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Conserved domains on  [gi|2217314263|ref|XP_047292847|]
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Fanconi anemia group J protein isoform X2 [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 ...
 245-881 6.37e-100

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: 333.99  E-value: 6.37e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  245 KIYFGTRTHKQIAQITRELRRTAYSGVPMTI---------LSSRDHTCVHPEVVGNFN---RNEKCMELLDGKNGKS--- 309
Cdd:TIGR00604   62 KIIYASRTHSQLEQATEELRKLMSYRTPRIGeespvsglsLASRKNLCLHPEVSKERQgkvVNGKCIKLTVSKIKEQrte 141

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  310 ------CYFYHGVHKISDQHTLqtFQGmcKAWDIEELVSLGKKLKACPYYTARELIQDADIIFCPYNYLLDAQIRESMDL 383
Cdd:TIGR00604  142 kpnvesCEFYENFDELREVEDL--LLS--EIMDIEDLVEYGELLGLCPYFATRKMLPFANIVLLPYQYLLDPKIRSAVSI 217

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  384 NLKEQVVILDEAHNIEDCARESASYSVTEVQLRFARDELDSmvnnnIRKKDHEPLRAVCCSLINWLEANAEYLVERDYES 463
Cdd:TIGR00604  218 ELKDSIVIFDEAHNLDNVCISSLSSNLSVRSLKRCSKEIAE-----YFEKIEERKEVDARKLLDELQKLVEGLKQEDLLT 292

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  464 ACKIWSGNEMLLTLhkmgITTATFPILQG---HFSAVLQKEEKispiYGKEEAREVPVISASTQIMLKGLF---MVLDYL 537
Cdd:TIGR00604  293 DEDIFLANPVLPKE----VLPEAVPGNIRiaeIFLHKLSRYLE----YLKDALKVLGVVSELPDAFLEHLKektFIDRPL 364

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  538 FRQNSRFAD-----------DYkIAIQQTYSWtNQIDISDKNGLLvlpKNKKRSRQKTAVH-VLNFWCLNPAVAFSDING 605
Cdd:TIGR00604  365 RFCSERLSNllreleithpeDF-SALVLLFTF-ATLVLTYTNGFL---EGIEPYENKTVPNpILKFMCLDPSIALKPLFE 439

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  606 KVQTIVLTSGTLSPMKSFSSELGVTFTIQLEANHIIKNSQVWVGTIGSGPKGRNLCATFQNTETFEFQDEVGALLLSVCQ 685
Cdd:TIGR00604  440 RVRSVILASGTLSPLDAFPRNLGFNPVSQDSPTHILKRENLLTLIVTRGSDQVPLSSTFEIRNDPSLVRNLGELLVEFSK 519

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  686 TVSQGILCFLPSYKLLEKLKERWLSTGLWHNLELVKTVIVEPQGGEKTnfDELLQVYYDAIKykgEKDGALLVAVCRGKV 765
Cdd:TIGR00604  520 IIPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVETKDAQET--SDALERYKQAVS---EGRGAVLLSVAGGKV 594

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  766 SEGLDFSDDNARAVITIGIPFPNVkdlqveLKRQYNDHHSKLRGLLPGRQ---WYEIQAYRALNQALGRCIRHRNDWGAL 842
Cdd:TIGR00604  595 SEGIDFCDDLGRAVIMVGIPYEYT------ESRILLARLEFLRDQYPIREnqdFYEFDAMRAVNQAIGRVIRHKDDYGSI 668

                          650       660       670
                   ....*....|....*....|....*....|....*....
gi 2217314263  843 ILVDDRFrnNPSRYISGLSKWVRQQIQHHSTFESALESL 881
Cdd:TIGR00604  669 VLLDKRY--ARSNKRKKLPKWIQDTIQSSDLNGMAISLT 705
PRK08074 super family cl35639
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 18-61 1.05e-04

bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated


The actual alignment was detected with superfamily member PRK08074:

Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 46.87  E-value: 1.05e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2217314263   18 PYKAYPSQLAMMNSILRGLNSKQHCLLESPTGSGKSLA-LLCSAL 61
Cdd:PRK08074   255 KYEKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAyLLPAAY 299
 
Name Accession Description Interval E-value
rad3 TIGR00604
DNA repair helicase (rad3); All proteins in this family for which funcitons are known are ...
 245-881 6.37e-100

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: 333.99  E-value: 6.37e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  245 KIYFGTRTHKQIAQITRELRRTAYSGVPMTI---------LSSRDHTCVHPEVVGNFN---RNEKCMELLDGKNGKS--- 309
Cdd:TIGR00604   62 KIIYASRTHSQLEQATEELRKLMSYRTPRIGeespvsglsLASRKNLCLHPEVSKERQgkvVNGKCIKLTVSKIKEQrte 141

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  310 ------CYFYHGVHKISDQHTLqtFQGmcKAWDIEELVSLGKKLKACPYYTARELIQDADIIFCPYNYLLDAQIRESMDL 383
Cdd:TIGR00604  142 kpnvesCEFYENFDELREVEDL--LLS--EIMDIEDLVEYGELLGLCPYFATRKMLPFANIVLLPYQYLLDPKIRSAVSI 217

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  384 NLKEQVVILDEAHNIEDCARESASYSVTEVQLRFARDELDSmvnnnIRKKDHEPLRAVCCSLINWLEANAEYLVERDYES 463
Cdd:TIGR00604  218 ELKDSIVIFDEAHNLDNVCISSLSSNLSVRSLKRCSKEIAE-----YFEKIEERKEVDARKLLDELQKLVEGLKQEDLLT 292

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  464 ACKIWSGNEMLLTLhkmgITTATFPILQG---HFSAVLQKEEKispiYGKEEAREVPVISASTQIMLKGLF---MVLDYL 537
Cdd:TIGR00604  293 DEDIFLANPVLPKE----VLPEAVPGNIRiaeIFLHKLSRYLE----YLKDALKVLGVVSELPDAFLEHLKektFIDRPL 364

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  538 FRQNSRFAD-----------DYkIAIQQTYSWtNQIDISDKNGLLvlpKNKKRSRQKTAVH-VLNFWCLNPAVAFSDING 605
Cdd:TIGR00604  365 RFCSERLSNllreleithpeDF-SALVLLFTF-ATLVLTYTNGFL---EGIEPYENKTVPNpILKFMCLDPSIALKPLFE 439

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  606 KVQTIVLTSGTLSPMKSFSSELGVTFTIQLEANHIIKNSQVWVGTIGSGPKGRNLCATFQNTETFEFQDEVGALLLSVCQ 685
Cdd:TIGR00604  440 RVRSVILASGTLSPLDAFPRNLGFNPVSQDSPTHILKRENLLTLIVTRGSDQVPLSSTFEIRNDPSLVRNLGELLVEFSK 519

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  686 TVSQGILCFLPSYKLLEKLKERWLSTGLWHNLELVKTVIVEPQGGEKTnfDELLQVYYDAIKykgEKDGALLVAVCRGKV 765
Cdd:TIGR00604  520 IIPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVETKDAQET--SDALERYKQAVS---EGRGAVLLSVAGGKV 594

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  766 SEGLDFSDDNARAVITIGIPFPNVkdlqveLKRQYNDHHSKLRGLLPGRQ---WYEIQAYRALNQALGRCIRHRNDWGAL 842
Cdd:TIGR00604  595 SEGIDFCDDLGRAVIMVGIPYEYT------ESRILLARLEFLRDQYPIREnqdFYEFDAMRAVNQAIGRVIRHKDDYGSI 668

                          650       660       670
                   ....*....|....*....|....*....|....*....
gi 2217314263  843 ILVDDRFrnNPSRYISGLSKWVRQQIQHHSTFESALESL 881
Cdd:TIGR00604  669 VLLDKRY--ARSNKRKKLPKWIQDTIQSSDLNGMAISLT 705
DEAD_2 pfam06733
DEAD_2; This represents a conserved region within a number of RAD3-like DNA-binding helicases ...
 248-415 1.83e-70

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: 232.93  E-value: 1.83e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  248 FGTRTHKQIAQITRELRRTAY-SGVPMTILSSRDHTCVHPEVV---GNFNRNEKCMELLDGKNGKSCYFYHGVHKISDQH 323
Cdd:pfam06733    1 YCSRTHSQLEQVVKELRRLPYyKKIRGLILGSRKNLCINPEVLklkKGNLVNERCRELVKSKARGSCPFYNNLEDLLKLR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  324 tlqtFQGMCKAWDIEELVSLGKKLKACPYYTARELIQDADIIFCPYNYLLDAQIRESMDLNLKEQVVILDEAHNIEDCAR 403
Cdd:pfam06733   81 ----DLLGDEVMDIEDLVELGEKLGICPYYLSRELIPDADIIILPYNYLLDPKIRESLSINLKNSIVIFDEAHNIEDVCI 156

                          170
                   ....*....|..
gi 2217314263  404 ESASYSVTEVQL 415
Cdd:pfam06733  157 ESASFSISRSQL 168
SF2_C_XPD cd18788
C-terminal helicase domain of xeroderma pigmentosum group D (XPD) family DEAD-like helicases; ...
 644-849 2.66e-69

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: 229.03  E-value: 2.66e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  644 SQVWVGTIGSGPKGRNLCATFQNTETFEFQDEVGALLLSVCQTVSQGILCFLPSYKLLEKLKERwlstglwhnlelvktv 723
Cdd:cd18788      1 DQVCPGIVGRGPDQQALNSKFQTREDEAVMDELGNLLLELCAVVPDGVLVFFPSYSYMERVVSR---------------- 64

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  724 ivepqggektnfdellqvyydaikykgekdGALLVAVCRGKVSEGLDFSDDNARAVITIGIPFPNVKDLQVELKRQYNdH 803
Cdd:cd18788     65 ------------------------------GALLLAVCRGKVSEGIDFSDDLGRAVIMVGIPYPNTKDPILKLKMDDL-E 113

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 2217314263  804 HSKLRGLLPGRQWYEIQAYRALNQALGRCIRHRNDWGALILVDDRF 849
Cdd:cd18788    114 YLRDKGLLTGEDWYTFQAMRAVNQAIGRAIRHKNDYGAIVLLDKRF 159
DEXDc2 smart00488
DEAD-like helicases superfamily;
15-427 2.41e-42

DEAD-like helicases superfamily;


Pssm-ID: 214693 [Multi-domain]  Cd Length: 289  Bit Score: 156.77  E-value: 2.41e-42
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263    15 IYFPYKAYPSQLAMMNSILRGLNSKQHCLLESPTGSGKSLALLCSALAWQQSLsgkpadEGVSEKAEVQLscccachskd 94
Cdd:smart00488    3 FYFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSF------PERIQKIKLIY---------- 66

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263    95 ftnndmnqgtsrhfnypstppserngtsstCQDspektTLAaklsakkqasiyrdenddfQVEKkrirpleTTQQIRKRH 174
Cdd:smart00488   67 ------------------------------LSR-----TVS-------------------EIEK-------RLEELRKLM 85

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263   175 CfgtevhnldakvdsgktvklnsplekinsfspqkppghcsrcccstkqgnsqessntikkdhtgkskiPKIYFGTRTHK 254
Cdd:smart00488   86 Q--------------------------------------------------------------------KVEYESDEESE 97

                           250       260       270       280       290       300       310       320
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263   255 QIAQITRELRRTAYSGVPMtILSSRDHTCVHPEV-----VGNFNrNEKCMELLDGK---------NGKSCYFYHGVHKIS 320
Cdd:smart00488   98 KQAQLLHELGREKPKVLGL-SLTSRKNLCLNPEVrtlkqNGLVV-DEVCRSLTASKarkyryenpKVERCPFYENTEFLL 175

                           330       340       350       360       370       380       390       400
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263   321 DQHTLQTfqgmcKAWDIEELVSLGKKLKACPYYTARELIQDADIIFCPYNYLLDAQIRESMDLNLKEQVVILDEAHNIED 400
Cdd:smart00488  176 VRDLLPA-----EVYDIEDLLELGKRLGGCPYFASRKAIEFANVVVLPYQYLLDPKIRQALSIELKDSIVIFDEAHNLDN 250

                           410       420
                    ....*....|....*....|....*..
gi 2217314263   401 CARESASYSVTEVQLRFARDELDSMVN 427
Cdd:smart00488  251 VCISALSSELSRRSLERAHKNIKKYFE 277
DinG COG1199
Rad3-related DNA helicase DinG [Replication, recombination and repair];
350-851 1.66e-38

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


Pssm-ID: 440812 [Multi-domain]  Cd Length: 629  Bit Score: 153.93  E-value: 1.66e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  350 CPYYTARELIQDADIIFCPYNYLLDAQIRESmDLNLKEQVVILDEAHNIEDCARESASYSVTEVQLRFARDELdsmvNNN 429
Cdd:COG1199    176 CPYELARRLAREADVVVVNHHLLFADLALGE-ELLPEDDVLIIDEAHNLPDRARDMFSAELSSRSLLRLLREL----RKL 250

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  430 IRKKDHEPLRAVCCSLINWLEANAEYLVERDyesackiwsgnEMLLTLHKMGITTATfpiLQGHFSAVLQKEEKISpiyg 509
Cdd:COG1199    251 GLRPGLKKLLDLLERLREALDDLFLALEEEE-----------ELRLALGELPDEPEE---LLEALDALRDALEALA---- 312

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  510 kEEAREVPVISAStqimLKGLFMVLDYLFRQNSRFADDYkiaiqqtyswtnqidiSDKNGLLVLPKNKKRSRqktavhvL 589
Cdd:COG1199    313 -EALEEELERLAE----LDALLERLEELLFALARFLRIA----------------EDEGYVRWLEREGGDVR-------L 364

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  590 NFWCLNPAVAFSD-INGKVQTIVLTSGTLSPMKSFS---SELGvtftIQLEANHII--------KNSQVWVGTIGSGPKG 657
Cdd:COG1199    365 HAAPLDPADLLRElLFSRARSVVLTSATLSVGGPFDyfaRRLG----LDEDARTLSlpspfdyeNQALLYVPRDLPRPSD 440

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  658 RNlcatfqntetfEFQDEVGALLLSVCQTVSQGILCFLPSYKLLEKLKERWLStglwhnlELVKTVIVepQG-GEKTnfd 736
Cdd:COG1199    441 RD-----------GYLEAIAEAIAELLEASGGNTLVLFTSYRALEQVAELLRE-------RLDIPVLV--QGdGSRE--- 497

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  737 ELLQvyydaiKYKGEKDGallVAVCRGKVSEGLDFSDDNARAVITIGIPFPNVKDLQVELKRQYNDHhsklRGLLPGRQW 816
Cdd:COG1199    498 ALLE------RFREGGNS---VLVGTGSFWEGVDLPGDALSLVIIVKLPFPPPDDPVLEARREALEA----RGGNGFMYA 564

                          490       500       510
                   ....*....|....*....|....*....|....*
gi 2217314263  817 YEIQAYRALNQALGRCIRHRNDWGALILVDDRFRN 851
Cdd:COG1199    565 YLPPAVIKLKQGAGRLIRSEEDRGVVVLLDRRLLT 599
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 18-61 1.05e-04

bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 46.87  E-value: 1.05e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2217314263   18 PYKAYPSQLAMMNSILRGLNSKQHCLLESPTGSGKSLA-LLCSAL 61
Cdd:PRK08074   255 KYEKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAyLLPAAY 299
DEAHc_DDX11_starthere cd17968
DEAH-box helicase domain of ATP-dependent DNA helicase DDX11; DDX11 (also called ChlR1) ...
 43-63 1.55e-03

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: 40.00  E-value: 1.55e-03
                           10        20
                   ....*....|....*....|.
gi 2217314263   43 LLESPTGSGKSLALLCSALAW 63
Cdd:cd17968      5 IFESPTGTGKSLSLICGALTW 25
DEXDc smart00487
DEAD-like helicases superfamily;
13-72 3.53e-03

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 40.17  E-value: 3.53e-03
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263    13 VKIYFPYKAYPSQLAMMNSILRGLnskQHCLLESPTGSGKSLALLCSALAWQQSLSGKPA 72
Cdd:smart00487    1 IEKFGFEPLRPYQKEAIEALLSGL---RDVILAAPTGSGKTLAALLPALEALKRGKGGRV 57
Lhr COG1201
Lhr-like helicase [Replication, recombination and repair];
23-74 7.43e-03

Lhr-like helicase [Replication, recombination and repair];


Pssm-ID: 440814 [Multi-domain]  Cd Length: 850  Bit Score: 40.47  E-value: 7.43e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2217314263   23 PSQLAMMNSILRGlnskQHCLLESPTGSGKSLALLCSALA--WQQSLSGKPADE 74
Cdd:COG1201     27 PPQREAWPAIAAG----ESTLLIAPTGSGKTLAAFLPALDelARRPRPGELPDG 76
dinG PRK11747
ATP-dependent DNA helicase DinG; Provisional
 350-425 8.90e-03

ATP-dependent DNA helicase DinG; Provisional


Pssm-ID: 236966 [Multi-domain]  Cd Length: 697  Bit Score: 40.20  E-value: 8.90e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  350 CPYYTARELIQDADIIFCpyNY-LLDAqireSMDL-------NLKEQVVILDEAHNIEDCARESASYSVTevqLRFARDE 421
Cdd:PRK11747   208 CPFFKARREIDEADVVVA--NHdLVLA----DLELgggvvlpDPENLLYVLDEGHHLPDVARDHFAASAE---LKGTADW 278


                   ....
gi 2217314263  422 LDSM 425
Cdd:PRK11747   279 LEKL 282
 
Name Accession Description Interval E-value
rad3 TIGR00604
DNA repair helicase (rad3); All proteins in this family for which funcitons are known are ...
 245-881 6.37e-100

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: 333.99  E-value: 6.37e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  245 KIYFGTRTHKQIAQITRELRRTAYSGVPMTI---------LSSRDHTCVHPEVVGNFN---RNEKCMELLDGKNGKS--- 309
Cdd:TIGR00604   62 KIIYASRTHSQLEQATEELRKLMSYRTPRIGeespvsglsLASRKNLCLHPEVSKERQgkvVNGKCIKLTVSKIKEQrte 141

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  310 ------CYFYHGVHKISDQHTLqtFQGmcKAWDIEELVSLGKKLKACPYYTARELIQDADIIFCPYNYLLDAQIRESMDL 383
Cdd:TIGR00604  142 kpnvesCEFYENFDELREVEDL--LLS--EIMDIEDLVEYGELLGLCPYFATRKMLPFANIVLLPYQYLLDPKIRSAVSI 217

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  384 NLKEQVVILDEAHNIEDCARESASYSVTEVQLRFARDELDSmvnnnIRKKDHEPLRAVCCSLINWLEANAEYLVERDYES 463
Cdd:TIGR00604  218 ELKDSIVIFDEAHNLDNVCISSLSSNLSVRSLKRCSKEIAE-----YFEKIEERKEVDARKLLDELQKLVEGLKQEDLLT 292

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  464 ACKIWSGNEMLLTLhkmgITTATFPILQG---HFSAVLQKEEKispiYGKEEAREVPVISASTQIMLKGLF---MVLDYL 537
Cdd:TIGR00604  293 DEDIFLANPVLPKE----VLPEAVPGNIRiaeIFLHKLSRYLE----YLKDALKVLGVVSELPDAFLEHLKektFIDRPL 364

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  538 FRQNSRFAD-----------DYkIAIQQTYSWtNQIDISDKNGLLvlpKNKKRSRQKTAVH-VLNFWCLNPAVAFSDING 605
Cdd:TIGR00604  365 RFCSERLSNllreleithpeDF-SALVLLFTF-ATLVLTYTNGFL---EGIEPYENKTVPNpILKFMCLDPSIALKPLFE 439

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  606 KVQTIVLTSGTLSPMKSFSSELGVTFTIQLEANHIIKNSQVWVGTIGSGPKGRNLCATFQNTETFEFQDEVGALLLSVCQ 685
Cdd:TIGR00604  440 RVRSVILASGTLSPLDAFPRNLGFNPVSQDSPTHILKRENLLTLIVTRGSDQVPLSSTFEIRNDPSLVRNLGELLVEFSK 519

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  686 TVSQGILCFLPSYKLLEKLKERWLSTGLWHNLELVKTVIVEPQGGEKTnfDELLQVYYDAIKykgEKDGALLVAVCRGKV 765
Cdd:TIGR00604  520 IIPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKLIFVETKDAQET--SDALERYKQAVS---EGRGAVLLSVAGGKV 594

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  766 SEGLDFSDDNARAVITIGIPFPNVkdlqveLKRQYNDHHSKLRGLLPGRQ---WYEIQAYRALNQALGRCIRHRNDWGAL 842
Cdd:TIGR00604  595 SEGIDFCDDLGRAVIMVGIPYEYT------ESRILLARLEFLRDQYPIREnqdFYEFDAMRAVNQAIGRVIRHKDDYGSI 668

                          650       660       670
                   ....*....|....*....|....*....|....*....
gi 2217314263  843 ILVDDRFrnNPSRYISGLSKWVRQQIQHHSTFESALESL 881
Cdd:TIGR00604  669 VLLDKRY--ARSNKRKKLPKWIQDTIQSSDLNGMAISLT 705
DEAD_2 pfam06733
DEAD_2; This represents a conserved region within a number of RAD3-like DNA-binding helicases ...
 248-415 1.83e-70

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: 232.93  E-value: 1.83e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  248 FGTRTHKQIAQITRELRRTAY-SGVPMTILSSRDHTCVHPEVV---GNFNRNEKCMELLDGKNGKSCYFYHGVHKISDQH 323
Cdd:pfam06733    1 YCSRTHSQLEQVVKELRRLPYyKKIRGLILGSRKNLCINPEVLklkKGNLVNERCRELVKSKARGSCPFYNNLEDLLKLR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  324 tlqtFQGMCKAWDIEELVSLGKKLKACPYYTARELIQDADIIFCPYNYLLDAQIRESMDLNLKEQVVILDEAHNIEDCAR 403
Cdd:pfam06733   81 ----DLLGDEVMDIEDLVELGEKLGICPYYLSRELIPDADIIILPYNYLLDPKIRESLSINLKNSIVIFDEAHNIEDVCI 156

                          170
                   ....*....|..
gi 2217314263  404 ESASYSVTEVQL 415
Cdd:pfam06733  157 ESASFSISRSQL 168
SF2_C_XPD cd18788
C-terminal helicase domain of xeroderma pigmentosum group D (XPD) family DEAD-like helicases; ...
 644-849 2.66e-69

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: 229.03  E-value: 2.66e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  644 SQVWVGTIGSGPKGRNLCATFQNTETFEFQDEVGALLLSVCQTVSQGILCFLPSYKLLEKLKERwlstglwhnlelvktv 723
Cdd:cd18788      1 DQVCPGIVGRGPDQQALNSKFQTREDEAVMDELGNLLLELCAVVPDGVLVFFPSYSYMERVVSR---------------- 64

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  724 ivepqggektnfdellqvyydaikykgekdGALLVAVCRGKVSEGLDFSDDNARAVITIGIPFPNVKDLQVELKRQYNdH 803
Cdd:cd18788     65 ------------------------------GALLLAVCRGKVSEGIDFSDDLGRAVIMVGIPYPNTKDPILKLKMDDL-E 113

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 2217314263  804 HSKLRGLLPGRQWYEIQAYRALNQALGRCIRHRNDWGALILVDDRF 849
Cdd:cd18788    114 YLRDKGLLTGEDWYTFQAMRAVNQAIGRAIRHKNDYGAIVLLDKRF 159
Helicase_C_2 pfam13307
Helicase C-terminal domain; This domain is found at the C-terminus of DEAD-box helicases.
 681-867 6.59e-59

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: 200.10  E-value: 6.59e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  681 LSVCQTVSQGILCFLPSYKLLEKLKERWLSTGLWhnleLVKTVIVEPQGGEktnFDELLQvyydaiKYKGEKDGALLVAV 760
Cdd:pfam13307    1 LRLLKVIPGGVLVFFPSYSYLEKVAERLKESGLE----KGIEIFVQPGEGS---REKLLE------EFKKKGKGAVLFGV 67

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  761 CRGKVSEGLDFSDDNARAVITIGIPFPNVKDLQVELKRQYNDHhsklRGLLPGRQWYEIQAYRALNQALGRCIRHRNDWG 840
Cdd:pfam13307   68 CGGSFSEGIDFPGDLLRAVIIVGLPFPNPDDPVVEAKREYLDS----KGGNPFNEWYLPQAVRAVNQAIGRLIRHENDYG 143

                          170       180
                   ....*....|....*....|....*..
gi 2217314263  841 ALILVDDRFRNNpsRYISGLSKWVRQQ 867
Cdd:pfam13307  144 AIVLLDSRFLTK--RYGKLLPKWLPPG 168
DEAHc_FancJ cd17970
DEAH-box helicase domain of Fanconi anemia group J protein and similar proteins; Fanconi ...
 39-399 7.32e-53

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: 183.32  E-value: 7.32e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263   39 KQHCLLESPTGSGKSLALLCSALAWQQSLSGKPADEGvsekaevqlscccachskdftnndmnqgtsrhfnypstppser 118
Cdd:cd17970      1 GQNALLESPTGTGKTLSLLCSTLAWRQSLKGKATSEG------------------------------------------- 37

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  119 ngtsstcqdspekttlaaklsakkqasiyrdenddfqvekkrirplettqqirkrhcfgtevhnldakvdsgktvklnsp 198
Cdd:cd17970        --------------------------------------------------------------------------------

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  199 lekinsfspqkppghcsrcccstkqgnsqessntikKDHTGKSKIPKIYFGTRTHKQIAQITRELRRTAYSGVPMTILSS 278
Cdd:cd17970     38 ------------------------------------SDGGGSGKIPKIIYASRTHSQLAQVVRELKRTAYKRPRMTILGS 81

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  279 RDHTCVHP--EVVGNFNRNEKCMELLDGKNgkscyfyhgvhkisdqhtlqtfqgmckawdieelvslgkklkacpyytar 356
Cdd:cd17970     82 RDHLCIHPviNKLSNQNANEACMALLSGKN-------------------------------------------------- 111

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|...
gi 2217314263  357 eliqDADIIFCPYNYLLDAQIRESMDLNLKEQVVILDEAHNIE 399
Cdd:cd17970    112 ----EADLVFCPYNYLLDPNIRRSMGLNLKGSVVIFDEAHNIE 150
DEXDc2 smart00488
DEAD-like helicases superfamily;
15-427 2.41e-42

DEAD-like helicases superfamily;


Pssm-ID: 214693 [Multi-domain]  Cd Length: 289  Bit Score: 156.77  E-value: 2.41e-42
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263    15 IYFPYKAYPSQLAMMNSILRGLNSKQHCLLESPTGSGKSLALLCSALAWQQSLsgkpadEGVSEKAEVQLscccachskd 94
Cdd:smart00488    3 FYFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSF------PERIQKIKLIY---------- 66

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263    95 ftnndmnqgtsrhfnypstppserngtsstCQDspektTLAaklsakkqasiyrdenddfQVEKkrirpleTTQQIRKRH 174
Cdd:smart00488   67 ------------------------------LSR-----TVS-------------------EIEK-------RLEELRKLM 85

                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263   175 CfgtevhnldakvdsgktvklnsplekinsfspqkppghcsrcccstkqgnsqessntikkdhtgkskiPKIYFGTRTHK 254
Cdd:smart00488   86 Q--------------------------------------------------------------------KVEYESDEESE 97

                           250       260       270       280       290       300       310       320
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263   255 QIAQITRELRRTAYSGVPMtILSSRDHTCVHPEV-----VGNFNrNEKCMELLDGK---------NGKSCYFYHGVHKIS 320
Cdd:smart00488   98 KQAQLLHELGREKPKVLGL-SLTSRKNLCLNPEVrtlkqNGLVV-DEVCRSLTASKarkyryenpKVERCPFYENTEFLL 175

                           330       340       350       360       370       380       390       400
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263   321 DQHTLQTfqgmcKAWDIEELVSLGKKLKACPYYTARELIQDADIIFCPYNYLLDAQIRESMDLNLKEQVVILDEAHNIED 400
Cdd:smart00488  176 VRDLLPA-----EVYDIEDLLELGKRLGGCPYFASRKAIEFANVVVLPYQYLLDPKIRQALSIELKDSIVIFDEAHNLDN 250

                           410       420
                    ....*....|....*....|....*..
gi 2217314263   401 CARESASYSVTEVQLRFARDELDSMVN 427
Cdd:smart00488  251 VCISALSSELSRRSLERAHKNIKKYFE 277
DinG COG1199
Rad3-related DNA helicase DinG [Replication, recombination and repair];
350-851 1.66e-38

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


Pssm-ID: 440812 [Multi-domain]  Cd Length: 629  Bit Score: 153.93  E-value: 1.66e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  350 CPYYTARELIQDADIIFCPYNYLLDAQIRESmDLNLKEQVVILDEAHNIEDCARESASYSVTEVQLRFARDELdsmvNNN 429
Cdd:COG1199    176 CPYELARRLAREADVVVVNHHLLFADLALGE-ELLPEDDVLIIDEAHNLPDRARDMFSAELSSRSLLRLLREL----RKL 250

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  430 IRKKDHEPLRAVCCSLINWLEANAEYLVERDyesackiwsgnEMLLTLHKMGITTATfpiLQGHFSAVLQKEEKISpiyg 509
Cdd:COG1199    251 GLRPGLKKLLDLLERLREALDDLFLALEEEE-----------ELRLALGELPDEPEE---LLEALDALRDALEALA---- 312

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  510 kEEAREVPVISAStqimLKGLFMVLDYLFRQNSRFADDYkiaiqqtyswtnqidiSDKNGLLVLPKNKKRSRqktavhvL 589
Cdd:COG1199    313 -EALEEELERLAE----LDALLERLEELLFALARFLRIA----------------EDEGYVRWLEREGGDVR-------L 364

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  590 NFWCLNPAVAFSD-INGKVQTIVLTSGTLSPMKSFS---SELGvtftIQLEANHII--------KNSQVWVGTIGSGPKG 657
Cdd:COG1199    365 HAAPLDPADLLRElLFSRARSVVLTSATLSVGGPFDyfaRRLG----LDEDARTLSlpspfdyeNQALLYVPRDLPRPSD 440

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  658 RNlcatfqntetfEFQDEVGALLLSVCQTVSQGILCFLPSYKLLEKLKERWLStglwhnlELVKTVIVepQG-GEKTnfd 736
Cdd:COG1199    441 RD-----------GYLEAIAEAIAELLEASGGNTLVLFTSYRALEQVAELLRE-------RLDIPVLV--QGdGSRE--- 497

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  737 ELLQvyydaiKYKGEKDGallVAVCRGKVSEGLDFSDDNARAVITIGIPFPNVKDLQVELKRQYNDHhsklRGLLPGRQW 816
Cdd:COG1199    498 ALLE------RFREGGNS---VLVGTGSFWEGVDLPGDALSLVIIVKLPFPPPDDPVLEARREALEA----RGGNGFMYA 564

                          490       500       510
                   ....*....|....*....|....*....|....*
gi 2217314263  817 YEIQAYRALNQALGRCIRHRNDWGALILVDDRFRN 851
Cdd:COG1199    565 YLPPAVIKLKQGAGRLIRSEEDRGVVVLLDRRLLT 599
HELICc2 smart00491
helicase superfamily c-terminal domain;
698-849 8.80e-38

helicase superfamily c-terminal domain;


Pssm-ID: 214694 [Multi-domain]  Cd Length: 142  Bit Score: 138.57  E-value: 8.80e-38
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263   698 YKLLEKLKERWLSTGLwhnLELVKTVIVEPQGGEKTNfdELLQVYYDAIkykgEKDGALLVAVCRGKVSEGLDFSDDNAR 777
Cdd:smart00491    1 YRYLEQVVEYWKENGI---LEINKPVFIEGKDSGETE--ELLEKYSAAC----EARGALLLAVARGKVSEGIDFPDDLGR 71

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2217314263   778 AVITIGIPFPNVKDLQVELKRQYNDhhsKLRGLLPGRQWYEIQAYRALNQALGRCIRHRNDWGALILVDDRF 849
Cdd:smart00491   72 AVIIVGIPFPNPDSPILRARLEYLD---EKGGIRPFDEVYLFDAMRALAQAIGRAIRHKNDYGVVVLLDKRY 140
DEAHc_XPD-like cd17915
DEAH-box helicase domain of XPD family DEAD-like helicases; The xeroderma pigmentosum group D ...
 242-399 4.02e-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: 4.02e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  242 KIPKIYFGTRTHKQIAQITRELRRTAYS-GVPMTILSSRDhtcvhpevvgnfnrnekcmelldgkngkscyfyhgvhkis 320
Cdd:cd17915     30 HKTKVLYCSRTHSQIEQIIRELRKLLEKrKIRALALSSRD---------------------------------------- 69

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2217314263  321 dqhtlqtfqgmckawdieelvslgkklkacpyytareliqdADIIFCPYNYLLDAQIRESMDLNLKEQVVILDEAHNIE 399
Cdd:cd17915     70 -----------------------------------------ADIVVLPYPYLLDARIREFIGIDLREQVVIIDEAHNLD 107
DEAHc_DDX11_starthere cd17968
DEAH-box helicase domain of ATP-dependent DNA helicase DDX11; DDX11 (also called ChlR1) ...
 340-398 3.04e-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: 45.00  E-value: 3.04e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2217314263  340 LVSLGKKLKAcpyytareliqdADIIFCPYNYLLDAQIRESMDLNLKEQVVILDEAHNI 398
Cdd:cd17968     57 LVSLGSRQPA------------AQVVVLPYQMLLHAATRKASGIKLKDQVVIIDEAHNL 103
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 18-61 1.05e-04

bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 46.87  E-value: 1.05e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2217314263   18 PYKAYPSQLAMMNSILRGLNSKQHCLLESPTGSGKSLA-LLCSAL 61
Cdd:PRK08074   255 KYEKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAyLLPAAY 299
DEAHc_XPD-like cd17915
DEAH-box helicase domain of XPD family DEAD-like helicases; The xeroderma pigmentosum group D ...
 604-637 1.81e-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: 42.80  E-value: 1.81e-04
                           10        20        30
                   ....*....|....*....|....*....|....
gi 2217314263  604 NGKVQTIVLTSGTLSPMKSFSSELGVTFTIQLEA 637
Cdd:cd17915    105 NLDERSVIITSGTLSPLDIYSKILGIRNMLVLAV 138
DEAHc_DDX11_starthere cd17968
DEAH-box helicase domain of ATP-dependent DNA helicase DDX11; DDX11 (also called ChlR1) ...
 43-63 1.55e-03

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: 40.00  E-value: 1.55e-03
                           10        20
                   ....*....|....*....|.
gi 2217314263   43 LLESPTGSGKSLALLCSALAW 63
Cdd:cd17968      5 IFESPTGTGKSLSLICGALTW 25
DEXDc smart00487
DEAD-like helicases superfamily;
13-72 3.53e-03

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 40.17  E-value: 3.53e-03
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263    13 VKIYFPYKAYPSQLAMMNSILRGLnskQHCLLESPTGSGKSLALLCSALAWQQSLSGKPA 72
Cdd:smart00487    1 IEKFGFEPLRPYQKEAIEALLSGL---RDVILAAPTGSGKTLAALLPALEALKRGKGGRV 57
DEAHc_XPD cd17969
DEAH-box helicase domain of TFIIH basal transcription factor complex helicase XPD subunit; ...
 34-65 4.37e-03

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: 39.34  E-value: 4.37e-03
                           10        20        30
                   ....*....|....*....|....*....|..
gi 2217314263   34 RGLNSKQHCLLESPTGSGKSLALLCSALAWQQ 65
Cdd:cd17969      5 RTLDAKGHCVLEMPSGTGKTVSLLSLIVAYQK 36
Lhr COG1201
Lhr-like helicase [Replication, recombination and repair];
23-74 7.43e-03

Lhr-like helicase [Replication, recombination and repair];


Pssm-ID: 440814 [Multi-domain]  Cd Length: 850  Bit Score: 40.47  E-value: 7.43e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2217314263   23 PSQLAMMNSILRGlnskQHCLLESPTGSGKSLALLCSALA--WQQSLSGKPADE 74
Cdd:COG1201     27 PPQREAWPAIAAG----ESTLLIAPTGSGKTLAAFLPALDelARRPRPGELPDG 76
dinG PRK11747
ATP-dependent DNA helicase DinG; Provisional
 350-425 8.90e-03

ATP-dependent DNA helicase DinG; Provisional


Pssm-ID: 236966 [Multi-domain]  Cd Length: 697  Bit Score: 40.20  E-value: 8.90e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217314263  350 CPYYTARELIQDADIIFCpyNY-LLDAqireSMDL-------NLKEQVVILDEAHNIEDCARESASYSVTevqLRFARDE 421
Cdd:PRK11747   208 CPFFKARREIDEADVVVA--NHdLVLA----DLELgggvvlpDPENLLYVLDEGHHLPDVARDHFAASAE---LKGTADW 278


                   ....
gi 2217314263  422 LDSM 425
Cdd:PRK11747   279 LEKL 282
 
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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