SOSUI

[…] of an intact na+/h+ exchanger domain (pfam: pf00999) by pfam (http://pfam.xfam.org/), and were named according to their similarity to arabidopsis homologous genes and phylogenetic relationship. sosui (http://harrier.nagahama-i-bio.ac.jp/sosui/sosui_submit.html) and psort (http://psort.hgc.jp/) were used to predict transmembrane domains and protein localization, respectively., […]

[…] was derived using clustal w with default parameters. protein domains were predicted by the pfam protein families database. the transmembrane domains with hydrophobic residues were predicted by the sosui algorithm., 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 […]

[…] molecular weight (mw) and isoelectric point (pi) of protein were calculated by compute pi/mw tool (http://web.expasy.org/compute_pi/) []. the transmembrane region of hn protein was predicted by the sosui system (http://harrier.nagahama-i-bio.ac.jp/sosui/sosui_submit.html) []. the alignment of nt and deduced amino acid (aa) sequences and calculation of evolutionary distance in nt substitutions […]

[…] of 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 [] and sosui [] were used to predict signal peptides and transmembrane helices. the predicted cdss were also used to search against the pfam protein family database []. the genbank database [] and the cog […]

[…] was also carried out using the clustalw program available at ddbj (http://www.ddbj.nig.ac.jp/). a phylogenetic tree was built using dendroscope. tm domains of the ppklrs were predicted using the sosui program (http://bp.nuap.nagoya-u.ac.jp/sosui/)., y190 strain yeast was grown on ypd medium [10 g/l yeast extract (nakalai tesque, kyoto, japan), 20 g/l peptone (nakalai tesque), and 20 g/l […]

[…] (ge healthcare). full-length cdnas were cloned using the smart race cdna amplification kit (clontech)., ncbi-blastp (http://blast.ncbi.nlm.nih.gov/blast.cgi), pfam (http://pfam.sanger.ac.uk/), and sosui (http://harrier.nagahama-i-bio.ac.jp/sosui/) were used to search for motifs in the nsd-1 sequence., recombinant autographa californica multiple nucleopolyhedroviruses (acmnpvs) were constructed […]

[…] and ecology, chinese academy of sciences) and dr. hong-li lian (shanghai jiao-tong university) for kindly supplying the tap-fusion vector and phb vector., http://harrier.nagahama-i-bio.ac.jp/sosui/sosui_submit.html , the supplementary material for this article can be found online at: […]

[…] for protein domain composition using the smart database () and pfam, prints, and tigrfams under interproscan (). tm domains were predicted using phobius (), tmhmm (), hmmtop (), gpcrhmm (), and sosui (). proteins containing domains other than pipk at the c terminus and those without tm domains were discarded. newly identified gpcr-pipks were then used in queries for iterative searches using […]

[…] it shares an average nucleotide identity (ani) of 73% (genbank accession number ku530220)., abt2graduatex2 gp29 has been identified as a putative class ii holin () by structural homology () and sosui analysis showing two transmembrane regions (). abt2graduatex2 gp29 is present in all current members of the bg cluster, where it forms a putative operon with gp28, a lysin, but it is absent […]

[…] intact if they revealed an open reading frame as well as intact splice sites., the amino acid sequences of the feline clca3 were analyzed in silico using the signalp 4.1 [], kyte–doolittle [], sosui [], hmmtop [], das [], psort ii [] and netnglyc (http://www.cbs.dtu.dk/services/netnglyc) software. putative proteolytic cleavage sites were identified by interspecies comparison of the amino […]