Target+Sp17+-+Alkaline+Phosphatase+(Clostridium+botulinum)

*Target (protein/gene name): alkaline phosphatase *NCBI Gene # or RefSeq#: Gene ID: 248 *Protein ID (NP or XP #) or Wolbachia#: *Organism (including strain): Clostridium botulinum Etiologic Risk Group (see link below): 2 */Disease Information (sort of like the Intro to your Mini Research Write up):

Botulism is a disease caused by the bacteria //clostridium botulinum//. Botulism occurs in humans when foods contaminated by this bacterium is consumed. The bacteria attack the immune system by releasing toxic spores in the intestines. Different types of diseases caused by this bacteria include foodborne botulism, infact botulism, wound botulism, etc. Symptoms of these diseases involve dropping eyelids, nausea and vomiting, muscle weakness, etc. The main treatment used to treat botulism is antibiotics.

Link to TDR Targets page (if present): http://www.tdrtargets.org/targets/view?gene_id=285537 Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.) Essentiality of this protein: Is it a monomer or multimer as biological unit? (make prediction at []): Monomer Complex of proteins?: Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1162816/pdf/biochemj00403-0154.pdf

*EC#: 3.1.3.1. Link to BRENDA EC# page: -- Show screenshot of BRENDA enzyme mechanism schematic <span style="font-family: Garamond,serif;">Enzyme Assay information (spectrophotometric, coupled assay ?, reagents): <span style="font-family: Garamond,serif;">-- link to Sigma (or other company) page for assay (see Sigma links below) <span style="font-family: Garamond,serif;">http://www.sigmaaldrich.com/technical-documents/protocols/biology/enzymatic-assay-of-alkaline-phosphatase-diethanolamine-assay.html <span style="font-family: Garamond,serif;">-- -or link (or citation) to paper that contains assay information <span style="font-family: Garamond,serif;">-- links to assay reagents (substrates) pages. <span style="font-family: Garamond,serif;">--- List cost and quantity of substrate reagents, supplier, and catalog #

<span style="font-family: Garamond,serif;">Structure (PDB or Homology model) <span style="font-family: Garamond,serif;">-- PDB # or closest PDB entry if using homology model: <span style="font-family: Garamond,serif;">-- For Homology Model option: <span style="font-family: Garamond,serif;"> Show pairwise alignment of your BLASTP search in NCBI against the PDB <span style="font-family: Garamond,serif;"> Query Coverage: <span style="font-family: Garamond,serif;"> Max % Identities: <span style="font-family: Garamond,serif;"> % Positives <span style="font-family: Garamond,serif;"> Chain used for homology: <span style="font-family: Garamond,serif; line-height: 0px; overflow: hidden;">

<span style="font-family: Garamond,serif;">http://www.rcsb.org/pdb/explore/explore.do?structureId=5TJ3

<span style="font-family: Garamond,serif;">Current Inhibitors: <span style="font-family: Garamond,serif;">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1162816/pdf/biochemj00403-0154.pdf <span style="font-family: Garamond,serif;">Expression Information (has it been expressed in bacterial cells): <span style="font-family: Garamond,serif;">Purification Method: <span style="font-family: Garamond,serif;">Image of protein (PyMol with features delineated and shown separately): <span style="font-family: Garamond,serif;">*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'): >5TJ3:A|PDBID|CHAIN|SEQUENCE MDIGIDSDPQKTNAVPRPKLVVGLVVDQMRWDYLYRYYSKYGEGGFKRMLNTGYSLNNVHIDYVPTVTAIGHTSIFTGSV PSIHGIAGNDWYDKELGKSVYCTSDETVQPVGTTSNSVGQHSPRNLWSTTVTDQLGLATNFTSKVVGVSLKDRASILPAG HNPTGAFWFDDTTGKFITSTYYTKELPKWVNDFNNKNVPAQLVANGWNTLLPINQYTESSEDNVEWEGLLGSKKTPTFPY TDLAKDYEAKKGLIRTTPFGNTLTLQMADAAIDGNQMGVDDITDFLTVNLASTDYVGHNFGPNSIEVEDTYLRLDRDLAD FFNNLDKKVGKGNYLVFLSADHGAAHSVGFMQAHKMPTGFFVEDMKKEMNAKLKQKFGADNIIAAAMNYQVYFDRKVLAD SKLELDDVRDYVMTELKKEPSVLYVLSTDEIWESSIPEPIKSRVINGYNWKRSGDIQIISKDGYLSAYSKKGTTHSVWNS YDSHIPLLFMGWGIKQGESNQPYHMTDIAPTVSSLLKIQFPSGAVGKPITEVIGRIEGRSAWSHPQFEK

<span style="font-family: Garamond,serif;">*length of your protein in Amino Acids: 549 <span style="font-family: Garamond,serif;">Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website: 61254.95 <span style="font-family: Garamond,serif;">Molar Extinction coefficient of your protein at 280 nm wavelength: 104740 <span style="font-family: Garamond,serif;">TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it. <span style="font-family: Garamond,serif;">*CDS Gene Sequence (paste as text only): code 1 mkqstialal lpllftpvtk artpempvle nraaqgdita pggarrltgd qtaalrdsls code code 61 dkpakniill igdgmgdsei taarnyaega ggffkgidal pltgqythya lnkktgkpdy code code 121 vtdsaasata wstgvktyng algvdihekd hptilemaka aglatgnvst aelqdatpaa code code 181 lvahvtsrkc ygpsatsekc pgnalekggk gsiteqllna radvtlggga ktfaetatag code code 241 ewqgktlreq aqargyqlvn daaslnsvte anqqkpllgl fadgnmpvrw lgpkatyhgn code code 301 idkpavtytp npqrndsvpt laqmtdkaie llsknekgff lqvegasidk qdhaanpcgq code code 361 igetvdldea vqralefakk egntlvivta dhahasqvva pdtkapgltq alntkdgavm code code 421 vmsygnseed sqehtgsqlr iaaygphaan vvgltdqtdl fytmkaalgl k code

<span style="font-family: Garamond,serif;">*GC% Content for gene: <span style="font-family: Garamond,serif;">*CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only): <span style="font-family: Garamond,serif;">*GC% Content for gene (codon optimized):

<span style="font-family: Garamond,serif;">Do Not Need this info for Spring (but still copy these lines to your Target page for now) <span style="font-family: Garamond,serif;">Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers): <span style="font-family: Garamond,serif;">(link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol) <span style="font-family: Garamond,serif;">-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.

<span style="font-family: Garamond,serif;">Primer design results for 'tail' primers (this is just 2 sequences): <span style="font-family: Garamond,serif;">**