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Conserved domains on  [gi|2714566624|ref|WP_341094877|]
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MULTISPECIES: ribonuclease H [unclassified Paenibacillus]

Protein Classification

ribonuclease H family protein( domain architecture ID 10483842)

ribonuclease H (RNaseH) family protein containing viroplasmin and RNaseH domains may function as an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_H_like super family cl14782
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 92-222 4.34e-68

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.


The actual alignment was detected with superfamily member cd13935:

Pssm-ID: 449355  Cd Length: 133  Bit Score: 205.06  E-value: 4.34e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2714566624  92 DSISVDVGTRGNPGPVEYKGVDTQTGDIIFSCGPIKKGTNNLGEFLAIVHALALLKKEGSNRTVYSDSLNAMKWVKQKKV 171
Cdd:cd13935     3 ESLCVDAACSGNPGIVEYRGVDTKTGEVLFHRGPFPGGTNNMGEFLAIVHALRYLKEKNSRKPIYSDSQTAIAWVKKKKA 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2714566624 172 ATTLPRDASTEEIWILIDRAERWLQSNTYDNKLLKWQTKEWGEIKADYGRK 222
Cdd:cd13935    83 KSTLVRNEKNAEIFKLVDRAEEWLSTHTYPNPILKWQTDKWGEIPADFGRK 133
Cauli_VI pfam01693
Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. ...
 5-42 4.07e-16

Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. The viroplasmin protein is encoded by gene VI and is the main component of viral inclusion bodies or viroplasms. Inclusions are the site of viral assembly, DNA synthesis and accumulation. Two domains exist within gene VI corresponding approximately to the 5' third and middle third of gene VI, these influence systemic infection in a light-dependent manner.


:

Pssm-ID: 460297 [Multi-domain]  Cd Length: 44  Bit Score: 69.36  E-value: 4.07e-16
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2714566624   5 KFYVVWEGKQPGVYGTWAECQAQTDHYTGAKYKSYESR 42
Cdd:pfam01693   1 KYYAVAKGRKPGIYTTWDECKAQVKGFPGAKYKSFKTR 38
 
Name Accession Description Interval E-value
RNase_H_bacteria_like cd13935
RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence ...
 92-222 4.34e-68

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: 205.06  E-value: 4.34e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2714566624  92 DSISVDVGTRGNPGPVEYKGVDTQTGDIIFSCGPIKKGTNNLGEFLAIVHALALLKKEGSNRTVYSDSLNAMKWVKQKKV 171
Cdd:cd13935     3 ESLCVDAACSGNPGIVEYRGVDTKTGEVLFHRGPFPGGTNNMGEFLAIVHALRYLKEKNSRKPIYSDSQTAIAWVKKKKA 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2714566624 172 ATTLPRDASTEEIWILIDRAERWLQSNTYDNKLLKWQTKEWGEIKADYGRK 222
Cdd:cd13935    83 KSTLVRNEKNAEIFKLVDRAEEWLSTHTYPNPILKWQTDKWGEIPADFGRK 133
Rnh1 COG3341
Ribonuclease HI-related protein, contains viroplasmin and RNaseH domains [General function ...
 2-222 5.45e-64

Ribonuclease HI-related protein, contains viroplasmin and RNaseH domains [General function prediction only];


Pssm-ID: 442570 [Multi-domain]  Cd Length: 203  Bit Score: 197.38  E-value: 5.45e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2714566624   2 AKQKFYVVWEGKQPGVYGTWAECQAQTDHYTGAKYKSYESRAAADAAYKAGWKGNwgtgasssasggskgkpaasrgrSA 81
Cdd:COG3341     1 KKKKFYAVWKGRKPGIYTTWDECKAQVKGFPGAKYKSFKTKEEAEAALNGNYEDY-----------------------KG 57

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2714566624  82 SVETSAEIDYDSISV--DVGTRGNPGPVEYKGVDTQTGDI----IFSCGPIKKGTNNLGEFLAIVHALALLKKEGSNRTV 155
Cdd:COG3341    58 KKKKLSEIELDSIAVyvDGSCSGNPGVYEYGGVDTKTGKEtfseLFHDGPFAEGTNNAGEFLAAVHALAYLKKKGSKLPI 137

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2714566624 156 YSDSLNAMKWVKqKKVATTLPRDASTEEIWILIDraerwlQSNTYDNKLLKWQT---KEWGEIKADYGRK 222
Cdd:COG3341   138 YSDYRGAISWVK-GKWKTKLERTQAYKELFDLIE------KKNTYENPFVKVKThsgDKWNEIPDDLARK 200
Cauli_VI pfam01693
Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. ...
 5-42 4.07e-16

Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. The viroplasmin protein is encoded by gene VI and is the main component of viral inclusion bodies or viroplasms. Inclusions are the site of viral assembly, DNA synthesis and accumulation. Two domains exist within gene VI corresponding approximately to the 5' third and middle third of gene VI, these influence systemic infection in a light-dependent manner.


Pssm-ID: 460297 [Multi-domain]  Cd Length: 44  Bit Score: 69.36  E-value: 4.07e-16
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2714566624   5 KFYVVWEGKQPGVYGTWAECQAQTDHYTGAKYKSYESR 42
Cdd:pfam01693   1 KYYAVAKGRKPGIYTTWDECKAQVKGFPGAKYKSFKTR 38
 
Name Accession Description Interval E-value
RNase_H_bacteria_like cd13935
RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence ...
 92-222 4.34e-68

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: 205.06  E-value: 4.34e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2714566624  92 DSISVDVGTRGNPGPVEYKGVDTQTGDIIFSCGPIKKGTNNLGEFLAIVHALALLKKEGSNRTVYSDSLNAMKWVKQKKV 171
Cdd:cd13935     3 ESLCVDAACSGNPGIVEYRGVDTKTGEVLFHRGPFPGGTNNMGEFLAIVHALRYLKEKNSRKPIYSDSQTAIAWVKKKKA 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2714566624 172 ATTLPRDASTEEIWILIDRAERWLQSNTYDNKLLKWQTKEWGEIKADYGRK 222
Cdd:cd13935    83 KSTLVRNEKNAEIFKLVDRAEEWLSTHTYPNPILKWQTDKWGEIPADFGRK 133
Rnh1 COG3341
Ribonuclease HI-related protein, contains viroplasmin and RNaseH domains [General function ...
 2-222 5.45e-64

Ribonuclease HI-related protein, contains viroplasmin and RNaseH domains [General function prediction only];


Pssm-ID: 442570 [Multi-domain]  Cd Length: 203  Bit Score: 197.38  E-value: 5.45e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2714566624   2 AKQKFYVVWEGKQPGVYGTWAECQAQTDHYTGAKYKSYESRAAADAAYKAGWKGNwgtgasssasggskgkpaasrgrSA 81
Cdd:COG3341     1 KKKKFYAVWKGRKPGIYTTWDECKAQVKGFPGAKYKSFKTKEEAEAALNGNYEDY-----------------------KG 57

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2714566624  82 SVETSAEIDYDSISV--DVGTRGNPGPVEYKGVDTQTGDI----IFSCGPIKKGTNNLGEFLAIVHALALLKKEGSNRTV 155
Cdd:COG3341    58 KKKKLSEIELDSIAVyvDGSCSGNPGVYEYGGVDTKTGKEtfseLFHDGPFAEGTNNAGEFLAAVHALAYLKKKGSKLPI 137

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2714566624 156 YSDSLNAMKWVKqKKVATTLPRDASTEEIWILIDraerwlQSNTYDNKLLKWQT---KEWGEIKADYGRK 222
Cdd:COG3341   138 YSDYRGAISWVK-GKWKTKLERTQAYKELFDLIE------KKNTYENPFVKVKThsgDKWNEIPDDLARK 200
Cauli_VI pfam01693
Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. ...
 5-42 4.07e-16

Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. The viroplasmin protein is encoded by gene VI and is the main component of viral inclusion bodies or viroplasms. Inclusions are the site of viral assembly, DNA synthesis and accumulation. Two domains exist within gene VI corresponding approximately to the 5' third and middle third of gene VI, these influence systemic infection in a light-dependent manner.


Pssm-ID: 460297 [Multi-domain]  Cd Length: 44  Bit Score: 69.36  E-value: 4.07e-16
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2714566624   5 KFYVVWEGKQPGVYGTWAECQAQTDHYTGAKYKSYESR 42
Cdd:pfam01693   1 KYYAVAKGRKPGIYTTWDECKAQVKGFPGAKYKSFKTR 38
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
94-168 3.57e-08

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 50.61  E-value: 3.57e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2714566624  94 ISVDVGTRGNPGPVEYkGVDTQTGDIIFS-CGPIKKGTNNLGEFLAIVHALALLKKEGSNR-TVYSDSLNAMKWVKQ 168
Cdd:COG0328     5 IYTDGACRGNPGPGGW-GAVIRYGGEEKElSGGLGDTTNNRAELTALIAALEALKELGPCEvEIYTDSQYVVNQITG 80
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 94-169 2.02e-06

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: 45.38  E-value: 2.02e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2714566624  94 ISVDVGTRGNPGPVEYKGV--DTQTGDIIFSCGPIKKGTNNLGEFLAIVHALALLKKEG-SNRTVYSDSLNAMKWVKQK 169
Cdd:cd06222     1 INVDGSCRGNPGPAGIGGVlrDHEGGWLGGFALKIGAPTALEAELLALLLALELALDLGyLKVIIESDSKYVVDLINSG 79
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 96-194 5.41e-05

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: 41.30  E-value: 5.41e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2714566624  96 VDVGTRGNPGPVEYkGV--DTQTGDIIFSCGPI-KKGTNNLGEFLAIVHALALLKKEGSNR-TVYSDS---LNAMK--W- 165
Cdd:cd09279     5 FDGASRGNPGPAGA-GVviYSPGGEVLELSERLgFPATNNEAEYEALIAGLELALELGAEKlEIYGDSqlvVNQLNgeYk 83

                          90       100
                  ....*....|....*....|....*....
gi 2714566624 166 VKQKKVATTLprdastEEIWILIDRAERW 194
Cdd:cd09279    84 VKNERLKPLL------EKVLELLAKFELV 106
 
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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