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Conserved domains on  [gi|1279228393|gb|PJE69800.1|]
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hypothetical protein COU98_00020 [Candidatus Staskawiczbacteria bacterium CG10_big_fil_rev_8_21_14_0_10_38_10]

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.

EC:  3.1.26.4
Gene Ontology:  GO:0003723|GO:0003677

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 ...
 4-138 5.03e-48

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: 151.09  E-value: 5.03e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279228393   4 LIVYTDGGSRGNPGLAAIGVVIADEKKNILkEYSQYLGDNLTNNEAEYKAVIFALKKIKALfgkkkiGEFDVEIMSDSEL 83
Cdd:cd09279     1 WTLYFDGASRGNPGPAGAGVVIYSPGGEVL-ELSERLGFPATNNEAEYEALIAGLELALEL------GAEKLEIYGDSQL 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1279228393  84 LIKQMQGLYKILEPKIQSLFVAVWNLKIDFKEVKFKLISREKNKEADKLVNEALD 138
Cdd:cd09279    74 VVNQLNGEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 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 ...
 4-138 5.03e-48

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: 151.09  E-value: 5.03e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279228393   4 LIVYTDGGSRGNPGLAAIGVVIADEKKNILkEYSQYLGDNLTNNEAEYKAVIFALKKIKALfgkkkiGEFDVEIMSDSEL 83
Cdd:cd09279     1 WTLYFDGASRGNPGPAGAGVVIYSPGGEVL-ELSERLGFPATNNEAEYEALIAGLELALEL------GAEKLEIYGDSQL 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1279228393  84 LIKQMQGLYKILEPKIQSLFVAVWNLKIDFKEVKFKLISREKNKEADKLVNEALD 138
Cdd:cd09279    74 VVNQLNGEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
2-137 4.60e-33

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 113.40  E-value: 4.60e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279228393   2 KKLIVYTDGGSRGNPGLAAIGVVIADekKNILKEYSQYLGDNlTNNEAEYKAVIFALKKIKALFGKKkigefdVEIMSDS 81
Cdd:COG0328     1 KMIEIYTDGACRGNPGPGGWGAVIRY--GGEEKELSGGLGDT-TNNRAELTALIAALEALKELGPCE------VEIYTDS 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1279228393  82 ELLIKQMQGLYKILEP------KIQSLFVAVWNLkIDFKEVKFKLISREK----NKEADKLVNEAL 137
Cdd:COG0328    72 QYVVNQITGWIHGWKKngwkpvKNPDLWQRLDEL-LARHKVTFEWVKGHAghpgNERADALANKAL 136
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 3-138 7.45e-29

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 108.14  E-value: 7.45e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279228393   3 KLIVYTDGGSRGNPGLAAIGVVIADE-KKNILKEYSQYLGdNLTNNEAEYKAVIFALKkikalfGKKKIGEFDVEIMSDS 81
Cdd:PRK07238    2 KVVVEADGGSRGNPGPAGYGAVVWDAdRGEVLAERAEAIG-RATNNVAEYRGLIAGLE------AAAELGATEVEVRMDS 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1279228393  82 ELLIKQMQGLYKILEPKIQSLFVAVWNLKIDFKEVKFKLISREKNKEADKLVNEALD 138
Cdd:PRK07238   75 KLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEAMD 131
RNAseHI_Thmprot NF041175
ribonuclease HI;
3-136 4.59e-24

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 90.41  E-value: 4.59e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279228393   3 KLIVYTDGGSR-GNP-GLAAIGVVIADEKKNILKEY---SQYLGDNLTNNEAEYKAVIFALKKIKALfgkkkiGEFDVEI 77
Cdd:NF041175    1 MAIGYFDGLCEpKNPgGIATYGYVIYLDNKRKIEGYglaAEPWSKDSTNNVAEYTGLICLLEKLLEL------GISEVII 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1279228393  78 MSDSELLIKQMQGLYKILEPKIQSLFVAVWNLKIDFKEVKFKLISREKNKEADKLVNEA 136
Cdd:NF041175   75 RGDSQLVIRQLNGEYKVKSPRIIPLYEKALELLSKFRSIEFEWVPREENKEADRLSRIA 133
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 8-136 1.36e-21

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: 83.47  E-value: 1.36e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279228393   8 TDGGSRGNPGLAAIGVVIADEKKNILKEYSQYLGDNLTNNEAEYKAVIFALKKIKALfGKKKIgefDVEimSDSELLIKQ 87
Cdd:pfam13456   2 FDGAFKCDSGLAGAGVVIRDPNGNVLLAGQKKLGPGASVLEAEAQALIIGLQLAWKL-GIRHL---IVE--GDSATVVQL 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1279228393  88 MQGLYKIlEPKIQSLFVAVWNLKIDFKEVKFKLISREKNKEADKLVNEA 136
Cdd:pfam13456  76 INGRSPK-QSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 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 ...
 4-138 5.03e-48

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: 151.09  E-value: 5.03e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279228393   4 LIVYTDGGSRGNPGLAAIGVVIADEKKNILkEYSQYLGDNLTNNEAEYKAVIFALKKIKALfgkkkiGEFDVEIMSDSEL 83
Cdd:cd09279     1 WTLYFDGASRGNPGPAGAGVVIYSPGGEVL-ELSERLGFPATNNEAEYEALIAGLELALEL------GAEKLEIYGDSQL 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1279228393  84 LIKQMQGLYKILEPKIQSLFVAVWNLKIDFKEVKFKLISREKNKEADKLVNEALD 138
Cdd:cd09279    74 VVNQLNGEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
2-137 4.60e-33

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 113.40  E-value: 4.60e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279228393   2 KKLIVYTDGGSRGNPGLAAIGVVIADekKNILKEYSQYLGDNlTNNEAEYKAVIFALKKIKALFGKKkigefdVEIMSDS 81
Cdd:COG0328     1 KMIEIYTDGACRGNPGPGGWGAVIRY--GGEEKELSGGLGDT-TNNRAELTALIAALEALKELGPCE------VEIYTDS 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1279228393  82 ELLIKQMQGLYKILEP------KIQSLFVAVWNLkIDFKEVKFKLISREK----NKEADKLVNEAL 137
Cdd:COG0328    72 QYVVNQITGWIHGWKKngwkpvKNPDLWQRLDEL-LARHKVTFEWVKGHAghpgNERADALANKAL 136
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 3-138 7.45e-29

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 108.14  E-value: 7.45e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279228393   3 KLIVYTDGGSRGNPGLAAIGVVIADE-KKNILKEYSQYLGdNLTNNEAEYKAVIFALKkikalfGKKKIGEFDVEIMSDS 81
Cdd:PRK07238    2 KVVVEADGGSRGNPGPAGYGAVVWDAdRGEVLAERAEAIG-RATNNVAEYRGLIAGLE------AAAELGATEVEVRMDS 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1279228393  82 ELLIKQMQGLYKILEPKIQSLFVAVWNLKIDFKEVKFKLISREKNKEADKLVNEALD 138
Cdd:PRK07238   75 KLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEAMD 131
RNAseHI_Thmprot NF041175
ribonuclease HI;
3-136 4.59e-24

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 90.41  E-value: 4.59e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279228393   3 KLIVYTDGGSR-GNP-GLAAIGVVIADEKKNILKEY---SQYLGDNLTNNEAEYKAVIFALKKIKALfgkkkiGEFDVEI 77
Cdd:NF041175    1 MAIGYFDGLCEpKNPgGIATYGYVIYLDNKRKIEGYglaAEPWSKDSTNNVAEYTGLICLLEKLLEL------GISEVII 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1279228393  78 MSDSELLIKQMQGLYKILEPKIQSLFVAVWNLKIDFKEVKFKLISREKNKEADKLVNEA 136
Cdd:NF041175   75 RGDSQLVIRQLNGEYKVKSPRIIPLYEKALELLSKFRSIEFEWVPREENKEADRLSRIA 133
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 6-134 5.26e-22

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: 84.67  E-value: 5.26e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279228393   6 VYTDGGSRGNPGLAAIGVVIADEKKNILKEYSQYLGdNLTNNEAEYKAVIFALKKIKALFGKKkigefdVEIMSDSELLI 85
Cdd:cd06222     1 INVDGSCRGNPGPAGIGGVLRDHEGGWLGGFALKIG-APTALEAELLALLLALELALDLGYLK------VIIESDSKYVV 73

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1279228393  86 KQMQGlYKILEPKIQSLFVAVWNLKIDFKEVKFKLISREKNKEADKLVN 134
Cdd:cd06222    74 DLINS-GSFKWSPNILLIEDILLLLSRFWSVKISHVPREGNQVADALAK 121
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 8-136 1.36e-21

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: 83.47  E-value: 1.36e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279228393   8 TDGGSRGNPGLAAIGVVIADEKKNILKEYSQYLGDNLTNNEAEYKAVIFALKKIKALfGKKKIgefDVEimSDSELLIKQ 87
Cdd:pfam13456   2 FDGAFKCDSGLAGAGVVIRDPNGNVLLAGQKKLGPGASVLEAEAQALIIGLQLAWKL-GIRHL---IVE--GDSATVVQL 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1279228393  88 MQGLYKIlEPKIQSLFVAVWNLKIDFKEVKFKLISREKNKEADKLVNEA 136
Cdd:pfam13456  76 INGRSPK-QSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 5-138 1.43e-14

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: 66.45  E-value: 1.43e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279228393   5 IVYTDGGSRGN--PGL-AAIGVVIADEK-KNILKEYSQYLGDNLTNNEAEYKAVIFALKKIKALFGKKKIGEFDVEIMSD 80
Cdd:cd13934     1 LVYIDGACRNNgrPDArAGYGVYFGPDSsYNVSGRLEDTGGHPQTSQRAELRAAIAALRFRSWIIDPDGEGLKTVVIATD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279228393  81 SELLIKQM---------------QG-------LYKILEPKIQSLfvavWNLKIdfkEVKFKLISREKNKEADKLVNEALD 138
Cdd:cd13934    81 SEYVVKGAtewipkwkrngwrtsKGkpvknrdLFELLLDEIEDL----EEGGV---EVQFWHVPRELNKEADRLAKAAAE 153
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 3-86 3.07e-13

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: 62.50  E-value: 3.07e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279228393   3 KLIVYTDGGSRGNPGLAAIGVVIadEKKNILKEYSQYLGdNLTNNEAEYKAVIFALKKIKAlfgkkkigEFDVEIMSDSE 82
Cdd:cd09278     1 EIVIYTDGACLGNPGPGGWAAVI--RYGDHEKELSGGEP-GTTNNRMELTAAIEALEALKE--------PCPVTIYTDSQ 69


                  ....
gi 1279228393  83 LLIK 86
Cdd:cd09278    70 YVIN 73
PRK07708 PRK07708
hypothetical protein; Validated
 4-140 9.84e-13

hypothetical protein; Validated


Pssm-ID: 181088 [Multi-domain]  Cd Length: 219  Bit Score: 62.74  E-value: 9.84e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279228393   4 LIVYTDGGSRGNPGLAAIGVVIADEKKNilKEY----SQYLGDNLTNNEAEYKAVIFALKKIKALfgkkKIGEFDVEIMS 79
Cdd:PRK07708   74 ILVYFDGGFDKETKLAGLGIVIYYKQGN--KRYrirrNAYIEGIYDNNEAEYAALYYAMQELEEL----GVKHEPVTFRG 147

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1279228393  80 DSELLIKQMQGLYKILEPKIQSlfvavWNLKIDFKEVKFKL------ISREKNKEADKLVNEALDNQ 140
Cdd:PRK07708  148 DSQVVLNQLAGEWPCYDEHLNH-----WLDRIEQKLKQLKLtpvyepISRKQNKEADQLATQALEGT 209
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 1-137 8.26e-11

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: 56.23  E-value: 8.26e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279228393   1 MKKLIVYTDGGSRGNPGLAAIGVVIADEKKNIlkeYSQYLGDNlTNNEAEYKAVIFALKKIKalFGKKkigefdVEIMSD 80
Cdd:pfam00075   1 PKAVTVYTDGSCLGNPGPGGAGAVLYRGHENI---SAPLPGRT-TNNRAELQAVIEALKALK--SPSK------VNIYTD 68

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1279228393  81 SELLIK---QMQGLYKILEPKIQSLFVAVWNLKIDF--------KEVKFKLISREK----NKEADKLVNEAL 137
Cdd:pfam00075  69 SQYVIGgitQWVHGWKKNGWPTTSEGKPVKNKDLWQllkalckkHQVYWQWVKGHAgnpgNEMADRLAKQGA 140
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 5-86 1.06e-09

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: 53.34  E-value: 1.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279228393   5 IVYTDGGSRGNPGLAA---IGVVIADE-KKNIlkeySQYL-GDNLTNNEAEYKAVIFALKKIKALFGKKkigefdVEIMS 79
Cdd:cd09280     1 VVYTDGSCLNNGKPGAragIGVYFGPGdPRNV----SEPLpGRKQTNNRAELLAVIHALEQAPEEGIRK------LEIRT 70


                  ....*..
gi 1279228393  80 DSELLIK 86
Cdd:cd09280    71 DSKYAIN 77
rnhA PRK13907
ribonuclease H; Provisional
 6-137 1.55e-09

ribonuclease H; Provisional


Pssm-ID: 139967 [Multi-domain]  Cd Length: 128  Bit Score: 52.75  E-value: 1.55e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1279228393   6 VYTDGGSRGNPGLAAIGVVIADEKKNIlkEYSQYLGdNLTNNEAEYKAVIFALKK-IKALFGKkkigefdVEIMSDSELL 84
Cdd:PRK13907    4 VYIDGASKGNPGPSGAGVFIKGVQPAV--QLSLPLG-TMSNHEAEYHALLAALKYcTEHNYNI-------VSFRTDSQLV 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1279228393  85 IKQMQGLY---KILEPKIQSLFVAVWNLKIDFkevkFKLISREKNKEADKLVNEAL 137
Cdd:PRK13907   74 ERAVEKEYaknKMFAPLLEEALQYIKSFDLFF----IKWIPSSQNKVADELARKAI 125
rnhA PRK00203
ribonuclease H; Reviewed
 1-62 1.09e-07

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 47.90  E-value: 1.09e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1279228393   1 MKKLIVYTDGGSRGNPGLAAIGVV-IADEKKnilKEYSQylGDNLT-NNEAEYKAVIFALKKIK 62
Cdd:PRK00203    1 MKQVEIYTDGACLGNPGPGGWGAIlRYKGHE---KELSG--GEALTtNNRMELMAAIEALEALK 59
 
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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