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Conserved domains on  [gi|156712384|emb|CAO00683|]
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phenylalanyl-tRNA synthase, partial [Lactobacillus helveticus]

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]; ...
 2-130 1.28e-89

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: 263.07  E-value: 1.28e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712384   2 TFYIDGEDLLRTQTSGDQARVLEKHdfsKSPLKMVGPGKVYRRDDDDATHSHQFMQMEGLVVDKNVTMSDLKGTLEMIAK 81
Cdd:COG0016  157 TFYIDDGLLLRTHTSPVQIRTMEKQ---KPPIRIIAPGRVYRRDESDATHSPMFHQVEGLVVDKGISFADLKGTLEEFAK 233

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 156712384  82 HVFGQDRATRLRPSYFPFTEPSVEMDVSCFNCDGKGCPICKYTGWIEVL 130
Cdd:COG0016  234 AFFGEDVKVRFRPSYFPFTEPSAEVDISCFICGGKGCRVCKGTGWLEIL 282
 
Name Accession Description Interval E-value
PheS COG0016
Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]; ...
 2-130 1.28e-89

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: 263.07  E-value: 1.28e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712384   2 TFYIDGEDLLRTQTSGDQARVLEKHdfsKSPLKMVGPGKVYRRDDDDATHSHQFMQMEGLVVDKNVTMSDLKGTLEMIAK 81
Cdd:COG0016  157 TFYIDDGLLLRTHTSPVQIRTMEKQ---KPPIRIIAPGRVYRRDESDATHSPMFHQVEGLVVDKGISFADLKGTLEEFAK 233

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 156712384  82 HVFGQDRATRLRPSYFPFTEPSVEMDVSCFNCDGKGCPICKYTGWIEVL 130
Cdd:COG0016  234 AFFGEDVKVRFRPSYFPFTEPSAEVDISCFICGGKGCRVCKGTGWLEIL 282
PheRS_alpha_core cd00496
Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class ...
 2-130 3.35e-60

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: 184.29  E-value: 3.35e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712384   2 TFYIDGED--LLRTQTSGDQARVLEKHdfsKSPLKMVGPGKVYRRDDDDATHSHQFMQMEGLVVDKNVTMSDLKGTLEMI 79
Cdd:cd00496   51 TFYINDPArlLLRTHTSAVQARALAKL---KPPIRIFSIGRVYRNDEIDATHLPEFHQIEGLVVDKGLTFADLKGTLEEF 127

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 156712384  80 AKHVFGQDRATRLRPSYFPFTEPSVEMDVSCFNCdgkgcpickyTGWIEVL 130
Cdd:cd00496  128 AKELFGPITKVRFRPSYFPFTEPSFEVDVYCPGC----------LGWLEIL 168
tRNA-synt_2d pfam01409
tRNA synthetases class II core domain (F); Other tRNA synthetase sub-families are too ...
 2-130 6.16e-56

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: 174.31  E-value: 6.16e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712384    2 TFYIDGED-------LLRTQTSGDQARVLEKHdfSKSPLKMVGPGKVYRRDDDDATHSHQFMQMEGLVVDKNVTMSDLKG 74
Cdd:pfam01409  67 TFYLKKPLkpvarrlLLRTHTTPVQARTLAKK--PKPPIKIFSIGRVFRRDQVDATHLPEFHQVEGLVVDENVTFADLKG 144

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 156712384   75 TLEMIAKHVFGQDRATRLRPSYFPFTEPSVEMDVScfncdgkgcpICKYTGWIEVL 130
Cdd:pfam01409 145 VLEEFLRKFFGFEVKVRFRPSYFPFTEPSAEVDVY----------VCKLGGWLEVG 190
pheS TIGR00468
phenylalanyl-tRNA synthetase, alpha subunit; Most phenylalanyl-tRNA synthetases are ...
 2-130 8.85e-54

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: 170.19  E-value: 8.85e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712384    2 TFYIDGEDLLRTQTSGDQARVLEKHDfsKSPLKMVGPGKVYRRDDDDATHSHQFMQMEGLVVDKNVTMSDLKGTLEMIAK 81
Cdd:TIGR00468 122 TFYIKDRLLLRTHTTAVQLRTMEEQE--KPPIRIFSPGRVFRNDTVDATHLPEFHQVEGLVIDKNISFTNLKGFLEEFLK 199

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 156712384   82 HVFGQdRATRLRPSYFPFTEPSVEMDVSCFNcdGKgcpickytGWIEVL 130
Cdd:TIGR00468 200 KMFGE-TEIRFRPSYFPFTEPSAEIDVYCPE--GK--------GWLEVL 237
pheS PRK04172
phenylalanine--tRNA ligase subunit alpha;
11-108 6.20e-29

phenylalanine--tRNA ligase subunit alpha;


Pssm-ID: 235239 [Multi-domain]  Cd Length: 489  Bit Score: 109.15  E-value: 6.20e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712384  11 LRTQTSGDQARVLEKHdfSKSPLKMVGPGKVYRRDDDDATHSHQFMQMEGLVVDKNVTMSDLKGTLEMIAKHvFGQDRaT 90
Cdd:PRK04172 331 LRTHTTALSARYLASR--PEPPQKYFSIGRVFRPDTIDATHLPEFYQLEGIVMGEDVSFRDLLGILKEFYKR-LGFEE-V 406

                         90
                 ....*....|....*...
gi 156712384  91 RLRPSYFPFTEPSVEMDV 108
Cdd:PRK04172 407 KFRPAYFPFTEPSVEVEV 424
 
Name Accession Description Interval E-value
PheS COG0016
Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]; ...
 2-130 1.28e-89

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: 263.07  E-value: 1.28e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712384   2 TFYIDGEDLLRTQTSGDQARVLEKHdfsKSPLKMVGPGKVYRRDDDDATHSHQFMQMEGLVVDKNVTMSDLKGTLEMIAK 81
Cdd:COG0016  157 TFYIDDGLLLRTHTSPVQIRTMEKQ---KPPIRIIAPGRVYRRDESDATHSPMFHQVEGLVVDKGISFADLKGTLEEFAK 233

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 156712384  82 HVFGQDRATRLRPSYFPFTEPSVEMDVSCFNCDGKGCPICKYTGWIEVL 130
Cdd:COG0016  234 AFFGEDVKVRFRPSYFPFTEPSAEVDISCFICGGKGCRVCKGTGWLEIL 282
PheRS_alpha_core cd00496
Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class ...
 2-130 3.35e-60

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: 184.29  E-value: 3.35e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712384   2 TFYIDGED--LLRTQTSGDQARVLEKHdfsKSPLKMVGPGKVYRRDDDDATHSHQFMQMEGLVVDKNVTMSDLKGTLEMI 79
Cdd:cd00496   51 TFYINDPArlLLRTHTSAVQARALAKL---KPPIRIFSIGRVYRNDEIDATHLPEFHQIEGLVVDKGLTFADLKGTLEEF 127

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 156712384  80 AKHVFGQDRATRLRPSYFPFTEPSVEMDVSCFNCdgkgcpickyTGWIEVL 130
Cdd:cd00496  128 AKELFGPITKVRFRPSYFPFTEPSFEVDVYCPGC----------LGWLEIL 168
tRNA-synt_2d pfam01409
tRNA synthetases class II core domain (F); Other tRNA synthetase sub-families are too ...
 2-130 6.16e-56

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: 174.31  E-value: 6.16e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712384    2 TFYIDGED-------LLRTQTSGDQARVLEKHdfSKSPLKMVGPGKVYRRDDDDATHSHQFMQMEGLVVDKNVTMSDLKG 74
Cdd:pfam01409  67 TFYLKKPLkpvarrlLLRTHTTPVQARTLAKK--PKPPIKIFSIGRVFRRDQVDATHLPEFHQVEGLVVDENVTFADLKG 144

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 156712384   75 TLEMIAKHVFGQDRATRLRPSYFPFTEPSVEMDVScfncdgkgcpICKYTGWIEVL 130
Cdd:pfam01409 145 VLEEFLRKFFGFEVKVRFRPSYFPFTEPSAEVDVY----------VCKLGGWLEVG 190
pheS TIGR00468
phenylalanyl-tRNA synthetase, alpha subunit; Most phenylalanyl-tRNA synthetases are ...
 2-130 8.85e-54

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: 170.19  E-value: 8.85e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712384    2 TFYIDGEDLLRTQTSGDQARVLEKHDfsKSPLKMVGPGKVYRRDDDDATHSHQFMQMEGLVVDKNVTMSDLKGTLEMIAK 81
Cdd:TIGR00468 122 TFYIKDRLLLRTHTTAVQLRTMEEQE--KPPIRIFSPGRVFRNDTVDATHLPEFHQVEGLVIDKNISFTNLKGFLEEFLK 199

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 156712384   82 HVFGQdRATRLRPSYFPFTEPSVEMDVSCFNcdGKgcpickytGWIEVL 130
Cdd:TIGR00468 200 KMFGE-TEIRFRPSYFPFTEPSAEIDVYCPE--GK--------GWLEVL 237
pheS PRK04172
phenylalanine--tRNA ligase subunit alpha;
11-108 6.20e-29

phenylalanine--tRNA ligase subunit alpha;


Pssm-ID: 235239 [Multi-domain]  Cd Length: 489  Bit Score: 109.15  E-value: 6.20e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712384  11 LRTQTSGDQARVLEKHdfSKSPLKMVGPGKVYRRDDDDATHSHQFMQMEGLVVDKNVTMSDLKGTLEMIAKHvFGQDRaT 90
Cdd:PRK04172 331 LRTHTTALSARYLASR--PEPPQKYFSIGRVFRPDTIDATHLPEFYQLEGIVMGEDVSFRDLLGILKEFYKR-LGFEE-V 406

                         90
                 ....*....|....*...
gi 156712384  91 RLRPSYFPFTEPSVEMDV 108
Cdd:PRK04172 407 KFRPAYFPFTEPSVEVEV 424
PLN02788 PLN02788
phenylalanine-tRNA synthetase
 2-130 2.77e-22

phenylalanine-tRNA synthetase


Pssm-ID: 215422 [Multi-domain]  Cd Length: 402  Bit Score: 90.21  E-value: 2.77e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712384   2 TFYIDGEDLLRTQTSGDQARVLEK-HDfsksplKMVGPGKVYRRDDDDATHSHQFMQMEGLVVDKNVTMS---------- 70
Cdd:PLN02788 122 TYYVDAQTVLRCHTSAHQAELLRAgHT------HFLVTGDVYRRDSIDATHYPVFHQMEGVRVFSPEEWEasgldgtdla 195

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 156712384  71 --DLKGTLEMIAKHVFGqDRATRLRPSYFPFTEPSVEMDVScFNCDgkgcpickytgWIEVL 130
Cdd:PLN02788 196 aeDLKKTLEGLARHLFG-DVEMRWVDAYFPFTNPSFELEIF-FKGE-----------WLEVL 244
PTZ00326 PTZ00326
phenylalanyl-tRNA synthetase alpha chain; Provisional
 10-105 1.61e-15

phenylalanyl-tRNA synthetase alpha chain; Provisional


Pssm-ID: 240361 [Multi-domain]  Cd Length: 494  Bit Score: 71.54  E-value: 1.61e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712384  10 LLRTQTSGDQARVLEK--HDFSK----SPLKMVGPGKVYRRDDDDATHSHQFMQMEGLVVDKNVTMSDLKGTLEMIakhv 83
Cdd:PTZ00326 329 ILRTHTTAVSARMLYKlaQEYKKtgpfKPKKYFSIDRVFRNETLDATHLAEFHQVEGFVIDRNLTLGDLIGTIREF---- 404

                         90       100
                 ....*....|....*....|....
gi 156712384  84 FGQDRATRLR--PSYFPFTEPSVE 105
Cdd:PTZ00326 405 FRRIGITKLRfkPAFNPYTEPSME 428
PLN02853 PLN02853
Probable phenylalanyl-tRNA synthetase alpha chain
 9-105 1.35e-14

Probable phenylalanyl-tRNA synthetase alpha chain


Pssm-ID: 215458 [Multi-domain]  Cd Length: 492  Bit Score: 68.93  E-value: 1.35e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712384   9 DLLRTQTSGDQARVLekHDFSKSPLKmvgPGK------VYRRDDDDATHSHQFMQMEGLVVDKNVTMSDLKGTLEmiakH 82
Cdd:PLN02853 318 NLLRTHTTAVSSRML--YKLAQKGFK---PKRyfsidrVFRNEAVDRTHLAEFHQVEGLVCDRGLTLGDLIGVLE----D 388

                         90       100
                 ....*....|....*....|....*
gi 156712384  83 VFGQDRATRLR--PSYFPFTEPSVE 105
Cdd:PLN02853 389 FFSRLGMTKLRfkPAYNPYTEPSME 413
pheS_mito TIGR00469
phenylalanyl-tRNA synthetase, mitochondrial; Unlike all other known phenylalanyl-tRNA ...
 2-79 4.64e-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: 50.07  E-value: 4.64e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712384    2 TFYIDGEDLLRTQTSGDQ----ARVLEKHDFSKSPLKMVGpgKVYRRDDDDATHSHQFMQMEGLVVDKnVTMSDL----K 73
Cdd:TIGR00469 101 CYYINEQHLLRAHTSAHElecfQGGLDDSDNIKSGFLISA--DVYRRDEIDKTHYPVFHQADGAAIRK-RTKADLfekeP 177


                  ....*.
gi 156712384   74 GTLEMI 79
Cdd:TIGR00469 178 GYIEKF 183
class_II_aaRS-like_core cd00768
Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA ...
 2-117 2.85e-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: 47.11  E-value: 2.85e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156712384   2 TFYIDGEDLLRTQTSGDQARVLEKHDFsKSPLKMVGPGKVYRRDDD--DATHSHQFMQMEGLVV----DKNVTMSDLKGT 75
Cdd:cd00768   46 GAENEEDLYLRPTLEPGLVRLFVSHIR-KLPLRLAEIGPAFRNEGGrrGLRRVREFTQLEGEVFgedgEEASEFEELIEL 124

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 156712384  76 LEMIAKHVFGQDRATRLRPSYFPFT----EPSVEMDVscFNCDGKG 117
Cdd:cd00768  125 TEELLRALGIKLDIVFVEKTPGEFSpggaGPGFEIEV--DHPEGRG 168
 
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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