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Conserved domains on  [gi|1958805712|ref|XP_038940697|]
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probable ATP-dependent RNA helicase DDX11 isoform X5 [Rattus norvegicus]

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 ...
 3-628 5.15e-145

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: 437.61  E-value: 5.15e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712   3 LCVNEDVKSLGSVHLMNDRCVDMQRRKHKKmrigedkpKRRRQKMQASCPFY-NHEQMELLRDEILLEVKDMEQLVALGK 81
Cdd:TIGR00604 108 LCLHPEVSKERQGKVVNGKCIKLTVSKIKE--------QRTEKPNVESCEFYeNFDELREVEDLLLSEIMDIEDLVEYGE 179

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712  82 EAQACPYYGSRFAIPAAQLVVLPYPMLLHAATRQAAGIRLQGQVVIIDEAHNLIDTITNIHSTEVNGSQLCQAHSQLLQY 161
Cdd:TIGR00604 180 LLGLCPYFATRKMLPFANIVLLPYQYLLDPKIRSAVSIELKDSIVIFDEAHNLDNVCISSLSSNLSVRSLKRCSKEIAEY 259

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 162 MERYRKRLKAKNLM----YIKQILYLLDKFVAVLGGNVKQNPSTQSLPQTGSELQSINdflfqsqVDNINLFKVQRYLEK 237
Cdd:TIGR00604 260 FEKIEERKEVDARKlldeLQKLVEGLKQEDLLTDEDIFLANPVLPKEVLPEAVPGNIR-------IAEIFLHKLSRYLEY 332

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 238 SMLSRKLFGFT-ECFGVVLPSLSDSEENRGLGGF-----QQFLKSLQSGPPEDsleegqavaLRPASPLMHIEAFLEALT 311
Cdd:TIGR00604 333 LKDALKVLGVVsELPDAFLEHLKEKTFIDRPLRFcserlSNLLRELEITHPED---------FSALVLLFTFATLVLTYT 403

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 312 TANQDGRVIVNRQgSVGQSSLKFLLLNPAVHFAQVVKECRALVIAGGTMQPVSDFREQLLACSGVEASRvvefscGHVIP 391
Cdd:TIGR00604 404 NGFLEGIEPYENK-TVPNPILKFMCLDPSIALKPLFERVRSVILASGTLSPLDAFPRNLGFNPVSQDSP------THILK 476

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 392 PDNILPLIICSGPSNQQLEFTYQRRELPQMMEETGRILCNLCNVVPGGMVCFLPSYEYLRQVHAHWDKTGLLARLSVRKK 471
Cdd:TIGR00604 477 RENLLTLIVTRGSDQVPLSSTFEIRNDPSLVRNLGELLVEFSKIIPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKL 556

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 472 IFQEPKRASQVEQVLTAYStciASCshSEGHltGALLLSVVGGKMSEGINFSDDLGRCVVMVGMPYPNIKSPELQEKMAY 551
Cdd:TIGR00604 557 IFVETKDAQETSDALERYK---QAV--SEGR--GAVLLSVAGGKVSEGIDFCDDLGRAVIMVGIPYEYTESRILLARLEF 629

                         570       580       590       600       610       620       630
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958805712 552 LDQTIPRTHGQPppgtvLIENLCMKAINQSIGRAIRHQKDFASIVLLDHRYARPSILAKLPAWIRDRVEVKATFGPA 628
Cdd:TIGR00604 630 LRDQYPIRENQD-----FYEFDAMRAVNQAIGRVIRHKDDYGSIVLLDKRYARSNKRKKLPKWIQDTIQSSDLNGMA 701
 
Name Accession Description Interval E-value
rad3 TIGR00604
DNA repair helicase (rad3); All proteins in this family for which funcitons are known are ...
 3-628 5.15e-145

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: 437.61  E-value: 5.15e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712   3 LCVNEDVKSLGSVHLMNDRCVDMQRRKHKKmrigedkpKRRRQKMQASCPFY-NHEQMELLRDEILLEVKDMEQLVALGK 81
Cdd:TIGR00604 108 LCLHPEVSKERQGKVVNGKCIKLTVSKIKE--------QRTEKPNVESCEFYeNFDELREVEDLLLSEIMDIEDLVEYGE 179

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712  82 EAQACPYYGSRFAIPAAQLVVLPYPMLLHAATRQAAGIRLQGQVVIIDEAHNLIDTITNIHSTEVNGSQLCQAHSQLLQY 161
Cdd:TIGR00604 180 LLGLCPYFATRKMLPFANIVLLPYQYLLDPKIRSAVSIELKDSIVIFDEAHNLDNVCISSLSSNLSVRSLKRCSKEIAEY 259

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 162 MERYRKRLKAKNLM----YIKQILYLLDKFVAVLGGNVKQNPSTQSLPQTGSELQSINdflfqsqVDNINLFKVQRYLEK 237
Cdd:TIGR00604 260 FEKIEERKEVDARKlldeLQKLVEGLKQEDLLTDEDIFLANPVLPKEVLPEAVPGNIR-------IAEIFLHKLSRYLEY 332

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 238 SMLSRKLFGFT-ECFGVVLPSLSDSEENRGLGGF-----QQFLKSLQSGPPEDsleegqavaLRPASPLMHIEAFLEALT 311
Cdd:TIGR00604 333 LKDALKVLGVVsELPDAFLEHLKEKTFIDRPLRFcserlSNLLRELEITHPED---------FSALVLLFTFATLVLTYT 403

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 312 TANQDGRVIVNRQgSVGQSSLKFLLLNPAVHFAQVVKECRALVIAGGTMQPVSDFREQLLACSGVEASRvvefscGHVIP 391
Cdd:TIGR00604 404 NGFLEGIEPYENK-TVPNPILKFMCLDPSIALKPLFERVRSVILASGTLSPLDAFPRNLGFNPVSQDSP------THILK 476

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 392 PDNILPLIICSGPSNQQLEFTYQRRELPQMMEETGRILCNLCNVVPGGMVCFLPSYEYLRQVHAHWDKTGLLARLSVRKK 471
Cdd:TIGR00604 477 RENLLTLIVTRGSDQVPLSSTFEIRNDPSLVRNLGELLVEFSKIIPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKL 556

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 472 IFQEPKRASQVEQVLTAYStciASCshSEGHltGALLLSVVGGKMSEGINFSDDLGRCVVMVGMPYPNIKSPELQEKMAY 551
Cdd:TIGR00604 557 IFVETKDAQETSDALERYK---QAV--SEGR--GAVLLSVAGGKVSEGIDFCDDLGRAVIMVGIPYEYTESRILLARLEF 629

                         570       580       590       600       610       620       630
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958805712 552 LDQTIPRTHGQPppgtvLIENLCMKAINQSIGRAIRHQKDFASIVLLDHRYARPSILAKLPAWIRDRVEVKATFGPA 628
Cdd:TIGR00604 630 LRDQYPIRENQD-----FYEFDAMRAVNQAIGRVIRHKDDYGSIVLLDKRYARSNKRKKLPKWIQDTIQSSDLNGMA 701
SF2_C_XPD cd18788
C-terminal helicase domain of xeroderma pigmentosum group D (XPD) family DEAD-like helicases; ...
 393-602 1.94e-66

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: 214.78  E-value: 1.94e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 393 DNILPLIICSGPSNQQLEFTYQRRELPQMMEETGRILCNLCNVVPGGMVCFLPSYEYLrqvhahwdktgllarlsvrkki 472
Cdd:cd18788     1 DQVCPGIVGRGPDQQALNSKFQTREDEAVMDELGNLLLELCAVVPDGVLVFFPSYSYM---------------------- 58

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 473 fqepkrasqvEQVLTaystciascshseghlTGALLLSVVGGKMSEGINFSDDLGRCVVMVGMPYPNIKSPELQEKMAYL 552
Cdd:cd18788    59 ----------ERVVS----------------RGALLLAVCRGKVSEGIDFSDDLGRAVIMVGIPYPNTKDPILKLKMDDL 112

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958805712 553 DqtIPRTHGQpPPGTVLIENLCMKAINQSIGRAIRHQKDFASIVLLDHRY 602
Cdd:cd18788   113 E--YLRDKGL-LTGEDWYTFQAMRAVNQAIGRAIRHKNDYGAIVLLDKRF 159
DEXDc2 smart00488
DEAD-like helicases superfamily;
3-173 2.72e-59

DEAD-like helicases superfamily;


Pssm-ID: 214693 [Multi-domain]  Cd Length: 289  Bit Score: 200.68  E-value: 2.72e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712    3 LCVNEDVKSLGSVHLMND-RCVDMQRRKHKkmrigedkPKRRRQKMQASCPFYNHEQMELLRDEILLEVKDMEQLVALGK 81
Cdd:smart00488 124 LCLNPEVRTLKQNGLVVDeVCRSLTASKAR--------KYRYENPKVERCPFYENTEFLLVRDLLPAEVYDIEDLLELGK 195

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712   82 EAQACPYYGSRFAIPAAQLVVLPYPMLLHAATRQAAGIRLQGQVVIIDEAHNLIDTITNIHSTEVNGSQLCQAHSQLLQY 161
Cdd:smart00488 196 RLGGCPYFASRKAIEFANVVVLPYQYLLDPKIRQALSIELKDSIVIFDEAHNLDNVCISALSSELSRRSLERAHKNIKKY 275

                          170
                   ....*....|....
gi 1958805712  162 MERYRK--RLKAKN 173
Cdd:smart00488 276 FERIEKirENDAKR 289
Helicase_C_2 pfam13307
Helicase C-terminal domain; This domain is found at the C-terminus of DEAD-box helicases.
 431-618 3.54e-58

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: 193.16  E-value: 3.54e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 431 NLCNVVPGGMVCFLPSYEYLRQVHAHWDKTGLlarlSVRKKIFQEPKRASqVEQVLTAYSTCiascshseghLTGALLLS 510
Cdd:pfam13307   2 RLLKVIPGGVLVFFPSYSYLEKVAERLKESGL----EKGIEIFVQPGEGS-REKLLEEFKKK----------GKGAVLFG 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 511 VVGGKMSEGINFSDDLGRCVVMVGMPYPNIKSPELQEKMAYLDQTiprthgQPPPGTVLIENLCMKAINQSIGRAIRHQK 590
Cdd:pfam13307  67 VCGGSFSEGIDFPGDLLRAVIIVGLPFPNPDDPVVEAKREYLDSK------GGNPFNEWYLPQAVRAVNQAIGRLIRHEN 140

                         170       180
                  ....*....|....*....|....*...
gi 1958805712 591 DFASIVLLDHRYARPSILAKLPAWIRDR 618
Cdd:pfam13307 141 DYGAIVLLDSRFLTKRYGKLLPKWLPPG 168
DinG COG1199
Rad3-related DNA helicase DinG [Replication, recombination and repair];
83-625 9.50e-29

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


Pssm-ID: 440812 [Multi-domain]  Cd Length: 629  Bit Score: 121.57  E-value: 9.50e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712  83 AQACPYYGSRFAIPAAQLVVLPYPMLL-HAATRQAagiRLQG-QVVIIDEAHNLIDTITNIHSTEVNGSQLcqahSQLLQ 160
Cdd:COG1199   173 YGVCPYELARRLAREADVVVVNHHLLFaDLALGEE---LLPEdDVLIIDEAHNLPDRARDMFSAELSSRSL----LRLLR 245

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 161 YMERYRKRLKAKNLMY-IKQILYLLDKFVAVLGGNVKQNPSTQSLPQTGSELQSindflfqsqvdniNLFKVQRYLEKsm 239
Cdd:COG1199   246 ELRKLGLRPGLKKLLDlLERLREALDDLFLALEEEEELRLALGELPDEPEELLE-------------ALDALRDALEA-- 310

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 240 LSRKLfgftecfgvvlpslsdSEENRGLGGFQQFLKSLQSgppedsleegqavalrpasplmHIEAFLEALTTANQDGRV 319
Cdd:COG1199   311 LAEAL----------------EEELERLAELDALLERLEE----------------------LLFALARFLRIAEDEGYV 352

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 320 -IVNRQGsvGQSSLKFLLLNPAVHFAQVV-KECRALVIAGGTMQ---PVSDFREQLlacsGVEAsRVVEFSCGHVIPPDN 394
Cdd:COG1199   353 rWLEREG--GDVRLHAAPLDPADLLRELLfSRARSVVLTSATLSvggPFDYFARRL----GLDE-DARTLSLPSPFDYEN 425

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 395 ILPLIICSGPSnqqlefTYQRRelPQMMEETGRILCNLCNVVPGGMVCFLPSYEYLRQVHAHwdktgLLARLsvRKKIFQ 474
Cdd:COG1199   426 QALLYVPRDLP------RPSDR--DGYLEAIAEAIAELLEASGGNTLVLFTSYRALEQVAEL-----LRERL--DIPVLV 490

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 475 EPK--RASQVEQvltaystciascsHSEGhlTGALLLSvvGGKMSEGINFSDDLGRCVVMVGMPYPNIKSPELQEKMAYL 552
Cdd:COG1199   491 QGDgsREALLER-------------FREG--GNSVLVG--TGSFWEGVDLPGDALSLVIIVKLPFPPPDDPVLEARREAL 553

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 553 DQTIprthGQP------PPGtvlienlcMKAINQSIGRAIRHQKDFASIVLLDHRYARPS----ILAKLPAWIRDRVEVK 622
Cdd:COG1199   554 EARG----GNGfmyaylPPA--------VIKLKQGAGRLIRSEEDRGVVVLLDRRLLTKRygkrFLDSLPPFRRTRPEEL 621


                  ...
gi 1958805712 623 ATF 625
Cdd:COG1199   622 RAF 624
 
Name Accession Description Interval E-value
rad3 TIGR00604
DNA repair helicase (rad3); All proteins in this family for which funcitons are known are ...
 3-628 5.15e-145

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: 437.61  E-value: 5.15e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712   3 LCVNEDVKSLGSVHLMNDRCVDMQRRKHKKmrigedkpKRRRQKMQASCPFY-NHEQMELLRDEILLEVKDMEQLVALGK 81
Cdd:TIGR00604 108 LCLHPEVSKERQGKVVNGKCIKLTVSKIKE--------QRTEKPNVESCEFYeNFDELREVEDLLLSEIMDIEDLVEYGE 179

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712  82 EAQACPYYGSRFAIPAAQLVVLPYPMLLHAATRQAAGIRLQGQVVIIDEAHNLIDTITNIHSTEVNGSQLCQAHSQLLQY 161
Cdd:TIGR00604 180 LLGLCPYFATRKMLPFANIVLLPYQYLLDPKIRSAVSIELKDSIVIFDEAHNLDNVCISSLSSNLSVRSLKRCSKEIAEY 259

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 162 MERYRKRLKAKNLM----YIKQILYLLDKFVAVLGGNVKQNPSTQSLPQTGSELQSINdflfqsqVDNINLFKVQRYLEK 237
Cdd:TIGR00604 260 FEKIEERKEVDARKlldeLQKLVEGLKQEDLLTDEDIFLANPVLPKEVLPEAVPGNIR-------IAEIFLHKLSRYLEY 332

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 238 SMLSRKLFGFT-ECFGVVLPSLSDSEENRGLGGF-----QQFLKSLQSGPPEDsleegqavaLRPASPLMHIEAFLEALT 311
Cdd:TIGR00604 333 LKDALKVLGVVsELPDAFLEHLKEKTFIDRPLRFcserlSNLLRELEITHPED---------FSALVLLFTFATLVLTYT 403

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 312 TANQDGRVIVNRQgSVGQSSLKFLLLNPAVHFAQVVKECRALVIAGGTMQPVSDFREQLLACSGVEASRvvefscGHVIP 391
Cdd:TIGR00604 404 NGFLEGIEPYENK-TVPNPILKFMCLDPSIALKPLFERVRSVILASGTLSPLDAFPRNLGFNPVSQDSP------THILK 476

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 392 PDNILPLIICSGPSNQQLEFTYQRRELPQMMEETGRILCNLCNVVPGGMVCFLPSYEYLRQVHAHWDKTGLLARLSVRKK 471
Cdd:TIGR00604 477 RENLLTLIVTRGSDQVPLSSTFEIRNDPSLVRNLGELLVEFSKIIPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKL 556

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 472 IFQEPKRASQVEQVLTAYStciASCshSEGHltGALLLSVVGGKMSEGINFSDDLGRCVVMVGMPYPNIKSPELQEKMAY 551
Cdd:TIGR00604 557 IFVETKDAQETSDALERYK---QAV--SEGR--GAVLLSVAGGKVSEGIDFCDDLGRAVIMVGIPYEYTESRILLARLEF 629

                         570       580       590       600       610       620       630
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958805712 552 LDQTIPRTHGQPppgtvLIENLCMKAINQSIGRAIRHQKDFASIVLLDHRYARPSILAKLPAWIRDRVEVKATFGPA 628
Cdd:TIGR00604 630 LRDQYPIRENQD-----FYEFDAMRAVNQAIGRVIRHKDDYGSIVLLDKRYARSNKRKKLPKWIQDTIQSSDLNGMA 701
SF2_C_XPD cd18788
C-terminal helicase domain of xeroderma pigmentosum group D (XPD) family DEAD-like helicases; ...
 393-602 1.94e-66

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: 214.78  E-value: 1.94e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 393 DNILPLIICSGPSNQQLEFTYQRRELPQMMEETGRILCNLCNVVPGGMVCFLPSYEYLrqvhahwdktgllarlsvrkki 472
Cdd:cd18788     1 DQVCPGIVGRGPDQQALNSKFQTREDEAVMDELGNLLLELCAVVPDGVLVFFPSYSYM---------------------- 58

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 473 fqepkrasqvEQVLTaystciascshseghlTGALLLSVVGGKMSEGINFSDDLGRCVVMVGMPYPNIKSPELQEKMAYL 552
Cdd:cd18788    59 ----------ERVVS----------------RGALLLAVCRGKVSEGIDFSDDLGRAVIMVGIPYPNTKDPILKLKMDDL 112

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958805712 553 DqtIPRTHGQpPPGTVLIENLCMKAINQSIGRAIRHQKDFASIVLLDHRY 602
Cdd:cd18788   113 E--YLRDKGL-LTGEDWYTFQAMRAVNQAIGRAIRHKNDYGAIVLLDKRF 159
DEXDc2 smart00488
DEAD-like helicases superfamily;
3-173 2.72e-59

DEAD-like helicases superfamily;


Pssm-ID: 214693 [Multi-domain]  Cd Length: 289  Bit Score: 200.68  E-value: 2.72e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712    3 LCVNEDVKSLGSVHLMND-RCVDMQRRKHKkmrigedkPKRRRQKMQASCPFYNHEQMELLRDEILLEVKDMEQLVALGK 81
Cdd:smart00488 124 LCLNPEVRTLKQNGLVVDeVCRSLTASKAR--------KYRYENPKVERCPFYENTEFLLVRDLLPAEVYDIEDLLELGK 195

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712   82 EAQACPYYGSRFAIPAAQLVVLPYPMLLHAATRQAAGIRLQGQVVIIDEAHNLIDTITNIHSTEVNGSQLCQAHSQLLQY 161
Cdd:smart00488 196 RLGGCPYFASRKAIEFANVVVLPYQYLLDPKIRQALSIELKDSIVIFDEAHNLDNVCISALSSELSRRSLERAHKNIKKY 275

                          170
                   ....*....|....
gi 1958805712  162 MERYRK--RLKAKN 173
Cdd:smart00488 276 FERIEKirENDAKR 289
Helicase_C_2 pfam13307
Helicase C-terminal domain; This domain is found at the C-terminus of DEAD-box helicases.
 431-618 3.54e-58

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: 193.16  E-value: 3.54e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 431 NLCNVVPGGMVCFLPSYEYLRQVHAHWDKTGLlarlSVRKKIFQEPKRASqVEQVLTAYSTCiascshseghLTGALLLS 510
Cdd:pfam13307   2 RLLKVIPGGVLVFFPSYSYLEKVAERLKESGL----EKGIEIFVQPGEGS-REKLLEEFKKK----------GKGAVLFG 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 511 VVGGKMSEGINFSDDLGRCVVMVGMPYPNIKSPELQEKMAYLDQTiprthgQPPPGTVLIENLCMKAINQSIGRAIRHQK 590
Cdd:pfam13307  67 VCGGSFSEGIDFPGDLLRAVIIVGLPFPNPDDPVVEAKREYLDSK------GGNPFNEWYLPQAVRAVNQAIGRLIRHEN 140

                         170       180
                  ....*....|....*....|....*...
gi 1958805712 591 DFASIVLLDHRYARPSILAKLPAWIRDR 618
Cdd:pfam13307 141 DYGAIVLLDSRFLTKRYGKLLPKWLPPG 168
HELICc2 smart00491
helicase superfamily c-terminal domain;
447-604 2.76e-52

helicase superfamily c-terminal domain;


Pssm-ID: 214694 [Multi-domain]  Cd Length: 142  Bit Score: 176.32  E-value: 2.76e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712  447 YEYLRQVHAHWDKTGLLARlsvRKKIFQEPKRASQVEQVLTAYSTCIASCshseghltGALLLSVVGGKMSEGINFSDDL 526
Cdd:smart00491   1 YRYLEQVVEYWKENGILEI---NKPVFIEGKDSGETEELLEKYSAACEAR--------GALLLAVARGKVSEGIDFPDDL 69

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958805712  527 GRCVVMVGMPYPNIKSPELQEKMAYLDQTiprthGQPPPGTVLIENLCMKAINQSIGRAIRHQKDFASIVLLDHRYAR 604
Cdd:smart00491  70 GRAVIIVGIPFPNPDSPILRARLEYLDEK-----GGIRPFDEVYLFDAMRALAQAIGRAIRHKNDYGVVVLLDKRYAR 142
DEAD_2 pfam06733
DEAD_2; This represents a conserved region within a number of RAD3-like DNA-binding helicases ...
 3-151 2.47e-46

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: 161.28  E-value: 2.47e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712   3 LCVNEDVKSLGSVHLMNDRCVDMQRRKHKKmrigedkpkrrrqkmqaSCPFY-NHEQMELLRDEILLEVKDMEQLVALGK 81
Cdd:pfam06733  36 LCINPEVLKLKKGNLVNERCRELVKSKARG-----------------SCPFYnNLEDLLKLRDLLGDEVMDIEDLVELGE 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712  82 EAQACPYYGSRFAIPAAQLVVLPYPMLLHAATRQAAGIRLQGQVVIIDEAHNLIDTITNIHSTEVNGSQL 151
Cdd:pfam06733  99 KLGICPYYLSRELIPDADIIILPYNYLLDPKIRESLSINLKNSIVIFDEAHNIEDVCIESASFSISRSQL 168
DinG COG1199
Rad3-related DNA helicase DinG [Replication, recombination and repair];
83-625 9.50e-29

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


Pssm-ID: 440812 [Multi-domain]  Cd Length: 629  Bit Score: 121.57  E-value: 9.50e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712  83 AQACPYYGSRFAIPAAQLVVLPYPMLL-HAATRQAagiRLQG-QVVIIDEAHNLIDTITNIHSTEVNGSQLcqahSQLLQ 160
Cdd:COG1199   173 YGVCPYELARRLAREADVVVVNHHLLFaDLALGEE---LLPEdDVLIIDEAHNLPDRARDMFSAELSSRSL----LRLLR 245

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 161 YMERYRKRLKAKNLMY-IKQILYLLDKFVAVLGGNVKQNPSTQSLPQTGSELQSindflfqsqvdniNLFKVQRYLEKsm 239
Cdd:COG1199   246 ELRKLGLRPGLKKLLDlLERLREALDDLFLALEEEEELRLALGELPDEPEELLE-------------ALDALRDALEA-- 310

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 240 LSRKLfgftecfgvvlpslsdSEENRGLGGFQQFLKSLQSgppedsleegqavalrpasplmHIEAFLEALTTANQDGRV 319
Cdd:COG1199   311 LAEAL----------------EEELERLAELDALLERLEE----------------------LLFALARFLRIAEDEGYV 352

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 320 -IVNRQGsvGQSSLKFLLLNPAVHFAQVV-KECRALVIAGGTMQ---PVSDFREQLlacsGVEAsRVVEFSCGHVIPPDN 394
Cdd:COG1199   353 rWLEREG--GDVRLHAAPLDPADLLRELLfSRARSVVLTSATLSvggPFDYFARRL----GLDE-DARTLSLPSPFDYEN 425

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 395 ILPLIICSGPSnqqlefTYQRRelPQMMEETGRILCNLCNVVPGGMVCFLPSYEYLRQVHAHwdktgLLARLsvRKKIFQ 474
Cdd:COG1199   426 QALLYVPRDLP------RPSDR--DGYLEAIAEAIAELLEASGGNTLVLFTSYRALEQVAEL-----LRERL--DIPVLV 490

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 475 EPK--RASQVEQvltaystciascsHSEGhlTGALLLSvvGGKMSEGINFSDDLGRCVVMVGMPYPNIKSPELQEKMAYL 552
Cdd:COG1199   491 QGDgsREALLER-------------FREG--GNSVLVG--TGSFWEGVDLPGDALSLVIIVKLPFPPPDDPVLEARREAL 553

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712 553 DQTIprthGQP------PPGtvlienlcMKAINQSIGRAIRHQKDFASIVLLDHRYARPS----ILAKLPAWIRDRVEVK 622
Cdd:COG1199   554 EARG----GNGfmyaylPPA--------VIKLKQGAGRLIRSEEDRGVVVLLDRRLLTKRygkrFLDSLPPFRRTRPEEL 621


                  ...
gi 1958805712 623 ATF 625
Cdd:COG1199   622 RAF 624
DEAHc_DDX11_starthere cd17968
DEAH-box helicase domain of ATP-dependent DNA helicase DDX11; DDX11 (also called ChlR1) ...
 75-135 1.98e-18

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: 81.98  E-value: 1.98e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958805712  75 QLVALGKEAQACPY--------YGSRfaIPAAQLVVLPYPMLLHAATRQAAGIRLQGQVVIIDEAHNLI 135
Cdd:cd17968    38 QLAQFVHEVQKSPFgkdvrlvsLGSR--QPAAQVVVLPYQMLLHAATRKASGIKLKDQVVIIDEAHNLI 104
DEAHc_XPD-like cd17915
DEAH-box helicase domain of XPD family DEAD-like helicases; The xeroderma pigmentosum group D ...
 70-135 1.23e-13

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: 68.23  E-value: 1.23e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958805712  70 VKDMEQLValgKEAQACPYYGSRFAIP----AAQLVVLPYPMLLHAATRQAAGIRLQGQVVIIDEAHNLI 135
Cdd:cd17915    41 HSQIEQII---RELRKLLEKRKIRALAlssrDADIVVLPYPYLLDARIREFIGIDLREQVVIIDEAHNLD 107
DEAHc_DDX11_starthere cd17968
DEAH-box helicase domain of ATP-dependent DNA helicase DDX11; DDX11 (also called ChlR1) ...
 350-379 1.61e-10

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: 59.26  E-value: 1.61e-10
                          10        20        30
                  ....*....|....*....|....*....|
gi 1958805712 350 CRALVIAGGTMQPVSDFREQLLACSGVEAS 379
Cdd:cd17968   105 CRAVIIAGGTMQPVADFKEQLLFSAGVTPE 134
DEAHc_FancJ cd17970
DEAH-box helicase domain of Fanconi anemia group J protein and similar proteins; Fanconi ...
 98-134 7.17e-07

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: 50.04  E-value: 7.17e-07
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1958805712  98 AQLVVLPYPMLLHAATRQAAGIRLQGQVVIIDEAHNL 134
Cdd:cd17970   113 ADLVFCPYNYLLDPNIRRSMGLNLKGSVVIFDEAHNI 149
DEAHc_XPD-like cd17915
DEAH-box helicase domain of XPD family DEAD-like helicases; The xeroderma pigmentosum group D ...
 349-378 7.49e-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: 37.41  E-value: 7.49e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1958805712 349 ECRALVIAGGTMQPVSDFREQLL-ACSGVEA 378
Cdd:cd17915   107 DERSVIITSGTLSPLDIYSKILGiRNMLVLA 137
 
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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