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Conserved domains on  [gi|219964674|gb|ACL68401|]
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polyprotein [Hepacivirus hominis]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Hepacivirus_RdRp cd23202
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
2434-2951 0e+00

RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the RdRp of RNA viruses belonging to the Hepacivirus genus within the family Flaviviridae, order Amarillovirales. The genus Hepacivirus includes hepatitis C virus, a major human pathogen causing progressive liver disease, and several other viruses of unknown pathogenicity that infect horses, rodents, bats, cows and primates. Infections are typically persistent and target the liver. Virions of Hepacivirus 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. 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: 438052  Cd Length: 518  Bit Score: 1142.27  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2434 CAAEEPKLPISPLSNSLLRHHNMVYATTSRSAT*RQKKVTFDRLQVVDQHYMTTLKEIKARASGVKAPTLSVEEACALTP 2513
Cdd:cd23202     1 CAAEEEKLPISPLSNSLLRHHNLVYSTTSRSASERQKKVTFDRLQVLDPHYDDVLKEAKARASGVKARLLSVEEACSLTP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2514 PHSAKSKFGYGAKDVRSLARKAVNHINSVWEDLLEDNVTPIPTTIMAKSEVFSVKPEKGGRKP*RLIVYPDLGVRVCEKR 2593
Cdd:cd23202    81 PHSARSKFGYGAKDVRSLSRKAVNHINSVWEDLLEDSETPIPTTIMAKNEVFCVTPEKGGRKPARLIVYPDLGVRVCEKM 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2594 ALYNVVQKLPQAVMGEAYGFQYSPAQRVERLLKSWNSKRVPMGFPYDTRCFDSTVTERDIQVEEEVYQCCDLDPEARKVI 2673
Cdd:cd23202   161 ALYDVAPKLPKAVMGEAYGFQYSPAQRVEFLLKMWRSKKTPMGFSYDTRCFDSTVTERDIRTEESIYQCCDLDPEARKAI 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2674 SSLTERLYKGGPMFN*KGDLCGYRRCRASGVFTTSFGNTLTCYLKATAAARAAGLKDYDMLVCGDDLVIIAESDGVEEDK 2753
Cdd:cd23202   241 RSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPTMLVCGDDLVVIAESAGVEEDA 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2754 QALRAFTEAMTRYSAPPGDAPQ*AYDLELITSCSSNVSVAHDAAGKRVYYLTRDPETPLARAAWETVRHTPVNSWLGNII 2833
Cdd:cd23202   321 AALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDATGKRYYYLTRDPTTPLARAAWETARHTPVNSWLGNII 400
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2834 LYAPTIWVRMVLMTHFFSILQSQEALERALDFDMYGVTYSITPLDLPAIIQRLHGLSAFTLHGYSPHELNRVAGSLRKLG 2913
Cdd:cd23202   401 MYAPTLWVRMVLMTHFFSILLAQEQLEKALDFEMYGNTYSIPPLDLPAIIQRLHGLSAFSLHGYSPRELNRVAAALRKLG 480
                         490       500       510
                  ....*....|....*....|....*....|....*...
gi 219964674 2914 VPPLRVWRHRARAVRAKLIAQGGKARICGIYLFNWAVK 2951
Cdd:cd23202   481 VPPLRAWRHRARAVRAKLIAQGGKAAICGKYLFNWAVK 518
HCV_NS1 super family cl03263
Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region ...
387-729 0e+00

Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region of hepatitis C virus varies greatly between viral isolates. E2 is thought to encode a structurally unconstrained envelope protein.


The actual alignment was detected with superfamily member pfam01560:

Pssm-ID: 110557  Cd Length: 344  Bit Score: 666.94  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   387 VSGGA*GHTTSGLASMF*RGPSQ*IQLINTNGSWHVNRTALNCNDSINTGFIAGLIYHWKFNSSGCPERLASCKRLSDFB 466
Cdd:pfam01560    2 VTGGSAARTTRGLVSLFSPGAKQNIQLINTNGSWHINRTALNCNDSLQTGFLASLFYTHRFNSSGCPERLASCRSIDDFR 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   467 QGWGGLGSSNISgPSDDKPYCWHYAPRPCGVVPAGKVCGPVYCFTPSPVVVGTTDRLGLPTYTWG*NETDVFLLNSTRPP 546
Cdd:pfam01560   82 QGWGPITYEETN-PEDQRPYCWHYPPRPCGIVPASSVCGPVYCFTPSPVVVGTTDRSGAPTYSWGENETDVFLLNNTRPP 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   547 SGGWFGCTWMNSTGFVKTCGASPCRV-TTSNGSWDCPTDCFRKHPDATYAKCGSGPWLTPRCMVHYPYRLWHYPCTVNYT 625
Cdd:pfam01560  161 QGNWFGCTWMNSTGFTKTCGAPPCRIgGDGNNTLLCPTDCFRKHPDATYTKCGSGPWLTPRCMVDYPYRLWHYPCTVNFT 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   626 IFKVRMYVGGIEHRLDAACNWTRGEPCGLEDRDRTELSPLLLSTTQWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGI 705
Cdd:pfam01560  241 IFKVRMYVGGVEHRLNAACNWTRGERCDLEDRDRSELSPLLLSTTEWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGL 320
                          330       340
                   ....*....|....*....|....
gi 219964674   706 GSSVVSWAIKWEYVVLAFLLLADA 729
Cdd:pfam01560  321 GSAVTSFAIKWEYVVLLFLLLADA 344
HCV_NS2 pfam01538
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ...
811-1005 1.64e-104

Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single polyprotein of about 3000 amino acids. Generation of the mature non-structural proteins relies on the activity of viral proteases. Cleavage at the NS2/NS3 junction is accomplished by a metal-dependent autoprotease encoded within NS2 and the N-terminus of NS3.


:

Pssm-ID: 366698  Cd Length: 195  Bit Score: 332.71  E-value: 1.64e-104
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   811 DAEVAGSLGGAVICLLTILTLSPWYKRWLAWIIWWLQYYLTRAEALLYVYIPPLEVRGGRDSLIILAVLLHPGLVFEVTK 890
Cdd:pfam01538    1 DTEDAGWLGAAVLSWITLFTLTPTYKGLLAKLLWWLQYCIARQEARLHVWVPPLGVRGGRDAVILLWCLAHPDLVFDVTK 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   891 HLLAILGPLYVLQASLLRIPYFVRAHALIKICGFVRGVAHGKFVQMAMLKLGALTGTYVYDHLTPLSDWAADGLKDLAVA 970
Cdd:pfam01538   81 ILLAILGPLYLLQASLLRVPYFVRAARLLRSCVLVRHLAGGKYVQMALLKLGRWTGTYLYDHLGPLSDWAAEGLRDLAVA 160
                          170       180       190
                   ....*....|....*....|....*....|....*
gi 219964674   971 LEPVIFTPMEKKVITWGADTAACGDIIRGLPVSAR 1005
Cdd:pfam01538  161 LEPVVFSPMECKIITWGADTAACGDIVHGLPVSAR 195
HCV_env super family cl03255
Hepatitis C virus envelope glycoprotein E1;
195-382 2.87e-101

Hepatitis C virus envelope glycoprotein E1;


The actual alignment was detected with superfamily member pfam01539:

Pssm-ID: 110536  Cd Length: 190  Bit Score: 323.37  E-value: 2.87e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   195 RNASGVYHITNDCPNSSIVYETEHQIMHLPGCVPCVRT*N*SRCWVPLTPTVAA*YPNAPLESMRRHVDLMVGAATMCSA 274
Cdd:pfam01539    3 RNISGSYHVTNDCSNSSITWQLADAVLHTPGCVPCEREGNTSRCWIAVTPNVAVRHRGALTTSLRTHVDMLVMAATLCSA 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   275 LYVGDVCGGIFLVGQMFSF*PRRHWTTQDCNCSIYTGHITGHRMAWDMMMNWSPTTTLVLAQVMRLPSALGDMFAGGHWG 354
Cdd:pfam01539   83 LYVGDLCGSVMLVSQLFTVSPQRHWFTQDCNCSIYPGHITGHRMAWDMMMNWSPTATMILAYALRVPEAVLDIIAGAHWG 162
                          170       180
                   ....*....|....*....|....*...
gi 219964674   355 VLAGLAFFSMQGNWAKVILVLFLFAGVD 382
Cdd:pfam01539  163 VLFGLAYFSMQGAWAKVLVILLLFAGVD 190
HCV_NS5a_C super family cl15181
HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C ...
2179-2420 1.01e-89

HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C virus. This family contains the C-terminal region of the NS5A protein. CC The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR.


The actual alignment was detected with superfamily member pfam12941:

Pssm-ID: 289693  Cd Length: 242  Bit Score: 292.61  E-value: 1.01e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2179 SHITAEAAARRLARGSPPSEASSSASQLSAPSLKATCTTNHHSPDADLIEANLLWRQEMGGNITRVESENKVVVLDSFEP 2258
Cdd:pfam12941    1 SHITAEAAGRRLARGSPPSMASSSASQLSAPSLKATCTANHDSPDAELIEANLLWRQEMGGNITRVESENKVVILDSFDP 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2259 LVAE*DSGEVSVPAEILRRSKRFPKPLPIWARPDYNPPLIZPWKQPDYTPPVVHGCALPPSKPTPVPPPRRKRAIVLTES 2338
Cdd:pfam12941   81 LVAEEDEREVSVPAEILRKSRRFAPALPVWARPDYNPLLVETWKKPDYEPPVVHGCPLPPPRSPPVPPPRKKRTVVLTES 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2339 NVSSALADLAAKVLSQPDADVDSGTGLTLPSEtstPDPPIADDRSDDGSFSSMPPLEGEPGDPDLTSDSWSTVSG---SE 2415
Cdd:pfam12941  161 TLPTALAELATKSFGSSSTSGITGDNTTTSSE---PAPSGCPPDSDVESYSSMPPLEGEPGDPDLSDGSWSTVSSgadTE 237

                   ....*
gi 219964674  2416 DVVCC 2420
Cdd:pfam12941  238 DVVCC 242
HCV_NS4b pfam01001
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
1728-1921 1.38e-82

Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. However, it is known that NS4b interacts with NS4a and NS3 to form a large replicase complex to direct the viral RNA replication.


:

Pssm-ID: 110032  Cd Length: 192  Bit Score: 270.02  E-value: 1.38e-82
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  1728 FKQKALGVLQVASARAQEATPVVQSNFAKLEQFWAKHMWNFVSGVQYLAGLSTLPGNPAIASLMSFTAAVTSPLTTQQTL 1807
Cdd:pfam01001    1 FAFKALGLLPPAIDKAESITPAVASLDTKFEQFWAKHMWNFRSGIQYLAGLYTLPRNPPLAVLASFLAGMTSPLPTHVRL 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  1808 LFNILGGWVASQIATPTASTAFVVSGLAGAAVGSVGLGKILVDILAGYGAGVAGAVVTFKIMSGEVPTTEDLVNLLPAIL 1887
Cdd:pfam01001   81 ALALLGGWGATQLGTPSGGLAFVGAGFAGAAVGSSWLGRVLVDVLGGYEAAVNAASLTFKIMSGELPTAEDLWNLLPCLL 160
                          170       180       190
                   ....*....|....*....|....*....|....
gi 219964674  1888 SPGALVVGVVCAAILRRHVgpGEGAVQWMNRLIA 1921
Cdd:pfam01001  161 SPGASVVGVALAALLRSHK--GEGAVQWMNRLLT 192
HCV_capsid pfam01543
Hepatitis C virus capsid protein;
2-115 2.65e-72

Hepatitis C virus capsid protein;


:

Pssm-ID: 144947  Cd Length: 121  Bit Score: 237.67  E-value: 2.65e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674     2 STNPKPQRKTKRNTNRRPMDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARR*EGRSWAQPGY 81
Cdd:pfam01543    1 STNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPEGRSWLSPGT 80
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 219964674    82 PWP------LYGNEG-CGWAGWLLSPRGSRPSWGPNDPRRR 115
Cdd:pfam01543   81 LGPstamraLYGNDGsCGWAGWLLPPRGSRPSWGQNDPRRR 121
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
1224-1366 3.08e-50

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


The actual alignment was detected with superfamily member cd17931:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 151  Bit Score: 175.43  E-value: 3.08e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 1224 QVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGSYMSKAhgiDPNIRSGVRTITTGA--PITYSTYG 1297
Cdd:cd17931     2 QLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGneIVDYMCHG 78
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 219964674 1298 KFLaDGGCGGGA---YDIIICDECHSTDSTTILGIGTVLDQAETaGVRLVVLATATPPGSITTPH---SNIEEIA 1366
Cdd:cd17931    79 TFT-CRLLSPKRvpnYNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDFE 151
HCV_NS5a_1b pfam08301
Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ...
2068-2168 2.25e-48

Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. This region corresponds to the 1b domain.


:

Pssm-ID: 149382  Cd Length: 102  Bit Score: 168.31  E-value: 2.25e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2068 GAGVPIPAPNYKFALWRVSAEEYVEIRRVGEFHYVTGMTQDNIkCPCQVPAPEFF--TEVDGVRLHRYAPPCKPLLRDEV 2145
Cdd:pfam08301    1 GPAVPLPPPNYGPALWRVGAEDYVEVVRVGDTHYVTATSCYNL-CPCQVPRPEFFapTEVDGVRVSWYAPPCKPLLVYEV 79
                           90       100
                   ....*....|....*....|...
gi 219964674  2146 QFTVGLNTFVVGSQLPCEPEPDV 2168
Cdd:pfam08301   80 GQSVGLDGYGVRSQLPCELEPDV 102
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
1362-1483 4.08e-43

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: 155.11  E-value: 4.08e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 1362 IEEIALPTTGEVPFYGKAIPleVIKGGRHLIFCHSKKKCDELAKQLSSLGLNAVAYYRGLDVSV---IPTSGDVVVCATD 1438
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 219964674 1439 ALMTGFTGNFDSVIDCNTSVIQTVDFSLDptFSIETT-TVPQDAVS 1483
Cdd:cd18806    79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAAS 122
HCV_core super family cl46603
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
116-190 7.65e-29

Hepatitis C virus core protein; The viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases. The N terminus of the core protein is involved in transcriptional repression.


The actual alignment was detected with superfamily member pfam01542:

Pssm-ID: 480943  Cd Length: 75  Bit Score: 111.69  E-value: 7.65e-29
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 219964674   116 SRNLGKVIDTLTCGFADLMGYIPLVGAPVGGVARALAHGVRAVEDGINYATGNLPGCSFSIFLLALLSCLTTPAS 190
Cdd:pfam01542    1 MRNLGKPIDKLKCGFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRATAKGNEPGCPFGIFLLALKACLPEGAS 75
HCV_p7 cd20903
Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for ...
747-795 1.29e-15

Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for virus production. The p7 monomer is comprised of 2 trans-membrane helices connected by a cytosolic loop, and oligomerizes to form cation-specific ion channels. These ion channels dissipate pH gradients in secretory vesicles potentially protecting acid-labile intracellular virions during egress (the rupturing of the infected cell and release of viral contents). p7 protein has at least two different functions in culture, one via the formation of these ion channels, the other through its specific interaction with the non-structural viral protein NS2. Several compounds targeting p7 have been investigated as anti-HCV drugs.


:

Pssm-ID: 411017  Cd Length: 58  Bit Score: 73.03  E-value: 1.29e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 219964674  747 AMANLININAMSAAGTYGLPYALLFFCVAWYVRG*LPA*AAYAACGMWP 795
Cdd:cd20903     1 ALENLVVLNAASAAGTHGLLWFLLFFCAAWYIKGRLVPAATYALLGLWP 49
HCV_NS5a pfam01506
Hepatitis C virus non-structural 5a protein membrane anchor; The molecular function of the ...
1975-1996 3.35e-07

Hepatitis C virus non-structural 5a protein membrane anchor; The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. The N-terminal region of the NS5a protein has been used in the construction of the alignment for this family. The C-terminal region has not been included because it is too heterogeneous.


:

Pssm-ID: 366682  Cd Length: 23  Bit Score: 48.35  E-value: 3.35e-07
                           10        20
                   ....*....|....*....|..
gi 219964674  1975 NWLREIWDWVCTVLSDFKSWLK 1996
Cdd:pfam01506    2 SWLWDIWDWVCRVLRDFKNWLK 23
 
Name Accession Description Interval E-value
Hepacivirus_RdRp cd23202
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
2434-2951 0e+00

RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the RdRp of RNA viruses belonging to the Hepacivirus genus within the family Flaviviridae, order Amarillovirales. The genus Hepacivirus includes hepatitis C virus, a major human pathogen causing progressive liver disease, and several other viruses of unknown pathogenicity that infect horses, rodents, bats, cows and primates. Infections are typically persistent and target the liver. Virions of Hepacivirus 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. 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: 438052  Cd Length: 518  Bit Score: 1142.27  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2434 CAAEEPKLPISPLSNSLLRHHNMVYATTSRSAT*RQKKVTFDRLQVVDQHYMTTLKEIKARASGVKAPTLSVEEACALTP 2513
Cdd:cd23202     1 CAAEEEKLPISPLSNSLLRHHNLVYSTTSRSASERQKKVTFDRLQVLDPHYDDVLKEAKARASGVKARLLSVEEACSLTP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2514 PHSAKSKFGYGAKDVRSLARKAVNHINSVWEDLLEDNVTPIPTTIMAKSEVFSVKPEKGGRKP*RLIVYPDLGVRVCEKR 2593
Cdd:cd23202    81 PHSARSKFGYGAKDVRSLSRKAVNHINSVWEDLLEDSETPIPTTIMAKNEVFCVTPEKGGRKPARLIVYPDLGVRVCEKM 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2594 ALYNVVQKLPQAVMGEAYGFQYSPAQRVERLLKSWNSKRVPMGFPYDTRCFDSTVTERDIQVEEEVYQCCDLDPEARKVI 2673
Cdd:cd23202   161 ALYDVAPKLPKAVMGEAYGFQYSPAQRVEFLLKMWRSKKTPMGFSYDTRCFDSTVTERDIRTEESIYQCCDLDPEARKAI 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2674 SSLTERLYKGGPMFN*KGDLCGYRRCRASGVFTTSFGNTLTCYLKATAAARAAGLKDYDMLVCGDDLVIIAESDGVEEDK 2753
Cdd:cd23202   241 RSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPTMLVCGDDLVVIAESAGVEEDA 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2754 QALRAFTEAMTRYSAPPGDAPQ*AYDLELITSCSSNVSVAHDAAGKRVYYLTRDPETPLARAAWETVRHTPVNSWLGNII 2833
Cdd:cd23202   321 AALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDATGKRYYYLTRDPTTPLARAAWETARHTPVNSWLGNII 400
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2834 LYAPTIWVRMVLMTHFFSILQSQEALERALDFDMYGVTYSITPLDLPAIIQRLHGLSAFTLHGYSPHELNRVAGSLRKLG 2913
Cdd:cd23202   401 MYAPTLWVRMVLMTHFFSILLAQEQLEKALDFEMYGNTYSIPPLDLPAIIQRLHGLSAFSLHGYSPRELNRVAAALRKLG 480
                         490       500       510
                  ....*....|....*....|....*....|....*...
gi 219964674 2914 VPPLRVWRHRARAVRAKLIAQGGKARICGIYLFNWAVK 2951
Cdd:cd23202   481 VPPLRAWRHRARAVRAKLIAQGGKAAICGKYLFNWAVK 518
HCV_NS1 pfam01560
Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region ...
387-729 0e+00

Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region of hepatitis C virus varies greatly between viral isolates. E2 is thought to encode a structurally unconstrained envelope protein.


Pssm-ID: 110557  Cd Length: 344  Bit Score: 666.94  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   387 VSGGA*GHTTSGLASMF*RGPSQ*IQLINTNGSWHVNRTALNCNDSINTGFIAGLIYHWKFNSSGCPERLASCKRLSDFB 466
Cdd:pfam01560    2 VTGGSAARTTRGLVSLFSPGAKQNIQLINTNGSWHINRTALNCNDSLQTGFLASLFYTHRFNSSGCPERLASCRSIDDFR 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   467 QGWGGLGSSNISgPSDDKPYCWHYAPRPCGVVPAGKVCGPVYCFTPSPVVVGTTDRLGLPTYTWG*NETDVFLLNSTRPP 546
Cdd:pfam01560   82 QGWGPITYEETN-PEDQRPYCWHYPPRPCGIVPASSVCGPVYCFTPSPVVVGTTDRSGAPTYSWGENETDVFLLNNTRPP 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   547 SGGWFGCTWMNSTGFVKTCGASPCRV-TTSNGSWDCPTDCFRKHPDATYAKCGSGPWLTPRCMVHYPYRLWHYPCTVNYT 625
Cdd:pfam01560  161 QGNWFGCTWMNSTGFTKTCGAPPCRIgGDGNNTLLCPTDCFRKHPDATYTKCGSGPWLTPRCMVDYPYRLWHYPCTVNFT 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   626 IFKVRMYVGGIEHRLDAACNWTRGEPCGLEDRDRTELSPLLLSTTQWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGI 705
Cdd:pfam01560  241 IFKVRMYVGGVEHRLNAACNWTRGERCDLEDRDRSELSPLLLSTTEWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGL 320
                          330       340
                   ....*....|....*....|....
gi 219964674   706 GSSVVSWAIKWEYVVLAFLLLADA 729
Cdd:pfam01560  321 GSAVTSFAIKWEYVVLLFLLLADA 344
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
2423-2934 0e+00

Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase enzymes from hepatitis C virus and various plant viruses.


Pssm-ID: 395794 [Multi-domain]  Cd Length: 486  Bit Score: 578.03  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2423 SYSWTGALVtpcAAEEPKLPIS-PLSNSLLRHHNMVYATTSRSAT*RQKKVTFDRLQVV--DQHYMTTLKEIKARASGVK 2499
Cdd:pfam00998    1 SYVWTGARP---AKERKILPITgPGSGLLFGVHNNSLVNLRRGLVERVFKVTFDRGGQLvpPKPYPGAFKELKYFASALV 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2500 APtlsVEEACALTPPHSAKSKFGYGAK-DVRSLARKAVNHINSVwEDLLEDNVTPIPTTIMAKSEVFsvkPEKGGRKP*R 2578
Cdd:pfam00998   78 SK---LGEATPLTPEHFAASYTGRKRKiYVKALESLAVKPVQRR-DAILKTFVKAEKINITAKPDPA---PRVIQPRPPR 150
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2579 LIVYPDLGVRVCEKRALYNVvqklPQAVMGEAYGFQYSPAQRVERLLKSWNSKRVPMGFPYDTRCFDSTVTERDIQVEEE 2658
Cdd:pfam00998  151 YNVEPGRYLRPCEKMIYKAI----DKAFGGPTVLKGYTPEQRGEILLKKWDSFKKPVAIGLDASRFDQHVSVEALRFEHS 226
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2659 VYQCCDLDPEarKVISSLTERLYKGGPMFN*KGDL-CGYRRCRASGVFTTSFGNTLTCYLKATAAARAAGlKDYDMLVCG 2737
Cdd:pfam00998  227 IYLAAFLGPE--ELIRLLTWQLYNGGPMYASDGQIkYGVRGCRMSGDMNTSLGNCLLMCLKVHAACKALG-IDARLLNNG 303
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2738 DDLVIIAESDGVEEDKQALrafTEAMTRYSaPPGDAPQ*AYDLELITSCSSNVSVAHDAAGKRVYYLTRDPETPLARAAW 2817
Cdd:pfam00998  304 DDCVVICESADLDEVKEAL---TEAFARYG-FTMKVEEPVYELELIEFCQSNPVFDGGKYGMVRNPLTSDSKDPLSRASW 379
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2818 ETVrhTPVNSWLGNIILYAPTIWVRMVLMTHFFSILQSQEALERALDFDMYGVTYSItpldlpaIIQRLHGLSAFTLHGY 2897
Cdd:pfam00998  380 ETA--TPAKSWLGAIGECGLSLWGGVPVLQHFYSCLLRNGGLEKAVSFEMYGKVYSD-------SGFRLHGLGAGSRHSY 450
                          490       500       510
                   ....*....|....*....|....*....|....*..
gi 219964674  2898 SPHELNRVAGSLrKLGVPPLRVWRHRARAVRAKLIAQ 2934
Cdd:pfam00998  451 EPTEEARVSFWL-AFGITPDEQWALEAYYDRLKLLRQ 486
HCV_NS2 pfam01538
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ...
811-1005 1.64e-104

Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single polyprotein of about 3000 amino acids. Generation of the mature non-structural proteins relies on the activity of viral proteases. Cleavage at the NS2/NS3 junction is accomplished by a metal-dependent autoprotease encoded within NS2 and the N-terminus of NS3.


Pssm-ID: 366698  Cd Length: 195  Bit Score: 332.71  E-value: 1.64e-104
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   811 DAEVAGSLGGAVICLLTILTLSPWYKRWLAWIIWWLQYYLTRAEALLYVYIPPLEVRGGRDSLIILAVLLHPGLVFEVTK 890
Cdd:pfam01538    1 DTEDAGWLGAAVLSWITLFTLTPTYKGLLAKLLWWLQYCIARQEARLHVWVPPLGVRGGRDAVILLWCLAHPDLVFDVTK 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   891 HLLAILGPLYVLQASLLRIPYFVRAHALIKICGFVRGVAHGKFVQMAMLKLGALTGTYVYDHLTPLSDWAADGLKDLAVA 970
Cdd:pfam01538   81 ILLAILGPLYLLQASLLRVPYFVRAARLLRSCVLVRHLAGGKYVQMALLKLGRWTGTYLYDHLGPLSDWAAEGLRDLAVA 160
                          170       180       190
                   ....*....|....*....|....*....|....*
gi 219964674   971 LEPVIFTPMEKKVITWGADTAACGDIIRGLPVSAR 1005
Cdd:pfam01538  161 LEPVVFSPMECKIITWGADTAACGDIVHGLPVSAR 195
HCV_env pfam01539
Hepatitis C virus envelope glycoprotein E1;
195-382 2.87e-101

Hepatitis C virus envelope glycoprotein E1;


Pssm-ID: 110536  Cd Length: 190  Bit Score: 323.37  E-value: 2.87e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   195 RNASGVYHITNDCPNSSIVYETEHQIMHLPGCVPCVRT*N*SRCWVPLTPTVAA*YPNAPLESMRRHVDLMVGAATMCSA 274
Cdd:pfam01539    3 RNISGSYHVTNDCSNSSITWQLADAVLHTPGCVPCEREGNTSRCWIAVTPNVAVRHRGALTTSLRTHVDMLVMAATLCSA 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   275 LYVGDVCGGIFLVGQMFSF*PRRHWTTQDCNCSIYTGHITGHRMAWDMMMNWSPTTTLVLAQVMRLPSALGDMFAGGHWG 354
Cdd:pfam01539   83 LYVGDLCGSVMLVSQLFTVSPQRHWFTQDCNCSIYPGHITGHRMAWDMMMNWSPTATMILAYALRVPEAVLDIIAGAHWG 162
                          170       180
                   ....*....|....*....|....*...
gi 219964674   355 VLAGLAFFSMQGNWAKVILVLFLFAGVD 382
Cdd:pfam01539  163 VLFGLAYFSMQGAWAKVLVILLLFAGVD 190
HCV_NS5a_C pfam12941
HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C ...
2179-2420 1.01e-89

HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C virus. This family contains the C-terminal region of the NS5A protein. CC The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR.


Pssm-ID: 289693  Cd Length: 242  Bit Score: 292.61  E-value: 1.01e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2179 SHITAEAAARRLARGSPPSEASSSASQLSAPSLKATCTTNHHSPDADLIEANLLWRQEMGGNITRVESENKVVVLDSFEP 2258
Cdd:pfam12941    1 SHITAEAAGRRLARGSPPSMASSSASQLSAPSLKATCTANHDSPDAELIEANLLWRQEMGGNITRVESENKVVILDSFDP 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2259 LVAE*DSGEVSVPAEILRRSKRFPKPLPIWARPDYNPPLIZPWKQPDYTPPVVHGCALPPSKPTPVPPPRRKRAIVLTES 2338
Cdd:pfam12941   81 LVAEEDEREVSVPAEILRKSRRFAPALPVWARPDYNPLLVETWKKPDYEPPVVHGCPLPPPRSPPVPPPRKKRTVVLTES 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2339 NVSSALADLAAKVLSQPDADVDSGTGLTLPSEtstPDPPIADDRSDDGSFSSMPPLEGEPGDPDLTSDSWSTVSG---SE 2415
Cdd:pfam12941  161 TLPTALAELATKSFGSSSTSGITGDNTTTSSE---PAPSGCPPDSDVESYSSMPPLEGEPGDPDLSDGSWSTVSSgadTE 237

                   ....*
gi 219964674  2416 DVVCC 2420
Cdd:pfam12941  238 DVVCC 242
HCV_NS4b pfam01001
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
1728-1921 1.38e-82

Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. However, it is known that NS4b interacts with NS4a and NS3 to form a large replicase complex to direct the viral RNA replication.


Pssm-ID: 110032  Cd Length: 192  Bit Score: 270.02  E-value: 1.38e-82
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  1728 FKQKALGVLQVASARAQEATPVVQSNFAKLEQFWAKHMWNFVSGVQYLAGLSTLPGNPAIASLMSFTAAVTSPLTTQQTL 1807
Cdd:pfam01001    1 FAFKALGLLPPAIDKAESITPAVASLDTKFEQFWAKHMWNFRSGIQYLAGLYTLPRNPPLAVLASFLAGMTSPLPTHVRL 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  1808 LFNILGGWVASQIATPTASTAFVVSGLAGAAVGSVGLGKILVDILAGYGAGVAGAVVTFKIMSGEVPTTEDLVNLLPAIL 1887
Cdd:pfam01001   81 ALALLGGWGATQLGTPSGGLAFVGAGFAGAAVGSSWLGRVLVDVLGGYEAAVNAASLTFKIMSGELPTAEDLWNLLPCLL 160
                          170       180       190
                   ....*....|....*....|....*....|....
gi 219964674  1888 SPGALVVGVVCAAILRRHVgpGEGAVQWMNRLIA 1921
Cdd:pfam01001  161 SPGASVVGVALAALLRSHK--GEGAVQWMNRLLT 192
HCV_capsid pfam01543
Hepatitis C virus capsid protein;
2-115 2.65e-72

Hepatitis C virus capsid protein;


Pssm-ID: 144947  Cd Length: 121  Bit Score: 237.67  E-value: 2.65e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674     2 STNPKPQRKTKRNTNRRPMDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARR*EGRSWAQPGY 81
Cdd:pfam01543    1 STNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPEGRSWLSPGT 80
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 219964674    82 PWP------LYGNEG-CGWAGWLLSPRGSRPSWGPNDPRRR 115
Cdd:pfam01543   81 LGPstamraLYGNDGsCGWAGWLLPPRGSRPSWGQNDPRRR 121
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
1224-1366 3.08e-50

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: 175.43  E-value: 3.08e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 1224 QVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGSYMSKAhgiDPNIRSGVRTITTGA--PITYSTYG 1297
Cdd:cd17931     2 QLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGneIVDYMCHG 78
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 219964674 1298 KFLaDGGCGGGA---YDIIICDECHSTDSTTILGIGTVLDQAETaGVRLVVLATATPPGSITTPH---SNIEEIA 1366
Cdd:cd17931    79 TFT-CRLLSPKRvpnYNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDFE 151
HCV_NS5a_1b pfam08301
Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ...
2068-2168 2.25e-48

Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. This region corresponds to the 1b domain.


Pssm-ID: 149382  Cd Length: 102  Bit Score: 168.31  E-value: 2.25e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2068 GAGVPIPAPNYKFALWRVSAEEYVEIRRVGEFHYVTGMTQDNIkCPCQVPAPEFF--TEVDGVRLHRYAPPCKPLLRDEV 2145
Cdd:pfam08301    1 GPAVPLPPPNYGPALWRVGAEDYVEVVRVGDTHYVTATSCYNL-CPCQVPRPEFFapTEVDGVRVSWYAPPCKPLLVYEV 79
                           90       100
                   ....*....|....*....|...
gi 219964674  2146 QFTVGLNTFVVGSQLPCEPEPDV 2168
Cdd:pfam08301   80 GQSVGLDGYGVRSQLPCELEPDV 102
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
1362-1483 4.08e-43

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: 155.11  E-value: 4.08e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 1362 IEEIALPTTGEVPFYGKAIPleVIKGGRHLIFCHSKKKCDELAKQLSSLGLNAVAYYRGLDVSV---IPTSGDVVVCATD 1438
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 219964674 1439 ALMTGFTGNFDSVIDCNTSVIQTVDFSLDptFSIETT-TVPQDAVS 1483
Cdd:cd18806    79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAAS 122
HCV_core pfam01542
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
116-190 7.65e-29

Hepatitis C virus core protein; The viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases. The N terminus of the core protein is involved in transcriptional repression.


Pssm-ID: 460245  Cd Length: 75  Bit Score: 111.69  E-value: 7.65e-29
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 219964674   116 SRNLGKVIDTLTCGFADLMGYIPLVGAPVGGVARALAHGVRAVEDGINYATGNLPGCSFSIFLLALLSCLTTPAS 190
Cdd:pfam01542    1 MRNLGKPIDKLKCGFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRATAKGNEPGCPFGIFLLALKACLPEGAS 75
HCV_p7 cd20903
Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for ...
747-795 1.29e-15

Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for virus production. The p7 monomer is comprised of 2 trans-membrane helices connected by a cytosolic loop, and oligomerizes to form cation-specific ion channels. These ion channels dissipate pH gradients in secretory vesicles potentially protecting acid-labile intracellular virions during egress (the rupturing of the infected cell and release of viral contents). p7 protein has at least two different functions in culture, one via the formation of these ion channels, the other through its specific interaction with the non-structural viral protein NS2. Several compounds targeting p7 have been investigated as anti-HCV drugs.


Pssm-ID: 411017  Cd Length: 58  Bit Score: 73.03  E-value: 1.29e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 219964674  747 AMANLININAMSAAGTYGLPYALLFFCVAWYVRG*LPA*AAYAACGMWP 795
Cdd:cd20903     1 ALENLVVLNAASAAGTHGLLWFLLFFCAAWYIKGRLVPAATYALLGLWP 49
DEXDc smart00487
DEAD-like helicases superfamily;
1228-1355 1.42e-13

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 72.14  E-value: 1.42e-13
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   1228 LHAPTGSGKSTKVPAAYAAQGY-----KVLVLNPSVAATLGFGSYMSKAHGIDPNIRSGVRT-----------ITTGAPI 1291
Cdd:smart00487   29 LAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGgdskreqlrklESGKTDI 108
                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 219964674   1292 TYSTYGKF---LADGGCGGGAYDIIICDECHSTDS----TTILGIGTVLDQAetagvRLVVLATATPPGSI 1355
Cdd:smart00487  109 LVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLDggfgDQLEKLLKLLPKN-----VQLLLLSATPPEEI 174
HCV_NS5a pfam01506
Hepatitis C virus non-structural 5a protein membrane anchor; The molecular function of the ...
1975-1996 3.35e-07

Hepatitis C virus non-structural 5a protein membrane anchor; The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. The N-terminal region of the NS5a protein has been used in the construction of the alignment for this family. The C-terminal region has not been included because it is too heterogeneous.


Pssm-ID: 366682  Cd Length: 23  Bit Score: 48.35  E-value: 3.35e-07
                           10        20
                   ....*....|....*....|..
gi 219964674  1975 NWLREIWDWVCTVLSDFKSWLK 1996
Cdd:pfam01506    2 SWLWDIWDWVCRVLRDFKNWLK 23
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1310-1361 3.50e-04

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 43.48  E-value: 3.50e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 219964674  1310 YDIIICDECHSTDSTTILGIG---TVLDQAETAgvrlVVLATATPPGSITT-PHSN 1361
Cdd:pfam07652   94 YEVIIMDEAHFTDPASIAARGyisTLVELGEAA----AIFMTATPPGTSDPfPESN 145
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
1228-1351 1.31e-03

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 44.25  E-value: 1.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 1228 LHAPTGSGKST---KVpAAYAAQGYKVLVLNPSVAATLGFgsyMSKAHGIDPNIRSGVRTITTGAPITYSTYGKFLADGG 1304
Cdd:COG1061   105 VVAPTGTGKTVlalAL-AAELLRGKRVLVLVPRRELLEQW---AEELRRFLGDPLAGGGKKDSDAPITVATYQSLARRAH 180
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 219964674 1305 CG--GGAYDIIICDECH--STDSTTILgigtvldqAETAGVRLVVLATATP 1351
Cdd:COG1061   181 LDelGDRFGLVIIDEAHhaGAPSYRRI--------LEAFPAAYRLGLTATP 223
 
Name Accession Description Interval E-value
Hepacivirus_RdRp cd23202
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
2434-2951 0e+00

RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the RdRp of RNA viruses belonging to the Hepacivirus genus within the family Flaviviridae, order Amarillovirales. The genus Hepacivirus includes hepatitis C virus, a major human pathogen causing progressive liver disease, and several other viruses of unknown pathogenicity that infect horses, rodents, bats, cows and primates. Infections are typically persistent and target the liver. Virions of Hepacivirus 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. 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: 438052  Cd Length: 518  Bit Score: 1142.27  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2434 CAAEEPKLPISPLSNSLLRHHNMVYATTSRSAT*RQKKVTFDRLQVVDQHYMTTLKEIKARASGVKAPTLSVEEACALTP 2513
Cdd:cd23202     1 CAAEEEKLPISPLSNSLLRHHNLVYSTTSRSASERQKKVTFDRLQVLDPHYDDVLKEAKARASGVKARLLSVEEACSLTP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2514 PHSAKSKFGYGAKDVRSLARKAVNHINSVWEDLLEDNVTPIPTTIMAKSEVFSVKPEKGGRKP*RLIVYPDLGVRVCEKR 2593
Cdd:cd23202    81 PHSARSKFGYGAKDVRSLSRKAVNHINSVWEDLLEDSETPIPTTIMAKNEVFCVTPEKGGRKPARLIVYPDLGVRVCEKM 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2594 ALYNVVQKLPQAVMGEAYGFQYSPAQRVERLLKSWNSKRVPMGFPYDTRCFDSTVTERDIQVEEEVYQCCDLDPEARKVI 2673
Cdd:cd23202   161 ALYDVAPKLPKAVMGEAYGFQYSPAQRVEFLLKMWRSKKTPMGFSYDTRCFDSTVTERDIRTEESIYQCCDLDPEARKAI 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2674 SSLTERLYKGGPMFN*KGDLCGYRRCRASGVFTTSFGNTLTCYLKATAAARAAGLKDYDMLVCGDDLVIIAESDGVEEDK 2753
Cdd:cd23202   241 RSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPTMLVCGDDLVVIAESAGVEEDA 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2754 QALRAFTEAMTRYSAPPGDAPQ*AYDLELITSCSSNVSVAHDAAGKRVYYLTRDPETPLARAAWETVRHTPVNSWLGNII 2833
Cdd:cd23202   321 AALRAFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDATGKRYYYLTRDPTTPLARAAWETARHTPVNSWLGNII 400
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2834 LYAPTIWVRMVLMTHFFSILQSQEALERALDFDMYGVTYSITPLDLPAIIQRLHGLSAFTLHGYSPHELNRVAGSLRKLG 2913
Cdd:cd23202   401 MYAPTLWVRMVLMTHFFSILLAQEQLEKALDFEMYGNTYSIPPLDLPAIIQRLHGLSAFSLHGYSPRELNRVAAALRKLG 480
                         490       500       510
                  ....*....|....*....|....*....|....*...
gi 219964674 2914 VPPLRVWRHRARAVRAKLIAQGGKARICGIYLFNWAVK 2951
Cdd:cd23202   481 VPPLRAWRHRARAVRAKLIAQGGKAAICGKYLFNWAVK 518
HCV_NS1 pfam01560
Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region ...
387-729 0e+00

Hepatitis C virus non-structural protein E2/NS1; The hypervariable region of the E2/NS1 region of hepatitis C virus varies greatly between viral isolates. E2 is thought to encode a structurally unconstrained envelope protein.


Pssm-ID: 110557  Cd Length: 344  Bit Score: 666.94  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   387 VSGGA*GHTTSGLASMF*RGPSQ*IQLINTNGSWHVNRTALNCNDSINTGFIAGLIYHWKFNSSGCPERLASCKRLSDFB 466
Cdd:pfam01560    2 VTGGSAARTTRGLVSLFSPGAKQNIQLINTNGSWHINRTALNCNDSLQTGFLASLFYTHRFNSSGCPERLASCRSIDDFR 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   467 QGWGGLGSSNISgPSDDKPYCWHYAPRPCGVVPAGKVCGPVYCFTPSPVVVGTTDRLGLPTYTWG*NETDVFLLNSTRPP 546
Cdd:pfam01560   82 QGWGPITYEETN-PEDQRPYCWHYPPRPCGIVPASSVCGPVYCFTPSPVVVGTTDRSGAPTYSWGENETDVFLLNNTRPP 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   547 SGGWFGCTWMNSTGFVKTCGASPCRV-TTSNGSWDCPTDCFRKHPDATYAKCGSGPWLTPRCMVHYPYRLWHYPCTVNYT 625
Cdd:pfam01560  161 QGNWFGCTWMNSTGFTKTCGAPPCRIgGDGNNTLLCPTDCFRKHPDATYTKCGSGPWLTPRCMVDYPYRLWHYPCTVNFT 240
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   626 IFKVRMYVGGIEHRLDAACNWTRGEPCGLEDRDRTELSPLLLSTTQWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGI 705
Cdd:pfam01560  241 IFKVRMYVGGVEHRLNAACNWTRGERCDLEDRDRSELSPLLLSTTEWQVLPCSFTTLPALSTGLIHLHQNIVDVQYLYGL 320
                          330       340
                   ....*....|....*....|....
gi 219964674   706 GSSVVSWAIKWEYVVLAFLLLADA 729
Cdd:pfam01560  321 GSAVTSFAIKWEYVVLLFLLLADA 344
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
2423-2934 0e+00

Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase enzymes from hepatitis C virus and various plant viruses.


Pssm-ID: 395794 [Multi-domain]  Cd Length: 486  Bit Score: 578.03  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2423 SYSWTGALVtpcAAEEPKLPIS-PLSNSLLRHHNMVYATTSRSAT*RQKKVTFDRLQVV--DQHYMTTLKEIKARASGVK 2499
Cdd:pfam00998    1 SYVWTGARP---AKERKILPITgPGSGLLFGVHNNSLVNLRRGLVERVFKVTFDRGGQLvpPKPYPGAFKELKYFASALV 77
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2500 APtlsVEEACALTPPHSAKSKFGYGAK-DVRSLARKAVNHINSVwEDLLEDNVTPIPTTIMAKSEVFsvkPEKGGRKP*R 2578
Cdd:pfam00998   78 SK---LGEATPLTPEHFAASYTGRKRKiYVKALESLAVKPVQRR-DAILKTFVKAEKINITAKPDPA---PRVIQPRPPR 150
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2579 LIVYPDLGVRVCEKRALYNVvqklPQAVMGEAYGFQYSPAQRVERLLKSWNSKRVPMGFPYDTRCFDSTVTERDIQVEEE 2658
Cdd:pfam00998  151 YNVEPGRYLRPCEKMIYKAI----DKAFGGPTVLKGYTPEQRGEILLKKWDSFKKPVAIGLDASRFDQHVSVEALRFEHS 226
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2659 VYQCCDLDPEarKVISSLTERLYKGGPMFN*KGDL-CGYRRCRASGVFTTSFGNTLTCYLKATAAARAAGlKDYDMLVCG 2737
Cdd:pfam00998  227 IYLAAFLGPE--ELIRLLTWQLYNGGPMYASDGQIkYGVRGCRMSGDMNTSLGNCLLMCLKVHAACKALG-IDARLLNNG 303
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2738 DDLVIIAESDGVEEDKQALrafTEAMTRYSaPPGDAPQ*AYDLELITSCSSNVSVAHDAAGKRVYYLTRDPETPLARAAW 2817
Cdd:pfam00998  304 DDCVVICESADLDEVKEAL---TEAFARYG-FTMKVEEPVYELELIEFCQSNPVFDGGKYGMVRNPLTSDSKDPLSRASW 379
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2818 ETVrhTPVNSWLGNIILYAPTIWVRMVLMTHFFSILQSQEALERALDFDMYGVTYSItpldlpaIIQRLHGLSAFTLHGY 2897
Cdd:pfam00998  380 ETA--TPAKSWLGAIGECGLSLWGGVPVLQHFYSCLLRNGGLEKAVSFEMYGKVYSD-------SGFRLHGLGAGSRHSY 450
                          490       500       510
                   ....*....|....*....|....*....|....*..
gi 219964674  2898 SPHELNRVAGSLrKLGVPPLRVWRHRARAVRAKLIAQ 2934
Cdd:pfam00998  451 EPTEEARVSFWL-AFGITPDEQWALEAYYDRLKLLRQ 486
ps-ssRNAv_Flaviviridae_RdRp cd23178
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ...
2554-2838 1.24e-131

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: 414.61  E-value: 1.24e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2554 IPTTIMAKSEVFSVKPEKGGRKP*RLIVYPDLGVRVCEKRALYNVVQKLPQAVMGEAYGFQYSPAQRVERLLKSWNSKRV 2633
Cdd:cd23178     1 IPTTIMPKNEVFCVEPGKGGRKPPRLIVYPDLGVRVAEKMALYDPVEVLPQVVGGSYYGFQYSPNQRVEILRKAWKSKKG 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2634 PMGFPYDTRCFDSTVTERDIQVEEEVYQCCDLdPEARKVISSLTERLYKGGPMFN*KGDLCGYRRCRASGVFTTSFGNTL 2713
Cdd:cd23178    81 PMAYSYDTRCFDSTVTEDDIQVEEEIYQACSL-KEARQAIVSITERLYVEGPMVNSDGQICGRRRCRASGVLTTSAGNT* 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2714 TCYLKATAAARAAGLKDYDMLVCGDDLVIIAESDGVEEDKQALRAFTEAMTRYSAPPGDAPQ*AYDLELITSCSSNVSVA 2793
Cdd:cd23178   160 TCYLK*LAACREAGIRLPTMLVCGDDCVVICESDGTQEDAALLAAFTEALTRYGKPPKDPPQPEYDLELIESCSHTVSEV 239
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 219964674 2794 HDAAGKRVYYLTRDPETPLARAAWETVRHTPVNSWLGNIILYAPT 2838
Cdd:cd23178   240 RMKDGRRLYYLTRDPTTPLARAAWETGRHEPINSWLGYIIMYALT 284
HCV_NS2 pfam01538
Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single ...
811-1005 1.64e-104

Hepatitis C virus non-structural protein NS2; The viral genome is translated into a single polyprotein of about 3000 amino acids. Generation of the mature non-structural proteins relies on the activity of viral proteases. Cleavage at the NS2/NS3 junction is accomplished by a metal-dependent autoprotease encoded within NS2 and the N-terminus of NS3.


Pssm-ID: 366698  Cd Length: 195  Bit Score: 332.71  E-value: 1.64e-104
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   811 DAEVAGSLGGAVICLLTILTLSPWYKRWLAWIIWWLQYYLTRAEALLYVYIPPLEVRGGRDSLIILAVLLHPGLVFEVTK 890
Cdd:pfam01538    1 DTEDAGWLGAAVLSWITLFTLTPTYKGLLAKLLWWLQYCIARQEARLHVWVPPLGVRGGRDAVILLWCLAHPDLVFDVTK 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   891 HLLAILGPLYVLQASLLRIPYFVRAHALIKICGFVRGVAHGKFVQMAMLKLGALTGTYVYDHLTPLSDWAADGLKDLAVA 970
Cdd:pfam01538   81 ILLAILGPLYLLQASLLRVPYFVRAARLLRSCVLVRHLAGGKYVQMALLKLGRWTGTYLYDHLGPLSDWAAEGLRDLAVA 160
                          170       180       190
                   ....*....|....*....|....*....|....*
gi 219964674   971 LEPVIFTPMEKKVITWGADTAACGDIIRGLPVSAR 1005
Cdd:pfam01538  161 LEPVVFSPMECKIITWGADTAACGDIVHGLPVSAR 195
HCV_env pfam01539
Hepatitis C virus envelope glycoprotein E1;
195-382 2.87e-101

Hepatitis C virus envelope glycoprotein E1;


Pssm-ID: 110536  Cd Length: 190  Bit Score: 323.37  E-value: 2.87e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   195 RNASGVYHITNDCPNSSIVYETEHQIMHLPGCVPCVRT*N*SRCWVPLTPTVAA*YPNAPLESMRRHVDLMVGAATMCSA 274
Cdd:pfam01539    3 RNISGSYHVTNDCSNSSITWQLADAVLHTPGCVPCEREGNTSRCWIAVTPNVAVRHRGALTTSLRTHVDMLVMAATLCSA 82
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   275 LYVGDVCGGIFLVGQMFSF*PRRHWTTQDCNCSIYTGHITGHRMAWDMMMNWSPTTTLVLAQVMRLPSALGDMFAGGHWG 354
Cdd:pfam01539   83 LYVGDLCGSVMLVSQLFTVSPQRHWFTQDCNCSIYPGHITGHRMAWDMMMNWSPTATMILAYALRVPEAVLDIIAGAHWG 162
                          170       180
                   ....*....|....*....|....*...
gi 219964674   355 VLAGLAFFSMQGNWAKVILVLFLFAGVD 382
Cdd:pfam01539  163 VLFGLAYFSMQGAWAKVLVILLLFAGVD 190
Pegivirus_RdRp cd23203
RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ...
2426-2917 2.32e-93

RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the RdRp of RNA viruses belonging to the Pegivirus genus within the family Flaviviridae, order Amarillovirales. Members of the Pegivirus genus are widely distributed in a range of mammalian species, in which they cause persistent infections. To date, they have not been clearly associated with disease. Virions of Pegivirus 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. 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: 438053  Cd Length: 476  Bit Score: 312.28  E-value: 2.32e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2426 WTGALVTpcAAEEPKLPIS-PLSNSLLRHHNMVYATTSRSAT*RQKKVTFDRLQ-VVDQHYMTTLKEIKARASGVKAPTL 2503
Cdd:cd23203     1 WSGAPLG--VGRPKPPPVTrPVGSHLRADATKVYVTDPDDVGERIEKVTIWRTPrVVDKFLRDAYNLALAKASATPSPGW 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2504 SVEEACALTPPHSAKskfGYGAK----DVRSLA-RKAVnhinsvwEDLLED---NVTPIPTTIMAKSEVFSVKpeKGGRK 2575
Cdd:cd23203    79 TYEEAVAKVRPGAAM---GHGSKvtvaDLKTPAgKKAV-------EECLNQiiaGGEEVPFTLTAKQEVFFQD--KKTRK 146
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2576 P*RLIVYPDLGVRVCEKRALYN--VVQKlpqAVMGEAYGFQYSPAQRVERLLKSWNSKRVPMGFPYDTRCFDSTVTERDI 2653
Cdd:cd23203   147 PPRLIVYPPLEFRVAEKMILGDpgRVAK---AVLGKAYGFQYTPNQRVKVLVDMWKSKRHPCAITVDATCFDSSITEEDV 223
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2654 QVEEEVYQCCDLDPEARKVISslteRLYKGGPMFN*KGDLCGYRRCRASGVFTTSFGNTLTCYLKATAAARAAGLKDYDM 2733
Cdd:cd23203   224 ARETEIYAAASDDPELVRALG----KYYAEGPMVNPEGVPVGERRCRASGVLTTSSSNSITCYLKVKAACRKAGLKNPSF 299
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2734 LVCGDDLVIIAESDGVEEdkqaLRAFTEAMTRYSAPPgdAPQ*AYDLELITSCSSNVSVAhDAAGKRVYYLTRDPETPLA 2813
Cdd:cd23203   300 LIHGDDCLIICERPEEDP----CDALKAALASYGYDC--EPQYHASLDTAESCSAYLAEC-NAGGGRHYFLSTDMRRPLA 372
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2814 RAAWEtvRHTPVNSWLGNIILYaPT--IwVRMVLMTHFFS-ILQSQEALERALDFDMYGVTYSItPLD-LPAIIQRLHGL 2889
Cdd:cd23203   373 RASSE--YGDPVASALGYILLY-PWhpI-TRYVLLPHLLTlAFRGGGTPDDLVTCQVHGNSYKF-PLKlLPRILVGLHGP 447
                         490       500
                  ....*....|....*....|....*...
gi 219964674 2890 SAFTLHGYSPHELNRVAGSLRKLGVPPL 2917
Cdd:cd23203   448 DCLRVTADSTKTLMEAGKALQAFGMRGL 475
HCV_NS5a_C pfam12941
HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C ...
2179-2420 1.01e-89

HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C virus. This family contains the C-terminal region of the NS5A protein. CC The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR.


Pssm-ID: 289693  Cd Length: 242  Bit Score: 292.61  E-value: 1.01e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2179 SHITAEAAARRLARGSPPSEASSSASQLSAPSLKATCTTNHHSPDADLIEANLLWRQEMGGNITRVESENKVVVLDSFEP 2258
Cdd:pfam12941    1 SHITAEAAGRRLARGSPPSMASSSASQLSAPSLKATCTANHDSPDAELIEANLLWRQEMGGNITRVESENKVVILDSFDP 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2259 LVAE*DSGEVSVPAEILRRSKRFPKPLPIWARPDYNPPLIZPWKQPDYTPPVVHGCALPPSKPTPVPPPRRKRAIVLTES 2338
Cdd:pfam12941   81 LVAEEDEREVSVPAEILRKSRRFAPALPVWARPDYNPLLVETWKKPDYEPPVVHGCPLPPPRSPPVPPPRKKRTVVLTES 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2339 NVSSALADLAAKVLSQPDADVDSGTGLTLPSEtstPDPPIADDRSDDGSFSSMPPLEGEPGDPDLTSDSWSTVSG---SE 2415
Cdd:pfam12941  161 TLPTALAELATKSFGSSSTSGITGDNTTTSSE---PAPSGCPPDSDVESYSSMPPLEGEPGDPDLSDGSWSTVSSgadTE 237

                   ....*
gi 219964674  2416 DVVCC 2420
Cdd:pfam12941  238 DVVCC 242
HCV_NS4b pfam01001
Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. ...
1728-1921 1.38e-82

Hepatitis C virus non-structural protein NS4b; No precise function has been assigned to NS4b. However, it is known that NS4b interacts with NS4a and NS3 to form a large replicase complex to direct the viral RNA replication.


Pssm-ID: 110032  Cd Length: 192  Bit Score: 270.02  E-value: 1.38e-82
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  1728 FKQKALGVLQVASARAQEATPVVQSNFAKLEQFWAKHMWNFVSGVQYLAGLSTLPGNPAIASLMSFTAAVTSPLTTQQTL 1807
Cdd:pfam01001    1 FAFKALGLLPPAIDKAESITPAVASLDTKFEQFWAKHMWNFRSGIQYLAGLYTLPRNPPLAVLASFLAGMTSPLPTHVRL 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  1808 LFNILGGWVASQIATPTASTAFVVSGLAGAAVGSVGLGKILVDILAGYGAGVAGAVVTFKIMSGEVPTTEDLVNLLPAIL 1887
Cdd:pfam01001   81 ALALLGGWGATQLGTPSGGLAFVGAGFAGAAVGSSWLGRVLVDVLGGYEAAVNAASLTFKIMSGELPTAEDLWNLLPCLL 160
                          170       180       190
                   ....*....|....*....|....*....|....
gi 219964674  1888 SPGALVVGVVCAAILRRHVgpGEGAVQWMNRLIA 1921
Cdd:pfam01001  161 SPGASVVGVALAALLRSHK--GEGAVQWMNRLLT 192
HCV_capsid pfam01543
Hepatitis C virus capsid protein;
2-115 2.65e-72

Hepatitis C virus capsid protein;


Pssm-ID: 144947  Cd Length: 121  Bit Score: 237.67  E-value: 2.65e-72
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674     2 STNPKPQRKTKRNTNRRPMDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARR*EGRSWAQPGY 81
Cdd:pfam01543    1 STNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPEGRSWLSPGT 80
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 219964674    82 PWP------LYGNEG-CGWAGWLLSPRGSRPSWGPNDPRRR 115
Cdd:pfam01543   81 LGPstamraLYGNDGsCGWAGWLLPPRGSRPSWGQNDPRRR 121
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
1224-1366 3.08e-50

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: 175.43  E-value: 3.08e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 1224 QVAHLHAPTGSGKSTKVPAAYAAQGY----KVLVLNPSVAATLGFGSYMSKAhgiDPNIRSGVRTITTGA--PITYSTYG 1297
Cdd:cd17931     2 QLTVLDLHPGAGKTTRVLPQIIREAIkkrlRTLVLAPTRVVAAEMYEALRGL---PIRYRTGAVKEEHGGneIVDYMCHG 78
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 219964674 1298 KFLaDGGCGGGA---YDIIICDECHSTDSTTILGIGTVLDQAETaGVRLVVLATATPPGSITTPH---SNIEEIA 1366
Cdd:cd17931    79 TFT-CRLLSPKRvpnYNLIIMDEAHFTDPASIAARGYIHTRVEM-GEAAVIFMTATPPGTVTPFPqsnHPIEDFE 151
HCV_NS5a_1b pfam08301
Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ...
2068-2168 2.25e-48

Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. This region corresponds to the 1b domain.


Pssm-ID: 149382  Cd Length: 102  Bit Score: 168.31  E-value: 2.25e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  2068 GAGVPIPAPNYKFALWRVSAEEYVEIRRVGEFHYVTGMTQDNIkCPCQVPAPEFF--TEVDGVRLHRYAPPCKPLLRDEV 2145
Cdd:pfam08301    1 GPAVPLPPPNYGPALWRVGAEDYVEVVRVGDTHYVTATSCYNL-CPCQVPRPEFFapTEVDGVRVSWYAPPCKPLLVYEV 79
                           90       100
                   ....*....|....*....|...
gi 219964674  2146 QFTVGLNTFVVGSQLPCEPEPDV 2168
Cdd:pfam08301   80 GQSVGLDGYGVRSQLPCELEPDV 102
SF2_C_viral cd18806
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
1362-1483 4.08e-43

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: 155.11  E-value: 4.08e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 1362 IEEIALPTTGEVPFYGKAIPleVIKGGRHLIFCHSKKKCDELAKQLSSLGLNAVAYYRGLDVSV---IPTSGDVVVCATD 1438
Cdd:cd18806     1 IEDVALEIPGRIWFYGKAWI--TIYGGKTVWFVHSKKKGNEIAACLSGLGKNVIQLYRKLDDTEypkIKTIDWDFVVTTD 78
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 219964674 1439 ALMTGFTGNFDSVIDCNTSVIQTVDFSLDptFSIETT-TVPQDAVS 1483
Cdd:cd18806    79 ISEMGANFDADRVIDCRTCVKPTILFSGD--FRVILTgPVPQTAAS 122
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
2536-2818 7.40e-37

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: 142.04  E-value: 7.40e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2536 VNHINSVWEDLLedNVTPIPTTIMAKSEVFsvKPEKGGRKP*RLIVYPDLGVRVCEKRALYNVVQKLPQAVMGEAYGFQY 2615
Cdd:cd01699     2 EKAVESLEDLPL--IRPDLVFTTFLKDELR--PLEKVEAGKTRLIQPRPLDYNIALRMYLGPFEAKLMKNRGGLPIAVGI 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2616 SPAQR-VERLLKSWNSKrVPMGFPYDTRCFDSTVTERDIQVEEEVYQCCDLDP---EARKVISSLTERLYkggPMFN*kG 2691
Cdd:cd01699    78 NPYSRdWTILANKLRSF-SPVAIALDYSRFDSSLSPQLLEAEHSIYNALYDDDdelERRNLLRSLTNNSL---HIGF--N 151
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2692 DLCGYRRCRASGVFTTSFGNTLTCYLK----ATAAARAAGLKDYDMLVCGDDLVIIAESDgveEDKQALRAFTEAMTRYS 2767
Cdd:cd01699   152 EVYKVRGGRPSGDPLTSIGNSIINCILvryaFRKLGGKSFFKNVRLLNYGDDCLLSVEKA---DDKFNLETLAEWLKEYG 228
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 219964674 2768 APPGDAPQ---*AYDLELITSCSSNVSVAHDaagkRVYYLTRDPETPLARAAWE 2818
Cdd:cd01699   229 LTMTDEDKvesPFRPLEEVEFLKRRFVLDEG----GGWRAPLDPSSILSKLSWS 278
HCV_core pfam01542
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
1-75 8.24e-33

Hepatitis C virus core protein; The viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases. The N terminus of the core protein is involved in transcriptional repression.


Pssm-ID: 460245  Cd Length: 75  Bit Score: 122.87  E-value: 8.24e-33
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 219964674     1 MSTNPKPQRKTKRNTNRRPMDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARR*EGRS 75
Cdd:pfam01542    1 MRNLGKPIDKLKCGFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRATAKGNEPGCPFGIFLLALKACLPEGAS 75
HCV_core pfam01542
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
116-190 7.65e-29

Hepatitis C virus core protein; The viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases. The N terminus of the core protein is involved in transcriptional repression.


Pssm-ID: 460245  Cd Length: 75  Bit Score: 111.69  E-value: 7.65e-29
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 219964674   116 SRNLGKVIDTLTCGFADLMGYIPLVGAPVGGVARALAHGVRAVEDGINYATGNLPGCSFSIFLLALLSCLTTPAS 190
Cdd:pfam01542    1 MRNLGKPIDKLKCGFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRATAKGNEPGCPFGIFLLALKACLPEGAS 75
HCV_p7 cd20903
Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for ...
747-795 1.29e-15

Hepatitis C virus p7 protein; Hepatitis C virus (HCV) p7 protein is a viroporin essential for virus production. The p7 monomer is comprised of 2 trans-membrane helices connected by a cytosolic loop, and oligomerizes to form cation-specific ion channels. These ion channels dissipate pH gradients in secretory vesicles potentially protecting acid-labile intracellular virions during egress (the rupturing of the infected cell and release of viral contents). p7 protein has at least two different functions in culture, one via the formation of these ion channels, the other through its specific interaction with the non-structural viral protein NS2. Several compounds targeting p7 have been investigated as anti-HCV drugs.


Pssm-ID: 411017  Cd Length: 58  Bit Score: 73.03  E-value: 1.29e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 219964674  747 AMANLININAMSAAGTYGLPYALLFFCVAWYVRG*LPA*AAYAACGMWP 795
Cdd:cd20903     1 ALENLVVLNAASAAGTHGLLWFLLFFCAAWYIKGRLVPAATYALLGLWP 49
DEXDc smart00487
DEAD-like helicases superfamily;
1228-1355 1.42e-13

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 72.14  E-value: 1.42e-13
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674   1228 LHAPTGSGKSTKVPAAYAAQGY-----KVLVLNPSVAATLGFGSYMSKAHGIDPNIRSGVRT-----------ITTGAPI 1291
Cdd:smart00487   29 LAAPTGSGKTLAALLPALEALKrgkggRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGgdskreqlrklESGKTDI 108
                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 219964674   1292 TYSTYGKF---LADGGCGGGAYDIIICDECHSTDS----TTILGIGTVLDQAetagvRLVVLATATPPGSI 1355
Cdd:smart00487  109 LVTTPGRLldlLENDKLSLSNVDLVILDEAHRLLDggfgDQLEKLLKLLPKN-----VQLLLLSATPPEEI 174
ps_ssRNAv_Tolivirales_RdRp cd23179
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ...
2615-2747 9.45e-11

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


Pssm-ID: 438029  Cd Length: 227  Bit Score: 64.47  E-value: 9.45e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2615 YSPAQRVERLLKSWNSKRVPMGFPYDTRCFDSTVTERDIQVEEEVY-QCCDLDPEARKVISslTERLYKGGPMFN*Kgdl 2693
Cdd:cd23179    64 LNPRQRANLIRRKWDEFDDPVVFSLDASRFDAHVSVELLRLEHSVYlACYPGDPELRKLLK--WQLVNKGRTSNGVK--- 138
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 219964674 2694 cgYRR--CRASGVFTTSFGNTLTCYLKATAAARAAGLKdYDMLVCGDDLVIIAESD 2747
Cdd:cd23179   139 --YKTrgGRMSGDMNTGLGNCLIMLAMVYAVLRELGIK-YDLLVDGDDALVFVERE 191
HCV_NS5a pfam01506
Hepatitis C virus non-structural 5a protein membrane anchor; The molecular function of the ...
1975-1996 3.35e-07

Hepatitis C virus non-structural 5a protein membrane anchor; The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. The N-terminal region of the NS5a protein has been used in the construction of the alignment for this family. The C-terminal region has not been included because it is too heterogeneous.


Pssm-ID: 366682  Cd Length: 23  Bit Score: 48.35  E-value: 3.35e-07
                           10        20
                   ....*....|....*....|..
gi 219964674  1975 NWLREIWDWVCTVLSDFKSWLK 1996
Cdd:pfam01506    2 SWLWDIWDWVCRVLRDFKNWLK 23
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
1386-1439 4.10e-06

C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. They 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: 350181 [Multi-domain]  Cd Length: 134  Bit Score: 48.74  E-value: 4.10e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 219964674 1386 KGGRHLIFCHSKKKCDELAKQLSSLGLNAVAYYRGL----DVSVIP---TSGDVVVCATDA 1439
Cdd:cd18794    29 LGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLepsdRRDVQRkwlRDKIQVIVATVA 89
Tombusvirus-like_RdRp cd23236
RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded ...
2593-2822 1.54e-05

RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within Procedovirinae subfamily; and related RdRps; This group contains the RdRp of RNA viruses belonging to the Tombusvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Tombusvirus is a genus of plant viruses. There are 17 species in the Tombusvirus genus: Artichoke mottled crinkle virus, Carnation Italian ringspot virus, Cucumber Bulgarian virus, Cucumber necrosis virus, Cymbidium ringspot virus, Eggplant mottled crinkle virus, Grapevine Algerian latent virus, Havel River virus, Lato River virus, Limonium flower distortion virus, Moroccan pepper virus, Neckar River virus, Pelargonium leaf curl virus, Pelargonium necrotic spot virus, Petunia asteroid mosaic virus, Sikte waterborne virus, and Tomato bushy stunt virus. Symptoms associated with this genus include mosaic. The name of the genus comes from Tomato bushy stunt virus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438086 [Multi-domain]  Cd Length: 474  Bit Score: 50.40  E-value: 1.54e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2593 RALYNVVQKLPQAVMGEAYGFQYSPAQRVERLLKS-WNSKRVPMGFPYDTRCFDSTVTERDIQVEEEVYQCcdLDPeARK 2671
Cdd:cd23236   158 RHMESKLMKAVDGVFGETTCIKGYTADEVGAIFRDkWDRFDKPVAIGLDASRFDQHCSVEALQFEHSFYRA--MYP-GNK 234
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2672 VISSLTE-RLYKGGPMFN*KGDLcGYRR--CRASGVFTTSFGNTLTCYLKATAAARAAGLKDYDMLVCGDDLVIIAESDG 2748
Cdd:cd23236   235 LLSKLLEwQLHNKGKGYVPDGTI-TYRKegCRMSGDINTSLGNYLLMCAMVYGYMRHLGINEFSLANCGDDCVLIVERRN 313
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2749 VEEDKQALRA--FTEAMTRYSAPPgdapq*AYDLELITSCSSN----------VSVAHDAAGKRVYYLT--RDPETplaR 2814
Cdd:cd23236   314 LKQVQGTLPEyfLNLGYTMKVEPP------VFQLEEVEFCQAHpvqfqggwkmVRNVRTAMSKDVHCVNniRDLAT---R 384

                  ....*...
gi 219964674 2815 AAWETVRH 2822
Cdd:cd23236   385 RAWSNAQH 392
Flavi_DEAD pfam07652
Flavivirus DEAD domain;
1310-1361 3.50e-04

Flavivirus DEAD domain;


Pssm-ID: 400138 [Multi-domain]  Cd Length: 146  Bit Score: 43.48  E-value: 3.50e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 219964674  1310 YDIIICDECHSTDSTTILGIG---TVLDQAETAgvrlVVLATATPPGSITT-PHSN 1361
Cdd:pfam07652   94 YEVIIMDEAHFTDPASIAARGyisTLVELGEAA----AIFMTATPPGTSDPfPESN 145
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
1230-1350 5.81e-04

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: 42.78  E-value: 5.81e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 1230 APTGSGKSTKV--PAAYAA--QGYKVLVLNPSVAATL-------GFGSYMSKAHGIDPNIRSGVRTITTG--APITYSTY 1296
Cdd:cd00046     8 APTGSGKTLAAllAALLLLlkKGKKVLVLVPTKALALqtaerlrELFGPGIRVAVLVGGSSAEEREKNKLgdADIIIATP 87
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 1297 GKF----LADGGCGGGAYDIIICDECHSTDSTT--ILGIGTVLDQAETAGVRlVVLATAT 1350
Cdd:cd00046    88 DMLlnllLREDRLFLKDLKLIIVDEAHALLIDSrgALILDLAVRKAGLKNAQ-VILLSAT 146
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
1230-1351 7.89e-04

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


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 42.29  E-value: 7.89e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 1230 APTGSGKST---KVPAAYAAQgyKVLVLNPSVA-------ATLGFGSymskaHGIDPNIRSGVRTITTGAPITYSTY--- 1296
Cdd:cd17926    25 LPTGSGKTLtalALIAYLKEL--RTLIVVPTDAlldqwkeRFEDFLG-----DSSIGLIGGGKKKDFDDANVVVATYqsl 97
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 219964674 1297 GKFLADGGCGGGAYDIIICDECHSTDSTTILGIgtvldqAETAGVRLVVLATATP 1351
Cdd:cd17926    98 SNLAEEEKDLFDQFGLLIVDEAHHLPAKTFSEI------LKELNAKYRLGLTATP 146
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
1382-1422 7.97e-04

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 42.11  E-value: 7.97e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 219964674 1382 LEVIKGGRHLIFCHSKKKCDELAKQLSSLGLNAVAYYRGLD 1422
Cdd:cd18787    22 LEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLS 62
ps-ssRNAv_RdRp-like cd23167
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
2699-2745 9.05e-04

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


Pssm-ID: 438017 [Multi-domain]  Cd Length: 73  Bit Score: 40.01  E-value: 9.05e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 219964674 2699 CRASGVFTTSFGNTLTCYLKAT-----AAARAAGLKDYDMLVCGDDLVIIAE 2745
Cdd:cd23167    22 GQPSGSPNTSADNSLINLLLARlalrkACGRAEFLNSVGILVYGDDSLVSVP 73
ResIII pfam04851
Type III restriction enzyme, res subunit;
1228-1319 1.02e-03

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 42.27  E-value: 1.02e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  1228 LHAPTGSGK---STKVPAAYAAQGY--KVLVLNPSVA----ATLGFGSYMSKAHGIdPNIRSG--VRTITTGAPITYSTY 1296
Cdd:pfam04851   28 IVMATGSGKtltAAKLIARLFKKGPikKVLFLVPRKDlleqALEEFKKFLPNYVEI-GEIISGdkKDESVDDNKIVVTTI 106
                           90       100
                   ....*....|....*....|....*...
gi 219964674  1297 GKF-----LADGGCGGGAYDIIICDECH 1319
Cdd:pfam04851  107 QSLykaleLASLELLPDFFDVIIIDEAH 134
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
1228-1351 1.31e-03

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 44.25  E-value: 1.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 1228 LHAPTGSGKST---KVpAAYAAQGYKVLVLNPSVAATLGFgsyMSKAHGIDPNIRSGVRTITTGAPITYSTYGKFLADGG 1304
Cdd:COG1061   105 VVAPTGTGKTVlalAL-AAELLRGKRVLVLVPRRELLEQW---AEELRRFLGDPLAGGGKKDSDAPITVATYQSLARRAH 180
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 219964674 1305 CG--GGAYDIIICDECH--STDSTTILgigtvldqAETAGVRLVVLATATP 1351
Cdd:COG1061   181 LDelGDRFGLVIIDEAHhaGAPSYRRI--------LEAFPAAYRLGLTATP 223
Gammacarmovirus_RdRp cd23242
RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense ...
2626-2832 5.23e-03

RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Gammacarmovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The single genus Carmovirus was split in 2015 into three genera, each retaining -carmovirus as part of their name: Alphacarmovirus, Betacarmovirus, and Gammacarmovirus. Most species have a narrow natural host range. However, different carmoviruses infect a wide range of both monocotyledonous and dicotyledonous plants. Viruses tend to remain localized, forming necrosis in artificially infected hosts. There are 4 species in the genus Gammacarmovirus: Cowpea mottle virus, Melon necrotic spot virus, Pea stem necrosis virus, and Soybean yellow mottle mosaic virus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438092  Cd Length: 476  Bit Score: 42.04  E-value: 5.23e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2626 KSWNSKRVPMGFPYDTRCFDSTVTERDIQVEEEVY-QCCDLDPEARKVIS-SLTERLYKGGPMFN*KgdlcgYRR--CRA 2701
Cdd:cd23242   185 DAWDSFVSPVAIGFDMKRFDQHVSRDALEWEHSVYlDAFCNDPYLAELLSwQLENKGVGYASDGSIK-----YKVdgCRM 259
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674 2702 SGVFTTSFGNTLTCYLKATAAARAAGLKdYDMLVCGDDLVIIAESDGVEEDK-QALRAFTE-AMTRYSAPPgdapq*AYD 2779
Cdd:cd23242   260 SGDMNTAMGNCLLACAITWDFFKGRGIK-ARLLNNGDDCVVITEKECAAAVVaGMVRHWRRfGFQCELECD------VYI 332
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 219964674 2780 LELITSCssNVSVAHDaaGKRvYYLTRDPETPLAR-----AAWETVRHTpvNSWLGNI 2832
Cdd:cd23242   333 LEHIEFC--QMRPVYD--GSK-YTMVRNPLVSLSKdsysvGPWNNIKHA--AKWVNAV 383
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
1224-1344 7.08e-03

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.


Pssm-ID: 433343 [Multi-domain]  Cd Length: 191  Bit Score: 40.24  E-value: 7.08e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219964674  1224 QVAHLHAPTGSGKST---KVPAAYAAQGYKVLVLNPSVAATLGfgsyMSKAHGIDpnirsgVRTIttgapitystyGKFL 1300
Cdd:pfam13604   19 RVAVLVGPAGTGKTTalkALREAWEAAGYRVIGLAPTGRAAKV----LGEELGIP------ADTI-----------AKLL 77
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 219964674  1301 A--DGGCGGGAYDIIICDECHSTDSTTILgigTVLDQAETAGVRLV 1344
Cdd:pfam13604   78 HrlGGRAGLDPGTLLIVDEAGMVGTRQMA---RLLKLAEDAGARVI 120
 
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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