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Conserved domains on  [gi|194473630|ref|NP_001123966|]
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ATP-dependent DNA helicase Q4 [Rattus norvegicus]

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];
484-849 6.76e-115

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: 366.77  E-value: 6.76e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  484 AEVFQVLEQL-GHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALLyakrSPCLTLVVSPLLSLMDDQVSDLP 562
Cdd:COG0514     3 DDALEVLKRVfGYDSFRPGQEEIIEAVLAGRDALVVMPTGGGKSLCYQLPALL----LPGLTLVVSPLIALMKDQVDALR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  563 SC-LKAACLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALVGcgakgPANLPPAAQLPPVAFAcIDEVHCLSQWSHNFRP 641
Cdd:COG0514    79 AAgIRAAFLNSSLSAEERREVLRALRAGELKLLYVAPERLLN-----PRFLELLRRLKISLFA-IDEAHCISQWGHDFRP 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  642 CYLRVcKVLREHMGVRCFLGLTATATRSTARDVAQHLGIAEELEVSGSASIPaNLHLSVS--MDRDSDQALVTLLQGdrf 719
Cdd:COG0514   153 DYRRL-GELRERLPNVPVLALTATATPRVRADIAEQLGLEDPRVFVGSFDRP-NLRLEVVpkPPDDKLAQLLDFLKE--- 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  720 RTLDSIIIYCARRKDTERVAALLRTclstvrdskpRGRGpetlAEAYHAGMCSQERKRVQQAFMQGHLRMVVATVAFGMG 799
Cdd:COG0514   228 HPGGSGIVYCLSRKKVEELAEWLRE----------AGIR----AAAYHAGLDAEEREANQDRFLRDEVDVIVATIAFGMG 293

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|
gi 194473630  800 LDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFLHPQGEDLWE 849
Cdd:COG0514   294 IDKPDVRFVIHYDLPKSIEAYYQEIGRAGRDGLPAEALLLYGPEDVAIQR 343
RecQL4_SLD2_NTD cd22289
N-terminal homeodomain-like domain of metazoan RecQ protein-like 4 (RecQL4), fungal DNA ...
 2-50 8.34e-18

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: 78.06  E-value: 8.34e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 194473630    2 ERLATVRAWLQDWERAFVRLHGRRPAKEDVEAAPEETRALYREYRNLKQ 50
Cdd:cd22289     1 ERLQELKIALKTWERAFAKKHGRKPTKDDIKAAPEEIKDLYKEYAKLKK 49
Drc1-Sld2 super family cl44400
DNA replication and checkpoint protein; Genome duplication is precisely regulated by ...
 4-170 3.49e-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.


The actual alignment was detected with superfamily member pfam11719:

Pssm-ID: 371692 [Multi-domain]  Cd Length: 391  Bit Score: 60.23  E-value: 3.49e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630     4 LATVRAWLQDWERAFVRLHGRRPAKEDVEAAPeETRALYREYRNLKQAVSQADDGHRVQ---KQSLAKAAEEEQepscwg 80
Cdd:pfam11719    1 ISQLKAEIKEWERAFAAKNGRKPSKDDIKKNP-EIAKKYKLYSKLKKGESIKTKTPSKPvklEARPKKRKHEST------ 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630    81 shlNRAATQNTQSIPKQSplssiqdygKRLKANLkntlqgGPTLSRklqhQKRSLSIVPTSRPPGPRTESPcPEQANDAL 160
Cdd:pfam11719   74 ---NKSPEKNSQSTPRKS---------KNIKSEL------GPTPQA----NGKVLSLFDLLSTPPKSSPLK-SKEVKTDV 130

                          170
                   ....*....|
gi 194473630   161 PQVPVPQPRQ 170
Cdd:pfam11719  131 SGTAIFTPSK 140
ZnF_C2HC smart00343
zinc finger;
394-408 2.40e-03

zinc finger;


:

Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 36.27  E-value: 2.40e-03
                            10
                    ....*....|....*
gi 194473630    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];
484-849 6.76e-115

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 366.77  E-value: 6.76e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  484 AEVFQVLEQL-GHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALLyakrSPCLTLVVSPLLSLMDDQVSDLP 562
Cdd:COG0514     3 DDALEVLKRVfGYDSFRPGQEEIIEAVLAGRDALVVMPTGGGKSLCYQLPALL----LPGLTLVVSPLIALMKDQVDALR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  563 SC-LKAACLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALVGcgakgPANLPPAAQLPPVAFAcIDEVHCLSQWSHNFRP 641
Cdd:COG0514    79 AAgIRAAFLNSSLSAEERREVLRALRAGELKLLYVAPERLLN-----PRFLELLRRLKISLFA-IDEAHCISQWGHDFRP 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  642 CYLRVcKVLREHMGVRCFLGLTATATRSTARDVAQHLGIAEELEVSGSASIPaNLHLSVS--MDRDSDQALVTLLQGdrf 719
Cdd:COG0514   153 DYRRL-GELRERLPNVPVLALTATATPRVRADIAEQLGLEDPRVFVGSFDRP-NLRLEVVpkPPDDKLAQLLDFLKE--- 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  720 RTLDSIIIYCARRKDTERVAALLRTclstvrdskpRGRGpetlAEAYHAGMCSQERKRVQQAFMQGHLRMVVATVAFGMG 799
Cdd:COG0514   228 HPGGSGIVYCLSRKKVEELAEWLRE----------AGIR----AAAYHAGLDAEEREANQDRFLRDEVDVIVATIAFGMG 293

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|
gi 194473630  800 LDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFLHPQGEDLWE 849
Cdd:COG0514   294 IDKPDVRFVIHYDLPKSIEAYYQEIGRAGRDGLPAEALLLYGPEDVAIQR 343
DEXHc_RecQ4-like cd18018
DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) ...
 487-689 2.66e-99

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: 313.81  E-value: 2.66e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  487 FQVLEQL-GHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALLYAKRSPCLTLVVSPLLSLMDDQVSDLPSCL 565
Cdd:cd18018     1 LKLLRRVfGHPSFRPGQEEAIARLLSGRSTLVVLPTGAGKSLCYQLPALLLRRRGPGLTLVVSPLIALMKDQVDALPRAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  566 KAACLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALVgcgakGPANLPPAAQLPPVAFACIDEVHCLSQWSHNFRPCYLR 645
Cdd:cd18018    81 KAAALNSSLTREERRRILEKLRAGEVKILYVSPERLV-----NESFRELLRQTPPISLLVVDEAHCISEWSHNFRPDYLR 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 194473630  646 VCKVLREHMGVRCFLGLTATATRSTARDVAQHLGIAEELEVSGS 689
Cdd:cd18018   156 LCRVLRELLGAPPVLALTATATKRVVEDIASHLGIPESGVVRGP 199
recQ_fam TIGR00614
ATP-dependent DNA helicase, RecQ family; All proteins in this family for which functions are ...
 494-842 1.65e-88

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: 294.76  E-value: 1.65e-88
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630   494 GHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALLyakrSPCLTLVVSPLLSLMDDQVSDLP-SCLKAACLHS 572
Cdd:TIGR00614    8 GLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALY----SDGITLVISPLISLMEDQVLQLQaLGIPATFLNS 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630   573 GMTKKQRESVLKKVRAAQVHVLIVSPEALvgCGAKGPANLPPAAQLPpvAFACIDEVHCLSQWSHNFRPCYlRVCKVLRE 652
Cdd:TIGR00614   84 AQTKEQQLNVLTDLKDGKIKLLYVTPEKI--SASNRLLQTLEERKGI--TLIAVDEAHCISQWGHDFRPDY-KALGSLKQ 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630   653 HMGVRCFLGLTATATRSTARDVAQHLGIAEELEVSGSASIPaNLHLSVsMDRDSD--QALVTLLQGdRFRTlDSIIIYCA 730
Cdd:TIGR00614  159 KFPNVPVMALTATASPSVREDILRQLNLLNPQIFCTSFDRP-NLYYEV-RRKTPKilEDLLRFIRK-EFEG-KSGIIYCP 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630   731 RRKDTERVAALLRTC-LStvrdskprgrgpetlAEAYHAGMCSQERKRVQQAFMQGHLRMVVATVAFGMGLDRPDVRAVL 809
Cdd:TIGR00614  235 SRKKVEQVAAELQKLgLA---------------AGAYHAGLEDSARDDVQHKFQRDEIQVVVATVAFGMGINKPDVRFVI 299

                          330       340       350
                   ....*....|....*....|....*....|...
gi 194473630   810 HLGLPPSFESYVQAIGRAGRDGKPAHCHLFLHP 842
Cdd:TIGR00614  300 HYSLPKSMESYYQESGRAGRDGLPSECHLFYAP 332
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 478-842 7.97e-79

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 271.97  E-value: 7.97e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  478 QVADTPAEVFQVL-EQLGHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALLYakrsPCLTLVVSPLLSLMDD 556
Cdd:PRK11057    5 EVLNLESLAKQVLqETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL----DGLTLVVSPLISLMKD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  557 QVSDL-PSCLKAACLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALVGCGAkgpanLPPAAQLPPVAFAcIDEVHCLSQW 635
Cdd:PRK11057   81 QVDQLlANGVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNF-----LEHLAHWNPALLA-VDEAHCISQW 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  636 SHNFRPCYlRVCKVLREHMGVRCFLGLTATATRSTARDVAQHLGIAEELEVSGSASIPANLHLSVSMDRDSDQaLVTLLQ 715
Cdd:PRK11057  155 GHDFRPEY-AALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYTLVEKFKPLDQ-LMRYVQ 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  716 GDRFRtldSIIIYCARRKDTERVAALLRtclstvrdskprGRGPEtlAEAYHAGMCSQERKRVQQAFMQGHLRMVVATVA 795
Cdd:PRK11057  233 EQRGK---SGIIYCNSRAKVEDTAARLQ------------SRGIS--AAAYHAGLDNDVRADVQEAFQRDDLQIVVATVA 295

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 194473630  796 FGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFLHP 842
Cdd:PRK11057  296 FGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDP 342
DpdF NF041063
protein DpdF;
493-843 1.75e-34

protein DpdF;


Pssm-ID: 468990 [Multi-domain]  Cd Length: 813  Bit Score: 142.74  E-value: 1.75e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  493 LGHHTFR-PGQERAVMRILS---GiSTLLV-LPTGAGKSLCYQLPALLYAKRSPcLTLVVSPLLSLMDDQVSDLPSCLKA 567
Cdd:NF041063  135 LGFTHYRsPGQREAVRAALLappG-STLIVnLPTGSGKSLVAQAPALLASRQGG-LTLVVVPTVALAIDQERRARELLRR 212

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  568 A--------CLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALVGcgakgpANLPP---AAQLPPVAFACIDEVHCLSQWS 636
Cdd:NF041063  213 AgpdlggplAWHGGLSAEERAAIRQRIRDGTQRILFTSPESLTG------SLRPAlfdAAEAGLLRYLVVDEAHLVDQWG 286

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  637 HNFRPCY----------LRVCKvlrEHMGVRCFLgLTATATRSTaRDVAQHL-GIAEELE-VSGSasipanlHL----SV 700
Cdd:NF041063  287 DGFRPEFqllaglrrslLRLAP---SGRPFRTLL-LSATLTEST-LDTLETLfGPPGPFIvVSAV-------QLrpepAY 354

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  701 SMDRDSDQAlvtllqgDRFRT-LDSI-------IIYCARRKDTERVAALLRtclstvrdSKPRGRgpetlAEAYHAGMCS 772
Cdd:NF041063  355 WVAKCDSEE-------ERRERvLEALrhlprplILYVTKVEDAEAWLQRLR--------AAGFRR-----VALFHGDTPD 414

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 194473630  773 QERKRVQQAFMQGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFLHPQ 843
Cdd:NF041063  415 AERERLIEQWRENELDIVVATSAFGLGMDKSDVRTVIHACVPETLDRFYQEVGRGGRDGKASLSLLIYTPD 485
DEXDc smart00487
DEAD-like helicases superfamily;
490-693 5.75e-25

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 103.73  E-value: 5.75e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630    490 LEQLGHHTFRPGQERAVMRILSGI-STLLVLPTGAGKSLCYQLPALLYAKRSP-CLTLVVSPLLSLMDDQVSDL-----P 562
Cdd:smart00487    1 IEKFGFEPLRPYQKEAIEALLSGLrDVILAAPTGSGKTLAALLPALEALKRGKgGRVLVLVPTRELAEQWAEELkklgpS 80

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630    563 SCLKAACLHSGMTKKQResvLKKVRAAQVHVLIVSPEALVGCGAKGPANlppaaqLPPVAFACIDEVHCLSQWshNFRPC 642
Cdd:smart00487   81 LGLKVVGLYGGDSKREQ---LRKLESGKTDILVTTPGRLLDLLENDKLS------LSNVDLVILDEAHRLLDG--GFGDQ 149

                           170       180       190       200       210
                    ....*....|....*....|....*....|....*....|....*....|.
gi 194473630    643 YLRVCKVLREHmgvRCFLGLTATATRSTARDVAQHLGIAEELEVSGSASIP 693
Cdd:smart00487  150 LEKLLKLLPKN---VQLLLLSATPPEEIENLLELFLNDPVFIDVGFTPLEP 197
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 499-672 1.60e-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: 1.60e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630   499 RPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPAL--LYAKRSPCLTLVVSPLLSLMDDQVSDL-----PSCLKAACLH 571
Cdd:pfam00270    1 TPIQAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALeaLDKLDNGPQALVLAPTRELAEQIYEELkklgkGLGLKVASLL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630   572 SGMTKKQRESVLKKvraaqVHVLIVSPEALVgcgakgpANLPPAAQLPPVAFACIDEVHCLSQWShnFRPCYLRVCKVLR 651
Cdd:pfam00270   81 GGDSRKEQLEKLKG-----PDILVGTPGRLL-------DLLQERKLLKNLKLLVLDEAHRLLDMG--FGPDLEEILRRLP 146

                          170       180
                   ....*....|....*....|.
gi 194473630   652 EHmgvRCFLGLTATATRSTAR 672
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 8.34e-18

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: 78.06  E-value: 8.34e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 194473630    2 ERLATVRAWLQDWERAFVRLHGRRPAKEDVEAAPEETRALYREYRNLKQ 50
Cdd:cd22289     1 ERLQELKIALKTWERAFAKKHGRKPTKDDIKAAPEEIKDLYKEYAKLKK 49
Drc1-Sld2 pfam11719
DNA replication and checkpoint protein; Genome duplication is precisely regulated by ...
 4-170 3.49e-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: 60.23  E-value: 3.49e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630     4 LATVRAWLQDWERAFVRLHGRRPAKEDVEAAPeETRALYREYRNLKQAVSQADDGHRVQ---KQSLAKAAEEEQepscwg 80
Cdd:pfam11719    1 ISQLKAEIKEWERAFAAKNGRKPSKDDIKKNP-EIAKKYKLYSKLKKGESIKTKTPSKPvklEARPKKRKHEST------ 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630    81 shlNRAATQNTQSIPKQSplssiqdygKRLKANLkntlqgGPTLSRklqhQKRSLSIVPTSRPPGPRTESPcPEQANDAL 160
Cdd:pfam11719   74 ---NKSPEKNSQSTPRKS---------KNIKSEL------GPTPQA----NGKVLSLFDLLSTPPKSSPLK-SKEVKTDV 130

                          170
                   ....*....|
gi 194473630   161 PQVPVPQPRQ 170
Cdd:pfam11719  131 SGTAIFTPSK 140
ZnF_C2HC smart00343
zinc finger;
394-408 2.40e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 36.27  E-value: 2.40e-03
                            10
                    ....*....|....*
gi 194473630    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];
484-849 6.76e-115

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 366.77  E-value: 6.76e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  484 AEVFQVLEQL-GHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALLyakrSPCLTLVVSPLLSLMDDQVSDLP 562
Cdd:COG0514     3 DDALEVLKRVfGYDSFRPGQEEIIEAVLAGRDALVVMPTGGGKSLCYQLPALL----LPGLTLVVSPLIALMKDQVDALR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  563 SC-LKAACLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALVGcgakgPANLPPAAQLPPVAFAcIDEVHCLSQWSHNFRP 641
Cdd:COG0514    79 AAgIRAAFLNSSLSAEERREVLRALRAGELKLLYVAPERLLN-----PRFLELLRRLKISLFA-IDEAHCISQWGHDFRP 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  642 CYLRVcKVLREHMGVRCFLGLTATATRSTARDVAQHLGIAEELEVSGSASIPaNLHLSVS--MDRDSDQALVTLLQGdrf 719
Cdd:COG0514   153 DYRRL-GELRERLPNVPVLALTATATPRVRADIAEQLGLEDPRVFVGSFDRP-NLRLEVVpkPPDDKLAQLLDFLKE--- 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  720 RTLDSIIIYCARRKDTERVAALLRTclstvrdskpRGRGpetlAEAYHAGMCSQERKRVQQAFMQGHLRMVVATVAFGMG 799
Cdd:COG0514   228 HPGGSGIVYCLSRKKVEELAEWLRE----------AGIR----AAAYHAGLDAEEREANQDRFLRDEVDVIVATIAFGMG 293

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|
gi 194473630  800 LDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFLHPQGEDLWE 849
Cdd:COG0514   294 IDKPDVRFVIHYDLPKSIEAYYQEIGRAGRDGLPAEALLLYGPEDVAIQR 343
DEXHc_RecQ4-like cd18018
DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) ...
 487-689 2.66e-99

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: 313.81  E-value: 2.66e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  487 FQVLEQL-GHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALLYAKRSPCLTLVVSPLLSLMDDQVSDLPSCL 565
Cdd:cd18018     1 LKLLRRVfGHPSFRPGQEEAIARLLSGRSTLVVLPTGAGKSLCYQLPALLLRRRGPGLTLVVSPLIALMKDQVDALPRAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  566 KAACLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALVgcgakGPANLPPAAQLPPVAFACIDEVHCLSQWSHNFRPCYLR 645
Cdd:cd18018    81 KAAALNSSLTREERRRILEKLRAGEVKILYVSPERLV-----NESFRELLRQTPPISLLVVDEAHCISEWSHNFRPDYLR 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 194473630  646 VCKVLREHMGVRCFLGLTATATRSTARDVAQHLGIAEELEVSGS 689
Cdd:cd18018   156 LCRVLRELLGAPPVLALTATATKRVVEDIASHLGIPESGVVRGP 199
recQ_fam TIGR00614
ATP-dependent DNA helicase, RecQ family; All proteins in this family for which functions are ...
 494-842 1.65e-88

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: 294.76  E-value: 1.65e-88
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630   494 GHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALLyakrSPCLTLVVSPLLSLMDDQVSDLP-SCLKAACLHS 572
Cdd:TIGR00614    8 GLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALY----SDGITLVISPLISLMEDQVLQLQaLGIPATFLNS 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630   573 GMTKKQRESVLKKVRAAQVHVLIVSPEALvgCGAKGPANLPPAAQLPpvAFACIDEVHCLSQWSHNFRPCYlRVCKVLRE 652
Cdd:TIGR00614   84 AQTKEQQLNVLTDLKDGKIKLLYVTPEKI--SASNRLLQTLEERKGI--TLIAVDEAHCISQWGHDFRPDY-KALGSLKQ 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630   653 HMGVRCFLGLTATATRSTARDVAQHLGIAEELEVSGSASIPaNLHLSVsMDRDSD--QALVTLLQGdRFRTlDSIIIYCA 730
Cdd:TIGR00614  159 KFPNVPVMALTATASPSVREDILRQLNLLNPQIFCTSFDRP-NLYYEV-RRKTPKilEDLLRFIRK-EFEG-KSGIIYCP 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630   731 RRKDTERVAALLRTC-LStvrdskprgrgpetlAEAYHAGMCSQERKRVQQAFMQGHLRMVVATVAFGMGLDRPDVRAVL 809
Cdd:TIGR00614  235 SRKKVEQVAAELQKLgLA---------------AGAYHAGLEDSARDDVQHKFQRDEIQVVVATVAFGMGINKPDVRFVI 299

                          330       340       350
                   ....*....|....*....|....*....|...
gi 194473630   810 HLGLPPSFESYVQAIGRAGRDGKPAHCHLFLHP 842
Cdd:TIGR00614  300 HYSLPKSMESYYQESGRAGRDGLPSECHLFYAP 332
recQ TIGR01389
ATP-dependent DNA helicase RecQ; The ATP-dependent DNA helicase RecQ of E. coli is about 600 ...
 487-843 3.95e-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: 297.75  E-value: 3.95e-88
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630   487 FQVL-EQLGHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALLYakrsPCLTLVVSPLLSLMDDQVSDLPSC- 564
Cdd:TIGR01389    2 QQVLkRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL----KGLTVVISPLISLMKDQVDQLRAAg 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630   565 LKAACLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALVGcgakgPANLPPAAQLPPVAFAcIDEVHCLSQWSHNFRPCYL 644
Cdd:TIGR01389   78 VAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQ-----DYFLNMLQRIPIALVA-VDEAHCVSQWGHDFRPEYQ 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630   645 RVCkVLREHMGVRCFLGLTATATRSTARDVAQHLGIAEELEVSGSASIPaNLHLSVSMDRDSDQALVTLLQGDRFRtldS 724
Cdd:TIGR01389  152 RLG-SLAERFPQVPRIALTATADAETRQDIRELLRLADANEFITSFDRP-NLRFSVVKKNNKQKFLLDYLKKHRGQ---S 226

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630   725 IIIYCARRKDTERVAALLRTclstvrdskprgRGPETLAeaYHAGMCSQERKRVQQAFMQGHLRMVVATVAFGMGLDRPD 804
Cdd:TIGR01389  227 GIIYASSRKKVEELAERLES------------QGISALA--YHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPN 292

                          330       340       350
                   ....*....|....*....|....*....|....*....
gi 194473630   805 VRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFLHPQ 843
Cdd:TIGR01389  293 VRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPA 331
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 478-842 7.97e-79

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 271.97  E-value: 7.97e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  478 QVADTPAEVFQVL-EQLGHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALLYakrsPCLTLVVSPLLSLMDD 556
Cdd:PRK11057    5 EVLNLESLAKQVLqETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL----DGLTLVVSPLISLMKD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  557 QVSDL-PSCLKAACLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALVGCGAkgpanLPPAAQLPPVAFAcIDEVHCLSQW 635
Cdd:PRK11057   81 QVDQLlANGVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNF-----LEHLAHWNPALLA-VDEAHCISQW 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  636 SHNFRPCYlRVCKVLREHMGVRCFLGLTATATRSTARDVAQHLGIAEELEVSGSASIPANLHLSVSMDRDSDQaLVTLLQ 715
Cdd:PRK11057  155 GHDFRPEY-AALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYTLVEKFKPLDQ-LMRYVQ 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  716 GDRFRtldSIIIYCARRKDTERVAALLRtclstvrdskprGRGPEtlAEAYHAGMCSQERKRVQQAFMQGHLRMVVATVA 795
Cdd:PRK11057  233 EQRGK---SGIIYCNSRAKVEDTAARLQ------------SRGIS--AAAYHAGLDNDVRADVQEAFQRDDLQIVVATVA 295

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 194473630  796 FGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFLHP 842
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 ...
 491-689 5.13e-66

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: 221.25  E-value: 5.13e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  491 EQLGHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALLyakrSPCLTLVVSPLLSLMDDQVSDLPS-CLKAAC 569
Cdd:cd17920     6 EVFGYDEFRPGQLEAINAVLAGRDVLVVMPTGGGKSLCYQLPALL----LDGVTLVVSPLISLMQDQVDRLQQlGIRAAA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  570 LHSGMTKKQRESVLKKVRAAQVHVLIVSPEALVgcgakGPANLPPAAQLP---PVAFACIDEVHCLSQWSHNFRPCYLRV 646
Cdd:cd17920    82 LNSTLSPEEKREVLLRIKNGQYKLLYVTPERLL-----SPDFLELLQRLPerkRLALIVVDEAHCVSQWGHDFRPDYLRL 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 194473630  647 CKVLREHMGVrCFLGLTATATRSTARDVAQHLGIAEELEVSGS 689
Cdd:cd17920   157 GRLRRALPGV-PILALTATATPEVREDILKRLGLRNPVIFRAS 198
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 695-839 6.66e-56

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: 189.73  E-value: 6.66e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  695 NLHLSVSMDRDSDQALVTLLQGDRFRTLDSIIIYCARRKDTERVAALLRTCLSTvrdskprgrgpetlAEAYHAGMCSQE 774
Cdd:cd18794     3 NLFYSVRPKDKKDEKLDLLKRIKVEHLGGSGIIYCLSRKECEQVAARLQSKGIS--------------AAAYHAGLEPSD 68

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 194473630  775 RKRVQQAFMQGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLF 839
Cdd:cd18794    69 RRDVQRKWLRDKIQVIVATVAFGMGIDKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECILF 133
PLN03137 PLN03137
ATP-dependent DNA helicase; Q4-like; Provisional
 494-839 3.20e-52

ATP-dependent DNA helicase; Q4-like; Provisional


Pssm-ID: 215597 [Multi-domain]  Cd Length: 1195  Bit Score: 200.89  E-value: 3.20e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  494 GHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALLyakrSPCLTLVVSPLLSLMDDQVSD-LPSCLKAACLHS 572
Cdd:PLN03137  457 GNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALI----CPGITLVISPLVSLIQDQIMNlLQANIPAASLSA 532

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  573 GMTKKQRESVLKKVRA--AQVHVLIVSPEALvgcgAKGPA---NLPPAAQLPPVAFACIDEVHCLSQWSHNFRPCYlRVC 647
Cdd:PLN03137  533 GMEWAEQLEILQELSSeySKYKLLYVTPEKV----AKSDSllrHLENLNSRGLLARFVIDEAHCVSQWGHDFRPDY-QGL 607

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  648 KVLREHMGVRCFLGLTATATRSTARDVAQHLGIAEELEVSGSASIPaNLHLSVSmdRDSDQALVTLLQGDRFRTLDSI-I 726
Cdd:PLN03137  608 GILKQKFPNIPVLALTATATASVKEDVVQALGLVNCVVFRQSFNRP-NLWYSVV--PKTKKCLEDIDKFIKENHFDECgI 684

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  727 IYCARRKDTERVAALLRTClstvrdskprgrGPEtlAEAYHAGMCSQERKRVQQAFMQGHLRMVVATVAFGMGLDRPDVR 806
Cdd:PLN03137  685 IYCLSRMDCEKVAERLQEF------------GHK--AAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVR 750

                         330       340       350
                  ....*....|....*....|....*....|...
gi 194473630  807 AVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLF 839
Cdd:PLN03137  751 FVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLY 783
DEXHc_RecQ1 cd18015
DEXH-box helicase domain of RecQ1; ATP-dependent DNA helicase Q1 (RecQ1) is part of the RecQ ...
 477-689 5.14e-38

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: 141.73  E-value: 5.14e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  477 GQVADTPAEVFQVleqlghHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALLyakrSPCLTLVVSPLLSLMDD 556
Cdd:cd18015     4 GKVKDTLKNVFKL------EKFRPLQLETINATMAGRDVFLVMPTGGGKSLCYQLPALC----SDGFTLVVSPLISLMED 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  557 QVSDLPSC-LKAACLHSGMTKKQRESVLKKVR--AAQVHVLIVSPEALvgcgAKGP---ANLPPAAQLPPVAFACIDEVH 630
Cdd:cd18015    74 QLMALKKLgISATMLNASSSKEHVKWVHAALTdkNSELKLLYVTPEKI----AKSKrfmSKLEKAYNAGRLARIAIDEVH 149

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 194473630  631 CLSQWSHNFRPCYlrvckvlrEHMGV--RCF-----LGLTATATRSTARDVAQHLGIAEELEVSGS 689
Cdd:cd18015   150 CCSQWGHDFRPDY--------KKLGIlkRQFpnvpiLGLTATATSKVLKDVQKILCIQKCLTFTAS 207
DpdF NF041063
protein DpdF;
493-843 1.75e-34

protein DpdF;


Pssm-ID: 468990 [Multi-domain]  Cd Length: 813  Bit Score: 142.74  E-value: 1.75e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  493 LGHHTFR-PGQERAVMRILS---GiSTLLV-LPTGAGKSLCYQLPALLYAKRSPcLTLVVSPLLSLMDDQVSDLPSCLKA 567
Cdd:NF041063  135 LGFTHYRsPGQREAVRAALLappG-STLIVnLPTGSGKSLVAQAPALLASRQGG-LTLVVVPTVALAIDQERRARELLRR 212

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  568 A--------CLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALVGcgakgpANLPP---AAQLPPVAFACIDEVHCLSQWS 636
Cdd:NF041063  213 AgpdlggplAWHGGLSAEERAAIRQRIRDGTQRILFTSPESLTG------SLRPAlfdAAEAGLLRYLVVDEAHLVDQWG 286

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  637 HNFRPCY----------LRVCKvlrEHMGVRCFLgLTATATRSTaRDVAQHL-GIAEELE-VSGSasipanlHL----SV 700
Cdd:NF041063  287 DGFRPEFqllaglrrslLRLAP---SGRPFRTLL-LSATLTEST-LDTLETLfGPPGPFIvVSAV-------QLrpepAY 354

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  701 SMDRDSDQAlvtllqgDRFRT-LDSI-------IIYCARRKDTERVAALLRtclstvrdSKPRGRgpetlAEAYHAGMCS 772
Cdd:NF041063  355 WVAKCDSEE-------ERRERvLEALrhlprplILYVTKVEDAEAWLQRLR--------AAGFRR-----VALFHGDTPD 414

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 194473630  773 QERKRVQQAFMQGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFLHPQ 843
Cdd:NF041063  415 AERERLIEQWRENELDIVVATSAFGLGMDKSDVRTVIHACVPETLDRFYQEVGRGGRDGKASLSLLIYTPD 485
DEXHc_RecQ5 cd18014
DEAH-box helicase domain of RecQ5; ATP-dependent DNA helicase Q5 (RecQ5) is part of the RecQ ...
 494-680 4.02e-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: 124.51  E-value: 4.02e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  494 GHHTFR-PGQERAVMRILSGISTLLV-LPTGAGKSLCYQLPALLYAKrspcLTLVVSPLLSLMDDQVSDLPSC-LKAACL 570
Cdd:cd18014     9 GHSDFKsPLQEKATMAVVKGNKDVFVcMPTGAGKSLCYQLPALLAKG----ITIVISPLIALIQDQVDHLKTLkIRVDSL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  571 HSGMTKKQRESVLKKVRAA--QVHVLIVSPEAlvgcgAKGPANLPPAAQLPP---VAFACIDEVHCLSQWSHNFRPCYLR 645
Cdd:cd18014    85 NSKLSAQERKRIIADLESEkpQTKFLYITPEM-----AATSSFQPLLSSLVSrnlLSYLVVDEAHCVSQWGHDFRPDYLR 159

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 194473630  646 VCKVLREHMGVRCfLGLTATATRSTARDVAQHLGI 680
Cdd:cd18014   160 LGALRSRYGHVPW-VALTATATPQVQEDIFAQLRL 193
DEXHc_RecQ3 cd18017
DEAH-box helicase domain of RecQ3; DEAD-like helicase RecQ3 (also called Werner syndrome ...
 491-680 4.57e-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: 124.12  E-value: 4.57e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  491 EQLGHHTFRPGQERAVMRIL-SGISTLLVLPTGAGKSLCYQLPALLYAKrspcLTLVVSPLLSLMDDQVSDLPSCLKAAC 569
Cdd:cd18017     6 EYFGHSSFRPVQWKVIRSVLeERRDNLVVMATGYGKSLCYQYPSVLLNS----LTLVISPLISLMEDQVLQLVMSNIPAC 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  570 LhsgMTKKQRESVLKKVRAAQVHVLIVSPEAlvgcGAKGPANLPP-AAQLPPVAfacIDEVHCLSQWSHNFRPCYlRVCK 648
Cdd:cd18017    82 F---LGSAQSQNVLDDIKMGKIRVIYVTPEF----VSKGLELLQQlRNGITLIA---IDEAHCVSQWGHDFRSSY-RHLG 150

                         170       180       190
                  ....*....|....*....|....*....|..
gi 194473630  649 VLREHMGVRCFLGLTATATRSTARDVAQHLGI 680
Cdd:cd18017   151 SIRNRLPNVPIVALTATATPSVRDDIIKNLNL 182
DEXHc_RecQ2_BLM cd18016
DEAH-box helicase domain of RecQ2; ATP-dependent DNA helicase Q2 (RecQ2, also called Bloom ...
 492-680 3.71e-28

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: 113.38  E-value: 3.71e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  492 QLGHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALLyakrSPCLTLVVSPLLSLMDDQVSDLPSC-LKAACL 570
Cdd:cd18016    12 KFGLHQFRTNQLEAINAALLGEDCFVLMPTGGGKSLCYQLPACV----SPGVTVVISPLRSLIVDQVQKLTSLdIPATYL 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  571 HSGMTKKQRESVLKKVRAAQ--VHVLIVSPEALVGCGAKGPA--NLPPAAQLppvAFACIDEVHCLSQWSHNFRPCYLRV 646
Cdd:cd18016    88 TGDKTDAEATKIYLQLSKKDpiIKLLYVTPEKISASNRLISTleNLYERKLL---ARFVIDEAHCVSQWGHDFRPDYKRL 164

                         170       180       190
                  ....*....|....*....|....*....|....
gi 194473630  647 cKVLREHMGVRCFLGLTATATRSTARDVAQHLGI 680
Cdd:cd18016   165 -NMLRQKFPSVPMMALTATATPRVQKDILNQLKM 197
DEXDc smart00487
DEAD-like helicases superfamily;
490-693 5.75e-25

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 103.73  E-value: 5.75e-25
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630    490 LEQLGHHTFRPGQERAVMRILSGI-STLLVLPTGAGKSLCYQLPALLYAKRSP-CLTLVVSPLLSLMDDQVSDL-----P 562
Cdd:smart00487    1 IEKFGFEPLRPYQKEAIEALLSGLrDVILAAPTGSGKTLAALLPALEALKRGKgGRVLVLVPTRELAEQWAEELkklgpS 80

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630    563 SCLKAACLHSGMTKKQResvLKKVRAAQVHVLIVSPEALVGCGAKGPANlppaaqLPPVAFACIDEVHCLSQWshNFRPC 642
Cdd:smart00487   81 LGLKVVGLYGGDSKREQ---LRKLESGKTDILVTTPGRLLDLLENDKLS------LSNVDLVILDEAHRLLDG--GFGDQ 149

                           170       180       190       200       210
                    ....*....|....*....|....*....|....*....|....*....|.
gi 194473630    643 YLRVCKVLREHmgvRCFLGLTATATRSTARDVAQHLGIAEELEVSGSASIP 693
Cdd:smart00487  150 LEKLLKLLPKN---VQLLLLSATPPEEIENLLELFLNDPVFIDVGFTPLEP 197
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 499-672 1.60e-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: 1.60e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630   499 RPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPAL--LYAKRSPCLTLVVSPLLSLMDDQVSDL-----PSCLKAACLH 571
Cdd:pfam00270    1 TPIQAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALeaLDKLDNGPQALVLAPTRELAEQIYEELkklgkGLGLKVASLL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630   572 SGMTKKQRESVLKKvraaqVHVLIVSPEALVgcgakgpANLPPAAQLPPVAFACIDEVHCLSQWShnFRPCYLRVCKVLR 651
Cdd:pfam00270   81 GGDSRKEQLEKLKG-----PDILVGTPGRLL-------DLLQERKLLKNLKLLVLDEAHRLLDMG--FGPDLEEILRRLP 146

                          170       180
                   ....*....|....*....|.
gi 194473630   652 EHmgvRCFLGLTATATRSTAR 672
Cdd:pfam00270  147 KK---RQILLLSATLPRNLED 164
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 473-834 3.12e-20

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: 96.83  E-value: 3.12e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  473 PGPLGQVADTPA----EVFQVLEQLGHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPAL--LYAKRSPClTLV 546
Cdd:COG1205    28 PAREARYAPWPDwlppELRAALKKRGIERLYSHQAEAIEAARAGKNVVIATPTASGKSLAYLLPVLeaLLEDPGAT-ALY 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  547 VSPLLSLMDDQVS-------DLPSCLKAACLHSGMTKKQRESVLKkvraaQVHVLIVSPEAL-VGcgakgpanLPPA--- 615
Cdd:COG1205   107 LYPTKALARDQLRrlrelaeALGLGVRVATYDGDTPPEERRWIRE-----HPDIVLTNPDMLhYG--------LLPHhtr 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  616 -AQLppvaFAC-----IDEVHCL-----SQWSHNFRPcYLRVCkvlrEHMGVRC-FLGLTAT-------ATRSTARDVaq 676
Cdd:COG1205   174 wARF----FRNlryvvIDEAHTYrgvfgSHVANVLRR-LRRIC----RHYGSDPqFILASATignpaehAERLTGRPV-- 242

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  677 hlgiaEELEVSGSAS------------IPANLHLSVSmdRDSDQALVTLLQGDRfRTldsiIIYCARRKDTERVAallrt 744
Cdd:COG1205   243 -----TVVDEDGSPRgertfvlwnpplVDDGIRRSAL--AEAARLLADLVREGL-RT----LVFTRSRRGAELLA----- 305

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  745 clSTVRDSKPRGRGPETLAeAYHAGMCSQERKRVQQAFMQGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAI 824
Cdd:COG1205   306 --RYARRALREPDLADRVA-AYRAGYLPEERREIERGLRSGELLGVVSTNALELGIDIGGLDAVVLAGYPGTRASFWQQA 382

                         410
                  ....*....|
gi 194473630  825 GRAGRDGKPA 834
Cdd:COG1205   383 GRAGRRGQDS 392
HELICc smart00490
helicase superfamily c-terminal domain;
763-831 7.73e-20

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 84.96  E-value: 7.73e-20
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 194473630    763 AEAYHAGMCSQERKRVQQAFMQGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDG 831
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 8.34e-18

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: 78.06  E-value: 8.34e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 194473630    2 ERLATVRAWLQDWERAFVRLHGRRPAKEDVEAAPEETRALYREYRNLKQ 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 ...
 726-834 3.74e-17

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: 79.61  E-value: 3.74e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  726 IIYCARRKDTERVAALLRTCLstvrdsKPRGRGPETLAeAYHAGMCSQERKRVQQAFMQGHLRMVVATVAFGMGLDRPDV 805
Cdd:cd18797    39 IVFCRSRKLAELLLRYLKARL------VEEGPLASKVA-SYRAGYLAEDRREIEAELFNGELLGVVATNALELGIDIGGL 111

                          90       100
                  ....*....|....*....|....*....
gi 194473630  806 RAVLHLGLPPSFESYVQAIGRAGRDGKPA 834
Cdd:cd18797   112 DAVVLAGYPGSLASLWQQAGRAGRRGKDS 140
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 708-831 3.76e-16

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: 75.32  E-value: 3.76e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630   708 QALVTLLQGDRFrtlDSIIIYCARRKDTERVAALLRTCLSTVRdskprgrgpetlaeaYHAGMCSQERKRVQQAFMQGHL 787
Cdd:pfam00271    4 EALLELLKKERG---GKVLIFSQTKKTLEAELLLEKEGIKVAR---------------LHGDLSQEEREEILEDFRKGKI 65

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 194473630   788 RMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDG 831
Cdd:pfam00271   66 DVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
499-839 2.03e-14

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 77.76  E-value: 2.03e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  499 RPGQERAVMRILSGIST-----LLVLPTGAGKSLCyqlpALLYAKR--SPCLTLVVSPLLSLMDDQVSDLPSCLKAACLH 571
Cdd:COG1061    82 RPYQQEALEALLAALERgggrgLVVAPTGTGKTVL----ALALAAEllRGKRVLVLVPRRELLEQWAEELRRFLGDPLAG 157

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  572 SGmtKKQRESvlkkvraaqvHVLIVSPEALvgcgakgpANLPPAAQLPP-VAFACIDEVHclsqwsHNFRPCYLRVckvl 650
Cdd:COG1061   158 GG--KKDSDA----------PITVATYQSL--------ARRAHLDELGDrFGLVIIDEAH------HAGAPSYRRI---- 207

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  651 REHMGVRCFLGLTATATRSTARDVAQHL--GIA-----EELEVSGsasIPANLH-LSVSMDRDSDQALVTLLQGDRFRTL 722
Cdd:COG1061   208 LEAFPAAYRLGLTATPFRSDGREILLFLfdGIVyeyslKEAIEDG---YLAPPEyYGIRVDLTDERAEYDALSERLREAL 284

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  723 DS---------------------IIIYCARRKDTERVAALLRTclstvrdskprgRGPEtlAEAYHAGMCSQERKRVQQA 781
Cdd:COG1061   285 AAdaerkdkilrellrehpddrkTLVFCSSVDHAEALAELLNE------------AGIR--AAVVTGDTPKKEREEILEA 350

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 194473630  782 FMQGHLRMVVATVAFGMGLDRPDVRAVLHLGlppSFES---YVQAIGRA--GRDGKPaHCHLF 839
Cdd:COG1061   351 FRDGELRILVTVDVLNEGVDVPRLDVAILLR---PTGSpreFIQRLGRGlrPAPGKE-DALVY 409
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 704-840 2.20e-14

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: 71.00  E-value: 2.20e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  704 RDSDQALVTLLQGDRFRTLDSIIIYCARRKDTERVAALLRTClstvrdskprgrgpETLAEAYHAGMCSQERKRVQQAFM 783
Cdd:cd18787     9 EEEEKKLLLLLLLLEKLKPGKAIIFVNTKKRVDRLAELLEEL--------------GIKVAALHGDLSQEERERALKKFR 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 194473630  784 QGHLRMVVAT-VAfGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFL 840
Cdd:cd18787    75 SGKVRVLVATdVA-ARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAGRKGTAITFV 131
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
483-832 2.26e-14

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 76.72  E-value: 2.26e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  483 PAEVFQVLEQLGHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPA---LLYAKRSPCLTLVVSPL--LSLmddQ 557
Cdd:COG0513    10 SPPLLKALAELGYTTPTPIQAQAIPLILAGRDVLGQAQTGTGKTAAFLLPLlqrLDPSRPRAPQALILAPTreLAL---Q 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  558 VSD--------LPscLKAACLHSGMT-KKQRESvLKKvraaQVHVLIVSP---EALVGcgaKGPANLppaaqlppvafac 625
Cdd:COG0513    87 VAEelrklakyLG--LRVATVYGGVSiGRQIRA-LKR----GVDIVVATPgrlLDLIE---RGALDL------------- 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  626 iDEVHCLsqwshnfrpcylrvckVLRE-----HMG----VRCFLGLT----------ATATRSTARDVAQHLGIAEELEV 686
Cdd:COG0513   144 -SGVETL----------------VLDEadrmlDMGfiedIERILKLLpkerqtllfsATMPPEIRKLAKRYLKNPVRIEV 206

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  687 SGSASIPANLHLSVSM--DRDSDQALVTLLQGDRFrtlDSIIIYCARRKDTERVAALLRtclstvrdskprGRGPEtlAE 764
Cdd:COG0513   207 APENATAETIEQRYYLvdKRDKLELLRRLLRDEDP---ERAIVFCNTKRGADRLAEKLQ------------KRGIS--AA 269

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 194473630  765 AYHAGMcSQ-ERKRVQQAFMQGHLRMVVAT-VAfGMGLDRPDVRAVLHLGLPPSFESYVQAIG---RAGRDGK 832
Cdd:COG0513   270 ALHGDL-SQgQRERALDAFRNGKIRVLVATdVA-ARGIDIDDVSHVINYDLPEDPEDYVHRIGrtgRAGAEGT 340
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 515-665 3.84e-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: 70.90  E-value: 3.84e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  515 TLLVLPTGAGKSLCYQLPALLYAKRSPCLTLVVSPLLSLMDDQVSDL----PSCLKAACLHSGMTKKQREsvlkKVRAAQ 590
Cdd:cd00046     4 VLITAPTGSGKTLAALLAALLLLLKKGKKVLVLVPTKALALQTAERLrelfGPGIRVAVLVGGSSAEERE----KNKLGD 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 194473630  591 VHVLIVSPEALVGCgakgpanLPPAAQL--PPVAFACIDEVHCLSQWSHNFRPCYLRVCKVLREHMGVrcfLGLTAT 665
Cdd:cd00046    80 ADIIIATPDMLLNL-------LLREDRLflKDLKLIIVDEAHALLIDSRGALILDLAVRKAGLKNAQV---ILLSAT 146
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
478-845 2.42e-12

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 71.08  E-value: 2.42e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  478 QVADTP-AEVFQVLEQLGHHTFRPGQERAVMR-ILSGISTLLVLPTGAGKSLCYQLpALLYAKRSPCLTLVVSPLLSLMD 555
Cdd:COG1204     2 KVAELPlEKVIEFLKERGIEELYPPQAEALEAgLLEGKNLVVSAPTASGKTLIAEL-AILKALLNGGKALYIVPLRALAS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  556 DQVSDLPSCLKAACLHSGMTKKQRESVLKkvRAAQVHVLIVSPE---ALVGCGAKgpanlppaaQLPPVAFACIDEVH-- 630
Cdd:COG1204    81 EKYREFKRDFEELGIKVGVSTGDYDSDDE--WLGRYDILVATPEkldSLLRNGPS---------WLRDVDLVVVDEAHli 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  631 -----------CLSqwshnfrpcylrvcKVLREHMGVRcFLGLTATA--------------TRSTARDVAQHLGIA--EE 683
Cdd:COG1204   150 ddesrgptlevLLA--------------RLRRLNPEAQ-IVALSATIgnaeeiaewldaelVKSDWRPVPLNEGVLydGV 214

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  684 LEVSGSASIPANLHLSVSMDrdsdqalvTLLQGDrfrtldSIIIYCARRKDTERVAALLRTCLSTVRDSKPRGR------ 757
Cdd:COG1204   215 LRFDDGSRRSKDPTLALALD--------LLEEGG------QVLVFVSSRRDAESLAKKLADELKRRLTPEEREEleelae 280

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  758 ---------GP-ETLAE------AYH-AGMCSQERKRVQQAFMQGHLRMVVAT--VAFGMGLdrPdVRAVL-----HLGL 813
Cdd:COG1204   281 ellevseetHTnEKLADclekgvAFHhAGLPSELRRLVEDAFREGLIKVLVATptLAAGVNL--P-ARRVIirdtkRGGM 357

                         410       420       430
                  ....*....|....*....|....*....|....
gi 194473630  814 PP--SFEsYVQAIGRAGRDGKpahchlflHPQGE 845
Cdd:COG1204   358 VPipVLE-FKQMAGRAGRPGY--------DPYGE 382
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 732-834 3.66e-11

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: 62.28  E-value: 3.66e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  732 RKDTERVAALLRtclstvrdSKPRGRGPETLAEAYHAGMCSQERKRVQQAFMQGHLRMVVATVAFGMGLDRPDVRAVLHL 811
Cdd:cd18796    48 RSQAERLAQRLR--------ELCPDRVPPDFIALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDVDLVIQI 119

                          90       100
                  ....*....|....*....|...
gi 194473630  812 GLPPSFESYVQAIGRAGRDGKPA 834
Cdd:cd18796   120 GSPKSVARLLQRLGRSGHRPGAA 142
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 790-839 6.02e-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: 6.02e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 194473630  790 VVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGK-PAHCHLF 839
Cdd:cd18785    26 LVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRGGKdEGEVILF 76
Drc1-Sld2 pfam11719
DNA replication and checkpoint protein; Genome duplication is precisely regulated by ...
 4-170 3.49e-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: 60.23  E-value: 3.49e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630     4 LATVRAWLQDWERAFVRLHGRRPAKEDVEAAPeETRALYREYRNLKQAVSQADDGHRVQ---KQSLAKAAEEEQepscwg 80
Cdd:pfam11719    1 ISQLKAEIKEWERAFAAKNGRKPSKDDIKKNP-EIAKKYKLYSKLKKGESIKTKTPSKPvklEARPKKRKHEST------ 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630    81 shlNRAATQNTQSIPKQSplssiqdygKRLKANLkntlqgGPTLSRklqhQKRSLSIVPTSRPPGPRTESPcPEQANDAL 160
Cdd:pfam11719   74 ---NKSPEKNSQSTPRKS---------KNIKSEL------GPTPQA----NGKVLSLFDLLSTPPKSSPLK-SKEVKTDV 130

                          170
                   ....*....|
gi 194473630   161 PQVPVPQPRQ 170
Cdd:pfam11719  131 SGTAIFTPSK 140
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 724-831 7.62e-09

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: 56.02  E-value: 7.62e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  724 SIIIYCARRKDTERVAALLRtclstvrdskprGRGpetlaeAYHAGMCSQERKRVQQAFMQGHLRMVVATVAFGMGLDRP 803
Cdd:cd18795    45 PVLVFCSSRKECEKTAKDLA------------GIA------FHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLP 106

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 194473630  804 DVRAVLhLGLP----------PSFEsYVQAIGRAGRDG 831
Cdd:cd18795   107 ARTVII-KGTQrydgkgyrelSPLE-YLQMIGRAGRPG 142
PRK09751 PRK09751
putative ATP-dependent helicase Lhr; Provisional
 727-828 8.95e-09

putative ATP-dependent helicase Lhr; Provisional


Pssm-ID: 137505 [Multi-domain]  Cd Length: 1490  Bit Score: 60.32  E-value: 8.95e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  727 IYCARRKDTERVAALLRTCLSTVRDSKPRGRG-PETLAEAYHAGMCSQERKRVQQAFMQGHLRMVVATVAFGMGLDRPDV 805
Cdd:PRK09751  267 LYAARLQRSPSIAVDAAHFESTSGATSNRVQSsDVFIARSHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAV 346

                          90       100
                  ....*....|....*....|...
gi 194473630  806 RAVLHLGLPPSFESYVQAIGRAG 828
Cdd:PRK09751  347 DLVIQVATPLSVASGLQRIGRAG 369
PTZ00110 PTZ00110
helicase; Provisional
 483-842 2.95e-08

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 57.86  E-value: 2.95e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  483 PAEVFQVLEQLGHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALLYAKRSPCL-------TLVVSPLLSLMD 555
Cdd:PTZ00110  138 PDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLrygdgpiVLVLAPTRELAE 217

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  556 dQVSD------LPSCLKAACLHSGMTKKQRESVLKKvraaQVHVLIVSPEALVGCGAKGPANLPPaaqlppVAFACIDEV 629
Cdd:PTZ00110  218 -QIREqcnkfgASSKIRNTVAYGGVPKRGQIYALRR----GVEILIACPGRLIDFLESNVTNLRR------VTYLVLDEA 286

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  630 HclSQWSHNFRPCYLRVCKVLREHmgvRCFLGLTATATR---STARDVAQHLGI---AEELEVSGSASIPANLHLsvsMD 703
Cdd:PTZ00110  287 D--RMLDMGFEPQIRKIVSQIRPD---RQTLMWSATWPKevqSLARDLCKEEPVhvnVGSLDLTACHNIKQEVFV---VE 358

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  704 RDSDQALVTLLQGDRFRTLDSIIIYCARRKDTERVAALLRTclstvrDSKPrgrgpetlAEAYHAGMCSQERKRVQQAFM 783
Cdd:PTZ00110  359 EHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRL------DGWP--------ALCIHGDKKQEERTWVLNEFK 424

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 194473630  784 QGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFLHP 842
Cdd:PTZ00110  425 TGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTP 483
PRK13767 PRK13767
ATP-dependent helicase; Provisional
 497-828 4.50e-08

ATP-dependent helicase; Provisional


Pssm-ID: 237497 [Multi-domain]  Cd Length: 876  Bit Score: 57.59  E-value: 4.50e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  497 TFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPAL---------------LYAkrspcltLVVSPLLSLMDD----- 556
Cdd:PRK13767   32 TFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIdelfrlgregeledkVYC-------LYVSPLRALNNDihrnl 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  557 --------QVS-----DLPScLKAACLHSGMTKKQRESVLKKvraaQVHVLIVSPEALvgcgakgpA---NLPPAAQ-LP 619
Cdd:PRK13767  105 eeplteirEIAkergeELPE-IRVAIRTGDTSSYEKQKMLKK----PPHILITTPESL--------AillNSPKFREkLR 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  620 PVAFACIDEVHCLSQwshNFRPCYLRVC-KVLREHMG---VRcfLGLTATAtrSTARDVAQHLGIAEELEVSGSASIpan 695
Cdd:PRK13767  172 TVKWVIVDEIHSLAE---NKRGVHLSLSlERLEELAGgefVR--IGLSATI--EPLEEVAKFLVGYEDDGEPRDCEI--- 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  696 lhLSVSMDRDSDQALVT----LLQGDR-------FRTLDSII-------IYCARRKDTERVAALLRTCLSTVRDskprgr 757
Cdd:PRK13767  242 --VDARFVKPFDIKVISpvddLIHTPAeeisealYETLHELIkehrttlIFTNTRSGAERVLYNLRKRFPEEYD------ 313

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 194473630  758 gpETLAEAYHAGMCSQERKRVQQAFMQGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAG 828
Cdd:PRK13767  314 --EDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAG 382
PTZ00424 PTZ00424
helicase 45; Provisional
 721-853 1.65e-07

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 55.22  E-value: 1.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  721 TLDSIIIYCARRKDTERVAALLRTCLSTVrdskprgrgpetlaEAYHAGMCSQERKRVQQAFMQGHLRMVVATVAFGMGL 800
Cdd:PTZ00424  266 TITQAIIYCNTRRKVDYLTKKMHERDFTV--------------SCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGI 331

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 194473630  801 DRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFLHPQG-EDLWELSRH 853
Cdd:PTZ00424  332 DVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDiEQLKEIERH 385
COG1202 COG1202
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
763-829 6.78e-07

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


Pssm-ID: 440815 [Multi-domain]  Cd Length: 790  Bit Score: 53.74  E-value: 6.78e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 194473630  763 AEAYHAGMCSQERKRVQQAFMQGHLRMVVATVAFGMGLDRPDVRAVlhlglppsFES------------YVQAIGRAGR 829
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 ...
 502-561 1.20e-06

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: 50.28  E-value: 1.20e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 194473630  502 QERAVMRILSGISTLLVLPTGAGKSLCYQLPAL--LYAKRSPClTLVVSPLLSLMDDQVSDL 561
Cdd:cd17923     5 QAEAIEAARAGRSVVVTTGTASGKSLCYQLPILeaLLRDPGSR-ALYLYPTKALAQDQLRSL 65
Lhr COG1201
Lhr-like helicase [Replication, recombination and repair];
497-828 2.71e-06

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


Pssm-ID: 440814 [Multi-domain]  Cd Length: 850  Bit Score: 51.64  E-value: 2.71e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  497 TFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALL-YAKRSP-------CLTLVVSPLLSL--------------M 554
Cdd:COG1201    24 APTPPQREAWPAIAAGESTLLIAPTGSGKTLAAFLPALDeLARRPRpgelpdgLRVLYISPLKALandiernlrapleeI 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  555 DDQVSDLPSCLKAAcLHSGMTKkQREsvlkkvRAAQV----HVLIVSPE--ALVGCGAKGPANLppaAQLPPVAfacIDE 628
Cdd:COG1201   104 GEAAGLPLPEIRVG-VRTGDTP-ASE------RQRQRrrppHILITTPEslALLLTSPDARELL---RGVRTVI---VDE 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  629 VHCL------SQWS------HNFRPCYLRVckvlrehmgvrcfLGLTATAtrstaRD---VAQHLGIAEELE----VSgs 689
Cdd:COG1201   170 IHALagskrgVHLAlslerlRALAPRPLQR-------------IGLSATV-----GPleeVARFLVGYEDPRpvtiVD-- 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  690 ASIPANLHLSV-SMDRDSD--------------QALVTLLQGDRfrtldSIIIYCARRKDTERVAALLRTclstvrdskp 754
Cdd:COG1201   230 AGAGKKPDLEVlVPVEDLIerfpwaghlwphlyPRVLDLIEAHR-----TTLVFTNTRSQAERLFQRLNE---------- 294

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 194473630  755 RGRGPETLAEAYHAGMCSQERKRVQQAFMQGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAG 828
Cdd:COG1201   295 LNPEDALPIAAHHGSLSREQRLEVEEALKAGELRAVVATSSLELGIDIGDVDLVIQVGSPKSVARLLQRIGRAG 368
DDXDc_reverse_gyrase cd17924
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ...
 508-597 3.49e-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: 48.86  E-value: 3.49e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  508 RILSGISTLLVLPTGAGKS---LCYQLPALLYAKRSpcltLVVSPLLSLMDdQVSD--------LPSCLKAACLHSGMTK 576
Cdd:cd17924    28 RLLRGKSFAIIAPTGVGKTtfgLATSLYLASKGKRS----YLIFPTKSLVK-QAYErlskyaekAGVEVKILVYHSRLKK 102

                          90       100
                  ....*....|....*....|.
gi 194473630  577 KQRESVLKKVRAAQVHVLIVS 597
Cdd:cd17924   103 KEKEELLEKIEKGDFDILVTT 123
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 498-665 4.19e-06

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: 47.69  E-value: 4.19e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  498 FRPGQERAVMRILSGIST---LLVLPTGAGKSLC-YQLPALLYAKRspclTLVVSPLLSLMDDQVSDLpsclkAACLHSG 573
Cdd:cd17926     1 LRPYQEEALEAWLAHKNNrrgILVLPTGSGKTLTaLALIAYLKELR----TLIVVPTDALLDQWKERF-----EDFLGDS 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  574 MTKKQRESVLKKVRAAQvhVLIVSPEALvgcgakgpANLPPAAQLPPVAFACI--DEVHCLS--QWSHnfrpcylrvckv 649
Cdd:cd17926    72 SIGLIGGGKKKDFDDAN--VVVATYQSL--------SNLAEEEKDLFDQFGLLivDEAHHLPakTFSE------------ 129

                         170
                  ....*....|....*.
gi 194473630  650 LREHMGVRCFLGLTAT 665
Cdd:cd17926   130 ILKELNAKYRLGLTAT 145
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 472-848 6.87e-06

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 50.17  E-value: 6.87e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  472 PPGPLGQVADT--PAEVFQVLEQLGHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALLY---------AKRS 540
Cdd:PLN00206  116 VPPPILSFSSCglPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRcctirsghpSEQR 195

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  541 PCLTLVVSPLLSLMDdQVSDlpsclKAACLHSGMTKKQRESVLKKVRAAQVHVLIVSPEALVGCgakgPANL-----PPA 615
Cdd:PLN00206  196 NPLAMVLTPTRELCV-QVED-----QAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGT----PGRLidllsKHD 265

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  616 AQLPPVAFACIDEVHCLSQwsHNFRPCYLRVCKVLREHMgvrcFLGLTATATRSTARdVAQHLgiAEELeVSGSASIPAN 695
Cdd:PLN00206  266 IELDNVSVLVLDEVDCMLE--RGFRDQVMQIFQALSQPQ----VLLFSATVSPEVEK-FASSL--AKDI-ILISIGNPNR 335

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  696 LHLSVSM------DRDSDQALVTLLQgDRFRTLDSIIIYCARRKDtervAALLRTCLSTVRDSKprgrgpetlAEAYHAG 769
Cdd:PLN00206  336 PNKAVKQlaiwveTKQKKQKLFDILK-SKQHFKPPAVVFVSSRLG----ADLLANAITVVTGLK---------ALSIHGE 401

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 194473630  770 MCSQERKRVQQAFMQGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFLHPQGEDLW 848
Cdd:PLN00206  402 KSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRNLF 480
DEADc_DDX5 cd18049
DEAD-box helicase domain of DEAD box protein 5; DDX5 (also called RNA helicase P68, HLR1, ...
 463-612 1.17e-05

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: 48.08  E-value: 1.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  463 CPTPVLPLYPpgplgqvADTPAEVFQVLEQLGHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALLYAKRSPC 542
Cdd:cd18049    19 CPKPVLNFYE-------ANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPF 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  543 LT-------LVVSPLLSLMdDQVSDLP-----SC-LKAACLHSGMTKKQRESVLKKvraaQVHVLIVSPEALVGCGAKGP 609
Cdd:cd18049    92 LErgdgpicLVLAPTRELA-QQVQQVAaeygrACrLKSTCIYGGAPKGPQIRDLER----GVEICIATPGRLIDFLEAGK 166


                  ...
gi 194473630  610 ANL 612
Cdd:cd18049   167 TNL 169
ResIII pfam04851
Type III restriction enzyme, res subunit;
496-665 1.30e-05

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 46.51  E-value: 1.30e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630   496 HTFRPGQERAVMRILSGIST-----LLVLPTGAGKSLCY-QLPALLYAKRSPCLTLVVSPLLSLMDDQVSDLPSCLKAAC 569
Cdd:pfam04851    2 LELRPYQIEAIENLLESIKNgqkrgLIVMATGSGKTLTAaKLIARLFKKGPIKKVLFLVPRKDLLEQALEEFKKFLPNYV 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630   570 LHSGMTKKQResvlKKVRAAQVHVLIVSPEALvgcgakGPANLPPAAQLPPVAFACI--DEVHCL--SQWSH---NFRPC 642
Cdd:pfam04851   82 EIGEIISGDK----KDESVDDNKIVVTTIQSL------YKALELASLELLPDFFDVIiiDEAHRSgaSSYRNileYFKPA 151

                          170       180
                   ....*....|....*....|...
gi 194473630   643 YLrvckvlrehmgvrcfLGLTAT 665
Cdd:pfam04851  152 FL---------------LGLTAT 159
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 497-685 2.82e-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: 46.10  E-value: 2.82e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  497 TFRPGQERAVMRI-LSGISTLLVLPTGAGKSLCYQLPALLYAKRSPCLTLVVSPLLSLMDDQVSDLPSCLKAACLHSGMt 575
Cdd:cd17921     1 LLNPIQREALRALyLSGDSVLVSAPTSSGKTLIAELAILRALATSGGKAVYIAPTRALVNQKEADLRERFGPLGKNVGL- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  576 kKQRESVLKKVRAAQVHVLIVSPEALVGCGAKGPANLppaaqLPPVAFACIDEVHCLSQWShnfRPCYLRVC--KVLREH 653
Cdd:cd17921    80 -LTGDPSVNKLLLAEADILVATPEKLDLLLRNGGERL-----IQDVRLVVVDEAHLIGDGE---RGVVLELLlsRLLRIN 150

                         170       180       190
                  ....*....|....*....|....*....|..
gi 194473630  654 MGVRcFLGLTATAtrSTARDVAQHLGIAEELE 685
Cdd:cd17921   151 KNAR-FVGLSATL--PNAEDLAEWLGVEDLIR 179
PRK04837 PRK04837
ATP-dependent RNA helicase RhlB; Provisional
 775-835 3.55e-05

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235314 [Multi-domain]  Cd Length: 423  Bit Score: 47.66  E-value: 3.55e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 194473630  775 RKRVQQAFMQGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAH 835
Cdd:PRK04837  294 RLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGH 354
DEXHc_LHR-like cd17922
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ...
 512-601 6.26e-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: 6.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  512 GISTLLVLPTGAGKSLCYQLPALL-YAKR--SPCLTLVVSPLLSLMDDQVSDLPSCLKAACL-------HSGMTKKQRES 581
Cdd:cd17922     1 GRNVLIAAPTGSGKTEAAFLPALSsLADEpeKGVQVLYISPLKALINDQERRLEEPLDEIDLeipvavrHGDTSQSEKAK 80

                          90       100
                  ....*....|....*....|
gi 194473630  582 VLKKVRaaqvHVLIVSPEAL 601
Cdd:cd17922    81 QLKNPP----GILITTPESL 96
DEADc_DDX17 cd18050
DEAD-box helicase domain of DEAD box protein 17; DDX17 (also called DEAD Box Protein P72 or ...
 463-612 1.22e-04

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: 45.39  E-value: 1.22e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  463 CPTPVLPLYPpgplgqvADTPAEVFQVLEQLGHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALLYAKRSP- 541
Cdd:cd18050    57 CPKPVFAFHQ-------ANFPQYVMDVLLDQNFKEPTPIQCQGFPLALSGRDMVGIAQTGSGKTLAYLLPAIVHINHQPy 129

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  542 --------CLTLVVSPLLSLMDDQVSD---LPSCLKAACLHSGMTKKQRESVLKKvraaQVHVLIVSPEALVGCGAKGPA 610
Cdd:cd18050   130 lergdgpiCLVLAPTRELAQQVQQVADdygKSSRLKSTCIYGGAPKGPQIRDLER----GVEICIATPGRLIDFLEAGKT 205


                  ..
gi 194473630  611 NL 612
Cdd:cd18050   206 NL 207
PRK01172 PRK01172
ATP-dependent DNA helicase;
660-831 2.89e-04

ATP-dependent DNA helicase;


Pssm-ID: 100801 [Multi-domain]  Cd Length: 674  Bit Score: 45.26  E-value: 2.89e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  660 LGLTATAtrSTARDVAQHLGIAeeLEVSGSASIPANL------HLSVSMDRDSDQALVTLLQgDRFRTLDSIIIYCARRK 733
Cdd:PRK01172  173 LALSATV--SNANELAQWLNAS--LIKSNFRPVPLKLgilyrkRLILDGYERSQVDINSLIK-ETVNDGGQVLVFVSSRK 247

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  734 DTERVAALLRTCLSTVRDSKPRGRG----PETLAEA-------YHAGMCSQERKRVQQAFMQGHLRMVVATVAFGMGLDR 802
Cdd:PRK01172  248 NAEDYAEMLIQHFPEFNDFKVSSENnnvyDDSLNEMlphgvafHHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNL 327

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 194473630  803 P-------DVRAVLHLGLPP-SFESYVQAIGRAGRDG 831
Cdd:PRK01172  328 ParlvivrDITRYGNGGIRYlSNMEIKQMIGRAGRPG 364
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 708-840 3.15e-04

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: 42.19  E-value: 3.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  708 QALVTLLQGDRFRTLDSI-IIYCARRkDTERV-AALLRTCLSTVRDSKPR---GRGPETlaEAYHAGMCSQERKRVQQAF 782
Cdd:cd18802    10 QKLIEILREYFPKTPDFRgIIFVERR-ATAVVlSRLLKEHPSTLAFIRCGfliGRGNSS--QRKRSLMTQRKQKETLDKF 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 194473630  783 MQGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGkpAHCHLFL 840
Cdd:cd18802    87 RDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPN--SKYILMV 142
DEADc cd00268
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ...
 488-602 5.28e-04

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: 42.43  E-value: 5.28e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  488 QVLEQLGHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPAL------LYAKRSPCLTLVVSPL--LSLmddQVS 559
Cdd:cd00268     3 KALKKLGFEKPTPIQAQAIPLILSGRDVIGQAQTGSGKTLAFLLPILekllpePKKKGRGPQALVLAPTreLAM---QIA 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 194473630  560 DL------PSCLKAACLHSGMTKKQRESVLKKvraaQVHVLIVSPEALV 602
Cdd:cd00268    80 EVarklgkGTGLKVAAIYGGAPIKKQIEALKK----GPDIVVGTPGRLL 124
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 565-595 5.75e-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: 41.34  E-value: 5.75e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 194473630  565 LKAACLHSGMTKKQRESVLKKVRAAQVHVLI 595
Cdd:cd18787    52 IKVAALHGDLSQEERERALKKFRSGKVRVLV 82
PRK01297 PRK01297
ATP-dependent RNA helicase RhlB; Provisional
 683-831 5.97e-04

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 234938 [Multi-domain]  Cd Length: 475  Bit Score: 43.75  E-value: 5.97e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  683 ELEVSGSASIPANLHLSVSMDRDSDQALVTLLQGDRFrtlDSIIIYCARRKDTERVAALLrtclstVRDskprgrgpetl 762
Cdd:PRK01297  299 EIEPENVASDTVEQHVYAVAGSDKYKLLYNLVTQNPW---ERVMVFANRKDEVRRIEERL------VKD----------- 358

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 194473630  763 aeAYHAGMCSQE-----RKRVQQAFMQGHLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDG 831
Cdd:PRK01297  359 --GINAAQLSGDvpqhkRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAG 430
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 531-597 7.78e-04

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: 40.27  E-value: 7.78e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 194473630   531 LPALLYAKRSPClTLVVSPLLSLMDDQVSDLPSCLKAACLHSGMTKKQRESVLKKVRAAQVHVLIVS 597
Cdd:pfam00271    6 LLELLKKERGGK-VLIFSQTKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVAT 71
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 707-840 7.96e-04

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 43.68  E-value: 7.96e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  707 DQALVTLLQGDRFrtlDSIIIYCARRKDTERVA-ALLRTCLSTVrdskprgrgpetlaeAYHAGMCSQERKRVQQAFMQG 785
Cdd:PRK11634  233 NEALVRFLEAEDF---DAAIIFVRTKNATLEVAeALERNGYNSA---------------ALNGDMNQALREQTLERLKDG 294

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 194473630  786 HLRMVVATVAFGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGKPAHCHLFL 840
Cdd:PRK11634  295 RLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFV 349
PRK00254 PRK00254
ski2-like helicase; Provisional
 726-829 1.58e-03

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 42.88  E-value: 1.58e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  726 IIYCARRKDTERVAALLRTCLSTVRDsKPRGRGPETLAEA--------------------YHAGMCSQERKRVQQAFMQG 785
Cdd:PRK00254  242 LVFVNTRRSAEKEALELAKKIKRFLT-KPELRALKELADSleenptneklkkalrggvafHHAGLGRTERVLIEDAFREG 320

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 194473630  786 HLRMVVATVAFGMGLDRPDVRAVL-------HLGLP--PSFESYvQAIGRAGR 829
Cdd:PRK00254  321 LIKVITATPTLSAGINLPAFRVIIrdtkrysNFGWEdiPVLEIQ-QMMGRAGR 372
DEADc_DDX43_DDX53 cd17958
DEAD-box helicase domain of DEAD box proteins 43 and 53; DDX43 (also called cancer/testis ...
 486-598 1.70e-03

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: 40.91  E-value: 1.70e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  486 VFQVLEQLGHHTFRPGQERAVMRILSGISTLLVLPTGAGKSLCYQLPALL--------YAKRSPCLTLVVSPLLSL---M 554
Cdd:cd17958     1 IMKEIKKQGFEKPSPIQSQAWPIILQGIDLIGVAQTGTGKTLAYLLPGFIhldlqpipREQRNGPGVLVLTPTRELalqI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 194473630  555 DDQVSD-LPSCLKAACLHSGMTKKQRESVLKKvraaQVHVLIVSP 598
Cdd:cd17958    81 EAECSKySYKGLKSVCVYGGGNRNEQIEDLSK----GVDIIIATP 121
DEADc_DDX28 cd17948
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box ...
 502-601 2.29e-03

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: 41.20  E-value: 2.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  502 QERAVMRILSGISTLLVLPTGAGKSLCYQLP---ALLYAK-------RSPcLTLVVSPLLSLMdDQVS--------DLPs 563
Cdd:cd17948    17 QKQGIPSILRGRNTLCAAETGSGKTLTYLLPiiqRLLRYKllaegpfNAP-RGLVITPSRELA-EQIGsvaqslteGLG- 93

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 194473630  564 cLKAACLHSGMTKKQresvLKKVRAAQVHVLIVSPEAL 601
Cdd:cd17948    94 -LKVKVITGGRTKRQ----IRNPHFEEVDILVATPGAL 126
ZnF_C2HC smart00343
zinc finger;
394-408 2.40e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 36.27  E-value: 2.40e-03
                            10
                    ....*....|....*
gi 194473630    394 TCFRCGQFGHWASQC 408
Cdd:smart00343    1 KCYNCGKEGHIARDC 15
DinG COG1199
Rad3-related DNA helicase DinG [Replication, recombination and repair];
491-540 2.41e-03

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


Pssm-ID: 440812 [Multi-domain]  Cd Length: 629  Bit Score: 42.22  E-value: 2.41e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 194473630  491 EQLGHHTFRPGQER---AVMRILSGISTLLVL-PTGAGKSLCYQLPALLYAKRS 540
Cdd:COG1199     8 LAFPGFEPRPGQREmaeAVARALAEGRHLLIEaGTGTGKTLAYLVPALLAARET 61
PRK02362 PRK02362
ATP-dependent DNA helicase;
760-845 2.89e-03

ATP-dependent DNA helicase;


Pssm-ID: 235032 [Multi-domain]  Cd Length: 737  Bit Score: 41.87  E-value: 2.89e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  760 ETLAEA-------YHAGMCSQERKRVQQAFMQGHLRMVVATVAFGMGLDRPDVRAVLH--------LGLPP-SFESYVQA 823
Cdd:PRK02362  296 KDLADCvakgaafHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRdyrrydggAGMQPiPVLEYHQM 375

                          90       100
                  ....*....|....*....|..
gi 194473630  824 IGRAGRDGkpahchlfLHPQGE 845
Cdd:PRK02362  376 AGRAGRPG--------LDPYGE 389
PRK11776 PRK11776
ATP-dependent RNA helicase DbpA; Provisional
 703-832 3.42e-03

ATP-dependent RNA helicase DbpA; Provisional


Pssm-ID: 236977 [Multi-domain]  Cd Length: 460  Bit Score: 41.33  E-value: 3.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  703 DRDSDQALVTLLQgdRFRTlDSIIIYCARRKDTERVAALLRtclstvrdskprGRGPETLAeaYHAGMCSQERKRVQQAF 782
Cdd:PRK11776  226 PDERLPALQRLLL--HHQP-ESCVVFCNTKKECQEVADALN------------AQGFSALA--LHGDLEQRDRDQVLVRF 288

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 194473630  783 MQGHLRMVVAT-VAfGMGLDRPDVRAVLHLGLPPSFESYVQAIGRAGRDGK 832
Cdd:PRK11776  289 ANRSCSVLVATdVA-ARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGS 338
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 766-840 6.23e-03

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: 38.23  E-value: 6.23e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  766 YHAGMCSQERKRVQQAFM--QGHLRMVVATVAFGMGL-----DRpdvraVLHLGLP--PSFESyvQAIGRAGRDG--KPA 834
Cdd:cd18793    57 LDGSTSSKERQKLVDRFNedPDIRVFLLSTKAGGVGLnltaaNR-----VILYDPWwnPAVEE--QAIDRAHRIGqkKPV 129


                  ....*.
gi 194473630  835 HCHLFL 840
Cdd:cd18793   130 VVYRLI 135
HELICc smart00490
helicase superfamily c-terminal domain;
565-597 7.10e-03

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 36.81  E-value: 7.10e-03
                            10        20        30
                    ....*....|....*....|....*....|...
gi 194473630    565 LKAACLHSGMTKKQRESVLKKVRAAQVHVLIVS 597
Cdd:smart00490   12 IKVARLHGGLSQEEREEILDKFNNGKIKVLVAT 44
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
 522-665 7.19e-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: 7.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194473630  522 GAGK-----SLCYQLpalLYAKRSPCLTLVVSPlLSLMDDQVSDL----PScLKAACLHSgmTKKQRESVLKKVRAAQVH 592
Cdd:cd17919    29 GLGKtlqaiAFLAYL---LKEGKERGPVLVVCP-LSVLENWEREFekwtPD-LRVVVYHG--SQRERAQIRAKEKLDKFD 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 194473630  593 VLIVSPEALVGCgakgpanlppAAQLPPVAFACI--DEVHCL----SQWShnfrpcylRVCKVLREHMgvRcfLGLTAT 665
Cdd:cd17919   102 VVLTTYETLRRD----------KASLRKFRWDLVvvDEAHRLknpkSQLS--------KALKALRAKR--R--LLLTGT 158
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 767-838 8.00e-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: 38.48  E-value: 8.00e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 194473630  767 HAGMCSQERKRVQQAFMQGHLRMVVATVAFGMGLDRPD--VRAVLH---LGLppsfESYVQAIGRAGRDGKPAHCHL 838
Cdd:cd18811    68 HGRLKSDEKDAVMAEFREGEVDILVSTTVIEVGVDVPNatVMVIEDaerFGL----SQLHQLRGRVGRGDHQSYCLL 140
 
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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