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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(typecarbohyd "N-linked (GlcNAc...)"
confidenceexperimental) reviewedyes
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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 sequences D-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
protein i.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
pattern Use the scanprosite tool at
http//www.expasy.org/tools/scanprosite/
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Step 2 Retrieve the matched human entries _at_
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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Step 3 Retrieve the sequences annotated as being
phosphorylated on a Thr
-gt 19 candidates to be manually checked .
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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 _at_ 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 database List 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 SIB Use
PSI Blast
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Do a PSI BLAST against UniProtKB
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Select sequence with a E value gt 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
proteins SMART  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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