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Conserved domains on  [gi|543171830|ref|YP_008532103|]
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Rnase H [Klebsiella phage 0507-KN2-1]

Protein Classification

ribonuclease HI( domain architecture ID 10001091)

type 1 ribonuclease H is involved in the removal of RNA from RNA/DNA hybrids during DNA replication, repair and transcription

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1-148 2.86e-36

Ribonuclease HI [Replication, recombination and repair];


:

Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 122.65  E-value: 2.86e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171830   1 MIEIYTDGASSPQTTQAaGWAFAVspISGGAQWnVFYGYLPPpSTNNIAELLGVINALKLLWKFSGCgernipKATIISD 80
Cdd:COG0328    2 MIEIYTDGACRGNPGPG-GWGAVI--RYGGEEK-ELSGGLGD-TTNNRAELTALIAALEALKELGPC------EVEIYTD 70

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 543171830  81 SQYVINSATKWRSKWEYEG-MPPKNTELLLDLfnmyDKVCSICELELKWVKGHAGTIGNEIADQWSVRA 148
Cdd:COG0328   71 SQYVVNQITGWIHGWKKNGwKPVKNPDLWQRL----DELLARHKVTFEWVKGHAGHPGNERADALANKA 135
 
Name Accession Description Interval E-value
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1-148 2.86e-36

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 122.65  E-value: 2.86e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171830   1 MIEIYTDGASSPQTTQAaGWAFAVspISGGAQWnVFYGYLPPpSTNNIAELLGVINALKLLWKFSGCgernipKATIISD 80
Cdd:COG0328    2 MIEIYTDGACRGNPGPG-GWGAVI--RYGGEEK-ELSGGLGD-TTNNRAELTALIAALEALKELGPC------EVEIYTD 70

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 543171830  81 SQYVINSATKWRSKWEYEG-MPPKNTELLLDLfnmyDKVCSICELELKWVKGHAGTIGNEIADQWSVRA 148
Cdd:COG0328   71 SQYVVNQITGWIHGWKKNGwKPVKNPDLWQRL----DELLARHKVTFEWVKGHAGHPGNERADALANKA 135
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 1-148 9.60e-35

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: 118.74  E-value: 9.60e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171830   1 MIEIYTDGASSPQTTqAAGWAFAVSP------ISGGAqwnvfygylpPPSTNNIAELLGVINALKLLwkfsgcgeRNIPK 74
Cdd:cd09278    1 EIVIYTDGACLGNPG-PGGWAAVIRYgdhekeLSGGE----------PGTTNNRMELTAAIEALEAL--------KEPCP 61

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171830  75 ATIISDSQYVINSATKWRSKWE------YEGMPPKNTELLLDLfnmyDKVCSICELELKWVKGHAGTIGNEIADQWSVRA 148
Cdd:cd09278   62 VTIYTDSQYVINGITKWIKGWKkngwktADGKPVKNRDLWQEL----DALLAGHKVTWEWVKGHAGHPGNERADRLANKA 137
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 2-150 2.36e-27

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: 100.14  E-value: 2.36e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171830    2 IEIYTDGASSPQTTQAaGWAFAVSpisGGAQwnVFYGYLPPPSTNNIAELLGVINALKLLWkfSGCgernipKATIISDS 81
Cdd:pfam00075   4 VTVYTDGSCLGNPGPG-GAGAVLY---RGHE--NISAPLPGRTTNNRAELQAVIEALKALK--SPS------KVNIYTDS 69

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 543171830   82 QYVINSATKWRSKWEYEGMPPKNTELLL---DLFNMYDKVCSICELELKWVKGHAGTIGNEIADQWSVRAKE 150
Cdd:pfam00075  70 QYVIGGITQWVHGWKKNGWPTTSEGKPVknkDLWQLLKALCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
rnhA PRK00203
ribonuclease H; Reviewed
 2-151 3.41e-21

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 84.49  E-value: 3.41e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171830   2 IEIYTDGASS--PQttqAAGWAfAVSpISGGAQWNVFYGYlpPPSTNNIAELLGVINALKLLwkfsgcgerNIP-KATII 78
Cdd:PRK00203   4 VEIYTDGACLgnPG---PGGWG-AIL-RYKGHEKELSGGE--ALTTNNRMELMAAIEALEAL---------KEPcEVTLY 67

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 543171830  79 SDSQYVINSATKWRSKWEYEG------MPPKNtellLDLFNMYDKVCSICELELKWVKGHAGTIGNEIADQWSVRAKEN 151
Cdd:PRK00203  68 TDSQYVRQGITEWIHGWKKNGwktadkKPVKN----VDLWQRLDAALKRHQIKWHWVKGHAGHPENERCDELARAGAEE 142
 
Name Accession Description Interval E-value
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
1-148 2.86e-36

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 122.65  E-value: 2.86e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171830   1 MIEIYTDGASSPQTTQAaGWAFAVspISGGAQWnVFYGYLPPpSTNNIAELLGVINALKLLWKFSGCgernipKATIISD 80
Cdd:COG0328    2 MIEIYTDGACRGNPGPG-GWGAVI--RYGGEEK-ELSGGLGD-TTNNRAELTALIAALEALKELGPC------EVEIYTD 70

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 543171830  81 SQYVINSATKWRSKWEYEG-MPPKNTELLLDLfnmyDKVCSICELELKWVKGHAGTIGNEIADQWSVRA 148
Cdd:COG0328   71 SQYVVNQITGWIHGWKKNGwKPVKNPDLWQRL----DELLARHKVTFEWVKGHAGHPGNERADALANKA 135
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 1-148 9.60e-35

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: 118.74  E-value: 9.60e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171830   1 MIEIYTDGASSPQTTqAAGWAFAVSP------ISGGAqwnvfygylpPPSTNNIAELLGVINALKLLwkfsgcgeRNIPK 74
Cdd:cd09278    1 EIVIYTDGACLGNPG-PGGWAAVIRYgdhekeLSGGE----------PGTTNNRMELTAAIEALEAL--------KEPCP 61

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171830  75 ATIISDSQYVINSATKWRSKWE------YEGMPPKNTELLLDLfnmyDKVCSICELELKWVKGHAGTIGNEIADQWSVRA 148
Cdd:cd09278   62 VTIYTDSQYVINGITKWIKGWKkngwktADGKPVKNRDLWQEL----DALLAGHKVTWEWVKGHAGHPGNERADRLANKA 137
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 4-143 1.56e-27

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: 100.72  E-value: 1.56e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171830   4 IYTDGASSPQTTQ--AAGWAFAVSPisgGAQWNVFYGYLPPPSTNNIAELLGVINALKLLWkfsgcgERNIPKATIISDS 81
Cdd:cd09280    2 VYTDGSCLNNGKPgaRAGIGVYFGP---GDPRNVSEPLPGRKQTNNRAELLAVIHALEQAP------EEGIRKLEIRTDS 72

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 543171830  82 QYVINSATKWRSKWE------YEGMPPKNTELLLDLFNMYDKvcSICELELKWVKGHAGTIGNEIADQ 143
Cdd:cd09280   73 KYAINCITKWIPKWKkngwktSKGKPVKNQDLIKELDKLLRK--RGIKVKFEHVKGHSGDPGNEEADR 138
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 2-150 2.36e-27

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: 100.14  E-value: 2.36e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171830    2 IEIYTDGASSPQTTQAaGWAFAVSpisGGAQwnVFYGYLPPPSTNNIAELLGVINALKLLWkfSGCgernipKATIISDS 81
Cdd:pfam00075   4 VTVYTDGSCLGNPGPG-GAGAVLY---RGHE--NISAPLPGRTTNNRAELQAVIEALKALK--SPS------KVNIYTDS 69

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 543171830   82 QYVINSATKWRSKWEYEGMPPKNTELLL---DLFNMYDKVCSICELELKWVKGHAGTIGNEIADQWSVRAKE 150
Cdd:pfam00075  70 QYVIGGITQWVHGWKKNGWPTTSEGKPVknkDLWQLLKALCKKHQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
rnhA PRK00203
ribonuclease H; Reviewed
 2-151 3.41e-21

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 84.49  E-value: 3.41e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171830   2 IEIYTDGASS--PQttqAAGWAfAVSpISGGAQWNVFYGYlpPPSTNNIAELLGVINALKLLwkfsgcgerNIP-KATII 78
Cdd:PRK00203   4 VEIYTDGACLgnPG---PGGWG-AIL-RYKGHEKELSGGE--ALTTNNRMELMAAIEALEAL---------KEPcEVTLY 67

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 543171830  79 SDSQYVINSATKWRSKWEYEG------MPPKNtellLDLFNMYDKVCSICELELKWVKGHAGTIGNEIADQWSVRAKEN 151
Cdd:PRK00203  68 TDSQYVRQGITEWIHGWKKNGwktadkKPVKN----VDLWQRLDAALKRHQIKWHWVKGHAGHPENERCDELARAGAEE 142
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 4-111 2.59e-17

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: 74.54  E-value: 2.59e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171830   4 IYTDGASSP--QTTQAAGWAFAVSPISGGAQWNVFYGYLPPPSTNNIAELLGVINALKLL-WKFSGCGERnIPKATIISD 80
Cdd:cd13934    2 VYIDGACRNngRPDARAGYGVYFGPDSSYNVSGRLEDTGGHPQTSQRAELRAAIAALRFRsWIIDPDGEG-LKTVVIATD 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 543171830  81 SQYVINSATKWRSKWE------YEGMPPKNTELLLDL 111
Cdd:cd13934   81 SEYVVKGATEWIPKWKrngwrtSKGKPVKNRDLFELL 117
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 4-150 3.37e-17

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: 73.41  E-value: 3.37e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171830   4 IYTDGASSPQttqAAGWAFAVSPISGGAQWnvfYGYLPPPSTNNIAELLGVINALKLLWKfsgcGERNIPKATIISDSQY 83
Cdd:cd09276    2 IYTDGSKLEG---SVGAGFVIYRGGEVISR---SYRLGTHASVFDAELEAILEALELALA----TARRARKVTIFTDSQS 71

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 543171830  84 VINSATKWRskweyegmPPKNTELLLDLFNMYDKVCSIC-ELELKWVKGHAGTIGNEIADQwsvRAKE 150
Cdd:cd09276   72 ALQALRNPR--------RSSGQVILIRILRLLRLLKAKGvKVRLRWVPGHVGIEGNEAADR---LAKE 128
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 4-142 2.30e-15

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: 68.49  E-value: 2.30e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171830   4 IYTDGASSPQTtQAAGWAFAVSPISGGaqWNVFYGYLPPPSTNNIAELLGVINALKLLWkfsgcgERNIPKATIISDSQY 83
Cdd:cd06222    1 INVDGSCRGNP-GPAGIGGVLRDHEGG--WLGGFALKIGAPTALEAELLALLLALELAL------DLGYLKVIIESDSKY 71

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 543171830  84 VINSATKWRSKWEyegmppKNTELLLDLfnmYDKVCSICELELKWVKGHagtiGNEIAD 142
Cdd:cd06222   72 VVDLINSGSFKWS------PNILLIEDI---LLLLSRFWSVKISHVPRE----GNQVAD 117
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 2-143 1.42e-12

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: 1.42e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171830   2 IEIYTDGASSPQTTQAAGWAFAVSPISGGAQWNVfygYLPPPSTNNIAELLGVINALKLLWkfsgcgERNIPKATIISDS 81
Cdd:cd09279    1 WTLYFDGASRGNPGPAGAGVVIYSPGGEVLELSE---RLGFPATNNEAEYEALIAGLELAL------ELGAEKLEIYGDS 71

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 543171830  82 QYVINSATK-WRSKweYEGMPPKNTEL--LLDLFnmydkvcsiCELELKWVKGHAgtigNEIADQ 143
Cdd:cd09279   72 QLVVNQLNGeYKVK--NERLKPLLEKVleLLAKF---------ELVELKWIPREQ----NKEADA 121
PRK06548 PRK06548
ribonuclease H; Provisional
 6-153 7.99e-12

ribonuclease H; Provisional


Pssm-ID: 75628 [Multi-domain]  Cd Length: 161  Bit Score: 60.21  E-value: 7.99e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171830   6 TDGaSSPQTTQAAGWAFAVSP---ISGGaqWNVfygylpppSTNNIAELlgviNALKLLWKFSGCGERNIpkaTIISDSQ 82
Cdd:PRK06548  10 TDG-SSLANPGPSGWAWYVDEntwDSGG--WDI--------ATNNIAEL----TAVRELLIATRHTDRPI---LILSDSK 71

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 543171830  83 YVINSATKWRSKWEY------EGMPPKNTELLLDLfnmyDKVCSICELELKWVKGHAGTIGNEIADQWSVRAKENSS 153
Cdd:PRK06548  72 YVINSLTKWVYSWKMrkwrkaDGKPVLNQEIIQEI----DSLMENRNIRMSWVNAHTGHPLNEAADSLARQAANNFS 144
RNase_HI_bacteria_like cd09277
Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; Ribonuclease H ...
 2-143 3.77e-06

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: 44.40  E-value: 3.77e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171830   2 IEIYTDGaSSPQTTQAAGWAFAVspISGGaQWNVFYGYLPPP---STNNIA-ELLGVINALKLlwkfsgCGERNIPKATI 77
Cdd:cd09277    1 VIAYVDG-SYNKETKKYGYGVVI--IKNG-KEEEFSGSGNDPeyaSMRNVAgEIKGAMKAIKY------AIENGIKKITI 70

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 543171830  78 ISDSQYVINSATK-WRSkweyegmppkNTELLLDLFNMYDKVCSICELELKWVKGHAGTIGNEIADQ 143
Cdd:cd09277   71 YYDYEGIEKWATGeWKA----------NKELTKEYKEFMQKYKKKIKIEFVKVKAHSGDKYNELADK 127
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 4-143 2.43e-04

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: 39.24  E-value: 2.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543171830   4 IYTDGASSPqttqaAGWAfAVSpisggaqWNVFY--GYLPPPSTNNIAELLGVINALKLlwkfsGCGERnipkATIISDS 81
Cdd:cd09273    2 VFTDGSSFK-----AGYA-IVS-------GTEIVeaQPLPPGTSAQRAELIALIQALEL-----AKGKP----VNIYTDS 59

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 543171830  82 QYVINSATKWRSKWEYEGM--PPKNTELLLDLFNMYD--KVCSICElelkwVKGHAG-----TIGNEIADQ 143
Cdd:cd09273   60 AYAVHALHLLETIGIERGFlkSIKNLSLFLQLLEAVQrpKPVAIIH-----IRAHSKlpgplAEGNAQADA 125
 
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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