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Gag-Pro-Pol-Env protein [Homo sapiens]
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 ... |
956-1168 | 1.37e-131 | ||||
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: 410.91 E-value: 1.37e-131
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HERV-K_env_2 | pfam13804 | Retro-transcribing viruses envelope glycoprotein; This family comes from human endogenous ... |
1798-1966 | 1.43e-119 | ||||
Retro-transcribing viruses envelope glycoprotein; This family comes from human endogenous retrovirus K envelope glycoproteins. : Pssm-ID: 290518 Cd Length: 169 Bit Score: 374.47 E-value: 1.43e-119
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Gag_p24 | pfam00607 | gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ... |
306-434 | 1.99e-47 | ||||
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro. : Pssm-ID: 459864 Cd Length: 128 Bit Score: 166.30 E-value: 1.99e-47
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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 ... |
1388-1512 | 8.79e-40 | ||||
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: 144.40 E-value: 8.79e-40
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RVP | pfam00077 | Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ... |
785-884 | 1.87e-39 | ||||
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: 142.51 E-value: 1.87e-39
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RVT_thumb | pfam06817 | Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ... |
1175-1240 | 1.57e-33 | ||||
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: 124.35 E-value: 1.57e-33
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Gag_p10 | pfam02337 | Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ... |
11-93 | 6.46e-33 | ||||
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins and encompasses the p10 region producing the p10 protein upon proteolytic cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. Some of the GAG polyproteins have alternate cleavage sites leading to the production of alternative and longer cleavage products (e.g. p19) the alignment of this family only covers the approximately N-terminal (GAG) 100 amino acid region of homology to p10. : Pssm-ID: 426727 Cd Length: 85 Bit Score: 123.22 E-value: 6.46e-33
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Gag_p24_C super family | cl44748 | Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ... |
434-512 | 1.16e-32 | ||||
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro. The actual alignment was detected with superfamily member pfam19317: Pssm-ID: 466038 Cd Length: 74 Bit Score: 122.20 E-value: 1.16e-32
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rve | pfam00665 | Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ... |
1569-1662 | 1.53e-27 | ||||
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: 108.17 E-value: 1.53e-27
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HIV-1-like_HR1-HR2 | cd09909 | heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human ... |
2184-2278 | 1.98e-27 | ||||
heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human immunodeficiency virus (HIV-1), and related domains; This domain family spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including human, simian, and feline immunodeficiency viruses (HIV, SIV, and FIV), bovine immunodeficiency-like virus (BIV), equine infectious anaemia virus (EIAV), and Jaagsiekte sheep retrovirus (JSRV), mouse mammary tumour virus (MMTV) and various ERVs including sheep enJSRV-26, and human ERVs (HERVs): HERV-K_c1q23.3 and HERV-K_c12q14.1. This domain belongs to a larger superfamily containing the HR1-HR2 domain of ERVs and infectious retroviruses, including Ebola virus, and Rous sarcoma virus. Proteins in this family lack the canonical CSK17-like immunosuppressive sequence, and the intrasubunit disulfide bond-forming CX6C motif found in linker region between HR1 and HR2 in the Ebola_RSV-like_HR1-HR2 family. N-terminal to the HR1-HR2 region is a fusion peptide (FP), and C-terminal is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1 helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some modern ERVs, those that integrated into the host genome post-speciation, have a currently active exogenous counterpart, such as JSRV. Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Included in this subgroup are ERVs from domestic sheep that are related to JSRV, the agent of transmissible lung cancer in sheep, for example enJSRV-26 that retains an intact genome. These endogenous JSRVs protect the sheep against JSRV infection and are required for sheep placental development. HERV-K_c12q14.1 is potentially a complete envelope protein; however, it does not appear to be fusogenic. : Pssm-ID: 197369 Cd Length: 128 Bit Score: 109.02 E-value: 1.98e-27
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trimeric_dUTPase | cd07557 | Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ... |
667-751 | 4.43e-20 | ||||
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA. It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface. : Pssm-ID: 143638 [Multi-domain] Cd Length: 92 Bit Score: 86.78 E-value: 4.43e-20
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zf-CCHC_5 | pfam14787 | GAG-polyprotein viral zinc-finger; |
578-613 | 7.52e-17 | ||||
GAG-polyprotein viral zinc-finger; : Pssm-ID: 373297 Cd Length: 36 Bit Score: 75.67 E-value: 7.52e-17
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Integrase_Zn | pfam02022 | Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ... |
1517-1552 | 7.79e-14 | ||||
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552. : Pssm-ID: 426567 Cd Length: 36 Bit Score: 67.01 E-value: 7.79e-14
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G-patch | pfam01585 | G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ... |
890-934 | 1.28e-13 | ||||
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines. : Pssm-ID: 396249 [Multi-domain] Cd Length: 45 Bit Score: 66.76 E-value: 1.28e-13
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PRK10263 super family | cl35903 | DNA translocase FtsK; Provisional |
172-313 | 1.78e-07 | ||||
DNA translocase FtsK; Provisional The actual alignment was detected with superfamily member PRK10263: Pssm-ID: 236669 [Multi-domain] Cd Length: 1355 Bit Score: 57.02 E-value: 1.78e-07
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AIR1 super family | cl34894 | Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ... |
545-601 | 9.19e-06 | ||||
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; The actual alignment was detected with superfamily member COG5082: Pssm-ID: 227414 [Multi-domain] Cd Length: 190 Bit Score: 48.69 E-value: 9.19e-06
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IN_DBD_C super family | cl02895 | Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ... |
1738-1778 | 2.77e-03 | ||||
Integrase DNA binding 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. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain. The actual alignment was detected with superfamily member pfam00552: Pssm-ID: 425747 Cd Length: 45 Bit Score: 37.76 E-value: 2.77e-03
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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 ... |
956-1168 | 1.37e-131 | ||||
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: 410.91 E-value: 1.37e-131
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HERV-K_env_2 | pfam13804 | Retro-transcribing viruses envelope glycoprotein; This family comes from human endogenous ... |
1798-1966 | 1.43e-119 | ||||
Retro-transcribing viruses envelope glycoprotein; This family comes from human endogenous retrovirus K envelope glycoproteins. Pssm-ID: 290518 Cd Length: 169 Bit Score: 374.47 E-value: 1.43e-119
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Gag_p24 | pfam00607 | gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ... |
306-434 | 1.99e-47 | ||||
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro. Pssm-ID: 459864 Cd Length: 128 Bit Score: 166.30 E-value: 1.99e-47
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RVT_1 | pfam00078 | Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ... |
999-1168 | 7.81e-46 | ||||
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: 164.01 E-value: 7.81e-46
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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 ... |
1388-1512 | 8.79e-40 | ||||
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: 144.40 E-value: 8.79e-40
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RVP | pfam00077 | Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ... |
785-884 | 1.87e-39 | ||||
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: 142.51 E-value: 1.87e-39
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RVT_thumb | pfam06817 | Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ... |
1175-1240 | 1.57e-33 | ||||
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: 124.35 E-value: 1.57e-33
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Gag_p10 | pfam02337 | Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ... |
11-93 | 6.46e-33 | ||||
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins and encompasses the p10 region producing the p10 protein upon proteolytic cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. Some of the GAG polyproteins have alternate cleavage sites leading to the production of alternative and longer cleavage products (e.g. p19) the alignment of this family only covers the approximately N-terminal (GAG) 100 amino acid region of homology to p10. Pssm-ID: 426727 Cd Length: 85 Bit Score: 123.22 E-value: 6.46e-33
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Gag_p24_C | pfam19317 | Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ... |
434-512 | 1.16e-32 | ||||
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro. Pssm-ID: 466038 Cd Length: 74 Bit Score: 122.20 E-value: 1.16e-32
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HIV_retropepsin_like | cd05482 | Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ... |
791-877 | 4.05e-30 | ||||
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: 115.06 E-value: 4.05e-30
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RNase_H | pfam00075 | RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ... |
1384-1513 | 1.87e-28 | ||||
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: 112.47 E-value: 1.87e-28
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rve | pfam00665 | Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ... |
1569-1662 | 1.53e-27 | ||||
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: 108.17 E-value: 1.53e-27
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HIV-1-like_HR1-HR2 | cd09909 | heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human ... |
2184-2278 | 1.98e-27 | ||||
heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human immunodeficiency virus (HIV-1), and related domains; This domain family spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including human, simian, and feline immunodeficiency viruses (HIV, SIV, and FIV), bovine immunodeficiency-like virus (BIV), equine infectious anaemia virus (EIAV), and Jaagsiekte sheep retrovirus (JSRV), mouse mammary tumour virus (MMTV) and various ERVs including sheep enJSRV-26, and human ERVs (HERVs): HERV-K_c1q23.3 and HERV-K_c12q14.1. This domain belongs to a larger superfamily containing the HR1-HR2 domain of ERVs and infectious retroviruses, including Ebola virus, and Rous sarcoma virus. Proteins in this family lack the canonical CSK17-like immunosuppressive sequence, and the intrasubunit disulfide bond-forming CX6C motif found in linker region between HR1 and HR2 in the Ebola_RSV-like_HR1-HR2 family. N-terminal to the HR1-HR2 region is a fusion peptide (FP), and C-terminal is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1 helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some modern ERVs, those that integrated into the host genome post-speciation, have a currently active exogenous counterpart, such as JSRV. Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Included in this subgroup are ERVs from domestic sheep that are related to JSRV, the agent of transmissible lung cancer in sheep, for example enJSRV-26 that retains an intact genome. These endogenous JSRVs protect the sheep against JSRV infection and are required for sheep placental development. HERV-K_c12q14.1 is potentially a complete envelope protein; however, it does not appear to be fusogenic. Pssm-ID: 197369 Cd Length: 128 Bit Score: 109.02 E-value: 1.98e-27
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transpos_IS481 | NF033577 | IS481 family transposase; null |
1569-1690 | 4.29e-21 | ||||
IS481 family transposase; null Pssm-ID: 468094 [Multi-domain] Cd Length: 283 Bit Score: 95.74 E-value: 4.29e-21
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trimeric_dUTPase | cd07557 | Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ... |
667-751 | 4.43e-20 | ||||
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA. It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface. Pssm-ID: 143638 [Multi-domain] Cd Length: 92 Bit Score: 86.78 E-value: 4.43e-20
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dUTPase | pfam00692 | dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate. |
668-754 | 4.23e-19 | ||||
dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate. Pssm-ID: 395562 [Multi-domain] Cd Length: 129 Bit Score: 85.42 E-value: 4.23e-19
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Tra5 | COG2801 | Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons]; |
1569-1684 | 7.17e-18 | ||||
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons]; Pssm-ID: 442053 [Multi-domain] Cd Length: 309 Bit Score: 86.75 E-value: 7.17e-18
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zf-CCHC_5 | pfam14787 | GAG-polyprotein viral zinc-finger; |
578-613 | 7.52e-17 | ||||
GAG-polyprotein viral zinc-finger; Pssm-ID: 373297 Cd Length: 36 Bit Score: 75.67 E-value: 7.52e-17
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transpos_IS3 | NF033516 | IS3 family transposase; |
1569-1683 | 2.02e-15 | ||||
IS3 family transposase; Pssm-ID: 468052 [Multi-domain] Cd Length: 369 Bit Score: 80.30 E-value: 2.02e-15
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dut | PRK00601 | dUTP diphosphatase; |
651-771 | 5.91e-14 | ||||
dUTP diphosphatase; Pssm-ID: 234802 [Multi-domain] Cd Length: 150 Bit Score: 71.35 E-value: 5.91e-14
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Dut | COG0756 | dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP ... |
650-771 | 6.33e-14 | ||||
dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP pyrophosphatase (dUTPase) is part of the Pathway/BioSystem: Thymidylate biosynthesis Pssm-ID: 440519 [Multi-domain] Cd Length: 143 Bit Score: 70.82 E-value: 6.33e-14
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dut | TIGR00576 | deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is ... |
668-771 | 6.53e-14 | ||||
deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is in maintaining the levels of dUTP in the cell to prevent dUTP incorporation into DNA during DNA replication. Pol proteins in viruses are very similar to this protein family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Changed role from 132 to 123. RTD [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism] Pssm-ID: 273149 [Multi-domain] Cd Length: 142 Bit Score: 70.73 E-value: 6.53e-14
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Integrase_Zn | pfam02022 | Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ... |
1517-1552 | 7.79e-14 | ||||
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552. Pssm-ID: 426567 Cd Length: 36 Bit Score: 67.01 E-value: 7.79e-14
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G-patch | pfam01585 | G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ... |
890-934 | 1.28e-13 | ||||
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines. Pssm-ID: 396249 [Multi-domain] Cd Length: 45 Bit Score: 66.76 E-value: 1.28e-13
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GP41 | pfam00517 | Retroviral envelope protein; This family includes envelope protein from a variety of ... |
2177-2276 | 1.26e-11 | ||||
Retroviral envelope protein; This family includes envelope protein from a variety of retroviruses. It includes the GP41 subunit of the envelope protein complex from human and simian immunodeficiency viruses (HIV and SIV) which mediate membrane fusion during viral entry. The family also includes bovine immunodeficiency virus, feline immunodeficiency virus and Equine infectious anaemia (EIAV). The family also includes the Gp36 protein from mouse mammary tumour virus (MMTV) and human endogenous retroviruses (HERVs). Pssm-ID: 395415 Cd Length: 197 Bit Score: 65.77 E-value: 1.26e-11
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G_patch | smart00443 | glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ... |
890-933 | 1.79e-11 | ||||
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins. Pssm-ID: 197727 [Multi-domain] Cd Length: 47 Bit Score: 60.64 E-value: 1.79e-11
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RnhA | COG0328 | Ribonuclease HI [Replication, recombination and repair]; |
1385-1512 | 1.00e-07 | ||||
Ribonuclease HI [Replication, recombination and repair]; Pssm-ID: 440097 [Multi-domain] Cd Length: 136 Bit Score: 52.92 E-value: 1.00e-07
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PRK10263 | PRK10263 | DNA translocase FtsK; Provisional |
172-313 | 1.78e-07 | ||||
DNA translocase FtsK; Provisional Pssm-ID: 236669 [Multi-domain] Cd Length: 1355 Bit Score: 57.02 E-value: 1.78e-07
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PHA02517 | PHA02517 | putative transposase OrfB; Reviewed |
1569-1743 | 5.29e-07 | ||||
putative transposase OrfB; Reviewed Pssm-ID: 222853 [Multi-domain] Cd Length: 277 Bit Score: 53.72 E-value: 5.29e-07
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AIR1 | COG5082 | Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ... |
545-601 | 9.19e-06 | ||||
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Pssm-ID: 227414 [Multi-domain] Cd Length: 190 Bit Score: 48.69 E-value: 9.19e-06
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zf-CCHC | pfam00098 | Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ... |
544-560 | 6.35e-05 | ||||
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger. Pssm-ID: 395050 [Multi-domain] Cd Length: 18 Bit Score: 41.74 E-value: 6.35e-05
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PBP1 | COG5180 | PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; ... |
117-305 | 8.00e-05 | ||||
PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; Pssm-ID: 444064 [Multi-domain] Cd Length: 548 Bit Score: 47.75 E-value: 8.00e-05
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ZnF_C2HC | smart00343 | zinc finger; |
545-560 | 3.17e-04 | ||||
zinc finger; Pssm-ID: 197667 [Multi-domain] Cd Length: 17 Bit Score: 39.73 E-value: 3.17e-04
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PTZ00368 | PTZ00368 | universal minicircle sequence binding protein (UMSBP); Provisional |
544-598 | 7.18e-04 | ||||
universal minicircle sequence binding protein (UMSBP); Provisional Pssm-ID: 173561 [Multi-domain] Cd Length: 148 Bit Score: 42.10 E-value: 7.18e-04
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IN_DBD_C | pfam00552 | Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ... |
1738-1778 | 2.77e-03 | ||||
Integrase DNA binding 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. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain. Pssm-ID: 425747 Cd Length: 45 Bit Score: 37.76 E-value: 2.77e-03
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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 ... |
956-1168 | 1.37e-131 | ||||
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: 410.91 E-value: 1.37e-131
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HERV-K_env_2 | pfam13804 | Retro-transcribing viruses envelope glycoprotein; This family comes from human endogenous ... |
1798-1966 | 1.43e-119 | ||||
Retro-transcribing viruses envelope glycoprotein; This family comes from human endogenous retrovirus K envelope glycoproteins. Pssm-ID: 290518 Cd Length: 169 Bit Score: 374.47 E-value: 1.43e-119
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Gag_p24 | pfam00607 | gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ... |
306-434 | 1.99e-47 | ||||
gag protein p24 N-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro. Pssm-ID: 459864 Cd Length: 128 Bit Score: 166.30 E-value: 1.99e-47
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RVT_1 | pfam00078 | Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ... |
999-1168 | 7.81e-46 | ||||
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: 164.01 E-value: 7.81e-46
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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 ... |
1388-1512 | 8.79e-40 | ||||
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: 144.40 E-value: 8.79e-40
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RVP | pfam00077 | Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ... |
785-884 | 1.87e-39 | ||||
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: 142.51 E-value: 1.87e-39
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RT_ZFREV_like | cd03715 | RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ... |
956-1168 | 1.12e-35 | ||||
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: 135.94 E-value: 1.12e-35
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RVT_thumb | pfam06817 | Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ... |
1175-1240 | 1.57e-33 | ||||
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: 124.35 E-value: 1.57e-33
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Gag_p10 | pfam02337 | Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins ... |
11-93 | 6.46e-33 | ||||
Retroviral GAG p10 protein; This family consists of various retroviral GAG (core) polyproteins and encompasses the p10 region producing the p10 protein upon proteolytic cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. Some of the GAG polyproteins have alternate cleavage sites leading to the production of alternative and longer cleavage products (e.g. p19) the alignment of this family only covers the approximately N-terminal (GAG) 100 amino acid region of homology to p10. Pssm-ID: 426727 Cd Length: 85 Bit Score: 123.22 E-value: 6.46e-33
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Gag_p24_C | pfam19317 | Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA ... |
434-512 | 1.16e-32 | ||||
Gag protein p24 C-terminal domain; p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro. Pssm-ID: 466038 Cd Length: 74 Bit Score: 122.20 E-value: 1.16e-32
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HIV_retropepsin_like | cd05482 | Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ... |
791-877 | 4.05e-30 | ||||
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: 115.06 E-value: 4.05e-30
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RNase_H | pfam00075 | RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ... |
1384-1513 | 1.87e-28 | ||||
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: 112.47 E-value: 1.87e-28
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rve | pfam00665 | Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ... |
1569-1662 | 1.53e-27 | ||||
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: 108.17 E-value: 1.53e-27
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HIV-1-like_HR1-HR2 | cd09909 | heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human ... |
2184-2278 | 1.98e-27 | ||||
heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human immunodeficiency virus (HIV-1), and related domains; This domain family spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including human, simian, and feline immunodeficiency viruses (HIV, SIV, and FIV), bovine immunodeficiency-like virus (BIV), equine infectious anaemia virus (EIAV), and Jaagsiekte sheep retrovirus (JSRV), mouse mammary tumour virus (MMTV) and various ERVs including sheep enJSRV-26, and human ERVs (HERVs): HERV-K_c1q23.3 and HERV-K_c12q14.1. This domain belongs to a larger superfamily containing the HR1-HR2 domain of ERVs and infectious retroviruses, including Ebola virus, and Rous sarcoma virus. Proteins in this family lack the canonical CSK17-like immunosuppressive sequence, and the intrasubunit disulfide bond-forming CX6C motif found in linker region between HR1 and HR2 in the Ebola_RSV-like_HR1-HR2 family. N-terminal to the HR1-HR2 region is a fusion peptide (FP), and C-terminal is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1 helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some modern ERVs, those that integrated into the host genome post-speciation, have a currently active exogenous counterpart, such as JSRV. Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Included in this subgroup are ERVs from domestic sheep that are related to JSRV, the agent of transmissible lung cancer in sheep, for example enJSRV-26 that retains an intact genome. These endogenous JSRVs protect the sheep against JSRV infection and are required for sheep placental development. HERV-K_c12q14.1 is potentially a complete envelope protein; however, it does not appear to be fusogenic. Pssm-ID: 197369 Cd Length: 128 Bit Score: 109.02 E-value: 1.98e-27
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RT_LTR | cd01647 | RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ... |
983-1130 | 1.14e-26 | ||||
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: 108.84 E-value: 1.14e-26
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transpos_IS481 | NF033577 | IS481 family transposase; null |
1569-1690 | 4.29e-21 | ||||
IS481 family transposase; null Pssm-ID: 468094 [Multi-domain] Cd Length: 283 Bit Score: 95.74 E-value: 4.29e-21
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trimeric_dUTPase | cd07557 | Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common ... |
667-751 | 4.43e-20 | ||||
Trimeric dUTP diphosphatases; Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA. It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface. Pssm-ID: 143638 [Multi-domain] Cd Length: 92 Bit Score: 86.78 E-value: 4.43e-20
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dUTPase | pfam00692 | dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate. |
668-754 | 4.23e-19 | ||||
dUTPase; dUTPase hydrolyses dUTP to dUMP and pyrophosphate. Pssm-ID: 395562 [Multi-domain] Cd Length: 129 Bit Score: 85.42 E-value: 4.23e-19
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Tra5 | COG2801 | Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons]; |
1569-1684 | 7.17e-18 | ||||
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons]; Pssm-ID: 442053 [Multi-domain] Cd Length: 309 Bit Score: 86.75 E-value: 7.17e-18
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zf-CCHC_5 | pfam14787 | GAG-polyprotein viral zinc-finger; |
578-613 | 7.52e-17 | ||||
GAG-polyprotein viral zinc-finger; Pssm-ID: 373297 Cd Length: 36 Bit Score: 75.67 E-value: 7.52e-17
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transpos_IS3 | NF033516 | IS3 family transposase; |
1569-1683 | 2.02e-15 | ||||
IS3 family transposase; Pssm-ID: 468052 [Multi-domain] Cd Length: 369 Bit Score: 80.30 E-value: 2.02e-15
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dut | PRK00601 | dUTP diphosphatase; |
651-771 | 5.91e-14 | ||||
dUTP diphosphatase; Pssm-ID: 234802 [Multi-domain] Cd Length: 150 Bit Score: 71.35 E-value: 5.91e-14
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Dut | COG0756 | dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP ... |
650-771 | 6.33e-14 | ||||
dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]; dUTP pyrophosphatase (dUTPase) is part of the Pathway/BioSystem: Thymidylate biosynthesis Pssm-ID: 440519 [Multi-domain] Cd Length: 143 Bit Score: 70.82 E-value: 6.33e-14
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dut | TIGR00576 | deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is ... |
668-771 | 6.53e-14 | ||||
deoxyuridine 5'-triphosphate nucleotidohydrolase (dut); The main function of these proteins is in maintaining the levels of dUTP in the cell to prevent dUTP incorporation into DNA during DNA replication. Pol proteins in viruses are very similar to this protein family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Changed role from 132 to 123. RTD [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism] Pssm-ID: 273149 [Multi-domain] Cd Length: 142 Bit Score: 70.73 E-value: 6.53e-14
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Integrase_Zn | pfam02022 | Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ... |
1517-1552 | 7.79e-14 | ||||
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552. Pssm-ID: 426567 Cd Length: 36 Bit Score: 67.01 E-value: 7.79e-14
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G-patch | pfam01585 | G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ... |
890-934 | 1.28e-13 | ||||
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines. Pssm-ID: 396249 [Multi-domain] Cd Length: 45 Bit Score: 66.76 E-value: 1.28e-13
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GP41 | pfam00517 | Retroviral envelope protein; This family includes envelope protein from a variety of ... |
2177-2276 | 1.26e-11 | ||||
Retroviral envelope protein; This family includes envelope protein from a variety of retroviruses. It includes the GP41 subunit of the envelope protein complex from human and simian immunodeficiency viruses (HIV and SIV) which mediate membrane fusion during viral entry. The family also includes bovine immunodeficiency virus, feline immunodeficiency virus and Equine infectious anaemia (EIAV). The family also includes the Gp36 protein from mouse mammary tumour virus (MMTV) and human endogenous retroviruses (HERVs). Pssm-ID: 395415 Cd Length: 197 Bit Score: 65.77 E-value: 1.26e-11
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G_patch | smart00443 | glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ... |
890-933 | 1.79e-11 | ||||
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins. Pssm-ID: 197727 [Multi-domain] Cd Length: 47 Bit Score: 60.64 E-value: 1.79e-11
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RNase_HI_eukaryote_like | cd09280 | Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ... |
1388-1507 | 1.84e-10 | ||||
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: 61.04 E-value: 1.84e-10
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RnhA | COG0328 | Ribonuclease HI [Replication, recombination and repair]; |
1385-1512 | 1.00e-07 | ||||
Ribonuclease HI [Replication, recombination and repair]; Pssm-ID: 440097 [Multi-domain] Cd Length: 136 Bit Score: 52.92 E-value: 1.00e-07
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PRK10263 | PRK10263 | DNA translocase FtsK; Provisional |
172-313 | 1.78e-07 | ||||
DNA translocase FtsK; Provisional Pssm-ID: 236669 [Multi-domain] Cd Length: 1355 Bit Score: 57.02 E-value: 1.78e-07
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RT_like | cd00304 | RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ... |
1044-1168 | 3.19e-07 | ||||
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: 50.43 E-value: 3.19e-07
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PHA02517 | PHA02517 | putative transposase OrfB; Reviewed |
1569-1743 | 5.29e-07 | ||||
putative transposase OrfB; Reviewed Pssm-ID: 222853 [Multi-domain] Cd Length: 277 Bit Score: 53.72 E-value: 5.29e-07
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PHA03094 | PHA03094 | dUTPase; Provisional |
694-772 | 6.17e-07 | ||||
dUTPase; Provisional Pssm-ID: 165376 [Multi-domain] Cd Length: 144 Bit Score: 50.92 E-value: 6.17e-07
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PLN02547 | PLN02547 | dUTP pyrophosphatase |
686-771 | 6.39e-07 | ||||
dUTP pyrophosphatase Pssm-ID: 215302 Cd Length: 157 Bit Score: 51.33 E-value: 6.39e-07
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PHA03379 | PHA03379 | EBNA-3A; Provisional |
178-324 | 9.90e-07 | ||||
EBNA-3A; Provisional Pssm-ID: 223066 [Multi-domain] Cd Length: 935 Bit Score: 54.29 E-value: 9.90e-07
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AIR1 | COG5082 | Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ... |
545-601 | 9.19e-06 | ||||
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Pssm-ID: 227414 [Multi-domain] Cd Length: 190 Bit Score: 48.69 E-value: 9.19e-06
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Dcd | COG0717 | dCTP deaminase [Nucleotide transport and metabolism]; dCTP deaminase is part of the Pathway ... |
694-759 | 3.44e-05 | ||||
dCTP deaminase [Nucleotide transport and metabolism]; dCTP deaminase is part of the Pathway/BioSystem: Thymidylate biosynthesis Pssm-ID: 440481 Cd Length: 180 Bit Score: 46.74 E-value: 3.44e-05
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RT_DIRS1 | cd03714 | RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ... |
1044-1168 | 4.60e-05 | ||||
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: 45.03 E-value: 4.60e-05
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zf-CCHC | pfam00098 | Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ... |
544-560 | 6.35e-05 | ||||
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger. Pssm-ID: 395050 [Multi-domain] Cd Length: 18 Bit Score: 41.74 E-value: 6.35e-05
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RP_RTVL_H_like | cd06095 | Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ... |
795-877 | 7.99e-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: 43.09 E-value: 7.99e-05
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PBP1 | COG5180 | PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; ... |
117-305 | 8.00e-05 | ||||
PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]; Pssm-ID: 444064 [Multi-domain] Cd Length: 548 Bit Score: 47.75 E-value: 8.00e-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 ... |
1388-1511 | 1.44e-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: 43.75 E-value: 1.44e-04
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PRK10263 | PRK10263 | DNA translocase FtsK; Provisional |
151-324 | 1.61e-04 | ||||
DNA translocase FtsK; Provisional Pssm-ID: 236669 [Multi-domain] Cd Length: 1355 Bit Score: 47.00 E-value: 1.61e-04
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RNase_HI_prokaryote_like | cd09278 | RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ... |
1387-1447 | 1.87e-04 | ||||
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: 43.63 E-value: 1.87e-04
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PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
158-261 | 2.43e-04 | ||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 46.86 E-value: 2.43e-04
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ZnF_C2HC | smart00343 | zinc finger; |
545-560 | 3.17e-04 | ||||
zinc finger; Pssm-ID: 197667 [Multi-domain] Cd Length: 17 Bit Score: 39.73 E-value: 3.17e-04
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PTZ00368 | PTZ00368 | universal minicircle sequence binding protein (UMSBP); Provisional |
544-598 | 7.18e-04 | ||||
universal minicircle sequence binding protein (UMSBP); Provisional Pssm-ID: 173561 [Multi-domain] Cd Length: 148 Bit Score: 42.10 E-value: 7.18e-04
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dnaA | PRK14086 | chromosomal replication initiator protein DnaA; |
167-305 | 1.48e-03 | ||||
chromosomal replication initiator protein DnaA; Pssm-ID: 237605 [Multi-domain] Cd Length: 617 Bit Score: 43.66 E-value: 1.48e-03
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PHA02703 | PHA02703 | ORF007 dUTPase; Provisional |
659-750 | 2.02e-03 | ||||
ORF007 dUTPase; Provisional Pssm-ID: 165079 Cd Length: 165 Bit Score: 41.12 E-value: 2.02e-03
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IN_DBD_C | pfam00552 | Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ... |
1738-1778 | 2.77e-03 | ||||
Integrase DNA binding 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. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain. Pssm-ID: 425747 Cd Length: 45 Bit Score: 37.76 E-value: 2.77e-03
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RNase_H_Dikarya_like | cd13934 | Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ... |
1389-1453 | 2.87e-03 | ||||
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many of which are uncharacterized. 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. Pssm-ID: 260014 [Multi-domain] Cd Length: 153 Bit Score: 40.64 E-value: 2.87e-03
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PRK02253 | PRK02253 | deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional |
694-751 | 3.20e-03 | ||||
deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional Pssm-ID: 179395 Cd Length: 167 Bit Score: 40.70 E-value: 3.20e-03
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PHA03124 | PHA03124 | dUTPase; Provisional |
668-752 | 3.23e-03 | ||||
dUTPase; Provisional Pssm-ID: 165396 [Multi-domain] Cd Length: 418 Bit Score: 42.24 E-value: 3.23e-03
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RNase_H_like | cd06222 | Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ... |
1389-1447 | 6.86e-03 | ||||
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: 38.83 E-value: 6.86e-03
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Blast search parameters | ||||
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