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Database of Supergene Family

Research Project

Project/Area Number 03558027
Research Category

Grant-in-Aid for Developmental Scientific Research (B)

Allocation TypeSingle-year Grants
Research Field 分子遺伝学・分子生理学
Research InstitutionKYOTO UNIVERSITY

Principal Investigator

MIYATA Takashi  Kyoto Univ. Biophysics, Professor, 理学部, 教授 (20022692)

Co-Investigator(Kenkyū-buntansha) OGITA Naoshi  Fujitu Information Processing System Laboratory Adviser, 顧問
HASEGAWA Masami  Institute of Statistical Mathematics Professor, 教授 (60011657)
Project Period (FY) 1991 – 1992
Project Status Completed (Fiscal Year 1992)
Budget Amount *help
¥16,600,000 (Direct Cost: ¥16,600,000)
Fiscal Year 1992: ¥4,800,000 (Direct Cost: ¥4,800,000)
Fiscal Year 1991: ¥11,800,000 (Direct Cost: ¥11,800,000)
KeywordsSupergene family / Alignment / Consensus sequence / motif / molecular phylogenetic tree / database / 超遺伝子族 / デ-タベ-ス / ホモロジ- / コンピュ-タ / タンパク質
Research Abstract

(1) For each of three protein families involved in cell adhesion, six protein families involved in signal transduction, ras-related GTP binding protein family, and other six protein families, the amino acid sequences were aligned among members, and the consensus sequence and weighted motifs of highly conserved segments were determined based on the alignment. phylogenetic trees representing branching orders of family members in evolution were also inferred. These data were included in our database of supergene family.
(2) A new method was developed to search sequences in database that show significant similarities with motifs of known family members : In this method a score system was introduced representing the frequency of occurrence of an amino acid on each amino acid position of the motif. On the basis of the score system, a statistical test was carried out for the observed sequence similarity.
(3) Applying the above method to three protein families involved in cell adhesion, we found sequence similarities between trk and immunoglobulin family members, between ret and cadherin family members, and between several tyrosine kinases and fibronectin type III family members.
(4) From the above results, we showed that known receptor type protein tyrosine kinases are classified into at least four groups, based on the structural differences of the extracellular domains. This classification in almost parallel to that based on a phylogenetic tree inferred from a sequence comparison of the kinase domains.

Report

(3 results)
  • 1992 Annual Research Report   Final Research Report Summary
  • 1991 Annual Research Report
  • Research Products

    (30 results)

All Other

All Publications (30 results)

  • [Publications] KUMA,K.,IWABE,N.and MIYATA,T.: "The immunoglobulin family" Current Opinion in Structural Biology. 1. 384-393 (1991)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1992 Final Research Report Summary
  • [Publications] KUMA,K.,IWABE,N.and MIYATA,T.: "Motifs of immunoglobulin-like domains:Neurotrophic factor receptors trk and trkB are members of the immunoglobulin family." Proc.Japan Acad.67B. 188-192 (1991)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1992 Final Research Report Summary
  • [Publications] HAYASHIDA,H.,KUMA,K.and MIYATA,T.: "Inter-chromosomal gene conversion as a possible mechanism for explaining divergence patterns of ZFY-related genes." J.Mol.Evol.35. 181-183 (1992)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1992 Final Research Report Summary
  • [Publications] KUMA,K.,MIYATA,T.and TAKEICHI,M.: "Proto-oncogene ret has cadherin-like repeats in the extracellular region." Proc.Japan Acad.68B. 106-108 (1992)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1992 Final Research Report Summary
  • [Publications] HASEGAWA,M.,HASHIMOTO,T.,ADACHI,J.,IWABE,N.and MIYATA,T.: "Early branchings in the evolution of eukaryotes:Ancient divergence of entamoeba that lacks mitochondria revealed by protein sequence data." J.Mol.Evol.

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1992 Final Research Report Summary
  • [Publications] KUMA,K.,IWABE,N.and MIYATA,T.: "Motifs of cadherin-and fibronectin type III-related sequences and evolution of the receptor type protein tyrosine kinases: Sequence similarity between proto-oncogene ret and cadherin family." Mol.Biol.Evol.

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1992 Final Research Report Summary
  • [Publications] Iwabe, N., Kuma, K., Kishino, H., Hasegawa, M. and Miyata, T.: "Evolution of RNA polymerases and branching patterns of the three major groups of archaebacteria." J.Mol.Evol.32. 70-78 (1991)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1992 Final Research Report Summary
  • [Publications] Kuma, K., Iwabe, N. and Miyata, T.: "The immunoglobulin family Current Opinion in Structural Biology 1" 384-393 (1991)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1992 Final Research Report Summary
  • [Publications] Nakano, K., Matuda, S., Yamanaka, T., Tsubouchi, H., Nakagawa, S., Titani, K., Ohta, S. and Miyata, T.: "Purification and molecular cloning of succinyltransferase of the rat a-ketoglutarate dehydrogenase complex." J.Biol. Chem.266. 19013-19017 (1991)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1992 Final Research Report Summary
  • [Publications] Kuma, K., Iwade, N. and Miyata, T.: "Motifs of immunoglobulin-like domains : Neurotrophic factor receptors trk and trkB are members of the immunoglobulin family." Proc.Japan Acad.67B. 188-192 (1991)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1992 Final Research Report Summary
  • [Publications] Hayashida, H., Kuma, K. and Miyata, T.: "Inter-chromosomal gene conversion as a possible mechanism for explaining devergence patterns of ZFY-related genes." J.Mol.Evol.35. 181-183 (1992)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1992 Final Research Report Summary
  • [Publications] Kuma, K., Miyata, T. and Takeichi, M.: "Proto-oncogene ret has cadherin-like repeats in the extracellular region." Proc.Japan Acad.68B. 106-108 (1992)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1992 Final Research Report Summary
  • [Publications] Hasegawa,M., Hashimoto,T., Adachi,J., Iwabe,N. and Miyata,T.: "Early branchings in the evolution of eukaryotes: Ancient divergence of entamoeba that lacks mitochondria revealed by protein sequence data." J.Mol.Evol.

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1992 Final Research Report Summary
  • [Publications] Kuma, K. and Miyata, T.: "Temporal and geographical patterns of dengue 1 virus evolution." J.Mol.Evol.

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1992 Final Research Report Summary
  • [Publications] Kuma, K., Iwade, N. and Miyata, T.: "Motifs of cadherin-and fibronectin type III-related sequences and evolution of the receptor type protein tyrosine kinases : Sequence similarity between proto-oncogene ret and cadherin family." Mol.Biol.Evol.

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1992 Final Research Report Summary
  • [Publications] Tokunaga, F., Muta, T., Iwanaga, S., Ichinose, A., Davie, E. W., Kuma, K. and Miyata, T.: "Limulus hemocyte transglutaminase II : Its cDNA cloning, amino acid sequence, and tissue localization." J.Biol.Chem.

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1992 Final Research Report Summary
  • [Publications] Fujita, Y., Mynlieff, M., Dirksen, R.T., Kim, M-S., Niidome, T., Nakai, J., Friedrich, T., Iwabe, N., Miyata, T., Mori, Y., and Beam, K. G.: "Primary structure and functional expression of the o-conotoxin-sensitive N-type calcium channel from rabbit brain." Neuron.

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1992 Final Research Report Summary
  • [Publications] Kuma, K. and Miyata, T.: "Global constraint and molecular evolutionary rate : Slowly evolving brain specific genes demonstrated by protein kinase and immunoglobulin supergene families." Proc.Natl.Acad.Sci. USA.

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1992 Final Research Report Summary
  • [Publications] Hayashida,H.,Kuma,K.and Miyata,T.: "Inter-chromosomal gene conversion as a possible mechanism for explaining divergence patterns of ZFY-related genes." J.Mol.Evol.35. 181-183 (1992)

    • Related Report
      1992 Annual Research Report
  • [Publications] Kuma,K.,Miyata,T.and Takeichi,M.: "Proto-oncogene ret has cadherin-like repeats in the extracellular region." Proc.Japan Acad.68B. 106-108 (1992)

    • Related Report
      1992 Annual Research Report
  • [Publications] Hasegawa,M.,Hashimoto,T.,Adachi,J.,Iwabe,N.and Miyata,T.: "Early branchings in the evolution of eukaryotes:Ancient divergence of entamoeda that lacks mitochondria revealed by protein sequence data." J.Mol.Evol.

    • Related Report
      1992 Annual Research Report
  • [Publications] Kuma,K.and Miyata,T.: "Temporal and Geographical patterns of dengue 1 verus evolution." J.Mol.Evol.

    • Related Report
      1992 Annual Research Report
  • [Publications] Kuma,K.,Iwabe,N.and Miyata,T.: "Motifs of cadherin-and fibronectin type III-related sequences and evolution of the receptor type protein tyrosine kinases:Sequence similarity between proto-oncogene ret and cadherin family." Mol.Biol.Evol.

    • Related Report
      1992 Annual Research Report
  • [Publications] Tokunaga,F.,Muta,T.,Iwanaga,S.,Ichinose,A.,Davie,E.W.,Kuma,K.and Miyata,T.: "Limulus hemocyte transglutaminase II:Its cDNA cloning,amino acid sequence,and tissue localization." J.Biol.chem.

    • Related Report
      1992 Annual Research Report
  • [Publications] Kuma,K.: "The immunoglobulin family" Current Opinion in Structural Biology. 1. 384-393 (1991)

    • Related Report
      1991 Annual Research Report
  • [Publications] Kuma,K.: "Motifs of immunoglobulin-like domains:Neurotrophic factor receptors trk and trkB are members of the immunoglobulin family." Proc.Japan Acad.67B. 188-192 (1991)

    • Related Report
      1991 Annual Research Report
  • [Publications] Iwabe,N.: "Evolution of RNA polymerases and branching patterns of the three major groups of archaebacteria." J.Mol.Evol.32. 70-78 (1991)

    • Related Report
      1991 Annual Research Report
  • [Publications] Matsuda,S.: "Purification and molecular cloning of succinyltransferase of the rat α-ketoglutarate dehydrogenase complex." J.Biol.Chem.266. 19013-19017 (1991)

    • Related Report
      1991 Annual Research Report
  • [Publications] Hayashida,H.: "Inter-chromosomal gene conversion as a possible mechanism for explaining divergence patterns of ZFY-related genes." J.Mol.Evol.

    • Related Report
      1991 Annual Research Report
  • [Publications] Hasegawa,M.: "Early branchings in the evolution of eukaryotes:Ancient divergence of entamoeba that lacks mitochondria revealed by protein sequence data." J.Mol.Evol.

    • Related Report
      1991 Annual Research Report

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Published: 1991-04-01   Modified: 2016-04-21  

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