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Volumn 17, Issue 11, 2016, Pages 1214-1226

Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains

Author keywords

GRAM domains; Gyp7p; pleckstrin homology (PH) domains; profile profile search; Saccharomyces cerevisiae; secondary structure prediction; structural bioinformatics; TBC1D15; Vid27p, Vps13p; YJL016W; YJL181C; YJR030C

Indexed keywords

FUNGAL PROTEIN; PLECKSTRIN; PROTEOME; MEMBRANE PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN;

EID: 84990882578     PISSN: 13989219     EISSN: 16000854     Source Type: Journal    
DOI: 10.1111/tra.12432     Document Type: Article
Times cited : (43)

References (75)
  • 1
    • 34548573170 scopus 로고    scopus 로고
    • Why are there still over 1000 uncharacterized yeast genes?
    • Pena-Castillo L, Hughes TR. Why are there still over 1000 uncharacterized yeast genes? Genetics. 2007;176:7-14.
    • (2007) Genetics , vol.176 , pp. 7-14
    • Pena-Castillo, L.1    Hughes, T.R.2
  • 2
    • 0032568596 scopus 로고    scopus 로고
    • Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
    • Brenner SE, Chothia C, Hubbard TJ. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci USA. 1998;95:6073-6078.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 6073-6078
    • Brenner, S.E.1    Chothia, C.2    Hubbard, T.J.3
  • 3
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3
  • 4
    • 0037440190 scopus 로고    scopus 로고
    • Finding weak similarities between proteins by sequence profile comparison
    • Panchenko AR. Finding weak similarities between proteins by sequence profile comparison. Nucleic Acids Res. 2003;31:683-689.
    • (2003) Nucleic Acids Res , vol.31 , pp. 683-689
    • Panchenko, A.R.1
  • 5
    • 0036307493 scopus 로고    scopus 로고
    • Within the twilight zone: a sensitive profile-profile comparison tool based on information theory
    • Yona G, Levitt M. Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J Mol Biol. 2002;315:1257-1275.
    • (2002) J Mol Biol , vol.315 , pp. 1257-1275
    • Yona, G.1    Levitt, M.2
  • 6
    • 70349775678 scopus 로고    scopus 로고
    • Exploration of uncharted regions of the protein universe
    • Jaroszewski L, Li Z, Krishna SS, et al. Exploration of uncharted regions of the protein universe. PLoS Biol. 2009;7:e1000205.
    • (2009) PLoS Biol , vol.7
    • Jaroszewski, L.1    Li, Z.2    Krishna, S.S.3
  • 7
    • 0035967880 scopus 로고    scopus 로고
    • FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
    • Shi J, Blundell TL, Mizuguchi K. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol. 2001;310:243-257.
    • (2001) J Mol Biol , vol.310 , pp. 243-257
    • Shi, J.1    Blundell, T.L.2    Mizuguchi, K.3
  • 8
    • 0344873345 scopus 로고    scopus 로고
    • On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles
    • Tang CL, Xie L, Koh IY, Posy S, Alexov E, Honig B. On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles. J Mol Biol. 2003;334:1043-1062.
    • (2003) J Mol Biol , vol.334 , pp. 1043-1062
    • Tang, C.L.1    Xie, L.2    Koh, I.Y.3    Posy, S.4    Alexov, E.5    Honig, B.6
  • 9
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics. 2005;21:951-960.
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Soding, J.1
  • 10
    • 79959834139 scopus 로고    scopus 로고
    • AlignHUSH: alignment of HMMs using structure and hydrophobicity information
    • Krishnadev O, Srinivasan N. AlignHUSH: alignment of HMMs using structure and hydrophobicity information. BMC Bioinform. 2011;12:275.
    • (2011) BMC Bioinform , vol.12 , pp. 275
    • Krishnadev, O.1    Srinivasan, N.2
  • 11
    • 0023305986 scopus 로고
    • Knowledge-based prediction of protein structures and the design of novel molecules
    • Blundell TL, Sibanda BL, Sternberg MJ, Thornton JM. Knowledge-based prediction of protein structures and the design of novel molecules. Nature. 1987;326:347-352.
    • (1987) Nature , vol.326 , pp. 347-352
    • Blundell, T.L.1    Sibanda, B.L.2    Sternberg, M.J.3    Thornton, J.M.4
  • 12
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol. 1999;292:195-202.
    • (1999) J Mol Biol , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 13
    • 80855132939 scopus 로고    scopus 로고
    • Assessment of template based protein structure predictions in CASP9
    • Mariani V, Kiefer F, Schmidt T, Haas J, Schwede T. Assessment of template based protein structure predictions in CASP9. Proteins. 2011;79(Suppl 10):37-58.
    • (2011) Proteins , vol.79 , pp. 37-58
    • Mariani, V.1    Kiefer, F.2    Schmidt, T.3    Haas, J.4    Schwede, T.5
  • 15
    • 0028856715 scopus 로고
    • Structural similarity between the pleckstrin homology domain and verotoxin: the problem of measuring and evaluating structural similarity
    • Orengo CA, Swindells MB, Michie AD, et al. Structural similarity between the pleckstrin homology domain and verotoxin: the problem of measuring and evaluating structural similarity. Protein Sci. 1995;4:1977-1983.
    • (1995) Protein Sci , vol.4 , pp. 1977-1983
    • Orengo, C.A.1    Swindells, M.B.2    Michie, A.D.3
  • 16
    • 84872115717 scopus 로고    scopus 로고
    • Pleckstrin homology (PH) domains and phosphoinositides
    • Lemmon MA. Pleckstrin homology (PH) domains and phosphoinositides. Biochem Soc Symp. 2007;74:81-93.
    • (2007) Biochem Soc Symp , vol.74 , pp. 81-93
    • Lemmon, M.A.1
  • 17
    • 0028860968 scopus 로고
    • Structure and ligand recognition of the phosphotyrosine binding domain of Shc
    • Zhou MM, Ravichandran KS, Olejniczak EF, et al. Structure and ligand recognition of the phosphotyrosine binding domain of Shc. Nature. 1995;378:584-592.
    • (1995) Nature , vol.378 , pp. 584-592
    • Zhou, M.M.1    Ravichandran, K.S.2    Olejniczak, E.F.3
  • 18
    • 0346156077 scopus 로고    scopus 로고
    • Crystal structure of a phosphoinositide phosphatase, MTMR2: insights into myotubular myopathy and Charcot-Marie-Tooth syndrome
    • Begley MJ, Taylor GS, Kim SA, Veine DM, Dixon JE, Stuckey JA. Crystal structure of a phosphoinositide phosphatase, MTMR2: insights into myotubular myopathy and Charcot-Marie-Tooth syndrome. Mol Cell. 2003;12:1391-1402.
    • (2003) Mol Cell , vol.12 , pp. 1391-1402
    • Begley, M.J.1    Taylor, G.S.2    Kim, S.A.3    Veine, D.M.4    Dixon, J.E.5    Stuckey, J.A.6
  • 19
    • 3042547173 scopus 로고    scopus 로고
    • TFIIH contains a PH domain involved in DNA nucleotide excision repair
    • Gervais V, Lamour V, Jawhari A, et al. TFIIH contains a PH domain involved in DNA nucleotide excision repair. Nat Struct Mol Biol. 2004;11:616-622.
    • (2004) Nat Struct Mol Biol , vol.11 , pp. 616-622
    • Gervais, V.1    Lamour, V.2    Jawhari, A.3
  • 21
    • 33645831773 scopus 로고    scopus 로고
    • A novel bipartite phospholipid-binding module in the neurofibromatosis type 1 protein
    • D'Angelo I, Welti S, Bonneau F, Scheffzek K. A novel bipartite phospholipid-binding module in the neurofibromatosis type 1 protein. EMBO Rep. 2006;7:174-179.
    • (2006) EMBO Rep , vol.7 , pp. 174-179
    • D'Angelo, I.1    Welti, S.2    Bonneau, F.3    Scheffzek, K.4
  • 22
    • 33645981584 scopus 로고    scopus 로고
    • ESCRT-I core and ESCRT-II GLUE domain structures reveal role for GLUE in linking to ESCRT-I and membranes
    • Teo H, Gill DJ, Sun J, et al. ESCRT-I core and ESCRT-II GLUE domain structures reveal role for GLUE in linking to ESCRT-I and membranes. Cell. 2006;125:99-111.
    • (2006) Cell , vol.125 , pp. 99-111
    • Teo, H.1    Gill, D.J.2    Sun, J.3
  • 23
    • 33646153980 scopus 로고    scopus 로고
    • The structure of the yFACT Pob3-M domain, its interaction with the DNA replication factor RPA, and a potential role in nucleosome deposition
    • VanDemark AP, Blanksma M, Ferris E, Heroux A, Hill CP, Formosa T. The structure of the yFACT Pob3-M domain, its interaction with the DNA replication factor RPA, and a potential role in nucleosome deposition. Mol Cell. 2006;22:363-374.
    • (2006) Mol Cell , vol.22 , pp. 363-374
    • VanDemark, A.P.1    Blanksma, M.2    Ferris, E.3    Heroux, A.4    Hill, C.P.5    Formosa, T.6
  • 24
    • 35348916034 scopus 로고    scopus 로고
    • Functional insights from structures of coactivator-associated arginine methyltransferase 1 domains
    • Troffer-Charlier N, Cura V, Hassenboehler P, Moras D, Cavarelli J. Functional insights from structures of coactivator-associated arginine methyltransferase 1 domains. EMBO J. 2007;26:4391-4401.
    • (2007) EMBO J , vol.26 , pp. 4391-4401
    • Troffer-Charlier, N.1    Cura, V.2    Hassenboehler, P.3    Moras, D.4    Cavarelli, J.5
  • 25
    • 77951227637 scopus 로고    scopus 로고
    • Structure-function study of the N-terminal domain of exocyst subunit Sec3
    • Baek K, Knodler A, Lee SH, et al. Structure-function study of the N-terminal domain of exocyst subunit Sec3. J Biol Chem. 2010;285:10424-10433.
    • (2010) J Biol Chem , vol.285 , pp. 10424-10433
    • Baek, K.1    Knodler, A.2    Lee, S.H.3
  • 26
    • 75049084956 scopus 로고    scopus 로고
    • Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain
    • Xu Q, Bateman A, Finn RD, et al. Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain. J Mol Biol. 2010;396:31-46.
    • (2010) J Mol Biol , vol.396 , pp. 31-46
    • Xu, Q.1    Bateman, A.2    Finn, R.D.3
  • 27
    • 84876275605 scopus 로고    scopus 로고
    • Structure of the Spt16 middle domain reveals functional features of the histone chaperone FACT
    • Kemble DJ, Whitby FG, Robinson H, McCullough LL, Formosa T, Hill CP. Structure of the Spt16 middle domain reveals functional features of the histone chaperone FACT. J Biol Chem. 2013;288:10188-10194.
    • (2013) J Biol Chem , vol.288 , pp. 10188-10194
    • Kemble, D.J.1    Whitby, F.G.2    Robinson, H.3    McCullough, L.L.4    Formosa, T.5    Hill, C.P.6
  • 28
    • 0007724488 scopus 로고    scopus 로고
    • The PH superfold: a structural scaffold for multiple functions
    • Blomberg N, Baraldi E, Nilges M, Saraste M. The PH superfold: a structural scaffold for multiple functions. Trends Biochem Sci. 1999;24:441-445.
    • (1999) Trends Biochem Sci , vol.24 , pp. 441-445
    • Blomberg, N.1    Baraldi, E.2    Nilges, M.3    Saraste, M.4
  • 30
    • 0034306454 scopus 로고    scopus 로고
    • GRAM, a novel domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins
    • Doerks T, Strauss M, Brendel M, Bork P. GRAM, a novel domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins. Trends Biochem Sci. 2000;25:483-485.
    • (2000) Trends Biochem Sci , vol.25 , pp. 483-485
    • Doerks, T.1    Strauss, M.2    Brendel, M.3    Bork, P.4
  • 32
    • 84925284236 scopus 로고    scopus 로고
    • Structure of myosin-1c tail bound to calmodulin provides insights into calcium-mediated conformational coupling
    • Lu Q, Li J, Ye F, Zhang M. Structure of myosin-1c tail bound to calmodulin provides insights into calcium-mediated conformational coupling. Nat Struct Mol Biol. 2015;22:81-88.
    • (2015) Nat Struct Mol Biol , vol.22 , pp. 81-88
    • Lu, Q.1    Li, J.2    Ye, F.3    Zhang, M.4
  • 33
    • 24344455560 scopus 로고    scopus 로고
    • Structural mechanism for sterol sensing and transport by OSBP-related proteins
    • Im YJ, Raychaudhuri S, Prinz WA, Hurley JH. Structural mechanism for sterol sensing and transport by OSBP-related proteins. Nature. 2005;437:154-158.
    • (2005) Nature , vol.437 , pp. 154-158
    • Im, Y.J.1    Raychaudhuri, S.2    Prinz, W.A.3    Hurley, J.H.4
  • 34
    • 0036087169 scopus 로고    scopus 로고
    • SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments
    • Gough J, Chothia C. SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments. Nucleic Acids Res. 2002;30:268-272.
    • (2002) Nucleic Acids Res , vol.30 , pp. 268-272
    • Gough, J.1    Chothia, C.2
  • 35
    • 84976865403 scopus 로고    scopus 로고
    • The Pfam protein families database: towards a more sustainable future
    • Finn RD, Coggill P, Eberhardt RY, et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016;44:D279-D285.
    • (2016) Nucleic Acids Res , vol.44 , pp. D279-D285
    • Finn, R.D.1    Coggill, P.2    Eberhardt, R.Y.3
  • 37
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy SR. Profile hidden Markov models. Bioinformatics. 1998;14:755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 38
    • 75549086991 scopus 로고    scopus 로고
    • Gene3D: merging structure and function for a Thousand genomes
    • Lees J, Yeats C, Redfern O, Clegg A, Orengo C. Gene3D: merging structure and function for a Thousand genomes. Nucleic Acids Res. 2010;38:D296-D300.
    • (2010) Nucleic Acids Res , vol.38 , pp. D296-D300
    • Lees, J.1    Yeats, C.2    Redfern, O.3    Clegg, A.4    Orengo, C.5
  • 39
    • 79959931985 scopus 로고    scopus 로고
    • HMMER web server: interactive sequence similarity searching
    • Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011;39:W29-W37.
    • (2011) Nucleic Acids Res , vol.39 , pp. W29-W37
    • Finn, R.D.1    Clements, J.2    Eddy, S.R.3
  • 40
    • 51349115095 scopus 로고    scopus 로고
    • Big data: The future of biocuration
    • Howe D, Costanzo M, Fey P, et al. Big data: The future of biocuration. Nature. 2008;455:47-50.
    • (2008) Nature , vol.455 , pp. 47-50
    • Howe, D.1    Costanzo, M.2    Fey, P.3
  • 41
    • 33750515229 scopus 로고    scopus 로고
    • Myo1c binds phosphoinositides through a putative pleckstrin homology domain
    • Hokanson DE, Laakso JM, Lin T, Sept D, Ostap EM. Myo1c binds phosphoinositides through a putative pleckstrin homology domain. Mol Biol Cell. 2006;17:4856-4865.
    • (2006) Mol Biol Cell , vol.17 , pp. 4856-4865
    • Hokanson, D.E.1    Laakso, J.M.2    Lin, T.3    Sept, D.4    Ostap, E.M.5
  • 43
    • 77957878139 scopus 로고    scopus 로고
    • Syt1p promotes activation of Arl1p at the late Golgi to recruit Imh1p
    • Chen KY, Tsai PC, Hsu JW, et al. Syt1p promotes activation of Arl1p at the late Golgi to recruit Imh1p. J Cell Sci. 2010;123:3478-3489.
    • (2010) J Cell Sci , vol.123 , pp. 3478-3489
    • Chen, K.Y.1    Tsai, P.C.2    Hsu, J.W.3
  • 44
    • 84863793694 scopus 로고    scopus 로고
    • The pleckstrin homology (PH) domain of the Arf exchange factor Brag2 is an allosteric binding site
    • Jian X, Gruschus JM, Sztul E, Randazzo PA. The pleckstrin homology (PH) domain of the Arf exchange factor Brag2 is an allosteric binding site. J Biol Chem. 2012;287:24273-24283.
    • (2012) J Biol Chem , vol.287 , pp. 24273-24283
    • Jian, X.1    Gruschus, J.M.2    Sztul, E.3    Randazzo, P.A.4
  • 45
    • 58149203231 scopus 로고    scopus 로고
    • InterPro: the integrative protein signature database
    • Hunter S, Apweiler R, Attwood TK, et al. InterPro: the integrative protein signature database. Nucleic Acids Res. 2009;37:D211-D215.
    • (2009) Nucleic Acids Res , vol.37 , pp. D211-D215
    • Hunter, S.1    Apweiler, R.2    Attwood, T.K.3
  • 46
    • 84858588614 scopus 로고    scopus 로고
    • Saccharomyces Genome Database: the genomics resource of budding yeast
    • Cherry JM, Hong EL, Amundsen C, et al. Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. 2012;40:D700-D705.
    • (2012) Nucleic Acids Res , vol.40 , pp. D700-D705
    • Cherry, J.M.1    Hong, E.L.2    Amundsen, C.3
  • 48
    • 63849246525 scopus 로고    scopus 로고
    • Protein structure prediction on the Web: a case study using the Phyre server
    • Kelley LA, Sternberg MJ. Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc. 2009;4:363-371.
    • (2009) Nat Protoc , vol.4 , pp. 363-371
    • Kelley, L.A.1    Sternberg, M.J.2
  • 49
    • 41049093228 scopus 로고    scopus 로고
    • Expansion of poxvirus RNA polymerase subunits sharing homology with corresponding subunits of RNA polymerase II
    • Knutson BA, Broyles SS. Expansion of poxvirus RNA polymerase subunits sharing homology with corresponding subunits of RNA polymerase II. Virus Genes. 2008;36:307-311.
    • (2008) Virus Genes , vol.36 , pp. 307-311
    • Knutson, B.A.1    Broyles, S.S.2
  • 50
    • 65949094575 scopus 로고    scopus 로고
    • Prediction of a caspase-like fold in Tannerella forsythia virulence factor PrtH
    • Pei J, Grishin NV. Prediction of a caspase-like fold in Tannerella forsythia virulence factor PrtH. Cell Cycle. 2009;8:1453-1455.
    • (2009) Cell Cycle , vol.8 , pp. 1453-1455
    • Pei, J.1    Grishin, N.V.2
  • 51
    • 58349112969 scopus 로고    scopus 로고
    • Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors
    • Bateman A, Finn RD, Sims PJ, Wiedmer T, Biegert A, Soding J. Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors. Bioinformatics. 2009;25:159-162.
    • (2009) Bioinformatics , vol.25 , pp. 159-162
    • Bateman, A.1    Finn, R.D.2    Sims, P.J.3    Wiedmer, T.4    Biegert, A.5    Soding, J.6
  • 52
    • 77955361329 scopus 로고    scopus 로고
    • Homology of SMP domains to the TULIP superfamily of lipid-binding proteins provides a structural basis for lipid exchange between ER and mitochondria
    • Kopec KO, Alva V, Lupas AN. Homology of SMP domains to the TULIP superfamily of lipid-binding proteins provides a structural basis for lipid exchange between ER and mitochondria. Bioinformatics. 2010;26:1927-1931.
    • (2010) Bioinformatics , vol.26 , pp. 1927-1931
    • Kopec, K.O.1    Alva, V.2    Lupas, A.N.3
  • 53
    • 77951978637 scopus 로고    scopus 로고
    • Insights into the domain and repeat architecture of target of rapamycin
    • Knutson BA. Insights into the domain and repeat architecture of target of rapamycin. J Struct Biol. 2010;170:354-363.
    • (2010) J Struct Biol , vol.170 , pp. 354-363
    • Knutson, B.A.1
  • 54
    • 79751476605 scopus 로고    scopus 로고
    • Yeast homologues of three BLOC-1 subunits highlight KxDL proteins as conserved interactors of BLOC-1
    • Hayes MJ, Bryon K, Satkurunathan J, Levine TP. Yeast homologues of three BLOC-1 subunits highlight KxDL proteins as conserved interactors of BLOC-1. Traffic. 2011;12:260-268.
    • (2011) Traffic , vol.12 , pp. 260-268
    • Hayes, M.J.1    Bryon, K.2    Satkurunathan, J.3    Levine, T.P.4
  • 55
    • 80052955293 scopus 로고    scopus 로고
    • Yeast Rrn7 and human TAF1B are TFIIB-related RNA polymerase I general transcription factors
    • Knutson BA, Hahn S. Yeast Rrn7 and human TAF1B are TFIIB-related RNA polymerase I general transcription factors. Science. 2011;333:1637-1640.
    • (2011) Science , vol.333 , pp. 1637-1640
    • Knutson, B.A.1    Hahn, S.2
  • 56
    • 79958720098 scopus 로고    scopus 로고
    • Expansion of type II CAAX proteases reveals evolutionary origin of gamma-secretase subunit APH-1
    • Pei J, Mitchell DA, Dixon JE, Grishin NV. Expansion of type II CAAX proteases reveals evolutionary origin of gamma-secretase subunit APH-1. J Mol Biol. 2011;410:18-26.
    • (2011) J Mol Biol , vol.410 , pp. 18-26
    • Pei, J.1    Mitchell, D.A.2    Dixon, J.E.3    Grishin, N.V.4
  • 57
    • 84874246696 scopus 로고    scopus 로고
    • The product of C9orf72, a gene strongly implicated in neurodegeneration, is structurally related to DENN Rab-GEFs
    • Levine TP, Daniels RD, Gatta AT, Wong LH, Hayes MJ. The product of C9orf72, a gene strongly implicated in neurodegeneration, is structurally related to DENN Rab-GEFs. Bioinformatics. 2013;29:499-503.
    • (2013) Bioinformatics , vol.29 , pp. 499-503
    • Levine, T.P.1    Daniels, R.D.2    Gatta, A.T.3    Wong, L.H.4    Hayes, M.J.5
  • 58
    • 84876431000 scopus 로고    scopus 로고
    • Discovery of new Longin and Roadblock domains that form platforms for small GTPases in ragulator and TRAPP-II
    • Levine TP, Daniels RD, Wong LH, Gatta AT, Gerondopoulos A, Barr FA. Discovery of new Longin and Roadblock domains that form platforms for small GTPases in ragulator and TRAPP-II. Small GTPases. 2013;4:62-69.
    • (2013) Small GTPases , vol.4 , pp. 62-69
    • Levine, T.P.1    Daniels, R.D.2    Wong, L.H.3    Gatta, A.T.4    Gerondopoulos, A.5    Barr, F.A.6
  • 59
    • 84902312762 scopus 로고    scopus 로고
    • Characterization of TSET, an ancient and widespread membrane trafficking complex
    • Hirst J, Schlacht A, Norcott JP, et al. Characterization of TSET, an ancient and widespread membrane trafficking complex. eLife. 2014;3:e02866.
    • (2014) eLife , vol.3
    • Hirst, J.1    Schlacht, A.2    Norcott, J.P.3
  • 60
    • 84856489442 scopus 로고    scopus 로고
    • HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
    • Remmert M, Biegert A, Hauser A, Soding J. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods. 2012;9:173-175.
    • (2012) Nat Methods , vol.9 , pp. 173-175
    • Remmert, M.1    Biegert, A.2    Hauser, A.3    Soding, J.4
  • 61
    • 0031762837 scopus 로고    scopus 로고
    • Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence
    • Gerstein M. Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence. Bioinformatics. 1998;14:707-714.
    • (1998) Bioinformatics , vol.14 , pp. 707-714
    • Gerstein, M.1
  • 62
    • 17744372267 scopus 로고    scopus 로고
    • The P5 protein from bacteriophage phi-6 is a distant homolog of lytic transglycosylases
    • Pei J, Grishin NV. The P5 protein from bacteriophage phi-6 is a distant homolog of lytic transglycosylases. Protein Sci. 2005;14:1370-1374.
    • (2005) Protein Sci , vol.14 , pp. 1370-1374
    • Pei, J.1    Grishin, N.V.2
  • 64
    • 1642367563 scopus 로고    scopus 로고
    • Genome-wide analysis of membrane targeting by S. cerevisiae pleckstrin homology domains
    • Yu JW, Mendrola JM, Audhya A, et al. Genome-wide analysis of membrane targeting by S. cerevisiae pleckstrin homology domains. Mol Cell. 2004;13:677-688.
    • (2004) Mol Cell , vol.13 , pp. 677-688
    • Yu, J.W.1    Mendrola, J.M.2    Audhya, A.3
  • 65
    • 84951019875 scopus 로고    scopus 로고
    • Ltc1 is an ER-localized sterol transporter and a component of ER-mitochondria and ER-vacuole contacts
    • Murley A, Sarsam RD, Toulmay A, Yamada J, Prinz WA, Nunnari J. Ltc1 is an ER-localized sterol transporter and a component of ER-mitochondria and ER-vacuole contacts. J Cell Biol. 2015;209:539-548.
    • (2015) J Cell Biol , vol.209 , pp. 539-548
    • Murley, A.1    Sarsam, R.D.2    Toulmay, A.3    Yamada, J.4    Prinz, W.A.5    Nunnari, J.6
  • 66
    • 0034282751 scopus 로고    scopus 로고
    • Localization of phosphatidylinositol 3-phosphate in yeast and mammalian cells
    • Gillooly DJ, Morrow IC, Lindsay M, et al. Localization of phosphatidylinositol 3-phosphate in yeast and mammalian cells. EMBO J. 2000;19:4577-4588.
    • (2000) EMBO J , vol.19 , pp. 4577-4588
    • Gillooly, D.J.1    Morrow, I.C.2    Lindsay, M.3
  • 67
    • 0037197804 scopus 로고    scopus 로고
    • Targeting of Golgi-specific pleckstrin homology domains involves both PtdIns 4-kinase-dependent and -independent components
    • Levine TP, Munro S. Targeting of Golgi-specific pleckstrin homology domains involves both PtdIns 4-kinase-dependent and -independent components. Curr Biol. 2002;12:695-704.
    • (2002) Curr Biol , vol.12 , pp. 695-704
    • Levine, T.P.1    Munro, S.2
  • 68
    • 84869118647 scopus 로고    scopus 로고
    • VPS13 regulates membrane morphogenesis during sporulation in Saccharomyces cerevisiae
    • Park JS, Neiman AM. VPS13 regulates membrane morphogenesis during sporulation in Saccharomyces cerevisiae. J Cell Sci. 2012;125:3004-3011.
    • (2012) J Cell Sci , vol.125 , pp. 3004-3011
    • Park, J.S.1    Neiman, A.M.2
  • 69
    • 84965190934 scopus 로고    scopus 로고
    • ER-mitochondrial junctions can be bypassed by dominant mutations in the endosomal protein Vps13
    • Lang AB, John Peter AT, Walter P, Kornmann B. ER-mitochondrial junctions can be bypassed by dominant mutations in the endosomal protein Vps13. J Cell Biol. 2015;210:883-890.
    • (2015) J Cell Biol , vol.210 , pp. 883-890
    • Lang, A.B.1    John Peter, A.T.2    Walter, P.3    Kornmann, B.4
  • 70
    • 84980002132 scopus 로고    scopus 로고
    • Yeast Vps13 promotes mitochondrial function and is localized at membrane contact sites
    • Park JS, Thorsness MK, Policastro R, et al. Yeast Vps13 promotes mitochondrial function and is localized at membrane contact sites. Mol Biol Cell. 2016;27:2435-2449.
    • (2016) Mol Biol Cell , vol.27 , pp. 2435-2449
    • Park, J.S.1    Thorsness, M.K.2    Policastro, R.3
  • 71
    • 0028609692 scopus 로고
    • Pleckstrin homology (PH) domains in signal transduction
    • Ingley E, Hemmings BA. Pleckstrin homology (PH) domains in signal transduction. J Cell Biochem. 1994;56:436-443.
    • (1994) J Cell Biochem , vol.56 , pp. 436-443
    • Ingley, E.1    Hemmings, B.A.2
  • 72
    • 77952108998 scopus 로고    scopus 로고
    • The functions of steryl glycosides come to those who wait: Recent advances in plants, fungi, bacteria and animals
    • Grille S, Zaslawski A, Thiele S, Plat J, Warnecke D. The functions of steryl glycosides come to those who wait: Recent advances in plants, fungi, bacteria and animals. Prog Lipid Res. 2010;49:262-288.
    • (2010) Prog Lipid Res , vol.49 , pp. 262-288
    • Grille, S.1    Zaslawski, A.2    Thiele, S.3    Plat, J.4    Warnecke, D.5
  • 73
    • 0022470653 scopus 로고
    • Overproduction-induced mislocalization of a yeast vacuolar protein allows isolation of its structural gene
    • Rothman JH, Hunter CP, Valls LA, Stevens TH. Overproduction-induced mislocalization of a yeast vacuolar protein allows isolation of its structural gene. Proc Natl Acad Sci USA. 1986;83:3248-3252.
    • (1986) Proc Natl Acad Sci USA , vol.83 , pp. 3248-3252
    • Rothman, J.H.1    Hunter, C.P.2    Valls, L.A.3    Stevens, T.H.4
  • 74
    • 23144452044 scopus 로고    scopus 로고
    • The HHpred interactive server for protein homology detection and structure prediction
    • Soding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 2005;33:W244-W248.
    • (2005) Nucleic Acids Res , vol.33 , pp. W244-W248
    • Soding, J.1    Biegert, A.2    Lupas, A.N.3
  • 75
    • 77954257799 scopus 로고    scopus 로고
    • ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
    • Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res. 2010;38:W529-W533.
    • (2010) Nucleic Acids Res , vol.38 , pp. W529-W533
    • Ashkenazy, H.1    Erez, E.2    Martz, E.3    Pupko, T.4    Ben-Tal, N.5


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