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Conserved domains on  [gi|503347016|ref|WP_013581677|]
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ribonuclease HI family protein [Granulicella tundricola]

Protein Classification

ribonuclease HI family protein( domain architecture ID 10174584)

ribonuclease HI family protein such as type 1 ribonuclease H, which is involved in the removal of RNA from RNA/DNA hybrids during DNA replication, repair and transcription; similar to Enterococcus faecalis hydrolase EbsB

CATH:  3.30.420.10
EC:  3.-.-.-
Gene Ontology:  GO:0004523|GO:0003676|GO:0000287|GO:0043137
PubMed:  19228198|19228197|16093691|16232566|2177653
SCOP:  4000541

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 12-139 1.81e-51

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: 161.87  E-value: 1.81e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016  12 IFAHCDGGSRGNPGPSGYGAVITDTGGQKIaELSEFLGIR-TNNYAEYSGLLAVLAYAVENKRLSLKVVSDSELMVKQIQ 90
Cdd:cd09279    1 WTLYFDGASRGNPGPAGAGVVIYSPGGEVL-ELSERLGFPaTNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLN 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 503347016  91 GKYKVNSPDLKPLWQEARDRIAKLKSFEISHALRHKNKDADALANQAMD 139
Cdd:cd09279   80 GEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
 
Name Accession Description Interval E-value
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 12-139 1.81e-51

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: 161.87  E-value: 1.81e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016  12 IFAHCDGGSRGNPGPSGYGAVITDTGGQKIaELSEFLGIR-TNNYAEYSGLLAVLAYAVENKRLSLKVVSDSELMVKQIQ 90
Cdd:cd09279    1 WTLYFDGASRGNPGPAGAGVVIYSPGGEVL-ELSERLGFPaTNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLN 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 503347016  91 GKYKVNSPDLKPLWQEARDRIAKLKSFEISHALRHKNKDADALANQAMD 139
Cdd:cd09279   80 GEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 16-173 2.14e-42

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 146.28  E-value: 2.14e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016  16 CDGGSRGNPGPSGYGAVITD-TGGQKIAELSEFLGIRTNNYAEYSGLLAVLAYAVENKRLSLKVVSDSELMVKQIQGKYK 94
Cdd:PRK07238   7 ADGGSRGNPGPAGYGAVVWDaDRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWK 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 503347016  95 VNSPDLKPLWQEARDRIAKLKSFEISHALRHKNKDADALANQAMDRGmKKGEYKATPTAPQITtrEPQKTVASPVALPA 173
Cdd:PRK07238  87 VKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEAMDAA-AGGEPWGPSAAAADA--DPAKSAAPPAPTAP 162
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
10-138 2.05e-37

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 126.50  E-value: 2.05e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016  10 ETIFAHCDGGSRGNPGPSGYGAVITDtgGQKIAELSEFLGIRTNNYAEYSGLLAVLAYAVENKRLSLKVVSDSELMVKQI 89
Cdd:COG0328    1 KMIEIYTDGACRGNPGPGGWGAVIRY--GGEEKELSGGLGDTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQI 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503347016  90 QGKY---------KVNSPDlkpLWQEArDRIAKLKSFEISHALRHK----NKDADALANQAM 138
Cdd:COG0328   79 TGWIhgwkkngwkPVKNPD---LWQRL-DELLARHKVTFEWVKGHAghpgNERADALANKAL 136
RNAseHI_Thmprot NF041175
ribonuclease HI;
23-137 1.01e-22

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 88.87  E-value: 1.01e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016  23 NPGPSG-YGAVITDTGGQKIaelsEFLGI--------RTNNYAEYSGLLAVLAYAVENKRLSLKVVSDSELMVKQIQGKY 93
Cdd:NF041175  14 NPGGIAtYGYVIYLDNKRKI----EGYGLaaepwskdSTNNVAEYTGLICLLEKLLELGISEVIIRGDSQLVIRQLNGEY 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 503347016  94 KVNSPDLKPLWQEARDRIAKLKSFEISHALRHKNKDADALANQA 137
Cdd:NF041175  90 KVKSPRIIPLYEKALELLSKFRSIEFEWVPREENKEADRLSRIA 133
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 16-137 1.75e-13

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: 64.21  E-value: 1.75e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016   16 CDGGSRGNPGPSGYGAVITDTGGQKIAELSEFLGIRTNNY-AEYSGLLAVLAYAVENKRLSLKVVSDSELMVKQIQGKyK 94
Cdd:pfam13456   2 FDGAFKCDSGLAGAGVVIRDPNGNVLLAGQKKLGPGASVLeAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGR-S 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 503347016   95 VNSPDLKPLWQEARDRIAKLKSFEISHALRHKNKDADALANQA 137
Cdd:pfam13456  81 PKQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
 
Name Accession Description Interval E-value
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 12-139 1.81e-51

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: 161.87  E-value: 1.81e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016  12 IFAHCDGGSRGNPGPSGYGAVITDTGGQKIaELSEFLGIR-TNNYAEYSGLLAVLAYAVENKRLSLKVVSDSELMVKQIQ 90
Cdd:cd09279    1 WTLYFDGASRGNPGPAGAGVVIYSPGGEVL-ELSERLGFPaTNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLN 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 503347016  91 GKYKVNSPDLKPLWQEARDRIAKLKSFEISHALRHKNKDADALANQAMD 139
Cdd:cd09279   80 GEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 16-173 2.14e-42

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 146.28  E-value: 2.14e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016  16 CDGGSRGNPGPSGYGAVITD-TGGQKIAELSEFLGIRTNNYAEYSGLLAVLAYAVENKRLSLKVVSDSELMVKQIQGKYK 94
Cdd:PRK07238   7 ADGGSRGNPGPAGYGAVVWDaDRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWK 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 503347016  95 VNSPDLKPLWQEARDRIAKLKSFEISHALRHKNKDADALANQAMDRGmKKGEYKATPTAPQITtrEPQKTVASPVALPA 173
Cdd:PRK07238  87 VKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEAMDAA-AGGEPWGPSAAAADA--DPAKSAAPPAPTAP 162
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
10-138 2.05e-37

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 126.50  E-value: 2.05e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016  10 ETIFAHCDGGSRGNPGPSGYGAVITDtgGQKIAELSEFLGIRTNNYAEYSGLLAVLAYAVENKRLSLKVVSDSELMVKQI 89
Cdd:COG0328    1 KMIEIYTDGACRGNPGPGGWGAVIRY--GGEEKELSGGLGDTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQI 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503347016  90 QGKY---------KVNSPDlkpLWQEArDRIAKLKSFEISHALRHK----NKDADALANQAM 138
Cdd:COG0328   79 TGWIhgwkkngwkPVKNPD---LWQRL-DELLARHKVTFEWVKGHAghpgNERADALANKAL 136
RNAseHI_Thmprot NF041175
ribonuclease HI;
23-137 1.01e-22

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 88.87  E-value: 1.01e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016  23 NPGPSG-YGAVITDTGGQKIaelsEFLGI--------RTNNYAEYSGLLAVLAYAVENKRLSLKVVSDSELMVKQIQGKY 93
Cdd:NF041175  14 NPGGIAtYGYVIYLDNKRKI----EGYGLaaepwskdSTNNVAEYTGLICLLEKLLELGISEVIIRGDSQLVIRQLNGEY 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 503347016  94 KVNSPDLKPLWQEARDRIAKLKSFEISHALRHKNKDADALANQA 137
Cdd:NF041175  90 KVKSPRIIPLYEKALELLSKFRSIEFEWVPREENKEADRLSRIA 133
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 16-135 4.13e-21

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


Pssm-ID: 259998 [Multi-domain]  Cd Length: 121  Bit Score: 84.29  E-value: 4.13e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016  16 CDGGSRGNPGPSGYGAVITDTGGQKIAELSEFLGIRTNNYAEYSGLLAVLAYAVENKRLSLKVVSDSELMVKQIQGKYKV 95
Cdd:cd06222    3 VDGSCRGNPGPAGIGGVLRDHEGGWLGGFALKIGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLINSGSFK 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 503347016  96 NSPDLKPLWQeARDRIAKLKSFEISHALRHKNKDADALAN 135
Cdd:cd06222   83 WSPNILLIED-ILLLLSRFWSVKISHVPREGNQVADALAK 121
rnhA PRK13907
ribonuclease H; Provisional
 12-138 1.37e-19

ribonuclease H; Provisional


Pssm-ID: 139967 [Multi-domain]  Cd Length: 128  Bit Score: 80.48  E-value: 1.37e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016  12 IFAHCDGGSRGNPGPSGYGAVITdtGGQKIAELSEFLGIRTNNYAEYSGLLAVLAYAVENKRLSLKVVSDSELMVKQIQG 91
Cdd:PRK13907   2 IEVYIDGASKGNPGPSGAGVFIK--GVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEK 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 503347016  92 KYKVNSPdLKPLWQEARDRIAKLKSFEISHALRHKNKDADALANQAM 138
Cdd:PRK13907  80 EYAKNKM-FAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAI 125
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 11-139 6.09e-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: 68.66  E-value: 6.09e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016  11 TIFAHCDGGSRGNPGPSGYGAVITDTGGQKiaELSEFLGIRTNNYAEYSGLLAVLAYAVENKRlsLKVVSDSELMVKQIQ 90
Cdd:cd09278    1 EIVIYTDGACLGNPGPGGWAAVIRYGDHEK--ELSGGEPGTTNNRMELTAAIEALEALKEPCP--VTIYTDSQYVINGIT 76

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 503347016  91 GKYK-------VNSpDLKP-----LWQEArDRIAKLKSFEI----SHALRHKNKDADALANQAMD 139
Cdd:cd09278   77 KWIKgwkkngwKTA-DGKPvknrdLWQEL-DALLAGHKVTWewvkGHAGHPGNERADRLANKAAD 139
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 16-137 1.75e-13

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: 64.21  E-value: 1.75e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016   16 CDGGSRGNPGPSGYGAVITDTGGQKIAELSEFLGIRTNNY-AEYSGLLAVLAYAVENKRLSLKVVSDSELMVKQIQGKyK 94
Cdd:pfam13456   2 FDGAFKCDSGLAGAGVVIRDPNGNVLLAGQKKLGPGASVLeAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGR-S 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 503347016   95 VNSPDLKPLWQEARDRIAKLKSFEISHALRHKNKDADALANQA 137
Cdd:pfam13456  81 PKQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
PRK07708 PRK07708
hypothetical protein; Validated
 9-139 3.40e-10

hypothetical protein; Validated


Pssm-ID: 181088 [Multi-domain]  Cd Length: 219  Bit Score: 57.35  E-value: 3.40e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016   9 PETIFAHCDGGSRGNPGPSGYGAVITDTGGQK---IAELSEFLGIRTNNYAEYSGLLavlaYAVEN------KRLSLKVV 79
Cdd:PRK07708  71 PHEILVYFDGGFDKETKLAGLGIVIYYKQGNKryrIRRNAYIEGIYDNNEAEYAALY----YAMQEleelgvKHEPVTFR 146

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 503347016  80 SDSELMVKQIQGKYKVNSPDLkplwQEARDRI-AKLKSFEISHAL----RHKNKDADALANQAMD 139
Cdd:PRK07708 147 GDSQVVLNQLAGEWPCYDEHL----NHWLDRIeQKLKQLKLTPVYepisRKQNKEADQLATQALE 207
rnhA PRK00203
ribonuclease H; Reviewed
 12-145 1.72e-09

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 54.06  E-value: 1.72e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016  12 IFAHCDGGSRGNPGPSGYGAVITDTGGQKiaELSEFLGIRTNNYAEysgLLAVLAyAVEnkrlSLK------VVSDSELM 85
Cdd:PRK00203   4 VEIYTDGACLGNPGPGGWGAILRYKGHEK--ELSGGEALTTNNRME---LMAAIE-ALE----ALKepcevtLYTDSQYV 73

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503347016  86 VKQIQG---KYKVN---SPDLKP-----LWQEArdrIAKLKSFEIS------HALRHKNKDADALANQAMDRGMKKG 145
Cdd:PRK00203  74 RQGITEwihGWKKNgwkTADKKPvknvdLWQRL---DAALKRHQIKwhwvkgHAGHPENERCDELARAGAEEATLED 147
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 10-137 5.51e-09

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: 52.76  E-value: 5.51e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016   10 ETIFahCDGGSRGNPGPSGYGAViTDTGGQKIAELSEflGIRTNNYAEYSGLLAVLAYAVENKRLSLkvVSDSELMVKQI 89
Cdd:pfam00075   4 VTVY--TDGSCLGNPGPGGAGAV-LYRGHENISAPLP--GRTTNNRAELQAVIEALKALKSPSKVNI--YTDSQYVIGGI 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 503347016   90 ----QGKYKVNSPDL--------KPLWQEARDRIAKlKSFEISHALRHK----NKDADALANQA 137
Cdd:pfam00075  77 tqwvHGWKKNGWPTTsegkpvknKDLWQLLKALCKK-HQVYWQWVKGHAgnpgNEMADRLAKQG 139
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 17-139 4.62e-07

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: 47.58  E-value: 4.62e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016  17 DGGSRGN--PGP-SGYGAVITDTGGQKIAELSEFLGI--RTNNYAEysgLLAVLA--------YAVENKRLS-LKVVSDS 82
Cdd:cd13934    5 DGACRNNgrPDArAGYGVYFGPDSSYNVSGRLEDTGGhpQTSQRAE---LRAAIAalrfrswiIDPDGEGLKtVVIATDS 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 503347016  83 ELMVKQI---------------QGKYKVNspdlKPLWQEARDRIAKLKSFEIS----HALRHKNKDADALANQAMD 139
Cdd:cd13934   82 EYVVKGAtewipkwkrngwrtsKGKPVKN----RDLFELLLDEIEDLEEGGVEvqfwHVPRELNKEADRLAKAAAE 153
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 15-137 5.24e-05

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: 41.78  E-value: 5.24e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016  15 HCDGGSRGNPGP---SGYGAVItdtGGQKIAELSEFLGIR--TNNYAEysgLLAVLaYAVEN----KRLSLKVVSDSELM 85
Cdd:cd09280    3 YTDGSCLNNGKPgarAGIGVYF---GPGDPRNVSEPLPGRkqTNNRAE---LLAVI-HALEQapeeGIRKLEIRTDSKYA 75

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503347016  86 VKQI--------------QGKYKV-NspdlKPLWQEARDRIAKLK-SFEISHALRHK----NKDADALANQA 137
Cdd:cd09280   76 INCItkwipkwkkngwktSKGKPVkN----QDLIKELDKLLRKRGiKVKFEHVKGHSgdpgNEEADRLAREG 143
PRK06548 PRK06548
ribonuclease H; Provisional
 12-139 6.67e-05

ribonuclease H; Provisional


Pssm-ID: 75628 [Multi-domain]  Cd Length: 161  Bit Score: 41.72  E-value: 6.67e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503347016  12 IFAHCDGGSRGNPGPSGYGAVIT----DTGGQKIAelseflgirTNNYAEYSGLLAVLAYAVENKRLSLkVVSDSELMVK 87
Cdd:PRK06548   6 IIAATDGSSLANPGPSGWAWYVDentwDSGGWDIA---------TNNIAELTAVRELLIATRHTDRPIL-ILSDSKYVIN 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 503347016  88 QIQ------GKYKVNSPDLKP-LWQEARDRIAKL-------KSFEISHALRHKNKDADALANQAMD 139
Cdd:PRK06548  76 SLTkwvyswKMRKWRKADGKPvLNQEIIQEIDSLmenrnirMSWVNAHTGHPLNEAADSLARQAAN 141
 
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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