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Conserved domains on  [gi|1958783975|ref|XP_038968555|]
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tRNA-dihydrouridine(20a/20b) synthase [NAD(P)+]-like isoform X3 [Rattus norvegicus]

Protein Classification

tRNA-dihydrouridine synthase family protein( domain architecture ID 10120048)

tRNA-dihydrouridine synthase family protein such as tRNA-dihydrouridine synthase, which catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs

CATH:  3.20.20.70
EC:  1.3.1.-
SCOP:  4000080

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
28-188 1.07e-50

Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present.


:

Pssm-ID: 239200 [Multi-domain]  Cd Length: 231  Bit Score: 163.43  E-value: 1.07e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783975  28 VKVCAPMVRYSNllklllscsfrrekiyvrpfsssftadsrLAFRTLVRKYSCDLCYTPMIVAADFVRSVKARDSEFTTN 107
Cdd:cd02801     1 KLILAPMVGVTD-----------------------------LPFRLLCRRYGADLVYTEMISAKALLRGNRKRLRLLTRN 51
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783975 108 QGDCPLIVQFAANDARLLSDAALIVCP-YASGIDINCGCPQRWAMADGYGACLINKPELVLDMVRQVRNRVENPrfsVSI 186
Cdd:cd02801    52 PEERPLIVQLGGSDPETLAEAAKIVEElGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIP---VTV 128

                  ..
gi 1958783975 187 KI 188
Cdd:cd02801   129 KI 130
 
Name Accession Description Interval E-value
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
28-188 1.07e-50

Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present.


Pssm-ID: 239200 [Multi-domain]  Cd Length: 231  Bit Score: 163.43  E-value: 1.07e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783975  28 VKVCAPMVRYSNllklllscsfrrekiyvrpfsssftadsrLAFRTLVRKYSCDLCYTPMIVAADFVRSVKARDSEFTTN 107
Cdd:cd02801     1 KLILAPMVGVTD-----------------------------LPFRLLCRRYGADLVYTEMISAKALLRGNRKRLRLLTRN 51
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783975 108 QGDCPLIVQFAANDARLLSDAALIVCP-YASGIDINCGCPQRWAMADGYGACLINKPELVLDMVRQVRNRVENPrfsVSI 186
Cdd:cd02801    52 PEERPLIVQLGGSDPETLAEAAKIVEElGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIP---VTV 128

                  ..
gi 1958783975 187 KI 188
Cdd:cd02801   129 KI 130
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
69-189 2.27e-33

Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD. Some family members may be targeted to the mitochondria and even have a role in mitochondria.


Pssm-ID: 426126  Cd Length: 309  Bit Score: 121.28  E-value: 2.27e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783975  69 LAFRTLVRKYSC-DLCYTPMIVAADFVRSVKARDSEFTTNQGDCPLIVQFAANDARLLSDAALIVCP-YASGIDINCGCP 146
Cdd:pfam01207  11 LPFRRLVREYGAgDLVYTEMVTAKAQLRPEKVRIRMLSELEEPTPLAVQLGGSDPALLAEAAKLVEDrGADGIDINMGCP 90
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1958783975 147 QRWAMADGYGACLINKPELVLDMVRQVRNRVENPrfsVSIKIS 189
Cdd:pfam01207  91 SKKVTRGGGGAALLRNPDLVAQIVKAVVKAVGIP---VTVKIR 130
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
69-188 2.10e-26

tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; tRNA-dihydrouridine synthase is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 439812 [Multi-domain]  Cd Length: 310  Bit Score: 102.86  E-value: 2.10e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783975  69 LAFRTLVRKYSCDLCYTPMIVAADFVRSVKARDSEFTTNQGDCPLIVQFAANDARLLSDAALIVCPY-ASGIDINCGCPq 147
Cdd:COG0042    20 RPFRRLCRELGAGLLYTEMVSARALLHGNRKTRRLLDFDPEEHPVAVQLFGSDPEELAEAARIAEELgADEIDINMGCP- 98
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1958783975 148 rwamAD-----GYGACLINKPELVLDMVRQVRNRVENPrfsVSIKI 188
Cdd:COG0042    99 ----VKkvtkgGAGAALLRDPELVAEIVKAVVEAVDVP---VTVKI 137
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
67-188 1.37e-11

putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family). This branch includes NifR3 itself, from Rhodobacter capsulatus. It excludes a broadly distributed but more sparsely populated subfamily that contains sll0926 from Synechocystis PCC6803, HI0634 from Haemophilus influenzae, and BB0225 from Borrelia burgdorferi. It also excludes a shorter and more distant archaeal subfamily.The function of nifR3, a member of this family, is unknown, but it is found in an operon with nitrogen-sensing two component regulators in Rhodobacter capsulatus.Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. [Unknown function, General]


Pssm-ID: 129820  Cd Length: 319  Bit Score: 62.00  E-value: 1.37e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783975  67 SRLAFRTLVRKYSCDLCYTPMIVAADFVR--SVKARDSEFTTNQGdcPLIVQFAANDARLLSDAALIVCPY-ASGIDINC 143
Cdd:TIGR00737  19 TDSPFRRLVAEYGAGLTVCEMVSSEAIVYdsQRTMRLLDIAEDET--PISVQLFGSDPDTMAEAAKINEELgADIIDINM 96
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1958783975 144 GCPQRWAMADGYGACLINKPELVLDMVRQVRNRVENPrfsVSIKI 188
Cdd:TIGR00737  97 GCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIP---VTVKI 138
PRK11815 PRK11815
tRNA dihydrouridine(20/20a) synthase DusA;
82-187 7.05e-10

tRNA dihydrouridine(20/20a) synthase DusA;


Pssm-ID: 236991 [Multi-domain]  Cd Length: 333  Bit Score: 57.45  E-value: 7.05e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783975  82 LCYTPMIVAADFVRSVKARDSEFttNQGDCPLIVQFAANDARLLSDAALIVCPYasG---IDINCGCP----QRWAmadg 154
Cdd:PRK11815   38 LLYTEMVTTGAIIHGDRERLLAF--DPEEHPVALQLGGSDPADLAEAAKLAEDW--GydeINLNVGCPsdrvQNGR---- 109
                          90       100       110
                  ....*....|....*....|....*....|...
gi 1958783975 155 YGACLINKPELVLDMVRQVRNRVENPrfsVSIK 187
Cdd:PRK11815  110 FGACLMAEPELVADCVKAMKDAVSIP---VTVK 139
 
Name Accession Description Interval E-value
DUS_like_FMN cd02801
Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze ...
28-188 1.07e-50

Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present.


Pssm-ID: 239200 [Multi-domain]  Cd Length: 231  Bit Score: 163.43  E-value: 1.07e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783975  28 VKVCAPMVRYSNllklllscsfrrekiyvrpfsssftadsrLAFRTLVRKYSCDLCYTPMIVAADFVRSVKARDSEFTTN 107
Cdd:cd02801     1 KLILAPMVGVTD-----------------------------LPFRLLCRRYGADLVYTEMISAKALLRGNRKRLRLLTRN 51
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783975 108 QGDCPLIVQFAANDARLLSDAALIVCP-YASGIDINCGCPQRWAMADGYGACLINKPELVLDMVRQVRNRVENPrfsVSI 186
Cdd:cd02801    52 PEERPLIVQLGGSDPETLAEAAKIVEElGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIP---VTV 128

                  ..
gi 1958783975 187 KI 188
Cdd:cd02801   129 KI 130
Dus pfam01207
Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double ...
69-189 2.27e-33

Dihydrouridine synthase (Dus); Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD. Some family members may be targeted to the mitochondria and even have a role in mitochondria.


Pssm-ID: 426126  Cd Length: 309  Bit Score: 121.28  E-value: 2.27e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783975  69 LAFRTLVRKYSC-DLCYTPMIVAADFVRSVKARDSEFTTNQGDCPLIVQFAANDARLLSDAALIVCP-YASGIDINCGCP 146
Cdd:pfam01207  11 LPFRRLVREYGAgDLVYTEMVTAKAQLRPEKVRIRMLSELEEPTPLAVQLGGSDPALLAEAAKLVEDrGADGIDINMGCP 90
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1958783975 147 QRWAMADGYGACLINKPELVLDMVRQVRNRVENPrfsVSIKIS 189
Cdd:pfam01207  91 SKKVTRGGGGAALLRNPDLVAQIVKAVVKAVGIP---VTVKIR 130
DusA COG0042
tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; ...
69-188 2.10e-26

tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; tRNA-dihydrouridine synthase is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 439812 [Multi-domain]  Cd Length: 310  Bit Score: 102.86  E-value: 2.10e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783975  69 LAFRTLVRKYSCDLCYTPMIVAADFVRSVKARDSEFTTNQGDCPLIVQFAANDARLLSDAALIVCPY-ASGIDINCGCPq 147
Cdd:COG0042    20 RPFRRLCRELGAGLLYTEMVSARALLHGNRKTRRLLDFDPEEHPVAVQLFGSDPEELAEAARIAEELgADEIDINMGCP- 98
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1958783975 148 rwamAD-----GYGACLINKPELVLDMVRQVRNRVENPrfsVSIKI 188
Cdd:COG0042    99 ----VKkvtkgGAGAALLRDPELVAEIVKAVVEAVDVP---VTVKI 137
nifR3_yhdG TIGR00737
putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 ...
67-188 1.37e-11

putative TIM-barrel protein, nifR3 family; This model represents one branch of COG0042 (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family). This branch includes NifR3 itself, from Rhodobacter capsulatus. It excludes a broadly distributed but more sparsely populated subfamily that contains sll0926 from Synechocystis PCC6803, HI0634 from Haemophilus influenzae, and BB0225 from Borrelia burgdorferi. It also excludes a shorter and more distant archaeal subfamily.The function of nifR3, a member of this family, is unknown, but it is found in an operon with nitrogen-sensing two component regulators in Rhodobacter capsulatus.Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. [Unknown function, General]


Pssm-ID: 129820  Cd Length: 319  Bit Score: 62.00  E-value: 1.37e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783975  67 SRLAFRTLVRKYSCDLCYTPMIVAADFVR--SVKARDSEFTTNQGdcPLIVQFAANDARLLSDAALIVCPY-ASGIDINC 143
Cdd:TIGR00737  19 TDSPFRRLVAEYGAGLTVCEMVSSEAIVYdsQRTMRLLDIAEDET--PISVQLFGSDPDTMAEAAKINEELgADIIDINM 96
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1958783975 144 GCPQRWAMADGYGACLINKPELVLDMVRQVRNRVENPrfsVSIKI 188
Cdd:TIGR00737  97 GCPVPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIP---VTVKI 138
yjbN TIGR00742
tRNA dihydrouridine synthase A; This model represents one branch of COG0042 (Predicted ...
71-187 4.89e-10

tRNA dihydrouridine synthase A; This model represents one branch of COG0042 (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family). It represents a distinct subset by a set of shared unique motifs, a conserved pattern of insertions/deletions relative to other nifR3 homologs, and by subclustering based on cross-genome bidirectional best hits. Members are found in species as diverse as the proteobacteria, a spirochete, a cyanobacterium, and Deinococcus radiodurans. NifR3 itself, a protein of unknown function associated with nitrogen regulation in Rhodobacter capsulatus, is not a member of this branch. Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129825  Cd Length: 318  Bit Score: 57.91  E-value: 4.89e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783975  71 FRTLVRKYSCD-LCYTPMIVAADFVRSVKARDSEFttNQGDCPLIVQFAANDARLLSDAALIVCPYA-SGIDINCGCPQR 148
Cdd:TIGR00742  16 FRYFLRLLSKHtLLYTEMITAKAIIHGDKKDILKF--SPEESPVALQLGGSDPNDLAKCAKIAEKRGyDEINLNVGCPSD 93
                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1958783975 149 WAMADGYGACLINKPELVLDMVRQVRNRVENPrfsVSIK 187
Cdd:TIGR00742  94 RVQNGNFGACLMGNADLVADCVKAMQEAVNIP---VTVK 129
PRK11815 PRK11815
tRNA dihydrouridine(20/20a) synthase DusA;
82-187 7.05e-10

tRNA dihydrouridine(20/20a) synthase DusA;


Pssm-ID: 236991 [Multi-domain]  Cd Length: 333  Bit Score: 57.45  E-value: 7.05e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783975  82 LCYTPMIVAADFVRSVKARDSEFttNQGDCPLIVQFAANDARLLSDAALIVCPYasG---IDINCGCP----QRWAmadg 154
Cdd:PRK11815   38 LLYTEMVTTGAIIHGDRERLLAF--DPEEHPVALQLGGSDPADLAEAAKLAEDW--GydeINLNVGCPsdrvQNGR---- 109
                          90       100       110
                  ....*....|....*....|....*....|...
gi 1958783975 155 YGACLINKPELVLDMVRQVRNRVENPrfsVSIK 187
Cdd:PRK11815  110 FGACLMAEPELVADCVKAMKDAVSIP---VTVK 139
PRK10415 PRK10415
tRNA-dihydrouridine synthase B; Provisional
71-188 1.52e-05

tRNA-dihydrouridine synthase B; Provisional


Pssm-ID: 182440  Cd Length: 321  Bit Score: 44.58  E-value: 1.52e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783975  71 FRTLVRKYSCDLCYTPMIVAADFV-RSVKARdseFTTNQGDCPLI--VQFAANDARLLSDAALI-VCPYASGIDINCGCP 146
Cdd:PRK10415   25 FRTLCYEMGAGLTVSEMMSSNPQVwESDKSR---LRMVHIDEPGIrtVQIAGSDPKEMADAARInVESGAQIIDINMGCP 101
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1958783975 147 QRWAMADGYGACLINKPELVLDMVRQVRNRVENPrfsVSIKI 188
Cdd:PRK10415  102 AKKVNRKLAGSALLQYPDLVKSILTEVVNAVDVP---VTLKI 140
PRK10550 PRK10550
tRNA dihydrouridine(16) synthase DusC;
138-188 1.54e-04

tRNA dihydrouridine(16) synthase DusC;


Pssm-ID: 236713  Cd Length: 312  Bit Score: 41.33  E-value: 1.54e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958783975 138 GIDINCGCPQRWAMADGYGACLINKPELVLDMVRQVRNRVENpRFSVSIKI 188
Cdd:PRK10550   91 GVDLNCGCPSKTVNGSGGGATLLKDPELIYQGAKAMREAVPA-HLPVTVKV 140
PRK07259 PRK07259
dihydroorotate dehydrogenase;
107-198 3.36e-03

dihydroorotate dehydrogenase;


Pssm-ID: 235982  Cd Length: 301  Bit Score: 37.44  E-value: 3.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958783975 107 NQGDCPLIVQFAAND-------ARLLSDAalivcPYASGIDINCGCPQrwamADGYGACLINKPELVLDMVRQVRNRVEN 179
Cdd:PRK07259   88 EEFDTPIIANVAGSTeeeyaevAEKLSKA-----PNVDAIELNISCPN----VKHGGMAFGTDPELAYEVVKAVKEVVKV 158
                          90
                  ....*....|....*....
gi 1958783975 180 PrfsVSIKISCNFEIIGSM 198
Cdd:PRK07259  159 P---VIVKLTPNVTDIVEI 174
 
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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