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/ huang-2006c-1 Systematic identification of the subproteome of Escherichia coli cell envelope reveals the interaction network of membrane proteins and membrane-associated peripheral proteins. ecoli Escherichia coli (strain K12) comig non denat gel comigration in non denaturing gel electrophoresis comig non denat gel ms participant Identification by mass spectrometry ms participant Huang CZ., Lin XM., Wu LN., Zhang DF., Liu D., Wang SY., Peng XX. Ecoli were cultured in luria broth medium. Membrane vesicle preparartions were used in subsequent assays. Protein complexes were in 0.5% Triton X-100 were isolated by the native-PAGE. Individual proteins in each complex were consequently resolved into a vertical line through the SDS-PADE gel and then identified by MS. wangpeng@xmu.edu.cn J. Proteome Res. (1535-3893) 2006 Only protein-protein interactions imex curation huang-2006c-4 Systematic identification of the subproteome of Escherichia coli cell envelope reveals the interaction network of membrane proteins and membrane-associated peripheral proteins. ecoli Escherichia coli (strain K12) comig non denat gel comigration in non denaturing gel electrophoresis comig non denat gel ms participant Identification by mass spectrometry ms participant Huang CZ., Lin XM., Wu LN., Zhang DF., Liu D., Wang SY., Peng XX. Ecoli were cultured in luria broth medium. Membrane vesicle preparartions were used in subsequent assays. Protein complexes were in 0.5% Triton X-100 were isolated by the native-PAGE. Individual proteins in each complex were consequently resolved into a vertical line through the SDS-PADE gel and then identified by MS. wangpeng@xmu.edu.cn J. Proteome Res. (1535-3893) 2006 Only protein-protein interactions imex curation huang-2006c-2 Systematic identification of the subproteome of Escherichia coli cell envelope reveals the interaction network of membrane proteins and membrane-associated peripheral proteins. ecoli Escherichia coli (strain K12) anti bait coip anti bait coimmunoprecipitation anti bait coip ms participant Identification by mass spectrometry ms participant Huang CZ., Lin XM., Wu LN., Zhang DF., Liu D., Wang SY., Peng XX. Ecoli were cultured in luria broth medium. Membrane vesicle preparartions were used in subsequent assays. Protein complexes were in 0.5% Triton X-100 were isolated by the native-PAGE. Individual proteins in each complex were consequently resolved into a vertical line through the SDS-PADE gel and then identified by MS. wangpeng@xmu.edu.cn J. Proteome Res. (1535-3893) 2006 Only protein-protein interactions imex curation huang-2006c-3 Systematic identification of the subproteome of Escherichia coli cell envelope reveals the interaction network of membrane proteins and membrane-associated peripheral proteins. ecoli Escherichia coli (strain K12) far western blotting far western blotting Affinity blotting Affinity blotting antibody detection identification by antibody antibody detection Huang CZ., Lin XM., Wu LN., Zhang DF., Liu D., Wang SY., Peng XX. Ecoli were cultured in luria broth medium. Membrane vesicle preparartions were used in subsequent assays. Protein complexes were in 0.5% Triton X-100 were isolated by the native-PAGE. Individual proteins in each complex were consequently resolved into a vertical line through the SDS-PADE gel and then identified by MS. wangpeng@xmu.edu.cn J. Proteome Res. (1535-3893) 2006 Only protein-protein interactions imex curation ompw_ecoli Outer membrane protein W yciD ompW b1256 JW1248 protein protein ecoli Escherichia coli (strain K12) MKKLTVAALAVTTLLSGSAFAHEAGEFFMRAGSATVRPTEGAGGTLGSLGGFSVTNNTQLGLTFTYMATDNIGVELLAATPFRHKIGTRATGDIATVHHLPPTLMAQWYFGDASSKFRPYVGAGINYTTFFDNGFNDHGKEAGLSDLSLKDSWGAAGQVGVDYLINRDWLVNMSVWYMDIDTTANYKLGGAQQHDSVRLDPWVFMFSAGYRF frdb_ecoli Fumarate reductase iron-sulfur subunit frdB Quinol-fumarate reductase iron-sulfur subunit JW4114 b4153 protein protein ecoli Escherichia coli (strain K12) MAEMKNLKIEVVRYNPEVDTAPHSAFYEVPYDATTSLLDALGYIKDNLAPDLSYRWSCRMAICGSCGMMVNNVPKLACKTFLRDYTDGMKVEALANFPIERDLVVDMTHFIESLEAIKPYIIGNSRTADQGTNIQTPAQMAKYHQFSGCINCGLCYAACPQFGLNPEFIGPAAITLAHRYNEDSRDHGKKERMAQLNSQNGVWSCTFVGYCSEVCPKHVDPAAAIQQGKVESSKDFLIATLKPR frda_ecoli Fumarate reductase flavoprotein subunit frdA Quinol-fumarate reductase flavoprotein subunit JW4115 b4154 protein protein ecoli Escherichia coli (strain K12) MQTFQADLAIVGAGGAGLRAAIAAAQANPNAKIALISKVYPMRSHTVAAEGGSAAVAQDHDSFEYHFHDTVAGGDWLCEQDVVDYFVHHCPTEMTQLELWGCPWSRRPDGSVNVRRFGGMKIERTWFAADKTGFHMLHTLFQTSLQFPQIQRFDEHFVLDILVDDGHVRGLVAMNMMEGTLVQIRANAVVMATGGAGRVYRYNTNGGIVTGDGMGMALSHGVPLRDMEFVQYHPTGLPGSGILMTEGCRGEGGILVNKNGYRYLQDYGMGPETPLGEPKNKYMELGPRDKVSQAFWHEWRKGNTISTPRGDVVYLDLRHLGEKKLHERLPFICELAKAYVGVDPVKEPIPVRPTAHYTMGGIETDQNCETRIKGLFAVGECSSVGLHGANRLGSNSLAELVVFGRLAGEQATERAATAGNGNEAAIEAQAAGVEQRLKDLVNQDGGENWAKIRDEMGLAMEEGCGIYRTPELMQKTIDKLAELQERFKRVRITDTSSVFNTDLLYTIELGHGLNVAECMAHSAMARKESRGAHQRLDEGCTERDDVNFLKHTLAFRDADGTTRLEYSDVKITTLPPAKRVYGGEADAADKAEAANKKEKANG slp_ecoli Outer membrane protein Slp slp b3506 JW3474 protein protein ecoli Escherichia coli (strain K12) MNMTKGALILSLSFLLAACSSIPQNIKGNNQPDIQKSFVAVHNQPGLYVGQQARFGGKVINVINGKTDTLLEISVLPLDSYAKPDIEANYQGRLLARQSGFLDPVNYRNHFVTILGTIQGEQPGFINKVPYNFLEVNMQGIQVWHLREVVNTTYNLWDYGYGAFWPEPGWGAPYYTNAVSQVTPELVK ydga_ecoli Protein YdgA ydgA b1614 JW1606 protein protein ecoli Escherichia coli (strain K12) MNKSLVAVGVIVALGVVWTGGAWYTGKKIETHLEDMVAQANAQLKLTAPESNLEVSYQNYHRGVFSSQLQLLVKPIAGKENPWIKSGQSVIFNESVDHGPFPLAQLKKLNLIPSMASIQTTLVNNEVSKPLFDMAKGETPFEINSRIGYSGDSSSDISLKPLNYEQKDEKVAFSGGEFQLNADRDGKAISLSGEAQSGRIDAVNEYNQKVQLTFNNLKTDGSSTLASFGERVGNQKLSLEKMTISVEGKELALLEGMEISGKSDLVNDGKTINSQLDYSLNSLKVQNQDLGSGKLTLKVGQIDGEAWHQFSQQYNAQTQALLAQPEIANNPELYQEKVTEAFFSALPLMLKGDPVITIAPLSWKNSQGESALNLSLFLKDPATTKEAPQTLAQEVDRSVKSLDAKLTIPVDMATEFMTQVAKLEGYQEDQAKKLAKQQVEGASAMGQMFRLTTLQDNTITTSLQYANGQITLNGQKMSLEDFVGMFAMPALNVPAVPAIPQQ ybjp_ecoli Uncharacterized lipoprotein YbjP ybjP b0865 JW0849 protein protein ecoli Escherichia coli (strain K12) MRYSKLTMLIPCALLLSACTTVTPAYKDNGTRSGPCVEGGPDNVAQQFYDYRILHRSNDITALRPYLSDKLATLLSDASRDNNHRELLTNDPFSSRTTLPDSAHVASASTIPNRDARNIPLRVDLKQGDQGWQDEVLMIQEGQCWVIDDVRYLGGSVHATAGTLRQSIENR odp1_eco57 Pyruvate dehydrogenase E1 component aceE Z0124 ECs0118 protein protein eco57 Escherichia coli O157:H7 MSERFPNDVDPIETRDWLQAIESVIREEGVERAQYLIDQLLAEARKGGVNVAAGTGISNYINTIPVEEQPEYPGNLELERRIRSAIRWNAIMTVLRASKKDLELGGHMASFQSSATIYDVCFNHFFRARNEQDGGDLVYFQGHISPGVYARAFLEGRLTQEQLDNFRQEVHGNGLSSYPHPKLMPEFWQFPTVSMGLGPIGAIYQAKFLKYLEHRGLKDTSKQTVYAFLGDGEMDEPESKGAITIATREKLDNLVFVINCNLQRLDGPVTGNGKIINELEGIFEGAGWNVIKVMWGSRWDELLRKDTSGKLIQLMNETVDGDYQTFKSKDGAYVREHFFGKYPETAALVADWTDEQIWALNRGGHDPKKIYAAFKKAQETKGKATVILAHTIKGYGMGDAAEGKNIAHQVKKMNMDGVRHIRDRFNVPVSDADIEKLPYITFPEGSEEHTYLHAQRQKLHGYLPSRQPNFTEKLELPSLQDFGALLEEQSKEISTTIAFVRALNVMLKNKSIKDRLVPIIADEARTFGMEGLFRQIGIYSPNGQQYTPQDREQVAYYKEDEKGQILQEGINELGAGCSWLAAATSYSTNNLPMIPFYIYYSMFGFQRIGDLCWAAGDQQARGFLIGGTSGRTTLNGEGLQHEDGHSHIQSLTIPNCISYDPAYAYEVAVIMHDGLERMYGEKQENVYYYITTLNENYHMPAMPEGAEEGIRKGIYKLETIEGSKGKVQLLGSGSILRHVREAAEILAKDYGVGSDVYSVTSFTELARDGQDCERWNMLHPLETPRVPYIAQVMNDAPAVASTDYMKLFAEQVRTYVPADDYRVLGTDGFGRSDSRENLRHHFEVDASYVVVAALGELAKRGEIDKKVVADAIAKFNIDADKVNPRLA metq_ecoli D-methionine-binding lipoprotein MetQ metQ b0197 JW0193 yaeC protein protein ecoli Escherichia coli (strain K12) MAFKFKTFAAVGALIGSLALVGCGQDEKDPNHIKVGVIVGAEQQVAEVAQKVAKDKYGLDVELVTFNDYVLPNEALSKGDIDANAFQHKPYLDQQLKDRGYKLVAVGNTFVYPIAGYSKKIKSLDELQDGSQVAVPNDPTNLGRSLLLLQKVGLIKLKDGVGLLPTVLDVVENPKNLKIVELEAPQLPRSLDDAQIALAVINTTYASQIGLTPAKDGIFVEDKESPYVNLIVTREDNKDAENVKKFVQAYQSDEVYEAANKVFNGGAVKGW dcea_ecoli Glutamate decarboxylase alpha gadA gadS b3517 JW3485 protein protein ecoli Escherichia coli (strain K12) MDQKLLTDFRSELLDSRFGAKAISTIAESKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT 86F963E710553E22 glpd_ecoli Aerobic glycerol-3-phosphate dehydrogenase glpD glyD b3426 JW3389 protein protein ecoli Escherichia coli (strain K12) METKDLIVIGGGINGAGIAADAAGRGLSVLMLEAQDLACATSSASSKLIHGGLRYLEHYEFRLVSEALAEREVLLKMAPHIAFPMRFRLPHRPHLRPAWMIRIGLFMYDHLGKRTSLPGSTGLRFGANSVLKPEIKRGFEYSDCWVDDARLVLANAQMVVRKGGEVLTRTRATSARRENGLWIVEAEDIDTGKKYSWQARGLVNATGPWVKQFFDDGMHLPSPYGIRLIKGSHIVVPRVHTQKQAYILQNEDKRIVFVIPWMDEFSIIGTTDVEYKGDPKAVKIEESEINYLLNVYNTHFKKQLSRDDIVWTYSGVRPLCDDESDSPQAITRDYTLDIHDENGKAPLLSVFGGKLTTYRKLAEHALEKLTPYYQGIGPAWTKESVLPGGAIEGDRDDYAARLRRRYPFLTESLARHYARTYGSNSELLLGNAGTVSDLGEDFGHEFYEAELKYLVDHEWVRRADDALWRRTKQGMWLNADQQSRVSQWLVEYTQQRLSLAS 1C4D341E9E4536AB atpb_ecoli ATP synthase subunit beta atpD papB uncD b3732 JW3710 ATP synthase F1 sector subunit beta F-ATPase subunit beta protein protein ecoli Escherichia coli (strain K12) MATGKIVQVIGAVVDVEFPQDAVPRVYDALEVQNGNERLVLEVQQQLGGGIVRTIAMGSSDGLRRGLDVKDLEHPIEVPVGKATLGRIMNVLGEPVDMKGEIGEEERWAIHRAAPSYEELSNSQELLETGIKVIDLMCPFAKGGKVGLFGGAGVGKTVNMMELIRNIAIEHSGYSVFAGVGERTREGNDFYHEMTDSNVIDKVSLVYGQMNEPPGNRLRVALTGLTMAEKFRDEGRDVLLFVDNIYRYTLAGTEVSALLGRMPSAVGYQPTLAEEMGVLQERITSTKTGSITSVQAVYVPADDLTDPSPATTFAHLDATVVLSRQIASLGIYPAVDPLDSTSRQLDPLVVGQEHYDTARGVQSILQRYQELKDIIAILGMDELSEEDKLVVARARKIQRFLSQPFFVAEVFTGSPGKYVSLKDTIRGFKGIMEGEYDHLPEQAFYMVGSIEEAVEKAKKL atpa_ecoli ATP synthase subunit alpha atpA papA uncA b3734 JW3712 ATP synthase F1 sector subunit alpha F-ATPase subunit alpha protein protein ecoli Escherichia coli (strain K12) MQLNSTEISELIKQRIAQFNVVSEAHNEGTIVSVSDGVIRIHGLADCMQGEMISLPGNRYAIALNLERDSVGAVVMGPYADLAEGMKVKCTGRILEVPVGRGLLGRVVNTLGAPIDGKGPLDHDGFSAVEAIAPGVIERQSVDQPVQTGYKAVDSMIPIGRGQRELIIGDRQTGKTALAIDAIINQRDSGIKCIYVAIGQKASTISNVVRKLEEHGALANTIVVVATASESAALQYLAPYAGCAMGEYFRDRGEDALIIYDDLSKQAVAYRQISLLLRRPPGREAFPGDVFYLHSRLLERAARVNAEYVEAFTKGEVKGKTGSLTALPIIETQAGDVSAFVPTNVISITDGQIFLETNLFNAGIRPAVNPGISVSRVGGAAQTKIMKKLSGGIRTALAQYRELAAFSQFASDLDDATRKQLDHGQKVTELLKQKQYAPMSVAQQSLVLFAAERGYLADVELSKIGSFEAALLAYVDRDHAPLMQEINQTGGYNDEIEGKLKGILDSFKATQSW pyrd_ecoli Dihydroorotate dehydrogenase (quinone) Dihydroorotate oxidase DHOdehase pyrD b0945 JW0928 protein protein ecoli Escherichia coli (strain K12) MYYPFVRKALFQLDPERAHEFTFQQLRRITGTPFEALVRQKVPAKPVNCMGLTFKNPLGLAAGLDKDGECIDALGAMGFGSIEIGTVTPRPQPGNDKPRLFRLVDAEGLINRMGFNNLGVDNLVENVKKAHYDGVLGINIGKNKDTPVEQGKDDYLICMEKIYAYAGYIAINISSPNTPGLRTLQYGEALDDLLTAIKNKQNDLQAMHHKYVPIAVKIAPDLSEEELIQVADSLVRHNIDGVIATNTTLDRSLVQGMKNCDQTGGLSGRPLQLKSTEIIRRLSLELNGRLPIIGVGGIDSVIAAREKIAAGASLVQIYSGFIFKGPPLIKEIVTHI 973227EAE6B83622 rl1_ecoli 50S ribosomal protein L1 rplA Large ribosomal subunit protein uL1 JW3947 b3984 protein protein ecoli Escherichia coli (strain K12) MAKLTKRMRVIREKVDATKQYDINEAIALLKELATAKFVESVDVAVNLGIDARKSDQNVRGATVLPHGTGRSVRVAVFTQGANAEAAKAAGAELVGMEDLADQIKKGEMNFDVVIASPDAMRVVGQLGQVLGPRGLMPNPKVGTVTPNVAEAVKNAKAGQVRYRNDKNGIIHTTIGKVDFDADKLKENLEALLVALKKAKPTQAKGVYIKKVSISTTMGAGVAVDQAGLSASVN rl9_ecoli 50S ribosomal protein L9 rplI Large ribosomal subunit protein bL9 JW4161 b4203 protein protein ecoli Escherichia coli (strain K12) MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAEVLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNGVLRTTGEHEVSFQVHSEVFAKVIVNVVAE dada_ecoli D-amino acid dehydrogenase dadA dadR b1189 JW1178 D-alanine dehydrogenase protein protein ecoli Escherichia coli (strain K12) MRVVILGSGVVGVASAWYLNQAGHEVTVIDREPGAALETSAANAGQISPGYAAPWAAPGVPLKAIKWMFQRHAPLAVRLDGTQFQLKWMWQMLRNCDTSHYMENKGRMVRLAEYSRDCLKALRAETNIQYEGRQGGTLQLFRTEQQYENATRDIAVLEDAGVPYQLLESSRLAEVEPALAEVAHKLTGGLQLPNDETGDCQLFTQNLARMAEQAGVKFRFNTPVDQLLCDGEQIYGVKCGDEVIKADAYVMAFGSYSTAMLKGIVDIPVYPLKGYSLTIPIAQEDGAPVSTILDETYKIAITRFDNRIRVGGMAEIVGFNTELLQPRRETLEMVVRDLYPRGGHVEQATFWTGLRPMTPDGTPVVGRTRFKNLWLNTGHGTLGWTMACGSGQLLSDLLSGRTPAIPYEDLSVARYSRGFTPSRPGHLHGAHS ace-frda-frdb 596686 N/A 596690 unspecified role unspecified role neutral component neutral component N/A 596691 unspecified role unspecified role neutral component neutral component N/A 596692 unspecified role unspecified role neutral component neutral component N/A 596693 unspecified role unspecified role neutral component neutral component N/A 596694 unspecified role unspecified role neutral component neutral component N/A 596695 unspecified role unspecified role neutral component neutral component N/A 596696 unspecified role unspecified role neutral component neutral component physical association physical association false false false Figure 3 Figure 4A Table 3 glpd-dcea-metq 596686 N/A 596697 unspecified role unspecified role neutral component neutral component N/A 596698 unspecified role unspecified role neutral component neutral component N/A 596699 unspecified role unspecified role neutral component neutral component physical association physical association false false false Figure 3 Table 3 atpa-atpb-dada-pyrid 596686 N/A 596700 unspecified role unspecified role neutral component neutral component N/A 596701 unspecified role unspecified role neutral component neutral component N/A 596702 unspecified role unspecified role neutral component neutral component N/A 596703 unspecified role unspecified role neutral component neutral component N/A 596704 unspecified role unspecified role neutral component neutral component N/A 596705 unspecified role unspecified role neutral component neutral component physical association physical association false false false Figure 3 Table 3 ydga 596687 N/A 596694 unspecified role unspecified role neutral component neutral component N/A 596694 unspecified role unspecified role neutral component neutral component physical association physical association false false false Figure 3 B YdgA was reported to be oligomeric. glpd-dcea-metq-1 596687 N/A 596693 unspecified role unspecified role neutral component neutral component N/A 596695 unspecified role unspecified role neutral component neutral component N/A 596698 unspecified role unspecified role neutral component neutral component N/A 596699 unspecified role unspecified role neutral component neutral component N/A 596697 unspecified role unspecified role neutral component neutral component physical association physical association false false false Figure 3 B atpa-atpb-dada 596687 N/A 596701 unspecified role unspecified role neutral component neutral component N/A 596700 unspecified role unspecified role neutral component neutral component N/A 596702 unspecified role unspecified role neutral component neutral component N/A 596705 unspecified role unspecified role neutral component neutral component physical association physical association false false false Figure 3 B ompw-acee-frdb-1 596688 N/A 596691 unspecified role unspecified role prey prey N/A 596696 unspecified role unspecified role prey prey N/A 596690 unspecified role unspecified role bait bait association association false false false Figure 4 D ompw-frdb 596689 N/A 596691 unspecified role unspecified role bait bait N/A 596690 unspecified role unspecified role prey prey physical association physical association false false false Figure 4 C