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Conserved domains on  [gi|1063729140|ref|NP_001318459|]
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methionine-tRNA ligase [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN02610 super family cl33529
probable methionyl-tRNA synthetase
 54-108 1.12e-15

probable methionyl-tRNA synthetase


The actual alignment was detected with superfamily member PLN02610:

Pssm-ID: 215329 [Multi-domain]  Cd Length: 801  Bit Score: 72.12  E-value: 1.12e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063729140  54 VSDTLFPWNDLQAKLNGEFLNNLGNSVNRALSFIAKHM----------IMQAEKHPKANAL------YVEE 108
Cdd:PLN02610  383 VSDTLFTWADLQAKLNSELLNNLGNFINRVLSFIAKPPgagygsvipdAPGAESHPLTKKLaekvgkLVEQ 453
tRNA_bindingDomain super family cl00320
The tRNA binding domain is also known as the Myf domain in literature. This domain is found in ...
 92-126 2.06e-07

The tRNA binding domain is also known as the Myf domain in literature. This domain is found in a diverse collection of tRNA binding proteins, including prokaryotic phenylalanyl tRNA synthetases (PheRS), methionyl-tRNA synthetases (MetRS), human tyrosyl-tRNA synthetase(hTyrRS), Saccharomyces cerevisiae Arc1p, Thermus thermophilus CsaA, Aquifex aeolicus Trbp111, human p43 and human EMAP-II. PheRS, MetRS and hTyrRS aminoacylate their cognate tRNAs. Arc1p is a transactivator of yeast methionyl-tRNA and glutamyl-tRNA synthetases. The molecular chaperones Trbp111 and CsaA also contain this domain. CsaA has export related activities; Trbp111 is structure-specific recognizing the L-shape of the tRNA fold. This domain has general tRNA binding properties. In a subset of this family this domain has the added capability of a cytokine. For example the p43 component of the Human aminoacyl-tRNA synthetase complex is cleaved to release EMAP-II cytokine. EMAP-II has multiple activities during apoptosis, angiogenesis and inflammation and participates in malignant transformation. An EMAP-II-like cytokine is released from hTyrRS upon cleavage. The active cytokine heptapeptide locates to this domain. For homodimeric members of this group which include CsaA, Trbp111 and Escherichia coli MetRS this domain acts as a dimerization domain.


The actual alignment was detected with superfamily member cd02799:

Pssm-ID: 444833 [Multi-domain]  Cd Length: 105  Bit Score: 46.07  E-value: 2.06e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063729140  92 IMQAEKHPKANALYVEEIDIGGGEinyrlrkCRTV 126
Cdd:cd02799    13 ILKVRKHPDADSLYVEEIDLGEEE-------PRTI 40
 
Name Accession Description Interval E-value
PLN02610 PLN02610
probable methionyl-tRNA synthetase
 54-108 1.12e-15

probable methionyl-tRNA synthetase


Pssm-ID: 215329 [Multi-domain]  Cd Length: 801  Bit Score: 72.12  E-value: 1.12e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063729140  54 VSDTLFPWNDLQAKLNGEFLNNLGNSVNRALSFIAKHM----------IMQAEKHPKANAL------YVEE 108
Cdd:PLN02610  383 VSDTLFTWADLQAKLNSELLNNLGNFINRVLSFIAKPPgagygsvipdAPGAESHPLTKKLaekvgkLVEQ 453
tRNA_bind_EMAP-II_like cd02799
tRNA-binding-domain-containing EMAP2-like proteins. This family contains a diverse fraction of ...
 92-126 2.06e-07

tRNA-binding-domain-containing EMAP2-like proteins. This family contains a diverse fraction of tRNA binding proteins, including Caenorhabditis elegans methionyl-tRNA synthetase (CeMetRS), human tyrosyl- tRNA synthetase (hTyrRS), Saccharomyces cerevisiae Arc1p, human p43 and EMAP2. CeMetRS and hTyrRS aminoacylate their cognate tRNAs. Arc1p is a transactivator of yeast methionyl-tRNA and glutamyl-tRNA synthetases. This domain has general tRNA binding properties. In a subset of this family this domain has the added capability of a cytokine. For example the p43 component of the Human aminoacyl-tRNA synthetase complex is cleaved to release EMAP-II cytokine. EMAP-II has multiple activities during apoptosis, angiogenesis and inflammation and participates in malignant transformation. A EMAP-II-like cytokine also is released from hTyrRS upon cleavage. The active cytokine heptapeptide locates to this domain.


Pssm-ID: 239198 [Multi-domain]  Cd Length: 105  Bit Score: 46.07  E-value: 2.06e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063729140  92 IMQAEKHPKANALYVEEIDIGGGEinyrlrkCRTV 126
Cdd:cd02799    13 ILKVRKHPDADSLYVEEIDLGEEE-------PRTI 40
PLN02610 PLN02610
probable methionyl-tRNA synthetase
 91-126 2.75e-07

probable methionyl-tRNA synthetase


Pssm-ID: 215329 [Multi-domain]  Cd Length: 801  Bit Score: 47.85  E-value: 2.75e-07
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1063729140  91 MIMQAEKHPKANALYVEEIDIGGGeinyrlrKCRTV 126
Cdd:PLN02610  649 LIVKAEKHPDADSLYVEEIDVGEG-------APRTV 677
MetG COG0143
Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Methionyl-tRNA ...
 54-90 3.52e-07

Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Methionyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases


Pssm-ID: 439913 [Multi-domain]  Cd Length: 544  Bit Score: 47.42  E-value: 3.52e-07
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1063729140  54 VSDTLFPWNDLQAKLNGEFLNNLGNSVNRALSFIAKH 90
Cdd:COG0143   361 GQDGDFSWEDFVARVNSDLANDLGNLASRTLSMIHKY 397
tRNA_bind pfam01588
Putative tRNA binding domain; This domain is found in prokaryotic methionyl-tRNA synthetases, ...
 92-116 2.40e-05

Putative tRNA binding domain; This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1), human tyrosyl-tRNA synthetase, and endothelial-monocyte activating polypeptide II. G4p1 binds specifically to tRNA form a complex with methionyl-tRNA synthetases. In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme. This domain may perform a common function in tRNA aminoacylation.


Pssm-ID: 396251 [Multi-domain]  Cd Length: 96  Bit Score: 40.30  E-value: 2.40e-05
                          10        20
                  ....*....|....*....|....*
gi 1063729140  92 IMQAEKHPKANALYVEEIDIGGGEI 116
Cdd:pfam01588   6 VVEAERHPNADKLLVCKVDVGEEEP 30
tRNA_bindingDomain cd02153
The tRNA binding domain is also known as the Myf domain in literature. This domain is found in ...
 92-116 3.94e-05

The tRNA binding domain is also known as the Myf domain in literature. This domain is found in a diverse collection of tRNA binding proteins, including prokaryotic phenylalanyl tRNA synthetases (PheRS), methionyl-tRNA synthetases (MetRS), human tyrosyl-tRNA synthetase(hTyrRS), Saccharomyces cerevisiae Arc1p, Thermus thermophilus CsaA, Aquifex aeolicus Trbp111, human p43 and human EMAP-II. PheRS, MetRS and hTyrRS aminoacylate their cognate tRNAs. Arc1p is a transactivator of yeast methionyl-tRNA and glutamyl-tRNA synthetases. The molecular chaperones Trbp111 and CsaA also contain this domain. CsaA has export related activities; Trbp111 is structure-specific recognizing the L-shape of the tRNA fold. This domain has general tRNA binding properties. In a subset of this family this domain has the added capability of a cytokine. For example the p43 component of the Human aminoacyl-tRNA synthetase complex is cleaved to release EMAP-II cytokine. EMAP-II has multiple activities during apoptosis, angiogenesis and inflammation and participates in malignant transformation. An EMAP-II-like cytokine is released from hTyrRS upon cleavage. The active cytokine heptapeptide locates to this domain. For homodimeric members of this group which include CsaA, Trbp111 and Escherichia coli MetRS this domain acts as a dimerization domain.


Pssm-ID: 239066 [Multi-domain]  Cd Length: 99  Bit Score: 39.81  E-value: 3.94e-05
                          10        20
                  ....*....|....*....|....*
gi 1063729140  92 IMQAEKHPKANALYVEEIDIGGGEI 116
Cdd:cd02153     6 IVEAEPHPNADKLYVLKVDIGEEKP 30
 
Name Accession Description Interval E-value
PLN02610 PLN02610
probable methionyl-tRNA synthetase
 54-108 1.12e-15

probable methionyl-tRNA synthetase


Pssm-ID: 215329 [Multi-domain]  Cd Length: 801  Bit Score: 72.12  E-value: 1.12e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063729140  54 VSDTLFPWNDLQAKLNGEFLNNLGNSVNRALSFIAKHM----------IMQAEKHPKANAL------YVEE 108
Cdd:PLN02610  383 VSDTLFTWADLQAKLNSELLNNLGNFINRVLSFIAKPPgagygsvipdAPGAESHPLTKKLaekvgkLVEQ 453
tRNA_bind_EMAP-II_like cd02799
tRNA-binding-domain-containing EMAP2-like proteins. This family contains a diverse fraction of ...
 92-126 2.06e-07

tRNA-binding-domain-containing EMAP2-like proteins. This family contains a diverse fraction of tRNA binding proteins, including Caenorhabditis elegans methionyl-tRNA synthetase (CeMetRS), human tyrosyl- tRNA synthetase (hTyrRS), Saccharomyces cerevisiae Arc1p, human p43 and EMAP2. CeMetRS and hTyrRS aminoacylate their cognate tRNAs. Arc1p is a transactivator of yeast methionyl-tRNA and glutamyl-tRNA synthetases. This domain has general tRNA binding properties. In a subset of this family this domain has the added capability of a cytokine. For example the p43 component of the Human aminoacyl-tRNA synthetase complex is cleaved to release EMAP-II cytokine. EMAP-II has multiple activities during apoptosis, angiogenesis and inflammation and participates in malignant transformation. A EMAP-II-like cytokine also is released from hTyrRS upon cleavage. The active cytokine heptapeptide locates to this domain.


Pssm-ID: 239198 [Multi-domain]  Cd Length: 105  Bit Score: 46.07  E-value: 2.06e-07
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063729140  92 IMQAEKHPKANALYVEEIDIGGGEinyrlrkCRTV 126
Cdd:cd02799    13 ILKVRKHPDADSLYVEEIDLGEEE-------PRTI 40
PLN02610 PLN02610
probable methionyl-tRNA synthetase
 91-126 2.75e-07

probable methionyl-tRNA synthetase


Pssm-ID: 215329 [Multi-domain]  Cd Length: 801  Bit Score: 47.85  E-value: 2.75e-07
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1063729140  91 MIMQAEKHPKANALYVEEIDIGGGeinyrlrKCRTV 126
Cdd:PLN02610  649 LIVKAEKHPDADSLYVEEIDVGEG-------APRTV 677
MetG COG0143
Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Methionyl-tRNA ...
 54-90 3.52e-07

Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Methionyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases


Pssm-ID: 439913 [Multi-domain]  Cd Length: 544  Bit Score: 47.42  E-value: 3.52e-07
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1063729140  54 VSDTLFPWNDLQAKLNGEFLNNLGNSVNRALSFIAKH 90
Cdd:COG0143   361 GQDGDFSWEDFVARVNSDLANDLGNLASRTLSMIHKY 397
metG PRK00133
methionyl-tRNA synthetase; Reviewed
 54-90 6.79e-07

methionyl-tRNA synthetase; Reviewed


Pssm-ID: 234655 [Multi-domain]  Cd Length: 673  Bit Score: 46.68  E-value: 6.79e-07
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1063729140  54 VSDTLFPWNDLQAKLNGEFLNNLGNSVNRALSFIAKH 90
Cdd:PRK00133  364 IDDLDFNWEDFQQRVNSELVGKVVNFASRTAGFINKR 400
tRNA_bind pfam01588
Putative tRNA binding domain; This domain is found in prokaryotic methionyl-tRNA synthetases, ...
 92-116 2.40e-05

Putative tRNA binding domain; This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1), human tyrosyl-tRNA synthetase, and endothelial-monocyte activating polypeptide II. G4p1 binds specifically to tRNA form a complex with methionyl-tRNA synthetases. In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme. This domain may perform a common function in tRNA aminoacylation.


Pssm-ID: 396251 [Multi-domain]  Cd Length: 96  Bit Score: 40.30  E-value: 2.40e-05
                          10        20
                  ....*....|....*....|....*
gi 1063729140  92 IMQAEKHPKANALYVEEIDIGGGEI 116
Cdd:pfam01588   6 VVEAERHPNADKLLVCKVDVGEEEP 30
tRNA_bindingDomain cd02153
The tRNA binding domain is also known as the Myf domain in literature. This domain is found in ...
 92-116 3.94e-05

The tRNA binding domain is also known as the Myf domain in literature. This domain is found in a diverse collection of tRNA binding proteins, including prokaryotic phenylalanyl tRNA synthetases (PheRS), methionyl-tRNA synthetases (MetRS), human tyrosyl-tRNA synthetase(hTyrRS), Saccharomyces cerevisiae Arc1p, Thermus thermophilus CsaA, Aquifex aeolicus Trbp111, human p43 and human EMAP-II. PheRS, MetRS and hTyrRS aminoacylate their cognate tRNAs. Arc1p is a transactivator of yeast methionyl-tRNA and glutamyl-tRNA synthetases. The molecular chaperones Trbp111 and CsaA also contain this domain. CsaA has export related activities; Trbp111 is structure-specific recognizing the L-shape of the tRNA fold. This domain has general tRNA binding properties. In a subset of this family this domain has the added capability of a cytokine. For example the p43 component of the Human aminoacyl-tRNA synthetase complex is cleaved to release EMAP-II cytokine. EMAP-II has multiple activities during apoptosis, angiogenesis and inflammation and participates in malignant transformation. An EMAP-II-like cytokine is released from hTyrRS upon cleavage. The active cytokine heptapeptide locates to this domain. For homodimeric members of this group which include CsaA, Trbp111 and Escherichia coli MetRS this domain acts as a dimerization domain.


Pssm-ID: 239066 [Multi-domain]  Cd Length: 99  Bit Score: 39.81  E-value: 3.94e-05
                          10        20
                  ....*....|....*....|....*
gi 1063729140  92 IMQAEKHPKANALYVEEIDIGGGEI 116
Cdd:cd02153     6 IVEAEPHPNADKLYVLKVDIGEEKP 30
tRNA-synt_1g pfam09334
tRNA synthetases class I (M); This family includes methionyl tRNA synthetases.
 55-83 1.53e-04

tRNA synthetases class I (M); This family includes methionyl tRNA synthetases.


Pssm-ID: 401322 [Multi-domain]  Cd Length: 387  Bit Score: 39.97  E-value: 1.53e-04
                          10        20
                  ....*....|....*....|....*....
gi 1063729140  55 SDTLFPWNDLQAKLNGEFLNNLGNSVNRA 83
Cdd:pfam09334 359 KDTDFSWEDFVERVNSELADDLGNLVNRV 387
Anticodon_Ia_Met cd07957
Anticodon-binding domain of methionyl tRNA synthetases; This domain is found in methionyl tRNA ...
 68-89 2.02e-03

Anticodon-binding domain of methionyl tRNA synthetases; This domain is found in methionyl tRNA synthetases (MetRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon (CAU). MetRS catalyzes the transfer of methionine to the 3'-end of its tRNA.


Pssm-ID: 153411 [Multi-domain]  Cd Length: 129  Bit Score: 35.93  E-value: 2.02e-03
                          10        20
                  ....*....|....*....|..
gi 1063729140  68 LNGEFLNNLGNSVNRALSFIAK 89
Cdd:cd07957     1 INSELANNLGNLVNRTLNMASK 22
 
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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