Sequence Alignment - Photosynthetic Reaction Center and PSII

Sequence Alignment - Photosynthetic Reaction Center and PSII


  The methods for obtaining the alignments are described in:
 
  • Eva-Maria Krammer, Pierre Sebban and G. Matthias Ullmann. Conservation of cofactor binding motifs and proton transfer pathways in photosynthetic reaction centers analyzed by profile Hidden Markov Models. Biochemistry , 48 : 1230-1243, 2009
    [PDF File] [Supporting Informations]

    •  
  • Eva-Maria Krammer, Mirco S. Till, Pierre Sebban and G. Matthias Ullmann Proton Transfer Pathways in Photosynthetic Reaction Centers Analyzed by Profile Hidden Markov Models and Network Calculations. J. Mol. Biol. , 388 : 631-343, 2009
    [PDF File] [Supporting Informations]

      Please cite these publications, if you use these alignments or the pHMM in your work.

    Alignments

  • ProfileAlignment_LD1.fasta:
    Fasta File containing the alignment of the L subunit (bRC) and the D1 subunit (PSII) used for the conservation analysis

  • ProfileAlignment_MD2.fasta:
    Fasta File containing the alignment t of the M subunit (bRC) and the D2 subunit (PSII) used for the conservation analysis

  • ProfileAlignment_H.fasta:
    Fasta File containing the alignment of the H subunit (bRC) used for the conservation analysis

    • The fasta files can for instance be viewed with cinem5 ( http://aig.cs.man.ac.uk/research/utopia/cinema/cinema.php).

    Profile Hidden Markov Models

  • LD1.hmm: HMM File for the subunit L/D1

  • MD2.hmm: HMM File for the subunit M/D2

  • H.hmm: HMM File for the subunit H


    Matthias Ullmann