catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within ...
2838-3404
0e+00
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Flavivirus genus within the family Flaviviridae, order Amarillovirales. The genus Flavivirus consists of more than 50 species of arthropod-borne viruses, with distinct groups infecting mosquitoes or ticks. Mammals and birds are the usual primary hosts, in which infections range from asymptomatic to severe or fatal hemorrhagic fever or neurological disease. Important human pathogens include yellow fever virus, dengue virus, Japanese encephalitis virus, West Nile virus and tick-borne encephalitis virus. Other members cause economically important diseases in domestic or wild animals. Virions of Flavivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. Translational initiation of genomic RNA is cap dependent in the case of members of the genus Flavivirus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.
:
Pssm-ID: 438054 [Multi-domain] Cd Length: 565 Bit Score: 1218.94 E-value: 0e+00
Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the ...
786-1140
3.30e-150
Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the flaviviruses. It contains 12 cysteines, and undergoes glycosylation in a similar manner to other NS proteins. Mutational analysis has strongly implied a role for NS1 in the early stages of RNA replication.
The actual alignment was detected with superfamily member pfam00948:
Pssm-ID: 279316 Cd Length: 360 Bit Score: 471.45 E-value: 3.30e-150
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific ...
2527-2760
2.49e-114
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Flaviviridae viruses, comprise a family of ss(+)RNA viruses, cap their mRNAs. The 2'OMTase activity is located in the non-structural protein 5 (NS5).
:
Pssm-ID: 467736 Cd Length: 225 Bit Score: 362.31 E-value: 2.49e-114
flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal ...
688-784
2.86e-46
flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal domain, containing a stem region followed by two transmembrane anchor domains, of the envelope protein E. This protein is cleaved from the large flavivirus polyprotein, which yields three structural and seven nonstructural proteins.
:
Pssm-ID: 213897 Cd Length: 97 Bit Score: 162.04 E-value: 2.86e-46
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
1830-1973
5.65e-46
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: 163.20 E-value: 5.65e-46
Immunoglobulin-like domain III (C-terminal domain) of Flavivirus envelope glycoprotein E; The ...
595-683
1.68e-39
Immunoglobulin-like domain III (C-terminal domain) of Flavivirus envelope glycoprotein E; The C-terminal domain (domain III) of Flavivirus glycoprotein E appears to be involved in low-affinity interactions with negatively charged glycoaminoglycans on the host cell surface. Domain III may also play a role in interactions with alpha-v-beta-3 integrins in West Nile virus, Japanese encephalitis virus, and Dengue virus. The interface between domain I and domain III appears to be destabilized by the low-pH environment of the endosome, and domain III may play a vital role in the conformational changes of envelope glycoprotein E that follow the clathrin-mediated endocytosis of viral particles and are a prerequisite to membrane fusion.
:
Pssm-ID: 213392 Cd Length: 91 Bit Score: 142.83 E-value: 1.68e-39
Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that ...
1518-1666
1.21e-31
Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that encodes a single polyprotein precursor. Processing of the polyprotein precursor into mature proteins is carried out by the host signal peptidase and by NS3 serine protease, which requires NS2B (pfam01002) as a cofactor.
:
Pssm-ID: 395758 Cd Length: 129 Bit Score: 121.78 E-value: 1.21e-31
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with a ...
220-294
3.36e-30
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with a membrane-anchored envelope comprised of 3 proteins called C, M and E. The envelope glycoprotein M is translated as a precursor, called prM. The precursor portion of the protein is the signal peptide for the protein's entry into the membrane. prM is cleaved to form M by the proprotein convertase furin in a late-stage cleavage event. Associated with this cleavage is a change in the infectivity and fusion activity of the virus.
:
Pssm-ID: 341208 Cd Length: 75 Bit Score: 115.42 E-value: 3.36e-30
Flavivirus polyprotein propeptide; The flaviviruses are small enveloped animal viruses ...
142-212
5.84e-15
Flavivirus polyprotein propeptide; The flaviviruses are small enveloped animal viruses containing a single positive strand genomic RNA. The genome encodes one large ORF a polyprotein which undergos proteolytic processing into mature viral peptide chains. This family consists of a propeptide region of approximately 90 amino acid length.
:
Pssm-ID: 366710 Cd Length: 78 Bit Score: 72.15 E-value: 5.84e-15
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within ...
2838-3404
0e+00
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Flavivirus genus within the family Flaviviridae, order Amarillovirales. The genus Flavivirus consists of more than 50 species of arthropod-borne viruses, with distinct groups infecting mosquitoes or ticks. Mammals and birds are the usual primary hosts, in which infections range from asymptomatic to severe or fatal hemorrhagic fever or neurological disease. Important human pathogens include yellow fever virus, dengue virus, Japanese encephalitis virus, West Nile virus and tick-borne encephalitis virus. Other members cause economically important diseases in domestic or wild animals. Virions of Flavivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. Translational initiation of genomic RNA is cap dependent in the case of members of the genus Flavivirus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.
Pssm-ID: 438054 [Multi-domain] Cd Length: 565 Bit Score: 1218.94 E-value: 0e+00
Flavivirus RNA-directed RNA polymerase, fingers and palm domains; Flaviviruses produce a large ...
2769-3218
0e+00
Flavivirus RNA-directed RNA polymerase, fingers and palm domains; Flaviviruses produce a large polyprotein from the ssRNA genome, encoding structural proteins required for virus assembly and non-structural (NS1-5) proteins involved in replication of the viral genome. This polyprotein is cleaved by viral and cellular proteases to produce mature viral proteins. NS5 is the largest mature viral protein and contains a N-terminal methyltransferase (MTase) domain separated by a short linker from the C-terminal RNA-directed RNA polymerase domain (RdRp) that adopts a characteriztic right-handed fingers-palm-thumb fold and possesses a number of short regions and motifs homologous to other RNA-directed RNA polymerases. This entry covers the fingers and palm domains of RNA-directed RNA polymerase (RdRp) from Flavivirus NS5. NS5 binds to a the stem loop A (SLA) at the 5' extremity of Flavivirus genome and regulates translation of the viral genome.
Pssm-ID: 460013 Cd Length: 451 Bit Score: 741.76 E-value: 0e+00
Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the ...
786-1140
3.30e-150
Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the flaviviruses. It contains 12 cysteines, and undergoes glycosylation in a similar manner to other NS proteins. Mutational analysis has strongly implied a role for NS1 in the early stages of RNA replication.
Pssm-ID: 279316 Cd Length: 360 Bit Score: 471.45 E-value: 3.30e-150
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific ...
2527-2760
2.49e-114
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Flaviviridae viruses, comprise a family of ss(+)RNA viruses, cap their mRNAs. The 2'OMTase activity is located in the non-structural protein 5 (NS5).
Pssm-ID: 467736 Cd Length: 225 Bit Score: 362.31 E-value: 2.49e-114
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
1684-1832
2.30e-52
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: 181.98 E-value: 2.30e-52
flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal ...
688-784
2.86e-46
flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal domain, containing a stem region followed by two transmembrane anchor domains, of the envelope protein E. This protein is cleaved from the large flavivirus polyprotein, which yields three structural and seven nonstructural proteins.
Pssm-ID: 213897 Cd Length: 97 Bit Score: 162.04 E-value: 2.86e-46
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
1830-1973
5.65e-46
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: 163.20 E-value: 5.65e-46
Immunoglobulin-like domain III (C-terminal domain) of Flavivirus envelope glycoprotein E; The ...
595-683
1.68e-39
Immunoglobulin-like domain III (C-terminal domain) of Flavivirus envelope glycoprotein E; The C-terminal domain (domain III) of Flavivirus glycoprotein E appears to be involved in low-affinity interactions with negatively charged glycoaminoglycans on the host cell surface. Domain III may also play a role in interactions with alpha-v-beta-3 integrins in West Nile virus, Japanese encephalitis virus, and Dengue virus. The interface between domain I and domain III appears to be destabilized by the low-pH environment of the endosome, and domain III may play a vital role in the conformational changes of envelope glycoprotein E that follow the clathrin-mediated endocytosis of viral particles and are a prerequisite to membrane fusion.
Pssm-ID: 213392 Cd Length: 91 Bit Score: 142.83 E-value: 1.68e-39
Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that ...
1518-1666
1.21e-31
Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that encodes a single polyprotein precursor. Processing of the polyprotein precursor into mature proteins is carried out by the host signal peptidase and by NS3 serine protease, which requires NS2B (pfam01002) as a cofactor.
Pssm-ID: 395758 Cd Length: 129 Bit Score: 121.78 E-value: 1.21e-31
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with a ...
220-294
3.36e-30
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with a membrane-anchored envelope comprised of 3 proteins called C, M and E. The envelope glycoprotein M is translated as a precursor, called prM. The precursor portion of the protein is the signal peptide for the protein's entry into the membrane. prM is cleaved to form M by the proprotein convertase furin in a late-stage cleavage event. Associated with this cleavage is a change in the infectivity and fusion activity of the virus.
Pssm-ID: 341208 Cd Length: 75 Bit Score: 115.42 E-value: 3.36e-30
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...
2571-2743
1.78e-26
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesized that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping.
Pssm-ID: 426399 Cd Length: 179 Bit Score: 108.83 E-value: 1.78e-26
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with virions ...
221-294
3.76e-19
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with virions comprised of 3 proteins called C, M and E. The envelope glycoprotein M is made as a precursor, called prM. The precursor portion of the protein is the signal peptide for the proteins entry into the membrane. prM is cleaved to form M in a late-stage cleavage event. Associated with this cleavage is a change in the infectivity and fusion activity of the virus.
Pssm-ID: 460022 Cd Length: 74 Bit Score: 84.17 E-value: 3.76e-19
Flavivirus polyprotein propeptide; The flaviviruses are small enveloped animal viruses ...
142-212
5.84e-15
Flavivirus polyprotein propeptide; The flaviviruses are small enveloped animal viruses containing a single positive strand genomic RNA. The genome encodes one large ORF a polyprotein which undergos proteolytic processing into mature viral peptide chains. This family consists of a propeptide region of approximately 90 amino acid length.
Pssm-ID: 366710 Cd Length: 78 Bit Score: 72.15 E-value: 5.84e-15
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ...
1778-1965
2.00e-04
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.
Pssm-ID: 273707 [Multi-domain] Cd Length: 359 Bit Score: 46.68 E-value: 2.00e-04
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
1872-1960
2.19e-03
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 40.27 E-value: 2.19e-03
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within ...
2838-3404
0e+00
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Flavivirus genus within the family Flaviviridae, order Amarillovirales. The genus Flavivirus consists of more than 50 species of arthropod-borne viruses, with distinct groups infecting mosquitoes or ticks. Mammals and birds are the usual primary hosts, in which infections range from asymptomatic to severe or fatal hemorrhagic fever or neurological disease. Important human pathogens include yellow fever virus, dengue virus, Japanese encephalitis virus, West Nile virus and tick-borne encephalitis virus. Other members cause economically important diseases in domestic or wild animals. Virions of Flavivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. Translational initiation of genomic RNA is cap dependent in the case of members of the genus Flavivirus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.
Pssm-ID: 438054 [Multi-domain] Cd Length: 565 Bit Score: 1218.94 E-value: 0e+00
Flavivirus RNA-directed RNA polymerase, fingers and palm domains; Flaviviruses produce a large ...
2769-3218
0e+00
Flavivirus RNA-directed RNA polymerase, fingers and palm domains; Flaviviruses produce a large polyprotein from the ssRNA genome, encoding structural proteins required for virus assembly and non-structural (NS1-5) proteins involved in replication of the viral genome. This polyprotein is cleaved by viral and cellular proteases to produce mature viral proteins. NS5 is the largest mature viral protein and contains a N-terminal methyltransferase (MTase) domain separated by a short linker from the C-terminal RNA-directed RNA polymerase domain (RdRp) that adopts a characteriztic right-handed fingers-palm-thumb fold and possesses a number of short regions and motifs homologous to other RNA-directed RNA polymerases. This entry covers the fingers and palm domains of RNA-directed RNA polymerase (RdRp) from Flavivirus NS5. NS5 binds to a the stem loop A (SLA) at the 5' extremity of Flavivirus genome and regulates translation of the viral genome.
Pssm-ID: 460013 Cd Length: 451 Bit Score: 741.76 E-value: 0e+00
Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the ...
786-1140
3.30e-150
Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the flaviviruses. It contains 12 cysteines, and undergoes glycosylation in a similar manner to other NS proteins. Mutational analysis has strongly implied a role for NS1 in the early stages of RNA replication.
Pssm-ID: 279316 Cd Length: 360 Bit Score: 471.45 E-value: 3.30e-150
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific ...
2527-2760
2.49e-114
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Flaviviridae viruses, comprise a family of ss(+)RNA viruses, cap their mRNAs. The 2'OMTase activity is located in the non-structural protein 5 (NS5).
Pssm-ID: 467736 Cd Length: 225 Bit Score: 362.31 E-value: 2.49e-114
Flavivirus RNA-directed RNA polymerase, thumb domain; Flaviviruses produce a large polyprotein ...
3224-3387
5.76e-80
Flavivirus RNA-directed RNA polymerase, thumb domain; Flaviviruses produce a large polyprotein from the ssRNA genome, encoding structural proteins required for virus assembly and non-structural (NS1-5) proteins involved in replication of the viral genome. This polyprotein is cleaved by viral and cellular proteases to produce mature viral proteins. NS5 is the largest mature viral protein and contains a N-terminal methyltransferase (MTase) domain separated by a short linker from the C-terminal RNA-directed RNA polymerase domain (RdRp) that adopts a characteriztic right-handed fingers-palm-thumb fold and possesses a number of short regions and motifs homologous to other RNA-directed RNA polymerases. This entry represents the thumb domain of NS5 RdRp. NS5 binds to a the stem loop A (SLA) at the 5' extremity of Flavivirus genome and regulates translation of the viral genome.
Pssm-ID: 466632 Cd Length: 164 Bit Score: 261.27 E-value: 5.76e-80
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ...
2968-3284
4.85e-69
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: 235.10 E-value: 4.85e-69
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
1684-1832
2.30e-52
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: 181.98 E-value: 2.30e-52
flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal ...
688-784
2.86e-46
flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal domain, containing a stem region followed by two transmembrane anchor domains, of the envelope protein E. This protein is cleaved from the large flavivirus polyprotein, which yields three structural and seven nonstructural proteins.
Pssm-ID: 213897 Cd Length: 97 Bit Score: 162.04 E-value: 2.86e-46
C-terminal helicase domain of viral helicase; Viral helicases in this family here are ...
1830-1973
5.65e-46
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: 163.20 E-value: 5.65e-46
Immunoglobulin-like domain III (C-terminal domain) of Flavivirus envelope glycoprotein E; The ...
595-683
1.68e-39
Immunoglobulin-like domain III (C-terminal domain) of Flavivirus envelope glycoprotein E; The C-terminal domain (domain III) of Flavivirus glycoprotein E appears to be involved in low-affinity interactions with negatively charged glycoaminoglycans on the host cell surface. Domain III may also play a role in interactions with alpha-v-beta-3 integrins in West Nile virus, Japanese encephalitis virus, and Dengue virus. The interface between domain I and domain III appears to be destabilized by the low-pH environment of the endosome, and domain III may play a vital role in the conformational changes of envelope glycoprotein E that follow the clathrin-mediated endocytosis of viral particles and are a prerequisite to membrane fusion.
Pssm-ID: 213392 Cd Length: 91 Bit Score: 142.83 E-value: 1.68e-39
Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that ...
1518-1666
1.21e-31
Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that encodes a single polyprotein precursor. Processing of the polyprotein precursor into mature proteins is carried out by the host signal peptidase and by NS3 serine protease, which requires NS2B (pfam01002) as a cofactor.
Pssm-ID: 395758 Cd Length: 129 Bit Score: 121.78 E-value: 1.21e-31
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with a ...
220-294
3.36e-30
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with a membrane-anchored envelope comprised of 3 proteins called C, M and E. The envelope glycoprotein M is translated as a precursor, called prM. The precursor portion of the protein is the signal peptide for the protein's entry into the membrane. prM is cleaved to form M by the proprotein convertase furin in a late-stage cleavage event. Associated with this cleavage is a change in the infectivity and fusion activity of the virus.
Pssm-ID: 341208 Cd Length: 75 Bit Score: 115.42 E-value: 3.36e-30
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...
2571-2743
1.78e-26
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesized that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping.
Pssm-ID: 426399 Cd Length: 179 Bit Score: 108.83 E-value: 1.78e-26
viral Cap-0 specific (nucleoside-2'-O-)-methyltransferase; Cap-0 specific (nucleoside-2'-O-) ...
2576-2763
1.71e-20
viral Cap-0 specific (nucleoside-2'-O-)-methyltransferase; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Some dsDNA and dsRNA viruses, like the bluetongue virus (BTV), a member of the Reoviridae family, and Vaccinia virus, a member of the Poxviridae family, as well as some ss(+)RNA viruses, like Flaviviridae and Nidovirales, cap their mRNAs and encode their own 2'OMTase. In BTV, all four reactions are catalyzed by a single protein, VP4. In Vaccinia, the activity is located in the processing factor of the poly(A) polymerase, VP39.
Pssm-ID: 467730 Cd Length: 179 Bit Score: 91.73 E-value: 1.71e-20
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with virions ...
221-294
3.76e-19
Flavivirus envelope glycoprotein M; Flaviviruses are small enveloped viruses with virions comprised of 3 proteins called C, M and E. The envelope glycoprotein M is made as a precursor, called prM. The precursor portion of the protein is the signal peptide for the proteins entry into the membrane. prM is cleaved to form M in a late-stage cleavage event. Associated with this cleavage is a change in the infectivity and fusion activity of the virus.
Pssm-ID: 460022 Cd Length: 74 Bit Score: 84.17 E-value: 3.76e-19
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
1684-1815
2.12e-15
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: 75.90 E-value: 2.12e-15
Flavivirus polyprotein propeptide; The flaviviruses are small enveloped animal viruses ...
142-212
5.84e-15
Flavivirus polyprotein propeptide; The flaviviruses are small enveloped animal viruses containing a single positive strand genomic RNA. The genome encodes one large ORF a polyprotein which undergos proteolytic processing into mature viral peptide chains. This family consists of a propeptide region of approximately 90 amino acid length.
Pssm-ID: 366710 Cd Length: 78 Bit Score: 72.15 E-value: 5.84e-15
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ...
1688-1816
2.58e-12
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 438707 [Multi-domain] Cd Length: 159 Bit Score: 67.48 E-value: 2.58e-12
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
2949-3259
2.36e-07
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: 55.37 E-value: 2.36e-07
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ...
1778-1990
5.65e-07
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I
Pssm-ID: 187770 [Multi-domain] Cd Length: 353 Bit Score: 54.74 E-value: 5.65e-07
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
1688-1816
4.34e-06
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350684 [Multi-domain] Cd Length: 146 Bit Score: 49.23 E-value: 4.34e-06
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ...
1778-1965
2.00e-04
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.
Pssm-ID: 273707 [Multi-domain] Cd Length: 359 Bit Score: 46.68 E-value: 2.00e-04
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
1872-1960
2.19e-03
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 40.27 E-value: 2.19e-03
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
1694-1817
2.81e-03
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 41.46 E-value: 2.81e-03
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
2956-3235
3.60e-03
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases.
Pssm-ID: 425815 Cd Length: 450 Bit Score: 42.78 E-value: 3.60e-03
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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Functional characterization of the conserved domain architecture found on the query.
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This image shows a graphical summary of conserved domains identified on the query sequence.
The Show Concise/Full Display button at the top of the page can be used to select the desired level of detail: only top scoring hits
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if a domain or superfamily has been annotated with functional sites (conserved features),
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click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.
The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
Click on the domain model's accession number to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.
To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page,
or click on the triangles, if present, that represent functional sites (conserved features)
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Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence.
(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
(labeled illustration) Full Display shows all domain models, in each hit category below, that meet or exceed the RPS-BLAST threshold for statistical significance.
(labeled illustration) Four types of hits can be shown, as available,
for each region on the query sequence:
specific hits meet or exceed a domain-specific e-value threshold
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and represent a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model
non-specific hits
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the domain superfamily to which the specific and non-specific hits belong
multi-domain models that were computationally detected and are likely to contain multiple single domains
Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool
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