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Conserved domains on  [gi|1087994243|gb|OGY67390|]
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MAG: hypothetical protein A3I89_03030 [Candidatus Harrisonbacteria bacterium RIFCSPLOWO2_02_FULL_41_11]

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
Rnh1 super family cl34588
Ribonuclease HI-related protein, contains viroplasmin and RNaseH domains [General function ...
 18-202 5.34e-16

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


The actual alignment was detected with superfamily member COG3341:

Pssm-ID: 442570 [Multi-domain]  Cd Length: 203  Bit Score: 72.96  E-value: 5.34e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1087994243  18 GVCDSWEECAKKVIGVTGARYRGFSDIKSAEYWLKQGAVYQESRQREKPNLLPG---IYFDA----GTGR-GQGVeisVT 89
Cdd:COG3341    15 GIYTTWDECKAQVKGFPGAKYKSFKTKEEAEAALNGNYEDYKGKKKKLSEIELDsiaVYVDGscsgNPGVyEYGG---VD 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1087994243  90 NEKGENLLNKvmpRKKINRHEKHlilkpvTNNYGELLALSYALKLAVKTGIKR-IFGDSRLIIDyWSQGKIRRAQVESAT 168
Cdd:COG3341    92 TKTGKETFSE---LFHDGPFAEG------TNNAGEFLAAVHALAYLKKKGSKLpIYSDYRGAIS-WVKGKWKTKLERTQA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1087994243 169 ----VRLAENTRKLRISFEksggKVEYVSGD---DNPADLG 202
Cdd:COG3341   162 ykelFDLIEKKNTYENPFV----KVKTHSGDkwnEIPDDLA 198
 
Name Accession Description Interval E-value
Rnh1 COG3341
Ribonuclease HI-related protein, contains viroplasmin and RNaseH domains [General function ...
 18-202 5.34e-16

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


Pssm-ID: 442570 [Multi-domain]  Cd Length: 203  Bit Score: 72.96  E-value: 5.34e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1087994243  18 GVCDSWEECAKKVIGVTGARYRGFSDIKSAEYWLKQGAVYQESRQREKPNLLPG---IYFDA----GTGR-GQGVeisVT 89
Cdd:COG3341    15 GIYTTWDECKAQVKGFPGAKYKSFKTKEEAEAALNGNYEDYKGKKKKLSEIELDsiaVYVDGscsgNPGVyEYGG---VD 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1087994243  90 NEKGENLLNKvmpRKKINRHEKHlilkpvTNNYGELLALSYALKLAVKTGIKR-IFGDSRLIIDyWSQGKIRRAQVESAT 168
Cdd:COG3341    92 TKTGKETFSE---LFHDGPFAEG------TNNAGEFLAAVHALAYLKKKGSKLpIYSDYRGAIS-WVKGKWKTKLERTQA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1087994243 169 ----VRLAENTRKLRISFEksggKVEYVSGD---DNPADLG 202
Cdd:COG3341   162 ykelFDLIEKKNTYENPFV----KVKTHSGDkwnEIPDDLA 198
Cauli_VI pfam01693
Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. ...
 13-50 3.75e-06

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: 42.39  E-value: 3.75e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1087994243  13 KNNQDGVCDSWEECAKKVIGVTGARYRGFSDIKSAEYW 50
Cdd:pfam01693   7 KGRKPGIYTTWDECKAQVKGFPGAKYKSFKTREEAEAF 44
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 72-152 1.92e-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: 42.46  E-value: 1.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1087994243  72 IYFDAGTgRGQ----GVEISVTNEKGEnllnkvmpRKKINRHekhlILKPVTNNYGELLALSYALKLAVKTGIKR--IFG 145
Cdd:cd09279     3 LYFDGAS-RGNpgpaGAGVVIYSPGGE--------VLELSER----LGFPATNNEAEYEALIAGLELALELGAEKleIYG 69


                  ....*..
gi 1087994243 146 DSRLIID 152
Cdd:cd09279    70 DSQLVVN 76
 
Name Accession Description Interval E-value
Rnh1 COG3341
Ribonuclease HI-related protein, contains viroplasmin and RNaseH domains [General function ...
 18-202 5.34e-16

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


Pssm-ID: 442570 [Multi-domain]  Cd Length: 203  Bit Score: 72.96  E-value: 5.34e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1087994243  18 GVCDSWEECAKKVIGVTGARYRGFSDIKSAEYWLKQGAVYQESRQREKPNLLPG---IYFDA----GTGR-GQGVeisVT 89
Cdd:COG3341    15 GIYTTWDECKAQVKGFPGAKYKSFKTKEEAEAALNGNYEDYKGKKKKLSEIELDsiaVYVDGscsgNPGVyEYGG---VD 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1087994243  90 NEKGENLLNKvmpRKKINRHEKHlilkpvTNNYGELLALSYALKLAVKTGIKR-IFGDSRLIIDyWSQGKIRRAQVESAT 168
Cdd:COG3341    92 TKTGKETFSE---LFHDGPFAEG------TNNAGEFLAAVHALAYLKKKGSKLpIYSDYRGAIS-WVKGKWKTKLERTQA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1087994243 169 ----VRLAENTRKLRISFEksggKVEYVSGD---DNPADLG 202
Cdd:COG3341   162 ykelFDLIEKKNTYENPFV----KVKTHSGDkwnEIPDDLA 198
Cauli_VI pfam01693
Caulimovirus viroplasmin; This family consists of various caulimovirus viroplasmin proteins. ...
 13-50 3.75e-06

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: 42.39  E-value: 3.75e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1087994243  13 KNNQDGVCDSWEECAKKVIGVTGARYRGFSDIKSAEYW 50
Cdd:pfam01693   7 KGRKPGIYTTWDECKAQVKGFPGAKYKSFKTREEAEAF 44
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 72-152 1.92e-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: 42.46  E-value: 1.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1087994243  72 IYFDAGTgRGQ----GVEISVTNEKGEnllnkvmpRKKINRHekhlILKPVTNNYGELLALSYALKLAVKTGIKR--IFG 145
Cdd:cd09279     3 LYFDGAS-RGNpgpaGAGVVIYSPGGE--------VLELSER----LGFPATNNEAEYEALIAGLELALELGAEKleIYG 69


                  ....*..
gi 1087994243 146 DSRLIID 152
Cdd:cd09279    70 DSQLVVN 76
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
119-161 4.20e-04

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 39.06  E-value: 4.20e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1087994243 119 TNNYGELLALSYALKLAVKTGIK--RIFGDSRLIIDY---WSQGKIRR 161
Cdd:COG0328    41 TNNRAELTALIAALEALKELGPCevEIYTDSQYVVNQitgWIHGWKKN 88
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 113-182 5.42e-04

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: 38.45  E-value: 5.42e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1087994243 113 LILKPVTNNYGELLALSYALKLAVKTGIKR--IFGDSRLIIDY---WSQGKIRRAQVESATVRLAENTRKLRISF 182
Cdd:cd06222    33 LKIGAPTALEAELLALLLALELALDLGYLKviIESDSKYVVDLinsGSFKWSPNILLIEDILLLLSRFWSVKISH 107
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 119-152 1.52e-03

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: 37.55  E-value: 1.52e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1087994243 119 TNNYGELLALSYALKLAVKTGIKR--IFGDSRLIID 152
Cdd:cd09280    42 TNNRAELLAVIHALEQAPEEGIRKleIRTDSKYAIN 77
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 124-200 1.85e-03

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: 36.86  E-value: 1.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1087994243 124 ELLALSYALKLAVKTGIKRI--FGDSRLIIDYWSQGKIRRAQVEsatvRLAENTRKLRISFEKSggKVEYVSGDDN-PAD 200
Cdd:pfam13456  44 EAQALIIGLQLAWKLGIRHLivEGDSATVVQLINGRSPKQSKLA----NLLDEIRKLLKRFESV--SFEHIPREQNrVAD 117
 
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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