HIV-1 Protease regions

Molecular rendering of protease dimer surface (slate blue) coupled to the antiretroviral Saquinavir (grey) highlighting protein domains. Crystallographic model generated through x-ray diffraction crystallography by Kovalevsky AY, 2010 (PDB:3OXC).

HIV-1 Protease domains

Molecular rendering of protease dimer surface (slate blue) coupled to the antiretroviral Saquinavir (grey) highlighting protein domains. Crystallographic model generated through x-ray diffraction crystallography by Kovalevsky AY, 2010 (PDB:3OXC).

Phylogeny of Mexican HIV-1 Protease-encoding nucleotide sequences

Phylogeny reconstructed using a Markov Chain Monte Carlo algorithm based Bayesian analysis suite (BEAUti and BEAST) using a general time reversible substitution model and strict clock for 777 Mexican HIV-1 nucleotide sequences.

Mexican HIV-1 Protease-encoding nucleotide sequence alignments

BBEdit text multiple alignment of the 777 Mexican HIV-1 nucleotide sequences along with HXB2 reference and consensus sequences for group M subtypes A1, A2, B, C, D, F1, F2, G & H and group O as performed using Clustal Omega and reformatted for unanimity to HXB2 reference using SURe.

Protease inhibitor resistance mutations in local HIV-1 Isolates

Primary and secondary protease inhibitor resistance mutations seen in 51 Mexican HIV-1 isolates are mapped unto a crystallographic model of a HIV-1 protease dimer coupled to the antiretroviral Saquinavir protease-inhibitor generated through x-ray diffraction crystallography (PDB:3OXC).

Phylogeny of local HIV-1 Protease-encoding nucleotide sequences

Phylogeny reconstructed using a Markov Chain Monte Carlo algorithm based Bayesian analysis suite (BEAUti and BEAST) using a general time reversible substitution model and log normal relaxed clock for 51 Mexican HIV-1 nucleotide sequences plus group M (subtypes A1, A2, B, C, D, F1, F2, G and H) and group O (as an outlier) consensus sequences.

Local HIV-1 Protease amino acid sequence alignments

Multiple alignment of the 51 Mexican HIV-1 amino acid sequences along with HXB2 reference and consensus sequences for group M subtypes A1, A2, B, C, D, F1, F2, G & H and group O as performed using Clustal Omega and reformatted for unanimity to HXB2 reference using SURe.

Local HIV-1 Protease-encoding nucleotide sequence alignments

Multiple alignment of the 51 Mexican HIV-1 nucleotide sequences along with HXB2 reference and consensus sequences for group M subtypes A1, A2, B, C, D, F1, F2, G & H and group O as performed using Clustal Omega and reformatted for unanimity to HXB2 reference using SURe.

Local HIV-1 Vif amino acid sequence alignments

Multiple alignment of the 86 nucleotide sequences was performed using Clustal Omega and reformatted for unanimity to the HXB2 reference using SURe.

Local HIV-1 Vif-encoding nucleotide sequence alignments

Multiple alignment of the 86 nucleotide sequences was performed using Clustal Omega and reformatted for unanimity to the HXB2 reference using SURe.

Phylogeny of Mexican HIV-1 Vif-encoding nucleotide sequences

Phylogeny reconstructed using a Markov Chain Monte Carlo algorithm based Bayesian analysis suite (BEAUti and BEAST) using a general time reversible substitution model and strict clock for 77 Mexican HIV-1 nucleotide sequences plus group M (subtypes A, B, C, D, F1, F2, G and H) and group O (as an outlier) consensus sequences.

Mexican Vif protein sequence alignment summary

Protein domains and functional regions are shaded to highlight functional regions and sites. These include tryptophans (W) involved in APOBEC3G binding, APOBEC3-protein family binding domains, the nuclear localization inhibitory signal, the MAPK phosphorylation sites, CBFβ interaction sites, the Cullin5 Zinc-binding domain, the Elongin B/C (BC) box, protease processing site, known phosphorylation sites, the Cullin5-box and the dimerization site..

Mexican Vif protein sequence entropy and amino acid frequency map

The frequency of the most common amino acids observed at each site in the 77 Mexican HIV-1 Vif sequences is shown in the continuous line while Shannon entropy level at each site is shown in bar graphs. Boxes indicate protein regions exhibiting low entropy levels..

HIV pol region sequence analysis and contig assembly

Nucleotide and aminoacid sequences in fasta format and their alignments for five Human Immunodeficiency Virus type-1 clinical isolates are included. This page includes links to nucleotide alignments, protein alignments, fasta files as well as to their original fragment and contig assembly document.

Genomic mapping of contigs unto HXB2 genome pictogram

Topological maps for the five contig clones depicting location of sequences as generated by REGA HIV-1 Subtyping tool.

SimPlot analysis and subtyping using bootscan plots of regional homology

Regional homology bootscan plots for the five sequenced contigs.

Recombinatorial analysis of cloned and sequenced samples

Recombinatorial analysis incorporating pictogram of HIV genome and bootscan analysis in a single image.

Clinical information capture form (v08) for MGDC-HIV (in spanish)

Includes a 7 page clinical and epidemiological data collection form in protable document format as used by our lab to summarize individual medical records.

CDC staging table (in spanish)

Includes single page HIV clinical staging table summarizing CDC's criteria based on both clinical and CD4 cell count data.