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Conserved domains on  [gi|1122810927|gb|APP93296|]
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polyprotein, partial [Kibale red colobus virus 1]

Protein Classification

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List of domain hits

 Name Accession Description Interval E-value
Arteriviridae_RdRp cd23189
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of ...
 317-639 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: 620.43  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  317 VSEVWQSVTPVTLKKQYCSKPKTRTILGTNGLISLGLRALLSGVTARFQLAGKDSPICLGKSKFQRSDIRITTRCLETDL 396
Cdd:cd23189      1 VRENWQTVTPCTLKKQYCSKKKTRTILGTNNLIALALRAALSGVTQGFMKAGFNSPIALGKNKFKPLQTPVLGRCLEADL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  397 ASCDRSTPALVRYFSTRLLFELACAERAIPLYVANCCHDLLVTQTSAVTKRGGLSSGDPITSIANTIYSLLLYTQHMVLS 476
Cdd:cd23189     81 ASCDRSTPAIVRWFAANLLFELACAEECLPSYVLNCCHDLLVTQSGAFTKRGGLSSGDPVTSISNTIYSLVIYTQHMVLS 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  477 AFKIGHPIALAFMQRRLTMEDLIKVQRFVVYSDDLVLLNEPEDFPNFVYWSDHLDLALGFKTCRSKTVITTNPGFLGCRF 556
Cdd:cd23189    161 ALKEGHPIGLKFLQDQLKFEDLLKVQPLLVYSDDLVLYAESPSFPNYHWWVEHLDLMLGFKTDPKKTVITDSPSFLGCRI 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  557 VDGW-LVPQRERVLAALAYHMSAKDVQQYYINAVAILSDASAMSVFDADWFGELVLGIANCAKTdGFTFPGVPYFLDFFT 635
Cdd:cd23189    241 INGRqLVPNRDRLLAALAYHMKASNVSEYYASAAAILMDACACLEYDPEWFEDLVVGIAECARK-DGYSFPGPPFFLFMW 319


                   ....
gi 1122810927  636 RVSG 639
Cdd:cd23189    320 EKLG 323
NendoU_av_Nsp11-like cd21160
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV ...
 1194-1313 2.25e-74

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: 242.23  E-value: 2.25e-74
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927 1194 YSTGRFEAGLRDYLDLKERQFAEEHAHAFIGDVKGTVVGGCHHITSRFLPPEIAPGAVTRVGVSSVGKAAKSLCTVTDVY 1273
Cdd:cd21160      1 FSTGRFELNSREYLDEGEREFAKKHPHAFIGDIKGTTVGGCHHITSKYLPPVLPAGSVVKVGVSSPGKAAKALCTVTDVY 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1122810927 1274 LPYLQPYTAPVTASKVYLVNVDQRACRLMVWRDKTMYFQE 1313
Cdd:cd21160     81 LPYLEPYLNPPTQSKVYKVNIDFKPVRLMVWKDATMYFQE 120
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 785-920 3.21e-54

N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.


The actual alignment was detected with superfamily member cd17937:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 137  Bit Score: 185.33  E-value: 3.21e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  785 ASVFVNGPPGSGKTTHIASQLTDGDVVYCPTHESLKAYSLLLPRCRFVVPRSADPSEYGSPSDSGPTLTLVAAGYVPGSR 864
Cdd:cd17937      2 ASTYIEGPPGCGKTFWLKKLVQPNDVLYVPTHATMLDMIKSLGPCRFVVPFGAPDLDFPTPSSSGPTVRLLAVGYTPGGK 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1122810927  865 HFIDEACYANPLDTLRILSKTPVTAIGDPHQLSPVKYTSCLFLFKYMKEQYLETVH 920
Cdd:cd17937     82 AFVDEACYCNPVDLARLLTQTPVTAFGDPNQLGPVGFASVFFLVDLMQREQLNVIY 137
M_cv_Nsp15-NTD_av_Nsp11-like super family cl41717
middle (M) domain of coronavirus Nonstructural protein 15 (Nsp15) and the N-terminal domain ...
 1094-1196 1.16e-43

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.


The actual alignment was detected with superfamily member cd21166:

Pssm-ID: 455122  Cd Length: 100  Bit Score: 153.64  E-value: 1.16e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927 1094 ISPLPRVATNLGFFYSPDLPKFFPIPKDLCAHWPVVTAINnpqWPHRLVVSLTRIHPKSSPATCAGYYVGDSLFIGVPSV 1173
Cdd:cd21166      1 PSPLPRVAHNLGFHFSPDLPGFPPIPEELAEHWPVVTNDN---WPNRLVVSLAPIDELSKPCISAGYYVGQSVFVGTPGV 77

                           90       100
                   ....*....|....*....|...
gi 1122810927 1174 VSYYLTLYENNQVKDLPPSIYST 1196
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 ...
 646-707 1.59e-31

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: 117.81  E-value: 1.59e-31
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1122810927  646 HVCGICASTASTSSRCGLYLCNLCAHRHQHCPVSSPFCAHDVGSKSCDGCSLDVLPGNTELD 707
Cdd:cd21405      1 RVCGICGSTAVTTSACGLDLCAYHAHFHQHCPVTSPFCGHPIGSKSCTMCSIPVVPGNDELD 62
1B_av_Nsp10-like cd21410
1B domain of arterivirus EAV Nsp10 helicase and related proteins; Helicases catalyze ...
 720-767 6.83e-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: 78.44  E-value: 6.83e-18
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1122810927  720 MTEVTVVDGFTNAEPGRYVWQHRPIMLRRDRNGCAIGLPDGTYAMKKL 767
Cdd:cd21410      2 EVTVEVVDGVTSAAPGRYQTRHGVVMVRRDIGGCIVDLPDGEYQVTPL 49
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 957-1016 2.93e-16

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: 75.17  E-value: 2.93e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1122810927  957 RGLVLTPYHRDR------------------HGNAITIDSSQGLTQDIATIYLPSPRSINRERAIVAITRARARLYIFD 1016
Cdd:cd18786     12 KGVVLTPYHRDRaylnqylqglsldefdlqLVGAITIDSSQGLTFDVVTLYLPTANSLTPRRLYVALTRARKRLVIYD 89
 
Name Accession Description Interval E-value
Arteriviridae_RdRp cd23189
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of ...
 317-639 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: 620.43  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  317 VSEVWQSVTPVTLKKQYCSKPKTRTILGTNGLISLGLRALLSGVTARFQLAGKDSPICLGKSKFQRSDIRITTRCLETDL 396
Cdd:cd23189      1 VRENWQTVTPCTLKKQYCSKKKTRTILGTNNLIALALRAALSGVTQGFMKAGFNSPIALGKNKFKPLQTPVLGRCLEADL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  397 ASCDRSTPALVRYFSTRLLFELACAERAIPLYVANCCHDLLVTQTSAVTKRGGLSSGDPITSIANTIYSLLLYTQHMVLS 476
Cdd:cd23189     81 ASCDRSTPAIVRWFAANLLFELACAEECLPSYVLNCCHDLLVTQSGAFTKRGGLSSGDPVTSISNTIYSLVIYTQHMVLS 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  477 AFKIGHPIALAFMQRRLTMEDLIKVQRFVVYSDDLVLLNEPEDFPNFVYWSDHLDLALGFKTCRSKTVITTNPGFLGCRF 556
Cdd:cd23189    161 ALKEGHPIGLKFLQDQLKFEDLLKVQPLLVYSDDLVLYAESPSFPNYHWWVEHLDLMLGFKTDPKKTVITDSPSFLGCRI 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  557 VDGW-LVPQRERVLAALAYHMSAKDVQQYYINAVAILSDASAMSVFDADWFGELVLGIANCAKTdGFTFPGVPYFLDFFT 635
Cdd:cd23189    241 INGRqLVPNRDRLLAALAYHMKASNVSEYYASAAAILMDACACLEYDPEWFEDLVVGIAECARK-DGYSFPGPPFFLFMW 319


                   ....
gi 1122810927  636 RVSG 639
Cdd:cd23189    320 EKLG 323
NendoU_av_Nsp11-like cd21160
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV ...
 1194-1313 2.25e-74

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: 242.23  E-value: 2.25e-74
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927 1194 YSTGRFEAGLRDYLDLKERQFAEEHAHAFIGDVKGTVVGGCHHITSRFLPPEIAPGAVTRVGVSSVGKAAKSLCTVTDVY 1273
Cdd:cd21160      1 FSTGRFELNSREYLDEGEREFAKKHPHAFIGDIKGTTVGGCHHITSKYLPPVLPAGSVVKVGVSSPGKAAKALCTVTDVY 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1122810927 1274 LPYLQPYTAPVTASKVYLVNVDQRACRLMVWRDKTMYFQE 1313
Cdd:cd21160     81 LPYLEPYLNPPTQSKVYKVNIDFKPVRLMVWKDATMYFQE 120
DEXXYc_viral_SF1-N cd17937
DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ...
 785-920 3.21e-54

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: 185.33  E-value: 3.21e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  785 ASVFVNGPPGSGKTTHIASQLTDGDVVYCPTHESLKAYSLLLPRCRFVVPRSADPSEYGSPSDSGPTLTLVAAGYVPGSR 864
Cdd:cd17937      2 ASTYIEGPPGCGKTFWLKKLVQPNDVLYVPTHATMLDMIKSLGPCRFVVPFGAPDLDFPTPSSSGPTVRLLAVGYTPGGK 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1122810927  865 HFIDEACYANPLDTLRILSKTPVTAIGDPHQLSPVKYTSCLFLFKYMKEQYLETVH 920
Cdd:cd17937     82 AFVDEACYCNPVDLARLLTQTPVTAFGDPNQLGPVGFASVFFLVDLMQREQLNVIY 137
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 199-614 1.72e-45

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: 171.44  E-value: 1.72e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  199 VCSTVPFGLELYIPTIPTTVLDYlDERPDTPVYLTKHGTEKAALEDLAKFDLSTQGFILPEVYSIVRSYLIKVIGYSPPI 278
Cdd:pfam00680   10 IPAYVPASLGPEDPRWARSYLNT-DPYVDDIKKYSRPKLPGPADERDKLLNRSAAKMVLSELRGVPKKANSTLIVYRAID 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  279 HTPATVPSN-DSHAGINGMRFSTR------LLQSIPNINSICEQAVS--EVWQSVTPVTLKKQYC-----------SKPK 338
Cdd:pfam00680   89 GVEQIDPLNwDTSAGYPYVGLGGKkgdlieHLKDGTEARELAERLAAdwEVLQNGTPLKLVYQTClkdelrplekvEKGK 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  339 TRTILGTNGLISLGLRALLSGVTARFQLAGKDSPICLGKSKFQRSDIRITTR-------CLETDLASCDRSTPALVRYFS 411
Cdd:pfam00680  169 TRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHPIQVGINPFDRGWPRLLRRlarfgdyVYELDYSGFDSSVPPWLIRFA 248

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  412 TRLLFELAC------AERAIPLYVanCCHDLLVTQTSAVTKRGGLSSGDPITSIANTIYSlLLYTQHMVLSAFKIGHPia 485
Cdd:pfam00680  249 FEILRELLGfpsnvkEWRAILELL--IYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVN-YLLILYALLKSLENDGP-- 323

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  486 lafmqrrlTMEDLIKVQRFVVYSDDLVLLNEPEDFPNFVYWSDHLDLaLGFKTCRSKTVITTNP-----GFLGCRFV--- 557
Cdd:pfam00680  324 --------RVCNLDKYFDFFTYGDDSLVAVSPDFDPVLDRLSPHLKE-LGLTITPAKKTFPVSReleevSFLKRTFRktp 394

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1122810927  558 DGWLVPQRERVLAALAYHMSAKdvqqyYINAVAILSDASAMSVFDADWFGELVLGIA 614
Cdd:pfam00680  395 GGYRPPLDRKRILAQLEYIRSK-----PVPSGQLENIRAYASHHGYEFYRDLLYRFV 446
NTD_av_Nsp11-like cd21166
N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; ...
 1094-1196 1.16e-43

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: 153.64  E-value: 1.16e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927 1094 ISPLPRVATNLGFFYSPDLPKFFPIPKDLCAHWPVVTAINnpqWPHRLVVSLTRIHPKSSPATCAGYYVGDSLFIGVPSV 1173
Cdd:cd21166      1 PSPLPRVAHNLGFHFSPDLPGFPPIPEELAEHWPVVTNDN---WPNRLVVSLAPIDELSKPCISAGYYVGQSVFVGTPGV 77

                           90       100
                   ....*....|....*....|...
gi 1122810927 1174 VSYYLTLYENNQVKDLPPSIYST 1196
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 ...
 646-707 1.59e-31

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: 117.81  E-value: 1.59e-31
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1122810927  646 HVCGICASTASTSSRCGLYLCNLCAHRHQHCPVSSPFCAHDVGSKSCDGCSLDVLPGNTELD 707
Cdd:cd21405      1 RVCGICGSTAVTTSACGLDLCAYHAHFHQHCPVTSPFCGHPIGSKSCTMCSIPVVPGNDELD 62
1B_av_Nsp10-like cd21410
1B domain of arterivirus EAV Nsp10 helicase and related proteins; Helicases catalyze ...
 720-767 6.83e-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: 78.44  E-value: 6.83e-18
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1122810927  720 MTEVTVVDGFTNAEPGRYVWQHRPIMLRRDRNGCAIGLPDGTYAMKKL 767
Cdd:cd21410      2 EVTVEVVDGVTSAAPGRYQTRHGVVMVRRDIGGCIVDLPDGEYQVTPL 49
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 957-1016 2.93e-16

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: 75.17  E-value: 2.93e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1122810927  957 RGLVLTPYHRDR------------------HGNAITIDSSQGLTQDIATIYLPSPRSINRERAIVAITRARARLYIFD 1016
Cdd:cd18786     12 KGVVLTPYHRDRaylnqylqglsldefdlqLVGAITIDSSQGLTFDVVTLYLPTANSLTPRRLYVALTRARKRLVIYD 89
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 789-1016 4.19e-09

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: 58.54  E-value: 4.19e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  789 VNGPPGSGKTTHIASQLTDGdVVYCPTHEslkaysllLPRCRFVVPrsadpseygsPSDSGPTLT--LVAAGYVPGSRHF 866
Cdd:pfam01443    3 VHGVPGCGKSTLIRKLLRTS-RVIRPTAE--------LRTEGKPDL----------PNLNVRTVDtfLMALLKPTGKILI 63

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  867 IDE-----ACYANPLdtLRILSKTPVTAIGDPHQlSPVKYTSCLFLFKYMkeqYLETVHRFSQNIADAIQPYYKQKLVSS 941
Cdd:pfam01443   64 LDEytllpPGYILLL--AAISGAKLVILFGDPLQ-IPYHSRAPSFLIPHF---PSSLSHRVGRRTTYLLPSLRAPILSAK 137

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  942 RPGVT---QVIYQTKFEPRG-LVLTPYHR-----DRHG-NAITIDSSQGLTQDIATIYL--PSPRSI---NRERAIVAIT 1006
Cdd:pfam01443  138 GFEVVverSGEYKVDYDPNGvLVLVYLTFtqalkESLGvRVTTVHEVQGLTFDSVTLVLdtDTDLLIisdSPEHLYVALT 217

                          250
                   ....*....|
gi 1122810927 1007 RARARLYIFD 1016
Cdd:pfam01443  218 RHRKSLHILT 227
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 968-1023 2.79e-05

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: 48.43  E-value: 2.79e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1122810927  968 RHGNAITIDSSQGLTQDIATIYLPS--PRSINRERAIVAITRARARLYIFDPHKQLAE 1023
Cdd:COG0507    440 ELAYAITVHKSQGSTFDRVILVLPSehSPLLSRELLYTALTRARELLTLVGDRDALAR 497
CoV_NSP15_C pfam19215
Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the ...
 1192-1304 1.01e-04

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: 44.24  E-value: 1.01e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927 1192 SIYSTGRFEAGL-------RDYLDLKERQFAEEH-------AHAFIGDVKGTVVGGCH--------HITSRFLPPEIAPG 1249
Cdd:pfam19215    2 TLFTQGRTLEDFvprstmeKDFLNMDQQQFIQKYgledlgfEHIVYGDFSKTTIGGLHllislvrlTKMGILKVEEFVPN 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1122810927 1250 AVTRVGVSSV----GKAAKSLCTVTDV----YLPYLQPYTAPVTaSKVYLVNVDQRACRLMVW 1304
Cdd:pfam19215   82 DDSTVKNCSVtyanDGSSKAVCTVLDLllddFVDILKSLDLSVV-SKVVTVNIDFQPVRFMLW 143
 
Name Accession Description Interval E-value
Arteriviridae_RdRp cd23189
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of ...
 317-639 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: 620.43  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  317 VSEVWQSVTPVTLKKQYCSKPKTRTILGTNGLISLGLRALLSGVTARFQLAGKDSPICLGKSKFQRSDIRITTRCLETDL 396
Cdd:cd23189      1 VRENWQTVTPCTLKKQYCSKKKTRTILGTNNLIALALRAALSGVTQGFMKAGFNSPIALGKNKFKPLQTPVLGRCLEADL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  397 ASCDRSTPALVRYFSTRLLFELACAERAIPLYVANCCHDLLVTQTSAVTKRGGLSSGDPITSIANTIYSLLLYTQHMVLS 476
Cdd:cd23189     81 ASCDRSTPAIVRWFAANLLFELACAEECLPSYVLNCCHDLLVTQSGAFTKRGGLSSGDPVTSISNTIYSLVIYTQHMVLS 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  477 AFKIGHPIALAFMQRRLTMEDLIKVQRFVVYSDDLVLLNEPEDFPNFVYWSDHLDLALGFKTCRSKTVITTNPGFLGCRF 556
Cdd:cd23189    161 ALKEGHPIGLKFLQDQLKFEDLLKVQPLLVYSDDLVLYAESPSFPNYHWWVEHLDLMLGFKTDPKKTVITDSPSFLGCRI 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  557 VDGW-LVPQRERVLAALAYHMSAKDVQQYYINAVAILSDASAMSVFDADWFGELVLGIANCAKTdGFTFPGVPYFLDFFT 635
Cdd:cd23189    241 INGRqLVPNRDRLLAALAYHMKASNVSEYYASAAAILMDACACLEYDPEWFEDLVVGIAECARK-DGYSFPGPPFFLFMW 319


                   ....
gi 1122810927  636 RVSG 639
Cdd:cd23189    320 EKLG 323
NendoU_av_Nsp11-like cd21160
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV ...
 1194-1313 2.25e-74

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: 242.23  E-value: 2.25e-74
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927 1194 YSTGRFEAGLRDYLDLKERQFAEEHAHAFIGDVKGTVVGGCHHITSRFLPPEIAPGAVTRVGVSSVGKAAKSLCTVTDVY 1273
Cdd:cd21160      1 FSTGRFELNSREYLDEGEREFAKKHPHAFIGDIKGTTVGGCHHITSKYLPPVLPAGSVVKVGVSSPGKAAKALCTVTDVY 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1122810927 1274 LPYLQPYTAPVTASKVYLVNVDQRACRLMVWRDKTMYFQE 1313
Cdd:cd21160     81 LPYLEPYLNPPTQSKVYKVNIDFKPVRLMVWKDATMYFQE 120
DEXXYc_viral_SF1-N cd17937
DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ...
 785-920 3.21e-54

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: 185.33  E-value: 3.21e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  785 ASVFVNGPPGSGKTTHIASQLTDGDVVYCPTHESLKAYSLLLPRCRFVVPRSADPSEYGSPSDSGPTLTLVAAGYVPGSR 864
Cdd:cd17937      2 ASTYIEGPPGCGKTFWLKKLVQPNDVLYVPTHATMLDMIKSLGPCRFVVPFGAPDLDFPTPSSSGPTVRLLAVGYTPGGK 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1122810927  865 HFIDEACYANPLDTLRILSKTPVTAIGDPHQLSPVKYTSCLFLFKYMKEQYLETVH 920
Cdd:cd17937     82 AFVDEACYCNPVDLARLLTQTPVTAFGDPNQLGPVGFASVFFLVDLMQREQLNVIY 137
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 199-614 1.72e-45

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: 171.44  E-value: 1.72e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  199 VCSTVPFGLELYIPTIPTTVLDYlDERPDTPVYLTKHGTEKAALEDLAKFDLSTQGFILPEVYSIVRSYLIKVIGYSPPI 278
Cdd:pfam00680   10 IPAYVPASLGPEDPRWARSYLNT-DPYVDDIKKYSRPKLPGPADERDKLLNRSAAKMVLSELRGVPKKANSTLIVYRAID 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  279 HTPATVPSN-DSHAGINGMRFSTR------LLQSIPNINSICEQAVS--EVWQSVTPVTLKKQYC-----------SKPK 338
Cdd:pfam00680   89 GVEQIDPLNwDTSAGYPYVGLGGKkgdlieHLKDGTEARELAERLAAdwEVLQNGTPLKLVYQTClkdelrplekvEKGK 168

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  339 TRTILGTNGLISLGLRALLSGVTARFQLAGKDSPICLGKSKFQRSDIRITTR-------CLETDLASCDRSTPALVRYFS 411
Cdd:pfam00680  169 TRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHPIQVGINPFDRGWPRLLRRlarfgdyVYELDYSGFDSSVPPWLIRFA 248

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  412 TRLLFELAC------AERAIPLYVanCCHDLLVTQTSAVTKRGGLSSGDPITSIANTIYSlLLYTQHMVLSAFKIGHPia 485
Cdd:pfam00680  249 FEILRELLGfpsnvkEWRAILELL--IYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVN-YLLILYALLKSLENDGP-- 323

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  486 lafmqrrlTMEDLIKVQRFVVYSDDLVLLNEPEDFPNFVYWSDHLDLaLGFKTCRSKTVITTNP-----GFLGCRFV--- 557
Cdd:pfam00680  324 --------RVCNLDKYFDFFTYGDDSLVAVSPDFDPVLDRLSPHLKE-LGLTITPAKKTFPVSReleevSFLKRTFRktp 394

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1122810927  558 DGWLVPQRERVLAALAYHMSAKdvqqyYINAVAILSDASAMSVFDADWFGELVLGIA 614
Cdd:pfam00680  395 GGYRPPLDRKRILAQLEYIRSK-----PVPSGQLENIRAYASHHGYEFYRDLLYRFV 446
NTD_av_Nsp11-like cd21166
N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins; ...
 1094-1196 1.16e-43

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: 153.64  E-value: 1.16e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927 1094 ISPLPRVATNLGFFYSPDLPKFFPIPKDLCAHWPVVTAINnpqWPHRLVVSLTRIHPKSSPATCAGYYVGDSLFIGVPSV 1173
Cdd:cd21166      1 PSPLPRVAHNLGFHFSPDLPGFPPIPEELAEHWPVVTNDN---WPNRLVVSLAPIDELSKPCISAGYYVGQSVFVGTPGV 77

                           90       100
                   ....*....|....*....|...
gi 1122810927 1174 VSYYLTLYENNQVKDLPPSIYST 1196
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 ...
 646-707 1.59e-31

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: 117.81  E-value: 1.59e-31
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1122810927  646 HVCGICASTASTSSRCGLYLCNLCAHRHQHCPVSSPFCAHDVGSKSCDGCSLDVLPGNTELD 707
Cdd:cd21405      1 RVCGICGSTAVTTSACGLDLCAYHAHFHQHCPVTSPFCGHPIGSKSCTMCSIPVVPGNDELD 62
ps-ssRNAv_Nidovirales_RdRp cd23168
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Nidovirales of ...
 323-559 5.80e-30

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: 121.70  E-value: 5.80e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  323 SVTPVTLKKQYCSKPKTRTILGTNGLISLGLRALLSGVTARFQLAGKD-SPICL-----GKSKFQR---SDIRITTRCLE 393
Cdd:cd23168      1 TLTQVNPKYAIQKKKRARTILGVSIISTDVGRQLHQAVLAAIVNTRSAnIVIIGtkfygGWHKMLRylyPGVIEDPVLMG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  394 TDLASCDRSTPALVRYFSTRLLFEL---ACAERAIP-LYVANCCH---DLLVTQTSAVTKRGGLSSGDPITSIANTIYSL 466
Cdd:cd23168     81 WDYPKCDRSVPNMLRYLANLLLASLydnCCNLSEIVhLLINECAQvlyDYVVYGGNLYRKPGGVSSGDSTTAISNSIYNY 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  467 LLYTQHMVLSAFkighpialafmqrrltmedlikvqrfvvYSDDLVLLNEPEDFPNFVY-WSDHLDLALGFKTCRSKTVI 545
Cdd:cd23168    161 FQTFIANVRLAI----------------------------LSDDGVACINPDLIDLGDVaSVSFFLASYYYTNNKKKYSS 212

                          250
                   ....*....|....
gi 1122810927  546 TTNPGFLGCRFVDG 559
Cdd:cd23168    213 TCWVEPHEFCSPHE 226
M_cv_Nsp15-NTD_av_Nsp11-like cd21163
middle (M) domain of coronavirus Nonstructural protein 15 (Nsp15) and the N-terminal domain ...
 1095-1196 7.73e-22

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: 92.40  E-value: 7.73e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927 1095 SPLPRVATNLGFFYSPDLPKFFPI--------------PKDLCAHWPVVTAINNP-------QWPHRLVVSLTRIHPKSS 1153
Cdd:cd21163      2 TPLPKVLRNLGVDFTPNFVLWDYEdtapffnttvckytPEELCEHLPVLYDDRYGgslerflSAPNAVLISLTKVKKYSI 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1122810927 1154 PAtCAGYYVGDSLFIGVPSVVSYYLTLYENNQVKDLPPSIYST 1196
Cdd:cd21163     82 PP-PAGAYLNGSVVVGTPKVVSFYLYKRKDGKFVTLPDTLFTQ 123
NendoU_nv cd21158
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural ...
 1194-1312 2.83e-20

Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural protein 15 (Nsp15), arterivirus Nsp11, torovirus endoribonuclease, and related proteins; Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. This family also includes torovirus NendoUs. Except for turkey coronavirus (TCoV) Nsp15, Mn2+ is generally essential for the catalytic activity of coronavirus Nsp15. Mn2+ is dispensable, and to some extent inhibits the activity of arterivirus (Porcine Reproductive and Respiratory Syndrome virus) PRRSV Nsp11. Coronavirus Nsp15 from Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), human Coronavirus 229E (HCoV229E), and murine hepatitis virus (MHV) form a functional hexamer while Porcine DeltaCoronavirus (PDCoV) Nsp15 has been shown to exist as a dimer and monomer in solution. Nsp11 from the arterivirus PRRSV is a dimer. NendoUs are distantly related to Xenopus laevis Mn(2+)-dependent uridylate-specific endoribonuclease (XendoU) which is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA.


Pssm-ID: 439157  Cd Length: 151  Bit Score: 88.86  E-value: 2.83e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927 1194 YSTGRFEAGlRDYLDLKERQFAEEHA---------------HAFIGDVKGTVVGGCHHITSRFLPP--------EIAPGA 1250
Cdd:cd21158      1 FTQGRNLQE-FLPRSDMERDFLPVDMdvfiekygleiyafeHVVYGDFSHTTLGGLHLVISLYKRFkegplpreEFIPND 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1122810927 1251 VT--RVGVSSVG-KAAKSLCTVTDVYLPYLQPYTAP---VTASKVYLVNVDQRACRLMVWRD----KTMYFQ 1312
Cdd:cd21158     80 STvkNYGVTSPGtKASKAVCTLIDLLLDDFVEILKSqdlEVVSKVVKVMIDFKEVRFMLWCKdgdvQTFYPQ 151
1B_av_Nsp10-like cd21410
1B domain of arterivirus EAV Nsp10 helicase and related proteins; Helicases catalyze ...
 720-767 6.83e-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: 78.44  E-value: 6.83e-18
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1122810927  720 MTEVTVVDGFTNAEPGRYVWQHRPIMLRRDRNGCAIGLPDGTYAMKKL 767
Cdd:cd21410      2 EVTVEVVDGVTSAAPGRYQTRHGVVMVRRDIGGCIVDLPDGEYQVTPL 49
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 957-1016 2.93e-16

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: 75.17  E-value: 2.93e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1122810927  957 RGLVLTPYHRDR------------------HGNAITIDSSQGLTQDIATIYLPSPRSINRERAIVAITRARARLYIFD 1016
Cdd:cd18786     12 KGVVLTPYHRDRaylnqylqglsldefdlqLVGAITIDSSQGLTFDVVTLYLPTANSLTPRRLYVALTRARKRLVIYD 89
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 789-1016 4.19e-09

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: 58.54  E-value: 4.19e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  789 VNGPPGSGKTTHIASQLTDGdVVYCPTHEslkaysllLPRCRFVVPrsadpseygsPSDSGPTLT--LVAAGYVPGSRHF 866
Cdd:pfam01443    3 VHGVPGCGKSTLIRKLLRTS-RVIRPTAE--------LRTEGKPDL----------PNLNVRTVDtfLMALLKPTGKILI 63

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  867 IDE-----ACYANPLdtLRILSKTPVTAIGDPHQlSPVKYTSCLFLFKYMkeqYLETVHRFSQNIADAIQPYYKQKLVSS 941
Cdd:pfam01443   64 LDEytllpPGYILLL--AAISGAKLVILFGDPLQ-IPYHSRAPSFLIPHF---PSSLSHRVGRRTTYLLPSLRAPILSAK 137

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  942 RPGVT---QVIYQTKFEPRG-LVLTPYHR-----DRHG-NAITIDSSQGLTQDIATIYL--PSPRSI---NRERAIVAIT 1006
Cdd:pfam01443  138 GFEVVverSGEYKVDYDPNGvLVLVYLTFtqalkESLGvRVTTVHEVQGLTFDSVTLVLdtDTDLLIisdSPEHLYVALT 217

                          250
                   ....*....|
gi 1122810927 1007 RARARLYIFD 1016
Cdd:pfam01443  218 RHRKSLHILT 227
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 336-574 9.34e-08

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: 55.37  E-value: 9.34e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  336 KPKTRTILGTNGLISLGLRALLSGVTARFQLAGKDSPICLGKSKFQR--SDIRITTRCLETDLASCDRS------TPALV 407
Cdd:cd01699     36 AGKTRLIQPRPLDYNIALRMYLGPFEAKLMKNRGGLPIAVGINPYSRdwTILANKLRSFSPVAIALDYSrfdsslSPQLL 115

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  408 RYFSTRLlfelacaERAIPLYVANCCHDLLVTQTSAVT---------KRGGLSSGDPITSIANTIYSLLlytqhMVLSAF 478
Cdd:cd01699    116 EAEHSIY-------NALYDDDDELERRNLLRSLTNNSLhigfnevykVRGGRPSGDPLTSIGNSIINCI-----LVRYAF 183

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  479 kighpialafmqRRLTMEDLIKVQRFVVYSDDLVL-LNEPEDFPNFVYWSDHLDlALGFK-TCRSKTVITTNPG----FL 552
Cdd:cd01699    184 ------------RKLGGKSFFKNVRLLNYGDDCLLsVEKADDKFNLETLAEWLK-EYGLTmTDEDKVESPFRPLeeveFL 250

                          250       260
                   ....*....|....*....|....*..
gi 1122810927  553 GCRFV----DGWLVP-QRERVLAALAY 574
Cdd:cd01699    251 KRRFVldegGGWRAPlDPSSILSKLSW 277
NendoU_tv_PToV-like cd21162
Nidoviral uridylate-specific endoribonuclease (NendoU) domain of Porcine torovirus (PToV) ...
 1194-1304 1.91e-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: 51.43  E-value: 1.91e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927 1194 YSTGRFEAglRDYLDLKERQFAEE--HAHAFIGDVK--GTVVGGCHHITSRF------LPPEIAPgavTRVGVSSVGKAA 1263
Cdd:cd21162      1 FSTGRLYN--LEHDPSYNFNVEQLpfNKHVFLGEFTevSTTIGGVHHVPALNgtkgsiIPSYVKP---IHTGLINVGKGV 75

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1122810927 1264 KSLCTVTDV----YLPYLQPYTAPVTASKVYLVNVDQRACRLMVW 1304
Cdd:cd21162     76 KRCTTLVDVcanqLYELVKQQINGVTVSKVIFINIDFQEVQFMVF 120
SF1_C_RecD cd18809
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ...
 959-1015 1.13e-06

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: 47.56  E-value: 1.13e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1122810927  959 LVLTPYHRDR--------HGNAITIDSSQGLTQDIATIYLPSPRS-INRERAIVAITRARARLYIF 1015
Cdd:cd18809     14 QVLAPTRKGGvdalnerlQAYAMTIHKSQGSEFDRVIVVLPTSHPmLSRGLLYTALTRARKLLTLV 79
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 968-1023 2.79e-05

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: 48.43  E-value: 2.79e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1122810927  968 RHGNAITIDSSQGLTQDIATIYLPS--PRSINRERAIVAITRARARLYIFDPHKQLAE 1023
Cdd:COG0507    440 ELAYAITVHKSQGSTFDRVILVLPSehSPLLSRELLYTALTRARELLTLVGDRDALAR 497
CoV_NSP15_C pfam19215
Coronavirus replicase NSP15, uridylate-specific endoribonuclease; This entry represents the ...
 1192-1304 1.01e-04

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: 44.24  E-value: 1.01e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927 1192 SIYSTGRFEAGL-------RDYLDLKERQFAEEH-------AHAFIGDVKGTVVGGCH--------HITSRFLPPEIAPG 1249
Cdd:pfam19215    2 TLFTQGRTLEDFvprstmeKDFLNMDQQQFIQKYgledlgfEHIVYGDFSKTTIGGLHllislvrlTKMGILKVEEFVPN 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1122810927 1250 AVTRVGVSSV----GKAAKSLCTVTDV----YLPYLQPYTAPVTaSKVYLVNVDQRACRLMVW 1304
Cdd:pfam19215   82 DDSTVKNCSVtyanDGSSKAVCTVLDLllddFVDILKSLDLSVV-SKVVTVNIDFQPVRFMLW 143
deltaCoV_RdRp cd21590
deltacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ...
 310-467 2.11e-04

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: 46.00  E-value: 2.11e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  310 NSICEQAVSEVWQSVTPVTLKKQYCSKPKTRTILGTNGLISLGLRALLSGVTARFQLAgKDSPICLGKSKFQRSDIRITT 389
Cdd:cd21590    523 NQLFEYTKRNVLPTLTQMNLKYAISAKDRARTVAGVSIISTMTNRQYHQKMLKSISLA-RNQTIVIGTTKFYGGWDNMLR 601

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  390 RCLET---------DLASCDRSTPALVRYFSTRLLF-ELACAERAIPLY-VAN-CCH---DLLVTQTSAVTKRGGLSSGD 454
Cdd:cd21590    602 RLMCNinnpilvgwDYPKCDRSMPNMLRIAASCLLArKHTCCNQSQRFYrLANeCCQvlsEVVVSGNNLYVKPGGTSSGD 681

                          170
                   ....*....|...
gi 1122810927  455 PITSIANTIYSLL 467
Cdd:cd21590    682 ATTAYANSVFNIL 694
HCoV_HKU1-like_RdRp cd21593
human coronavirus HKU1 RNA-dependent RNA polymerase, also known as non-structural protein 12, ...
 320-522 3.80e-04

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: 45.34  E-value: 3.80e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  320 VWQSVTPVTLKKQYCSKPKTRTILGTnglislglrALLSGVTARF--------QLAGKDSPICLGKSKFQRSDIRITTRC 391
Cdd:cd21593    528 VLPTLTQMNLKYAISAKNRARTVAGV---------SILSTMTGRMfhqkclksIAATRGVPVVIGTTKFYGGWDDMLRRL 598

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  392 LET---------DLASCDRSTPALVRYFSTRLLFEL--ACAERAIPLY-VANCCHDLL----VTQTSAVTKRGGLSSGDP 455
Cdd:cd21593    599 IKDvdnpvlmgwDYPKCDRAMPNILRIVSSLVLARKhdSCCSHGDRFYrLANECAQVLseivMCGGCYYVKPGGTSSGDA 678

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1122810927  456 ITSIANTIYSLLLYTQHMVLSAFKI-GHPIalafmqRRLTMEDLIKVQRFVVYSDDLV---LLNEPEDFPN 522
Cdd:cd21593    679 TTAFANSVFNICQAVSANVCSLMACnGHKI------EDLSIRELQKRLYSNVYRSDYVdptFVNEYYEFLN 743
MERS-CoV-like_RdRp cd21592
Middle East respiratory syndrome-related coronavirus RNA-dependent RNA polymerase, also known ...
 320-470 1.26e-03

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: 43.49  E-value: 1.26e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  320 VWQSVTPVTLKKQYCSKPKTRTILGTNGLISLGLRALLSGVTaRFQLAGKDSPICLGKSKFQRS-DIRITT--------R 390
Cdd:cd21592    534 VIPTITQMNLKYAISAKNRARTVAGVSILSTMTNRQYHQKML-KSMAATRGATCVIGTTKFYGGwDFMLKTlykdvdnpH 612

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  391 CLETDLASCDRSTPALVRYFSTRLL---FELACAERAIPLYVANCCHDLL----VTQTSAVTKRGGLSSGDPITSIANTI 463
Cdd:cd21592    613 LMGWDYPKCDRAMPNMCRIFASLILarkHGTCCTTRDRFYRLANECAQVLseyvLCGGGYYVKPGGTSSGDATTAYANSV 692


                   ....*..
gi 1122810927  464 YSLLLYT 470
Cdd:cd21592    693 FNILQAT 699
batCoV-HKU9-like_RdRp cd21596
Bat coronavirus HKU9 RNA-dependent RNA polymerase, also known as non-structural protein 12, ...
 320-466 2.35e-03

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


Pssm-ID: 394898  Cd Length: 929  Bit Score: 42.72  E-value: 2.35e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  320 VWQSVTPVTLKKQYCSKPKTRTILGTNGLISLGLRALLSGVTARFQlAGKDSPICLGKSKFQRSDIR-ITTRC------- 391
Cdd:cd21596    532 VLPTITQMNLKYAISAKNRARTVAGVSIASTMTNRQFHQKMLKSIA-AARGASVVIGTTKFYGGWNRmLRTLCegvenph 610

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  392 -LETDLASCDRSTPALVRYFSTRLLFE--LACAERAIPLY-VANCC----HDLLVTQTSAVTKRGGLSSGDPITSIANTI 463
Cdd:cd21596    611 lMGWDYPKCDRAMPNLLRIFASLILARkhSTCCNASERFYrLANECaqvlSEMVLCGGGFYVKPGGTSSGDSTTAYANSV 690


                   ...
gi 1122810927  464 YSL 466
Cdd:cd21596    691 FNI 693
gammaCoV_RdRp cd21587
gammacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ...
 320-502 6.90e-03

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: 41.02  E-value: 6.90e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  320 VWQSVTPVTLKKQYCSKPKTRTILGTNGLISLGLR-----ALLSGVTARfqlagkDSPICLGKSKFQ---RSDIRITTRC 391
Cdd:cd21587    534 VLPTITQMNLKYAISAKNRARTVAGVSILSTMTNRqfhqkVLKSIVNTR------NAPVVIGTTKFYggwDNMLRNLIQG 607

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1122810927  392 LET------DLASCDRSTPALVRYFSTRLL---FELAC--AERAIPLYvaNCCHDLL---VTQTSAV-TKRGGLSSGDPI 456
Cdd:cd21587    608 VEDpilmgwDYPKCDRAMPNLLRIAASLVLarkHTNCCtwSERIYRLY--NECAQVLsetVLATGGIyVKPGGTSSGDAT 685

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1122810927  457 TSIANTIYSLLLYTQHMVLSafkighpiALAFMQRRLTMEDLIKVQ 502
Cdd:cd21587    686 TAYANSVFNIIQATSANVAR--------LLSVITRDIVYDDIKSLQ 723
 
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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