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Conserved domains on  [gi|52000773|sp|P63135|]
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RecName: Full=Endogenous retrovirus group K member 7 Pol protein; AltName: Full=HERV-K(III) Pol protein; AltName: Full=HERV-K102 Pol protein; AltName: Full=HERV-K_1q22 provirus ancestral Pol protein; Includes: RecName: Full=Reverse transcriptase; Short=RT; Includes: RecName: Full=Ribonuclease H; Short=RNase H; Includes: RecName: Full=Integrase; Short=IN

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 33-245 2.35e-135

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: 415.14  E-value: 2.35e-135
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773   33 PVWVNQWPLPKQKLEALHLLANEQLEKGHIEPSFSPWNSPVFVIQKKSGKWRMLTDLRAVNAVIQPMGPLQPGLPSPAMI 112
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773  113 PKDWPLIIIDLKDCFFTIPLAEQDCEKFAFTIPAINNKEPATRFQWKVLPQGMLNSPTICQTFVGRALQPVREKFSDCYI 192
Cdd:cd01645   81 PKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 52000773  193 IHYIDDILCAAETRDKLIDCYTFLQAEVANAGLAIASDKIQTSTPFHYLGMQI 245
Cdd:cd01645  161 YHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
HERV-K_env_2 pfam13804
Retro-transcribing viruses envelope glycoprotein; This family comes from human endogenous ...
 875-1043 5.13e-126

Retro-transcribing viruses envelope glycoprotein; This family comes from human endogenous retrovirus K envelope glycoproteins.


:

Pssm-ID: 290518  Cd Length: 169  Bit Score: 387.95  E-value: 5.13e-126
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773    875 PVTWMDNPIEIYVNDSVWVPGPIDDRCPAKPEEEGMMINISIGYRYPPICLGRAPGCLMPAVQNWLVEVPTVSPISRFTY 954
Cdd:pfam13804    1 AVTWMDNPIEVYVNDSVWVPGPIDDRCPAKPEEEGMMINISIGYRYPPICLGRAPGCLMPAVQNWLVEVPTVSPISRFTY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773    955 HMVSGMSLRPRVNYLQDFSYQRSLKFRPKGKPCPKEIPKESKNTEVLVWEECVANSAVILQNNEFGTIIDWAPRGQFYHN 1034
Cdd:pfam13804   81 HMVSGMSLRPRVNYLQDFSYQRSLKFRPKGKPCPKEIPKESKNTEVLVWEECVANSAVILQNNEFGTIIDWAPRGQFYHN 160


                   ....*....
gi 52000773   1035 CSGQTQSCP 1043
Cdd:pfam13804  161 CSGQTQSCP 169
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 465-589 7.78e-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: 144.02  E-value: 7.78e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773  465 TVFTDGSS--NGKAAYTGPkERVIKTPYQ---SAQRAELVAVITVLQDF-DQPINIISDSAYVVQATRDVETALIKYSM- 537
Cdd:cd09273    1 TVFTDGSSfkAGYAIVSGT-EIVEAQPLPpgtSAQRAELIALIQALELAkGKPVNIYTDSAYAVHALHLLETIGIERGFl 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 52000773  538 -DDQLNQLFNLLQQTVrKRNFPFYITHIRAHTNLPGPLTKANEQADLLVSSAL 589
Cdd:cd09273   80 kSIKNLSLFLQLLEAV-QRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
HIV-1-like_HR1-HR2 cd09909
heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human ...
 1261-1386 5.69e-35

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: 130.21  E-value: 5.69e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773 1261 VNDWQKNSTRLWNSQSSIDQ--KLANQINDLRQTVIWMGDRLMSLEHRFQLQCDWNTsDFCITPQIYNESEHHWDMVRRH 1338
Cdd:cd09909    1 VQARQLLVTRVQQQQSLIDAieKLEHLLNLLYWVVKQLGARVQALEFRLKIQCHLNL-WGCVTKQPYCHTDVPWNRSWNH 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 52000773 1339 LQGREDNLTLDISKLKEQIFEASKAHLNLVPGTEAIAGV-ADGLANLNP 1386
Cdd:cd09909   80 LQGNDNWISLTWQEWENKIDDLEEKILNLLEEAQNQLEKlADGLLSLDP 128
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 253-317 6.18e-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: 122.04  E-value: 6.18e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 52000773    253 QKIEIRKDTLKTLNDFQKLLGDINWIRPTLGIPTYAMSNLFSILRGDSDLNSKRILTPEATKEIK 317
Cdd:pfam06817    2 QKLQLRKDHLKTLNDFQKLLGDINWIRPYLGITTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 646-739 1.48e-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: 107.79  E-value: 1.48e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773    646 PNALWQMDVTHVPSF--GRLSYVHVTVDTYSHFIWATCQTGE-STSHVKKHLLSCFAVMG-VPEKIKTDNGPGYCSKAFQ 721
Cdd:pfam00665    1 PNQLWQGDFTYIRIPggGGKLYLLVIVDDFSREILAWALSSEmDAELVLDALERAIAFRGgVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 52000773    722 KFLSQWKISHTTGIPYNS 739
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 594-628 2.90e-13

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: 65.09  E-value: 2.90e-13
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 52000773    594 ELHALTHVNAAGLKNKFDVTWKQAKDIVQHCTQCQ 628
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35
IN_DBD_C super family cl02895
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 815-855 4.14e-04

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: 39.30  E-value: 4.14e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 52000773    815 WKDNKNKTWE-IGKVITWGRGFACVsPGENQLPVWIPTRHLK 855
Cdd:pfam00552    3 WKDLLNGLWKgPDPLLWWGRGAVCV-PQDASDPQWVPERLLK 43
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 33-245 2.35e-135

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: 415.14  E-value: 2.35e-135
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773   33 PVWVNQWPLPKQKLEALHLLANEQLEKGHIEPSFSPWNSPVFVIQKKSGKWRMLTDLRAVNAVIQPMGPLQPGLPSPAMI 112
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773  113 PKDWPLIIIDLKDCFFTIPLAEQDCEKFAFTIPAINNKEPATRFQWKVLPQGMLNSPTICQTFVGRALQPVREKFSDCYI 192
Cdd:cd01645   81 PKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 52000773  193 IHYIDDILCAAETRDKLIDCYTFLQAEVANAGLAIASDKIQTSTPFHYLGMQI 245
Cdd:cd01645  161 YHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
HERV-K_env_2 pfam13804
Retro-transcribing viruses envelope glycoprotein; This family comes from human endogenous ...
 875-1043 5.13e-126

Retro-transcribing viruses envelope glycoprotein; This family comes from human endogenous retrovirus K envelope glycoproteins.


Pssm-ID: 290518  Cd Length: 169  Bit Score: 387.95  E-value: 5.13e-126
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773    875 PVTWMDNPIEIYVNDSVWVPGPIDDRCPAKPEEEGMMINISIGYRYPPICLGRAPGCLMPAVQNWLVEVPTVSPISRFTY 954
Cdd:pfam13804    1 AVTWMDNPIEVYVNDSVWVPGPIDDRCPAKPEEEGMMINISIGYRYPPICLGRAPGCLMPAVQNWLVEVPTVSPISRFTY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773    955 HMVSGMSLRPRVNYLQDFSYQRSLKFRPKGKPCPKEIPKESKNTEVLVWEECVANSAVILQNNEFGTIIDWAPRGQFYHN 1034
Cdd:pfam13804   81 HMVSGMSLRPRVNYLQDFSYQRSLKFRPKGKPCPKEIPKESKNTEVLVWEECVANSAVILQNNEFGTIIDWAPRGQFYHN 160


                   ....*....
gi 52000773   1035 CSGQTQSCP 1043
Cdd:pfam13804  161 CSGQTQSCP 169
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 76-245 3.92e-45

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: 161.70  E-value: 3.92e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773     76 IQKKS-GKWRML----TDLRAVNAVIQP-------MGPLQPGLPSPAM-IPKDWPLIIIDLKDCFFTIPLAEQDCEKFAF 142
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773    143 TIPAINNK----EPATRFQWKVLPQGMLNSPTICQTFVGRALQPVREKFsDCYIIHYIDDILCAAETRDKLIDCYTFLQA 218
Cdd:pfam00078   81 TTPPININwngeLSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRA-GLTLVRYADDILIFSKSEEEHQEALEEVLE 159

                          170       180       190
                   ....*....|....*....|....*....|
gi 52000773    219 EVANAGLAIASDKIQ---TSTPFHYLGMQI 245
Cdd:pfam00078  160 WLKESGLKINPEKTQfflKSKEVKYLGVTL 189
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 465-589 7.78e-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: 144.02  E-value: 7.78e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773  465 TVFTDGSS--NGKAAYTGPkERVIKTPYQ---SAQRAELVAVITVLQDF-DQPINIISDSAYVVQATRDVETALIKYSM- 537
Cdd:cd09273    1 TVFTDGSSfkAGYAIVSGT-EIVEAQPLPpgtSAQRAELIALIQALELAkGKPVNIYTDSAYAVHALHLLETIGIERGFl 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 52000773  538 -DDQLNQLFNLLQQTVrKRNFPFYITHIRAHTNLPGPLTKANEQADLLVSSAL 589
Cdd:cd09273   80 kSIKNLSLFLQLLEAV-QRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
HIV-1-like_HR1-HR2 cd09909
heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human ...
 1261-1386 5.69e-35

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: 130.21  E-value: 5.69e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773 1261 VNDWQKNSTRLWNSQSSIDQ--KLANQINDLRQTVIWMGDRLMSLEHRFQLQCDWNTsDFCITPQIYNESEHHWDMVRRH 1338
Cdd:cd09909    1 VQARQLLVTRVQQQQSLIDAieKLEHLLNLLYWVVKQLGARVQALEFRLKIQCHLNL-WGCVTKQPYCHTDVPWNRSWNH 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 52000773 1339 LQGREDNLTLDISKLKEQIFEASKAHLNLVPGTEAIAGV-ADGLANLNP 1386
Cdd:cd09909   80 LQGNDNWISLTWQEWENKIDDLEEKILNLLEEAQNQLEKlADGLLSLDP 128
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 253-317 6.18e-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: 122.04  E-value: 6.18e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 52000773    253 QKIEIRKDTLKTLNDFQKLLGDINWIRPTLGIPTYAMSNLFSILRGDSDLNSKRILTPEATKEIK 317
Cdd:pfam06817    2 QKLQLRKDHLKTLNDFQKLLGDINWIRPYLGITTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 461-590 1.17e-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: 1.17e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773    461 ENALTVFTDGSSN-----GKAAYTGPKERV-IKTPY---QSAQRAELVAVITVLQD--FDQPINIISDSAYVVQ-ATRDV 528
Cdd:pfam00075    1 PKAVTVYTDGSCLgnpgpGGAGAVLYRGHEnISAPLpgrTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGgITQWV 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 52000773    529 ETAlIKYSMDDQLNQ-------LFNLLQQTVRKRNfpFYITHIRAHTNLPGpltkaNEQADLLVSSALI 590
Cdd:pfam00075   81 HGW-KKNGWPTTSEGkpvknkdLWQLLKALCKKHQ--VYWQWVKGHAGNPG-----NEMADRLAKQGAE 141
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 646-739 1.48e-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: 107.79  E-value: 1.48e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773    646 PNALWQMDVTHVPSF--GRLSYVHVTVDTYSHFIWATCQTGE-STSHVKKHLLSCFAVMG-VPEKIKTDNGPGYCSKAFQ 721
Cdd:pfam00665    1 PNQLWQGDFTYIRIPggGGKLYLLVIVDDFSREILAWALSSEmDAELVLDALERAIAFRGgVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 52000773    722 KFLSQWKISHTTGIPYNS 739
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
transpos_IS481 NF033577
IS481 family transposase; null
 646-767 2.58e-21

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 95.74  E-value: 2.58e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773   646 PNALWQMDVTHVPSF---GRLsYVHVTVDTYSHFIWATCQTGESTSHVKKHLLSCFAVMGVP-EKIKTDNGPGYCSKA-- 719
Cdd:NF033577  127 PGELWHIDIKKLGRIpdvGRL-YLHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGIPiRRVLTDNGSEFRSRAhg 205

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 52000773   720 FQKFLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQKEGGDSKE 767
Cdd:NF033577  206 FELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEFAYARPYESLAE 253
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
646-761 4.66e-18

Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 86.75  E-value: 4.66e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773  646 PNALWQMDVTHVPSFGRLSYVHVTVDTYSHFI--WATCQTgESTSHVKKHLLSCFAVMGVPEK--IKTDNGPGYCSKAFQ 721
Cdd:COG2801  148 PNQVWVTDITYIPTAEGWLYLAAVIDLFSREIvgWSVSDS-MDAELVVDALEMAIERRGPPKPliLHSDNGSQYTSKAYQ 226

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 52000773  722 KFLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQKE 761
Cdd:COG2801  227 ELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYELLYRRR 266
transpos_IS3 NF033516
IS3 family transposase;
646-760 1.20e-15

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 80.30  E-value: 1.20e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773   646 PNALWQMDVTHVPSFGRLSYVHVTVDTYSHFI--WATcQTGESTSHVKKHLLSCFAVMGVPEK--IKTDNGPGYCSKAFQ 721
Cdd:NF033516  215 PNQVWVTDITYIRTAEGWLYLAVVLDLFSREIvgWSV-STSMSAELVLDALEMAIEWRGKPEGliLHSDNGSQYTSKAYR 293

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 52000773   722 KFLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQK 760
Cdd:NF033516  294 EWLKEHGITQSMSRPGNCWDNAVAESFFGTLKRECLYRR 332
GP41 pfam00517
Retroviral envelope protein; This family includes envelope protein from a variety of ...
 1254-1393 3.87e-15

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: 75.40  E-value: 3.87e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773   1254 SVQSVNFVNDWQKNSTRLWNSQSSIDQKLANQINDLRQTVIWMGDRLMSLEHRFQLQCDWNTSDFCITPQIYNESEhHWD 1333
Cdd:pfam00517    9 SIQAATLVDGLQYNVTKVMGTQQDIDKKLEARLSALEDVVRVLGEQVQSLKFRMKLQCHANYKWICVTKVPYNASD-PWD 87

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 52000773   1334 MVRRHLQG--REDNLTLDISKLKEQIFEASKAHLNLVPGTEAIAGVADGLANLNPVT---WVKTI 1393
Cdd:pfam00517   88 KVKKHLQGiwNNTEVSYDLLQLHNLIEDIQNQQEKTLNELDTLDNWAQSLFNWFPSLnslWRSYI 152
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 594-628 2.90e-13

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: 65.09  E-value: 2.90e-13
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 52000773    594 ELHALTHVNAAGLKNKFDVTWKQAKDIVQHCTQCQ 628
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
462-589 6.24e-08

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 52.92  E-value: 6.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773  462 NALTVFTDGSSN---GKAAY-----TGPKERVIKTPYQSA--QRAELVAVITVLQ----DFDQPINIISDSAYVVQATRD 527
Cdd:COG0328    1 KMIEIYTDGACRgnpGPGGWgavirYGGEEKELSGGLGDTtnNRAELTALIAALEalkeLGPCEVEIYTDSQYVVNQITG 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 52000773  528 VETALIKYSMDDQLNQ-LFNLLQQTVRKRNFPFyiTHIRAHTNLPGpltkaNEQADLLVSSAL 589
Cdd:COG0328   81 WIHGWKKNGWKPVKNPdLWQRLDELLARHKVTF--EWVKGHAGHPG-----NERADALANKAL 136
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 646-820 3.22e-07

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 53.72  E-value: 3.22e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773   646 PNALWQMDVTHVPSFGRLSYVHVTVDTYSHFI--WATCQTGESTsHVKKHLLSCFAVMGVPEK--IKTDNGPGYCSKAFQ 721
Cdd:PHA02517  109 PNQLWVADFTYVSTWQGWVYVAFIIDVFARRIvgWRVSSSMDTD-FVLDALEQALWARGRPGGliHHSDKGSQYVSLAYT 187

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773   722 KFLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQKEGGDSKEcttpqmqlnLALYTLNFLNIYRNQTTTSAEQHLT 801
Cdd:PHA02517  188 QRLKEAGIRASTGSRGDSYDNAPAESINGLYKAEVIHRVSWKNREE---------VELATLEWVAWYNNRRLHERLGYTP 258

                         170
                  ....*....|....*....
gi 52000773   802 gkknsPHEGKLIWWKDNKN 820
Cdd:PHA02517  259 -----PAEAEKAYYASIGN 272
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 815-855 4.14e-04

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: 39.30  E-value: 4.14e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 52000773    815 WKDNKNKTWE-IGKVITWGRGFACVsPGENQLPVWIPTRHLK 855
Cdd:pfam00552    3 WKDLLNGLWKgPDPLLWWGRGAVCV-PQDASDPQWVPERLLK 43
 
Name Accession Description Interval E-value
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 33-245 2.35e-135

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: 415.14  E-value: 2.35e-135
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773   33 PVWVNQWPLPKQKLEALHLLANEQLEKGHIEPSFSPWNSPVFVIQKKSGKWRMLTDLRAVNAVIQPMGPLQPGLPSPAMI 112
Cdd:cd01645    1 PVWIKQWPLTEEKLEALTELVTEQLKEGHIEPSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHPAAL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773  113 PKDWPLIIIDLKDCFFTIPLAEQDCEKFAFTIPAINNKEPATRFQWKVLPQGMLNSPTICQTFVGRALQPVREKFSDCYI 192
Cdd:cd01645   81 PKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVI 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 52000773  193 IHYIDDILCAAETRDKLIDCYTFLQAEVANAGLAIASDKIQTSTPFHYLGMQI 245
Cdd:cd01645  161 YHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEPPFQYLGYEL 213
HERV-K_env_2 pfam13804
Retro-transcribing viruses envelope glycoprotein; This family comes from human endogenous ...
 875-1043 5.13e-126

Retro-transcribing viruses envelope glycoprotein; This family comes from human endogenous retrovirus K envelope glycoproteins.


Pssm-ID: 290518  Cd Length: 169  Bit Score: 387.95  E-value: 5.13e-126
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773    875 PVTWMDNPIEIYVNDSVWVPGPIDDRCPAKPEEEGMMINISIGYRYPPICLGRAPGCLMPAVQNWLVEVPTVSPISRFTY 954
Cdd:pfam13804    1 AVTWMDNPIEVYVNDSVWVPGPIDDRCPAKPEEEGMMINISIGYRYPPICLGRAPGCLMPAVQNWLVEVPTVSPISRFTY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773    955 HMVSGMSLRPRVNYLQDFSYQRSLKFRPKGKPCPKEIPKESKNTEVLVWEECVANSAVILQNNEFGTIIDWAPRGQFYHN 1034
Cdd:pfam13804   81 HMVSGMSLRPRVNYLQDFSYQRSLKFRPKGKPCPKEIPKESKNTEVLVWEECVANSAVILQNNEFGTIIDWAPRGQFYHN 160


                   ....*....
gi 52000773   1035 CSGQTQSCP 1043
Cdd:pfam13804  161 CSGQTQSCP 169
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 76-245 3.92e-45

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: 161.70  E-value: 3.92e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773     76 IQKKS-GKWRML----TDLRAVNAVIQP-------MGPLQPGLPSPAM-IPKDWPLIIIDLKDCFFTIPLAEQDCEKFAF 142
Cdd:pfam00078    1 IPKKGkGKYRPIsllsIDYKALNKIIVKrlkpenlDSPPQPGFRPGLAkLKKAKWFLKLDLKKAFDQVPLDELDRKLTAF 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773    143 TIPAINNK----EPATRFQWKVLPQGMLNSPTICQTFVGRALQPVREKFsDCYIIHYIDDILCAAETRDKLIDCYTFLQA 218
Cdd:pfam00078   81 TTPPININwngeLSGGRYEWKGLPQGLVLSPALFQLFMNELLRPLRKRA-GLTLVRYADDILIFSKSEEEHQEALEEVLE 159

                          170       180       190
                   ....*....|....*....|....*....|
gi 52000773    219 EVANAGLAIASDKIQ---TSTPFHYLGMQI 245
Cdd:pfam00078  160 WLKESGLKINPEKTQfflKSKEVKYLGVTL 189
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 465-589 7.78e-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: 144.02  E-value: 7.78e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773  465 TVFTDGSS--NGKAAYTGPkERVIKTPYQ---SAQRAELVAVITVLQDF-DQPINIISDSAYVVQATRDVETALIKYSM- 537
Cdd:cd09273    1 TVFTDGSSfkAGYAIVSGT-EIVEAQPLPpgtSAQRAELIALIQALELAkGKPVNIYTDSAYAVHALHLLETIGIERGFl 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 52000773  538 -DDQLNQLFNLLQQTVrKRNFPFYITHIRAHTNLPGPLTKANEQADLLVSSAL 589
Cdd:cd09273   80 kSIKNLSLFLQLLEAV-QRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
RT_ZFREV_like cd03715
RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the ...
 33-245 3.45e-37

RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.


Pssm-ID: 239685 [Multi-domain]  Cd Length: 210  Bit Score: 139.41  E-value: 3.45e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773   33 PVWVNQWPLPKQKLEALHLLANEQLEKGHIEPSFSPWNSPVFVIQKKSG-KWRMLTDLRAVNAVIqpmGPLQPGLPSPAM 111
Cdd:cd03715    1 PVNQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGnDYRMVQDLRLVNQAV---LPIHPAVPNPYT 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773  112 I-----PKDWPLIIIDLKDCFFTIPLAEQDCEKFAFTIPAinnkepaTRFQWKVLPQGMLNSPTICQTFVGRALQPVREK 186
Cdd:cd03715   78 LlsllpPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEG-------QQYTFTRLPQGFKNSPTLFHEALARDLAPFPLE 150

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773  187 FSDCYIIHYIDDILCAAETRDKLIDCYTFLQAEVANAGLAIASDKIQ-TSTPFHYLGMQI 245
Cdd:cd03715  151 HEGTILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQiCRAEVKFLGVVW 210
HIV-1-like_HR1-HR2 cd09909
heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human ...
 1261-1386 5.69e-35

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: 130.21  E-value: 5.69e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773 1261 VNDWQKNSTRLWNSQSSIDQ--KLANQINDLRQTVIWMGDRLMSLEHRFQLQCDWNTsDFCITPQIYNESEHHWDMVRRH 1338
Cdd:cd09909    1 VQARQLLVTRVQQQQSLIDAieKLEHLLNLLYWVVKQLGARVQALEFRLKIQCHLNL-WGCVTKQPYCHTDVPWNRSWNH 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 52000773 1339 LQGREDNLTLDISKLKEQIFEASKAHLNLVPGTEAIAGV-ADGLANLNP 1386
Cdd:cd09909   80 LQGNDNWISLTWQEWENKIDDLEEKILNLLEEAQNQLEKlADGLLSLDP 128
RVT_thumb pfam06817
Reverse transcriptase thumb domain; This domain is known as the thumb domain. It is composed ...
 253-317 6.18e-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: 122.04  E-value: 6.18e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 52000773    253 QKIEIRKDTLKTLNDFQKLLGDINWIRPTLGIPTYAMSNLFSILRGDSDLNSKRILTPEATKEIK 317
Cdd:pfam06817    2 QKLQLRKDHLKTLNDFQKLLGDINWIRPYLGITTYDLKPLFSLLRGDSDLTSPRTLTEEAEEALQ 66
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 461-590 1.17e-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: 1.17e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773    461 ENALTVFTDGSSN-----GKAAYTGPKERV-IKTPY---QSAQRAELVAVITVLQD--FDQPINIISDSAYVVQ-ATRDV 528
Cdd:pfam00075    1 PKAVTVYTDGSCLgnpgpGGAGAVLYRGHEnISAPLpgrTTNNRAELQAVIEALKAlkSPSKVNIYTDSQYVIGgITQWV 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 52000773    529 ETAlIKYSMDDQLNQ-------LFNLLQQTVRKRNfpFYITHIRAHTNLPGpltkaNEQADLLVSSALI 590
Cdd:pfam00075   81 HGW-KKNGWPTTSEGkpvknkdLWQLLKALCKKHQ--VYWQWVKGHAGNPG-----NEMADRLAKQGAE 141
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 646-739 1.48e-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: 107.79  E-value: 1.48e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773    646 PNALWQMDVTHVPSF--GRLSYVHVTVDTYSHFIWATCQTGE-STSHVKKHLLSCFAVMG-VPEKIKTDNGPGYCSKAFQ 721
Cdd:pfam00665    1 PNQLWQGDFTYIRIPggGGKLYLLVIVDDFSREILAWALSSEmDAELVLDALERAIAFRGgVPLIIHSDNGSEYTSKAFR 80

                           90
                   ....*....|....*...
gi 52000773    722 KFLSQWKISHTTGIPYNS 739
Cdd:pfam00665   81 EFLKDLGIKPSFSRPGNP 98
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 60-207 7.94e-27

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


Pssm-ID: 238825  Cd Length: 177  Bit Score: 108.45  E-value: 7.94e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773   60 GHIEPSFSPWNSPVFVIQKKSGKWRMLTDLRAVNAVIQPM-GPlqpgLPSP----AMIPKDWPLIIIDLKDCFFTIPLAE 134
Cdd:cd01647    1 GIIEPSSSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDrYP----LPTIdellEELAGAKVFSKLDLRSGYHQIPLAE 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 52000773  135 QDCEKFAFTIpainnkePATRFQWKVLPQGMLNSPTICQTFVGRALQPVREKFsdcyIIHYIDDILCAAETRD 207
Cdd:cd01647   77 ESRPKTAFRT-------PFGLYEYTRMPFGLKNAPATFQRLMNKILGDLLGDF----VEVYLDDILVYSKTEE 138
transpos_IS481 NF033577
IS481 family transposase; null
 646-767 2.58e-21

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 95.74  E-value: 2.58e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773   646 PNALWQMDVTHVPSF---GRLsYVHVTVDTYSHFIWATCQTGESTSHVKKHLLSCFAVMGVP-EKIKTDNGPGYCSKA-- 719
Cdd:NF033577  127 PGELWHIDIKKLGRIpdvGRL-YLHTAIDDHSRFAYAELYPDETAETAADFLRRAFAEHGIPiRRVLTDNGSEFRSRAhg 205

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 52000773   720 FQKFLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQKEGGDSKE 767
Cdd:NF033577  206 FELALAELGIEHRRTRPYHPQTNGKVERFHRTLKDEFAYARPYESLAE 253
Tra5 COG2801
Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];
646-761 4.66e-18

Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442053 [Multi-domain]  Cd Length: 309  Bit Score: 86.75  E-value: 4.66e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773  646 PNALWQMDVTHVPSFGRLSYVHVTVDTYSHFI--WATCQTgESTSHVKKHLLSCFAVMGVPEK--IKTDNGPGYCSKAFQ 721
Cdd:COG2801  148 PNQVWVTDITYIPTAEGWLYLAAVIDLFSREIvgWSVSDS-MDAELVVDALEMAIERRGPPKPliLHSDNGSQYTSKAYQ 226

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 52000773  722 KFLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQKE 761
Cdd:COG2801  227 ELLKKLGITQSMSRPGNPQDNAFIESFFGTLKYELLYRRR 266
transpos_IS3 NF033516
IS3 family transposase;
646-760 1.20e-15

IS3 family transposase;


Pssm-ID: 468052 [Multi-domain]  Cd Length: 369  Bit Score: 80.30  E-value: 1.20e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773   646 PNALWQMDVTHVPSFGRLSYVHVTVDTYSHFI--WATcQTGESTSHVKKHLLSCFAVMGVPEK--IKTDNGPGYCSKAFQ 721
Cdd:NF033516  215 PNQVWVTDITYIRTAEGWLYLAVVLDLFSREIvgWSV-STSMSAELVLDALEMAIEWRGKPEGliLHSDNGSQYTSKAYR 293

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 52000773   722 KFLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQK 760
Cdd:NF033516  294 EWLKEHGITQSMSRPGNCWDNAVAESFFGTLKRECLYRR 332
GP41 pfam00517
Retroviral envelope protein; This family includes envelope protein from a variety of ...
 1254-1393 3.87e-15

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: 75.40  E-value: 3.87e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773   1254 SVQSVNFVNDWQKNSTRLWNSQSSIDQKLANQINDLRQTVIWMGDRLMSLEHRFQLQCDWNTSDFCITPQIYNESEhHWD 1333
Cdd:pfam00517    9 SIQAATLVDGLQYNVTKVMGTQQDIDKKLEARLSALEDVVRVLGEQVQSLKFRMKLQCHANYKWICVTKVPYNASD-PWD 87

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 52000773   1334 MVRRHLQG--REDNLTLDISKLKEQIFEASKAHLNLVPGTEAIAGVADGLANLNPVT---WVKTI 1393
Cdd:pfam00517   88 KVKKHLQGiwNNTEVSYDLLQLHNLIEDIQNQQEKTLNELDTLDNWAQSLFNWFPSLnslWRSYI 152
Integrase_Zn pfam02022
Integrase Zinc binding domain; Integrase mediates integration of a DNA copy of the viral ...
 594-628 2.90e-13

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: 65.09  E-value: 2.90e-13
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 52000773    594 ELHALTHVNAAGLKNKFDVTWKQAKDIVQHCTQCQ 628
Cdd:pfam02022    1 ELHSLHHVNAKALRKKFGITRKQARDIVQSCPTCQ 35
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 465-584 1.14e-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: 1.14e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773  465 TVFTDGSS--NGKAA-------YTGPK------ERVIKtPYQSAQRAELVAVITVLQDFDQ----PINIISDSAYVVQA- 524
Cdd:cd09280    1 VVYTDGSClnNGKPGaragigvYFGPGdprnvsEPLPG-RKQTNNRAELLAVIHALEQAPEegirKLEIRTDSKYAINCi 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 52000773  525 TRDVETALIKYSMDDQLNQLFN--LLQQTV---RKRNFPFYITHIRAHTNLPGpltkaNEQADLL 584
Cdd:cd09280   80 TKWIPKWKKNGWKTSKGKPVKNqdLIKELDkllRKRGIKVKFEHVKGHSGDPG-----NEEADRL 139
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
462-589 6.24e-08

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 52.92  E-value: 6.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773  462 NALTVFTDGSSN---GKAAY-----TGPKERVIKTPYQSA--QRAELVAVITVLQ----DFDQPINIISDSAYVVQATRD 527
Cdd:COG0328    1 KMIEIYTDGACRgnpGPGGWgavirYGGEEKELSGGLGDTtnNRAELTALIAALEalkeLGPCEVEIYTDSQYVVNQITG 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 52000773  528 VETALIKYSMDDQLNQ-LFNLLQQTVRKRNFPFyiTHIRAHTNLPGpltkaNEQADLLVSSAL 589
Cdd:COG0328   81 WIHGWKKNGWKPVKNPdLWQRLDELLARHKVTF--EWVKGHAGHPG-----NERADALANKAL 136
PHA02517 PHA02517
putative transposase OrfB; Reviewed
 646-820 3.22e-07

putative transposase OrfB; Reviewed


Pssm-ID: 222853 [Multi-domain]  Cd Length: 277  Bit Score: 53.72  E-value: 3.22e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773   646 PNALWQMDVTHVPSFGRLSYVHVTVDTYSHFI--WATCQTGESTsHVKKHLLSCFAVMGVPEK--IKTDNGPGYCSKAFQ 721
Cdd:PHA02517  109 PNQLWVADFTYVSTWQGWVYVAFIIDVFARRIvgWRVSSSMDTD-FVLDALEQALWARGRPGGliHHSDKGSQYVSLAYT 187

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773   722 KFLSQWKISHTTGIPYNSQGQAIVERTNRTLKTQLVKQKEGGDSKEcttpqmqlnLALYTLNFLNIYRNQTTTSAEQHLT 801
Cdd:PHA02517  188 QRLKEAGIRASTGSRGDSYDNAPAESINGLYKAEVIHRVSWKNREE---------VELATLEWVAWYNNRRLHERLGYTP 258

                         170
                  ....*....|....*....
gi 52000773   802 gkknsPHEGKLIWWKDNKN 820
Cdd:PHA02517  259 -----PAEAEKAYYASIGN 272
RT_like cd00304
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
 121-245 1.34e-06

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: 48.12  E-value: 1.34e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773  121 IDLKDCFFTIPLaeqdcekfaftipainnkepatrfqwkvlPQGMLNSPTICQTFVGRALQPVREKFSDCYIIHYIDDIL 200
Cdd:cd00304    1 FDVKSFFTSIPL-----------------------------PQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLV 51

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 52000773  201 CAAETRDKLIDCYTFLQAEvANAGLAIASDKIQTST---PFHYLGMQI 245
Cdd:cd00304   52 VIAKSEQQAVKKRELEEFL-ARLGLNLSDEKTQFTEkekKFKFLGILV 98
RT_DIRS1 cd03714
RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members ...
 121-245 4.32e-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: 44.26  E-value: 4.32e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773  121 IDLKDCFFTIPLAEQ--DCEKFAFTIPAinnkepatrFQWKVLPQGMLNSPTICQTFVGRALQPVREKFSDcyIIHYIDD 198
Cdd:cd03714    1 VDLKDAYFHIPILPRsrDLLGFAWQGET---------YQFKALPFGLSLAPRVFTKVVEALLAPLRLLGVR--IFSYLDD 69

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 52000773  199 ILCAAET---RDKLIDCytFLQAEVANAGLAIASDKiQTSTPFH---YLGMQI 245
Cdd:cd03714   70 LLIIASSiktSEAVLRH--LRATLLANLGFTLNLEK-SKLGPTQritFLGLEL 119
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 465-588 9.00e-05

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: 9.00e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773  465 TVFTDGSSNGK---AAYTGPKERVIKT------PYQSAQRAELVAV------ITVLQDFDQPINIISDSAYVVQATRDVE 529
Cdd:cd09276    1 VIYTDGSKLEGsvgAGFVIYRGGEVISrsyrlgTHASVFDAELEAIlealelALATARRARKVTIFTDSQSALQALRNPR 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 52000773  530 TalikySMDDQLNQLFNLLQQTVRKRNFPFYITHIRAHTNLPGpltkaNEQADLLVSSA 588
Cdd:cd09276   81 R-----SSGQVILIRILRLLRLLKAKGVKVRLRWVPGHVGIEG-----NEAADRLAKEA 129
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 464-524 1.78e-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: 43.24  E-value: 1.78e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 52000773  464 LTVFTDGSS---NGKAAY-----TGPKERVIKTPYQSA--QRAELVAVITVLQDF--DQPINIISDSAYVVQA 524
Cdd:cd09278    2 IVIYTDGAClgnPGPGGWaavirYGDHEKELSGGEPGTtnNRMELTAAIEALEALkePCPVTIYTDSQYVING 74
IN_DBD_C pfam00552
Integrase DNA binding domain; Integrase mediates integration of a DNA copy of the viral genome ...
 815-855 4.14e-04

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: 39.30  E-value: 4.14e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 52000773    815 WKDNKNKTWE-IGKVITWGRGFACVsPGENQLPVWIPTRHLK 855
Cdd:pfam00552    3 WKDLLNGLWKgPDPLLWWGRGAVCV-PQDASDPQWVPERLLK 43
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 466-524 2.16e-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: 40.26  E-value: 2.16e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52000773  466 VFTDG--SSNGKAA-------YTGPK---------ERVIKTPyQSAQRAELVAVITVLQDFDQPIN----------IISD 517
Cdd:cd13934    2 VYIDGacRNNGRPDaragygvYFGPDssynvsgrlEDTGGHP-QTSQRAELRAAIAALRFRSWIIDpdgeglktvvIATD 80


                 ....*..
gi 52000773  518 SAYVVQA 524
Cdd:cd13934   81 SEYVVKG 87
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 466-524 4.30e-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: 4.30e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 52000773  466 VFTDGSS---NGKAAY----TGPKERVI-----KTPYQSAQRAELVAVITVLQ----DFDQPINIISDSAYVVQA 524
Cdd:cd06222    1 INVDGSCrgnPGPAGIggvlRDHEGGWLggfalKIGAPTALEAELLALLLALElaldLGYLKVIIESDSKYVVDL 75
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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