AmphipaSeeK help

A brief introduction to AmhpipaSeeK

AmphipaSeeK is a prediction method of amphipathic in-plane membrane anchors (IPM anchors) in protein sequences. IPM anchoring is a particular type of membrane interaction found as well as in monotopic proteins (e.g. NonStructural protein 5A of the Hepatitis C virus [1]) and in polytopic proteins (e.g. gp41 from the Human Immunodeficiency Virus [2]). AmphipaSeeK has been initally developed with a set of 21 monotopic membrane proteins including an experimentally characterized IPM anchor. The set is currently extended to IPM segments found in transmembrane proteins. To date, 7 transmembrane proteins are included in the data set.

[ ! ] AmphipaSeeK is not a prediction method of transmembrane segments or monotopic proteins. It only tells if a protein sequence potentially contains an IPM anchor [ ! ]

AmphipaSeeK uses a SVM classifier based on Gaussian kernel. The classification process requires a Gram matrix derived from a substitution matrix (currently : PHAT [3]). This part of AmphipaSeeK code come from the M-SVM source code distributed by Yann Guermeur under the GNU public License. M-SVM is a Multiclass Support Vector Machine, for details see [4]. Additionally, AmphipaSeeK automatically generates a multiple alignment to compute a weighted average prediction. Homologous to your query sequence are retrieve from the UniProt database. If no homologous sequence is retrived, the prediction will be computed on your query only. The computation of the average prediction uses the Squid-1.9g library distributed by Stephen Eddy under the GNU Public License.

If you use AmphipaSeeK in a publication, please cite :
Sapay N, Guermeur Y, and Deléage G (2006) prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier, BMC Bioinformatics, 7:255.

References :

  1. Sapay N, Montserret R, Chipot C, Brass V, Deléage G, Moradpour D, and Penin F (2006) NMR structure and molecular dynamics of the in-plane membrane anchor of the monotopic NonStructural protein 5A (NS5A) from the Bovine Viral Diarrhea Virus (BVDV), Biochemistry, 45(7):2221-2233.
  2. Schibli DJ, Montelaro RC, and Vogel HJ (2001) The membrane-proximal tryptophan-rich region of the HIV glycoprotein, gp41, forms a well-defined helix in dodecylphosphocholine micelles, Biochemistry, 40(32):9570-9578.
  3. Ng PC, Henikoff JG and Henikoff S (2001) PHAT: a transmembrane-specific substitution matrix. predicted hydrophobic and transmembrane, Bioinformatics, 16(9):760-766.
  4. Guermeur Y, Lifchitz A, and Vert R. (2004) A kernel for protein secondary structure prediction, In Schölkopf B, Tsuda K and Vert JP, editors, Kernel Methods in Computational Biology.

List of known IPM anchored proteins currently used in AmphipaSeeK

1   ADP Ribosylation Factor 1 [ UniProt ] [ abstract ]
2   ADP Ribosylation Factor GTPase Activating Protein 1 [ UniProt ] [ abstract ]
3   Aerobic Glycerol-3-Phosphate Dehydrogenase [ UniProt ] [ abstract ]
4   Cholinephosphate CytidylylTransferase α [ UniProt ] [ abstract ]
5   Coat Protein γ [ UniProt ] [ abstract ]
6   Core protein [ UniProt ] [ abstract ]
7   Dense Granule Protein 2 [ UniProt ] [ abstract ]
8   DnaA, chromosomal replication initiator protein [ UniProt ] [ abstract ]
9   Epsin 1 [ UniProt ] [ abstract ]
10   G protein-coupled Receptor Kinase 5 [ UniProt ] [ abstract ]
11   Glucose-specific IIa component [ UniProt ] [ abstract ]
12   Lactophorin (Proteose-Peptone Component 3) [ UniProt ] [ abstract ]
13   Myelin Basic Protein [ UniProt ] [ abstract ]
14   NonSpecific Lipid-Transfer Protein (Sterol Carrier Protein 2) [ UniProt ] [ abstract ]
15   NonStructural protein 5A - Hepatitis C Virus [ UniProt ] [ abstract ]
16   NonStructural protein 5A - GB virus A [ UniProt ] submitted
17   NonStructural protein 5A - GB virus B [ UniProt ] submitted
18   NonStructural protein 5A - GB virus C [ UniProt ] submitted
19   NonStructural protein 5A - Bovine Viral Diarrhea Virus [ UniProt ] [ abstract ]
20   NonStructural Protein 1 [ UniProt ] [ abstract ]
21   NonStructural protein 2C - Poliovirus [ UniProt ] [ abstract ]
22   NonStructural protein 2C - Foot and Mout Disease Virus [ UniProt ] [ abstract ]
23   Penicillin Binding Protein 5 (D-alanyl-D-alanine carboxypeptidase 5) [ UniProt ] [ abstract ]
24   Penicillin Binding Protein 6 (D-alanyl-D-alanine carboxypeptidase 6) [ UniProt ] [ abstract ]
25   PhosphoDiEsterase 4A cAMP specific (RD1) [ UniProt ] [ abstract ]
26   Prostaglandin H2 synthase - isoforme 1 [ UniProt ] [ abstract ]
27   Prostaglandin H2 synthase - isoforme 2 [ UniProt ] [ abstract ]
28   SAR1 [ UniProt ] [ abstract ]
29   Septum site-determining protein minD [ UniProt ] [ abstract ]
30   Squalene-Hopene Cyclase [ UniProt ] [ abstract ]

List of transmembrane proteins including a known IPM anchor currently used in AmphipaSeeK

1   crcA (PagP) [ UniProt ] [ abstract ]
2   GP41 [ UniProt ] [ abstract ]
3   Kcsa [ UniProt ] [ abstract ]
4   KirBac [ UniProt ] [ abstract ]
5   M2 [ UniProt ] [ abstract ]
6   Major Coat Protein [ UniProt ] [ abstract ]
7   Amine Oxidase B [ UniProt ] [ abstract ]
8   VPU [ UniProt ] [ abstract ]

Availability in NPS@

AmphipaSeeK is available :

Paste your protein sequence and submit! By default, AmphipaSeeK will compute a prediction as sensitive as possible, based on the set of 21 + 7 membrane proteins. This corresponds to the option [1] . For more specific prediction, you can try option [3]. If you really the most specific efficiency, try option [6]. Supplemental options are provided to help you to analyze AmphipaSeeK results, including :
  1. the secondary structure prediction to looking for putative α-helical segments.
  2. the hydrophobic moment μH calculation to measures the amphipathy along the sequence.
  3. a basic smoothing function to avoid predicted IPM anchors made of a single residue.

[ ! ] Analyses options are not used by AmphipaSeeK to compute a predictions. They are just a help [ ! ]

Parameters

NPS@ AmphipaSeeK output example

The output is divided into 1 HTML page and 4 text files.

References


User : public@52.91.245.237. Last modification time : Thu May 12 14:35:13 2016. Current time : Thu Dec 13 20:16:38 2018