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Brix Domain Proteins

This page supplies supplementary material for the manuscript

"The Brix domain protein family - a key to the ribosomal biogenesis pathway"
by Frank Eisenhaber, Christian Wechselberger, Guenther Kreil

Acknowledgements to:
M. Breitenbach, F.M. Jantsch, G. Lepperdinger
for sharing experimental data with respect to Brix and yol077c with us prior to publication, for discussion of the sequence analysis results and for carefully reading the manuscript.

You might want to know:
  1. Sequences and alignments
    fasta-file with the X. laevis Brix sequence (AF319877)
    Members of the Brix domain protein superfamily
    The search history of the Brix domain superfamily and its internal structure
    fasta-file of Brix Domain Proteins
    Clustal-formatted grand alignment of Brix proteins
    The same alignment in postscript and colour
  2. HMMs and domain locations
    The HMM for global domain searches
    The HMM for local/fragmented domain searches
    The domain boundaries for Brix domain proteins (hmmsearch output)

    Reference for HMM: Eddy SR.
    Profile hidden Markov models.
    Bioinformatics. 1998;14(9):755-63.

  3. Compositions and sequence lengths
    Charged AA in the regions flanking the Brix domain
    Length of Brix domain proteins

  4. supplementary information kindly supplied by Mensur Dlakic (University Michigan - Medical School) from June 12th, 2001
    another alignment of Brix proteins in color
    this alignment in MSF format
    the corresponding HMM for global domain searches
    the corresponding HMM for fragmented domain searches
    the search output from SWISS-ALL

Features of four Brix domain proteins with unusually large sequence length in their family indicating possible gene prediction or genome assembly inaccuracies:

The length of proteins in the Peter Pan family and in group 1 of hypothetical proteins is typically <475 residues (346-475 residues and 295-434 residues respectively). But four proteins (all of them are hypothetical, conceptual translations of genomic sequences) have an extraordinary length of ~700 residues.

Reference for IMPALA:
Schaffer AA, Wolf YI, Ponting CP, Koonin EV, Aravind L, Altschul SF
IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices.
Bioinformatics 1999 Dec;15(12):1000-11

Last modified: Feb 2001