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Conserved domains on  [gi|1132371565|ref|YP_009337425|]
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hypothetical protein 1 [Wenzhou bivalvia virus 3]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ps-ssRNAv_Nodaviridae_RdRp cd23173
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Nodaviridae of ...
 655-890 5.84e-89

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Nodaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Nodaviridae, order Nodamuvirales. The family name Nodaviridae, derives from the Japanese village of Nodamura where Nodamura virus was first isolated from Culex tritaeniorhynchus mosquitoes. Virions are non-enveloped and spherical in shape with icosahedral symmetry and diameters ranging from 25 to 33 nm. The members of the two genera in this family infect insects (Alphanodavirus) or fish (Betanodavirus). Alphanodavirus infection results in the stunting, paralysis and death of the insect host. The infection of fish by betanodaviruses such as striped jack nervous necrosis virus or red-spotted grouper nervous necrosis virus causes neural necrosis, encephalopathy or retinopathy and is associated with behavioral abnormalities and high mortality, posing significant problems for marine aquaculture. The genome consists of two molecules of (+)ssRNA: RNA1 and RNA2. 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: 438023  Cd Length: 236  Bit Score: 286.33  E-value: 5.84e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132371565  655 IIETFQKNEVYGKLADPRTISQVDPRTKLAYSMFYMVISEEILKPQPWYTFGKTPKEMAERVAYIATGADSVVMGDFSRM 734
Cdd:cd23173     14 LVKAFIKREAYAKPKDPRNISTVDPEHTLKLSRYTYAFKEEVLKNQPWYAPGKTPKEIAERVQEIASSSDGVIETDYSRF 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132371565  735 DATISN-LGRHLTTSIMMRAFHPSYHEELQTLLQRQCHRTCFTRFGVKYTSGTSRLSGSPETSGHNTIENAFIAYLALRM 813
Cdd:cd23173     94 DGTISEwLRRNVEFAAYLRWFHPEYRAELLKLLDAEINCPARTKTGVKYDPGVSRLSGSPTTTDGNTIINAFVSYCALRE 173

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1132371565  814 TKDEDgnwierDRAYRILCTrteFGGDDSIMfslgPGITEETYCKAASKMGLKATCQVLQRwDLGVNFLARFFSRHV 890
Cdd:cd23173    174 TGYSP------EEAFALLGL---YYGDDGLS----DNLPAEALEKVAKDLGLKLKIEVVRP-GQPVTFLGRVFPDPW 236
Noda_Vmethyltr pfam19222
Nodavirus Vmethyltransferase; This entry represents a family of nodavirus proteins that is ...
 214-362 5.05e-57

Nodavirus Vmethyltransferase; This entry represents a family of nodavirus proteins that is homologous to pfam01660. These proteins are likely methytransferases involved in mRNA capping.


:

Pssm-ID: 408991  Cd Length: 148  Bit Score: 193.61  E-value: 5.05e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132371565  214 PIFAKVGgaHTHPEAASERNAMGPYFKRLAAMMGRDLFMYSLSNADIKaDTRGNKTMYWPKDLLVPHTAALPKETDMIGV 293
Cdd:pfam19222    1 PVPRKSG--HSHPEAAAERTAATRTIHAAIRSAGYEPYVVSPSRRDQD-NTDGSRYYYWAKDLRQPYRNDPITDGHVIVM 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1132371565  294 VDCDWYLDMNDLLtRYVVTWAIYGLNPTEPGGKVKNGDFTFINNVLHYSITGGANYKHELWDWNRETIC 362
Cdd:pfam19222   78 IDVDYYVDMNEWL-SLGRPILMYTFVPTEVAGRDKDYAFTIKDNVVHYHVSGGADYSHELWDYNGDTVS 145
BAT super family cl37898
GAF and HTH_10 associated domain; GAF-HTH_assoc domain is always found between GAF-2 and ...
 980-1023 2.33e-03

GAF and HTH_10 associated domain; GAF-HTH_assoc domain is always found between GAF-2 and HTH_10 domains on bacterio-opsin activator proteins. The exact function is not known.


The actual alignment was detected with superfamily member pfam15915:

Pssm-ID: 435017  Cd Length: 156  Bit Score: 39.85  E-value: 2.33e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1132371565  980 VQFPNDNEVDNFhIDYLREAYPDIEYVAFREWLDDVKTPEEFMR 1023
Cdd:pfam15915  114 VEVPPDADVREV-VEALEERYPDVELVARRERERPVRTRQEFRA 156
 
Name Accession Description Interval E-value
ps-ssRNAv_Nodaviridae_RdRp cd23173
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Nodaviridae of ...
 655-890 5.84e-89

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Nodaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Nodaviridae, order Nodamuvirales. The family name Nodaviridae, derives from the Japanese village of Nodamura where Nodamura virus was first isolated from Culex tritaeniorhynchus mosquitoes. Virions are non-enveloped and spherical in shape with icosahedral symmetry and diameters ranging from 25 to 33 nm. The members of the two genera in this family infect insects (Alphanodavirus) or fish (Betanodavirus). Alphanodavirus infection results in the stunting, paralysis and death of the insect host. The infection of fish by betanodaviruses such as striped jack nervous necrosis virus or red-spotted grouper nervous necrosis virus causes neural necrosis, encephalopathy or retinopathy and is associated with behavioral abnormalities and high mortality, posing significant problems for marine aquaculture. The genome consists of two molecules of (+)ssRNA: RNA1 and RNA2. 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: 438023  Cd Length: 236  Bit Score: 286.33  E-value: 5.84e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132371565  655 IIETFQKNEVYGKLADPRTISQVDPRTKLAYSMFYMVISEEILKPQPWYTFGKTPKEMAERVAYIATGADSVVMGDFSRM 734
Cdd:cd23173     14 LVKAFIKREAYAKPKDPRNISTVDPEHTLKLSRYTYAFKEEVLKNQPWYAPGKTPKEIAERVQEIASSSDGVIETDYSRF 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132371565  735 DATISN-LGRHLTTSIMMRAFHPSYHEELQTLLQRQCHRTCFTRFGVKYTSGTSRLSGSPETSGHNTIENAFIAYLALRM 813
Cdd:cd23173     94 DGTISEwLRRNVEFAAYLRWFHPEYRAELLKLLDAEINCPARTKTGVKYDPGVSRLSGSPTTTDGNTIINAFVSYCALRE 173

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1132371565  814 TKDEDgnwierDRAYRILCTrteFGGDDSIMfslgPGITEETYCKAASKMGLKATCQVLQRwDLGVNFLARFFSRHV 890
Cdd:cd23173    174 TGYSP------EEAFALLGL---YYGDDGLS----DNLPAEALEKVAKDLGLKLKIEVVRP-GQPVTFLGRVFPDPW 236
Noda_Vmethyltr pfam19222
Nodavirus Vmethyltransferase; This entry represents a family of nodavirus proteins that is ...
 214-362 5.05e-57

Nodavirus Vmethyltransferase; This entry represents a family of nodavirus proteins that is homologous to pfam01660. These proteins are likely methytransferases involved in mRNA capping.


Pssm-ID: 408991  Cd Length: 148  Bit Score: 193.61  E-value: 5.05e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132371565  214 PIFAKVGgaHTHPEAASERNAMGPYFKRLAAMMGRDLFMYSLSNADIKaDTRGNKTMYWPKDLLVPHTAALPKETDMIGV 293
Cdd:pfam19222    1 PVPRKSG--HSHPEAAAERTAATRTIHAAIRSAGYEPYVVSPSRRDQD-NTDGSRYYYWAKDLRQPYRNDPITDGHVIVM 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1132371565  294 VDCDWYLDMNDLLtRYVVTWAIYGLNPTEPGGKVKNGDFTFINNVLHYSITGGANYKHELWDWNRETIC 362
Cdd:pfam19222   78 IDVDYYVDMNEWL-SLGRPILMYTFVPTEVAGRDKDYAFTIKDNVVHYHVSGGADYSHELWDYNGDTVS 145
BAT pfam15915
GAF and HTH_10 associated domain; GAF-HTH_assoc domain is always found between GAF-2 and ...
 980-1023 2.33e-03

GAF and HTH_10 associated domain; GAF-HTH_assoc domain is always found between GAF-2 and HTH_10 domains on bacterio-opsin activator proteins. The exact function is not known.


Pssm-ID: 435017  Cd Length: 156  Bit Score: 39.85  E-value: 2.33e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1132371565  980 VQFPNDNEVDNFhIDYLREAYPDIEYVAFREWLDDVKTPEEFMR 1023
Cdd:pfam15915  114 VEVPPDADVREV-VEALEERYPDVELVARRERERPVRTRQEFRA 156
 
Name Accession Description Interval E-value
ps-ssRNAv_Nodaviridae_RdRp cd23173
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Nodaviridae of ...
 655-890 5.84e-89

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Nodaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Nodaviridae, order Nodamuvirales. The family name Nodaviridae, derives from the Japanese village of Nodamura where Nodamura virus was first isolated from Culex tritaeniorhynchus mosquitoes. Virions are non-enveloped and spherical in shape with icosahedral symmetry and diameters ranging from 25 to 33 nm. The members of the two genera in this family infect insects (Alphanodavirus) or fish (Betanodavirus). Alphanodavirus infection results in the stunting, paralysis and death of the insect host. The infection of fish by betanodaviruses such as striped jack nervous necrosis virus or red-spotted grouper nervous necrosis virus causes neural necrosis, encephalopathy or retinopathy and is associated with behavioral abnormalities and high mortality, posing significant problems for marine aquaculture. The genome consists of two molecules of (+)ssRNA: RNA1 and RNA2. 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: 438023  Cd Length: 236  Bit Score: 286.33  E-value: 5.84e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132371565  655 IIETFQKNEVYGKLADPRTISQVDPRTKLAYSMFYMVISEEILKPQPWYTFGKTPKEMAERVAYIATGADSVVMGDFSRM 734
Cdd:cd23173     14 LVKAFIKREAYAKPKDPRNISTVDPEHTLKLSRYTYAFKEEVLKNQPWYAPGKTPKEIAERVQEIASSSDGVIETDYSRF 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132371565  735 DATISN-LGRHLTTSIMMRAFHPSYHEELQTLLQRQCHRTCFTRFGVKYTSGTSRLSGSPETSGHNTIENAFIAYLALRM 813
Cdd:cd23173     94 DGTISEwLRRNVEFAAYLRWFHPEYRAELLKLLDAEINCPARTKTGVKYDPGVSRLSGSPTTTDGNTIINAFVSYCALRE 173

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1132371565  814 TKDEDgnwierDRAYRILCTrteFGGDDSIMfslgPGITEETYCKAASKMGLKATCQVLQRwDLGVNFLARFFSRHV 890
Cdd:cd23173    174 TGYSP------EEAFALLGL---YYGDDGLS----DNLPAEALEKVAKDLGLKLKIEVVRP-GQPVTFLGRVFPDPW 236
Noda_Vmethyltr pfam19222
Nodavirus Vmethyltransferase; This entry represents a family of nodavirus proteins that is ...
 214-362 5.05e-57

Nodavirus Vmethyltransferase; This entry represents a family of nodavirus proteins that is homologous to pfam01660. These proteins are likely methytransferases involved in mRNA capping.


Pssm-ID: 408991  Cd Length: 148  Bit Score: 193.61  E-value: 5.05e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132371565  214 PIFAKVGgaHTHPEAASERNAMGPYFKRLAAMMGRDLFMYSLSNADIKaDTRGNKTMYWPKDLLVPHTAALPKETDMIGV 293
Cdd:pfam19222    1 PVPRKSG--HSHPEAAAERTAATRTIHAAIRSAGYEPYVVSPSRRDQD-NTDGSRYYYWAKDLRQPYRNDPITDGHVIVM 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1132371565  294 VDCDWYLDMNDLLtRYVVTWAIYGLNPTEPGGKVKNGDFTFINNVLHYSITGGANYKHELWDWNRETIC 362
Cdd:pfam19222   78 IDVDYYVDMNEWL-SLGRPILMYTFVPTEVAGRDKDYAFTIKDNVVHYHVSGGADYSHELWDYNGDTVS 145
ps-ssRNAv_CBPV-like_RdRp cd23174
catalytic core domain of RNA-dependent RNA polymerase (RdRp) chronic bee paralysis virus (CBPV) ...
 656-871 6.13e-16

catalytic core domain of RNA-dependent RNA polymerase (RdRp) chronic bee paralysis virus (CBPV) and related positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of the chronic bee paralysis virus (CBPV) and related (+)ssRNA viruses. The CBPV is the causative agent of severe, usually fatal, paralysis in adult honey bees. CBPV has not been assigned to any group or class of viruses because it has a unique genome organization and virion morphology. However, analyses of the nucleic acid sequence showed similarities between the RdRp of CBPV and the RdRps of Tombusviruses, Nodaviruses, Lake Sinai virus 1 and 2 as well as the Anopheline associated C virus (AACV). CBPV was one of the first viruses in honey bees to be described and isolated as it causes characteristic signs of disease in adult honey bees. 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: 438024  Cd Length: 229  Bit Score: 78.29  E-value: 6.13e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132371565  656 IETFQKNEVYGKLADPRTISqvdPRTKLAYSMF--YMVISEEILKPQPWYTFGKTPKEMAERVAYIATgADSVVMGDFSR 733
Cdd:cd23174     16 IKNFVKNETTAKFVDPRNIS---PRSDEFLVVVgpYISAIEHAAVHCPFLIKGLTPKKRCDKLSWLTE-YERFLEIDFSR 91

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132371565  734 MDATIS-NLGRHLTTSIMMRAFHPSYHEELQTLLQRQCHRTCFTRFGVKYTSGTSRLSGSPETSGHNTIENAFIAYLALR 812
Cdd:cd23174     92 FDMTLMkDLLRIVELRFLLDPYTQRAHQLFIAFMLYTLTNVGVSRFGTHYKRDGTRCSGDPHTSIGNGFLNAFIIWLCLR 171

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132371565  813 mtKDEDGNWierdrayrilctRTEFGGDDSIMFSLGPGITE-ETYCKAASKMGLKATCQV 871
Cdd:cd23174    172 --KLPTNSW------------QSAHEGDDGIIGLRANVVNQvEYNLKFLSCLGFRAKIRV 217
ps_ssRNAv_Tolivirales_RdRp cd23179
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ...
 659-845 6.28e-10

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of positive-sense single-stranded RNA (+ssRNA) viruses; This family contains the catalytic core domain of RdRp of Tolivirales, an order of (+)ssRNA viruses which infect insects and plants. The virions are non-enveloped, spherical, and have an icosahedral capsid. The name Tolivirales, is derived from "tombusvirus-like" with the suffix -virales indicating a virus order. This order includes two families: Carmotetraviridae and Tombusviridae. 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: 438029  Cd Length: 227  Bit Score: 60.61  E-value: 6.28e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132371565  659 FQKNEVYGKLADPRTISQVDPRTKLAYS--------MFYMVISEEILKpQPWYTFGKTPKEMAERVAYIATG-ADSVVMG 729
Cdd:cd23179      9 AEKYNPLAKNKKPRMIQPRSPRYNLELArylkpiehALYGALDAGRGG-TRVVAKGLNPRQRANLIRRKWDEfDDPVVFS 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132371565  730 -DFSRMDATISNLGRHLTTSIMMRAFhpSYHEELQTLLQRQCHRTCFTRFGVKYTSGTSRLSGSPETSGHNTIENAFIAY 808
Cdd:cd23179     88 lDASRFDAHVSVELLRLEHSVYLACY--PGDPELRKLLKWQLVNKGRTSNGVKYKTRGGRMSGDMNTGLGNCLIMLAMVY 165

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 1132371565  809 LALRmtkdedgnwiERDRAYRILCTrtefgGDDSIMF 845
Cdd:cd23179    166 AVLR----------ELGIKYDLLVD-----GDDALVF 187
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 658-845 1.84e-06

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


Pssm-ID: 238843 [Multi-domain]  Cd Length: 278  Bit Score: 50.74  E-value: 1.84e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132371565  658 TFQKNEV-------YGKladPRTISQVDPRTKLAYSMFYMVISEEILKP--QPWYTFGKTP-----KEMAERvayIATGA 723
Cdd:cd01699     22 TFLKDELrplekveAGK---TRLIQPRPLDYNIALRMYLGPFEAKLMKNrgGLPIAVGINPysrdwTILANK---LRSFS 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132371565  724 DSVVMGDFSRMDATISNLGRHLTTSIMMRAFHPSYHEELQTLLQRQCHRTCFTRFGVKYTSGTSRLSGSPETSGHNTIEN 803
Cdd:cd01699     96 PVAIALDYSRFDSSLSPQLLEAEHSIYNALYDDDDELERRNLLRSLTNNSLHIGFNEVYKVRGGRPSGDPLTSIGNSIIN 175

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 1132371565  804 AFIAYLALRMTKDEdgnwiERDRAYRILCTrtefgGDDSIMF 845
Cdd:cd01699    176 CILVRYAFRKLGGK-----SFFKNVRLLNY-----GDDCLLS 207
ps-ssRNAv-Picornavirales cd23169
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...
 718-889 1.27e-05

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This family contains the catalytic core domain of RdRp of Picornavirales, an order of (+)ssRNA viruses. The order Picornavirales comprises viruses that historically are referred to as picorna-like viruses and which are classified into eight virus families: Caliciviridae, Dicistroviridae, Iflaviridae, Marnaviridae, Picornaviridae, Polycipiviridae, Secoviridae, and Solinviviridae. All known genomes of Picornavirales members encode proteins with helicase, 3C-like protease, and RdRp domains, as well as capsid proteins with related structures, although the genome organizations can differ among viruses. The picornavirus genome is replicated via a negative-sense (-) RNA intermediate by the viral RdRp, named 3Dpol, which uses VPg (the product of 3B) as a primer to initiate the replication process. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438019  Cd Length: 309  Bit Score: 48.75  E-value: 1.27e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132371565  718 YIATGADSVVMGDFSRMDATISnlgrhltTSIMMRAFH-----------PSYHEELQTLLQRQCHRTCfTRFGVKYTSGT 786
Cdd:cd23169     73 RLLKKGPNIFAGDYSNFDGSLP-------PDVMEAAFDiindwydeyvdDEDERVRKVLFEELINTIH-LVGNLVYQVHG 144

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132371565  787 SRLSGSPETSGHNTIENAFIAYLALRMTKDEDgNWIERDRAYRILCTrtefgGDDSIMfSLGPGITE----ETYCKAASK 862
Cdd:cd23169    145 GNPSGNPLTTIINSIVNLLYIRYAWLRITGLT-SLSDFKKNVRLVTY-----GDDVII-SVSDEVKDefnfVTISEFLKE 217

                          170       180       190
                   ....*....|....*....|....*....|...
gi 1132371565  863 MGLKAT------CQVLQRWDLGVNFLARFFSRH 889
Cdd:cd23169    218 LGITYTdadksgDIVPYRPLEEVTFLKRGFRPH 250
BAT pfam15915
GAF and HTH_10 associated domain; GAF-HTH_assoc domain is always found between GAF-2 and ...
 980-1023 2.33e-03

GAF and HTH_10 associated domain; GAF-HTH_assoc domain is always found between GAF-2 and HTH_10 domains on bacterio-opsin activator proteins. The exact function is not known.


Pssm-ID: 435017  Cd Length: 156  Bit Score: 39.85  E-value: 2.33e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1132371565  980 VQFPNDNEVDNFhIDYLREAYPDIEYVAFREWLDDVKTPEEFMR 1023
Cdd:pfam15915  114 VEVPPDADVREV-VEALEERYPDVELVARRERERPVRTRQEFRA 156
 
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.
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