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
Multiple alignment (ClustalW) -[LAPIQ]-N-[HAYRCS]-[ST]-[KLESGM]
301 protein (within the set of 1000 proteins) are N-glycosylated according to the UniProtKB annotation…!
Scan Prosite with the official pattern The official pattern also match with bacteria sequences (false positives)
PRATT pattern with 20 sequences D-K-T-G-T-[IL]-T-x(3)-[ILMV]-x-[FILV]
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 )
The pattern missed some Zn finger in the same protein i.e. Q24174 Pattern Profile Not found with the pattern
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
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…)
Discriminators (Signatures, descriptors) for the Zinc finger C2H2 type domain can be found in Prosite (Pattern and Profile) and Pfam (HMM)
Step 1: scan UniProtKB/Swiss-Prot with the pattern Use the ‘scanprosite’ tool at http://www.expasy.org/tools/scanprosite/
Step 2: Retrieve the matched human entries @ UniProt (go at the end of the Scan Prosite result page: click on ‘Matched UniProtKB entries’)
Step 3: Retrieve the sequences annotated as being ‘phosphorylated on a Thr’
Step 3: Retrieve the sequences annotated as being ‘phosphorylated on a Thr’ -> 19 candidates to be manually checked ….
InterPro shema PFAM Graphical view
Blast @ NCBI against Swiss-Prot NCBI: Color key for alignment scores
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)….