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Conserved domains on  [gi|1883540343|ref|NP_001372836|]
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antiviral innate immune response receptor RIG-I isoform 2 [Homo sapiens]

Protein Classification

DEXHc_RIG-I_DDX58 and SF2_C_dicer domain-containing protein( domain architecture ID 13102736)

protein containing domains CARD_RIG-I_r2, DEXHc_RIG-I_DDX58, SF2_C_dicer, and RIG-I_C

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEXHc_RIG-I_DDX58 cd18073
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ...
 241-440 2.12e-139

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: 413.45  E-value: 2.12e-139
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 241 FKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQQKSVFSKYFERHG-- 318
Cdd:cd18073     1 FKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFATKVPVYEQQKSVFSKYFERHGyr 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 319 VTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSG 398
Cdd:cd18073    81 VTGISGATAENVPVEQIIENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSGNHPYNMIMFRYLDQKLGGSSG 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1883540343 399 PLPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATV 440
Cdd:cd18073   161 PLPQIIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATV 202
MPH1 super family cl34113
ERCC4-related helicase [Replication, recombination and repair];
243-767 2.42e-52

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: 195.72  E-value: 2.42e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 243 PRNYQLELALPAMKgKNTIICAPTGCGKTFVSLLICEHHLKKfpqgQKGKVVFFANQIPVYEQQKSVFSKYFERHGvTGI 322
Cdd:COG1111     4 RRLYQLNLAASALR-KNTLVVLPTGLGKTAVALLVIAERLHK----KGGKVLFLAPTKPLVEQHAEFFKEALNIPE-DEI 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 323 SGATAENVPVEQ--IVENNDIIILTPQILVNNLKKGTIpSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKlggssgPL 400
Cdd:COG1111    78 VVFTGEVSPEKRkeLWEKARIIVATPQVIENDLIAGRI-DLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDA------KD 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 401 PQVIGLTASVGvgdakNTDEALDYICKlcaSLdasVIATVKHNLEELEQVV-YKPQKFFRKVESRISDKFKYIIAQLmrd 479
Cdd:COG1111   151 PLILGMTASPG-----SDEEKIEEVCE---NL---GIENVEVRTEEDPDVApYVHDTEVEWIRVELPEELKEIRDLL--- 216

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 480 TESLAKRIcKDLENLSQIQNREFGTQKYE--QWIVTVQKacmvfQMPDKDEEsrickalflytshlrKYNDALIISEHAR 557
Cdd:COG1111   217 NEVLDDRL-KKLKELGVIVSTSPDLSKKDllALQKKLQR-----RIREDDSE---------------GYRAISILAEALK 275

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 558 MKDALDY--------LKDFFSNVRAAGFDEIEQDLTQRF--EEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETI 627
Cdd:COG1111   276 LRHALELletqgveaLLRYLERLEEEARSSGGSKASKRLvsDPRFRKAMRLAEEADIEHPKLSKLREILKEQLGTNPDSR 355

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 628 TILFVKTR----ALVDALKNwiEGnpklsfLKPGILTGRGKTNQNTGMTLPAQKCILDAFKAsGDHNILIATSVADEGID 703
Cdd:COG1111   356 IIVFTQYRdtaeMIVEFLSE--PG------IKAGRFVGQASKEGDKGLTQKEQIEILERFRA-GEFNVLVATSVAEEGLD 426

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1883540343 704 IAQCNLVILYEYVGNVIKMIQTRGR-GRARGSKCFLLTSNAGVIEK-EQINMYKEKMMNDSILRLQ 767
Cdd:COG1111   427 IPEVDLVIFYEPVPSEIRSIQRKGRtGRKREGRVVVLIAKGTRDEAyYWSSRRKEKKMKSILKKLK 492
RIG-I_C cd15805
C-terminal domain of Retinoic acid-inducible gene (RIG)-I protein, a cytoplasmic viral RNA ...
 803-916 9.94e-52

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: 176.31  E-value: 9.94e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 803 NKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCArqNCSHDWGIHVKYKTFEI 882
Cdd:cd15805     1 SYKLLCGKCKTFACNSDDIRVIKESHHVVIDPSFKERYTTKPHPKPKTFDGFEKKGKIFCK--KCGHDWGIMASYKIQNL 78

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1883540343 883 PVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPF 916
Cdd:cd15805    79 PVLKIESFVVENPVTGQQLLFRKWKDVPFAIKEF 112
CARD_RIG-I_r2 cd08817
Caspase activation and recruitment domain found in RIG-I, second repeat; Caspase activation ...
 100-189 4.73e-43

Caspase activation and recruitment domain found in RIG-I, second repeat; Caspase activation and recruitment domain (CARD) found in RIG-I (Retinoic acid Inducible Gene I, also known as Ddx58), second repeat. RIG-I is a cytoplasmic RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. RIG-I contains two N-terminal CARD domains and a C-terminal RNA helicase. 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, RIG-I recognizes different sets of viruses compared to MDA5, a related RNA helicase. RIG-I 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: 260076  Cd Length: 91  Bit Score: 151.06  E-value: 4.73e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 100 LEEYRLLLKRLQPEFKTRIIPTDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLALEKE- 178
Cdd:cd08817     1 LEEHRQLLKRIEPSFTKRIKPRDLIPYLSDCLIDRECEEILQIEEQKGMIAGAEKLVECLLRSDKENWPKTLKLALEKCg 80

                          90
                  ....*....|.
gi 1883540343 179 RNKFSELWIVE 189
Cdd:cd08817    81 YDAASELWPDE 91
DD super family cl14633
Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) ...
 2-92 1.20e-39

Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. 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. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer.


The actual alignment was detected with superfamily member cd08816:

Pssm-ID: 472698  Cd Length: 90  Bit Score: 141.43  E-value: 1.20e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343   2 TTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNnKGPMEAATLFLKFLLELQEEGWFRGFLDALDHAG 81
Cdd:cd08816     1 TALEKRNLRCYRDYIEKILRPSYVLGFMTTWLEDELVERILSEEE-KGVTEAAQLFLDAVLQLEEEGWFQGFLDALLAAG 79

                          90
                  ....*....|.
gi 1883540343  82 YSGLYEAIESW 92
Cdd:cd08816    80 YTGLCEAIENW 90
 
Name Accession Description Interval E-value
DEXHc_RIG-I_DDX58 cd18073
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ...
 241-440 2.12e-139

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: 413.45  E-value: 2.12e-139
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 241 FKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQQKSVFSKYFERHG-- 318
Cdd:cd18073     1 FKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFATKVPVYEQQKSVFSKYFERHGyr 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 319 VTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSG 398
Cdd:cd18073    81 VTGISGATAENVPVEQIIENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSGNHPYNMIMFRYLDQKLGGSSG 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1883540343 399 PLPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATV 440
Cdd:cd18073   161 PLPQIIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATV 202
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
243-767 2.42e-52

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 195.72  E-value: 2.42e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 243 PRNYQLELALPAMKgKNTIICAPTGCGKTFVSLLICEHHLKKfpqgQKGKVVFFANQIPVYEQQKSVFSKYFERHGvTGI 322
Cdd:COG1111     4 RRLYQLNLAASALR-KNTLVVLPTGLGKTAVALLVIAERLHK----KGGKVLFLAPTKPLVEQHAEFFKEALNIPE-DEI 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 323 SGATAENVPVEQ--IVENNDIIILTPQILVNNLKKGTIpSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKlggssgPL 400
Cdd:COG1111    78 VVFTGEVSPEKRkeLWEKARIIVATPQVIENDLIAGRI-DLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDA------KD 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 401 PQVIGLTASVGvgdakNTDEALDYICKlcaSLdasVIATVKHNLEELEQVV-YKPQKFFRKVESRISDKFKYIIAQLmrd 479
Cdd:COG1111   151 PLILGMTASPG-----SDEEKIEEVCE---NL---GIENVEVRTEEDPDVApYVHDTEVEWIRVELPEELKEIRDLL--- 216

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 480 TESLAKRIcKDLENLSQIQNREFGTQKYE--QWIVTVQKacmvfQMPDKDEEsrickalflytshlrKYNDALIISEHAR 557
Cdd:COG1111   217 NEVLDDRL-KKLKELGVIVSTSPDLSKKDllALQKKLQR-----RIREDDSE---------------GYRAISILAEALK 275

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 558 MKDALDY--------LKDFFSNVRAAGFDEIEQDLTQRF--EEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETI 627
Cdd:COG1111   276 LRHALELletqgveaLLRYLERLEEEARSSGGSKASKRLvsDPRFRKAMRLAEEADIEHPKLSKLREILKEQLGTNPDSR 355

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 628 TILFVKTR----ALVDALKNwiEGnpklsfLKPGILTGRGKTNQNTGMTLPAQKCILDAFKAsGDHNILIATSVADEGID 703
Cdd:COG1111   356 IIVFTQYRdtaeMIVEFLSE--PG------IKAGRFVGQASKEGDKGLTQKEQIEILERFRA-GEFNVLVATSVAEEGLD 426

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1883540343 704 IAQCNLVILYEYVGNVIKMIQTRGR-GRARGSKCFLLTSNAGVIEK-EQINMYKEKMMNDSILRLQ 767
Cdd:COG1111   427 IPEVDLVIFYEPVPSEIRSIQRKGRtGRKREGRVVVLIAKGTRDEAyYWSSRRKEKKMKSILKKLK 492
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 607-740 5.97e-52

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: 178.17  E-value: 5.97e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 607 PKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPK-LSFLKPGILTGRGKTNQNT--GMTLPAQKCILDAF 683
Cdd:cd18802     7 PKLQKLIEILREYFPKTPDFRGIIFVERRATAVVLSRLLKEHPStLAFIRCGFLIGRGNSSQRKrsLMTQRKQKETLDKF 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1883540343 684 KAsGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLT 740
Cdd:cd18802    87 RD-GELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIG-I_C cd15805
C-terminal domain of Retinoic acid-inducible gene (RIG)-I protein, a cytoplasmic viral RNA ...
 803-916 9.94e-52

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: 176.31  E-value: 9.94e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 803 NKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCArqNCSHDWGIHVKYKTFEI 882
Cdd:cd15805     1 SYKLLCGKCKTFACNSDDIRVIKESHHVVIDPSFKERYTTKPHPKPKTFDGFEKKGKIFCK--KCGHDWGIMASYKIQNL 78

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1883540343 883 PVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPF 916
Cdd:cd15805    79 PVLKIESFVVENPVTGQQLLFRKWKDVPFAIKEF 112
RIG-I_C-RD pfam11648
C-terminal domain of RIG-I; This family of proteins represents the regulatory domain RD of ...
 804-921 4.27e-51

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: 174.74  E-value: 4.27e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 804 KKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSR-PHPKPKQFSSFEKRAKIFCArqNCSHDWGIHVKYKTFEI 882
Cdd:pfam11648   1 VKLLCRKCKKFVCSGSDIRKIENSHHVVVNPDFKERYIVKePHKKPKSFEDWEPGGKISCK--KCGQDWGIMMKYKGVEL 78

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1883540343 883 PVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEM 921
Cdd:pfam11648  79 PVLKIKSFVVETPATGRRKTKKKWKDVPFEVPEFDYTEY 117
PRK13766 PRK13766
Hef nuclease; Provisional
 243-805 9.01e-49

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 185.85  E-value: 9.01e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 243 PRNYQLELALPAMKgKNTIICAPTGCGKTFVSLLICEHHLKKFPqgqkGKVVFFANQIPVYEQQKSVFSKYFerhgvtgi 322
Cdd:PRK13766   16 ARLYQQLLAATALK-KNTLVVLPTGLGKTAIALLVIAERLHKKG----GKVLILAPTKPLVEQHAEFFRKFL-------- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 323 sgataeNVPVEQIV---------------ENNDIIILTPQILVNNLKKGTIpSLSIFTLMIFDECHNTSKQHPYNMIMFN 387
Cdd:PRK13766   83 ------NIPEEKIVvftgevspekraelwEKAKVIVATPQVIENDLIAGRI-SLEDVSLLIFDEAHRAVGNYAYVYIAER 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 388 YLDQklggSSGPLpqVIGLTASVGVGDAKntdealdyicklcasldasvIATVKHNLeeleqvvykpqkFFRKVESRISD 467
Cdd:PRK13766  156 YHED----AKNPL--VLGLTASPGSDEEK--------------------IKEVCENL------------GIEHVEVRTED 197

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 468 -----------KFKYIIAQL---MRDTESLAKRICKD----LENLSQIQNREFGTQKYEqwIVTVQKAcmVFQMPDKDEE 529
Cdd:PRK13766  198 dpdvkpyvhkvKIEWVRVELpeeLKEIRDLLNEALKDrlkkLKELGVIVSISPDVSKKE--LLGLQKK--LQQEIANDDS 273

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 530 SriCKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQrfEEKLQELESVSRDPSNENPKL 609
Cdd:PRK13766  274 E--GYEAISILAEAMKLRHAVELLETQGVEALRRYLERLREEARSSGGSKASKRLVE--DPRFRKAVRKAKELDIEHPKL 349

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 610 EDLCFILQEEYHLNPETITILFVKTR----ALVDALKnwIEGnpklsfLKPGILTGRGKTNQNTGMTLPAQKCILDAFKA 685
Cdd:PRK13766  350 EKLREIVKEQLGKNPDSRIIVFTQYRdtaeKIVDLLE--KEG------IKAVRFVGQASKDGDKGMSQKEQIEILDKFRA 421

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 686 sGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRARGSKCFLLtsnagVIEKEQ------INMYKEKM 758
Cdd:PRK13766  422 -GEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRtGRQEEGRVVVL-----IAKGTRdeayywSSRRKEKK 495

                         570       580       590       600
                  ....*....|....*....|....*....|....*....|....*..
gi 1883540343 759 MNDSILRLQTWDEAVFREKILHIQTHEKFiRDSQEKPKPVPDKENKK 805
Cdd:PRK13766  496 MKEELKNLKGILNKKLQELDEEQKGEEEE-KDEQLSLDDFVKSKGKE 541
CARD_RIG-I_r2 cd08817
Caspase activation and recruitment domain found in RIG-I, second repeat; Caspase activation ...
 100-189 4.73e-43

Caspase activation and recruitment domain found in RIG-I, second repeat; Caspase activation and recruitment domain (CARD) found in RIG-I (Retinoic acid Inducible Gene I, also known as Ddx58), second repeat. RIG-I is a cytoplasmic RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. RIG-I contains two N-terminal CARD domains and a C-terminal RNA helicase. 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, RIG-I recognizes different sets of viruses compared to MDA5, a related RNA helicase. RIG-I 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: 260076  Cd Length: 91  Bit Score: 151.06  E-value: 4.73e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 100 LEEYRLLLKRLQPEFKTRIIPTDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLALEKE- 178
Cdd:cd08817     1 LEEHRQLLKRIEPSFTKRIKPRDLIPYLSDCLIDRECEEILQIEEQKGMIAGAEKLVECLLRSDKENWPKTLKLALEKCg 80

                          90
                  ....*....|.
gi 1883540343 179 RNKFSELWIVE 189
Cdd:cd08817    81 YDAASELWPDE 91
RIG-I_C pfam18119
RIG-I receptor C-terminal domain; This is the C-terminal domain of Innate Immune ...
 456-599 1.19e-41

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: 149.03  E-value: 1.19e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 456 KFFRKVESRISDKFKYIIAQLMRDTESLAKRIcKDLENLSQIQNREFGTQKYEQWIVTVQKACMVfqmpDKDEESRICka 535
Cdd:pfam18119   2 KFVVKVTSRKEDPFGDIIKDIMSKIEDHLNKS-YNLDDLSKLKPSDKGTQKYEQWIVTLQKKGAE----DPEEERRVC-- 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1883540343 536 LFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVS 599
Cdd:pfam18119  75 RALCTEHLRKYNDALIINDDARTKDALEYLLKFLKELKETKFDETERKLYRLFEEKREELQRLA 138
CARD_RIG-I_r1 cd08816
Caspase activation and recruitment domain found in RIG-I, first repeat; Caspase activation and ...
 2-92 1.20e-39

Caspase activation and recruitment domain found in RIG-I, first repeat; Caspase activation and recruitment domain (CARD) found in RIG-I (Retinoic acid Inducible Gene I, also known as Ddx58), first repeat. RIG-I is a cytoplasmic RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. RIG-I contains two N-terminal CARD domains and a C-terminal RNA helicase. 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, RIG-I recognizes different sets of viruses compared to MDA5, a related RNA helicase. RIG-I 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: 260075  Cd Length: 90  Bit Score: 141.43  E-value: 1.20e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343   2 TTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNnKGPMEAATLFLKFLLELQEEGWFRGFLDALDHAG 81
Cdd:cd08816     1 TALEKRNLRCYRDYIEKILRPSYVLGFMTTWLEDELVERILSEEE-KGVTEAAQLFLDAVLQLEEEGWFQGFLDALLAAG 79

                          90
                  ....*....|.
gi 1883540343  82 YSGLYEAIESW 92
Cdd:cd08816    80 YTGLCEAIENW 90
CARD_2 pfam16739
Caspase recruitment domain; In the probable ATP-dependent RNA helicase DDX58 this CARD domain ...
 1-93 1.41e-36

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: 132.72  E-value: 1.41e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343   1 MTTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNNKGPMEAATLFLKFLLELQEEGWFRGFLDALDHA 80
Cdd:pfam16739   1 EDDEYRRLLRLFRPRLKDTIKPTEILPHLPECLTEDDKERIRAETNNKGNTAAAELLLDRLVRSDREGWFRAFLDALRKT 80

                          90
                  ....*....|...
gi 1883540343  81 GYSGLYEAIESWD 93
Cdd:pfam16739  81 GHDGLAEELEGEY 93
CARD_2 pfam16739
Caspase recruitment domain; In the probable ATP-dependent RNA helicase DDX58 this CARD domain ...
 99-190 1.88e-28

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: 109.60  E-value: 1.88e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343  99 KLEEYRLLLKRLQPEFKTRIIPTDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLALEK- 177
Cdd:pfam16739   1 EDDEYRRLLRLFRPRLKDTIKPTEILPHLPECLTEDDKERIRAETNNKGNTAAAELLLDRLVRSDREGWFRAFLDALRKt 80

                          90
                  ....*....|...
gi 1883540343 178 ERNKFSELWIVEK 190
Cdd:pfam16739  81 GHDGLAEELEGEY 93
DEXDc smart00487
DEAD-like helicases superfamily;
235-408 2.44e-20

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 90.24  E-value: 2.44e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343  235 TNLYSPFKPRNYQLELALPAMKG-KNTIICAPTGCGKTFVSLLICEHHLKKfpqGQKGKVVFFANQIPVYEQQKSVFSKY 313
Cdd:smart00487   1 IEKFGFEPLRPYQKEAIEALLSGlRDVILAAPTGSGKTLAALLPALEALKR---GKGGRVLVLVPTRELAEQWAEELKKL 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343  314 FERHG---VTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIpSLSIFTLMIFDECHNTSKQHPYNMIMfnyld 390
Cdd:smart00487  78 GPSLGlkvVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKL-SLSNVDLVILDEAHRLLDGGFGDQLE----- 151

                          170
                   ....*....|....*...
gi 1883540343  391 qKLGGSSGPLPQVIGLTA 408
Cdd:smart00487 152 -KLLKLLPKNVQLLLLSA 168
ResIII pfam04851
Type III restriction enzyme, res subunit;
241-408 7.03e-15

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 73.09  E-value: 7.03e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 241 FKPRNYQLE-----LALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPqgqKGKVVFFANQIPVYEQQKSVFSKYFE 315
Cdd:pfam04851   2 LELRPYQIEaienlLESIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGP---IKKVLFLVPRKDLLEQALEEFKKFLP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 316 RHGVTGISGATAENvpvEQIVENNDIIILTPQILVNNLKKGTIPSLS-IFTLMIFDECHNTSKQHpYNMImFNYLDQklg 394
Cdd:pfam04851  79 NYVEIGEIISGDKK---DESVDDNKIVVTTIQSLYKALELASLELLPdFFDVIIIDEAHRSGASS-YRNI-LEYFKP--- 150

                         170
                  ....*....|....
gi 1883540343 395 gssgplPQVIGLTA 408
Cdd:pfam04851 151 ------AFLLGLTA 158
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
247-501 4.09e-13

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 73.01  E-value: 4.09e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 247 QLElALPA--MKGKNTIICAPTGCGKTFV-SLLICEHHLKkfpqgqKGKVVF------FANQipVYEQqksvFSKYFERH 317
Cdd:COG1204    27 QAE-ALEAglLEGKNLVVSAPTASGKTLIaELAILKALLN------GGKALYivplraLASE--KYRE----FKRDFEEL 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 318 GVTgISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPsLSIFTLMIFDECHntskqhpynmimfnYLDQklgGSS 397
Cdd:COG1204    94 GIK-VGVSTGDYDSDDEWLGRYDILVATPEKLDSLLRNGPSW-LRDVDLVVVDEAH--------------LIDD---ESR 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 398 GPL--------------PQVIGLTASVGvgdakNTDEALDYicklcasLDASVIAT----VkhnleELEQVVYKPQKF-F 458
Cdd:COG1204   155 GPTlevllarlrrlnpeAQIVALSATIG-----NAEEIAEW-------LDAELVKSdwrpV-----PLNEGVLYDGVLrF 217

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1883540343 459 RKVESRISDKFKYIIAQLM-------------RDTESLAKRICKDLENLSQIQNRE 501
Cdd:COG1204   218 DDGSRRSKDPTLALALDLLeeggqvlvfvssrRDAESLAKKLADELKRRLTPEERE 273
HELICc smart00490
helicase superfamily c-terminal domain;
670-731 1.63e-10

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 57.99  E-value: 1.63e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1883540343  670 GMTLPAQKCILDAFKaSGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRA 731
Cdd:smart00490  20 GLSQEEREEILDKFN-NGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRaGRA 81
uvsW PHA02558
UvsW helicase; Provisional
 232-394 8.76e-05

UvsW helicase; Provisional


Pssm-ID: 222875 [Multi-domain]  Cd Length: 501  Bit Score: 46.16  E-value: 8.76e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 232 VSDTNLYS---PFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFpqgqKGKVVFFANQIPVYEQQKS 308
Cdd:PHA02558  101 VSSLEIYSgnkKIEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLENY----EGKVLIIVPTTSLVTQMID 176

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 309 VFSKY--FERHGVTGISGATAENVpveqiveNNDIIILTPQILVNNLKKgtipSLSIFTLMIFDECH-NTSKQHPYNMIM 385
Cdd:PHA02558  177 DFVDYrlFPREAMHKIYSGTAKDT-------DAPIVVSTWQSAVKQPKE----WFDQFGMVIVDECHlFTGKSLTSIITK 245


                  ....*....
gi 1883540343 386 FNYLDQKLG 394
Cdd:PHA02558  246 LDNCKFKFG 254
DEXH_lig_assoc TIGR04121
DEXH box helicase, DNA ligase-associated; Members of this protein family are DEAD/DEAH box ...
 241-272 8.92e-03

DEXH box helicase, DNA ligase-associated; Members of this protein family are DEAD/DEAH box helicases found associated with a bacterial ATP-dependent DNA ligase, part of a four-gene system that occurs in about 12 % of prokaryotic reference genomes. The actual motif in this family is DE[VILW]H.


Pssm-ID: 274994 [Multi-domain]  Cd Length: 804  Bit Score: 39.84  E-value: 8.92e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1883540343 241 FKPRNYQLELALPAMKGKNTIICAPTGCGKTF 272
Cdd:TIGR04121  12 WTPRPFQLEMWAAALEGRSGLLIAPTGSGKTL 43
 
Name Accession Description Interval E-value
DEXHc_RIG-I_DDX58 cd18073
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ...
 241-440 2.12e-139

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: 413.45  E-value: 2.12e-139
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 241 FKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQQKSVFSKYFERHG-- 318
Cdd:cd18073     1 FKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFATKVPVYEQQKSVFSKYFERHGyr 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 319 VTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSG 398
Cdd:cd18073    81 VTGISGATAENVPVEQIIENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSGNHPYNMIMFRYLDQKLGGSSG 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1883540343 399 PLPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATV 440
Cdd:cd18073   161 PLPQIIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATV 202
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 241-440 4.73e-115

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: 350.24  E-value: 4.73e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 241 FKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFP-QGQKGKVVFFANQIPVYEQQKSVFSKYFER-HG 318
Cdd:cd18036     1 LELRNYQLELVLPALRGKNTIICAPTGSGKTRVAVYICRHHLEKRRsAGEKGRVVVLVNKVPLVEQQLEKFFKYFRKgYK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 319 VTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTI---PSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLgG 395
Cdd:cd18036    81 VTGLSGDSSHKVSFGQIVKASDVIICTPQILINNLLSGREeerVYLSDFSLLIFDECHHTQKEHPYNKIMRMYLDKKL-S 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1883540343 396 SSGPLPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATV 440
Cdd:cd18036   160 SQGPLPQILGLTASPGVGGARSFEEALEHILKLCANLDASVIATV 204
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 241-440 1.84e-111

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: 340.56  E-value: 1.84e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 241 FKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQQKSVFSKYFERHG-- 318
Cdd:cd17927     1 FKPRNYQLELAQPALKGKNTIICLPTGSGKTFVAVLICEHHLKKFPAGRKGKVVFLANKVPLVEQQKEVFRKHFERPGyk 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 319 VTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLgGSSG 398
Cdd:cd17927    81 VTGLSGDTSENVSVEQIVESSDVIIVTPQILVNDLKSGTIVSLSDFSLLVFDECHNTTKNHPYNEIMFRYLDQKL-GSSG 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1883540343 399 PLPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATV 440
Cdd:cd17927   160 PLPQILGLTASPGVGGAKNTEEALEHICKLCANLDISVIATV 201
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
243-767 2.42e-52

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 195.72  E-value: 2.42e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 243 PRNYQLELALPAMKgKNTIICAPTGCGKTFVSLLICEHHLKKfpqgQKGKVVFFANQIPVYEQQKSVFSKYFERHGvTGI 322
Cdd:COG1111     4 RRLYQLNLAASALR-KNTLVVLPTGLGKTAVALLVIAERLHK----KGGKVLFLAPTKPLVEQHAEFFKEALNIPE-DEI 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 323 SGATAENVPVEQ--IVENNDIIILTPQILVNNLKKGTIpSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKlggssgPL 400
Cdd:COG1111    78 VVFTGEVSPEKRkeLWEKARIIVATPQVIENDLIAGRI-DLDDVSLLIFDEAHRAVGNYAYVYIAERYHEDA------KD 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 401 PQVIGLTASVGvgdakNTDEALDYICKlcaSLdasVIATVKHNLEELEQVV-YKPQKFFRKVESRISDKFKYIIAQLmrd 479
Cdd:COG1111   151 PLILGMTASPG-----SDEEKIEEVCE---NL---GIENVEVRTEEDPDVApYVHDTEVEWIRVELPEELKEIRDLL--- 216

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 480 TESLAKRIcKDLENLSQIQNREFGTQKYE--QWIVTVQKacmvfQMPDKDEEsrickalflytshlrKYNDALIISEHAR 557
Cdd:COG1111   217 NEVLDDRL-KKLKELGVIVSTSPDLSKKDllALQKKLQR-----RIREDDSE---------------GYRAISILAEALK 275

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 558 MKDALDY--------LKDFFSNVRAAGFDEIEQDLTQRF--EEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETI 627
Cdd:COG1111   276 LRHALELletqgveaLLRYLERLEEEARSSGGSKASKRLvsDPRFRKAMRLAEEADIEHPKLSKLREILKEQLGTNPDSR 355

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 628 TILFVKTR----ALVDALKNwiEGnpklsfLKPGILTGRGKTNQNTGMTLPAQKCILDAFKAsGDHNILIATSVADEGID 703
Cdd:COG1111   356 IIVFTQYRdtaeMIVEFLSE--PG------IKAGRFVGQASKEGDKGLTQKEQIEILERFRA-GEFNVLVATSVAEEGLD 426

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1883540343 704 IAQCNLVILYEYVGNVIKMIQTRGR-GRARGSKCFLLTSNAGVIEK-EQINMYKEKMMNDSILRLQ 767
Cdd:COG1111   427 IPEVDLVIFYEPVPSEIRSIQRKGRtGRKREGRVVVLIAKGTRDEAyYWSSRRKEKKMKSILKKLK 492
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 607-740 5.97e-52

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: 178.17  E-value: 5.97e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 607 PKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPK-LSFLKPGILTGRGKTNQNT--GMTLPAQKCILDAF 683
Cdd:cd18802     7 PKLQKLIEILREYFPKTPDFRGIIFVERRATAVVLSRLLKEHPStLAFIRCGFLIGRGNSSQRKrsLMTQRKQKETLDKF 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1883540343 684 KAsGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLT 740
Cdd:cd18802    87 RD-GELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRARAPNSKYILMV 142
RIG-I_C cd15805
C-terminal domain of Retinoic acid-inducible gene (RIG)-I protein, a cytoplasmic viral RNA ...
 803-916 9.94e-52

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: 176.31  E-value: 9.94e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 803 NKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCArqNCSHDWGIHVKYKTFEI 882
Cdd:cd15805     1 SYKLLCGKCKTFACNSDDIRVIKESHHVVIDPSFKERYTTKPHPKPKTFDGFEKKGKIFCK--KCGHDWGIMASYKIQNL 78

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1883540343 883 PVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPF 916
Cdd:cd15805    79 PVLKIESFVVENPVTGQQLLFRKWKDVPFAIKEF 112
RIG-I_C-RD pfam11648
C-terminal domain of RIG-I; This family of proteins represents the regulatory domain RD of ...
 804-921 4.27e-51

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: 174.74  E-value: 4.27e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 804 KKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSR-PHPKPKQFSSFEKRAKIFCArqNCSHDWGIHVKYKTFEI 882
Cdd:pfam11648   1 VKLLCRKCKKFVCSGSDIRKIENSHHVVVNPDFKERYIVKePHKKPKSFEDWEPGGKISCK--KCGQDWGIMMKYKGVEL 78

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1883540343 883 PVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEM 921
Cdd:pfam11648  79 PVLKIKSFVVETPATGRRKTKKKWKDVPFEVPEFDYTEY 117
MDA5_ID cd12090
Insert domain of MDA5; MDA5 (melanoma-differentiation-associated gene 5, also known as IFIH1), ...
 467-602 2.28e-49

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: 170.19  E-value: 2.28e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 467 DKFKYIIAQLMRDTESLAKRICKDlenlsqIQNREFGTQKYEQWIVTVQKACMVFqmpdkdeesrICKALFLYTSHLRKY 546
Cdd:cd12090     1 DPFGDIIKKLMTDIEELLKMTPPD------IQPREFGTQKYEQWVVTLEKKAAKL----------GNRALRTCAEHLRKY 64

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1883540343 547 NDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDP 602
Cdd:cd12090    65 NDALLINDTARMKDALQYLKEFYTNLKEAKFDETERFLTDLFEENLEELKKLARDP 120
DEXHc_RLR-2 cd18074
DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma ...
 244-440 8.67e-49

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: 172.35  E-value: 8.67e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 244 RNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHL-KKFPQGQKGKVVFFANQIPVYEQQ-KSVFSKYFERH-GVT 320
Cdd:cd18074     4 RDYQMEVAKPALEGKNIIICLPTGSGKTRVAVYITKDHLdKKRKASEPGKVIVLVNKVPLVEQHyRKEFNPFLKHWyQVI 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 321 GISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPS-----LSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGG 395
Cdd:cd18074    84 GLSGDSQLKISFPEVVKRYDVIICTAQILENSLLNATEEEdegvqLSDFSLIIIDECHHTQKEAVYNNIMRRYLKQKIKN 163

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1883540343 396 SSG--------PLPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATV 440
Cdd:cd18074   164 RKQkkenkpliPLPQILGLTASPGVGGAKNNKKAEEHILKICANLDAFRIMTV 216
PRK13766 PRK13766
Hef nuclease; Provisional
 243-805 9.01e-49

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 185.85  E-value: 9.01e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 243 PRNYQLELALPAMKgKNTIICAPTGCGKTFVSLLICEHHLKKFPqgqkGKVVFFANQIPVYEQQKSVFSKYFerhgvtgi 322
Cdd:PRK13766   16 ARLYQQLLAATALK-KNTLVVLPTGLGKTAIALLVIAERLHKKG----GKVLILAPTKPLVEQHAEFFRKFL-------- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 323 sgataeNVPVEQIV---------------ENNDIIILTPQILVNNLKKGTIpSLSIFTLMIFDECHNTSKQHPYNMIMFN 387
Cdd:PRK13766   83 ------NIPEEKIVvftgevspekraelwEKAKVIVATPQVIENDLIAGRI-SLEDVSLLIFDEAHRAVGNYAYVYIAER 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 388 YLDQklggSSGPLpqVIGLTASVGVGDAKntdealdyicklcasldasvIATVKHNLeeleqvvykpqkFFRKVESRISD 467
Cdd:PRK13766  156 YHED----AKNPL--VLGLTASPGSDEEK--------------------IKEVCENL------------GIEHVEVRTED 197

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 468 -----------KFKYIIAQL---MRDTESLAKRICKD----LENLSQIQNREFGTQKYEqwIVTVQKAcmVFQMPDKDEE 529
Cdd:PRK13766  198 dpdvkpyvhkvKIEWVRVELpeeLKEIRDLLNEALKDrlkkLKELGVIVSISPDVSKKE--LLGLQKK--LQQEIANDDS 273

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 530 SriCKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQrfEEKLQELESVSRDPSNENPKL 609
Cdd:PRK13766  274 E--GYEAISILAEAMKLRHAVELLETQGVEALRRYLERLREEARSSGGSKASKRLVE--DPRFRKAVRKAKELDIEHPKL 349

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 610 EDLCFILQEEYHLNPETITILFVKTR----ALVDALKnwIEGnpklsfLKPGILTGRGKTNQNTGMTLPAQKCILDAFKA 685
Cdd:PRK13766  350 EKLREIVKEQLGKNPDSRIIVFTQYRdtaeKIVDLLE--KEG------IKAVRFVGQASKDGDKGMSQKEQIEILDKFRA 421

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 686 sGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRARGSKCFLLtsnagVIEKEQ------INMYKEKM 758
Cdd:PRK13766  422 -GEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRtGRQEEGRVVVL-----IAKGTRdeayywSSRRKEKK 495

                         570       580       590       600
                  ....*....|....*....|....*....|....*....|....*..
gi 1883540343 759 MNDSILRLQTWDEAVFREKILHIQTHEKFiRDSQEKPKPVPDKENKK 805
Cdd:PRK13766  496 MKEELKNLKGILNKKLQELDEEQKGEEEE-KDEQLSLDDFVKSKGKE 541
DEXHc_RLR-3 cd18075
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ...
 244-439 1.24e-44

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: 160.02  E-value: 1.24e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 244 RNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKkfpQGQKGKVVFFANQIPVYEQQ-KSVFSKYFERHGVTGI 322
Cdd:cd18075     4 HGYQWEVVAPALRGKNSIIWLPTGAGKTRAAVYVARRHLE---TKRGAKVAVLVNKVHLVDQHlEKEFHVLLDKYTVTAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 323 SGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPS---LSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSsGP 399
Cdd:cd18075    81 SGDSSHKCFFGQLARGSDVVICTAQILQNALLSGEEEAhveLTDFSLLVIDECHHTHKEAVYNKIMLSYLEKKLSRQ-GD 159

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1883540343 400 LPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIAT 439
Cdd:cd18075   160 LPQILGLTASPGTGGATSFDGAVEHILQICANLDTWVIMS 199
CARD_RIG-I_r2 cd08817
Caspase activation and recruitment domain found in RIG-I, second repeat; Caspase activation ...
 100-189 4.73e-43

Caspase activation and recruitment domain found in RIG-I, second repeat; Caspase activation and recruitment domain (CARD) found in RIG-I (Retinoic acid Inducible Gene I, also known as Ddx58), second repeat. RIG-I is a cytoplasmic RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. RIG-I contains two N-terminal CARD domains and a C-terminal RNA helicase. 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, RIG-I recognizes different sets of viruses compared to MDA5, a related RNA helicase. RIG-I 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: 260076  Cd Length: 91  Bit Score: 151.06  E-value: 4.73e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 100 LEEYRLLLKRLQPEFKTRIIPTDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLALEKE- 178
Cdd:cd08817     1 LEEHRQLLKRIEPSFTKRIKPRDLIPYLSDCLIDRECEEILQIEEQKGMIAGAEKLVECLLRSDKENWPKTLKLALEKCg 80

                          90
                  ....*....|.
gi 1883540343 179 RNKFSELWIVE 189
Cdd:cd08817    81 YDAASELWPDE 91
RIG-I_C pfam18119
RIG-I receptor C-terminal domain; This is the C-terminal domain of Innate Immune ...
 456-599 1.19e-41

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: 149.03  E-value: 1.19e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 456 KFFRKVESRISDKFKYIIAQLMRDTESLAKRIcKDLENLSQIQNREFGTQKYEQWIVTVQKACMVfqmpDKDEESRICka 535
Cdd:pfam18119   2 KFVVKVTSRKEDPFGDIIKDIMSKIEDHLNKS-YNLDDLSKLKPSDKGTQKYEQWIVTLQKKGAE----DPEEERRVC-- 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1883540343 536 LFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVS 599
Cdd:pfam18119  75 RALCTEHLRKYNDALIINDDARTKDALEYLLKFLKELKETKFDETERKLYRLFEEKREELQRLA 138
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 241-442 4.60e-41

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: 149.72  E-value: 4.60e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 241 FKPRNYQLELALPAMKgKNTIICAPTGCGKTFVS-LLICEHHLKKFPQGQKGKVVFF-ANQIPVYEQQKSVFSKYFErHG 318
Cdd:cd18034     1 FTPRSYQLELFEAALK-RNTIVVLPTGSGKTLIAvMLIKEMGELNRKEKNPKKRAVFlVPTVPLVAQQAEAIRSHTD-LK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 319 VTGISGATAENVPVEQI----VENNDIIILTPQILVNNLKKGTIpSLSIFTLMIFDECHNTSKQHPYNMIMFNYldqKLG 394
Cdd:cd18034    79 VGEYSGEMGVDKWTKERwkeeLEKYDVLVMTAQILLDALRHGFL-SLSDINLLIFDECHHATGDHPYARIMKEF---YHL 154

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1883540343 395 GSSGPLPQVIGLTASVgVGDAKNTDEALDYICKLCASLDaSVIATVKH 442
Cdd:cd18034   155 EGRTSRPRILGLTASP-VNGKGDPKSVEKKIQQLEELLN-STIKTVSD 200
CARD_RIG-I_r1 cd08816
Caspase activation and recruitment domain found in RIG-I, first repeat; Caspase activation and ...
 2-92 1.20e-39

Caspase activation and recruitment domain found in RIG-I, first repeat; Caspase activation and recruitment domain (CARD) found in RIG-I (Retinoic acid Inducible Gene I, also known as Ddx58), first repeat. RIG-I is a cytoplasmic RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. RIG-I contains two N-terminal CARD domains and a C-terminal RNA helicase. 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, RIG-I recognizes different sets of viruses compared to MDA5, a related RNA helicase. RIG-I 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: 260075  Cd Length: 90  Bit Score: 141.43  E-value: 1.20e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343   2 TTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNnKGPMEAATLFLKFLLELQEEGWFRGFLDALDHAG 81
Cdd:cd08816     1 TALEKRNLRCYRDYIEKILRPSYVLGFMTTWLEDELVERILSEEE-KGVTEAAQLFLDAVLQLEEEGWFQGFLDALLAAG 79

                          90
                  ....*....|.
gi 1883540343  82 YSGLYEAIESW 92
Cdd:cd08816    80 YTGLCEAIENW 90
CARD_2 pfam16739
Caspase recruitment domain; In the probable ATP-dependent RNA helicase DDX58 this CARD domain ...
 1-93 1.41e-36

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: 132.72  E-value: 1.41e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343   1 MTTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNNKGPMEAATLFLKFLLELQEEGWFRGFLDALDHA 80
Cdd:pfam16739   1 EDDEYRRLLRLFRPRLKDTIKPTEILPHLPECLTEDDKERIRAETNNKGNTAAAELLLDRLVRSDREGWFRAFLDALRKT 80

                          90
                  ....*....|...
gi 1883540343  81 GYSGLYEAIESWD 93
Cdd:pfam16739  81 GHDGLAEELEGEY 93
RLR_C cd15804
C-terminal domain of Retinoic acid-inducible gene (RIG)-I-like Receptors; Retinoic ...
 805-916 1.42e-36

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: 133.21  E-value: 1.42e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 805 KLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFS-SFEKRAKIFCArqNCSHDWGIHVKYKTFEIP 883
Cdd:cd15804     2 TLLCKKCSAFACNSDDIRKIEGSHHVVIDPDFLERVKIEEDPKKKKKFeDTQILGKIKCK--KCGHDWGTMMKYKGVELP 79

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1883540343 884 VIKIESFVVEDIaTGVQTLYSKWKDFHFEKIPF 916
Cdd:cd15804    80 VLKIKNFVFVDE-DEERATKKKWKDVPFAIPEI 111
RLR_C_like cd15803
C-terminal domain of Retinoic acid-inducible gene (RIG)-I-like Receptors, Cereblon (CRBN), and ...
 806-890 1.60e-34

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: 126.48  E-value: 1.60e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 806 LLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQ-FSSFEKRAKIFCArqNCSHDWGIHVKYKTFEIPV 884
Cdd:cd15803     1 LLCKNCSALACTGEDIRVIELCHHVVYKPAFKNNYNVIGRPSTVHkWFDGYAWGIISCK--ICSSHWGWHFTYKPQKLPV 78


                  ....*.
gi 1883540343 885 IKIESF 890
Cdd:cd15803    79 LKRESF 84
CARD_2 pfam16739
Caspase recruitment domain; In the probable ATP-dependent RNA helicase DDX58 this CARD domain ...
 99-190 1.88e-28

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: 109.60  E-value: 1.88e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343  99 KLEEYRLLLKRLQPEFKTRIIPTDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLALEK- 177
Cdd:pfam16739   1 EDDEYRRLLRLFRPRLKDTIKPTEILPHLPECLTEDDKERIRAETNNKGNTAAAELLLDRLVRSDREGWFRAFLDALRKt 80

                          90
                  ....*....|...
gi 1883540343 178 ERNKFSELWIVEK 190
Cdd:pfam16739  81 GHDGLAEELEGEY 93
helicase_insert_domain cd12088
helicase_insert_domain; helicase_insert_domain; This helical domain can be found inserted in a ...
 535-602 9.83e-22

helicase_insert_domain; helicase_insert_domain; This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases, like archaeal Hef helicase, MDA5-like helicases and FancM-like helicases. The exact function of this domain is unknown, but seems to play a role in interaction with nucleotides and/or the stabilization of the nucleotide complex.


Pssm-ID: 277187  Cd Length: 82  Bit Score: 89.84  E-value: 9.83e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1883540343 535 ALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDP 602
Cdd:cd12088    15 LKLLYTAHLRKLNDALELLEDAGIWDALKYIKMFFTEVREGIFDELERKLTLRFDEKLQKLIALSRDP 82
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 257-408 1.89e-20

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: 88.61  E-value: 1.89e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 257 GKNTIICAPTGCGKTFVSLLICEHHLKKfpqgQKGKVVFFANQIPVYEQQKSVFSKYFERHG-VTGISGATAENVPVEQI 335
Cdd:cd00046     1 GENVLITAPTGSGKTLAALLAALLLLLK----KGKKVLVLVPTKALALQTAERLRELFGPGIrVAVLVGGSSAEEREKNK 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1883540343 336 VENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYnMIMFNYLDQKLGgssGPLPQVIGLTA 408
Cdd:cd00046    77 LGDADIIIATPDMLLNLLLREDRLFLKDLKLIIVDEAHALLIDSRG-ALILDLAVRKAG---LKNAQVILLSA 145
DEXDc smart00487
DEAD-like helicases superfamily;
235-408 2.44e-20

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 90.24  E-value: 2.44e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343  235 TNLYSPFKPRNYQLELALPAMKG-KNTIICAPTGCGKTFVSLLICEHHLKKfpqGQKGKVVFFANQIPVYEQQKSVFSKY 313
Cdd:smart00487   1 IEKFGFEPLRPYQKEAIEALLSGlRDVILAAPTGSGKTLAALLPALEALKR---GKGGRVLVLVPTRELAEQWAEELKKL 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343  314 FERHG---VTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIpSLSIFTLMIFDECHNTSKQHPYNMIMfnyld 390
Cdd:smart00487  78 GPSLGlkvVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKL-SLSNVDLVILDEAHRLLDGGFGDQLE----- 151

                          170
                   ....*....|....*...
gi 1883540343  391 qKLGGSSGPLPQVIGLTA 408
Cdd:smart00487 152 -KLLKLLPKNVQLLLLSA 168
CARD_IPS-1_RIG-I cd08789
Caspase activation and recruitment domains (CARDs) found in IPS-1 and RIG-I-like RNA helicases; ...
 2-92 9.55e-20

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: 84.82  E-value: 9.55e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343   2 TTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNNKGPMEAATLFLKFLLELQEEGWFRGFLDALDHAG 81
Cdd:cd08789     1 TDDEKQLLQCYRATVERSLDVVYVLPYLTDCLPDEDRERIRAAEENRGNSGAAALLLNTLLQLEKEGWFRGFLDALRATG 80

                          90
                  ....*....|.
gi 1883540343  82 YSGLYEAIESW 92
Cdd:cd08789    81 YTGARELIDNW 91
DEXDc_FANCM cd18033
DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ...
 244-437 2.06e-19

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: 86.61  E-value: 2.06e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 244 RNYQLELALPAMKgKNTIICAPTGCGKTFVSLLICEHHLKKFPqgqKGKVVFFANQIPVYEQQKSVFskyferHGVTGI- 322
Cdd:cd18033     4 RDYQFTIVQKALF-QNTLVALPTGLGKTFIAAVVMLNYYRWFP---KGKIVFMAPTKPLVSQQIEAC------YKITGIp 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 323 SGATAE---NVPVE---QIVENNDIIILTPQILVNNLKKGTIPSLSIfTLMIFDECHNTSKQHPYNMIMfnyldQKLGGS 396
Cdd:cd18033    74 SSQTAEltgSVPPTkraELWASKRVFFLTPQTLENDLKEGDCDPKSI-VCLVIDEAHRATGNYAYCQVV-----RELMRY 147

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1883540343 397 SGPLpQVIGLTASVGVGdakntdeaLDYICKLCASLDASVI 437
Cdd:cd18033   148 NSHF-RILALTATPGSK--------LEAVQQVIDNLLISHI 179
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 242-411 2.46e-19

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: 86.41  E-value: 2.46e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 242 KPRNYQLELALPAMKGkNTIICAPTGCGKTFVSLLICEHHLKKfpqgQKGKVVFFANQIPVYEQQKSVFSKYFERHG-VT 320
Cdd:cd18035     2 ERRLYQVLIAAVALNG-NTLIVLPTGLGKTIIAILVAADRLTK----KGGKVLILAPSRPLVEQHAENLKRVLNIPDkIT 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 321 GISGATAENvPVEQIVENNDIIILTPQILVNNLKKGTIpSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQklggSSGPL 400
Cdd:cd18035    77 SLTGEVKPE-ERAERWDASKIIVATPQVIENDLLAGRI-TLDDVSLLIFDEAHHAVGNYAYVYIAHRYKRE----ANNPL 150

                         170
                  ....*....|.
gi 1883540343 401 pqVIGLTASVG 411
Cdd:cd18035   151 --ILGLTASPG 159
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 607-739 6.47e-19

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: 83.94  E-value: 6.47e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 607 PKLEDLCFILQEEYHLNPETIT---ILFVKTRALVDALKNWIEGNPKLsfLKPGILTGRGKTNQNTGMTLPAQKCILDAF 683
Cdd:cd18801     9 PKLEKLEEIVKEHFKKKQEGSDtrvIIFSEFRDSAEEIVNFLSKIRPG--IRATRFIGQASGKSSKGMSQKEQKEVIEQF 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1883540343 684 KAsGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRARGSKCFLL 739
Cdd:cd18801    87 RK-GGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMIQRMGRtGRKRQGRVVVL 142
CARD_IPS-1_RIG-I cd08789
Caspase activation and recruitment domains (CARDs) found in IPS-1 and RIG-I-like RNA helicases; ...
 100-186 2.84e-17

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: 77.50  E-value: 2.84e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 100 LEEYRLLLKRLQPEFKTRIIPTDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLAL-EKE 178
Cdd:cd08789     1 TDDEKQLLQCYRATVERSLDVVYVLPYLTDCLPDEDRERIRAAEENRGNSGAAALLLNTLLQLEKEGWFRGFLDALrATG 80


                  ....*...
gi 1883540343 179 RNKFSELW 186
Cdd:cd08789    81 YTGARELI 88
LGP2_C cd15806
C-terminal domain of Laboratory of Genetics and Physiology 2 (LGP2), a cytoplasmic viral RNA ...
 805-917 5.37e-16

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: 74.76  E-value: 5.37e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 805 KLLCRKCKALACYTADVRVIEECHYTVLGDAFKECF-VSRPHPKPKQFSSFEKRAKIFCArqNCSHDWGIHVKYKTFEIP 883
Cdd:cd15806     2 QLLCRNCFVAVAHGSDLRKVEGTHHVNINPNFSRYYkVGGKPILIRTFEDWEPGGTISCS--NCGQVWGMEMIYKSVLLP 79

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1883540343 884 VIKIESFVVEDIATGVQtlYSKWKDFHFEKIPFD 917
Cdd:cd15806    80 VLSIKNFVLETPEGRRQ--AKKWKDVPFSVEEFD 111
ResIII pfam04851
Type III restriction enzyme, res subunit;
241-408 7.03e-15

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 73.09  E-value: 7.03e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 241 FKPRNYQLE-----LALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPqgqKGKVVFFANQIPVYEQQKSVFSKYFE 315
Cdd:pfam04851   2 LELRPYQIEaienlLESIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGP---IKKVLFLVPRKDLLEQALEEFKKFLP 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 316 RHGVTGISGATAENvpvEQIVENNDIIILTPQILVNNLKKGTIPSLS-IFTLMIFDECHNTSKQHpYNMImFNYLDQklg 394
Cdd:pfam04851  79 NYVEIGEIISGDKK---DESVDDNKIVVTTIQSLYKALELASLELLPdFFDVIIIDEAHRSGASS-YRNI-LEYFKP--- 150

                         170
                  ....*....|....
gi 1883540343 395 gssgplPQVIGLTA 408
Cdd:pfam04851 151 ------AFLLGLTA 158
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 608-731 1.20e-14

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: 70.70  E-value: 1.20e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 608 KLEDLCFILQEEYHLNpetiTILFVKTRALVDAlknwiegnpKLSFLKPGILTGR--GKTNQNTgmtlpaQKCILDAFKa 685
Cdd:pfam00271   2 KLEALLELLKKERGGK----VLIFSQTKKTLEA---------ELLLEKEGIKVARlhGDLSQEE------REEILEDFR- 61

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1883540343 686 SGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRA 731
Cdd:pfam00271  62 KGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRaGRA 108
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 245-374 1.98e-14

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: 72.29  E-value: 1.98e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 245 NYQLELALPAM-KGKNTIICAPTGCGKTFVSLLICEHHLKKfpqgQKGKVVFFANQIPVYEQQKSVFSKYFERHG--VTG 321
Cdd:cd17921     4 PIQREALRALYlSGDSVLVSAPTSSGKTLIAELAILRALAT----SGGKAVYIAPTRALVNQKEADLRERFGPLGknVGL 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1883540343 322 ISGATAENvpvEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHN 374
Cdd:cd17921    80 LTGDPSVN---KLLLAEADILVATPEKLDLLLRNGGERLIQDVRLVVVDEAHL 129
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 243-376 7.85e-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: 69.64  E-value: 7.85e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 243 PRNYQLElALPAMKGKNT----IICAPTGCGKTFVSL-LICEHHlkkfpqgqKGKVVFFANQIPVYEQQKSVFSKYFERH 317
Cdd:cd17926     1 LRPYQEE-ALEAWLAHKNnrrgILVLPTGSGKTLTALaLIAYLK--------ELRTLIVVPTDALLDQWKERFEDFLGDS 71

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1883540343 318 GVTGISGataenvPVEQIVENNDIIILTPQILVNNLKKGTIPSLSiFTLMIFDECHNTS 376
Cdd:cd17926    72 SIGLIGG------GKKKDFDDANVVVATYQSLSNLAEEEKDLFDQ-FGLLIVDEAHHLP 123
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
234-735 2.28e-13

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 73.91  E-value: 2.28e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 234 DTNLYSPFKPRNYQLE-----LALPAMKGKNTIICAPTGCGKTFVSLLICEHHLkkfpqgQKGKVVFFANQIPVYEQQKS 308
Cdd:COG1061    72 DEASGTSFELRPYQQEalealLAALERGGGRGLVVAPTGTGKTVLALALAAELL------RGKRVLVLVPRRELLEQWAE 145

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 309 VFSKYFERHGVTGISGATAEnvpveqivennDIIILTPQILVNNLKKGTIPSLsiFTLMIFDECHN-TSKQhpYNMIMfN 387
Cdd:COG1061   146 ELRRFLGDPLAGGGKKDSDA-----------PITVATYQSLARRAHLDELGDR--FGLVIIDEAHHaGAPS--YRRIL-E 209

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 388 YLDQKLggssgplpqVIGLTASVGVGDAKNTDealdyicklcasldasviatvkhnLEELEQVVYkpqkffrkvesrisd 467
Cdd:COG1061   210 AFPAAY---------RLGLTATPFRSDGREIL------------------------LFLFDGIVY--------------- 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 468 kfKYIIAQLMRDtESLAKRICkdlenlsqiqnrefgtqkyeqwivtvqkacmvfqMPDKDEESRICKALFLYTSHLRKyn 547
Cdd:COG1061   242 --EYSLKEAIED-GYLAPPEY----------------------------------YGIRVDLTDERAEYDALSERLRE-- 282

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 548 daLIISEHARMKDALDYLKDFFSNVRAagfdeieqdltqrfeeklqelesvsrdpsnenpkledlcfilqeeyhlnpeti 627
Cdd:COG1061   283 --ALAADAERKDKILRELLREHPDDRK----------------------------------------------------- 307

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 628 TILFVKTRALVDALKNWIEGNpklsFLKPGILTGRgktnqntgMTLPAQKCILDAFKAsGDHNILIATSVADEGIDIAQC 707
Cdd:COG1061   308 TLVFCSSVDHAEALAELLNEA----GIRAAVVTGD--------TPKKEREEILEAFRD-GELRILVTVDVLNEGVDVPRL 374

                         490       500
                  ....*....|....*....|....*....
gi 1883540343 708 NLVILYEYVGNVIKMIQTRGRG-RARGSK 735
Cdd:COG1061   375 DVAILLRPTGSPREFIQRLGRGlRPAPGK 403
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
247-501 4.09e-13

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 73.01  E-value: 4.09e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 247 QLElALPA--MKGKNTIICAPTGCGKTFV-SLLICEHHLKkfpqgqKGKVVF------FANQipVYEQqksvFSKYFERH 317
Cdd:COG1204    27 QAE-ALEAglLEGKNLVVSAPTASGKTLIaELAILKALLN------GGKALYivplraLASE--KYRE----FKRDFEEL 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 318 GVTgISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPsLSIFTLMIFDECHntskqhpynmimfnYLDQklgGSS 397
Cdd:COG1204    94 GIK-VGVSTGDYDSDDEWLGRYDILVATPEKLDSLLRNGPSW-LRDVDLVVVDEAH--------------LIDD---ESR 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 398 GPL--------------PQVIGLTASVGvgdakNTDEALDYicklcasLDASVIAT----VkhnleELEQVVYKPQKF-F 458
Cdd:COG1204   155 GPTlevllarlrrlnpeAQIVALSATIG-----NAEEIAEW-------LDAELVKSdwrpV-----PLNEGVLYDGVLrF 217

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1883540343 459 RKVESRISDKFKYIIAQLM-------------RDTESLAKRICKDLENLSQIQNRE 501
Cdd:COG1204   218 DDGSRRSKDPTLALALDLLeeggqvlvfvssrRDAESLAKKLADELKRRLTPEERE 273
MDA5_C cd15807
C-terminal domain of Melanoma differentiation-associated protein 5, a cytoplasmic viral RNA ...
 806-908 4.77e-13

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: 66.36  E-value: 4.77e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 806 LLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPK-PKQFSSFEKRAKIFCarQNCSHDWGIHVKYKTFEIPV 884
Cdd:cd15807     6 FLCKNCSVLVCSGEDIQVIEKMHHVNVTPEFKELYIKRENKAlQEKLADYQTNGEIIC--KTCGQAWGTMMVHKGLELPC 83

                          90       100
                  ....*....|....*....|....
gi 1883540343 885 IKIESFVVEDIATGVQTLYSKWKD 908
Cdd:cd15807    84 LKIRNFVVTFKNNSTKKTYKKWVE 107
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 246-373 5.74e-13

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: 67.65  E-value: 5.74e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 246 YQLELALPAMKGKNTIICAPTGCGKTFVSLL-ICEHHLKKFPqgqKGKVVFFANQIPVYEQQKSVFSKYFERHGVTGISG 324
Cdd:pfam00270   3 IQAEAIPAILEGRDVLVQAPTGSGKTLAFLLpALEALDKLDN---GPQALVLAPTRELAEQIYEELKKLGKGLGLKVASL 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1883540343 325 ATAENVPVE-QIVENNDIIILTPQILVNNLKKgtIPSLSIFTLMIFDECH 373
Cdd:pfam00270  80 LGGDSRKEQlEKLKGPDILVGTPGRLLDLLQE--RKLLKNLKLLVLDEAH 127
HELICc smart00490
helicase superfamily c-terminal domain;
670-731 1.63e-10

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 57.99  E-value: 1.63e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1883540343  670 GMTLPAQKCILDAFKaSGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRA 731
Cdd:smart00490  20 GLSQEEREEILDKFN-NGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRaGRA 81
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 243-418 6.65e-10

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: 58.73  E-value: 6.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 243 PRNYQLElALPAM-----KGKNTI-ICAPTGCGKTFVSLLICEHHLKkfpQGQKGKVVFFANQIPVYEQQKSVFSKYFER 316
Cdd:cd18032     1 PRYYQQE-AIEALeeareKGQRRAlLVMATGTGKTYTAAFLIKRLLE---ANRKKRILFLAHREELLEQAERSFKEVLPD 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 317 HGVTGISGATAEnvpveqiVENNDIIILTPQILVNNlKKGTIPSLSIFTLMIFDECH-NTSKQhpYNMImFNYLDQKLgg 395
Cdd:cd18032    77 GSFGNLKGGKKK-------PDDARVVFATVQTLNKR-KRLEKFPPDYFDLIIIDEAHhAIASS--YRKI-LEYFEPAF-- 143

                         170       180
                  ....*....|....*....|...
gi 1883540343 396 ssgplpqVIGLTASVGVGDAKNT 418
Cdd:cd18032   144 -------LLGLTATPERTDGLDT 159
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
 579-728 1.35e-07

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


Pssm-ID: 350176 [Multi-domain]  Cd Length: 153  Bit Score: 51.87  E-value: 1.35e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 579 EIEQDLTQRFEEKLQELE--SVSRDPSNENP-KLEDLCFILQeeYHLNPETItILFVKTralVDALKNWIEGnpklsFLK 655
Cdd:cd18789     3 EIRCPMTPEFYREYLGLGahRKRRLLAAMNPnKLRALEELLK--RHEQGDKI-IVFTDN---VEALYRYAKR-----LLK 71

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1883540343 656 PGILtgrGKTNQNTGMTlpaqkcILDAFKaSGDHNILIATSVADEGIDIAQCN-LVILYEYVGNVIKMIQTRGR 728
Cdd:cd18789    72 PFIT---GETPQSEREE------ILQNFR-EGEYNTLVVSKVGDEGIDLPEANvAIQISGHGGSRRQEAQRLGR 135
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 690-740 3.02e-07

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: 48.47  E-value: 3.02e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1883540343 690 NILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGR-GRA--RGSKCFLLT 740
Cdd:cd18785    24 EILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRaGRGgkDEGEVILFV 77
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 607-714 3.24e-07

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: 50.20  E-value: 3.24e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 607 PKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPklsfLKPGILTGrgktnqntGMTLPAQKCILDAFKaS 686
Cdd:cd18787     9 EEEEKKLLLLLLLLEKLKPGKAIIFVNTKKRVDRLAELLEELG----IKVAALHG--------DLSQEERERALKKFR-S 75

                          90       100
                  ....*....|....*....|....*...
gi 1883540343 687 GDHNILIATSVADEGIDIAQCNLVILYE 714
Cdd:cd18787    76 GKVRVLVATDVAARGLDIPGVDHVINYD 103
DEADc_DDX52 cd17957
DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ...
 251-371 1.52e-06

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: 49.90  E-value: 1.52e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 251 ALPAM-KGKNTIICAPTGCGKTFVSLLICEHHLKKfPQGQKG--KVVF-----FANQIpVYEQQKSVFSKYFERHGVTGI 322
Cdd:cd17957    20 AIPILlHGRDLLACAPTGSGKTLAFLIPILQKLGK-PRKKKGlrALILaptreLASQI-YRELLKLSKGTGLRIVLLSKS 97

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1883540343 323 SGATAENVPVEqiVENNDIIILTPQILVNNLKKGTIpSLSIFTLMIFDE 371
Cdd:cd17957    98 LEAKAKDGPKS--ITKYDILVSTPLRLVFLLKQGPI-DLSSVEYLVLDE 143
CARD_IPS1 cd08811
Caspase activation and recruitment domain (CARD) found in IPS-1; Caspase activation and ...
 101-177 1.20e-05

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: 44.66  E-value: 1.20e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1883540343 101 EEYRLLLKRLQPEFKTRIIPTDIISDLSeCLINQECEEILQICSTKGMMAGAEKLVECLLRsdKENWPKTLKLALEK 177
Cdd:cd08811     4 DKEYKYLRRNMGVFCHDIKVSEIIPYLP-CLTRSDRDEILAKKDMSGNRDTAWTLLDHLQR--RPGWVEDFIKALRN 77
DEXHc_Brr2_2 cd18021
C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type ...
 259-404 5.85e-05

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


Pssm-ID: 350779 [Multi-domain]  Cd Length: 191  Bit Score: 44.94  E-value: 5.85e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 259 NTIICAPTGCGKTFVSLLICEHHLKkfpQGQKGKVVFFAnqiPVYEQQKSVFSKYFERHG------VTGISGATAENVpv 332
Cdd:cd18021    21 NVFVGAPTGSGKTVCAELALLRHWR---QNPKGRAVYIA---PMQELVDARYKDWRAKFGpllgkkVVKLTGETSTDL-- 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1883540343 333 eQIVENNDIIILTPQ---ILVNNLK-KGTIPSLSiftLMIFDECHntskqhpynMImfnyldqklGGSSGPLPQVI 404
Cdd:cd18021    93 -KLLAKSDVILATPEqwdVLSRRWKqRKNVQSVE---LFIADELH---------LI---------GGENGPVYEVV 146
uvsW PHA02558
UvsW helicase; Provisional
 232-394 8.76e-05

UvsW helicase; Provisional


Pssm-ID: 222875 [Multi-domain]  Cd Length: 501  Bit Score: 46.16  E-value: 8.76e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 232 VSDTNLYS---PFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFpqgqKGKVVFFANQIPVYEQQKS 308
Cdd:PHA02558  101 VSSLEIYSgnkKIEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLENY----EGKVLIIVPTTSLVTQMID 176

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 309 VFSKY--FERHGVTGISGATAENVpveqiveNNDIIILTPQILVNNLKKgtipSLSIFTLMIFDECH-NTSKQHPYNMIM 385
Cdd:PHA02558  177 DFVDYrlFPREAMHKIYSGTAKDT-------DAPIVVSTWQSAVKQPKE----WFDQFGMVIVDECHlFTGKSLTSIITK 245


                  ....*....
gi 1883540343 386 FNYLDQKLG 394
Cdd:PHA02558  246 LDNCKFKFG 254
DEADc cd00268
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ...
 249-372 1.13e-04

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


Pssm-ID: 350669 [Multi-domain]  Cd Length: 196  Bit Score: 43.97  E-value: 1.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 249 ELALP-AMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFF--------ANQIpvyeqqKSVFSKYFERHG- 318
Cdd:cd00268    18 AQAIPlILSGRDVIGQAQTGSGKTLAFLLPILEKLLPEPKKKGRGPQALvlaptrelAMQI------AEVARKLGKGTGl 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1883540343 319 -VTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIpSLSIFTLMIFDEC 372
Cdd:cd00268    92 kVAAIYGGAPIKKQIEALKKGPDIVVGTPGRLLDLIERGKL-DLSNVKYLVLDEA 145
PTZ00110 PTZ00110
helicase; Provisional
 679-756 1.54e-04

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 45.53  E-value: 1.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 679 ILDAFKaSGDHNILIATSVADEGIDIAQCNLVILYEYVGNV---IKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYK 755
Cdd:PTZ00110  419 VLNEFK-TGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIedyVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVKVLR 497


                  .
gi 1883540343 756 E 756
Cdd:PTZ00110  498 E 498
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
608-714 1.55e-04

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 45.14  E-value: 1.55e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 608 KLEDLCFILQEEyhlNPETiTILFVKTRALVDALKNWIEGNpklsflkpGI----LTGrgktnqntGMTLPAQKCILDAF 683
Cdd:COG0513   228 KLELLRRLLRDE---DPER-AIVFCNTKRGADRLAEKLQKR--------GIsaaaLHG--------DLSQGQRERALDAF 287

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1883540343 684 KaSGDHNILIATSVADEGIDIAQCNLVILYE 714
Cdd:COG0513   288 R-NGKIRVLVATDVAARGIDIDDVSHVINYD 317
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 242-371 1.77e-04

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 44.93  E-value: 1.77e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 242 KPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVF--------FANQipVYEQQKSvFSKY 313
Cdd:PRK11192   23 RPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRIliltptreLAMQ--VADQARE-LAKH 99

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1883540343 314 fERHGVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLmIFDE 371
Cdd:PRK11192  100 -THLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETL-ILDE 155
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 624-714 1.77e-04

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: 42.46  E-value: 1.77e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 624 PETITILFVKTRALVDALKNWIEGNPK-----------------LSFLKPGILTGRGKTNQNTGMTlpaqkcILDAFKAS 686
Cdd:cd18793     3 PKIEEVVSGKLEALLELLEELREPGEKvlifsqftdtldileeaLRERGIKYLRLDGSTSSKERQK------LVDRFNED 76

                          90       100
                  ....*....|....*....|....*....
gi 1883540343 687 GDHNI-LIATSVADEGIDIAQCNLVILYE 714
Cdd:cd18793    77 PDIRVfLLSTKAGGVGLNLTAANRVILYD 105
DEXHc_HFM1 cd18023
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ...
 245-347 2.86e-04

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: 43.11  E-value: 2.86e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 245 NYQLELALPAM--KGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKG--KVVFFAnQIPVYEQQKsvFSKYFERHGVT 320
Cdd:cd18023     3 NRIQSEVFPDLlySDKNFVVSAPTGSGKTVLFELAILRLLKERNPLPWGnrKVVYIA-PIKALCSEK--YDDWKEKFGPL 79

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1883540343 321 GIS-----GATaENVPVEQIvENNDIIILTPQ 347
Cdd:cd18023    80 GLScaeltGDT-EMDDTFEI-QDADIILTTPE 109
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
 256-439 4.98e-04

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: 41.94  E-value: 4.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 256 KGKNTIICAPTGCGKTFVSLLICEHHLKKfpqgqKGKVVFFANQIPVYEQQKSVFSKYFE---RHGV-TGISGATAENVP 331
Cdd:cd18028    16 KGENLLISIPTASGKTLIAEMAMVNTLLE-----GGKALYLVPLRALASEKYEEFKKLEEiglKVGIsTGDYDEDDEWLG 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 332 veqiveNNDIIILTPQILvNNLKKGTIPSLSIFTLMIFDECHNTSkqhpynmimfnylDQKLGG----------SSGPLP 401
Cdd:cd18028    91 ------DYDIIVATYEKF-DSLLRHSPSWLRDVGVVVVDEIHLIS-------------DEERGPtlesivarlrRLNPNT 150

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1883540343 402 QVIGLTASVGvgdakNTDEaldyickLCASLDASVIAT 439
Cdd:cd18028   151 QIIGLSATIG-----NPDE-------LAEWLNAELVES 176
CARD_MDA5_r2 cd08819
Caspase activation and recruitment domain found in MDA5, second repeat; Caspase activation and ...
 33-87 7.43e-04

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: 39.62  E-value: 7.43e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1883540343  33 FREEEVQYIQAEKNNKGPMEAATLFLKFLLElQEEGWFRGFLDALDHAGYSGLYE 87
Cdd:cd08819    33 LTAEDRERILAATENHGNRSGARELLSRIVR-QKEGWFSKFLQALRETEHNNLAE 86
PRK00254 PRK00254
ski2-like helicase; Provisional
 254-411 8.00e-04

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 43.27  E-value: 8.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 254 AMKGKNTIICAPTGCGKTFVSLLICEHHLKKfpqgQKGKVVFFANQIPVYEQQKSVFsKYFERHGVTgISGATAENVPVE 333
Cdd:PRK00254   36 VLEGKNLVLAIPTASGKTLVAEIVMVNKLLR----EGGKAVYLVPLKALAEEKYREF-KDWEKLGLR-VAMTTGDYDSTD 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 334 QIVENNDIIILTPQILVNNLKKGTiPSLSIFTLMIFDECH---NTSKQHPYNMIMFNYLDQKlggssgplpQVIGLTASV 410
Cdd:PRK00254  110 EWLGKYDIIIATAEKFDSLLRHGS-SWIKDVKLVVADEIHligSYDRGATLEMILTHMLGRA---------QILGLSATV 179


                  .
gi 1883540343 411 G 411
Cdd:PRK00254  180 G 180
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
240-373 8.69e-04

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


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 43.00  E-value: 8.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 240 PFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLkkfpqgQKGKVVFF-------ANQipvyeqqksvfsK 312
Cdd:COG4581    23 GFELDPFQEEAILALEAGRSVLVAAPTGSGKTLVAEFAIFLAL------ARGRRSFYtapikalSNQ------------K 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1883540343 313 YF---ERHG------VTGisgataenvpveQIVENND--IIILTPQILvNNLKKGTIPSLSIFTLMIFDECH 373
Cdd:COG4581    85 FFdlvERFGaenvglLTG------------DASVNPDapIVVMTTEIL-RNMLYREGADLEDVGVVVMDEFH 143
DEXHc_Brr2_1 cd18019
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD ...
 259-373 1.56e-03

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: 40.82  E-value: 1.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 259 NTIICAPTGCGKTFVSLLICEHHLKKF--PQG----QKGKVVFFANQIPVYEQQKSVFSKYFERHGVTgISGATAENVPV 332
Cdd:cd18019    35 NLLLCAPTGAGKTNVALLTILREIGKHrnPDGtinlDAFKIVYIAPMKALVQEMVGNFSKRLAPYGIT-VAELTGDQQLT 113

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1883540343 333 EQIVENNDIIILTPQIL-VNNLKKGTIPSLSIFTLMIFDECH 373
Cdd:cd18019   114 KEQISETQIIVTTPEKWdIITRKSGDRTYTQLVRLIIIDEIH 155
DEXHc_DDX60 cd18025
DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an ...
 242-373 2.17e-03

DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an IFN-inducible cytoplasmic helicase that plays a role in RIG-I-mediated type I interferon (IFN) nuclease-mediated viral RNA degradation. DDX60 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350783 [Multi-domain]  Cd Length: 192  Bit Score: 40.43  E-value: 2.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 242 KPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKkfpQGQKGKVVFFA------NQI--PVYEQqksvFSKY 313
Cdd:cd18025     1 NPDAWQRELLDIVDRRESALIVAPTSSGKTFISYYCMEKVLR---ESDDGVVVYVAptkalvNQVvaEVYAR----FSKK 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1883540343 314 FERHGVTGISGATAENvpVEQIVENNDIIILTPQILVNNLkkgTIPSLSIFT----LMIFDECH 373
Cdd:cd18025    74 YPPSGKSLWGVFTRDY--RHNNPMNCQVLITVPECLEILL---LSPHNASWVprikYVIFDEIH 132
SF2_C_Hrq cd18797
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...
 628-734 3.04e-03

C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350184 [Multi-domain]  Cd Length: 146  Bit Score: 39.16  E-value: 3.04e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 628 TILFVKTRALVDALKNWIEGN-PKLSFLKPGILTGRGktnqntgmTLPAQ--KCILDAFKaSGDHNILIATSVADEGIDI 704
Cdd:cd18797    38 TIVFCRSRKLAELLLRYLKARlVEEGPLASKVASYRA--------GYLAEdrREIEAELF-NGELLGVVATNALELGIDI 108

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1883540343 705 AQCNLVILYEYVGNVIKMIQTRGR-GRARGS 734
Cdd:cd18797   109 GGLDAVVLAGYPGSLASLWQQAGRaGRRGKD 139
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 244-591 3.72e-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: 40.84  E-value: 3.72e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 244 RNYQLELALPAMKGKN--TIICAPTGCGKTFVSLLICEHHLKKFpQGQKgkvVFFAnqIPvY----EQQKSVFSKYFER- 316
Cdd:COG1203   132 QNEALELALEAAEEEPglFILTAPTGGGKTEAALLFALRLAAKH-GGRR---IIYA--LP-FtsiiNQTYDRLRDLFGEd 204

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 317 ----HGVTGISGATAENVPVEQIVE--------NNDIIILTP-QILVNNLKKGTIPSLSIFTLM----IFDECHNtskqh 379
Cdd:COG1203   205 vllhHSLADLDLLEEEEEYESEARWlkllkelwDAPVVVTTIdQLFESLFSNRKGQERRLHNLAnsviILDEVQA----- 279

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 380 pYNMIMFNYLdqklggssgplpqvigltasvgvgdakntDEALDYIcklcASLDASVI---AT-----VKHNLEELEQVV 451
Cdd:COG1203   280 -YPPYMLALL-----------------------------LRLLEWL----KNLGGSVIlmtATlppllREELLEAYELIP 325

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 452 YKPQKFFRKVESRISDKFKYIIAQLmrDTESLAKRICKDLenlsqiqnrefgtQKYEQ--WIV-TVQKACMVFQ-MPDKD 527
Cdd:COG1203   326 DEPEELPEYFRAFVRKRVELKEGPL--SDEELAELILEAL-------------HKGKSvlVIVnTVKDAQELYEaLKEKL 390

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1883540343 528 EESRICkalflytsHLrkyndaliiseHARMkdaldYLKDffsnvRAagfdEIEQDLTQRFEEK 591
Cdd:COG1203   391 PDEEVY--------LL-----------HSRF-----CPAD-----RS----EIEKEIKERLERG 421
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 679-739 4.02e-03

C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350186 [Multi-domain]  Cd Length: 116  Bit Score: 37.92  E-value: 4.02e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1883540343 679 ILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRG-RARGSKCFLL 739
Cdd:cd18799    50 LILLFFGELKPPILVTVDLLTTGVDIPEVDNVVFLRPTESRTLFLQMLGRGlRLHEGKDFFT 111
DEXHc_cas3 cd17930
DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase ...
 257-373 4.99e-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: 39.20  E-value: 4.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1883540343 257 GKNTIICAPTGCGKTFVSLLIcehHLKKFPQGQKGKVVF------FANQIpvYEQQKSVFSKYFER------HGVTGISG 324
Cdd:cd17930     1 PGLVILEAPTGSGKTEAALLW---ALKLAARGGKRRIIYalptraTINQM--YERIREILGRLDDEdkvlllHSKAALEL 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1883540343 325 ATAENVPVEQIVENND------------IIILTP-QILVNNLK-KGTIPSLSIF--TLMIFDECH 373
Cdd:cd17930    76 LESDEEPDDDPVEAVDwalllkrswlapIVVTTIdQLLESLLKyKHFERRLHGLanSVVVLDEVQ 140
DEXH_lig_assoc TIGR04121
DEXH box helicase, DNA ligase-associated; Members of this protein family are DEAD/DEAH box ...
 241-272 8.92e-03

DEXH box helicase, DNA ligase-associated; Members of this protein family are DEAD/DEAH box helicases found associated with a bacterial ATP-dependent DNA ligase, part of a four-gene system that occurs in about 12 % of prokaryotic reference genomes. The actual motif in this family is DE[VILW]H.


Pssm-ID: 274994 [Multi-domain]  Cd Length: 804  Bit Score: 39.84  E-value: 8.92e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1883540343 241 FKPRNYQLELALPAMKGKNTIICAPTGCGKTF 272
Cdd:TIGR04121  12 WTPRPFQLEMWAAALEGRSGLLIAPTGSGKTL 43
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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