IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/ araki-2013-2 yeast Saccharomyces cerevisiae Baker's yeast affinity chrom affinity chromatography technology Affinity purification Affinity purification affinity chrom anti tag western anti tag western blot anti tag western Araki Y., Ku WC., Akioka M., May AI., Hayashi Y., Arisaka F., Ishihama Y., Ohsumi Y., Araki Y., Ku WC., Akioka M., May AI., Hayashi Y., Arisaka F., Ishihama Y., Ohsumi Y. yohsumi@iri.titech.ac.jp The Journal of cell biology 2013 Only protein-protein interactions imex curation imex curation araki-2013-1 yeast Saccharomyces cerevisiae Baker's yeast affinity chrom affinity chromatography technology Affinity purification Affinity purification affinity chrom sequence tag sequence tag identification sequence tag Araki Y., Ku WC., Akioka M., May AI., Hayashi Y., Arisaka F., Ishihama Y., Ohsumi Y., Araki Y., Ku WC., Akioka M., May AI., Hayashi Y., Arisaka F., Ishihama Y., Ohsumi Y. yohsumi@iri.titech.ac.jp The Journal of cell biology 2013 Only protein-protein interactions imex curation imex curation araki-2013-3 yeast Saccharomyces cerevisiae Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid predetermined predetermined participant predetermined Araki Y., Ku WC., Akioka M., May AI., Hayashi Y., Arisaka F., Ishihama Y., Ohsumi Y., Araki Y., Ku WC., Akioka M., May AI., Hayashi Y., Arisaka F., Ishihama Y., Ohsumi Y. yohsumi@iri.titech.ac.jp The Journal of cell biology 2013 Only protein-protein interactions imex curation imex curation araki-2013-4 yeast Saccharomyces cerevisiae Baker's yeast pull down pull down western blot western blot Immuno blot Immuno blot Araki Y., Ku WC., Akioka M., May AI., Hayashi Y., Arisaka F., Ishihama Y., Ohsumi Y., Araki Y., Ku WC., Akioka M., May AI., Hayashi Y., Arisaka F., Ishihama Y., Ohsumi Y. yohsumi@iri.titech.ac.jp The Journal of cell biology 2013 Only protein-protein interactions imex curation imex curation araki-2013-5 ecoli Escherichia coli (strain K12) molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column weight by comassie molecular weight estimation by coomasie staining weight by comassie Araki Y., Ku WC., Akioka M., May AI., Hayashi Y., Arisaka F., Ishihama Y., Ohsumi Y., Araki Y., Ku WC., Akioka M., May AI., Hayashi Y., Arisaka F., Ishihama Y., Ohsumi Y. TAP-tagged Atg14 proteins were precipitated with magnetic beads coupled with rabbit IgG. Bound proteins were eluted with TEV protease, the eluate was separated by size exclusion chromatography on a Superdex 200 column. yohsumi@iri.titech.ac.jp The Journal of cell biology 2013 Only protein-protein interactions imex curation imex curation araki-2013-6 ecoli Escherichia coli (strain K12) solution sedimentati cosedimentation in solution solution sedimentati predetermined predetermined participant predetermined Araki Y., Ku WC., Akioka M., May AI., Hayashi Y., Arisaka F., Ishihama Y., Ohsumi Y., Araki Y., Ku WC., Akioka M., May AI., Hayashi Y., Arisaka F., Ishihama Y., Ohsumi Y. Non-tagged Atg38 was purified by Mono Q chromatography yohsumi@iri.titech.ac.jp The Journal of cell biology 2013 Only protein-protein interactions imex curation imex curation araki-2013-7 yeast Saccharomyces cerevisiae Baker's yeast molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column anti tag western anti tag western blot anti tag western Araki Y., Ku WC., Akioka M., May AI., Hayashi Y., Arisaka F., Ishihama Y., Ohsumi Y., Araki Y., Ku WC., Akioka M., May AI., Hayashi Y., Arisaka F., Ishihama Y., Ohsumi Y. TAP-tagged Atg14 proteins were precipitated with magnetic beads coupled with rabbit IgG. Bound proteins were eluted with TEV protease, the eluate was separated by size exclusion chromatography on a Superdex 200 column. yohsumi@iri.titech.ac.jp The Journal of cell biology 2013 Only protein-protein interactions imex curation imex curation atg14_yeast Autophagy-related protein 14 ATG14 APG14 YBR128C YBR1003 CVT12 Cytoplasm to vacuole targeting protein 12 protein protein yeast Saccharomyces cerevisiae Baker's yeast MHCPICHHRAHVVYCAHCINTSPSLLLKLKLDLILLKDENKELNGKVEQILNEAMNYDQLDIKRMEKKKDPLMNSLMKLDVLRMKKNNNLIRHRIEQLNERIYSKRNHISELKVEIDNYKCYKVGTGTDKLREQVEISDAKNKLAQVSKICESARDYKLNLLNNWFVIQKLQDNFQIPFAIAFQPLISLKNFRILPLAITNDSINIMWKYISFFSDILMIKLPYTNKICEQPMFEFSDSIQTVVQRLIKLIINILQICRHLKLVPSTPMDIPWLLDQYDVDGLFYNMVKRNKMKCRSVSLYWTFGMLYSMVLDNMNNPQRGHPARRTAPPPTVTGPHDRWYVVG 202039BC7EC8BB16 vps34_yeast Phosphatidylinositol 3-kinase VPS34 VPS34 END12 PEP15 Vacuolar protein sorting-associated protein 34 Vacuolar protein-targeting protein 29 Carboxypeptidase Y-deficient protein 15 VPL7 VPT29 L9672.10 YLR240W protein protein yeast Saccharomyces cerevisiae Baker's yeast MSLNNITFCVSQDLDVPLKVKIKSLEGHKPLLKPSQKILNPELMLIGSNVFPSSDLIVSLQVFDKERNRNLTLPIYTPYIPFRNSRTWDYWLTLPIRIKQLTFSSHLRIILWEYNGSKQIPFFNLETSIFNLKDCTLKRGFESLKFRYDVIDHCEVVTDNKDQENLNKYFQGEFTRLPWLDEITISKLRKQRENRTWPQGTFVLNLEFPMLELPVVFIEREIMNTQMNIPTLKNNPGLSTDLREPNRNDPQIKISLGDKYHSTLKFYDPDQPNNDPIEEKYRRLERASKNANLDKQVKPDIKKRDYLNKIINYPPGTKLTAHEKGSIWKYRYYLMNNKKALTKLLQSTNLREESERVEVLELMDSWAEIDIDDALELLGSTFKNLSVRSYAVNRLKKASDKELELYLLQLVEAVCFENLSTFSDKSNSEFTIVDAVSSQKLSGDSMLLSTSHANQKLLKSISSESETSGTESLPIVISPLAEFLIRRALVNPRLGSFFYWYLKSESEDKPYLDQILSSFWSRLDKKSRNILNDQVRLINVLRECCETIKRLKDTTAKKMELLVHLLETKVRPLVKVRPIALPLDPDVLICDVCPETSKVFKSSLSPLKITFKTTLNQPYHLMFKVGDDLRQDQLVVQIISLMNELLKNENVDLKLTPYKILATGPQEGAIEFIPNDTLASILSKYHGILGYLKLHYPDENATLGVQGWVLDNFVKSCAGYCVITYILGVGDRHLDNLLVTPDGHFFHADFGYILGQDPKPFPPLMKLPPQIIEAFGGAESSNYDKFRSYCFVAYSILRRNAGLILNLFELMKTSNIPDIRIDPNGAILRVRERFNLNMSEEDATVHFQNLINDSVNALLPIVIDHLHNLAQYWRT 806E3404EF260287 atg38_yeast Autophagy-related protein 38 ATG38 L8167.20 YLR211C protein protein yeast Saccharomyces cerevisiae Baker's yeast MSTLAEVYTIIEDAEQECRKGDFTNAKAKYQEAIEVLGPQNENLSQNKLSSDVTQAIDLLKQDITAKIQELELLIEKQSSEENNIGMVNNNMLIGSVILNNKSPINGISNARNWDNPAYQDTLSPINDPLLMSILNRLQFNLNNDIQLKTEGGKNSKNSEMKINLRLEQFKKELVLYEQKKFKEYGMKIDEITKENKKLANEIGRLRERWDSLVESAKQRRDKQKN vps15_yeast Serine/threonine-protein kinase VPS15 VPS15 GRD8 VPL19 YBR0825 YBR097W VAC4 Vacuolar protein sorting-associated protein 15 Golgi-retention defective mutant protein 8 protein protein yeast Saccharomyces cerevisiae Baker's yeast MGAQLSLVVQASPSIAIFSYIDVLEEVHYVSQLNSSRFLKTCKALDPNGEIVIKVFIKPKDQYSLRPFLQRIRAQSFKLGQLPHVLNYSKLIETNRAGYMIRQHLKNNLYDRLSLRPYLQDIELKFIAFQLLNALKDIHNLNIVHGDIKTENILVTSWNWCILTDFAAFIKPVYLPEDNPGEFLFYFDTSKRRTCYLAPERFNSKLYQDGKSNNGRLTKEMDIFSLGCVIAEIFAEGRPIFNLSQLFKYKSNSYDVNREFLMEEMNSTDLRNLVLDMIQLDPSKRLSCDELLNKYRGIFFPDYFYTFIYDYFRNLVTMTTSTPISDNTCTNSTLEDNVKLLDETTEKIYRDFSQICHCLDFPLIKDGGEIGSDPPILESYKIEIEISRFLNTNLYFPQNYHLVLQQFTKVSEKIKSVKEECALLFISYLSHSIRSIVSTATKLKNLELLAVFAQFVSDENKIDRVVPYFVCCFEDSDQDVQALSLLTLIQVLTSVRKLNQLNENIFVDYLLPRLKRLLISNRQNTNYLRIVFANCLSDLAIIINRFQEFTFAQHCNDNSMDNNTEIMESSTKYSAKLIQSVEDLTVSFLTDNDTYVKMALLQNILPLCKFFGRERTNDIILSHLITYLNDKDPALRVSLIQTISGISILLGTVTLEQYILPLLIQTITDSEELVVISVLQSLKSLFKTGLIRKKYYIDISKTTSPLLLHPNNWIRQFTLMIIIEIINKLSKAEVYCILYPIIRPFFEFDVEFNFKSMISCCKQPVSRSVYNLLCSWSVRASKSLFWKKIITNHVDSFGNNRIEFITKNYSSKNYGFNKRDTKSSSSLKGIKTSSTVYSHDNKEIPLTAEDRNWIDKFHIIGLTEKDIWKIVALRGYVIRTARVMAANPDFPYNNSNYRPLVQNSPPNLNLTNIMPRNIFFDVEFAEESTSEGQDSNLENQQIYKYDESEKDSNKLNINGSKQLSTVMDINGSLIFKNKSIATTTSNLKNVFVQLEPTSYHMHSPNHGLKDNANVKPERKVVVSNSYEGDVESIEKFLSTFKILPPLRDYKEFGPIQEIVRSPNMGNLRGKLIATLMENEPNSITSSAVSPGETPYLITGSDQGVIKIWNLKEIIVGEVYSSSLTYDCSSTVTQITMIPNFDAFAVSSKDGQIIVLKVNHYQQESEVKFLNCECIRKINLKNFGKNEYAVRMRAFVNEEKSLLVALTNLSRVIIFDIRTLERLQIIENSPRHGAVSSICIDEECCVLILGTTRGIIDIWDIRFNVLIRSWSFGDHAPITHVEVCQFYGKNSVIVVGGSSKTFLTIWNFVKGHCQYAFINSDEQPSMEHFLPIEKGLEELNFCGIRSLNALSTISVSNDKILLTDEATSSIVMFSLNELSSSKAVISPSRFSDVFIPTQVTANLTMLLRKMKRTSTHSVDDSLYHHDIINSISTCEVDETPLLVACDNSGLIGIFQ 247EBA5531E41FFB becn1_yeast Vacuolar protein sorting-associated protein 30 VPS30 APG6 VPT30 YPL120W LPH7 ATG6 Autophagy-related protein 6 protein protein yeast Saccharomyces cerevisiae Baker's yeast MKCQTCHLPLQLDPSLEGLSLTQRNLLLSNNSIITATNENVISNKGIEAADNCGPQIPKERLRRLGEIQNIKDLNLKDDKLITDSFVFLNHDDDDNANITSNSREDQRYGNANGNDNKKANSDTSDGTSTFRDHDEEEQEATDEDENQQIQLNSKTLSTQVNAMTNVFNILSSQTNIDFPICQDCCNILINRLKSEYDDAIKERDTYAQFLSKLESQNKEISESNKEKQYSHNLSEKENLKKEEERLLDQLLRLEMTDDDLDGELVRLQEKKVQLENEKLQKLSDQNLMDLNNIQFNKNLQSLKLQYELSLNQLDKLRKINIFNATFKISHSGPFATINGLRLGSIPESVVPWKEINAALGQLILLLATINKNLKINLVDYELQPMGSFSKIKKRMVNSVEYNNSTTNAPGDWLILPVYYDENFNLGRIFRKETKFDKSLETTLEIISEITRQLSTIASSYSSQTLTTSQDESSMNNANDVENSTSILELPYIMNKDKINGLSVKLHGSSPNLEWTTAMKFLLTNVKWLLAFSSNLLSKSITLSPTVNYNDKTISGN 4BA74B614CABE1C0 atg15_yeast Putative lipase ATG15 ATG15 AUT5 CVT17 YCR068W YCR68W Autophagy-related protein 15 Cytoplasm to vacuole targeting protein 17 protein protein yeast Saccharomyces cerevisiae Baker's yeast MLHKSPSRKRFASPLHLGCILTLTVLCLIAYYFALPDYLSVGKSSSRGAMDQKSDGTFRLKSIYRHGVGANHRLHQRLEVTPEVISAAGMLYQETTTQGQDFEDQEPLWTTNAEYATTNPFDFEFELRRMPLLMKRMKERDPEFIESYIYGETYMTEEEEHAMWIDDDIVAPNITDRGTVVSLALMSSNAYVRIPQTGDWRNVTEPWNETEPEDFGWDGDGIRGHVFYNEVENIVVLSIKGTSAQGLPGSGEDETTGNDKINDNLLFSCCCARVSYLWTTVCDCYVKSYICDESCLEKELRRKDRFYSAVVDIYKGVLKEYPDAAIWVTGHSLGGALASLLGRTFGLPAVAFESPGELLPSKRLHLPFPPGLPSYMEGIWHFGHNADPIFMGTCNGASSSCSLVGYAMETACHTGRVCVYDVVNDKGWSVNMFNHRIHKVIDEVLLGYEQAAKCVEPEPCVDCYNWKFIPSRDWESSSRLITKTKSHAAPTTTTRTTATTTSSSTCVGRNWLGFCTKYEL B56ABAB72B999019 atg9_yeast Autophagy-related protein 9 ATG9 APG9 AUT9 CVT7 YDL149W D1560 Cytoplasm to vacuole targeting protein 7 protein protein yeast Saccharomyces cerevisiae Baker's yeast MERDEYQLPNSHGKNTFLSRIFGLQSDEVNPSLNSQEMSNFPLPDIERGSSLLHSTNDSREDVDENDLRVPESDQGTSTEEEDEVDEEQVQAYAPQISDGLDGDHQLNSVTSKENVLETEKSNLERLVEGSTDDSVPKVGQLSSEEEEDNEFINNDGFDDDTPLFQKSKIHEFSSKKSNTIEDGKRPLFFRHILQNNRPQRDTQKLFTSSNAIHHDKDKSANNGPRNINGNQKHGTKYFGSATQPRFTGSPLNNTNRFTKLFPLRKPNLLSNISVLNNTPEDRINTLSVKERALWKWANVENLDIFLQDVYNYYLGNGFYCIILEKILNICTLLFVVFVSTYMGHCVDYSKLPTSHRVSDIIIDKCYSNSITGFTKFFLWMFYFFVILKIVQLYFDVQKLSELQNFYKYLLNISDDELQTLPWQNVIQQLMYLKDQNAMTANVVEVKAKNRIDAHDVANRIMRRENYLIALYNSDILNLSLPIPLFRTNVLTKTLEWNINLCVMGFVFNESGFIKQSILKPSQREFTREELQKRFMLAGFLNIILAPFLVTYFVLLYFFRYFNEYKTSPGSIGARQYTPIAEWKFREYNELYHIFKKRISLSTTLANKYVDQFPKEKTNLFLKFVSFICGSFVAILAFLTVFDPENFLNFEITSDRSVIFYITILGAIWSVSRNTITQEYHVFDPEETLKELYEYTHYLPKEWEGRYHKEEIKLEFCKLYNLRIVILLRELTSLMITPFVLWFSLPSSAGRIVDFFRENSEYVDGLGYVCKYAMFNMKNIDGEDTHSMDEDSLTKKIAVNGSHTLNSKRRSKFTAEDHSDKDLANNKMLQSYVYFMDDYSNSENLTGKYQLPAKKGYPNNEGDSFLNNKYSWRKQFQPGQKPELFRIGKHALGPGHNISPAIYSTRNPGKNWDNNNNGDDIKNGTNNATAKNDDNNGNNDHEYVLTESFLDSGAFPNHDVIDHNKMLNSNYNGNGILNKGGVLGLVKEYYKKSDVGR vps38_yeast Vacuolar protein sorting-associated protein 38 VPS38 VPL17 YLR360W L8039.11 protein protein yeast Saccharomyces cerevisiae Baker's yeast MKRFLLSRRQRHLRMICFHNISLFRANGDSKLIKEYGDGFIPCFFILESIRGELLYVSEVQSGSLRKLSFQELPKLTGASTMIVLKLVGLVPSDILCTISSDKNGIIDDKWCVLCTYTIDLNKLQPINEDTVLITGTNAPVLDLIDGSYTLAAEKIKPLKGLVSSHKRNISQVKIKFSLAYSSLLKLNKLLEYSSQVHEEINEISSKIEDDFLSLKNQNHWYMRTVQKSIETLEKEVLQRKKSKKNIEMAQLESNDTINHSKTELSLMSQDESINDDYGSIYSRFVQIKDRLDQLRFKKLYQLIGIFHSTDLFNSDRGYIYFEKPSSVNDVINRLKLKPLNIEILLRQAGESTKHREYVNSQLGYYLLFLHLTAIQIFKAPLPYRLMYYGSTSVIDSQYPLYFTDQMISKHQAKLIKAIHYFNADILQFKQILENYRPT 70141E084D185015 atg14-vps34-1 1931652 N/A 1931659 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931660 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931661 unspecified role unspecified role ancillary ancillary association association false false false Fig. 4A, Supp Fig. 3B Interaction not observed in ATG38-/- cells atg38-vps15-1 1931652 N/A 1931659 unspecified role unspecified role ancillary ancillary N/A 1931662 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931661 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false association association false false false Fig. 1B, 1D Interaction not observed in ATG14-/- cells atg38-vps30-1 1931652 N/A 1931659 unspecified role unspecified role ancillary ancillary N/A 1931663 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931661 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false association association false false false Fig. 1B, 1D Interaction not observed in ATG14-/- cells atg38-atg14-1 1931652 N/A 1931659 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931661 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Fig. 1B, Supp. 1D atg38-vps34-1 1931652 N/A 1931659 unspecified role unspecified role ancillary ancillary N/A 1931660 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931661 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false association association false false false Fig. 1D, Supp Fig. 1B Interaction not observed in ATG14-/- cells atg14-vps15-2 1931652 N/A 1931659 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931662 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931661 unspecified role unspecified role ancillary ancillary association association false false false Fig. 4A Interaction not observed in ATG38-/- cells vps30-atg14-2 1931652 N/A 1931659 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931663 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Fig. 4A Interaction observed in ATG38-/- cells atg14-atg38-3 1931652 N/A 1931663 unspecified role unspecified role prey prey region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931659 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931660 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931661 unspecified role unspecified role prey prey region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false association association false false false Fig. 4D The association of Atg14 with Vps30 was found to be resistant to washes with high concentrations of salt. In contrast, Vps34 and Atg38 detached from Atg14–Vps30 in a concentration-dependent manner. atg14-vps34-2 1931652 N/A 1931660 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931659 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931661 unspecified role unspecified role ancillary ancillary region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false Fig. 7A Interaction not observed in ATG38-/- cells. Use of tags showed that ATG38 was required to be a homodimer to stabilise this interaction. atg14-vps15-3 1931652 N/A 1931662 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931659 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931661 unspecified role unspecified role ancillary ancillary region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false association association false false false Fig. 7A Interaction not observed in ATG38-/- cells. Use of tags showed that ATG38 was required to be a homodimer to stabilise this interaction. atg38-atg15-1 1931652 N/A 1931661 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931664 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Supp. Fig. 2A atg14-atg9-1 1931652 N/A 1931659 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931665 unspecified role unspecified role prey prey region gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Supp Fig. 3A Interaction observed in ATG38-/- cells atg14-vps15-4 1931652 N/A 1931659 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931662 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931661 unspecified role unspecified role ancillary ancillary association association false false false Fig. 4Ai Interaction not observed in ATG38-/- cells atg14-vps34-3 1931652 N/A 1931659 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931660 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931661 unspecified role unspecified role ancillary ancillary association association false false false Fig. 4Ai Interaction not observed in ATG38-/- cells atg14-vps30-1 1931652 N/A 1931659 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931663 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Fig. 4Ai Interaction observed in ATG38-/- cells vps34-atg14-1 1931653 N/A 1931663 unspecified role unspecified role prey prey N/A 1931661 unspecified role unspecified role prey prey N/A 1931659 unspecified role unspecified role prey prey N/A 1931666 unspecified role unspecified role prey prey N/A 1931662 unspecified role unspecified role prey prey N/A 1931660 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false association association false false false Fig. 1A atg14-atg38-1 1931653 N/A 1931660 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931661 unspecified role unspecified role prey prey N/A 1931659 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931663 unspecified role unspecified role prey prey N/A 1931662 unspecified role unspecified role prey prey association association false false false Fig. 1C atg14-atg38-2 1931653 N/A 1931660 unspecified role unspecified role prey prey region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931661 unspecified role unspecified role bait bait region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931659 unspecified role unspecified role prey prey N/A 1931663 unspecified role unspecified role prey prey N/A 1931662 unspecified role unspecified role prey prey association association false false false Fig. 1Cx atg14-atg38-4 1931654 N/A 1931659 unspecified role unspecified role bait bait N/A 1931661 unspecified role unspecified role prey prey region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false Fig. 5A, 5B, Supp. Fig. 2D vps34-atg38-1 1931654 N/A 1931660 unspecified role unspecified role bait bait N/A 1931661 unspecified role unspecified role prey prey physical association physical association false false false Fig. 5A, Supp. Fig 2B atg38-atg38-1 1931654 N/A 1931661 unspecified role unspecified role prey prey region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false N/A 1931661 unspecified role unspecified role bait bait region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false 1931792 1931790 physical association physical association false false false Fig. 6A atg38-vps15-2 1931655 N/A 1931660 unspecified role unspecified role prey prey vps15 binding region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region tap tagged calmodulin binding peptide plus protein a tag CBP-ProtA tagged CBP-ProtA tagged tap tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false yeast Saccharomyces cerevisiae Baker's yeast N/A 1931662 unspecified role unspecified role prey prey vps34 binding region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false yeast Saccharomyces cerevisiae Baker's yeast N/A 1931661 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) 1931798 1931795 physical association physical association false false false Fig. 5C atg38-atg38-2 1931656 N/A 1931661 unspecified role unspecified role neutral component neutral component N/A 1931661 unspecified role unspecified role neutral component neutral component direct interaction direct interaction false false false Fig. 6B The molecular mass of the native form of Atg38 was distributed around 50–80 kD, suggesting either a homodimer or homotrimer. atg38-atg38-3 1931657 N/A 1931661 unspecified role unspecified role neutral component neutral component Stoichiometry: 2.0 direct interaction direct interaction false false false Fig. 6C Sedimentation coefficient = 3.0 S in solution. This indicates that Atg38 exists as a particle of 50.2 kD, which is consistent with the molecular mass of a dimer. atg14-atg38-5 1931658 N/A 1931663 unspecified role unspecified role neutral component neutral component region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931659 unspecified role unspecified role neutral component neutral component region cam tag calmodulin binding protein tag cam tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931660 unspecified role unspecified role neutral component neutral component region ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 1931661 unspecified role unspecified role neutral component neutral component c-terminal flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false physical association physical association false false false Supp. Fig. 1C