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Conserved domains on  [gi|2308551904|ref|WP_261243358|]
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ribonuclease H family protein [Arcobacter lacus]

Protein Classification

ribonuclease H family protein( domain architecture ID 10174616)

ribonuclease H (RNase H) family protein may function as an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; similar to Acanthamoeba polyphaga mimivirus ribonuclease H

CATH:  3.30.420.10
EC:  3.1.26.4
Gene Ontology:  GO:0004523|GO:0003676|GO:0000287|GO:0043137
PubMed:  19228197|16232566|2177653|16093691|19228198
SCOP:  4000541

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 ...
 103-245 3.25e-46

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: 151.56  E-value: 3.25e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 103 KIYCDGACSGNPG-NAGSGLAVYSNKKNP----VLLYGayiENGTNNIAELNALFQALTIASQTTSENIIsIFTDSKYAI 177
Cdd:cd09280     1 VVYTDGSCLNNGKpGARAGIGVYFGPGDPrnvsEPLPG---RKQTNNRAELLAVIHALEQAPEEGIRKLE-IRTDSKYAI 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2308551904 178 DCITTWAYSWKKNGWSKKGGE-IKNLELIQEAHYLYEKIKNKIEITHVKGHSGIEGNELADRMAVNAIK 245
Cdd:cd09280    77 NCITKWIPKWKKNGWKTSKGKpVKNQDLIKELDKLLRKRGIKVKFEHVKGHSGDPGNEEADRLAREGAD 145
 
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 ...
 103-245 3.25e-46

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: 151.56  E-value: 3.25e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 103 KIYCDGACSGNPG-NAGSGLAVYSNKKNP----VLLYGayiENGTNNIAELNALFQALTIASQTTSENIIsIFTDSKYAI 177
Cdd:cd09280     1 VVYTDGSCLNNGKpGARAGIGVYFGPGDPrnvsEPLPG---RKQTNNRAELLAVIHALEQAPEEGIRKLE-IRTDSKYAI 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2308551904 178 DCITTWAYSWKKNGWSKKGGE-IKNLELIQEAHYLYEKIKNKIEITHVKGHSGIEGNELADRMAVNAIK 245
Cdd:cd09280    77 NCITKWIPKWKKNGWKTSKGKpVKNQDLIKELDKLLRKRGIKVKFEHVKGHSGDPGNEEADRLAREGAD 145
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
100-244 7.09e-46

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 150.38  E-value: 7.09e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 100 EHIKIYCDGACSGNPGNAGSGLAVYSNKKnpVLLYGAYIENGTNNIAELNALFQALTIASQTTSENIIsIFTDSKYAIDC 179
Cdd:COG0328     1 KMIEIYTDGACRGNPGPGGWGAVIRYGGE--EKELSGGLGDTTNNRAELTALIAALEALKELGPCEVE-IYTDSQYVVNQ 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2308551904 180 ITTWAYSWKKNGWSKkggeIKNLELIQEAHYLYEKIknKIEITHVKGHSGIEGNELADRMAVNAI 244
Cdd:COG0328    78 ITGWIHGWKKNGWKP----VKNPDLWQRLDELLARH--KVTFEWVKGHAGHPGNERADALANKAL 136
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 104-245 1.26e-37

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: 129.42  E-value: 1.26e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 104 IYCDGACSGNPGNAGSGLAVYSNKKNpvlLYGAYIENGTNNIAELNALFQALtiaSQTTSENIISIFTDSKYAIDCITTW 183
Cdd:pfam00075   6 VYTDGSCLGNPGPGGAGAVLYRGHEN---ISAPLPGRTTNNRAELQAVIEAL---KALKSPSKVNIYTDSQYVIGGITQW 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2308551904 184 AYSWKKNGW--SKKGGEIKNLELIQEAHYLYEKikNKIEITHVKGHSGIEGNELADRMAVNAIK 245
Cdd:pfam00075  80 VHGWKKNGWptTSEGKPVKNKDLWQLLKALCKK--HQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
rnhA PRK00203
ribonuclease H; Reviewed
 101-249 4.16e-29

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 107.60  E-value: 4.16e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 101 HIKIYCDGACSGNPGNAGSG-LAVYSNKKNpvLLYGAYiENGTNNIAELNALFQALTIASQTTSeniISIFTDSKYAIDC 179
Cdd:PRK00203    3 QVEIYTDGACLGNPGPGGWGaILRYKGHEK--ELSGGE-ALTTNNRMELMAAIEALEALKEPCE---VTLYTDSQYVRQG 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2308551904 180 ITTWAYSWKKNGWSKKGGE-IKNLELIQEahyLYEKIK-NKIEITHVKGHSGIEGNELADRMAVNAIKEKNE 249
Cdd:PRK00203   77 ITEWIHGWKKNGWKTADKKpVKNVDLWQR---LDAALKrHQIKWHWVKGHAGHPENERCDELARAGAEEATL 145
 
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 ...
 103-245 3.25e-46

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: 151.56  E-value: 3.25e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 103 KIYCDGACSGNPG-NAGSGLAVYSNKKNP----VLLYGayiENGTNNIAELNALFQALTIASQTTSENIIsIFTDSKYAI 177
Cdd:cd09280     1 VVYTDGSCLNNGKpGARAGIGVYFGPGDPrnvsEPLPG---RKQTNNRAELLAVIHALEQAPEEGIRKLE-IRTDSKYAI 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2308551904 178 DCITTWAYSWKKNGWSKKGGE-IKNLELIQEAHYLYEKIKNKIEITHVKGHSGIEGNELADRMAVNAIK 245
Cdd:cd09280    77 NCITKWIPKWKKNGWKTSKGKpVKNQDLIKELDKLLRKRGIKVKFEHVKGHSGDPGNEEADRLAREGAD 145
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
100-244 7.09e-46

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 150.38  E-value: 7.09e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 100 EHIKIYCDGACSGNPGNAGSGLAVYSNKKnpVLLYGAYIENGTNNIAELNALFQALTIASQTTSENIIsIFTDSKYAIDC 179
Cdd:COG0328     1 KMIEIYTDGACRGNPGPGGWGAVIRYGGE--EKELSGGLGDTTNNRAELTALIAALEALKELGPCEVE-IYTDSQYVVNQ 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2308551904 180 ITTWAYSWKKNGWSKkggeIKNLELIQEAHYLYEKIknKIEITHVKGHSGIEGNELADRMAVNAI 244
Cdd:COG0328    78 ITGWIHGWKKNGWKP----VKNPDLWQRLDELLARH--KVTFEWVKGHAGHPGNERADALANKAL 136
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 102-245 5.26e-44

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: 145.70  E-value: 5.26e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 102 IKIYCDGACSGNPGNAGSGLAVYSNKKNPVLLYGAyiENGTNNIAELNALFQALTIASQTtseNIISIFTDSKYAIDCIT 181
Cdd:cd09278     2 IVIYTDGACLGNPGPGGWAAVIRYGDHEKELSGGE--PGTTNNRMELTAAIEALEALKEP---CPVTIYTDSQYVINGIT 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2308551904 182 TWAYSWKKNGWSK-KGGEIKNLELIQEAHYLYEkiKNKIEITHVKGHSGIEGNELADRMAVNAIK 245
Cdd:cd09278    77 KWIKGWKKNGWKTaDGKPVKNRDLWQELDALLA--GHKVTWEWVKGHAGHPGNERADRLANKAAD 139
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 104-245 1.26e-37

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: 129.42  E-value: 1.26e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 104 IYCDGACSGNPGNAGSGLAVYSNKKNpvlLYGAYIENGTNNIAELNALFQALtiaSQTTSENIISIFTDSKYAIDCITTW 183
Cdd:pfam00075   6 VYTDGSCLGNPGPGGAGAVLYRGHEN---ISAPLPGRTTNNRAELQAVIEAL---KALKSPSKVNIYTDSQYVIGGITQW 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2308551904 184 AYSWKKNGW--SKKGGEIKNLELIQEAHYLYEKikNKIEITHVKGHSGIEGNELADRMAVNAIK 245
Cdd:pfam00075  80 VHGWKKNGWptTSEGKPVKNKDLWQLLKALCKK--HQVYWQWVKGHAGNPGNEMADRLAKQGAE 141
rnhA PRK00203
ribonuclease H; Reviewed
 101-249 4.16e-29

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 107.60  E-value: 4.16e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 101 HIKIYCDGACSGNPGNAGSG-LAVYSNKKNpvLLYGAYiENGTNNIAELNALFQALTIASQTTSeniISIFTDSKYAIDC 179
Cdd:PRK00203    3 QVEIYTDGACLGNPGPGGWGaILRYKGHEK--ELSGGE-ALTTNNRMELMAAIEALEALKEPCE---VTLYTDSQYVRQG 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2308551904 180 ITTWAYSWKKNGWSKKGGE-IKNLELIQEahyLYEKIK-NKIEITHVKGHSGIEGNELADRMAVNAIKEKNE 249
Cdd:PRK00203   77 ITEWIHGWKKNGWKTADKKpVKNVDLWQR---LDAALKrHQIKWHWVKGHAGHPENERCDELARAGAEEATL 145
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 104-240 5.62e-21

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: 86.48  E-value: 5.62e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 104 IYCDGACSGN-PGNAGSGLAVYSNKKNP----VLLYGAYIENGTNNIAELNALFQALTIASQTTSENIIS-----IFTDS 173
Cdd:cd13934     2 VYIDGACRNNgRPDARAGYGVYFGPDSSynvsGRLEDTGGHPQTSQRAELRAAIAALRFRSWIIDPDGEGlktvvIATDS 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2308551904 174 KYAIDCITTWAYSWKKNGW-SKKGGEIKNLELIQEahyLYEKI----KNKIEIT--HVKGhsgiEGNELADRMA 240
Cdd:cd13934    82 EYVVKGATEWIPKWKRNGWrTSKGKPVKNRDLFEL---LLDEIedleEGGVEVQfwHVPR----ELNKEADRLA 148
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 104-240 6.86e-21

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: 85.06  E-value: 6.86e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 104 IYCDGACSGNPGNAGSGLAVYSNKKNPVLLYGAYIENGTNNIAELNALFQALTIASQTTSENIIsIFTDSKYAIDCITTW 183
Cdd:cd06222     1 INVDGSCRGNPGPAGIGGVLRDHEGGWLGGFALKIGAPTALEAELLALLLALELALDLGYLKVI-IESDSKYVVDLINSG 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2308551904 184 AYSWkkngwskkggeIKNLELIQEAHYLYEKIKNkIEITHVKGhsgiEGNELADRMA 240
Cdd:cd06222    80 SFKW-----------SPNILLIEDILLLLSRFWS-VKISHVPR----EGNQVADALA 120
PRK06548 PRK06548
ribonuclease H; Provisional
 107-243 2.31e-18

ribonuclease H; Provisional


Pssm-ID: 75628 [Multi-domain]  Cd Length: 161  Bit Score: 79.86  E-value: 2.31e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 107 DGACSGNPGNAGSGLAVYSNKKNPvllyGAYiENGTNNIAELNALfQALTIASQTTSENIIsIFTDSKYAIDCITTWAYS 186
Cdd:PRK06548   11 DGSSLANPGPSGWAWYVDENTWDS----GGW-DIATNNIAELTAV-RELLIATRHTDRPIL-ILSDSKYVINSLTKWVYS 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2308551904 187 WKKNGWSKKGGE-IKNLELIQEAHYLYEkiKNKIEITHVKGHSGIEGNELADRMAVNA 243
Cdd:PRK06548   84 WKMRKWRKADGKpVLNQEIIQEIDSLME--NRNIRMSWVNAHTGHPLNEAADSLARQA 139
PRK08719 PRK08719
ribonuclease H; Reviewed
 101-245 7.27e-17

ribonuclease H; Reviewed


Pssm-ID: 236334 [Multi-domain]  Cd Length: 147  Bit Score: 75.28  E-value: 7.27e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 101 HIKIYCDGACSGNPG---NAGSGLAVYSNKKNPVLLYGAYIENGTNNI-AELNALFQALTIASQTTSeniisIFTDSKYA 176
Cdd:PRK08719    4 SYSIYIDGAAPNNQHgcvRGGIGLVVYDEAGEIVDEQSITVNRYTDNAeLELLALIEALEYARDGDV-----IYSDSDYC 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 177 IDCITTWAYSWKKNGWSKKGGE-IKNLELIQEAHYLyeKIKNKIEITHVKGHSGIEGNELADRMAVNAIK 245
Cdd:PRK08719   79 VRGFNEWLDTWKQKGWRKSDKKpVANRDLWQQVDEL--RARKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 104-240 9.91e-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: 74.56  E-value: 9.91e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 104 IYCDGacSGNPGNAGSGLAVYSNKKNPVLLYGAyienGTNN---IAELNALFQALTIASQTTSENI-ISIFTDSKYAIDC 179
Cdd:cd09276     2 IYTDG--SKLEGSVGAGFVIYRGGEVISRSYRL----GTHAsvfDAELEAILEALELALATARRARkVTIFTDSQSALQA 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2308551904 180 ITTWAYSWkkngwskkggeikNLELIQEAHYLYEKIKNK---IEITHVKGHSGIEGNELADRMA 240
Cdd:cd09276    76 LRNPRRSS-------------GQVILIRILRLLRLLKAKgvkVRLRWVPGHVGIEGNEAADRLA 126
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 102-240 7.55e-15

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: 69.42  E-value: 7.55e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 102 IKIYCDGACSGNPGNAGSGLAVYSNKKNpVLLYGAYI-ENGTNNIAELNALFQALTIASQTTSENiISIFTDSKYAIDCI 180
Cdd:cd09279     1 WTLYFDGASRGNPGPAGAGVVIYSPGGE-VLELSERLgFPATNNEAEYEALIAGLELALELGAEK-LEIYGDSQLVVNQL 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2308551904 181 ttwayswkkngwsKKGGEIKNLELIQeahyLYEKIKN------KIEITHVKGhsgiEGNELADRMA 240
Cdd:cd09279    79 -------------NGEYKVKNERLKP----LLEKVLEllakfeLVELKWIPR----EQNKEADALA 123
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 104-240 1.25e-12

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: 63.51  E-value: 1.25e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 104 IYCDGACSGNpgnagsGLAVYSNKKnpVLLYGAYIENGTNNIAELNALFQALTIASQTTseniISIFTDSKYAIDCITTW 183
Cdd:cd09273     2 VFTDGSSFKA------GYAIVSGTE--IVEAQPLPPGTSAQRAELIALIQALELAKGKP----VNIYTDSAYAVHALHLL 69

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2308551904 184 AYSWKKNGWSKkggEIKNLELIQEahyLYEKI--KNKIEITHVKGHSG-----IEGNELADRMA 240
Cdd:cd09273    70 ETIGIERGFLK---SIKNLSLFLQ---LLEAVqrPKPVAIIHIRAHSKlpgplAEGNAQADAAA 127
RNase_HI_bacteria_like cd09277
Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; Ribonuclease H ...
 102-244 1.29e-07

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: 49.41  E-value: 1.29e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 102 IKIYCDGACSGNPGNAGSGLAVYSNKKnPVLLYGAYIEN---GTNNIA-ELNALFQALTIASqttSENI--ISIFTDskY 175
Cdd:cd09277     1 VIAYVDGSYNKETKKYGYGVVIIKNGK-EEEFSGSGNDPeyaSMRNVAgEIKGAMKAIKYAI---ENGIkkITIYYD--Y 74

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2308551904 176 AidCITTWAY-SWKKNgwskkggeiknLELIQEAHYLYEKIKNKIEIT--HVKGHSGIEGNELADRMAVNAI 244
Cdd:cd09277    75 E--GIEKWATgEWKAN-----------KELTKEYKEFMQKYKKKIKIEfvKVKAHSGDKYNELADKLAKKAL 133
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 104-174 6.95e-06

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 46.51  E-value: 6.95e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2308551904 104 IYCDGACSGNPGNAGSGLAVYSNKKNPVLL-YGAYIENGTNNIAELNALFQALTIASQTTSENiISIFTDSK 174
Cdd:PRK07238    5 VEADGGSRGNPGPAGYGAVVWDADRGEVLAeRAEAIGRATNNVAEYRGLIAGLEAAAELGATE-VEVRMDSK 75
rnhA PRK13907
ribonuclease H; Provisional
 102-174 3.17e-04

ribonuclease H; Provisional


Pssm-ID: 139967 [Multi-domain]  Cd Length: 128  Bit Score: 39.65  E-value: 3.17e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2308551904 102 IKIYCDGACSGNPGNAGSGlaVYSNKKNPVLLYGAYIENGTNNIAELNALFQALTIASQtTSENIISIFTDSK 174
Cdd:PRK13907    2 IEVYIDGASKGNPGPSGAG--VFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTE-HNYNIVSFRTDSQ 71
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 106-240 4.75e-04

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: 39.17  E-value: 4.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 106 CDGACSGNPGNAGSGlAVYSNKKNPVLLYGAYIENGTNN--IAELNALFQALTIASQTTSENIIsIFTDSKYAIDCIttw 183
Cdd:pfam13456   2 FDGAFKCDSGLAGAG-VVIRDPNGNVLLAGQKKLGPGASvlEAEAQALIIGLQLAWKLGIRHLI-VEGDSATVVQLI--- 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2308551904 184 ayswkkNGWSKKGGEIKNleliqeahyLYEKIKN------KIEITHVKghsgIEGNELADRMA 240
Cdd:pfam13456  77 ------NGRSPKQSKLAN---------LLDEIRKllkrfeSVSFEHIP----REQNRVADTLA 120
RNase_H_bacteria_like cd13935
RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence ...
 105-219 1.52e-03

RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; This family includes bacterial ribonuclease H (RNase H) enzymes. RNases are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. 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. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260015  Cd Length: 133  Bit Score: 37.88  E-value: 1.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2308551904 105 YC-DGACSGNPGnagsgLAVY---SNKKNPVLLYGAYIENGTNNIAELNALFQALTIASQTTSEniISIFTDSKYAIdci 180
Cdd:cd13935     5 LCvDAACSGNPG-----IVEYrgvDTKTGEVLFHRGPFPGGTNNMGEFLAIVHALRYLKEKNSR--KPIYSDSQTAI--- 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2308551904 181 ttwaySWKKNGWSK-------KGGEIknLELIQEA-HYL-YEKIKNKI 219
Cdd:cd13935    75 -----AWVKKKKAKstlvrneKNAEI--FKLVDRAeEWLsTHTYPNPI 115
 
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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