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Conserved domains on  [gi|3377833|gb|AAC28206|]
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contains similarity to Nicotiana tabacum probable integrase (GB:X80830) [Arabidopsis thaliana]

Protein Classification

transposase( domain architecture ID 10328791)

transposase is an enzyme that binds to the end of a transposon and catalyzes the movement of the transposon to another part of the genome by a cut and paste mechanism or a replicative transposition mechanism; similar to Geobacillus stearothermophilus insertion sequence element IS5376

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 ...
 1-68 8.34e-23

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 cd09279:

Pssm-ID: 449355 [Multi-domain]  Cd Length: 128  Bit Score: 92.54  E-value: 8.34e-23
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 3377833    1 MGIRDIHAHSDSQLVISQFHGEYEAKDERMEAYLELVKTLTQQFESFELTMIPRGENTSADALAALAY 68
Cdd:cd09279  60 LGAEKLEIYGDSQLVVNQLNGEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQAL 127
rve super family cl47583
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 237-315 1.00e-04

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


The actual alignment was detected with superfamily member pfam00665:

Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 40.76  E-value: 1.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3377833    237 PFMKWSMDVVgPMEASGGKKKLKnLLV------------------TEKQVEDFLWENIVCRHGIPYEIITDNGTNLTSGK 298
Cdd:pfam00665   1 PNQLWQGDFT-YIRIPGGGGKLY-LLVivddfsreilawalssemDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKA 78

                          90
                  ....*....|....*..
gi 3377833    299 IKAFCDKCKIRLTISTP 315
Cdd:pfam00665  79 FREFLKDLGIKPSFSRP 95
 
Name Accession Description Interval E-value
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 1-68 8.34e-23

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: 92.54  E-value: 8.34e-23
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 3377833    1 MGIRDIHAHSDSQLVISQFHGEYEAKDERMEAYLELVKTLTQQFESFELTMIPRGENTSADALAALAY 68
Cdd:cd09279  60 LGAEKLEIYGDSQLVVNQLNGEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQAL 127
RNAseHI_Thmprot NF041175
ribonuclease HI;
2-68 5.28e-13

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 65.76  E-value: 5.28e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 3377833     2 GIRDIHAHSDSQLVISQFHGEYEAKDERMEAYLELVKTLTQQFESFELTMIPRGENTSADALAALAY 68
Cdd:NF041175  68 GISEVIIRGDSQLVIRQLNGEYKVKSPRIIPLYEKALELLSKFRSIEFEWVPREENKEADRLSRIAY 134
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 2-67 4.83e-07

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: 48.03  E-value: 4.83e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 3377833      2 GIRDIHAHSDSQLVISQFHGEyEAKDERMEAYLELVKTLTQQFESFELTMIPRGENTSADALAALA 67
Cdd:pfam13456  59 GIRHLIVEGDSATVVQLINGR-SPKQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 237-315 1.00e-04

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 40.76  E-value: 1.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3377833    237 PFMKWSMDVVgPMEASGGKKKLKnLLV------------------TEKQVEDFLWENIVCRHGIPYEIITDNGTNLTSGK 298
Cdd:pfam00665   1 PNQLWQGDFT-YIRIPGGGGKLY-LLVivddfsreilawalssemDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKA 78

                          90
                  ....*....|....*..
gi 3377833    299 IKAFCDKCKIRLTISTP 315
Cdd:pfam00665  79 FREFLKDLGIKPSFSRP 95
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 1-67 5.37e-04

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 41.50  E-value: 5.37e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 3377833     1 MGIRDIHAHSDSQLVISQFHGEYEAKDERMEAYLELVKTLTQQFESFELTMIPRGENTSADALAALA 67
Cdd:PRK07238  63 LGATEVEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEA 129
 
Name Accession Description Interval E-value
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
 1-68 8.34e-23

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: 92.54  E-value: 8.34e-23
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 3377833    1 MGIRDIHAHSDSQLVISQFHGEYEAKDERMEAYLELVKTLTQQFESFELTMIPRGENTSADALAALAY 68
Cdd:cd09279  60 LGAEKLEIYGDSQLVVNQLNGEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQAL 127
RNAseHI_Thmprot NF041175
ribonuclease HI;
2-68 5.28e-13

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 65.76  E-value: 5.28e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 3377833     2 GIRDIHAHSDSQLVISQFHGEYEAKDERMEAYLELVKTLTQQFESFELTMIPRGENTSADALAALAY 68
Cdd:NF041175  68 GISEVIIRGDSQLVIRQLNGEYKVKSPRIIPLYEKALELLSKFRSIEFEWVPREENKEADRLSRIAY 134
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 2-67 4.83e-07

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: 48.03  E-value: 4.83e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 3377833      2 GIRDIHAHSDSQLVISQFHGEyEAKDERMEAYLELVKTLTQQFESFELTMIPRGENTSADALAALA 67
Cdd:pfam13456  59 GIRHLIVEGDSATVVQLINGR-SPKQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 237-315 1.00e-04

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 40.76  E-value: 1.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3377833    237 PFMKWSMDVVgPMEASGGKKKLKnLLV------------------TEKQVEDFLWENIVCRHGIPYEIITDNGTNLTSGK 298
Cdd:pfam00665   1 PNQLWQGDFT-YIRIPGGGGKLY-LLVivddfsreilawalssemDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKA 78

                          90
                  ....*....|....*..
gi 3377833    299 IKAFCDKCKIRLTISTP 315
Cdd:pfam00665  79 FREFLKDLGIKPSFSRP 95
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 1-67 5.37e-04

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 41.50  E-value: 5.37e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 3377833     1 MGIRDIHAHSDSQLVISQFHGEYEAKDERMEAYLELVKTLTQQFESFELTMIPRGENTSADALAALA 67
Cdd:PRK07238  63 LGATEVEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEA 129
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 1-64 3.39e-03

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: 37.29  E-value: 3.39e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 3377833    1 MGIRDIHAHSDSQLVISQFHGEYEAKDERMEAYLELVKTLTQqFESFELTMIPRGENTSADALA 64
Cdd:cd06222  58 LGYLKVIIESDSKYVVDLINSGSFKWSPNILLIEDILLLLSR-FWSVKISHVPREGNQVADALA 120
 
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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