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Conserved domains on  [gi|1731040072|gb|TYK27876|]
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uncharacterized protein E5676_scaffold384G00590 [Cucumis melo var. makuwa]

Protein Classification

Ty1/Copia family ribonuclease HI( domain architecture ID 10276979)

Ty1/Copia family ribonuclease HI in long-term repeat (LTR) retroelements is involved in the 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

EC:  2.7.7.49
Gene Ontology:  GO:0003964|GO:0032197|GO:0003723

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 168-245 1.46e-33

Ty1/Copia 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 eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing 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. The Ty1/Copia family is widely distributed among the genomes of plants, fungi, and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


:

Pssm-ID: 260004  Cd Length: 140  Bit Score: 125.66  E-value: 1.46e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731040072 168 YCDADWAGSGDDRK----------------------------TEAEYIIAGSGCTQLIWMKNMLHEYGLDQD-TMTLYCD 218
Cdd:cd09272     3 YSDADWAGDPDDRRstsgyvfflgggpiswkskkqttvalssTEAEYIALAEAAKEALWLRRLLEELGIPLDgPTTIYCD 82

                          90       100
                  ....*....|....*....|....*..
gi 1731040072 219 NMSAIDISKNPVQHSRTKHIDIRHHFI 245
Cdd:cd09272    83 NQSAIALAKNPVFHSRTKHIDIRYHFI 109
RVT_2 super family cl06662
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1-100 1.03e-23

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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


The actual alignment was detected with superfamily member pfam07727:

Pssm-ID: 400190  Cd Length: 243  Bit Score: 100.74  E-value: 1.03e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731040072   1 MDVKSAFLNGYLNEEVYVAQPKGFVDSEHPKNVFKLNKALYGLKQAPRAWYELLT----------------VYLRG---- 60
Cdd:pfam07727  81 MDVSSAFLNGDIDEEIYVKQPPGFNIDNESGKVWQLNKSLYGLKQAPYMWNTCITkvlmdlnfepdtaesgMYCRGfgen 160

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1731040072  61 -------------------LVNNFINIMQSEFEMSMVGELSYFLGLQIKQKNDGIFISQ 100
Cdd:pfam07727 161 klivglyvddmfitgsditIINDFKLELAKHFKMKDLGDISEFLGIEFIQIAGGIRLSQ 219
Transposase_32 pfam20167
Putative plant transposon protein; This entry represents a likely transposon related protein ...
 484-641 2.84e-15

Putative plant transposon protein; This entry represents a likely transposon related protein from plants. This entry appears related to ORF1 from the ATHILA group of Arabidopsis thaliana retrotransposons pfam03078.


:

Pssm-ID: 466318  Cd Length: 177  Bit Score: 74.47  E-value: 2.84e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731040072 484 ELIRELIVNLPDEFSNPSspdYQTVHIRWFKFVISPTVINGFLGNIVDIDCSPSCPT--EILATVLSGGTlsTWPVN-GI 560
Cdd:pfam20167  18 TLVREFYANAPELVPDDK---VYSSYVRGKRIDFSPETINEFLEICQFGLYLEEGKTleDLARVLCVPGG--RWLRNlGI 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731040072 561 PAAALSIKYATLHKIGIANWFPSSHASSISAALGTFLYQICNDDKVDTGAFVYNQLLRHVGSFGVKVPIALPRFFSSLLL 640
Cdd:pfam20167  93 RKADLNPAAKYWFGFIRSNLMPSSNESDLTHDRALLLYCILKGKPINLGRIIIDEIKMCARSKNSKTPLPFPSLITRLCR 172


                  .
gi 1731040072 641 H 641
Cdd:pfam20167 173 R 173
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 269-458 9.86e-05

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 46.08  E-value: 9.86e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731040072  269 APNVTISSPPPVRQARESLRPESVpevgesSLPISPTMHVPRAPEVVVSDMDSDDQDDSSSIEGVFIPTPGGPRrSPAIP 348
Cdd:PHA03247  2770 APPAAPAAGPPRRLTRPAVASLSE------SRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPT-APPPP 2842

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731040072  349 SGYSP-------FVHPS---RSKSPASKPDVVPAhISGNTTVAHEEQTGVSRNEDHFAsFNQDDIPPEDIPPSTNDPTAP 418
Cdd:PHA03247  2843 PGPPPpslplggSVAPGgdvRRRPPSRSPAAKPA-APARPPVRRLARPAVSRSTESFA-LPPDQPERPPQPQAPPPPQPQ 2920

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 1731040072  419 STEGRIESPQPPKRKTQQVRRNITTKTGRKRTPTNIPSVP 458
Cdd:PHA03247  2921 PQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVP 2960
 
Name Accession Description Interval E-value
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 168-245 1.46e-33

Ty1/Copia 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 eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing 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. The Ty1/Copia family is widely distributed among the genomes of plants, fungi, and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260004  Cd Length: 140  Bit Score: 125.66  E-value: 1.46e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731040072 168 YCDADWAGSGDDRK----------------------------TEAEYIIAGSGCTQLIWMKNMLHEYGLDQD-TMTLYCD 218
Cdd:cd09272     3 YSDADWAGDPDDRRstsgyvfflgggpiswkskkqttvalssTEAEYIALAEAAKEALWLRRLLEELGIPLDgPTTIYCD 82

                          90       100
                  ....*....|....*....|....*..
gi 1731040072 219 NMSAIDISKNPVQHSRTKHIDIRHHFI 245
Cdd:cd09272    83 NQSAIALAKNPVFHSRTKHIDIRYHFI 109
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1-100 1.03e-23

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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


Pssm-ID: 400190  Cd Length: 243  Bit Score: 100.74  E-value: 1.03e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731040072   1 MDVKSAFLNGYLNEEVYVAQPKGFVDSEHPKNVFKLNKALYGLKQAPRAWYELLT----------------VYLRG---- 60
Cdd:pfam07727  81 MDVSSAFLNGDIDEEIYVKQPPGFNIDNESGKVWQLNKSLYGLKQAPYMWNTCITkvlmdlnfepdtaesgMYCRGfgen 160

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1731040072  61 -------------------LVNNFINIMQSEFEMSMVGELSYFLGLQIKQKNDGIFISQ 100
Cdd:pfam07727 161 klivglyvddmfitgsditIINDFKLELAKHFKMKDLGDISEFLGIEFIQIAGGIRLSQ 219
Transposase_32 pfam20167
Putative plant transposon protein; This entry represents a likely transposon related protein ...
 484-641 2.84e-15

Putative plant transposon protein; This entry represents a likely transposon related protein from plants. This entry appears related to ORF1 from the ATHILA group of Arabidopsis thaliana retrotransposons pfam03078.


Pssm-ID: 466318  Cd Length: 177  Bit Score: 74.47  E-value: 2.84e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731040072 484 ELIRELIVNLPDEFSNPSspdYQTVHIRWFKFVISPTVINGFLGNIVDIDCSPSCPT--EILATVLSGGTlsTWPVN-GI 560
Cdd:pfam20167  18 TLVREFYANAPELVPDDK---VYSSYVRGKRIDFSPETINEFLEICQFGLYLEEGKTleDLARVLCVPGG--RWLRNlGI 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731040072 561 PAAALSIKYATLHKIGIANWFPSSHASSISAALGTFLYQICNDDKVDTGAFVYNQLLRHVGSFGVKVPIALPRFFSSLLL 640
Cdd:pfam20167  93 RKADLNPAAKYWFGFIRSNLMPSSNESDLTHDRALLLYCILKGKPINLGRIIIDEIKMCARSKNSKTPLPFPSLITRLCR 172


                  .
gi 1731040072 641 H 641
Cdd:pfam20167 173 R 173
PHA03247 PHA03247
large tegument protein UL36; Provisional
 269-458 9.86e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 46.08  E-value: 9.86e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731040072  269 APNVTISSPPPVRQARESLRPESVpevgesSLPISPTMHVPRAPEVVVSDMDSDDQDDSSSIEGVFIPTPGGPRrSPAIP 348
Cdd:PHA03247  2770 APPAAPAAGPPRRLTRPAVASLSE------SRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPT-APPPP 2842

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731040072  349 SGYSP-------FVHPS---RSKSPASKPDVVPAhISGNTTVAHEEQTGVSRNEDHFAsFNQDDIPPEDIPPSTNDPTAP 418
Cdd:PHA03247  2843 PGPPPpslplggSVAPGgdvRRRPPSRSPAAKPA-APARPPVRRLARPAVSRSTESFA-LPPDQPERPPQPQAPPPPQPQ 2920

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 1731040072  419 STEGRIESPQPPKRKTQQVRRNITTKTGRKRTPTNIPSVP 458
Cdd:PHA03247  2921 PQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVP 2960
 
Name Accession Description Interval E-value
RNase_HI_RT_Ty1 cd09272
Ty1/Copia family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 168-245 1.46e-33

Ty1/Copia 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 eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing 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. The Ty1/Copia family is widely distributed among the genomes of plants, fungi, and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260004  Cd Length: 140  Bit Score: 125.66  E-value: 1.46e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731040072 168 YCDADWAGSGDDRK----------------------------TEAEYIIAGSGCTQLIWMKNMLHEYGLDQD-TMTLYCD 218
Cdd:cd09272     3 YSDADWAGDPDDRRstsgyvfflgggpiswkskkqttvalssTEAEYIALAEAAKEALWLRRLLEELGIPLDgPTTIYCD 82

                          90       100
                  ....*....|....*....|....*..
gi 1731040072 219 NMSAIDISKNPVQHSRTKHIDIRHHFI 245
Cdd:cd09272    83 NQSAIALAKNPVFHSRTKHIDIRYHFI 109
RVT_2 pfam07727
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1-100 1.03e-23

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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.


Pssm-ID: 400190  Cd Length: 243  Bit Score: 100.74  E-value: 1.03e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731040072   1 MDVKSAFLNGYLNEEVYVAQPKGFVDSEHPKNVFKLNKALYGLKQAPRAWYELLT----------------VYLRG---- 60
Cdd:pfam07727  81 MDVSSAFLNGDIDEEIYVKQPPGFNIDNESGKVWQLNKSLYGLKQAPYMWNTCITkvlmdlnfepdtaesgMYCRGfgen 160

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1731040072  61 -------------------LVNNFINIMQSEFEMSMVGELSYFLGLQIKQKNDGIFISQ 100
Cdd:pfam07727 161 klivglyvddmfitgsditIINDFKLELAKHFKMKDLGDISEFLGIEFIQIAGGIRLSQ 219
Transposase_32 pfam20167
Putative plant transposon protein; This entry represents a likely transposon related protein ...
 484-641 2.84e-15

Putative plant transposon protein; This entry represents a likely transposon related protein from plants. This entry appears related to ORF1 from the ATHILA group of Arabidopsis thaliana retrotransposons pfam03078.


Pssm-ID: 466318  Cd Length: 177  Bit Score: 74.47  E-value: 2.84e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731040072 484 ELIRELIVNLPDEFSNPSspdYQTVHIRWFKFVISPTVINGFLGNIVDIDCSPSCPT--EILATVLSGGTlsTWPVN-GI 560
Cdd:pfam20167  18 TLVREFYANAPELVPDDK---VYSSYVRGKRIDFSPETINEFLEICQFGLYLEEGKTleDLARVLCVPGG--RWLRNlGI 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731040072 561 PAAALSIKYATLHKIGIANWFPSSHASSISAALGTFLYQICNDDKVDTGAFVYNQLLRHVGSFGVKVPIALPRFFSSLLL 640
Cdd:pfam20167  93 RKADLNPAAKYWFGFIRSNLMPSSNESDLTHDRALLLYCILKGKPINLGRIIIDEIKMCARSKNSKTPLPFPSLITRLCR 172


                  .
gi 1731040072 641 H 641
Cdd:pfam20167 173 R 173
PHA03247 PHA03247
large tegument protein UL36; Provisional
 269-458 9.86e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 46.08  E-value: 9.86e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731040072  269 APNVTISSPPPVRQARESLRPESVpevgesSLPISPTMHVPRAPEVVVSDMDSDDQDDSSSIEGVFIPTPGGPRrSPAIP 348
Cdd:PHA03247  2770 APPAAPAAGPPRRLTRPAVASLSE------SRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPT-APPPP 2842

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1731040072  349 SGYSP-------FVHPS---RSKSPASKPDVVPAhISGNTTVAHEEQTGVSRNEDHFAsFNQDDIPPEDIPPSTNDPTAP 418
Cdd:PHA03247  2843 PGPPPpslplggSVAPGgdvRRRPPSRSPAAKPA-APARPPVRRLARPAVSRSTESFA-LPPDQPERPPQPQAPPPPQPQ 2920

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 1731040072  419 STEGRIESPQPPKRKTQQVRRNITTKTGRKRTPTNIPSVP 458
Cdd:PHA03247  2921 PQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVP 2960
 
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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