LDCI_ECOLI
ID LDCI_ECOLI Reviewed; 715 AA.
AC P0A9H3; P23892; Q2M6H2;
DT 19-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2005, sequence version 1.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=Inducible lysine decarboxylase {ECO:0000303|PubMed:4590109};
DE Short=LDCI;
DE EC=4.1.1.18 {ECO:0000269|PubMed:4590109};
GN Name=cadA; Synonyms=ldcI; OrderedLocusNames=b4131, JW4092;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1556085; DOI=10.1128/jb.174.8.2659-2669.1992;
RA Meng S.-Y., Bennett G.N.;
RT "Nucleotide sequence of the Escherichia coli cad operon: a system for
RT neutralization of low extracellular pH.";
RL J. Bacteriol. 174:2659-2669(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=7610040; DOI=10.1093/nar/23.12.2105;
RA Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.;
RT "Analysis of the Escherichia coli genome VI: DNA sequence of the region
RT from 92.8 through 100 minutes.";
RL Nucleic Acids Res. 23:2105-2119(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-280, AND INDUCTION.
RC STRAIN=JLS821;
RX PubMed=1370290; DOI=10.1128/jb.174.2.530-540.1992;
RA Watson N., Dunyak D.S., Rosey E.L., Slonczewski J.L., Olson E.R.;
RT "Identification of elements involved in transcriptional regulation of the
RT Escherichia coli cad operon by external pH.";
RL J. Bacteriol. 174:530-540(1992).
RN [6]
RP PROTEIN SEQUENCE OF 1-7 AND 358-372, AND PYRIDOXAL PHOSPHATE AT LYS-367.
RX PubMed=4204273; DOI=10.1021/bi00701a006;
RA Sabo D.L., Fischer E.H.;
RT "Chemical properties of Escherichia coli lysine decarboxylase including a
RT segment of its pyridoxal 5'-phosphate binding site.";
RL Biochemistry 13:670-676(1974).
RN [7]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 358-372.
RC STRAIN=K12;
RX PubMed=2527331; DOI=10.1111/j.1365-2958.1989.tb00208.x;
RA Auger E.A., Redding K.E., Plumb T., Childs L.C., Meng S.Y., Bennett G.N.;
RT "Construction of lac fusions to the inducible arginine- and lysine
RT decarboxylase genes of Escherichia coli K12.";
RL Mol. Microbiol. 3:609-620(1989).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, AND SUBUNIT.
RX PubMed=4590109; DOI=10.1021/bi00701a005;
RA Sabo D.L., Boeker E.A., Byers B., Waron H., Fischer E.H.;
RT "Purification and physical properties of inducible Escherichia coli lysine
RT decarboxylase.";
RL Biochemistry 13:662-670(1974).
RN [9]
RP INDUCTION BY CADC.
RX PubMed=8808945; DOI=10.1128/jb.178.18.5522-5528.1996;
RA Neely M.N., Olson E.R.;
RT "Kinetics of expression of the Escherichia coli cad operon as a function of
RT pH and lysine.";
RL J. Bacteriol. 178:5522-5528(1996).
RN [10]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [11]
RP INDUCTION.
RX PubMed=16491024; DOI=10.1159/000090346;
RA Kuper C., Jung K.;
RT "CadC-mediated activation of the cadBA promoter in Escherichia coli.";
RL J. Mol. Microbiol. Biotechnol. 10:26-39(2005).
RN [12]
RP SUBUNIT, AND INTERACTION WITH RAVA.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=16301313; DOI=10.1074/jbc.m511172200;
RA Snider J., Gutsche I., Lin M., Baby S., Cox B., Butland G., Greenblatt J.,
RA Emili A., Houry W.A.;
RT "Formation of a distinctive complex between the inducible bacterial lysine
RT decarboxylase and a novel AAA+ ATPase.";
RL J. Biol. Chem. 281:1532-1546(2006).
RN [13]
RP FUNCTION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=17209032; DOI=10.1128/jb.01306-06;
RA Moreau P.L.;
RT "The lysine decarboxylase CadA protects Escherichia coli starved of
RT phosphate against fermentation acids.";
RL J. Bacteriol. 189:2249-2261(2007).
RN [14]
RP TRANSCRIPTIONAL REGULATION BY LRP.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=21441513; DOI=10.1128/jb.00815-10;
RA Ruiz J., Haneburger I., Jung K.;
RT "Identification of ArgP and Lrp as transcriptional regulators of lysP, the
RT gene encoding the specific lysine permease of Escherichia coli.";
RL J. Bacteriol. 193:2536-2548(2011).
RN [15]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS), SUBUNIT, AND ACTIVITY REGULATION.
RX PubMed=21278708; DOI=10.1038/emboj.2011.5;
RA Kanjee U., Gutsche I., Alexopoulos E., Zhao B., El Bakkouri M.,
RA Thibault G., Liu K., Ramachandran S., Snider J., Pai E.F., Houry W.A.;
RT "Linkage between the bacterial acid stress and stringent responses: the
RT structure of the inducible lysine decarboxylase.";
RL EMBO J. 30:931-944(2011).
RN [16]
RP STRUCTURE BY ELECTRON MICROSCOPY (7.50 ANGSTROMS), SUBUNIT, AND INTERACTION
RP WITH RAVA.
RX PubMed=25097238; DOI=10.7554/elife.03653;
RA Malet H., Liu K., El Bakkouri M., Chan S.W., Effantin G., Bacia M.,
RA Houry W.A., Gutsche I.;
RT "Assembly principles of a unique cage formed by hexameric and decameric E.
RT coli proteins.";
RL Elife 3:E03653-E03653(2014).
RN [17]
RP STRUCTURE BY ELECTRON MICROSCOPY (6.10 ANGSTROMS) OF 1-711, SUBUNIT, AND
RP INTERACTION WITH RAVA.
RX PubMed=27080013; DOI=10.1038/srep24601;
RA Kandiah E., Carriel D., Perard J., Malet H., Bacia M., Liu K., Chan S.W.,
RA Houry W.A., Ollagnier de Choudens S., Elsen S., Gutsche I.;
RT "Structural insights into the Escherichia coli lysine decarboxylases and
RT molecular determinants of interaction with the AAA+ ATPase RavA.";
RL Sci. Rep. 6:24601-24601(2016).
CC -!- FUNCTION: Inducible lysine decarboxylase that catalyzes the proton-
CC dependent decarboxylation of L-lysine to produce the polyamine
CC cadaverine and carbon dioxide (PubMed:4590109). Plays a role in pH
CC homeostasis by consuming protons and neutralizing the acidic by-
CC products of carbohydrate fermentation (PubMed:17209032).
CC {ECO:0000269|PubMed:17209032, ECO:0000269|PubMed:4590109}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + L-lysine = cadaverine + CO2; Xref=Rhea:RHEA:22352,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:32551,
CC ChEBI:CHEBI:58384; EC=4.1.1.18;
CC Evidence={ECO:0000269|PubMed:4590109};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC -!- ACTIVITY REGULATION: Inhibited by ppGpp, also known as the alarmone.
CC {ECO:0000269|PubMed:21278708}.
CC -!- SUBUNIT: Homodecamer; built of five dimers associated in a 5-fold
CC symmetrical double-ring (PubMed:27080013, PubMed:16301313,
CC PubMed:4590109, PubMed:21278708, PubMed:25097238). Interacts (via C-
CC terminus) with RavA (PubMed:16301313, PubMed:25097238,
CC PubMed:27080013). {ECO:0000269|PubMed:16301313,
CC ECO:0000269|PubMed:21278708, ECO:0000269|PubMed:25097238,
CC ECO:0000269|PubMed:27080013, ECO:0000269|PubMed:4590109}.
CC -!- INTERACTION:
CC P0A9H3; P0A9H3: cadA; NbExp=8; IntAct=EBI-545922, EBI-545922;
CC P0A9H3; P52095: ldcC; NbExp=5; IntAct=EBI-545922, EBI-545944;
CC P0A9H3; P31473: ravA; NbExp=13; IntAct=EBI-545922, EBI-561223;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- INDUCTION: Part of the cadB-cadA operon, which is under the control of
CC the Pcad promoter (PubMed:16491024). Expression is regulated by CadC
CC (PubMed:1370290, PubMed:8808945, PubMed:16491024). Induction occurs
CC under conditions of low pH with excess lysine and anaerobiosis
CC (PubMed:1370290, PubMed:8808945, PubMed:16491024). The global regulator
CC Lrp has also a positive effect on the expression of the cadBA operon
CC when cells are exposed to moderate acidic stress in the presence of
CC lysine (PubMed:21441513). Repressed by H-NS under non-inducing
CC conditions (PubMed:16491024). {ECO:0000269|PubMed:1370290,
CC ECO:0000269|PubMed:16491024, ECO:0000269|PubMed:21441513,
CC ECO:0000269|PubMed:8808945}.
CC -!- SIMILARITY: Belongs to the Orn/Lys/Arg decarboxylase class-I family.
CC {ECO:0000305}.
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DR EMBL; M76411; AAA23536.1; -; Genomic_DNA.
DR EMBL; U14003; AAA97031.1; -; Genomic_DNA.
DR EMBL; U00096; AAC77092.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78134.1; -; Genomic_DNA.
DR EMBL; M67452; AAA23533.1; -; Genomic_DNA.
DR PIR; B41842; B41842.
DR RefSeq; NP_418555.1; NC_000913.3.
DR RefSeq; WP_001295383.1; NZ_STEB01000014.1.
DR PDB; 3N75; X-ray; 2.00 A; A/B/C/D/E=1-715.
DR PDB; 3Q16; X-ray; 4.10 A; A/B/C/D/E=1-715.
DR PDB; 4UPB; EM; 11.00 A; A/B=1-715.
DR PDB; 4UPF; EM; 7.50 A; A=1-715.
DR PDB; 5FKX; EM; 6.10 A; A=1-711.
DR PDB; 5FL2; EM; 6.20 A; A=1-711.
DR PDB; 6YN5; EM; 2.70 A; A/B/C/D/E/F/G/H/I/J=1-711.
DR PDB; 6YN6; EM; 3.28 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T=1-711.
DR PDBsum; 3N75; -.
DR PDBsum; 3Q16; -.
DR PDBsum; 4UPB; -.
DR PDBsum; 4UPF; -.
DR PDBsum; 5FKX; -.
DR PDBsum; 5FL2; -.
DR PDBsum; 6YN5; -.
DR PDBsum; 6YN6; -.
DR AlphaFoldDB; P0A9H3; -.
DR SMR; P0A9H3; -.
DR BioGRID; 4260777; 2.
DR DIP; DIP-35646N; -.
DR IntAct; P0A9H3; 20.
DR MINT; P0A9H3; -.
DR STRING; 511145.b4131; -.
DR jPOST; P0A9H3; -.
DR PaxDb; P0A9H3; -.
DR PRIDE; P0A9H3; -.
DR EnsemblBacteria; AAC77092; AAC77092; b4131.
DR EnsemblBacteria; BAE78134; BAE78134; BAE78134.
DR GeneID; 66671957; -.
DR GeneID; 948643; -.
DR KEGG; ecj:JW4092; -.
DR KEGG; eco:b4131; -.
DR PATRIC; fig|1411691.4.peg.2568; -.
DR EchoBASE; EB0129; -.
DR eggNOG; COG1982; Bacteria.
DR HOGENOM; CLU_014292_3_0_6; -.
DR InParanoid; P0A9H3; -.
DR OMA; NCHKSVF; -.
DR PhylomeDB; P0A9H3; -.
DR BioCyc; EcoCyc:LYSDECARBOX-MON; -.
DR BioCyc; MetaCyc:LYSDECARBOX-MON; -.
DR BRENDA; 4.1.1.18; 2026.
DR EvolutionaryTrace; P0A9H3; -.
DR PRO; PR:P0A9H3; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0097216; F:guanosine tetraphosphate binding; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0008923; F:lysine decarboxylase activity; IDA:EcoCyc.
DR GO; GO:0006554; P:lysine catabolic process; IMP:EcoliWiki.
DR CDD; cd00615; Orn_deC_like; 1.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR InterPro; IPR005308; OKR_de-COase_N.
DR InterPro; IPR011193; Orn/lys/arg_de-COase.
DR InterPro; IPR000310; Orn/Lys/Arg_deCO2ase_major_dom.
DR InterPro; IPR008286; Prn/Lys/Arg_de-COase_C.
DR InterPro; IPR036633; Prn/Lys/Arg_de-COase_C_sf.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR Pfam; PF01276; OKR_DC_1; 1.
DR Pfam; PF03711; OKR_DC_1_C; 1.
DR Pfam; PF03709; OKR_DC_1_N; 1.
DR PIRSF; PIRSF009393; Orn_decarb; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
DR SUPFAM; SSF55904; SSF55904; 1.
DR PROSITE; PS00703; OKR_DC_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Decarboxylase; Direct protein sequencing; Lyase;
KW Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..715
FT /note="Inducible lysine decarboxylase"
FT /id="PRO_0000201138"
FT MOD_RES 367
FT /note="N6-(pyridoxal phosphate)lysine"
FT STRAND 3..7
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 13..28
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 32..34
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 39..48
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 52..58
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 59..73
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 78..82
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 91..93
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 94..96
FT /evidence="ECO:0007829|PDB:6YN5"
FT STRAND 99..103
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 110..128
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 131..142
FT /evidence="ECO:0007829|PDB:3N75"
FT TURN 151..155
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 156..160
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 162..171
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 173..177
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 185..187
FT /evidence="ECO:0007829|PDB:3N75"
FT TURN 190..193
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 196..208
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 211..218
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 219..231
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 237..243
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 246..254
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 258..262
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 277..280
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 282..291
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 299..306
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 310..313
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 315..321
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 325..330
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 337..339
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 341..343
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 350..352
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 358..363
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 376..382
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 386..395
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 403..416
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 418..445
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 446..448
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 452..455
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 461..463
FT /evidence="ECO:0007829|PDB:6YN5"
FT STRAND 481..486
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 490..494
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 496..498
FT /evidence="ECO:0007829|PDB:6YN5"
FT HELIX 511..520
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 526..529
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 532..536
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 543..561
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 566..569
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 571..576
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 578..581
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 586..599
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 602..609
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 610..612
FT /evidence="ECO:0007829|PDB:6YN5"
FT STRAND 615..618
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 620..628
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 632..636
FT /evidence="ECO:0007829|PDB:3N75"
FT HELIX 637..639
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 644..647
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 649..652
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 663..665
FT /evidence="ECO:0007829|PDB:6YN5"
FT HELIX 667..669
FT /evidence="ECO:0007829|PDB:6YN5"
FT HELIX 670..682
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 692..694
FT /evidence="ECO:0007829|PDB:3N75"
FT STRAND 696..698
FT /evidence="ECO:0007829|PDB:6YN5"
FT STRAND 704..709
FT /evidence="ECO:0007829|PDB:3N75"
SQ SEQUENCE 715 AA; 81260 MW; B9776622A0AE0190 CRC64;
MNVIAILNHM GVYFKEEPIR ELHRALERLN FQIVYPNDRD DLLKLIENNA RLCGVIFDWD
KYNLELCEEI SKMNENLPLY AFANTYSTLD VSLNDLRLQI SFFEYALGAA EDIANKIKQT
TDEYINTILP PLTKALFKYV REGKYTFCTP GHMGGTAFQK SPVGSLFYDF FGPNTMKSDI
SISVSELGSL LDHSGPHKEA EQYIARVFNA DRSYMVTNGT STANKIVGMY SAPAGSTILI
DRNCHKSLTH LMMMSDVTPI YFRPTRNAYG ILGGIPQSEF QHATIAKRVK ETPNATWPVH
AVITNSTYDG LLYNTDFIKK TLDVKSIHFD SAWVPYTNFS PIYEGKCGMS GGRVEGKVIY
ETQSTHKLLA AFSQASMIHV KGDVNEETFN EAYMMHTTTS PHYGIVASTE TAAAMMKGNA
GKRLINGSIE RAIKFRKEIK RLRTESDGWF FDVWQPDHID TTECWPLRSD STWHGFKNID
NEHMYLDPIK VTLLTPGMEK DGTMSDFGIP ASIVAKYLDE HGIVVEKTGP YNLLFLFSIG
IDKTKALSLL RALTDFKRAF DLNLRVKNML PSLYREDPEF YENMRIQELA QNIHKLIVHH
NLPDLMYRAF EVLPTMVMTP YAAFQKELHG MTEEVYLDEM VGRINANMIL PYPPGVPLVM
PGEMITEESR PVLEFLQMLC EIGAHYPGFE TDIHGAYRQA DGRYTVKVLK EESKK
