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Conserved domains on  [gi|1722905558|gb|TXD31918|]
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ribonuclease HI family protein, partial [Lujinxingia vulgaris]

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 ...
 1-91 4.39e-37

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: 124.12  E-value: 4.39e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722905558   1 GFNCTNNMAEYEACALAVQATIASNVKLFKVYGDSTLVIHQLRGEWETRDPKLIPYKAYIKELAKTFDEISFHHVPREEN 80
Cdd:cd09279    37 GFPATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLNGEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQN 116

                          90
                  ....*....|.
gi 1722905558  81 QMADALATLAS 91
Cdd:cd09279   117 KEADALANQAL 127
 
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 ...
 1-91 4.39e-37

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: 124.12  E-value: 4.39e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722905558   1 GFNCTNNMAEYEACALAVQATIASNVKLFKVYGDSTLVIHQLRGEWETRDPKLIPYKAYIKELAKTFDEISFHHVPREEN 80
Cdd:cd09279    37 GFPATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLNGEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQN 116

                          90
                  ....*....|.
gi 1722905558  81 QMADALATLAS 91
Cdd:cd09279   117 KEADALANQAL 127
RNAseHI_Thmprot NF041175
ribonuclease HI;
3-90 5.38e-24

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 91.18  E-value: 5.38e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722905558   3 NCTNNMAEYEACALAVQATIASNVKLFKVYGDSTLVIHQLRGEWETRDPKLIPYKAYIKELAKTFDEISFHHVPREENQM 82
Cdd:NF041175   46 DSTNNVAEYTGLICLLEKLLELGISEVIIRGDSQLVIRQLNGEYKVKSPRIIPLYEKALELLSKFRSIEFEWVPREENKE 125


                  ....*...
gi 1722905558  83 ADALATLA 90
Cdd:NF041175  126 ADRLSRIA 133
RnaseHI_Halo NF041306
ribonuclease HI;
5-90 1.08e-22

ribonuclease HI;


Pssm-ID: 469203  Cd Length: 197  Bit Score: 89.30  E-value: 1.08e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722905558   5 TNNMAEYEACALAVQATIASNVKLFKVYGDSTLVIHQLRGEWETRDPKLIPYKAYIKELAKTFDEISFHHVPREENQMAD 84
Cdd:NF041306  109 TNNQAEYEALIRALEAAADYGFDEVEVRGDSELIVKQVRGEWDTNDPDLRERRVRVRELLEGFDDWSIEHVPREINERAD 188


                  ....*.
gi 1722905558  85 ALATLA 90
Cdd:NF041306  189 ELANEA 194
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 5-90 9.36e-16

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: 69.22  E-value: 9.36e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722905558   5 TNNMAEYEACALAVQATIASNVKLFKVYGDSTLVIHQLRGEWETRdPKLIPYKAYIKELAKTFDEISFHHVPREENQMAD 84
Cdd:pfam13456  39 SVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGRSPKQ-SKLANLLDEIRKLLKRFESVSFEHIPREQNRVAD 117


                  ....*.
gi 1722905558  85 ALATLA 90
Cdd:pfam13456 118 TLAKMA 123
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 5-90 1.59e-14

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 69.62  E-value: 1.59e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722905558   5 TNNMAEYEA------CALAVQATIASnvklfkVYGDSTLVIHQLRGEWETRDPKLIPYKAYIKELAKTFDEISFHHVPRE 78
Cdd:PRK07238   44 TNNVAEYRGliagleAAAELGATEVE------VRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRA 117

                          90
                  ....*....|..
gi 1722905558  79 ENQMADALATLA 90
Cdd:PRK07238  118 RNAHADRLANEA 129
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
5-90 2.08e-14

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 66.02  E-value: 2.08e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722905558   5 TNNMAEYEACALAVQATIASNVKLFKVYGDSTLVIHQLRG---EWETRDPKLIPYKAYIKELAK--TFDEISFHHVPRE- 78
Cdd:COG0328    41 TNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQITGwihGWKKNGWKPVKNPDLWQRLDEllARHKVTFEWVKGHa 120

                          90
                  ....*....|....*
gi 1722905558  79 ---ENQMADALATLA 90
Cdd:COG0328   121 ghpGNERADALANKA 135
 
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 ...
 1-91 4.39e-37

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: 124.12  E-value: 4.39e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722905558   1 GFNCTNNMAEYEACALAVQATIASNVKLFKVYGDSTLVIHQLRGEWETRDPKLIPYKAYIKELAKTFDEISFHHVPREEN 80
Cdd:cd09279    37 GFPATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLNGEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQN 116

                          90
                  ....*....|.
gi 1722905558  81 QMADALATLAS 91
Cdd:cd09279   117 KEADALANQAL 127
RNAseHI_Thmprot NF041175
ribonuclease HI;
3-90 5.38e-24

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 91.18  E-value: 5.38e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722905558   3 NCTNNMAEYEACALAVQATIASNVKLFKVYGDSTLVIHQLRGEWETRDPKLIPYKAYIKELAKTFDEISFHHVPREENQM 82
Cdd:NF041175   46 DSTNNVAEYTGLICLLEKLLELGISEVIIRGDSQLVIRQLNGEYKVKSPRIIPLYEKALELLSKFRSIEFEWVPREENKE 125


                  ....*...
gi 1722905558  83 ADALATLA 90
Cdd:NF041175  126 ADRLSRIA 133
RnaseHI_Halo NF041306
ribonuclease HI;
5-90 1.08e-22

ribonuclease HI;


Pssm-ID: 469203  Cd Length: 197  Bit Score: 89.30  E-value: 1.08e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722905558   5 TNNMAEYEACALAVQATIASNVKLFKVYGDSTLVIHQLRGEWETRDPKLIPYKAYIKELAKTFDEISFHHVPREENQMAD 84
Cdd:NF041306  109 TNNQAEYEALIRALEAAADYGFDEVEVRGDSELIVKQVRGEWDTNDPDLRERRVRVRELLEGFDDWSIEHVPREINERAD 188


                  ....*.
gi 1722905558  85 ALATLA 90
Cdd:NF041306  189 ELANEA 194
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 4-87 1.36e-16

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


Pssm-ID: 259998 [Multi-domain]  Cd Length: 121  Bit Score: 71.58  E-value: 1.36e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722905558   4 CTNNMAEYEACALAVQATIASNVKLFKVYGDSTLVIHQLRGEWETRDPKLIPYKAyIKELAKTFDEISFHHVPREENQMA 83
Cdd:cd06222    38 PTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLINSGSFKWSPNILLIED-ILLLLSRFWSVKISHVPREGNQVA 116


                  ....
gi 1722905558  84 DALA 87
Cdd:cd06222   117 DALA 120
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 5-90 9.36e-16

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: 69.22  E-value: 9.36e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722905558   5 TNNMAEYEACALAVQATIASNVKLFKVYGDSTLVIHQLRGEWETRdPKLIPYKAYIKELAKTFDEISFHHVPREENQMAD 84
Cdd:pfam13456  39 SVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGRSPKQ-SKLANLLDEIRKLLKRFESVSFEHIPREQNRVAD 117


                  ....*.
gi 1722905558  85 ALATLA 90
Cdd:pfam13456 118 TLAKMA 123
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 5-90 1.59e-14

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 69.62  E-value: 1.59e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722905558   5 TNNMAEYEA------CALAVQATIASnvklfkVYGDSTLVIHQLRGEWETRDPKLIPYKAYIKELAKTFDEISFHHVPRE 78
Cdd:PRK07238   44 TNNVAEYRGliagleAAAELGATEVE------VRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRA 117

                          90
                  ....*....|..
gi 1722905558  79 ENQMADALATLA 90
Cdd:PRK07238  118 RNAHADRLANEA 129
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
5-90 2.08e-14

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 66.02  E-value: 2.08e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722905558   5 TNNMAEYEACALAVQATIASNVKLFKVYGDSTLVIHQLRG---EWETRDPKLIPYKAYIKELAK--TFDEISFHHVPRE- 78
Cdd:COG0328    41 TNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQITGwihGWKKNGWKPVKNPDLWQRLDEllARHKVTFEWVKGHa 120

                          90
                  ....*....|....*
gi 1722905558  79 ---ENQMADALATLA 90
Cdd:COG0328   121 ghpGNERADALANKA 135
PRK07708 PRK07708
hypothetical protein; Validated
 5-90 1.73e-09

hypothetical protein; Validated


Pssm-ID: 181088 [Multi-domain]  Cd Length: 219  Bit Score: 54.65  E-value: 1.73e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722905558   5 TNNMAEYEACALAVQATIASNVKLFKV--YGDSTLVIHQLRGEWETRDPKLIPYKAYIKELAKTFD-EISFHHVPREENQ 81
Cdd:PRK07708  117 DNNEAEYAALYYAMQELEELGVKHEPVtfRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKlTPVYEPISRKQNK 196


                  ....*....
gi 1722905558  82 MADALATLA 90
Cdd:PRK07708  197 EADQLATQA 205
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 5-92 2.18e-07

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: 47.56  E-value: 2.18e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722905558   5 TNNMAEYEACALAVQATIASNVKLFKVYGDSTLVIH--------QLRGEWETRDPKLIPYKAYIKELAKTFDE----ISF 72
Cdd:cd09280    42 TNNRAELLAVIHALEQAPEEGIRKLEIRTDSKYAINcitkwipkWKKNGWKTSKGKPVKNQDLIKELDKLLRKrgikVKF 121

                          90       100
                  ....*....|....*....|....
gi 1722905558  73 HHVP----REENQMADALATLASM 92
Cdd:cd09280   122 EHVKghsgDPGNEEADRLAREGAD 145
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 5-90 3.68e-05

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: 41.80  E-value: 3.68e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722905558   5 TNNMAEYEACALAVQ----ATIASNVKLFKVY--GDSTLV-------IHQ--LRGeWETRDPKLIPYKAYIKELAKTFD- 68
Cdd:cd13934    45 TSQRAELRAAIAALRfrswIIDPDGEGLKTVViaTDSEYVvkgatewIPKwkRNG-WRTSKGKPVKNRDLFELLLDEIEd 123

                          90       100
                  ....*....|....*....|....*...
gi 1722905558  69 ------EISFHHVPREENQMADALATLA 90
Cdd:cd13934   124 leeggvEVQFWHVPRELNKEADRLAKAA 151
RNase_HI_bacteria_like cd09277
Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus; Ribonuclease H ...
 10-87 1.62e-03

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: 36.69  E-value: 1.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1722905558  10 EYEACALAVQATIASNVKLFKVYGDSTLVIHQLRGEWETRDPKLIPYKAYIKELAKTFDeISFHHVPR----EENQMADA 85
Cdd:cd09277    49 EIKGAMKAIKYAIENGIKKITIYYDYEGIEKWATGEWKANKELTKEYKEFMQKYKKKIK-IEFVKVKAhsgdKYNELADK 127


                  ..
gi 1722905558  86 LA 87
Cdd:cd09277   128 LA 129
 
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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