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Conserved domains on  [gi|1229801214|ref|XP_022154440|]
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uncharacterized protein LOC111021711 [Momordica charantia]

Protein Classification

ribonuclease H family protein( domain architecture ID 10153149)

ribonuclease H (RNaseH) family protein containing a reverse transcriptase (RT)-like domain; may be an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner

CATH:  3.30.420.10
EC:  3.1.26.4
Gene Ontology:  GO:0003723|GO:0004540
PubMed:  16093691
SCOP:  4000541

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 138-258 2.18e-15

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: 70.81  E-value: 2.18e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1229801214 138 INVDTACKLSNSRTGIGVVCQNDKGEIIVAMIRKLDVfYEPLQVETLAILEGL---WLTQCLDLIfvqVDSDSQNSINLI 214
Cdd:cd06222     1 INVDGSCRGNPGPAGIGGVLRDHEGGWLGGFALKIGA-PTALEAELLALLLALelaLDLGYLKVI---IESDSKYVVDLI 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1229801214 215 SQEYDPSHQPNVWVDDIHMCAINFIDILFMHIQRSSSNVTHRLA 258
Cdd:cd06222    77 NSGSFKWSPNILLIEDILLLLSRFWSVKISHVPREGNQVADALA 120
 
Name Accession Description Interval E-value
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 138-258 2.18e-15

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: 70.81  E-value: 2.18e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1229801214 138 INVDTACKLSNSRTGIGVVCQNDKGEIIVAMIRKLDVfYEPLQVETLAILEGL---WLTQCLDLIfvqVDSDSQNSINLI 214
Cdd:cd06222     1 INVDGSCRGNPGPAGIGGVLRDHEGGWLGGFALKIGA-PTALEAELLALLLALelaLDLGYLKVI---IESDSKYVVDLI 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1229801214 215 SQEYDPSHQPNVWVDDIHMCAINFIDILFMHIQRSSSNVTHRLA 258
Cdd:cd06222    77 NSGSFKWSPNILLIEDILLLLSRFWSVKISHVPREGNQVADALA 120
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 139-261 4.90e-14

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: 67.29  E-value: 4.90e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1229801214 139 NVDTACKLSNSRTGIGVVCQNDKGEIIVAMIRKLDVFYEPLQVETLAILEGLWLtqCLDLIF--VQVDSDSQNSINLISQ 216
Cdd:pfam13456   1 NFDGAFKCDSGLAGAGVVIRDPNGNVLLAGQKKLGPGASVLEAEAQALIIGLQL--AWKLGIrhLIVEGDSATVVQLING 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1229801214 217 EYDPSHQPNVWVDDIHMCAINFIDILFMHIQRSSSNVTHRLASTA 261
Cdd:pfam13456  79 RSPKQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
 
Name Accession Description Interval E-value
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 138-258 2.18e-15

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: 70.81  E-value: 2.18e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1229801214 138 INVDTACKLSNSRTGIGVVCQNDKGEIIVAMIRKLDVfYEPLQVETLAILEGL---WLTQCLDLIfvqVDSDSQNSINLI 214
Cdd:cd06222     1 INVDGSCRGNPGPAGIGGVLRDHEGGWLGGFALKIGA-PTALEAELLALLLALelaLDLGYLKVI---IESDSKYVVDLI 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1229801214 215 SQEYDPSHQPNVWVDDIHMCAINFIDILFMHIQRSSSNVTHRLA 258
Cdd:cd06222    77 NSGSFKWSPNILLIEDILLLLSRFWSVKISHVPREGNQVADALA 120
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 139-261 4.90e-14

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: 67.29  E-value: 4.90e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1229801214 139 NVDTACKLSNSRTGIGVVCQNDKGEIIVAMIRKLDVFYEPLQVETLAILEGLWLtqCLDLIF--VQVDSDSQNSINLISQ 216
Cdd:pfam13456   1 NFDGAFKCDSGLAGAGVVIRDPNGNVLLAGQKKLGPGASVLEAEAQALIIGLQL--AWKLGIrhLIVEGDSATVVQLING 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1229801214 217 EYDPSHQPNVWVDDIHMCAINFIDILFMHIQRSSSNVTHRLASTA 261
Cdd:pfam13456  79 RSPKQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 136-263 3.98e-03

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: 36.68  E-value: 3.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1229801214 136 VKINVDTACKLSNSRTGIGVVCQNDKGEIIvamirkldVFYEPL-------QVETLAILEGlwLTQCLDLIFVQVD--SD 206
Cdd:cd09279     1 WTLYFDGASRGNPGPAGAGVVIYSPGGEVL--------ELSERLgfpatnnEAEYEALIAG--LELALELGAEKLEiyGD 70

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1229801214 207 SQ---NSINLISQEYDPSHQPnvWVDDIHMCAINFIDILFMHIQRSSSNVTHRLASTAIS 263
Cdd:cd09279    71 SQlvvNQLNGEYKVKNERLKP--LLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
 
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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