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Conserved domains on  [gi|1981092546|ref|NP_001380343|]
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tRNA:m(4)X modification enzyme TRM13 homolog isoform 7 [Homo sapiens]

Protein Classification

tRNA:m(4)X modification enzyme TRM13 family protein( domain architecture ID 10569703)

tRNA:m(4)X modification enzyme TRM13 family protein similar to Oryza sativa TRM13, a tRNA methylase that catalyzes 2'-O-methyladenosine (Am) nucleoside formation on tRNA(Gly)(GCC) in vitro

CATH:  2.20.25.110
EC:  2.1.1.-
Gene Ontology:  GO:0008757|GO:1904047|GO:0030488|GO:0008270
PubMed:  12504684|12826405|17210253|12665246
SCOP:  3000118

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AdoMet_MTases super family cl17173
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 151-260 3.87e-42

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


The actual alignment was detected with superfamily member pfam05206:

Pssm-ID: 473071  Cd Length: 256  Bit Score: 144.75  E-value: 3.87e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1981092546 151 KQQASILGNIENLKLLGPRRCFVEFGAGKGKLSHWVDIALKDAEK--VHFILVEKVTTRFKVDGKHRKKNS--VFERLQI 226
Cdd:pfam05206   1 IQQSSLIGNLEELGLLNPDSAYVEFGAGRGELSRYVNQCIQEDKLgnSGYVLIDRASNRMKFDRKIRKDESepIIKRLRI 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1981092546 227 DIQHLCLNKIPVLrEEKLPVVGIGKHLCGMATGF 260
Cdd:pfam05206  81 DIKDLNLDAVLSL-EDGSPVVAVSKHLCGAATDL 113
zf-TRM13_CCCH pfam11722
CCCH zinc finger in TRM13 protein; This domain is found at the N-terminus of TRM13 ...
 17-45 7.48e-12

CCCH zinc finger in TRM13 protein; This domain is found at the N-terminus of TRM13 methyltransferase proteins. It is presumed to be a zinc binding domain.


:

Pssm-ID: 463331  Cd Length: 29  Bit Score: 58.29  E-value: 7.48e-12
                          10        20
                  ....*....|....*....|....*....
gi 1981092546  17 GRCGYYVEKKKRFCRMVVAAGKRFCGEHA 45
Cdd:pfam11722   1 LRCEFFLPRKKRFCGMTRKKGSKYCGEHL 29
zf-U11-48K pfam05253
U11-48K-like CHHC zinc finger; This zinc binding domain has four conserved zinc chelating ...
 56-80 2.14e-06

U11-48K-like CHHC zinc finger; This zinc binding domain has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function.


:

Pssm-ID: 461603  Cd Length: 25  Bit Score: 43.20  E-value: 2.14e-06
                          10        20
                  ....*....|....*....|....*
gi 1981092546  56 RILCPLDPKHTVYEDQLAKHLKKCN 80
Cdd:pfam05253   1 LVPCPYNPSHRVPESRLEKHLKKCP 25
 
Name Accession Description Interval E-value
TRM13 pfam05206
Methyltransferase TRM13; This is a family of eukaryotic proteins which are responsible for 2 ...
 151-260 3.87e-42

Methyltransferase TRM13; This is a family of eukaryotic proteins which are responsible for 2'-O-methylation of tRNA at position 4. TRM13 shows no sequence similarity to other known methyltransferases.


Pssm-ID: 398743  Cd Length: 256  Bit Score: 144.75  E-value: 3.87e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1981092546 151 KQQASILGNIENLKLLGPRRCFVEFGAGKGKLSHWVDIALKDAEK--VHFILVEKVTTRFKVDGKHRKKNS--VFERLQI 226
Cdd:pfam05206   1 IQQSSLIGNLEELGLLNPDSAYVEFGAGRGELSRYVNQCIQEDKLgnSGYVLIDRASNRMKFDRKIRKDESepIIKRLRI 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1981092546 227 DIQHLCLNKIPVLrEEKLPVVGIGKHLCGMATGF 260
Cdd:pfam05206  81 DIKDLNLDAVLSL-EDGSPVVAVSKHLCGAATDL 113
zf-TRM13_CCCH pfam11722
CCCH zinc finger in TRM13 protein; This domain is found at the N-terminus of TRM13 ...
 17-45 7.48e-12

CCCH zinc finger in TRM13 protein; This domain is found at the N-terminus of TRM13 methyltransferase proteins. It is presumed to be a zinc binding domain.


Pssm-ID: 463331  Cd Length: 29  Bit Score: 58.29  E-value: 7.48e-12
                          10        20
                  ....*....|....*....|....*....
gi 1981092546  17 GRCGYYVEKKKRFCRMVVAAGKRFCGEHA 45
Cdd:pfam11722   1 LRCEFFLPRKKRFCGMTRKKGSKYCGEHL 29
zf-U11-48K pfam05253
U11-48K-like CHHC zinc finger; This zinc binding domain has four conserved zinc chelating ...
 56-80 2.14e-06

U11-48K-like CHHC zinc finger; This zinc binding domain has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function.


Pssm-ID: 461603  Cd Length: 25  Bit Score: 43.20  E-value: 2.14e-06
                          10        20
                  ....*....|....*....|....*
gi 1981092546  56 RILCPLDPKHTVYEDQLAKHLKKCN 80
Cdd:pfam05253   1 LVPCPYNPSHRVPESRLEKHLKKCP 25
 
Name Accession Description Interval E-value
TRM13 pfam05206
Methyltransferase TRM13; This is a family of eukaryotic proteins which are responsible for 2 ...
 151-260 3.87e-42

Methyltransferase TRM13; This is a family of eukaryotic proteins which are responsible for 2'-O-methylation of tRNA at position 4. TRM13 shows no sequence similarity to other known methyltransferases.


Pssm-ID: 398743  Cd Length: 256  Bit Score: 144.75  E-value: 3.87e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1981092546 151 KQQASILGNIENLKLLGPRRCFVEFGAGKGKLSHWVDIALKDAEK--VHFILVEKVTTRFKVDGKHRKKNS--VFERLQI 226
Cdd:pfam05206   1 IQQSSLIGNLEELGLLNPDSAYVEFGAGRGELSRYVNQCIQEDKLgnSGYVLIDRASNRMKFDRKIRKDESepIIKRLRI 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1981092546 227 DIQHLCLNKIPVLrEEKLPVVGIGKHLCGMATGF 260
Cdd:pfam05206  81 DIKDLNLDAVLSL-EDGSPVVAVSKHLCGAATDL 113
zf-TRM13_CCCH pfam11722
CCCH zinc finger in TRM13 protein; This domain is found at the N-terminus of TRM13 ...
 17-45 7.48e-12

CCCH zinc finger in TRM13 protein; This domain is found at the N-terminus of TRM13 methyltransferase proteins. It is presumed to be a zinc binding domain.


Pssm-ID: 463331  Cd Length: 29  Bit Score: 58.29  E-value: 7.48e-12
                          10        20
                  ....*....|....*....|....*....
gi 1981092546  17 GRCGYYVEKKKRFCRMVVAAGKRFCGEHA 45
Cdd:pfam11722   1 LRCEFFLPRKKRFCGMTRKKGSKYCGEHL 29
zf-U11-48K pfam05253
U11-48K-like CHHC zinc finger; This zinc binding domain has four conserved zinc chelating ...
 56-80 2.14e-06

U11-48K-like CHHC zinc finger; This zinc binding domain has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function.


Pssm-ID: 461603  Cd Length: 25  Bit Score: 43.20  E-value: 2.14e-06
                          10        20
                  ....*....|....*....|....*
gi 1981092546  56 RILCPLDPKHTVYEDQLAKHLKKCN 80
Cdd:pfam05253   1 LVPCPYNPSHRVPESRLEKHLKKCP 25
 
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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