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gag-pol fusion polyprotein precursor, partial [HIV-1 CRF26_A5U:08GQ323]
pol protein( domain architecture ID 10442199)
HIV-1 pol protein containing the pepsin-like aspartate protease, reverse transcriptase (RT), RT thumb, and RT connection domains; RT catalyzes the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes
List of domain hits
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Name | Accession | Description | Interval | E-value | ||||
RT_Rtv | cd01645 | RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ... |
172-388 | 9.20e-118 | ||||
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs. : Pssm-ID: 238823 [Multi-domain] Cd Length: 213 Bit Score: 348.12 E-value: 9.20e-118
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RVT_connect | pfam06815 | Reverse transcriptase connection domain; This domain is known as the connection domain. This ... |
472-573 | 1.16e-35 | ||||
Reverse transcriptase connection domain; This domain is known as the connection domain. This domain lies between the thumb and palm domains. : Pssm-ID: 462013 Cd Length: 102 Bit Score: 129.49 E-value: 1.16e-35
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RVP | pfam00077 | Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ... |
60-153 | 6.57e-31 | ||||
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026). : Pssm-ID: 425454 Cd Length: 101 Bit Score: 115.93 E-value: 6.57e-31
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RVT_thumb | pfam06817 | Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ... |
395-458 | 5.33e-21 | ||||
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle. : Pssm-ID: 429135 Cd Length: 66 Bit Score: 86.61 E-value: 5.33e-21
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Name | Accession | Description | Interval | E-value | ||||
RT_Rtv | cd01645 | RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ... |
172-388 | 9.20e-118 | ||||
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs. Pssm-ID: 238823 [Multi-domain] Cd Length: 213 Bit Score: 348.12 E-value: 9.20e-118
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RVT_1 | pfam00078 | Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ... |
217-388 | 1.10e-44 | ||||
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. Pssm-ID: 395031 [Multi-domain] Cd Length: 189 Bit Score: 157.08 E-value: 1.10e-44
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RVT_connect | pfam06815 | Reverse transcriptase connection domain; This domain is known as the connection domain. This ... |
472-573 | 1.16e-35 | ||||
Reverse transcriptase connection domain; This domain is known as the connection domain. This domain lies between the thumb and palm domains. Pssm-ID: 462013 Cd Length: 102 Bit Score: 129.49 E-value: 1.16e-35
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RVP | pfam00077 | Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ... |
60-153 | 6.57e-31 | ||||
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026). Pssm-ID: 425454 Cd Length: 101 Bit Score: 115.93 E-value: 6.57e-31
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HIV_retropepsin_like | cd05482 | Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ... |
66-146 | 3.19e-21 | ||||
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A. Pssm-ID: 133149 Cd Length: 87 Bit Score: 88.09 E-value: 3.19e-21
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RVT_thumb | pfam06817 | Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ... |
395-458 | 5.33e-21 | ||||
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle. Pssm-ID: 429135 Cd Length: 66 Bit Score: 86.61 E-value: 5.33e-21
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Name | Accession | Description | Interval | E-value | ||||
RT_Rtv | cd01645 | RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ... |
172-388 | 9.20e-118 | ||||
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs. Pssm-ID: 238823 [Multi-domain] Cd Length: 213 Bit Score: 348.12 E-value: 9.20e-118
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RVT_1 | pfam00078 | Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ... |
217-388 | 1.10e-44 | ||||
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. Pssm-ID: 395031 [Multi-domain] Cd Length: 189 Bit Score: 157.08 E-value: 1.10e-44
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RVT_connect | pfam06815 | Reverse transcriptase connection domain; This domain is known as the connection domain. This ... |
472-573 | 1.16e-35 | ||||
Reverse transcriptase connection domain; This domain is known as the connection domain. This domain lies between the thumb and palm domains. Pssm-ID: 462013 Cd Length: 102 Bit Score: 129.49 E-value: 1.16e-35
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RT_ZFREV_like | cd03715 | RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ... |
173-376 | 1.33e-32 | ||||
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses. Pssm-ID: 239685 [Multi-domain] Cd Length: 210 Bit Score: 124.38 E-value: 1.33e-32
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RVP | pfam00077 | Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ... |
60-153 | 6.57e-31 | ||||
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026). Pssm-ID: 425454 Cd Length: 101 Bit Score: 115.93 E-value: 6.57e-31
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RT_LTR | cd01647 | RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ... |
209-365 | 6.41e-27 | ||||
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses. Pssm-ID: 238825 Cd Length: 177 Bit Score: 107.30 E-value: 6.41e-27
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HIV_retropepsin_like | cd05482 | Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ... |
66-146 | 3.19e-21 | ||||
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A. Pssm-ID: 133149 Cd Length: 87 Bit Score: 88.09 E-value: 3.19e-21
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RVT_thumb | pfam06817 | Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ... |
395-458 | 5.33e-21 | ||||
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed of a four helix bundle. Pssm-ID: 429135 Cd Length: 66 Bit Score: 86.61 E-value: 5.33e-21
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RT_like | cd00304 | RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ... |
303-388 | 2.22e-17 | ||||
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Pssm-ID: 238185 [Multi-domain] Cd Length: 98 Bit Score: 77.39 E-value: 2.22e-17
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RT_DIRS1 | cd03714 | RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ... |
263-379 | 2.98e-08 | ||||
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase. Pssm-ID: 239684 [Multi-domain] Cd Length: 119 Bit Score: 52.35 E-value: 2.98e-08
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RP_RTVL_H_like | cd06095 | Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ... |
66-146 | 4.90e-05 | ||||
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family includes aspartate proteases from retroelements with LTR (long terminal repeats) including the RTVL_H family of human endogenous retrovirus-like elements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A. Pssm-ID: 133159 Cd Length: 86 Bit Score: 41.93 E-value: 4.90e-05
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gag-asp_proteas | pfam13975 | gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ... |
66-147 | 7.37e-05 | ||||
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins. Pssm-ID: 464060 Cd Length: 92 Bit Score: 41.79 E-value: 7.37e-05
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Asp_protease_2 | pfam13650 | Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ... |
66-143 | 3.61e-04 | ||||
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix. Pssm-ID: 433378 Cd Length: 90 Bit Score: 39.58 E-value: 3.61e-04
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RT_pepA17 | cd01644 | RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ... |
264-346 | 8.56e-03 | ||||
RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements. Pssm-ID: 238822 Cd Length: 213 Bit Score: 38.05 E-value: 8.56e-03
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Blast search parameters | ||||
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