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Conserved domains on  [gi|1735226158|gb|KAA0067952|]
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uncharacterized protein E6C27_scaffold138G001360 [Cucumis melo var. makuwa]

Protein Classification

Graphical summary

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List of domain hits

 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 ...
 285-408 4.25e-40

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: 144.15  E-value: 4.25e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158 285 WTMLFDGASNELEH--GIGVVLISPEGKVFPLTTKLCFECTHNIVEYEACIMGLQVACDMSIKKLKVLGDSMLVIHQVKE 362
Cdd:cd09279     1 WTLYFDGASRGNPGpaGAGVVIYSPGGEVLELSERLGFPATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLNG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1735226158 363 EWETRDAKLVPYIQYVTKLSQNFEKISFNHVLKEDNQMADALATLA 408
Cdd:cd09279    81 EYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQA 126
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1-82 5.49e-32

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


:

Pssm-ID: 238825  Cd Length: 177  Bit Score: 122.70  E-value: 5.49e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158   1 MPFGLKNAGATYQRAMVTLFHDMMHKEIEVYLDDMITKSKADEDHTTTLQKIFHRLRKYQLKLNPSKCTFGATSGKLLGF 80
Cdd:cd01647    96 MPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFLGH 175


                  ..
gi 1735226158  81 IV 82
Cdd:cd01647   176 IV 177
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 129-232 1.79e-26

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


:

Pssm-ID: 465565  Cd Length: 104  Bit Score: 104.51  E-value: 1.79e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158 129 PGRPLILYLTVLESSMGGVLGQHDlSKKKEHAIYYLSKKFTDYESRYSMLERTCCALVWTAHRLRQYMLYHTTCLISKMN 208
Cdd:pfam17917   2 PSKPFILETDASDYGIGAVLSQKD-EDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHK 80

                          90       100
                  ....*....|....*....|....
gi 1735226158 209 PIKYIFEKPSLSGRITKWQVLLSE 232
Cdd:pfam17917  81 PLKYLFTPKELNGRLARWALFLQE 104
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 495-552 7.99e-06

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


:

Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 44.16  E-value: 7.99e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1735226158 495 VDEEEAKQIMTNIHEGicgthaNGH-----MMARqiLRSGYYWTTMESDCIKYARKCKKCQIY 552
Cdd:pfam17921   1 VPKSLRKEILKEAHDS------GGHlgiekTLAR--LRRRYWWPGMRKDVKKYVKSCETCQRR 55
 
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 ...
 285-408 4.25e-40

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: 144.15  E-value: 4.25e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158 285 WTMLFDGASNELEH--GIGVVLISPEGKVFPLTTKLCFECTHNIVEYEACIMGLQVACDMSIKKLKVLGDSMLVIHQVKE 362
Cdd:cd09279     1 WTLYFDGASRGNPGpaGAGVVIYSPGGEVLELSERLGFPATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLNG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1735226158 363 EWETRDAKLVPYIQYVTKLSQNFEKISFNHVLKEDNQMADALATLA 408
Cdd:cd09279    81 EYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQA 126
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1-82 5.49e-32

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


Pssm-ID: 238825  Cd Length: 177  Bit Score: 122.70  E-value: 5.49e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158   1 MPFGLKNAGATYQRAMVTLFHDMMHKEIEVYLDDMITKSKADEDHTTTLQKIFHRLRKYQLKLNPSKCTFGATSGKLLGF 80
Cdd:cd01647    96 MPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFLGH 175


                  ..
gi 1735226158  81 IV 82
Cdd:cd01647   176 IV 177
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 129-232 1.79e-26

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 104.51  E-value: 1.79e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158 129 PGRPLILYLTVLESSMGGVLGQHDlSKKKEHAIYYLSKKFTDYESRYSMLERTCCALVWTAHRLRQYMLYHTTCLISKMN 208
Cdd:pfam17917   2 PSKPFILETDASDYGIGAVLSQKD-EDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHK 80

                          90       100
                  ....*....|....*....|....
gi 1735226158 209 PIKYIFEKPSLSGRITKWQVLLSE 232
Cdd:pfam17917  81 PLKYLFTPKELNGRLARWALFLQE 104
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 144-252 6.84e-25

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; 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. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in 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. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 100.64  E-value: 6.84e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158 144 MGGVLGQHDlSKKKEHAIYYLSKKFTDYESRYSMLERTCCALVWTAHRLRQYMLYHTTCLISKMNPIKYIFEKPSLSGRI 223
Cdd:cd09274    11 IGAVLSQED-DDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLLTQKDLNGRL 89

                          90       100
                  ....*....|....*....|....*....
gi 1735226158 224 TKWQVLLSEYNIVYVTKKAiKGSTVVDHL 252
Cdd:cd09274    90 ARWLLLLSEFDFEIEYRPG-KENVVADAL 117
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 289-408 8.19e-18

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: 80.39  E-value: 8.19e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158 289 FDGASNELEH--GIGVVLISPEGKVF-----PLTTKLCFEcthnIVEYEACIMGLQVACDMSIKKLKVLGDSMLVIHQVK 361
Cdd:pfam13456   2 FDGAFKCDSGlaGAGVVIRDPNGNVLlagqkKLGPGASVL----EAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLIN 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1735226158 362 EEWETRDaKLVPYIQYVTKLSQNFEKISFNHVLKEDNQMADALATLA 408
Cdd:pfam13456  78 GRSPKQS-KLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1-82 3.58e-13

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 68.87  E-value: 3.58e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158   1 MPFGLKNAGATYQRAMVTLFHDMMHKE---IEVYLDDMITKSKADEDHTTTLQKIFHRLRKYQLKLNPSKCTF--GATSG 75
Cdd:pfam00078 103 LPQGLVLSPALFQLFMNELLRPLRKRAgltLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFflKSKEV 182


                  ....*..
gi 1735226158  76 KLLGFIV 82
Cdd:pfam00078 183 KYLGVTL 189
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
289-409 3.63e-09

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 56.01  E-value: 3.63e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158 289 FDGAS--NELEHGIGVVLISPE-----GKVFPLTTklcfectHNIVEYEACIMGLQVACDMSIKKLKVLGDSMLVIHQVK 361
Cdd:COG0328     7 TDGACrgNPGPGGWGAVIRYGGeekelSGGLGDTT-------NNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQIT 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1735226158 362 E---EWETRDAKLV---PYIQYVTKLSQNfEKISFNHV----LKEDNQMADALATLAV 409
Cdd:COG0328    80 GwihGWKKNGWKPVknpDLWQRLDELLAR-HKVTFEWVkghaGHPGNERADALANKAL 136
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 323-408 7.50e-06

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 49.21  E-value: 7.50e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158 323 THNIVEYEACIMGLQVACDMSIKKLKVLGDSMLVIHQVKEEWETRDAKLVPYIQYVTKLSQNFEKISFNHVLKEDNQMAD 402
Cdd:PRK07238   44 TNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHAD 123


                  ....*.
gi 1735226158 403 ALATLA 408
Cdd:PRK07238  124 RLANEA 129
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 495-552 7.99e-06

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 44.16  E-value: 7.99e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1735226158 495 VDEEEAKQIMTNIHEGicgthaNGH-----MMARqiLRSGYYWTTMESDCIKYARKCKKCQIY 552
Cdd:pfam17921   1 VPKSLRKEILKEAHDS------GGHlgiekTLAR--LRRRYWWPGMRKDVKKYVKSCETCQRR 55
 
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 ...
 285-408 4.25e-40

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: 144.15  E-value: 4.25e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158 285 WTMLFDGASNELEH--GIGVVLISPEGKVFPLTTKLCFECTHNIVEYEACIMGLQVACDMSIKKLKVLGDSMLVIHQVKE 362
Cdd:cd09279     1 WTLYFDGASRGNPGpaGAGVVIYSPGGEVLELSERLGFPATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLNG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1735226158 363 EWETRDAKLVPYIQYVTKLSQNFEKISFNHVLKEDNQMADALATLA 408
Cdd:cd09279    81 EYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQA 126
RT_LTR cd01647
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long ...
 1-82 5.49e-32

RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.


Pssm-ID: 238825  Cd Length: 177  Bit Score: 122.70  E-value: 5.49e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158   1 MPFGLKNAGATYQRAMVTLFHDMMHKEIEVYLDDMITKSKADEDHTTTLQKIFHRLRKYQLKLNPSKCTFGATSGKLLGF 80
Cdd:cd01647    96 MPFGLKNAPATFQRLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFLGH 175


                  ..
gi 1735226158  81 IV 82
Cdd:cd01647   176 IV 177
RT_RNaseH pfam17917
RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) ...
 129-232 1.79e-26

RNase H-like domain found in reverse transcriptase; DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.


Pssm-ID: 465565  Cd Length: 104  Bit Score: 104.51  E-value: 1.79e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158 129 PGRPLILYLTVLESSMGGVLGQHDlSKKKEHAIYYLSKKFTDYESRYSMLERTCCALVWTAHRLRQYMLYHTTCLISKMN 208
Cdd:pfam17917   2 PSKPFILETDASDYGIGAVLSQKD-EDGKERPIAYASRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRKFTVYTDHK 80

                          90       100
                  ....*....|....*....|....
gi 1735226158 209 PIKYIFEKPSLSGRITKWQVLLSE 232
Cdd:pfam17917  81 PLKYLFTPKELNGRLARWALFLQE 104
RNase_HI_RT_Ty3 cd09274
Ty3/Gypsy family of RNase HI in long-term repeat retroelements; Ribonuclease H (RNase H) ...
 144-252 6.84e-25

Ty3/Gypsy family of RNase HI in long-term repeat retroelements; 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. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in 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. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260006 [Multi-domain]  Cd Length: 121  Bit Score: 100.64  E-value: 6.84e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158 144 MGGVLGQHDlSKKKEHAIYYLSKKFTDYESRYSMLERTCCALVWTAHRLRQYMLYHTTCLISKMNPIKYIFEKPSLSGRI 223
Cdd:cd09274    11 IGAVLSQED-DDGKERPIAFFSRKLTPAERNYSTTEKELLAIVWALKKFRHYLLGRPFTVYTDHKALKYLLTQKDLNGRL 89

                          90       100
                  ....*....|....*....|....*....
gi 1735226158 224 TKWQVLLSEYNIVYVTKKAiKGSTVVDHL 252
Cdd:cd09274    90 ARWLLLLSEFDFEIEYRPG-KENVVADAL 117
RT_RNaseH_2 pfam17919
RNase H-like domain found in reverse transcriptase;
103-195 8.52e-25

RNase H-like domain found in reverse transcriptase;


Pssm-ID: 465567 [Multi-domain]  Cd Length: 100  Bit Score: 99.50  E-value: 8.52e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158 103 WNEDCEKAFNKIKQYLQSPPVLIPLAPGRPLILYLTVLESSMGGVLGQHDlSKKKEHAIYYLSKKFTDYESRYSMLERTC 182
Cdd:pfam17919   1 WTEECQKAFEKLKQALTSAPVLAHPDPDKPFILETDASDYGIGAVLSQED-DDGGERPIAYASRKLSPAERNYSTTEKEL 79

                          90
                  ....*....|...
gi 1735226158 183 CALVWTAHRLRQY 195
Cdd:pfam17919  80 LAIVFALKKFRHY 92
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 289-408 8.19e-18

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: 80.39  E-value: 8.19e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158 289 FDGASNELEH--GIGVVLISPEGKVF-----PLTTKLCFEcthnIVEYEACIMGLQVACDMSIKKLKVLGDSMLVIHQVK 361
Cdd:pfam13456   2 FDGAFKCDSGlaGAGVVIRDPNGNVLlagqkKLGPGASVL----EAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLIN 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1735226158 362 EEWETRDaKLVPYIQYVTKLSQNFEKISFNHVLKEDNQMADALATLA 408
Cdd:pfam13456  78 GRSPKQS-KLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAKMA 123
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 289-405 4.64e-17

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: 78.12  E-value: 4.64e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158 289 FDGAS--NELEHGIGVVLISPEGKVFPLTTKLCFECTHNIVEYEACIMGLQVACDMSIKKLKVLGDSMLVIHQVKeEWET 366
Cdd:cd06222     3 VDGSCrgNPGPAGIGGVLRDHEGGWLGGFALKIGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLIN-SGSF 81

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1735226158 367 RDAKLVPYIQYVTKLSQNFEKISFNHVLKEDNQMADALA 405
Cdd:cd06222    82 KWSPNILLIEDILLLLSRFWSVKISHVPREGNQVADALA 120
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 1-82 3.58e-13

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 68.87  E-value: 3.58e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158   1 MPFGLKNAGATYQRAMVTLFHDMMHKE---IEVYLDDMITKSKADEDHTTTLQKIFHRLRKYQLKLNPSKCTF--GATSG 75
Cdd:pfam00078 103 LPQGLVLSPALFQLFMNELLRPLRKRAgltLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEKTQFflKSKEV 182


                  ....*..
gi 1735226158  76 KLLGFIV 82
Cdd:pfam00078 183 KYLGVTL 189
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
289-409 3.63e-09

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 56.01  E-value: 3.63e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158 289 FDGAS--NELEHGIGVVLISPE-----GKVFPLTTklcfectHNIVEYEACIMGLQVACDMSIKKLKVLGDSMLVIHQVK 361
Cdd:COG0328     7 TDGACrgNPGPGGWGAVIRYGGeekelSGGLGDTT-------NNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQIT 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1735226158 362 E---EWETRDAKLV---PYIQYVTKLSQNfEKISFNHV----LKEDNQMADALATLAV 409
Cdd:COG0328    80 GwihGWKKNGWKPVknpDLWQRLDELLAR-HKVTFEWVkghaGHPGNERADALANKAL 136
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 323-408 7.50e-06

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 49.21  E-value: 7.50e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158 323 THNIVEYEACIMGLQVACDMSIKKLKVLGDSMLVIHQVKEEWETRDAKLVPYIQYVTKLSQNFEKISFNHVLKEDNQMAD 402
Cdd:PRK07238   44 TNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHAD 123


                  ....*.
gi 1735226158 403 ALATLA 408
Cdd:PRK07238  124 RLANEA 129
Integrase_H2C2 pfam17921
Integrase zinc binding domain; This zinc binding domain is found in a wide variety of ...
 495-552 7.99e-06

Integrase zinc binding domain; This zinc binding domain is found in a wide variety of integrase proteins.


Pssm-ID: 465569 [Multi-domain]  Cd Length: 58  Bit Score: 44.16  E-value: 7.99e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1735226158 495 VDEEEAKQIMTNIHEGicgthaNGH-----MMARqiLRSGYYWTTMESDCIKYARKCKKCQIY 552
Cdd:pfam17921   1 VPKSLRKEILKEAHDS------GGHlgiekTLAR--LRRRYWWPGMRKDVKKYVKSCETCQRR 55
PRK07708 PRK07708
hypothetical protein; Validated
 237-408 4.00e-05

hypothetical protein; Validated


Pssm-ID: 181088 [Multi-domain]  Cd Length: 219  Bit Score: 45.80  E-value: 4.00e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158 237 YVTKKAIKGSTVVDHL----AAQLVADYEPM----RIDFPDEN-----IFLVEKNAKDHET----WTMLFDGA--SNELE 297
Cdd:PRK07708    9 YKTKKGLQTELTSDWMnieeALQLAEDFEKTgrvkELEFYDEMdtewsLKELKKLSKEVEEepheILVYFDGGfdKETKL 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158 298 HGIGVVL-ISPEGKVFPLTTKLCFEC--THNIVEYEACIMGLQVACDMSIKKLKVL--GDSMLVIHQVKEEWETRDAKLV 372
Cdd:PRK07708   89 AGLGIVIyYKQGNKRYRIRRNAYIEGiyDNNEAEYAALYYAMQELEELGVKHEPVTfrGDSQVVLNQLAGEWPCYDEHLN 168

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1735226158 373 PYIQYVT------KLSQNFEKISfnhvlKEDNQMADALATLA 408
Cdd:PRK07708  169 HWLDRIEqklkqlKLTPVYEPIS-----RKQNKEADQLATQA 205
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 323-410 3.71e-04

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: 41.78  E-value: 3.71e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1735226158 323 THNIVEYEACIMGLQVACDMSIKKLKVLGDSMLVIHQV--------KEEWETRDAKLV---PYIQYVTKLSQNFE-KISF 390
Cdd:cd09280    42 TNNRAELLAVIHALEQAPEEGIRKLEIRTDSKYAINCItkwipkwkKNGWKTSKGKPVknqDLIKELDKLLRKRGiKVKF 121

                          90       100
                  ....*....|....*....|....*
gi 1735226158 391 NHVlK-----EDNQMADALATLAVM 410
Cdd:cd09280   122 EHV-KghsgdPGNEEADRLAREGAD 145
 
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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