ID DNLI1_YEAST Reviewed; 755 AA.
AC P04819; D6VRI7; Q12736;
DT 13-AUG-1987, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 27-MAR-2024, entry version 229.
DE RecName: Full=DNA ligase 1;
DE EC=6.5.1.1 {ECO:0000255|PROSITE-ProRule:PRU10135};
DE AltName: Full=DNA ligase I;
DE AltName: Full=Polydeoxyribonucleotide synthase [ATP] 1;
DE Flags: Precursor;
GN Name=CDC9; OrderedLocusNames=YDL164C;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3909103; DOI=10.1093/nar/13.23.8323;
RA Barker D.G., White J.H.M., Johnston L.H.;
RT "The nucleotide sequence of the DNA ligase gene (CDC9) from Saccharomyces
RT cerevisiae: a gene which is cell-cycle regulated and induced in response to
RT DNA damage.";
RL Nucleic Acids Res. 13:8323-8337(1985).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169867;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 610-755.
RC STRAIN=ATCC 38626 / AH22 / NRRL Y-12843;
RX PubMed=8483449; DOI=10.1007/bf00279438;
RA Wehner E.P., Rao E., Brendel M.;
RT "Molecular structure and genetic regulation of SFA, a gene responsible for
RT resistance to formaldehyde in Saccharomyces cerevisiae, and
RT characterization of its protein product.";
RL Mol. Gen. Genet. 237:351-358(1993).
RN [6]
RP ALTERNATIVE INITIATION.
RX PubMed=10531002; DOI=10.1016/s0960-9822(99)80477-1;
RA Willer M., Rainey M., Pullen T., Stirling C.J.;
RT "The yeast CDC9 gene encodes both a nuclear and a mitochondrial form of DNA
RT ligase I.";
RL Curr. Biol. 9:1085-1094(1999).
RN [7]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-58 AND SER-75, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=17287358; DOI=10.1073/pnas.0607084104;
RA Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
RA Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
RT "Analysis of phosphorylation sites on proteins from Saccharomyces
RT cerevisiae by electron transfer dissociation (ETD) mass spectrometry.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-58 AND SER-75, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-75; SER-119 AND SER-123, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [11]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2 (ISOFORM NUCLEAR), CLEAVAGE OF
RP INITIATOR METHIONINE [LARGE SCALE ANALYSIS] (ISOFORM NUCLEAR), AND
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., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
CC -!- FUNCTION: DNA ligase that seals nicks in double-stranded DNA during DNA
CC replication, DNA recombination and DNA repair. The mitochondrial form
CC is required for mitochondrial DNA maintenance but is non-essential
CC while the nuclear form is essential for cell viability.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP +
CC diphosphate.; EC=6.5.1.1; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU10135};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC -!- SUBCELLULAR LOCATION: [Isoform Mitochondrial]: Mitochondrion.
CC -!- SUBCELLULAR LOCATION: [Isoform Nuclear]: Nucleus.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative initiation; Named isoforms=2;
CC Name=Mitochondrial;
CC IsoId=P04819-1; Sequence=Displayed;
CC Name=Nuclear;
CC IsoId=P04819-2; Sequence=VSP_018719;
CC -!- MISCELLANEOUS: Cdc9 is included within the category of so-called 'start
CC genes', encoding proteins which are required in early G1, when the cell
CC is faced with the option of initiating a further cell cycle.
CC -!- MISCELLANEOUS: Present with 149 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- MISCELLANEOUS: [Isoform Nuclear]: Produced by alternative initiation at
CC Met-24 of isoform Mitochondrial. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
CC {ECO:0000305}.
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DR EMBL; X03246; CAA27005.1; -; Genomic_DNA.
DR EMBL; Z67750; CAA91582.1; -; Genomic_DNA.
DR EMBL; Z74212; CAA98737.1; -; Genomic_DNA.
DR EMBL; AY723764; AAU09681.1; -; Genomic_DNA.
DR EMBL; X68020; CAA48158.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA11697.1; -; Genomic_DNA.
DR PIR; S61049; LQBYPX.
DR RefSeq; NP_010117.1; NM_001180224.1. [P04819-1]
DR PDB; 2OD8; X-ray; 2.80 A; B=32-53.
DR PDBsum; 2OD8; -.
DR AlphaFoldDB; P04819; -.
DR SMR; P04819; -.
DR BioGRID; 31901; 483.
DR DIP; DIP-5630N; -.
DR ELM; P04819; -.
DR IntAct; P04819; 37.
DR MINT; P04819; -.
DR STRING; 4932.YDL164C; -.
DR iPTMnet; P04819; -.
DR MaxQB; P04819; -.
DR PaxDb; 4932-YDL164C; -.
DR PeptideAtlas; P04819; -.
DR EnsemblFungi; YDL164C_mRNA; YDL164C; YDL164C. [P04819-1]
DR GeneID; 851391; -.
DR KEGG; sce:YDL164C; -.
DR AGR; SGD:S000002323; -.
DR SGD; S000002323; CDC9.
DR VEuPathDB; FungiDB:YDL164C; -.
DR eggNOG; KOG0967; Eukaryota.
DR GeneTree; ENSGT00940000157783; -.
DR HOGENOM; CLU_005138_4_1_1; -.
DR InParanoid; P04819; -.
DR OMA; WIKYKRD; -.
DR OrthoDB; 961at2759; -.
DR BioCyc; YEAST:G3O-29556-MONOMER; -.
DR Reactome; R-SCE-5358565; Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha).
DR Reactome; R-SCE-5358606; Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta).
DR Reactome; R-SCE-69183; Processive synthesis on the lagging strand.
DR BioGRID-ORCS; 851391; 6 hits in 10 CRISPR screens.
DR EvolutionaryTrace; P04819; -.
DR PRO; PR:P04819; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; P04819; Protein.
DR GO; GO:0005739; C:mitochondrion; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003910; F:DNA ligase (ATP) activity; IDA:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006284; P:base-excision repair; IMP:SGD.
DR GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
DR GO; GO:0071897; P:DNA biosynthetic process; IEA:InterPro.
DR GO; GO:0006266; P:DNA ligation; IDA:SGD.
DR GO; GO:0006310; P:DNA recombination; IMP:SGD.
DR GO; GO:0006273; P:lagging strand elongation; IDA:SGD.
DR GO; GO:0035753; P:maintenance of DNA trinucleotide repeats; IMP:SGD.
DR GO; GO:0000278; P:mitotic cell cycle; IMP:SGD.
DR GO; GO:0006289; P:nucleotide-excision repair; IMP:SGD.
DR GO; GO:1903461; P:Okazaki fragment processing involved in mitotic DNA replication; IBA:GO_Central.
DR CDD; cd07900; Adenylation_DNA_ligase_I_Euk; 1.
DR CDD; cd07969; OBF_DNA_ligase_I; 1.
DR Gene3D; 3.30.1490.70; -; 1.
DR Gene3D; 1.10.3260.10; DNA ligase, ATP-dependent, N-terminal domain; 1.
DR Gene3D; 3.30.470.30; DNA ligase/mRNA capping enzyme; 1.
DR Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1.
DR IDEAL; IID50307; -.
DR InterPro; IPR000977; DNA_ligase_ATP-dep.
DR InterPro; IPR012309; DNA_ligase_ATP-dep_C.
DR InterPro; IPR012310; DNA_ligase_ATP-dep_cent.
DR InterPro; IPR016059; DNA_ligase_ATP-dep_CS.
DR InterPro; IPR012308; DNA_ligase_ATP-dep_N.
DR InterPro; IPR036599; DNA_ligase_N_sf.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR NCBIfam; TIGR00574; dnl1; 1.
DR PANTHER; PTHR45674:SF4; DNA LIGASE 1; 1.
DR PANTHER; PTHR45674; DNA LIGASE 1/3 FAMILY MEMBER; 1.
DR Pfam; PF04679; DNA_ligase_A_C; 1.
DR Pfam; PF01068; DNA_ligase_A_M; 1.
DR Pfam; PF04675; DNA_ligase_A_N; 1.
DR SUPFAM; SSF117018; ATP-dependent DNA ligase DNA-binding domain; 1.
DR SUPFAM; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1.
DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR PROSITE; PS00697; DNA_LIGASE_A1; 1.
DR PROSITE; PS00333; DNA_LIGASE_A2; 1.
DR PROSITE; PS50160; DNA_LIGASE_A3; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Alternative initiation; ATP-binding; Cell cycle;
KW Cell division; DNA damage; DNA recombination; DNA repair; DNA replication;
KW Ligase; Magnesium; Metal-binding; Mitochondrion; Nucleotide-binding;
KW Nucleus; Phosphoprotein; Reference proteome; Transit peptide.
FT TRANSIT 1..44
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 45..755
FT /note="DNA ligase 1"
FT /id="PRO_0000007274"
FT REGION 47..79
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 97..127
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 309..318
FT /note="Interaction with target DNA"
FT /evidence="ECO:0000250"
FT REGION 493..495
FT /note="Interaction with target DNA"
FT /evidence="ECO:0000250"
FT COMPBIAS 61..79
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 419
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10135"
FT BINDING 417
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 424
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 440
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 472
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 571
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 576
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 590
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 596
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT SITE 164
FT /note="Interaction with target DNA"
FT /evidence="ECO:0000250"
FT SITE 441
FT /note="Interaction with target DNA"
FT /evidence="ECO:0000250"
FT SITE 622
FT /note="Interaction with target DNA"
FT /evidence="ECO:0000250"
FT SITE 647
FT /note="Interaction with target DNA"
FT /evidence="ECO:0000250"
FT MOD_RES 58
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17287358,
FT ECO:0007744|PubMed:18407956"
FT MOD_RES 75
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17287358,
FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198"
FT MOD_RES 119
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 123
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT VAR_SEQ 1..23
FT /note="Missing (in isoform Nuclear)"
FT /evidence="ECO:0000305"
FT /id="VSP_018719"
FT CONFLICT 69
FT /note="D -> E (in Ref. 1; CAA27005)"
FT /evidence="ECO:0000305"
FT CONFLICT 186
FT /note="L -> V (in Ref. 1; CAA27005)"
FT /evidence="ECO:0000305"
FT CONFLICT 671
FT /note="G -> E (in Ref. 5; CAA48158)"
FT /evidence="ECO:0000305"
FT CONFLICT 724
FT /note="R -> I (in Ref. 5; CAA48158)"
FT /evidence="ECO:0000305"
FT HELIX 41..44
FT /evidence="ECO:0007829|PDB:2OD8"
FT INIT_MET P04819-2:1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22814378"
FT MOD_RES P04819-2:2
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:22814378"
SQ SEQUENCE 755 AA; 84828 MW; B7C2ECAF5C61CAE7 CRC64;
MRRLLTGCLL SSARPLKSRL PLLMSSSLPS SAGKKPKQAT LARFFTSMKN KPTEGTPSPK
KSSKHMLEDR MDNVSGEEEY ATKKLKQTAV THTVAAPSSM GSNFSSIPSS APSSGVADSP
QQSQRLVGEV EDALSSNNND HYSSNIPYSE VCEVFNKIEA ISSRLEIIRI CSDFFIKIMK
QSSKNLIPTT YLFINRLGPD YEAGLELGLG ENLLMKTISE TCGKSMSQIK LKYKDIGDLG
EIAMGARNVQ PTMFKPKPLT VGEVFKNLRA IAKTQGKDSQ LKKMKLIKRM LTACKGIEAK
FLIRSLESKL RIGLAEKTVL ISLSKALLLH DENREDSPDK DVPMDVLESA QQKIRDAFCQ
VPNYEIVINS CLEHGIMNLD KYCTLRPGIP LKPMLAKPTK AINEVLDRFQ GETFTSEYKY
DGERAQVHLL NDGTMRIYSR NGENMTERYP EINITDFIQD LDTTKNLILD CEAVAWDKDQ
GKILPFQVLS TRKRKDVELN DVKVKVCLFA FDILCYNDER LINKSLKERR EYLTKVTKVV
PGEFQYATQI TTNNLDELQK FLDESVNHSC EGLMVKMLEG PESHYEPSKR SRNWLKLKKD
YLEGVGDSLD LCVLGAYYGR GKRTGTYGGF LLGCYNQDTG EFETCCKIGT GFSDEMLQLL
HDRLTPTIID GPKATFVFDS SAEPDVWFEP TTLFEVLTAD LSLSPIYKAG SATFDKGVSL
RFPRFLRIRE DKGVEDATSS DQIVELYENQ SHMQN
//
