pol protein, partial [Human immunodeficiency virus 2]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||
| ps-ssRNAv_RdRp-like super family | cl40470 | conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ... |
190-406 | 4.37e-109 | ||||
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model. The actual alignment was detected with superfamily member cd01645: Pssm-ID: 477363 [Multi-domain] Cd Length: 213 Bit Score: 329.24 E-value: 4.37e-109
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| RVT_connect | pfam06815 | Reverse transcriptase connection domain; This domain is known as the connection domain. This ... |
490-590 | 3.90e-58 | ||||
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: 191.89 E-value: 3.90e-58
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| RNase_H | pfam00075 | RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ... |
606-709 | 1.75e-26 | ||||
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers. : Pssm-ID: 395028 [Multi-domain] Cd Length: 141 Bit Score: 105.15 E-value: 1.75e-26
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| RVT_thumb | pfam06817 | Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ... |
413-468 | 8.52e-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: 8.52e-21
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| HIV_retropepsin_like | cd05482 | Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ... |
84-164 | 2.39e-20 | ||||
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: 85.78 E-value: 2.39e-20
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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 ... |
190-406 | 4.37e-109 | ||||
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: 329.24 E-value: 4.37e-109
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| RVT_connect | pfam06815 | Reverse transcriptase connection domain; This domain is known as the connection domain. This ... |
490-590 | 3.90e-58 | ||||
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: 191.89 E-value: 3.90e-58
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| RVT_1 | pfam00078 | Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ... |
235-406 | 2.68e-41 | ||||
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: 148.99 E-value: 2.68e-41
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| RNase_H | pfam00075 | RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ... |
606-709 | 1.75e-26 | ||||
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers. Pssm-ID: 395028 [Multi-domain] Cd Length: 141 Bit Score: 105.15 E-value: 1.75e-26
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| RVT_thumb | pfam06817 | Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ... |
413-468 | 8.52e-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: 8.52e-21
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| HIV_retropepsin_like | cd05482 | Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ... |
84-164 | 2.39e-20 | ||||
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: 85.78 E-value: 2.39e-20
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| RVP | pfam00077 | Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ... |
78-171 | 1.33e-17 | ||||
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: 78.56 E-value: 1.33e-17
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| RnhA | COG0328 | Ribonuclease HI [Replication, recombination and repair]; |
612-674 | 1.46e-07 | ||||
Ribonuclease HI [Replication, recombination and repair]; Pssm-ID: 440097 [Multi-domain] Cd Length: 136 Bit Score: 51.00 E-value: 1.46e-07
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| RNase_HI_prokaryote_like | cd09278 | RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ... |
612-674 | 1.38e-06 | ||||
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD), residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability. Pssm-ID: 260010 [Multi-domain] Cd Length: 139 Bit Score: 48.25 E-value: 1.38e-06
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| COG3577 | COG3577 | Predicted aspartyl protease [General function prediction only]; |
82-169 | 9.65e-06 | ||||
Predicted aspartyl protease [General function prediction only]; Pssm-ID: 442797 Cd Length: 152 Bit Score: 46.09 E-value: 9.65e-06
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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 ... |
190-406 | 4.37e-109 | ||||
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: 329.24 E-value: 4.37e-109
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| RVT_connect | pfam06815 | Reverse transcriptase connection domain; This domain is known as the connection domain. This ... |
490-590 | 3.90e-58 | ||||
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: 191.89 E-value: 3.90e-58
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| RVT_1 | pfam00078 | Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ... |
235-406 | 2.68e-41 | ||||
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: 148.99 E-value: 2.68e-41
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| RT_ZFREV_like | cd03715 | RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ... |
194-394 | 1.92e-37 | ||||
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: 139.02 E-value: 1.92e-37
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| RT_LTR | cd01647 | RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ... |
227-376 | 3.72e-31 | ||||
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: 120.01 E-value: 3.72e-31
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| RNase_H | pfam00075 | RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ... |
606-709 | 1.75e-26 | ||||
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers. Pssm-ID: 395028 [Multi-domain] Cd Length: 141 Bit Score: 105.15 E-value: 1.75e-26
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| RVT_thumb | pfam06817 | Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ... |
413-468 | 8.52e-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: 8.52e-21
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| HIV_retropepsin_like | cd05482 | Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ... |
84-164 | 2.39e-20 | ||||
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: 85.78 E-value: 2.39e-20
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| RVP | pfam00077 | Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ... |
78-171 | 1.33e-17 | ||||
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: 78.56 E-value: 1.33e-17
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| RT_like | cd00304 | RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ... |
321-406 | 9.40e-15 | ||||
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: 70.46 E-value: 9.40e-15
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| RT_DIRS1 | cd03714 | RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ... |
281-404 | 2.05e-12 | ||||
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: 64.29 E-value: 2.05e-12
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| gag-asp_proteas | pfam13975 | gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ... |
84-163 | 2.22e-08 | ||||
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: 51.81 E-value: 2.22e-08
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| RT_pepA17 | cd01644 | RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ... |
275-386 | 7.14e-08 | ||||
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: 53.46 E-value: 7.14e-08
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| RnhA | COG0328 | Ribonuclease HI [Replication, recombination and repair]; |
612-674 | 1.46e-07 | ||||
Ribonuclease HI [Replication, recombination and repair]; Pssm-ID: 440097 [Multi-domain] Cd Length: 136 Bit Score: 51.00 E-value: 1.46e-07
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| Asp_protease_2 | pfam13650 | Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ... |
84-161 | 2.87e-07 | ||||
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: 48.82 E-value: 2.87e-07
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| RNase_HI_prokaryote_like | cd09278 | RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ... |
612-674 | 1.38e-06 | ||||
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD), residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability. Pssm-ID: 260010 [Multi-domain] Cd Length: 139 Bit Score: 48.25 E-value: 1.38e-06
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| RNase_H_like | cd06222 | Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ... |
612-708 | 4.12e-06 | ||||
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions. Pssm-ID: 259998 [Multi-domain] Cd Length: 121 Bit Score: 46.54 E-value: 4.12e-06
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| RNase_HI_RT_Bel | cd09273 | Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ... |
610-709 | 7.42e-06 | ||||
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Pssm-ID: 260005 [Multi-domain] Cd Length: 131 Bit Score: 45.79 E-value: 7.42e-06
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| COG3577 | COG3577 | Predicted aspartyl protease [General function prediction only]; |
82-169 | 9.65e-06 | ||||
Predicted aspartyl protease [General function prediction only]; Pssm-ID: 442797 Cd Length: 152 Bit Score: 46.09 E-value: 9.65e-06
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| RNase_HI_eukaryote_like | cd09280 | Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ... |
612-673 | 1.61e-05 | ||||
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at their N-termini called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. Pssm-ID: 260012 [Multi-domain] Cd Length: 145 Bit Score: 45.25 E-value: 1.61e-05
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| retropepsin_like_bacteria | cd05483 | Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria ... |
81-163 | 4.24e-05 | ||||
Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria aspartate proteases is a subfamily of retropepsin-like protease family, which includes enzymes from retrovirus and retrotransposons. While fungal and mammalian pepsin-like aspartate proteases are bilobal proteins with structurally related N- and C-termini, this family of bacteria aspartate proteases is half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. 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 proteases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A. Pssm-ID: 133150 Cd Length: 96 Bit Score: 42.62 E-value: 4.24e-05
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| Rnase_HI_RT_non_LTR | cd09276 | non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ... |
610-709 | 5.34e-04 | ||||
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retrotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Pssm-ID: 260008 [Multi-domain] Cd Length: 131 Bit Score: 40.66 E-value: 5.34e-04
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| retropepsin_like | cd00303 | Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ... |
84-164 | 1.20e-03 | ||||
Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, 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: 133136 Cd Length: 92 Bit Score: 38.47 E-value: 1.20e-03
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| RNase_HI_like | cd09279 | RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ... |
612-708 | 4.45e-03 | ||||
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties. Pssm-ID: 260011 [Multi-domain] Cd Length: 128 Bit Score: 37.84 E-value: 4.45e-03
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