Figure 1.
Flow chart for annotating individual proteins in H. Pylori 26695 strain.
Figure 2.
Comparison of H. pylori 26695 proteome functional classes in Pylorigene database and current annotation studies.
Figure 3.
Coverage of H. pylori 26695 structural proteome (A) Distribution of structural classes in H. pylori 26695 proteome according to SCOP classification.
(B) Distribution of major structural folds across H.pylori 26695 proteome.
Figure 4.
Modelling and structural analysis of HP0773.
(A) Sequence alignment of HP0773 and its structural template PDB_ID: 2GJL_A used for modelling. Ligand binding residues are shown in black boxes. (B) Superimposition of HP0773 model (yellow) with its template structure PDB_ID: 2GJL_A (purple). (C) In the HP0773 model, CastP predicted cofactor binding pocket is shown in green surface. (D) Superimposition of the predicted ligand binding site of model with the template structure. (E) Association of the FMN cofactor to the predicted binding site of model (residues in yellow) based on high similarity to a known FMN binding site of template 2GJL (residues in blue). Cofactor FMN is represented in ball and stick model, carbon- green, oxygen- red, nitrogen- blue and phosphorus- orange.
Figure 5.
Modelling and structural analysis of HP1214.
(A) Sequence alignment of HP1214 and its structural template PDB_ID: 1WD5_A. (B) Superimposition of HP1214 model (yellow) with its template structure PDB_ID: 1WD5_A (purple). (C) In the model structure HP1214, CastP predicted cofactor binding pocket is shown in light blue surface (D) Superimposition of the predicted ligand binding site of model with the template structure. (E) Structure based sequence alignment of HP1214 with PDB_ID: 3G6W_D, residues involved in ligand binding are shown by black boxes, residues of the loop region involved in the dimer formation are shown in blue boxes while red boxes indicate residues involved in the formation of inserted loop. (F) Association of the PRPP ligand to the predicted binding site (residues in yellow) based on high similarity to a known PRPP binding site of template which is PDB_ID: 3G6W_D (residues in blue). PRPP is represented in ball and stick model, carbon- green, oxygen- red, nitrogen- blue and phosphorus- orange.
Figure 6.
Modelling and structural analysis of HP1504.
(A) Sequence alignment of HP1504 and its template PDB_ID: 3LPM_A used for modelling. (B) Structural superimposition of HP1504 model (yellow) with its structural template PDB_ID: 3LPM_A (purple). (C) In the model structure HP1504, CastP predicted ligand binding pocket is shown in blue surface. (D) Superimposition of the predicted ligand binding site of model with the template structure. (E) Structure based sequence alignment of HP1504 sequence with PDB_ID: 2ZWV_A, residues involved in ligand binding are shown in black boxes. (F) Association of the SAH ligand to the predicted binding site (residues in yellow) based on high similarity to a known SAH binding site of template which is PDB_ID: 2ZWV_A (residues in blue). SAH is represented in ball and stick model, carbon- green, oxygen- red, nitrogen- blue and phosphorus- orange.