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Conserved domains on  [gi|755404252|gb|AJJ21414|]
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RNase H family protein [Yersinia intermedia]

Protein Classification

ribonuclease HI( domain architecture ID 10791836)

type 1 ribonuclease H is involved in the removal of RNA from RNA/DNA hybrids during DNA replication, repair and transcription

EC:  3.1.26.4
Gene Ontology:  GO:0004523

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rnhA PRK00203
ribonuclease H; Reviewed
 3-151 4.54e-111

ribonuclease H; Reviewed


:

Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 311.38  E-value: 4.54e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252   3 KQVEIFTDGSCLGNPGPGGYGAIMRYKQHEKTFSAGYRLTTNNRMELMAAIVALEALTSPCQVTLSTDSQYVRQGITQWI 82
Cdd:PRK00203   2 KQVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKEPCEVTLYTDSQYVRQGITEWI 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 755404252  83 HNWKKRGWKTTDRKPVRNVDLWQRLDLAIQGHTVQWEWVKGHAGHPENERCDELARLAANSPTQDDIGY 151
Cdd:PRK00203  82 HGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWVKGHAGHPENERCDELARAGAEEATLEDTGY 150
 
Name Accession Description Interval E-value
rnhA PRK00203
ribonuclease H; Reviewed
 3-151 4.54e-111

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 311.38  E-value: 4.54e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252   3 KQVEIFTDGSCLGNPGPGGYGAIMRYKQHEKTFSAGYRLTTNNRMELMAAIVALEALTSPCQVTLSTDSQYVRQGITQWI 82
Cdd:PRK00203   2 KQVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKEPCEVTLYTDSQYVRQGITEWI 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 755404252  83 HNWKKRGWKTTDRKPVRNVDLWQRLDLAIQGHTVQWEWVKGHAGHPENERCDELARLAANSPTQDDIGY 151
Cdd:PRK00203  82 HGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWVKGHAGHPENERCDELARAGAEEATLEDTGY 150
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 4-142 1.23e-93

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: 267.04  E-value: 1.23e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252   4 QVEIFTDGSCLGNPGPGGYGAIMRYKQHEKTFSAGYRLTTNNRMELMAAIVALEALTSPCQVTLSTDSQYVRQGITQWIH 83
Cdd:cd09278    1 EIVIYTDGACLGNPGPGGWAAVIRYGDHEKELSGGEPGTTNNRMELTAAIEALEALKEPCPVTIYTDSQYVINGITKWIK 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 755404252  84 NWKKRGWKTTDRKPVRNVDLWQRLDLAIQGHTVQWEWVKGHAGHPENERCDELARLAAN 142
Cdd:cd09278   81 GWKKNGWKTADGKPVKNRDLWQELDALLAGHKVTWEWVKGHAGHPGNERADRLANKAAD 139
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
3-141 7.58e-82

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 237.05  E-value: 7.58e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252   3 KQVEIFTDGSCLGNPGPGGYGAIMRYKQHEKTFSAGYRLTTNNRMELMAAIVALEALT--SPCQVTLSTDSQYVRQGITQ 80
Cdd:COG0328    1 KMIEIYTDGACRGNPGPGGWGAVIRYGGEEKELSGGLGDTTNNRAELTALIAALEALKelGPCEVEIYTDSQYVVNQITG 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 755404252  81 WIHNWKKRGWkttdrKPVRNVDLWQRLDLAIQGHTVQWEWVKGHAGHPENERCDELARLAA 141
Cdd:COG0328   81 WIHGWKKNGW-----KPVKNPDLWQRLDELLARHKVTFEWVKGHAGHPGNERADALANKAL 136
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 3-141 5.75e-75

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: 219.94  E-value: 5.75e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252    3 KQVEIFTDGSCLGNPGPGGYGAIMrYKQHEkTFSAGYRL-TTNNRMELMAAIVALEALTSPCQVTLSTDSQYVRQGITQW 81
Cdd:pfam00075   2 KAVTVYTDGSCLGNPGPGGAGAVL-YRGHE-NISAPLPGrTTNNRAELQAVIEALKALKSPSKVNIYTDSQYVIGGITQW 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 755404252   82 IHNWKKRGWKTTDR-KPVRNVDLWQRLDLAIQGHTVQWEWVKGHAGHPENERCDELARLAA 141
Cdd:pfam00075  80 VHGWKKNGWPTTSEgKPVKNKDLWQLLKALCKKHQVYWQWVKGHAGNPGNEMADRLAKQGA 140
 
Name Accession Description Interval E-value
rnhA PRK00203
ribonuclease H; Reviewed
 3-151 4.54e-111

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 311.38  E-value: 4.54e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252   3 KQVEIFTDGSCLGNPGPGGYGAIMRYKQHEKTFSAGYRLTTNNRMELMAAIVALEALTSPCQVTLSTDSQYVRQGITQWI 82
Cdd:PRK00203   2 KQVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKEPCEVTLYTDSQYVRQGITEWI 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 755404252  83 HNWKKRGWKTTDRKPVRNVDLWQRLDLAIQGHTVQWEWVKGHAGHPENERCDELARLAANSPTQDDIGY 151
Cdd:PRK00203  82 HGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWVKGHAGHPENERCDELARAGAEEATLEDTGY 150
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 4-142 1.23e-93

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: 267.04  E-value: 1.23e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252   4 QVEIFTDGSCLGNPGPGGYGAIMRYKQHEKTFSAGYRLTTNNRMELMAAIVALEALTSPCQVTLSTDSQYVRQGITQWIH 83
Cdd:cd09278    1 EIVIYTDGACLGNPGPGGWAAVIRYGDHEKELSGGEPGTTNNRMELTAAIEALEALKEPCPVTIYTDSQYVINGITKWIK 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 755404252  84 NWKKRGWKTTDRKPVRNVDLWQRLDLAIQGHTVQWEWVKGHAGHPENERCDELARLAAN 142
Cdd:cd09278   81 GWKKNGWKTADGKPVKNRDLWQELDALLAGHKVTWEWVKGHAGHPGNERADRLANKAAD 139
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
3-141 7.58e-82

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 237.05  E-value: 7.58e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252   3 KQVEIFTDGSCLGNPGPGGYGAIMRYKQHEKTFSAGYRLTTNNRMELMAAIVALEALT--SPCQVTLSTDSQYVRQGITQ 80
Cdd:COG0328    1 KMIEIYTDGACRGNPGPGGWGAVIRYGGEEKELSGGLGDTTNNRAELTALIAALEALKelGPCEVEIYTDSQYVVNQITG 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 755404252  81 WIHNWKKRGWkttdrKPVRNVDLWQRLDLAIQGHTVQWEWVKGHAGHPENERCDELARLAA 141
Cdd:COG0328   81 WIHGWKKNGW-----KPVKNPDLWQRLDELLARHKVTFEWVKGHAGHPGNERADALANKAL 136
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 3-141 5.75e-75

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: 219.94  E-value: 5.75e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252    3 KQVEIFTDGSCLGNPGPGGYGAIMrYKQHEkTFSAGYRL-TTNNRMELMAAIVALEALTSPCQVTLSTDSQYVRQGITQW 81
Cdd:pfam00075   2 KAVTVYTDGSCLGNPGPGGAGAVL-YRGHE-NISAPLPGrTTNNRAELQAVIEALKALKSPSKVNIYTDSQYVIGGITQW 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 755404252   82 IHNWKKRGWKTTDR-KPVRNVDLWQRLDLAIQGHTVQWEWVKGHAGHPENERCDELARLAA 141
Cdd:pfam00075  80 VHGWKKNGWPTTSEgKPVKNKDLWQLLKALCKKHQVYWQWVKGHAGNPGNEMADRLAKQGA 140
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 7-141 3.09e-48

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: 152.33  E-value: 3.09e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252   7 IFTDGSCLGNPGPG---GYGAimrY--KQHEKTFSAgyRLT----TNNRMELMAAIVALE-ALTSPCQ-VTLSTDSQYVR 75
Cdd:cd09280    2 VYTDGSCLNNGKPGaraGIGV---YfgPGDPRNVSE--PLPgrkqTNNRAELLAVIHALEqAPEEGIRkLEIRTDSKYAI 76

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 755404252  76 QGITQWIHNWKKRGWKTTDRKPVRNVDLWQRLD--LAIQGHTVQWEWVKGHAGHPENERCDELARLAA 141
Cdd:cd09280   77 NCITKWIPKWKKNGWKTSKGKPVKNQDLIKELDklLRKRGIKVKFEHVKGHSGDPGNEEADRLAREGA 144
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 7-142 2.74e-32

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: 112.29  E-value: 2.74e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252   7 IFTDGSCLGNPGPG---GYGAIMRykqHEKTFSAGYRLT-------TNNRMELMAAIVALEALT--------SPCQVTLS 68
Cdd:cd13934    2 VYIDGACRNNGRPDaraGYGVYFG---PDSSYNVSGRLEdtgghpqTSQRAELRAAIAALRFRSwiidpdgeGLKTVVIA 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 755404252  69 TDSQYVRQGITQWIHNWKKRGWKTTDRKPVRNVDLWQRLDLAIQ-----GHTVQWEWVKGHaghpENERCDELARLAAN 142
Cdd:cd13934   79 TDSEYVVKGATEWIPKWKRNGWRTSKGKPVKNRDLFELLLDEIEdleegGVEVQFWHVPRE----LNKEADRLAKAAAE 153
PRK06548 PRK06548
ribonuclease H; Provisional
 9-143 5.50e-30

ribonuclease H; Provisional


Pssm-ID: 75628 [Multi-domain]  Cd Length: 161  Bit Score: 106.82  E-value: 5.50e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252   9 TDGSCLGNPGPGGYGaimrYKQHEKTF-SAGYRLTTNNRMELMAA---IVALEALTSPcqVTLSTDSQYVRQGITQWIHN 84
Cdd:PRK06548  10 TDGSSLANPGPSGWA----WYVDENTWdSGGWDIATNNIAELTAVrelLIATRHTDRP--ILILSDSKYVINSLTKWVYS 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 755404252  85 WKKRGWKTTDRKPVRNVDLWQRLDLAIQGHTVQWEWVKGHAGHPENERCDELARLAANS 143
Cdd:PRK06548  84 WKMRKWRKADGKPVLNQEIIQEIDSLMENRNIRMSWVNAHTGHPLNEAADSLARQAANN 142
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 7-138 2.02e-23

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: 88.53  E-value: 2.02e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252   7 IFTDGSCLGNPGPGGYGAIMRYKQHEKTFSAGY--RLTTNNRMELMAAIVALE-ALTSPC-QVTLSTDSQYVRQGITQWI 82
Cdd:cd06222    1 INVDGSCRGNPGPAGIGGVLRDHEGGWLGGFALkiGAPTALEAELLALLLALElALDLGYlKVIIESDSKYVVDLINSGS 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 755404252  83 HNWKKRGwkttdrkpvrnVDLWQRLDLAIQGHTVQWEWVKGhaghPENERCDELAR 138
Cdd:cd06222   81 FKWSPNI-----------LLIEDILLLLSRFWSVKISHVPR----EGNQVADALAK 121
PRK08719 PRK08719
ribonuclease H; Reviewed
 40-141 5.16e-20

ribonuclease H; Reviewed


Pssm-ID: 236334 [Multi-domain]  Cd Length: 147  Bit Score: 80.68  E-value: 5.16e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252  40 RLTTNNRMELMAAIVALEALTSPCQVTlsTDSQYVRQGITQWIHNWKKRGWKTTDRKPVRNVDLWQRLDLAIQGHTVQWE 119
Cdd:PRK08719  46 RYTDNAELELLALIEALEYARDGDVIY--SDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVEVE 123

                         90       100
                 ....*....|....*....|..
gi 755404252 120 WVKGHAGHPENERCDELARLAA 141
Cdd:PRK08719 124 KVTAHSGIEGNEAADMLAQAAA 145
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 7-141 5.51e-16

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: 69.55  E-value: 5.51e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252   7 IFTDGSclGNPGPGGYGAImrYKQHEKTFSAGYRLTTNNRM---ELMAAIVALEALTSPC----QVTLSTDSQYVRQGIt 79
Cdd:cd09276    2 IYTDGS--KLEGSVGAGFV--IYRGGEVISRSYRLGTHASVfdaELEAILEALELALATArrarKVTIFTDSQSALQAL- 76

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 755404252  80 qwihnwkkRGWKTTDRKPVRNVDLWQRLDLAIQGHTVQWEWVKGHAGHPENERCDELARLAA 141
Cdd:cd09276   77 --------RNPRRSSGQVILIRILRLLRLLKAKGVKVRLRWVPGHVGIEGNEAADRLAKEAA 130
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 5-141 3.81e-14

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: 64.80  E-value: 3.81e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252   5 VEIFTDGSCLGNPGPGGYGAIMRY---KQHEKTFSAGYRlTTNNRMELMAAIVALEALTS--PCQVTLSTDSQYV-RQgi 78
Cdd:cd09279    1 WTLYFDGASRGNPGPAGAGVVIYSpggEVLELSERLGFP-ATNNEAEYEALIAGLELALElgAEKLEIYGDSQLVvNQ-- 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 755404252  79 tqwIH-NWKkrgwkttdrkpVRNVDLwQRL-----DLAIQGHTVQWEWVKGHaghpENERCDELARLAA 141
Cdd:cd09279   78 ---LNgEYK-----------VKNERL-KPLlekvlELLAKFELVELKWIPRE----QNKEADALANQAL 127
RNase_HI_bacteria_like cd09277
Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; Ribonuclease H ...
 5-140 8.61e-08

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: 48.25  E-value: 8.61e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252   5 VEIFTDGSCLGNPGPGGYGAIMRYKQHEKTFSAGYRLTTNNRM-----ELMAAIVALE-ALTS-PCQVTLSTDsqYvrQG 77
Cdd:cd09277    1 VIAYVDGSYNKETKKYGYGVVIIKNGKEEEFSGSGNDPEYASMrnvagEIKGAMKAIKyAIENgIKKITIYYD--Y--EG 76

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 755404252  78 ITQWI-HNWKkrgwkttdrkpvRNVDLWQR----LDLAIQGHTVQWEWVKGHAGHPENERCDELARLA 140
Cdd:cd09277   77 IEKWAtGEWK------------ANKELTKEykefMQKYKKKIKIEFVKVKAHSGDKYNELADKLAKKA 132
rnhA PRK13907
ribonuclease H; Provisional
 5-80 3.82e-06

ribonuclease H; Provisional


Pssm-ID: 139967 [Multi-domain]  Cd Length: 128  Bit Score: 43.89  E-value: 3.82e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 755404252   5 VEIFTDGSCLGNPGPGGYGAIMRYKQHEKTFSAGYRLTTNNRMELMAAIVALEALT--SPCQVTLSTDSQYVRQGITQ 80
Cdd:PRK13907   2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTehNYNIVSFRTDSQLVERAVEK 79
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 4-140 5.27e-05

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 41.89  E-value: 5.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252   4 QVEIFTDGSCLGNPGPGGYGAIMRYKQHEKTF---SAGYRLTTNNRMELMAAIVALEAL--TSPCQVTLSTDSQYVrqgI 78
Cdd:PRK07238   2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLaerAEAIGRATNNVAEYRGLIAGLEAAaeLGATEVEVRMDSKLV---V 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 755404252  79 TQWIHNWKKrgwKTTDRKPvrnvdLWQRL-DLAIQGHTVQWEWVkghaghP--ENERCDELARLA 140
Cdd:PRK07238  79 EQMSGRWKV---KHPDMKP-----LAAQArELASQFGRVTYTWI------PraRNAHADRLANEA 129
RNase_HI_RT_DIRS1 cd09275
DIRS1 family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 6-83 8.22e-05

DIRS1 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 eukaryotes. 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. The structural features of DIRS1-group elements are different from typical LTR elements. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260007  Cd Length: 120  Bit Score: 39.96  E-value: 8.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252   6 EIFTDGSclGNpgpgGYGAIMRYKQHEKTFSAGYRLTTNNRMELMAAIVALEAL---TSPCQVTLSTDS----QYV-RQG 77
Cdd:cd09275    1 VLFTDAS--LS----GWGAYLLNSRAHGPWSADERNKHINLLELKAVLLALQHFaaeLKNRKILIRTDNttavAYInKQG 74


                 ....*.
gi 755404252  78 ITQWIH 83
Cdd:cd09275   75 GTSSPP 80
RNase_HI_RT_Bel cd09273
Bel/Pao family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) enzymes ...
 7-141 1.15e-04

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: 39.63  E-value: 1.15e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252   7 IFTDGSCLGNpgpgGYGAIMRYKQHEKTfsAGYRLTTNNRMELMAAIVALEaLTSPCQVTLSTDSQYVRQGITQWIHNWK 86
Cdd:cd09273    2 VFTDGSSFKA----GYAIVSGTEIVEAQ--PLPPGTSAQRAELIALIQALE-LAKGKPVNIYTDSAYAVHALHLLETIGI 74

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 755404252  87 KRGWkttdRKPVRNVDLWQRLDLAIQ-------GHtvqwewVKGHAGHPE-----NERCDELARLAA 141
Cdd:cd09273   75 ERGF----LKSIKNLSLFLQLLEAVQrpkpvaiIH------IRAHSKLPGplaegNAQADAAAKQAA 131
RNase_H_bacteria_like cd13935
RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence ...
 10-124 4.60e-04

RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; This family includes bacterial ribonuclease H (RNase H) enzymes. RNases are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260015  Cd Length: 133  Bit Score: 37.88  E-value: 4.60e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252  10 DGSCLGNPGPGGYGAIMRyKQHEKTFSAG-YRLTTNNRMELMAAIVALEALTSP-CQVTLSTDSQYVRqgitQWIhnwKK 87
Cdd:cd13935    8 DAACSGNPGIVEYRGVDT-KTGEVLFHRGpFPGGTNNMGEFLAIVHALRYLKEKnSRKPIYSDSQTAI----AWV---KK 79

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 755404252  88 RGWKTTDRKPVRNVDLWQRLDLAIqghtvqwEWVKGH 124
Cdd:cd13935   80 KKAKSTLVRNEKNAEIFKLVDRAE-------EWLSTH 109
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 8-140 4.02e-03

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: 35.32  E-value: 4.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252    8 FTDGSCLGNPGPGGYGAIMRYKQHEKTFSAGYRL-TTNNRM--ELMAAIVALEA---LTSPcQVTLSTDSQYVRQGITQw 81
Cdd:pfam13456   1 NFDGAFKCDSGLAGAGVVIRDPNGNVLLAGQKKLgPGASVLeaEAQALIIGLQLawkLGIR-HLIVEGDSATVVQLING- 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 755404252   82 ihnwkkrgwKTTDRKPVRNVdLWQRLDLAIQGHTVQWEWVkghagHPENERC-DELARLA 140
Cdd:pfam13456  79 ---------RSPKQSKLANL-LDEIRKLLKRFESVSFEHI-----PREQNRVaDTLAKMA 123
 
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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