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Database: UniProt
Entry: Q9NR12
LinkDB: Q9NR12
Original site: Q9NR12 
ID   PDLI7_HUMAN             Reviewed;         457 AA.
AC   Q9NR12; Q14250; Q5XG82; Q6NVZ5; Q96C91; Q9BXB8; Q9BXB9;
DT   06-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2000, sequence version 1.
DT   26-NOV-2014, entry version 123.
DE   RecName: Full=PDZ and LIM domain protein 7;
DE   AltName: Full=LIM mineralization protein;
DE            Short=LMP;
DE   AltName: Full=Protein enigma;
GN   Name=PDLIM7; Synonyms=ENIGMA;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC   Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND INTERACTION WITH
RP   INSR.
RX   PubMed=7929196;
RA   Wu R.-Y., Gill G.N.;
RT   "LIM domain recognition of a tyrosine-containing tight turn.";
RL   J. Biol. Chem. 269:25085-25090(1994).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2 AND 3), FUNCTION, TISSUE
RP   SPECIFICITY, AND ALTERNATIVE SPLICING.
RC   TISSUE=Heart;
RX   PubMed=11874232; DOI=10.1359/jbmr.2002.17.3.406;
RA   Liu Y., Hair G.A., Boden S.D., Viggeswarapu M., Titus L.;
RT   "Overexpressed LIM mineralization proteins do not require LIM domains
RT   to induce bone.";
RL   J. Bone Miner. Res. 17:406-414(2002).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RC   TISSUE=Neuroepithelium;
RA   Borrello M.G., Billaud M., Mercalli E., Ghizzoni S., Bidaud C.;
RT   "Enigma sequence and interaction with Ret.";
RL   Submitted (MAY-2000) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 4; 5 AND 6).
RC   TISSUE=Brain, Kidney, Mammary gland, and Uterus;
RX   PubMed=15489334; DOI=10.1101/gr.2596504;
RG   The MGC Project Team;
RT   "The status, quality, and expansion of the NIH full-length cDNA
RT   project: the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
RN   [5]
RP   PROTEIN SEQUENCE OF 6-17; 94-103 AND 246-258, AND IDENTIFICATION BY
RP   MASS SPECTROMETRY.
RC   TISSUE=Platelet;
RA   Bienvenut W.V., Claeys D.;
RL   Submitted (NOV-2005) to UniProtKB.
RN   [6]
RP   INTERACTION WITH PKC.
RX   PubMed=8940095; DOI=10.1074/jbc.271.49.31029;
RA   Kuroda S., Tokunaga C., Kiyohara Y., Higuchi O., Konishi H.,
RA   Mizuno K., Gill G.N., Kikkawa U.;
RT   "Protein-protein interaction of zinc finger LIM domains with protein
RT   kinase C.";
RL   J. Biol. Chem. 271:31029-31032(1996).
RN   [7]
RP   SUBCELLULAR LOCATION, AND INTERACTION WITH RET AND SHC1.
RX   PubMed=9528800;
RA   Durick K., Gill G.N., Taylor S.S.;
RT   "Shc and Enigma are both required for mitogenic signaling by
RT   Ret/ptc2.";
RL   Mol. Cell. Biol. 18:2298-2308(1998).
RN   [8]
RP   INTERACTION WITH TPM2, AND MUTAGENESIS OF 15-GLY-PHE-16 AND HIS-63.
RX   PubMed=10359609; DOI=10.1091/mbc.10.6.1973;
RA   Guy P.M., Kenny D.A., Gill G.N.;
RT   "The PDZ domain of the LIM protein enigma binds to beta-tropomyosin.";
RL   Mol. Biol. Cell 10:1973-1984(1999).
RN   [9]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-247, AND IDENTIFICATION
RP   BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   TISSUE=Cervix carcinoma;
RX   PubMed=18669648; DOI=10.1073/pnas.0805139105;
RA   Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
RA   Elledge S.J., Gygi S.P.;
RT   "A quantitative atlas of mitotic phosphorylation.";
RL   Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
RN   [10]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   TISSUE=Cervix carcinoma;
RX   PubMed=20068231; DOI=10.1126/scisignal.2000475;
RA   Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
RA   Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S.,
RA   Mann M.;
RT   "Quantitative phosphoproteomics reveals widespread full
RT   phosphorylation site occupancy during mitosis.";
RL   Sci. Signal. 3:RA3-RA3(2010).
RN   [11]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA   Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
RA   Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
RT   "Initial characterization of the human central proteome.";
RL   BMC Syst. Biol. 5:17-17(2011).
RN   [12]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA   Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA   Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E.,
RA   Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K.,
RA   Aldabe R.;
RT   "N-terminal acetylome analyses and functional insights of the N-
RT   terminal acetyltransferase NatB.";
RL   Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN   [13]
RP   X-RAY CRYSTALLOGRAPHY (1.11 ANGSTROMS) OF 1-84.
RG   Structural genomics consortium (SGC);
RT   "Structure of the PDZ domain of human PDLIM7 bound to a C-terminal
RT   extension from human beta-tropomyosin.";
RL   Submitted (FEB-2009) to the PDB data bank.
RN   [14]
RP   VARIANT [LARGE SCALE ANALYSIS] ASN-450.
RX   PubMed=16959974; DOI=10.1126/science.1133427;
RA   Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D.,
RA   Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S.,
RA   Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J.,
RA   Dawson D., Willson J.K.V., Gazdar A.F., Hartigan J., Wu L., Liu C.,
RA   Parmigiani G., Park B.H., Bachman K.E., Papadopoulos N.,
RA   Vogelstein B., Kinzler K.W., Velculescu V.E.;
RT   "The consensus coding sequences of human breast and colorectal
RT   cancers.";
RL   Science 314:268-274(2006).
CC   -!- FUNCTION: May function as a scaffold on which the coordinated
CC       assembly of proteins can occur. May play a role as an adapter
CC       that, via its PDZ domain, localizes LIM-binding proteins to actin
CC       filaments of both skeletal muscle and nonmuscle tissues. Involved
CC       in both of the two fundamental mechanisms of bone formation,
CC       direct bone formation (e.g. embryonic flat bones mandible and
CC       cranium), and endochondral bone formation (e.g. embryonic long
CC       bone development). Plays a role during fracture repair. Involved
CC       in BMP6 signaling pathway (By similarity). {ECO:0000250}.
CC   -!- SUBUNIT: Binds via its LIM zinc-binding 3 domain (LIM 3) to
CC       endocytic codes of INSR, but not with those of IGF1R, LDLR, TFRC,
CC       or EGFR. Interacts with various PKC isoforms through the LIM zinc-
CC       binding domains. Binds to RET in a phosphorylation-independent
CC       manner via its LIM zinc-binding domain 2 (LIM 2). Probably part of
CC       a complex with SHC and the RET dimer. Interacts with TPM2.
CC       Interacts with TBX4 and TBX5 (By similarity). {ECO:0000250}.
CC   -!- INTERACTION:
CC       P09022:Hoxa1 (xeno); NbExp=3; IntAct=EBI-350517, EBI-3957603;
CC       Q9NRR5:UBQLN4; NbExp=2; IntAct=EBI-350517, EBI-711226;
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}. Cytoplasm,
CC       cytoskeleton {ECO:0000250}. Note=Colocalizes with RET to the cell
CC       periphery and in some cytoskeletal components. Colocalizes with
CC       TPM2 near the Z line in muscle. Colocalizes with TBX4 and TBX5 to
CC       actin filaments (By similarity). {ECO:0000250}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=6;
CC       Name=1; Synonyms=LMP-1;
CC         IsoId=Q9NR12-1; Sequence=Displayed;
CC       Name=2; Synonyms=LMP-2;
CC         IsoId=Q9NR12-2; Sequence=VSP_016509;
CC         Note=Did not induce bone induction.;
CC       Name=3; Synonyms=LMP-3;
CC         IsoId=Q9NR12-3; Sequence=VSP_016510, VSP_016513;
CC         Note=Same activity as isoform 1 in bone nodule induction.;
CC       Name=4;
CC         IsoId=Q9NR12-4; Sequence=VSP_016511, VSP_016516;
CC         Note=No experimental confirmation available.;
CC       Name=5;
CC         IsoId=Q9NR12-5; Sequence=VSP_016514;
CC         Note=May be produced at very low levels due to a premature stop
CC         codon in the mRNA, leading to nonsense-mediated mRNA decay. No
CC         experimental confirmation available.;
CC       Name=6;
CC         IsoId=Q9NR12-6; Sequence=VSP_016512, VSP_016515;
CC         Note=No experimental confirmation available.;
CC   -!- TISSUE SPECIFICITY: Isoform 1 and isoform 2 are expressed
CC       ubiquitously, however, isoform 2 predominates in skeletal muscle,
CC       isoform 1 is more abundant in lung, spleen, leukocytes and fetal
CC       liver. {ECO:0000269|PubMed:11874232}.
CC   -!- DOMAIN: The LIM zinc-binding 2 (LIM 2) domain interacts with TBX4.
CC       {ECO:0000250}.
CC   -!- DOMAIN: The LIM zinc-binding 3 (LIM 3) domain provides the
CC       structural basis for recognition of tyrosine-containing tight turn
CC       structures. This domain is necessary and sufficient for
CC       interaction with TBX5 (By similarity). {ECO:0000250}.
CC   -!- DOMAIN: Anchored to cell periphery via its N-terminal PDZ domain.
CC   -!- SIMILARITY: Contains 3 LIM zinc-binding domains.
CC       {ECO:0000255|PROSITE-ProRule:PRU00125}.
CC   -!- SIMILARITY: Contains 1 PDZ (DHR) domain. {ECO:0000255|PROSITE-
CC       ProRule:PRU00143}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAC37565.1; Type=Frameshift; Positions=103, 128, 161, 183, 195, 245; Evidence={ECO:0000305};
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DR   EMBL; L35240; AAC37565.1; ALT_FRAME; Genomic_DNA.
DR   EMBL; AF345904; AAK30567.1; -; mRNA.
DR   EMBL; AF345905; AAK30568.1; -; mRNA.
DR   EMBL; AF345906; AAK30569.1; -; mRNA.
DR   EMBL; AF265209; AAF76152.1; -; mRNA.
DR   EMBL; BC001093; AAH01093.1; -; mRNA.
DR   EMBL; BC014521; AAH14521.1; -; mRNA.
DR   EMBL; BC067806; -; NOT_ANNOTATED_CDS; mRNA.
DR   EMBL; BC084575; AAH84575.1; -; mRNA.
DR   CCDS; CCDS4422.1; -. [Q9NR12-1]
DR   CCDS; CCDS4423.1; -. [Q9NR12-2]
DR   CCDS; CCDS4424.1; -. [Q9NR12-6]
DR   PIR; A55050; A55050.
DR   RefSeq; NP_005442.2; NM_005451.4. [Q9NR12-1]
DR   RefSeq; NP_976227.1; NM_203352.2. [Q9NR12-2]
DR   RefSeq; NP_998801.1; NM_213636.2. [Q9NR12-6]
DR   UniGene; Hs.533040; -.
DR   UniGene; Hs.736984; -.
DR   PDB; 2Q3G; X-ray; 1.11 A; A/B=1-84.
DR   PDBsum; 2Q3G; -.
DR   ProteinModelPortal; Q9NR12; -.
DR   SMR; Q9NR12; 1-84, 278-451.
DR   BioGrid; 114682; 49.
DR   IntAct; Q9NR12; 27.
DR   MINT; MINT-94304; -.
DR   STRING; 9606.ENSP00000348099; -.
DR   PhosphoSite; Q9NR12; -.
DR   DMDM; 74752914; -.
DR   MaxQB; Q9NR12; -.
DR   PaxDb; Q9NR12; -.
DR   PRIDE; Q9NR12; -.
DR   DNASU; 9260; -.
DR   Ensembl; ENST00000355572; ENSP00000347776; ENSG00000196923. [Q9NR12-6]
DR   Ensembl; ENST00000355841; ENSP00000348099; ENSG00000196923. [Q9NR12-1]
DR   Ensembl; ENST00000359895; ENSP00000352964; ENSG00000196923. [Q9NR12-2]
DR   Ensembl; ENST00000393551; ENSP00000377182; ENSG00000196923. [Q9NR12-4]
DR   Ensembl; ENST00000486828; ENSP00000439157; ENSG00000196923. [Q9NR12-5]
DR   Ensembl; ENST00000493815; ENSP00000431236; ENSG00000196923. [Q9NR12-3]
DR   GeneID; 9260; -.
DR   KEGG; hsa:9260; -.
DR   UCSC; uc003mha.1; human. [Q9NR12-1]
DR   UCSC; uc003mhb.1; human. [Q9NR12-2]
DR   UCSC; uc003mhf.3; human. [Q9NR12-4]
DR   UCSC; uc003mhg.1; human. [Q9NR12-6]
DR   CTD; 9260; -.
DR   GeneCards; GC05M176912; -.
DR   HGNC; HGNC:22958; PDLIM7.
DR   HPA; HPA018794; -.
DR   HPA; HPA048815; -.
DR   MIM; 605903; gene.
DR   neXtProt; NX_Q9NR12; -.
DR   PharmGKB; PA128394546; -.
DR   eggNOG; NOG286537; -.
DR   GeneTree; ENSGT00760000118910; -.
DR   HOVERGEN; HBG051478; -.
DR   InParanoid; Q9NR12; -.
DR   OMA; WPGPTAP; -.
DR   OrthoDB; EOG7HXCQB; -.
DR   PhylomeDB; Q9NR12; -.
DR   TreeFam; TF106408; -.
DR   ChiTaRS; PDLIM7; human.
DR   EvolutionaryTrace; Q9NR12; -.
DR   GeneWiki; PDLIM7; -.
DR   GenomeRNAi; 9260; -.
DR   NextBio; 34707; -.
DR   PRO; PR:Q9NR12; -.
DR   Bgee; Q9NR12; -.
DR   CleanEx; HS_PDLIM7; -.
DR   ExpressionAtlas; Q9NR12; baseline and differential.
DR   Genevestigator; Q9NR12; -.
DR   GO; GO:0015629; C:actin cytoskeleton; IDA:HPA.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-KW.
DR   GO; GO:0005925; C:focal adhesion; IDA:HPA.
DR   GO; GO:0005634; C:nucleus; IDA:HPA.
DR   GO; GO:0001726; C:ruffle; IEA:Ensembl.
DR   GO; GO:0001725; C:stress fiber; IEA:Ensembl.
DR   GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR   GO; GO:0030036; P:actin cytoskeleton organization; IEA:Ensembl.
DR   GO; GO:0030154; P:cell differentiation; IEA:UniProtKB-KW.
DR   GO; GO:0007275; P:multicellular organismal development; IEA:UniProtKB-KW.
DR   GO; GO:0001503; P:ossification; IEA:UniProtKB-KW.
DR   GO; GO:0045669; P:positive regulation of osteoblast differentiation; IEA:Ensembl.
DR   GO; GO:0006898; P:receptor-mediated endocytosis; TAS:ProtInc.
DR   Gene3D; 2.10.110.10; -; 3.
DR   Gene3D; 2.30.42.10; -; 1.
DR   InterPro; IPR001478; PDZ.
DR   InterPro; IPR001781; Znf_LIM.
DR   Pfam; PF00412; LIM; 3.
DR   Pfam; PF00595; PDZ; 1.
DR   SMART; SM00132; LIM; 3.
DR   SMART; SM00228; PDZ; 1.
DR   SUPFAM; SSF50156; SSF50156; 1.
DR   PROSITE; PS00478; LIM_DOMAIN_1; 2.
DR   PROSITE; PS50023; LIM_DOMAIN_2; 3.
DR   PROSITE; PS50106; PDZ; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Alternative splicing; Complete proteome; Cytoplasm;
KW   Cytoskeleton; Developmental protein; Differentiation;
KW   Direct protein sequencing; LIM domain; Metal-binding; Osteogenesis;
KW   Phosphoprotein; Polymorphism; Reference proteome; Repeat; Zinc.
FT   CHAIN         1    457       PDZ and LIM domain protein 7.
FT                                /FTId=PRO_0000075881.
FT   DOMAIN        1     85       PDZ. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00143}.
FT   DOMAIN      280    338       LIM zinc-binding 1. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00125}.
FT   DOMAIN      339    398       LIM zinc-binding 2. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00125}.
FT   DOMAIN      399    457       LIM zinc-binding 3. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00125}.
FT   MOD_RES     247    247       Phosphoserine.
FT                                {ECO:0000269|PubMed:18669648}.
FT   VAR_SEQ      94    133       ASAPAADPPRYTFAPSVSLNKTARPFGAPPPADSAPQQNG
FT                                -> VQTPDK (in isoform 2).
FT                                {ECO:0000303|PubMed:11874232}.
FT                                /FTId=VSP_016509.
FT   VAR_SEQ     134    153       QPLRPLVPDASKQRLMENTE -> CRPLTNSRSDRWSQMPA
FT                                SSG (in isoform 3).
FT                                {ECO:0000303|PubMed:11874232}.
FT                                /FTId=VSP_016510.
FT   VAR_SEQ     154    457       Missing (in isoform 3).
FT                                {ECO:0000303|PubMed:11874232}.
FT                                /FTId=VSP_016513.
FT   VAR_SEQ     191    287       SQVPRTEAPAPASSTPQEPWPGPTAPSPTSRPPWAVDPAFA
FT                                ERYAPDKTSTVLTRHSQPATPTPLQSRTSIVQAAAGGVPGG
FT                                GSNNGKTPVCHQCHK -> RPYRPQPYQPPALGCGPCVCRA
FT                                LCPGQNEHSADPAQPAGHAHAAAEPHLHCAGSCRRGARRGQ
FT                                QQRQDSRVSPVPQGHPGPLPGGAGPRVPPGGVCV (in
FT                                isoform 4).
FT                                {ECO:0000303|PubMed:15489334}.
FT                                /FTId=VSP_016511.
FT   VAR_SEQ     191    222       SQVPRTEAPAPASSTPQEPWPGPTAPSPTSRP -> REKYV
FT                                LELQSPRYTRLRDWHHQRSAHVLNVQS (in isoform
FT                                6). {ECO:0000303|PubMed:15489334}.
FT                                /FTId=VSP_016512.
FT   VAR_SEQ     192    457       Missing (in isoform 5).
FT                                {ECO:0000303|PubMed:15489334}.
FT                                /FTId=VSP_016514.
FT   VAR_SEQ     223    457       Missing (in isoform 6).
FT                                {ECO:0000303|PubMed:15489334}.
FT                                /FTId=VSP_016515.
FT   VAR_SEQ     288    457       Missing (in isoform 4).
FT                                {ECO:0000303|PubMed:15489334}.
FT                                /FTId=VSP_016516.
FT   VARIANT     326    326       A -> T (in dbSNP:rs2306764).
FT                                /FTId=VAR_050168.
FT   VARIANT     450    450       K -> N (in a breast cancer sample;
FT                                somatic mutation).
FT                                {ECO:0000269|PubMed:16959974}.
FT                                /FTId=VAR_036193.
FT   MUTAGEN      15     16       GF->AA: Loss of binding to TPM2.
FT                                {ECO:0000269|PubMed:10359609}.
FT   MUTAGEN      63     63       H->A: Loss of binding to TPM2.
FT                                {ECO:0000269|PubMed:10359609}.
FT   CONFLICT    138    138       P -> Q (in Ref. 4; BC067806).
FT                                {ECO:0000305}.
FT   STRAND        1     12       {ECO:0000244|PDB:2Q3G}.
FT   STRAND       16     21       {ECO:0000244|PDB:2Q3G}.
FT   HELIX        22     24       {ECO:0000244|PDB:2Q3G}.
FT   STRAND       26     33       {ECO:0000244|PDB:2Q3G}.
FT   HELIX        38     41       {ECO:0000244|PDB:2Q3G}.
FT   STRAND       49     53       {ECO:0000244|PDB:2Q3G}.
FT   HELIX        58     60       {ECO:0000244|PDB:2Q3G}.
FT   HELIX        63     71       {ECO:0000244|PDB:2Q3G}.
FT   STRAND       76     84       {ECO:0000244|PDB:2Q3G}.
SQ   SEQUENCE   457 AA;  49845 MW;  AA37F9E8E987D990 CRC64;
     MDSFKVVLEG PAPWGFRLQG GKDFNVPLSI SRLTPGGKAA QAGVAVGDWV LSIDGENAGS
     LTHIEAQNKI RACGERLSLG LSRAQPVQSK PQKASAPAAD PPRYTFAPSV SLNKTARPFG
     APPPADSAPQ QNGQPLRPLV PDASKQRLME NTEDWRPRPG TGQSRSFRIL AHLTGTEFMQ
     DPDEEHLKKS SQVPRTEAPA PASSTPQEPW PGPTAPSPTS RPPWAVDPAF AERYAPDKTS
     TVLTRHSQPA TPTPLQSRTS IVQAAAGGVP GGGSNNGKTP VCHQCHKVIR GRYLVALGHA
     YHPEEFVCSQ CGKVLEEGGF FEEKGAIFCP PCYDVRYAPS CAKCKKKITG EIMHALKMTW
     HVHCFTCAAC KTPIRNRAFY MEEGVPYCER DYEKMFGTKC HGCDFKIDAG DRFLEALGFS
     WHDTCFVCAI CQINLEGKTF YSKKDRPLCK SHAFSHV
//
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