Because of the inter-species conservation of protein-coding sequences we were able to predict the presumptive DNA sequence encoding amino- and carboxyl-termini of various TMC proteins by comparing human and murine genomic TMC sequence.
Its presumptive lipobox sequence is LGAC, containing the indispensible cysteine in position 30, indicating that SsTroA is not released into the environment but rather inserted into the plasma membrane via a diacylglyceryl anchor.
These analyses defined the presumptive promoter sequence and TSS of the A20 gene.
An HMM was built from the N-terminal region of collected BA_2677 homologs in order to represent the presumptive leader sequence.
The evolutionary conservation of these motifs was also analyzed by first assembling presumptive UTR sequences of annotated genes in T. congolense, T. cruzi, and Leishmania major using Splicemodel predictions, and then assembling the sequences into regulated groups based on the assumption that these orthologous genes are regulated in the same way as in T. brucei.
It is reasonable to assume that this discrepancy and the lack of identifiable terminal inverted repeats (TIR) (discussed below) is an assembly artifact due to omission of the presumptive repeat sequences in the terminal regions of pLMP1046.
It should also be noted that E. coli possesses only five DnaA boxes, whereas M.tb has 13 presumptive DnaA box sequences that bear little sequence similarity to any of the E. coli DnaA boxes [5], [8].
Importantly, the molecular weight of this protein and pI revealed by 2D (69.1 and 5.4 correspondently) practically coincide with those of Hsp68 deduced basing on the presumptive hsp68 gene sequence located in phage 7 and 7b of O. pardalina (69.14 kD and 5.36).
The AGC [ 28] acts as a repository for presumptive full-length sequences from multiple sources, including: AESTdb, sequences parsed from existing databases (e.g. NCBI), and sequences derived from the community at large.
The sequences were of high quality, although one problematic area due to a presumptive context-specific sequencing error causing motif located in exon 1 of the DSP gene was detected.
