Supplementary data for sequence-structure-function analyses of protein families

To accompany the following paper:

LacI/RbsB family

• Phylogenetic tree and functional group predictions
• Table of binding site matches
• LacI binding site match alignment
• RbsB binding site match alignment
• LacI/RbsB family whole domain alignment (MSF)

SubI family

• Phylogenetic tree and functional group predictions
• Table of binding site matches
• ModA binding site match alignment
• SubI family whole domain alignment (MSF)

Software

• AlignmentBuilder: Iterative alignment building Perl script using HMMER2.1 and BLAST
• Perl scripts used to integrate protein-ligand contacts with multiple algnments are also available to academic users. Please contact the authors to get the latest versions, which we are trying to make more user friendly.

To accompany the following paper:

OEP family (outer-membrane efflux proteins)

• OEP family (whole proteins)
• OEP symmetry (N and C halves aligned with each other)

PEP family (periplasmic efflux proteins)

• PEP-Lipoyl domain homology
• MexC subfamily coiled-coil region
• MexC subfamily (PSI-BLAST-generated)
• HlyD subfamily (PSI-BLAST-generated)
• Combined PEP family alignment: this is the newest alignment, which combines both of the subfamiles and contains a handful of Gram-negative bacteria. The central, coiled-coil section of this alignment is uncertain, but many proteins could be added with by using an iterative HMM method of alignment-building..

The above alignments are in MSF format.

PSI-BLAST is available at http://www.ncbi.nlm.nih.gov/cgi-bin/BLAST/nph-psi_blast.

• MAPF Perl5 program for predicting transmembrane beta strands in outer membrane porins from input multiple alignments in MSF format. Requires GNUPLOT for postscript output. (Use caution to ensure that long lines are not split when cutting and pasting code.)