Multiple sequence analysis of polygalacturonases and invertases and phase shift in conserved motifs

Multiple sequence analysis by programs, such as ClustalW and T-COFFEE, is one of the important tools in bioinformatics. These programs are used to predict conserved motifs among related or unrelated proteins and nucleic acids that are of functional importance. However, it is observed that the conserved motifs in protein sequence analysis from some organisms especially from archae bacteria, extremophilic organisms and fungi do not align with other conserved sequences all the time and the conserved motif(s) in these organisms may be slightly shifted, either side of the conserved motif aligned for all the other organisms. Even one protein sequence is not aligned with others; the ClustalW or T-COFFEE does not mark the whole block as the conserved motif even though the particular motif is conserved among others. This is a serious problem as the investigator may miss important and functional motif(s) because of such misalignments. But a careful manual analysis of the aligned sequences will solve such anomaly. This is substantiated with two examples; one from polygalacturonase sequences analysis and the other from invertase sequences analysis using ClustalW, T-COFFEE, DIALIGN and MAFFT algorithms.