Search for ancient patterns in protein sequences

Journal of Molecular Evolution

Volumn 42, Issue 2, 1996, Pages 224-233

  Thode, Guillermo ^a   García Ranea, Juan Antonio ^a   Jimenez, Juan ^a  

^a UNIVERSITY OF MÁLAGA   (Spain)

Author keywords

Ancient patterns; Molecular evolution; Nonrelated proteins; Sequence footprints

Indexed keywords

DNA; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; DATA BASE; EVOLUTION; EXON; HUMAN; NONHUMAN; PHYLOGENY;

AMINO ACID SEQUENCE; ANIMALS; CDC2 PROTEIN KINASE; DATABASES, FACTUAL; DNA, VIRAL; EVOLUTION, MOLECULAR; GEMINIVIRIDAE; HUMANS; MICE; MOLECULAR SEQUENCE DATA; ORNITHINE DECARBOXYLASE; PROTEINS; READING FRAMES; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0029897953     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF02198848     Document Type: Article

References (27)

1. Bairoch A (1993) The PROSITE dictionary of sites and patterns in proteins, its current status. Nucleic Acids Res 21:3097-3103
2. Bairoch A, Boeckmann B (1993) The SWISS-PROT protein sequence data bank, recent developments. Nucleic Acids Res 21:3093-3096
3. Baron M, Norman DG, Campbell ID (1991) Protein modules. Trends Biosci 16:13-17
4. Blum ML, Down JA, Gurnett AM, Carrington M, Turner MJ, Wiley DC (1993) A structural motif in the variant surface glycoproteins of Trypanosoma brucei. Nature 362:603-609
5. Brenner S, Lerner RA (1992) Encoded combinatorial chemistry. Proc Natl Acad Sci USA 89:5381-5383
6. Claverie JM (1993) Database of ancient sequences. Nature 364:19-20
7. Doolittle RF (1985) The genealogy of some recently evolved vertebrate proteins. Trends Biosci 10:233-237
8. Doolittle RF (1994) Convergent evolution: the need to be explicit. Trends Biosci 19:15-18
9. Feldmann H, et al. (1994) Complete DNA sequence of yeast chromosome II. EMBO J 24:5795-5809
10. Gibson T, Thompson JD, Blocker A, Kouzarides T (1994) Evidence for a protein domain superfamily shared by the cyclins, TFIIB and RB/p107. Nucleic Acids Res 22:946-952
11. Goffeau A (1994) Genes in search of functions. Nature 369:101-102
12. Green P, Lipman D, Hillier L, Waterston R, State D, Claverie JM (1993) Ancient conserved regions in new gene sequences and the protein databases. Science 259:1711-1716
13. Holm L, Ouzounis C, Sander C, Tuparev G, Vriend G (1992) A data-base of protein structure families with common folding motifs. Protein Sci 1:1691-1698
14. Houghten RA, Pinilla C, Blondelle SE, Appel JR, Dooley CT, Cuervo JH (1991) Generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery. Nature 354:84-86
15. Jimenez J, Alphey L, Nurse P, Glover M (1990) Complementation of fission yeast cdc2ts and cdc25ts mutants identifies two cell cycle genes from Drosophila: a cdc2 homologue and string. EMBO J 9:3565-3571
16. Karlin S, Ost F, Blaisdell BE (1989) Patterns in DNA and amino acid sequences and their statistical significance. In: Waterman MS, Mathematical methods for DNA sequences. CRC Press, Boca Raton, FL, pp 133-157
17. Kuma KI, Iwabe N, Miyata T (1993) Motifs of cadherin- and fibronectin type III-related sequences and evolution of the receptor-type-protein tyrosine kinases: sequence similarity between protooncogene ret and Cadherin family. Mol Biol Evol 10:539-551
18. Kemp BE, Pearson RB (1990) Protein kinase recognition sequence motifs. Trends Biosci 15:342-346
19. Lazarowitz SG (1992) Geminiviruses: genome structure and gene function. Crit Rev Plant Sci 11:327-349
20. Mayer BJ, Ren R, Clark KL, Baltimore D (1993) A putative modular domain present in diverse signalling proteins. Cell 73:629-630
21. Oliver SG, et al. (1992) The complete DNA sequence of yeast chromosome III. Nature 357:38-46
22. Pongor S, Skerl V, CserzÖ M, Hátsági Z, Simon G, Bevilacqua V (1993) The SBASE protein domain library, release 2.0: a collection of annotated protein sequence segments. Nucleic Acids Res 21: 3111-3115
23. Poulin R, Lu L, Ackermann B, Bey P, Pegg AE (1992) Mechanism of the irreversible inactivation of mouse ornithine decarboxylase by alpha-difluoromethyl ornithine - characterization of sequences at the inhibitor and coenzyme binding-sites. J Biol Chem 267:150-158
24. Sander C, Schneider R (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment proteins. Struct Funct Genet 9:56-68
25. Sato A, Nishimura S, Ohkubo T, Kyogoku Y, Koyama S, Kobayashi M, Yasuda T, Kobayashi Y (1992) H-1-NMR assignment and secondary structure of human insulin-like growth factor-I (IGF-I) in solution. J Biochem 111:529-536
26. Sternberg MJE (1991) Library of common protein motifs. Nature 349: 111
27. Sternberg MJE, Islam SA (1991) Protein sequences - homologies and motifs. TIBTECH 9:300-302