YFVdelCME-mVenus [Cloning vector pYFVdelCME-mVenus]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||||
| Flavivirus_RdRp | cd23204 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within ... |
2461-3027 | 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: 1276.72 E-value: 0e+00
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| Flavi_NS1 | pfam00948 | Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the ... |
409-762 | 0e+00 | |||||||||
Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the flaviviruses. It contains 12 cysteines, and undergoes glycosylation in a similar manner to other NS proteins. Mutational analysis has strongly implied a role for NS1 in the early stages of RNA replication. : Pssm-ID: 279316 Cd Length: 360 Bit Score: 740.32 E-value: 0e+00
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| Flavi_NS4B | pfam01349 | Flavivirus non-structural protein NS4B; Flaviviruses encode a single polyprotein. This is ... |
1891-2134 | 1.04e-143 | |||||||||
Flavivirus non-structural protein NS4B; Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4B protein is small and poorly conserved among the Flaviviruses. NS4B contains multiple hydrophobic potential membrane spanning regions. NS4B may form membrane components of the viral replication complex and could be involved in membrane localization of NS3 and pfam00972. : Pssm-ID: 279665 Cd Length: 248 Bit Score: 447.55 E-value: 1.04e-143
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| capping_2-OMTase_Flaviviridae | cd20761 | Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific ... |
2147-2377 | 7.23e-114 | |||||||||
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Flaviviridae viruses, comprise a family of ss(+)RNA viruses, cap their mRNAs. The 2'OMTase activity is located in the non-structural protein 5 (NS5). : Pssm-ID: 467736 Cd Length: 225 Bit Score: 361.15 E-value: 7.23e-114
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| Flavi_NS2A | pfam01005 | Flavivirus non-structural protein NS2A; NS2A is a hydrophobic protein about 25 kDa is size. ... |
768-953 | 1.09e-92 | |||||||||
Flavivirus non-structural protein NS2A; NS2A is a hydrophobic protein about 25 kDa is size. NS2A is cleaved from NS1 by a membrane bound host protease. NS2A has been found to associate with the dsRNA within the vesicle packages. It has also been found that NS2A associates with the known replicase components and so NS2A has been postulated to be part of this replicase complex. : Pssm-ID: 279359 Cd Length: 215 Bit Score: 299.83 E-value: 1.09e-92
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| Flavi_DEAD | pfam07652 | Flavivirus DEAD domain; |
1308-1453 | 3.95e-92 | |||||||||
Flavivirus DEAD domain; : Pssm-ID: 400138 [Multi-domain] Cd Length: 146 Bit Score: 295.40 E-value: 3.95e-92
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| Flavi_NS4A | pfam01350 | Flavivirus non-structural protein NS4A; Flaviviruses encode a single polyprotein. This is ... |
1745-1888 | 1.72e-78 | |||||||||
Flavivirus non-structural protein NS4A; Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4A protein is small and poorly conserved among the Flaviviruses. NS4A contains multiple hydrophobic potential membrane spanning regions. NS4A has only been found in cells infected by Kunjin virus. : Pssm-ID: 279666 Cd Length: 144 Bit Score: 256.37 E-value: 1.72e-78
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| Flavi_NS2B super family | cl03063 | Flavivirus non-structural protein NS2B; Flaviviruses encode a single polyprotein. This is ... |
987-1113 | 3.50e-68 | |||||||||
Flavivirus non-structural protein NS2B; Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. All, but two, are cleaved by the NS2B-NS3 protease complex. The actual alignment was detected with superfamily member pfam01002: Pssm-ID: 279357 Cd Length: 127 Bit Score: 226.04 E-value: 3.50e-68
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| Ubl_ubiquitin | cd01803 | ubiquitin-like (Ubl) domain found in ubiquitin; Ubiquitin is a protein modifier in eukaryotes ... |
288-362 | 1.74e-51 | |||||||||
ubiquitin-like (Ubl) domain found in ubiquitin; Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. Ubiquitin-like (Ubl) proteins have similar ubiquitin beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ubiquitin (Ub)and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Ub includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains. : Pssm-ID: 340501 [Multi-domain] Cd Length: 76 Bit Score: 176.10 E-value: 1.74e-51
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| Peptidase_S7 | pfam00949 | Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that ... |
1138-1289 | 2.06e-48 | |||||||||
Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that encodes a single polyprotein precursor. Processing of the polyprotein precursor into mature proteins is carried out by the host signal peptidase and by NS3 serine protease, which requires NS2B (pfam01002) as a cofactor. : Pssm-ID: 395758 Cd Length: 129 Bit Score: 169.54 E-value: 2.06e-48
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| P-loop_NTPase super family | cl38936 | P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ... |
1455-1597 | 1.49e-44 | |||||||||
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families. The actual alignment was detected with superfamily member cd18806: Pssm-ID: 476819 [Multi-domain] Cd Length: 145 Bit Score: 158.96 E-value: 1.49e-44
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| GFP super family | cl08319 | Green fluorescent protein; |
46-241 | 2.05e-15 | |||||||||
Green fluorescent protein; The actual alignment was detected with superfamily member pfam01353: Pssm-ID: 426217 Cd Length: 211 Bit Score: 77.61 E-value: 2.05e-15
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| flavi_E_stem super family | cl16990 | flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal ... |
373-407 | 3.86e-05 | |||||||||
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. The actual alignment was detected with superfamily member TIGR04240: Pssm-ID: 213897 Cd Length: 97 Bit Score: 44.94 E-value: 3.86e-05
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| Name | Accession | Description | Interval | E-value | |||||||||
| Flavivirus_RdRp | cd23204 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within ... |
2461-3027 | 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: 1276.72 E-value: 0e+00
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| Flavi_NS5 | pfam00972 | Flavivirus RNA-directed RNA polymerase, fingers and palm domains; Flaviviruses produce a large ... |
2392-2844 | 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: 953.24 E-value: 0e+00
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| Flavi_NS1 | pfam00948 | Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the ... |
409-762 | 0e+00 | |||||||||
Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the flaviviruses. It contains 12 cysteines, and undergoes glycosylation in a similar manner to other NS proteins. Mutational analysis has strongly implied a role for NS1 in the early stages of RNA replication. Pssm-ID: 279316 Cd Length: 360 Bit Score: 740.32 E-value: 0e+00
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| Flavi_NS4B | pfam01349 | Flavivirus non-structural protein NS4B; Flaviviruses encode a single polyprotein. This is ... |
1891-2134 | 1.04e-143 | |||||||||
Flavivirus non-structural protein NS4B; Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4B protein is small and poorly conserved among the Flaviviruses. NS4B contains multiple hydrophobic potential membrane spanning regions. NS4B may form membrane components of the viral replication complex and could be involved in membrane localization of NS3 and pfam00972. Pssm-ID: 279665 Cd Length: 248 Bit Score: 447.55 E-value: 1.04e-143
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| capping_2-OMTase_Flaviviridae | cd20761 | Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific ... |
2147-2377 | 7.23e-114 | |||||||||
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Flaviviridae viruses, comprise a family of ss(+)RNA viruses, cap their mRNAs. The 2'OMTase activity is located in the non-structural protein 5 (NS5). Pssm-ID: 467736 Cd Length: 225 Bit Score: 361.15 E-value: 7.23e-114
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| Flavi_NS2A | pfam01005 | Flavivirus non-structural protein NS2A; NS2A is a hydrophobic protein about 25 kDa is size. ... |
768-953 | 1.09e-92 | |||||||||
Flavivirus non-structural protein NS2A; NS2A is a hydrophobic protein about 25 kDa is size. NS2A is cleaved from NS1 by a membrane bound host protease. NS2A has been found to associate with the dsRNA within the vesicle packages. It has also been found that NS2A associates with the known replicase components and so NS2A has been postulated to be part of this replicase complex. Pssm-ID: 279359 Cd Length: 215 Bit Score: 299.83 E-value: 1.09e-92
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| Flavi_DEAD | pfam07652 | Flavivirus DEAD domain; |
1308-1453 | 3.95e-92 | |||||||||
Flavivirus DEAD domain; Pssm-ID: 400138 [Multi-domain] Cd Length: 146 Bit Score: 295.40 E-value: 3.95e-92
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| Flavi_NS4A | pfam01350 | Flavivirus non-structural protein NS4A; Flaviviruses encode a single polyprotein. This is ... |
1745-1888 | 1.72e-78 | |||||||||
Flavivirus non-structural protein NS4A; Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4A protein is small and poorly conserved among the Flaviviruses. NS4A contains multiple hydrophobic potential membrane spanning regions. NS4A has only been found in cells infected by Kunjin virus. Pssm-ID: 279666 Cd Length: 144 Bit Score: 256.37 E-value: 1.72e-78
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| Flavi_NS2B | pfam01002 | Flavivirus non-structural protein NS2B; Flaviviruses encode a single polyprotein. This is ... |
987-1113 | 3.50e-68 | |||||||||
Flavivirus non-structural protein NS2B; Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. All, but two, are cleaved by the NS2B-NS3 protease complex. Pssm-ID: 279357 Cd Length: 127 Bit Score: 226.04 E-value: 3.50e-68
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| DEXHc_viral_Ns3 | cd17931 | DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ... |
1312-1459 | 5.35e-58 | |||||||||
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350689 [Multi-domain] Cd Length: 151 Bit Score: 197.77 E-value: 5.35e-58
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| Ubl_ubiquitin | cd01803 | ubiquitin-like (Ubl) domain found in ubiquitin; Ubiquitin is a protein modifier in eukaryotes ... |
288-362 | 1.74e-51 | |||||||||
ubiquitin-like (Ubl) domain found in ubiquitin; Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. Ubiquitin-like (Ubl) proteins have similar ubiquitin beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ubiquitin (Ub)and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Ub includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains. Pssm-ID: 340501 [Multi-domain] Cd Length: 76 Bit Score: 176.10 E-value: 1.74e-51
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| Peptidase_S7 | pfam00949 | Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that ... |
1138-1289 | 2.06e-48 | |||||||||
Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that encodes a single polyprotein precursor. Processing of the polyprotein precursor into mature proteins is carried out by the host signal peptidase and by NS3 serine protease, which requires NS2B (pfam01002) as a cofactor. Pssm-ID: 395758 Cd Length: 129 Bit Score: 169.54 E-value: 2.06e-48
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| SF2_C_viral | cd18806 | C-terminal helicase domain of viral helicase; Viral helicases in this family here are ... |
1455-1597 | 1.49e-44 | |||||||||
C-terminal helicase domain of viral helicase; Viral helicases in this family here are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350193 [Multi-domain] Cd Length: 145 Bit Score: 158.96 E-value: 1.49e-44
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| UBI4 | COG5272 | Ubiquitin [Posttranslational modification, protein turnover, chaperones]; |
288-357 | 1.91e-41 | |||||||||
Ubiquitin [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 444084 [Multi-domain] Cd Length: 213 Bit Score: 153.02 E-value: 1.91e-41
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| UBQ | smart00213 | Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ... |
288-357 | 3.70e-32 | |||||||||
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression Pssm-ID: 214563 [Multi-domain] Cd Length: 72 Bit Score: 120.83 E-value: 3.70e-32
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| ubiquitin | pfam00240 | Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ... |
289-357 | 7.69e-32 | |||||||||
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites. Pssm-ID: 459726 [Multi-domain] Cd Length: 72 Bit Score: 119.97 E-value: 7.69e-32
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| FtsJ | pfam01728 | FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ... |
2195-2366 | 1.33e-27 | |||||||||
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesized that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping. Pssm-ID: 426399 Cd Length: 179 Bit Score: 111.91 E-value: 1.33e-27
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| PTZ00044 | PTZ00044 | ubiquitin; Provisional |
288-362 | 7.24e-24 | |||||||||
ubiquitin; Provisional Pssm-ID: 185411 [Multi-domain] Cd Length: 76 Bit Score: 97.20 E-value: 7.24e-24
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| GFP | pfam01353 | Green fluorescent protein; |
46-241 | 2.05e-15 | |||||||||
Green fluorescent protein; Pssm-ID: 426217 Cd Length: 211 Bit Score: 77.61 E-value: 2.05e-15
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
1302-1448 | 2.40e-12 | |||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 68.67 E-value: 2.40e-12
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| rad23 | TIGR00601 | UV excision repair protein Rad23; All proteins in this family for which functions are known ... |
288-347 | 1.15e-09 | |||||||||
UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273167 [Multi-domain] Cd Length: 378 Bit Score: 63.38 E-value: 1.15e-09
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
1318-1441 | 1.55e-07 | |||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 56.96 E-value: 1.55e-07
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| flavi_E_stem | TIGR04240 | flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal ... |
373-407 | 3.86e-05 | |||||||||
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: 44.94 E-value: 3.86e-05
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
1494-1585 | 5.69e-04 | |||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 41.04 E-value: 5.69e-04
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| Cfa | COG2230 | Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport ... |
2199-2252 | 1.18e-03 | |||||||||
Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport and metabolism]; Pssm-ID: 441831 [Multi-domain] Cd Length: 158 Bit Score: 42.22 E-value: 1.18e-03
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| cas3_core | TIGR01587 | CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
1403-1527 | 7.14e-03 | |||||||||
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model. Pssm-ID: 273707 [Multi-domain] Cd Length: 359 Bit Score: 41.67 E-value: 7.14e-03
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| Name | Accession | Description | Interval | E-value | |||||||||
| Flavivirus_RdRp | cd23204 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within ... |
2461-3027 | 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: 1276.72 E-value: 0e+00
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| Flavi_NS5 | pfam00972 | Flavivirus RNA-directed RNA polymerase, fingers and palm domains; Flaviviruses produce a large ... |
2392-2844 | 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: 953.24 E-value: 0e+00
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| Flavi_NS1 | pfam00948 | Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the ... |
409-762 | 0e+00 | |||||||||
Flavivirus non-structural Protein NS1; The NS1 protein is well conserved amongst the flaviviruses. It contains 12 cysteines, and undergoes glycosylation in a similar manner to other NS proteins. Mutational analysis has strongly implied a role for NS1 in the early stages of RNA replication. Pssm-ID: 279316 Cd Length: 360 Bit Score: 740.32 E-value: 0e+00
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| Flavi_NS4B | pfam01349 | Flavivirus non-structural protein NS4B; Flaviviruses encode a single polyprotein. This is ... |
1891-2134 | 1.04e-143 | |||||||||
Flavivirus non-structural protein NS4B; Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4B protein is small and poorly conserved among the Flaviviruses. NS4B contains multiple hydrophobic potential membrane spanning regions. NS4B may form membrane components of the viral replication complex and could be involved in membrane localization of NS3 and pfam00972. Pssm-ID: 279665 Cd Length: 248 Bit Score: 447.55 E-value: 1.04e-143
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| capping_2-OMTase_Flaviviridae | cd20761 | Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific ... |
2147-2377 | 7.23e-114 | |||||||||
Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Flaviviridae viruses, comprise a family of ss(+)RNA viruses, cap their mRNAs. The 2'OMTase activity is located in the non-structural protein 5 (NS5). Pssm-ID: 467736 Cd Length: 225 Bit Score: 361.15 E-value: 7.23e-114
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| Flavi_NS5_thumb | pfam20483 | Flavivirus RNA-directed RNA polymerase, thumb domain; Flaviviruses produce a large polyprotein ... |
2848-3011 | 3.42e-96 | |||||||||
Flavivirus RNA-directed RNA polymerase, thumb domain; Flaviviruses produce a large polyprotein from the ssRNA genome, encoding structural proteins required for virus assembly and non-structural (NS1-5) proteins involved in replication of the viral genome. This polyprotein is cleaved by viral and cellular proteases to produce mature viral proteins. NS5 is the largest mature viral protein and contains a N-terminal methyltransferase (MTase) domain separated by a short linker from the C-terminal RNA-directed RNA polymerase domain (RdRp) that adopts a characteriztic right-handed fingers-palm-thumb fold and possesses a number of short regions and motifs homologous to other RNA-directed RNA polymerases. This entry represents the thumb domain of NS5 RdRp. NS5 binds to a the stem loop A (SLA) at the 5' extremity of Flavivirus genome and regulates translation of the viral genome. Pssm-ID: 466632 Cd Length: 164 Bit Score: 307.88 E-value: 3.42e-96
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| Flavi_NS2A | pfam01005 | Flavivirus non-structural protein NS2A; NS2A is a hydrophobic protein about 25 kDa is size. ... |
768-953 | 1.09e-92 | |||||||||
Flavivirus non-structural protein NS2A; NS2A is a hydrophobic protein about 25 kDa is size. NS2A is cleaved from NS1 by a membrane bound host protease. NS2A has been found to associate with the dsRNA within the vesicle packages. It has also been found that NS2A associates with the known replicase components and so NS2A has been postulated to be part of this replicase complex. Pssm-ID: 279359 Cd Length: 215 Bit Score: 299.83 E-value: 1.09e-92
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| Flavi_DEAD | pfam07652 | Flavivirus DEAD domain; |
1308-1453 | 3.95e-92 | |||||||||
Flavivirus DEAD domain; Pssm-ID: 400138 [Multi-domain] Cd Length: 146 Bit Score: 295.40 E-value: 3.95e-92
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| ps-ssRNAv_Flaviviridae_RdRp | cd23178 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ... |
2591-2909 | 3.48e-80 | |||||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Flaviviridae, order Amarillovirales. Flaviviridae, is a family of small, enveloped viruses with RNA genomes of 9-13 kb. Most infect mammals and birds. Many flaviviruses are host-specific and pathogenic, such as hepatitis C virus in the genus Hepacivirus. The majority of known members in the genus Flavivirus are arthropod borne, and many are important human and veterinary pathogens (e.g., yellow fever virus, dengue virus). Virions are typically spherical in shape with a lipid envelope. Virions have a single, small, basic capsid (C) protein and two (genera Flavivirus, Hepacivirus and Pegivirus) or three (genus Pestivirus) envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. Translational initiation of genomic RNA is cap dependent in the case of members of the genus Flavivirus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438028 Cd Length: 284 Bit Score: 267.08 E-value: 3.48e-80
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| Flavi_NS4A | pfam01350 | Flavivirus non-structural protein NS4A; Flaviviruses encode a single polyprotein. This is ... |
1745-1888 | 1.72e-78 | |||||||||
Flavivirus non-structural protein NS4A; Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4A protein is small and poorly conserved among the Flaviviruses. NS4A contains multiple hydrophobic potential membrane spanning regions. NS4A has only been found in cells infected by Kunjin virus. Pssm-ID: 279666 Cd Length: 144 Bit Score: 256.37 E-value: 1.72e-78
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| Flavi_NS2B | pfam01002 | Flavivirus non-structural protein NS2B; Flaviviruses encode a single polyprotein. This is ... |
987-1113 | 3.50e-68 | |||||||||
Flavivirus non-structural protein NS2B; Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. All, but two, are cleaved by the NS2B-NS3 protease complex. Pssm-ID: 279357 Cd Length: 127 Bit Score: 226.04 E-value: 3.50e-68
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| DEXHc_viral_Ns3 | cd17931 | DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ... |
1312-1459 | 5.35e-58 | |||||||||
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350689 [Multi-domain] Cd Length: 151 Bit Score: 197.77 E-value: 5.35e-58
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| Ubl_ubiquitin | cd01803 | ubiquitin-like (Ubl) domain found in ubiquitin; Ubiquitin is a protein modifier in eukaryotes ... |
288-362 | 1.74e-51 | |||||||||
ubiquitin-like (Ubl) domain found in ubiquitin; Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. Ubiquitin-like (Ubl) proteins have similar ubiquitin beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ubiquitin (Ub)and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Ub includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains. Pssm-ID: 340501 [Multi-domain] Cd Length: 76 Bit Score: 176.10 E-value: 1.74e-51
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| Peptidase_S7 | pfam00949 | Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that ... |
1138-1289 | 2.06e-48 | |||||||||
Peptidase S7, Flavivirus NS3 serine protease; The viral genome is a positive strand RNA that encodes a single polyprotein precursor. Processing of the polyprotein precursor into mature proteins is carried out by the host signal peptidase and by NS3 serine protease, which requires NS2B (pfam01002) as a cofactor. Pssm-ID: 395758 Cd Length: 129 Bit Score: 169.54 E-value: 2.06e-48
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| SF2_C_viral | cd18806 | C-terminal helicase domain of viral helicase; Viral helicases in this family here are ... |
1455-1597 | 1.49e-44 | |||||||||
C-terminal helicase domain of viral helicase; Viral helicases in this family here are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350193 [Multi-domain] Cd Length: 145 Bit Score: 158.96 E-value: 1.49e-44
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| capping_2-OMTase_viral | cd20754 | viral Cap-0 specific (nucleoside-2'-O-)-methyltransferase; Cap-0 specific (nucleoside-2'-O-) ... |
2199-2377 | 6.93e-42 | |||||||||
viral Cap-0 specific (nucleoside-2'-O-)-methyltransferase; Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Some dsDNA and dsRNA viruses, like the bluetongue virus (BTV), a member of the Reoviridae family, and Vaccinia virus, a member of the Poxviridae family, as well as some ss(+)RNA viruses, like Flaviviridae and Nidovirales, cap their mRNAs and encode their own 2'OMTase. In BTV, all four reactions are catalyzed by a single protein, VP4. In Vaccinia, the activity is located in the processing factor of the poly(A) polymerase, VP39. Pssm-ID: 467730 Cd Length: 179 Bit Score: 152.98 E-value: 6.93e-42
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| UBI4 | COG5272 | Ubiquitin [Posttranslational modification, protein turnover, chaperones]; |
288-357 | 1.91e-41 | |||||||||
Ubiquitin [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 444084 [Multi-domain] Cd Length: 213 Bit Score: 153.02 E-value: 1.91e-41
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| Ubl_NEDD8 | cd01806 | ubiquitin-like (Ubl) domain found in neural precursor cell expressed developmentally ... |
289-362 | 4.40e-33 | |||||||||
ubiquitin-like (Ubl) domain found in neural precursor cell expressed developmentally down-regulated protein 8 (NEDD8) and similar proteins; NEDD8, also termed Neddylin, or RELATED TO UBIQUITIN (RUB/Rub1p) in plant and yeast, is a ubiquitin-like protein that conjugates to nuclear proteins in a manner analogous to ubiquitination and sentrinization. It modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. NEDD8 deamidation and its inhibition of Cullin-RING ubiquitin ligases (CRLs) activity are responsible for Cycle-inhibiting factor (Cif)/Cif homolog in Burkholderia pseudomallei (CHBP)-induced cytopathic effect. NEDD8 contains a single conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. Polyubiquitination, signals for a diverse set of cellular events via different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the epsilon-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. Ubl NEDD8, contains many of the same lysines (K6, K11, K27, K33, K48) as Ub, where K27 has an role (other than conjugation) in the mechanism of protein neddylation. Pssm-ID: 340504 [Multi-domain] Cd Length: 74 Bit Score: 123.65 E-value: 4.40e-33
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| UBQ | smart00213 | Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ... |
288-357 | 3.70e-32 | |||||||||
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression Pssm-ID: 214563 [Multi-domain] Cd Length: 72 Bit Score: 120.83 E-value: 3.70e-32
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| ubiquitin | pfam00240 | Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ... |
289-357 | 7.69e-32 | |||||||||
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites. Pssm-ID: 459726 [Multi-domain] Cd Length: 72 Bit Score: 119.97 E-value: 7.69e-32
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| FtsJ | pfam01728 | FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ... |
2195-2366 | 1.33e-27 | |||||||||
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesized that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping. Pssm-ID: 426399 Cd Length: 179 Bit Score: 111.91 E-value: 1.33e-27
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| Ubl_ubiquitin_like | cd17039 | ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ... |
289-356 | 2.13e-27 | |||||||||
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like (Ubl) proteins have a similar ubiquitin (Ub) beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ub and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some Ubl domains have adaptor roles in Ub-signaling by mediating protein-protein interaction. Prokaryotic sulfur carrier proteins are Ub-related proteins that can be activated in an ATP-dependent manner. Polyubiquitination signals for a diverse set of cellular events via different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the epsilon-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. One of these seven lysine residues (K27, Ub numbering) is conserved in this Ubl_ubiquitin_like family. K27-linked Ub chains are versatile and can be recognized by several downstream receptor proteins. K27 has roles beyond chain linkage, such as in Ubl NEDD8 (which contains many of the same lysines (K6, K11, K27, K33, K48) as Ub) where K27 has a role (other than conjugation) in the mechanism of protein neddylation. Pssm-ID: 340559 [Multi-domain] Cd Length: 68 Bit Score: 107.30 E-value: 2.13e-27
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| PTZ00044 | PTZ00044 | ubiquitin; Provisional |
288-362 | 7.24e-24 | |||||||||
ubiquitin; Provisional Pssm-ID: 185411 [Multi-domain] Cd Length: 76 Bit Score: 97.20 E-value: 7.24e-24
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| Ubl_ZFAND4 | cd01802 | ubiquitin-like (Ubl) domain found in AN1-type zinc finger protein 4 (ZFAND4) and similar ... |
289-360 | 7.52e-23 | |||||||||
ubiquitin-like (Ubl) domain found in AN1-type zinc finger protein 4 (ZFAND4) and similar proteins; ZFAND4, also termed AN1-type zinc finger and ubiquitin domain-containing protein-like 1 (ANUBL1), may function as an oncogene that promotes proliferation and regulates relevant tumor suppressor genes in gastric cancer, suggesting a role in gastric cancer initiation and progression. ZFAND4contains an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions, as well as a C-terminal AN1-type zinc finger. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal Ubl domain of ZFAND4 does not undergo proteolytic processing. Pssm-ID: 340500 [Multi-domain] Cd Length: 74 Bit Score: 94.32 E-value: 7.52e-23
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| Ubl2_ISG15 | cd01810 | ubiquitin-like (Ubl) domain 2 found in interferon-stimulated gene 15 (ISG15) and similar ... |
288-360 | 7.27e-22 | |||||||||
ubiquitin-like (Ubl) domain 2 found in interferon-stimulated gene 15 (ISG15) and similar proteins; ISG15, also termed interferon-induced 15 kDa protein, or interferon-induced 17 kDa protein (IP17), or ubiquitin cross-reactive protein (UCRP), is an antiviral interferon-induced ubiquitin-like protein that upon viral infection it modifies cellular and viral proteins by mechanisms similar to ubiquitination. Although ISG15 has properties similar to those of other ubiquitin-like (Ubl) molecules, it is a unique member of the Ubl superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system. ISG15 contains two tandem Ubl domains with a beta-grasp Ubl fold. This family corresponds to the second Ubl domain. Pssm-ID: 340508 [Multi-domain] Cd Length: 74 Bit Score: 91.74 E-value: 7.27e-22
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| Ubl_AtUPL5_like | cd16107 | ubiquitin-like (Ubl) domain found in Arabidopsis thaliana ubiquitin-protein ligase 5 (AtUPL5) ... |
288-356 | 8.08e-22 | |||||||||
ubiquitin-like (Ubl) domain found in Arabidopsis thaliana ubiquitin-protein ligase 5 (AtUPL5) and similar proteins; Arabidopsis thaliana AtUPL5, also termed HECT-type E3 ubiquitin transferase UPL5, is an E3 ubiquitin-protein ligase that contains a ubiquitin-like domain (Ubl), a C-type lectin-binding domain, a leucine zipper and a HECT domain. HECT domain containing-ubiquitin-protein ligases have more than one member in different genomes, these proteins have been classified into four sub-families (UPL1/2, UPL3/4, UPL5 and UPL6/7). AtUPL5 fUPL5 regulates leaf senescence in Arabidopsis through degradation of the transcription factor WRKY53. Pssm-ID: 340524 Cd Length: 70 Bit Score: 91.41 E-value: 8.08e-22
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| Ubl_Rad23 | cd01805 | ubiquitin-like (Ubl) domain found in the Rad23 protein family; The Rad23 family includes the ... |
288-353 | 2.22e-20 | |||||||||
ubiquitin-like (Ubl) domain found in the Rad23 protein family; The Rad23 family includes the yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe), their mammalian orthologs HR23A and HR23B, and putative DNA repair proteins from plants. Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ubiquitinylated proteins and participate in translocating polyubiquitinated proteins to the proteasome. Rad23 proteins carry an ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. The Ubl domain is responsible for the binding to proteasome. The UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates, which suggests Rad23 proteins might be involved in certain pathways of Ub metabolism. Both the Ubl domain and the XPC-binding domain are necessary for efficient NER function of Rad23 proteins. Pssm-ID: 340503 [Multi-domain] Cd Length: 72 Bit Score: 87.23 E-value: 2.22e-20
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| Ubl2_FAT10 | cd17053 | ubiquitin-like (Ubl) domain 2 found in leukocyte antigen F (HLA-F) adjacent transcript 10 ... |
288-356 | 2.74e-20 | |||||||||
ubiquitin-like (Ubl) domain 2 found in leukocyte antigen F (HLA-F) adjacent transcript 10 (FAT10) and similar proteins; FAT10, also termed ubiquitin D (UBD), or diubiquitin, is a cytokine-inducible ubiquitin-like (Ubl) modifer that is highly expressed in the thymus, and targets substrates covalently for 26S proteasomal degradation. It is also associated with cancer development, antigen processing and antimicrobial defense, chromosomal stability and cell cycle regulation. FAT10 is presented on immune cells and under the inflammatory conditions, is synergistically induced by interferon gamma (IFNgamma) and tumor necrosis factor (TNFalpha) in the non-immune (liver parenchymal) cells. FAT10 contains two Ubl domains. The family corresponds to the second Ubl domain of FAT10. Some family members contain only one Ubl domain. Pssm-ID: 340573 Cd Length: 71 Bit Score: 87.02 E-value: 2.74e-20
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| Ubl_Dsk2p_like | cd16106 | ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein ... |
291-356 | 2.37e-19 | |||||||||
ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein Dsk2p and similar proteins; The family contains several fungal multiubiquitin receptors, including Saccharomyces cerevisiae Dsk2p and Schizosaccharomyces pombe Dph1p, both of which have been characterized as shuttle proteins transporting ubiquitinated substrates destined for degradation from the E3 ligase to the 26S proteasome. They interact with the proteasome through their N-terminal ubiquitin-like domain (Ubl) and with ubiquitin (Ub) through their C-terminal Ub-associated domain (UBA). S. cerevisiae Dsk2p is a nuclear-enriched protein that may involve in the ubiquitin-proteasome proteolytic pathway through interacting with K48-linked polyubiquitin and the proteasome. Moreover, it has been implicated in spindle pole duplication through assisting in Cdc31 assembly into the new spindle pole body (SPB). S. pombe Dph1p is an ubiquitin (Ub0 receptor working in concert with the class V myosin, Myo52, to target the degradation of the S. pombe CLIP-170 homolog, Tip1. It also can protect Ub chains against disassembly by deubiquitinating enzymes. Pssm-ID: 340523 [Multi-domain] Cd Length: 73 Bit Score: 84.23 E-value: 2.37e-19
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| Ubl_UBL4A_like | cd01807 | ubiquitin-like (Ubl) domain found in ubiquitin-like proteins UBL4A and similar proteins; UBL4A, ... |
288-356 | 2.79e-18 | |||||||||
ubiquitin-like (Ubl) domain found in ubiquitin-like proteins UBL4A and similar proteins; UBL4A, also termed GdX, is a ubiquitously expressed ubiquitin-like (Ubl) protein that forms a complex with partner proteins and participates in the protein processing through endoplasmic reticulum (ER), acting as a chaperone. As a key component of the BCL2-associated athanogene 6 (BAG6) chaperone complex, UBL4A plays a role in mediating DNA damage signaling and cell death. UBL4A also regulates insulin-induced Akt plasma membrane translocation through promotion of Arp2/3-dependent actin branching. Moreover, UBL4A specifically stabilizes the TC45/STAT3 association and promotes dephosphorylation of STAT3 to repress tumorigenesis. UBL4B is testis-specific, and encoded by an X-derived retrogene Ubl4b, which is specifically expressed in post-meiotic germ cells in mammals. As a germ cell-specific cytoplasmic protein, UBL4B is not present in somatic cells. Moreover, UBL4B is present in elongated spermatids, but not in spermatocytes and round spermatids, suggesting its function is restricted to late spermiogenesis. The function of UBL4A may be compensated by either UBL4B or other Ubl proteins in normal conditions. Both UBL4A and UBL4B contain a conserved Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. Pssm-ID: 340505 [Multi-domain] Cd Length: 72 Bit Score: 81.26 E-value: 2.79e-18
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| Ubiquitin_like_fold | cd00196 | Beta-grasp ubiquitin-like fold; Ubiquitin is a protein modifier that is involved in various ... |
289-356 | 2.89e-16 | |||||||||
Beta-grasp ubiquitin-like fold; Ubiquitin is a protein modifier that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. The ubiquitination process comprises a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. Ubiquitin-like proteins have similar ubiquitin beta-grasp fold and attach to other proteins in a ubiquitin-like manner but with biochemically distinct roles. Ubiquitin and ubiquitin-like proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some other ubiquitin-like domains have adaptor roles in ubiquitin-signaling by mediating protein-protein interaction. In addition to Ubiquitin-like (Ubl) domain, Ras-associating (RA) domain, F0/F1 sub-domain of FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, TGS (ThrRS, GTPase and SpoT) domain, Ras-binding domain (RBD), Ubiquitin regulatory domain X (UBX), Dublecortin-like domain, and RING finger- and WD40-associated ubiquitin-like (RAWUL) domain have beta-grasp ubiquitin-like folds, and are included in this superfamily. Pssm-ID: 340450 Cd Length: 68 Bit Score: 75.44 E-value: 2.89e-16
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| Rad60-SLD | pfam11976 | Ubiquitin-2 like Rad60 SUMO-like; The small ubiquitin-related modifier SUMO-1 is a Ub/Ubl ... |
288-357 | 1.27e-15 | |||||||||
Ubiquitin-2 like Rad60 SUMO-like; The small ubiquitin-related modifier SUMO-1 is a Ub/Ubl family member, and although SUMO-1 shares structural similarity to Ub, SUMO's cellular functions remain distinct insomuch as SUMO modification alters protein function through changes in activity, cellular localization, or by protecting substrates from ubiquitination. Rad60 family members contain functionally enigmatic, integral SUMO-like domains (SLDs). Despite their divergence from SUMO, each Rad60 SLD interacts with a subset of SUMO pathway enzymes: SLD2 specifically binds the SUMO E2 conjugating enzyme (Ubc9)), whereas SLD1 binds the SUMO E1 (Fub2, also called Uba2) activating and E3 (Pli1, also called Siz1 and Siz2) specificity enzymes. Structural analysis of PDB:2uyz reveals a mechanistic basis for the near-synonymous roles of Rad60 and SUMO in survival of genotoxic stress and suggest unprecedented DNA-damage-response functions for SLDs in regulating SUMOylation. The Rad60 branch of this family is also known as RENi (Rad60-Esc2-Nip45), and biologically it should be two distinct families SUMO and RENi (Rad60-Esc2-Nip45). Pssm-ID: 403255 [Multi-domain] Cd Length: 72 Bit Score: 73.75 E-value: 1.27e-15
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| GFP | pfam01353 | Green fluorescent protein; |
46-241 | 2.05e-15 | |||||||||
Green fluorescent protein; Pssm-ID: 426217 Cd Length: 211 Bit Score: 77.61 E-value: 2.05e-15
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| Ubl_FUBI | cd01793 | ubiquitin-like (Ubl) domain found in ubiquitin-like protein FUBI and similar proteins; FUBI is ... |
288-362 | 9.42e-15 | |||||||||
ubiquitin-like (Ubl) domain found in ubiquitin-like protein FUBI and similar proteins; FUBI is a pro-apoptotic regulatory gene FAU encoding ubiquitin-like protein with ribosomal protein S30 as a C-terminal extension. FUBI functions as a tumor suppressor protein that may be involved in the ATP-dependent proteolytic activity of ubiquitin. The N-terminal ubiquitin-like (Ubl) domain of FUBI has the beta-grasp Ubl fold, and it may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8. Pssm-ID: 340491 Cd Length: 74 Bit Score: 71.16 E-value: 9.42e-15
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| Ubl_parkin | cd01798 | ubiquitin-like (Ubl) domain found in parkin and similar proteins; Parkin, also termed ... |
289-356 | 2.36e-14 | |||||||||
ubiquitin-like (Ubl) domain found in parkin and similar proteins; Parkin, also termed Parkinson juvenile disease protein 2, is a RBR-type E3 ubiquitin-protein ligase that is associated with recessive early onset Parkinson's disease (PD), and exerts a protective effect against dopamine-induced alpha-synuclein-dependent cell toxicity. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Parkin functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, RHOT1/MIRO1, MFN1, MFN2, STUB1, SNCAIP, SEPT5, TOMM20, USP30, ZNF746 and AIMP2. It mediates monoubiquitination as well as Lys-6-, Lys-11-, Lys-48- and Lys-63-linked polyubiquitination of substrates depending on the context. Parkin may enhance cell viability and protects dopaminergic neurons from oxidative stress-mediated death by regulating mitochondrial function. It also limits the production of reactive oxygen species (ROS), and regulates cyclin-E during neuronal apoptosis. Moreover, parkin displays a ubiquitin ligase-independent function in transcriptional repression of p53. Parkin contains an N-terminal ubiquitin-like (Ubl) domain and a C-terminal RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain use an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. Pssm-ID: 340496 Cd Length: 74 Bit Score: 70.02 E-value: 2.36e-14
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| Ubl2_OASL | cd16103 | ubiquitin-like (Ubl) domain 2 found in 2'-5'-oligoadenylate synthase-like protein (OASL) and ... |
288-357 | 5.07e-14 | |||||||||
ubiquitin-like (Ubl) domain 2 found in 2'-5'-oligoadenylate synthase-like protein (OASL) and similar proteins; OASL, also termed 2'-5'-OAS-related protein (2'-5'-OAS-RP), or 59 kDa 2'-5'-oligoadenylate synthase-like protein, or thyroid receptor-interacting protein 14, or TR-interacting protein 14 (TRIP-14), or p59 OASL (p59OASL), is an interferon (IFN)-induced antiviral protein that plays an important role in the IFNs-mediated antiviral signaling pathway. It inhibits respiratory syncytial virus replication and is targeted by the viral nonstructural protein 1 (NS1). It also displays antiviral activity against encephalomyocarditis virus (EMCV) and hepatitis C virus (HCV) via an alternative antiviral pathway independent of RNase L. Moreover, OASL does not have 2'-5'-OAS activity, but can bind double-stranded RNA (dsRNA) to enhance RIG-I signaling. OASL belongs to the 2'-5' oligoadenylate synthase (OAS) family. While each member of this family has a conserved N-terminal OAS catalytic domain, only OASL has two tandem C-terminal ubiquitin-like (Ubl) repeats, which are required for its antiviral activity. This family corresponds to the second Ubl domain. Pssm-ID: 340520 [Multi-domain] Cd Length: 72 Bit Score: 69.24 E-value: 5.07e-14
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| Ubl_BAG6 | cd01809 | ubiquitin-like (Ubl) domain found in BCL2-associated athanogene 6 (BAG6) and similar proteins; ... |
288-356 | 5.56e-14 | |||||||||
ubiquitin-like (Ubl) domain found in BCL2-associated athanogene 6 (BAG6) and similar proteins; BAG6, also termed large proline-rich protein BAG6, or BAG family molecular chaperone regulator 6, or HLA-B-associated transcript 3 (Bat3), or protein Scythe, or protein G3, is a nucleo-cytoplasmic shuttling chaperone protein that is highly conserved in eukaryotes. It functions in two distinct biological pathways, ubiquitin-mediated protein degradation of defective polypeptides and tail-anchored transmembrane protein biogenesis in mammals. BAG6 is a component of the heterotrimeric BAG6 sortase complex composed of BAG6, transmembrane recognition complex 35 (TRC35) and ubiquitin-like protein 4A (UBL4A). The BAG6 complex together with the cochaperone small, glutamine-rich, tetratricopeptide repeat-containing, protein alpha (SGTA) plays a role in the biogenesis of tail-anchored membrane proteins and subsequently shown to regulate the ubiquitination and proteasomal degradation of mislocalized proteins. Moreover, BAG6 acts as an apoptotic regulator that binds reaper, a potent apoptotic inducer. BAG6/reaper is thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules. It is also likely a key regulator of the molecular chaperone Heat Shock Protein A2 (HSPA2) stability/function in human germ cells. Furthermore, aspartyl protease-mediated cleavage of BAG6 is necessary for autophagy and fungal resistance in plants. BAG6 contains a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, which provides a platform for discriminating substrates with shorter hydrophobicity stretches as a signal for defective proteins. Pssm-ID: 340507 [Multi-domain] Cd Length: 71 Bit Score: 68.91 E-value: 5.56e-14
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| Ubl_TAFs_like | cd17064 | ubiquitin-like (Ubl) domain found in plant TBP-associated factors (TAFs) and similar proteins; ... |
288-356 | 5.42e-13 | |||||||||
ubiquitin-like (Ubl) domain found in plant TBP-associated factors (TAFs) and similar proteins; TAFs, also termed transcription initiation factor TFIID subunits, or TAFII250 subunits, are components of the TFIID complex, a multisubunit protein complex involved in promoter recognition and essential for mediating regulation of RNA polymerase transcription. TAFs is the core scaffold of the TFIID complex, which is comprised of the TATA binding protein (TBP) and 12-15 TAFs. TAFs contain a ubiquitin-like (Ubl) domain and a Bromo domain. Pssm-ID: 340584 [Multi-domain] Cd Length: 72 Bit Score: 66.32 E-value: 5.42e-13
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| SF2-N | cd00046 | N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
1309-1440 | 2.39e-12 | |||||||||
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region. Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 67.04 E-value: 2.39e-12
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| DEXDc | smart00487 | DEAD-like helicases superfamily; |
1302-1448 | 2.40e-12 | |||||||||
DEAD-like helicases superfamily; Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 68.67 E-value: 2.40e-12
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| Ubl1_ISG15 | cd01792 | ubiquitin-like (Ubl) domain 1 found in interferon-stimulated gene 15 (ISG15) and similar ... |
288-357 | 1.01e-11 | |||||||||
ubiquitin-like (Ubl) domain 1 found in interferon-stimulated gene 15 (ISG15) and similar proteins; ISG15, also termed interferon-induced 15 kDa protein, or interferon-induced 17 kDa protein (IP17), or ubiquitin cross-reactive protein (UCRP), is an antiviral interferon-induced ubiquitin-like protein (Ubl) that upon viral infection, modifies cellular and viral proteins by mechanisms similar to ubiquitination. Although ISG15 has properties similar to those of other Ubl molecules, it is a unique member of the Ubl superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system. ISG15 contains two tandem Ubl domains with a beta-grasp Ubl fold. This family corresponds to the first Ubl domain. Pssm-ID: 340490 Cd Length: 75 Bit Score: 62.94 E-value: 1.01e-11
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| Ubl_UBTD | cd01794 | ubiquitin-like (Ubl) domain found in ubiquitin domain-containing proteins UBTD1, UBTD2, and ... |
295-349 | 1.26e-11 | |||||||||
ubiquitin-like (Ubl) domain found in ubiquitin domain-containing proteins UBTD1, UBTD2, and similar proteins; This family represents a group of ubiquitin-like (Ubl) domain-containing proteins evolutionarily conserved and found in metazoa, fungi, and plants. They may regulate the activity and/or specificity of E2 ubiquitin conjugating enzymes belonging to the UBE2D family. Members in this family contain an N-terminal ubiquitin binding domain (UBD) and a C-terminal Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. Pssm-ID: 340492 Cd Length: 69 Bit Score: 62.31 E-value: 1.26e-11
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| DEXHc_RHA-like | cd17917 | DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ... |
1312-1441 | 2.17e-11 | |||||||||
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 438707 [Multi-domain] Cd Length: 159 Bit Score: 64.40 E-value: 2.17e-11
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| Ubl1_FAT10 | cd17052 | ubiquitin-like (Ubl) domain 1 found in leukocyte antigen F (HLA-F) adjacent transcript 10 ... |
291-357 | 1.01e-10 | |||||||||
ubiquitin-like (Ubl) domain 1 found in leukocyte antigen F (HLA-F) adjacent transcript 10 (FAT10) and similar proteins; FAT10, also termed ubiquitin D (UBD), or diubiquitin, is a cytokine-inducible ubiquitin-like (Ubl) modifer that is highly expressed in the thymus, and targets substrates covalently for 26S proteasomal degradation. It is also associated with cancer development, antigen processing and antimicrobial defense, chromosomal stability and cell cycle regulation. FAT10 is presented on immune cells and under the inflammatory conditions, is synergistically induced by interferon gamma (IFNgamma) and tumor necrosis factor (TNFalpha) in the non-immune (liver parenchymal) cells. FAT10 contains two Ubl domains. The family corresponds to the first Ubl domain of FAT10. Some family members contain only one Ubl domain. Pssm-ID: 340572 [Multi-domain] Cd Length: 74 Bit Score: 59.98 E-value: 1.01e-10
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| Ubl_PLICs | cd01808 | ubiquitin-like (Ubl) domain found in eukaryotic protein linking integrin-associated protein ... |
289-356 | 1.73e-10 | |||||||||
ubiquitin-like (Ubl) domain found in eukaryotic protein linking integrin-associated protein (IAP, also known as CD47) with cytoskeleton (PLIC) proteins; The PLIC proteins (or ubiquilins) family contains human homologs of the yeast ubiquitin-like (Ubl) Dsk2 protein, PLIC-1 (also termed ubiquilin-1), PLIC-2 (also termed ubiquilin-2, or Chap1), PLIC-3 (also termed ubiquilin-3) and PLIC-4 (also termed ubiquilin-4, ataxin-1 interacting ubiquitin-like protein, A1Up, connexin43-interacting protein of 75 kDa, or CIP75), and mouse PLIC proteins. They are ubiquitin (Ub)-binding adaptor proteins involved in all protein degradation pathways through delivering ubiquitinated substrates to proteasomes. They also promote autophagy-dependent cell survival during nutrient starvation. PLIC-1 regulates the function of the thrombospondin receptor CD47 and G protein signaling. It plays a role in TLR4-mediated signaling through interacting with the Toll/interleukin-1 receptor (TIR) domain of TLR4. It also inhibits the TLR3-Trif antiviral pathway by reducing the abundance of Trif. Moreover, PLIC-1 binds to gamma-aminobutyric acid receptors (GABAARs) and modulates the Ub-dependent, proteasomal degradation of GABAARs. Furthermore, PLIC-1 acts as a molecular chaperone regulating amyloid precursor protein (APP) biosynthesis, trafficking, and degradation by stimulating K63-linked polyubiquitination of lysine 688 in the APP intracellular domain. In addition, PLIC-1 is involved in the protein aggregation-stress pathway via associating with the Ub-interacting motif (UIM) proteins ataxin 3, HSJ1a, and epidermal growth factor substrate 15 (EPS15). PLIC-2 is a protein that binds the ATPase domain of the HSP70-like Stch protein. It functions as a negative regulator of G protein-coupled receptor (GPCR) endocytosis. It also involved in amyotrophic lateral sclerosis (ALS)-related dementia. PLIC-3 is encoded by UbiquilinN3, a testis-specific gene. It shows high sequence similarity with the Xenopus protein XDRP1, a nuclear phosphoprotein that binds to the N-terminus of cyclin A and inhibits Ca2+-induced degradation of cyclin A, but not cyclin B. PLIC-4 is an ubiquitin-like (Ubl) nuclear protein that interacts with ataxin-1 and further links ataxin-1 with the chaperone and Ub-proteasome pathways. It also binds to the non-ubiquitinated gap junction protein connexin43 (Cx43) and regulates the turnover of Cx43 through the proteasomal pathway. PLIC proteins contain an N-terminal Ubl domain that is responsible for the binding of Ub-interacting motifs (UIMs) expressed by proteasomes and endocytic adaptors, and C-terminal Ub-associated (UBA) domain that interacts with Ub chains present on proteins destined for proteasomal degradation. In addition, mammalian PLIC2 proteins have an extra collagen-like motif region, which is absent in other PLIC proteins and the yeast Dsk2 protein. Pssm-ID: 340506 [Multi-domain] Cd Length: 73 Bit Score: 59.18 E-value: 1.73e-10
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| Ubl_Ddi1_like | cd01796 | ubiquitin-like (Ubl) domain found in the eukaryotic Ddi1 family; The eukaryotic Ddi1 family, ... |
288-348 | 2.10e-10 | |||||||||
ubiquitin-like (Ubl) domain found in the eukaryotic Ddi1 family; The eukaryotic Ddi1 family, including yeast aspartyl protease DNA-damage inducible 1 (Ddi1) and Ddi1-like proteins from vertebrates and other eukaryotes, has been characterized by containing an N-terminal ubiquitin-like (Ubl) domain and a conserved retroviral aspartyl-protease-like domain (RVP) that is important in cell-cycle control. Yeast Ddi1 and many family members also contain a C-terminal ubiquitin-association (UBA) domain, however, Ddi1-like proteins from all vertebrates lack the UBA domain. Ddi1, also termed v-SNARE-master 1 (Vsm1), is an ubiquitin receptor involved in the cell cycle and late secretory pathway in Saccharomyces cerevisiae. It functions as an UBA-Ubl shuttle protein that is required for the proteasome to enable ubiquitin-dependent degradation of its ligands. For instance, Ddi1 plays an essential role in the final stages of proteasomal degradation of Ho endonuclease and of its cognate FBP, Ufo1. Moreover, Ddi1 and its associated protein Rad23p play a cooperative role as negative regulators in yeast PHO pathway. This family also includes mammalian regulatory solute carrier protein family 1 member 1 (RSC1A1), also termed transporter regulator RS1 (RS1), which mediates transcriptional and post-transcriptional regulation of Na(+)-D-glucose cotransporter SGLT1. Ddi1-like proteins play a significant role in cell cycle control, growth control, and trafficking in yeast and may play a crucial role in embryogenesis in higher eukaryotes. Pssm-ID: 340494 [Multi-domain] Cd Length: 73 Bit Score: 59.11 E-value: 2.10e-10
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| Ubl_SF3a120 | cd01800 | ubiquitin-like (Ubl) domain found in splicing factor 3A 120kDa subunit (SF3a120) and similar ... |
294-357 | 3.14e-10 | |||||||||
ubiquitin-like (Ubl) domain found in splicing factor 3A 120kDa subunit (SF3a120) and similar proteins; Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit SF3a120, also termed splicing factor 3A subunit 1 (SF3A1), or spliceosome-associated protein 114 (SAP114), is the U2 snRNP-specific protein that is critical for spliceosome assembly and normal splicing events. During splicing, SF3a120, together with the U2 snRNP and other proteins, are recruited to the 3' splicing site to generate the splicing complex A after the recognition of the 3' splicing site. SF3a120 contains two N-terminal SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, as well as a C-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. Pssm-ID: 340498 Cd Length: 84 Bit Score: 58.74 E-value: 3.14e-10
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| Ubl_UHRF2 | cd17123 | ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing ... |
289-347 | 3.18e-10 | |||||||||
ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2, also termed Np95/ICBP90-like RING finger protein (NIRF), or Np95-likeRING finger protein, or nuclear protein 97, or nuclear zinc finger protein Np97, or RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2, was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131(ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (Ubl), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a set- and ring-associated (SRA) domain, and a C-terminal RING finger. Pssm-ID: 340643 Cd Length: 74 Bit Score: 58.34 E-value: 3.18e-10
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| Ubl_UHRF | cd01797 | ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing ... |
289-347 | 5.43e-10 | |||||||||
ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing proteins, UHRF1 and UHRF2, and similar proteins; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma, gastric cancer, esophageal squamous cell carcinoma, colorectal cancer, prostate cancer, and breast cancer. UHRF1 can acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumor suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (Ubl), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a set- and ring-associated (SRA) domain, and a C-terminal RING finger. Pssm-ID: 340495 Cd Length: 74 Bit Score: 57.76 E-value: 5.43e-10
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| rad23 | TIGR00601 | UV excision repair protein Rad23; All proteins in this family for which functions are known ... |
288-347 | 1.15e-09 | |||||||||
UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 273167 [Multi-domain] Cd Length: 378 Bit Score: 63.38 E-value: 1.15e-09
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| Ubl1_OASL | cd01811 | ubiquitin-like (Ubl) domain 1 found in 2'-5'-oligoadenylate synthase-like protein (OASL) and ... |
288-356 | 3.85e-09 | |||||||||
ubiquitin-like (Ubl) domain 1 found in 2'-5'-oligoadenylate synthase-like protein (OASL) and similar proteins; OASL, also termed 2'-5'-OAS-related protein (2'-5'-OAS-RP), or 59 kDa 2'-5'-oligoadenylate synthase-like protein, or thyroid receptor-interacting protein 14, or TR-interacting protein 14 (TRIP-14), or p59 OASL (p59OASL), is an interferon (IFN)-induced antiviral protein that plays an important role in the IFNs-mediated antiviral signaling pathway. It inhibits respiratory syncytial virus replication and is targeted by the viral nonstructural protein 1 (NS1). It also displays antiviral activity against encephalomyocarditis virus (EMCV) and hepatitis C virus (HCV) via an alternative antiviral pathway independent of RNase L. Moreover, OASL does not have 2'-5'-OAS activity, but can bind double-stranded RNA (dsRNA) to enhance RIG-I signaling. OASL belongs to the 2'-5' oligoadenylate synthase (OAS) family. While each member of this family has a conserved N-terminal OAS catalytic domain, only OASL has two tandem C-terminal ubiquitin-like (Ubl) repeats, which is required for its antiviral activity. This family corresponds to the first Ubl domain. Pssm-ID: 340509 Cd Length: 75 Bit Score: 55.40 E-value: 3.85e-09
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| Ubl_UBTD1 | cd17120 | ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein 1 (UBTD1); UBTD1 is ... |
291-357 | 1.98e-08 | |||||||||
ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein 1 (UBTD1); UBTD1 is the mammalian homolog of the mitochondrial Dc-UbP/UBTD2 protein, both of which contain an N-terminal ubiquitin binding domain (UBD) and a C-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. UBTD1 stably interacts with the UBE2D family of E2 ubiquitin conjugating enzymes. As a tumor suppressor, UBTD1 plays a pivotal role in in regulating cellular senescence that mediates p53 function. It is also involved in MDM2 ubiquitination and degradation. Pssm-ID: 340640 Cd Length: 69 Bit Score: 53.40 E-value: 1.98e-08
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| Ubl_HR23A | cd17126 | ubiquitin-like (Ubl) domain found in UV excision repair protein RAD23 homolog A (HR23A); HR23A, ... |
288-351 | 6.76e-08 | |||||||||
ubiquitin-like (Ubl) domain found in UV excision repair protein RAD23 homolog A (HR23A); HR23A, also termed RAD23A, is a DNA repair protein that binds to 19S subunit of the 26S proteasome and shuttles ubiquitinated proteins to the proteasome for degradation, which is required for efficient nucleotide excision repair (NER), a primary mechanism for removing UV-induced DNA lesions. HR23A also plays a critical role in the interaction of HIV-1 viral protein R (Vpr) with the proteasome, especially facilitating Vpr to promote protein poly-ubiquitination. HR23A contains an N-terminal ubiquitin-like (Ubl) domain that binds proteasomes and two C-terminal ubiquitin-associated (UBA) domains that bind ubiquitin or multi-ubiquitinated substrates. In addition, it has a XPC protein-binding domain that might be necessary for its efficient NER function. Pssm-ID: 340646 Cd Length: 76 Bit Score: 51.98 E-value: 6.76e-08
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| SSL2 | COG1061 | Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
1318-1441 | 1.55e-07 | |||||||||
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 56.96 E-value: 1.55e-07
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| Ubl_USP48 | cd01795 | ubiquitin-like (Ubl) domain found in ubiquitin-specific-processing protease 48 (USP48) and ... |
295-356 | 1.56e-07 | |||||||||
ubiquitin-like (Ubl) domain found in ubiquitin-specific-processing protease 48 (USP48) and similar proteins; USP48, also termed USP31, or deubiquitinating enzyme 48, or ubiquitin thioesterase 48, or ubiquitin carboxyl-terminal hydrolase 48, belongs to the ubiquitin specific protease (USP) family that is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin (Ub)and ubiquitin-like (Ubl) adducts. While the USP proteins have a conserved catalytic core domain, USP48 differs in its domain architecture. It contains an N-terminal USP domain, three DUSP (domain present in ubiquitin-specific protease) domains, and a C-terminal Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. USP48 is a deubiquitinating enzyme that interacts with TNF receptor-associated factor 2 (TRAF2) and has been implicated in activation of nuclear factor-kappaB (NF-kappaB). Moreover, as a nuclear deubiquitinase regulated by casein kinase 2 (CK2), USP48 controls the ubiquitin/proteasome-system (UPS)-dependent turnover of activated NF-kappaB/RelA in the nucleus together with the COP9 signalosome, suggesting a role of USP48 in a timely control of immune responses. Pssm-ID: 340493 [Multi-domain] Cd Length: 99 Bit Score: 51.52 E-value: 1.56e-07
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| DEXHc_RE | cd17926 | DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
1313-1441 | 1.72e-07 | |||||||||
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350684 [Multi-domain] Cd Length: 146 Bit Score: 53.08 E-value: 1.72e-07
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| Ubl_UHRF1 | cd17122 | ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing ... |
289-357 | 1.76e-07 | |||||||||
ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing protein 1(UHRF1); UHRF1, also termed inverted CCAAT box-binding protein of 90 kDa, or nuclear protein 95, or nuclear zinc finger protein Np95 (Np95), or RING finger protein 106, or transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1, is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma, gastric cancer, esophageal squamous cell carcinoma, colorectal cancer, prostate cancer, and breast cancer. UHRF1 can acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumor suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21.Moreover, UHRF1-dependent repression of factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination ofTIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (Ubl), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitination has an essential role in maintenance DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibits both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1. Pssm-ID: 340642 Cd Length: 74 Bit Score: 50.64 E-value: 1.76e-07
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| Ubl_HR23B | cd16126 | ubiquitin-like (Ubl) domain found in UV excision repair protein RAD23 homolog B (HR23B); HR23B, ... |
288-351 | 2.50e-07 | |||||||||
ubiquitin-like (Ubl) domain found in UV excision repair protein RAD23 homolog B (HR23B); HR23B, also termed xeroderma pigmentosum group C (XPC) repair-complementing complex 58 kDa protein (p58), is tightly complexed with XPC protein to form the XPC-HR23B complex. Although it displays a high affinity for both single- and double-stranded DNA, the XPC-HR23B complex functions as a global genome repair (GGR)-specific repair factor that is specifically involved in global genome but not transcription-coupled nucleotide excision repair (NER). HR23B also interacts specifically with S5a subunit of the human 26S proteasome, and plays an important role in shuttling ubiquitinated cargo proteins to the proteasome. HR23B contains an N-terminal ubiquitin-like (Ubl) domain that binds proteasomes and two C-terminal ubiquitin-associated (UBA) domains that bind ubiquitin or multi-ubiquitinated substrates. In addition, it has a XPC protein-binding domain that might be necessary for its efficient NER function. Pssm-ID: 340543 Cd Length: 78 Bit Score: 50.49 E-value: 2.50e-07
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| Ubl1_FAF1 | cd17129 | ubiquitin-like (Ubl) domain 1 found in FAS-associated factor 1 (FAF1) and similar proteins; ... |
297-356 | 4.57e-07 | |||||||||
ubiquitin-like (Ubl) domain 1 found in FAS-associated factor 1 (FAF1) and similar proteins; FAF1, also termed UBX domain-containing protein 12 (UBXD12), or UBX domain-containing protein 3A (UBXN3A), belongs to the UBXD family of proteins that contains the ubiquitin (Ub) regulatory domain X (UBX) with a beta-grasp ubiquitin-like (Ubl) fold, but without the C-terminal double glycine motif. The UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. In addition, FAF1 contains two tandem Ubl domains, which show high structural similarity with the UBX domain. FAF1 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. The FAF1-p97 complex inhibits the proteasomal protein degradation in which p97 acts as a co-chaperone. Moreover, FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF1 is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kappaB (NF-kappaB) by interfering with the nuclear translocation of the p65 subunit. Although the precise role of FAF1 in the ubiquitination pathway remains unclear, FAF1 interacts with valosin-containing protein (VCP), which is involved in the ubiquitin-proteosome pathway. The family corresponds to the first Ubl domain. Pssm-ID: 340649 Cd Length: 73 Bit Score: 49.57 E-value: 4.57e-07
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| Ubl_midnolin | cd01804 | ubiquitin-like (Ubl) domain found in midnolin and similar proteins; Midnolin, also termed ... |
288-356 | 5.32e-07 | |||||||||
ubiquitin-like (Ubl) domain found in midnolin and similar proteins; Midnolin, also termed midbrain nucleolar protein, is a nucleolar protein that may be involved in regulation of genes related to neurogenesis in the nucleolus. It is strongly expressed at the mesencephalon (midbrain) of the embryo in day 12.5 (E12.5) mice and its expression is developmentally regulated. Midnolin plays a role in cellular signaling of adult tissues and regulates glucokinase enzyme activity in pancreatic beta cells. It can also control development via regulation of mRNA transport in cells. Midnolin contains an N-terminal conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. Pssm-ID: 340502 Cd Length: 70 Bit Score: 49.19 E-value: 5.32e-07
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| HepA | COG0553 | Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
1318-1441 | 9.32e-07 | |||||||||
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair]; Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 54.85 E-value: 9.32e-07
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| Ubl_NUB1 | cd17062 | ubiquitin-like (Ubl) domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins; NUB1, ... |
299-359 | 1.19e-06 | |||||||||
ubiquitin-like (Ubl) domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins; NUB1, also termed negative regulator of ubiquitin-like proteins 1, or renal carcinoma antigen NY-REN-18, or protein BS4, is a NEDD8-interacting protein that can be induced by interferon. It functions as a strong post-transcriptional down-regulator of the NEDD8 expression and plays critical roles in regulating many biological events, such as cell growth, NF-kappaB signaling, and biological responses to hypoxia. NUB1 can also interact with aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1), which may function in the regulation of cell cycle progression. NUB1 contains a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, three ubiquitin-associated domains (UBA), a bipartite nuclear localization signal (NLS) and a PEST motif. Pssm-ID: 340582 Cd Length: 78 Bit Score: 48.29 E-value: 1.19e-06
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| Ubl_HOIL1 | cd01799 | ubiquitin-like (Ubl) domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and ... |
298-356 | 1.29e-06 | |||||||||
ubiquitin-like (Ubl) domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins; HOIL-1, also termed RBCK1, or HOIL-1L, or RanBP-type and C3HC4-type zinc finger-containing protein 1, HBV-associated factor 4, or Hepatitis B virus X-associated protein 4, or RING finger protein 54 (RNF54), or ubiquitin-conjugating enzyme 7-interacting protein 3, or UbcM4-interacting protein 28 (UIP28), together with E3 ubiquitin-protein ligase RNF31 (also known as HOIP) and SHANK-associated RH domain interacting protein (SHARPIN), forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis through conjugation of linear polyubiquitin chains to NF-kappaB essential modulator (also known as NEMO or IKBKG). HOIL-1 plays a crucial role in TNF-alpha-mediated NF-kappaB activation. It also functions as an ubiquitin-protein ligase E3 that interacts with not only PKCbeta but also PKCzeta. It can recognize heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. HOIL-1 contains an N-terminal ubiqutin-like (UBL) domain and an Npl4 zinc-finger (NZF) domain, which regulate the interaction with the LUBAC subunit RNF31 and ubiquitin, respectively. The NZF domain belongs to RanBP2-type zinc finger (zf-RanBP2) domain superfamily. In addition, HOIL-1 has a RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain use an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. Pssm-ID: 340497 Cd Length: 81 Bit Score: 48.36 E-value: 1.29e-06
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| Ubl_UBTD2 | cd17121 | ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein 2 (UBTD2); UBTD2, ... |
288-357 | 1.61e-06 | |||||||||
ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein 2 (UBTD2); UBTD2, also termed dendritic cell-derived ubiquitin-like protein (DC-UbP), or ubiquitin-like protein SB72, is a potential ubiquitin shuttle protein firstly identified in dendritic cells and implicated in apoptosis. It binds proteins involved in the ubiquitination pathway and may play an important role in regulating protein ubiquitination and delivery of ubiquitinated substrates in eukaryotic cells. UBTD2 is expressed in tumor cells but not in normal human adult tissue suggesting a role in tumorogenesis. It can potentially regulate the stability of proteins involved in various physiological processes relevant to many disease phenotypes, such as ageing and cancer. UBTD2 reconciles protein ubiquitination and deubiquitination via linking UbE1 and USP5 enzymes. Pssm-ID: 340641 Cd Length: 75 Bit Score: 48.05 E-value: 1.61e-06
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| Ubl_HERP | cd01790 | ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress ... |
300-356 | 4.32e-06 | |||||||||
ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress protein HERP; HERP is an endoplasmic reticulum (ER) integral membrane protein containing an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. The Ubl domain is required for the degradation of HERP itself as well as for HERP-mediated anti-apoptotic effects. HERP is induced by the ER stress response pathway and is involved in improving the balance of folding capacity and protein loads in the ER. There are two types of HERP, HERP1 and HERP2, which are encoded by the HERPUD1 and HERPUD2 genes, respectively. Pssm-ID: 340488 Cd Length: 78 Bit Score: 46.86 E-value: 4.32e-06
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| RNA_dep_RNAP | cd01699 | RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ... |
2572-2881 | 4.54e-06 | |||||||||
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage. RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D structure of the catalytic center of a wide range of RdRps, including those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing a number of conserved amino acid residues. This subfamily represents the RNA-dependent RNA polymerases from all positive-strand RNA eukaryotic viruses with no DNA stage. Pssm-ID: 238843 [Multi-domain] Cd Length: 278 Bit Score: 51.13 E-value: 4.54e-06
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| Ubl_TMUB1_like | cd17057 | ubiquitin-like (Ubl) domain found in transmembrane and ubiquitin-like domain-containing ... |
302-357 | 3.10e-05 | |||||||||
ubiquitin-like (Ubl) domain found in transmembrane and ubiquitin-like domain-containing proteins TMUB1, TMUB2, and similar proteins; TMUB1, also termed dendritic cell-derived ubiquitin-like protein (DULP), or hepatocyte odd protein shuttling protein, or ubiquitin-like protein SB144, or HOPS, is highly expressed in the nervous system. It is involved in the termination of liver regeneration and plays a negative role in interleukin-6-induced hepatocyte proliferation. The overexpression of Tmub1 has been shown to play a role in the inhibition of cell proliferation. TMUB1 has been implicated in the regulation of locomotor activity and wakefulness in mice, perhaps acting through its interaction with CAMLG. It also facilitates the recycling of AMPA receptors into synaptic membrane in cultured primary neurons. TMUB1 contains transmembrane domains and a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. TMUB2 is an uncharacterized transmembrane domain and Ubl domain-containing protein that shows high sequence similarity to TMUB1. Pssm-ID: 340577 Cd Length: 74 Bit Score: 44.52 E-value: 3.10e-05
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| flavi_E_stem | TIGR04240 | flavivirus envelope glycoprotein E, stem/anchor domain; This model describes the C-terminal ... |
373-407 | 3.86e-05 | |||||||||
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: 44.94 E-value: 3.86e-05
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| Ubl_MUBs_plant | cd01814 | ubiquitin-like (Ubl) domain found in plant membrane-anchored ubiquitin-fold proteins (MUBs); ... |
304-357 | 8.55e-05 | |||||||||
ubiquitin-like (Ubl) domain found in plant membrane-anchored ubiquitin-fold proteins (MUBs); The plant MUBs belong to a family of ubiquitin-fold proteins that are plasma membrane-anchored by prenylation. They may serve as docking site to facilitate the association of specific E2s to the plasma membrane. MUBs contain a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. Pssm-ID: 340512 Cd Length: 89 Bit Score: 43.52 E-value: 8.55e-05
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| Ubl1_ANKUB1 | cd17050 | ubiquitin-like (Ubl) domain 1 found in Ankyrin repeat and ubiquitin domain-containing 1 ... |
289-357 | 1.02e-04 | |||||||||
ubiquitin-like (Ubl) domain 1 found in Ankyrin repeat and ubiquitin domain-containing 1 (ANKUB1) and similar proteins; ANKUB1 is an uncharacterized protein with two tandem ubiquitin-like (Ubl) domains located at the N-terminal of Ankyrin repeats (ANK). The Ubl domain may have an adaptor role in ubiquitin (Ub)-signaling by mediating protein-protein interaction. Ubl proteins have a beta-grasp Ubl fold and attach to other proteins in a Ubl manner with biochemically distinct roles. The ankyrin repeats have been identified in numerous proteins with diverse functions. The family corresponds to the first Ubl domain. Pssm-ID: 340570 Cd Length: 79 Bit Score: 43.06 E-value: 1.02e-04
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| Ubl_UBLCP1 | cd01813 | ubiquitin-like (Ubl) domain found in ubiquitin-like domain-containing CTD phosphatase 1 ... |
296-348 | 1.05e-04 | |||||||||
ubiquitin-like (Ubl) domain found in ubiquitin-like domain-containing CTD phosphatase 1 (UBLCP1) and similar proteins; UBLCP1 is a 26S proteasome phosphatase that regulates nuclear proteasome activity. It is localized in the nucleus and it contains conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, which directly interacts with the proteasome. Knockdown of UBLCP1 in cells promotes 26S proteasome assembly and selectively enhances nuclear proteasome activity. UBLCP1 may also play a role in the regulation of phosphorylation state of RNA polymerase II C-terminal domain, a key event during mRNA metabolism. Pssm-ID: 340511 Cd Length: 74 Bit Score: 42.94 E-value: 1.05e-04
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| Ubl_TECR_like | cd01801 | ubiquitin-like (Ubl) domain found in trans-2,3-enoyl-CoA reductase (TECR) and similar proteins; ... |
288-353 | 1.44e-04 | |||||||||
ubiquitin-like (Ubl) domain found in trans-2,3-enoyl-CoA reductase (TECR) and similar proteins; This family includes TECR and many TECR-like proteins, such as TECRL. TECR, also termed very-long-chain enoyl-CoA reductase, or synaptic glycoprotein SC2, or TER, or GPSN2, is a synaptic glycoprotein that catalyzes the fourth reaction in the synthesis of very long-chain fatty acids (VLCFA) which is the reduction step of the microsomal fatty acyl-elongation process. Diseases involving perturbations to normal synthesis and degradation of VLCFA (e.g. adrenoleukodystrophy and Zellweger syndrome) have significant neurological consequences. The mammalian TECR P182L mutation causes nonsyndromic mental retardation. Deletion of the yeast TECR (TSC13) homolog is lethal. TECR contains an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions, as well as a C-terminal catalytic domain. TECRL, also termed steroid 5-alpha-reductase 2-like 2 protein (SRD5A2L2), is associated with life-threatening inherited arrhythmias displaying features of both long QT syndrome (LQTS) and catecholaminergic polymorphic ventricular tachycardia (CPVT). Both TECR and TECRL contain an N-terminal Ubl domain with a beta-grasp Ubl fold, and a C-terminal catalytic domain. Pssm-ID: 340499 [Multi-domain] Cd Length: 77 Bit Score: 42.66 E-value: 1.44e-04
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| Ubiquitin_2 | pfam14560 | Ubiquitin-like domain; This entry contains ubiquitin-like domains. |
305-356 | 2.28e-04 | |||||||||
Ubiquitin-like domain; This entry contains ubiquitin-like domains. Pssm-ID: 405277 Cd Length: 83 Bit Score: 42.13 E-value: 2.28e-04
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| DEXHc_Snf | cd17919 | DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
1318-1441 | 2.91e-04 | |||||||||
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350677 [Multi-domain] Cd Length: 182 Bit Score: 44.48 E-value: 2.91e-04
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| Ubl_UBFD1 | cd17047 | ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein UBFD1 and similar ... |
297-356 | 3.70e-04 | |||||||||
ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein UBFD1 and similar proteins; UBFD1, also termed ubiquitin-binding protein homolog (UBPH), is a polyubiquitin binding protein containing a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. It may play a role as nuclear factor-kappaB (NF-kappaB) regulator. Pssm-ID: 340567 Cd Length: 70 Bit Score: 41.08 E-value: 3.70e-04
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| Ubl_TBCB | cd01789 | ubiquitin-like (Ubl) domain found in tubulin-folding cofactor B (TBCB) and similar proteins; ... |
305-356 | 5.45e-04 | |||||||||
ubiquitin-like (Ubl) domain found in tubulin-folding cofactor B (TBCB) and similar proteins; TBCB, also termed cytoskeleton-associated protein 1, or cytoskeleton-associated protein CKAPI, or tubulin-specific chaperone B, is one of protein cofactors A through E that is required for the folding of tubulins prior to their incorporation into microtubules and heterodimer assembly. TBCB comprises an N-terminal ubiquitin-like (Ubl) domain and a C-terminal cytoskeleton-associated protein with glycine-rich segment (CAP-Gly) domain. The Ubl domain of TBCB is essential for proper folding and assembly of tubulin alpha. It has a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. TBC-A through E are necessary for the biogenesis of microtubules and for cell viability. Pssm-ID: 340487 Cd Length: 80 Bit Score: 41.02 E-value: 5.45e-04
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| HELICc | smart00490 | helicase superfamily c-terminal domain; |
1494-1585 | 5.69e-04 | |||||||||
helicase superfamily c-terminal domain; Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 41.04 E-value: 5.69e-04
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| Cas3_I | cd09639 | CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
1403-1608 | 6.53e-04 | |||||||||
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I Pssm-ID: 187770 [Multi-domain] Cd Length: 353 Bit Score: 44.73 E-value: 6.53e-04
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| DEAD | pfam00270 | DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
1319-1448 | 6.98e-04 | |||||||||
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 43.00 E-value: 6.98e-04
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| Ubl_BAG1 | cd01812 | ubiquitin-like (Ubl) domain found in BAG family molecular chaperone regulator 1 (BAG1) and ... |
299-356 | 1.06e-03 | |||||||||
ubiquitin-like (Ubl) domain found in BAG family molecular chaperone regulator 1 (BAG1) and similar proteins; BAG1, also termed Bcl-2-associated athanogene 1, or HAP, is a multifunctional protein involved in a variety of cellular functions such as apoptosis, transcription, and proliferative pathways, as well as in cell signaling and differentiation. It delivers chaperone-recognized unfolded substrates to the proteasome for degradation. BAG1 functions as a co-chaperone for Hsp70/Hsc70 to increase Hsp70 foldase activity. It also suppresses apoptosis and enhances neuronal differentiation. As an anti-apoptotic factor, BAG1 interacts with tau and regulates its proteasomal degradation. It also binds to BCR-ABL with a high affinity, and directly routes immature BCR-ABL for proteasomal degradation. It acts as a potential therapeutic target in Parkinson's disease. It also modulates huntingtin toxicity, aggregation, degradation, and subcellular distribution, suggesting a role in Huntington's disease. There are at least four isoforms of Bag1 protein that are formed by alternative initiation of translation within a common mRNA. BAG1 contains an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, and a C-terminal BAG domain. Pssm-ID: 340510 [Multi-domain] Cd Length: 77 Bit Score: 39.95 E-value: 1.06e-03
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| Cfa | COG2230 | Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport ... |
2199-2252 | 1.18e-03 | |||||||||
Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport and metabolism]; Pssm-ID: 441831 [Multi-domain] Cd Length: 158 Bit Score: 42.22 E-value: 1.18e-03
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| Ubl_ElonginB | cd01788 | ubiquitin-like (Ubl) domain found in transcription elongation factor B (Elongin B) and similar ... |
297-347 | 1.46e-03 | |||||||||
ubiquitin-like (Ubl) domain found in transcription elongation factor B (Elongin B) and similar proteins; Elongin B, also termed Elongin 18 kDa subunit, or EloB, or RNA polymerase II transcription factor SIII subunit B (SIII p18), is part of an E3 ubiquitin ligase complex called VEC that activates ubiquitination by the E2 ubiquitin-conjugating enzyme Ubc5. VEC is composed of von Hippel-Lindau tumor suppressor protein (pVHL), elongin C, cullin 2, NEDD8, and Rbx1. ElonginB binds elonginC to form the elonginBC complex which is a positive regulator of RNA polymerase II elongation factor Elongin A. The BC complex then binds VHL (von Hippel-Lindau) tumor suppressor protein to form a VCB ternary complex. Elongin B has a ubiquitin-like (Ubl) domain. Ub has a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. Ub is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Pssm-ID: 340486 Cd Length: 101 Bit Score: 40.36 E-value: 1.46e-03
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| Ubl_TBK1_like | cd12219 | ubiquitin-like (Ubl) domain found in non-canonical Inhibitor of kappa B kinases IKKepsilon and ... |
293-351 | 1.54e-03 | |||||||||
ubiquitin-like (Ubl) domain found in non-canonical Inhibitor of kappa B kinases IKKepsilon and TBK1, and similar proteins; IKKepsilon and TBK1 (TRAF family member-associated NF-kappaB activator-binding kinase 1) are non-canonical members of IKK family. They have been characterized as activators of nuclear factor-kappaB (NF-kappaB), but they are not essential for NF-kappaB activation. They play critical roles in antiviral response via phosphorylation and activation of transcription factors IRF3, IRF7, STAT1 and STAT3. They are also involved in the survival, tumorigenesis and development of various cancers. Both IKKepsilon and TBK1 contain an N-terminal protein kinase domain followed a ubiquitin-like (Ubl) domain. The Ubl domain acts as a protein-protein interaction domain, and has been implicated in regulating kinase activity, which modulates interactions in the interferon pathway. Pssm-ID: 340518 Cd Length: 77 Bit Score: 39.52 E-value: 1.54e-03
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| SF2_C | cd18785 | C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
1479-1596 | 1.55e-03 | |||||||||
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. Pssm-ID: 350172 [Multi-domain] Cd Length: 77 Bit Score: 39.61 E-value: 1.55e-03
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| Ubl_AtNPL4_like | cd17055 | ubiquitin-like (Ubl) domain found in Arabidopsis thaliana NPL4-like proteins NPL4-1, NPL4-2, ... |
301-355 | 3.24e-03 | |||||||||
ubiquitin-like (Ubl) domain found in Arabidopsis thaliana NPL4-like proteins NPL4-1, NPL4-2, and similar proteins; The family includes a group of uncharacterized plant ubiquitin-like (Ubl) domain-containing proteins, including Arabidopsis thaliana NPL4-like protein 1 and NPL4-like protein 2. Pssm-ID: 340575 Cd Length: 73 Bit Score: 38.74 E-value: 3.24e-03
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| DEXHc_HrpB | cd17990 | DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ... |
1299-1440 | 6.57e-03 | |||||||||
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA two-partner secretion (TPS) system, a secretion pathway important to the secretion of large virulence-associated proteins. HrpB belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 438711 [Multi-domain] Cd Length: 174 Bit Score: 40.01 E-value: 6.57e-03
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| cas3_core | TIGR01587 | CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
1403-1527 | 7.14e-03 | |||||||||
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model. Pssm-ID: 273707 [Multi-domain] Cd Length: 359 Bit Score: 41.67 E-value: 7.14e-03
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| MFS_1 | pfam07690 | Major Facilitator Superfamily; |
755-1026 | 7.52e-03 | |||||||||
Major Facilitator Superfamily; Pssm-ID: 429598 [Multi-domain] Cd Length: 344 Bit Score: 41.25 E-value: 7.52e-03
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