probable ATP-dependent RNA helicase DDX58 [Latimeria chalumnae]
Protein Classification
MDA5_ID and RIG-I_C domain-containing protein( domain architecture ID 13102814)
protein containing domains DD, DEAD-like_helicase_N, MDA5_ID, and RIG-I_C
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||||
| DEAD-like_helicase_N super family | cl28899 | N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ... |
245-447 | 1.32e-109 | |||||||||
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region. The actual alignment was detected with superfamily member cd18073: Pssm-ID: 475120 [Multi-domain] Cd Length: 202 Bit Score: 336.02 E-value: 1.32e-109
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| RIG-I_C | cd15805 | C-terminal domain of Retinoic acid-inducible gene (RIG)-I protein, a cytoplasmic viral RNA ... |
811-925 | 9.65e-59 | |||||||||
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: 195.95 E-value: 9.65e-59
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| MPH1 super family | cl34113 | ERCC4-related helicase [Replication, recombination and repair]; |
248-806 | 9.64e-57 | |||||||||
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: 208.82 E-value: 9.64e-57
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| DD super family | cl14633 | Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) ... |
2-91 | 3.62e-37 | |||||||||
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: 134.50 E-value: 3.62e-37
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| DD super family | cl14633 | Death Domain Superfamily of protein-protein interaction domains; The Death Domain (DD) ... |
99-186 | 2.77e-29 | |||||||||
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 cd08817: Pssm-ID: 472698 Cd Length: 91 Bit Score: 111.77 E-value: 2.77e-29
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| 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 ... |
245-447 | 1.32e-109 | |||||||||
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: 336.02 E-value: 1.32e-109
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| RIG-I_C | cd15805 | C-terminal domain of Retinoic acid-inducible gene (RIG)-I protein, a cytoplasmic viral RNA ... |
811-925 | 9.65e-59 | |||||||||
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: 195.95 E-value: 9.65e-59
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| MPH1 | COG1111 | ERCC4-related helicase [Replication, recombination and repair]; |
248-806 | 9.64e-57 | |||||||||
ERCC4-related helicase [Replication, recombination and repair]; Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 208.82 E-value: 9.64e-57
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| PRK13766 | PRK13766 | Hef nuclease; Provisional |
248-811 | 3.64e-49 | |||||||||
Hef nuclease; Provisional Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 187.00 E-value: 3.64e-49
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| RIG-I_C | pfam18119 | RIG-I receptor C-terminal domain; This is the C-terminal domain of Innate Immune ... |
462-605 | 1.27e-44 | |||||||||
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: 157.50 E-value: 1.27e-44
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| RIG-I_C-RD | pfam11648 | C-terminal domain of RIG-I; This family of proteins represents the regulatory domain RD of ... |
813-925 | 8.93e-44 | |||||||||
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: 154.33 E-value: 8.93e-44
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| MDA5_ID | cd12090 | Insert domain of MDA5; MDA5 (melanoma-differentiation-associated gene 5, also known as IFIH1), ... |
474-608 | 2.78e-43 | |||||||||
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: 152.86 E-value: 2.78e-43
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| CARD_RIG-I_r1 | cd08816 | Caspase activation and recruitment domain found in RIG-I, first repeat; Caspase activation and ... |
2-91 | 3.62e-37 | |||||||||
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: 134.50 E-value: 3.62e-37
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| CARD_RIG-I_r2 | cd08817 | Caspase activation and recruitment domain found in RIG-I, second repeat; Caspase activation ... |
99-186 | 2.77e-29 | |||||||||
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: 111.77 E-value: 2.77e-29
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| CARD_2 | pfam16739 | Caspase recruitment domain; In the probable ATP-dependent RNA helicase DDX58 this CARD domain ... |
98-190 | 1.63e-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: 1.63e-28
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
239-452 | 8.02e-19 | |||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 85.62 E-value: 8.02e-19
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| CARD_2 | pfam16739 | Caspase recruitment domain; In the probable ATP-dependent RNA helicase DDX58 this CARD domain ... |
1-92 | 4.26e-18 | |||||||||
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: 79.94 E-value: 4.26e-18
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
244-415 | 8.39e-14 | |||||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 70.01 E-value: 8.39e-14
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
676-738 | 1.83e-10 | |||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 57.99 E-value: 1.83e-10
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| BRR2 | COG1204 | Replicative superfamily II helicase [Replication, recombination and repair]; |
246-418 | 3.32e-09 | |||||||||
Replicative superfamily II helicase [Replication, recombination and repair]; Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 60.29 E-value: 3.32e-09
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| 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 ... |
245-447 | 1.32e-109 | |||||||||
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: 336.02 E-value: 1.32e-109
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| DEXHc_RIG-I | cd17927 | DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
245-447 | 5.71e-87 | |||||||||
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: 276.24 E-value: 5.71e-87
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| DEXHc_RLR | cd18036 | DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
245-447 | 7.46e-80 | |||||||||
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: 257.40 E-value: 7.46e-80
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| RIG-I_C | cd15805 | C-terminal domain of Retinoic acid-inducible gene (RIG)-I protein, a cytoplasmic viral RNA ... |
811-925 | 9.65e-59 | |||||||||
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: 195.95 E-value: 9.65e-59
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| MPH1 | COG1111 | ERCC4-related helicase [Replication, recombination and repair]; |
248-806 | 9.64e-57 | |||||||||
ERCC4-related helicase [Replication, recombination and repair]; Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 208.82 E-value: 9.64e-57
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| PRK13766 | PRK13766 | Hef nuclease; Provisional |
248-811 | 3.64e-49 | |||||||||
Hef nuclease; Provisional Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 187.00 E-value: 3.64e-49
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| DEXHc_dicer | cd18034 | DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
246-432 | 6.13e-46 | |||||||||
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: 163.59 E-value: 6.13e-46
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| DEXHc_RLR-2 | cd18074 | DEXH-box helicase domain of RLR-2; RIG-I-like receptor 2 (RLR-2, also known as melanoma ... |
245-447 | 1.02e-44 | |||||||||
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: 160.80 E-value: 1.02e-44
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| RIG-I_C | pfam18119 | RIG-I receptor C-terminal domain; This is the C-terminal domain of Innate Immune ... |
462-605 | 1.27e-44 | |||||||||
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: 157.50 E-value: 1.27e-44
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| RIG-I_C-RD | pfam11648 | C-terminal domain of RIG-I; This family of proteins represents the regulatory domain RD of ... |
813-925 | 8.93e-44 | |||||||||
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: 154.33 E-value: 8.93e-44
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| MDA5_ID | cd12090 | Insert domain of MDA5; MDA5 (melanoma-differentiation-associated gene 5, also known as IFIH1), ... |
474-608 | 2.78e-43 | |||||||||
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: 152.86 E-value: 2.78e-43
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| SF2_C_dicer | cd18802 | C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
613-746 | 2.95e-42 | |||||||||
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: 150.82 E-value: 2.95e-42
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| DEXHc_RLR-3 | cd18075 | DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ... |
245-446 | 1.02e-40 | |||||||||
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: 148.47 E-value: 1.02e-40
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| CARD_RIG-I_r1 | cd08816 | Caspase activation and recruitment domain found in RIG-I, first repeat; Caspase activation and ... |
2-91 | 3.62e-37 | |||||||||
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: 134.50 E-value: 3.62e-37
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| RLR_C | cd15804 | C-terminal domain of Retinoic acid-inducible gene (RIG)-I-like Receptors; Retinoic ... |
813-925 | 1.07e-34 | |||||||||
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: 128.20 E-value: 1.07e-34
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| CARD_RIG-I_r2 | cd08817 | Caspase activation and recruitment domain found in RIG-I, second repeat; Caspase activation ... |
99-186 | 2.77e-29 | |||||||||
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: 111.77 E-value: 2.77e-29
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| CARD_2 | pfam16739 | Caspase recruitment domain; In the probable ATP-dependent RNA helicase DDX58 this CARD domain ... |
98-190 | 1.63e-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: 1.63e-28
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| LGP2_C | cd15806 | C-terminal domain of Laboratory of Genetics and Physiology 2 (LGP2), a cytoplasmic viral RNA ... |
813-925 | 1.44e-19 | |||||||||
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: 84.78 E-value: 1.44e-19
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
239-452 | 8.02e-19 | |||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 85.62 E-value: 8.02e-19
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| SF2_C_FANCM_Hef | cd18801 | C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
613-745 | 1.27e-18 | |||||||||
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: 83.17 E-value: 1.27e-18
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| DEXHc_Hef | cd18035 | DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
248-444 | 1.40e-18 | |||||||||
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: 84.49 E-value: 1.40e-18
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| CARD_IPS-1_RIG-I | cd08789 | Caspase activation and recruitment domains (CARDs) found in IPS-1 and RIG-I-like RNA helicases; ... |
99-186 | 2.73e-18 | |||||||||
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: 80.58 E-value: 2.73e-18
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| CARD_2 | pfam16739 | Caspase recruitment domain; In the probable ATP-dependent RNA helicase DDX58 this CARD domain ... |
1-92 | 4.26e-18 | |||||||||
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: 79.94 E-value: 4.26e-18
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| DEXDc_FANCM | cd18033 | DEAH-box helicase domain of FANCM; Fanconi anemia group M (FANCM) protein is a DNA-dependent ... |
247-435 | 4.70e-18 | |||||||||
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: 82.76 E-value: 4.70e-18
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
261-415 | 1.92e-17 | |||||||||
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: 80.14 E-value: 1.92e-17
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| RLR_C_like | cd15803 | C-terminal domain of Retinoic acid-inducible gene (RIG)-I-like Receptors, Cereblon (CRBN), and ... |
814-897 | 1.11e-16 | |||||||||
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: 75.63 E-value: 1.11e-16
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| DEXHc_Ski2 | cd17921 | DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
249-380 | 6.36e-16 | |||||||||
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: 76.53 E-value: 6.36e-16
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| Helicase_C | pfam00271 | Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
621-738 | 1.55e-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: 70.32 E-value: 1.55e-14
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| ResIII | pfam04851 | Type III restriction enzyme, res subunit; |
244-415 | 8.39e-14 | |||||||||
Type III restriction enzyme, res subunit; Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 70.01 E-value: 8.39e-14
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| CARD_IPS-1_RIG-I | cd08789 | Caspase activation and recruitment domains (CARDs) found in IPS-1 and RIG-I-like RNA helicases; ... |
2-91 | 1.12e-13 | |||||||||
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: 67.48 E-value: 1.12e-13
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| MDA5_C | cd15807 | C-terminal domain of Melanoma differentiation-associated protein 5, a cytoplasmic viral RNA ... |
814-925 | 1.71e-12 | |||||||||
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: 64.82 E-value: 1.71e-12
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
244-741 | 3.78e-12 | |||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 70.05 E-value: 3.78e-12
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| DEXHc_RE | cd17926 | DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
247-381 | 1.45e-11 | |||||||||
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: 63.09 E-value: 1.45e-11
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| helicase_insert_domain | cd12088 | helicase_insert_domain; helicase_insert_domain; This helical domain can be found inserted in a ... |
540-608 | 1.60e-11 | |||||||||
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: 60.95 E-value: 1.60e-11
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| CARD_IPS1 | cd08811 | Caspase activation and recruitment domain (CARD) found in IPS-1; Caspase activation and ... |
112-184 | 2.00e-11 | |||||||||
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: 60.83 E-value: 2.00e-11
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
248-379 | 3.51e-11 | |||||||||
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: 62.65 E-value: 3.51e-11
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
676-738 | 1.83e-10 | |||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 57.99 E-value: 1.83e-10
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| BRR2 | COG1204 | Replicative superfamily II helicase [Replication, recombination and repair]; |
246-418 | 3.32e-09 | |||||||||
Replicative superfamily II helicase [Replication, recombination and repair]; Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 60.29 E-value: 3.32e-09
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| DEXHc_Brr2_1 | cd18019 | N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD ... |
241-379 | 2.31e-07 | |||||||||
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD box helicase that mediates spliceosome catalytic activation. It is a stable subunit of the spliceosome, required during splicing catalysis and spliceosome disassembly. Brr2 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350777 [Multi-domain] Cd Length: 214 Bit Score: 52.37 E-value: 2.31e-07
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| SF2_C_DEAD | cd18787 | C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
621-720 | 4.70e-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: 49.81 E-value: 4.70e-07
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| DEXHc_RE_I_III_res | cd18032 | DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
247-379 | 4.79e-07 | |||||||||
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: 50.64 E-value: 4.79e-07
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| DEXHc_Brr2_2 | cd18021 | C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type ... |
263-425 | 6.68e-07 | |||||||||
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: 50.72 E-value: 6.68e-07
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| SF2_C | cd18785 | C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
696-746 | 9.09e-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: 47.31 E-value: 9.09e-07
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| DEXHc_HFM1 | cd18023 | DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ... |
262-353 | 1.42e-06 | |||||||||
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: 50.05 E-value: 1.42e-06
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| DEXHc_DDX60 | cd18025 | DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an ... |
250-379 | 2.13e-05 | |||||||||
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: 46.21 E-value: 2.13e-05
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| DEADc_DDX28 | cd17948 | DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box ... |
245-377 | 6.69e-05 | |||||||||
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box polypeptide 28) plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function. DDX28 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: 350706 [Multi-domain] Cd Length: 231 Bit Score: 45.44 E-value: 6.69e-05
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| SF2_C_SNF | cd18793 | C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ... |
613-720 | 8.26e-05 | |||||||||
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: 43.23 E-value: 8.26e-05
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| SF2_C_XPB | cd18789 | C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
611-710 | 1.13e-04 | |||||||||
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: 43.39 E-value: 1.13e-04
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| DEXHc_archSki2 | cd18028 | DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
259-418 | 1.52e-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: 43.48 E-value: 1.52e-04
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| PTZ00110 | PTZ00110 | helicase; Provisional |
611-784 | 2.42e-04 | |||||||||
helicase; Provisional Pssm-ID: 240273 [Multi-domain] Cd Length: 545 Bit Score: 44.76 E-value: 2.42e-04
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| SrmB | COG0513 | Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
627-813 | 2.69e-04 | |||||||||
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 44.37 E-value: 2.69e-04
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| Dob10 | COG4581 | Superfamily II RNA helicase [Replication, recombination and repair]; |
245-286 | 2.96e-04 | |||||||||
Superfamily II RNA helicase [Replication, recombination and repair]; Pssm-ID: 443638 [Multi-domain] Cd Length: 751 Bit Score: 44.54 E-value: 2.96e-04
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| SF2_C_EcoAI-like | cd18799 | C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
631-735 | 3.20e-04 | |||||||||
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: 41.01 E-value: 3.20e-04
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| DEXHc_POLQ-like | cd18026 | DEXH-box helicase domain of DNA polymerase theta; DNA polymerase theta (POLQ) is important in ... |
257-418 | 3.46e-04 | |||||||||
DEXH-box helicase domain of DNA polymerase theta; DNA polymerase theta (POLQ) is important in the repair of genomic double-strand breaks (DSBs). POLQ contains an N-terminal type II DEAD box helicase domain which contains the ATP-binding region. Pssm-ID: 350784 [Multi-domain] Cd Length: 202 Bit Score: 42.59 E-value: 3.46e-04
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| HsdR | COG4096 | Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
243-415 | 5.97e-04 | |||||||||
Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms]; Pssm-ID: 443272 [Multi-domain] Cd Length: 806 Bit Score: 43.68 E-value: 5.97e-04
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| DEXHc_cas3 | cd17930 | DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase ... |
261-324 | 6.76e-04 | |||||||||
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: 41.51 E-value: 6.76e-04
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| DEADc_DDX54 | cd17959 | DEAD-box helicase domain of DEAD box protein 54; DDX54 interacts in a hormone-dependent manner ... |
260-377 | 9.16e-04 | |||||||||
DEAD-box helicase domain of DEAD box protein 54; DDX54 interacts in a hormone-dependent manner with nuclear receptors, and represses their transcriptional activity. DDX54 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350717 [Multi-domain] Cd Length: 205 Bit Score: 41.52 E-value: 9.16e-04
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| DEADc_DDX55 | cd17960 | DEAD-box helicase domain of DEAD box protein 55; DDX55 is a member of the DEAD-box helicases, ... |
261-377 | 1.94e-03 | |||||||||
DEAD-box helicase domain of DEAD box protein 55; DDX55 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350718 [Multi-domain] Cd Length: 202 Bit Score: 40.64 E-value: 1.94e-03
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| SF2_C_Hrq | cd18797 | C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ... |
633-745 | 2.13e-03 | |||||||||
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350184 [Multi-domain] Cd Length: 146 Bit Score: 39.55 E-value: 2.13e-03
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| HepA | COG0553 | Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
600-720 | 3.05e-03 | |||||||||
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair]; Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 41.36 E-value: 3.05e-03
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| CARD_MDA5_r2 | cd08819 | Caspase activation and recruitment domain found in MDA5, second repeat; Caspase activation and ... |
116-184 | 3.89e-03 | |||||||||
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: 37.31 E-value: 3.89e-03
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| DEXHc_Hrq1-like | cd17923 | DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a ... |
247-418 | 3.98e-03 | |||||||||
DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. Hrq1 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350681 [Multi-domain] Cd Length: 182 Bit Score: 39.49 E-value: 3.98e-03
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| Cas3 | COG1203 | CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
246-320 | 5.94e-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: 40.45 E-value: 5.94e-03
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| DEXHc_RecQ | cd17920 | DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ... |
241-277 | 6.17e-03 | |||||||||
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box helicase superfamily is a family of highly conserved DNA repair helicases. This domain contains the ATP-binding region. Pssm-ID: 350678 [Multi-domain] Cd Length: 200 Bit Score: 39.05 E-value: 6.17e-03
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| DEADc_DDX56 | cd17961 | DEAD-box helicase domain of DEAD box protein 56; DDX56 is a helicase required for assembly of ... |
258-377 | 8.65e-03 | |||||||||
DEAD-box helicase domain of DEAD box protein 56; DDX56 is a helicase required for assembly of infectious West Nile virus particles. New research suggests that DDX56 relocalizes to the site of virus assembly during WNV infection and that its interaction with WNV capsid in the cytoplasm may occur transiently during virion morphogenesis. DDX56 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. Pssm-ID: 350719 [Multi-domain] Cd Length: 206 Bit Score: 38.72 E-value: 8.65e-03
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