RecName: Full=Replicase polyprotein 1ab; Short=pp1ab; AltName: Full=ORF1ab polyprotein; Contains: RecName: Full=Putative papain-like proteinase; Short=PL-PRO; AltName: Full=Non-structural protein 1; Short=nsp1; Contains: RecName: Full=Non-structural protein 2; Short=nsp2; Contains: RecName: Full=3C-like serine proteinase; Short=3CLSP; AltName: Full=M-PRO; AltName: Full=nsp3; AltName: Full=p27; Contains: RecName: Full=Non-structural protein 4; Short=nsp4; Contains: RecName: Full=Non-structural protein 5; Short=nsp5; Contains: RecName: Full=Non-structural protein 6; Short=nsp6; Contains: RecName: Full=Non-structural protein 7; Short=nsp7; Contains: RecName: Full=Non-structural protein 8; Short=nsp8; Contains: RecName: Full=RNA-directed RNA polymerase; Short=Pol; Short=RdRp; AltName: Full=nsp
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||
| Tobaniviridae_RdRp | cd23186 | catalytic core domain of RNA-dependent RNA polymerase (RdRP) in the Tobaniviridae family of ... |
4947-5384 | 0e+00 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRP) in the Tobaniviridae family of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Tobaniviridae, order Nidovirales. Tobaniviridae RNA viruses infect vertebrates; their host organisms include mammals, fish, and snakes. Member viruses have a viral envelope and (+)ssRNA genome. The genome size of Tobaniviruses ranges from 20 to 32 kilobases. The family is the only member of the suborder Tornidovirineae. The family Tobaniviridae has four subfamilies (Piscanivirinae, Remotovirinae, Remotovirinae, and Torovirinae) and eight genera (Bafinivirus, Oncotshavirus, Bostovirus, Infratovirus, Pregotovirus, Sectovirus, Tiruvirus, and Torovirus). The Tobaniviridae family belongs to the order Nidovirales, which currently comprises 88 formally recognized virus species of (+)ssRNA viruses, which are classified into nine virus families across seven different suborders. The structure of Tobaniviridae RdRp contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. : Pssm-ID: 438036 Cd Length: 401 Bit Score: 696.45 E-value: 0e+00
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| Corona_NS2A super family | cl20291 | Coronavirus NS2A protein; This family contains a number of corona virus non-structural ... |
4403-4641 | 2.38e-113 | |||||||
Coronavirus NS2A protein; This family contains a number of corona virus non-structural proteins of unknown function. The family also includes a polymerase protein fragment from Berne virus and does not seem to be related to the pfam04753 Coronavirus NS2 family. This family is part of the 2H phosphoesterase superfamily. The actual alignment was detected with superfamily member pfam05213: Pssm-ID: 282997 Cd Length: 267 Bit Score: 362.48 E-value: 2.38e-113
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| NendoU_tv_PToV-like | cd21162 | Nidoviral uridylate-specific endoribonuclease (NendoU) domain of Porcine torovirus (PToV) ... |
6456-6593 | 7.19e-72 | |||||||
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of Porcine torovirus (PToV) endoribonuclease and related proteins; Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. The Porcine torovirus (PToV) strain PToV-NPL/2013 NendoU domain is located at the N-terminus of the ORF1ab replicase polyprotein, between regions annotated as Nonstructural proteins 11 (Nsp11) and 13 (Nsp13). This subfamily belongs to a family which includes Nsp15 from coronaviruses and Nsp11 from arteriviruses, which may participate in the viral replication process and in the evasion of the host immune system. These vary in their requirement for Mn2+. Coronavirus Nsp15 generally form functional hexamers, with the exception of Porcine DeltaCoronavirus (PDCoV) Nsp15 which exists as a dimer and a monomer in solution. Arterivirus (Porcine Reproductive and Respiratory Syndrome virus) PRRSV Nsp11 is a dimer. NendoUs are distantly related to Xenopus laevis Mn(2+)-dependent uridylate-specific endoribonuclease (XendoU) which is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA. : Pssm-ID: 394913 Cd Length: 133 Bit Score: 237.87 E-value: 7.19e-72
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| capping_2-OMTase_Nidovirales | cd20762 | Cap-0 specific (nucleoside-2'-O-)-methyltransferase of nidovirales; Cap-0 specific ... |
6630-6803 | 1.08e-64 | |||||||
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of nidovirales; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Nidovirales viruses, which comprise a family of ss(+)RNA viruses, cap their mRNAs. For one member, coronavirus, the 2'OMTase activity is located in the non-structural protein 16 (Nsp16). For others, the 2'OMTase activity may be located in replicase polyprotein 1ab. : Pssm-ID: 467737 Cd Length: 175 Bit Score: 219.11 E-value: 1.08e-64
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| unc_tv_SF1_Hel-like | cd21413 | uncharacterized domain which connects the Cys/His rich zinc-binding (ZBD) and linker to the ... |
5562-5640 | 1.48e-49 | |||||||
uncharacterized domain which connects the Cys/His rich zinc-binding (ZBD) and linker to the first helicase domain of tornidovirus SF1 helicase and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Helicases in this family belong to helicase superfamily 1 (SF1) and include tornidovirus helicases such as Breda virus serotype 1 (BoTV-1) SF1 helicase encoded on ORF1b. They are related to the SF1 family nidoviral replication helicases which include Severe Acute Respiratory Syndrome coronavirus (SARS) non-structural protein 13 (SARS-Nsp13), a component of the viral RNA synthesis replication and transcription complex (RTC). SARS-Nsp13 is a multidomain protein; its other domains include an N-terminal Cys/His rich zinc-binding domain (ZBD) and a SF1 helicase core. The location of the uncharacterized domain represented in this tornidovirus group resembles that of the 1B domain in SARS-Nsp13 helicase; it connects the zinc-binding domain (ZBD) and linker to the first helicase domain. : Pssm-ID: 394819 Cd Length: 79 Bit Score: 171.75 E-value: 1.48e-49
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| Macro_X_Nsp3-like | cd21557 | X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The ... |
1713-1844 | 2.00e-43 | |||||||
X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The X-domain, also called Mac1, is the macrodomain found in riboviral non-structural protein 3 (Nsp3), including the Nsp3 of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) as well as SARS-CoV-2, and other coronaviruses (alpha-, beta-, gamma-, and deltacoronavirus), among others. The SARS-CoV-2 Nsp3 Mac1 is highly conserved among all CoVs, and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. It appears to counter host-mediated antiviral ADP-ribosylation, a post-translational modification that is part of the host response to viral infections. Mac1 is essential for pathogenesis in multiple animal models of CoV infection, implicating it as a virulence factor and potential therapeutic target. Assays show that the de-MARylating activity leads to a rapid loss of substrate, and that Mac1 could not hydrolyze poly-ADP-ribose; thus, Mac1 is a MAR-hydrolase (mono-ADP ribosylhydrolase). Mac1 was originally named ADP-ribose-1"-phosphatase (ADRP) based on data demonstrating that it could remove the phosphate group from ADP-ribose-1"-phosphate; however, activity was modest and was unclear why this would impact a virus infection. This family also includes the X-domain of Avian infectious bronchitis virus (IBV) strain Beaudette coronavirus that does not bind ADP-ribose; the triple glycine sequence found in the X-domains of SARS-CoV and human coronavirus 229E (HCoV229E), which are involved in ADP-ribose binding, is not conserved in the IBV X-domain. SARS-CoVs have two other macrodomains referred to as the SUD-N (N-terminal subdomain, or Mac2) and SUD-M (middle SUD subdomain, or Mac3) of the SARS-unique domain (SUD), which also do not bind ADP-ribose; these bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). SARS-CoV SUD-N and SUD-M are not included in this group. : Pssm-ID: 438957 Cd Length: 127 Bit Score: 156.18 E-value: 2.00e-43
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| ZBD_tv_SF1_Hel-like | cd21403 | Cys/His rich zinc-binding domain (CH/ZBD) of tornidovirus SF1 helicase and related proteins; ... |
5413-5507 | 1.33e-37 | |||||||
Cys/His rich zinc-binding domain (CH/ZBD) of tornidovirus SF1 helicase and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. This tornidovirus group includes White bream virus (WBV) SF1 helicase encoded on ORF1b and belongs to helicase superfamily 1 (SF1). The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. Members of this group belong to a family of nindoviral replication helicases which include includes Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) non-structural protein 13 (SARS-Nsp13), a component of the viral RNA synthesis replication and transcription complex (RTC). The SARS-Nsp13 CH/ZBD is indispensable for helicase activity and interacts with SARS-Nsp12, the RNA-dependent RNA polymerase. : Pssm-ID: 394810 Cd Length: 95 Bit Score: 138.24 E-value: 1.33e-37
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| CoV_Nsp13-helicase super family | cl41748 | helicase domain of coronavirus non-structural protein 13; This model represents the helicase ... |
5630-5950 | 3.28e-12 | |||||||
helicase domain of coronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from alpha-, beta-, gamma-, and deltacoronavirus, including pathogenic human viruses such as Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core. The actual alignment was detected with superfamily member cd21718: Pssm-ID: 425379 [Multi-domain] Cd Length: 341 Bit Score: 71.79 E-value: 3.28e-12
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| CoV_Nsp14 super family | cl40464 | nonstructural protein 14 of coronavirus; Nonstructural protein 14 (Nsp14) of coronavirus (CoV) ... |
6077-6186 | 4.30e-06 | |||||||
nonstructural protein 14 of coronavirus; Nonstructural protein 14 (Nsp14) of coronavirus (CoV) plays an important role in viral replication and transcription. It consists of 2 domains with different enzymatic activities: an N-terminal exoribonuclease (ExoN) domain and a C-terminal cap (guanine-N7) methyltransferase (N7-MTase) domain. ExoN is important for proofreading and therefore, the prevention of lethal mutations. The association of Nsp14 with Nsp10 stimulates its ExoN activity; the complex hydrolyzes double-stranded RNA in a 3' to 5' direction as well as a single mismatched nucleotide at the 3'-end mimicking an erroneous replication product. The Nsp10/Nsp14 complex may function in a replicative mismatch repair mechanism. N7-MTase functions in mRNA capping. Nsp14 can methylate GTP, dGTP as well as cap analogs GpppG, GpppA and m7GpppG. The accumulation of m7GTP or Nsp14 has been found to interfere with protein translation of cellular mRNAs. The actual alignment was detected with superfamily member cd21528: Pssm-ID: 424095 Cd Length: 518 Bit Score: 53.62 E-value: 4.30e-06
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| eMpr super family | cl42390 | V8-like Glu-specific endopeptidase [Posttranslational modification, protein turnover, ... |
3284-3430 | 6.79e-06 | |||||||
V8-like Glu-specific endopeptidase [Posttranslational modification, protein turnover, chaperones]; The actual alignment was detected with superfamily member COG3591: Pssm-ID: 442810 [Multi-domain] Cd Length: 194 Bit Score: 50.45 E-value: 6.79e-06
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| ND5 super family | cl31795 | NADH dehydrogenase subunit 5; Provisional |
3042-3162 | 2.52e-04 | |||||||
NADH dehydrogenase subunit 5; Provisional The actual alignment was detected with superfamily member MTH00095: Pssm-ID: 177158 [Multi-domain] Cd Length: 527 Bit Score: 47.60 E-value: 2.52e-04
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| Peptidase_C19 super family | cl02553 | Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ... |
1867-1945 | 7.37e-03 | |||||||
Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. The actual alignment was detected with superfamily member pfam00443: Pssm-ID: 470612 [Multi-domain] Cd Length: 310 Bit Score: 42.43 E-value: 7.37e-03
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| Name | Accession | Description | Interval | E-value | |||||||
| Tobaniviridae_RdRp | cd23186 | catalytic core domain of RNA-dependent RNA polymerase (RdRP) in the Tobaniviridae family of ... |
4947-5384 | 0e+00 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRP) in the Tobaniviridae family of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Tobaniviridae, order Nidovirales. Tobaniviridae RNA viruses infect vertebrates; their host organisms include mammals, fish, and snakes. Member viruses have a viral envelope and (+)ssRNA genome. The genome size of Tobaniviruses ranges from 20 to 32 kilobases. The family is the only member of the suborder Tornidovirineae. The family Tobaniviridae has four subfamilies (Piscanivirinae, Remotovirinae, Remotovirinae, and Torovirinae) and eight genera (Bafinivirus, Oncotshavirus, Bostovirus, Infratovirus, Pregotovirus, Sectovirus, Tiruvirus, and Torovirus). The Tobaniviridae family belongs to the order Nidovirales, which currently comprises 88 formally recognized virus species of (+)ssRNA viruses, which are classified into nine virus families across seven different suborders. The structure of Tobaniviridae RdRp contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438036 Cd Length: 401 Bit Score: 696.45 E-value: 0e+00
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| Corona_NS2A | pfam05213 | Coronavirus NS2A protein; This family contains a number of corona virus non-structural ... |
4403-4641 | 2.38e-113 | |||||||
Coronavirus NS2A protein; This family contains a number of corona virus non-structural proteins of unknown function. The family also includes a polymerase protein fragment from Berne virus and does not seem to be related to the pfam04753 Coronavirus NS2 family. This family is part of the 2H phosphoesterase superfamily. Pssm-ID: 282997 Cd Length: 267 Bit Score: 362.48 E-value: 2.38e-113
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| NendoU_tv_PToV-like | cd21162 | Nidoviral uridylate-specific endoribonuclease (NendoU) domain of Porcine torovirus (PToV) ... |
6456-6593 | 7.19e-72 | |||||||
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of Porcine torovirus (PToV) endoribonuclease and related proteins; Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. The Porcine torovirus (PToV) strain PToV-NPL/2013 NendoU domain is located at the N-terminus of the ORF1ab replicase polyprotein, between regions annotated as Nonstructural proteins 11 (Nsp11) and 13 (Nsp13). This subfamily belongs to a family which includes Nsp15 from coronaviruses and Nsp11 from arteriviruses, which may participate in the viral replication process and in the evasion of the host immune system. These vary in their requirement for Mn2+. Coronavirus Nsp15 generally form functional hexamers, with the exception of Porcine DeltaCoronavirus (PDCoV) Nsp15 which exists as a dimer and a monomer in solution. Arterivirus (Porcine Reproductive and Respiratory Syndrome virus) PRRSV Nsp11 is a dimer. NendoUs are distantly related to Xenopus laevis Mn(2+)-dependent uridylate-specific endoribonuclease (XendoU) which is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA. Pssm-ID: 394913 Cd Length: 133 Bit Score: 237.87 E-value: 7.19e-72
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| capping_2-OMTase_Nidovirales | cd20762 | Cap-0 specific (nucleoside-2'-O-)-methyltransferase of nidovirales; Cap-0 specific ... |
6630-6803 | 1.08e-64 | |||||||
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of nidovirales; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Nidovirales viruses, which comprise a family of ss(+)RNA viruses, cap their mRNAs. For one member, coronavirus, the 2'OMTase activity is located in the non-structural protein 16 (Nsp16). For others, the 2'OMTase activity may be located in replicase polyprotein 1ab. Pssm-ID: 467737 Cd Length: 175 Bit Score: 219.11 E-value: 1.08e-64
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| unc_tv_SF1_Hel-like | cd21413 | uncharacterized domain which connects the Cys/His rich zinc-binding (ZBD) and linker to the ... |
5562-5640 | 1.48e-49 | |||||||
uncharacterized domain which connects the Cys/His rich zinc-binding (ZBD) and linker to the first helicase domain of tornidovirus SF1 helicase and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Helicases in this family belong to helicase superfamily 1 (SF1) and include tornidovirus helicases such as Breda virus serotype 1 (BoTV-1) SF1 helicase encoded on ORF1b. They are related to the SF1 family nidoviral replication helicases which include Severe Acute Respiratory Syndrome coronavirus (SARS) non-structural protein 13 (SARS-Nsp13), a component of the viral RNA synthesis replication and transcription complex (RTC). SARS-Nsp13 is a multidomain protein; its other domains include an N-terminal Cys/His rich zinc-binding domain (ZBD) and a SF1 helicase core. The location of the uncharacterized domain represented in this tornidovirus group resembles that of the 1B domain in SARS-Nsp13 helicase; it connects the zinc-binding domain (ZBD) and linker to the first helicase domain. Pssm-ID: 394819 Cd Length: 79 Bit Score: 171.75 E-value: 1.48e-49
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| Macro_X_Nsp3-like | cd21557 | X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The ... |
1713-1844 | 2.00e-43 | |||||||
X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The X-domain, also called Mac1, is the macrodomain found in riboviral non-structural protein 3 (Nsp3), including the Nsp3 of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) as well as SARS-CoV-2, and other coronaviruses (alpha-, beta-, gamma-, and deltacoronavirus), among others. The SARS-CoV-2 Nsp3 Mac1 is highly conserved among all CoVs, and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. It appears to counter host-mediated antiviral ADP-ribosylation, a post-translational modification that is part of the host response to viral infections. Mac1 is essential for pathogenesis in multiple animal models of CoV infection, implicating it as a virulence factor and potential therapeutic target. Assays show that the de-MARylating activity leads to a rapid loss of substrate, and that Mac1 could not hydrolyze poly-ADP-ribose; thus, Mac1 is a MAR-hydrolase (mono-ADP ribosylhydrolase). Mac1 was originally named ADP-ribose-1"-phosphatase (ADRP) based on data demonstrating that it could remove the phosphate group from ADP-ribose-1"-phosphate; however, activity was modest and was unclear why this would impact a virus infection. This family also includes the X-domain of Avian infectious bronchitis virus (IBV) strain Beaudette coronavirus that does not bind ADP-ribose; the triple glycine sequence found in the X-domains of SARS-CoV and human coronavirus 229E (HCoV229E), which are involved in ADP-ribose binding, is not conserved in the IBV X-domain. SARS-CoVs have two other macrodomains referred to as the SUD-N (N-terminal subdomain, or Mac2) and SUD-M (middle SUD subdomain, or Mac3) of the SARS-unique domain (SUD), which also do not bind ADP-ribose; these bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). SARS-CoV SUD-N and SUD-M are not included in this group. Pssm-ID: 438957 Cd Length: 127 Bit Score: 156.18 E-value: 2.00e-43
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| ZBD_tv_SF1_Hel-like | cd21403 | Cys/His rich zinc-binding domain (CH/ZBD) of tornidovirus SF1 helicase and related proteins; ... |
5413-5507 | 1.33e-37 | |||||||
Cys/His rich zinc-binding domain (CH/ZBD) of tornidovirus SF1 helicase and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. This tornidovirus group includes White bream virus (WBV) SF1 helicase encoded on ORF1b and belongs to helicase superfamily 1 (SF1). The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. Members of this group belong to a family of nindoviral replication helicases which include includes Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) non-structural protein 13 (SARS-Nsp13), a component of the viral RNA synthesis replication and transcription complex (RTC). The SARS-Nsp13 CH/ZBD is indispensable for helicase activity and interacts with SARS-Nsp12, the RNA-dependent RNA polymerase. Pssm-ID: 394810 Cd Length: 95 Bit Score: 138.24 E-value: 1.33e-37
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| A1pp | smart00506 | Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by ... |
1712-1829 | 2.68e-16 | |||||||
Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by reciprocal PSI-BLAST searches (unpublished results, and Pehrson _ Fuji). Pssm-ID: 214701 Cd Length: 133 Bit Score: 78.89 E-value: 2.68e-16
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| PRK00431 | PRK00431 | ADP-ribose-binding protein; |
1709-1857 | 1.42e-15 | |||||||
ADP-ribose-binding protein; Pssm-ID: 234759 Cd Length: 177 Bit Score: 78.35 E-value: 1.42e-15
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| YmdB | COG2110 | O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ... |
1709-1857 | 2.05e-15 | |||||||
O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ribosomal structure and biogenesis]; Pssm-ID: 441713 Cd Length: 168 Bit Score: 77.52 E-value: 2.05e-15
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| Macro | pfam01661 | Macro domain; The Macro or A1pp domain is a module of about 180 amino acids which can bind ... |
1716-1820 | 4.86e-14 | |||||||
Macro domain; The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent: in certain cases it is believed to bind non-covalently; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein. This domain is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein 4 and also in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alpha-viruses and coronaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria and eukaryotes. The 3D structure of the SARS-CoV Macro domain has a mixed alpha/beta fold consisting of a central seven-stranded twisted mixed beta sheet sandwiched between two alpha helices on one face, and three on the other. The final alpha-helix, located on the edge of the central beta-sheet, forms the C terminus of the protein. The crystal structure of AF1521 (a Macro domain-only protein from Archaeoglobus fulgidus) has also been reported and compared with other Macro domain containing proteins. Several Macro domain only proteins are shorter than AF1521, and appear to lack either the first strand of the beta-sheet or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site. Pssm-ID: 460286 Cd Length: 116 Bit Score: 71.83 E-value: 4.86e-14
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| CoV_Methyltr_2 | pfam06460 | Coronavirus 2'-O-methyltransferase; This domain covers the NSP16 region of the coronavirus ... |
6614-6775 | 6.05e-14 | |||||||
Coronavirus 2'-O-methyltransferase; This domain covers the NSP16 region of the coronavirus polyprotein. The SARS-CoV RNA cap SAM-dependent (nucleoside-2'-O-)-methyltransferase (2'-O-MTase) is a heterodimer comprising SARS-CoV nsp10 and nsp16. When bound to nsp10, nsp16 is active as a type-0 RNA cap-dependent 2'-O-MTase, ie., active only when the cap guanine is methylated at its N7 position. Nsp10 binds to nsp16 through an activation surface area in nsp10, and the resulting complex exhibits RNA cap (nucleoside-2'-O)-methyltransferase activity. Nsp10 is a double zinc finger protein together with nsp4, nsp5, nsp12, nsp14, and nsp16, nsp10 has been found to be essential in the assembly of a functional replication/transcription complex. Nsp16 adopts a typical fold of the S-adenosylmethionine-dependent methyltransferase (SAM) family as defined initially for the catechol O-MTase but it lacks several elements of the canonical MTase fold, such as helices B and C. The nsp16 topology matches those of dengue virus NS5 N-terminal domain and of vaccinia virus VP39 MTases. Pssm-ID: 461919 Cd Length: 296 Bit Score: 76.37 E-value: 6.05e-14
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| CoV_Nsp13-helicase | cd21718 | helicase domain of coronavirus non-structural protein 13; This model represents the helicase ... |
5630-5950 | 3.28e-12 | |||||||
helicase domain of coronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from alpha-, beta-, gamma-, and deltacoronavirus, including pathogenic human viruses such as Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core. Pssm-ID: 409652 [Multi-domain] Cd Length: 341 Bit Score: 71.79 E-value: 3.28e-12
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| CoV_NSP15_C | pfam19215 | Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the ... |
6453-6592 | 1.90e-11 | |||||||
Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the C-terminal domain of coronavirus non-structural protein 15 (NSP15 or nsp15). NSP15 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. This domain exhibits endoribonuclease activity designated EndoU, highly conserved in all known CoVs and is part of the replicase-transcriptase complex that plays important roles in virus replication and transcription. NSP15 is a Uridylate-specific endoribonuclease that cleaves the 5'-polyuridines from negative-sense viral RNA, termed PUN RNA either upstream or downstream of uridylates, at GUU or GU to produce molecules with 2',3'-cyclic phosphate ends. PUN RNA is a CoV MDA5-dependent pathogen-associated molecular pattern (PAMP). Pssm-ID: 465999 Cd Length: 155 Bit Score: 65.82 E-value: 1.90e-11
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| RdRP_1 | pfam00680 | Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ... |
5040-5194 | 2.08e-11 | |||||||
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases. Pssm-ID: 425815 Cd Length: 450 Bit Score: 70.52 E-value: 2.08e-11
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| RecD | COG0507 | ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
5655-5787 | 3.71e-09 | |||||||
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair]; Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 63.46 E-value: 3.71e-09
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| recD | TIGR01447 | exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ... |
5661-5787 | 4.53e-07 | |||||||
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273631 [Multi-domain] Cd Length: 582 Bit Score: 56.69 E-value: 4.53e-07
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| CoV_Nsp14 | cd21528 | nonstructural protein 14 of coronavirus; Nonstructural protein 14 (Nsp14) of coronavirus (CoV) ... |
6077-6186 | 4.30e-06 | |||||||
nonstructural protein 14 of coronavirus; Nonstructural protein 14 (Nsp14) of coronavirus (CoV) plays an important role in viral replication and transcription. It consists of 2 domains with different enzymatic activities: an N-terminal exoribonuclease (ExoN) domain and a C-terminal cap (guanine-N7) methyltransferase (N7-MTase) domain. ExoN is important for proofreading and therefore, the prevention of lethal mutations. The association of Nsp14 with Nsp10 stimulates its ExoN activity; the complex hydrolyzes double-stranded RNA in a 3' to 5' direction as well as a single mismatched nucleotide at the 3'-end mimicking an erroneous replication product. The Nsp10/Nsp14 complex may function in a replicative mismatch repair mechanism. N7-MTase functions in mRNA capping. Nsp14 can methylate GTP, dGTP as well as cap analogs GpppG, GpppA and m7GpppG. The accumulation of m7GTP or Nsp14 has been found to interfere with protein translation of cellular mRNAs. Pssm-ID: 394955 Cd Length: 518 Bit Score: 53.62 E-value: 4.30e-06
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| eMpr | COG3591 | V8-like Glu-specific endopeptidase [Posttranslational modification, protein turnover, ... |
3284-3430 | 6.79e-06 | |||||||
V8-like Glu-specific endopeptidase [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 442810 [Multi-domain] Cd Length: 194 Bit Score: 50.45 E-value: 6.79e-06
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| ThpR | COG1514 | RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and ... |
4410-4565 | 3.61e-05 | |||||||
RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and biogenesis]; Pssm-ID: 441123 [Multi-domain] Cd Length: 181 Bit Score: 48.10 E-value: 3.61e-05
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| ND5 | MTH00095 | NADH dehydrogenase subunit 5; Provisional |
3042-3162 | 2.52e-04 | |||||||
NADH dehydrogenase subunit 5; Provisional Pssm-ID: 177158 [Multi-domain] Cd Length: 527 Bit Score: 47.60 E-value: 2.52e-04
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| cv_Nsp4_TM | cd21473 | coronavirus non-structural protein 4 (Nsp4) transmembrane domain; Nsp4 may be involved in ... |
3062-3149 | 5.72e-04 | |||||||
coronavirus non-structural protein 4 (Nsp4) transmembrane domain; Nsp4 may be involved in coronavirus-induced membrane remodeling. In order to assemble the replication-transcription complex (RTC), coronavirus induces the rearrangement of host endoplasmic reticulum (ER) membrane into double membrane vesicles (DMVs), zippered ER, or ER spherules. DMV formation has been observed in SARS-CoV cells overexpressing the three transmembrane-containing non-structural proteins of viral replicase polyprotein 1ab: Nsp3, Nsp4 and Nsp6. Together, Nsp3, Nsp4, and Nsp6 have the ability to induce the formation of DMVs that are similar to those seen in SARS-CoV-infected cells. Pssm-ID: 394836 Cd Length: 376 Bit Score: 46.43 E-value: 5.72e-04
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| CbiQ | pfam02361 | Cobalt transport protein; This family consists of various cobalt transport proteins Most of ... |
3094-3193 | 8.16e-04 | |||||||
Cobalt transport protein; This family consists of various cobalt transport proteins Most of which are found in Cobalamin (Vitamin B12) biosynthesis operons. In Salmonella the cbiN cbiQ (product CbiQ in this family) and cbiO are likely to form an active cobalt transport system. Pssm-ID: 396782 Cd Length: 215 Bit Score: 44.63 E-value: 8.16e-04
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| AAA_19 | pfam13245 | AAA domain; |
5662-5787 | 1.02e-03 | |||||||
AAA domain; Pssm-ID: 433059 [Multi-domain] Cd Length: 136 Bit Score: 42.98 E-value: 1.02e-03
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| PotE | COG0531 | Serine transporter YbeC, amino acid:H+ symporter family [Amino acid transport and metabolism]; |
3059-3167 | 3.10e-03 | |||||||
Serine transporter YbeC, amino acid:H+ symporter family [Amino acid transport and metabolism]; Pssm-ID: 440297 [Multi-domain] Cd Length: 438 Bit Score: 44.12 E-value: 3.10e-03
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| UCH | pfam00443 | Ubiquitin carboxyl-terminal hydrolase; |
1867-1945 | 7.37e-03 | |||||||
Ubiquitin carboxyl-terminal hydrolase; Pssm-ID: 425685 [Multi-domain] Cd Length: 310 Bit Score: 42.43 E-value: 7.37e-03
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| Name | Accession | Description | Interval | E-value | ||||||||||||
| Tobaniviridae_RdRp | cd23186 | catalytic core domain of RNA-dependent RNA polymerase (RdRP) in the Tobaniviridae family of ... |
4947-5384 | 0e+00 | ||||||||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRP) in the Tobaniviridae family of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Tobaniviridae, order Nidovirales. Tobaniviridae RNA viruses infect vertebrates; their host organisms include mammals, fish, and snakes. Member viruses have a viral envelope and (+)ssRNA genome. The genome size of Tobaniviruses ranges from 20 to 32 kilobases. The family is the only member of the suborder Tornidovirineae. The family Tobaniviridae has four subfamilies (Piscanivirinae, Remotovirinae, Remotovirinae, and Torovirinae) and eight genera (Bafinivirus, Oncotshavirus, Bostovirus, Infratovirus, Pregotovirus, Sectovirus, Tiruvirus, and Torovirus). The Tobaniviridae family belongs to the order Nidovirales, which currently comprises 88 formally recognized virus species of (+)ssRNA viruses, which are classified into nine virus families across seven different suborders. The structure of Tobaniviridae RdRp contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438036 Cd Length: 401 Bit Score: 696.45 E-value: 0e+00
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| Corona_NS2A | pfam05213 | Coronavirus NS2A protein; This family contains a number of corona virus non-structural ... |
4403-4641 | 2.38e-113 | ||||||||||||
Coronavirus NS2A protein; This family contains a number of corona virus non-structural proteins of unknown function. The family also includes a polymerase protein fragment from Berne virus and does not seem to be related to the pfam04753 Coronavirus NS2 family. This family is part of the 2H phosphoesterase superfamily. Pssm-ID: 282997 Cd Length: 267 Bit Score: 362.48 E-value: 2.38e-113
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| NendoU_tv_PToV-like | cd21162 | Nidoviral uridylate-specific endoribonuclease (NendoU) domain of Porcine torovirus (PToV) ... |
6456-6593 | 7.19e-72 | ||||||||||||
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of Porcine torovirus (PToV) endoribonuclease and related proteins; Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. The Porcine torovirus (PToV) strain PToV-NPL/2013 NendoU domain is located at the N-terminus of the ORF1ab replicase polyprotein, between regions annotated as Nonstructural proteins 11 (Nsp11) and 13 (Nsp13). This subfamily belongs to a family which includes Nsp15 from coronaviruses and Nsp11 from arteriviruses, which may participate in the viral replication process and in the evasion of the host immune system. These vary in their requirement for Mn2+. Coronavirus Nsp15 generally form functional hexamers, with the exception of Porcine DeltaCoronavirus (PDCoV) Nsp15 which exists as a dimer and a monomer in solution. Arterivirus (Porcine Reproductive and Respiratory Syndrome virus) PRRSV Nsp11 is a dimer. NendoUs are distantly related to Xenopus laevis Mn(2+)-dependent uridylate-specific endoribonuclease (XendoU) which is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA. Pssm-ID: 394913 Cd Length: 133 Bit Score: 237.87 E-value: 7.19e-72
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| capping_2-OMTase_Nidovirales | cd20762 | Cap-0 specific (nucleoside-2'-O-)-methyltransferase of nidovirales; Cap-0 specific ... |
6630-6803 | 1.08e-64 | ||||||||||||
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of nidovirales; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Nidovirales viruses, which comprise a family of ss(+)RNA viruses, cap their mRNAs. For one member, coronavirus, the 2'OMTase activity is located in the non-structural protein 16 (Nsp16). For others, the 2'OMTase activity may be located in replicase polyprotein 1ab. Pssm-ID: 467737 Cd Length: 175 Bit Score: 219.11 E-value: 1.08e-64
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| unc_tv_SF1_Hel-like | cd21413 | uncharacterized domain which connects the Cys/His rich zinc-binding (ZBD) and linker to the ... |
5562-5640 | 1.48e-49 | ||||||||||||
uncharacterized domain which connects the Cys/His rich zinc-binding (ZBD) and linker to the first helicase domain of tornidovirus SF1 helicase and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Helicases in this family belong to helicase superfamily 1 (SF1) and include tornidovirus helicases such as Breda virus serotype 1 (BoTV-1) SF1 helicase encoded on ORF1b. They are related to the SF1 family nidoviral replication helicases which include Severe Acute Respiratory Syndrome coronavirus (SARS) non-structural protein 13 (SARS-Nsp13), a component of the viral RNA synthesis replication and transcription complex (RTC). SARS-Nsp13 is a multidomain protein; its other domains include an N-terminal Cys/His rich zinc-binding domain (ZBD) and a SF1 helicase core. The location of the uncharacterized domain represented in this tornidovirus group resembles that of the 1B domain in SARS-Nsp13 helicase; it connects the zinc-binding domain (ZBD) and linker to the first helicase domain. Pssm-ID: 394819 Cd Length: 79 Bit Score: 171.75 E-value: 1.48e-49
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| ps-ssRNAv_Nidovirales_RdRp | cd23168 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Nidovirales of ... |
5030-5329 | 1.78e-48 | ||||||||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Nidovirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This family contains the catalytic core domain of RdRP of Nidovirales, an order of enveloped, (+)ssRNA viruses which infect vertebrates and invertebrates. Host organisms include mammals, birds, reptiles, amphibians, fish, arthropods, mollusks, and helminths. The order Nidovirales currently comprises 88 formally recognized virus species of (+)ssRNA viruses which are classified into nine virus families: Abyssoviridae, Arteriviridae, Coronaviridae, Euroniviridae, Medioniviridae, Mesoniviridae, Mononiviridae, Roniviridae, and Tobaniviridae. Based on the genome size, the members of the order Nidovirales can be divided into two groups, large and small nidoviruses. The genomes of the large nidoviruses are well over 25 kb in length with size differences in the 5 kb range. Planarian secretory cell nidovirus (PSCNV), only member of the Mononiviridae family, has the largest known non-segmented RNA genome of 41.1 kb; its host is the planarian flatworm. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438018 [Multi-domain] Cd Length: 310 Bit Score: 177.55 E-value: 1.78e-48
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| Macro_X_Nsp3-like | cd21557 | X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The ... |
1713-1844 | 2.00e-43 | ||||||||||||
X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The X-domain, also called Mac1, is the macrodomain found in riboviral non-structural protein 3 (Nsp3), including the Nsp3 of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) as well as SARS-CoV-2, and other coronaviruses (alpha-, beta-, gamma-, and deltacoronavirus), among others. The SARS-CoV-2 Nsp3 Mac1 is highly conserved among all CoVs, and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. It appears to counter host-mediated antiviral ADP-ribosylation, a post-translational modification that is part of the host response to viral infections. Mac1 is essential for pathogenesis in multiple animal models of CoV infection, implicating it as a virulence factor and potential therapeutic target. Assays show that the de-MARylating activity leads to a rapid loss of substrate, and that Mac1 could not hydrolyze poly-ADP-ribose; thus, Mac1 is a MAR-hydrolase (mono-ADP ribosylhydrolase). Mac1 was originally named ADP-ribose-1"-phosphatase (ADRP) based on data demonstrating that it could remove the phosphate group from ADP-ribose-1"-phosphate; however, activity was modest and was unclear why this would impact a virus infection. This family also includes the X-domain of Avian infectious bronchitis virus (IBV) strain Beaudette coronavirus that does not bind ADP-ribose; the triple glycine sequence found in the X-domains of SARS-CoV and human coronavirus 229E (HCoV229E), which are involved in ADP-ribose binding, is not conserved in the IBV X-domain. SARS-CoVs have two other macrodomains referred to as the SUD-N (N-terminal subdomain, or Mac2) and SUD-M (middle SUD subdomain, or Mac3) of the SARS-unique domain (SUD), which also do not bind ADP-ribose; these bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). SARS-CoV SUD-N and SUD-M are not included in this group. Pssm-ID: 438957 Cd Length: 127 Bit Score: 156.18 E-value: 2.00e-43
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| NendoU_nv | cd21158 | Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural ... |
6456-6592 | 1.06e-38 | ||||||||||||
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural protein 15 (Nsp15), arterivirus Nsp11, torovirus endoribonuclease, and related proteins; Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. This family also includes torovirus NendoUs. Except for turkey coronavirus (TCoV) Nsp15, Mn2+ is generally essential for the catalytic activity of coronavirus Nsp15. Mn2+ is dispensable, and to some extent inhibits the activity of arterivirus (Porcine Reproductive and Respiratory Syndrome virus) PRRSV Nsp11. Coronavirus Nsp15 from Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), human Coronavirus 229E (HCoV229E), and murine hepatitis virus (MHV) form a functional hexamer while Porcine DeltaCoronavirus (PDCoV) Nsp15 has been shown to exist as a dimer and monomer in solution. Nsp11 from the arterivirus PRRSV is a dimer. NendoUs are distantly related to Xenopus laevis Mn(2+)-dependent uridylate-specific endoribonuclease (XendoU) which is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA. Pssm-ID: 439157 Cd Length: 151 Bit Score: 143.55 E-value: 1.06e-38
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| ZBD_tv_SF1_Hel-like | cd21403 | Cys/His rich zinc-binding domain (CH/ZBD) of tornidovirus SF1 helicase and related proteins; ... |
5413-5507 | 1.33e-37 | ||||||||||||
Cys/His rich zinc-binding domain (CH/ZBD) of tornidovirus SF1 helicase and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. This tornidovirus group includes White bream virus (WBV) SF1 helicase encoded on ORF1b and belongs to helicase superfamily 1 (SF1). The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. Members of this group belong to a family of nindoviral replication helicases which include includes Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) non-structural protein 13 (SARS-Nsp13), a component of the viral RNA synthesis replication and transcription complex (RTC). The SARS-Nsp13 CH/ZBD is indispensable for helicase activity and interacts with SARS-Nsp12, the RNA-dependent RNA polymerase. Pssm-ID: 394810 Cd Length: 95 Bit Score: 138.24 E-value: 1.33e-37
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| MERS-CoV-like_RdRp | cd21592 | Middle East respiratory syndrome-related coronavirus RNA-dependent RNA polymerase, also known ... |
4660-5383 | 1.50e-31 | ||||||||||||
Middle East respiratory syndrome-related coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the C lineage: responsible for replication and transcription of the viral RNA genome; This group contains the RNA-dependent RNA polymerase (RdRp) of Middle East respiratory syndrome (MERS)-related CoV, bat-CoV HKU5, and similar proteins from betacoronaviruses in the merbecovirus subgenera (C lineage). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which has been shown to potently inhibit MERS RdRp. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 394896 Cd Length: 931 Bit Score: 137.10 E-value: 1.50e-31
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| CoV_RdRp | cd21530 | coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible ... |
4736-5364 | 8.76e-30 | ||||||||||||
coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome; This family contains the RNA-dependent RNA polymerase of alpha-, beta-, gamma-, delta-coronaviruses, including three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2, also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which shows potential for the treatment of SARS-CoV-2 viral infections. The structure of SARS-CoV-2 Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438015 Cd Length: 928 Bit Score: 131.50 E-value: 8.76e-30
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| SARS-CoV-like_RdRp | cd21591 | Severe acute respiratory syndrome coronavirus RNA-dependent RNA polymerase, also known as ... |
4662-5364 | 4.57e-29 | ||||||||||||
Severe acute respiratory syndrome coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the B lineage: responsible for replication and transcription of the viral RNA genome; This group contains the RNA-dependent RNA polymerase (RdRp) of Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2 (also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus), and similar proteins from betacoronaviruses in the sarbecovirus subgenera (B lineage). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which shows potential for the treatment of SARS-CoV-2 viral infections. The structure of SARS-CoV-2 Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. Recent studies have shown that the SARS-CoV-2 RdRp requires two iron-sulfur clusters to function optimally. Earlier studies had mistakenly identified these iron-sulfur cluster binding sites for zinc-binding sites, likely because iron-sulfur clusters degrade easily under standard experimental conditions.The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 394895 Cd Length: 928 Bit Score: 129.05 E-value: 4.57e-29
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| HCoV_HKU1-like_RdRp | cd21593 | human coronavirus HKU1 RNA-dependent RNA polymerase, also known as non-structural protein 12, ... |
4909-5387 | 2.14e-27 | ||||||||||||
human coronavirus HKU1 RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the A lineage: responsible for replication and transcription of the viral RNA genome; This group contains the RNA-dependent RNA polymerase (RdRp) of human coronavirus HKU1, murine hepatitis virus, and similar proteins from betacoronaviruses in the embecovirus subgenera (A lineage). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 394897 Cd Length: 925 Bit Score: 123.53 E-value: 2.14e-27
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| batCoV-HKU9-like_RdRp | cd21596 | Bat coronavirus HKU9 RNA-dependent RNA polymerase, also known as non-structural protein 12, ... |
4928-5389 | 9.97e-27 | ||||||||||||
Bat coronavirus HKU9 RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the D lineage: responsible for replication and transcription of the viral RNA genome; This group contains the RNA-dependent RNA polymerase (RdRp) of bat coronavirus HKU9 and similar proteins from betacoronaviruses in the nobecovirus subgenera (D lineage). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 394898 Cd Length: 929 Bit Score: 121.30 E-value: 9.97e-27
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| betaCoV_RdRp | cd21589 | betacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ... |
4909-5364 | 5.63e-25 | ||||||||||||
betacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome; This subfamily contains the RNA-dependent RNA polymerase (RdRp) of betacoronaviruses, including the RdRps from three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2, also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which shows potential for the treatment of SARS-CoV-2 viral infections. The structure of SARS-CoV-2 Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438016 Cd Length: 925 Bit Score: 115.65 E-value: 5.63e-25
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| Macro_Af1521_BAL-like | cd02907 | macrodomain, Af1521-like family; Macrodomains are found in a variety of proteins with diverse ... |
1709-1820 | 6.41e-24 | ||||||||||||
macrodomain, Af1521-like family; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. The macrodomains in this family show similarity to Af1521, a protein from Archaeoglobus fulgidus containing a stand-alone macrodomain. Af1521 binds ADP-ribose and exhibits phosphatase activity toward ADP-ribose-1"-monophosphate (Appr-1"-p). Also included in this family are the N-terminal (or first) macrodomains of BAL (B-aggressive lymphoma) proteins which contain multiple macrodomains, such as the first macrodomain of mono-ADP-ribosyltransferase PARP14 (PARP-14, also known as ADP-ribosyltransferase diphtheria toxin-like 8, ATRD8, B aggressive lymphoma protein 2, or BAL2). Most BAL proteins also contain a C-terminal PARP active site and are also named as PARPs. Human BAL1 (or PARP-9) was originally identified as a risk-related gene in diffuse large B-cell lymphoma that promotes malignant B-cell migration. Some BAL family proteins exhibit PARP activity. Poly (ADP-ribosyl)ation is an immediate DNA-damage-dependent post-translational modification of histones and other nuclear proteins. BAL proteins may also function as transcriptional repressors. Pssm-ID: 394877 [Multi-domain] Cd Length: 158 Bit Score: 101.41 E-value: 6.41e-24
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| gammaCoV_RdRp | cd21587 | gammacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ... |
4930-5383 | 2.60e-23 | ||||||||||||
gammacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome; This subfamily contains the RNA-dependent RNA polymerase (RdRp) of gammacoronaviruses, including the RdRp of avian infectious bronchitis virus (IBV) and similar proteins. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 394891 Cd Length: 931 Bit Score: 110.36 E-value: 2.60e-23
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| deltaCoV_RdRp | cd21590 | deltacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ... |
4736-5323 | 8.15e-22 | ||||||||||||
deltacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome; This subfamily contains the RNA-dependent RNA polymerase (RdRp) of deltacoronaviruses. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which has been shown to inhibit human endemic and zoonotic deltacoronaviruses with a highly divergent RdRp. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 394894 Cd Length: 928 Bit Score: 105.32 E-value: 8.15e-22
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| capping_2-OMTase_deltaCoV_Nsp16 | cd23530 | Cap-0 specific (nucleoside-2'-O-)-methyltransferase of deltacoronavirus, also called ... |
6630-6774 | 2.88e-18 | ||||||||||||
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of deltacoronavirus, also called non-structural protein 16; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. The deltacoronavirus (deltaCoV) 2'OMTase activity is located in the non-structural protein 16 (Nsp16). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Nsp16 requires Nsp10 to bind both m7GpppA-RNA substrate and SAM cofactor; the structure suggests that Nsp10 may stabilize the SAM-binding pocket and extend the substrate RNA-binding groove of Nsp16. Pssm-ID: 467742 Cd Length: 183 Bit Score: 86.37 E-value: 2.88e-18
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| alphaCoV_RdRp | cd21588 | alphacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ... |
4909-5363 | 4.98e-17 | ||||||||||||
alphacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome; This subfamily contains the RNA-dependent RNA polymerase (RdRp) of alphacoronaviruses, including human coronaviruses (HCoVs), HCoV-NL63, and HCoV-229E. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 394892 Cd Length: 924 Bit Score: 89.78 E-value: 4.98e-17
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| A1pp | smart00506 | Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by ... |
1712-1829 | 2.68e-16 | ||||||||||||
Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by reciprocal PSI-BLAST searches (unpublished results, and Pehrson _ Fuji). Pssm-ID: 214701 Cd Length: 133 Bit Score: 78.89 E-value: 2.68e-16
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| Arteriviridae_RdRp | cd23189 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of ... |
5096-5372 | 1.10e-15 | ||||||||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Arteriviridae, order Nidovirales. Member viruses have a viral envelope and (+)ssRNA genome. The overall genome organization of the Arteriviruses are highly similar to the Coronaviruses; however, they lack the spike proteins of the coronaviruses. The family members include equine arteritis virus (EAV), porcine reproductive and respiratory syndrome virus (PRRSV), lactate dehydrogenase elevating virus of mice, and simian hemorrhagic fever virus (SHFV). The structure of Arteriviridae RdRp contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438039 [Multi-domain] Cd Length: 323 Bit Score: 81.92 E-value: 1.10e-15
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| PRK00431 | PRK00431 | ADP-ribose-binding protein; |
1709-1857 | 1.42e-15 | ||||||||||||
ADP-ribose-binding protein; Pssm-ID: 234759 Cd Length: 177 Bit Score: 78.35 E-value: 1.42e-15
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| YmdB | COG2110 | O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ... |
1709-1857 | 2.05e-15 | ||||||||||||
O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ribosomal structure and biogenesis]; Pssm-ID: 441713 Cd Length: 168 Bit Score: 77.52 E-value: 2.05e-15
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| Macro | pfam01661 | Macro domain; The Macro or A1pp domain is a module of about 180 amino acids which can bind ... |
1716-1820 | 4.86e-14 | ||||||||||||
Macro domain; The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent: in certain cases it is believed to bind non-covalently; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein. This domain is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein 4 and also in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alpha-viruses and coronaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria and eukaryotes. The 3D structure of the SARS-CoV Macro domain has a mixed alpha/beta fold consisting of a central seven-stranded twisted mixed beta sheet sandwiched between two alpha helices on one face, and three on the other. The final alpha-helix, located on the edge of the central beta-sheet, forms the C terminus of the protein. The crystal structure of AF1521 (a Macro domain-only protein from Archaeoglobus fulgidus) has also been reported and compared with other Macro domain containing proteins. Several Macro domain only proteins are shorter than AF1521, and appear to lack either the first strand of the beta-sheet or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site. Pssm-ID: 460286 Cd Length: 116 Bit Score: 71.83 E-value: 4.86e-14
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| Macro_OAADPr_deacetylase | cd02908 | macrodomain, O-acetyl-ADP-ribose (OAADPr) family; Macrodomains are found in a variety of ... |
1712-1845 | 5.28e-14 | ||||||||||||
macrodomain, O-acetyl-ADP-ribose (OAADPr) family; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. This family includes eukaryotic macrodomain proteins such as human MacroD1 and MacroD2, and bacterial proteins such as Escherichia coli YmdB; these have been shown to be O-acetyl-ADP-ribose (OAADPr) deacetylases that efficiently catalyze the hydrolysis of OAADPr to produce ADP-ribose and free acetate. OAADPr is a sirtuin reaction product generated from the NAD+-dependent protein deacetylation reactions and has been implicated as a signaling molecule. By acting on mono-ADP-ribosylated substrates, OAADPr deacetylases may reverse cellular ADP-ribosylation. Pssm-ID: 438955 Cd Length: 166 Bit Score: 73.32 E-value: 5.28e-14
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| CoV_Methyltr_2 | pfam06460 | Coronavirus 2'-O-methyltransferase; This domain covers the NSP16 region of the coronavirus ... |
6614-6775 | 6.05e-14 | ||||||||||||
Coronavirus 2'-O-methyltransferase; This domain covers the NSP16 region of the coronavirus polyprotein. The SARS-CoV RNA cap SAM-dependent (nucleoside-2'-O-)-methyltransferase (2'-O-MTase) is a heterodimer comprising SARS-CoV nsp10 and nsp16. When bound to nsp10, nsp16 is active as a type-0 RNA cap-dependent 2'-O-MTase, ie., active only when the cap guanine is methylated at its N7 position. Nsp10 binds to nsp16 through an activation surface area in nsp10, and the resulting complex exhibits RNA cap (nucleoside-2'-O)-methyltransferase activity. Nsp10 is a double zinc finger protein together with nsp4, nsp5, nsp12, nsp14, and nsp16, nsp10 has been found to be essential in the assembly of a functional replication/transcription complex. Nsp16 adopts a typical fold of the S-adenosylmethionine-dependent methyltransferase (SAM) family as defined initially for the catechol O-MTase but it lacks several elements of the canonical MTase fold, such as helices B and C. The nsp16 topology matches those of dengue virus NS5 N-terminal domain and of vaccinia virus VP39 MTases. Pssm-ID: 461919 Cd Length: 296 Bit Score: 76.37 E-value: 6.05e-14
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| capping_2-OMTase_CoV_Nsp16 | cd23526 | Cap-0 specific (nucleoside-2'-O-)-methyltransferase of Coronavirus, also called non-structural ... |
6630-6775 | 1.74e-13 | ||||||||||||
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of Coronavirus, also called non-structural protein 16; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Coronavirus (CoV) 2'OMTase activity is located in the non-structural protein 16 (Nsp16). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Nsp16 requires Nsp10 to bind both m7GpppA-RNA substrate and SAM cofactor; the structure suggests that Nsp10 may stabilize the SAM-binding pocket and extend the substrate RNA-binding groove of Nsp16. Pssm-ID: 467738 Cd Length: 191 Bit Score: 72.49 E-value: 1.74e-13
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| capping_2-OMTase_gammaCoV_Nsp16 | cd23529 | Cap-0 specific (nucleoside-2'-O-)-methyltransferase of gammacoronavirus, also called ... |
6630-6775 | 4.45e-13 | ||||||||||||
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of gammacoronavirus, also called non-structural protein 16; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. The gammacoronavirus (gammaCoV) 2'OMTase activity is located in the non-structural protein 16 (Nsp16). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Nsp16 requires Nsp10 to bind both m7GpppA-RNA substrate and SAM cofactor; the structure suggests that Nsp10 may stabilize the SAM-binding pocket and extend the substrate RNA-binding groove of Nsp16. Pssm-ID: 467741 Cd Length: 196 Bit Score: 71.45 E-value: 4.45e-13
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| CoV_Nsp13-helicase | cd21718 | helicase domain of coronavirus non-structural protein 13; This model represents the helicase ... |
5630-5950 | 3.28e-12 | ||||||||||||
helicase domain of coronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from alpha-, beta-, gamma-, and deltacoronavirus, including pathogenic human viruses such as Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core. Pssm-ID: 409652 [Multi-domain] Cd Length: 341 Bit Score: 71.79 E-value: 3.28e-12
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| Macro_SF | cd02749 | macrodomain superfamily; Macrodomains are found in a variety of proteins with diverse cellular ... |
1713-1831 | 1.03e-11 | ||||||||||||
macrodomain superfamily; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Macrodomains include the yeast macrodomain Poa1 which is a phosphatase of ADP-ribose-1"-phosphate, a by-product of tRNA splicing. Some macrodomains have ADPr-unrelated binding partners such as the coronavirus SUD-N (N-terminal subdomain) and SUD-M (middle subdomain) of the SARS-unique domain (SUD) which bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). Macrodomains regulate a wide variety of cellular and organismal processes, including DNA damage repair, signal transduction, and immune response. Pssm-ID: 394871 Cd Length: 121 Bit Score: 65.50 E-value: 1.03e-11
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| capping_2-OMTase_alphaCoV_Nsp16 | cd23527 | Cap-0 specific (nucleoside-2'-O-)-methyltransferase of alphacoronavirus, also called ... |
6630-6775 | 1.12e-11 | ||||||||||||
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of alphacoronavirus, also called non-structural protein 16; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. The alphacoronavirus (alphaCoV) 2'OMTase activity is located in the non-structural protein 16 (Nsp16). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Nsp16 requires Nsp10 to bind both m7GpppA-RNA substrate and SAM cofactor; the structure suggests that Nsp10 may stabilize the SAM-binding pocket and extend the substrate RNA-binding groove of Nsp16. Pssm-ID: 467739 Cd Length: 193 Bit Score: 67.43 E-value: 1.12e-11
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| CoV_NSP15_C | pfam19215 | Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the ... |
6453-6592 | 1.90e-11 | ||||||||||||
Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the C-terminal domain of coronavirus non-structural protein 15 (NSP15 or nsp15). NSP15 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. This domain exhibits endoribonuclease activity designated EndoU, highly conserved in all known CoVs and is part of the replicase-transcriptase complex that plays important roles in virus replication and transcription. NSP15 is a Uridylate-specific endoribonuclease that cleaves the 5'-polyuridines from negative-sense viral RNA, termed PUN RNA either upstream or downstream of uridylates, at GUU or GU to produce molecules with 2',3'-cyclic phosphate ends. PUN RNA is a CoV MDA5-dependent pathogen-associated molecular pattern (PAMP). Pssm-ID: 465999 Cd Length: 155 Bit Score: 65.82 E-value: 1.90e-11
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| RdRP_1 | pfam00680 | Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ... |
5040-5194 | 2.08e-11 | ||||||||||||
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases. Pssm-ID: 425815 Cd Length: 450 Bit Score: 70.52 E-value: 2.08e-11
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| DEXXQc_Upf1-like | cd17934 | DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ... |
5662-5817 | 4.88e-11 | ||||||||||||
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to 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: 438708 [Multi-domain] Cd Length: 121 Bit Score: 63.41 E-value: 4.88e-11
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| capping_2-OMTase_betaCoV_Nsp16 | cd23528 | Cap-0 specific (nucleoside-2'-O-)-methyltransferase of betacoronavirus, also called ... |
6617-6775 | 1.14e-10 | ||||||||||||
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of betacoronavirus, also called non-structural protein 16; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. The betacoronavirus (betaCoV) 2'OMTase activity is located in the non-structural protein 16 (Nsp16). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Nsp16 requires Nsp10 to bind both m7GpppA-RNA substrate and SAM cofactor; the structure suggests that Nsp10 may stabilize the SAM-binding pocket and extend the substrate RNA-binding groove of Nsp16. Pssm-ID: 467740 Cd Length: 216 Bit Score: 65.10 E-value: 1.14e-10
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| deltaCoV_Nsp13-helicase | cd21721 | helicase domain of deltacoronavirus non-structural protein 13; This model represents the ... |
5660-5940 | 1.63e-10 | ||||||||||||
helicase domain of deltacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from deltacoronavirus, including Bulbul coronavirus (CoV) HKU11 and Common moorhen CoV HKU21. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core. Pssm-ID: 409654 [Multi-domain] Cd Length: 342 Bit Score: 66.49 E-value: 1.63e-10
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| RecD | COG0507 | ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
5655-5787 | 3.71e-09 | ||||||||||||
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair]; Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 63.46 E-value: 3.71e-09
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| DEXSc_RecD-like | cd17933 | DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ... |
5654-5787 | 6.60e-09 | ||||||||||||
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD 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: 350691 [Multi-domain] Cd Length: 155 Bit Score: 58.33 E-value: 6.60e-09
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| gammaCoV_Nsp13-helicase | cd21720 | helicase domain of gammacoronavirus non-structural protein 13; This model represents the ... |
5663-5940 | 4.40e-08 | ||||||||||||
helicase domain of gammacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from gammacoronavirus, including Avian infectious bronchitis virus. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Coronavirus (CoV) Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core. Pssm-ID: 409653 [Multi-domain] Cd Length: 343 Bit Score: 59.16 E-value: 4.40e-08
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| NendoU_av_Nsp11-like | cd21160 | Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV ... |
6456-6592 | 5.92e-08 | ||||||||||||
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV Nonstructural protein 11 (Nsp11), and related proteins; Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. Mn2+ is dispensable, and to some extent inhibits the activity of arterivirus (Porcine Reproductive and Respiratory Syndrome virus) PRRSV Nsp11. This Nsp11 exists as a dimer. NendoUs are distantly related to Xenopus laevis Mn(2+)-dependent uridylate-specific endoribonuclease (XendoU) which is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA. Pssm-ID: 394911 Cd Length: 120 Bit Score: 54.64 E-value: 5.92e-08
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| Medioniviridae_RdRp | cd23188 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the Medioniviridae family of ... |
5035-5361 | 4.03e-07 | ||||||||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the Medioniviridae family of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Medioniviridae, order Nidovirales. Member viruses have a viral envelope and (+)ssRNA genome. The Medioniviridae subgenera includes Turrinivirus and Balbicanovirus. The structure of Medioniviridae RdRp contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438038 Cd Length: 391 Bit Score: 56.24 E-value: 4.03e-07
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| recD | TIGR01447 | exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ... |
5661-5787 | 4.53e-07 | ||||||||||||
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273631 [Multi-domain] Cd Length: 582 Bit Score: 56.69 E-value: 4.53e-07
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| DEXXYc_viral_SF1-N | cd17937 | DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ... |
5663-5816 | 4.85e-07 | ||||||||||||
DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. The members here contain arterivirus equine arteritis virus (EAV) non-structural protein (nsp)10. Nsp10 is composed of two domains, ZBD (ATPase) and HEL1 (helicase) along with 2 additional non-enzymatic domains that are thought to regulate HEL1 function. The helicase activity depends on the extensive relay of interactions between the ZBD and HEL1 domains. The arterivirus helicase structurally resembles the cellular Upf1 helicase, suggesting that nidoviruses may also use their helicases for post-transcriptional quality control of their large RNA genomes. The proteins here 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: 350695 [Multi-domain] Cd Length: 137 Bit Score: 52.44 E-value: 4.85e-07
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| DNA2 | COG1112 | Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]; |
5750-5948 | 1.26e-06 | ||||||||||||
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]; Pssm-ID: 440729 [Multi-domain] Cd Length: 819 Bit Score: 55.52 E-value: 1.26e-06
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| CoV_Nsp14 | cd21528 | nonstructural protein 14 of coronavirus; Nonstructural protein 14 (Nsp14) of coronavirus (CoV) ... |
6077-6186 | 4.30e-06 | ||||||||||||
nonstructural protein 14 of coronavirus; Nonstructural protein 14 (Nsp14) of coronavirus (CoV) plays an important role in viral replication and transcription. It consists of 2 domains with different enzymatic activities: an N-terminal exoribonuclease (ExoN) domain and a C-terminal cap (guanine-N7) methyltransferase (N7-MTase) domain. ExoN is important for proofreading and therefore, the prevention of lethal mutations. The association of Nsp14 with Nsp10 stimulates its ExoN activity; the complex hydrolyzes double-stranded RNA in a 3' to 5' direction as well as a single mismatched nucleotide at the 3'-end mimicking an erroneous replication product. The Nsp10/Nsp14 complex may function in a replicative mismatch repair mechanism. N7-MTase functions in mRNA capping. Nsp14 can methylate GTP, dGTP as well as cap analogs GpppG, GpppA and m7GpppG. The accumulation of m7GTP or Nsp14 has been found to interfere with protein translation of cellular mRNAs. Pssm-ID: 394955 Cd Length: 518 Bit Score: 53.62 E-value: 4.30e-06
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| eMpr | COG3591 | V8-like Glu-specific endopeptidase [Posttranslational modification, protein turnover, ... |
3284-3430 | 6.79e-06 | ||||||||||||
V8-like Glu-specific endopeptidase [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 442810 [Multi-domain] Cd Length: 194 Bit Score: 50.45 E-value: 6.79e-06
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| DEXXQc_SMUBP2 | cd18044 | DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ... |
5656-5792 | 8.17e-06 | ||||||||||||
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, or IGHMBP2) is a 5' to 3' helicase that unwinds RNA and DNA duplexes in an ATP-dependent reaction. It is a DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence (5'-GGGCT-3') related to the immunoglobulin mu chain switch region. The IGHMBP2 gene is responsible for Charcot-Marie-Tooth disease (CMT) type 2S and spinal muscular atrophy with respiratory distress type 1 (SMARD1). It is also thought to play a role in frontotemporal dementia (FTD) with amyotrophic lateral sclerosis (ALS) and major depressive disorder (MDD). SMUBP2 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: 350802 [Multi-domain] Cd Length: 191 Bit Score: 50.30 E-value: 8.17e-06
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| ZBD_nv_SF1_Hel-like | cd21399 | Cys/His rich zinc-binding domain (CH/ZBD) of nidovirus helicases including coronavirus Nsp13 ... |
5416-5479 | 2.10e-05 | ||||||||||||
Cys/His rich zinc-binding domain (CH/ZBD) of nidovirus helicases including coronavirus Nsp13 and arterivirus Nsp10, and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. This nidovirus family includes Severe Acute Respiratory Syndrome coronavirus (SARS) non-structural protein 13 (SARS-Nsp13) and equine arteritis virus (EAV) Nsp10 helicase, and belongs to helicase superfamily 1 (SF1). The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. SARS-Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). The SARS-Nsp13 CH/ZBD is indispensable for helicase activity and interacts with SARS-Nsp12, the RNA-dependent RNA polymerase. SARS-Nsp12 can enhance the helicase activity of SARS-Nsp13. SARS-Nsp13 and EAV Nsp10 are multidomain proteins; their other domains include a 1B regulatory domain and a SF1 helicase core. Pssm-ID: 394806 Cd Length: 71 Bit Score: 45.64 E-value: 2.10e-05
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| ThpR | COG1514 | RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and ... |
4410-4565 | 3.61e-05 | ||||||||||||
RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and biogenesis]; Pssm-ID: 441123 [Multi-domain] Cd Length: 181 Bit Score: 48.10 E-value: 3.61e-05
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| betaCoV_Nsp13-helicase | cd21722 | helicase domain of betacoronavirus non-structural protein 13; This model represents the ... |
5645-5827 | 5.51e-05 | ||||||||||||
helicase domain of betacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from betacoronavirus, including pathogenic human viruses such as Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core. Pssm-ID: 409655 [Multi-domain] Cd Length: 340 Bit Score: 49.41 E-value: 5.51e-05
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| NendoU_cv_Nsp15-like | cd21161 | Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural ... |
6539-6592 | 1.33e-04 | ||||||||||||
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural Protein 15 (Nsp15) and related proteins; Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. Except for turkey coronavirus (TCoV) Nsp15, Mn2+ is generally essential for the catalytic activity of coronavirus Nsp15. Coronavirus Nsp15 from Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), human Coronavirus 229E (HCoV229E), and murine hepatitis virus (MHV) form a functional hexamer while Porcine DeltaCoronavirus (PDCoV) Nsp15 has been shown to exist as a dimer and a monomer in solution. NendoUs are distantly related to Xenopus laevis Mn(2+)-dependent uridylate-specific endoribonuclease (XendoU) which is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA. Pssm-ID: 439158 Cd Length: 151 Bit Score: 45.72 E-value: 1.33e-04
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| ZBD_UPF1_nv_SF1_Hel-like | cd21343 | Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 helicase, nidovirus SF1 helicases ... |
5416-5479 | 1.35e-04 | ||||||||||||
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 helicase, nidovirus SF1 helicases including coronavirus Nsp13 and arterivirus Nsp10, and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands, and are classified based on the arrangement of conserved motifs into six superfamilies. Members of this family belong to helicase superfamily 1 (SF1) and include nidoviral helicases such as Severe Acute Respiratory Syndrome coronavirus (SARS) non-structural protein 13 (SARS-Nsp13) and equine arteritis virus (EAV) Nsp10, as well as eukaryotic UPF1 helicase. The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. UPF1 participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. The CH/ZBD of UPF1 interacts with UPF2, a factor also involved in NMD. SARS-Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). The SARS-Nsp13 CH/ZBD is indispensable for helicase activity and interacts with SARS-Nsp12, the RNA-dependent RNA polymerase. SARS-Nsp12 can enhance the helicase activity of SARS-Nsp13. UPF1, SARS-Nsp13 and EAV Nsp10 are multidomain proteins; their other domains include a 1B regulatory domain and a SF1 helicase core. Pssm-ID: 439166 Cd Length: 70 Bit Score: 43.25 E-value: 1.35e-04
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| ND5 | MTH00095 | NADH dehydrogenase subunit 5; Provisional |
3042-3162 | 2.52e-04 | ||||||||||||
NADH dehydrogenase subunit 5; Provisional Pssm-ID: 177158 [Multi-domain] Cd Length: 527 Bit Score: 47.60 E-value: 2.52e-04
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| AKAP7_NLS | pfam10469 | AKAP7 2'5' RNA ligase-like domain; AKAP7_NLS is the N-terminal domain of the cyclic ... |
4407-4519 | 2.95e-04 | ||||||||||||
AKAP7 2'5' RNA ligase-like domain; AKAP7_NLS is the N-terminal domain of the cyclic AMP-dependent protein kinase A, PKA, anchor protein AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes. AKAP7_NLS carries the nuclear localization signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein. Binding to the regulatory subunits RI and RII of PKA is mediated via the family AKAP7_RIRII_bdg. at the C-terminus. This family represents a region that contains two 2'5' RNA ligase like domains pfam02834. Presumably this domain carried out some as yet unknown enzymatic function. Pssm-ID: 402204 [Multi-domain] Cd Length: 207 Bit Score: 45.72 E-value: 2.95e-04
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| cv_Nsp4_TM | cd21473 | coronavirus non-structural protein 4 (Nsp4) transmembrane domain; Nsp4 may be involved in ... |
3062-3149 | 5.72e-04 | ||||||||||||
coronavirus non-structural protein 4 (Nsp4) transmembrane domain; Nsp4 may be involved in coronavirus-induced membrane remodeling. In order to assemble the replication-transcription complex (RTC), coronavirus induces the rearrangement of host endoplasmic reticulum (ER) membrane into double membrane vesicles (DMVs), zippered ER, or ER spherules. DMV formation has been observed in SARS-CoV cells overexpressing the three transmembrane-containing non-structural proteins of viral replicase polyprotein 1ab: Nsp3, Nsp4 and Nsp6. Together, Nsp3, Nsp4, and Nsp6 have the ability to induce the formation of DMVs that are similar to those seen in SARS-CoV-infected cells. Pssm-ID: 394836 Cd Length: 376 Bit Score: 46.43 E-value: 5.72e-04
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| CbiQ | pfam02361 | Cobalt transport protein; This family consists of various cobalt transport proteins Most of ... |
3094-3193 | 8.16e-04 | ||||||||||||
Cobalt transport protein; This family consists of various cobalt transport proteins Most of which are found in Cobalamin (Vitamin B12) biosynthesis operons. In Salmonella the cbiN cbiQ (product CbiQ in this family) and cbiO are likely to form an active cobalt transport system. Pssm-ID: 396782 Cd Length: 215 Bit Score: 44.63 E-value: 8.16e-04
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| AAA_19 | pfam13245 | AAA domain; |
5662-5787 | 1.02e-03 | ||||||||||||
AAA domain; Pssm-ID: 433059 [Multi-domain] Cd Length: 136 Bit Score: 42.98 E-value: 1.02e-03
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| DEXXQc_Helz-like | cd18038 | DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ... |
5667-5787 | 2.41e-03 | ||||||||||||
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and similar proteins. Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. All 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: 350796 [Multi-domain] Cd Length: 229 Bit Score: 43.38 E-value: 2.41e-03
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| PRK04143 | PRK04143 | protein-ADP-ribose hydrolase; |
1712-1819 | 2.81e-03 | ||||||||||||
protein-ADP-ribose hydrolase; Pssm-ID: 235225 Cd Length: 264 Bit Score: 43.43 E-value: 2.81e-03
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| PotE | COG0531 | Serine transporter YbeC, amino acid:H+ symporter family [Amino acid transport and metabolism]; |
3059-3167 | 3.10e-03 | ||||||||||||
Serine transporter YbeC, amino acid:H+ symporter family [Amino acid transport and metabolism]; Pssm-ID: 440297 [Multi-domain] Cd Length: 438 Bit Score: 44.12 E-value: 3.10e-03
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| EcfT | cd16914 | T component of ECF-type transporters; The transmembrane component (T component) of the energy ... |
3057-3153 | 4.04e-03 | ||||||||||||
T component of ECF-type transporters; The transmembrane component (T component) of the energy coupling-factor (ECF)-type transporter is a transmembrane protein important for vitamin uptake in prokaryotes. In addition to the T component, energy-coupling factor (ECF) transporters contain an energy-coupling module that consists of two ATP-binding proteins (known as the A and A' components) and a substrate-binding (S) component. ECF transporters comprise a subgroup of ATP-binding cassette (ABC) transporters that do not make use of water-soluble substrate binding proteins or domains, but instead employ integral membrane proteins for substrate binding, the S component, in contrast to classical ABC importers. The T component links the S component to the ATP-binding subcomplex that is composed of the A and A' components. Pssm-ID: 410987 Cd Length: 233 Bit Score: 42.53 E-value: 4.04e-03
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| SF1_C | cd18786 | C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
5874-5940 | 4.97e-03 | ||||||||||||
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Similar to SF2 helicases, they do not form toroidal, predominantly hexameric structures like SF3-6. SF1 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: 350173 [Multi-domain] Cd Length: 89 Bit Score: 39.73 E-value: 4.97e-03
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| UCH | pfam00443 | Ubiquitin carboxyl-terminal hydrolase; |
1867-1945 | 7.37e-03 | ||||||||||||
Ubiquitin carboxyl-terminal hydrolase; Pssm-ID: 425685 [Multi-domain] Cd Length: 310 Bit Score: 42.43 E-value: 7.37e-03
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