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Conserved domains on  [gi|1868518084|ref|XP_035325751|]
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putative zinc knuckle [Colletotrichum scovillei]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 715-847 4.39e-39

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: 141.59  E-value: 4.39e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084  715 HIYTDGSGIDGQIGAAAVCTTT--QQTRKSHMGddTTSTVYAGELQGIVLALEMAqadKESGNSRSKIFIHTDNQAAIRS 792
Cdd:cd09276      1 VIYTDGSKLEGSVGAGFVIYRGgeVISRSYRLG--THASVFDAELEAILEALELA---LATARRARKVTIFTDSQSALQA 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1868518084  793 SAKPKGKSGAYLLKIIAEKTQALREQGLEVELRWVPAHIGIQGNEAADIAAKEAT 847
Cdd:cd09276     76 LRNPRRSSGQVILIRILRLLRLLKAKGVKVRLRWVPGHVGIEGNEAADRLAKEAA 130
Exo_endo_phos_2 pfam14529
Endonuclease-reverse transcriptase; This domain represents the endonuclease region of ...
 90-213 7.37e-24

Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.


:

Pssm-ID: 434019 [Multi-domain]  Cd Length: 118  Bit Score: 97.43  E-value: 7.37e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084   90 LVLHNVYNPspREEDRQPVLQQLRTTLETHRHVEQIVVGDFNLHHELWGGSDIRapDREATELLDLMGDMNLT-SQLRAG 168
Cdd:pfam14529    1 ILIISVYCP--PSDQLRNLLDTLEDILRSLDRPPIIIGGDFNAHHPLWGSNSTD--VSRGEELIEFLNEHGLNlLNLPKS 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1868518084  169 TITYEEGDHRTTIDLYLVTVGLVnrmIRCEVDHNIDHDSDHLPIA 213
Cdd:pfam14529   77 GPTFISSNGDSTIDLTLTSDPLA---VRVLSDLGPDSGSDHRPIA 118
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 12-131 5.76e-05

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


:

Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 44.91  E-value: 5.76e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084   12 NYDIIAIQEPWRNPYSATTHH-PAKDRFHLCYPSSEENGPARVCFFINKKLDHS--RWQFREVSRDLCTLVIATDDDAET 88
Cdd:pfam03372   30 DPDVVALQETDDDDASRLLLAlLAYGGFLSYGGPGGGGGGGGVAILSRYPLSSVilVDLGEFGDPALRGAIAPFAGVLVV 109

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1868518084   89 SLVLHNVYNPSPREEDRQPVLQQLRTTLET--HRHVEQIVVGDFN 131
Cdd:pfam03372  110 PLVLTLAPHASPRLARDEQRADLLLLLLALlaPRSEPVILAGDFN 154
 
Name Accession Description Interval E-value
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 715-847 4.39e-39

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: 141.59  E-value: 4.39e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084  715 HIYTDGSGIDGQIGAAAVCTTT--QQTRKSHMGddTTSTVYAGELQGIVLALEMAqadKESGNSRSKIFIHTDNQAAIRS 792
Cdd:cd09276      1 VIYTDGSKLEGSVGAGFVIYRGgeVISRSYRLG--THASVFDAELEAILEALELA---LATARRARKVTIFTDSQSALQA 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1868518084  793 SAKPKGKSGAYLLKIIAEKTQALREQGLEVELRWVPAHIGIQGNEAADIAAKEAT 847
Cdd:cd09276     76 LRNPRRSSGQVILIRILRLLRLLKAKGVKVRLRWVPGHVGIEGNEAADRLAKEAA 130
Exo_endo_phos_2 pfam14529
Endonuclease-reverse transcriptase; This domain represents the endonuclease region of ...
 90-213 7.37e-24

Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.


Pssm-ID: 434019 [Multi-domain]  Cd Length: 118  Bit Score: 97.43  E-value: 7.37e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084   90 LVLHNVYNPspREEDRQPVLQQLRTTLETHRHVEQIVVGDFNLHHELWGGSDIRapDREATELLDLMGDMNLT-SQLRAG 168
Cdd:pfam14529    1 ILIISVYCP--PSDQLRNLLDTLEDILRSLDRPPIIIGGDFNAHHPLWGSNSTD--VSRGEELIEFLNEHGLNlLNLPKS 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1868518084  169 TITYEEGDHRTTIDLYLVTVGLVnrmIRCEVDHNIDHDSDHLPIA 213
Cdd:pfam14529   77 GPTFISSNGDSTIDLTLTSDPLA---VRVLSDLGPDSGSDHRPIA 118
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
715-846 4.33e-12

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 64.48  E-value: 4.33e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084  715 HIYTDGS--GIDGQIGAAAVCTTTQQtRKSHMGD--DTTSTVyaGELQGIVLALEMAqadKESGNSRskIFIHTDNQAAI 790
Cdd:COG0328      4 EIYTDGAcrGNPGPGGWGAVIRYGGE-EKELSGGlgDTTNNR--AELTALIAALEAL---KELGPCE--VEIYTDSQYVV 75

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084  791 RSSAK--PKGKSGAYLLKIIAEKTQALRE--QGLEVELRWVPAHIGIQGNEAADIAAKEA 846
Cdd:COG0328     76 NQITGwiHGWKKNGWKPVKNPDLWQRLDEllARHKVTFEWVKGHAGHPGNERADALANKA 135
R1-I-EN cd09077
Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat ...
 14-216 1.44e-11

Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197311 [Multi-domain]  Cd Length: 205  Bit Score: 64.62  E-value: 1.44e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084   14 DIIAIQEPWRNPysatthhpakdRFHLCYPSSEENgpaRVCFFINKKLDHSRWQFREVSRDLCTLVIatdddaeTSLVLH 93
Cdd:cd09077     28 DIALIQEPYLVP-----------VNNPNWVTDESG---RAAIVVSDRLPRKPIQRLSLGLGIVAARV-------GGITVV 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084   94 NVYNPsPRE--EDRQPVLQQLRTTLETHRHvEQIVVGDFNLHHELWGGsdiRAPDREATELLDLMGDMNLTSQLRAGTIT 171
Cdd:cd09077     87 SCYAP-PSEslEEFEEYLENLVRIVRGLSR-PVIIGGDFNAWSPAWGS---KRTDRRGRLLEDWIANLGLVLLNDGNSPT 161

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 1868518084  172 YEEGDHRTTIDLYLVTVGLVNRMIRCEVDhNIDHDSDHLPIATSL 216
Cdd:cd09077    162 FVRPRGTSIIDVTFCSPSLARRISNWRVL-EDETLSDHRYIRFTI 205
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 716-846 2.01e-09

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: 57.00  E-value: 2.01e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084  716 IYTDGS--GIDGQIGAAAVCTTTQQTRKSHMGDDTTSTVyaGELQGIVLALemaQADKESgnsrSKIFIHTDNQAAI--- 790
Cdd:pfam00075    6 VYTDGSclGNPGPGGAGAVLYRGHENISAPLPGRTTNNR--AELQAVIEAL---KALKSP----SKVNIYTDSQYVIggi 76

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1868518084  791 --------------RSSAKP-KGKSGAYLLKIIAEKTQalreqgleVELRWVPAHIGIQGNEAADIAAKEA 846
Cdd:pfam00075   77 tqwvhgwkkngwptTSEGKPvKNKDLWQLLKALCKKHQ--------VYWQWVKGHAGNPGNEMADRLAKQG 139
XthA COG0708
Exonuclease III [Replication, recombination and repair];
64-212 8.29e-06

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 48.53  E-value: 8.29e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084   64 SRWQFREVSRDLCTLviatDDDAE--------TSLVLHNVYNPS--PREEDRQPV--------LQQLRTTLETHRHVeqI 125
Cdd:COG0708     69 SRLPPEDVRRGLGGD----EFDAEgryieadfGGVRVVSLYVPNggSVGSEKFDYklrfldalRAYLAELLAPGRPL--I 142

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084  126 VVGDFNL-HHELwggsDIRAP------------DREA-TELLDLmgdmNLTSQLRAgtiTYEEGDHRTT----------- 180
Cdd:COG0708    143 LCGDFNIaPTEI----DVKNPkanlknagflpeERAWfDRLLEL----GLVDAFRA---LHPDVEGQYTwwsyragafar 211

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 1868518084  181 -----IDLYLVTVGLVNRMIRCEVDHNIDHD---SDHLPI 212
Cdd:COG0708    212 nrgwrIDYILASPALADRLKDAGIDREPRGDerpSDHAPV 251
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 12-131 5.76e-05

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 44.91  E-value: 5.76e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084   12 NYDIIAIQEPWRNPYSATTHH-PAKDRFHLCYPSSEENGPARVCFFINKKLDHS--RWQFREVSRDLCTLVIATDDDAET 88
Cdd:pfam03372   30 DPDVVALQETDDDDASRLLLAlLAYGGFLSYGGPGGGGGGGGVAILSRYPLSSVilVDLGEFGDPALRGAIAPFAGVLVV 109

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1868518084   89 SLVLHNVYNPSPREEDRQPVLQQLRTTLET--HRHVEQIVVGDFN 131
Cdd:pfam03372  110 PLVLTLAPHASPRLARDEQRADLLLLLLALlaPRSEPVILAGDFN 154
 
Name Accession Description Interval E-value
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 715-847 4.39e-39

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: 141.59  E-value: 4.39e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084  715 HIYTDGSGIDGQIGAAAVCTTT--QQTRKSHMGddTTSTVYAGELQGIVLALEMAqadKESGNSRSKIFIHTDNQAAIRS 792
Cdd:cd09276      1 VIYTDGSKLEGSVGAGFVIYRGgeVISRSYRLG--THASVFDAELEAILEALELA---LATARRARKVTIFTDSQSALQA 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1868518084  793 SAKPKGKSGAYLLKIIAEKTQALREQGLEVELRWVPAHIGIQGNEAADIAAKEAT 847
Cdd:cd09276     76 LRNPRRSSGQVILIRILRLLRLLKAKGVKVRLRWVPGHVGIEGNEAADRLAKEAA 130
Exo_endo_phos_2 pfam14529
Endonuclease-reverse transcriptase; This domain represents the endonuclease region of ...
 90-213 7.37e-24

Endonuclease-reverse transcriptase; This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49.


Pssm-ID: 434019 [Multi-domain]  Cd Length: 118  Bit Score: 97.43  E-value: 7.37e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084   90 LVLHNVYNPspREEDRQPVLQQLRTTLETHRHVEQIVVGDFNLHHELWGGSDIRapDREATELLDLMGDMNLT-SQLRAG 168
Cdd:pfam14529    1 ILIISVYCP--PSDQLRNLLDTLEDILRSLDRPPIIIGGDFNAHHPLWGSNSTD--VSRGEELIEFLNEHGLNlLNLPKS 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1868518084  169 TITYEEGDHRTTIDLYLVTVGLVnrmIRCEVDHNIDHDSDHLPIA 213
Cdd:pfam14529   77 GPTFISSNGDSTIDLTLTSDPLA---VRVLSDLGPDSGSDHRPIA 118
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
715-846 4.33e-12

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 64.48  E-value: 4.33e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084  715 HIYTDGS--GIDGQIGAAAVCTTTQQtRKSHMGD--DTTSTVyaGELQGIVLALEMAqadKESGNSRskIFIHTDNQAAI 790
Cdd:COG0328      4 EIYTDGAcrGNPGPGGWGAVIRYGGE-EKELSGGlgDTTNNR--AELTALIAALEAL---KELGPCE--VEIYTDSQYVV 75

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084  791 RSSAK--PKGKSGAYLLKIIAEKTQALRE--QGLEVELRWVPAHIGIQGNEAADIAAKEA 846
Cdd:COG0328     76 NQITGwiHGWKKNGWKPVKNPDLWQRLDEllARHKVTFEWVKGHAGHPGNERADALANKA 135
R1-I-EN cd09077
Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat ...
 14-216 1.44e-11

Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197311 [Multi-domain]  Cd Length: 205  Bit Score: 64.62  E-value: 1.44e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084   14 DIIAIQEPWRNPysatthhpakdRFHLCYPSSEENgpaRVCFFINKKLDHSRWQFREVSRDLCTLVIatdddaeTSLVLH 93
Cdd:cd09077     28 DIALIQEPYLVP-----------VNNPNWVTDESG---RAAIVVSDRLPRKPIQRLSLGLGIVAARV-------GGITVV 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084   94 NVYNPsPRE--EDRQPVLQQLRTTLETHRHvEQIVVGDFNLHHELWGGsdiRAPDREATELLDLMGDMNLTSQLRAGTIT 171
Cdd:cd09077     87 SCYAP-PSEslEEFEEYLENLVRIVRGLSR-PVIIGGDFNAWSPAWGS---KRTDRRGRLLEDWIANLGLVLLNDGNSPT 161

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 1868518084  172 YEEGDHRTTIDLYLVTVGLVNRMIRCEVDhNIDHDSDHLPIATSL 216
Cdd:cd09077    162 FVRPRGTSIIDVTFCSPSLARRISNWRVL-EDETLSDHRYIRFTI 205
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 715-847 4.24e-11

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: 61.81  E-value: 4.24e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084  715 HIYTDGSGID-GQIGAAA---VCTTTQQTRKSHM---GDDTTSTVyaGELQGIVLALEMAQADkesgnSRSKIFIHTDNQ 787
Cdd:cd09280      1 VVYTDGSCLNnGKPGARAgigVYFGPGDPRNVSEplpGRKQTNNR--AELLAVIHALEQAPEE-----GIRKLEIRTDSK 73

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1868518084  788 AAIRS---------SAKPKGKSGAY-----LLKIIAEKtqaLREQGLEVELRWVPAHIGIQGNEAADIAAKEAT 847
Cdd:cd09280     74 YAINCitkwipkwkKNGWKTSKGKPvknqdLIKELDKL---LRKRGIKVKFEHVKGHSGDPGNEEADRLAREGA 144
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 716-846 2.01e-09

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: 57.00  E-value: 2.01e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084  716 IYTDGS--GIDGQIGAAAVCTTTQQTRKSHMGDDTTSTVyaGELQGIVLALemaQADKESgnsrSKIFIHTDNQAAI--- 790
Cdd:pfam00075    6 VYTDGSclGNPGPGGAGAVLYRGHENISAPLPGRTTNNR--AELQAVIEAL---KALKSP----SKVNIYTDSQYVIggi 76

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1868518084  791 --------------RSSAKP-KGKSGAYLLKIIAEKTQalreqgleVELRWVPAHIGIQGNEAADIAAKEA 846
Cdd:pfam00075   77 tqwvhgwkkngwptTSEGKPvKNKDLWQLLKALCKKHQ--------VYWQWVKGHAGNPGNEMADRLAKQG 139
RNase_HI_bacteria_like cd09277
Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; Ribonuclease H ...
 714-847 7.89e-08

Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; 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 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. Some bacteria distinguished from other bacterial RNase HI in the presence of a hybrid binding domain (HBD) at the N-terminus which is commonly present at the N-termini of eukaryotic RNase HI. It has been reported that this domain is required for dimerization and processivity of RNase HI upon binding to RNA-DNA hybrids.


Pssm-ID: 260009 [Multi-domain]  Cd Length: 133  Bit Score: 52.10  E-value: 7.89e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084  714 AHIYTDGSGID--GQIGAAAVCTT--TQQTRKSHMGDDTTSTVY--AGELQGIVLALEMAQAdkesgNSRSKIFIHTDNQ 787
Cdd:cd09277      1 VIAYVDGSYNKetKKYGYGVVIIKngKEEEFSGSGNDPEYASMRnvAGEIKGAMKAIKYAIE-----NGIKKITIYYDYE 75

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1868518084  788 AaIRSSAKpkgksGAYllKIIAEKTQALRE------QGLEVELRWVPAHIGIQGNEAADIAAKEAT 847
Cdd:cd09277     76 G-IEKWAT-----GEW--KANKELTKEYKEfmqkykKKIKIEFVKVKAHSGDKYNELADKLAKKAL 133
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 716-844 8.22e-08

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: 51.93  E-value: 8.22e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084  716 IYTDGSGID--GQIGAAAVCTTTQQT----RKSHMGddtTSTVYAGELQGIVLALEMAqadkeSGNSRSKIFIHTDNQAA 789
Cdd:cd06222      1 INVDGSCRGnpGPAGIGGVLRDHEGGwlggFALKIG---APTALEAELLALLLALELA-----LDLGYLKVIIESDSKYV 72

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1868518084  790 IRSSAKPKGKSGAYLLkIIAEKTQALREQGlEVELRWVPAHigiqGNEAADIAAK 844
Cdd:cd06222     73 VDLINSGSFKWSPNIL-LIEDILLLLSRFW-SVKISHVPRE----GNQVADALAK 121
XthA COG0708
Exonuclease III [Replication, recombination and repair];
64-212 8.29e-06

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 48.53  E-value: 8.29e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084   64 SRWQFREVSRDLCTLviatDDDAE--------TSLVLHNVYNPS--PREEDRQPV--------LQQLRTTLETHRHVeqI 125
Cdd:COG0708     69 SRLPPEDVRRGLGGD----EFDAEgryieadfGGVRVVSLYVPNggSVGSEKFDYklrfldalRAYLAELLAPGRPL--I 142

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084  126 VVGDFNL-HHELwggsDIRAP------------DREA-TELLDLmgdmNLTSQLRAgtiTYEEGDHRTT----------- 180
Cdd:COG0708    143 LCGDFNIaPTEI----DVKNPkanlknagflpeERAWfDRLLEL----GLVDAFRA---LHPDVEGQYTwwsyragafar 211

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 1868518084  181 -----IDLYLVTVGLVNRMIRCEVDHNIDHD---SDHLPI 212
Cdd:COG0708    212 nrgwrIDYILASPALADRLKDAGIDREPRGDerpSDHAPV 251
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 715-846 1.39e-05

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: 45.94  E-value: 1.39e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084  715 HIYTDGS--GIDGqIGAAAVCTTTQQTRKSHMG--DDTTSTVyaGELQGIVLALEMAQADkesgnsrSKIFIHTDNQaai 790
Cdd:cd09278      3 VIYTDGAclGNPG-PGGWAAVIRYGDHEKELSGgePGTTNNR--MELTAAIEALEALKEP-------CPVTIYTDSQ--- 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084  791 rssakpkgksgaYLLKIIAE----------KT------------QALRE--QGLEVELRWVPAHIGIQGNEAADIAAKEA 846
Cdd:cd09278     70 ------------YVINGITKwikgwkkngwKTadgkpvknrdlwQELDAllAGHKVTWEWVKGHAGHPGNERADRLANKA 137
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 10-209 2.18e-05

Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197310 [Multi-domain]  Cd Length: 236  Bit Score: 46.96  E-value: 2.18e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084   10 IDNYDIIAIQEpwrnpysatTHHPAKDRFHLC-------YPSSEENGPARVCFFINKKLDHSR--WQFREVSRdlctLVI 80
Cdd:cd09076     24 RKKLDILGLQE---------THWTGEGELKKKreggtilYSGSDSGKSRGVAILLSKTAANKLleYTKVVSGR----IIM 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084   81 ATDDDAETSLVLHNVYNPSPR-EEDRQPVLQQLRTTLETHRHVEQ-IVVGDFNLH----HELWGGSDIRApDREATELLD 154
Cdd:cd09076     91 VRFKIKGKRLTIINVYAPTARdEEEKEEFYDQLQDVLDKVPRHDTlIIGGDFNAVlgpkDDGRKGLDKRN-ENGERALSA 169

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1868518084  155 LMGDMNL-----TSQLRAGTITYEEGDH--RTTIDLYLVTVGLVNRMIRCEVDHNIdhDSDH 209
Cdd:cd09076    170 LIEEHDLvdvwrENNPKTREYTWRSPDHgsRSRIDRILVSKRLRVKVKKTKITPGA--GSDH 229
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 12-131 5.76e-05

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 44.91  E-value: 5.76e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1868518084   12 NYDIIAIQEPWRNPYSATTHH-PAKDRFHLCYPSSEENGPARVCFFINKKLDHS--RWQFREVSRDLCTLVIATDDDAET 88
Cdd:pfam03372   30 DPDVVALQETDDDDASRLLLAlLAYGGFLSYGGPGGGGGGGGVAILSRYPLSSVilVDLGEFGDPALRGAIAPFAGVLVV 109

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1868518084   89 SLVLHNVYNPSPREEDRQPVLQQLRTTLET--HRHVEQIVVGDFN 131
Cdd:pfam03372  110 PLVLTLAPHASPRLARDEQRADLLLLLLALlaPRSEPVILAGDFN 154
 
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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