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Conserved domains on  [gi|398314562|gb|AFO73512|]
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ORF1b [Cloning vector prMLVB4/5 GP5ecto]

Protein Classification

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List of domain hits

 Name Accession Description Interval E-value
Arteriviridae_RdRp cd23189
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of ...
 317-643 1.10e-176

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: 528.75  E-value: 1.10e-176
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  317 MKSNLQTATMATCKRQYCSKYKIRSILGTNNYIGLGLRACLSGVTAAFQKAGKdGSPIYLGKSKFDPIP-APDKYCLETD 395
Cdd:cd23189     1 VRENWQTVTPCTLKKQYCSKKKTRTILGTNNLIALALRAALSGVTQGFMKAGF-NSPIALGKNKFKPLQtPVLGRCLEAD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  396 LESCDRSTPALVRWFATNLIFELAGQPELVHSYVLNCCHDLVVAGSVAFTKRGGLSSGDPITSISNTIYSLVLYTQHMLL 475
Cdd:cd23189    80 LASCDRSTPAIVRWFAANLLFELACAEECLPSYVLNCCHDLLVTQSGAFTKRGGLSSGDPVTSISNTIYSLVIYTQHMVL 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  476 CGLEGYFPEIAeKYLDGSLELRDMFKYVRVYIYSDDVVLTTPNQHYaASFDRWVPHLQALLGFKVDPKKTVNTSSPSFLG 555
Cdd:cd23189   160 SALKEGHPIGL-KFLQDQLKFEDLLKVQPLLVYSDDLVLYAESPSF-PNYHWWVEHLDLMLGFKTDPKKTVITDSPSFLG 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  556 CRfkqVDGKCYLASLQDRVTRSLLYHIGAKNPSEYYEAAVSIFKDSIICC--DEDWWTDLHRRISGAARTDGvEFPTIEM 633
Cdd:cd23189   238 CR---IINGRQLVPNRDRLLAALAYHMKASNVSEYYASAAAILMDACACLeyDPEWFEDLVVGIAECARKDG-YSFPGPP 313

                         330
                  ....*....|
gi 398314562  634 LTSFRTKQYE 643
Cdd:cd23189   314 FFLFMWEKLG 323
NendoU_av_Nsp11-like cd21160
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV ...
 1210-1329 1.56e-68

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: 225.66  E-value: 1.56e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562 1210 FSSGRFETNSRVFLDEAEEKFAAAHPHACLGEINKSTVGGSHFIFSQYLPPLLPAGAVALVGASLAGKAAKAACSVVDVY 1289
Cdd:cd21160     1 FSTGRFELNSREYLDEGEREFAKKHPHAFIGDIKGTTVGGCHHITSKYLPPVLPAGSVVKVGVSSPGKAAKALCTVTDVY 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 398314562 1290 APSFEPYLHPETLSRVYKIMIDFKPCRLMVWRNATFYVQE 1329
Cdd:cd21160    81 LPYLEPYLNPPTQSKVYKVNIDFKPVRLMVWKDATMYFQE 120
DEXXYc_viral_SF1-N cd17937
DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ...
 794-938 5.33e-58

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: 196.12  E-value: 5.33e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  794 AASEYVEGPPGSGKTFHLVKDVLAvvgSATLVVPTHASMLDCINKLKQAGADPYFVVPkytVLDFPRPGSGNITVRLPQV 873
Cdd:cd17937     1 AASTYIEGPPGCGKTFWLKKLVQP---NDVLYVPTHATMLDMIKSLGPCRFVVPFGAP---DLDFPTPSSSGPTVRLLAV 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 398314562  874 G-TSEGETFVDEVAYFSPVDLARILTQGRVKGYGDLNQLGCVGPASVprnLWLRHFVSLEPLRVCH 938
Cdd:cd17937    75 GyTPGGKAFVDEACYCNPVDLARLLTQTPVTAFGDPNQLGPVGFASV---FFLVDLMQREQLNVIY 137
NTD_av_Nsp11-like cd21166
N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; ...
 1114-1212 4.85e-54

N-terminal domain (NTD) of arterivirus 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. Coronavirus Nsp15 NendoUs have an N-terminal domain, a middle (M) domain and a C-terminal catalytic (NendoU) domain. Arterivirus Nsp11 has an N-terminal domain (NTD) and a C-terminal NendoU catalytic domain. The NTD of Nsp11 superimposes onto the M-domain 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. Oligomerization of Porcine DeltaCoronavirus (PDCoV) Nsp15 differs from that of the other coronaviruses; it has been shown to exist as a dimer and a monomer in solution. Nsp11 from the arterivirus PRRSV functions as a dimer. PRRSV Nsp11 has been shown to induce STAT2 degradation to inhibit interferon signaling; mutagenesis revealed that the amino acid residue K59 located at the NTD of Nsp11 is indispensable for inducing STAT2 reduction.


:

Pssm-ID: 394904  Cd Length: 100  Bit Score: 183.30  E-value: 4.85e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562 1114 ISCLPRVAQNLGYHYSPDLPGFCPIPKELAEHWPVVSNDRYPNCLQITLQQVCELSKPC-SAGYMVGQSVFVQTPGVTSY 1192
Cdd:cd21166     1 PSPLPRVAHNLGFHFSPDLPGFPPIPEELAEHWPVVTNDNWPNRLVVSLAPIDELSKPCiSAGYYVGQSVFVGTPGVTSY 80

                          90       100
                  ....*....|....*....|
gi 398314562 1193 WLTEWVDGKARALPDSLFSS 1212
Cdd:cd21166    81 YLTLFVDGKARALPDSLFST 100
zf-RING_13 super family cl39407
RING/Ubox like zinc-binding domain; This is a zinc binding domain found in nidovirus helicase. ...
 644-711 8.40e-45

RING/Ubox like zinc-binding domain; This is a zinc binding domain found in nidovirus helicase. It includes includes 12 or 13 conserved Cys/His residues. Amino acid substitutions in ZBD or the adjacent spacer that connects it to the downstream domain can profoundly affect EAV (equine arteritis virus) helicase activity and RNA synthesis, with most replacements of conserved Cys or His residues yielding replication-negative virus phenotypes.


The actual alignment was detected with superfamily member pfam17977:

Pssm-ID: 375459  Cd Length: 68  Bit Score: 156.03  E-value: 8.40e-45
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398314562   644 SAVCTVCGAAPVAKSACGGWFCGNCVPYHVGHCHTTSLFANCGHDIMYRSTYCTMCEGSPKQMVPKVP 711
Cdd:pfam17977    1 SAVCTVCGAAPVAKSACGGWFCGNCVPYHAGHCHTTSLFANCGHDIMYRSTYCTMCEGSPKQMVPKVP 68
Rep_1B pfam17873
Replicase polyprotein 1ab; This entry relates to a regulatory domain found in replicase ...
 726-778 4.96e-31

Replicase polyprotein 1ab; This entry relates to a regulatory domain found in replicase polyprotein 1ab found in Arterivirus. Structural studies of arterivirus helicase (nsp10), indicate that this domain undergoes conformational changes on substrate binding. Besides the large conformational change, it is suggested that the regions at the surface of domain 1B not directly involved in DNA binding may become flexible. For example, domain 1B residues Arg95, Gly125 and Ala131 become disordered after DNA binding. Together with domains 1A and 2A it forms a nucleic acid-binding channel where the single-stranded part of the DNA substrate is bound to.


:

Pssm-ID: 375396  Cd Length: 53  Bit Score: 115.96  E-value: 4.96e-31
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 398314562   726 SKEELTLVVADGRTTSPPGRYKVGHKVVAVVADVGGNIVFGCGPGSHIAVPLQ 778
Cdd:pfam17873    1 SKEELTLVVADGRTTSPPGRYKVGHKVVAVVADVGGNIVFGCGPGSHIAVPLQ 53
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 974-1033 4.90e-20

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: 85.95  E-value: 4.90e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398314562  974 KGVVITAYHKDRG------------------LGHRTIDSIQGCTFPVVTLRLPTPQSLTRPRAVVAVTRASQELYIYD 1033
Cdd:cd18786    12 KGVVLTPYHRDRAylnqylqglsldefdlqlVGAITIDSSQGLTFDVVTLYLPTANSLTPRRLYVALTRARKRLVIYD 89
DUF3756 pfam12581
Protein of unknown function (DUF3756); This domain family is found in viruses, and is ...
 1357-1397 3.81e-17

Protein of unknown function (DUF3756); This domain family is found in viruses, and is approximately 40 amino acids in length.


:

Pssm-ID: 315289  Cd Length: 41  Bit Score: 76.37  E-value: 3.81e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 398314562  1357 VASGYRTNALVAPQAKISIGAYAAEWALSTEPPPAGYAIVR 1397
Cdd:pfam12581    1 LASGYRTNALVAPQAKISIGAYAAEWALSTEPPPAGYAIVR 41
 
Name Accession Description Interval E-value
Arteriviridae_RdRp cd23189
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of ...
 317-643 1.10e-176

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: 528.75  E-value: 1.10e-176
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  317 MKSNLQTATMATCKRQYCSKYKIRSILGTNNYIGLGLRACLSGVTAAFQKAGKdGSPIYLGKSKFDPIP-APDKYCLETD 395
Cdd:cd23189     1 VRENWQTVTPCTLKKQYCSKKKTRTILGTNNLIALALRAALSGVTQGFMKAGF-NSPIALGKNKFKPLQtPVLGRCLEAD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  396 LESCDRSTPALVRWFATNLIFELAGQPELVHSYVLNCCHDLVVAGSVAFTKRGGLSSGDPITSISNTIYSLVLYTQHMLL 475
Cdd:cd23189    80 LASCDRSTPAIVRWFAANLLFELACAEECLPSYVLNCCHDLLVTQSGAFTKRGGLSSGDPVTSISNTIYSLVIYTQHMVL 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  476 CGLEGYFPEIAeKYLDGSLELRDMFKYVRVYIYSDDVVLTTPNQHYaASFDRWVPHLQALLGFKVDPKKTVNTSSPSFLG 555
Cdd:cd23189   160 SALKEGHPIGL-KFLQDQLKFEDLLKVQPLLVYSDDLVLYAESPSF-PNYHWWVEHLDLMLGFKTDPKKTVITDSPSFLG 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  556 CRfkqVDGKCYLASLQDRVTRSLLYHIGAKNPSEYYEAAVSIFKDSIICC--DEDWWTDLHRRISGAARTDGvEFPTIEM 633
Cdd:cd23189   238 CR---IINGRQLVPNRDRLLAALAYHMKASNVSEYYASAAAILMDACACLeyDPEWFEDLVVGIAECARKDG-YSFPGPP 313

                         330
                  ....*....|
gi 398314562  634 LTSFRTKQYE 643
Cdd:cd23189   314 FFLFMWEKLG 323
NendoU_av_Nsp11-like cd21160
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV ...
 1210-1329 1.56e-68

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: 225.66  E-value: 1.56e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562 1210 FSSGRFETNSRVFLDEAEEKFAAAHPHACLGEINKSTVGGSHFIFSQYLPPLLPAGAVALVGASLAGKAAKAACSVVDVY 1289
Cdd:cd21160     1 FSTGRFELNSREYLDEGEREFAKKHPHAFIGDIKGTTVGGCHHITSKYLPPVLPAGSVVKVGVSSPGKAAKALCTVTDVY 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 398314562 1290 APSFEPYLHPETLSRVYKIMIDFKPCRLMVWRNATFYVQE 1329
Cdd:cd21160    81 LPYLEPYLNPPTQSKVYKVNIDFKPVRLMVWKDATMYFQE 120
DEXXYc_viral_SF1-N cd17937
DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ...
 794-938 5.33e-58

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: 196.12  E-value: 5.33e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  794 AASEYVEGPPGSGKTFHLVKDVLAvvgSATLVVPTHASMLDCINKLKQAGADPYFVVPkytVLDFPRPGSGNITVRLPQV 873
Cdd:cd17937     1 AASTYIEGPPGCGKTFWLKKLVQP---NDVLYVPTHATMLDMIKSLGPCRFVVPFGAP---DLDFPTPSSSGPTVRLLAV 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 398314562  874 G-TSEGETFVDEVAYFSPVDLARILTQGRVKGYGDLNQLGCVGPASVprnLWLRHFVSLEPLRVCH 938
Cdd:cd17937    75 GyTPGGKAFVDEACYCNPVDLARLLTQTPVTAFGDPNQLGPVGFASV---FFLVDLMQREQLNVIY 137
NTD_av_Nsp11-like cd21166
N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; ...
 1114-1212 4.85e-54

N-terminal domain (NTD) of arterivirus 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. Coronavirus Nsp15 NendoUs have an N-terminal domain, a middle (M) domain and a C-terminal catalytic (NendoU) domain. Arterivirus Nsp11 has an N-terminal domain (NTD) and a C-terminal NendoU catalytic domain. The NTD of Nsp11 superimposes onto the M-domain 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. Oligomerization of Porcine DeltaCoronavirus (PDCoV) Nsp15 differs from that of the other coronaviruses; it has been shown to exist as a dimer and a monomer in solution. Nsp11 from the arterivirus PRRSV functions as a dimer. PRRSV Nsp11 has been shown to induce STAT2 degradation to inhibit interferon signaling; mutagenesis revealed that the amino acid residue K59 located at the NTD of Nsp11 is indispensable for inducing STAT2 reduction.


Pssm-ID: 394904  Cd Length: 100  Bit Score: 183.30  E-value: 4.85e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562 1114 ISCLPRVAQNLGYHYSPDLPGFCPIPKELAEHWPVVSNDRYPNCLQITLQQVCELSKPC-SAGYMVGQSVFVQTPGVTSY 1192
Cdd:cd21166     1 PSPLPRVAHNLGFHFSPDLPGFPPIPEELAEHWPVVTNDNWPNRLVVSLAPIDELSKPCiSAGYYVGQSVFVGTPGVTSY 80

                          90       100
                  ....*....|....*....|
gi 398314562 1193 WLTEWVDGKARALPDSLFSS 1212
Cdd:cd21166    81 YLTLFVDGKARALPDSLFST 100
zf-RING_13 pfam17977
RING/Ubox like zinc-binding domain; This is a zinc binding domain found in nidovirus helicase. ...
 644-711 8.40e-45

RING/Ubox like zinc-binding domain; This is a zinc binding domain found in nidovirus helicase. It includes includes 12 or 13 conserved Cys/His residues. Amino acid substitutions in ZBD or the adjacent spacer that connects it to the downstream domain can profoundly affect EAV (equine arteritis virus) helicase activity and RNA synthesis, with most replacements of conserved Cys or His residues yielding replication-negative virus phenotypes.


Pssm-ID: 375459  Cd Length: 68  Bit Score: 156.03  E-value: 8.40e-45
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398314562   644 SAVCTVCGAAPVAKSACGGWFCGNCVPYHVGHCHTTSLFANCGHDIMYRSTYCTMCEGSPKQMVPKVP 711
Cdd:pfam17977    1 SAVCTVCGAAPVAKSACGGWFCGNCVPYHAGHCHTTSLFANCGHDIMYRSTYCTMCEGSPKQMVPKVP 68
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 235-585 1.89e-34

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: 138.70  E-value: 1.89e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562   235 PAAETALCGDLEKYNLSTQGFVLPSVFSMVRAYLKEEIGDAPPLYLPSTVPSK-NSQAGINGAEFPTRSLQSYCLIDDM- 312
Cdd:pfam00680   45 PKLPGPADERDKLLNRSAAKMVLSELRGVPKKANSTLIVYRAIDGVEQIDPLNwDTSAGYPYVGLGGKKGDLIEHLKDGt 124

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562   313 ----VSQSMKSN---LQTATMATCKRQYC-----------SKYKIRSILGTNNYIGLGLRACLSGVTAAFQKAGKDGsPI 374
Cdd:pfam00680  125 eareLAERLAADwevLQNGTPLKLVYQTClkdelrplekvEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFH-PI 203

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562   375 YLGKSKFDP--------IPAPDKYCLETDLESCDRSTPALVRWFATNLIFELAGQPELVHSYVLN----CCHDLVVAGSV 442
Cdd:pfam00680  204 QVGINPFDRgwprllrrLARFGDYVYELDYSGFDSSVPPWLIRFAFEILRELLGFPSNVKEWRAIlellIYTPIALPNGT 283

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562   443 AFTKRGGLSSGDPITSISNTIYSlVLYTQHMLLCGLEGYFPEIAEkyldgslelrdMFKYVRVYIYSDDVVLTTPNQhYA 522
Cdd:pfam00680  284 VFKKTGGLPSGSPFTSIINSIVN-YLLILYALLKSLENDGPRVCN-----------LDKYFDFFTYGDDSLVAVSPD-FD 350

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398314562   523 ASFDRWVPHLqALLGFKVDPKKTVNTSSP-----SFLGCRFKQVDGKcYLASLQDRVTRSLLYHIGAK 585
Cdd:pfam00680  351 PVLDRLSPHL-KELGLTITPAKKTFPVSReleevSFLKRTFRKTPGG-YRPPLDRKRILAQLEYIRSK 416
Rep_1B pfam17873
Replicase polyprotein 1ab; This entry relates to a regulatory domain found in replicase ...
 726-778 4.96e-31

Replicase polyprotein 1ab; This entry relates to a regulatory domain found in replicase polyprotein 1ab found in Arterivirus. Structural studies of arterivirus helicase (nsp10), indicate that this domain undergoes conformational changes on substrate binding. Besides the large conformational change, it is suggested that the regions at the surface of domain 1B not directly involved in DNA binding may become flexible. For example, domain 1B residues Arg95, Gly125 and Ala131 become disordered after DNA binding. Together with domains 1A and 2A it forms a nucleic acid-binding channel where the single-stranded part of the DNA substrate is bound to.


Pssm-ID: 375396  Cd Length: 53  Bit Score: 115.96  E-value: 4.96e-31
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 398314562   726 SKEELTLVVADGRTTSPPGRYKVGHKVVAVVADVGGNIVFGCGPGSHIAVPLQ 778
Cdd:pfam17873    1 SKEELTLVVADGRTTSPPGRYKVGHKVVAVVADVGGNIVFGCGPGSHIAVPLQ 53
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 974-1033 4.90e-20

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: 85.95  E-value: 4.90e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398314562  974 KGVVITAYHKDRG------------------LGHRTIDSIQGCTFPVVTLRLPTPQSLTRPRAVVAVTRASQELYIYD 1033
Cdd:cd18786    12 KGVVLTPYHRDRAylnqylqglsldefdlqlVGAITIDSSQGLTFDVVTLYLPTANSLTPRRLYVALTRARKRLVIYD 89
ZBD_av_Nsp10-like cd21405
Cys/His rich zinc-binding domain (CH/ZBD) of arterivirus EAV Nsp10 helicase and related ...
 645-711 4.11e-19

Cys/His rich zinc-binding domain (CH/ZBD) of arterivirus EAV Nsp10 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. Members of this arterivirus group belong to helicase superfamily 1 (SF1) and include helicases such Equine arteritis virus (EAV) Nsp10 helicase encoded on ORF1b. 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. SARS-Nsp12 can enhance the helicase activity of SARS-Nsp13.


Pssm-ID: 439169  Cd Length: 62  Bit Score: 82.37  E-value: 4.11e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 398314562  645 AVCTVCGAAPVAKSACGGWFCGNCVPYHVgHCHTTSLFanCGHDImyRSTYCTMCEGSPKQMVPKVP 711
Cdd:cd21405     1 RVCGICGSTAVTTSACGLDLCAYHAHFHQ-HCPVTSPF--CGHPI--GSKSCTMCSIPVVPGNDELD 62
DUF3756 pfam12581
Protein of unknown function (DUF3756); This domain family is found in viruses, and is ...
 1357-1397 3.81e-17

Protein of unknown function (DUF3756); This domain family is found in viruses, and is approximately 40 amino acids in length.


Pssm-ID: 315289  Cd Length: 41  Bit Score: 76.37  E-value: 3.81e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 398314562  1357 VASGYRTNALVAPQAKISIGAYAAEWALSTEPPPAGYAIVR 1397
Cdd:pfam12581    1 LASGYRTNALVAPQAKISIGAYAAEWALSTEPPPAGYAIVR 41
1B_nv_SF1_Hel-like cd21406
1B domain of nidovirus helicases including coronavirus Nsp13 and arterivirus Nsp10, and ...
 730-777 5.31e-11

1B domain 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. Members of this nidoviral 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. SARS-Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). They belong to a larger SF1 helicase family which also includes eukaryotic UPF1-like helicases. UPF1, EAV Nsp10 and SARS-Nsp13 are multidomain proteins with an N-terminal Cys/His rich zinc-binding domain (CH/ZBD), a 1B domain and a SF1 helicase core. The 1B domain is involved in nucleic acid substrate binding; the 1B domain of EAV Nsp10 undergoes large conformational change upon substrate binding, and together with the 1A and 2A domains of the helicase core form a channel that accommodates the single stranded nucleic acids.


Pssm-ID: 439171  Cd Length: 48  Bit Score: 59.11  E-value: 5.31e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 398314562  730 LTLVVADGRTTSPPGRYKVGHKVVAVVADVGGNIVFGCGPGSHIAVPL 777
Cdd:cd21406     1 LIATVARGLTLSRPGRYTGYHGEVAVERGDDGNIVFGCTPGGDIFVLL 48
CoV_NSP15_C pfam19215
Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the ...
 1207-1328 4.49e-09

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: 56.96  E-value: 4.49e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  1207 DSLFSSGRFETN-------SRVFLDEAEEKFAAAHP-------HACLGEINKSTVGGSHFIFSQYLPPLLPAGAVALVGA 1272
Cdd:pfam19215    1 DTLFTQGRTLEDfvprstmEKDFLNMDQQQFIQKYGledlgfeHIVYGDFSKTTIGGLHLLISLVRLTKMGILKVEEFVP 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 398314562  1273 SLA------------GKAAKAACSVVDVYAPSFEP---YLHPETLSRVYKIMIDFKPCRLMVWRN----ATFYVQ 1328
Cdd:pfam19215   81 NDDstvkncsvtyanDGSSKAVCTVLDLLLDDFVDilkSLDLSVVSKVVTVNIDFQPVRFMLWCKdgkvQTFYPQ 155
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 799-1033 1.27e-06

Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.


Pssm-ID: 366646 [Multi-domain]  Cd Length: 227  Bit Score: 51.23  E-value: 1.27e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562   799 VEGPPGSGKTfHLVKDVL--AVVGSATLVVPTHASMlDCINKlkqagaDPYFVVpkyTVLDFPRPGSGNITV-----RLP 871
Cdd:pfam01443    3 VHGVPGCGKS-TLIRKLLrtSRVIRPTAELRTEGKP-DLPNL------NVRTVD---TFLMALLKPTGKILIldeytLLP 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562   872 QvgtseGEtfVDEVAYFSPVDLArILTqgrvkgyGDLNQLGCvgPASVPRNLWLRHFVSL---EPLRVCHRFGAAVCD-L 947
Cdd:pfam01443   72 P-----GY--ILLLAAISGAKLV-ILF-------GDPLQIPY--HSRAPSFLIPHFPSSLshrVGRRTTYLLPSLRAPiL 134

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562   948 IKGIYPYYEPAPHTTKVVFVPNPdFEKGVVITAYHKD-RGLGHR--TIDSIQGCTFPVVTLRLPTPQSL-----TRPRAV 1019
Cdd:pfam01443  135 SAKGFEVVVERSGEYKVDYDPNG-VLVLVYLTFTQALkESLGVRvtTVHEVQGLTFDSVTLVLDTDTDLliisdSPEHLY 213

                          250
                   ....*....|....
gi 398314562  1020 VAVTRASQELYIYD 1033
Cdd:pfam01443  214 VALTRHRKSLHILT 227
 
Name Accession Description Interval E-value
Arteriviridae_RdRp cd23189
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of ...
 317-643 1.10e-176

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: 528.75  E-value: 1.10e-176
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  317 MKSNLQTATMATCKRQYCSKYKIRSILGTNNYIGLGLRACLSGVTAAFQKAGKdGSPIYLGKSKFDPIP-APDKYCLETD 395
Cdd:cd23189     1 VRENWQTVTPCTLKKQYCSKKKTRTILGTNNLIALALRAALSGVTQGFMKAGF-NSPIALGKNKFKPLQtPVLGRCLEAD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  396 LESCDRSTPALVRWFATNLIFELAGQPELVHSYVLNCCHDLVVAGSVAFTKRGGLSSGDPITSISNTIYSLVLYTQHMLL 475
Cdd:cd23189    80 LASCDRSTPAIVRWFAANLLFELACAEECLPSYVLNCCHDLLVTQSGAFTKRGGLSSGDPVTSISNTIYSLVIYTQHMVL 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  476 CGLEGYFPEIAeKYLDGSLELRDMFKYVRVYIYSDDVVLTTPNQHYaASFDRWVPHLQALLGFKVDPKKTVNTSSPSFLG 555
Cdd:cd23189   160 SALKEGHPIGL-KFLQDQLKFEDLLKVQPLLVYSDDLVLYAESPSF-PNYHWWVEHLDLMLGFKTDPKKTVITDSPSFLG 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  556 CRfkqVDGKCYLASLQDRVTRSLLYHIGAKNPSEYYEAAVSIFKDSIICC--DEDWWTDLHRRISGAARTDGvEFPTIEM 633
Cdd:cd23189   238 CR---IINGRQLVPNRDRLLAALAYHMKASNVSEYYASAAAILMDACACLeyDPEWFEDLVVGIAECARKDG-YSFPGPP 313

                         330
                  ....*....|
gi 398314562  634 LTSFRTKQYE 643
Cdd:cd23189   314 FFLFMWEKLG 323
ps-ssRNAv_Nidovirales_RdRp cd23168
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Nidovirales of ...
 323-642 1.58e-88

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: 290.42  E-value: 1.58e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  323 TATMATCKRQYCSKYKIRSILGTNNYIGLGLRACLSGVTAAFQKAGKDGSPI-----YLGKSKFDPIPAP----DKYCLE 393
Cdd:cd23168     1 TLTQVNPKYAIQKKKRARTILGVSIISTDVGRQLHQAVLAAIVNTRSANIVIigtkfYGGWHKMLRYLYPgvieDPVLMG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  394 TDLESCDRSTPALVRWFATNLIFEL----AGQPELVHSYVLNCCH---DLVVAGSVAFTKRGGLSSGDPITSISNTIYSL 466
Cdd:cd23168    81 WDYPKCDRSVPNMLRYLANLLLASLydncCNLSEIVHLLINECAQvlyDYVVYGGNLYRKPGGVSSGDSTTAISNSIYNY 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  467 VLYTQHMllcglegyfpeiaekyldgslelrdmfkyVRVYIYSDDVVLTTPNQHYAASFDRWVPHLQALLGFKVDPKKTV 546
Cdd:cd23168   161 FQTFIAN-----------------------------VRLAILSDDGVACINPDLIDLGDVASVSFFLASYYYTNNKKKYS 211

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  547 NTSSPSFLGcrFKQVDGKCYLASLQDRVTRSLLYHIGAKNPSEYYEAAVSIFKDSIICCDEDWWTDLHRRISGAART--- 623
Cdd:cd23168   212 STCWVEPHE--FCSPHEFKSDDKYQDRVERVYLPIPDPSRMLSACLLVDTRTKTDILLMIERLISILIDAYPLTFHTktl 289

                         330       340
                  ....*....|....*....|.
gi 398314562  624 --DGVEFPTIEMLTSFRTKQY 642
Cdd:cd23168   290 pvNIEYAPLILLLLDYIKKLS 310
NendoU_av_Nsp11-like cd21160
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV ...
 1210-1329 1.56e-68

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: 225.66  E-value: 1.56e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562 1210 FSSGRFETNSRVFLDEAEEKFAAAHPHACLGEINKSTVGGSHFIFSQYLPPLLPAGAVALVGASLAGKAAKAACSVVDVY 1289
Cdd:cd21160     1 FSTGRFELNSREYLDEGEREFAKKHPHAFIGDIKGTTVGGCHHITSKYLPPVLPAGSVVKVGVSSPGKAAKALCTVTDVY 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 398314562 1290 APSFEPYLHPETLSRVYKIMIDFKPCRLMVWRNATFYVQE 1329
Cdd:cd21160    81 LPYLEPYLNPPTQSKVYKVNIDFKPVRLMVWKDATMYFQE 120
DEXXYc_viral_SF1-N cd17937
DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ...
 794-938 5.33e-58

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: 196.12  E-value: 5.33e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  794 AASEYVEGPPGSGKTFHLVKDVLAvvgSATLVVPTHASMLDCINKLKQAGADPYFVVPkytVLDFPRPGSGNITVRLPQV 873
Cdd:cd17937     1 AASTYIEGPPGCGKTFWLKKLVQP---NDVLYVPTHATMLDMIKSLGPCRFVVPFGAP---DLDFPTPSSSGPTVRLLAV 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 398314562  874 G-TSEGETFVDEVAYFSPVDLARILTQGRVKGYGDLNQLGCVGPASVprnLWLRHFVSLEPLRVCH 938
Cdd:cd17937    75 GyTPGGKAFVDEACYCNPVDLARLLTQTPVTAFGDPNQLGPVGFASV---FFLVDLMQREQLNVIY 137
NTD_av_Nsp11-like cd21166
N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; ...
 1114-1212 4.85e-54

N-terminal domain (NTD) of arterivirus 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. Coronavirus Nsp15 NendoUs have an N-terminal domain, a middle (M) domain and a C-terminal catalytic (NendoU) domain. Arterivirus Nsp11 has an N-terminal domain (NTD) and a C-terminal NendoU catalytic domain. The NTD of Nsp11 superimposes onto the M-domain 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. Oligomerization of Porcine DeltaCoronavirus (PDCoV) Nsp15 differs from that of the other coronaviruses; it has been shown to exist as a dimer and a monomer in solution. Nsp11 from the arterivirus PRRSV functions as a dimer. PRRSV Nsp11 has been shown to induce STAT2 degradation to inhibit interferon signaling; mutagenesis revealed that the amino acid residue K59 located at the NTD of Nsp11 is indispensable for inducing STAT2 reduction.


Pssm-ID: 394904  Cd Length: 100  Bit Score: 183.30  E-value: 4.85e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562 1114 ISCLPRVAQNLGYHYSPDLPGFCPIPKELAEHWPVVSNDRYPNCLQITLQQVCELSKPC-SAGYMVGQSVFVQTPGVTSY 1192
Cdd:cd21166     1 PSPLPRVAHNLGFHFSPDLPGFPPIPEELAEHWPVVTNDNWPNRLVVSLAPIDELSKPCiSAGYYVGQSVFVGTPGVTSY 80

                          90       100
                  ....*....|....*....|
gi 398314562 1193 WLTEWVDGKARALPDSLFSS 1212
Cdd:cd21166    81 YLTLFVDGKARALPDSLFST 100
zf-RING_13 pfam17977
RING/Ubox like zinc-binding domain; This is a zinc binding domain found in nidovirus helicase. ...
 644-711 8.40e-45

RING/Ubox like zinc-binding domain; This is a zinc binding domain found in nidovirus helicase. It includes includes 12 or 13 conserved Cys/His residues. Amino acid substitutions in ZBD or the adjacent spacer that connects it to the downstream domain can profoundly affect EAV (equine arteritis virus) helicase activity and RNA synthesis, with most replacements of conserved Cys or His residues yielding replication-negative virus phenotypes.


Pssm-ID: 375459  Cd Length: 68  Bit Score: 156.03  E-value: 8.40e-45
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398314562   644 SAVCTVCGAAPVAKSACGGWFCGNCVPYHVGHCHTTSLFANCGHDIMYRSTYCTMCEGSPKQMVPKVP 711
Cdd:pfam17977    1 SAVCTVCGAAPVAKSACGGWFCGNCVPYHAGHCHTTSLFANCGHDIMYRSTYCTMCEGSPKQMVPKVP 68
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 235-585 1.89e-34

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: 138.70  E-value: 1.89e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562   235 PAAETALCGDLEKYNLSTQGFVLPSVFSMVRAYLKEEIGDAPPLYLPSTVPSK-NSQAGINGAEFPTRSLQSYCLIDDM- 312
Cdd:pfam00680   45 PKLPGPADERDKLLNRSAAKMVLSELRGVPKKANSTLIVYRAIDGVEQIDPLNwDTSAGYPYVGLGGKKGDLIEHLKDGt 124

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562   313 ----VSQSMKSN---LQTATMATCKRQYC-----------SKYKIRSILGTNNYIGLGLRACLSGVTAAFQKAGKDGsPI 374
Cdd:pfam00680  125 eareLAERLAADwevLQNGTPLKLVYQTClkdelrplekvEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFH-PI 203

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562   375 YLGKSKFDP--------IPAPDKYCLETDLESCDRSTPALVRWFATNLIFELAGQPELVHSYVLN----CCHDLVVAGSV 442
Cdd:pfam00680  204 QVGINPFDRgwprllrrLARFGDYVYELDYSGFDSSVPPWLIRFAFEILRELLGFPSNVKEWRAIlellIYTPIALPNGT 283

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562   443 AFTKRGGLSSGDPITSISNTIYSlVLYTQHMLLCGLEGYFPEIAEkyldgslelrdMFKYVRVYIYSDDVVLTTPNQhYA 522
Cdd:pfam00680  284 VFKKTGGLPSGSPFTSIINSIVN-YLLILYALLKSLENDGPRVCN-----------LDKYFDFFTYGDDSLVAVSPD-FD 350

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398314562   523 ASFDRWVPHLqALLGFKVDPKKTVNTSSP-----SFLGCRFKQVDGKcYLASLQDRVTRSLLYHIGAK 585
Cdd:pfam00680  351 PVLDRLSPHL-KELGLTITPAKKTFPVSReleevSFLKRTFRKTPGG-YRPPLDRKRILAQLEYIRSK 416
Rep_1B pfam17873
Replicase polyprotein 1ab; This entry relates to a regulatory domain found in replicase ...
 726-778 4.96e-31

Replicase polyprotein 1ab; This entry relates to a regulatory domain found in replicase polyprotein 1ab found in Arterivirus. Structural studies of arterivirus helicase (nsp10), indicate that this domain undergoes conformational changes on substrate binding. Besides the large conformational change, it is suggested that the regions at the surface of domain 1B not directly involved in DNA binding may become flexible. For example, domain 1B residues Arg95, Gly125 and Ala131 become disordered after DNA binding. Together with domains 1A and 2A it forms a nucleic acid-binding channel where the single-stranded part of the DNA substrate is bound to.


Pssm-ID: 375396  Cd Length: 53  Bit Score: 115.96  E-value: 4.96e-31
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 398314562   726 SKEELTLVVADGRTTSPPGRYKVGHKVVAVVADVGGNIVFGCGPGSHIAVPLQ 778
Cdd:pfam17873    1 SKEELTLVVADGRTTSPPGRYKVGHKVVAVVADVGGNIVFGCGPGSHIAVPLQ 53
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 796-938 1.13e-26

DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. 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. SF1 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: 438706 [Multi-domain]  Cd Length: 121  Bit Score: 106.03  E-value: 1.13e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  796 SEYVEGPPGSGKTFHLVKDVLAVV-------GSATLVVPTHASMLDCinklkqagadpyfvvpkytvldfprpgsgnitv 868
Cdd:cd17914     1 LSLIQGPPGTGKTRVLVKIVAALMqnkngepGRILLVTPTNKAAAQL--------------------------------- 47

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  869 rlpqvgtseGETFVDEVAYFSPVDLAR----ILTQGRVKGYGDLNQLGCVGPASVP---------RNLWLRHFVSLEPLR 935
Cdd:cd17914    48 ---------DNILVDEAAQILEPETSRlidlALDQGRVILVGDHDQLGPVWRGAVLakicneqslFTRLVRLGVSLIRLQ 118


                  ...
gi 398314562  936 VCH 938
Cdd:cd17914   119 VQY 121
M_cv_Nsp15-NTD_av_Nsp11-like cd21163
middle (M) domain of coronavirus Nonstructural protein 15 (Nsp15) and the N-terminal domain ...
 1115-1211 1.87e-25

middle (M) domain of coronavirus Nonstructural protein 15 (Nsp15) and the N-terminal domain (NTD) of arterivirus 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. Coronavirus Nsp15 NendoUs have an N-terminal domain, a middle (M) domain, and a C-terminal catalytic (NendoU) domain. Arterivirus Nsp11 has an N-terminal domain (NTD) and a C-terminal catalytic (NendoU) domain. The NTD of Nsp11 superimposes onto the M-domain 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. Oligomerization of Porcine DeltaCoronavirus (PDCoV) Nsp15 differs from that of other coronavirus members; it has been shown to exist as a dimer and a monomer in solution. Nsp11 from the arterivirus PRRSV functions as a dimer.


Pssm-ID: 439159  Cd Length: 123  Bit Score: 102.80  E-value: 1.87e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562 1115 SCLPRVAQNLGYHYSPDLPGFCPI--------------PKELAEHWPVVSNDRY----------PNCLQITLQQVCELSK 1170
Cdd:cd21163     2 TPLPKVLRNLGVDFTPNFVLWDYEdtapffnttvckytPEELCEHLPVLYDDRYggslerflsaPNAVLISLTKVKKYSI 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 398314562 1171 PCSAGYMVGQSVFVQTPGVTSYWLTEWVDGKARALPDSLFS 1211
Cdd:cd21163    82 PPPAGAYLNGSVVVGTPKVVSFYLYKRKDGKFVTLPDTLFT 122
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 974-1033 4.90e-20

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: 85.95  E-value: 4.90e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398314562  974 KGVVITAYHKDRG------------------LGHRTIDSIQGCTFPVVTLRLPTPQSLTRPRAVVAVTRASQELYIYD 1033
Cdd:cd18786    12 KGVVLTPYHRDRAylnqylqglsldefdlqlVGAITIDSSQGLTFDVVTLYLPTANSLTPRRLYVALTRARKRLVIYD 89
NendoU_nv cd21158
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural ...
 1210-1328 8.58e-20

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: 87.70  E-value: 8.58e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562 1210 FSSGRFE-------TNSRVFLDEAEEKFAA-------AHPHACLGEINKSTVGGSHFIFSQYL---PPLLPAG------- 1265
Cdd:cd21158     1 FTQGRNLqeflprsDMERDFLPVDMDVFIEkygleiyAFEHVVYGDFSHTTLGGLHLVISLYKrfkEGPLPREefipnds 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 398314562 1266 AVALVGASLAG-KAAKAACSVVDVYAPSFEPYLHP---ETLSRVYKIMIDFKPCRLMVWRN----ATFYVQ 1328
Cdd:cd21158    81 TVKNYGVTSPGtKASKAVCTLIDLLLDDFVEILKSqdlEVVSKVVKVMIDFKEVRFMLWCKdgdvQTFYPQ 151
ZBD_av_Nsp10-like cd21405
Cys/His rich zinc-binding domain (CH/ZBD) of arterivirus EAV Nsp10 helicase and related ...
 645-711 4.11e-19

Cys/His rich zinc-binding domain (CH/ZBD) of arterivirus EAV Nsp10 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. Members of this arterivirus group belong to helicase superfamily 1 (SF1) and include helicases such Equine arteritis virus (EAV) Nsp10 helicase encoded on ORF1b. 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. SARS-Nsp12 can enhance the helicase activity of SARS-Nsp13.


Pssm-ID: 439169  Cd Length: 62  Bit Score: 82.37  E-value: 4.11e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 398314562  645 AVCTVCGAAPVAKSACGGWFCGNCVPYHVgHCHTTSLFanCGHDImyRSTYCTMCEGSPKQMVPKVP 711
Cdd:cd21405     1 RVCGICGSTAVTTSACGLDLCAYHAHFHQ-HCPVTSPF--CGHPI--GSKSCTMCSIPVVPGNDELD 62
DUF3756 pfam12581
Protein of unknown function (DUF3756); This domain family is found in viruses, and is ...
 1357-1397 3.81e-17

Protein of unknown function (DUF3756); This domain family is found in viruses, and is approximately 40 amino acids in length.


Pssm-ID: 315289  Cd Length: 41  Bit Score: 76.37  E-value: 3.81e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 398314562  1357 VASGYRTNALVAPQAKISIGAYAAEWALSTEPPPAGYAIVR 1397
Cdd:pfam12581    1 LASGYRTNALVAPQAKISIGAYAAEWALSTEPPPAGYAIVR 41
ZBD_nv_SF1_Hel-like cd21399
Cys/His rich zinc-binding domain (CH/ZBD) of nidovirus helicases including coronavirus Nsp13 ...
 645-702 7.58e-13

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: 64.90  E-value: 7.58e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 398314562  645 AVCTVCGAAP-VAKSAC--GGWFCGNCVPYHVG-HCHTTSLFAN------CG-HDIMYRSTYC--TMCEGS 702
Cdd:cd21399     1 GVCYVCGSQTsLRCGTCirRPFFCCKCCYDHVIqTCHKTVLLASpyvcagCGeSDITLLYTGGdsYRCVDH 71
ZBD_UPF1_nv_SF1_Hel-like cd21343
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 helicase, nidovirus SF1 helicases ...
 646-702 5.30e-11

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: 59.81  E-value: 5.30e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  646 VCTVCGAAP-VAKSAC--GGWFCGNCVPYHVG-HCHTTSLFA------NCG-HDIMYR--STYCTMCEGS 702
Cdd:cd21343     1 ACYVCGSHTvVRCGTCirRPWFCNSCIYDHLIrTKHKEVLLAspyvcaGCGeSDITLLyfGGVSYRCVDH 70
1B_nv_SF1_Hel-like cd21406
1B domain of nidovirus helicases including coronavirus Nsp13 and arterivirus Nsp10, and ...
 730-777 5.31e-11

1B domain 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. Members of this nidoviral 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. SARS-Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). They belong to a larger SF1 helicase family which also includes eukaryotic UPF1-like helicases. UPF1, EAV Nsp10 and SARS-Nsp13 are multidomain proteins with an N-terminal Cys/His rich zinc-binding domain (CH/ZBD), a 1B domain and a SF1 helicase core. The 1B domain is involved in nucleic acid substrate binding; the 1B domain of EAV Nsp10 undergoes large conformational change upon substrate binding, and together with the 1A and 2A domains of the helicase core form a channel that accommodates the single stranded nucleic acids.


Pssm-ID: 439171  Cd Length: 48  Bit Score: 59.11  E-value: 5.31e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 398314562  730 LTLVVADGRTTSPPGRYKVGHKVVAVVADVGGNIVFGCGPGSHIAVPL 777
Cdd:cd21406     1 LIATVARGLTLSRPGRYTGYHGEVAVERGDDGNIVFGCTPGGDIFVLL 48
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 403-580 1.71e-09

RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage. RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D structure of the catalytic center of a wide range of RdRps, including those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing a number of conserved amino acid residues. This subfamily represents the RNA-dependent RNA polymerases from all positive-strand RNA eukaryotic viruses with no DNA stage.


Pssm-ID: 238843 [Multi-domain]  Cd Length: 278  Bit Score: 60.37  E-value: 1.71e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  403 TPALVRWfATNLIFELAGQP------ELVHSYVLNCCHDLvvaGSVAFTKRGGLSSGDPITSISNTIYslvlytqHMLLC 476
Cdd:cd01699   111 SPQLLEA-EHSIYNALYDDDdelerrNLLRSLTNNSLHIG---FNEVYKVRGGRPSGDPLTSIGNSII-------NCILV 179

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  477 glEGYFPEIAEKYldgslelrdMFKYVRVYIYSDDVVLTTPNQHYAASFDRWVPHLqALLGFKV-DPKKTVNTSSP---- 551
Cdd:cd01699   180 --RYAFRKLGGKS---------FFKNVRLLNYGDDCLLSVEKADDKFNLETLAEWL-KEYGLTMtDEDKVESPFRPleev 247

                         170       180       190
                  ....*....|....*....|....*....|
gi 398314562  552 SFLGCRFKQVDGKCYLASLQ-DRVTRSLLY 580
Cdd:cd01699   248 EFLKRRFVLDEGGGWRAPLDpSSILSKLSW 277
CoV_NSP15_C pfam19215
Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the ...
 1207-1328 4.49e-09

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: 56.96  E-value: 4.49e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  1207 DSLFSSGRFETN-------SRVFLDEAEEKFAAAHP-------HACLGEINKSTVGGSHFIFSQYLPPLLPAGAVALVGA 1272
Cdd:pfam19215    1 DTLFTQGRTLEDfvprstmEKDFLNMDQQQFIQKYGledlgfeHIVYGDFSKTTIGGLHLLISLVRLTKMGILKVEEFVP 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 398314562  1273 SLA------------GKAAKAACSVVDVYAPSFEP---YLHPETLSRVYKIMIDFKPCRLMVWRN----ATFYVQ 1328
Cdd:pfam19215   81 NDDstvkncsvtyanDGSSKAVCTVLDLLLDDFVDilkSLDLSVVSKVVTVNIDFQPVRFMLWCKdgkvQTFYPQ 155
ps-ssRNAv-Picornavirales cd23169
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...
 406-580 4.32e-08

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This family contains the catalytic core domain of RdRp of Picornavirales, an order of (+)ssRNA viruses. The order Picornavirales comprises viruses that historically are referred to as picorna-like viruses and which are classified into eight virus families: Caliciviridae, Dicistroviridae, Iflaviridae, Marnaviridae, Picornaviridae, Polycipiviridae, Secoviridae, and Solinviviridae. All known genomes of Picornavirales members encode proteins with helicase, 3C-like protease, and RdRp domains, as well as capsid proteins with related structures, although the genome organizations can differ among viruses. The picornavirus genome is replicated via a negative-sense (-) RNA intermediate by the viral RdRp, named 3Dpol, which uses VPg (the product of 3B) as a primer to initiate the replication process. 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: 438019  Cd Length: 309  Bit Score: 56.45  E-value: 4.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  406 LVRWFATNLIFElagQPELVHSYVLNCCHDLVVAGSVAFTKRGGLSSGDPIT----SISNTIYSLVLYTQHMllcglegy 481
Cdd:cd23169   105 INDWYDEYVDDE---DERVRKVLFEELINTIHLVGNLVYQVHGGNPSGNPLTtiinSIVNLLYIRYAWLRIT-------- 173

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  482 fpeiaekyldGSLELRDMFKYVRVYIYSDDVVLTTpNQHYAASFD-RWVPHLQALLGFKV-DPKKT------VNTSSPSF 553
Cdd:cd23169   174 ----------GLTSLSDFKKNVRLVTYGDDVIISV-SDEVKDEFNfVTISEFLKELGITYtDADKSgdivpyRPLEEVTF 242

                         170       180
                  ....*....|....*....|....*...
gi 398314562  554 LGCRFKQVDGK-CYLASLQDRVTRSLLY 580
Cdd:cd23169   243 LKRGFRPHPTPgLVLAPLDLESIEEQLN 270
NendoU_tv_PToV-like cd21162
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of Porcine torovirus (PToV) ...
 1210-1329 8.40e-08

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: 52.59  E-value: 8.40e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562 1210 FSSGRFETNSRVFLDEAEEKFAAAHPHACLGEINK--STVGGSHFI-------FSQYLPPLLPAGAVALVgaslAGKAAK 1280
Cdd:cd21162     1 FSTGRLYNLEHDPSYNFNVEQLPFNKHVFLGEFTEvsTTIGGVHHVpalngtkGSIIPSYVKPIHTGLIN----VGKGVK 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 398314562 1281 AACSVVDVYAPSFEPYLHPE----TLSRVYKIMIDFKPCRLMVWRN----ATFYVQE 1329
Cdd:cd21162    77 RCTTLVDVCANQLYELVKQQingvTVSKVIFINIDFQEVQFMVFASegdiQTAYPQK 133
Caliciviridae_RdRp cd23192
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of ...
 389-563 2.14e-07

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Caliciviridae, order Picornavirales. Member viruses have a viral (+)ssRNA genome, which is not segmented. The family Caliciviridae, includes eleven genera: seven genera of which infect mammals (Lagovirus, Norovirus, Nebovirus, Recovirus, Sapovirus, Valovirus, and Vesivirus), two genera of which infect birds (Bavovirus, Nacovirus), and two genera of which infect fish (Minovirus and Salovirus). Each genus includes 1-2 species. Human noroviruses are a leading cause of acute gastroenteritis in humans. Furthermore, unclassified caliciviruses have been detected in geese, yellowfin seabream, greater green snake, arctic lamprey, frogs and various Australian birds, highlighting the wide host range of viruses in the family Caliciviridae. 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: 438042  Cd Length: 310  Bit Score: 54.58  E-value: 2.14e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  389 KYCLETDLESCDrST--PALVRwFATNLIFELAGQPELVHSyvlnCCHDL-----VVAGSVAFTKRGGLSSGDPITSISN 461
Cdd:cd23192    78 RYHYCLDYSKWD-STqsPAVTA-AAIDILADLSEETPLRDS----VVETLssppmGIFDDVIFVTKRGLPSGMPFTSVIN 151

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  462 TIyslvlytQHMLLCgleGYFpeIAEKYLDGSLELRDMFKYVRVYIYSDDVVLTTPNqHYAASFDrWVPHLQALLGFK-V 540
Cdd:cd23192   152 SL-------NHWLLF---SAA--VLKAYELVGIYTGNVFDEADFFTYGDDGVYAMPP-ATASVMD-EIIENLKSYGLKpT 217

                         170       180
                  ....*....|....*....|....*...
gi 398314562  541 DPKKTVN-----TSSPSFLGCRFKQVDG 563
Cdd:cd23192   218 AADKTENpdippLQGPVFLKRTFVRTPG 245
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 799-1033 1.27e-06

Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.


Pssm-ID: 366646 [Multi-domain]  Cd Length: 227  Bit Score: 51.23  E-value: 1.27e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562   799 VEGPPGSGKTfHLVKDVL--AVVGSATLVVPTHASMlDCINKlkqagaDPYFVVpkyTVLDFPRPGSGNITV-----RLP 871
Cdd:pfam01443    3 VHGVPGCGKS-TLIRKLLrtSRVIRPTAELRTEGKP-DLPNL------NVRTVD---TFLMALLKPTGKILIldeytLLP 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562   872 QvgtseGEtfVDEVAYFSPVDLArILTqgrvkgyGDLNQLGCvgPASVPRNLWLRHFVSL---EPLRVCHRFGAAVCD-L 947
Cdd:pfam01443   72 P-----GY--ILLLAAISGAKLV-ILF-------GDPLQIPY--HSRAPSFLIPHFPSSLshrVGRRTTYLLPSLRAPiL 134

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562   948 IKGIYPYYEPAPHTTKVVFVPNPdFEKGVVITAYHKD-RGLGHR--TIDSIQGCTFPVVTLRLPTPQSL-----TRPRAV 1019
Cdd:pfam01443  135 SAKGFEVVVERSGEYKVDYDPNG-VLVLVYLTFTQALkESLGVRvtTVHEVQGLTFDSVTLVLDTDTDLliisdSPEHLY 213

                          250
                   ....*....|....
gi 398314562  1020 VAVTRASQELYIYD 1033
Cdd:pfam01443  214 VALTRHRKSLHILT 227
1B_av_Nsp10-like cd21410
1B domain of arterivirus EAV Nsp10 helicase and related proteins; Helicases catalyze ...
 728-777 2.00e-06

1B domain of arterivirus EAV Nsp10 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. Members of this subfamily belong to helicase superfamily 1 (SF1) and include arterivirus helicases such Equine arteritis virus (EAV) Nsp10 helicase encoded on ORF1b. EAV Nsp10 is a multidomain protein; its other domains include an N-terminal Cys/His rich zinc-binding domain (CH/ZBD) and a SF1 helicase core. The 1B domain is involved in nucleic acid substrate binding; the 1B domain of EAV Nsp10 undergoes large conformational change upon substrate binding, and together with the 1A and 2A domains of the helicase core form a channel that accommodates the single stranded nucleic acids.


Pssm-ID: 439172  Cd Length: 49  Bit Score: 46.08  E-value: 2.00e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 398314562  728 EELTLVVADGRTTSPPGRYKVGHKVVAVVADVGGNIVFGCGpGSHIAVPL 777
Cdd:cd21410     1 VEVTVEVVDGVTSAAPGRYQTRHGVVMVRRDIGGCIVDLPD-GEYQVTPL 49
NendoU_cv_Nsp15-like cd21161
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural ...
 1236-1328 1.09e-05

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: 46.87  E-value: 1.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562 1236 HACLGEINKSTVGGSHFIFSQ---------YLPPLLPAGAV---ALVGASLAGkAAKAACSVVDVYAPSFEPYL---HPE 1300
Cdd:cd21161    41 HIVYGDFSKPTIGGLHLLIGLvrlkkegklYVEEFHNSDSTvqnYFVTDANNG-SSKQVCTVVDLLLDDFVDILksqDLS 119

                          90       100       110
                  ....*....|....*....|....*....|..
gi 398314562 1301 TLSRVYKIMIDFKPCRLMVW----RNATFYVQ 1328
Cdd:cd21161   120 VVSKVVTVSIDYKPIRFMLWckdgKVKTFYPQ 151
ps-ssRNA_Picornaviridae cd23193
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of ...
 415-566 7.46e-05

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Picornaviridae, order Picornavirales. The Picornaviridae family consists of small, icosahedral viruses with (+)ssRNA genomes. Characteristic features of all members of the family Picornaviridae are three capsid proteins with beta-barrel folding, polyprotein processing by virus-encoded cysteine proteinase(s), and replication by an RdRp with a YGDD sequence motif. The family Picornaviridae comprises 68 genera containing 158 species, but many viruses are presently awaiting classification. The established genera of the family include: Aphthovirus, Avisivirus, Crohivirus, Enterovirus, Teschovirus, Cardiovirus, Erbovirus, Kobuvirus, Hepatovirus, Parechovirus, Aquamavirus, Avihepatovirus, Avisivirus, Cosavirus, Dicipivirus, Fipivirus, Gallivirus, Hunnivirus, Kunsagivirus, Limnipivirus, Megrivirus, Mischivirus, Mosavirus, Oscivirus, Pasivirus, Passerivirus, Rabovirus, Rosavirus, Sakobuvirus, Salivirus, Sapelovirus, Senecavirus, Sicinivirus, and Tremovirus. The Picornaviridae contains many important human and animal pathogens including enteroviruses (such as poliovirus, enterovirus, coxsackievirus, and rhinovirus), cardioviruses (such as encephalomyocarditis virus and Theiler's virus), hepatitis A virus and foot-and-mouth disease virus. Infection with various picornaviruses may cause encephalitis, febrile rash illnesses (hand-foot-and-mouth disease), aseptic meningitis, hepatitis, conjunctivitis, herpangina, myositis and myocarditis, and the common cold. 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: 438043  Cd Length: 345  Bit Score: 46.77  E-value: 7.46e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  415 IFELAGQPELVHSYVLNCCHDLVVAGSVAFTKRGGLSSGDPITSISNTIYSLVLYTQHMLLCGLegyfpeiaekyldgsl 494
Cdd:cd23193   160 LAECHGDPELVLRYLEPIINSKHVVGDERYTVEGGMPSGCPCTSILNSICNNLVVRYALLETGK---------------- 223

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398314562  495 elrDMFKYVRVYIYSDDVVLTTPNQHyaaSFDRWVPHLQALLGFKV---DPKKTVNTSSPS---FLGCRFKQVDGKCY 566
Cdd:cd23193   224 ---FDPDEYYILAYGDDVLVSTDEPI---DPSDLAEFYKKYFGMTVtpaDKSSDFPESSPIedvFLKRRFFVPDGTFL 295
Dicistroviridae_RdRp cd23194
RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense ...
 400-514 1.61e-04

RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the RdRp of RNA viruses belonging to the family Dicistroviridae, order Picornavirales. Dicistroviridae is a family of small non-enveloped viruses with a (+)ssRNA genome of approximately 8-10 kilobases. The family contains 3 genera: Aparavirus, Cripavirus, and Triatovirus. All members infect arthropod hosts with some having devastating economic consequences, such as acute bee paralysis virus, Kashmir bee virus, and Israeli acute paralysis virus in domesticated honeybees, and taura syndrome virus and mud crab virus in the seafood industry. On the contrary, host specificity and other desirable traits make several members of this group amenable to development as biopesticides for insect control, such as Solenopsis invicta virus 1 against fire ants, and triatoma virus against triatomine bugs that vector Chagas disease. Members in the family Dicistroviridae have similarity to viruses in the Picornavirales members (Iflaviridae, Picornaviridae, Marnaviridae and Secoviridae). The genomes of viruses of these taxa encode proteins with helicase, 3C-like protease, and RdRp domains, as well as capsid proteins with related structures, although the genome organizations can differ among viruses. 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: 438044 [Multi-domain]  Cd Length: 315  Bit Score: 45.57  E-value: 1.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  400 DRSTPALVRWfatnLIFElagqpELVHSYVLncCHDLVVAgsvaFTKrgGLSSGDPITSISNTIYSLVLYTQHMLLCGLE 479
Cdd:cd23194   116 DGEENALIRR----VLWE-----DIVNSVHI--CGGYVYQ----WTH--SQPSGNPLTAIINSIYNSIIMRYVYLLLTKE 178

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 398314562  480 GYFPeiaekyldgslELRDMFKYVRVYIYSDDVVL 514
Cdd:cd23194   179 AGLM-----------TMSDFNKHVSMVSYGDDNVI 202
Mosavirus_RdRp cd23225
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Mosavirus of ...
 388-542 2.22e-03

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Mosavirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Mosavirus genus within the family Picornaviridae, order Picornavirales. The Mosavirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus includes two species: Mosavirus A, which found in the feces of a canyon mouse (Peromyscus crinitus), and Mosavirus B, which contains marmot mosavirus. Mosavirus stands for mouse stool-associated picornavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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: 438075  Cd Length: 378  Bit Score: 42.21  E-value: 2.22e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  388 DKYCLETDLESCDRSTP-ALVRWFATNLIFELAG-QPELVHSYVLNCCHDLVVAGSVAFTKRGGLSSGDPITSISNTIYS 465
Cdd:cd23225   139 DRYVFDLDYKAFDSTHPtAMFNLLAERFFTERNGfDQQAVRIFLNGLSDSDHVYEGKHFRIRGGLPSGCPCTSILNTVIN 218

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398314562  466 LVLYTQHMLlcglegyfpeiaekyldGSLELRDM-FKYVRVYIYSDDVVLTTPNQHYAASFDRWvphLQALLGFKVDP 542
Cdd:cd23225   219 NIIVRAAIL-----------------GAYQIDTVdFQKFRMLAYGDDVVYATPQPIKPQDLADW---LHANTNYKVTP 276
deltaCoV_RdRp cd21590
deltacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ...
 395-467 2.41e-03

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: 42.54  E-value: 2.41e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 398314562  395 DLESCDRSTPALVRWFATNLI---FELAGQPELVHSYVLNCCH---DLVVAGSVAFTKRGGLSSGDPITSISNTIYSLV 467
Cdd:cd21590   616 DYPKCDRSMPNMLRIAASCLLarkHTCCNQSQRFYRLANECCQvlsEVVVSGNNLYVKPGGTSSGDATTAYANSVFNIL 694
ps-ssRNAv_RdRp-like cd23167
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 449-517 5.94e-03

conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model.


Pssm-ID: 438017 [Multi-domain]  Cd Length: 73  Bit Score: 36.93  E-value: 5.94e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 398314562  449 GLSSGDPITSISNTIYSLVLytqhMLLCGLEGYFPEIAekyldgslelrdmFKYVRVYIYSDDVVLTTP 517
Cdd:cd23167    22 GQPSGSPNTSADNSLINLLL----ARLALRKACGRAEF-------------LNSVGILVYGDDSLVSVP 73
batCoV-HKU9-like_RdRp cd21596
Bat coronavirus HKU9 RNA-dependent RNA polymerase, also known as non-structural protein 12, ...
 305-466 6.96e-03

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: 41.18  E-value: 6.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  305 SYCLIDDMVSQSMKSNLQTATMATCKRQYCSKYKIRSILGTNNYIGLGLRACLSGVTAAFqkAGKDGSPIYLGKSKF--- 381
Cdd:cd21596   517 SYADQDELFAYTKRNVLPTITQMNLKYAISAKNRARTVAGVSIASTMTNRQFHQKMLKSI--AAARGASVVIGTTKFygg 594

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398314562  382 ---------DPIPAPdkYCLETDLESCDRSTPALVRWFATNLIFE----LAGQPELVHSYVLNCCH---DLVVAGSVAFT 445
Cdd:cd21596   595 wnrmlrtlcEGVENP--HLMGWDYPKCDRAMPNLLRIFASLILARkhstCCNASERFYRLANECAQvlsEMVLCGGGFYV 672

                         170       180
                  ....*....|....*....|.
gi 398314562  446 KRGGLSSGDPITSISNTIYSL 466
Cdd:cd21596   673 KPGGTSSGDSTTAYANSVFNI 693
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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