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Conserved domains on  [gi|1848664397|gb|QKI28838|]
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polyprotein [Brassica caulorapa potyvirus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ps-ssRNAv_Potyviridae_RdRp cd23175
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of ...
 2446-2681 6.77e-169

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Potyviridae, order: Patatavirales. Potyviridae, is the largest family of RNA plant viruses, members of which have (+)ssRNA genomes and flexuous filamentous particles. The family is divided into eight genera: Brambyvirus, Bymovirus, Ipomovirus, Macluravirus, Poacevirus, Potyvirus, Rymovirus, and Tritimovirus. Most genomes are monopartite but those of members of the genus Bymovirus are bipartite. Some members cause serious disease epidemics in cultivated plants. 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: 438025  Cd Length: 236  Bit Score: 519.31  E-value: 6.77e-169
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2446 GYKGLWNGSLKAELRPLEKVRANKTRTFTAAPIDTLLGAKVCVDDFNNEFYSKNLKCPWTVGMTKFYGGWDKLMRSLPDG 2525
Cdd:cd23175      1 GKMGVWNGSLKAELRPIEKVEANKTRTFTAAPIDTLLGGKVCVDDFNNQFYSLHLKAPWTVGITKFYGGWDKLLRKLPDG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2526 WLYCHADGSQFDSSLTPALLNAVLIIRSFYMEDWWVGQEMLENLYAEIVYTPILAPDGTIFKKFRGNNSGQPSTVVDNTL 2605
Cdd:cd23175     81 WVYCDADGSQFDSSLTPYLINAVLRIRLHFMEDWDIGEQMLRNLYTEIVYTPILTPDGTIVKKFKGNNSGQPSTVVDNTL 160

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1848664397 2606 MVVISIYYACMKFGWNHEDIENKLVFFANGDDLILAVKDEDSGLLDNMSSSFCDLGLNYDFSERTHKREDLWFMSH 2681
Cdd:cd23175    161 MVMIAMYYALLKLGIDFEEIDERCVFFCNGDDLLIAVSPEHEHILDTFSSSFSELGLNYDFSSRTRDKEELWFMSH 236
Peptidase_C6 super family cl20022
Helper component proteinase; This protein is found in genome polyproteins of potyviruses.
 329-766 2.25e-112

Helper component proteinase; This protein is found in genome polyproteins of potyviruses.


The actual alignment was detected with superfamily member pfam00851:

Pssm-ID: 279223  Cd Length: 440  Bit Score: 365.86  E-value: 2.25e-112
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  329 FRPRPDHVCKVDHNNEECGELAAIFCQALFPVVKLSCQTCREKLSRVSFEEFKDSLNANFIIHKDKWDSFKEGSHYDNIF 408
Cdd:pfam00851    3 SRLPSDHTPYESSNNELIGRLARMLVAAIIPKGHLYCKTCALRVIKSKRADIVNALSKAKQRGMLEFGKERDRFIYDERV 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  409 --KLIKVATQATQNLKLSSEVTKLVQNHTSTHMKPIQDVNKALMKGSLVTQNELDLALKQLLEMTQWFKNHMHLTGEEAL 486
Cdd:pfam00851   83 liKLFELQAPPPYKIATITEITTICCGSDDDPFAHIRIIMKVLAEPNLADVSGWQPASGSLLLLARHLKNRHTSIQAGNS 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  487 KTFRNKRSSKAMinpsllCDNQLDKNGNFVWGERGYHSKRLFKNFFEEVIPSEGYTK-YVVRNFPNGTRKLAIGSLIVPL 565
Cdd:pfam00851  163 SMFHNSLAGAQN------WDNQIDRNQVRIWGQRNEEAMPFFKKAFDEIQLLNATSQvANARKHYLGTRKLSTGDLDILR 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  566 NLDRARTALLGESI--EKKPLTS-ACVSQQNGNYIHSCCCVTMDDGTPMYSELKSPTKRHLVIGASGDPKYIDLPASEAE 642
Cdd:pfam00851  237 KYQDLYEFVQKSETsySKADNTSgACLTMKNDKYFYSCGCKTGVDGSKMYSPLYCPTKQHVRIHRVEDNMQIPLPTFHDA 316

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  643 RMYIAKEGYCYLNIFLAMLVNVNENEAKDFTKMIRDVLIPMLGQWPSLMDVATAAYILGVFHPETRCAELPRILVDHATQ 722
Cdd:pfam00851  317 TVYEANEGYCYINQFLAMLVGFINEDEMEFYKNQMNQIVLNLGAWPTFEDYAVECRAISLDYPKVRGAPLPIILVSHATK 396

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....
gi 1848664397  723 TMHVIDSYGSLTVGYHVLKAGTVNHLIQFASNDLQSEMKHYRVG 766
Cdd:pfam00851  397 TIHVVDQFGSINQGYHALKAATVGELVDLAHKKVEGEMLTYKVG 440
Poty_coat super family cl02961
Potyvirus coat protein;
2846-3077 1.70e-97

Potyvirus coat protein;


The actual alignment was detected with superfamily member pfam00767:

Pssm-ID: 279151  Cd Length: 243  Bit Score: 314.93  E-value: 1.70e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2846 DVNAGSHGKI-VPRLSKITKKMSLPRVKGNVILD-IDHLLEYKPDQIELYNTRASHQQFASWFNQVKTEYDLNEQQ-MGV 2922
Cdd:pfam00767    1 DVAAATSITFeVPRRKGFGALWRPPKQKGAATPNrIEKLKKYLPDQNDISNTRATQAQLNDWYEAVRDDYGQTEEEfMDT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2923 VMNGFMVWCIENGTSPDIN--GVW-----VMMDGNEQVEYPLKPIVENAKPTLRQIMHHFSDAAEA-YIEMRNAEAPYMP 2994
Cdd:pfam00767   81 ILPGWIVWCIENGTSPENRkaGSWravimAMMEDEEQVLYPIEPIIINAQPTLRQIMRHFSDLARAqYAESRNQGKPYMP 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2995 RYGLLRNLRDRSLARYAFDFYEVNSKTPERAREAVAQMKAAALSNVSSRLFGLDGNVATTSEDTERHTARDVNRNMHTLL 3074
Cdd:pfam00767  161 KGGLKAGLADASLAAYAFDFYEDTSHDTARAREVHHQMKAAAVSGIKIRLFALAGPGSGQEEDTERHTVEDVAEGIHSLG 240


                   ...
gi 1848664397 3075 GVN 3077
Cdd:pfam00767  241 GAQ 243
Peptidase_S30 pfam01577
Potyvirus P1 protease; The potyviridae family positive stand RNA viruses with genome encoding ...
 74-309 1.14e-73

Potyvirus P1 protease; The potyviridae family positive stand RNA viruses with genome encoding a polyprotein. members include zucchini yellow mosaic virus, and turnip mosaic viruses which cause considerable losses of crops worldwide. This family consists of a C terminus region from various plant potyvirus P1 proteins (found at the N terminus of the polyprotein). The C terminus of P1 is a serine-type protease responsible for autocatalytic cleavage between P1 and the helper component protease pfam00851. The entire P1 protein may be involved in virus-host interactions.


:

Pssm-ID: 250716  Cd Length: 245  Bit Score: 246.47  E-value: 1.14e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397   74 EMKFRLTRNEMSKVKKGPNGRIILRKPSKQRVFARIEQDKAARMEEAIFLEGNYDDSITTLESVLPSEVTRNVDVSLRSP 153
Cdd:pfam01577    6 KVAERLLRKEMSKIKQEKKGRIILRKLSPAQVAKKREKLKREEREERQFLQGAYASIVSKITPIGTDKVSKTESVSFRTP 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  154 FYKRTYKKERKRVAQKQIVQAP-LNSLCTRILKIARNKNIPVEMIGNKKAKHTLIFKRFRGYFVGKVSVAHEEGRMRHTE 232
Cdd:pfam01577   86 YYKRTTKKMKKKKKKKKVVMSDkINYLIRQVLKIAKKKGKPVELIGKKKKRTRVTFKRKGGSRLLKVSLAHERGKRRRRD 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  233 MSYEQFKWILKAICQVTHTERIREEDIK-PGCSGWVLGTNHTLTKRYSRLPHLVIRGRDDDGIVNALEPVLF--YSEFDH 309
Cdd:pfam01577  166 LSLDNFTQKLALHCAKTTTRHLRVDDIKlKGDSGLVLNTRKLLGFGRSRLPLFVVRGRHNGKLVDARSKVSEsvMHSIEH 245
Poty_PP super family cl07169
Potyviridae polyprotein; This domain is found in polyproteins of the viral Potyviridae taxon.
 1549-1821 2.23e-60

Potyviridae polyprotein; This domain is found in polyproteins of the viral Potyviridae taxon.


The actual alignment was detected with superfamily member pfam08440:

Pssm-ID: 285618  Cd Length: 277  Bit Score: 209.65  E-value: 2.23e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1549 AAALSFAYGLPVTTHGVSTNILGKCTVKQMRCALNFELTPFFTTHLIRHDGSMHPLIHEELKQFKLRDSEMVLNKVALPH 1628
Cdd:pfam08440    1 AALLCFAYNVPPVTDNVDVALFGTCTREQVLTAQQFELSPFLMANMVAPDGSMPPVIYDLFKKLLLRDGAVPLCSSYNPL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1629 QFVSQWMDQSEYERIGVHVQCHE-GTRIPFYTNGVPDKVYEKIWKCIQEHKNDAIFGKLSSACS-TKVSYTLSTDPAALP 1706
Cdd:pfam08440   81 RASSNWLTVSEYERIGNDKHIHVkAVKIPFHCKDLSEDFNIKLAEAVKKCRSTSLARFIVDAVNfIKTAYKLSTDPKSVG 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1707 RTIAIIDHLLAEEMMKRNHFDT-ISSAVTGYSFSLAGIADSFRKRYMRDHTAHNIAILQQARAQLLEFnSKNVNINNLSD 1785
Cdd:pfam08440  161 RTLLIVGELLVEQRSKLEQLLHhQSESVGRYLFGLCTLNYCLRGRYAKDRLDENINRLENVRSQLGEF-SITSDYDELEE 239

                          250       260       270
                   ....*....|....*....|....*....|....*...
gi 1848664397 1786 L--EGIGVIKSVVLQSKQEVSNFLGLRGKWDGRKFSND 1821
Cdd:pfam08440  240 LfiENYECAAYVHHQSKTQKFIDLKLKGIYNYTLIASD 277
Peptidase_C4 super family cl24133
Peptidase family C4; This peptidase is present in the nuclear inclusion protein of potyviruses.
 2041-2273 5.39e-51

Peptidase family C4; This peptidase is present in the nuclear inclusion protein of potyviruses.


The actual alignment was detected with superfamily member pfam00863:

Pssm-ID: 279235  Cd Length: 243  Bit Score: 181.44  E-value: 5.39e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2041 ESKSIYKGVRDYNGISTIVCQLTNDSDGLKETMYGIGYGPIIITNGHLFRKNNG--TLLVKSWHGEFTVKNTTTLKVHFI 2118
Cdd:pfam00863    2 EDKSIAKGLRDYHHIASNLAALEYYCGDHKGEIHGICHGDKIITPAHLFKEACGndTLKIQSKHGLFDLEALDRQKIEEL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2119 EGKDVVLVRMPKDFPPFKSNASFRAPKREERACLVGTNFQEKSLRSTVSESSMTIPEG--TGSYWIHWISTNEGDCGLPM 2196
Cdd:pfam00863   82 CGQDIIVIKGPIDMPPAKMRLIFRAPIQCERAVLIGCRRDDNGDRFEKSDESAIFPLGkeNGGFWKHGCDTKLGDCGGPI 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2197 VSTTDGKIIGVHG-----LASTVSSKNYFVPFTDDFIATHLSKLDDLTWTQHWLWQPSKIAWGTLNLIDEQPGPEFRISN 2271
Cdd:pfam00863  162 IACDDMDIIGFHGgrlmqLGANNSLAHIFAALNDDFIEMFAEMETAKGFQRKWKFNADKVEWGRLDLTSNQPSGAFKIQK 241


                   ..
gi 1848664397 2272 LV 2273
Cdd:pfam00863  242 LI 243
DEXDc smart00487
DEAD-like helicases superfamily;
1236-1389 2.01e-21

DEAD-like helicases superfamily;


:

Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 94.87  E-value: 2.01e-21
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  1236 EIASSSEGEFLVRGAVGSGKSTSLPAHLA------KKGKVLLLEPTRPLAENVSRQLA--GDPFFQNVTLRMRGLNCF-- 1305
Cdd:smart00487   18 EALLSGLRDVILAAPTGSGKTLAALLPALealkrgKGGRVLVLVPTRELAEQWAEELKklGPSLGLKVVGLYGGDSKReq 97

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  1306 ------GSSNITVMTSGFAFHYYVNNPHQLMEFDFVIIDECHVTDSATiaFNCALKEY----NFAGKLIKVSATPPGREC 1375
Cdd:smart00487   98 lrklesGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGG--FGDQLEKLlkllPKNVQLLLLSATPPEEIE 175

                           170
                    ....*....|....
gi 1848664397  1376 DFDTQFAVKVKTED 1389
Cdd:smart00487  176 NLLELFLNDPVFID 189
HELICc smart00490
helicase superfamily c-terminal domain;
1426-1524 1.52e-12

helicase superfamily c-terminal domain;


:

Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 65.31  E-value: 1.52e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  1426 DMLSKLLTERQFSVTKVDGRTMQLGKTTIETHGTSQKPHFIVATNIIENGVTL-DVECVVDFGLkvvaeldsenrcvryn 1504
Cdd:smart00490    1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLpGVDLVIIYDL---------------- 64

                            90       100
                    ....*....|....*....|
gi 1848664397  1505 kkSVSYGERIQRLGRVWRPK 1524
Cdd:smart00490   65 --PWSPASYIQRIGRAGRAG 82
ps-ssRNAv_RdRp-like super family cl40470
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 2356-2522 3.44e-03

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


The actual alignment was detected with superfamily member cd21589:

Pssm-ID: 477363  Cd Length: 925  Bit Score: 43.23  E-value: 3.44e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2356 DFFKYNKP--VTVNQLDH-----DKFLEAVDGvirmmcdfefnECrfITDPEEIYNSLNMKAAIGAQYRGKKKEYFEGLD 2428
Cdd:cd21589    447 NYYKYNLPtmVDIKQLLFvlevvYKYFEIYDG-----------GC--IPASQVIVNNYDKSAGYPFNKFGKARLYYEALS 513

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2429 dFDRERLLFQSCERlfNGYKGLWNGSLKAELrplekvrANKTRTFTAApidtllGAKVCVDDFNNEFYSKNLK------- 2501
Cdd:cd21589    514 -FEEQDEIYAYTKR--NVLPTLTQMNLKYAI-------SAKNRARTVA------GVSILSTMTGRMFHQKCLKsiaatrg 577

                          170       180
                   ....*....|....*....|.
gi 1848664397 2502 CPWTVGMTKFYGGWDKLMRSL 2522
Cdd:cd21589    578 VPVVIGTTKFYGGWDDMLRRL 598
 
Name Accession Description Interval E-value
ps-ssRNAv_Potyviridae_RdRp cd23175
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of ...
 2446-2681 6.77e-169

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Potyviridae, order: Patatavirales. Potyviridae, is the largest family of RNA plant viruses, members of which have (+)ssRNA genomes and flexuous filamentous particles. The family is divided into eight genera: Brambyvirus, Bymovirus, Ipomovirus, Macluravirus, Poacevirus, Potyvirus, Rymovirus, and Tritimovirus. Most genomes are monopartite but those of members of the genus Bymovirus are bipartite. Some members cause serious disease epidemics in cultivated plants. 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: 438025  Cd Length: 236  Bit Score: 519.31  E-value: 6.77e-169
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2446 GYKGLWNGSLKAELRPLEKVRANKTRTFTAAPIDTLLGAKVCVDDFNNEFYSKNLKCPWTVGMTKFYGGWDKLMRSLPDG 2525
Cdd:cd23175      1 GKMGVWNGSLKAELRPIEKVEANKTRTFTAAPIDTLLGGKVCVDDFNNQFYSLHLKAPWTVGITKFYGGWDKLLRKLPDG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2526 WLYCHADGSQFDSSLTPALLNAVLIIRSFYMEDWWVGQEMLENLYAEIVYTPILAPDGTIFKKFRGNNSGQPSTVVDNTL 2605
Cdd:cd23175     81 WVYCDADGSQFDSSLTPYLINAVLRIRLHFMEDWDIGEQMLRNLYTEIVYTPILTPDGTIVKKFKGNNSGQPSTVVDNTL 160

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1848664397 2606 MVVISIYYACMKFGWNHEDIENKLVFFANGDDLILAVKDEDSGLLDNMSSSFCDLGLNYDFSERTHKREDLWFMSH 2681
Cdd:cd23175    161 MVMIAMYYALLKLGIDFEEIDERCVFFCNGDDLLIAVSPEHEHILDTFSSSFSELGLNYDFSSRTRDKEELWFMSH 236
Peptidase_C6 pfam00851
Helper component proteinase; This protein is found in genome polyproteins of potyviruses.
 329-766 2.25e-112

Helper component proteinase; This protein is found in genome polyproteins of potyviruses.


Pssm-ID: 279223  Cd Length: 440  Bit Score: 365.86  E-value: 2.25e-112
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  329 FRPRPDHVCKVDHNNEECGELAAIFCQALFPVVKLSCQTCREKLSRVSFEEFKDSLNANFIIHKDKWDSFKEGSHYDNIF 408
Cdd:pfam00851    3 SRLPSDHTPYESSNNELIGRLARMLVAAIIPKGHLYCKTCALRVIKSKRADIVNALSKAKQRGMLEFGKERDRFIYDERV 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  409 --KLIKVATQATQNLKLSSEVTKLVQNHTSTHMKPIQDVNKALMKGSLVTQNELDLALKQLLEMTQWFKNHMHLTGEEAL 486
Cdd:pfam00851   83 liKLFELQAPPPYKIATITEITTICCGSDDDPFAHIRIIMKVLAEPNLADVSGWQPASGSLLLLARHLKNRHTSIQAGNS 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  487 KTFRNKRSSKAMinpsllCDNQLDKNGNFVWGERGYHSKRLFKNFFEEVIPSEGYTK-YVVRNFPNGTRKLAIGSLIVPL 565
Cdd:pfam00851  163 SMFHNSLAGAQN------WDNQIDRNQVRIWGQRNEEAMPFFKKAFDEIQLLNATSQvANARKHYLGTRKLSTGDLDILR 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  566 NLDRARTALLGESI--EKKPLTS-ACVSQQNGNYIHSCCCVTMDDGTPMYSELKSPTKRHLVIGASGDPKYIDLPASEAE 642
Cdd:pfam00851  237 KYQDLYEFVQKSETsySKADNTSgACLTMKNDKYFYSCGCKTGVDGSKMYSPLYCPTKQHVRIHRVEDNMQIPLPTFHDA 316

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  643 RMYIAKEGYCYLNIFLAMLVNVNENEAKDFTKMIRDVLIPMLGQWPSLMDVATAAYILGVFHPETRCAELPRILVDHATQ 722
Cdd:pfam00851  317 TVYEANEGYCYINQFLAMLVGFINEDEMEFYKNQMNQIVLNLGAWPTFEDYAVECRAISLDYPKVRGAPLPIILVSHATK 396

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....
gi 1848664397  723 TMHVIDSYGSLTVGYHVLKAGTVNHLIQFASNDLQSEMKHYRVG 766
Cdd:pfam00851  397 TIHVVDQFGSINQGYHALKAATVGELVDLAHKKVEGEMLTYKVG 440
Poty_coat pfam00767
Potyvirus coat protein;
2846-3077 1.70e-97

Potyvirus coat protein;


Pssm-ID: 279151  Cd Length: 243  Bit Score: 314.93  E-value: 1.70e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2846 DVNAGSHGKI-VPRLSKITKKMSLPRVKGNVILD-IDHLLEYKPDQIELYNTRASHQQFASWFNQVKTEYDLNEQQ-MGV 2922
Cdd:pfam00767    1 DVAAATSITFeVPRRKGFGALWRPPKQKGAATPNrIEKLKKYLPDQNDISNTRATQAQLNDWYEAVRDDYGQTEEEfMDT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2923 VMNGFMVWCIENGTSPDIN--GVW-----VMMDGNEQVEYPLKPIVENAKPTLRQIMHHFSDAAEA-YIEMRNAEAPYMP 2994
Cdd:pfam00767   81 ILPGWIVWCIENGTSPENRkaGSWravimAMMEDEEQVLYPIEPIIINAQPTLRQIMRHFSDLARAqYAESRNQGKPYMP 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2995 RYGLLRNLRDRSLARYAFDFYEVNSKTPERAREAVAQMKAAALSNVSSRLFGLDGNVATTSEDTERHTARDVNRNMHTLL 3074
Cdd:pfam00767  161 KGGLKAGLADASLAAYAFDFYEDTSHDTARAREVHHQMKAAAVSGIKIRLFALAGPGSGQEEDTERHTVEDVAEGIHSLG 240


                   ...
gi 1848664397 3075 GVN 3077
Cdd:pfam00767  241 GAQ 243
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 2330-2741 2.43e-85

Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases.


Pssm-ID: 425815  Cd Length: 450  Bit Score: 288.15  E-value: 2.43e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2330 AEASAYFRPLMGEYQPSKLNKEAFKKDFFKYNKP---VTVNQLDHDKFLEA----------VDGVIRMMCDFEFNecrfi 2396
Cdd:pfam00680   12 AYVPASLGPEDPRWARSYLNTDPYVDDIKKYSRPklpGPADERDKLLNRSAakmvlselrgVPKKANSTLIVYRA----- 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2397 TDPEEIYNSLNMKAAIGAQY---RGKKKEYFEGLDDFDRERLLFQSCE------RLFNGYKGLWNGSLKAELRPLEKVRA 2467
Cdd:pfam00680   87 IDGVEQIDPLNWDTSAGYPYvglGGKKGDLIEHLKDGTEARELAERLAadwevlQNGTPLKLVYQTCLKDELRPLEKVEK 166

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2468 NKTRTFTAAPIDTLLGAKVCVDDFNNEFYSKNLKCPWTVGMTKFYGGWDKLMRSL--PDGWLYChADGSQFDSSLTPALL 2545
Cdd:pfam00680  167 GKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHPIQVGINPFDRGWPRLLRRLarFGDYVYE-LDYSGFDSSVPPWLI 245

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2546 NAVL-IIRSFYMEDWWVGQEmlENLYAEIVYTPILAPDGTIFKKFRGNNSGQPSTVVDNTLMVVISIYYA----CMKFGW 2620
Cdd:pfam00680  246 RFAFeILRELLGFPSNVKEW--RAILELLIYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYAllksLENDGP 323

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2621 NHEDIENKLVFFANGDDLILAVKDEDSGLLDNMSSSFCDLGLNYDFSERT----HKREDLWFMSHQAMLVDGMYIPKLEK 2696
Cdd:pfam00680  324 RVCNLDKYFDFFTYGDDSLVAVSPDFDPVLDRLSPHLKELGLTITPAKKTfpvsRELEEVSFLKRTFRKTPGGYRPPLDR 403

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*.
gi 1848664397 2697 ERIVSILEWDRSKEIMH-RTEAICaAMIEAWGHTELLQEIRKFYLW 2741
Cdd:pfam00680  404 KRILAQLEYIRSKPVPSgQLENIR-AYASHHGYEFYRDLLYRFVEW 448
Peptidase_S30 pfam01577
Potyvirus P1 protease; The potyviridae family positive stand RNA viruses with genome encoding ...
 74-309 1.14e-73

Potyvirus P1 protease; The potyviridae family positive stand RNA viruses with genome encoding a polyprotein. members include zucchini yellow mosaic virus, and turnip mosaic viruses which cause considerable losses of crops worldwide. This family consists of a C terminus region from various plant potyvirus P1 proteins (found at the N terminus of the polyprotein). The C terminus of P1 is a serine-type protease responsible for autocatalytic cleavage between P1 and the helper component protease pfam00851. The entire P1 protein may be involved in virus-host interactions.


Pssm-ID: 250716  Cd Length: 245  Bit Score: 246.47  E-value: 1.14e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397   74 EMKFRLTRNEMSKVKKGPNGRIILRKPSKQRVFARIEQDKAARMEEAIFLEGNYDDSITTLESVLPSEVTRNVDVSLRSP 153
Cdd:pfam01577    6 KVAERLLRKEMSKIKQEKKGRIILRKLSPAQVAKKREKLKREEREERQFLQGAYASIVSKITPIGTDKVSKTESVSFRTP 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  154 FYKRTYKKERKRVAQKQIVQAP-LNSLCTRILKIARNKNIPVEMIGNKKAKHTLIFKRFRGYFVGKVSVAHEEGRMRHTE 232
Cdd:pfam01577   86 YYKRTTKKMKKKKKKKKVVMSDkINYLIRQVLKIAKKKGKPVELIGKKKKRTRVTFKRKGGSRLLKVSLAHERGKRRRRD 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  233 MSYEQFKWILKAICQVTHTERIREEDIK-PGCSGWVLGTNHTLTKRYSRLPHLVIRGRDDDGIVNALEPVLF--YSEFDH 309
Cdd:pfam01577  166 LSLDNFTQKLALHCAKTTTRHLRVDDIKlKGDSGLVLNTRKLLGFGRSRLPLFVVRGRHNGKLVDARSKVSEsvMHSIEH 245
Poty_PP pfam08440
Potyviridae polyprotein; This domain is found in polyproteins of the viral Potyviridae taxon.
 1549-1821 2.23e-60

Potyviridae polyprotein; This domain is found in polyproteins of the viral Potyviridae taxon.


Pssm-ID: 285618  Cd Length: 277  Bit Score: 209.65  E-value: 2.23e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1549 AAALSFAYGLPVTTHGVSTNILGKCTVKQMRCALNFELTPFFTTHLIRHDGSMHPLIHEELKQFKLRDSEMVLNKVALPH 1628
Cdd:pfam08440    1 AALLCFAYNVPPVTDNVDVALFGTCTREQVLTAQQFELSPFLMANMVAPDGSMPPVIYDLFKKLLLRDGAVPLCSSYNPL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1629 QFVSQWMDQSEYERIGVHVQCHE-GTRIPFYTNGVPDKVYEKIWKCIQEHKNDAIFGKLSSACS-TKVSYTLSTDPAALP 1706
Cdd:pfam08440   81 RASSNWLTVSEYERIGNDKHIHVkAVKIPFHCKDLSEDFNIKLAEAVKKCRSTSLARFIVDAVNfIKTAYKLSTDPKSVG 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1707 RTIAIIDHLLAEEMMKRNHFDT-ISSAVTGYSFSLAGIADSFRKRYMRDHTAHNIAILQQARAQLLEFnSKNVNINNLSD 1785
Cdd:pfam08440  161 RTLLIVGELLVEQRSKLEQLLHhQSESVGRYLFGLCTLNYCLRGRYAKDRLDENINRLENVRSQLGEF-SITSDYDELEE 239

                          250       260       270
                   ....*....|....*....|....*....|....*...
gi 1848664397 1786 L--EGIGVIKSVVLQSKQEVSNFLGLRGKWDGRKFSND 1821
Cdd:pfam08440  240 LfiENYECAAYVHHQSKTQKFIDLKLKGIYNYTLIASD 277
Peptidase_C4 pfam00863
Peptidase family C4; This peptidase is present in the nuclear inclusion protein of potyviruses.
 2041-2273 5.39e-51

Peptidase family C4; This peptidase is present in the nuclear inclusion protein of potyviruses.


Pssm-ID: 279235  Cd Length: 243  Bit Score: 181.44  E-value: 5.39e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2041 ESKSIYKGVRDYNGISTIVCQLTNDSDGLKETMYGIGYGPIIITNGHLFRKNNG--TLLVKSWHGEFTVKNTTTLKVHFI 2118
Cdd:pfam00863    2 EDKSIAKGLRDYHHIASNLAALEYYCGDHKGEIHGICHGDKIITPAHLFKEACGndTLKIQSKHGLFDLEALDRQKIEEL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2119 EGKDVVLVRMPKDFPPFKSNASFRAPKREERACLVGTNFQEKSLRSTVSESSMTIPEG--TGSYWIHWISTNEGDCGLPM 2196
Cdd:pfam00863   82 CGQDIIVIKGPIDMPPAKMRLIFRAPIQCERAVLIGCRRDDNGDRFEKSDESAIFPLGkeNGGFWKHGCDTKLGDCGGPI 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2197 VSTTDGKIIGVHG-----LASTVSSKNYFVPFTDDFIATHLSKLDDLTWTQHWLWQPSKIAWGTLNLIDEQPGPEFRISN 2271
Cdd:pfam00863  162 IACDDMDIIGFHGgrlmqLGANNSLAHIFAALNDDFIEMFAEMETAKGFQRKWKFNADKVEWGRLDLTSNQPSGAFKIQK 241


                   ..
gi 1848664397 2272 LV 2273
Cdd:pfam00863  242 LI 243
DEXDc smart00487
DEAD-like helicases superfamily;
1236-1389 2.01e-21

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 94.87  E-value: 2.01e-21
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  1236 EIASSSEGEFLVRGAVGSGKSTSLPAHLA------KKGKVLLLEPTRPLAENVSRQLA--GDPFFQNVTLRMRGLNCF-- 1305
Cdd:smart00487   18 EALLSGLRDVILAAPTGSGKTLAALLPALealkrgKGGRVLVLVPTRELAEQWAEELKklGPSLGLKVVGLYGGDSKReq 97

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  1306 ------GSSNITVMTSGFAFHYYVNNPHQLMEFDFVIIDECHVTDSATiaFNCALKEY----NFAGKLIKVSATPPGREC 1375
Cdd:smart00487   98 lrklesGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGG--FGDQLEKLlkllPKNVQLLLLSATPPEEIE 175

                           170
                    ....*....|....
gi 1848664397  1376 DFDTQFAVKVKTED 1389
Cdd:smart00487  176 NLLELFLNDPVFID 189
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1252-1372 2.47e-13

DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350689 [Multi-domain]  Cd Length: 151  Bit Score: 69.89  E-value: 2.47e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1252 GSGKSTSLPAHLAKKG-----KVLLLEPTRPLAENVSRQLAGDPFFQNVTLRMRGLNcfGSSNITVMTSGFaFHYYVNNP 1326
Cdd:cd17931     11 GAGKTTRVLPQIIREAikkrlRTLVLAPTRVVAAEMYEALRGLPIRYRTGAVKEEHG--GNEIVDYMCHGT-FTCRLLSP 87

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1848664397 1327 HQLMEFDFVIIDECHVTDSATIAF--NCALKEYNFAGKLIKVSATPPG 1372
Cdd:cd17931     88 KRVPNYNLIIMDEAHFTDPASIAArgYIHTRVEMGEAAVIFMTATPPG 135
HELICc smart00490
helicase superfamily c-terminal domain;
1426-1524 1.52e-12

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 65.31  E-value: 1.52e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  1426 DMLSKLLTERQFSVTKVDGRTMQLGKTTIETHGTSQKPHFIVATNIIENGVTL-DVECVVDFGLkvvaeldsenrcvryn 1504
Cdd:smart00490    1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLpGVDLVIIYDL---------------- 64

                            90       100
                    ....*....|....*....|
gi 1848664397  1505 kkSVSYGERIQRLGRVWRPK 1524
Cdd:smart00490   65 --PWSPASYIQRIGRAGRAG 82
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 1410-1524 1.78e-11

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 63.38  E-value: 1.78e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1410 QHGNNILVYVASYNEVDmLSKLLTERQFSVTKVDGRTMQLGKTTIETHGTSQKPHFIVATNIIENGVTL-DVECVVDFGL 1488
Cdd:pfam00271   13 ERGGKVLIFSQTKKTLE-AELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLpDVDLVINYDL 91

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1848664397 1489 kvvaeldsenrcvrynKKSVSygERIQRLGRVWRPK 1524
Cdd:pfam00271   92 ----------------PWNPA--SYIQRIGRAGRAG 109
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 1246-1371 7.30e-10

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 60.33  E-value: 7.30e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1246 LVRGAVGSGKSTS--LPA-----HLAKKGKVLLLEPTRPLAENVSRQL--AGDPFFQNVTLRMRG------LNCFGSSNI 1310
Cdd:pfam00270   18 LVQAPTGSGKTLAflLPAlealdKLDNGPQALVLAPTRELAEQIYEELkkLGKGLGLKVASLLGGdsrkeqLEKLKGPDI 97

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1848664397 1311 TVMTSGFaFHYYVNNPHQLMEFDFVIIDECHVTDSatIAFNCALKEY----NFAGKLIKVSATPP 1371
Cdd:pfam00270   98 LVGTPGR-LLDLLQERKLLKNLKLLVLDEAHRLLD--MGFGPDLEEIlrrlPKKRQILLLSATLP 159
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
1252-1341 5.43e-04

HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 45.84  E-value: 5.43e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1252 GSGKSTSLPAHLA-----KKGKVLLLEPTRPLAENVSRQLA---GDPFFQNVTLRMRGLNCFGSSN-ITVMTSGfafhyy 1322
Cdd:COG1643     36 GAGKTTQLPLALLelgwgAGGRIGMLEPRRLAARAAAERMAeelGEPVGETVGYRVRFEDKVSAATrIEVVTEG------ 109

                           90       100
                   ....*....|....*....|....*
gi 1848664397 1323 V------NNPhQLMEFDFVIIDECH 1341
Cdd:COG1643    110 IllrelqRDP-ELEGVDTVIFDEFH 133
betaCoV_RdRp cd21589
betacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ...
 2356-2522 3.44e-03

betacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome; This subfamily contains the RNA-dependent RNA polymerase (RdRp) of betacoronaviruses, including the RdRps from three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2, also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which shows potential for the treatment of SARS-CoV-2 viral infections. The structure of SARS-CoV-2 Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438016  Cd Length: 925  Bit Score: 43.23  E-value: 3.44e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2356 DFFKYNKP--VTVNQLDH-----DKFLEAVDGvirmmcdfefnECrfITDPEEIYNSLNMKAAIGAQYRGKKKEYFEGLD 2428
Cdd:cd21589    447 NYYKYNLPtmVDIKQLLFvlevvYKYFEIYDG-----------GC--IPASQVIVNNYDKSAGYPFNKFGKARLYYEALS 513

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2429 dFDRERLLFQSCERlfNGYKGLWNGSLKAELrplekvrANKTRTFTAApidtllGAKVCVDDFNNEFYSKNLK------- 2501
Cdd:cd21589    514 -FEEQDEIYAYTKR--NVLPTLTQMNLKYAI-------SAKNRARTVA------GVSILSTMTGRMFHQKCLKsiaatrg 577

                          170       180
                   ....*....|....*....|.
gi 1848664397 2502 CPWTVGMTKFYGGWDKLMRSL 2522
Cdd:cd21589    578 VPVVIGTTKFYGGWDDMLRRL 598
 
Name Accession Description Interval E-value
ps-ssRNAv_Potyviridae_RdRp cd23175
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of ...
 2446-2681 6.77e-169

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Potyviridae, order: Patatavirales. Potyviridae, is the largest family of RNA plant viruses, members of which have (+)ssRNA genomes and flexuous filamentous particles. The family is divided into eight genera: Brambyvirus, Bymovirus, Ipomovirus, Macluravirus, Poacevirus, Potyvirus, Rymovirus, and Tritimovirus. Most genomes are monopartite but those of members of the genus Bymovirus are bipartite. Some members cause serious disease epidemics in cultivated plants. 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: 438025  Cd Length: 236  Bit Score: 519.31  E-value: 6.77e-169
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2446 GYKGLWNGSLKAELRPLEKVRANKTRTFTAAPIDTLLGAKVCVDDFNNEFYSKNLKCPWTVGMTKFYGGWDKLMRSLPDG 2525
Cdd:cd23175      1 GKMGVWNGSLKAELRPIEKVEANKTRTFTAAPIDTLLGGKVCVDDFNNQFYSLHLKAPWTVGITKFYGGWDKLLRKLPDG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2526 WLYCHADGSQFDSSLTPALLNAVLIIRSFYMEDWWVGQEMLENLYAEIVYTPILAPDGTIFKKFRGNNSGQPSTVVDNTL 2605
Cdd:cd23175     81 WVYCDADGSQFDSSLTPYLINAVLRIRLHFMEDWDIGEQMLRNLYTEIVYTPILTPDGTIVKKFKGNNSGQPSTVVDNTL 160

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1848664397 2606 MVVISIYYACMKFGWNHEDIENKLVFFANGDDLILAVKDEDSGLLDNMSSSFCDLGLNYDFSERTHKREDLWFMSH 2681
Cdd:cd23175    161 MVMIAMYYALLKLGIDFEEIDERCVFFCNGDDLLIAVSPEHEHILDTFSSSFSELGLNYDFSSRTRDKEELWFMSH 236
Peptidase_C6 pfam00851
Helper component proteinase; This protein is found in genome polyproteins of potyviruses.
 329-766 2.25e-112

Helper component proteinase; This protein is found in genome polyproteins of potyviruses.


Pssm-ID: 279223  Cd Length: 440  Bit Score: 365.86  E-value: 2.25e-112
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  329 FRPRPDHVCKVDHNNEECGELAAIFCQALFPVVKLSCQTCREKLSRVSFEEFKDSLNANFIIHKDKWDSFKEGSHYDNIF 408
Cdd:pfam00851    3 SRLPSDHTPYESSNNELIGRLARMLVAAIIPKGHLYCKTCALRVIKSKRADIVNALSKAKQRGMLEFGKERDRFIYDERV 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  409 --KLIKVATQATQNLKLSSEVTKLVQNHTSTHMKPIQDVNKALMKGSLVTQNELDLALKQLLEMTQWFKNHMHLTGEEAL 486
Cdd:pfam00851   83 liKLFELQAPPPYKIATITEITTICCGSDDDPFAHIRIIMKVLAEPNLADVSGWQPASGSLLLLARHLKNRHTSIQAGNS 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  487 KTFRNKRSSKAMinpsllCDNQLDKNGNFVWGERGYHSKRLFKNFFEEVIPSEGYTK-YVVRNFPNGTRKLAIGSLIVPL 565
Cdd:pfam00851  163 SMFHNSLAGAQN------WDNQIDRNQVRIWGQRNEEAMPFFKKAFDEIQLLNATSQvANARKHYLGTRKLSTGDLDILR 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  566 NLDRARTALLGESI--EKKPLTS-ACVSQQNGNYIHSCCCVTMDDGTPMYSELKSPTKRHLVIGASGDPKYIDLPASEAE 642
Cdd:pfam00851  237 KYQDLYEFVQKSETsySKADNTSgACLTMKNDKYFYSCGCKTGVDGSKMYSPLYCPTKQHVRIHRVEDNMQIPLPTFHDA 316

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  643 RMYIAKEGYCYLNIFLAMLVNVNENEAKDFTKMIRDVLIPMLGQWPSLMDVATAAYILGVFHPETRCAELPRILVDHATQ 722
Cdd:pfam00851  317 TVYEANEGYCYINQFLAMLVGFINEDEMEFYKNQMNQIVLNLGAWPTFEDYAVECRAISLDYPKVRGAPLPIILVSHATK 396

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....
gi 1848664397  723 TMHVIDSYGSLTVGYHVLKAGTVNHLIQFASNDLQSEMKHYRVG 766
Cdd:pfam00851  397 TIHVVDQFGSINQGYHALKAATVGELVDLAHKKVEGEMLTYKVG 440
Poty_coat pfam00767
Potyvirus coat protein;
2846-3077 1.70e-97

Potyvirus coat protein;


Pssm-ID: 279151  Cd Length: 243  Bit Score: 314.93  E-value: 1.70e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2846 DVNAGSHGKI-VPRLSKITKKMSLPRVKGNVILD-IDHLLEYKPDQIELYNTRASHQQFASWFNQVKTEYDLNEQQ-MGV 2922
Cdd:pfam00767    1 DVAAATSITFeVPRRKGFGALWRPPKQKGAATPNrIEKLKKYLPDQNDISNTRATQAQLNDWYEAVRDDYGQTEEEfMDT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2923 VMNGFMVWCIENGTSPDIN--GVW-----VMMDGNEQVEYPLKPIVENAKPTLRQIMHHFSDAAEA-YIEMRNAEAPYMP 2994
Cdd:pfam00767   81 ILPGWIVWCIENGTSPENRkaGSWravimAMMEDEEQVLYPIEPIIINAQPTLRQIMRHFSDLARAqYAESRNQGKPYMP 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2995 RYGLLRNLRDRSLARYAFDFYEVNSKTPERAREAVAQMKAAALSNVSSRLFGLDGNVATTSEDTERHTARDVNRNMHTLL 3074
Cdd:pfam00767  161 KGGLKAGLADASLAAYAFDFYEDTSHDTARAREVHHQMKAAAVSGIKIRLFALAGPGSGQEEDTERHTVEDVAEGIHSLG 240


                   ...
gi 1848664397 3075 GVN 3077
Cdd:pfam00767  241 GAQ 243
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 2330-2741 2.43e-85

Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases.


Pssm-ID: 425815  Cd Length: 450  Bit Score: 288.15  E-value: 2.43e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2330 AEASAYFRPLMGEYQPSKLNKEAFKKDFFKYNKP---VTVNQLDHDKFLEA----------VDGVIRMMCDFEFNecrfi 2396
Cdd:pfam00680   12 AYVPASLGPEDPRWARSYLNTDPYVDDIKKYSRPklpGPADERDKLLNRSAakmvlselrgVPKKANSTLIVYRA----- 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2397 TDPEEIYNSLNMKAAIGAQY---RGKKKEYFEGLDDFDRERLLFQSCE------RLFNGYKGLWNGSLKAELRPLEKVRA 2467
Cdd:pfam00680   87 IDGVEQIDPLNWDTSAGYPYvglGGKKGDLIEHLKDGTEARELAERLAadwevlQNGTPLKLVYQTCLKDELRPLEKVEK 166

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2468 NKTRTFTAAPIDTLLGAKVCVDDFNNEFYSKNLKCPWTVGMTKFYGGWDKLMRSL--PDGWLYChADGSQFDSSLTPALL 2545
Cdd:pfam00680  167 GKTRLVWGEPVEYLLLERAFFDPFNQAFMLNNGFHPIQVGINPFDRGWPRLLRRLarFGDYVYE-LDYSGFDSSVPPWLI 245

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2546 NAVL-IIRSFYMEDWWVGQEmlENLYAEIVYTPILAPDGTIFKKFRGNNSGQPSTVVDNTLMVVISIYYA----CMKFGW 2620
Cdd:pfam00680  246 RFAFeILRELLGFPSNVKEW--RAILELLIYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYAllksLENDGP 323

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2621 NHEDIENKLVFFANGDDLILAVKDEDSGLLDNMSSSFCDLGLNYDFSERT----HKREDLWFMSHQAMLVDGMYIPKLEK 2696
Cdd:pfam00680  324 RVCNLDKYFDFFTYGDDSLVAVSPDFDPVLDRLSPHLKELGLTITPAKKTfpvsRELEEVSFLKRTFRKTPGGYRPPLDR 403

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*.
gi 1848664397 2697 ERIVSILEWDRSKEIMH-RTEAICaAMIEAWGHTELLQEIRKFYLW 2741
Cdd:pfam00680  404 KRILAQLEYIRSKPVPSgQLENIR-AYASHHGYEFYRDLLYRFVEW 448
Peptidase_S30 pfam01577
Potyvirus P1 protease; The potyviridae family positive stand RNA viruses with genome encoding ...
 74-309 1.14e-73

Potyvirus P1 protease; The potyviridae family positive stand RNA viruses with genome encoding a polyprotein. members include zucchini yellow mosaic virus, and turnip mosaic viruses which cause considerable losses of crops worldwide. This family consists of a C terminus region from various plant potyvirus P1 proteins (found at the N terminus of the polyprotein). The C terminus of P1 is a serine-type protease responsible for autocatalytic cleavage between P1 and the helper component protease pfam00851. The entire P1 protein may be involved in virus-host interactions.


Pssm-ID: 250716  Cd Length: 245  Bit Score: 246.47  E-value: 1.14e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397   74 EMKFRLTRNEMSKVKKGPNGRIILRKPSKQRVFARIEQDKAARMEEAIFLEGNYDDSITTLESVLPSEVTRNVDVSLRSP 153
Cdd:pfam01577    6 KVAERLLRKEMSKIKQEKKGRIILRKLSPAQVAKKREKLKREEREERQFLQGAYASIVSKITPIGTDKVSKTESVSFRTP 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  154 FYKRTYKKERKRVAQKQIVQAP-LNSLCTRILKIARNKNIPVEMIGNKKAKHTLIFKRFRGYFVGKVSVAHEEGRMRHTE 232
Cdd:pfam01577   86 YYKRTTKKMKKKKKKKKVVMSDkINYLIRQVLKIAKKKGKPVELIGKKKKRTRVTFKRKGGSRLLKVSLAHERGKRRRRD 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  233 MSYEQFKWILKAICQVTHTERIREEDIK-PGCSGWVLGTNHTLTKRYSRLPHLVIRGRDDDGIVNALEPVLF--YSEFDH 309
Cdd:pfam01577  166 LSLDNFTQKLALHCAKTTTRHLRVDDIKlKGDSGLVLNTRKLLGFGRSRLPLFVVRGRHNGKLVDARSKVSEsvMHSIEH 245
Poty_PP pfam08440
Potyviridae polyprotein; This domain is found in polyproteins of the viral Potyviridae taxon.
 1549-1821 2.23e-60

Potyviridae polyprotein; This domain is found in polyproteins of the viral Potyviridae taxon.


Pssm-ID: 285618  Cd Length: 277  Bit Score: 209.65  E-value: 2.23e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1549 AAALSFAYGLPVTTHGVSTNILGKCTVKQMRCALNFELTPFFTTHLIRHDGSMHPLIHEELKQFKLRDSEMVLNKVALPH 1628
Cdd:pfam08440    1 AALLCFAYNVPPVTDNVDVALFGTCTREQVLTAQQFELSPFLMANMVAPDGSMPPVIYDLFKKLLLRDGAVPLCSSYNPL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1629 QFVSQWMDQSEYERIGVHVQCHE-GTRIPFYTNGVPDKVYEKIWKCIQEHKNDAIFGKLSSACS-TKVSYTLSTDPAALP 1706
Cdd:pfam08440   81 RASSNWLTVSEYERIGNDKHIHVkAVKIPFHCKDLSEDFNIKLAEAVKKCRSTSLARFIVDAVNfIKTAYKLSTDPKSVG 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1707 RTIAIIDHLLAEEMMKRNHFDT-ISSAVTGYSFSLAGIADSFRKRYMRDHTAHNIAILQQARAQLLEFnSKNVNINNLSD 1785
Cdd:pfam08440  161 RTLLIVGELLVEQRSKLEQLLHhQSESVGRYLFGLCTLNYCLRGRYAKDRLDENINRLENVRSQLGEF-SITSDYDELEE 239

                          250       260       270
                   ....*....|....*....|....*....|....*...
gi 1848664397 1786 L--EGIGVIKSVVLQSKQEVSNFLGLRGKWDGRKFSND 1821
Cdd:pfam08440  240 LfiENYECAAYVHHQSKTQKFIDLKLKGIYNYTLIASD 277
Peptidase_C4 pfam00863
Peptidase family C4; This peptidase is present in the nuclear inclusion protein of potyviruses.
 2041-2273 5.39e-51

Peptidase family C4; This peptidase is present in the nuclear inclusion protein of potyviruses.


Pssm-ID: 279235  Cd Length: 243  Bit Score: 181.44  E-value: 5.39e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2041 ESKSIYKGVRDYNGISTIVCQLTNDSDGLKETMYGIGYGPIIITNGHLFRKNNG--TLLVKSWHGEFTVKNTTTLKVHFI 2118
Cdd:pfam00863    2 EDKSIAKGLRDYHHIASNLAALEYYCGDHKGEIHGICHGDKIITPAHLFKEACGndTLKIQSKHGLFDLEALDRQKIEEL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2119 EGKDVVLVRMPKDFPPFKSNASFRAPKREERACLVGTNFQEKSLRSTVSESSMTIPEG--TGSYWIHWISTNEGDCGLPM 2196
Cdd:pfam00863   82 CGQDIIVIKGPIDMPPAKMRLIFRAPIQCERAVLIGCRRDDNGDRFEKSDESAIFPLGkeNGGFWKHGCDTKLGDCGGPI 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2197 VSTTDGKIIGVHG-----LASTVSSKNYFVPFTDDFIATHLSKLDDLTWTQHWLWQPSKIAWGTLNLIDEQPGPEFRISN 2271
Cdd:pfam00863  162 IACDDMDIIGFHGgrlmqLGANNSLAHIFAALNDDFIEMFAEMETAKGFQRKWKFNADKVEWGRLDLTSNQPSGAFKIQK 241


                   ..
gi 1848664397 2272 LV 2273
Cdd:pfam00863  242 LI 243
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 2441-2705 3.32e-46

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: 169.00  E-value: 3.32e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2441 ERLFNGYKGLWNGSLKAELRPLEKVRANKTRTFTAAPIDTLLGAKVCVDDFNNEFYSKNLKCPWTVGMTKFYGGWDKLMR 2520
Cdd:cd01699     10 DLPLIRPDLVFTTFLKDELRPLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKNRGGLPIAVGINPYSRDWTILAN 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2521 SL-PDGWLYCHADGSQFDSSLTPALLNAVL-IIRSFYMEDWWvgqEMLENLYAEIVYTPilAPDGT--IFKKFRGNNSGQ 2596
Cdd:cd01699     90 KLrSFSPVAIALDYSRFDSSLSPQLLEAEHsIYNALYDDDDE---LERRNLLRSLTNNS--LHIGFneVYKVRGGRPSGD 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2597 PSTVVDNTLMVVISIYYACMKFGWNHEDIENKLVFfaNGDDLILAVKDEDS-GLLDNMSSSFCDLGLNYDFSERTH---- 2671
Cdd:cd01699    165 PLTSIGNSIINCILVRYAFRKLGGKSFFKNVRLLN--YGDDCLLSVEKADDkFNLETLAEWLKEYGLTMTDEDKVEspfr 242

                          250       260       270
                   ....*....|....*....|....*....|....*
gi 1848664397 2672 KREDLWFMSHQAMLVDG-MYIPKLEKERIVSILEW 2705
Cdd:cd01699    243 PLEEVEFLKRRFVLDEGgGWRAPLDPSSILSKLSW 277
ps-ssRNAv-Picornavirales cd23169
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...
 2450-2745 5.58e-36

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


Pssm-ID: 438019  Cd Length: 309  Bit Score: 140.42  E-value: 5.58e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2450 LWNGSLKAELRPLEKVRANKTRTFTAAPIDTLLGAKVCVDDFNNEFYSKNLKCPWTVGMTKFYGGWDKLMRSLPDGWLYC 2529
Cdd:cd23169      2 IFVDCLKDELRPIEKVKAGKTRLFSASPLDYTIAFRKYFGDFIAAFQKNRIKLEHAVGINPDSVEWTRLYRRLLKKGPNI 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2530 HA-DGSQFDSSLTPALLNAVL-IIRSFYMEDW-WVGQEMLENLYAEIVYTPILApDGTIFKKFRGNNSGQPSTVVDNTLM 2606
Cdd:cd23169     82 FAgDYSNFDGSLPPDVMEAAFdIINDWYDEYVdDEDERVRKVLFEELINTIHLV-GNLVYQVHGGNPSGNPLTTIINSIV 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2607 VVISIYYA---CMKfGWNHEDIENKLVFFANGDDLILAVKDEDSGLLDN--MSSSFCDLGLNY------DFSERTHKRED 2675
Cdd:cd23169    161 NLLYIRYAwlrITG-LTSLSDFKKNVRLVTYGDDVIISVSDEVKDEFNFvtISEFLKELGITYtdadksGDIVPYRPLEE 239

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1848664397 2676 LWFMSH--QAMLVDGMYIPKLEKERIVSILEWDRsKEIMHRTEAICAAMIEAWghtELLQEIRKFYLWFVEK 2745
Cdd:cd23169    240 VTFLKRgfRPHPTPGLVLAPLDLESIEEQLNWTR-KEDDLLEATIENARAALL---LAFGHGPEYYNKFRQK 307
DEXDc smart00487
DEAD-like helicases superfamily;
1236-1389 2.01e-21

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 94.87  E-value: 2.01e-21
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  1236 EIASSSEGEFLVRGAVGSGKSTSLPAHLA------KKGKVLLLEPTRPLAENVSRQLA--GDPFFQNVTLRMRGLNCF-- 1305
Cdd:smart00487   18 EALLSGLRDVILAAPTGSGKTLAALLPALealkrgKGGRVLVLVPTRELAEQWAEELKklGPSLGLKVVGLYGGDSKReq 97

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  1306 ------GSSNITVMTSGFAFHYYVNNPHQLMEFDFVIIDECHVTDSATiaFNCALKEY----NFAGKLIKVSATPPGREC 1375
Cdd:smart00487   98 lrklesGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGG--FGDQLEKLlkllPKNVQLLLLSATPPEEIE 175

                           170
                    ....*....|....
gi 1848664397  1376 DFDTQFAVKVKTED 1389
Cdd:smart00487  176 NLLELFLNDPVFID 189
ps-ssRNA_Picornaviridae cd23193
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of ...
 2404-2657 4.64e-18

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


Pssm-ID: 438043  Cd Length: 345  Bit Score: 88.37  E-value: 4.64e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2404 NSLNMKAAIGAQY--RGKKKEYfegLDDFDRERLLFQSCERLF-----NGYKGLWNGSLKAELRPLEKVRANKTRTFTAA 2476
Cdd:cd23193      9 DPIDLNTSPGYPYttQGLRRRD---LIDNDKGGVSPLLEEEEQvlldlDGPDVVFTTFLKDELRPKEKVKAGKTRVIEAA 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2477 PIDTLLGAKVCVDDFNNEFYSKNlkCPWT---VGMTKFYGgWDKLMRSLPDGWLYChADGSQFDSSLTPALLN-AVLIIR 2552
Cdd:cd23193     86 PLDYVIAGRMVFGRLFAQFHSNP--GILTgsaVGCNPDTD-WTRLFASLKQDNVYD-LDYSGFDASLSSQLFEaAVEVLA 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2553 SFYMEDwwvgqEMLENLYAEIVY-TPILapDGTIFKKFRGNNSGQPSTVVDNTLMVVISIYYACMKFGwnHEDIENkLVF 2631
Cdd:cd23193    162 ECHGDP-----ELVLRYLEPIINsKHVV--GDERYTVEGGMPSGCPCTSILNSICNNLVVRYALLETG--KFDPDE-YYI 231

                          250       260
                   ....*....|....*....|....*...
gi 1848664397 2632 FANGDDLILAVKDE--DSGLLDNMSSSF 2657
Cdd:cd23193    232 LAYGDDVLVSTDEPidPSDLAEFYKKYF 259
Nora-virus_RdRp cd23200
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in a novel picorna-like ...
 2455-2737 4.53e-16

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in a novel picorna-like Drosophila virus, Nora virus; This group contains the catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the unclassified Nora virus, a new picorna-like virus family. Nora virus has a (+)ssRNA genome followed by a poly(A) tail. Unlike other picorna-like viruses, the genome has four open reading frames (ORFs). One ORF encodes a picornavirus-like cassette of proteins for virus replication, including an iflavirus-like RdRp and a helicase that is related to those of mammalian picornaviruses. The three other ORFs are not closely related to any previously described viruses. Nora virus is present as a persistent infection in several tested laboratory stocks and wild-caught flies. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438050  Cd Length: 306  Bit Score: 81.89  E-value: 4.53e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2455 LKAELRPLEKVRANKTRTFTAAPIDTLLGAKVCVDDFNNEFYSKNLKCPWTVGMTKFYGGWDKLMRSLPDGWLYCHADGS 2534
Cdd:cd23200      7 LKDQPIKIAQAKSGRTRVFHCIPVDLILFSGALYGPYKEAYTKAGLKCYHAVGIDPKSVGWQQLATYMTKHPNYFDADYK 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2535 QFDSSLTPALLNAVL-IIRSFYME---DWWVGQEMLENLYAeivYTPILAPDGTIFKKFRGNNSGQPSTVVDNTLMVVIS 2610
Cdd:cd23200     87 NYDKYLHRQVFKAVRkIQRSVIQQvcpDKWDKARAVEELDA---IDTYVVDYQTVYKTNRGNKSGSYTTTIDNCLANDIY 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2611 IYYACMKF--GWNHEDIENKLVFFANGDDLILAVKDEDSGLLDNMS--SSFCDLGL-----NYDFSER-THKREDLWFMS 2680
Cdd:cd23200    164 GLYAWVKTtgLRSLWDYRQNVSSVAFGDDIIKSVSDEYKDKYNYCTyrDVLNATGHimtpgSKDGEEKpFTSFENLQFLK 243

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1848664397 2681 HQAMLVDGMYIPKLEKERIVSILEWD--RSKEIMHRTEAICAAMIEA--WGHtELLQEIRK 2737
Cdd:cd23200    244 RGFKLENGMVLAPLLQRSIEGPFVWTdiREDQITVWVNLVQEQLIEAalWGE-EYYNELCQ 303
Dicistroviridae_RdRp cd23194
RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense ...
 2449-2664 5.47e-16

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


Pssm-ID: 438044 [Multi-domain]  Cd Length: 315  Bit Score: 81.78  E-value: 5.47e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2449 GLWNGSLKAELRPLEKVRANKTRTFTAAPIDTLLGAKVCVDDFNNEFYSKNLKCPWTVGMTKFYGGWDKLMRSL-PDGwl 2527
Cdd:cd23194      6 HVFVDTLKDERRPIEKVDAGKTRVFSAGPMDYTIAFRMYFLGFVAHLMRNRIDNEIAVGTNVYSLDWDKLARKLlSKG-- 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2528 YCHADG--SQFDSSLTPALLNAVL-IIRSFYMEDWwvgqemlEN------LYAEIVYTPILApDGTIFKKFRGNNSGQPS 2598
Cdd:cd23194     84 DKVIAGdfSNFDGSLNPQILWAILdIINEWYDDGE-------ENalirrvLWEDIVNSVHIC-GGYVYQWTHSQPSGNPL 155

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1848664397 2599 TVVDNTLMVVISIYYACMKFG-----WNHEDIENKLVFFANGDDLILAVKDEDSGLL--DNMSSSFCDLGLNY 2664
Cdd:cd23194    156 TAIINSIYNSIIMRYVYLLLTkeaglMTMSDFNKHVSMVSYGDDNVINVSDEVSEWFnqLTITEAMAEIGMTY 228
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1252-1372 2.47e-13

DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350689 [Multi-domain]  Cd Length: 151  Bit Score: 69.89  E-value: 2.47e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1252 GSGKSTSLPAHLAKKG-----KVLLLEPTRPLAENVSRQLAGDPFFQNVTLRMRGLNcfGSSNITVMTSGFaFHYYVNNP 1326
Cdd:cd17931     11 GAGKTTRVLPQIIREAikkrlRTLVLAPTRVVAAEMYEALRGLPIRYRTGAVKEEHG--GNEIVDYMCHGT-FTCRLLSP 87

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1848664397 1327 HQLMEFDFVIIDECHVTDSATIAF--NCALKEYNFAGKLIKVSATPPG 1372
Cdd:cd17931     88 KRVPNYNLIIMDEAHFTDPASIAArgYIHTRVEMGEAAVIFMTATPPG 135
HELICc smart00490
helicase superfamily c-terminal domain;
1426-1524 1.52e-12

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 65.31  E-value: 1.52e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397  1426 DMLSKLLTERQFSVTKVDGRTMQLGKTTIETHGTSQKPHFIVATNIIENGVTL-DVECVVDFGLkvvaeldsenrcvryn 1504
Cdd:smart00490    1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLpGVDLVIIYDL---------------- 64

                            90       100
                    ....*....|....*....|
gi 1848664397  1505 kkSVSYGERIQRLGRVWRPK 1524
Cdd:smart00490   65 --PWSPASYIQRIGRAGRAG 82
Caliciviridae_RdRp cd23192
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of ...
 2454-2663 7.95e-12

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Caliciviridae, order Picornavirales. Member viruses have a viral (+)ssRNA genome, which is not segmented. The family Caliciviridae, includes eleven genera: seven genera of which infect mammals (Lagovirus, Norovirus, Nebovirus, Recovirus, Sapovirus, Valovirus, and Vesivirus), two genera of which infect birds (Bavovirus, Nacovirus), and two genera of which infect fish (Minovirus and Salovirus). Each genus includes 1-2 species. Human noroviruses are a leading cause of acute gastroenteritis in humans. Furthermore, unclassified caliciviruses have been detected in geese, yellowfin seabream, greater green snake, arctic lamprey, frogs and various Australian birds, highlighting the wide host range of viruses in the family Caliciviridae. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438042  Cd Length: 310  Bit Score: 69.21  E-value: 7.95e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2454 SLKAELRPLEKVRANKTRTFTAAPIDTLLGAKVCVDDFNNEFYSKNLKCPWTVGMTKFYGGWDKLMRSL-PDGWLYChAD 2532
Cdd:cd23192      6 ALKDELRPVEKIAEGKRRLLWGCDVGVTLVAAAAFGPVADALKAVCPTGPIAVGINMDSEDVEVIFERLsGFRYHYC-LD 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2533 GSQFDSSLTPALLNAVL-IIRSFYMEDWWVgQEMLENLYAeivyTPILAPDGTIFKKFRGNNSGQPSTVVDNTL--MVVI 2609
Cdd:cd23192     85 YSKWDSTQSPAVTAAAIdILADLSEETPLR-DSVVETLSS----PPMGIFDDVIFVTKRGLPSGMPFTSVINSLnhWLLF 159

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1848664397 2610 S--IYYACMKFGWNHEDIENKLVFFANGDDLILAVKDEDSGLLDNMSSSFCDLGLN 2663
Cdd:cd23192    160 SaaVLKAYELVGIYTGNVFDEADFFTYGDDGVYAMPPATASVMDEIIENLKSYGLK 215
ps-ssRNAv_Astroviridae_RdRp cd23172
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of ...
 2450-2645 8.54e-12

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Astroviridae, order, Stellavirales. Astrovirus has a non-segmented, (+)ssRNA genome within a non-enveloped icosahedral capsid. The family Astroviridae comprises two genera, Mamastrovirus, which infect mammals, and Avastrovirus, which infect birds. Astroviruses have been isolated from stools from a wide variety of mammals and birds. Human astroviruses have been shown to be an important cause of gastroenteritis in young children. Duck astrovirus causes an often-fatal hepatitis in ducklings. Astroviruses infecting turkeys, guinea fowl and chickens affect multiple organs, including the kidney and thymus. 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: 438022  Cd Length: 243  Bit Score: 67.88  E-value: 8.54e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2450 LWNGSLKAELRPLEKVRANKTRTFTAAP-IDTLLGAkvCVD-DFNNEFYSKNLKCPWTVGMTKFYGGWDKLMRSLPD-GW 2526
Cdd:cd23172      3 LWYLFLKKEILKKEKIEDGDIRQILCPDpIFARIGA--RFEqDQNNLMKERTLTNEGQVGWSPFYGGFDARVRRLGSkGN 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2527 LYCHADGSQFDSSLTPALLNAVLIIRSFYMEDwwVGQEMLENLYAEIV----YTPILAPDGTIFKKFRGNNSGQPSTVVD 2602
Cdd:cd23172     81 YFVEFDWTRFDGTIPAELFRHIRKLRWSFLDP--EKTEENRKVYDWYVhnllNRYVLLPTGEVTRVTKGNPSGQISTTMD 158

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 1848664397 2603 NTLmvVISIYYACMKFGWNHEDIENKLVFFAN------GDDLILAVKDE 2645
Cdd:cd23172    159 NCM--VNTFLTAFEFAYVYGPKTGTLKELWDNydtivyGDDRLSGYPSL 205
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 1410-1524 1.78e-11

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 63.38  E-value: 1.78e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1410 QHGNNILVYVASYNEVDmLSKLLTERQFSVTKVDGRTMQLGKTTIETHGTSQKPHFIVATNIIENGVTL-DVECVVDFGL 1488
Cdd:pfam00271   13 ERGGKVLIFSQTKKTLE-AELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLpDVDLVINYDL 91

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1848664397 1489 kvvaeldsenrcvrynKKSVSygERIQRLGRVWRPK 1524
Cdd:pfam00271   92 ----------------PWNPA--SYIQRIGRAGRAG 109
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 1246-1371 7.30e-10

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 60.33  E-value: 7.30e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1246 LVRGAVGSGKSTS--LPA-----HLAKKGKVLLLEPTRPLAENVSRQL--AGDPFFQNVTLRMRG------LNCFGSSNI 1310
Cdd:pfam00270   18 LVQAPTGSGKTLAflLPAlealdKLDNGPQALVLAPTRELAEQIYEELkkLGKGLGLKVASLLGGdsrkeqLEKLKGPDI 97

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1848664397 1311 TVMTSGFaFHYYVNNPHQLMEFDFVIIDECHVTDSatIAFNCALKEY----NFAGKLIKVSATPP 1371
Cdd:pfam00270   98 LVGTPGR-LLDLLQERKLLKNLKLLVLDEAHRLLD--MGFGPDLEEIlrrlPKKRQILLLSATLP 159
Aalivirus_RdRp cd23216
RNA-dependent RNA polymerase (RdRp) in the genus Aalivirus of positive-sense single-stranded ...
 2406-2651 6.68e-09

RNA-dependent RNA polymerase (RdRp) in the genus Aalivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Aalivirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. Aalivirus is a new picornavirus found in ducks in China. It is most closely related to duck hepatitis A virus (genus Avihepatovirus) and to avisivirus A1 (genus Avisivirus). The name "aalivirus" is derived from Avihepatovirus/Avisivirus-like virus. RdRps are multi-domain proteins that play a pivotal role in enterovirus replication. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438066  Cd Length: 337  Bit Score: 60.45  E-value: 6.68e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2406 LNMKAAIGAQYRGKKKEyfegldDFDRERLLFQSCERLFNGYKGLWNGSLKAELRPLEKVRANKTRTFTAAPIDTLLGAK 2485
Cdd:cd23216     12 IDWQTSPGLKYKGRTKA------DLVQDPKFKEDVKEILAGKPTFFTTYLKDELRSIEKIANGNTRAIEAANFDHVVAWR 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2486 VCVDDFNNEFYSKNLKCP-WTVGMTKfYGGWDKLMRSLPdgWLYCHADGSQFDSSLTPALLN-AVLIIRSFYMEdwwvgQ 2563
Cdd:cd23216     86 QVMGNIVKQLFSDHDRVTgFAPGMNP-YTHFDSLMDQVK--WNVLALDFKKFDGSLSPQVMEeAVDILASFHDM-----P 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2564 EMLENLYAEIVYTPILAPDGTIFKKfRGNNSGQPSTVVDNT---LMVVISIYYAcmkfgwnhEDIE-NKLVFFANGDDLI 2639
Cdd:cd23216    158 QMVVDIHKHTIYSTNVVSDETWFVE-GGMCSGSPCTTVLNTicnLLVNTTILLS--------EGIQpDNFYIAAYGDDTI 228

                          250
                   ....*....|..
gi 1848664397 2640 LAVKDEDSGLLD 2651
Cdd:cd23216    229 ISVDGLSSSLPD 240
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 1252-1341 8.20e-09

DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA two-partner secretion (TPS) system, a secretion pathway important to the secretion of large virulence-associated proteins. HrpB belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438711 [Multi-domain]  Cd Length: 174  Bit Score: 57.34  E-value: 8.20e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1252 GSGKSTSLPAHLA-----KKGKVLLLEPTRPLAENVSRQLA---GDPFFQNVTLRMRGLNCFG-SSNITVMTSGFAFHYY 1322
Cdd:cd17990     27 GAGKTTRVPLALLaelwiAGGKIIVLEPRRVAARAAARRLAtllGEAPGETVGYRVRGESRVGrRTRVEVVTEGVLLRRL 106

                           90
                   ....*....|....*....
gi 1848664397 1323 VNNPhQLMEFDFVIIDECH 1341
Cdd:cd17990    107 QRDP-ELSGVGAVILDEFH 124
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 1244-1369 3.33e-08

N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 55.10  E-value: 3.33e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1244 EFLVRGAVGSGKST--SLPAHLA---KKGKVLLLEPTRPLAENVSRQLaGDPFFQNVTLRM---------RGLNCFGSSN 1309
Cdd:cd00046      3 NVLITAPTGSGKTLaaLLAALLLllkKGKKVLVLVPTKALALQTAERL-RELFGPGIRVAVlvggssaeeREKNKLGDAD 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1848664397 1310 ITVMTSGFAFHYYV-NNPHQLMEFDFVIIDECHVTDSAT-IAFNCALKEYNFAGKLIKV---SAT 1369
Cdd:cd00046     82 IIIATPDMLLNLLLrEDRLFLKDLKLIIVDEAHALLIDSrGALILDLAVRKAGLKNAQVillSAT 146
ps-ssRNAv_RdRp-like cd23167
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 2528-2642 4.01e-07

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


Pssm-ID: 438017 [Multi-domain]  Cd Length: 73  Bit Score: 49.64  E-value: 4.01e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2528 YCHADGSQFDSSLTPALLNAvliirsfymedwwvgqemlenlyaeivytpilapdgtifkkfrGNNSGQPSTVVDNTLMV 2607
Cdd:cd23167      2 VVESDYSGFDSSISPDLLKA-------------------------------------------GQPSGSPNTSADNSLIN 38

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1848664397 2608 VISIYYACMKFGWNHEDIENkLVFFANGDDLILAV 2642
Cdd:cd23167     39 LLLARLALRKACGRAEFLNS-VGILVYGDDSLVSV 72
Marnaviridae_RdRp cd23195
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Marnaviridae of ...
 2451-2645 6.55e-07

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


Pssm-ID: 438045  Cd Length: 310  Bit Score: 53.99  E-value: 6.55e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2451 WNGSLKAELRPLEKvraNKTRTFTAAPID-TLLGAK----VCvddfnnEFYSKN-LKCPWTVGMTKFYGGWDKLMRSL-P 2523
Cdd:cd23195      3 FKACLKDEPTKLTK---DKVRVFQAAPVAlQLLVRKyflpIA------RFLQMNpLLSECAVGINAQSPEWEELYEHLtK 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2524 DGWLYCHA-DGSQFDSSLTPALLNA---VLIIRSFYMEDWwvGQEML---ENLYAEIVYtPILAPDGTIFKKFRGNNSGQ 2596
Cdd:cd23195     74 FGEDRIIAgDYSKYDKRMSAQLILAafkILIDIAAKSGGY--SEEDLkimRGIATDIAY-PLVDFNGDLIQFFGSNPSGH 150

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1848664397 2597 PSTVVDNTLmvVISIYyacMKFGWNHEDIENKLVFFAN-------GDDLILAVKDE 2645
Cdd:cd23195    151 PLTVIINSI--VNSLY---MRYAYYSLYPEKEVPPFRDvvalmtyGDDNIMSVSPG 201
Parechovirus_RdRp cd23217
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Parechovirus of ...
 2404-2645 7.65e-07

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


Pssm-ID: 438067  Cd Length: 371  Bit Score: 54.10  E-value: 7.65e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2404 NSLNMKAAIGAQY--RGKKKEYFEGLDDFDRERLLFQSCERLFNG-YKG-----LWNGSLKAELRPLEKVRANKTRTFTA 2475
Cdd:cd23217      9 NSLDLSTSPGYKYvkSGYKKRDLLSLEPFSVSPQLEKDVKDKLHAvYKGnqpttIFNACLKDELRKLDKIAQGKTRCIEA 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2476 APIDTLLGAKVCVDDFNNEFY-SKNLKCPWTVGMTKfYGGWDKLMRSLPDgwlYCHA-DGSQFDSSLTPALLnavliirs 2553
Cdd:cd23217     89 CSIDYVIAYRVVMSSLYEAIYqTPCQELGLAVGMNP-WTDWDFMINALNP---YNYGlDYSSYDGSLSEMLM-------- 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2554 fymedwWVGQEMLENLYAE-----IVYTPILAPDGTIFKKF----RGNNSGQPSTVVDNTLM-VVISIYYACMKfgwnHE 2623
Cdd:cd23217    157 ------WEAVEVLAYCHESpdlvmQLHKPVINSDHVVMDERwlvhGGMPSGSPCTTVLNSICnLLVCIYLAYLQ----SP 226

                          250       260
                   ....*....|....*....|..
gi 1848664397 2624 DIENKLVFFanGDDLILAVKDE 2645
Cdd:cd23217    227 GIECLPIVY--GDDVIFSVSSE 246
Polycipiviridae_RdRp cd23198
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Polycipiviridae of ...
 2456-2645 4.89e-06

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


Pssm-ID: 438048  Cd Length: 317  Bit Score: 51.26  E-value: 4.89e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2456 KAELRPLEKVRAN-----KTRTFTAAPIDTLLG-AKVCVDDFNNEFYSKNLKCPWTVGMTKFYGGWDKLMRslpdgWLYC 2529
Cdd:cd23198      8 KDELRPIYKALGDpqtppKTRSVTCMNVYYILAwRRVTLDFWASMHRAADGNFPFCPGINPEGPDWNRLYH-----YLNR 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2530 HADGSQFDSS-----LTPALLNAVLIIRSFYMEDWWVGQ--EMLENLYAEIVYTPILAPDgTIFKKFRGNNSGQPSTVVD 2602
Cdd:cd23198     83 HPNAVDFDVSnwdghLPAELFYAVLDIIKTVLGLKPNSPnaKVIYSILTEVMNCHIQFED-IIYQKLRGLISGFPGTAEV 161

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 1848664397 2603 NTLMVVISIYYACMKFGWNHEDIENKLVFFAN------GDDLILAVKDE 2645
Cdd:cd23198    162 NTLAHWLLIYYIYLYLAQNTIYDMTITAFLRNvsaifyGDDIIITISDE 210
DEXHc_RHA-like cd17917
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ...
 1246-1341 5.41e-06

DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438707 [Multi-domain]  Cd Length: 159  Bit Score: 49.00  E-value: 5.41e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1246 LVRGAVGSGKSTSLPAHLA-------KKGKVLLLEPTR----PLAENVSRQLaGDPFFQNVTLRMRGLNCFGS-SNITVM 1313
Cdd:cd17917      5 VIVGETGSGKTTQVPQFLLedglakgGKGRIVCTQPRRiaaiSVAERVAEER-GEKLGEEVGYQIRFESKTSSkTRIKFC 83

                           90       100
                   ....*....|....*....|....*...
gi 1848664397 1314 TSGFAFHYYVNNPhQLMEFDFVIIDECH 1341
Cdd:cd17917     84 TDGILLRELLSDP-LLSGYSHVILDEAH 110
CoV_RdRp cd21530
coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible ...
 2305-2609 6.34e-06

coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome; This family contains the RNA-dependent RNA polymerase of alpha-, beta-, gamma-, delta-coronaviruses, including three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2, also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which shows potential for the treatment of SARS-CoV-2 viral infections. The structure of SARS-CoV-2 Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438015  Cd Length: 928  Bit Score: 52.15  E-value: 6.34e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2305 AQSALVTKHVVKgkcP-FFEEYLQTHAEASAYFR-----PLMGEYQPSKLNKEAFKKDFFKYNKPVTvnqLDHDKFLEAV 2378
Cdd:cd21530    396 ALSSGIAFQTVK---PgHFNKDFYDFAVSKGFFKegssvELKHFFFAQDGNAAISDYDYYRYNLPTM---LDIRQLLFCL 469

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2379 DGVIRMmcdFEFNECRFITDPEEIYNSLNMKAAIGAQYRGKKKEYFEGLDdFDRERLLFQSCERlfNGYKGLWNGSLKAE 2458
Cdd:cd21530    470 EVVDKY---FDCYEGGCINANQVVVTNLDKSAGFPFNKFGKARLYYDSMS-YEEQDALFAYTKR--NVLPTITQMNLKYA 543

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2459 LRPLEKVRanktrtftaapidTLLGAKVCVDDFNNEFYSKNLKC-------PWTVGMTKFYGGWDKLMRSLPD------- 2524
Cdd:cd21530    544 ISAKNRAR-------------TVAGVSILSTMTNRQFHQKLLKSivntrnaTVVIGTTKFYGGWDNMLRTLYSgvenpml 610

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2525 -GWLYCHADgsqfdssltPALLNAVLIIRSFYMEDWWVG----QEMLENLYAEI--VYTPILAPDGTIFKKFRGNNSGQP 2597
Cdd:cd21530    611 mGWDYPKCD---------RAMPNMLRIAASLVLARKHTNcctlSHRFYRLANECaqVLSEVVMSGGGLYVKPGGTSSGDA 681

                          330
                   ....*....|..
gi 1848664397 2598 STVVDNTLMVVI 2609
Cdd:cd21530    682 TTAYANSVFNIC 693
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 1250-1370 7.47e-06

DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 48.07  E-value: 7.47e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1250 AVGSGKST---SLPAHLaKKGKVLLLEPTRPLAENVSRQLAGdpFFQNVTLRMRG---LNCFGSSNITVMTSGFAFHYyv 1323
Cdd:cd17926     26 PTGSGKTLtalALIAYL-KELRTLIVVPTDALLDQWKERFED--FLGDSSIGLIGggkKKDFDDANVVVATYQSLSNL-- 100

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1848664397 1324 NNPHQLM--EFDFVIIDECHVTDSATiaFNCALKEYNfAGKLIKVSATP 1370
Cdd:cd17926    101 AEEEKDLfdQFGLLIVDEAHHLPAKT--FSEILKELN-AKYRLGLTATP 146
gammaCoV_RdRp cd21587
gammacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ...
 2322-2609 1.72e-05

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


Pssm-ID: 394891  Cd Length: 931  Bit Score: 50.65  E-value: 1.72e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2322 FEEYLQTHAEASAYFR-----PLMGEYQPSKLNKEAFKKDFFKYNKPVTVnqlDHDKFLEAVDGVIRMmcdFEFNECRFI 2396
Cdd:cd21587    415 FNKDFYDFAEKAGMFKegssiPLKHFFYPQTGNAAINDYDYYRYNRPTMF---DIRQLLFCLEVTSKY---FECYEGGCI 488

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2397 TDPEEIYNSLNMKAAIGAQYRGKKKEYFEGldDFDRERLLFQSCERlfNGYKGLWNGSLKAELrplekvrANKTRTFTAA 2476
Cdd:cd21587    489 PASQVVVNNLDKSAGYPFNKFGKARLYYEM--SLEEQDQLFESTKK--NVLPTITQMNLKYAI-------SAKNRARTVA 557

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2477 pidtllGAKVCVDDFNNEFYSKNLK-------CPWTVGMTKFYGGWDKLMRSLPD--------GWLYCHADGSQfdsslt 2541
Cdd:cd21587    558 ------GVSILSTMTNRQFHQKVLKsivntrnAPVVIGTTKFYGGWDNMLRNLIQgvedpilmGWDYPKCDRAM------ 625

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1848664397 2542 PALL----NAVLIIRSFYMEDWWVGQEMLENLYAEIVYTPILApDGTIFKKFRGNNSGQPSTVVDNTLMVVI 2609
Cdd:cd21587    626 PNLLriaaSLVLARKHTNCCTWSERIYRLYNECAQVLSETVLA-TGGIYVKPGGTSSGDATTAYANSVFNII 696
Iflaviridae_RdRp cd23197
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Iflaviridae of ...
 2455-2617 2.43e-05

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


Pssm-ID: 438047  Cd Length: 319  Bit Score: 49.09  E-value: 2.43e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2455 LKAELRPLEKVRA-NKTRTFTAAPIDTLLGAKVCVDDFNNEFYSKNLKCPWTVGMTKFYGGWDKLMRSL-PDGWLYCHAD 2532
Cdd:cd23197     12 LKDELRPSEKLRRfGGTRVFSVPPLELVLNSRRFLLPFMDAFQSFPIEAHHAIGLNPNSGDWRRLRDTLlEKGPCLLQMD 91

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2533 GSQFDSSLTPALLNAVLIIRSFYMEDWWVGQEMLENLYAEIVY---TPILAPDGTIFKKFRGNNSGQPSTVVDNTLMVVI 2609
Cdd:cd23197     92 YKNYSDAIPKECVAKAFHIIVDYYRKWHCLTVEIENALKTLFLdtaDAELLVYGDVFKVNNGVLAGHPMTSVVNSVVNLI 171


                   ....*...
gi 1848664397 2610 SIYYACMK 2617
Cdd:cd23197    172 LMNYMWIK 179
Aphthovirus_RdRp cd23210
RNA-dependent RNA polymerase (RdRp) in the Aphthovirus genus of positive-sense single-stranded ...
 2447-2641 1.24e-04

RNA-dependent RNA polymerase (RdRp) in the Aphthovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the Aphthovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. This genus includes species such as bovine rhinitis A virus, bovine rhinitis B virus, equine rhinitis A virus, and food-and-mouth disease virus (FMDV). Aphthoviruses primarily infect via the upper respiratory tract. FMDV infects mainly cloven-hoofed animals, but has been isolated from at least 70 species of mammals. Aphthoviruses are non-enveloped and have an icosahedral capsid with a diameter of around 27 to 30 nm. The assembled viral capsid contains a single copy of the RNA genome and 60 copies of the four viral capsid proteins VP1, VP2, VP3, and VP4. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438060  Cd Length: 458  Bit Score: 47.63  E-value: 1.24e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2447 YKGLWNGSLKAELRPLEKVRANKTRTFTAAPIDTLLGAKVCVDDFNNEFYSKN-------LKCPWTVGMTKFyGGWDKLM 2519
Cdd:cd23210    148 YKFACQTFLKDEIRPMEKVRAGKTRIVDVLPVEHILYTRMMIGRFCAQMHSNNgpqigsaVGCNPDVDWQRF-GTHFAQY 226

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2520 RSLPDgwlychADGSQFDSSLTPALLNAVLiiRSFYMEDW-------WVGQEMLENLYAEivytpilapDGTIFKKFRGN 2592
Cdd:cd23210    227 RNVWD------VDYSAFDANHCSDAMNIMF--EEVFRTEFgfhpnaeWILKTLVNTEHAY---------ENKRITVEGGM 289

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2593 NSGQPSTVVDNTLMVVISIYYACMKfgwNHEDIE-NKLVFFANGDDLILA 2641
Cdd:cd23210    290 PSGCSATSIINTILNNIYVLYALRR---HYEGVElDTYTMISYGDDIVVA 336
ResIII pfam04851
Type III restriction enzyme, res subunit;
1245-1371 1.25e-04

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 44.97  E-value: 1.25e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1245 FLVRGAVGSGK---STSLPAHLAKKG---KVLLLEPTRPLAEnvsrQLAGDpfFQNVTLRMRGLNCFGSSNiTVMTSGFA 1318
Cdd:pfam04851   26 GLIVMATGSGKtltAAKLIARLFKKGpikKVLFLVPRKDLLE----QALEE--FKKFLPNYVEIGEIISGD-KKDESVDD 98

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1848664397 1319 FHYYVNNPHQLM-------------EFDFVIIDECHvtDSATIAFNcALKEYNFAGKLIKVSATPP 1371
Cdd:pfam04851   99 NKIVVTTIQSLYkalelaslellpdFFDVIIIDEAH--RSGASSYR-NILEYFKPAFLLGLTATPE 161
Avisivirus_RdRp cd23231
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Avisivirus of ...
 2413-2643 1.39e-04

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


Pssm-ID: 438081  Cd Length: 362  Bit Score: 47.19  E-value: 1.39e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2413 GAQYRGKKKEyfEGLDD--FDRERL---------LFQSCERLFNGYkglwngsLKAELRPLEKVRANKTRTFTAAPIDTL 2481
Cdd:cd23231     18 GDKYKGKTKA--QLVDDkkFKADVMnlvrfngdpNREPPDVYFTTY-------LKDELRPKEKAKAGKTRVISAASFDYT 88

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2482 LGAKVCVDDFNNEFYSKNLKCPWTVGMTKfYGGWDKLMRSLpdgWLYC-HADGSQFDSSLTPALL-NAVLIIRSFYMEDW 2559
Cdd:cd23231     89 IACRMVFGPILRQLFAWGREFGFGPGLNP-YTHFDELYDKI---LPFViCLDYSGFDGSLSSELMfHAAQVIACFSEKPE 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2560 WVGQE-MLENLYAEIVYTPILAPDGtifkkfrGNNSGQPSTVVDNTLMVVISIYYACMKFGWnheDIENKLVfFANGDDL 2638
Cdd:cd23231    165 AIMASaELTIGSTERVSDEVWYVYG-------GMPSGSPWTTTLNTICNLLMCYTYLLDMGH---CWSETFV-VAYGDDV 233


                   ....*
gi 1848664397 2639 ILAVK 2643
Cdd:cd23231    234 VISAN 238
HCoV_HKU1-like_RdRp cd21593
human coronavirus HKU1 RNA-dependent RNA polymerase, also known as non-structural protein 12, ...
 2356-2627 2.83e-04

human coronavirus HKU1 RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the A lineage: responsible for replication and transcription of the viral RNA genome; This group contains the RNA-dependent RNA polymerase (RdRp) of human coronavirus HKU1, murine hepatitis virus, and similar proteins from betacoronaviruses in the embecovirus subgenera (A lineage). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 394897  Cd Length: 925  Bit Score: 46.88  E-value: 2.83e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2356 DFFKYNKPVTVnqlDHDKFLEAVDGVIRMmcdFEFNECRFITDPEEIYNSLNMKAAIGAQYRGKKKEYFEGLDdFDRERL 2435
Cdd:cd21593    447 NYYKYNLPTMV---DIKQLLFVLEVVYKY---FEIYDGGCIPASQVIVNNYDKSAGYPFNKFGKARLYYEALS-FEEQDD 519

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2436 LFQSCERlfNGYKGLWNGSLKAELRPlekvrANKTRTFTAAPIDTLLGAKVcvddfnneFYSKNLK-------CPWTVGM 2508
Cdd:cd21593    520 IYAYTKR--NVLPTLTQMNLKYAISA-----KNRARTVAGVSILSTMTGRM--------FHQKCLKsiaatrgVPVVIGT 584

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2509 TKFYGGWDKLMRSLPD--------GWLYCHADgsqfdssltPALLNAVLIIRSFYM---EDWWVGQE----MLENLYAEi 2573
Cdd:cd21593    585 TKFYGGWDDMLRRLIKdvdnpvlmGWDYPKCD---------RAMPNILRIVSSLVLarkHDSCCSHGdrfyRLANECAQ- 654

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1848664397 2574 VYTPILAPDGTIFKKFRGNNSGQPSTVVDNTLMVVISIYYA--CMKFGWNHEDIEN 2627
Cdd:cd21593    655 VLSEIVMCGGCYYVKPGGTSSGDATTAFANSVFNICQAVSAnvCSLMACNGHKIED 710
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1252-1372 3.87e-04

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 43.09  E-value: 3.87e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1252 GSGKSTS-LPAHL----AKKGKVLLLEPTRPLAENVSRQLAGDP--FFQNVTLRMRGlncfGSSNITVMTSGfAFHYYVN 1324
Cdd:pfam07652   12 GAGKTRKvLPELVreciDRRLRTLVLAPTRVVLAEMEEALRGLPirYHTPAVSSEHT----GREIVDVMCHA-TFTQRLL 86

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1848664397 1325 NPHQLMEFDFVIIDECHVTDSATIA---FNCALKEYNFAgKLIKVSATPPG 1372
Cdd:pfam07652   87 SPVRVPNYEVIIMDEAHFTDPASIAargYISTLVELGEA-AAIFMTATPPG 136
Mosavirus_RdRp cd23225
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Mosavirus of ...
 2402-2641 4.00e-04

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Mosavirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Mosavirus genus within the family Picornaviridae, order Picornavirales. The Mosavirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus includes two species: Mosavirus A, which found in the feces of a canyon mouse (Peromyscus crinitus), and Mosavirus B, which contains marmot mosavirus. Mosavirus stands for mouse stool-associated picornavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438075  Cd Length: 378  Bit Score: 45.68  E-value: 4.00e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2402 IYNSLNMKAAIGAQY--RGKK-------KEYFEGLDDFDRERLLfQSCERLFNGY-KGLWNGSLKAELRPLEKVRANKTR 2471
Cdd:cd23225      8 ISDAMDMTKAVGYPYclDSIKrldlveiKETENGKVYLPTERLV-EETEKFFTGEeKPKFVTFLKDEVRSNEKIKQGKTR 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2472 TFTAAPIDTLLGAKVCVDDfnneFYSKNLKCPWTvGMTKFYG-----GWDKLMRSLPDGWLYcHADGSQFDSSLTPALLN 2546
Cdd:cd23225     87 IVDASPFPYAIAGRMVMQN----FMSNMMRCNGT-EVGSAVGcdpdtEWTRYFFELCDRYVF-DLDYKAFDSTHPTAMFN 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2547 avLIIRSFYMEDWWVGQE----MLENLY-AEIVYtpilapDGTIFKKFRGNNSGQPSTVVDNTLMVVIsIYYACMKFGWN 2621
Cdd:cd23225    161 --LLAERFFTERNGFDQQavriFLNGLSdSDHVY------EGKHFRIRGGLPSGCPCTSILNTVINNI-IVRAAILGAYQ 231

                          250       260
                   ....*....|....*....|.
gi 1848664397 2622 HEDIE-NKLVFFANGDDLILA 2641
Cdd:cd23225    232 IDTVDfQKFRMLAYGDDVVYA 252
ps-ssRNAv_Nidovirales_RdRp cd23168
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Nidovirales of ...
 2476-2616 4.04e-04

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Nidovirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This family contains the catalytic core domain of RdRP of Nidovirales, an order of enveloped, (+)ssRNA viruses which infect vertebrates and invertebrates. Host organisms include mammals, birds, reptiles, amphibians, fish, arthropods, mollusks, and helminths. The order Nidovirales currently comprises 88 formally recognized virus species of (+)ssRNA viruses which are classified into nine virus families: Abyssoviridae, Arteriviridae, Coronaviridae, Euroniviridae, Medioniviridae, Mesoniviridae, Mononiviridae, Roniviridae, and Tobaniviridae. Based on the genome size, the members of the order Nidovirales can be divided into two groups, large and small nidoviruses. The genomes of the large nidoviruses are well over 25 kb in length with size differences in the 5 kb range. Planarian secretory cell nidovirus (PSCNV), only member of the Mononiviridae family, has the largest known non-segmented RNA genome of 41.1 kb; its host is the planarian flatworm. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438018 [Multi-domain]  Cd Length: 310  Bit Score: 45.43  E-value: 4.04e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2476 APIDTLLGAKVCVDDFNNEFYSKNLK-----CPWTVGM--TKFYGGWDKLMRSL-PDGWLYCH---ADGSQFDSSlTPAL 2544
Cdd:cd23168     15 KRARTILGVSIISTDVGRQLHQAVLAaivntRSANIVIigTKFYGGWHKMLRYLyPGVIEDPVlmgWDYPKCDRS-VPNM 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2545 ---LNAVLIIRSF-----YMEDW-WVGQEMLENLYAEIVYtpilapDGTIFKKFRGNNSGQPSTVVDNTLM---VVISIY 2612
Cdd:cd23168     94 lryLANLLLASLYdnccnLSEIVhLLINECAQVLYDYVVY------GGNLYRKPGGVSSGDSTTAISNSIYnyfQTFIAN 167


                   ....
gi 1848664397 2613 YACM 2616
Cdd:cd23168    168 VRLA 171
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
1252-1341 5.43e-04

HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 45.84  E-value: 5.43e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1252 GSGKSTSLPAHLA-----KKGKVLLLEPTRPLAENVSRQLA---GDPFFQNVTLRMRGLNCFGSSN-ITVMTSGfafhyy 1322
Cdd:COG1643     36 GAGKTTQLPLALLelgwgAGGRIGMLEPRRLAARAAAERMAeelGEPVGETVGYRVRFEDKVSAATrIEVVTEG------ 109

                           90       100
                   ....*....|....*....|....*
gi 1848664397 1323 V------NNPhQLMEFDFVIIDECH 1341
Cdd:COG1643    110 IllrelqRDP-ELEGVDTVIFDEFH 133
Aquamavirus_RdRp cd23220
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Aquamavirus of ...
 2406-2728 1.10e-03

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Aquamavirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Aquamavirus genus within the family Picornaviridae, order Picornavirales. The Aquamavirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Aquamavirus is a genus containing a single species, Aquamavirus A. This species consists of the previously named seal picornavirus 1, now to be called seal aquamavirus A1. Recently other aquamaviruses have been discovered in bears and seals (unassigned aquamaviruses). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438070  Cd Length: 338  Bit Score: 43.93  E-value: 1.10e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2406 LNMKAAIGAQYRG-KKKEYFEGLDDFDRERLLfQSCERLFNGYKGL-WNGSLKAELRPLEKVRANKTRTFTAAPIDTLLG 2483
Cdd:cd23220     12 LNFNGTAGAKYPGmNRRQLLLPLNPQVRDDVV-KLAGDVGNGTATVvFETFMKDELRPKEKIESGKTRIVESCPLDYLLL 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2484 AKVCVDDFNNEFYSKNlkcPWTVGMT---KFYGGWDKLMRSLPDgWLYChADGSQFDSSLTPALLNAvliirsfymedww 2560
Cdd:cd23220     91 YRMVMLKSMIWWYNSD---CIKTGVApgmNVYTDFVPMVKQFKK-IKYC-LDFSAYDSTLSDEILAA------------- 152

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2561 vGQEMLENL-----YAEIVYTPILAP----DGTIFKKFRGNNSGQPSTVVDNTLMVVISIYYACMKFgwnheDIENKlVF 2631
Cdd:cd23220    153 -GVEVLACTsavpsYVRKLHAPIICShhwhNNVVDLVLGGMPSGAPCTSVLNSIVNVLMARYICALM-----DIDYP-VM 225

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2632 FANGDDLILAVKDE--DSGLLDNMSSSFCDLGLNYDFSERTHKREDLWFMSHQAMLVDGMYI--PKLEKERIVSILEWDR 2707
Cdd:cd23220    226 VAYGDDNVVSFDEEidIERMVSLYKTEFGVTATNHDKTPVPRPMANPVFLKRRLRFNPDLNIqfPVLPLGEMIDRMCWTR 305

                          330       340
                   ....*....|....*....|.
gi 1848664397 2708 SKEimHRTEAICAAMIEAWGH 2728
Cdd:cd23220    306 GPE--HLSDQTFSFAIELAGY 324
ps-ssRNAv_Flaviviridae_RdRp cd23178
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ...
 2532-2689 1.79e-03

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Flaviviridae, order Amarillovirales. Flaviviridae, is a family of small, enveloped viruses with RNA genomes of 9-13 kb. Most infect mammals and birds. Many flaviviruses are host-specific and pathogenic, such as hepatitis C virus in the genus Hepacivirus. The majority of known members in the genus Flavivirus are arthropod borne, and many are important human and veterinary pathogens (e.g., yellow fever virus, dengue virus). Virions are typically spherical in shape with a lipid envelope. Virions have a single, small, basic capsid (C) protein and two (genera Flavivirus, Hepacivirus and Pegivirus) or three (genus Pestivirus) envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. Translational initiation of genomic RNA is cap dependent in the case of members of the genus Flavivirus. 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: 438028  Cd Length: 284  Bit Score: 43.27  E-value: 1.79e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2532 DGSQFDSSLTPA-LLNAVLIIRSFYMEDWWVG-QEMLENLYAEivyTPILAPDGTIFKKFRGNNSGQPSTVVDNTLMVVI 2609
Cdd:cd23178     87 DTRCFDSTVTEDdIQVEEEIYQACSLKEARQAiVSITERLYVE---GPMVNSDGQICGRRRCRASGVLTTSAGNT*TCYL 163

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2610 SIYYACMKFGwnhedIENKlVFFANGDDLIL----AVKDEDSGLLDNMSSSFCDLG-LNYDFSERTHKREDLWFMSH--- 2681
Cdd:cd23178    164 K*LAACREAG-----IRLP-TMLVCGDDCVVicesDGTQEDAALLAAFTEALTRYGkPPKDPPQPEYDLELIESCSHtvs 237


                   ....*...
gi 1848664397 2682 QAMLVDGM 2689
Cdd:cd23178    238 EVRMKDGR 245
betaCoV_RdRp cd21589
betacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: ...
 2356-2522 3.44e-03

betacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome; This subfamily contains the RNA-dependent RNA polymerase (RdRp) of betacoronaviruses, including the RdRps from three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2, also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which shows potential for the treatment of SARS-CoV-2 viral infections. The structure of SARS-CoV-2 Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438016  Cd Length: 925  Bit Score: 43.23  E-value: 3.44e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2356 DFFKYNKP--VTVNQLDH-----DKFLEAVDGvirmmcdfefnECrfITDPEEIYNSLNMKAAIGAQYRGKKKEYFEGLD 2428
Cdd:cd21589    447 NYYKYNLPtmVDIKQLLFvlevvYKYFEIYDG-----------GC--IPASQVIVNNYDKSAGYPFNKFGKARLYYEALS 513

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2429 dFDRERLLFQSCERlfNGYKGLWNGSLKAELrplekvrANKTRTFTAApidtllGAKVCVDDFNNEFYSKNLK------- 2501
Cdd:cd21589    514 -FEEQDEIYAYTKR--NVLPTLTQMNLKYAI-------SAKNRARTVA------GVSILSTMTGRMFHQKCLKsiaatrg 577

                          170       180
                   ....*....|....*....|.
gi 1848664397 2502 CPWTVGMTKFYGGWDKLMRSL 2522
Cdd:cd21589    578 VPVVIGTTKFYGGWDDMLRRL 598
DEXHc_TDRD9 cd17988
DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also ...
 1246-1344 5.29e-03

DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also known as HIG-1or NET54 or C14orf75) is a part of the nuclear PIWI-interacting RNA (piRNA) pathway essential for transposon silencing and male fertility TDRD9 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350746 [Multi-domain]  Cd Length: 180  Bit Score: 40.56  E-value: 5.29e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 1246 LVRGAVGSGKSTSLPA----HLAKKGK---VLLLEPTRPLAENVSRQLAGDPFFQNVTL--RMRGLNCFGS--SNITVMT 1314
Cdd:cd17988     21 IIKGATGCGKTTQLPQfildHYYKRGKycnIVVTQPRRIAAISIARRVSQEREWTLGSLvgYQVGLERPASeeTRLIYCT 100

                           90       100       110
                   ....*....|....*....|....*....|
gi 1848664397 1315 SGFAFHYYVNNPHqLMEFDFVIIDECHVTD 1344
Cdd:cd17988    101 TGVLLQKLINNKT-LTEYTHIILDEVHERD 129
ps_ssRNAv_Tolivirales_RdRp cd23179
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ...
 2515-2658 6.65e-03

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of positive-sense single-stranded RNA (+ssRNA) viruses; This family contains the catalytic core domain of RdRp of Tolivirales, an order of (+)ssRNA viruses which infect insects and plants. The virions are non-enveloped, spherical, and have an icosahedral capsid. The name Tolivirales, is derived from "tombusvirus-like" with the suffix -virales indicating a virus order. This order includes two families: Carmotetraviridae and Tombusviridae. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438029  Cd Length: 227  Bit Score: 40.97  E-value: 6.65e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1848664397 2515 WDKlMRSLPDGWLYChADGSQFDSSLTPALLNAVliiRSFYME----DWWVgQEMLENLYAEIVYTpilaPDGTIFKKFR 2590
Cdd:cd23179     74 RRK-WDEFDDPVVFS-LDASRFDAHVSVELLRLE---HSVYLAcypgDPEL-RKLLKWQLVNKGRT----SNGVKYKTRG 143

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1848664397 2591 GNNSGQPSTVVDNTLMVVISIYYACMKFGWnhedienKLVFFANGDDLILAVKDEDSGLLDNMSSSFC 2658
Cdd:cd23179    144 GRMSGDMNTGLGNCLIMLAMVYAVLRELGI-------KYDLLVDGDDALVFVEREDLERLLEEFAEFF 204
 
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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