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Conserved domains on  [gi|1773654335|gb|QGD14181|]
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ORF1a/b polyprotein [Porcine reproductive and respiratory syndrome virus 2]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Arteriviridae_RdRp cd23189
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of ...
 2811-3133 0e+00

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: 657.41  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2811 VRENWQTVTPCTLKKQYCGKKKTRTILGTNNFIALAHRAALSGVTQGFMKKAFNSPIALGKNKFKELQTPVLGRCLEADL 2890
Cdd:cd23189      1 VRENWQTVTPCTLKKQYCSKKKTRTILGTNNLIALALRAALSGVTQGFMKAGFNSPIALGKNKFKPLQTPVLGRCLEADL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2891 ASCDRSTPAIVRWFAANLLYELACAEEHLPSYVLNCCHDLLVTQSGAVTKRGGLSSGDPITSVSNTIYSLVIYAQHMVLS 2970
Cdd:cd23189     81 ASCDRSTPAIVRWFAANLLFELACAEECLPSYVLNCCHDLLVTQSGAFTKRGGLSSGDPVTSISNTIYSLVIYTQHMVLS 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2971 YFKSGHPHGLLFLQDQLKFEDMLKVQPLIVYSDDLVLYAESPTMPNYHWWVEHLNLMLGFQTDPKKTAITDSPSFLGCRI 3050
Cdd:cd23189    161 ALKEGHPIGLKFLQDQLKFEDLLKVQPLLVYSDDLVLYAESPSFPNYHWWVEHLDLMLGFKTDPKKTVITDSPSFLGCRI 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3051 INGRQLVPNRDRILAALAYHMKASNVSEYYAAAAAILMDSCACLEYDPEWFEELVVGIAQCARKDGYSFPGPPFFLSMWE 3130
Cdd:cd23189    241 INGRQLVPNRDRLLAALAYHMKASNVSEYYASAAAILMDACACLEYDPEWFEDLVVGIAECARKDGYSFPGPPFFLFMWE 320


                   ...
gi 1773654335 3131 KLR 3133
Cdd:cd23189    321 KLG 323
NSP2-B_epitope pfam14757
Immunogenic region of nsp2 protein of arterivirus polyprotein; This domain is in a ...
 823-1069 1.07e-168

Immunogenic region of nsp2 protein of arterivirus polyprotein; This domain is in a non-essential part of the nsp2 (non-structural protein) subunit section of the arterivirus polyprotein. This domain carries seven small sequence-regions that are predicted to be potential B-cell epitopes.


:

Pssm-ID: 373272  Cd Length: 272  Bit Score: 520.55  E-value: 1.07e-168
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335  823 KTKSVKSLLENKPVPAPRRKVRSDCGSPILMGDNVPNGWEDSTVGGPLDLSAPSEPMTPLSEPVL------ISRPVTSLS 896
Cdd:pfam14757   20 KTKSVKSLPENKPVPAPRRKVRSDCGSPVLMGDNVPNGWEDLTVGGPLDLPTPSEPMTPLSEPVLvpalqhIPRPVTPLS 99

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335  897 VPAPVPAPRRAVSRPMTPSSEPIFVSALRHKFQQVEKANLAAAAPMYQDEPLDLSASSQTEYEASPLTPPQNVGILEVRG 976
Cdd:pfam14757  100 GPAPVPAPRRTVSRPMTPLSEPIFVSAPRHKFQQVEEANLAATTLTCQDEPLDLSASSQTEYEASPLAPLQNMGILEAGG 179

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335  977 QEAEEVLSEISDILNDTNPAPVSSSSSLSSVRITRPKYSAQAIIDSGGPCSGHLQREKEACLRIMREACDAAKLSDPATQ 1056
Cdd:pfam14757  180 QEAEEVLSEISDILNDINPAPVSSSSSLSSVKITRPKYSAQAIIDSGGPCSGHLQKEKEACLSIMREACDATKLSDPATQ 259

                          250
                   ....*....|...
gi 1773654335 1057 EWLSRMWDRVDML 1069
Cdd:pfam14757  260 EWLSRMWDRVDML 272
Peptidase_S32 pfam05579
Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing ...
 1711-2008 9.87e-163

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


:

Pssm-ID: 253263  Cd Length: 297  Bit Score: 504.70  E-value: 9.87e-163
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 1711 LTILWLVFFLISVNMPSGILAVVLLVSLWLLGRYTNIAGLVTPYDIHHYTSGPRGVAALATAPDGTYLAAVRRAALTGRT 1790
Cdd:pfam05579    1 LTMLWVQFFLVFVNFWAGVAALVVLISLWLLARYTNVAGLVTPYDIHLVTSSPRGAAALATAPEGTYLAAVRRAALTGRT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 1791 MLFTPSQLGSLLEGAFRTRKPSLNTVNVVGSSMGSGGVFTIDGKIRCVTAAHVLTGNSARVSGVGFNQMLDFDVKGDFAI 1870
Cdd:pfam05579   81 CLFVPSNFGSVLEGLFRTRKPALNVVSVFGSSSGSGGVFTINGNVVVVTASHVLGGNKARVSGVGFNQMLTFKTNGDYAF 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 1871 ADCPNWQGAAPKTQFCaDGWTGRAYWLTSSGVEPGVIGSGFAFCFTACGDSGSPVITEAGELVGVHTGSNKQGGGIVTRP 1950
Cdd:pfam05579  161 AVVAEWPGAAPKLKFA-QGYTGRAYWSTSTGVEPGLLGKGFAFCFTKCGDSGSPVITEDGNLVGVHTGSNKRGSGMVTTP 239

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1773654335 1951 SGQFCNVAPIKLSELSEFFAGPKVPLGDVKVGSHIIKDTCEVPSDLCALLAAKPELEG 2008
Cdd:pfam05579  240 SGKTLGMAPVKLSELSKHFAGPGVPVPTVKLPKNIIVDVEAVPSDLAALLESLPNLEG 297
Pdase_C33_assoc pfam14756
Peptidase_C33-associated domain; The nsps or non-structural protein subunits of the ...
 536-682 3.15e-96

Peptidase_C33-associated domain; The nsps or non-structural protein subunits of the arteriviral polyproteins such as porcine arterivirus PRRSV and equine arterivirus EAV are auto-cleaved into functional units. the function of this particular domain is not known.


:

Pssm-ID: 258893  Cd Length: 147  Bit Score: 307.34  E-value: 3.15e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335  536 GFPDVVEVSGFDPACLDRLAEIMHLPSSVIPAALAEMSDDFNRLASPAATVWTVSQFFARHRGGEHPDQVCLGKIINLCQ 615
Cdd:pfam14756    1 GSPDAVEVSGFDPACLDRLAGVMHLPSSAIPAALAELSGDSDRPVSPATTVWTVSQFYARHSGGEHPDQVCLGKIISLCQ 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1773654335  616 VIEECCCSRNKANRATPEEVAAKIDQYLRGAASLGECLAKLEMARPPSAMDTSFDWNVVLPGVETAN 682
Cdd:pfam14756   81 VIEDCCCSQNKTNRVTPEEVAAKIDQYLRGAASLEECLARLEKARPPSVLDTSFDWDVVLPGVEAAN 147
NendoU_av_Nsp11-like cd21160
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV ...
 3681-3799 3.77e-77

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: 251.47  E-value: 3.77e-77
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3681 FSTGRIEVDCRGYLDDREREVAESLPHAFIGDVKGTTVGGCHHVTSKYLPRFLPKESVAVVGVSSPGKAAKAVCTLTDVY 3760
Cdd:cd21160      1 FSTGRFELNSREYLDEGEREFAKKHPHAFIGDIKGTTVGGCHHITSKYLPPVLPAGSVVKVGVSSPGKAAKALCTVTDVY 80

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1773654335 3761 LPDLEAYLHPETQSKCWKVMLDFKEVRLMVWKDKTAYFQ 3799
Cdd:cd21160     81 LPYLEPYLNPPTQSKVYKVNIDFKPVRLMVWKDATMYFQ 119
Peptidase_C32 pfam05411
Equine arteritis virus putative proteinase; These proteins are characterized by a region that ...
 256-382 1.46e-73

Equine arteritis virus putative proteinase; These proteins are characterized by a region that has been proposed to have peptidase activity involved in viral polyprotein processing in replication.


:

Pssm-ID: 398854  Cd Length: 127  Bit Score: 241.68  E-value: 1.46e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335  256 QHGCLPADTVPEGNCWWCLFDLLPPEVQNKEIRRANQFGYQTKHGVPGKYLQRRLQVNGLRAVTDTDGPIVVQYFSVRES 335
Cdd:pfam05411    1 QHGCLPADTVPEGKCWLKLFDHLPWEVQCKEIRLADQFGYQTKHGVQGKYLQRRLQVNGLRAVVDQNGPIIVQAFSVPES 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1773654335  336 WIRHFRLAEEPSLPGFEDLLRIRVEPNTSPLGGKGEKIFRFGSHKWY 382
Cdd:pfam05411   81 WIRHLKLADEPVPPGFVDLLRFRVVPNTEPLAKTPEKIFRFGSHKWY 127
DEXXYc_viral_SF1-N cd17937
DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ...
 3279-3414 4.12e-72

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: 238.10  E-value: 4.12e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3279 LRSRFIIGPPGAGKTYWLLQQVQDGDVIYTPTHQTMLDMIRALGTCRFNVPAGTT-LQFPAPSRTGPWVRILAGGWCPGK 3357
Cdd:cd17937      1 AASTYIEGPPGCGKTFWLKKLVQPNDVLYVPTHATMLDMIKSLGPCRFVVPFGAPdLDFPTPSSSGPTVRLLAVGYTPGG 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1773654335 3358 NSFLDEAAYCNHLDVLRLLSKTTLTCLGDFKQLHPVGFDSHCYVFDIMPQTQLKTIW 3414
Cdd:cd17937     81 KAFVDEACYCNPVDLARLLTQTPVTAFGDPNQLGPVGFASVFFLVDLMQREQLNVIY 137
Peptidase_C31 pfam05410
Porcine arterivirus-type cysteine proteinase alpha; Corresponds to Merops family C31. These ...
 57-161 2.16e-67

Porcine arterivirus-type cysteine proteinase alpha; Corresponds to Merops family C31. These peptidases are involved in viral polyprotein processing in replication.


:

Pssm-ID: 461643  Cd Length: 105  Bit Score: 223.26  E-value: 2.16e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335   57 LRWTLPRAFPTVECSPAGACWLSAIFPIARMTSGNLNFQQRMVRVAAEIYRAGQLTPAVLKALQVYERGCRWYPIVGPVP 136
Cdd:pfam05410    1 LTWEAPITYPTVECRPGGLCWLSAIFPIARMTSGNHNFQQRLVFVASVVYRDGKLTPKHLEELQVYERGCRWYPITGPVP 80

                           90       100
                   ....*....|....*....|....*
gi 1773654335  137 GVAVHANSLHVSDKPFPGATHVLTN 161
Cdd:pfam05410   81 GIALYANSVHVSDEPFPGATHVLTN 105
Arteri_nsp7a pfam16749
Arterivirus nonstructural protein 7 alpha; Nonstructural protein 7 alpha is likely to have a ...
 2195-2322 3.11e-65

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: 218.04  E-value: 3.11e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2195 LTGALAMRLNDEDLDFLTKWTDFKCFVSASNMRNAAGQFIEAAYAKALRIELAQLVQVDKVRGTLAKLEAFADTVAPQLS 2274
Cdd:pfam16749    1 LTAALACALSDDDLDFLSQLVDCKAFVSASNMRNALGDFIESAYAKALRASLASVVAVAKSRRALAKLEDFADTVSPQLS 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1773654335 2275 PGDIVVALGHTPVGSIFDLKVGGTKHTLQVIETRVLAGSKMTVARVVD 2322
Cdd:pfam16749   81 PGDPVVLLGKTPVGEIFDIYVGDTKHVLRPIETRVVAGSKCTICTVVV 128
Peptidase_C33 pfam05412
Equine arterivirus Nsp2-type cysteine proteinase; Corresponds to Merops family C33. These ...
 429-535 2.92e-59

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: 200.14  E-value: 2.92e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335  429 YSPPADGNCGWHCISAITNRMVNSKFETTLPERVRPSDDWATDEDLVNAIQILRLPAALDRNGACAGAKYVLKLEGEHWT 508
Cdd:pfam05412    2 YSPPGDGACGWHCISAIANRMFNDKFTTTLTECSRPSDDWASDQDLVQAIQTLRLPATLDRNGACPSAKYKLKLVGQHWT 81

                           90       100
                   ....*....|....*....|....*..
gi 1773654335  509 VSVTPGMTPSLLPLECVQGCCEHTSGL 535
Cdd:pfam05412   82 VTVRKGMAPGLLSPECVRGVCGHEGGL 108
NTD_av_Nsp11-like cd21166
N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; ...
 3581-3683 2.50e-51

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: 177.14  E-value: 2.50e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3581 SSPLPKVAHNLGFYFSPDLTQFAKLPVDLAPHWPVVTTQNnekWPDRLVASLRPVHKYSRACIGAGYMVGPSVFLGTPGV 3660
Cdd:cd21166      1 PSPLPRVAHNLGFHFSPDLPGFPPIPEELAEHWPVVTNDN---WPNRLVVSLAPIDELSKPCISAGYYVGQSVFVGTPGV 77

                           90       100
                   ....*....|....*....|...
gi 1773654335 3661 VSYYLTKFVKGEAQVLPETVFST 3683
Cdd:cd21166     78 TSYYLTLFVDGKARALPDSLFST 100
ZBD_av_Nsp10-like cd21405
Cys/His rich zinc-binding domain (CH/ZBD) of arterivirus EAV Nsp10 helicase and related ...
 3142-3202 2.37e-30

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: 115.50  E-value: 2.37e-30
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1773654335 3142 RMCGYCGAPAPYATACGLDVCIYHTHFHQHCPVIIW-CGHPAGSGSCSECKPPLGKGTSPLD 3202
Cdd:cd21405      1 RVCGICGSTAVTTSACGLDLCAYHAHFHQHCPVTSPfCGHPIGSKSCTMCSIPVVPGNDELD 62
av_Nsp3_ER-remodelling cd22528
intracellular membrane remodeller motif of arterivirus non-structural protein 3 (Nsp3); This ...
 1594-1651 3.23e-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: 89.30  E-value: 3.23e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1773654335 1594 GVYVTSVGSCGAGTNDPWCTNPFAVPGYGPGSLCTSRLCISQHGLTLPlTALVAGFGL 1651
Cdd:cd22528      1 GLYLQSPVSCGIGTNDPFCRNPFGVPVVGTQGVCHSGYCASAQGISLP-TSLLTQLSS 57
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 3450-3509 4.97e-21

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: 90.19  E-value: 4.97e-21
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1773654335 3450 YGQVLTPYHRDR------------------EDGAITIDSSQGATFDVVTLHLPTKDSLNRQRALVAITRARHAIFVYD 3509
Cdd:cd18786     12 KGVVLTPYHRDRaylnqylqglsldefdlqLVGAITIDSSQGLTFDVVTLYLPTANSLTPRRLYVALTRARKRLVIYD 89
1B_av_Nsp10-like cd21410
1B domain of arterivirus EAV Nsp10 helicase and related proteins; Helicases catalyze ...
 3214-3262 4.62e-18

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: 80.36  E-value: 4.62e-18
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1773654335 3214 RTVIMHVEQGLTPLDPGRYQTRRGLVSVRRGIRGNEVDLPDGDYASTAL 3262
Cdd:cd21410      1 VEVTVEVVDGVTSAAPGRYQTRHGVVMVRRDIGGCIVDLPDGEYQVTPL 49
ND5 super family cl33350
NADH dehydrogenase subunit 5; Provisional
 1235-1303 1.51e-03

NADH dehydrogenase subunit 5; Provisional


The actual alignment was detected with superfamily member MTH00063:

Pssm-ID: 214414 [Multi-domain]  Cd Length: 522  Bit Score: 44.48  E-value: 1.51e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 1235 VFFS-HLFKSDSGYSPGDWGFAAFTLFCLFLCYSYPFFGFVPLLGVFSGSSRRVRMGVFGCWLAFAVGLF 1303
Cdd:MTH00063   334 VFFSkHFLLSSFSSVVFNVSLLLVVILCVFLSYLYSFRLCLILFGVKSSLSSGVRFLFFNSGLMVFLWLF 403
 
Name Accession Description Interval E-value
Arteriviridae_RdRp cd23189
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of ...
 2811-3133 0e+00

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: 657.41  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2811 VRENWQTVTPCTLKKQYCGKKKTRTILGTNNFIALAHRAALSGVTQGFMKKAFNSPIALGKNKFKELQTPVLGRCLEADL 2890
Cdd:cd23189      1 VRENWQTVTPCTLKKQYCSKKKTRTILGTNNLIALALRAALSGVTQGFMKAGFNSPIALGKNKFKPLQTPVLGRCLEADL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2891 ASCDRSTPAIVRWFAANLLYELACAEEHLPSYVLNCCHDLLVTQSGAVTKRGGLSSGDPITSVSNTIYSLVIYAQHMVLS 2970
Cdd:cd23189     81 ASCDRSTPAIVRWFAANLLFELACAEECLPSYVLNCCHDLLVTQSGAFTKRGGLSSGDPVTSISNTIYSLVIYTQHMVLS 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2971 YFKSGHPHGLLFLQDQLKFEDMLKVQPLIVYSDDLVLYAESPTMPNYHWWVEHLNLMLGFQTDPKKTAITDSPSFLGCRI 3050
Cdd:cd23189    161 ALKEGHPIGLKFLQDQLKFEDLLKVQPLLVYSDDLVLYAESPSFPNYHWWVEHLDLMLGFKTDPKKTVITDSPSFLGCRI 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3051 INGRQLVPNRDRILAALAYHMKASNVSEYYAAAAAILMDSCACLEYDPEWFEELVVGIAQCARKDGYSFPGPPFFLSMWE 3130
Cdd:cd23189    241 INGRQLVPNRDRLLAALAYHMKASNVSEYYASAAAILMDACACLEYDPEWFEDLVVGIAECARKDGYSFPGPPFFLFMWE 320


                   ...
gi 1773654335 3131 KLR 3133
Cdd:cd23189    321 KLG 323
NSP2-B_epitope pfam14757
Immunogenic region of nsp2 protein of arterivirus polyprotein; This domain is in a ...
 823-1069 1.07e-168

Immunogenic region of nsp2 protein of arterivirus polyprotein; This domain is in a non-essential part of the nsp2 (non-structural protein) subunit section of the arterivirus polyprotein. This domain carries seven small sequence-regions that are predicted to be potential B-cell epitopes.


Pssm-ID: 373272  Cd Length: 272  Bit Score: 520.55  E-value: 1.07e-168
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335  823 KTKSVKSLLENKPVPAPRRKVRSDCGSPILMGDNVPNGWEDSTVGGPLDLSAPSEPMTPLSEPVL------ISRPVTSLS 896
Cdd:pfam14757   20 KTKSVKSLPENKPVPAPRRKVRSDCGSPVLMGDNVPNGWEDLTVGGPLDLPTPSEPMTPLSEPVLvpalqhIPRPVTPLS 99

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335  897 VPAPVPAPRRAVSRPMTPSSEPIFVSALRHKFQQVEKANLAAAAPMYQDEPLDLSASSQTEYEASPLTPPQNVGILEVRG 976
Cdd:pfam14757  100 GPAPVPAPRRTVSRPMTPLSEPIFVSAPRHKFQQVEEANLAATTLTCQDEPLDLSASSQTEYEASPLAPLQNMGILEAGG 179

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335  977 QEAEEVLSEISDILNDTNPAPVSSSSSLSSVRITRPKYSAQAIIDSGGPCSGHLQREKEACLRIMREACDAAKLSDPATQ 1056
Cdd:pfam14757  180 QEAEEVLSEISDILNDINPAPVSSSSSLSSVKITRPKYSAQAIIDSGGPCSGHLQKEKEACLSIMREACDATKLSDPATQ 259

                          250
                   ....*....|...
gi 1773654335 1057 EWLSRMWDRVDML 1069
Cdd:pfam14757  260 EWLSRMWDRVDML 272
Peptidase_S32 pfam05579
Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing ...
 1711-2008 9.87e-163

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


Pssm-ID: 253263  Cd Length: 297  Bit Score: 504.70  E-value: 9.87e-163
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 1711 LTILWLVFFLISVNMPSGILAVVLLVSLWLLGRYTNIAGLVTPYDIHHYTSGPRGVAALATAPDGTYLAAVRRAALTGRT 1790
Cdd:pfam05579    1 LTMLWVQFFLVFVNFWAGVAALVVLISLWLLARYTNVAGLVTPYDIHLVTSSPRGAAALATAPEGTYLAAVRRAALTGRT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 1791 MLFTPSQLGSLLEGAFRTRKPSLNTVNVVGSSMGSGGVFTIDGKIRCVTAAHVLTGNSARVSGVGFNQMLDFDVKGDFAI 1870
Cdd:pfam05579   81 CLFVPSNFGSVLEGLFRTRKPALNVVSVFGSSSGSGGVFTINGNVVVVTASHVLGGNKARVSGVGFNQMLTFKTNGDYAF 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 1871 ADCPNWQGAAPKTQFCaDGWTGRAYWLTSSGVEPGVIGSGFAFCFTACGDSGSPVITEAGELVGVHTGSNKQGGGIVTRP 1950
Cdd:pfam05579  161 AVVAEWPGAAPKLKFA-QGYTGRAYWSTSTGVEPGLLGKGFAFCFTKCGDSGSPVITEDGNLVGVHTGSNKRGSGMVTTP 239

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1773654335 1951 SGQFCNVAPIKLSELSEFFAGPKVPLGDVKVGSHIIKDTCEVPSDLCALLAAKPELEG 2008
Cdd:pfam05579  240 SGKTLGMAPVKLSELSKHFAGPGVPVPTVKLPKNIIVDVEAVPSDLAALLESLPNLEG 297
Pdase_C33_assoc pfam14756
Peptidase_C33-associated domain; The nsps or non-structural protein subunits of the ...
 536-682 3.15e-96

Peptidase_C33-associated domain; The nsps or non-structural protein subunits of the arteriviral polyproteins such as porcine arterivirus PRRSV and equine arterivirus EAV are auto-cleaved into functional units. the function of this particular domain is not known.


Pssm-ID: 258893  Cd Length: 147  Bit Score: 307.34  E-value: 3.15e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335  536 GFPDVVEVSGFDPACLDRLAEIMHLPSSVIPAALAEMSDDFNRLASPAATVWTVSQFFARHRGGEHPDQVCLGKIINLCQ 615
Cdd:pfam14756    1 GSPDAVEVSGFDPACLDRLAGVMHLPSSAIPAALAELSGDSDRPVSPATTVWTVSQFYARHSGGEHPDQVCLGKIISLCQ 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1773654335  616 VIEECCCSRNKANRATPEEVAAKIDQYLRGAASLGECLAKLEMARPPSAMDTSFDWNVVLPGVETAN 682
Cdd:pfam14756   81 VIEDCCCSQNKTNRVTPEEVAAKIDQYLRGAASLEECLARLEKARPPSVLDTSFDWDVVLPGVEAAN 147
NendoU_av_Nsp11-like cd21160
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV ...
 3681-3799 3.77e-77

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: 251.47  E-value: 3.77e-77
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3681 FSTGRIEVDCRGYLDDREREVAESLPHAFIGDVKGTTVGGCHHVTSKYLPRFLPKESVAVVGVSSPGKAAKAVCTLTDVY 3760
Cdd:cd21160      1 FSTGRFELNSREYLDEGEREFAKKHPHAFIGDIKGTTVGGCHHITSKYLPPVLPAGSVVKVGVSSPGKAAKALCTVTDVY 80

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1773654335 3761 LPDLEAYLHPETQSKCWKVMLDFKEVRLMVWKDKTAYFQ 3799
Cdd:cd21160     81 LPYLEPYLNPPTQSKVYKVNIDFKPVRLMVWKDATMYFQ 119
Peptidase_C32 pfam05411
Equine arteritis virus putative proteinase; These proteins are characterized by a region that ...
 256-382 1.46e-73

Equine arteritis virus putative proteinase; These proteins are characterized by a region that has been proposed to have peptidase activity involved in viral polyprotein processing in replication.


Pssm-ID: 398854  Cd Length: 127  Bit Score: 241.68  E-value: 1.46e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335  256 QHGCLPADTVPEGNCWWCLFDLLPPEVQNKEIRRANQFGYQTKHGVPGKYLQRRLQVNGLRAVTDTDGPIVVQYFSVRES 335
Cdd:pfam05411    1 QHGCLPADTVPEGKCWLKLFDHLPWEVQCKEIRLADQFGYQTKHGVQGKYLQRRLQVNGLRAVVDQNGPIIVQAFSVPES 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1773654335  336 WIRHFRLAEEPSLPGFEDLLRIRVEPNTSPLGGKGEKIFRFGSHKWY 382
Cdd:pfam05411   81 WIRHLKLADEPVPPGFVDLLRFRVVPNTEPLAKTPEKIFRFGSHKWY 127
DEXXYc_viral_SF1-N cd17937
DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ...
 3279-3414 4.12e-72

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: 238.10  E-value: 4.12e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3279 LRSRFIIGPPGAGKTYWLLQQVQDGDVIYTPTHQTMLDMIRALGTCRFNVPAGTT-LQFPAPSRTGPWVRILAGGWCPGK 3357
Cdd:cd17937      1 AASTYIEGPPGCGKTFWLKKLVQPNDVLYVPTHATMLDMIKSLGPCRFVVPFGAPdLDFPTPSSSGPTVRLLAVGYTPGG 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1773654335 3358 NSFLDEAAYCNHLDVLRLLSKTTLTCLGDFKQLHPVGFDSHCYVFDIMPQTQLKTIW 3414
Cdd:cd17937     81 KAFVDEACYCNPVDLARLLTQTPVTAFGDPNQLGPVGFASVFFLVDLMQREQLNVIY 137
Peptidase_C31 pfam05410
Porcine arterivirus-type cysteine proteinase alpha; Corresponds to Merops family C31. These ...
 57-161 2.16e-67

Porcine arterivirus-type cysteine proteinase alpha; Corresponds to Merops family C31. These peptidases are involved in viral polyprotein processing in replication.


Pssm-ID: 461643  Cd Length: 105  Bit Score: 223.26  E-value: 2.16e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335   57 LRWTLPRAFPTVECSPAGACWLSAIFPIARMTSGNLNFQQRMVRVAAEIYRAGQLTPAVLKALQVYERGCRWYPIVGPVP 136
Cdd:pfam05410    1 LTWEAPITYPTVECRPGGLCWLSAIFPIARMTSGNHNFQQRLVFVASVVYRDGKLTPKHLEELQVYERGCRWYPITGPVP 80

                           90       100
                   ....*....|....*....|....*
gi 1773654335  137 GVAVHANSLHVSDKPFPGATHVLTN 161
Cdd:pfam05410   81 GIALYANSVHVSDEPFPGATHVLTN 105
Arteri_nsp7a pfam16749
Arterivirus nonstructural protein 7 alpha; Nonstructural protein 7 alpha is likely to have a ...
 2195-2322 3.11e-65

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: 218.04  E-value: 3.11e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2195 LTGALAMRLNDEDLDFLTKWTDFKCFVSASNMRNAAGQFIEAAYAKALRIELAQLVQVDKVRGTLAKLEAFADTVAPQLS 2274
Cdd:pfam16749    1 LTAALACALSDDDLDFLSQLVDCKAFVSASNMRNALGDFIESAYAKALRASLASVVAVAKSRRALAKLEDFADTVSPQLS 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1773654335 2275 PGDIVVALGHTPVGSIFDLKVGGTKHTLQVIETRVLAGSKMTVARVVD 2322
Cdd:pfam16749   81 PGDPVVLLGKTPVGEIFDIYVGDTKHVLRPIETRVVAGSKCTICTVVV 128
Peptidase_C33 pfam05412
Equine arterivirus Nsp2-type cysteine proteinase; Corresponds to Merops family C33. These ...
 429-535 2.92e-59

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: 200.14  E-value: 2.92e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335  429 YSPPADGNCGWHCISAITNRMVNSKFETTLPERVRPSDDWATDEDLVNAIQILRLPAALDRNGACAGAKYVLKLEGEHWT 508
Cdd:pfam05412    2 YSPPGDGACGWHCISAIANRMFNDKFTTTLTECSRPSDDWASDQDLVQAIQTLRLPATLDRNGACPSAKYKLKLVGQHWT 81

                           90       100
                   ....*....|....*....|....*..
gi 1773654335  509 VSVTPGMTPSLLPLECVQGCCEHTSGL 535
Cdd:pfam05412   82 VTVRKGMAPGLLSPECVRGVCGHEGGL 108
NTD_av_Nsp11-like cd21166
N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; ...
 3581-3683 2.50e-51

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: 177.14  E-value: 2.50e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3581 SSPLPKVAHNLGFYFSPDLTQFAKLPVDLAPHWPVVTTQNnekWPDRLVASLRPVHKYSRACIGAGYMVGPSVFLGTPGV 3660
Cdd:cd21166      1 PSPLPRVAHNLGFHFSPDLPGFPPIPEELAEHWPVVTNDN---WPNRLVVSLAPIDELSKPCISAGYYVGQSVFVGTPGV 77

                           90       100
                   ....*....|....*....|...
gi 1773654335 3661 VSYYLTKFVKGEAQVLPETVFST 3683
Cdd:cd21166     78 TSYYLTLFVDGKARALPDSLFST 100
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 2704-3110 1.60e-41

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: 161.04  E-value: 1.60e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2704 YVPTIPASVLDYL--DSRPDCPKQLTEHGCEDAALRDLSKYDLSTQGFVLPGVLRLVRKYLFAHVGKCPPVHRPSTYPAK 2781
Cdd:pfam00680   18 LGPEDPRWARSYLntDPYVDDIKKYSRPKLPGPADERDKLLNRSAAKMVLSELRGVPKKANSTLIVYRAIDGVEQIDPLN 97

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2782 -NSMAGINGNRFPTK------DIQSVPEIDVLCAQ--AVRENWQTVTPCTLKKQYCGKK-----------KTRTILGTNN 2841
Cdd:pfam00680   98 wDTSAGYPYVGLGGKkgdlieHLKDGTEARELAERlaADWEVLQNGTPLKLVYQTCLKDelrplekvekgKTRLVWGEPV 177

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2842 FIALAHRAALSGVTQGFMKKAFNSPIALGKNKFkELQTPVLGR--------CLEADLASCDRSTPAIVRWFAANLLYELA 2913
Cdd:pfam00680  178 EYLLLERAFFDPFNQAFMLNNGFHPIQVGINPF-DRGWPRLLRrlarfgdyVYELDYSGFDSSVPPWLIRFAFEILRELL 256

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2914 CAEEHLPSYVLN----CCHDLLVTQSGAVTKRGGLSSGDPITSVSNTIYSlVIYAQHMVLSYFKSGHPHGLLFlqdqlkf 2989
Cdd:pfam00680  257 GFPSNVKEWRAIlellIYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVN-YLLILYALLKSLENDGPRVCNL------- 328

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2990 edmLKVQPLIVYSDDLVLYAESPTMPNYHWWVEHLNLmLGFQTDPKKTAITDSP-----SFLGCRIINGRQLV---PNRD 3061
Cdd:pfam00680  329 ---DKYFDFFTYGDDSLVAVSPDFDPVLDRLSPHLKE-LGLTITPAKKTFPVSReleevSFLKRTFRKTPGGYrppLDRK 404

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3062 RILAALAY-HMKASNVSEYYAAAAAILMdscacleYDPEWFEELVVGIAQ 3110
Cdd:pfam00680  405 RILAQLEYiRSKPVPSGQLENIRAYASH-------HGYEFYRDLLYRFVE 447
ZBD_av_Nsp10-like cd21405
Cys/His rich zinc-binding domain (CH/ZBD) of arterivirus EAV Nsp10 helicase and related ...
 3142-3202 2.37e-30

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: 115.50  E-value: 2.37e-30
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1773654335 3142 RMCGYCGAPAPYATACGLDVCIYHTHFHQHCPVIIW-CGHPAGSGSCSECKPPLGKGTSPLD 3202
Cdd:cd21405      1 RVCGICGSTAVTTSACGLDLCAYHAHFHQHCPVTSPfCGHPIGSKSCTMCSIPVVPGNDELD 62
av_Nsp3_ER-remodelling cd22528
intracellular membrane remodeller motif of arterivirus non-structural protein 3 (Nsp3); This ...
 1594-1651 3.23e-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: 89.30  E-value: 3.23e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1773654335 1594 GVYVTSVGSCGAGTNDPWCTNPFAVPGYGPGSLCTSRLCISQHGLTLPlTALVAGFGL 1651
Cdd:cd22528      1 GLYLQSPVSCGIGTNDPFCRNPFGVPVVGTQGVCHSGYCASAQGISLP-TSLLTQLSS 57
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 3450-3509 4.97e-21

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: 90.19  E-value: 4.97e-21
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1773654335 3450 YGQVLTPYHRDR------------------EDGAITIDSSQGATFDVVTLHLPTKDSLNRQRALVAITRARHAIFVYD 3509
Cdd:cd18786     12 KGVVLTPYHRDRaylnqylqglsldefdlqLVGAITIDSSQGLTFDVVTLYLPTANSLTPRRLYVALTRARKRLVIYD 89
1B_av_Nsp10-like cd21410
1B domain of arterivirus EAV Nsp10 helicase and related proteins; Helicases catalyze ...
 3214-3262 4.62e-18

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: 80.36  E-value: 4.62e-18
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1773654335 3214 RTVIMHVEQGLTPLDPGRYQTRRGLVSVRRGIRGNEVDLPDGDYASTAL 3262
Cdd:cd21410      1 VEVTVEVVDGVTSAAPGRYQTRHGVVMVRRDIGGCIVDLPDGEYQVTPL 49
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 3286-3509 5.96e-10

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: 62.40  E-value: 5.96e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3286 GPPGAGKTYWLLQQVQDGdVIYTPTHqtmldmirALGTCRFNVPagttlqfpaPSRTGPWVR--ILAGGWCPGKNSFLDE 3363
Cdd:pfam01443    5 GVPGCGKSTLIRKLLRTS-RVIRPTA--------ELRTEGKPDL---------PNLNVRTVDtfLMALLKPTGKILILDE 66

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3364 ---AAYCNHLDVLRLLSKTTLTCLGDFKQLHPVGFDSHCYVfdimPQTQLKTIWRFGQNICDAIQPDYRDKLVSM---VN 3437
Cdd:pfam01443   67 ytlLPPGYILLLAAISGAKLVILFGDPLQIPYHSRAPSFLI----PHFPSSLSHRVGRRTTYLLPSLRAPILSAKgfeVV 142

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3438 TTR-----VTYVEKPVKYGQVLTPYHRDRED---GAITIDSSQGATFDVVTLHLPTKDSL-----NRQRALVAITRARHA 3504
Cdd:pfam01443  143 VERsgeykVDYDPNGVLVLVYLTFTQALKESlgvRVTTVHEVQGLTFDSVTLVLDTDTDLliisdSPEHLYVALTRHRKS 222


                   ....*
gi 1773654335 3505 IFVYD 3509
Cdd:pfam01443  223 LHILT 227
CoV_NSP15_C pfam19215
Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the ...
 3679-3797 7.12e-09

Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the C-terminal domain of coronavirus non-structural protein 15 (NSP15 or nsp15). NSP15 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. This domain exhibits endoribonuclease activity designated EndoU, highly conserved in all known CoVs and is part of the replicase-transcriptase complex that plays important roles in virus replication and transcription. NSP15 is a Uridylate-specific endoribonuclease that cleaves the 5'-polyuridines from negative-sense viral RNA, termed PUN RNA either upstream or downstream of uridylates, at GUU or GU to produce molecules with 2',3'-cyclic phosphate ends. PUN RNA is a CoV MDA5-dependent pathogen-associated molecular pattern (PAMP).


Pssm-ID: 465999  Cd Length: 155  Bit Score: 57.34  E-value: 7.12e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3679 TVFSTGRIEVDCRGyLDDREREVAESLPHAFI---------------GDVKGTTVGGCH-------------HVTSKYLP 3730
Cdd:pfam19215    2 TLFTQGRTLEDFVP-RSTMEKDFLNMDQQQFIqkygledlgfehivyGDFSKTTIGGLHllislvrltkmgiLKVEEFVP 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1773654335 3731 -RFLPKESVAVVGVSSPGkaAKAVCTLTDVYLPDLEA---YLHPETQSKCWKVMLDFKEVRLMVW-KD---KTAY 3797
Cdd:pfam19215   81 nDDSTVKNCSVTYANDGS--SKAVCTVLDLLLDDFVDilkSLDLSVVSKVVTVNIDFQPVRFMLWcKDgkvQTFY 153
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 3465-3517 7.83e-07

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 54.98  E-value: 7.83e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1773654335 3465 AITIDSSQGATFDVVTLHLPTKDS--LNRQRALVAITRARHAIFVYDPHRQLQSM 3517
Cdd:COG0507    444 AITVHKSQGSTFDRVILVLPSEHSplLSRELLYTALTRARELLTLVGDRDALARA 498
ND5 MTH00063
NADH dehydrogenase subunit 5; Provisional
 1235-1303 1.51e-03

NADH dehydrogenase subunit 5; Provisional


Pssm-ID: 214414 [Multi-domain]  Cd Length: 522  Bit Score: 44.48  E-value: 1.51e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 1235 VFFS-HLFKSDSGYSPGDWGFAAFTLFCLFLCYSYPFFGFVPLLGVFSGSSRRVRMGVFGCWLAFAVGLF 1303
Cdd:MTH00063   334 VFFSkHFLLSSFSSVVFNVSLLLVVILCVFLSYLYSFRLCLILFGVKSSLSSGVRFLFFNSGLMVFLWLF 403
UvrD_C_2 pfam13538
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ...
 3465-3508 6.59e-03

UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.


Pssm-ID: 463913 [Multi-domain]  Cd Length: 52  Bit Score: 37.55  E-value: 6.59e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1773654335 3465 AITIDSSQGATFDVVTLHLPTKDS-----LNRQRALVAITRARHAIFVY 3508
Cdd:pfam13538    4 ALTVHKAQGSEFPAVFLVDPDLTAhyhsmLRRRLLYTAVTRARKKLVLV 52
 
Name Accession Description Interval E-value
Arteriviridae_RdRp cd23189
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of ...
 2811-3133 0e+00

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: 657.41  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2811 VRENWQTVTPCTLKKQYCGKKKTRTILGTNNFIALAHRAALSGVTQGFMKKAFNSPIALGKNKFKELQTPVLGRCLEADL 2890
Cdd:cd23189      1 VRENWQTVTPCTLKKQYCSKKKTRTILGTNNLIALALRAALSGVTQGFMKAGFNSPIALGKNKFKPLQTPVLGRCLEADL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2891 ASCDRSTPAIVRWFAANLLYELACAEEHLPSYVLNCCHDLLVTQSGAVTKRGGLSSGDPITSVSNTIYSLVIYAQHMVLS 2970
Cdd:cd23189     81 ASCDRSTPAIVRWFAANLLFELACAEECLPSYVLNCCHDLLVTQSGAFTKRGGLSSGDPVTSISNTIYSLVIYTQHMVLS 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2971 YFKSGHPHGLLFLQDQLKFEDMLKVQPLIVYSDDLVLYAESPTMPNYHWWVEHLNLMLGFQTDPKKTAITDSPSFLGCRI 3050
Cdd:cd23189    161 ALKEGHPIGLKFLQDQLKFEDLLKVQPLLVYSDDLVLYAESPSFPNYHWWVEHLDLMLGFKTDPKKTVITDSPSFLGCRI 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3051 INGRQLVPNRDRILAALAYHMKASNVSEYYAAAAAILMDSCACLEYDPEWFEELVVGIAQCARKDGYSFPGPPFFLSMWE 3130
Cdd:cd23189    241 INGRQLVPNRDRLLAALAYHMKASNVSEYYASAAAILMDACACLEYDPEWFEDLVVGIAECARKDGYSFPGPPFFLFMWE 320


                   ...
gi 1773654335 3131 KLR 3133
Cdd:cd23189    321 KLG 323
NSP2-B_epitope pfam14757
Immunogenic region of nsp2 protein of arterivirus polyprotein; This domain is in a ...
 823-1069 1.07e-168

Immunogenic region of nsp2 protein of arterivirus polyprotein; This domain is in a non-essential part of the nsp2 (non-structural protein) subunit section of the arterivirus polyprotein. This domain carries seven small sequence-regions that are predicted to be potential B-cell epitopes.


Pssm-ID: 373272  Cd Length: 272  Bit Score: 520.55  E-value: 1.07e-168
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335  823 KTKSVKSLLENKPVPAPRRKVRSDCGSPILMGDNVPNGWEDSTVGGPLDLSAPSEPMTPLSEPVL------ISRPVTSLS 896
Cdd:pfam14757   20 KTKSVKSLPENKPVPAPRRKVRSDCGSPVLMGDNVPNGWEDLTVGGPLDLPTPSEPMTPLSEPVLvpalqhIPRPVTPLS 99

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335  897 VPAPVPAPRRAVSRPMTPSSEPIFVSALRHKFQQVEKANLAAAAPMYQDEPLDLSASSQTEYEASPLTPPQNVGILEVRG 976
Cdd:pfam14757  100 GPAPVPAPRRTVSRPMTPLSEPIFVSAPRHKFQQVEEANLAATTLTCQDEPLDLSASSQTEYEASPLAPLQNMGILEAGG 179

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335  977 QEAEEVLSEISDILNDTNPAPVSSSSSLSSVRITRPKYSAQAIIDSGGPCSGHLQREKEACLRIMREACDAAKLSDPATQ 1056
Cdd:pfam14757  180 QEAEEVLSEISDILNDINPAPVSSSSSLSSVKITRPKYSAQAIIDSGGPCSGHLQKEKEACLSIMREACDATKLSDPATQ 259

                          250
                   ....*....|...
gi 1773654335 1057 EWLSRMWDRVDML 1069
Cdd:pfam14757  260 EWLSRMWDRVDML 272
Peptidase_S32 pfam05579
Equine arteritis virus serine endopeptidase S32; Serine peptidases involved in processing ...
 1711-2008 9.87e-163

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


Pssm-ID: 253263  Cd Length: 297  Bit Score: 504.70  E-value: 9.87e-163
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 1711 LTILWLVFFLISVNMPSGILAVVLLVSLWLLGRYTNIAGLVTPYDIHHYTSGPRGVAALATAPDGTYLAAVRRAALTGRT 1790
Cdd:pfam05579    1 LTMLWVQFFLVFVNFWAGVAALVVLISLWLLARYTNVAGLVTPYDIHLVTSSPRGAAALATAPEGTYLAAVRRAALTGRT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 1791 MLFTPSQLGSLLEGAFRTRKPSLNTVNVVGSSMGSGGVFTIDGKIRCVTAAHVLTGNSARVSGVGFNQMLDFDVKGDFAI 1870
Cdd:pfam05579   81 CLFVPSNFGSVLEGLFRTRKPALNVVSVFGSSSGSGGVFTINGNVVVVTASHVLGGNKARVSGVGFNQMLTFKTNGDYAF 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 1871 ADCPNWQGAAPKTQFCaDGWTGRAYWLTSSGVEPGVIGSGFAFCFTACGDSGSPVITEAGELVGVHTGSNKQGGGIVTRP 1950
Cdd:pfam05579  161 AVVAEWPGAAPKLKFA-QGYTGRAYWSTSTGVEPGLLGKGFAFCFTKCGDSGSPVITEDGNLVGVHTGSNKRGSGMVTTP 239

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1773654335 1951 SGQFCNVAPIKLSELSEFFAGPKVPLGDVKVGSHIIKDTCEVPSDLCALLAAKPELEG 2008
Cdd:pfam05579  240 SGKTLGMAPVKLSELSKHFAGPGVPVPTVKLPKNIIVDVEAVPSDLAALLESLPNLEG 297
Pdase_C33_assoc pfam14756
Peptidase_C33-associated domain; The nsps or non-structural protein subunits of the ...
 536-682 3.15e-96

Peptidase_C33-associated domain; The nsps or non-structural protein subunits of the arteriviral polyproteins such as porcine arterivirus PRRSV and equine arterivirus EAV are auto-cleaved into functional units. the function of this particular domain is not known.


Pssm-ID: 258893  Cd Length: 147  Bit Score: 307.34  E-value: 3.15e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335  536 GFPDVVEVSGFDPACLDRLAEIMHLPSSVIPAALAEMSDDFNRLASPAATVWTVSQFFARHRGGEHPDQVCLGKIINLCQ 615
Cdd:pfam14756    1 GSPDAVEVSGFDPACLDRLAGVMHLPSSAIPAALAELSGDSDRPVSPATTVWTVSQFYARHSGGEHPDQVCLGKIISLCQ 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1773654335  616 VIEECCCSRNKANRATPEEVAAKIDQYLRGAASLGECLAKLEMARPPSAMDTSFDWNVVLPGVETAN 682
Cdd:pfam14756   81 VIEDCCCSQNKTNRVTPEEVAAKIDQYLRGAASLEECLARLEKARPPSVLDTSFDWDVVLPGVEAAN 147
NendoU_av_Nsp11-like cd21160
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV ...
 3681-3799 3.77e-77

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: 251.47  E-value: 3.77e-77
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3681 FSTGRIEVDCRGYLDDREREVAESLPHAFIGDVKGTTVGGCHHVTSKYLPRFLPKESVAVVGVSSPGKAAKAVCTLTDVY 3760
Cdd:cd21160      1 FSTGRFELNSREYLDEGEREFAKKHPHAFIGDIKGTTVGGCHHITSKYLPPVLPAGSVVKVGVSSPGKAAKALCTVTDVY 80

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1773654335 3761 LPDLEAYLHPETQSKCWKVMLDFKEVRLMVWKDKTAYFQ 3799
Cdd:cd21160     81 LPYLEPYLNPPTQSKVYKVNIDFKPVRLMVWKDATMYFQ 119
Peptidase_C32 pfam05411
Equine arteritis virus putative proteinase; These proteins are characterized by a region that ...
 256-382 1.46e-73

Equine arteritis virus putative proteinase; These proteins are characterized by a region that has been proposed to have peptidase activity involved in viral polyprotein processing in replication.


Pssm-ID: 398854  Cd Length: 127  Bit Score: 241.68  E-value: 1.46e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335  256 QHGCLPADTVPEGNCWWCLFDLLPPEVQNKEIRRANQFGYQTKHGVPGKYLQRRLQVNGLRAVTDTDGPIVVQYFSVRES 335
Cdd:pfam05411    1 QHGCLPADTVPEGKCWLKLFDHLPWEVQCKEIRLADQFGYQTKHGVQGKYLQRRLQVNGLRAVVDQNGPIIVQAFSVPES 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 1773654335  336 WIRHFRLAEEPSLPGFEDLLRIRVEPNTSPLGGKGEKIFRFGSHKWY 382
Cdd:pfam05411   81 WIRHLKLADEPVPPGFVDLLRFRVVPNTEPLAKTPEKIFRFGSHKWY 127
DEXXYc_viral_SF1-N cd17937
DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ...
 3279-3414 4.12e-72

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: 238.10  E-value: 4.12e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3279 LRSRFIIGPPGAGKTYWLLQQVQDGDVIYTPTHQTMLDMIRALGTCRFNVPAGTT-LQFPAPSRTGPWVRILAGGWCPGK 3357
Cdd:cd17937      1 AASTYIEGPPGCGKTFWLKKLVQPNDVLYVPTHATMLDMIKSLGPCRFVVPFGAPdLDFPTPSSSGPTVRLLAVGYTPGG 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1773654335 3358 NSFLDEAAYCNHLDVLRLLSKTTLTCLGDFKQLHPVGFDSHCYVFDIMPQTQLKTIW 3414
Cdd:cd17937     81 KAFVDEACYCNPVDLARLLTQTPVTAFGDPNQLGPVGFASVFFLVDLMQREQLNVIY 137
Peptidase_C31 pfam05410
Porcine arterivirus-type cysteine proteinase alpha; Corresponds to Merops family C31. These ...
 57-161 2.16e-67

Porcine arterivirus-type cysteine proteinase alpha; Corresponds to Merops family C31. These peptidases are involved in viral polyprotein processing in replication.


Pssm-ID: 461643  Cd Length: 105  Bit Score: 223.26  E-value: 2.16e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335   57 LRWTLPRAFPTVECSPAGACWLSAIFPIARMTSGNLNFQQRMVRVAAEIYRAGQLTPAVLKALQVYERGCRWYPIVGPVP 136
Cdd:pfam05410    1 LTWEAPITYPTVECRPGGLCWLSAIFPIARMTSGNHNFQQRLVFVASVVYRDGKLTPKHLEELQVYERGCRWYPITGPVP 80

                           90       100
                   ....*....|....*....|....*
gi 1773654335  137 GVAVHANSLHVSDKPFPGATHVLTN 161
Cdd:pfam05410   81 GIALYANSVHVSDEPFPGATHVLTN 105
Arteri_nsp7a pfam16749
Arterivirus nonstructural protein 7 alpha; Nonstructural protein 7 alpha is likely to have a ...
 2195-2322 3.11e-65

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: 218.04  E-value: 3.11e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2195 LTGALAMRLNDEDLDFLTKWTDFKCFVSASNMRNAAGQFIEAAYAKALRIELAQLVQVDKVRGTLAKLEAFADTVAPQLS 2274
Cdd:pfam16749    1 LTAALACALSDDDLDFLSQLVDCKAFVSASNMRNALGDFIESAYAKALRASLASVVAVAKSRRALAKLEDFADTVSPQLS 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1773654335 2275 PGDIVVALGHTPVGSIFDLKVGGTKHTLQVIETRVLAGSKMTVARVVD 2322
Cdd:pfam16749   81 PGDPVVLLGKTPVGEIFDIYVGDTKHVLRPIETRVVAGSKCTICTVVV 128
Peptidase_C33 pfam05412
Equine arterivirus Nsp2-type cysteine proteinase; Corresponds to Merops family C33. These ...
 429-535 2.92e-59

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: 200.14  E-value: 2.92e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335  429 YSPPADGNCGWHCISAITNRMVNSKFETTLPERVRPSDDWATDEDLVNAIQILRLPAALDRNGACAGAKYVLKLEGEHWT 508
Cdd:pfam05412    2 YSPPGDGACGWHCISAIANRMFNDKFTTTLTECSRPSDDWASDQDLVQAIQTLRLPATLDRNGACPSAKYKLKLVGQHWT 81

                           90       100
                   ....*....|....*....|....*..
gi 1773654335  509 VSVTPGMTPSLLPLECVQGCCEHTSGL 535
Cdd:pfam05412   82 VTVRKGMAPGLLSPECVRGVCGHEGGL 108
NTD_av_Nsp11-like cd21166
N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; ...
 3581-3683 2.50e-51

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: 177.14  E-value: 2.50e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3581 SSPLPKVAHNLGFYFSPDLTQFAKLPVDLAPHWPVVTTQNnekWPDRLVASLRPVHKYSRACIGAGYMVGPSVFLGTPGV 3660
Cdd:cd21166      1 PSPLPRVAHNLGFHFSPDLPGFPPIPEELAEHWPVVTNDN---WPNRLVVSLAPIDELSKPCISAGYYVGQSVFVGTPGV 77

                           90       100
                   ....*....|....*....|...
gi 1773654335 3661 VSYYLTKFVKGEAQVLPETVFST 3683
Cdd:cd21166     78 TSYYLTLFVDGKARALPDSLFST 100
NendoU_nv cd21158
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural ...
 3681-3799 1.74e-43

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: 156.65  E-value: 1.74e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3681 FSTGRIEvDCRGYLDDREREVA---------------ESLPHAFIGDVKGTTVGGCHHVTSKY-------LPRFLPK--- 3735
Cdd:cd21158      1 FTQGRNL-QEFLPRSDMERDFLpvdmdvfiekygleiYAFEHVVYGDFSHTTLGGLHLVISLYkrfkegpLPREEFIpnd 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1773654335 3736 ESVAVVGVSSPG-KAAKAVCTLTDVYLPDLEAYLHP---ETQSKCWKVMLDFKEVRLMVWKD----KTAYFQ 3799
Cdd:cd21158     80 STVKNYGVTSPGtKASKAVCTLIDLLLDDFVEILKSqdlEVVSKVVKVMIDFKEVRFMLWCKdgdvQTFYPQ 151
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 2704-3110 1.60e-41

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: 161.04  E-value: 1.60e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2704 YVPTIPASVLDYL--DSRPDCPKQLTEHGCEDAALRDLSKYDLSTQGFVLPGVLRLVRKYLFAHVGKCPPVHRPSTYPAK 2781
Cdd:pfam00680   18 LGPEDPRWARSYLntDPYVDDIKKYSRPKLPGPADERDKLLNRSAAKMVLSELRGVPKKANSTLIVYRAIDGVEQIDPLN 97

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2782 -NSMAGINGNRFPTK------DIQSVPEIDVLCAQ--AVRENWQTVTPCTLKKQYCGKK-----------KTRTILGTNN 2841
Cdd:pfam00680   98 wDTSAGYPYVGLGGKkgdlieHLKDGTEARELAERlaADWEVLQNGTPLKLVYQTCLKDelrplekvekgKTRLVWGEPV 177

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2842 FIALAHRAALSGVTQGFMKKAFNSPIALGKNKFkELQTPVLGR--------CLEADLASCDRSTPAIVRWFAANLLYELA 2913
Cdd:pfam00680  178 EYLLLERAFFDPFNQAFMLNNGFHPIQVGINPF-DRGWPRLLRrlarfgdyVYELDYSGFDSSVPPWLIRFAFEILRELL 256

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2914 CAEEHLPSYVLN----CCHDLLVTQSGAVTKRGGLSSGDPITSVSNTIYSlVIYAQHMVLSYFKSGHPHGLLFlqdqlkf 2989
Cdd:pfam00680  257 GFPSNVKEWRAIlellIYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVN-YLLILYALLKSLENDGPRVCNL------- 328

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2990 edmLKVQPLIVYSDDLVLYAESPTMPNYHWWVEHLNLmLGFQTDPKKTAITDSP-----SFLGCRIINGRQLV---PNRD 3061
Cdd:pfam00680  329 ---DKYFDFFTYGDDSLVAVSPDFDPVLDRLSPHLKE-LGLTITPAKKTFPVSReleevSFLKRTFRKTPGGYrppLDRK 404

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3062 RILAALAY-HMKASNVSEYYAAAAAILMdscacleYDPEWFEELVVGIAQ 3110
Cdd:pfam00680  405 RILAQLEYiRSKPVPSGQLENIRAYASH-------HGYEFYRDLLYRFVE 447
ps-ssRNAv_Nidovirales_RdRp cd23168
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Nidovirales of ...
 2817-3077 7.25e-33

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: 131.71  E-value: 7.25e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2817 TVTPCTLKKQYCGKKKTRTILGTNNFIALAHRAALSGVTQgFMKKAFNSPIALGKNKF-----KELQTPVLGR-----CL 2886
Cdd:cd23168      1 TLTQVNPKYAIQKKKRARTILGVSIISTDVGRQLHQAVLA-AIVNTRSANIVIIGTKFyggwhKMLRYLYPGViedpvLM 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2887 EADLASCDRSTPAIVRWFAANLLYEL---ACAEEHLP-SYVLNCCH---DLLVTQSGAVTKRGGLSSGDPITSVSNTIYS 2959
Cdd:cd23168     80 GWDYPKCDRSVPNMLRYLANLLLASLydnCCNLSEIVhLLINECAQvlyDYVVYGGNLYRKPGGVSSGDSTTAISNSIYN 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2960 LVIYAQHMVLSYFksghphgllflqdqlkfedmlkvqplivYSDDLVLYAESPTMPNYHW-WVEHLNLMLGFQTDPKKTA 3038
Cdd:cd23168    160 YFQTFIANVRLAI----------------------------LSDDGVACINPDLIDLGDVaSVSFFLASYYYTNNKKKYS 211

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1773654335 3039 ITDSPSFLGCR-----IING---------RQLVPNRDRILAALAYHMKASNVS 3077
Cdd:cd23168    212 STCWVEPHEFCsphefKSDDkyqdrvervYLPIPDPSRMLSACLLVDTRTKTD 264
ZBD_av_Nsp10-like cd21405
Cys/His rich zinc-binding domain (CH/ZBD) of arterivirus EAV Nsp10 helicase and related ...
 3142-3202 2.37e-30

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: 115.50  E-value: 2.37e-30
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1773654335 3142 RMCGYCGAPAPYATACGLDVCIYHTHFHQHCPVIIW-CGHPAGSGSCSECKPPLGKGTSPLD 3202
Cdd:cd21405      1 RVCGICGSTAVTTSACGLDLCAYHAHFHQHCPVTSPfCGHPIGSKSCTMCSIPVVPGNDELD 62
M_cv_Nsp15-NTD_av_Nsp11-like cd21163
middle (M) domain of coronavirus Nonstructural protein 15 (Nsp15) and the N-terminal domain ...
 3581-3683 9.84e-27

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: 107.80  E-value: 9.84e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3581 SSPLPKVAHNLGFYFSPDLTQF--------------AKLPVDLAPHWPVVTTQNNE-------KWPDRLVASLRPVHKYS 3639
Cdd:cd21163      1 STPLPKVLRNLGVDFTPNFVLWdyedtapffnttvcKYTPEELCEHLPVLYDDRYGgslerflSAPNAVLISLTKVKKYS 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1773654335 3640 RACIgAGYMVGPSVFLGTPGVVSYYLTKFVKGEAQVLPETVFST 3683
Cdd:cd21163     81 IPPP-AGAYLNGSVVVGTPKVVSFYLYKRKDGKFVTLPDTLFTQ 123
Tobaniviridae_RdRp cd23186
catalytic core domain of RNA-dependent RNA polymerase (RdRP) in the Tobaniviridae family of ...
 2742-3152 3.46e-22

catalytic core domain of RNA-dependent RNA polymerase (RdRP) in the Tobaniviridae family of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Tobaniviridae, order Nidovirales. Tobaniviridae RNA viruses infect vertebrates; their host organisms include mammals, fish, and snakes. Member viruses have a viral envelope and (+)ssRNA genome. The genome size of Tobaniviruses ranges from 20 to 32 kilobases. The family is the only member of the suborder Tornidovirineae. The family Tobaniviridae has four subfamilies (Piscanivirinae, Remotovirinae, Remotovirinae, and Torovirinae) and eight genera (Bafinivirus, Oncotshavirus, Bostovirus, Infratovirus, Pregotovirus, Sectovirus, Tiruvirus, and Torovirus). The Tobaniviridae family belongs to the order Nidovirales, which currently comprises 88 formally recognized virus species of (+)ssRNA viruses, which are classified into nine virus families across seven different suborders. The structure of Tobaniviridae RdRp contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438036  Cd Length: 401  Bit Score: 102.47  E-value: 3.46e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2742 YDLSTQGFVLPGVLRLVRKYLFAHVGKCPPVHRPSTY-PAKNSM--AGINGNRFPTKDI-QSVPE--IDVLCAQAVRENW 2815
Cdd:cd23186      2 YDYQGPLFLDPHILKFLYEYMLKDFSSYATDARFTYHePGKPRLssMGVGLRGFKQDAVyQALPEdfIDRLLELAKKTPL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2816 QTVTPCTLKKQYCGKKKTRTILGTNNFIALAHRAALSGVTQGFMKKAFN---------SPIALGKNKFKELQTPVLGRC- 2885
Cdd:cd23186     82 PFSTKIITKFALTKKARARTIAACSFIASTIFRFLHKPVTNNMVKQAQNnighcligvSKFNLGFDKFLRSRYGGIEDYn 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2886 -LEADLASCDRSTPAIVRWFAANLLYELAcaeeHLPSY---VLNCCHDLLVTQ---SGAV-TKRGGLSSGDPITSVSNTI 2957
Cdd:cd23186    162 vFGSDYTKCDRSFPLVFRALAAALLYELG----GWDPKnhlFVNEIFAFMLDFvfiGGHIfNKPGGTSSGDATTAFSNTL 237

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2958 YSlviyaqHMVLSYFKSGHPHGLLFLqdqlkfedmlkvqplivySDDLVLYA--ESPTMPNYHWWVEHLNLMLGFQTDPK 3035
Cdd:cd23186    238 YN------YMVHLYVQFQTFYFFNFL------------------SDDSFILSkpEAFPIFTTENFSRKLQTILHTTVDQT 293

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3036 K--TAITDSPSFLGCRI--INGR-QLVPNRDRILAALAYHMKASNVSEYYAAAAAILmdscacleydpewfEELVVgiaq 3110
Cdd:cd23186    294 KawSASGHIHEFCSSHIeeVNGVyQFIPDPNRLLAGLLITGKASDVDLDIWRTVAIL--------------AELAV---- 355

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|..
gi 1773654335 3111 carkdgYSFPGPPFFLSMWEKLRSNHEGKKSRmcgYCGAPAP 3152
Cdd:cd23186    356 ------YSRVDPAFFNALFQLFQNKHAEFVTK---YGVNPLP 388
av_Nsp3_ER-remodelling cd22528
intracellular membrane remodeller motif of arterivirus non-structural protein 3 (Nsp3); This ...
 1594-1651 3.23e-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: 89.30  E-value: 3.23e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1773654335 1594 GVYVTSVGSCGAGTNDPWCTNPFAVPGYGPGSLCTSRLCISQHGLTLPlTALVAGFGL 1651
Cdd:cd22528      1 GLYLQSPVSCGIGTNDPFCRNPFGVPVVGTQGVCHSGYCASAQGISLP-TSLLTQLSS 57
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 3450-3509 4.97e-21

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: 90.19  E-value: 4.97e-21
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1773654335 3450 YGQVLTPYHRDR------------------EDGAITIDSSQGATFDVVTLHLPTKDSLNRQRALVAITRARHAIFVYD 3509
Cdd:cd18786     12 KGVVLTPYHRDRaylnqylqglsldefdlqLVGAITIDSSQGLTFDVVTLYLPTANSLTPRRLYVALTRARKRLVIYD 89
1B_av_Nsp10-like cd21410
1B domain of arterivirus EAV Nsp10 helicase and related proteins; Helicases catalyze ...
 3214-3262 4.62e-18

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: 80.36  E-value: 4.62e-18
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1773654335 3214 RTVIMHVEQGLTPLDPGRYQTRRGLVSVRRGIRGNEVDLPDGDYASTAL 3262
Cdd:cd21410      1 VEVTVEVVDGVTSAAPGRYQTRHGVVMVRRDIGGCIVDLPDGEYQVTPL 49
1B_nv_SF1_Hel-like cd21406
1B domain of nidovirus helicases including coronavirus Nsp13 and arterivirus Nsp10, and ...
 3216-3262 4.04e-15

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: 71.82  E-value: 4.04e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1773654335 3216 VIMHVEQGLTPLDPGRYQTRRGLVSVRRGIRGNEVDLPD-GDYASTAL 3262
Cdd:cd21406      1 LIATVARGLTLSRPGRYTGYHGEVAVERGDDGNIVFGCTpGGDIFVLL 48
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 3286-3509 5.96e-10

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: 62.40  E-value: 5.96e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3286 GPPGAGKTYWLLQQVQDGdVIYTPTHqtmldmirALGTCRFNVPagttlqfpaPSRTGPWVR--ILAGGWCPGKNSFLDE 3363
Cdd:pfam01443    5 GVPGCGKSTLIRKLLRTS-RVIRPTA--------ELRTEGKPDL---------PNLNVRTVDtfLMALLKPTGKILILDE 66

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3364 ---AAYCNHLDVLRLLSKTTLTCLGDFKQLHPVGFDSHCYVfdimPQTQLKTIWRFGQNICDAIQPDYRDKLVSM---VN 3437
Cdd:pfam01443   67 ytlLPPGYILLLAAISGAKLVILFGDPLQIPYHSRAPSFLI----PHFPSSLSHRVGRRTTYLLPSLRAPILSAKgfeVV 142

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3438 TTR-----VTYVEKPVKYGQVLTPYHRDRED---GAITIDSSQGATFDVVTLHLPTKDSL-----NRQRALVAITRARHA 3504
Cdd:pfam01443  143 VERsgeykVDYDPNGVLVLVYLTFTQALKESlgvRVTTVHEVQGLTFDSVTLVLDTDTDLliisdSPEHLYVALTRHRKS 222


                   ....*
gi 1773654335 3505 IFVYD 3509
Cdd:pfam01443  223 LHILT 227
CoV_NSP15_C pfam19215
Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the ...
 3679-3797 7.12e-09

Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the C-terminal domain of coronavirus non-structural protein 15 (NSP15 or nsp15). NSP15 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. This domain exhibits endoribonuclease activity designated EndoU, highly conserved in all known CoVs and is part of the replicase-transcriptase complex that plays important roles in virus replication and transcription. NSP15 is a Uridylate-specific endoribonuclease that cleaves the 5'-polyuridines from negative-sense viral RNA, termed PUN RNA either upstream or downstream of uridylates, at GUU or GU to produce molecules with 2',3'-cyclic phosphate ends. PUN RNA is a CoV MDA5-dependent pathogen-associated molecular pattern (PAMP).


Pssm-ID: 465999  Cd Length: 155  Bit Score: 57.34  E-value: 7.12e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3679 TVFSTGRIEVDCRGyLDDREREVAESLPHAFI---------------GDVKGTTVGGCH-------------HVTSKYLP 3730
Cdd:pfam19215    2 TLFTQGRTLEDFVP-RSTMEKDFLNMDQQQFIqkygledlgfehivyGDFSKTTIGGLHllislvrltkmgiLKVEEFVP 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1773654335 3731 -RFLPKESVAVVGVSSPGkaAKAVCTLTDVYLPDLEA---YLHPETQSKCWKVMLDFKEVRLMVW-KD---KTAY 3797
Cdd:pfam19215   81 nDDSTVKNCSVTYANDGS--SKAVCTVLDLLLDDFVDilkSLDLSVVSKVVTVNIDFQPVRFMLWcKDgkvQTFY 153
SF1_C_RecD cd18809
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ...
 3452-3508 4.38e-08

C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350196 [Multi-domain]  Cd Length: 80  Bit Score: 52.95  E-value: 4.38e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1773654335 3452 QVLTPYHRDREDG--------AITIDSSQGATFDVVTLHLPTKDSLNRQRAL-VAITRARHAIFVY 3508
Cdd:cd18809     14 QVLAPTRKGGVDAlnerlqayAMTIHKSQGSEFDRVIVVLPTSHPMLSRGLLyTALTRARKLLTLV 79
NendoU_cv_Nsp15-like cd21161
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural ...
 3705-3797 1.20e-07

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: 53.81  E-value: 1.20e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3705 LPHAFIGDVKGTTVGGCHHVTSKYLPRFLPKESVAVVGVSS-----------PGKAAKAVCTLTDVYLPD---LEAYLHP 3770
Cdd:cd21161     39 FEHIVYGDFSKPTIGGLHLLIGLVRLKKEGKLYVEEFHNSDstvqnyfvtdaNNGSSKQVCTVVDLLLDDfvdILKSQDL 118

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1773654335 3771 ETQSKCWKVMLDFKEVRLMVW-KD---KTAY 3797
Cdd:cd21161    119 SVVSKVVTVSIDYKPIRFMLWcKDgkvKTFY 149
HCoV_HKU1-like_RdRp cd21593
human coronavirus HKU1 RNA-dependent RNA polymerase, also known as non-structural protein 12, ...
 2733-2960 2.18e-07

human coronavirus HKU1 RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the A lineage: responsible for replication and transcription of the viral RNA genome; This group contains the RNA-dependent RNA polymerase (RdRp) of human coronavirus HKU1, murine hepatitis virus, and similar proteins from betacoronaviruses in the embecovirus subgenera (A lineage). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 394897  Cd Length: 925  Bit Score: 57.28  E-value: 2.18e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2733 DAALRDLS--KYDLSTQGFV--LPGVLRLVRKYLFAHVGKCPPVHRPSTYPAKNSmAGINGNRFPTKDIQ----SVPEID 2804
Cdd:cd21593    440 NAAITDYNyyKYNLPTMVDIkqLLFVLEVVYKYFEIYDGGCIPASQVIVNNYDKS-AGYPFNKFGKARLYyealSFEEQD 518

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2805 VLCAQAVRENWQTVTPCTLKKQYCGKKKTRTILGTNNFIALAHRAalsgvtqgFMKKAFNS-------PIALGKNKF--- 2874
Cdd:cd21593    519 DIYAYTKRNVLPTLTQMNLKYAISAKNRARTVAGVSILSTMTGRM--------FHQKCLKSiaatrgvPVVIGTTKFygg 590

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2875 ---------KELQTPVLgrcLEADLASCDRSTPAIVRWFAANLL---YELACAEEHLPSYVLNCCHDLL--VTQSGAV-- 2938
Cdd:cd21593    591 wddmlrrliKDVDNPVL---MGWDYPKCDRAMPNILRIVSSLVLarkHDSCCSHGDRFYRLANECAQVLseIVMCGGCyy 667

                          250       260
                   ....*....|....*....|..
gi 1773654335 2939 TKRGGLSSGDPITSVSNTIYSL 2960
Cdd:cd21593    668 VKPGGTSSGDATTAFANSVFNI 689
NendoU_tv_PToV-like cd21162
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of Porcine torovirus (PToV) ...
 3681-3799 3.20e-07

Nidoviral uridylate-specific endoribonuclease (NendoU) domain of Porcine torovirus (PToV) endoribonuclease and related proteins; Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. The Porcine torovirus (PToV) strain PToV-NPL/2013 NendoU domain is located at the N-terminus of the ORF1ab replicase polyprotein, between regions annotated as Nonstructural proteins 11 (Nsp11) and 13 (Nsp13). This subfamily belongs to a family which includes Nsp15 from coronaviruses and Nsp11 from arteriviruses, which may participate in the viral replication process and in the evasion of the host immune system. These vary in their requirement for Mn2+. Coronavirus Nsp15 generally form functional hexamers, with the exception of Porcine DeltaCoronavirus (PDCoV) Nsp15 which exists as a dimer and a monomer in solution. Arterivirus (Porcine Reproductive and Respiratory Syndrome virus) PRRSV Nsp11 is a dimer. NendoUs are distantly related to Xenopus laevis Mn(2+)-dependent uridylate-specific endoribonuclease (XendoU) which is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA.


Pssm-ID: 394913  Cd Length: 133  Bit Score: 52.20  E-value: 3.20e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 3681 FSTGRIEVDCRgylDDREREVAESLP---HAFIGDVK--GTTVGGCHHVTSKYLPRF--LPKESVAVVGVS-SPGKAAKA 3752
Cdd:cd21162      1 FSTGRLYNLEH---DPSYNFNVEQLPfnkHVFLGEFTevSTTIGGVHHVPALNGTKGsiIPSYVKPIHTGLiNVGKGVKR 77

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1773654335 3753 VCTLTDVYLPDLEAYLHPE----TQSKCWKVMLDFKEVRLMVW----KDKTAYFQ 3799
Cdd:cd21162     78 CTTLVDVCANQLYELVKQQingvTVSKVIFINIDFQEVQFMVFasegDIQTAYPQ 132
Caliciviridae_RdRp cd23192
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of ...
 2832-3103 4.37e-07

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Caliciviridae, order Picornavirales. Member viruses have a viral (+)ssRNA genome, which is not segmented. The family Caliciviridae, includes eleven genera: seven genera of which infect mammals (Lagovirus, Norovirus, Nebovirus, Recovirus, Sapovirus, Valovirus, and Vesivirus), two genera of which infect birds (Bavovirus, Nacovirus), and two genera of which infect fish (Minovirus and Salovirus). Each genus includes 1-2 species. Human noroviruses are a leading cause of acute gastroenteritis in humans. Furthermore, unclassified caliciviruses have been detected in geese, yellowfin seabream, greater green snake, arctic lamprey, frogs and various Australian birds, highlighting the wide host range of viruses in the family Caliciviridae. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438042  Cd Length: 310  Bit Score: 54.96  E-value: 4.37e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2832 KTRTILGTNNFIALAHRAALSGVTQGFMKKAFNSPIALGKNK--------FKELQTpvLGRCLEADLASCDrST--PAIV 2901
Cdd:cd23192     21 KRRLLWGCDVGVTLVAAAAFGPVADALKAVCPTGPIAVGINMdsedveviFERLSG--FRYHYCLDYSKWD-STqsPAVT 97

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2902 RwFAANLLYElaCAEEHlpSYVLNCCHDLLVTQSG-----AVTKRGGLSSGDPITSVSNTIyslviyaQHMVL---SYFK 2973
Cdd:cd23192     98 A-AAIDILAD--LSEET--PLRDSVVETLSSPPMGifddvIFVTKRGLPSGMPFTSVINSL-------NHWLLfsaAVLK 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2974 SGHPHGLLflqdqlkFEDMLKVQPLIVYSDDLVLYAESPTMPNYHWWVEHLNLmLGFQ-TDPKKTA-----ITDSPSFLg 3047
Cdd:cd23192    166 AYELVGIY-------TGNVFDEADFFTYGDDGVYAMPPATASVMDEIIENLKS-YGLKpTAADKTEnpdipPLQGPVFL- 236

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1773654335 3048 criinGRQLVPNRDRILAAL--------AYHMKASNVSEYYAAAAAILMDS------CACLE---YDPEWFEE 3103
Cdd:cd23192    237 -----KRTFVRTPGGWRALLdrssilrqLYWVKGPNTHDWTEPPTEIDHEArtvqleNVLLEaaqHGPEFYEK 304
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 3465-3517 7.83e-07

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 54.98  E-value: 7.83e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1773654335 3465 AITIDSSQGATFDVVTLHLPTKDS--LNRQRALVAITRARHAIFVYDPHRQLQSM 3517
Cdd:COG0507    444 AITVHKSQGSTFDRVILVLPSEHSplLSRELLYTALTRARELLTLVGDRDALARA 498
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 2830-3069 5.35e-06

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: 51.13  E-value: 5.35e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2830 KKKTRTILGTNNFIALAHRAALSGVTQGFMKKAFNSPIALGKNKFKELQTPVLGRCLEAD--LASCDRS------TPAIV 2901
Cdd:cd01699     36 AGKTRLIQPRPLDYNIALRMYLGPFEAKLMKNRGGLPIAVGINPYSRDWTILANKLRSFSpvAIALDYSrfdsslSPQLL 115

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2902 RWFA--ANLLYELaCAEEHLPSYVLNCCHDLLVTQSGAV-TKRGGLSSGDPITSVSNTIYSlviyaqHMVLSYFKSghph 2978
Cdd:cd01699    116 EAEHsiYNALYDD-DDELERRNLLRSLTNNSLHIGFNEVyKVRGGRPSGDPLTSIGNSIIN------CILVRYAFR---- 184

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2979 gllflqdQLKFEDMLKVQPLIVYSDDLVLYAESPTMP-NYHWWVEHLNlMLGF-QTDPKKTAITDSP----SFLGCRII- 3051
Cdd:cd01699    185 -------KLGGKSFFKNVRLLNYGDDCLLSVEKADDKfNLETLAEWLK-EYGLtMTDEDKVESPFRPleevEFLKRRFVl 256

                          250       260
                   ....*....|....*....|.
gi 1773654335 3052 -NGRQLVP--NRDRILAALAY 3069
Cdd:cd01699    257 dEGGGWRAplDPSSILSKLSW 277
ps-ssRNAv-Picornavirales cd23169
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...
 2822-3067 6.35e-05

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: 48.36  E-value: 6.35e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2822 TLKKQYCGKKKTRTILGTN-NFIaLAHRAALSGVTQGFMKKAFNSPIALGKNK--------FKELQTpVLGRCLEADLAS 2892
Cdd:cd23169     11 LRPIEKVKAGKTRLFSASPlDYT-IAFRKYFGDFIAAFQKNRIKLEHAVGINPdsvewtrlYRRLLK-KGPNIFAGDYSN 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2893 CDRSTPA---------IVRWFAANLLYELACAEEHLPSYVLNCCHdllvtQSGAVT--KRGGLSSGDPITSVSNTIYSLv 2961
Cdd:cd23169     89 FDGSLPPdvmeaafdiINDWYDEYVDDEDERVRKVLFEELINTIH-----LVGNLVyqVHGGNPSGNPLTTIINSIVNL- 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2962 IYaqhMVLSYFKSGHPHGLLFLQDQLKFedmlkvqplIVYSDDLVL-----YAESPTMPNYHWWVEHLNLMLgfqTDPKK 3036
Cdd:cd23169    163 LY---IRYAWLRITGLTSLSDFKKNVRL---------VTYGDDVIIsvsdeVKDEFNFVTISEFLKELGITY---TDADK 227

                          250       260       270
                   ....*....|....*....|....*....|....*..
gi 1773654335 3037 TAIT------DSPSFLGCRIIngrqLVPNRDRILAAL 3067
Cdd:cd23169    228 SGDIvpyrplEEVTFLKRGFR----PHPTPGLVLAPL 260
betaCoV_RdRp cd21589
betacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ...
 2733-2960 6.80e-05

betacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome; This subfamily contains the RNA-dependent RNA polymerase (RdRp) of betacoronaviruses, including the RdRps from three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2, also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which shows potential for the treatment of SARS-CoV-2 viral infections. The structure of SARS-CoV-2 Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438016  Cd Length: 925  Bit Score: 49.01  E-value: 6.80e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2733 DAALRDLS--KYDLSTQGFV--LPGVLRLVRKYLFAHVGKCPPVHRPSTYPAKNSmAGINGNRFPTK----DIQSVPEID 2804
Cdd:cd21589    440 NAAITDYNyyKYNLPTMVDIkqLLFVLEVVYKYFEIYDGGCIPASQVIVNNYDKS-AGYPFNKFGKArlyyEALSFEEQD 518

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2805 VLCAQAVRENWQTVTPCTLKKQYCGKKKTRTILGTnnfialahrAALSGVT-QGFMKKAFNS-------PIALGKNKF-- 2874
Cdd:cd21589    519 EIYAYTKRNVLPTLTQMNLKYAISAKNRARTVAGV---------SILSTMTgRMFHQKCLKSiaatrgvPVVIGTTKFyg 589

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2875 ----------KELQTPVLgrcLEADLASCDRSTPAIVRWFAANLL---YELACAEEHLPSYVLNCCHDLL---VTQSGAV 2938
Cdd:cd21589    590 gwddmlrrliKDVDNPVL---MGWDYPKCDRAMPNILRIVSSLVLarkHDTCCSHSDRFYRLANECAQVLseiVMCGGCY 666

                          250       260
                   ....*....|....*....|...
gi 1773654335 2939 -TKRGGLSSGDPITSVSNTIYSL 2960
Cdd:cd21589    667 yVKPGGTSSGDATTAFANSVFNI 689
CoV_RdRp cd21530
coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible ...
 2733-2961 9.40e-05

coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome; This family contains the RNA-dependent RNA polymerase of alpha-, beta-, gamma-, delta-coronaviruses, including three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2, also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which shows potential for the treatment of SARS-CoV-2 viral infections. The structure of SARS-CoV-2 Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438015  Cd Length: 928  Bit Score: 48.68  E-value: 9.40e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2733 DAALRDLSKYDLSTQGFV----LPGVLRLVRKYLFAHVGKCPPVHRPSTYPAKNSmAGINGNRFPTK----DIQSVPEID 2804
Cdd:cd21530    443 NAAISDYDYYRYNLPTMLdirqLLFCLEVVDKYFDCYEGGCINANQVVVTNLDKS-AGFPFNKFGKArlyyDSMSYEEQD 521

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2805 VLCAQAVRENWQTVTPCTLKKQYCGKKKTRTILGTNNFIALAHRAalsgVTQGFMKK---AFNSPIALGKNKF------- 2874
Cdd:cd21530    522 ALFAYTKRNVLPTITQMNLKYAISAKNRARTVAGVSILSTMTNRQ----FHQKLLKSivnTRNATVVIGTTKFyggwdnm 597

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2875 -----KELQTPVLgrcLEADLASCDRSTPAIVRWFAANLL---YELACAEEHLPSYVLNCCHDLL----VTQSGAVTKRG 2942
Cdd:cd21530    598 lrtlySGVENPML---MGWDYPKCDRAMPNMLRIAASLVLarkHTNCCTLSHRFYRLANECAQVLsevvMSGGGLYVKPG 674

                          250
                   ....*....|....*....
gi 1773654335 2943 GLSSGDPITSVSNTIYSLV 2961
Cdd:cd21530    675 GTSSGDATTAYANSVFNIC 693
MERS-CoV-like_RdRp cd21592
Middle East respiratory syndrome-related coronavirus RNA-dependent RNA polymerase, also known ...
 2799-2961 1.23e-04

Middle East respiratory syndrome-related coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the C lineage: responsible for replication and transcription of the viral RNA genome; This group contains the RNA-dependent RNA polymerase (RdRp) of Middle East respiratory syndrome (MERS)-related CoV, bat-CoV HKU5, and similar proteins from betacoronaviruses in the merbecovirus subgenera (C lineage). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which has been shown to potently inhibit MERS RdRp. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 394896  Cd Length: 931  Bit Score: 48.12  E-value: 1.23e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2799 SVPEIDVLCAQAVRENWQTVTPCTLKKQYCGKKKTRTILGTNNFIALAHRAALSGVTQGfMKKAFNSPIALGKNKF---- 2874
Cdd:cd21592    519 SYQEQDELFAMTKRNVIPTITQMNLKYAISAKNRARTVAGVSILSTMTNRQYHQKMLKS-MAATRGATCVIGTTKFyggw 597

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2875 --------KELQTPVLgrcLEADLASCDRSTPAIVRWFAANLL---YELACAEEHLPSYVLNCCHDLL----VTQSGAVT 2939
Cdd:cd21592    598 dfmlktlyKDVDNPHL---MGWDYPKCDRAMPNMCRIFASLILarkHGTCCTTRDRFYRLANECAQVLseyvLCGGGYYV 674

                          170       180
                   ....*....|....*....|..
gi 1773654335 2940 KRGGLSSGDPITSVSNTIYSLV 2961
Cdd:cd21592    675 KPGGTSSGDATTAYANSVFNIL 696
gammaCoV_RdRp cd21587
gammacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ...
 2755-2961 2.05e-04

gammacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome; This subfamily contains the RNA-dependent RNA polymerase (RdRp) of gammacoronaviruses, including the RdRp of avian infectious bronchitis virus (IBV) and similar proteins. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 394891  Cd Length: 931  Bit Score: 47.57  E-value: 2.05e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2755 LRLVRKYLFAHVGKCPPVHRPSTYPAKNSmAGINGNRFPTKDI---QSVPEIDVLCAQAVRENWQTVTPCTLKKQYCGKK 2831
Cdd:cd21587    473 LEVTSKYFECYEGGCIPASQVVVNNLDKS-AGYPFNKFGKARLyyeMSLEEQDQLFESTKKNVLPTITQMNLKYAISAKN 551

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2832 KTRTILGTNNFIALAHRAALSGVTQGFMKKAfNSPIALGKNKF------------KELQTPVLgrcLEADLASCDRSTPA 2899
Cdd:cd21587    552 RARTVAGVSILSTMTNRQFHQKVLKSIVNTR-NAPVVIGTTKFyggwdnmlrnliQGVEDPIL---MGWDYPKCDRAMPN 627

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1773654335 2900 IVRWFAANLL---YELACAEEHLPSYVLNCCHDLL----VTQSGAVTKRGGLSSGDPITSVSNTIYSLV 2961
Cdd:cd21587    628 LLRIAASLVLarkHTNCCTWSERIYRLYNECAQVLsetvLATGGIYVKPGGTSSGDATTAYANSVFNII 696
SARS-CoV-like_RdRp cd21591
Severe acute respiratory syndrome coronavirus RNA-dependent RNA polymerase, also known as ...
 2738-2960 4.50e-04

Severe acute respiratory syndrome coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the B lineage: responsible for replication and transcription of the viral RNA genome; This group contains the RNA-dependent RNA polymerase (RdRp) of Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2 (also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus), and similar proteins from betacoronaviruses in the sarbecovirus subgenera (B lineage). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which shows potential for the treatment of SARS-CoV-2 viral infections. The structure of SARS-CoV-2 Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. Recent studies have shown that the SARS-CoV-2 RdRp requires two iron-sulfur clusters to function optimally. Earlier studies had mistakenly identified these iron-sulfur cluster binding sites for zinc-binding sites, likely because iron-sulfur clusters degrade easily under standard experimental conditions.The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 394895  Cd Length: 928  Bit Score: 46.62  E-value: 4.50e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2738 DLSKYDLSTQGFV--LPGVLRLVRKYLFAHVGKCPPVHRPSTYPAKNSmAGINGNRFPTK----DIQSVPEIDVLCAQAV 2811
Cdd:cd21591    450 DYYRYNLPTMCDIrqLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKS-AGFPFNKWGKArlyyDSMSYEDQDALFAYTK 528

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2812 RENWQTVTPCTLKKQYCGKKKTRTILGTNNFIALAHR----------AALSGVTQGF-MKKAFNSPIALGKNKFKELQTP 2880
Cdd:cd21591    529 RNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRqfhqkllksiAATRGATVVIgTSKFYGGWHNMLKTVYSDVENP 608

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2881 VLgrcLEADLASCDRSTPAIVRWFAANLL---YELACAEEHLPSYVLNCCHDLL---VTQSGAV-TKRGGLSSGDPITSV 2953
Cdd:cd21591    609 HL---MGWDYPKCDRAMPNMLRIMASLVLarkHTTCCSLSHRFYRLANECAQVLsemVMCGGSLyVKPGGTSSGDATTAY 685


                   ....*..
gi 1773654335 2954 SNTIYSL 2960
Cdd:cd21591    686 ANSVFNI 692
batCoV-HKU9-like_RdRp cd21596
Bat coronavirus HKU9 RNA-dependent RNA polymerase, also known as non-structural protein 12, ...
 2738-2960 5.51e-04

Bat coronavirus HKU9 RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the D lineage: responsible for replication and transcription of the viral RNA genome; This group contains the RNA-dependent RNA polymerase (RdRp) of bat coronavirus HKU9 and similar proteins from betacoronaviruses in the nobecovirus subgenera (D lineage). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 394898  Cd Length: 929  Bit Score: 46.18  E-value: 5.51e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2738 DLSKYDLSTQGFV--LPGVLRLVRKYLFAHVGKCPPVHRPSTYPAKNSmAGINGNRFPTKDIQ----SVPEIDVLCAQAV 2811
Cdd:cd21596    451 DYYRYNLPTMCDIkqLLFSLEVVDKYFDCYDGGCLQASQVVVANYDKS-AGFPFNKFGKARLYyeslSYADQDELFAYTK 529

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2812 RENWQTVTPCTLKKQYCGKKKTRTILGTNNFIALAHRAALSGVTQGfMKKAFNSPIALGKNKF-----KELQTPVLG--- 2883
Cdd:cd21596    530 RNVLPTITQMNLKYAISAKNRARTVAGVSIASTMTNRQFHQKMLKS-IAAARGASVVIGTTKFyggwnRMLRTLCEGven 608

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2884 -RCLEADLASCDRSTPAIVRWFAANLL---YELACAEEHLPSYVLNCC----HDLLVTQSGAVTKRGGLSSGDPITSVSN 2955
Cdd:cd21596    609 pHLMGWDYPKCDRAMPNLLRIFASLILarkHSTCCNASERFYRLANECaqvlSEMVLCGGGFYVKPGGTSSGDSTTAYAN 688


                   ....*
gi 1773654335 2956 TIYSL 2960
Cdd:cd21596    689 SVFNI 693
deltaCoV_RdRp cd21590
deltacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ...
 2817-2961 1.04e-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: 45.23  E-value: 1.04e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2817 TVTPCTLKKQYCGKKKTRTILGTNNFIALAHRAalsgVTQGFMKK---AFNSPIALGKNKFKELQTPVLGRCLEA----- 2888
Cdd:cd21590    536 TLTQMNLKYAISAKDRARTVAGVSIISTMTNRQ----YHQKMLKSislARNQTIVIGTTKFYGGWDNMLRRLMCNinnpi 611

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 2889 ----DLASCDRSTPAIVRWFAANLL-YELACAEEHLPSYVL--NCCH---DLLVTQSGAVTKRGGLSSGDPITSVSNTIY 2958
Cdd:cd21590    612 lvgwDYPKCDRSMPNMLRIAASCLLaRKHTCCNQSQRFYRLanECCQvlsEVVVSGNNLYVKPGGTSSGDATTAYANSVF 691


                   ...
gi 1773654335 2959 SLV 2961
Cdd:cd21590    692 NIL 694
ND5 MTH00063
NADH dehydrogenase subunit 5; Provisional
 1235-1303 1.51e-03

NADH dehydrogenase subunit 5; Provisional


Pssm-ID: 214414 [Multi-domain]  Cd Length: 522  Bit Score: 44.48  E-value: 1.51e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1773654335 1235 VFFS-HLFKSDSGYSPGDWGFAAFTLFCLFLCYSYPFFGFVPLLGVFSGSSRRVRMGVFGCWLAFAVGLF 1303
Cdd:MTH00063   334 VFFSkHFLLSSFSSVVFNVSLLLVVILCVFLSYLYSFRLCLILFGVKSSLSSGVRFLFFNSGLMVFLWLF 403
CoV_Nsp13-helicase cd21718
helicase domain of coronavirus non-structural protein 13; This model represents the helicase ...
 3467-3520 2.09e-03

helicase domain of coronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from alpha-, beta-, gamma-, and deltacoronavirus, including pathogenic human viruses such as Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core.


Pssm-ID: 409652 [Multi-domain]  Cd Length: 341  Bit Score: 43.67  E-value: 2.09e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1773654335 3467 TIDSSQGATFDVVTLHLPTKD--SLNRQRALVAITRARHAIFVYdpHRQLQSMFDL 3520
Cdd:cd21718    282 TVDSSQGSEYDYVIFCQTTDTahALNINRFNVAITRAKHGILVI--MRDENDLYNA 335
UvrD_C_2 pfam13538
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ...
 3465-3508 6.59e-03

UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.


Pssm-ID: 463913 [Multi-domain]  Cd Length: 52  Bit Score: 37.55  E-value: 6.59e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1773654335 3465 AITIDSSQGATFDVVTLHLPTKDS-----LNRQRALVAITRARHAIFVY 3508
Cdd:pfam13538    4 ALTVHKAQGSEFPAVFLVDPDLTAhyhsmLRRRLLYTAVTRARKKLVLV 52
 
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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