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Conserved domains on  [gi|6323890|ref|NP_013961|]
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RNA-DNA hybrid ribonuclease [Saccharomyces cerevisiae S288C]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 190-345 2.00e-48

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: 159.65  E-value: 2.00e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890  190 VYCDGSSFGNGTSSSRAGYGAYFEGAPEENISEPLLSGAQTNNRAEIEAVSEALKKIWekltnEKEKVNYQIKTDSEYVT 269
Cdd:cd09280   2 VYTDGSCLNNGKPGARAGIGVYFGPGDPRNVSEPLPGRKQTNNRAELLAVIHALEQAP-----EEGIRKLEIRTDSKYAI 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890  270 KLLNDRYMTYD-----NKKLEGLPNSDLIVPLVQRFVkvkkyyelnkecfKNNGKFQIEWVKGHDGDPGNEMADFLAKKG 344
Cdd:cd09280  77 NCITKWIPKWKkngwkTSKGKPVKNQDLIKELDKLLR-------------KRGIKVKFEHVKGHSGDPGNEEADRLAREG 143


                .
gi 6323890  345 A 345
Cdd:cd09280 144 A 144
Cauli_VI pfam01693
Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. ...
 7-49 5.08e-19

Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. The viroplasmin protein is encoded by gene VI and is the main component of viral inclusion bodies or viroplasms. Inclusions are the site of viral assembly, DNA synthesis and accumulation. Two domains exist within gene VI corresponding approximately to the 5' third and middle third of gene VI, these influence systemic infection in a light-dependent manner.


:

Pssm-ID: 460297 [Multi-domain]  Cd Length: 44  Bit Score: 78.99  E-value: 5.08e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 6323890      7 FYAVRKGRETGIYNTWNECKNQVDGYGGAIYKKFNSYEQAKSF 49
Cdd:pfam01693   2 YYAVAKGRKPGIYTTWDECKAQVKGFPGAKYKSFKTREEAEAF 44
Cauli_VI super family cl38054
Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. ...
 108-153 4.39e-05

Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. The viroplasmin protein is encoded by gene VI and is the main component of viral inclusion bodies or viroplasms. Inclusions are the site of viral assembly, DNA synthesis and accumulation. Two domains exist within gene VI corresponding approximately to the 5' third and middle third of gene VI, these influence systemic infection in a light-dependent manner.


The actual alignment was detected with superfamily member pfam01693:

Pssm-ID: 460297 [Multi-domain]  Cd Length: 44  Bit Score: 40.08  E-value: 4.39e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 6323890    108 FYSVKSNvpnIESKIFNNWKDCQAYVKHKRGITFKKFEDQLAAENF 153
Cdd:pfam01693   2 YYAVAKG---RKPGIYTTWDECKAQVKGFPGAKYKSFKTREEAEAF 44
 
Name Accession Description Interval E-value
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 190-345 2.00e-48

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: 159.65  E-value: 2.00e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890  190 VYCDGSSFGNGTSSSRAGYGAYFEGAPEENISEPLLSGAQTNNRAEIEAVSEALKKIWekltnEKEKVNYQIKTDSEYVT 269
Cdd:cd09280   2 VYTDGSCLNNGKPGARAGIGVYFGPGDPRNVSEPLPGRKQTNNRAELLAVIHALEQAP-----EEGIRKLEIRTDSKYAI 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890  270 KLLNDRYMTYD-----NKKLEGLPNSDLIVPLVQRFVkvkkyyelnkecfKNNGKFQIEWVKGHDGDPGNEMADFLAKKG 344
Cdd:cd09280  77 NCITKWIPKWKkngwkTSKGKPVKNQDLIKELDKLLR-------------KRGIKVKFEHVKGHSGDPGNEEADRLAREG 143


                .
gi 6323890  345 A 345
Cdd:cd09280 144 A 144
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 185-346 4.91e-40

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: 137.89  E-value: 4.91e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890    185 NKSMNVYCDGSSFGNgTSSSRAGYGAYFEgapEENISEPLlSGAQTNNRAEIEAVSEALK--KIWEKLTnekekvnyqIK 262
Cdd:pfam00075   1 PKAVTVYTDGSCLGN-PGPGGAGAVLYRG---HENISAPL-PGRTTNNRAELQAVIEALKalKSPSKVN---------IY 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890    263 TDSEYVTK-LLNDRYMTydnkKLEGLPNSDLIVPlvqrfVKVKKYYELNKECFKNnGKFQIEWVKGHDGDPGNEMADFLA 341
Cdd:pfam00075  67 TDSQYVIGgITQWVHGW----KKNGWPTTSEGKP-----VKNKDLWQLLKALCKK-HQVYWQWVKGHAGNPGNEMADRLA 136


                  ....*
gi 6323890    342 KKGAS 346
Cdd:pfam00075 137 KQGAE 141
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
186-345 3.29e-24

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 96.07  E-value: 3.29e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890  186 KSMNVYCDGSSFGNgtsSSRAGYGAYF-EGAPEENISEPLlsGAQTNNRAEIEAVSEALKKIwekLTNEKEKVnyQIKTD 264
Cdd:COG0328   1 KMIEIYTDGACRGN---PGPGGWGAVIrYGGEEKELSGGL--GDTTNNRAELTALIAALEAL---KELGPCEV--EIYTD 70

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890  265 SEYVTKLLNDRYMTYDNKKLEGLPNSDLivplvqrfvkVKKYYELNKECfknngKFQIEWVKGHDGDPGNEMADFLAKKG 344
Cdd:COG0328  71 SQYVVNQITGWIHGWKKNGWKPVKNPDL----------WQRLDELLARH-----KVTFEWVKGHAGHPGNERADALANKA 135


                .
gi 6323890  345 A 345
Cdd:COG0328 136 L 136
Cauli_VI pfam01693
Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. ...
 7-49 5.08e-19

Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. The viroplasmin protein is encoded by gene VI and is the main component of viral inclusion bodies or viroplasms. Inclusions are the site of viral assembly, DNA synthesis and accumulation. Two domains exist within gene VI corresponding approximately to the 5' third and middle third of gene VI, these influence systemic infection in a light-dependent manner.


Pssm-ID: 460297 [Multi-domain]  Cd Length: 44  Bit Score: 78.99  E-value: 5.08e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 6323890      7 FYAVRKGRETGIYNTWNECKNQVDGYGGAIYKKFNSYEQAKSF 49
Cdd:pfam01693   2 YYAVAKGRKPGIYTTWDECKAQVKGFPGAKYKSFKTREEAEAF 44
Rnh1 COG3341
Ribonuclease HI-related protein, contains viroplasmin and RNaseH domains [General function ...
 7-57 1.77e-18

Ribonuclease HI-related protein, contains viroplasmin and RNaseH domains [General function prediction only];


Pssm-ID: 442570 [Multi-domain]  Cd Length: 203  Bit Score: 82.59  E-value: 1.77e-18
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 6323890    7 FYAVRKGRETGIYNTWNECKNQVDGYGGAIYKKFNSYEQAKSFLGQPNTTS 57
Cdd:COG3341   5 FYAVWKGRKPGIYTTWDECKAQVKGFPGAKYKSFKTKEEAEAALNGNYEDY 55
rnhA PRK00203
ribonuclease H; Reviewed
 186-347 2.33e-13

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 66.77  E-value: 2.33e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890   186 KSMNVYCDGSSFGN-GtsssRAGYGAY--FEGAPEEniseplLSGAQ---TNNRAEIEAVSEALKKIwekltneKEKVNY 259
Cdd:PRK00203   2 KQVEIYTDGACLGNpG----PGGWGAIlrYKGHEKE------LSGGEaltTNNRMELMAAIEALEAL-------KEPCEV 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890   260 QIKTDSEYVTKLLND--------RYMTYDNKKLEglpNSDLIvplvqrfvkvKKYYELNKecfknngKFQIE--WVKGHD 329
Cdd:PRK00203  65 TLYTDSQYVRQGITEwihgwkknGWKTADKKPVK---NVDLW----------QRLDAALK-------RHQIKwhWVKGHA 124

                        170
                 ....*....|....*...
gi 6323890   330 GDPGNEMADFLAKKGASR 347
Cdd:PRK00203 125 GHPENERCDELARAGAEE 142
Cauli_VI pfam01693
Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. ...
 108-153 4.39e-05

Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. The viroplasmin protein is encoded by gene VI and is the main component of viral inclusion bodies or viroplasms. Inclusions are the site of viral assembly, DNA synthesis and accumulation. Two domains exist within gene VI corresponding approximately to the 5' third and middle third of gene VI, these influence systemic infection in a light-dependent manner.


Pssm-ID: 460297 [Multi-domain]  Cd Length: 44  Bit Score: 40.08  E-value: 4.39e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 6323890    108 FYSVKSNvpnIESKIFNNWKDCQAYVKHKRGITFKKFEDQLAAENF 153
Cdd:pfam01693   2 YYAVAKG---RKPGIYTTWDECKAQVKGFPGAKYKSFKTREEAEAF 44
 
Name Accession Description Interval E-value
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 190-345 2.00e-48

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: 159.65  E-value: 2.00e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890  190 VYCDGSSFGNGTSSSRAGYGAYFEGAPEENISEPLLSGAQTNNRAEIEAVSEALKKIWekltnEKEKVNYQIKTDSEYVT 269
Cdd:cd09280   2 VYTDGSCLNNGKPGARAGIGVYFGPGDPRNVSEPLPGRKQTNNRAELLAVIHALEQAP-----EEGIRKLEIRTDSKYAI 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890  270 KLLNDRYMTYD-----NKKLEGLPNSDLIVPLVQRFVkvkkyyelnkecfKNNGKFQIEWVKGHDGDPGNEMADFLAKKG 344
Cdd:cd09280  77 NCITKWIPKWKkngwkTSKGKPVKNQDLIKELDKLLR-------------KRGIKVKFEHVKGHSGDPGNEEADRLAREG 143


                .
gi 6323890  345 A 345
Cdd:cd09280 144 A 144
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 185-346 4.91e-40

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: 137.89  E-value: 4.91e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890    185 NKSMNVYCDGSSFGNgTSSSRAGYGAYFEgapEENISEPLlSGAQTNNRAEIEAVSEALK--KIWEKLTnekekvnyqIK 262
Cdd:pfam00075   1 PKAVTVYTDGSCLGN-PGPGGAGAVLYRG---HENISAPL-PGRTTNNRAELQAVIEALKalKSPSKVN---------IY 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890    263 TDSEYVTK-LLNDRYMTydnkKLEGLPNSDLIVPlvqrfVKVKKYYELNKECFKNnGKFQIEWVKGHDGDPGNEMADFLA 341
Cdd:pfam00075  67 TDSQYVIGgITQWVHGW----KKNGWPTTSEGKP-----VKNKDLWQLLKALCKK-HQVYWQWVKGHAGNPGNEMADRLA 136


                  ....*
gi 6323890    342 KKGAS 346
Cdd:pfam00075 137 KQGAE 141
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
186-345 3.29e-24

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 96.07  E-value: 3.29e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890  186 KSMNVYCDGSSFGNgtsSSRAGYGAYF-EGAPEENISEPLlsGAQTNNRAEIEAVSEALKKIwekLTNEKEKVnyQIKTD 264
Cdd:COG0328   1 KMIEIYTDGACRGN---PGPGGWGAVIrYGGEEKELSGGL--GDTTNNRAELTALIAALEAL---KELGPCEV--EIYTD 70

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890  265 SEYVTKLLNDRYMTYDNKKLEGLPNSDLivplvqrfvkVKKYYELNKECfknngKFQIEWVKGHDGDPGNEMADFLAKKG 344
Cdd:COG0328  71 SQYVVNQITGWIHGWKKNGWKPVKNPDL----------WQRLDELLARH-----KVTFEWVKGHAGHPGNERADALANKA 135


                .
gi 6323890  345 A 345
Cdd:COG0328 136 L 136
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 190-345 8.52e-22

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: 89.46  E-value: 8.52e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890  190 VYCDGSSFGNgtsSSRAGYGAYFEgapeENISEPLLSGAQ---TNNRAEIEAVSEALKKIwekltneKEKVNYQIKTDSE 266
Cdd:cd09278   4 IYTDGACLGN---PGPGGWAAVIR----YGDHEKELSGGEpgtTNNRMELTAAIEALEAL-------KEPCPVTIYTDSQ 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890  267 YVTKLLNDRY--------MTYDNKKLEglpNSDLIvplvqrfvkvKKYYELNkecfkNNGKFQIEWVKGHDGDPGNEMAD 338
Cdd:cd09278  70 YVINGITKWIkgwkkngwKTADGKPVK---NRDLW----------QELDALL-----AGHKVTWEWVKGHAGHPGNERAD 131


                ....*..
gi 6323890  339 FLAKKGA 345
Cdd:cd09278 132 RLANKAA 138
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 190-270 3.16e-19

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: 83.02  E-value: 3.16e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890  190 VYCDGSSFGNGTSSSRAGYGAYFEGAPEENISEPL---LSGAQTNNRAEIEAVSEALKKIWEKLTNEKEKVN-YQIKTDS 265
Cdd:cd13934   2 VYIDGACRNNGRPDARAGYGVYFGPDSSYNVSGRLedtGGHPQTSQRAELRAAIAALRFRSWIIDPDGEGLKtVVIATDS 81


                ....*
gi 6323890  266 EYVTK 270
Cdd:cd13934  82 EYVVK 86
Cauli_VI pfam01693
Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. ...
 7-49 5.08e-19

Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. The viroplasmin protein is encoded by gene VI and is the main component of viral inclusion bodies or viroplasms. Inclusions are the site of viral assembly, DNA synthesis and accumulation. Two domains exist within gene VI corresponding approximately to the 5' third and middle third of gene VI, these influence systemic infection in a light-dependent manner.


Pssm-ID: 460297 [Multi-domain]  Cd Length: 44  Bit Score: 78.99  E-value: 5.08e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 6323890      7 FYAVRKGRETGIYNTWNECKNQVDGYGGAIYKKFNSYEQAKSF 49
Cdd:pfam01693   2 YYAVAKGRKPGIYTTWDECKAQVKGFPGAKYKSFKTREEAEAF 44
Rnh1 COG3341
Ribonuclease HI-related protein, contains viroplasmin and RNaseH domains [General function ...
 7-57 1.77e-18

Ribonuclease HI-related protein, contains viroplasmin and RNaseH domains [General function prediction only];


Pssm-ID: 442570 [Multi-domain]  Cd Length: 203  Bit Score: 82.59  E-value: 1.77e-18
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 6323890    7 FYAVRKGRETGIYNTWNECKNQVDGYGGAIYKKFNSYEQAKSFLGQPNTTS 57
Cdd:COG3341   5 FYAVWKGRKPGIYTTWDECKAQVKGFPGAKYKSFKTKEEAEAALNGNYEDY 55
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 189-346 1.54e-13

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: 66.86  E-value: 1.54e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890  189 NVYCDGSSFGNGTsssraGYGAY-FEGAPEENISEPLlSGAQTNNRAEIEAVSEALKKIWeKLTNEKEKVNyqIKTDSEY 267
Cdd:cd09276   1 VIYTDGSKLEGSV-----GAGFViYRGGEVISRSYRL-GTHASVFDAELEAILEALELAL-ATARRARKVT--IFTDSQS 71

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6323890  268 VTKLLNDRYMTydnkkleglPNSDLIVPLVQRFvkvkkyyelnKECFKNNGKFQIEWVKGHDGDPGNEMADFLAKKGAS 346
Cdd:cd09276  72 ALQALRNPRRS---------SGQVILIRILRLL----------RLLKAKGVKVRLRWVPGHVGIEGNEAADRLAKEAAS 131
rnhA PRK00203
ribonuclease H; Reviewed
 186-347 2.33e-13

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 66.77  E-value: 2.33e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890   186 KSMNVYCDGSSFGN-GtsssRAGYGAY--FEGAPEEniseplLSGAQ---TNNRAEIEAVSEALKKIwekltneKEKVNY 259
Cdd:PRK00203   2 KQVEIYTDGACLGNpG----PGGWGAIlrYKGHEKE------LSGGEaltTNNRMELMAAIEALEAL-------KEPCEV 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890   260 QIKTDSEYVTKLLND--------RYMTYDNKKLEglpNSDLIvplvqrfvkvKKYYELNKecfknngKFQIE--WVKGHD 329
Cdd:PRK00203  65 TLYTDSQYVRQGITEwihgwkknGWKTADKKPVK---NVDLW----------QRLDAALK-------RHQIKwhWVKGHA 124

                        170
                 ....*....|....*...
gi 6323890   330 GDPGNEMADFLAKKGASR 347
Cdd:PRK00203 125 GHPENERCDELARAGAEE 142
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 190-342 2.79e-13

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: 65.80  E-value: 2.79e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890  190 VYCDGSSFGNGtssSRAGYGAYF---EGAPEENISEPLlsGAQTNNRAEIEAVSEALKKIWEKltNEKEKVnyqIKTDSE 266
Cdd:cd06222   1 INVDGSCRGNP---GPAGIGGVLrdhEGGWLGGFALKI--GAPTALEAELLALLLALELALDL--GYLKVI---IESDSK 70

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6323890  267 YVTKLLNDRymtydnkkleglpnsdlivplVQRFVKVKKYYELNKECFKNNGKFQIEWVKGhdgdPGNEMADFLAK 342
Cdd:cd06222  71 YVVDLINSG---------------------SFKWSPNILLIEDILLLLSRFWSVKISHVPR----EGNQVADALAK 121
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 190-346 1.13e-11

RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; 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. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties.


Pssm-ID: 260011 [Multi-domain]  Cd Length: 128  Bit Score: 61.33  E-value: 1.13e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890  190 VYCDGSSFGNgtsSSRAGYGA--YFEGAPEENISEPLLSGAqTNNRAEIEAVSEALKKIwekLTNEKEKVnyQIKTDSEY 267
Cdd:cd09279   3 LYFDGASRGN---PGPAGAGVviYSPGGEVLELSERLGFPA-TNNEAEYEALIAGLELA---LELGAEKL--EIYGDSQL 73

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6323890  268 VTKLLNDRYMTYdNKKLeglpnsdlivplvqrfvkvKKYYELNKECFKNNGKFQIEWVKGHDgdpgNEMADFLAKKGAS 346
Cdd:cd09279  74 VVNQLNGEYKVK-NERL-------------------KPLLEKVLELLAKFELVELKWIPREQ----NKEADALANQALD 128
RNase_HI_bacteria_like cd09277
Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; Ribonuclease H ...
 304-344 2.49e-05

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: 43.24  E-value: 2.49e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 6323890  304 KKYYELNKECFKnngKFQIEW--VKGHDGDPGNEMADFLAKKG 344
Cdd:cd09277  93 KEYKEFMQKYKK---KIKIEFvkVKAHSGDKYNELADKLAKKA 132
Cauli_VI pfam01693
Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. ...
 108-153 4.39e-05

Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. The viroplasmin protein is encoded by gene VI and is the main component of viral inclusion bodies or viroplasms. Inclusions are the site of viral assembly, DNA synthesis and accumulation. Two domains exist within gene VI corresponding approximately to the 5' third and middle third of gene VI, these influence systemic infection in a light-dependent manner.


Pssm-ID: 460297 [Multi-domain]  Cd Length: 44  Bit Score: 40.08  E-value: 4.39e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 6323890    108 FYSVKSNvpnIESKIFNNWKDCQAYVKHKRGITFKKFEDQLAAENF 153
Cdd:pfam01693   2 YYAVAKG---RKPGIYTTWDECKAQVKGFPGAKYKSFKTREEAEAF 44
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 189-345 4.88e-05

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: 42.71  E-value: 4.88e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890  189 NVYCDGSSFGngtsssrAGYGAYFEgaPEENISEPLLSG--AQtnnRAEIEAVSEALKkiweklTNEKEKVNyqIKTDSE 266
Cdd:cd09273   1 TVFTDGSSFK-------AGYAIVSG--TEIVEAQPLPPGtsAQ---RAELIALIQALE------LAKGKPVN--IYTDSA 60

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323890  267 YVTKLLNDRYMTYdnkKLEGLPNSDLIVPLVQRFVKVkkyYELNKECFknngkfqIEWVKGHDGDP-----GNEMADFLA 341
Cdd:cd09273  61 YAVHALHLLETIG---IERGFLKSIKNLSLFLQLLEA---VQRPKPVA-------IIHIRAHSKLPgplaeGNAQADAAA 127


                ....
gi 6323890  342 KKGA 345
Cdd:cd09273 128 KQAA 131
 
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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