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Conserved domains on  [gi|15232041|ref|NP_189756|]
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non-LTR retroelement reverse transcriptase [Arabidopsis thaliana]

Protein Classification

ribonuclease H family protein( domain architecture ID 54171)

ribonuclease H (RNase H) family protein 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 ...
 124-185 8.03e-10

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 pfam13456:

Pssm-ID: 449355 [Multi-domain]  Cd Length: 123  Bit Score: 54.58  E-value: 8.03e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15232041   124 NNNVSQAGRSKGQHCSMSMEAELQALVMAMQHVWSKGYKKVIFEGDNLRLSSFLRKIKPTSK 185
Cdd:pfam13456  23 NGNVLLAGQKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGRSPKQS 84
 
Name Accession Description Interval E-value
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 124-185 8.03e-10

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: 54.58  E-value: 8.03e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15232041   124 NNNVSQAGRSKGQHCSMSMEAELQALVMAMQHVWSKGYKKVIFEGDNLRLSSFLRKIKPTSK 185
Cdd:pfam13456  23 NGNVLLAGQKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGRSPKQS 84
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 124-170 1.19e-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: 45.77  E-value: 1.19e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 15232041 124 NNNVSQAGRSKGQHCSMSMEAELQALVMAMQHVWSKGYKKVIFEGDN 170
Cdd:cd06222  23 HEGGWLGGFALKIGAPTALEAELLALLLALELALDLGYLKVIIESDS 69
 
Name Accession Description Interval E-value
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 124-185 8.03e-10

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: 54.58  E-value: 8.03e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15232041   124 NNNVSQAGRSKGQHCSMSMEAELQALVMAMQHVWSKGYKKVIFEGDNLRLSSFLRKIKPTSK 185
Cdd:pfam13456  23 NGNVLLAGQKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGRSPKQS 84
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 124-170 1.19e-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: 45.77  E-value: 1.19e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 15232041 124 NNNVSQAGRSKGQHCSMSMEAELQALVMAMQHVWSKGYKKVIFEGDN 170
Cdd:cd06222  23 HEGGWLGGFALKIGAPTALEAELLALLLALELALDLGYLKVIIESDS 69
 
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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