NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1696124467|ref|XP_029559156|]
View 

interferon-induced helicase C domain-containing protein 1 isoform X2 [Salmo trutta]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 307-521 2.11e-126

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


The actual alignment was detected with superfamily member cd18074:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 216  Bit Score: 382.29  E-value: 2.11e-126
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  307 IVLRDYQMDVARPALEGKNIIICLPTGSGKTRVAVYITKEHLDSRRKEGRPGKVVVLVNKVPLVEQHYSTEFWKFLKNKY 386
Cdd:cd18074      1 LTLRDYQMEVAKPALEGKNIIICLPTGSGKTRVAVYITKDHLDKKRKASEPGKVIVLVNKVPLVEQHYRKEFNPFLKHWY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  387 KVERVSGDSQLKISFTDIVQKNDIVICTAQILENYLERAHSGDDDGIKLSDLSLIVIDECHHTQKGGVYNHIMIRYLKQK 466
Cdd:cd18074     81 QVIGLSGDSQLKISFPEVVKRYDVIICTAQILENSLLNATEEEDEGVQLSDFSLIIIDECHHTQKEAVYNNIMRRYLKQK 160

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1696124467  467 HKNAKLKKEQKDTVDIPQILGLTASPGVGGAKKIEKAEEHILRICANLDAYKIMT 521
Cdd:cd18074    161 IKNRKQKKENKPLIPLPQILGLTASPGVGGAKNNKKAEEHILKICANLDAFRIMT 215
RLR_C_like super family cl13152
C-terminal domain of Retinoic acid-inducible gene (RIG)-I-like Receptors, Cereblon (CRBN), and ...
 875-989 3.08e-60

C-terminal domain of Retinoic acid-inducible gene (RIG)-I-like Receptors, Cereblon (CRBN), and similar protein domains; Retinoic acid-inducible gene (RIG)-I-like Receptors (RLRs) are cytoplasmic RNA receptors that recognize non-self RNA and act as molecular sensors to detect viral pathogens. They play crucial roles in innate antiviral responses, including the production of proinflammatory cytokines and type I interferon. There are three RLRs in vertebrates, RIG-I, LGP2, and MDA5. They are characterized by a central DExD/H-box helicase domain and a C-terminal domain, both of which are responsible for binding viral RNA. Cereblon is part of an E3 ubiquitin ligase complex, together with damaged DNA binding protein 1 (DDB1), CUL4A and ROC1. Cereblon interacts directly with DDB1, although the C-terminal domain characterized here does not contribute to that interaction. The C-terminal domain of Cereblon was shown to contain the binding site for thalidomide and its analogs, a class of teratogenic drugs that exhibit an antiproliferative effect on myelomas. Mutations in CRBN, some of which map onto the C-terminal domain, were associated with autosomal recessive mental retardation, which may have to do with interactions between CRBN and ion channels in the brain. RLRs and Cereblon contain a common conserved zinc binding site in their C-terminal domains.


The actual alignment was detected with superfamily member cd15807:

Pssm-ID: 472430  Cd Length: 117  Bit Score: 201.18  E-value: 3.08e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  875 PSKVKFSCRSCNKPVCSGEDVEIIENMHRVNVTPQFKELFIQRENTSLVKRLLDYETNGFIACKDCGQRWGSMMLYRGIE 954
Cdd:cd15807      1 PSLITFLCKNCSVLVCSGEDIQVIEKMHHVNVTPEFKELYIKRENKALQEKLADYQTNGEIICKTCGQAWGTMMVHKGLE 80

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1696124467  955 CPCLHVKNFLVTYDE--KKKNINKWSELGIQLPAFDY 989
Cdd:cd15807     81 LPCLKIRNFVVTFKNnsTKKTYKKWVELPITFPAFDY 117
MPH1 super family cl34113
ERCC4-related helicase [Replication, recombination and repair];
310-851 1.13e-51

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


The actual alignment was detected with superfamily member COG1111:

Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 194.56  E-value: 1.13e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  310 RDYQMDVARPALEgKNIIICLPTGSGKTRVAVYITKEHLDSRRkegrpGKVVVLVNKVPLVEQHYSTeFWKFLK-NKYKV 388
Cdd:COG1111      5 RLYQLNLAASALR-KNTLVVLPTGLGKTAVALLVIAERLHKKG-----GKVLFLAPTKPLVEQHAEF-FKEALNiPEDEI 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  389 ERVSGDSQLKISfTDIVQKNDIVICTAQILENYLERAHsgdddgIKLSDLSLIVIDECHHTQKGGVYNHIMIRYLKQKHK 468
Cdd:COG1111     78 VVFTGEVSPEKR-KELWEKARIIVATPQVIENDLIAGR------IDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKD 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  469 naklkkeqkdtvdiPQILGLTASPGvggaKKIEKAEEhilrICANLdaykimtgnlgenkkephkKIATAEERKE-DPfg 547
Cdd:COG1111    151 --------------PLILGMTASPG----SDEEKIEE----VCENL-------------------GIENVEVRTEeDP-- 187

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  548 DV---IKGImNAIHVHAELNPTC-------------------DLGTQNYEQWVV-QKEQNAAKEENQK------------ 592
Cdd:COG1111    188 DVapyVHDT-EVEWIRVELPEELkeirdllnevlddrlkklkELGVIVSTSPDLsKKDLLALQKKLQRrireddsegyra 266

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  593 VRVCAEHLR-QYneALYLGKTirmwDAFSFLDKYFdEELKKKvapEDEEAIIKTDTErflftLFKDSKV-KLQELAKLPQ 670
Cdd:COG1111    267 ISILAEALKlRH--ALELLET----QGVEALLRYL-ERLEEE---ARSSGGSKASKR-----LVSDPRFrKAMRLAEEAD 331

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  671 YENNSLAKLRTKILHEFTSREKARGIIFTKTRRSAIALAQWVQENskfeevGVKACHVIGGGGQSVVKPMTAAEQRDVLN 750
Cdd:COG1111    332 IEHPKLSKLREILKEQLGTNPDSRIIVFTQYRDTAEMIVEFLSEP------GIKAGRFVGQASKEGDKGLTQKEQIEILE 405

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  751 KFQNAEVNLLIATTVAEEGLDIAACNFVIRYELVTNEIAMIQARGR-GRAEDSS-YTLVAgEGSgvaeRESVNEY----R 824
Cdd:COG1111    406 RFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRtGRKREGRvVVLIA-KGT----RDEAYYWssrrK 480

                          570       580
                   ....*....|....*....|....*...
gi 1696124467  825 EKMMSKAIDKVKK-LDQDEYEKRIKEFQ 851
Cdd:COG1111    481 EKKMKSILKKLKKlLDKQEKEKLKESAQ 508
CARD_MDA5_r2 cd08819
Caspase activation and recruitment domain found in MDA5, second repeat; Caspase activation and ...
 108-199 2.28e-48

Caspase activation and recruitment domain found in MDA5, second repeat; Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), second repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.


:

Pssm-ID: 260078  Cd Length: 92  Bit Score: 166.35  E-value: 2.28e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  108 NDNCVRLIELLSPSLLEMKTTDVCWDCFSKDILTAEDREIILAECQNRGNMGGARELLRRIVRFPPGWFSIFLKALQNTE 187
Cdd:cd08819      1 NDQCVRLIQLLQPTLVDMKTTDVCDKCLEKGLLTAEDRERILAATENHGNRSGARELLSRIVRQKEGWFSKFLQALRETE 80

                           90
                   ....*....|..
gi 1696124467  188 HKNLFKELTGES 199
Cdd:cd08819     81 HNNLAEELTGED 92
CARD_MDA5_r1 cd08818
Caspase activation and recruitment domain found in MDA5, first repeat; Caspase activation and ...
 7-99 2.29e-43

Caspase activation and recruitment domain found in MDA5, first repeat; Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), first repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.


:

Pssm-ID: 260077  Cd Length: 92  Bit Score: 152.07  E-value: 2.29e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467    7 NDANICLIEDFRPRLRKLIEVEFVLDHLNFLDNDNKDLIRTKARKESNLKAVDLLIDTIIRiRPLPNGWFREFVDALSAG 86
Cdd:cd08818      1 DENFLYLISCFRPRLKRLIVVEPVLDYLHFLSPEQKERIRQKARTEGNLAAADLLIDAVEK-GPHPPGWFREFVDALEQG 79

                           90
                   ....*....|...
gi 1696124467   87 GCKHAATYVEDSP 99
Cdd:cd08818     80 GCDLAARYVNPSL 92
 
Name Accession Description Interval E-value
DEXHc_RLR-2 cd18074
DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma ...
 307-521 2.11e-126

DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma differentiation-associated protein 5 or Mda5 and IFIH1) is a viral double-stranded RNA (dsRNA) receptor that shares sequence similarity and signaling pathways with RIG-I, yet plays essential functions in antiviral immunity through distinct specificity for viral RNA. RLR-2 recognizes the internal duplex structure, whereas RIG-I recognizes the terminus of dsRNA. RLR-2 uses direct protein-protein contacts to stack along dsRNA in a head-to-tail arrangement. The signaling domain (tandem CARD), which decorates the outside of the core RLR-2 filament, also has an intrinsic propensity to oligomerize into an elongated structure that activates the signaling adaptor, MAVS. RLR-2 uses long dsRNA as a signaling platform to cooperatively assemble the core filament, which in turn promotes stochastic assembly of the tandem CARD oligomers for signaling. LGP2 appears to positively and negatively regulate RLR-2 and RIG-I signaling, respectively. RLR-2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350832 [Multi-domain]  Cd Length: 216  Bit Score: 382.29  E-value: 2.11e-126
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  307 IVLRDYQMDVARPALEGKNIIICLPTGSGKTRVAVYITKEHLDSRRKEGRPGKVVVLVNKVPLVEQHYSTEFWKFLKNKY 386
Cdd:cd18074      1 LTLRDYQMEVAKPALEGKNIIICLPTGSGKTRVAVYITKDHLDKKRKASEPGKVIVLVNKVPLVEQHYRKEFNPFLKHWY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  387 KVERVSGDSQLKISFTDIVQKNDIVICTAQILENYLERAHSGDDDGIKLSDLSLIVIDECHHTQKGGVYNHIMIRYLKQK 466
Cdd:cd18074     81 QVIGLSGDSQLKISFPEVVKRYDVIICTAQILENSLLNATEEEDEGVQLSDFSLIIIDECHHTQKEAVYNNIMRRYLKQK 160

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1696124467  467 HKNAKLKKEQKDTVDIPQILGLTASPGVGGAKKIEKAEEHILRICANLDAYKIMT 521
Cdd:cd18074    161 IKNRKQKKENKPLIPLPQILGLTASPGVGGAKNNKKAEEHILKICANLDAFRIMT 215
MDA5_C cd15807
C-terminal domain of Melanoma differentiation-associated protein 5, a cytoplasmic viral RNA ...
 875-989 3.08e-60

C-terminal domain of Melanoma differentiation-associated protein 5, a cytoplasmic viral RNA receptor; Melanoma differentiation-associated protein 5 (MDA5) is also called Interferon-induced helicase C domain-containing protein 1 (IFIH1) or RIG-I-like receptor 2 (RLR-2). It is one of three members of the RLR family. RLRs are cytoplasmic RNA receptors that recognize non-self RNA and act as molecular sensors to detect viral pathogens. It has been shown to detect viruses from the Picornaviridae and Caliciviridae families. RLRs are characterized by a central DExD/H-box helicase domain and a C-terminal domain, both of which are responsible for binding viral RNA. The helicase domain catalyzes the unwinding of double stranded RNA in an ATP-dependent manner. RIG-I and MDA5 also contain two N-terminal caspase activation and recruitment domains (CARDs), which initiate downstream signaling upon viral RNA sensing.


Pssm-ID: 276945  Cd Length: 117  Bit Score: 201.18  E-value: 3.08e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  875 PSKVKFSCRSCNKPVCSGEDVEIIENMHRVNVTPQFKELFIQRENTSLVKRLLDYETNGFIACKDCGQRWGSMMLYRGIE 954
Cdd:cd15807      1 PSLITFLCKNCSVLVCSGEDIQVIEKMHHVNVTPEFKELYIKRENKALQEKLADYQTNGEIICKTCGQAWGTMMVHKGLE 80

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1696124467  955 CPCLHVKNFLVTYDE--KKKNINKWSELGIQLPAFDY 989
Cdd:cd15807     81 LPCLKIRNFVVTFKNnsTKKTYKKWVELPITFPAFDY 117
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
310-851 1.13e-51

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 194.56  E-value: 1.13e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  310 RDYQMDVARPALEgKNIIICLPTGSGKTRVAVYITKEHLDSRRkegrpGKVVVLVNKVPLVEQHYSTeFWKFLK-NKYKV 388
Cdd:COG1111      5 RLYQLNLAASALR-KNTLVVLPTGLGKTAVALLVIAERLHKKG-----GKVLFLAPTKPLVEQHAEF-FKEALNiPEDEI 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  389 ERVSGDSQLKISfTDIVQKNDIVICTAQILENYLERAHsgdddgIKLSDLSLIVIDECHHTQKGGVYNHIMIRYLKQKHK 468
Cdd:COG1111     78 VVFTGEVSPEKR-KELWEKARIIVATPQVIENDLIAGR------IDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKD 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  469 naklkkeqkdtvdiPQILGLTASPGvggaKKIEKAEEhilrICANLdaykimtgnlgenkkephkKIATAEERKE-DPfg 547
Cdd:COG1111    151 --------------PLILGMTASPG----SDEEKIEE----VCENL-------------------GIENVEVRTEeDP-- 187

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  548 DV---IKGImNAIHVHAELNPTC-------------------DLGTQNYEQWVV-QKEQNAAKEENQK------------ 592
Cdd:COG1111    188 DVapyVHDT-EVEWIRVELPEELkeirdllnevlddrlkklkELGVIVSTSPDLsKKDLLALQKKLQRrireddsegyra 266

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  593 VRVCAEHLR-QYneALYLGKTirmwDAFSFLDKYFdEELKKKvapEDEEAIIKTDTErflftLFKDSKV-KLQELAKLPQ 670
Cdd:COG1111    267 ISILAEALKlRH--ALELLET----QGVEALLRYL-ERLEEE---ARSSGGSKASKR-----LVSDPRFrKAMRLAEEAD 331

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  671 YENNSLAKLRTKILHEFTSREKARGIIFTKTRRSAIALAQWVQENskfeevGVKACHVIGGGGQSVVKPMTAAEQRDVLN 750
Cdd:COG1111    332 IEHPKLSKLREILKEQLGTNPDSRIIVFTQYRDTAEMIVEFLSEP------GIKAGRFVGQASKEGDKGLTQKEQIEILE 405

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  751 KFQNAEVNLLIATTVAEEGLDIAACNFVIRYELVTNEIAMIQARGR-GRAEDSS-YTLVAgEGSgvaeRESVNEY----R 824
Cdd:COG1111    406 RFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRtGRKREGRvVVLIA-KGT----RDEAYYWssrrK 480

                          570       580
                   ....*....|....*....|....*...
gi 1696124467  825 EKMMSKAIDKVKK-LDQDEYEKRIKEFQ 851
Cdd:COG1111    481 EKKMKSILKKLKKlLDKQEKEKLKESAQ 508
RIG-I_C-RD pfam11648
C-terminal domain of RIG-I; This family of proteins represents the regulatory domain RD of ...
 878-992 6.63e-50

C-terminal domain of RIG-I; This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependant dimerization. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity.


Pssm-ID: 463318  Cd Length: 117  Bit Score: 171.66  E-value: 6.63e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  878 VKFSCRSCNKPVCSGEDVEIIENMHRVNVTPQFKELFIQRENTSLVKRLLDYETNGFIACKDCGQRWGSMMLYRGIECPC 957
Cdd:pfam11648    1 VKLLCRKCKKFVCSGSDIRKIENSHHVVVNPDFKERYIVKEPHKKPKSFEDWEPGGKISCKKCGQDWGIMMKYKGVELPV 80

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1696124467  958 LHVKNFLVTYDEKK--KNINKWSELGIQLPAFDYAEH 992
Cdd:pfam11648   81 LKIKSFVVETPATGrrKTKKKWKDVPFEVPEFDYTEY 117
CARD_MDA5_r2 cd08819
Caspase activation and recruitment domain found in MDA5, second repeat; Caspase activation and ...
 108-199 2.28e-48

Caspase activation and recruitment domain found in MDA5, second repeat; Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), second repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.


Pssm-ID: 260078  Cd Length: 92  Bit Score: 166.35  E-value: 2.28e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  108 NDNCVRLIELLSPSLLEMKTTDVCWDCFSKDILTAEDREIILAECQNRGNMGGARELLRRIVRFPPGWFSIFLKALQNTE 187
Cdd:cd08819      1 NDQCVRLIQLLQPTLVDMKTTDVCDKCLEKGLLTAEDRERILAATENHGNRSGARELLSRIVRQKEGWFSKFLQALRETE 80

                           90
                   ....*....|..
gi 1696124467  188 HKNLFKELTGES 199
Cdd:cd08819     81 HNNLAEELTGED 92
PRK13766 PRK13766
Hef nuclease; Provisional
 304-930 1.24e-46

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 180.07  E-value: 1.24e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  304 KDVIVLRDYQMDVARPALEgKNIIICLPTGSGKTRVAVYITKEhldsrRKEGRPGKVVVLVNKVPLVEQHYSTeFWKFLK 383
Cdd:PRK13766    11 PNTIEARLYQQLLAATALK-KNTLVVLPTGLGKTAIALLVIAE-----RLHKKGGKVLILAPTKPLVEQHAEF-FRKFLN 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  384 nkykvervsGDSQLKISFT---------DIVQKNDIVICTAQILENYL--ERahsgdddgIKLSDLSLIVIDECHHTQKG 452
Cdd:PRK13766    84 ---------IPEEKIVVFTgevspekraELWEKAKVIVATPQVIENDLiaGR--------ISLEDVSLLIFDEAHRAVGN 146

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  453 GVYNHIMIRYLKQKHKnaklkkeqkdtvdiPQILGLTASPGvggakkieKAEEHILRICANL--DAYKIMTGN------- 523
Cdd:PRK13766   147 YAYVYIAERYHEDAKN--------------PLVLGLTASPG--------SDEEKIKEVCENLgiEHVEVRTEDdpdvkpy 204

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  524 LGENKKEPhKKIATAEERKEdpfgdvIKGIMNAIhVHAELNPTCDLG-TQNYEQWVVQKEQNAAKEE-NQKVR----VCA 597
Cdd:PRK13766   205 VHKVKIEW-VRVELPEELKE------IRDLLNEA-LKDRLKKLKELGvIVSISPDVSKKELLGLQKKlQQEIAnddsEGY 276

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  598 EHLRQYNEALYLGKTIRMWDA--FSFLDKYFDEELKKKVAPEDEEAiiktdTERflftLFKDSKV-KLQELAKLPQYENN 674
Cdd:PRK13766   277 EAISILAEAMKLRHAVELLETqgVEALRRYLERLREEARSSGGSKA-----SKR----LVEDPRFrKAVRKAKELDIEHP 347

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  675 SLAKLRTKILHEFTSREKARGIIFTKTRRSAIALAQWVQENskfeevGVKACHVIGGGGQSVVKPMTAAEQRDVLNKFQN 754
Cdd:PRK13766   348 KLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVDLLEKE------GIKAVRFVGQASKDGDKGMSQKEQIEILDKFRA 421

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  755 AEVNLLIATTVAEEGLDIAACNFVIRYELVTNEIAMIQARGR-GRAEDSS-YTLVAgEGSgvaeRES----VNEYREKMM 828
Cdd:PRK13766   422 GEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRtGRQEEGRvVVLIA-KGT----RDEayywSSRRKEKKM 496

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  829 SKAIDKVKKLDQDEYEKRIKEFQIQAIMEERVRTTKKKQKGMKKESPSKVKFSCRSCNKPVCSGEDVEIIENmhrvnvtp 908
Cdd:PRK13766   497 KEELKNLKGILNKKLQELDEEQKGEEEEKDEQLSLDDFVKSKGKEEEEEEEKEEKDKETEEDEPEGPKIIVD-------- 568

                          650       660
                   ....*....|....*....|..
gi 1696124467  909 qfkelfiQRENTSLVKRLLDYE 930
Cdd:PRK13766   569 -------SRELRSNVARHLKRL 583
CARD_MDA5_r1 cd08818
Caspase activation and recruitment domain found in MDA5, first repeat; Caspase activation and ...
 7-99 2.29e-43

Caspase activation and recruitment domain found in MDA5, first repeat; Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), first repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.


Pssm-ID: 260077  Cd Length: 92  Bit Score: 152.07  E-value: 2.29e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467    7 NDANICLIEDFRPRLRKLIEVEFVLDHLNFLDNDNKDLIRTKARKESNLKAVDLLIDTIIRiRPLPNGWFREFVDALSAG 86
Cdd:cd08818      1 DENFLYLISCFRPRLKRLIVVEPVLDYLHFLSPEQKERIRQKARTEGNLAAADLLIDAVEK-GPHPPGWFREFVDALEQG 79

                           90
                   ....*....|...
gi 1696124467   87 GCKHAATYVEDSP 99
Cdd:cd08818     80 GCDLAARYVNPSL 92
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 676-808 2.53e-40

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: 145.43  E-value: 2.53e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  676 LAKLRtKILHEFTSREK-ARGIIFTKTRRSAIALAQWVQENSKfEEVGVKACHVIGGG--GQSVVKPMTAAEQRDVLNKF 752
Cdd:cd18802      9 LQKLI-EILREYFPKTPdFRGIIFVERRATAVVLSRLLKEHPS-TLAFIRCGFLIGRGnsSQRKRSLMTQRKQKETLDKF 86

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1696124467  753 QNAEVNLLIATTVAEEGLDIAACNFVIRYELVTNEIAMIQARGRGRAEDSSYTLVA 808
Cdd:cd18802     87 RDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIG-I_C pfam18119
RIG-I receptor C-terminal domain; This is the C-terminal domain of Innate Immune ...
 532-666 3.13e-35

RIG-I receptor C-terminal domain; This is the C-terminal domain of Innate Immune Pattern-Recognition Receptor RIG-I present in homo sapiens. RIG-I is a key cytosolic pattern-recognition receptors of the vertebrate innate immune system that form the first line of defense against RNA viral infection. RNA binding to RIG-I is mediated both by the C-terminal domain and by the helicase domain. The C-terminal domain specifically binds the 5'triphosphate end with a 10-fold higher affinity compared to 5'OH-dsRNA.


Pssm-ID: 465656  Cd Length: 139  Bit Score: 130.92  E-value: 3.13e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  532 HKKIATAEERKEDPFGDVIKGIMNAIHVHAELN---------PTCDLGTQNYEQWVVQKEQNAAKEENQKVRVC----AE 598
Cdd:pfam18119    1 DKFVVKVTSRKEDPFGDIIKDIMSKIEDHLNKSynlddlsklKPSDKGTQKYEQWIVTLQKKGAEDPEEERRVCralcTE 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1696124467  599 HLRQYNEALYLGKTIRMWDAFSFLDKYFDEELKKKVAPedeeaiiktdTERFLFTLFKDSKVKLQELA 666
Cdd:pfam18119   81 HLRKYNDALIINDDARTKDALEYLLKFLKELKETKFDE----------TERKLYRLFEEKREELQRLA 138
DEXDc smart00487
DEAD-like helicases superfamily;
309-510 7.17e-26

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 106.04  E-value: 7.17e-26
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467   309 LRDYQMDVARPALEG-KNIIICLPTGSGKTRVAVYITKEHLdsrrKEGRPGKVVVLVNKVPLVEQHYSTEFWKFLKNKYK 387
Cdd:smart00487    9 LRPYQKEAIEALLSGlRDVILAAPTGSGKTLAALLPALEAL----KRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLK 84

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467   388 VERVSGDSQLKISFTDIVQKN-DIVICTAQILENYLERahsgddDGIKLSDLSLIVIDECHHTqKGGVYNHIMIRYLKQK 466
Cdd:smart00487   85 VVGLYGGDSKREQLRKLESGKtDILVTTPGRLLDLLEN------DKLSLSNVDLVILDEAHRL-LDGGFGDQLEKLLKLL 157

                           170       180       190       200
                    ....*....|....*....|....*....|....*....|....
gi 1696124467   467 HKNaklkkeqkdtvdiPQILGLTASPGVGGAKKIEKAEEHILRI 510
Cdd:smart00487  158 PKN-------------VQLLLLSATPPEEIENLLELFLNDPVFI 188
CARD_2 pfam16739
Caspase recruitment domain; In the probable ATP-dependent RNA helicase DDX58 this CARD domain ...
 107-199 4.71e-23

Caspase recruitment domain; In the probable ATP-dependent RNA helicase DDX58 this CARD domain is found near the N-terminus and interacts with the C-terminal domain.


Pssm-ID: 465251  Cd Length: 93  Bit Score: 94.20  E-value: 4.71e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  107 ENDNCVRLIELLSPSLLE-MKTTDVCWDCfsKDILTAEDREIILAECQNRGNMGGARELLRRIVR-FPPGWFSIFLKALQ 184
Cdd:pfam16739    1 EDDEYRRLLRLFRPRLKDtIKPTEILPHL--PECLTEDDKERIRAETNNKGNTAAAELLLDRLVRsDREGWFRAFLDALR 78

                           90
                   ....*....|....*
gi 1696124467  185 NTEHKNLFKELTGES 199
Cdd:pfam16739   79 KTGHDGLAEELEGEY 93
ResIII pfam04851
Type III restriction enzyme, res subunit;
307-492 1.84e-17

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 80.79  E-value: 1.84e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  307 IVLRDYQMDVARPALEG-----KNIIICLPTGSGKTRVAVYITKEhldsRRKEGRPGKVVVLVNKVPLVEQHYStEFWKF 381
Cdd:pfam04851    2 LELRPYQIEAIENLLESikngqKRGLIVMATGSGKTLTAAKLIAR----LFKKGPIKKVLFLVPRKDLLEQALE-EFKKF 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  382 LKNKYKV-ERVSGDSQLKisftdIVQKNDIVICTAQ----ILENYLERAHSGDDDgiklsdlsLIVIDECHHTQKGGvYN 456
Cdd:pfam04851   77 LPNYVEIgEIISGDKKDE-----SVDDNKIVVTTIQslykALELASLELLPDFFD--------VIIIDEAHRSGASS-YR 142

                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 1696124467  457 HImIRYLKQKHknaklkkeqkdtvdipqILGLTASP 492
Cdd:pfam04851  143 NI-LEYFKPAF-----------------LLGLTATP 160
CARD_2 pfam16739
Caspase recruitment domain; In the probable ATP-dependent RNA helicase DDX58 this CARD domain ...
 13-99 2.84e-17

Caspase recruitment domain; In the probable ATP-dependent RNA helicase DDX58 this CARD domain is found near the N-terminus and interacts with the C-terminal domain.


Pssm-ID: 465251  Cd Length: 93  Bit Score: 77.63  E-value: 2.84e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467   13 LIEDFRPRLRKLIEVEFVLDHL-NFLDNDNKDLIRTKARKESNLKAVDLLIDTIIRIRPLpnGWFREFVDALSAGGCKHA 91
Cdd:pfam16739    8 LLRLFRPRLKDTIKPTEILPHLpECLTEDDKERIRAETNNKGNTAAAELLLDRLVRSDRE--GWFRAFLDALRKTGHDGL 85


                   ....*...
gi 1696124467   92 ATYVEDSP 99
Cdd:pfam16739   86 AEELEGEY 93
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
321-500 3.32e-13

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 73.39  E-value: 3.32e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  321 LEGKNIIICLPTGSGKTRVAVYITKEHLDsrrkegRPGKVVVLvnkVP---LVEQHYStEFWKFLKNK-YKVERVSGDSQ 396
Cdd:COG1204     36 LEGKNLVVSAPTASGKTLIAELAILKALL------NGGKALYI---VPlraLASEKYR-EFKRDFEELgIKVGVSTGDYD 105

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  397 LKIsftDIVQKNDIVICTAqilenylERAHSGDDDGIK-LSDLSLIVIDECHH---TQKGGVYNHIMirylkqkhknAKL 472
Cdd:COG1204    106 SDD---EWLGRYDILVATP-------EKLDSLLRNGPSwLRDVDLVVVDEAHLiddESRGPTLEVLL----------ARL 165

                          170       180
                   ....*....|....*....|....*...
gi 1696124467  473 KKEQKDtvdiPQILGLtaSPGVGGAKKI 500
Cdd:COG1204    166 RRLNPE----AQIVAL--SATIGNAEEI 187
HELICc smart00490
helicase superfamily c-terminal domain;
717-799 4.69e-13

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 65.31  E-value: 4.69e-13
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467   717 KFEEVGVKACHVIGGggqsvvkpMTAAEQRDVLNKFQNAEVNLLIATTVAEEGLDIAACNFVIRYELVTNEIAMIQARGR 796
Cdd:smart00490    6 LLKELGIKVARLHGG--------LSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGR 77


                    ....
gi 1696124467   797 -GRA 799
Cdd:smart00490   78 aGRA 81
PRK00254 PRK00254
ski2-like helicase; Provisional
 320-493 1.92e-07

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 55.21  E-value: 1.92e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  320 ALEGKNIIICLPTGSGKTRVAVYITKEHLdsrRKEGrpGKVVVLVNKVPLVEQHYStEFWKFLKNKYKVERVSGDSQlki 399
Cdd:PRK00254    36 VLEGKNLVLAIPTASGKTLVAEIVMVNKL---LREG--GKAVYLVPLKALAEEKYR-EFKDWEKLGLRVAMTTGDYD--- 106

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  400 SFTDIVQKNDIVICTAQILENYLERAHSGdddgikLSDLSLIVIDECHhtqkggvynhimirYLKQKHKNAKLKKEQKDT 479
Cdd:PRK00254   107 STDEWLGKYDIIIATAEKFDSLLRHGSSW------IKDVKLVVADEIH--------------LIGSYDRGATLEMILTHM 166

                          170
                   ....*....|....
gi 1696124467  480 VDIPQILGLTASPG 493
Cdd:PRK00254   167 LGRAQILGLSATVG 180
 
Name Accession Description Interval E-value
DEXHc_RLR-2 cd18074
DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma ...
 307-521 2.11e-126

DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma differentiation-associated protein 5 or Mda5 and IFIH1) is a viral double-stranded RNA (dsRNA) receptor that shares sequence similarity and signaling pathways with RIG-I, yet plays essential functions in antiviral immunity through distinct specificity for viral RNA. RLR-2 recognizes the internal duplex structure, whereas RIG-I recognizes the terminus of dsRNA. RLR-2 uses direct protein-protein contacts to stack along dsRNA in a head-to-tail arrangement. The signaling domain (tandem CARD), which decorates the outside of the core RLR-2 filament, also has an intrinsic propensity to oligomerize into an elongated structure that activates the signaling adaptor, MAVS. RLR-2 uses long dsRNA as a signaling platform to cooperatively assemble the core filament, which in turn promotes stochastic assembly of the tandem CARD oligomers for signaling. LGP2 appears to positively and negatively regulate RLR-2 and RIG-I signaling, respectively. RLR-2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350832 [Multi-domain]  Cd Length: 216  Bit Score: 382.29  E-value: 2.11e-126
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  307 IVLRDYQMDVARPALEGKNIIICLPTGSGKTRVAVYITKEHLDSRRKEGRPGKVVVLVNKVPLVEQHYSTEFWKFLKNKY 386
Cdd:cd18074      1 LTLRDYQMEVAKPALEGKNIIICLPTGSGKTRVAVYITKDHLDKKRKASEPGKVIVLVNKVPLVEQHYRKEFNPFLKHWY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  387 KVERVSGDSQLKISFTDIVQKNDIVICTAQILENYLERAHSGDDDGIKLSDLSLIVIDECHHTQKGGVYNHIMIRYLKQK 466
Cdd:cd18074     81 QVIGLSGDSQLKISFPEVVKRYDVIICTAQILENSLLNATEEEDEGVQLSDFSLIIIDECHHTQKEAVYNNIMRRYLKQK 160

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1696124467  467 HKNAKLKKEQKDTVDIPQILGLTASPGVGGAKKIEKAEEHILRICANLDAYKIMT 521
Cdd:cd18074    161 IKNRKQKKENKPLIPLPQILGLTASPGVGGAKNNKKAEEHILKICANLDAFRIMT 215
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 307-521 9.20e-89

DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350794 [Multi-domain]  Cd Length: 204  Bit Score: 282.44  E-value: 9.20e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  307 IVLRDYQMDVARPALEGKNIIICLPTGSGKTRVAVYITKEHLDSRRKEGRPGKVVVLVNKVPLVEQHySTEFWKFLKNKY 386
Cdd:cd18036      1 LELRNYQLELVLPALRGKNTIICAPTGSGKTRVAVYICRHHLEKRRSAGEKGRVVVLVNKVPLVEQQ-LEKFFKYFRKGY 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  387 KVERVSGDSQLKISFTDIVQKNDIVICTAQILENYLERAHSGDDdgIKLSDLSLIVIDECHHTQKGGVYNHIMIRYLKQK 466
Cdd:cd18036     80 KVTGLSGDSSHKVSFGQIVKASDVIICTPQILINNLLSGREEER--VYLSDFSLLIFDECHHTQKEHPYNKIMRMYLDKK 157

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1696124467  467 hknaklkkeQKDTVDIPQILGLTASPGVGGAKKIEKAEEHILRICANLDAYKIMT 521
Cdd:cd18036    158 ---------LSSQGPLPQILGLTASPGVGGARSFEEALEHILKLCANLDASVIAT 203
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 309-521 6.27e-84

DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350685 [Multi-domain]  Cd Length: 201  Bit Score: 269.30  E-value: 6.27e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  309 LRDYQMDVARPALEGKNIIICLPTGSGKTRVAVYITKEHLDSRRkEGRPGKVVVLVNKVPLVEQHYSTEFWKFLKNKYKV 388
Cdd:cd17927      3 PRNYQLELAQPALKGKNTIICLPTGSGKTFVAVLICEHHLKKFP-AGRKGKVVFLANKVPLVEQQKEVFRKHFERPGYKV 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  389 ERVSGDSQLKISFTDIVQKNDIVICTAQILENYLErahSGDDdgIKLSDLSLIVIDECHHTQKGGVYNHIMIRYLKQKHK 468
Cdd:cd17927     82 TGLSGDTSENVSVEQIVESSDVIIVTPQILVNDLK---SGTI--VSLSDFSLLVFDECHNTTKNHPYNEIMFRYLDQKLG 156

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1696124467  469 NAKlkkeqkdtvDIPQILGLTASPGVGGAKKIEKAEEHILRICANLDAYKIMT 521
Cdd:cd17927    157 SSG---------PLPQILGLTASPGVGGAKNTEEALEHICKLCANLDISVIAT 200
DEXHc_RLR-3 cd18075
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ...
 309-521 6.72e-77

DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of genetics and physiology 2 or LGP2 and DHX58) appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. RLR-3 resembles a chimera combining a MDA5-like helicase domain and RIG-I like CTD supporting both stem and end binding. RNA binding is required for RLR-3-mediated enhancement of MDA5 activation. RLR-3 end-binding may promote nucleation of MDA5 oligomerization on dsRNA. RLR-3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350833 [Multi-domain]  Cd Length: 200  Bit Score: 250.16  E-value: 6.72e-77
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  309 LRDYQMDVARPALEGKNIIICLPTGSGKTRVAVYITKEHLDSRRKegrpGKVVVLVNKVPLVEQHYSTEFWKFLKnKYKV 388
Cdd:cd18075      3 LHGYQWEVVAPALRGKNSIIWLPTGAGKTRAAVYVARRHLETKRG----AKVAVLVNKVHLVDQHLEKEFHVLLD-KYTV 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  389 ERVSGDSQLKISFTDIVQKNDIVICTAQILENYLErahSGDDDG-IKLSDLSLIVIDECHHTQKGGVYNHIMIRYLKQKh 467
Cdd:cd18075     78 TAISGDSSHKCFFGQLARGSDVVICTAQILQNALL---SGEEEAhVELTDFSLLVIDECHHTHKEAVYNKIMLSYLEKK- 153

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1696124467  468 knakLKKEQkdtvDIPQILGLTASPGVGGAKKIEKAEEHILRICANLDAYKIMT 521
Cdd:cd18075    154 ----LSRQG----DLPQILGLTASPGTGGATSFDGAVEHILQICANLDTWVIMS 199
MDA5_C cd15807
C-terminal domain of Melanoma differentiation-associated protein 5, a cytoplasmic viral RNA ...
 875-989 3.08e-60

C-terminal domain of Melanoma differentiation-associated protein 5, a cytoplasmic viral RNA receptor; Melanoma differentiation-associated protein 5 (MDA5) is also called Interferon-induced helicase C domain-containing protein 1 (IFIH1) or RIG-I-like receptor 2 (RLR-2). It is one of three members of the RLR family. RLRs are cytoplasmic RNA receptors that recognize non-self RNA and act as molecular sensors to detect viral pathogens. It has been shown to detect viruses from the Picornaviridae and Caliciviridae families. RLRs are characterized by a central DExD/H-box helicase domain and a C-terminal domain, both of which are responsible for binding viral RNA. The helicase domain catalyzes the unwinding of double stranded RNA in an ATP-dependent manner. RIG-I and MDA5 also contain two N-terminal caspase activation and recruitment domains (CARDs), which initiate downstream signaling upon viral RNA sensing.


Pssm-ID: 276945  Cd Length: 117  Bit Score: 201.18  E-value: 3.08e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  875 PSKVKFSCRSCNKPVCSGEDVEIIENMHRVNVTPQFKELFIQRENTSLVKRLLDYETNGFIACKDCGQRWGSMMLYRGIE 954
Cdd:cd15807      1 PSLITFLCKNCSVLVCSGEDIQVIEKMHHVNVTPEFKELYIKRENKALQEKLADYQTNGEIICKTCGQAWGTMMVHKGLE 80

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1696124467  955 CPCLHVKNFLVTYDE--KKKNINKWSELGIQLPAFDY 989
Cdd:cd15807     81 LPCLKIRNFVVTFKNnsTKKTYKKWVELPITFPAFDY 117
DEXHc_RIG-I_DDX58 cd18073
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ...
 309-521 6.67e-57

DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called DEAD box protein 58 (DDX58), is a pathogen-recognition receptor that recognizes viral 5'-triphosphates carrying double-stranded RNA. Upon binding to these microbe-associated molecular patterns (MAMPs), RIG-I forms oligomers and promotes downstream processes that result in type I interferon production and induction of an antiviral state. The optimal ligand for RIG-I has been found to be base-paired or double-stranded RNA (dsRNA) molecules containing a 5' triphosphate (5'-ppp-dsRNA). RIG-I contains two N-terminal caspase activation and recruitment domains (CARDs), which are required for interaction with IPS-1, a superfamily 2 helicase/translocase/ATPase (SF2) domain and a C-terminal regulatory/repressor domain (RD). RIG-I is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350831 [Multi-domain]  Cd Length: 202  Bit Score: 195.04  E-value: 6.67e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  309 LRDYQMDVARPALEGKNIIICLPTGSGKTRVAVYITKEHLDsRRKEGRPGKVVVLVNKVPLVEQHYSTEFWKFLKNKYKV 388
Cdd:cd18073      3 PRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLK-KFPQGQKGKVVFFATKVPVYEQQKSVFSKYFERHGYRV 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  389 ERVSGDSQLKISFTDIVQKNDIVICTAQILENYLERAHSGdddgiKLSDLSLIVIDECHHTQKGGVYNHIMIRYLKQKHK 468
Cdd:cd18073     82 TGISGATAENVPVEQIIENNDIIILTPQILVNNLKKGTIP-----SLSIFTLMIFDECHNTSGNHPYNMIMFRYLDQKLG 156

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1696124467  469 NAklkkeqkdTVDIPQILGLTASPGVGGAKKIEKAEEHILRICANLDAYKIMT 521
Cdd:cd18073    157 GS--------SGPLPQIIGLTASVGVGDAKNTDEALDYICKLCASLDASVIAT 201
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
310-851 1.13e-51

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 194.56  E-value: 1.13e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  310 RDYQMDVARPALEgKNIIICLPTGSGKTRVAVYITKEHLDSRRkegrpGKVVVLVNKVPLVEQHYSTeFWKFLK-NKYKV 388
Cdd:COG1111      5 RLYQLNLAASALR-KNTLVVLPTGLGKTAVALLVIAERLHKKG-----GKVLFLAPTKPLVEQHAEF-FKEALNiPEDEI 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  389 ERVSGDSQLKISfTDIVQKNDIVICTAQILENYLERAHsgdddgIKLSDLSLIVIDECHHTQKGGVYNHIMIRYLKQKHK 468
Cdd:COG1111     78 VVFTGEVSPEKR-KELWEKARIIVATPQVIENDLIAGR------IDLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDAKD 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  469 naklkkeqkdtvdiPQILGLTASPGvggaKKIEKAEEhilrICANLdaykimtgnlgenkkephkKIATAEERKE-DPfg 547
Cdd:COG1111    151 --------------PLILGMTASPG----SDEEKIEE----VCENL-------------------GIENVEVRTEeDP-- 187

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  548 DV---IKGImNAIHVHAELNPTC-------------------DLGTQNYEQWVV-QKEQNAAKEENQK------------ 592
Cdd:COG1111    188 DVapyVHDT-EVEWIRVELPEELkeirdllnevlddrlkklkELGVIVSTSPDLsKKDLLALQKKLQRrireddsegyra 266

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  593 VRVCAEHLR-QYneALYLGKTirmwDAFSFLDKYFdEELKKKvapEDEEAIIKTDTErflftLFKDSKV-KLQELAKLPQ 670
Cdd:COG1111    267 ISILAEALKlRH--ALELLET----QGVEALLRYL-ERLEEE---ARSSGGSKASKR-----LVSDPRFrKAMRLAEEAD 331

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  671 YENNSLAKLRTKILHEFTSREKARGIIFTKTRRSAIALAQWVQENskfeevGVKACHVIGGGGQSVVKPMTAAEQRDVLN 750
Cdd:COG1111    332 IEHPKLSKLREILKEQLGTNPDSRIIVFTQYRDTAEMIVEFLSEP------GIKAGRFVGQASKEGDKGLTQKEQIEILE 405

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  751 KFQNAEVNLLIATTVAEEGLDIAACNFVIRYELVTNEIAMIQARGR-GRAEDSS-YTLVAgEGSgvaeRESVNEY----R 824
Cdd:COG1111    406 RFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRtGRKREGRvVVLIA-KGT----RDEAYYWssrrK 480

                          570       580
                   ....*....|....*....|....*...
gi 1696124467  825 EKMMSKAIDKVKK-LDQDEYEKRIKEFQ 851
Cdd:COG1111    481 EKKMKSILKKLKKlLDKQEKEKLKESAQ 508
RIG-I_C-RD pfam11648
C-terminal domain of RIG-I; This family of proteins represents the regulatory domain RD of ...
 878-992 6.63e-50

C-terminal domain of RIG-I; This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependant dimerization. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity.


Pssm-ID: 463318  Cd Length: 117  Bit Score: 171.66  E-value: 6.63e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  878 VKFSCRSCNKPVCSGEDVEIIENMHRVNVTPQFKELFIQRENTSLVKRLLDYETNGFIACKDCGQRWGSMMLYRGIECPC 957
Cdd:pfam11648    1 VKLLCRKCKKFVCSGSDIRKIENSHHVVVNPDFKERYIVKEPHKKPKSFEDWEPGGKISCKKCGQDWGIMMKYKGVELPV 80

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1696124467  958 LHVKNFLVTYDEKK--KNINKWSELGIQLPAFDYAEH 992
Cdd:pfam11648   81 LKIKSFVVETPATGrrKTKKKWKDVPFEVPEFDYTEY 117
CARD_MDA5_r2 cd08819
Caspase activation and recruitment domain found in MDA5, second repeat; Caspase activation and ...
 108-199 2.28e-48

Caspase activation and recruitment domain found in MDA5, second repeat; Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), second repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.


Pssm-ID: 260078  Cd Length: 92  Bit Score: 166.35  E-value: 2.28e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  108 NDNCVRLIELLSPSLLEMKTTDVCWDCFSKDILTAEDREIILAECQNRGNMGGARELLRRIVRFPPGWFSIFLKALQNTE 187
Cdd:cd08819      1 NDQCVRLIQLLQPTLVDMKTTDVCDKCLEKGLLTAEDRERILAATENHGNRSGARELLSRIVRQKEGWFSKFLQALRETE 80

                           90
                   ....*....|..
gi 1696124467  188 HKNLFKELTGES 199
Cdd:cd08819     81 HNNLAEELTGED 92
PRK13766 PRK13766
Hef nuclease; Provisional
 304-930 1.24e-46

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 180.07  E-value: 1.24e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  304 KDVIVLRDYQMDVARPALEgKNIIICLPTGSGKTRVAVYITKEhldsrRKEGRPGKVVVLVNKVPLVEQHYSTeFWKFLK 383
Cdd:PRK13766    11 PNTIEARLYQQLLAATALK-KNTLVVLPTGLGKTAIALLVIAE-----RLHKKGGKVLILAPTKPLVEQHAEF-FRKFLN 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  384 nkykvervsGDSQLKISFT---------DIVQKNDIVICTAQILENYL--ERahsgdddgIKLSDLSLIVIDECHHTQKG 452
Cdd:PRK13766    84 ---------IPEEKIVVFTgevspekraELWEKAKVIVATPQVIENDLiaGR--------ISLEDVSLLIFDEAHRAVGN 146

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  453 GVYNHIMIRYLKQKHKnaklkkeqkdtvdiPQILGLTASPGvggakkieKAEEHILRICANL--DAYKIMTGN------- 523
Cdd:PRK13766   147 YAYVYIAERYHEDAKN--------------PLVLGLTASPG--------SDEEKIKEVCENLgiEHVEVRTEDdpdvkpy 204

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  524 LGENKKEPhKKIATAEERKEdpfgdvIKGIMNAIhVHAELNPTCDLG-TQNYEQWVVQKEQNAAKEE-NQKVR----VCA 597
Cdd:PRK13766   205 VHKVKIEW-VRVELPEELKE------IRDLLNEA-LKDRLKKLKELGvIVSISPDVSKKELLGLQKKlQQEIAnddsEGY 276

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  598 EHLRQYNEALYLGKTIRMWDA--FSFLDKYFDEELKKKVAPEDEEAiiktdTERflftLFKDSKV-KLQELAKLPQYENN 674
Cdd:PRK13766   277 EAISILAEAMKLRHAVELLETqgVEALRRYLERLREEARSSGGSKA-----SKR----LVEDPRFrKAVRKAKELDIEHP 347

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  675 SLAKLRTKILHEFTSREKARGIIFTKTRRSAIALAQWVQENskfeevGVKACHVIGGGGQSVVKPMTAAEQRDVLNKFQN 754
Cdd:PRK13766   348 KLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVDLLEKE------GIKAVRFVGQASKDGDKGMSQKEQIEILDKFRA 421

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  755 AEVNLLIATTVAEEGLDIAACNFVIRYELVTNEIAMIQARGR-GRAEDSS-YTLVAgEGSgvaeRES----VNEYREKMM 828
Cdd:PRK13766   422 GEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRtGRQEEGRvVVLIA-KGT----RDEayywSSRRKEKKM 496

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  829 SKAIDKVKKLDQDEYEKRIKEFQIQAIMEERVRTTKKKQKGMKKESPSKVKFSCRSCNKPVCSGEDVEIIENmhrvnvtp 908
Cdd:PRK13766   497 KEELKNLKGILNKKLQELDEEQKGEEEEKDEQLSLDDFVKSKGKEEEEEEEKEEKDKETEEDEPEGPKIIVD-------- 568

                          650       660
                   ....*....|....*....|..
gi 1696124467  909 qfkelfiQRENTSLVKRLLDYE 930
Cdd:PRK13766   569 -------SRELRSNVARHLKRL 583
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 309-517 9.09e-45

DEXH-box helicase domain of 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. Dicers exist throughout eukaryotes, and a subset have 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 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350792 [Multi-domain]  Cd Length: 200  Bit Score: 160.51  E-value: 9.09e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  309 LRDYQMDVARPALEgKNIIICLPTGSGKTRVAVYITKEHLDSRRKEGRPGKVVV-LVNKVPLVEQHYstefwKFLKN--K 385
Cdd:cd18034      3 PRSYQLELFEAALK-RNTIVVLPTGSGKTLIAVMLIKEMGELNRKEKNPKKRAVfLVPTVPLVAQQA-----EAIRShtD 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  386 YKVERVSG----DSQLKISFTDIVQKNDIVICTAQILENYLERAHsgdddgIKLSDLSLIVIDECHHTQKGGVYNHIMir 461
Cdd:cd18034     77 LKVGEYSGemgvDKWTKERWKEELEKYDVLVMTAQILLDALRHGF------LSLSDINLLIFDECHHATGDHPYARIM-- 148

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1696124467  462 ylkQKHKNAKLKKEQkdtvdiPQILGLTASPgVGGAKKIEKAEEHILRICANLDAY 517
Cdd:cd18034    149 ---KEFYHLEGRTSR------PRILGLTASP-VNGKGDPKSVEKKIQQLEELLNST 194
CARD_MDA5_r1 cd08818
Caspase activation and recruitment domain found in MDA5, first repeat; Caspase activation and ...
 7-99 2.29e-43

Caspase activation and recruitment domain found in MDA5, first repeat; Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), first repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.


Pssm-ID: 260077  Cd Length: 92  Bit Score: 152.07  E-value: 2.29e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467    7 NDANICLIEDFRPRLRKLIEVEFVLDHLNFLDNDNKDLIRTKARKESNLKAVDLLIDTIIRiRPLPNGWFREFVDALSAG 86
Cdd:cd08818      1 DENFLYLISCFRPRLKRLIVVEPVLDYLHFLSPEQKERIRQKARTEGNLAAADLLIDAVEK-GPHPPGWFREFVDALEQG 79

                           90
                   ....*....|...
gi 1696124467   87 GCKHAATYVEDSP 99
Cdd:cd08818     80 GCDLAARYVNPSL 92
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 676-808 2.53e-40

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: 145.43  E-value: 2.53e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  676 LAKLRtKILHEFTSREK-ARGIIFTKTRRSAIALAQWVQENSKfEEVGVKACHVIGGG--GQSVVKPMTAAEQRDVLNKF 752
Cdd:cd18802      9 LQKLI-EILREYFPKTPdFRGIIFVERRATAVVLSRLLKEHPS-TLAFIRCGFLIGRGnsSQRKRSLMTQRKQKETLDKF 86

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1696124467  753 QNAEVNLLIATTVAEEGLDIAACNFVIRYELVTNEIAMIQARGRGRAEDSSYTLVA 808
Cdd:cd18802     87 RDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
MDA5_ID cd12090
Insert domain of MDA5; MDA5 (melanoma-differentiation-associated gene 5, also known as IFIH1), ...
 544-669 8.81e-36

Insert domain of MDA5; MDA5 (melanoma-differentiation-associated gene 5, also known as IFIH1), as well as RIG-I (Retinoic acid Inducible Gene I, also known as DDX58) and LPG2 (also known as DHX58), contain two N-terminal CARD domains and a C-terminal SF2 helicase domain. They are cytoplasmic DEAD box RNA helicases acting as key innate immune pattern-recognition receptor (PRRs) that play an important role in host antiviral response by sensing incoming viral RNA. Their SF2 helicase domain is comprised of 3 structural domains, the 2 generally conserved helicase domains and a helical domain inserted between the two domains. The inserted domain is involved in conformational changes upon ligand binding.


Pssm-ID: 277189  Cd Length: 120  Bit Score: 131.67  E-value: 8.81e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  544 DPFGDVIKGIMNAIHVHAEL----NPTCDLGTQNYEQWVVQKEQNAAKEENQKVRVCAEHLRQYNEALYLGKTIRMWDAF 619
Cdd:cd12090      1 DPFGDIIKKLMTDIEELLKMtppdIQPREFGTQKYEQWVVTLEKKAAKLGNRALRTCAEHLRKYNDALLINDTARMKDAL 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 1696124467  620 SFLDKYFDEElkkKVAPEDEeaiiktdTERFLFTLFKDSKVKLQELAKLP 669
Cdd:cd12090     81 QYLKEFYTNL---KEAKFDE-------TERFLTDLFEENLEELKKLARDP 120
RIG-I_C pfam18119
RIG-I receptor C-terminal domain; This is the C-terminal domain of Innate Immune ...
 532-666 3.13e-35

RIG-I receptor C-terminal domain; This is the C-terminal domain of Innate Immune Pattern-Recognition Receptor RIG-I present in homo sapiens. RIG-I is a key cytosolic pattern-recognition receptors of the vertebrate innate immune system that form the first line of defense against RNA viral infection. RNA binding to RIG-I is mediated both by the C-terminal domain and by the helicase domain. The C-terminal domain specifically binds the 5'triphosphate end with a 10-fold higher affinity compared to 5'OH-dsRNA.


Pssm-ID: 465656  Cd Length: 139  Bit Score: 130.92  E-value: 3.13e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  532 HKKIATAEERKEDPFGDVIKGIMNAIHVHAELN---------PTCDLGTQNYEQWVVQKEQNAAKEENQKVRVC----AE 598
Cdd:pfam18119    1 DKFVVKVTSRKEDPFGDIIKDIMSKIEDHLNKSynlddlsklKPSDKGTQKYEQWIVTLQKKGAEDPEEERRVCralcTE 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1696124467  599 HLRQYNEALYLGKTIRMWDAFSFLDKYFDEELKKKVAPedeeaiiktdTERFLFTLFKDSKVKLQELA 666
Cdd:pfam18119   81 HLRKYNDALIINDDARTKDALEYLLKFLKELKETKFDE----------TERKLYRLFEEKREELQRLA 138
LGP2_C cd15806
C-terminal domain of Laboratory of Genetics and Physiology 2 (LGP2), a cytoplasmic viral RNA ...
 878-989 9.41e-30

C-terminal domain of Laboratory of Genetics and Physiology 2 (LGP2), a cytoplasmic viral RNA receptor; Laboratory of Genetics and Physiology 2 (LGP2) is one of three members of the RIG-I-like Receptor (RLR) family. RLRs are cytoplasmic RNA receptors that recognize non-self RNA and act as molecular sensors to detect viral pathogens. They are characterized by a central DExD/H-box helicase domain and a C-terminal domain, both of which are responsible for binding viral RNA. LGP2 lacks the caspase activation and recruitment domains (CARDs) that are present in other RLRs, which initiate downstream signaling upon viral RNA sensing. LGP2 may play a regulatory role in RLR signaling, and may cooperate with either RIG-I or MDA5 to sense viral RNA.


Pssm-ID: 276944  Cd Length: 112  Bit Score: 114.05  E-value: 9.41e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  878 VKFSCRSCNKPVCSGEDVEIIENMHRVNVTPQFKELFIQRENTSLVKRLLDYETNGFIACKDCGQRWGSMMLYRGIECPC 957
Cdd:cd15806      1 VQLLCRNCFVAVAHGSDLRKVEGTHHVNINPNFSRYYKVGGKPILIRTFEDWEPGGTISCSNCGQVWGMEMIYKSVLLPV 80

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1696124467  958 LHVKNFLVTYDEKKKNINKWSELGIQLPAFDY 989
Cdd:cd15806     81 LSIKNFVLETPEGRRQAKKWKDVPFSVEEFDF 112
RLR_C cd15804
C-terminal domain of Retinoic acid-inducible gene (RIG)-I-like Receptors; Retinoic ...
 878-987 1.22e-27

C-terminal domain of Retinoic acid-inducible gene (RIG)-I-like Receptors; Retinoic acid-inducible gene (RIG)-I-like Receptors (RLRs) are cytoplasmic RNA receptors that recognize non-self RNA and act as molecular sensors to detect viral pathogens. They play crucial roles in innate antiviral responses, including the production of proinflammatory cytokines and type I interferon. There are three RLRs in vertebrates, RIG-I, LGP2, and MDA5. They are characterized by a central DExD/H-box helicase domain and a C-terminal domain, both of which are responsible for binding viral RNA. The helicase domain catalyzes the unwinding of double stranded RNA in an ATP-dependent manner. RIG-I and MDA5 also contain two N-terminal caspase activation and recruitment domains (CARDs), which initiate downstream signaling upon viral RNA sensing. They may detect partially overlapping viral substrates, including dengue virus, West Nile virus (WNV), reoviruses, and several paramyxoviruses (such as measles virus and Sendai virus). LGP2 lacks CARD and may play a regulatory role in RLR signaling. It may cooperate with either RIG-I or MDA5 to sense viral RNA.


Pssm-ID: 276942  Cd Length: 111  Bit Score: 108.17  E-value: 1.22e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  878 VKFSCRSCNKPVCSGEDVEIIENMHRVNVTPQFKELFIQRENTSLVKRLLDYETNGFIACKDCGQRWGSMMLYRGIECPC 957
Cdd:cd15804      1 FTLLCKKCSAFACNSDDIRKIEGSHHVVIDPDFLERVKIEEDPKKKKKFEDTQILGKIKCKKCGHDWGTMMKYKGVELPV 80

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1696124467  958 LHVKNF-LVTYDEKKKNINKWSELGIQLPAF 987
Cdd:cd15804     81 LKIKNFvFVDEDEERATKKKWKDVPFAIPEI 111
DEXDc smart00487
DEAD-like helicases superfamily;
309-510 7.17e-26

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 106.04  E-value: 7.17e-26
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467   309 LRDYQMDVARPALEG-KNIIICLPTGSGKTRVAVYITKEHLdsrrKEGRPGKVVVLVNKVPLVEQHYSTEFWKFLKNKYK 387
Cdd:smart00487    9 LRPYQKEAIEALLSGlRDVILAAPTGSGKTLAALLPALEAL----KRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLK 84

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467   388 VERVSGDSQLKISFTDIVQKN-DIVICTAQILENYLERahsgddDGIKLSDLSLIVIDECHHTqKGGVYNHIMIRYLKQK 466
Cdd:smart00487   85 VVGLYGGDSKREQLRKLESGKtDILVTTPGRLLDLLEN------DKLSLSNVDLVILDEAHRL-LDGGFGDQLEKLLKLL 157

                           170       180       190       200
                    ....*....|....*....|....*....|....*....|....
gi 1696124467   467 HKNaklkkeqkdtvdiPQILGLTASPGVGGAKKIEKAEEHILRI 510
Cdd:smart00487  158 PKN-------------VQLLLLSATPPEEIENLLELFLNDPVFI 188
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 323-490 4.24e-23

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


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 96.32  E-value: 4.24e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  323 GKNIIICLPTGSGKTRVAVYITKEHLDSRRKegrpgKVVVLVNKVPLVEQHYsTEFWKFLKNKYKVERVSGDSQLKISFT 402
Cdd:cd00046      1 GENVLITAPTGSGKTLAALLAALLLLLKKGK-----KVLVLVPTKALALQTA-ERLRELFGPGIRVAVLVGGSSAEEREK 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  403 DIVQKNDIVICTAQILENYLERAHsgdddGIKLSDLSLIVIDECHHTQKGGVYNHIMIRYLkqkhknakLKKEQKDtvdi 482
Cdd:cd00046     75 NKLGDADIIIATPDMLLNLLLRED-----RLFLKDLKLIIVDEAHALLIDSRGALILDLAV--------RKAGLKN---- 137


                   ....*...
gi 1696124467  483 PQILGLTA 490
Cdd:cd00046    138 AQVILLSA 145
CARD_2 pfam16739
Caspase recruitment domain; In the probable ATP-dependent RNA helicase DDX58 this CARD domain ...
 107-199 4.71e-23

Caspase recruitment domain; In the probable ATP-dependent RNA helicase DDX58 this CARD domain is found near the N-terminus and interacts with the C-terminal domain.


Pssm-ID: 465251  Cd Length: 93  Bit Score: 94.20  E-value: 4.71e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  107 ENDNCVRLIELLSPSLLE-MKTTDVCWDCfsKDILTAEDREIILAECQNRGNMGGARELLRRIVR-FPPGWFSIFLKALQ 184
Cdd:pfam16739    1 EDDEYRRLLRLFRPRLKDtIKPTEILPHL--PECLTEDDKERIRAETNNKGNTAAAELLLDRLVRsDREGWFRAFLDALR 78

                           90
                   ....*....|....*
gi 1696124467  185 NTEHKNLFKELTGES 199
Cdd:pfam16739   79 KTGHDGLAEELEGEY 93
RLR_C_like cd15803
C-terminal domain of Retinoic acid-inducible gene (RIG)-I-like Receptors, Cereblon (CRBN), and ...
 880-963 2.06e-22

C-terminal domain of Retinoic acid-inducible gene (RIG)-I-like Receptors, Cereblon (CRBN), and similar protein domains; Retinoic acid-inducible gene (RIG)-I-like Receptors (RLRs) are cytoplasmic RNA receptors that recognize non-self RNA and act as molecular sensors to detect viral pathogens. They play crucial roles in innate antiviral responses, including the production of proinflammatory cytokines and type I interferon. There are three RLRs in vertebrates, RIG-I, LGP2, and MDA5. They are characterized by a central DExD/H-box helicase domain and a C-terminal domain, both of which are responsible for binding viral RNA. Cereblon is part of an E3 ubiquitin ligase complex, together with damaged DNA binding protein 1 (DDB1), CUL4A and ROC1. Cereblon interacts directly with DDB1, although the C-terminal domain characterized here does not contribute to that interaction. The C-terminal domain of Cereblon was shown to contain the binding site for thalidomide and its analogs, a class of teratogenic drugs that exhibit an antiproliferative effect on myelomas. Mutations in CRBN, some of which map onto the C-terminal domain, were associated with autosomal recessive mental retardation, which may have to do with interactions between CRBN and ion channels in the brain. RLRs and Cereblon contain a common conserved zinc binding site in their C-terminal domains.


Pssm-ID: 276941  Cd Length: 84  Bit Score: 92.20  E-value: 2.06e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  880 FSCRSCNKPVCSGEDVEIIENMHRVNVTPQFKELFIQRENTSLVKRLLDYETNGFIACKDCGQRWGSMMLYRGIECPCLH 959
Cdd:cd15803      1 LLCKNCSALACTGEDIRVIELCHHVVYKPAFKNNYNVIGRPSTVHKWFDGYAWGIISCKICSSHWGWHFTYKPQKLPVLK 80


                   ....
gi 1696124467  960 VKNF 963
Cdd:cd15803     81 RESF 84
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 310-514 3.93e-22

DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350793 [Multi-domain]  Cd Length: 181  Bit Score: 94.89  E-value: 3.93e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  310 RDYQMDVARPALEGKNIIIcLPTGSGKTRVAVYITKEHLdsrrkEGRPGKVVVLVNKVPLVEQHYSTeFWKFLKNKYKVE 389
Cdd:cd18035      4 RLYQVLIAAVALNGNTLIV-LPTGLGKTIIAILVAADRL-----TKKGGKVLILAPSRPLVEQHAEN-LKRVLNIPDKIT 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  390 RVSGDSQLKiSFTDIVQKNDIVICTAQILENYL--ERahsgdddgIKLSDLSLIVIDECHHTQKGGVYNHIMIRYlkqkh 467
Cdd:cd18035     77 SLTGEVKPE-ERAERWDASKIIVATPQVIENDLlaGR--------ITLDDVSLLIFDEAHHAVGNYAYVYIAHRY----- 142

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 1696124467  468 knaklKKEQKDtvdiPQILGLTASPGvggakkieKAEEHILRICANL 514
Cdd:cd18035    143 -----KREANN----PLILGLTASPG--------SDKEKIMEICENL 172
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 682-799 5.20e-18

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: 80.33  E-value: 5.20e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  682 KILHEFTSREKARGIIFTKTRRSaialaqwVQENSKFEEVGVKACHVIGGggqsvvkpMTAAEQRDVLNKFQNAEVNLLI 761
Cdd:pfam00271    5 ALLELLKKERGGKVLIFSQTKKT-------LEAELLLEKEGIKVARLHGD--------LSQEEREEILEDFRKGKIDVLV 69

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1696124467  762 ATTVAEEGLDIAACNFVIRYELVTNEIAMIQARGR-GRA 799
Cdd:pfam00271   70 ATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRaGRA 108
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 311-500 7.01e-18

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


Pssm-ID: 350679 [Multi-domain]  Cd Length: 181  Bit Score: 82.31  E-value: 7.01e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  311 DYQMDVARPA-LEGKNIIICLPTGSGKTRVAVYITkehLDSRRKEGrpGKVVVLVNKVPLVEQHYStEFWKFLKNKYK-V 388
Cdd:cd17921      4 PIQREALRALyLSGDSVLVSAPTSSGKTLIAELAI---LRALATSG--GKAVYIAPTRALVNQKEA-DLRERFGPLGKnV 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  389 ERVSGDSQLKIsftDIVQKNDIVICTAQILENYLERAHSGdddgiKLSDLSLIVIDECH---HTQKGGVYNHImIRYLKQ 465
Cdd:cd17921     78 GLLTGDPSVNK---LLLAEADILVATPEKLDLLLRNGGER-----LIQDVRLVVVDEAHligDGERGVVLELL-LSRLLR 148

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 1696124467  466 KHKNAklkkeqkdtvdipQILGLtaSPGVGGAKKI 500
Cdd:cd17921    149 INKNA-------------RFVGL--SATLPNAEDL 168
ResIII pfam04851
Type III restriction enzyme, res subunit;
307-492 1.84e-17

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 80.79  E-value: 1.84e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  307 IVLRDYQMDVARPALEG-----KNIIICLPTGSGKTRVAVYITKEhldsRRKEGRPGKVVVLVNKVPLVEQHYStEFWKF 381
Cdd:pfam04851    2 LELRPYQIEAIENLLESikngqKRGLIVMATGSGKTLTAAKLIAR----LFKKGPIKKVLFLVPRKDLLEQALE-EFKKF 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  382 LKNKYKV-ERVSGDSQLKisftdIVQKNDIVICTAQ----ILENYLERAHSGDDDgiklsdlsLIVIDECHHTQKGGvYN 456
Cdd:pfam04851   77 LPNYVEIgEIISGDKKDE-----SVDDNKIVVTTIQslykALELASLELLPDFFD--------VIIIDEAHRSGASS-YR 142

                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 1696124467  457 HImIRYLKQKHknaklkkeqkdtvdipqILGLTASP 492
Cdd:pfam04851  143 NI-LEYFKPAF-----------------LLGLTATP 160
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 310-492 2.15e-17

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


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 80.36  E-value: 2.15e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  310 RDYQMDVARPALEGKNIIICLPTGSGKTRVAVYITKEHLDsrrKEGRPGKVVVLVNKVPLVEQHYStEFWKFLKN-KYKV 388
Cdd:pfam00270    1 TPIQAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALEALD---KLDNGPQALVLAPTRELAEQIYE-ELKKLGKGlGLKV 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  389 ERVSGDSQLKISFTDIvQKNDIVICTAQILENYLERAHsgdddgiKLSDLSLIVIDECHHTQKGGVYNHI--MIRYLKQK 466
Cdd:pfam00270   77 ASLLGGDSRKEQLEKL-KGPDILVGTPGRLLDLLQERK-------LLKNLKLLVLDEAHRLLDMGFGPDLeeILRRLPKK 148

                          170       180
                   ....*....|....*....|....*.
gi 1696124467  467 HknaklkkeqkdtvdipQILGLTASP 492
Cdd:pfam00270  149 R----------------QILLLSATL 158
CARD_2 pfam16739
Caspase recruitment domain; In the probable ATP-dependent RNA helicase DDX58 this CARD domain ...
 13-99 2.84e-17

Caspase recruitment domain; In the probable ATP-dependent RNA helicase DDX58 this CARD domain is found near the N-terminus and interacts with the C-terminal domain.


Pssm-ID: 465251  Cd Length: 93  Bit Score: 77.63  E-value: 2.84e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467   13 LIEDFRPRLRKLIEVEFVLDHL-NFLDNDNKDLIRTKARKESNLKAVDLLIDTIIRIRPLpnGWFREFVDALSAGGCKHA 91
Cdd:pfam16739    8 LLRLFRPRLKDTIKPTEILPHLpECLTEDDKERIRAETNNKGNTAAAELLLDRLVRSDRE--GWFRAFLDALRKTGHDGL 85


                   ....*...
gi 1696124467   92 ATYVEDSP 99
Cdd:pfam16739   86 AEELEGEY 93
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 694-801 2.46e-16

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: 77.01  E-value: 2.46e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  694 RGIIFTKTRRSAIALAQWVQENSKfeevGVKACHVIGGGGQSVVKPMTAAEQRDVLNKFQNAEVNLLIATTVAEEGLDIA 773
Cdd:cd18801     32 RVIIFSEFRDSAEEIVNFLSKIRP----GIRATRFIGQASGKSSKGMSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIG 107

                           90       100
                   ....*....|....*....|....*....
gi 1696124467  774 ACNFVIRYELVTNEIAMIQARGR-GRAED 801
Cdd:cd18801    108 EVDLIICYDASPSPIRMIQRMGRtGRKRQ 136
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
297-797 3.80e-16

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 82.77  E-value: 3.80e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  297 AAAESPPKDVIVLRDYQMD-----VARPALEGKNIIICLPTGSGKTRVAVYITKEHLdsrrkegRPGKVVVLVNKVPLVE 371
Cdd:COG1061     69 EAGDEASGTSFELRPYQQEalealLAALERGGGRGLVVAPTGTGKTVLALALAAELL-------RGKRVLVLVPRRELLE 141

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  372 QhYSTEFWKFLKNkykveRVSGDSQLKISFtdivqknDIVICTAQILENYLERAHSGDDDGiklsdlsLIVIDECHHTQk 451
Cdd:COG1061    142 Q-WAEELRRFLGD-----PLAGGGKKDSDA-------PITVATYQSLARRAHLDELGDRFG-------LVIIDEAHHAG- 200

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  452 GGVYNHImIRYLKQKHknaklkkeqkdtvdipqILGLTASPGVGGAKKIEkaeehiLRICANLdAYKImtgnlgenkkep 531
Cdd:COG1061    201 APSYRRI-LEAFPAAY-----------------RLGLTATPFRSDGREIL------LFLFDGI-VYEY------------ 243

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  532 hkkiataeerkedPFGDVIKGimnaihvhaelnptcdlgtqnyeqwvvqkeqnaakeenqkvrvcaEHLRQYnealylgk 611
Cdd:COG1061    244 -------------SLKEAIED---------------------------------------------GYLAPP-------- 257

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  612 tirmwDAFSFLDKYFDEELKKKVAPEDEEAIIKTDTERflftlfKDSKVKlqelaklpqyennslaklrtKILHEFTSRE 691
Cdd:COG1061    258 -----EYYGIRVDLTDERAEYDALSERLREALAADAER------KDKILR--------------------ELLREHPDDR 306

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  692 KarGIIFTKTRRSAIALAQwvqensKFEEVGVKACHVIGGggqsvvkpMTAAEQRDVLNKFQNAEVNLLIATTVAEEGLD 771
Cdd:COG1061    307 K--TLVFCSSVDHAEALAE------LLNEAGIRAAVVTGD--------TPKKEREEILEAFRDGELRILVTVDVLNEGVD 370

                          490       500
                   ....*....|....*....|....*...
gi 1696124467  772 IAACNFVI--RYelVTNEIAMIQARGRG 797
Cdd:COG1061    371 VPRLDVAIllRP--TGSPREFIQRLGRG 396
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 309-492 6.05e-15

DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350790 [Multi-domain]  Cd Length: 163  Bit Score: 73.36  E-value: 6.05e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  309 LRDYQMDvARPALEG------KNIIICLPTGSGKTRVAVYITKEHLDSRRKEgrpgKVVVLVNKVPLVEQHySTEFWKFL 382
Cdd:cd18032      1 PRYYQQE-AIEALEEarekgqRRALLVMATGTGKTYTAAFLIKRLLEANRKK----RILFLAHREELLEQA-ERSFKEVL 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  383 --KNKYKVErvsgdsQLKISFTDIvqknDIVICTAQILeNYLERAHSGDDDgiklsDLSLIVIDECHHTQKGGvYNHImI 460
Cdd:cd18032     75 pdGSFGNLK------GGKKKPDDA----RVVFATVQTL-NKRKRLEKFPPD-----YFDLIIIDEAHHAIASS-YRKI-L 136

                          170       180       190
                   ....*....|....*....|....*....|..
gi 1696124467  461 RYLKQKHknaklkkeqkdtvdipqILGLTASP 492
Cdd:cd18032    137 EYFEPAF-----------------LLGLTATP 151
RIG-I_C cd15805
C-terminal domain of Retinoic acid-inducible gene (RIG)-I protein, a cytoplasmic viral RNA ...
 879-987 1.52e-14

C-terminal domain of Retinoic acid-inducible gene (RIG)-I protein, a cytoplasmic viral RNA receptor; Retinoic acid-inducible gene (RIG)-I protein, also called DEAD box protein 58 (DDX58), is one of three members of the RIG-I-like Receptor (RLR) family. RLRs are cytoplasmic RNA receptors that recognize non-self RNA and act as molecular sensors to detect viral pathogens. RIG-I is activated by blunt-ended double-stranded RNA with or without a 5'-triphosphate (ppp), by single-stranded RNA marked by a 5'-ppp and by polyuridine sequences. It has been found to confer resistance to many negative-sense RNA viruses, including orthomyxoviruses, rhabdoviruses, bunyaviruses, and paramyxoviruses, as well as the positive-strand hepatitis C virus. RLRs are characterized by a central DExD/H-box helicase domain and a C-terminal domain, both of which are responsible for binding viral RNA. The helicase domain catalyzes the unwinding of double stranded RNA in an ATP-dependent manner. RIG-I and MDA5 also contain two N-terminal caspase activation and recruitment domains (CARDs), which initiate downstream signaling upon viral RNA sensing.


Pssm-ID: 276943  Cd Length: 112  Bit Score: 70.77  E-value: 1.52e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  879 KFSCRSCNKPVCSGEDVEIIENMHRVNVTPQFKELFIQRENTSlVKRLLDYETNGFIACKDCGQRWGSMMLYRGIECPCL 958
Cdd:cd15805      3 KLLCGKCKTFACNSDDIRVIKESHHVVIDPSFKERYTTKPHPK-PKTFDGFEKKGKIFCKKCGHDWGIMASYKIQNLPVL 81

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1696124467  959 HVKNFLV--TYDEKKKNINKWSELGIQLPAF 987
Cdd:cd15805     82 KIESFVVenPVTGQQLLFRKWKDVPFAIKEF 112
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 309-492 3.65e-14

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


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 70.80  E-value: 3.65e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  309 LRDYQ---MDVARPALEGKNIIICLPTGSGKTRVAVYITKEhldsrRKEGRpgkVVVLVNKVPLVEQHYStEFWKFLKNK 385
Cdd:cd17926      1 LRPYQeeaLEAWLAHKNNRRGILVLPTGSGKTLTALALIAY-----LKELR---TLIVVPTDALLDQWKE-RFEDFLGDS 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  386 YkVERVSGDSqlKISFTDIvqknDIVICTAQILENYLERAHSGDDDGiklsdlSLIVIDECHHtqkggvYNHIMIRYLkQ 465
Cdd:cd17926     72 S-IGLIGGGK--KKDFDDA----NVVVATYQSLSNLAEEEKDLFDQF------GLLIVDEAHH------LPAKTFSEI-L 131

                          170       180
                   ....*....|....*....|....*..
gi 1696124467  466 KHKNAKLKkeqkdtvdipqiLGLTASP 492
Cdd:cd17926    132 KELNAKYR------------LGLTATP 146
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
321-500 3.32e-13

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 73.39  E-value: 3.32e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  321 LEGKNIIICLPTGSGKTRVAVYITKEHLDsrrkegRPGKVVVLvnkVP---LVEQHYStEFWKFLKNK-YKVERVSGDSQ 396
Cdd:COG1204     36 LEGKNLVVSAPTASGKTLIAELAILKALL------NGGKALYI---VPlraLASEKYR-EFKRDFEELgIKVGVSTGDYD 105

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  397 LKIsftDIVQKNDIVICTAqilenylERAHSGDDDGIK-LSDLSLIVIDECHH---TQKGGVYNHIMirylkqkhknAKL 472
Cdd:COG1204    106 SDD---EWLGRYDILVATP-------EKLDSLLRNGPSwLRDVDLVVVDEAHLiddESRGPTLEVLL----------ARL 165

                          170       180
                   ....*....|....*....|....*...
gi 1696124467  473 KKEQKDtvdiPQILGLtaSPGVGGAKKI 500
Cdd:COG1204    166 RRLNPE----AQIVAL--SATIGNAEEI 187
HELICc smart00490
helicase superfamily c-terminal domain;
717-799 4.69e-13

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 65.31  E-value: 4.69e-13
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467   717 KFEEVGVKACHVIGGggqsvvkpMTAAEQRDVLNKFQNAEVNLLIATTVAEEGLDIAACNFVIRYELVTNEIAMIQARGR 796
Cdd:smart00490    6 LLKELGIKVARLHGG--------LSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGR 77


                    ....
gi 1696124467   797 -GRA 799
Cdd:smart00490   78 aGRA 81
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 671-799 5.92e-13

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: 66.76  E-value: 5.92e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  671 YENNSLAKLRTKILHEFTSREKARGIIFTKTRRSAIALAQwvqensKFEEVGVKACHVIGGggqsvvkpMTAAEQRDVLN 750
Cdd:cd18787      6 VVVEEEEKKLLLLLLLLEKLKPGKAIIFVNTKKRVDRLAE------LLEELGIKVAALHGD--------LSQEERERALK 71

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1696124467  751 KFQNAEVNLLIATTVAEEGLDIAACNFVIRYELVTNEIAMIQaR-GR-GRA 799
Cdd:cd18787     72 KFRSGKVRVLVATDVAARGLDIPGVDHVINYDLPRDAEDYVH-RiGRtGRA 121
DEXDc_FANCM cd18033
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ...
 309-519 3.54e-11

DEAH-box helicase domain of FANCM; 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. In complex with CENPS and CENPX, it binds double-stranded DNA (dsDNA), fork-structured DNA (fsDNA), and Holliday junction substrates. Its ATP-dependent DNA branch migration activity can process branched DNA structures such as a movable replication fork. This activity is strongly stimulated in the presence of CENPS and CENPX. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, it strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA. FANCM is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350791 [Multi-domain]  Cd Length: 182  Bit Score: 63.11  E-value: 3.54e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  309 LRDYQMDVARPALEgKNIIICLPTGSGKTRVAVYITKEHLDSRRKegrpGKVVVLVNKVPLVEQHystefwkfLKNKYKV 388
Cdd:cd18033      3 LRDYQFTIVQKALF-QNTLVALPTGLGKTFIAAVVMLNYYRWFPK----GKIVFMAPTKPLVSQQ--------IEACYKI 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  389 ERVSGDSQlkISFTDIVQKND---------IVICTAQILENYLERahsGDDDgikLSDLSLIVIDECHHTQKGGVYNHIM 459
Cdd:cd18033     70 TGIPSSQT--AELTGSVPPTKraelwaskrVFFLTPQTLENDLKE---GDCD---PKSIVCLVIDEAHRATGNYAYCQVV 141

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  460 iRYLKQKHKNAKlkkeqkdtvdipqILGLTASPGvggaKKIEKAEEhilrICANLDAYKI 519
Cdd:cd18033    142 -RELMRYNSHFR-------------ILALTATPG----SKLEAVQQ----VIDNLLISHI 179
CARD_IPS-1_RIG-I cd08789
Caspase activation and recruitment domains (CARDs) found in IPS-1 and RIG-I-like RNA helicases; ...
 109-198 5.24e-11

Caspase activation and recruitment domains (CARDs) found in IPS-1 and RIG-I-like RNA helicases; Caspase activation and recruitment domains (CARDs) found in IPS-1 (Interferon beta promoter stimulator protein 1) and Retinoic acid Inducible Gene I (RIG-I)-like DEAD box helicases. RIG-I-like helicases and IPS-1 play important roles in the induction of interferons in response to viral infection. They are crucial in triggering innate immunity and in developing adaptive immunity against viral pathogens. RIG-I-like helicases, including MDA5 and RIG-I, contain two N-terminal CARD domains and a C-terminal DEAD box RNA helicase domain. They are cytoplasmic RNA helicases that play an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. MDA5 and RIG-I associate with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.


Pssm-ID: 260057  Cd Length: 91  Bit Score: 59.78  E-value: 5.24e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  109 DNCVRLIELLSPSLLE-MKTTDVCWDCfsKDILTAEDREIILAECQNRGNMGGARELLRRIVRF-PPGWFSIFLKALQNT 186
Cdd:cd08789      2 DDEKQLLQCYRATVERsLDVVYVLPYL--TDCLPDEDRERIRAAEENRGNSGAAALLLNTLLQLeKEGWFRGFLDALRAT 79

                           90
                   ....*....|..
gi 1696124467  187 EHKNLfKELTGE 198
Cdd:cd08789     80 GYTGA-RELIDN 90
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
307-447 1.47e-09

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


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 61.88  E-value: 1.47e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  307 IVLRDYQMDVARPALEGKNIIICLPTGSGKTRVAVYITKEHLdsrrKEGR------PGKVvvlvnkvpLVEQhystefwK 380
Cdd:COG4581     24 FELDPFQEEAILALEAGRSVLVAAPTGSGKTLVAEFAIFLAL----ARGRrsfytaPIKA--------LSNQ-------K 84

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1696124467  381 F--LKNKYKVERVS---GDSQLkisftdivqkN---DIVICTAQILENYLERahsgddDGIKLSDLSLIVIDECH 447
Cdd:COG4581     85 FfdLVERFGAENVGlltGDASV----------NpdaPIVVMTTEILRNMLYR------EGADLEDVGVVVMDEFH 143
DEADc cd00268
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ...
 313-446 1.55e-09

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: 58.61  E-value: 1.55e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  313 QMDVARPALEGKNIIICLPTGSGKTrvAVYI--TKEHLDSRRKEGRPG-KVVVLvnkVP---LVEQHYStEFWKFLKNK- 385
Cdd:cd00268     17 QAQAIPLILSGRDVIGQAQTGSGKT--LAFLlpILEKLLPEPKKKGRGpQALVL---APtreLAMQIAE-VARKLGKGTg 90

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1696124467  386 YKVERVSGDSQLKISFTDIVQKNDIVICT-AQILEnYLERAHsgdddgIKLSDLSLIVIDEC 446
Cdd:cd00268     91 LKVAAIYGGAPIKKQIEALKKGPDIVVGTpGRLLD-LIERGK------LDLSNVKYLVLDEA 145
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
680-861 1.84e-09

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 60.93  E-value: 1.84e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  680 RTKILHEFTSREKA-RGIIFTKTRRSAIALAQWVQENskfeevGVKAChVIGGG-GQSvvkpmtaaeQRD-VLNKFQNAE 756
Cdd:COG0513    228 KLELLRRLLRDEDPeRAIVFCNTKRGADRLAEKLQKR------GISAA-ALHGDlSQG---------QRErALDAFRNGK 291

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  757 VNLLIATTVAEEGLDIAACNFVIRYELVTNE------IamiqarGR-GRAEDS--SYTLVAGEgsgvaERESVNEYrEKM 827
Cdd:COG0513    292 IRVLVATDVAARGIDIDDVSHVINYDLPEDPedyvhrI------GRtGRAGAEgtAISLVTPD-----ERRLLRAI-EKL 359

                          170       180       190
                   ....*....|....*....|....*....|....
gi 1696124467  828 MSKAIdKVKKLDQDEYEKRIKEFQIQAIMEERVR 861
Cdd:COG0513    360 IGQKI-EEEELPGFEPVEEKRLERLKPKIKEKLK 392
HsdR COG4096
Type I site-specific restriction endonuclease, part of a restriction-modification system ...
 299-456 1.16e-08

Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms];


Pssm-ID: 443272 [Multi-domain]  Cd Length: 806  Bit Score: 59.08  E-value: 1.16e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  299 AESPPKDVIVLRDYQMDVARPALE----GKN-IIICLPTGSGKTRVAVYITKEHLDSRRKEgrpgKVVVLVNKVPLVEQH 373
Cdd:COG4096    149 ATEPYNDGIALRYYQIEAIRRVEEaiakGQRrALLVMATGTGKTRTAIALIYRLLKAGRAK----RILFLADRNALVDQA 224

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  374 YsTEFWKFLKNKYKvervsgdsqlkisFTDIVQKN-------DIVICTAQILENYLErahsGDDDGIKLSDLS-----LI 441
Cdd:COG4096    225 K-NAFKPFLPDLDA-------------FTKLYNKSkdidksaRVYFSTYQTMMNRID----GEEEEPGYRQFPpdffdLI 286

                          170
                   ....*....|....*
gi 1696124467  442 VIDECHHtqkgGVYN 456
Cdd:COG4096    287 IIDECHR----GIYS 297
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
 321-500 3.46e-08

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


Pssm-ID: 350786 [Multi-domain]  Cd Length: 177  Bit Score: 54.26  E-value: 3.46e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  321 LEGKNIIICLPTGSGKTRVA-VYITKEHLDSrrkegrpGKVVVLVNKVPLVEQHYsTEFWKFLKNKYKVERVSGDSQLKi 399
Cdd:cd18028     15 LKGENLLISIPTASGKTLIAeMAMVNTLLEG-------GKALYLVPLRALASEKY-EEFKKLEEIGLKVGISTGDYDED- 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  400 sfTDIVQKNDIVICTAQILENYLERAHSgdddgiKLSDLSLIVIDECHHT---QKGGVYNHIMIRyLKQKHKNAklkkeq 476
Cdd:cd18028     86 --DEWLGDYDIIVATYEKFDSLLRHSPS------WLRDVGVVVVDEIHLIsdeERGPTLESIVAR-LRRLNPNT------ 150

                          170       180
                   ....*....|....*....|....
gi 1696124467  477 kdtvdipQILGLTASpgVGGAKKI 500
Cdd:cd18028    151 -------QIIGLSAT--IGNPDEL 165
PRK00254 PRK00254
ski2-like helicase; Provisional
 320-493 1.92e-07

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 55.21  E-value: 1.92e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  320 ALEGKNIIICLPTGSGKTRVAVYITKEHLdsrRKEGrpGKVVVLVNKVPLVEQHYStEFWKFLKNKYKVERVSGDSQlki 399
Cdd:PRK00254    36 VLEGKNLVLAIPTASGKTLVAEIVMVNKL---LREG--GKAVYLVPLKALAEEKYR-EFKDWEKLGLRVAMTTGDYD--- 106

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  400 SFTDIVQKNDIVICTAQILENYLERAHSGdddgikLSDLSLIVIDECHhtqkggvynhimirYLKQKHKNAKLKKEQKDT 479
Cdd:PRK00254   107 STDEWLGKYDIIIATAEKFDSLLRHGSSW------IKDVKLVVADEIH--------------LIGSYDRGATLEMILTHM 166

                          170
                   ....*....|....
gi 1696124467  480 VDIPQILGLTASPG 493
Cdd:PRK00254   167 LGRAQILGLSATVG 180
CARD cd01671
Caspase activation and recruitment domain: a protein-protein interaction domain; Caspase ...
 110-195 2.31e-07

Caspase activation and recruitment domain: a protein-protein interaction domain; Caspase activation and recruitment domains (CARDs) are death domains (DDs) found associated with caspases. Caspases are aspartate-specific cysteine proteases with functions in apoptosis, immune signaling, inflammation, and host-defense mechanisms. In addition to caspases, proteins containing CARDs include adaptor proteins such as RAIDD, CARD9, and RIG-I-like helicases, which can form multiprotein complexes and play important roles in mediating the signals to induce immune and inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.


Pssm-ID: 260018 [Multi-domain]  Cd Length: 79  Bit Score: 49.05  E-value: 2.31e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  110 NCVRLIEllspsllEMKTTDVCWDCFSKDILTAEDREIILAECQNRGnmgGARELLRRIVRFPPGWFSIFLKALQNTEHK 189
Cdd:cd01671      4 NRVELVE-------DLDVEDILDHLIQKGVLTEEDKEEILSEKTRQD---KARKLLDILPRRGPKAFEVFCEALRETGQP 73


                   ....*.
gi 1696124467  190 NLFKEL 195
Cdd:cd01671     74 HLAELL 79
DEXHc_Brr2_1 cd18019
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD ...
 313-491 8.82e-07

N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD box helicase that mediates spliceosome catalytic activation. It is a stable subunit of the spliceosome, required during splicing catalysis and spliceosome disassembly. Brr2 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350777 [Multi-domain]  Cd Length: 214  Bit Score: 50.83  E-value: 8.82e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  313 QMDVARPALEGK-NIIICLPTGSGKTRVAVY-ITKEHLDSRRKEGRPG----KVVVLVNKVPLVeQHYSTEFWKFLKN-K 385
Cdd:cd18019     22 QSKLFPAAFETDeNLLLCAPTGAGKTNVALLtILREIGKHRNPDGTINldafKIVYIAPMKALV-QEMVGNFSKRLAPyG 100

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  386 YKVERVSGDSQL---KISFTDIV----QKNDIVIctaqilenylerAHSGDDDGIKLsdLSLIVIDECH--HTQKGGVYN 456
Cdd:cd18019    101 ITVAELTGDQQLtkeQISETQIIvttpEKWDIIT------------RKSGDRTYTQL--VRLIIIDEIHllHDDRGPVLE 166

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 1696124467  457 HIMIRYLKQkhknaklkkeQKDTVDIPQILGLTAS 491
Cdd:cd18019    167 SIVARTIRQ----------IEQTQEYVRLVGLSAT 191
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 758-807 1.05e-06

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: 47.31  E-value: 1.05e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1696124467  758 NLLIATTVAEEGLDIAACNFVIRYELVTNEIAMIQARGR-GRAEDSSYTLV 807
Cdd:cd18785     24 EILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRaGRGGKDEGEVI 74
DEXHc_RE_I_HsdR cd18030
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of ...
 332-470 1.75e-06

DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of type I restriction-modification enzymes contains the DNA cleavage and ATP-dependent DNA translocation activities of the heteromeric complex. It is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350788 [Multi-domain]  Cd Length: 208  Bit Score: 49.92  E-value: 1.75e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  332 TGSGKTRVAVYITKEhldSRRKEGRPgKVVVLVNKVPLVEQHYSTeFWKFlkNKYKVERVSGDSQLKISFTDIvqKNDIV 411
Cdd:cd18030     56 QGSGKSLTMFKAAKL---LIEDPKNP-KVVFVVDRKDLDYQTSST-FSRF--AAEDVVRANSTKELKELLKNL--SGGII 126

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1696124467  412 ICTAQILEN---YLERAHSGDDDGIklsdlsLIVIDECHHTQKGGvynhiMIRYLKQKHKNA 470
Cdd:cd18030    127 VTTIQKFNNavkEESKPVLIYRKNI------VVIVDEAHRSQFGE-----LAKALKKALPNA 177
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 677-796 2.72e-06

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 47.86  E-value: 2.72e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  677 AKLRT--KILHE-FTSREKArgIIFTKTRRSAIALAQWVQENskfeevGVKACHVIGGggqsvvkpMTAAEQRDVLNKFQ 753
Cdd:cd18793     11 GKLEAllELLEElREPGEKV--LIFSQFTDTLDILEEALRER------GIKYLRLDGS--------TSSKERQKLVDRFN 74

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1696124467  754 NAE---VnLLIATTVAEEGLDIAACNFVIRYELVTNEIAMIQARGR 796
Cdd:cd18793     75 EDPdirV-FLLSTKAGGVGLNLTAANRVILYDPWWNPAVEEQAIDR 119
DEXHc_POLQ-like cd18026
DEXH-box helicase domain of DNA polymerase theta; DNA polymerase theta (POLQ) is important in ...
 319-447 3.50e-06

DEXH-box helicase domain of DNA polymerase theta; DNA polymerase theta (POLQ) is important in the repair of genomic double-strand breaks (DSBs). POLQ contains an N-terminal type II DEAD box helicase domain which contains the ATP-binding region.


Pssm-ID: 350784 [Multi-domain]  Cd Length: 202  Bit Score: 48.75  E-value: 3.50e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  319 PALEGKNIIICLPTGSGKTRVA-VYITKEHLDSRRKegrpgkvVVLVnkVPLV----EQHYSTEfwKFLKNK-YKVERVS 392
Cdd:cd18026     29 GLLEGRNLVYSLPTSGGKTLVAeILMLKRLLERRKK-------ALFV--LPYVsivqEKVDALS--PLFEELgFRVEGYA 97

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1696124467  393 GDSqlKISFTDIVQKNDIVICTaqilenyLERAHSGDDDGI---KLSDLSLIVIDECH 447
Cdd:cd18026     98 GNK--GRSPPKRRKSLSVAVCT-------IEKANSLVNSLIeegRLDELGLVVVDELH 146
CARD_IPS-1_RIG-I cd08789
Caspase activation and recruitment domains (CARDs) found in IPS-1 and RIG-I-like RNA helicases; ...
 13-97 4.32e-06

Caspase activation and recruitment domains (CARDs) found in IPS-1 and RIG-I-like RNA helicases; Caspase activation and recruitment domains (CARDs) found in IPS-1 (Interferon beta promoter stimulator protein 1) and Retinoic acid Inducible Gene I (RIG-I)-like DEAD box helicases. RIG-I-like helicases and IPS-1 play important roles in the induction of interferons in response to viral infection. They are crucial in triggering innate immunity and in developing adaptive immunity against viral pathogens. RIG-I-like helicases, including MDA5 and RIG-I, contain two N-terminal CARD domains and a C-terminal DEAD box RNA helicase domain. They are cytoplasmic RNA helicases that play an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. MDA5 and RIG-I associate with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.


Pssm-ID: 260057  Cd Length: 91  Bit Score: 45.91  E-value: 4.32e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467   13 LIEDFRPRLRKLIEVEFVLDHL-NFLDNDNKDLIRTKARKESNLKAVDLLIDTIIRIRPlpNGWFREFVDALSAGGCKHA 91
Cdd:cd08789      7 LLQCYRATVERSLDVVYVLPYLtDCLPDEDRERIRAAEENRGNSGAAALLLNTLLQLEK--EGWFRGFLDALRATGYTGA 84


                   ....*.
gi 1696124467   92 ATYVED 97
Cdd:cd08789     85 RELIDN 90
CARD_IPS1 cd08811
Caspase activation and recruitment domain (CARD) found in IPS-1; Caspase activation and ...
 140-198 4.61e-06

Caspase activation and recruitment domain (CARD) found in IPS-1; Caspase activation and recruitment domain (CARD) found in IPS-1 (Interferon beta promoter stimulator protein 1), also known as CARDIF, VISA or MAVS. IPS-1 is an adaptor protein that plays an important role in interferon induction in response to viral infection. It is crucial in triggering innate immunity and in developing adaptive immunity against viral pathogens. The CARD of IPS-1 associates with the CARDs of two RNA helicases, RIG-I and MDA5, which bind viral DNA in the cytoplasm during the initial stage of intracellular antiviral response, leading to the induction of type I interferons. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.


Pssm-ID: 260073  Cd Length: 92  Bit Score: 45.81  E-value: 4.61e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1696124467  140 LTAEDREIILAECQNRGNMGGARELLRRIVRfPPGWFSIFLKALQNTEHKNLFKELTGE 198
Cdd:cd08811     33 LTRSDRDEILAKKDMSGNRDTAWTLLDHLQR-RPGWVEDFIKALRNCELGHLADELERV 90
DEXHc_TRCF cd17991
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ...
 328-492 8.27e-06

DEXH/Q-box 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 member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350749 [Multi-domain]  Cd Length: 193  Bit Score: 47.57  E-value: 8.27e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  328 ICLPTGSGKTRVAvyitkehLDSRRKEGRPGK-VVVLVNKVPLVEQHYSTeFWKFLKN-KYKVERVSG---DSQLKISFT 402
Cdd:cd17991     41 ICGDVGFGKTEVA-------MRAAFKAVLSGKqVAVLVPTTLLAQQHYET-FKERFANfPVNVELLSRfttAAEQREILE 112

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  403 DI-VQKNDIVICTAQILEnylerahsgddDGIKLSDLSLIVIDEchhTQKGGVynhimirylKQKHKNAKLKKEqkdtVD 481
Cdd:cd17991    113 GLkEGKVDIVIGTHRLLS-----------KDVEFKNLGLLIIDE---EQRFGV---------KQKEKLKELRPN----VD 165

                          170
                   ....*....|.
gi 1696124467  482 ipqILGLTASP 492
Cdd:cd17991    166 ---VLTLSATP 173
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 295-796 8.73e-06

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 49.84  E-value: 8.73e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  295 IAAAAESPPKDVIV-LRDYQMD----VARPALEGKNIIICLPTGSGKTRVAvyITkeHLDSRRKEGRPGKVVVLVnkvP- 368
Cdd:COG0553    227 LREALESLPAGLKAtLRPYQLEgaawLLFLRRLGLGGLLADDMGLGKTIQA--LA--LLLELKERGLARPVLIVA---Pt 299

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  369 -LVEQhYSTEFWKFLKNkYKVERVSGDSQlKISFTDIVQKNDIVICTAQILENYLERahsgdddgIKLSDLSLIVIDECH 447
Cdd:COG0553    300 sLVGN-WQRELAKFAPG-LRVLVLDGTRE-RAKGANPFEDADLVITSYGLLRRDIEL--------LAAVDWDLVILDEAQ 368

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  448 H-----TQkggvyNHIMIRYLKQKHKnaklkkeqkdtvdipqiLGLTASPgvggakkIE-KAEEH--ILRIcanldaykI 519
Cdd:COG0553    369 HiknpaTK-----RAKAVRALKARHR-----------------LALTGTP-------VEnRLEELwsLLDF--------L 411

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  520 MTGNLG---ENKKEPHKKIATAEERKEDPFGDVIKGIMnaihvhaeLNPTcdlgtqnyeqwvvqKEQNAA-----KEENQ 591
Cdd:COG0553    412 NPGLLGslkAFRERFARPIEKGDEEALERLRRLLRPFL--------LRRT--------------KEDVLKdlpekTEETL 469

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  592 KVRVCAEHLRQYNEALylgktirmwdafsfldKYFDEELKKKVAPEDEEAIIKTDTerflftlfkdskvKLQELAKLPQ- 670
Cdd:COG0553    470 YVELTPEQRALYEAVL----------------EYLRRELEGAEGIRRRGLILAALT-------------RLRQICSHPAl 520

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  671 -------YENNS--LAKLRTKILHEFTSREKArgIIFTKTRRSAIALAQWVQENskfeevGVKACHVIGGggqsvvkpmT 741
Cdd:COG0553    521 lleegaeLSGRSakLEALLELLEELLAEGEKV--LVFSQFTDTLDLLEERLEER------GIEYAYLHGG---------T 583

                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1696124467  742 AAEQRD-VLNKFQN---AEVnLLIATTVAEEGLDIAACNFVIRYELVTNEIAMIQARGR 796
Cdd:COG0553    584 SAEERDeLVDRFQEgpeAPV-FLISLKAGGEGLNLTAADHVIHYDLWWNPAVEEQAIDR 641
CARD pfam00619
Caspase recruitment domain; Motif contained in proteins involved in apoptotic signaling. ...
 108-198 8.96e-06

Caspase recruitment domain; Motif contained in proteins involved in apoptotic signaling. Predicted to possess a DEATH (pfam00531) domain-like fold.


Pssm-ID: 459874 [Multi-domain]  Cd Length: 85  Bit Score: 44.86  E-value: 8.96e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  108 NDNCVRLIEllspsllEMKTTDVCWD-CFSKDILTAEDREIIlaeCQNRGNMGGARELLRRIVRFPPGWFSIFLKALQNt 186
Cdd:pfam00619    5 KKNRVALVE-------RLGTLDGLLDyLLEKNVLTEEEEEKI---KANPTRLDKARELLDLVLKKGPKACQIFLEALKE- 73

                           90
                   ....*....|..
gi 1696124467  187 EHKNLFKELTGE 198
Cdd:pfam00619   74 GDPDLASDLEGL 85
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 680-783 1.15e-05

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 49.17  E-value: 1.15e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  680 RTKIL-HEFTSREKARGIIFTKTRRSAIALAQWVQENskfeevGVKACHVIGgggqsvvkPMTAAEQRDVLNKFQNAEVN 758
Cdd:PRK11192   232 KTALLcHLLKQPEVTRSIVFVRTRERVHELAGWLRKA------GINCCYLEG--------EMVQAKRNEAIKRLTDGRVN 297

                           90       100
                   ....*....|....*....|....*
gi 1696124467  759 LLIATTVAEEGLDIAACNFVIRYEL 783
Cdd:PRK11192   298 VLVATDVAARGIDIDDVSHVINFDM 322
PTZ00110 PTZ00110
helicase; Provisional
 663-825 1.24e-05

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 49.00  E-value: 1.24e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  663 QELAKLPQYENnslaKLRTKILHEFTSREKARGIIFTKTRRSAIALAQWVQENskfeevGVKACHVIGGGGQSvvkpmta 742
Cdd:PTZ00110   352 QEVFVVEEHEK----RGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLD------GWPALCIHGDKKQE------- 414

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  743 aEQRDVLNKFQNAEVNLLIATTVAEEGLDIAACNFVIRYEL---VTNEIAMIQARGRGRAEDSSYTLVAGEGSGVAeRES 819
Cdd:PTZ00110   415 -ERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFpnqIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLA-RDL 492


                   ....*.
gi 1696124467  820 VNEYRE 825
Cdd:PTZ00110   493 VKVLRE 498
DEXHc_ASCC3_1 cd18020
N-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ...
 324-465 1.09e-04

N-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; Activating signal cointegrator 1 complex subunit 3 (ASCC3) is a type II DEAD box helicase that plays a role in the repair of N-alkylated nucleotides. ASCC3 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350778 [Multi-domain]  Cd Length: 199  Bit Score: 44.34  E-value: 1.09e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  324 KNIIICLPTGSGKTRVA----VYITKEHLDSRRKEGRPGKVVVLVNKVPLVEQHYSTEFWKFLKN-KYKVERVSGDSQLk 398
Cdd:cd18020     18 ENMLICAPTGAGKTNIAmltiLHEIRQHVNQGGVIKKDDFKIVYIAPMKALAAEMVEKFSKRLAPlGIKVKELTGDMQL- 96

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1696124467  399 iSFTDIVQKNDIVicTAQILENYLERAHSGDDDGIKLsdLSLIVIDECH--HTQKGGVYNHIMIRYLKQ 465
Cdd:cd18020     97 -TKKEIAETQIIV--TTPEKWDVVTRKSSGDVALSQL--VRLLIIDEVHllHDDRGPVIESLVARTLRQ 160
SF2_C_Hrq cd18797
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...
 690-807 1.23e-04

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: 43.40  E-value: 1.23e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  690 REKARGIIFTKTRRSAIALAQWVQENSKFEEVGVKACHVIGGGgqsvvkpMTAAEQRDVLNKFQNAEVNLLIATTVAEEG 769
Cdd:cd18797     33 RAGVKTIVFCRSRKLAELLLRYLKARLVEEGPLASKVASYRAG-------YLAEDRREIEAELFNGELLGVVATNALELG 105

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1696124467  770 LDIAACNFVIRYELVTNEIAMIQARGR-GRAEDSSYTLV 807
Cdd:cd18797    106 IDIGGLDAVVLAGYPGSLASLWQQAGRaGRRGKDSLVIL 144
DEADc_DDX56 cd17961
DEAD-box helicase domain of DEAD box protein 56; DDX56 is a helicase required for assembly of ...
 320-445 1.35e-04

DEAD-box helicase domain of DEAD box protein 56; DDX56 is a helicase required for assembly of infectious West Nile virus particles. New research suggests that DDX56 relocalizes to the site of virus assembly during WNV infection and that its interaction with WNV capsid in the cytoplasm may occur transiently during virion morphogenesis. DDX56 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: 350719 [Multi-domain]  Cd Length: 206  Bit Score: 44.11  E-value: 1.35e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  320 ALEGKNIIICLPTGSGKTrvAVY---ITKEHLDSRRKEGRPG--KVVVLVNKVPLVEQHYST--EFWKFLKNKYKVERVS 392
Cdd:cd17961     28 ALEGKDILARARTGSGKT--AAYalpIIQKILKAKAESGEEQgtRALILVPTRELAQQVSKVleQLTAYCRKDVRVVNLS 105

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1696124467  393 GDSqlkisfTDIVQKN------DIVICTAQILENYLERAHSGDddgikLSDLSLIVIDE 445
Cdd:cd17961    106 ASS------SDSVQRAllaekpDIVVSTPARLLSHLESGSLLL-----LSTLKYLVIDE 153
DEADc_DDX52 cd17957
DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ...
 313-445 2.35e-04

DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ubiquitously expressed in testis, endometrium, and other tissues in humans. DDX52 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: 350715 [Multi-domain]  Cd Length: 198  Bit Score: 43.35  E-value: 2.35e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  313 QMdVARP-ALEGKNIIICLPTGSGKTrVAVYI-TKEHLDSRRKEGRPgKVVVLVNKVPLVEQHYsTEFWKFLKNK-YKVE 389
Cdd:cd17957     17 QM-QAIPiLLHGRDLLACAPTGSGKT-LAFLIpILQKLGKPRKKKGL-RALILAPTRELASQIY-RELLKLSKGTgLRIV 92

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1696124467  390 RVSGDSQLKISFTDI-VQKNDIVICTAQILENYLErahsgdDDGIKLSDLSLIVIDE 445
Cdd:cd17957     93 LLSKSLEAKAKDGPKsITKYDILVSTPLRLVFLLK------QGPIDLSSVEYLVLDE 143
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
 309-448 6.20e-04

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


Pssm-ID: 350677 [Multi-domain]  Cd Length: 182  Bit Score: 41.78  E-value: 6.20e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  309 LRDYQMD----VARPALEGKNIIICLPTGSGKTRVAV-YITkeHLdsRRKEGRPGKVVVLVnkvPL-VEQHYSTEFWKFL 382
Cdd:cd17919      1 LRPYQLEglnfLLELYENGPGGILADEMGLGKTLQAIaFLA--YL--LKEGKERGPVLVVC---PLsVLENWEREFEKWT 73

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1696124467  383 KN-KYKVERVSGDSQLKISFTDIVQKNDIVICTAQILENYLERAHSGdddgiklsDLSLIVIDECHH 448
Cdd:cd17919     74 PDlRVVVYHGSQRERAQIRAKEKLDKFDVVLTTYETLRRDKASLRKF--------RWDLVVVDEAHR 132
CARD cd01671
Caspase activation and recruitment domain: a protein-protein interaction domain; Caspase ...
 14-94 1.00e-03

Caspase activation and recruitment domain: a protein-protein interaction domain; Caspase activation and recruitment domains (CARDs) are death domains (DDs) found associated with caspases. Caspases are aspartate-specific cysteine proteases with functions in apoptosis, immune signaling, inflammation, and host-defense mechanisms. In addition to caspases, proteins containing CARDs include adaptor proteins such as RAIDD, CARD9, and RIG-I-like helicases, which can form multiprotein complexes and play important roles in mediating the signals to induce immune and inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.


Pssm-ID: 260018 [Multi-domain]  Cd Length: 79  Bit Score: 38.65  E-value: 1.00e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467   14 IEDFRPRLRKLIEVEFVLDHL---NFLDNDNKDLIRtkaRKESNLKAVDLLIDTIIRiRplPNGWFREFVDALSAGGCKH 90
Cdd:cd01671      1 LRKNRVELVEDLDVEDILDHLiqkGVLTEEDKEEIL---SEKTRQDKARKLLDILPR-R--GPKAFEVFCEALRETGQPH 74


                   ....
gi 1696124467   91 AATY 94
Cdd:cd01671     75 LAEL 78
DEXHc_RecG cd17918
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ...
 309-447 1.12e-03

DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase RecG family is part of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350676 [Multi-domain]  Cd Length: 180  Bit Score: 41.25  E-value: 1.12e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  309 LRDYQMDVARPalEGKNIIICLPTGSGKTRVAVYITKEHLDsrrkegRPGKVVVLVNKVPLVEQHYStEFWKFLKNkYKV 388
Cdd:cd17918     24 IKDIEKDLHSP--EPMDRLLSGDVGSGKTLVALGAALLAYK------NGKQVAILVPTEILAHQHYE-EARKFLPF-INV 93

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1696124467  389 ERVSGDSQlkisfTDIVQKNDIVICTAQILenYLERahsgdddgiKLSDLSLIVIDECH 447
Cdd:cd17918     94 ELVTGGTK-----AQILSGISLLVGTHALL--HLDV---------KFKNLDLVIVDEQH 136
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 300-447 1.37e-03

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


Pssm-ID: 440816 [Multi-domain]  Cd Length: 535  Bit Score: 42.38  E-value: 1.37e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  300 ESPPKDVIVLRDYQMDVARPALE-GKNI-IICLPTGSGKTRVAVYITKEHLDsrrKEGRPGKVVVL-------------- 363
Cdd:COG1203    122 SKPRTPINPLQNEALELALEAAEeEPGLfILTAPTGGGKTEAALLFALRLAA---KHGGRRIIYALpftsiinqtydrlr 198

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  364 -VNKVPLVEQHYSTEFwKFLKNKYKVERVSGDSQLKISFTDivqkNDIVICTA-QILEnYLERAHSGDDdgIKLSDL--S 439
Cdd:COG1203    199 dLFGEDVLLHHSLADL-DLLEEEEEYESEARWLKLLKELWD----APVVVTTIdQLFE-SLFSNRKGQE--RRLHNLanS 270


                   ....*...
gi 1696124467  440 LIVIDECH 447
Cdd:COG1203    271 VIILDEVQ 278
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 677-798 1.74e-03

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: 39.50  E-value: 1.74e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  677 AKLRTKILHEFTSREK---ARGIIFTKTRRSAIALAQWVQENskfeevGVKACHVIGGggqsvvkpMTAAEQRDVLNKFQ 753
Cdd:cd18794     12 DKKDEKLDLLKRIKVEhlgGSGIIYCLSRKECEQVAARLQSK------GISAAAYHAG--------LEPSDRRDVQRKWL 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1696124467  754 NAEVNLLIATTVAEEGLDIAACNFVIRYELVTNEIAMIQARGR-GR 798
Cdd:cd18794     78 RDKIQVIVATVAFGMGIDKPDVRFVIHYSLPKSMESYYQESGRaGR 123
DEADc_DDX43_DDX53 cd17958
DEAD-box helicase domain of DEAD box proteins 43 and 53; DDX43 (also called cancer/testis ...
 321-459 1.82e-03

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


Pssm-ID: 350716 [Multi-domain]  Cd Length: 197  Bit Score: 40.53  E-value: 1.82e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  321 LEGKNIIICLPTGSGKTRVAVYITKEHLDS----RRKEGRPGkVVVLVNKVPLVeQHYSTEFWKFLKNKYKVERVSGDSQ 396
Cdd:cd17958     25 LQGIDLIGVAQTGTGKTLAYLLPGFIHLDLqpipREQRNGPG-VLVLTPTRELA-LQIEAECSKYSYKGLKSVCVYGGGN 102

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1696124467  397 LKISFTDIVQKNDIVICTAQILeNYLERAHSgdddgIKLSDLSLIVIDECHHTQKGGVYNHIM 459
Cdd:cd17958    103 RNEQIEDLSKGVDIIIATPGRL-NDLQMNNV-----INLKSITYLVLDEADRMLDMGFEPQIR 159
PRK01172 PRK01172
ATP-dependent DNA helicase;
309-447 2.35e-03

ATP-dependent DNA helicase;


Pssm-ID: 100801 [Multi-domain]  Cd Length: 674  Bit Score: 41.79  E-value: 2.35e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  309 LRDYQMDVARPALEGKNIIICLPTGSGKTRVAVYITKEHLDSRRKEgrpgkvVVLVNKVPLVEQHYStEFWKFLKNKYKV 388
Cdd:PRK01172    23 LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLAGLKS------IYIVPLRSLAMEKYE-ELSRLRSLGMRV 95

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  389 ERVSGDSQlkiSFTDIVQKNDIVICTAqilenylERAHSG-DDDGIKLSDLSLIVIDECH 447
Cdd:PRK01172    96 KISIGDYD---DPPDFIKRYDVVILTS-------EKADSLiHHDPYIINDVGLIVADEIH 145
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
 740-804 3.54e-03

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: 39.17  E-value: 3.54e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1696124467  740 MTAAEQRDVLNKFQNAEVNLLIATTVAEEGLDIAACNFVI-----RYELVTneiaMIQARGR-GRAEDSSY 804
Cdd:cd18792     70 MTEDEKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIiedadRFGLSQ----LHQLRGRvGRGKHQSY 136
DEXHc_HFM1 cd18023
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ...
 324-447 3.57e-03

DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box helicase, required for crossover formation and complete synapsis of homologous chromosomes during meiosis. HFM1 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350781 [Multi-domain]  Cd Length: 206  Bit Score: 40.03  E-value: 3.57e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  324 KNIIICLPTGSGKTrVAVYITKEHLDSRRKEGRPG--KVVVLVNKVPLVEQHYSTEFWKFLKNKYKVERVSGDSQLKiSF 401
Cdd:cd18023     18 KNFVVSAPTGSGKT-VLFELAILRLLKERNPLPWGnrKVVYIAPIKALCSEKYDDWKEKFGPLGLSCAELTGDTEMD-DT 95

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1696124467  402 TDIvQKNDIVICTAQILENYLERAHsgdDDGIKLSDLSLIVIDECH 447
Cdd:cd18023     96 FEI-QDADIILTTPEKWDSMTRRWR---DNGNLVQLVALVLIDEVH 137
DEXHc_cas3 cd17930
DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase ...
 323-447 3.76e-03

DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase responsible for degradation of dsDNA. The two enzymatic units of Cas3, a histidine-aspartate (HD) nuclease and a Superfamily 2 (SF2) helicase, may be expressed from separate genes as Cas3' (SF2 helicase) and Cas3'' (HD nuclease) or may be fused as a single HD-SF2 polypeptide. The nucleolytic activity of most Cas3 enzymes is transition metal ion-dependent. Cas3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350688 [Multi-domain]  Cd Length: 186  Bit Score: 39.58  E-value: 3.76e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  323 GKNIIICLPTGSGKTRVAVYItkeHLDSRRKEGRPGKVVVLvnkvP---LVEQHYS--TEFWKFLKNKYKV-------ER 390
Cdd:cd17930      1 PGLVILEAPTGSGKTEAALLW---ALKLAARGGKRRIIYAL----PtraTINQMYEriREILGRLDDEDKVlllhskaAL 73

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1696124467  391 VSGDSQLKISFTDIVQKND-----------IVICTA-QILENYLerAHSGDDdgIKLSDL--SLIVIDECH 447
Cdd:cd17930     74 ELLESDEEPDDDPVEAVDWalllkrswlapIVVTTIdQLLESLL--KYKHFE--RRLHGLanSVVVLDEVQ 140
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 740-810 3.88e-03

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


Pssm-ID: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 39.25  E-value: 3.88e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1696124467  740 MTAAEQRDVLNKFQNAEVNLLIATTVAEEGLDIAACNFVI-----RYELVTneiaMIQARGR-GRAEDSSYT-LVAGE 810
Cdd:cd18811     71 LKSDEKDAVMAEFREGEVDILVSTTVIEVGVDVPNATVMViedaeRFGLSQ----LHQLRGRvGRGDHQSYClLVYKD 144
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
 309-448 6.23e-03

DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350769 [Multi-domain]  Cd Length: 207  Bit Score: 39.19  E-value: 6.23e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  309 LRDYQMDVARPALEGK--NIIICLPTGSGKTRVAVYITKEHLDsrrkEGRPGKVVVLVNKvPLVEQhystefWKF-LKNK 385
Cdd:cd18011      1 PLPHQIDAVLRALRKPpvRLLLADEVGLGKTIEAGLIIKELLL----RGDAKRVLILCPA-SLVEQ------WQDeLQDK 69

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1696124467  386 YKVERVSGDS----QLKISFTDIVQKNDIVICTAQILenyleRAHSGDDDGIKLSDLSLIVIDECHH 448
Cdd:cd18011     70 FGLPFLILDRetaaQLRRLIGNPFEEFPIVIVSLDLL-----KRSEERRGLLLSEEWDLVVVDEAHK 131
uvsW PHA02558
UvsW helicase; Provisional
 310-375 6.81e-03

UvsW helicase; Provisional


Pssm-ID: 222875 [Multi-domain]  Cd Length: 501  Bit Score: 39.99  E-value: 6.81e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1696124467  310 RDYQMDVARPALEGKNIIICLPTGSGKTRVAVYITKEHLDSRRkegrpGKVVVLVNKVPLVEQHYS 375
Cdd:PHA02558   116 HWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLENYE-----GKVLIIVPTTSLVTQMID 176
DEADc_DDX55 cd17960
DEAD-box helicase domain of DEAD box protein 55; DDX55 is a member of the DEAD-box helicases, ...
 321-445 8.88e-03

DEAD-box helicase domain of DEAD box protein 55; DDX55 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: 350718 [Multi-domain]  Cd Length: 202  Bit Score: 38.71  E-value: 8.88e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1696124467  321 LEGKNIIICLPTGSGKTRVAVYITKEHLDSRRKEGRPGKV--VVLVNKVPLVEQHYS--TEFWKFLKNKYKVERVSGDSQ 396
Cdd:cd17960     25 LSNKDVVVEAVTGSGKTLAFLIPVLEILLKRKANLKKGQVgaLIISPTRELATQIYEvlQSFLEHHLPKLKCQLLIGGTN 104

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 1696124467  397 LKISFTDIVQKN-DIVICTAQILENYLERAHsgddDGIKLSDLSLIVIDE 445
Cdd:cd17960    105 VEEDVKKFKRNGpNILVGTPGRLEELLSRKA----DKVKVKSLEVLVLDE 150
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH