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Conserved domains on  [gi|1109646387|emb|SHM70487|]
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Uncharacterized conserved protein YbaR, Trm112 family [Salegentibacter salegens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Trm112_arch super family cl40492
methytransferase partner Trm112; This HMM describes an archaeal branch of a small protein, ...
 1-60 2.13e-15

methytransferase partner Trm112; This HMM describes an archaeal branch of a small protein, Trm112, that is conserved in the three domains of life and that serves as general activator of methyltransferases for RNA or protein.


The actual alignment was detected with superfamily member NF038101:

Pssm-ID: 411682 [Multi-domain]  Cd Length: 59  Bit Score: 63.75  E-value: 2.13e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109646387  1 MRISTIDKLCCPFDKNDLDLTAISKDlDGKIIEGFLSCAKCKRIYPIIKGIPIMNPDEYR 60
Cdd:NF038101   1 MKESLMDILCCPVCKGDLELEVDEED-DEEIIEGTLTCTACGEDYPIEDGIPNLLPPDMR 59
 
Name Accession Description Interval E-value
Trm112_arch NF038101
methytransferase partner Trm112; This HMM describes an archaeal branch of a small protein, ...
 1-60 2.13e-15

methytransferase partner Trm112; This HMM describes an archaeal branch of a small protein, Trm112, that is conserved in the three domains of life and that serves as general activator of methyltransferases for RNA or protein.


Pssm-ID: 411682 [Multi-domain]  Cd Length: 59  Bit Score: 63.75  E-value: 2.13e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109646387  1 MRISTIDKLCCPFDKNDLDLTAISKDlDGKIIEGFLSCAKCKRIYPIIKGIPIMNPDEYR 60
Cdd:NF038101   1 MKESLMDILCCPVCKGDLELEVDEED-DEEIIEGTLTCTACGEDYPIEDGIPNLLPPDMR 59
Trm112 COG2835
RNA methyltransferase activator Trm112/YbaR [Translation, ribosomal structure and biogenesis];
1-68 7.31e-15

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


Pssm-ID: 442083 [Multi-domain]  Cd Length: 60  Bit Score: 62.59  E-value: 7.31e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1109646387  1 MRISTIDKLCCPFDKNDLDLTAIskdldgkiiEGFLSCAKCKRIYPIIKGIPIMNPDEYREFKLEAPL 68
Cdd:COG2835    1 MDPRLLEILACPVCKGPLELDKE---------EGELVCTACGLAYPIRDGIPVLLPDEARPLSEDEEF 59
Trm112p pfam03966
Trm112p-like protein; The function of this family is uncertain. The bacterial members are ...
 5-50 1.25e-05

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: 38.69  E-value: 1.25e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 1109646387  5 TIDKLCCPFDKNDLDLtaiskDLDGKIIEGFLSCAKCKRIYPIIKG 50
Cdd:pfam03966  4 LLEILACPLCKGPLHL-----LLEYDIEEGELVCPECGLAYPIRDG 44
Trm112-like cd21089
eukaryotic tRNA methyltransferase 112, a partner protein of both rRNA/tRNA and protein ...
 31-54 7.17e-05

eukaryotic tRNA methyltransferase 112, a partner protein of both rRNA/tRNA and protein methyltransferases, and similar proteins; This family contains eukaryotic tRNA methyltransferase 112 (Trm112)-like proteins such as human multifunctional methyltransferase subunit Trm112 protein, which acts as an activator of both rRNA/tRNA and protein methyltransferases. Trm112 acts as an obligate activating platform for at least four methyltransferases (MTase) involved in the modification of 18S rRNA (Bud23), tRNA (Trm9 and Trm11) and translation termination factor eRF1 (Mtq2) in eukaryotes. Hence, Trm112 is at a nexus between ribosome synthesis and function. Trm112 is a partner protein of N6amt1 (N6 -adenine-specific DNA methyltransferase 1), which is suggested to be the N6-adenine DNA methyltransferase (MTase) in human cells. Trm112 binds to a hydrophobic surface of N6amt1, stabilizing its structure but not directly contributing to substrate binding and catalysis. In Yarrowia lipolytica, it forms a complex with Trm9 methyltransferase, which is involved in the 5-methoxycarbonylmethyluridine (mcm(5)U) modification of the tRNA anticodon wobble position and hence promotes translational fidelity. In Saccharomyces cerevisiae, Trm112 (also called Ynr046w or tRNA methyltransferase 112) is a zinc binding protein that is plurifunctional and a component of the eRF1 methyltransferase, putatively containing a zinc finger signature motif.


Pssm-ID: 411041  Cd Length: 117  Bit Score: 38.30  E-value: 7.17e-05
                          10        20
                  ....*....|....*....|....
gi 1109646387  31 IIEGFLSCAKCKRIYPIIKGIPIM 54
Cdd:cd21089    92 VVEGELVCPETGRKFPISNGIPNM 115
 
Name Accession Description Interval E-value
Trm112_arch NF038101
methytransferase partner Trm112; This HMM describes an archaeal branch of a small protein, ...
 1-60 2.13e-15

methytransferase partner Trm112; This HMM describes an archaeal branch of a small protein, Trm112, that is conserved in the three domains of life and that serves as general activator of methyltransferases for RNA or protein.


Pssm-ID: 411682 [Multi-domain]  Cd Length: 59  Bit Score: 63.75  E-value: 2.13e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1109646387  1 MRISTIDKLCCPFDKNDLDLTAISKDlDGKIIEGFLSCAKCKRIYPIIKGIPIMNPDEYR 60
Cdd:NF038101   1 MKESLMDILCCPVCKGDLELEVDEED-DEEIIEGTLTCTACGEDYPIEDGIPNLLPPDMR 59
Trm112 COG2835
RNA methyltransferase activator Trm112/YbaR [Translation, ribosomal structure and biogenesis];
1-68 7.31e-15

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


Pssm-ID: 442083 [Multi-domain]  Cd Length: 60  Bit Score: 62.59  E-value: 7.31e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1109646387  1 MRISTIDKLCCPFDKNDLDLTAIskdldgkiiEGFLSCAKCKRIYPIIKGIPIMNPDEYREFKLEAPL 68
Cdd:COG2835    1 MDPRLLEILACPVCKGPLELDKE---------EGELVCTACGLAYPIRDGIPVLLPDEARPLSEDEEF 59
Trm112p pfam03966
Trm112p-like protein; The function of this family is uncertain. The bacterial members are ...
 5-50 1.25e-05

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: 38.69  E-value: 1.25e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 1109646387  5 TIDKLCCPFDKNDLDLtaiskDLDGKIIEGFLSCAKCKRIYPIIKG 50
Cdd:pfam03966  4 LLEILACPLCKGPLHL-----LLEYDIEEGELVCPECGLAYPIRDG 44
Trm112-like cd21089
eukaryotic tRNA methyltransferase 112, a partner protein of both rRNA/tRNA and protein ...
 31-54 7.17e-05

eukaryotic tRNA methyltransferase 112, a partner protein of both rRNA/tRNA and protein methyltransferases, and similar proteins; This family contains eukaryotic tRNA methyltransferase 112 (Trm112)-like proteins such as human multifunctional methyltransferase subunit Trm112 protein, which acts as an activator of both rRNA/tRNA and protein methyltransferases. Trm112 acts as an obligate activating platform for at least four methyltransferases (MTase) involved in the modification of 18S rRNA (Bud23), tRNA (Trm9 and Trm11) and translation termination factor eRF1 (Mtq2) in eukaryotes. Hence, Trm112 is at a nexus between ribosome synthesis and function. Trm112 is a partner protein of N6amt1 (N6 -adenine-specific DNA methyltransferase 1), which is suggested to be the N6-adenine DNA methyltransferase (MTase) in human cells. Trm112 binds to a hydrophobic surface of N6amt1, stabilizing its structure but not directly contributing to substrate binding and catalysis. In Yarrowia lipolytica, it forms a complex with Trm9 methyltransferase, which is involved in the 5-methoxycarbonylmethyluridine (mcm(5)U) modification of the tRNA anticodon wobble position and hence promotes translational fidelity. In Saccharomyces cerevisiae, Trm112 (also called Ynr046w or tRNA methyltransferase 112) is a zinc binding protein that is plurifunctional and a component of the eRF1 methyltransferase, putatively containing a zinc finger signature motif.


Pssm-ID: 411041  Cd Length: 117  Bit Score: 38.30  E-value: 7.17e-05
                          10        20
                  ....*....|....*....|....
gi 1109646387  31 IIEGFLSCAKCKRIYPIIKGIPIM 54
Cdd:cd21089    92 VVEGELVCPETGRKFPISNGIPNM 115
 
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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