guy.perriere@univ-lyon1.fr Ple Bioinformatique Lyonnais - PowerPoint PPT Presentation

guy.perriere@univ-lyon1.fr

Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

« L’hypothèse du génome » : mise en évidence du fait que différends organismes utilisent préférentielle- ment certains jeux de codons syno- nymes (Grantham et al., Nucleic Acids Res. , 8 :1893-1912, 1980) Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

Nucléotides Protéines (1) Protéines (2) EMBL TrEMBL SWISS-PROT GenBank GenPept PIR † DDBJ NRL_3D Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

NRDB UniProtKB SWISS-PROT SWISS-PROT PIR † TrEMBL GenPept PIR † PDB Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

ID M19233; SV 1; linear; genomic DNA; STD; HUM; 851 BP. XX AC M19233; XX DT 16-JUL-1988 (Rel. 16, Created) DT 14-NOV-2006 (Rel. 89, Last updated, Version 13) XX DE Human alpha-amylase-1 gene, exon 6. XX KW amylase. XX OS Homo sapiens (human) OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; OC Homo. XX RN [1] RP 1-851 RX PUBMED; 2442579. RA Handy D.E., Larsen S.H., Karn R.C., Hodes M.E.; RT "Identification of a human salivary amylase gene. Partial sequence of RT genomic DNA suggests a mode of regulation different from that of mouse, RT Amy1"; RL Mol. Biol. Med. 4(3):145-155(1987). … Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

CC Draft entry and computer-readable sequence for [1] kindly provided CC by D.E.Handy, 06-JAN-1988. XX FH Key Location/Qualifiers FH FT source 1..851 FT /organism="Homo sapiens" FT /map="1p21" FT /mol_type="genomic DNA" FT /tissue_type="salivary gland" FT /db_xref="taxon:9606" FT CDS join(M17883.1:988..1155,M17883.1:1504..1650, FT M17883.1:2451..2648,M17883.1:3098..3328,625..758) FT /partial FT /codon_start=1 FT /gene="AMY1A" FT /product="alpha-amylase" FT /db_xref="GDB:120544" FT /db_xref="GOA:P04745" FT /db_xref="HGNC:474" FT /db_xref="UniProtKB/Swiss-Prot:P04745" FT /protein_id="AAA57345.1" FT /translation="MKLFWLLFTIGFCWAQYSSNTQQGRTSIVHLFEWRWVDIALECER FT YLAPKGFGGVQVSPPNENVAIHNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNV FT GVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDI … Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

… FT intron <1..624 FT /gene="AMY1A" FT /number=5 FT /note="G00-120-544" FT exon 625..758 FT /gene="AMY1A" FT /number=6 FT /note="G00-120-544" FT intron 759..>851 FT /gene="AMY1A" FT /number=6 FT /note="G00-120-544" SQ Sequence 851 BP; 284 A; 133 C; 162 G; 272 T; 0 other; tcttacctcc tctcttactt acaggcatat ctaattcttt atcacaacag gttttatgga 60 ggtacacaga atgtaggata ctgataatag ttatgtcttt gttttctttg gaaaatgaaa 120 tgaaatgagt taatatttat caaaaaaagt gagtcagata gtaaatatcg tattcctgtg 180 agctgttatt attatcattg atgtacaaga ctaaaaatta ggtaagtatt ctcacaggac 240 aacaggtaac tttgacatta tgtttctttc aatattgtag tgtatacttt atcaaaaaaa 300 … ttttttttcc taaatttctt ctaggtaatt gatctgggtg gtgagccaat taaaagcagt 660 gactactttg gtaatggccg ggtgacagaa ttcaagtatg gtgcaaaact cggcacagtt 720 attcgcaagt ggactggaga gaagatgtct tacttaaagt aaataaatac aacttttccc 780 ctgaactatt tcatagactg ttagtcatac taccccagtg cgagttatct tctggaacat 840 ttcttattca g 851 // Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

 {  {  { Duplications partielles ou complètes dans les séquences Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

ID AMPA_ECOLI Reviewed; 503 AA. AC P68767; P11648; Q2M649; DT 21-DEC-2004, integrated into UniProtKB/Swiss-Prot. DT 21-DEC-2004, sequence version 1. DT 22-JUL-2008, entry version 40. DE RecName: Full=Cytosol aminopeptidase; DE EC=3.4.11.1; DE AltName: Full=Leucine aminopeptidase; DE Short=LAP; DE AltName: Full=Leucyl aminopeptidase; DE AltName: Full=Aminopeptidase A/I; GN Name=pepA; Synonyms=carP, xerB; OrderedLocusNames=b4260, JW4217; OS Escherichia coli (strain K12). OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; OC Enterobacteriaceae; Escherichia. OX NCBI_TaxID=83333; ... RN [3] RP SEQUENCE FROM N.A. RC STRAIN=K12 / MG1655; RX MEDLINE=95334362; PubMed=7610040; RA Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., RA Blattner F.R.; RT "Analysis of the Escherichia coli genome VI: DNA sequence of the RT region from 92.8 through 100 minutes."; RL Nucleic Acids Res. 23:2105-2119(1995). Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

CC -!- FUNCTION: Presumably involved in the processing and regular CC turnover of intracellular proteins. Catalyzes the removal of CC unsubstituted N-terminal amino acids from various peptides. CC Required for plasmid ColE1 site-specific recombination but not in CC its aminopeptidase activity. Could act as a structural component CC of the putative nucleoprotein complex in which the Xer CC recombination reaction takes place. CC -!- CATALYTIC ACTIVITY: Release of an N-terminal amino acid, Xaa-|- CC Yaa-, in which Xaa is preferably Leu, but may be other amino acids CC including Pro although not Arg or Lys, and Yaa may be Pro. Amino CC acid amides and methyl esters are also readily hydrolyzed, but CC rates on arylamides are exceedingly low. CC -!- COFACTOR: Binds 2 manganese ions per subunit (By similarity). CC -!- ENZYME REGULATION: Inhibited by zinc and EDTA. CC -!- SUBUNIT: Homohexamer. CC -!- SIMILARITY: Belongs to the peptidase M17 family. CC -!- CAUTION: The ligation for manganese is based on the ligation for CC zinc, an inhibitor, in the crystallographic structure reported in CC PubMed:10449417. The ligation for manganese in the active form of CC the enzyme may differ. DR EMBL; X15130; CAA33225.1; -; Genomic_DNA. DR EMBL; X86443; CAA60164.1; -; Genomic_DNA. … Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

KW 3D-structure; Aminopeptidase; Complete proteome; KW Direct protein sequencing; Hydrolase; Manganese; Metal-binding; KW Protease. FT CHAIN 1 503 Cytosol aminopeptidase. FT /FTId=PRO_0000165750. FT ACT_SITE 282 282 Potential. FT ACT_SITE 356 356 Potential. FT METAL 270 270 Manganese 2 (Probable). FT METAL 275 275 Manganese 1 (Probable). … FT METAL 354 354 Manganese 2 (Probable). FT MUTAGEN 354 354 E->A: Loss of activity. FT STRAND 2 6 FT HELIX 10 12 FT STRAND 18 23 FT TURN 24 26 … SQ SEQUENCE 503 AA; 54880 MW; 643DED17EAC44DCD CRC64; MEFSVKSGSP EKQRSACIVV GVFEPRRLSP IAEQLDKISD GYISALLRRG ELEGKPGQTL LLHHVPNVLS ERILLIGCGK ERELDERQYK QVIQKTINTL NDTGSMEAVC FLTELHVKGR NNYWKVRQAV ETAKETLYSF DQLKTNKSEP RRPLRKMVFN VPTRRELTSG ERAIQHGLAI … DVLTYVERFE PEAVIDVATL TGACVIALGH HITGLMANHN PLAHELIAAS EQSGDRAWRL PLGDEYQEQL ESNFADMANI GGRPGGAITA GCFLSRFTRK YNWAHLDIAG TAWRSGKAKG ATGRPVALLA QFLLNRAGFN G Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr

Banque Source Construction PROSITE SWISS-PROT Expressions régulières ( patterns ) eMOTIF BLOCKS/PRINTS Expression régulières floues PRINTS UniProt Motifs alignés ( fingerprints ) BLOCKS UniProt Motifs pondérés Profile UniProt Matrices de pondération (profils) Pfam UniProt/ProDom Modèles de Markov Cachés (HMM) Pôle Bioinformatique Lyonnais – http://pbil.univ-lyon1.fr