The major outer membrane protein of the Chlamydiaceae family has been sequenced in different biovars and serotypes of Chlamydia. Nucleotide and amino acid sequence alignments for the major outer membrane protein have been constructed for different biovars and serotypes: 1) An intraspecies alignment contains representative serotypes of the various Chlamydia trachomatis biovars; 2) An interspecies alignment contains representative sequences from the different species; 3) An alignment of all MOMP sequences encompasses all MOMP sequences longer than 315 aa, which have a corresonding DNA sequence, contained in GenBank under the Chlamydiaceae node of the NCBI taxonomy tree. In these alignments the sequence names are GenBank gi numbers. The Chlamydia MOMP Data Table contains each protein and nucleotide GenBank entry along with a brief description and reference. The Chlamydia MOMP References Table contains the complete references.
Alignments are presented for both nucleotide and protein sequences. Nucleotide alignments are codon aligned, that is to say insertions and deletions maintain the coding potential of the sequence. Nucleotide alignments are essentially a back translation of the protein alignments. Protein alignments were generated with Clustal W and manually examined. Phylogenetic trees were constructed for both proteins and nucleotides (first and second codon positions) and were in agreement.
Secondary structure analysis of the Chlamydia trachomatis intraspecies protein alignment was performed using the Network Protein Sequence Analysis web site. Five secondary structure prediction tools (DPM, DSC, PHD, SIMPA96 and SOPM) were used. A majority rule secondary structure consensus of these five prediction tools was calculated, one for each protein sequence. An intraspecies secondary structure consensus (majority rule) was then generated using each individual secondary structure consensuses. The letters in the alignment correspond to various secondary structures: H or h corresponds to alpha helices, E or e to extended strands, C or c to random coils and ? to ambiguous states.
The alignment of N-linked glycosylation sites, cysteine residues and serine-linked sites for the intraspecies C. trachomatis MOMP data set was generated using a C program developed by Rhoshel Lenroot of LANL. The alignment shows the N-linked glycosylation sites as 'X', the cysteine residues as 'C' and the serine-linked sites as 'S'. Dots represent all other amino acids in the alignment.Nucleotide Alignments
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