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Protein Overview: VPS41

General Information:
Name(s) found: VPS41 / YDR080W [SGD]
Description(s) found:
Found 30 descriptions.
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  • Vacuolar membrane protein that is a subunit of the homotypic vacuole fusion and vacuole protein sorting (HOPS) complex; essential for membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of protein transport [SGD]
    • Organism: Saccharomyces cerevisiae
    Length: 992 amino acids

    Gene Ontology:
    Cellular Component: endosome [IDALink to PubMed article]
    fungal-type vacuole [IDALink to PubMed article]
    vacuolar membrane [IDALink to PubMed article]
    HOPS complex [IPILink to PubMed article]
    Biological Process: vacuolar protein processing [IMPLink to PubMed article]
    vacuole organization [IMPLink to PubMed article]
    protein transport [IMPLink to PubMed article]
    vacuole fusion, non-autophagic [IDALink to PubMed article][IMPLink to PubMed article]
    Molecular Function: Rab guanyl-nucleotide exchange factor activity [IPILink to PubMed article]


    Sequence:
    Sequence:
    [PDR BLAST]
    [ProtParam] 
          1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTTDNHQNDS VLDQQSGERT IDESNSISDE NNVDNKREDV NVTSPTKSVS CISQAENGVA  60
   61 SRTDESTITG SATDAETGDD DDDDDDDDDE DEDDEDEPPL LKYTRISQLP KNFFQRDSIS 120
  121 SCLFGDTFFA FGTHSGILHL TTCAFEPIKT IKCHRSSILC INTDGKYFAT GSIDGTVIIG 180
  181 SMDDPQNITQ YDFKRPINSV ALHSNFQASR MFVSGGMAGD VVLSQRNWLG NRIDIVLNKK 240
  241 KKKKTRKDDL SSDMKGPIMG IYTMGDLILW MDDDGITFCD VPTRSQLLNI PFPSRIFNVQ 300
  301 DVRPDLFRPH VHFLESDRVV IGWGSNIWLF KVSFTKDSNS IKSGDSNSQS NNMSHFNPTT 360
  361 NIGSLLSSAA SSFRGTPDKK VELECHFTVS MLITGLASFK DDQLLCLGFD IDIEEEATID 420
  421 EDMKEGKNFS KRPENLLAKG NAPELKIVDL FNGDEIYNDE VIMKNYEKLS INDYHLGKHI 480
  481 DKTTPEYYLI SSNDAIRVQE LSLKDHFDWF MERKQYYKAW KIGKYVIGSE ERFSIGLKFL 540
  541 NSLVTKKDWG TLVDHLNIIF EETLNSLDSN SYDVTQNVLK EWADIIEILI TSGNIVEIAP 600
  601 LIPKKPALRK SVYDDVLHYF LANDMINKFH EYITKWDLKL FSVEDFEEEL ETRIEAASEP 660
  661 TASSKEEGSN ITYRTELVHL YLKENKYTKA IPHLLKAKDL RALTIIKIQN LLPQYLDQIV 720
  721 DIILLPYKGE ISHISKLSIF EIQTIFNKPI DLLFENRHTI SVARIYEIFE HDCPKSFKKI 780
  781 LFCYLIKFLD TDDSFMISPY ENQLIELYSE YDRQSLLPFL QKHNNYNVES AIEVCSSKLG 840
  841 LYNELIYLWG KIGETKKALS LIIDELKNPQ LAIDFVKNWG DSELWEFMIN YSLDKPNFTK 900
  901 AILTCSDETS EIYLKVIRGM SDDLQIDNLQ DIIKHIVQEN SLSLEVRDNI LVIINDETKK 960
  961 FANEFLKIRS QGKLFQVDES DIEINDDLNG VL

    Protein Complex Data

      PUBLICATION TOPOLOGY COCOMPLEXED PROTEINS
    View Details Riffle et al. (2010) (Unpublished Data) PEP3 PEP5 VPS16 VPS33 VPS41 VPS8
    View Details (MIPS) Mewes HW, et al. (2004) VAM6 VPS41
    View Details Gavin AC, et al. (2006) PEP3 PEP5 VAM6 VPS16 VPS33 VPS41 VPS8
    View Details Gavin AC, et al. (2002) ATP8 LUC7 PEP3 PEP5 SNU71 VAM6 VPS16 VPS33 VPS41 VPS8
    View Details Ho Y, et al. (2002) RCK2 VPS41

    Mass Spectrometry Data

    The following runs contain data for this protein:

      BAIT COMMENTS PUBLICATION
    View Run CEP3 sample cbf3 from feb 2005 Sandall S, et all (2006)
    View Run ZDS1 Sample 2- cpn2 from june 2005 McCusker D, et al (2007)
    View Run ZDS1 Sample 3 - cpn + atp, from june 2005 McCusker D, et al (2007)
    View Run VAM3 sample: hx3 Hao Xu, et al. (2010)
    View Run VAM3 Sample: HX11 - both fusion and trans-SNARE complex formation take place. Hao Xu, et al. (2010)
    View Run VAM3 Sample: HX12 - trans-SNARE complex formation and fusion are inhibited (control). Hao Xu, et al. (2010)
    View Run VAM3 Sample: HX13 - trans-SNARE complex forms but fusion is blocked. Hao Xu, et al. (2010)
    View Run VAM3 Sample: HX14 - mixture in detergent (control). Hao Xu, et al. (2010)
    View Run VAM3 hx23: mixture in detergent (control) Investigating Vam3p, Nyv1p and their partners in trans-SNARE complex Hao Xu, et al. (2010)
    View Run MLP2 #31 Asynchronous Prep (Protease cleavage) Keck JM, et al. (2011)

    Yeast Two-Hybrid Data

    The following interactions contain this protein:

    NOT SHOWING SINGLE HITS. [ Show Single Hits ]

    [View our yeast two-hybrid interpretation guidelines.]

    No yeast two-hybrid interactions found for this protein.

    Microscopy / Localization Data

    New Feature: Upload Your Own Microscopy Data

      PROTEIN(S) PUBLICATION
    View Data VPS41 Huh WK, et al. (2003)

    Protein Structure Data


    [What does the above image mean?]
    [View Top Sequence Alignments] [Show Ginzu Version Information]

    Domains predicted:

    #   Region(s) Method Confidence Match Description
    1 View Details [1..375] PSI-BLAST 57.0 Tup1, C-terminal domain
    2 View Details [376..478] PSI-BLAST 68.30103 beta1-subunit of the signal-transducing G protein heterotrimer
    3 View Details [479..992] ORFEUS 12.83 Clathrin heavy chain proximal leg segment

    Functions predicted (by domain):

    # Gene Ontology predictions
    1
    Term Confidence Notes
  • cytoskeletal protein binding
    		•  2.20122168933317 bayes_pls_golite062009
  • binding
    		•  1.99637157021613 bayes_pls_golite062009
  • actin binding
    		•  1.40054662654509 bayes_pls_golite062009
  • protein binding
    		•  1.21879977456466 bayes_pls_golite062009
  • transporter activity
    		•  1.21549336905926 bayes_pls_golite062009
  • tubulin binding
    		•  1.10875870970504 bayes_pls_golite062009
  • microtubule binding
    		•  1.03769395387791 bayes_pls_golite062009
  • substrate-specific transporter activity
    		•  0.734793983890004 bayes_pls_golite062009
  • nucleic acid binding
    		•  0.624115832843391 bayes_pls_golite062009
  • hydrolase activity
    		•  0.36638536879917 bayes_pls_golite062009
  • transcription repressor activity
    		•  0.328276176504109 bayes_pls_golite062009
  • transcription regulator activity
    		•  0.282387003961579 bayes_pls_golite062009
  • dynein binding
    		•  0.180120691665679 bayes_pls_golite062009
  • structural molecule activity
    		•  0.0588151480189092 bayes_pls_golite062009
  • nucleoside-triphosphatase activity
    		•  0.00585398682921312 bayes_pls_golite062009
    2
    Term Confidence Notes
  • cytoskeletal protein binding
    		•  2.20122168933317 bayes_pls_golite062009
  • binding
    		•  1.99637157021613 bayes_pls_golite062009
  • actin binding
    		•  1.40054662654509 bayes_pls_golite062009
  • protein binding
    		•  1.21879977456466 bayes_pls_golite062009
  • transporter activity
    		•  1.21549336905926 bayes_pls_golite062009
  • tubulin binding
    		•  1.10875870970504 bayes_pls_golite062009
  • microtubule binding
    		•  1.03769395387791 bayes_pls_golite062009
  • substrate-specific transporter activity
    		•  0.734793983890004 bayes_pls_golite062009
  • nucleic acid binding
    		•  0.624115832843391 bayes_pls_golite062009
  • hydrolase activity
    		•  0.36638536879917 bayes_pls_golite062009
  • transcription repressor activity
    		•  0.328276176504109 bayes_pls_golite062009
  • transcription regulator activity
    		•  0.282387003961579 bayes_pls_golite062009
  • dynein binding
    		•  0.180120691665679 bayes_pls_golite062009
  • structural molecule activity
    		•  0.0588151480189092 bayes_pls_golite062009
  • nucleoside-triphosphatase activity
    		•  0.00585398682921312 bayes_pls_golite062009
    3
    Term Confidence Notes
  • protein transporter activity
    		•  2.99345877012947 bayes_pls_golite062009
  • binding
    		•  2.53151481871847 bayes_pls_golite062009
  • transporter activity
    		•  2.3766833486706 bayes_pls_golite062009
  • substrate-specific transporter activity
    		•  2.12926593993985 bayes_pls_golite062009
  • cytoskeletal protein binding
    		•  1.67265990792668 bayes_pls_golite062009
  • protein binding
    		•  1.61131270705552 bayes_pls_golite062009
  • transmembrane transporter activity
    		•  1.2724388835449 bayes_pls_golite062009
  • protein transmembrane transporter activity
    		•  1.12112006227201 bayes_pls_golite062009
  • substrate-specific transmembrane transporter activity
    		•  1.04982314606251 bayes_pls_golite062009
  • nucleic acid binding
    		•  1.0110931222658 bayes_pls_golite062009
  • actin binding
    		•  0.864076688656138 bayes_pls_golite062009
  • hydrolase activity
    		•  0.648465506487331 bayes_pls_golite062009
  • signal sequence binding
    		•  0.279693431859311 bayes_pls_golite062009
  • active transmembrane transporter activity
    		•  0.260663498540354 bayes_pls_golite062009
  • ion transmembrane transporter activity
    		•  0.256036243669218 bayes_pls_golite062009
  • structural molecule activity
    		•  0.244712400498315 bayes_pls_golite062009
  • nuclear localization sequence binding
    		•  0.241630311762028 bayes_pls_golite062009
  • RNA binding
    		•  0.235569865745441 bayes_pls_golite062009
  • primary active transmembrane transporter activity
    		•  0.234271600707329 bayes_pls_golite062009
  • P-P-bond-hydrolysis-driven transmembrane transporter activity
    		•  0.225395946682209 bayes_pls_golite062009
  • hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances
    		•  0.186601655036333 bayes_pls_golite062009
  • ATPase activity, coupled to movement of substances
    		•  0.183072614802483 bayes_pls_golite062009
  • ATPase activity, coupled to transmembrane movement of substances
    		•  0.182751938544977 bayes_pls_golite062009
  • transcription regulator activity
    		•  0.111971004877048 bayes_pls_golite062009
  • nucleoside-triphosphatase activity
    		•  0.109435859778099 bayes_pls_golite062009
  • clathrin binding
    		•  0.0923079381755934 bayes_pls_golite062009
  • pyrophosphatase activity
    		•  0.0728493557966827 bayes_pls_golite062009
  • hydrolase activity, acting on acid anhydrides
    		•  0.0641324729536009 bayes_pls_golite062009
  • hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
    		•  0.0615190129942244 bayes_pls_golite062009
  • cation transmembrane transporter activity
    		•  0.0475280280823402 bayes_pls_golite062009
  • signal transducer activity
    		•  0.0143632526449453 bayes_pls_golite062009
  • molecular transducer activity
    		•  0.0143632526449453 bayes_pls_golite062009


    Reference: Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076


    Philius Transmembrane Prediction:

    Protein predicted to be: GLOBULAR (No transmembrane regions or signal peptide)
    Confidence of classification: 0.95

    Source: Reynolds et al. (2008)

    YRC Informatics Platform - Version 3.0
    Created and Maintained by: Michael Riffle