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Conserved domains on  [gi|568993644|ref|XP_006521609|]
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ATP-dependent DNA helicase Q4 isoform X1 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RecQ super family cl33925
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
485-844 9.26e-116

Superfamily II DNA helicase RecQ [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0514:

Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 370.24  E-value: 9.26e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  485 AEVFQALERL-GYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALLyaqrSPCLTLVVSPLLSLMDDQVSDLP 563
Cdd:COG0514     3 DDALEVLKRVfGYDSFRPGQEEIIEAVLAGRDALVVMPTGGGKSLCYQLPALL----LPGLTLVVSPLIALMKDQVDALR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  564 SC-LKAACLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALvgcgaRGPGSLPQAAQLPPIAFAcIDEVHCLSQWSHNFRP 642
Cdd:COG0514    79 AAgIRAAFLNSSLSAEERREVLRALRAGELKLLYVAPERL-----LNPRFLELLRRLKISLFA-IDEAHCISQWGHDFRP 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  643 CYLRVcKVLREHMGVRCFLGLTATATRSTARDVAQHLGIAGEFELSGSANIPaNLHLSVS--MDRDSDQALVTLLQGdrf 720
Cdd:COG0514   153 DYRRL-GELRERLPNVPVLALTATATPRVRADIAEQLGLEDPRVFVGSFDRP-NLRLEVVpkPPDDKLAQLLDFLKE--- 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  721 RTLDSVIIYCTRRKDTERVAALLRTclsmvgdsrpRGcgpeaI-AEAYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGM 799
Cdd:COG0514   228 HPGGSGIVYCLSRKKVEELAEWLRE----------AG-----IrAAAYHAGLDAEEREANQDRFLRDEVDVIVATIAFGM 292

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*
gi 568993644  800 GLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFMHPQ 844
Cdd:COG0514   293 GIDKPDVRFVIHYDLPKSIEAYYQEIGRAGRDGLPAEALLLYGPE 337
RecQL4_SLD2_NTD cd22289
N-terminal homeodomain-like domain of metazoan RecQ protein-like 4 (RecQL4), fungal DNA ...
 2-50 1.66e-19

N-terminal homeodomain-like domain of metazoan RecQ protein-like 4 (RecQL4), fungal DNA replication regulator SLD2 and similar proteins; RecQL4, also called ATP-dependent DNA helicase Q4, or DNA helicase, RecQ-like type 4 (RecQ4), or RTS, is a DNA-dependent ATPase that may modulate chromosome segregation. This family also includes fungal DNA replication regulator SLD2, also known as DNA replication and checkpoint protein 1 (DRC1), which functions with DPB11 to control DNA replication and the S-phase checkpoint. It is also required for the proper activation of RAD53 in response to DNA damage and replication blocks. This model corresponds to the N-terminal domain of RecQL4 and SLD2, which is a homeodomain-like DNA interaction motif.


:

Pssm-ID: 412085  Cd Length: 49  Bit Score: 83.06  E-value: 1.66e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 568993644    2 ERLATVRARLQEWERAFARLHGRRPAKGDVEAAPEETRALYREYRNLKQ 50
Cdd:cd22289     1 ERLQELKIALKTWERAFAKKHGRKPTKDDIKAAPEEIKDLYKEYAKLKK 49
ZnF_C2HC smart00343
zinc finger;
394-408 2.33e-03

zinc finger;


:

Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 36.65  E-value: 2.33e-03
                            10
                    ....*....|....*
gi 568993644    394 TCFRCGQFGHWASQC 408
Cdd:smart00343    1 KCYNCGKEGHIARDC 15
 
Name Accession Description Interval E-value
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
485-844 9.26e-116

Superfamily II DNA helicase RecQ [Replication, recombination and repair];


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 370.24  E-value: 9.26e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  485 AEVFQALERL-GYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALLyaqrSPCLTLVVSPLLSLMDDQVSDLP 563
Cdd:COG0514     3 DDALEVLKRVfGYDSFRPGQEEIIEAVLAGRDALVVMPTGGGKSLCYQLPALL----LPGLTLVVSPLIALMKDQVDALR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  564 SC-LKAACLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALvgcgaRGPGSLPQAAQLPPIAFAcIDEVHCLSQWSHNFRP 642
Cdd:COG0514    79 AAgIRAAFLNSSLSAEERREVLRALRAGELKLLYVAPERL-----LNPRFLELLRRLKISLFA-IDEAHCISQWGHDFRP 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  643 CYLRVcKVLREHMGVRCFLGLTATATRSTARDVAQHLGIAGEFELSGSANIPaNLHLSVS--MDRDSDQALVTLLQGdrf 720
Cdd:COG0514   153 DYRRL-GELRERLPNVPVLALTATATPRVRADIAEQLGLEDPRVFVGSFDRP-NLRLEVVpkPPDDKLAQLLDFLKE--- 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  721 RTLDSVIIYCTRRKDTERVAALLRTclsmvgdsrpRGcgpeaI-AEAYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGM 799
Cdd:COG0514   228 HPGGSGIVYCLSRKKVEELAEWLRE----------AG-----IrAAAYHAGLDAEEREANQDRFLRDEVDVIVATIAFGM 292

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*
gi 568993644  800 GLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFMHPQ 844
Cdd:COG0514   293 GIDKPDVRFVIHYDLPKSIEAYYQEIGRAGRDGLPAEALLLYGPE 337
DEXHc_RecQ4-like cd18018
DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) ...
 488-690 2.14e-98

DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Mutations cause Rothmund-Thomson/RAPADILINO/Baller-Gerold syndrome.


Pssm-ID: 350776 [Multi-domain]  Cd Length: 201  Bit Score: 311.88  E-value: 2.14e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  488 FQALERL-GYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALLYAQRSPCLTLVVSPLLSLMDDQVSDLPSCL 566
Cdd:cd18018     1 LKLLRRVfGHPSFRPGQEEAIARLLSGRSTLVVLPTGAGKSLCYQLPALLLRRRGPGLTLVVSPLIALMKDQVDALPRAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  567 KAACLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALvgcgaRGPGSLPQAAQLPPIAFACIDEVHCLSQWSHNFRPCYLR 646
Cdd:cd18018    81 KAAALNSSLTREERRRILEKLRAGEVKILYVSPERL-----VNESFRELLRQTPPISLLVVDEAHCISEWSHNFRPDYLR 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 568993644  647 VCKVLREHMGVRCFLGLTATATRSTARDVAQHLGIAGEFELSGS 690
Cdd:cd18018   156 LCRVLRELLGAPPVLALTATATKRVVEDIASHLGIPESGVVRGP 199
recQ_fam TIGR00614
ATP-dependent DNA helicase, RecQ family; All proteins in this family for which functions are ...
 495-843 1.77e-90

ATP-dependent DNA helicase, RecQ family; All proteins in this family for which functions are known are 3'-5' DNA-DNA helicases. These proteins are used for recombination, recombinational repair, and possibly maintenance of chromosome stability. 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: 129701 [Multi-domain]  Cd Length: 470  Bit Score: 300.53  E-value: 1.77e-90
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644   495 GYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALLyaqrSPCLTLVVSPLLSLMDDQVSDLP-SCLKAACLHS 573
Cdd:TIGR00614    8 GLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALY----SDGITLVISPLISLMEDQVLQLQaLGIPATFLNS 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644   574 GMTKKQRESVLKKVRAAQVHVLIVSPEALvgCGARGPGSLPQAAQLppIAFACIDEVHCLSQWSHNFRPCYlRVCKVLRE 653
Cdd:TIGR00614   84 AQTKEQQLNVLTDLKDGKIKLLYVTPEKI--SASNRLLQTLEERKG--ITLIAVDEAHCISQWGHDFRPDY-KALGSLKQ 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644   654 HMGVRCFLGLTATATRSTARDVAQHLGIAGEFELSGSANIPaNLHLSVsMDRDSD--QALVTLLQGdRFRTlDSVIIYCT 731
Cdd:TIGR00614  159 KFPNVPVMALTATASPSVREDILRQLNLLNPQIFCTSFDRP-NLYYEV-RRKTPKilEDLLRFIRK-EFEG-KSGIIYCP 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644   732 RRKDTERVAALLRTclsmVGDSrprgcgpeaiAEAYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRPDVRAVLH 811
Cdd:TIGR00614  235 SRKKVEQVAAELQK----LGLA----------AGAYHAGLEDSARDDVQHKFQRDEIQVVVATVAFGMGINKPDVRFVIH 300

                          330       340       350
                   ....*....|....*....|....*....|..
gi 568993644   812 LGLPPSFESYVQAIGRAGRDGKPAHCHLFMHP 843
Cdd:TIGR00614  301 YSLPKSMESYYQESGRAGRDGLPSECHLFYAP 332
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 479-843 1.19e-79

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 274.67  E-value: 1.19e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  479 QVAETPAEVFQAL-ERLGYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALLYaqrsPCLTLVVSPLLSLMDD 557
Cdd:PRK11057    5 EVLNLESLAKQVLqETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL----DGLTLVVSPLISLMKD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  558 QVSDL-PSCLKAACLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALVGcgargPGSLPQAAQLPPIAFAcIDEVHCLSQW 636
Cdd:PRK11057   81 QVDQLlANGVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMM-----DNFLEHLAHWNPALLA-VDEAHCISQW 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  637 SHNFRPCYlRVCKVLREHMGVRCFLGLTATATRSTARDVAQHLGIAGEFELSGSANIPANLHLSVSMDRDSDQaLVTLLQ 716
Cdd:PRK11057  155 GHDFRPEY-AALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYTLVEKFKPLDQ-LMRYVQ 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  717 GDRFRtldSVIIYCTRRKDTERVAALLRTclsmvgdsrpRGCGpeaiAEAYHAGMSSQERRRVQQAFMRGHLRMVVATVA 796
Cdd:PRK11057  233 EQRGK---SGIIYCNSRAKVEDTAARLQS----------RGIS----AAAYHAGLDNDVRADVQEAFQRDDLQIVVATVA 295

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 568993644  797 FGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFMHP 843
Cdd:PRK11057  296 FGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDP 342
DpdF NF041063
protein DpdF;
476-844 2.74e-39

protein DpdF;


Pssm-ID: 468990 [Multi-domain]  Cd Length: 813  Bit Score: 158.15  E-value: 2.74e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  476 PLGQVAETPAEVFQAlERLGYRAFR-PGQERAIMRILS---GiSTLLV-LPTGAGKSLCYQLPALLYAQRSPcLTLVVSP 550
Cdd:NF041063  118 LRRTLEPVPGDPFLA-EALGFTHYRsPGQREAVRAALLappG-STLIVnLPTGSGKSLVAQAPALLASRQGG-LTLVVVP 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  551 LLSLMDDQVSDLPSCLKAA--------CLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALVGCGARgpgSLPQAAQLPPI 622
Cdd:NF041063  195 TVALAIDQERRARELLRRAgpdlggplAWHGGLSAEERAAIRQRIRDGTQRILFTSPESLTGSLRP---ALFDAAEAGLL 271

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  623 AFACIDEVHCLSQWSHNFRPCY----------LRVCKvlrEHMGVRCFLgLTATATRSTaRDVAQHL-GIAGEFEL-SGS 690
Cdd:NF041063  272 RYLVVDEAHLVDQWGDGFRPEFqllaglrrslLRLAP---SGRPFRTLL-LSATLTEST-LDTLETLfGPPGPFIVvSAV 346

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  691 anipanlHL----SVSMDRDSDQAlvtllqgDRFRT-LDSV-------IIYCTRRKDTERVAALLRTclsmVGDSRprgc 758
Cdd:NF041063  347 -------QLrpepAYWVAKCDSEE-------ERRERvLEALrhlprplILYVTKVEDAEAWLQRLRA----AGFRR---- 404

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  759 gpeaiAEAYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCH 838
Cdd:NF041063  405 -----VALFHGDTPDAERERLIEQWRENELDIVVATSAFGLGMDKSDVRTVIHACVPETLDRFYQEVGRGGRDGKASLSL 479


                  ....*.
gi 568993644  839 LFMHPQ 844
Cdd:NF041063  480 LIYTPD 485
DEXDc smart00487
DEAD-like helicases superfamily;
491-679 4.60e-25

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 104.11  E-value: 4.60e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644    491 LERLGYRAFRPGQERAIMRILSGI-STLLVLPTGAGKSLCYQLPALLYAQRSP-CLTLVVSPLLSLMDDQVSDL-----P 563
Cdd:smart00487    1 IEKFGFEPLRPYQKEAIEALLSGLrDVILAAPTGSGKTLAALLPALEALKRGKgGRVLVLVPTRELAEQWAEELkklgpS 80

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644    564 SCLKAACLHSGMTKKQResvLKKVRAAQVHVLIVSPEALVGCGARGPGSLPQaaqlppIAFACIDEVHCLSQWshNFRPC 643
Cdd:smart00487   81 LGLKVVGLYGGDSKREQ---LRKLESGKTDILVTTPGRLLDLLENDKLSLSN------VDLVILDEAHRLLDG--GFGDQ 149

                           170       180       190
                    ....*....|....*....|....*....|....*.
gi 568993644    644 YLRVCKVLREHmgvRCFLGLTATATRSTARDVAQHL 679
Cdd:smart00487  150 LEKLLKLLPKN---VQLLLLSATPPEEIENLLELFL 182
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 500-673 1.74e-24

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 101.17  E-value: 1.74e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644   500 RPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPAL--LYAQRSPCLTLVVSPLLSLMDDQVSDL-----PSCLKAACLH 572
Cdd:pfam00270    1 TPIQAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALeaLDKLDNGPQALVLAPTRELAEQIYEELkklgkGLGLKVASLL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644   573 SGMTKKQRESVLKKvraaqVHVLIVSPEALVgcgargpGSLPQAAQLPPIAFACIDEVHCLSQWShnFRPCYLRVCKVLR 652
Cdd:pfam00270   81 GGDSRKEQLEKLKG-----PDILVGTPGRLL-------DLLQERKLLKNLKLLVLDEAHRLLDMG--FGPDLEEILRRLP 146

                          170       180
                   ....*....|....*....|.
gi 568993644   653 EHmgvRCFLGLTATATRSTAR 673
Cdd:pfam00270  147 KK---RQILLLSATLPRNLED 164
RecQL4_SLD2_NTD cd22289
N-terminal homeodomain-like domain of metazoan RecQ protein-like 4 (RecQL4), fungal DNA ...
 2-50 1.66e-19

N-terminal homeodomain-like domain of metazoan RecQ protein-like 4 (RecQL4), fungal DNA replication regulator SLD2 and similar proteins; RecQL4, also called ATP-dependent DNA helicase Q4, or DNA helicase, RecQ-like type 4 (RecQ4), or RTS, is a DNA-dependent ATPase that may modulate chromosome segregation. This family also includes fungal DNA replication regulator SLD2, also known as DNA replication and checkpoint protein 1 (DRC1), which functions with DPB11 to control DNA replication and the S-phase checkpoint. It is also required for the proper activation of RAD53 in response to DNA damage and replication blocks. This model corresponds to the N-terminal domain of RecQL4 and SLD2, which is a homeodomain-like DNA interaction motif.


Pssm-ID: 412085  Cd Length: 49  Bit Score: 83.06  E-value: 1.66e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 568993644    2 ERLATVRARLQEWERAFARLHGRRPAKGDVEAAPEETRALYREYRNLKQ 50
Cdd:cd22289     1 ERLQELKIALKTWERAFAKKHGRKPTKDDIKAAPEEIKDLYKEYAKLKK 49
Drc1-Sld2 pfam11719
DNA replication and checkpoint protein; Genome duplication is precisely regulated by ...
 4-49 9.88e-09

DNA replication and checkpoint protein; Genome duplication is precisely regulated by cyclin-dependent kinases CDKs, which bring about the onset of S phase by activating replication origins and then prevent re-licensing of origins until mitosis is completed. The optimum sequence motif for CDK phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found to have at least 11 potential phosphorylation sites. Drc1 is required for DNA synthesis and S-M replication checkpoint control. Drc1 associates with Cdc2 and is phosphorylated at the onset of S phase when Cdc2 is activated. Thus Cdc2 promotes DNA replication by phosphorylating Drc1 and regulating its association with Cut5. Sld2 and Sld3 represent the minimal set of S-CDK substrates required for DNA replication.


Pssm-ID: 371692 [Multi-domain]  Cd Length: 391  Bit Score: 59.07  E-value: 9.88e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 568993644     4 LATVRARLQEWERAFARLHGRRPAKGDVEAAPeETRALYREYRNLK 49
Cdd:pfam11719    1 ISQLKAEIKEWERAFAAKNGRKPSKDDIKKNP-EIAKKYKLYSKLK 45
ZnF_C2HC smart00343
zinc finger;
394-408 2.33e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 36.65  E-value: 2.33e-03
                            10
                    ....*....|....*
gi 568993644    394 TCFRCGQFGHWASQC 408
Cdd:smart00343    1 KCYNCGKEGHIARDC 15
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 393-410 9.83e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 34.81  E-value: 9.83e-03
                           10
                   ....*....|....*...
gi 568993644   393 DTCFRCGQFGHWASQCSQ 410
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
 
Name Accession Description Interval E-value
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
485-844 9.26e-116

Superfamily II DNA helicase RecQ [Replication, recombination and repair];


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 370.24  E-value: 9.26e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  485 AEVFQALERL-GYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALLyaqrSPCLTLVVSPLLSLMDDQVSDLP 563
Cdd:COG0514     3 DDALEVLKRVfGYDSFRPGQEEIIEAVLAGRDALVVMPTGGGKSLCYQLPALL----LPGLTLVVSPLIALMKDQVDALR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  564 SC-LKAACLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALvgcgaRGPGSLPQAAQLPPIAFAcIDEVHCLSQWSHNFRP 642
Cdd:COG0514    79 AAgIRAAFLNSSLSAEERREVLRALRAGELKLLYVAPERL-----LNPRFLELLRRLKISLFA-IDEAHCISQWGHDFRP 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  643 CYLRVcKVLREHMGVRCFLGLTATATRSTARDVAQHLGIAGEFELSGSANIPaNLHLSVS--MDRDSDQALVTLLQGdrf 720
Cdd:COG0514   153 DYRRL-GELRERLPNVPVLALTATATPRVRADIAEQLGLEDPRVFVGSFDRP-NLRLEVVpkPPDDKLAQLLDFLKE--- 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  721 RTLDSVIIYCTRRKDTERVAALLRTclsmvgdsrpRGcgpeaI-AEAYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGM 799
Cdd:COG0514   228 HPGGSGIVYCLSRKKVEELAEWLRE----------AG-----IrAAAYHAGLDAEEREANQDRFLRDEVDVIVATIAFGM 292

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*
gi 568993644  800 GLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFMHPQ 844
Cdd:COG0514   293 GIDKPDVRFVIHYDLPKSIEAYYQEIGRAGRDGLPAEALLLYGPE 337
DEXHc_RecQ4-like cd18018
DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) ...
 488-690 2.14e-98

DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Mutations cause Rothmund-Thomson/RAPADILINO/Baller-Gerold syndrome.


Pssm-ID: 350776 [Multi-domain]  Cd Length: 201  Bit Score: 311.88  E-value: 2.14e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  488 FQALERL-GYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALLYAQRSPCLTLVVSPLLSLMDDQVSDLPSCL 566
Cdd:cd18018     1 LKLLRRVfGHPSFRPGQEEAIARLLSGRSTLVVLPTGAGKSLCYQLPALLLRRRGPGLTLVVSPLIALMKDQVDALPRAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  567 KAACLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALvgcgaRGPGSLPQAAQLPPIAFACIDEVHCLSQWSHNFRPCYLR 646
Cdd:cd18018    81 KAAALNSSLTREERRRILEKLRAGEVKILYVSPERL-----VNESFRELLRQTPPISLLVVDEAHCISEWSHNFRPDYLR 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 568993644  647 VCKVLREHMGVRCFLGLTATATRSTARDVAQHLGIAGEFELSGS 690
Cdd:cd18018   156 LCRVLRELLGAPPVLALTATATKRVVEDIASHLGIPESGVVRGP 199
recQ_fam TIGR00614
ATP-dependent DNA helicase, RecQ family; All proteins in this family for which functions are ...
 495-843 1.77e-90

ATP-dependent DNA helicase, RecQ family; All proteins in this family for which functions are known are 3'-5' DNA-DNA helicases. These proteins are used for recombination, recombinational repair, and possibly maintenance of chromosome stability. 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: 129701 [Multi-domain]  Cd Length: 470  Bit Score: 300.53  E-value: 1.77e-90
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644   495 GYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALLyaqrSPCLTLVVSPLLSLMDDQVSDLP-SCLKAACLHS 573
Cdd:TIGR00614    8 GLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALY----SDGITLVISPLISLMEDQVLQLQaLGIPATFLNS 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644   574 GMTKKQRESVLKKVRAAQVHVLIVSPEALvgCGARGPGSLPQAAQLppIAFACIDEVHCLSQWSHNFRPCYlRVCKVLRE 653
Cdd:TIGR00614   84 AQTKEQQLNVLTDLKDGKIKLLYVTPEKI--SASNRLLQTLEERKG--ITLIAVDEAHCISQWGHDFRPDY-KALGSLKQ 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644   654 HMGVRCFLGLTATATRSTARDVAQHLGIAGEFELSGSANIPaNLHLSVsMDRDSD--QALVTLLQGdRFRTlDSVIIYCT 731
Cdd:TIGR00614  159 KFPNVPVMALTATASPSVREDILRQLNLLNPQIFCTSFDRP-NLYYEV-RRKTPKilEDLLRFIRK-EFEG-KSGIIYCP 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644   732 RRKDTERVAALLRTclsmVGDSrprgcgpeaiAEAYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRPDVRAVLH 811
Cdd:TIGR00614  235 SRKKVEQVAAELQK----LGLA----------AGAYHAGLEDSARDDVQHKFQRDEIQVVVATVAFGMGINKPDVRFVIH 300

                          330       340       350
                   ....*....|....*....|....*....|..
gi 568993644   812 LGLPPSFESYVQAIGRAGRDGKPAHCHLFMHP 843
Cdd:TIGR00614  301 YSLPKSMESYYQESGRAGRDGLPSECHLFYAP 332
recQ TIGR01389
ATP-dependent DNA helicase RecQ; The ATP-dependent DNA helicase RecQ of E. coli is about 600 ...
 488-844 3.78e-88

ATP-dependent DNA helicase RecQ; The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273594 [Multi-domain]  Cd Length: 591  Bit Score: 298.14  E-value: 3.78e-88
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644   488 FQALER-LGYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALLYaqrsPCLTLVVSPLLSLMDDQVSDLPSC- 565
Cdd:TIGR01389    2 QQVLKRtFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL----KGLTVVISPLISLMKDQVDQLRAAg 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644   566 LKAACLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALVGcgargPGSLPQAAQLPPIAFAcIDEVHCLSQWSHNFRPCYL 645
Cdd:TIGR01389   78 VAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQ-----DYFLNMLQRIPIALVA-VDEAHCVSQWGHDFRPEYQ 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644   646 RVCkVLREHMGVRCFLGLTATATRSTARDVAQHLGIAGEFELSGSANIPaNLHLSVSMDRDSDQALVTLLQGDRFRtldS 725
Cdd:TIGR01389  152 RLG-SLAERFPQVPRIALTATADAETRQDIRELLRLADANEFITSFDRP-NLRFSVVKKNNKQKFLLDYLKKHRGQ---S 226

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644   726 VIIYCTRRKDTERVAALLRTClsmvgdsrprgcGPEAIAeaYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRPD 805
Cdd:TIGR01389  227 GIIYASSRKKVEELAERLESQ------------GISALA--YHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPN 292

                          330       340       350
                   ....*....|....*....|....*....|....*....
gi 568993644   806 VRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFMHPQ 844
Cdd:TIGR01389  293 VRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPA 331
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 479-843 1.19e-79

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 274.67  E-value: 1.19e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  479 QVAETPAEVFQAL-ERLGYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALLYaqrsPCLTLVVSPLLSLMDD 557
Cdd:PRK11057    5 EVLNLESLAKQVLqETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL----DGLTLVVSPLISLMKD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  558 QVSDL-PSCLKAACLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALVGcgargPGSLPQAAQLPPIAFAcIDEVHCLSQW 636
Cdd:PRK11057   81 QVDQLlANGVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMM-----DNFLEHLAHWNPALLA-VDEAHCISQW 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  637 SHNFRPCYlRVCKVLREHMGVRCFLGLTATATRSTARDVAQHLGIAGEFELSGSANIPANLHLSVSMDRDSDQaLVTLLQ 716
Cdd:PRK11057  155 GHDFRPEY-AALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYTLVEKFKPLDQ-LMRYVQ 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  717 GDRFRtldSVIIYCTRRKDTERVAALLRTclsmvgdsrpRGCGpeaiAEAYHAGMSSQERRRVQQAFMRGHLRMVVATVA 796
Cdd:PRK11057  233 EQRGK---SGIIYCNSRAKVEDTAARLQS----------RGIS----AAAYHAGLDNDVRADVQEAFQRDDLQIVVATVA 295

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 568993644  797 FGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFMHP 843
Cdd:PRK11057  296 FGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDP 342
DEXHc_RecQ cd17920
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ...
 492-690 1.51e-65

DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box helicase superfamily is a family of highly conserved DNA repair helicases. This domain contains the ATP-binding region.


Pssm-ID: 350678 [Multi-domain]  Cd Length: 200  Bit Score: 220.10  E-value: 1.51e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  492 ERLGYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALLyaqrSPCLTLVVSPLLSLMDDQVSDLPS-CLKAAC 570
Cdd:cd17920     6 EVFGYDEFRPGQLEAINAVLAGRDVLVVMPTGGGKSLCYQLPALL----LDGVTLVVSPLISLMQDQVDRLQQlGIRAAA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  571 LHSGMTKKQRESVLKKVRAAQVHVLIVSPEALVGCGARgpGSLPQAAQLPPIAFACIDEVHCLSQWSHNFRPCYLRVCKV 650
Cdd:cd17920    82 LNSTLSPEEKREVLLRIKNGQYKLLYVTPERLLSPDFL--ELLQRLPERKRLALIVVDEAHCVSQWGHDFRPDYLRLGRL 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 568993644  651 LREHMGVrCFLGLTATATRSTARDVAQHLGIAGEFELSGS 690
Cdd:cd17920   160 RRALPGV-PILALTATATPEVREDILKRLGLRNPVIFRAS 198
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 696-840 3.60e-55

C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. 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: 350181 [Multi-domain]  Cd Length: 134  Bit Score: 187.80  E-value: 3.60e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  696 NLHLSVSMDRDSDQALVTLLQGDRFRTLDSVIIYCTRRKDTERVAALLRTClsmvGDSrprgcgpeaiAEAYHAGMSSQE 775
Cdd:cd18794     3 NLFYSVRPKDKKDEKLDLLKRIKVEHLGGSGIIYCLSRKECEQVAARLQSK----GIS----------AAAYHAGLEPSD 68

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568993644  776 RRRVQQAFMRGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLF 840
Cdd:cd18794    69 RRDVQRKWLRDKIQVIVATVAFGMGIDKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECILF 133
PLN03137 PLN03137
ATP-dependent DNA helicase; Q4-like; Provisional
 495-840 4.07e-52

ATP-dependent DNA helicase; Q4-like; Provisional


Pssm-ID: 215597 [Multi-domain]  Cd Length: 1195  Bit Score: 200.89  E-value: 4.07e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  495 GYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALLyaqrSPCLTLVVSPLLSLMDDQVSDL-PSCLKAACLHS 573
Cdd:PLN03137  457 GNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALI----CPGITLVISPLVSLIQDQIMNLlQANIPAASLSA 532

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  574 GMTKKQRESVLKKVRA--AQVHVLIVSPEALVGCGA--RGPGSLPQAAQLPPIAfacIDEVHCLSQWSHNFRPCYlRVCK 649
Cdd:PLN03137  533 GMEWAEQLEILQELSSeySKYKLLYVTPEKVAKSDSllRHLENLNSRGLLARFV---IDEAHCVSQWGHDFRPDY-QGLG 608

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  650 VLREHMGVRCFLGLTATATRSTARDVAQHLGIAGEFELSGSANIPaNLHLSVSmdRDSDQALVTLLQGDRFRTLDSV-II 728
Cdd:PLN03137  609 ILKQKFPNIPVLALTATATASVKEDVVQALGLVNCVVFRQSFNRP-NLWYSVV--PKTKKCLEDIDKFIKENHFDECgII 685

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  729 YCTRRKDTERVAALLRTClsmvGDSrprgcgpeaiAEAYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRPDVRA 808
Cdd:PLN03137  686 YCLSRMDCEKVAERLQEF----GHK----------AAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRF 751

                         330       340       350
                  ....*....|....*....|....*....|..
gi 568993644  809 VLHLGLPPSFESYVQAIGRAGRDGKPAHCHLF 840
Cdd:PLN03137  752 VIHHSLPKSIEGYHQECGRAGRDGQRSSCVLY 783
DEXHc_RecQ1 cd18015
DEXH-box helicase domain of RecQ1; ATP-dependent DNA helicase Q1 (RecQ1) is part of the RecQ ...
 478-692 5.35e-40

DEXH-box helicase domain of RecQ1; ATP-dependent DNA helicase Q1 (RecQ1) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350773 [Multi-domain]  Cd Length: 209  Bit Score: 147.51  E-value: 5.35e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  478 GQVAETPAEVFQaLErlgyrAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALLyaqrSPCLTLVVSPLLSLMDD 557
Cdd:cd18015     4 GKVKDTLKNVFK-LE-----KFRPLQLETINATMAGRDVFLVMPTGGGKSLCYQLPALC----SDGFTLVVSPLISLMED 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  558 QVSDLPSC-LKAACLHSGMTKKQRESVLKKVR--AAQVHVLIVSPEALVGcGARGPGSLPQAAQLPPIAFACIDEVHCLS 634
Cdd:cd18015    74 QLMALKKLgISATMLNASSSKEHVKWVHAALTdkNSELKLLYVTPEKIAK-SKRFMSKLEKAYNAGRLARIAIDEVHCCS 152

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568993644  635 QWSHNFRPCYlrvckvlrEHMGV--RCF-----LGLTATATRSTARDVAQHLGIAGEFELSGSAN 692
Cdd:cd18015   153 QWGHDFRPDY--------KKLGIlkRQFpnvpiLGLTATATSKVLKDVQKILCIQKCLTFTASFN 209
DpdF NF041063
protein DpdF;
476-844 2.74e-39

protein DpdF;


Pssm-ID: 468990 [Multi-domain]  Cd Length: 813  Bit Score: 158.15  E-value: 2.74e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  476 PLGQVAETPAEVFQAlERLGYRAFR-PGQERAIMRILS---GiSTLLV-LPTGAGKSLCYQLPALLYAQRSPcLTLVVSP 550
Cdd:NF041063  118 LRRTLEPVPGDPFLA-EALGFTHYRsPGQREAVRAALLappG-STLIVnLPTGSGKSLVAQAPALLASRQGG-LTLVVVP 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  551 LLSLMDDQVSDLPSCLKAA--------CLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALVGCGARgpgSLPQAAQLPPI 622
Cdd:NF041063  195 TVALAIDQERRARELLRRAgpdlggplAWHGGLSAEERAAIRQRIRDGTQRILFTSPESLTGSLRP---ALFDAAEAGLL 271

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  623 AFACIDEVHCLSQWSHNFRPCY----------LRVCKvlrEHMGVRCFLgLTATATRSTaRDVAQHL-GIAGEFEL-SGS 690
Cdd:NF041063  272 RYLVVDEAHLVDQWGDGFRPEFqllaglrrslLRLAP---SGRPFRTLL-LSATLTEST-LDTLETLfGPPGPFIVvSAV 346

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  691 anipanlHL----SVSMDRDSDQAlvtllqgDRFRT-LDSV-------IIYCTRRKDTERVAALLRTclsmVGDSRprgc 758
Cdd:NF041063  347 -------QLrpepAYWVAKCDSEE-------ERRERvLEALrhlprplILYVTKVEDAEAWLQRLRA----AGFRR---- 404

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  759 gpeaiAEAYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCH 838
Cdd:NF041063  405 -----VALFHGDTPDAERERLIEQWRENELDIVVATSAFGLGMDKSDVRTVIHACVPETLDRFYQEVGRGGRDGKASLSL 479


                  ....*.
gi 568993644  839 LFMHPQ 844
Cdd:NF041063  480 LIYTPD 485
DEXHc_RecQ3 cd18017
DEAH-box helicase domain of RecQ3; DEAD-like helicase RecQ3 (also called Werner syndrome ...
 495-681 1.16e-32

DEAH-box helicase domain of RecQ3; DEAD-like helicase RecQ3 (also called Werner syndrome ATP-dependent helicase or WRN) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Mutations cause Werner's syndrome.


Pssm-ID: 350775 [Multi-domain]  Cd Length: 193  Bit Score: 125.66  E-value: 1.16e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  495 GYRAFRPGQERAIMRIL-SGISTLLVLPTGAGKSLCYQLPALLYAQrspcLTLVVSPLLSLMDDQVSDLPSCLKAACLhs 573
Cdd:cd18017     9 GHSSFRPVQWKVIRSVLeERRDNLVVMATGYGKSLCYQYPSVLLNS----LTLVISPLISLMEDQVLQLVMSNIPACF-- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  574 gMTKKQRESVLKKVRAAQVHVLIVSPEAlvgcGARGPGSLPQ-AAQLPPIAfacIDEVHCLSQWSHNFRPCYlRVCKVLR 652
Cdd:cd18017    83 -LGSAQSQNVLDDIKMGKIRVIYVTPEF----VSKGLELLQQlRNGITLIA---IDEAHCVSQWGHDFRSSY-RHLGSIR 153

                         170       180
                  ....*....|....*....|....*....
gi 568993644  653 EHMGVRCFLGLTATATRSTARDVAQHLGI 681
Cdd:cd18017   154 NRLPNVPIVALTATATPSVRDDIIKNLNL 182
DEXHc_RecQ5 cd18014
DEAH-box helicase domain of RecQ5; ATP-dependent DNA helicase Q5 (RecQ5) is part of the RecQ ...
 495-681 3.13e-32

DEAH-box helicase domain of RecQ5; ATP-dependent DNA helicase Q5 (RecQ5) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350772 [Multi-domain]  Cd Length: 205  Bit Score: 124.89  E-value: 3.13e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  495 GYRAFR-PGQERAIMRILSGISTLLV-LPTGAGKSLCYQLPALLYAQrspcLTLVVSPLLSLMDDQVSDLPSC-LKAACL 571
Cdd:cd18014     9 GHSDFKsPLQEKATMAVVKGNKDVFVcMPTGAGKSLCYQLPALLAKG----ITIVISPLIALIQDQVDHLKTLkIRVDSL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  572 HSGMTKKQRESVLKKVRAA--QVHVLIVSPEAlvgcgARGPGSLPQAAQLPP---IAFACIDEVHCLSQWSHNFRPCYLR 646
Cdd:cd18014    85 NSKLSAQERKRIIADLESEkpQTKFLYITPEM-----AATSSFQPLLSSLVSrnlLSYLVVDEAHCVSQWGHDFRPDYLR 159

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 568993644  647 VCKVLREHMGVRCfLGLTATATRSTARDVAQHLGI 681
Cdd:cd18014   160 LGALRSRYGHVPW-VALTATATPQVQEDIFAQLRL 193
DEXHc_RecQ2_BLM cd18016
DEAH-box helicase domain of RecQ2; ATP-dependent DNA helicase Q2 (RecQ2, also called Bloom ...
 493-681 1.38e-29

DEAH-box helicase domain of RecQ2; ATP-dependent DNA helicase Q2 (RecQ2, also called Bloom syndrome protein homolog or BLM) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Mutations in RecQ2 cause Bloom syndrome.


Pssm-ID: 350774 [Multi-domain]  Cd Length: 208  Bit Score: 117.24  E-value: 1.38e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  493 RLGYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALLyaqrSPCLTLVVSPLLSLMDDQVSDLPSC-LKAACL 571
Cdd:cd18016    12 KFGLHQFRTNQLEAINAALLGEDCFVLMPTGGGKSLCYQLPACV----SPGVTVVISPLRSLIVDQVQKLTSLdIPATYL 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  572 HSGMTKKQRESVLKKVRAAQ--VHVLIVSPEAlVGCGARGPGSLPQAAQLPPIAFACIDEVHCLSQWSHNFRPCYLRVcK 649
Cdd:cd18016    88 TGDKTDAEATKIYLQLSKKDpiIKLLYVTPEK-ISASNRLISTLENLYERKLLARFVIDEAHCVSQWGHDFRPDYKRL-N 165

                         170       180       190
                  ....*....|....*....|....*....|..
gi 568993644  650 VLREHMGVRCFLGLTATATRSTARDVAQHLGI 681
Cdd:cd18016   166 MLRQKFPSVPMMALTATATPRVQKDILNQLKM 197
DEXDc smart00487
DEAD-like helicases superfamily;
491-679 4.60e-25

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 104.11  E-value: 4.60e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644    491 LERLGYRAFRPGQERAIMRILSGI-STLLVLPTGAGKSLCYQLPALLYAQRSP-CLTLVVSPLLSLMDDQVSDL-----P 563
Cdd:smart00487    1 IEKFGFEPLRPYQKEAIEALLSGLrDVILAAPTGSGKTLAALLPALEALKRGKgGRVLVLVPTRELAEQWAEELkklgpS 80

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644    564 SCLKAACLHSGMTKKQResvLKKVRAAQVHVLIVSPEALVGCGARGPGSLPQaaqlppIAFACIDEVHCLSQWshNFRPC 643
Cdd:smart00487   81 LGLKVVGLYGGDSKREQ---LRKLESGKTDILVTTPGRLLDLLENDKLSLSN------VDLVILDEAHRLLDG--GFGDQ 149

                           170       180       190
                    ....*....|....*....|....*....|....*.
gi 568993644    644 YLRVCKVLREHmgvRCFLGLTATATRSTARDVAQHL 679
Cdd:smart00487  150 LEKLLKLLPKN---VQLLLLSATPPEEIENLLELFL 182
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 500-673 1.74e-24

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 101.17  E-value: 1.74e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644   500 RPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPAL--LYAQRSPCLTLVVSPLLSLMDDQVSDL-----PSCLKAACLH 572
Cdd:pfam00270    1 TPIQAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALeaLDKLDNGPQALVLAPTRELAEQIYEELkklgkGLGLKVASLL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644   573 SGMTKKQRESVLKKvraaqVHVLIVSPEALVgcgargpGSLPQAAQLPPIAFACIDEVHCLSQWShnFRPCYLRVCKVLR 652
Cdd:pfam00270   81 GGDSRKEQLEKLKG-----PDILVGTPGRLL-------DLLQERKLLKNLKLLVLDEAHRLLDMG--FGPDLEEILRRLP 146

                          170       180
                   ....*....|....*....|.
gi 568993644   653 EHmgvRCFLGLTATATRSTAR 673
Cdd:pfam00270  147 KK---RQILLLSATLPRNLED 164
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 474-835 8.51e-23

ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, recombination and repair];


Pssm-ID: 440818 [Multi-domain]  Cd Length: 758  Bit Score: 105.30  E-value: 8.51e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  474 PGPLGQVAETPA----EVFQALERLGYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPAL--LYAQRSPClTLV 547
Cdd:COG1205    28 PAREARYAPWPDwlppELRAALKKRGIERLYSHQAEAIEAARAGKNVVIATPTASGKSLAYLLPVLeaLLEDPGAT-ALY 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  548 VSPLLSLMDDQVS-------DLPSCLKAACLHSGMTKKQRESVLKkvraaQVHVLIVSPEAL-VGCgargpgsLPQAAQL 619
Cdd:COG1205   107 LYPTKALARDQLRrlrelaeALGLGVRVATYDGDTPPEERRWIRE-----HPDIVLTNPDMLhYGL-------LPHHTRW 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  620 PPIaFAC-----IDEVHCL-----SQWSHNFRPcYLRVCkvlrEHMGVRC-FLGLTAT-------ATRSTARDVAQhlgI 681
Cdd:COG1205   175 ARF-FRNlryvvIDEAHTYrgvfgSHVANVLRR-LRRIC----RHYGSDPqFILASATignpaehAERLTGRPVTV---V 245

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  682 AGEFELSGSANI----PANLHLSVSMDRDSDQA-LVTLLQGDRFRTldsvIIYCTRRKDTERVAALLRtclsmvgDSRPR 756
Cdd:COG1205   246 DEDGSPRGERTFvlwnPPLVDDGIRRSALAEAArLLADLVREGLRT----LVFTRSRRGAELLARYAR-------RALRE 314

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568993644  757 GCGPEAIAeAYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPA 835
Cdd:COG1205   315 PDLADRVA-AYRAGYLPEERREIERGLRSGELLGVVSTNALELGIDIGGLDAVVLAGYPGTRASFWQQAGRAGRRGQDS 392
HELICc smart00490
helicase superfamily c-terminal domain;
764-832 5.13e-21

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 88.42  E-value: 5.13e-21
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568993644    764 AEAYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDG 832
Cdd:smart00490   14 VARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82
RecQL4_SLD2_NTD cd22289
N-terminal homeodomain-like domain of metazoan RecQ protein-like 4 (RecQL4), fungal DNA ...
 2-50 1.66e-19

N-terminal homeodomain-like domain of metazoan RecQ protein-like 4 (RecQL4), fungal DNA replication regulator SLD2 and similar proteins; RecQL4, also called ATP-dependent DNA helicase Q4, or DNA helicase, RecQ-like type 4 (RecQ4), or RTS, is a DNA-dependent ATPase that may modulate chromosome segregation. This family also includes fungal DNA replication regulator SLD2, also known as DNA replication and checkpoint protein 1 (DRC1), which functions with DPB11 to control DNA replication and the S-phase checkpoint. It is also required for the proper activation of RAD53 in response to DNA damage and replication blocks. This model corresponds to the N-terminal domain of RecQL4 and SLD2, which is a homeodomain-like DNA interaction motif.


Pssm-ID: 412085  Cd Length: 49  Bit Score: 83.06  E-value: 1.66e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 568993644    2 ERLATVRARLQEWERAFARLHGRRPAKGDVEAAPEETRALYREYRNLKQ 50
Cdd:cd22289     1 ERLQELKIALKTWERAFAKKHGRKPTKDDIKAAPEEIKDLYKEYAKLKK 49
SF2_C_Hrq cd18797
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...
 727-835 2.32e-18

C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. 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: 350184 [Multi-domain]  Cd Length: 146  Bit Score: 83.08  E-value: 2.32e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  727 IIYCTRRKDTERVAALLRTCLsmvgdsRPRGCGPEAIAeAYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRPDV 806
Cdd:cd18797    39 IVFCRSRKLAELLLRYLKARL------VEEGPLASKVA-SYRAGYLAEDRREIEAELFNGELLGVVATNALELGIDIGGL 111

                          90       100
                  ....*....|....*....|....*....
gi 568993644  807 RAVLHLGLPPSFESYVQAIGRAGRDGKPA 835
Cdd:cd18797   112 DAVVLAGYPGSLASLWQQAGRAGRRGKDS 140
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 709-832 1.35e-17

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 79.56  E-value: 1.35e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644   709 QALVTLLQGDRFrtlDSVIIYCTRRKDTErvAALLRTCLSMvgdsrprgcgpeaIAEAYHAGMSSQERRRVQQAFMRGHL 788
Cdd:pfam00271    4 EALLELLKKERG---GKVLIFSQTKKTLE--AELLLEKEGI-------------KVARLHGDLSQEEREEILEDFRKGKI 65

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 568993644   789 RMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDG 832
Cdd:pfam00271   66 DVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 705-840 2.64e-15

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise 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. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 73.70  E-value: 2.64e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  705 RDSDQALVTLLQGDRFRTLDSVIIYCTRRKDTERVAALLRTClsmvgdsrprgcGPEAIAeaYHAGMSSQERRRVQQAFM 784
Cdd:cd18787     9 EEEEKKLLLLLLLLEKLKPGKAIIFVNTKKRVDRLAELLEEL------------GIKVAA--LHGDLSQEERERALKKFR 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 568993644  785 RGHLRMVVAT-VAfGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLF 840
Cdd:cd18787    75 SGKVRVLVATdVA-ARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAGRKGTAITF 130
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
479-833 3.17e-15

Replicative superfamily II helicase [Replication, recombination and repair];


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 80.32  E-value: 3.17e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  479 QVAETP-AEVFQALERLGYRAFRPGQERAIMR-ILSGISTLLVLPTGAGKSLCYQLpALLYAQRSPCLTLVVSPLLSLMD 556
Cdd:COG1204     2 KVAELPlEKVIEFLKERGIEELYPPQAEALEAgLLEGKNLVVSAPTASGKTLIAEL-AILKALLNGGKALYIVPLRALAS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  557 DQVSDLPSCLKAACLHSGMTKKQRESVLKkvRAAQVHVLIVSPEALVgcgargpgSL--PQAAQLPPIAFACIDEVH--- 631
Cdd:COG1204    81 EKYREFKRDFEELGIKVGVSTGDYDSDDE--WLGRYDILVATPEKLD--------SLlrNGPSWLRDVDLVVVDEAHlid 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  632 ----------CLSqwshnfrpcylrvcKVLREHMGVRcFLGLTATA--------------TRSTARDVAQHLGIA--GEF 685
Cdd:COG1204   151 desrgptlevLLA--------------RLRRLNPEAQ-IVALSATIgnaeeiaewldaelVKSDWRPVPLNEGVLydGVL 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  686 ELSGSANIPANLHLSVSMDrdsdqalvTLLQGDrfrtldSVIIYCTRRKDTERVAALLRTCLSMVGDSRPRGCGPEAIAE 765
Cdd:COG1204   216 RFDDGSRRSKDPTLALALD--------LLEEGG------QVLVFVSSRRDAESLAKKLADELKRRLTPEEREELEELAEE 281

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  766 ----------------------AYH-AGMSSQERRRVQQAFMRGHLRMVVAT--VAFGMGLdrPdVRAVL-----HLGLP 815
Cdd:COG1204   282 llevseethtnekladclekgvAFHhAGLPSELRRLVEDAFREGLIKVLVATptLAAGVNL--P-ARRVIirdtkRGGMV 358

                         410       420
                  ....*....|....*....|
gi 568993644  816 P--SFEsYVQAIGRAGRDGK 833
Cdd:COG1204   359 PipVLE-FKQMAGRAGRPGY 377
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
500-840 8.48e-15

Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 78.91  E-value: 8.48e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  500 RPGQERAIMRILSGIST-----LLVLPTGAGKSLcyqLPALLYAQ-RSPCLTLVVSPLLSLMDDQVSDLPSCLKAACLHS 573
Cdd:COG1061    82 RPYQQEALEALLAALERgggrgLVVAPTGTGKTV---LALALAAElLRGKRVLVLVPRRELLEQWAEELRRFLGDPLAGG 158

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  574 GmtKKQRESvlkkvraaqvHVLIVSPEALvgcgargpGSLPQAAQLPP-IAFACIDEVHclsqwsHNFRPCYLRVckvlR 652
Cdd:COG1061   159 G--KKDSDA----------PITVATYQSL--------ARRAHLDELGDrFGLVIIDEAH------HAGAPSYRRI----L 208

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  653 EHMGVRCFLGLTATATRSTARDVAQHL--GIAGEF---ELSgSANIPANLH-LSVSMDRDSDQALVTLLQGDRFRTLDS- 725
Cdd:COG1061   209 EAFPAAYRLGLTATPFRSDGREILLFLfdGIVYEYslkEAI-EDGYLAPPEyYGIRVDLTDERAEYDALSERLREALAAd 287

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  726 --------------------VIIYCTRRKDTERVAALLRTclsmvgdsrpRGCGPEAIaeayHAGMSSQERRRVQQAFMR 785
Cdd:COG1061   288 aerkdkilrellrehpddrkTLVFCSSVDHAEALAELLNE----------AGIRAAVV----TGDTPKKEREEILEAFRD 353

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  786 GHLRMVVATVAFGMGLDRPDVRAVLHLGlppSFES---YVQAIGRA--GRDGKPaHCHLF 840
Cdd:COG1061   354 GELRILVTVDVLNEGVDVPRLDVAILLR---PTGSpreFIQRLGRGlrPAPGKE-DALVY 409
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 516-666 1.67e-14

N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 72.05  E-value: 1.67e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  516 TLLVLPTGAGKSLCYQLPALLYAQRSPCLTLVVSPLLSLMDDQVSDL----PSCLKAACLHSGMTKKQREsvlkKVRAAQ 591
Cdd:cd00046     4 VLITAPTGSGKTLAALLAALLLLLKKGKKVLVLVPTKALALQTAERLrelfGPGIRVAVLVGGSSAEERE----KNKLGD 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568993644  592 VHVLIVSPEALVGCGARGPGSLpqaaqLPPIAFACIDEVHCLSQWSHNFRPCYLRVCKVLREHMGVrcfLGLTAT 666
Cdd:cd00046    80 ADIIIATPDMLLNLLLREDRLF-----LKDLKLIIVDEAHALLIDSRGALILDLAVRKAGLKNAQV---ILLSAT 146
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
484-833 1.00e-13

Superfamily II DNA and RNA helicase [Replication, recombination and repair];


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 74.80  E-value: 1.00e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  484 PAEVFQALERLGYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPA---LLYAQRSPCLTLVVSPL--LSLmddQ 558
Cdd:COG0513    10 SPPLLKALAELGYTTPTPIQAQAIPLILAGRDVLGQAQTGTGKTAAFLLPLlqrLDPSRPRAPQALILAPTreLAL---Q 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  559 VSD--------LPscLKAACLHSGMT-KKQRESvLKKvraaQVHVLivspealVGCgargPGSLpqaaqlppiafacID- 628
Cdd:COG0513    87 VAEelrklakyLG--LRVATVYGGVSiGRQIRA-LKR----GVDIV-------VAT----PGRL-------------LDl 135

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  629 ---------EVHCLsqwshnfrpcylrvckVLRE-----HMG----VRCFLGLT----------ATATRSTARDVAQHLG 680
Cdd:COG0513   136 iergaldlsGVETL----------------VLDEadrmlDMGfiedIERILKLLpkerqtllfsATMPPEIRKLAKRYLK 199

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  681 IAGEFELSGSANIPANLHLSVSM--DRDSDQALVTLLQGDRFrtlDSVIIYCTRRKDTERVAALLRTclsmvgdsrpRGc 758
Cdd:COG0513   200 NPVRIEVAPENATAETIEQRYYLvdKRDKLELLRRLLRDEDP---ERAIVFCNTKRGADRLAEKLQK----------RG- 265

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568993644  759 gpeAIAEAYHAGMSSQERRRVQQAFMRGHLRMVVAT-VAfGMGLDRPDVRAVLHLGLPPSFESYVQAIG---RAGRDGK 833
Cdd:COG0513   266 ---ISAAALHGDLSQGQRERALDAFRNGKIRVLVATdVA-ARGIDIDDVSHVINYDLPEDPEDYVHRIGrtgRAGAEGT 340
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 725-841 4.25e-12

C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. 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: 350183 [Multi-domain]  Cd Length: 150  Bit Score: 65.36  E-value: 4.25e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  725 SVIIYCTRRKDTERVAALLRtclsmvgdSRPRGCGPEAIAEAYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRP 804
Cdd:cd18796    40 STLVFTNTRSQAERLAQRLR--------ELCPDRVPPDFIALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIG 111

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 568993644  805 DVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFM 841
Cdd:cd18796   112 DVDLVIQIGSPKSVARLLQRLGRSGHRPGAASKGRLV 148
PTZ00110 PTZ00110
helicase; Provisional
 474-843 2.54e-10

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 64.79  E-value: 2.54e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  474 PGPLGQVAET--PAEVFQALERLGYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALLYAQRSPCL------- 544
Cdd:PTZ00110  126 PKPVVSFEYTsfPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLrygdgpi 205

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  545 TLVVSPLLSLMDdQVSD------LPSCLKAACLHSGMTKKQRESVLKKvraaQVHVLIVSPEALVGCGARGPGSLPQaaq 618
Cdd:PTZ00110  206 VLVLAPTRELAE-QIREqcnkfgASSKIRNTVAYGGVPKRGQIYALRR----GVEILIACPGRLIDFLESNVTNLRR--- 277

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  619 lppIAFACIDEVHclSQWSHNFRPCYLRVCKVLREHmgvRCFLGLTATATR---STARDVAQHLGI---AGEFELSGSAN 692
Cdd:PTZ00110  278 ---VTYLVLDEAD--RMLDMGFEPQIRKIVSQIRPD---RQTLMWSATWPKevqSLARDLCKEEPVhvnVGSLDLTACHN 349

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  693 IPANLHLsvsMDRDSDQALVTLLQGDRFRTLDSVIIYCTRRKDTERVAALLRTclsmvgDSRPRGCgpeaiaeaYHAGMS 772
Cdd:PTZ00110  350 IKQEVFV---VEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRL------DGWPALC--------IHGDKK 412

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568993644  773 SQERRRVQQAFMRGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFMHP 843
Cdd:PTZ00110  413 QEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTP 483
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 725-832 2.74e-10

C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. This family includes spliceosomal Brr2 RNA helicase, ASCC3 (involved in the repair of N-alkylated nucleotides), Mtr4 (involved in processing of structured RNAs), DDX60 (involved in viral RNA degradation), and other proteins. Ski2-like RNA helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. 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: 350182 [Multi-domain]  Cd Length: 154  Bit Score: 60.26  E-value: 2.74e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  725 SVIIYCTRRKDTERVAALLRtclsmvgdsrprGCGpeaiaeAYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRP 804
Cdd:cd18795    45 PVLVFCSSRKECEKTAKDLA------------GIA------FHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLP 106

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 568993644  805 DVRAVLhLGLP----------PSFEsYVQAIGRAGRDG 832
Cdd:cd18795   107 ARTVII-KGTQrydgkgyrelSPLE-YLQMIGRAGRPG 142
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 791-841 5.92e-10

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The 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: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 56.56  E-value: 5.92e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 568993644  791 VVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGK-PAHCHLFM 841
Cdd:cd18785    26 LVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRGGKdEGEVILFV 77
Lhr COG1201
Lhr-like helicase [Replication, recombination and repair];
496-829 6.90e-10

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


Pssm-ID: 440814 [Multi-domain]  Cd Length: 850  Bit Score: 63.58  E-value: 6.90e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  496 YRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALL-YAQRSP-------CLTLVVSPLLSL------------- 554
Cdd:COG1201    22 FGAPTPPQREAWPAIAAGESTLLIAPTGSGKTLAAFLPALDeLARRPRpgelpdgLRVLYISPLKALandiernlraple 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  555 -MDDQVSDLPSCLKAAcLHSGMTKkQREsvlkkvRAAQV----HVLIVSPEALvgcgargpgSL----PQAAQLppiaFA 625
Cdd:COG1201   102 eIGEAAGLPLPEIRVG-VRTGDTP-ASE------RQRQRrrppHILITTPESL---------ALlltsPDAREL----LR 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  626 C-----IDEVHCL------SQWS------HNFRPCYLRVckvlrehmgvrcfLGLTATAtrstaRDVAQhlgiAGEFeLS 688
Cdd:COG1201   161 GvrtviVDEIHALagskrgVHLAlslerlRALAPRPLQR-------------IGLSATV-----GPLEE----VARF-LV 217

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  689 GS----------ANIPANLHLSV-SMDRDSD--------------QALVTLLQGDRfrtldSVIIYC-TRRKdTERVAAL 742
Cdd:COG1201   218 GYedprpvtivdAGAGKKPDLEVlVPVEDLIerfpwaghlwphlyPRVLDLIEAHR-----TTLVFTnTRSQ-AERLFQR 291

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  743 LRtclsmvgdsRPRGCGPEAIAeAYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYV 822
Cdd:COG1201   292 LN---------ELNPEDALPIA-AHHGSLSREQRLEVEEALKAGELRAVVATSSLELGIDIGDVDLVIQVGSPKSVARLL 361


                  ....*..
gi 568993644  823 QAIGRAG 829
Cdd:COG1201   362 QRIGRAG 368
PRK09751 PRK09751
putative ATP-dependent helicase Lhr; Provisional
 728-829 8.06e-10

putative ATP-dependent helicase Lhr; Provisional


Pssm-ID: 137505 [Multi-domain]  Cd Length: 1490  Bit Score: 63.79  E-value: 8.06e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  728 IYCTRRKDTERVAALLRTCLSMVGDSRPRGCG-PEAIAEAYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRPDV 806
Cdd:PRK09751  267 LYAARLQRSPSIAVDAAHFESTSGATSNRVQSsDVFIARSHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAV 346

                          90       100
                  ....*....|....*....|...
gi 568993644  807 RAVLHLGLPPSFESYVQAIGRAG 829
Cdd:PRK09751  347 DLVIQVATPLSVASGLQRIGRAG 369
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 473-865 2.08e-09

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 61.73  E-value: 2.08e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  473 PPGPLGQVAET--PAEVFQALERLGYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPAL----------LYAQR 540
Cdd:PLN00206  116 VPPPILSFSSCglPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIIsrcctirsghPSEQR 195

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  541 SPcLTLVVSPLLSLMDdQVSDlpsclKAACLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALVGCgargPGSL-----PQ 615
Cdd:PLN00206  196 NP-LAMVLTPTRELCV-QVED-----QAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGT----PGRLidllsKH 264

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  616 AAQLPPIAFACIDEVHCLSQwsHNFRPCYLRVCKVLREHMgvrcFLGLTATATRSTARdVAQHLGIAGEFELSGSANIP- 694
Cdd:PLN00206  265 DIELDNVSVLVLDEVDCMLE--RGFRDQVMQIFQALSQPQ----VLLFSATVSPEVEK-FASSLAKDIILISIGNPNRPn 337

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  695 -ANLHLSVSMD-RDSDQALVTLLQgDRFRTLDSVIIYCTRRKDtervAALLRTCLSMVGDSRprgcgpeaiAEAYHAGMS 772
Cdd:PLN00206  338 kAVKQLAIWVEtKQKKQKLFDILK-SKQHFKPPAVVFVSSRLG----ADLLANAITVVTGLK---------ALSIHGEKS 403

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  773 SQERRRVQQAFMRGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFMHPQvGSPISPD 852
Cdd:PLN00206  404 MKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEE-DRNLFPE 482

                         410
                  ....*....|....*.
gi 568993644  853 ---QDRPRGSTIPRPL 865
Cdd:PLN00206  483 lvaLLKSSGAAIPREL 498
PRK13767 PRK13767
ATP-dependent helicase; Provisional
 496-829 8.16e-09

ATP-dependent helicase; Provisional


Pssm-ID: 237497 [Multi-domain]  Cd Length: 876  Bit Score: 60.28  E-value: 8.16e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  496 YRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPAL---------------LYAqrspcltLVVSPLLSLMDD--- 557
Cdd:PRK13767   30 FGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIdelfrlgregeledkVYC-------LYVSPLRALNNDihr 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  558 ----------QVS-----DLPScLKAACLHSGMTKKQRESVLKKvraaQVHVLIVSPE----ALVGcgargpgslPQAAQ 618
Cdd:PRK13767  103 nleeplteirEIAkergeELPE-IRVAIRTGDTSSYEKQKMLKK----PPHILITTPEslaiLLNS---------PKFRE 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  619 -LPPIAFACIDEVHCLSQwshNFRPCYLRVC-KVLREHMG---VRcfLGLTATAtrSTARDVAQHLGIAGEFELSGSANI 693
Cdd:PRK13767  169 kLRTVKWVIVDEIHSLAE---NKRGVHLSLSlERLEELAGgefVR--IGLSATI--EPLEEVAKFLVGYEDDGEPRDCEI 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  694 panlhLSVSMDRDSDQALVT----LLQGDR-------FRTLDSVI-------IYCTRRKDTERVAALLRTCLSMVGDSrp 755
Cdd:PRK13767  242 -----VDARFVKPFDIKVISpvddLIHTPAeeisealYETLHELIkehrttlIFTNTRSGAERVLYNLRKRFPEEYDE-- 314

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568993644  756 rgcgpEAIaEAYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAG 829
Cdd:PRK13767  315 -----DNI-GAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAG 382
Drc1-Sld2 pfam11719
DNA replication and checkpoint protein; Genome duplication is precisely regulated by ...
 4-49 9.88e-09

DNA replication and checkpoint protein; Genome duplication is precisely regulated by cyclin-dependent kinases CDKs, which bring about the onset of S phase by activating replication origins and then prevent re-licensing of origins until mitosis is completed. The optimum sequence motif for CDK phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found to have at least 11 potential phosphorylation sites. Drc1 is required for DNA synthesis and S-M replication checkpoint control. Drc1 associates with Cdc2 and is phosphorylated at the onset of S phase when Cdc2 is activated. Thus Cdc2 promotes DNA replication by phosphorylating Drc1 and regulating its association with Cut5. Sld2 and Sld3 represent the minimal set of S-CDK substrates required for DNA replication.


Pssm-ID: 371692 [Multi-domain]  Cd Length: 391  Bit Score: 59.07  E-value: 9.88e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 568993644     4 LATVRARLQEWERAFARLHGRRPAKGDVEAAPeETRALYREYRNLK 49
Cdd:pfam11719    1 ISQLKAEIKEWERAFAAKNGRKPSKDDIKKNP-EIAKKYKLYSKLK 45
PTZ00424 PTZ00424
helicase 45; Provisional
 722-833 1.03e-07

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 55.99  E-value: 1.03e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  722 TLDSVIIYCTRRKDTERVAALLR----TCLSMVGDsrprgcgpeaiaeayhagMSSQERRRVQQAFMRGHLRMVVATVAF 797
Cdd:PTZ00424  266 TITQAIIYCNTRRKVDYLTKKMHerdfTVSCMHGD------------------MDQKDRDLIMREFRSGSTRVLITTDLL 327

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 568993644  798 GMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGK 833
Cdd:PTZ00424  328 ARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGR 363
COG1202 COG1202
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
764-830 1.68e-07

Superfamily II helicase, archaea-specific [Replication, recombination and repair];


Pssm-ID: 440815 [Multi-domain]  Cd Length: 790  Bit Score: 55.67  E-value: 1.68e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568993644  764 AEAYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRPDVRAVlhlglppsFES------------YVQAIGRAGR 830
Cdd:COG1202   451 AAPYHAGLDYGERKKVERRFADQELAAVVTTAALAAGVDFPASQVI--------FDSlamgiewlsvqeFHQMLGRAGR 521
DEXHc_Hrq1-like cd17923
DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a ...
 503-562 2.73e-07

DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. Hrq1 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350681 [Multi-domain]  Cd Length: 182  Bit Score: 52.20  E-value: 2.73e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568993644  503 QERAIMRILSGISTLLVLPTGAGKSLCYQLPAL--LYAQRSPClTLVVSPLLSLMDDQVSDL 562
Cdd:cd17923     5 QAEAIEAARAGRSVVVTTGTASGKSLCYQLPILeaLLRDPGSR-ALYLYPTKALAQDQLRSL 65
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 499-666 3.98e-07

DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 50.77  E-value: 3.98e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  499 FRPGQERAIMRILSGIST---LLVLPTGAGKSLC-YQLPALLYAQRspclTLVVSPLLSLMDDQVSDLpsclkAACLHSG 574
Cdd:cd17926     1 LRPYQEEALEAWLAHKNNrrgILVLPTGSGKTLTaLALIAYLKELR----TLIVVPTDALLDQWKERF-----EDFLGDS 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  575 MTKKQRESVLKKVRAAQvhVLIVSPEALVGCGARGPGSLPQAAQLppIAfaciDEVHCLS--QWSHnfrpcylrvckvLR 652
Cdd:cd17926    72 SIGLIGGGKKKDFDDAN--VVVATYQSLSNLAEEEKDLFDQFGLL--IV----DEAHHLPakTFSE------------IL 131

                         170
                  ....*....|....
gi 568993644  653 EHMGVRCFLGLTAT 666
Cdd:cd17926   132 KELNAKYRLGLTAT 145
DEADc cd00268
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ...
 489-603 2.63e-06

DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise 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: 350669 [Multi-domain]  Cd Length: 196  Bit Score: 49.36  E-value: 2.63e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  489 QALERLGYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPAL------LYAQRSPCLTLVVSPL--LSLmddQVS 560
Cdd:cd00268     3 KALKKLGFEKPTPIQAQAIPLILSGRDVIGQAQTGSGKTLAFLLPILekllpePKKKGRGPQALVLAPTreLAM---QIA 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 568993644  561 DL------PSCLKAACLHSGMTKKQRESVLKKvraaQVHVLIVSPEALV 603
Cdd:cd00268    80 EVarklgkGTGLKVAAIYGGAPIKKQIEALKK----GPDIVVGTPGRLL 124
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 727-832 3.61e-06

C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. 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: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 47.97  E-value: 3.61e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  727 IIYCTRR----------KDTERVAALLRtCLSMVGDSRprgcgpeaIAEAYHAGMSSQERRRVQQAFMRGHLRMVVATVA 796
Cdd:cd18802    29 IIFVERRatavvlsrllKEHPSTLAFIR-CGFLIGRGN--------SSQRKRSLMTQRKQKETLDKFRDGELNLLIATSV 99

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 568993644  797 FGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDG 832
Cdd:cd18802   100 LEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPN 135
DDXDc_reverse_gyrase cd17924
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ...
 507-598 8.50e-06

DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350682 [Multi-domain]  Cd Length: 189  Bit Score: 47.71  E-value: 8.50e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  507 IMRILSGISTLLVLPTGAGKS---LCYQLPALLYAQRSpcltLVVSPLLSLMDdQVSD--------LPSCLKAACLHSGM 575
Cdd:cd17924    26 AKRLLRGKSFAIIAPTGVGKTtfgLATSLYLASKGKRS----YLIFPTKSLVK-QAYErlskyaekAGVEVKILVYHSRL 100

                          90       100
                  ....*....|....*....|...
gi 568993644  576 TKKQRESVLKKVRAAQVHVLIVS 598
Cdd:cd17924   101 KKKEKEELLEKIEKGDFDILVTT 123
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 499-686 1.62e-05

DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350679 [Multi-domain]  Cd Length: 181  Bit Score: 46.87  E-value: 1.62e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  499 FRPGQERAIMRI-LSGISTLLVLPTGAGKSLCYQLPALLYAQRSPCLTLVVSPLLSLMDDQVSDLPSCLKAACLHSGMtk 577
Cdd:cd17921     2 LNPIQREALRALyLSGDSVLVSAPTSSGKTLIAELAILRALATSGGKAVYIAPTRALVNQKEADLRERFGPLGKNVGL-- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  578 KQRESVLKKVRAAQVHVLIVSPEALVGCGARGPGSLPQAAQLppiafACIDEVHCLSQWShnfRPCYLRVC--KVLREHM 655
Cdd:cd17921    80 LTGDPSVNKLLLAEADILVATPEKLDLLLRNGGERLIQDVRL-----VVVDEAHLIGDGE---RGVVLELLlsRLLRINK 151

                         170       180       190
                  ....*....|....*....|....*....|.
gi 568993644  656 GVRcFLGLTATAtrSTARDVAQHLGIAGEFE 686
Cdd:cd17921   152 NAR-FVGLSATL--PNAEDLAEWLGVEDLIR 179
PRK01297 PRK01297
ATP-dependent RNA helicase RhlB; Provisional
 420-832 2.37e-05

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 234938 [Multi-domain]  Cd Length: 475  Bit Score: 48.37  E-value: 2.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  420 EGDRDDKQPISTLEEVAQRTGTASCHHSAGEETQPAAPELQVPHCPTPMSPLYPPGP-------LGQVAETPAE------ 486
Cdd:PRK01297   11 KGEAEQPAPAPPSPAAAPAPPPPAKTAAPATKAAAPAAAAPRAEKPKKDKPRRERKPkpaslwkLEDFVVEPQEgktrfh 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  487 -------VFQALERLGYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALLYAQRSPC---------LTLVVSP 550
Cdd:PRK01297   91 dfnlapeLMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPpkerymgepRALIIAP 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  551 LLSLMDDQVSDLPSCLKAACLH-----SGMT-KKQresvLKKVRAAQVHVLIVSPEALVGCGARGPGSLPQaaqlppIAF 624
Cdd:PRK01297  171 TRELVVQIAKDAAALTKYTGLNvmtfvGGMDfDKQ----LKQLEARFCDILVATPGRLLDFNQRGEVHLDM------VEV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  625 ACIDEVHCLsqWSHNFRPcylRVCKVLRE--HMGVRCFLGLTATATRSTARDVAQHL--GIAGEFELSGSANIPANLHLS 700
Cdd:PRK01297  241 MVLDEADRM--LDMGFIP---QVRQIIRQtpRKEERQTLLFSATFTDDVMNLAKQWTtdPAIVEIEPENVASDTVEQHVY 315

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  701 VSMDRDSDQALVTLLQGDRFrtlDSVIIYCTRRKDTERVAALLRTclsmvgdsrprgcgpEAIAEAYHAGMSSQERR-RV 779
Cdd:PRK01297  316 AVAGSDKYKLLYNLVTQNPW---ERVMVFANRKDEVRRIEERLVK---------------DGINAAQLSGDVPQHKRiKT 377

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|...
gi 568993644  780 QQAFMRGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDG 832
Cdd:PRK01297  378 LEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAG 430
DEADc_DDX47 cd17954
DEAD-box helicase domain of DEAD box protein 47; DDX47 (also called E4-DEAD box protein) can ...
 485-603 2.46e-05

DEAD-box helicase domain of DEAD box protein 47; DDX47 (also called E4-DEAD box protein) can shuttle between the nucleus and the cytoplasm, and has an RNA-independent ATPase activity. DX47 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: 350712 [Multi-domain]  Cd Length: 203  Bit Score: 46.54  E-value: 2.46e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  485 AEVFQALERLGYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPAL--LYAQRSPCLTLVVSPLLSL---MDDQV 559
Cdd:cd17954     9 EELCEACEKLGWKKPTKIQEEAIPVALQGRDIIGLAETGSGKTAAFALPILqaLLENPQRFFALVLAPTRELaqqISEQF 88

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 568993644  560 SDLPSC--LKAACLHSGMTKKQRESVLKKvraaQVHVLIVSPEALV 603
Cdd:cd17954    89 EALGSSigLKSAVLVGGMDMMAQAIALAK----KPHVIVATPGRLV 130
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
480-832 2.87e-05

Superfamily II RNA helicase [Replication, recombination and repair];


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 48.40  E-value: 2.87e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  480 VAETPAEVFQALERL-GYRAFR--PGQERAIMRILSGISTLLVLPTGAGKSL-----CYQlpALLYAQRSPCLTlvvsPL 551
Cdd:COG4581     4 SPARADARLEALADFaEERGFEldPFQEEAILALEAGRSVLVAAPTGSGKTLvaefaIFL--ALARGRRSFYTA----PI 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  552 --LSLmddqvsdlpsclkaaclhsgmtKKQRESVlKKVRAAQVHVL----IVSPEALVGCG----------ARGPGslpq 615
Cdd:COG4581    78 kaLSN----------------------QKFFDLV-ERFGAENVGLLtgdaSVNPDAPIVVMtteilrnmlyREGAD---- 130

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  616 aaqLPPIAFACIDEVHCLSQwshNFR-----------PCYLRvckvlrehmgvrcFLGLTATAtrSTARDVAQHL-GIAG 683
Cdd:COG4581   131 ---LEDVGVVVMDEFHYLAD---PDRgwvweepiihlPARVQ-------------LVLLSATV--GNAEEFAEWLtRVRG 189

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  684 EFELSGSANIPANLHLSVSM-DRDSDQALVT---LLQGDRFRTLDS--------VIIYC-TRRKDTERVAALLRTCLS-- 748
Cdd:COG4581   190 ETAVVVSEERPVPLEFHYLVtPRLFPLFRVNpelLRPPSRHEVIEEldrggllpAIVFIfSRRGCDEAAQQLLSARLTtk 269

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  749 --------MVGD-------------SRPRGCGpeaIAeAYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRPdVR 807
Cdd:COG4581   270 eeraeireAIDEfaedfsvlfgktlSRLLRRG---IA-VHHAGMLPKYRRLVEELFQAGLLKVVFATDTLAVGINMP-AR 344

                         410       420       430
                  ....*....|....*....|....*....|....*.
gi 568993644  808 AVL-----------HLGLPPSfeSYVQAIGRAGRDG 832
Cdd:COG4581   345 TVVftklskfdgerHRPLTAR--EFHQIAGRAGRRG 378
ResIII pfam04851
Type III restriction enzyme, res subunit;
499-666 4.59e-05

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 44.97  E-value: 4.59e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644   499 FRPGQERAIMRILSGIST-----LLVLPTGAGKSLCY-QLPALLYAQRSPCLTLVVSPLLSLMDDQVSDLPSCLKAACLH 572
Cdd:pfam04851    4 LRPYQIEAIENLLESIKNgqkrgLIVMATGSGKTLTAaKLIARLFKKGPIKKVLFLVPRKDLLEQALEEFKKFLPNYVEI 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644   573 SGMTKKQResvlKKVRAAQVHVLIVSPEALVGCgargpgSLPQAAQLPPIAFACI--DEVHCL--SQWSH---NFRPCYL 645
Cdd:pfam04851   84 GEIISGDK----KDESVDDNKIVVTTIQSLYKA------LELASLELLPDFFDVIiiDEAHRSgaSSYRNileYFKPAFL 153

                          170       180
                   ....*....|....*....|.
gi 568993644   646 rvckvlrehmgvrcfLGLTAT 666
Cdd:pfam04851  154 ---------------LGLTAT 159
DEXHc_LHR-like cd17922
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ...
 513-633 6.42e-05

DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases from the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350680 [Multi-domain]  Cd Length: 166  Bit Score: 44.88  E-value: 6.42e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  513 GISTLLVLPTGAGKSLCYQLPAL--LYAQRSPCL-TLVVSPLLSLMDDQVSDLPSCLKAACL-------HSGMTKKQRES 582
Cdd:cd17922     1 GRNVLIAAPTGSGKTEAAFLPALssLADEPEKGVqVLYISPLKALINDQERRLEEPLDEIDLeipvavrHGDTSQSEKAK 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 568993644  583 VLKKVRaaqvHVLIVSPEAL----VGCGARGpgslpqaaQLPPIAFACIDEVHCL 633
Cdd:cd17922    81 QLKNPP----GILITTPESLelllVNKKLRE--------LFAGLRYVVVDEIHAL 123
PRK04837 PRK04837
ATP-dependent RNA helicase RhlB; Provisional
 776-836 8.26e-05

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235314 [Multi-domain]  Cd Length: 423  Bit Score: 46.50  E-value: 8.26e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568993644  776 RRRVQQAFMRGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAH 836
Cdd:PRK04837  294 RLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGH 354
DEADc_DDX43_DDX53 cd17958
DEAD-box helicase domain of DEAD box proteins 43 and 53; DDX43 (also called cancer/testis ...
 487-599 1.03e-04

DEAD-box helicase domain of DEAD box proteins 43 and 53; DDX43 (also called cancer/testis antigen 13 or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 is also called cancer/testis antigen 26 or DEAD-Box Protein CAGE. Both DDX46 and DDX53 are members 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: 350716 [Multi-domain]  Cd Length: 197  Bit Score: 44.76  E-value: 1.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  487 VFQALERLGYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALL--------YAQRSPCLTLVVSPLLSL---M 555
Cdd:cd17958     1 IMKEIKKQGFEKPSPIQSQAWPIILQGIDLIGVAQTGTGKTLAYLLPGFIhldlqpipREQRNGPGVLVLTPTRELalqI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 568993644  556 DDQVSD-LPSCLKAACLHSGMTKKQRESVLKKvraaQVHVLIVSP 599
Cdd:cd17958    81 EAECSKySYKGLKSVCVYGGGNRNEQIEDLSK----GVDIIIATP 121
DEADc_DDX28 cd17948
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box ...
 487-602 1.18e-04

DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box polypeptide 28) plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function. DDX28 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: 350706 [Multi-domain]  Cd Length: 231  Bit Score: 45.05  E-value: 1.18e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  487 VFQALERLGYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALLYAQRSPCLT---------LVVSPLLSLMdD 557
Cdd:cd17948     1 LVEILQRQGITKPTTVQKQGIPSILRGRNTLCAAETGSGKTLTYLLPIIQRLLRYKLLAegpfnaprgLVITPSRELA-E 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 568993644  558 QVS--------DLPscLKAACLHSGMTKKQresvLKKVRAAQVHVLIVSPEAL 602
Cdd:cd17948    80 QIGsvaqslteGLG--LKVKVITGGRTKRQ----IRNPHFEEVDILVATPGAL 126
PRK01172 PRK01172
ATP-dependent DNA helicase;
726-865 1.51e-04

ATP-dependent DNA helicase;


Pssm-ID: 100801 [Multi-domain]  Cd Length: 674  Bit Score: 46.03  E-value: 1.51e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  726 VIIYCTRRKDTERVAALLRTCLSMVGD----SRPRGCGPEAIAEA-------YHAGMSSQERRRVQQAFMRGHLRMVVAT 794
Cdd:PRK01172  239 VLVFVSSRKNAEDYAEMLIQHFPEFNDfkvsSENNNVYDDSLNEMlphgvafHHAGLSNEQRRFIEEMFRNRYIKVIVAT 318

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568993644  795 VAFGMGLDRP-------DVRAVLHLGLPP-SFESYVQAIGRAGRDGKPAHCHLFMHpqVGSPISPDQDRPRGSTIPRPL 865
Cdd:PRK01172  319 PTLAAGVNLParlvivrDITRYGNGGIRYlSNMEIKQMIGRAGRPGYDQYGIGYIY--AASPASYDAAKKYLSGEPEPV 395
DEADc_DDX5 cd18049
DEAD-box helicase domain of DEAD box protein 5; DDX5 (also called RNA helicase P68, HLR1, ...
 464-603 3.48e-04

DEAD-box helicase domain of DEAD box protein 5; DDX5 (also called RNA helicase P68, HLR1, G17P1, or HUMP68) is involved in pathways that include the alteration of RNA structures, plays a role as a coregulator of transcription, a regulator of splicing, and in the processing of small noncoding RNAs. It synergizes with DDX17 and SRA1 RNA to activate MYOD1 transcriptional activity and is involved in skeletal muscle differentiation. Dysregulation of this gene may play a role in cancer development. DDX5 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: 350807 [Multi-domain]  Cd Length: 234  Bit Score: 43.84  E-value: 3.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  464 CPTPMSPLYPpgplgqvAETPAEVFQALERLGYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALLYAQRSPC 543
Cdd:cd18049    19 CPKPVLNFYE-------ANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPF 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568993644  544 LT-------LVVSPLLSLMdDQVSDLP-----SC-LKAACLHSGMTKKQRESVLKKvraaQVHVLIVSPEALV 603
Cdd:cd18049    92 LErgdgpicLVLAPTRELA-QQVQQVAaeygrACrLKSTCIYGGAPKGPQIRDLER----GVEICIATPGRLI 159
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 767-841 3.79e-04

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. 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: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 41.69  E-value: 3.79e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  767 YHAGMSSQERRRVQQAFMR--GHLRMVVATVAFGMGL-----DRpdvraVLHLGLP--PSFESyvQAIGRAGRDG--KPA 835
Cdd:cd18793    57 LDGSTSSKERQKLVDRFNEdpDIRVFLLSTKAGGVGLnltaaNR-----VILYDPWwnPAVEE--QAIDRAHRIGqkKPV 129


                  ....*.
gi 568993644  836 HCHLFM 841
Cdd:cd18793   130 VVYRLI 135
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 566-609 4.25e-04

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise 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. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 41.72  E-value: 4.25e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 568993644  566 LKAACLHSGMTKKQRESVLKKVRAAQVHVLIVSPEAlvgcgARG 609
Cdd:cd18787    52 IKVAALHGDLSQEERERALKKFRSGKVRVLVATDVA-----ARG 90
PRK11776 PRK11776
ATP-dependent RNA helicase DbpA; Provisional
 704-833 4.36e-04

ATP-dependent RNA helicase DbpA; Provisional


Pssm-ID: 236977 [Multi-domain]  Cd Length: 460  Bit Score: 44.41  E-value: 4.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  704 DRDSDQALVTLLQgdRFRTlDSVIIYCTRRKDTERVAALLRtclsMVGDSrprgcgpeaiAEAYHAGMSSQERRRVQQAF 783
Cdd:PRK11776  226 PDERLPALQRLLL--HHQP-ESCVVFCNTKKECQEVADALN----AQGFS----------ALALHGDLEQRDRDQVLVRF 288

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 568993644  784 MRGHLRMVVAT-VAfGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGK 833
Cdd:PRK11776  289 ANRSCSVLVATdVA-ARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGS 338
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 708-841 8.21e-04

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 43.68  E-value: 8.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  708 DQALVTLLQGDRFrtlDSVIIYCTRRKDTERVA-ALLRTCLSmvgdsrprgcgpeaiAEAYHAGMSSQERRRVQQAFMRG 786
Cdd:PRK11634  233 NEALVRFLEAEDF---DAAIIFVRTKNATLEVAeALERNGYN---------------SAALNGDMNQALREQTLERLKDG 294

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 568993644  787 HLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFM 841
Cdd:PRK11634  295 RLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFV 349
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 532-598 1.09e-03

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 39.89  E-value: 1.09e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568993644   532 LPALLYAQRSPClTLVVSPLLSLMDDQVSDLPSCLKAACLHSGMTKKQRESVLKKVRAAQVHVLIVS 598
Cdd:pfam00271    6 LLELLKKERGGK-VLIFSQTKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVAT 71
DEADc_DDX17 cd18050
DEAD-box helicase domain of DEAD box protein 17; DDX17 (also called DEAD Box Protein P72 or ...
 464-603 1.97e-03

DEAD-box helicase domain of DEAD box protein 17; DDX17 (also called DEAD Box Protein P72 or DEAD Box Protein P82) has a wide variety of functions including regulating the alternative splicing of exons exhibiting specific features such as the inclusion of AC-rich alternative exons in CD44 transcripts, playing a role in innate immunity, and promoting mRNA degradation mediated by the antiviral zinc-finger protein ZC3HAV1 in an ATPase-dependent manner. DDX17 synergizes with DDX5 and SRA1 RNA to activate MYOD1 transcriptional activity and is involved in skeletal muscle differentiation. DDX17 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: 350808 [Multi-domain]  Cd Length: 271  Bit Score: 41.53  E-value: 1.97e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  464 CPTPMSPLYPpgplgqvAETPAEVFQALERLGYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPALLYAQRSP- 542
Cdd:cd18050    57 CPKPVFAFHQ-------ANFPQYVMDVLLDQNFKEPTPIQCQGFPLALSGRDMVGIAQTGSGKTLAYLLPAIVHINHQPy 129

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568993644  543 --------CLTLVVSPLLSLMDDQVSD---LPSCLKAACLHSGMTKKQRESVLKKvraaQVHVLIVSPEALV 603
Cdd:cd18050   130 lergdgpiCLVLAPTRELAQQVQQVADdygKSSRLKSTCIYGGAPKGPQIRDLER----GVEICIATPGRLI 197
ZnF_C2HC smart00343
zinc finger;
394-408 2.33e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 36.65  E-value: 2.33e-03
                            10
                    ....*....|....*
gi 568993644    394 TCFRCGQFGHWASQC 408
Cdd:smart00343    1 KCYNCGKEGHIARDC 15
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 727-833 2.91e-03

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 41.47  E-value: 2.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  727 IIYCTRRKDTERVAALLRTclsmvgdsrprgcgpEAIAEAYHAGMSSQERRrvQQA---FMRGHLRMVVAT-VAfGMGLD 802
Cdd:PRK11192  249 IVFVRTRERVHELAGWLRK---------------AGINCCYLEGEMVQAKR--NEAikrLTDGRVNVLVATdVA-ARGID 310

                          90       100       110
                  ....*....|....*....|....*....|.
gi 568993644  803 RPDVRAVLHLGLPPSFESYVQAIGRAGRDGK 833
Cdd:PRK11192  311 IDDVSHVINFDMPRSADTYLHRIGRTGRAGR 341
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 768-848 3.29e-03

C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. 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: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 39.63  E-value: 3.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  768 HAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRPD--VRAVLH---LGLppsfESYVQAIGRAGRDGKPAHCHLFMH 842
Cdd:cd18811    68 HGRLKSDEKDAVMAEFREGEVDILVSTTVIEVGVDVPNatVMVIEDaerFGL----SQLHQLRGRVGRGDHQSYCLLVYK 143


                  ....*.
gi 568993644  843 PQVGSP 848
Cdd:cd18811   144 DPLTET 149
PRK00254 PRK00254
ski2-like helicase; Provisional
 767-830 6.09e-03

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 40.96  E-value: 6.09e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568993644  767 YHAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRPDVRAVL-------HLGLP--PSFESYvQAIGRAGR 830
Cdd:PRK00254  301 HHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIrdtkrysNFGWEdiPVLEIQ-QMMGRAGR 372
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
 523-666 6.42e-03

DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350677 [Multi-domain]  Cd Length: 182  Bit Score: 39.09  E-value: 6.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  523 GAGK-----SLCYQLpalLYAQRSPCLTLVVSPlLSLMDDQVSDL----PScLKAACLHSgmTKKQRESVLKKVRAAQVH 593
Cdd:cd17919    29 GLGKtlqaiAFLAYL---LKEGKERGPVLVVCP-LSVLENWEREFekwtPD-LRVVVYHG--SQRERAQIRAKEKLDKFD 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568993644  594 VLIVSPEALVGCgargpgslpqAAQLPPIAFACI--DEVHCL----SQWShnfrpcylRVCKVLREHMgvRcfLGLTAT 666
Cdd:cd17919   102 VVLTTYETLRRD----------KASLRKFRWDLVvvDEAHRLknpkSQLS--------KALKALRAKR--R--LLLTGT 158
PRK02362 PRK02362
ATP-dependent DNA helicase;
767-832 6.73e-03

ATP-dependent DNA helicase;


Pssm-ID: 235032 [Multi-domain]  Cd Length: 737  Bit Score: 40.71  E-value: 6.73e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568993644  767 YHAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRPDVRAVLH--------LGLPP-SFESYVQAIGRAGRDG 832
Cdd:PRK02362  309 HHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRdyrrydggAGMQPiPVLEYHQMAGRAGRPG 383
DEADc_DDX46 cd17953
DEAD-box helicase domain of DEAD box protein 46; DDX46 (also called Prp5-like DEAD-box protein) ...
 464-542 6.78e-03

DEAD-box helicase domain of DEAD box protein 46; DDX46 (also called Prp5-like DEAD-box protein) is a component of the 17S U2 snRNP complex. It plays an important role in pre-mRNA splicing and has a role in antiviral innate immunity. DDX46 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: 350711 [Multi-domain]  Cd Length: 222  Bit Score: 39.67  E-value: 6.78e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568993644  464 CPTPMSPLYPPGplgqvaeTPAEVFQALERLGYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLPAL--LYAQRS 541
Cdd:cd17953     7 CPKPIQKWSQCG-------LSEKVLDLIKKLGYEKPTPIQAQALPAIMSGRDVIGIAKTGSGKTLAFLLPMFrhIKDQRP 79


                  .
gi 568993644  542 P 542
Cdd:cd17953    80 V 80
PRK10590 PRK10590
ATP-dependent RNA helicase RhlE; Provisional
 764-830 6.81e-03

ATP-dependent RNA helicase RhlE; Provisional


Pssm-ID: 236722 [Multi-domain]  Cd Length: 456  Bit Score: 40.56  E-value: 6.81e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568993644  764 AEAYHAGMSSQERRRVQQAFMRGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGR 830
Cdd:PRK10590  272 SAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGR 338
HELICc smart00490
helicase superfamily c-terminal domain;
566-598 7.40e-03

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 36.81  E-value: 7.40e-03
                            10        20        30
                    ....*....|....*....|....*....|...
gi 568993644    566 LKAACLHSGMTKKQRESVLKKVRAAQVHVLIVS 598
Cdd:smart00490   12 IKVARLHGGLSQEEREEILDKFNNGKIKVLVAT 44
DEADc_DDX54 cd17959
DEAD-box helicase domain of DEAD box protein 54; DDX54 interacts in a hormone-dependent manner ...
 486-533 7.89e-03

DEAD-box helicase domain of DEAD box protein 54; DDX54 interacts in a hormone-dependent manner with nuclear receptors, and represses their transcriptional activity. DDX54 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: 350717 [Multi-domain]  Cd Length: 205  Bit Score: 39.21  E-value: 7.89e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 568993644  486 EVFQALERLGYRAFRPGQERAIMRILSGISTLLVLPTGAGKSLCYQLP 533
Cdd:cd17959    11 PLLRAIKKKGYKVPTPIQRKTIPLILDGRDVVAMARTGSGKTAAFLIP 58
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 393-410 9.83e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 34.81  E-value: 9.83e-03
                           10
                   ....*....|....*...
gi 568993644   393 DTCFRCGQFGHWASQCSQ 410
Cdd:pfam00098    1 GKCYNCGEPGHIARDCPK 18
 
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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