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Conserved domains on  [gi|898325230|ref|WP_049585246|]
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MULTISPECIES: Trm112 family protein [Photorhabdus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Trm112p super family cl01066
Trm112p-like protein; The function of this family is uncertain. The bacterial members are ...
 1-59 1.05e-27

Trm112p-like protein; The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. Trm112p is required for tRNA methylation in S. cerevisiae and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices.


The actual alignment was detected with superfamily member PRK11827:

Pssm-ID: 470054  Cd Length: 60  Bit Score: 93.90  E-value: 1.05e-27
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 898325230  1 MDHRLLEIIACPVCNGKLSYDKENFELICKLDRLAFPVRDGIPVLLDHEARELPLDEEK 59
Cdd:PRK11827  1 MDHRLLEIIACPVCNGKLWYNQEKQELICKLDNLAFPLRDGIPVLLETEARVLTADESK 59
 
Name Accession Description Interval E-value
PRK11827 PRK11827
protein YcaR;
1-59 1.05e-27

protein YcaR;


Pssm-ID: 183328  Cd Length: 60  Bit Score: 93.90  E-value: 1.05e-27
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 898325230  1 MDHRLLEIIACPVCNGKLSYDKENFELICKLDRLAFPVRDGIPVLLDHEARELPLDEEK 59
Cdd:PRK11827  1 MDHRLLEIIACPVCNGKLWYNQEKQELICKLDNLAFPLRDGIPVLLETEARVLTADESK 59
Trm112 COG2835
RNA methyltransferase activator Trm112/YbaR [Translation, ribosomal structure and biogenesis];
1-59 1.09e-25

RNA methyltransferase activator Trm112/YbaR [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442083 [Multi-domain]  Cd Length: 60  Bit Score: 88.40  E-value: 1.09e-25
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 898325230  1 MDHRLLEIIACPVCNGKLSYDKENFELICKLDRLAFPVRDGIPVLLDHEARELPLDEEK 59
Cdd:COG2835   1 MDPRLLEILACPVCKGPLELDKEEGELVCTACGLAYPIRDGIPVLLPDEARPLSEDEEF 59
Trm112p pfam03966
Trm112p-like protein; The function of this family is uncertain. The bacterial members are ...
 2-41 3.49e-10

Trm112p-like protein; The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. Trm112p is required for tRNA methylation in S. cerevisiae and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices.


Pssm-ID: 397869  Cd Length: 44  Bit Score: 49.09  E-value: 3.49e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 898325230   2 DHRLLEIIACPVCNGKLS----YDKENFELICKLDRLAFPVRDG 41
Cdd:pfam03966  1 DLLLLEILACPLCKGPLHllleYDIEEGELVCPECGLAYPIRDG 44
 
Name Accession Description Interval E-value
PRK11827 PRK11827
protein YcaR;
1-59 1.05e-27

protein YcaR;


Pssm-ID: 183328  Cd Length: 60  Bit Score: 93.90  E-value: 1.05e-27
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 898325230  1 MDHRLLEIIACPVCNGKLSYDKENFELICKLDRLAFPVRDGIPVLLDHEARELPLDEEK 59
Cdd:PRK11827  1 MDHRLLEIIACPVCNGKLWYNQEKQELICKLDNLAFPLRDGIPVLLETEARVLTADESK 59
Trm112 COG2835
RNA methyltransferase activator Trm112/YbaR [Translation, ribosomal structure and biogenesis];
1-59 1.09e-25

RNA methyltransferase activator Trm112/YbaR [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442083 [Multi-domain]  Cd Length: 60  Bit Score: 88.40  E-value: 1.09e-25
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 898325230  1 MDHRLLEIIACPVCNGKLSYDKENFELICKLDRLAFPVRDGIPVLLDHEARELPLDEEK 59
Cdd:COG2835   1 MDPRLLEILACPVCKGPLELDKEEGELVCTACGLAYPIRDGIPVLLPDEARPLSEDEEF 59
Trm112p pfam03966
Trm112p-like protein; The function of this family is uncertain. The bacterial members are ...
 2-41 3.49e-10

Trm112p-like protein; The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. Trm112p is required for tRNA methylation in S. cerevisiae and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices.


Pssm-ID: 397869  Cd Length: 44  Bit Score: 49.09  E-value: 3.49e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 898325230   2 DHRLLEIIACPVCNGKLS----YDKENFELICKLDRLAFPVRDG 41
Cdd:pfam03966  1 DLLLLEILACPLCKGPLHllleYDIEEGELVCPECGLAYPIRDG 44
 
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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