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Conserved domains on  [gi|1907169074|ref|XP_036021580|]
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uncharacterized protein Gm54333 [Mus musculus]

Protein Classification

RNase_HI_RT_Bel and rve domain-containing protein( domain architecture ID 10873193)

protein containing domains RNase_HI_RT_Bel, zf-H2C2, and rve

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
109-249 5.13e-58

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: 187.55  E-value: 5.13e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907169074 109 TWYTDGSSFlqegqrKAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFATAHVHGEIYR 188
Cdd:cd09273     1 TVFTDGSSF------KAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGI 74
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907169074 189 RRGLLtsegKEIKNKGEILALLKALFLPKRLSIIHCPGHQKGNSAEAKGNRMADQAAREAA 249
Cdd:cd09273    75 ERGFL----KSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
zf-H2C2 super family cl07828
His(2)-Cys(2) zinc finger; This domain binds to histone upstream activating sequence (UAS) ...
270-365 2.60e-48

His(2)-Cys(2) zinc finger; This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters. Added to clan to resolve overlaps with pfam16721 but neither are classic zf_C2H2 zinc-fingers.


The actual alignment was detected with superfamily member pfam16721:

Pssm-ID: 447530  Cd Length: 96  Bit Score: 161.05  E-value: 2.60e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907169074 270 DFFHYTETDIKNLQELGATYDREKKYWVLQGKPVMPDQFTFELLDFLHQLTHLSYQKMRALLDRKESPYYMLNKDKILHE 349
Cdd:pfam16721   1 EHFHYTVTDIKDLTKLGAIYDKTKKYWVYQGKPVMPDQFTFELLDFLHQLTHLSFSKMKALLERSHSPYYMLNRDRTLKN 80
                          90
                  ....*....|....*.
gi 1907169074 350 VAESCQACVQVNASKA 365
Cdd:pfam16721  81 ITETCKACAQVNASKS 96
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
378-452 4.08e-19

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


:

Pssm-ID: 425808 [Multi-domain]  Cd Length: 98  Bit Score: 81.98  E-value: 4.08e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907169074 378 PGTHWEIDFTEVK-PGLYGYKYLLVFVDTFSGWVEAFPTKHETAKVVTKKLLEEIF-PRFGMPQVLGTDNGPAFVSQ 452
Cdd:pfam00665   1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIaFRGGVPLIIHSDNGSEYTSK 77
 
Name Accession Description Interval E-value
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
109-249 5.13e-58

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: 187.55  E-value: 5.13e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907169074 109 TWYTDGSSFlqegqrKAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFATAHVHGEIYR 188
Cdd:cd09273     1 TVFTDGSSF------KAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGI 74
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907169074 189 RRGLLtsegKEIKNKGEILALLKALFLPKRLSIIHCPGHQKGNSAEAKGNRMADQAAREAA 249
Cdd:cd09273    75 ERGFL----KSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
zf-H3C2 pfam16721
Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers ...
270-365 2.60e-48

Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers found on Gag-Pol polyproteins from mouse retroviruses. Added to clan to resolve overlaps with zf-H2C2, but neither are true members.


Pssm-ID: 293326  Cd Length: 96  Bit Score: 161.05  E-value: 2.60e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907169074 270 DFFHYTETDIKNLQELGATYDREKKYWVLQGKPVMPDQFTFELLDFLHQLTHLSYQKMRALLDRKESPYYMLNKDKILHE 349
Cdd:pfam16721   1 EHFHYTVTDIKDLTKLGAIYDKTKKYWVYQGKPVMPDQFTFELLDFLHQLTHLSFSKMKALLERSHSPYYMLNRDRTLKN 80
                          90
                  ....*....|....*.
gi 1907169074 350 VAESCQACVQVNASKA 365
Cdd:pfam16721  81 ITETCKACAQVNASKS 96
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
109-249 1.93e-40

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: 141.75  E-value: 1.93e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907169074 109 TWYTDGSSFLQEGQRKAGAAVTTETEvIWAKALPAGTSAQRAELIALTQALK-MAEGKKLNVYTDSRYAFATAH--VHGE 185
Cdd:pfam00075   5 TVYTDGSCLGNPGPGGAGAVLYRGHE-NISAPLPGRTTNNRAELQAVIEALKaLKSPSKVNIYTDSQYVIGGITqwVHGW 83
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907169074 186 IYRRRGlLTSEGKEIKNKgEILALLKALFLPKRLSIIHCPGHqKGNsaeaKGNRMADQAAREAA 249
Cdd:pfam00075  84 KKNGWP-TTSEGKPVKNK-DLWQLLKALCKKHQVYWQWVKGH-AGN----PGNEMADRLAKQGA 140
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
378-452 4.08e-19

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 425808 [Multi-domain]  Cd Length: 98  Bit Score: 81.98  E-value: 4.08e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907169074 378 PGTHWEIDFTEVK-PGLYGYKYLLVFVDTFSGWVEAFPTKHETAKVVTKKLLEEIF-PRFGMPQVLGTDNGPAFVSQ 452
Cdd:pfam00665   1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIaFRGGVPLIIHSDNGSEYTSK 77
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
111-250 1.74e-14

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 223405 [Multi-domain]  Cd Length: 154  Bit Score: 70.85  E-value: 1.74e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907169074 111 YTDGSSFLQEGQRKAGAAV--TTETEVIWAKAlpAGTSAQRAELIALTQALKMAEGKK---LNVYTDSRYAFATAHVHGE 185
Cdd:COG0328     7 FTDGACLGNPGPGGWGAVLryGDGEKELSGGE--GRTTNNRAELRALIEALEALKELGaceVTLYTDSKYVVEGITRWIV 84
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907169074 186 IYRRRGLLTSEGKEIKNKG---EILALLKALflpKRLSIIHCPGHQkGNsaeaKGNRMADQAAREAAM 250
Cdd:COG0328    85 KWKKNGWKTADKKPVKNKDlweELDELLKRH---ELVFWEWVKGHA-GH----PENERADQLAREAAR 144
rnhA PRK00203
ribonuclease H; Reviewed
143-249 1.88e-03

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 38.65  E-value: 1.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907169074 143 AGTSAQRAELIALTQALKM-AEGKKLNVYTDSRY---AFaTAHVHGeiYRRRGLLTSEGKEIKNKGEILALLKALflpKR 218
Cdd:PRK00203   39 ALTTNNRMELMAAIEALEAlKEPCEVTLYTDSQYvrqGI-TEWIHG--WKKNGWKTADKKPVKNVDLWQRLDAAL---KR 112
                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1907169074 219 lsiihcpgHQ------KGNSAEAkGNRMADQAAREAA 249
Cdd:PRK00203  113 --------HQikwhwvKGHAGHP-ENERCDELARAGA 140
 
Name Accession Description Interval E-value
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
109-249 5.13e-58

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: 187.55  E-value: 5.13e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907169074 109 TWYTDGSSFlqegqrKAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFATAHVHGEIYR 188
Cdd:cd09273     1 TVFTDGSSF------KAGYAIVSGTEIVEAQPLPPGTSAQRAELIALIQALELAKGKPVNIYTDSAYAVHALHLLETIGI 74
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907169074 189 RRGLLtsegKEIKNKGEILALLKALFLPKRLSIIHCPGHQKGNSAEAKGNRMADQAAREAA 249
Cdd:cd09273    75 ERGFL----KSIKNLSLFLQLLEAVQRPKPVAIIHIRAHSKLPGPLAEGNAQADAAAKQAA 131
zf-H3C2 pfam16721
Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers ...
270-365 2.60e-48

Zinc-finger like, probable DNA-binding; This is a family of probably DNA-binding zinc-fingers found on Gag-Pol polyproteins from mouse retroviruses. Added to clan to resolve overlaps with zf-H2C2, but neither are true members.


Pssm-ID: 293326  Cd Length: 96  Bit Score: 161.05  E-value: 2.60e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907169074 270 DFFHYTETDIKNLQELGATYDREKKYWVLQGKPVMPDQFTFELLDFLHQLTHLSYQKMRALLDRKESPYYMLNKDKILHE 349
Cdd:pfam16721   1 EHFHYTVTDIKDLTKLGAIYDKTKKYWVYQGKPVMPDQFTFELLDFLHQLTHLSFSKMKALLERSHSPYYMLNRDRTLKN 80
                          90
                  ....*....|....*.
gi 1907169074 350 VAESCQACVQVNASKA 365
Cdd:pfam16721  81 ITETCKACAQVNASKS 96
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
109-249 1.93e-40

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: 141.75  E-value: 1.93e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907169074 109 TWYTDGSSFLQEGQRKAGAAVTTETEvIWAKALPAGTSAQRAELIALTQALK-MAEGKKLNVYTDSRYAFATAH--VHGE 185
Cdd:pfam00075   5 TVYTDGSCLGNPGPGGAGAVLYRGHE-NISAPLPGRTTNNRAELQAVIEALKaLKSPSKVNIYTDSQYVIGGITqwVHGW 83
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907169074 186 IYRRRGlLTSEGKEIKNKgEILALLKALFLPKRLSIIHCPGHqKGNsaeaKGNRMADQAAREAA 249
Cdd:pfam00075  84 KKNGWP-TTSEGKPVKNK-DLWQLLKALCKKHQVYWQWVKGH-AGN----PGNEMADRLAKQGA 140
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
111-250 8.56e-21

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: 88.39  E-value: 8.56e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907169074 111 YTDGSsFLQEGQR--KAGAAVtteteviW---------AKALP--AGTSaQRAELIALTQALKMA---EGKKLNVYTDSR 174
Cdd:cd09280     3 YTDGS-CLNNGKPgaRAGIGV-------YfgpgdprnvSEPLPgrKQTN-NRAELLAVIHALEQApeeGIRKLEIRTDSK 73
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907169074 175 YAFATAHVHGEIYRRRGLLTSEGKEIKNKGEILALLKAL-FLPKRLSIIHCPGHQkGNsaeaKGNRMADQAAREAAM 250
Cdd:cd09280    74 YAINCITKWIPKWKKNGWKTSKGKPVKNQDLIKELDKLLrKRGIKVKFEHVKGHS-GD----PGNEEADRLAREGAD 145
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
378-452 4.08e-19

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 425808 [Multi-domain]  Cd Length: 98  Bit Score: 81.98  E-value: 4.08e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907169074 378 PGTHWEIDFTEVK-PGLYGYKYLLVFVDTFSGWVEAFPTKHETAKVVTKKLLEEIF-PRFGMPQVLGTDNGPAFVSQ 452
Cdd:pfam00665   1 PNQLWQGDFTYIRiPGGGGKLYLLVIVDDFSREILAWALSSEMDAELVLDALERAIaFRGGVPLIIHSDNGSEYTSK 77
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
111-249 1.17e-15

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: 73.67  E-value: 1.17e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907169074 111 YTDGSSFLQEGqrKAG--AAVTTETEVIWAKALPAGTSAQRAELIALTQALKMA-EGKKLNVYTDSRYAF--ATAHVHGe 185
Cdd:cd09278     5 YTDGACLGNPG--PGGwaAVIRYGDHEKELSGGEPGTTNNRMELTAAIEALEALkEPCPVTIYTDSQYVIngITKWIKG- 81
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907169074 186 iYRRRGLLTSEGKEIKNKGEILALLKALfLPKRLSIIHCPGHQkGNsaeaKGNRMADQAAREAA 249
Cdd:cd09278    82 -WKKNGWKTADGKPVKNRDLWQELDALL-AGHKVTWEWVKGHA-GH----PGNERADRLANKAA 138
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
110-246 5.44e-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: 71.19  E-value: 5.44e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907169074 110 WYTDGSSFLQEGQRKAGAAVT-TETEVIWAKALPAGT-SAQRAELIALTQALKMA---EGKKLNVYTDSRYAFatahvhg 184
Cdd:cd06222     1 INVDGSCRGNPGPAGIGGVLRdHEGGWLGGFALKIGApTALEAELLALLLALELAldlGYLKVIIESDSKYVV------- 73
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907169074 185 eiyrrRGLLTSEGKEIKNKGEILALLKALFLPKRLSIIHCPGhqkgnsaeaKGNRMADQAAR 246
Cdd:cd06222    74 -----DLINSGSFKWSPNILLIEDILLLLSRFWSVKISHVPR---------EGNQVADALAK 121
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
111-250 1.74e-14

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 223405 [Multi-domain]  Cd Length: 154  Bit Score: 70.85  E-value: 1.74e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907169074 111 YTDGSSFLQEGQRKAGAAV--TTETEVIWAKAlpAGTSAQRAELIALTQALKMAEGKK---LNVYTDSRYAFATAHVHGE 185
Cdd:COG0328     7 FTDGACLGNPGPGGWGAVLryGDGEKELSGGE--GRTTNNRAELRALIEALEALKELGaceVTLYTDSKYVVEGITRWIV 84
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907169074 186 IYRRRGLLTSEGKEIKNKG---EILALLKALflpKRLSIIHCPGHQkGNsaeaKGNRMADQAAREAAM 250
Cdd:COG0328    85 KWKKNGWKTADKKPVKNKDlweELDELLKRH---ELVFWEWVKGHA-GH----PENERADQLAREAAR 144
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
111-249 1.28e-13

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: 67.63  E-value: 1.28e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907169074 111 YTDGSSflQEGQRKAGAAVTTETEVI-WAKALPAGTSAQRAELIALTQALKMA-----EGKKLNVYTDSRYAFA----TA 180
Cdd:cd09276     3 YTDGSK--LEGSVGAGFVIYRGGEVIsRSYRLGTHASVFDAELEAILEALELAlatarRARKVTIFTDSQSALQalrnPR 80
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907169074 181 HVHGEIYRRRGLLTSegKEIKNKGeilallkalflpKRLSIIHCPGHQkgnsaEAKGNRMADQAAREAA 249
Cdd:cd09276    81 RSSGQVILIRILRLL--RLLKAKG------------VKVRLRWVPGHV-----GIEGNEAADRLAKEAA 130
zf-H2C2 pfam09337
His(2)-Cys(2) zinc finger; This domain binds to histone upstream activating sequence (UAS) ...
317-357 5.53e-12

His(2)-Cys(2) zinc finger; This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters. Added to clan to resolve overlaps with pfam16721 but neither are classic zf_C2H2 zinc-fingers.


Pssm-ID: 430537  Cd Length: 39  Bit Score: 60.03  E-value: 5.53e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1907169074 317 HQLTHLSYQKMRALLDRKespYYMLNKDKILHEVAESCQAC 357
Cdd:pfam09337   1 HALTHLGINKLTALLARK---YHWLGIKETVSEVISSCVAC 38
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
111-249 6.06e-07

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: 48.24  E-value: 6.06e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907169074 111 YTDGSSFLQEGQRKAGAAVTTETEVIW--AKALPAGTSAQRAELIALTQALKMAEG---KKLNVYTDSRyaFATAHVHGE 185
Cdd:cd09279     4 YFDGASRGNPGPAGAGVVIYSPGGEVLelSERLGFPATNNEAEYEALIAGLELALElgaEKLEIYGDSQ--LVVNQLNGE 81
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907169074 186 IyrrrglltsegkEIKNKG------EILALLKALflpKRLSIIHCPGHQkgnsaeakgNRMADQAAREAA 249
Cdd:cd09279    82 Y------------KVKNERlkplleKVLELLAKF---ELVELKWIPREQ---------NKEADALANQAL 127
rnhA PRK00203
ribonuclease H; Reviewed
143-249 1.88e-03

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 38.65  E-value: 1.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907169074 143 AGTSAQRAELIALTQALKM-AEGKKLNVYTDSRY---AFaTAHVHGeiYRRRGLLTSEGKEIKNKGEILALLKALflpKR 218
Cdd:PRK00203   39 ALTTNNRMELMAAIEALEAlKEPCEVTLYTDSQYvrqGI-TEWIHG--WKKNGWKTADKKPVKNVDLWQRLDAAL---KR 112
                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1907169074 219 lsiihcpgHQ------KGNSAEAkGNRMADQAAREAA 249
Cdd:PRK00203  113 --------HQikwhwvKGHAGHP-ENERCDELARAGA 140
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
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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