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Conserved domains on  [gi|700588962|gb|AIU94742|]
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polyprotein [Naranjal virus]

Protein Classification

Graphical summary

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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 ...
 2844-3411 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: 1293.29  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 2844 MINQVVKMVSKPWDALNSVTSISMTDTTPFGQQRVFKEKVDTKAPEPPRGVAEAMDMVADWVWMILSRKKKPRLCTREEF 2923
Cdd:cd23204     1 MVNGVVKLLSKPWDVIEMVTQMAMTDTTPFGQQRVFKEKVDTKAPEPPEGTRKIMRIVNEWLWKFLARKKKPRLCTREEF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 2924 KAKVNGHAAMGAVFEEEQQWQTAREAVEDPEFWDLVDKERALHLEGRCETCVYNMMGKREKKLGEFGKAKGSRAIWYMWL 3003
Cdd:cd23204    81 IAKVRSNAALGAVFEEQNQWKSAREAVEDPRFWELVDEERELHLEGKCETCVYNMMGKREKKLGEFGKAKGSRAIWYMWL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3004 GARFLEFEALGFLNEDHWLSRENSYAGVEGLGLQRLGYVLRDISYRPGGKMYADDTAGWDTRITEKDLENEAKITEKMEG 3083
Cdd:cd23204   161 GARFLEFEALGFLNEDHWASRENSGGGVEGIGLQYLGYILREISKKPGGKMYADDTAGWDTRITEADLEDEEKILEYMEG 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3084 EHKKLAKAIIELTYKHKVVKVMRPGPGGKTFMDVISREDQRGSGQVVTYALNTYTNMVAQLIRCAEAEGVLTPDMRErsl 3163
Cdd:cd23204   241 EHRKLAEAIFELTYQNKVVKVMRPGPGGGTVMDVISRRDQRGSGQVVTYALNTFTNMKVQLIRMMEGEGVITPEDLE--- 317

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3164 TKQERYALTLWLDMEGVKRLKKMAISGDDCVVKSEDERFATALYFLNAMAKVRKDIQEWKPSSGWLDWQEVPFCSHHFKE 3243
Cdd:cd23204   318 TAPRLKRVEDWLEENGEERLSRMAVSGDDCVVKPIDDRFATALTFLNDMGKVRKDIQEWEPSKGWNDWEEVPFCSHHFHE 397

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3244 LQLKDGRSIVVPCRHQDELVGRARVSPGAAWGVRESAGLAKAYAQMWKLMYFHRRDLRLMANAICSAVPKDWVPTGRTTW 3323
Cdd:cd23204   398 LIMKDGRTLVVPCRDQDELIGRARVSPGAGWSLRETACLSKAYAQMWLLMYFHRRDLRLMANAICSAVPVDWVPTGRTTW 477

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3324 SIHGKGEWMTNEDMLEVWNRVWIRENPYMTDKTEVHDWKEIPYLGKREDQWCGSLIGSRARATWAENIWVAVNQVRAKIG 3403
Cdd:cd23204   478 SIHAKGEWMTTEDMLEVWNRVWIEDNPWMEDKTPVTSWRDVPYLGKREDQWCGSLIGLRSRATWAKNIQTAVNQVRSLIG 557


                  ....*...
gi 700588962 3404 KEEYLDYL 3411
Cdd:cd23204   558 NEEYRDYL 565
Flavi_NS1 super family cl03032
Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the ...
 797-1149 5.11e-160

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: 499.57  E-value: 5.11e-160
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962   797 GCAVDIERRELKCGTGIFIMDDVESWRDEYSFHPSSPKKLAASIVEAVESGTCGIRTVNRMEHKMWESIENELNAILEEN 876
Cdd:pfam00948    2 GCAINFGGRELKCGDGIFIFNDSDDWLEKYKFQADDPKKLAAAIGAAFEEGKCGINSADRLEHEMWKQIADEINAIFEEN 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962   877 EQDITVVVKDLENPAPKGFKRL---PL--VEKELKYGWKKWGATFFKHPERKNTTFLVDGPSGPECPNSQRAWNSFHVED 951
Cdd:pfam00948   82 DMDFSVVVGDPKGILAQGKKMIrphPFehIRDGLKYGWKSWGKAKIFGADRKNGSFIIDGKNRKECPDNNRAWNIFEIED 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962   952 FGFGVFKTSVWMELNDQVTEVCDTKMIGTGIKNNKAVHSDLGYWIESR-KNHSWEISRARLIETKSCIWPRSHTLWSDGV 1030
Cdd:pfam00948  162 FGFGIFTTNIWLDARDEYTIDCDGRILGAAIKDKKAAHADMGFWIESHeKNETWKIARAEAIDVKECEWPKSHTIWGNGV 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  1031 EETQLIIPKSLGGPRSRHNMRNGYKTQVNGPWNLIPLDIKFEECPGTSVTVTQNCGGRGPSARSTTASGKIIAEWCCKDC 1110
Cdd:pfam00948  242 EESEMFIPKIIGGPISQHNHIPGYFTQTAGPWHLGKLELDFDACEGTSVIIDEHCDGRGKSLRSTTDSGKTIHEWCCRSC 321

                          330       340       350
                   ....*....|....*....|....*....|....*....
gi 700588962  1111 VLPPLTFRHGETCWYGMEIRPMKEKEENLVKSKVSAGDG 1149
Cdd:pfam00948  322 TLPPLRFHGEDGCWYGMEIRPRKEHEEHLVKSMVSAGEG 360
capping_2-OMTase_Flaviviridae cd20761
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific ...
 2531-2766 2.34e-125

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: 393.90  E-value: 2.34e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 2531 TLGEKWKHMLNSMDKYEFSRYKVNGIFEVDreparmalanglvTGGHAVSRGSAKLRWMVERGAVRPTGRVIDLGCGRGG 2610
Cdd:cd20761     1 TLGEKWKDRLNALSKEEFDAYKKRGVVEVA-------------TKGHAVSRGYAKLRWLVERGYVKPSGKVVDLGCGRGG 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 2611 WSYYCATLKQVQEVRGFTKGGEGHEEPKMVQSYGWNIVTLKSGVDVFHRPAEMGDTILCDIGESSATPEIEEARTLRVLD 2690
Cdd:cd20761    68 WSQYAAGLPKVTEVRGYTLGGPGHEEPRLVQSYGWNLVRLKSGVDVFYRPPERCDTLLCDIGESSPSPEVEEERTLRVLD 147

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 700588962 2691 MIEPWLKNKP--EFCIKVLCPYRPKVIEKLSALQRQYGGGLLRVPLSRNSTHEMYWTSGTAGNIINAVNLTSKVLIHR 2766
Cdd:cd20761   148 LVEKWLERNPtaNFCIKVLCPYHPEVIELLERLQRKGGGGLVRVPLSRNSTHEMYFVSGARGNIVNSVNMTSRLLLNR 225
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1690-1835 1.79e-94

Flavivirus DEAD domain;


:

Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 302.33  E-value: 1.79e-94
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  1690 KKKLTVLDLHPGAGKTRKVLPRLLQEALEKRLRTVVLAPTRVVAAEMAEALKGMPIRYQTSAVTASHQGNEIIDLMCHAT 1769
Cdd:pfam07652    1 KGTLTVLDLHPGAGKTRKVLPELVRECIDRRLRTLVLAPTRVVLAEMEEALRGLPIRYHTPAVSSEHTGREIVDVMCHAT 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 700588962  1770 FTSRLMQPHKVPNYNLYIMDEAHFTDPASIAARGFISTKVSLGEAAAVFMTATPPGSDNPFPASNA 1835
Cdd:pfam07652   81 FTQRLLSPVRVPNYEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFMTATPPGTSDPFPESNA 146
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1837-1981 2.78e-70

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: 232.92  E-value: 2.78e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 1837 ITDTEAQIPDKAWSSGFDWITEYEGKTVWFVPSVRMGNEIAACLGKAKKKVIQLSRRTFNTEYPKCKQGDWDFVVTTDIS 1916
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWITIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEYPKIKTIDWDFVVTTDIS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 700588962 1917 EMGANFKATRVIDSRRAIKPSIMSDQEERVVLSGPLPISPASAAQRRGRIGRNPNQLGDEYVFSG 1981
Cdd:cd18806    81 EMGANFDADRVIDCRTCVKPTILFSGDFRVILTGPVPQTAASAAQRRGRTGRNPAQERDIYRFVG 145
flavi_E_stem TIGR04240
flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal ...
 698-794 1.13e-47

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: 166.27  E-value: 1.13e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962   698 GGAFSTTMKGAKRLAILGDAAWDFGSIGGVFNSMGKAVHQLFGGVFRTLFGGMSWLSRIFIGVLCVWIGINARDHTIAVS 777
Cdd:TIGR04240    1 GKAFELTMRGAERMAILGDAAWDFGSVGGVFTSIGKALHQVFGGAFRALFGGVSWITKILIGVLLIWLGLNSRNTTLSLT 80

                           90
                   ....*....|....*..
gi 700588962   778 MLAVGGVLLFLSVSVNA 794
Cdd:TIGR04240   81 FLAVGGILLFLTTGVGA 97
Flavi_E_C cd12149
Immunoglobulin-like domain III (C-terminal domain) of Flavivirus envelope glycoprotein E; The ...
 603-693 8.53e-44

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: 154.77  E-value: 8.53e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  603 SFKMEKSPADTGHGTVVLDISYQGSEAPCKVPIVITPNLAEIEPVGRLVSAHPVVTGKNVRTMIEVEPPYGDSYIIIGTG 682
Cdd:cd12149     1 KFSWKKEPADTGHGTVVMEVKYSGTDAPCRIPVRVVDSGSGGENVGRLITVNPIITNANSKVFIEVEPPFGDSYIVVGVG 80

                          90
                  ....*....|.
gi 700588962  683 DGKLKQHWYKK 693
Cdd:cd12149    81 DTRLKHQWFQK 91
Flavi_capsid pfam01003
Flavivirus capsid protein C; Flaviviruses are small enveloped viruses with virions comprised ...
 6-123 2.44e-34

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: 128.99  E-value: 2.44e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962     6 GKPGVGRVVNMLKRTATNAasPVRLAKRLLGEAFSGRGPLRVILAVIAFFRFTAIKMSPALLKKWGTVEKGAALAIMKSF 85
Cdd:pfam01003    1 GKPGKGRGVNMLKRGAKRV--PLKKTKRKTGQLLDGRGPLRLVLAFLAFFRFTAIAPTPGLKKRWRTVPKRQAIKHLRKF 78

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 700588962    86 KKEIGNMLDTVSRRKTKGKKKRSSESSA-MLILMVASMA 123
Cdd:pfam01003   79 KKEVGTLLDGLNRRGKRRSKRGGWTGLLlMLGLLTLVLA 117
Flavi_NS4A super family cl03176
Flavivirus non-structural protein NS4A; Flaviviruses encode a single polyprotein. This is ...
 2132-2270 1.73e-33

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: 127.71  E-value: 1.73e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  2132 VGKLPEHLGARLKDSIDVLYLAFTAEAGSRPHREAMHELPAALETILVFALLMALTGTTFFLLMRHKGINKMGYGMIVMT 2211
Cdd:pfam01350    6 IGELPDFLAKKAGEALDNISMFHHSEEGGKAYRHALEELPDAIEILMLFALAALLTGGMTIFFLSGKGIGKMSIALGCMA 85

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 700588962  2212 AVGGLLWYGNIQAPKIAGILLLTFLLMVVLIPEPEKQRSIQDNQLALAVLGCLVFLGTV 2270
Cdd:pfam01350   86 ACGALLFLAGVEPHHIAASIIIEFFLMVLLIPEPDQQRSIQDNQLAYLIIGILFLISAL 144
Flavi_M cd17038
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with a ...
 218-292 2.22e-33

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: 124.67  E-value: 2.22e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 700588962  218 STAFPQHTESTLATRRESWLNTDVAMKHLVKVETWALRNPGFAFVAITLGWMLGNSTSQKIIFTLLLLLVAPAYS 292
Cdd:cd17038     1 SVAIPPHGTGGLTTRKETWLSTSNGKEHLTRVERWVLRNPGYALAAVALAWMLGSSTTQRVIIIVLLLLVAPAYA 75
Peptidase_S7 pfam00949
Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that ...
 1522-1670 1.12e-31

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: 121.78  E-value: 1.12e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  1522 TENGVYRIFANRLFGRVQVGVGVMQDGVFHTMWHVTRGAALRSGDGRLDPYWGDVRKDLISYGGPWKLEGKWDGtsevql 1601
Cdd:pfam00949    1 LTDGILRFFQSSLLGRSQRGVGVLQEGVFHTMWHPTRGTKLHTQGIKTSPSWASVKQDLVDYGGSWKFQGKWLG------ 74

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  1602 vavapkEKVKNVqttpgvfktpNGEVGAITLDFPAGSSGSPIINKNGEVIGLYGNGLMMGD-AYASAIAQ 1670
Cdd:pfam00949   75 ------EEYQQY----------GYGLGITDLNLSSGSSGSLVLNQNKQIVGIYFATVEVDDnSFVVGLAQ 128
Flavi_NS2A super family cl03066
Flavivirus non-structural protein NS2A; NS2A is a hydrophobic protein about 25 kDa is size. ...
 1158-1339 1.48e-23

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: 101.46  E-value: 1.48e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  1158 GLLVAMLVTQEGLRKRWATRHIVVASLAMLAAMITGNITYMDLGRYIILLGATFAEMNSGGDIM-----HLALVAVFKVQ 1232
Cdd:pfam01005    1 GLLCIMIAIEEVLRKRQGPKMLLTGGLALFGALLMGQLTLLDLIKLCIAVGLHFHEMANAGDAMgmgttYLALIAAFRIR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  1233 PGFLVGFLLKRRWTPRESMLLAISACF----------------------MHLVFSDFQTD-LTSLAHNFSLALLVLRAVI 1289
Cdd:pfam01005   81 PGFAIGFGFRRLTSPRERLLLTLGAALvasvelpnsleeiadggamgimMLKLLTDFQSHgLWATLLALSFCILTFNAHA 160

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 700588962  1290 QTDVSSVTLPVLSMMAPAFQFSVLGTFRMAVAIYVVANLMLSRKNDAVKK 1339
Cdd:pfam01005  161 ARKAMAMILPIMALFTPLCLAEVRLAAMFFCAVVIIGVLHQNFKDTSMQK 210
 
Name Accession Description Interval E-value
Flavivirus_RdRp cd23204
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within ...
 2844-3411 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: 1293.29  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 2844 MINQVVKMVSKPWDALNSVTSISMTDTTPFGQQRVFKEKVDTKAPEPPRGVAEAMDMVADWVWMILSRKKKPRLCTREEF 2923
Cdd:cd23204     1 MVNGVVKLLSKPWDVIEMVTQMAMTDTTPFGQQRVFKEKVDTKAPEPPEGTRKIMRIVNEWLWKFLARKKKPRLCTREEF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 2924 KAKVNGHAAMGAVFEEEQQWQTAREAVEDPEFWDLVDKERALHLEGRCETCVYNMMGKREKKLGEFGKAKGSRAIWYMWL 3003
Cdd:cd23204    81 IAKVRSNAALGAVFEEQNQWKSAREAVEDPRFWELVDEERELHLEGKCETCVYNMMGKREKKLGEFGKAKGSRAIWYMWL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3004 GARFLEFEALGFLNEDHWLSRENSYAGVEGLGLQRLGYVLRDISYRPGGKMYADDTAGWDTRITEKDLENEAKITEKMEG 3083
Cdd:cd23204   161 GARFLEFEALGFLNEDHWASRENSGGGVEGIGLQYLGYILREISKKPGGKMYADDTAGWDTRITEADLEDEEKILEYMEG 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3084 EHKKLAKAIIELTYKHKVVKVMRPGPGGKTFMDVISREDQRGSGQVVTYALNTYTNMVAQLIRCAEAEGVLTPDMRErsl 3163
Cdd:cd23204   241 EHRKLAEAIFELTYQNKVVKVMRPGPGGGTVMDVISRRDQRGSGQVVTYALNTFTNMKVQLIRMMEGEGVITPEDLE--- 317

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3164 TKQERYALTLWLDMEGVKRLKKMAISGDDCVVKSEDERFATALYFLNAMAKVRKDIQEWKPSSGWLDWQEVPFCSHHFKE 3243
Cdd:cd23204   318 TAPRLKRVEDWLEENGEERLSRMAVSGDDCVVKPIDDRFATALTFLNDMGKVRKDIQEWEPSKGWNDWEEVPFCSHHFHE 397

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3244 LQLKDGRSIVVPCRHQDELVGRARVSPGAAWGVRESAGLAKAYAQMWKLMYFHRRDLRLMANAICSAVPKDWVPTGRTTW 3323
Cdd:cd23204   398 LIMKDGRTLVVPCRDQDELIGRARVSPGAGWSLRETACLSKAYAQMWLLMYFHRRDLRLMANAICSAVPVDWVPTGRTTW 477

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3324 SIHGKGEWMTNEDMLEVWNRVWIRENPYMTDKTEVHDWKEIPYLGKREDQWCGSLIGSRARATWAENIWVAVNQVRAKIG 3403
Cdd:cd23204   478 SIHAKGEWMTTEDMLEVWNRVWIEDNPWMEDKTPVTSWRDVPYLGKREDQWCGSLIGLRSRATWAKNIQTAVNQVRSLIG 557


                  ....*...
gi 700588962 3404 KEEYLDYL 3411
Cdd:cd23204   558 NEEYRDYL 565
Flavi_NS5 pfam00972
Flavivirus RNA-directed RNA polymerase, fingers and palm domains; Flaviviruses produce a large ...
 2776-3228 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: 782.21  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  2776 YEKDVNLGSGTRAVTVKRKAPDMEKIGPRIKKLREEHSSSWCYDEMNPYRTWNYHGSYEVKPTGSASSMINQVVKMVSKP 2855
Cdd:pfam00972    2 YEADVILGIGTRSVATDKEPLNKEIIGERIERIKNEHMTTWFYDEDNPYRTWAYHGSYETKTSGSASSMVNGVVRLLTKP 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  2856 WDALNSVTSISMTDTTPFGQQRVFKEKVDTKAPEPPRGVAEAMDMVADWVWMILSRKKKPRLCTREEFKAKVNGHAAMGA 2935
Cdd:pfam00972   82 WDVIEEVTRIAMTDTTPFGQQRVFKEKVDTRAPDPPAGTRQIMKVVNRWLWRHLAREKNPRLCTKEEFIAKVRSNAAIGA 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  2936 VFEEEQQWQTAREAVEDPEFWDLVDKERALHLEGRCETCVYNMMGKREKKLGEFGKAKGSRAIWYMWLGARFLEFEALGF 3015
Cdd:pfam00972  162 YFEEEEQWKTANEAVQDPRFWELVDRERELHQQGRCRTCVYNMMGKREKKLGEFGKAKGSRAIWYMWLGARFLEFEALGF 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  3016 LNEDHWLSRENSYAGVEGLGLQRLGYVLRDISYRPGGKMYADDTAGWDTRITEKDLENEAKITEKMEGEHKKLAKAIIEL 3095
Cdd:pfam00972  242 LNEDHWASRENSGGGVEGIGLQYLGYILRDLAAMPGGGMYADDTAGWDTRITEADLDNEAEITNYMEPHHKKLAQAVMKM 321

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  3096 TYKHKVVKVMRPGPGGKTFMDVISREDQRGSGQVVTYALNTYTNMVAQLIRCAEAEGVLTPDMRErSLTKQERyaLTLWL 3175
Cdd:pfam00972  322 TYQNKVVKVLRPAPGGKTVMDVISRRDQRGSGQVVTYALNTFTNLKVQLIRMMEAEMVIHHQHLQ-DCDESER--VEAWL 398

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 700588962  3176 DMEGVKRLKKMAISGDDCVVKSEDERFATALYFLNAMAKVRKDIQEWKPSSGW 3228
Cdd:pfam00972  399 TEHGCDRLKRMAVSGDDCVVKPIDDRFALALSHLNDMGKVRKDISEWQPSKGW 451
Flavi_NS1 pfam00948
Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the ...
 797-1149 5.11e-160

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: 499.57  E-value: 5.11e-160
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962   797 GCAVDIERRELKCGTGIFIMDDVESWRDEYSFHPSSPKKLAASIVEAVESGTCGIRTVNRMEHKMWESIENELNAILEEN 876
Cdd:pfam00948    2 GCAINFGGRELKCGDGIFIFNDSDDWLEKYKFQADDPKKLAAAIGAAFEEGKCGINSADRLEHEMWKQIADEINAIFEEN 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962   877 EQDITVVVKDLENPAPKGFKRL---PL--VEKELKYGWKKWGATFFKHPERKNTTFLVDGPSGPECPNSQRAWNSFHVED 951
Cdd:pfam00948   82 DMDFSVVVGDPKGILAQGKKMIrphPFehIRDGLKYGWKSWGKAKIFGADRKNGSFIIDGKNRKECPDNNRAWNIFEIED 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962   952 FGFGVFKTSVWMELNDQVTEVCDTKMIGTGIKNNKAVHSDLGYWIESR-KNHSWEISRARLIETKSCIWPRSHTLWSDGV 1030
Cdd:pfam00948  162 FGFGIFTTNIWLDARDEYTIDCDGRILGAAIKDKKAAHADMGFWIESHeKNETWKIARAEAIDVKECEWPKSHTIWGNGV 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  1031 EETQLIIPKSLGGPRSRHNMRNGYKTQVNGPWNLIPLDIKFEECPGTSVTVTQNCGGRGPSARSTTASGKIIAEWCCKDC 1110
Cdd:pfam00948  242 EESEMFIPKIIGGPISQHNHIPGYFTQTAGPWHLGKLELDFDACEGTSVIIDEHCDGRGKSLRSTTDSGKTIHEWCCRSC 321

                          330       340       350
                   ....*....|....*....|....*....|....*....
gi 700588962  1111 VLPPLTFRHGETCWYGMEIRPMKEKEENLVKSKVSAGDG 1149
Cdd:pfam00948  322 TLPPLRFHGEDGCWYGMEIRPRKEHEEHLVKSMVSAGEG 360
capping_2-OMTase_Flaviviridae cd20761
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific ...
 2531-2766 2.34e-125

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: 393.90  E-value: 2.34e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 2531 TLGEKWKHMLNSMDKYEFSRYKVNGIFEVDreparmalanglvTGGHAVSRGSAKLRWMVERGAVRPTGRVIDLGCGRGG 2610
Cdd:cd20761     1 TLGEKWKDRLNALSKEEFDAYKKRGVVEVA-------------TKGHAVSRGYAKLRWLVERGYVKPSGKVVDLGCGRGG 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 2611 WSYYCATLKQVQEVRGFTKGGEGHEEPKMVQSYGWNIVTLKSGVDVFHRPAEMGDTILCDIGESSATPEIEEARTLRVLD 2690
Cdd:cd20761    68 WSQYAAGLPKVTEVRGYTLGGPGHEEPRLVQSYGWNLVRLKSGVDVFYRPPERCDTLLCDIGESSPSPEVEEERTLRVLD 147

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 700588962 2691 MIEPWLKNKP--EFCIKVLCPYRPKVIEKLSALQRQYGGGLLRVPLSRNSTHEMYWTSGTAGNIINAVNLTSKVLIHR 2766
Cdd:cd20761   148 LVEKWLERNPtaNFCIKVLCPYHPEVIELLERLQRKGGGGLVRVPLSRNSTHEMYFVSGARGNIVNSVNMTSRLLLNR 225
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1690-1835 1.79e-94

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 302.33  E-value: 1.79e-94
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  1690 KKKLTVLDLHPGAGKTRKVLPRLLQEALEKRLRTVVLAPTRVVAAEMAEALKGMPIRYQTSAVTASHQGNEIIDLMCHAT 1769
Cdd:pfam07652    1 KGTLTVLDLHPGAGKTRKVLPELVRECIDRRLRTLVLAPTRVVLAEMEEALRGLPIRYHTPAVSSEHTGREIVDVMCHAT 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 700588962  1770 FTSRLMQPHKVPNYNLYIMDEAHFTDPASIAARGFISTKVSLGEAAAVFMTATPPGSDNPFPASNA 1835
Cdd:pfam07652   81 FTQRLLSPVRVPNYEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFMTATPPGTSDPFPESNA 146
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1691-1841 1.44e-79

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: 259.79  E-value: 1.44e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 1691 KKLTVLDLHPGAGKTRKVLPRLLQEALEKRLRTVVLAPTRVVAAEMAEALKGMPIRYQTSAVTASHQGNEIIDLMCHATF 1770
Cdd:cd17931     1 GQLTVLDLHPGAGKTTRVLPQIIREAIKKRLRTLVLAPTRVVAAEMYEALRGLPIRYRTGAVKEEHGGNEIVDYMCHGTF 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 700588962 1771 TSRLMQPHKVPNYNLYIMDEAHFTDPASIAARGFISTKVSLGEAAAVFMTATPPGSDNPFPASNAPITDTE 1841
Cdd:cd17931    81 TCRLLSPKRVPNYNLIIMDEAHFTDPASIAARGYIHTRVEMGEAAVIFMTATPPGTVTPFPQSNHPIEDFE 151
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1837-1981 2.78e-70

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: 232.92  E-value: 2.78e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 1837 ITDTEAQIPDKAWSSGFDWITEYEGKTVWFVPSVRMGNEIAACLGKAKKKVIQLSRRTFNTEYPKCKQGDWDFVVTTDIS 1916
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWITIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEYPKIKTIDWDFVVTTDIS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 700588962 1917 EMGANFKATRVIDSRRAIKPSIMSDQEERVVLSGPLPISPASAAQRRGRIGRNPNQLGDEYVFSG 1981
Cdd:cd18806    81 EMGANFDADRVIDCRTCVKPTILFSGDFRVILTGPVPQTAASAAQRRGRTGRNPAQERDIYRFVG 145
flavi_E_stem TIGR04240
flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal ...
 698-794 1.13e-47

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: 166.27  E-value: 1.13e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962   698 GGAFSTTMKGAKRLAILGDAAWDFGSIGGVFNSMGKAVHQLFGGVFRTLFGGMSWLSRIFIGVLCVWIGINARDHTIAVS 777
Cdd:TIGR04240    1 GKAFELTMRGAERMAILGDAAWDFGSVGGVFTSIGKALHQVFGGAFRALFGGVSWITKILIGVLLIWLGLNSRNTTLSLT 80

                           90
                   ....*....|....*..
gi 700588962   778 MLAVGGVLLFLSVSVNA 794
Cdd:TIGR04240   81 FLAVGGILLFLTTGVGA 97
Flavi_E_C cd12149
Immunoglobulin-like domain III (C-terminal domain) of Flavivirus envelope glycoprotein E; The ...
 603-693 8.53e-44

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: 154.77  E-value: 8.53e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  603 SFKMEKSPADTGHGTVVLDISYQGSEAPCKVPIVITPNLAEIEPVGRLVSAHPVVTGKNVRTMIEVEPPYGDSYIIIGTG 682
Cdd:cd12149     1 KFSWKKEPADTGHGTVVMEVKYSGTDAPCRIPVRVVDSGSGGENVGRLITVNPIITNANSKVFIEVEPPFGDSYIVVGVG 80

                          90
                  ....*....|.
gi 700588962  683 DGKLKQHWYKK 693
Cdd:cd12149    81 DTRLKHQWFQK 91
Flavi_capsid pfam01003
Flavivirus capsid protein C; Flaviviruses are small enveloped viruses with virions comprised ...
 6-123 2.44e-34

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: 128.99  E-value: 2.44e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962     6 GKPGVGRVVNMLKRTATNAasPVRLAKRLLGEAFSGRGPLRVILAVIAFFRFTAIKMSPALLKKWGTVEKGAALAIMKSF 85
Cdd:pfam01003    1 GKPGKGRGVNMLKRGAKRV--PLKKTKRKTGQLLDGRGPLRLVLAFLAFFRFTAIAPTPGLKKRWRTVPKRQAIKHLRKF 78

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 700588962    86 KKEIGNMLDTVSRRKTKGKKKRSSESSA-MLILMVASMA 123
Cdd:pfam01003   79 KKEVGTLLDGLNRRGKRRSKRGGWTGLLlMLGLLTLVLA 117
Flavi_NS4A pfam01350
Flavivirus non-structural protein NS4A; Flaviviruses encode a single polyprotein. This is ...
 2132-2270 1.73e-33

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: 127.71  E-value: 1.73e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  2132 VGKLPEHLGARLKDSIDVLYLAFTAEAGSRPHREAMHELPAALETILVFALLMALTGTTFFLLMRHKGINKMGYGMIVMT 2211
Cdd:pfam01350    6 IGELPDFLAKKAGEALDNISMFHHSEEGGKAYRHALEELPDAIEILMLFALAALLTGGMTIFFLSGKGIGKMSIALGCMA 85

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 700588962  2212 AVGGLLWYGNIQAPKIAGILLLTFLLMVVLIPEPEKQRSIQDNQLALAVLGCLVFLGTV 2270
Cdd:pfam01350   86 ACGALLFLAGVEPHHIAASIIIEFFLMVLLIPEPDQQRSIQDNQLAYLIIGILFLISAL 144
Flavi_M cd17038
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with a ...
 218-292 2.22e-33

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: 124.67  E-value: 2.22e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 700588962  218 STAFPQHTESTLATRRESWLNTDVAMKHLVKVETWALRNPGFAFVAITLGWMLGNSTSQKIIFTLLLLLVAPAYS 292
Cdd:cd17038     1 SVAIPPHGTGGLTTRKETWLSTSNGKEHLTRVERWVLRNPGYALAAVALAWMLGSSTTQRVIIIVLLLLVAPAYA 75
Flavi_glycop_C pfam02832
Flavivirus glycoprotein, immunoglobulin-like domain;
596-692 5.40e-33

Flavivirus glycoprotein, immunoglobulin-like domain;


Pssm-ID: 280922  Cd Length: 97  Bit Score: 124.38  E-value: 5.40e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962   596 TYAQCTGSFKMEKSPADTGHGTVVLDISYQGSEAPCKVPIVITPNLAEIEPVGRLVSAHPVVTGKNVRTMIEVEPPYGDS 675
Cdd:pfam02832    1 SYKICTDKFFFEKEPADTGHGTVLMQVKVEGKDAPCKIPVFSADDEKAAINKGILITANPIASDKDDEVLIEAEPPFGDS 80

                           90
                   ....*....|....*..
gi 700588962   676 YIIIGTGDGKLKQHWYK 692
Cdd:pfam02832   81 YIIVGAGDKALKLQWFK 97
Peptidase_S7 pfam00949
Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that ...
 1522-1670 1.12e-31

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: 121.78  E-value: 1.12e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  1522 TENGVYRIFANRLFGRVQVGVGVMQDGVFHTMWHVTRGAALRSGDGRLDPYWGDVRKDLISYGGPWKLEGKWDGtsevql 1601
Cdd:pfam00949    1 LTDGILRFFQSSLLGRSQRGVGVLQEGVFHTMWHPTRGTKLHTQGIKTSPSWASVKQDLVDYGGSWKFQGKWLG------ 74

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  1602 vavapkEKVKNVqttpgvfktpNGEVGAITLDFPAGSSGSPIINKNGEVIGLYGNGLMMGD-AYASAIAQ 1670
Cdd:pfam00949   75 ------EEYQQY----------GYGLGITDLNLSSGSSGSLVLNQNKQIVGIYFATVEVDDnSFVVGLAQ 128
Flavi_NS2A pfam01005
Flavivirus non-structural protein NS2A; NS2A is a hydrophobic protein about 25 kDa is size. ...
 1158-1339 1.48e-23

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: 101.46  E-value: 1.48e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  1158 GLLVAMLVTQEGLRKRWATRHIVVASLAMLAAMITGNITYMDLGRYIILLGATFAEMNSGGDIM-----HLALVAVFKVQ 1232
Cdd:pfam01005    1 GLLCIMIAIEEVLRKRQGPKMLLTGGLALFGALLMGQLTLLDLIKLCIAVGLHFHEMANAGDAMgmgttYLALIAAFRIR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  1233 PGFLVGFLLKRRWTPRESMLLAISACF----------------------MHLVFSDFQTD-LTSLAHNFSLALLVLRAVI 1289
Cdd:pfam01005   81 PGFAIGFGFRRLTSPRERLLLTLGAALvasvelpnsleeiadggamgimMLKLLTDFQSHgLWATLLALSFCILTFNAHA 160

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 700588962  1290 QTDVSSVTLPVLSMMAPAFQFSVLGTFRMAVAIYVVANLMLSRKNDAVKK 1339
Cdd:pfam01005  161 ARKAMAMILPIMALFTPLCLAEVRLAAMFFCAVVIIGVLHQNFKDTSMQK 210
Flavi_M pfam01004
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with virions ...
 220-292 5.79e-23

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: 94.96  E-value: 5.79e-23
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 700588962   220 AFPQHTESTLATRRESWLNTDVAMKHLVKVETWALRNPGFAFVAITLGWMLGNSTSQKIIFTLLLLLVAPAYS 292
Cdd:pfam01004    2 ALPPHVGLGLETRTETWMSSRGAWKQLQKVETWALRNPGFTVIALFIAHLIGSSITQKVIIFILLLLVTPAYS 74
FtsJ pfam01728
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...
 2579-2744 6.08e-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: 92.65  E-value: 6.08e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  2579 VSRGSAKLRWMVER-GAVRPTGRVIDLGCGRGGWSYYCATLKqVQEVRGFTKGGEGHEEPKM---VQSYGWNI---VTLK 2651
Cdd:pfam01728    2 RSRAAYKLLEIDEKfGLLKPGKTVLDLGAAPGGWSQVALQRG-AGKVVGVDLGPMQLWKPRNdpgVTFIQGDIrdpETLD 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  2652 SGVDVFHRPAemgDTILCDIGES-SATPEIEEARTLR----VLDMIEPWLKNKPEFCIKVLCpyRPKVIEKLSALQRQYG 2726
Cdd:pfam01728   81 LLEELLGRKV---DLVLSDGSPFiSGNKVLDHLRSLDlvkaALEVALELLRKGGNFVCKVFQ--GEDFSELLYLLKLGFE 155

                          170
                   ....*....|....*....
gi 700588962  2727 GGLLRVP-LSRNSTHEMYW 2744
Cdd:pfam01728  156 KVGVFKPpASRPESSEEYL 174
DEXDc smart00487
DEAD-like helicases superfamily;
1694-1825 1.81e-07

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 54.42  E-value: 1.81e-07
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962   1694 TVLDLHPGAGKTRkVLPRLLQEAL--EKRLRTVVLAPTRV----VAAEMAEALKGMPIR--YQTSAVTASHQGNEIIDLM 1765
Cdd:smart00487   27 VILAAPTGSGKTL-AALLPALEALkrGKGGRVLVLVPTRElaeqWAEELKKLGPSLGLKvvGLYGGDSKREQLRKLESGK 105

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 700588962   1766 CHATFTS--RLMQ-----PHKVPNYNLYIMDEAHFTDPASiaARGFISTKVSLGEAAA--VFMTATPPG 1825
Cdd:smart00487  106 TDILVTTpgRLLDllendKLSLSNVDLVILDEAHRLLDGG--FGDQLEKLLKLLPKNVqlLLLSATPPE 172
Cfa COG2230
Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport ...
 2584-2628 1.58e-05

Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport and metabolism];


Pssm-ID: 441831 [Multi-domain]  Cd Length: 158  Bit Score: 47.62  E-value: 1.58e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 700588962 2584 AKLRWMVERGAVRPTGRVIDLGCGRGGWSYYCATLKQVQeVRGFT 2628
Cdd:COG2230    38 AKLDLILRKLGLKPGMRVLDIGCGWGGLALYLARRYGVR-VTGVT 81
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
1700-1828 1.12e-04

Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 48.10  E-value: 1.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 1700 PGAGKTRkVLPRLLQEALEKRlRTVVLAPTRVVAAEMAEALKGmpIRYQTSAVTASHQGNEIIDLMCHATFTSRLMQPHK 1779
Cdd:COG1061   109 TGTGKTV-LALALAAELLRGK-RVLVLVPRRELLEQWAEELRR--FLGDPLAGGGKKDSDAPITVATYQSLARRAHLDEL 184

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 700588962 1780 VPNYNLYIMDEAHFTdPASI---AARGFISTKVsLGeaaavfMTATPPGSDN 1828
Cdd:COG1061   185 GDRFGLVIIDEAHHA-GAPSyrrILEAFPAAYR-LG------LTATPFRSDG 228
HELICc smart00490
helicase superfamily c-terminal domain;
1875-1968 1.20e-04

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 42.97  E-value: 1.20e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962   1875 EIAACLGKAKKKVIQLSRRTFNTE----YPKCKQGDWDFVVTTDISEMGANFK-ATRVIDSRraikpsimsdqeervvls 1949
Cdd:smart00490    2 ELAELLKELGIKVARLHGGLSQEEreeiLDKFNNGKIKVLVATDVAERGLDLPgVDLVIIYD------------------ 63

                            90
                    ....*....|....*....
gi 700588962   1950 gpLPISPASAAQRRGRIGR 1968
Cdd:smart00490   64 --LPWSPASYIQRIGRAGR 80
 
Name Accession Description Interval E-value
Flavivirus_RdRp cd23204
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within ...
 2844-3411 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: 1293.29  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 2844 MINQVVKMVSKPWDALNSVTSISMTDTTPFGQQRVFKEKVDTKAPEPPRGVAEAMDMVADWVWMILSRKKKPRLCTREEF 2923
Cdd:cd23204     1 MVNGVVKLLSKPWDVIEMVTQMAMTDTTPFGQQRVFKEKVDTKAPEPPEGTRKIMRIVNEWLWKFLARKKKPRLCTREEF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 2924 KAKVNGHAAMGAVFEEEQQWQTAREAVEDPEFWDLVDKERALHLEGRCETCVYNMMGKREKKLGEFGKAKGSRAIWYMWL 3003
Cdd:cd23204    81 IAKVRSNAALGAVFEEQNQWKSAREAVEDPRFWELVDEERELHLEGKCETCVYNMMGKREKKLGEFGKAKGSRAIWYMWL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3004 GARFLEFEALGFLNEDHWLSRENSYAGVEGLGLQRLGYVLRDISYRPGGKMYADDTAGWDTRITEKDLENEAKITEKMEG 3083
Cdd:cd23204   161 GARFLEFEALGFLNEDHWASRENSGGGVEGIGLQYLGYILREISKKPGGKMYADDTAGWDTRITEADLEDEEKILEYMEG 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3084 EHKKLAKAIIELTYKHKVVKVMRPGPGGKTFMDVISREDQRGSGQVVTYALNTYTNMVAQLIRCAEAEGVLTPDMRErsl 3163
Cdd:cd23204   241 EHRKLAEAIFELTYQNKVVKVMRPGPGGGTVMDVISRRDQRGSGQVVTYALNTFTNMKVQLIRMMEGEGVITPEDLE--- 317

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3164 TKQERYALTLWLDMEGVKRLKKMAISGDDCVVKSEDERFATALYFLNAMAKVRKDIQEWKPSSGWLDWQEVPFCSHHFKE 3243
Cdd:cd23204   318 TAPRLKRVEDWLEENGEERLSRMAVSGDDCVVKPIDDRFATALTFLNDMGKVRKDIQEWEPSKGWNDWEEVPFCSHHFHE 397

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3244 LQLKDGRSIVVPCRHQDELVGRARVSPGAAWGVRESAGLAKAYAQMWKLMYFHRRDLRLMANAICSAVPKDWVPTGRTTW 3323
Cdd:cd23204   398 LIMKDGRTLVVPCRDQDELIGRARVSPGAGWSLRETACLSKAYAQMWLLMYFHRRDLRLMANAICSAVPVDWVPTGRTTW 477

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3324 SIHGKGEWMTNEDMLEVWNRVWIRENPYMTDKTEVHDWKEIPYLGKREDQWCGSLIGSRARATWAENIWVAVNQVRAKIG 3403
Cdd:cd23204   478 SIHAKGEWMTTEDMLEVWNRVWIEDNPWMEDKTPVTSWRDVPYLGKREDQWCGSLIGLRSRATWAKNIQTAVNQVRSLIG 557


                  ....*...
gi 700588962 3404 KEEYLDYL 3411
Cdd:cd23204   558 NEEYRDYL 565
Flavi_NS5 pfam00972
Flavivirus RNA-directed RNA polymerase, fingers and palm domains; Flaviviruses produce a large ...
 2776-3228 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: 782.21  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  2776 YEKDVNLGSGTRAVTVKRKAPDMEKIGPRIKKLREEHSSSWCYDEMNPYRTWNYHGSYEVKPTGSASSMINQVVKMVSKP 2855
Cdd:pfam00972    2 YEADVILGIGTRSVATDKEPLNKEIIGERIERIKNEHMTTWFYDEDNPYRTWAYHGSYETKTSGSASSMVNGVVRLLTKP 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  2856 WDALNSVTSISMTDTTPFGQQRVFKEKVDTKAPEPPRGVAEAMDMVADWVWMILSRKKKPRLCTREEFKAKVNGHAAMGA 2935
Cdd:pfam00972   82 WDVIEEVTRIAMTDTTPFGQQRVFKEKVDTRAPDPPAGTRQIMKVVNRWLWRHLAREKNPRLCTKEEFIAKVRSNAAIGA 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  2936 VFEEEQQWQTAREAVEDPEFWDLVDKERALHLEGRCETCVYNMMGKREKKLGEFGKAKGSRAIWYMWLGARFLEFEALGF 3015
Cdd:pfam00972  162 YFEEEEQWKTANEAVQDPRFWELVDRERELHQQGRCRTCVYNMMGKREKKLGEFGKAKGSRAIWYMWLGARFLEFEALGF 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  3016 LNEDHWLSRENSYAGVEGLGLQRLGYVLRDISYRPGGKMYADDTAGWDTRITEKDLENEAKITEKMEGEHKKLAKAIIEL 3095
Cdd:pfam00972  242 LNEDHWASRENSGGGVEGIGLQYLGYILRDLAAMPGGGMYADDTAGWDTRITEADLDNEAEITNYMEPHHKKLAQAVMKM 321

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  3096 TYKHKVVKVMRPGPGGKTFMDVISREDQRGSGQVVTYALNTYTNMVAQLIRCAEAEGVLTPDMRErSLTKQERyaLTLWL 3175
Cdd:pfam00972  322 TYQNKVVKVLRPAPGGKTVMDVISRRDQRGSGQVVTYALNTFTNLKVQLIRMMEAEMVIHHQHLQ-DCDESER--VEAWL 398

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 700588962  3176 DMEGVKRLKKMAISGDDCVVKSEDERFATALYFLNAMAKVRKDIQEWKPSSGW 3228
Cdd:pfam00972  399 TEHGCDRLKRMAVSGDDCVVKPIDDRFALALSHLNDMGKVRKDISEWQPSKGW 451
Flavi_NS1 pfam00948
Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the ...
 797-1149 5.11e-160

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: 499.57  E-value: 5.11e-160
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962   797 GCAVDIERRELKCGTGIFIMDDVESWRDEYSFHPSSPKKLAASIVEAVESGTCGIRTVNRMEHKMWESIENELNAILEEN 876
Cdd:pfam00948    2 GCAINFGGRELKCGDGIFIFNDSDDWLEKYKFQADDPKKLAAAIGAAFEEGKCGINSADRLEHEMWKQIADEINAIFEEN 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962   877 EQDITVVVKDLENPAPKGFKRL---PL--VEKELKYGWKKWGATFFKHPERKNTTFLVDGPSGPECPNSQRAWNSFHVED 951
Cdd:pfam00948   82 DMDFSVVVGDPKGILAQGKKMIrphPFehIRDGLKYGWKSWGKAKIFGADRKNGSFIIDGKNRKECPDNNRAWNIFEIED 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962   952 FGFGVFKTSVWMELNDQVTEVCDTKMIGTGIKNNKAVHSDLGYWIESR-KNHSWEISRARLIETKSCIWPRSHTLWSDGV 1030
Cdd:pfam00948  162 FGFGIFTTNIWLDARDEYTIDCDGRILGAAIKDKKAAHADMGFWIESHeKNETWKIARAEAIDVKECEWPKSHTIWGNGV 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  1031 EETQLIIPKSLGGPRSRHNMRNGYKTQVNGPWNLIPLDIKFEECPGTSVTVTQNCGGRGPSARSTTASGKIIAEWCCKDC 1110
Cdd:pfam00948  242 EESEMFIPKIIGGPISQHNHIPGYFTQTAGPWHLGKLELDFDACEGTSVIIDEHCDGRGKSLRSTTDSGKTIHEWCCRSC 321

                          330       340       350
                   ....*....|....*....|....*....|....*....
gi 700588962  1111 VLPPLTFRHGETCWYGMEIRPMKEKEENLVKSKVSAGDG 1149
Cdd:pfam00948  322 TLPPLRFHGEDGCWYGMEIRPRKEHEEHLVKSMVSAGEG 360
capping_2-OMTase_Flaviviridae cd20761
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific ...
 2531-2766 2.34e-125

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: 393.90  E-value: 2.34e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 2531 TLGEKWKHMLNSMDKYEFSRYKVNGIFEVDreparmalanglvTGGHAVSRGSAKLRWMVERGAVRPTGRVIDLGCGRGG 2610
Cdd:cd20761     1 TLGEKWKDRLNALSKEEFDAYKKRGVVEVA-------------TKGHAVSRGYAKLRWLVERGYVKPSGKVVDLGCGRGG 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 2611 WSYYCATLKQVQEVRGFTKGGEGHEEPKMVQSYGWNIVTLKSGVDVFHRPAEMGDTILCDIGESSATPEIEEARTLRVLD 2690
Cdd:cd20761    68 WSQYAAGLPKVTEVRGYTLGGPGHEEPRLVQSYGWNLVRLKSGVDVFYRPPERCDTLLCDIGESSPSPEVEEERTLRVLD 147

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 700588962 2691 MIEPWLKNKP--EFCIKVLCPYRPKVIEKLSALQRQYGGGLLRVPLSRNSTHEMYWTSGTAGNIINAVNLTSKVLIHR 2766
Cdd:cd20761   148 LVEKWLERNPtaNFCIKVLCPYHPEVIELLERLQRKGGGGLVRVPLSRNSTHEMYFVSGARGNIVNSVNMTSRLLLNR 225
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1690-1835 1.79e-94

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 302.33  E-value: 1.79e-94
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  1690 KKKLTVLDLHPGAGKTRKVLPRLLQEALEKRLRTVVLAPTRVVAAEMAEALKGMPIRYQTSAVTASHQGNEIIDLMCHAT 1769
Cdd:pfam07652    1 KGTLTVLDLHPGAGKTRKVLPELVRECIDRRLRTLVLAPTRVVLAEMEEALRGLPIRYHTPAVSSEHTGREIVDVMCHAT 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 700588962  1770 FTSRLMQPHKVPNYNLYIMDEAHFTDPASIAARGFISTKVSLGEAAAVFMTATPPGSDNPFPASNA 1835
Cdd:pfam07652   81 FTQRLLSPVRVPNYEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFMTATPPGTSDPFPESNA 146
Flavi_NS5_thumb pfam20483
Flavivirus RNA-directed RNA polymerase, thumb domain; Flaviviruses produce a large polyprotein ...
 3232-3395 1.59e-87

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: 283.22  E-value: 1.59e-87
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  3232 QEVPFCSHHFKELQLKDGRSIVVPCRHQDELVGRARVSPGAAWGVRESAGLAKAYAQMWKLMYFHRRDLRLMANAICSAV 3311
Cdd:pfam20483    1 EEVDFCSHHYEKLTFKDGRTIVVPTRDQDEIIAKSRIRPGGDWSLDETAWLSKAYANMWLVNYFHLRTARALGFAYKSAV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  3312 PKDWVPTGRTTWSIHGKGEWMTNEDMLEVWNRVWIRENPYMTDKTEVHDWKEIPYLGKREDQWCGSLIGSRARATWAENI 3391
Cdd:pfam20483   81 PPNWVPTGRTTGSIHRPGPWMTPEDMLDVWNRVWFGESTHMPDGFRVRSWRHVGYLKKREEKLYDSLIGLRNRAYWRSNL 160


                   ....
gi 700588962  3392 WVAV 3395
Cdd:pfam20483  161 HLDV 164
ps-ssRNAv_Flaviviridae_RdRp cd23178
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ...
 2974-3293 2.57e-84

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: 279.02  E-value: 2.57e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 2974 CVYNMMGKREKKLGEFGK--AKGSRAIWYMWLGARFLEFEALGFLNEDHWLSRENSYAGVEGLGLQRlGYVLRDISYRP- 3050
Cdd:cd23178     1 IPTTIMPKNEVFCVEPGKggRKPPRLIVYPDLGVRVAEKMALYDPVEVLPQVVGGSYYGFQYSPNQR-VEILRKAWKSKk 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3051 GGKMYADDTAGWDTRITEKDLENEAKITEKME-GEHKKLAKAIIELTYKHKVVKVMRpgpggktfMDVISREDQRGSGQV 3129
Cdd:cd23178    80 GPMAYSYDTRCFDSTVTEDDIQVEEEIYQACSlKEARQAIVSITERLYVEGPMVNSD--------GQICGRRRCRASGVL 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3130 VTYALNTYTNMVAQLIRCAEAEgvltpdmrersltkqeryaltlwldmegvKRLKKMAISGDDCVVKSEDE-------RF 3202
Cdd:cd23178   152 TTSAGNT*TCYLK*LAACREAG-----------------------------IRLPTMLVCGDDCVVICESDgtqedaaLL 202

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3203 ATALYFLNAMAKVRKDiqewkPSSGWLDWQEVPFCSHHFKELQLKDGRSIVVPCRHQDELVGRARVSPGAAwgvrESAGL 3282
Cdd:cd23178   203 AAFTEALTRYGKPPKD-----PPQPEYDLELIESCSHTVSEVRMKDGRRLYYLTRDPTTPLARAAWETGRH----EPINS 273

                         330
                  ....*....|.
gi 700588962 3283 AKAYAQMWKLM 3293
Cdd:cd23178   274 WLGYIIMYALT 284
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1691-1841 1.44e-79

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: 259.79  E-value: 1.44e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 1691 KKLTVLDLHPGAGKTRKVLPRLLQEALEKRLRTVVLAPTRVVAAEMAEALKGMPIRYQTSAVTASHQGNEIIDLMCHATF 1770
Cdd:cd17931     1 GQLTVLDLHPGAGKTTRVLPQIIREAIKKRLRTLVLAPTRVVAAEMYEALRGLPIRYRTGAVKEEHGGNEIVDYMCHGTF 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 700588962 1771 TSRLMQPHKVPNYNLYIMDEAHFTDPASIAARGFISTKVSLGEAAAVFMTATPPGSDNPFPASNAPITDTE 1841
Cdd:cd17931    81 TCRLLSPKRVPNYNLIIMDEAHFTDPASIAARGYIHTRVEMGEAAVIFMTATPPGTVTPFPQSNHPIEDFE 151
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1837-1981 2.78e-70

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: 232.92  E-value: 2.78e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 1837 ITDTEAQIPDKAWSSGFDWITEYEGKTVWFVPSVRMGNEIAACLGKAKKKVIQLSRRTFNTEYPKCKQGDWDFVVTTDIS 1916
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWITIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEYPKIKTIDWDFVVTTDIS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 700588962 1917 EMGANFKATRVIDSRRAIKPSIMSDQEERVVLSGPLPISPASAAQRRGRIGRNPNQLGDEYVFSG 1981
Cdd:cd18806    81 EMGANFDADRVIDCRTCVKPTILFSGDFRVILTGPVPQTAASAAQRRGRTGRNPAQERDIYRFVG 145
flavi_E_stem TIGR04240
flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal ...
 698-794 1.13e-47

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: 166.27  E-value: 1.13e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962   698 GGAFSTTMKGAKRLAILGDAAWDFGSIGGVFNSMGKAVHQLFGGVFRTLFGGMSWLSRIFIGVLCVWIGINARDHTIAVS 777
Cdd:TIGR04240    1 GKAFELTMRGAERMAILGDAAWDFGSVGGVFTSIGKALHQVFGGAFRALFGGVSWITKILIGVLLIWLGLNSRNTTLSLT 80

                           90
                   ....*....|....*..
gi 700588962   778 MLAVGGVLLFLSVSVNA 794
Cdd:TIGR04240   81 FLAVGGILLFLTTGVGA 97
Flavi_E_C cd12149
Immunoglobulin-like domain III (C-terminal domain) of Flavivirus envelope glycoprotein E; The ...
 603-693 8.53e-44

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: 154.77  E-value: 8.53e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  603 SFKMEKSPADTGHGTVVLDISYQGSEAPCKVPIVITPNLAEIEPVGRLVSAHPVVTGKNVRTMIEVEPPYGDSYIIIGTG 682
Cdd:cd12149     1 KFSWKKEPADTGHGTVVMEVKYSGTDAPCRIPVRVVDSGSGGENVGRLITVNPIITNANSKVFIEVEPPFGDSYIVVGVG 80

                          90
                  ....*....|.
gi 700588962  683 DGKLKQHWYKK 693
Cdd:cd12149    81 DTRLKHQWFQK 91
Flavi_capsid pfam01003
Flavivirus capsid protein C; Flaviviruses are small enveloped viruses with virions comprised ...
 6-123 2.44e-34

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: 128.99  E-value: 2.44e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962     6 GKPGVGRVVNMLKRTATNAasPVRLAKRLLGEAFSGRGPLRVILAVIAFFRFTAIKMSPALLKKWGTVEKGAALAIMKSF 85
Cdd:pfam01003    1 GKPGKGRGVNMLKRGAKRV--PLKKTKRKTGQLLDGRGPLRLVLAFLAFFRFTAIAPTPGLKKRWRTVPKRQAIKHLRKF 78

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 700588962    86 KKEIGNMLDTVSRRKTKGKKKRSSESSA-MLILMVASMA 123
Cdd:pfam01003   79 KKEVGTLLDGLNRRGKRRSKRGGWTGLLlMLGLLTLVLA 117
Flavi_NS4A pfam01350
Flavivirus non-structural protein NS4A; Flaviviruses encode a single polyprotein. This is ...
 2132-2270 1.73e-33

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: 127.71  E-value: 1.73e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  2132 VGKLPEHLGARLKDSIDVLYLAFTAEAGSRPHREAMHELPAALETILVFALLMALTGTTFFLLMRHKGINKMGYGMIVMT 2211
Cdd:pfam01350    6 IGELPDFLAKKAGEALDNISMFHHSEEGGKAYRHALEELPDAIEILMLFALAALLTGGMTIFFLSGKGIGKMSIALGCMA 85

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 700588962  2212 AVGGLLWYGNIQAPKIAGILLLTFLLMVVLIPEPEKQRSIQDNQLALAVLGCLVFLGTV 2270
Cdd:pfam01350   86 ACGALLFLAGVEPHHIAASIIIEFFLMVLLIPEPDQQRSIQDNQLAYLIIGILFLISAL 144
Flavi_M cd17038
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with a ...
 218-292 2.22e-33

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: 124.67  E-value: 2.22e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 700588962  218 STAFPQHTESTLATRRESWLNTDVAMKHLVKVETWALRNPGFAFVAITLGWMLGNSTSQKIIFTLLLLLVAPAYS 292
Cdd:cd17038     1 SVAIPPHGTGGLTTRKETWLSTSNGKEHLTRVERWVLRNPGYALAAVALAWMLGSSTTQRVIIIVLLLLVAPAYA 75
Flavi_glycop_C pfam02832
Flavivirus glycoprotein, immunoglobulin-like domain;
596-692 5.40e-33

Flavivirus glycoprotein, immunoglobulin-like domain;


Pssm-ID: 280922  Cd Length: 97  Bit Score: 124.38  E-value: 5.40e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962   596 TYAQCTGSFKMEKSPADTGHGTVVLDISYQGSEAPCKVPIVITPNLAEIEPVGRLVSAHPVVTGKNVRTMIEVEPPYGDS 675
Cdd:pfam02832    1 SYKICTDKFFFEKEPADTGHGTVLMQVKVEGKDAPCKIPVFSADDEKAAINKGILITANPIASDKDDEVLIEAEPPFGDS 80

                           90
                   ....*....|....*..
gi 700588962   676 YIIIGTGDGKLKQHWYK 692
Cdd:pfam02832   81 YIIVGAGDKALKLQWFK 97
Peptidase_S7 pfam00949
Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that ...
 1522-1670 1.12e-31

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: 121.78  E-value: 1.12e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  1522 TENGVYRIFANRLFGRVQVGVGVMQDGVFHTMWHVTRGAALRSGDGRLDPYWGDVRKDLISYGGPWKLEGKWDGtsevql 1601
Cdd:pfam00949    1 LTDGILRFFQSSLLGRSQRGVGVLQEGVFHTMWHPTRGTKLHTQGIKTSPSWASVKQDLVDYGGSWKFQGKWLG------ 74

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  1602 vavapkEKVKNVqttpgvfktpNGEVGAITLDFPAGSSGSPIINKNGEVIGLYGNGLMMGD-AYASAIAQ 1670
Cdd:pfam00949   75 ------EEYQQY----------GYGLGITDLNLSSGSSGSLVLNQNKQIVGIYFATVEVDDnSFVVGLAQ 128
Flavi_NS2A pfam01005
Flavivirus non-structural protein NS2A; NS2A is a hydrophobic protein about 25 kDa is size. ...
 1158-1339 1.48e-23

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: 101.46  E-value: 1.48e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  1158 GLLVAMLVTQEGLRKRWATRHIVVASLAMLAAMITGNITYMDLGRYIILLGATFAEMNSGGDIM-----HLALVAVFKVQ 1232
Cdd:pfam01005    1 GLLCIMIAIEEVLRKRQGPKMLLTGGLALFGALLMGQLTLLDLIKLCIAVGLHFHEMANAGDAMgmgttYLALIAAFRIR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  1233 PGFLVGFLLKRRWTPRESMLLAISACF----------------------MHLVFSDFQTD-LTSLAHNFSLALLVLRAVI 1289
Cdd:pfam01005   81 PGFAIGFGFRRLTSPRERLLLTLGAALvasvelpnsleeiadggamgimMLKLLTDFQSHgLWATLLALSFCILTFNAHA 160

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 700588962  1290 QTDVSSVTLPVLSMMAPAFQFSVLGTFRMAVAIYVVANLMLSRKNDAVKK 1339
Cdd:pfam01005  161 ARKAMAMILPIMALFTPLCLAEVRLAAMFFCAVVIIGVLHQNFKDTSMQK 210
Flavi_M pfam01004
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with virions ...
 220-292 5.79e-23

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: 94.96  E-value: 5.79e-23
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 700588962   220 AFPQHTESTLATRRESWLNTDVAMKHLVKVETWALRNPGFAFVAITLGWMLGNSTSQKIIFTLLLLLVAPAYS 292
Cdd:pfam01004    2 ALPPHVGLGLETRTETWMSSRGAWKQLQKVETWALRNPGFTVIALFIAHLIGSSITQKVIIFILLLLVTPAYS 74
FtsJ pfam01728
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...
 2579-2744 6.08e-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: 92.65  E-value: 6.08e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  2579 VSRGSAKLRWMVER-GAVRPTGRVIDLGCGRGGWSYYCATLKqVQEVRGFTKGGEGHEEPKM---VQSYGWNI---VTLK 2651
Cdd:pfam01728    2 RSRAAYKLLEIDEKfGLLKPGKTVLDLGAAPGGWSQVALQRG-AGKVVGVDLGPMQLWKPRNdpgVTFIQGDIrdpETLD 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962  2652 SGVDVFHRPAemgDTILCDIGES-SATPEIEEARTLR----VLDMIEPWLKNKPEFCIKVLCpyRPKVIEKLSALQRQYG 2726
Cdd:pfam01728   81 LLEELLGRKV---DLVLSDGSPFiSGNKVLDHLRSLDlvkaALEVALELLRKGGNFVCKVFQ--GEDFSELLYLLKLGFE 155

                          170
                   ....*....|....*....
gi 700588962  2727 GGLLRVP-LSRNSTHEMYW 2744
Cdd:pfam01728  156 KVGVFKPpASRPESSEEYL 174
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 1692-1822 5.55e-20

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: 89.00  E-value: 5.55e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 1692 KLTVLDLHPGAGKTRKVLPRLLQEALEKRLRTVVLAPTRVVAAEMAEALK-----GMPIRYQTSAVTASHQ-----GNEI 1761
Cdd:cd00046     2 ENVLITAPTGSGKTLAALLAALLLLLKKGKKVLVLVPTKALALQTAERLRelfgpGIRVAVLVGGSSAEEReknklGDAD 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 700588962 1762 IDLMCHATFTSRLMQ--PHKVPNYNLYIMDEAHFTDPASIAARGFIST--KVSLGEAAAVFMTAT 1822
Cdd:cd00046    82 IIIATPDMLLNLLLRedRLFLKDLKLIIVDEAHALLIDSRGALILDLAvrKAGLKNAQVILLSAT 146
capping_2-OMTase_viral cd20754
viral Cap-0 specific (nucleoside-2'-O-)-methyltransferase; Cap-0 specific (nucleoside-2'-O-) ...
 2584-2743 1.23e-14

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: 74.79  E-value: 1.23e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 2584 AKLRWMVERGAVRPT-GRVIDLGCGRGGWSYYCATLKQVQEVRGFTkggegheePKMVQSYGWNIVTLKSGvDVFHR--- 2659
Cdd:cd20754     2 AKLLQLEEYFLYKPEkMRVIYIGCAPGGWLYYLRDWFEGTLWVGFD--------PRDTDPLGYNNVITVNK-FFDHEhtk 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 2660 ---PAEMGDTILCDIGE--SSATPEiEEARTLRVLDMIEPWLKNKPE----FCIKVLCPYrpkviekLSALQRQYGGGLL 2730
Cdd:cd20754    73 lkfLPNKKDLLICDIRSdrSSHVTK-EEDTTESFLTLQEGYIATKLAkvgsICVKVRAPD-------LKDDGHFSSGTLF 144

                         170
                  ....*....|...
gi 700588962 2731 RVPLsRNSTHEMY 2743
Cdd:cd20754   145 PQPY-AASSSEMR 156
DEXHc_RHA-like cd17917
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ...
 1694-1823 1.67e-13

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: 70.95  E-value: 1.67e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 1694 TVLDLHPGAGKTRKVLPRLLQEALEK--RLRTVVLAPTRV--------VAAEMAEALkGMPIRYQT---SAVTAshqgNE 1760
Cdd:cd17917     4 VVIVGETGSGKTTQVPQFLLEDGLAKggKGRIVCTQPRRIaaisvaerVAEERGEKL-GEEVGYQIrfeSKTSS----KT 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 700588962 1761 IIDLMCHATFTSRLMQPHKVPNYNLYIMDEAHFTDPASIAARGFISTKVSLGEAA-AVFMTATP 1823
Cdd:cd17917    79 RIKFCTDGILLRELLSDPLLSGYSHVILDEAHERSLDTDFLLGLLKDLLRKRPDLkVILMSATL 142
DEXDc smart00487
DEAD-like helicases superfamily;
1694-1825 1.81e-07

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 54.42  E-value: 1.81e-07
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962   1694 TVLDLHPGAGKTRkVLPRLLQEAL--EKRLRTVVLAPTRV----VAAEMAEALKGMPIR--YQTSAVTASHQGNEIIDLM 1765
Cdd:smart00487   27 VILAAPTGSGKTL-AALLPALEALkrGKGGRVLVLVPTRElaeqWAEELKKLGPSLGLKvvGLYGGDSKREQLRKLESGK 105

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 700588962   1766 CHATFTS--RLMQ-----PHKVPNYNLYIMDEAHFTDPASiaARGFISTKVSLGEAAA--VFMTATPPG 1825
Cdd:smart00487  106 TDILVTTpgRLLDllendKLSLSNVDLVILDEAHRLLDGG--FGDQLEKLLKLLPKNVqlLLLSATPPE 172
Cfa COG2230
Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport ...
 2584-2628 1.58e-05

Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport and metabolism];


Pssm-ID: 441831 [Multi-domain]  Cd Length: 158  Bit Score: 47.62  E-value: 1.58e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 700588962 2584 AKLRWMVERGAVRPTGRVIDLGCGRGGWSYYCATLKQVQeVRGFT 2628
Cdd:COG2230    38 AKLDLILRKLGLKPGMRVLDIGCGWGGLALYLARRYGVR-VTGVT 81
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
1700-1828 1.12e-04

Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 48.10  E-value: 1.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 1700 PGAGKTRkVLPRLLQEALEKRlRTVVLAPTRVVAAEMAEALKGmpIRYQTSAVTASHQGNEIIDLMCHATFTSRLMQPHK 1779
Cdd:COG1061   109 TGTGKTV-LALALAAELLRGK-RVLVLVPRRELLEQWAEELRR--FLGDPLAGGGKKDSDAPITVATYQSLARRAHLDEL 184

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 700588962 1780 VPNYNLYIMDEAHFTdPASI---AARGFISTKVsLGeaaavfMTATPPGSDN 1828
Cdd:COG1061   185 GDRFGLVIIDEAHHA-GAPSyrrILEAFPAAYR-LG------LTATPFRSDG 228
HELICc smart00490
helicase superfamily c-terminal domain;
1875-1968 1.20e-04

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 42.97  E-value: 1.20e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962   1875 EIAACLGKAKKKVIQLSRRTFNTE----YPKCKQGDWDFVVTTDISEMGANFK-ATRVIDSRraikpsimsdqeervvls 1949
Cdd:smart00490    2 ELAELLKELGIKVARLHGGLSQEEreeiLDKFNNGKIKVLVATDVAERGLDLPgVDLVIIYD------------------ 63

                            90
                    ....*....|....*....
gi 700588962   1950 gpLPISPASAAQRRGRIGR 1968
Cdd:smart00490   64 --LPWSPASYIQRIGRAGR 80
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 1695-1823 3.38e-04

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: 43.45  E-value: 3.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 1695 VLDLHPGAGKTrkVLPRLLQEALeKRLRTVVLAPTRVVAAEMAEALK----GMPIRYQTSAVTASHQGNEIIdlmcHATF 1770
Cdd:cd17926    22 ILVLPTGSGKT--LTALALIAYL-KELRTLIVVPTDALLDQWKERFEdflgDSSIGLIGGGKKKDFDDANVV----VATY 94

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 700588962 1771 TS--RLMQPHK--VPNYNLYIMDEAHftdpaSIAARGFISTKVSLGEAAAVFMTATP 1823
Cdd:cd17926    95 QSlsNLAEEEKdlFDQFGLLIVDEAH-----HLPAKTFSEILKELNAKYRLGLTATP 146
Pestivirus_RdRp cd23201
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Pestivirus, within ...
 3058-3294 1.47e-03

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Pestivirus, 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 Pestivirus genus within the family Flaviviridae, order Amarillovirales. Members of the genus Pestivirus infect pigs and ruminants, including cattle, sheep, goats and wild ruminants, and are transmitted through contact with infected secretions (respiratory droplets, urine or feces). Infections may be subclinical or cause enteric, hemorrhagic or wasting diseases, including those by the economically important bovine viral diarrhea virus and classical swine fever virus. Virions of Pestivirus have a single, small, basic capsid (C) protein and three 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. 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: 438051  Cd Length: 579  Bit Score: 44.24  E-value: 1.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3058 DTAGWDTRITEKDLENEAKITE---KmegehKKLAKAIIELTYKHKVVKVMrPGPGgktfmDVISREDQRGSGQVVTYAL 3134
Cdd:cd23201   249 DTKAWDTQVTSKDLRLIGEIQKyyyK-----KKWHKFIDTLTEHMVEVPVI-TADG-----EVYIRKGQRGSGQPDTSAG 317

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3135 NTYTNMVAQLIRCAEAEGVltpdmrersltkqeryaltlwlDMEGVKRLKKMAISGDDCVVKSED---ERFAT-ALYFLN 3210
Cdd:cd23201   318 NSMLNVLTMIYAFCEATGV----------------------PYKSFNRVAKIHVCGDDGFLITEKglgEKFASkGVQILH 375

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 3211 AMAKVRKDIQEWKPSSGwLDWQEVPFCSHHFKELQLKDGRSIVVPCRHQDELVGR--ARVSPGaawGVRESAGLAKAYAQ 3288
Cdd:cd23201   376 EAGKPQKITEGDKMKVA-YRFEDIEFCSHTPIPVRWSDNTSSYMPGRDTATILSKmaTRLDSS---GERGTEAYEKAVAF 451


                  ....*.
gi 700588962 3289 MWKLMY 3294
Cdd:cd23201   452 SFLLMY 457
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 1695-1792 3.00e-03

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


Pssm-ID: 438711 [Multi-domain]  Cd Length: 174  Bit Score: 41.55  E-value: 3.00e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 700588962 1695 VLDLHPGAGKTRKVLPRLLQEALEKRLRTVVLAPTRV----VAAEMAEALK-------GMPIRYQTSAVTASHqgneiID 1763
Cdd:cd17990    21 VLEAPPGAGKTTRVPLALLAELWIAGGKIIVLEPRRVaaraAARRLATLLGeapgetvGYRVRGESRVGRRTR-----VE 95

                          90       100
                  ....*....|....*....|....*....
gi 700588962 1764 LMCHATFTSRLMQPHKVPNYNLYIMDEAH 1792
Cdd:cd17990    96 VVTEGVLLRRLQRDPELSGVGAVILDEFH 124
 
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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