SOSUI

[…] derived using clustal w with default parameters48. protein domains were predicted by the pfam protein families database49. the transmembrane domains with hydrophobic residues were predicted by the sosui algorithm50., to screen wcr active targets, 400 to 800 base pair regions of randomly selected non- redundant cdna clones were amplified using taq dna polymerase with a pair of gene specific […]

[…] (‹0.05 for saouhsc_02307, saouhsc_02309, saouhsc_02866, and abd31816.1) compared to proteins with expected size. this indicates that these specific hypothetical proteins may not be in the mfs., sosui calculates the average hydrophobicity of a protein. if hydrophobicity exists, the server labels that portion of the protein as a transmembrane region. table 6 details transmembrane regions […]

[…] the average hydrophobicity of a protein. if hydrophobicity exists, the server labels that portion of the protein as a transmembrane region. table 6 details transmembrane regions as described by the sosui server. mfs proteins typically have 11 to 13 transmembrane regions, so saouhsc_02307, saouhsc_02309, saouhsc_02620, and abd31816.1 are unlikely functioning mfs proteins because they have half […]

[…] and abd31816.1 are unlikely functioning mfs proteins because they have half or less of the necessary number of transmembrane regions. since glpt and lacy had 10 transmembrane regions per sosui (data not shown), it is still possible that saouhsc_02752 and abd31642.1 are related to mfs proteins based on this analysis., finally, potential mfs hypothetical proteins should have similar […]

[…] the genomic sequences was completed using the ncbi prokaryotic genome annotation pipeline which was combined using best-placed reference protein set and the gene caller genemarks+. signalp [30] and sosui [31] were used to predict signal peptides and transmembrane helices. the predicted cdss were also used to search against the pfam protein family database [32]. the genbank database [33] […]