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Conserved domains on  [gi|1824670810|gb|QIQ51487|]
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phenylalanine tRNA synthetase alpha subunit, 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]; ...
 1-133 5.91e-98

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: 284.25  E-value: 5.91e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670810   1 MQETFYITNELLMRSQTSPMQARTMEKHdftKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTLLA 80
Cdd:COG0016   154 MQDTFYIDDGLLLRTHTSPVQIRTMEKQ---KPPIRIIAPGRVYRRDESDATHSPMFHQVEGLVVDKGISFADLKGTLEE 230

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1824670810  81 MCQHVFGADRTIRLRPSYFPFTEPSVEVDVSCFRCGGKGCPVCKYTGWIEVLG 133
Cdd:COG0016   231 FAKAFFGEDVKVRFRPSYFPFTEPSAEVDISCFICGGKGCRVCKGTGWLEILG 283
 
Name Accession Description Interval E-value
PheS COG0016
Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]; ...
 1-133 5.91e-98

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: 284.25  E-value: 5.91e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670810   1 MQETFYITNELLMRSQTSPMQARTMEKHdftKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTLLA 80
Cdd:COG0016   154 MQDTFYIDDGLLLRTHTSPVQIRTMEKQ---KPPIRIIAPGRVYRRDESDATHSPMFHQVEGLVVDKGISFADLKGTLEE 230

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1824670810  81 MCQHVFGADRTIRLRPSYFPFTEPSVEVDVSCFRCGGKGCPVCKYTGWIEVLG 133
Cdd:COG0016   231 FAKAFFGEDVKVRFRPSYFPFTEPSAEVDISCFICGGKGCRVCKGTGWLEILG 283
PheRS_alpha_core cd00496
Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class ...
 1-133 1.27e-61

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: 188.14  E-value: 1.27e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670810   1 MQETFYITNE--LLMRSQTSPMQARTMEKHdftKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTL 78
Cdd:cd00496    48 MQDTFYINDParLLLRTHTSAVQARALAKL---KPPIRIFSIGRVYRNDEIDATHLPEFHQIEGLVVDKGLTFADLKGTL 124

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1824670810  79 LAMCQHVFGADRTIRLRPSYFPFTEPSVEVDVSCFRCggkgcpvckyTGWIEVLG 133
Cdd:cd00496   125 EEFAKELFGPITKVRFRPSYFPFTEPSFEVDVYCPGC----------LGWLEILG 169
tRNA-synt_2d pfam01409
tRNA synthetases class II core domain (F); Other tRNA synthetase sub-families are too ...
 1-133 3.95e-61

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: 187.79  E-value: 3.95e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670810   1 MQETFYI-------TNELLMRSQTSPMQARTMEKHdfTKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMAD 73
Cdd:pfam01409  64 MQDTFYLkkplkpvARRLLLRTHTTPVQARTLAKK--PKPPIKIFSIGRVFRRDQVDATHLPEFHQVEGLVVDENVTFAD 141

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670810  74 LKGTLLAMCQHVFGADRTIRLRPSYFPFTEPSVEVDVScfrcggkgcpVCKYTGWIEVLG 133
Cdd:pfam01409 142 LKGVLEEFLRKFFGFEVKVRFRPSYFPFTEPSAEVDVY----------VCKLGGWLEVGG 191
pheS TIGR00468
phenylalanyl-tRNA synthetase, alpha subunit; Most phenylalanyl-tRNA synthetases are ...
 1-133 9.03e-58

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: 180.59  E-value: 9.03e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670810   1 MQETFYITNELLMRSQTSPMQARTMEKHDftKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTLLA 80
Cdd:TIGR00468 119 MQDTFYIKDRLLLRTHTTAVQLRTMEEQE--KPPIRIFSPGRVFRNDTVDATHLPEFHQVEGLVIDKNISFTNLKGFLEE 196

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1824670810  81 MCQHVFGAdRTIRLRPSYFPFTEPSVEVDVSCFRcgGKgcpvckytGWIEVLG 133
Cdd:TIGR00468 197 FLKKMFGE-TEIRFRPSYFPFTEPSAEIDVYCPE--GK--------GWLEVLG 238
pheS PRK04172
phenylalanine--tRNA ligase subunit alpha;
11-133 1.05e-25

phenylalanine--tRNA ligase subunit alpha;


Pssm-ID: 235239 [Multi-domain]  Cd Length: 489  Bit Score: 100.29  E-value: 1.05e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670810  11 LLMRSQTSPMQARTMEKHdfTKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTlLAMCQHVFGADR 90
Cdd:PRK04172  329 LVLRTHTTALSARYLASR--PEPPQKYFSIGRVFRPDTIDATHLPEFYQLEGIVMGEDVSFRDLLGI-LKEFYKRLGFEE 405

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1824670810  91 tIRLRPSYFPFTEPSVEVDVscfRCGGKgcpvckytGWIEVLG 133
Cdd:PRK04172  406 -VKFRPAYFPFTEPSVEVEV---YHEGL--------GWVELGG 436
 
Name Accession Description Interval E-value
PheS COG0016
Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]; ...
 1-133 5.91e-98

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: 284.25  E-value: 5.91e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670810   1 MQETFYITNELLMRSQTSPMQARTMEKHdftKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTLLA 80
Cdd:COG0016   154 MQDTFYIDDGLLLRTHTSPVQIRTMEKQ---KPPIRIIAPGRVYRRDESDATHSPMFHQVEGLVVDKGISFADLKGTLEE 230

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1824670810  81 MCQHVFGADRTIRLRPSYFPFTEPSVEVDVSCFRCGGKGCPVCKYTGWIEVLG 133
Cdd:COG0016   231 FAKAFFGEDVKVRFRPSYFPFTEPSAEVDISCFICGGKGCRVCKGTGWLEILG 283
PheRS_alpha_core cd00496
Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class ...
 1-133 1.27e-61

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: 188.14  E-value: 1.27e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670810   1 MQETFYITNE--LLMRSQTSPMQARTMEKHdftKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTL 78
Cdd:cd00496    48 MQDTFYINDParLLLRTHTSAVQARALAKL---KPPIRIFSIGRVYRNDEIDATHLPEFHQIEGLVVDKGLTFADLKGTL 124

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1824670810  79 LAMCQHVFGADRTIRLRPSYFPFTEPSVEVDVSCFRCggkgcpvckyTGWIEVLG 133
Cdd:cd00496   125 EEFAKELFGPITKVRFRPSYFPFTEPSFEVDVYCPGC----------LGWLEILG 169
tRNA-synt_2d pfam01409
tRNA synthetases class II core domain (F); Other tRNA synthetase sub-families are too ...
 1-133 3.95e-61

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: 187.79  E-value: 3.95e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670810   1 MQETFYI-------TNELLMRSQTSPMQARTMEKHdfTKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMAD 73
Cdd:pfam01409  64 MQDTFYLkkplkpvARRLLLRTHTTPVQARTLAKK--PKPPIKIFSIGRVFRRDQVDATHLPEFHQVEGLVVDENVTFAD 141

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670810  74 LKGTLLAMCQHVFGADRTIRLRPSYFPFTEPSVEVDVScfrcggkgcpVCKYTGWIEVLG 133
Cdd:pfam01409 142 LKGVLEEFLRKFFGFEVKVRFRPSYFPFTEPSAEVDVY----------VCKLGGWLEVGG 191
pheS TIGR00468
phenylalanyl-tRNA synthetase, alpha subunit; Most phenylalanyl-tRNA synthetases are ...
 1-133 9.03e-58

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: 180.59  E-value: 9.03e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670810   1 MQETFYITNELLMRSQTSPMQARTMEKHDftKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTLLA 80
Cdd:TIGR00468 119 MQDTFYIKDRLLLRTHTTAVQLRTMEEQE--KPPIRIFSPGRVFRNDTVDATHLPEFHQVEGLVIDKNISFTNLKGFLEE 196

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1824670810  81 MCQHVFGAdRTIRLRPSYFPFTEPSVEVDVSCFRcgGKgcpvckytGWIEVLG 133
Cdd:TIGR00468 197 FLKKMFGE-TEIRFRPSYFPFTEPSAEIDVYCPE--GK--------GWLEVLG 238
pheS PRK04172
phenylalanine--tRNA ligase subunit alpha;
11-133 1.05e-25

phenylalanine--tRNA ligase subunit alpha;


Pssm-ID: 235239 [Multi-domain]  Cd Length: 489  Bit Score: 100.29  E-value: 1.05e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670810  11 LLMRSQTSPMQARTMEKHdfTKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTlLAMCQHVFGADR 90
Cdd:PRK04172  329 LVLRTHTTALSARYLASR--PEPPQKYFSIGRVFRPDTIDATHLPEFYQLEGIVMGEDVSFRDLLGI-LKEFYKRLGFEE 405

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1824670810  91 tIRLRPSYFPFTEPSVEVDVscfRCGGKgcpvckytGWIEVLG 133
Cdd:PRK04172  406 -VKFRPAYFPFTEPSVEVEV---YHEGL--------GWVELGG 436
PLN02788 PLN02788
phenylalanine-tRNA synthetase
 3-133 1.15e-19

phenylalanine-tRNA synthetase


Pssm-ID: 215422 [Multi-domain]  Cd Length: 402  Bit Score: 82.89  E-value: 1.15e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670810   3 ETFYITNELLMRSQTSPMQARTMEKhdftkGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVI-------DKHITM---- 71
Cdd:PLN02788  121 DTYYVDAQTVLRCHTSAHQAELLRA-----GHTHFLVTGDVYRRDSIDATHYPVFHQMEGVRVfspeeweASGLDGtdla 195

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1824670810  72 -ADLKGTLLAMCQHVFGaDRTIRLRPSYFPFTEPSVEVDVscfrcggkgcpvcKYTG-WIEVLG 133
Cdd:PLN02788  196 aEDLKKTLEGLARHLFG-DVEMRWVDAYFPFTNPSFELEI-------------FFKGeWLEVLG 245
PLN02853 PLN02853
Probable phenylalanyl-tRNA synthetase alpha chain
 12-108 7.19e-15

Probable phenylalanyl-tRNA synthetase alpha chain


Pssm-ID: 215458 [Multi-domain]  Cd Length: 492  Bit Score: 69.70  E-value: 7.19e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670810  12 LMRSQTSPMQARTMEK---HDFTkgPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTL------LAMC 82
Cdd:PLN02853  319 LLRTHTTAVSSRMLYKlaqKGFK--PKRYFSIDRVFRNEAVDRTHLAEFHQVEGLVCDRGLTLGDLIGVLedffsrLGMT 396

                          90       100
                  ....*....|....*....|....*.
gi 1824670810  83 QhvfgadrtIRLRPSYFPFTEPSVEV 108
Cdd:PLN02853  397 K--------LRFKPAYNPYTEPSMEI 414
PTZ00326 PTZ00326
phenylalanyl-tRNA synthetase alpha chain; Provisional
 12-108 1.13e-14

phenylalanyl-tRNA synthetase alpha chain; Provisional


Pssm-ID: 240361 [Multi-domain]  Cd Length: 494  Bit Score: 69.23  E-value: 1.13e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670810  12 LMRSQTSPMQARTMEK--HDFTKG----PLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKHITMADLKGTLLAMCQHV 85
Cdd:PTZ00326  329 ILRTHTTAVSARMLYKlaQEYKKTgpfkPKKYFSIDRVFRNETLDATHLAEFHQVEGFVIDRNLTLGDLIGTIREFFRRI 408

                          90       100
                  ....*....|....*....|...
gi 1824670810  86 fGADRtIRLRPSYFPFTEPSVEV 108
Cdd:PTZ00326  409 -GITK-LRFKPAFNPYTEPSMEI 429
pheS_mito TIGR00469
phenylalanyl-tRNA synthetase, mitochondrial; Unlike all other known phenylalanyl-tRNA ...
 3-74 6.06e-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: 49.69  E-value: 6.06e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1824670810   3 ETFYITNELLMRSQTSPMQARTMEK--HDFTKGPLKMISPGVVYRRDDDDATHSHQFHQMEGLVIDKhITMADL 74
Cdd:TIGR00469 100 DCYYINEQHLLRAHTSAHELECFQGglDDSDNIKSGFLISADVYRRDEIDKTHYPVFHQADGAAIRK-RTKADL 172
class_II_aaRS-like_core cd00768
Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA ...
 9-108 2.76e-07

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: 47.50  E-value: 2.76e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1824670810   9 NELLMRSQTSPMQARTMEKHDFtKGPLKMISPGVVYRRDDD--DATHSHQFHQMEGLV----IDKHITMADLKGTLLAMC 82
Cdd:cd00768    51 EDLYLRPTLEPGLVRLFVSHIR-KLPLRLAEIGPAFRNEGGrrGLRRVREFTQLEGEVfgedGEEASEFEELIELTEELL 129

                          90       100
                  ....*....|....*....|....*.
gi 1824670810  83 QHVFGADRTIRLRPSYFPFTEPSVEV 108
Cdd:cd00768   130 RALGIKLDIVFVEKTPGEFSPGGAGP 155
 
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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