NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1464222874|ref|WP_116899868|]
View 

tRNA (adenine(22)-N(1))-methyltransferase TrmK [Thermaerobacter sp. PB12/4term]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 426-553 6.75e-61

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: 197.31  E-value: 6.75e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 426 WRLHTDGAARGNPGPAGIGVVLVGPDGAVaERIARFIGE-ATNNVAEYTALVTGLQRALERGARRLDVYSDSELMVRQLN 504
Cdd:cd09279     1 WTLYFDGASRGNPGPAGAGVVIYSPGGEV-LELSERLGFpATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLN 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1464222874 505 GQYRVKNEGLKPLFEQAARLAAQFELVRFIHVPRERNREADRLANQGID 553
Cdd:cd09279    80 GEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
TrmK COG2384
tRNA A22 N1-methylase [Translation, ribosomal structure and biogenesis]; tRNA A22 N1-methylase ...
 5-130 7.39e-36

tRNA A22 N1-methylase [Translation, ribosomal structure and biogenesis]; tRNA A22 N1-methylase is part of the Pathway/BioSystem: tRNA modification


:

Pssm-ID: 441950  Cd Length: 228  Bit Score: 133.76  E-value: 7.39e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874   5 RLGPRLEALLDMLGRVEVLADIGTDHGLLPVTAVLRGRARRAIATDLRAAPLAAARRLVEDTGTQDRIELRQGPGLLPLR 84
Cdd:COG2384     1 KLSKRLQAIASLVPKGARVADIGTDHAYLPIYLVKNGIIKKAIAGDVNEGPLEKAKKNVKKYGLEDKIEVRLGDGLEVLE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1464222874  85 PGEAGTVVISGLHGETIAAILRAGAGRLEPGTRLLLQPTRGAAALR 130
Cdd:COG2384    81 PGEVDTIVIAGMGGELIADILEAGKDKLKSVKRLILQPNTGAEELR 126
 
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 ...
 426-553 6.75e-61

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: 197.31  E-value: 6.75e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 426 WRLHTDGAARGNPGPAGIGVVLVGPDGAVaERIARFIGE-ATNNVAEYTALVTGLQRALERGARRLDVYSDSELMVRQLN 504
Cdd:cd09279     1 WTLYFDGASRGNPGPAGAGVVIYSPGGEV-LELSERLGFpATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLN 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1464222874 505 GQYRVKNEGLKPLFEQAARLAAQFELVRFIHVPRERNREADRLANQGID 553
Cdd:cd09279    80 GEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
426-552 1.11e-36

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 133.05  E-value: 1.11e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 426 WRLHTDGAARGNPGPAGIGVVLVgpDGAVAERIARFIGEATNNVAEYTALVTGLQRALERGARRLDVYSDSELMVRQLNG 505
Cdd:COG0328     3 IEIYTDGACRGNPGPGGWGAVIR--YGGEEKELSGGLGDTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQITG 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 506 QY---------RVKNeglKPLFEQAARLAAQfELVRFIHVPRER----NREADRLANQGI 552
Cdd:COG0328    81 WIhgwkkngwkPVKN---PDLWQRLDELLAR-HKVTFEWVKGHAghpgNERADALANKAL 136
TrmK COG2384
tRNA A22 N1-methylase [Translation, ribosomal structure and biogenesis]; tRNA A22 N1-methylase ...
 5-130 7.39e-36

tRNA A22 N1-methylase [Translation, ribosomal structure and biogenesis]; tRNA A22 N1-methylase is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441950  Cd Length: 228  Bit Score: 133.76  E-value: 7.39e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874   5 RLGPRLEALLDMLGRVEVLADIGTDHGLLPVTAVLRGRARRAIATDLRAAPLAAARRLVEDTGTQDRIELRQGPGLLPLR 84
Cdd:COG2384     1 KLSKRLQAIASLVPKGARVADIGTDHAYLPIYLVKNGIIKKAIAGDVNEGPLEKAKKNVKKYGLEDKIEVRLGDGLEVLE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1464222874  85 PGEAGTVVISGLHGETIAAILRAGAGRLEPGTRLLLQPTRGAAALR 130
Cdd:COG2384    81 PGEVDTIVIAGMGGELIADILEAGKDKLKSVKRLILQPNTGAEELR 126
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 431-566 1.24e-35

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 137.42  E-value: 1.24e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 431 DGAARGNPGPAGIGVVLVGPD-GAVAERIARFIGEATNNVAEYTALVTGLQRALERGARRLDVYSDSELMVRQLNGQYRV 509
Cdd:PRK07238    8 DGGSRGNPGPAGYGAVVWDADrGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWKV 87

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1464222874 510 KNEGLKPLFEQAARLAAQFELVRFIHVPRERNREADRLANQGIDQGTGGAQGAPGPV 566
Cdd:PRK07238   88 KHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEAMDAAAGGEPWGPSAA 144
Methyltransf_18 pfam12847
Methyltransferase domain; Protein in this family function as methyltransferases.
 6-130 5.75e-35

Methyltransferase domain; Protein in this family function as methyltransferases.


Pssm-ID: 463730  Cd Length: 151  Bit Score: 128.70  E-value: 5.75e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874   6 LGPRLEALLDMLGRVEVLADIGTDHGLLPVTAVLRGRARRAIATDLRAAPLAAARRLVEDTGTQDRIELRQGPGLLPLRP 85
Cdd:pfam12847   1 LSKRLQAIASLVPPGSRVADIGTDHAYLPIYLVKNGIAPKAIASDINEGPLEKARENIEKYGLEDRIEVRLGDGLEVLEP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1464222874  86 GEAGTVVISGLHGETIAAILRAGAGRLEPGTRLLLQPTRGAAALR 130
Cdd:pfam12847  81 GEVDTIVIAGMGGELIIDILEAGPEVLKSVKRLILQPQSDIEELR 125
RNAseHI_Thmprot NF041175
ribonuclease HI;
437-550 1.03e-32

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 122.38  E-value: 1.03e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 437 NPGpaGI---GVVLVGPDGAVAER--IAR--FIGEATNNVAEYTALVTGLQRALERGARRLDVYSDSELMVRQLNGQYRV 509
Cdd:NF041175   14 NPG--GIatyGYVIYLDNKRKIEGygLAAepWSKDSTNNVAEYTGLICLLEKLLELGISEVIIRGDSQLVIRQLNGEYKV 91

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1464222874 510 KNEGLKPLFEQAARLAAQFELVRFIHVPRERNREADRLANQ 550
Cdd:NF041175   92 KSPRIIPLYEKALELLSKFRSIEFEWVPREENKEADRLSRI 132
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 430-549 4.77e-24

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: 97.34  E-value: 4.77e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 430 TDGAARGNPGPAGIGVVLVGPDGAV-AERIARFIGEATNNVAEYTALVTGLQRALERGARRLDVYSDSELMVRQLNGQyR 508
Cdd:pfam13456   2 FDGAFKCDSGLAGAGVVIRDPNGNVlLAGQKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGR-S 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1464222874 509 VKNEGLKPLFEQAARLAAQFELVRFIHVPRERNREADRLAN 549
Cdd:pfam13456  81 PKQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAK 121
Sortase_D_1 cd05828
Sortase domain found in subfamily 1 of the class D family of sortases; Class D sortases are ...
 67-125 1.23e-03

Sortase domain found in subfamily 1 of the class D family of sortases; Class D sortases are cysteine transpeptidases distributed in Gram-positive bacteria (mainly present in Firmicutes). The prototypical subfamily 1 of class D sortase from Bacillus anthracis (named Ba-SrtC) covalently attaches proteins bearing a noncanonical LPNTA sorting signal, such as the BasH and BasI proteins, to the peptidoglycan of the cell wall that facilitate sporulation. BasH is exclusively anchored to the forespore cell wall envelope, while BasI is attached to the diaminopimelic acid moiety of the peptidoglycan of predivisional cells. Ba-SrtC lacks the N-terminal signal peptide and membrane anchor. The family also includes many class D sortase homologs from Gram-negative bacteria, but the functions of these enzymes are unknown.


Pssm-ID: 320677  Cd Length: 127  Bit Score: 39.02  E-value: 1.23e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1464222874  67 GTQDRIeLRQGPGLLPL--RPGEAGTVVISGlHGETIAAILragaGRLEPGTRLLLQPTRG 125
Cdd:cd05828    21 GTSGEA-LAFGPGHLPGsaLPGEGGNVVIAG-HRDTHFRFL----KDLKVGDEITLETSGG 75
 
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 ...
 426-553 6.75e-61

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: 197.31  E-value: 6.75e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 426 WRLHTDGAARGNPGPAGIGVVLVGPDGAVaERIARFIGE-ATNNVAEYTALVTGLQRALERGARRLDVYSDSELMVRQLN 504
Cdd:cd09279     1 WTLYFDGASRGNPGPAGAGVVIYSPGGEV-LELSERLGFpATNNEAEYEALIAGLELALELGAEKLEIYGDSQLVVNQLN 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1464222874 505 GQYRVKNEGLKPLFEQAARLAAQFELVRFIHVPRERNREADRLANQGID 553
Cdd:cd09279    80 GEYKVKNERLKPLLEKVLELLAKFELVELKWIPREQNKEADALANQALD 128
RnhA COG0328
Ribonuclease HI [Replication, recombination and repair];
426-552 1.11e-36

Ribonuclease HI [Replication, recombination and repair];


Pssm-ID: 440097 [Multi-domain]  Cd Length: 136  Bit Score: 133.05  E-value: 1.11e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 426 WRLHTDGAARGNPGPAGIGVVLVgpDGAVAERIARFIGEATNNVAEYTALVTGLQRALERGARRLDVYSDSELMVRQLNG 505
Cdd:COG0328     3 IEIYTDGACRGNPGPGGWGAVIR--YGGEEKELSGGLGDTTNNRAELTALIAALEALKELGPCEVEIYTDSQYVVNQITG 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 506 QY---------RVKNeglKPLFEQAARLAAQfELVRFIHVPRER----NREADRLANQGI 552
Cdd:COG0328    81 WIhgwkkngwkPVKN---PDLWQRLDELLAR-HKVTFEWVKGHAghpgNERADALANKAL 136
TrmK COG2384
tRNA A22 N1-methylase [Translation, ribosomal structure and biogenesis]; tRNA A22 N1-methylase ...
 5-130 7.39e-36

tRNA A22 N1-methylase [Translation, ribosomal structure and biogenesis]; tRNA A22 N1-methylase is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441950  Cd Length: 228  Bit Score: 133.76  E-value: 7.39e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874   5 RLGPRLEALLDMLGRVEVLADIGTDHGLLPVTAVLRGRARRAIATDLRAAPLAAARRLVEDTGTQDRIELRQGPGLLPLR 84
Cdd:COG2384     1 KLSKRLQAIASLVPKGARVADIGTDHAYLPIYLVKNGIIKKAIAGDVNEGPLEKAKKNVKKYGLEDKIEVRLGDGLEVLE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1464222874  85 PGEAGTVVISGLHGETIAAILRAGAGRLEPGTRLLLQPTRGAAALR 130
Cdd:COG2384    81 PGEVDTIVIAGMGGELIADILEAGKDKLKSVKRLILQPNTGAEELR 126
PRK07238 PRK07238
bifunctional RNase H/acid phosphatase; Provisional
 431-566 1.24e-35

bifunctional RNase H/acid phosphatase; Provisional


Pssm-ID: 180903 [Multi-domain]  Cd Length: 372  Bit Score: 137.42  E-value: 1.24e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 431 DGAARGNPGPAGIGVVLVGPD-GAVAERIARFIGEATNNVAEYTALVTGLQRALERGARRLDVYSDSELMVRQLNGQYRV 509
Cdd:PRK07238    8 DGGSRGNPGPAGYGAVVWDADrGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWKV 87

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1464222874 510 KNEGLKPLFEQAARLAAQFELVRFIHVPRERNREADRLANQGIDQGTGGAQGAPGPV 566
Cdd:PRK07238   88 KHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEAMDAAAGGEPWGPSAA 144
Methyltransf_18 pfam12847
Methyltransferase domain; Protein in this family function as methyltransferases.
 6-130 5.75e-35

Methyltransferase domain; Protein in this family function as methyltransferases.


Pssm-ID: 463730  Cd Length: 151  Bit Score: 128.70  E-value: 5.75e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874   6 LGPRLEALLDMLGRVEVLADIGTDHGLLPVTAVLRGRARRAIATDLRAAPLAAARRLVEDTGTQDRIELRQGPGLLPLRP 85
Cdd:pfam12847   1 LSKRLQAIASLVPPGSRVADIGTDHAYLPIYLVKNGIAPKAIASDINEGPLEKARENIEKYGLEDRIEVRLGDGLEVLEP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1464222874  86 GEAGTVVISGLHGETIAAILRAGAGRLEPGTRLLLQPTRGAAALR 130
Cdd:pfam12847  81 GEVDTIVIAGMGGELIIDILEAGPEVLKSVKRLILQPQSDIEELR 125
RNAseHI_Thmprot NF041175
ribonuclease HI;
437-550 1.03e-32

ribonuclease HI;


Pssm-ID: 469086 [Multi-domain]  Cd Length: 144  Bit Score: 122.38  E-value: 1.03e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 437 NPGpaGI---GVVLVGPDGAVAER--IAR--FIGEATNNVAEYTALVTGLQRALERGARRLDVYSDSELMVRQLNGQYRV 509
Cdd:NF041175   14 NPG--GIatyGYVIYLDNKRKIEGygLAAepWSKDSTNNVAEYTGLICLLEKLLELGISEVIIRGDSQLVIRQLNGEYKV 91

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1464222874 510 KNEGLKPLFEQAARLAAQFELVRFIHVPRERNREADRLANQ 550
Cdd:NF041175   92 KSPRIIPLYEKALELLSKFRSIEFEWVPREENKEADRLSRI 132
RNase_H_like cd06222
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
 428-549 2.54e-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: 109.33  E-value: 2.54e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 428 LHTDGAARGNPGPAGIGVVLVGPDGAVAERIARFIGEATNNVAEYTALVTGLQRALERGARRLDVYSDSELMVRQLNGQY 507
Cdd:cd06222     1 INVDGSCRGNPGPAGIGGVLRDHEGGWLGGFALKIGAPTALEAELLALLLALELALDLGYLKVIIESDSKYVVDLINSGS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1464222874 508 RVKNEGLKpLFEQAARLAAQFELVRFIHVPRERNREADRLAN 549
Cdd:cd06222    81 FKWSPNIL-LIEDILLLLSRFWSVKISHVPREGNQVADALAK 121
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
 430-549 4.77e-24

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: 97.34  E-value: 4.77e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 430 TDGAARGNPGPAGIGVVLVGPDGAV-AERIARFIGEATNNVAEYTALVTGLQRALERGARRLDVYSDSELMVRQLNGQyR 508
Cdd:pfam13456   2 FDGAFKCDSGLAGAGVVIRDPNGNVlLAGQKKLGPGASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGR-S 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1464222874 509 VKNEGLKPLFEQAARLAAQFELVRFIHVPRERNREADRLAN 549
Cdd:pfam13456  81 PKQSKLANLLDEIRKLLKRFESVSFEHIPREQNRVADTLAK 121
TrmK pfam04816
tRNA (adenine(22)-N(1))-methyltransferase; tRNA_MT is a family of bacterial tRNA (adenine(22) ...
 23-130 1.30e-20

tRNA (adenine(22)-N(1))-methyltransferase; tRNA_MT is a family of bacterial tRNA (adenine(22)-N(1))-methyltransferase enzymes with a Rossmann-like fold. This enzyme carries out the function of N1-adenosine methylation at position 22 of bacterial tRNA.


Pssm-ID: 428139  Cd Length: 205  Bit Score: 90.07  E-value: 1.30e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874  23 LADIGTDHGLLPVTAVLRGRARRAIATDLRAAPLAAARRLVEDTGTQDRIELRQGPGLLPLRPGE-AGTVVISGLHGETI 101
Cdd:pfam04816   1 LADIGSDHAYLPIYLVQNNLASFAIAGEVNAGPLQSAVNNVAKSGLTERIDVRLGDGLAVIELEDvIDVIVIAGMGGTLI 80

                          90       100
                  ....*....|....*....|....*....
gi 1464222874 102 AAILRAGAGRLEPGTRLLLQPTRGAAALR 130
Cdd:pfam04816  81 REILEEGKDKLAGVKRLILQPNINPEDLR 109
rnhA PRK13907
ribonuclease H; Provisional
 428-554 4.53e-18

ribonuclease H; Provisional


Pssm-ID: 139967 [Multi-domain]  Cd Length: 128  Bit Score: 80.48  E-value: 4.53e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 428 LHTDGAARGNPGPAGIGVVLVGPDGAVAERIArfIGEATNNVAEYTALVTGLQRALERGARRLDVYSDSELMVRQLNGQY 507
Cdd:PRK13907    4 VYIDGASKGNPGPSGAGVFIKGVQPAVQLSLP--LGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEY 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1464222874 508 rVKNEGLKPLFEQAARLAAQFELVRFIHVPRERNREADRLANQGIDQ 554
Cdd:PRK13907   82 -AKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAILQ 127
RNase_HI_eukaryote_like cd09280
Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic ...
 427-553 9.57e-17

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: 77.22  E-value: 9.57e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 427 RLHTDGAARGNPGP---AGIGVVlVGPDGA--VAERIARfiGEATNNVAEYTALVTGLQRALERGARRLDVYSDSELMVR 501
Cdd:cd09280     1 VVYTDGSCLNNGKPgarAGIGVY-FGPGDPrnVSEPLPG--RKQTNNRAELLAVIHALEQAPEEGIRKLEIRTDSKYAIN 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1464222874 502 QLNGQYR--------------VKNeglKPLFEQAARLAAQFEL-VRFIHVP----RERNREADRLANQGID 553
Cdd:cd09280    78 CITKWIPkwkkngwktskgkpVKN---QDLIKELDKLLRKRGIkVKFEHVKghsgDPGNEEADRLAREGAD 145
RNase_HI_prokaryote_like cd09278
RNase HI family found mainly in prokaryotes; Ribonuclease H (RNase H) is classified into two ...
 428-553 2.18e-16

RNase HI family found mainly in prokaryotes; 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. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability.


Pssm-ID: 260010 [Multi-domain]  Cd Length: 139  Bit Score: 75.98  E-value: 2.18e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 428 LHTDGAARGNPGPAGIGVVLVgpDGAVAERIARFIGEATNNVAEYTALVTGLqRALERGaRRLDVYSDSELMVR------ 501
Cdd:cd09278     4 IYTDGACLGNPGPGGWAAVIR--YGDHEKELSGGEPGTTNNRMELTAAIEAL-EALKEP-CPVTIYTDSQYVINgitkwi 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1464222874 502 ---QLNGqYR------VKNeglKPLFEQAARLAAQFElVRFIHVP----RERNREADRLANQGID 553
Cdd:cd09278    80 kgwKKNG-WKtadgkpVKN---RDLWQELDALLAGHK-VTWEWVKghagHPGNERADRLANKAAD 139
RNase_H pfam00075
RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral ...
 428-552 8.90e-15

RNase H; RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.


Pssm-ID: 395028 [Multi-domain]  Cd Length: 141  Bit Score: 71.64  E-value: 8.90e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 428 LHTDGAARGNPGPAGIGVVLVGPDgavAERIARFIGEATNNVAEYTALVTGLQrALERGaRRLDVYSDSELMVRQLN--- 504
Cdd:pfam00075   6 VYTDGSCLGNPGPGGAGAVLYRGH---ENISAPLPGRTTNNRAELQAVIEALK-ALKSP-SKVNIYTDSQYVIGGITqwv 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1464222874 505 -----GQYRVKNEGlKPLF----EQAARLAAQFELVRFIHVP----RERNREADRLANQGI 552
Cdd:pfam00075  81 hgwkkNGWPTTSEG-KPVKnkdlWQLLKALCKKHQVYWQWVKghagNPGNEMADRLAKQGA 140
RNase_H_Dikarya_like cd13934
Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many ...
 428-553 1.22e-12

Fungal (dikarya) Ribonuclease H, uncharacterized; This family contains dikarya RNase H, many of which are uncharacterized. 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.


Pssm-ID: 260014 [Multi-domain]  Cd Length: 153  Bit Score: 65.68  E-value: 1.22e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 428 LHTDGAARGNPGP---AGIGVVlVGPD--GAVAERIARFIGEA-TNNVAEYTALVTGLQRA------LERGARRLDVYSD 495
Cdd:cd13934     2 VYIDGACRNNGRPdarAGYGVY-FGPDssYNVSGRLEDTGGHPqTSQRAELRAAIAALRFRswiidpDGEGLKTVVIATD 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1464222874 496 SELMVR---------QLNG-----QYRVKN-EGLKPLFEQAARLAAQFELVRFIHVPRERNREADRLANQGID 553
Cdd:cd13934    81 SEYVVKgatewipkwKRNGwrtskGKPVKNrDLFELLLDEIEDLEEGGVEVQFWHVPRELNKEADRLAKAAAE 153
rnhA PRK00203
ribonuclease H; Reviewed
 428-561 3.77e-10

ribonuclease H; Reviewed


Pssm-ID: 178927 [Multi-domain]  Cd Length: 150  Bit Score: 58.30  E-value: 3.77e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 428 LHTDGAARGNPGPAGIGVVLVGPDgavAERIArFIGEA--TNNVAEYTALVTGLqRALERgARRLDVYSDSELMVRQLNG 505
Cdd:PRK00203    6 IYTDGACLGNPGPGGWGAILRYKG---HEKEL-SGGEAltTNNRMELMAAIEAL-EALKE-PCEVTLYTDSQYVRQGITE 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1464222874 506 -----QYR---------VKNEGL-KPLFEQAARLAAQFELVRFiHVPRERNREADRLANQGIDQGTGGAQG 561
Cdd:PRK00203   80 wihgwKKNgwktadkkpVKNVDLwQRLDAALKRHQIKWHWVKG-HAGHPENERCDELARAGAEEATLEDTG 149
PRK07708 PRK07708
hypothetical protein; Validated
 431-553 7.66e-10

hypothetical protein; Validated


Pssm-ID: 181088 [Multi-domain]  Cd Length: 219  Bit Score: 59.28  E-value: 7.66e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 431 DGAARGNPGPAGIGVVLVGPDGAVAERI---ARFIGEATNNVAEYTALVTGLQRALERGARRLDV--YSDSELMVRQLNG 505
Cdd:PRK07708   79 DGGFDKETKLAGLGIVIYYKQGNKRYRIrrnAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVtfRGDSQVVLNQLAG 158

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1464222874 506 QYRVKNEGLKPLFEQAARLAAQFELV-RFIHVPRERNREADRLANQGID 553
Cdd:PRK07708  159 EWPCYDEHLNHWLDRIEQKLKQLKLTpVYEPISRKQNKEADQLATQALE 207
RNase_H_bacteria_like cd13935
RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence ...
 431-531 7.30e-05

RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner; This family includes bacterial ribonuclease H (RNase H) enzymes. RNases 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. 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. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.


Pssm-ID: 260015  Cd Length: 133  Bit Score: 42.89  E-value: 7.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 431 DGAARGNPGPagigVVLVGPDGAVAERIARF--IGEATNNVAEYTALVTGLQRALERGARRlDVYSDSelmvrqLNGQYR 508
Cdd:cd13935     8 DAACSGNPGI----VEYRGVDTKTGEVLFHRgpFPGGTNNMGEFLAIVHALRYLKEKNSRK-PIYSDS------QTAIAW 76

                          90       100
                  ....*....|....*....|...
gi 1464222874 509 VKNEGLKPLFEQAARLAAQFELV 531
Cdd:cd13935    77 VKKKKAKSTLVRNEKNAEIFKLV 99
Rnase_HI_RT_non_LTR cd09276
non-LTR RNase HI domain of reverse transcriptases; Ribonuclease H (RNase H) is classified into ...
 430-551 1.03e-03

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: 39.51  E-value: 1.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1464222874 430 TDGAarGNPGPAGIGVVlvGPDGAVAERIARFIG-EATNNVAEYTALVTGLQRALE--RGARRLDVYSDSELMVRQLNGQ 506
Cdd:cd09276     4 TDGS--KLEGSVGAGFV--IYRGGEVISRSYRLGtHASVFDAELEAILEALELALAtaRRARKVTIFTDSQSALQALRNP 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1464222874 507 YRVKNEGLKPLFEQAARLAAQFEL-VRFIHVPRER----NREADRLANQG 551
Cdd:cd09276    80 RRSSGQVILIRILRLLRLLKAKGVkVRLRWVPGHVgiegNEAADRLAKEA 129
Sortase_D_1 cd05828
Sortase domain found in subfamily 1 of the class D family of sortases; Class D sortases are ...
 67-125 1.23e-03

Sortase domain found in subfamily 1 of the class D family of sortases; Class D sortases are cysteine transpeptidases distributed in Gram-positive bacteria (mainly present in Firmicutes). The prototypical subfamily 1 of class D sortase from Bacillus anthracis (named Ba-SrtC) covalently attaches proteins bearing a noncanonical LPNTA sorting signal, such as the BasH and BasI proteins, to the peptidoglycan of the cell wall that facilitate sporulation. BasH is exclusively anchored to the forespore cell wall envelope, while BasI is attached to the diaminopimelic acid moiety of the peptidoglycan of predivisional cells. Ba-SrtC lacks the N-terminal signal peptide and membrane anchor. The family also includes many class D sortase homologs from Gram-negative bacteria, but the functions of these enzymes are unknown.


Pssm-ID: 320677  Cd Length: 127  Bit Score: 39.02  E-value: 1.23e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1464222874  67 GTQDRIeLRQGPGLLPL--RPGEAGTVVISGlHGETIAAILragaGRLEPGTRLLLQPTRG 125
Cdd:cd05828    21 GTSGEA-LAFGPGHLPGsaLPGEGGNVVIAG-HRDTHFRFL----KDLKVGDEITLETSGG 75
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH