mpidb The Microbial Protein Interaction Database fagan-2009-3 Structural insights into the molecular organization of the S-layer from Clostridium difficile. in vitro In vitro elisa enzyme linked immunosorbent assay ELISA ELISA elisa antibody detection identification by antibody antibody detection Fagan R.P., Albesa-Jové D., Qazi O., Svergun D.I., Brown K.A., Fairweather N.F. Mol. Microbiol. (0950-382X) 2009 Only protein-protein interactions imex curation fagan-2009-1 Structural insights into the molecular organization of the S-layer from Clostridium difficile. clod6 Clostridium difficile (strain 630) Clostridium difficile comig non denat gel comigration in non denaturing gel electrophoresis comig non denat gel polyclonal western polyclonal antibody western blot polyclonal western Fagan R.P., Albesa-Jové D., Qazi O., Svergun D.I., Brown K.A., Fairweather N.F. Mol. Microbiol. (0950-382X) 2009 Only protein-protein interactions imex curation fagan-2009-2 Structural insights into the molecular organization of the S-layer from Clostridium difficile. in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Fagan R.P., Albesa-Jové D., Qazi O., Svergun D.I., Brown K.A., Fairweather N.F. Mol. Microbiol. (0950-382X) 2009 Only protein-protein interactions imex curation q183m8_clod6 CD630_27930 slpA protein protein clod6 Clostridium difficile (strain 630) Clostridium difficile MNKKNIAIAMSGLTVLASAAPVFAATTGTQGYTVVKNDWKKAVKQLQDGLKDNSIGKITVSFNDGVVGEVAPKSANKKADRDAAAEKLYNLVNTQLDKLGDGDYVDFSVDYNLENKIITNQADAEAIVTKLNSLNEKTLIDIATKDTFGMVSKTQDSEGKNVAATKALKVKDVATFGLKSGGSEDTGYVVEMKAGAVEDKYGKVGDSTAGIAINLPSTGLEYAGKGTTIDFNKTLKVDVTGGSTPSAVAVSGFVTKDDTDLAKSGTINVRVINAKEESIDIDASSYTSAENLAKRYVFDPDEISEAYKAIVALQNDGIESNLVQLVNGKYQVIFYPEGKRLETKSANDTIASQDTPAKVVIKANKLKDLKDYVDDLKTYNNTYSNVVTVAGEDRIETAIELSSKYYNSDDKNAITDKAVNDIVLVGSTSIVDGLVASPLASEKTAPLLLTSKDKLDSSVKSEIKRVMNLKSDTGINTSKKVYLAGGVNSISKDVENELKNMGLKVTRLSGEDRYETSLAIADEIGLDNDKAFVVGGTGLADAMSIAPVASQLKDGDATPIVVVDGKAKEISDDAKSFLGTSDVDIIGGKNSVSKEIEESIDSATGKTPDRISGDDRQATNAEVLKEDDYFTDGEVVNYFVAKDGSTKEDQLVDALAAAPIAGRFKESPAPIILATDTLSSDQNVAVSKAVPKDGGTNLVQVGKGIASSVINKMKDLLDM slpa-slpa-3 1335317 n/a 1335320 unspecified role unspecified role prey prey c-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false low mw slpa required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli n/a 1335320 unspecified role unspecified role bait bait high mw slp sufficient to bind sufficient binding region sufficient to bind range range certain certain sequence position certain false c-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false ecolx Escherichia coli direct interaction direct interaction false false false 1335317 Fig. 4A, 4B slpa-slpa-4 1335317 n/a 1335320 unspecified role unspecified role bait bait c-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false low mw slpa required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false ecolx Escherichia coli n/a 1335320 unspecified role unspecified role prey prey high mw slp required to bind necessary binding region required to bind certain certain sequence position certain certain certain sequence position certain false c-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false ecolx Escherichia coli direct interaction direct interaction false false false 1335317 Fig. 4C, 4D slpa-slpa 1335318 n/a 1335320 unspecified role unspecified role neutral component neutral component high mw slp sufficient to bind sufficient binding region sufficient to bind range range certain certain sequence position certain false n/a 1335320 unspecified role unspecified role neutral component neutral component low mw slpa sufficient to bind sufficient binding region sufficient to bind range range range range false 1335339 1335337 physical association physical association false false false Figure 2 slpa-slpa-1 1335319 n/a 1335320 unspecified role unspecified role neutral component neutral component high mw slp sufficient to bind sufficient binding region sufficient to bind range range certain certain sequence position certain false c-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false ecolx Escherichia coli n/a 1335320 unspecified role unspecified role neutral component neutral component low mw slpa sufficient to bind sufficient binding region sufficient to bind range range range range false c-terminal his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false ecolx Escherichia coli 1335345 1335342 direct interaction direct interaction false false false Figure 2B DIP Database of Interacting Proteins 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ dip@mbi.ucla.edu 611 Young Drive East; Los Angeles CA 90095; USA http://dip.doe-mbi.ucla.edu/ czyzewski-2012-1 ecolx Escherichia coli x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Czyzewski BK., Wang DN. DIP original experiment: DIP-249445X Nature 2012 IMEx Identification and characterization of a bacterial hydrosulphide ion channel. Czyzewski BK., Wang DN. Only protein-protein interactions imex curation aksyuk-2011-1 ecolx Escherichia coli 3d-em 3D electron microscopy 3D-EM electron tomog predetermined predetermined participant predetermined Aksyuk AA., Kurochkina LP., Fokine A., Forouhar F., Mesyanzhinov VV., Tong L., Rossmann MG. DIP original experiment: DIP-220180X Structure (London, England : 1993) 2011 IMEx Structural conservation of the myoviridae phage tail sheath protein fold. Aksyuk AA., Kurochkina LP., Fokine A., Forouhar F., Mesyanzhinov VV., Tong L., Rossmann MG. Only protein-protein interactions imex curation q186b7_clod6 CD630_22300 protein protein clod6 Clostridium difficile (strain 630) Clostridium difficile MHKETLDKLTNAAINKINLLNTSKVKYLVSSAFAGLYVGIGILLIFTIGGLLTDAGSPMTKIVMGLSFAIALSLVIMTGTELFTGNNMVMSAGMLNKGVSIKDTSKIWAYSWVGNLIGALVLGIIFVGTGLVDKGPVAEFFANTAASKASMPFTALFFRGILCNILVCVSVLCSFRTNSDTAKIIMIFLCLFAFITSGFEHSVANMTIYSVSLFSPTISTVTIGGAIYNLVAVTLGNIVGGALFMGLGTYILGKEKLN q184a3_clod6 CD630_09540 CD630_29100 protein protein clod6 Clostridium difficile (strain 630) Clostridium difficile MALGGGTFVTQNKILPGSYINFISAKRATSSLSDRGIVAIPLELDWGIDEDVFQVTSDDFEKYSVKYFGYDYTHEKLKGLRDLFKNIRLGYFYKLNKGVKASCTIATAKYSGIRGNDLKVTVTTNIDDNAKFDVVTLLDNKKVDTQIAKVITDLQDNDYITWKKDATLEASAGLVFTGGTNGEAVTGAEYQAFLDKIESYSFNALGCLATTTEIKSLFVEFTKRMRDKVGAKFQTVLYKKSDADYEGVVSVENKIKEIGLVESSLIYWAAGAIAGCDINKSNTNKKYDGEFDVDVNYTQIQLEEALKTGKFIFHKVGDEVHVLEDINTFVSFTDDKNDDFSSNQSVRVLDQIANDIATLFNEKYLGKVPNDKAGRISFWNDVVKHHKELENIRAIEDFKTDDVSVELGNDKKTVIVSDAVKVINAMSKLYMTVSVN q186b7_pepd6-1 3237939 N/A 3237940 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false q184a3_pepd6-1 3233786 N/A 3233787 unspecified role unspecified role unspecified role unspecified role ecolx Escherichia coli direct interaction direct interaction false false false MINT MINT, Dpt of Biology, University of Rome Tor Vergata MINT http://mint.bio.uniroma2.it/mint url>http://mint.bio.uniroma2.it/mint/ https://mint.bio.uniroma2.it MINT-[0-9]+ https://mint.bio.uniroma2.it/index.php/results-interactions/?id=${ac} The Molecular INTeraction database (MINT) is a relational database designed to store interactions between biological molecules. http://mint.bio.uniroma2.it http://mint.bio.uniroma2.it/mint anonymous-2014z-1 Clostridium difficile sortase recognizes a (S/P)PXTG sequence motif and can accommodate diaminopimelic acid as a substrate for transpeptidation in vitro In vitro enzymatic study enzymatic study ms participant Identification by mass spectrometry ms participant P.Hensbergen@lumc.nl 2014 imex curation van Leeuwen H.C., Klychnikov O.I., Menks M.A., Kuijper E.J., Drijfhout J.W., Hensbergen P.J. FEBS Lett. (0014-5793) Only protein-protein interactions q183r6_clod6 CD630_28310 protein protein clod6 Clostridium difficile (strain 630) Clostridium difficile MKKGNRKALLISLIMILSMVVSTIYPTVSYASELGENSQIQSGSTNSSTGEEKESDNKKPEQTPEKDKATDNKKPEQTPEEEKPTDNKKPEQTPEEDKSTDNKKPEQTPEGEKPIDNKKPEQIPEEDKSTDNKKSEQALEDEKPLDNKNTEKTPEEDNLLEDENLLKVLEEELNEENEDYGFVVKINNNTIETESMKKISFNLTYTPTSKGIQAGDSITFKVPDVFNKVNLDYTSECFDKTESNGEYTLTFRELPNGQSVMQGKIGLEAYVKKVDEDTNAKIHIETTGKIESGSGDIDVEIKPGDKTDVPDAKGTLKKLVEGKKSTTVFMPVKNKDINYSIQVNEKQEELKDIILYDELPEGLTLINGSVSVVTSDGKEVSDFNIEQSKNSISVNFGNIDKSYTVKYKARISDKNAKHGNKYKNVARIESDGKKIQEDDATVSIFDRGDDYLLTKGHSGATNITQVGQVINYQISINDDKSPISNVVITDNIPEGMRLTTSGEAGHDFRVVEIPMNGSWTPWSKEKIANNISYKVEEKRNESGQVDKVITGFTINLSKEEVESKFFIAYTLKVISIEDSYINRAVLDANNSEIDKNDEINFKKNSGLISAKKEVDKKVLNSSDNQIVKYKINMSTYGVYDAGQVNLLDEVNSVLEISNIKYSDNLELKKEAGDGKNTIRLVNKYEFKQIKEGEPVQSWVTFDANFTNVKVGETIRNVAQINGSSPPGVETTKQGYAFEAKKVDALDKNVLSGAKFNLEDAFGNIVVKDLVSDEDGIIQSSVKNPGTYYLVEIMAPRGYEKLKDKIKVEIGNKDIGRIVDIGNIENIRQENPPVNPPAPPNTDEPIVNPPVPPSTDKPRKPSSSSDTEDTIVINPPVPPSEDIINPPIPEVLNPPVPPSEEMIETPVKQIIPIPEVVKPSVSEEKNNKVKDDTLVNPPVPPKTGDSTTIIGEILLVIGAIVGLIVLRRNKNTN q183f3_clod6 CD630_27180 protein protein clod6 Clostridium difficile (strain 630) Clostridium difficile MKKLYRIVINIILVLVILYSGFNIYSKLTKYNHDTKISSELQKKEYKKEDLSKINSDFKFWLSVENTNINYPVVQSKDNSYYLDKDFYKKDSISGTLFMDYRNKSIDDKNIIIYGHNMKNKTMFNNLNKFKDADFFKKNNKIKITLNGKEFLYDVFSAYIVESDYDYLKTNFNNESDYQNYINDITSKSLYKSPIKVNSNDKIVTLSTCTYEFDDARMVIHGRLI q17zz0_clod6 CD630_32460 protein protein clod6 Clostridium difficile (strain 630) Clostridium difficile MKTKIKKSSIISLVIAFSMVFTAFTPIVSYADEVTSNDTILNGEEQSNGQTPDVEKPSDGQVPGGEKPSDSQVPDGEKPSDGQVPDGEKPSDGQIPDGEKPSDGQIPDGEKPSDGQIPDGEKPSDGQMPDGEKTSDSQTPDVEKPSDGQMPDGEKPLDEQTPEEEKPLEEEIVIEEMSLKQDIDKILDMTLSQINKIVYNFWEDEEDVKADEQSEINQVFTSEDSFISLWYDKKAKVKNSCLLKEIDGSDRPYHDLRFDDITKTLTFDYVIKGLVGASSKDDKYVIEGEDGEQTAFCYNNHLRPPSSNGKSPYLPAEDFNGQENQNEEAVKSILYAGSEFDGFGYKQQFNLGGEENELMTYSATQSAIWIILGQMDEQERLKQYQGSINLCDKLIERAKTEEERAEYQKKKEVAINIKAYLEALLKAGREELKPNNTGKPSLSNGLTKINFEKNEDGTYETEAVALVGYSGVVKLRLPDGVTAYDVDGNIIGTGEVEISTQQKFKLKSVGKPDAKANISAVSYDYIFPKAIQYYKAVLDLGQKDHSSSLPSSKQNLLSYTIEKKNGQEVNFNIGLPTDDDDVVNPPVPPIDDDVVNPPVPPTDDTNGHKPKPSPPIDDTVINPPVPPMDDTIINPPVPPTEDAVLNPPVPPMEDAVLNPPVPPTDDTVLNPPVPPVSDTVEKTPELSRDDTIVKSPKTGDETQLMSYVFISVIAICGLAYQCKIKRN g6b7g2-q183f3 1569610 n/a CD3246 1569611 ms participant Identification by mass spectrometry ms participant enzyme target enzyme target substrate substrate neutral component neutral component purified purified range binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false n/a C. difficile sortase B (CD2718) 1569612 predetermined predetermined participant predetermined enzyme enzyme neutral component neutral component purified purified his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false range binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false cleavage cleavage reaction cleavage false false false f2 t1 sf2 sf4 q17zz0-q183f3 1569610 n/a CD2831 1569613 ms participant Identification by mass spectrometry ms participant enzyme target enzyme target substrate substrate neutral component neutral component purified purified range binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false Q183R6:p.Pro940Leu mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false n/a C. difficile sortase B (CD2718) 1569612 predetermined predetermined participant predetermined enzyme enzyme neutral component neutral component purified purified range binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false his tag his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false cleavage cleavage reaction cleavage false false false f3 t1 sf3