NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1125811701|ref|YP_009329972|]
View 

hypothetical protein 1 [Hubei myriapoda virus 3]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
ps-ssRNAv-Picornavirales cd23169
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...
1697-1995 2.65e-58

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: 204.37  E-value: 2.65e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1697 IYEVCPKDEVRKLKKIyDTPQTRIFTPGPFQHSITYRMYFHAAVALVRECRLKLPMKVGMNPFGDEVDYMVRKAISKGTN 1776
Cdd:cd23169      2 IFVDCLKDELRPIEKV-KAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNRIKLEHAVGINPDSVEWTRLYRRLLKKGPN 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1777 CFDGDFSHYDASHPLFLVRSAMNVFHRVAVETTErdprltpelfakqlEDERIIREGIMRADLQPFISIDGHLVQFSGGV 1856
Cdd:cd23169     81 IFAGDYSNFDGSLPPDVMEAAFDIINDWYDEYVD--------------DEDERVRKVLFEELINTIHLVGNLVYQVHGGN 146
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1857 FSGQPATTDLNGILNFMYIYYAWLNIMKDqpelQNMAAFLHHCEFLCFGDDNILFTSDKILKKFNLQTVHDVLEKHLdvI 1936
Cdd:cd23169    147 PSGNPLTTIINSIVNLLYIRYAWLRITGL----TSLSDFKKNVRLVTYGDDVIISVSDEVKDEFNFVTISEFLKELG--I 220
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1125811701 1937 LLGSSKDKNNIEKFHHFTEAEFLKRKFVLKGDKFTM--PLVDESIVKMLEWTTGPKHIYAT 1995
Cdd:cd23169    221 TYTDADKSGDIVPYRPLEEVTFLKRGFRPHPTPGLVlaPLDLESIEEQLNWTRKEDDLLEA 281
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
459-561 3.58e-19

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.


:

Pssm-ID: 459992  Cd Length: 102  Bit Score: 84.58  E-value: 3.58e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701  459 IWIAGPHMQGKSQVVNTIVDKLSE-LHQRKLTTYTR-SFDKYWTGYCFQDVVIYDEFmkthgvDGRPDAMELQEFFTCNS 536
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKkLGLPKDSVYSRnPDDDFWDGYTGQPVVIIDDF------GQNPDGPDEAELIRLVS 74
                           90       100
                   ....*....|....*....|....*...
gi 1125811701  537 TA---LNLAAVEEKGRKFASKYIIICSN 561
Cdd:pfam00910   75 STpypPPMAALEEKGTPFTSKFVIVTSN 102
AlkB super family cl43793
Alkylated DNA repair dioxygenase AlkB [Replication, recombination and repair];
2054-2102 1.02e-06

Alkylated DNA repair dioxygenase AlkB [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG3145:

Pssm-ID: 442379  Cd Length: 200  Bit Score: 51.70  E-value: 1.02e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1125811701 2054 PYEYNGGQHQPKRIPKIFRDL-------FHFDFNGVLINYYPDTSSGIPWHRDNEE 2102
Cdd:COG3145     70 GYRYSGTDPEPPPWPPALLALkrrveaaAGFPFNSCLLNLYRDGQDRMGWHQDDEE 125
 
Name Accession Description Interval E-value
ps-ssRNAv-Picornavirales cd23169
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...
1697-1995 2.65e-58

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: 204.37  E-value: 2.65e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1697 IYEVCPKDEVRKLKKIyDTPQTRIFTPGPFQHSITYRMYFHAAVALVRECRLKLPMKVGMNPFGDEVDYMVRKAISKGTN 1776
Cdd:cd23169      2 IFVDCLKDELRPIEKV-KAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNRIKLEHAVGINPDSVEWTRLYRRLLKKGPN 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1777 CFDGDFSHYDASHPLFLVRSAMNVFHRVAVETTErdprltpelfakqlEDERIIREGIMRADLQPFISIDGHLVQFSGGV 1856
Cdd:cd23169     81 IFAGDYSNFDGSLPPDVMEAAFDIINDWYDEYVD--------------DEDERVRKVLFEELINTIHLVGNLVYQVHGGN 146
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1857 FSGQPATTDLNGILNFMYIYYAWLNIMKDqpelQNMAAFLHHCEFLCFGDDNILFTSDKILKKFNLQTVHDVLEKHLdvI 1936
Cdd:cd23169    147 PSGNPLTTIINSIVNLLYIRYAWLRITGL----TSLSDFKKNVRLVTYGDDVIISVSDEVKDEFNFVTISEFLKELG--I 220
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1125811701 1937 LLGSSKDKNNIEKFHHFTEAEFLKRKFVLKGDKFTM--PLVDESIVKMLEWTTGPKHIYAT 1995
Cdd:cd23169    221 TYTDADKSGDIVPYRPLEEVTFLKRGFRPHPTPGLVlaPLDLESIEEQLNWTRKEDDLLEA 281
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
1544-1989 2.61e-36

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: 144.86  E-value: 2.61e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1544 FAPTILSDLDPRLTDDDGIPkcEIIRPEIFKWKRVFDYGNMDKdlMKKTIEDVTERIVDvAKASGKKTRVLTKSEALNGC 1623
Cdd:pfam00680   13 YVPASLGPEDPRWARSYLNT--DPYVDDIKKYSRPKLPGPADE--RDKLLNRSAAKMVL-SELRGVPKKANSTLIVYRAI 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1624 SLYEVSNPIDKHSSVGIPLKNLFTQSRGKYHYLKfneqkqfwsidmEKECGKVLNNLCDQLIDTYRRGDNPVLIYEVCPK 1703
Cdd:pfam00680   88 DGVEQIDPLNWDTSAGYPYVGLGGKKGDLIEHLK------------DGTEARELAERLAADWEVLQNGTPLKLVYQTCLK 155
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1704 DEVRKLKKIyDTPQTRIFTPGPFQHSITYRMYFHAAVALVRECRLKLPMKVGMNPFGDEVDYMVRKAISKGTNCFDGDFS 1783
Cdd:pfam00680  156 DELRPLEKV-EKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHPIQVGINPFDRGWPRLLRRLARFGDYVYELDYS 234
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1784 HYDASHPLFLVRSAMNVFHrvavETTERDPRLTpelfakqlEDERIIREGIMRadlqPFISIDGHLVQFSGGVFSGQPAT 1863
Cdd:pfam00680  235 GFDSSVPPWLIRFAFEILR----ELLGFPSNVK--------EWRAILELLIYT----PIALPNGTVFKKTGGLPSGSPFT 298
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1864 TDLNGILNFMYIYYAWLN-IMKDQPELQNmaaFLHHCEFLCFGDDNILFTS-------DKI---LKKFNLqTVHDvlekh 1932
Cdd:pfam00680  299 SIINSIVNYLLILYALLKsLENDGPRVCN---LDKYFDFFTYGDDSLVAVSpdfdpvlDRLsphLKELGL-TITP----- 369
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1125811701 1933 ldvillgsskDKNNIEKFHHFTEAEFLKRKFVLKGDKFTMPLVDESIVKMLEWTTGP 1989
Cdd:pfam00680  370 ----------AKKTFPVSRELEEVSFLKRTFRKTPGGYRPPLDRKRILAQLEYIRSK 416
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
459-561 3.58e-19

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.


Pssm-ID: 459992  Cd Length: 102  Bit Score: 84.58  E-value: 3.58e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701  459 IWIAGPHMQGKSQVVNTIVDKLSE-LHQRKLTTYTR-SFDKYWTGYCFQDVVIYDEFmkthgvDGRPDAMELQEFFTCNS 536
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKkLGLPKDSVYSRnPDDDFWDGYTGQPVVIIDDF------GQNPDGPDEAELIRLVS 74
                           90       100
                   ....*....|....*....|....*...
gi 1125811701  537 TA---LNLAAVEEKGRKFASKYIIICSN 561
Cdd:pfam00910   75 STpypPPMAALEEKGTPFTSKFVIVTSN 102
AlkB COG3145
Alkylated DNA repair dioxygenase AlkB [Replication, recombination and repair];
2054-2102 1.02e-06

Alkylated DNA repair dioxygenase AlkB [Replication, recombination and repair];


Pssm-ID: 442379  Cd Length: 200  Bit Score: 51.70  E-value: 1.02e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1125811701 2054 PYEYNGGQHQPKRIPKIFRDL-------FHFDFNGVLINYYPDTSSGIPWHRDNEE 2102
Cdd:COG3145     70 GYRYSGTDPEPPPWPPALLALkrrveaaAGFPFNSCLLNLYRDGQDRMGWHQDDEE 125
 
Name Accession Description Interval E-value
ps-ssRNAv-Picornavirales cd23169
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...
1697-1995 2.65e-58

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: 204.37  E-value: 2.65e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1697 IYEVCPKDEVRKLKKIyDTPQTRIFTPGPFQHSITYRMYFHAAVALVRECRLKLPMKVGMNPFGDEVDYMVRKAISKGTN 1776
Cdd:cd23169      2 IFVDCLKDELRPIEKV-KAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNRIKLEHAVGINPDSVEWTRLYRRLLKKGPN 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1777 CFDGDFSHYDASHPLFLVRSAMNVFHRVAVETTErdprltpelfakqlEDERIIREGIMRADLQPFISIDGHLVQFSGGV 1856
Cdd:cd23169     81 IFAGDYSNFDGSLPPDVMEAAFDIINDWYDEYVD--------------DEDERVRKVLFEELINTIHLVGNLVYQVHGGN 146
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1857 FSGQPATTDLNGILNFMYIYYAWLNIMKDqpelQNMAAFLHHCEFLCFGDDNILFTSDKILKKFNLQTVHDVLEKHLdvI 1936
Cdd:cd23169    147 PSGNPLTTIINSIVNLLYIRYAWLRITGL----TSLSDFKKNVRLVTYGDDVIISVSDEVKDEFNFVTISEFLKELG--I 220
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1125811701 1937 LLGSSKDKNNIEKFHHFTEAEFLKRKFVLKGDKFTM--PLVDESIVKMLEWTTGPKHIYAT 1995
Cdd:cd23169    221 TYTDADKSGDIVPYRPLEEVTFLKRGFRPHPTPGLVlaPLDLESIEEQLNWTRKEDDLLEA 281
Marnaviridae_RdRp cd23195
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Marnaviridae of ...
1697-1992 8.48e-41

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Marnaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Marnaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. They are mono- or dicistronic, have a polyadenylate tail and have conserved motifs for RNA helicase, RdRp, and structural protein domains. The first RNA virus isolated and characterized that infects a marine protist was Heterosigma akashiwo RNA virus (HaRNAV) in the genus Marnavirus, that infects the toxic bloom-forming Raphidophyte alga, Heterosigma akashiwo. Recently, it has undergone a major taxonomic revision and now includes 20 species within 7 genera, which include Bacillarnavirus, Kusarnavirus, Labyrnavirus, Locarnavirus, Marnavirus, Salisharnavirus, and Sogarnavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438045  Cd Length: 310  Bit Score: 154.14  E-value: 8.48e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1697 IYEVCPKDEVRKLKKiydtPQTRIFTPGPFQHSITYRMYFHAAVALVRECRLKLPMKVGMNPFGDEVDYMVRKAISKGT- 1775
Cdd:cd23195      2 IFKACLKDEPTKLTK----DKVRVFQAAPVALQLLVRKYFLPIARFLQMNPLLSECAVGINAQSPEWEELYEHLTKFGEd 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1776 NCFDGDFSHYDASHPLFLVRSAMNVFhrvaVETTERDPRLTpelfakqlEDERIIREGIMrADL-QPFISIDGHLVQFSG 1854
Cdd:cd23195     78 RIIAGDYSKYDKRMSAQLILAAFKIL----IDIAAKSGGYS--------EEDLKIMRGIA-TDIaYPLVDFNGDLIQFFG 144
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1855 GVFSGQPATTDLNGILNFMYIYYAWLNIMKDQPElqnmAAFLHHCEFLCFGDDNILFTSDKILkKFNLQTVHDVLEKHlD 1934
Cdd:cd23195    145 SNPSGHPLTVIINSIVNSLYMRYAYYSLYPEKEV----PPFRDVVALMTYGDDNIMSVSPGYP-WFNHTSIAEFLAKI-G 218
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1935 VILLGSSKDKnNIEKFHHFTEAEFLKRKFVLKGD--KFTMPLVDESIVKMLEWTTGPKHI 1992
Cdd:cd23195    219 IKYTMADKEA-ESVPFIHISEADFLKRKFVFDPElgVYVGPLDEDSIFKSLHCYLKSKVL 277
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
1694-1986 1.35e-40

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: 152.44  E-value: 1.35e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1694 PVLIYEVCPKDEVRKLKKIYDtPQTRIFTPGPFQHSITYRMYFHAAVALVRECRLKLPMKVGMNPFGDEVDYMVRKAISK 1773
Cdd:cd01699     16 PDLVFTTFLKDELRPLEKVEA-GKTRLIQPRPLDYNIALRMYLGPFEAKLMKNRGGLPIAVGINPYSRDWTILANKLRSF 94
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1774 GTNCFDGDFSHYDASHPlflvRSAMNVFHRVAVETTERDprltPELFAKQLederiIREGIMRadlqpFISI-DGHLVQF 1852
Cdd:cd01699     95 SPVAIALDYSRFDSSLS----PQLLEAEHSIYNALYDDD----DELERRNL-----LRSLTNN-----SLHIgFNEVYKV 156
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1853 SGGVFSGQPATTDLNGILNFMYIYYAWLNIMKDqpelqnmaAFLHHCEFLCFGDDNILFTSDKiLKKFNLQTVHDVLEKh 1932
Cdd:cd01699    157 RGGRPSGDPLTSIGNSIINCILVRYAFRKLGGK--------SFFKNVRLLNYGDDCLLSVEKA-DDKFNLETLAEWLKE- 226
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1125811701 1933 ldvilLG---SSKDKNNIEkFHHFTEAEFLKRKFVLKGD-KFTMPLVDESIVKMLEWT 1986
Cdd:cd01699    227 -----YGltmTDEDKVESP-FRPLEEVEFLKRRFVLDEGgGWRAPLDPSSILSKLSWS 278
Dicistroviridae_RdRp cd23194
RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense ...
1703-1986 2.49e-37

RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the RdRp of RNA viruses belonging to the family Dicistroviridae, order Picornavirales. Dicistroviridae is a family of small non-enveloped viruses with a (+)ssRNA genome of approximately 8-10 kilobases. The family contains 3 genera: Aparavirus, Cripavirus, and Triatovirus. All members infect arthropod hosts with some having devastating economic consequences, such as acute bee paralysis virus, Kashmir bee virus, and Israeli acute paralysis virus in domesticated honeybees, and taura syndrome virus and mud crab virus in the seafood industry. On the contrary, host specificity and other desirable traits make several members of this group amenable to development as biopesticides for insect control, such as Solenopsis invicta virus 1 against fire ants, and triatoma virus against triatomine bugs that vector Chagas disease. Members in the family Dicistroviridae have similarity to viruses in the Picornavirales members (Iflaviridae, Picornaviridae, Marnaviridae and Secoviridae). The genomes of viruses of these taxa encode proteins with helicase, 3C-like protease, and RdRp domains, as well as capsid proteins with related structures, although the genome organizations can differ among viruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438044 [Multi-domain]  Cd Length: 315  Bit Score: 144.18  E-value: 2.49e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1703 KDEVRKLKKIyDTPQTRIFTPGPFQHSITYRMYFHAAVALVRECRLKLPMKVGMNPFGDEVDYMVRKAISKGTNCFDGDF 1782
Cdd:cd23194     13 KDERRPIEKV-DAGKTRVFSAGPMDYTIAFRMYFLGFVAHLMRNRIDNEIAVGTNVYSLDWDKLARKLLSKGDKVIAGDF 91
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1783 SHYDASHPLFLVRSAMNVFHRvavetterdprltpelFAKQLEDERIIREGIMRADLQPFISIDGHLVQFSGGVFSGQPA 1862
Cdd:cd23194     92 SNFDGSLNPQILWAILDIINE----------------WYDDGEENALIRRVLWEDIVNSVHICGGYVYQWTHSQPSGNPL 155
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1863 TTDLNGILNFMYIYYAWLNIMKDQPeLQNMAAFLHHCEFLCFGDDNILFTSDKILKKFNLQTVHDVLEKhldvilLG--- 1939
Cdd:cd23194    156 TAIINSIYNSIIMRYVYLLLTKEAG-LMTMSDFNKHVSMVSYGDDNVINVSDEVSEWFNQLTITEAMAE------IGmty 228
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1940 SSKDKN-NIEKFHHFTEAEFLKRKFVLKGDK--FTMPLVDESIVKMLEWT 1986
Cdd:cd23194    229 TDETKTgEIVPYRSLEEVSFLKRGFRYDDDLgrWVAPLDLDTILEMPNWV 278
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
1544-1989 2.61e-36

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: 144.86  E-value: 2.61e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1544 FAPTILSDLDPRLTDDDGIPkcEIIRPEIFKWKRVFDYGNMDKdlMKKTIEDVTERIVDvAKASGKKTRVLTKSEALNGC 1623
Cdd:pfam00680   13 YVPASLGPEDPRWARSYLNT--DPYVDDIKKYSRPKLPGPADE--RDKLLNRSAAKMVL-SELRGVPKKANSTLIVYRAI 87
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1624 SLYEVSNPIDKHSSVGIPLKNLFTQSRGKYHYLKfneqkqfwsidmEKECGKVLNNLCDQLIDTYRRGDNPVLIYEVCPK 1703
Cdd:pfam00680   88 DGVEQIDPLNWDTSAGYPYVGLGGKKGDLIEHLK------------DGTEARELAERLAADWEVLQNGTPLKLVYQTCLK 155
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1704 DEVRKLKKIyDTPQTRIFTPGPFQHSITYRMYFHAAVALVRECRLKLPMKVGMNPFGDEVDYMVRKAISKGTNCFDGDFS 1783
Cdd:pfam00680  156 DELRPLEKV-EKGKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHPIQVGINPFDRGWPRLLRRLARFGDYVYELDYS 234
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1784 HYDASHPLFLVRSAMNVFHrvavETTERDPRLTpelfakqlEDERIIREGIMRadlqPFISIDGHLVQFSGGVFSGQPAT 1863
Cdd:pfam00680  235 GFDSSVPPWLIRFAFEILR----ELLGFPSNVK--------EWRAILELLIYT----PIALPNGTVFKKTGGLPSGSPFT 298
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1864 TDLNGILNFMYIYYAWLN-IMKDQPELQNmaaFLHHCEFLCFGDDNILFTS-------DKI---LKKFNLqTVHDvlekh 1932
Cdd:pfam00680  299 SIINSIVNYLLILYALLKsLENDGPRVCN---LDKYFDFFTYGDDSLVAVSpdfdpvlDRLsphLKELGL-TITP----- 369
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1125811701 1933 ldvillgsskDKNNIEKFHHFTEAEFLKRKFVLKGDKFTMPLVDESIVKMLEWTTGP 1989
Cdd:pfam00680  370 ----------AKKTFPVSRELEEVSFLKRTFRKTPGGYRPPLDRKRILAQLEYIRSK 416
Secoviridae_RdRp cd23196
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Secoviridae of ...
1701-1990 1.61e-23

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Secoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Secoviridae, order Picornavirales. Members of the family Secoviridae are non-enveloped viruses with mono- or bipartite (RNA-1 and RNA-2) linear (+)ssRNA genomes of 9 to 13.7 kilobases in total. Secoviruses are related to picornaviruses and are classified in the order Picornavirales. The majority of known members infect dicotyledonous plants and many are important plant pathogens (e.g., grapevine fanleaf virus and rice tungro spherical virus). The Secoviridae includes 8 genera (Comovirus, Fabavirus, Nepovirus, Cheravirus, Sadwavirus, Torradovirus, Sequivirus, and Waikavirus) as well as unassigned species (strawberry latent ringspot virus-MEN 454, strawberry mottle virus-Thompson, black raspberry necrosis virus- 1, chocolate lily virus A-KP2, and Dioscorea mosaic associated virus-goiana). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438046  Cd Length: 309  Bit Score: 103.62  E-value: 1.61e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1701 CPKDEVRKLKKIYDTPQTRIFTPGPFQHSITYRMYFHAAVALVRECRLKLPMKVGMNPFGDEVDYMVRKAISKGTNCFDG 1780
Cdd:cd23196      6 CPKDERLKKRKVLEKPKTRLFDVLPMEYNLLLRKYFLNFVRFIQANRHRLPCQVGINPYSREWTTLYDRLAEKSDTALNC 85
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1781 DFSHYDAshplFLVRSAMNVFhrvavetterdprltPELFAKQLEDERIIREGimRADLQPFI---SIDGHLV-QFSGGV 1856
Cdd:cd23196     86 DYSRFDG----LLSHQVYVWI---------------ADMINRLYGDGDEAKAR--RNLLMMFCgrrSICGRQVyMVRGGM 144
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1857 FSGQPATTDLNGILNFMYIYYAWLNIMKDQPelQNMaaFLHHCEFLCFGDDNILFTSDKILKKFNLQTVHDVLEKHLDVI 1936
Cdd:cd23196    145 PSGCALTVIINSIFNEILIRYVYRKVVPRPA--RNN--FNKYVRLVVYGDDNLISVKEEIIPYFDGPVIKKEMAKVGVTI 220
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1125811701 1937 LLGSSKDKNNIEkFHHFTEAEFLKRKFVLKGD-KFTMPLVDESIVKMLEWTTGPK 1990
Cdd:cd23196    221 TDGTDKTSPTLE-RKPLESLDFLKRGFRVQSDgLVVAPLDKTSLYSRLHYVTAGG 274
ps-ssRNA_Picornaviridae cd23193
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of ...
1630-1986 2.81e-23

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Picornaviridae, order Picornavirales. The Picornaviridae family consists of small, icosahedral viruses with (+)ssRNA genomes. Characteristic features of all members of the family Picornaviridae are three capsid proteins with beta-barrel folding, polyprotein processing by virus-encoded cysteine proteinase(s), and replication by an RdRp with a YGDD sequence motif. The family Picornaviridae comprises 68 genera containing 158 species, but many viruses are presently awaiting classification. The established genera of the family include: Aphthovirus, Avisivirus, Crohivirus, Enterovirus, Teschovirus, Cardiovirus, Erbovirus, Kobuvirus, Hepatovirus, Parechovirus, Aquamavirus, Avihepatovirus, Avisivirus, Cosavirus, Dicipivirus, Fipivirus, Gallivirus, Hunnivirus, Kunsagivirus, Limnipivirus, Megrivirus, Mischivirus, Mosavirus, Oscivirus, Pasivirus, Passerivirus, Rabovirus, Rosavirus, Sakobuvirus, Salivirus, Sapelovirus, Senecavirus, Sicinivirus, and Tremovirus. The Picornaviridae contains many important human and animal pathogens including enteroviruses (such as poliovirus, enterovirus, coxsackievirus, and rhinovirus), cardioviruses (such as encephalomyocarditis virus and Theiler's virus), hepatitis A virus and foot-and-mouth disease virus. Infection with various picornaviruses may cause encephalitis, febrile rash illnesses (hand-foot-and-mouth disease), aseptic meningitis, hepatitis, conjunctivitis, herpangina, myositis and myocarditis, and the common cold. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438043  Cd Length: 345  Bit Score: 103.78  E-value: 2.81e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1630 NPIDKHSSVGIPLKnlftqSRGKYhylkfneQKQFWSIDMEKECGKVLNNLCDqlidtYRRGDNPVLIYEVCPKDEVRKL 1709
Cdd:cd23193      9 DPIDLNTSPGYPYT-----TQGLR-------RRDLIDNDKGGVSPLLEEEEQV-----LLDLDGPDVVFTTFLKDELRPK 71
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1710 KKIYDTpQTRIFTPGPFQHSITYRMYFhaavalvreCRL----------KLPMKVGMNPFGDEVDYMvrkAISKGTNCFD 1779
Cdd:cd23193     72 EKVKAG-KTRVIEAAPLDYVIAGRMVF---------GRLfaqfhsnpgiLTGSAVGCNPDTDWTRLF---ASLKQDNVYD 138
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1780 GDFSHYDASHPLFLvrsamnvFHRVAvetterdprltpELFAKQLEDEriirEGIMRAdLQPfISIDGHLV-----QFSG 1854
Cdd:cd23193    139 LDYSGFDASLSSQL-------FEAAV------------EVLAECHGDP----ELVLRY-LEP-IINSKHVVgderyTVEG 193
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1855 GVFSGQPATTDLNGILNFMYIYYAWLNIMKDQPElqnmaaflhHCEFLCFGDDNILFTSDKILKKFnlqtVHDVLEKHLD 1934
Cdd:cd23193    194 GMPSGCPCTSILNSICNNLVVRYALLETGKFDPD---------EYYILAYGDDVLVSTDEPIDPSD----LAEFYKKYFG 260
                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1125811701 1935 VILLGSSKDknNIEKFHHFTEAEFLKRKFVLKGDKF----TMPLvdESIVKMLEWT 1986
Cdd:cd23193    261 MTVTPADKS--SDFPESSPIEDVFLKRRFFVPDGTFlihpVMDL--ETLEQSLMWC 312
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
459-561 3.58e-19

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.


Pssm-ID: 459992  Cd Length: 102  Bit Score: 84.58  E-value: 3.58e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701  459 IWIAGPHMQGKSQVVNTIVDKLSE-LHQRKLTTYTR-SFDKYWTGYCFQDVVIYDEFmkthgvDGRPDAMELQEFFTCNS 536
Cdd:pfam00910    1 IWLYGPPGCGKSTLAKYLARALLKkLGLPKDSVYSRnPDDDFWDGYTGQPVVIIDDF------GQNPDGPDEAELIRLVS 74
                           90       100
                   ....*....|....*....|....*...
gi 1125811701  537 TA---LNLAAVEEKGRKFASKYIIICSN 561
Cdd:pfam00910   75 STpypPPMAALEEKGTPFTSKFVIVTSN 102
Hepatovirus_RdRp cd23215
RNA-dependent RNA polymerase (RdRp) in the genus Hepatovirus of positive-sense single-stranded ...
1696-1985 3.72e-18

RNA-dependent RNA polymerase (RdRp) in the genus Hepatovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Hepatovirus genus within the family Picornaviridae, order Picornavirales. Hepatoviruses are 27- to 32-nm, nonenveloped, icosahedral viruses with a (+)ssRNA linear genome of approximately 7.5-kb. The Hepatovirus genus has nine species, Hepatovirus A-I, of which Hepatovirus A is responsible for a self-limiting viral hepatitis in human beings and may be transmitted by the fecal-oral route during acute infection or by the ingestion of uncooked contaminated shellfish. RdRps are multi-domain proteins that play a pivotal role in enterovirus replication. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of hepatoviruses. 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: 438065  Cd Length: 464  Bit Score: 89.91  E-value: 3.72e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1696 LIYEVCPKDEVRKLKKIYDTpQTRIFTPGPFQHSITYRMYFHAAVALVR-ECRLKLPMKVGMNPFGDEvDYMVRKAISKG 1774
Cdd:cd23215    135 VVYTTCPKDELRPLEKVLES-KTRAIDACPLDFTIICRMFWGPAISYFQlNPGFHTGVAVGIDPDRDW-DALFKTMIRFG 212
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1775 TNCFDGDFSHYDASHPLFLVRSAMNVFHRVAVetterdprlTPELFAKQLEDEriiregimradlqpfISIDGHLV---- 1850
Cdd:cd23215    213 DYGIDLDFSSFDASLSPFMIREACRVLSELSG---------VPDHQGQALINT---------------IIYSKHLLynlc 268
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1851 -QFSGGVFSGQPATTDLNGILNFMYIYYAWLNIMKDQPELqnmaaFLHHCEFLCFGDD-NILFTSDKILKkfNLQTVHDV 1928
Cdd:cd23215    269 yHVCGSMPSGSPCTSLLNSIVNNVNLYYVFSKIFKKSPVF-----FYDAVKFLCYGDDvLIVFSRDLEIK--NLDKLGQR 341
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1125811701 1929 LEKHLDVILLGSSKDKNNIEKFHHFTEAEFLKRKFVLKGDKFTMPLVDESIVKMLEW 1985
Cdd:cd23215    342 IQDEFKLLGMTATSADKGEPQVVPVSELTFLKRSFNLIEDRFRPAISEKTIWSLVAW 398
Limnipivirus_RdRp cd23228
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Limnipivirus of ...
1619-1994 6.58e-16

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Limnipivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Limnipivirus genus within the family Picornaviridae, order Picornavirales. The Limnipivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus contains three species, Limnipivirus A (bluegill picornavirus 1), Limnipivirus B (carp picornavirus 1) and Limnipivirus C (fathead minnow picornavirus 1). Limnipiviruses infect freshwater fishes. The virus can be grown in various fish cell lines. Experimental infection of bluegills with bluegill picornavirus induces morbidity (inflammation and redness at the base of fins, exophthalmia, abdomen distension, internal hemorrhaging and ascites) and mortality. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438078  Cd Length: 390  Bit Score: 82.23  E-value: 6.58e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1619 ALNGCSLyevsNPIDKHSSVGIPLKNLFTQsrgKYHYLKFNEQKQFWSIDMekecgkvLNNLCDQLIDTYRRGDNPVLIY 1698
Cdd:cd23228      1 AITGAGT----NPIDKNTSPGLKYTRDGLK---KSDLYTIDEDGNVVVSDM-------LRADVEAWEELIQSGGYPTTLF 66
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1699 EVCPKDEVRKLKKIyDTPQTRIFTPGPFQHSITYRMYFHAAVALVRECRLKLP-MKVGMNPFGDevDYMVRKAISKGTNC 1777
Cdd:cd23228     67 TACLKDELRSDEKV-ALGKTRVIEAAELDYVVAYRMYMSSIYSDLYNAYAGDTgIAAGINPPAD--GHRLREELSQYDSF 143
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1778 FDGDFSHYDASHPLFLVRSAMnvfhrvavetterdprltpELFAKQLEDERIIREgimradLQPFISIDGHLV-----QF 1852
Cdd:cd23228    144 LALDYSRFDGSLPEMLMRAAV-------------------EILADLHEDPDLVRR------LHETVIISKHLVvdedwTV 198
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1853 SGGVFSGQPATTDLNGILNFMYIYYAWLNIMkDQPElQNMAAFLHHCEFL--CFGDDNILFTSDKILKKFNLQTVHDVLe 1930
Cdd:cd23228    199 KGGMPSGSPCTTVLNCICNLLVLEYAFLVHF-GVYE-DDDGVGLPQCDYLsvVYGDDCIVAYNGMEMGLAFAETIEDTF- 275
                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1125811701 1931 kHLDVILLGSSKDKNNIEkfhhFTEAEFLKRKFV----LKGDKFTMPLVDESIVKMLEW----TTGPKHIYA 1994
Cdd:cd23228    276 -GMEVTPASKVGDHFNVE----LHEVEFLKRKFFafetEEYDRIALRLSENTIVQSLMWmrnlKTFPDQVQS 342
Aphthovirus_RdRp cd23210
RNA-dependent RNA polymerase (RdRp) in the Aphthovirus genus of positive-sense single-stranded ...
1519-1984 5.34e-15

RNA-dependent RNA polymerase (RdRp) in the Aphthovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the Aphthovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. This genus includes species such as bovine rhinitis A virus, bovine rhinitis B virus, equine rhinitis A virus, and food-and-mouth disease virus (FMDV). Aphthoviruses primarily infect via the upper respiratory tract. FMDV infects mainly cloven-hoofed animals, but has been isolated from at least 70 species of mammals. Aphthoviruses are non-enveloped and have an icosahedral capsid with a diameter of around 27 to 30 nm. The assembled viral capsid contains a single copy of the RNA genome and 60 copies of the four viral capsid proteins VP1, VP2, VP3, and VP4. 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: 438060  Cd Length: 458  Bit Score: 79.99  E-value: 5.34e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1519 DQKTHLPIKTQYHRSILHPPWHEHtFAPTILSDLDPRLtdDDGIPKCEIIrpeIFKWKRVFDYGNMDKDLMKKTIEDVTE 1598
Cdd:cd23210      3 EERVHVMRKTKLAPTVAHGVFNPE-FGPAALSNKDPRL--NEGVVLDEVI---FSKHKGDTKMSAEDKALFRRCAADYAS 76
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1599 RIVDVAkasGKKTRVLTKSEALNGCSLYEVSNPidkHSSVGIPLKnLFTQSRGKYhylkfneqkqfwsIDMEKecGKVLN 1678
Cdd:cd23210     77 RLHSVL---GTANAPLSIYEAIKGVDGLDAMEP---DTAPGLPWA-LQGKRRGAL-------------IDFEN--GTVGP 134
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1679 NLCDQLiDTYRRGDNPvLIYEVCPKDEVRKLKKIyDTPQTRIFTPGPFQHSITYRMYFHAAVALVRECR-LKLPMKVGMN 1757
Cdd:cd23210    135 EVEAAL-KLMEKREYK-FACQTFLKDEIRPMEKV-RAGKTRIVDVLPVEHILYTRMMIGRFCAQMHSNNgPQIGSAVGCN 211
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1758 PfgdEVDYM-VRKAISKGTNCFDGDFSHYDASHplflVRSAMNV-FHRVAVETTERDPRLtpELFAKQLEDERIIREgim 1835
Cdd:cd23210    212 P---DVDWQrFGTHFAQYRNVWDVDYSAFDANH----CSDAMNImFEEVFRTEFGFHPNA--EWILKTLVNTEHAYE--- 279
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1836 radlQPFISIDGhlvqfsgGVFSGQPATTDLNGILNFMYIYYAwlnIMKDQPELQnmaafLHHCEFLCFGDDnILFTSDK 1915
Cdd:cd23210    280 ----NKRITVEG-------GMPSGCSATSIINTILNNIYVLYA---LRRHYEGVE-----LDTYTMISYGDD-IVVASDY 339
                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1916 ILkkfNLQTVHDVLEKHLDVILLGSSKDKNNIEKfHHFTEAEFLKRKFVL-KGDKFTMPLVDesiVKMLE 1984
Cdd:cd23210    340 DL---DFEALKPHFKSLGQTITPADKSDKGFVLG-HSITDVTFLKRHFHMdYGTGFYKPVMA---SKTLE 402
Nora-virus_RdRp cd23200
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in a novel picorna-like ...
1703-1986 9.30e-15

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in a novel picorna-like Drosophila virus, Nora virus; This group contains the catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the unclassified Nora virus, a new picorna-like virus family. Nora virus has a (+)ssRNA genome followed by a poly(A) tail. Unlike other picorna-like viruses, the genome has four open reading frames (ORFs). One ORF encodes a picornavirus-like cassette of proteins for virus replication, including an iflavirus-like RdRp and a helicase that is related to those of mammalian picornaviruses. The three other ORFs are not closely related to any previously described viruses. Nora virus is present as a persistent infection in several tested laboratory stocks and wild-caught flies. 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: 438050  Cd Length: 306  Bit Score: 77.65  E-value: 9.30e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1703 KDEVRKLKKIyDTPQTRIFTPGPFQHSITYRMYFHAAVALVRECRLKLPMKVGMNPFGDEVDYMVrKAISKGTNCFDGDF 1782
Cdd:cd23200      8 KDQPIKIAQA-KSGRTRVFHCIPVDLILFSGALYGPYKEAYTKAGLKCYHAVGIDPKSVGWQQLA-TYMTKHPNYFDADY 85
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1783 SHYDAS-HPLF---LVRSAMNVFHRVAvetterdprltPELFAKQledeRIIREgimradlqpFISIDGHLVQFSG---- 1854
Cdd:cd23200     86 KNYDKYlHRQVfkaVRKIQRSVIQQVC-----------PDKWDKA----RAVEE---------LDAIDTYVVDYQTvykt 141
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1855 --GVFSGQPATTDLNGILNFMYIYYAWLNIMKdqpeLQNMAAFLHHCEFLCFGDDNILFTSDKILKKFNLQTVHDVLEKH 1932
Cdd:cd23200    142 nrGNKSGSYTTTIDNCLANDIYGLYAWVKTTG----LRSLWDYRQNVSSVAFGDDIIKSVSDEYKDKYNYCTYRDVLNAT 217
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1125811701 1933 LDVILLGSskdKNNIEK-FHHFTEAEFLKRKFVLKGDKFTMPLVDESIVKMLEWT 1986
Cdd:cd23200    218 GHIMTPGS---KDGEEKpFTSFENLQFLKRGFKLENGMVLAPLLQRSIEGPFVWT 269
Megrivirus_RdRp cd23223
RNA-dependent RNA polymerase (RdRp) in the genus Megrivirus of positive-sense single-stranded ...
1543-1964 1.94e-14

RNA-dependent RNA polymerase (RdRp) in the genus Megrivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Megrivirus genus within the family Picornaviridae, order Picornavirales. The Megrivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. The genus Megrivirus contains a five species Megrivirus A, Megrivirus B, Megrivirus C, Megrivirus D and Megrivirus E. The name Megrivirus is derived from the turkey genus name Meleagris. Megrivirus A is comprised of turkey hepatitis virus 1 (THV-1), duck megrivirus and goose megrivirus 1. Megrivirus B contains the mesiviruses. Megrivirus D contains harrier picornavirus 1 (HaPV-1). Megrivirus E was found in an Adelie penguin. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438073  Cd Length: 432  Bit Score: 77.96  E-value: 1.94e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1543 TFAPTILSDLDPRLtdDDGIPKCEII----RPEIFKWKRV---FDYgnMDKDLMKKtiedvterivdVAKASGKKTRVLT 1615
Cdd:cd23223      8 THGPAALTNKDKRL--EEGVDLDDVMfskhVPDHPGWPTLepaMSY--VVEDLMHK-----------LGFSKDEPVPMWT 72
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1616 KSEALNGcslYEVSNPIDKHSSVGIPLKnlfTQSRGKYHYLKFNEQKQFWSIDMEKECGKVLNNLCDQLIDTYRrgdnpv 1695
Cdd:cd23223     73 LEQAING---EGVMDGIDMGQSPGYPYN---AQGRSRRSFFEWNGEKWQPTEELKKEVDHALKDPDDFYFSTFL------ 140
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1696 liyevcpKDEVRKLKKIyDTPQTRIFTPGPFQHSITYRMYFHAAV-ALVRECRLKLPMKVGMNPFGDEVDYMVRKAISKG 1774
Cdd:cd23223    141 -------KDELRPLEKV-KAGKTRLVDGDSLPRILAMRMVFGPLFeAMLRKNGPEIHSAVGCNPDTDWTRYYHEMGPDSF 212
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1775 TNCFDGDFSHYDAShplflvrsamnvfhrvavetterDPRLTPELFAKQLEDeriiregIMRADLQPFIS--------ID 1846
Cdd:cd23223    213 PYCFDLDYSCFDST-----------------------EPKIAFRLMAKYLKP-------YFSVDVTPFFEalatskhvYG 262
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1847 GHLVQFSGGVFSGQPATTDLNGILNFMYIYYAWLNiMKDQPElqnmaaflhHCEFLCFGDDNILFTSDKILKKfnlqTVH 1926
Cdd:cd23223    263 DKAYEMEGGMPSGCVGTSMFNCINNSAFIVSALIA-LKISPE---------DCAWICYGDDVIISTDEKALSK----RIA 328
                          410       420       430
                   ....*....|....*....|....*....|....*...
gi 1125811701 1927 DVLEKHLDVILLGSSKDKNNIEKfHHFTEAEFLKRKFV 1964
Cdd:cd23223    329 DFYHKNTNLVVTPASKSGDFPET-STIYDVTFLKRFFQ 365
Iflaviridae_RdRp cd23197
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Iflaviridae of ...
1703-1965 3.78e-14

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Iflaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Iflaviridae, order Picornavirales. Iflaviridae is a family of small non-enveloped viruses with (+)ssRNA genomes of approximately 9-11 kilobases in length encoding a single polyprotein. All members infect arthropod hosts with the majority infecting insects. Beneficial and pest insects serve as hosts and infections can be symptomless (Nilaparvata lugens honeydew virus 1), cause developmental abnormalities (deformed wing virus, Varroa destructor virus 1, sacbrood virus), behavioral changes (deformed wing virus, Varroa destructor virus 1, slow bee paralysis virus, sacbrood virus) and premature mortality (deformed wing virus, Varroa destructor virus 1, slow bee paralysis virus, infectious flacherie virus, sacbrood virus). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438047  Cd Length: 319  Bit Score: 76.06  E-value: 3.78e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1703 KDEVRKLKKIYDTPQTRIFTPGPFQHSITYRMYFHAAVALVRECRLKLPMKVGMNPFGDEVDYMVRKAISKGTNCFDGDF 1782
Cdd:cd23197     13 KDELRPSEKLRRFGGTRVFSVPPLELVLNSRRFLLPFMDAFQSFPIEAHHAIGLNPNSGDWRRLRDTLLEKGPCLLQMDY 92
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1783 SHYDASHPLFLVRSAmnvFHrVAVETTERDPRLTPE--LFAKQLEDERIIREGImradlqpfisIDGHLVQFSGGVFSGQ 1860
Cdd:cd23197     93 KNYSDAIPKECVAKA---FH-IIVDYYRKWHCLTVEieNALKTLFLDTADAELL----------VYGDVFKVNNGVLAGH 158
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1861 PATTDLNGILNFMYIYYAWLNIMKdqpelQNMAAFLHHCEFLCFGDDNILFTSDKILKKFNLQTVHDVLEKhLDVILLGS 1940
Cdd:cd23197    159 PMTSVVNSVVNLILMNYMWIKITR-----RRASEFFKLTYIIVMGDDVVISLPKQLTEEFDCRKICAEFAK-YDIKVTDS 232
                          250       260
                   ....*....|....*....|....*.
gi 1125811701 1941 SKDKNNIEK-FHHFTEAEFLKRKFVL 1965
Cdd:cd23197    233 EKNLTGEPKpYDSFDKFEFLSRGFSD 258
Cardiovirus_RdRp cd23211
RNA-dependent RNA polymerase (RdRp) in the Cardiovirus genus of positive-sense single-stranded ...
1511-1985 6.19e-14

RNA-dependent RNA polymerase (RdRp) in the Cardiovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Cardiovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. Vertebrates serve as natural hosts for the cardioviruses. There are currently six species in the genus: Cardiovirus A-F. Diseases associated with cardioviruses include: myocarditis, encephalitis, multiple sclerosis, and type 1 diabetes. Cardiovirus A is composed of only one serotype, encephalomycarditis virus (EMCV) which causes encephalomyocarditis and reproductive disease in pigs. Cardiovirus B comprises 15 genetic types, Theiler's murine encephalomyelitis virus (TMEV), Vilyuisk human encephalomyelitis virus (VHEV), thera virus (formerly named Theiler-like virus of rats), Saffold virus (SAFV) types 1 to 11, and genet fecal theilovirus (from Geneta geneta). Of these types, only VHEV and SAFV are thought to cause infection in humans. Thus far, Cardiovirus C has only been observed in the brown rat. 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: 438061  Cd Length: 460  Bit Score: 76.80  E-value: 6.19e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1511 GAAVVAKFDQKTHLPIKTQYHRSILHPPWhEHTFAPTILSDLDPRlTDDDGIPKCeiirpeifkwkrvFDYGNMDKDLMK 1590
Cdd:cd23211      1 GALVRIGTGPVVHVPRKTKLRRTVAHPVF-QPKFEPAVLSKYDPR-TDKDVDEVA-------------FSKHTTNQESLP 65
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1591 KTIEDV-TERIVDVAKASGKKTRVLTKSEALNGcslYEVSNPIDKHSSVGIPlknlFTQSRGKYHYLKFNEQKQFwsIDM 1669
Cdd:cd23211     66 PVFRMVaKEYANRVFTLLGKDNGRLTVEQAVLG---LEGMDPMEKDTSPGLP----YTQQGLRRTDVVDFETATM--IPF 136
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1670 EKECGKVLNNlcdqlidtyrrGDNPVLIYEVCPKDEVRKLKKIYDTpQTRIFTPGPFQHSITYRMYF-HAAVALVRECRL 1748
Cdd:cd23211    137 LAEAHRKMVE-----------GDYSDVVYQSFLKDEIRPIEKVQAA-KTRIVDVPPFEHCILGRQLLgRFASKFQTNPGL 204
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1749 KLPMKVGMNPFGDEVDYMVrkAISKGTNCFDGDFSHYDASHPLFLVRSAMNVFHrvaveTTER--DPRLtpelfAKQLED 1826
Cdd:cd23211    205 ELGSAIGCDPDVDWTAFAV--ALSGFKYVYDVDYSNFDSTHSTAMFELLIENFF-----TEENgfDPRI-----GEYLRS 272
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1827 ERIIREgimradlqpfiSIDGHLVQFSGGVFSGQPATTDLNGILNFMYIyYAWLNIMKDQPELQNMaaflhhcEFLCFGD 1906
Cdd:cd23211    273 LAVSRH-----------AYEERRVLIRGGLPSGCAATSMLNTIMNNIII-RAGLYLTYKNFEFDDI-------KVLSYGD 333
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1907 DNILFTSDKIlkKFNLqtVHDVLEKHLDVILLGSSKDKNNIEKfhHFTEAEFLKRKFVLKGDKFTMPLVDESIVK-MLEW 1985
Cdd:cd23211    334 DLLVATNYQI--DFNL--VKARLAKFGYKITPANKTSTFPLTS--TLEDVVFLKRKFVKENSYLYRPVMDRENLKaMLSY 407
Cosavirus_RdRp cd23226
RNA-dependent RNA polymerase (RdRp) in the genus Cosavirus of positive-sense single-stranded ...
1544-1985 3.75e-13

RNA-dependent RNA polymerase (RdRp) in the genus Cosavirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Cosavirus genus within the family Picornaviridae, order Picornavirales. The Cosavirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus consists of five species Cosavirus A, Cosavirus B, Cosavirus D, Cosavirus E and Cosavirus F. The candidate species, Cosavirus C, remains unclassified due to a lack of full genome sequence data. Cosaviruses (formerly called Dekaviruses) have been identified in the stools of south Asian children. Cosaviruses are most closely related to members of the Cardiovirus and Senecavirus genera, but they lack a leader polypeptide. The name Cosavirus stands for common stool-associated picornavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438076  Cd Length: 461  Bit Score: 74.28  E-value: 3.75e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1544 FAPTILSDLDPRLtdDDGIPkceiirpeifkwkrvFDYGNMDKDLMKKTIEDVTERIVDVA--------KASGKKTRVLT 1615
Cdd:cd23226     33 YGPAVLSKNDPRL--DPDVD---------------FDKVIFSKHVANVVIDEDTSFWNALKmsaqiyaeKFKGVDFSPLT 95
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1616 KSEALNGCSLYEVSNPidkHSSVGIPlknlFTQSRGKYhyLKFNEqkqfwsidmekecGKVLNNLCDQLIDTYRRGDNPV 1695
Cdd:cd23226     96 VEEAILGIPGLDRMDP---NTASGLP----YTKTRRQM--IDFQE-------------GKILDPELQERLDTWLSGKQPE 153
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1696 LIYEVCPKDEVRKLKKIyDTPQTRIFTPGPFQHSITYRMYFHAAVALVR-ECRLKLPMKVGMNP------FGdevdymvr 1768
Cdd:cd23226    154 MLYQTFLKDEIRPIEKV-KAGKTRIIDVTPLDHVLAFRIVLGRFMAHFHnNYGFELGSAVGCDPdvawanFG-------- 224
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1769 KAISKGTNCFDGDFSHYDASHPLFLVRSAMNVFHRvavETTERDPRLTpeLFAKQL-------EDERIIREgimradlqp 1841
Cdd:cd23226    225 FALSSKKYQYDFDYSNFDASHSESIFELLKQFVFT---KDNGFDHRCS--LMIDSLvtsthcyEDQRMTIR--------- 290
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1842 fisidghlvqfsGGVFSGQPATTDLNGILNFMY----IYYAWLNIMKDQPELqnmaaflhhcefLCFGDDnILFTSDKIL 1917
Cdd:cd23226    291 ------------GGLPSGTSGTSVINTIINNIIfkaaLYHTYSNFEWDDVQM------------LAYGDD-IVAASDCLL 345
                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1125811701 1918 kkfNLQTVHDVLeKHLDVILLGSSKDKNNIEKfhHFTEAEFLKRKFVlKGDKFTMPLVD-ESIVKMLEW 1985
Cdd:cd23226    346 ---DLDRVKYFM-ALIGYKITPADKGEKFIPK--DMQNIQFLKRSFR-KVAGVWAPIMDlENLQAMLSW 407
Polycipiviridae_RdRp cd23198
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Polycipiviridae of ...
1702-1963 5.30e-13

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Polycipiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Polycipiviridae (polycistronic picorna-like viruses), order Picornavirales. Polycipiviridae is a family of picorna-like viruses with non-segmented, linear, (+)ssRNA genomes of approximately 10-12 kb. Their genomes are polycistronic, with four (or more) consecutive 5'-proximal open reading frames (ORFs) encoding structural (and possibly other) proteins and a long 3' ORF encoding the replication polyprotein. Members of species within the family are typically found in ants, with Apple picorna-like virus 1 and the unnamed Polycipiviridae virus in fruit bat stool as exceptions. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438048  Cd Length: 317  Bit Score: 72.45  E-value: 5.30e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1702 PKDEVRKLKKIYDTPQTriftPgPFQHSIT-YRMYFHAA---------VALVRECRLKLPMKVGMNPFGDEvdymvrkai 1771
Cdd:cd23198      7 PKDELRPIYKALGDPQT----P-PKTRSVTcMNVYYILAwrrvtldfwASMHRAADGNFPFCPGINPEGPD--------- 72
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1772 skGTNCFdgdfsHYDASHPlflvrsamnvfHRVAVETTERDPRLTPELFAKQLEderiIREGIMRADLQPFIS------- 1844
Cdd:cd23198     73 --WNRLY-----HYLNRHP-----------NAVDFDVSNWDGHLPAELFYAVLD----IIKTVLGLKPNSPNAkviysil 130
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1845 ---IDGHlVQFSG-------GVFSGQPATTDLNGILNFMYIYYAWLNIMKDQPELQNMAAFLHHCEFLCFGDDNILFTSD 1914
Cdd:cd23198    131 tevMNCH-IQFEDiiyqklrGLISGFPGTAEVNTLAHWLLIYYIYLYLAQNTIYDMTITAFLRNVSAIFYGDDIIITISD 209
                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*....
gi 1125811701 1915 KILKKFNLQTVHDVLEKHlDVILLGSSKDKnNIEKFHHFTEAEFLKRKF 1963
Cdd:cd23198    210 EILHWFNGKTIQRMYEEH-GYPVTSAAKDT-EIPESKPLSDCQFLKSSW 256
Caliciviridae_RdRp cd23192
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of ...
1697-2015 7.27e-13

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: 71.91  E-value: 7.27e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1697 IYEVCPKDEVRKLKKIYDTpQTRIFTPGPFQHSITYRMYFHA-AVALVRECRLkLPMKVGMNPFGDEVDYMVrKAISKGT 1775
Cdd:cd23192      2 AYALALKDELRPVEKIAEG-KRRLLWGCDVGVTLVAAAAFGPvADALKAVCPT-GPIAVGINMDSEDVEVIF-ERLSGFR 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1776 NCFDGDFSHYDASHPLFLVRSAMNVFhrvaVETTERDPrltpelfakqlederiIREGIMRADLQPFISI-DGHLVQFSG 1854
Cdd:cd23192     79 YHYCLDYSKWDSTQSPAVTAAAIDIL----ADLSEETP----------------LRDSVVETLSSPPMGIfDDVIFVTKR 138
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1855 GVFSGQPATTDLNGILNFMYIYYAwlnIMKDQPELQNMAAFLHHCE-FLCFGDDNILFTSDKILKKFNlqTVHDVLEKhl 1933
Cdd:cd23192    139 GLPSGMPFTSVINSLNHWLLFSAA---VLKAYELVGIYTGNVFDEAdFFTYGDDGVYAMPPATASVMD--EIIENLKS-- 211
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1934 dVILLGSSKDKNNIEKFHHFTEAEFLKRKFVLKGDKFTMPLVDESIVKMLEWTTGPKHIYATRKLIRPPKQNKIIQIPNI 2013
Cdd:cd23192    212 -YGLKPTAADKTENPDIPPLQGPVFLKRTFVRTPGGWRALLDRSSILRQLYWVKGPNTHDWTEPPTEIDHEARTVQLENV 290

                   ..
gi 1125811701 2014 QL 2015
Cdd:cd23192    291 LL 292
Fipivirus_RdRp cd23229
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Fipivirus of ...
1632-1986 2.06e-12

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Fipivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Fipivirus genus within the family Picornaviridae, order Picornavirales. The Fipivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus contains five species: Fipivirus A (Wuhan sharpbelly picornavirus 2), Fipivirus B (Wuhan sharpbelly picornavirus 3), Fipivirus C (Wenling crossorhombus picornavirus), Fipivirus D (Wenling jack mackerels picornavirus) and Fipivirus E (Wenling banjofish picornavirus 1). All contain viruses from fish. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438079  Cd Length: 394  Bit Score: 71.38  E-value: 2.06e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1632 IDKHSSVGIPLKNlftQSRGKYHYLKFNEQKQFwsidMEKECGKVLNNLCDQLIDtYRRGDNPVLIYEVCPKDEVRKLKK 1711
Cdd:cd23229     11 LDMKTSAGYPWCE---QNQKKKDKIKLLAGKNF----LVRPLREVVHIVVDWYIM-PPDMPKPEIKYVVYLKDELLSSDK 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1712 IyDTPQTRIFTPGPFQHSITYRMYFHAAVALVR--ECRLKLPM--KVGMNPfgdEVDYMVRKAISKGTNCFDGDFSHYDA 1787
Cdd:cd23229     83 V-KMGRTRWICAAPVQLVCAWKKVFGRAIAAIHleSVTDGKSTgcAVGMDP---ETAWTDIALARPGWPVIALDYSNFDG 158
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1788 SHPLFLVRSAMNVFHRVAVETTERDPRLtpelfAKQLEDERIIregimradlqpfisIDGHLVQFSGGVFSGQPATTDLN 1867
Cdd:cd23229    159 SLQSFVITGAVRILGYIAGLPDGQSYRL-----AEFVYDVKQI--------------VGKYLYTTVGPLPSGCPSTSIIG 219
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1868 GILNFMYIYYAWLNIMKdqpelQNMAAFLHHCEFLCFGDDNILFTSDKILkkFNLQTVHDVLEKHLDVILLGSSkDKNNI 1947
Cdd:cd23229    220 SLCNVLMLLYTLSHATG-----QRYSAFRDWMHVVTYGDDVLVFVHPEVV--VVLDTLAHEMYLVFGVTATDAT-DKRAP 291
                          330       340       350       360
                   ....*....|....*....|....*....|....*....|..
gi 1125811701 1948 EKFHHFTEAEFLKRKFVLKGD--KFTMPLVD-ESIVKMLEWT 1986
Cdd:cd23229    292 PQLRELSNVTFLKRGFRQCSSvpFLVHPTMDkSTIYQMLAWK 333
Parechovirus_RdRp cd23217
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Parechovirus of ...
1676-1962 2.38e-09

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Parechovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the Parechovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. The Parechovirus genus is comprised of six species, Parechovirus A (formerly named Human parechovirus), Parechovirus B (formerly named Ljungan virus), Parechovirus C (Sebokele virus) and Parechovirus D (ferret parechovirus), Parechovirus E (falcon parechovirus) and Parechovirus F (gecko parechovirus). Humans, ferrets, and various rodents serve as natural hosts. Human parechoviruses may cause gastrointestinal or respiratory illness in infants, and have been implicated in cases of myocarditis and encephalitis. Human parechoviruses replicate in the respiratory and gastrointestinal tract. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438067  Cd Length: 371  Bit Score: 61.81  E-value: 2.38e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1676 VLNNLCDQLIDTYRRGDNPVLIYEVCPKDEVRKLKKIyDTPQTRIFTPGPFQHSITYRMYFHAAV-ALVRECRLKLPMKV 1754
Cdd:cd23217     42 QLEKDVKDKLHAVYKGNQPTTIFNACLKDELRKLDKI-AQGKTRCIEACSIDYVIAYRVVMSSLYeAIYQTPCQELGLAV 120
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1755 GMNPFGDeVDYMVRKAISKGtncFDGDFSHYDASHPLFLVRSAMNVfhrvaVETTERDPRLTPELFAKQLEDERIIREGI 1834
Cdd:cd23217    121 GMNPWTD-WDFMINALNPYN---YGLDYSSYDGSLSEMLMWEAVEV-----LAYCHESPDLVMQLHKPVINSDHVVMDER 191
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1835 MradlqpfisidghlvQFSGGVFSGQPATTDLNGILNFMY-IYYAWLNimkdQPELQnmaaflhhCEFLCFGDDNILFTS 1913
Cdd:cd23217    192 W---------------LVHGGMPSGSPCTTVLNSICNLLVcIYLAYLQ----SPGIE--------CLPIVYGDDVIFSVS 244
                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*....
gi 1125811701 1914 DKILKKFNLQTVHDVLEKHLdvillgSSKDKNNIEKFHHFTEAEFLKRK 1962
Cdd:cd23217    245 SEIDPEYLVSSAADSFGMEV------TGSDKDEPPSLLPRMEVEFLKRT 287
Kunsagivirus_RdRp cd23219
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Kunsagivirus of ...
1690-1990 1.23e-07

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Kunsagivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Kunsagivirus genus within the family Picornaviridae, order Picornavirales. The Kunsagivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Kunsagivirus is a new picornavirus genus containing a three species. Viral RNA of kunsagivirus A1 was detected in feces of an apparently healthy European roller (Coracias garrulus), of kunsagivirus B1 (bat kunsagivirus) in feces of the fruit bat Eidolon helvum, and of kunsagivirus C1 (bakunsavirus) in wild baboons (Papio cynocephalus). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438069  Cd Length: 346  Bit Score: 56.03  E-value: 1.23e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1690 RGDNPVLIYEVCPKDEVRKLKKIYDTpQTRIFTPGPFQHSITYRMYFhaaVALVRECRLKLPMKVGMNPfGDEVDYMVRK 1769
Cdd:cd23219     55 SGGAGEVKFSSFLKDELRPLSKIRSG-DTRVVECSSLDYTVAFRMQF---LRVLQMCYGSDPTLTGLAP-GMNVYTDMLP 129
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1770 AISK---GTNCFdgDFSHYDASHPLflvrsamNVFHRVAvetterdprltpELFAKQLEDERIIREGimradLQPFIsID 1846
Cdd:cd23219    130 LCTSlydYNLCL--DFSKYDSRLPL-------QVMHRVA------------QLISNLTPDPQVSMRL-----FQPII-IS 182
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1847 GHLV-----QFSGGVFSGQPATTDLNGILNFMYIYYAwlnIMKDQPELqnmaaflhHCEFLCFGDDNILFTSDKIlkkfN 1921
Cdd:cd23219    183 THIVgsyevVVEGGMPSGCPITTIMNSVCNVVMTSYA---MLLLDPDS--------DFWPVAYGDDNIVSTRKPI----D 247
                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1125811701 1922 LQTVHDVLEKHLDVILlgSSKDKNNIEKFHHFTEAEFLKRKFVLKGDkFTMP---LVDESIVKMLEWTTGPK 1990
Cdd:cd23219    248 TELFCSILNEEFGMIL--TGADKTTTVQAVPPMSVDFLKRRLRYTPE-FPLPvpvLPLDSMLSRICWCKGET 316
Mischivirus_RdRp cd23227
RNA-dependent RNA polymerase (RdRp) in the genus Mischivirus of positive-sense single-stranded ...
1523-1965 2.09e-07

RNA-dependent RNA polymerase (RdRp) in the genus Mischivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Mischivirus genus within the family Picornaviridae, order Picornavirales. The Mischivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Mischivirus is a picornavirus genus containing five species Mischivirus A, Mischivirus B, Mischivirus C, Mischivirus D and the proposed Mischivirus E. The name is derived from the name originally given to the virus, Miniopterus schreibersii picornavirus, which was found in the common bent-wing bat (aka Schreiber's long-fingered bat or Schreiber's bat) in China and is most closely related to the cardioviruses. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438077  Cd Length: 466  Bit Score: 56.11  E-value: 2.09e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1523 HLPIKTQYHRSILHPPWHEHTfAPTILSDLDPRLTdddgipkceiirPEIFKWKRVFDYGNMDKDLMKKTIEDVTERIVD 1602
Cdd:cd23227     13 HVPRKTKLRKSPAYPIFKPDA-GPAVLSKNDPRLA------------EGVDFDKQVFSKHSANQKEYPKAFRRMARWYAD 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1603 -VAKASGKKTRVLTKSEALNGCSLYEVsnpIDKHSSVGIPlknlFTQSRGKYHYLkfneqkqfwsIDMEKecGKVLNNLC 1681
Cdd:cd23227     80 rVFTYLGKDNGPLSVKDAIKGIDNLDA---MDPTTSPGLP----YSAAGIKRTDL----------LDFDT--GEIISPAL 140
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1682 DQLIDTYRRGDNPVLIYEVCPKDEVRKLKKIyDTPQTRIFTPGPFQHSITYRMY-------FHAAVALVrecrlkLPMKV 1754
Cdd:cd23227    141 RAEYNKYVSGDYSDHVFQTFLKDEIRSEEKI-KAGKTRIVDVPSLAHVIIGRVLlgkfcskFQASPGTE------LGSAI 213
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1755 GMNPFGDEVDYMVRkaISKGTNCFDGDFSHYDASHPLFLVRSAMNVFHrvavetTER---DPRLTPEL----FAKQ-LED 1826
Cdd:cd23227    214 GCNPDWDWTYFAHQ--LMERQWCYDIDYSNFDSTHGTGMFELLIDCFF------TPEngfSPAVAPYLrslaFSKHaWMD 285
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1827 ERIiregimradlqpfisidghlvQFSGGVFSGQPATTDLNGILNFMYIyYAWLNIMKDQPELQNMAAflhhcefLCFGD 1906
Cdd:cd23227    286 KRY---------------------KIEGGLPSGCSATSVLNTVMNNIII-RALLSLTYKNFHPEDVLV-------LAYGD 336
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1125811701 1907 DnILFTSDKILkKFNLqtVHDVLEKHlDVILLGSSKDKNNIEKFHHFTEAEFLKRKFVL 1965
Cdd:cd23227    337 D-LLVASDYQL-DFNR--VREKAAEH-TLYKLTTANKAPDFPETSTLLDCQFLKRKFVL 390
Teschovirus_RdRp cd23212
RNA-dependent RNA polymerase (RdRp) in the Teschovirus genus of positive-sense single-stranded ...
1703-1985 5.64e-07

RNA-dependent RNA polymerase (RdRp) in the Teschovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Teschovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. Teschoviruses are emerging pathogens and infect the porcine population only. There are two species in this genus, including Teschovirus A (previously Porcine teschovirus), which is responsible for the porcine enteroviral encephalomyelitis disease caused in pigs, and Teschovirus B. Teschovirus is also known by several other names including Teschen disease, Talfan disease, poliomyelitis suum, benign enzootic paresis, Klobauk disease and contagious porcine paralysis. Teschovirus has a single-stranded, linear, non-segmented RNA genome. The RNA genome is positively sensed meaning that it has the same polarity as the mRNA and no reverse transcription is necessary. 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: 438062  Cd Length: 354  Bit Score: 54.24  E-value: 5.64e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1703 KDEVRKLKKIYDTpQTRIFTPGPFQHSITYRMYFHAAVALVRecrlKLP-----MKVGMNPfgdEVDYMVRKAISKGTNC 1777
Cdd:cd23212     79 KDELRPKEKVQAG-KTRVIDVAGFGHAIVGRMLFGRLFAFFH----KNPgwntgSAVGVNP---DLAWTQIFYTAPSRNV 150
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1778 FDGDFSHYDASHP--LF-LVRSAMNVFHRVAVETTERDPRLtpelFAKQLEDERIIRegimradlqpfisidghlvqFSG 1854
Cdd:cd23212    151 LAMDYSGFDASHTsgMFcILKHFLTTLGYGTLQLSYIDSLC----YSKHHWDDETYR--------------------LDG 206
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1855 GVFSGQPATTDLNGILNFMyIYYAWLNIMKDQPelqnmaaflhhCEFLCFGDDNILFTSDKIlkkfnlqTVHDVLEKHLD 1934
Cdd:cd23212    207 GLPSGCSGTTIFNTIMNNI-VARAAASYAAEGP-----------VGILCYGDDILVSSPEKF-------PVSDWLEFYSK 267
                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1125811701 1935 VILLGSSKDKNNIEKFHHFTEAEFLKRKFVLKGdKFTMPLVDES-IVKMLEW 1985
Cdd:cd23212    268 TPYKVTAADKSEQIDWRDITQCTFLKRGFVLDG-SLVRPVMEEQhLAELLKW 318
AlkB COG3145
Alkylated DNA repair dioxygenase AlkB [Replication, recombination and repair];
2054-2102 1.02e-06

Alkylated DNA repair dioxygenase AlkB [Replication, recombination and repair];


Pssm-ID: 442379  Cd Length: 200  Bit Score: 51.70  E-value: 1.02e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1125811701 2054 PYEYNGGQHQPKRIPKIFRDL-------FHFDFNGVLINYYPDTSSGIPWHRDNEE 2102
Cdd:COG3145     70 GYRYSGTDPEPPPWPPALLALkrrveaaAGFPFNSCLLNLYRDGQDRMGWHQDDEE 125
Avisivirus_RdRp cd23231
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Avisivirus of ...
1694-1988 3.16e-06

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Avisivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Avisivirus genus within the family Picornaviridae, order Picornavirales. The Avisivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Avisivirus is a picornavirus genus containing three species Avisivirus A, Avisivirus B and Avisivirus C. The name Avisivirus is derived from Avihepato sister-clade. Turkeys serve as natural hosts. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438081  Cd Length: 362  Bit Score: 51.82  E-value: 3.16e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1694 PVLIYEVC-PKDEVRKLKKIyDTPQTRIFTPGPFQHSITYRMYFHAAVALVRECRLKLPMKVGMNPFgDEVDYMVRKAIs 1772
Cdd:cd23231     53 PPDVYFTTyLKDELRPKEKA-KAGKTRVISAASFDYTIACRMVFGPILRQLFAWGREFGFGPGLNPY-THFDELYDKIL- 129
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1773 kgTNCFDGDFSHYDASHPLFLVRSAMNVfhrvaVETTERDPrltpelfakqlederiirEGIMRADLQPFIS---IDGHL 1849
Cdd:cd23231    130 --PFVICLDYSGFDGSLSSELMFHAAQV-----IACFSEKP------------------EAIMASAELTIGSterVSDEV 184
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1850 VQFSGGVFSGQPATTDLNGILNfMYIYYAWLNIMKdqpelqnmaaflHHCE---FLCFGDDNILFTSdkilKKFNLQTVH 1926
Cdd:cd23231    185 WYVYGGMPSGSPWTTTLNTICN-LLMCYTYLLDMG------------HCWSetfVVAYGDDVVISAN----IKHNLEGIE 247
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1125811701 1927 DVLEKHLDVILLGSSKDKNNIEKFHHftEAEFLKR--KFVLKGDKFTMPLVDESIVKMLEWTTG 1988
Cdd:cd23231    248 QWFKTKFGATVTPSDKQGKITWTTKN--NMEFLKRrpKQLDFLPKIVGALDLDNMLDRIQWTKG 309
ps-ssRNAv_RdRp-like cd23167
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
1855-1910 6.89e-06

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


Pssm-ID: 438017 [Multi-domain]  Cd Length: 73  Bit Score: 45.79  E-value: 6.89e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1125811701 1855 GVFSGQPATTDLNGILNFMYIYYAWLNIMKDqpelqnmAAFLHHCEFLCFGDDNIL 1910
Cdd:cd23167     22 GQPSGSPNTSADNSLINLLLARLALRKACGR-------AEFLNSVGILVYGDDSLV 70
Solinviviridae_RdRp cd23199
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Solinviviridae of ...
1754-1992 6.40e-04

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Solinviviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Solinviviridae, order Picornavirales. Solinviviridae is a family of picorna/calici-like viruses with non-segmented, linear, (+)ssRNA genomes of approximately 10-11 kb. Members of two species within the family infect ants but related unclassified virus sequences derive from a large variety of insects and other arthropods. Phylogenetic analysis of RdRp amino acid sequences shows that members of the two classified solinvivirus species form part of a large and very diverse group of arthropod-infecting viruses within the picorna/calici-like group of viruses. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg (viral protein genome-linked)-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438049  Cd Length: 323  Bit Score: 44.27  E-value: 6.40e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1754 VGMNPFGDEVDYMVRkaISKGTNCFDGDFSHYDASHPLFLVRSAMNVFhrVAVETTERDPRLTpelfakqlederiireg 1833
Cdd:cd23199     73 VGCNPYATFHKFATK--FFKFKNFFSCDYKNFDRTIPKCVFEDFRDML--IQANPHMKNEIYA----------------- 131
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1834 iMRADLQPFISIDGH-LVQFSGGVFSGQPATTDLNGILNFMYIYYAWLNIMK----DQPELQNMAAFLhHCEFLcFGDDN 1908
Cdd:cd23199    132 -CFQTIIDRIQVSGNsILLVHGGMPSGCVPTAPLNSKVNDIMIYTAYVNILRradrGDITSYRYYRDL-VCRLF-YGDDV 208
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1909 ILFTSDKILKKFNLQTVHDVLeKHLDVILLGSSKDKNNIEKFHHFTEAEFLKRKFVLKGDKFTM---PLVDESIVKMLEW 1985
Cdd:cd23199    209 IIAVDDSIADIFNCQTLSEEM-KILFGMNMTDGSKSDIIPKFETIETLSFISRFFRPLKHQENFivgALKKISIQTHFYY 287

                   ....*....
gi 1125811701 1986 TTG--PKHI 1992
Cdd:cd23199    288 ATDdtPEHF 296
Crohivirus_RdRp cd23232
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Crohivirus of ...
1618-1873 3.50e-03

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Crohivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Crohivirus genus within the family Picornaviridae, order Picornavirales. The Crohivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Crohivirus is a new genus containing two species, Crohivirus A and Crohivirus B. Crohivirus A (Crohivirus 1, CroV-1) is a novel picornavirus found the lesser red musk shrew (Crocidura hirta) which is found in southern Africa. The genome sequence is most closely related to the parechoviruses. Crohivirus B consists of a virus which has been found in the straw-colored fruit bat (Eidolon helvum). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438082  Cd Length: 373  Bit Score: 42.01  E-value: 3.50e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1618 EALNGCSLYEVSNPIDKHSSVGIPLKNLFTQSRGkyhylkfneqkqFWSidmekecgKVLNNLCDQLIDTYRRGDNPVLI 1697
Cdd:cd23232      7 EEGDEHALDLKTSPGFKYVQMGLKKTDLVNRPNK------------FIH--------PILRNDVRLIFDEMAKGQMPVVT 66
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1698 YEVCPKDEVRKLKKIyDTPQTRIFTPGPFQHSITYRMYFHAAVALVRECRLKLP-MKVGMNPFGDEvDYMVRkaiSKGTN 1776
Cdd:cd23232     67 FTAHLKDELRKLEKI-RSGKTRCIEACDFDYTVAHKMMFGTLYKAIYDTPGIITgLAVGMNPWKDW-ELIQQ---SLFKY 141
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1125811701 1777 CFDGDFSHYDASHPLFLVRSAMNVFhrvaVETTERdPRLTPELFAKQLEDERIIREgimradlqpfisidgHLVQFSGGV 1856
Cdd:cd23232    142 NYDFDYKTFDGSLSRELMLHAVDIL----SACVEN-DEMAKLMLSVVVESVHLVLD---------------QKWNVSGGM 201
                          250
                   ....*....|....*..
gi 1125811701 1857 FSGQPATTDLNGILNFM 1873
Cdd:cd23232    202 PSGSPCTTVLNSVCNLI 218
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH