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Conserved domains on  [gi|1768928482|gb|KAB8213079|]
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ribonuclease H-like domain-containing protein [Aspergillus novoparasiticus]

Protein Classification

RNase_H_Dikarya_like domain-containing protein( domain architecture ID 10195359)

RNase_H_Dikarya_like domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 134-290 1.38e-80

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: 241.33  E-value: 1.38e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 134 LIYTDGACLDNGRANPRAGCSFVFKPSTPqpkglGSVHFRLEDDGPtgeaHPQTSNRAELRAVIAALRFRFW----PGEG 209
Cdd:cd13934     1 LVYIDGACRNNGRPDARAGYGVYFGPDSS-----YNVSGRLEDTGG----HPQTSQRAELRAAIAALRFRSWiidpDGEG 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 210 FTSLLIATDSEYVVEGVTSWVRGWLQRGWRTRTGSVVKNRDLWECILGEIERWDGHGMQVKFWRIPRDWNKEADYHAKIA 289
Cdd:cd13934    72 LKTVVIATDSEYVVKGATEWIPKWKRNGWRTSKGKPVKNRDLFELLLDEIEDLEEGGVEVQFWHVPRELNKEADRLAKAA 151


                  .
gi 1768928482 290 A 290
Cdd:cd13934   152 A 152
 
Name Accession Description Interval E-value
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 134-290 1.38e-80

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: 241.33  E-value: 1.38e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 134 LIYTDGACLDNGRANPRAGCSFVFKPSTPqpkglGSVHFRLEDDGPtgeaHPQTSNRAELRAVIAALRFRFW----PGEG 209
Cdd:cd13934     1 LVYIDGACRNNGRPDARAGYGVYFGPDSS-----YNVSGRLEDTGG----HPQTSQRAELRAAIAALRFRSWiidpDGEG 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 210 FTSLLIATDSEYVVEGVTSWVRGWLQRGWRTRTGSVVKNRDLWECILGEIERWDGHGMQVKFWRIPRDWNKEADYHAKIA 289
Cdd:cd13934    72 LKTVVIATDSEYVVKGATEWIPKWKRNGWRTSKGKPVKNRDLFELLLDEIEDLEEGGVEVQFWHVPRELNKEADRLAKAA 151


                  .
gi 1768928482 290 A 290
Cdd:cd13934   152 A 152
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
135-290 5.94e-28

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 105.31  E-value: 5.94e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 135 IYTDGACLDNgranpragcsfvfkpstPQPKGLGSVhfrLEDDGPT-----GEAHpQTSNRAELRAVIAALRFrfWPGEG 209
Cdd:COG0328     5 IYTDGACRGN-----------------PGPGGWGAV---IRYGGEEkelsgGLGD-TTNNRAELTALIAALEA--LKELG 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 210 FTSLLIATDSEYVVEGVTSWVRGWLQRGWRTrtgsvVKNRDLWECILGEIERwdgHgmQVKFWRIPR----DWNKEADYH 285
Cdd:COG0328    62 PCEVEIYTDSQYVVNQITGWIHGWKKNGWKP-----VKNPDLWQRLDELLAR---H--KVTFEWVKGhaghPGNERADAL 131


                  ....*
gi 1768928482 286 AKIAA 290
Cdd:COG0328   132 ANKAL 136
rnhA PRK00203
ribonuclease H; Reviewed
 135-300 5.19e-22

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 89.89  E-value: 5.19e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 135 IYTDGACLDNgranpragcsfvfkpstPQPKGLGSV-----HFRlEDDGptGEAHpQTSNRAELRAVIAALRFRFWPgeg 209
Cdd:PRK00203    6 IYTDGACLGN-----------------PGPGGWGAIlrykgHEK-ELSG--GEAL-TTNNRMELMAAIEALEALKEP--- 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 210 fTSLLIATDSEYVVEGVTSWVRGWLQRGWRTRTGSVVKNRDLWECILGEIERwdgHgmQVKfWRiprdW---------NK 280
Cdd:PRK00203   62 -CEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR---H--QIK-WH----WvkghaghpeNE 130

                         170       180
                  ....*....|....*....|
gi 1768928482 281 EADYHAKIAASEDTIERFTD 300
Cdd:PRK00203  131 RCDELARAGAEEATLEDTGY 150
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 135-291 5.43e-21

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: 87.05  E-value: 5.43e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 135 IYTDGACLDNgranpragcsfvfkpstPQPKGLGSVHFRLEDDGPTGEAHPQTSNRAELRAVIAALRFRFWPgegfTSLL 214
Cdd:pfam00075   6 VYTDGSCLGN-----------------PGPGGAGAVLYRGHENISAPLPGRTTNNRAELQAVIEALKALKSP----SKVN 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 215 IATDSEYVVEGVTSWVRGWLQRGWR-TRTGSVVKNRDLWECILGEIERwdghgMQVKFWRIP----RDWNKEADYHAKIA 289
Cdd:pfam00075  65 IYTDSQYVIGGITQWVHGWKKNGWPtTSEGKPVKNKDLWQLLKALCKK-----HQVYWQWVKghagNPGNEMADRLAKQG 139


                  ..
gi 1768928482 290 AS 291
Cdd:pfam00075 140 AE 141
 
Name Accession Description Interval E-value
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 134-290 1.38e-80

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: 241.33  E-value: 1.38e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 134 LIYTDGACLDNGRANPRAGCSFVFKPSTPqpkglGSVHFRLEDDGPtgeaHPQTSNRAELRAVIAALRFRFW----PGEG 209
Cdd:cd13934     1 LVYIDGACRNNGRPDARAGYGVYFGPDSS-----YNVSGRLEDTGG----HPQTSQRAELRAAIAALRFRSWiidpDGEG 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 210 FTSLLIATDSEYVVEGVTSWVRGWLQRGWRTRTGSVVKNRDLWECILGEIERWDGHGMQVKFWRIPRDWNKEADYHAKIA 289
Cdd:cd13934    72 LKTVVIATDSEYVVKGATEWIPKWKRNGWRTSKGKPVKNRDLFELLLDEIEDLEEGGVEVQFWHVPRELNKEADRLAKAA 151


                  .
gi 1768928482 290 A 290
Cdd:cd13934   152 A 152
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 135-290 2.91e-35

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: 124.60  E-value: 2.91e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 135 IYTDGACLDNGRANPRAGCSFVFKPSTPQpkglgSVHFRLEDdgptgeaHPQTSNRAELRAVIAALRFRfwPGEGFTSLL 214
Cdd:cd09280     2 VYTDGSCLNNGKPGARAGIGVYFGPGDPR-----NVSEPLPG-------RKQTNNRAELLAVIHALEQA--PEEGIRKLE 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 215 IATDSEYVVEGVTSWVRGWLQRGWRTRTGSVVKNRDLWECILgeiERWDGHGMQVKFWRIP----RDWNKEADYHAKIAA 290
Cdd:cd09280    68 IRTDSKYAINCITKWIPKWKKNGWKTSKGKPVKNQDLIKELD---KLLRKRGIKVKFEHVKghsgDPGNEEADRLAREGA 144
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
135-290 5.94e-28

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 105.31  E-value: 5.94e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 135 IYTDGACLDNgranpragcsfvfkpstPQPKGLGSVhfrLEDDGPT-----GEAHpQTSNRAELRAVIAALRFrfWPGEG 209
Cdd:COG0328     5 IYTDGACRGN-----------------PGPGGWGAV---IRYGGEEkelsgGLGD-TTNNRAELTALIAALEA--LKELG 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 210 FTSLLIATDSEYVVEGVTSWVRGWLQRGWRTrtgsvVKNRDLWECILGEIERwdgHgmQVKFWRIPR----DWNKEADYH 285
Cdd:COG0328    62 PCEVEIYTDSQYVVNQITGWIHGWKKNGWKP-----VKNPDLWQRLDELLAR---H--KVTFEWVKGhaghPGNERADAL 131


                  ....*
gi 1768928482 286 AKIAA 290
Cdd:COG0328   132 ANKAL 136
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 135-290 4.65e-27

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: 102.95  E-value: 4.65e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 135 IYTDGACLDNgranpragcsfvfkpstPQPKGLGSVhfrLEDDGPT-----GEAHpQTSNRAELRAVIAALRfRFWPGEg 209
Cdd:cd09278     4 IYTDGACLGN-----------------PGPGGWAAV---IRYGDHEkelsgGEPG-TTNNRMELTAAIEALE-ALKEPC- 60

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 210 ftSLLIATDSEYVVEGVTSWVRGWLQRGWRTRTGSVVKNRDLWECILGEIERwdgHgmQVKF-W-----RIPrdWNKEAD 283
Cdd:cd09278    61 --PVTIYTDSQYVINGITKWIKGWKKNGWKTADGKPVKNRDLWQELDALLAG---H--KVTWeWvkghaGHP--GNERAD 131


                  ....*..
gi 1768928482 284 YHAKIAA 290
Cdd:cd09278   132 RLANKAA 138
rnhA PRK00203
ribonuclease H; Reviewed
 135-300 5.19e-22

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 89.89  E-value: 5.19e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 135 IYTDGACLDNgranpragcsfvfkpstPQPKGLGSV-----HFRlEDDGptGEAHpQTSNRAELRAVIAALRFRFWPgeg 209
Cdd:PRK00203    6 IYTDGACLGN-----------------PGPGGWGAIlrykgHEK-ELSG--GEAL-TTNNRMELMAAIEALEALKEP--- 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 210 fTSLLIATDSEYVVEGVTSWVRGWLQRGWRTRTGSVVKNRDLWECILGEIERwdgHgmQVKfWRiprdW---------NK 280
Cdd:PRK00203   62 -CEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR---H--QIK-WH----WvkghaghpeNE 130

                         170       180
                  ....*....|....*....|
gi 1768928482 281 EADYHAKIAASEDTIERFTD 300
Cdd:PRK00203  131 RCDELARAGAEEATLEDTGY 150
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 135-291 5.43e-21

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: 87.05  E-value: 5.43e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 135 IYTDGACLDNgranpragcsfvfkpstPQPKGLGSVHFRLEDDGPTGEAHPQTSNRAELRAVIAALRFRFWPgegfTSLL 214
Cdd:pfam00075   6 VYTDGSCLGN-----------------PGPGGAGAVLYRGHENISAPLPGRTTNNRAELQAVIEALKALKSP----SKVN 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 215 IATDSEYVVEGVTSWVRGWLQRGWR-TRTGSVVKNRDLWECILGEIERwdghgMQVKFWRIP----RDWNKEADYHAKIA 289
Cdd:pfam00075  65 IYTDSQYVIGGITQWVHGWKKNGWPtTSEGKPVKNKDLWQLLKALCKK-----HQVYWQWVKghagNPGNEMADRLAKQG 139


                  ..
gi 1768928482 290 AS 291
Cdd:pfam00075 140 AE 141
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 135-287 7.99e-15

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


Pssm-ID: 259998 [Multi-domain]  Cd Length: 121  Bit Score: 69.65  E-value: 7.99e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 135 IYTDGACLDNGRanpRAGCSFVFKPSTpqpkglGSVHFrleddGPTGEAHPQTSNRAELRAVIAALRFrfWPGEGFTSLL 214
Cdd:cd06222     1 INVDGSCRGNPG---PAGIGGVLRDHE------GGWLG-----GFALKIGAPTALEAELLALLLALEL--ALDLGYLKVI 64

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1768928482 215 IATDSEYVVEGVTSWVRGWLQRGwrtrtgsvvknrdlweCILGEIERWDGHGMQVKFWRIPRDWNKEADYHAK 287
Cdd:cd06222    65 IESDSKYVVDLINSGSFKWSPNI----------------LLIEDILLLLSRFWSVKISHVPREGNQVADALAK 121
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 135-291 2.97e-10

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: 57.10  E-value: 2.97e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 135 IYTDGACldngRANP-RAGCSFVFKPSTPQPKglgSVHFRLEddgptgeaHPQTSNRAELRAVIAALRF--RFwpgeGFT 211
Cdd:cd09279     3 LYFDGAS----RGNPgPAGAGVVIYSPGGEVL---ELSERLG--------FPATNNEAEYEALIAGLELalEL----GAE 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 212 SLLIATDSEYVVEGVtswvrgwlQRGWRtrtgsvVKNRDLwECILGEIERWDGHGMQVKFWRIPRDWNKEADYHAKIAAS 291
Cdd:cd09279    64 KLEIYGDSQLVVNQL--------NGEYK------VKNERL-KPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
PRK08719 PRK08719
ribonuclease H; Reviewed
 187-255 5.79e-10

ribonuclease H; Reviewed


Pssm-ID: 236334 [Multi-domain]  Cd Length: 147  Bit Score: 56.79  E-value: 5.79e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1768928482 187 TSNRAELRAVIAALRFrfwPGEGFtslLIATDSEYVVEGVTSWVRGWLQRGWRTRTGSVVKNRDLWECI 255
Cdd:PRK08719   49 DNAELELLALIEALEY---ARDGD---VIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQV 111
PRK06548 PRK06548
ribonuclease H; Provisional
 128-251 1.65e-06

ribonuclease H; Provisional


Pssm-ID: 75628 [Multi-domain]  Cd Length: 161  Bit Score: 47.12  E-value: 1.65e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768928482 128 TNNELfLIYTDGACLDNgranpragcsfvfkpstPQPKGLGsvHFRLEDDGPTGEAHPQTSNRAELRAV---IAALRFRF 204
Cdd:PRK06548    2 TNNEI-IAATDGSSLAN-----------------PGPSGWA--WYVDENTWDSGGWDIATNNIAELTAVrelLIATRHTD 61

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1768928482 205 WPgegftsLLIATDSEYVVEGVTSWVRGWLQRGWRTRTGSVVKNRDL 251
Cdd:PRK06548   62 RP------ILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEI 102
 
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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