Putative orthologous gene clusters to P. fijiensis PKS10-2, from P. fuligena and P. cruenta.

For each gene in the putative biosynthetic cluster, the table indicates the description in Fig 10, the accession of the putative P. fijiensis homolog protein in cases where they are each other’s best blast hit, the scaffold wherein the P. fuligena or P. cruenta gene is located, the location along the scaffold, the gene orientation, the protein accession of the sequence if one has been annotated, the Interpro and KOG descriptions, and the conserved domains identified in the Conserved Domain Database (CDD) via blastp or blastx, via the CDD v3.18–55570 PSSMs or NCBI_curated—16212 PSSMs databases. Blastx or blastp analysis was done for each gene or protein sequence using the non-redundant protein sequence database on NCBI, and the top ten hits are indicated with species wherein they are found, description of the sequence, bitscore, E-value, percent sequence identity, and accession. If predicted protein sequences were previously annotated, then reciprocal blastp searches were used to identify homologs of P. fijiensis sequences, conserved domains were identified in the CDD database using blastp, and blastp analysis was used to identify the top ten hits from the non-redundant protein sequence database on NCBI. If predicted protein sequences were not previously annotated, then putative genes were identified from the P. fuligena and P. cruenta genomes using tblastn of P. fijiensis cluster genes as queries, blastx was used to verify that they were reciprocal best hits, blastx was used to identify conserved domains, and blastx was used to identify the top ten hits from the non-redundant protein sequence database on NCBI. A) The putative biosynthetic cluster for P. fuligena; B) The putative biosynthetic cluster for P. cruenta. (XLSX)本表格针对推定生物合成基因簇中的每一个基因，列明了如下信息：图10中的基因描述、若二者互为最优BLAST比对匹配时斐济假尾孢菌（P. fijiensis）同源蛋白的登录号、烟霉假尾孢菌（P. fuligena）或豌豆假尾孢菌（P. cruenta）基因所在的基因组支架序列、该基因在支架序列上的位置、基因转录方向、若已完成注释则对应的蛋白质登录号、Interpro及KOG数据库注释信息，以及通过BLASTp或BLASTx，基于保守结构域数据库（CDD）的CDD v3.18–55570位置特异性得分矩阵（PSSMs）或NCBI手工注释的16212个PSSMs数据库所鉴定得到的保守结构域。 本研究针对每一条基因或蛋白质序列，采用NCBI非冗余蛋白质序列数据库开展BLASTx或BLASTp分析，所得到的前10条匹配序列信息包括其来源物种、序列描述、比特得分、期望阈值（E值）、序列一致性百分比及登录号。 若预测得到的蛋白质序列已完成预先注释，则采用双向BLASTp比对鉴定斐济假尾孢菌序列的同源基因；通过BLASTp在CDD数据库中鉴定保守结构域；并采用BLASTp分析从NCBI非冗余蛋白质序列数据库中获取前10条匹配序列。 若预测得到的蛋白质序列未完成预先注释，则以斐济假尾孢菌基因簇基因为查询序列，通过tblastn从烟霉假尾孢菌和豌豆假尾孢菌基因组中鉴定推定基因；采用BLASTx验证二者为双向最优匹配；通过BLASTx鉴定保守结构域；并采用BLASTx从NCBI非冗余蛋白质序列数据库中获取前10条匹配序列。 A) 烟霉假尾孢菌（P. fuligena）推定生物合成基因簇；B) 豌豆假尾孢菌（P. cruenta）推定生物合成基因簇。（XLSX）