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Conserved domains on  [gi|1404637347|gb|PZN08420|]
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MAG: ribonuclease H [Bacillota bacterium]

Protein Classification

ribonuclease HI family protein( domain architecture ID 10174584)

ribonuclease HI family protein such as type 1 ribonuclease H, which is involved in the removal of RNA from RNA/DNA hybrids during DNA replication, repair and transcription.

EC:  3.1.26.4
Gene Ontology:  GO:0003723|GO:0003677

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 8-135 4.43e-65

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: 193.84  E-value: 4.43e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347   8 WRLHTDGAARGNPGPAGIGVVLIDPHGQVAEQlARYIGT-ATNNVAEYTALIAGLERALARGARRLDVYSDSELMVRQLN 86
Cdd:cd09279     1 WTLYFDGASRGNPGPAGAGVVIYSPGGEVLEL-SERLGFpATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLN 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1404637347  87 GEYRVKHEGLKPLYHRVRELAACFDAVRFIHVPRERNREADRLANRGID 135
Cdd:cd09279    80 GEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
 
Name Accession Description Interval E-value
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 8-135 4.43e-65

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: 193.84  E-value: 4.43e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347   8 WRLHTDGAARGNPGPAGIGVVLIDPHGQVAEQlARYIGT-ATNNVAEYTALIAGLERALARGARRLDVYSDSELMVRQLN 86
Cdd:cd09279     1 WTLYFDGASRGNPGPAGAGVVIYSPGGEVLEL-SERLGFpATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLN 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1404637347  87 GEYRVKHEGLKPLYHRVRELAACFDAVRFIHVPRERNREADRLANRGID 135
Cdd:cd09279    80 GEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 13-139 1.29e-46

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 154.75  E-value: 1.29e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347  13 DGAARGNPGPAGIGVVLIDP-HGQVAEQLARYIGTATNNVAEYTALIAGLERALARGARRLDVYSDSELMVRQLNGEYRV 91
Cdd:PRK07238    8 DGGSRGNPGPAGYGAVVWDAdRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWKV 87

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1404637347  92 KHEGLKPLYHRVRELAACFDAVRFIHVPRERNREADRLANRGIDQGAA 139
Cdd:PRK07238   88 KHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEAMDAAAG 135
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
8-134 8.06e-41

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 132.66  E-value: 8.06e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347   8 WRLHTDGAARGNPGPAGIGVVLIDphGQVAEQLARYIGTATNNVAEYTALIAGLERALARGARRLDVYSDSELMVRQLNG 87
Cdd:COG0328     3 IEIYTDGACRGNPGPGGWGAVIRY--GGEEKELSGGLGDTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQITG 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347  88 EY---------RVKHeglKPLYHRVRELAACFDaVRFIHVPRER----NREADRLANRGI 134
Cdd:COG0328    81 WIhgwkkngwkPVKN---PDLWQRLDELLARHK-VTFEWVKGHAghpgNERADALANKAL 136
RNAseHI_Thmprot NF041175
ribonuclease HI;
19-132 6.46e-37

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 123.16  E-value: 6.46e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347  19 NPGpaGI---GVVLIDPHGQVAEQ--LAR--YIGTATNNVAEYTALIAGLERALARGARRLDVYSDSELMVRQLNGEYRV 91
Cdd:NF041175   14 NPG--GIatyGYVIYLDNKRKIEGygLAAepWSKDSTNNVAEYTGLICLLEKLLELGISEVIIRGDSQLVIRQLNGEYKV 91

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1404637347  92 KHEGLKPLYHRVRELAACFDAVRFIHVPRERNREADRLANR 132
Cdd:NF041175   92 KSPRIIPLYEKALELLSKFRSIEFEWVPREENKEADRLSRI 132
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 12-133 1.04e-31

Reverse transcriptase-like; This domain is found in plants and appears to be part of a retrotransposon.


Pssm-ID: 433223 [Multi-domain]  Cd Length: 123  Bit Score: 109.28  E-value: 1.04e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347  12 TDGAARGNPGPAGIGVVLIDPHGQV-AEQLARYIGTATNNVAEYTALIAGLERALARGARRLDVYSDSELMVRQLNGEyR 90
Cdd:pfam13456   2 FDGAFKCDSGLAGAGVVIRDPNGNVlLAGQKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGR-S 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1404637347  91 VKHEGLKPLYHRVRELAACFDAVRFIHVPRERNREADRLANRG 133
Cdd:pfam13456  81 PKQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
 
Name Accession Description Interval E-value
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 8-135 4.43e-65

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: 193.84  E-value: 4.43e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347   8 WRLHTDGAARGNPGPAGIGVVLIDPHGQVAEQlARYIGT-ATNNVAEYTALIAGLERALARGARRLDVYSDSELMVRQLN 86
Cdd:cd09279     1 WTLYFDGASRGNPGPAGAGVVIYSPGGEVLEL-SERLGFpATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLN 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1404637347  87 GEYRVKHEGLKPLYHRVRELAACFDAVRFIHVPRERNREADRLANRGID 135
Cdd:cd09279    80 GEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 13-139 1.29e-46

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 154.75  E-value: 1.29e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347  13 DGAARGNPGPAGIGVVLIDP-HGQVAEQLARYIGTATNNVAEYTALIAGLERALARGARRLDVYSDSELMVRQLNGEYRV 91
Cdd:PRK07238    8 DGGSRGNPGPAGYGAVVWDAdRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWKV 87

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1404637347  92 KHEGLKPLYHRVRELAACFDAVRFIHVPRERNREADRLANRGIDQGAA 139
Cdd:PRK07238   88 KHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEAMDAAAG 135
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
8-134 8.06e-41

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 132.66  E-value: 8.06e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347   8 WRLHTDGAARGNPGPAGIGVVLIDphGQVAEQLARYIGTATNNVAEYTALIAGLERALARGARRLDVYSDSELMVRQLNG 87
Cdd:COG0328     3 IEIYTDGACRGNPGPGGWGAVIRY--GGEEKELSGGLGDTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQITG 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347  88 EY---------RVKHeglKPLYHRVRELAACFDaVRFIHVPRER----NREADRLANRGI 134
Cdd:COG0328    81 WIhgwkkngwkPVKN---PDLWQRLDELLARHK-VTFEWVKGHAghpgNERADALANKAL 136
RNAseHI_Thmprot NF041175
ribonuclease HI;
19-132 6.46e-37

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 123.16  E-value: 6.46e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347  19 NPGpaGI---GVVLIDPHGQVAEQ--LAR--YIGTATNNVAEYTALIAGLERALARGARRLDVYSDSELMVRQLNGEYRV 91
Cdd:NF041175   14 NPG--GIatyGYVIYLDNKRKIEGygLAAepWSKDSTNNVAEYTGLICLLEKLLELGISEVIIRGDSQLVIRQLNGEYKV 91

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1404637347  92 KHEGLKPLYHRVRELAACFDAVRFIHVPRERNREADRLANR 132
Cdd:NF041175   92 KSPRIIPLYEKALELLSKFRSIEFEWVPREENKEADRLSRI 132
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 12-133 1.04e-31

Reverse transcriptase-like; This domain is found in plants and appears to be part of a retrotransposon.


Pssm-ID: 433223 [Multi-domain]  Cd Length: 123  Bit Score: 109.28  E-value: 1.04e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347  12 TDGAARGNPGPAGIGVVLIDPHGQV-AEQLARYIGTATNNVAEYTALIAGLERALARGARRLDVYSDSELMVRQLNGEyR 90
Cdd:pfam13456   2 FDGAFKCDSGLAGAGVVIRDPNGNVlLAGQKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGR-S 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1404637347  91 VKHEGLKPLYHRVRELAACFDAVRFIHVPRERNREADRLANRG 133
Cdd:pfam13456  81 PKQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 10-131 1.13e-29

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: 103.93  E-value: 1.13e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347  10 LHTDGAARGNPGPAGIGVVLIDPHGQVAEQLARYIGTATNNVAEYTALIAGLERALARGARRLDVYSDSELMVRQLNGEY 89
Cdd:cd06222     1 INVDGSCRGNPGPAGIGGVLRDHEGGWLGGFALKIGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLINSGS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1404637347  90 RVKHEGLKPLYHRVRELAAcFDAVRFIHVPRERNREADRLAN 131
Cdd:cd06222    81 FKWSPNILLIEDILLLLSR-FWSVKISHVPREGNQVADALAK 121
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 10-135 4.51e-18

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: 74.83  E-value: 4.51e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347  10 LHTDGAARGNPGPAGIGVVLIDPhGQVAEQLARYIGTaTNNVAEYTALIAGLErALARGaRRLDVYSDSELMVR------ 83
Cdd:cd09278     4 IYTDGACLGNPGPGGWAAVIRYG-DHEKELSGGEPGT-TNNRMELTAAIEALE-ALKEP-CPVTIYTDSQYVINgitkwi 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1404637347  84 ---QLNGeYR------VKHeglKPLYHRVRELAACFDaVRFIHVP----RERNREADRLANRGID 135
Cdd:cd09278    80 kgwKKNG-WKtadgkpVKN---RDLWQELDALLAGHK-VTWEWVKghagHPGNERADRLANKAAD 139
rnhA PRK13907
ribonuclease H; Provisional
 10-136 2.05e-17

ribonuclease H; Provisional


Pssm-ID: 139967 [Multi-domain]  Cd Length: 128  Bit Score: 72.78  E-value: 2.05e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347  10 LHTDGAARGNPGPAGIGVVLidpHG-QVAEQLARYIGTATNNVAEYTALIAGLERALARGARRLDVYSDSELMVRQLNGE 88
Cdd:PRK13907    4 VYIDGASKGNPGPSGAGVFI---KGvQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1404637347  89 YrVKHEGLKPLYHRVRELAACFDAVRFIHVPRERNREADRLANRGIDQ 136
Cdd:PRK13907   81 Y-AKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAILQ 127
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 10-135 7.66e-16

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: 69.53  E-value: 7.66e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347  10 LHTDGAARGNPGP---AGIGVVL-IDPHGQVAEQLARYIGTA-TNNVAEYTALIAGLERA------LARGARRLDVYSDS 78
Cdd:cd13934     2 VYIDGACRNNGRPdarAGYGVYFgPDSSYNVSGRLEDTGGHPqTSQRAELRAAIAALRFRswiidpDGEGLKTVVIATDS 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1404637347  79 ELMVR---------QLNG-----EYRVKH-EGLKPLYHRVRELAACFDAVRFIHVPRERNREADRLANRGID 135
Cdd:cd13934    82 EYVVKgatewipkwKRNGwrtskGKPVKNrDLFELLLDEIEDLEEGGVEVQFWHVPRELNKEADRLAKAAAE 153
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 10-134 7.41e-15

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: 66.63  E-value: 7.41e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347  10 LHTDGAARGNPGPAGIGVVLIDPHGQVAEQLAryiGTATNNVAEYTALIAGLErALARGaRRLDVYSDSELMVRQLN--- 86
Cdd:pfam00075   6 VYTDGSCLGNPGPGGAGAVLYRGHENISAPLP---GRTTNNRAELQAVIEALK-ALKSP-SKVNIYTDSQYVIGGITqwv 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1404637347  87 -----GEYRVKHEGL----KPLYHRVRELAACfDAVRFIHVP----RERNREADRLANRGI 134
Cdd:pfam00075  81 hgwkkNGWPTTSEGKpvknKDLWQLLKALCKK-HQVYWQWVKghagNPGNEMADRLAKQGA 140
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 9-135 9.63e-14

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: 63.74  E-value: 9.63e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347   9 RLHTDGAARGNPGP---AGIGVVLIDPHGQ-VAEQLARYIgtATNNVAEYTALIAGLERALARGARRLDVYSDSELMVRQ 84
Cdd:cd09280     1 VVYTDGSCLNNGKPgarAGIGVYFGPGDPRnVSEPLPGRK--QTNNRAELLAVIHALEQAPEEGIRKLEIRTDSKYAINC 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1404637347  85 LNgEYRVKHE-------GLKPLYHR------VRELAACFDAVRFIHVP----RERNREADRLANRGID 135
Cdd:cd09280    79 IT-KWIPKWKkngwktsKGKPVKNQdlikelDKLLRKRGIKVKFEHVKghsgDPGNEEADRLAREGAD 145
rnhA PRK00203
ribonuclease H; Reviewed
 10-82 4.75e-11

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 56.76  E-value: 4.75e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1404637347  10 LHTDGAARGNPGPAGIGVVLIdpHGQVAEQLARYIGTATNNVAEYTALIAGLErALARgARRLDVYSDSELMV 82
Cdd:PRK00203    6 IYTDGACLGNPGPGGWGAILR--YKGHEKELSGGEALTTNNRMELMAAIEALE-ALKE-PCEVTLYTDSQYVR 74
PRK07708 PRK07708
hypothetical protein; Validated
 13-135 5.99e-07

hypothetical protein; Validated


Pssm-ID: 181088 [Multi-domain]  Cd Length: 219  Bit Score: 46.57  E-value: 5.99e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347  13 DGAARGNPGPAGIGVVLIDPHGQVAEQL---ARYIGTATNNVAEYTALIAGLERALARGARRLDV--YSDSELMVRQLNG 87
Cdd:PRK07708   79 DGGFDKETKLAGLGIVIYYKQGNKRYRIrrnAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVtfRGDSQVVLNQLAG 158

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1404637347  88 EYRVKHEGLKPLYHRVRELAACFD-AVRFIHVPRERNREADRLANRGID 135
Cdd:PRK07708  159 EWPCYDEHLNHWLDRIEQKLKQLKlTPVYEPISRKQNKEADQLATQALE 207
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 12-133 1.39e-04

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: 39.12  E-value: 1.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347  12 TDGAarGNPGPAGIGVVLIDphGQVAEQLARYIGT-ATNNVAEYTALIAGLERAL--ARGARRLDVYSDSELMVRQLNGE 88
Cdd:cd09276     4 TDGS--KLEGSVGAGFVIYR--GGEVISRSYRLGThASVFDAELEAILEALELALatARRARKVTIFTDSQSALQALRNP 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1404637347  89 YRVK-HEGLKPLYHRVRELAACFDAVRFIHVPRER----NREADRLANRG 133
Cdd:cd09276    80 RRSSgQVILIRILRLLRLLKAKGVKVRLRWVPGHVgiegNEAADRLAKEA 129
PRK08719 PRK08719
ribonuclease H; Reviewed
 7-86 2.23e-04

ribonuclease H; Reviewed


Pssm-ID: 236334 [Multi-domain]  Cd Length: 147  Bit Score: 38.69  E-value: 2.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1404637347   7 PWRLHTDGAARGNPG---PAGIGVVLIDPHGQVAEQLARYI-GTATNNVAEYTALIAGLERAlargaRRLDV-YSDSELM 81
Cdd:PRK08719    4 SYSIYIDGAAPNNQHgcvRGGIGLVVYDEAGEIVDEQSITVnRYTDNAELELLALIEALEYA-----RDGDViYSDSDYC 78


                  ....*
gi 1404637347  82 VRQLN 86
Cdd:PRK08719   79 VRGFN 83
 
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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