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Conserved domains on  [gi|1907078725|ref|XP_036012018|]
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ATP-dependent RNA helicase DDX50 isoform X4 [Mus musculus]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 11423699)

DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SrmB super family cl33924
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
1-232 1.68e-70

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


The actual alignment was detected with superfamily member COG0513:

Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 228.88  E-value: 1.68e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725   1 MLDLGFAEQVEDIIHesyKTDSEDnpQTLLFSATCPQWVYKVAKKYMKSrYEQVDLVGKmtQKAATTVEHLAIQCHWSQR 80
Cdd:COG0513   157 MLDMGFIEDIERILK---LLPKER--QTLLFSATMPPEIRKLAKRYLKN-PVRIEVAPE--NATAETIEQRYYLVDKRDK 228

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  81 PAVIGDVLQVYSgsEGRAIIFCETKKNVTEMAmnphiKQ------NAQCLHGDIAQSQREITLKGFREGSFKVLVATNVA 154
Cdd:COG0513   229 LELLRRLLRDED--PERAIVFCNTKRGADRLA-----EKlqkrgiSAAALHGDLSQGQRERALDAFRNGKIRVLVATDVA 301

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907078725 155 ARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICVCFYQPRERGQLRYVEQKAGITFKRVGVPSTMDLVKSK 232
Cdd:COG0513   302 ARGIDIDDVSHVINYDLPEDPEDYVHRIGRTGRAGAEGTAISLVTPDERRLLRAIEKLIGQKIEEEELPGFEPVEEKR 379
GUCT_RHII_Gualpha_beta cd12936
RNA-binding GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA ...
 274-365 3.89e-50

RNA-binding GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA helicase II/Gubeta (RH-II/Gubeta) and similar proteins; This subfamily corresponds to the Gu C-terminal (GUCT) domain of RH-II/Gualpha and RH-II/Gubeta, two paralogues found in vertebrates. RH-II/Gualpha, also termed nucleolar RNA helicase 2, or DEAD box protein 21, or nucleolar RNA helicase Gu, is a bifunctional enzyme that displays independent RNA-unwinding and RNA-folding activities. It unwinds double-stranded RNA in the 5' to 3' direction in the presence of Mg2+ through the domains in its N-terminal region. In contrast, it folds single-stranded RNA in an ATP-dependent manner and its C-terminal region is responsible for the Mg2+ independent RNA-foldase activity. RH-II/Gualpha consists of a DEAD box helicase domain (DEAD), a helicase conserved C-terminal domain (helicase_C), and a GUCT followed by three FRGQR repeats and one PRGQR sequence. The DEAD and helicase_C domains may play critical roles in the RNA-helicase activity of RH-II/Gualpha. The function of GUCT domain remains unclear. The C-terminal region responsible for the RNA-foldase activity does not overlap with the GUCT domain. RH-II/Gubeta, also termed ATP-dependent RNA helicase DDX50, or DEAD box protein 50, or nucleolar protein Gu2, shows significant sequence homology with RH-II/Gualpha. It contains a DEAD domain, a helicase_C domain, and a GUCT domain followed by an arginine-serine-rich sequence but not (F/P)RGQR repeats in RH-II/Gualpha. Both RH-II/Gualpha and RH-II/Gubeta localize to nucleoli, suggesting roles in ribosomal RNA production, but RH-II/Gubeta also localizes to nuclear speckles containing the splicing factor SC35, suggesting its possible involvement in pre-mRNA splicing. In contrast to RH-II/Gualpha, RH-II/Gubeta has RNA-unwinding activity, but no RNA-folding activity.


:

Pssm-ID: 240593  Cd Length: 93  Bit Score: 164.93  E-value: 3.89e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725 274 HISGASSFEPRSLITSDKGFVTMTLESPEEIQDVSCAWKELNRKLSSNAVSHVTRMCLLKGNMGVCFDVPTSESERLQAE 353
Cdd:cd12936     1 HISGATSKEQRSLLNSDKGFVTMALRCSEEIPNRSYAWKELKEKLGVDADAHISRMCLLKGRMGVCFDVPTAEVESIQAE 80

                          90
                  ....*....|...
gi 1907078725 354 WHDS-DWILSVPA 365
Cdd:cd12936    81 WHDSrRWQLSVAT 93
 
Name Accession Description Interval E-value
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
1-232 1.68e-70

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 228.88  E-value: 1.68e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725   1 MLDLGFAEQVEDIIHesyKTDSEDnpQTLLFSATCPQWVYKVAKKYMKSrYEQVDLVGKmtQKAATTVEHLAIQCHWSQR 80
Cdd:COG0513   157 MLDMGFIEDIERILK---LLPKER--QTLLFSATMPPEIRKLAKRYLKN-PVRIEVAPE--NATAETIEQRYYLVDKRDK 228

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  81 PAVIGDVLQVYSgsEGRAIIFCETKKNVTEMAmnphiKQ------NAQCLHGDIAQSQREITLKGFREGSFKVLVATNVA 154
Cdd:COG0513   229 LELLRRLLRDED--PERAIVFCNTKRGADRLA-----EKlqkrgiSAAALHGDLSQGQRERALDAFRNGKIRVLVATDVA 301

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907078725 155 ARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICVCFYQPRERGQLRYVEQKAGITFKRVGVPSTMDLVKSK 232
Cdd:COG0513   302 ARGIDIDDVSHVINYDLPEDPEDYVHRIGRTGRAGAEGTAISLVTPDERRLLRAIEKLIGQKIEEEELPGFEPVEEKR 379
GUCT_RHII_Gualpha_beta cd12936
RNA-binding GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA ...
 274-365 3.89e-50

RNA-binding GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA helicase II/Gubeta (RH-II/Gubeta) and similar proteins; This subfamily corresponds to the Gu C-terminal (GUCT) domain of RH-II/Gualpha and RH-II/Gubeta, two paralogues found in vertebrates. RH-II/Gualpha, also termed nucleolar RNA helicase 2, or DEAD box protein 21, or nucleolar RNA helicase Gu, is a bifunctional enzyme that displays independent RNA-unwinding and RNA-folding activities. It unwinds double-stranded RNA in the 5' to 3' direction in the presence of Mg2+ through the domains in its N-terminal region. In contrast, it folds single-stranded RNA in an ATP-dependent manner and its C-terminal region is responsible for the Mg2+ independent RNA-foldase activity. RH-II/Gualpha consists of a DEAD box helicase domain (DEAD), a helicase conserved C-terminal domain (helicase_C), and a GUCT followed by three FRGQR repeats and one PRGQR sequence. The DEAD and helicase_C domains may play critical roles in the RNA-helicase activity of RH-II/Gualpha. The function of GUCT domain remains unclear. The C-terminal region responsible for the RNA-foldase activity does not overlap with the GUCT domain. RH-II/Gubeta, also termed ATP-dependent RNA helicase DDX50, or DEAD box protein 50, or nucleolar protein Gu2, shows significant sequence homology with RH-II/Gualpha. It contains a DEAD domain, a helicase_C domain, and a GUCT domain followed by an arginine-serine-rich sequence but not (F/P)RGQR repeats in RH-II/Gualpha. Both RH-II/Gualpha and RH-II/Gubeta localize to nucleoli, suggesting roles in ribosomal RNA production, but RH-II/Gubeta also localizes to nuclear speckles containing the splicing factor SC35, suggesting its possible involvement in pre-mRNA splicing. In contrast to RH-II/Gualpha, RH-II/Gubeta has RNA-unwinding activity, but no RNA-folding activity.


Pssm-ID: 240593  Cd Length: 93  Bit Score: 164.93  E-value: 3.89e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725 274 HISGASSFEPRSLITSDKGFVTMTLESPEEIQDVSCAWKELNRKLSSNAVSHVTRMCLLKGNMGVCFDVPTSESERLQAE 353
Cdd:cd12936     1 HISGATSKEQRSLLNSDKGFVTMALRCSEEIPNRSYAWKELKEKLGVDADAHISRMCLLKGRMGVCFDVPTAEVESIQAE 80

                          90
                  ....*....|...
gi 1907078725 354 WHDS-DWILSVPA 365
Cdd:cd12936    81 WHDSrRWQLSVAT 93
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 68-198 5.31e-49

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 163.45  E-value: 5.31e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  68 VEHLAIQCHWSQRPAVIGDVLqVYSGSEGRAIIFCETKKNVTEMAMN-PHIKQNAQCLHGDIAQSQREITLKGFREGSFK 146
Cdd:cd18787     1 IKQLYVVVEEEEKKLLLLLLL-LEKLKPGKAIIFVNTKKRVDRLAELlEELGIKVAALHGDLSQEERERALKKFRSGKVR 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1907078725 147 VLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICVCFY 198
Cdd:cd18787    80 VLVATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAGRKGTAITFV 131
PRK11776 PRK11776
ATP-dependent RNA helicase DbpA; Provisional
 1-224 6.96e-43

ATP-dependent RNA helicase DbpA; Provisional


Pssm-ID: 236977 [Multi-domain]  Cd Length: 460  Bit Score: 156.89  E-value: 6.96e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725   1 MLDLGFAEQVEDIIHESYKTDsednpQTLLFSATCPQWVYKVAKKYMKSRYE-QVDlvgkmTQKAATTVEHLAIQCHWSQ 79
Cdd:PRK11776  159 MLDMGFQDAIDAIIRQAPARR-----QTLLFSATYPEGIAAISQRFQRDPVEvKVE-----STHDLPAIEQRFYEVSPDE 228

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  80 RPAVIGDVLQVY---SgsegrAIIFCETKKNVTEMA--MNpHIKQNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVA 154
Cdd:PRK11776  229 RLPALQRLLLHHqpeS-----CVVFCNTKKECQEVAdaLN-AQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVA 302

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725 155 ARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICVCFYQPRERGQLRYVEQKAGITFKRVGVPS 224
Cdd:PRK11776  303 ARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAIEDYLGRKLNWEPLPS 372
GUCT pfam08152
GUCT (NUC152) domain; This is the C terminal domain found in the RNA helicase II / Gu protein ...
 277-371 1.15e-37

GUCT (NUC152) domain; This is the C terminal domain found in the RNA helicase II / Gu protein family.


Pssm-ID: 462378  Cd Length: 96  Bit Score: 132.28  E-value: 1.15e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725 277 GASSFEPRSLITSDKGFVTMTLESPEEIQDVSCAWKELNRKLSSNAVSHVTRMCLLKGNMGVCFDVPTSESERLQAEWHD 356
Cdd:pfam08152   1 GYTEIKQRSLLSSEEGFVTLLLTSSREIRTPGYAWSILRRNLSEEIADKVKGMRLTKDKMGAVFDVPSELVEEFLAGWED 80

                          90
                  ....*....|....*.
gi 1907078725 357 SD-WILSVPAKLPEIE 371
Cdd:pfam08152  81 SRgVTLEVATELPELQ 96
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 79-189 8.60e-34

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: 122.32  E-value: 8.60e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  79 QRPAVIGDVLQVYSGseGRAIIFCETKKNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGL 158
Cdd:pfam00271   1 EKLEALLELLKKERG--GKVLIFSQTKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGL 78

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1907078725 159 DIPEVDLVIQSSPPQDVESYIHRSGRTGRAG 189
Cdd:pfam00271  79 DLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
HELICc smart00490
helicase superfamily c-terminal domain;
120-189 3.60e-26

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 100.75  E-value: 3.60e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  120 NAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAG 189
Cdd:smart00490  13 KVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82
uvrb TIGR00631
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ...
 97-190 1.13e-05

excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273185 [Multi-domain]  Cd Length: 655  Bit Score: 47.68  E-value: 1.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  97 RAIIFCETKK---NVTEMAMNPHIKqnAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLV-IQSSpp 172
Cdd:TIGR00631 444 RVLVTTLTKKmaeDLTDYLKELGIK--VRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVaILDA-- 519

                          90       100
                  ....*....|....*....|...
gi 1907078725 173 qDVESYIhRSGRT-----GRAGR 190
Cdd:TIGR00631 520 -DKEGFL-RSERSliqtiGRAAR 540
 
Name Accession Description Interval E-value
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
1-232 1.68e-70

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 228.88  E-value: 1.68e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725   1 MLDLGFAEQVEDIIHesyKTDSEDnpQTLLFSATCPQWVYKVAKKYMKSrYEQVDLVGKmtQKAATTVEHLAIQCHWSQR 80
Cdd:COG0513   157 MLDMGFIEDIERILK---LLPKER--QTLLFSATMPPEIRKLAKRYLKN-PVRIEVAPE--NATAETIEQRYYLVDKRDK 228

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  81 PAVIGDVLQVYSgsEGRAIIFCETKKNVTEMAmnphiKQ------NAQCLHGDIAQSQREITLKGFREGSFKVLVATNVA 154
Cdd:COG0513   229 LELLRRLLRDED--PERAIVFCNTKRGADRLA-----EKlqkrgiSAAALHGDLSQGQRERALDAFRNGKIRVLVATDVA 301

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907078725 155 ARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICVCFYQPRERGQLRYVEQKAGITFKRVGVPSTMDLVKSK 232
Cdd:COG0513   302 ARGIDIDDVSHVINYDLPEDPEDYVHRIGRTGRAGAEGTAISLVTPDERRLLRAIEKLIGQKIEEEELPGFEPVEEKR 379
GUCT_RHII_Gualpha_beta cd12936
RNA-binding GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA ...
 274-365 3.89e-50

RNA-binding GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA helicase II/Gubeta (RH-II/Gubeta) and similar proteins; This subfamily corresponds to the Gu C-terminal (GUCT) domain of RH-II/Gualpha and RH-II/Gubeta, two paralogues found in vertebrates. RH-II/Gualpha, also termed nucleolar RNA helicase 2, or DEAD box protein 21, or nucleolar RNA helicase Gu, is a bifunctional enzyme that displays independent RNA-unwinding and RNA-folding activities. It unwinds double-stranded RNA in the 5' to 3' direction in the presence of Mg2+ through the domains in its N-terminal region. In contrast, it folds single-stranded RNA in an ATP-dependent manner and its C-terminal region is responsible for the Mg2+ independent RNA-foldase activity. RH-II/Gualpha consists of a DEAD box helicase domain (DEAD), a helicase conserved C-terminal domain (helicase_C), and a GUCT followed by three FRGQR repeats and one PRGQR sequence. The DEAD and helicase_C domains may play critical roles in the RNA-helicase activity of RH-II/Gualpha. The function of GUCT domain remains unclear. The C-terminal region responsible for the RNA-foldase activity does not overlap with the GUCT domain. RH-II/Gubeta, also termed ATP-dependent RNA helicase DDX50, or DEAD box protein 50, or nucleolar protein Gu2, shows significant sequence homology with RH-II/Gualpha. It contains a DEAD domain, a helicase_C domain, and a GUCT domain followed by an arginine-serine-rich sequence but not (F/P)RGQR repeats in RH-II/Gualpha. Both RH-II/Gualpha and RH-II/Gubeta localize to nucleoli, suggesting roles in ribosomal RNA production, but RH-II/Gubeta also localizes to nuclear speckles containing the splicing factor SC35, suggesting its possible involvement in pre-mRNA splicing. In contrast to RH-II/Gualpha, RH-II/Gubeta has RNA-unwinding activity, but no RNA-folding activity.


Pssm-ID: 240593  Cd Length: 93  Bit Score: 164.93  E-value: 3.89e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725 274 HISGASSFEPRSLITSDKGFVTMTLESPEEIQDVSCAWKELNRKLSSNAVSHVTRMCLLKGNMGVCFDVPTSESERLQAE 353
Cdd:cd12936     1 HISGATSKEQRSLLNSDKGFVTMALRCSEEIPNRSYAWKELKEKLGVDADAHISRMCLLKGRMGVCFDVPTAEVESIQAE 80

                          90
                  ....*....|...
gi 1907078725 354 WHDS-DWILSVPA 365
Cdd:cd12936    81 WHDSrRWQLSVAT 93
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 68-198 5.31e-49

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 163.45  E-value: 5.31e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  68 VEHLAIQCHWSQRPAVIGDVLqVYSGSEGRAIIFCETKKNVTEMAMN-PHIKQNAQCLHGDIAQSQREITLKGFREGSFK 146
Cdd:cd18787     1 IKQLYVVVEEEEKKLLLLLLL-LEKLKPGKAIIFVNTKKRVDRLAELlEELGIKVAALHGDLSQEERERALKKFRSGKVR 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1907078725 147 VLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICVCFY 198
Cdd:cd18787    80 VLVATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAGRKGTAITFV 131
PRK11776 PRK11776
ATP-dependent RNA helicase DbpA; Provisional
 1-224 6.96e-43

ATP-dependent RNA helicase DbpA; Provisional


Pssm-ID: 236977 [Multi-domain]  Cd Length: 460  Bit Score: 156.89  E-value: 6.96e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725   1 MLDLGFAEQVEDIIHESYKTDsednpQTLLFSATCPQWVYKVAKKYMKSRYE-QVDlvgkmTQKAATTVEHLAIQCHWSQ 79
Cdd:PRK11776  159 MLDMGFQDAIDAIIRQAPARR-----QTLLFSATYPEGIAAISQRFQRDPVEvKVE-----STHDLPAIEQRFYEVSPDE 228

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  80 RPAVIGDVLQVY---SgsegrAIIFCETKKNVTEMA--MNpHIKQNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVA 154
Cdd:PRK11776  229 RLPALQRLLLHHqpeS-----CVVFCNTKKECQEVAdaLN-AQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVA 302

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725 155 ARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICVCFYQPRERGQLRYVEQKAGITFKRVGVPS 224
Cdd:PRK11776  303 ARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAIEDYLGRKLNWEPLPS 372
GUCT pfam08152
GUCT (NUC152) domain; This is the C terminal domain found in the RNA helicase II / Gu protein ...
 277-371 1.15e-37

GUCT (NUC152) domain; This is the C terminal domain found in the RNA helicase II / Gu protein family.


Pssm-ID: 462378  Cd Length: 96  Bit Score: 132.28  E-value: 1.15e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725 277 GASSFEPRSLITSDKGFVTMTLESPEEIQDVSCAWKELNRKLSSNAVSHVTRMCLLKGNMGVCFDVPTSESERLQAEWHD 356
Cdd:pfam08152   1 GYTEIKQRSLLSSEEGFVTLLLTSSREIRTPGYAWSILRRNLSEEIADKVKGMRLTKDKMGAVFDVPSELVEEFLAGWED 80

                          90
                  ....*....|....*.
gi 1907078725 357 SD-WILSVPAKLPEIE 371
Cdd:pfam08152  81 SRgVTLEVATELPELQ 96
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 1-224 7.23e-36

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 139.98  E-value: 7.23e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725   1 MLDLGFAEQVEDIIHESyktdsEDNPQTLLFSATCPQWVYKVAKKYMKSRYEQvdlvgkMTQKAATTVEHLAiQCHWSQR 80
Cdd:PRK11634  161 MLRMGFIEDVETIMAQI-----PEGHQTALFSATMPEAIRRITRRFMKEPQEV------RIQSSVTTRPDIS-QSYWTVW 228

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  81 PAVIGDVLQVYSGSEG--RAIIFCETKKNVTEMAMNPHIK-QNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARG 157
Cdd:PRK11634  229 GMRKNEALVRFLEAEDfdAAIIFVRTKNATLEVAEALERNgYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARG 308

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907078725 158 LDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICVCFYQPRERGQLRYVEQKAGITFKRVGVPS 224
Cdd:PRK11634  309 LDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNIERTMKLTIPEVELPN 375
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 79-189 8.60e-34

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: 122.32  E-value: 8.60e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  79 QRPAVIGDVLQVYSGseGRAIIFCETKKNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGL 158
Cdd:pfam00271   1 EKLEALLELLKKERG--GKVLIFSQTKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGL 78

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1907078725 159 DIPEVDLVIQSSPPQDVESYIHRSGRTGRAG 189
Cdd:pfam00271  79 DLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
GUCT cd12929
RNA-binding GUCT domain found in the RNA helicase II/Gu protein family; This family includes ...
 292-364 5.92e-33

RNA-binding GUCT domain found in the RNA helicase II/Gu protein family; This family includes vertebrate RNA helicase II/Gualpha (RH-II/Gualpha) and RNA helicase II/Gubeta (RH-II/Gubeta), both of which consist of a DEAD box helicase domain (DEAD), a helicase conserved C-terminal domain, and a Gu C-terminal (GUCT) domain. They localize to nucleoli, suggesting roles in ribosomal RNA production, but RH-II/Gubeta also localizes to nuclear speckles containing the splicing factor SC35, suggesting its possible involvement in pre-mRNA splicing. In contrast to RH-II/Gualpha, RH-II/Gubeta has RNA-unwinding activity, but no RNA-folding activity. The family also contains plant DEAD-box ATP-dependent RNA helicase 7 (RH7 or PRH75), Thermus thermophilus heat resistant RNA-dependent ATPase (Hera) and similar proteins. RH7 is a new nucleus-localized member of the DEAD-box protein family from higher plants. It displays a weak ATPase activity which is barely stimulated by RNA ligands. RH7 contains an N-terminal KDES domain rich in lysine, glutamic acid, aspartic acid, and serine residues, seven highly conserved helicase motifs in the central region, a GUCT domain, and a C-terminal GYR domain harboring a large number of glycine residues interrupted by either arginines or tyrosines. Thermus thermophilus Hera is a DEAD box helicase that binds fragments of 23S rRNA and RNase P RNA via its C-terminal domain. It contains a helicase core that harbors two RecA-like domains termed RecA_N and RecA_C, a dimerization domain (DD), and a C-terminal RNA-binding domain (RBD) that reveals a compact, RRM-like fold and shows sequence similarity with the typical GUCT domain found in the RNA helicase II/Gu protein family.


Pssm-ID: 240592  Cd Length: 72  Bit Score: 118.97  E-value: 5.92e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907078725 292 GFVTMTLESPEEIQDVSCAWKELNRKLSSNaVSHVTRMCLLKGNMGVCFDVPTSESERLQAEWHDSDWILSVP 364
Cdd:cd12929     1 GWVTYKLEGPRLIQSLSRLVALLKRQLLSN-VSEVGKVAELEGNGGFYFDVRPEARERLQAEPEVAGLRLEVA 72
DEADc_DDX21_DDX50 cd17944
DEAD-box helicase domain of DEAD box proteins 21 and 50; DDX21 (also called Gu-Alpha and ...
 1-55 4.79e-32

DEAD-box helicase domain of DEAD box proteins 21 and 50; DDX21 (also called Gu-Alpha and nucleolar RNA helicase 2) is an RNA helicase that acts as a sensor of the transcriptional status of both RNA polymerase (Pol) I and II. It promotes ribosomal RNA (rRNA) processing and transcription from polymerase II (Pol II) and binds various RNAs, such as rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs. DDX50 (also called Gu-Beta, Nucleolar Protein Gu2, and malignant cell derived RNA helicase). DDX21 and DDX50 have similar genomic structures and are in tandem orientation on chromosome 10, suggesting that the two genes arose by gene duplication in evolution. Diseases associated with DDX21 include stomach disease and cerebral creatine deficiency syndrome 3. Diseases associated with DDX50 include rectal disease. Both are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. Their name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.


Pssm-ID: 350702 [Multi-domain]  Cd Length: 202  Bit Score: 121.11  E-value: 4.79e-32
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907078725   1 MLDLGFAEQVEDIIHESYKTDSEDNPQTLLFSATCPQWVYKVAKKYMKSRYEQVD 55
Cdd:cd17944   148 MLDMGFAEQVEEILSVSYKKDSEDNPQTLLFSATCPDWVYNVAKKYMKSQYEQVD 202
PTZ00110 PTZ00110
helicase; Provisional
 1-200 7.47e-32

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 127.58  E-value: 7.47e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725   1 MLDLGFAEQVEDIIhesyktdSEDNP--QTLLFSATCPQWVYKVAKKYMKSRYEQVDlVGKMTQKAATTVEHLAIQCHWS 78
Cdd:PTZ00110  289 MLDMGFEPQIRKIV-------SQIRPdrQTLMWSATWPKEVQSLARDLCKEEPVHVN-VGSLDLTACHNIKQEVFVVEEH 360

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  79 QRPAVIGDVLQVYSGSEGRAIIFCETKKN----VTEMAMN--PhikqnAQCLHGDIAQSQREITLKGFREGSFKVLVATN 152
Cdd:PTZ00110  361 EKRGKLKMLLQRIMRDGDKILIFVETKKGadflTKELRLDgwP-----ALCIHGDKKQEERTWVLNEFKTGKSPIMIATD 435

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1907078725 153 VAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICVCFYQP 200
Cdd:PTZ00110  436 VASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTP 483
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 1-212 9.77e-31

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 122.74  E-value: 9.77e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725   1 MLDLGFAEQVEDIIHESY--KtdsednpQTLLFSATCP-QWVYKVAKKYMK---------SRYEQvdlvGKMTQ--KAAT 66
Cdd:PRK11192  159 MLDMGFAQDIETIAAETRwrK-------QTLLFSATLEgDAVQDFAERLLNdpveveaepSRRER----KKIHQwyYRAD 227

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  67 TVEH-LAIQCHWSQRPAVigdvlqvysgseGRAIIFCETKKNVTEMAMNPHiKQNAQC--LHGDIAQSQREITLKGFREG 143
Cdd:PRK11192  228 DLEHkTALLCHLLKQPEV------------TRSIVFVRTRERVHELAGWLR-KAGINCcyLEGEMVQAKRNEAIKRLTDG 294

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907078725 144 SFKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICVCFYQPRERGQL----RYVEQK 212
Cdd:PRK11192  295 RVNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLLgkieRYIEEP 367
PRK01297 PRK01297
ATP-dependent RNA helicase RhlB; Provisional
 1-214 2.55e-27

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 234938 [Multi-domain]  Cd Length: 475  Bit Score: 113.85  E-value: 2.55e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725   1 MLDLGFAEQVEDIIHEsykTDSEDNPQTLLFSATCPQWVYKVAKKYMksrYEQVDLVGKMTQKAATTVEHLAIQCHWSQR 80
Cdd:PRK01297  249 MLDMGFIPQVRQIIRQ---TPRKEERQTLLFSATFTDDVMNLAKQWT---TDPAIVEIEPENVASDTVEQHVYAVAGSDK 322

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  81 PAVIGDVlqVYSGSEGRAIIFCETKKNVTEMamNPHIKQ---NAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARG 157
Cdd:PRK01297  323 YKLLYNL--VTQNPWERVMVFANRKDEVRRI--EERLVKdgiNAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRG 398

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907078725 158 LDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICVCFYQPRERGQLRYVEQKAG 214
Cdd:PRK01297  399 IHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPEIEELLG 455
PTZ00424 PTZ00424
helicase 45; Provisional
 1-211 4.21e-27

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 112.23  E-value: 4.21e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725   1 MLDLGFAEQvediIHESYKTDSEDnPQTLLFSATCPQWVYKVAKKYMKsryeqvDLVGKMTQKAATTVE-----HLAIQC 75
Cdd:PTZ00424  182 MLSRGFKGQ----IYDVFKKLPPD-VQVALFSATMPNEILELTTKFMR------DPKRILVKKDELTLEgirqfYVAVEK 250

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  76 HwSQRPAVIGDVLQVYSGSEgrAIIFCETKKNVTEMAMNPHIKQ-NAQCLHGDIAQSQREITLKGFREGSFKVLVATNVA 154
Cdd:PTZ00424  251 E-EWKFDTLCDLYETLTITQ--AIIYCNTRRKVDYLTKKMHERDfTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLL 327

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907078725 155 ARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICVCFYQPRERGQLRYVEQ 211
Cdd:PTZ00424  328 ARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIER 384
HELICc smart00490
helicase superfamily c-terminal domain;
120-189 3.60e-26

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 100.75  E-value: 3.60e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  120 NAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAG 189
Cdd:smart00490  13 KVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82
PRK04537 PRK04537
ATP-dependent RNA helicase RhlB; Provisional
 1-212 8.96e-23

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235307 [Multi-domain]  Cd Length: 572  Bit Score: 100.80  E-value: 8.96e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725   1 MLDLGFaeqVEDIIHESYKTDSEDNPQTLLFSATCPQWVYKVAKKYMKsryEQVDLVGKMTQKAATTVEHlaiQCHWSQR 80
Cdd:PRK04537  171 MFDLGF---IKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMN---EPEKLVVETETITAARVRQ---RIYFPAD 241

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  81 PAVIGDVLQVYSGSEG-RAIIFCETKKNVTEMAMNphIKQNAQ---CLHGDIAQSQREITLKGFREGSFKVLVATNVAAR 156
Cdd:PRK04537  242 EEKQTLLLGLLSRSEGaRTMVFVNTKAFVERVART--LERHGYrvgVLSGDVPQKKRESLLNRFQKGQLEILVATDVAAR 319

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725 157 GLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICVCFYQPRERGQL----RYVEQK 212
Cdd:PRK04537  320 GLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYAMSLpdieAYIEQK 379
PRK04837 PRK04837
ATP-dependent RNA helicase RhlB; Provisional
 97-197 3.43e-21

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235314 [Multi-domain]  Cd Length: 423  Bit Score: 95.04  E-value: 3.43e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  97 RAIIFCETKKNVTE----MAMNPHikqNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPP 172
Cdd:PRK04837  257 RAIIFANTKHRCEEiwghLAADGH---RVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLP 333

                          90       100
                  ....*....|....*....|....*
gi 1907078725 173 QDVESYIHRSGRTGRAGRTGICVCF 197
Cdd:PRK04837  334 DDCEDYVHRIGRTGRAGASGHSISL 358
GUCT_RH7_like cd12937
RNA-binding GUCT domain found in plant DEAD-box ATP-dependent RNA helicase 7 (RH7) and similar ...
 284-368 3.53e-17

RNA-binding GUCT domain found in plant DEAD-box ATP-dependent RNA helicase 7 (RH7) and similar proteins; This subfamily corresponds to the Gu C-terminal (GUCT) domain of RH7 and similar proteins. RH7, also termed plant RNA helicase 75 (PRH75), is a new nucleus-localized member of the DEAD-box protein family from higher plants. It displays a weak ATPase activity which is barely stimulated by RNA ligands. RH7 contains an N-terminal KDES domain rich in lysine, glutamic acid, aspartic acid, and serine residues, seven highly conserved helicase motifs in the central region, a GUCT domain, and a C-terminal GYR domain harboring a large number of glycine residues interrupted by either arginines or tyrosines. RH7 is RNA specific and harbors two possible RNA-binding motifs, the helicase motif VI (HRIGRTGR) and the C-terminal glycine-rich GYR domain.


Pssm-ID: 240594  Cd Length: 86  Bit Score: 76.07  E-value: 3.53e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725 284 RSLITSDKGFVTMTLESPEEIQDVSCAWKELNRKLSSNAVSHVTRMCLLKGNMGVCFDVPTSESERLQAEWHDSDWI-LS 362
Cdd:cd12937     1 RSLLTSHEGYTTLLLKSNTPIRSPGYVWNALRRYLPEDIVESIKGMTLTADGKGAVFDVPSELIEEFLSAWVDKRGVtLE 80


                  ....*.
gi 1907078725 363 VPAKLP 368
Cdd:cd12937    81 VATELP 86
PRK10590 PRK10590
ATP-dependent RNA helicase RhlE; Provisional
 1-223 9.82e-17

ATP-dependent RNA helicase RhlE; Provisional


Pssm-ID: 236722 [Multi-domain]  Cd Length: 456  Bit Score: 82.16  E-value: 9.82e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725   1 MLDLGFaeqvediIHESYKTDSEDNP--QTLLFSATCPQWVYKVAKKYMKSRyEQVDLVgkmtqKAATTVEHLAIQCHWS 78
Cdd:PRK10590  161 MLDMGF-------IHDIRRVLAKLPAkrQNLLFSATFSDDIKALAEKLLHNP-LEIEVA-----RRNTASEQVTQHVHFV 227

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  79 QR-------PAVIGDvlqvysGSEGRAIIFCETKKNVTEMAmnphiKQ------NAQCLHGDIAQSQREITLKGFREGSF 145
Cdd:PRK10590  228 DKkrkrellSQMIGK------GNWQQVLVFTRTKHGANHLA-----EQlnkdgiRSAAIHGNKSQGARTRALADFKSGDI 296

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725 146 KVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTG-----ICVcfyqpRERGQLRYVEQKAGITFKRV 220
Cdd:PRK10590  297 RVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGealslVCV-----DEHKLLRDIEKLLKKEIPRI 371


                  ...
gi 1907078725 221 GVP 223
Cdd:PRK10590  372 AIP 374
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 1-197 1.03e-15

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 79.06  E-value: 1.03e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725   1 MLDLGFAEQVEDIIHesyktdSEDNPQTLLFSATCPQWVYKVAKKYMKSRYeqVDLVGKmTQKAATTVEHLAIQCHWSQR 80
Cdd:PLN00206  282 MLERGFRDQVMQIFQ------ALSQPQVLLFSATVSPEVEKFASSLAKDII--LISIGN-PNRPNKAVKQLAIWVETKQK 352

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  81 PAVIGDVLQ----------VYSGSEGRAIIFCETKKNVTEMamnphikqNAQCLHGDIAQSQREITLKGFREGSFKVLVA 150
Cdd:PLN00206  353 KQKLFDILKskqhfkppavVFVSSRLGADLLANAITVVTGL--------KALSIHGEKSMKERREVMKSFLVGEVPVIVA 424

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1907078725 151 TNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICVCF 197
Cdd:PLN00206  425 TGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVF 471
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
95-189 8.37e-15

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 76.69  E-value: 8.37e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  95 EGRAIIFCE---TKKNVTEMAMNPHIK------QNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDL 165
Cdd:COG1111   353 DSRIIVFTQyrdTAEMIVEFLSEPGIKagrfvgQASKEGDKGLTQKEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDL 432

                          90       100
                  ....*....|....*....|....*..
gi 1907078725 166 VIQSSPpqdVES---YIHRSGRTGRAG 189
Cdd:COG1111   433 VIFYEP---VPSeirSIQRKGRTGRKR 456
PRK13766 PRK13766
Hef nuclease; Provisional
 97-195 6.29e-14

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 74.14  E-value: 6.29e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  97 RAIIFCE---TKKNVTEMAMNPHIK------QNAQclHGDIAQSQRE--ITLKGFREGSFKVLVATNVAARGLDIPEVDL 165
Cdd:PRK13766  367 RIIVFTQyrdTAEKIVDLLEKEGIKavrfvgQASK--DGDKGMSQKEqiEILDKFRAGEFNVLVSTSVAEEGLDIPSVDL 444

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1907078725 166 VIQSSP-PQDVESyIHRSGRTGRaGRTGICV 195
Cdd:PRK13766  445 VIFYEPvPSEIRS-IQRKGRTGR-QEEGRVV 473
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 95-198 7.19e-14

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: 68.39  E-value: 7.19e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  95 EGRAIIFCETKKNVTEMAMnpHIKQN---AQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSP 171
Cdd:cd18794    30 GGSGIIYCLSRKECEQVAA--RLQSKgisAAAYHAGLEPSDRRDVQRKWLRDKIQVIVATVAFGMGIDKPDVRFVIHYSL 107

                          90       100
                  ....*....|....*....|....*..
gi 1907078725 172 PQDVESYIHRSGRTGRAGRTGICVCFY 198
Cdd:cd18794   108 PKSMESYYQESGRAGRDGLPSECILFY 134
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 93-192 4.06e-13

C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is 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. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef 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: 350188 [Multi-domain]  Cd Length: 143  Bit Score: 66.23  E-value: 4.06e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  93 GSEGRAIIFCETKKNVTEMA-----MNPHIK-------QNAQCLHGdIAQSQREITLKGFREGSFKVLVATNVAARGLDI 160
Cdd:cd18801    28 GSDTRVIIFSEFRDSAEEIVnflskIRPGIRatrfigqASGKSSKG-MSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDI 106

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1907078725 161 PEVDLVI----QSSPPQdvesYIHRSGRTGRaGRTG 192
Cdd:cd18801   107 GEVDLIIcydaSPSPIR----MIQRMGRTGR-KRQG 137
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 86-188 1.24e-12

C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 64.92  E-value: 1.24e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  86 DVLQVYSGSEG--RAIIFCETKknVTEMAMNPHIKQNAQCLHG------------------DIAQSQREITLKGFREGSF 145
Cdd:cd18802    14 EILREYFPKTPdfRGIIFVERR--ATAVVLSRLLKEHPSTLAFircgfligrgnssqrkrsLMTQRKQKETLDKFRDGEL 91

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1907078725 146 KVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRtGRA 188
Cdd:cd18802    92 NLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGR-ARA 133
DEADc cd00268
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ...
 1-48 4.43e-12

DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350669 [Multi-domain]  Cd Length: 196  Bit Score: 64.77  E-value: 4.43e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1907078725   1 MLDLGFAEQVEDIIHESYKtdsedNPQTLLFSATCPQWVYKVAKKYMK 48
Cdd:cd00268   148 MLDMGFEEDVEKILSALPK-----DRQTLLFSATLPEEVKELAKKFLK 190
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 125-187 7.46e-11

C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350183 [Multi-domain]  Cd Length: 150  Bit Score: 59.97  E-value: 7.46e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907078725 125 HGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGR 187
Cdd:cd18796    75 HGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDVDLVIQIGSPKSVARLLQRLGRSGH 137
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 144-198 1.40e-10

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 57.33  E-value: 1.40e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907078725 144 SFKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAG-RTGICVCFY 198
Cdd:cd18785    22 SLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRGGkDEGEVILFV 77
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
 96-190 1.85e-10

C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350176 [Multi-domain]  Cd Length: 153  Bit Score: 59.19  E-value: 1.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  96 GRAIIFCETKKNVTEMAmnphIKQNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQ-SSPPQD 174
Cdd:cd18789    50 DKIIVFTDNVEALYRYA----KRLLKPFITGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEANVAIQiSGHGGS 125

                          90
                  ....*....|....*.
gi 1907078725 175 VESYIHRSGRTGRAGR 190
Cdd:cd18789   126 RRQEAQRLGRILRPKK 141
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
82-184 1.04e-09

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 60.42  E-value: 1.04e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  82 AVIGDVLQVYsGSEGRAIIFCETKKNVTEMA-MNPHIKQNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDI 160
Cdd:COG1061   293 KILRELLREH-PDDRKTLVFCSSVDHAEALAeLLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDV 371

                          90       100
                  ....*....|....*....|....
gi 1907078725 161 PEVDLVIQSSPPQDVESYIHRSGR 184
Cdd:COG1061   372 PRLDVAILLRPTGSPREFIQRLGR 395
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
99-208 1.33e-09

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 59.77  E-value: 1.33e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  99 IIFCETKKNVTEMAmnPHIKQN---AQCLHGDIAQSQREITLKGFREGSFKVLVATNvaARGL--DIPEVDLVIQSSPPQ 173
Cdd:COG0514   234 IVYCLSRKKVEELA--EWLREAgirAAAYHAGLDAEEREANQDRFLRDEVDVIVATI--AFGMgiDKPDVRFVIHYDLPK 309

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1907078725 174 DVESYIHRSGRTGRAGRTGICVCFYQPRERGQLRY 208
Cdd:COG0514   310 SIEAYYQEIGRAGRDGLPAEALLLYGPEDVAIQRF 344
DEADc_MSS116 cd17964
DEAD-box helicase domain of DEAD-box helicase Mss116; Mss116 is an RNA chaperone important for ...
 1-55 4.74e-09

DEAD-box helicase domain of DEAD-box helicase Mss116; Mss116 is an RNA chaperone important for mitochondrial group I and II intron splicing, translational activation, and RNA end processing. Mss116 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350722 [Multi-domain]  Cd Length: 211  Bit Score: 56.05  E-value: 4.74e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907078725   1 MLDLGFAEQVEDIIhESYKTDSEDNPQTLLFSATCPQWVYKVAKKYMKSRYEQVD 55
Cdd:cd17964   158 LLDMGFRPDLEQIL-RHLPEKNADPRQTLLFSATVPDEVQQIARLTLKKDYKFID 211
PRK09751 PRK09751
putative ATP-dependent helicase Lhr; Provisional
 121-206 4.39e-08

putative ATP-dependent helicase Lhr; Provisional


Pssm-ID: 137505 [Multi-domain]  Cd Length: 1490  Bit Score: 55.70  E-value: 4.39e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  121 AQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTG-RAGrtGICVCFYQ 199
Cdd:PRK09751   304 ARSHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGhQVG--GVSKGLFF 381


                   ....*..
gi 1907078725  200 PRERGQL 206
Cdd:PRK09751   382 PRTRRDL 388
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
 97-190 6.33e-07

C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II), and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA. Its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350177 [Multi-domain]  Cd Length: 171  Bit Score: 49.17  E-value: 6.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  97 RAIIFCETKK---NVTEMAMNPHIKqnAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLV-IQSSpp 172
Cdd:cd18790    29 RVLVTTLTKRmaeDLTEYLQELGVK--VRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVaILDA-- 104

                          90       100
                  ....*....|....*....|...
gi 1907078725 173 qDVESYIhRSGRT-----GRAGR 190
Cdd:cd18790   105 -DKEGFL-RSETSliqtiGRAAR 125
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 133-195 8.18e-07

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: 51.37  E-value: 8.18e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907078725 133 REITlKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTGICV 195
Cdd:COG1205   334 REIE-RGLRSGELLGVVSTNALELGIDIGGLDAVVLAGYPGTRASFWQQAGRAGRRGQDSLVV 395
DEADc_DDX3_DDX4 cd17967
DEAD-box helicase domain of ATP-dependent RNA helicases DDX3 and DDX4; This subfamily includes ...
 1-48 1.13e-06

DEAD-box helicase domain of ATP-dependent RNA helicases DDX3 and DDX4; This subfamily includes Drosophila melanogaster Vasa, which is essential for development. DEAD box protein 3 (DDX3) has been reported to display a high level of RNA-independent ATPase activity stimulated by both RNA and DNA. DEAD box protein 4 (DDX4, also known as VASA homolog) is an ATP-dependent RNA helicase required during spermatogenesis and is essential for the germline integrity. DDX3 and DDX4 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350725 [Multi-domain]  Cd Length: 221  Bit Score: 49.41  E-value: 1.13e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1907078725   1 MLDLGFAEQVEDIIHESYKTDSEDNpQTLLFSATCPQWVYKVAKKYMK 48
Cdd:cd17967   164 MLDMGFEPQIRKIVEHPDMPPKGER-QTLMFSATFPREIQRLAADFLK 210
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 90-167 1.22e-06

C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins 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: 350186 [Multi-domain]  Cd Length: 116  Bit Score: 47.17  E-value: 1.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  90 VYSGSEGRAIIFCETKKNVTEMA-----MNPhikqNAQCLHGDIAQSQRE---ITLKGFREGSFKVLVATNVAARGLDIP 161
Cdd:cd18799     1 PYKYVEIKTLIFCVSIEHAEFMAeafneAGI----DAVALNSDYSDRERGdeaLILLFFGELKPPILVTVDLLTTGVDIP 76


                  ....*.
gi 1907078725 162 EVDLVI 167
Cdd:cd18799    77 EVDNVV 82
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 99-207 1.44e-06

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 50.48  E-value: 1.44e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  99 IIFCETKKNVTEMA---MNPHIKQNAqcLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDV 175
Cdd:PRK11057  240 IIYCNSRAKVEDTAarlQSRGISAAA--YHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNI 317

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1907078725 176 ESYIHRSGRTGRAGRTGICVCFYQPRERGQLR 207
Cdd:PRK11057  318 ESYYQETGRAGRDGLPAEAMLFYDPADMAWLR 349
DEADc_DDX4 cd18052
DEAD-box helicase domain of DEAD box protein 4; DEAD box protein 4 (DDX4, also known as VASA ...
 1-51 3.56e-06

DEAD-box helicase domain of DEAD box protein 4; DEAD box protein 4 (DDX4, also known as VASA homolog) is an ATP-dependent RNA helicase required during spermatogenesis and is essential for the germline integrity. DEAD-box helicases are a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350810 [Multi-domain]  Cd Length: 264  Bit Score: 48.42  E-value: 3.56e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907078725   1 MLDLGFAEQVEDIIhESYKTDSEDNPQTLLFSATCPQWVYKVAKKYMKSRY 51
Cdd:cd18052   206 MLDMGFGPEIRKLV-SEPGMPSKEDRQTLMFSATFPEEIQRLAAEFLKEDY 255
GUCT_Hera cd12938
RNA-binding GUCT-like domain found in Thermus thermophilus heat resistant RNA-dependent ATPase ...
 283-353 3.87e-06

RNA-binding GUCT-like domain found in Thermus thermophilus heat resistant RNA-dependent ATPase (Hera) and similar proteins; This subfamily corresponds to the Gu C-terminal (GUCT)-like domain of Hera and similar proteins. Thermus thermophilus Hera is a DEAD box helicase that binds fragments of 23S rRNA and RNase P RNA via its C-terminal domain. It contains a helicase core that harbors two RecA-like domains termed RecA_N and RecA_C, a dimerization domain (DD), and a C-terminal RNA-binding domain (RBD) that reveals a compact, RRM-like fold and shows sequence similarity with GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA helicase II/Gubeta (RH-II/Gubeta) and plant DEAD-box ATP-dependent RNA helicase 7 (RH7 or PRH75).


Pssm-ID: 240595  Cd Length: 74  Bit Score: 44.60  E-value: 3.87e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907078725 283 PRSLITSDKGFVTMTLESPEEIQ--DVSCAWKELNRKLSSNavshVTRMCLLKGNMGVCFDVPTSESERLQAE 353
Cdd:cd12938     1 PRSLLTGEEGWTTLQLTGSRLLPpgSVRRAVGLLSRAAADG----VGKIRILADAGGAVFDLPEEIAKELLAK 69
SF2_C_Hrq cd18797
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...
 97-190 6.16e-06

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: 45.71  E-value: 6.16e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  97 RAIIFCETKKNVTEM-----AMNPHIKQNAQCLH----GDIAQSQREITlKGFREGSFKVLVATNVAARGLDIPEVDLVI 167
Cdd:cd18797    37 KTIVFCRSRKLAELLlrylkARLVEEGPLASKVAsyraGYLAEDRREIE-AELFNGELLGVVATNALELGIDIGGLDAVV 115

                          90       100
                  ....*....|....*....|...
gi 1907078725 168 QSSPPQDVESYIHRSGRTGRAGR 190
Cdd:cd18797   116 LAGYPGSLASLWQQAGRAGRRGK 138
PLN03137 PLN03137
ATP-dependent DNA helicase; Q4-like; Provisional
 99-198 6.77e-06

ATP-dependent DNA helicase; Q4-like; Provisional


Pssm-ID: 215597 [Multi-domain]  Cd Length: 1195  Bit Score: 48.74  E-value: 6.77e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725   99 IIFCETK---KNVTEMAMnpHIKQNAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDV 175
Cdd:PLN03137   684 IIYCLSRmdcEKVAERLQ--EFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSI 761

                           90       100
                   ....*....|....*....|...
gi 1907078725  176 ESYIHRSGRTGRAGRTGICVCFY 198
Cdd:PLN03137   762 EGYHQECGRAGRDGQRSSCVLYY 784
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
 124-207 9.26e-06

C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350197 [Multi-domain]  Cd Length: 151  Bit Score: 45.41  E-value: 9.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725 124 LHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHR-SGRTGRAGRTGICVCFYQPR- 201
Cdd:cd18810    57 AHGQMTENELEEVMLEFAKGEYDILVCTTIIESGIDIPNANTIIIERADKFGLAQLYQlRGRVGRSKERAYAYFLYPDQk 136


                  ....*....
gi 1907078725 202 ---ERGQLR 207
Cdd:cd18810   137 kltEDALKR 145
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
 124-207 1.10e-05

C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. 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: 350179 [Multi-domain]  Cd Length: 160  Bit Score: 45.34  E-value: 1.10e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725 124 LHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHR-SGRTGRAGRTGICVCFYQPR- 201
Cdd:cd18792    66 LHGKMTEDEKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQlRGRVGRGKHQSYCYLLYPDPk 145


                  ....*....
gi 1907078725 202 ---ERGQLR 207
Cdd:cd18792   146 kltETAKKR 154
uvrb TIGR00631
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ...
 97-190 1.13e-05

excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273185 [Multi-domain]  Cd Length: 655  Bit Score: 47.68  E-value: 1.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  97 RAIIFCETKK---NVTEMAMNPHIKqnAQCLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLV-IQSSpp 172
Cdd:TIGR00631 444 RVLVTTLTKKmaeDLTDYLKELGIK--VRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVaILDA-- 519

                          90       100
                  ....*....|....*....|...
gi 1907078725 173 qDVESYIhRSGRT-----GRAGR 190
Cdd:TIGR00631 520 -DKEGFL-RSERSliqtiGRAAR 540
DEADc_DDX23 cd17945
DEAD-box helicase domain of DEAD box protein 23; DDX23 (also called U5 snRNP 100kD protein and ...
 1-49 3.98e-05

DEAD-box helicase domain of DEAD box protein 23; DDX23 (also called U5 snRNP 100kD protein and PRP28 homolog) is involved in pre-mRNA splicing and its phosphorylated form (by SRPK2) is required for spliceosomal B complex formation. Diseases associated with DDX23 include distal hereditary motor neuropathy, type II. DDX23 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350703 [Multi-domain]  Cd Length: 220  Bit Score: 44.62  E-value: 3.98e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907078725   1 MLDLGFAEQVEDIIH----ESYKTDSEDNP-----------QTLLFSATCPQWVYKVAKKYMKS 49
Cdd:cd17945   152 MIDMGFEPQVTKILDampvSNKKPDTEEAEklaasgkhryrQTMMFTATMPPAVEKIAKGYLRR 215
SF2_C_reverse_gyrase cd18798
C-terminal helicase domain of the reverse gyrase; Reverse gyrase modifies the topological ...
 137-212 4.70e-05

C-terminal helicase domain of the reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350185 [Multi-domain]  Cd Length: 174  Bit Score: 43.83  E-value: 4.70e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725 137 LKGFREGSFKVLVAT----NVAARGLDIPE-VDLVIQSSPPqdVESYIHRSGRTGR--AGR--TGICVCFYQPRE----- 202
Cdd:cd18798    65 LEKFEEGEIDVLIGVasyyGVLVRGIDLPErIKYAIFYGVP--VTTYIQASGRTSRlyAGGltKGLSVVLVDDPElfeal 142

                          90
                  ....*....|..
gi 1907078725 203 --RGQLRYVEQK 212
Cdd:cd18798   143 kkRLKLILDEFI 154
Lhr COG1201
Lhr-like helicase [Replication, recombination and repair];
125-206 8.29e-05

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


Pssm-ID: 440814 [Multi-domain]  Cd Length: 850  Bit Score: 45.09  E-value: 8.29e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725 125 HGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQ-SSPPQdVESYIHRSGRTG-RAGRT--GICVcfyqP 200
Cdd:COG1201   307 HGSLSREQRLEVEEALKAGELRAVVATSSLELGIDIGDVDLVIQvGSPKS-VARLLQRIGRAGhRVGEVskGRLV----P 381


                  ....*.
gi 1907078725 201 RERGQL 206
Cdd:COG1201   382 THRDEL 387
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
96-196 9.60e-05

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 44.50  E-value: 9.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  96 GRAIIFCETKKNVTEMA------MNPHIKQN-------------------------AQCL-------HGDIAQSQREITL 137
Cdd:COG1204   240 GQVLVFVSSRRDAESLAkkladeLKRRLTPEereeleelaeellevseethtneklADCLekgvafhHAGLPSELRRLVE 319

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907078725 138 KGFREGSFKVLVATNVAARGLDIPeVDLVIqssppqdVESYiHRSGRT-----------GRAGRTG-------ICVC 196
Cdd:COG1204   320 DAFREGLIKVLVATPTLAAGVNLP-ARRVI-------IRDT-KRGGMVpipvlefkqmaGRAGRPGydpygeaILVA 387
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 124-200 2.00e-04

C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 41.56  E-value: 2.00e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907078725 124 LHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHR-SGRTGRAGRTGICVCFYQP 200
Cdd:cd18811    67 LHGRLKSDEKDAVMAEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQlRGRVGRGDHQSYCLLVYKD 144
DEADc_DDX5_DDX17 cd17966
DEAD-box helicase domain of ATP-dependent RNA helicases DDX5 and DDX17; DDX5 and DDX17 are ...
 1-54 3.14e-04

DEAD-box helicase domain of ATP-dependent RNA helicases DDX5 and DDX17; DDX5 and DDX17 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350724 [Multi-domain]  Cd Length: 197  Bit Score: 41.59  E-value: 3.14e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907078725   1 MLDLGFAEQVEDIIhesyktdSEDNP--QTLLFSATCPQWVYKVAKKYMKSrYEQV 54
Cdd:cd17966   149 MLDMGFEPQIRKIV-------DQIRPdrQTLMWSATWPKEVRRLAEDFLKD-YIQV 196
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 98-193 3.38e-04

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: 41.00  E-value: 3.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  98 AIIFCETKKNVTEMAMN-----PHikqnaqclHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPeVDLVIqsspp 172
Cdd:cd18795    46 VLVFCSSRKECEKTAKDlagiaFH--------HAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLP-ARTVI----- 111

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1907078725 173 qdVESYIHRSGRT-------------GRAGRTGI 193
Cdd:cd18795   112 --IKGTQRYDGKGyrelspleylqmiGRAGRPGF 143
PRK05298 PRK05298
excinuclease ABC subunit UvrB;
124-166 6.18e-04

excinuclease ABC subunit UvrB;


Pssm-ID: 235395 [Multi-domain]  Cd Length: 652  Bit Score: 42.34  E-value: 6.18e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1907078725 124 LHGDIAQSQR-EItLKGFREGSFKVLVATNVAARGLDIPEVDLV 166
Cdd:PRK05298  476 LHSDIDTLERvEI-IRDLRLGEFDVLVGINLLREGLDIPEVSLV 518
UvrB COG0556
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
124-166 7.76e-04

Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];


Pssm-ID: 440322 [Multi-domain]  Cd Length: 657  Bit Score: 41.92  E-value: 7.76e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1907078725 124 LHGDIAQSQR-EItLKGFREGSFKVLVATNVAARGLDIPEVDLV 166
Cdd:COG0556   473 LHSDIDTLERvEI-IRDLRLGEFDVLVGINLLREGLDLPEVSLV 515
DEADc_DDX27 cd17947
DEAD-box helicase domain of DEAD box protein 27; DDX27 (also called RHLP, deficiency of ...
 1-34 1.20e-03

DEAD-box helicase domain of DEAD box protein 27; DDX27 (also called RHLP, deficiency of ribosomal subunits protein 1 homolog, and probable ATP-dependent RNA helicase DDX27) is involved in the processing of 5.8S and 28S ribosomal RNAs. More specifically, the encoded protein localizes to the nucleolus, where it interacts with the PeBoW complex to ensure proper 3' end formation of 47S rRNA. DDX27 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350705 [Multi-domain]  Cd Length: 196  Bit Score: 39.93  E-value: 1.20e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1907078725   1 MLDLGFAEQVEDIIHESYKTDsednpQTLLFSAT 34
Cdd:cd17947   148 MLEEGFADELKEILRLCPRTR-----QTMLFSAT 176
DEADc_DDX6 cd17940
DEAD-box helicase domain of DEAD box protein 6; DEAD box protein 6 (DDX6, also known as Rck or ...
 1-52 2.03e-03

DEAD-box helicase domain of DEAD box protein 6; DEAD box protein 6 (DDX6, also known as Rck or p54) participates in mRNA regulation mediated by miRNA-mediated silencing. It also plays a role in global and transcript-specific messenger RNA (mRNA) storage, translational repression, and decay. It is a member of the DEAD-box helicase family, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350698 [Multi-domain]  Cd Length: 201  Bit Score: 39.20  E-value: 2.03e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1907078725   1 MLDLGFAEQVEDIIHESYKtdsedNPQTLLFSATCPQWVYKVAKKYMKSRYE 52
Cdd:cd17940   153 LLSQDFQPIIEKILNFLPK-----ERQILLFSATFPLTVKNFMDRHMHNPYE 199
DEAD-like_helicase_C cd09300
C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases ...
 147-192 2.38e-03

C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases is composed of two superfamilies, SF1 and SF2, that share almost identical folds and extensive structural similarity in their catalytic core. Helicases are involved in ATP-dependent RNA or DNA unwinding. Two distinct types of helicases exist, those forming toroidal, predominantly hexameric structures, and those that do not. SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Their conserved 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: 350171 [Multi-domain]  Cd Length: 59  Bit Score: 36.37  E-value: 2.38e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1907078725 147 VLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTG 192
Cdd:cd09300     8 VLIAVN*ALTGFDAPELNTIIVDKNLRSYRGLNQAFGRANRIYTFG 53
DEADc_DDX43_DDX53 cd17958
DEAD-box helicase domain of DEAD box proteins 43 and 53; DDX43 (also called cancer/testis ...
 1-48 3.05e-03

DEAD-box helicase domain of DEAD box proteins 43 and 53; DDX43 (also called cancer/testis antigen 13 or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 is also called cancer/testis antigen 26 or DEAD-Box Protein CAGE. Both DDX46 and DDX53 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350716 [Multi-domain]  Cd Length: 197  Bit Score: 38.60  E-value: 3.05e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1907078725   1 MLDLGFAEQVEDIIhesykTDSEDNPQTLLFSATCPQWVYKVAKKYMK 48
Cdd:cd17958   149 MLDMGFEPQIRKIL-----LDIRPDRQTIMTSATWPDGVRRLAQSYLK 191
DEADc_DDX59 cd17962
DEAD-box helicase domain of DEAD box protein 59; DDX59 plays an important role in lung cancer ...
 1-48 3.13e-03

DEAD-box helicase domain of DEAD box protein 59; DDX59 plays an important role in lung cancer development by promoting DNA replication. DDX59 knockdown mice showed reduced cell proliferation, anchorage-independent cell growth, and reduction of tumor formation. Recent work shows that EGFR and Ras regulate DDX59 during lung cancer development. Diseases associated with DDX59 (also called zinc finger HIT domain-containing protein 5) include orofaciodigital syndrome V and orofaciodigital syndrome. DDX59 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350720 [Multi-domain]  Cd Length: 193  Bit Score: 38.68  E-value: 3.13e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1907078725   1 MLDLGFAEQVEDIIHesyktDSEDNPQTLLFSATCPQWVYKVAKKYMK 48
Cdd:cd17962   145 MLKMGFQQQVLDILE-----NISHDHQTILVSATIPRGIEQLAGQLLQ 187
SF2_C_RHA cd18791
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ...
 123-198 3.49e-03

C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family members 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: 350178 [Multi-domain]  Cd Length: 171  Bit Score: 38.28  E-value: 3.49e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725 123 CLHGDIAQS-QREI---TLKGFRegsfKVLVATNVAARGLDIPEVDLVIqssppqD-----VESYIHRSG---------- 183
Cdd:cd18791    79 PLHSSLPPEeQQRVfepPPPGVR----KVVLATNIAETSITIPGVVYVI------DsglvkEKVYDPRTGlsslvtvwis 148

                          90       100
                  ....*....|....*....|...
gi 1907078725 184 ------RTGRAGRT--GICVCFY 198
Cdd:cd18791   149 kasaeqRAGRAGRTrpGKCYRLY 171
DEADc_DDX10 cd17941
DEAD-box helicase domain of DEAD box protein 10; Fusion of the DDX10 gene and the nucleoporin ...
 1-44 4.06e-03

DEAD-box helicase domain of DEAD box protein 10; Fusion of the DDX10 gene and the nucleoporin gene, NUP98, by inversion 11 (p15q22) chromosome translocation is found in the patients with de novo or therapy-related myeloid malignancies. Diseases associated with DDX10 (also known as DDX10-NUP98 Fusion Protein Type 2) include myelodysplastic syndrome and leukemia, acute myeloid. DDX10 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350699 [Multi-domain]  Cd Length: 198  Bit Score: 38.43  E-value: 4.06e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1907078725   1 MLDLGFAEQVEDIIHESYKTDsednpQTLLFSATCPQWVYKVAK 44
Cdd:cd17941   148 ILDMGFKETLDAIVENLPKSR-----QTLLFSATQTKSVKDLAR 186
DEADc_DDX46 cd17953
DEAD-box helicase domain of DEAD box protein 46; DDX46 (also called Prp5-like DEAD-box protein) ...
 1-52 4.06e-03

DEAD-box helicase domain of DEAD box protein 46; DDX46 (also called Prp5-like DEAD-box protein) is a component of the 17S U2 snRNP complex. It plays an important role in pre-mRNA splicing and has a role in antiviral innate immunity. DDX46 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350711 [Multi-domain]  Cd Length: 222  Bit Score: 38.51  E-value: 4.06e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1907078725   1 MLDLGFAEQVEDIIhESYKTDSednpQTLLFSATCPQWVYKVAKKYMKSRYE 52
Cdd:cd17953   174 MFDMGFEPQIMKIV-NNIRPDR----QTVLFSATFPRKVEALARKVLHKPIE 220
DEADc_DDX54 cd17959
DEAD-box helicase domain of DEAD box protein 54; DDX54 interacts in a hormone-dependent manner ...
 1-36 5.69e-03

DEAD-box helicase domain of DEAD box protein 54; DDX54 interacts in a hormone-dependent manner with nuclear receptors, and represses their transcriptional activity. DDX54 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350717 [Multi-domain]  Cd Length: 205  Bit Score: 38.05  E-value: 5.69e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1907078725   1 MLDLGFAEQVEDIIHESyktdsEDNPQTLLFSATCP 36
Cdd:cd17959   157 LFEMGFAEQLHEILSRL-----PENRQTLLFSATLP 187
cas3_core TIGR01587
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ...
 84-190 6.10e-03

CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.


Pssm-ID: 273707 [Multi-domain]  Cd Length: 359  Bit Score: 38.59  E-value: 6.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  84 IGDVLQVYSgSEGRAIIFCETKKNVTEMAMNPHIKQNAQC---LHGDIAQSQRE----ITLKGFREGSFK-VLVATNVAA 155
Cdd:TIGR01587 212 LERLLEFIK-KGGSIAIIVNTVDRAQEFYQQLKEKAPEEEiilYHSRFTEKDRAkkeaELLREMKKSNEKfVIVATQVIE 290

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1907078725 156 RGLDIpEVDLVIQSSPPQDveSYIHRSGRTGRAGR 190
Cdd:TIGR01587 291 ASLDI-SADVMITELAPID--SLIQRLGRLHRYGR 322
Cas3_I cd09639
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ...
 94-190 7.06e-03

CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I


Pssm-ID: 187770 [Multi-domain]  Cd Length: 353  Bit Score: 38.56  E-value: 7.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078725  94 SEGRAIIFCETKKNVTEMAMNphIKQNAQC-----LHGDIAQSQR----EITLKGFREGSFKVLVATNVAARGLDIpEVD 164
Cdd:cd09639   217 KGGSVAIIVNTVDRAQEFYQQ--LKEKGPEeeimlIHSRFTEKDRakkeAELLLEFKKSEKFVIVATQVIEASLDI-SVD 293

                          90       100
                  ....*....|....*....|....*.
gi 1907078725 165 LVIQSSPPQDveSYIHRSGRTGRAGR 190
Cdd:cd09639   294 VMITELAPID--SLIQRLGRLHRYGE 317
DEADc_EIF4A cd17939
DEAD-box helicase domain of eukaryotic initiation factor 4A; The eukaryotic initiation ...
 1-47 7.67e-03

DEAD-box helicase domain of eukaryotic initiation factor 4A; The eukaryotic initiation factor-4A (eIF4A) family consists of 3 proteins EIF4A1, EIF4A2, and EIF4A3. These factors are required for the binding of mRNA to 40S ribosomal subunits. In addition these proteins are helicases that function to unwind double-stranded RNA. EIF4A proteins are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350697 [Multi-domain]  Cd Length: 199  Bit Score: 37.69  E-value: 7.67e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1907078725   1 MLDLGFAEQVEDIIHESYKtdsedNPQTLLFSATCPQWVYKVAKKYM 47
Cdd:cd17939   151 MLSRGFKDQIYDIFQFLPP-----ETQVVLFSATMPHEVLEVTKKFM 192
 
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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