User:Tiffykt/Assignments 1

Assignment 2 Full name: Tiffany Tong Organism: Assigned: Monday September 27, 2010 Due date: Monday October 18, 2010

= Retrieve = Objectives:

Procedure:
 * 1) Go to the NCBI site and search Mbp1 AND "saccharomyces cerevisiae"[organism].
 * 2) From the results given, click on Protein. On the following page, on the right hand side click on the RefSeq record link.
 * 3) Retrieve the FASTA record, which is displayed below:
 * >gi|6320147|ref|NP_010227.1| Mbp1p [Saccharomyces cerevisiae S288c]
 * MSNQIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGF
 * GKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDFTQTDGSASPPPAPKHHHASKVDRKKAIRSASTSAIMET
 * KRNNKKAEENQFQSSKILGNPTAAPRKRGRPVGSTRGSRRKLGVNLQRSQSDMGFPRPAIPNSSISTTQL
 * PSIRSTMGPQSPTLGILEEERHDSRQQQPQQNNSAQFKEIDLEDGLSSDVEPSQQLQQVFNQNTGFVPQQ
 * QSSLIQTQQTESMATSVSSSPSLPTSPGDFADSNPFEERFPGGGTSPIISMIPRYPVTSRPQTSDINDKV
 * NKYLSKLVDYFISNEMKSNKSLPQVLLHPPPHSAPYIDAPIDPELHTAFHWACSMGNLPIAEALYEAGTS
 * IRSTNSQGQTPLMRSSLFHNSYTRRTFPRIFQLLHETVFDIDSQSQTVIHHIVKRKSTTPSAVYYLDVVL
 * SKIKDFSPQYRIELLLNTQDKNGDTALHIASKNGDVVFFNTLVKMGALTTISNKEGLTANEIMNQQYEQM
 * MIQNGTNQHVNSSNTDLNIHVNTNNIETKNDVNSMVIMSPVSPSDYITYPSQIATNISRNIPNVVNSMKQ
 * MASIYNDLHEQHDNEIKSLQKTLKSISKTKIQVSLKTLEVLKESSKDENGEAQTNDDFEILSRLQEQNTK
 * KLRKRLIRYKRLIKQKLEYRQTVLLNKLIEDETQATTNNTVEKDNNTLERLELAQELTMLQLQRKNKLSS
 * LVKKFEDNAKIHKYRRIIREGTEMNIEEVDSSLDVILQTLIANNNKNKGAEQIITISNANSHA


 * 1) Go to the UniProt ID-Mapping site and search for the Mbp1 protein record using the RefSeq ID (NP_010227.1). The corresponding UniProtKB Accession number is: D6VRU0.

Results:
 * The UniProtKB accession number for the S. cerevisae Mbp1 proteins is P39678.

Conclusions:
 * The UniProt ID-Mapping tool can be used to find the UniProtKB accession number of an organism with the NCBI RedSeq identifier.

=Analyse=

saccharomyces cerevisiae Mbp1 - domain annotations
Objectives:

Procedure:
 * 1) Go to the SMART site and search for the S. cerevisae Mbp1 protein using its accession number (P39678), check off the following options: PFAM domains, internal repeats, and intrinsic protein disorder.

Results:
 * Domain features of the S. cerevisae Mbp1 protein are highlighted:
 * MSNQIYSARYSGVD VYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGF
 * GKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDFTQTDGSASP PPAPKHHHASKVDRKKAIRSASTSAIMET
 * KRNNKKAEENQFQSSKILGNPTAAPRKRGRPVGSTRGSRRKLGVNLQRSQSDMGFPRPAIPNSSISTTQL
 * PSIRSTMGPQSPTLGILEEERHDSR QQQPQQ NNSAQFKEIDLEDGLSSDVEPSQQLQQVFNQNTGFVP QQ
 * QQSSLIQTQQTESMATSVSSSPSLPTSP GDFADSNPFEERFPGGGTSPIISMIPRYPVTSRPQTSDINDKV
 * NKYLSKLVDYFISNEMKSNKSLPQVLLHPPPHSAPYIDAPIDP ELHTAFHWACSMGNLPIAEALYEAGTS
 * IRS TNS QGQTPLMRSSLFHNSYTRRTFPRIFQLLHETVFDIDS QSQTVIHHIVKRKSTTPSAVYYLDVVL
 * SKIKDFSPQYRIELLLNTQDKS NGDTALHIASKNGDVVFFNTLVKMGALTTI SNKEGLTANEIMNQQYEQM
 * MIQNGTNQHVNSSNTDLNIHVNTNNIETKNDVNSMVIMSPVSPSDYITYPSQIATNISRNIPNVVNSMKQ
 * MA SIYNDLHEQHDNEIKSLQKTLKS ISKTKIQVSLKTLEVLKESSKDENGEAQTNDDFEILSRLQEQNT K
 * KLRKRLIRYKRLIKQKL EYRQTVLLNKLIEDETQATTNNTVEKDNNTLERLELAQELTMLQLQRKNKLSS
 * LVKKFEDNAKIHKYRRIIREGTEMNIEEVDSSLDVILQTLIANNNKNKGAEQIITISNANSHA


 * Domain features: Pfam:KilA-N, low complexity , low complexity , ANK , ANK , ANK , coiled-coil , and low complexity.

Conclusions:

APSES domains
Objectives:

Procedure:
 * 1) Go to the NCBI RefSeq record for S. cerevisae Mbp1 protein. Under the Analyze this sequence menu, click on Identify Conserved Domains.
 * 2) Click on the [+] to expand the record for pfam04383.

Results:
 * The NCBI and SMART definition of the KilA-N (APSES) domain in Mbp1 do not coincide.
 * Domain boundaries as defined by the NCBI and by SMART in my FASTA sequence:
 * MSNQIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGF
 * GKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDFTQTDGSASPPPAPKHHHASKVDRKKAIRSASTSAIMET
 * KRNNKKAEENQFQSSKILGNPTAAPRKRGRPVGSTRGSRRKLGVNLQRSQSDMGFPRPAIPNSSISTTQL
 * PSIRSTMGPQSPTLGILEEERHDSRQQQPQQNNSAQFKEIDLEDGLSSDVEPSQQLQQVFNQNTGFVPQQ
 * QSSLIQTQQTESMATSVSSSPSLPTSPGDFADSNPFEERFPGGGTSPIISMIPRYPVTSRPQTSDINDKV
 * NKYLSKLVDYFISNEMKSNKSLPQVLLHPPPHSAPYIDAPIDPELHTAFHWACSMGNLPIAEALYEAGTS
 * IRSTNSQGQTPLMRSSLFHNSYTRRTFPRIFQLLHETVFDIDSQSQTVIHHIVKRKSTTPSAVYYLDVVL
 * SKIKDFSPQYRIELLLNTQDKNGDTALHIASKNGDVVFFNTLVKMGALTTISNKEGLTANEIMNQQYEQM
 * MIQNGTNQHVNSSNTDLNIHVNTNNIETKNDVNSMVIMSPVSPSDYITYPSQIATNISRNIPNVVNSMKQ
 * MASIYNDLHEQHDNEIKSLQKTLKSISKTKIQVSLKTLEVLKESSKDENGEAQTNDDFEILSRLQEQNTK
 * KLRKRLIRYKRLIKQKLEYRQTVLLNKLIEDETQATTNNTVEKDNNTLERLELAQELTMLQLQRKNKLSS
 * LVKKFEDNAKIHKYRRIIREGTEMNIEEVDSSLDVILQTLIANNNKNKGAEQIITISNANSHA



Conclusions:

APSES domain structure
Objectives:

Procedure:
 * 1) Go to PDB site and search for Mbp1 co-ordinates using search query Mbp1 AND Saccharomyces cerevisiae 

Results:

Conclusions:

DNA binding site
Objectives:

Procedure:

Results:

Conclusions: