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Conserved domains on  [gi|15217749|ref|NP_174108|]
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Polynucleotidyl transferase, ribonuclease H-like superfamily protein [Arabidopsis thaliana]

Protein Classification

RNase_H_like domain-containing protein( domain architecture ID 10603123)

RNase_H_like domain-containing protein

Graphical summary

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List of domain hits

 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 ...
 63-182 2.17e-37

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: 126.23  E-value: 2.17e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15217749    63 NFDGSFVNGDVKSKAGWVVRDSNGSYLLAGQAIGRKVDNALESEIQALIISMQHCWSHGYKRVCFEGDNKMLFDLING-S 141
Cdd:pfam13456   1 NFDGAFKCDSGLAGAGVVIRDPNGNVLLAGQKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGrS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 15217749   142 KVYFGVHNWIRDIHWWLRKFESIHFNWIRRHHNTPADILAK 182
Cdd:pfam13456  81 PKQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAK 121
 
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 ...
 63-182 2.17e-37

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: 126.23  E-value: 2.17e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15217749    63 NFDGSFVNGDVKSKAGWVVRDSNGSYLLAGQAIGRKVDNALESEIQALIISMQHCWSHGYKRVCFEGDNKMLFDLING-S 141
Cdd:pfam13456   1 NFDGAFKCDSGLAGAGVVIRDPNGNVLLAGQKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGrS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 15217749   142 KVYFGVHNWIRDIHWWLRKFESIHFNWIRRHHNTPADILAK 182
Cdd:pfam13456  81 PKQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAK 121
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 62-182 2.63e-28

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: 103.16  E-value: 2.63e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15217749  62 CNFDGSFVNGDVKSKAGWVVRDSNGSYLlAGQAIGRKVDNALESEIQALIISMQHCWSHGYKRVCFEGDNKMLFDLIN-G 140
Cdd:cd06222   1 INVDGSCRGNPGPAGIGGVLRDHEGGWL-GGFALKIGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLINsG 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 15217749 141 SKVYFGVHNWIRDIHWWLRKFESIHFNWIRRHHNTPADILAK 182
Cdd:cd06222  80 SFKWSPNILLIEDILLLLSRFWSVKISHVPREGNQVADALAK 121
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
77-183 1.57e-05

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 42.91  E-value: 1.57e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15217749  77 AGWVVRDSNGSYLLAGQAigRKVDNaLESEIQALIISMQHCWSHGYKRVCFEGDNKMLFDLINGSKVYFGVHNW--IRDI 154
Cdd:COG0328  20 WGAVIRYGGEEKELSGGL--GDTTN-NRAELTALIAALEALKELGPCEVEIYTDSQYVVNQITGWIHGWKKNGWkpVKNP 96

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 15217749 155 HWW-----LRKFESIHFNWIRRHH----NTPADILAKA 183
Cdd:COG0328  97 DLWqrldeLLARHKVTFEWVKGHAghpgNERADALANK 134
rnhA PRK13907
ribonuclease H; Provisional
 104-187 3.68e-05

ribonuclease H; Provisional


Pssm-ID: 139967 [Multi-domain]  Cd Length: 128  Bit Score: 41.96  E-value: 3.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15217749  104 ESEIQALIISMQHCWSHGYKRVCFEGDNKMLFDLIN----GSKVYFGVhnwIRDIHWWLRKFESIHFNWIRRHHNTPADI 179
Cdd:PRK13907  43 EAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEkeyaKNKMFAPL---LEEALQYIKSFDLFFIKWIPSSQNKVADE 119


                 ....*....
gi 15217749  180 LA-KAPLQN 187
Cdd:PRK13907 120 LArKAILQN 128
 
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 ...
 63-182 2.17e-37

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: 126.23  E-value: 2.17e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15217749    63 NFDGSFVNGDVKSKAGWVVRDSNGSYLLAGQAIGRKVDNALESEIQALIISMQHCWSHGYKRVCFEGDNKMLFDLING-S 141
Cdd:pfam13456   1 NFDGAFKCDSGLAGAGVVIRDPNGNVLLAGQKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGrS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 15217749   142 KVYFGVHNWIRDIHWWLRKFESIHFNWIRRHHNTPADILAK 182
Cdd:pfam13456  81 PKQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAK 121
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 62-182 2.63e-28

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: 103.16  E-value: 2.63e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15217749  62 CNFDGSFVNGDVKSKAGWVVRDSNGSYLlAGQAIGRKVDNALESEIQALIISMQHCWSHGYKRVCFEGDNKMLFDLIN-G 140
Cdd:cd06222   1 INVDGSCRGNPGPAGIGGVLRDHEGGWL-GGFALKIGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLINsG 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 15217749 141 SKVYFGVHNWIRDIHWWLRKFESIHFNWIRRHHNTPADILAK 182
Cdd:cd06222  80 SFKWSPNILLIEDILLLLSRFWSVKISHVPREGNQVADALAK 121
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 60-182 2.54e-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: 64.03  E-value: 2.54e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15217749  60 IKCNFDGSFVNGDVKSKAGWVVRDSNGSYLLAGQAIGRKVDNaLESEIQALIISMQHCWSHGYKRVCFEGDNKMLFDLIN 139
Cdd:cd09279   1 WTLYFDGASRGNPGPAGAGVVIYSPGGEVLELSERLGFPATN-NEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLN 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 15217749 140 G-----SKVYFGVHNWIRDIhwwLRKFESIHFNWIRRHHNTPADILAK 182
Cdd:cd09279  80 GeykvkNERLKPLLEKVLEL---LAKFELVELKWIPREQNKEADALAN 124
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
77-183 1.57e-05

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 42.91  E-value: 1.57e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15217749  77 AGWVVRDSNGSYLLAGQAigRKVDNaLESEIQALIISMQHCWSHGYKRVCFEGDNKMLFDLINGSKVYFGVHNW--IRDI 154
Cdd:COG0328  20 WGAVIRYGGEEKELSGGL--GDTTN-NRAELTALIAALEALKELGPCEVEIYTDSQYVVNQITGWIHGWKKNGWkpVKNP 96

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 15217749 155 HWW-----LRKFESIHFNWIRRHH----NTPADILAKA 183
Cdd:COG0328  97 DLWqrldeLLARHKVTFEWVKGHAghpgNERADALANK 134
rnhA PRK13907
ribonuclease H; Provisional
 104-187 3.68e-05

ribonuclease H; Provisional


Pssm-ID: 139967 [Multi-domain]  Cd Length: 128  Bit Score: 41.96  E-value: 3.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15217749  104 ESEIQALIISMQHCWSHGYKRVCFEGDNKMLFDLIN----GSKVYFGVhnwIRDIHWWLRKFESIHFNWIRRHHNTPADI 179
Cdd:PRK13907  43 EAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEkeyaKNKMFAPL---LEEALQYIKSFDLFFIKWIPSSQNKVADE 119


                 ....*....
gi 15217749  180 LA-KAPLQN 187
Cdd:PRK13907 120 LArKAILQN 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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