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Conserved domains on  [gi|2443764052|ref|WP_273306006|]
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Rossmann-like and DUF2520 domain-containing protein [Barnesiella viscericola]

Protein Classification

Rossmann-like and DUF2520 domain-containing protein( domain architecture ID 11475612)

Rossmann-like and DUF2520 domain-containing protein may function as an oxidoreductase

CATH:  3.40.50.720
EC:  1.-.-.-
Gene Ontology:  GO:0070403|GO:0016491
PubMed:  30945211|25704928
SCOP:  4000116

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
COG5495 COG5495
Predicted oxidoreductase, contains short-chain dehydrogenase (SDR) and DUF2520 domains ...
1-253 2.47e-99

Predicted oxidoreductase, contains short-chain dehydrogenase (SDR) and DUF2520 domains [General function prediction only];


:

Pssm-ID: 444246 [Multi-domain]  Cd Length: 286  Bit Score: 291.72  E-value: 2.47e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443764052   1 MKIILIGAGNLATRLALALQAKGLAPEWVYSRTEESARRLSEQLPHShYTTRLDSLPSDGDLYIFAVKDSVLPQLLSAMP 80
Cdd:COG5495     4 MKIGIIGAGRVGTALAAALRAAGHEVVGVYSRSPASAERAAALLGAV-PALDLEELAAEADLVLLAVPDDAIAEVAAGLA 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443764052  81 ANAG-----LWVHTAGSVDREVFRPYTNR---YGVFYPMQTFSKERAV--DFDDIPFFIEANsEADTARLHDLAARLSGK 150
Cdd:COG5495    83 AAGAlrpgqLVVHTSGALGSDVLAPAARAgalTGSFHPLQTFSGPREDleRLAGIPFAIEGD-EEALPVLEALAEALGGE 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443764052 151 VYRADSEQRKYLHLAAVFACNFTNHLYALCDRILQEHNL--PFEAMLPLIRETAAKVADMSPFDAQTGPAIRYDQNIIAK 228
Cdd:COG5495   162 PFVIDSEQRPLYHAAAVFASNFLVTLVALAAELLEAAGLedAFDALLPLIRETLDNILELGPAAALTGPAARGDAGTVAK 241
                         250       260
                  ....*....|....*....|....*..
gi 2443764052 229 QEALL--TDPTMREIYTLLSRSIHETH 253
Cdd:COG5495   242 HLAALaeLDPELAELYRALSRSTLELA 268
 
Name Accession Description Interval E-value
COG5495 COG5495
Predicted oxidoreductase, contains short-chain dehydrogenase (SDR) and DUF2520 domains ...
1-253 2.47e-99

Predicted oxidoreductase, contains short-chain dehydrogenase (SDR) and DUF2520 domains [General function prediction only];


Pssm-ID: 444246 [Multi-domain]  Cd Length: 286  Bit Score: 291.72  E-value: 2.47e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443764052   1 MKIILIGAGNLATRLALALQAKGLAPEWVYSRTEESARRLSEQLPHShYTTRLDSLPSDGDLYIFAVKDSVLPQLLSAMP 80
Cdd:COG5495     4 MKIGIIGAGRVGTALAAALRAAGHEVVGVYSRSPASAERAAALLGAV-PALDLEELAAEADLVLLAVPDDAIAEVAAGLA 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443764052  81 ANAG-----LWVHTAGSVDREVFRPYTNR---YGVFYPMQTFSKERAV--DFDDIPFFIEANsEADTARLHDLAARLSGK 150
Cdd:COG5495    83 AAGAlrpgqLVVHTSGALGSDVLAPAARAgalTGSFHPLQTFSGPREDleRLAGIPFAIEGD-EEALPVLEALAEALGGE 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443764052 151 VYRADSEQRKYLHLAAVFACNFTNHLYALCDRILQEHNL--PFEAMLPLIRETAAKVADMSPFDAQTGPAIRYDQNIIAK 228
Cdd:COG5495   162 PFVIDSEQRPLYHAAAVFASNFLVTLVALAAELLEAAGLedAFDALLPLIRETLDNILELGPAAALTGPAARGDAGTVAK 241
                         250       260
                  ....*....|....*....|....*..
gi 2443764052 229 QEALL--TDPTMREIYTLLSRSIHETH 253
Cdd:COG5495   242 HLAALaeLDPELAELYRALSRSTLELA 268
DUF2520 pfam10728
Domain of unknown function (DUF2520); This presumed domain is found C-terminal to a ...
125-248 7.95e-55

Domain of unknown function (DUF2520); This presumed domain is found C-terminal to a Rossmann-like domain suggesting that these proteins are oxidoreductases.


Pssm-ID: 463182  Cd Length: 126  Bit Score: 172.64  E-value: 7.95e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443764052 125 IPFFIEANSEAdTARLHDLAARLSGKVYRADSEQRKYLHLAAVFACNFTNHLYALCDRILQEHNLP--FEAMLPLIRETA 202
Cdd:pfam10728   1 IPFGIEGDEEA-LAVLEALAESLGGKVFEIDSEQRKLYHAAAVFASNFLVTLYALAAELLEEAGLPeaFEALLPLIRETL 79
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2443764052 203 AKVADMSPFDAQTGPAIRYDQNIIAKQ-EALLTDPTMREIYTLLSRS 248
Cdd:pfam10728  80 DNILELGPVAALTGPVARGDAGTVAKHlAALADDPELAELYRLLSRS 126
PRK11880 PRK11880
pyrroline-5-carboxylate reductase; Reviewed
1-87 1.43e-06

pyrroline-5-carboxylate reductase; Reviewed


Pssm-ID: 237008 [Multi-domain]  Cd Length: 267  Bit Score: 48.22  E-value: 1.43e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443764052   1 MKIILIGAGNLATRLALALQAKGLAPE--WVYSRTEESARRLSEQLpHSHYTTRLDSLPSDGDLYIFAVKDSVLPQLLSA 78
Cdd:PRK11880    3 KKIGFIGGGNMASAIIGGLLASGVPAKdiIVSDPSPEKRAALAEEY-GVRAATDNQEAAQEADVVVLAVKPQVMEEVLSE 81

                  ....*....
gi 2443764052  79 MPANAGLWV 87
Cdd:PRK11880   82 LKGQLDKLV 90
NAD_bind_Glutamyl_tRNA_reduct cd05213
NADP-binding domain of glutamyl-tRNA reductase; Glutamyl-tRNA reductase catalyzes the ...
2-45 2.85e-03

NADP-binding domain of glutamyl-tRNA reductase; Glutamyl-tRNA reductase catalyzes the conversion of glutamyl-tRNA to glutamate-1-semialdehyde, initiating the synthesis of tetrapyrrole. Whereas tRNAs are generally associated with peptide bond formation in protein translation, here the tRNA activates glutamate in the initiation of tetrapyrrole biosynthesis in archaea, plants and many bacteria. In the first step, activated glutamate is reduced to glutamate-1-semi-aldehyde via the NADPH dependent glutamyl-tRNA reductase. Glutamyl-tRNA reductase forms a V-shaped dimer. Each monomer has 3 domains: an N-terminal catalytic domain, a classic nucleotide binding domain, and a C-terminal dimerization domain. Although the representative structure 1GPJ lacks a bound NADPH, a theoretical binding pocket has been described. (PMID 11172694). Amino acid dehydrogenase (DH)-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts.


Pssm-ID: 133452 [Multi-domain]  Cd Length: 311  Bit Score: 38.40  E-value: 2.85e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2443764052   2 KIILIGAGNLATRLALALQAKGLAPEWVYSRTEESARRLSEQLP 45
Cdd:cd05213   180 KVLVIGAGEMGELAAKHLAAKGVAEITIANRTYERAEELAKELG 223
 
Name Accession Description Interval E-value
COG5495 COG5495
Predicted oxidoreductase, contains short-chain dehydrogenase (SDR) and DUF2520 domains ...
1-253 2.47e-99

Predicted oxidoreductase, contains short-chain dehydrogenase (SDR) and DUF2520 domains [General function prediction only];


Pssm-ID: 444246 [Multi-domain]  Cd Length: 286  Bit Score: 291.72  E-value: 2.47e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443764052   1 MKIILIGAGNLATRLALALQAKGLAPEWVYSRTEESARRLSEQLPHShYTTRLDSLPSDGDLYIFAVKDSVLPQLLSAMP 80
Cdd:COG5495     4 MKIGIIGAGRVGTALAAALRAAGHEVVGVYSRSPASAERAAALLGAV-PALDLEELAAEADLVLLAVPDDAIAEVAAGLA 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443764052  81 ANAG-----LWVHTAGSVDREVFRPYTNR---YGVFYPMQTFSKERAV--DFDDIPFFIEANsEADTARLHDLAARLSGK 150
Cdd:COG5495    83 AAGAlrpgqLVVHTSGALGSDVLAPAARAgalTGSFHPLQTFSGPREDleRLAGIPFAIEGD-EEALPVLEALAEALGGE 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443764052 151 VYRADSEQRKYLHLAAVFACNFTNHLYALCDRILQEHNL--PFEAMLPLIRETAAKVADMSPFDAQTGPAIRYDQNIIAK 228
Cdd:COG5495   162 PFVIDSEQRPLYHAAAVFASNFLVTLVALAAELLEAAGLedAFDALLPLIRETLDNILELGPAAALTGPAARGDAGTVAK 241
                         250       260
                  ....*....|....*....|....*..
gi 2443764052 229 QEALL--TDPTMREIYTLLSRSIHETH 253
Cdd:COG5495   242 HLAALaeLDPELAELYRALSRSTLELA 268
DUF2520 pfam10728
Domain of unknown function (DUF2520); This presumed domain is found C-terminal to a ...
125-248 7.95e-55

Domain of unknown function (DUF2520); This presumed domain is found C-terminal to a Rossmann-like domain suggesting that these proteins are oxidoreductases.


Pssm-ID: 463182  Cd Length: 126  Bit Score: 172.64  E-value: 7.95e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443764052 125 IPFFIEANSEAdTARLHDLAARLSGKVYRADSEQRKYLHLAAVFACNFTNHLYALCDRILQEHNLP--FEAMLPLIRETA 202
Cdd:pfam10728   1 IPFGIEGDEEA-LAVLEALAESLGGKVFEIDSEQRKLYHAAAVFASNFLVTLYALAAELLEEAGLPeaFEALLPLIRETL 79
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2443764052 203 AKVADMSPFDAQTGPAIRYDQNIIAKQ-EALLTDPTMREIYTLLSRS 248
Cdd:pfam10728  80 DNILELGPVAALTGPVARGDAGTVAKHlAALADDPELAELYRLLSRS 126
ProC COG0345
Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism]; ...
1-83 1.26e-08

Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism]; Pyrroline-5-carboxylate reductase is part of the Pathway/BioSystem: Proline biosynthesis


Pssm-ID: 440114 [Multi-domain]  Cd Length: 267  Bit Score: 54.30  E-value: 1.26e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443764052   1 MKIILIGAGNLATRLALALQAKGLAPE--WVYSRTEESARRLSEQLpHSHYTTRLDSLPSDGDLYIFAVK----DSVLPQ 74
Cdd:COG0345     3 MKIGFIGAGNMGSAIIKGLLKSGVPPEdiIVSDRSPERLEALAERY-GVRVTTDNAEAAAQADVVVLAVKpqdlAEVLEE 81

                  ....*....
gi 2443764052  75 LLSAMPANA 83
Cdd:COG0345    82 LAPLLDPDK 90
PRK11880 PRK11880
pyrroline-5-carboxylate reductase; Reviewed
1-87 1.43e-06

pyrroline-5-carboxylate reductase; Reviewed


Pssm-ID: 237008 [Multi-domain]  Cd Length: 267  Bit Score: 48.22  E-value: 1.43e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443764052   1 MKIILIGAGNLATRLALALQAKGLAPE--WVYSRTEESARRLSEQLpHSHYTTRLDSLPSDGDLYIFAVKDSVLPQLLSA 78
Cdd:PRK11880    3 KKIGFIGGGNMASAIIGGLLASGVPAKdiIVSDPSPEKRAALAEEY-GVRAATDNQEAAQEADVVVLAVKPQVMEEVLSE 81

                  ....*....
gi 2443764052  79 MPANAGLWV 87
Cdd:PRK11880   82 LKGQLDKLV 90
AspD COG1712
L-aspartate dehydrogenase, NAD(P)-dependent [Amino acid transport and metabolism];
1-78 2.14e-05

L-aspartate dehydrogenase, NAD(P)-dependent [Amino acid transport and metabolism];


Pssm-ID: 441318 [Multi-domain]  Cd Length: 263  Bit Score: 44.79  E-value: 2.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443764052   1 MKIILIGAGNLATRLALALQAKGLAPEWVYSRTEESARRLSEQLPHSHYTTRLDSLPSDGDLYI-----FAVKDSVlPQL 75
Cdd:COG1712     1 MRIGLIGCGAIGSEVAEALADAGVELVAVYDRDPERAEALLASLGARVVSDVDELLAADPDLVVeaasqAAVREHG-PAV 79

                  ...
gi 2443764052  76 LSA 78
Cdd:COG1712    80 LEA 82
F420_oxidored pfam03807
NADP oxidoreductase coenzyme F420-dependent;
6-80 1.19e-04

NADP oxidoreductase coenzyme F420-dependent;


Pssm-ID: 397743 [Multi-domain]  Cd Length: 92  Bit Score: 39.91  E-value: 1.19e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2443764052   6 IGAGNLATRLALALQAKGlaPEWVY---SRTEESARRLSEQLPHSHYTTRLDSLPSDGDLYIFAVKDSVLPQLLSAMP 80
Cdd:pfam03807   3 IGAGNMGEALARGLVAAG--PHEVVvanSRNPEKAEELAEEYGVGATAVDNEEAAEEADVVFLAVKPEDAPDVLSELS 78
PLN02688 PLN02688
pyrroline-5-carboxylate reductase
1-82 2.32e-04

pyrroline-5-carboxylate reductase


Pssm-ID: 178291 [Multi-domain]  Cd Length: 266  Bit Score: 41.48  E-value: 2.32e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443764052   1 MKIILIGAGNLATRLALALQAKGLAP--EWVYSRTEESARRLSEQLPHSHYTTRLDSLPSDGDLYIFAVKDSVLPQLLSA 78
Cdd:PLN02688    1 FRVGFIGAGKMAEAIARGLVASGVVPpsRISTADDSNPARRDVFQSLGVKTAASNTEVVKSSDVIILAVKPQVVKDVLTE 80

                  ....
gi 2443764052  79 MPAN 82
Cdd:PLN02688   81 LRPL 84
Rossmann-like pfam10727
Rossmann-like domain; This family of proteins contain a Rossmann-like domain.
5-104 4.58e-04

Rossmann-like domain; This family of proteins contain a Rossmann-like domain.


Pssm-ID: 287672 [Multi-domain]  Cd Length: 127  Bit Score: 39.07  E-value: 4.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2443764052   5 LIGAGNLATRLALALQAKGLAPEWVYSRTEESARRLSEQLPHSHYTTRLDSLpSDGDLYIFAVKDSVLPQLLSAMpANAG 84
Cdd:pfam10727  15 IISAGRVGTALGAALERAGHVVVGISAISAASRERAERRLPDTPVLPVPDVA-ARAELLLLAVPDAELPGLVEGL-AATG 92
                          90       100
                  ....*....|....*....|....*.
gi 2443764052  85 LW------VHTAGSVDREVFRPYTNR 104
Cdd:pfam10727  93 AVragtivAHTSGANGVGILAPLTEQ 118
Shikimate_DH pfam01488
Shikimate / quinate 5-dehydrogenase; This family contains both shikimate and quinate ...
2-58 1.04e-03

Shikimate / quinate 5-dehydrogenase; This family contains both shikimate and quinate dehydrogenases. Shikimate 5-dehydrogenase catalyzes the conversion of shikimate to 5-dehydroshikimate. This reaction is part of the shikimate pathway which is involved in the biosynthesis of aromatic amino acids. Quinate 5-dehydrogenase catalyzes the conversion of quinate to 5-dehydroquinate. This reaction is part of the quinate pathway where quinic acid is exploited as a source of carbon in prokaryotes and microbial eukaryotes. Both the shikimate and quinate pathways share two common pathway metabolites 3-dehydroquinate and dehydroshikimate.


Pssm-ID: 460229 [Multi-domain]  Cd Length: 136  Bit Score: 38.32  E-value: 1.04e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2443764052   2 KIILIGAGNLATRLALALQAKGLAPEWVYSRTEESARRLSEQLPHSHYTTrLDSLPS 58
Cdd:pfam01488  14 KVLLIGAGEMGELVAKHLLAKGAKEVTIANRTIERAQELAEKFGGVEALP-LDDLKE 69
NAD_bind_Glutamyl_tRNA_reduct cd05213
NADP-binding domain of glutamyl-tRNA reductase; Glutamyl-tRNA reductase catalyzes the ...
2-45 2.85e-03

NADP-binding domain of glutamyl-tRNA reductase; Glutamyl-tRNA reductase catalyzes the conversion of glutamyl-tRNA to glutamate-1-semialdehyde, initiating the synthesis of tetrapyrrole. Whereas tRNAs are generally associated with peptide bond formation in protein translation, here the tRNA activates glutamate in the initiation of tetrapyrrole biosynthesis in archaea, plants and many bacteria. In the first step, activated glutamate is reduced to glutamate-1-semi-aldehyde via the NADPH dependent glutamyl-tRNA reductase. Glutamyl-tRNA reductase forms a V-shaped dimer. Each monomer has 3 domains: an N-terminal catalytic domain, a classic nucleotide binding domain, and a C-terminal dimerization domain. Although the representative structure 1GPJ lacks a bound NADPH, a theoretical binding pocket has been described. (PMID 11172694). Amino acid dehydrogenase (DH)-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts.


Pssm-ID: 133452 [Multi-domain]  Cd Length: 311  Bit Score: 38.40  E-value: 2.85e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2443764052   2 KIILIGAGNLATRLALALQAKGLAPEWVYSRTEESARRLSEQLP 45
Cdd:cd05213   180 KVLVIGAGEMGELAAKHLAAKGVAEITIANRTYERAEELAKELG 223
hemA PRK00045
glutamyl-tRNA reductase; Reviewed
2-58 4.40e-03

glutamyl-tRNA reductase; Reviewed


Pssm-ID: 234592 [Multi-domain]  Cd Length: 423  Bit Score: 37.86  E-value: 4.40e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2443764052   2 KIILIGAGNLATRLALALQAKGLAPEWVYSRTEESARRLSEQLPHShyTTRLDSLPS 58
Cdd:PRK00045  184 KVLVIGAGEMGELVAKHLAEKGVRKITVANRTLERAEELAEEFGGE--AIPLDELPE 238
 
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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