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Conserved domains on  [gi|1143619699|gb|AQM55436|]
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hypothetical protein 1 [San Bernardo virus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Kitaviridae_RdRp cd23254
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of ...
 2039-2305 1.01e-170

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Kitaviridae, order Martellivirales. The family Kitaviridae is composed of five recognized species among the three genera: Blueberry necrotic ring blotch virus and Tea plant necrotic ring blotch virus (genus Blunervirus); Citrus leprosis virus C and Citrus leprosis virus C2 (genus Cilevirus); and Hibiscus green spot virus 2 (genus Higrevirus). Although related, there are considerable physical and genetic distinctions between members of the different genera. For example, cile- and higreviruses are associated with a bacilliform virion, whereas a spherical virion has been observed for the lone blunervirus for which microscopy has been reported. Moreover, the replication-associated polyproteins are encoded by a single genomic RNA for cile- and higreviruses, but are split between two genomic RNAs for blunerviruses. 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: 438104  Cd Length: 267  Bit Score: 524.02  E-value: 1.01e-170
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2039 NSYSFSIKRKPKPNLTVDATRSYLALQTIVYHEKPINAMFCSVFREIKKRVTSSLLPHVKIFCDMSAEEFEEILNRDIPI 2118
Cdd:cd23254      1 NVYSFMIKRNPKPNLTVDAAYKYPALQTIAYHDKDINAIFCPIFRELKKRLLAVLKPNFVIFTDMSPEDFEELLNRRFPP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2119 EKLHKILEKLEIDISKYDKSQRELALEFECKLMRRFGVSEDIIELWYNAHILTEVYDRNTKLKALIPYQRKSGDASTFIG 2198
Cdd:cd23254     81 EVLSKLLHKLEIDISKYDKSQGELALLFECKLMRRFGVPEELVELWFNAHVLTTLYDRTNKLKALVEYQRKSGDASTFFG 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2199 NTLFLMAVISDLIPISQMDLALFSGDDSLIYGLGLKKYKNAQHFGLKFNLEIKFFEFEHSYFCSKFLLPVNGRWRFTPCP 2278
Cdd:cd23254    161 NTLFLMAVLADLFDLSDLELALFSGDDSLLFGRNLLDYDDSQHFALKFNLESKFLNYKYPYFCSKFLLPVGGRWYFVPDP 240

                          250       260
                   ....*....|....*....|....*..
gi 1143619699 2279 VKFMTKLGRHDMVNFEHVEQYRVSFAD 2305
Cdd:cd23254    241 VKLLTKLGRHDLVNWEHVEEYRISLKD 267
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 1353-1618 5.15e-33

Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.


:

Pssm-ID: 366646 [Multi-domain]  Cd Length: 227  Bit Score: 128.65  E-value: 5.15e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 1353 GIVQAGPGCGKTTYVVNnsvpphVSGASNVLLATTEgkyDYIDRLQKKYNRiftkdqlsHVRTLASFLVNPhKNVKSSVL 1432
Cdd:pfam01443    1 IVVHGVPGCGKSTLIRK------LLRTSRVIRPTAE---LRTEGKPDLPNL--------NVRTVDTFLMAL-LKPTGKIL 62

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 1433 IIDEALMSHPGQIFFAISLSGATTVKLLGDRLQIPFVNRTPAFPtkfdkLPDFVPVVETLY---ISYRCRTDVVARLDAE 1509
Cdd:pfam01443   63 ILDEYTLLPPGYILLLAAISGAKLVILFGDPLQIPYHSRAPSFL-----IPHFPSSLSHRVgrrTTYLLPSLRAPILSAK 137

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 1510 YLKCNAPlgvNKGLMSVHYSPNTckvvkicnddfpkDPNVQYLVFTQpekTILKNLKLHVSTVHEYQGKEAKEIRVVRLN 1589
Cdd:pfam01443  138 GFEVVVE---RSGEYKVDYDPNG-------------VLVLVYLTFTQ---ALKESLGVRVTTVHEVQGLTFDSVTLVLDT 198

                          250       260
                   ....*....|....*....|....*....
gi 1143619699 1590 AQPQTEIYKRFNYALVALTRHTEKLTYYT 1618
Cdd:pfam01443  199 DTDLLIISDSPEHLYVALTRHRKSLHILT 227
Vmethyltransf super family cl46422
Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ...
 82-354 2.11e-12

Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily.


The actual alignment was detected with superfamily member pfam01660:

Pssm-ID: 480762  Cd Length: 308  Bit Score: 70.40  E-value: 2.11e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699   82 LSKEDQDKLRRtfcmFNLDFTKASNCSG-HPFWRAHRKLsemrMLNsaritpTCRPSVGYDVVYKDVGGNPTTHFSRNEE 160
Cdd:pfam01660    5 LSPEAQELLEN----LGIEFSPYSVTPHsHPAAKALENL----LLE------VLPSYLPNPSTVLDIKGSKLRHLKRGNP 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699  161 YVHTCAPLLSnnddkrrsaYKEVLRRTDRDNkcVRLHLEQNSRVICNRRSQNC---AIKAEVLIFLHSSYDMSAEDIADS 237
Cdd:pfam01660   71 NVHCCNPILD---------PRDVARYPEAFS--LEKSLGNGEDLRPTNTFEDCrvlAPTTSYAFMHDSLHDWSPEELADL 139

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699  238 MHRADAR-VAYGCFHFNPRVLYEKEGKLSNGMYFKKlVVNGRLHirfwFENDN--QEGYEHDYlTYLSLVRTFRIKStck 314
Cdd:pfam01660  140 FLRKPKLeRLYATLVFPPELLFGDKESLYPELYTFW-YKGDRFH----FYPDGhlGGSYTHPL-NLLSWLTTSKIHL--- 210

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|.
gi 1143619699  315 KNPRYYNVQFDVTEDDTTFFTIRHSD-NGNIPRSNPYRVFT 354
Cdd:pfam01660  211 PGGFTYTVERLESRGAHHLFKITRGDgLTPKVIVPDSRTFG 251
AdoMet_MTases super family cl17173
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 806-992 9.85e-11

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


The actual alignment was detected with superfamily member pfam01728:

Pssm-ID: 473071  Cd Length: 179  Bit Score: 62.99  E-value: 9.85e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699  806 YVCRSGLKTAEMFTRFftNDIESAFSI----GGPGGEVEFLCDRGIRT-FGatktdlIDfspaVRHHLFTQLLGD----T 876
Cdd:pfam01728    1 YRSRAAYKLLEIDEKF--GLLKPGKTVldlgAAPGGWSQVALQRGAGKvVG------VD----LGPMQLWKPRNDpgvtF 68

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699  877 YDGDITDLSNIisfgKSVRKYYSEGVDFFGGDAA-DSSRENEID-LKSMSHLLSWEILCCItVLKEGGCAYFKVFDllSH 954
Cdd:pfam01728   69 IQGDIRDPETL----DLLEELLGRKVDLVLSDGSpFISGNKVLDhLRSLDLVKAALEVALE-LLRKGGNFVCKVFQ--GE 141

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 1143619699  955 KNPSLIHYLHSHFDDVQVVKLETSRSASTELHIICRGF 992
Cdd:pfam01728  142 DFSELLYLLKLGFEKVGVFKPPASRPESSEEYLVCLGF 179
 
Name Accession Description Interval E-value
Kitaviridae_RdRp cd23254
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of ...
 2039-2305 1.01e-170

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Kitaviridae, order Martellivirales. The family Kitaviridae is composed of five recognized species among the three genera: Blueberry necrotic ring blotch virus and Tea plant necrotic ring blotch virus (genus Blunervirus); Citrus leprosis virus C and Citrus leprosis virus C2 (genus Cilevirus); and Hibiscus green spot virus 2 (genus Higrevirus). Although related, there are considerable physical and genetic distinctions between members of the different genera. For example, cile- and higreviruses are associated with a bacilliform virion, whereas a spherical virion has been observed for the lone blunervirus for which microscopy has been reported. Moreover, the replication-associated polyproteins are encoded by a single genomic RNA for cile- and higreviruses, but are split between two genomic RNAs for blunerviruses. 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: 438104  Cd Length: 267  Bit Score: 524.02  E-value: 1.01e-170
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2039 NSYSFSIKRKPKPNLTVDATRSYLALQTIVYHEKPINAMFCSVFREIKKRVTSSLLPHVKIFCDMSAEEFEEILNRDIPI 2118
Cdd:cd23254      1 NVYSFMIKRNPKPNLTVDAAYKYPALQTIAYHDKDINAIFCPIFRELKKRLLAVLKPNFVIFTDMSPEDFEELLNRRFPP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2119 EKLHKILEKLEIDISKYDKSQRELALEFECKLMRRFGVSEDIIELWYNAHILTEVYDRNTKLKALIPYQRKSGDASTFIG 2198
Cdd:cd23254     81 EVLSKLLHKLEIDISKYDKSQGELALLFECKLMRRFGVPEELVELWFNAHVLTTLYDRTNKLKALVEYQRKSGDASTFFG 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2199 NTLFLMAVISDLIPISQMDLALFSGDDSLIYGLGLKKYKNAQHFGLKFNLEIKFFEFEHSYFCSKFLLPVNGRWRFTPCP 2278
Cdd:cd23254    161 NTLFLMAVLADLFDLSDLELALFSGDDSLLFGRNLLDYDDSQHFALKFNLESKFLNYKYPYFCSKFLLPVGGRWYFVPDP 240

                          250       260
                   ....*....|....*....|....*..
gi 1143619699 2279 VKFMTKLGRHDMVNFEHVEQYRVSFAD 2305
Cdd:cd23254    241 VKLLTKLGRHDLVNWEHVEEYRISLKD 267
RdRP_2 pfam00978
RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ...
 1910-2314 4.27e-87

RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins: 2A protein from bromoviruses putative RNA dependent RNA polymerase from tobamoviruses Non structural polyprotein from togaviruses


Pssm-ID: 395779  Cd Length: 440  Bit Score: 292.62  E-value: 4.27e-87
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 1910 NSDLDLEMGQLTYAPvlGVQLNRRFDN---LRPILKTPMPHMRDYNTRELMLALQKRNRNVPYMNGTVDFDKSSDEMLDN 1986
Cdd:pfam00978    1 TSDISLDLDDCRLDP--SKSKPKPKDKepyLVPVLRTAAPSPRQNTLKEVLLALKKRNFNVPELQESVDLDDTAERVAER 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 1987 LLRECFDPALLEFHtrEPVSISCNSVSDWLSGQ-PPAVKGMIVP-SFAMHCSALNSYSFSIKRKPKPNLTVDATRSYLAL 2064
Cdd:pfam00978   79 FKKSFLDKEKLDKL--DPIINTTENVSRWLDKQsGKKAAQLKLDdLVPLHEVDLDRYKHMIKSDVKPKLDLSPQSERPAL 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2065 QTIVYHEKPINAMFCSVFREIKKRVTSSLLPHVKIFCDMSAEEFEEilnrdiPIEKLHKILEKLEIDISKYDKSQRELAL 2144
Cdd:pfam00978  157 QTITYHDKGVTAYFSPIFRELFERLLYVLKPKIVFPTGMTSSLIAE------HFEFLDASEDFLEIDFSKFDKSQGELHL 230

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2145 EFECKLMRRFGVSEDIIELWYNAHILTEVYDRNTKLKALIPYQRKSGDASTFIGNTLFLMAVISDLIPISQMDLALFSGD 2224
Cdd:pfam00978  231 LVQLEILKLLGLDPELADLWFKFHRQSYIKDRKNGVGFSVDYQRKSGDANTYLGNTLVTMAMLASVYDLEKIDCAAFSGD 310

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2225 DSLIYglGLKKYKN-AQHFGLKFNLEIKFFEFEHSYFCSKFLLPVNGRWRFTPCPVKFMTKLGR-HDMVNFEHVEQYRVS 2302
Cdd:pfam00978  311 DSLIF--SPKPIEDpASRFATLFNMEAKVFDPSVPYFCSKFLLEVDGGAFFVPDPLKLLQKLGKkKIPDDEQHLDEIFTS 388

                          410
                   ....*....|..
gi 1143619699 2303 FADTVKNYADYH 2314
Cdd:pfam00978  389 LCDLTKSFNDDC 400
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 1353-1618 5.15e-33

Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.


Pssm-ID: 366646 [Multi-domain]  Cd Length: 227  Bit Score: 128.65  E-value: 5.15e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 1353 GIVQAGPGCGKTTYVVNnsvpphVSGASNVLLATTEgkyDYIDRLQKKYNRiftkdqlsHVRTLASFLVNPhKNVKSSVL 1432
Cdd:pfam01443    1 IVVHGVPGCGKSTLIRK------LLRTSRVIRPTAE---LRTEGKPDLPNL--------NVRTVDTFLMAL-LKPTGKIL 62

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 1433 IIDEALMSHPGQIFFAISLSGATTVKLLGDRLQIPFVNRTPAFPtkfdkLPDFVPVVETLY---ISYRCRTDVVARLDAE 1509
Cdd:pfam01443   63 ILDEYTLLPPGYILLLAAISGAKLVILFGDPLQIPYHSRAPSFL-----IPHFPSSLSHRVgrrTTYLLPSLRAPILSAK 137

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 1510 YLKCNAPlgvNKGLMSVHYSPNTckvvkicnddfpkDPNVQYLVFTQpekTILKNLKLHVSTVHEYQGKEAKEIRVVRLN 1589
Cdd:pfam01443  138 GFEVVVE---RSGEYKVDYDPNG-------------VLVLVYLTFTQ---ALKESLGVRVTTVHEVQGLTFDSVTLVLDT 198

                          250       260
                   ....*....|....*....|....*....
gi 1143619699 1590 AQPQTEIYKRFNYALVALTRHTEKLTYYT 1618
Cdd:pfam01443  199 DTDLLIISDSPEHLYVALTRHRKSLHILT 227
Vmethyltransf pfam01660
Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ...
 82-354 2.11e-12

Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily.


Pssm-ID: 396298  Cd Length: 308  Bit Score: 70.40  E-value: 2.11e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699   82 LSKEDQDKLRRtfcmFNLDFTKASNCSG-HPFWRAHRKLsemrMLNsaritpTCRPSVGYDVVYKDVGGNPTTHFSRNEE 160
Cdd:pfam01660    5 LSPEAQELLEN----LGIEFSPYSVTPHsHPAAKALENL----LLE------VLPSYLPNPSTVLDIKGSKLRHLKRGNP 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699  161 YVHTCAPLLSnnddkrrsaYKEVLRRTDRDNkcVRLHLEQNSRVICNRRSQNC---AIKAEVLIFLHSSYDMSAEDIADS 237
Cdd:pfam01660   71 NVHCCNPILD---------PRDVARYPEAFS--LEKSLGNGEDLRPTNTFEDCrvlAPTTSYAFMHDSLHDWSPEELADL 139

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699  238 MHRADAR-VAYGCFHFNPRVLYEKEGKLSNGMYFKKlVVNGRLHirfwFENDN--QEGYEHDYlTYLSLVRTFRIKStck 314
Cdd:pfam01660  140 FLRKPKLeRLYATLVFPPELLFGDKESLYPELYTFW-YKGDRFH----FYPDGhlGGSYTHPL-NLLSWLTTSKIHL--- 210

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|.
gi 1143619699  315 KNPRYYNVQFDVTEDDTTFFTIRHSD-NGNIPRSNPYRVFT 354
Cdd:pfam01660  211 PGGFTYTVERLESRGAHHLFKITRGDgLTPKVIVPDSRTFG 251
FtsJ pfam01728
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...
 806-992 9.85e-11

FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesized that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping.


Pssm-ID: 426399  Cd Length: 179  Bit Score: 62.99  E-value: 9.85e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699  806 YVCRSGLKTAEMFTRFftNDIESAFSI----GGPGGEVEFLCDRGIRT-FGatktdlIDfspaVRHHLFTQLLGD----T 876
Cdd:pfam01728    1 YRSRAAYKLLEIDEKF--GLLKPGKTVldlgAAPGGWSQVALQRGAGKvVG------VD----LGPMQLWKPRNDpgvtF 68

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699  877 YDGDITDLSNIisfgKSVRKYYSEGVDFFGGDAA-DSSRENEID-LKSMSHLLSWEILCCItVLKEGGCAYFKVFDllSH 954
Cdd:pfam01728   69 IQGDIRDPETL----DLLEELLGRKVDLVLSDGSpFISGNKVLDhLRSLDLVKAALEVALE-LLRKGGNFVCKVFQ--GE 141

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 1143619699  955 KNPSLIHYLHSHFDDVQVVKLETSRSASTELHIICRGF 992
Cdd:pfam01728  142 DFSELLYLLKLGFEKVGVFKPPASRPESSEEYLVCLGF 179
RlmE COG0293
23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ [Translation, ribosomal structure and ...
 920-992 5.32e-05

23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ [Translation, ribosomal structure and biogenesis]; 23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440062 [Multi-domain]  Cd Length: 208  Bit Score: 46.60  E-value: 5.32e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699  920 LKSMsHL--LSWEIlcCITVLKEGGCAYFKVF------DLLshknpsliHYLHSHFDDVQVVKLETSRSASTELHIICRG 991
Cdd:COG0293    137 ARSM-YLveLALDF--ARKVLKPGGAFVVKVFqgegfdELL--------KELKKLFKKVKHRKPKASRARSSEVYLVAKG 205


                   .
gi 1143619699  992 F 992
Cdd:COG0293    206 F 206
 
Name Accession Description Interval E-value
Kitaviridae_RdRp cd23254
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of ...
 2039-2305 1.01e-170

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Kitaviridae, order Martellivirales. The family Kitaviridae is composed of five recognized species among the three genera: Blueberry necrotic ring blotch virus and Tea plant necrotic ring blotch virus (genus Blunervirus); Citrus leprosis virus C and Citrus leprosis virus C2 (genus Cilevirus); and Hibiscus green spot virus 2 (genus Higrevirus). Although related, there are considerable physical and genetic distinctions between members of the different genera. For example, cile- and higreviruses are associated with a bacilliform virion, whereas a spherical virion has been observed for the lone blunervirus for which microscopy has been reported. Moreover, the replication-associated polyproteins are encoded by a single genomic RNA for cile- and higreviruses, but are split between two genomic RNAs for blunerviruses. 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: 438104  Cd Length: 267  Bit Score: 524.02  E-value: 1.01e-170
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2039 NSYSFSIKRKPKPNLTVDATRSYLALQTIVYHEKPINAMFCSVFREIKKRVTSSLLPHVKIFCDMSAEEFEEILNRDIPI 2118
Cdd:cd23254      1 NVYSFMIKRNPKPNLTVDAAYKYPALQTIAYHDKDINAIFCPIFRELKKRLLAVLKPNFVIFTDMSPEDFEELLNRRFPP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2119 EKLHKILEKLEIDISKYDKSQRELALEFECKLMRRFGVSEDIIELWYNAHILTEVYDRNTKLKALIPYQRKSGDASTFIG 2198
Cdd:cd23254     81 EVLSKLLHKLEIDISKYDKSQGELALLFECKLMRRFGVPEELVELWFNAHVLTTLYDRTNKLKALVEYQRKSGDASTFFG 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2199 NTLFLMAVISDLIPISQMDLALFSGDDSLIYGLGLKKYKNAQHFGLKFNLEIKFFEFEHSYFCSKFLLPVNGRWRFTPCP 2278
Cdd:cd23254    161 NTLFLMAVLADLFDLSDLELALFSGDDSLLFGRNLLDYDDSQHFALKFNLESKFLNYKYPYFCSKFLLPVGGRWYFVPDP 240

                          250       260
                   ....*....|....*....|....*..
gi 1143619699 2279 VKFMTKLGRHDMVNFEHVEQYRVSFAD 2305
Cdd:cd23254    241 VKLLTKLGRHDLVNWEHVEEYRISLKD 267
Virgaviridae_RdRp cd23251
RNA-dependent RNA polymerase (RdRp) in the family Virgaviridae of positive-sense ...
 1900-2313 1.27e-96

RNA-dependent RNA polymerase (RdRp) in the family Virgaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Virgaviridae, order Martellivirales. The Virgaviridae is a family of plant viruses with rod-shaped virions, a (+)ssRNA genome with a 3'-terminal tRNA-like structure and a replication protein similar to those of the alpha-like supergroup. Plants serve as natural hosts. The name of the family is derived from the Latin word virga (rod), as all viruses in this family are rod-shaped. There are currently 59 species in this family, divided among seven genera: Goravirus, Furovirus, Hordeivirus, Pecluvirus, Pomovirus, Tobamovirus, and Tobravirus. 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: 438101  Cd Length: 427  Bit Score: 319.57  E-value: 1.27e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 1900 DQSFDAWDVRNSDLDLEMGQLTYAPVLGVQLNRRFDNLRPILKTPMPHMRDYNTRELMLALQKRNRNVPYMNGTVDFDKS 1979
Cdd:cd23251      8 DSDFDGYTVATSDINLNVEDCTLDPSKSVKVWQEKEGLKPVLRTAMPEKRQNGLLESLLALIKRNMAAPKLQGAVNEFET 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 1980 SDEMLDNLLRECFDPALLefhTREPVSIScNSVSDWLSGQPPAVKG-MIVPSFAMHCSALNSYSFSIKRKPKPNLTVDAT 2058
Cdd:cd23251     88 IERVIKKAKDVFFDEDLI---DRSPLSTR-ESFLRWWDKQSTTARAqLLADDRVLDEIDVCTYNFMIKNDVKPKLDLSPQ 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2059 RSYLALQTIVYHEKPINAMFCSVFREIKKRVTSSLLPHVKIFCDMSAEEFEEILnRDIPIEKLHKILEkleIDISKYDKS 2138
Cdd:cd23251    164 SEYAALQTVVYPDKIVNALFGPIFKEINERILSALDPHVVFNTRMTAEELNETV-EFLDPDEEYDALE---IDFSKFDKS 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2139 QRELALEFECKLMRRFGVSEDIIELWYNAHILTEVYDRNTKLKALIPYQRKSGDASTFIGNTLFLMAVISDLIPISQMDL 2218
Cdd:cd23251    240 KTSLHIRAVIELYKLFGLDGMLAFLWEKSQCQTTVKDRQNGIKAYLLYQQKSGNCDTYGSNTWSAALALLSMLPLEKAIF 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2219 ALFSGDDSLIY-GLGLKKYKNAQHFGLKFNLEIKFFEFEHSYFCSKFLLPVNGRWRFTPCPVKFMTKLGRHDMVNFEHVE 2297
Cdd:cd23251    320 MIFGGDDSLILfPKGLVIPDPCRRLASLWNFECKLFKFKYGYFCGKFLLKHGDGYIFYPDPLKLITKLGRKDIKDGEHLS 399

                          410
                   ....*....|....*.
gi 1143619699 2298 QYRVSFADTVKNYADY 2313
Cdd:cd23251    400 EIFVSICDNYKSYRDY 415
RdRP_2 pfam00978
RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ...
 1910-2314 4.27e-87

RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins: 2A protein from bromoviruses putative RNA dependent RNA polymerase from tobamoviruses Non structural polyprotein from togaviruses


Pssm-ID: 395779  Cd Length: 440  Bit Score: 292.62  E-value: 4.27e-87
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 1910 NSDLDLEMGQLTYAPvlGVQLNRRFDN---LRPILKTPMPHMRDYNTRELMLALQKRNRNVPYMNGTVDFDKSSDEMLDN 1986
Cdd:pfam00978    1 TSDISLDLDDCRLDP--SKSKPKPKDKepyLVPVLRTAAPSPRQNTLKEVLLALKKRNFNVPELQESVDLDDTAERVAER 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 1987 LLRECFDPALLEFHtrEPVSISCNSVSDWLSGQ-PPAVKGMIVP-SFAMHCSALNSYSFSIKRKPKPNLTVDATRSYLAL 2064
Cdd:pfam00978   79 FKKSFLDKEKLDKL--DPIINTTENVSRWLDKQsGKKAAQLKLDdLVPLHEVDLDRYKHMIKSDVKPKLDLSPQSERPAL 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2065 QTIVYHEKPINAMFCSVFREIKKRVTSSLLPHVKIFCDMSAEEFEEilnrdiPIEKLHKILEKLEIDISKYDKSQRELAL 2144
Cdd:pfam00978  157 QTITYHDKGVTAYFSPIFRELFERLLYVLKPKIVFPTGMTSSLIAE------HFEFLDASEDFLEIDFSKFDKSQGELHL 230

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2145 EFECKLMRRFGVSEDIIELWYNAHILTEVYDRNTKLKALIPYQRKSGDASTFIGNTLFLMAVISDLIPISQMDLALFSGD 2224
Cdd:pfam00978  231 LVQLEILKLLGLDPELADLWFKFHRQSYIKDRKNGVGFSVDYQRKSGDANTYLGNTLVTMAMLASVYDLEKIDCAAFSGD 310

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2225 DSLIYglGLKKYKN-AQHFGLKFNLEIKFFEFEHSYFCSKFLLPVNGRWRFTPCPVKFMTKLGR-HDMVNFEHVEQYRVS 2302
Cdd:pfam00978  311 DSLIF--SPKPIEDpASRFATLFNMEAKVFDPSVPYFCSKFLLEVDGGAFFVPDPLKLLQKLGKkKIPDDEQHLDEIFTS 388

                          410
                   ....*....|..
gi 1143619699 2303 FADTVKNYADYH 2314
Cdd:pfam00978  389 LCDLTKSFNDDC 400
ps-ssRNAv_Martellivirales_RdRp cd23208
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Martellivirales of ...
 2039-2230 6.53e-62

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Martellivirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Martellivirales, class Alsuviricetes. The order Martellivirales consists of seven families: Bromoviridae, Closteroviridae, Endornaviridae, Kitaviridae, Mayoviridae, Togaviridae, and Virgaviridae. 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: 438058 [Multi-domain]  Cd Length: 190  Bit Score: 210.30  E-value: 6.53e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2039 NSYSFSIKRKPKPNLTVDATRSYLALQTIVYHEKPINAMFCSVFREIKKRVTSSLLPHVKIFCDMsaeEFEEILNRDIPI 2118
Cdd:cd23208      1 DKYEMMIKSDVKPKLDLTAQQEYPKLQTIVYHDKNITAIFCPIFKELFERLLSCLKKKVVIYTGM---MTSAELNDFISA 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2119 EKLHKILEKLEIDISKYDKSQRELALEFECKLMRRFGVSEDIIELWYNAHILTEVYDRNTKLKALIPYQRKSGDASTFIG 2198
Cdd:cd23208     78 LHLESGYYVLEIDFSKFDKSQGALHLLTELLILRRLGVDEPLLVLWEFAHTQSTTRDINNGISFETAYQRKSGDAFTYFG 157

                          170       180       190
                   ....*....|....*....|....*....|..
gi 1143619699 2199 NTLFLMAVISDLIPISQMDLALFSGDDSLIYG 2230
Cdd:cd23208    158 NTLVTMAALLDVLDLEKIVCIAFGGDDSLIFS 189
Closteroviridae_RdRp cd23253
RNA-dependent RNA polymerase (RdRp) in the family Closteroviridae of positive-sense ...
 2039-2287 2.90e-55

RNA-dependent RNA polymerase (RdRp) in the family Closteroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Closteroviridae, order Martellivirales. Viruses in the family Closteroviridae have a mono-, bi- or tripartite (+)ssRNA genome of 13-19 kb, and non-enveloped, filamentous particles 650-2200 nm long and 12 nm in diameter. They infect plants, mainly dicots, many of which are fruit crops. Members of the family are classified into four genera: Ampelovirus, Closterovirus, Crinivirus and Velarivirus. Their genetic diversity is primarily influenced by strong negative selection and recombination. Closteroviridae viruses are mostly phloem-restricted and induce specific cytoplasmic aggregates of virus particles intermingled with membranous vesicles derived from the endoplasmic reticulum and possibly mitochondria. Their transmission is by aphids, whiteflies, pseudococcid mealybugs or soft scale insects in a semi-persistent manner. 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: 438103  Cd Length: 266  Bit Score: 194.32  E-value: 2.90e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2039 NSYSFSIKRKPKPNLTVDATRSYLALQTIVYHEKPINAMFCSVFREIKKRVTSSLLPHVKIFCDMSAEEFEEILNRDI-- 2116
Cdd:cd23253      1 TSFKLMVKGDMKPKLDSSSLSKYPPGQNIVYHERAINAFFSPIFLEVFDRIKYCLSDKIILYSGMNLEELASLIRSKLgd 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2117 PIEKLHKIleklEIDISKYDKSQRELALEFECKLMRRFGVSEDIIELWYnahiLTEVYDRNTK----LKALIPYQRKSGD 2192
Cdd:cd23253     81 PLDEYKTV----EIDFSKFDKSQGVLFKVYEELVYKFFGFSEELYDNWK----CSEYFSCRATsdsgVSLELGAQRRTGS 152

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2193 ASTFIGNTLFLMAVISDLIPISQMDLALFSGDDSLIyglgLKKYK---NAQHFGLKFNLEIKFFEFEHSYFCSKFLLPVN 2269
Cdd:cd23253    153 PNTWLGNTLVTLGILSSSYDLDDIDLLLVSGDDSLI----FSKKPlpnKANEINLDFGFEAKFIENSVPYFCSKFIIEDR 228

                          250
                   ....*....|....*...
gi 1143619699 2270 GRWRFTPCPVKFMTKLGR 2287
Cdd:cd23253    229 GKIKVVPDPVKLFEKLSV 246
Mayoviridae_RdRp cd23256
RNA-dependent RNA polymerase (RdRp) in the family Mayoviridae of positive-sense ...
 2023-2308 2.66e-39

RNA-dependent RNA polymerase (RdRp) in the family Mayoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Mayoviridae, order Martellivirales. The Mayoviridae family consists of two genera, Idaeovirus and Pteridovirus. The genus Idaeovirus contains Raspberry bushy dwarf virus (RBDV), named after the host with which it was first associated (red raspberry, Rubus idaeu) and the disease which is characterized by bushiness (stunting and proliferation of canes); RBDV has recently been found causing an infection in grapevines. RBDV occurs in all tissues of the plant, including seed and pollen, and is transmitted in association with pollen, both vertically to the seed and horizontally to the pollinated plant; this is the only known method of natural spread of RBDV. 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: 438106  Cd Length: 329  Bit Score: 150.28  E-value: 2.66e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2023 VKGMIVPSFAMHCSALNSYSFSIKRKPKPNLTVDATRSYLALQTIVYHEKPINAMFCSVFREIKKRVTSSLLPHVKIFCD 2102
Cdd:cd23256     17 VGNKVNDPVVLALTSLNKYSHMIKRDRKPVLTTAVQSEYTKAATITYHDKDITQVATPIFRQFKTRLLACKKSNLCIPLD 96

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2103 MSAEEFEEILNRDIPIEKLHKIleklEIDISKYDKSQRELALEFECKLMRRFGVSEDIIELWYNAHILTEVYDRNTKLKA 2182
Cdd:cd23256     97 HDHDISGWLTNRHLGSENGTFT----EIDFSKFDKSQGELHQLIQDLILLRFGCDPEFVSLWSTAHRSSSIKDQNVGISF 172

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2183 LIPYQRKSGDASTFIGNTLFLMAVISDLI---PISQMDLALFSGDDSLIYGLGLKKYkNAQHFGLKFNLEIKFFEFEHSY 2259
Cdd:cd23256    173 KTDFQRRTGDAFTFLGNSLVTAVMLAYVLsfeDEKKIRYMLVGGDDSLICSYGPISV-PLEPLSTIFNMSCKLIQPSCPY 251

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2260 FCSKFLLPVNGRWRFTPCPVKFMTKLGRHDMV-NFEHVEQYRVSFADTVK 2308
Cdd:cd23256    252 FASRYIIRVGDEILCVPDPYKLLVKMGRKDIPdNEASLEEVRTGLADSAK 301
Bromoviridae_RdRp cd23252
RNA-dependent RNA polymerase (RdRp) in the family Bromoviridae of positive-sense ...
 1937-2286 6.71e-38

RNA-dependent RNA polymerase (RdRp) in the family Bromoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Bromoviridae, order Martellivirales. The Bromoviridae family of plant viruses contains tri-segmented, (+)ssRNA viruses with a total genome size of about 8 kb. There are six genera in this family: Alfamovirus, Anulavirus, Bromovirus, Cucumovirus, Ilarvirus, and Oleavirus. Bromoviridae virions are variable in morphology (spherical or bacilliform) and are transmitted mechanically, in/on the pollen and non-persistently by insect vectors. Members of the family cause major disease epidemics in fruit, vegetable and fodder crops such as tomato, cucurbits, bananas, and alfalfa. 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: 438102  Cd Length: 332  Bit Score: 146.22  E-value: 6.71e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 1937 LRPILKTPMPHMRDYNTRELMLALQKRNRNVPYMNGTVDFDKSSDEMLDNLLRECFDPALLEFHtrepvsiscnsvsdwl 2016
Cdd:cd23252     26 LEPVLNTGSGSKRVGTQREALLAIKKRNANVPELGDSVDLDRVSNAVANRFLTTVIDVDRLDKY---------------- 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2017 sgqppavkgmivpsfaMHCsalnsysfsIKRKPKPnlTVDAT----RSYLAlqTIVYHEKPINAMFCSVFReikkrvtss 2092
Cdd:cd23252     90 ----------------MHM---------IKSDLKP--VEDDSlhveRPVPA--TITYHKKGIVMQFSPLFL--------- 131

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2093 llphvkifcdMSAEEFEEILNRD--IPIEKLHKILEK-----------LEIDISKYDKSQRELALEFECKLMRRFGVSED 2159
Cdd:cd23252    132 ----------AAFERLLRCLRSKivIPSGKIHQLFMIdpsvlnaskhfKEIDFSKFDKSQGELHHEIQEHILNALGCPAP 201

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2160 IIELWYNAHILTEVYDRNTKLKALIPYQRKSGDASTFIGNTLFLMAVIS---DLIPiSQMDLALFSGDDSLIYGLGLKKY 2236
Cdd:cd23252    202 FTKWWFDFHRRSYISDRRAGVGFSVDFQRRTGDAFTYLGNTLVTLAELAyvyDLDD-PNFDFVVASGDDSLIGSVEPLPR 280

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1143619699 2237 KNAQHFGLKFNLEIKffeFEHS--YFCSKFLL--PVNGRWRFT-PCPVKFMTKLG 2286
Cdd:cd23252    281 DDEDLFTTLFNFEAK---FPHNqpFICSKFLLsdEFGDENVFSvPDPLKLLQRLG 332
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 1353-1618 5.15e-33

Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.


Pssm-ID: 366646 [Multi-domain]  Cd Length: 227  Bit Score: 128.65  E-value: 5.15e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 1353 GIVQAGPGCGKTTYVVNnsvpphVSGASNVLLATTEgkyDYIDRLQKKYNRiftkdqlsHVRTLASFLVNPhKNVKSSVL 1432
Cdd:pfam01443    1 IVVHGVPGCGKSTLIRK------LLRTSRVIRPTAE---LRTEGKPDLPNL--------NVRTVDTFLMAL-LKPTGKIL 62

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 1433 IIDEALMSHPGQIFFAISLSGATTVKLLGDRLQIPFVNRTPAFPtkfdkLPDFVPVVETLY---ISYRCRTDVVARLDAE 1509
Cdd:pfam01443   63 ILDEYTLLPPGYILLLAAISGAKLVILFGDPLQIPYHSRAPSFL-----IPHFPSSLSHRVgrrTTYLLPSLRAPILSAK 137

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 1510 YLKCNAPlgvNKGLMSVHYSPNTckvvkicnddfpkDPNVQYLVFTQpekTILKNLKLHVSTVHEYQGKEAKEIRVVRLN 1589
Cdd:pfam01443  138 GFEVVVE---RSGEYKVDYDPNG-------------VLVLVYLTFTQ---ALKESLGVRVTTVHEVQGLTFDSVTLVLDT 198

                          250       260
                   ....*....|....*....|....*....
gi 1143619699 1590 AQPQTEIYKRFNYALVALTRHTEKLTYYT 1618
Cdd:pfam01443  199 DTDLLIISDSPEHLYVALTRHRKSLHILT 227
ps-ssRNAv_Alsuviricetes_RdRp cd23182
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the class Alsuviricetes of ...
 2040-2230 7.72e-30

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the class Alsuviricetes of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the class Alsuviricetes, phylum: Kitrinoviricota. Alsuviricetes is a class of [(+)ssRNA] viruses which infect eukaryotes. The name of the group is a syllabic abbreviation of "alpha supergroup" with the suffix -viricetes indicating a virus class. The class Alsuviricetes includes three orders: Hepelivirales, Martellivirales, and Tymovirales. 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: 438032 [Multi-domain]  Cd Length: 187  Bit Score: 118.08  E-value: 7.72e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2040 SYSFSIKRKPKPNLTvDATRSYLALQTIVYHEKPINAMFCSVFREIKKRVTSSLLPHVKIF--CDMSAEEFEEILNRDIP 2117
Cdd:cd23182      2 DIDFLIKTQQKVSPK-TPFNTGKAGQTIAAHSKSINFVLGPWIRYLEERLRDGSRTHRYSNglMDEEEAMLSQWKINHVP 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2118 IEKLhkilekLEIDISKYDKSQRELALEFECKLMRRFGVSEDIIELWYNAHILTEVYDRNTKLKALIPYQRKSGDASTFI 2197
Cdd:cd23182     81 HATF------VSNDYTAFDKSHNGESLLLEAAIMRRIGTPAAAPNLFIELHGKRTLRAKVLGGSGELDGMRDSGAAWTYC 154

                          170       180       190
                   ....*....|....*....|....*....|...
gi 1143619699 2198 GNTLFLMAVISDLIPISQMdLALFSGDDSLIYG 2230
Cdd:cd23182    155 RNTDYNLAVMLSLYRLKVK-PAAFSGDDSLLCG 186
Endornaviridae_RdRp cd23255
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Endornaviridae of ...
 2067-2228 1.74e-23

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Endornaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Endornaviridae, order Martellivirales. The family Endornaviridae includes viruses with linear (+)ssRNA genomes that range from 9.7 to 17.6 kb. The family consists of two genera, Alphaendornavirus and Betaendornavirus. Alphaendornavirus includes species whose members infect plants, fungi and oomycetes, while the genus Betaendornavirus includes species whose members infect ascomycete fungi. Plant endornaviruses are transmitted only through the gametes. A conserved RNA-dependent RNA polymerase domain located in the C-terminal region of the polyprotein is a feature common to all endornaviruses. 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: 438105  Cd Length: 237  Bit Score: 101.46  E-value: 1.74e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2067 IVYHEKPINAMFCSVFREIKKRVTSSLLPHVkIFCD-MSAEEFEEILNrdipieKLHKILEKLEIDISKYDKSQRELALE 2145
Cdd:cd23255     61 IVWQRKGICAIFSPIFNEAKKRLKSLLKPKV-VYADgLTPDELSARLR------LVKNVKYFFEDDLSKQDRQTDKPIID 133

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2146 FECKLMRRFGVSEDIIELWYNAHILTevYDRNTKLKALIPYQRKSGDASTFIGNTLFLMAVISDLIP--ISQMDLALFSG 2223
Cdd:cd23255    134 VEMELYKLLGVDPNVIELWREVHENW--RFKGKGVRGVGDAMRLTGQATTALGNVITNLLVHSRLVKrnGSNLKLMLVLG 211


                   ....*
gi 1143619699 2224 DDSLI 2228
Cdd:cd23255    212 DDNLI 216
Togaviridae_RdRp cd23250
RNA-dependent RNA polymerase (RdRp) in the family Togaviridae of positive-sense ...
 1937-2310 1.95e-14

RNA-dependent RNA polymerase (RdRp) in the family Togaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Togaviridae, order Martellivirales. Togaviridae is a family of small, enveloped viruses with [(+)ssRNA] genomes of 10-12 kb, and contains a single genus, Alphavirus. Alphavirus includes a large number of species that are mostly mosquito-borne and pathogenic in their vertebrate hosts. Many are important human and veterinary pathogens (e.g., chikungunya virus, eastern equine encephalitis virus). The genus Alphavirus mainly consists of mosquito-borne viruses although other hematophagous insects, including ticks, lice, and cliff swallow bugs, have been implicated in transmission. Vertebrate hosts include humans, non-human primates, equids, birds, amphibians, reptiles, rodents, and pigs. There are two aquatic alphaviruses, southern elephant seal virus and salmon pancreas disease virus, infecting sea mammals and fish respectively. Interestingly, Eilat virus (EILV) has been shown to only infect insect cells and is incapable of replicating in vertebrate cells. 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: 438100  Cd Length: 458  Bit Score: 78.27  E-value: 1.95e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 1937 LRPILKTPMPHMRDYNTRELMLALQKRNRNVPYMNGTVDFDKSSDEMldnllrECF------DPALLEFHtREPVSISCN 2010
Cdd:cd23250     29 HQPQIRSAVPSPFQNTLQNVLAAATKRNCNVTQMRELPTLDSAAFNV------ECFkkfacnNEYWEEFK-EKPIRLTTE 101

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2011 SVSDWLSG-QPPAVKGMIVPSFA---MHCSALNSYSFSIKRKPKPNLTVDATRSYLALQTIVYHEKPINAMFCSVFREIK 2086
Cdd:cd23250    102 NVTTYVTKlKGPKAAALFAKTHNlvpLQEVPMDRFVMDMKRDVKVTPGTKHTEERPKVQVIQAADPLATAYLCGIHRELV 181

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2087 KRVTSSLLPHVKIFCDMSAEEFEEILNrdipiEKLHKILEKLEIDISKYDKSQ-RELALEfECKLMRRFGVSEDIIELWY 2165
Cdd:cd23250    182 RRLNAVLLPNIHTLFDMSAEDFDAIIA-----EHFQPGDKVLETDIASFDKSQdDAMALT-ALMILEDLGVDQELLDLIE 255

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2166 NA-------HILTevydrNTKLK--ALIpyqrKSGDASTFIGNTLFLMAVISDLIP--ISQMDLALFSGDDSLIYGLGLK 2234
Cdd:cd23250    256 AAfgeitsvHLPT-----GTRFKfgAMM----KSGMFLTLFVNTVLNIVIASRVLRerLTNSRCAAFIGDDNIVHGVVSD 326

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2235 KYKnAQHFGLKFNLEIKFFEFE----HSYFCSKFLL--PVNGrwrfTPC----PVKFMTKLGRHDMVNFEHVEQYRVSFA 2304
Cdd:cd23250    327 KLM-ADRCATWLNMEVKIIDAVigekPPYFCGGFILydSVTG----TACrvadPLKRLFKLGKPLPADDEQDEDRRRALH 401


                   ....*.
gi 1143619699 2305 DTVKNY 2310
Cdd:cd23250    402 DEVKRW 407
ps-ssRNA_RdRp_Tymovirales cd23207
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Tymovirales of ...
 2048-2230 3.44e-13

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Tymovirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Tymovirales. The Tymovirales order contains viruses that mostly infect plants, have a single molecule of (+)ssRNA, and which are united by the similarities in their replication-associated polyproteins. Tymovirales contains five families (Alpha-, Beta-, Delta- and Gammaflexiviridae and Tymoviridae) and groups mostly plant-infecting agents, although a few Tymovirales members have either fungal or insect hosts. Botrytis virus F (BVF), isolated from the fungus Botrytis cinerea, is a flexuous mycovirus that is typical of members of the genus Mycoflexivirus (family Gammaflexiviridae). 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: 438057 [Multi-domain]  Cd Length: 188  Bit Score: 70.12  E-value: 3.44e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2048 KPKPNLTVDATrsylALQTIVYHEKPINAMFCSVFREIKKRVTSSLLPHVKIFCDMSAEEFEEILnrdipieKLH-KILE 2126
Cdd:cd23207     21 KKDEKIFSDAK----AGQTLALFHDQIILRFGPYARYMRRFINADLPPNIYIHCGKTPEDLSKWC-------KEHwQHGP 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2127 KLEIDISKYDKSQRELALEFECKLMRRFGVSEDIIELWynAHILTEVYdrnTKLKALIPyQRKSGDASTFIGNTLFLMAV 2206
Cdd:cd23207     90 STANDYTAFDQSQDGEFVVFEVLLMRHLHIPDDLIELY--VDIKTNAY---SHLGPLSI-MRLTGEPGTFDFNTDYNLAL 163

                          170       180
                   ....*....|....*....|....*....
gi 1143619699 2207 IsdlipISQMDL-----ALFSGDDSLIYG 2230
Cdd:cd23207    164 T-----YAKYDLppgtpICFSGDDSVANG 187
Vmethyltransf pfam01660
Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ...
 82-354 2.11e-12

Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily.


Pssm-ID: 396298  Cd Length: 308  Bit Score: 70.40  E-value: 2.11e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699   82 LSKEDQDKLRRtfcmFNLDFTKASNCSG-HPFWRAHRKLsemrMLNsaritpTCRPSVGYDVVYKDVGGNPTTHFSRNEE 160
Cdd:pfam01660    5 LSPEAQELLEN----LGIEFSPYSVTPHsHPAAKALENL----LLE------VLPSYLPNPSTVLDIKGSKLRHLKRGNP 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699  161 YVHTCAPLLSnnddkrrsaYKEVLRRTDRDNkcVRLHLEQNSRVICNRRSQNC---AIKAEVLIFLHSSYDMSAEDIADS 237
Cdd:pfam01660   71 NVHCCNPILD---------PRDVARYPEAFS--LEKSLGNGEDLRPTNTFEDCrvlAPTTSYAFMHDSLHDWSPEELADL 139

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699  238 MHRADAR-VAYGCFHFNPRVLYEKEGKLSNGMYFKKlVVNGRLHirfwFENDN--QEGYEHDYlTYLSLVRTFRIKStck 314
Cdd:pfam01660  140 FLRKPKLeRLYATLVFPPELLFGDKESLYPELYTFW-YKGDRFH----FYPDGhlGGSYTHPL-NLLSWLTTSKIHL--- 210

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|.
gi 1143619699  315 KNPRYYNVQFDVTEDDTTFFTIRHSD-NGNIPRSNPYRVFT 354
Cdd:pfam01660  211 PGGFTYTVERLESRGAHHLFKITRGDgLTPKVIVPDSRTFG 251
ps-ssRNAv_Hepelivirales_RdRp cd23209
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of ...
 2041-2230 2.96e-12

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Hepelivirales, class Alsuviricetes. This Hepelivirales order consists of four families: Alphatetraviridae, Benyviridae, Hepeviridae, and Matonaviridae. 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: 438059 [Multi-domain]  Cd Length: 183  Bit Score: 67.51  E-value: 2.96e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2041 YSFSIK--RKPKPNLTVDATRsylALQTIVYHEKPINAMFCSVFREIKKRVTSSLLPHVKIFCDMSAEEFEEILNrdipi 2118
Cdd:cd23209      3 ITFFQKdcRKFTDCEPVAHGK---AGQGISAWSKELCFVFGPWFRALEKILRRALKPNVLYANGHEAEPFVDKIN----- 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2119 EKLHKILekLEIDISKYDKSQRELALEFECKLMRRFGVSEDIIELWYN---AHILTEVYDRntklkALIPYQRKSGDAST 2195
Cdd:cd23209     75 QAHSAVF--IENDFTEFDSTQNLFSLLVELEILEACGMPPALAELYRAlraKWTLQAREGS-----LEGTCKKTSGEPGT 147

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 1143619699 2196 FIGNTLFLMAVISDLIPISQMDLALFSGDDSLIYG 2230
Cdd:cd23209    148 LLHNTIWNMAVMMHMVRGGVRKAAAFKGDDSVVCC 182
Hepeviridae_RdRp cd23259
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Hepeviridae of ...
 2065-2234 1.19e-11

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Hepeviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Hepeviridae, order Hepelivirales. The family Hepeviridae includes enterically transmitted small non-enveloped [(+)ssRNA viruses. It includes the genera Piscihepevirus, whose members infect fish, and Orthohepevirus, whose members infect mammals and birds. Members of the genus Orthohepevirus include hepatitis E virus, which is responsible for self-limiting acute hepatitis in humans and several mammalian species; the infection may become chronic in immunocompromised individuals. Avian hepatitis E virus causes hepatitis-splenomegaly syndrome in chickens. Hepeviridae genomes (approximately 7.2 kb) have 5' methyl G caps and 3' poly (A) tails, and contain three ORFS. They have two mRNAs, a genome length and a subgenomic mRNA: the genome-length mRNA is translated to produce proteins required for RNA replication while the subgenomic mRNA is used to produce the capsid protein. Some of the capsid protein is glycosylated, which is an unusual finding for an unenveloped virus. 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: 438109  Cd Length: 274  Bit Score: 67.85  E-value: 1.19e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2065 QTIVYHEKPINAMFCSVFREIKKRVTSSLLPHVkIFCDMSAEEfeeILNRDIPIEKLHKILEKleiDISKYDKSQRELAL 2144
Cdd:cd23259     90 QGISAWSKTFCALFGPWFRAIEKAIVALLPPNI-FYGDAYEES---VFSAAVAGAGSCRVFEN---DFSEFDSTQNNFSL 162

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2145 EFECKLMRRFGVSEDIIELWynaHILTEVYDRNTKLKALIPYQRK-SGDASTFIGNTLFLMAVISDLIPISQMDLALFSG 2223
Cdd:cd23259    163 GLECEIMEECGMPQWLVRLY---HLVRSAWVLQAPKESLRGFWKKhSGEPGTLLWNTVWNMAVIAHCYEFRDLAVAAFKG 239

                          170       180
                   ....*....|....*....|....*.
gi 1143619699 2224 DDS---------------LIYGLGLK 2234
Cdd:cd23259    240 DDSvvlcsdyrqsrnaaaLIAGCGLK 265
FtsJ pfam01728
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...
 806-992 9.85e-11

FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesized that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping.


Pssm-ID: 426399  Cd Length: 179  Bit Score: 62.99  E-value: 9.85e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699  806 YVCRSGLKTAEMFTRFftNDIESAFSI----GGPGGEVEFLCDRGIRT-FGatktdlIDfspaVRHHLFTQLLGD----T 876
Cdd:pfam01728    1 YRSRAAYKLLEIDEKF--GLLKPGKTVldlgAAPGGWSQVALQRGAGKvVG------VD----LGPMQLWKPRNDpgvtF 68

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699  877 YDGDITDLSNIisfgKSVRKYYSEGVDFFGGDAA-DSSRENEID-LKSMSHLLSWEILCCItVLKEGGCAYFKVFDllSH 954
Cdd:pfam01728   69 IQGDIRDPETL----DLLEELLGRKVDLVLSDGSpFISGNKVLDhLRSLDLVKAALEVALE-LLRKGGNFVCKVFQ--GE 141

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 1143619699  955 KNPSLIHYLHSHFDDVQVVKLETSRSASTELHIICRGF 992
Cdd:pfam01728  142 DFSELLYLLKLGFEKVGVFKPPASRPESSEEYLVCLGF 179
Gammaflexiviridae_RdRp cd23249
RNA-dependent RNA polymerase (RdRp) in the family Gammaflexiviridae of positive-sense ...
 1990-2228 1.27e-08

RNA-dependent RNA polymerase (RdRp) in the family Gammaflexiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Tymovirales; This group contains the RdRp of RNA viruses belonging to the family Gammaflexiviridae, order Tymovirales. Virions within the Gammaflexiviridae family are flexuous filaments of 720 nm modal length and about 13 nm in diameter. Members of the Tymovirales order are mainly plant pathogens that are characterized by similarities in their replication-associated polyproteins, which account for the majority of their genomic coding capacity. They are considered to form a group, phylogenetically, referred to as flexiviruses, with filamentous virions. 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: 438099  Cd Length: 354  Bit Score: 59.53  E-value: 1.27e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 1990 ECFDPALLEFHTREpvsiscNSVSdwLSGQPPAVKGMIV----PSFAMHCSALNSYSFSIKRKPKPNltVDATrsylALQ 2065
Cdd:cd23249     31 TFNDSLLYECRTEN------DTVH--LTSKPPATLINNAersdPSWSLHMIELFIKGQTVTKLGKMG--SDAT----AGQ 96

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2066 TIVYHEKPINAMFCSVFREIKKRVTSSLLPHVKIFCDMSAEEFEEILNRDIPIEklhkiLEKLEIDISKYDKSQRELALE 2145
Cdd:cd23249     97 SIASFRAQVLLAWGPLARYLDRRIRALLPPHIYIHSGRTNEDFERFVAAHWDFT-----RESTEGDYTAFDASQDADFLN 171

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2146 FECKLMRRFGVSEDIIELWYNAHILTevydrnTKLKALIPYQRKSGDASTFIGNTLFLMAVISDLIPISQMDLALFSGDD 2225
Cdd:cd23249    172 FETLLMRALGVPLDLIEAYLEMKASI------TSHLGPLAIMRFSGEVWTYLFNTLGNMAYTAAKYEVPPPVPRVYGGDD 245


                   ...
gi 1143619699 2226 SLI 2228
Cdd:cd23249    246 KSI 248
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 2128-2228 1.51e-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: 52.29  E-value: 1.51e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2128 LEIDISKYDKSQRELALEFECKLMRRFGVSEDIIELWynaHILTEVYDRNTKLKALIPYQRK----SGDASTFIGNTLFL 2203
Cdd:cd01699     99 IALDYSRFDSSLSPQLLEAEHSIYNALYDDDDELERR---NLLRSLTNNSLHIGFNEVYKVRggrpSGDPLTSIGNSIIN 175

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1143619699 2204 MAVISD----LIPISQMDLALFS--GDDSLI 2228
Cdd:cd01699    176 CILVRYafrkLGGKSFFKNVRLLnyGDDCLL 206
Tymoviridae_RdRp cd23247
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tymoviridae of ...
 2131-2268 2.59e-05

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tymoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Tymovirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Tymoviridae, order Tymovirales. Virions of the family Tymoviridae are isometric, non-enveloped, about 30 nm in diameter, and contain a single molecule of (+)ssRNA constituting 25#35% of the particle weight. There are 42 species in this family, assigned to three genera (Maculavirus, Marafivirus, and Tymovirus), with two species unassigned to a genus. Members of the Tymovirales order are mainly plant pathogens that are characterized by similarities in their replication-associated polyproteins, which account for the majority of their genomic coding capacity. They are considered to form a group, phylogenetically, referred to as flexiviruses, with filamentous virions. 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: 438097  Cd Length: 373  Bit Score: 49.11  E-value: 2.59e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2131 DISKYDKSQRELALEFECKLMRRFGVSEDIIELwyNAHILTEVydrNTKLKALIpYQRKSGDASTFIGNTLFLMAVISdl 2210
Cdd:cd23247    173 DYTAFDQSQHGEAVVFERLKMERLSIPQHLIDL--HVHLKTNV---STQFGPLT-CMRLTGEPGTYDDNTDYNLAVIY-- 244

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2211 ipiSQMDLA----LFSGDDSLIYGL--------GLKKYknaqhFGLKFNLEIKffefEHSYFCSKFLLPV 2268
Cdd:cd23247    245 ---SQYDISstpiMVSGDDSVIDGVpperpswpAIKPL-----LHLRFKTETT----RYPLFCGYYVGPA 302
RlmE COG0293
23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ [Translation, ribosomal structure and ...
 920-992 5.32e-05

23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ [Translation, ribosomal structure and biogenesis]; 23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440062 [Multi-domain]  Cd Length: 208  Bit Score: 46.60  E-value: 5.32e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699  920 LKSMsHL--LSWEIlcCITVLKEGGCAYFKVF------DLLshknpsliHYLHSHFDDVQVVKLETSRSASTELHIICRG 991
Cdd:COG0293    137 ARSM-YLveLALDF--ARKVLKPGGAFVVKVFqgegfdELL--------KELKKLFKKVKHRKPKASRARSSEVYLVAKG 205


                   .
gi 1143619699  992 F 992
Cdd:COG0293    206 F 206
Benyviridae_RdRp cd23257
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Benyviridae of ...
 2041-2211 2.11e-04

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Benyviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Benyviridae, order Hepelivirales. The Benyviridae is a family of plant viruses with rod-shaped virions. Their genomes are multipartite (+)ssRNAs with 5' m7G-cap and 3' poly(A) and there is post-translational cleavage of the viral replicase. Beet necrotic yellow vein virus belongs to the genus Benyvirus and is the cause of 'rhizomania' disease of sugar beet. This widespread soil-borne disease can severely reduce sugar beet growth and beet sucrose production. BNYVV RNA1 contains one open reading frame (ORF) encoding a replicase protein that harbors motifs for methyltransferase, helicase, papain-like protease, and RdRp. 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: 438107 [Multi-domain]  Cd Length: 188  Bit Score: 44.53  E-value: 2.11e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2041 YSFSIK--RKPKPNLTVDATRsylALQTIVYHEKPINAMFCSVFREIKKRVTSSLLPHVKIFCDMSAEEFEEILN---RD 2115
Cdd:cd23257      3 YRFQLKdiEKPLKDPETDLAK---AGQGILAWSKEAHVKFMVAFRVLNDLLLKSLNSNVVYDNTMSETEFVGKINaamNT 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2116 IPIEKLHKIlekleIDISKYDKSQRELALEFECKLMRRFGVSEDIIElWYNAhiLTEVYDRNTK-LKALIPYQRKSGDAS 2194
Cdd:cd23257     80 VPDSAINGV-----IDAAACDSGQGVFTQLIERYIYAALGISDFFLD-WYFS--FREKYVMQSRyVRAHMSYVKTSGEPG 151

                          170
                   ....*....|....*..
gi 1143619699 2195 TFIGNTLFLMAVISDLI 2211
Cdd:cd23257    152 TLLGNTILMGAMLNAML 168
Deltaflexiviridae_RdRp cd23248
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Deltaflexiviridae ...
 2131-2230 2.86e-03

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Deltaflexiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Tymovirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Deltaflexiviridae, order Tymovirales. Deltaflexiviridae consists of one genus (Deltaflexivirus) and three species: Fusarium deltaflexivirus 1, Sclerotinia deltaflexivirus 1, and Soybean-associated deltaflexivirus 1. Members of the Tymovirales order are mainly plant pathogens that are characterized by similarities in their replication-associated polyproteins, which account for the majority of their genomic coding capacity. They are considered to form a group, phylogenetically, referred to as flexiviruses, with filamentous virions. 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: 438098  Cd Length: 279  Bit Score: 42.09  E-value: 2.86e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1143619699 2131 DISKYDKSQRELALEFECKLMRRFGVSEDIIELWYNAHILTEVYdrntkLKALIPYQrKSGDASTFIGNTLFLMAVISDL 2210
Cdd:cd23248    138 DYTAWDSGCDHVFLEFDLWLMDLCGFPEEYIEKYRFERLNTRSY-----LGPHMPRQ-ESGDRWTWILNTLRNAALTGAS 211

                           90       100
                   ....*....|....*....|
gi 1143619699 2211 IPISQMDLALFSGDDSLIYG 2230
Cdd:cd23248    212 LDCPPGTPACFSGDDSVLLG 231
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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