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Conserved domains on  [gi|2082373814|ref|XP_042957608|]
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phenylalanine--tRNA ligase alpha subunit, cytoplasmic-like [Carya illinoinensis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN02853 super family cl30523
Probable phenylalanyl-tRNA synthetase alpha chain
 1-92 4.32e-78

Probable phenylalanyl-tRNA synthetase alpha chain


The actual alignment was detected with superfamily member PLN02853:

Pssm-ID: 215458 [Multi-domain]  Cd Length: 492  Bit Score: 236.88  E-value: 4.32e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373814   1 MSKLRFKPAYNPYTEPSMEIFSYHEGFGKWVEVGNSGMFRPEMLLPMGLPEDVRVIAWGLSLERPAMILYGINNIRDLSG 80
Cdd:PLN02853  395 MTKLRFKPAYNPYTEPSMEIFSYHEGLKKWVEVGNSGMFRPEMLLPMGLPEDVNVIAWGLSLERPTMILYGIDNIRDLFG 474

                          90
                  ....*....|..
gi 2082373814  81 HKVDLGLIQTNP 92
Cdd:PLN02853  475 HKVDLGLIKRNP 486
 
Name Accession Description Interval E-value
PLN02853 PLN02853
Probable phenylalanyl-tRNA synthetase alpha chain
 1-92 4.32e-78

Probable phenylalanyl-tRNA synthetase alpha chain


Pssm-ID: 215458 [Multi-domain]  Cd Length: 492  Bit Score: 236.88  E-value: 4.32e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373814   1 MSKLRFKPAYNPYTEPSMEIFSYHEGFGKWVEVGNSGMFRPEMLLPMGLPEDVRVIAWGLSLERPAMILYGINNIRDLSG 80
Cdd:PLN02853  395 MTKLRFKPAYNPYTEPSMEIFSYHEGLKKWVEVGNSGMFRPEMLLPMGLPEDVNVIAWGLSLERPTMILYGIDNIRDLFG 474

                          90
                  ....*....|..
gi 2082373814  81 HKVDLGLIQTNP 92
Cdd:PLN02853  475 HKVDLGLIKRNP 486
PheRS_alpha_core cd00496
Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class ...
 3-84 1.05e-45

Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer.


Pssm-ID: 238277 [Multi-domain]  Cd Length: 218  Bit Score: 145.77  E-value: 1.05e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373814   3 KLRFKPAYNPYTEPSMEIFSYHEGFGKWVEVGNSGMFRPEMLLPMGLPEDVRVIAWGLSLERPAMILYGINNIRDLSGHK 82
Cdd:cd00496   137 KVRFRPSYFPFTEPSFEVDVYCPGCLGWLEILGCGMVRPEVLENAGIDEEYSGFAFGIGLERLAMLKYGIPDIRLFYSND 216


                  ..
gi 2082373814  83 VD 84
Cdd:cd00496   217 LR 218
tRNA-synt_2d pfam01409
tRNA synthetases class II core domain (F); Other tRNA synthetase sub-families are too ...
 3-84 1.35e-42

tRNA synthetases class II core domain (F); Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only phenylalanyl-tRNA synthetases. This is the core catalytic domain.


Pssm-ID: 396130 [Multi-domain]  Cd Length: 245  Bit Score: 138.87  E-value: 1.35e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373814   3 KLRFKPAYNPYTEPSMEIFSYHEGFGKWVEVGNSGMFRPEMLLPMGLPEDVRVIAWGLSLERPAMILYGINNIRDLSGHK 82
Cdd:pfam01409 159 KVRFRPSYFPFTEPSAEVDVYVCKLGGWLEVGGAGMVHPNVLEAVGIDEDYSGFAFGLGVERLAMLKYGIDDIRDLYEND 238


                  ..
gi 2082373814  83 VD 84
Cdd:pfam01409 239 LR 240
pheS TIGR00468
phenylalanyl-tRNA synthetase, alpha subunit; Most phenylalanyl-tRNA synthetases are ...
 3-92 1.62e-38

phenylalanyl-tRNA synthetase, alpha subunit; Most phenylalanyl-tRNA synthetases are heterodimeric, with 2 alpha (pheS) and 2 beta (pheT) subunits. This model describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this model. An interesting feature of the alignment of all sequences captured by this model is a deep split between non-spirochete bacterial examples and all other examples; supporting this split is a relative deletion of about 50 residues in the former set between two motifs well conserved throughout the alignment. [Protein synthesis, tRNA aminoacylation]


Pssm-ID: 273095 [Multi-domain]  Cd Length: 293  Bit Score: 129.74  E-value: 1.62e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373814   3 KLRFKPAYNPYTEPSMEIFSYH-EGFGkWVEVGNSGMFRPEMLLPMGLPEDVRVIAWGLSLERPAMILYGINNIRDLSGH 81
Cdd:TIGR00468 206 EIRFRPSYFPFTEPSAEIDVYCpEGKG-WLEVLGAGMFRPEVLEPMGIDPTYPGFAWGIGIERLAMLKYGITDIRDLYEN 284

                          90
                  ....*....|.
gi 2082373814  82 kvDLGLIQTNP 92
Cdd:TIGR00468 285 --DLRFLRQFK 293
 
Name Accession Description Interval E-value
PLN02853 PLN02853
Probable phenylalanyl-tRNA synthetase alpha chain
 1-92 4.32e-78

Probable phenylalanyl-tRNA synthetase alpha chain


Pssm-ID: 215458 [Multi-domain]  Cd Length: 492  Bit Score: 236.88  E-value: 4.32e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373814   1 MSKLRFKPAYNPYTEPSMEIFSYHEGFGKWVEVGNSGMFRPEMLLPMGLPEDVRVIAWGLSLERPAMILYGINNIRDLSG 80
Cdd:PLN02853  395 MTKLRFKPAYNPYTEPSMEIFSYHEGLKKWVEVGNSGMFRPEMLLPMGLPEDVNVIAWGLSLERPTMILYGIDNIRDLFG 474

                          90
                  ....*....|..
gi 2082373814  81 HKVDLGLIQTNP 92
Cdd:PLN02853  475 HKVDLGLIKRNP 486
PTZ00326 PTZ00326
phenylalanyl-tRNA synthetase alpha chain; Provisional
 1-85 7.43e-66

phenylalanyl-tRNA synthetase alpha chain; Provisional


Pssm-ID: 240361 [Multi-domain]  Cd Length: 494  Bit Score: 205.20  E-value: 7.43e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373814   1 MSKLRFKPAYNPYTEPSMEIFSYHEGFGKWVEVGNSGMFRPEMLLPMGLPEDVRVIAWGLSLERPAMILYGINNIRDLSG 80
Cdd:PTZ00326  410 ITKLRFKPAFNPYTEPSMEIFGYHPGLKKWVEVGNSGIFRPEMLRPMGFPEDVTVIAWGLSLERPTMIKYGIKNIRDLFG 489


                  ....*
gi 2082373814  81 HKVDL 85
Cdd:PTZ00326  490 HKVDL 494
PheRS_alpha_core cd00496
Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class ...
 3-84 1.05e-45

Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer.


Pssm-ID: 238277 [Multi-domain]  Cd Length: 218  Bit Score: 145.77  E-value: 1.05e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373814   3 KLRFKPAYNPYTEPSMEIFSYHEGFGKWVEVGNSGMFRPEMLLPMGLPEDVRVIAWGLSLERPAMILYGINNIRDLSGHK 82
Cdd:cd00496   137 KVRFRPSYFPFTEPSFEVDVYCPGCLGWLEILGCGMVRPEVLENAGIDEEYSGFAFGIGLERLAMLKYGIPDIRLFYSND 216


                  ..
gi 2082373814  83 VD 84
Cdd:cd00496   217 LR 218
tRNA-synt_2d pfam01409
tRNA synthetases class II core domain (F); Other tRNA synthetase sub-families are too ...
 3-84 1.35e-42

tRNA synthetases class II core domain (F); Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only phenylalanyl-tRNA synthetases. This is the core catalytic domain.


Pssm-ID: 396130 [Multi-domain]  Cd Length: 245  Bit Score: 138.87  E-value: 1.35e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373814   3 KLRFKPAYNPYTEPSMEIFSYHEGFGKWVEVGNSGMFRPEMLLPMGLPEDVRVIAWGLSLERPAMILYGINNIRDLSGHK 82
Cdd:pfam01409 159 KVRFRPSYFPFTEPSAEVDVYVCKLGGWLEVGGAGMVHPNVLEAVGIDEDYSGFAFGLGVERLAMLKYGIDDIRDLYEND 238


                  ..
gi 2082373814  83 VD 84
Cdd:pfam01409 239 LR 240
pheS PRK04172
phenylalanine--tRNA ligase subunit alpha;
1-89 6.96e-39

phenylalanine--tRNA ligase subunit alpha;


Pssm-ID: 235239 [Multi-domain]  Cd Length: 489  Bit Score: 134.57  E-value: 6.96e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373814   1 MSKLRFKPAYNPYTEPSMEIFSYHEGFGkWVEVGNSGMFRPEMLLPMGLpeDVRVIAWGLSLERPAMILYGINNIRDLsg 80
Cdd:PRK04172  403 FEEVKFRPAYFPFTEPSVEVEVYHEGLG-WVELGGAGIFRPEVLEPLGI--DVPVLAWGLGIERLAMLRLGLDDIRDL-- 477


                  ....*....
gi 2082373814  81 HKVDLGLIQ 89
Cdd:PRK04172  478 YSSDIEWLR 486
pheS TIGR00468
phenylalanyl-tRNA synthetase, alpha subunit; Most phenylalanyl-tRNA synthetases are ...
 3-92 1.62e-38

phenylalanyl-tRNA synthetase, alpha subunit; Most phenylalanyl-tRNA synthetases are heterodimeric, with 2 alpha (pheS) and 2 beta (pheT) subunits. This model describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this model. An interesting feature of the alignment of all sequences captured by this model is a deep split between non-spirochete bacterial examples and all other examples; supporting this split is a relative deletion of about 50 residues in the former set between two motifs well conserved throughout the alignment. [Protein synthesis, tRNA aminoacylation]


Pssm-ID: 273095 [Multi-domain]  Cd Length: 293  Bit Score: 129.74  E-value: 1.62e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2082373814   3 KLRFKPAYNPYTEPSMEIFSYH-EGFGkWVEVGNSGMFRPEMLLPMGLPEDVRVIAWGLSLERPAMILYGINNIRDLSGH 81
Cdd:TIGR00468 206 EIRFRPSYFPFTEPSAEIDVYCpEGKG-WLEVLGAGMFRPEVLEPMGIDPTYPGFAWGIGIERLAMLKYGITDIRDLYEN 284

                          90
                  ....*....|.
gi 2082373814  82 kvDLGLIQTNP 92
Cdd:TIGR00468 285 --DLRFLRQFK 293
PLN02788 PLN02788
phenylalanine-tRNA synthetase
 4-76 1.19e-12

phenylalanine-tRNA synthetase


Pssm-ID: 215422 [Multi-domain]  Cd Length: 402  Bit Score: 61.70  E-value: 1.19e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2082373814   4 LRFKPAYNPYTEPSMEIFSYHEGfgKWVEVGNSGMFRPEMLLPMGLPeDVRVIAWGLSLERPAMILYGINNIR 76
Cdd:PLN02788  216 MRWVDAYFPFTNPSFELEIFFKG--EWLEVLGCGVTEQEILKNNGRS-DNVAWAFGLGLERLAMVLFDIPDIR 285
pheS_mito TIGR00469
phenylalanyl-tRNA synthetase, mitochondrial; Unlike all other known phenylalanyl-tRNA ...
 3-76 1.69e-10

phenylalanyl-tRNA synthetase, mitochondrial; Unlike all other known phenylalanyl-tRNA synthetases, the mitochondrial form demonstrated from yeast is monomeric. It is similar to but longer than the alpha subunit (PheS) of the alpha 2 beta 2 form found in Bacteria, Archaea, and eukaryotes, and shares the characteristic motifs of class II aminoacyl-tRNA ligases. This model models the experimental example from Saccharomyces cerevisiae (designated MSF1) and its orthologs from other eukaryotic species. [Protein synthesis, tRNA aminoacylation]


Pssm-ID: 129561 [Multi-domain]  Cd Length: 460  Bit Score: 55.85  E-value: 1.69e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2082373814   3 KLRFKPAYNPYTEPSMEIFSYHEGfgKWVEVGNSGMFRPEMLLPMGL-PEDVRVIAWGLSLERPAMILYGINNIR 76
Cdd:TIGR00469 264 KVRWIDAYFPFTAPSWEIEIWFKD--EWLELCGCGIIRHDILLRAGVhPSETIGWAFGLGLDRIAMLLFDIPDIR 336
 
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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