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Conserved domains on  [gi|100913204|ref|NP_004390|]
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ATP-dependent DNA helicase DDX11 isoform 2 [Homo sapiens]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 1003081)

DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA; similar to human ATP-dependent DNA helicase DDX11

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
rad3 super family cl36704
DNA repair helicase (rad3); All proteins in this family for which funcitons are known are ...
227-843 1.07e-130

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]


The actual alignment was detected with superfamily member TIGR00604:

Pssm-ID: 273169 [Multi-domain]  Cd Length: 705  Bit Score: 407.57  E-value: 1.07e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  227 TKIYYCSRTHSQLAQFVHEVKK--SPFGK------DVRLVSLGSRQNLCVNEDVKSLGSVQLINDRCVDMQRSRHEKKkg 298
Cdd:TIGR00604  61 RKIIYASRTHSQLEQATEELRKlmSYRTPrigeesPVSGLSLASRKNLCLHPEVSKERQGKVVNGKCIKLTVSKIKEQ-- 138
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  299 aeeekpkRRRQEKQAACPFY-NHEQMGLLRDEALAEVKDMEQLLALGKEARACPYYGSRLAIPAAQLVVLPYQMLLHAAT 377
Cdd:TIGR00604 139 -------RTEKPNVESCEFYeNFDELREVEDLLLSEIMDIEDLVEYGELLGLCPYFATRKMLPFANIVLLPYQYLLDPKI 211
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  378 RQAAGIRLQDQVVIIDEAHNLIDTITGMHSVEVSGSQLCQAHSQLLQYVERYGKRLKAKNLMYLKQILYLLEKFVAVlgg 457
Cdd:TIGR00604 212 RSAVSIELKDSIVIFDEAHNLDNVCISSLSSNLSVRSLKRCSKEIAEYFEKIEERKEVDARKLLDELQKLVEGLKQE--- 288
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  458 NIKQNPNTQSLSQTGTELKTINDFLFQSQIDNINLFKVQRYCEKSMISRKLFGFTERYGAVFSSR--EQPKLAGFQQFLQ 535
Cdd:TIGR00604 289 DLLTDEDIFLANPVLPKEVLPEAVPGNIRIAEIFLHKLSRYLEYLKDALKVLGVVSELPDAFLEHlkEKTFIDRPLRFCS 368
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  536 SlqpRTTEAL--AAPADESQAStlrPASPLMHIQGFLAALTTANQDGRvILSRQGSLSQSTLKFLLLNPAVHFAQVVKEC 613
Cdd:TIGR00604 369 E---RLSNLLreLEITHPEDFS---ALVLLFTFATLVLTYTNGFLEGI-EPYENKTVPNPILKFMCLDPSIALKPLFERV 441
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  614 RAVVIAGGTMQPVSDFRQQLlacaGVEAerVVEFSCGHVIPPDNILPLVICSGISNQPLEFTFQKRELP----------- 682
Cdd:TIGR00604 442 RSVILASGTLSPLDAFPRNL----GFNP--VSQDSPTHILKRENLLTLIVTRGSDQVPLSSTFEIRNDPslvrnlgellv 515
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  683 ---------------------------------------QMIFQEPKSAHQVEQVLLAYSrciQACGQERgqvtGALLLS 723
Cdd:TIGR00604 516 efskiipdgivvffpsysylenivstwkemgileniekkKLIFVETKDAQETSDALERYK---QAVSEGR----GAVLLS 588
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  724 VVGGKMSEGINFSDNLGRCVVMVGMPFPNIRSAELQEKMAYLDQTLPRAPGQappgkALVENLCMKAVNQSIGRAIRHQK 803
Cdd:TIGR00604 589 VAGGKVSEGIDFCDDLGRAVIMVGIPYEYTESRILLARLEFLRDQYPIRENQ-----DFYEFDAMRAVNQAIGRVIRHKD 663
                         650       660       670       680
                  ....*....|....*....|....*....|....*....|
gi 100913204  804 DFASVVLLDQRYARPPVLAKLPAWIRARVEVKATFGPAIA 843
Cdd:TIGR00604 664 DYGSIVLLDKRYARSNKRKKLPKWIQDTIQSSDLNGMAIS 703
 
Name Accession Description Interval E-value
rad3 TIGR00604
DNA repair helicase (rad3); All proteins in this family for which funcitons are known are ...
227-843 1.07e-130

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: 407.57  E-value: 1.07e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  227 TKIYYCSRTHSQLAQFVHEVKK--SPFGK------DVRLVSLGSRQNLCVNEDVKSLGSVQLINDRCVDMQRSRHEKKkg 298
Cdd:TIGR00604  61 RKIIYASRTHSQLEQATEELRKlmSYRTPrigeesPVSGLSLASRKNLCLHPEVSKERQGKVVNGKCIKLTVSKIKEQ-- 138
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  299 aeeekpkRRRQEKQAACPFY-NHEQMGLLRDEALAEVKDMEQLLALGKEARACPYYGSRLAIPAAQLVVLPYQMLLHAAT 377
Cdd:TIGR00604 139 -------RTEKPNVESCEFYeNFDELREVEDLLLSEIMDIEDLVEYGELLGLCPYFATRKMLPFANIVLLPYQYLLDPKI 211
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  378 RQAAGIRLQDQVVIIDEAHNLIDTITGMHSVEVSGSQLCQAHSQLLQYVERYGKRLKAKNLMYLKQILYLLEKFVAVlgg 457
Cdd:TIGR00604 212 RSAVSIELKDSIVIFDEAHNLDNVCISSLSSNLSVRSLKRCSKEIAEYFEKIEERKEVDARKLLDELQKLVEGLKQE--- 288
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  458 NIKQNPNTQSLSQTGTELKTINDFLFQSQIDNINLFKVQRYCEKSMISRKLFGFTERYGAVFSSR--EQPKLAGFQQFLQ 535
Cdd:TIGR00604 289 DLLTDEDIFLANPVLPKEVLPEAVPGNIRIAEIFLHKLSRYLEYLKDALKVLGVVSELPDAFLEHlkEKTFIDRPLRFCS 368
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  536 SlqpRTTEAL--AAPADESQAStlrPASPLMHIQGFLAALTTANQDGRvILSRQGSLSQSTLKFLLLNPAVHFAQVVKEC 613
Cdd:TIGR00604 369 E---RLSNLLreLEITHPEDFS---ALVLLFTFATLVLTYTNGFLEGI-EPYENKTVPNPILKFMCLDPSIALKPLFERV 441
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  614 RAVVIAGGTMQPVSDFRQQLlacaGVEAerVVEFSCGHVIPPDNILPLVICSGISNQPLEFTFQKRELP----------- 682
Cdd:TIGR00604 442 RSVILASGTLSPLDAFPRNL----GFNP--VSQDSPTHILKRENLLTLIVTRGSDQVPLSSTFEIRNDPslvrnlgellv 515
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  683 ---------------------------------------QMIFQEPKSAHQVEQVLLAYSrciQACGQERgqvtGALLLS 723
Cdd:TIGR00604 516 efskiipdgivvffpsysylenivstwkemgileniekkKLIFVETKDAQETSDALERYK---QAVSEGR----GAVLLS 588
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  724 VVGGKMSEGINFSDNLGRCVVMVGMPFPNIRSAELQEKMAYLDQTLPRAPGQappgkALVENLCMKAVNQSIGRAIRHQK 803
Cdd:TIGR00604 589 VAGGKVSEGIDFCDDLGRAVIMVGIPYEYTESRILLARLEFLRDQYPIRENQ-----DFYEFDAMRAVNQAIGRVIRHKD 663
                         650       660       670       680
                  ....*....|....*....|....*....|....*....|
gi 100913204  804 DFASVVLLDQRYARPPVLAKLPAWIRARVEVKATFGPAIA 843
Cdd:TIGR00604 664 DYGSIVLLDKRYARSNKRKKLPKWIQDTIQSSDLNGMAIS 703
DEXDc2 smart00488
DEAD-like helicases superfamily;
11-437 4.11e-102

DEAD-like helicases superfamily;


Pssm-ID: 214693 [Multi-domain]  Cd Length: 289  Bit Score: 318.17  E-value: 4.11e-102
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204    11 IHFPFPFTPYSIQEDFMAELYRVLEAGKIGIFESPTGTGKSLSLICGALSWLRDFEQKKreeearlletgtgplhdekde 90
Cdd:smart00488   1 LLFYFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERI--------------------- 59
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204    91 slclssscegaagtprPAGEPAWVTQFVqkkeerdlvdrlkaeqarrKQREERLQQLQHRVQLKyaakrlrqeeeerenl 170
Cdd:smart00488  60 ----------------QKIKLIYLSRTV-------------------SEIEKRLEELRKLMQKV---------------- 88
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204   171 lrlsremletgpeaerleqlesgeeelvlaEYESDEEkkvasrvdededdleeehitkiyycsrtHSQLAQFVHEVKKsp 250
Cdd:smart00488  89 ------------------------------EYESDEE----------------------------SEKQAQLLHELGR-- 108
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204   251 FGKDVRLVSLGSRQNLCVNEDVKSLGSVQLIND-RCVDMQRSRHEKKkgaeeekpkRRRQEKQAACPFYNHEQMGLLRDE 329
Cdd:smart00488 109 EKPKVLGLSLTSRKNLCLNPEVRTLKQNGLVVDeVCRSLTASKARKY---------RYENPKVERCPFYENTEFLLVRDL 179
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204   330 ALAEVKDMEQLLALGKEARACPYYGSRLAIPAAQLVVLPYQMLLHAATRQAAGIRLQDQVVIIDEAHNLIDTITGMHSVE 409
Cdd:smart00488 180 LPAEVYDIEDLLELGKRLGGCPYFASRKAIEFANVVVLPYQYLLDPKIRQALSIELKDSIVIFDEAHNLDNVCISALSSE 259
                          410       420       430
                   ....*....|....*....|....*....|
gi 100913204   410 VSGSQLCQAHSQLLQYVERYGK--RLKAKN 437
Cdd:smart00488 260 LSRRSLERAHKNIKKYFERIEKirENDAKR 289
DEAD_2 pfam06733
DEAD_2; This represents a conserved region within a number of RAD3-like DNA-binding helicases ...
231-415 6.59e-72

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: 233.31  E-value: 6.59e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  231 YCSRTHSQLAQFVHEVKKSPFGKDVRLVSLGSRQNLCVNEDVKSLGSVQLINDRCVDMQRSRHEkkkgaeeekpkrrrqe 310
Cdd:pfam06733   1 YCSRTHSQLEQVVKELRRLPYYKKIRGLILGSRKNLCINPEVLKLKKGNLVNERCRELVKSKAR---------------- 64
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  311 kqAACPFY-NHEQMGLLRDEALAEVKDMEQLLALGKEARACPYYGSRLAIPAAQLVVLPYQMLLHAATRQAAGIRLQDQV 389
Cdd:pfam06733  65 --GSCPFYnNLEDLLKLRDLLGDEVMDIEDLVELGEKLGICPYYLSRELIPDADIIILPYNYLLDPKIRESLSINLKNSI 142
                         170       180
                  ....*....|....*....|....*.
gi 100913204  390 VIIDEAHNLIDTITGMHSVEVSGSQL 415
Cdd:pfam06733 143 VIFDEAHNIEDVCIESASFSISRSQL 168
SF2_C_XPD cd18788
C-terminal helicase domain of xeroderma pigmentosum group D (XPD) family DEAD-like helicases; ...
656-815 1.52e-46

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: 163.54  E-value: 1.52e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 656 DNILPLVICSGISNQPLEFTFQKRELPQMIfqepksaHQVEQVLLAYSRCIQAcG----------QERGQVTGALLLSVV 725
Cdd:cd18788    1 DQVCPGIVGRGPDQQALNSKFQTREDEAVM-------DELGNLLLELCAVVPD-GvlvffpsysyMERVVSRGALLLAVC 72
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 726 GGKMSEGINFSDNLGRCVVMVGMPFPNIRSAELQEKMAYLDqtLPRAPGQaPPGKALVENLCMKAVNQSIGRAIRHQKDF 805
Cdd:cd18788   73 RGKVSEGIDFSDDLGRAVIMVGIPYPNTKDPILKLKMDDLE--YLRDKGL-LTGEDWYTFQAMRAVNQAIGRAIRHKNDY 149
                        170
                 ....*....|
gi 100913204 806 ASVVLLDQRY 815
Cdd:cd18788  150 GAIVLLDKRF 159
DinG COG1199
Rad3-related DNA helicase DinG [Replication, recombination and repair];
347-838 7.46e-21

Rad3-related DNA helicase DinG [Replication, recombination and repair];


Pssm-ID: 440812 [Multi-domain]  Cd Length: 629  Bit Score: 97.69  E-value: 7.46e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 347 ARACPYYGSRLAIPAAQLVVLPYQMLL-HAATRQAagIRLQDQVVIIDEAHNLIDTITGMHSVEVSGSQLcqahSQLLQY 425
Cdd:COG1199  173 YGVCPYELARRLAREADVVVVNHHLLFaDLALGEE--LLPEDDVLIIDEAHNLPDRARDMFSAELSSRSL----LRLLRE 246
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 426 VERYGKRLKAKNLMY-LKQILYLLEKFVAVLGGNIKQNPNTQSLSQTGTELKTINDFLFQSqidninLFKVQRYCEKSMi 504
Cdd:COG1199  247 LRKLGLRPGLKKLLDlLERLREALDDLFLALEEEEELRLALGELPDEPEELLEALDALRDA------LEALAEALEEEL- 319
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 505 srklfgfterygavfssREQPKLAGFQQFLQSLQPRTTEALAAPADEsqastlrpasplmhiqGFLAALTTANQDGRVIL 584
Cdd:COG1199  320 -----------------ERLAELDALLERLEELLFALARFLRIAEDE----------------GYVRWLEREGGDVRLHA 366
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 585 SrqgslsqstlkflLLNPAVHFAQVV-KECRAVVIAGGTMQ---PVSDFRQQLlacaGVEAErVVEFSCGHVIPPDNILP 660
Cdd:COG1199  367 A-------------PLDPADLLRELLfSRARSVVLTSATLSvggPFDYFARRL----GLDED-ARTLSLPSPFDYENQAL 428
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 661 LVICSGIS--NQPLEFTFQK-RELPQMIFQEPK-------SAHQVEQVllaYSRCIQACG-----QERGQVT-------- 717
Cdd:COG1199  429 LYVPRDLPrpSDRDGYLEAIaEAIAELLEASGGntlvlftSYRALEQV---AELLRERLDipvlvQGDGSREallerfre 505
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 718 --GALLLSvvGGKMSEGINFSDNLGRCVVMVGMPFPNIRSAELQEKMAYLDQ---------TLPRApgqappgkalvenl 786
Cdd:COG1199  506 ggNSVLVG--TGSFWEGVDLPGDALSLVIIVKLPFPPPDDPVLEARREALEArggngfmyaYLPPA-------------- 569
                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 100913204 787 cMKAVNQSIGRAIRHQKDFASVVLLDQRYARPPV----LAKLPAWIRARVEVKATF 838
Cdd:COG1199  570 -VIKLKQGAGRLIRSEEDRGVVVLLDRRLLTKRYgkrfLDSLPPFRRTRPEELRAF 624
 
Name Accession Description Interval E-value
rad3 TIGR00604
DNA repair helicase (rad3); All proteins in this family for which funcitons are known are ...
227-843 1.07e-130

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: 407.57  E-value: 1.07e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  227 TKIYYCSRTHSQLAQFVHEVKK--SPFGK------DVRLVSLGSRQNLCVNEDVKSLGSVQLINDRCVDMQRSRHEKKkg 298
Cdd:TIGR00604  61 RKIIYASRTHSQLEQATEELRKlmSYRTPrigeesPVSGLSLASRKNLCLHPEVSKERQGKVVNGKCIKLTVSKIKEQ-- 138
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  299 aeeekpkRRRQEKQAACPFY-NHEQMGLLRDEALAEVKDMEQLLALGKEARACPYYGSRLAIPAAQLVVLPYQMLLHAAT 377
Cdd:TIGR00604 139 -------RTEKPNVESCEFYeNFDELREVEDLLLSEIMDIEDLVEYGELLGLCPYFATRKMLPFANIVLLPYQYLLDPKI 211
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  378 RQAAGIRLQDQVVIIDEAHNLIDTITGMHSVEVSGSQLCQAHSQLLQYVERYGKRLKAKNLMYLKQILYLLEKFVAVlgg 457
Cdd:TIGR00604 212 RSAVSIELKDSIVIFDEAHNLDNVCISSLSSNLSVRSLKRCSKEIAEYFEKIEERKEVDARKLLDELQKLVEGLKQE--- 288
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  458 NIKQNPNTQSLSQTGTELKTINDFLFQSQIDNINLFKVQRYCEKSMISRKLFGFTERYGAVFSSR--EQPKLAGFQQFLQ 535
Cdd:TIGR00604 289 DLLTDEDIFLANPVLPKEVLPEAVPGNIRIAEIFLHKLSRYLEYLKDALKVLGVVSELPDAFLEHlkEKTFIDRPLRFCS 368
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  536 SlqpRTTEAL--AAPADESQAStlrPASPLMHIQGFLAALTTANQDGRvILSRQGSLSQSTLKFLLLNPAVHFAQVVKEC 613
Cdd:TIGR00604 369 E---RLSNLLreLEITHPEDFS---ALVLLFTFATLVLTYTNGFLEGI-EPYENKTVPNPILKFMCLDPSIALKPLFERV 441
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  614 RAVVIAGGTMQPVSDFRQQLlacaGVEAerVVEFSCGHVIPPDNILPLVICSGISNQPLEFTFQKRELP----------- 682
Cdd:TIGR00604 442 RSVILASGTLSPLDAFPRNL----GFNP--VSQDSPTHILKRENLLTLIVTRGSDQVPLSSTFEIRNDPslvrnlgellv 515
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  683 ---------------------------------------QMIFQEPKSAHQVEQVLLAYSrciQACGQERgqvtGALLLS 723
Cdd:TIGR00604 516 efskiipdgivvffpsysylenivstwkemgileniekkKLIFVETKDAQETSDALERYK---QAVSEGR----GAVLLS 588
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  724 VVGGKMSEGINFSDNLGRCVVMVGMPFPNIRSAELQEKMAYLDQTLPRAPGQappgkALVENLCMKAVNQSIGRAIRHQK 803
Cdd:TIGR00604 589 VAGGKVSEGIDFCDDLGRAVIMVGIPYEYTESRILLARLEFLRDQYPIRENQ-----DFYEFDAMRAVNQAIGRVIRHKD 663
                         650       660       670       680
                  ....*....|....*....|....*....|....*....|
gi 100913204  804 DFASVVLLDQRYARPPVLAKLPAWIRARVEVKATFGPAIA 843
Cdd:TIGR00604 664 DYGSIVLLDKRYARSNKRKKLPKWIQDTIQSSDLNGMAIS 703
DEXDc2 smart00488
DEAD-like helicases superfamily;
11-437 4.11e-102

DEAD-like helicases superfamily;


Pssm-ID: 214693 [Multi-domain]  Cd Length: 289  Bit Score: 318.17  E-value: 4.11e-102
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204    11 IHFPFPFTPYSIQEDFMAELYRVLEAGKIGIFESPTGTGKSLSLICGALSWLRDFEQKKreeearlletgtgplhdekde 90
Cdd:smart00488   1 LLFYFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERI--------------------- 59
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204    91 slclssscegaagtprPAGEPAWVTQFVqkkeerdlvdrlkaeqarrKQREERLQQLQHRVQLKyaakrlrqeeeerenl 170
Cdd:smart00488  60 ----------------QKIKLIYLSRTV-------------------SEIEKRLEELRKLMQKV---------------- 88
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204   171 lrlsremletgpeaerleqlesgeeelvlaEYESDEEkkvasrvdededdleeehitkiyycsrtHSQLAQFVHEVKKsp 250
Cdd:smart00488  89 ------------------------------EYESDEE----------------------------SEKQAQLLHELGR-- 108
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204   251 FGKDVRLVSLGSRQNLCVNEDVKSLGSVQLIND-RCVDMQRSRHEKKkgaeeekpkRRRQEKQAACPFYNHEQMGLLRDE 329
Cdd:smart00488 109 EKPKVLGLSLTSRKNLCLNPEVRTLKQNGLVVDeVCRSLTASKARKY---------RYENPKVERCPFYENTEFLLVRDL 179
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204   330 ALAEVKDMEQLLALGKEARACPYYGSRLAIPAAQLVVLPYQMLLHAATRQAAGIRLQDQVVIIDEAHNLIDTITGMHSVE 409
Cdd:smart00488 180 LPAEVYDIEDLLELGKRLGGCPYFASRKAIEFANVVVLPYQYLLDPKIRQALSIELKDSIVIFDEAHNLDNVCISALSSE 259
                          410       420       430
                   ....*....|....*....|....*....|
gi 100913204   410 VSGSQLCQAHSQLLQYVERYGK--RLKAKN 437
Cdd:smart00488 260 LSRRSLERAHKNIKKYFERIEKirENDAKR 289
DEAD_2 pfam06733
DEAD_2; This represents a conserved region within a number of RAD3-like DNA-binding helicases ...
231-415 6.59e-72

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: 233.31  E-value: 6.59e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  231 YCSRTHSQLAQFVHEVKKSPFGKDVRLVSLGSRQNLCVNEDVKSLGSVQLINDRCVDMQRSRHEkkkgaeeekpkrrrqe 310
Cdd:pfam06733   1 YCSRTHSQLEQVVKELRRLPYYKKIRGLILGSRKNLCINPEVLKLKKGNLVNERCRELVKSKAR---------------- 64
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  311 kqAACPFY-NHEQMGLLRDEALAEVKDMEQLLALGKEARACPYYGSRLAIPAAQLVVLPYQMLLHAATRQAAGIRLQDQV 389
Cdd:pfam06733  65 --GSCPFYnNLEDLLKLRDLLGDEVMDIEDLVELGEKLGICPYYLSRELIPDADIIILPYNYLLDPKIRESLSINLKNSI 142
                         170       180
                  ....*....|....*....|....*.
gi 100913204  390 VIIDEAHNLIDTITGMHSVEVSGSQL 415
Cdd:pfam06733 143 VIFDEAHNIEDVCIESASFSISRSQL 168
HELICc2 smart00491
helicase superfamily c-terminal domain;
680-817 4.85e-48

helicase superfamily c-terminal domain;


Pssm-ID: 214694 [Multi-domain]  Cd Length: 142  Bit Score: 167.07  E-value: 4.85e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204   680 ELPQMIFQEPKSAHQVEQVLLAYSRCIQACGqergqvtgALLLSVVGGKMSEGINFSDNLGRCVVMVGMPFPNIRSAELQ 759
Cdd:smart00491  18 EINKPVFIEGKDSGETEELLEKYSAACEARG--------ALLLAVARGKVSEGIDFPDDLGRAVIIVGIPFPNPDSPILR 89
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 100913204   760 EKMAYLDQTlprapGQAPPGKALVENLCMKAVNQSIGRAIRHQKDFASVVLLDQRYAR 817
Cdd:smart00491  90 ARLEYLDEK-----GGIRPFDEVYLFDAMRALAQAIGRAIRHKNDYGVVVLLDKRYAR 142
SF2_C_XPD cd18788
C-terminal helicase domain of xeroderma pigmentosum group D (XPD) family DEAD-like helicases; ...
656-815 1.52e-46

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: 163.54  E-value: 1.52e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 656 DNILPLVICSGISNQPLEFTFQKRELPQMIfqepksaHQVEQVLLAYSRCIQAcG----------QERGQVTGALLLSVV 725
Cdd:cd18788    1 DQVCPGIVGRGPDQQALNSKFQTREDEAVM-------DELGNLLLELCAVVPD-GvlvffpsysyMERVVSRGALLLAVC 72
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 726 GGKMSEGINFSDNLGRCVVMVGMPFPNIRSAELQEKMAYLDqtLPRAPGQaPPGKALVENLCMKAVNQSIGRAIRHQKDF 805
Cdd:cd18788   73 RGKVSEGIDFSDDLGRAVIMVGIPYPNTKDPILKLKMDDLE--YLRDKGL-LTGEDWYTFQAMRAVNQAIGRAIRHKNDY 149
                        170
                 ....*....|
gi 100913204 806 ASVVLLDQRY 815
Cdd:cd18788  150 GAIVLLDKRF 159
Helicase_C_2 pfam13307
Helicase C-terminal domain; This domain is found at the C-terminus of DEAD-box helicases.
680-829 4.62e-41

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: 148.09  E-value: 4.62e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  680 ELPQMIFQEPKSAhQVEQVLLAYSRCiqacgqergqVTGALLLSVVGGKMSEGINFSDNLGRCVVMVGMPFPNIRSAELQ 759
Cdd:pfam13307  34 EKGIEIFVQPGEG-SREKLLEEFKKK----------GKGAVLFGVCGGSFSEGIDFPGDLLRAVIIVGLPFPNPDDPVVE 102
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204  760 EKMAYLDQTLPRapgqapPGKALVENLCMKAVNQSIGRAIRHQKDFASVVLLDQRYARPPVLAKLPAWIR 829
Cdd:pfam13307 103 AKREYLDSKGGN------PFNEWYLPQAVRAVNQAIGRLIRHENDYGAIVLLDSRFLTKRYGKLLPKWLP 166
DEAHc_DDX11_starthere cd17968
DEAH-box helicase domain of ATP-dependent DNA helicase DDX11; DDX11 (also called ChlR1) ...
226-399 7.27e-34

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: 126.67  E-value: 7.27e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 226 ITKIYYCSRTHSQLAQFVHEVKKSPFGKDVRLVSLGSRQnlcvnedvkslgsvqlindrcvdmqrsrhekkkgaeeekpk 305
Cdd:cd17968   26 LTKIYYCSRTHSQLAQFVHEVQKSPFGKDVRLVSLGSRQ----------------------------------------- 64
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 306 rrrqekqaacpfynheqmgllrdealaevkdmeqllalgkearacpyygsrlaiPAAQLVVLPYQMLLHAATRQAAGIRL 385
Cdd:cd17968   65 ------------------------------------------------------PAAQVVVLPYQMLLHAATRKASGIKL 90
                        170
                 ....*....|....
gi 100913204 386 QDQVVIIDEAHNLI 399
Cdd:cd17968   91 KDQVVIIDEAHNLI 104
DEAHc_XPD-like cd17915
DEAH-box helicase domain of XPD family DEAD-like helicases; The xeroderma pigmentosum group D ...
225-399 2.94e-21

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: 90.57  E-value: 2.94e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 225 HITKIYYCSRTHSQLAQFVHEVKKSPFGKDVRLVSLGSRqnlcvnedvkslgsvqlindrcvdmqrsrhekkkgaeeekp 304
Cdd:cd17915   30 HKTKVLYCSRTHSQIEQIIRELRKLLEKRKIRALALSSR----------------------------------------- 68
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 305 krrrqekqaacpfynheqmgllrdealaevkdmeqllalgkearacpyygsrlaipAAQLVVLPYQMLLHAATRQAAGIR 384
Cdd:cd17915   69 --------------------------------------------------------DADIVVLPYPYLLDARIREFIGID 92
                        170
                 ....*....|....*
gi 100913204 385 LQDQVVIIDEAHNLI 399
Cdd:cd17915   93 LREQVVIIDEAHNLD 107
DinG COG1199
Rad3-related DNA helicase DinG [Replication, recombination and repair];
347-838 7.46e-21

Rad3-related DNA helicase DinG [Replication, recombination and repair];


Pssm-ID: 440812 [Multi-domain]  Cd Length: 629  Bit Score: 97.69  E-value: 7.46e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 347 ARACPYYGSRLAIPAAQLVVLPYQMLL-HAATRQAagIRLQDQVVIIDEAHNLIDTITGMHSVEVSGSQLcqahSQLLQY 425
Cdd:COG1199  173 YGVCPYELARRLAREADVVVVNHHLLFaDLALGEE--LLPEDDVLIIDEAHNLPDRARDMFSAELSSRSL----LRLLRE 246
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 426 VERYGKRLKAKNLMY-LKQILYLLEKFVAVLGGNIKQNPNTQSLSQTGTELKTINDFLFQSqidninLFKVQRYCEKSMi 504
Cdd:COG1199  247 LRKLGLRPGLKKLLDlLERLREALDDLFLALEEEEELRLALGELPDEPEELLEALDALRDA------LEALAEALEEEL- 319
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 505 srklfgfterygavfssREQPKLAGFQQFLQSLQPRTTEALAAPADEsqastlrpasplmhiqGFLAALTTANQDGRVIL 584
Cdd:COG1199  320 -----------------ERLAELDALLERLEELLFALARFLRIAEDE----------------GYVRWLEREGGDVRLHA 366
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 585 SrqgslsqstlkflLLNPAVHFAQVV-KECRAVVIAGGTMQ---PVSDFRQQLlacaGVEAErVVEFSCGHVIPPDNILP 660
Cdd:COG1199  367 A-------------PLDPADLLRELLfSRARSVVLTSATLSvggPFDYFARRL----GLDED-ARTLSLPSPFDYENQAL 428
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 661 LVICSGIS--NQPLEFTFQK-RELPQMIFQEPK-------SAHQVEQVllaYSRCIQACG-----QERGQVT-------- 717
Cdd:COG1199  429 LYVPRDLPrpSDRDGYLEAIaEAIAELLEASGGntlvlftSYRALEQV---AELLRERLDipvlvQGDGSREallerfre 505
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 718 --GALLLSvvGGKMSEGINFSDNLGRCVVMVGMPFPNIRSAELQEKMAYLDQ---------TLPRApgqappgkalvenl 786
Cdd:COG1199  506 ggNSVLVG--TGSFWEGVDLPGDALSLVIIVKLPFPPPDDPVLEARREALEArggngfmyaYLPPA-------------- 569
                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 100913204 787 cMKAVNQSIGRAIRHQKDFASVVLLDQRYARPPV----LAKLPAWIRARVEVKATF 838
Cdd:COG1199  570 -VIKLKQGAGRLIRSEEDRGVVVLLDRRLLTKRYgkrfLDSLPPFRRTRPEELRAF 624
DEAHc_FancJ cd17970
DEAH-box helicase domain of Fanconi anemia group J protein and similar proteins; Fanconi ...
226-398 2.28e-20

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: 89.33  E-value: 2.28e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 226 ITKIYYCSRTHSQLAQFVHEVKKSPFgKDVRLVSLGSRQNLCVNEDVKSLGSvqlindrcvdmqrsrhekkkgaeeekpk 305
Cdd:cd17970   46 IPKIIYASRTHSQLAQVVRELKRTAY-KRPRMTILGSRDHLCIHPVINKLSN---------------------------- 96
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913204 306 rrrQEKQAACpfynheqMGLLRDEALAEvkdmeqllalgkearacpyygsrlaipaaqLVVLPYQMLLHAATRQAAGIRL 385
Cdd:cd17970   97 ---QNANEAC-------MALLSGKNEAD------------------------------LVFCPYNYLLDPNIRRSMGLNL 136
                        170
                 ....*....|...
gi 100913204 386 QDQVVIIDEAHNL 398
Cdd:cd17970  137 KGSVVIFDEAHNI 149
DEAHc_DDX11_starthere cd17968
DEAH-box helicase domain of ATP-dependent DNA helicase DDX11; DDX11 (also called ChlR1) ...
613-642 6.45e-12

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: 63.88  E-value: 6.45e-12
                         10        20        30
                 ....*....|....*....|....*....|
gi 100913204 613 CRAVVIAGGTMQPVSDFRQQLLACAGVEAE 642
Cdd:cd17968  105 CRAVIIAGGTMQPVADFKEQLLFSAGVTPE 134
DEAHc_XPD-like cd17915
DEAH-box helicase domain of XPD family DEAD-like helicases; The xeroderma pigmentosum group D ...
612-642 4.92e-04

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: 41.26  E-value: 4.92e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 100913204 612 ECRAVVIAGGTMQPVSDFRQQLL-ACAGVEAE 642
Cdd:cd17915  107 DERSVIITSGTLSPLDIYSKILGiRNMLVLAV 138
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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