University of Illinos at Chicago
 
Pattern of Amino Acid Substitution in Transmembrane Segments of β-Barrel Membrane Proteins
David Jimenez-Morales and Jie Liang

Supporting Material

Main · Substitution Rate and Scoring Matrices · Multiple Sequence Alignments · Data Set · BBTM-SearchTool
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Substitution Rate and bbTM Scoring Matrices
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A Bayesian Monte Carlo approach based on the technique of Markov chain Monte Carlo was used to estimate the posterior mean values of the instantaneous rates of residue substitution, using the selected set of sequences homologous to the template protein and its phylogenetic tree. The entries qij of the matrix Q are substitution rates of amino acid residues for the 20 amino acids at an infinitesimally small time interval. Q takes the form Q = D/2*S + S*D/2, where D is a diagonal matrix with values taken from the amino acid composition of the set of aligned sequences studied, and S is a symmetric matrix with 0 values in diagonal elements, and whose off-diagonal entries are estimated. Phylogenetic trees were obtained using a maximum likelihood method based on the entire length of the protein sequences.

TM-ALL region

The fragments embedded within the outer membrane region.

- Symmetric Q-all matrix (S to A) - bubble plot
- bbTM-all scoring matrix



 

TM-OUT region

Amino Acids facing the lipid interface, from the fragments embedded within the outer membrane region.

- Symmetric Q-out matrix (S to A) - bubble plot
- bbTM-out scoring matrix

 
Residues facing the interior of the beta barrel pore

TM-IN region

Amino Acids facing the interior of the beta barrel pore, from the fragments embedded within the outer membrane region.

- Symmetric Q-in matrix (S to A) - bubble plot
- bbTM-in scoring matrix

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Multiple Sequence Alignments
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Multiple sequence aligments of the beta barrel membrane proteins used in this study.

ScrY: Sucrose-Specific Porin (PDB:1A0S)
OmpA: Protein A (PDB:1BXW)
~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _
Omp32: Anion-selective porin (PDB:1E54)
FepA: Ferric enterobactin receptor (PDB:1FEP)
- ~ = ~ = ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ -
OmpT: Protease (PDB:1I78)
FecA: Transporter (PDB:1KMO)
- ~ = ~ = ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ -
BtuB: Cobalamin transporter (PDB:1NQE)
Phospholipase A (PDB: 1QD6)
- ~ = ~ = ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ -
OMPX: Protein X (PDB: 1QJ8)
lamB: Maltoporin (PDB:2MPR)
- ~ = ~ = ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ -
OmpF: Porin (PDB:2OMF)  

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Data Set
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Set of sequences used in this study

> dataset nrbigswiss.fasta: non-rendudant dat set containing known and predicted beta barrel membrane from TMBprof and Swiss-Prot database
> dataset chalmemrandom.fasta: random sequences obtained from fully shuffled sequences of 385 α- helical and β-barrel membrane proteins from different organisms. These random sequences preserve the same amino acid composition as membrane proteins
> oMBp.fasta: (for other MemBrane proteins) consists of membrane proteins with a different architecture (non-β-barrel). These were selected based on annotations of “SUBCELLULAR LOCATION: Cell membrane” from Eukaryota and Archaea. In total, 10,951 protein sequences (1,061 from Archaea and 9,890 from Eukaryota).

> Globular.fasta: 127,485 globular protein sequences from Uniprot with annotations that lack the word “membrane” (16,814 Archaea and 110,671 Eukaryota).

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David Jimenez-Morales and Jie Liang

Dept of Bioengineering/ Bioinformatics Program
University of Illinois at Chicago
Chicago, Illinois, United States of America