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Conserved domains on  [gi|17137476|ref|NP_477315|]
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ribonuclease H1, isoform A [Drosophila melanogaster]

Protein Classification

ribonuclease H family protein( domain architecture ID 10483817)

ribonuclease H (RNaseH) family protein containing a reverse transcriptase (RT)-like domain; may be an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner

EC:  3.1.26.4
Gene Ontology:  GO:0003723|GO:0004523

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 ...
 183-326 1.73e-74

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: 225.91  E-value: 1.73e-74
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476 183 IVYTDGSCIGNGRAGACAGYGVYFGKNHQLNAAKPVEGRV-TNNVGEIQAAIHAIKTALDLGIQKLCISTDSQFLINSIT 261
Cdd:cd09280   1 VVYTDGSCLNNGKPGARAGIGVYFGPGDPRNVSEPLPGRKqTNNRAELLAVIHALEQAPEEGIRKLEIRTDSKYAINCIT 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17137476 262 LWVAGWKKRDWKLKNNQPVKNVVDFKELDKLLQENNITVKWNYVEAHKGIEGNEMADKLARQGSA 326
Cdd:cd09280  81 KWIPKWKKNGWKTSKGKPVKNQDLIKELDKLLRKRGIKVKFEHVKGHSGDPGNEEADRLAREGAD 145
Cauli_VI pfam01693
Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. ...
 18-60 1.42e-19

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


:

Pssm-ID: 460297 [Multi-domain]  Cd Length: 44  Bit Score: 80.53  E-value: 1.42e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 17137476    18 FYAVASGRRSGVYGSWAECEEQVKGFKNAKYKKFKTRQEADQF 60
Cdd:pfam01693   2 YYAVAKGRKPGIYTTWDECKAQVKGFPGAKYKSFKTREEAEAF 44
 
Name Accession Description Interval E-value
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 183-326 1.73e-74

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: 225.91  E-value: 1.73e-74
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476 183 IVYTDGSCIGNGRAGACAGYGVYFGKNHQLNAAKPVEGRV-TNNVGEIQAAIHAIKTALDLGIQKLCISTDSQFLINSIT 261
Cdd:cd09280   1 VVYTDGSCLNNGKPGARAGIGVYFGPGDPRNVSEPLPGRKqTNNRAELLAVIHALEQAPEEGIRKLEIRTDSKYAINCIT 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17137476 262 LWVAGWKKRDWKLKNNQPVKNVVDFKELDKLLQENNITVKWNYVEAHKGIEGNEMADKLARQGSA 326
Cdd:cd09280  81 KWIPKWKKNGWKTSKGKPVKNQDLIKELDKLLRKRGIKVKFEHVKGHSGDPGNEEADRLAREGAD 145
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 179-325 4.31e-51

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: 166.01  E-value: 4.31e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476   179 EGYVIVYTDGSCIGNGRAGaCAGYGVYFGKNhqlNAAKPVEGRVTNNVGEIQAAIHAIKtALDLGiQKLCISTDSQFLIN 258
Cdd:pfam00075   1 PKAVTVYTDGSCLGNPGPG-GAGAVLYRGHE---NISAPLPGRTTNNRAELQAVIEALK-ALKSP-SKVNIYTDSQYVIG 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17137476   259 SITLWVAGWKKRDWKLKNNQ-PVKNVVDFKELDKLLQenNITVKWNYVEAHKGIEGNEMADKLARQGS 325
Cdd:pfam00075  75 GITQWVHGWKKNGWPTTSEGkPVKNKDLWQLLKALCK--KHQVYWQWVKGHAGNPGNEMADRLAKQGA 140
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
182-324 1.31e-38

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 133.43  E-value: 1.31e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476 182 VIVYTDGSCIGN-GRAGacagYGVYFGKNHQLNAAKPVEGRVTNNVGEIQAAIHAIKTALDLGIQKLCISTDSQFLINSI 260
Cdd:COG0328   3 IEIYTDGACRGNpGPGG----WGAVIRYGGEEKELSGGLGDTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQI 78

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17137476 261 TLWVAGWKKRDWKlknnqPVKNVVDFKELDKLLQENNITVKWnyVEAHKGIEGNEMADKLARQG 324
Cdd:COG0328  79 TGWIHGWKKNGWK-----PVKNPDLWQRLDELLARHKVTFEW--VKGHAGHPGNERADALANKA 135
rnhA PRK00203
ribonuclease H; Reviewed
 182-324 4.49e-34

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 122.24  E-value: 4.49e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476  182 VIVYTDGSCIGNGRAGacaGYGV---YFGKNHQLNAAKPVegrVTNNVGEIQAAIHAIKtALdlgiQKLC---ISTDSQF 255
Cdd:PRK00203   4 VEIYTDGACLGNPGPG---GWGAilrYKGHEKELSGGEAL---TTNNRMELMAAIEALE-AL----KEPCevtLYTDSQY 72

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17137476  256 LINSITLWVAGWKKRDWKLKNNQPVKNVVDFKELDKLLQENNITvkWNYVEAHKGIEGNEMADKLARQG 324
Cdd:PRK00203  73 VRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIK--WHWVKGHAGHPENERCDELARAG 139
Cauli_VI pfam01693
Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. ...
 18-60 1.42e-19

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


Pssm-ID: 460297 [Multi-domain]  Cd Length: 44  Bit Score: 80.53  E-value: 1.42e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 17137476    18 FYAVASGRRSGVYGSWAECEEQVKGFKNAKYKKFKTRQEADQF 60
Cdd:pfam01693   2 YYAVAKGRKPGIYTTWDECKAQVKGFPGAKYKSFKTREEAEAF 44
RNAseHI_Thmprot NF041175
ribonuclease HI;
182-332 1.02e-08

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 53.43  E-value: 1.02e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476  182 VIVYTDGSCIGNGRAG-ACAGYGVYFGKNHQLN----AAKPVEGRVTNNVGEIQAAIHAIKTALDLGIQKLCISTDSQFL 256
Cdd:NF041175   2 AIGYFDGLCEPKNPGGiATYGYVIYLDNKRKIEgyglAAEPWSKDSTNNVAEYTGLICLLEKLLELGISEVIIRGDSQLV 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476  257 INSITlwvagwkkRDWKLKNNQ--PVknvvdFKELDKLLQE-NNITVKWnyveahkgI--EGNEMADKLARQGSALYKQK 331
Cdd:NF041175  82 IRQLN--------GEYKVKSPRiiPL-----YEKALELLSKfRSIEFEW--------VprEENKEADRLSRIAYELVLKG 140


                 .
gi 17137476  332 N 332
Cdd:NF041175 141 K 141
 
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 ...
 183-326 1.73e-74

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: 225.91  E-value: 1.73e-74
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476 183 IVYTDGSCIGNGRAGACAGYGVYFGKNHQLNAAKPVEGRV-TNNVGEIQAAIHAIKTALDLGIQKLCISTDSQFLINSIT 261
Cdd:cd09280   1 VVYTDGSCLNNGKPGARAGIGVYFGPGDPRNVSEPLPGRKqTNNRAELLAVIHALEQAPEEGIRKLEIRTDSKYAINCIT 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17137476 262 LWVAGWKKRDWKLKNNQPVKNVVDFKELDKLLQENNITVKWNYVEAHKGIEGNEMADKLARQGSA 326
Cdd:cd09280  81 KWIPKWKKNGWKTSKGKPVKNQDLIKELDKLLRKRGIKVKFEHVKGHSGDPGNEEADRLAREGAD 145
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 179-325 4.31e-51

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: 166.01  E-value: 4.31e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476   179 EGYVIVYTDGSCIGNGRAGaCAGYGVYFGKNhqlNAAKPVEGRVTNNVGEIQAAIHAIKtALDLGiQKLCISTDSQFLIN 258
Cdd:pfam00075   1 PKAVTVYTDGSCLGNPGPG-GAGAVLYRGHE---NISAPLPGRTTNNRAELQAVIEALK-ALKSP-SKVNIYTDSQYVIG 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17137476   259 SITLWVAGWKKRDWKLKNNQ-PVKNVVDFKELDKLLQenNITVKWNYVEAHKGIEGNEMADKLARQGS 325
Cdd:pfam00075  75 GITQWVHGWKKNGWPTTSEGkPVKNKDLWQLLKALCK--KHQVYWQWVKGHAGNPGNEMADRLAKQGA 140
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 182-324 1.53e-40

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: 138.77  E-value: 1.53e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476 182 VIVYTDGSCIGNGRAGACAGYGVYFGKNHQLNAAkpvEGRVTNNVGEIQAAIHAIKTALDlgIQKLCISTDSQFLINSIT 261
Cdd:cd09278   2 IVIYTDGACLGNPGPGGWAAVIRYGDHEKELSGG---EPGTTNNRMELTAAIEALEALKE--PCPVTIYTDSQYVINGIT 76

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17137476 262 LWVAGWKKRDWKLKNNQPVKNVVDFKELDKLLQENNITVKWnyVEAHKGIEGNEMADKLARQG 324
Cdd:cd09278  77 KWIKGWKKNGWKTADGKPVKNRDLWQELDALLAGHKVTWEW--VKGHAGHPGNERADRLANKA 137
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
182-324 1.31e-38

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 133.43  E-value: 1.31e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476 182 VIVYTDGSCIGN-GRAGacagYGVYFGKNHQLNAAKPVEGRVTNNVGEIQAAIHAIKTALDLGIQKLCISTDSQFLINSI 260
Cdd:COG0328   3 IEIYTDGACRGNpGPGG----WGAVIRYGGEEKELSGGLGDTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQI 78

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17137476 261 TLWVAGWKKRDWKlknnqPVKNVVDFKELDKLLQENNITVKWnyVEAHKGIEGNEMADKLARQG 324
Cdd:COG0328  79 TGWIHGWKKNGWK-----PVKNPDLWQRLDELLARHKVTFEW--VKGHAGHPGNERADALANKA 135
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 183-324 1.77e-37

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: 131.17  E-value: 1.77e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476 183 IVYTDGSCIGNGRAGACAGYGVYFGKNHQLNAAKPVEGRV----TNNVGEIQAAIHAIK------TALDLGIQKLCISTD 252
Cdd:cd13934   1 LVYIDGACRNNGRPDARAGYGVYFGPDSSYNVSGRLEDTGghpqTSQRAELRAAIAALRfrswiiDPDGEGLKTVVIATD 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17137476 253 SQFLINSITLWVAGWKKRDWKLKNNQPVKNVVDFKELDKL---LQENNITVKWNYVEAhkgiEGNEMADKLARQG 324
Cdd:cd13934  81 SEYVVKGATEWIPKWKRNGWRTSKGKPVKNRDLFELLLDEiedLEEGGVEVQFWHVPR----ELNKEADRLAKAA 151
rnhA PRK00203
ribonuclease H; Reviewed
 182-324 4.49e-34

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 122.24  E-value: 4.49e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476  182 VIVYTDGSCIGNGRAGacaGYGV---YFGKNHQLNAAKPVegrVTNNVGEIQAAIHAIKtALdlgiQKLC---ISTDSQF 255
Cdd:PRK00203   4 VEIYTDGACLGNPGPG---GWGAilrYKGHEKELSGGEAL---TTNNRMELMAAIEALE-AL----KEPCevtLYTDSQY 72

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17137476  256 LINSITLWVAGWKKRDWKLKNNQPVKNVVDFKELDKLLQENNITvkWNYVEAHKGIEGNEMADKLARQG 324
Cdd:PRK00203  73 VRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIK--WHWVKGHAGHPENERCDELARAG 139
Rnh1 COG3341
Ribonuclease HI-related protein, contains viroplasmin and RNaseH domains [General function ...
 16-324 1.24e-33

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


Pssm-ID: 442570 [Multi-domain]  Cd Length: 203  Bit Score: 122.65  E-value: 1.24e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476  16 MAFYAVASGRRSGVYGSWAECEEQVKGFKNAKYKKFKTRQEADQFVNGCKsyapqdvavplgkekaslaswknsiEVNKN 95
Cdd:COG3341   3 KKFYAVWKGRKPGIYTTWDECKAQVKGFPGAKYKSFKTKEEAEAALNGNY-------------------------EDYKG 57

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476  96 PKYTDEWPEEDhdlaeddlnaamnevegdpkpsnssnlpdilnrkrkgttsgdkrnkiprhasqvseatglkqvgafqfe 175
Cdd:COG3341  58 KKKKLSEIELD--------------------------------------------------------------------- 68

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476 176 idaegYVIVYTDGSCIGN-GRagacAGYGVYFGKNHQLNAAKP------VEGRvtNNVGEIQAAIHAIKTALDLGIqKLC 248
Cdd:COG3341  69 -----SIAVYVDGSCSGNpGV----YEYGGVDTKTGKETFSELfhdgpfAEGT--NNAGEFLAAVHALAYLKKKGS-KLP 136

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17137476 249 ISTDSQFLINsitlwvagWKKRDWKLKNNQPVKNVVDFKELDKllqENNITVKWNYVEAHKGIEGNEMADKLARQG 324
Cdd:COG3341 137 IYSDYRGAIS--------WVKGKWKTKLERTQAYKELFDLIEK---KNTYENPFVKVKTHSGDKWNEIPDDLARKA 201
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 184-322 6.82e-20

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: 83.90  E-value: 6.82e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476 184 VYTDGSCIGNGRagaCAGYGVYF--GKNHQLNAAKPVEGRVTNNVGEIQAAIHAIKTALDLGIQKLCISTDSQFLINSIT 261
Cdd:cd06222   1 INVDGSCRGNPG---PAGIGGVLrdHEGGWLGGFALKIGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLIN 77

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17137476 262 LWVAGWKKrdwklknnqpvKNVVDFKELDKLLQENNITVKWNYVeahkgiEGNEMADKLAR 322
Cdd:cd06222  78 SGSFKWSP-----------NILLIEDILLLLSRFWSVKISHVPR------EGNQVADALAK 121
Cauli_VI pfam01693
Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. ...
 18-60 1.42e-19

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


Pssm-ID: 460297 [Multi-domain]  Cd Length: 44  Bit Score: 80.53  E-value: 1.42e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 17137476    18 FYAVASGRRSGVYGSWAECEEQVKGFKNAKYKKFKTRQEADQF 60
Cdd:pfam01693   2 YYAVAKGRKPGIYTTWDECKAQVKGFPGAKYKSFKTREEAEAF 44
PRK06548 PRK06548
ribonuclease H; Provisional
 182-333 6.86e-19

ribonuclease H; Provisional


Pssm-ID: 75628 [Multi-domain]  Cd Length: 161  Bit Score: 82.17  E-value: 6.86e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476  182 VIVYTDGSCIGNGragACAGYGVYFGKNHQLNAAKPVegrVTNNVGEIqAAIHAIKTALDLGIQKLCISTDSQFLINSIT 261
Cdd:PRK06548   6 IIAATDGSSLANP---GPSGWAWYVDENTWDSGGWDI---ATNNIAEL-TAVRELLIATRHTDRPILILSDSKYVINSLT 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17137476  262 LWVAGWKKRDWKLKNNQPVKNVVDFKELDKLLQENNITVKWnyVEAHKGIEGNEMADKLARQGSALYKQKNG 333
Cdd:PRK06548  79 KWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENRNIRMSW--VNAHTGHPLNEAADSLARQAANNFSTRSA 148
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 182-325 3.00e-16

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: 74.05  E-value: 3.00e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476 182 VIVYTDGSCIGN-GRAGAcaGYGVYFGKNHQLNAAKPVEGRVTNNVGEIQAAIHAIKTALDLGIQKLCISTDSQFLINSI 260
Cdd:cd09279   1 WTLYFDGASRGNpGPAGA--GVVIYSPGGEVLELSERLGFPATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQL 78

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476 261 tlwvagwkKRDWKLKNN--QPVknvvdFKELDKLLQE-NNITVKWnyveahkgI--EGNEMADKLARQGS 325
Cdd:cd09279  79 --------NGEYKVKNErlKPL-----LEKVLELLAKfELVELKW--------IprEQNKEADALANQAL 127
RNase_HI_bacteria_like cd09277
Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; Ribonuclease H ...
 182-324 1.22e-14

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: 69.82  E-value: 1.22e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476 182 VIVYTDGSCIgngRAGACAGYGVYFGKNhqlNAAKPVEGRVTN-------NV-GEIQAAIHAIKTALDLGIQKLCISTDS 253
Cdd:cd09277   1 VIAYVDGSYN---KETKKYGYGVVIIKN---GKEEEFSGSGNDpeyasmrNVaGEIKGAMKAIKYAIENGIKKITIYYDY 74

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17137476 254 QflinSITLWVAGwkkrDWKLKNNQpVKNVVDFkeLDKLLQEnnITVKWNYVEAHKGIEGNEMADKLARQG 324
Cdd:cd09277  75 E----GIEKWATG----EWKANKEL-TKEYKEF--MQKYKKK--IKIEFVKVKAHSGDKYNELADKLAKKA 132
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 184-326 1.58e-14

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: 69.17  E-value: 1.58e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476 184 VYTDGSCIgNGRAGAcaGYGVY-FGKNHQLNAAKPVEGRVTNnvGEIQAAIHAIKTAL--DLGIQKLCISTDSQFLINSI 260
Cdd:cd09276   2 IYTDGSKL-EGSVGA--GFVIYrGGEVISRSYRLGTHASVFD--AELEAILEALELALatARRARKVTIFTDSQSALQAL 76

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17137476 261 tlwvagwkkRDWKLKNNQPVknVVDFKELDKLLQENNITVKWNYVEAHKGIEGNEMADKLARQGSA 326
Cdd:cd09276  77 ---------RNPRRSSGQVI--LIRILRLLRLLKAKGVKVRLRWVPGHVGIEGNEAADRLAKEAAS 131
PRK08719 PRK08719
ribonuclease H; Reviewed
 178-327 1.13e-12

ribonuclease H; Reviewed


Pssm-ID: 236334 [Multi-domain]  Cd Length: 147  Bit Score: 64.50  E-value: 1.13e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476  178 AEGYVIVYTDGSCiGNGRAGaCAGYG---VYFGKNHQL--NAAKPVEGRVTNNVGEIQAAIHAIKTALDLGIqklcISTD 252
Cdd:PRK08719   1 MRASYSIYIDGAA-PNNQHG-CVRGGiglVVYDEAGEIvdEQSITVNRYTDNAELELLALIEALEYARDGDV----IYSD 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17137476  253 SQFLINSITLWVAGWKKRDWKLKNNQPVKNVVDFKELDKLLQENNITVKwnYVEAHKGIEGNEMADKLARQGSAL 327
Cdd:PRK08719  75 SDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVEVE--KVTAHSGIEGNEAADMLAQAAAEL 147
RNAseHI_Thmprot NF041175
ribonuclease HI;
182-332 1.02e-08

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 53.43  E-value: 1.02e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476  182 VIVYTDGSCIGNGRAG-ACAGYGVYFGKNHQLN----AAKPVEGRVTNNVGEIQAAIHAIKTALDLGIQKLCISTDSQFL 256
Cdd:NF041175   2 AIGYFDGLCEPKNPGGiATYGYVIYLDNKRKIEgyglAAEPWSKDSTNNVAEYTGLICLLEKLLELGISEVIIRGDSQLV 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476  257 INSITlwvagwkkRDWKLKNNQ--PVknvvdFKELDKLLQE-NNITVKWnyveahkgI--EGNEMADKLARQGSALYKQK 331
Cdd:NF041175  82 IRQLN--------GEYKVKSPRiiPL-----YEKALELLSKfRSIEFEW--------VprEENKEADRLSRIAYELVLKG 140


                 .
gi 17137476  332 N 332
Cdd:NF041175 141 K 141
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 184-323 3.46e-07

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: 48.49  E-value: 3.46e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476 184 VYTDGSCIGngragacAGYGVYFGKNHQLnaAKPVEGRVTNNVGEIQAAIHAIKTALDlgiQKLCISTDSQFLINSITLW 263
Cdd:cd09273   2 VFTDGSSFK-------AGYAIVSGTEIVE--AQPLPPGTSAQRAELIALIQALELAKG---KPVNIYTDSAYAVHALHLL 69

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17137476 264 VAGWKKRdwklKNNQPVKNVVDFKELDKLLQENN---ITvkwnYVEAHKG-----IEGNEMADKLARQ 323
Cdd:cd09273  70 ETIGIER----GFLKSIKNLSLFLQLLEAVQRPKpvaII----HIRAHSKlpgplAEGNAQADAAAKQ 129
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 214-322 1.48e-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: 40.71  E-value: 1.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476   214 AAKPVEGRVTNNVGEIQAAIHAIKTALDLGIQKLCISTDSQFLINSITlwvAGWKKRDwklknnqPVKNVVDfkELDKLL 293
Cdd:pfam13456  30 GQKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLIN---GRSPKQS-------KLANLLD--EIRKLL 97

                          90       100       110
                  ....*....|....*....|....*....|
gi 17137476   294 QE-NNITVKWNYVeahkgiEGNEMADKLAR 322
Cdd:pfam13456  98 KRfESVSFEHIPR------EQNRVADTLAK 121
PRK07708 PRK07708
hypothetical protein; Validated
 175-258 5.02e-03

hypothetical protein; Validated


Pssm-ID: 181088 [Multi-domain]  Cd Length: 219  Bit Score: 37.71  E-value: 5.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17137476  175 EIDAEGY-VIVYTDGSC-IGNGRAGAcaGYGVYF---GKNHQLNAAKPVEGRVTNNVGEIQAAIHAIKTALDLGIQKLCI 249
Cdd:PRK07708  66 EVEEEPHeILVYFDGGFdKETKLAGL--GIVIYYkqgNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPV 143

                         90
                 ....*....|.
gi 17137476  250 S--TDSQFLIN 258
Cdd:PRK07708 144 TfrGDSQVVLN 154
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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