Minimotif miner 2nd release: a database and web system for motif search

Rajasekaran, Sanguthevar; Balla, Sudha; Gradie, Patrick R.; Gryk, Michael R.; Kadaveru, Krishna; Kundeti, Vamsi; Maciejewski, Mark W.; Tian, Mi; Rubino, Nicholas; Vyas, Jay; Schiller, Martin

doi:10.1093/nar/gkn865

Cited by 60 publications

(73 citation statements)

References 34 publications

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“…There is much still to learn. An analysis of the P2X7R sequence using Minimotif Miner Scan [85][86][87] and focusing on the C terminus has allowed us to find many new and previously undiscovered motifs and domains listed in Table 1.…”

Section: What Is Expected For the Future?mentioning

confidence: 99%

C terminus of the P2X7 receptor: treasure hunting

Costa-Junior

Vieira

Coutinho‐Silva

2011

Purinergic Signalling

107

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P2X receptor (P2XR) is a family of the ATPgated ion channel family and can permeabilize the plasma membrane to small cations such as potassium, sodium, and calcium, resulting in cellular depolarization. There are seven P2XR that have been described and cloned, with 45% identity in amino acid sequence. Each P2X receptors has two transmembrane domains that are separated by an extracellular loop and an intracellular N and C terminus. Unlike the other P2X receptors, the P2X7R has a larger C terminus with an extra 200 amino acid residues compared with the other receptors. The C terminus of the P2X7R has been implicated in regulating receptor function including signaling pathway activation, cellular localization, proteinprotein interactions, and post-translational modification (PTM). In the present review, we discuss the role of the P2X7R C terminus in regards to receptor function, describe the specific domains and motifs found therein and compare the C terminus sequence with others proteins to discover predicted domains or sites of PTM.

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Section: What Is Expected For the Future?mentioning

confidence: 99%

C terminus of the P2X7 receptor: treasure hunting

Costa-Junior

Vieira

Coutinho‐Silva

2011

Purinergic Signalling

107

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“…There are several available linear motif databases, such as the Eukaryotic Linear Motif (ELM) database (http://elm.eu. org) [26], Minimotif Miner [27], [28], [29] and Scansite [2]. We choose the ELM database to collect our data sets, as it contains comprehensive resource of biologically validated linear motifs and provides detailed annotations for each motif [30] [31].…”

Section: Results On Real-world Data Sets With Protein Sequencesmentioning

confidence: 99%

An Efficient Exact Algorithm for the Motif Stem Search Problem over Large Alphabets

Huo

Vitter

et al. 2015

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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In recent years, there has been an increasing interest in planted (l, d) motif search (PMS) with applications to discovering significant segments in biological sequences. However, there has been little discussion about PMS over large alphabets. This paper focuses on motif stem search (MSS), which is recently introduced to search motifs on large-alphabet inputs. A motif stem is an l-length string with some wildcards. The goal of the MSS problem is to find a set of stems that represents a superset of all (l , d) motifs present in the input sequences, and the superset is expected to be as small as possible. The three main contributions of this paper are as follows: (1) We build motif stem representation more precisely by using regular expressions. (2) We give a method for generating all possible motif stems without redundant wildcards. (3) We propose an efficient exact algorithm, called StemFinder, for solving the MSS problem. Compared with the previous MSS algorithms, StemFinder runs much faster and reports fewer stems which represent a smaller superset of all (l, d) motifs. StemFinder is freely available at http://sites.google.com/site/feqond/stemfinder.

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“…For bioinformatic analysis, a number of individual Web-based programs were employed. For phosphorylation site predictions, two programs were used, NetPhosK and MiniMotif Miner (4,5,31). For protein identification, the raw mass spectra data files were converted into an mgf file format and searched against a Dictyostelium database using the program Mascot (29), licensed through the CBC-UIC Research Resources Center Proteomics and Informatics Services Facility at the University of Illinois at Chicago.…”

Section: Methodsmentioning

confidence: 99%

Uncovering a Role for the Tail of the Dictyostelium discoideum SadA Protein in Cell-Substrate Adhesion

Kowal¹,

Chisholm²

2011

Eukaryotic Cell

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Previous work from our laboratory showed that the Dictyostelium discoideum SadA protein plays a central role in cell-substrate adhesion. SadA null cells exhibit a loss of adhesion, a disrupted actin cytoskeleton, and a cytokinesis defect. How SadA mediates these phenotypes is unknown. This work addresses the mechanism of SadA function, demonstrating an important role for the C-terminal cytoplasmic tail in SadA function. We found that a SadA tailless mutant was unable to rescue the sadA adhesion deficiency, and overexpression of the SadA tail domain reduced adhesion in wild-type cells. We also show that SadA is closely associated with the actin cytoskeleton. Mutagenesis studies suggested that four serine residues in the tail, S924/S925 and S940/ S941, may regulate association of SadA with the actin cytoskeleton. Glutathione S-transferase pull-down assays identified at least one likely interaction partner of the SadA tail, cortexillin I, a known actin bundling protein.Thus, our data demonstrate an important role for the carboxy-terminal cytoplasmic tail in SadA function and strongly suggest that a phosphorylation event in this tail regulates an interaction with cortexillin I. Based on our data, we propose a model for the function of SadA.

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Minimotif miner 2nd release: a database and web system for motif search

Cited by 60 publications

References 34 publications

C terminus of the P2X7 receptor: treasure hunting

C terminus of the P2X7 receptor: treasure hunting

An Efficient Exact Algorithm for the Motif Stem Search Problem over Large Alphabets

Uncovering a Role for the Tail of the Dictyostelium discoideum SadA Protein in Cell-Substrate Adhesion

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