34个参数完成，7个未成功，2个删除。
This commit is contained in:
fy3047957834
@@ -12,25 +12,31 @@ def keep_txt_to_file(code, script_path):
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f.write(code)
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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",
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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",
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title="chart", dpi=100, width=10, height=6, title_font_size=12, ):
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midwest = pd.read_csv(file_path) # 导入文件
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plt.figure(figsize=(width, height), dpi=dpi, facecolor='w', edgecolor='k')
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plt.figure(figsize=(int(width), int(height)), dpi=int(dpi), facecolor='w', edgecolor='k')
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categories = np.unique(midwest[group_by_column])
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group_by_column = np.unique(midwest[group_by_column])
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colors = [
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plt.cm.Set1(i / float(len(group_by_column) - 1)) for i in range(len(group_by_column))
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plt.cm.Set1(i / float(len(categories) - 1)) for i in range(len(categories))
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]
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for i, category in enumerate(group_by_column):
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plt.scatter(midwest.keys()[0],
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midwest.keys()[1],
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data=midwest.loc[midwest[midwest.keys()[2]] == category, :],
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for i, category in enumerate(categories):
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plt.scatter(x_column_name,
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y_column_name,
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data=midwest.loc[midwest.category == category, :],
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s=20,
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c=colors[i],
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color=colors[i],
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label=str(category))
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plt.gca().set(
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xlim=(0.0, 0.1),
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ylim=(0, 90000),
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)
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# xy轴的刻度
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plt.xticks(rotation=x_scale_font_angle, fontsize=10)
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plt.yticks(rotation=y_scale_font_angle, fontsize=10)
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@@ -53,7 +59,7 @@ def scatter_plot(file_path, chart_out_path, out_path, x_scale_font_angle, y_scal
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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,
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title, title_font_size, x_scale_font_angle, y_scale_font_angle, x_name, y_name, color):
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title, title_font_size, x_name, y_name, color):
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df = pd.read_csv(file_path)
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group_by_range = [group_by_range.split("-")[0], group_by_range.split("-")[1]]
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df_select = df.loc[df[group_by_column].isin(group_by_range), :]
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@@ -73,9 +79,6 @@ def Each_regression_line_in_its_own_column(file_path, chart_out_path, out_path,
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plt.title(title, fontsize=int(title_font_size))
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plt.savefig(f"{chart_out_path}") # 保存图片
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plt.xticks(rotation=x_scale_font_angle, fontsize=10)
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plt.yticks(rotation=y_scale_font_angle, fontsize=10)
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# xy轴的名称
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plt.xlabel(x_name, fontdict={'fontsize': 10})
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plt.ylabel(y_name, fontdict={'fontsize': 10})
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@@ -86,7 +89,7 @@ def Each_regression_line_in_its_own_column(file_path, chart_out_path, out_path,
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def Jittering_with_stripplot(file_path, chart_out_path, out_path, x_column_name, y_column_name,
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title, title_font_size, x_scale_font_angle, y_scale_font_angle, x_name, y_name, color):
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title, title_font_size, x_name, y_name, color):
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df = pd.read_csv(file_path)
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fig, ax = plt.subplots(figsize=(5, 3), dpi=180)
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print(fig, ax)
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@@ -105,9 +108,6 @@ def Jittering_with_stripplot(file_path, chart_out_path, out_path, x_column_name,
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plt.legend(fontsize=10)
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plt.xticks(rotation=x_scale_font_angle, fontsize=10)
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plt.yticks(rotation=y_scale_font_angle, fontsize=10)
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# xy轴的名称
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plt.xlabel(x_name, fontdict={'fontsize': 10})
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plt.ylabel(y_name, fontdict={'fontsize': 10})
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@@ -118,7 +118,7 @@ def Jittering_with_stripplot(file_path, chart_out_path, out_path, x_column_name,
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def Marginal_Histogram(file_path, chart_out_path, out_path, x_column_name, y_column_name,
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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'):
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title, x_name, y_name, chart_bar_x_color='#0078d4', chart_bar_y_color='#098154'):
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df = pd.read_csv(file_path)
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# Create Fig and gridspec
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@@ -156,8 +156,6 @@ def Marginal_Histogram(file_path, chart_out_path, out_path, x_column_name, y_col
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orientation='horizontal',
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color=chart_bar_y_color)
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ax_main.title.set_fontsize(fontsize=int(title_font_size))
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ax_main.set(title=title,
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xlabel=x_name,
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ylabel=y_name)
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@@ -173,16 +171,13 @@ def Marginal_Histogram(file_path, chart_out_path, out_path, x_column_name, y_col
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plt.legend(fontsize=10)
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plt.xticks(rotation=x_scale_font_angle, fontsize=10)
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plt.yticks(rotation=y_scale_font_angle, fontsize=10)
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plt.savefig(f"{out_path}.png")
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plt.savefig(f"{out_path}.svg")
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plt.savefig(f"{out_path}.pdf")
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def Correllogram(file_path, chart_out_path, out_path,
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title, title_font_size, x_scale_font_angle, y_scale_font_angle, x_name, y_name, font_size, font_color, weight):
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title, title_font_size, font_size, font_color, weight):
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df = pd.read_csv(file_path)
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plt.figure(figsize=(9.4, 4.25), dpi=200)
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sns.heatmap(
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@@ -204,13 +199,6 @@ def Correllogram(file_path, chart_out_path, out_path,
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plt.legend(fontsize=10)
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plt.xticks(rotation=x_scale_font_angle, fontsize=10)
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plt.yticks(rotation=y_scale_font_angle, fontsize=10)
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# xy轴的名称
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plt.xlabel(x_name, fontdict={'fontsize': 10})
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plt.ylabel(y_name, fontdict={'fontsize': 10})
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plt.savefig(f"{out_path}.png")
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plt.savefig(f"{out_path}.svg")
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plt.savefig(f"{out_path}.pdf")
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@@ -375,7 +363,7 @@ def Diverging_Bars_vertical(file_path, chart_out_path, out_path, x_column_name,
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def Ordered_Bar_Chart(file_path, chart_out_path, out_path, x_column_name, y_column_name,
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title, title_font_size, x_scale_font_angle, y_scale_font_angle, x_name, y_name, color):
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title, title_font_size, y_scale_font_angle, x_name, y_name, color):
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df_raw = pd.read_csv(file_path)
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df = df_raw[[x_column_name, y_column_name]].groupby(y_column_name).apply(lambda x: x.mean())
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df.sort_values(x_column_name, inplace=True)
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@@ -393,7 +381,6 @@ def Ordered_Bar_Chart(file_path, chart_out_path, out_path, x_column_name, y_colu
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alpha=0.7,
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linewidth=20)
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plt.xticks(rotation=x_scale_font_angle, fontsize=10)
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plt.yticks(rotation=y_scale_font_angle, fontsize=10)
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# Annotate Text
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@@ -524,7 +511,7 @@ def Dot_Plot(file_path, chart_out_path, out_path, x_column_name, y_column_name,
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plt.yticks(rotation=y_scale_font_angle, fontsize=10)
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plt.ylabel(y_name, fontsize=12)
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plt.ylabel(x_name, fontsize=12)
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plt.xlabel(x_name, fontsize=12)
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plt.title(title, fontsize=int(title_font_size))
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@@ -1016,7 +1003,7 @@ def Population_Pyramid(file_path, chart_out_path, out_path,
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# 测试文件 mpg.csv
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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,
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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,
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title_font_size, title):
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df_raw = pd.read_csv(file_path)
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@@ -1033,10 +1020,10 @@ def Waffle_Chart(file_path, chart_out_path, out_path, rows_number, group_by_colu
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plots={
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'111': {
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'values':
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df[data_column],
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df['counts'],
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'labels': [
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"{0} ({1})".format(n[0], n[1])
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for n in df[[group_by_column, data_column]].itertuples()
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for n in df[[group_by_column, 'counts']].itertuples()
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],
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'legend': {
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'loc': 'upper left',
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@@ -1089,7 +1076,7 @@ def Pie_Chart(file_path, chart_out_path, out_path, y_name, title, group_by_colum
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# 测试文件 mpg.csv
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def Treemap(file_path, chart_out_path, out_path, title, group_by_column, data_column, title_font_size):
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def Treemap(file_path, chart_out_path, out_path, title, group_by_column, title_font_size):
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import squarify
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df_raw = pd.read_csv(file_path)
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@@ -1097,7 +1084,7 @@ def Treemap(file_path, chart_out_path, out_path, title, group_by_column, data_co
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# Prepare Data
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df = df_raw.groupby(group_by_column).size().reset_index(name='counts')
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labels = df.apply(lambda x: str(x[0]) + "\n (" + str(x[1]) + ")", axis=1)
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sizes = df[data_column].values.tolist()
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sizes = df['counts'].values.tolist()
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colors = [plt.cm.Set2(i / float(len(labels))) for i in range(len(labels))]
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# Draw Plot
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@@ -1490,7 +1477,7 @@ def Dendrogram(file_path, chart_out_path, out_path,
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def Composition_Bar(file_path, chart_out_path, out_path, title, caption, subtitle, x_name, y_name, title_font_size, x_font_size,
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y_font_size, x_scale_font_size, y_scale_font_size, x_scale_font_angle, y_scale_font_angle,
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x_font_color, y_font_color, x_scale_font_color, y_scale_font_color, title_font_color, background_color):
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x_font_color, y_font_color, x_scale_font_color, y_scale_font_color, title_font_color):
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code = f"""
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datas <- read.csv("{file_path}")
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@@ -1512,7 +1499,6 @@ gg <- g + geom_bar(stat="identity", width = 0.5, fill="tomato2") +
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x="{x_name}",
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y="{y_name}") +
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theme(title=element_text(size={title_font_size}, color="{title_font_color}"),
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plot.background_color = element_rect(fill="{background_color}", color="{background_color}"),
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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}),
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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}"))
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@@ -2389,7 +2375,7 @@ dev.off()
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def Distribution_Box_1(file_path, chart_out_path, out_path, title, caption, subtitle, x_name, y_name, title_font_size,
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x_font_size, y_font_size, x_scale_font_size, y_scale_font_size, x_scale_font_angle, y_scale_font_angle,
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x_font_color, y_font_color, x_scale_font_color, y_scale_font_color, title_font_color, background_color, line_color):
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x_font_color, y_font_color, x_scale_font_color, y_scale_font_color, title_font_color, line_color):
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file_path = file_path.replace("\\", "\\\\")
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code = f"""
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@@ -2410,7 +2396,6 @@ gg <- g + geom_boxplot(varwidth=T, fill="plum", color="{line_color}") +
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x="{x_name}",
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y="{y_name}") +
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theme(title=element_text(size={title_font_size}, color="{title_font_color}"),
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plot.background_color = element_rect(fill="{background_color}", color="{background_color}"),
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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}),
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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}"))
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@@ -2873,7 +2858,7 @@ dev.off()
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# 实例文件 Group_HierarchicalTree.csv
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def Group_HierarchicalTree(file_path, chart_out_path, out_path, title, caption, subtitle, title_font_size,
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title_font_color, background_color):
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title_font_color):
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file_path = file_path.replace("\\", "\\\\")
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code = f"""
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@@ -2889,8 +2874,7 @@ hc <- hclust(dist(datas), "ave") # hierarchical clustering
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gg <- ggdendrogram(hc, rotate = TRUE, size = 2) + labs(title="{title}",
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subtitle="{subtitle}",
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caption="{caption}") +
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theme(title=element_text(size={title_font_size}, color="{title_font_color}"),
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plot.background_color = element_rect(fill="{background_color}", color="{background_color}"))
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theme(title=element_text(size={title_font_size}, color="{title_font_color}"))
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png("{chart_out_path}",width=900,height=408)
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plot(gg)
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@@ -367,6 +367,7 @@ class="layui-input" style="height: 25px; width:80px;margin-top: 6px">
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else:
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fl = "hex"
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code += """
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%s = "#000000"
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layui.use('colorpicker', function()
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{
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var $ = layui.$
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@@ -384,7 +385,7 @@ class="layui-input" style="height: 25px; width:80px;margin-top: 6px">
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});
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})
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""" % (i, random_color(), fl, i + "_")
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""" % (i + '_', i, random_color(), fl, i + "_")
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return code
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BIN
db.sqlite3
BIN
db.sqlite3
Binary file not shown.
@@ -1,89 +0,0 @@
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HMMER：
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在线使用：https://www.ebi.ac.uk/Tools/hmmer/search/phmmer
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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）
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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
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phmmer:功能：与Blastp类似，使用一个蛋白质序列搜索蛋白质序列库
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格式：phmmer [-options] <query seqfile> <target seqdb>
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输入：你要检测的fasta格式的序列和你要搜索的数据库
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输出匹配的序列和特征：含有score,Taxonomy,Domain,Download
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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
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jackhmmer:功能：与psiBlast类似，蛋白质序列迭代搜索蛋白质序列库
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格式：jackhmmer [-options] <query seqfile> <target seqdb>
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输入：你要检测的fasta格式的序列和你要搜索的数据库
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输出：匹配的序列及特征，含有score,Taxonomy,Domain,Download
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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
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hmmalign:功能 多重序列比对
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格式： hmmalign [-options] <hmmfile> <seqfile>
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输入：输入是fasta文件
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输出：Stockholm 格式的多重序列比对文件
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参数：输入文件序列格式包括FASTA、EMBL、GenBank、UniProt
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输出比对文件格式包括Stockholm、Pfam、A2M、PSIBLAST
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hmmbuild:功能：建立参考数据的隐马尔可科夫模型
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格式： hmmbuild [-options] <hmmfile output> <alignment file input>
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输入：多重序列比对的文件（Stockholm file）
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输出：建立的这些多重序列比对的隐马尔可科夫模型
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参数：输入文件支持很多生物数据格式如：CLUSTALW, SELEX, GCG MSF
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输出文件命名时的后缀为.hmm
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hmmscan:使用序列搜索HMM库
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格式： hmmscan [-options] <hmm database> <query seqfile>
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输入：hmm数据库和查询序列文件
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输出：含有Score和Download，hmm数据库所匹配的序列
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参数：HMM数据库有Pfam,TIGRFAM,Gene3D,Superfamily,PIRSF,TreeFam
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hmmsearch:功能：在数据库中寻找已经建立好的模体）
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格式： hmmsearch [options] <query hmmfile> <target seqfile>
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输入：建立好的参考数据模型、要搜索的数据库
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输出：输出结果
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参数：比较序列文件可以是FASTA、EMBL/UniProt、Genbank格式
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输出选项：
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-o：直接输出结果到文件，不是标准输出
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--tblout：tblout格式输出
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--domtblout：domtblout格式输出
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--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] <hmmfile>
|
||||
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] <hmmfile>
|
||||
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] <hmmfile>
|
||||
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] <hmmfile (single)>
|
||||
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] <hmmfile> <key> (retrieves HMM named <key>)
|
||||
hmmfetch [options] -f <hmmfile> <keyfile> (retrieves all HMMs in <keyfile>)
|
||||
hmmfetch [options] --index <hmmfile> (indexes <hmmfile>)
|
||||
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] <hmmfile>
|
||||
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
|
||||
|
||||
@@ -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
|
||||
//
|
||||
@@ -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
|
||||
//
|
||||
@@ -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
|
||||
@@ -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
|
||||
//
|
||||
@@ -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
|
||||
@@ -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] <query seqfile> <target seqdb>
|
||||
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] <query seqfile> <target seqdb>
|
||||
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] <hmmfile> <seqfile>
|
||||
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] <hmmfile output> <alignment file input>
|
||||
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] <hmm database> <query seqfile>
|
||||
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] <query hmmfile> <target seqfile>
|
||||
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] <hmmfile>
|
||||
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] <hmmfile>
|
||||
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] <hmmfile>
|
||||
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] <hmmfile (single)>
|
||||
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] <hmmfile> <key> (retrieves HMM named <key>)
|
||||
hmmfetch [options] -f <hmmfile> <keyfile> (retrieves all HMMs in <keyfile>)
|
||||
hmmfetch [options] --index <hmmfile> (indexes <hmmfile>)
|
||||
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] <hmmfile>
|
||||
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
|
||||
|
||||
@@ -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
|
||||
|
||||
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Before Width: | Height: | Size: 30 KiB |
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static/img_eg/example_chart/Pairwise_Plot.png
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After Width: | Height: | Size: 147 KiB |
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static/img_eg/show_index_chart/Pairwise_Plot.png
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After Width: | Height: | Size: 147 KiB |
Reference in New Issue
Block a user