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Conserved domains on  [gi|1487103480|gb|AYF59092|]
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replicase ORF1ab polyprotein [Equine arteritis virus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IFR3_antag super family cl20679
Papain-like auto-proteinase; The replicase polyproteins of the Nidoviruses such as, porcine ...
 1-249 6.54e-176

Papain-like auto-proteinase; The replicase polyproteins of the Nidoviruses such as, porcine arterivirus PRRSV, equine arterivirus EAV, human coronavirus 229E, and severe acute respiratory syndrome coronavirus (SARS-CoV), are predicted to be cleaved into 14 non-structural proteins (nsps) by the nsp4 main proteinase pfam05579 and three accessory proteinases residing in nsp1-alpha, nsp1-beta and nsp2. This family is the two nsp1 proteins that together act in a papain-like way to separate off the rest of the various functional domains of the polyprotein. Once inside the host cell, this nsp1 interferes with the regulation of interferon, thereby enabling the virus to replicate.


The actual alignment was detected with superfamily member pfam14754:

Pssm-ID: 291424  Cd Length: 249  Bit Score: 540.03  E-value: 6.54e-176
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480    1 MATFSATGFGGSFVRDWSLDLPDACEHGAGLCCEVDGSTLCAECLRGCEGMEQCPGLFMGLLKLASPVPVGHKFLIGWYR 80
Cdd:pfam14754    1 MATFSATGFGGSFVRDWSLDLPDACEHGAGLCCEVDGSTLCAECFRGCEGMEQCPGLFMGLLKLASPVPVGHKFLIGWYR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480   81 AAKVTGRYNFLELLQHPAFAQLRVVDARLAIEEASVFISTDHASAKRFPGARFALTPVYANAWVVSPAANSLIVTIDQEQ 160
Cdd:pfam14754   81 AAKVTGRYNFLELLQHPAFAQLRVVDARLAIEEASVFISTDHASAKRFPGARFALTPVYANAWVVSPAANSLIVTTDQEQ 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480  161 DGFCWLKLLPPDRREAGLRLYYNHYREQRTGWLSKTGLRLWLGDLGLGINASSGGLKFHIMRGSPQRAWHITTRSCKLKS 240
Cdd:pfam14754  161 DGFCWLKLLPPDRREAGLRLYYNHYREQRTGWLSKTGLRLWLGDLGLGINASSGGLKFHIMRGSPQRAWHITTRSCKLKS 240


                   ....*....
gi 1487103480  241 YYVCDISEA 249
Cdd:pfam14754  241 YYVCDISEA 249
Arteriviridae_RdRp cd23189
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of ...
 2044-2370 4.22e-169

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: 523.74  E-value: 4.22e-169
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2044 MNSNLQTATMATCKRQYCSKYKIRSILGTNNYIGLGLRACLSGVTAAFQKAGKdGSPIYLGKSKFDPIP-APDKYCLETD 2122
Cdd:cd23189      1 VRENWQTVTPCTLKKQYCSKKKTRTILGTNNLIALALRAALSGVTQGFMKAGF-NSPIALGKNKFKPLQtPVLGRCLEAD 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2123 LESCDRSTPALVRWFATNLIFELAGQPELVHSYVLNCCHDLVVAGSVAFTKRGGLSSGDPITSISNTIYSLVLYTQHMLL 2202
Cdd:cd23189     80 LASCDRSTPAIVRWFAANLLFELACAEECLPSYVLNCCHDLLVTQSGAFTKRGGLSSGDPVTSISNTIYSLVIYTQHMVL 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2203 CGLEGYFPEIAeKYLDGSLELRDMFKYVRVYIYSDDVVLTTPNQHYaASFDRWVPHLQALLGFKVDPKKTVNTSSPSFLG 2282
Cdd:cd23189    160 SALKEGHPIGL-KFLQDQLKFEDLLKVQPLLVYSDDLVLYAESPSF-PNYHWWVEHLDLMLGFKTDPKKTVITDSPSFLG 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2283 CRfkqVDGKCYLASLQDRVTRSLLYHIGAKNPSEYYEAAVSIFKDSIICC--DEDWWTDLHHRISSAARTDGvEFPTVEM 2360
Cdd:cd23189    238 CR---IINGRQLVPNRDRLLAALAYHMKASNVSEYYASAAAILMDACACLeyDPEWFEDLVVGIAECARKDG-YSFPGPP 313

                          330
                   ....*....|
gi 1487103480 2361 LTSFRTKQYE 2370
Cdd:cd23189    314 FFLFMWEKLG 323
Peptidase_S32 super family cl21733
Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing ...
 963-1269 2.78e-139

Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing nidovirus polyprotein.


The actual alignment was detected with superfamily member pfam05579:

Pssm-ID: 253263  Cd Length: 297  Bit Score: 437.29  E-value: 2.78e-139
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480  963 LATLFVNLFfpqaaLVTMGYWACVAALAVYSLMGLRVK-VNVPMCVTPAHFLLLARSAGQSReqmlrVSAAAPTNSLLGV 1041
Cdd:pfam05579    1 LTMLWVQFF-----LVFVNFWAGVAALVVLISLWLLARyTNVAGLVTPYDIHLVTSSPRGAA-----ALATAPEGTYLAA 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 1042 ARDCYVTGTTRLYIPKEGGMVFEGLFRSPKARGNVGFVAGSSYGTGSVWARDNEVVVLTASHVVGrANMATLKIGDTMLT 1121
Cdd:pfam05579   71 VRRAALTGRTCLFVPSNFGSVLEGLFRTRKPALNVVSVFGSSSGSGGVFTINGNVVVVTASHVLG-GNKARVSGVGFNQM 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 1122 LTFKKNGDFAEAVTtqSELPGHWPQLHFAQPTTGPASWCTATGDEEGLLSGEVCLAWTTSGDSGSAVVQGDA-VVGIHTG 1200
Cdd:pfam05579  150 LTFKTNGDYAFAVV--AEWPGAAPKLKFAQGYTGRAYWSTSTGVEPGLLGKGFAFCFTKCGDSGSPVITEDGnLVGVHTG 227

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 1201 SNTSGVAYVTTPSGKLLGADTVTLSSLSKHFTGPLTSIPK-DIPDNIIADVDTVPRSLAMLIDGLSNRES 1269
Cdd:pfam05579  228 SNKRGSGMVTTPSGKTLGMAPVKLSELSKHFAGPGVPVPTvKLPKNIIVDVEAVPSDLAALLESLPNLEG 297
Nsp2_AV pfam14755
Nsp2, transmembrane domain; This domain is found in Nsp2 protein of the RNA-arteriviruses, ...
 361-508 6.17e-88

Nsp2, transmembrane domain; This domain is found in Nsp2 protein of the RNA-arteriviruses, such as porcine arterivirus PRRSV and equine arterivirus EAV, which is a tetraspanning transmembrane protein. This domain resides adjacent to the peptidase C33 catalytic domain of Nsp2.


:

Pssm-ID: 373271 [Multi-domain]  Cd Length: 148  Bit Score: 283.41  E-value: 6.17e-88
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480  361 GPPPAPVSAAVLDHILEAATFGNVRVVTTEEQSRPVPAPRARPSVNSSGDDKDPAPVPPVPKPRTKLVKPNPTQAPIPAP 440
Cdd:pfam14755    1 GPPPAPVSASVLDHILEAATFGNVRVVATEEQQRPVPAPRTRPSASSSGDVKDPATVPPVPKPRTKLAKPSPTQAPTPAP 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1487103480  441 RTRPPGASAQEPPVNAETASASASKWRVAKTVYNSAERCRAELVQRARSVGDVLFQALPLKTPAVQRY 508
Cdd:pfam14755   81 RTRLQDASKQEPPVGTAAAPASAPKWRVAKTVYSSAERIRTELVQRARSIGDVLVQALPLKTPAVQRY 148
NendoU_av_Nsp11-like cd21160
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV ...
 2937-3056 5.10e-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: 225.28  E-value: 5.10e-68
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2937 FSSGRFETNSRAFLDDAEEKFAAAHPHACLGEITKSTVGGSHFIFSQYLPPLLPADAVALVGASLAGKAAKAACSVVDVY 3016
Cdd:cd21160      1 FSTGRFELNSREYLDEGEREFAKKHPHAFIGDIKGTTVGGCHHITSKYLPPVLPAGSVVKVGVSSPGKAAKALCTVTDVY 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1487103480 3017 APSFEPYLHPETLSRVYKIMIDFKPCRLMVWRNATFYVQE 3056
Cdd:cd21160     81 LPYLEPYLNPPTQSKVYKVNIDFKPVRLMVWKDATMYFQE 120
DEXXYc_viral_SF1-N cd17937
DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ...
 2521-2665 1.48e-56

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: 193.04  E-value: 1.48e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2521 AASEYVEGPPGSGKTFHLVKDVLAvvgSATLVVPTHASMLDCINKLKQEGADPYFVVPkytVLDFPRPGSGNITVRLPQV 2600
Cdd:cd17937      1 AASTYIEGPPGCGKTFWLKKLVQP---NDVLYVPTHATMLDMIKSLGPCRFVVPFGAP---DLDFPTPSSSGPTVRLLAV 74

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1487103480 2601 G-TSEGETFVDEVAYFSPVDLARILTQGRVKGYGDLNQLGCVGPASVprdLWLRHFVSLEPLRACH 2665
Cdd:cd17937     75 GyTPGGKAFVDEACYCNPVDLARLLTQTPVTAFGDPNQLGPVGFASV---FFLVDLMQREQLNVIY 137
NTD_av_Nsp11-like cd21166
N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; ...
 2841-2939 3.27e-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: 184.84  E-value: 3.27e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2841 ISCLPRVAQNLGYHYSPDLPGFCPIPKELAEHWPVVSNDRYPNCLQITLQQVCELSKPC-SAGYMVGQSVFVQTPGVTSY 2919
Cdd:cd21166      1 PSPLPRVAHNLGFHFSPDLPGFPPIPEELAEHWPVVTNDNWPNRLVVSLAPIDELSKPCiSAGYYVGQSVFVGTPGVTSY 80

                           90       100
                   ....*....|....*....|
gi 1487103480 2920 WLTEWVDGKARALPDSLFSS 2939
Cdd:cd21166     81 YLTLFVDGKARALPDSLFST 100
Arteri_nsp7a pfam16749
Arterivirus nonstructural protein 7 alpha; Nonstructural protein 7 alpha is likely to have a ...
 1454-1573 8.36e-48

Arterivirus nonstructural protein 7 alpha; Nonstructural protein 7 alpha is likely to have a role in viral RNA synthesis.


:

Pssm-ID: 374774  Cd Length: 128  Bit Score: 167.58  E-value: 8.36e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 1454 LTAALA-ALTDDDFQFLSDVLDCRAVRSAMNLRAALTSFQVAQYRNILNASLQIDRDAARSRRLMAKLADFA--VEQEVT 1530
Cdd:pfam16749    1 LTAALAcALSDDDLDFLSQLVDCKAFVSASNMRNALGDFIESAYAKALRASLASVVAVAKSRRALAKLEDFAdtVSPQLS 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1487103480 1531 AGDRVVVIdGLDRMAHFKD------DLVLVPLTTKVVGGSRCTICDVVK 1573
Cdd:pfam16749   81 PGDPVVLL-GKTPVGEIFDiyvgdtKHVLRPIETRVVAGSKCTICTVVV 128
zf-RING_13 super family cl39407
RING/Ubox like zinc-binding domain; This is a zinc binding domain found in nidovirus helicase. ...
 2371-2438 9.18e-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: 156.80  E-value: 9.18e-45
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1487103480 2371 SAVCTVCGAAPVAKSACGGWFCGNCVPYHVGHCHTTSLFANCGHDIMYRSTYCTMCEGSPKQMVPKVP 2438
Cdd:pfam17977    1 SAVCTVCGAAPVAKSACGGWFCGNCVPYHAGHCHTTSLFANCGHDIMYRSTYCTMCEGSPKQMVPKVP 68
Rep_1B super family cl39350
Replicase polyprotein 1ab; This entry relates to a regulatory domain found in replicase ...
 2453-2505 3.84e-30

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.


The actual alignment was detected with superfamily member pfam17873:

Pssm-ID: 375396  Cd Length: 53  Bit Score: 114.42  E-value: 3.84e-30
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1487103480 2453 SKEELTLIVADGRTTSPPGRYKVGHKVVAVVADVGGNIVFGCGPGSHLAVPLQ 2505
Cdd:pfam17873    1 SKEELTLVVADGRTTSPPGRYKVGHKVVAVVADVGGNIVFGCGPGSHIAVPLQ 53
av_Nsp3_ER-remodelling cd22528
intracellular membrane remodeller motif of arterivirus non-structural protein 3 (Nsp3); This ...
 846-902 4.26e-21

intracellular membrane remodeller motif of arterivirus non-structural protein 3 (Nsp3); This domain is present in subunit Nsp3 of RNA-arteriviruses, such as porcine arterivirus PRRSV and equine arterivirus EAV. Nsp3 proteins are localized to the ER and appear to be essential for formation of double-membrane vesicles that originate from the ER during the life-cycle of the virus. Arterivirus Nsp3 is a predicted tetra-spanning transmembrane protein containing four transmembrane helices, with the N- and C-termini of the protein residing in the cytoplasm. It contains a cluster of four highly conserved cysteine residues that are predicted to reside in the first luminal domain of the protein. These conserved cysteines play a key role in the formation of double-membrane vesicles (DMVs); mutagenesis of each completely blocked DMV formation.


:

Pssm-ID: 412095  Cd Length: 57  Bit Score: 88.92  E-value: 4.26e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1487103480  846 STFTCLPIKCGIGTRDPFCRRVFSVPVTKTQEHCHAGMCASAEGISLDSLGLSQLQS 902
Cdd:cd22528      1 GLYLQSPVSCGIGTNDPFCRNPFGVPVVGTQGVCHSGYCASAQGISLPTSLLTQLSS 57
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 2701-2760 1.09e-19

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: 1.09e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1487103480 2701 KGVVITAYHKDRG------------------LGHRTIDSIQGCTFPVVTLRLPTPQSLTRPRAVVAVTRASQELYIYD 2760
Cdd:cd18786     12 KGVVLTPYHRDRAylnqylqglsldefdlqlVGAITIDSSQGLTFDVVTLYLPTANSLTPRRLYVALTRARKRLVIYD 89
DUF3756 pfam12581
Protein of unknown function (DUF3756); This domain family is found in viruses, and is ...
 3084-3124 8.01e-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: 8.01e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1487103480 3084 VASGYRTNALVAPQAKISIGAYAAEWALSTEPPPAGYAIVR 3124
Cdd:pfam12581    1 LASGYRTNALVAPQAKISIGAYAAEWALSTEPPPAGYAIVR 41
Peptidase_C33 super family cl05135
Equine arterivirus Nsp2-type cysteine proteinase; Corresponds to Merops family C33. These ...
 261-357 1.39e-13

Equine arterivirus Nsp2-type cysteine proteinase; Corresponds to Merops family C33. These peptidases are involved in viral polyprotein processing in replication.


The actual alignment was detected with superfamily member pfam05412:

Pssm-ID: 114153  Cd Length: 108  Bit Score: 69.17  E-value: 1.39e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480  261 GYNPPGDGACGYRCLAFMNGATAVSAGCS--------SDLWCDDELAYRVFQLSpTFTVTIPGGRVCPNAKHVMICDKQH 332
Cdd:pfam05412    1 GYSPPGDGACGWHCISAIANRMFNDKFTTtltecsrpSDDWASDQDLVQAIQTL-RLPATLDRNGACPSAKYKLKLVGQH 79

                           90       100
                   ....*....|....*....|....*.
gi 1487103480  333 WRVKRAKGVGL-CLDESCFRGTCNCQ 357
Cdd:pfam05412   80 WTVTVRKGMAPgLLSPECVRGVCGHE 105
 
Name Accession Description Interval E-value
IFR3_antag pfam14754
Papain-like auto-proteinase; The replicase polyproteins of the Nidoviruses such as, porcine ...
 1-249 6.54e-176

Papain-like auto-proteinase; The replicase polyproteins of the Nidoviruses such as, porcine arterivirus PRRSV, equine arterivirus EAV, human coronavirus 229E, and severe acute respiratory syndrome coronavirus (SARS-CoV), are predicted to be cleaved into 14 non-structural proteins (nsps) by the nsp4 main proteinase pfam05579 and three accessory proteinases residing in nsp1-alpha, nsp1-beta and nsp2. This family is the two nsp1 proteins that together act in a papain-like way to separate off the rest of the various functional domains of the polyprotein. Once inside the host cell, this nsp1 interferes with the regulation of interferon, thereby enabling the virus to replicate.


Pssm-ID: 291424  Cd Length: 249  Bit Score: 540.03  E-value: 6.54e-176
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480    1 MATFSATGFGGSFVRDWSLDLPDACEHGAGLCCEVDGSTLCAECLRGCEGMEQCPGLFMGLLKLASPVPVGHKFLIGWYR 80
Cdd:pfam14754    1 MATFSATGFGGSFVRDWSLDLPDACEHGAGLCCEVDGSTLCAECFRGCEGMEQCPGLFMGLLKLASPVPVGHKFLIGWYR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480   81 AAKVTGRYNFLELLQHPAFAQLRVVDARLAIEEASVFISTDHASAKRFPGARFALTPVYANAWVVSPAANSLIVTIDQEQ 160
Cdd:pfam14754   81 AAKVTGRYNFLELLQHPAFAQLRVVDARLAIEEASVFISTDHASAKRFPGARFALTPVYANAWVVSPAANSLIVTTDQEQ 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480  161 DGFCWLKLLPPDRREAGLRLYYNHYREQRTGWLSKTGLRLWLGDLGLGINASSGGLKFHIMRGSPQRAWHITTRSCKLKS 240
Cdd:pfam14754  161 DGFCWLKLLPPDRREAGLRLYYNHYREQRTGWLSKTGLRLWLGDLGLGINASSGGLKFHIMRGSPQRAWHITTRSCKLKS 240


                   ....*....
gi 1487103480  241 YYVCDISEA 249
Cdd:pfam14754  241 YYVCDISEA 249
Arteriviridae_RdRp cd23189
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of ...
 2044-2370 4.22e-169

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: 523.74  E-value: 4.22e-169
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2044 MNSNLQTATMATCKRQYCSKYKIRSILGTNNYIGLGLRACLSGVTAAFQKAGKdGSPIYLGKSKFDPIP-APDKYCLETD 2122
Cdd:cd23189      1 VRENWQTVTPCTLKKQYCSKKKTRTILGTNNLIALALRAALSGVTQGFMKAGF-NSPIALGKNKFKPLQtPVLGRCLEAD 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2123 LESCDRSTPALVRWFATNLIFELAGQPELVHSYVLNCCHDLVVAGSVAFTKRGGLSSGDPITSISNTIYSLVLYTQHMLL 2202
Cdd:cd23189     80 LASCDRSTPAIVRWFAANLLFELACAEECLPSYVLNCCHDLLVTQSGAFTKRGGLSSGDPVTSISNTIYSLVIYTQHMVL 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2203 CGLEGYFPEIAeKYLDGSLELRDMFKYVRVYIYSDDVVLTTPNQHYaASFDRWVPHLQALLGFKVDPKKTVNTSSPSFLG 2282
Cdd:cd23189    160 SALKEGHPIGL-KFLQDQLKFEDLLKVQPLLVYSDDLVLYAESPSF-PNYHWWVEHLDLMLGFKTDPKKTVITDSPSFLG 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2283 CRfkqVDGKCYLASLQDRVTRSLLYHIGAKNPSEYYEAAVSIFKDSIICC--DEDWWTDLHHRISSAARTDGvEFPTVEM 2360
Cdd:cd23189    238 CR---IINGRQLVPNRDRLLAALAYHMKASNVSEYYASAAAILMDACACLeyDPEWFEDLVVGIAECARKDG-YSFPGPP 313

                          330
                   ....*....|
gi 1487103480 2361 LTSFRTKQYE 2370
Cdd:cd23189    314 FFLFMWEKLG 323
Peptidase_S32 pfam05579
Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing ...
 963-1269 2.78e-139

Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing nidovirus polyprotein.


Pssm-ID: 253263  Cd Length: 297  Bit Score: 437.29  E-value: 2.78e-139
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480  963 LATLFVNLFfpqaaLVTMGYWACVAALAVYSLMGLRVK-VNVPMCVTPAHFLLLARSAGQSReqmlrVSAAAPTNSLLGV 1041
Cdd:pfam05579    1 LTMLWVQFF-----LVFVNFWAGVAALVVLISLWLLARyTNVAGLVTPYDIHLVTSSPRGAA-----ALATAPEGTYLAA 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 1042 ARDCYVTGTTRLYIPKEGGMVFEGLFRSPKARGNVGFVAGSSYGTGSVWARDNEVVVLTASHVVGrANMATLKIGDTMLT 1121
Cdd:pfam05579   71 VRRAALTGRTCLFVPSNFGSVLEGLFRTRKPALNVVSVFGSSSGSGGVFTINGNVVVVTASHVLG-GNKARVSGVGFNQM 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 1122 LTFKKNGDFAEAVTtqSELPGHWPQLHFAQPTTGPASWCTATGDEEGLLSGEVCLAWTTSGDSGSAVVQGDA-VVGIHTG 1200
Cdd:pfam05579  150 LTFKTNGDYAFAVV--AEWPGAAPKLKFAQGYTGRAYWSTSTGVEPGLLGKGFAFCFTKCGDSGSPVITEDGnLVGVHTG 227

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 1201 SNTSGVAYVTTPSGKLLGADTVTLSSLSKHFTGPLTSIPK-DIPDNIIADVDTVPRSLAMLIDGLSNRES 1269
Cdd:pfam05579  228 SNKRGSGMVTTPSGKTLGMAPVKLSELSKHFAGPGVPVPTvKLPKNIIVDVEAVPSDLAALLESLPNLEG 297
Nsp2_AV pfam14755
Nsp2, transmembrane domain; This domain is found in Nsp2 protein of the RNA-arteriviruses, ...
 361-508 6.17e-88

Nsp2, transmembrane domain; This domain is found in Nsp2 protein of the RNA-arteriviruses, such as porcine arterivirus PRRSV and equine arterivirus EAV, which is a tetraspanning transmembrane protein. This domain resides adjacent to the peptidase C33 catalytic domain of Nsp2.


Pssm-ID: 373271 [Multi-domain]  Cd Length: 148  Bit Score: 283.41  E-value: 6.17e-88
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480  361 GPPPAPVSAAVLDHILEAATFGNVRVVTTEEQSRPVPAPRARPSVNSSGDDKDPAPVPPVPKPRTKLVKPNPTQAPIPAP 440
Cdd:pfam14755    1 GPPPAPVSASVLDHILEAATFGNVRVVATEEQQRPVPAPRTRPSASSSGDVKDPATVPPVPKPRTKLAKPSPTQAPTPAP 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1487103480  441 RTRPPGASAQEPPVNAETASASASKWRVAKTVYNSAERCRAELVQRARSVGDVLFQALPLKTPAVQRY 508
Cdd:pfam14755   81 RTRLQDASKQEPPVGTAAAPASAPKWRVAKTVYSSAERIRTELVQRARSIGDVLVQALPLKTPAVQRY 148
NendoU_av_Nsp11-like cd21160
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV ...
 2937-3056 5.10e-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: 225.28  E-value: 5.10e-68
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2937 FSSGRFETNSRAFLDDAEEKFAAAHPHACLGEITKSTVGGSHFIFSQYLPPLLPADAVALVGASLAGKAAKAACSVVDVY 3016
Cdd:cd21160      1 FSTGRFELNSREYLDEGEREFAKKHPHAFIGDIKGTTVGGCHHITSKYLPPVLPAGSVVKVGVSSPGKAAKALCTVTDVY 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1487103480 3017 APSFEPYLHPETLSRVYKIMIDFKPCRLMVWRNATFYVQE 3056
Cdd:cd21160     81 LPYLEPYLNPPTQSKVYKVNIDFKPVRLMVWKDATMYFQE 120
DEXXYc_viral_SF1-N cd17937
DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ...
 2521-2665 1.48e-56

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: 193.04  E-value: 1.48e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2521 AASEYVEGPPGSGKTFHLVKDVLAvvgSATLVVPTHASMLDCINKLKQEGADPYFVVPkytVLDFPRPGSGNITVRLPQV 2600
Cdd:cd17937      1 AASTYIEGPPGCGKTFWLKKLVQP---NDVLYVPTHATMLDMIKSLGPCRFVVPFGAP---DLDFPTPSSSGPTVRLLAV 74

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1487103480 2601 G-TSEGETFVDEVAYFSPVDLARILTQGRVKGYGDLNQLGCVGPASVprdLWLRHFVSLEPLRACH 2665
Cdd:cd17937     75 GyTPGGKAFVDEACYCNPVDLARLLTQTPVTAFGDPNQLGPVGFASV---FFLVDLMQREQLNVIY 137
NTD_av_Nsp11-like cd21166
N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; ...
 2841-2939 3.27e-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: 184.84  E-value: 3.27e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2841 ISCLPRVAQNLGYHYSPDLPGFCPIPKELAEHWPVVSNDRYPNCLQITLQQVCELSKPC-SAGYMVGQSVFVQTPGVTSY 2919
Cdd:cd21166      1 PSPLPRVAHNLGFHFSPDLPGFPPIPEELAEHWPVVTNDNWPNRLVVSLAPIDELSKPCiSAGYYVGQSVFVGTPGVTSY 80

                           90       100
                   ....*....|....*....|
gi 1487103480 2920 WLTEWVDGKARALPDSLFSS 2939
Cdd:cd21166     81 YLTLFVDGKARALPDSLFST 100
Arteri_nsp7a pfam16749
Arterivirus nonstructural protein 7 alpha; Nonstructural protein 7 alpha is likely to have a ...
 1454-1573 8.36e-48

Arterivirus nonstructural protein 7 alpha; Nonstructural protein 7 alpha is likely to have a role in viral RNA synthesis.


Pssm-ID: 374774  Cd Length: 128  Bit Score: 167.58  E-value: 8.36e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 1454 LTAALA-ALTDDDFQFLSDVLDCRAVRSAMNLRAALTSFQVAQYRNILNASLQIDRDAARSRRLMAKLADFA--VEQEVT 1530
Cdd:pfam16749    1 LTAALAcALSDDDLDFLSQLVDCKAFVSASNMRNALGDFIESAYAKALRASLASVVAVAKSRRALAKLEDFAdtVSPQLS 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1487103480 1531 AGDRVVVIdGLDRMAHFKD------DLVLVPLTTKVVGGSRCTICDVVK 1573
Cdd:pfam16749   81 PGDPVVLL-GKTPVGEIFDiyvgdtKHVLRPIETRVVAGSKCTICTVVV 128
zf-RING_13 pfam17977
RING/Ubox like zinc-binding domain; This is a zinc binding domain found in nidovirus helicase. ...
 2371-2438 9.18e-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: 156.80  E-value: 9.18e-45
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1487103480 2371 SAVCTVCGAAPVAKSACGGWFCGNCVPYHVGHCHTTSLFANCGHDIMYRSTYCTMCEGSPKQMVPKVP 2438
Cdd:pfam17977    1 SAVCTVCGAAPVAKSACGGWFCGNCVPYHAGHCHTTSLFANCGHDIMYRSTYCTMCEGSPKQMVPKVP 68
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 1971-2312 6.08e-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: 138.31  E-value: 6.08e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 1971 DLEKYNLSTQGFVLPSVFSMVRAYLKEEIGDAPPLYLPSTVPSK-NSQAGINGAEFPTKSLQSYCLIDDM-----VSRSM 2044
Cdd:pfam00680   54 RDKLLNRSAAKMVLSELRGVPKKANSTLIVYRAIDGVEQIDPLNwDTSAGYPYVGLGGKKGDLIEHLKDGteareLAERL 133

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2045 NSN---LQTATMATCKRQYC-----------SKYKIRSILGTNNYIGLGLRACLSGVTAAFQKAGKDGsPIYLGKSKFDP 2110
Cdd:pfam00680  134 AADwevLQNGTPLKLVYQTClkdelrplekvEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFH-PIQVGINPFDR 212

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2111 --------IPAPDKYCLETDLESCDRSTPALVRWFATNLIFELAGQPELVHSYVLN----CCHDLVVAGSVAFTKRGGLS 2178
Cdd:pfam00680  213 gwprllrrLARFGDYVYELDYSGFDSSVPPWLIRFAFEILRELLGFPSNVKEWRAIlellIYTPIALPNGTVFKKTGGLP 292

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2179 SGDPITSISNTIYSlVLYTQHMLLCGLEGYFPEIAEkyldgslelrdMFKYVRVYIYSDDVVLTTPNQhYAASFDRWVPH 2258
Cdd:pfam00680  293 SGSPFTSIINSIVN-YLLILYALLKSLENDGPRVCN-----------LDKYFDFFTYGDDSLVAVSPD-FDPVLDRLSPH 359

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1487103480 2259 LqALLGFKVDPKKTVNTSSP-----SFLGCRFKQVDGKcYLASLQDRVTRSLLYHIGAK 2312
Cdd:pfam00680  360 L-KELGLTITPAKKTFPVSReleevSFLKRTFRKTPGG-YRPPLDRKRILAQLEYIRSK 416
Rep_1B pfam17873
Replicase polyprotein 1ab; This entry relates to a regulatory domain found in replicase ...
 2453-2505 3.84e-30

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: 114.42  E-value: 3.84e-30
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1487103480 2453 SKEELTLIVADGRTTSPPGRYKVGHKVVAVVADVGGNIVFGCGPGSHLAVPLQ 2505
Cdd:pfam17873    1 SKEELTLVVADGRTTSPPGRYKVGHKVVAVVADVGGNIVFGCGPGSHIAVPLQ 53
av_Nsp3_ER-remodelling cd22528
intracellular membrane remodeller motif of arterivirus non-structural protein 3 (Nsp3); This ...
 846-902 4.26e-21

intracellular membrane remodeller motif of arterivirus non-structural protein 3 (Nsp3); This domain is present in subunit Nsp3 of RNA-arteriviruses, such as porcine arterivirus PRRSV and equine arterivirus EAV. Nsp3 proteins are localized to the ER and appear to be essential for formation of double-membrane vesicles that originate from the ER during the life-cycle of the virus. Arterivirus Nsp3 is a predicted tetra-spanning transmembrane protein containing four transmembrane helices, with the N- and C-termini of the protein residing in the cytoplasm. It contains a cluster of four highly conserved cysteine residues that are predicted to reside in the first luminal domain of the protein. These conserved cysteines play a key role in the formation of double-membrane vesicles (DMVs); mutagenesis of each completely blocked DMV formation.


Pssm-ID: 412095  Cd Length: 57  Bit Score: 88.92  E-value: 4.26e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1487103480  846 STFTCLPIKCGIGTRDPFCRRVFSVPVTKTQEHCHAGMCASAEGISLDSLGLSQLQS 902
Cdd:cd22528      1 GLYLQSPVSCGIGTNDPFCRNPFGVPVVGTQGVCHSGYCASAQGISLPTSLLTQLSS 57
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 2701-2760 1.09e-19

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: 1.09e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1487103480 2701 KGVVITAYHKDRG------------------LGHRTIDSIQGCTFPVVTLRLPTPQSLTRPRAVVAVTRASQELYIYD 2760
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 ...
 2372-2438 5.72e-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: 83.14  E-value: 5.72e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1487103480 2372 AVCTVCGAAPVAKSACGGWFCGNCVPYHVgHCHTTSLFanCGHDImyRSTYCTMCEGSPKQMVPKVP 2438
Cdd:cd21405      1 RVCGICGSTAVTTSACGLDLCAYHAHFHQ-HCPVTSPF--CGHPI--GSKSCTMCSIPVVPGNDELD 62
DUF3756 pfam12581
Protein of unknown function (DUF3756); This domain family is found in viruses, and is ...
 3084-3124 8.01e-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: 8.01e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1487103480 3084 VASGYRTNALVAPQAKISIGAYAAEWALSTEPPPAGYAIVR 3124
Cdd:pfam12581    1 LASGYRTNALVAPQAKISIGAYAAEWALSTEPPPAGYAIVR 41
Peptidase_C33 pfam05412
Equine arterivirus Nsp2-type cysteine proteinase; Corresponds to Merops family C33. These ...
 261-357 1.39e-13

Equine arterivirus Nsp2-type cysteine proteinase; Corresponds to Merops family C33. These peptidases are involved in viral polyprotein processing in replication.


Pssm-ID: 114153  Cd Length: 108  Bit Score: 69.17  E-value: 1.39e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480  261 GYNPPGDGACGYRCLAFMNGATAVSAGCS--------SDLWCDDELAYRVFQLSpTFTVTIPGGRVCPNAKHVMICDKQH 332
Cdd:pfam05412    1 GYSPPGDGACGWHCISAIANRMFNDKFTTtltecsrpSDDWASDQDLVQAIQTL-RLPATLDRNGACPSAKYKLKLVGQH 79

                           90       100
                   ....*....|....*....|....*.
gi 1487103480  333 WRVKRAKGVGL-CLDESCFRGTCNCQ 357
Cdd:pfam05412   80 WTVTVRKGMAPgLLSPECVRGVCGHE 105
CoV_NSP15_C pfam19215
Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the ...
 2934-3055 7.71e-10

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: 60.04  E-value: 7.71e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2934 DSLFSSGRFETN-------SRAFLDDAEEKFAAAHP-------HACLGEITKSTVGGSHFIFSQYLPPLLPADAVALVGA 2999
Cdd:pfam19215    1 DTLFTQGRTLEDfvprstmEKDFLNMDQQQFIQKYGledlgfeHIVYGDFSKTTIGGLHLLISLVRLTKMGILKVEEFVP 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1487103480 3000 SLA------------GKAAKAACSVVDVYAPSFEP---YLHPETLSRVYKIMIDFKPCRLMVWRN----ATFYVQ 3055
Cdd:pfam19215   81 NDDstvkncsvtyanDGSSKAVCTVLDLLLDDFVDilkSLDLSVVSKVVTVNIDFQPVRFMLWCKdgkvQTFYPQ 155
1B_nv_SF1_Hel-like cd21406
1B domain of nidovirus helicases including coronavirus Nsp13 and arterivirus Nsp10, and ...
 2457-2504 1.08e-09

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: 56.03  E-value: 1.08e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1487103480 2457 LTLIVADGRTTSPPGRYKVGHKVVAVVADVGGNIVFGCGPGSHLAVPL 2504
Cdd:cd21406      1 LIATVARGLTLSRPGRYTGYHGEVAVERGDDGNIVFGCTPGGDIFVLL 48
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 2526-2760 1.27e-05

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: 49.30  E-value: 1.27e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2526 VEGPPGSGKTfHLVKDVL--AVVGSATLVVPTHASMlDCINKlkqegaDPYFVVpkyTVLDFPRPGSGNITV-----RLP 2598
Cdd:pfam01443    3 VHGVPGCGKS-TLIRKLLrtSRVIRPTAELRTEGKP-DLPNL------NVRTVD---TFLMALLKPTGKILIldeytLLP 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2599 QvgtseGEtfVDEVAYFSPVDLArILTqgrvkgyGDLNQLGCvgPASVPRDLWLRHFVSL---EPLRACHRFGAAVCD-L 2674
Cdd:pfam01443   72 P-----GY--ILLLAAISGAKLV-ILF-------GDPLQIPY--HSRAPSFLIPHFPSSLshrVGRRTTYLLPSLRAPiL 134

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2675 IKGIYPYYEPAPHTTKVVFVPNPdFEKGVVITAYHKD-RGLGHR--TIDSIQGCTFPVVTLRLPTPQSL-----TRPRAV 2746
Cdd:pfam01443  135 SAKGFEVVVERSGEYKVDYDPNG-VLVLVYLTFTQALkESLGVRvtTVHEVQGLTFDSVTLVLDTDTDLliisdSPEHLY 213

                          250
                   ....*....|....
gi 1487103480 2747 VAVTRASQELYIYD 2760
Cdd:pfam01443  214 VALTRHRKSLHILT 227
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
360-470 1.95e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 44.10  E-value: 1.95e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480  360 SGPPPAPVSAAVLDHILEAA-TFGNVRVVTTEEQSRPVPAPRARPSVNSSGDDKDPAPVPPVPKPRTKLVKPNPTQAPIP 438
Cdd:PRK12323   379 AAPVAQPAPAAAAPAAAAPApAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPAPAAAP 458

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1487103480  439 APRTRPPGASAQEPPVNAETASASASKWRVAK 470
Cdd:PRK12323   459 AAAARPAAAGPRPVAAAAAAAPARAAPAAAPA 490
 
Name Accession Description Interval E-value
IFR3_antag pfam14754
Papain-like auto-proteinase; The replicase polyproteins of the Nidoviruses such as, porcine ...
 1-249 6.54e-176

Papain-like auto-proteinase; The replicase polyproteins of the Nidoviruses such as, porcine arterivirus PRRSV, equine arterivirus EAV, human coronavirus 229E, and severe acute respiratory syndrome coronavirus (SARS-CoV), are predicted to be cleaved into 14 non-structural proteins (nsps) by the nsp4 main proteinase pfam05579 and three accessory proteinases residing in nsp1-alpha, nsp1-beta and nsp2. This family is the two nsp1 proteins that together act in a papain-like way to separate off the rest of the various functional domains of the polyprotein. Once inside the host cell, this nsp1 interferes with the regulation of interferon, thereby enabling the virus to replicate.


Pssm-ID: 291424  Cd Length: 249  Bit Score: 540.03  E-value: 6.54e-176
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480    1 MATFSATGFGGSFVRDWSLDLPDACEHGAGLCCEVDGSTLCAECLRGCEGMEQCPGLFMGLLKLASPVPVGHKFLIGWYR 80
Cdd:pfam14754    1 MATFSATGFGGSFVRDWSLDLPDACEHGAGLCCEVDGSTLCAECFRGCEGMEQCPGLFMGLLKLASPVPVGHKFLIGWYR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480   81 AAKVTGRYNFLELLQHPAFAQLRVVDARLAIEEASVFISTDHASAKRFPGARFALTPVYANAWVVSPAANSLIVTIDQEQ 160
Cdd:pfam14754   81 AAKVTGRYNFLELLQHPAFAQLRVVDARLAIEEASVFISTDHASAKRFPGARFALTPVYANAWVVSPAANSLIVTTDQEQ 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480  161 DGFCWLKLLPPDRREAGLRLYYNHYREQRTGWLSKTGLRLWLGDLGLGINASSGGLKFHIMRGSPQRAWHITTRSCKLKS 240
Cdd:pfam14754  161 DGFCWLKLLPPDRREAGLRLYYNHYREQRTGWLSKTGLRLWLGDLGLGINASSGGLKFHIMRGSPQRAWHITTRSCKLKS 240


                   ....*....
gi 1487103480  241 YYVCDISEA 249
Cdd:pfam14754  241 YYVCDISEA 249
Arteriviridae_RdRp cd23189
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of ...
 2044-2370 4.22e-169

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: 523.74  E-value: 4.22e-169
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2044 MNSNLQTATMATCKRQYCSKYKIRSILGTNNYIGLGLRACLSGVTAAFQKAGKdGSPIYLGKSKFDPIP-APDKYCLETD 2122
Cdd:cd23189      1 VRENWQTVTPCTLKKQYCSKKKTRTILGTNNLIALALRAALSGVTQGFMKAGF-NSPIALGKNKFKPLQtPVLGRCLEAD 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2123 LESCDRSTPALVRWFATNLIFELAGQPELVHSYVLNCCHDLVVAGSVAFTKRGGLSSGDPITSISNTIYSLVLYTQHMLL 2202
Cdd:cd23189     80 LASCDRSTPAIVRWFAANLLFELACAEECLPSYVLNCCHDLLVTQSGAFTKRGGLSSGDPVTSISNTIYSLVIYTQHMVL 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2203 CGLEGYFPEIAeKYLDGSLELRDMFKYVRVYIYSDDVVLTTPNQHYaASFDRWVPHLQALLGFKVDPKKTVNTSSPSFLG 2282
Cdd:cd23189    160 SALKEGHPIGL-KFLQDQLKFEDLLKVQPLLVYSDDLVLYAESPSF-PNYHWWVEHLDLMLGFKTDPKKTVITDSPSFLG 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2283 CRfkqVDGKCYLASLQDRVTRSLLYHIGAKNPSEYYEAAVSIFKDSIICC--DEDWWTDLHHRISSAARTDGvEFPTVEM 2360
Cdd:cd23189    238 CR---IINGRQLVPNRDRLLAALAYHMKASNVSEYYASAAAILMDACACLeyDPEWFEDLVVGIAECARKDG-YSFPGPP 313

                          330
                   ....*....|
gi 1487103480 2361 LTSFRTKQYE 2370
Cdd:cd23189    314 FFLFMWEKLG 323
Peptidase_S32 pfam05579
Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing ...
 963-1269 2.78e-139

Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing nidovirus polyprotein.


Pssm-ID: 253263  Cd Length: 297  Bit Score: 437.29  E-value: 2.78e-139
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480  963 LATLFVNLFfpqaaLVTMGYWACVAALAVYSLMGLRVK-VNVPMCVTPAHFLLLARSAGQSReqmlrVSAAAPTNSLLGV 1041
Cdd:pfam05579    1 LTMLWVQFF-----LVFVNFWAGVAALVVLISLWLLARyTNVAGLVTPYDIHLVTSSPRGAA-----ALATAPEGTYLAA 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 1042 ARDCYVTGTTRLYIPKEGGMVFEGLFRSPKARGNVGFVAGSSYGTGSVWARDNEVVVLTASHVVGrANMATLKIGDTMLT 1121
Cdd:pfam05579   71 VRRAALTGRTCLFVPSNFGSVLEGLFRTRKPALNVVSVFGSSSGSGGVFTINGNVVVVTASHVLG-GNKARVSGVGFNQM 149

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 1122 LTFKKNGDFAEAVTtqSELPGHWPQLHFAQPTTGPASWCTATGDEEGLLSGEVCLAWTTSGDSGSAVVQGDA-VVGIHTG 1200
Cdd:pfam05579  150 LTFKTNGDYAFAVV--AEWPGAAPKLKFAQGYTGRAYWSTSTGVEPGLLGKGFAFCFTKCGDSGSPVITEDGnLVGVHTG 227

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 1201 SNTSGVAYVTTPSGKLLGADTVTLSSLSKHFTGPLTSIPK-DIPDNIIADVDTVPRSLAMLIDGLSNRES 1269
Cdd:pfam05579  228 SNKRGSGMVTTPSGKTLGMAPVKLSELSKHFAGPGVPVPTvKLPKNIIVDVEAVPSDLAALLESLPNLEG 297
Nsp2_AV pfam14755
Nsp2, transmembrane domain; This domain is found in Nsp2 protein of the RNA-arteriviruses, ...
 361-508 6.17e-88

Nsp2, transmembrane domain; This domain is found in Nsp2 protein of the RNA-arteriviruses, such as porcine arterivirus PRRSV and equine arterivirus EAV, which is a tetraspanning transmembrane protein. This domain resides adjacent to the peptidase C33 catalytic domain of Nsp2.


Pssm-ID: 373271 [Multi-domain]  Cd Length: 148  Bit Score: 283.41  E-value: 6.17e-88
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480  361 GPPPAPVSAAVLDHILEAATFGNVRVVTTEEQSRPVPAPRARPSVNSSGDDKDPAPVPPVPKPRTKLVKPNPTQAPIPAP 440
Cdd:pfam14755    1 GPPPAPVSASVLDHILEAATFGNVRVVATEEQQRPVPAPRTRPSASSSGDVKDPATVPPVPKPRTKLAKPSPTQAPTPAP 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1487103480  441 RTRPPGASAQEPPVNAETASASASKWRVAKTVYNSAERCRAELVQRARSVGDVLFQALPLKTPAVQRY 508
Cdd:pfam14755   81 RTRLQDASKQEPPVGTAAAPASAPKWRVAKTVYSSAERIRTELVQRARSIGDVLVQALPLKTPAVQRY 148
ps-ssRNAv_Nidovirales_RdRp cd23168
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Nidovirales of ...
 2050-2369 3.15e-87

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: 288.49  E-value: 3.15e-87
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2050 TATMATCKRQYCSKYKIRSILGTNNYIGLGLRACLSGVTAAFQKAGKDGSPI-----YLGKSKFDPIPAP----DKYCLE 2120
Cdd:cd23168      1 TLTQVNPKYAIQKKKRARTILGVSIISTDVGRQLHQAVLAAIVNTRSANIVIigtkfYGGWHKMLRYLYPgvieDPVLMG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2121 TDLESCDRSTPALVRWFATNLIFEL----AGQPELVHSYVLNCCH---DLVVAGSVAFTKRGGLSSGDPITSISNTIYSL 2193
Cdd:cd23168     81 WDYPKCDRSVPNMLRYLANLLLASLydncCNLSEIVHLLINECAQvlyDYVVYGGNLYRKPGGVSSGDSTTAISNSIYNY 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2194 VLYTQHMllcglegyfpeiaekyldgslelrdmfkyVRVYIYSDDVVLTTPNQHYAASFDRWVPHLQALLGFKVDPKKTV 2273
Cdd:cd23168    161 FQTFIAN-----------------------------VRLAILSDDGVACINPDLIDLGDVASVSFFLASYYYTNNKKKYS 211

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2274 NTSSPSFLGcrFKQVDGKCYLASLQDRVTRSLLYHIGAKNPSEYYEAAVSIFKDSIICCDEDWWTDLHHRISSAART--- 2350
Cdd:cd23168    212 STCWVEPHE--FCSPHEFKSDDKYQDRVERVYLPIPDPSRMLSACLLVDTRTKTDILLMIERLISILIDAYPLTFHTktl 289

                          330       340
                   ....*....|....*....|.
gi 1487103480 2351 --DGVEFPTVEMLTSFRTKQY 2369
Cdd:cd23168    290 pvNIEYAPLILLLLDYIKKLS 310
NendoU_av_Nsp11-like cd21160
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV ...
 2937-3056 5.10e-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: 225.28  E-value: 5.10e-68
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2937 FSSGRFETNSRAFLDDAEEKFAAAHPHACLGEITKSTVGGSHFIFSQYLPPLLPADAVALVGASLAGKAAKAACSVVDVY 3016
Cdd:cd21160      1 FSTGRFELNSREYLDEGEREFAKKHPHAFIGDIKGTTVGGCHHITSKYLPPVLPAGSVVKVGVSSPGKAAKALCTVTDVY 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1487103480 3017 APSFEPYLHPETLSRVYKIMIDFKPCRLMVWRNATFYVQE 3056
Cdd:cd21160     81 LPYLEPYLNPPTQSKVYKVNIDFKPVRLMVWKDATMYFQE 120
DEXXYc_viral_SF1-N cd17937
DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ...
 2521-2665 1.48e-56

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: 193.04  E-value: 1.48e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2521 AASEYVEGPPGSGKTFHLVKDVLAvvgSATLVVPTHASMLDCINKLKQEGADPYFVVPkytVLDFPRPGSGNITVRLPQV 2600
Cdd:cd17937      1 AASTYIEGPPGCGKTFWLKKLVQP---NDVLYVPTHATMLDMIKSLGPCRFVVPFGAP---DLDFPTPSSSGPTVRLLAV 74

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1487103480 2601 G-TSEGETFVDEVAYFSPVDLARILTQGRVKGYGDLNQLGCVGPASVprdLWLRHFVSLEPLRACH 2665
Cdd:cd17937     75 GyTPGGKAFVDEACYCNPVDLARLLTQTPVTAFGDPNQLGPVGFASV---FFLVDLMQREQLNVIY 137
NTD_av_Nsp11-like cd21166
N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; ...
 2841-2939 3.27e-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: 184.84  E-value: 3.27e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2841 ISCLPRVAQNLGYHYSPDLPGFCPIPKELAEHWPVVSNDRYPNCLQITLQQVCELSKPC-SAGYMVGQSVFVQTPGVTSY 2919
Cdd:cd21166      1 PSPLPRVAHNLGFHFSPDLPGFPPIPEELAEHWPVVTNDNWPNRLVVSLAPIDELSKPCiSAGYYVGQSVFVGTPGVTSY 80

                           90       100
                   ....*....|....*....|
gi 1487103480 2920 WLTEWVDGKARALPDSLFSS 2939
Cdd:cd21166     81 YLTLFVDGKARALPDSLFST 100
Arteri_nsp7a pfam16749
Arterivirus nonstructural protein 7 alpha; Nonstructural protein 7 alpha is likely to have a ...
 1454-1573 8.36e-48

Arterivirus nonstructural protein 7 alpha; Nonstructural protein 7 alpha is likely to have a role in viral RNA synthesis.


Pssm-ID: 374774  Cd Length: 128  Bit Score: 167.58  E-value: 8.36e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 1454 LTAALA-ALTDDDFQFLSDVLDCRAVRSAMNLRAALTSFQVAQYRNILNASLQIDRDAARSRRLMAKLADFA--VEQEVT 1530
Cdd:pfam16749    1 LTAALAcALSDDDLDFLSQLVDCKAFVSASNMRNALGDFIESAYAKALRASLASVVAVAKSRRALAKLEDFAdtVSPQLS 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1487103480 1531 AGDRVVVIdGLDRMAHFKD------DLVLVPLTTKVVGGSRCTICDVVK 1573
Cdd:pfam16749   81 PGDPVVLL-GKTPVGEIFDiyvgdtKHVLRPIETRVVAGSKCTICTVVV 128
zf-RING_13 pfam17977
RING/Ubox like zinc-binding domain; This is a zinc binding domain found in nidovirus helicase. ...
 2371-2438 9.18e-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: 156.80  E-value: 9.18e-45
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1487103480 2371 SAVCTVCGAAPVAKSACGGWFCGNCVPYHVGHCHTTSLFANCGHDIMYRSTYCTMCEGSPKQMVPKVP 2438
Cdd:pfam17977    1 SAVCTVCGAAPVAKSACGGWFCGNCVPYHAGHCHTTSLFANCGHDIMYRSTYCTMCEGSPKQMVPKVP 68
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 1971-2312 6.08e-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: 138.31  E-value: 6.08e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 1971 DLEKYNLSTQGFVLPSVFSMVRAYLKEEIGDAPPLYLPSTVPSK-NSQAGINGAEFPTKSLQSYCLIDDM-----VSRSM 2044
Cdd:pfam00680   54 RDKLLNRSAAKMVLSELRGVPKKANSTLIVYRAIDGVEQIDPLNwDTSAGYPYVGLGGKKGDLIEHLKDGteareLAERL 133

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2045 NSN---LQTATMATCKRQYC-----------SKYKIRSILGTNNYIGLGLRACLSGVTAAFQKAGKDGsPIYLGKSKFDP 2110
Cdd:pfam00680  134 AADwevLQNGTPLKLVYQTClkdelrplekvEKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFH-PIQVGINPFDR 212

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2111 --------IPAPDKYCLETDLESCDRSTPALVRWFATNLIFELAGQPELVHSYVLN----CCHDLVVAGSVAFTKRGGLS 2178
Cdd:pfam00680  213 gwprllrrLARFGDYVYELDYSGFDSSVPPWLIRFAFEILRELLGFPSNVKEWRAIlellIYTPIALPNGTVFKKTGGLP 292

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2179 SGDPITSISNTIYSlVLYTQHMLLCGLEGYFPEIAEkyldgslelrdMFKYVRVYIYSDDVVLTTPNQhYAASFDRWVPH 2258
Cdd:pfam00680  293 SGSPFTSIINSIVN-YLLILYALLKSLENDGPRVCN-----------LDKYFDFFTYGDDSLVAVSPD-FDPVLDRLSPH 359

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1487103480 2259 LqALLGFKVDPKKTVNTSSP-----SFLGCRFKQVDGKcYLASLQDRVTRSLLYHIGAK 2312
Cdd:pfam00680  360 L-KELGLTITPAKKTFPVSReleevSFLKRTFRKTPGG-YRPPLDRKRILAQLEYIRSK 416
Rep_1B pfam17873
Replicase polyprotein 1ab; This entry relates to a regulatory domain found in replicase ...
 2453-2505 3.84e-30

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: 114.42  E-value: 3.84e-30
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1487103480 2453 SKEELTLIVADGRTTSPPGRYKVGHKVVAVVADVGGNIVFGCGPGSHLAVPLQ 2505
Cdd:pfam17873    1 SKEELTLVVADGRTTSPPGRYKVGHKVVAVVADVGGNIVFGCGPGSHIAVPLQ 53
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 2523-2665 1.64e-25

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: 103.72  E-value: 1.64e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2523 SEYVEGPPGSGKTFHLVKDVLAVV-------GSATLVVPTHASMLDCinklkqegadpyfvvpkytvldfprpgsgnitv 2595
Cdd:cd17914      1 LSLIQGPPGTGKTRVLVKIVAALMqnkngepGRILLVTPTNKAAAQL--------------------------------- 47

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2596 rlpqvgtseGETFVDEVAYFSPVDLAR----ILTQGRVKGYGDLNQLGCVGPASVP---------RDLWLRHFVSLEPLR 2662
Cdd:cd17914     48 ---------DNILVDEAAQILEPETSRlidlALDQGRVILVGDHDQLGPVWRGAVLakicneqslFTRLVRLGVSLIRLQ 118


                   ...
gi 1487103480 2663 ACH 2665
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 ...
 2842-2938 1.82e-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: 103.57  E-value: 1.82e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2842 SCLPRVAQNLGYHYSPDLPGFCPI--------------PKELAEHWPVVSNDRY----------PNCLQITLQQVCELSK 2897
Cdd:cd21163      2 TPLPKVLRNLGVDFTPNFVLWDYEdtapffnttvckytPEELCEHLPVLYDDRYggslerflsaPNAVLISLTKVKKYSI 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1487103480 2898 PCSAGYMVGQSVFVQTPGVTSYWLTEWVDGKARALPDSLFS 2938
Cdd:cd21163     82 PPPAGAYLNGSVVVGTPKVVSFYLYKRKDGKFVTLPDTLFT 122
av_Nsp3_ER-remodelling cd22528
intracellular membrane remodeller motif of arterivirus non-structural protein 3 (Nsp3); This ...
 846-902 4.26e-21

intracellular membrane remodeller motif of arterivirus non-structural protein 3 (Nsp3); This domain is present in subunit Nsp3 of RNA-arteriviruses, such as porcine arterivirus PRRSV and equine arterivirus EAV. Nsp3 proteins are localized to the ER and appear to be essential for formation of double-membrane vesicles that originate from the ER during the life-cycle of the virus. Arterivirus Nsp3 is a predicted tetra-spanning transmembrane protein containing four transmembrane helices, with the N- and C-termini of the protein residing in the cytoplasm. It contains a cluster of four highly conserved cysteine residues that are predicted to reside in the first luminal domain of the protein. These conserved cysteines play a key role in the formation of double-membrane vesicles (DMVs); mutagenesis of each completely blocked DMV formation.


Pssm-ID: 412095  Cd Length: 57  Bit Score: 88.92  E-value: 4.26e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1487103480  846 STFTCLPIKCGIGTRDPFCRRVFSVPVTKTQEHCHAGMCASAEGISLDSLGLSQLQS 902
Cdd:cd22528      1 GLYLQSPVSCGIGTNDPFCRNPFGVPVVGTQGVCHSGYCASAQGISLPTSLLTQLSS 57
NendoU_nv cd21158
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural ...
 2937-3055 1.84e-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: 90.40  E-value: 1.84e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2937 FSSGRFETNsRAFLDDAEEKFAA---------------AHPHACLGEITKSTVGGSHFIFSQYLPP---------LLPAD 2992
Cdd:cd21158      1 FTQGRNLQE-FLPRSDMERDFLPvdmdvfiekygleiyAFEHVVYGDFSHTTLGGLHLVISLYKRFkegplpreeFIPND 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1487103480 2993 -AVALVGASLAG-KAAKAACSVVDVYAPSFEPYLHP---ETLSRVYKIMIDFKPCRLMVWRN----ATFYVQ 3055
Cdd:cd21158     80 sTVKNYGVTSPGtKASKAVCTLIDLLLDDFVEILKSqdlEVVSKVVKVMIDFKEVRFMLWCKdgdvQTFYPQ 151
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 2701-2760 1.09e-19

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: 1.09e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1487103480 2701 KGVVITAYHKDRG------------------LGHRTIDSIQGCTFPVVTLRLPTPQSLTRPRAVVAVTRASQELYIYD 2760
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 ...
 2372-2438 5.72e-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: 83.14  E-value: 5.72e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1487103480 2372 AVCTVCGAAPVAKSACGGWFCGNCVPYHVgHCHTTSLFanCGHDImyRSTYCTMCEGSPKQMVPKVP 2438
Cdd:cd21405      1 RVCGICGSTAVTTSACGLDLCAYHAHFHQ-HCPVTSPF--CGHPI--GSKSCTMCSIPVVPGNDELD 62
DUF3756 pfam12581
Protein of unknown function (DUF3756); This domain family is found in viruses, and is ...
 3084-3124 8.01e-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: 8.01e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1487103480 3084 VASGYRTNALVAPQAKISIGAYAAEWALSTEPPPAGYAIVR 3124
Cdd:pfam12581    1 LASGYRTNALVAPQAKISIGAYAAEWALSTEPPPAGYAIVR 41
Peptidase_C33 pfam05412
Equine arterivirus Nsp2-type cysteine proteinase; Corresponds to Merops family C33. These ...
 261-357 1.39e-13

Equine arterivirus Nsp2-type cysteine proteinase; Corresponds to Merops family C33. These peptidases are involved in viral polyprotein processing in replication.


Pssm-ID: 114153  Cd Length: 108  Bit Score: 69.17  E-value: 1.39e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480  261 GYNPPGDGACGYRCLAFMNGATAVSAGCS--------SDLWCDDELAYRVFQLSpTFTVTIPGGRVCPNAKHVMICDKQH 332
Cdd:pfam05412    1 GYSPPGDGACGWHCISAIANRMFNDKFTTtltecsrpSDDWASDQDLVQAIQTL-RLPATLDRNGACPSAKYKLKLVGQH 79

                           90       100
                   ....*....|....*....|....*.
gi 1487103480  333 WRVKRAKGVGL-CLDESCFRGTCNCQ 357
Cdd:pfam05412   80 WTVTVRKGMAPgLLSPECVRGVCGHE 105
ZBD_nv_SF1_Hel-like cd21399
Cys/His rich zinc-binding domain (CH/ZBD) of nidovirus helicases including coronavirus Nsp13 ...
 2372-2429 6.44e-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: 66.06  E-value: 6.44e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1487103480 2372 AVCTVCGAAP-VAKSAC--GGWFCGNCVPYHVG-HCHTTSLFAN------CG-HDIMYRSTYC--TMCEGS 2429
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 ...
 2373-2429 5.52e-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: 60.58  E-value: 5.52e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2373 VCTVCGAAP-VAKSAC--GGWFCGNCVPYHVG-HCHTTSLFA------NCG-HDIMYR--STYCTMCEGS 2429
Cdd:cd21343      1 ACYVCGSHTvVRCGTCirRPWFCNSCIYDHLIrTKHKEVLLAspyvcaGCGeSDITLLyfGGVSYRCVDH 70
CoV_NSP15_C pfam19215
Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the ...
 2934-3055 7.71e-10

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: 60.04  E-value: 7.71e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2934 DSLFSSGRFETN-------SRAFLDDAEEKFAAAHP-------HACLGEITKSTVGGSHFIFSQYLPPLLPADAVALVGA 2999
Cdd:pfam19215    1 DTLFTQGRTLEDfvprstmEKDFLNMDQQQFIQKYGledlgfeHIVYGDFSKTTIGGLHLLISLVRLTKMGILKVEEFVP 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1487103480 3000 SLA------------GKAAKAACSVVDVYAPSFEP---YLHPETLSRVYKIMIDFKPCRLMVWRN----ATFYVQ 3055
Cdd:pfam19215   81 NDDstvkncsvtyanDGSSKAVCTVLDLLLDDFVDilkSLDLSVVSKVVTVNIDFQPVRFMLWCKdgkvQTFYPQ 155
1B_nv_SF1_Hel-like cd21406
1B domain of nidovirus helicases including coronavirus Nsp13 and arterivirus Nsp10, and ...
 2457-2504 1.08e-09

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: 56.03  E-value: 1.08e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1487103480 2457 LTLIVADGRTTSPPGRYKVGHKVVAVVADVGGNIVFGCGPGSHLAVPL 2504
Cdd:cd21406      1 LIATVARGLTLSRPGRYTGYHGEVAVERGDDGNIVFGCTPGGDIFVLL 48
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 2130-2307 2.86e-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: 61.15  E-value: 2.86e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2130 TPALVRWfATNLIFELAGQP------ELVHSYVLNCCHDLvvaGSVAFTKRGGLSSGDPITSISNTIYslvlytqHMLLC 2203
Cdd:cd01699    111 SPQLLEA-EHSIYNALYDDDdelerrNLLRSLTNNSLHIG---FNEVYKVRGGRPSGDPLTSIGNSII-------NCILV 179

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2204 glEGYFPEIAEKYldgslelrdMFKYVRVYIYSDDVVLTTPNQHYAASFDRWVPHLqALLGFKV-DPKKTVNTSSP---- 2278
Cdd:cd01699    180 --RYAFRKLGGKS---------FFKNVRLLNYGDDCLLSVEKADDKFNLETLAEWL-KEYGLTMtDEDKVESPFRPleev 247

                          170       180       190
                   ....*....|....*....|....*....|
gi 1487103480 2279 SFLGCRFKQVDGKCYLASLQ-DRVTRSLLY 2307
Cdd:cd01699    248 EFLKRRFVLDEGGGWRAPLDpSSILSKLSW 277
NendoU_tv_PToV-like cd21162
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of Porcine torovirus (PToV) ...
 2937-3056 1.62e-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: 55.67  E-value: 1.62e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2937 FSSGRFETNSRAFLDDAEEKFAAAHPHACLGEITK--STVGGSHFI--FSQYLPPLLPADAVALVGASLA-GKAAKAACS 3011
Cdd:cd21162      1 FSTGRLYNLEHDPSYNFNVEQLPFNKHVFLGEFTEvsTTIGGVHHVpaLNGTKGSIIPSYVKPIHTGLINvGKGVKRCTT 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1487103480 3012 VVDVYAPSFEPYLHPE----TLSRVYKIMIDFKPCRLMVWRN----ATFYVQE 3056
Cdd:cd21162     81 LVDVCANQLYELVKQQingvTVSKVIFINIDFQEVQFMVFASegdiQTAYPQK 133
ps-ssRNAv-Picornavirales cd23169
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...
 2133-2307 1.02e-07

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: 1.02e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2133 LVRWFATNLIFElagQPELVHSYVLNCCHDLVVAGSVAFTKRGGLSSGDPIT----SISNTIYSLVLYTQHMllcglegy 2208
Cdd:cd23169    105 INDWYDEYVDDE---DERVRKVLFEELINTIHLVGNLVYQVHGGNPSGNPLTtiinSIVNLLYIRYAWLRIT-------- 173

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2209 fpeiaekyldGSLELRDMFKYVRVYIYSDDVVLTTpNQHYAASFD-RWVPHLQALLGFKV-DPKKT------VNTSSPSF 2280
Cdd:cd23169    174 ----------GLTSLSDFKKNVRLVTYGDDVIISV-SDEVKDEFNfVTISEFLKELGITYtDADKSgdivpyRPLEEVTF 242

                          170       180
                   ....*....|....*....|....*...
gi 1487103480 2281 LGCRFKQVDGK-CYLASLQDRVTRSLLY 2307
Cdd:cd23169    243 LKRGFRPHPTPgLVLAPLDLESIEEQLN 270
Caliciviridae_RdRp cd23192
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of ...
 2116-2290 7.74e-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: 53.81  E-value: 7.74e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2116 KYCLETDLESCDrST--PALVRwFATNLIFELAGQPELVHSyvlnCCHDL-----VVAGSVAFTKRGGLSSGDPITSISN 2188
Cdd:cd23192     78 RYHYCLDYSKWD-STqsPAVTA-AAIDILADLSEETPLRDS----VVETLssppmGIFDDVIFVTKRGLPSGMPFTSVIN 151

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2189 TIyslvlytQHMLLCgleGYFpeIAEKYLDGSLELRDMFKYVRVYIYSDDVVLTTPNqHYAASFDrWVPHLQALLGFK-V 2267
Cdd:cd23192    152 SL-------NHWLLF---SAA--VLKAYELVGIYTGNVFDEADFFTYGDDGVYAMPP-ATASVMD-EIIENLKSYGLKpT 217

                          170       180
                   ....*....|....*....|....*...
gi 1487103480 2268 DPKKTVN-----TSSPSFLGCRFKQVDG 2290
Cdd:cd23192    218 AADKTENpdippLQGPVFLKRTFVRTPG 245
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 2526-2760 1.27e-05

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: 49.30  E-value: 1.27e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2526 VEGPPGSGKTfHLVKDVL--AVVGSATLVVPTHASMlDCINKlkqegaDPYFVVpkyTVLDFPRPGSGNITV-----RLP 2598
Cdd:pfam01443    3 VHGVPGCGKS-TLIRKLLrtSRVIRPTAELRTEGKP-DLPNL------NVRTVD---TFLMALLKPTGKILIldeytLLP 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2599 QvgtseGEtfVDEVAYFSPVDLArILTqgrvkgyGDLNQLGCvgPASVPRDLWLRHFVSL---EPLRACHRFGAAVCD-L 2674
Cdd:pfam01443   72 P-----GY--ILLLAAISGAKLV-ILF-------GDPLQIPY--HSRAPSFLIPHFPSSLshrVGRRTTYLLPSLRAPiL 134

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2675 IKGIYPYYEPAPHTTKVVFVPNPdFEKGVVITAYHKD-RGLGHR--TIDSIQGCTFPVVTLRLPTPQSL-----TRPRAV 2746
Cdd:pfam01443  135 SAKGFEVVVERSGEYKVDYDPNG-VLVLVYLTFTQALkESLGVRvtTVHEVQGLTFDSVTLVLDTDTDLliisdSPEHLY 213

                          250
                   ....*....|....
gi 1487103480 2747 VAVTRASQELYIYD 2760
Cdd:pfam01443  214 VALTRHRKSLHILT 227
NendoU_cv_Nsp15-like cd21161
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural ...
 2963-3055 1.51e-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: 47.64  E-value: 1.51e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2963 HACLGEITKSTVGGSHFIFSQ---------YLPPLLPADAV---ALVGASLAGkAAKAACSVVDVYAPSFEPYL---HPE 3027
Cdd:cd21161     41 HIVYGDFSKPTIGGLHLLIGLvrlkkegklYVEEFHNSDSTvqnYFVTDANNG-SSKQVCTVVDLLLDDFVDILksqDLS 119

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1487103480 3028 TLSRVYKIMIDFKPCRLMVW----RNATFYVQ 3055
Cdd:cd21161    120 VVSKVVTVSIDYKPIRFMLWckdgKVKTFYPQ 151
1B_av_Nsp10-like cd21410
1B domain of arterivirus EAV Nsp10 helicase and related proteins; Helicases catalyze ...
 2455-2504 4.29e-05

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: 43.00  E-value: 4.29e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2455 EELTLIVADGRTTSPPGRYKVGHKVVAVVADVGGNIVFGCGpGSHLAVPL 2504
Cdd:cd21410      1 VEVTVEVVDGVTSAAPGRYQTRHGVVMVRRDIGGCIVDLPD-GEYQVTPL 49
ps-ssRNA_Picornaviridae cd23193
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of ...
 2142-2293 1.39e-04

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: 47.16  E-value: 1.39e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2142 IFELAGQPELVHSYVLNCCHDLVVAGSVAFTKRGGLSSGDPITSISNTIYSLVLYTQHMLLCGLegyfpeiaekyldgsl 2221
Cdd:cd23193    160 LAECHGDPELVLRYLEPIINSKHVVGDERYTVEGGMPSGCPCTSILNSICNNLVVRYALLETGK---------------- 223

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1487103480 2222 elrDMFKYVRVYIYSDDVVLTTPNQHyaaSFDRWVPHLQALLGFKV---DPKKTVNTSSPS---FLGCRFKQVDGKCY 2293
Cdd:cd23193    224 ---FDPDEYYILAYGDDVLVSTDEPI---DPSDLAEFYKKYFGMTVtpaDKSSDFPESSPIedvFLKRRFFVPDGTFL 295
Dicistroviridae_RdRp cd23194
RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense ...
 2127-2241 3.75e-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: 3.75e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2127 DRSTPALVRWfatnLIFElagqpELVHSYVLncCHDLVVAgsvaFTKrgGLSSGDPITSISNTIYSLVLYTQHMLLCGLE 2206
Cdd:cd23194    116 DGEENALIRR----VLWE-----DIVNSVHI--CGGYVYQ----WTH--SQPSGNPLTAIINSIYNSIIMRYVYLLLTKE 178

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1487103480 2207 GYFPeiaekyldgslELRDMFKYVRVYIYSDDVVL 2241
Cdd:cd23194    179 AGLM-----------TMSDFNKHVSMVSYGDDNVI 202
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
360-470 1.95e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 44.10  E-value: 1.95e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480  360 SGPPPAPVSAAVLDHILEAA-TFGNVRVVTTEEQSRPVPAPRARPSVNSSGDDKDPAPVPPVPKPRTKLVKPNPTQAPIP 438
Cdd:PRK12323   379 AAPVAQPAPAAAAPAAAAPApAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPAPAAAP 458

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1487103480  439 APRTRPPGASAQEPPVNAETASASASKWRVAK 470
Cdd:PRK12323   459 AAAARPAAAGPRPVAAAAAAAPARAAPAAAPA 490
Mosavirus_RdRp cd23225
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Mosavirus of ...
 2115-2269 3.71e-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: 42.59  E-value: 3.71e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1487103480 2115 DKYCLETDLESCDRSTP-ALVRWFATNLIFELAG-QPELVHSYVLNCCHDLVVAGSVAFTKRGGLSSGDPITSISNTIYS 2192
Cdd:cd23225    139 DRYVFDLDYKAFDSTHPtAMFNLLAERFFTERNGfDQQAVRIFLNGLSDSDHVYEGKHFRIRGGLPSGCPCTSILNTVIN 218

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1487103480 2193 LVLYTQHMLlcglegyfpeiaekyldGSLELRDM-FKYVRVYIYSDDVVLTTPNQHYAASFDRWvphLQALLGFKVDP 2269
Cdd:cd23225    219 NIIVRAAIL-----------------GAYQIDTVdFQKFRMLAYGDDVVYATPQPIKPQDLADW---LHANTNYKVTP 276
deltaCoV_RdRp cd21590
deltacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ...
 2122-2194 4.38e-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: 42.92  E-value: 4.38e-03
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gi 1487103480 2122 DLESCDRSTPALVRWFATNLI---FELAGQPELVHSYVLNCCH---DLVVAGSVAFTKRGGLSSGDPITSISNTIYSLV 2194
Cdd:cd21590    616 DYPKCDRSMPNMLRIAASCLLarkHTCCNQSQRFYRLANECCQvlsEVVVSGNNLYVKPGGTSSGDATTAYANSVFNIL 694
 
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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