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Conserved domains on  [gi|156712354|emb|CAO00668|]
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phenylalanyl-tRNA synthase, partial [Fructilactobacillus sanfranciscensis]

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]; ...
 1-130 1.18e-90

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: 265.76  E-value: 1.18e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712354   1 DTFYITKEILMRTHTSPMQARSLEKHdfsKGPLKMISPGVVFRRDTDDPTHSHQFHQVEGIMIDKHITMADLKGTLETMT 80
Cdd:COG0016  156 DTFYIDDGLLLRTHTSPVQIRTMEKQ---KPPIRIIAPGRVYRRDESDATHSPMFHQVEGLVVDKGISFADLKGTLEEFA 232

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 156712354  81 HKLFGDKFKVRLRPSYFPFTEPSVEADITCMNCGGKGCDVCKGSGWIEVL 130
Cdd:COG0016  233 KAFFGEDVKVRFRPSYFPFTEPSAEVDISCFICGGKGCRVCKGTGWLEIL 282
 
Name Accession Description Interval E-value
PheS COG0016
Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]; ...
 1-130 1.18e-90

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: 265.76  E-value: 1.18e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712354   1 DTFYITKEILMRTHTSPMQARSLEKHdfsKGPLKMISPGVVFRRDTDDPTHSHQFHQVEGIMIDKHITMADLKGTLETMT 80
Cdd:COG0016  156 DTFYIDDGLLLRTHTSPVQIRTMEKQ---KPPIRIIAPGRVYRRDESDATHSPMFHQVEGLVVDKGISFADLKGTLEEFA 232

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 156712354  81 HKLFGDKFKVRLRPSYFPFTEPSVEADITCMNCGGKGCDVCKGSGWIEVL 130
Cdd:COG0016  233 KAFFGEDVKVRFRPSYFPFTEPSAEVDISCFICGGKGCRVCKGTGWLEIL 282
PheRS_alpha_core cd00496
Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class ...
 1-130 6.75e-59

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: 180.82  E-value: 6.75e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712354   1 DTFYITKE--ILMRTHTSPMQARSLEKHdfsKGPLKMISPGVVFRRDTDDPTHSHQFHQVEGIMIDKHITMADLKGTLET 78
Cdd:cd00496   50 DTFYINDParLLLRTHTSAVQARALAKL---KPPIRIFSIGRVYRNDEIDATHLPEFHQIEGLVVDKGLTFADLKGTLEE 126

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 156712354  79 MTHKLFGDKFKVRLRPSYFPFTEPSVEADITCMNCGgkgcdvckgsGWIEVL 130
Cdd:cd00496  127 FAKELFGPITKVRFRPSYFPFTEPSFEVDVYCPGCL----------GWLEIL 168
tRNA-synt_2d pfam01409
tRNA synthetases class II core domain (F); Other tRNA synthetase sub-families are too ...
 1-130 8.26e-59

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: 181.62  E-value: 8.26e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712354    1 DTFYI-------TKEILMRTHTSPMQARSLEKHdfSKGPLKMISPGVVFRRDTDDPTHSHQFHQVEGIMIDKHITMADLK 73
Cdd:pfam01409  66 DTFYLkkplkpvARRLLLRTHTTPVQARTLAKK--PKPPIKIFSIGRVFRRDQVDATHLPEFHQVEGLVVDENVTFADLK 143

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 156712354   74 GTLETMTHKLFGDKFKVRLRPSYFPFTEPSVEADITcmncggkgcdVCKGSGWIEVL 130
Cdd:pfam01409 144 GVLEEFLRKFFGFEVKVRFRPSYFPFTEPSAEVDVY----------VCKLGGWLEVG 190
pheS TIGR00468
phenylalanyl-tRNA synthetase, alpha subunit; Most phenylalanyl-tRNA synthetases are ...
 1-130 3.31e-55

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: 174.04  E-value: 3.31e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712354    1 DTFYITKEILMRTHTSPMQARSLEKHDfsKGPLKMISPGVVFRRDTDDPTHSHQFHQVEGIMIDKHITMADLKGTLETMT 80
Cdd:TIGR00468 121 DTFYIKDRLLLRTHTTAVQLRTMEEQE--KPPIRIFSPGRVFRNDTVDATHLPEFHQVEGLVIDKNISFTNLKGFLEEFL 198

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 156712354   81 HKLFGDKfKVRLRPSYFPFTEPSVEADITCMNcggkgcdvckGSGWIEVL 130
Cdd:TIGR00468 199 KKMFGET-EIRFRPSYFPFTEPSAEIDVYCPE----------GKGWLEVL 237
pheS PRK04172
phenylalanine--tRNA ligase subunit alpha;
5-130 2.25e-31

phenylalanine--tRNA ligase subunit alpha;


Pssm-ID: 235239 [Multi-domain]  Cd Length: 489  Bit Score: 115.70  E-value: 2.25e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712354   5 ITKEILMRTHTSPMQARSLEKHdfSKGPLKMISPGVVFRRDTDDPTHSHQFHQVEGIMIDKHITMADLKGTLETMTHKLf 84
Cdd:PRK04172 325 IAKRLVLRTHTTALSARYLASR--PEPPQKYFSIGRVFRPDTIDATHLPEFYQLEGIVMGEDVSFRDLLGILKEFYKRL- 401

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 156712354  85 GDKfKVRLRPSYFPFTEPSVEADITcmncggkgcdvCKGSGWIEVL 130
Cdd:PRK04172 402 GFE-EVKFRPAYFPFTEPSVEVEVY-----------HEGLGWVELG 435
 
Name Accession Description Interval E-value
PheS COG0016
Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]; ...
 1-130 1.18e-90

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: 265.76  E-value: 1.18e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712354   1 DTFYITKEILMRTHTSPMQARSLEKHdfsKGPLKMISPGVVFRRDTDDPTHSHQFHQVEGIMIDKHITMADLKGTLETMT 80
Cdd:COG0016  156 DTFYIDDGLLLRTHTSPVQIRTMEKQ---KPPIRIIAPGRVYRRDESDATHSPMFHQVEGLVVDKGISFADLKGTLEEFA 232

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 156712354  81 HKLFGDKFKVRLRPSYFPFTEPSVEADITCMNCGGKGCDVCKGSGWIEVL 130
Cdd:COG0016  233 KAFFGEDVKVRFRPSYFPFTEPSAEVDISCFICGGKGCRVCKGTGWLEIL 282
PheRS_alpha_core cd00496
Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class ...
 1-130 6.75e-59

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: 180.82  E-value: 6.75e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712354   1 DTFYITKE--ILMRTHTSPMQARSLEKHdfsKGPLKMISPGVVFRRDTDDPTHSHQFHQVEGIMIDKHITMADLKGTLET 78
Cdd:cd00496   50 DTFYINDParLLLRTHTSAVQARALAKL---KPPIRIFSIGRVYRNDEIDATHLPEFHQIEGLVVDKGLTFADLKGTLEE 126

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 156712354  79 MTHKLFGDKFKVRLRPSYFPFTEPSVEADITCMNCGgkgcdvckgsGWIEVL 130
Cdd:cd00496  127 FAKELFGPITKVRFRPSYFPFTEPSFEVDVYCPGCL----------GWLEIL 168
tRNA-synt_2d pfam01409
tRNA synthetases class II core domain (F); Other tRNA synthetase sub-families are too ...
 1-130 8.26e-59

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: 181.62  E-value: 8.26e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712354    1 DTFYI-------TKEILMRTHTSPMQARSLEKHdfSKGPLKMISPGVVFRRDTDDPTHSHQFHQVEGIMIDKHITMADLK 73
Cdd:pfam01409  66 DTFYLkkplkpvARRLLLRTHTTPVQARTLAKK--PKPPIKIFSIGRVFRRDQVDATHLPEFHQVEGLVVDENVTFADLK 143

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 156712354   74 GTLETMTHKLFGDKFKVRLRPSYFPFTEPSVEADITcmncggkgcdVCKGSGWIEVL 130
Cdd:pfam01409 144 GVLEEFLRKFFGFEVKVRFRPSYFPFTEPSAEVDVY----------VCKLGGWLEVG 190
pheS TIGR00468
phenylalanyl-tRNA synthetase, alpha subunit; Most phenylalanyl-tRNA synthetases are ...
 1-130 3.31e-55

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: 174.04  E-value: 3.31e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712354    1 DTFYITKEILMRTHTSPMQARSLEKHDfsKGPLKMISPGVVFRRDTDDPTHSHQFHQVEGIMIDKHITMADLKGTLETMT 80
Cdd:TIGR00468 121 DTFYIKDRLLLRTHTTAVQLRTMEEQE--KPPIRIFSPGRVFRNDTVDATHLPEFHQVEGLVIDKNISFTNLKGFLEEFL 198

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 156712354   81 HKLFGDKfKVRLRPSYFPFTEPSVEADITCMNcggkgcdvckGSGWIEVL 130
Cdd:TIGR00468 199 KKMFGET-EIRFRPSYFPFTEPSAEIDVYCPE----------GKGWLEVL 237
pheS PRK04172
phenylalanine--tRNA ligase subunit alpha;
5-130 2.25e-31

phenylalanine--tRNA ligase subunit alpha;


Pssm-ID: 235239 [Multi-domain]  Cd Length: 489  Bit Score: 115.70  E-value: 2.25e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712354   5 ITKEILMRTHTSPMQARSLEKHdfSKGPLKMISPGVVFRRDTDDPTHSHQFHQVEGIMIDKHITMADLKGTLETMTHKLf 84
Cdd:PRK04172 325 IAKRLVLRTHTTALSARYLASR--PEPPQKYFSIGRVFRPDTIDATHLPEFYQLEGIVMGEDVSFRDLLGILKEFYKRL- 401

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 156712354  85 GDKfKVRLRPSYFPFTEPSVEADITcmncggkgcdvCKGSGWIEVL 130
Cdd:PRK04172 402 GFE-EVKFRPAYFPFTEPSVEVEVY-----------HEGLGWVELG 435
PLN02788 PLN02788
phenylalanine-tRNA synthetase
 1-130 4.11e-20

phenylalanine-tRNA synthetase


Pssm-ID: 215422 [Multi-domain]  Cd Length: 402  Bit Score: 84.04  E-value: 4.11e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712354   1 DTFYITKEILMRTHTSPMQARSLEKhdfskGPLKMISPGVVFRRDTDDPTHSHQFHQVEGI-------MIDKHITM---- 69
Cdd:PLN02788 121 DTYYVDAQTVLRCHTSAHQAELLRA-----GHTHFLVTGDVYRRDSIDATHYPVFHQMEGVrvfspeeWEASGLDGtdla 195

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 156712354  70 -ADLKGTLETMTHKLFGDkFKVRLRPSYFPFTEPSVEADItcmNCGGKgcdvckgsgWIEVL 130
Cdd:PLN02788 196 aEDLKKTLEGLARHLFGD-VEMRWVDAYFPFTNPSFELEI---FFKGE---------WLEVL 244
PLN02853 PLN02853
Probable phenylalanyl-tRNA synthetase alpha chain
 10-105 1.57e-19

Probable phenylalanyl-tRNA synthetase alpha chain


Pssm-ID: 215458 [Multi-domain]  Cd Length: 492  Bit Score: 82.80  E-value: 1.57e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712354  10 LMRTHTSPMQARSLekHDFSKG---PLKMISPGVVFRRDTDDPTHSHQFHQVEGIMIDKHITMADLKGTLETMTHKLfGD 86
Cdd:PLN02853 319 LLRTHTTAVSSRML--YKLAQKgfkPKRYFSIDRVFRNEAVDRTHLAEFHQVEGLVCDRGLTLGDLIGVLEDFFSRL-GM 395

                         90
                 ....*....|....*....
gi 156712354  87 KfKVRLRPSYFPFTEPSVE 105
Cdd:PLN02853 396 T-KLRFKPAYNPYTEPSME 413
PTZ00326 PTZ00326
phenylalanyl-tRNA synthetase alpha chain; Provisional
 7-105 3.45e-19

phenylalanyl-tRNA synthetase alpha chain; Provisional


Pssm-ID: 240361 [Multi-domain]  Cd Length: 494  Bit Score: 81.94  E-value: 3.45e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712354   7 KEILmRTHTSPMQARSLEK--HDFSKG----PLKMISPGVVFRRDTDDPTHSHQFHQVEGIMIDKHITMADLKGTLETMT 80
Cdd:PTZ00326 327 KNIL-RTHTTAVSARMLYKlaQEYKKTgpfkPKKYFSIDRVFRNETLDATHLAEFHQVEGFVIDRNLTLGDLIGTIREFF 405

                         90       100
                 ....*....|....*....|....*
gi 156712354  81 HKLFGDkfKVRLRPSYFPFTEPSVE 105
Cdd:PTZ00326 406 RRIGIT--KLRFKPAFNPYTEPSME 428
class_II_aaRS-like_core cd00768
Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA ...
 12-124 1.30e-08

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: 50.96  E-value: 1.30e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712354  12 RTHTSPMQARSLEKHDFsKGPLKMISPGVVFR--RDTDDPTHSHQFHQVEGIM----IDKHITMADLKGTLETMTHKLFG 85
Cdd:cd00768   56 RPTLEPGLVRLFVSHIR-KLPLRLAEIGPAFRneGGRRGLRRVREFTQLEGEVfgedGEEASEFEELIELTEELLRALGI 134

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 156712354  86 DKFKVRLRPSYFPFTEPSVEA--DITCMNCGGKGCDVCKGS 124
Cdd:cd00768  135 KLDIVFVEKTPGEFSPGGAGPgfEIEVDHPEGRGLEIGSGG 175
pheS_mito TIGR00469
phenylalanyl-tRNA synthetase, mitochondrial; Unlike all other known phenylalanyl-tRNA ...
 1-84 2.43e-08

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: 50.84  E-value: 2.43e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712354    1 DTFYITKEILMRTHTSPMQARSLEK--HDFSKGPLKMISPGVVFRRDTDDPTHSHQFHQVEGIMIDKhITMADLkGTLET 78
Cdd:TIGR00469 100 DCYYINEQHLLRAHTSAHELECFQGglDDSDNIKSGFLISADVYRRDEIDKTHYPVFHQADGAAIRK-RTKADL-FEKEP 177


                  ....*.
gi 156712354   79 MTHKLF 84
Cdd:TIGR00469 178 GYIEKF 183
 
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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