corrections
DESCRIPTION
Corrections. N-linked glycosylation (GlcNac): Look at the Swiss-Prot annotation (in a random ‘glycosylated’ entry). Query:. annotation:(type:carbohyd "N-linked (GlcNAc...)" confidence:experimental) reviewed:yes. Taxonomic distribution. TPNLI N DTME. Multiple alignment (ClustalW). - PowerPoint PPT PresentationTRANSCRIPT
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Corrections
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N-linked glycosylation (GlcNac):
Look at the Swiss-Prot annotation (in a random ‘glycosylated’ entry)
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Query:
annotation:(type:carbohyd "N-linked (GlcNAc...)" confidence:experimental) reviewed:yes
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Taxonomic distribution
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TPNLINDTME
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Multiple alignment (ClustalW)
-[LAPIQ]-N-[HAYRCS]-[ST]-[KLESGM]
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N-glycosylation does not occur in Bacteria: …false positive !
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301 protein (within the set of 1000 proteins) are N-glycosylated according to the UniProtKB annotation…!
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Scan Prosite with the official pattern
The official pattern also match with bacteria sequences (false positives)
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PRATT pattern with 20 sequencesD-K-T-G-T-[IL]-T-x(3)-[ILMV]-x-[FILV]
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AT31_HUMAN:
SIMILARITY: Belongs to the cation transport ATPase (P-type) family. Type V subfamily. The pattern is a discriminator for ATP ase family (Cation-transporting )
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C-x(2,4)-C-x(3)-[LIVMFYWC]-x(8)-H-x(3,5)-H
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Pattern scan
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The pattern missed some Zn finger in the same proteini.e. Q24174
Pattern
Profile
Not found with the pattern
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The pattern:
C - X(2,4) - C - X(3) - [LIVMFYWC] - X(8) - H - X(3,5) – H
Should includes:
YRCVLCGTVAKSRNSLHSHMSrQHRGIST
C-X(2,4)-C-X(3)-[LIVMFYWCA]-X(8)-H-X(3,5)-H
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Yes !
But:
The pattern becomes less restrictive.You get more sequences which should not be here.(As the results are limited to 1000, the number of hits is not the same…)
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Discriminators (Signatures, descriptors) for the Zinc finger C2H2 type domain can be found in Prosite (Pattern and Profile) and Pfam (HMM)
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Step 1: scan UniProtKB/Swiss-Prot with the patternUse the ‘scanprosite’ tool at http://www.expasy.org/tools/scanprosite/
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Step 2: Retrieve the matched human entries @ UniProt(go at the end of the Scan Prosite result page: click on ‘Matched UniProtKB entries’)
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Step 3: Retrieve the sequences annotated as being ‘phosphorylated on a Thr’
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-> 19 candidates to be manually checked ….
Step 3: Retrieve the sequences annotated as being ‘phosphorylated on a Thr’
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InterPro scan results
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InterPro : other shema (Graphical view from UniProtKB)
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InterPro shema
PFAM Graphical view
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Prosite Graphical view
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Blast @ NCBI against Swiss-Prot
NCBI: Color key for alignment scores
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NCBI Swiss-Prot does not contain the alternative sequences (i.e. P28175-2) –!! NCBI gives the ‘version number’ of the Swiss-Prot sequence (i.e. Q8BU25.2)….
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UniProt: Color code for identity scores (not alignment !)
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UniProt: Color code for identity scores (not alignment !)
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ProDom databaseList of proteins sharing at least a common domain…
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1) BLAST at www.uniprot.org
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2) PROSITE tools
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You are lucky: domains are rarely not annotated in the different domain/family databases !
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3) Construct a profile with My hits at SIBUse PSI Blast
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Do a PSI BLAST against UniProtKB
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Select sequence with a E value > 0.001 and do a second cycle
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Look at the MSA
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Construct a profile with the MSA
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The profile
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The profile hits
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Construct a HMM with the MSA
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The HMM
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The HMM hits
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- Look at the Goloco data in InterPro. How many proteins (and/or hits) are found by the different methods ?
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http://www.ebi.ac.uk/interpro/
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According to InterPro: Goloco domain is described by at least one of the different methods (PFAM, Prosite, Smart)
PFAM: 167 proteins Prosite: 192 proteinsSMART: 1 proteins These different numbers are the consequence of the interval between the different releases of the different databases (including the sequence databases (UniProtKB). It may also be due to the different methods used (HMM, profile…)
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Look for the HMM for the Goloco domain in PFAM
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Look for the HMM for the Goloco domain in PFAM
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Download the HMM matrix
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the HMM matrix
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