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

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

« L’hypothèse du génome » : mise en évidence du fait que différends

• rganismes utilisent préférentielle-

ment certains jeux de codons syno- nymes (Grantham et al., Nucleic Acids Res., 8:1893-1912, 1980)

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Nucléotides EMBL GenBank DDBJ Protéines (1) TrEMBL GenPept Protéines (2) SWISS-PROT PIR† NRL_3D

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NRDB SWISS-PROT PIR† GenPept PDB UniProtKB SWISS-PROT TrEMBL PIR†

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

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

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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). …

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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 …

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… 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 //

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 {  {  {

Duplications partielles ou complètes dans les séquences

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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).

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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. …

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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

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Banque PROSITE eMOTIF PRINTS BLOCKS Profile Pfam Construction Expressions régulières (patterns) Expression régulières floues Motifs alignés (fingerprints) Motifs pondérés Matrices de pondération (profils) Modèles de Markov Cachés (HMM) Source SWISS-PROT BLOCKS/PRINTS UniProt UniProt UniProt UniProt/ProDom

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Motifs simples Motifs multiples Alignements de domaines entiers

Profils (Profile) HMM (Pfam) Patterns flous (eMOTIF) Patterns exacts (PROSITE) Motifs alignés (PRINTS) Matrices de pondération (BLOCKS)

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ID BACTERIAL_OPSIN_1; PATTERN. AC PS00950; DT JUN-1994 (CREATED); JUN-1994 (DATA UPDATE); JUL-1998 (INFO UPDATE). DE Bacterial rhodopsins signature 1. PA R-Y-x-[DT]-W-x-[LIVMF]-[ST]-T-P-[LIVM](3). NR /RELEASE=38,80000; NR /TOTAL=22(22); /POSITIVE=22(22); /UNKNOWN=0(0); /FALSE_POS=0(0); NR /FALSE_NEG=1; /PARTIAL=1; CC /TAXO-RANGE=A????; /MAX-REPEAT=1; DR P19585, BAC1_HALS1, T; P29563, BAC2_HALS2, T; P96787, BAC3_HALSD, T; DR Q48334, BAC3_HALVA, T; P33970, BACH_HALHM, T; Q48315, BACH_HALHP, T; DR Q48314, BACH_HALHS, T; P16102, BACH_HALSP, T; P33742, BACH_HALSS, T; DR P94853, BACH_HALVA, T; P15647, BACH_NATPH, T; Q57101, BACR_HALAR, T; DR P02945, BACR_HALHA, T; P33969, BACR_HALHM, T; P33971, BACR_HALHP, T; DR P33972, BACR_HALHS, T; Q53496, BACR_HALSR, T; P94854, BACR_HALVA, T; DR P25964, BACS_HALHA, T; P33743, BACS_HALSS, T; P71411, BACT_HALSA, T; DR P42196, BACT_NATPH, T; DR Q53461, BACH_HALAR, P; DR P42197, BACT_HALVA, N; 3D 1BRD; 2BRD; 1BRR; 1BRX; 1BAC; 1BAD; 1BHA; 1BHB; 1BCT; 1AP9; 1AT9; 1SR1; DO PDOC00291; //

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gc; BACTRLOPSIN gx; PR00251 gn; COMPOUND(7) ga; 11-NOV-1993; UPDATE 06-JUN-1999 gt; Bacterial opsin signature gp; PRINTS; PR00237 GPCRRHODOPSN; PR00247 GPCRCAMP; PR00248 GPCRMGR gp; PRINTS; PR00249 GPCRSECRETIN; PR00250 GPCRSTE2; PR00899 GPCRSTE3 gp; PRINTS; PR00238 OPSIN gp; INTERPRO; IPR001425 gp; PROSITE; PS00950 BACTERIAL_OPSIN_1; PS00327 BACTERIAL_OPSIN_RET gp; BLOCKS; BL00327 gp; PFAM; PF01036 Bac_rhodopsin gp; PDB; 1BRD gp; SCOP; 1BRD bb; gr; 1. OESTERHELT, D. AND TITTOR, J. gr; Two pumps, one principle - Light-driven ion-transport in halobacteria. gr; TRENDS BIOCHEM.SCI. 14(2) 57-61 (1989).

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cd; 7| 15 15 15 15 15 15 15 cd; 6| 0 1 1 1 1 1 1 cd; 5| 0 1 1 0 1 1 1 cd; 4| 0 1 1 0 0 1 1 cd; 3| 0 0 2 2 0 1 1 cd; 2| 0 0 0 0 0 0 0 cd; --+------------------------------------ cd; | 1 2 3 4 5 6 7 bb; tp; BACH_HALHP BACH_HALHS BACH_HALVA BAC3_HALSD tp; BAC2_HALS2 BACH_NATPH BACH_HALSS BAC1_HALS1 tp; BACR_HALAR BACR_HALVA BACH_HALSP BACR_HALSR tp; BACR_HALHA BACS_HALHA BACS_HALSS bb; sn; Codes involving 6 elements st; BAC3_HALVA bb; sn; Codes involving 5 elements st; BACT_NATPH bb; sn; Codes involving 4 elements st; BACT_HALVA

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im; INITIAL MOTIF-SETS im; ------------------ ic; BACTRLOPSIN1 il; 20 it; Bacterial opsin TM motif I - 1 id; LYINIALAGLSILLFVFMTR BACH_NATPH 37 37 id; AYLGGAVALIVGVAFVWLLY BACS_HALHA 6 6 id; LWVNVALAGIAILVFVYMGR BACH_HALSP 32 32 id; LWLGIGTLLMLIGTFYFIVK BAC1_HALS1 22 22 id; IWLALGTALMGLGTLYFLVK BACR_HALHA 23 23 bb; ic; BACTRLOPSIN2 il; 21 it; Bacterial opsin TM motif II - 1 id; IAVSTILVPVVSIASYTGLAS BACH_NATPH 66 9 id; ALAPLAIIPVFAGLSYVGMAY BACS_HALHA 36 10 id; IWGATLMIPLVSISSYLGLLS BACH_HALSP 61 9 id; YYSITILVPGIASAAYLSMFF BAC1_HALS1 53 11 id; FYAITTLVPAIAFTMYLSMLL BACR_HALHA 54 11

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InterPro

profile prodom pfam prints prosite

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Accession IPR001425 Name Bacterial rhodopsin Type Family Dates 08-OCT-1999 (created) 28-FEB-2000 (last modified) Signatures PROSITE PS00327 BACTERIAL_OPSIN_RET PROSITE PS00950 BACTERIAL_OPSIN_1 PRINTS BACTRLOPSIN PFAM PF01036 Bac_rhodopsin Abstract The bacterial opsins are retinal-binding proteins that provide light-dependent ion transport and sensory functions to a family

• f halophilic bacteria [1, 2] ]. They are integral membrane

proteins believed to contain seven transmembrane (TM) domains, the last of which contains the attachment point for retinal (a conserved lysine). ... Example s * Q48315 BACH_HALHP: Halorhodopsin * Q53496 BACR_HALSR: Cruxrhodopsin * P15647 BACH_NATPH * P96787 BAC3_HALSD: Archaearhodopsin View examples ...

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Systèmes GXD (Mouse Gene Expression Database) The Stanford Microarray Database GDB (Genome Data Base) EMG (Encyclopedia of Mouse Genome) MGD (Mouse Genome Database) INE (Integrated Rice Genome Explorer) SWISS-2DPAGE PDD (Protein Disease Database) Sub2D (B. subtilis 2D Protein Index) PDB (Protein Data Bank) MMDB (Molecular Modelling Data Base) NRL_3D (Non-Redundant Library of 3D Structures) SCOP (Structural Classification of Proteins) ALFRED (Allele Frequency Database) DIP (Database of Interacting proteins) BIND (Biomolecular Interaction Network Database) Données Expression des gènes Cartographie Quantification Structures 3D Polymorphisme Interactions moléculaires

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