Search Options

The ARABI-COIL search form provides several search options to identify coiled-coil proteins of interest for the user:

• Search by sequence identifier (e.g. GenBank accession number).
  Multiple sequence search is possible by entering multiple identifiers.
• Search by annotation keyword (e.g. myosin).
• Search by sequence features using the Refining Search Options.

Refining Search Options

Length of Sequence

• Limits the search to proteins of specified length (in amino acids).

Length of Coiled-Coil Domain

• Limits the search to proteins containing a coiled-coil domain of specified length (in amino acids).

Coiled-Coil Coverage

• Limits the search to proteins with a specified percentage of all amino acids predicted to form a coiled-coil structure.
• Available for full length sequence as well as N-terminal, central, and C-terminal thirds of the total protein length (combinations possible).

This feature allows the user to pre-select a certain coiled-coil domain structure, e.g. N-terminal or C-terminal coiled-coil domains.

Number of Transmembrane Domains

• Limits the search to proteins predicted to contain the specified number of transmembrane domains.

Predicted Localization

• Limits the search to proteins predicted to be localized in the specified cell compartment.

Explanation of Output Data

The details page for each protein entry provides the user with the following information about the protein:

General Information

• Sequence identifiers:
  AGI Gene Locus Number, GenBank Accession Number, links to sequence databases.
• Description:
  Functional annotation of the protein, if available.
• Publications:
  References to published data about the protein, if available.
• Sequence Length.

Coiled-Coil Prediction Data

• Schematic diagram of distribution of coiled-coil domains over protein length.
• Number of coiled-coil domains in the sequence.
• Length of the longest coiled-coiled domain in the sequence (in amino acids).
• Percentage of entire sequence predicted to form a coiled-coil.
• Percentage of N-terminal third, middle, and C-terminal thirds of sequence predicted to form a coiled-coil.
• Largest coiled-coil probability predicted by MultiCoil in entire sequence.
  Coiled-coil domains were predicted using a cut-off probability score of 0.5 in MultiCoil. The maximum probability score is 1. Higher scores indicate more reliable coiled-coil prediction.
• Position (start and end) of individual predicted coiled-coil domains.
• Lengths of individual predicted coiled-coil domains.
• Maximum intra-domain gap for individual predicted coiled-coil domains.
  Gaps of up to 25 amino acids between coiled-coil domains predicted by MultiCoil were ignored in favor of treating those domains as a single coiled-coil.

Transmembrane Properties

• Number of transmembrane helices predicted to be present in the sequence by a variety of programs/databases.

Predicted Localization

Predictions for the following localizations are included in the Arabi-Coil database:

• Chloroplast (cTP)
• Mitochondria (mTP)
• Secretory Pathway (SP)
• Nucleus (NLS)
• Other (no N-terminal signal predicted, includes nuclear proteins)

All probability scores for targeting predictions are in the range of 0 (low probability) to 1 (high probability). Scores for ChloroP (0.4 - 0.6 range in raw output) were adjusted to 0 -1 range for better comparability. Hits in the PredictNLS database were given a score of 1.

Results above cut-off values for two confidence levels of scores at 0.5 (low confidence) and 0.75 (high confidence) are marked in yellow and red, respectively.

Selection of Long Coiled-Coil Proteins

Prediction Programs Used

The following programs and prediction servers were used to generate data for the Arabi-Coil Database.

MultiCoil - prediction of two- and three-stranded coiled-coils
http://multicoil.lcs.mit.edu/cgi-bin/multicoil
Wolf, E., Kim, P.S., and Berger, B. (1997): MultiCoil: A Program for Predicting Two- and Three-Stranded Coiled Coils. Protein Sci. 6: 1179-1189.

Center for Biological Sequence Analysis Prediction Servers
http://www.cbs.dtu.dk/services

ChloroP 1.1 - prediction of chloroplast transit peptide
http://www.cbs.dtu.dk/services/ChloroP
Emanuelsson, O., Nielsen, H., and von Heijne, G. (1999): ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci. 8: 978-984.

SignalP V2.0 - prediction of signal peptide
http://www.cbs.dtu.dk/services/SignalP
Neural Network:
Nielsen, H., Engelbrecht, J., Brunak, S., and von Heijne, G. (1997): A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Int. J. Neural. Syst. 8: 581-599.

Hidden Markov Model:
Nielsen, H., and Krogh, A. (1998): Prediction of signal peptides and signal anchors by a hidden Markov model. Proc. Int. Conf. Intell. Syst. Mol. Biol. 6: 122-130.

TargetP v1.01 - prediction of subcellular location
http://www.cbs.dtu.dk/services/TargetP
Emanuelsson, O., Nielsen, H., Brunak, S., and von Heijne, G. (2000): Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol. 300: 1005-1016.

TMHMM (v. 2.0) - prediction of transmembrane helices
http://www.cbs.dtu.dk/services/TMHMM
Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E.L.L. (2001): Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 305: 567-580.

Other Prediction Servers

HMMTOP - prediction of transmembrane helices and topology
http://www.enzim.hu/hmmtop
Tusnády, G.E., and Simon, I. (1998): Principles Governing Amino Acid Composition of Integral Membrane Proteins: Applications to Topology Prediction. J. Mol. Biol. 283: 489-506.

MITOPROT - prediction of mitochondrial targeting
http://mips.gsf.de/cgi-bin/proj/medgen/mitofilter
Claros, M.G., and Vincens, P (1996). Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur. J. Biochem. 241: 779-786.

Predotar - prediction of mitochondrial and plastid targeting sequences
http://genoplante-info.infobiogen.fr/predotar/predotar.html

PredictNLS server - prediction of nuclear localization signals
http://cubic.bioc.columbia.edu/predictNLS/
Cokol, M., Nair, R., and Rost, B. (2000): Finding Nuclear localization signals. EMBO Rep. 1: 411-415.

PSORT - prediction of protein sorting signals and localization
http://psort.nibb.ac.jp
Nakai, K., and Horton, P. (1999): PSORT: a program for detecting the sorting signals of proteins and predicting their subcellular localization. Trends Biochem. Sci. 24: 34-35.

Release History and Updates

version 1.0 - released Nov. 04, 2003

Reference:

Annkatrin Rose, Sankaraganesh Manikantan, Shannon J. Schraegle, Michael A. Maloy, Eric A. Stahlberg, and Iris Meier (2004). Genome-wide Identification of Arabidopsis Coiled-Coil Proteins and Establishment of the ARABI-COIL Database. Plant Physiol. 134, 927-939. - Abstract at NCBI PubMed

A.R., I.M. (corresponding author): Department of Plant Cellular and Molecular Biology and Plant Biotechnology Center, The Ohio State University, 1060 Carmack Road, Columbus, OH 43210, USA

S.M., S.J.S. (webmaster), M.A.M., E.A.S.: Ohio Supercomputer Center, 1224 Kinnear Road, Columbus, OH 43212, USA

The ARABI-COIL database was made possible with support from the National Science Foundation Project 2010 and the Ohio Supercomputer Center.