LOW QUALITY PROTEIN: uncharacterized protein LOC121677304 [Arvicola amphibius]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||
| Gag_p30 super family | cl03444 | Gag P30 core shell protein; According to Swiss-Prot annotation this protein is the viral core ... |
228-432 | 6.46e-130 | ||||
Gag P30 core shell protein; According to Swiss-Prot annotation this protein is the viral core shell protein. P30 is essential for viral assembly. The actual alignment was detected with superfamily member pfam02093: Pssm-ID: 426597 Cd Length: 208 Bit Score: 403.28 E-value: 6.46e-130
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| RT_ZFREV_like | cd03715 | RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ... |
706-921 | 2.98e-104 | ||||
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: 331.62 E-value: 2.98e-104
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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 ... |
1168-1308 | 3.49e-51 | ||||
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: 176.76 E-value: 3.49e-51
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| Gag_MA | pfam01140 | Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved ... |
2-113 | 2.11e-48 | ||||
Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved in pathogenicity. : Pssm-ID: 426076 [Multi-domain] Cd Length: 126 Bit Score: 168.71 E-value: 2.11e-48
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| MLVIN_C super family | cl40013 | Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ... |
1645-1727 | 1.27e-32 | ||||
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain (CTD) which can be found in murine leukemia virus (MLV) integrase (IN) proteins. The MLV IN C-terminal domain interacts with the bromo and extraterminal (BET) proteins through the ET domain. This interaction provides a structural basis for global in vivo integration-site preferences andt disruption of this interaction through truncation mutations affects the global targeting profile of MLV. The CTD consists an SH3 fold followed by a long unstructured tail. The actual alignment was detected with superfamily member pfam18697: Pssm-ID: 436671 Cd Length: 83 Bit Score: 121.86 E-value: 1.27e-32
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| zf-H2C2 super family | cl07828 | H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ... |
1335-1426 | 6.98e-27 | ||||
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters. The actual alignment was detected with superfamily member pfam16721: Pssm-ID: 447530 Cd Length: 96 Bit Score: 105.97 E-value: 6.98e-27
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| rve | pfam00665 | Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ... |
1439-1534 | 3.20e-23 | ||||
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site. : Pssm-ID: 459897 [Multi-domain] Cd Length: 98 Bit Score: 95.46 E-value: 3.20e-23
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| pepsin_retropepsin_like super family | cl11403 | Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular ... |
541-630 | 9.25e-23 | ||||
Cellular and retroviral pepsin-like aspartate proteases; This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin 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. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family). The actual alignment was detected with superfamily member pfam00077: Pssm-ID: 472175 Cd Length: 101 Bit Score: 94.36 E-value: 9.25e-23
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| RT_RNaseH super family | cl39037 | RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ... |
1009-1114 | 2.93e-15 | ||||
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain. The actual alignment was detected with superfamily member pfam17917: Pssm-ID: 465565 Cd Length: 104 Bit Score: 72.93 E-value: 2.93e-15
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| Gag_p12 super family | cl03117 | Gag polyprotein, inner coat protein p12; The retroviral p12 is a virion structural protein. ... |
151-214 | 1.16e-12 | ||||
Gag polyprotein, inner coat protein p12; The retroviral p12 is a virion structural protein. p12 is proline rich. The function carried out by p12 in assembly and replication is unknown. p12 is associated with pathogenicity of the virus. The actual alignment was detected with superfamily member pfam01141: Pssm-ID: 279483 [Multi-domain] Cd Length: 85 Bit Score: 65.16 E-value: 1.16e-12
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| Name | Accession | Description | Interval | E-value | |||||
| Gag_p30 | pfam02093 | Gag P30 core shell protein; According to Swiss-Prot annotation this protein is the viral core ... |
228-432 | 6.46e-130 | |||||
Gag P30 core shell protein; According to Swiss-Prot annotation this protein is the viral core shell protein. P30 is essential for viral assembly. Pssm-ID: 426597 Cd Length: 208 Bit Score: 403.28 E-value: 6.46e-130
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| RT_ZFREV_like | cd03715 | RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ... |
706-921 | 2.98e-104 | |||||
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: 331.62 E-value: 2.98e-104
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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 ... |
1168-1308 | 3.49e-51 | |||||
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: 176.76 E-value: 3.49e-51
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| Gag_MA | pfam01140 | Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved ... |
2-113 | 2.11e-48 | |||||
Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved in pathogenicity. Pssm-ID: 426076 [Multi-domain] Cd Length: 126 Bit Score: 168.71 E-value: 2.11e-48
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| RNase_H | pfam00075 | RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ... |
1164-1308 | 1.51e-33 | |||||
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: 126.72 E-value: 1.51e-33
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| MLVIN_C | pfam18697 | Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ... |
1645-1727 | 1.27e-32 | |||||
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain (CTD) which can be found in murine leukemia virus (MLV) integrase (IN) proteins. The MLV IN C-terminal domain interacts with the bromo and extraterminal (BET) proteins through the ET domain. This interaction provides a structural basis for global in vivo integration-site preferences andt disruption of this interaction through truncation mutations affects the global targeting profile of MLV. The CTD consists an SH3 fold followed by a long unstructured tail. Pssm-ID: 436671 Cd Length: 83 Bit Score: 121.86 E-value: 1.27e-32
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| RVT_1 | pfam00078 | Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ... |
749-921 | 1.81e-32 | |||||
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: 125.49 E-value: 1.81e-32
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| zf-H3C2 | pfam16721 | Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers ... |
1335-1426 | 6.98e-27 | |||||
Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers found on Gag-Pol polyproteins from mouse retroviruses. Added to clan to resolve overlaps with zf-H2C2, but neither are true members. Pssm-ID: 293326 Cd Length: 96 Bit Score: 105.97 E-value: 6.98e-27
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| rve | pfam00665 | Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ... |
1439-1534 | 3.20e-23 | |||||
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site. Pssm-ID: 459897 [Multi-domain] Cd Length: 98 Bit Score: 95.46 E-value: 3.20e-23
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| RVP | pfam00077 | Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ... |
541-630 | 9.25e-23 | |||||
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: 94.36 E-value: 9.25e-23
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| RP_RTVL_H_like | cd06095 | Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ... |
542-623 | 9.59e-23 | |||||
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: 93.94 E-value: 9.59e-23
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| transpos_IS481 | NF033577 | IS481 family transposase; null |
1365-1587 | 2.79e-15 | |||||
IS481 family transposase; null Pssm-ID: 468094 [Multi-domain] Cd Length: 283 Bit Score: 78.40 E-value: 2.79e-15
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| RT_RNaseH | pfam17917 | RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ... |
1009-1114 | 2.93e-15 | |||||
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain. Pssm-ID: 465565 Cd Length: 104 Bit Score: 72.93 E-value: 2.93e-15
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| Gag_p12 | pfam01141 | Gag polyprotein, inner coat protein p12; The retroviral p12 is a virion structural protein. ... |
151-214 | 1.16e-12 | |||||
Gag polyprotein, inner coat protein p12; The retroviral p12 is a virion structural protein. p12 is proline rich. The function carried out by p12 in assembly and replication is unknown. p12 is associated with pathogenicity of the virus. Pssm-ID: 279483 [Multi-domain] Cd Length: 85 Bit Score: 65.16 E-value: 1.16e-12
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| Tra5 | COG2801 | Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons]; |
1297-1549 | 1.01e-10 | |||||
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons]; Pssm-ID: 442053 [Multi-domain] Cd Length: 309 Bit Score: 64.79 E-value: 1.01e-10
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| RnhA | COG0328 | Ribonuclease HI [Replication, recombination and repair]; |
1170-1306 | 5.80e-08 | |||||
Ribonuclease HI [Replication, recombination and repair]; Pssm-ID: 440097 [Multi-domain] Cd Length: 136 Bit Score: 53.31 E-value: 5.80e-08
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| COG3577 | COG3577 | Predicted aspartyl protease [General function prediction only]; |
541-633 | 8.98e-06 | |||||
Predicted aspartyl protease [General function prediction only]; Pssm-ID: 442797 Cd Length: 152 Bit Score: 47.25 E-value: 8.98e-06
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| transpos_ISNCY_2 | NF033594 | ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes ... |
1459-1557 | 5.58e-04 | |||||
ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes several apparently unrelated families of transposases. Members of this family resemble the transposases of ISNCY family elements such as IS1202, ISTde1, ISKpn21, and ISCARN1. Pssm-ID: 468103 [Multi-domain] Cd Length: 367 Bit Score: 44.40 E-value: 5.58e-04
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| Tra8 | COG2826 | Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons]; |
1414-1553 | 5.96e-03 | |||||
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons]; Pssm-ID: 442074 [Multi-domain] Cd Length: 325 Bit Score: 41.02 E-value: 5.96e-03
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| Name | Accession | Description | Interval | E-value | |||||
| Gag_p30 | pfam02093 | Gag P30 core shell protein; According to Swiss-Prot annotation this protein is the viral core ... |
228-432 | 6.46e-130 | |||||
Gag P30 core shell protein; According to Swiss-Prot annotation this protein is the viral core shell protein. P30 is essential for viral assembly. Pssm-ID: 426597 Cd Length: 208 Bit Score: 403.28 E-value: 6.46e-130
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| RT_ZFREV_like | cd03715 | RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ... |
706-921 | 2.98e-104 | |||||
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: 331.62 E-value: 2.98e-104
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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 ... |
1168-1308 | 3.49e-51 | |||||
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: 176.76 E-value: 3.49e-51
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| Gag_MA | pfam01140 | Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved ... |
2-113 | 2.11e-48 | |||||
Matrix protein (MA), p15; The matrix protein, p15, is encoded by the gag gene. MA is involved in pathogenicity. Pssm-ID: 426076 [Multi-domain] Cd Length: 126 Bit Score: 168.71 E-value: 2.11e-48
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| RT_Rtv | cd01645 | RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ... |
706-921 | 5.47e-39 | |||||
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: 145.12 E-value: 5.47e-39
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| RT_LTR | cd01647 | RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ... |
733-919 | 2.87e-35 | |||||
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: 133.10 E-value: 2.87e-35
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| RNase_H | pfam00075 | RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ... |
1164-1308 | 1.51e-33 | |||||
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: 126.72 E-value: 1.51e-33
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| MLVIN_C | pfam18697 | Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain ... |
1645-1727 | 1.27e-32 | |||||
Murine leukemia virus (MLV) integrase (IN) C-terminal domain; This is the C-terminal domain (CTD) which can be found in murine leukemia virus (MLV) integrase (IN) proteins. The MLV IN C-terminal domain interacts with the bromo and extraterminal (BET) proteins through the ET domain. This interaction provides a structural basis for global in vivo integration-site preferences andt disruption of this interaction through truncation mutations affects the global targeting profile of MLV. The CTD consists an SH3 fold followed by a long unstructured tail. Pssm-ID: 436671 Cd Length: 83 Bit Score: 121.86 E-value: 1.27e-32
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| RVT_1 | pfam00078 | Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ... |
749-921 | 1.81e-32 | |||||
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: 125.49 E-value: 1.81e-32
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| zf-H3C2 | pfam16721 | Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers ... |
1335-1426 | 6.98e-27 | |||||
Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers found on Gag-Pol polyproteins from mouse retroviruses. Added to clan to resolve overlaps with zf-H2C2, but neither are true members. Pssm-ID: 293326 Cd Length: 96 Bit Score: 105.97 E-value: 6.98e-27
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| rve | pfam00665 | Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ... |
1439-1534 | 3.20e-23 | |||||
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site. Pssm-ID: 459897 [Multi-domain] Cd Length: 98 Bit Score: 95.46 E-value: 3.20e-23
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| RVP | pfam00077 | Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ... |
541-630 | 9.25e-23 | |||||
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: 94.36 E-value: 9.25e-23
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| RP_RTVL_H_like | cd06095 | Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ... |
542-623 | 9.59e-23 | |||||
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: 93.94 E-value: 9.59e-23
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| RNase_HI_eukaryote_like | cd09280 | Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ... |
1170-1308 | 1.04e-15 | |||||
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: 75.68 E-value: 1.04e-15
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| transpos_IS481 | NF033577 | IS481 family transposase; null |
1365-1587 | 2.79e-15 | |||||
IS481 family transposase; null Pssm-ID: 468094 [Multi-domain] Cd Length: 283 Bit Score: 78.40 E-value: 2.79e-15
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| RT_RNaseH | pfam17917 | RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ... |
1009-1114 | 2.93e-15 | |||||
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain. Pssm-ID: 465565 Cd Length: 104 Bit Score: 72.93 E-value: 2.93e-15
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| RT_RNaseH_2 | pfam17919 | RNase H-like domain found in reverse transcriptase; |
984-1064 | 4.30e-14 | |||||
RNase H-like domain found in reverse transcriptase; Pssm-ID: 465567 [Multi-domain] Cd Length: 100 Bit Score: 69.45 E-value: 4.30e-14
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| RT_like | cd00304 | RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ... |
835-921 | 1.88e-13 | |||||
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: 67.76 E-value: 1.88e-13
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| Gag_p12 | pfam01141 | Gag polyprotein, inner coat protein p12; The retroviral p12 is a virion structural protein. ... |
151-214 | 1.16e-12 | |||||
Gag polyprotein, inner coat protein p12; The retroviral p12 is a virion structural protein. p12 is proline rich. The function carried out by p12 in assembly and replication is unknown. p12 is associated with pathogenicity of the virus. Pssm-ID: 279483 [Multi-domain] Cd Length: 85 Bit Score: 65.16 E-value: 1.16e-12
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| RNase_H_like | cd06222 | Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ... |
1169-1305 | 1.64e-11 | |||||
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: 63.10 E-value: 1.64e-11
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| RT_DIRS1 | cd03714 | RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ... |
797-921 | 4.65e-11 | |||||
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: 61.59 E-value: 4.65e-11
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| RNase_HI_prokaryote_like | cd09278 | RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ... |
1170-1308 | 9.30e-11 | |||||
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: 61.34 E-value: 9.30e-11
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| Tra5 | COG2801 | Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons]; |
1297-1549 | 1.01e-10 | |||||
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons]; Pssm-ID: 442053 [Multi-domain] Cd Length: 309 Bit Score: 64.79 E-value: 1.01e-10
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| zf-H2C2 | pfam09337 | H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements ... |
1378-1419 | 5.30e-09 | |||||
H2C2 zinc finger; This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters. Pssm-ID: 430537 Cd Length: 39 Bit Score: 53.10 E-value: 5.30e-09
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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 ... |
1170-1308 | 6.50e-09 | |||||
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: 55.69 E-value: 6.50e-09
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| RnhA | COG0328 | Ribonuclease HI [Replication, recombination and repair]; |
1170-1306 | 5.80e-08 | |||||
Ribonuclease HI [Replication, recombination and repair]; Pssm-ID: 440097 [Multi-domain] Cd Length: 136 Bit Score: 53.31 E-value: 5.80e-08
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| gag-asp_proteas | pfam13975 | gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ... |
542-622 | 1.02e-07 | |||||
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: 51.42 E-value: 1.02e-07
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| retropepsin_like | cd00303 | Retropepsins; pepsin-like aspartate proteases; The family includes pepsin-like aspartate ... |
542-623 | 4.22e-06 | |||||
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: 46.56 E-value: 4.22e-06
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| COG3577 | COG3577 | Predicted aspartyl protease [General function prediction only]; |
541-633 | 8.98e-06 | |||||
Predicted aspartyl protease [General function prediction only]; Pssm-ID: 442797 Cd Length: 152 Bit Score: 47.25 E-value: 8.98e-06
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| Asp_protease_2 | pfam13650 | Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ... |
542-621 | 5.37e-05 | |||||
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: 43.43 E-value: 5.37e-05
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| retropepsin_like_bacteria | cd05483 | Bacterial aspartate proteases, retropepsin-like protease family; This family of bacteria ... |
542-597 | 6.28e-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: 43.39 E-value: 6.28e-05
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| HIV_retropepsin_like | cd05482 | Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ... |
542-623 | 3.60e-04 | |||||
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: 41.10 E-value: 3.60e-04
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| transpos_ISNCY_2 | NF033594 | ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes ... |
1459-1557 | 5.58e-04 | |||||
ISNCY family transposase; The ISNCY insertion sequence family, as defined by ISFinder, encodes several apparently unrelated families of transposases. Members of this family resemble the transposases of ISNCY family elements such as IS1202, ISTde1, ISKpn21, and ISCARN1. Pssm-ID: 468103 [Multi-domain] Cd Length: 367 Bit Score: 44.40 E-value: 5.58e-04
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| RT_pepA17 | cd01644 | RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT ... |
798-896 | 8.68e-04 | |||||
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: 42.68 E-value: 8.68e-04
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| Tra8 | COG2826 | Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons]; |
1414-1553 | 5.96e-03 | |||||
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons]; Pssm-ID: 442074 [Multi-domain] Cd Length: 325 Bit Score: 41.02 E-value: 5.96e-03
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