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Conserved domains on  [gi|67633766|gb|AAY78807|]
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putative reverse transcriptase/RNA-dependent DNA polymerase [Arabidopsis thaliana]

Protein Classification

ribonuclease H family protein( domain architecture ID 10623310)

ribonuclease H family protein with a zinc-binding domain that may be associated with an LTR retrotransposon, 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 cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 430-550 1.78e-27

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: 107.01  E-value: 1.78e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67633766 430 CNTDATWNRDNERCGIGWVLRNEKGEVKWmGARALPKLKSVLEAELEAMRWAVLSLSRFQYNYVIFESDSQVLIEILNND 509
Cdd:cd06222   1 INVDGSCRGNPGPAGIGGVLRDHEGGWLG-GFALKIGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLINSG 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 67633766 510 EIWPSLKPT-IQDLQRLLSQFTEVKFVFIPREGNTLAERVAR 550
Cdd:cd06222  80 SFKWSPNILlIEDILLLLSRFWSVKISHVPREGNQVADALAK 121
zf-RVT pfam13966
zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of ...
 223-316 6.09e-15

zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of a putative reverse transcriptase.


:

Pssm-ID: 433612  Cd Length: 84  Bit Score: 69.99  E-value: 6.09e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67633766   223 YTVKSGYWVLTQIINKrsspqevsepslNPIYQKIWKSQTSPKIQHFLWKCLSNSLPVAGALAYRHLSKESACIRCPSCK 302
Cdd:pfam13966   1 FSVKSAYNLLRQKRPK------------VDWAKLIWKKKAPPKVKFFLWLALRNRLPTADRLKKRGIPIDSRCPLCGQEE 68

                          90
                  ....*....|....
gi 67633766   303 ETVNHLLFKCTFAR 316
Cdd:pfam13966  69 ETIDHLFFSCPFAR 82
 
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 ...
 430-550 1.78e-27

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: 107.01  E-value: 1.78e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67633766 430 CNTDATWNRDNERCGIGWVLRNEKGEVKWmGARALPKLKSVLEAELEAMRWAVLSLSRFQYNYVIFESDSQVLIEILNND 509
Cdd:cd06222   1 INVDGSCRGNPGPAGIGGVLRDHEGGWLG-GFALKIGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLINSG 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 67633766 510 EIWPSLKPT-IQDLQRLLSQFTEVKFVFIPREGNTLAERVAR 550
Cdd:cd06222  80 SFKWSPNILlIEDILLLLSRFWSVKISHVPREGNQVADALAK 121
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 431-552 1.32e-22

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: 93.10  E-value: 1.32e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67633766   431 NTDATWNRDNERCGIGWVLRNEKGEVKWMGARALPKLKSVLEAELEAMRWAV---LSLSrfqYNYVIFESDSQVLIEILN 507
Cdd:pfam13456   1 NFDGAFKCDSGLAGAGVVIRDPNGNVLLAGQKKLGPGASVLEAEAQALIIGLqlaWKLG---IRHLIVEGDSATVVQLIN 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 67633766   508 NDE-IWPSLKPTIQDLQRLLSQFTEVKFVFIPREGNTLAERVARES 552
Cdd:pfam13456  78 GRSpKQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
zf-RVT pfam13966
zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of ...
 223-316 6.09e-15

zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of a putative reverse transcriptase.


Pssm-ID: 433612  Cd Length: 84  Bit Score: 69.99  E-value: 6.09e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67633766   223 YTVKSGYWVLTQIINKrsspqevsepslNPIYQKIWKSQTSPKIQHFLWKCLSNSLPVAGALAYRHLSKESACIRCPSCK 302
Cdd:pfam13966   1 FSVKSAYNLLRQKRPK------------VDWAKLIWKKKAPPKVKFFLWLALRNRLPTADRLKKRGIPIDSRCPLCGQEE 68

                          90
                  ....*....|....
gi 67633766   303 ETVNHLLFKCTFAR 316
Cdd:pfam13966  69 ETIDHLFFSCPFAR 82
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
444-553 3.77e-05

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 43.68  E-value: 3.77e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67633766 444 GIGWVLRnEKGEVKWMGARAlpKLKSVLEAELEAMRWAVLSLSRFQYNYVIFESDSQVLIEILN---------------N 508
Cdd:COG0328  19 GWGAVIR-YGGEEKELSGGL--GDTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQITgwihgwkkngwkpvkN 95

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 67633766 509 DEIWpslkptiQDLQRLLSQFtEVKFVFIPRE----GNTLAERVARESL 553
Cdd:COG0328  96 PDLW-------QRLDELLARH-KVTFEWVKGHaghpGNERADALANKAL 136
 
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 ...
 430-550 1.78e-27

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: 107.01  E-value: 1.78e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67633766 430 CNTDATWNRDNERCGIGWVLRNEKGEVKWmGARALPKLKSVLEAELEAMRWAVLSLSRFQYNYVIFESDSQVLIEILNND 509
Cdd:cd06222   1 INVDGSCRGNPGPAGIGGVLRDHEGGWLG-GFALKIGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLINSG 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 67633766 510 EIWPSLKPT-IQDLQRLLSQFTEVKFVFIPREGNTLAERVAR 550
Cdd:cd06222  80 SFKWSPNILlIEDILLLLSRFWSVKISHVPREGNQVADALAK 121
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 431-552 1.32e-22

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: 93.10  E-value: 1.32e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67633766   431 NTDATWNRDNERCGIGWVLRNEKGEVKWMGARALPKLKSVLEAELEAMRWAV---LSLSrfqYNYVIFESDSQVLIEILN 507
Cdd:pfam13456   1 NFDGAFKCDSGLAGAGVVIRDPNGNVLLAGQKKLGPGASVLEAEAQALIIGLqlaWKLG---IRHLIVEGDSATVVQLIN 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 67633766   508 NDE-IWPSLKPTIQDLQRLLSQFTEVKFVFIPREGNTLAERVARES 552
Cdd:pfam13456  78 GRSpKQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
zf-RVT pfam13966
zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of ...
 223-316 6.09e-15

zinc-binding in reverse transcriptase; This domain would appear to be a zinc-binding region of a putative reverse transcriptase.


Pssm-ID: 433612  Cd Length: 84  Bit Score: 69.99  E-value: 6.09e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67633766   223 YTVKSGYWVLTQIINKrsspqevsepslNPIYQKIWKSQTSPKIQHFLWKCLSNSLPVAGALAYRHLSKESACIRCPSCK 302
Cdd:pfam13966   1 FSVKSAYNLLRQKRPK------------VDWAKLIWKKKAPPKVKFFLWLALRNRLPTADRLKKRGIPIDSRCPLCGQEE 68

                          90
                  ....*....|....
gi 67633766   303 ETVNHLLFKCTFAR 316
Cdd:pfam13966  69 ETIDHLFFSCPFAR 82
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 428-554 7.90e-13

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: 65.57  E-value: 7.90e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67633766 428 VKCNTDATWNRDNERCGIGWVLRNEKGEVkWMGARALPKLKSVLEAELEAMRWAVLSLSRFQYNYVIFESDSQVLIEILN 507
Cdd:cd09279   1 WTLYFDGASRGNPGPAGAGVVIYSPGGEV-LELSERLGFPATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLN 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 67633766 508 NDeiW----PSLKPTIQDLQRLLSQFTEVKFVFIPREGNTLAERVARESLS 554
Cdd:cd09279  80 GE--YkvknERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
444-553 3.77e-05

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 43.68  E-value: 3.77e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67633766 444 GIGWVLRnEKGEVKWMGARAlpKLKSVLEAELEAMRWAVLSLSRFQYNYVIFESDSQVLIEILN---------------N 508
Cdd:COG0328  19 GWGAVIR-YGGEEKELSGGL--GDTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQITgwihgwkkngwkpvkN 95

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 67633766 509 DEIWpslkptiQDLQRLLSQFtEVKFVFIPRE----GNTLAERVARESL 553
Cdd:COG0328  96 PDLW-------QRLDELLARH-KVTFEWVKGHaghpGNERADALANKAL 136
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 432-554 5.67e-05

non-LTR RNase HI domain of reverse transcriptases; 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). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retrotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260008 [Multi-domain]  Cd Length: 131  Bit Score: 42.98  E-value: 5.67e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 67633766 432 TDATwnRDNERCGIGWVLRNEKGEVKWMGAraLPKLKSVLEAEL----EAMRWAvLSLSRFQYNYVIFeSDSQVLIEILN 507
Cdd:cd09276   4 TDGS--KLEGSVGAGFVIYRGGEVISRSYR--LGTHASVFDAELeailEALELA-LATARRARKVTIF-TDSQSALQALR 77

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 67633766 508 NDEI---WPSLKPTIQDLQRLLSQFTEVKFVFIPR----EGNTLAERVARESLS 554
Cdd:cd09276  78 NPRRssgQVILIRILRLLRLLKAKGVKVRLRWVPGhvgiEGNEAADRLAKEAAS 131
 
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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