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Conserved domains on  [gi|690375824|gb|AIR72170|]
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phenylalanyl-tRNA synthase, partial [Lacticaseibacillus rhamnosus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PheS super family cl33741
Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]; ...
 1-117 2.82e-86

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


The actual alignment was detected with superfamily member COG0016:

Pssm-ID: 439787 [Multi-domain]  Cd Length: 339  Bit Score: 253.82  E-value: 2.82e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690375824   1 MQARTMEKHdftKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTLLAMCQHVFGADRTIRLRPSYF 80
Cdd:COG0016  173 VQIRTMEKQ---KPPIRIIAPGRVYRRDESDATHSPMFHQVEGLVVDKGISFADLKGTLEEFAKAFFGEDVKVRFRPSYF 249

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 690375824  81 PFTEPSVEVDVSCFRCGGKGCPVCKYTGWIEVLGAGM 117
Cdd:COG0016  250 PFTEPSAEVDISCFICGGKGCRVCKGTGWLEILGCGM 286
 
Name Accession Description Interval E-value
PheS COG0016
Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]; ...
 1-117 2.82e-86

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


Pssm-ID: 439787 [Multi-domain]  Cd Length: 339  Bit Score: 253.82  E-value: 2.82e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690375824   1 MQARTMEKHdftKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTLLAMCQHVFGADRTIRLRPSYF 80
Cdd:COG0016  173 VQIRTMEKQ---KPPIRIIAPGRVYRRDESDATHSPMFHQVEGLVVDKGISFADLKGTLEEFAKAFFGEDVKVRFRPSYF 249

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 690375824  81 PFTEPSVEVDVSCFRCGGKGCPVCKYTGWIEVLGAGM 117
Cdd:COG0016  250 PFTEPSAEVDISCFICGGKGCRVCKGTGWLEILGCGM 286
PheRS_alpha_core cd00496
Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class ...
 1-117 4.54e-55

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: 170.80  E-value: 4.54e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690375824   1 MQARTMEKHdftKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTLLAMCQHVFGADRTIRLRPSYF 80
Cdd:cd00496   69 VQARALAKL---KPPIRIFSIGRVYRNDEIDATHLPEFHQIEGLVVDKGLTFADLKGTLEEFAKELFGPITKVRFRPSYF 145

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 690375824  81 PFTEPSVEVDVSCFRCggkgcpvckyTGWIEVLGAGM 117
Cdd:cd00496  146 PFTEPSFEVDVYCPGC----------LGWLEILGCGM 172
tRNA-synt_2d pfam01409
tRNA synthetases class II core domain (F); Other tRNA synthetase sub-families are too ...
 1-117 8.44e-55

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: 170.84  E-value: 8.44e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690375824    1 MQARTMEKHdfTKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTLLAMCQHVFGADRTIRLRPSYF 80
Cdd:pfam01409  90 VQARTLAKK--PKPPIKIFSIGRVFRRDQVDATHLPEFHQVEGLVVDENVTFADLKGVLEEFLRKFFGFEVKVRFRPSYF 167

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 690375824   81 PFTEPSVEVDVScfrcggkgcpVCKYTGWIEVLGAGM 117
Cdd:pfam01409 168 PFTEPSAEVDVY----------VCKLGGWLEVGGAGM 194
pheS TIGR00468
phenylalanyl-tRNA synthetase, alpha subunit; Most phenylalanyl-tRNA synthetases are ...
 2-117 2.21e-49

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: 158.63  E-value: 2.21e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690375824    2 QARTMEKHDftKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTLLAMCQHVFGAdRTIRLRPSYFP 81
Cdd:TIGR00468 139 QLRTMEEQE--KPPIRIFSPGRVFRNDTVDATHLPEFHQVEGLVIDKNISFTNLKGFLEEFLKKMFGE-TEIRFRPSYFP 215

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 690375824   82 FTEPSVEVDVSCFRcgGKgcpvckytGWIEVLGAGM 117
Cdd:TIGR00468 216 FTEPSAEIDVYCPE--GK--------GWLEVLGAGM 241
pheS PRK04172
phenylalanine--tRNA ligase subunit alpha;
13-117 4.11e-27

phenylalanine--tRNA ligase subunit alpha;


Pssm-ID: 235239 [Multi-domain]  Cd Length: 489  Bit Score: 103.37  E-value: 4.11e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690375824  13 KGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTlLAMCQHVFGADRtIRLRPSYFPFTEPSVEVDVs 92
Cdd:PRK04172 348 EPPQKYFSIGRVFRPDTIDATHLPEFYQLEGIVMGEDVSFRDLLGI-LKEFYKRLGFEE-VKFRPAYFPFTEPSVEVEV- 424

                         90       100
                 ....*....|....*....|....*
gi 690375824  93 cfRCGGKgcpvckytGWIEVLGAGM 117
Cdd:PRK04172 425 --YHEGL--------GWVELGGAGI 439
 
Name Accession Description Interval E-value
PheS COG0016
Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]; ...
 1-117 2.82e-86

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


Pssm-ID: 439787 [Multi-domain]  Cd Length: 339  Bit Score: 253.82  E-value: 2.82e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690375824   1 MQARTMEKHdftKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTLLAMCQHVFGADRTIRLRPSYF 80
Cdd:COG0016  173 VQIRTMEKQ---KPPIRIIAPGRVYRRDESDATHSPMFHQVEGLVVDKGISFADLKGTLEEFAKAFFGEDVKVRFRPSYF 249

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 690375824  81 PFTEPSVEVDVSCFRCGGKGCPVCKYTGWIEVLGAGM 117
Cdd:COG0016  250 PFTEPSAEVDISCFICGGKGCRVCKGTGWLEILGCGM 286
PheRS_alpha_core cd00496
Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class ...
 1-117 4.54e-55

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: 170.80  E-value: 4.54e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690375824   1 MQARTMEKHdftKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTLLAMCQHVFGADRTIRLRPSYF 80
Cdd:cd00496   69 VQARALAKL---KPPIRIFSIGRVYRNDEIDATHLPEFHQIEGLVVDKGLTFADLKGTLEEFAKELFGPITKVRFRPSYF 145

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 690375824  81 PFTEPSVEVDVSCFRCggkgcpvckyTGWIEVLGAGM 117
Cdd:cd00496  146 PFTEPSFEVDVYCPGC----------LGWLEILGCGM 172
tRNA-synt_2d pfam01409
tRNA synthetases class II core domain (F); Other tRNA synthetase sub-families are too ...
 1-117 8.44e-55

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: 170.84  E-value: 8.44e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690375824    1 MQARTMEKHdfTKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTLLAMCQHVFGADRTIRLRPSYF 80
Cdd:pfam01409  90 VQARTLAKK--PKPPIKIFSIGRVFRRDQVDATHLPEFHQVEGLVVDENVTFADLKGVLEEFLRKFFGFEVKVRFRPSYF 167

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 690375824   81 PFTEPSVEVDVScfrcggkgcpVCKYTGWIEVLGAGM 117
Cdd:pfam01409 168 PFTEPSAEVDVY----------VCKLGGWLEVGGAGM 194
pheS TIGR00468
phenylalanyl-tRNA synthetase, alpha subunit; Most phenylalanyl-tRNA synthetases are ...
 2-117 2.21e-49

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: 158.63  E-value: 2.21e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690375824    2 QARTMEKHDftKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTLLAMCQHVFGAdRTIRLRPSYFP 81
Cdd:TIGR00468 139 QLRTMEEQE--KPPIRIFSPGRVFRNDTVDATHLPEFHQVEGLVIDKNISFTNLKGFLEEFLKKMFGE-TEIRFRPSYFP 215

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 690375824   82 FTEPSVEVDVSCFRcgGKgcpvckytGWIEVLGAGM 117
Cdd:TIGR00468 216 FTEPSAEIDVYCPE--GK--------GWLEVLGAGM 241
pheS PRK04172
phenylalanine--tRNA ligase subunit alpha;
13-117 4.11e-27

phenylalanine--tRNA ligase subunit alpha;


Pssm-ID: 235239 [Multi-domain]  Cd Length: 489  Bit Score: 103.37  E-value: 4.11e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690375824  13 KGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTlLAMCQHVFGADRtIRLRPSYFPFTEPSVEVDVs 92
Cdd:PRK04172 348 EPPQKYFSIGRVFRPDTIDATHLPEFYQLEGIVMGEDVSFRDLLGI-LKEFYKRLGFEE-VKFRPAYFPFTEPSVEVEV- 424

                         90       100
                 ....*....|....*....|....*
gi 690375824  93 cfRCGGKgcpvckytGWIEVLGAGM 117
Cdd:PRK04172 425 --YHEGL--------GWVELGGAGI 439
PLN02788 PLN02788
phenylalanine-tRNA synthetase
 22-116 4.57e-16

phenylalanine-tRNA synthetase


Pssm-ID: 215422 [Multi-domain]  Cd Length: 402  Bit Score: 72.49  E-value: 4.57e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690375824  22 GVVYRRDDDDATHSHQFHQMEGLVI-------DKHITM-----ADLKGTLLAMCQHVFGaDRTIRLRPSYFPFTEPSVEV 89
Cdd:PLN02788 154 GDVYRRDSIDATHYPVFHQMEGVRVfspeeweASGLDGtdlaaEDLKKTLEGLARHLFG-DVEMRWVDAYFPFTNPSFEL 232

                         90       100
                 ....*....|....*....|....*...
gi 690375824  90 DVscfrcggkgcpvcKYTG-WIEVLGAG 116
Cdd:PLN02788 233 EI-------------FFKGeWLEVLGCG 247
PTZ00326 PTZ00326
phenylalanyl-tRNA synthetase alpha chain; Provisional
 24-89 1.35e-14

phenylalanyl-tRNA synthetase alpha chain; Provisional


Pssm-ID: 240361 [Multi-domain]  Cd Length: 494  Bit Score: 68.07  E-value: 1.35e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 690375824  24 VYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTLLAMCQHVfGADRtIRLRPSYFPFTEPSVEV 89
Cdd:PTZ00326 366 VFRNETLDATHLAEFHQVEGFVIDRNLTLGDLIGTIREFFRRI-GITK-LRFKPAFNPYTEPSMEI 429
PLN02853 PLN02853
Probable phenylalanyl-tRNA synthetase alpha chain
 15-89 3.12e-14

Probable phenylalanyl-tRNA synthetase alpha chain


Pssm-ID: 215458 [Multi-domain]  Cd Length: 492  Bit Score: 67.01  E-value: 3.12e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690375824  15 PLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTL------LAMCQhvfgadrtIRLRPSYFPFTEPSVE 88
Cdd:PLN02853 342 PKRYFSIDRVFRNEAVDRTHLAEFHQVEGLVCDRGLTLGDLIGVLedffsrLGMTK--------LRFKPAYNPYTEPSME 413


                 .
gi 690375824  89 V 89
Cdd:PLN02853 414 I 414
class_II_aaRS-like_core cd00768
Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA ...
 1-89 5.75e-06

Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of 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. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial ATP phosphoribosyltransferase regulatory subunit HisZ.


Pssm-ID: 238391 [Multi-domain]  Cd Length: 211  Bit Score: 43.26  E-value: 5.75e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 690375824   1 MQARTMEKHDFtKGPLKMISPGVVYRRDDD--DATHSHQFHQMEGLV----IDKHITMADLKGTLLAMCQHVFGADRTIR 74
Cdd:cd00768   62 GLVRLFVSHIR-KLPLRLAEIGPAFRNEGGrrGLRRVREFTQLEGEVfgedGEEASEFEELIELTEELLRALGIKLDIVF 140

                         90
                 ....*....|....*
gi 690375824  75 LRPSYFPFTEPSVEV 89
Cdd:cd00768  141 VEKTPGEFSPGGAGP 155
pheS_mito TIGR00469
phenylalanyl-tRNA synthetase, mitochondrial; Unlike all other known phenylalanyl-tRNA ...
 22-55 2.18e-04

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: 39.29  E-value: 2.18e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 690375824   22 GVVYRRDDDDATHSHQFHQMEGLVIDKhITMADL 55
Cdd:TIGR00469 140 ADVYRRDEIDKTHYPVFHQADGAAIRK-RTKADL 172
 
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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