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Conserved domains on  [gi|3288890|gb|AAC35899|]
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polyprotein [Yellow fever 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 ...
 2827-3393 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: 1272.87  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  2827 MVNGVIKILTYPWDRIEEVTRMAMTDTTPFGQQRVFKEKVDTRAKDPPAGTRKIMKVVNRWLFRHLAREKNPRLCTKEEF 2906
Cdd:cd23204    1 MVNGVVKLLSKPWDVIEMVTQMAMTDTTPFGQQRVFKEKVDTKAPEPPEGTRKIMRIVNEWLWKFLARKKKPRLCTREEF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  2907 IAKVRSHAAIGAYLEEQEQWKTANEAVQDPKFWELVDEERKLHQQGRCRTCVYNMMGKREKKLSEFGKAKGSRAIWYMWL 2986
Cdd:cd23204   81 IAKVRSNAALGAVFEEQNQWKSAREAVEDPRFWELVDEERELHLEGKCETCVYNMMGKREKKLGEFGKAKGSRAIWYMWL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  2987 GARYLEFEALGFLNEDHWASRENSGGGVEGIGLQYLGYVIRDLAAMDGGGFYADDTAGWDTRITEADLDDEQEILNYMSP 3066
Cdd:cd23204  161 GARFLEFEALGFLNEDHWASRENSGGGVEGIGLQYLGYILREISKKPGGKMYADDTAGWDTRITEADLEDEEKILEYMEG 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  3067 HHKKLAQAVMEMTYKNKVVKVLRPAPGGKAYMDVISRRDQRGSGQVVTYALNTITNLKVQLIRMAEAEMVIHHQHVQdcD 3146
Cdd:cd23204  241 EHRKLAEAIFELTYQNKVVKVMRPGPGGGTVMDVISRRDQRGSGQVVTYALNTFTNMKVQLIRMMEGEGVITPEDLE--T 318

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  3147 ESVLTRLEAWLTEHGCNRLKRMAVSGDDCVVRPIDDRFGLALSHLNAMSKVRKDISEWQPSKGWNDWENVPFCSHHFHEL 3226
Cdd:cd23204  319 APRLKRVEDWLEENGEERLSRMAVSGDDCVVKPIDDRFATALTFLNDMGKVRKDIQEWEPSKGWNDWEEVPFCSHHFHEL 398

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  3227 QLKDGRRIVVPCREQDELIGRGRVSPGNGWMIKETACLSKAYANMWSLMYFHKRDMRLLSLAVSSAVPTSWVPQGRTTWS 3306
Cdd:cd23204  399 IMKDGRTLVVPCRDQDELIGRARVSPGAGWSLRETACLSKAYAQMWLLMYFHRRDLRLMANAICSAVPVDWVPTGRTTWS 478

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  3307 IHGKGEWMTTEDMLEVWNRVWITNNPHMQDKTMVKKWRDVPYLTKRQDKLCGSLIGMTNRATWASHIHLVIHRIRTLIGQ 3386
Cdd:cd23204  479 IHAKGEWMTTEDMLEVWNRVWIEDNPWMEDKTPVTSWRDVPYLGKREDQWCGSLIGLRSRATWAKNIQTAVNQVRSLIGN 558


                 ....*..
gi 3288890  3387 EKYTDYL 3393
Cdd:cd23204  559 EEYRDYL 565
Flavi_NS1 pfam00948
Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the ...
 780-1133 0e+00

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: 736.47  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     780 QGCAINFGKRELKCGDGIFIFRDSDDWLNKYSYYPEDPVKLASIVKASFEEGKCGLNSVDSLEHEMWRSRADEINAIFEE 859
Cdd:pfam00948    1 QGCAINFGGRELKCGDGIFIFNDSDDWLEKYKFQADDPKKLAAAIGAAFEEGKCGINSADRLEHEMWKQIADEINAIFEE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     860 NEVDISVVVQDPKNVYQRGT-----HPFSRIRDGLQYGWKTWGKNLVFSPGRKNGSFIIDGKSRKECPFSNRVWNSFQIE 934
Cdd:pfam00948   81 NDMDFSVVVGDPKGILAQGKkmirpHPFEHIRDGLKYGWKSWGKAKIFGADRKNGSFIIDGKNRKECPDNNRAWNIFEIE 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     935 EFGTGVFTTRVYMDAVFEYTIDCDGSILGAAVNGKKSAHGSPTFWMGSHEVNGTWMIHTLEALDYKECEWPLTHTI-GTS 1013
Cdd:pfam00948  161 DFGFGIFTTNIWLDARDEYTIDCDGRILGAAIKDKKAAHADMGFWIESHEKNETWKIARAEAIDVKECEWPKSHTIwGNG 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1014 VEESEMFMPRSIGGPVSSHNHIPGYKVQTNGPWMQVPLEVKREACPGTSVIIDGNCDGRGKSTRSTTDSGKVIPEWCCRS 1093
Cdd:pfam00948  241 VEESEMFIPKIIGGPISQHNHIPGYFTQTAGPWHLGKLELDFDACEGTSVIIDEHCDGRGKSLRSTTDSGKTIHEWCCRS 320

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|
gi 3288890    1094 CTMPPVSFHGSDGCWYPMEIRPRKTHESHLVRSWVTAGEI 1133
Cdd:pfam00948  321 CTLPPLRFHGEDGCWYGMEIRPRKEHEEHLVKSMVSAGEG 360
Flavi_glycoprot pfam00869
Flavivirus glycoprotein, central and dimerization domains;
287-579 0e+00

Flavivirus glycoprotein, central and dimerization domains;


:

Pssm-ID: 395698  Cd Length: 300  Bit Score: 585.10  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     287 HCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDRPAEVRKVCYNAVLTHVKINDKCPSTGEAH 366
Cdd:pfam00869    1 HCIGIGDRDFIEGLHGATWVDATLEHDKCVTTMAKDKPSLDIELEKTAIDNPAELRKLCIEAKISHTKIDDKCPSQGEAH 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     367 LAEENEGDNACKRTYSDRGWGNGCGLFGKGSIVACAKFTCAKSMSLFEVDQTKIQYVIRAQLHVGAKQENWTTDIK---T 443
Cdd:pfam00869   81 LAEENDGDFACKRTFSDRGHGNGCGLFGKGSIIACAKFKCAKKLEGFEVDQEKIKYSIIAQLHTGAKHENGNEDIEhgtI 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     444 LKFDALSGSQEVEFIGYGKATLECQVQTAVDFGNSYIAEMETESWIVDRQWAQDLTLPWQSG---SGGVWREMHHLVEFE 520
Cdd:pfam00869  161 AKFDALAGSQEIEFIDYGAATLDCQPQTALDFGEMVIAEMEKESWIVDKQWALDLPLPWQSGastSGETWNEMDHLVEFE 240

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     521 PPHAATIRVLALGNQEGSLKTALTGAMRV-TKDTNDNNLYKLHGGHVSCRVKLSALTLKG 579
Cdd:pfam00869  241 PAHAAKIEVLALGNQEGALHTALTGAMEIqTKDTNDNNLYKIFAGHLKCRLKLDALTLKG 300
Flavi_NS4B pfam01349
Flavivirus non-structural protein NS4B; Flaviviruses encode a single polyprotein. This is ...
 2257-2500 5.76e-142

Flavivirus non-structural protein NS4B; Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4B protein is small and poorly conserved among the Flaviviruses. NS4B contains multiple hydrophobic potential membrane spanning regions. NS4B may form membrane components of the viral replication complex and could be involved in membrane localization of NS3 and pfam00972.


:

Pssm-ID: 279665  Cd Length: 248  Bit Score: 442.93  E-value: 5.76e-142
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2257 NELGMLEKTKEDLFGKKNLIPSSASPWSWPDLDLKPGAAWTVYVGIVTMLSPMLHHWIKVEYGNLSLSGIAQSASVLSFM 2336
Cdd:pfam01349    1 NELGLLEKTKEDLFGIGHAAAENAHHAAMLDLDLHPAAAWTLYAGATTIISPMLHHTIENETANISLSAIANQAAILMFL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2337 DKGIPFMKMNISVIMLLVSGWNSITVMPLLCGIGCAMLHWSLILPGIKAQQSKLAQRRVFHGVAKNPVVDGNPTVDIEEA 2416
Cdd:pfam01349   81 DKGIPFMKMDIGVILLALGCWNQINPLPLLAAIFCAMAHWAIIGPGIKAKASKEAQKRTAAGIAENPTVDGIPAIDIDEA 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2417 PEMPALY----EKKLALYLLLALSLASVAMCRTPFSLAEGIVLASAASGPLIEGNTSLLWNGPMAVSMTGVMRGNHYAFV 2492
Cdd:pfam01349  161 PEMPALYdakfEKKLALILLLALCLAQIALCRTPFALAEGITLASAALGPLIEGNPGKFWNGPIAVSMAGIFRGNHLAFA 240


                   ....*...
gi 3288890    2493 GVMYNLWK 2500
Cdd:pfam01349  241 GLAFNLMK 248
capping_2-OMTase_Flaviviridae cd20761
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific ...
 2513-2743 9.23e-114

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: 360.77  E-value: 9.23e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  2513 TLGEVWKRELNLLDKRQFELYKRTDIVEVDrdtarrhlaegkvDTGVAVSRGTAKLRWFHERGYVKLEGRVIDLGCGRGG 2592
Cdd:cd20761    1 TLGEKWKDRLNALSKEEFDAYKKRGVVEVA-------------TKGHAVSRGYAKLRWLVERGYVKPSGKVVDLGCGRGG 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  2593 WCYYAAAQKEVSGVKGFTLGRDGHEKPMNVQSLGWNIITFKDKTDIHRLEPVKCDTLLCDIGESSSSSVTEGERTVRVLD 2672
Cdd:cd20761   68 WSQYAAGLPKVTEVRGYTLGGPGHEEPRLVQSYGWNLVRLKSGVDVFYRPPERCDTLLCDIGESSPSPEVEEERTLRVLD 147

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 3288890  2673 TVEKWLACGVD-NFCVKVLAPYMPDVLEKLELLQRRFGGTVIRNPLSRNSTHEMYYVSGARSNVTFTVNQTS 2743
Cdd:cd20761  148 LVEKWLERNPTaNFCIKVLCPYHPEVIELLERLQRKGGGGLVRVPLSRNSTHEMYFVSGARGNIVNSVNMTS 219
Flavi_NS2A pfam01005
Flavivirus non-structural protein NS2A; NS2A is a hydrophobic protein about 25 kDa is size. ...
 1139-1324 1.49e-92

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: 299.83  E-value: 1.49e-92
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1139 GLVSMMIAMEVVLRKRQGPKQMLVGGVVLLGAMLVGQVTLLDLLKLTVAVGLHFHEMNNGGDAM-----YMALIAAFSIR 1213
Cdd:pfam01005    1 GLLCIMIAIEEVLRKRQGPKMLLTGGLALFGALLMGQLTLLDLIKLCIAVGLHFHEMANAGDAMgmgttYLALIAAFRIR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1214 PGLLIGFGLRTLWSPRERLVLTLGAAMV----------EIALGGVMG-------------GLWKYLNAVSLCILTINAVA 1270
Cdd:pfam01005   81 PGFAIGFGFRRLTSPRERLLLTLGAALVasvelpnsleEIADGGAMGimmlklltdfqshGLWATLLALSFCILTFNAHA 160

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....
gi 3288890    1271 SRKASNTILPLMALLTPVTMAEVRLAAMFFCAVVIIGVLHQNFKDTSMQKTIPL 1324
Cdd:pfam01005  161 ARKAMAMILPIMALFTPLCLAEVRLAAMFFCAVVIIGVLHQNFKDTSMQKTTWI 214
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1674-1819 5.43e-92

Flavivirus DEAD domain;


:

Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 295.01  E-value: 5.43e-92
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1674 KGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGLDVKFHTQAFSAHGSGREVIDAMCHAT 1753
Cdd:pfam07652    1 KGTLTVLDLHPGAGKTRKVLPELVRECIDRRLRTLVLAPTRVVLAEMEEALRGLPIRYHTPAVSSEHTGREIVDVMCHAT 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 3288890    1754 LTYRMLEPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRARANESATILMTATPPGTSDEFPHSNG 1819
Cdd:pfam07652   81 FTQRLLSPVRVPNYEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFMTATPPGTSDPFPESNA 146
Flavi_NS4A pfam01350
Flavivirus non-structural protein NS4A; Flaviviruses encode a single polyprotein. This is ...
 2111-2254 1.83e-78

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: 256.37  E-value: 1.83e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2111 EVLVVLSELPDFLAKKGGEAMDTISVFLHSEEGSRAYRNALSMMPEAMTIVMLFILAGLLTSGMVIFFMSPKGISRMSMA 2190
Cdd:pfam01350    1 DLILEIGELPDFLAKKAGEALDNISMFHHSEEGGKAYRHALEELPDAIEILMLFALAALLTGGMTIFFLSGKGIGKMSIA 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 3288890    2191 MGTMAGCGYLMFLGGVKPTHISYIMLIFFVLMVVVIPEPGQQRSIQDNQVAYLIIGILTLVSAV 2254
Cdd:pfam01350   81 LGCMAACGALLFLAGVEPHHIAASIIIEFFLMVLLIPEPDQQRSIQDNQLAYLIIGILFLISAL 144
Flavi_NS2B super family cl03063
Flavivirus non-structural protein NS2B; Flaviviruses encode a single polyprotein. This is ...
 1358-1484 1.22e-68

Flavivirus non-structural protein NS2B; Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. All, but two, are cleaved by the NS2B-NS3 protease complex.


The actual alignment was detected with superfamily member pfam01002:

Pssm-ID: 279357  Cd Length: 127  Bit Score: 227.58  E-value: 1.22e-68
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1358 VNEALAAAGLVGVLAGLAFQEMENFLGPIAVGGLLMMLVSVAGRVDGLELKKLGEVSWEEEAEISGSSARYDVALSEQGE 1437
Cdd:pfam01002    1 LNEAIAAAGIVGILAGLAFKEDENFAGPIAAGGLLIACVSIAGRSADLELEKAAEVSWEEEAEHSGASANIDVALQDDGE 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 3288890    1438 FKLLSEEKVPWDQVVMTSLALVGAALHPFALLLVLAGWLFHVRGARR 1484
Cdd:pfam01002   81 FKIKDEEKDDTDQILLKALALAGAALHPFAILATLAGWLFHQKGAQR 127
Flavi_glycop_C pfam02832
Flavivirus glycoprotein, immunoglobulin-like domain;
581-676 4.90e-57

Flavivirus glycoprotein, immunoglobulin-like domain;


:

Pssm-ID: 280922  Cd Length: 97  Bit Score: 192.94  E-value: 4.90e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     581 SYKICTDKMFFVKNPTDTGHGTVVMQVKV-SKGAPCRIPVIVADDLTAAINKGILVTVNPIASTNDDEVLIEVNPPFGDS 659
Cdd:pfam02832    1 SYKICTDKFFFEKEPADTGHGTVLMQVKVeGKDAPCKIPVFSADDEKAAINKGILITANPIASDKDDEVLIEAEPPFGDS 80

                           90
                   ....*....|....*..
gi 3288890     660 YIIVGRGDSRLTYQWHK 676
Cdd:pfam02832   81 YIIVGAGDKALKLQWFK 97
Peptidase_S7 pfam00949
Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that ...
 1504-1655 2.31e-48

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: 169.54  E-value: 2.31e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1504 LEDGIYGIFQSTFLGASQRGVGVAQGGVFHTMWHVTRGAFLVRNGKKLIPSWASVKEDLVAYGGSWKLEGRWDGeEEVQL 1583
Cdd:pfam00949    1 LTDGILRFFQSSLLGRSQRGVGVLQEGVFHTMWHPTRGTKLHTQGIKTSPSWASVKQDLVDYGGSWKFQGKWLG-EEYQQ 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 3288890    1584 IaavpgknvvnvqtkpslfkvrnGGEIGAVALDYPSGTSGSPIVNRNGEVIGLYGNGILVGDNSFVSAISQT 1655
Cdd:pfam00949   80 Y----------------------GYGLGITDLNLSSGSSGSLVLNQNKQIVGIYFATVEVDDNSFVVGLAQL 129
flavi_E_stem TIGR04240
flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal ...
 682-778 7.88e-48

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: 166.66  E-value: 7.88e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     682 GKLFTQTMKGVERLAVMGDTAWDFSSAGGFFTSVGKGIHTVFGSAFQGLFGGLNWITKVIMGAVLIWVGINTRNMTMSMS 761
Cdd:TIGR04240    1 GKAFELTMRGAERMAILGDAAWDFGSVGGVFTSIGKALHQVFGGAFRALFGGVSWITKILIGVLLIWLGLNSRNTTLSLT 80

                           90
                   ....*....|....*..
gi 3288890     762 MILVGVIMMFLSLGVGA 778
Cdd:TIGR04240   81 FLAVGGILLFLTTGVGA 97
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 1821-1963 2.69e-44

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd18806:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 145  Bit Score: 158.58  E-value: 2.69e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  1821 IEDVQTDIPSEPWNTGHDWILADKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYPTIKQKKPDFILATDIA 1900
Cdd:cd18806    1 IEDVALEIPGRIWFYGKAWITIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEYPKIKTIDWDFVVTTDIS 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 3288890  1901 EMGANLCVERVLDCRTAFKPVLVDEGR-KVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS 1963
Cdd:cd18806   81 EMGANFDADRVIDCRTCVKPTILFSGDfRVILTGPVPQTAASAAQRRGRTGRNPAQERDIYRFV 144
Flavi_M pfam01004
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with virions ...
 212-285 2.48e-38

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: 138.87  E-value: 2.48e-38
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 3288890     212 IDLPTHENHGLKTRQEKWMTGRMGERQLQKIERWFVRNPFFAVTALTIAYLVGSNMTQRVVIALLVLAVGPAYS 285
Cdd:pfam01004    1 VALPPHVGLGLETRTETWMSSRGAWKQLQKVETWALRNPGFTVIALFIAHLIGSSITQKVIIFILLLLVTPAYS 74
Flavi_capsid pfam01003
Flavivirus capsid protein C; Flaviviruses are small enveloped viruses with virions comprised ...
 5-125 4.92e-26

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: 105.10  E-value: 4.92e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890       5 KAQGKTLGVNMVRRGV-RSLSNKIKQKTKQIGNRPGPSRGVQGFIFFFLFnilTGKKITAHLKRLWKMLDPRQGLAVLRK 83
Cdd:pfam01003    1 GKPGKGRGVNMLKRGAkRVPLKKTKRKTGQLLDGRGPLRLVLAFLAFFRF---TAIAPTPGLKKRWRTVPKRQAIKHLRK 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 3288890      84 VKRVVASLMRGLSSRKRRShdvlTVQFLILGMLLMTGGVTLV 125
Cdd:pfam01003   78 FKKEVGTLLDGLNRRGKRR----SKRGGWTGLLLMLGLLTLV 115
Flavi_propep pfam01570
Flavivirus polyprotein propeptide; The flaviviruses are small enveloped animal viruses ...
 132-203 2.09e-15

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


:

Pssm-ID: 366710  Cd Length: 78  Bit Score: 73.69  E-value: 2.09e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 3288890     132 LLNVTSEDLGKTFSVGTGNCTTNILEAKYWCPDSMEYNCPNLSPREEPDDIDCWCYGVENVRVAYGKCDSAG 203
Cdd:pfam01570    7 LLNVTSEDLGKTFSVGTGNCTTNILEAKYWCPDSMEYNCPNLSPREEPDDIDCWCYGVENVRVAYGKCDSAG 78
 
Name Accession Description Interval E-value
Flavivirus_RdRp cd23204
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within ...
 2827-3393 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: 1272.87  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  2827 MVNGVIKILTYPWDRIEEVTRMAMTDTTPFGQQRVFKEKVDTRAKDPPAGTRKIMKVVNRWLFRHLAREKNPRLCTKEEF 2906
Cdd:cd23204    1 MVNGVVKLLSKPWDVIEMVTQMAMTDTTPFGQQRVFKEKVDTKAPEPPEGTRKIMRIVNEWLWKFLARKKKPRLCTREEF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  2907 IAKVRSHAAIGAYLEEQEQWKTANEAVQDPKFWELVDEERKLHQQGRCRTCVYNMMGKREKKLSEFGKAKGSRAIWYMWL 2986
Cdd:cd23204   81 IAKVRSNAALGAVFEEQNQWKSAREAVEDPRFWELVDEERELHLEGKCETCVYNMMGKREKKLGEFGKAKGSRAIWYMWL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  2987 GARYLEFEALGFLNEDHWASRENSGGGVEGIGLQYLGYVIRDLAAMDGGGFYADDTAGWDTRITEADLDDEQEILNYMSP 3066
Cdd:cd23204  161 GARFLEFEALGFLNEDHWASRENSGGGVEGIGLQYLGYILREISKKPGGKMYADDTAGWDTRITEADLEDEEKILEYMEG 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  3067 HHKKLAQAVMEMTYKNKVVKVLRPAPGGKAYMDVISRRDQRGSGQVVTYALNTITNLKVQLIRMAEAEMVIHHQHVQdcD 3146
Cdd:cd23204  241 EHRKLAEAIFELTYQNKVVKVMRPGPGGGTVMDVISRRDQRGSGQVVTYALNTFTNMKVQLIRMMEGEGVITPEDLE--T 318

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  3147 ESVLTRLEAWLTEHGCNRLKRMAVSGDDCVVRPIDDRFGLALSHLNAMSKVRKDISEWQPSKGWNDWENVPFCSHHFHEL 3226
Cdd:cd23204  319 APRLKRVEDWLEENGEERLSRMAVSGDDCVVKPIDDRFATALTFLNDMGKVRKDIQEWEPSKGWNDWEEVPFCSHHFHEL 398

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  3227 QLKDGRRIVVPCREQDELIGRGRVSPGNGWMIKETACLSKAYANMWSLMYFHKRDMRLLSLAVSSAVPTSWVPQGRTTWS 3306
Cdd:cd23204  399 IMKDGRTLVVPCRDQDELIGRARVSPGAGWSLRETACLSKAYAQMWLLMYFHRRDLRLMANAICSAVPVDWVPTGRTTWS 478

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  3307 IHGKGEWMTTEDMLEVWNRVWITNNPHMQDKTMVKKWRDVPYLTKRQDKLCGSLIGMTNRATWASHIHLVIHRIRTLIGQ 3386
Cdd:cd23204  479 IHAKGEWMTTEDMLEVWNRVWIEDNPWMEDKTPVTSWRDVPYLGKREDQWCGSLIGLRSRATWAKNIQTAVNQVRSLIGN 558


                 ....*..
gi 3288890  3387 EKYTDYL 3393
Cdd:cd23204  559 EEYRDYL 565
Flavi_NS5 pfam00972
Flavivirus RNA-directed RNA polymerase, fingers and palm domains; Flaviviruses produce a large ...
 2758-3210 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: 950.15  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2758 TLEADVILPIGTRSVETDKGPLDKEAIEERVERIKSEYMTSWFYDNDNPYRTWHYCGSYVTKTSGSAASMVNGVIKILTY 2837
Cdd:pfam00972    1 TYEADVILGIGTRSVATDKEPLNKEIIGERIERIKNEHMTTWFYDEDNPYRTWAYHGSYETKTSGSASSMVNGVVRLLTK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2838 PWDRIEEVTRMAMTDTTPFGQQRVFKEKVDTRAKDPPAGTRKIMKVVNRWLFRHLAREKNPRLCTKEEFIAKVRSHAAIG 2917
Cdd:pfam00972   81 PWDVIEEVTRIAMTDTTPFGQQRVFKEKVDTRAPDPPAGTRQIMKVVNRWLWRHLAREKNPRLCTKEEFIAKVRSNAAIG 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2918 AYLEEQEQWKTANEAVQDPKFWELVDEERKLHQQGRCRTCVYNMMGKREKKLSEFGKAKGSRAIWYMWLGARYLEFEALG 2997
Cdd:pfam00972  161 AYFEEEEQWKTANEAVQDPRFWELVDRERELHQQGRCRTCVYNMMGKREKKLGEFGKAKGSRAIWYMWLGARFLEFEALG 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2998 FLNEDHWASRENSGGGVEGIGLQYLGYVIRDLAAMDGGGFYADDTAGWDTRITEADLDDEQEILNYMSPHHKKLAQAVME 3077
Cdd:pfam00972  241 FLNEDHWASRENSGGGVEGIGLQYLGYILRDLAAMPGGGMYADDTAGWDTRITEADLDNEAEITNYMEPHHKKLAQAVMK 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    3078 MTYKNKVVKVLRPAPGGKAYMDVISRRDQRGSGQVVTYALNTITNLKVQLIRMAEAEMVIHHQHVQDCDESvlTRLEAWL 3157
Cdd:pfam00972  321 MTYQNKVVKVLRPAPGGKTVMDVISRRDQRGSGQVVTYALNTFTNLKVQLIRMMEAEMVIHHQHLQDCDES--ERVEAWL 398

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 3288890    3158 TEHGCNRLKRMAVSGDDCVVRPIDDRFGLALSHLNAMSKVRKDISEWQPSKGW 3210
Cdd:pfam00972  399 TEHGCDRLKRMAVSGDDCVVKPIDDRFALALSHLNDMGKVRKDISEWQPSKGW 451
Flavi_NS1 pfam00948
Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the ...
 780-1133 0e+00

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: 736.47  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     780 QGCAINFGKRELKCGDGIFIFRDSDDWLNKYSYYPEDPVKLASIVKASFEEGKCGLNSVDSLEHEMWRSRADEINAIFEE 859
Cdd:pfam00948    1 QGCAINFGGRELKCGDGIFIFNDSDDWLEKYKFQADDPKKLAAAIGAAFEEGKCGINSADRLEHEMWKQIADEINAIFEE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     860 NEVDISVVVQDPKNVYQRGT-----HPFSRIRDGLQYGWKTWGKNLVFSPGRKNGSFIIDGKSRKECPFSNRVWNSFQIE 934
Cdd:pfam00948   81 NDMDFSVVVGDPKGILAQGKkmirpHPFEHIRDGLKYGWKSWGKAKIFGADRKNGSFIIDGKNRKECPDNNRAWNIFEIE 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     935 EFGTGVFTTRVYMDAVFEYTIDCDGSILGAAVNGKKSAHGSPTFWMGSHEVNGTWMIHTLEALDYKECEWPLTHTI-GTS 1013
Cdd:pfam00948  161 DFGFGIFTTNIWLDARDEYTIDCDGRILGAAIKDKKAAHADMGFWIESHEKNETWKIARAEAIDVKECEWPKSHTIwGNG 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1014 VEESEMFMPRSIGGPVSSHNHIPGYKVQTNGPWMQVPLEVKREACPGTSVIIDGNCDGRGKSTRSTTDSGKVIPEWCCRS 1093
Cdd:pfam00948  241 VEESEMFIPKIIGGPISQHNHIPGYFTQTAGPWHLGKLELDFDACEGTSVIIDEHCDGRGKSLRSTTDSGKTIHEWCCRS 320

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|
gi 3288890    1094 CTMPPVSFHGSDGCWYPMEIRPRKTHESHLVRSWVTAGEI 1133
Cdd:pfam00948  321 CTLPPLRFHGEDGCWYGMEIRPRKEHEEHLVKSMVSAGEG 360
Flavi_glycoprot pfam00869
Flavivirus glycoprotein, central and dimerization domains;
287-579 0e+00

Flavivirus glycoprotein, central and dimerization domains;


Pssm-ID: 395698  Cd Length: 300  Bit Score: 585.10  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     287 HCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDRPAEVRKVCYNAVLTHVKINDKCPSTGEAH 366
Cdd:pfam00869    1 HCIGIGDRDFIEGLHGATWVDATLEHDKCVTTMAKDKPSLDIELEKTAIDNPAELRKLCIEAKISHTKIDDKCPSQGEAH 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     367 LAEENEGDNACKRTYSDRGWGNGCGLFGKGSIVACAKFTCAKSMSLFEVDQTKIQYVIRAQLHVGAKQENWTTDIK---T 443
Cdd:pfam00869   81 LAEENDGDFACKRTFSDRGHGNGCGLFGKGSIIACAKFKCAKKLEGFEVDQEKIKYSIIAQLHTGAKHENGNEDIEhgtI 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     444 LKFDALSGSQEVEFIGYGKATLECQVQTAVDFGNSYIAEMETESWIVDRQWAQDLTLPWQSG---SGGVWREMHHLVEFE 520
Cdd:pfam00869  161 AKFDALAGSQEIEFIDYGAATLDCQPQTALDFGEMVIAEMEKESWIVDKQWALDLPLPWQSGastSGETWNEMDHLVEFE 240

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     521 PPHAATIRVLALGNQEGSLKTALTGAMRV-TKDTNDNNLYKLHGGHVSCRVKLSALTLKG 579
Cdd:pfam00869  241 PAHAAKIEVLALGNQEGALHTALTGAMEIqTKDTNDNNLYKIFAGHLKCRLKLDALTLKG 300
Flavi_NS4B pfam01349
Flavivirus non-structural protein NS4B; Flaviviruses encode a single polyprotein. This is ...
 2257-2500 5.76e-142

Flavivirus non-structural protein NS4B; Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4B protein is small and poorly conserved among the Flaviviruses. NS4B contains multiple hydrophobic potential membrane spanning regions. NS4B may form membrane components of the viral replication complex and could be involved in membrane localization of NS3 and pfam00972.


Pssm-ID: 279665  Cd Length: 248  Bit Score: 442.93  E-value: 5.76e-142
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2257 NELGMLEKTKEDLFGKKNLIPSSASPWSWPDLDLKPGAAWTVYVGIVTMLSPMLHHWIKVEYGNLSLSGIAQSASVLSFM 2336
Cdd:pfam01349    1 NELGLLEKTKEDLFGIGHAAAENAHHAAMLDLDLHPAAAWTLYAGATTIISPMLHHTIENETANISLSAIANQAAILMFL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2337 DKGIPFMKMNISVIMLLVSGWNSITVMPLLCGIGCAMLHWSLILPGIKAQQSKLAQRRVFHGVAKNPVVDGNPTVDIEEA 2416
Cdd:pfam01349   81 DKGIPFMKMDIGVILLALGCWNQINPLPLLAAIFCAMAHWAIIGPGIKAKASKEAQKRTAAGIAENPTVDGIPAIDIDEA 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2417 PEMPALY----EKKLALYLLLALSLASVAMCRTPFSLAEGIVLASAASGPLIEGNTSLLWNGPMAVSMTGVMRGNHYAFV 2492
Cdd:pfam01349  161 PEMPALYdakfEKKLALILLLALCLAQIALCRTPFALAEGITLASAALGPLIEGNPGKFWNGPIAVSMAGIFRGNHLAFA 240


                   ....*...
gi 3288890    2493 GVMYNLWK 2500
Cdd:pfam01349  241 GLAFNLMK 248
capping_2-OMTase_Flaviviridae cd20761
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific ...
 2513-2743 9.23e-114

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: 360.77  E-value: 9.23e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  2513 TLGEVWKRELNLLDKRQFELYKRTDIVEVDrdtarrhlaegkvDTGVAVSRGTAKLRWFHERGYVKLEGRVIDLGCGRGG 2592
Cdd:cd20761    1 TLGEKWKDRLNALSKEEFDAYKKRGVVEVA-------------TKGHAVSRGYAKLRWLVERGYVKPSGKVVDLGCGRGG 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  2593 WCYYAAAQKEVSGVKGFTLGRDGHEKPMNVQSLGWNIITFKDKTDIHRLEPVKCDTLLCDIGESSSSSVTEGERTVRVLD 2672
Cdd:cd20761   68 WSQYAAGLPKVTEVRGYTLGGPGHEEPRLVQSYGWNLVRLKSGVDVFYRPPERCDTLLCDIGESSPSPEVEEERTLRVLD 147

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 3288890  2673 TVEKWLACGVD-NFCVKVLAPYMPDVLEKLELLQRRFGGTVIRNPLSRNSTHEMYYVSGARSNVTFTVNQTS 2743
Cdd:cd20761  148 LVEKWLERNPTaNFCIKVLCPYHPEVIELLERLQRKGGGGLVRVPLSRNSTHEMYFVSGARGNIVNSVNMTS 219
Flavi_NS2A pfam01005
Flavivirus non-structural protein NS2A; NS2A is a hydrophobic protein about 25 kDa is size. ...
 1139-1324 1.49e-92

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: 299.83  E-value: 1.49e-92
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1139 GLVSMMIAMEVVLRKRQGPKQMLVGGVVLLGAMLVGQVTLLDLLKLTVAVGLHFHEMNNGGDAM-----YMALIAAFSIR 1213
Cdd:pfam01005    1 GLLCIMIAIEEVLRKRQGPKMLLTGGLALFGALLMGQLTLLDLIKLCIAVGLHFHEMANAGDAMgmgttYLALIAAFRIR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1214 PGLLIGFGLRTLWSPRERLVLTLGAAMV----------EIALGGVMG-------------GLWKYLNAVSLCILTINAVA 1270
Cdd:pfam01005   81 PGFAIGFGFRRLTSPRERLLLTLGAALVasvelpnsleEIADGGAMGimmlklltdfqshGLWATLLALSFCILTFNAHA 160

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....
gi 3288890    1271 SRKASNTILPLMALLTPVTMAEVRLAAMFFCAVVIIGVLHQNFKDTSMQKTIPL 1324
Cdd:pfam01005  161 ARKAMAMILPIMALFTPLCLAEVRLAAMFFCAVVIIGVLHQNFKDTSMQKTTWI 214
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1674-1819 5.43e-92

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 295.01  E-value: 5.43e-92
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1674 KGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGLDVKFHTQAFSAHGSGREVIDAMCHAT 1753
Cdd:pfam07652    1 KGTLTVLDLHPGAGKTRKVLPELVRECIDRRLRTLVLAPTRVVLAEMEEALRGLPIRYHTPAVSSEHTGREIVDVMCHAT 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 3288890    1754 LTYRMLEPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRARANESATILMTATPPGTSDEFPHSNG 1819
Cdd:pfam07652   81 FTQRLLSPVRVPNYEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFMTATPPGTSDPFPESNA 146
Flavi_NS4A pfam01350
Flavivirus non-structural protein NS4A; Flaviviruses encode a single polyprotein. This is ...
 2111-2254 1.83e-78

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: 256.37  E-value: 1.83e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2111 EVLVVLSELPDFLAKKGGEAMDTISVFLHSEEGSRAYRNALSMMPEAMTIVMLFILAGLLTSGMVIFFMSPKGISRMSMA 2190
Cdd:pfam01350    1 DLILEIGELPDFLAKKAGEALDNISMFHHSEEGGKAYRHALEELPDAIEILMLFALAALLTGGMTIFFLSGKGIGKMSIA 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 3288890    2191 MGTMAGCGYLMFLGGVKPTHISYIMLIFFVLMVVVIPEPGQQRSIQDNQVAYLIIGILTLVSAV 2254
Cdd:pfam01350   81 LGCMAACGALLFLAGVEPHHIAASIIIEFFLMVLLIPEPDQQRSIQDNQLAYLIIGILFLISAL 144
Flavi_NS2B pfam01002
Flavivirus non-structural protein NS2B; Flaviviruses encode a single polyprotein. This is ...
 1358-1484 1.22e-68

Flavivirus non-structural protein NS2B; Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. All, but two, are cleaved by the NS2B-NS3 protease complex.


Pssm-ID: 279357  Cd Length: 127  Bit Score: 227.58  E-value: 1.22e-68
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1358 VNEALAAAGLVGVLAGLAFQEMENFLGPIAVGGLLMMLVSVAGRVDGLELKKLGEVSWEEEAEISGSSARYDVALSEQGE 1437
Cdd:pfam01002    1 LNEAIAAAGIVGILAGLAFKEDENFAGPIAAGGLLIACVSIAGRSADLELEKAAEVSWEEEAEHSGASANIDVALQDDGE 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 3288890    1438 FKLLSEEKVPWDQVVMTSLALVGAALHPFALLLVLAGWLFHVRGARR 1484
Cdd:pfam01002   81 FKIKDEEKDDTDQILLKALALAGAALHPFAILATLAGWLFHQKGAQR 127
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1678-1825 6.01e-58

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: 197.77  E-value: 6.01e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  1678 TVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGLDVKFHTQAFSAHGSGREVIDAMCHATLTYR 1757
Cdd:cd17931    4 TVLDLHPGAGKTTRVLPQIIREAIKKRLRTLVLAPTRVVAAEMYEALRGLPIRYRTGAVKEEHGGNEIVDYMCHGTFTCR 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 3288890  1758 MLEPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRARANESATILMTATPPGTSDEFPHSNGEIEDVQ 1825
Cdd:cd17931   84 LLSPKRVPNYNLIIMDEAHFTDPASIAARGYIHTRVEMGEAAVIFMTATPPGTVTPFPQSNHPIEDFE 151
Flavi_glycop_C pfam02832
Flavivirus glycoprotein, immunoglobulin-like domain;
581-676 4.90e-57

Flavivirus glycoprotein, immunoglobulin-like domain;


Pssm-ID: 280922  Cd Length: 97  Bit Score: 192.94  E-value: 4.90e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     581 SYKICTDKMFFVKNPTDTGHGTVVMQVKV-SKGAPCRIPVIVADDLTAAINKGILVTVNPIASTNDDEVLIEVNPPFGDS 659
Cdd:pfam02832    1 SYKICTDKFFFEKEPADTGHGTVLMQVKVeGKDAPCKIPVFSADDEKAAINKGILITANPIASDKDDEVLIEAEPPFGDS 80

                           90
                   ....*....|....*..
gi 3288890     660 YIIVGRGDSRLTYQWHK 676
Cdd:pfam02832   81 YIIVGAGDKALKLQWFK 97
Peptidase_S7 pfam00949
Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that ...
 1504-1655 2.31e-48

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: 169.54  E-value: 2.31e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1504 LEDGIYGIFQSTFLGASQRGVGVAQGGVFHTMWHVTRGAFLVRNGKKLIPSWASVKEDLVAYGGSWKLEGRWDGeEEVQL 1583
Cdd:pfam00949    1 LTDGILRFFQSSLLGRSQRGVGVLQEGVFHTMWHPTRGTKLHTQGIKTSPSWASVKQDLVDYGGSWKFQGKWLG-EEYQQ 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 3288890    1584 IaavpgknvvnvqtkpslfkvrnGGEIGAVALDYPSGTSGSPIVNRNGEVIGLYGNGILVGDNSFVSAISQT 1655
Cdd:pfam00949   80 Y----------------------GYGLGITDLNLSSGSSGSLVLNQNKQIVGIYFATVEVDDNSFVVGLAQL 129
flavi_E_stem TIGR04240
flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal ...
 682-778 7.88e-48

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: 166.66  E-value: 7.88e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     682 GKLFTQTMKGVERLAVMGDTAWDFSSAGGFFTSVGKGIHTVFGSAFQGLFGGLNWITKVIMGAVLIWVGINTRNMTMSMS 761
Cdd:TIGR04240    1 GKAFELTMRGAERMAILGDAAWDFGSVGGVFTSIGKALHQVFGGAFRALFGGVSWITKILIGVLLIWLGLNSRNTTLSLT 80

                           90
                   ....*....|....*..
gi 3288890     762 MILVGVIMMFLSLGVGA 778
Cdd:TIGR04240   81 FLAVGGILLFLTTGVGA 97
Flavi_E_C cd12149
Immunoglobulin-like domain III (C-terminal domain) of Flavivirus envelope glycoprotein E; The ...
 588-677 1.45e-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: 157.08  E-value: 1.45e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890   588 KMFFVKNPTDTGHGTVVMQVKVSK-GAPCRIPVIVADDLTAAINKGILVTVNPIASTNDDEVLIEVNPPFGDSYIIVGRG 666
Cdd:cd12149    1 KFSWKKEPADTGHGTVVMEVKYSGtDAPCRIPVRVVDSGSGGENVGRLITVNPIITNANSKVFIEVEPPFGDSYIVVGVG 80

                         90
                 ....*....|.
gi 3288890   667 DSRLTYQWHKE 677
Cdd:cd12149   81 DTRLKHQWFQK 91
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1821-1963 2.69e-44

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: 158.58  E-value: 2.69e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  1821 IEDVQTDIPSEPWNTGHDWILADKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYPTIKQKKPDFILATDIA 1900
Cdd:cd18806    1 IEDVALEIPGRIWFYGKAWITIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEYPKIKTIDWDFVVTTDIS 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 3288890  1901 EMGANLCVERVLDCRTAFKPVLVDEGR-KVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS 1963
Cdd:cd18806   81 EMGANFDADRVIDCRTCVKPTILFSGDfRVILTGPVPQTAASAAQRRGRTGRNPAQERDIYRFV 144
Flavi_M pfam01004
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with virions ...
 212-285 2.48e-38

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: 138.87  E-value: 2.48e-38
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 3288890     212 IDLPTHENHGLKTRQEKWMTGRMGERQLQKIERWFVRNPFFAVTALTIAYLVGSNMTQRVVIALLVLAVGPAYS 285
Cdd:pfam01004    1 VALPPHVGLGLETRTETWMSSRGAWKQLQKVETWALRNPGFTVIALFIAHLIGSSITQKVIIFILLLLVTPAYS 74
Flavi_M cd17038
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with a ...
 211-285 8.03e-31

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: 117.35  E-value: 8.03e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 3288890   211 AIDLPTHENHGLKTRQEKWMTGRMGERQLQKIERWFVRNPFFAVTALTIAYLVGSNMTQRVVIALLVLAVGPAYS 285
Cdd:cd17038    1 SVAIPPHGTGGLTTRKETWLSTSNGKEHLTRVERWVLRNPGYALAAVALAWMLGSSTTQRVIIIVLLLLVAPAYA 75
FtsJ pfam01728
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...
 2561-2732 1.48e-27

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: 111.91  E-value: 1.48e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2561 VSRGTAKLRWFHER-GYVKLEGRVIDLGCGRGGWCYYaAAQKEVSGVKGFTLGRDGHEKPMNVQslgwNIITFkdKTDIH 2639
Cdd:pfam01728    2 RSRAAYKLLEIDEKfGLLKPGKTVLDLGAAPGGWSQV-ALQRGAGKVVGVDLGPMQLWKPRNDP----GVTFI--QGDIR 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2640 RLEPV---------KCDTLLCDIGESSSS-SVTEGERTVRVLDTVEKW----LACGvDNFCVKVLapYMPDVLEKLELLQ 2705
Cdd:pfam01728   75 DPETLdlleellgrKVDLVLSDGSPFISGnKVLDHLRSLDLVKAALEValelLRKG-GNFVCKVF--QGEDFSELLYLLK 151

                          170       180
                   ....*....|....*....|....*...
gi 3288890    2706 RRFGGTVIRNP-LSRNSTHEMYYVSGAR 2732
Cdd:pfam01728  152 LGFEKVGVFKPpASRPESSEEYLVCLGF 179
Flavi_capsid pfam01003
Flavivirus capsid protein C; Flaviviruses are small enveloped viruses with virions comprised ...
 5-125 4.92e-26

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: 105.10  E-value: 4.92e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890       5 KAQGKTLGVNMVRRGV-RSLSNKIKQKTKQIGNRPGPSRGVQGFIFFFLFnilTGKKITAHLKRLWKMLDPRQGLAVLRK 83
Cdd:pfam01003    1 GKPGKGRGVNMLKRGAkRVPLKKTKRKTGQLLDGRGPLRLVLAFLAFFRF---TAIAPTPGLKKRWRTVPKRQAIKHLRK 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 3288890      84 VKRVVASLMRGLSSRKRRShdvlTVQFLILGMLLMTGGVTLV 125
Cdd:pfam01003   78 FKKEVGTLLDGLNRRGKRR----SKRGGWTGLLLMLGLLTLV 115
Flavi_propep pfam01570
Flavivirus polyprotein propeptide; The flaviviruses are small enveloped animal viruses ...
 132-203 2.09e-15

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


Pssm-ID: 366710  Cd Length: 78  Bit Score: 73.69  E-value: 2.09e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 3288890     132 LLNVTSEDLGKTFSVGTGNCTTNILEAKYWCPDSMEYNCPNLSPREEPDDIDCWCYGVENVRVAYGKCDSAG 203
Cdd:pfam01570    7 LLNVTSEDLGKTFSVGTGNCTTNILEAKYWCPDSMEYNCPNLSPREEPDDIDCWCYGVENVRVAYGKCDSAG 78
DEXDc smart00487
DEAD-like helicases superfamily;
1668-1814 2.25e-12

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 68.67  E-value: 2.25e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     1668 IPTMLKKGMTTVLDFHPGAGKTRRFLpQILAECARRRL--RTLVLAPTRV----VLSEMKEAFHGLDVKFHTQ--AFSAH 1739
Cdd:smart00487   17 IEALLSGLRDVILAAPTGSGKTLAAL-LPALEALKRGKggRVLVLVPTRElaeqWAEELKKLGPSLGLKVVGLygGDSKR 95

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     1740 GSGREVIDAMCHATL-TYRML------EPTRVVNWEVIIMDEAHFLDPASIAARgWAAHRARANESA-TILMTATPPGTS 1811
Cdd:smart00487   96 EQLRKLESGKTDILVtTPGRLldllenDKLSLSNVDLVILDEAHRLLDGGFGDQ-LEKLLKLLPKNVqLLLLSATPPEEI 174


                    ...
gi 3288890     1812 DEF 1814
Cdd:smart00487  175 ENL 177
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
1684-1807 1.75e-07

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 56.96  E-value: 1.75e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  1684 PGAGKTRrflpqILAECARR---RLRTLVLAPTRVVLSEMKEAFHgldvKFHTQAFSAHG---SGREVIDAMcHATLTYR 1757
Cdd:COG1061  109 TGTGKTV-----LALALAAEllrGKRVLVLVPRRELLEQWAEELR----RFLGDPLAGGGkkdSDAPITVAT-YQSLARR 178

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 3288890  1758 MLEPTRVVNWEVIIMDEAHfldpaSIAARGWAAHRARANESATILMTATP 1807
Cdd:COG1061  179 AHLDELGDRFGLVIIDEAH-----HAGAPSYRRILEAFPAAYRLGLTATP 223
HELICc smart00490
helicase superfamily c-terminal domain;
1860-1951 5.90e-04

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 41.04  E-value: 5.90e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     1860 MAASLRKAGKSVVVLNRKTFEREYPTI----KQKKPDFILATDIAEMGANL-CVERVLDCRtafkpvlvdegrkvaikgp 1934
Cdd:smart00490    3 LAELLKELGIKVARLHGGLSQEEREEIldkfNNGKIKVLVATDVAERGLDLpGVDLVIIYD------------------- 63

                            90
                    ....*....|....*..
gi 3288890     1935 LRISASSAAQRRGRIGR 1951
Cdd:smart00490   64 LPWSPASYIQRIGRAGR 80
Cfa COG2230
Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport ...
 2565-2618 1.23e-03

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


Pssm-ID: 441831 [Multi-domain]  Cd Length: 158  Bit Score: 42.22  E-value: 1.23e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 3288890  2565 TAKLRWFHERGYVKLEGRVIDLGCGRGGWCYYAAAQKEVSgVKGFTLGRDGHEK 2618
Cdd:COG2230   37 EAKLDLILRKLGLKPGMRVLDIGCGWGGLALYLARRYGVR-VTGVTLSPEQLEY 89
cas3_core TIGR01587
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ...
 1769-1893 8.04e-03

CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.


Pssm-ID: 273707 [Multi-domain]  Cd Length: 359  Bit Score: 41.67  E-value: 8.04e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1769 VIIMDEAHFLDPASIAARGWAAHRARANESATILMTATPPGTSDEFPHSNGEIEDVQTDIPSEPWN-TGHDWILADKRpt 1847
Cdd:TIGR01587  127 LLIFDEVHFYDEYTLALILAVLEVLKDNDVPILLMSATLPKFLKEYAEKIGYVEFNEPLDLKEERRfENHRFILIESD-- 204

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 3288890    1848 awFLPSIRAANVMAASLRKAGKSVVVLNrkTFERE---YPTIKQKKPDF 1893
Cdd:TIGR01587  205 --KVGEISSLERLLEFIKKGGSIAIIVN--TVDRAqefYQQLKEKAPEE 249
 
Name Accession Description Interval E-value
Flavivirus_RdRp cd23204
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within ...
 2827-3393 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: 1272.87  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  2827 MVNGVIKILTYPWDRIEEVTRMAMTDTTPFGQQRVFKEKVDTRAKDPPAGTRKIMKVVNRWLFRHLAREKNPRLCTKEEF 2906
Cdd:cd23204    1 MVNGVVKLLSKPWDVIEMVTQMAMTDTTPFGQQRVFKEKVDTKAPEPPEGTRKIMRIVNEWLWKFLARKKKPRLCTREEF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  2907 IAKVRSHAAIGAYLEEQEQWKTANEAVQDPKFWELVDEERKLHQQGRCRTCVYNMMGKREKKLSEFGKAKGSRAIWYMWL 2986
Cdd:cd23204   81 IAKVRSNAALGAVFEEQNQWKSAREAVEDPRFWELVDEERELHLEGKCETCVYNMMGKREKKLGEFGKAKGSRAIWYMWL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  2987 GARYLEFEALGFLNEDHWASRENSGGGVEGIGLQYLGYVIRDLAAMDGGGFYADDTAGWDTRITEADLDDEQEILNYMSP 3066
Cdd:cd23204  161 GARFLEFEALGFLNEDHWASRENSGGGVEGIGLQYLGYILREISKKPGGKMYADDTAGWDTRITEADLEDEEKILEYMEG 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  3067 HHKKLAQAVMEMTYKNKVVKVLRPAPGGKAYMDVISRRDQRGSGQVVTYALNTITNLKVQLIRMAEAEMVIHHQHVQdcD 3146
Cdd:cd23204  241 EHRKLAEAIFELTYQNKVVKVMRPGPGGGTVMDVISRRDQRGSGQVVTYALNTFTNMKVQLIRMMEGEGVITPEDLE--T 318

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  3147 ESVLTRLEAWLTEHGCNRLKRMAVSGDDCVVRPIDDRFGLALSHLNAMSKVRKDISEWQPSKGWNDWENVPFCSHHFHEL 3226
Cdd:cd23204  319 APRLKRVEDWLEENGEERLSRMAVSGDDCVVKPIDDRFATALTFLNDMGKVRKDIQEWEPSKGWNDWEEVPFCSHHFHEL 398

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  3227 QLKDGRRIVVPCREQDELIGRGRVSPGNGWMIKETACLSKAYANMWSLMYFHKRDMRLLSLAVSSAVPTSWVPQGRTTWS 3306
Cdd:cd23204  399 IMKDGRTLVVPCRDQDELIGRARVSPGAGWSLRETACLSKAYAQMWLLMYFHRRDLRLMANAICSAVPVDWVPTGRTTWS 478

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  3307 IHGKGEWMTTEDMLEVWNRVWITNNPHMQDKTMVKKWRDVPYLTKRQDKLCGSLIGMTNRATWASHIHLVIHRIRTLIGQ 3386
Cdd:cd23204  479 IHAKGEWMTTEDMLEVWNRVWIEDNPWMEDKTPVTSWRDVPYLGKREDQWCGSLIGLRSRATWAKNIQTAVNQVRSLIGN 558


                 ....*..
gi 3288890  3387 EKYTDYL 3393
Cdd:cd23204  559 EEYRDYL 565
Flavi_NS5 pfam00972
Flavivirus RNA-directed RNA polymerase, fingers and palm domains; Flaviviruses produce a large ...
 2758-3210 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: 950.15  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2758 TLEADVILPIGTRSVETDKGPLDKEAIEERVERIKSEYMTSWFYDNDNPYRTWHYCGSYVTKTSGSAASMVNGVIKILTY 2837
Cdd:pfam00972    1 TYEADVILGIGTRSVATDKEPLNKEIIGERIERIKNEHMTTWFYDEDNPYRTWAYHGSYETKTSGSASSMVNGVVRLLTK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2838 PWDRIEEVTRMAMTDTTPFGQQRVFKEKVDTRAKDPPAGTRKIMKVVNRWLFRHLAREKNPRLCTKEEFIAKVRSHAAIG 2917
Cdd:pfam00972   81 PWDVIEEVTRIAMTDTTPFGQQRVFKEKVDTRAPDPPAGTRQIMKVVNRWLWRHLAREKNPRLCTKEEFIAKVRSNAAIG 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2918 AYLEEQEQWKTANEAVQDPKFWELVDEERKLHQQGRCRTCVYNMMGKREKKLSEFGKAKGSRAIWYMWLGARYLEFEALG 2997
Cdd:pfam00972  161 AYFEEEEQWKTANEAVQDPRFWELVDRERELHQQGRCRTCVYNMMGKREKKLGEFGKAKGSRAIWYMWLGARFLEFEALG 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2998 FLNEDHWASRENSGGGVEGIGLQYLGYVIRDLAAMDGGGFYADDTAGWDTRITEADLDDEQEILNYMSPHHKKLAQAVME 3077
Cdd:pfam00972  241 FLNEDHWASRENSGGGVEGIGLQYLGYILRDLAAMPGGGMYADDTAGWDTRITEADLDNEAEITNYMEPHHKKLAQAVMK 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    3078 MTYKNKVVKVLRPAPGGKAYMDVISRRDQRGSGQVVTYALNTITNLKVQLIRMAEAEMVIHHQHVQDCDESvlTRLEAWL 3157
Cdd:pfam00972  321 MTYQNKVVKVLRPAPGGKTVMDVISRRDQRGSGQVVTYALNTFTNLKVQLIRMMEAEMVIHHQHLQDCDES--ERVEAWL 398

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|...
gi 3288890    3158 TEHGCNRLKRMAVSGDDCVVRPIDDRFGLALSHLNAMSKVRKDISEWQPSKGW 3210
Cdd:pfam00972  399 TEHGCDRLKRMAVSGDDCVVKPIDDRFALALSHLNDMGKVRKDISEWQPSKGW 451
Flavi_NS1 pfam00948
Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the ...
 780-1133 0e+00

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: 736.47  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     780 QGCAINFGKRELKCGDGIFIFRDSDDWLNKYSYYPEDPVKLASIVKASFEEGKCGLNSVDSLEHEMWRSRADEINAIFEE 859
Cdd:pfam00948    1 QGCAINFGGRELKCGDGIFIFNDSDDWLEKYKFQADDPKKLAAAIGAAFEEGKCGINSADRLEHEMWKQIADEINAIFEE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     860 NEVDISVVVQDPKNVYQRGT-----HPFSRIRDGLQYGWKTWGKNLVFSPGRKNGSFIIDGKSRKECPFSNRVWNSFQIE 934
Cdd:pfam00948   81 NDMDFSVVVGDPKGILAQGKkmirpHPFEHIRDGLKYGWKSWGKAKIFGADRKNGSFIIDGKNRKECPDNNRAWNIFEIE 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     935 EFGTGVFTTRVYMDAVFEYTIDCDGSILGAAVNGKKSAHGSPTFWMGSHEVNGTWMIHTLEALDYKECEWPLTHTI-GTS 1013
Cdd:pfam00948  161 DFGFGIFTTNIWLDARDEYTIDCDGRILGAAIKDKKAAHADMGFWIESHEKNETWKIARAEAIDVKECEWPKSHTIwGNG 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1014 VEESEMFMPRSIGGPVSSHNHIPGYKVQTNGPWMQVPLEVKREACPGTSVIIDGNCDGRGKSTRSTTDSGKVIPEWCCRS 1093
Cdd:pfam00948  241 VEESEMFIPKIIGGPISQHNHIPGYFTQTAGPWHLGKLELDFDACEGTSVIIDEHCDGRGKSLRSTTDSGKTIHEWCCRS 320

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|
gi 3288890    1094 CTMPPVSFHGSDGCWYPMEIRPRKTHESHLVRSWVTAGEI 1133
Cdd:pfam00948  321 CTLPPLRFHGEDGCWYGMEIRPRKEHEEHLVKSMVSAGEG 360
Flavi_glycoprot pfam00869
Flavivirus glycoprotein, central and dimerization domains;
287-579 0e+00

Flavivirus glycoprotein, central and dimerization domains;


Pssm-ID: 395698  Cd Length: 300  Bit Score: 585.10  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     287 HCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDRPAEVRKVCYNAVLTHVKINDKCPSTGEAH 366
Cdd:pfam00869    1 HCIGIGDRDFIEGLHGATWVDATLEHDKCVTTMAKDKPSLDIELEKTAIDNPAELRKLCIEAKISHTKIDDKCPSQGEAH 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     367 LAEENEGDNACKRTYSDRGWGNGCGLFGKGSIVACAKFTCAKSMSLFEVDQTKIQYVIRAQLHVGAKQENWTTDIK---T 443
Cdd:pfam00869   81 LAEENDGDFACKRTFSDRGHGNGCGLFGKGSIIACAKFKCAKKLEGFEVDQEKIKYSIIAQLHTGAKHENGNEDIEhgtI 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     444 LKFDALSGSQEVEFIGYGKATLECQVQTAVDFGNSYIAEMETESWIVDRQWAQDLTLPWQSG---SGGVWREMHHLVEFE 520
Cdd:pfam00869  161 AKFDALAGSQEIEFIDYGAATLDCQPQTALDFGEMVIAEMEKESWIVDKQWALDLPLPWQSGastSGETWNEMDHLVEFE 240

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     521 PPHAATIRVLALGNQEGSLKTALTGAMRV-TKDTNDNNLYKLHGGHVSCRVKLSALTLKG 579
Cdd:pfam00869  241 PAHAAKIEVLALGNQEGALHTALTGAMEIqTKDTNDNNLYKIFAGHLKCRLKLDALTLKG 300
Flavi_NS4B pfam01349
Flavivirus non-structural protein NS4B; Flaviviruses encode a single polyprotein. This is ...
 2257-2500 5.76e-142

Flavivirus non-structural protein NS4B; Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4B protein is small and poorly conserved among the Flaviviruses. NS4B contains multiple hydrophobic potential membrane spanning regions. NS4B may form membrane components of the viral replication complex and could be involved in membrane localization of NS3 and pfam00972.


Pssm-ID: 279665  Cd Length: 248  Bit Score: 442.93  E-value: 5.76e-142
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2257 NELGMLEKTKEDLFGKKNLIPSSASPWSWPDLDLKPGAAWTVYVGIVTMLSPMLHHWIKVEYGNLSLSGIAQSASVLSFM 2336
Cdd:pfam01349    1 NELGLLEKTKEDLFGIGHAAAENAHHAAMLDLDLHPAAAWTLYAGATTIISPMLHHTIENETANISLSAIANQAAILMFL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2337 DKGIPFMKMNISVIMLLVSGWNSITVMPLLCGIGCAMLHWSLILPGIKAQQSKLAQRRVFHGVAKNPVVDGNPTVDIEEA 2416
Cdd:pfam01349   81 DKGIPFMKMDIGVILLALGCWNQINPLPLLAAIFCAMAHWAIIGPGIKAKASKEAQKRTAAGIAENPTVDGIPAIDIDEA 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2417 PEMPALY----EKKLALYLLLALSLASVAMCRTPFSLAEGIVLASAASGPLIEGNTSLLWNGPMAVSMTGVMRGNHYAFV 2492
Cdd:pfam01349  161 PEMPALYdakfEKKLALILLLALCLAQIALCRTPFALAEGITLASAALGPLIEGNPGKFWNGPIAVSMAGIFRGNHLAFA 240


                   ....*...
gi 3288890    2493 GVMYNLWK 2500
Cdd:pfam01349  241 GLAFNLMK 248
capping_2-OMTase_Flaviviridae cd20761
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific ...
 2513-2743 9.23e-114

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: 360.77  E-value: 9.23e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  2513 TLGEVWKRELNLLDKRQFELYKRTDIVEVDrdtarrhlaegkvDTGVAVSRGTAKLRWFHERGYVKLEGRVIDLGCGRGG 2592
Cdd:cd20761    1 TLGEKWKDRLNALSKEEFDAYKKRGVVEVA-------------TKGHAVSRGYAKLRWLVERGYVKPSGKVVDLGCGRGG 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  2593 WCYYAAAQKEVSGVKGFTLGRDGHEKPMNVQSLGWNIITFKDKTDIHRLEPVKCDTLLCDIGESSSSSVTEGERTVRVLD 2672
Cdd:cd20761   68 WSQYAAGLPKVTEVRGYTLGGPGHEEPRLVQSYGWNLVRLKSGVDVFYRPPERCDTLLCDIGESSPSPEVEEERTLRVLD 147

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 3288890  2673 TVEKWLACGVD-NFCVKVLAPYMPDVLEKLELLQRRFGGTVIRNPLSRNSTHEMYYVSGARSNVTFTVNQTS 2743
Cdd:cd20761  148 LVEKWLERNPTaNFCIKVLCPYHPEVIELLERLQRKGGGGLVRVPLSRNSTHEMYFVSGARGNIVNSVNMTS 219
Flavi_NS5_thumb pfam20483
Flavivirus RNA-directed RNA polymerase, thumb domain; Flaviviruses produce a large polyprotein ...
 3214-3377 7.01e-96

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: 307.11  E-value: 7.01e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    3214 ENVPFCSHHFHELQLKDGRRIVVPCREQDELIGRGRVSPGNGWMIKETACLSKAYANMWSLMYFHKRDMRLLSLAVSSAV 3293
Cdd:pfam20483    1 EEVDFCSHHYEKLTFKDGRTIVVPTRDQDEIIAKSRIRPGGDWSLDETAWLSKAYANMWLVNYFHLRTARALGFAYKSAV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    3294 PTSWVPQGRTTWSIHGKGEWMTTEDMLEVWNRVWITNNPHMQDKTMVKKWRDVPYLTKRQDKLCGSLIGMTNRATWASHI 3373
Cdd:pfam20483   81 PPNWVPTGRTTGSIHRPGPWMTPEDMLDVWNRVWFGESTHMPDGFRVRSWRHVGYLKKREEKLYDSLIGLRNRAYWRSNL 160


                   ....
gi 3288890    3374 HLVI 3377
Cdd:pfam20483  161 HLDV 164
Flavi_NS2A pfam01005
Flavivirus non-structural protein NS2A; NS2A is a hydrophobic protein about 25 kDa is size. ...
 1139-1324 1.49e-92

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: 299.83  E-value: 1.49e-92
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1139 GLVSMMIAMEVVLRKRQGPKQMLVGGVVLLGAMLVGQVTLLDLLKLTVAVGLHFHEMNNGGDAM-----YMALIAAFSIR 1213
Cdd:pfam01005    1 GLLCIMIAIEEVLRKRQGPKMLLTGGLALFGALLMGQLTLLDLIKLCIAVGLHFHEMANAGDAMgmgttYLALIAAFRIR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1214 PGLLIGFGLRTLWSPRERLVLTLGAAMV----------EIALGGVMG-------------GLWKYLNAVSLCILTINAVA 1270
Cdd:pfam01005   81 PGFAIGFGFRRLTSPRERLLLTLGAALVasvelpnsleEIADGGAMGimmlklltdfqshGLWATLLALSFCILTFNAHA 160

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....
gi 3288890    1271 SRKASNTILPLMALLTPVTMAEVRLAAMFFCAVVIIGVLHQNFKDTSMQKTIPL 1324
Cdd:pfam01005  161 ARKAMAMILPIMALFTPLCLAEVRLAAMFFCAVVIIGVLHQNFKDTSMQKTTWI 214
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1674-1819 5.43e-92

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 295.01  E-value: 5.43e-92
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1674 KGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGLDVKFHTQAFSAHGSGREVIDAMCHAT 1753
Cdd:pfam07652    1 KGTLTVLDLHPGAGKTRKVLPELVRECIDRRLRTLVLAPTRVVLAEMEEALRGLPIRYHTPAVSSEHTGREIVDVMCHAT 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 3288890    1754 LTYRMLEPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRARANESATILMTATPPGTSDEFPHSNG 1819
Cdd:pfam07652   81 FTQRLLSPVRVPNYEVIIMDEAHFTDPASIAARGYISTLVELGEAAAIFMTATPPGTSDPFPESNA 146
ps-ssRNAv_Flaviviridae_RdRp cd23178
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ...
 2957-3275 1.13e-80

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: 268.62  E-value: 1.13e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  2957 CVYNMMGKREKKLSEFGK--AKGSRAIWYMWLGARYLEFEALGFLNEDHWASRENSGGGVEGIGLQYLGYVIRDLAAMDG 3034
Cdd:cd23178    1 IPTTIMPKNEVFCVEPGKggRKPPRLIVYPDLGVRVAEKMALYDPVEVLPQVVGGSYYGFQYSPNQRVEILRKAWKSKKG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  3035 GGFYADDTAGWDTRITEADLDDEQEILNYMSP-HHKKLAQAVMEMTYKNKVVKVLRpapggkayMDVISRRDQRGSGQVV 3113
Cdd:cd23178   81 PMAYSYDTRCFDSTVTEDDIQVEEEIYQACSLkEARQAIVSITERLYVEGPMVNSD--------GQICGRRRCRASGVLT 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  3114 TYALNTITNLKVQLIRMAEAEmvihhqhvqdcdesvltrleawltehgcNRLKRMAVSGDDCVVRPIDD-------RFGL 3186
Cdd:cd23178  153 TSAGNT*TCYLK*LAACREAG----------------------------IRLPTMLVCGDDCVVICESDgtqedaaLLAA 204

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  3187 ALSHLNAMSKVRKDisewqPSKGWNDWENVPFCSHHFHELQLKDGRRIVVPCREQDELIGRGRVSPGNGwmikETACLSK 3266
Cdd:cd23178  205 FTEALTRYGKPPKD-----PPQPEYDLELIESCSHTVSEVRMKDGRRLYYLTRDPTTPLARAAWETGRH----EPINSWL 275


                 ....*....
gi 3288890  3267 AYANMWSLM 3275
Cdd:cd23178  276 GYIIMYALT 284
Flavi_NS4A pfam01350
Flavivirus non-structural protein NS4A; Flaviviruses encode a single polyprotein. This is ...
 2111-2254 1.83e-78

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: 256.37  E-value: 1.83e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2111 EVLVVLSELPDFLAKKGGEAMDTISVFLHSEEGSRAYRNALSMMPEAMTIVMLFILAGLLTSGMVIFFMSPKGISRMSMA 2190
Cdd:pfam01350    1 DLILEIGELPDFLAKKAGEALDNISMFHHSEEGGKAYRHALEELPDAIEILMLFALAALLTGGMTIFFLSGKGIGKMSIA 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 3288890    2191 MGTMAGCGYLMFLGGVKPTHISYIMLIFFVLMVVVIPEPGQQRSIQDNQVAYLIIGILTLVSAV 2254
Cdd:pfam01350   81 LGCMAACGALLFLAGVEPHHIAASIIIEFFLMVLLIPEPDQQRSIQDNQLAYLIIGILFLISAL 144
Flavi_NS2B pfam01002
Flavivirus non-structural protein NS2B; Flaviviruses encode a single polyprotein. This is ...
 1358-1484 1.22e-68

Flavivirus non-structural protein NS2B; Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. All, but two, are cleaved by the NS2B-NS3 protease complex.


Pssm-ID: 279357  Cd Length: 127  Bit Score: 227.58  E-value: 1.22e-68
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1358 VNEALAAAGLVGVLAGLAFQEMENFLGPIAVGGLLMMLVSVAGRVDGLELKKLGEVSWEEEAEISGSSARYDVALSEQGE 1437
Cdd:pfam01002    1 LNEAIAAAGIVGILAGLAFKEDENFAGPIAAGGLLIACVSIAGRSADLELEKAAEVSWEEEAEHSGASANIDVALQDDGE 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 3288890    1438 FKLLSEEKVPWDQVVMTSLALVGAALHPFALLLVLAGWLFHVRGARR 1484
Cdd:pfam01002   81 FKIKDEEKDDTDQILLKALALAGAALHPFAILATLAGWLFHQKGAQR 127
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 1678-1825 6.01e-58

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: 197.77  E-value: 6.01e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  1678 TVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGLDVKFHTQAFSAHGSGREVIDAMCHATLTYR 1757
Cdd:cd17931    4 TVLDLHPGAGKTTRVLPQIIREAIKKRLRTLVLAPTRVVAAEMYEALRGLPIRYRTGAVKEEHGGNEIVDYMCHGTFTCR 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 3288890  1758 MLEPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRARANESATILMTATPPGTSDEFPHSNGEIEDVQ 1825
Cdd:cd17931   84 LLSPKRVPNYNLIIMDEAHFTDPASIAARGYIHTRVEMGEAAVIFMTATPPGTVTPFPQSNHPIEDFE 151
Flavi_glycop_C pfam02832
Flavivirus glycoprotein, immunoglobulin-like domain;
581-676 4.90e-57

Flavivirus glycoprotein, immunoglobulin-like domain;


Pssm-ID: 280922  Cd Length: 97  Bit Score: 192.94  E-value: 4.90e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     581 SYKICTDKMFFVKNPTDTGHGTVVMQVKV-SKGAPCRIPVIVADDLTAAINKGILVTVNPIASTNDDEVLIEVNPPFGDS 659
Cdd:pfam02832    1 SYKICTDKFFFEKEPADTGHGTVLMQVKVeGKDAPCKIPVFSADDEKAAINKGILITANPIASDKDDEVLIEAEPPFGDS 80

                           90
                   ....*....|....*..
gi 3288890     660 YIIVGRGDSRLTYQWHK 676
Cdd:pfam02832   81 YIIVGAGDKALKLQWFK 97
Peptidase_S7 pfam00949
Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that ...
 1504-1655 2.31e-48

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: 169.54  E-value: 2.31e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1504 LEDGIYGIFQSTFLGASQRGVGVAQGGVFHTMWHVTRGAFLVRNGKKLIPSWASVKEDLVAYGGSWKLEGRWDGeEEVQL 1583
Cdd:pfam00949    1 LTDGILRFFQSSLLGRSQRGVGVLQEGVFHTMWHPTRGTKLHTQGIKTSPSWASVKQDLVDYGGSWKFQGKWLG-EEYQQ 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 3288890    1584 IaavpgknvvnvqtkpslfkvrnGGEIGAVALDYPSGTSGSPIVNRNGEVIGLYGNGILVGDNSFVSAISQT 1655
Cdd:pfam00949   80 Y----------------------GYGLGITDLNLSSGSSGSLVLNQNKQIVGIYFATVEVDDNSFVVGLAQL 129
flavi_E_stem TIGR04240
flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal ...
 682-778 7.88e-48

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: 166.66  E-value: 7.88e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     682 GKLFTQTMKGVERLAVMGDTAWDFSSAGGFFTSVGKGIHTVFGSAFQGLFGGLNWITKVIMGAVLIWVGINTRNMTMSMS 761
Cdd:TIGR04240    1 GKAFELTMRGAERMAILGDAAWDFGSVGGVFTSIGKALHQVFGGAFRALFGGVSWITKILIGVLLIWLGLNSRNTTLSLT 80

                           90
                   ....*....|....*..
gi 3288890     762 MILVGVIMMFLSLGVGA 778
Cdd:TIGR04240   81 FLAVGGILLFLTTGVGA 97
Flavi_E_C cd12149
Immunoglobulin-like domain III (C-terminal domain) of Flavivirus envelope glycoprotein E; The ...
 588-677 1.45e-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: 157.08  E-value: 1.45e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890   588 KMFFVKNPTDTGHGTVVMQVKVSK-GAPCRIPVIVADDLTAAINKGILVTVNPIASTNDDEVLIEVNPPFGDSYIIVGRG 666
Cdd:cd12149    1 KFSWKKEPADTGHGTVVMEVKYSGtDAPCRIPVRVVDSGSGGENVGRLITVNPIITNANSKVFIEVEPPFGDSYIVVGVG 80

                         90
                 ....*....|.
gi 3288890   667 DSRLTYQWHKE 677
Cdd:cd12149   81 DTRLKHQWFQK 91
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
 1821-1963 2.69e-44

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: 158.58  E-value: 2.69e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  1821 IEDVQTDIPSEPWNTGHDWILADKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYPTIKQKKPDFILATDIA 1900
Cdd:cd18806    1 IEDVALEIPGRIWFYGKAWITIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEYPKIKTIDWDFVVTTDIS 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 3288890  1901 EMGANLCVERVLDCRTAFKPVLVDEGR-KVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYS 1963
Cdd:cd18806   81 EMGANFDADRVIDCRTCVKPTILFSGDfRVILTGPVPQTAASAAQRRGRTGRNPAQERDIYRFV 144
capping_2-OMTase_viral cd20754
viral Cap-0 specific (nucleoside-2'-O-)-methyltransferase; Cap-0 specific (nucleoside-2'-O-) ...
 2565-2743 6.07e-42

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: 152.98  E-value: 6.07e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  2565 TAKLRWFHERGYVKLE-GRVIDLGCGRGGWCYYAAAQKEVSGVKGFTLGRDGHekpmnvqsLGWNIITFKDKTDIHRLE- 2642
Cdd:cd20754    1 QAKLLQLEEYFLYKPEkMRVIYIGCAPGGWLYYLRDWFEGTLWVGFDPRDTDP--------LGYNNVITVNKFFDHEHTk 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  2643 ----PVKCDTLLCDIGESSSSSVT-EGERTVRVLDTVEKWLAC---GVDNFCVKVLAPYMPDVleklellQRRFGGTVIR 2714
Cdd:cd20754   73 lkflPNKKDLLICDIRSDRSSHVTkEEDTTESFLTLQEGYIATklaKVGSICVKVRAPDLKDD-------GHFSSGTLFP 145

                        170       180       190
                 ....*....|....*....|....*....|....
gi 3288890  2715 NPLsRNSTHEMYYVSG----ARSNVTF-TVNQTS 2743
Cdd:cd20754  146 QPY-AASSSEMRLFSAnydaSQIKVVKaDVEKYE 178
Flavi_M pfam01004
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with virions ...
 212-285 2.48e-38

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: 138.87  E-value: 2.48e-38
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 3288890     212 IDLPTHENHGLKTRQEKWMTGRMGERQLQKIERWFVRNPFFAVTALTIAYLVGSNMTQRVVIALLVLAVGPAYS 285
Cdd:pfam01004    1 VALPPHVGLGLETRTETWMSSRGAWKQLQKVETWALRNPGFTVIALFIAHLIGSSITQKVIIFILLLLVTPAYS 74
Flavi_M cd17038
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with a ...
 211-285 8.03e-31

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: 117.35  E-value: 8.03e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 3288890   211 AIDLPTHENHGLKTRQEKWMTGRMGERQLQKIERWFVRNPFFAVTALTIAYLVGSNMTQRVVIALLVLAVGPAYS 285
Cdd:cd17038    1 SVAIPPHGTGGLTTRKETWLSTSNGKEHLTRVERWVLRNPGYALAAVALAWMLGSSTTQRVIIIVLLLLVAPAYA 75
FtsJ pfam01728
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...
 2561-2732 1.48e-27

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: 111.91  E-value: 1.48e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2561 VSRGTAKLRWFHER-GYVKLEGRVIDLGCGRGGWCYYaAAQKEVSGVKGFTLGRDGHEKPMNVQslgwNIITFkdKTDIH 2639
Cdd:pfam01728    2 RSRAAYKLLEIDEKfGLLKPGKTVLDLGAAPGGWSQV-ALQRGAGKVVGVDLGPMQLWKPRNDP----GVTFI--QGDIR 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    2640 RLEPV---------KCDTLLCDIGESSSS-SVTEGERTVRVLDTVEKW----LACGvDNFCVKVLapYMPDVLEKLELLQ 2705
Cdd:pfam01728   75 DPETLdlleellgrKVDLVLSDGSPFISGnKVLDHLRSLDLVKAALEValelLRKG-GNFVCKVF--QGEDFSELLYLLK 151

                          170       180
                   ....*....|....*....|....*...
gi 3288890    2706 RRFGGTVIRNP-LSRNSTHEMYYVSGAR 2732
Cdd:pfam01728  152 LGFEKVGVFKPpASRPESSEEYLVCLGF 179
Flavi_capsid pfam01003
Flavivirus capsid protein C; Flaviviruses are small enveloped viruses with virions comprised ...
 5-125 4.92e-26

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: 105.10  E-value: 4.92e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890       5 KAQGKTLGVNMVRRGV-RSLSNKIKQKTKQIGNRPGPSRGVQGFIFFFLFnilTGKKITAHLKRLWKMLDPRQGLAVLRK 83
Cdd:pfam01003    1 GKPGKGRGVNMLKRGAkRVPLKKTKRKTGQLLDGRGPLRLVLAFLAFFRF---TAIAPTPGLKKRWRTVPKRQAIKHLRK 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 3288890      84 VKRVVASLMRGLSSRKRRShdvlTVQFLILGMLLMTGGVTLV 125
Cdd:pfam01003   78 FKKEVGTLLDGLNRRGKRR----SKRGGWTGLLLMLGLLTLV 115
Flavi_propep pfam01570
Flavivirus polyprotein propeptide; The flaviviruses are small enveloped animal viruses ...
 132-203 2.09e-15

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


Pssm-ID: 366710  Cd Length: 78  Bit Score: 73.69  E-value: 2.09e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 3288890     132 LLNVTSEDLGKTFSVGTGNCTTNILEAKYWCPDSMEYNCPNLSPREEPDDIDCWCYGVENVRVAYGKCDSAG 203
Cdd:pfam01570    7 LLNVTSEDLGKTFSVGTGNCTTNILEAKYWCPDSMEYNCPNLSPREEPDDIDCWCYGVENVRVAYGKCDSAG 78
DEXDc smart00487
DEAD-like helicases superfamily;
1668-1814 2.25e-12

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 68.67  E-value: 2.25e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     1668 IPTMLKKGMTTVLDFHPGAGKTRRFLpQILAECARRRL--RTLVLAPTRV----VLSEMKEAFHGLDVKFHTQ--AFSAH 1739
Cdd:smart00487   17 IEALLSGLRDVILAAPTGSGKTLAAL-LPALEALKRGKggRVLVLVPTRElaeqWAEELKKLGPSLGLKVVGLygGDSKR 95

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     1740 GSGREVIDAMCHATL-TYRML------EPTRVVNWEVIIMDEAHFLDPASIAARgWAAHRARANESA-TILMTATPPGTS 1811
Cdd:smart00487   96 EQLRKLESGKTDILVtTPGRLldllenDKLSLSNVDLVILDEAHRLLDGGFGDQ-LEKLLKLLPKNVqLLLLSATPPEEI 174


                    ...
gi 3288890     1812 DEF 1814
Cdd:smart00487  175 ENL 177
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 1675-1806 2.68e-12

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: 67.04  E-value: 2.68e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  1675 GMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGL-DVKFHTQAFSaHGS----------GR 1743
Cdd:cd00046    1 GENVLITAPTGSGKTLAALLAALLLLLKKGKKVLVLVPTKALALQTAERLRELfGPGIRVAVLV-GGSsaeereknklGD 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 3288890  1744 EVIDAMCHATLTYRMLEPTRVV--NWEVIIMDEAHFLDPASIAARGWAA--HRARANESATILMTAT 1806
Cdd:cd00046   80 ADIIIATPDMLLNLLLREDRLFlkDLKLIIVDEAHALLIDSRGALILDLavRKAGLKNAQVILLSAT 146
DEXHc_RHA-like cd17917
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ...
 1678-1807 2.77e-11

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: 64.40  E-value: 2.77e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  1678 TVLDFHPGAGKTRRfLPQILAE---CARRRLRTLVLAPTRV--------VLSEMKEAfHGLDVKFHTQaFSAHGSGREVI 1746
Cdd:cd17917    4 VVIVGETGSGKTTQ-VPQFLLEdglAKGGKGRIVCTQPRRIaaisvaerVAEERGEK-LGEEVGYQIR-FESKTSSKTRI 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 3288890  1747 DAMCHATLTYRMLEPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRARANESAT-ILMTATP 1807
Cdd:cd17917   81 KFCTDGILLRELLSDPLLSGYSHVILDEAHERSLDTDFLLGLLKDLLRKRPDLKvILMSATL 142
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
1684-1807 1.75e-07

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 56.96  E-value: 1.75e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  1684 PGAGKTRrflpqILAECARR---RLRTLVLAPTRVVLSEMKEAFHgldvKFHTQAFSAHG---SGREVIDAMcHATLTYR 1757
Cdd:COG1061  109 TGTGKTV-----LALALAAEllrGKRVLVLVPRRELLEQWAEELR----RFLGDPLAGGGkkdSDAPITVAT-YQSLARR 178

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 3288890  1758 MLEPTRVVNWEVIIMDEAHfldpaSIAARGWAAHRARANESATILMTATP 1807
Cdd:COG1061  179 AHLDELGDRFGLVIIDEAH-----HAGAPSYRRILEAFPAAYRLGLTATP 223
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 1679-1807 1.93e-07

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: 53.08  E-value: 1.93e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  1679 VLDFHPGAGKTrrfLPQILAECARRRLRTLVLAPTRVVLSEMKEAFhgldvkfhTQAFSAH-----GSGREVIDAMCHAT 1753
Cdd:cd17926   22 ILVLPTGSGKT---LTALALIAYLKELRTLIVVPTDALLDQWKERF--------EDFLGDSsigliGGGKKKDFDDANVV 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 3288890  1754 LT-----YRMLEPTRVV--NWEVIIMDEAHfldpaSIAARGWAAHRARANESATILMTATP 1807
Cdd:cd17926   91 VAtyqslSNLAEEEKDLfdQFGLLIVDEAH-----HLPAKTFSEILKELNAKYRLGLTATP 146
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 1684-1807 9.27e-07

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 54.85  E-value: 9.27e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  1684 PGAGKTrrflPQILAECARRRL-----RTLVLAPTRVV---LSEMKEAFHGLDVKFHtqafsaHGSGREV--IDAMCHAT 1753
Cdd:COG0553  269 MGLGKT----IQALALLLELKErglarPVLIVAPTSLVgnwQRELAKFAPGLRVLVL------DGTRERAkgANPFEDAD 338

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 3288890  1754 L---TY----RMLEPTRVVNWEVIIMDEAHFL-DPASIAARgwAAHRARAneSATILMTATP 1807
Cdd:COG0553  339 LvitSYgllrRDIELLAAVDWDLVILDEAQHIkNPATKRAK--AVRALKA--RHRLALTGTP 396
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 2938-3247 4.89e-06

RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage. RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D structure of the catalytic center of a wide range of RdRps, including those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing a number of conserved amino acid residues. This subfamily represents the RNA-dependent RNA polymerases from all positive-strand RNA eukaryotic viruses with no DNA stage.


Pssm-ID: 238843 [Multi-domain]  Cd Length: 278  Bit Score: 51.13  E-value: 4.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  2938 FWELVDEERKLHQQGR---CRTCVynmmgKREKKLSEFGKAKGSRAIW-----YMWLGARYLefealgflneDHWASR-- 3007
Cdd:cd01699    1 LEKAVESLEDLPLIRPdlvFTTFL-----KDELRPLEKVEAGKTRLIQprpldYNIALRMYL----------GPFEAKlm 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  3008 ENSGGGVEGIGL---QYLGYVIRDLAAMDGGGFYADDTAGWDTRITEADLDDEQEILNYMSPHHKKLAQAVMEMTYKNKV 3084
Cdd:cd01699   66 KNRGGLPIAVGInpySRDWTILANKLRSFSPVAIALDYSRFDSSLSPQLLEAEHSIYNALYDDDDELERRNLLRSLTNNS 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  3085 VKVLrpapggkaYMDVISRRDQRGSGQVVTYALNTITNlkvqlirmaeaEMVIHHqhvqdcdesvltrleAWLTEHGCNR 3164
Cdd:cd01699  146 LHIG--------FNEVYKVRGGRPSGDPLTSIGNSIIN-----------CILVRY---------------AFRKLGGKSF 191

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  3165 LK--RMAVSGDDCV--VRPIDDRFglalsHLNAMSKVRKDI-----SEWQPSKGWNDWENVPFCSHHFhelqLKDGRRIV 3235
Cdd:cd01699  192 FKnvRLLNYGDDCLlsVEKADDKF-----NLETLAEWLKEYgltmtDEDKVESPFRPLEEVEFLKRRF----VLDEGGGW 262

                        330
                 ....*....|..
gi 3288890  3236 VPCREQDELIGR 3247
Cdd:cd01699  263 RAPLDPSSILSK 274
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
 1684-1807 3.22e-04

DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350677 [Multi-domain]  Cd Length: 182  Bit Score: 44.48  E-value: 3.22e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  1684 PGAGKTRR---FLpQILAECARRRLRTLVLAPTRVVLSEMKEA---FHGLDVkfhtqaFSAHGSGREVIDAMCHATL--- 1754
Cdd:cd17919   28 MGLGKTLQaiaFL-AYLLKEGKERGPVLVVCPLSVLENWEREFekwTPDLRV------VVYHGSQRERAQIRAKEKLdkf 100

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 3288890  1755 -----TYRML----EPTRVVNWEVIIMDEAHFL-DPASIAARgwAAHRARANesATILMTATP 1807
Cdd:cd17919  101 dvvltTYETLrrdkASLRKFRWDLVVVDEAHRLkNPKSQLSK--ALKALRAK--RRLLLTGTP 159
HELICc smart00490
helicase superfamily c-terminal domain;
1860-1951 5.90e-04

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 41.04  E-value: 5.90e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890     1860 MAASLRKAGKSVVVLNRKTFEREYPTI----KQKKPDFILATDIAEMGANL-CVERVLDCRtafkpvlvdegrkvaikgp 1934
Cdd:smart00490    3 LAELLKELGIKVARLHGGLSQEEREEIldkfNNGKIKVLVATDVAERGLDLpGVDLVIIYD------------------- 63

                            90
                    ....*....|....*..
gi 3288890     1935 LRISASSAAQRRGRIGR 1951
Cdd:smart00490   64 LPWSPASYIQRIGRAGR 80
Cas3_I cd09639
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ...
 1769-1974 7.36e-04

CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I


Pssm-ID: 187770 [Multi-domain]  Cd Length: 353  Bit Score: 44.73  E-value: 7.36e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  1769 VIIMDEAHFLDPASIAARGWAAHRARANESATILMTATPPGTSDEFPHSNGEIEDVQTdIPSEPWNTGHDWILADKRpta 1848
Cdd:cd09639  126 LLIFDEVHFYDEYTLALILAVLEVLKDNDVPILLMSATLPKFLKEYAEKIGYVEENEP-LDLKPNERAPFIKIESDK--- 201

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  1849 wfLPSIRAANVMAASLRKAGKSVVVLN-------------RKTFEREYPTI--------------------KQKKPDFIL 1895
Cdd:cd09639  202 --VGEISSLERLLEFIKKGGSVAIIVNtvdraqefyqqlkEKGPEEEIMLIhsrftekdrakkeaelllefKKSEKFVIV 279

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  1896 ATDIAEMGANLCVErvldcrtafkpVLVDEgrkvaikgplrIS-ASSAAQRRGRIGRNPNRDGDSYYYSEPTSENNAHHV 1974
Cdd:cd09639  280 ATQVIEASLDISVD-----------VMITE-----------LApIDSLIQRLGRLHRYGEKNGEEVYIITDAPDGKGQKP 337
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 1685-1814 7.84e-04

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


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 43.00  E-value: 7.84e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1685 GAGKTRRF-LPqILAECARRR--LRTLVLAPTRV----VLSEMKEAFHGLDVKFHtqafSAHG--SGREVIDAMCHATLT 1755
Cdd:pfam00270   24 GSGKTLAFlLP-ALEALDKLDngPQALVLAPTRElaeqIYEELKKLGKGLGLKVA----SLLGgdSRKEQLEKLKGPDIL 98

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 3288890    1756 Y-------RMLEPTRVV-NWEVIIMDEAH-FLDPASIAarGWAAHRARANESA-TILMTATPPGTSDEF 1814
Cdd:pfam00270   99 VgtpgrllDLLQERKLLkNLKLLVLDEAHrLLDMGFGP--DLEEILRRLPKKRqILLLSATLPRNLEDL 165
Cfa COG2230
Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport ...
 2565-2618 1.23e-03

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


Pssm-ID: 441831 [Multi-domain]  Cd Length: 158  Bit Score: 42.22  E-value: 1.23e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 3288890  2565 TAKLRWFHERGYVKLEGRVIDLGCGRGGWCYYAAAQKEVSgVKGFTLGRDGHEK 2618
Cdd:COG2230   37 EAKLDLILRKLGLKPGMRVLDIGCGWGGLALYLARRYGVR-VTGVTLSPEQLEY 89
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 1845-1962 2.06e-03

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


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 39.61  E-value: 2.06e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  1845 RPTAWFLPSIRAANVMAASLrkagkSVVVlnrktfereyptikqkkpdfilATDIAEMGanlcvervldcrtafkpVLVD 1924
Cdd:cd18785    4 VKIIVFTNSIEHAEEIASSL-----EILV----------------------ATNVLGEG-----------------IDVP 39

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 3288890  1925 EGRKVAIKGPlRISASSAAQRRGRIGRNPNRDGDSYYY 1962
Cdd:cd18785   40 SLDTVIFFDP-PSSAASYIQRVGRAGRGGKDEGEVILF 76
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 1665-1806 7.39e-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: 40.01  E-value: 7.39e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890  1665 LQEIPTMLKKGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVV-------LSEMKEAFHGLDVKFHTQAFS 1737
Cdd:cd17990    7 LPALRAALDAGGQVVLEAPPGAGKTTRVPLALLAELWIAGGKIIVLEPRRVAaraaarrLATLLGEAPGETVGYRVRGES 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 3288890  1738 AhGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAH--FLDPASIAARGWAAHRARANESATILMTAT 1806
Cdd:cd17990   87 R-VGRRTRVEVVTEGVLLRRLQRDPELSGVGAVILDEFHerSLDADLALALLLEVQQLLRDDLRLLAMSAT 156
cas3_core TIGR01587
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ...
 1769-1893 8.04e-03

CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.


Pssm-ID: 273707 [Multi-domain]  Cd Length: 359  Bit Score: 41.67  E-value: 8.04e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3288890    1769 VIIMDEAHFLDPASIAARGWAAHRARANESATILMTATPPGTSDEFPHSNGEIEDVQTDIPSEPWN-TGHDWILADKRpt 1847
Cdd:TIGR01587  127 LLIFDEVHFYDEYTLALILAVLEVLKDNDVPILLMSATLPKFLKEYAEKIGYVEFNEPLDLKEERRfENHRFILIESD-- 204

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 3288890    1848 awFLPSIRAANVMAASLRKAGKSVVVLNrkTFERE---YPTIKQKKPDF 1893
Cdd:TIGR01587  205 --KVGEISSLERLLEFIKKGGSIAIIVN--TVDRAqefYQQLKEKAPEE 249
 
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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