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Systematic search for putative new domain families in Mycoplasma gallisepticum genome

Chilamakuri CS Reddy12, Sane Sudha Rani2, Bernard Offmann1* and R Sowdhamini2*

Author Affiliations

1 Université de La Réunion, Equipe de Bioinformatique, Laboratoire de Biochimie et Génétique Moléculaire, 15 ave René Cassin, 97715 Saint Denis Messag Cedex 09, La Réunion, France

2 National Centre for Biological Sciences, GKVK Campus, Bellary Road, 560065 Bangalore, India

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BMC Research Notes 2010, 3:98  doi:10.1186/1756-0500-3-98

Published: 12 April 2010

Additional files

Additional file 1:

Supplemental Table ST1 Predicted putative new domain families. In our analysis, some of the unassigned regions shared homologues (at least 5 hits in PSI-BLAST search), but failed to associate with any Pfam domain in Hmmpfam search. We performed multiple sequence alignments to assess sequence conservation. 63 unassigned regions showed good conservation which may indicate putative new domain family. In the table, second column indicates the protein-id and third column (UR = Unassigned Region) indicates the start and end points of unassigned regions. Fourth column indicates the percentage secondary structural content in the unassigned region by using PSIPRED program. Fifth column indicates the total number of hits in the PSI-BLAST search and the sixth column indicates the number of PDB hits in PSI-BLAST search. Seventh column indicates the number of different species among the PSI-BLAST hits and eighth column indicates number of transmembrane helices which indicates whether protein is likely to be membrane-bound or not.

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Additional file 2:

Supplemental Table ST1 PfamB associations in the unassigned regions. 63 unassigned sequences were used to search against PfamB database (Pfam 24), only 20 unassigned sequences were associated with at least one PfamB domain. Unassigned sequence id along with start and end residues are showed in column two, PfamB start and end residue numbers are shown in column three, PfamB ids are shown in column four and the Expectation values with which PfamB domains associated are shown in the last column.

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