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Conserved domains on  [gi|1034641786|ref|XP_016864318|]
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probable ATP-dependent RNA helicase DDX60-like isoform X3 [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 ...
 743-894 8.54e-72

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: 238.42  E-value: 8.54e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786  743 IPNAWQQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDVGVVVYVAPAKSLVGQVAATVENRFTKTL-PAGRT 821
Cdd:cd18025      1 NPDAWQRELLDIVDRRESALIVAPTSSGKTFISYYCMEKVLRESDDGVVVYVAPTKALVNQVVAEVYARFSKKYpPSGKS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786  822 LCGAFTRDYCHN-VLNCQV--------------------------------HYLGREVGAKFWELLLVIIRCPFLVLSAT 868
Cdd:cd18025     81 LWGVFTRDYRHNnPMNCQVlitvpecleilllsphnaswvprikyvifdeiHSIGQSEDGAVWEQLLLLIPCPFLALSAT 160

                          170       180
                   ....*....|....*....|....*.
gi 1034641786  869 INNPNLLTKWLQSVKQYWKQADKIME 894
Cdd:cd18025    161 IGNPQKFHEWLQSVQRARKAELKKIE 186
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 1199-1293 6.06e-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: 6.06e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1199 FTRHGKELKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFAQDSVY-------LDALN 1271
Cdd:cd18795     51 SSRKECEKTAKDLAGIAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLPARTVIIKGTQRYdgkgyreLSPLE 130

                           90       100
                   ....*....|....*....|..
gi 1034641786 1272 YRQMSGRAGRRGQDLLGNVYFF 1293
Cdd:cd18795    131 YLQMIGRAGRPGFDTRGEAIIM 152
BRR2 super family cl34180
Replicative superfamily II helicase [Replication, recombination and repair];
1132-1384 6.52e-21

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


The actual alignment was detected with superfamily member COG1204:

Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 98.81  E-value: 6.52e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1132 ISTKKNpkkAEKLerkkvyrAEYI-NFLENLKILEISEDctyadVKALHTEITRNKDSTLErvlprvrftrhGKELKALA 1210
Cdd:COG1204    246 VSSRRD---AESL-------AKKLaDELKRRLTPEEREE-----LEELAEELLEVSEETHT-----------NEKLADCL 299

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1211 QRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFA----QDSVYLDALNYRQMSGRAGRRGQDL 1286
Cdd:COG1204    300 EKGVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRdtkrGGMVPIPVLEFKQMAGRAGRPGYDP 379

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1287 LGNVYFFDIPLPK----IKRLLASSVPELRGQfpLSITLVLRLMLLAS----KGDDPEDakakVLSVLKHSLLSFkrRRA 1358
Cdd:COG1204    380 YGEAILVAKSSDEadelFERYILGEPEPIRSK--LANESALRTHLLALiasgFANSREE----LLDFLENTFYAY--QYD 451

                          250       260
                   ....*....|....*....|....*.
gi 1034641786 1359 METLKLYFLFSLQLLIKEDYLNKKGN 1384
Cdd:COG1204    452 KGDLEEVVDDALEFLLENGFIEEDGD 477
 
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 ...
 743-894 8.54e-72

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: 238.42  E-value: 8.54e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786  743 IPNAWQQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDVGVVVYVAPAKSLVGQVAATVENRFTKTL-PAGRT 821
Cdd:cd18025      1 NPDAWQRELLDIVDRRESALIVAPTSSGKTFISYYCMEKVLRESDDGVVVYVAPTKALVNQVVAEVYARFSKKYpPSGKS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786  822 LCGAFTRDYCHN-VLNCQV--------------------------------HYLGREVGAKFWELLLVIIRCPFLVLSAT 868
Cdd:cd18025     81 LWGVFTRDYRHNnPMNCQVlitvpecleilllsphnaswvprikyvifdeiHSIGQSEDGAVWEQLLLLIPCPFLALSAT 160

                          170       180
                   ....*....|....*....|....*.
gi 1034641786  869 INNPNLLTKWLQSVKQYWKQADKIME 894
Cdd:cd18025    161 IGNPQKFHEWLQSVQRARKAELKKIE 186
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 1199-1293 6.06e-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: 6.06e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1199 FTRHGKELKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFAQDSVY-------LDALN 1271
Cdd:cd18795     51 SSRKECEKTAKDLAGIAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLPARTVIIKGTQRYdgkgyreLSPLE 130

                           90       100
                   ....*....|....*....|..
gi 1034641786 1272 YRQMSGRAGRRGQDLLGNVYFF 1293
Cdd:cd18795    131 YLQMIGRAGRPGFDTRGEAIIM 152
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
1200-1358 6.26e-28

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


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 122.36  E-value: 6.26e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1200 TRHGKELKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFAQDS-------VYLDALNY 1272
Cdd:COG4581    288 VLFGKTLSRLLRRGIAVHHAGMLPKYRRLVEELFQAGLLKVVFATDTLAVGINMPARTVVFTKLSkfdgerhRPLTAREF 367

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1273 RQMSGRAGRRGQDLLGNVY-----FFDiplPKIKRLLASSVPE-LRGQFPLSITLVLRlmLLASKGddPEDAKAkvlsVL 1346
Cdd:COG4581    368 HQIAGRAGRRGIDTEGHVVvlapeHDD---PKKFARLASARPEpLRSSFRPSYNMVLN--LLARPG--LERARE----LL 436

                          170
                   ....*....|..
gi 1034641786 1347 KHSLLSFKRRRA 1358
Cdd:COG4581    437 EDSFAQFQADRS 448
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
1132-1384 6.52e-21

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 98.81  E-value: 6.52e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1132 ISTKKNpkkAEKLerkkvyrAEYI-NFLENLKILEISEDctyadVKALHTEITRNKDSTLErvlprvrftrhGKELKALA 1210
Cdd:COG1204    246 VSSRRD---AESL-------AKKLaDELKRRLTPEEREE-----LEELAEELLEVSEETHT-----------NEKLADCL 299

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1211 QRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFA----QDSVYLDALNYRQMSGRAGRRGQDL 1286
Cdd:COG1204    300 EKGVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRdtkrGGMVPIPVLEFKQMAGRAGRPGYDP 379

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1287 LGNVYFFDIPLPK----IKRLLASSVPELRGQfpLSITLVLRLMLLAS----KGDDPEDakakVLSVLKHSLLSFkrRRA 1358
Cdd:COG1204    380 YGEAILVAKSSDEadelFERYILGEPEPIRSK--LANESALRTHLLALiasgFANSREE----LLDFLENTFYAY--QYD 451

                          250       260
                   ....*....|....*....|....*.
gi 1034641786 1359 METLKLYFLFSLQLLIKEDYLNKKGN 1384
Cdd:COG1204    452 KGDLEEVVDDALEFLLENGFIEEDGD 477
HELICc smart00490
helicase superfamily c-terminal domain;
1207-1283 4.23e-11

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 60.30  E-value: 4.23e-11
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1034641786  1207 KALAQRGIGY--HHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFaQDSVYLDALNYRQMSGRAGRRG 1283
Cdd:smart00490    5 ELLKELGIKVarLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI-IYDLPWSPASYIQRIGRAGRAG 82
PRK02362 PRK02362
ATP-dependent DNA helicase;
1176-1285 7.04e-11

ATP-dependent DNA helicase;


Pssm-ID: 235032 [Multi-domain]  Cd Length: 737  Bit Score: 67.29  E-value: 7.04e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1176 KALHTEITRNKDSTLERVLPRVRFTRHGKELKALA---QRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIH 1252
Cdd:PRK02362   265 SALKKTLTAAERAELAELAEEIREVSDTETSKDLAdcvAKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLN 344

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1034641786 1253 MPCKSVV------FAQDS--VYLDALNYRQMSGRAGRRGQD 1285
Cdd:PRK02362   345 LPARRVIirdyrrYDGGAgmQPIPVLEYHQMAGRAGRPGLD 385
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
725-868 1.38e-08

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 59.65  E-value: 1.38e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786  725 HYLIRDERKDRDPRVQ-DFIPNAWQQELLD-----VVDKNESAVIVAPTSSGKTYASYYCMEKVLResdVGVVVYVAPAK 798
Cdd:COG1061     61 ELAEAEALEAGDEASGtSFELRPYQQEALEallaaLERGGGRGLVVAPTGTGKTVLALALAAELLR---GKRVLVLVPRR 137

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786  799 SLVGQVAATVENRFTKTLPAGrtlcGAFTRDYCHNVL-------NCQVHYLGRE-----------VGAKFWELLLVIIRC 860
Cdd:COG1061    138 ELLEQWAEELRRFLGDPLAGG----GKKDSDAPITVAtyqslarRAHLDELGDRfglviideahhAGAPSYRRILEAFPA 213


                   ....*....
gi 1034641786  861 PFLV-LSAT 868
Cdd:COG1061    214 AYRLgLTAT 222
DEXDc smart00487
DEAD-like helicases superfamily;
742-815 2.17e-06

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 50.18  E-value: 2.17e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034641786   742 FIPNAWQQELLD-VVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDVGVVVYVAPAKSLVGQVAATVENRFTKT 815
Cdd:smart00487    7 EPLRPYQKEAIEaLLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSL 81
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 1204-1283 2.39e-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: 47.98  E-value: 2.39e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1204 KELKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFAQDSVYlDALNYRQMSGRAGRRG 1283
Cdd:pfam00271   31 ELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPW-NPASYIQRIGRAGRAG 109
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 748-812 4.49e-06

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: 48.39  E-value: 4.49e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034641786  748 QQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDVGV-VVYVAPAKSLVGQVAATVENRF 812
Cdd:pfam00270    4 QAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALEALDKLDNGPqALVLAPTRELAEQIYEELKKLG 69
 
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 ...
 743-894 8.54e-72

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: 238.42  E-value: 8.54e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786  743 IPNAWQQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDVGVVVYVAPAKSLVGQVAATVENRFTKTL-PAGRT 821
Cdd:cd18025      1 NPDAWQRELLDIVDRRESALIVAPTSSGKTFISYYCMEKVLRESDDGVVVYVAPTKALVNQVVAEVYARFSKKYpPSGKS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786  822 LCGAFTRDYCHN-VLNCQV--------------------------------HYLGREVGAKFWELLLVIIRCPFLVLSAT 868
Cdd:cd18025     81 LWGVFTRDYRHNnPMNCQVlitvpecleilllsphnaswvprikyvifdeiHSIGQSEDGAVWEQLLLLIPCPFLALSAT 160

                          170       180
                   ....*....|....*....|....*.
gi 1034641786  869 INNPNLLTKWLQSVKQYWKQADKIME 894
Cdd:cd18025    161 IGNPQKFHEWLQSVQRARKAELKKIE 186
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 1199-1293 6.06e-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: 6.06e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1199 FTRHGKELKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFAQDSVY-------LDALN 1271
Cdd:cd18795     51 SSRKECEKTAKDLAGIAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLPARTVIIKGTQRYdgkgyreLSPLE 130

                           90       100
                   ....*....|....*....|..
gi 1034641786 1272 YRQMSGRAGRRGQDLLGNVYFF 1293
Cdd:cd18795    131 YLQMIGRAGRPGFDTRGEAIIM 152
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
1200-1358 6.26e-28

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


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 122.36  E-value: 6.26e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1200 TRHGKELKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFAQDS-------VYLDALNY 1272
Cdd:COG4581    288 VLFGKTLSRLLRRGIAVHHAGMLPKYRRLVEELFQAGLLKVVFATDTLAVGINMPARTVVFTKLSkfdgerhRPLTAREF 367

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1273 RQMSGRAGRRGQDLLGNVY-----FFDiplPKIKRLLASSVPE-LRGQFPLSITLVLRlmLLASKGddPEDAKAkvlsVL 1346
Cdd:COG4581    368 HQIAGRAGRRGIDTEGHVVvlapeHDD---PKKFARLASARPEpLRSSFRPSYNMVLN--LLARPG--LERARE----LL 436

                          170
                   ....*....|..
gi 1034641786 1347 KHSLLSFKRRRA 1358
Cdd:COG4581    437 EDSFAQFQADRS 448
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 745-882 2.98e-22

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: 95.79  E-value: 2.98e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786  745 NAWQQELLD-VVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDvGVVVYVAPAKSLVGQVAAtvenRFTKTLPAGRTLC 823
Cdd:cd17921      3 NPIQREALRaLYLSGDSVLVSAPTSSGKTLIAELAILRALATSG-GKAVYIAPTRALVNQKEA----DLRERFGPLGKNV 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786  824 GAFTRDYCHN---VLNCQV-------------------------------HYLGREVGAKFWELLLVIIR-----CPFLV 864
Cdd:cd17921     78 GLLTGDPSVNkllLAEADIlvatpekldlllrnggerliqdvrlvvvdeaHLIGDGERGVVLELLLSRLLrinknARFVG 157

                          170
                   ....*....|....*...
gi 1034641786  865 LSATINNPNLLTKWLQSV 882
Cdd:cd17921    158 LSATLPNAEDLAEWLGVE 175
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
1132-1384 6.52e-21

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 98.81  E-value: 6.52e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1132 ISTKKNpkkAEKLerkkvyrAEYI-NFLENLKILEISEDctyadVKALHTEITRNKDSTLErvlprvrftrhGKELKALA 1210
Cdd:COG1204    246 VSSRRD---AESL-------AKKLaDELKRRLTPEEREE-----LEELAEELLEVSEETHT-----------NEKLADCL 299

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1211 QRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFA----QDSVYLDALNYRQMSGRAGRRGQDL 1286
Cdd:COG1204    300 EKGVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRdtkrGGMVPIPVLEFKQMAGRAGRPGYDP 379

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1287 LGNVYFFDIPLPK----IKRLLASSVPELRGQfpLSITLVLRLMLLAS----KGDDPEDakakVLSVLKHSLLSFkrRRA 1358
Cdd:COG1204    380 YGEAILVAKSSDEadelFERYILGEPEPIRSK--LANESALRTHLLALiasgFANSREE----LLDFLENTFYAY--QYD 451

                          250       260
                   ....*....|....*....|....*.
gi 1034641786 1359 METLKLYFLFSLQLLIKEDYLNKKGN 1384
Cdd:COG1204    452 KGDLEEVVDDALEFLLENGFIEEDGD 477
HELICc smart00490
helicase superfamily c-terminal domain;
1207-1283 4.23e-11

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 60.30  E-value: 4.23e-11
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1034641786  1207 KALAQRGIGY--HHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFaQDSVYLDALNYRQMSGRAGRRG 1283
Cdd:smart00490    5 ELLKELGIKVarLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI-IYDLPWSPASYIQRIGRAGRAG 82
PRK02362 PRK02362
ATP-dependent DNA helicase;
1176-1285 7.04e-11

ATP-dependent DNA helicase;


Pssm-ID: 235032 [Multi-domain]  Cd Length: 737  Bit Score: 67.29  E-value: 7.04e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1176 KALHTEITRNKDSTLERVLPRVRFTRHGKELKALA---QRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIH 1252
Cdd:PRK02362   265 SALKKTLTAAERAELAELAEEIREVSDTETSKDLAdcvAKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLN 344

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1034641786 1253 MPCKSVV------FAQDS--VYLDALNYRQMSGRAGRRGQD 1285
Cdd:PRK02362   345 LPARRVIirdyrrYDGGAgmQPIPVLEYHQMAGRAGRPGLD 385
PRK01172 PRK01172
ATP-dependent DNA helicase;
1206-1288 1.52e-09

ATP-dependent DNA helicase;


Pssm-ID: 100801 [Multi-domain]  Cd Length: 674  Bit Score: 62.98  E-value: 1.52e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1206 LKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVV------FAQD-SVYLDALNYRQMSGR 1278
Cdd:PRK01172   280 LNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIvrditrYGNGgIRYLSNMEIKQMIGR 359

                           90
                   ....*....|
gi 1034641786 1279 AGRRGQDLLG 1288
Cdd:PRK01172   360 AGRPGYDQYG 369
PRK00254 PRK00254
ski2-like helicase; Provisional
 1204-1288 4.74e-09

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 61.37  E-value: 4.74e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1204 KELKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFAQDSVYLD-------ALNYRQMS 1276
Cdd:PRK00254   288 EKLKKALRGGVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNfgwedipVLEIQQMM 367

                           90
                   ....*....|..
gi 1034641786 1277 GRAGRRGQDLLG 1288
Cdd:PRK00254   368 GRAGRPKYDEVG 379
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
725-868 1.38e-08

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 59.65  E-value: 1.38e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786  725 HYLIRDERKDRDPRVQ-DFIPNAWQQELLD-----VVDKNESAVIVAPTSSGKTYASYYCMEKVLResdVGVVVYVAPAK 798
Cdd:COG1061     61 ELAEAEALEAGDEASGtSFELRPYQQEALEallaaLERGGGRGLVVAPTGTGKTVLALALAAELLR---GKRVLVLVPRR 137

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786  799 SLVGQVAATVENRFTKTLPAGrtlcGAFTRDYCHNVL-------NCQVHYLGRE-----------VGAKFWELLLVIIRC 860
Cdd:COG1061    138 ELLEQWAEELRRFLGDPLAGG----GKKDSDAPITVAtyqslarRAHLDELGDRfglviideahhAGAPSYRRILEAFPA 213


                   ....*....
gi 1034641786  861 PFLV-LSAT 868
Cdd:COG1061    214 AYRLgLTAT 222
DEXDc smart00487
DEAD-like helicases superfamily;
742-815 2.17e-06

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 50.18  E-value: 2.17e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034641786   742 FIPNAWQQELLD-VVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDVGVVVYVAPAKSLVGQVAATVENRFTKT 815
Cdd:smart00487    7 EPLRPYQKEAIEaLLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSL 81
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 1204-1283 2.39e-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: 47.98  E-value: 2.39e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1204 KELKALAQRGIGYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFAQDSVYlDALNYRQMSGRAGRRG 1283
Cdd:pfam00271   31 ELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPW-NPASYIQRIGRAGRAG 109
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 748-812 4.49e-06

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: 48.39  E-value: 4.49e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034641786  748 QQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDVGV-VVYVAPAKSLVGQVAATVENRF 812
Cdd:pfam00270    4 QAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALEALDKLDNGPqALVLAPTRELAEQIYEELKKLG 69
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 1175-1284 1.78e-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: 46.49  E-value: 1.78e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1175 VKALHTEITRNKdSTL---------ERVLPRVRFtRHGKELKALAqrgIGYHHSSMYFKEKEFVEILFVKGLIRVVTATE 1245
Cdd:cd18796     28 YAEVIFLLERHK-STLvftntrsqaERLAQRLRE-LCPDRVPPDF---IALHHGSLSRELREEVEAALKRGDLKVVVATS 102

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1034641786 1246 TLALGIHM-PCKSVVfaQDSVYLDALNYRQMSGRAGRRGQ 1284
Cdd:cd18796    103 SLELGIDIgDVDLVI--QIGSPKSVARLLQRLGRSGHRPG 140
DEXHc_HFM1 cd18023
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ...
 745-880 3.79e-05

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: 46.58  E-value: 3.79e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786  745 NAWQQELL-DVVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDVG-----VVVYVAPAKSLVGQVAATVENRFTktlPA 818
Cdd:cd18023      3 NRIQSEVFpDLLYSDKNFVVSAPTGSGKTVLFELAILRLLKERNPLpwgnrKVVYIAPIKALCSEKYDDWKEKFG---PL 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786  819 GRTlCGAFTRDY----------CHNVLNC---------------------------QVHYLGREVGA------------- 848
Cdd:cd18023     80 GLS-CAELTGDTemddtfeiqdADIILTTpekwdsmtrrwrdngnlvqlvalvlidEVHIIKENRGAtlevvvsrmktls 158

                          170       180       190
                   ....*....|....*....|....*....|...
gi 1034641786  849 KFWELL-LVIIRCPFLVLSATINNPNLLTKWLQ 880
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 ...
 742-884 8.90e-05

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: 45.51  E-value: 8.90e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786  742 FIPNAWQQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDvgVVVYVAPAKSLVGQVAATVENRFTKTlpagrt 821
Cdd:cd18024     31 FTLDPFQKTAIACIERNESVLVSAHTSAGKTVVAEYAIAQSLRDKQ--RVIYTSPIKALSNQKYRELQEEFGDV------ 102

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786  822 lcGAFTRDYCHN-----------------------------VLNCQVHYL-GREVGAkFWE--LLLVIIRCPFLVLSATI 869
Cdd:cd18024    103 --GLMTGDVTINpnasclvmtteilrsmlyrgseimrevawVIFDEIHYMrDKERGV-VWEetIILLPDKVRYVFLSATI 179

                          170
                   ....*....|....*
gi 1034641786  870 NNPNLLTKWLQSVKQ 884
Cdd:cd18024    180 PNARQFAEWICKIHK 194
DEXHc_ASCC3_2 cd18022
C-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ...
 758-816 1.71e-04

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: 44.29  E-value: 1.71e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1034641786  758 NESAVIVAPTSSGKTYASYYCMEKVLRESDVGVVVYVAPAKSLVGQVAATVENRFTKTL 816
Cdd:cd18022     17 DNNVLLGAPTGSGKTIAAELAMFRAFNKYPGSKVVYIAPLKALVRERVDDWKKRFEEKL 75
COG1202 COG1202
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
1216-1291 1.82e-04

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


Pssm-ID: 440815 [Multi-domain]  Cd Length: 790  Bit Score: 46.42  E-value: 1.82e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1216 YHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMPCKSVVFaqDSVYL--DALN---YRQMSGRAGRRGQDLLGNV 1290
Cdd:COG1202    453 PYHAGLDYGERKKVERRFADQELAAVVTTAALAAGVDFPASQVIF--DSLAMgiEWLSvqeFHQMLGRAGRPDYHDRGKV 530


                   .
gi 1034641786 1291 Y 1291
Cdd:COG1202    531 Y 531
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 742-812 5.25e-04

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: 43.23  E-value: 5.25e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034641786  742 FIPNAWQQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVLRE----SDVGVVVYVAPAKSLVGQvAATVENRF 812
Cdd:cd18036      1 LELRNYQLELVLPALRGKNTIICAPTGSGKTRVAVYICRHHLEKrrsaGEKGRVVVLVNKVPLVEQ-QLEKFFKY 74
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 1207-1284 7.95e-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: 7.95e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786 1207 KALAQRGI--GYHHSSMYFKEKEFVEILFVKGLIRVVTATETLALGIHMP-CKSVVFAqdSVYLDALNYRQMSGRAGRRG 1283
Cdd:cd18794     48 ARLQSKGIsaAAYHAGLEPSDRRDVQRKWLRDKIQVIVATVAFGMGIDKPdVRFVIHY--SLPKSMESYYQESGRAGRDG 125


                   .
gi 1034641786 1284 Q 1284
Cdd:cd18794    126 L 126
ResIII pfam04851
Type III restriction enzyme, res subunit;
741-824 1.06e-03

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 41.50  E-value: 1.06e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786  741 DFIPNAWQQELLD-----VVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDVGVVVYVAPAKSLVGQvaatVENRFTKT 815
Cdd:pfam04851    1 KLELRPYQIEAIEnllesIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPRKDLLEQ----ALEEFKKF 76


                   ....*....
gi 1034641786  816 LPAGRTLCG 824
Cdd:pfam04851   77 LPNYVEIGE 85
DEXHc_LHR-like cd17922
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ...
 758-800 1.10e-03

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: 41.41  E-value: 1.10e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1034641786  758 NESAVIVAPTSSGKTYASYYC-MEKVLRESDVGV-VVYVAPAKSL 800
Cdd:cd17922      1 GRNVLIAAPTGSGKTEAAFLPaLSSLADEPEKGVqVLYISPLKAL 45
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 744-814 2.60e-03

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: 40.88  E-value: 2.60e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034641786  744 PNAWQQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVL---RESDVGVVVYVAPAKSLVGQVAATVENRFTK 814
Cdd:cd17927      3 PRNYQLELAQPALKGKNTIICLPTGSGKTFVAVLICEHHLkkfPAGRKGKVVFLANKVPLVEQQKEVFRKHFER 76
SF2_C_Hrq cd18797
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...
 1236-1287 3.41e-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: 3.41e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1034641786 1236 GLIRVVTATETLALGIhmpcksvvfaqDSVYLDAL----------NYRQMSGRAGRRGQDLL 1287
Cdd:cd18797     91 GELLGVVATNALELGI-----------DIGGLDAVvlagypgslaSLWQQAGRAGRRGKDSL 141
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 745-812 4.95e-03

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: 41.61  E-value: 4.95e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1034641786  745 NAWQQELLDVVDKNESA-----VIVAPTSSGKTYASYYCMEKVLRESDVGVVVYVAPAKSLVGQVAATVENRF 812
Cdd:COG1203    129 NPLQNEALELALEAAEEepglfILTAPTGGGKTEAALLFALRLAAKHGGRRIIYALPFTSIINQTYDRLRDLF 201
Lhr COG1201
Lhr-like helicase [Replication, recombination and repair];
744-800 5.15e-03

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


Pssm-ID: 440814 [Multi-domain]  Cd Length: 850  Bit Score: 41.63  E-value: 5.15e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034641786  744 PNAWQQELLDVVDKNESAVIVAPTSSGKTYASYY-CMEKVLRESDVGV------VVYVAPAKSL 800
Cdd:COG1201     25 PTPPQREAWPAIAAGESTLLIAPTGSGKTLAAFLpALDELARRPRPGElpdglrVLYISPLKAL 88
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 748-817 5.59e-03

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: 39.81  E-value: 5.59e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034641786  748 QQELLDVVDKNESAVIVAPTSSGKTYASYYCMEKVLRESDvGVVVYVAPAKSLVGQVAATVENRFTKTLP 817
Cdd:cd18035      6 YQVLIAAVALNGNTLIVLPTGLGKTIIAILVAADRLTKKG-GKVLILAPSRPLVEQHAENLKRVLNIPDK 74
 
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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