDPRAEPRFN 1793
Cdd:cd05534 312 QKILEKSLRILFETKDLSTVKSYLQRQWSKLLQGRVSIQDFIFAKEVRLGTYKEGATLPAGAIVALRRMEKDPRAEPQYG 391
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2124384683 1794 ERVPYIVVFSplhPSKAKLSDMVIHPKYYIADRmgtstsnqvmihntrqKYRLHYNYYITRQLLPSLDRLFSLCFVNCN 1872
Cdd:cd05534 392 ERVPYVVVRG---EPGSRLIDLVVSPEEFLADP----------------SLRLDAEYYITKQIIPALDRLFNLVGVDVQ 451
|
|
| DNA_pol_B |
pfam00136 |
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one ... |
1390-1864 |
1.10e-100 |
|
DNA polymerase family B; This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities.
Pssm-ID: 395085 Cd Length: 439 Bit Score: 331.50 E-value: 1.10e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1390 SVLNRGSQYRVESMMLRLARLYNYVALSPTRKQVME---QAAieclpLVMEPQSKLYTNPVIVLDFQSLYPSIIIAYNLC 1466
Cdd:pfam00136 5 RVLEGGQQIRVESCLLRLALEEGFILPDRPSAKGDEdgyQGA-----TVIEPKKGFYDKPVLVLDFNSLYPSIIQAHNLC 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1467 YSTCLGkmayvdqkksklgtldgyePNSELRKLlkhreEGKSIEEDILITPNQCLFVKPNVRQGILPRMCTEILNTRVMV 1546
Cdd:pfam00136 80 YTTLVR-------------------SVDEANNL-----PPEDNLITVECTPRGVYFVKDHVREGLLPKLLKDLLAKRKAI 135
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1547 KQAMKETSkeDTETQRILNARQLGLKLIANVTYGYTSANfSGRMPLSDLADAIVQLARQTLENAIETVNQRFKGKCRVAY 1626
Cdd:pfam00136 136 KKLLKEET--DPFERAILDKQQLALKITANSVYGFTGFA-NGRLPCLPIAASVTAIGREMLENTKDLVEGMYTYNFRVIY 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1627 GDTDSLFVECIDSTKEEAFKLGKEIVKIVTNSN-PKPITLQMERVFHPSFLVSKKRYVGLAFENPSQTkGTLFCKGIEAV 1705
Cdd:pfam00136 213 GDTDSVFIEFGGKDVEEAMKIGDELAEHVNQDLfKSPIKLEFEKVYKPLLLISKKKYAGLKYTAPSNF-NKLDMKGVDLV 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1706 RRDNCLMVRSLMEKSLEILFETLD----FSLVKSYLSRQFYRIISEKCSLQDFIFWKKVKLGYYKSEKNLPPSARVAIRE 1781
Cdd:pfam00136 292 RRDNCPLVKEVIKKVLDLLLSDRGlpvgLEFVISILNDARSDLRNNKVPLEKFVISKELSKPPDNYKSKNLPHVEVALRM 371
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1782 MQRDPRAePRFNERVPYIVVFSPLHPSKAKLSDMVIHPKYYIADrmgtstsnqvmihntrqKYRLHYNYYITRQLLPSLD 1861
Cdd:pfam00136 372 NKRNGEA-PEVGDRIPYVIVKAAKGLKNLLIYERAEDPEYVLEN-----------------NLPIDYEYYFSNQLIPPVA 433
|
...
gi 2124384683 1862 RLF 1864
Cdd:pfam00136 434 RLL 436
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
1130-2007 |
6.93e-94 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 330.45 E-value: 6.93e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1130 IEChVTTRADFLPNPIYDPVQAIiicsqncadvanstESILLLNRDLEDN--DTIQHKLTCIPLNFDRFYEFKTEQDLLN 1207
Cdd:PTZ00166 271 IEC-IKLKGLGFPEAENDPVIQI--------------SSVVTNQGDEEEPltKFIFTLKECASIAGANVLSFETEKELLL 335
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1208 GFIDFICKEDPDILLGYEMQTEGLGYLIERGfTVLGKNICYDLSRAIfyqnenKANNTNKDKR-QDKIMKKAQeyarNKQ 1286
Cdd:PTZ00166 336 AWAEFVIAVDPDFLTGYNIINFDLPYLLNRA-KALKLNDFKYLGRIK------STRSVIKDSKfSSKQMGTRE----SKE 404
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1287 sgVMIKGRVVINVWRLMNGEMKLDMYTLHNVAFNILGKRIPYYSYQTLSELSNSCQHRKdsfeyRIILQYYYKKASITLE 1366
Cdd:PTZ00166 405 --INIEGRIQFDVMDLIRRDYKLKSYSLNYVSFEFLKEQKEDVHYSIISDLQNGSPETR-----RRIAVYCLKDAILPLR 477
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1367 LLNYLDFLNRTGELAKVFGIEFFSVLNRGSQYRVESMMLRLARLYNYVALSPTRKQVMEQAAIEClPLVMEPQSKLYTNP 1446
Cdd:PTZ00166 478 LLDKLLLIYNYVEMARVTGTPIGWLLTRGQQIKVTSQLLRKCKKLNYVIPTVKYSGGGSEEKYEG-ATVLEPKKGFYDEP 556
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1447 VIVLDFQSLYPSIIIAYNLCYSTCLgkmayvdqkksklgtldgyePNSELRKLlkhreegksiEEDILI-TPNQCLFVKP 1525
Cdd:PTZ00166 557 IATLDFASLYPSIMIAHNLCYSTLV--------------------PPNDANNY----------PEDTYVtTPTGDKFVKK 606
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1526 NVRQGILPRMCTEILNTRVMVKQAMKETSkeDTETQRILNARQLGLKLIANVTYGYTSANFSGRMPLSDLADAIVQLARQ 1605
Cdd:PTZ00166 607 EVRKGILPLIVEELIAARKKAKKEMKDEK--DPLLKKVLNGRQLALKISANSVYGYTGAQVGGQLPCLEVSTSITSFGRQ 684
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1606 TLENAIETVNQRF------KGKCRVAYGDTDSLFVECIDSTKEEAFKLGKEIVKIVTNSNPKPITLQMERVFHPSFLVSK 1679
Cdd:PTZ00166 685 MIDKTKELVEKHYtkangyKHDATVIYGDTDSVMVKFGTDDIQEAMDLGKEAAERISKKFLKPIKLEFEKVYCPYLLMNK 764
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1680 KRYVGLAFENPsQTKGTLFCKGIEAVRRDNCLMVRSLMEKSLEILFETLDFSLVKSYLSRQFYRIISEKCSLQDFIFWKk 1759
Cdd:PTZ00166 765 KRYAGLLYTNP-EKYDKIDCKGIETVRRDNCLLVQQMVETVLNKILIEKDVESAIEFTKGKISDLLQNRIDISLLVITK- 842
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1760 vKLGYYKSEKNLPPSArVAIREMQRDPRAEPRFNERVPYIVVfsplHPSK-AKLSDMVIHPKYyiadrmgtstsnqVMIH 1838
Cdd:PTZ00166 843 -SLGKDDYEGRLAHVE-LAKKLRQRDPGSAPNVGDRVSYVIV----KGAKgAPQYERAEDPLY-------------VLEN 903
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1839 NTrqkyRLHYNYYItRQLLPSLDRLFSLCFVNCNVWYMNLPKRDVYLMAdwrkqlfrKSKNFIERYFKpISLPCVSCGAI 1918
Cdd:PTZ00166 904 NI----PIDTQYYL-DQIKNPLLRIFEGVMDNPDSLFSGEHTRHITISS--------SSKGGLSKFVK-KQLQCLGCKSV 969
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1919 IdcktlnkvegaatdlsSQEPLCPKCKEYPLVLLLRLRSVERNK--NMLSEL---CRHCNHEL--DVTngllpyskvpsi 1991
Cdd:PTZ00166 970 I----------------KEGALCDNCNQNKEPSIYGKKLAKRRHkeAEYSQLwtqCQRCQGSLhqEVI------------ 1021
|
890
....*....|....*.
gi 2124384683 1992 eekCMSLECPILFSKV 2007
Cdd:PTZ00166 1022 ---CTNRDCPIFYRRK 1034
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
1124-1865 |
2.26e-78 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 277.86 E-value: 2.26e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1124 NINVMSIECHVTTRADFlPNPIYD-PVqaIIICSQNCADVanstESILLLNRDlEDNDTIQHkltciplnfdrfyeFKTE 1202
Cdd:COG0417 159 KLKVLSFDIEVSTPRGF-PDPERDgPI--ISIGLAGSDGE----KKVLMLGRE-GVDFEVEY--------------FDDE 216
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1203 QDLLNGFIDFICKEDPDILLGYEMQTEGLGYLIERgFTVLGKNIcyDLSRaifyqnenkanntnkDKRQDKIMKkaqeya 1282
Cdd:COG0417 217 KALLEAFFEIIREYDPDIIIGWNVDNFDLPYLQKR-AERLGIPL--DLGR---------------DGSEPSWRE------ 272
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1283 RNKQSGVMIKGRVVINVWR-LMNGEMKLDMYTLHNVAFNILGKRIPYYSYQTLSELSNscqHRKDSFeyriiLQYYYKKA 1361
Cdd:COG0417 273 HGGQGFASIPGRVVIDLYDaLKSATYKFKSYSLDAVAEELLGEGKLIVDGGEIERLWD---DDKPAL-----AEYNLRDA 344
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1362 SITLELLNYLDFLNRTGELAKVFGIEFFSVLNRGSQYRVESMMLRLARLYNYVAlsPTRKQVMEQA---AIeclplVMEP 1438
Cdd:COG0417 345 ELTLRIFEKTLLLPFLIELSRITGLPLDDVGRAGSSAAFENLLLPEAHRRGYLA--PNKGEIKGEAypgGY-----VLDP 417
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1439 QSKLYTNpVIVLDFQSLYPSIIIAYNLCYSTclgkmayvdqkksklgtLDgyepnselrkllkhrEEGKSIEEDILITPN 1518
Cdd:COG0417 418 KPGLYEN-VLVLDFKSLYPSIIRTFNISPET-----------------LV---------------EGGEEPCGDEDVAPG 464
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1519 Q-CLFVKPnvRQGILPRMCTEILNTRVMVKQAMKETSKEDTEtQRILNARQLGLKLIANVTYGYT-SANFsgrmPLSD-- 1594
Cdd:COG0417 465 FgHRFCRE--PKGILPSILEELWDERDEAKKKMKKAKPDSEE-YRLYDALQQALKILMNSFYGVLgSEGC----RFYDpe 537
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1595 LADAIVQLARQTLENAIETVNQRfkGKcRVAYGDTDSLFVECIDSTKEEAFKLGKEIVKIVTNSNPKPITLQMERVFHPS 1674
Cdd:COG0417 538 LAESITARGREIIKQTIEKAEEL--GY-KVIYGDTDSLFVWLPKASLEEAIEIGKELAEEINAWWPSGLELEFEKHYRRF 614
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1675 FLV-SKKRYVGLaFENpsqtkGTLFCKGIEAVRRDNCLMVRSLMEKSLEILFETLDFSLVKSYLSRQFYRIISEKCSLQD 1753
Cdd:COG0417 615 FFPgSKKRYAGL-TED-----GKIDIKGLEAVRSDWTELAKEFQQEVYERILKEEDVEKAVEYVRDVIEKLRAGEVDLDD 688
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1754 FIFWKKV--KLGYYksEKNLPPSARVAIREMQRDPRAEPRfnERVPYIVVfsplhpsKAKLSdmvihPKYYIADRMGTSt 1831
Cdd:COG0417 689 LVIRKRLrkPLSEY--EKNVPPHVRAARKLDERGRPYQRG--DKISYVIT-------KGGGR-----VEPVELAKERES- 751
|
730 740 750
....*....|....*....|....*....|....
gi 2124384683 1832 snqvmihntrqkyRLHYNYYITRQLLPSLDRLFS 1865
Cdd:COG0417 752 -------------EIDYDYYIEKQLKPTADRILE 772
|
|
| POLBc_delta |
cd05533 |
DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
1435-1864 |
7.89e-76 |
|
DNA polymerase type-B delta 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. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand.
Pssm-ID: 99916 Cd Length: 393 Bit Score: 257.96 E-value: 7.89e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1435 VMEPQSKLYTNPVIVLDFQSLYPSIIIAYNLCYSTclgkmayvdqkksklgtldgyepnselrkLLKHREEGKSIEEDIL 1514
Cdd:cd05533 8 VIEPIKGYYDVPIATLDFASLYPSIMMAHNLCYTT-----------------------------LLNKNTAKKLPPEDYI 58
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1515 ITPNQCLFVKPNVRQGILPRMCTEILNTRVMVKQAMKETskEDTETQRILNARQLGLKLIANVTYGYTSANfSGRMPLSD 1594
Cdd:cd05533 59 KTPNGDYFVKSSVRKGLLPEILEELLAARKRAKKDLKEE--TDPFKKAVLDGRQLALKISANSVYGFTGAT-VGKLPCLE 135
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1595 LADAIVQLARQTLENAIETVNQRFKGK------CRVAYGDTDSLFVECIDSTKEEAFKLGKEIVKIVTNSNPKPITLQME 1668
Cdd:cd05533 136 ISSSVTSFGRQMIEKTKKLVEEKYTKAngyshdAKVIYGDTDSVMVKFGVSDVEEAMKLGKEAAEYVSKKFIKPIKLEFE 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1669 RVFHPSFLVSKKRYVGLAFENPsQTKGTLFCKGIEAVRRDNCLMVRSLMEKSLEILFETLDFSLVKSYLSRQFYRIISEK 1748
Cdd:cd05533 216 KVYFPYLLINKKRYAGLLWTNP-DKHDKMDTKGIETVRRDNCLLVQNVVETCLNKILIERDVEGAIEFVKGVISDLLQNK 294
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1749 CSLQDFIFWKkvklGYYKSEKNLP-PSARV--AIREMQRDPRAEPRFNERVPYIVVFSplhPSKAKLSDMVIHPKYyiad 1825
Cdd:cd05533 295 IDISLLVITK----ALTKTADDYAgKQAHVelAERMRKRDPGSAPNVGDRVPYVIIKG---AKGAKAYEKAEDPIY---- 363
|
410 420 430
....*....|....*....|....*....|....*....
gi 2124384683 1826 rmgtstsnqVMIHNtrqkYRLHYNYYITRQLLPSLDRLF 1864
Cdd:cd05533 364 ---------VLENN----IPIDTQYYLENQLSKPLLRIF 389
|
|
| POLBc |
smart00486 |
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), ... |
1124-1636 |
5.99e-72 |
|
DNA polymerase type-B family; DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases
Pssm-ID: 214691 [Multi-domain] Cd Length: 474 Bit Score: 249.76 E-value: 5.99e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1124 NINVMSIECHVTTRADFLPNPiYDPVQAIIicsQNCADVANSTESILLLNRDLEDNDTIQHKLTCIplnfdrfYEFKTEQ 1203
Cdd:smart00486 2 PLKILSFDIETYTDGGNFPDA-EIFDDEII---QISLVINDGDKKGANRRILFTLGTCKEIDGIEV-------YEFNNEK 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1204 DLLNGFIDFICKEDPDILLGYEMQTEGLGYLIERgFTVLGKNICYDLSRAIFYQNENKANNTNKDKRQDKIMKKaqeyar 1283
Cdd:smart00486 71 ELLLAFFEFIKKYDPDIIYGHNISNFDLPYIISR-LEKLKIDPLSKIGRLKIGLRIPNKKPLFGSKSFGLSDIK------ 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1284 nkqsgVMIKGRVVINVWRLMNGEMKLDMYTLHNVAFNILGKRIPYYSYQTLSELSNScqhrkDSFEYRIILQYYYKKASI 1363
Cdd:smart00486 144 -----VYIKGRLVIDLYRLYKNKLKLPSYKLDTVAEYLLGKEKDDLPYKDIPELYNG-----NYEERDELLRYCIQDAVL 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1364 TLELLNYLDFLNRTGELAKVFGIEFFSVLNRGSQYRVESMMLRLARLYNYVAlsPTRKQVMEQAAIECL--------PLV 1435
Cdd:smart00486 214 TLKLFNKLNVIPLIIELARIAGIPLRRTLYYGSQIRVESLLLREAKKNNYIL--PSKELYDFKGSEPDLkkkvkyegGKV 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1436 MEPQSKLYTNPVIVLDFQSLYPSIIIAYNLCYSTCLGKmayvdqkksklgtldgyepNSELRKLLKHREEGKSIEEDIli 1515
Cdd:smart00486 292 LEPKKGFYDNPVLVLDFNSLYPSIIIAHNLCYSTLVGV-------------------GEVVIKGDLIIPEDLLTIKYE-- 350
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1516 TPNQCLFVKPNVRQGILPRMCTEILNTRVMVKQAMKETSKEDTETQRILNARQLGLKLIANVTYGYTSANFSgRMPLSDL 1595
Cdd:smart00486 351 KGNKYRFVKKNIRKGILPKLLKKLLDKRKEIKKLMKKEKDESEELKKLLDSRQLALKLTANSVYGYLGFTNS-RLPCKPL 429
|
490 500 510 520
....*....|....*....|....*....|....*....|...
gi 2124384683 1596 ADAIVQLARQTLENAIETVNQRFKGKC--RVAYGDTDSLFVEC 1636
Cdd:smart00486 430 AASVTALGREILEKTKELIEENGYPKPgfKVIYGDTDSIFVTK 472
|
|
| POLBc |
cd00145 |
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ... |
1431-1746 |
8.92e-61 |
|
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is made up of distinct domains and sub-domains. The polymerase domain of DNA polymerase type B (Pol domain) is responsible for the template-directed polymerization of dNTPs onto the growing primer strand of duplex DNA that is usually magnesium dependent. In general, the architecture of the Pol domain has been likened to a right hand with fingers, thumb, and palm sub-domains with a deep groove to accommodate the nucleic acid substrate. There are a few conserved motifs in the Pol domain of family B DNA polymerases. The conserved aspartic acid residues in the DTDS motifs of the palm sub-domain is crucial for binding to divalent metal ion and is suggested to be important for polymerase catalysis.
Pssm-ID: 99912 [Multi-domain] Cd Length: 323 Bit Score: 212.23 E-value: 8.92e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1431 CLPLVMEPqSKLYTNPVIVLDFQSLYPSIIIAYNLCYSTCLGKMAYVDqkksklgtLDGYEPNselrkllkhreegksie 1510
Cdd:cd00145 4 EGGYVFDP-IPGLYENVIVLDFKSLYPSIIITYNLSPTTLVGNGEIAA--------PEDYIGV----------------- 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1511 edilitpnqcLFVKPNVRQGILPRMCTEILNTRVMVKQAMKEtSKEDTETQRILNARQLGLKLIANVTYGYTSANFSgRM 1590
Cdd:cd00145 58 ----------GFRSPKDRKGLLPRILEELLNFRDEAKKRMKA-AKLAPEERVLYDNRQQALKVLANSFYGYLGAKFF-RF 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1591 PLSDLADAIVQLARQTLENAIETVNQRfkgKCRVAYGDTDSLFVEC-IDSTKEEAFKLGKEIVKIVTnsNPKPITLQMER 1669
Cdd:cd00145 126 YDPEVAASITSFGREIIQDTIALVEEH---GARVIYGDTDSIFVSLpKMGTKEDAIKEGREILQELA--DEHLLELEFEK 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1670 VFHPSFLVSKKRYVGLAFEnPSQTKGTLFCKGIEAVRRDNCLMVRSLMEKSLEILFE---TLDFslVKSYLSR--QFYRI 1744
Cdd:cd00145 201 VYLPFFLGKKKRYAGLDIW-KGQDEGKIDIKGLETRRRDSPPLVKKFQKEVLELILEeerKVEA--VKEYIDEldKVKYV 277
|
..
gi 2124384683 1745 IS 1746
Cdd:cd00145 278 VT 279
|
|
| DNA_polB_zeta_exo |
cd05778 |
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA ... |
1123-1369 |
4.22e-53 |
|
inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis.
Pssm-ID: 99821 [Multi-domain] Cd Length: 231 Bit Score: 186.29 E-value: 4.22e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1123 QNINVMSIECHVTTRADFLPNPIYDPVQAIIICSQN--CADVANSTESILLLNRDLEDNDTIQHKLTCIPlnFDRFYEFK 1200
Cdd:cd05778 2 QHLTILSLEVHVNTRGDLLPDPEFDPISAIFYCIDDdvSPFILDANKVGVIIVDELKSNASNGRIRSGLS--GIPVEVVE 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1201 TEQDLLNGFIDFICKEDPDILLGYEMQTEGLGYLIERGFTVLGKNICYDLSRAIFYQNENKANNTNkdkrqdkimkkaqE 1280
Cdd:cd05778 80 SELELFEELIDLVRRFDPDILSGYEIQRSSWGYLIERAAALGIDDLLDEISRVPSDSNGKFGDRDD-------------E 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1281 YARNKQSGVMIKGRVVINVWRLMNGEMKLDMYTLHNVAFNILGKRIPYYSYQTLSEL--SNSCQHRKdsfeyrIILQYYY 1358
Cdd:cd05778 147 WGYTHTSGIKIVGRHILNVWRLMRSELALTNYTLENVVYHVLHQRIPLYSNKTLTEWykSGSASERW------RVLEYYL 220
|
250
....*....|.
gi 2124384683 1359 KKASITLELLN 1369
Cdd:cd05778 221 KRVRLNLEILD 231
|
|
| POLBc_alpha |
cd05532 |
DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases ... |
1434-1864 |
1.82e-48 |
|
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.
Pssm-ID: 99915 Cd Length: 400 Bit Score: 178.93 E-value: 1.82e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1434 LVMEPQSKLYTNPVIVLDFQSLYPSIIIAYNLCYSTClgkmayvdqkksklgtldgyepnselrkllkHREEGKSIEEDI 1513
Cdd:cd05532 12 LVLEPKKGLYDKFILLLDFNSLYPSIIQEYNICFTTV-------------------------------DRADPDDEDDEE 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1514 LITPNqclfvkPNVRQGILPRMCTEILNTRVMVKQAMKetsKEDTETQR-ILNARQLGLKLIANVTYGYTSANFSgRMPL 1592
Cdd:cd05532 61 PPLPP------SDQEKGILPRIIRKLVERRRQVKKLMK---SEKDPDKKaQLDIRQLALKLTANSMYGCLGFSYS-RFYA 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1593 SDLADAIVQLARQTLENAIETVNQRfkgKCRVAYGDTDSLFVECIDSTKEEAFKLGKEIVKIVtNSNPKPITLQMERVFH 1672
Cdd:cd05532 131 KPLAALITSKGREILQKTKDLVEKM---NLEVIYGDTDSIMINTGTTDYEEAKKLGNKIKKEV-NKSYKKLEIDIDGVFK 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1673 PSFLVSKKRYVGLAFENPSQTKGTLFCKGIEAVRRDNCLMVRSLMEKSLEILFETLD----FSLVKSYLSRQFYRIISEK 1748
Cdd:cd05532 207 RLLLLKKKKYAALKVVDDDKGKLKKEVKGLDIVRRDWCPLSKEIGNYVLDQILSDKSrediVENIHEYLRKINEDLRNGK 286
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1749 CSLQDFIFWKKV--KLGYYKSEKNLpPSARVAIREMQRDPRAEPrfNERVPYIVVFSPLHPSkakLSDMVIHPkyyiadr 1826
Cdd:cd05532 287 IPLEKFIITKQLtkNPEEYPDKKSL-PHVQVALRMNKRGRKVKA--GDTIPYIICKDGSSKS---LADRAYHP------- 353
|
410 420 430
....*....|....*....|....*....|....*...
gi 2124384683 1827 mgtstsNQVMIHNTRQkyrLHYNYYITRQLLPSLDRLF 1864
Cdd:cd05532 354 ------DEVKKNENLK---IDIEYYLSQQILPPISRLC 382
|
|
| PRK05762 |
PRK05762 |
DNA polymerase II; Reviewed |
1199-1862 |
1.95e-47 |
|
DNA polymerase II; Reviewed
Pssm-ID: 235595 [Multi-domain] Cd Length: 786 Bit Score: 184.29 E-value: 1.95e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1199 FKTEQDLLNGFIDFICKEDPDILLGYEMQTEGLGYLIERGfTVLGknICYDLSRaifyqnenkaNNTNKDKRQDKimkka 1278
Cdd:PRK05762 200 VADEKALLEKFNAWFAEHDPDVIIGWNVVQFDLRLLQERA-ERYG--IPLRLGR----------DGSELEWREHP----- 261
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1279 qeyARNKQSGVMIKGRVVINVWR-LMNGEMKLDMYTLHNVAFNIL--GKRIpYYSYQTLSELSNSCQHRKDsfeyrIILQ 1355
Cdd:PRK05762 262 ---FRSGYGFASVPGRLVLDGIDaLKSATWVFDSFSLEYVSQRLLgeGKAI-DDPYDRMDEIDRRFAEDKP-----ALAR 332
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1356 YYYKKASITLELLNYLDFLNRTGELAKVFGIEffsvLNR--GSQYRVESMMLRLARLYNYVAlsPTRKQVMEQAAieclP 1433
Cdd:PRK05762 333 YNLKDCELVTRIFEKTKLLPFLLERATVTGLP----LDRvgGSVAAFEHLYLPRAHRAGYVA--PNLGERPGEAS----P 402
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1434 --LVMEPQSKLYTNpVIVLDFQSLYPSIIIAYNLCYstclgkMAYVdqkksklgtldgyepnselrkllkhrEEGKSIEE 1511
Cdd:PRK05762 403 ggYVMDSKPGLYDS-VLVLDFKSLYPSIIRTFNIDP------DGLV--------------------------EGLAQPPE 449
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1512 DILITPNQCLFVKPnvrQGILPRMCTEILNTRVMVKQAMKEtskedtetqrilnARQLGLKLIANVTYGYTSANFSgRMP 1591
Cdd:PRK05762 450 ESVAGFLGARFSRE---KHFLPEIVERLWEGRDEAKREMNK-------------PLSQAIKIIMNAFYGVLGSSGC-RFF 512
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1592 LSDLADAIVQLARQTLENAIETVNQR-FKgkcrVAYGDTDSLFVEC-IDSTKEEAFKLGKEIVKIVTNSNPKPIT----- 1664
Cdd:PRK05762 513 DPRLASSITMRGHEIMKQTRELIEAQgYQ----VIYGDTDSTFVWLgGAHDEEDAAKIGRALVQEINQWWQEHLQqefgl 588
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1665 -----LQMERVFHPSFLV--------SKKRYVGLAfeNPSQTKGTLFCKGIEAVRRDNCLMVRSLMEKSLEILFETLDfs 1731
Cdd:PRK05762 589 esaleLEFEKHYRRFFMPtirgaeegSKKRYAGLI--QEGDGDGRIVFKGLETVRTDWTPLAKEFQQELYERIFRGEP-- 664
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1732 lVKSYLSRQFYRIISEKCSlQDFIFWKKV--KLGYYksEKNLPPSARVAIR--EMQRDPRAEPRF--NERVPYIVVFSpl 1805
Cdd:PRK05762 665 -YVDYVREVIDKLRAGELD-EKLVYRKRLrrPLDEY--QRNVPPHVRAARLadEMGYKVGRPLQYqnGGKIGYVITVN-- 738
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*..
gi 2124384683 1806 hpSKAKLSDmvihpkyyiadrmgtstsnqvmihntrQKYRLHYNYYITRQLLPSLDR 1862
Cdd:PRK05762 739 --GPEPLEY---------------------------RKSPIDYDYYIEKQLQPVADR 766
|
|
| POLBc_B3 |
cd05536 |
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in ... |
1434-1862 |
2.78e-38 |
|
DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces.
Pssm-ID: 99919 Cd Length: 371 Bit Score: 148.24 E-value: 2.78e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1434 LVMEPQSKLYTNpVIVLDFQSLYPSIIIAYNLCYSTclgkmaYVDQKKSklgtldgyEPNSELRKLLKHReegKSIEedi 1513
Cdd:cd05536 8 IVLEPEKGLHEN-IVVLDFSSLYPSIMIKYNISPDT------LVREGCE--------DCDVEPQVGHKFR---KDPP--- 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1514 litpnqclfvkpnvrqGILPRMCTEILNTRVMVKQAMKETSKEDTEtQRILNARQLGLKLIANVTYGYTSANfSGRMPLS 1593
Cdd:cd05536 67 ----------------GFIPSVLEDLLEERRRIKEKMKKLDPESEE-YKLLDERQRAIKILANSFYGYMGWA-NARWYCK 128
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1594 DLADAIVQLARQTLENAIETVNQR-FKgkcrVAYGDTDSLFVecidsTKEEAFKLGKEIVKIVTNSNPK-PITLQMERVF 1671
Cdd:cd05536 129 ECAEAVTAWGREYIKTTIKIAEEKgFK----VIYGDTDSLFV-----KIDGADAVKKKVKKLLKYINEElPLELEIEKFY 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1672 HPSFLVSKKRYVGLAFEnpsqtkGTLFCKGIEAVRRDNCLMVRSLMEKSLEILFETLDFSLVKSYLSRQFYRIISEKCSL 1751
Cdd:cd05536 200 KRGFFVTKKRYAGLTED------GKIDVVGLEVVRRDWSEIAKETQARVLEAILKEGDVEEAVKIVKEVIEKLKRGEVPP 273
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1752 QDFIFWKKV--KLGYYKSEknlPPSARVAIREMQRDPRAEPrfNERVPYIVVFSPLHPS-KAKLSDMVihpkyyiadrmg 1828
Cdd:cd05536 274 EKLVIWKQLtkDLSEYKAT---GPHVAAAKKLAKRGYKVRP--GTKIGYVIVKGSGKISdRAYPYDMV------------ 336
|
410 420 430
....*....|....*....|....*....|....
gi 2124384683 1829 tstsnqvmihntRQKYRLHYNYYITRQLLPSLDR 1862
Cdd:cd05536 337 ------------DEKHKYDAEYYIDNQVLPAVLR 358
|
|
| pol2 |
TIGR00592 |
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA ... |
1199-1864 |
4.77e-36 |
|
DNA polymerase (pol2); All proteins in this superfamily for which functions are known are DNA polymerases.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273159 [Multi-domain] Cd Length: 1172 Bit Score: 150.21 E-value: 4.77e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1199 FKTEQDLLNGFIDFICKEDPDILLGYEMQTEGLGYLIERgftvlgknicydlsraifyqnenkaNNTNKDKRQDKIMKKA 1278
Cdd:TIGR00592 581 LATERALIKKFMAKVKKIDPDEIVGHDYQQRALKVLANR-------------------------INDLKIPTWSKIGRLR 635
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1279 QEYARNKQSGVMIKGRVVINVWRLMNGEMKLDMYTLHNVAFNILGK-RIPYYSYQTLSELSNSCQHRKdsfeyriILQYY 1357
Cdd:TIGR00592 636 RSPKFGRRFGERTCGRMICDVEISAKELIRCKSYDLSELVQQILKTeRKVIPIDNINNMYSESSSLTY-------LLEHT 708
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1358 YKKASITLELLNYLDFLNRTGELAKVFGIEFFSVLNRGSQYRVESMMLRLARLYNYVA--LSPTRKQ------------- 1422
Cdd:TIGR00592 709 WKDAMFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVpdKQIFRKQqklgdedeeidgy 788
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1423 VMEQAAIECLPLVMEPQSKLYTNPVIVLDFQSLYPSIIIAYNLCYSTclgkmayVDQKKSklgtldgyepnselrkllkh 1502
Cdd:TIGR00592 789 KKGKKAAYAGGLVLEPKVGLYDKYVLLMDFNSLYPSIIQEFNICFTT-------VQQKVD-------------------- 841
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1503 reegksiEEDILITPNqclfvkPNVRQGILPRMCTEILNTRVMVKQAMKETSKEDTETQriLNARQLGLKLIANVTYGYT 1582
Cdd:TIGR00592 842 -------EDELPELPD------SELEMGILPRELRKLVERRKEVKKLMKQDLNPDLRLQ--YDIRQKALKLTANSMYGCL 906
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1583 SANFSgRMPLSDLADAIVQLARQTLENAIETVNQRFkgkCRVAYGDTDSLFVECIDSTKEEAFKLGKEIVKIVtNSNPKP 1662
Cdd:TIGR00592 907 GYSKS-RFYAKPLAALVTAKGREILEHTRQLVEEMN---LEVIYGDTDSIMINTPGTKYEEVFKIGKEFKSEV-NKLYKL 981
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1663 ITLQMERVFHPSFLVSKKRYVGLAFENPSQTKGT--LFCKGIEAVRRDNCLMVRSLMEKSLE-ILFE-TLDFSL--VKSY 1736
Cdd:TIGR00592 982 LELDIDGVFKRLLLLKKKKYAAIKVEGDSDGNYTtkQEVKGLDIVRRDWSPLAKETGKKVLDtILSDkDVEEAVeeVQEV 1061
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1737 LSRQFYRIISEKCSLQDFIFWKKVKLGY--YKSEKNLpPSARVAIREMQRDPRAEPRfNERVPYIVVfsplhPSKAKLSD 1814
Cdd:TIGR00592 1062 LEKIGKNVLNGEVPLEKFVINKQLTRDPkdYPDGASL-PHVHVALRINARGGRKVKA-GDVVSYVIC-----KDGGNLSA 1134
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1815 MvihPKYYIADRMGTSTSNqvMIHNTrqkyrlhyNYYITRQLLPSLDRLF 1864
Cdd:TIGR00592 1135 R---QRAYALEELQRKHNN--LIYDT--------QYYLEHQIHPVVLRIL 1171
|
|
| BAH |
smart00439 |
Bromo adjacent homology domain; |
558-688 |
2.38e-23 |
|
Bromo adjacent homology domain;
Pssm-ID: 214664 [Multi-domain] Cd Length: 121 Bit Score: 96.98 E-value: 2.38e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 558 DVSVGEFVYLRAP-KNCKPYIACVI-----DKNNQSKIVTVRWFYRPEETKGGVRDWNGENEVFLISHCDTNLIDTVIGK 631
Cdd:smart00439 1 TISVGDFVLVEPDdADEPYYIGRIEeifetKKNSESKMVRVRWFYRPEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGK 80
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 2124384683 632 CNVLFVDKYFkdlptnivvdnffieeKLPEEFVEQSKDTYFCRFEYSVKNNSFRKIS 688
Cdd:smart00439 81 CNVLYKSDYP----------------GLRPEGSIGEPDVFFCESAYDPEKGSFKKLP 121
|
|
| BAH |
pfam01426 |
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been ... |
557-688 |
1.77e-20 |
|
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction.
Pssm-ID: 460207 Cd Length: 120 Bit Score: 88.90 E-value: 1.77e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 557 EDVSVGEFVYLRAPKNCKPYIACVI-----DKNNQSKIVTVRWFYRPEETKGGVRDWNGENEVFLISHCDTNLIDTVIGK 631
Cdd:pfam01426 1 ETYSVGDFVLVEPDDADEPYYVARIeelfeDTKNGKKMVRVQWFYRPEETVHRAGKAFNKDELFLSDEEDDVPLSAIIGK 80
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 2124384683 632 CNVLFVDKYFKDLPTNIVVDnffieeklpeefveqskDTYFCRFEYSVKNNSFRKIS 688
Cdd:pfam01426 81 CSVLHKSDLESLDPYKIKEP-----------------DDFFCELLYDPKTKSFKKLP 120
|
|
| PRK05761 |
PRK05761 |
DNA-directed DNA polymerase I; |
1434-1780 |
3.67e-20 |
|
DNA-directed DNA polymerase I;
Pssm-ID: 235594 [Multi-domain] Cd Length: 787 Bit Score: 97.84 E-value: 3.67e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1434 LVMEPQSKLYTNpVIVLDFQSLYPSIIIAYNLCYSTclgkmayVDQkksklgtldgyePNSELRKLLKHREEGKSIEEDi 1513
Cdd:PRK05761 411 LVFQPPPGIFFN-VYVLDFASLYPSIIVKWNLSPET-------VRI------------PECKCHYDDEVPELGHSVCDD- 469
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1514 litpnqclfvkpnvRQGILPRMCTEILNTRVMVKQAMKETSKEDTETQRILNARQLGLKLIANVTYGYTSA-NFS-GRMP 1591
Cdd:PRK05761 470 --------------RPGLTSVLVGLLRDFRVKIYKKKAKDPNLDEERRAWYDVVQRALKVFLNASYGVFGAeNFKlYRIE 535
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1592 LsdlADAIVQLARQTLenaIETVNQRFKGKCRVAYGDTDSLFVEciDSTKEEAFKLGKEIVKIVTnsnpkpITLQMERVF 1671
Cdd:PRK05761 536 V---AESITALGREIL---LSTKKKAEELGLKVLYGDTDSLFVW--GPTKESLEELIKEIEERTG------IDLEVDKTY 601
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1672 HpsFLV---SKKRYVGLAFEnpsqtkGTLFCKGIEAVRRDNCLMVRSLMEKSLEILFET---LDFSLVKSYLSRQFYRII 1745
Cdd:PRK05761 602 D--WVAfsgLKKNYFGVLKD------GKVKIKGIVAKKRNTPEFVKELQREVLEVLKSIrspEDVEKVKDEIEDVLKRYY 673
|
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 2124384683 1746 SE----KCSLQDFIFwkKVKLGYYKSE--KNLPPSARVAIR 1780
Cdd:PRK05761 674 EKlrakDYPLDELAI--RVRLSKPLDEytKNTPQHVKAALQ 712
|
|
| POLBc_Pol_II |
cd05537 |
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
1434-1866 |
3.34e-19 |
|
DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Pssm-ID: 99920 Cd Length: 371 Bit Score: 91.94 E-value: 3.34e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1434 LVMEPQSKLYTNpVIVLDFQSLYPSIIIAYNlcystclgkmayVDqkksKLGTLDGyepnselrklLKHREEGKSIEedi 1513
Cdd:cd05537 7 YVMDSKPGLYKN-VLVLDFKSLYPSIIRTFL------------ID----PLGLIEG----------LKAPDPEDLIP--- 56
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1514 liTPNQCLFVKpnvRQGILPRMCTEILNTRVMVKQAMKEtskedtetqrilnARQLGLKLIANVTYGYTSAN----FSGR 1589
Cdd:cd05537 57 --GFLGARFSR---EKHILPDLIARLWAARDEAKREKNA-------------PLSQAIKIIMNSFYGVLGSTgcrfFDPR 118
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1590 mplsdLADAIV----QLARQTLEnAIETVNQRfkgkcrVAYGDTDSLFVEC-IDSTKEEAFKLGKEIVKIVTNSNPKPIT 1664
Cdd:cd05537 119 -----LASSITlrghEIMKQTRA-WIEQQGYQ------VIYGDTDSTFVWLgEELDAAEAQAIGKELASQINQWWAQKLK 186
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1665 ----------LQMERVFHPSFLV--------SKKRYVGLAFENpsqTKGTLFCKGIEAVRRDNCLMVRSLMEKSLEILFE 1726
Cdd:cd05537 187 eefglesfleIEFETHYSRFFMPtirgsdegSKKRYAGLKSTD---GGDELVFKGLETVRSDWTPLARQFQKELYERVFN 263
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1727 TLDF-SLVKSYLSRQFYRIISEKcslqdFIFWKKV--KLGYYksEKNLPPSARVA-IREMQRDPRAEPRFNERVPYIVvf 1802
Cdd:cd05537 264 DEPYeGFIKETVEELLAGELDEL-----LVYRKRLrrPLSEY--TKNVPPHVQAArLADQINRELGRPRQYQWIEYVI-- 334
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2124384683 1803 splhpskaklsdmvihpkyyiadrmgtsTSNQVMIHNTRQKyRLHYNYYITRQLLPSLDRLFSL 1866
Cdd:cd05537 335 ----------------------------TVNGPEPLEYRTS-PLDYQHYIDKQLKPIADSILPF 369
|
|
| DEDDy_DNA_polB_exo |
cd05160 |
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of ... |
1125-1368 |
2.24e-18 |
|
DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon and zeta), and eukaryotic viral and plasmid-borne enzymes. Nuclear DNA polymerases alpha and zeta lack the four conserved acidic metal-binding residues. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Pssm-ID: 176646 [Multi-domain] Cd Length: 199 Bit Score: 85.48 E-value: 2.24e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1125 INVMSIEChvtTRADFLPNPIYDPVQAIiicsqNCADVANSTESILLLNRDLEDNDTIQHKLTCIplnfdrfYEFKTEQD 1204
Cdd:cd05160 1 VLSFDIET---TPPVGGPEPDRDPIICI-----TYADSFDGVKVVFLLKTSTVGDDIEFIDGIEV-------EYFADEKE 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1205 LLNGFIDFICKEDPDILLGYEMQTEGLGYLIERGFTvLGKNICYDLSRAIfyqnenkanntnkdkrqdKIMKKAQEYARN 1284
Cdd:cd05160 66 LLKRFFDIIREYDPDILTGYNIDDFDLPYLLKRAEA-LGIKLTDGIYRRS------------------GGEKSSGSTERI 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1285 KqsgvmIKGRVVINVWRLMNGEMKLDMYTLHNVAFNILGKRIPYYSYQTLSELSNSCQHRKdsfeyriILQYYYKKASIT 1364
Cdd:cd05160 127 A-----VKGRVVFDLLAAYKRDFKLKSYTLDAVAEELLGEGKEKVDGEIIEDAEWEEDPER-------LIEYNLKDAELT 194
|
....
gi 2124384683 1365 LELL 1368
Cdd:cd05160 195 LQIL 198
|
|
| POLBc_B2 |
cd05531 |
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in ... |
1434-1823 |
4.52e-17 |
|
DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Pssm-ID: 99914 Cd Length: 352 Bit Score: 85.09 E-value: 4.52e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1434 LVMEPQSKLYTNpVIVLDFQSLYPSIIIAYNLCYstclgkmayvdqkksklGTLDGYEPNSELRKLLKHREEGKsieedi 1513
Cdd:cd05531 9 LVFQPEPGLYEN-VAQIDFSSMYPSIIVKYNISP-----------------ETINCRCCECRDHVYLGHRICLK------ 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1514 litpnqclfvkpnvRQGILPrmctEILNTRVMVKQAMKETSKEDTetqrILNARQLGLKLIANVTYGYT---SANFsGRM 1590
Cdd:cd05531 65 --------------RRGFLP----EVLEPLLERRLEYKRLKKEED----PYAGRQKALKWILVTSFGYLgykNAKF-GRI 121
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1591 plsDLADAIVQLARQTLENAIE-TVNQRFkgkcRVAYGDTDSLFVECIDSTKEEAFKLGKEI-VKIVTNSNPKPItlqme 1668
Cdd:cd05531 122 ---EVHEAITAYGRKILLRAKEiAEEMGF----RVLHGIVDSLWIQGRGDIEELAREIEERTgIPLKLEGHYDWI----- 189
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1669 rVFHPSF--LVSKKRYVGLaFENpsqtkGTLFCKGIEAVRRDNCLMVRSLMEKSLEILFETLDFSLVKSYLSR-----QF 1741
Cdd:cd05531 190 -VFLPERdgLGAPNRYFGR-LSD-----GEMKVRGIELRRRDTPPFVKKFQEEALDILASAKTPEELLKLREEaldlfRR 262
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1742 YRIISEKCSLQDFIFWKKVklGYYKSE-KNLPPSARVAIREMQRDPRAeprfNERVPYIVVFSPlHPSKAKLSDMVIHPK 1820
Cdd:cd05531 263 YLQRLREGDLEDLIIEKKI--SKRSSEyKVLASTALKALRAKGVSVVP----GMKIEYIVRDGK-RPVPDLGNDEGYDTK 335
|
...
gi 2124384683 1821 YYI 1823
Cdd:cd05531 336 YYR 338
|
|
| BAH_BAHCC1 |
cd04714 |
BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. ... |
557-677 |
4.87e-17 |
|
BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Pssm-ID: 240065 Cd Length: 121 Bit Score: 78.98 E-value: 4.87e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 557 EDVSVGEFVYLRAPKNCK-PYIACV----IDKNNQSKiVTVRWFYRPEETKGGVRDWNGENEVFLISHCDTNLIDTVIGK 631
Cdd:cd04714 2 EIIRVGDCVLFKSPGRPSlPYVARIeslwEDPEGNMV-VRVKWYYRPEETKGGRKPNHGEKELFASDHQDENSVQTIEHK 80
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 2124384683 632 CNVLFVDKYFKDLPTNIVVDNffieeklpeefveqSKDTYFCRFEY 677
Cdd:cd04714 81 CYVLTFAEYERLARVKKKPQD--------------GVDFYYCAGTY 112
|
|
| BAH |
cd04370 |
BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). ... |
560-688 |
7.72e-17 |
|
BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Pssm-ID: 239835 [Multi-domain] Cd Length: 123 Bit Score: 78.59 E-value: 7.72e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 560 SVGEFVYLR---APKNCKPYIACVID---KNNQSKIVTVRWFYRPEETKGGVRDWNGENEVFLISHCDTNLIDTVIGKCN 633
Cdd:cd04370 5 EVGDSVYVEpddSIKSDPPYIARIEElweDTNGSKQVKVRWFYRPEETPKGLSPFALRRELFLSDHLDEIPVESIIGKCK 84
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*
gi 2124384683 634 VLFVDKYFKDLPTNIVVDNffieeklpeefveqskDTYFCRFEYSVKNNSFRKIS 688
Cdd:cd04370 85 VLFVSEFEGLKQRPNKIDT----------------DDFFCRLAYDPTTKEFKALE 123
|
|
| BAH_polybromo |
cd04717 |
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human ... |
559-687 |
7.78e-16 |
|
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Pssm-ID: 240068 Cd Length: 121 Bit Score: 75.70 E-value: 7.78e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 559 VSVGEFVYLRAPKNCKPYIACVIDK----NNQSKIVTVRWFYRPEETKGGVRDWNGENEVFLISHCDTNLIDTVIGKCNV 634
Cdd:cd04717 4 YRVGDCVYVANPEDPSKPIIFRIERlwkdEDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGKCAV 83
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|...
gi 2124384683 635 LFVDKYFKDLPTNIvvdnffieeklPEEfveqskDTYFCRFEYSVKNNSFRKI 687
Cdd:cd04717 84 MDVKDYIKGRPTEI-----------SEE------DVYVCESRYNESAKSFKKI 119
|
|
| PHA03036 |
PHA03036 |
DNA polymerase; Provisional |
1435-1728 |
2.54e-12 |
|
DNA polymerase; Provisional
Pssm-ID: 222962 [Multi-domain] Cd Length: 1004 Bit Score: 72.36 E-value: 2.54e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1435 VMEPQSKLYTNPVIVLDFQSLYPSIIIAYNLCYSTCLGKMAYVDQKKSKLGtldgyepNSELRKLLKH----------RE 1504
Cdd:PHA03036 535 VFAPKQKMFDNNVLIFDYNSLYPNVCIFGNLSPETLVGVVVNDNRLEAEIN-------KQELRRKYPYpryiyvhcepRS 607
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1505 EGKSIEedILITPNQclfvkpnvRQGILPRMCTEILNTRVMVKQAMKETSkeDTETQRILNARQLGLKLIANVTYG---- 1580
Cdd:PHA03036 608 PDLVSE--IAVFDRR--------IEGIIPKLLKTFLEERARYKKLLKEAT--SSVEKAIYDSMQYTYKIVANSVYGlmgf 675
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1581 YTSANFS----------GRMPL---------SDLADAIVQLARQTL------ENAIET-------VNQRFKgkCRVAYGD 1628
Cdd:PHA03036 676 RNSALYSyasaksctaiGRNMIkylnsvlngSKLINGKLILANCPInpffkdDRSIDTnydtnlpVEYNFT--FRSVYGD 753
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1629 TDSLFVECIDSTKEEAFKLGKEIVKIVTNSN-PKPITLQMERVFHPSFLVSKKRYVGLAFENPSQTKGTL--FCKGIEAV 1705
Cdd:PHA03036 754 TDSVFLEINTKDVDKSIKIAKELERIINEKVlFDNFKIEFEAVYKNLIMQSKKKYTTLKYIASSTDGSVPerVNKGTSET 833
|
330 340
....*....|....*....|...
gi 2124384683 1706 RRDNCLMVRSLMEKSLEILFETL 1728
Cdd:PHA03036 834 RRDVSKFHKYMIKIYKTRLLDML 856
|
|
| POLBc_B1 |
cd05530 |
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in ... |
1434-1778 |
4.14e-12 |
|
DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases.
Pssm-ID: 99913 Cd Length: 372 Bit Score: 70.07 E-value: 4.14e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1434 LVMEPQSKLYTNpVIVLDFQSLYPSIIIAYNLCYSTclgkmayVDQKKSKLGTldgYEPNSELRKLLKHREegksieedi 1513
Cdd:cd05530 17 IVLEPPPGIFFN-VVVLDFASLYPSIIKVWNLSYET-------VNCPHCECKT---NEVPEVGHWVCKKRP--------- 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1514 litpnqclfvkpnvrqGILPRMCTEILNTRVMV-KQAMKetSKEDTETQRIL-NARQLGLKLIANVTYG-YTSANFsgrm 1590
Cdd:cd05530 77 ----------------GITSQIIGLLRDLRVKIyKKKAK--DKSLDEEMRQWyDVVQSAMKVFINASYGvFGAENF---- 134
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1591 PLSDL--ADAIVQLAR----QTLENAIETvnqrfkgKCRVAYGDTDSLFVEciDSTKEeafKLgKEIVKIVtnSNPKPIT 1664
Cdd:cd05530 135 PLYCPpvAESTTALGRyiitSTIKKAREL-------GLKVLYGDTDSLFLW--NPPQE---QL-EDLVEWV--EKELGLD 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1665 LQMERVF-HPSFLVSKKRYVGLAFEnpsqtkGTLFCKGIEAVRRDNCLMVRSLMEKSLEILFETL---DFSLVKSYLSRQ 1740
Cdd:cd05530 200 LELDKEYrYVVFSGLKKNYLGVTKD------GSVDIKGLLGKKRNTPEFVKELFYEVIEILSAVNspeDFEKAREKIRDI 273
|
330 340 350 360
....*....|....*....|....*....|....*....|....
gi 2124384683 1741 ----FYRIISEKCSLQDFIFwkKVKLGYYKSE--KNLPPSARVA 1778
Cdd:cd05530 274 vkgvYKRLKKKEYTLDQLAF--KVMLSKPPEEytKNTPQHVKAA 315
|
|
| DNA_polB_delta_exo |
cd05777 |
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; ... |
1125-1323 |
3.07e-11 |
|
DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase; The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues necessary for metal binding and catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation.
Pssm-ID: 99820 [Multi-domain] Cd Length: 230 Bit Score: 65.29 E-value: 3.07e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1125 INVMS--IECHVTTRAdfLPNPIYDPVqaIIICSqncadvanstesilLLNRDLEDNDTIQHKLT---CIPLNFDRFYEF 1199
Cdd:cd05777 7 LRILSfdIECAGRKGV--FPEPEKDPV--IQIAN--------------VVTRQGEGEPFIRNIFTlktCAPIVGAQVFSF 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1200 KTEQDLLNGFIDFICKEDPDILLGYEMQTEGLGYLIERG-------FTVLG--KNICYDLSRAIFyQNENKANNTNKDkr 1270
Cdd:cd05777 69 ETEEELLLAWRDFVQEVDPDIITGYNICNFDLPYLLERAkalklntFPFLGriKNIKSTIKDTTF-SSKQMGTRETKE-- 145
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 2124384683 1271 qdkimkkaqeyarnkqsgVMIKGRVVINVWRLMNGEMKLDMYTLHNVAFNILG 1323
Cdd:cd05777 146 ------------------INIEGRIQFDLLQVIQRDYKLRSYSLNSVSAHFLG 180
|
|
| BAH_plant_3 |
cd04713 |
BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH ... |
560-639 |
4.98e-10 |
|
BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Pssm-ID: 240064 Cd Length: 146 Bit Score: 59.79 E-value: 4.98e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 560 SVGEFVYLRAPKNCKPYIACVIDKNNQSK---IVTVRWFYRPEET-KGGVRDWNGE--NEVFLISHCDTNLIDTVIGKCN 633
Cdd:cd04713 22 RLEDCVLLVPEDDQKPYIAIIKDIYKQEEgslKLEVQWLYRPEEIeKKKGGNWKAEdpRELFYSFHRDEVPAESVLHPCK 101
|
....*.
gi 2124384683 634 VLFVDK 639
Cdd:cd04713 102 VAFVPK 107
|
|
| PTZ00166 |
PTZ00166 |
DNA polymerase delta catalytic subunit; Provisional |
1-280 |
5.56e-09 |
|
DNA polymerase delta catalytic subunit; Provisional
Pssm-ID: 240301 [Multi-domain] Cd Length: 1054 Bit Score: 61.58 E-value: 5.56e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1 MLLQVLSLEYSLCLPQALfDDRKCSFFGGRSIDlVPIMHVYGtIQETKQKACLHIHQLYPYFMLSFPYELfleegEENDH 80
Cdd:PTZ00166 42 LVFFQLDADYTEKDDKSQ-GNPHNTVSGVRHVE-VPIIRLYG-VTKEGHSVLVNVHNFFPYFYIEAPPNF-----LPEDS 113
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 81 SNLKRTDNLLLKLnmrkvsdfihvlgntieqtfhrslygtslqqyqnmqqqnskqdQSVYKHQRQFIHDIVVVTGTPFYG 160
Cdd:PTZ00166 114 QKLKRELNAQLSE-------------------------------------------QSQFKKYQNTVLDIEIVKKESLMY 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 161 YWFNPQL-FLKVYVYNPSHVGKMAAMF--GNSSVMGH-----KFSVYEAHIPFSLQFMMDYNVYGMGDLSVEKvffrlpf 232
Cdd:PTZ00166 151 YKGNGEKdFLKITVQLPKMVPRLRSLIesGVVVCGGGwdgirLFQTYESNVPFVLRFLIDNNITGGSWLTLPK------- 223
|
250 260 270 280
....*....|....*....|....*....|....*....|....*...
gi 2124384683 233 haadndneNTQKISSQNatnygtilpenvKRLSKCEIEMDIFSRDVLN 280
Cdd:PTZ00166 224 --------GKYKIRPPK------------KKTSTCQIEVDCSYEDLIP 251
|
|
| DNA_polB_Kod1_like_exo |
cd05780 |
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B ... |
1200-1371 |
6.39e-07 |
|
DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show similarity to eukaryotic DNA polymerases involved in DNA replication. Some archaea possess multiple family-B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family-B DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.
Pssm-ID: 99823 [Multi-domain] Cd Length: 195 Bit Score: 51.97 E-value: 6.39e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1200 KTEQDLLNGFIDFICKEDPDILLGYEMQTEGLGYLIERGFTVlgkNICYDLSRaifyqnenkanntnkDKRQDKIMKKAQ 1279
Cdd:cd05780 54 KTEKEMIKRFIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKL---GIELDLGR---------------DGSEIKIQRGGF 115
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1280 EYArnkqsgVMIKGRVVINVWRLMNGEMKLDMYTLHNVAFNILGKRIPYYSYQTLSELSNSCQHRKDSFEYRiilqyyYK 1359
Cdd:cd05780 116 NNA------SEIKGRIHVDLYPVARRTLNLTRYTLERVYEELFGIEKEDVPGEEIAEAWDSGENLERLFRYS------ME 183
|
170
....*....|..
gi 2124384683 1360 KASITLELLNYL 1371
Cdd:cd05780 184 DAKYTYEIGKEF 195
|
|
| DNA_pol_B_exo1 |
pfam03104 |
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and ... |
1197-1317 |
7.35e-05 |
|
DNA polymerase family B, exonuclease domain; This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold.
Pssm-ID: 397292 Cd Length: 333 Bit Score: 47.03 E-value: 7.35e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1197 YEFKTEQDLLNGFIDFICKEDPDILLGYEMQteglgylierGFTvlgknICYDLSRAifyqNENKANNTNKDKRQDKIM- 1275
Cdd:pfam03104 229 FEFPSEKELLRRFFEFIRQYDPDIITGYNGD----------NFD-----WPYILNRA----KELYIVKLSSIGRLNRGGr 289
|
90 100 110 120
....*....|....*....|....*....|....*....|....
gi 2124384683 1276 KKAQE--YARNKQSGVMIKGRVVINVWRLMNGEMKLDMYTLHNV 1317
Cdd:pfam03104 290 SKVREigFGTRSYEKVKISGRLHLDLYRVIKRDYKLPSYKLNAV 333
|
|
| PolB |
COG0417 |
DNA polymerase B elongation subunit [Replication, recombination and repair]; |
147-224 |
8.95e-05 |
|
DNA polymerase B elongation subunit [Replication, recombination and repair];
Pssm-ID: 440186 [Multi-domain] Cd Length: 794 Bit Score: 47.51 E-value: 8.95e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2124384683 147 IHDIVVVTGTPFYGywfNPQLFLKVYVYNPSHVGKMAamfgnSSVMGHKFSVYEAHIPFSLQFMMDYNVYGMGDLSVE 224
Cdd:COG0417 64 ITEVEPVKLKSFFG---EPVPVLKIYTRDPRDVRELR-----DRLKEGGIDVYEADIRFHDRYLIDRFLTPGVWYEGE 133
|
|
| BAH_DCM_I |
cd04712 |
BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) ... |
582-658 |
1.89e-04 |
|
BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Pssm-ID: 240063 Cd Length: 130 Bit Score: 43.16 E-value: 1.89e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 582 DKNNQSKIVTVRWFYRPEETKGGVRDWngENEVFLISHCDT---NLIDTVI-GKCNV-LFVDKYFKDLPTNIVVDNFFIE 656
Cdd:cd04712 43 KGSDGSKMFHGRWLYRGCDTVLGNYAN--ERELFLTNECTClelDLLSTEIkGVHKVdWSGTPWGKGLPEFFVRQSYYWP 120
|
..
gi 2124384683 657 EK 658
Cdd:cd04712 121 ER 122
|
|
| POLBc_Pol_II_B |
cd05538 |
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, ... |
1446-1800 |
3.60e-04 |
|
DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication.
Pssm-ID: 99921 Cd Length: 347 Bit Score: 45.17 E-value: 3.60e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1446 PVIVLDFQSLYPSIIIAYNLCystclgkmayvdqkksklgtldgyePNSElrkllkhreegksieedilitpnqclfvkp 1525
Cdd:cd05538 18 PIVHADVASLYPSIMLAYRIC-------------------------PARD------------------------------ 42
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1526 nvRQGILPRMCTEILNTRVMVKQAMKETSkeDTETQRILNARQLGLKLIANVTYGYTSanfSGRMPLSD--LADAIVQLA 1603
Cdd:cd05538 43 --SLGIFLALLKYLVELRLAAKESARAAA--RPAERDAFKAKQAAFKVLINSFYGYLG---TGLHAFSDpeAAAEVTRLG 115
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1604 RQTLENAIETVNQRfkgKCRVAYGDTDSLFV---ECIDSTKEEafklgKEIVKIVTNSNPKPITLQMERVFHPSFLVSKK 1680
Cdd:cd05538 116 RELLKLMIRWLRRR---GATPVEVDTDGIYFippNGVDTEDEE-----EELVRELSSTLPKGITVEFDGRYRAMFSYKIK 187
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1681 RYVGLAFENPSQTKGTLFckgieaVRRDNCLMVRSLMEKSLEILFETlDFSLVKSYLSRQFYRIISEKCSLQDFIFWKKV 1760
Cdd:cd05538 188 NYALLDYDGKLIVKGSAF------RSRGIEPFLREFLREAVRLLLQG-DGAGVHDLYEDYLRRLRSHELPISDLARTETL 260
|
330 340 350 360
....*....|....*....|....*....|....*....|..
gi 2124384683 1761 K--LGYYKSEKNLPPSARVAIREMQRDPRAEPRFNERVPYIV 1800
Cdd:cd05538 261 KesPEEYLQKVRAGKRNPAAAYEIALARPREWRAGDRVTYYV 302
|
|
| BAH_plant_2 |
cd04718 |
BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH ... |
583-688 |
8.05e-04 |
|
BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Pssm-ID: 240069 Cd Length: 148 Bit Score: 41.80 E-value: 8.05e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 583 KNNQSKIVTVRWFYRPEETKGGVRDWNGENEVFLISHCDTNLIDTVIGKCNVlfvdkyfkdlptnivvdnffieeKLPEE 662
Cdd:cd04718 63 EENGTYWYAARWYTLPEETHMGRQPHNLRRELYLTNDFADIEMECILRHCSV-----------------------KCPKE 119
|
90 100
....*....|....*....|....*....
gi 2124384683 663 FVEQS---KDTYFCRFEYSVKNNSFRKIS 688
Cdd:cd04718 120 FRDASndgDDVFLCEYEYDVHWQSFKRLA 148
|
|
| zf-C4pol |
pfam14260 |
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears ... |
1912-2006 |
1.36e-03 |
|
C4-type zinc-finger of DNA polymerase delta; In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1. Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1.
Pssm-ID: 464119 Cd Length: 68 Bit Score: 38.89 E-value: 1.36e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1912 CVSCGAiidcktlnkvegaatdlsSQEPLCPKCKEYPLVL----LLRLRSVERNKNMLSELCRHCNHELDvtngllpysk 1987
Cdd:pfam14260 1 CLGCGA------------------PEEPLCKNCRSDPQASylelLSRLRELERRFNRLWTICQRCQGSLH---------- 52
|
90
....*....|....*....
gi 2124384683 1988 vpsIEEKCMSLECPILFSK 2006
Cdd:pfam14260 53 ---EEVLCDSRDCPVFYMR 68
|
|
| BAH_plantDCM_I |
cd04716 |
BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5) ... |
560-689 |
1.93e-03 |
|
BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Pssm-ID: 240067 Cd Length: 122 Bit Score: 40.12 E-value: 1.93e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 560 SVGEFVYLRAPKNCKPYIACVID---KNNQSKIVTVRWFYRPEETKGGVRDWNGENE-VFLISHCDTNLIDTVIGKCNVL 635
Cdd:cd04716 5 NLGDDAYVQGGEGEEPFICKITEffeGTDGKTYFTAQWFYRAEDTVIERQATNHDKKrVFYSEIKNDNPLDCLISKVKIL 84
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....
gi 2124384683 636 FVDkyfkdlptnivvdnffIEEKLPEEFVEQSKDTYFCRFEYSVKNNSFRKISS 689
Cdd:cd04716 85 QVP----------------PNVGTKRKKPNSEKCDYYYDMEYCVPYSTFQTLRN 122
|
|
| DNA_polB_B3_exo |
cd05781 |
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar ... |
1125-1237 |
5.15e-03 |
|
DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases; The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaea possess multiple family-B DNA polymerases. B3 is mainly found in crenarchaea. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B-DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases.
Pssm-ID: 99824 [Multi-domain] Cd Length: 188 Bit Score: 40.00 E-value: 5.15e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2124384683 1125 INVMSIECHVTTRADFlPNPIYDPVqaIIICSQNcadvanstesilllnrdleDNDTIQHKLTciplnfdrfyEFKTEQD 1204
Cdd:cd05781 3 LKTLAFDIEVYSKYGT-PNPRRDPI--IVISLAT-------------------SNGDVEFILA----------EGLDDRK 50
|
90 100 110
....*....|....*....|....*....|...
gi 2124384683 1205 LLNGFIDFICKEDPDILLGYEMQTEGLGYLIER 1237
Cdd:cd05781 51 IIREFVKYVKEYDPDIIVGYNSNAFDWPYLVER 83
|
|
| |
