The lytic process, however, is not catastrophic; rather it follows a step-wise sequence of events (Ertel et al., 1993; Peterlin et al., 2012).
Also in this case, our results support previous data [ 73], which argue for a distributive/step-wise sequence of events for PCNA poly-ubiquitylation, starting from ubiquitin activation to its covalent linkage on mono-ubiquitylated PCNA.
The benchmark study was performed using a set of 200 non-homologous protein chains collected from the PDB by Zhang and Skolnick [ 7] with a pair wise sequence identity of less than 30%.
Many benefits can be gained from the use of genomic scaffolds: they reduce the number of pair wise sequence comparisons, they are often less error-prone than ESTs and they ensure that phylogenetically divergent transcripts with shared domains (such as paralogues, chimeras and repeat-containing transcripts) are not placed in the same cluster.
Scheme 5 Synthesis of 6b in step wise sequence.
Codon-wise sequence alignment of cytb haplotypes from populations of different Gerbillus species, together with outgroup haplotypes, exposed most of the segregation sites which were probably enough for speciation events between different taxa.
A database of 71 TIM barrel proteins has been previously developed (http://www.cbrc.jp/~gromiha/tim/proteinlist.html [15]) from the SCOP [41] and HOMSTRAD [42] databases, with a pair-wise sequence homology of <25%.
The pair-wise sequence identity of C2 domains was determined using needle, a global alignment tool within EMBOSS [ 29].
Pair-wise sequence comparisons of all gene indices were performed using BLASTN [ 20] and an E value cutoff of 10-10 was used as a minimum cutoff for significant sequence similarity at the nucleotide level.
From the pair-wise sequence alignment of each PPK protein and the template, multiple structural models were generated by MODELER with default homology modeling protocol (Sali and Blundell 1993).
The function Bridge extracts a circle-wise ordered sequence of F gap adjacent facets and bridges the gap between a pair of consecutive F out facets.
