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Conserved domains on  [gi|828763558|gb|AKK75109|]
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237kDa protein [Beet necrotic yellow vein virus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Benyviridae_RdRp cd23257
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Benyviridae of ...
 1752-1939 1.58e-128

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: 400.84  E-value: 1.58e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1752 KLYRFQLKDIEKPLKDPETDLAKAGQGILAWSKEAHVKFMVAFRVLNDLLLKSLNSNVVYDNTMSETEFVGKINAAMNIV 1831
Cdd:cd23257     1 RLYRFQLKDIEKPLKDPETDLAKAGQGILAWSKEAHVKFMVAFRVLNDLLLKSLNSNVVYDNTMSETEFVGKINAAMNTV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1832 PDSAINGVIDAAACDSGQGVFTQLIERHIYAALGISDFFLDWYFSFREKYVMQSRYVRAHMSYVKTSGEPGTLLGNTILM 1911
Cdd:cd23257    81 PDSAINGVIDAAACDSGQGVFTQLIERYIYAALGISDFFLDWYFSFREKYVMQSRYVRAHMSYVKTSGEPGTLLGNTILM 160

                         170       180
                  ....*....|....*....|....*...
gi 828763558 1912 GAMLNAMLRGTGPFCMAMKGDDGFKRQA 1939
Cdd:cd23257   161 GAMLNAMLRGTGPFCMAMKGDDGFKRQA 188
Peptidase_C36 pfam05415
Beet necrotic yellow vein furovirus-type papain-like endopeptidase; Corresponds to Merops ...
 1-104 2.52e-54

Beet necrotic yellow vein furovirus-type papain-like endopeptidase; Corresponds to Merops family C36. This protease involved in processing the viral polyprotein.


:

Pssm-ID: 461645  Cd Length: 104  Bit Score: 184.90  E-value: 2.52e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558     1 MADSFGFTPMEVLLFGGESVQLLTSDMPIDVQWGFVHSTRCYALWKDDLIHLNPLLKYSQRIAKRWERLVSGFVGPVPLD 80
Cdd:pfam05415    1 MADSFGFNCLEVAIFECEGVQLEKLDMLIDANAGFLDKTHAWALKKDDLIHLDCLLFADALIAKMWEKLLSDFPGDLPLD 80

                           90       100
                   ....*....|....*....|....
gi 828763558    81 KLLSLLAKLMRYCVNMGVSVQEIY 104
Cdd:pfam05415   81 KDGAGLAKLLHLCGKEGDGHFEAA 104
Peptidase_C36 super family cl05138
Beet necrotic yellow vein furovirus-type papain-like endopeptidase; Corresponds to Merops ...
 1285-1388 6.03e-52

Beet necrotic yellow vein furovirus-type papain-like endopeptidase; Corresponds to Merops family C36. This protease involved in processing the viral polyprotein.


The actual alignment was detected with superfamily member pfam05415:

Pssm-ID: 461645  Cd Length: 104  Bit Score: 178.35  E-value: 6.03e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558  1285 NLVSRPNNCLVVAISECLGVTLEKLDNLMQAKAVTLDKYHAWLSKKSPSTWQDCRMFADALKVSMYVKVLSDKPYDLTYE 1364
Cdd:pfam05415    1 MADSFGFNCLEVAIFECEGVQLEKLDMLIDANAGFLDKTHAWALKKDDLIHLDCLLFADALIAKMWEKLLSDFPGDLPLD 80

                           90       100
                   ....*....|....*....|....
gi 828763558  1365 VDGAGSSVTLHLVGKESDGHFIAA 1388
Cdd:pfam05415   81 KDGAGLAKLLHLCGKEGDGHFEAA 104
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 940-1181 3.23e-32

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: 126.34  E-value: 3.23e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558   940 VKGGPGTGKSFLIRSLADPIRDLVvaPFIKLRSDyqnqRVGDE--LLSWDFHTPHKALDVTGKQIIFVDEFTAYDWRLLA 1017
Cdd:pfam01443    3 VHGVPGCGKSTLIRKLLRTSRVIR--PTAELRTE----GKPDLpnLNVRTVDTFLMALLKPTGKILILDEYTLLPPGYIL 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558  1018 VLAYRNHAHTIYLVGDEQQTGIQEGRGEGISILNKIDLSKVSTHVPIMNFRNPVRDVKVLNylfGSRMVPMSSVEKGFSF 1097
Cdd:pfam01443   77 LLAAISGAKLVILFGDPLQIPYHSRAPSFLIPHFPSSLSHRVGRRTTYLLPSLRAPILSAK---GFEVVVERSGEYKVDY 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558  1098 gdikefsSLSNIPDTKIIHYSDETGEHMmpdyvrGVSKTTVRANQGSTYDNVVLPVLPSDLKLI--NSAELNLVALSRHR 1175
Cdd:pfam01443  154 -------DPNGVLVLVYLTFTQALKESL------GVRVTTVHEVQGLTFDSVTLVLDTDTDLLIisDSPEHLYVALTRHR 220


                   ....*.
gi 828763558  1176 NKLTIL 1181
Cdd:pfam01443  221 KSLHIL 226
 
Name Accession Description Interval E-value
Benyviridae_RdRp cd23257
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Benyviridae of ...
 1752-1939 1.58e-128

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: 400.84  E-value: 1.58e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1752 KLYRFQLKDIEKPLKDPETDLAKAGQGILAWSKEAHVKFMVAFRVLNDLLLKSLNSNVVYDNTMSETEFVGKINAAMNIV 1831
Cdd:cd23257     1 RLYRFQLKDIEKPLKDPETDLAKAGQGILAWSKEAHVKFMVAFRVLNDLLLKSLNSNVVYDNTMSETEFVGKINAAMNTV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1832 PDSAINGVIDAAACDSGQGVFTQLIERHIYAALGISDFFLDWYFSFREKYVMQSRYVRAHMSYVKTSGEPGTLLGNTILM 1911
Cdd:cd23257    81 PDSAINGVIDAAACDSGQGVFTQLIERYIYAALGISDFFLDWYFSFREKYVMQSRYVRAHMSYVKTSGEPGTLLGNTILM 160

                         170       180
                  ....*....|....*....|....*...
gi 828763558 1912 GAMLNAMLRGTGPFCMAMKGDDGFKRQA 1939
Cdd:cd23257   161 GAMLNAMLRGTGPFCMAMKGDDGFKRQA 188
Peptidase_C36 pfam05415
Beet necrotic yellow vein furovirus-type papain-like endopeptidase; Corresponds to Merops ...
 1-104 2.52e-54

Beet necrotic yellow vein furovirus-type papain-like endopeptidase; Corresponds to Merops family C36. This protease involved in processing the viral polyprotein.


Pssm-ID: 461645  Cd Length: 104  Bit Score: 184.90  E-value: 2.52e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558     1 MADSFGFTPMEVLLFGGESVQLLTSDMPIDVQWGFVHSTRCYALWKDDLIHLNPLLKYSQRIAKRWERLVSGFVGPVPLD 80
Cdd:pfam05415    1 MADSFGFNCLEVAIFECEGVQLEKLDMLIDANAGFLDKTHAWALKKDDLIHLDCLLFADALIAKMWEKLLSDFPGDLPLD 80

                           90       100
                   ....*....|....*....|....
gi 828763558    81 KLLSLLAKLMRYCVNMGVSVQEIY 104
Cdd:pfam05415   81 KDGAGLAKLLHLCGKEGDGHFEAA 104
Peptidase_C36 pfam05415
Beet necrotic yellow vein furovirus-type papain-like endopeptidase; Corresponds to Merops ...
 1285-1388 6.03e-52

Beet necrotic yellow vein furovirus-type papain-like endopeptidase; Corresponds to Merops family C36. This protease involved in processing the viral polyprotein.


Pssm-ID: 461645  Cd Length: 104  Bit Score: 178.35  E-value: 6.03e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558  1285 NLVSRPNNCLVVAISECLGVTLEKLDNLMQAKAVTLDKYHAWLSKKSPSTWQDCRMFADALKVSMYVKVLSDKPYDLTYE 1364
Cdd:pfam05415    1 MADSFGFNCLEVAIFECEGVQLEKLDMLIDANAGFLDKTHAWALKKDDLIHLDCLLFADALIAKMWEKLLSDFPGDLPLD 80

                           90       100
                   ....*....|....*....|....
gi 828763558  1365 VDGAGSSVTLHLVGKESDGHFIAA 1388
Cdd:pfam05415   81 KDGAGLAKLLHLCGKEGDGHFEAA 104
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 940-1181 3.23e-32

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: 126.34  E-value: 3.23e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558   940 VKGGPGTGKSFLIRSLADPIRDLVvaPFIKLRSDyqnqRVGDE--LLSWDFHTPHKALDVTGKQIIFVDEFTAYDWRLLA 1017
Cdd:pfam01443    3 VHGVPGCGKSTLIRKLLRTSRVIR--PTAELRTE----GKPDLpnLNVRTVDTFLMALLKPTGKILILDEYTLLPPGYIL 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558  1018 VLAYRNHAHTIYLVGDEQQTGIQEGRGEGISILNKIDLSKVSTHVPIMNFRNPVRDVKVLNylfGSRMVPMSSVEKGFSF 1097
Cdd:pfam01443   77 LLAAISGAKLVILFGDPLQIPYHSRAPSFLIPHFPSSLSHRVGRRTTYLLPSLRAPILSAK---GFEVVVERSGEYKVDY 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558  1098 gdikefsSLSNIPDTKIIHYSDETGEHMmpdyvrGVSKTTVRANQGSTYDNVVLPVLPSDLKLI--NSAELNLVALSRHR 1175
Cdd:pfam01443  154 -------DPNGVLVLVYLTFTQALKESL------GVRVTTVHEVQGLTFDSVTLVLDTDTDLLIisDSPEHLYVALTRHR 220


                   ....*.
gi 828763558  1176 NKLTIL 1181
Cdd:pfam01443  221 KSLHIL 226
RdRP_2 pfam00978
RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ...
 1691-2015 3.24e-16

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: 83.46  E-value: 3.24e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558  1691 SSTQDSVARMVAQLFVSDCLVPNVADTFSASnlwRIMDKAMHDMVTK---NYQGQMEEEFTR-----NAKLYRFQLKDIE 1762
Cdd:pfam00978   65 SVDLDDTAERVAERFKKSFLDKEKLDKLDPI---INTTENVSRWLDKqsgKKAAQLKLDDLVplhevDLDRYKHMIKSDV 141

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558  1763 KPLKDPETDL-AKAGQGILAWSKEAHVKFMVAFRVLNDLLLKSLNSNVVYdntmseteFVGKINAAMNI---VPDSAING 1838
Cdd:pfam00978  142 KPKLDLSPQSeRPALQTITYHDKGVTAYFSPIFRELFERLLYVLKPKIVF--------PTGMTSSLIAEhfeFLDASEDF 213

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558  1839 V-IDAAACDSGQGVFTQLIERHIYAALGISDFFLDWYFSFREK-YVMQSRY-VRAHMSYVKTSGEPGTLLGNTILMGAML 1915
Cdd:pfam00978  214 LeIDFSKFDKSQGELHLLVQLEILKLLGLDPELADLWFKFHRQsYIKDRKNgVGFSVDYQRKSGDANTYLGNTLVTMAML 293

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558  1916 NAMLRGTGPFCMAMKGDDgfkrqaNLKINDQMLKLIKKETVLDFKLDL-----NVPiTFCG-YALSNGHLFPSVS---RK 1986
Cdd:pfam00978  294 ASVYDLEKIDCAAFSGDD------SLIFSPKPIEDPASRFATLFNMEAkvfdpSVP-YFCSkFLLEVDGGAFFVPdplKL 366

                          330       340       350
                   ....*....|....*....|....*....|
gi 828763558  1987 LTKI-AAHRFREYKHFCEYQESLRDWIKNL 2015
Cdd:pfam00978  367 LQKLgKKKIPDDEQHLDEIFTSLCDLTKSF 396
SF1_C_RecD cd18809
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ...
 1136-1180 4.51e-04

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


Pssm-ID: 350196 [Multi-domain]  Cd Length: 80  Bit Score: 40.62  E-value: 4.51e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 828763558 1136 TTVRANQGSTYDNVVLPVLPSDLKLinSAELNLVALSRHRNKLTI 1180
Cdd:cd18809    36 MTIHKSQGSEFDRVIVVLPTSHPML--SRGLLYTALTRARKLLTL 78
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 1142-1185 5.36e-04

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


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 44.97  E-value: 5.36e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 828763558 1142 QGSTYDNVVLpVLPSDLKLINSAELNLVALSRHRNKLTILLDND 1185
Cdd:COG0507   451 QGSTFDRVIL-VLPSEHSPLLSRELLYTALTRARELLTLVGDRD 493
 
Name Accession Description Interval E-value
Benyviridae_RdRp cd23257
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Benyviridae of ...
 1752-1939 1.58e-128

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: 400.84  E-value: 1.58e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1752 KLYRFQLKDIEKPLKDPETDLAKAGQGILAWSKEAHVKFMVAFRVLNDLLLKSLNSNVVYDNTMSETEFVGKINAAMNIV 1831
Cdd:cd23257     1 RLYRFQLKDIEKPLKDPETDLAKAGQGILAWSKEAHVKFMVAFRVLNDLLLKSLNSNVVYDNTMSETEFVGKINAAMNTV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1832 PDSAINGVIDAAACDSGQGVFTQLIERHIYAALGISDFFLDWYFSFREKYVMQSRYVRAHMSYVKTSGEPGTLLGNTILM 1911
Cdd:cd23257    81 PDSAINGVIDAAACDSGQGVFTQLIERYIYAALGISDFFLDWYFSFREKYVMQSRYVRAHMSYVKTSGEPGTLLGNTILM 160

                         170       180
                  ....*....|....*....|....*...
gi 828763558 1912 GAMLNAMLRGTGPFCMAMKGDDGFKRQA 1939
Cdd:cd23257   161 GAMLNAMLRGTGPFCMAMKGDDGFKRQA 188
ps-ssRNAv_Hepelivirales_RdRp cd23209
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of ...
 1754-1938 9.41e-76

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: 249.71  E-value: 9.41e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1754 YRFQLKDIEKPLKDPETDLAKAGQGILAWSKEAHVKFMVAFRVLNDLLLKSLNSNVVYDNTMSETEFVGKINAAMnivpd 1833
Cdd:cd23209     3 ITFFQKDCRKFTDCEPVAHGKAGQGISAWSKELCFVFGPWFRALEKILRRALKPNVLYANGHEAEPFVDKINQAH----- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1834 SAINGVIDAAACDSGQGVFTQLIERHIYAALGISDFFLDWYFSFREKYVMQSRYVRAHMSYVKTSGEPGTLLGNTILMGA 1913
Cdd:cd23209    78 SAVFIENDFTEFDSTQNLFSLLVELEILEACGMPPALAELYRALRAKWTLQAREGSLEGTCKKTSGEPGTLLHNTIWNMA 157

                         170       180
                  ....*....|....*....|....*
gi 828763558 1914 MLNAMLRGTGPFCMAMKGDDGFKRQ 1938
Cdd:cd23209   158 VMMHMVRGGVRKAAAFKGDDSVVCC 182
Peptidase_C36 pfam05415
Beet necrotic yellow vein furovirus-type papain-like endopeptidase; Corresponds to Merops ...
 1-104 2.52e-54

Beet necrotic yellow vein furovirus-type papain-like endopeptidase; Corresponds to Merops family C36. This protease involved in processing the viral polyprotein.


Pssm-ID: 461645  Cd Length: 104  Bit Score: 184.90  E-value: 2.52e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558     1 MADSFGFTPMEVLLFGGESVQLLTSDMPIDVQWGFVHSTRCYALWKDDLIHLNPLLKYSQRIAKRWERLVSGFVGPVPLD 80
Cdd:pfam05415    1 MADSFGFNCLEVAIFECEGVQLEKLDMLIDANAGFLDKTHAWALKKDDLIHLDCLLFADALIAKMWEKLLSDFPGDLPLD 80

                           90       100
                   ....*....|....*....|....
gi 828763558    81 KLLSLLAKLMRYCVNMGVSVQEIY 104
Cdd:pfam05415   81 KDGAGLAKLLHLCGKEGDGHFEAA 104
Peptidase_C36 pfam05415
Beet necrotic yellow vein furovirus-type papain-like endopeptidase; Corresponds to Merops ...
 1285-1388 6.03e-52

Beet necrotic yellow vein furovirus-type papain-like endopeptidase; Corresponds to Merops family C36. This protease involved in processing the viral polyprotein.


Pssm-ID: 461645  Cd Length: 104  Bit Score: 178.35  E-value: 6.03e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558  1285 NLVSRPNNCLVVAISECLGVTLEKLDNLMQAKAVTLDKYHAWLSKKSPSTWQDCRMFADALKVSMYVKVLSDKPYDLTYE 1364
Cdd:pfam05415    1 MADSFGFNCLEVAIFECEGVQLEKLDMLIDANAGFLDKTHAWALKKDDLIHLDCLLFADALIAKMWEKLLSDFPGDLPLD 80

                           90       100
                   ....*....|....*....|....
gi 828763558  1365 VDGAGSSVTLHLVGKESDGHFIAA 1388
Cdd:pfam05415   81 KDGAGLAKLLHLCGKEGDGHFEAA 104
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 940-1181 3.23e-32

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: 126.34  E-value: 3.23e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558   940 VKGGPGTGKSFLIRSLADPIRDLVvaPFIKLRSDyqnqRVGDE--LLSWDFHTPHKALDVTGKQIIFVDEFTAYDWRLLA 1017
Cdd:pfam01443    3 VHGVPGCGKSTLIRKLLRTSRVIR--PTAELRTE----GKPDLpnLNVRTVDTFLMALLKPTGKILILDEYTLLPPGYIL 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558  1018 VLAYRNHAHTIYLVGDEQQTGIQEGRGEGISILNKIDLSKVSTHVPIMNFRNPVRDVKVLNylfGSRMVPMSSVEKGFSF 1097
Cdd:pfam01443   77 LLAAISGAKLVILFGDPLQIPYHSRAPSFLIPHFPSSLSHRVGRRTTYLLPSLRAPILSAK---GFEVVVERSGEYKVDY 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558  1098 gdikefsSLSNIPDTKIIHYSDETGEHMmpdyvrGVSKTTVRANQGSTYDNVVLPVLPSDLKLI--NSAELNLVALSRHR 1175
Cdd:pfam01443  154 -------DPNGVLVLVYLTFTQALKESL------GVRVTTVHEVQGLTFDSVTLVLDTDTDLLIisDSPEHLYVALTRHR 220


                   ....*.
gi 828763558  1176 NKLTIL 1181
Cdd:pfam01443  221 KSLHIL 226
RdRP_2 pfam00978
RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ...
 1691-2015 3.24e-16

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: 83.46  E-value: 3.24e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558  1691 SSTQDSVARMVAQLFVSDCLVPNVADTFSASnlwRIMDKAMHDMVTK---NYQGQMEEEFTR-----NAKLYRFQLKDIE 1762
Cdd:pfam00978   65 SVDLDDTAERVAERFKKSFLDKEKLDKLDPI---INTTENVSRWLDKqsgKKAAQLKLDDLVplhevDLDRYKHMIKSDV 141

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558  1763 KPLKDPETDL-AKAGQGILAWSKEAHVKFMVAFRVLNDLLLKSLNSNVVYdntmseteFVGKINAAMNI---VPDSAING 1838
Cdd:pfam00978  142 KPKLDLSPQSeRPALQTITYHDKGVTAYFSPIFRELFERLLYVLKPKIVF--------PTGMTSSLIAEhfeFLDASEDF 213

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558  1839 V-IDAAACDSGQGVFTQLIERHIYAALGISDFFLDWYFSFREK-YVMQSRY-VRAHMSYVKTSGEPGTLLGNTILMGAML 1915
Cdd:pfam00978  214 LeIDFSKFDKSQGELHLLVQLEILKLLGLDPELADLWFKFHRQsYIKDRKNgVGFSVDYQRKSGDANTYLGNTLVTMAML 293

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558  1916 NAMLRGTGPFCMAMKGDDgfkrqaNLKINDQMLKLIKKETVLDFKLDL-----NVPiTFCG-YALSNGHLFPSVS---RK 1986
Cdd:pfam00978  294 ASVYDLEKIDCAAFSGDD------SLIFSPKPIEDPASRFATLFNMEAkvfdpSVP-YFCSkFLLEVDGGAFFVPdplKL 366

                          330       340       350
                   ....*....|....*....|....*....|
gi 828763558  1987 LTKI-AAHRFREYKHFCEYQESLRDWIKNL 2015
Cdd:pfam00978  367 LQKLgKKKIPDDEQHLDEIFTSLCDLTKSF 396
Hepeviridae_RdRp cd23259
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Hepeviridae of ...
 1756-1933 1.88e-13

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: 72.86  E-value: 1.88e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1756 FQlKDIEKPLKDPETDLAKAGQGILAWSKEAHVKFMVAFRVLNDLLLKSLNSNVVYDNTMSETEFVGKINAAmnivPDSA 1835
Cdd:cd23259    70 FQ-KDCNKFTTDETIAHGKVGQGISAWSKTFCALFGPWFRAIEKAIVALLPPNIFYGDAYEESVFSAAVAGA----GSCR 144

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1836 I--NgviDAAACDSGQGVFTQLIERHIYAALGISDFFLDWYFSFREKYVMQSRYVRAHMSYVKTSGEPGTLLGNTILMGA 1913
Cdd:cd23259   145 VfeN---DFSEFDSTQNNFSLGLECEIMEECGMPQWLVRLYHLVRSAWVLQAPKESLRGFWKKHSGEPGTLLWNTVWNMA 221

                         170       180
                  ....*....|....*....|
gi 828763558 1914 MLNAMLRGTGPFCMAMKGDD 1933
Cdd:cd23259   222 VIAHCYEFRDLAVAAFKGDD 241
ps-ssRNAv_Martellivirales_RdRp cd23208
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Martellivirales of ...
 1754-1933 2.10e-10

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: 62.00  E-value: 2.10e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1754 YRFQLKDIEKP-LKDPETDLAKAGQGILAWSKEAHVKFMVAFRVLNDLLLKSLNSNVVYdntmseteFVGKINAA-MN-- 1829
Cdd:cd23208     3 YEMMIKSDVKPkLDLTAQQEYPKLQTIVYHDKNITAIFCPIFKELFERLLSCLKKKVVI--------YTGMMTSAeLNdf 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1830 IVPDSAINGV----IDAAACDSGQGVFTQLIERHIYAALGISDFFLD-WYFSFREKYVMQSR-YVRAHMSYVKTSGEPGT 1903
Cdd:cd23208    75 ISALHLESGYyvleIDFSKFDKSQGALHLLTELLILRRLGVDEPLLVlWEFAHTQSTTRDINnGISFETAYQRKSGDAFT 154

                         170       180       190
                  ....*....|....*....|....*....|
gi 828763558 1904 LLGNTILMGAMLNAMLRGTGPFCMAMKGDD 1933
Cdd:cd23208   155 YFGNTLVTMAALLDVLDLEKIVCIAFGGDD 184
Kitaviridae_RdRp cd23254
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of ...
 1754-2010 2.76e-09

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: 60.24  E-value: 2.76e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1754 YRFQLKDIEKP-LKDPETDLAKAGQGILAWSKEAHVKFMVAFRVLNDLLLKSLNSNVVYDNTMSETEFVGKINaaMNIVP 1832
Cdd:cd23254     3 YSFMIKRNPKPnLTVDAAYKYPALQTIAYHDKDINAIFCPIFRELKKRLLAVLKPNFVIFTDMSPEDFEELLN--RRFPP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1833 DSAINGV----IDAAACDSGQGVFTQLIERHIYAALGISDFFLD-WYFSFREKYV--MQSRyVRAHMSYVKTSGEPGTLL 1905
Cdd:cd23254    81 EVLSKLLhkleIDISKYDKSQGELALLFECKLMRRFGVPEELVElWFNAHVLTTLydRTNK-LKALVEYQRKSGDASTFF 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1906 GNTI-LMGAMLNAM-LRGtgpFCMAM-KGDDG--FKRQANLKINDQMLKLI----KKetVLDFKLdlnvpITFCGYAL-- 1974
Cdd:cd23254   160 GNTLfLMAVLADLFdLSD---LELALfSGDDSllFGRNLLDYDDSQHFALKfnleSK--FLNYKY-----PYFCSKFLlp 229

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 828763558 1975 -SNGHLF-PSVSRKLTKIAAHRFREYKHFCEYQESLRD 2010
Cdd:cd23254   230 vGGRWYFvPDPVKLLTKLGRHDLVNWEHVEEYRISLKD 267
ps-ssRNAv_Alsuviricetes_RdRp cd23182
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the class Alsuviricetes of ...
 1754-1935 1.74e-07

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: 53.37  E-value: 1.74e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1754 YRFQLKDIEKPLKDPETDLAKAGQGILAWSKEAHVKFMVAFRVLNDLLLKSLNSNVVYDNTMSETEfVGKINAAMNIVPd 1833
Cdd:cd23182     3 IDFLIKTQQKVSPKTPFNTGKAGQTIAAHSKSINFVLGPWIRYLEERLRDGSRTHRYSNGLMDEEE-AMLSQWKINHVP- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1834 SAINGVIDAAACDSGQGVFTQLIERHIYAALGISDFFLDWyfsFREKYVmqSRYVR-------AHMSYVKTSGEPGTLLG 1906
Cdd:cd23182    81 HATFVSNDYTAFDKSHNGESLLLEAAIMRRIGTPAAAPNL---FIELHG--KRTLRakvlggsGELDGMRDSGAAWTYCR 155

                         170       180
                  ....*....|....*....|....*....
gi 828763558 1907 NTILMGAMLNAMLRGTGPFcMAMKGDDGF 1935
Cdd:cd23182   156 NTDYNLAVMLSLYRLKVKP-AAFSGDDSL 183
Closteroviridae_RdRp cd23253
RNA-dependent RNA polymerase (RdRp) in the family Closteroviridae of positive-sense ...
 1790-1933 3.69e-07

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: 53.72  E-value: 3.69e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1790 FMVAFRVLNDLLLKSLNSNVVYDNTMSETEFVGKINAAMNIVPDSAINGVIDAAACDSGQGVFTQLIERHIYAALGISDF 1869
Cdd:cd23253    40 FSPIFLEVFDRIKYCLSDKIILYSGMNLEELASLIRSKLGDPLDEYKTVEIDFSKFDKSQGVLFKVYEELVYKFFGFSEE 119

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 828763558 1870 FLD-WYFS-FREKYVMQSRYVRAHMSYVKTSGEPGTLLGNTILMGAMLNAMLRGTGPFCMAMKGDD 1933
Cdd:cd23253   120 LYDnWKCSeYFSCRATSDSGVSLELGAQRRTGSPNTWLGNTLVTLGILSSSYDLDDIDLLLVSGDD 185
Alphatetraviridae_RdRp cd23258
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Alphatetraviridae of ...
 1756-1935 5.93e-07

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Alphatetraviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Alphatetraviridae, order Hepelivirales. The Alphatetraviridae is a family of (+)ssRNA viruses with nonenveloped icosahedral T=4 viral particles; they restrictively infect insects, particularly the Lepidoptera. The Alphatetraviridae family includes two genera representing viruses with a monopartite (Betatetravirus) and bipartite (Omegatetravirus) genome organization. Under a previous classification, this Alphatetraviridae family was included in a single group of tetraviruses along with two other families: Carmotetraviridae (single species) and Permutotetraviridae. Neither of these two families is now included in this Alphatetraviridae family: Carmotetraviridae is now classified into a different order, Tolivirales; Permutotetraviridae is a permuted RdRp and not included in this RdRp hierarchy. Alphatetravirus replicases include three conserved functional domains, namely methytransferase (MT), helicase (HEL) and RdRp domains, that are characteristic of all members of the alpha-like virus superfamily. 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: 438108  Cd Length: 184  Bit Score: 51.90  E-value: 5.93e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1756 FQLKDIEKPLKDPETDLaKAGQGILAWSKEAHVKFMVAFRVLNDLLLKSlNSNVVYDNTMSETEFVGKINAAMNIVPDSA 1835
Cdd:cd23258     5 FLMKTQQKVSPKPINTG-KVGQGIAAHSKSLNFVLAAWVRILEEILRTG-SRTVRYSNGLPDEEEAMLLEAKINQVPHAT 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1836 INGV----IDAAACDSGQGVFTQLIERHIYAALGISdffldwYFSFREKyvmqSRYVRA------HMSYVKTSGEPGTLL 1905
Cdd:cd23258    83 FVSAdwteFDTAHNNVSELLFAALLERIGTPAAAVN------LFRERCG----KRTLRAkglgsvEVDGLLDSGAVWTIC 152

                         170       180       190
                  ....*....|....*....|....*....|
gi 828763558 1906 GNTILMGAMLNAMLRGTGpfCMAMKGDDGF 1935
Cdd:cd23258   153 RNTIFSAGVMLTLFRGVK--FAAFKGDDSL 180
Matonaviridae_RdRp cd23260
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Matonaviridae of ...
 1774-2010 7.35e-05

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Matonaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Matonaviridae, order Hepelivirales. Members of the family Matonaviridae have a (+)ssRNA genome enclosed by an icosahedral capsid. Matonaviridae has a single genus, Rubivirus, which contains three species: Rubivirus rubella (commonly called rubella virus), Rubivirus ruteetense (commonly called ruhugu virus), and Rubivirus strelense (commonly called rustrela virus). Rubella virus (RuV) is the etiologic agent of the disease rubella (also called German measles). RuV is transmitted only between humans via the respiratory route, and is the main cause of congenital rubella syndrome (severe congenital birth defects, miscarriage, and stillbirth) when infection occurs during the first trimester of pregnancy. In vitro studies with cell lines showed that RuV has an apoptotic effect on certain cell types; there is evidence for a p53-dependent mechanism. 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: 438110  Cd Length: 257  Bit Score: 46.51  E-value: 7.35e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1774 KAGQGILAWSKEAHVKFMVAFRVLNDLLLKSLNSN--VVYDNTMSETEFVGKINAAMNIVPdsaingvIDAAACDSGQGV 1851
Cdd:cd23260    22 KAGLEIRAWAKDWVQVMSPHFRAIQKIILRALRPQflVAAGHTEAEVDAWWQAHYSPNAVE-------VDFTEFDMNQTL 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1852 FTQLIERHIYAAL----GISDffldwYFSFRE-KYVMQSRYVRAHMSYVKTSGEPGTLLGNTILmgAMlnamlrgtgpfC 1926
Cdd:cd23260    95 ATRDVELEISASLlglpSAED-----YRALRAgSYCLLRDLASTETGCERTSGEPATLLHNTLV--AM-----------C 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1927 MAMKGDDGFKRQANLKINDQMLKLIKKETVLD------FKLDL---NVPI--------TFCGYALSNGHLFPSVSRKLTK 1989
Cdd:cd23260   157 MAMRMVPKGVRWAGIFQGDDMVIFLPEGARRAalrwtpAELGLfgfHIPVkhvatatpSFCGHVGSAAGLFHDVLHLAIK 236

                         250       260
                  ....*....|....*....|.
gi 828763558 1990 IAAHRFrEYKHFCEYQESLRD 2010
Cdd:cd23260   237 LLCRRF-DPDVLEEQQVAMLD 256
Bromoviridae_RdRp cd23252
RNA-dependent RNA polymerase (RdRp) in the family Bromoviridae of positive-sense ...
 1840-1933 2.23e-04

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: 45.68  E-value: 2.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 828763558 1840 IDAAACDSGQGVFTQLIERHIYAALGISDFFLDWYFSFREKYVMQSRYVRAHMS--YVKTSGEPGTLLGNTILMGAMLNA 1917
Cdd:cd23252   172 IDFSKFDKSQGELHHEIQEHILNALGCPAPFTKWWFDFHRRSYISDRRAGVGFSvdFQRRTGDAFTYLGNTLVTLAELAY 251

                          90
                  ....*....|....*...
gi 828763558 1918 M--LRGTGPFCMAMKGDD 1933
Cdd:cd23252   252 VydLDDPNFDFVVASGDD 269
SF1_C_RecD cd18809
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ...
 1136-1180 4.51e-04

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


Pssm-ID: 350196 [Multi-domain]  Cd Length: 80  Bit Score: 40.62  E-value: 4.51e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 828763558 1136 TTVRANQGSTYDNVVLPVLPSDLKLinSAELNLVALSRHRNKLTI 1180
Cdd:cd18809    36 MTIHKSQGSEFDRVIVVLPTSHPML--SRGLLYTALTRARKLLTL 78
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 1142-1185 5.36e-04

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


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 44.97  E-value: 5.36e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 828763558 1142 QGSTYDNVVLpVLPSDLKLINSAELNLVALSRHRNKLTILLDND 1185
Cdd:COG0507   451 QGSTFDRVIL-VLPSEHSPLLSRELLYTALTRARELLTLVGDRD 493
 
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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