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Conserved domains on  [gi|380295140|gb|AFD50747|]
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polyprotein [Chaoyang virus]

Protein Classification

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List of domain hits

 Name Accession Description Interval E-value
Flavivirus_RdRp cd23204
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within ...
 2849-3416 0e+00

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Flavivirus genus within the family Flaviviridae, order Amarillovirales. The genus Flavivirus consists of more than 50 species of arthropod-borne viruses, with distinct groups infecting mosquitoes or ticks. Mammals and birds are the usual primary hosts, in which infections range from asymptomatic to severe or fatal hemorrhagic fever or neurological disease. Important human pathogens include yellow fever virus, dengue virus, Japanese encephalitis virus, West Nile virus and tick-borne encephalitis virus. Other members cause economically important diseases in domestic or wild animals. Virions of Flavivirus have a single, small, basic capsid (C) protein and two 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: 438054 [Multi-domain]  Cd Length: 565  Bit Score: 1249.37  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 2849 MINGVVKELTHPWDTNSGVTNVCMTDTTPFGQQRVFKEKVDTKAMEPPTGTREVMRIVNRWLTNYLSRTKKPRLCTPDEF 2928
Cdd:cd23204     1 MVNGVVKLLSKPWDVIEMVTQMAMTDTTPFGQQRVFKEKVDTKAPEPPEGTRKIMRIVNEWLWKFLARKKKPRLCTREEF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 2929 IAKVNSDAALGTMFNDQGNWPSAKDAVRDHGFWRQVDIERQHHLEGRCVSCVYNMMGKREKKLTEFGRAKGSRAIWYMWL 3008
Cdd:cd23204    81 IAKVRSNAALGAVFEEQNQWKSAREAVEDPRFWELVDEERELHLEGKCETCVYNMMGKREKKLGEFGKAKGSRAIWYMWL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 3009 GARYLEFEALGFLNEDHWLSRENSKGGVEGIGLQYLGYILEDMGGMTGGQMYADDTAGWDTKITNADLEDEMEITKLMAH 3088
Cdd:cd23204   161 GARFLEFEALGFLNEDHWASRENSGGGVEGIGLQYLGYILREISKKPGGKMYADDTAGWDTRITEADLEDEEKILEYMEG 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 3089 THKKLATAIMNLTYMNKVVRVMRPGKGGKTLMDIISRKDQRGSGQVVTYPLNTWTNLKVQLIRMAEGEGVILPEDTlsLT 3168
Cdd:cd23204   241 EHRKLAEAIFELTYQNKVVKVMRPGPGGGTVMDVISRRDQRGSGQVVTYALNTFTNMKVQLIRMMEGEGVITPEDL--ET 318

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 3169 GCSRRNLEMWLVRNGEERLTRIAASGDDVVVKPIDDRFAEALHFLNSMAKIRKDINEWKPSTGWNSWEGVPFCSHHFHKL 3248
Cdd:cd23204   319 APRLKRVEDWLEENGEERLSRMAVSGDDCVVKPIDDRFATALTFLNDMGKVRKDIQEWEPSKGWNDWEEVPFCSHHFHEL 398

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 3249 SLKDGRTLTVPCRDQDELIGRARVSPGAGWTLRETAGLSKAYAQMWMLIHFHRRDLRTIAFAICSAVPKDWVPTGRTSWS 3328
Cdd:cd23204   399 IMKDGRTLVVPCRDQDELIGRARVSPGAGWSLRETACLSKAYAQMWLLMYFHRRDLRLMANAICSAVPVDWVPTGRTTWS 478

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 3329 IHARGEWMTNEDMLAVWNRVWITENPYMFNKETIHDWRDVPYLRKQLDKNCGSMIGVRSRATWAENIRVSVNQVRGYIGK 3408
Cdd:cd23204   479 IHAKGEWMTTEDMLEVWNRVWIEDNPWMEDKTPVTSWRDVPYLGKREDQWCGSLIGLRSRATWAKNIQTAVNQVRSLIGN 558


                  ....*...
gi 380295140 3409 hENYLDYL 3416
Cdd:cd23204   559 -EEYRDYL 565
Flavi_NS1 super family cl03032
Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the ...
 794-1146 1.10e-154

Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the flaviviruses. It contains 12 cysteines, and undergoes glycosylation in a similar manner to other NS proteins. Mutational analysis has strongly implied a role for NS1 in the early stages of RNA replication.


The actual alignment was detected with superfamily member pfam00948:

Pssm-ID: 279316  Cd Length: 360  Bit Score: 484.16  E-value: 1.10e-154
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   794 GCSLDITHREIKCGDGIFIFRDAGGWRDKYVFHPGSPKTLAAAIWKGWNDGICGVRSATRMEHEMWKQIENELNGILEEN 873
Cdd:pfam00948    2 GCAINFGGRELKCGDGIFIFNDSDDWLEKYKFQADDPKKLAAAIGAAFEEGKCGINSADRLEHEMWKQIADEINAIFEEN 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   874 DIKLSVVVKNANGTYPRGTKS-----LTRNTTGLQYGWKSWGKTMFVSVPIAENTFIIDGNDEGECASDKRAWNTFKIEE 948
Cdd:pfam00948   82 DMDFSVVVGDPKGILAQGKKMirphpFEHIRDGLKYGWKSWGKAKIFGADRKNGSFIIDGKNRKECPDNNRAWNIFEIED 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   949 FGTGIMKTKVFLDLADAQTEYCDTELLGAAVKGNKSVHGDPGLWMTASKESGDWKLESLSMTESRRCLWPDSHTIWGRGV 1028
Cdd:pfam00948  162 FGFGIFTTNIWLDARDEYTIDCDGRILGAAIKDKKAAHADMGFWIESHEKNETWKIARAEAIDVKECEWPKSHTIWGNGV 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  1029 LESKLILPSMFGGPVSHMNTRPGYATQLSGPWNNVPLDVVFEECPGTKVVVENNCTNRGESIRSTTDSGKIIPEWCCRKC 1108
Cdd:pfam00948  242 EESEMFIPKIIGGPISQHNHIPGYFTQTAGPWHLGKLELDFDACEGTSVIIDEHCDGRGKSLRSTTDSGKTIHEWCCRSC 321

                          330       340       350
                   ....*....|....*....|....*....|....*...
gi 380295140  1109 TMPPLTYRTPDGCWYAMEIRPKKASEESLLRSKVSAGT 1146
Cdd:pfam00948  322 TLPPLRFHGEDGCWYGMEIRPRKEHEEHLVKSMVSAGE 359
capping_2-OMTase_Flaviviridae cd20761
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific ...
 2534-2771 2.60e-118

Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Flaviviridae viruses, comprise a family of ss(+)RNA viruses, cap their mRNAs. The 2'OMTase activity is located in the non-structural protein 5 (NS5).


:

Pssm-ID: 467736  Cd Length: 225  Bit Score: 373.87  E-value: 2.60e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 2534 TRGMEWKRKLNAMNKETFQRYRRDGIVEVDrtaarealksgnvTGGHAVSRGSAKLRWLVDKGYLRLMGDVTDLGCGRGG 2613
Cdd:cd20761     1 TLGEKWKDRLNALSKEEFDAYKKRGVVEVA-------------TKGHAVSRGYAKLRWLVERGYVKPSGKVVDLGCGRGG 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 2614 WCYYAAAQRNVVSVRGFTKGGDGHEEPIPVQTYGWNIVTLRSKVDVFYMPTHMTDTLLCDIGESSSNMLVEEERTLRVLN 2693
Cdd:cd20761    68 WSQYAAGLPKVTEVRGYTLGGPGHEEPRLVQSYGWNLVRLKSGVDVFYRPPERCDTLLCDIGESSPSPEVEEERTLRVLD 147

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 380295140 2694 LFEEWIRKSKPTHFCCKVLAPYMPNVLEKIDKLMKVHGGALVRVPLSRNSTHEMYWVSDARGNAMNAVASLSRTLLDR 2771
Cdd:cd20761   148 LVEKWLERNPTANFCIKVLCPYHPEVIELLERLQRKGGGGLVRVPLSRNSTHEMYFVSGARGNIVNSVNMTSRLLLNR 225
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1689-1834 3.73e-85

Flavivirus DEAD domain;


:

Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 275.37  E-value: 3.73e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  1689 KGKLSVMDLHPGAGKTRKVLPQVLKEAVAKKLKTLVLAPTRVVAKEMHGALAGLPVRYQTSAVETKGSGNELIDVMCHAT 1768
Cdd:pfam07652    1 KGTLTVLDLHPGAGKTRKVLPELVRECIDRRLRTLVLAPTRVVLAEMEEALRGLPIRYHTPAVSSEHTGREIVDVMCHAT 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 380295140  1769 FTYRQLTPGRMVNYQLYVMDEAHFTDPASIAARGIIATRVKLGEAAAIFMTATPPGTLDAFPESNS 1834
Cdd:pfam07652   81 FTQRLLSPVRVPNYEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFMTATPPGTSDPFPESNA 146
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1836-1980 1.54e-63

C-terminal helicase domain of viral helicase; Viral helicases in this family here are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


:

Pssm-ID: 350193 [Multi-domain]  Cd Length: 145  Bit Score: 213.66  E-value: 1.54e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 1836 IEDEEREIPDKAWSTGFEWITDYTGKTVWFVPSIRTGNIIASCLARTGKKCVVLNSKTFNDEFPKTKSGTWDFVITTDIS 1915
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWITIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEYPKIKTIDWDFVVTTDIS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 380295140 1916 EMGANFKASRVIDCRTSIKPTLAYVPSERVVLGSPKPISPASAAQRRGRVGRDPTQLGDQYIYGG 1980
Cdd:cd18806    81 EMGANFDADRVIDCRTCVKPTILFSGDFRVILTGPVPQTAASAAQRRGRTGRNPAQERDIYRFVG 145
Flavi_E_C cd12149
Immunoglobulin-like domain III (C-terminal domain) of Flavivirus envelope glycoprotein E; The ...
 599-688 9.49e-47

Immunoglobulin-like domain III (C-terminal domain) of Flavivirus envelope glycoprotein E; The C-terminal domain (domain III) of Flavivirus glycoprotein E appears to be involved in low-affinity interactions with negatively charged glycoaminoglycans on the host cell surface. Domain III may also play a role in interactions with alpha-v-beta-3 integrins in West Nile virus, Japanese encephalitis virus, and Dengue virus. The interface between domain I and domain III appears to be destabilized by the low-pH environment of the endosome, and domain III may play a vital role in the conformational changes of envelope glycoprotein E that follow the clathrin-mediated endocytosis of viral particles and are a prerequisite to membrane fusion.


:

Pssm-ID: 213392  Cd Length: 91  Bit Score: 163.24  E-value: 9.49e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  599 AFTFAKRPVDTGHGTVVFQVSYAGTDAPCKIPVAVTDKPN-GEHVGRLVTAHPFIAKQNEKAVVEVEPPFGDSYIEIGAG 677
Cdd:cd12149     1 KFSWKKEPADTGHGTVVMEVKYSGTDAPCRIPVRVVDSGSgGENVGRLITVNPIITNANSKVFIEVEPPFGDSYIVVGVG 80

                          90
                  ....*....|.
gi 380295140  678 TTKISEAWHKP 688
Cdd:cd12149    81 DTRLKHQWFQK 91
flavi_E_stem TIGR04240
flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal ...
 693-789 4.25e-40

flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal domain, containing a stem region followed by two transmembrane anchor domains, of the envelope protein E. This protein is cleaved from the large flavivirus polyprotein, which yields three structural and seven nonstructural proteins.


:

Pssm-ID: 213897  Cd Length: 97  Bit Score: 144.70  E-value: 4.25e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   693 GNALALSYKGMKRITAMGEHAWDFGSIGGFFSSMGKAVHHVFGSLFRTLFGGIGWMAKILIGALLIWLGISTRDRMLATS 772
Cdd:TIGR04240    1 GKAFELTMRGAERMAILGDAAWDFGSVGGVFTSIGKALHQVFGGAFRALFGGVSWITKILIGVLLIWLGLNSRNTTLSLT 80

                           90
                   ....*....|....*..
gi 380295140   773 FILTGSILLYLATTTVG 789
Cdd:TIGR04240   81 FLAVGGILLFLTTGVGA 97
Flavi_NS4A super family cl03176
Flavivirus non-structural protein NS4A; Flaviviruses encode a single polyprotein. This is ...
 2128-2270 1.34e-35

Flavivirus non-structural protein NS4A; Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4A protein is small and poorly conserved among the Flaviviruses. NS4A contains multiple hydrophobic potential membrane spanning regions. NS4A has only been found in cells infected by Kunjin virus.


The actual alignment was detected with superfamily member pfam01350:

Pssm-ID: 279666  Cd Length: 144  Bit Score: 133.49  E-value: 1.34e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  2128 IIEVLGKLPQHFADKTIDAADTFKTVLTATPGSRAYRLAVDNLPDAAETAIFVTMVGFMTMGILIFLMAPKGMTRMSLGF 2207
Cdd:pfam01350    2 LILEIGELPDFLAKKAGEALDNISMFHHSEEGGKAYRHALEELPDAIEILMLFALAALLTGGMTIFFLSGKGIGKMSIAL 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 380295140  2208 MTIMAATYFLWASGMAGYQIAAMQLVAFILFVVLVPEPGSQRSVQDNTIAMVLIGILSIAALI 2270
Cdd:pfam01350   82 GCMAACGALLFLAGVEPHHIAASIIIEFFLMVLLIPEPDQQRSIQDNQLAYLIIGILFLISAL 144
Flavi_M cd17038
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with a ...
 217-292 5.82e-30

Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with a membrane-anchored envelope comprised of 3 proteins called C, M and E. The envelope glycoprotein M is translated as a precursor, called prM. The precursor portion of the protein is the signal peptide for the protein's entry into the membrane. prM is cleaved to form M by the proprotein convertase furin in a late-stage cleavage event. Associated with this cleavage is a change in the infectivity and fusion activity of the virus.


:

Pssm-ID: 341208  Cd Length: 75  Bit Score: 114.65  E-value: 5.82e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 380295140  217 SVALAPHGTGNLHTGeAPMWKSHTDASKYLQRVERWALRNPGYLGILVAIGWLLGKTTAQRVIYITLLVLIGPAYS 292
Cdd:cd17038     1 SVAIPPHGTGGLTTR-KETWLSTSNGKEHLTRVERWVLRNPGYALAAVALAWMLGSSTTQRVIIIVLLLLVAPAYA 75
Peptidase_S7 pfam00949
Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that ...
 1521-1671 3.56e-29

Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that encodes a single polyprotein precursor. Processing of the polyprotein precursor into mature proteins is carried out by the host signal peptidase and by NS3 serine protease, which requires NS2B (pfam01002) as a cofactor.


:

Pssm-ID: 395758  Cd Length: 129  Bit Score: 114.84  E-value: 3.56e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  1521 EDGCYRVMSRRLIGSTQVGVGVMKDSVFHTMWHVTRGASLTSGNGRMDPYWADVREDLISYGGPWKLNSTWDGsSEVQLI 1600
Cdd:pfam00949    2 TDGILRFFQSSLLGRSQRGVGVLQEGVFHTMWHPTRGTKLHTQGIKTSPSWASVKQDLVDYGGSWKFQGKWLG-EEYQQY 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 380295140  1601 avqpqkipenvqttpgrfvmsdGTEVGAVVLDYPSGTSGSPIVDKDGNVVGLYGNGVMLNDSTYASAIAQS 1671
Cdd:pfam00949   81 ----------------------GYGLGITDLNLSSGSSGSLVLNQNKQIVGIYFATVEVDDNSFVVGLAQL 129
Flavi_NS2A super family cl03066
Flavivirus non-structural protein NS2A; NS2A is a hydrophobic protein about 25 kDa is size. ...
 1156-1338 4.23e-17

Flavivirus non-structural protein NS2A; NS2A is a hydrophobic protein about 25 kDa is size. NS2A is cleaved from NS1 by a membrane bound host protease. NS2A has been found to associate with the dsRNA within the vesicle packages. It has also been found that NS2A associates with the known replicase components and so NS2A has been postulated to be part of this replicase complex.


The actual alignment was detected with superfamily member pfam01005:

Pssm-ID: 279359  Cd Length: 215  Bit Score: 82.97  E-value: 4.23e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  1156 GLLVLIIFVQEGLKRRMTSRYIMLAALGLLLAAVLGDLTYNDIARYLIMVGVAFAEMNNGGDLI-----HLALIATFKVQ 1230
Cdd:pfam01005    1 GLLCIMIAIEEVLRKRQGPKMLLTGGLALFGALLMGQLTLLDLIKLCIAVGLHFHEMANAGDAMgmgttYLALIAAFRIR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  1231 PGYLLFFLLRKQWSPRESTILASAA----------------------VVLQICAAAWQSTKSMQVLNALAMGWLYIRAIV 1288
Cdd:pfam01005   81 PGFAIGFGFRRLTSPRERLLLTLGAalvasvelpnsleeiadggamgIMMLKLLTDFQSHGLWATLLALSFCILTFNAHA 160

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 380295140  1289 VPGALSKAMPLICMCVPGVLSLTPHAIRVSMVTLAAGTLIKGTKGTSVRK 1338
Cdd:pfam01005  161 ARKAMAMILPIMALFTPLCLAEVRLAAMFFCAVVIIGVLHQNFKDTSMQK 210
Flavi_propep pfam01570
Flavivirus polyprotein propeptide; The flaviviruses are small enveloped animal viruses ...
 152-209 3.29e-14

Flavivirus polyprotein propeptide; The flaviviruses are small enveloped animal viruses containing a single positive strand genomic RNA. The genome encodes one large ORF a polyprotein which undergos proteolytic processing into mature viral peptide chains. This family consists of a propeptide region of approximately 90 amino acid length.


:

Pssm-ID: 366710  Cd Length: 78  Bit Score: 70.22  E-value: 3.29e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 380295140   152 AVGNGSCIVMATDVGTWCEDTVTYLCPKLDGAAEPDDIDCWCKVV-SVYVTYGRCRRDG 209
Cdd:pfam01570   20 SVGTGNCTTNILEAKYWCPDSMEYNCPNLSPREEPDDIDCWCYGVeNVRVAYGKCDSAG 78
Flavi_capsid super family cl03064
Flavivirus capsid protein C; Flaviviruses are small enveloped viruses with virions comprised ...
 6-122 7.60e-13

Flavivirus capsid protein C; Flaviviruses are small enveloped viruses with virions comprised of 3 proteins called C, M and E. Multiple copies of the C protein form the nucleocapsid, which contains the ssRNA molecule.


The actual alignment was detected with superfamily member pfam01003:

Pssm-ID: 366413  Cd Length: 117  Bit Score: 67.74  E-value: 7.60e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140     6 KKPGR-RAIDIVRRALPRVSgpkkvLKKATQTVMESLAG---IRATVAYLLYMTFLGNKVSKATRAKFRSAKKSDLIKIL 81
Cdd:pfam01003    1 GKPGKgRGVNMLKRGAKRVP-----LKKTKRKTGQLLDGrgpLRLVLAFLAFFRFTAIAPTPGLKKRWRTVPKRQAIKHL 75

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 380295140    82 SSFKRTVTNLLASVQKRKRK--AKRSVTTPSMALILLTMsCMA 122
Cdd:pfam01003   76 RKFKKEVGTLLDGLNRRGKRrsKRGGWTGLLLMLGLLTL-VLA 117
 
Name Accession Description Interval E-value
Flavivirus_RdRp cd23204
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within ...
 2849-3416 0e+00

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Flavivirus genus within the family Flaviviridae, order Amarillovirales. The genus Flavivirus consists of more than 50 species of arthropod-borne viruses, with distinct groups infecting mosquitoes or ticks. Mammals and birds are the usual primary hosts, in which infections range from asymptomatic to severe or fatal hemorrhagic fever or neurological disease. Important human pathogens include yellow fever virus, dengue virus, Japanese encephalitis virus, West Nile virus and tick-borne encephalitis virus. Other members cause economically important diseases in domestic or wild animals. Virions of Flavivirus have a single, small, basic capsid (C) protein and two 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: 438054 [Multi-domain]  Cd Length: 565  Bit Score: 1249.37  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 2849 MINGVVKELTHPWDTNSGVTNVCMTDTTPFGQQRVFKEKVDTKAMEPPTGTREVMRIVNRWLTNYLSRTKKPRLCTPDEF 2928
Cdd:cd23204     1 MVNGVVKLLSKPWDVIEMVTQMAMTDTTPFGQQRVFKEKVDTKAPEPPEGTRKIMRIVNEWLWKFLARKKKPRLCTREEF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 2929 IAKVNSDAALGTMFNDQGNWPSAKDAVRDHGFWRQVDIERQHHLEGRCVSCVYNMMGKREKKLTEFGRAKGSRAIWYMWL 3008
Cdd:cd23204    81 IAKVRSNAALGAVFEEQNQWKSAREAVEDPRFWELVDEERELHLEGKCETCVYNMMGKREKKLGEFGKAKGSRAIWYMWL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 3009 GARYLEFEALGFLNEDHWLSRENSKGGVEGIGLQYLGYILEDMGGMTGGQMYADDTAGWDTKITNADLEDEMEITKLMAH 3088
Cdd:cd23204   161 GARFLEFEALGFLNEDHWASRENSGGGVEGIGLQYLGYILREISKKPGGKMYADDTAGWDTRITEADLEDEEKILEYMEG 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 3089 THKKLATAIMNLTYMNKVVRVMRPGKGGKTLMDIISRKDQRGSGQVVTYPLNTWTNLKVQLIRMAEGEGVILPEDTlsLT 3168
Cdd:cd23204   241 EHRKLAEAIFELTYQNKVVKVMRPGPGGGTVMDVISRRDQRGSGQVVTYALNTFTNMKVQLIRMMEGEGVITPEDL--ET 318

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 3169 GCSRRNLEMWLVRNGEERLTRIAASGDDVVVKPIDDRFAEALHFLNSMAKIRKDINEWKPSTGWNSWEGVPFCSHHFHKL 3248
Cdd:cd23204   319 APRLKRVEDWLEENGEERLSRMAVSGDDCVVKPIDDRFATALTFLNDMGKVRKDIQEWEPSKGWNDWEEVPFCSHHFHEL 398

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 3249 SLKDGRTLTVPCRDQDELIGRARVSPGAGWTLRETAGLSKAYAQMWMLIHFHRRDLRTIAFAICSAVPKDWVPTGRTSWS 3328
Cdd:cd23204   399 IMKDGRTLVVPCRDQDELIGRARVSPGAGWSLRETACLSKAYAQMWLLMYFHRRDLRLMANAICSAVPVDWVPTGRTTWS 478

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 3329 IHARGEWMTNEDMLAVWNRVWITENPYMFNKETIHDWRDVPYLRKQLDKNCGSMIGVRSRATWAENIRVSVNQVRGYIGK 3408
Cdd:cd23204   479 IHAKGEWMTTEDMLEVWNRVWIEDNPWMEDKTPVTSWRDVPYLGKREDQWCGSLIGLRSRATWAKNIQTAVNQVRSLIGN 558


                  ....*...
gi 380295140 3409 hENYLDYL 3416
Cdd:cd23204   559 -EEYRDYL 565
Flavi_NS5 pfam00972
Flavivirus RNA-directed RNA polymerase, fingers and palm domains; Flaviviruses produce a large ...
 2781-3232 0e+00

Flavivirus RNA-directed RNA polymerase, fingers and palm domains; Flaviviruses produce a large polyprotein from the ssRNA genome, encoding structural proteins required for virus assembly and non-structural (NS1-5) proteins involved in replication of the viral genome. This polyprotein is cleaved by viral and cellular proteases to produce mature viral proteins. NS5 is the largest mature viral protein and contains a N-terminal methyltransferase (MTase) domain separated by a short linker from the C-terminal RNA-directed RNA polymerase domain (RdRp) that adopts a characteriztic right-handed fingers-palm-thumb fold and possesses a number of short regions and motifs homologous to other RNA-directed RNA polymerases. This entry covers the fingers and palm domains of RNA-directed RNA polymerase (RdRp) from Flavivirus NS5. NS5 binds to a the stem loop A (SLA) at the 5' extremity of Flavivirus genome and regulates translation of the viral genome.


Pssm-ID: 460013  Cd Length: 451  Bit Score: 741.38  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  2781 WEDDVNLGTGTRAVNSVADPPNWDKIGLRVRKLEQEYKASWMYDAEHPYKTWTYHGSYETSTSGSASSMINGVVKELTHP 2860
Cdd:pfam00972    2 YEADVILGIGTRSVATDKEPLNKEIIGERIERIKNEHMTTWFYDEDNPYRTWAYHGSYETKTSGSASSMVNGVVRLLTKP 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  2861 WDTNSGVTNVCMTDTTPFGQQRVFKEKVDTKAMEPPTGTREVMRIVNRWLTNYLSRTKKPRLCTPDEFIAKVNSDAALGT 2940
Cdd:pfam00972   82 WDVIEEVTRIAMTDTTPFGQQRVFKEKVDTRAPDPPAGTRQIMKVVNRWLWRHLAREKNPRLCTKEEFIAKVRSNAAIGA 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  2941 MFNDQGNWPSAKDAVRDHGFWRQVDIERQHHLEGRCVSCVYNMMGKREKKLTEFGRAKGSRAIWYMWLGARYLEFEALGF 3020
Cdd:pfam00972  162 YFEEEEQWKTANEAVQDPRFWELVDRERELHQQGRCRTCVYNMMGKREKKLGEFGKAKGSRAIWYMWLGARFLEFEALGF 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  3021 LNEDHWLSRENSKGGVEGIGLQYLGYILEDMGGMTGGQMYADDTAGWDTKITNADLEDEMEITKLMAHTHKKLATAIMNL 3100
Cdd:pfam00972  242 LNEDHWASRENSGGGVEGIGLQYLGYILRDLAAMPGGGMYADDTAGWDTRITEADLDNEAEITNYMEPHHKKLAQAVMKM 321

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  3101 TYMNKVVRVMRPGKGGKTLMDIISRKDQRGSGQVVTYPLNTWTNLKVQLIRMAEGEGVILPEDTLSLTGCSRrnLEMWLV 3180
Cdd:pfam00972  322 TYQNKVVKVLRPAPGGKTVMDVISRRDQRGSGQVVTYALNTFTNLKVQLIRMMEAEMVIHHQHLQDCDESER--VEAWLT 399

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 380295140  3181 RNGEERLTRIAASGDDVVVKPIDDRFAEALHFLNSMAKIRKDINEWKPSTGW 3232
Cdd:pfam00972  400 EHGCDRLKRMAVSGDDCVVKPIDDRFALALSHLNDMGKVRKDISEWQPSKGW 451
Flavi_NS1 pfam00948
Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the ...
 794-1146 1.10e-154

Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the flaviviruses. It contains 12 cysteines, and undergoes glycosylation in a similar manner to other NS proteins. Mutational analysis has strongly implied a role for NS1 in the early stages of RNA replication.


Pssm-ID: 279316  Cd Length: 360  Bit Score: 484.16  E-value: 1.10e-154
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   794 GCSLDITHREIKCGDGIFIFRDAGGWRDKYVFHPGSPKTLAAAIWKGWNDGICGVRSATRMEHEMWKQIENELNGILEEN 873
Cdd:pfam00948    2 GCAINFGGRELKCGDGIFIFNDSDDWLEKYKFQADDPKKLAAAIGAAFEEGKCGINSADRLEHEMWKQIADEINAIFEEN 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   874 DIKLSVVVKNANGTYPRGTKS-----LTRNTTGLQYGWKSWGKTMFVSVPIAENTFIIDGNDEGECASDKRAWNTFKIEE 948
Cdd:pfam00948   82 DMDFSVVVGDPKGILAQGKKMirphpFEHIRDGLKYGWKSWGKAKIFGADRKNGSFIIDGKNRKECPDNNRAWNIFEIED 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   949 FGTGIMKTKVFLDLADAQTEYCDTELLGAAVKGNKSVHGDPGLWMTASKESGDWKLESLSMTESRRCLWPDSHTIWGRGV 1028
Cdd:pfam00948  162 FGFGIFTTNIWLDARDEYTIDCDGRILGAAIKDKKAAHADMGFWIESHEKNETWKIARAEAIDVKECEWPKSHTIWGNGV 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  1029 LESKLILPSMFGGPVSHMNTRPGYATQLSGPWNNVPLDVVFEECPGTKVVVENNCTNRGESIRSTTDSGKIIPEWCCRKC 1108
Cdd:pfam00948  242 EESEMFIPKIIGGPISQHNHIPGYFTQTAGPWHLGKLELDFDACEGTSVIIDEHCDGRGKSLRSTTDSGKTIHEWCCRSC 321

                          330       340       350
                   ....*....|....*....|....*....|....*...
gi 380295140  1109 TMPPLTYRTPDGCWYAMEIRPKKASEESLLRSKVSAGT 1146
Cdd:pfam00948  322 TLPPLRFHGEDGCWYGMEIRPRKEHEEHLVKSMVSAGE 359
capping_2-OMTase_Flaviviridae cd20761
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific ...
 2534-2771 2.60e-118

Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Flaviviridae viruses, comprise a family of ss(+)RNA viruses, cap their mRNAs. The 2'OMTase activity is located in the non-structural protein 5 (NS5).


Pssm-ID: 467736  Cd Length: 225  Bit Score: 373.87  E-value: 2.60e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 2534 TRGMEWKRKLNAMNKETFQRYRRDGIVEVDrtaarealksgnvTGGHAVSRGSAKLRWLVDKGYLRLMGDVTDLGCGRGG 2613
Cdd:cd20761     1 TLGEKWKDRLNALSKEEFDAYKKRGVVEVA-------------TKGHAVSRGYAKLRWLVERGYVKPSGKVVDLGCGRGG 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 2614 WCYYAAAQRNVVSVRGFTKGGDGHEEPIPVQTYGWNIVTLRSKVDVFYMPTHMTDTLLCDIGESSSNMLVEEERTLRVLN 2693
Cdd:cd20761    68 WSQYAAGLPKVTEVRGYTLGGPGHEEPRLVQSYGWNLVRLKSGVDVFYRPPERCDTLLCDIGESSPSPEVEEERTLRVLD 147

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 380295140 2694 LFEEWIRKSKPTHFCCKVLAPYMPNVLEKIDKLMKVHGGALVRVPLSRNSTHEMYWVSDARGNAMNAVASLSRTLLDR 2771
Cdd:cd20761   148 LVEKWLERNPTANFCIKVLCPYHPEVIELLERLQRKGGGGLVRVPLSRNSTHEMYFVSGARGNIVNSVNMTSRLLLNR 225
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1689-1834 3.73e-85

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 275.37  E-value: 3.73e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  1689 KGKLSVMDLHPGAGKTRKVLPQVLKEAVAKKLKTLVLAPTRVVAKEMHGALAGLPVRYQTSAVETKGSGNELIDVMCHAT 1768
Cdd:pfam07652    1 KGTLTVLDLHPGAGKTRKVLPELVRECIDRRLRTLVLAPTRVVLAEMEEALRGLPIRYHTPAVSSEHTGREIVDVMCHAT 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 380295140  1769 FTYRQLTPGRMVNYQLYVMDEAHFTDPASIAARGIIATRVKLGEAAAIFMTATPPGTLDAFPESNS 1834
Cdd:pfam07652   81 FTQRLLSPVRVPNYEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFMTATPPGTSDPFPESNA 146
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1690-1840 1.92e-71

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: 236.29  E-value: 1.92e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 1690 GKLSVMDLHPGAGKTRKVLPQVLKEAVAKKLKTLVLAPTRVVAKEMHGALAGLPVRYQTSAVETKGSGNELIDVMCHATF 1769
Cdd:cd17931     1 GQLTVLDLHPGAGKTTRVLPQIIREAIKKRLRTLVLAPTRVVAAEMYEALRGLPIRYRTGAVKEEHGGNEIVDYMCHGTF 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 380295140 1770 TYRQLTPGRMVNYQLYVMDEAHFTDPASIAARGIIATRVKLGEAAAIFMTATPPGTLDAFPESNSHIEDEE 1840
Cdd:cd17931    81 TCRLLSPKRVPNYNLIIMDEAHFTDPASIAARGYIHTRVEMGEAAVIFMTATPPGTVTPFPQSNHPIEDFE 151
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1836-1980 1.54e-63

C-terminal helicase domain of viral helicase; Viral helicases in this family here are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350193 [Multi-domain]  Cd Length: 145  Bit Score: 213.66  E-value: 1.54e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 1836 IEDEEREIPDKAWSTGFEWITDYTGKTVWFVPSIRTGNIIASCLARTGKKCVVLNSKTFNDEFPKTKSGTWDFVITTDIS 1915
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWITIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEYPKIKTIDWDFVVTTDIS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 380295140 1916 EMGANFKASRVIDCRTSIKPTLAYVPSERVVLGSPKPISPASAAQRRGRVGRDPTQLGDQYIYGG 1980
Cdd:cd18806    81 EMGANFDADRVIDCRTCVKPTILFSGDFRVILTGPVPQTAASAAQRRGRTGRNPAQERDIYRFVG 145
Flavi_E_C cd12149
Immunoglobulin-like domain III (C-terminal domain) of Flavivirus envelope glycoprotein E; The ...
 599-688 9.49e-47

Immunoglobulin-like domain III (C-terminal domain) of Flavivirus envelope glycoprotein E; The C-terminal domain (domain III) of Flavivirus glycoprotein E appears to be involved in low-affinity interactions with negatively charged glycoaminoglycans on the host cell surface. Domain III may also play a role in interactions with alpha-v-beta-3 integrins in West Nile virus, Japanese encephalitis virus, and Dengue virus. The interface between domain I and domain III appears to be destabilized by the low-pH environment of the endosome, and domain III may play a vital role in the conformational changes of envelope glycoprotein E that follow the clathrin-mediated endocytosis of viral particles and are a prerequisite to membrane fusion.


Pssm-ID: 213392  Cd Length: 91  Bit Score: 163.24  E-value: 9.49e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  599 AFTFAKRPVDTGHGTVVFQVSYAGTDAPCKIPVAVTDKPN-GEHVGRLVTAHPFIAKQNEKAVVEVEPPFGDSYIEIGAG 677
Cdd:cd12149     1 KFSWKKEPADTGHGTVVMEVKYSGTDAPCRIPVRVVDSGSgGENVGRLITVNPIITNANSKVFIEVEPPFGDSYIVVGVG 80

                          90
                  ....*....|.
gi 380295140  678 TTKISEAWHKP 688
Cdd:cd12149    81 DTRLKHQWFQK 91
flavi_E_stem TIGR04240
flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal ...
 693-789 4.25e-40

flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal domain, containing a stem region followed by two transmembrane anchor domains, of the envelope protein E. This protein is cleaved from the large flavivirus polyprotein, which yields three structural and seven nonstructural proteins.


Pssm-ID: 213897  Cd Length: 97  Bit Score: 144.70  E-value: 4.25e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   693 GNALALSYKGMKRITAMGEHAWDFGSIGGFFSSMGKAVHHVFGSLFRTLFGGIGWMAKILIGALLIWLGISTRDRMLATS 772
Cdd:TIGR04240    1 GKAFELTMRGAERMAILGDAAWDFGSVGGVFTSIGKALHQVFGGAFRALFGGVSWITKILIGVLLIWLGLNSRNTTLSLT 80

                           90
                   ....*....|....*..
gi 380295140   773 FILTGSILLYLATTTVG 789
Cdd:TIGR04240   81 FLAVGGILLFLTTGVGA 97
Flavi_NS4A pfam01350
Flavivirus non-structural protein NS4A; Flaviviruses encode a single polyprotein. This is ...
 2128-2270 1.34e-35

Flavivirus non-structural protein NS4A; Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4A protein is small and poorly conserved among the Flaviviruses. NS4A contains multiple hydrophobic potential membrane spanning regions. NS4A has only been found in cells infected by Kunjin virus.


Pssm-ID: 279666  Cd Length: 144  Bit Score: 133.49  E-value: 1.34e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  2128 IIEVLGKLPQHFADKTIDAADTFKTVLTATPGSRAYRLAVDNLPDAAETAIFVTMVGFMTMGILIFLMAPKGMTRMSLGF 2207
Cdd:pfam01350    2 LILEIGELPDFLAKKAGEALDNISMFHHSEEGGKAYRHALEELPDAIEILMLFALAALLTGGMTIFFLSGKGIGKMSIAL 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 380295140  2208 MTIMAATYFLWASGMAGYQIAAMQLVAFILFVVLVPEPGSQRSVQDNTIAMVLIGILSIAALI 2270
Cdd:pfam01350   82 GCMAACGALLFLAGVEPHHIAASIIIEFFLMVLLIPEPDQQRSIQDNQLAYLIIGILFLISAL 144
Flavi_glycop_C pfam02832
Flavivirus glycoprotein, immunoglobulin-like domain;
592-687 2.63e-30

Flavivirus glycoprotein, immunoglobulin-like domain;


Pssm-ID: 280922  Cd Length: 97  Bit Score: 116.67  E-value: 2.63e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   592 TYVTCAQAFTFAKRPVDTGHGTVVFQVSYAGTDAPCKIPVAVTDKPNGE-HVGRLVTAHPFIAKQNEKAVVEVEPPFGDS 670
Cdd:pfam02832    1 SYKICTDKFFFEKEPADTGHGTVLMQVKVEGKDAPCKIPVFSADDEKAAiNKGILITANPIASDKDDEVLIEAEPPFGDS 80

                           90
                   ....*....|....*..
gi 380295140   671 YIEIGAGTTKISEAWHK 687
Cdd:pfam02832   81 YIIVGAGDKALKLQWFK 97
Flavi_M cd17038
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with a ...
 217-292 5.82e-30

Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with a membrane-anchored envelope comprised of 3 proteins called C, M and E. The envelope glycoprotein M is translated as a precursor, called prM. The precursor portion of the protein is the signal peptide for the protein's entry into the membrane. prM is cleaved to form M by the proprotein convertase furin in a late-stage cleavage event. Associated with this cleavage is a change in the infectivity and fusion activity of the virus.


Pssm-ID: 341208  Cd Length: 75  Bit Score: 114.65  E-value: 5.82e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 380295140  217 SVALAPHGTGNLHTGeAPMWKSHTDASKYLQRVERWALRNPGYLGILVAIGWLLGKTTAQRVIYITLLVLIGPAYS 292
Cdd:cd17038     1 SVAIPPHGTGGLTTR-KETWLSTSNGKEHLTRVERWVLRNPGYALAAVALAWMLGSSTTQRVIIIVLLLLVAPAYA 75
Peptidase_S7 pfam00949
Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that ...
 1521-1671 3.56e-29

Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that encodes a single polyprotein precursor. Processing of the polyprotein precursor into mature proteins is carried out by the host signal peptidase and by NS3 serine protease, which requires NS2B (pfam01002) as a cofactor.


Pssm-ID: 395758  Cd Length: 129  Bit Score: 114.84  E-value: 3.56e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  1521 EDGCYRVMSRRLIGSTQVGVGVMKDSVFHTMWHVTRGASLTSGNGRMDPYWADVREDLISYGGPWKLNSTWDGsSEVQLI 1600
Cdd:pfam00949    2 TDGILRFFQSSLLGRSQRGVGVLQEGVFHTMWHPTRGTKLHTQGIKTSPSWASVKQDLVDYGGSWKFQGKWLG-EEYQQY 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 380295140  1601 avqpqkipenvqttpgrfvmsdGTEVGAVVLDYPSGTSGSPIVDKDGNVVGLYGNGVMLNDSTYASAIAQS 1671
Cdd:pfam00949   81 ----------------------GYGLGITDLNLSSGSSGSLVLNQNKQIVGIYFATVEVDDNSFVVGLAQL 129
FtsJ pfam01728
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...
 2582-2751 1.61e-21

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


Pssm-ID: 426399  Cd Length: 179  Bit Score: 94.58  E-value: 1.61e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  2582 VSRGSAKLRWLVDK-GYLRLMGDVTDLGCGRGGWCYYaAAQRNVVSVRGFTKGGDGHEEPIPVQtygwNIVTLRskVDVF 2660
Cdd:pfam01728    2 RSRAAYKLLEIDEKfGLLKPGKTVLDLGAAPGGWSQV-ALQRGAGKVVGVDLGPMQLWKPRNDP----GVTFIQ--GDIR 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  2661 YMPTHMT---------DTLLCDIGESSSNML-VEEERTLRVLNLFEEWIRK--SKPTHFCCKVLapYMPNVLEKIDKLMK 2728
Cdd:pfam01728   75 DPETLDLleellgrkvDLVLSDGSPFISGNKvLDHLRSLDLVKAALEVALEllRKGGNFVCKVF--QGEDFSELLYLLKL 152

                          170       180
                   ....*....|....*....|....
gi 380295140  2729 VHGGALVRVP-LSRNSTHEMYWVS 2751
Cdd:pfam01728  153 GFEKVGVFKPpASRPESSEEYLVC 176
Flavi_M pfam01004
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with virions ...
 218-292 3.27e-17

Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with virions comprised of 3 proteins called C, M and E. The envelope glycoprotein M is made as a precursor, called prM. The precursor portion of the protein is the signal peptide for the proteins entry into the membrane. prM is cleaved to form M in a late-stage cleavage event. Associated with this cleavage is a change in the infectivity and fusion activity of the virus.


Pssm-ID: 460022  Cd Length: 74  Bit Score: 78.39  E-value: 3.27e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 380295140   218 VALAPHGTGNLHTgEAPMWKSHTDASKYLQRVERWALRNPGYLGILVAIGWLLGKTTAQRVIYITLLVLIGPAYS 292
Cdd:pfam01004    1 VALPPHVGLGLET-RTETWMSSRGAWKQLQKVETWALRNPGFTVIALFIAHLIGSSITQKVIIFILLLLVTPAYS 74
Flavi_NS2A pfam01005
Flavivirus non-structural protein NS2A; NS2A is a hydrophobic protein about 25 kDa is size. ...
 1156-1338 4.23e-17

Flavivirus non-structural protein NS2A; NS2A is a hydrophobic protein about 25 kDa is size. NS2A is cleaved from NS1 by a membrane bound host protease. NS2A has been found to associate with the dsRNA within the vesicle packages. It has also been found that NS2A associates with the known replicase components and so NS2A has been postulated to be part of this replicase complex.


Pssm-ID: 279359  Cd Length: 215  Bit Score: 82.97  E-value: 4.23e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  1156 GLLVLIIFVQEGLKRRMTSRYIMLAALGLLLAAVLGDLTYNDIARYLIMVGVAFAEMNNGGDLI-----HLALIATFKVQ 1230
Cdd:pfam01005    1 GLLCIMIAIEEVLRKRQGPKMLLTGGLALFGALLMGQLTLLDLIKLCIAVGLHFHEMANAGDAMgmgttYLALIAAFRIR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  1231 PGYLLFFLLRKQWSPRESTILASAA----------------------VVLQICAAAWQSTKSMQVLNALAMGWLYIRAIV 1288
Cdd:pfam01005   81 PGFAIGFGFRRLTSPRERLLLTLGAalvasvelpnsleeiadggamgIMMLKLLTDFQSHGLWATLLALSFCILTFNAHA 160

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 380295140  1289 VPGALSKAMPLICMCVPGVLSLTPHAIRVSMVTLAAGTLIKGTKGTSVRK 1338
Cdd:pfam01005  161 ARKAMAMILPIMALFTPLCLAEVRLAAMFFCAVVIIGVLHQNFKDTSMQK 210
Flavi_propep pfam01570
Flavivirus polyprotein propeptide; The flaviviruses are small enveloped animal viruses ...
 152-209 3.29e-14

Flavivirus polyprotein propeptide; The flaviviruses are small enveloped animal viruses containing a single positive strand genomic RNA. The genome encodes one large ORF a polyprotein which undergos proteolytic processing into mature viral peptide chains. This family consists of a propeptide region of approximately 90 amino acid length.


Pssm-ID: 366710  Cd Length: 78  Bit Score: 70.22  E-value: 3.29e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 380295140   152 AVGNGSCIVMATDVGTWCEDTVTYLCPKLDGAAEPDDIDCWCKVV-SVYVTYGRCRRDG 209
Cdd:pfam01570   20 SVGTGNCTTNILEAKYWCPDSMEYNCPNLSPREEPDDIDCWCYGVeNVRVAYGKCDSAG 78
Flavi_capsid pfam01003
Flavivirus capsid protein C; Flaviviruses are small enveloped viruses with virions comprised ...
 6-122 7.60e-13

Flavivirus capsid protein C; Flaviviruses are small enveloped viruses with virions comprised of 3 proteins called C, M and E. Multiple copies of the C protein form the nucleocapsid, which contains the ssRNA molecule.


Pssm-ID: 366413  Cd Length: 117  Bit Score: 67.74  E-value: 7.60e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140     6 KKPGR-RAIDIVRRALPRVSgpkkvLKKATQTVMESLAG---IRATVAYLLYMTFLGNKVSKATRAKFRSAKKSDLIKIL 81
Cdd:pfam01003    1 GKPGKgRGVNMLKRGAKRVP-----LKKTKRKTGQLLDGrgpLRLVLAFLAFFRFTAIAPTPGLKKRWRTVPKRQAIKHL 75

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 380295140    82 SSFKRTVTNLLASVQKRKRK--AKRSVTTPSMALILLTMsCMA 122
Cdd:pfam01003   76 RKFKKEVGTLLDGLNRRGKRrsKRGGWTGLLLMLGLLTL-VLA 117
DEXDc smart00487
DEAD-like helicases superfamily;
1684-1855 4.55e-07

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 53.26  E-value: 4.55e-07
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   1684 PDMLKKGKLSVMDLHPGAGKTRkVLPQVLKEAVAKKL--KTLVLAPTRVVAKEMHGALA--GLPVRYQTSAVETKGSGNE 1759
Cdd:smart00487   18 EALLSGLRDVILAAPTGSGKTL-AALLPALEALKRGKggRVLVLVPTRELAEQWAEELKklGPSLGLKVVGLYGGDSKRE 96

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   1760 LIDVM----CHATFTyrqlTPGRMV-----------NYQLYVMDEAHFTDPASiaARGIIATRVKLGEAAA--IFMTATP 1822
Cdd:smart00487   97 QLRKLesgkTDILVT----TPGRLLdllendklslsNVDLVILDEAHRLLDGG--FGDQLEKLLKLLPKNVqlLLLSATP 170

                           170       180       190
                    ....*....|....*....|....*....|...
gi 380295140   1823 PGTLDAFpeSNSHIEDEEREIPDKAWSTGFEWI 1855
Cdd:smart00487  171 PEEIENL--LELFLNDPVFIDVGFTPLEPIEQF 201
HELICc smart00490
helicase superfamily c-terminal domain;
1874-1968 7.70e-06

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 46.44  E-value: 7.70e-06
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   1874 IIASCLARTGKKCVVLNSKTFNDE----FPKTKSGTWDFVITTDISEMGANFK-ASRVIDCRTsikptlayvpservvlg 1948
Cdd:smart00490    2 ELAELLKELGIKVARLHGGLSQEEreeiLDKFNNGKIKVLVATDVAERGLDLPgVDLVIIYDL----------------- 64

                            90       100
                    ....*....|....*....|
gi 380295140   1949 spkPISPASAAQRRGRVGRD 1968
Cdd:smart00490   65 ---PWSPASYIQRIGRAGRA 81
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 1860-1967 2.86e-03

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: 39.89  E-value: 2.86e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  1860 GKTVWFVPSIRTGNIiASCLARTGKKCVVLNSKTFNDE-------FPKTKSgtwDFVITTDISEMGANFK-ASRVIDCRT 1931
Cdd:pfam00271   16 GKVLIFSQTKKTLEA-ELLLEKEGIKVARLHGDLSQEEreeiledFRKGKI---DVLVATDVAERGLDLPdVDLVINYDL 91

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 380295140  1932 sikptlayvpservvlgspkPISPASAAQRRGRVGR 1967
Cdd:pfam00271   92 --------------------PWNPASYIQRIGRAGR 107
 
Name Accession Description Interval E-value
Flavivirus_RdRp cd23204
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within ...
 2849-3416 0e+00

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Flavivirus genus within the family Flaviviridae, order Amarillovirales. The genus Flavivirus consists of more than 50 species of arthropod-borne viruses, with distinct groups infecting mosquitoes or ticks. Mammals and birds are the usual primary hosts, in which infections range from asymptomatic to severe or fatal hemorrhagic fever or neurological disease. Important human pathogens include yellow fever virus, dengue virus, Japanese encephalitis virus, West Nile virus and tick-borne encephalitis virus. Other members cause economically important diseases in domestic or wild animals. Virions of Flavivirus have a single, small, basic capsid (C) protein and two 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: 438054 [Multi-domain]  Cd Length: 565  Bit Score: 1249.37  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 2849 MINGVVKELTHPWDTNSGVTNVCMTDTTPFGQQRVFKEKVDTKAMEPPTGTREVMRIVNRWLTNYLSRTKKPRLCTPDEF 2928
Cdd:cd23204     1 MVNGVVKLLSKPWDVIEMVTQMAMTDTTPFGQQRVFKEKVDTKAPEPPEGTRKIMRIVNEWLWKFLARKKKPRLCTREEF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 2929 IAKVNSDAALGTMFNDQGNWPSAKDAVRDHGFWRQVDIERQHHLEGRCVSCVYNMMGKREKKLTEFGRAKGSRAIWYMWL 3008
Cdd:cd23204    81 IAKVRSNAALGAVFEEQNQWKSAREAVEDPRFWELVDEERELHLEGKCETCVYNMMGKREKKLGEFGKAKGSRAIWYMWL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 3009 GARYLEFEALGFLNEDHWLSRENSKGGVEGIGLQYLGYILEDMGGMTGGQMYADDTAGWDTKITNADLEDEMEITKLMAH 3088
Cdd:cd23204   161 GARFLEFEALGFLNEDHWASRENSGGGVEGIGLQYLGYILREISKKPGGKMYADDTAGWDTRITEADLEDEEKILEYMEG 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 3089 THKKLATAIMNLTYMNKVVRVMRPGKGGKTLMDIISRKDQRGSGQVVTYPLNTWTNLKVQLIRMAEGEGVILPEDTlsLT 3168
Cdd:cd23204   241 EHRKLAEAIFELTYQNKVVKVMRPGPGGGTVMDVISRRDQRGSGQVVTYALNTFTNMKVQLIRMMEGEGVITPEDL--ET 318

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 3169 GCSRRNLEMWLVRNGEERLTRIAASGDDVVVKPIDDRFAEALHFLNSMAKIRKDINEWKPSTGWNSWEGVPFCSHHFHKL 3248
Cdd:cd23204   319 APRLKRVEDWLEENGEERLSRMAVSGDDCVVKPIDDRFATALTFLNDMGKVRKDIQEWEPSKGWNDWEEVPFCSHHFHEL 398

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 3249 SLKDGRTLTVPCRDQDELIGRARVSPGAGWTLRETAGLSKAYAQMWMLIHFHRRDLRTIAFAICSAVPKDWVPTGRTSWS 3328
Cdd:cd23204   399 IMKDGRTLVVPCRDQDELIGRARVSPGAGWSLRETACLSKAYAQMWLLMYFHRRDLRLMANAICSAVPVDWVPTGRTTWS 478

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 3329 IHARGEWMTNEDMLAVWNRVWITENPYMFNKETIHDWRDVPYLRKQLDKNCGSMIGVRSRATWAENIRVSVNQVRGYIGK 3408
Cdd:cd23204   479 IHAKGEWMTTEDMLEVWNRVWIEDNPWMEDKTPVTSWRDVPYLGKREDQWCGSLIGLRSRATWAKNIQTAVNQVRSLIGN 558


                  ....*...
gi 380295140 3409 hENYLDYL 3416
Cdd:cd23204   559 -EEYRDYL 565
Flavi_NS5 pfam00972
Flavivirus RNA-directed RNA polymerase, fingers and palm domains; Flaviviruses produce a large ...
 2781-3232 0e+00

Flavivirus RNA-directed RNA polymerase, fingers and palm domains; Flaviviruses produce a large polyprotein from the ssRNA genome, encoding structural proteins required for virus assembly and non-structural (NS1-5) proteins involved in replication of the viral genome. This polyprotein is cleaved by viral and cellular proteases to produce mature viral proteins. NS5 is the largest mature viral protein and contains a N-terminal methyltransferase (MTase) domain separated by a short linker from the C-terminal RNA-directed RNA polymerase domain (RdRp) that adopts a characteriztic right-handed fingers-palm-thumb fold and possesses a number of short regions and motifs homologous to other RNA-directed RNA polymerases. This entry covers the fingers and palm domains of RNA-directed RNA polymerase (RdRp) from Flavivirus NS5. NS5 binds to a the stem loop A (SLA) at the 5' extremity of Flavivirus genome and regulates translation of the viral genome.


Pssm-ID: 460013  Cd Length: 451  Bit Score: 741.38  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  2781 WEDDVNLGTGTRAVNSVADPPNWDKIGLRVRKLEQEYKASWMYDAEHPYKTWTYHGSYETSTSGSASSMINGVVKELTHP 2860
Cdd:pfam00972    2 YEADVILGIGTRSVATDKEPLNKEIIGERIERIKNEHMTTWFYDEDNPYRTWAYHGSYETKTSGSASSMVNGVVRLLTKP 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  2861 WDTNSGVTNVCMTDTTPFGQQRVFKEKVDTKAMEPPTGTREVMRIVNRWLTNYLSRTKKPRLCTPDEFIAKVNSDAALGT 2940
Cdd:pfam00972   82 WDVIEEVTRIAMTDTTPFGQQRVFKEKVDTRAPDPPAGTRQIMKVVNRWLWRHLAREKNPRLCTKEEFIAKVRSNAAIGA 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  2941 MFNDQGNWPSAKDAVRDHGFWRQVDIERQHHLEGRCVSCVYNMMGKREKKLTEFGRAKGSRAIWYMWLGARYLEFEALGF 3020
Cdd:pfam00972  162 YFEEEEQWKTANEAVQDPRFWELVDRERELHQQGRCRTCVYNMMGKREKKLGEFGKAKGSRAIWYMWLGARFLEFEALGF 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  3021 LNEDHWLSRENSKGGVEGIGLQYLGYILEDMGGMTGGQMYADDTAGWDTKITNADLEDEMEITKLMAHTHKKLATAIMNL 3100
Cdd:pfam00972  242 LNEDHWASRENSGGGVEGIGLQYLGYILRDLAAMPGGGMYADDTAGWDTRITEADLDNEAEITNYMEPHHKKLAQAVMKM 321

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  3101 TYMNKVVRVMRPGKGGKTLMDIISRKDQRGSGQVVTYPLNTWTNLKVQLIRMAEGEGVILPEDTLSLTGCSRrnLEMWLV 3180
Cdd:pfam00972  322 TYQNKVVKVLRPAPGGKTVMDVISRRDQRGSGQVVTYALNTFTNLKVQLIRMMEAEMVIHHQHLQDCDESER--VEAWLT 399

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|..
gi 380295140  3181 RNGEERLTRIAASGDDVVVKPIDDRFAEALHFLNSMAKIRKDINEWKPSTGW 3232
Cdd:pfam00972  400 EHGCDRLKRMAVSGDDCVVKPIDDRFALALSHLNDMGKVRKDISEWQPSKGW 451
Flavi_NS1 pfam00948
Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the ...
 794-1146 1.10e-154

Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the flaviviruses. It contains 12 cysteines, and undergoes glycosylation in a similar manner to other NS proteins. Mutational analysis has strongly implied a role for NS1 in the early stages of RNA replication.


Pssm-ID: 279316  Cd Length: 360  Bit Score: 484.16  E-value: 1.10e-154
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   794 GCSLDITHREIKCGDGIFIFRDAGGWRDKYVFHPGSPKTLAAAIWKGWNDGICGVRSATRMEHEMWKQIENELNGILEEN 873
Cdd:pfam00948    2 GCAINFGGRELKCGDGIFIFNDSDDWLEKYKFQADDPKKLAAAIGAAFEEGKCGINSADRLEHEMWKQIADEINAIFEEN 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   874 DIKLSVVVKNANGTYPRGTKS-----LTRNTTGLQYGWKSWGKTMFVSVPIAENTFIIDGNDEGECASDKRAWNTFKIEE 948
Cdd:pfam00948   82 DMDFSVVVGDPKGILAQGKKMirphpFEHIRDGLKYGWKSWGKAKIFGADRKNGSFIIDGKNRKECPDNNRAWNIFEIED 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   949 FGTGIMKTKVFLDLADAQTEYCDTELLGAAVKGNKSVHGDPGLWMTASKESGDWKLESLSMTESRRCLWPDSHTIWGRGV 1028
Cdd:pfam00948  162 FGFGIFTTNIWLDARDEYTIDCDGRILGAAIKDKKAAHADMGFWIESHEKNETWKIARAEAIDVKECEWPKSHTIWGNGV 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  1029 LESKLILPSMFGGPVSHMNTRPGYATQLSGPWNNVPLDVVFEECPGTKVVVENNCTNRGESIRSTTDSGKIIPEWCCRKC 1108
Cdd:pfam00948  242 EESEMFIPKIIGGPISQHNHIPGYFTQTAGPWHLGKLELDFDACEGTSVIIDEHCDGRGKSLRSTTDSGKTIHEWCCRSC 321

                          330       340       350
                   ....*....|....*....|....*....|....*...
gi 380295140  1109 TMPPLTYRTPDGCWYAMEIRPKKASEESLLRSKVSAGT 1146
Cdd:pfam00948  322 TLPPLRFHGEDGCWYGMEIRPRKEHEEHLVKSMVSAGE 359
capping_2-OMTase_Flaviviridae cd20761
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific ...
 2534-2771 2.60e-118

Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Flaviviridae viruses, comprise a family of ss(+)RNA viruses, cap their mRNAs. The 2'OMTase activity is located in the non-structural protein 5 (NS5).


Pssm-ID: 467736  Cd Length: 225  Bit Score: 373.87  E-value: 2.60e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 2534 TRGMEWKRKLNAMNKETFQRYRRDGIVEVDrtaarealksgnvTGGHAVSRGSAKLRWLVDKGYLRLMGDVTDLGCGRGG 2613
Cdd:cd20761     1 TLGEKWKDRLNALSKEEFDAYKKRGVVEVA-------------TKGHAVSRGYAKLRWLVERGYVKPSGKVVDLGCGRGG 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 2614 WCYYAAAQRNVVSVRGFTKGGDGHEEPIPVQTYGWNIVTLRSKVDVFYMPTHMTDTLLCDIGESSSNMLVEEERTLRVLN 2693
Cdd:cd20761    68 WSQYAAGLPKVTEVRGYTLGGPGHEEPRLVQSYGWNLVRLKSGVDVFYRPPERCDTLLCDIGESSPSPEVEEERTLRVLD 147

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 380295140 2694 LFEEWIRKSKPTHFCCKVLAPYMPNVLEKIDKLMKVHGGALVRVPLSRNSTHEMYWVSDARGNAMNAVASLSRTLLDR 2771
Cdd:cd20761   148 LVEKWLERNPTANFCIKVLCPYHPEVIELLERLQRKGGGGLVRVPLSRNSTHEMYFVSGARGNIVNSVNMTSRLLLNR 225
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1689-1834 3.73e-85

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 275.37  E-value: 3.73e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  1689 KGKLSVMDLHPGAGKTRKVLPQVLKEAVAKKLKTLVLAPTRVVAKEMHGALAGLPVRYQTSAVETKGSGNELIDVMCHAT 1768
Cdd:pfam07652    1 KGTLTVLDLHPGAGKTRKVLPELVRECIDRRLRTLVLAPTRVVLAEMEEALRGLPIRYHTPAVSSEHTGREIVDVMCHAT 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 380295140  1769 FTYRQLTPGRMVNYQLYVMDEAHFTDPASIAARGIIATRVKLGEAAAIFMTATPPGTLDAFPESNS 1834
Cdd:pfam07652   81 FTQRLLSPVRVPNYEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFMTATPPGTSDPFPESNA 146
Flavi_NS5_thumb pfam20483
Flavivirus RNA-directed RNA polymerase, thumb domain; Flaviviruses produce a large polyprotein ...
 3236-3399 1.22e-80

Flavivirus RNA-directed RNA polymerase, thumb domain; Flaviviruses produce a large polyprotein from the ssRNA genome, encoding structural proteins required for virus assembly and non-structural (NS1-5) proteins involved in replication of the viral genome. This polyprotein is cleaved by viral and cellular proteases to produce mature viral proteins. NS5 is the largest mature viral protein and contains a N-terminal methyltransferase (MTase) domain separated by a short linker from the C-terminal RNA-directed RNA polymerase domain (RdRp) that adopts a characteriztic right-handed fingers-palm-thumb fold and possesses a number of short regions and motifs homologous to other RNA-directed RNA polymerases. This entry represents the thumb domain of NS5 RdRp. NS5 binds to a the stem loop A (SLA) at the 5' extremity of Flavivirus genome and regulates translation of the viral genome.


Pssm-ID: 466632  Cd Length: 164  Bit Score: 263.19  E-value: 1.22e-80
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  3236 EGVPFCSHHFHKLSLKDGRTLTVPCRDQDELIGRARVSPGAGWTLRETAGLSKAYAQMWMLIHFHRRDLRTIAFAICSAV 3315
Cdd:pfam20483    1 EEVDFCSHHYEKLTFKDGRTIVVPTRDQDEIIAKSRIRPGGDWSLDETAWLSKAYANMWLVNYFHLRTARALGFAYKSAV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  3316 PKDWVPTGRTSWSIHARGEWMTNEDMLAVWNRVWITENPYMFNKETIHDWRDVPYLRKQLDKNCGSMIGVRSRATWAENI 3395
Cdd:pfam20483   81 PPNWVPTGRTTGSIHRPGPWMTPEDMLDVWNRVWFGESTHMPDGFRVRSWRHVGYLKKREEKLYDSLIGLRNRAYWRSNL 160


                   ....
gi 380295140  3396 RVSV 3399
Cdd:pfam20483  161 HLDV 164
ps-ssRNAv_Flaviviridae_RdRp cd23178
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ...
 2979-3296 3.13e-72

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: 244.35  E-value: 3.13e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 2979 CVYNMMGKREKKLTEFGR--AKGSRAIWYMWLGARYLEFEALGFLNEDHWLSRENSKGGVEGIGLQyLGYILEDM-GGMT 3055
Cdd:cd23178     1 IPTTIMPKNEVFCVEPGKggRKPPRLIVYPDLGVRVAEKMALYDPVEVLPQVVGGSYYGFQYSPNQ-RVEILRKAwKSKK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 3056 GGQMYADDTAGWDTKITNADLEDEMEITKLMA-HTHKKLATAIMNLTYMNKVVRVMRpgkggktlMDIISRKDQRGSGQV 3134
Cdd:cd23178    80 GPMAYSYDTRCFDSTVTEDDIQVEEEIYQACSlKEARQAIVSITERLYVEGPMVNSD--------GQICGRRRCRASGVL 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 3135 VTYPLNTWTNLKVQLIRMAEgegvilpedtlsltgcsrrnlemwlvrnGEERLTRIAASGDDVVVKPIDD-------RFA 3207
Cdd:cd23178   152 TTSAGNT*TCYLK*LAACRE----------------------------AGIRLPTMLVCGDDCVVICESDgtqedaaLLA 203

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 3208 EALHFLNSMAKIRKDinewkPSTGWNSWEGVPFCSHHFHKLSLKDGRTLTVPCRDQDELIGRARVSPGAGwtlrETAGLS 3287
Cdd:cd23178   204 AFTEALTRYGKPPKD-----PPQPEYDLELIESCSHTVSEVRMKDGRRLYYLTRDPTTPLARAAWETGRH----EPINSW 274


                  ....*....
gi 380295140 3288 KAYAQMWML 3296
Cdd:cd23178   275 LGYIIMYAL 283
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1690-1840 1.92e-71

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: 236.29  E-value: 1.92e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 1690 GKLSVMDLHPGAGKTRKVLPQVLKEAVAKKLKTLVLAPTRVVAKEMHGALAGLPVRYQTSAVETKGSGNELIDVMCHATF 1769
Cdd:cd17931     1 GQLTVLDLHPGAGKTTRVLPQIIREAIKKRLRTLVLAPTRVVAAEMYEALRGLPIRYRTGAVKEEHGGNEIVDYMCHGTF 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 380295140 1770 TYRQLTPGRMVNYQLYVMDEAHFTDPASIAARGIIATRVKLGEAAAIFMTATPPGTLDAFPESNSHIEDEE 1840
Cdd:cd17931    81 TCRLLSPKRVPNYNLIIMDEAHFTDPASIAARGYIHTRVEMGEAAVIFMTATPPGTVTPFPQSNHPIEDFE 151
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1836-1980 1.54e-63

C-terminal helicase domain of viral helicase; Viral helicases in this family here are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350193 [Multi-domain]  Cd Length: 145  Bit Score: 213.66  E-value: 1.54e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 1836 IEDEEREIPDKAWSTGFEWITDYTGKTVWFVPSIRTGNIIASCLARTGKKCVVLNSKTFNDEFPKTKSGTWDFVITTDIS 1915
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWITIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEYPKIKTIDWDFVVTTDIS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 380295140 1916 EMGANFKASRVIDCRTSIKPTLAYVPSERVVLGSPKPISPASAAQRRGRVGRDPTQLGDQYIYGG 1980
Cdd:cd18806    81 EMGANFDADRVIDCRTCVKPTILFSGDFRVILTGPVPQTAASAAQRRGRTGRNPAQERDIYRFVG 145
Flavi_E_C cd12149
Immunoglobulin-like domain III (C-terminal domain) of Flavivirus envelope glycoprotein E; The ...
 599-688 9.49e-47

Immunoglobulin-like domain III (C-terminal domain) of Flavivirus envelope glycoprotein E; The C-terminal domain (domain III) of Flavivirus glycoprotein E appears to be involved in low-affinity interactions with negatively charged glycoaminoglycans on the host cell surface. Domain III may also play a role in interactions with alpha-v-beta-3 integrins in West Nile virus, Japanese encephalitis virus, and Dengue virus. The interface between domain I and domain III appears to be destabilized by the low-pH environment of the endosome, and domain III may play a vital role in the conformational changes of envelope glycoprotein E that follow the clathrin-mediated endocytosis of viral particles and are a prerequisite to membrane fusion.


Pssm-ID: 213392  Cd Length: 91  Bit Score: 163.24  E-value: 9.49e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  599 AFTFAKRPVDTGHGTVVFQVSYAGTDAPCKIPVAVTDKPN-GEHVGRLVTAHPFIAKQNEKAVVEVEPPFGDSYIEIGAG 677
Cdd:cd12149     1 KFSWKKEPADTGHGTVVMEVKYSGTDAPCRIPVRVVDSGSgGENVGRLITVNPIITNANSKVFIEVEPPFGDSYIVVGVG 80

                          90
                  ....*....|.
gi 380295140  678 TTKISEAWHKP 688
Cdd:cd12149    81 DTRLKHQWFQK 91
flavi_E_stem TIGR04240
flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal ...
 693-789 4.25e-40

flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal domain, containing a stem region followed by two transmembrane anchor domains, of the envelope protein E. This protein is cleaved from the large flavivirus polyprotein, which yields three structural and seven nonstructural proteins.


Pssm-ID: 213897  Cd Length: 97  Bit Score: 144.70  E-value: 4.25e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   693 GNALALSYKGMKRITAMGEHAWDFGSIGGFFSSMGKAVHHVFGSLFRTLFGGIGWMAKILIGALLIWLGISTRDRMLATS 772
Cdd:TIGR04240    1 GKAFELTMRGAERMAILGDAAWDFGSVGGVFTSIGKALHQVFGGAFRALFGGVSWITKILIGVLLIWLGLNSRNTTLSLT 80

                           90
                   ....*....|....*..
gi 380295140   773 FILTGSILLYLATTTVG 789
Cdd:TIGR04240   81 FLAVGGILLFLTTGVGA 97
Flavi_NS4A pfam01350
Flavivirus non-structural protein NS4A; Flaviviruses encode a single polyprotein. This is ...
 2128-2270 1.34e-35

Flavivirus non-structural protein NS4A; Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4A protein is small and poorly conserved among the Flaviviruses. NS4A contains multiple hydrophobic potential membrane spanning regions. NS4A has only been found in cells infected by Kunjin virus.


Pssm-ID: 279666  Cd Length: 144  Bit Score: 133.49  E-value: 1.34e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  2128 IIEVLGKLPQHFADKTIDAADTFKTVLTATPGSRAYRLAVDNLPDAAETAIFVTMVGFMTMGILIFLMAPKGMTRMSLGF 2207
Cdd:pfam01350    2 LILEIGELPDFLAKKAGEALDNISMFHHSEEGGKAYRHALEELPDAIEILMLFALAALLTGGMTIFFLSGKGIGKMSIAL 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 380295140  2208 MTIMAATYFLWASGMAGYQIAAMQLVAFILFVVLVPEPGSQRSVQDNTIAMVLIGILSIAALI 2270
Cdd:pfam01350   82 GCMAACGALLFLAGVEPHHIAASIIIEFFLMVLLIPEPDQQRSIQDNQLAYLIIGILFLISAL 144
Flavi_glycop_C pfam02832
Flavivirus glycoprotein, immunoglobulin-like domain;
592-687 2.63e-30

Flavivirus glycoprotein, immunoglobulin-like domain;


Pssm-ID: 280922  Cd Length: 97  Bit Score: 116.67  E-value: 2.63e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   592 TYVTCAQAFTFAKRPVDTGHGTVVFQVSYAGTDAPCKIPVAVTDKPNGE-HVGRLVTAHPFIAKQNEKAVVEVEPPFGDS 670
Cdd:pfam02832    1 SYKICTDKFFFEKEPADTGHGTVLMQVKVEGKDAPCKIPVFSADDEKAAiNKGILITANPIASDKDDEVLIEAEPPFGDS 80

                           90
                   ....*....|....*..
gi 380295140   671 YIEIGAGTTKISEAWHK 687
Cdd:pfam02832   81 YIIVGAGDKALKLQWFK 97
Flavi_M cd17038
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with a ...
 217-292 5.82e-30

Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with a membrane-anchored envelope comprised of 3 proteins called C, M and E. The envelope glycoprotein M is translated as a precursor, called prM. The precursor portion of the protein is the signal peptide for the protein's entry into the membrane. prM is cleaved to form M by the proprotein convertase furin in a late-stage cleavage event. Associated with this cleavage is a change in the infectivity and fusion activity of the virus.


Pssm-ID: 341208  Cd Length: 75  Bit Score: 114.65  E-value: 5.82e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 380295140  217 SVALAPHGTGNLHTGeAPMWKSHTDASKYLQRVERWALRNPGYLGILVAIGWLLGKTTAQRVIYITLLVLIGPAYS 292
Cdd:cd17038     1 SVAIPPHGTGGLTTR-KETWLSTSNGKEHLTRVERWVLRNPGYALAAVALAWMLGSSTTQRVIIIVLLLLVAPAYA 75
Peptidase_S7 pfam00949
Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that ...
 1521-1671 3.56e-29

Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that encodes a single polyprotein precursor. Processing of the polyprotein precursor into mature proteins is carried out by the host signal peptidase and by NS3 serine protease, which requires NS2B (pfam01002) as a cofactor.


Pssm-ID: 395758  Cd Length: 129  Bit Score: 114.84  E-value: 3.56e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  1521 EDGCYRVMSRRLIGSTQVGVGVMKDSVFHTMWHVTRGASLTSGNGRMDPYWADVREDLISYGGPWKLNSTWDGsSEVQLI 1600
Cdd:pfam00949    2 TDGILRFFQSSLLGRSQRGVGVLQEGVFHTMWHPTRGTKLHTQGIKTSPSWASVKQDLVDYGGSWKFQGKWLG-EEYQQY 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 380295140  1601 avqpqkipenvqttpgrfvmsdGTEVGAVVLDYPSGTSGSPIVDKDGNVVGLYGNGVMLNDSTYASAIAQS 1671
Cdd:pfam00949   81 ----------------------GYGLGITDLNLSSGSSGSLVLNQNKQIVGIYFATVEVDDNSFVVGLAQL 129
FtsJ pfam01728
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...
 2582-2751 1.61e-21

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


Pssm-ID: 426399  Cd Length: 179  Bit Score: 94.58  E-value: 1.61e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  2582 VSRGSAKLRWLVDK-GYLRLMGDVTDLGCGRGGWCYYaAAQRNVVSVRGFTKGGDGHEEPIPVQtygwNIVTLRskVDVF 2660
Cdd:pfam01728    2 RSRAAYKLLEIDEKfGLLKPGKTVLDLGAAPGGWSQV-ALQRGAGKVVGVDLGPMQLWKPRNDP----GVTFIQ--GDIR 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  2661 YMPTHMT---------DTLLCDIGESSSNML-VEEERTLRVLNLFEEWIRK--SKPTHFCCKVLapYMPNVLEKIDKLMK 2728
Cdd:pfam01728   75 DPETLDLleellgrkvDLVLSDGSPFISGNKvLDHLRSLDLVKAALEVALEllRKGGNFVCKVF--QGEDFSELLYLLKL 152

                          170       180
                   ....*....|....*....|....
gi 380295140  2729 VHGGALVRVP-LSRNSTHEMYWVS 2751
Cdd:pfam01728  153 GFEKVGVFKPpASRPESSEEYLVC 176
capping_2-OMTase_viral cd20754
viral Cap-0 specific (nucleoside-2'-O-)-methyltransferase; Cap-0 specific (nucleoside-2'-O-) ...
 2587-2755 6.43e-19

viral Cap-0 specific (nucleoside-2'-O-)-methyltransferase; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Some dsDNA and dsRNA viruses, like the bluetongue virus (BTV), a member of the Reoviridae family, and Vaccinia virus, a member of the Poxviridae family, as well as some ss(+)RNA viruses, like Flaviviridae and Nidovirales, cap their mRNAs and encode their own 2'OMTase. In BTV, all four reactions are catalyzed by a single protein, VP4. In Vaccinia, the activity is located in the processing factor of the poly(A) polymerase, VP39.


Pssm-ID: 467730  Cd Length: 179  Bit Score: 87.11  E-value: 6.43e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 2587 AKLRWLVDKG-YLRLMGDVTDLGCGRGGWCYYAAAQRNVVSVRGFTKGGDGHeepipvqtYGWNIVTLRSKVDVF----- 2660
Cdd:cd20754     2 AKLLQLEEYFlYKPEKMRVIYIGCAPGGWLYYLRDWFEGTLWVGFDPRDTDP--------LGYNNVITVNKFFDHehtkl 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 2661 YMPTHMTDTLLCDIGESSSNML-VEEERTLRVLNLFEEWI--RKSKPTHFCCKVLAPYMPNVLEKidklmkvHGGALVRV 2737
Cdd:cd20754    74 KFLPNKKDLLICDIRSDRSSHVtKEEDTTESFLTLQEGYIatKLAKVGSICVKVRAPDLKDDGHF-------SSGTLFPQ 146

                         170
                  ....*....|....*...
gi 380295140 2738 PLsRNSTHEMYWVSDARG 2755
Cdd:cd20754   147 PY-AASSSEMRLFSANYD 163
Flavi_M pfam01004
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with virions ...
 218-292 3.27e-17

Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with virions comprised of 3 proteins called C, M and E. The envelope glycoprotein M is made as a precursor, called prM. The precursor portion of the protein is the signal peptide for the proteins entry into the membrane. prM is cleaved to form M in a late-stage cleavage event. Associated with this cleavage is a change in the infectivity and fusion activity of the virus.


Pssm-ID: 460022  Cd Length: 74  Bit Score: 78.39  E-value: 3.27e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 380295140   218 VALAPHGTGNLHTgEAPMWKSHTDASKYLQRVERWALRNPGYLGILVAIGWLLGKTTAQRVIYITLLVLIGPAYS 292
Cdd:pfam01004    1 VALPPHVGLGLET-RTETWMSSRGAWKQLQKVETWALRNPGFTVIALFIAHLIGSSITQKVIIFILLLLVTPAYS 74
Flavi_NS2A pfam01005
Flavivirus non-structural protein NS2A; NS2A is a hydrophobic protein about 25 kDa is size. ...
 1156-1338 4.23e-17

Flavivirus non-structural protein NS2A; NS2A is a hydrophobic protein about 25 kDa is size. NS2A is cleaved from NS1 by a membrane bound host protease. NS2A has been found to associate with the dsRNA within the vesicle packages. It has also been found that NS2A associates with the known replicase components and so NS2A has been postulated to be part of this replicase complex.


Pssm-ID: 279359  Cd Length: 215  Bit Score: 82.97  E-value: 4.23e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  1156 GLLVLIIFVQEGLKRRMTSRYIMLAALGLLLAAVLGDLTYNDIARYLIMVGVAFAEMNNGGDLI-----HLALIATFKVQ 1230
Cdd:pfam01005    1 GLLCIMIAIEEVLRKRQGPKMLLTGGLALFGALLMGQLTLLDLIKLCIAVGLHFHEMANAGDAMgmgttYLALIAAFRIR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  1231 PGYLLFFLLRKQWSPRESTILASAA----------------------VVLQICAAAWQSTKSMQVLNALAMGWLYIRAIV 1288
Cdd:pfam01005   81 PGFAIGFGFRRLTSPRERLLLTLGAalvasvelpnsleeiadggamgIMMLKLLTDFQSHGLWATLLALSFCILTFNAHA 160

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 380295140  1289 VPGALSKAMPLICMCVPGVLSLTPHAIRVSMVTLAAGTLIKGTKGTSVRK 1338
Cdd:pfam01005  161 ARKAMAMILPIMALFTPLCLAEVRLAAMFFCAVVIIGVLHQNFKDTSMQK 210
Flavi_propep pfam01570
Flavivirus polyprotein propeptide; The flaviviruses are small enveloped animal viruses ...
 152-209 3.29e-14

Flavivirus polyprotein propeptide; The flaviviruses are small enveloped animal viruses containing a single positive strand genomic RNA. The genome encodes one large ORF a polyprotein which undergos proteolytic processing into mature viral peptide chains. This family consists of a propeptide region of approximately 90 amino acid length.


Pssm-ID: 366710  Cd Length: 78  Bit Score: 70.22  E-value: 3.29e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 380295140   152 AVGNGSCIVMATDVGTWCEDTVTYLCPKLDGAAEPDDIDCWCKVV-SVYVTYGRCRRDG 209
Cdd:pfam01570   20 SVGTGNCTTNILEAKYWCPDSMEYNCPNLSPREEPDDIDCWCYGVeNVRVAYGKCDSAG 78
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 1690-1821 1.74e-13

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: 70.51  E-value: 1.74e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 1690 GKLSVMDLHPGAGKTRKVLPQVLKEAVAKKLKTLVLAPTRVVAKEMHGALA-----GLPVRYQTSAV-----ETKGSGNE 1759
Cdd:cd00046     1 GENVLITAPTGSGKTLAALLAALLLLLKKGKKVLVLVPTKALALQTAERLRelfgpGIRVAVLVGGSsaeerEKNKLGDA 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 380295140 1760 LIDVMCHATFT--YRQLTPGRMVNYQLYVMDEAHFTDPASIAARGIIAT--RVKLGEAAAIFMTAT 1821
Cdd:cd00046    81 DIIIATPDMLLnlLLREDRLFLKDLKLIIVDEAHALLIDSRGALILDLAvrKAGLKNAQVILLSAT 146
Flavi_capsid pfam01003
Flavivirus capsid protein C; Flaviviruses are small enveloped viruses with virions comprised ...
 6-122 7.60e-13

Flavivirus capsid protein C; Flaviviruses are small enveloped viruses with virions comprised of 3 proteins called C, M and E. Multiple copies of the C protein form the nucleocapsid, which contains the ssRNA molecule.


Pssm-ID: 366413  Cd Length: 117  Bit Score: 67.74  E-value: 7.60e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140     6 KKPGR-RAIDIVRRALPRVSgpkkvLKKATQTVMESLAG---IRATVAYLLYMTFLGNKVSKATRAKFRSAKKSDLIKIL 81
Cdd:pfam01003    1 GKPGKgRGVNMLKRGAKRVP-----LKKTKRKTGQLLDGrgpLRLVLAFLAFFRFTAIAPTPGLKKRWRTVPKRQAIKHL 75

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 380295140    82 SSFKRTVTNLLASVQKRKRK--AKRSVTTPSMALILLTMsCMA 122
Cdd:pfam01003   76 RKFKKEVGTLLDGLNRRGKRrsKRGGWTGLLLMLGLLTL-VLA 117
DEXHc_RHA-like cd17917
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ...
 1694-1832 1.65e-12

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: 67.87  E-value: 1.65e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 1694 VMDLHPGAGKTRKVLPQVLKEAVAK--KLKTLVLAPTRV--------VAKEMHGALaGLPVRYQTSAvETKGSGNELIDV 1763
Cdd:cd17917     5 VIVGETGSGKTTQVPQFLLEDGLAKggKGRIVCTQPRRIaaisvaerVAEERGEKL-GEEVGYQIRF-ESKTSSKTRIKF 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 380295140 1764 MCHATFTYRQLTPGRMVNYQLYVMDEAHFTDPASIAARGIIATRV-KLGEAAAIFMTATP-PGTLDAFPES 1832
Cdd:cd17917    83 CTDGILLRELLSDPLLSGYSHVILDEAHERSLDTDFLLGLLKDLLrKRPDLKVILMSATLdAEKFSSYFGG 153
DEXDc smart00487
DEAD-like helicases superfamily;
1684-1855 4.55e-07

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 53.26  E-value: 4.55e-07
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   1684 PDMLKKGKLSVMDLHPGAGKTRkVLPQVLKEAVAKKL--KTLVLAPTRVVAKEMHGALA--GLPVRYQTSAVETKGSGNE 1759
Cdd:smart00487   18 EALLSGLRDVILAAPTGSGKTL-AALLPALEALKRGKggRVLVLVPTRELAEQWAEELKklGPSLGLKVVGLYGGDSKRE 96

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   1760 LIDVM----CHATFTyrqlTPGRMV-----------NYQLYVMDEAHFTDPASiaARGIIATRVKLGEAAA--IFMTATP 1822
Cdd:smart00487   97 QLRKLesgkTDILVT----TPGRLLdllendklslsNVDLVILDEAHRLLDGG--FGDQLEKLLKLLPKNVqlLLLSATP 170

                           170       180       190
                    ....*....|....*....|....*....|...
gi 380295140   1823 PGTLDAFpeSNSHIEDEEREIPDKAWSTGFEWI 1855
Cdd:smart00487  171 PEEIENL--LELFLNDPVFIDVGFTPLEPIEQF 201
HELICc smart00490
helicase superfamily c-terminal domain;
1874-1968 7.70e-06

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 46.44  E-value: 7.70e-06
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140   1874 IIASCLARTGKKCVVLNSKTFNDE----FPKTKSGTWDFVITTDISEMGANFK-ASRVIDCRTsikptlayvpservvlg 1948
Cdd:smart00490    2 ELAELLKELGIKVARLHGGLSQEEreeiLDKFNNGKIKVLVATDVAERGLDLPgVDLVIIYDL----------------- 64

                            90       100
                    ....*....|....*....|
gi 380295140   1949 spkPISPASAAQRRGRVGRD 1968
Cdd:smart00490   65 ---PWSPASYIQRIGRAGRA 81
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 1860-1967 2.86e-03

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: 39.89  E-value: 2.86e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140  1860 GKTVWFVPSIRTGNIiASCLARTGKKCVVLNSKTFNDE-------FPKTKSgtwDFVITTDISEMGANFK-ASRVIDCRT 1931
Cdd:pfam00271   16 GKVLIFSQTKKTLEA-ELLLEKEGIKVARLHGDLSQEEreeiledFRKGKI---DVLVATDVAERGLDLPdVDLVINYDL 91

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 380295140  1932 sikptlayvpservvlgspkPISPASAAQRRGRVGR 1967
Cdd:pfam00271   92 --------------------PWNPASYIQRIGRAGR 107
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 1861-1978 4.08e-03

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 38.45  E-value: 4.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 1861 KTVWFVPSIRTGNIIASCLArtgkkcvvlnsktfndefpktksgtwdFVITTDISEMGANFK-ASRVIDCRtsikptlay 1939
Cdd:cd18785     5 KIIVFTNSIEHAEEIASSLE---------------------------ILVATNVLGEGIDVPsLDTVIFFD--------- 48

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 380295140 1940 vpservvlgspKPISPASAAQRRGRVGRdPTQLGDQYIY 1978
Cdd:cd18785    49 -----------PPSSAASYIQRVGRAGR-GGKDEGEVIL 75
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 1688-1822 6.00e-03

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: 39.98  E-value: 6.00e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 380295140 1688 KKGKLSVMDLHPGAGKTrkVLPQVLKEAvAKKLKTLVLAPTRVVAKEMHGALA---GLPVRYQTSAVETKGSGNELIDVm 1764
Cdd:cd17926    16 KNNRRGILVLPTGSGKT--LTALALIAY-LKELRTLIVVPTDALLDQWKERFEdflGDSSIGLIGGGKKKDFDDANVVV- 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 380295140 1765 chATFT--YRQLTPGRMV--NYQLYVMDEAHftdpaSIAARGIIATRVKLGEAAAIFMTATP 1822
Cdd:cd17926    92 --ATYQslSNLAEEEKDLfdQFGLLIVDEAH-----HLPAKTFSEILKELNAKYRLGLTATP 146
 
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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