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Conserved domains on  [gi|2462599686|ref|XP_054207200|]
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probable ATP-dependent RNA helicase DDX60-like isoform X1 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 743-926 1.14e-102

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


The actual alignment was detected with superfamily member cd18025:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 192  Bit Score: 326.63  E-value: 1.14e-102
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  743 IPNAWQQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDVGVVVYVAPAKSLVGQVAATVENRFTKTL-PAGRT 821
Cdd:cd18025      1 NPDAWQRELLDIVDRRESALIVAPTSSGKTFISYYCMEKVLRESDDGVVVYVAPTKALVNQVVAEVYARFSKKYpPSGKS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  822 LCGAFTRDYRHN-VLNCQVLITVPECFEILLLAPHRQKWVERIRYVIFDEVHYLGREVGAKFWELLLVIIRCPFLVLSAT 900
Cdd:cd18025     81 LWGVFTRDYRHNnPMNCQVLITVPECLEILLLSPHNASWVPRIKYVIFDEIHSIGQSEDGAVWEQLLLLIPCPFLALSAT 160

                          170       180
                   ....*....|....*....|....*.
gi 2462599686  901 INNPNLLTKWLQSVKQYWKQADKIME 926
Cdd:cd18025    161 IGNPQKFHEWLQSVQRARKAELKKIE 186
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 1231-1325 6.19e-34

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd18795:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 154  Bit Score: 128.44  E-value: 6.19e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1231 FTRHGKELKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFAQDSVY-------LDALN 1303
Cdd:cd18795     51 SSRKECEKTAKDLAGIAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLPARTVIIKGTQRYdgkgyreLSPLE 130

                           90       100
                   ....*....|....*....|..
gi 2462599686 1304 YRQMSGRAGRRGQDLLGNVYFF 1325
Cdd:cd18795    131 YLQMIGRAGRPGFDTRGEAIIM 152
Dob10 super family cl34780
Superfamily II RNA helicase [Replication, recombination and repair];
748-1390 1.34e-30

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


The actual alignment was detected with superfamily member COG4581:

Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 130.83  E-value: 1.34e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  748 QQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVLRESdvGVVVYVAPAKSLVGQVAATVENRFtktlpaGRTLCGAFT 827
Cdd:COG4581     30 QEEAILALEAGRSVLVAAPTGSGKTLVAEFAIFLALARG--RRSFYTAPIKALSNQKFFDLVERF------GAENVGLLT 101

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  828 RDYRHNVlNCQVLI-TVpecfEIL---LLAPHRQkwVERIRYVIFDEVHYLG-REVGAkFWELllVIIRCP----FLVLS 898
Cdd:COG4581    102 GDASVNP-DAPIVVmTT----EILrnmLYREGAD--LEDVGVVVMDEFHYLAdPDRGW-VWEE--PIIHLParvqLVLLS 171

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  899 ATINNPNLLTKWLQSVKQywkqadkimeekcisekqadkclnflqdhsyknqsyEVRLVLCGERYNDLEKHICsvkhddv 978
Cdd:COG4581    172 ATVGNAEEFAEWLTRVRG------------------------------------ETAVVVSEERPVPLEFHYL------- 208

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  979 yfdhfhpcaaLTTDIIEKYGFPPDLTLTPQesiqlydtmaqVWETwpraqelcpeefilfknkivikkldarkyeenlka 1058
Cdd:COG4581    209 ----------VTPRLFPLFRVNPELLRPPS-----------RHEV----------------------------------- 232

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1059 eltnwikngqvkkvkrvlknlspdslssskdmvkmfpllVEKLRQMDKLPAIFFLFKnddvgkRAGsvctflektetksh 1138
Cdd:COG4581    233 ---------------------------------------IEELDRGGLLPAIVFIFS------RRG-------------- 253

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1139 phteCHSYVFAIdevlekvrkTQKRISTKKnpkkaeklERKKVYRAeyinflenlkILEISEDCTyadvkalhteitrnk 1218
Cdd:COG4581    254 ----CDEAAQQL---------LSARLTTKE--------ERAEIREA----------IDEFAEDFS--------------- 287

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1219 dstldrvlprvrfTRHGKELKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFAQDS-- 1296
Cdd:COG4581    288 -------------VLFGKTLSRLLRRGIAVHHAGMLPKYRRLVEELFQAGLLKVVFATDTLAVGINMPARTVVFTKLSkf 354

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1297 -----VYLDALNYRQMSGRAGRRGQDLLGNVY-----FFDiplPKIKRLLASSVPE-LRGQFPLSITLVLRlmLLASKGd 1365
Cdd:COG4581    355 dgerhRPLTAREFHQIAGRAGRRGIDTEGHVVvlapeHDD---PKKFARLASARPEpLRSSFRPSYNMVLN--LLARPG- 428

                          650       660
                   ....*....|....*....|....*
gi 2462599686 1366 dPEDAKAkvlsVLKHSLLSFKRRRA 1390
Cdd:COG4581    429 -LERARE----LLEDSFAQFQADRS 448
 
Name Accession Description Interval E-value
DEXHc_DDX60 cd18025
DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an ...
 743-926 1.14e-102

DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an IFN-inducible cytoplasmic helicase that plays a role in RIG-I-mediated type I interferon (IFN) nuclease-mediated viral RNA degradation. DDX60 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: 350783 [Multi-domain]  Cd Length: 192  Bit Score: 326.63  E-value: 1.14e-102
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  743 IPNAWQQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDVGVVVYVAPAKSLVGQVAATVENRFTKTL-PAGRT 821
Cdd:cd18025      1 NPDAWQRELLDIVDRRESALIVAPTSSGKTFISYYCMEKVLRESDDGVVVYVAPTKALVNQVVAEVYARFSKKYpPSGKS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  822 LCGAFTRDYRHN-VLNCQVLITVPECFEILLLAPHRQKWVERIRYVIFDEVHYLGREVGAKFWELLLVIIRCPFLVLSAT 900
Cdd:cd18025     81 LWGVFTRDYRHNnPMNCQVLITVPECLEILLLSPHNASWVPRIKYVIFDEIHSIGQSEDGAVWEQLLLLIPCPFLALSAT 160

                          170       180
                   ....*....|....*....|....*.
gi 2462599686  901 INNPNLLTKWLQSVKQYWKQADKIME 926
Cdd:cd18025    161 IGNPQKFHEWLQSVQRARKAELKKIE 186
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 1231-1325 6.19e-34

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: 128.44  E-value: 6.19e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1231 FTRHGKELKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFAQDSVY-------LDALN 1303
Cdd:cd18795     51 SSRKECEKTAKDLAGIAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLPARTVIIKGTQRYdgkgyreLSPLE 130

                           90       100
                   ....*....|....*....|..
gi 2462599686 1304 YRQMSGRAGRRGQDLLGNVYFF 1325
Cdd:cd18795    131 YLQMIGRAGRPGFDTRGEAIIM 152
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
748-1390 1.34e-30

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


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 130.83  E-value: 1.34e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  748 QQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVLRESdvGVVVYVAPAKSLVGQVAATVENRFtktlpaGRTLCGAFT 827
Cdd:COG4581     30 QEEAILALEAGRSVLVAAPTGSGKTLVAEFAIFLALARG--RRSFYTAPIKALSNQKFFDLVERF------GAENVGLLT 101

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  828 RDYRHNVlNCQVLI-TVpecfEIL---LLAPHRQkwVERIRYVIFDEVHYLG-REVGAkFWELllVIIRCP----FLVLS 898
Cdd:COG4581    102 GDASVNP-DAPIVVmTT----EILrnmLYREGAD--LEDVGVVVMDEFHYLAdPDRGW-VWEE--PIIHLParvqLVLLS 171

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  899 ATINNPNLLTKWLQSVKQywkqadkimeekcisekqadkclnflqdhsyknqsyEVRLVLCGERYNDLEKHICsvkhddv 978
Cdd:COG4581    172 ATVGNAEEFAEWLTRVRG------------------------------------ETAVVVSEERPVPLEFHYL------- 208

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  979 yfdhfhpcaaLTTDIIEKYGFPPDLTLTPQesiqlydtmaqVWETwpraqelcpeefilfknkivikkldarkyeenlka 1058
Cdd:COG4581    209 ----------VTPRLFPLFRVNPELLRPPS-----------RHEV----------------------------------- 232

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1059 eltnwikngqvkkvkrvlknlspdslssskdmvkmfpllVEKLRQMDKLPAIFFLFKnddvgkRAGsvctflektetksh 1138
Cdd:COG4581    233 ---------------------------------------IEELDRGGLLPAIVFIFS------RRG-------------- 253

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1139 phteCHSYVFAIdevlekvrkTQKRISTKKnpkkaeklERKKVYRAeyinflenlkILEISEDCTyadvkalhteitrnk 1218
Cdd:COG4581    254 ----CDEAAQQL---------LSARLTTKE--------ERAEIREA----------IDEFAEDFS--------------- 287

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1219 dstldrvlprvrfTRHGKELKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFAQDS-- 1296
Cdd:COG4581    288 -------------VLFGKTLSRLLRRGIAVHHAGMLPKYRRLVEELFQAGLLKVVFATDTLAVGINMPARTVVFTKLSkf 354

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1297 -----VYLDALNYRQMSGRAGRRGQDLLGNVY-----FFDiplPKIKRLLASSVPE-LRGQFPLSITLVLRlmLLASKGd 1365
Cdd:COG4581    355 dgerhRPLTAREFHQIAGRAGRRGIDTEGHVVvlapeHDD---PKKFARLASARPEpLRSSFRPSYNMVLN--LLARPG- 428

                          650       660
                   ....*....|....*....|....*
gi 2462599686 1366 dPEDAKAkvlsVLKHSLLSFKRRRA 1390
Cdd:COG4581    429 -LERARE----LLEDSFAQFQADRS 448
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 748-902 4.08e-17

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: 80.36  E-value: 4.08e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  748 QQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDVGV-VVYVAPAKSLVGQVAATVENRFTKTLPAGRTLCGAF 826
Cdd:pfam00270    4 QAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALEALDKLDNGPqALVLAPTRELAEQIYEELKKLGKGLGLKVASLLGGD 83

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462599686  827 TRDYRHNVL-NCQVLITVPECFEILLlapHRQKWVERIRYVIFDEVHYLGREVGAKFWELLLVIIR--CPFLVLSATIN 902
Cdd:pfam00270   84 SRKEQLEKLkGPDILVGTPGRLLDLL---QERKLLKNLKLLVLDEAHRLLDMGFGPDLEEILRRLPkkRQILLLSATLP 159
DEXDc smart00487
DEAD-like helicases superfamily;
742-911 1.03e-16

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 80.61  E-value: 1.03e-16
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686   742 FIPNAWQQELLD-VVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDVGVVVYVAPAKSLVGQVAATVENRFTKTLPAGR 820
Cdd:smart00487    7 EPLRPYQKEAIEaLLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKVV 86

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686   821 TLCGAFTRDYRHNVL---NCQVLITVPECFEILLLapHRQKWVERIRYVIFDEVHYLGrevGAKFWELLLVIIR-----C 892
Cdd:smart00487   87 GLYGGDSKREQLRKLesgKTDILVTTPGRLLDLLE--NDKLSLSNVDLVILDEAHRLL---DGGFGDQLEKLLKllpknV 161

                           170
                    ....*....|....*....
gi 2462599686   893 PFLVLSATINNPNLLTKWL 911
Cdd:smart00487  162 QLLLLSATPPEEIENLLEL 180
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
725-900 4.02e-15

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 80.45  E-value: 4.02e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  725 HYLIRDERKDRDPRVQ-DFIPNAWQQELLD-----VVDKNESAVIVAPTSSGKTYASYYCMEKVLResdVGVVVYVAPAK 798
Cdd:COG1061     61 ELAEAEALEAGDEASGtSFELRPYQQEALEallaaLERGGGRGLVVAPTGTGKTVLALALAAELLR---GKRVLVLVPRR 137

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  799 SLVGQVAATVENRFTKTLPAGrtlcGAFTRDYRHNVLNCQVLITvpecfeilllAPHRQKWVERIRYVIFDEVHYLgrev 878
Cdd:COG1061    138 ELLEQWAEELRRFLGDPLAGG----GKKDSDAPITVATYQSLAR----------RAHLDELGDRFGLVIIDEAHHA---- 199

                          170       180
                   ....*....|....*....|...
gi 2462599686  879 GAKFWELLLVIIRCPFLV-LSAT 900
Cdd:COG1061    200 GAPSYRRILEAFPAAYRLgLTAT 222
HELICc smart00490
helicase superfamily c-terminal domain;
1239-1315 5.09e-11

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 60.30  E-value: 5.09e-11
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462599686  1239 KALAQRGIGY--HHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFaQDSVYLDALNYRQMSGRAGRRG 1315
Cdd:smart00490    5 ELLKELGIKVarLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI-IYDLPWSPASYIQRIGRAGRAG 82
PRK02362 PRK02362
ATP-dependent DNA helicase;
1208-1317 9.22e-11

ATP-dependent DNA helicase;


Pssm-ID: 235032 [Multi-domain]  Cd Length: 737  Bit Score: 66.90  E-value: 9.22e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1208 KALHTEITRNKDSTLDRVLPRVRFTRHGKELKALA---QRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIH 1284
Cdd:PRK02362   265 SALKKTLTAAERAELAELAEEIREVSDTETSKDLAdcvAKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLN 344

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2462599686 1285 MPCKSVV------FAQDS--VYLDALNYRQMSGRAGRRGQD 1317
Cdd:PRK02362   345 LPARRVIirdyrrYDGGAgmQPIPVLEYHQMAGRAGRPGLD 385
PRK00254 PRK00254
ski2-like helicase; Provisional
 757-919 2.14e-09

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 62.53  E-value: 2.14e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  757 KNESAVIVAPTSSGKTYASYYCM-EKVLRESdvGVVVYVAPAKSLvgqvAATVENRFTKTLPAGRTLCGAfTRDYRHN-- 833
Cdd:PRK00254    38 EGKNLVLAIPTASGKTLVAEIVMvNKLLREG--GKAVYLVPLKAL----AEEKYREFKDWEKLGLRVAMT-TGDYDSTde 110

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  834 -VLNCQVLITVPECFEILLlaPHRQKWVERIRYVIFDEVHYLG-REVGAKFwELLL--VIIRCPFLVLSATINNPNLLTK 909
Cdd:PRK00254   111 wLGKYDIIIATAEKFDSLL--RHGSSWIKDVKLVVADEIHLIGsYDRGATL-EMILthMLGRAQILGLSATVGNAEELAE 187

                          170
                   ....*....|..
gi 2462599686  910 WLQS--VKQYWK 919
Cdd:PRK00254   188 WLNAelVVSDWR 199
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 1236-1315 2.59e-06

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: 47.59  E-value: 2.59e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1236 KELKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFAQDSVYlDALNYRQMSGRAGRRG 1315
Cdd:pfam00271   31 ELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPW-NPASYIQRIGRAGRAG 109
COG1202 COG1202
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
1248-1323 1.92e-04

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


Pssm-ID: 440815 [Multi-domain]  Cd Length: 790  Bit Score: 46.42  E-value: 1.92e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1248 YHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFaqDSVYL--DALN---YRQMSGRAGRRGQDLLGNV 1322
Cdd:COG1202    453 PYHAGLDYGERKKVERRFADQELAAVVTTAALAAGVDFPASQVIF--DSLAMgiEWLSvqeFHQMLGRAGRPDYHDRGKV 530


                   .
gi 2462599686 1323 Y 1323
Cdd:COG1202    531 Y 531
 
Name Accession Description Interval E-value
DEXHc_DDX60 cd18025
DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an ...
 743-926 1.14e-102

DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an IFN-inducible cytoplasmic helicase that plays a role in RIG-I-mediated type I interferon (IFN) nuclease-mediated viral RNA degradation. DDX60 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: 350783 [Multi-domain]  Cd Length: 192  Bit Score: 326.63  E-value: 1.14e-102
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  743 IPNAWQQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDVGVVVYVAPAKSLVGQVAATVENRFTKTL-PAGRT 821
Cdd:cd18025      1 NPDAWQRELLDIVDRRESALIVAPTSSGKTFISYYCMEKVLRESDDGVVVYVAPTKALVNQVVAEVYARFSKKYpPSGKS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  822 LCGAFTRDYRHN-VLNCQVLITVPECFEILLLAPHRQKWVERIRYVIFDEVHYLGREVGAKFWELLLVIIRCPFLVLSAT 900
Cdd:cd18025     81 LWGVFTRDYRHNnPMNCQVLITVPECLEILLLSPHNASWVPRIKYVIFDEIHSIGQSEDGAVWEQLLLLIPCPFLALSAT 160

                          170       180
                   ....*....|....*....|....*.
gi 2462599686  901 INNPNLLTKWLQSVKQYWKQADKIME 926
Cdd:cd18025    161 IGNPQKFHEWLQSVQRARKAELKKIE 186
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 745-914 2.99e-41

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: 150.10  E-value: 2.99e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  745 NAWQQELLD-VVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDvGVVVYVAPAKSLVGQVAAtvenRFTKTLPAGRTLC 823
Cdd:cd17921      3 NPIQREALRaLYLSGDSVLVSAPTSSGKTLIAELAILRALATSG-GKAVYIAPTRALVNQKEA----DLRERFGPLGKNV 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  824 GAFTRDYRHN---VLNCQVLITVPECFEILLLAPHrQKWVERIRYVIFDEVHYLGREVGAKFWELLLVIIR-----CPFL 895
Cdd:cd17921     78 GLLTGDPSVNkllLAEADILVATPEKLDLLLRNGG-ERLIQDVRLVVVDEAHLIGDGERGVVLELLLSRLLrinknARFV 156

                          170
                   ....*....|....*....
gi 2462599686  896 VLSATINNPNLLTKWLQSV 914
Cdd:cd17921    157 GLSATLPNAEDLAEWLGVE 175
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 1231-1325 6.19e-34

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: 128.44  E-value: 6.19e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1231 FTRHGKELKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFAQDSVY-------LDALN 1303
Cdd:cd18795     51 SSRKECEKTAKDLAGIAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLPARTVIIKGTQRYdgkgyreLSPLE 130

                           90       100
                   ....*....|....*....|..
gi 2462599686 1304 YRQMSGRAGRRGQDLLGNVYFF 1325
Cdd:cd18795    131 YLQMIGRAGRPGFDTRGEAIIM 152
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
748-1390 1.34e-30

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


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 130.83  E-value: 1.34e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  748 QQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVLRESdvGVVVYVAPAKSLVGQVAATVENRFtktlpaGRTLCGAFT 827
Cdd:COG4581     30 QEEAILALEAGRSVLVAAPTGSGKTLVAEFAIFLALARG--RRSFYTAPIKALSNQKFFDLVERF------GAENVGLLT 101

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  828 RDYRHNVlNCQVLI-TVpecfEIL---LLAPHRQkwVERIRYVIFDEVHYLG-REVGAkFWELllVIIRCP----FLVLS 898
Cdd:COG4581    102 GDASVNP-DAPIVVmTT----EILrnmLYREGAD--LEDVGVVVMDEFHYLAdPDRGW-VWEE--PIIHLParvqLVLLS 171

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  899 ATINNPNLLTKWLQSVKQywkqadkimeekcisekqadkclnflqdhsyknqsyEVRLVLCGERYNDLEKHICsvkhddv 978
Cdd:COG4581    172 ATVGNAEEFAEWLTRVRG------------------------------------ETAVVVSEERPVPLEFHYL------- 208

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  979 yfdhfhpcaaLTTDIIEKYGFPPDLTLTPQesiqlydtmaqVWETwpraqelcpeefilfknkivikkldarkyeenlka 1058
Cdd:COG4581    209 ----------VTPRLFPLFRVNPELLRPPS-----------RHEV----------------------------------- 232

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1059 eltnwikngqvkkvkrvlknlspdslssskdmvkmfpllVEKLRQMDKLPAIFFLFKnddvgkRAGsvctflektetksh 1138
Cdd:COG4581    233 ---------------------------------------IEELDRGGLLPAIVFIFS------RRG-------------- 253

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1139 phteCHSYVFAIdevlekvrkTQKRISTKKnpkkaeklERKKVYRAeyinflenlkILEISEDCTyadvkalhteitrnk 1218
Cdd:COG4581    254 ----CDEAAQQL---------LSARLTTKE--------ERAEIREA----------IDEFAEDFS--------------- 287

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1219 dstldrvlprvrfTRHGKELKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFAQDS-- 1296
Cdd:COG4581    288 -------------VLFGKTLSRLLRRGIAVHHAGMLPKYRRLVEELFQAGLLKVVFATDTLAVGINMPARTVVFTKLSkf 354

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1297 -----VYLDALNYRQMSGRAGRRGQDLLGNVY-----FFDiplPKIKRLLASSVPE-LRGQFPLSITLVLRlmLLASKGd 1365
Cdd:COG4581    355 dgerhRPLTAREFHQIAGRAGRRGIDTEGHVVvlapeHDD---PKKFARLASARPEpLRSSFRPSYNMVLN--LLARPG- 428

                          650       660
                   ....*....|....*....|....*
gi 2462599686 1366 dPEDAKAkvlsVLKHSLLSFKRRRA 1390
Cdd:COG4581    429 -LERARE----LLEDSFAQFQADRS 448
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
748-1416 7.46e-26

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 114.22  E-value: 7.46e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  748 QQELLD-VVDKNESAVIVAPTSSGKTYASYYCMEKVLRESdvGVVVYVAPAKSLVGQVaatvENRFTKTLPAGRTLCGAF 826
Cdd:COG1204     27 QAEALEaGLLEGKNLVVSAPTASGKTLIAELAILKALLNG--GKALYIVPLRALASEK----YREFKRDFEELGIKVGVS 100

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  827 TRDYRHN---VLNCQVLITVPECFEILLLapHRQKWVERIRYVIFDEVHYLG-REVGAKFwELLLVIIR--CP---FLVL 897
Cdd:COG1204    101 TGDYDSDdewLGRYDILVATPEKLDSLLR--NGPSWLRDVDLVVVDEAHLIDdESRGPTL-EVLLARLRrlNPeaqIVAL 177

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  898 SATINNPNLLTKWLqsvkqywkqadkimeekcisekqadkclnflqdhsyknqsyEVRLVLCGERYNDLEKHIcsVKHDD 977
Cdd:COG1204    178 SATIGNAEEIAEWL-----------------------------------------DAELVKSDWRPVPLNEGV--LYDGV 214

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  978 VYFDhfhpcaalttdiiekygfppDLTLTPQESIQlydtmaqvwetwpraqelcpeefilfknKIVIKKLDarkyeenlk 1057
Cdd:COG1204    215 LRFD--------------------DGSRRSKDPTL----------------------------ALALDLLE--------- 237

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1058 aeltnwiKNGQVkkvkrvlknlspdslssskdmvkmfpllveklrqmdklpAIFflfknddvgkragsvctflektetks 1137
Cdd:COG1204    238 -------EGGQV---------------------------------------LVF-------------------------- 245

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1138 hphtechsyvfaidevlekvrktqkrISTKKNpkkAEKLerkkvyrAEYI-NFLENLKILEISEDctyadVKALHTEITR 1216
Cdd:COG1204    246 --------------------------VSSRRD---AESL-------AKKLaDELKRRLTPEEREE-----LEELAEELLE 284

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1217 NKDSTLDrvlprvrftrhGKELKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFA--- 1293
Cdd:COG1204    285 VSEETHT-----------NEKLADCLEKGVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRdtk 353

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1294 -QDSVYLDALNYRQMSGRAGRRGQDLLGNVYFFDIPLPK----IKRLLASSVPELRGQfpLSITLVLRLMLLASKGDDPE 1368
Cdd:COG1204    354 rGGMVPIPVLEFKQMAGRAGRPGYDPYGEAILVAKSSDEadelFERYILGEPEPIRSK--LANESALRTHLLALIASGFA 431

                          650       660       670       680
                   ....*....|....*....|....*....|....*....|....*...
gi 2462599686 1369 DAKAKVLSVLKHSLLSFkrRRAMETLKLYFLFSLQLLIKEDYLNKKGN 1416
Cdd:COG1204    432 NSREELLDFLENTFYAY--QYDKGDLEEVVDDALEFLLENGFIEEDGD 477
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 748-902 4.08e-17

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: 80.36  E-value: 4.08e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  748 QQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDVGV-VVYVAPAKSLVGQVAATVENRFTKTLPAGRTLCGAF 826
Cdd:pfam00270    4 QAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALEALDKLDNGPqALVLAPTRELAEQIYEELKKLGKGLGLKVASLLGGD 83

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462599686  827 TRDYRHNVL-NCQVLITVPECFEILLlapHRQKWVERIRYVIFDEVHYLGREVGAKFWELLLVIIR--CPFLVLSATIN 902
Cdd:pfam00270   84 SRKEQLEKLkGPDILVGTPGRLLDLL---QERKLLKNLKLLVLDEAHRLLDMGFGPDLEEILRRLPkkRQILLLSATLP 159
DEXDc smart00487
DEAD-like helicases superfamily;
742-911 1.03e-16

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 80.61  E-value: 1.03e-16
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686   742 FIPNAWQQELLD-VVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDVGVVVYVAPAKSLVGQVAATVENRFTKTLPAGR 820
Cdd:smart00487    7 EPLRPYQKEAIEaLLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKVV 86

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686   821 TLCGAFTRDYRHNVL---NCQVLITVPECFEILLLapHRQKWVERIRYVIFDEVHYLGrevGAKFWELLLVIIR-----C 892
Cdd:smart00487   87 GLYGGDSKREQLRKLesgKTDILVTTPGRLLDLLE--NDKLSLSNVDLVILDEAHRLL---DGGFGDQLEKLLKllpknV 161

                           170
                    ....*....|....*....
gi 2462599686   893 PFLVLSATINNPNLLTKWL 911
Cdd:smart00487  162 QLLLLSATPPEEIENLLEL 180
DEXHc_LHR-like cd17922
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ...
 758-911 3.88e-16

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: 77.62  E-value: 3.88e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  758 NESAVIVAPTSSGKTYASYYC-MEKVLRESDVGV-VVYVAPAKSLVGQVAA-------------TVENRFTKTLPAGRTl 822
Cdd:cd17922      1 GRNVLIAAPTGSGKTEAAFLPaLSSLADEPEKGVqVLYISPLKALINDQERrleepldeidleiPVAVRHGDTSQSEKA- 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  823 cgAFTRDYRHnvlncqVLITVPECFEILLLAPHRQKWVERIRYVIFDEVH-YLGREVGAKFwELLLV----IIRCPFLV- 896
Cdd:cd17922     80 --KQLKNPPG------ILITTPESLELLLVNKKLRELFAGLRYVVVDEIHaLLGSKRGVQL-ELLLErlrkLTGRPLRRi 150

                          170
                   ....*....|....*.
gi 2462599686  897 -LSATINNPNLLTKWL 911
Cdd:cd17922    151 gLSATLGNLEEAAAFL 166
DEXHc_ASCC3_2 cd18022
C-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ...
 758-911 3.49e-15

C-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; Activating signal cointegrator 1 complex subunit 3 (ASCC3) is a type II DEAD box helicase that plays a role in the repair of N-alkylated nucleotides. ASCC3 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: 350780 [Multi-domain]  Cd Length: 189  Bit Score: 75.49  E-value: 3.49e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  758 NESAVIVAPTSSGKTYASYYCMEKVLRESDVGVVVYVAPAKSLVGQVAATVENRFTKTLpaGRT---LCGAFTRDYRhNV 834
Cdd:cd18022     17 DNNVLLGAPTGSGKTIAAELAMFRAFNKYPGSKVVYIAPLKALVRERVDDWKKRFEEKL--GKKvveLTGDVTPDMK-AL 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  835 LNCQVLITVPECFEILLLAPHRQKWVERIRYVIFDEVHYLGREVGAkfweLLLVII-RCPFLV-----------LSATIN 902
Cdd:cd18022     94 ADADIIITTPEKWDGISRSWQTREYVQQVSLIIIDEIHLLGSDRGP----VLEVIVsRMNYISsqtekpvrlvgLSTALA 169


                   ....*....
gi 2462599686  903 NPNLLTKWL 911
Cdd:cd18022    170 NAGDLANWL 178
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
725-900 4.02e-15

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 80.45  E-value: 4.02e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  725 HYLIRDERKDRDPRVQ-DFIPNAWQQELLD-----VVDKNESAVIVAPTSSGKTYASYYCMEKVLResdVGVVVYVAPAK 798
Cdd:COG1061     61 ELAEAEALEAGDEASGtSFELRPYQQEALEallaaLERGGGRGLVVAPTGTGKTVLALALAAELLR---GKRVLVLVPRR 137

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  799 SLVGQVAATVENRFTKTLPAGrtlcGAFTRDYRHNVLNCQVLITvpecfeilllAPHRQKWVERIRYVIFDEVHYLgrev 878
Cdd:COG1061    138 ELLEQWAEELRRFLGDPLAGG----GKKDSDAPITVATYQSLAR----------RAHLDELGDRFGLVIIDEAHHA---- 199

                          170       180
                   ....*....|....*....|...
gi 2462599686  879 GAKFWELLLVIIRCPFLV-LSAT 900
Cdd:COG1061    200 GAPSYRRILEAFPAAYRLgLTAT 222
DEXHc_HFM1 cd18023
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ...
 745-912 5.87e-15

DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box helicase, required for crossover formation and complete synapsis of homologous chromosomes during meiosis. HFM1 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: 350781 [Multi-domain]  Cd Length: 206  Bit Score: 75.47  E-value: 5.87e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  745 NAWQQELL-DVVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDVG-----VVVYVAPAKSLVGQVAATVENRFTktlPA 818
Cdd:cd18023      3 NRIQSEVFpDLLYSDKNFVVSAPTGSGKTVLFELAILRLLKERNPLpwgnrKVVYIAPIKALCSEKYDDWKEKFG---PL 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  819 GRTlCGAFTRDYR----HNVLNCQVLITVPECFE-ILLLAPHRQKWVERIRYVIFDEVHYLGREVGA------------- 880
Cdd:cd18023     80 GLS-CAELTGDTEmddtFEIQDADIILTTPEKWDsMTRRWRDNGNLVQLVALVLIDEVHIIKENRGAtlevvvsrmktls 158

                          170       180       190
                   ....*....|....*....|....*....|...
gi 2462599686  881 KFWELL-LVIIRCPFLVLSATINNPNLLTKWLQ 912
Cdd:cd18023    159 SSSELRgSTVRPMRFVAVSATIPNIEDLAEWLG 191
DEXHc_Mtr4-like cd18024
DEXH-box helicase domain of ATP-dependent RNA helicase Mtr4; Mtr4 (also known as DOB1 or ...
 742-916 7.55e-13

DEXH-box helicase domain of ATP-dependent RNA helicase Mtr4; Mtr4 (also known as DOB1 or SKIV2L2) is a type II DEAD box helicase that plays a role in the processing of structured RNAs, including the maturation of 5.8S ribosomal RNA (rRNA)and is part of the TRAMP complex that is involved in exosome-mediated degradation of aberrant RNAs. Mtr4 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: 350782 [Multi-domain]  Cd Length: 205  Bit Score: 69.39  E-value: 7.55e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  742 FIPNAWQQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDvgVVVYVAPAKSLVGQVAATVENRFTKTlpagrt 821
Cdd:cd18024     31 FTLDPFQKTAIACIERNESVLVSAHTSAGKTVVAEYAIAQSLRDKQ--RVIYTSPIKALSNQKYRELQEEFGDV------ 102

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  822 lcGAFTRDYRHN-VLNCQVLITvpecfEILLLAPHRQKWVER-IRYVIFDEVHYL-GREVGAkFWE--LLLVIIRCPFLV 896
Cdd:cd18024    103 --GLMTGDVTINpNASCLVMTT-----EILRSMLYRGSEIMReVAWVIFDEIHYMrDKERGV-VWEetIILLPDKVRYVF 174

                          170       180
                   ....*....|....*....|
gi 2462599686  897 LSATINNPNLLTKWLQSVKQ 916
Cdd:cd18024    175 LSATIPNARQFAEWICKIHK 194
ResIII pfam04851
Type III restriction enzyme, res subunit;
741-902 1.07e-12

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 67.70  E-value: 1.07e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  741 DFIPNAWQQELLD-----VVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDVGVVVYVAPAKSLVGQvaatVENRFTKT 815
Cdd:pfam04851    1 KLELRPYQIEAIEnllesIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPRKDLLEQ----ALEEFKKF 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  816 LPAGRTLCGAFT-RDYRHNVLNCQVLITVPECFEILLLAPHRQKWVERIRYVIFDEVHYLgrevGAKFWELLLVIIRCPF 894
Cdd:pfam04851   77 LPNYVEIGEIISgDKKDESVDDNKIVVTTIQSLYKALELASLELLPDFFDVIIIDEAHRS----GASSYRNILEYFKPAF 152


                   ....*....
gi 2462599686  895 LV-LSATIN 902
Cdd:pfam04851  153 LLgLTATPE 161
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
 748-911 1.55e-12

DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type 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: 350786 [Multi-domain]  Cd Length: 177  Bit Score: 67.74  E-value: 1.55e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  748 QQELLD-VVDKNESAVIVAPTSSGKTYASYYCMEKVLRESdvGVVVYVAPAKSLVGQVAatveNRFTKTLPAGRTlCGAF 826
Cdd:cd18028      6 QAEAVRaGLLKGENLLISIPTASGKTLIAEMAMVNTLLEG--GKALYLVPLRALASEKY----EEFKKLEEIGLK-VGIS 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  827 TRDYR---HNVLNCQVLITVPECFEILLlaPHRQKWVERIRYVIFDEVHYLGREVGAKFWELLLVIIR-----CPFLVLS 898
Cdd:cd18028     79 TGDYDeddEWLGDYDIIVATYEKFDSLL--RHSPSWLRDVGVVVVDEIHLISDEERGPTLESIVARLRrlnpnTQIIGLS 156

                          170
                   ....*....|...
gi 2462599686  899 ATINNPNLLTKWL 911
Cdd:cd18028    157 ATIGNPDELAEWL 169
HELICc smart00490
helicase superfamily c-terminal domain;
1239-1315 5.09e-11

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 60.30  E-value: 5.09e-11
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462599686  1239 KALAQRGIGY--HHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFaQDSVYLDALNYRQMSGRAGRRG 1315
Cdd:smart00490    5 ELLKELGIKVarLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI-IYDLPWSPASYIQRIGRAGRAG 82
DEXHc_SKIV2L cd18027
DEXH-box helicase domain of SKIV2L; Superkiller viralicidic activity 2-like (SKIV2L, also ...
 742-916 8.15e-11

DEXH-box helicase domain of SKIV2L; Superkiller viralicidic activity 2-like (SKIV2L, also called SKI2 or DHX13) plays a role in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. SKIV2L 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: 350785 [Multi-domain]  Cd Length: 179  Bit Score: 62.67  E-value: 8.15e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  742 FIPNAWQQELLDVVDKNESAVIVAPTSSGKTYASYYCMekVLRESDVGVVVYVAPAKSLVGQVAATVENRFTKTlpagrt 821
Cdd:cd18027      7 FELDVFQKQAILHLEAGDSVFVAAHTSAGKTVVAEYAI--ALAQKHMTRTIYTSPIKALSNQKFRDFKNTFGDV------ 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  822 lcGAFTRDYR-HNVLNCQVLITvpecfEILLLAPHRQKWVER-IRYVIFDEVHYLGREVGAKFWELLLVII--RCPFLVL 897
Cdd:cd18027     79 --GLITGDVQlNPEASCLIMTT-----EILRSMLYNGSDVIRdLEWVIFDEVHYINDAERGVVWEEVLIMLpdHVSIILL 151

                          170
                   ....*....|....*....
gi 2462599686  898 SATINNPNLLTKWLQSVKQ 916
Cdd:cd18027    152 SATVPNTVEFADWIGRIKK 170
PRK02362 PRK02362
ATP-dependent DNA helicase;
1208-1317 9.22e-11

ATP-dependent DNA helicase;


Pssm-ID: 235032 [Multi-domain]  Cd Length: 737  Bit Score: 66.90  E-value: 9.22e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1208 KALHTEITRNKDSTLDRVLPRVRFTRHGKELKALA---QRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIH 1284
Cdd:PRK02362   265 SALKKTLTAAERAELAELAEEIREVSDTETSKDLAdcvAKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLN 344

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2462599686 1285 MPCKSVV------FAQDS--VYLDALNYRQMSGRAGRRGQD 1317
Cdd:PRK02362   345 LPARRVIirdyrrYDGGAgmQPIPVLEYHQMAGRAGRPGLD 385
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 758-900 2.28e-10

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: 60.49  E-value: 2.28e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  758 NESAVIVAPTSSGKTYASYYCMEKVLRESDVGVVvYVAPAKSLVGQVAATVENRFTKTLPagrtlCGAFTRDY----RHN 833
Cdd:cd00046      1 GENVLITAPTGSGKTLAALLAALLLLLKKGKKVL-VLVPTKALALQTAERLRELFGPGIR-----VAVLVGGSsaeeREK 74

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462599686  834 V--LNCQVLITVPECFEILLLaPHRQKWVERIRYVIFDEVH-YLGREVGAkfWELLLVIIR-----CPFLVLSAT 900
Cdd:cd00046     75 NklGDADIIIATPDMLLNLLL-REDRLFLKDLKLIIVDEAHaLLIDSRGA--LILDLAVRKaglknAQVILLSAT 146
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 747-900 1.12e-09

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: 58.47  E-value: 1.12e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  747 WQQELLDVVDKNES---AVIVAPTSSGKTYASYYCMEKVLRESdvgvVVYVAPAKSLVGQVAAtvenRFTKTLPaGRTLc 823
Cdd:cd17926      4 YQEEALEAWLAHKNnrrGILVLPTGSGKTLTALALIAYLKELR----TLIVVPTDALLDQWKE----RFEDFLG-DSSI- 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  824 GAFTRDYRHNVLNCQVLITVPECFEILL---LAPHRQKWverirYVIFDEVHYLgrevGAKFWELLLVIIRCPFLV-LSA 899
Cdd:cd17926     74 GLIGGGKKKDFDDANVVVATYQSLSNLAeeeKDLFDQFG-----LLIVDEAHHL----PAKTFSEILKELNAKYRLgLTA 144


                   .
gi 2462599686  900 T 900
Cdd:cd17926    145 T 145
PRK01172 PRK01172
ATP-dependent DNA helicase;
1238-1320 1.59e-09

ATP-dependent DNA helicase;


Pssm-ID: 100801 [Multi-domain]  Cd Length: 674  Bit Score: 62.59  E-value: 1.59e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1238 LKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVV------FAQD-SVYLDALNYRQMSGR 1310
Cdd:PRK01172   280 LNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIvrditrYGNGgIRYLSNMEIKQMIGR 359

                           90
                   ....*....|
gi 2462599686 1311 AGRRGQDLLG 1320
Cdd:PRK01172   360 AGRPGYDQYG 369
PRK00254 PRK00254
ski2-like helicase; Provisional
 757-919 2.14e-09

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 62.53  E-value: 2.14e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  757 KNESAVIVAPTSSGKTYASYYCM-EKVLRESdvGVVVYVAPAKSLvgqvAATVENRFTKTLPAGRTLCGAfTRDYRHN-- 833
Cdd:PRK00254    38 EGKNLVLAIPTASGKTLVAEIVMvNKLLREG--GKAVYLVPLKAL----AEEKYREFKDWEKLGLRVAMT-TGDYDSTde 110

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  834 -VLNCQVLITVPECFEILLlaPHRQKWVERIRYVIFDEVHYLG-REVGAKFwELLL--VIIRCPFLVLSATINNPNLLTK 909
Cdd:PRK00254   111 wLGKYDIIIATAEKFDSLL--RHGSSWIKDVKLVVADEIHLIGsYDRGATL-EMILthMLGRAQILGLSATVGNAEELAE 187

                          170
                   ....*....|..
gi 2462599686  910 WLQS--VKQYWK 919
Cdd:PRK00254   188 WLNAelVVSDWR 199
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 748-904 2.81e-09

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: 62.16  E-value: 2.81e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  748 QQELLDVVDKNESAVIVAPTSSGKTYAsyYC---MEKVLRESDvGVVVYVAPAKSLV-GQVAATveNRFTKTLPAG---R 820
Cdd:COG1205     61 QAEAIEAARAGKNVVIATPTASGKSLA--YLlpvLEALLEDPG-ATALYLYPTKALArDQLRRL--RELAEALGLGvrvA 135

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  821 TLCGAFTRDYRHNVL-NCQVLITVPEcfeiLL---LAPHRQKWV---ERIRYVIFDEVHY----LGREVGAkfwelllvI 889
Cdd:COG1205    136 TYDGDTPPEERRWIReHPDIVLTNPD----MLhygLLPHHTRWArffRNLRYVVIDEAHTyrgvFGSHVAN--------V 203

                          170       180
                   ....*....|....*....|....*..
gi 2462599686  890 IR-----CP-------FLVLSATINNP 904
Cdd:COG1205    204 LRrlrriCRhygsdpqFILASATIGNP 230
PRK00254 PRK00254
ski2-like helicase; Provisional
 1236-1320 5.70e-09

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 60.99  E-value: 5.70e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1236 KELKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFAQDSVYLD-------ALNYRQMS 1308
Cdd:PRK00254   288 EKLKKALRGGVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNfgwedipVLEIQQMM 367

                           90
                   ....*....|..
gi 2462599686 1309 GRAGRRGQDLLG 1320
Cdd:PRK00254   368 GRAGRPKYDEVG 379
DEXHc_Brr2_2 cd18021
C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type ...
 745-880 1.22e-08

C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD box helicase that mediates spliceosome catalytic activation. It is a stable subunit of the spliceosome, required during splicing catalysis and spliceosome disassembly. Brr2 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: 350779 [Multi-domain]  Cd Length: 191  Bit Score: 56.50  E-value: 1.22e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  745 NAWQQELLDVV-DKNESAVIVAPTSSGKTYASYYCMEKVLRESDVGVVVYVAPAKSLVGQVAATVENRFTKTLpaGRT-- 821
Cdd:cd18021      5 NPIQTQVFNSLyNTDDNVFVGAPTGSGKTVCAELALLRHWRQNPKGRAVYIAPMQELVDARYKDWRAKFGPLL--GKKvv 82

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  822 -LCGAFTRDYRHnVLNCQVLITVPECFEILLLAPHRQKWVERIRYVIFDEVHYLGREVGA 880
Cdd:cd18021     83 kLTGETSTDLKL-LAKSDVILATPEQWDVLSRRWKQRKNVQSVELFIADELHLIGGENGP 141
DEXHc_Brr2_1 cd18019
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD ...
 756-903 2.90e-08

N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD box helicase that mediates spliceosome catalytic activation. It is a stable subunit of the spliceosome, required during splicing catalysis and spliceosome disassembly. Brr2 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: 350777 [Multi-domain]  Cd Length: 214  Bit Score: 55.84  E-value: 2.90e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  756 DKNESAVIVAPTSSGKTYASYYCMEKVL---RESDVGV------VVYVAPAKSLVGQVAATVENRFTktlPAGRTLcGAF 826
Cdd:cd18019     31 ETDENLLLCAPTGAGKTNVALLTILREIgkhRNPDGTInldafkIVYIAPMKALVQEMVGNFSKRLA---PYGITV-AEL 106

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  827 TRDY---RHNVLNCQVLITVPECFEILLLAPHRQKWVERIRYVIFDEVHYLGREVGAKFWELLLVIIR--------CPFL 895
Cdd:cd18019    107 TGDQqltKEQISETQIIVTTPEKWDIITRKSGDRTYTQLVRLIIIDEIHLLHDDRGPVLESIVARTIRqieqtqeyVRLV 186


                   ....*...
gi 2462599686  896 VLSATINN 903
Cdd:cd18019    187 GLSATLPN 194
DEXHc_Hrq1-like cd17923
DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a ...
 759-904 4.06e-08

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: 54.90  E-value: 4.06e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  759 ESAVIVAPTSSGKTYAsyY---CMEKVLRESDVgVVVYVAPAKSLvgqvAATVENRFTKTLPA--GRTLCGAFTRDYRHN 833
Cdd:cd17923     16 RSVVVTTGTASGKSLC--YqlpILEALLRDPGS-RALYLYPTKAL----AQDQLRSLRELLEQlgLGIRVATYDGDTPRE 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  834 V------LNCQVLITVPECFEILLLAPHRQ--KWVERIRYVIFDEVHY----LGREVGAKFWELL---------LVIIRC 892
Cdd:cd17923     89 ErraiirNPPRILLTNPDMLHYALLPHHDRwaRFLRNLRYVVLDEAHTyrgvFGSHVALLLRRLRrlcrrygadPQFILT 168

                          170
                   ....*....|..
gi 2462599686  893 pflvlSATINNP 904
Cdd:cd17923    169 -----SATIGNP 175
Lhr COG1201
Lhr-like helicase [Replication, recombination and repair];
744-911 3.17e-07

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


Pssm-ID: 440814 [Multi-domain]  Cd Length: 850  Bit Score: 55.49  E-value: 3.17e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  744 PNAWQQELLDVVDKNESAVIVAPTSSGKTYASYY-CMEKVLRESDVGV------VVYVAPAKSL--------------VG 802
Cdd:COG1201     25 PTPPQREAWPAIAAGESTLLIAPTGSGKTLAAFLpALDELARRPRPGElpdglrVLYISPLKALandiernlrapleeIG 104

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  803 QVAA------TVENRFTKTLPAGRTlcgAFTRDYRHnvlncqVLITVPECFEILLLAPHRQKWVERIRYVIFDEVHYLgr 876
Cdd:COG1201    105 EAAGlplpeiRVGVRTGDTPASERQ---RQRRRPPH------ILITTPESLALLLTSPDARELLRGVRTVIVDEIHAL-- 173

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 2462599686  877 eVGAK---FWELLL----VIIRCPFLV--LSATINNPNLLTKWL 911
Cdd:COG1201    174 -AGSKrgvHLALSLerlrALAPRPLQRigLSATVGPLEEVARFL 216
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 742-877 2.13e-06

DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) are members 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: 350794 [Multi-domain]  Cd Length: 204  Bit Score: 50.17  E-value: 2.13e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  742 FIPNAWQQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVLRE----SDVGVVVYVAPAKSLVGQvAATVENRFTKTLP 817
Cdd:cd18036      1 LELRNYQLELVLPALRGKNTIICAPTGSGKTRVAVYICRHHLEKrrsaGEKGRVVVLVNKVPLVEQ-QLEKFFKYFRKGY 79

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462599686  818 AGRTLCGAFTRD--YRHNVLNCQVLITVPECFEILLLAPHRQKWVERIRY--VIFDEVHYLGRE 877
Cdd:cd18036     80 KVTGLSGDSSHKvsFGQIVKASDVIICTPQILINNLLSGREEERVYLSDFslLIFDECHHTQKE 143
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 748-872 2.14e-06

DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef is a member 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: 350793 [Multi-domain]  Cd Length: 181  Bit Score: 49.82  E-value: 2.14e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  748 QQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDvGVVVYVAPAKSLVGQVAATVENRFTKTLPAGrTLCGAFT 827
Cdd:cd18035      6 YQVLIAAVALNGNTLIVLPTGLGKTIIAILVAADRLTKKG-GKVLILAPSRPLVEQHAENLKRVLNIPDKIT-SLTGEVK 83

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 2462599686  828 RDYRHNVLN-CQVLITVPECFEILLLAPHRQkwVERIRYVIFDEVH 872
Cdd:cd18035     84 PEERAERWDaSKIIVATPQVIENDLLAGRIT--LDDVSLLIFDEAH 127
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 1236-1315 2.59e-06

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: 47.59  E-value: 2.59e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1236 KELKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFAQDSVYlDALNYRQMSGRAGRRG 1315
Cdd:pfam00271   31 ELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPW-NPASYIQRIGRAGRAG 109
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 745-900 5.91e-06

CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 440816 [Multi-domain]  Cd Length: 535  Bit Score: 50.85  E-value: 5.91e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  745 NAWQQELLDVVDKNESA-----VIVAPTSSGKTYASYYCMEKVLRESDVGVVVYVAPAKSLVGQVAATVENRFT------ 813
Cdd:COG1203    129 NPLQNEALELALEAAEEepglfILTAPTGGGKTEAALLFALRLAAKHGGRRIIYALPFTSIINQTYDRLRDLFGedvllh 208

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  814 --KTLPAGRTLCGAFTRDYRHNVLNCQVL---ITVpeC-----FEILLLA-PHRQKWVERIRY--VIFDEVHYLgrevGA 880
Cdd:COG1203    209 hsLADLDLLEEEEEYESEARWLKLLKELWdapVVV--TtidqlFESLFSNrKGQERRLHNLANsvIILDEVQAY----PP 282

                          170       180
                   ....*....|....*....|....*.
gi 2462599686  881 KFWELLLVIIR------CPFLVLSAT 900
Cdd:COG1203    283 YMLALLLRLLEwlknlgGSVILMTAT 308
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 744-872 1.56e-05

DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is 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: 350685 [Multi-domain]  Cd Length: 201  Bit Score: 47.81  E-value: 1.56e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  744 PNAWQQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVL---RESDVGVVVYVAPAKSLVGQVAATVENRFTKtlPAGR 820
Cdd:cd17927      3 PRNYQLELAQPALKGKNTIICLPTGSGKTFVAVLICEHHLkkfPAGRKGKVVFLANKVPLVEQQKEVFRKHFER--PGYK 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462599686  821 TlcGAFTRDYRHNVLN------CQVLITVPECFEILLLApHRQKWVERIRYVIFDEVH 872
Cdd:cd17927     81 V--TGLSGDTSENVSVeqivesSDVIIVTPQILVNDLKS-GTIVSLSDFSLLVFDECH 135
DEXHc_ASCC3_1 cd18020
N-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ...
 745-880 2.85e-05

N-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; Activating signal cointegrator 1 complex subunit 3 (ASCC3) is a type II DEAD box helicase that plays a role in the repair of N-alkylated nucleotides. ASCC3 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: 350778 [Multi-domain]  Cd Length: 199  Bit Score: 47.04  E-value: 2.85e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  745 NAWQQELLDVVDK-NESAVIVAPTSSGKTYASYYCMEKVLRES---------DVGVVVYVAPAKSLvgqvAATVENRFTK 814
Cdd:cd18020      3 NRIQSLVFPVAYKtNENMLICAPTGAGKTNIAMLTILHEIRQHvnqggvikkDDFKIVYIAPMKAL----AAEMVEKFSK 78

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  815 TLPAGRTLCGAFTRDY---RHNVLNCQVLITVPECFEILLL-APHRQKWVERIRYVIFDEVHYLGREVGA 880
Cdd:cd18020     79 RLAPLGIKVKELTGDMqltKKEIAETQIIVTTPEKWDVVTRkSSGDVALSQLVRLLIIDEVHLLHDDRGP 148
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 1232-1316 2.93e-05

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: 45.72  E-value: 2.93e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1232 TRHGKE-----LKALA-QRG----IGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHM-PCKSVVfaQDSVYLD 1300
Cdd:cd18796     47 TRSQAErlaqrLRELCpDRVppdfIALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIgDVDLVI--QIGSPKS 124

                           90
                   ....*....|....*.
gi 2462599686 1301 ALNYRQMSGRAGRRGQ 1316
Cdd:cd18796    125 VARLLQRLGRSGHRPG 140
PRK13767 PRK13767
ATP-dependent helicase; Provisional
 755-874 7.90e-05

ATP-dependent helicase; Provisional


Pssm-ID: 237497 [Multi-domain]  Cd Length: 876  Bit Score: 47.57  E-value: 7.90e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  755 VDKNESAVIVAPTSSGKTYASY---------YCMEKVLRESdvgV-VVYVAPAKSL-----------VGQVAATVENRfT 813
Cdd:PRK13767    44 IHEGKNVLISSPTGSGKTLAAFlaiidelfrLGREGELEDK---VyCLYVSPLRALnndihrnleepLTEIREIAKER-G 119

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462599686  814 KTLP----AGRTlcGAFTRDYRHNVLN--CQVLITVPECFEILLLAPH-RQKwVERIRYVIFDEVHYL 874
Cdd:PRK13767   120 EELPeirvAIRT--GDTSSYEKQKMLKkpPHILITTPESLAILLNSPKfREK-LRTVKWVIVDEIHSL 184
COG1202 COG1202
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
1248-1323 1.92e-04

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


Pssm-ID: 440815 [Multi-domain]  Cd Length: 790  Bit Score: 46.42  E-value: 1.92e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1248 YHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFaqDSVYL--DALN---YRQMSGRAGRRGQDLLGNV 1322
Cdd:COG1202    453 PYHAGLDYGERKKVERRFADQELAAVVTTAALAAGVDFPASQVIF--DSLAMgiEWLSvqeFHQMLGRAGRPDYHDRGKV 530


                   .
gi 2462599686 1323 Y 1323
Cdd:COG1202    531 Y 531
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 1239-1316 8.03e-04

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: 41.43  E-value: 8.03e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686 1239 KALAQRGI--GYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMP-CKSVVFAqdSVYLDALNYRQMSGRAGRRG 1315
Cdd:cd18794     48 ARLQSKGIsaAAYHAGLEPSDRRDVQRKWLRDKIQVIVATVAFGMGIDKPdVRFVIHY--SLPKSMESYYQESGRAGRDG 125


                   .
gi 2462599686 1316 Q 1316
Cdd:cd18794    126 L 126
SF2_C_Hrq cd18797
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...
 1268-1319 3.48e-03

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: 39.55  E-value: 3.48e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462599686 1268 GLIRVVTATETLALGIhmpcksvvfaqDSVYLDAL----------NYRQMSGRAGRRGQDLL 1319
Cdd:cd18797     91 GELLGVVATNALELGI-----------DIGGLDAVvlagypgslaSLWQQAGRAGRRGKDSL 141
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
748-879 7.93e-03

ERCC4-related helicase [Replication, recombination and repair];


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 40.87  E-value: 7.93e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462599686  748 QQELLDVVdKNESAVIVAPTSSGKTYASYYCMEKVLRESDvGVVVYVAPAKSLVGQVAATvenrFTKTLPAGRTLCGAFT 827
Cdd:COG1111      8 QLNLAASA-LRKNTLVVLPTGLGKTAVALLVIAERLHKKG-GKVLFLAPTKPLVEQHAEF----FKEALNIPEDEIVVFT 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462599686  828 ----RDYRHNVLN-CQVLITVPECFEILLLAphrqkwvERIR-----YVIFDEVHylgREVG 879
Cdd:COG1111     82 gevsPEKRKELWEkARIIVATPQVIENDLIA-------GRIDlddvsLLIFDEAH---RAVG 133
 
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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