diff --git a/chart/charts.py b/chart/charts.py index 38f688e..587964f 100644 --- a/chart/charts.py +++ b/chart/charts.py @@ -12,25 +12,31 @@ def keep_txt_to_file(code, script_path): f.write(code) -def scatter_plot(file_path, chart_out_path, out_path, x_scale_font_angle, y_scale_font_angle, group_by_column='color', x_name="x", y_name="y", +def scatter_plot(file_path, chart_out_path, out_path, x_scale_font_angle, y_scale_font_angle, x_column_name, y_column_name, group_by_column='category', x_name="x", y_name="y", title="chart", dpi=100, width=10, height=6, title_font_size=12, ): midwest = pd.read_csv(file_path) # 导入文件 - plt.figure(figsize=(width, height), dpi=dpi, facecolor='w', edgecolor='k') + plt.figure(figsize=(int(width), int(height)), dpi=int(dpi), facecolor='w', edgecolor='k') + + categories = np.unique(midwest[group_by_column]) - group_by_column = np.unique(midwest[group_by_column]) colors = [ - plt.cm.Set1(i / float(len(group_by_column) - 1)) for i in range(len(group_by_column)) + plt.cm.Set1(i / float(len(categories) - 1)) for i in range(len(categories)) ] - for i, category in enumerate(group_by_column): - plt.scatter(midwest.keys()[0], - midwest.keys()[1], - data=midwest.loc[midwest[midwest.keys()[2]] == category, :], + for i, category in enumerate(categories): + plt.scatter(x_column_name, + y_column_name, + data=midwest.loc[midwest.category == category, :], s=20, - c=colors[i], + color=colors[i], label=str(category)) + plt.gca().set( + xlim=(0.0, 0.1), + ylim=(0, 90000), + ) + # xy轴的刻度 plt.xticks(rotation=x_scale_font_angle, fontsize=10) plt.yticks(rotation=y_scale_font_angle, fontsize=10) @@ -53,7 +59,7 @@ def scatter_plot(file_path, chart_out_path, out_path, x_scale_font_angle, y_scal def Each_regression_line_in_its_own_column(file_path, chart_out_path, out_path, group_by_column, group_by_range, x_column_name, y_column_name, - title, title_font_size, x_scale_font_angle, y_scale_font_angle, x_name, y_name, color): + title, title_font_size, x_name, y_name, color): df = pd.read_csv(file_path) group_by_range = [group_by_range.split("-")[0], group_by_range.split("-")[1]] df_select = df.loc[df[group_by_column].isin(group_by_range), :] @@ -73,9 +79,6 @@ def Each_regression_line_in_its_own_column(file_path, chart_out_path, out_path, plt.title(title, fontsize=int(title_font_size)) plt.savefig(f"{chart_out_path}") # 保存图片 - plt.xticks(rotation=x_scale_font_angle, fontsize=10) - plt.yticks(rotation=y_scale_font_angle, fontsize=10) - # xy轴的名称 plt.xlabel(x_name, fontdict={'fontsize': 10}) plt.ylabel(y_name, fontdict={'fontsize': 10}) @@ -86,7 +89,7 @@ def Each_regression_line_in_its_own_column(file_path, chart_out_path, out_path, def Jittering_with_stripplot(file_path, chart_out_path, out_path, x_column_name, y_column_name, - title, title_font_size, x_scale_font_angle, y_scale_font_angle, x_name, y_name, color): + title, title_font_size, x_name, y_name, color): df = pd.read_csv(file_path) fig, ax = plt.subplots(figsize=(5, 3), dpi=180) print(fig, ax) @@ -105,9 +108,6 @@ def Jittering_with_stripplot(file_path, chart_out_path, out_path, x_column_name, plt.legend(fontsize=10) - plt.xticks(rotation=x_scale_font_angle, fontsize=10) - plt.yticks(rotation=y_scale_font_angle, fontsize=10) - # xy轴的名称 plt.xlabel(x_name, fontdict={'fontsize': 10}) plt.ylabel(y_name, fontdict={'fontsize': 10}) @@ -118,7 +118,7 @@ def Jittering_with_stripplot(file_path, chart_out_path, out_path, x_column_name, def Marginal_Histogram(file_path, chart_out_path, out_path, x_column_name, y_column_name, - title, title_font_size, x_scale_font_angle, y_scale_font_angle, x_name, y_name, chart_bar_x_color='#0078d4', chart_bar_y_color='#098154'): + title, x_name, y_name, chart_bar_x_color='#0078d4', chart_bar_y_color='#098154'): df = pd.read_csv(file_path) # Create Fig and gridspec @@ -156,8 +156,6 @@ def Marginal_Histogram(file_path, chart_out_path, out_path, x_column_name, y_col orientation='horizontal', color=chart_bar_y_color) - ax_main.title.set_fontsize(fontsize=int(title_font_size)) - ax_main.set(title=title, xlabel=x_name, ylabel=y_name) @@ -173,16 +171,13 @@ def Marginal_Histogram(file_path, chart_out_path, out_path, x_column_name, y_col plt.legend(fontsize=10) - plt.xticks(rotation=x_scale_font_angle, fontsize=10) - plt.yticks(rotation=y_scale_font_angle, fontsize=10) - plt.savefig(f"{out_path}.png") plt.savefig(f"{out_path}.svg") plt.savefig(f"{out_path}.pdf") def Correllogram(file_path, chart_out_path, out_path, - title, title_font_size, x_scale_font_angle, y_scale_font_angle, x_name, y_name, font_size, font_color, weight): + title, title_font_size, font_size, font_color, weight): df = pd.read_csv(file_path) plt.figure(figsize=(9.4, 4.25), dpi=200) sns.heatmap( @@ -204,13 +199,6 @@ def Correllogram(file_path, chart_out_path, out_path, plt.legend(fontsize=10) - plt.xticks(rotation=x_scale_font_angle, fontsize=10) - plt.yticks(rotation=y_scale_font_angle, fontsize=10) - - # xy轴的名称 - plt.xlabel(x_name, fontdict={'fontsize': 10}) - plt.ylabel(y_name, fontdict={'fontsize': 10}) - plt.savefig(f"{out_path}.png") plt.savefig(f"{out_path}.svg") plt.savefig(f"{out_path}.pdf") @@ -375,7 +363,7 @@ def Diverging_Bars_vertical(file_path, chart_out_path, out_path, x_column_name, def Ordered_Bar_Chart(file_path, chart_out_path, out_path, x_column_name, y_column_name, - title, title_font_size, x_scale_font_angle, y_scale_font_angle, x_name, y_name, color): + title, title_font_size, y_scale_font_angle, x_name, y_name, color): df_raw = pd.read_csv(file_path) df = df_raw[[x_column_name, y_column_name]].groupby(y_column_name).apply(lambda x: x.mean()) df.sort_values(x_column_name, inplace=True) @@ -393,7 +381,6 @@ def Ordered_Bar_Chart(file_path, chart_out_path, out_path, x_column_name, y_colu alpha=0.7, linewidth=20) - plt.xticks(rotation=x_scale_font_angle, fontsize=10) plt.yticks(rotation=y_scale_font_angle, fontsize=10) # Annotate Text @@ -524,7 +511,7 @@ def Dot_Plot(file_path, chart_out_path, out_path, x_column_name, y_column_name, plt.yticks(rotation=y_scale_font_angle, fontsize=10) plt.ylabel(y_name, fontsize=12) - plt.ylabel(x_name, fontsize=12) + plt.xlabel(x_name, fontsize=12) plt.title(title, fontsize=int(title_font_size)) @@ -1016,7 +1003,7 @@ def Population_Pyramid(file_path, chart_out_path, out_path, # 测试文件 mpg.csv -def Waffle_Chart(file_path, chart_out_path, out_path, rows_number, group_by_column, data_column, x_scale_font_angle, y_scale_font_angle, y_name, x_name, +def Waffle_Chart(file_path, chart_out_path, out_path, rows_number, group_by_column, x_scale_font_angle, y_scale_font_angle, y_name, x_name, title_font_size, title): df_raw = pd.read_csv(file_path) @@ -1033,10 +1020,10 @@ def Waffle_Chart(file_path, chart_out_path, out_path, rows_number, group_by_colu plots={ '111': { 'values': - df[data_column], + df['counts'], 'labels': [ "{0} ({1})".format(n[0], n[1]) - for n in df[[group_by_column, data_column]].itertuples() + for n in df[[group_by_column, 'counts']].itertuples() ], 'legend': { 'loc': 'upper left', @@ -1089,7 +1076,7 @@ def Pie_Chart(file_path, chart_out_path, out_path, y_name, title, group_by_colum # 测试文件 mpg.csv -def Treemap(file_path, chart_out_path, out_path, title, group_by_column, data_column, title_font_size): +def Treemap(file_path, chart_out_path, out_path, title, group_by_column, title_font_size): import squarify df_raw = pd.read_csv(file_path) @@ -1097,7 +1084,7 @@ def Treemap(file_path, chart_out_path, out_path, title, group_by_column, data_co # Prepare Data df = df_raw.groupby(group_by_column).size().reset_index(name='counts') labels = df.apply(lambda x: str(x[0]) + "\n (" + str(x[1]) + ")", axis=1) - sizes = df[data_column].values.tolist() + sizes = df['counts'].values.tolist() colors = [plt.cm.Set2(i / float(len(labels))) for i in range(len(labels))] # Draw Plot @@ -1490,7 +1477,7 @@ def Dendrogram(file_path, chart_out_path, out_path, def Composition_Bar(file_path, chart_out_path, out_path, title, caption, subtitle, x_name, y_name, title_font_size, x_font_size, y_font_size, x_scale_font_size, y_scale_font_size, x_scale_font_angle, y_scale_font_angle, - x_font_color, y_font_color, x_scale_font_color, y_scale_font_color, title_font_color, background_color): + x_font_color, y_font_color, x_scale_font_color, y_scale_font_color, title_font_color): code = f""" datas <- read.csv("{file_path}") @@ -1512,7 +1499,6 @@ gg <- g + geom_bar(stat="identity", width = 0.5, fill="tomato2") + x="{x_name}", y="{y_name}") + theme(title=element_text(size={title_font_size}, color="{title_font_color}"), - plot.background_color = element_rect(fill="{background_color}", color="{background_color}"), axis.text.x=element_text(color="{x_scale_font_color}", size={x_scale_font_size}, angle={x_scale_font_angle}, vjust=0.6), axis.text.y=element_text(color="{y_scale_font_color}", size={y_scale_font_size}, angle={y_scale_font_angle}), axis.title.x=element_text(size={x_font_size}, color="{x_font_color}"), axis.title.y=element_text(size={y_font_size}, color="{y_font_color}")) @@ -2389,7 +2375,7 @@ dev.off() def Distribution_Box_1(file_path, chart_out_path, out_path, title, caption, subtitle, x_name, y_name, title_font_size, x_font_size, y_font_size, x_scale_font_size, y_scale_font_size, x_scale_font_angle, y_scale_font_angle, - x_font_color, y_font_color, x_scale_font_color, y_scale_font_color, title_font_color, background_color, line_color): + x_font_color, y_font_color, x_scale_font_color, y_scale_font_color, title_font_color, line_color): file_path = file_path.replace("\\", "\\\\") code = f""" @@ -2410,7 +2396,6 @@ gg <- g + geom_boxplot(varwidth=T, fill="plum", color="{line_color}") + x="{x_name}", y="{y_name}") + theme(title=element_text(size={title_font_size}, color="{title_font_color}"), - plot.background_color = element_rect(fill="{background_color}", color="{background_color}"), axis.text.x=element_text(color="{x_scale_font_color}", size={x_scale_font_size}, angle={x_scale_font_angle}, vjust=0.6), axis.text.y=element_text(color="{y_scale_font_color}", size={y_scale_font_size}, angle={y_scale_font_angle}), axis.title.x=element_text(size={x_font_size}, color="{x_font_color}"), axis.title.y=element_text(size={y_font_size}, color="{y_font_color}")) @@ -2873,7 +2858,7 @@ dev.off() # 实例文件 Group_HierarchicalTree.csv def Group_HierarchicalTree(file_path, chart_out_path, out_path, title, caption, subtitle, title_font_size, - title_font_color, background_color): + title_font_color): file_path = file_path.replace("\\", "\\\\") code = f""" @@ -2889,8 +2874,7 @@ hc <- hclust(dist(datas), "ave") # hierarchical clustering gg <- ggdendrogram(hc, rotate = TRUE, size = 2) + labs(title="{title}", subtitle="{subtitle}", caption="{caption}") + - theme(title=element_text(size={title_font_size}, color="{title_font_color}"), - plot.background_color = element_rect(fill="{background_color}", color="{background_color}")) + theme(title=element_text(size={title_font_size}, color="{title_font_color}")) png("{chart_out_path}",width=900,height=408) plot(gg) diff --git a/chart/tools.py b/chart/tools.py index eca0f7a..035ea2e 100644 --- a/chart/tools.py +++ b/chart/tools.py @@ -367,6 +367,7 @@ class="layui-input" style="height: 25px; width:80px;margin-top: 6px"> else: fl = "hex" code += """ + %s = "#000000" layui.use('colorpicker', function() { var $ = layui.$ @@ -384,7 +385,7 @@ class="layui-input" style="height: 25px; width:80px;margin-top: 6px"> }); }) - """ % (i, random_color(), fl, i + "_") + """ % (i + '_', i, random_color(), fl, i + "_") return code diff --git a/db.sqlite3 b/db.sqlite3 index 3abb927..c6e28f6 100644 Binary files a/db.sqlite3 and b/db.sqlite3 differ diff --git a/file_keep/chart/file/3170120442021135 b/file_keep/chart/file/3170120442021135 deleted file mode 100644 index 96e57e5..0000000 --- a/file_keep/chart/file/3170120442021135 +++ /dev/null @@ -1,89 +0,0 @@ -HMMER： -在线使用：https://www.ebi.ac.uk/Tools/hmmer/search/phmmer -下载：http://hmmer.janelia.org/static/binaries/hmmer3.0_windows.zip（将网址放在迅雷网盘进行下载，该文件含有readme.txt可参考使用） - -功能：用于搜索同源蛋白序列以及蛋白序列对位排序，比如从序列数据库中，找同源的序列，或者对一个一个新的基因功能进行鉴定，使用hmmer比使用blast有着更高的灵敏度和更高的搜索速度，HMMER的程序如下，注意每个程序都是输出文件在前面，输入文件在后面 -phmmer:功能：与Blastp类似，使用一个蛋白质序列搜索蛋白质序列库 -格式：phmmer [-options] -输入：你要检测的fasta格式的序列和你要搜索的数据库 -输出匹配的序列和特征：含有score,Taxonomy,Domain,Download -参数：输入的文件格式为fasta格式，蛋白质序列库常用的包括Reference Proteomes,UniProtKB,SwissProt,PDB,Ensembl,输出格式包括tblout、domtblout等，蛋白质数据库需要下载 -jackhmmer:功能：与psiBlast类似，蛋白质序列迭代搜索蛋白质序列库 -格式：jackhmmer [-options] -输入：你要检测的fasta格式的序列和你要搜索的数据库 -输出：匹配的序列及特征，含有score,Taxonomy,Domain,Download -参数：输入的文件格式为fasta格式，蛋白质序列库常用的有Reference Proteomes,UniProtKB,SwissProt,PDB,Ensembl，蛋白质数据库需要下载 -hmmalign:功能 多重序列比对 -格式： hmmalign [-options] -输入：输入是fasta文件 -输出：Stockholm 格式的多重序列比对文件 -参数：输入文件序列格式包括FASTA、EMBL、GenBank、UniProt -输出比对文件格式包括Stockholm、Pfam、A2M、PSIBLAST -hmmbuild:功能：建立参考数据的隐马尔可科夫模型 -格式： hmmbuild [-options] -输入：多重序列比对的文件（Stockholm file） -输出：建立的这些多重序列比对的隐马尔可科夫模型 -参数：输入文件支持很多生物数据格式如：CLUSTALW, SELEX, GCG MSF -输出文件命名时的后缀为.hmm -hmmscan:使用序列搜索HMM库 -格式： hmmscan [-options] -输入：hmm数据库和查询序列文件 -输出：含有Score和Download，hmm数据库所匹配的序列 -参数：HMM数据库有Pfam,TIGRFAM,Gene3D,Superfamily,PIRSF,TreeFam -hmmsearch:功能：在数据库中寻找已经建立好的模体） -格式： hmmsearch [options] -输入：建立好的参考数据模型、要搜索的数据库 -输出：输出结果 -参数：比较序列文件可以是FASTA、EMBL/UniProt、Genbank格式 -输出选项： --o：直接输出结果到文件，不是标准输出 ---tblout：tblout格式输出 ---domtblout：domtblout格式输出 ---pfamtblout：pfamtblout格式输出 -输出结果中分为两类，一类是针对序列的（full sequence），另一类是针对domain的（主要基于一条序列存在多个domain）。 -结果按照E-values值从小到大排序，形式与blast类似。 -其中target name是每个目标序列的名称； -query name是查询序列的名称； -score是比对得分，分值越高说明越相似； -E-value目标序列的期望值（统计意义）； -最重要的是E-value值，值越小，越可信，相当于一个统计量。 -hmmsim：功能没找到 -格式： hmmsim [-options] -输入：hmm格式的文件 -输出：以sequence为名的一行（2.out） -hmmstat:显示HMM数据库的统计信息 -格式： hmmstat [-options] -输入：hmm格式的文件 -输出：有idx为名的那一行，含有name,accession,nseq,eff_nseq,M,relent,info,p relE,compKL -输出显示：# hmmstat :: display summary statistics for a profile file -# HMMER 3.0 (March 2010); http://hmmer.org/ -# Copyright (C) 2010 Howard Hughes Medical Institute. -# Freely distributed under the GNU General Public License (GPLv3). -# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -# -# idx name accession nseq eff_nseq M relent info p relE compKL -# ---- -------------------- ------------ -------- -------- ------ ------ ------ ------ ------ -1 sequence - 1 0.39 172 0.59 0.59 0.51 0.03 -hmmconvert:功能：转换HMM格式 -格式：hmmconvert [-options] -输入：hmm格式的文件 -输出：hmm格式转换后的文件 -hmmemit:功能：从HMM模型中，得到一个模式序列 -格式： hmmemit [-options] -输入：hmm格式的文件 -输出：模式序列 -输出显示：>sequence-sample1 -IQYNNDSKLYLSLTRGVFKSSKVLAQVSKPPGIDTGTIHTTRRKRIVVDSETKSHELLDT -AGDRYFSFDDYLRRATTLVFLFALNRLRHFRKRNTLCEKIMELHGGDNFPNMLVKSEVSD -QISELDSEQCSLKPLGNAYKIPHVLAGNDVSKENDTGVLQLVRTIRQYIVRTGP -hmmfetch:功能：通过名字或者接受号从HMM库中取回一个HMM模型 -格式： hmmfetch [options] (retrieves HMM named ) -hmmfetch [options] -f (retrieves all HMMs in ) -hmmfetch [options] --index (indexes ) -输入：hmm文件和HMM模型的名字或接受号 -输出：为这个名字或接受号的HMM模型 -hmmpress:格式化HMM数据库，包括压缩和创建索引，以便于hmmscan搜索使用 -格式：hmmpress [-options] -输入：hmm格式的文件 -输出：可获得H3F格式的文件，H3I格式的文件，H3M格式的文件，H3P格式的文件 - diff --git a/file_keep/chart/file/3180030092021304 b/file_keep/chart/file/3180030092021304 deleted file mode 100644 index 57ee9fc..0000000 --- a/file_keep/chart/file/3180030092021304 +++ /dev/null @@ -1,529 +0,0 @@ -LOCUS NC_005816 9609 bp DNA circular BCT 21-JUL-2008 -DEFINITION Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete - sequence. -ACCESSION NC_005816 -VERSION NC_005816.1 GI:45478711 -DBLINK Project: 58037 -KEYWORDS . -SOURCE Yersinia pestis biovar Microtus str. 91001 - ORGANISM Yersinia pestis biovar Microtus str. 91001 - Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; - Enterobacteriaceae; Yersinia. -REFERENCE 1 (bases 1 to 9609) - AUTHORS Zhou,D., Tong,Z., Song,Y., Han,Y., Pei,D., Pang,X., Zhai,J., Li,M., - Cui,B., Qi,Z., Jin,L., Dai,R., Du,Z., Wang,J., Guo,Z., Wang,J., - Huang,P. and Yang,R. - TITLE Genetics of metabolic variations between Yersinia pestis biovars - and the proposal of a new biovar, microtus - JOURNAL J. Bacteriol. 186 (15), 5147-5152 (2004) - PUBMED 15262951 -REFERENCE 2 (bases 1 to 9609) - AUTHORS Song,Y., Tong,Z., Wang,J., Wang,L., Guo,Z., Han,Y., Zhang,J., - Pei,D., Zhou,D., Qin,H., Pang,X., Han,Y., Zhai,J., Li,M., Cui,B., - Qi,Z., Jin,L., Dai,R., Chen,F., Li,S., Ye,C., Du,Z., Lin,W., - Wang,J., Yu,J., Yang,H., Wang,J., Huang,P. and Yang,R. - TITLE Complete genome sequence of Yersinia pestis strain 91001, an - isolate avirulent to humans - JOURNAL DNA Res. 11 (3), 179-197 (2004) - PUBMED 15368893 -REFERENCE 3 (bases 1 to 9609) - CONSRTM NCBI Genome Project - TITLE Direct Submission - JOURNAL Submitted (16-MAR-2004) National Center for Biotechnology - Information, NIH, Bethesda, MD 20894, USA -REFERENCE 4 (bases 1 to 9609) - AUTHORS Song,Y., Tong,Z., Wang,L., Han,Y., Zhang,J., Pei,D., Wang,J., - Zhou,D., Han,Y., Pang,X., Zhai,J., Chen,F., Qin,H., Wang,J., Li,S., - Guo,Z., Ye,C., Du,Z., Lin,W., Wang,J., Yu,J., Yang,H., Wang,J., - Huang,P. and Yang,R. - TITLE Direct Submission - JOURNAL Submitted (24-APR-2003) The Institute of Microbiology and - Epidemiology, Academy of Military Medical Sciences, No. 20, - Dongdajie Street, Fengtai District, Beijing 100071, People's - Republic of China -COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final - NCBI review. The reference sequence was derived from AE017046. - COMPLETENESS: full length. -FEATURES Location/Qualifiers - source 1..9609 - /organism="Yersinia pestis biovar Microtus str. 91001" - /mol_type="genomic DNA" - /strain="91001" - /db_xref="taxon:229193" - /plasmid="pPCP1" - /biovar="Microtus" - repeat_region 1..1954 - gene 87..1109 - /locus_tag="YP_pPCP01" - /db_xref="GeneID:2767718" - CDS 87..1109 - /locus_tag="YP_pPCP01" - /note="similar to corresponding CDS from previously - sequenced pPCP plasmid of Yersinia pestis KIM (AF053945) - and CO92 (AL109969), also many transposase entries for - insertion sequence IS100 of Yersinia pestis. Contains - IS21-like element transposase, HTH domain - (Interpro|IPR007101)" - /codon_start=1 - /transl_table=11 - /product="putative transposase" - /protein_id="NP_995567.1" - /db_xref="GI:45478712" - /db_xref="GeneID:2767718" - /translation="MVTFETVMEIKILHKQGMSSRAIARELGISRNTVKRYLQAKSEP - PKYTPRPAVASLLDEYRDYIRQRIADAHPYKIPATVIAREIRDQGYRGGMTILRAFIR - SLSVPQEQEPAVRFETEPGRQMQVDWGTMRNGRSPLHVFVAVLGYSRMLYIEFTDNMR - YDTLETCHRNAFRFFGGVPREVLYDNMKTVVLQRDAYQTGQHRFHPSLWQFGKEMGFS - PRLCRPFRAQTKGKVERMVQYTRNSFYIPLMTRLRPMGITVDVETANRHGLRWLHDVA - NQRKHETIQARPCDRWLEEQQSMLALPPEKKEYDVHLDENLVNFDKHPLHHPLSIYDS - FCRGVA" - misc_feature 87..959 - /locus_tag="YP_pPCP01" - /note="Transposase and inactivated derivatives [DNA - replication, recombination, and repair]; Region: COG4584" - /db_xref="CDD:34222" - misc_feature <111..209 - /locus_tag="YP_pPCP01" - /note="Helix-turn-helix domain of Hin and related - proteins, a family of DNA-binding domains unique to - bacteria and represented by the Hin protein of Salmonella. - The basic HTH domain is a simple fold comprised of three - core helices that form a right-handed...; Region: - HTH_Hin_like; cl01116" - /db_xref="CDD:186341" - misc_feature 438..812 - /locus_tag="YP_pPCP01" - /note="Integrase core domain; Region: rve; cl01316" - /db_xref="CDD:194099" - gene 1106..1888 - /locus_tag="YP_pPCP02" - /db_xref="GeneID:2767716" - CDS 1106..1888 - /locus_tag="YP_pPCP02" - /note="similar to corresponding CDS form previously - sequenced pPCP plasmid of Yersinia pestis KIM (AF053945) - and CO92 (AL109969), also many ATP-binding protein entries - for insertion sequence IS100 of Yersinia pestis. Contains - Chaperonin clpA/B (Interpro|IPR001270). Contains - ATP/GTP-binding site motif A (P-loop) (Interpro|IPR001687, - Molecular Function: ATP binding (GO:0005524)). Contains - Bacterial chromosomal replication initiator protein, DnaA - (Interpro|IPR001957, Molecular Function: DNA binding - (GO:0003677), Molecular Function: DNA replication origin - binding (GO:0003688), Molecular Function: ATP binding - (GO:0005524), Biological Process: DNA replication - initiation (GO:0006270), Biological Process: regulation of - DNA replication (GO:0006275)). Contains AAA ATPase - (Interpro|IPR003593, Molecular Function: nucleotide - binding (GO:0000166))" - /codon_start=1 - /transl_table=11 - /product="transposase/IS protein" - /protein_id="NP_995568.1" - /db_xref="GI:45478713" - /db_xref="GeneID:2767716" - /translation="MMMELQHQRLMALAGQLQLESLISAAPALSQQAVDQEWSYMDFL - EHLLHEEKLARHQRKQAMYTRMAAFPAVKTFEEYDFTFATGAPQKQLQSLRSLSFIER - NENIVLLGPSGVGKTHLAIAMGYEAVRAGIKVRFTTAADLLLQLSTAQRQGRYKTTLQ - RGVMAPRLLIIDEIGYLPFSQEEAKLFFQVIAKRYEKSAMILTSNLPFGQWDQTFAGD - AALTSAMLDRILHHSHVVQIKGESYRLRQKRKAGVIAEANPE" - misc_feature 1109..1885 - /locus_tag="YP_pPCP02" - /note="transposase/IS protein; Provisional; Region: - PRK09183" - /db_xref="CDD:181681" - misc_feature 1367..>1669 - /locus_tag="YP_pPCP02" - /note="The AAA+ (ATPases Associated with a wide variety of - cellular Activities) superfamily represents an ancient - group of ATPases belonging to the ASCE (for additional - strand, catalytic E) division of the P-loop NTPase fold. - The ASCE division also includes...; Region: AAA; cd00009" - /db_xref="CDD:99707" - misc_feature 1433..1456 - /locus_tag="YP_pPCP02" - /note="Walker A motif; other site" - /db_xref="CDD:99707" - misc_feature order(1436..1459,1619..1621) - /locus_tag="YP_pPCP02" - /note="ATP binding site [chemical binding]; other site" - /db_xref="CDD:99707" - misc_feature 1607..1624 - /locus_tag="YP_pPCP02" - /note="Walker B motif; other site" - /db_xref="CDD:99707" - gene 2925..3119 - /gene="rop" - /locus_tag="YP_pPCP03" - /gene_synonym="rom" - /db_xref="GeneID:2767717" - CDS 2925..3119 - /gene="rop" - /locus_tag="YP_pPCP03" - /gene_synonym="rom" - /note="Best Blastp hit =gi|16082682|ref|NP_395229.1| - (NC_003132) putative replication regulatory protein - [Yersinia pestis], gi|5763813|emb|CAB531 66.1| (AL109969) - putative replication regulatory protein [Yersinia pestis]; - similar to gb|AAK91579.1| (AY048853), RNAI modulator - protein Rom [Salmonella choleraesuis], Contains Regulatory - protein Rop (Interpro|IPR000769)" - /codon_start=1 - /transl_table=11 - /product="putative replication regulatory protein" - /protein_id="NP_995569.1" - /db_xref="GI:45478714" - /db_xref="GeneID:2767717" - /translation="MNKQQQTALNMARFIRSQSLILLEKLDALDADEQAAMCERLHEL - AEELQNSIQARFEAESETGT" - misc_feature 2925..3107 - /gene="rop" - /locus_tag="YP_pPCP03" - /gene_synonym="rom" - /note="Rop protein; Region: Rop; pfam01815" - /db_xref="CDD:145136" - gene 3486..3857 - /locus_tag="YP_pPCP04" - /db_xref="GeneID:2767720" - CDS 3486..3857 - /locus_tag="YP_pPCP04" - /note="Best Blastp hit = gi|321919|pir||JQ1541 - hypothetical 16.9K protein - Salmonella typhi murium - plasmid NTP16." - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /protein_id="NP_995570.1" - /db_xref="GI:45478715" - /db_xref="GeneID:2767720" - /translation="MSKKRRPQKRPRRRRFFHRLRPPDEHHKNRRSSQRWRNPTGLKD - TRRFPPEAPSCALLFRPCRLPDTSPPFSLREAWRFLIAHAVGISVRCRSFAPSWAVCT - NPPFSPTTAPYPVTIVLSPTR" - misc_feature 3498..3626 - /locus_tag="YP_pPCP04" - /note="ProfileScan match to entry PS50323 ARG_RICH, - E-value 8.981" - gene 4343..4780 - /gene="pim" - /locus_tag="YP_pPCP05" - /db_xref="GeneID:2767712" - CDS 4343..4780 - /gene="pim" - /locus_tag="YP_pPCP05" - /note="similar to many previously sequenced pesticin - immunity protein entries of Yersinia pestis plasmid pPCP, - e.g. gi| 16082683|,ref|NP_395230.1| (NC_003132) , - gi|1200166|emb|CAA90861.1| (Z54145 ) , gi|1488655| - emb|CAA63439.1| (X92856) , gi|2996219|gb|AAC62543.1| - (AF053945) , and gi|5763814|emb|CAB531 67.1| (AL109969)" - /codon_start=1 - /transl_table=11 - /product="pesticin immunity protein" - /protein_id="NP_995571.1" - /db_xref="GI:45478716" - /db_xref="GeneID:2767712" - /translation="MGGGMISKLFCLALIFLSSSGLAEKNTYTAKDILQNLELNTFGN - SLSHGIYGKQTTFKQTEFTNIKSNTKKHIALINKDNSWMISLKILGIKRDEYTVCFED - FSLIRPPTYVAIHPLLIKKVKSGNFIVVKEIKKSIPGCTVYYH" - gene complement(4815..5888) - /gene="pst" - /locus_tag="YP_pPCP06" - /db_xref="GeneID:2767721" - CDS complement(4815..5888) - /gene="pst" - /locus_tag="YP_pPCP06" - /note="Best Blastp hit =|16082684|ref|NP_395231.1| - (NC_003132) pesticin [Yersinia pestis], - gi|984824|gb|AAA75369.1| (U31974) pesticin [Yersinia - pestis], gi|1488654|emb|CAA63438.1| (X92856) pesticin - [Yersinia pestis], gi|2996220|gb|AAC62544.1| (AF053945) - pesticin [Yersinia pestis], gi|5763815|emb|CAB53168.1| - (AL1099 69) pesticin [Yersinia pestis]" - /codon_start=1 - /transl_table=11 - /product="pesticin" - /protein_id="NP_995572.1" - /db_xref="GI:45478717" - /db_xref="GeneID:2767721" - /translation="MSDTMVVNGSGGVPAFLFSGSTLSSYRPNFEANSITIALPHYVD - LPGRSNFKLMYIMGFPIDTEMEKDSEYSNKIRQESKISKTEGTVSYEQKITVETGQEK - DGVKVYRVMVLEGTIAESIEHLDKKENEDILNNNRNRIVLADNTVINFDNISQLKEFL - RRSVNIVDHDIFSSNGFEGFNPTSHFPSNPSSDYFNSTGVTFGSGVDLGQRSKQDLLN - DGVPQYIADRLDGYYMLRGKEAYDKVRTAPLTLSDNEAHLLSNIYIDKFSHKIEGLFN - DANIGLRFSDLPLRTRTALVSIGYQKGFKLSRTAPTVWNKVIAKDWNGLVNAFNNIVD - GMSDRRKREGALVQKDIDSGLLK" - variation 5910..5911 - /note="compared to AF053945" - /replace="" - variation 5933^5934 - /note="compared to AL109969" - /replace="a" - variation 5933^5934 - /note="compared to AF053945" - /replace="aa" - variation 5948 - /note="compared to AL109969" - /replace="c" - gene 6005..6421 - /locus_tag="YP_pPCP07" - /db_xref="GeneID:2767719" - CDS 6005..6421 - /locus_tag="YP_pPCP07" - /note="Best Blastp hit = gi|16082685|ref|NP_395232.1| - (NC_003132) hypothetical protein [Yersinia pestis], - gi|5763816|emb|CAB53169.1| (AL109969) hypothetical protein - [Yersinia pestis]" - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /protein_id="NP_995573.1" - /db_xref="GI:45478718" - /db_xref="GeneID:2767719" - /translation="MKFHFCDLNHSYKNQEGKIRSRKTAPGNIRKKQKGDNVSKTKSG - RHRLSKTDKRLLAALVVAGYEERTARDLIQKHVYTLTQADLRHLVSEISNGVGQSQAY - DAIYQARRIRLARKYLSGKKPEGVEPREGQEREDLP" - variation 6525 - /note="compared to AF053945 and AL109969" - /replace="c" - gene 6664..7602 - /gene="pla" - /locus_tag="YP_pPCP08" - /db_xref="GeneID:2767715" - CDS 6664..7602 - /gene="pla" - /locus_tag="YP_pPCP08" - /EC_number="3.4.23.48" - /note="outer membrane protease; involved in virulence in - many organisms; OmpT; IcsP; SopA; Pla; PgtE; omptin; in - Escherichia coli OmpT can degrade antimicrobial peptides; - in Yersinia Pla activates plasminogen during infection; in - Shigella flexneria SopA cleaves the autotransporter IcsA" - /codon_start=1 - /transl_table=11 - /product="outer membrane protease" - /protein_id="NP_995574.1" - /db_xref="GI:45478719" - /db_xref="GeneID:2767715" - /translation="MKKSSIVATIITILSGSANAASSQLIPNISPDSFTVAASTGMLS - GKSHEMLYDAETGRKISQLDWKIKNVAILKGDISWDPYSFLTLNARGWTSLASGSGNM - DDYDWMNENQSEWTDHSSHPATNVNHANEYDLNVKGWLLQDENYKAGITAGYQETRFS - WTATGGSYSYNNGAYTGNFPKGVRVIGYNQRFSMPYIGLAGQYRINDFELNALFKFSD - WVRAHDNDEHYMRDLTFREKTSGSRYYGTVINAGYYVTPNAKVFAEFTYSKYDEGKGG - TQIIDKNSGDSVSIGGDAAGISNKNYTVTAGLQYRF" - misc_feature 6664..7599 - /gene="pla" - /locus_tag="YP_pPCP08" - /note="Omptin family; Region: Omptin; cl01886" - /db_xref="CDD:186487" - gene complement(7789..8088) - /locus_tag="YP_pPCP09" - /db_xref="GeneID:2767713" - CDS complement(7789..8088) - /locus_tag="YP_pPCP09" - /note="Best Blastp hit = gi|16082687|ref|NP_395234.1| - (NC_003132) putative transcriptional regulator [Yersinia - pestis], gi|5763818|emb|CAB53171.1| (AL109969) putative - transcriptional regulator [Yersinia pestis]." - /codon_start=1 - /transl_table=11 - /product="putative transcriptional regulator" - /protein_id="NP_995575.1" - /db_xref="GI:45478720" - /db_xref="GeneID:2767713" - /translation="MRTLDEVIASRSPESQTRIKEMADEMILEVGLQMMREELQLSQK - QVAEAMGISQPAVTKLEQRGNDLKLATLKRYVEAMGGKLSLDVELPTGRRVAFHV" - misc_feature complement(7837..7995) - /locus_tag="YP_pPCP09" - /note="Helix-turn-helix XRE-family like proteins. - Prokaryotic DNA binding proteins belonging to the - xenobiotic response element family of transcriptional - regulators; Region: HTH_XRE; cl09100" - /db_xref="CDD:195788" - gene complement(8088..8360) - /locus_tag="YP_pPCP10" - /db_xref="GeneID:2767714" - CDS complement(8088..8360) - /locus_tag="YP_pPCP10" - /note="Best Blastp hit = gi|16082688|ref|NP_395235.1| - (NC_003132) hypothetical protein [ Yersinia pestis], - gi|5763819|emb|CAB53172.1| (AL109969) hypothetical protein - [Yersinia pestis]" - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /protein_id="NP_995576.1" - /db_xref="GI:45478721" - /db_xref="GeneID:2767714" - /translation="MADLKKLQVYGPELPRPYADTVKGSRYKNMKELRVQFSGRPIRA - FYAFDPIRRAIVLCAGDKSNDKRFYEKLVRIAEDEFTAHLNTLESK" - misc_feature complement(8091..>8357) - /locus_tag="YP_pPCP10" - /note="Phage derived protein Gp49-like (DUF891); Region: - Gp49; cl01470" - /db_xref="CDD:194142" - variation 8529^8530 - /note="compared to AL109969" - /replace="tt" -ORIGIN - 1 tgtaacgaac ggtgcaatag tgatccacac ccaacgcctg aaatcagatc cagggggtaa - 61 tctgctctcc tgattcagga gagtttatgg tcacttttga gacagttatg gaaattaaaa - 121 tcctgcacaa gcagggaatg agtagccggg cgattgccag agaactgggg atctcccgca - 181 ataccgttaa acgttatttg caggcaaaat ctgagccgcc aaaatatacg ccgcgacctg - 241 ctgttgcttc actcctggat gaataccggg attatattcg tcaacgcatc gccgatgctc - 301 atccttacaa aatcccggca acggtaatcg ctcgcgagat cagagaccag ggatatcgtg - 361 gcggaatgac cattctcagg gcattcattc gttctctctc ggttcctcag gagcaggagc - 421 ctgccgttcg gttcgaaact gaacccggac gacagatgca ggttgactgg ggcactatgc - 481 gtaatggtcg ctcaccgctt cacgtgttcg ttgctgttct cggatacagc cgaatgctgt - 541 acatcgaatt cactgacaat atgcgttatg acacgctgga gacctgccat cgtaatgcgt - 601 tccgcttctt tggtggtgtg ccgcgcgaag tgttgtatga caatatgaaa actgtggttc - 661 tgcaacgtga cgcatatcag accggtcagc accggttcca tccttcgctg tggcagttcg - 721 gcaaggagat gggcttctct ccccgactgt gtcgcccctt cagggcacag actaaaggta - 781 aggtggaacg gatggtgcag tacacccgta acagttttta catcccacta atgactcgcc - 841 tgcgcccgat ggggatcact gtcgatgttg aaacagccaa ccgccacggt ctgcgctggc - 901 tgcacgatgt cgctaaccaa cgaaagcatg aaacaatcca ggcccgtccc tgcgatcgct - 961 ggctcgaaga gcagcagtcc atgctggcac tgcctccgga gaaaaaagag tatgacgtgc - 1021 atcttgatga aaatctggtg aacttcgaca aacaccccct gcatcatcca ctctccatct - 1081 acgactcatt ctgcagagga gtggcgtgat gatggaactg caacatcaac gactgatggc - 1141 gctcgccggg cagttgcaac tggaaagcct tataagcgca gcgcctgcgc tgtcacaaca - 1201 ggcagtagac caggaatgga gttatatgga cttcctggag catctgcttc atgaagaaaa - 1261 actggcacgt catcaacgta aacaggcgat gtatacccga atggcagcct tcccggcggt - 1321 gaaaacgttc gaagagtatg acttcacatt cgccaccgga gcaccgcaga agcaactcca - 1381 gtcgttacgc tcactcagct tcatagaacg taatgaaaat atcgtattac tggggccatc - 1441 aggtgtgggg aaaacccatc tggcaatagc gatgggctat gaagcagtcc gtgcaggtat - 1501 caaagttcgc ttcacaacag cagcagatct gttacttcag ttatctacgg cacaacgtca - 1561 gggccgttat aaaacgacgc ttcagcgtgg agtaatggcc ccccgcctgc tcatcattga - 1621 tgaaataggc tatctgccgt tcagtcagga agaagcaaag ctgttcttcc aggtcatcgc - 1681 taaacgttac gaaaagagcg caatgatcct gacatccaat ctgccgttcg ggcagtggga - 1741 tcaaacgttc gccggtgatg cagcactgac ctcagcgatg ctggaccgta tcttacacca - 1801 ctcacatgtc gttcaaatca aaggagaaag ctatcgactc agacagaaac gaaaggccgg - 1861 ggttatagca gaagctaatc ctgagtaaaa cggtggatca atattgggcc gttggtggag - 1921 atataagtgg atcacttttc atccgtcgtt gacaccctga tgaattcacg tgttcacgcc - 1981 tgaataacaa gaatgccgga gatacgcagt catatttttt acacaattct ctaatcccga - 2041 caaggtcgta ggtcgttata ggaaaattct tagcaccatt ccggaacaat cagaacagca - 2101 ggccatgaac gactgacaac attacgaata taaaaaacgc acccgggcca gacattcccc - 2161 ctactgatta aaccagccgg acttgtccac ggaacggtct ttttaaaccg acacacagtc - 2221 tgagtacaga tacatgtcac gatgatgcag gattagcgga agagtgtgag cacgtttccg - 2281 ggaactgtgg tgaaccatag ctcaatattc gagtgagggc ataccggaaa cgcgctcaga - 2341 ttcgttgtaa cgcgattttc cgtaccgggc aattttttca gttgtttttt cgtttcatgt - 2401 cgtcagaaac gttctgagcg cgtttccggc atctgatgct acgcaaacca tccccatggt - 2461 cagttgacag ccggaaacac gcgggtgtcg ttttagcgta tcgacgggac ggcgtcgaga - 2521 agcacaaaaa acagatgttg tactcagtca gttgttttac agacagcact gcggcagatt - 2581 gaaaaagtac cgtactttca ggaatgtcca gaaaccatgt gtcagacttc gttctccccc - 2641 ttccgggtga atttttttgt catccgttca ggaatctctt tataacgatt actccatttc - 2701 aggatttttt atgtggcgtt tactacaggc aggatattca aaggcaaaaa aatcccccgg - 2761 aacaggcgga acccggacag ggggagaacg aatcgctaaa taattttcgt agttgtattt - 2821 cccatcgttg ctactgcaac gggatgaatt tgccgcagtt tatcctgtaa aacaatcctg - 2881 atttactcac actccacata tcactgacgg agcacaacgg aatagtgaac aaacaacaac - 2941 aaactgcgct gaatatggcg cgatttatca gaagccagag cctgatactg cttgaaaaac - 3001 tggatgctct ggatgccgac gagcaggcgg ccatgtgtga acgactgcac gaactcgcgg - 3061 aagaactcca gaacagcatc caggctcgct ttgaagccga aagtgaaaca ggaacataac - 3121 gaagctcccg gagacggtca cagcttgtct gtgaacggat gccgggagca gacaagcccg - 3181 tcagggcgcg tcagcgggtt ttagcgggtg tcggggcgca gccatgaccc agtcacgtag - 3241 cgatagcgga gtgtatactg gcttagtcat gcggcatcag tgcggattgt atgaaaagtg - 3301 caccatgtac ggtgtgaaat gccgcacaga tgcgtaagga gaacatgcag atgccgatgc - 3361 tcttccgctt cctcgctcac tgactcgctg cgctcggtcg ttcggctgcg gcgagcggtg - 3421 tctgctcact caaaagcggt gatactgtta tccacacaat caggggataa cgccggaaag - 3481 aacatgtgag caaaaaacga agaccccaga aaaggccgcg ccggaggcgc tttttccata - 3541 ggctccgccc ccctgacgag catcacaaaa atcgacgctc aagtcagagg tggcgaaacc - 3601 cgacaggact taaagatacc aggcgtttcc ccccggaagc tccctcgtgc gctctcctgt - 3661 tccgaccctg ccgcttaccg gatacctctc cgcctttctc ccttcgggaa gcgtggcgct - 3721 ttctcatagc tcacgctgtt ggtatctcag ttcggtgtag gtcgttcgct ccaagctggg - 3781 ctgtgtgcac gaaccccccg ttcagcccga ccactgcgcc ttatccggta actatcgtct - 3841 tgagtccaac ccggtaagac acgactttac gccactggca gcagccattg gtaactgaaa - 3901 agtggattta gatacgcaga actcttgaag ttgaagcctt atcgcggcta cactgaaagg - 3961 acagcatttg gtatctgtgc tccacttaag ccagctacca caggttagaa agcctgagaa - 4021 acttctaacc ttcgaaagaa cccacgcctg agaacgtggg ttttttcgtt tacaggcagc - 4081 agattacgcg cagaaaaaaa ggatctcaag aagatccttt gatcttttct actgaattgc - 4141 gctcccgatc agttcagcag aagattatga tggggttcta tgggtattgc tgcggtaaca - 4201 cccatgttac ttgaggttgt atgtagtctg tgtagaatta tacacataag gcttaaactg - 4261 ctcttttttt tcaatatgca attggaagtt cattgactac ataaatagat tattccaaat - 4321 aatttattta tgtaagaaca ggatgggagg gggaatgatc tcaaagttat tttgcttggc - 4381 tctcatattt ttatcatcaa gtggccttgc agaaaaaaac acatatacag caaaagacat - 4441 cttgcaaaac ctagaattaa atacctttgg caattcattg tctcatggca tctatgggaa - 4501 acagacaacc ttcaagcaaa ccgagtttac aaatattaaa agcaacacca aaaaacacat - 4561 tgcacttatc aataaagaca actcatggat gatatcatta aaaatactag gaattaagag - 4621 agatgagtat actgtctgtt ttgaagattt ctctctaata agaccgccaa catatgtagc - 4681 catacatcct ctacttataa aaaaagtaaa atctggaaac tttatagtag tgaaagaaat - 4741 aaagaaatct atccctggtt gcactgtata ttatcattaa tagcaagccc ctcattatta - 4801 tgaggggctc atggttattt taacaatcca ctatcgatat ctttttgcac cagagcgccc - 4861 tctcgtttac gtctgtcaga cattccatca acaatattat taaaagcatt tacaaggcca - 4921 ttccagtctt ttgcgataac tttattccat actgtgggag cagttctgga taacttaaac - 4981 cctttttgat atccaataga caccagtgct gtacgggttc tcaacggtaa atcgctgaac - 5041 cgaagaccga tattagcgtc attgaaaaga ccttcaatct tatgtgagaa tttatcaata - 5101 taaatattag ataagagatg agcttcatta tcagaaagcg tcagaggtgc tgttctcact - 5161 ttatcataag cctccttccc tcgaagcata taatacccat caagtctatc tgcaatatac - 5221 tgagggacac cgtcattcaa taaatcctgt ttgcttcgct gaccaaggtc aaccccggaa - 5281 ccgaatgtaa caccggtact gttaaaataa tcgctactag gattagacgg aaaatgactt - 5341 gtcggattaa acccttcaaa accattactg gagaaaatat cgtggtcaac aatatttacc - 5401 gaacgacgta aaaattcctt cagttgacta atattgtcaa agttaatgac agtgttgtcc - 5461 gctaggacga tgcgatttcg gttattattc agaatgtctt cgttctcttt cttatcgaga - 5521 tgttcaatag attcggcaat cgttccctca agaaccatga cacggtagac tttcacaccg - 5581 tctttttcct gacctgtttc aacagttatt ttctgttcgt aagacacggt cccttcagtt - 5641 tttgaaattt tactttcctg gcggatctta tttgaatatt cactgtcttt ctccatctcc - 5701 gtatcaatcg gaaaccccat aatgtacatc agtttaaaat tactccggcc aggcagatcc - 5761 acataatgtg gtaatgcaat tgtaatcgaa ttagcttcaa aatttggtct gtaactgctt - 5821 aatgtacttc cggaaaagag aaaagccgga acaccacctg aaccattcac taccattgta - 5881 tctgacataa aaattcctct ttaacacata aaaaaaacaa taagttaaaa aaatactgta - 5941 cataaaagca ctgtttttat gtacagtaat aaaattacgc cgctttattt tctctgtcaa - 6001 taatatgaaa tttcattttt gtgatctgaa tcactcttat aaaaatcagg aagggaagat - 6061 tcgcagcaga aaaacagcac cgggtaacat cagaaaaaaa cagaaaggag ataacgtgag - 6121 caaaacaaaa tctggtcgcc accgactgag caaaacagac aaacgcctgc tggctgcact - 6181 tgtcgttgcc ggatacgaag aacggacagc ccgtgacctc atccagaaac acgtttacac - 6241 actgacacag gccgacctgc gccatctggt cagtgaaatc agtaacggtg tgggacagtc - 6301 acaggcctac gatgcgattt accaggcgag acgcattcgt ctcgcccgta aatacctgag - 6361 cggaaaaaaa ccggaagggg tggaaccccg ggaagggcag gaacgggaag atttaccata - 6421 actcccgtta tcagtaccat cggctcaacg ctcgttgtcg gatctgaaaa attcgctcaa - 6481 aagatcatat ttccctggat attttccacc gtttcttatg tgagaaaagt cacataattc - 6541 tgtcagacga cgagaaaacg gatatcgatt attgtttaat atttttacat tattaaaaat - 6601 gaaattagat aatcagatac aaataatatg ttttcgttca tgcagagaga ttaagggtgt - 6661 ctaatgaaga aaagttctat tgtggcaacc attataacta ttctgtccgg gagtgctaat - 6721 gcagcatcat ctcagttaat accaaatata tcccctgaca gctttacagt tgcagcctcc - 6781 accgggatgc tgagtggaaa gtctcatgaa atgctttatg acgcagaaac aggaagaaag - 6841 atcagccagt tagactggaa gatcaaaaat gtcgctatcc tgaaaggtga tatatcctgg - 6901 gatccatact catttctgac cctgaatgcc agggggtgga cgtctctggc ttccgggtca - 6961 ggtaatatgg atgactacga ctggatgaat gaaaatcaat ctgagtggac agatcactca - 7021 tctcatcctg ctacaaatgt taatcatgcc aatgaatatg acctcaatgt gaaaggctgg - 7081 ttactccagg atgagaatta taaagcaggt ataacagcag gatatcagga aacacgtttc - 7141 agttggacag ctacaggtgg ttcatatagt tataataatg gagcttatac cggaaacttc - 7201 ccgaaaggag tgcgggtaat aggttataac cagcgctttt ctatgccata tattggactt - 7261 gcaggccagt atcgcattaa tgattttgag ttaaatgcat tatttaaatt cagcgactgg - 7321 gttcgggcac atgataatga tgagcactat atgagagatc ttactttccg tgagaagaca - 7381 tccggctcac gttattatgg taccgtaatt aacgctggat attatgtcac acctaatgcc - 7441 aaagtctttg cggaatttac atacagtaaa tatgatgagg gcaaaggagg tactcagatc - 7501 attgataaga atagtggaga ttctgtctct attggcggag atgctgccgg tatttccaat - 7561 aaaaattata ctgtgacggc gggtctgcaa tatcgcttct gaaaaataca gatcatatct - 7621 ctcttttcat cctcccctag cggggaggat gtctgtggaa aggaggttgg tgtttgacca - 7681 accttcagat gtgtgaaaaa tcaccttttt caccataatg acggggcgct cattctgttg - 7741 ttttgccttg acattctcca cgtctttcag ggcatggaga aggtcaaatt agacatggaa - 7801 cgctactctc cttcctgtag gaagctcaac atccaagctt aatttgcctc ccattgcttc - 7861 aacgtaacgc tttaacgtcg ccagctttaa atcatttccg cgctgctcca gctttgttac - 7921 tgctggctgg cttataccca tcgcctcagc aacttgtttt tgtgataact ggagttcttc - 7981 acgcatcatc tgcaagccga cctcaagaat catctcatct gccatttctt taattcgtgt - 8041 ctggctttca ggtgaacgac tggcaatcac ctcatctaat gttctcatta cttgctctcc - 8101 agtgtgttca gatgtgctgt aaattcatcc tcagctatac gcaccagttt ttcataaaac - 8161 cgcttatcat tacttttatc tcctgcacaa agaacgatag cccgacgaat cggatcgaac - 8221 gcataaaagg ctcttatcgg acggccagaa aactgaacgc gaagctcttt catatttttg - 8281 taccgagaac ctttcacggt atcggcatat ggcctgggta actcaggtcc gtaaacctgt - 8341 agctttttca aatcagccaa aaccttttcc tgaagagcgt cttcttgctc atttagccag - 8401 tcgtcaaatc gctggctaaa aagtaccatc cacatgctca accctataac ctgtagctta - 8461 ccccactaac aatataacct acgagttata ttttcaagaa aagctggcta tttaacataa - 8521 cggcaatttg tacgcaccac tgaaatgcgt tcagcgcgat cacggcaaca gacaggcaaa - 8581 aatagcaaca aacctcccga aaaaccgccg cgatcgcgcc tgataaattt taaccttatg - 8641 catatctatg cagccaggcg aatcacgaac gaattgcctg cctgatgtaa ctgaaacggg - 8701 tgttttttcc tgatttggtg ggcgtggaag acggaacatg aacgggaaaa cagaattcat - 8761 gccagatgag cgcgatctgg caattaaggc aaaacacagc aacaaagaca cgccagaatc - 8821 gcgcccggat atgttttaac gcgattttca gactcagaca aattcagcag aatgctactc - 8881 cattcaccgg gctgatggtg aatacatgcg tatccaggat gagtacattt ctggctctgc - 8941 cacagctctg tctgttggca gctttcgcct gtccggaaac ctgcttaaaa cgctcccgaa - 9001 aggcctctga accagaaagc aacaaaacac aggccattaa gtaaatcgcg ttaaaacacg - 9061 tctgatggat tgctgcaaaa aaaagtccct aatggagcag ggactgttaa acccagtgaa - 9121 tagcgtctaa attaaagtaa gaatacgacc aggtactctt cagaaaagag attaatccac - 9181 cgcacagaat aatcaacagt aaaaacaaac aaccctgatt ttttattttt ctttttttcg - 9241 ataaaaacaa aattaaagaa ataattaatc agaacattcc ttaacttcag ggcattgcct - 9301 gtgttccatt ttgtgattag tctgaaactt ccgaaggtgg ataacacccg gtattttttt - 9361 gctcacataa agcccctcct tcaggcagag gggctttttc tttgccacca cataaaaaag - 9421 gccctcacag gaggtgttct gtgagggcgt atgataagga ctgaatcgat ggttaatatg - 9481 tctagtcctg acttttgcat ctccgaatat aaaaccctgt ttaacggcat gcaaaaccaa - 9541 aaaataaaaa tgtgacatcg caatgccaga taatattgac gcatgaggga atgcgtaccc - 9601 cgacccctg -// diff --git a/file_keep/chart/file/3200140572021372 b/file_keep/chart/file/3200140572021372 deleted file mode 100644 index 57ee9fc..0000000 --- a/file_keep/chart/file/3200140572021372 +++ /dev/null @@ -1,529 +0,0 @@ -LOCUS NC_005816 9609 bp DNA circular BCT 21-JUL-2008 -DEFINITION Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete - sequence. -ACCESSION NC_005816 -VERSION NC_005816.1 GI:45478711 -DBLINK Project: 58037 -KEYWORDS . -SOURCE Yersinia pestis biovar Microtus str. 91001 - ORGANISM Yersinia pestis biovar Microtus str. 91001 - Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; - Enterobacteriaceae; Yersinia. -REFERENCE 1 (bases 1 to 9609) - AUTHORS Zhou,D., Tong,Z., Song,Y., Han,Y., Pei,D., Pang,X., Zhai,J., Li,M., - Cui,B., Qi,Z., Jin,L., Dai,R., Du,Z., Wang,J., Guo,Z., Wang,J., - Huang,P. and Yang,R. - TITLE Genetics of metabolic variations between Yersinia pestis biovars - and the proposal of a new biovar, microtus - JOURNAL J. Bacteriol. 186 (15), 5147-5152 (2004) - PUBMED 15262951 -REFERENCE 2 (bases 1 to 9609) - AUTHORS Song,Y., Tong,Z., Wang,J., Wang,L., Guo,Z., Han,Y., Zhang,J., - Pei,D., Zhou,D., Qin,H., Pang,X., Han,Y., Zhai,J., Li,M., Cui,B., - Qi,Z., Jin,L., Dai,R., Chen,F., Li,S., Ye,C., Du,Z., Lin,W., - Wang,J., Yu,J., Yang,H., Wang,J., Huang,P. and Yang,R. - TITLE Complete genome sequence of Yersinia pestis strain 91001, an - isolate avirulent to humans - JOURNAL DNA Res. 11 (3), 179-197 (2004) - PUBMED 15368893 -REFERENCE 3 (bases 1 to 9609) - CONSRTM NCBI Genome Project - TITLE Direct Submission - JOURNAL Submitted (16-MAR-2004) National Center for Biotechnology - Information, NIH, Bethesda, MD 20894, USA -REFERENCE 4 (bases 1 to 9609) - AUTHORS Song,Y., Tong,Z., Wang,L., Han,Y., Zhang,J., Pei,D., Wang,J., - Zhou,D., Han,Y., Pang,X., Zhai,J., Chen,F., Qin,H., Wang,J., Li,S., - Guo,Z., Ye,C., Du,Z., Lin,W., Wang,J., Yu,J., Yang,H., Wang,J., - Huang,P. and Yang,R. - TITLE Direct Submission - JOURNAL Submitted (24-APR-2003) The Institute of Microbiology and - Epidemiology, Academy of Military Medical Sciences, No. 20, - Dongdajie Street, Fengtai District, Beijing 100071, People's - Republic of China -COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final - NCBI review. The reference sequence was derived from AE017046. - COMPLETENESS: full length. -FEATURES Location/Qualifiers - source 1..9609 - /organism="Yersinia pestis biovar Microtus str. 91001" - /mol_type="genomic DNA" - /strain="91001" - /db_xref="taxon:229193" - /plasmid="pPCP1" - /biovar="Microtus" - repeat_region 1..1954 - gene 87..1109 - /locus_tag="YP_pPCP01" - /db_xref="GeneID:2767718" - CDS 87..1109 - /locus_tag="YP_pPCP01" - /note="similar to corresponding CDS from previously - sequenced pPCP plasmid of Yersinia pestis KIM (AF053945) - and CO92 (AL109969), also many transposase entries for - insertion sequence IS100 of Yersinia pestis. Contains - IS21-like element transposase, HTH domain - (Interpro|IPR007101)" - /codon_start=1 - /transl_table=11 - /product="putative transposase" - /protein_id="NP_995567.1" - /db_xref="GI:45478712" - /db_xref="GeneID:2767718" - /translation="MVTFETVMEIKILHKQGMSSRAIARELGISRNTVKRYLQAKSEP - PKYTPRPAVASLLDEYRDYIRQRIADAHPYKIPATVIAREIRDQGYRGGMTILRAFIR - SLSVPQEQEPAVRFETEPGRQMQVDWGTMRNGRSPLHVFVAVLGYSRMLYIEFTDNMR - YDTLETCHRNAFRFFGGVPREVLYDNMKTVVLQRDAYQTGQHRFHPSLWQFGKEMGFS - PRLCRPFRAQTKGKVERMVQYTRNSFYIPLMTRLRPMGITVDVETANRHGLRWLHDVA - NQRKHETIQARPCDRWLEEQQSMLALPPEKKEYDVHLDENLVNFDKHPLHHPLSIYDS - FCRGVA" - misc_feature 87..959 - /locus_tag="YP_pPCP01" - /note="Transposase and inactivated derivatives [DNA - replication, recombination, and repair]; Region: COG4584" - /db_xref="CDD:34222" - misc_feature <111..209 - /locus_tag="YP_pPCP01" - /note="Helix-turn-helix domain of Hin and related - proteins, a family of DNA-binding domains unique to - bacteria and represented by the Hin protein of Salmonella. - The basic HTH domain is a simple fold comprised of three - core helices that form a right-handed...; Region: - HTH_Hin_like; cl01116" - /db_xref="CDD:186341" - misc_feature 438..812 - /locus_tag="YP_pPCP01" - /note="Integrase core domain; Region: rve; cl01316" - /db_xref="CDD:194099" - gene 1106..1888 - /locus_tag="YP_pPCP02" - /db_xref="GeneID:2767716" - CDS 1106..1888 - /locus_tag="YP_pPCP02" - /note="similar to corresponding CDS form previously - sequenced pPCP plasmid of Yersinia pestis KIM (AF053945) - and CO92 (AL109969), also many ATP-binding protein entries - for insertion sequence IS100 of Yersinia pestis. Contains - Chaperonin clpA/B (Interpro|IPR001270). Contains - ATP/GTP-binding site motif A (P-loop) (Interpro|IPR001687, - Molecular Function: ATP binding (GO:0005524)). Contains - Bacterial chromosomal replication initiator protein, DnaA - (Interpro|IPR001957, Molecular Function: DNA binding - (GO:0003677), Molecular Function: DNA replication origin - binding (GO:0003688), Molecular Function: ATP binding - (GO:0005524), Biological Process: DNA replication - initiation (GO:0006270), Biological Process: regulation of - DNA replication (GO:0006275)). Contains AAA ATPase - (Interpro|IPR003593, Molecular Function: nucleotide - binding (GO:0000166))" - /codon_start=1 - /transl_table=11 - /product="transposase/IS protein" - /protein_id="NP_995568.1" - /db_xref="GI:45478713" - /db_xref="GeneID:2767716" - /translation="MMMELQHQRLMALAGQLQLESLISAAPALSQQAVDQEWSYMDFL - EHLLHEEKLARHQRKQAMYTRMAAFPAVKTFEEYDFTFATGAPQKQLQSLRSLSFIER - NENIVLLGPSGVGKTHLAIAMGYEAVRAGIKVRFTTAADLLLQLSTAQRQGRYKTTLQ - RGVMAPRLLIIDEIGYLPFSQEEAKLFFQVIAKRYEKSAMILTSNLPFGQWDQTFAGD - AALTSAMLDRILHHSHVVQIKGESYRLRQKRKAGVIAEANPE" - misc_feature 1109..1885 - /locus_tag="YP_pPCP02" - /note="transposase/IS protein; Provisional; Region: - PRK09183" - /db_xref="CDD:181681" - misc_feature 1367..>1669 - /locus_tag="YP_pPCP02" - /note="The AAA+ (ATPases Associated with a wide variety of - cellular Activities) superfamily represents an ancient - group of ATPases belonging to the ASCE (for additional - strand, catalytic E) division of the P-loop NTPase fold. - The ASCE division also includes...; Region: AAA; cd00009" - /db_xref="CDD:99707" - misc_feature 1433..1456 - /locus_tag="YP_pPCP02" - /note="Walker A motif; other site" - /db_xref="CDD:99707" - misc_feature order(1436..1459,1619..1621) - /locus_tag="YP_pPCP02" - /note="ATP binding site [chemical binding]; other site" - /db_xref="CDD:99707" - misc_feature 1607..1624 - /locus_tag="YP_pPCP02" - /note="Walker B motif; other site" - /db_xref="CDD:99707" - gene 2925..3119 - /gene="rop" - /locus_tag="YP_pPCP03" - /gene_synonym="rom" - /db_xref="GeneID:2767717" - CDS 2925..3119 - /gene="rop" - /locus_tag="YP_pPCP03" - /gene_synonym="rom" - /note="Best Blastp hit =gi|16082682|ref|NP_395229.1| - (NC_003132) putative replication regulatory protein - [Yersinia pestis], gi|5763813|emb|CAB531 66.1| (AL109969) - putative replication regulatory protein [Yersinia pestis]; - similar to gb|AAK91579.1| (AY048853), RNAI modulator - protein Rom [Salmonella choleraesuis], Contains Regulatory - protein Rop (Interpro|IPR000769)" - /codon_start=1 - /transl_table=11 - /product="putative replication regulatory protein" - /protein_id="NP_995569.1" - /db_xref="GI:45478714" - /db_xref="GeneID:2767717" - /translation="MNKQQQTALNMARFIRSQSLILLEKLDALDADEQAAMCERLHEL - AEELQNSIQARFEAESETGT" - misc_feature 2925..3107 - /gene="rop" - /locus_tag="YP_pPCP03" - /gene_synonym="rom" - /note="Rop protein; Region: Rop; pfam01815" - /db_xref="CDD:145136" - gene 3486..3857 - /locus_tag="YP_pPCP04" - /db_xref="GeneID:2767720" - CDS 3486..3857 - /locus_tag="YP_pPCP04" - /note="Best Blastp hit = gi|321919|pir||JQ1541 - hypothetical 16.9K protein - Salmonella typhi murium - plasmid NTP16." - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /protein_id="NP_995570.1" - /db_xref="GI:45478715" - /db_xref="GeneID:2767720" - /translation="MSKKRRPQKRPRRRRFFHRLRPPDEHHKNRRSSQRWRNPTGLKD - TRRFPPEAPSCALLFRPCRLPDTSPPFSLREAWRFLIAHAVGISVRCRSFAPSWAVCT - NPPFSPTTAPYPVTIVLSPTR" - misc_feature 3498..3626 - /locus_tag="YP_pPCP04" - /note="ProfileScan match to entry PS50323 ARG_RICH, - E-value 8.981" - gene 4343..4780 - /gene="pim" - /locus_tag="YP_pPCP05" - /db_xref="GeneID:2767712" - CDS 4343..4780 - /gene="pim" - /locus_tag="YP_pPCP05" - /note="similar to many previously sequenced pesticin - immunity protein entries of Yersinia pestis plasmid pPCP, - e.g. gi| 16082683|,ref|NP_395230.1| (NC_003132) , - gi|1200166|emb|CAA90861.1| (Z54145 ) , gi|1488655| - emb|CAA63439.1| (X92856) , gi|2996219|gb|AAC62543.1| - (AF053945) , and gi|5763814|emb|CAB531 67.1| (AL109969)" - /codon_start=1 - /transl_table=11 - /product="pesticin immunity protein" - /protein_id="NP_995571.1" - /db_xref="GI:45478716" - /db_xref="GeneID:2767712" - /translation="MGGGMISKLFCLALIFLSSSGLAEKNTYTAKDILQNLELNTFGN - SLSHGIYGKQTTFKQTEFTNIKSNTKKHIALINKDNSWMISLKILGIKRDEYTVCFED - FSLIRPPTYVAIHPLLIKKVKSGNFIVVKEIKKSIPGCTVYYH" - gene complement(4815..5888) - /gene="pst" - /locus_tag="YP_pPCP06" - /db_xref="GeneID:2767721" - CDS complement(4815..5888) - /gene="pst" - /locus_tag="YP_pPCP06" - /note="Best Blastp hit =|16082684|ref|NP_395231.1| - (NC_003132) pesticin [Yersinia pestis], - gi|984824|gb|AAA75369.1| (U31974) pesticin [Yersinia - pestis], gi|1488654|emb|CAA63438.1| (X92856) pesticin - [Yersinia pestis], gi|2996220|gb|AAC62544.1| (AF053945) - pesticin [Yersinia pestis], gi|5763815|emb|CAB53168.1| - (AL1099 69) pesticin [Yersinia pestis]" - /codon_start=1 - /transl_table=11 - /product="pesticin" - /protein_id="NP_995572.1" - /db_xref="GI:45478717" - /db_xref="GeneID:2767721" - /translation="MSDTMVVNGSGGVPAFLFSGSTLSSYRPNFEANSITIALPHYVD - LPGRSNFKLMYIMGFPIDTEMEKDSEYSNKIRQESKISKTEGTVSYEQKITVETGQEK - DGVKVYRVMVLEGTIAESIEHLDKKENEDILNNNRNRIVLADNTVINFDNISQLKEFL - RRSVNIVDHDIFSSNGFEGFNPTSHFPSNPSSDYFNSTGVTFGSGVDLGQRSKQDLLN - DGVPQYIADRLDGYYMLRGKEAYDKVRTAPLTLSDNEAHLLSNIYIDKFSHKIEGLFN - DANIGLRFSDLPLRTRTALVSIGYQKGFKLSRTAPTVWNKVIAKDWNGLVNAFNNIVD - GMSDRRKREGALVQKDIDSGLLK" - variation 5910..5911 - /note="compared to AF053945" - /replace="" - variation 5933^5934 - /note="compared to AL109969" - /replace="a" - variation 5933^5934 - /note="compared to AF053945" - /replace="aa" - variation 5948 - /note="compared to AL109969" - /replace="c" - gene 6005..6421 - /locus_tag="YP_pPCP07" - /db_xref="GeneID:2767719" - CDS 6005..6421 - /locus_tag="YP_pPCP07" - /note="Best Blastp hit = gi|16082685|ref|NP_395232.1| - (NC_003132) hypothetical protein [Yersinia pestis], - gi|5763816|emb|CAB53169.1| (AL109969) hypothetical protein - [Yersinia pestis]" - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /protein_id="NP_995573.1" - /db_xref="GI:45478718" - /db_xref="GeneID:2767719" - /translation="MKFHFCDLNHSYKNQEGKIRSRKTAPGNIRKKQKGDNVSKTKSG - RHRLSKTDKRLLAALVVAGYEERTARDLIQKHVYTLTQADLRHLVSEISNGVGQSQAY - DAIYQARRIRLARKYLSGKKPEGVEPREGQEREDLP" - variation 6525 - /note="compared to AF053945 and AL109969" - /replace="c" - gene 6664..7602 - /gene="pla" - /locus_tag="YP_pPCP08" - /db_xref="GeneID:2767715" - CDS 6664..7602 - /gene="pla" - /locus_tag="YP_pPCP08" - /EC_number="3.4.23.48" - /note="outer membrane protease; involved in virulence in - many organisms; OmpT; IcsP; SopA; Pla; PgtE; omptin; in - Escherichia coli OmpT can degrade antimicrobial peptides; - in Yersinia Pla activates plasminogen during infection; in - Shigella flexneria SopA cleaves the autotransporter IcsA" - /codon_start=1 - /transl_table=11 - /product="outer membrane protease" - /protein_id="NP_995574.1" - /db_xref="GI:45478719" - /db_xref="GeneID:2767715" - /translation="MKKSSIVATIITILSGSANAASSQLIPNISPDSFTVAASTGMLS - GKSHEMLYDAETGRKISQLDWKIKNVAILKGDISWDPYSFLTLNARGWTSLASGSGNM - DDYDWMNENQSEWTDHSSHPATNVNHANEYDLNVKGWLLQDENYKAGITAGYQETRFS - WTATGGSYSYNNGAYTGNFPKGVRVIGYNQRFSMPYIGLAGQYRINDFELNALFKFSD - WVRAHDNDEHYMRDLTFREKTSGSRYYGTVINAGYYVTPNAKVFAEFTYSKYDEGKGG - TQIIDKNSGDSVSIGGDAAGISNKNYTVTAGLQYRF" - misc_feature 6664..7599 - /gene="pla" - /locus_tag="YP_pPCP08" - /note="Omptin family; Region: Omptin; cl01886" - /db_xref="CDD:186487" - gene complement(7789..8088) - /locus_tag="YP_pPCP09" - /db_xref="GeneID:2767713" - CDS complement(7789..8088) - /locus_tag="YP_pPCP09" - /note="Best Blastp hit = gi|16082687|ref|NP_395234.1| - (NC_003132) putative transcriptional regulator [Yersinia - pestis], gi|5763818|emb|CAB53171.1| (AL109969) putative - transcriptional regulator [Yersinia pestis]." - /codon_start=1 - /transl_table=11 - /product="putative transcriptional regulator" - /protein_id="NP_995575.1" - /db_xref="GI:45478720" - /db_xref="GeneID:2767713" - /translation="MRTLDEVIASRSPESQTRIKEMADEMILEVGLQMMREELQLSQK - QVAEAMGISQPAVTKLEQRGNDLKLATLKRYVEAMGGKLSLDVELPTGRRVAFHV" - misc_feature complement(7837..7995) - /locus_tag="YP_pPCP09" - /note="Helix-turn-helix XRE-family like proteins. - Prokaryotic DNA binding proteins belonging to the - xenobiotic response element family of transcriptional - regulators; Region: HTH_XRE; cl09100" - /db_xref="CDD:195788" - gene complement(8088..8360) - /locus_tag="YP_pPCP10" - /db_xref="GeneID:2767714" - CDS complement(8088..8360) - /locus_tag="YP_pPCP10" - /note="Best Blastp hit = gi|16082688|ref|NP_395235.1| - (NC_003132) hypothetical protein [ Yersinia pestis], - gi|5763819|emb|CAB53172.1| (AL109969) hypothetical protein - [Yersinia pestis]" - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /protein_id="NP_995576.1" - /db_xref="GI:45478721" - /db_xref="GeneID:2767714" - /translation="MADLKKLQVYGPELPRPYADTVKGSRYKNMKELRVQFSGRPIRA - FYAFDPIRRAIVLCAGDKSNDKRFYEKLVRIAEDEFTAHLNTLESK" - misc_feature complement(8091..>8357) - /locus_tag="YP_pPCP10" - /note="Phage derived protein Gp49-like (DUF891); Region: - Gp49; cl01470" - /db_xref="CDD:194142" - variation 8529^8530 - /note="compared to AL109969" - /replace="tt" -ORIGIN - 1 tgtaacgaac ggtgcaatag tgatccacac ccaacgcctg aaatcagatc cagggggtaa - 61 tctgctctcc tgattcagga gagtttatgg tcacttttga gacagttatg gaaattaaaa - 121 tcctgcacaa gcagggaatg agtagccggg cgattgccag agaactgggg atctcccgca - 181 ataccgttaa acgttatttg caggcaaaat ctgagccgcc aaaatatacg ccgcgacctg - 241 ctgttgcttc actcctggat gaataccggg attatattcg tcaacgcatc gccgatgctc - 301 atccttacaa aatcccggca acggtaatcg ctcgcgagat cagagaccag ggatatcgtg - 361 gcggaatgac cattctcagg gcattcattc gttctctctc ggttcctcag gagcaggagc - 421 ctgccgttcg gttcgaaact gaacccggac gacagatgca ggttgactgg ggcactatgc - 481 gtaatggtcg ctcaccgctt cacgtgttcg ttgctgttct cggatacagc cgaatgctgt - 541 acatcgaatt cactgacaat atgcgttatg acacgctgga gacctgccat cgtaatgcgt - 601 tccgcttctt tggtggtgtg ccgcgcgaag tgttgtatga caatatgaaa actgtggttc - 661 tgcaacgtga cgcatatcag accggtcagc accggttcca tccttcgctg tggcagttcg - 721 gcaaggagat gggcttctct ccccgactgt gtcgcccctt cagggcacag actaaaggta - 781 aggtggaacg gatggtgcag tacacccgta acagttttta catcccacta atgactcgcc - 841 tgcgcccgat ggggatcact gtcgatgttg aaacagccaa ccgccacggt ctgcgctggc - 901 tgcacgatgt cgctaaccaa cgaaagcatg aaacaatcca ggcccgtccc tgcgatcgct - 961 ggctcgaaga gcagcagtcc atgctggcac tgcctccgga gaaaaaagag tatgacgtgc - 1021 atcttgatga aaatctggtg aacttcgaca aacaccccct gcatcatcca ctctccatct - 1081 acgactcatt ctgcagagga gtggcgtgat gatggaactg caacatcaac gactgatggc - 1141 gctcgccggg cagttgcaac tggaaagcct tataagcgca gcgcctgcgc tgtcacaaca - 1201 ggcagtagac caggaatgga gttatatgga cttcctggag catctgcttc atgaagaaaa - 1261 actggcacgt catcaacgta aacaggcgat gtatacccga atggcagcct tcccggcggt - 1321 gaaaacgttc gaagagtatg acttcacatt cgccaccgga gcaccgcaga agcaactcca - 1381 gtcgttacgc tcactcagct tcatagaacg taatgaaaat atcgtattac tggggccatc - 1441 aggtgtgggg aaaacccatc tggcaatagc gatgggctat gaagcagtcc gtgcaggtat - 1501 caaagttcgc ttcacaacag cagcagatct gttacttcag ttatctacgg cacaacgtca - 1561 gggccgttat aaaacgacgc ttcagcgtgg agtaatggcc ccccgcctgc tcatcattga - 1621 tgaaataggc tatctgccgt tcagtcagga agaagcaaag ctgttcttcc aggtcatcgc - 1681 taaacgttac gaaaagagcg caatgatcct gacatccaat ctgccgttcg ggcagtggga - 1741 tcaaacgttc gccggtgatg cagcactgac ctcagcgatg ctggaccgta tcttacacca - 1801 ctcacatgtc gttcaaatca aaggagaaag ctatcgactc agacagaaac gaaaggccgg - 1861 ggttatagca gaagctaatc ctgagtaaaa cggtggatca atattgggcc gttggtggag - 1921 atataagtgg atcacttttc atccgtcgtt gacaccctga tgaattcacg tgttcacgcc - 1981 tgaataacaa gaatgccgga gatacgcagt catatttttt acacaattct ctaatcccga - 2041 caaggtcgta ggtcgttata ggaaaattct tagcaccatt ccggaacaat cagaacagca - 2101 ggccatgaac gactgacaac attacgaata taaaaaacgc acccgggcca gacattcccc - 2161 ctactgatta aaccagccgg acttgtccac ggaacggtct ttttaaaccg acacacagtc - 2221 tgagtacaga tacatgtcac gatgatgcag gattagcgga agagtgtgag cacgtttccg - 2281 ggaactgtgg tgaaccatag ctcaatattc gagtgagggc ataccggaaa cgcgctcaga - 2341 ttcgttgtaa cgcgattttc cgtaccgggc aattttttca gttgtttttt cgtttcatgt - 2401 cgtcagaaac gttctgagcg cgtttccggc atctgatgct acgcaaacca tccccatggt - 2461 cagttgacag ccggaaacac gcgggtgtcg ttttagcgta tcgacgggac ggcgtcgaga - 2521 agcacaaaaa acagatgttg tactcagtca gttgttttac agacagcact gcggcagatt - 2581 gaaaaagtac cgtactttca ggaatgtcca gaaaccatgt gtcagacttc gttctccccc - 2641 ttccgggtga atttttttgt catccgttca ggaatctctt tataacgatt actccatttc - 2701 aggatttttt atgtggcgtt tactacaggc aggatattca aaggcaaaaa aatcccccgg - 2761 aacaggcgga acccggacag ggggagaacg aatcgctaaa taattttcgt agttgtattt - 2821 cccatcgttg ctactgcaac gggatgaatt tgccgcagtt tatcctgtaa aacaatcctg - 2881 atttactcac actccacata tcactgacgg agcacaacgg aatagtgaac aaacaacaac - 2941 aaactgcgct gaatatggcg cgatttatca gaagccagag cctgatactg cttgaaaaac - 3001 tggatgctct ggatgccgac gagcaggcgg ccatgtgtga acgactgcac gaactcgcgg - 3061 aagaactcca gaacagcatc caggctcgct ttgaagccga aagtgaaaca ggaacataac - 3121 gaagctcccg gagacggtca cagcttgtct gtgaacggat gccgggagca gacaagcccg - 3181 tcagggcgcg tcagcgggtt ttagcgggtg tcggggcgca gccatgaccc agtcacgtag - 3241 cgatagcgga gtgtatactg gcttagtcat gcggcatcag tgcggattgt atgaaaagtg - 3301 caccatgtac ggtgtgaaat gccgcacaga tgcgtaagga gaacatgcag atgccgatgc - 3361 tcttccgctt cctcgctcac tgactcgctg cgctcggtcg ttcggctgcg gcgagcggtg - 3421 tctgctcact caaaagcggt gatactgtta tccacacaat caggggataa cgccggaaag - 3481 aacatgtgag caaaaaacga agaccccaga aaaggccgcg ccggaggcgc tttttccata - 3541 ggctccgccc ccctgacgag catcacaaaa atcgacgctc aagtcagagg tggcgaaacc - 3601 cgacaggact taaagatacc aggcgtttcc ccccggaagc tccctcgtgc gctctcctgt - 3661 tccgaccctg ccgcttaccg gatacctctc cgcctttctc ccttcgggaa gcgtggcgct - 3721 ttctcatagc tcacgctgtt ggtatctcag ttcggtgtag gtcgttcgct ccaagctggg - 3781 ctgtgtgcac gaaccccccg ttcagcccga ccactgcgcc ttatccggta actatcgtct - 3841 tgagtccaac ccggtaagac acgactttac gccactggca gcagccattg gtaactgaaa - 3901 agtggattta gatacgcaga actcttgaag ttgaagcctt atcgcggcta cactgaaagg - 3961 acagcatttg gtatctgtgc tccacttaag ccagctacca caggttagaa agcctgagaa - 4021 acttctaacc ttcgaaagaa cccacgcctg agaacgtggg ttttttcgtt tacaggcagc - 4081 agattacgcg cagaaaaaaa ggatctcaag aagatccttt gatcttttct actgaattgc - 4141 gctcccgatc agttcagcag aagattatga tggggttcta tgggtattgc tgcggtaaca - 4201 cccatgttac ttgaggttgt atgtagtctg tgtagaatta tacacataag gcttaaactg - 4261 ctcttttttt tcaatatgca attggaagtt cattgactac ataaatagat tattccaaat - 4321 aatttattta tgtaagaaca ggatgggagg gggaatgatc tcaaagttat tttgcttggc - 4381 tctcatattt ttatcatcaa gtggccttgc agaaaaaaac acatatacag caaaagacat - 4441 cttgcaaaac ctagaattaa atacctttgg caattcattg tctcatggca tctatgggaa - 4501 acagacaacc ttcaagcaaa ccgagtttac aaatattaaa agcaacacca aaaaacacat - 4561 tgcacttatc aataaagaca actcatggat gatatcatta aaaatactag gaattaagag - 4621 agatgagtat actgtctgtt ttgaagattt ctctctaata agaccgccaa catatgtagc - 4681 catacatcct ctacttataa aaaaagtaaa atctggaaac tttatagtag tgaaagaaat - 4741 aaagaaatct atccctggtt gcactgtata ttatcattaa tagcaagccc ctcattatta - 4801 tgaggggctc atggttattt taacaatcca ctatcgatat ctttttgcac cagagcgccc - 4861 tctcgtttac gtctgtcaga cattccatca acaatattat taaaagcatt tacaaggcca - 4921 ttccagtctt ttgcgataac tttattccat actgtgggag cagttctgga taacttaaac - 4981 cctttttgat atccaataga caccagtgct gtacgggttc tcaacggtaa atcgctgaac - 5041 cgaagaccga tattagcgtc attgaaaaga ccttcaatct tatgtgagaa tttatcaata - 5101 taaatattag ataagagatg agcttcatta tcagaaagcg tcagaggtgc tgttctcact - 5161 ttatcataag cctccttccc tcgaagcata taatacccat caagtctatc tgcaatatac - 5221 tgagggacac cgtcattcaa taaatcctgt ttgcttcgct gaccaaggtc aaccccggaa - 5281 ccgaatgtaa caccggtact gttaaaataa tcgctactag gattagacgg aaaatgactt - 5341 gtcggattaa acccttcaaa accattactg gagaaaatat cgtggtcaac aatatttacc - 5401 gaacgacgta aaaattcctt cagttgacta atattgtcaa agttaatgac agtgttgtcc - 5461 gctaggacga tgcgatttcg gttattattc agaatgtctt cgttctcttt cttatcgaga - 5521 tgttcaatag attcggcaat cgttccctca agaaccatga cacggtagac tttcacaccg - 5581 tctttttcct gacctgtttc aacagttatt ttctgttcgt aagacacggt cccttcagtt - 5641 tttgaaattt tactttcctg gcggatctta tttgaatatt cactgtcttt ctccatctcc - 5701 gtatcaatcg gaaaccccat aatgtacatc agtttaaaat tactccggcc aggcagatcc - 5761 acataatgtg gtaatgcaat tgtaatcgaa ttagcttcaa aatttggtct gtaactgctt - 5821 aatgtacttc cggaaaagag aaaagccgga acaccacctg aaccattcac taccattgta - 5881 tctgacataa aaattcctct ttaacacata aaaaaaacaa taagttaaaa aaatactgta - 5941 cataaaagca ctgtttttat gtacagtaat aaaattacgc cgctttattt tctctgtcaa - 6001 taatatgaaa tttcattttt gtgatctgaa tcactcttat aaaaatcagg aagggaagat - 6061 tcgcagcaga aaaacagcac cgggtaacat cagaaaaaaa cagaaaggag ataacgtgag - 6121 caaaacaaaa tctggtcgcc accgactgag caaaacagac aaacgcctgc tggctgcact - 6181 tgtcgttgcc ggatacgaag aacggacagc ccgtgacctc atccagaaac acgtttacac - 6241 actgacacag gccgacctgc gccatctggt cagtgaaatc agtaacggtg tgggacagtc - 6301 acaggcctac gatgcgattt accaggcgag acgcattcgt ctcgcccgta aatacctgag - 6361 cggaaaaaaa ccggaagggg tggaaccccg ggaagggcag gaacgggaag atttaccata - 6421 actcccgtta tcagtaccat cggctcaacg ctcgttgtcg gatctgaaaa attcgctcaa - 6481 aagatcatat ttccctggat attttccacc gtttcttatg tgagaaaagt cacataattc - 6541 tgtcagacga cgagaaaacg gatatcgatt attgtttaat atttttacat tattaaaaat - 6601 gaaattagat aatcagatac aaataatatg ttttcgttca tgcagagaga ttaagggtgt - 6661 ctaatgaaga aaagttctat tgtggcaacc attataacta ttctgtccgg gagtgctaat - 6721 gcagcatcat ctcagttaat accaaatata tcccctgaca gctttacagt tgcagcctcc - 6781 accgggatgc tgagtggaaa gtctcatgaa atgctttatg acgcagaaac aggaagaaag - 6841 atcagccagt tagactggaa gatcaaaaat gtcgctatcc tgaaaggtga tatatcctgg - 6901 gatccatact catttctgac cctgaatgcc agggggtgga cgtctctggc ttccgggtca - 6961 ggtaatatgg atgactacga ctggatgaat gaaaatcaat ctgagtggac agatcactca - 7021 tctcatcctg ctacaaatgt taatcatgcc aatgaatatg acctcaatgt gaaaggctgg - 7081 ttactccagg atgagaatta taaagcaggt ataacagcag gatatcagga aacacgtttc - 7141 agttggacag ctacaggtgg ttcatatagt tataataatg gagcttatac cggaaacttc - 7201 ccgaaaggag tgcgggtaat aggttataac cagcgctttt ctatgccata tattggactt - 7261 gcaggccagt atcgcattaa tgattttgag ttaaatgcat tatttaaatt cagcgactgg - 7321 gttcgggcac atgataatga tgagcactat atgagagatc ttactttccg tgagaagaca - 7381 tccggctcac gttattatgg taccgtaatt aacgctggat attatgtcac acctaatgcc - 7441 aaagtctttg cggaatttac atacagtaaa tatgatgagg gcaaaggagg tactcagatc - 7501 attgataaga atagtggaga ttctgtctct attggcggag atgctgccgg tatttccaat - 7561 aaaaattata ctgtgacggc gggtctgcaa tatcgcttct gaaaaataca gatcatatct - 7621 ctcttttcat cctcccctag cggggaggat gtctgtggaa aggaggttgg tgtttgacca - 7681 accttcagat gtgtgaaaaa tcaccttttt caccataatg acggggcgct cattctgttg - 7741 ttttgccttg acattctcca cgtctttcag ggcatggaga aggtcaaatt agacatggaa - 7801 cgctactctc cttcctgtag gaagctcaac atccaagctt aatttgcctc ccattgcttc - 7861 aacgtaacgc tttaacgtcg ccagctttaa atcatttccg cgctgctcca gctttgttac - 7921 tgctggctgg cttataccca tcgcctcagc aacttgtttt tgtgataact ggagttcttc - 7981 acgcatcatc tgcaagccga cctcaagaat catctcatct gccatttctt taattcgtgt - 8041 ctggctttca ggtgaacgac tggcaatcac ctcatctaat gttctcatta cttgctctcc - 8101 agtgtgttca gatgtgctgt aaattcatcc tcagctatac gcaccagttt ttcataaaac - 8161 cgcttatcat tacttttatc tcctgcacaa agaacgatag cccgacgaat cggatcgaac - 8221 gcataaaagg ctcttatcgg acggccagaa aactgaacgc gaagctcttt catatttttg - 8281 taccgagaac ctttcacggt atcggcatat ggcctgggta actcaggtcc gtaaacctgt - 8341 agctttttca aatcagccaa aaccttttcc tgaagagcgt cttcttgctc atttagccag - 8401 tcgtcaaatc gctggctaaa aagtaccatc cacatgctca accctataac ctgtagctta - 8461 ccccactaac aatataacct acgagttata ttttcaagaa aagctggcta tttaacataa - 8521 cggcaatttg tacgcaccac tgaaatgcgt tcagcgcgat cacggcaaca gacaggcaaa - 8581 aatagcaaca aacctcccga aaaaccgccg cgatcgcgcc tgataaattt taaccttatg - 8641 catatctatg cagccaggcg aatcacgaac gaattgcctg cctgatgtaa ctgaaacggg - 8701 tgttttttcc tgatttggtg ggcgtggaag acggaacatg aacgggaaaa cagaattcat - 8761 gccagatgag cgcgatctgg caattaaggc aaaacacagc aacaaagaca cgccagaatc - 8821 gcgcccggat atgttttaac gcgattttca gactcagaca aattcagcag aatgctactc - 8881 cattcaccgg gctgatggtg aatacatgcg tatccaggat gagtacattt ctggctctgc - 8941 cacagctctg tctgttggca gctttcgcct gtccggaaac ctgcttaaaa cgctcccgaa - 9001 aggcctctga accagaaagc aacaaaacac aggccattaa gtaaatcgcg ttaaaacacg - 9061 tctgatggat tgctgcaaaa aaaagtccct aatggagcag ggactgttaa acccagtgaa - 9121 tagcgtctaa attaaagtaa gaatacgacc aggtactctt cagaaaagag attaatccac - 9181 cgcacagaat aatcaacagt aaaaacaaac aaccctgatt ttttattttt ctttttttcg - 9241 ataaaaacaa aattaaagaa ataattaatc agaacattcc ttaacttcag ggcattgcct - 9301 gtgttccatt ttgtgattag tctgaaactt ccgaaggtgg ataacacccg gtattttttt - 9361 gctcacataa agcccctcct tcaggcagag gggctttttc tttgccacca cataaaaaag - 9421 gccctcacag gaggtgttct gtgagggcgt atgataagga ctgaatcgat ggttaatatg - 9481 tctagtcctg acttttgcat ctccgaatat aaaaccctgt ttaacggcat gcaaaaccaa - 9541 aaaataaaaa tgtgacatcg caatgccaga taatattgac gcatgaggga atgcgtaccc - 9601 cgacccctg -// diff --git a/file_keep/chart/file/3200140572021372.fasta b/file_keep/chart/file/3200140572021372.fasta deleted file mode 100644 index b9db7a9..0000000 --- a/file_keep/chart/file/3200140572021372.fasta +++ /dev/null @@ -1,162 +0,0 @@ ->NC_005816.1 Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence -TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATCCAGGGGGTAA -TCTGCTCTCCTGATTCAGGAGAGTTTATGGTCACTTTTGAGACAGTTATGGAAATTAAAA -TCCTGCACAAGCAGGGAATGAGTAGCCGGGCGATTGCCAGAGAACTGGGGATCTCCCGCA -ATACCGTTAAACGTTATTTGCAGGCAAAATCTGAGCCGCCAAAATATACGCCGCGACCTG -CTGTTGCTTCACTCCTGGATGAATACCGGGATTATATTCGTCAACGCATCGCCGATGCTC -ATCCTTACAAAATCCCGGCAACGGTAATCGCTCGCGAGATCAGAGACCAGGGATATCGTG -GCGGAATGACCATTCTCAGGGCATTCATTCGTTCTCTCTCGGTTCCTCAGGAGCAGGAGC -CTGCCGTTCGGTTCGAAACTGAACCCGGACGACAGATGCAGGTTGACTGGGGCACTATGC -GTAATGGTCGCTCACCGCTTCACGTGTTCGTTGCTGTTCTCGGATACAGCCGAATGCTGT -ACATCGAATTCACTGACAATATGCGTTATGACACGCTGGAGACCTGCCATCGTAATGCGT -TCCGCTTCTTTGGTGGTGTGCCGCGCGAAGTGTTGTATGACAATATGAAAACTGTGGTTC -TGCAACGTGACGCATATCAGACCGGTCAGCACCGGTTCCATCCTTCGCTGTGGCAGTTCG -GCAAGGAGATGGGCTTCTCTCCCCGACTGTGTCGCCCCTTCAGGGCACAGACTAAAGGTA -AGGTGGAACGGATGGTGCAGTACACCCGTAACAGTTTTTACATCCCACTAATGACTCGCC -TGCGCCCGATGGGGATCACTGTCGATGTTGAAACAGCCAACCGCCACGGTCTGCGCTGGC -TGCACGATGTCGCTAACCAACGAAAGCATGAAACAATCCAGGCCCGTCCCTGCGATCGCT -GGCTCGAAGAGCAGCAGTCCATGCTGGCACTGCCTCCGGAGAAAAAAGAGTATGACGTGC -ATCTTGATGAAAATCTGGTGAACTTCGACAAACACCCCCTGCATCATCCACTCTCCATCT -ACGACTCATTCTGCAGAGGAGTGGCGTGATGATGGAACTGCAACATCAACGACTGATGGC -GCTCGCCGGGCAGTTGCAACTGGAAAGCCTTATAAGCGCAGCGCCTGCGCTGTCACAACA -GGCAGTAGACCAGGAATGGAGTTATATGGACTTCCTGGAGCATCTGCTTCATGAAGAAAA -ACTGGCACGTCATCAACGTAAACAGGCGATGTATACCCGAATGGCAGCCTTCCCGGCGGT -GAAAACGTTCGAAGAGTATGACTTCACATTCGCCACCGGAGCACCGCAGAAGCAACTCCA -GTCGTTACGCTCACTCAGCTTCATAGAACGTAATGAAAATATCGTATTACTGGGGCCATC -AGGTGTGGGGAAAACCCATCTGGCAATAGCGATGGGCTATGAAGCAGTCCGTGCAGGTAT -CAAAGTTCGCTTCACAACAGCAGCAGATCTGTTACTTCAGTTATCTACGGCACAACGTCA -GGGCCGTTATAAAACGACGCTTCAGCGTGGAGTAATGGCCCCCCGCCTGCTCATCATTGA -TGAAATAGGCTATCTGCCGTTCAGTCAGGAAGAAGCAAAGCTGTTCTTCCAGGTCATCGC -TAAACGTTACGAAAAGAGCGCAATGATCCTGACATCCAATCTGCCGTTCGGGCAGTGGGA -TCAAACGTTCGCCGGTGATGCAGCACTGACCTCAGCGATGCTGGACCGTATCTTACACCA -CTCACATGTCGTTCAAATCAAAGGAGAAAGCTATCGACTCAGACAGAAACGAAAGGCCGG -GGTTATAGCAGAAGCTAATCCTGAGTAAAACGGTGGATCAATATTGGGCCGTTGGTGGAG -ATATAAGTGGATCACTTTTCATCCGTCGTTGACACCCTGATGAATTCACGTGTTCACGCC -TGAATAACAAGAATGCCGGAGATACGCAGTCATATTTTTTACACAATTCTCTAATCCCGA -CAAGGTCGTAGGTCGTTATAGGAAAATTCTTAGCACCATTCCGGAACAATCAGAACAGCA -GGCCATGAACGACTGACAACATTACGAATATAAAAAACGCACCCGGGCCAGACATTCCCC -CTACTGATTAAACCAGCCGGACTTGTCCACGGAACGGTCTTTTTAAACCGACACACAGTC -TGAGTACAGATACATGTCACGATGATGCAGGATTAGCGGAAGAGTGTGAGCACGTTTCCG -GGAACTGTGGTGAACCATAGCTCAATATTCGAGTGAGGGCATACCGGAAACGCGCTCAGA -TTCGTTGTAACGCGATTTTCCGTACCGGGCAATTTTTTCAGTTGTTTTTTCGTTTCATGT -CGTCAGAAACGTTCTGAGCGCGTTTCCGGCATCTGATGCTACGCAAACCATCCCCATGGT -CAGTTGACAGCCGGAAACACGCGGGTGTCGTTTTAGCGTATCGACGGGACGGCGTCGAGA -AGCACAAAAAACAGATGTTGTACTCAGTCAGTTGTTTTACAGACAGCACTGCGGCAGATT -GAAAAAGTACCGTACTTTCAGGAATGTCCAGAAACCATGTGTCAGACTTCGTTCTCCCCC -TTCCGGGTGAATTTTTTTGTCATCCGTTCAGGAATCTCTTTATAACGATTACTCCATTTC -AGGATTTTTTATGTGGCGTTTACTACAGGCAGGATATTCAAAGGCAAAAAAATCCCCCGG -AACAGGCGGAACCCGGACAGGGGGAGAACGAATCGCTAAATAATTTTCGTAGTTGTATTT -CCCATCGTTGCTACTGCAACGGGATGAATTTGCCGCAGTTTATCCTGTAAAACAATCCTG -ATTTACTCACACTCCACATATCACTGACGGAGCACAACGGAATAGTGAACAAACAACAAC -AAACTGCGCTGAATATGGCGCGATTTATCAGAAGCCAGAGCCTGATACTGCTTGAAAAAC -TGGATGCTCTGGATGCCGACGAGCAGGCGGCCATGTGTGAACGACTGCACGAACTCGCGG -AAGAACTCCAGAACAGCATCCAGGCTCGCTTTGAAGCCGAAAGTGAAACAGGAACATAAC -GAAGCTCCCGGAGACGGTCACAGCTTGTCTGTGAACGGATGCCGGGAGCAGACAAGCCCG -TCAGGGCGCGTCAGCGGGTTTTAGCGGGTGTCGGGGCGCAGCCATGACCCAGTCACGTAG -CGATAGCGGAGTGTATACTGGCTTAGTCATGCGGCATCAGTGCGGATTGTATGAAAAGTG -CACCATGTACGGTGTGAAATGCCGCACAGATGCGTAAGGAGAACATGCAGATGCCGATGC -TCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTG -TCTGCTCACTCAAAAGCGGTGATACTGTTATCCACACAATCAGGGGATAACGCCGGAAAG -AACATGTGAGCAAAAAACGAAGACCCCAGAAAAGGCCGCGCCGGAGGCGCTTTTTCCATA -GGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACC -CGACAGGACTTAAAGATACCAGGCGTTTCCCCCCGGAAGCTCCCTCGTGCGCTCTCCTGT -TCCGACCCTGCCGCTTACCGGATACCTCTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCT -TTCTCATAGCTCACGCTGTTGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGG -CTGTGTGCACGAACCCCCCGTTCAGCCCGACCACTGCGCCTTATCCGGTAACTATCGTCT -TGAGTCCAACCCGGTAAGACACGACTTTACGCCACTGGCAGCAGCCATTGGTAACTGAAA -AGTGGATTTAGATACGCAGAACTCTTGAAGTTGAAGCCTTATCGCGGCTACACTGAAAGG -ACAGCATTTGGTATCTGTGCTCCACTTAAGCCAGCTACCACAGGTTAGAAAGCCTGAGAA -ACTTCTAACCTTCGAAAGAACCCACGCCTGAGAACGTGGGTTTTTTCGTTTACAGGCAGC -AGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACTGAATTGC -GCTCCCGATCAGTTCAGCAGAAGATTATGATGGGGTTCTATGGGTATTGCTGCGGTAACA -CCCATGTTACTTGAGGTTGTATGTAGTCTGTGTAGAATTATACACATAAGGCTTAAACTG -CTCTTTTTTTTCAATATGCAATTGGAAGTTCATTGACTACATAAATAGATTATTCCAAAT -AATTTATTTATGTAAGAACAGGATGGGAGGGGGAATGATCTCAAAGTTATTTTGCTTGGC -TCTCATATTTTTATCATCAAGTGGCCTTGCAGAAAAAAACACATATACAGCAAAAGACAT -CTTGCAAAACCTAGAATTAAATACCTTTGGCAATTCATTGTCTCATGGCATCTATGGGAA -ACAGACAACCTTCAAGCAAACCGAGTTTACAAATATTAAAAGCAACACCAAAAAACACAT -TGCACTTATCAATAAAGACAACTCATGGATGATATCATTAAAAATACTAGGAATTAAGAG -AGATGAGTATACTGTCTGTTTTGAAGATTTCTCTCTAATAAGACCGCCAACATATGTAGC -CATACATCCTCTACTTATAAAAAAAGTAAAATCTGGAAACTTTATAGTAGTGAAAGAAAT -AAAGAAATCTATCCCTGGTTGCACTGTATATTATCATTAATAGCAAGCCCCTCATTATTA -TGAGGGGCTCATGGTTATTTTAACAATCCACTATCGATATCTTTTTGCACCAGAGCGCCC -TCTCGTTTACGTCTGTCAGACATTCCATCAACAATATTATTAAAAGCATTTACAAGGCCA -TTCCAGTCTTTTGCGATAACTTTATTCCATACTGTGGGAGCAGTTCTGGATAACTTAAAC -CCTTTTTGATATCCAATAGACACCAGTGCTGTACGGGTTCTCAACGGTAAATCGCTGAAC -CGAAGACCGATATTAGCGTCATTGAAAAGACCTTCAATCTTATGTGAGAATTTATCAATA -TAAATATTAGATAAGAGATGAGCTTCATTATCAGAAAGCGTCAGAGGTGCTGTTCTCACT -TTATCATAAGCCTCCTTCCCTCGAAGCATATAATACCCATCAAGTCTATCTGCAATATAC -TGAGGGACACCGTCATTCAATAAATCCTGTTTGCTTCGCTGACCAAGGTCAACCCCGGAA -CCGAATGTAACACCGGTACTGTTAAAATAATCGCTACTAGGATTAGACGGAAAATGACTT -GTCGGATTAAACCCTTCAAAACCATTACTGGAGAAAATATCGTGGTCAACAATATTTACC -GAACGACGTAAAAATTCCTTCAGTTGACTAATATTGTCAAAGTTAATGACAGTGTTGTCC -GCTAGGACGATGCGATTTCGGTTATTATTCAGAATGTCTTCGTTCTCTTTCTTATCGAGA -TGTTCAATAGATTCGGCAATCGTTCCCTCAAGAACCATGACACGGTAGACTTTCACACCG -TCTTTTTCCTGACCTGTTTCAACAGTTATTTTCTGTTCGTAAGACACGGTCCCTTCAGTT -TTTGAAATTTTACTTTCCTGGCGGATCTTATTTGAATATTCACTGTCTTTCTCCATCTCC -GTATCAATCGGAAACCCCATAATGTACATCAGTTTAAAATTACTCCGGCCAGGCAGATCC -ACATAATGTGGTAATGCAATTGTAATCGAATTAGCTTCAAAATTTGGTCTGTAACTGCTT -AATGTACTTCCGGAAAAGAGAAAAGCCGGAACACCACCTGAACCATTCACTACCATTGTA -TCTGACATAAAAATTCCTCTTTAACACATAAAAAAAACAATAAGTTAAAAAAATACTGTA -CATAAAAGCACTGTTTTTATGTACAGTAATAAAATTACGCCGCTTTATTTTCTCTGTCAA -TAATATGAAATTTCATTTTTGTGATCTGAATCACTCTTATAAAAATCAGGAAGGGAAGAT -TCGCAGCAGAAAAACAGCACCGGGTAACATCAGAAAAAAACAGAAAGGAGATAACGTGAG -CAAAACAAAATCTGGTCGCCACCGACTGAGCAAAACAGACAAACGCCTGCTGGCTGCACT -TGTCGTTGCCGGATACGAAGAACGGACAGCCCGTGACCTCATCCAGAAACACGTTTACAC -ACTGACACAGGCCGACCTGCGCCATCTGGTCAGTGAAATCAGTAACGGTGTGGGACAGTC -ACAGGCCTACGATGCGATTTACCAGGCGAGACGCATTCGTCTCGCCCGTAAATACCTGAG -CGGAAAAAAACCGGAAGGGGTGGAACCCCGGGAAGGGCAGGAACGGGAAGATTTACCATA -ACTCCCGTTATCAGTACCATCGGCTCAACGCTCGTTGTCGGATCTGAAAAATTCGCTCAA -AAGATCATATTTCCCTGGATATTTTCCACCGTTTCTTATGTGAGAAAAGTCACATAATTC -TGTCAGACGACGAGAAAACGGATATCGATTATTGTTTAATATTTTTACATTATTAAAAAT -GAAATTAGATAATCAGATACAAATAATATGTTTTCGTTCATGCAGAGAGATTAAGGGTGT -CTAATGAAGAAAAGTTCTATTGTGGCAACCATTATAACTATTCTGTCCGGGAGTGCTAAT -GCAGCATCATCTCAGTTAATACCAAATATATCCCCTGACAGCTTTACAGTTGCAGCCTCC -ACCGGGATGCTGAGTGGAAAGTCTCATGAAATGCTTTATGACGCAGAAACAGGAAGAAAG -ATCAGCCAGTTAGACTGGAAGATCAAAAATGTCGCTATCCTGAAAGGTGATATATCCTGG -GATCCATACTCATTTCTGACCCTGAATGCCAGGGGGTGGACGTCTCTGGCTTCCGGGTCA -GGTAATATGGATGACTACGACTGGATGAATGAAAATCAATCTGAGTGGACAGATCACTCA -TCTCATCCTGCTACAAATGTTAATCATGCCAATGAATATGACCTCAATGTGAAAGGCTGG -TTACTCCAGGATGAGAATTATAAAGCAGGTATAACAGCAGGATATCAGGAAACACGTTTC -AGTTGGACAGCTACAGGTGGTTCATATAGTTATAATAATGGAGCTTATACCGGAAACTTC -CCGAAAGGAGTGCGGGTAATAGGTTATAACCAGCGCTTTTCTATGCCATATATTGGACTT -GCAGGCCAGTATCGCATTAATGATTTTGAGTTAAATGCATTATTTAAATTCAGCGACTGG -GTTCGGGCACATGATAATGATGAGCACTATATGAGAGATCTTACTTTCCGTGAGAAGACA -TCCGGCTCACGTTATTATGGTACCGTAATTAACGCTGGATATTATGTCACACCTAATGCC -AAAGTCTTTGCGGAATTTACATACAGTAAATATGATGAGGGCAAAGGAGGTACTCAGATC -ATTGATAAGAATAGTGGAGATTCTGTCTCTATTGGCGGAGATGCTGCCGGTATTTCCAAT -AAAAATTATACTGTGACGGCGGGTCTGCAATATCGCTTCTGAAAAATACAGATCATATCT -CTCTTTTCATCCTCCCCTAGCGGGGAGGATGTCTGTGGAAAGGAGGTTGGTGTTTGACCA -ACCTTCAGATGTGTGAAAAATCACCTTTTTCACCATAATGACGGGGCGCTCATTCTGTTG -TTTTGCCTTGACATTCTCCACGTCTTTCAGGGCATGGAGAAGGTCAAATTAGACATGGAA -CGCTACTCTCCTTCCTGTAGGAAGCTCAACATCCAAGCTTAATTTGCCTCCCATTGCTTC -AACGTAACGCTTTAACGTCGCCAGCTTTAAATCATTTCCGCGCTGCTCCAGCTTTGTTAC -TGCTGGCTGGCTTATACCCATCGCCTCAGCAACTTGTTTTTGTGATAACTGGAGTTCTTC -ACGCATCATCTGCAAGCCGACCTCAAGAATCATCTCATCTGCCATTTCTTTAATTCGTGT -CTGGCTTTCAGGTGAACGACTGGCAATCACCTCATCTAATGTTCTCATTACTTGCTCTCC -AGTGTGTTCAGATGTGCTGTAAATTCATCCTCAGCTATACGCACCAGTTTTTCATAAAAC -CGCTTATCATTACTTTTATCTCCTGCACAAAGAACGATAGCCCGACGAATCGGATCGAAC -GCATAAAAGGCTCTTATCGGACGGCCAGAAAACTGAACGCGAAGCTCTTTCATATTTTTG -TACCGAGAACCTTTCACGGTATCGGCATATGGCCTGGGTAACTCAGGTCCGTAAACCTGT -AGCTTTTTCAAATCAGCCAAAACCTTTTCCTGAAGAGCGTCTTCTTGCTCATTTAGCCAG -TCGTCAAATCGCTGGCTAAAAAGTACCATCCACATGCTCAACCCTATAACCTGTAGCTTA -CCCCACTAACAATATAACCTACGAGTTATATTTTCAAGAAAAGCTGGCTATTTAACATAA -CGGCAATTTGTACGCACCACTGAAATGCGTTCAGCGCGATCACGGCAACAGACAGGCAAA -AATAGCAACAAACCTCCCGAAAAACCGCCGCGATCGCGCCTGATAAATTTTAACCTTATG -CATATCTATGCAGCCAGGCGAATCACGAACGAATTGCCTGCCTGATGTAACTGAAACGGG -TGTTTTTTCCTGATTTGGTGGGCGTGGAAGACGGAACATGAACGGGAAAACAGAATTCAT -GCCAGATGAGCGCGATCTGGCAATTAAGGCAAAACACAGCAACAAAGACACGCCAGAATC -GCGCCCGGATATGTTTTAACGCGATTTTCAGACTCAGACAAATTCAGCAGAATGCTACTC -CATTCACCGGGCTGATGGTGAATACATGCGTATCCAGGATGAGTACATTTCTGGCTCTGC -CACAGCTCTGTCTGTTGGCAGCTTTCGCCTGTCCGGAAACCTGCTTAAAACGCTCCCGAA -AGGCCTCTGAACCAGAAAGCAACAAAACACAGGCCATTAAGTAAATCGCGTTAAAACACG -TCTGATGGATTGCTGCAAAAAAAAGTCCCTAATGGAGCAGGGACTGTTAAACCCAGTGAA -TAGCGTCTAAATTAAAGTAAGAATACGACCAGGTACTCTTCAGAAAAGAGATTAATCCAC -CGCACAGAATAATCAACAGTAAAAACAAACAACCCTGATTTTTTATTTTTCTTTTTTTCG -ATAAAAACAAAATTAAAGAAATAATTAATCAGAACATTCCTTAACTTCAGGGCATTGCCT -GTGTTCCATTTTGTGATTAGTCTGAAACTTCCGAAGGTGGATAACACCCGGTATTTTTTT -GCTCACATAAAGCCCCTCCTTCAGGCAGAGGGGCTTTTTCTTTGCCACCACATAAAAAAG -GCCCTCACAGGAGGTGTTCTGTGAGGGCGTATGATAAGGACTGAATCGATGGTTAATATG -TCTAGTCCTGACTTTTGCATCTCCGAATATAAAACCCTGTTTAACGGCATGCAAAACCAA -AAAATAAAAATGTGACATCGCAATGCCAGATAATATTGACGCATGAGGGAATGCGTACCC -CGACCCCTG diff --git a/file_keep/chart/file/3200210232021637 b/file_keep/chart/file/3200210232021637 deleted file mode 100644 index 57ee9fc..0000000 --- a/file_keep/chart/file/3200210232021637 +++ /dev/null @@ -1,529 +0,0 @@ -LOCUS NC_005816 9609 bp DNA circular BCT 21-JUL-2008 -DEFINITION Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete - sequence. -ACCESSION NC_005816 -VERSION NC_005816.1 GI:45478711 -DBLINK Project: 58037 -KEYWORDS . -SOURCE Yersinia pestis biovar Microtus str. 91001 - ORGANISM Yersinia pestis biovar Microtus str. 91001 - Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; - Enterobacteriaceae; Yersinia. -REFERENCE 1 (bases 1 to 9609) - AUTHORS Zhou,D., Tong,Z., Song,Y., Han,Y., Pei,D., Pang,X., Zhai,J., Li,M., - Cui,B., Qi,Z., Jin,L., Dai,R., Du,Z., Wang,J., Guo,Z., Wang,J., - Huang,P. and Yang,R. - TITLE Genetics of metabolic variations between Yersinia pestis biovars - and the proposal of a new biovar, microtus - JOURNAL J. Bacteriol. 186 (15), 5147-5152 (2004) - PUBMED 15262951 -REFERENCE 2 (bases 1 to 9609) - AUTHORS Song,Y., Tong,Z., Wang,J., Wang,L., Guo,Z., Han,Y., Zhang,J., - Pei,D., Zhou,D., Qin,H., Pang,X., Han,Y., Zhai,J., Li,M., Cui,B., - Qi,Z., Jin,L., Dai,R., Chen,F., Li,S., Ye,C., Du,Z., Lin,W., - Wang,J., Yu,J., Yang,H., Wang,J., Huang,P. and Yang,R. - TITLE Complete genome sequence of Yersinia pestis strain 91001, an - isolate avirulent to humans - JOURNAL DNA Res. 11 (3), 179-197 (2004) - PUBMED 15368893 -REFERENCE 3 (bases 1 to 9609) - CONSRTM NCBI Genome Project - TITLE Direct Submission - JOURNAL Submitted (16-MAR-2004) National Center for Biotechnology - Information, NIH, Bethesda, MD 20894, USA -REFERENCE 4 (bases 1 to 9609) - AUTHORS Song,Y., Tong,Z., Wang,L., Han,Y., Zhang,J., Pei,D., Wang,J., - Zhou,D., Han,Y., Pang,X., Zhai,J., Chen,F., Qin,H., Wang,J., Li,S., - Guo,Z., Ye,C., Du,Z., Lin,W., Wang,J., Yu,J., Yang,H., Wang,J., - Huang,P. and Yang,R. - TITLE Direct Submission - JOURNAL Submitted (24-APR-2003) The Institute of Microbiology and - Epidemiology, Academy of Military Medical Sciences, No. 20, - Dongdajie Street, Fengtai District, Beijing 100071, People's - Republic of China -COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final - NCBI review. The reference sequence was derived from AE017046. - COMPLETENESS: full length. -FEATURES Location/Qualifiers - source 1..9609 - /organism="Yersinia pestis biovar Microtus str. 91001" - /mol_type="genomic DNA" - /strain="91001" - /db_xref="taxon:229193" - /plasmid="pPCP1" - /biovar="Microtus" - repeat_region 1..1954 - gene 87..1109 - /locus_tag="YP_pPCP01" - /db_xref="GeneID:2767718" - CDS 87..1109 - /locus_tag="YP_pPCP01" - /note="similar to corresponding CDS from previously - sequenced pPCP plasmid of Yersinia pestis KIM (AF053945) - and CO92 (AL109969), also many transposase entries for - insertion sequence IS100 of Yersinia pestis. Contains - IS21-like element transposase, HTH domain - (Interpro|IPR007101)" - /codon_start=1 - /transl_table=11 - /product="putative transposase" - /protein_id="NP_995567.1" - /db_xref="GI:45478712" - /db_xref="GeneID:2767718" - /translation="MVTFETVMEIKILHKQGMSSRAIARELGISRNTVKRYLQAKSEP - PKYTPRPAVASLLDEYRDYIRQRIADAHPYKIPATVIAREIRDQGYRGGMTILRAFIR - SLSVPQEQEPAVRFETEPGRQMQVDWGTMRNGRSPLHVFVAVLGYSRMLYIEFTDNMR - YDTLETCHRNAFRFFGGVPREVLYDNMKTVVLQRDAYQTGQHRFHPSLWQFGKEMGFS - PRLCRPFRAQTKGKVERMVQYTRNSFYIPLMTRLRPMGITVDVETANRHGLRWLHDVA - NQRKHETIQARPCDRWLEEQQSMLALPPEKKEYDVHLDENLVNFDKHPLHHPLSIYDS - FCRGVA" - misc_feature 87..959 - /locus_tag="YP_pPCP01" - /note="Transposase and inactivated derivatives [DNA - replication, recombination, and repair]; Region: COG4584" - /db_xref="CDD:34222" - misc_feature <111..209 - /locus_tag="YP_pPCP01" - /note="Helix-turn-helix domain of Hin and related - proteins, a family of DNA-binding domains unique to - bacteria and represented by the Hin protein of Salmonella. - The basic HTH domain is a simple fold comprised of three - core helices that form a right-handed...; Region: - HTH_Hin_like; cl01116" - /db_xref="CDD:186341" - misc_feature 438..812 - /locus_tag="YP_pPCP01" - /note="Integrase core domain; Region: rve; cl01316" - /db_xref="CDD:194099" - gene 1106..1888 - /locus_tag="YP_pPCP02" - /db_xref="GeneID:2767716" - CDS 1106..1888 - /locus_tag="YP_pPCP02" - /note="similar to corresponding CDS form previously - sequenced pPCP plasmid of Yersinia pestis KIM (AF053945) - and CO92 (AL109969), also many ATP-binding protein entries - for insertion sequence IS100 of Yersinia pestis. Contains - Chaperonin clpA/B (Interpro|IPR001270). Contains - ATP/GTP-binding site motif A (P-loop) (Interpro|IPR001687, - Molecular Function: ATP binding (GO:0005524)). Contains - Bacterial chromosomal replication initiator protein, DnaA - (Interpro|IPR001957, Molecular Function: DNA binding - (GO:0003677), Molecular Function: DNA replication origin - binding (GO:0003688), Molecular Function: ATP binding - (GO:0005524), Biological Process: DNA replication - initiation (GO:0006270), Biological Process: regulation of - DNA replication (GO:0006275)). Contains AAA ATPase - (Interpro|IPR003593, Molecular Function: nucleotide - binding (GO:0000166))" - /codon_start=1 - /transl_table=11 - /product="transposase/IS protein" - /protein_id="NP_995568.1" - /db_xref="GI:45478713" - /db_xref="GeneID:2767716" - /translation="MMMELQHQRLMALAGQLQLESLISAAPALSQQAVDQEWSYMDFL - EHLLHEEKLARHQRKQAMYTRMAAFPAVKTFEEYDFTFATGAPQKQLQSLRSLSFIER - NENIVLLGPSGVGKTHLAIAMGYEAVRAGIKVRFTTAADLLLQLSTAQRQGRYKTTLQ - RGVMAPRLLIIDEIGYLPFSQEEAKLFFQVIAKRYEKSAMILTSNLPFGQWDQTFAGD - AALTSAMLDRILHHSHVVQIKGESYRLRQKRKAGVIAEANPE" - misc_feature 1109..1885 - /locus_tag="YP_pPCP02" - /note="transposase/IS protein; Provisional; Region: - PRK09183" - /db_xref="CDD:181681" - misc_feature 1367..>1669 - /locus_tag="YP_pPCP02" - /note="The AAA+ (ATPases Associated with a wide variety of - cellular Activities) superfamily represents an ancient - group of ATPases belonging to the ASCE (for additional - strand, catalytic E) division of the P-loop NTPase fold. - The ASCE division also includes...; Region: AAA; cd00009" - /db_xref="CDD:99707" - misc_feature 1433..1456 - /locus_tag="YP_pPCP02" - /note="Walker A motif; other site" - /db_xref="CDD:99707" - misc_feature order(1436..1459,1619..1621) - /locus_tag="YP_pPCP02" - /note="ATP binding site [chemical binding]; other site" - /db_xref="CDD:99707" - misc_feature 1607..1624 - /locus_tag="YP_pPCP02" - /note="Walker B motif; other site" - /db_xref="CDD:99707" - gene 2925..3119 - /gene="rop" - /locus_tag="YP_pPCP03" - /gene_synonym="rom" - /db_xref="GeneID:2767717" - CDS 2925..3119 - /gene="rop" - /locus_tag="YP_pPCP03" - /gene_synonym="rom" - /note="Best Blastp hit =gi|16082682|ref|NP_395229.1| - (NC_003132) putative replication regulatory protein - [Yersinia pestis], gi|5763813|emb|CAB531 66.1| (AL109969) - putative replication regulatory protein [Yersinia pestis]; - similar to gb|AAK91579.1| (AY048853), RNAI modulator - protein Rom [Salmonella choleraesuis], Contains Regulatory - protein Rop (Interpro|IPR000769)" - /codon_start=1 - /transl_table=11 - /product="putative replication regulatory protein" - /protein_id="NP_995569.1" - /db_xref="GI:45478714" - /db_xref="GeneID:2767717" - /translation="MNKQQQTALNMARFIRSQSLILLEKLDALDADEQAAMCERLHEL - AEELQNSIQARFEAESETGT" - misc_feature 2925..3107 - /gene="rop" - /locus_tag="YP_pPCP03" - /gene_synonym="rom" - /note="Rop protein; Region: Rop; pfam01815" - /db_xref="CDD:145136" - gene 3486..3857 - /locus_tag="YP_pPCP04" - /db_xref="GeneID:2767720" - CDS 3486..3857 - /locus_tag="YP_pPCP04" - /note="Best Blastp hit = gi|321919|pir||JQ1541 - hypothetical 16.9K protein - Salmonella typhi murium - plasmid NTP16." - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /protein_id="NP_995570.1" - /db_xref="GI:45478715" - /db_xref="GeneID:2767720" - /translation="MSKKRRPQKRPRRRRFFHRLRPPDEHHKNRRSSQRWRNPTGLKD - TRRFPPEAPSCALLFRPCRLPDTSPPFSLREAWRFLIAHAVGISVRCRSFAPSWAVCT - NPPFSPTTAPYPVTIVLSPTR" - misc_feature 3498..3626 - /locus_tag="YP_pPCP04" - /note="ProfileScan match to entry PS50323 ARG_RICH, - E-value 8.981" - gene 4343..4780 - /gene="pim" - /locus_tag="YP_pPCP05" - /db_xref="GeneID:2767712" - CDS 4343..4780 - /gene="pim" - /locus_tag="YP_pPCP05" - /note="similar to many previously sequenced pesticin - immunity protein entries of Yersinia pestis plasmid pPCP, - e.g. gi| 16082683|,ref|NP_395230.1| (NC_003132) , - gi|1200166|emb|CAA90861.1| (Z54145 ) , gi|1488655| - emb|CAA63439.1| (X92856) , gi|2996219|gb|AAC62543.1| - (AF053945) , and gi|5763814|emb|CAB531 67.1| (AL109969)" - /codon_start=1 - /transl_table=11 - /product="pesticin immunity protein" - /protein_id="NP_995571.1" - /db_xref="GI:45478716" - /db_xref="GeneID:2767712" - /translation="MGGGMISKLFCLALIFLSSSGLAEKNTYTAKDILQNLELNTFGN - SLSHGIYGKQTTFKQTEFTNIKSNTKKHIALINKDNSWMISLKILGIKRDEYTVCFED - FSLIRPPTYVAIHPLLIKKVKSGNFIVVKEIKKSIPGCTVYYH" - gene complement(4815..5888) - /gene="pst" - /locus_tag="YP_pPCP06" - /db_xref="GeneID:2767721" - CDS complement(4815..5888) - /gene="pst" - /locus_tag="YP_pPCP06" - /note="Best Blastp hit =|16082684|ref|NP_395231.1| - (NC_003132) pesticin [Yersinia pestis], - gi|984824|gb|AAA75369.1| (U31974) pesticin [Yersinia - pestis], gi|1488654|emb|CAA63438.1| (X92856) pesticin - [Yersinia pestis], gi|2996220|gb|AAC62544.1| (AF053945) - pesticin [Yersinia pestis], gi|5763815|emb|CAB53168.1| - (AL1099 69) pesticin [Yersinia pestis]" - /codon_start=1 - /transl_table=11 - /product="pesticin" - /protein_id="NP_995572.1" - /db_xref="GI:45478717" - /db_xref="GeneID:2767721" - /translation="MSDTMVVNGSGGVPAFLFSGSTLSSYRPNFEANSITIALPHYVD - LPGRSNFKLMYIMGFPIDTEMEKDSEYSNKIRQESKISKTEGTVSYEQKITVETGQEK - DGVKVYRVMVLEGTIAESIEHLDKKENEDILNNNRNRIVLADNTVINFDNISQLKEFL - RRSVNIVDHDIFSSNGFEGFNPTSHFPSNPSSDYFNSTGVTFGSGVDLGQRSKQDLLN - DGVPQYIADRLDGYYMLRGKEAYDKVRTAPLTLSDNEAHLLSNIYIDKFSHKIEGLFN - DANIGLRFSDLPLRTRTALVSIGYQKGFKLSRTAPTVWNKVIAKDWNGLVNAFNNIVD - GMSDRRKREGALVQKDIDSGLLK" - variation 5910..5911 - /note="compared to AF053945" - /replace="" - variation 5933^5934 - /note="compared to AL109969" - /replace="a" - variation 5933^5934 - /note="compared to AF053945" - /replace="aa" - variation 5948 - /note="compared to AL109969" - /replace="c" - gene 6005..6421 - /locus_tag="YP_pPCP07" - /db_xref="GeneID:2767719" - CDS 6005..6421 - /locus_tag="YP_pPCP07" - /note="Best Blastp hit = gi|16082685|ref|NP_395232.1| - (NC_003132) hypothetical protein [Yersinia pestis], - gi|5763816|emb|CAB53169.1| (AL109969) hypothetical protein - [Yersinia pestis]" - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /protein_id="NP_995573.1" - /db_xref="GI:45478718" - /db_xref="GeneID:2767719" - /translation="MKFHFCDLNHSYKNQEGKIRSRKTAPGNIRKKQKGDNVSKTKSG - RHRLSKTDKRLLAALVVAGYEERTARDLIQKHVYTLTQADLRHLVSEISNGVGQSQAY - DAIYQARRIRLARKYLSGKKPEGVEPREGQEREDLP" - variation 6525 - /note="compared to AF053945 and AL109969" - /replace="c" - gene 6664..7602 - /gene="pla" - /locus_tag="YP_pPCP08" - /db_xref="GeneID:2767715" - CDS 6664..7602 - /gene="pla" - /locus_tag="YP_pPCP08" - /EC_number="3.4.23.48" - /note="outer membrane protease; involved in virulence in - many organisms; OmpT; IcsP; SopA; Pla; PgtE; omptin; in - Escherichia coli OmpT can degrade antimicrobial peptides; - in Yersinia Pla activates plasminogen during infection; in - Shigella flexneria SopA cleaves the autotransporter IcsA" - /codon_start=1 - /transl_table=11 - /product="outer membrane protease" - /protein_id="NP_995574.1" - /db_xref="GI:45478719" - /db_xref="GeneID:2767715" - /translation="MKKSSIVATIITILSGSANAASSQLIPNISPDSFTVAASTGMLS - GKSHEMLYDAETGRKISQLDWKIKNVAILKGDISWDPYSFLTLNARGWTSLASGSGNM - DDYDWMNENQSEWTDHSSHPATNVNHANEYDLNVKGWLLQDENYKAGITAGYQETRFS - WTATGGSYSYNNGAYTGNFPKGVRVIGYNQRFSMPYIGLAGQYRINDFELNALFKFSD - WVRAHDNDEHYMRDLTFREKTSGSRYYGTVINAGYYVTPNAKVFAEFTYSKYDEGKGG - TQIIDKNSGDSVSIGGDAAGISNKNYTVTAGLQYRF" - misc_feature 6664..7599 - /gene="pla" - /locus_tag="YP_pPCP08" - /note="Omptin family; Region: Omptin; cl01886" - /db_xref="CDD:186487" - gene complement(7789..8088) - /locus_tag="YP_pPCP09" - /db_xref="GeneID:2767713" - CDS complement(7789..8088) - /locus_tag="YP_pPCP09" - /note="Best Blastp hit = gi|16082687|ref|NP_395234.1| - (NC_003132) putative transcriptional regulator [Yersinia - pestis], gi|5763818|emb|CAB53171.1| (AL109969) putative - transcriptional regulator [Yersinia pestis]." - /codon_start=1 - /transl_table=11 - /product="putative transcriptional regulator" - /protein_id="NP_995575.1" - /db_xref="GI:45478720" - /db_xref="GeneID:2767713" - /translation="MRTLDEVIASRSPESQTRIKEMADEMILEVGLQMMREELQLSQK - QVAEAMGISQPAVTKLEQRGNDLKLATLKRYVEAMGGKLSLDVELPTGRRVAFHV" - misc_feature complement(7837..7995) - /locus_tag="YP_pPCP09" - /note="Helix-turn-helix XRE-family like proteins. - Prokaryotic DNA binding proteins belonging to the - xenobiotic response element family of transcriptional - regulators; Region: HTH_XRE; cl09100" - /db_xref="CDD:195788" - gene complement(8088..8360) - /locus_tag="YP_pPCP10" - /db_xref="GeneID:2767714" - CDS complement(8088..8360) - /locus_tag="YP_pPCP10" - /note="Best Blastp hit = gi|16082688|ref|NP_395235.1| - (NC_003132) hypothetical protein [ Yersinia pestis], - gi|5763819|emb|CAB53172.1| (AL109969) hypothetical protein - [Yersinia pestis]" - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /protein_id="NP_995576.1" - /db_xref="GI:45478721" - /db_xref="GeneID:2767714" - /translation="MADLKKLQVYGPELPRPYADTVKGSRYKNMKELRVQFSGRPIRA - FYAFDPIRRAIVLCAGDKSNDKRFYEKLVRIAEDEFTAHLNTLESK" - misc_feature complement(8091..>8357) - /locus_tag="YP_pPCP10" - /note="Phage derived protein Gp49-like (DUF891); Region: - Gp49; cl01470" - /db_xref="CDD:194142" - variation 8529^8530 - /note="compared to AL109969" - /replace="tt" -ORIGIN - 1 tgtaacgaac ggtgcaatag tgatccacac ccaacgcctg aaatcagatc cagggggtaa - 61 tctgctctcc tgattcagga gagtttatgg tcacttttga gacagttatg gaaattaaaa - 121 tcctgcacaa gcagggaatg agtagccggg cgattgccag agaactgggg atctcccgca - 181 ataccgttaa acgttatttg caggcaaaat ctgagccgcc aaaatatacg ccgcgacctg - 241 ctgttgcttc actcctggat gaataccggg attatattcg tcaacgcatc gccgatgctc - 301 atccttacaa aatcccggca acggtaatcg ctcgcgagat cagagaccag ggatatcgtg - 361 gcggaatgac cattctcagg gcattcattc gttctctctc ggttcctcag gagcaggagc - 421 ctgccgttcg gttcgaaact gaacccggac gacagatgca ggttgactgg ggcactatgc - 481 gtaatggtcg ctcaccgctt cacgtgttcg ttgctgttct cggatacagc cgaatgctgt - 541 acatcgaatt cactgacaat atgcgttatg acacgctgga gacctgccat cgtaatgcgt - 601 tccgcttctt tggtggtgtg ccgcgcgaag tgttgtatga caatatgaaa actgtggttc - 661 tgcaacgtga cgcatatcag accggtcagc accggttcca tccttcgctg tggcagttcg - 721 gcaaggagat gggcttctct ccccgactgt gtcgcccctt cagggcacag actaaaggta - 781 aggtggaacg gatggtgcag tacacccgta acagttttta catcccacta atgactcgcc - 841 tgcgcccgat ggggatcact gtcgatgttg aaacagccaa ccgccacggt ctgcgctggc - 901 tgcacgatgt cgctaaccaa cgaaagcatg aaacaatcca ggcccgtccc tgcgatcgct - 961 ggctcgaaga gcagcagtcc atgctggcac tgcctccgga gaaaaaagag tatgacgtgc - 1021 atcttgatga aaatctggtg aacttcgaca aacaccccct gcatcatcca ctctccatct - 1081 acgactcatt ctgcagagga gtggcgtgat gatggaactg caacatcaac gactgatggc - 1141 gctcgccggg cagttgcaac tggaaagcct tataagcgca gcgcctgcgc tgtcacaaca - 1201 ggcagtagac caggaatgga gttatatgga cttcctggag catctgcttc atgaagaaaa - 1261 actggcacgt catcaacgta aacaggcgat gtatacccga atggcagcct tcccggcggt - 1321 gaaaacgttc gaagagtatg acttcacatt cgccaccgga gcaccgcaga agcaactcca - 1381 gtcgttacgc tcactcagct tcatagaacg taatgaaaat atcgtattac tggggccatc - 1441 aggtgtgggg aaaacccatc tggcaatagc gatgggctat gaagcagtcc gtgcaggtat - 1501 caaagttcgc ttcacaacag cagcagatct gttacttcag ttatctacgg cacaacgtca - 1561 gggccgttat aaaacgacgc ttcagcgtgg agtaatggcc ccccgcctgc tcatcattga - 1621 tgaaataggc tatctgccgt tcagtcagga agaagcaaag ctgttcttcc aggtcatcgc - 1681 taaacgttac gaaaagagcg caatgatcct gacatccaat ctgccgttcg ggcagtggga - 1741 tcaaacgttc gccggtgatg cagcactgac ctcagcgatg ctggaccgta tcttacacca - 1801 ctcacatgtc gttcaaatca aaggagaaag ctatcgactc agacagaaac gaaaggccgg - 1861 ggttatagca gaagctaatc ctgagtaaaa cggtggatca atattgggcc gttggtggag - 1921 atataagtgg atcacttttc atccgtcgtt gacaccctga tgaattcacg tgttcacgcc - 1981 tgaataacaa gaatgccgga gatacgcagt catatttttt acacaattct ctaatcccga - 2041 caaggtcgta ggtcgttata ggaaaattct tagcaccatt ccggaacaat cagaacagca - 2101 ggccatgaac gactgacaac attacgaata taaaaaacgc acccgggcca gacattcccc - 2161 ctactgatta aaccagccgg acttgtccac ggaacggtct ttttaaaccg acacacagtc - 2221 tgagtacaga tacatgtcac gatgatgcag gattagcgga agagtgtgag cacgtttccg - 2281 ggaactgtgg tgaaccatag ctcaatattc gagtgagggc ataccggaaa cgcgctcaga - 2341 ttcgttgtaa cgcgattttc cgtaccgggc aattttttca gttgtttttt cgtttcatgt - 2401 cgtcagaaac gttctgagcg cgtttccggc atctgatgct acgcaaacca tccccatggt - 2461 cagttgacag ccggaaacac gcgggtgtcg ttttagcgta tcgacgggac ggcgtcgaga - 2521 agcacaaaaa acagatgttg tactcagtca gttgttttac agacagcact gcggcagatt - 2581 gaaaaagtac cgtactttca ggaatgtcca gaaaccatgt gtcagacttc gttctccccc - 2641 ttccgggtga atttttttgt catccgttca ggaatctctt tataacgatt actccatttc - 2701 aggatttttt atgtggcgtt tactacaggc aggatattca aaggcaaaaa aatcccccgg - 2761 aacaggcgga acccggacag ggggagaacg aatcgctaaa taattttcgt agttgtattt - 2821 cccatcgttg ctactgcaac gggatgaatt tgccgcagtt tatcctgtaa aacaatcctg - 2881 atttactcac actccacata tcactgacgg agcacaacgg aatagtgaac aaacaacaac - 2941 aaactgcgct gaatatggcg cgatttatca gaagccagag cctgatactg cttgaaaaac - 3001 tggatgctct ggatgccgac gagcaggcgg ccatgtgtga acgactgcac gaactcgcgg - 3061 aagaactcca gaacagcatc caggctcgct ttgaagccga aagtgaaaca ggaacataac - 3121 gaagctcccg gagacggtca cagcttgtct gtgaacggat gccgggagca gacaagcccg - 3181 tcagggcgcg tcagcgggtt ttagcgggtg tcggggcgca gccatgaccc agtcacgtag - 3241 cgatagcgga gtgtatactg gcttagtcat gcggcatcag tgcggattgt atgaaaagtg - 3301 caccatgtac ggtgtgaaat gccgcacaga tgcgtaagga gaacatgcag atgccgatgc - 3361 tcttccgctt cctcgctcac tgactcgctg cgctcggtcg ttcggctgcg gcgagcggtg - 3421 tctgctcact caaaagcggt gatactgtta tccacacaat caggggataa cgccggaaag - 3481 aacatgtgag caaaaaacga agaccccaga aaaggccgcg ccggaggcgc tttttccata - 3541 ggctccgccc ccctgacgag catcacaaaa atcgacgctc aagtcagagg tggcgaaacc - 3601 cgacaggact taaagatacc aggcgtttcc ccccggaagc tccctcgtgc gctctcctgt - 3661 tccgaccctg ccgcttaccg gatacctctc cgcctttctc ccttcgggaa gcgtggcgct - 3721 ttctcatagc tcacgctgtt ggtatctcag ttcggtgtag gtcgttcgct ccaagctggg - 3781 ctgtgtgcac gaaccccccg ttcagcccga ccactgcgcc ttatccggta actatcgtct - 3841 tgagtccaac ccggtaagac acgactttac gccactggca gcagccattg gtaactgaaa - 3901 agtggattta gatacgcaga actcttgaag ttgaagcctt atcgcggcta cactgaaagg - 3961 acagcatttg gtatctgtgc tccacttaag ccagctacca caggttagaa agcctgagaa - 4021 acttctaacc ttcgaaagaa cccacgcctg agaacgtggg ttttttcgtt tacaggcagc - 4081 agattacgcg cagaaaaaaa ggatctcaag aagatccttt gatcttttct actgaattgc - 4141 gctcccgatc agttcagcag aagattatga tggggttcta tgggtattgc tgcggtaaca - 4201 cccatgttac ttgaggttgt atgtagtctg tgtagaatta tacacataag gcttaaactg - 4261 ctcttttttt tcaatatgca attggaagtt cattgactac ataaatagat tattccaaat - 4321 aatttattta tgtaagaaca ggatgggagg gggaatgatc tcaaagttat tttgcttggc - 4381 tctcatattt ttatcatcaa gtggccttgc agaaaaaaac acatatacag caaaagacat - 4441 cttgcaaaac ctagaattaa atacctttgg caattcattg tctcatggca tctatgggaa - 4501 acagacaacc ttcaagcaaa ccgagtttac aaatattaaa agcaacacca aaaaacacat - 4561 tgcacttatc aataaagaca actcatggat gatatcatta aaaatactag gaattaagag - 4621 agatgagtat actgtctgtt ttgaagattt ctctctaata agaccgccaa catatgtagc - 4681 catacatcct ctacttataa aaaaagtaaa atctggaaac tttatagtag tgaaagaaat - 4741 aaagaaatct atccctggtt gcactgtata ttatcattaa tagcaagccc ctcattatta - 4801 tgaggggctc atggttattt taacaatcca ctatcgatat ctttttgcac cagagcgccc - 4861 tctcgtttac gtctgtcaga cattccatca acaatattat taaaagcatt tacaaggcca - 4921 ttccagtctt ttgcgataac tttattccat actgtgggag cagttctgga taacttaaac - 4981 cctttttgat atccaataga caccagtgct gtacgggttc tcaacggtaa atcgctgaac - 5041 cgaagaccga tattagcgtc attgaaaaga ccttcaatct tatgtgagaa tttatcaata - 5101 taaatattag ataagagatg agcttcatta tcagaaagcg tcagaggtgc tgttctcact - 5161 ttatcataag cctccttccc tcgaagcata taatacccat caagtctatc tgcaatatac - 5221 tgagggacac cgtcattcaa taaatcctgt ttgcttcgct gaccaaggtc aaccccggaa - 5281 ccgaatgtaa caccggtact gttaaaataa tcgctactag gattagacgg aaaatgactt - 5341 gtcggattaa acccttcaaa accattactg gagaaaatat cgtggtcaac aatatttacc - 5401 gaacgacgta aaaattcctt cagttgacta atattgtcaa agttaatgac agtgttgtcc - 5461 gctaggacga tgcgatttcg gttattattc agaatgtctt cgttctcttt cttatcgaga - 5521 tgttcaatag attcggcaat cgttccctca agaaccatga cacggtagac tttcacaccg - 5581 tctttttcct gacctgtttc aacagttatt ttctgttcgt aagacacggt cccttcagtt - 5641 tttgaaattt tactttcctg gcggatctta tttgaatatt cactgtcttt ctccatctcc - 5701 gtatcaatcg gaaaccccat aatgtacatc agtttaaaat tactccggcc aggcagatcc - 5761 acataatgtg gtaatgcaat tgtaatcgaa ttagcttcaa aatttggtct gtaactgctt - 5821 aatgtacttc cggaaaagag aaaagccgga acaccacctg aaccattcac taccattgta - 5881 tctgacataa aaattcctct ttaacacata aaaaaaacaa taagttaaaa aaatactgta - 5941 cataaaagca ctgtttttat gtacagtaat aaaattacgc cgctttattt tctctgtcaa - 6001 taatatgaaa tttcattttt gtgatctgaa tcactcttat aaaaatcagg aagggaagat - 6061 tcgcagcaga aaaacagcac cgggtaacat cagaaaaaaa cagaaaggag ataacgtgag - 6121 caaaacaaaa tctggtcgcc accgactgag caaaacagac aaacgcctgc tggctgcact - 6181 tgtcgttgcc ggatacgaag aacggacagc ccgtgacctc atccagaaac acgtttacac - 6241 actgacacag gccgacctgc gccatctggt cagtgaaatc agtaacggtg tgggacagtc - 6301 acaggcctac gatgcgattt accaggcgag acgcattcgt ctcgcccgta aatacctgag - 6361 cggaaaaaaa ccggaagggg tggaaccccg ggaagggcag gaacgggaag atttaccata - 6421 actcccgtta tcagtaccat cggctcaacg ctcgttgtcg gatctgaaaa attcgctcaa - 6481 aagatcatat ttccctggat attttccacc gtttcttatg tgagaaaagt cacataattc - 6541 tgtcagacga cgagaaaacg gatatcgatt attgtttaat atttttacat tattaaaaat - 6601 gaaattagat aatcagatac aaataatatg ttttcgttca tgcagagaga ttaagggtgt - 6661 ctaatgaaga aaagttctat tgtggcaacc attataacta ttctgtccgg gagtgctaat - 6721 gcagcatcat ctcagttaat accaaatata tcccctgaca gctttacagt tgcagcctcc - 6781 accgggatgc tgagtggaaa gtctcatgaa atgctttatg acgcagaaac aggaagaaag - 6841 atcagccagt tagactggaa gatcaaaaat gtcgctatcc tgaaaggtga tatatcctgg - 6901 gatccatact catttctgac cctgaatgcc agggggtgga cgtctctggc ttccgggtca - 6961 ggtaatatgg atgactacga ctggatgaat gaaaatcaat ctgagtggac agatcactca - 7021 tctcatcctg ctacaaatgt taatcatgcc aatgaatatg acctcaatgt gaaaggctgg - 7081 ttactccagg atgagaatta taaagcaggt ataacagcag gatatcagga aacacgtttc - 7141 agttggacag ctacaggtgg ttcatatagt tataataatg gagcttatac cggaaacttc - 7201 ccgaaaggag tgcgggtaat aggttataac cagcgctttt ctatgccata tattggactt - 7261 gcaggccagt atcgcattaa tgattttgag ttaaatgcat tatttaaatt cagcgactgg - 7321 gttcgggcac atgataatga tgagcactat atgagagatc ttactttccg tgagaagaca - 7381 tccggctcac gttattatgg taccgtaatt aacgctggat attatgtcac acctaatgcc - 7441 aaagtctttg cggaatttac atacagtaaa tatgatgagg gcaaaggagg tactcagatc - 7501 attgataaga atagtggaga ttctgtctct attggcggag atgctgccgg tatttccaat - 7561 aaaaattata ctgtgacggc gggtctgcaa tatcgcttct gaaaaataca gatcatatct - 7621 ctcttttcat cctcccctag cggggaggat gtctgtggaa aggaggttgg tgtttgacca - 7681 accttcagat gtgtgaaaaa tcaccttttt caccataatg acggggcgct cattctgttg - 7741 ttttgccttg acattctcca cgtctttcag ggcatggaga aggtcaaatt agacatggaa - 7801 cgctactctc cttcctgtag gaagctcaac atccaagctt aatttgcctc ccattgcttc - 7861 aacgtaacgc tttaacgtcg ccagctttaa atcatttccg cgctgctcca gctttgttac - 7921 tgctggctgg cttataccca tcgcctcagc aacttgtttt tgtgataact ggagttcttc - 7981 acgcatcatc tgcaagccga cctcaagaat catctcatct gccatttctt taattcgtgt - 8041 ctggctttca ggtgaacgac tggcaatcac ctcatctaat gttctcatta cttgctctcc - 8101 agtgtgttca gatgtgctgt aaattcatcc tcagctatac gcaccagttt ttcataaaac - 8161 cgcttatcat tacttttatc tcctgcacaa agaacgatag cccgacgaat cggatcgaac - 8221 gcataaaagg ctcttatcgg acggccagaa aactgaacgc gaagctcttt catatttttg - 8281 taccgagaac ctttcacggt atcggcatat ggcctgggta actcaggtcc gtaaacctgt - 8341 agctttttca aatcagccaa aaccttttcc tgaagagcgt cttcttgctc atttagccag - 8401 tcgtcaaatc gctggctaaa aagtaccatc cacatgctca accctataac ctgtagctta - 8461 ccccactaac aatataacct acgagttata ttttcaagaa aagctggcta tttaacataa - 8521 cggcaatttg tacgcaccac tgaaatgcgt tcagcgcgat cacggcaaca gacaggcaaa - 8581 aatagcaaca aacctcccga aaaaccgccg cgatcgcgcc tgataaattt taaccttatg - 8641 catatctatg cagccaggcg aatcacgaac gaattgcctg cctgatgtaa ctgaaacggg - 8701 tgttttttcc tgatttggtg ggcgtggaag acggaacatg aacgggaaaa cagaattcat - 8761 gccagatgag cgcgatctgg caattaaggc aaaacacagc aacaaagaca cgccagaatc - 8821 gcgcccggat atgttttaac gcgattttca gactcagaca aattcagcag aatgctactc - 8881 cattcaccgg gctgatggtg aatacatgcg tatccaggat gagtacattt ctggctctgc - 8941 cacagctctg tctgttggca gctttcgcct gtccggaaac ctgcttaaaa cgctcccgaa - 9001 aggcctctga accagaaagc aacaaaacac aggccattaa gtaaatcgcg ttaaaacacg - 9061 tctgatggat tgctgcaaaa aaaagtccct aatggagcag ggactgttaa acccagtgaa - 9121 tagcgtctaa attaaagtaa gaatacgacc aggtactctt cagaaaagag attaatccac - 9181 cgcacagaat aatcaacagt aaaaacaaac aaccctgatt ttttattttt ctttttttcg - 9241 ataaaaacaa aattaaagaa ataattaatc agaacattcc ttaacttcag ggcattgcct - 9301 gtgttccatt ttgtgattag tctgaaactt ccgaaggtgg ataacacccg gtattttttt - 9361 gctcacataa agcccctcct tcaggcagag gggctttttc tttgccacca cataaaaaag - 9421 gccctcacag gaggtgttct gtgagggcgt atgataagga ctgaatcgat ggttaatatg - 9481 tctagtcctg acttttgcat ctccgaatat aaaaccctgt ttaacggcat gcaaaaccaa - 9541 aaaataaaaa tgtgacatcg caatgccaga taatattgac gcatgaggga atgcgtaccc - 9601 cgacccctg -// diff --git a/file_keep/chart/file/3200210232021637.fasta b/file_keep/chart/file/3200210232021637.fasta deleted file mode 100644 index b9db7a9..0000000 --- a/file_keep/chart/file/3200210232021637.fasta +++ /dev/null @@ -1,162 +0,0 @@ ->NC_005816.1 Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence -TGTAACGAACGGTGCAATAGTGATCCACACCCAACGCCTGAAATCAGATCCAGGGGGTAA -TCTGCTCTCCTGATTCAGGAGAGTTTATGGTCACTTTTGAGACAGTTATGGAAATTAAAA -TCCTGCACAAGCAGGGAATGAGTAGCCGGGCGATTGCCAGAGAACTGGGGATCTCCCGCA -ATACCGTTAAACGTTATTTGCAGGCAAAATCTGAGCCGCCAAAATATACGCCGCGACCTG -CTGTTGCTTCACTCCTGGATGAATACCGGGATTATATTCGTCAACGCATCGCCGATGCTC -ATCCTTACAAAATCCCGGCAACGGTAATCGCTCGCGAGATCAGAGACCAGGGATATCGTG -GCGGAATGACCATTCTCAGGGCATTCATTCGTTCTCTCTCGGTTCCTCAGGAGCAGGAGC -CTGCCGTTCGGTTCGAAACTGAACCCGGACGACAGATGCAGGTTGACTGGGGCACTATGC -GTAATGGTCGCTCACCGCTTCACGTGTTCGTTGCTGTTCTCGGATACAGCCGAATGCTGT -ACATCGAATTCACTGACAATATGCGTTATGACACGCTGGAGACCTGCCATCGTAATGCGT -TCCGCTTCTTTGGTGGTGTGCCGCGCGAAGTGTTGTATGACAATATGAAAACTGTGGTTC -TGCAACGTGACGCATATCAGACCGGTCAGCACCGGTTCCATCCTTCGCTGTGGCAGTTCG -GCAAGGAGATGGGCTTCTCTCCCCGACTGTGTCGCCCCTTCAGGGCACAGACTAAAGGTA -AGGTGGAACGGATGGTGCAGTACACCCGTAACAGTTTTTACATCCCACTAATGACTCGCC -TGCGCCCGATGGGGATCACTGTCGATGTTGAAACAGCCAACCGCCACGGTCTGCGCTGGC -TGCACGATGTCGCTAACCAACGAAAGCATGAAACAATCCAGGCCCGTCCCTGCGATCGCT -GGCTCGAAGAGCAGCAGTCCATGCTGGCACTGCCTCCGGAGAAAAAAGAGTATGACGTGC -ATCTTGATGAAAATCTGGTGAACTTCGACAAACACCCCCTGCATCATCCACTCTCCATCT -ACGACTCATTCTGCAGAGGAGTGGCGTGATGATGGAACTGCAACATCAACGACTGATGGC -GCTCGCCGGGCAGTTGCAACTGGAAAGCCTTATAAGCGCAGCGCCTGCGCTGTCACAACA -GGCAGTAGACCAGGAATGGAGTTATATGGACTTCCTGGAGCATCTGCTTCATGAAGAAAA -ACTGGCACGTCATCAACGTAAACAGGCGATGTATACCCGAATGGCAGCCTTCCCGGCGGT -GAAAACGTTCGAAGAGTATGACTTCACATTCGCCACCGGAGCACCGCAGAAGCAACTCCA -GTCGTTACGCTCACTCAGCTTCATAGAACGTAATGAAAATATCGTATTACTGGGGCCATC -AGGTGTGGGGAAAACCCATCTGGCAATAGCGATGGGCTATGAAGCAGTCCGTGCAGGTAT -CAAAGTTCGCTTCACAACAGCAGCAGATCTGTTACTTCAGTTATCTACGGCACAACGTCA -GGGCCGTTATAAAACGACGCTTCAGCGTGGAGTAATGGCCCCCCGCCTGCTCATCATTGA -TGAAATAGGCTATCTGCCGTTCAGTCAGGAAGAAGCAAAGCTGTTCTTCCAGGTCATCGC -TAAACGTTACGAAAAGAGCGCAATGATCCTGACATCCAATCTGCCGTTCGGGCAGTGGGA -TCAAACGTTCGCCGGTGATGCAGCACTGACCTCAGCGATGCTGGACCGTATCTTACACCA -CTCACATGTCGTTCAAATCAAAGGAGAAAGCTATCGACTCAGACAGAAACGAAAGGCCGG -GGTTATAGCAGAAGCTAATCCTGAGTAAAACGGTGGATCAATATTGGGCCGTTGGTGGAG -ATATAAGTGGATCACTTTTCATCCGTCGTTGACACCCTGATGAATTCACGTGTTCACGCC -TGAATAACAAGAATGCCGGAGATACGCAGTCATATTTTTTACACAATTCTCTAATCCCGA -CAAGGTCGTAGGTCGTTATAGGAAAATTCTTAGCACCATTCCGGAACAATCAGAACAGCA -GGCCATGAACGACTGACAACATTACGAATATAAAAAACGCACCCGGGCCAGACATTCCCC -CTACTGATTAAACCAGCCGGACTTGTCCACGGAACGGTCTTTTTAAACCGACACACAGTC -TGAGTACAGATACATGTCACGATGATGCAGGATTAGCGGAAGAGTGTGAGCACGTTTCCG -GGAACTGTGGTGAACCATAGCTCAATATTCGAGTGAGGGCATACCGGAAACGCGCTCAGA -TTCGTTGTAACGCGATTTTCCGTACCGGGCAATTTTTTCAGTTGTTTTTTCGTTTCATGT -CGTCAGAAACGTTCTGAGCGCGTTTCCGGCATCTGATGCTACGCAAACCATCCCCATGGT -CAGTTGACAGCCGGAAACACGCGGGTGTCGTTTTAGCGTATCGACGGGACGGCGTCGAGA -AGCACAAAAAACAGATGTTGTACTCAGTCAGTTGTTTTACAGACAGCACTGCGGCAGATT -GAAAAAGTACCGTACTTTCAGGAATGTCCAGAAACCATGTGTCAGACTTCGTTCTCCCCC -TTCCGGGTGAATTTTTTTGTCATCCGTTCAGGAATCTCTTTATAACGATTACTCCATTTC -AGGATTTTTTATGTGGCGTTTACTACAGGCAGGATATTCAAAGGCAAAAAAATCCCCCGG -AACAGGCGGAACCCGGACAGGGGGAGAACGAATCGCTAAATAATTTTCGTAGTTGTATTT -CCCATCGTTGCTACTGCAACGGGATGAATTTGCCGCAGTTTATCCTGTAAAACAATCCTG -ATTTACTCACACTCCACATATCACTGACGGAGCACAACGGAATAGTGAACAAACAACAAC -AAACTGCGCTGAATATGGCGCGATTTATCAGAAGCCAGAGCCTGATACTGCTTGAAAAAC -TGGATGCTCTGGATGCCGACGAGCAGGCGGCCATGTGTGAACGACTGCACGAACTCGCGG -AAGAACTCCAGAACAGCATCCAGGCTCGCTTTGAAGCCGAAAGTGAAACAGGAACATAAC -GAAGCTCCCGGAGACGGTCACAGCTTGTCTGTGAACGGATGCCGGGAGCAGACAAGCCCG -TCAGGGCGCGTCAGCGGGTTTTAGCGGGTGTCGGGGCGCAGCCATGACCCAGTCACGTAG -CGATAGCGGAGTGTATACTGGCTTAGTCATGCGGCATCAGTGCGGATTGTATGAAAAGTG -CACCATGTACGGTGTGAAATGCCGCACAGATGCGTAAGGAGAACATGCAGATGCCGATGC -TCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTG -TCTGCTCACTCAAAAGCGGTGATACTGTTATCCACACAATCAGGGGATAACGCCGGAAAG -AACATGTGAGCAAAAAACGAAGACCCCAGAAAAGGCCGCGCCGGAGGCGCTTTTTCCATA -GGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACC -CGACAGGACTTAAAGATACCAGGCGTTTCCCCCCGGAAGCTCCCTCGTGCGCTCTCCTGT -TCCGACCCTGCCGCTTACCGGATACCTCTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCT -TTCTCATAGCTCACGCTGTTGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGG -CTGTGTGCACGAACCCCCCGTTCAGCCCGACCACTGCGCCTTATCCGGTAACTATCGTCT -TGAGTCCAACCCGGTAAGACACGACTTTACGCCACTGGCAGCAGCCATTGGTAACTGAAA -AGTGGATTTAGATACGCAGAACTCTTGAAGTTGAAGCCTTATCGCGGCTACACTGAAAGG -ACAGCATTTGGTATCTGTGCTCCACTTAAGCCAGCTACCACAGGTTAGAAAGCCTGAGAA -ACTTCTAACCTTCGAAAGAACCCACGCCTGAGAACGTGGGTTTTTTCGTTTACAGGCAGC -AGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACTGAATTGC -GCTCCCGATCAGTTCAGCAGAAGATTATGATGGGGTTCTATGGGTATTGCTGCGGTAACA -CCCATGTTACTTGAGGTTGTATGTAGTCTGTGTAGAATTATACACATAAGGCTTAAACTG -CTCTTTTTTTTCAATATGCAATTGGAAGTTCATTGACTACATAAATAGATTATTCCAAAT -AATTTATTTATGTAAGAACAGGATGGGAGGGGGAATGATCTCAAAGTTATTTTGCTTGGC -TCTCATATTTTTATCATCAAGTGGCCTTGCAGAAAAAAACACATATACAGCAAAAGACAT -CTTGCAAAACCTAGAATTAAATACCTTTGGCAATTCATTGTCTCATGGCATCTATGGGAA -ACAGACAACCTTCAAGCAAACCGAGTTTACAAATATTAAAAGCAACACCAAAAAACACAT -TGCACTTATCAATAAAGACAACTCATGGATGATATCATTAAAAATACTAGGAATTAAGAG -AGATGAGTATACTGTCTGTTTTGAAGATTTCTCTCTAATAAGACCGCCAACATATGTAGC -CATACATCCTCTACTTATAAAAAAAGTAAAATCTGGAAACTTTATAGTAGTGAAAGAAAT -AAAGAAATCTATCCCTGGTTGCACTGTATATTATCATTAATAGCAAGCCCCTCATTATTA -TGAGGGGCTCATGGTTATTTTAACAATCCACTATCGATATCTTTTTGCACCAGAGCGCCC -TCTCGTTTACGTCTGTCAGACATTCCATCAACAATATTATTAAAAGCATTTACAAGGCCA -TTCCAGTCTTTTGCGATAACTTTATTCCATACTGTGGGAGCAGTTCTGGATAACTTAAAC -CCTTTTTGATATCCAATAGACACCAGTGCTGTACGGGTTCTCAACGGTAAATCGCTGAAC -CGAAGACCGATATTAGCGTCATTGAAAAGACCTTCAATCTTATGTGAGAATTTATCAATA -TAAATATTAGATAAGAGATGAGCTTCATTATCAGAAAGCGTCAGAGGTGCTGTTCTCACT -TTATCATAAGCCTCCTTCCCTCGAAGCATATAATACCCATCAAGTCTATCTGCAATATAC -TGAGGGACACCGTCATTCAATAAATCCTGTTTGCTTCGCTGACCAAGGTCAACCCCGGAA -CCGAATGTAACACCGGTACTGTTAAAATAATCGCTACTAGGATTAGACGGAAAATGACTT -GTCGGATTAAACCCTTCAAAACCATTACTGGAGAAAATATCGTGGTCAACAATATTTACC -GAACGACGTAAAAATTCCTTCAGTTGACTAATATTGTCAAAGTTAATGACAGTGTTGTCC -GCTAGGACGATGCGATTTCGGTTATTATTCAGAATGTCTTCGTTCTCTTTCTTATCGAGA -TGTTCAATAGATTCGGCAATCGTTCCCTCAAGAACCATGACACGGTAGACTTTCACACCG -TCTTTTTCCTGACCTGTTTCAACAGTTATTTTCTGTTCGTAAGACACGGTCCCTTCAGTT -TTTGAAATTTTACTTTCCTGGCGGATCTTATTTGAATATTCACTGTCTTTCTCCATCTCC -GTATCAATCGGAAACCCCATAATGTACATCAGTTTAAAATTACTCCGGCCAGGCAGATCC -ACATAATGTGGTAATGCAATTGTAATCGAATTAGCTTCAAAATTTGGTCTGTAACTGCTT -AATGTACTTCCGGAAAAGAGAAAAGCCGGAACACCACCTGAACCATTCACTACCATTGTA -TCTGACATAAAAATTCCTCTTTAACACATAAAAAAAACAATAAGTTAAAAAAATACTGTA -CATAAAAGCACTGTTTTTATGTACAGTAATAAAATTACGCCGCTTTATTTTCTCTGTCAA -TAATATGAAATTTCATTTTTGTGATCTGAATCACTCTTATAAAAATCAGGAAGGGAAGAT -TCGCAGCAGAAAAACAGCACCGGGTAACATCAGAAAAAAACAGAAAGGAGATAACGTGAG -CAAAACAAAATCTGGTCGCCACCGACTGAGCAAAACAGACAAACGCCTGCTGGCTGCACT -TGTCGTTGCCGGATACGAAGAACGGACAGCCCGTGACCTCATCCAGAAACACGTTTACAC -ACTGACACAGGCCGACCTGCGCCATCTGGTCAGTGAAATCAGTAACGGTGTGGGACAGTC -ACAGGCCTACGATGCGATTTACCAGGCGAGACGCATTCGTCTCGCCCGTAAATACCTGAG -CGGAAAAAAACCGGAAGGGGTGGAACCCCGGGAAGGGCAGGAACGGGAAGATTTACCATA -ACTCCCGTTATCAGTACCATCGGCTCAACGCTCGTTGTCGGATCTGAAAAATTCGCTCAA -AAGATCATATTTCCCTGGATATTTTCCACCGTTTCTTATGTGAGAAAAGTCACATAATTC -TGTCAGACGACGAGAAAACGGATATCGATTATTGTTTAATATTTTTACATTATTAAAAAT -GAAATTAGATAATCAGATACAAATAATATGTTTTCGTTCATGCAGAGAGATTAAGGGTGT -CTAATGAAGAAAAGTTCTATTGTGGCAACCATTATAACTATTCTGTCCGGGAGTGCTAAT -GCAGCATCATCTCAGTTAATACCAAATATATCCCCTGACAGCTTTACAGTTGCAGCCTCC -ACCGGGATGCTGAGTGGAAAGTCTCATGAAATGCTTTATGACGCAGAAACAGGAAGAAAG -ATCAGCCAGTTAGACTGGAAGATCAAAAATGTCGCTATCCTGAAAGGTGATATATCCTGG -GATCCATACTCATTTCTGACCCTGAATGCCAGGGGGTGGACGTCTCTGGCTTCCGGGTCA -GGTAATATGGATGACTACGACTGGATGAATGAAAATCAATCTGAGTGGACAGATCACTCA -TCTCATCCTGCTACAAATGTTAATCATGCCAATGAATATGACCTCAATGTGAAAGGCTGG -TTACTCCAGGATGAGAATTATAAAGCAGGTATAACAGCAGGATATCAGGAAACACGTTTC -AGTTGGACAGCTACAGGTGGTTCATATAGTTATAATAATGGAGCTTATACCGGAAACTTC -CCGAAAGGAGTGCGGGTAATAGGTTATAACCAGCGCTTTTCTATGCCATATATTGGACTT -GCAGGCCAGTATCGCATTAATGATTTTGAGTTAAATGCATTATTTAAATTCAGCGACTGG -GTTCGGGCACATGATAATGATGAGCACTATATGAGAGATCTTACTTTCCGTGAGAAGACA -TCCGGCTCACGTTATTATGGTACCGTAATTAACGCTGGATATTATGTCACACCTAATGCC -AAAGTCTTTGCGGAATTTACATACAGTAAATATGATGAGGGCAAAGGAGGTACTCAGATC -ATTGATAAGAATAGTGGAGATTCTGTCTCTATTGGCGGAGATGCTGCCGGTATTTCCAAT -AAAAATTATACTGTGACGGCGGGTCTGCAATATCGCTTCTGAAAAATACAGATCATATCT -CTCTTTTCATCCTCCCCTAGCGGGGAGGATGTCTGTGGAAAGGAGGTTGGTGTTTGACCA -ACCTTCAGATGTGTGAAAAATCACCTTTTTCACCATAATGACGGGGCGCTCATTCTGTTG -TTTTGCCTTGACATTCTCCACGTCTTTCAGGGCATGGAGAAGGTCAAATTAGACATGGAA -CGCTACTCTCCTTCCTGTAGGAAGCTCAACATCCAAGCTTAATTTGCCTCCCATTGCTTC -AACGTAACGCTTTAACGTCGCCAGCTTTAAATCATTTCCGCGCTGCTCCAGCTTTGTTAC -TGCTGGCTGGCTTATACCCATCGCCTCAGCAACTTGTTTTTGTGATAACTGGAGTTCTTC -ACGCATCATCTGCAAGCCGACCTCAAGAATCATCTCATCTGCCATTTCTTTAATTCGTGT -CTGGCTTTCAGGTGAACGACTGGCAATCACCTCATCTAATGTTCTCATTACTTGCTCTCC -AGTGTGTTCAGATGTGCTGTAAATTCATCCTCAGCTATACGCACCAGTTTTTCATAAAAC -CGCTTATCATTACTTTTATCTCCTGCACAAAGAACGATAGCCCGACGAATCGGATCGAAC -GCATAAAAGGCTCTTATCGGACGGCCAGAAAACTGAACGCGAAGCTCTTTCATATTTTTG -TACCGAGAACCTTTCACGGTATCGGCATATGGCCTGGGTAACTCAGGTCCGTAAACCTGT -AGCTTTTTCAAATCAGCCAAAACCTTTTCCTGAAGAGCGTCTTCTTGCTCATTTAGCCAG -TCGTCAAATCGCTGGCTAAAAAGTACCATCCACATGCTCAACCCTATAACCTGTAGCTTA -CCCCACTAACAATATAACCTACGAGTTATATTTTCAAGAAAAGCTGGCTATTTAACATAA -CGGCAATTTGTACGCACCACTGAAATGCGTTCAGCGCGATCACGGCAACAGACAGGCAAA -AATAGCAACAAACCTCCCGAAAAACCGCCGCGATCGCGCCTGATAAATTTTAACCTTATG -CATATCTATGCAGCCAGGCGAATCACGAACGAATTGCCTGCCTGATGTAACTGAAACGGG -TGTTTTTTCCTGATTTGGTGGGCGTGGAAGACGGAACATGAACGGGAAAACAGAATTCAT -GCCAGATGAGCGCGATCTGGCAATTAAGGCAAAACACAGCAACAAAGACACGCCAGAATC -GCGCCCGGATATGTTTTAACGCGATTTTCAGACTCAGACAAATTCAGCAGAATGCTACTC -CATTCACCGGGCTGATGGTGAATACATGCGTATCCAGGATGAGTACATTTCTGGCTCTGC -CACAGCTCTGTCTGTTGGCAGCTTTCGCCTGTCCGGAAACCTGCTTAAAACGCTCCCGAA -AGGCCTCTGAACCAGAAAGCAACAAAACACAGGCCATTAAGTAAATCGCGTTAAAACACG -TCTGATGGATTGCTGCAAAAAAAAGTCCCTAATGGAGCAGGGACTGTTAAACCCAGTGAA -TAGCGTCTAAATTAAAGTAAGAATACGACCAGGTACTCTTCAGAAAAGAGATTAATCCAC -CGCACAGAATAATCAACAGTAAAAACAAACAACCCTGATTTTTTATTTTTCTTTTTTTCG -ATAAAAACAAAATTAAAGAAATAATTAATCAGAACATTCCTTAACTTCAGGGCATTGCCT -GTGTTCCATTTTGTGATTAGTCTGAAACTTCCGAAGGTGGATAACACCCGGTATTTTTTT -GCTCACATAAAGCCCCTCCTTCAGGCAGAGGGGCTTTTTCTTTGCCACCACATAAAAAAG -GCCCTCACAGGAGGTGTTCTGTGAGGGCGTATGATAAGGACTGAATCGATGGTTAATATG -TCTAGTCCTGACTTTTGCATCTCCGAATATAAAACCCTGTTTAACGGCATGCAAAACCAA -AAAATAAAAATGTGACATCGCAATGCCAGATAATATTGACGCATGAGGGAATGCGTACCC -CGACCCCTG diff --git a/file_keep/chart/file/5140330442021126 b/file_keep/chart/file/5140330442021126 deleted file mode 100644 index 96e57e5..0000000 --- a/file_keep/chart/file/5140330442021126 +++ /dev/null @@ -1,89 +0,0 @@ -HMMER： -在线使用：https://www.ebi.ac.uk/Tools/hmmer/search/phmmer -下载：http://hmmer.janelia.org/static/binaries/hmmer3.0_windows.zip（将网址放在迅雷网盘进行下载，该文件含有readme.txt可参考使用） - -功能：用于搜索同源蛋白序列以及蛋白序列对位排序，比如从序列数据库中，找同源的序列，或者对一个一个新的基因功能进行鉴定，使用hmmer比使用blast有着更高的灵敏度和更高的搜索速度，HMMER的程序如下，注意每个程序都是输出文件在前面，输入文件在后面 -phmmer:功能：与Blastp类似，使用一个蛋白质序列搜索蛋白质序列库 -格式：phmmer [-options] -输入：你要检测的fasta格式的序列和你要搜索的数据库 -输出匹配的序列和特征：含有score,Taxonomy,Domain,Download -参数：输入的文件格式为fasta格式，蛋白质序列库常用的包括Reference Proteomes,UniProtKB,SwissProt,PDB,Ensembl,输出格式包括tblout、domtblout等，蛋白质数据库需要下载 -jackhmmer:功能：与psiBlast类似，蛋白质序列迭代搜索蛋白质序列库 -格式：jackhmmer [-options] -输入：你要检测的fasta格式的序列和你要搜索的数据库 -输出：匹配的序列及特征，含有score,Taxonomy,Domain,Download -参数：输入的文件格式为fasta格式，蛋白质序列库常用的有Reference Proteomes,UniProtKB,SwissProt,PDB,Ensembl，蛋白质数据库需要下载 -hmmalign:功能 多重序列比对 -格式： hmmalign [-options] -输入：输入是fasta文件 -输出：Stockholm 格式的多重序列比对文件 -参数：输入文件序列格式包括FASTA、EMBL、GenBank、UniProt -输出比对文件格式包括Stockholm、Pfam、A2M、PSIBLAST -hmmbuild:功能：建立参考数据的隐马尔可科夫模型 -格式： hmmbuild [-options] -输入：多重序列比对的文件（Stockholm file） -输出：建立的这些多重序列比对的隐马尔可科夫模型 -参数：输入文件支持很多生物数据格式如：CLUSTALW, SELEX, GCG MSF -输出文件命名时的后缀为.hmm -hmmscan:使用序列搜索HMM库 -格式： hmmscan [-options] -输入：hmm数据库和查询序列文件 -输出：含有Score和Download，hmm数据库所匹配的序列 -参数：HMM数据库有Pfam,TIGRFAM,Gene3D,Superfamily,PIRSF,TreeFam -hmmsearch:功能：在数据库中寻找已经建立好的模体） -格式： hmmsearch [options] -输入：建立好的参考数据模型、要搜索的数据库 -输出：输出结果 -参数：比较序列文件可以是FASTA、EMBL/UniProt、Genbank格式 -输出选项： --o：直接输出结果到文件，不是标准输出 ---tblout：tblout格式输出 ---domtblout：domtblout格式输出 ---pfamtblout：pfamtblout格式输出 -输出结果中分为两类，一类是针对序列的（full sequence），另一类是针对domain的（主要基于一条序列存在多个domain）。 -结果按照E-values值从小到大排序，形式与blast类似。 -其中target name是每个目标序列的名称； -query name是查询序列的名称； -score是比对得分，分值越高说明越相似； -E-value目标序列的期望值（统计意义）； -最重要的是E-value值，值越小，越可信，相当于一个统计量。 -hmmsim：功能没找到 -格式： hmmsim [-options] -输入：hmm格式的文件 -输出：以sequence为名的一行（2.out） -hmmstat:显示HMM数据库的统计信息 -格式： hmmstat [-options] -输入：hmm格式的文件 -输出：有idx为名的那一行，含有name,accession,nseq,eff_nseq,M,relent,info,p relE,compKL -输出显示：# hmmstat :: display summary statistics for a profile file -# HMMER 3.0 (March 2010); http://hmmer.org/ -# Copyright (C) 2010 Howard Hughes Medical Institute. -# Freely distributed under the GNU General Public License (GPLv3). -# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -# -# idx name accession nseq eff_nseq M relent info p relE compKL -# ---- -------------------- ------------ -------- -------- ------ ------ ------ ------ ------ -1 sequence - 1 0.39 172 0.59 0.59 0.51 0.03 -hmmconvert:功能：转换HMM格式 -格式：hmmconvert [-options] -输入：hmm格式的文件 -输出：hmm格式转换后的文件 -hmmemit:功能：从HMM模型中，得到一个模式序列 -格式： hmmemit [-options] -输入：hmm格式的文件 -输出：模式序列 -输出显示：>sequence-sample1 -IQYNNDSKLYLSLTRGVFKSSKVLAQVSKPPGIDTGTIHTTRRKRIVVDSETKSHELLDT -AGDRYFSFDDYLRRATTLVFLFALNRLRHFRKRNTLCEKIMELHGGDNFPNMLVKSEVSD -QISELDSEQCSLKPLGNAYKIPHVLAGNDVSKENDTGVLQLVRTIRQYIVRTGP -hmmfetch:功能：通过名字或者接受号从HMM库中取回一个HMM模型 -格式： hmmfetch [options] (retrieves HMM named ) -hmmfetch [options] -f (retrieves all HMMs in ) -hmmfetch [options] --index (indexes ) -输入：hmm文件和HMM模型的名字或接受号 -输出：为这个名字或接受号的HMM模型 -hmmpress:格式化HMM数据库，包括压缩和创建索引，以便于hmmscan搜索使用 -格式：hmmpress [-options] -输入：hmm格式的文件 -输出：可获得H3F格式的文件，H3I格式的文件，H3M格式的文件，H3P格式的文件 - diff --git a/file_keep/chart/file/5140430432021117 b/file_keep/chart/file/5140430432021117 deleted file mode 100644 index 6b6eb82..0000000 --- a/file_keep/chart/file/5140430432021117 +++ /dev/null @@ -1,45 +0,0 @@ -# blast - -## 建立数据库 - -```shell -makeblastdb -in Arabidopsis_thaliana.TAIR10.dna.toplevel.fa -dbtype nucl -out TAIR10 -parse_seqids - --in # 输入文件 --dbtype # 类型 nucl 核酸 prot 蛋白 --out # 输出文件位置和名字 --parse_seqids # -``` - -## 比对 - -``` -blastn -``` - --query: 检索文件 - --query_loc : 指定检索的位置 - --strand： 搜索正义链还是反义链，还是都要 - -out : 输出文件 - --remote： 可以用NCBI的远程数据库， 一般与 -db nr - --evalue 科学计数法，比如说1e3，定义期望值阈值。E值表明在随机的情况下，其它序列与 - - - - - - - - - - - - - -### 比对 - diff --git a/file_keep/chart/img/8180000562021492.pdf b/file_keep/chart/img/8180000562021492.pdf deleted file mode 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