Les II,

2. FBW 06-10-2011 Wim Van Criekinge

10. Sequence entries gene 10317..12529 /gene="ZK822.4" CDS join (10317..10375,10714..10821,10874..10912,10960..11013, 11061..11114,11169..11222,11346..11739,11859..11912, 11962..12195,12242..12529) /gene="ZK822.4" /codon_start=1 /protein_id="CAA98068.1" /db_xref="PID:g3881817" /db_xref="GI:3881817" /db_xref="SPTREMBL:Q23615" /translation="MHRHTYRKLYWNLGADGFSQGNADASVSAGSSGSNFLSGLQNSS FGQAVMGGINTYNQAKNSSGGNWQTAVANSSVGNFFQNGIDFFNGMKNGTQNFLDTDT IQETIGNSSFGEVVQTGVEFFNNIKNGNSPFQGDASSVMSQFVPFLANASAEAKAEFY TILPNFGNMTIAEFETAVNAWAAKYNLTDEVEAFNERSKNATVVAEEHANVVVMNLPN VLNNLKAISSDKNQTVVEMHTRMMAYVNSLDDDTRDIVFIFFRNLLPPQFKKSKCVDQ GNFLTNMYNKASDFFAGRNNRTDGEGSFWSGQGQNGNSGGSGFSSFFNNFNGQGNGNG NGAQNPMIGMFNNFMKKNNITADEANAAMADGGASIQILPAISAGWGDVAQVKIGGDF KIAVEEETKTTKKNKKQQQQANKNKNKNKKKTTIAPEAAIDANIAAEVHTQVL"

13. FEATURES Location/Qualifiers source 1..756 /organism="Listeria ivanovii" /strain="ATCC 19119" /db_xref="taxon:1638" RBS 95..100 /gene="sod" gene 95..746 /gene="sod" CDS 109..717 /gene="sod" /EC_number="1.15.1.1" /codon_start=1 /product="superoxide dismutase" /db_xref="PID:g44011" /db_xref="SWISS-PROT:P28763" /transl_table=11 /translation="MTYELPKLPYTYDALEPNFDKETMEIHYTKHHNIYVTKL NEAVSGHAELASKPGEELVANLDSVPEEIRGAVRNHGGGHANHTLFWSSLSPN GGGAPTGNLKAAIESEFGTFDEFKEKFNAAAAARFGSGWAWLVVNNGKLEIVS TANQDSPLSEGKTPVLGLDVWEHAYYLKFQNRRPEYIDTFWNVINWDERNKRF DAAK" terminator 723..746 /gene="sod"

15. BASE COUNT 247 a 136 c 151 g 222 t ORIGIN 1 cgttatttaa ggtgttacat agttctatgg aaatagggtc tatacctttc gccttacaat 61 gtaatttctt ttcacataaa taataaacaa tccgaggagg aatttttaat gacttacgaa 121 ttaccaaaat taccttatac ttatgatgct ttggagccga attttgataa agaaacaatg 181 gaaattcact atacaaagca ccacaatatt tatgtaacaa aactaaatga agcagtctca 241 ggacacgcag aacttgcaag taaacctggg gaagaattag ttgctaatct agatagcgtt 301 cctgaagaaa ttcgtggcgc agtacgtaac cacggtggtg gacatgctaa ccatacttta 361 ttctggtcta gtcttagccc aaatggtggt ggtgctccaa ctggtaactt aaaagcagca 421 atcgaaagcg aattcggcac atttgatgaa ttcaaagaaa aattcaatgc ggcagctgcg 481 gctcgttttg gttcaggatg ggcatggcta gtagtgaaca atggtaaact agaaattgtt 541 tccactgcta accaagattc tccacttagc gaaggtaaaa ctccagttct tggcttagat 601 gtttgggaac atgcttatta tcttaaattc caaaaccgtc gtcctgaata cattgacaca 661 ttttggaatg taattaactg ggatgaacga aataaacgct ttgacgcagc aaaataatta 721 tcgaaaggct cacttaggtg ggtcttttta tttcta //

29. Vector Trimming

47. CC -!- FUNCTION: CYTOKINE WITH A WIDE VARIETY OF FUNCTIONS: IT CAN CC CAUSE CYTOLYSIS OF CERTAIN TUMOR CELL LINES, IT IS IMPLICATED CC IN THE INDUCTION OF CACHEXIA, IT IS A POTENT PYROGEN CAUSING CC FEVER BY DIRECT ACTION OR BY STIMULATION OF IL-1 SECRETION, IT CC CAN STIMULATE CELL PROLIFERATION & INDUCE CELL DIFFERENTIATION CC UNDER CERTAIN CONDITIONS. Comments CC -!- SUBUNIT: HOMOTRIMER. CC -!- SUBCELLULAR LOCATION: TYPE II MEMBRANE PROTEIN. ALSO EXISTS AS CC AN EXTRACELLULAR SOLUBLE FORM. CC -!- PTM: THE SOLUBLE FORM DERIVES FROM THE MEMBRANE FORM BY CC PROTEOLYTIC PROCESSING. CC -!- DISEASE: CACHEXIA ACCOMPANIES A VARIETY OF DISEASES, INCLUDING CC CANCER AND INFECTION, AND IS CHARACTERIZED BY GENERAL ILL CC HEALTH AND MALNUTRITION. CC -!- SIMILARITY: BELONGS TO THE TUMOR NECROSIS FACTOR FAMILY. DR EMBL; X02910; G37210; -. Database Cross-references DR EMBL; M16441; G339741; -. DR EMBL; X01394; G37220; -. DR EMBL; M10988; G339738; -. DR EMBL; M26331; G339764; -. DR EMBL; Z15026; G37212; -. DR PIR; B23784; QWHUN. DR PIR; A44189; A44189. DR PDB; 1TNF; 15-JAN-91. DR PDB; 2TUN; 31-JAN-94.

48. KW CYTOKINE; CYTOTOXIN; TRANSMEMBRANE; GLYCOPROTEIN; SIGNAL-ANCHOR; KW MYRISTYLATION; 3D-STRUCTURE. KeyWord FT PROPEP 1 76 Feature Table FT CHAIN 77 233 TUMOR NECROSIS FACTOR. FT TRANSMEM 36 56 SIGNAL-ANCHOR (TYPE-II PROTEIN). FT LIPID 19 19 MYRISTATE. FT LIPID 20 20 MYRISTATE. FT DISULFID 145 177 FT MUTAGEN 105 105 L->S: LOW ACTIVITY. FT MUTAGEN 108 108 R->W: BIOLOGICALLY INACTIVE. FT MUTAGEN 112 112 L->F: BIOLOGICALLY INACTIVE. FT MUTAGEN 162 162 S->F: BIOLOGICALLY INACTIVE. FT MUTAGEN 167 167 V->A,D: BIOLOGICALLY INACTIVE. FT MUTAGEN 222 222 E->K: BIOLOGICALLY INACTIVE. FT CONFLICT 63 63 F -> S (IN REF. 5). FT STRAND 89 93 FT TURN 99 100 FT TURN 109 110 FT STRAND 112 113 FT TURN 115 116 FT STRAND 118 119 FT STRAND 124 125

49. FT STRAND 130 143 FT STRAND 152 159 FT STRAND 166 170 FT STRAND 173 174 FT TURN 183 184 FT STRAND 189 202 FT TURN 204 205 FT STRAND 207 212 FT HELIX 215 217 FT STRAND 218 218 FT STRAND 227 232 SQ SEQUENCE 233 AA; 25644 MW; 666D7069 CRC32; MSTESMIRDV ELAEEALPKK TGGPQGSRRC LFLSLFSFLI VAGATTLFCL LHFGVIGPQR EEFPRDLSLI SPLAQAVRSS SRTPSDKPVA HVVANPQAEG QLQWLNRRAN ALLANGVELR DNQLVVPSEG LYLIYSQVLF KGQGCPSTHV LLTHTISRIA VSYQTKVNLL SAIKSPCQRE TPEGAEAKPW YEPIYLGGVF QLEKGDRLSA EINRPDYLDF AESGQVYFGI IAL //

53. understanding molecular structure is critical to the understanding of biology because because structure determines function

55. • the drug morphine has chemical groups that are functionally equivalent to the natural endorphins found in the human body From Structure to Function

56. • the drug morphine has chemical groups that are functionally equivalent to the natural endorphins found in the human body • the receptor molecules located at the synapse (between two neurons) bind morphine much the same way as endorphins • therefore, morphine is able to attenuate the pain response From Structure to Function

60. PDB Content Growth

61. PDB Growth in New Folds

73. Relational Terminology ID NAME PHONE EMP_ID 201 Unisports 55-2066101 12 202 Simms Atheletics 81-20101 14 203 Delhi Sports 91-10351 14 204 Womansport 1-206-104-0103 11 Row (Tuple) Column (Attribute) CUSTOMER Table (Relation)

76. A simple datamodel (tables and relations) Prot_id name seq Species_id 1 GTM1_HUMAN MGTDHG… 1 2 GTM1_RAT MGHJADSW.. 2 3 GTM2_HUMAN MVSDBSVD.. 1 Species_id name Full Lineage 1 human Homo Sapiens … 2 rat Rattus rattus

78. BioSQL

84. Example 3-tier model in biological database http://www.bioinformatics.be Example of different interface to the same back-end database (MySQL)

96. BioMart - Single access point - Generic interface

97. BioMart - ‘Out of the box’ website

102. Single interface