|
Name |
Accession |
Description |
Interval |
E-value |
| rad3 |
TIGR00604 |
DNA repair helicase (rad3); All proteins in this family for which funcitons are known are ... |
59-651 |
2.71e-109 |
|
DNA repair helicase (rad3); All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. 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: 273169 [Multi-domain] Cd Length: 705 Bit Score: 345.55 E-value: 2.71e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 59 LRLFPYEP-YPQQLKFMKDAETVLDKGGVLVAEACNGFGKTVCALSSALATGRR------IIYATRTHEQVRQVLREIEQ 131
Cdd:TIGR00604 3 LVYFPYEKiYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEkpevrkIIYASRTHSQLEQATEELRK 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 132 INK------KAGTDFSAVALASRQNLCLNQICRSLPQTEAVEA-CRVLRNS------------RRCPY------KSQFSF 186
Cdd:TIGR00604 83 LMSyrtpriGEESPVSGLSLASRKNLCLHPEVSKERQGKVVNGkCIKLTVSkikeqrtekpnvESCEFyenfdeLREVED 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 187 LGSSLPPvlSTRRLLNYGRTKGICPYYLSRKISQDCTVVVAPYQYIFNESIRATVGLDINGKVLVFDEAHNADKIGQEVL 266
Cdd:TIGR00604 163 LLLSEIM--DIEDLVEYGELLGLCPYFATRKMLPFANIVLLPYQYLLDPKIRSAVSIELKDSIVIFDEAHNLDNVCISSL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 267 SDTLSERGLDNAVRELE---------------------------------------------------------LVGVPS 289
Cdd:TIGR00604 241 SSNLSVRSLKRCSKEIAeyfekieerkevdarklldelqklveglkqedlltdediflanpvlpkevlpeavpgNIRIAE 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 290 VFIGKLTDYLEKT---------VREEPvvKPGSQLFKDLTEVLGEdLSFIVESFKpmvDEIREKRISRGEVPVCYLNGLL 360
Cdd:TIGR00604 321 IFLHKLSRYLEYLkdalkvlgvVSELP--DAFLEHLKEKTFIDRP-LRFCSERLS---NLLRELEITHPEDFSALVLLFT 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 361 NFLLLVDSSEKESYVAIYRKSASGLNLV-EYRCLDPSLAIKPVIEEAHAALIMSGTLSPLDLFTEVLGLSEAETRTYSAI 439
Cdd:TIGR00604 395 FATLVLTYTNGFLEGIEPYENKTVPNPIlKFMCLDPSIALKPLFERVRSVILASGTLSPLDAFPRNLGFNPVSQDSPTHI 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 440 AKPENVRTYV------DISVTTKFQERSA-DMLKLYGERISKLAKNVPNGVLIFFPQRRLMNEAVAIWRRNGFIRRRGRr 512
Cdd:TIGR00604 475 LKRENLLTLIvtrgsdQVPLSSTFEIRNDpSLVRNLGELLVEFSKIIPDGIVVFFPSYSYLENIVSTWKEMGILENIEK- 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 513 lflgKKIVFVEGTRATENARIVDEYKKAARTDQGAVLFAVFRGRNAEGSNFPYEEARGVFNVGLPYADYHDPLVKAQIGF 592
Cdd:TIGR00604 554 ----KKLIFVETKDAQETSDALERYKQAVSEGRGAVLLSVAGGKVSEGIDFCDDLGRAVIMVGIPYEYTESRILLARLEF 629
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1231988176 593 FNRKKS-RLGELWYLMDAFRAANQAMGRGIRHRDDWCRFYLMDRRYATHWK--FISKWAVEN 651
Cdd:TIGR00604 630 LRDQYPiRENQDFYEFDAMRAVNQAIGRVIRHKDDYGSIVLLDKRYARSNKrkKLPKWIQDT 691
|
|
| DinG |
COG1199 |
Rad3-related DNA helicase DinG [Replication, recombination and repair]; |
54-639 |
4.81e-64 |
|
Rad3-related DNA helicase DinG [Replication, recombination and repair];
Pssm-ID: 440812 [Multi-domain] Cd Length: 629 Bit Score: 223.26 E-value: 4.81e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 54 PQKGFLRLFP-YEPYPQQLKFMKDAETVLDKGGVLVAEACNGFGKT----VCALSSALATGRRIIYATRTHEQVRQVL-R 127
Cdd:COG1199 2 DDGLLALAFPgFEPRPGQREMAEAVARALAEGRHLLIEAGTGTGKTlaylVPALLAARETGKKVVISTATKALQEQLVeK 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 128 EIEQINKKAGTDFSAVALASRQN-LCLNQICRSLPQTEAVEACRVLRNSRRCPYKSQFSFLGSSLPPVLSTR--RLLNYG 204
Cdd:COG1199 82 DLPLLRKALGLPLRVALLKGRSNyLCLRRLEQALQEGDDLDDEELLLARILAWASETWTGDRDELPLPEDDElwRQVTSD 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 205 RTK---------GICPYYLSRKISQDCTVVVAPYQYIFNESIRATVGLDiNGKVLVFDEAHNADKIGQEVLSDTLSERGL 275
Cdd:COG1199 162 ADNclgrrcpyyGVCPYELARRLAREADVVVVNHHLLFADLALGEELLP-EDDVLIIDEAHNLPDRARDMFSAELSSRSL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 276 DNAVRELELVGVPS------VFIGKLTDYLE---KTVREEPVVKPGSQLFKDLTEVLGEDLSFIVESFKPMVDEIREKRI 346
Cdd:COG1199 241 LRLLRELRKLGLRPglkkllDLLERLREALDdlfLALEEEEELRLALGELPDEPEELLEALDALRDALEALAEALEEELE 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 347 SRGEVPVCYLNGLLNFLLL---VDSSEKESYVAIYRKSASGLNLvEYRCLDPSLAIKPVI-EEAHAALIMSGTLS---PL 419
Cdd:COG1199 321 RLAELDALLERLEELLFALarfLRIAEDEGYVRWLEREGGDVRL-HAAPLDPADLLRELLfSRARSVVLTSATLSvggPF 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 420 DLFTEVLGLS-EAETRTYSAIAKPENVRTYVDISVTTKFQERsADMLKLYGERISKLAKNVPNGVLIFFPQRRLMNEAVA 498
Cdd:COG1199 400 DYFARRLGLDeDARTLSLPSPFDYENQALLYVPRDLPRPSDR-DGYLEAIAEAIAELLEASGGNTLVLFTSYRALEQVAE 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 499 IWRRNGFIRrrgrrlflgkkiVFVEGTRATEnaRIVDEYKKaartDQGAVLFAVfrGRNAEGSNFPYEEARGVFNVGLPY 578
Cdd:COG1199 479 LLRERLDIP------------VLVQGDGSRE--ALLERFRE----GGNSVLVGT--GSFWEGVDLPGDALSLVIIVKLPF 538
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1231988176 579 ADYHDPLVKAQIGFFnrkKSRLGELW---YLMDAFRAANQAMGRGIRHRDDWCRFYLMDRRYAT 639
Cdd:COG1199 539 PPPDDPVLEARREAL---EARGGNGFmyaYLPPAVIKLKQGAGRLIRSEEDRGVVVLLDRRLLT 599
|
|
| DEXDc2 |
smart00488 |
DEAD-like helicases superfamily; |
61-282 |
2.20e-48 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214693 [Multi-domain] Cd Length: 289 Bit Score: 171.41 E-value: 2.20e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 61 LFPYEPYPQQLKFMKDAETVLDKGGVLVAEACNGFGKTVCALSSALATGRR---------IIYATRTHEQVRQVLREIEQ 131
Cdd:smart00488 4 YFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSfperiqkikLIYLSRTVSEIEKRLEELRK 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 132 INK---------------------KAGTDFSAVALASRQNLCLNQICRSLPQTEAV--EACRVLRNSR------------ 176
Cdd:smart00488 84 LMQkveyesdeesekqaqllhelgREKPKVLGLSLTSRKNLCLNPEVRTLKQNGLVvdEVCRSLTASKarkyryenpkve 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 177 RCPYKSQFSFLG--SSLPP-VLSTRRLLNYGRTKGICPYYLSRKISQDCTVVVAPYQYIFNESIRATVGLDINGKVLVFD 253
Cdd:smart00488 164 RCPFYENTEFLLvrDLLPAeVYDIEDLLELGKRLGGCPYFASRKAIEFANVVVLPYQYLLDPKIRQALSIELKDSIVIFD 243
|
250 260
....*....|....*....|....*....
gi 1231988176 254 EAHNADKIGQEVLSDTLSERGLDNAVREL 282
Cdd:smart00488 244 EAHNLDNVCISALSSELSRRSLERAHKNI 272
|
|
| Helicase_C_2 |
pfam13307 |
Helicase C-terminal domain; This domain is found at the C-terminus of DEAD-box helicases. |
473-647 |
3.68e-45 |
|
Helicase C-terminal domain; This domain is found at the C-terminus of DEAD-box helicases.
Pssm-ID: 463840 [Multi-domain] Cd Length: 168 Bit Score: 158.49 E-value: 3.68e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 473 SKLAKNVPNGVLIFFPQRRLMNEAVAIWRRNGFIRrrgrrlflgKKIVFVEGTRAtENARIVDEYKKAARtdqGAVLFAV 552
Cdd:pfam13307 1 LRLLKVIPGGVLVFFPSYSYLEKVAERLKESGLEK---------GIEIFVQPGEG-SREKLLEEFKKKGK---GAVLFGV 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 553 FRGRNAEGSNFPYEEARGVFNVGLPYADYHDPLVKAQIGFFNRKKSRLGELWYLMDAFRAANQAMGRGIRHRDDWCRFYL 632
Cdd:pfam13307 68 CGGSFSEGIDFPGDLLRAVIIVGLPFPNPDDPVVEAKREYLDSKGGNPFNEWYLPQAVRAVNQAIGRLIRHENDYGAIVL 147
|
170
....*....|....*..
gi 1231988176 633 MDRRYAT--HWKFISKW 647
Cdd:pfam13307 148 LDSRFLTkrYGKLLPKW 164
|
|
| SF2_C_XPD |
cd18788 |
C-terminal helicase domain of xeroderma pigmentosum group D (XPD) family DEAD-like helicases; ... |
451-637 |
3.95e-30 |
|
C-terminal helicase domain of xeroderma pigmentosum group D (XPD) family DEAD-like helicases; The xeroderma pigmentosum group D (XPD)-like family members are DEAD-box helicases belonging to superfamily (SF)2. This family includes DDX11 (also called ChlR1), a protein involved in maintaining chromosome transmission fidelity and genome stability, the TFIIH basal transcription factor complex XPD subunit, and FANCJ (also known as BRIP1), a DNA helicase required for the maintenance of chromosomal stability. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350175 [Multi-domain] Cd Length: 159 Bit Score: 116.16 E-value: 3.95e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 451 ISVTTKFQER-SADMLKLYGERISKLAKNVPNGVLIFFPQRRLMNEAVAiwrrngfirrrgrrlflgkkivfvegtrate 529
Cdd:cd18788 15 QALNSKFQTReDEAVMDELGNLLLELCAVVPDGVLVFFPSYSYMERVVS------------------------------- 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 530 narivdeykkaartdQGAVLFAVFRGRNAEGSNFPYEEARGVFNVGLPYADYHDPLVKAQIGF--FNRKKSRL-GELWYL 606
Cdd:cd18788 64 ---------------RGALLLAVCRGKVSEGIDFSDDLGRAVIMVGIPYPNTKDPILKLKMDDleYLRDKGLLtGEDWYT 128
|
170 180 190
....*....|....*....|....*....|.
gi 1231988176 607 MDAFRAANQAMGRGIRHRDDWCRFYLMDRRY 637
Cdd:cd18788 129 FQAMRAVNQAIGRAIRHKNDYGAIVLLDKRF 159
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rad3 |
TIGR00604 |
DNA repair helicase (rad3); All proteins in this family for which funcitons are known are ... |
59-651 |
2.71e-109 |
|
DNA repair helicase (rad3); All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. 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: 273169 [Multi-domain] Cd Length: 705 Bit Score: 345.55 E-value: 2.71e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 59 LRLFPYEP-YPQQLKFMKDAETVLDKGGVLVAEACNGFGKTVCALSSALATGRR------IIYATRTHEQVRQVLREIEQ 131
Cdd:TIGR00604 3 LVYFPYEKiYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEkpevrkIIYASRTHSQLEQATEELRK 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 132 INK------KAGTDFSAVALASRQNLCLNQICRSLPQTEAVEA-CRVLRNS------------RRCPY------KSQFSF 186
Cdd:TIGR00604 83 LMSyrtpriGEESPVSGLSLASRKNLCLHPEVSKERQGKVVNGkCIKLTVSkikeqrtekpnvESCEFyenfdeLREVED 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 187 LGSSLPPvlSTRRLLNYGRTKGICPYYLSRKISQDCTVVVAPYQYIFNESIRATVGLDINGKVLVFDEAHNADKIGQEVL 266
Cdd:TIGR00604 163 LLLSEIM--DIEDLVEYGELLGLCPYFATRKMLPFANIVLLPYQYLLDPKIRSAVSIELKDSIVIFDEAHNLDNVCISSL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 267 SDTLSERGLDNAVRELE---------------------------------------------------------LVGVPS 289
Cdd:TIGR00604 241 SSNLSVRSLKRCSKEIAeyfekieerkevdarklldelqklveglkqedlltdediflanpvlpkevlpeavpgNIRIAE 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 290 VFIGKLTDYLEKT---------VREEPvvKPGSQLFKDLTEVLGEdLSFIVESFKpmvDEIREKRISRGEVPVCYLNGLL 360
Cdd:TIGR00604 321 IFLHKLSRYLEYLkdalkvlgvVSELP--DAFLEHLKEKTFIDRP-LRFCSERLS---NLLRELEITHPEDFSALVLLFT 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 361 NFLLLVDSSEKESYVAIYRKSASGLNLV-EYRCLDPSLAIKPVIEEAHAALIMSGTLSPLDLFTEVLGLSEAETRTYSAI 439
Cdd:TIGR00604 395 FATLVLTYTNGFLEGIEPYENKTVPNPIlKFMCLDPSIALKPLFERVRSVILASGTLSPLDAFPRNLGFNPVSQDSPTHI 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 440 AKPENVRTYV------DISVTTKFQERSA-DMLKLYGERISKLAKNVPNGVLIFFPQRRLMNEAVAIWRRNGFIRRRGRr 512
Cdd:TIGR00604 475 LKRENLLTLIvtrgsdQVPLSSTFEIRNDpSLVRNLGELLVEFSKIIPDGIVVFFPSYSYLENIVSTWKEMGILENIEK- 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 513 lflgKKIVFVEGTRATENARIVDEYKKAARTDQGAVLFAVFRGRNAEGSNFPYEEARGVFNVGLPYADYHDPLVKAQIGF 592
Cdd:TIGR00604 554 ----KKLIFVETKDAQETSDALERYKQAVSEGRGAVLLSVAGGKVSEGIDFCDDLGRAVIMVGIPYEYTESRILLARLEF 629
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1231988176 593 FNRKKS-RLGELWYLMDAFRAANQAMGRGIRHRDDWCRFYLMDRRYATHWK--FISKWAVEN 651
Cdd:TIGR00604 630 LRDQYPiRENQDFYEFDAMRAVNQAIGRVIRHKDDYGSIVLLDKRYARSNKrkKLPKWIQDT 691
|
|
| DinG |
COG1199 |
Rad3-related DNA helicase DinG [Replication, recombination and repair]; |
54-639 |
4.81e-64 |
|
Rad3-related DNA helicase DinG [Replication, recombination and repair];
Pssm-ID: 440812 [Multi-domain] Cd Length: 629 Bit Score: 223.26 E-value: 4.81e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 54 PQKGFLRLFP-YEPYPQQLKFMKDAETVLDKGGVLVAEACNGFGKT----VCALSSALATGRRIIYATRTHEQVRQVL-R 127
Cdd:COG1199 2 DDGLLALAFPgFEPRPGQREMAEAVARALAEGRHLLIEAGTGTGKTlaylVPALLAARETGKKVVISTATKALQEQLVeK 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 128 EIEQINKKAGTDFSAVALASRQN-LCLNQICRSLPQTEAVEACRVLRNSRRCPYKSQFSFLGSSLPPVLSTR--RLLNYG 204
Cdd:COG1199 82 DLPLLRKALGLPLRVALLKGRSNyLCLRRLEQALQEGDDLDDEELLLARILAWASETWTGDRDELPLPEDDElwRQVTSD 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 205 RTK---------GICPYYLSRKISQDCTVVVAPYQYIFNESIRATVGLDiNGKVLVFDEAHNADKIGQEVLSDTLSERGL 275
Cdd:COG1199 162 ADNclgrrcpyyGVCPYELARRLAREADVVVVNHHLLFADLALGEELLP-EDDVLIIDEAHNLPDRARDMFSAELSSRSL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 276 DNAVRELELVGVPS------VFIGKLTDYLE---KTVREEPVVKPGSQLFKDLTEVLGEDLSFIVESFKPMVDEIREKRI 346
Cdd:COG1199 241 LRLLRELRKLGLRPglkkllDLLERLREALDdlfLALEEEEELRLALGELPDEPEELLEALDALRDALEALAEALEEELE 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 347 SRGEVPVCYLNGLLNFLLL---VDSSEKESYVAIYRKSASGLNLvEYRCLDPSLAIKPVI-EEAHAALIMSGTLS---PL 419
Cdd:COG1199 321 RLAELDALLERLEELLFALarfLRIAEDEGYVRWLEREGGDVRL-HAAPLDPADLLRELLfSRARSVVLTSATLSvggPF 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 420 DLFTEVLGLS-EAETRTYSAIAKPENVRTYVDISVTTKFQERsADMLKLYGERISKLAKNVPNGVLIFFPQRRLMNEAVA 498
Cdd:COG1199 400 DYFARRLGLDeDARTLSLPSPFDYENQALLYVPRDLPRPSDR-DGYLEAIAEAIAELLEASGGNTLVLFTSYRALEQVAE 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 499 IWRRNGFIRrrgrrlflgkkiVFVEGTRATEnaRIVDEYKKaartDQGAVLFAVfrGRNAEGSNFPYEEARGVFNVGLPY 578
Cdd:COG1199 479 LLRERLDIP------------VLVQGDGSRE--ALLERFRE----GGNSVLVGT--GSFWEGVDLPGDALSLVIIVKLPF 538
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1231988176 579 ADYHDPLVKAQIGFFnrkKSRLGELW---YLMDAFRAANQAMGRGIRHRDDWCRFYLMDRRYAT 639
Cdd:COG1199 539 PPPDDPVLEARREAL---EARGGNGFmyaYLPPAVIKLKQGAGRLIRSEEDRGVVVLLDRRLLT 599
|
|
| DEXDc2 |
smart00488 |
DEAD-like helicases superfamily; |
61-282 |
2.20e-48 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214693 [Multi-domain] Cd Length: 289 Bit Score: 171.41 E-value: 2.20e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 61 LFPYEPYPQQLKFMKDAETVLDKGGVLVAEACNGFGKTVCALSSALATGRR---------IIYATRTHEQVRQVLREIEQ 131
Cdd:smart00488 4 YFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSfperiqkikLIYLSRTVSEIEKRLEELRK 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 132 INK---------------------KAGTDFSAVALASRQNLCLNQICRSLPQTEAV--EACRVLRNSR------------ 176
Cdd:smart00488 84 LMQkveyesdeesekqaqllhelgREKPKVLGLSLTSRKNLCLNPEVRTLKQNGLVvdEVCRSLTASKarkyryenpkve 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 177 RCPYKSQFSFLG--SSLPP-VLSTRRLLNYGRTKGICPYYLSRKISQDCTVVVAPYQYIFNESIRATVGLDINGKVLVFD 253
Cdd:smart00488 164 RCPFYENTEFLLvrDLLPAeVYDIEDLLELGKRLGGCPYFASRKAIEFANVVVLPYQYLLDPKIRQALSIELKDSIVIFD 243
|
250 260
....*....|....*....|....*....
gi 1231988176 254 EAHNADKIGQEVLSDTLSERGLDNAVREL 282
Cdd:smart00488 244 EAHNLDNVCISALSSELSRRSLERAHKNI 272
|
|
| Helicase_C_2 |
pfam13307 |
Helicase C-terminal domain; This domain is found at the C-terminus of DEAD-box helicases. |
473-647 |
3.68e-45 |
|
Helicase C-terminal domain; This domain is found at the C-terminus of DEAD-box helicases.
Pssm-ID: 463840 [Multi-domain] Cd Length: 168 Bit Score: 158.49 E-value: 3.68e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 473 SKLAKNVPNGVLIFFPQRRLMNEAVAIWRRNGFIRrrgrrlflgKKIVFVEGTRAtENARIVDEYKKAARtdqGAVLFAV 552
Cdd:pfam13307 1 LRLLKVIPGGVLVFFPSYSYLEKVAERLKESGLEK---------GIEIFVQPGEG-SREKLLEEFKKKGK---GAVLFGV 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 553 FRGRNAEGSNFPYEEARGVFNVGLPYADYHDPLVKAQIGFFNRKKSRLGELWYLMDAFRAANQAMGRGIRHRDDWCRFYL 632
Cdd:pfam13307 68 CGGSFSEGIDFPGDLLRAVIIVGLPFPNPDDPVVEAKREYLDSKGGNPFNEWYLPQAVRAVNQAIGRLIRHENDYGAIVL 147
|
170
....*....|....*..
gi 1231988176 633 MDRRYAT--HWKFISKW 647
Cdd:pfam13307 148 LDSRFLTkrYGKLLPKW 164
|
|
| DEAD_2 |
pfam06733 |
DEAD_2; This represents a conserved region within a number of RAD3-like DNA-binding helicases ... |
114-275 |
8.14e-39 |
|
DEAD_2; This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin. RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast.
Pssm-ID: 399602 [Multi-domain] Cd Length: 168 Bit Score: 140.86 E-value: 8.14e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 114 YATRTHEQVRQVLREIEQINKKAgtDFSAVALASRQNLCLNQICRSLPQTEAV-EACRVLRNSR---RCPYKSQFSFLGS 189
Cdd:pfam06733 1 YCSRTHSQLEQVVKELRRLPYYK--KIRGLILGSRKNLCINPEVLKLKKGNLVnERCRELVKSKargSCPFYNNLEDLLK 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 190 S----LPPVLSTRRLLNYGRTKGICPYYLSRKISQDCTVVVAPYQYIFNESIRATVGLDINGKVLVFDEAHNADKIGQEV 265
Cdd:pfam06733 79 LrdllGDEVMDIEDLVELGEKLGICPYYLSRELIPDADIIILPYNYLLDPKIRESLSINLKNSIVIFDEAHNIEDVCIES 158
|
170
....*....|
gi 1231988176 266 LSDTLSERGL 275
Cdd:pfam06733 159 ASFSISRSQL 168
|
|
| HELICc2 |
smart00491 |
helicase superfamily c-terminal domain; |
517-639 |
2.33e-32 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 214694 [Multi-domain] Cd Length: 142 Bit Score: 122.00 E-value: 2.33e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 517 KKIVFVEGTRATENARIVDEYKKAARTdQGAVLFAVFRGRNAEGSNFPYEEARGVFNVGLPYADYHDPLVKAQIGFFNRK 596
Cdd:smart00491 20 NKPVFIEGKDSGETEELLEKYSAACEA-RGALLLAVARGKVSEGIDFPDDLGRAVIIVGIPFPNPDSPILRARLEYLDEK 98
|
90 100 110 120
....*....|....*....|....*....|....*....|....
gi 1231988176 597 -KSRLGELWYLMDAFRAANQAMGRGIRHRDDWCRFYLMDRRYAT 639
Cdd:smart00491 99 gGIRPFDEVYLFDAMRALAQAIGRAIRHKNDYGVVVLLDKRYAR 142
|
|
| SF2_C_XPD |
cd18788 |
C-terminal helicase domain of xeroderma pigmentosum group D (XPD) family DEAD-like helicases; ... |
451-637 |
3.95e-30 |
|
C-terminal helicase domain of xeroderma pigmentosum group D (XPD) family DEAD-like helicases; The xeroderma pigmentosum group D (XPD)-like family members are DEAD-box helicases belonging to superfamily (SF)2. This family includes DDX11 (also called ChlR1), a protein involved in maintaining chromosome transmission fidelity and genome stability, the TFIIH basal transcription factor complex XPD subunit, and FANCJ (also known as BRIP1), a DNA helicase required for the maintenance of chromosomal stability. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350175 [Multi-domain] Cd Length: 159 Bit Score: 116.16 E-value: 3.95e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 451 ISVTTKFQER-SADMLKLYGERISKLAKNVPNGVLIFFPQRRLMNEAVAiwrrngfirrrgrrlflgkkivfvegtrate 529
Cdd:cd18788 15 QALNSKFQTReDEAVMDELGNLLLELCAVVPDGVLVFFPSYSYMERVVS------------------------------- 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 530 narivdeykkaartdQGAVLFAVFRGRNAEGSNFPYEEARGVFNVGLPYADYHDPLVKAQIGF--FNRKKSRL-GELWYL 606
Cdd:cd18788 64 ---------------RGALLLAVCRGKVSEGIDFSDDLGRAVIMVGIPYPNTKDPILKLKMDDleYLRDKGLLtGEDWYT 128
|
170 180 190
....*....|....*....|....*....|.
gi 1231988176 607 MDAFRAANQAMGRGIRHRDDWCRFYLMDRRY 637
Cdd:cd18788 129 FQAMRAVNQAIGRAIRHKNDYGAIVLLDKRF 159
|
|
| DEAHc_FancJ |
cd17970 |
DEAH-box helicase domain of Fanconi anemia group J protein and similar proteins; Fanconi ... |
90-284 |
7.89e-21 |
|
DEAH-box helicase domain of Fanconi anemia group J protein and similar proteins; Fanconi anemia group J protein (FACJ or FANCJ, also known as BRIP1) is a DNA helicase required for the maintenance of chromosomal stability. It plays a role in the repair of DNA double-strand breaks by homologous recombination dependent on its interaction with BRCA1. FANCJ belongs to the DEAD-box helicase family, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350728 [Multi-domain] Cd Length: 181 Bit Score: 90.48 E-value: 7.89e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 90 EACNGFGKTVCALSSALA-----TGR---------------RIIYATRTHEQVRQVLREieqINKKAGTDFSAVALASRQ 149
Cdd:cd17970 7 ESPTGTGKTLSLLCSTLAwrqslKGKatsegsdgggsgkipKIIYASRTHSQLAQVVRE---LKRTAYKRPRMTILGSRD 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 150 NLCLNQICRSLPQTEAVEACRVLRNSRrcpyksqfsflgsslppvlstrrllnygrtkgicpyylsrkisQDCTVVVAPY 229
Cdd:cd17970 84 HLCIHPVINKLSNQNANEACMALLSGK-------------------------------------------NEADLVFCPY 120
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 1231988176 230 QYIFNESIRATVGLDINGKVLVFDEAHNADKIGQEVLSDTLSErgLDNAVRELEL 284
Cdd:cd17970 121 NYLLDPNIRRSMGLNLKGSVVIFDEAHNIEVRTIILTSGTLSP--LDSFASELGT 173
|
|
| HBB |
pfam06777 |
Helical and beta-bridge domain; HBB is the domain on DEAD-box eukaryotic DNA repair helicases ... |
286-459 |
6.12e-15 |
|
Helical and beta-bridge domain; HBB is the domain on DEAD-box eukaryotic DNA repair helicases (EC:3.6.1.-) that appears to be a unique fold. It's conformation is of alpha-helices 12-16 plus a short beta-bridge to the FeS-cluster domain at the N-terminal. The full-length XPD protein verifies the presence of damage to DNA and allows DNA repair to proceed. XPD is an assembly of several domains to form a doughnut-shaped molecule that is able to separate two DNA strands and scan the DNA for damage. HBB helps to form the overall DNA-clamping architecture. This family represents a conserved region within a number of eukaryotic DNA repair helicases (EC:3.6.1.-).
Pssm-ID: 462008 Cd Length: 190 Bit Score: 73.57 E-value: 6.12e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 286 GVPSVFIGKLTDYLektVREEPVvkPGSQLFKDLTEVLGEDLSFIVESFKPMV---DEIREKRISRGEVPVCYLNGLLNF 362
Cdd:pfam06777 23 GLREAYEARLEDYV---LSEVPV--LPDEILEEAVPGNIRSAEHFLAFLKRLVeygKARREVKIVKSESPRSFLSHLGEF 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 363 LLLVDSSEKESYVAIYRKSaSGLNLVEYrCLDPSLAIKPViEEAHAALIMSGTLSPLDLFTEVLGLsEAETRTYSAIAKP 442
Cdd:pfam06777 98 LLAWLSSDSEDYVFLVSRE-EGPSLEAV-CIDPSKPLRFL-AERLSSLLMSGTLTPLEDYSDLMGL-EAKLKKFPSPFPK 173
|
170
....*....|....*..
gi 1231988176 443 ENVRTYVDISVTTKFQE 459
Cdd:pfam06777 174 ENLIVLFATLVSTYYKG 190
|
|
| DEAHc_XPD-like |
cd17915 |
DEAH-box helicase domain of XPD family DEAD-like helicases; The xeroderma pigmentosum group D ... |
84-273 |
2.71e-11 |
|
DEAH-box helicase domain of XPD family DEAD-like helicases; The xeroderma pigmentosum group D (XPD)-like family members are DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350673 [Multi-domain] Cd Length: 138 Bit Score: 61.68 E-value: 2.71e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 84 GGVLVAEACNGFGKTVCALSSALATGR-----RIIYATRTHEQVRQVLREIEQInkKAGTDFSAVALASRqnlclnqicr 158
Cdd:cd17915 1 GGHVALESPTGSGKTLSLLCSALSYQRefhktKVLYCSRTHSQIEQIIRELRKL--LEKRKIRALALSSR---------- 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 159 slpqteaveacrvlrnsrrcpyksqfsflgsslppvlstrrllnygrtkgicpyylsrkisqDCTVVVAPYQYIFNESIR 238
Cdd:cd17915 69 --------------------------------------------------------------DADIVVLPYPYLLDARIR 86
|
170 180 190
....*....|....*....|....*....|....*
gi 1231988176 239 ATVGLDINGKVLVFDEAHNADKIGQEVLSDTLSER 273
Cdd:cd17915 87 EFIGIDLREQVVIIDEAHNLDERSVIITSGTLSPL 121
|
|
| DEAHc_DDX11_starthere |
cd17968 |
DEAH-box helicase domain of ATP-dependent DNA helicase DDX11; DDX11 (also called ChlR1) ... |
84-257 |
5.55e-05 |
|
DEAH-box helicase domain of ATP-dependent DNA helicase DDX11; DDX11 (also called ChlR1) encodes a protein of the conserved family of Iron-Sulfur (Fe-S) cluster DNA helicases and is thought to function in maintaining chromosome transmission fidelity and genome stability. Mutations in the Chl1 human homologs ChlR1/DDX11 and BACH1/BRIP1/FANCJ collectively result in Warsaw Breakage Syndrome, Fanconi anemia, cell aneuploidy and breast and ovarian cancers. DDX11 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350726 Cd Length: 134 Bit Score: 43.46 E-value: 5.55e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 84 GGVLVAEACNGFGKTVCALSSALATGRRIIYATRTHEQVRQVLREIEQinKKAGTDFSAVALASRQnlclnqicrslPQT 163
Cdd:cd17968 1 GKVGIFESPTGTGKSLSLICGALTWLTKIYYCSRTHSQLAQFVHEVQK--SPFGKDVRLVSLGSRQ-----------PAA 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 164 EaveacrvlrnsrrcpyksqfsflgsslppvlstrrllnygrtkgicpyylsrkisqdctVVVAPYQYIFNESIRATVGL 243
Cdd:cd17968 68 Q-----------------------------------------------------------VVVLPYQMLLHAATRKASGI 88
|
170
....*....|....
gi 1231988176 244 DINGKVLVFDEAHN 257
Cdd:cd17968 89 KLKDQVVIIDEAHN 102
|
|
| DEAHc_XPD |
cd17969 |
DEAH-box helicase domain of TFIIH basal transcription factor complex helicase XPD subunit; ... |
198-271 |
7.78e-04 |
|
DEAH-box helicase domain of TFIIH basal transcription factor complex helicase XPD subunit; TFIIH can be resolved biochemically into a seven subunit core complex containing XPD/Rad3, XPB/Ssl2, p62/Tfb1, p52/Tfb2, p44/Ssl1, p34/Tfb4, and p8/Tfb5 and a three subunit Cdk Activating Kinase (CAK) complex containing CDK7/Kin28, cyclin H/Ccl1, and MAT1/Tfb3. XPD interacts directly with p44, which stimulates XPD helicase activity. XPD/Rad3 also interacts directly with the CAK via its MAT1/Tfb3 subunit inhibiting the helicase activity of XPD. XPD is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350727 [Multi-domain] Cd Length: 157 Bit Score: 40.49 E-value: 7.78e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1231988176 198 RRLLNY-----GRTKGICPYYLSrkiSQDCTVVVAPYQYIFNESIRATVGLDINGK-VLVFDEAHNADKIGQEVLSDTLS 271
Cdd:cd17969 63 RKLMDYyekqtGEKPNFLGLALS---SRHANVVVYSYHYLLDPKIAELVSKELSKKsVVVFDEAHNIDFQSVVITSGTLS 139
|
|
| DEAHc_XPD-like |
cd17915 |
DEAH-box helicase domain of XPD family DEAD-like helicases; The xeroderma pigmentosum group D ... |
402-431 |
2.42e-03 |
|
DEAH-box helicase domain of XPD family DEAD-like helicases; The xeroderma pigmentosum group D (XPD)-like family members are DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350673 [Multi-domain] Cd Length: 138 Bit Score: 38.57 E-value: 2.42e-03
10 20 30
....*....|....*....|....*....|....*
gi 1231988176 402 VIEEAH-----AALIMSGTLSPLDLFTEVLGLSEA 431
Cdd:cd17915 99 IIDEAHnlderSVIITSGTLSPLDIYSKILGIRNM 133
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
224-273 |
3.68e-03 |
|
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.
Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 38.54 E-value: 3.68e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|
gi 1231988176 224 VVVAPYQYIFNESIRATVGLDINGKVLVFDEAHNADKIGQEVLSDTLSER 273
Cdd:cd00046 82 IIIATPDMLLNLLLREDRLFLKDLKLIIVDEAHALLIDSRGALILDLAVR 131
|
|
| |
