bioroebe 0.10.80

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Files changed (802) hide show
  1. checksums.yaml +7 -0
  2. data/LICENSE.md +428 -0
  3. data/README.md +9280 -0
  4. data/bin/advanced_dotplot +7 -0
  5. data/bin/align_open_reading_frames +12 -0
  6. data/bin/all_positions_of_this_nucleotide +7 -0
  7. data/bin/aminoacid_composition +7 -0
  8. data/bin/aminoacid_frequencies +12 -0
  9. data/bin/aminoacid_substitution +7 -0
  10. data/bin/automatically_rename_this_fasta_file +7 -0
  11. data/bin/base_composition +7 -0
  12. data/bin/batch_create_windows_executables +7 -0
  13. data/bin/biomart_console +11 -0
  14. data/bin/bioroebe +27 -0
  15. data/bin/bioroebe_controller +10 -0
  16. data/bin/bioshell +26 -0
  17. data/bin/blosum_2D_table +12 -0
  18. data/bin/calculate_n50_value +12 -0
  19. data/bin/chunked_display +12 -0
  20. data/bin/codon_frequency +9 -0
  21. data/bin/codon_to_aminoacid +30 -0
  22. data/bin/colourize_this_fasta_sequence +14 -0
  23. data/bin/compact_fasta_file +7 -0
  24. data/bin/complement +7 -0
  25. data/bin/complementary_dna_strand +12 -0
  26. data/bin/complementary_rna_strand +12 -0
  27. data/bin/compseq +7 -0
  28. data/bin/consensus_sequence +17 -0
  29. data/bin/count_AT +12 -0
  30. data/bin/count_GC +12 -0
  31. data/bin/create_random_aminoacids +7 -0
  32. data/bin/decode_this_aminoacid_sequence +20 -0
  33. data/bin/deduce_aminoacid_sequence +13 -0
  34. data/bin/deduce_most_likely_aminoacid_sequence +7 -0
  35. data/bin/display_aminoacid_table +12 -0
  36. data/bin/display_open_reading_frames +7 -0
  37. data/bin/dna_to_aminoacid_sequence +7 -0
  38. data/bin/dna_to_rna +7 -0
  39. data/bin/downcase_chunked_display +12 -0
  40. data/bin/download_this_pdb +7 -0
  41. data/bin/fasta_index +7 -0
  42. data/bin/fetch_data_from_uniprot +12 -0
  43. data/bin/filter_away_invalid_nucleotides +12 -0
  44. data/bin/find_substring +19 -0
  45. data/bin/genbank_to_fasta +7 -0
  46. data/bin/hamming_distance +12 -0
  47. data/bin/input_as_dna +12 -0
  48. data/bin/is_palindrome +13 -0
  49. data/bin/leading_five_prime +7 -0
  50. data/bin/levensthein +7 -0
  51. data/bin/longest_ORF +14 -0
  52. data/bin/longest_substring +12 -0
  53. data/bin/n_stop_codons_in_this_sequence +15 -0
  54. data/bin/open_reading_frames +14 -0
  55. data/bin/overwrite_fasta_header +7 -0
  56. data/bin/palindrome_2D_structure +7 -0
  57. data/bin/palindrome_generator +7 -0
  58. data/bin/parse_fasta +7 -0
  59. data/bin/partner_nucleotide +9 -0
  60. data/bin/possible_codons_for_this_aminoacid +12 -0
  61. data/bin/random_dna_sequence +12 -0
  62. data/bin/random_sequence +12 -0
  63. data/bin/raw_hamming_distance +12 -0
  64. data/bin/return_longest_substring_via_LCS_algorithm +7 -0
  65. data/bin/reverse_complement +7 -0
  66. data/bin/reverse_sequence +7 -0
  67. data/bin/ruler +12 -0
  68. data/bin/scan_this_input_for_startcodons +12 -0
  69. data/bin/short_aminoacid_letter_from_long_aminoacid_name +7 -0
  70. data/bin/show_atomic_composition +7 -0
  71. data/bin/show_codon_usage +12 -0
  72. data/bin/show_fasta_header +7 -0
  73. data/bin/show_nucleotide_sequence +7 -0
  74. data/bin/show_this_codon_table +7 -0
  75. data/bin/show_this_dna_sequence +7 -0
  76. data/bin/showorf +14 -0
  77. data/bin/simplify_fasta +7 -0
  78. data/bin/sort_aminoacid_based_on_its_hydrophobicity +7 -0
  79. data/bin/split_this_fasta_file_into_chromosomes +7 -0
  80. data/bin/strict_filter_away_invalid_aminoacids +7 -0
  81. data/bin/taxonomy +63 -0
  82. data/bin/three_to_one +7 -0
  83. data/bin/to_rna +7 -0
  84. data/bin/trailing_three_prime +7 -0
  85. data/bin/trypsin_digest +7 -0
  86. data/bin/upcase_this_aminoacid_sequence_and_remove_numbers +7 -0
  87. data/bioroebe.gemspec +97 -0
  88. data/doc/IUPAC_aminoacids_code.md +36 -0
  89. data/doc/IUPAC_nucleotide_code.md +19 -0
  90. data/doc/README.gen +9237 -0
  91. data/doc/blosum.md +5 -0
  92. data/doc/compatibility/BIO_PHP.md +37 -0
  93. data/doc/compatibility/README.md +3 -0
  94. data/doc/compatibility/emboss.md +56 -0
  95. data/doc/extensive_usage_example.md +35 -0
  96. data/doc/german_names_for_the_aminoacids.md +27 -0
  97. data/doc/instructions_for_the_taxonomy_subproject.md +504 -0
  98. data/doc/legacy_paths.md +9 -0
  99. data/doc/pdb_ATOM_entry.md +33 -0
  100. data/doc/quality_control/README.md +2 -0
  101. data/doc/quality_control/commandline_applications.md +13 -0
  102. data/doc/resources.md +23 -0
  103. data/doc/setup.rb +1655 -0
  104. data/doc/statistics/statistics.md +41 -0
  105. data/doc/todo/README.md +5 -0
  106. data/doc/todo/bioroebe_GUI_todo.md +15 -0
  107. data/doc/todo/bioroebe_todo.md +2823 -0
  108. data/doc/using_biomart.md +258 -0
  109. data/html/test.html +144 -0
  110. data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +118 -0
  111. data/lib/bioroebe/aminoacids/aminoacids_mass_table.rb +118 -0
  112. data/lib/bioroebe/aminoacids/codon_percentage.rb +189 -0
  113. data/lib/bioroebe/aminoacids/colourize_hydrophilic_and_hydrophobic_aminoacids.rb +110 -0
  114. data/lib/bioroebe/aminoacids/create_random_aminoacids.rb +221 -0
  115. data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +460 -0
  116. data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +231 -0
  117. data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +184 -0
  118. data/lib/bioroebe/annotations/README.md +2 -0
  119. data/lib/bioroebe/annotations/create_annotation_format.rb +208 -0
  120. data/lib/bioroebe/autoinclude.rb +7 -0
  121. data/lib/bioroebe/base/base.rb +35 -0
  122. data/lib/bioroebe/base/colours.rb +14 -0
  123. data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +275 -0
  124. data/lib/bioroebe/base/commandline_application/README.md +7 -0
  125. data/lib/bioroebe/base/commandline_application/aminoacids.rb +33 -0
  126. data/lib/bioroebe/base/commandline_application/commandline_application.rb +37 -0
  127. data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +144 -0
  128. data/lib/bioroebe/base/commandline_application/directory.rb +33 -0
  129. data/lib/bioroebe/base/commandline_application/extract.rb +22 -0
  130. data/lib/bioroebe/base/commandline_application/misc.rb +485 -0
  131. data/lib/bioroebe/base/commandline_application/opn.rb +47 -0
  132. data/lib/bioroebe/base/commandline_application/reset.rb +40 -0
  133. data/lib/bioroebe/base/commandline_application/warnings.rb +36 -0
  134. data/lib/bioroebe/base/commandline_application/write_what_into.rb +29 -0
  135. data/lib/bioroebe/base/initialize.rb +18 -0
  136. data/lib/bioroebe/base/misc.rb +94 -0
  137. data/lib/bioroebe/base/namespace.rb +16 -0
  138. data/lib/bioroebe/base/prototype/README.md +12 -0
  139. data/lib/bioroebe/base/prototype/e_and_ee.rb +24 -0
  140. data/lib/bioroebe/base/prototype/misc.rb +108 -0
  141. data/lib/bioroebe/base/prototype/mkdir.rb +20 -0
  142. data/lib/bioroebe/base/prototype/prototype.rb +21 -0
  143. data/lib/bioroebe/base/prototype/reset.rb +26 -0
  144. data/lib/bioroebe/base/reset.rb +11 -0
  145. data/lib/bioroebe/biomart/LICENSE.md +27 -0
  146. data/lib/bioroebe/biomart/attribute.rb +77 -0
  147. data/lib/bioroebe/biomart/biomart.rb +227 -0
  148. data/lib/bioroebe/biomart/database.rb +128 -0
  149. data/lib/bioroebe/biomart/dataset.rb +572 -0
  150. data/lib/bioroebe/biomart/filter.rb +97 -0
  151. data/lib/bioroebe/biomart/server.rb +152 -0
  152. data/lib/bioroebe/blosum/blosum.rb +88 -0
  153. data/lib/bioroebe/calculate/calculate_blosum_score.rb +145 -0
  154. data/lib/bioroebe/calculate/calculate_gc_content.rb +301 -0
  155. data/lib/bioroebe/calculate/calculate_levensthein_distance.rb +100 -0
  156. data/lib/bioroebe/calculate/calculate_melting_temperature.rb +398 -0
  157. data/lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb +304 -0
  158. data/lib/bioroebe/calculate/calculate_the_position_specific_scoring_matrix.rb +166 -0
  159. data/lib/bioroebe/cell/README.md +1 -0
  160. data/lib/bioroebe/cell/cell.rb +63 -0
  161. data/lib/bioroebe/cleave_and_digest/README.md +2 -0
  162. data/lib/bioroebe/cleave_and_digest/cleave.rb +80 -0
  163. data/lib/bioroebe/cleave_and_digest/digestion.rb +75 -0
  164. data/lib/bioroebe/cleave_and_digest/trypsin.rb +192 -0
  165. data/lib/bioroebe/codon_tables/README.md +9 -0
  166. data/lib/bioroebe/codon_tables/frequencies/287_Pseudomonas_aeruginosa.yml +101 -0
  167. data/lib/bioroebe/codon_tables/frequencies/3702_Arabidopsis_thaliana.yml +77 -0
  168. data/lib/bioroebe/codon_tables/frequencies/4932_Saccharomyces_cerevisiae.yml +103 -0
  169. data/lib/bioroebe/codon_tables/frequencies/7227_Drosophila_melanogaster.yml +71 -0
  170. data/lib/bioroebe/codon_tables/frequencies/83333_Escherichia_coli_K12.yml +103 -0
  171. data/lib/bioroebe/codon_tables/frequencies/9606_Homo_sapiens.yml +123 -0
  172. data/lib/bioroebe/codon_tables/frequencies/9685_Felis_catus.yml +78 -0
  173. data/lib/bioroebe/codon_tables/frequencies/README.md +10 -0
  174. data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +337 -0
  175. data/lib/bioroebe/codons/README.md +28 -0
  176. data/lib/bioroebe/codons/codon_table.rb +416 -0
  177. data/lib/bioroebe/codons/codon_tables.rb +123 -0
  178. data/lib/bioroebe/codons/codons.rb +517 -0
  179. data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +102 -0
  180. data/lib/bioroebe/codons/detect_minimal_codon.rb +180 -0
  181. data/lib/bioroebe/codons/determine_optimal_codons.rb +74 -0
  182. data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +380 -0
  183. data/lib/bioroebe/codons/sanitize_codon_frequency.rb +144 -0
  184. data/lib/bioroebe/codons/show_codon_tables.rb +130 -0
  185. data/lib/bioroebe/codons/show_codon_usage.rb +197 -0
  186. data/lib/bioroebe/codons/show_this_codon_table.rb +573 -0
  187. data/lib/bioroebe/codons/start_codons.rb +105 -0
  188. data/lib/bioroebe/colours/colour_schemes/README.md +10 -0
  189. data/lib/bioroebe/colours/colour_schemes/array_available_colour_schemes.rb +38 -0
  190. data/lib/bioroebe/colours/colour_schemes/buried.rb +70 -0
  191. data/lib/bioroebe/colours/colour_schemes/colour_scheme.rb +101 -0
  192. data/lib/bioroebe/colours/colour_schemes/colour_scheme_demo.rb +262 -0
  193. data/lib/bioroebe/colours/colour_schemes/helix.rb +65 -0
  194. data/lib/bioroebe/colours/colour_schemes/hydropathy.rb +70 -0
  195. data/lib/bioroebe/colours/colour_schemes/nucleotide.rb +47 -0
  196. data/lib/bioroebe/colours/colour_schemes/score.rb +112 -0
  197. data/lib/bioroebe/colours/colour_schemes/simple.rb +42 -0
  198. data/lib/bioroebe/colours/colour_schemes/strand.rb +65 -0
  199. data/lib/bioroebe/colours/colour_schemes/taylor.rb +58 -0
  200. data/lib/bioroebe/colours/colour_schemes/turn.rb +65 -0
  201. data/lib/bioroebe/colours/colour_schemes/zappo.rb +59 -0
  202. data/lib/bioroebe/colours/colourize_sequence.rb +262 -0
  203. data/lib/bioroebe/colours/colours.rb +119 -0
  204. data/lib/bioroebe/colours/misc_colours.rb +80 -0
  205. data/lib/bioroebe/colours/rev.rb +41 -0
  206. data/lib/bioroebe/colours/sdir.rb +21 -0
  207. data/lib/bioroebe/colours/sfancy.rb +21 -0
  208. data/lib/bioroebe/colours/sfile.rb +21 -0
  209. data/lib/bioroebe/colours/simp.rb +21 -0
  210. data/lib/bioroebe/colours/swarn.rb +29 -0
  211. data/lib/bioroebe/colours/use_colours.rb +27 -0
  212. data/lib/bioroebe/configuration/configuration.rb +114 -0
  213. data/lib/bioroebe/configuration/constants.rb +35 -0
  214. data/lib/bioroebe/constants/GUIs.rb +79 -0
  215. data/lib/bioroebe/constants/aminoacids_and_proteins.rb +146 -0
  216. data/lib/bioroebe/constants/base_directory.rb +120 -0
  217. data/lib/bioroebe/constants/carriage_return.rb +14 -0
  218. data/lib/bioroebe/constants/codon_tables.rb +77 -0
  219. data/lib/bioroebe/constants/database_constants.rb +107 -0
  220. data/lib/bioroebe/constants/files_and_directories.rb +579 -0
  221. data/lib/bioroebe/constants/misc.rb +189 -0
  222. data/lib/bioroebe/constants/newline.rb +14 -0
  223. data/lib/bioroebe/constants/nucleotides.rb +114 -0
  224. data/lib/bioroebe/constants/regex.rb +28 -0
  225. data/lib/bioroebe/constants/roebe.rb +38 -0
  226. data/lib/bioroebe/constants/row_terminator.rb +16 -0
  227. data/lib/bioroebe/constants/tabulator.rb +14 -0
  228. data/lib/bioroebe/constants/unicode.rb +12 -0
  229. data/lib/bioroebe/constants/urls.rb +50 -0
  230. data/lib/bioroebe/conversions/README.md +3 -0
  231. data/lib/bioroebe/conversions/convert_aminoacid_to_dna.rb +298 -0
  232. data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +569 -0
  233. data/lib/bioroebe/count/README.md +1 -0
  234. data/lib/bioroebe/count/count_amount_of_aminoacids.rb +352 -0
  235. data/lib/bioroebe/count/count_amount_of_nucleotides.rb +491 -0
  236. data/lib/bioroebe/count/count_at.rb +39 -0
  237. data/lib/bioroebe/count/count_gc.rb +43 -0
  238. data/lib/bioroebe/css/README.md +5 -0
  239. data/lib/bioroebe/css/project.css +121 -0
  240. data/lib/bioroebe/data/README.md +10 -0
  241. data/lib/bioroebe/data/bam/README.md +1 -0
  242. data/lib/bioroebe/data/data.txt +192 -0
  243. data/lib/bioroebe/data/fasta/GFP_mutant_3_coding_sequence.fasta +12 -0
  244. data/lib/bioroebe/data/fasta/alu_elements.fasta +42 -0
  245. data/lib/bioroebe/data/fasta/lady_slippers_orchid.fasta +1197 -0
  246. data/lib/bioroebe/data/fasta/loxP.fasta +2 -0
  247. data/lib/bioroebe/data/fasta/ls_orchid.fasta +1197 -0
  248. data/lib/bioroebe/data/fasta/pax6_in_mouse.fasta +1 -0
  249. data/lib/bioroebe/data/fasta/test.fasta +7 -0
  250. data/lib/bioroebe/data/fasta/test_DNA.fasta +1 -0
  251. data/lib/bioroebe/data/fastq/fastq_example_file.fastq +32 -0
  252. data/lib/bioroebe/data/fastq/fastq_example_file_SP1.fastq +1000 -0
  253. data/lib/bioroebe/data/fastq/one_random_fastq_entry.fastq +4 -0
  254. data/lib/bioroebe/data/genbank/sample_file.genbank +15 -0
  255. data/lib/bioroebe/data/genbank/standard.fasta +3 -0
  256. data/lib/bioroebe/data/gff/Escherichia_coli_K12_plasmid_F_DNA_NC_002483.1.gff3 +345 -0
  257. data/lib/bioroebe/data/gff/sample.gff +2 -0
  258. data/lib/bioroebe/data/gff/test_gene.gff +4 -0
  259. data/lib/bioroebe/data/gff/transcripts.gff +16 -0
  260. data/lib/bioroebe/data/gtf/README.md +1 -0
  261. data/lib/bioroebe/data/json/example_config.json +48 -0
  262. data/lib/bioroebe/data/pdb/1VII.pdb +754 -0
  263. data/lib/bioroebe/data/pdb/ala_phe_ala.pdb +228 -0
  264. data/lib/bioroebe/data/pdb/rcsb_pdb_1VII.fasta +2 -0
  265. data/lib/bioroebe/data/phylip/README.md +11 -0
  266. data/lib/bioroebe/data/phylip/example.phylip +7 -0
  267. data/lib/bioroebe/data/svg/example.svg +301 -0
  268. data/lib/bioroebe/databases/README.md +1 -0
  269. data/lib/bioroebe/databases/download_taxonomy_database.rb +102 -0
  270. data/lib/bioroebe/dotplots/README.md +5 -0
  271. data/lib/bioroebe/dotplots/advanced_dotplot.rb +256 -0
  272. data/lib/bioroebe/dotplots/dotplot.rb +184 -0
  273. data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +191 -0
  274. data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +102 -0
  275. data/lib/bioroebe/electron_microscopy/generate_em2em_file.rb +122 -0
  276. data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +197 -0
  277. data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +282 -0
  278. data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +131 -0
  279. data/lib/bioroebe/encoding/README.md +2 -0
  280. data/lib/bioroebe/encoding/encoding.rb +45 -0
  281. data/lib/bioroebe/enzymes/README.md +2 -0
  282. data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +46 -0
  283. data/lib/bioroebe/enzymes/restriction_enzyme.rb +200 -0
  284. data/lib/bioroebe/enzymes/restriction_enzymes_file.rb +72 -0
  285. data/lib/bioroebe/enzymes/return_restriction_enzyme_sequence_and_cut_position.rb +80 -0
  286. data/lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb +65 -0
  287. data/lib/bioroebe/enzymes/show_restriction_enzymes.rb +119 -0
  288. data/lib/bioroebe/exceptions/README.md +2 -0
  289. data/lib/bioroebe/exceptions/exceptions.rb +17 -0
  290. data/lib/bioroebe/ext/LICENCE.md +5 -0
  291. data/lib/bioroebe/ext/README.md +7 -0
  292. data/lib/bioroebe/ext/main.cpp +45 -0
  293. data/lib/bioroebe/ext/nucleotide.cpp +24 -0
  294. data/lib/bioroebe/ext/nussinov_algorithm.cpp +348 -0
  295. data/lib/bioroebe/ext/sequence +0 -0
  296. data/lib/bioroebe/ext/sequence.cpp +162 -0
  297. data/lib/bioroebe/fasta_and_fastq/README.md +6 -0
  298. data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +88 -0
  299. data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +151 -0
  300. data/lib/bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb +111 -0
  301. data/lib/bioroebe/fasta_and_fastq/download_fasta.rb +248 -0
  302. data/lib/bioroebe/fasta_and_fastq/fasta_defline/README.md +2 -0
  303. data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +113 -0
  304. data/lib/bioroebe/fasta_and_fastq/fasta_parser.rb +167 -0
  305. data/lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb +131 -0
  306. data/lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb +87 -0
  307. data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb +50 -0
  308. data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb +86 -0
  309. data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb +117 -0
  310. data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb +981 -0
  311. data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +27 -0
  312. data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb +156 -0
  313. data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb +128 -0
  314. data/lib/bioroebe/fasta_and_fastq/parse_fasta/run.rb +20 -0
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  655. data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +230 -0
  656. data/lib/bioroebe/utility_scripts/compacter.rb +131 -0
  657. data/lib/bioroebe/utility_scripts/compseq/compseq.rb +529 -0
  658. data/lib/bioroebe/utility_scripts/consensus_sequence.rb +374 -0
  659. data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +130 -0
  660. data/lib/bioroebe/utility_scripts/determine_antigenic_areas.rb +115 -0
  661. data/lib/bioroebe/utility_scripts/determine_missing_nucleotides_percentage.rb +137 -0
  662. data/lib/bioroebe/utility_scripts/display_open_reading_frames/determine.rb +73 -0
  663. data/lib/bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb +31 -0
  664. data/lib/bioroebe/utility_scripts/display_open_reading_frames/initialize.rb +37 -0
  665. data/lib/bioroebe/utility_scripts/display_open_reading_frames/menu.rb +49 -0
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  670. data/lib/bioroebe/utility_scripts/download_files_from_rebase.rb +72 -0
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  678. data/lib/bioroebe/utility_scripts/show_this_dna_sequence.rb +148 -0
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  680. data/lib/bioroebe/utility_scripts/showorf/help.rb +33 -0
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  690. data/lib/bioroebe/with_gui.rb +18 -0
  691. data/lib/bioroebe/www/bioroebe.cgi +44 -0
  692. data/lib/bioroebe/www/embeddable_interface.rb +686 -0
  693. data/lib/bioroebe/www/sinatra/sinatra.rb +1013 -0
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  705. data/lib/bioroebe/yaml/aminoacids/amino_acids_three_to_one.yml +34 -0
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  751. data/lib/bioroebe/yaml/configuration/try_to_use_matplotlib.yml +1 -0
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  753. data/lib/bioroebe/yaml/configuration/use_this_database.yml +1 -0
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  758. data/lib/bioroebe/yaml/fasta_and_fastq/fastq_quality_schemes.yml +44 -0
  759. data/lib/bioroebe/yaml/genomes/README.md +16 -0
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  762. data/lib/bioroebe/yaml/laboratory/README.md +1 -0
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  785. data/lib/bioroebe/yaml/sequences/README.md +2 -0
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  790. data/spec/testing_toplevel_method_editor.rb +20 -0
  791. data/spec/testing_toplevel_method_url.rb +15 -0
  792. data/spec/testing_toplevel_method_verbose.rb +13 -0
  793. data/test/advanced_svg_example.rb +307 -0
  794. data/test/testing_bioroebe.rb +25 -0
  795. data/test/testing_codons.rb +45 -0
  796. data/test/testing_dna_to_rna_conversion.rb +15 -0
  797. data/test/testing_parse_pdb_file.rb +23 -0
  798. data/test/testing_reverse_complement.rb +32 -0
  799. data/test/testing_svg_component_of_bioroebe.rb +311 -0
  800. data/test/testing_svg_component_of_bioroebe_from_json_dataset.rb +34 -0
  801. data/test/testing_taxonomy.rb +22 -0
  802. metadata +1059 -0
data/lib/bioroebe/data/fastq/one_random_fastq_entry.fastq ADDED
@@ -0,0 +1,4 @@
1
+ @AZ1:233:B399NACCC:2:1203:7689:2153
2
+ GTTGTTCTTGATGAGCCATGAGGAAGGCATGCCAAATTAAAATACTGGTGCGAATTTAAT
3
+ +
4
+ CCFFFFHHHHHJJJJJEIFJIJIJJJIJIJJJJCDGHIIGIGIGIGJIIIIJIJIJIIIH
data/lib/bioroebe/data/genbank/sample_file.genbank ADDED
@@ -0,0 +1,15 @@
1
+ LOCUS tmpseq_0 96 bp linear 01-MAY-2021
2
+ DEFINITION No definition line found.
3
+ ACCESSION tmpseq_0
4
+ VERSION
5
+ KEYWORDS .
6
+ SOURCE Unknown.
7
+ ORGANISM Unknown.
8
+ Unclassified.
9
+ FEATURES Location/Qualifiers
10
+ source 1..96
11
+ BASE COUNT 16 a 24 c 40 g 16 t
12
+ ORIGIN
13
+ 1 atggggcctg caatggggcc tgcaatgggg cctgcaatgg ggcctgcaat ggggcctgca
14
+ 61 atggggcctg caatggggcc tgcaatgggg cctgca
15
+ //
data/lib/bioroebe/data/genbank/standard.fasta ADDED
@@ -0,0 +1,3 @@
1
+ > genbank file
2
+ ATGGGGCCTGCAATGGGGCCTGCAATGGGGCCTGCAATGGGGCCTGCAATGGGGCCTGCA
3
+ ATGGGGCCTGCAATGGGGCCTGCAATGGGGCCTGCA
data/lib/bioroebe/data/gff/Escherichia_coli_K12_plasmid_F_DNA_NC_002483.1.gff3 ADDED
@@ -0,0 +1,345 @@
1
+ ##sequence-region NC_002483.1 1 99159
2
+ ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=83333
3
+ NC_002483.1 RefSeq region 1 99159 . + . ID=NC_002483.1:1..99159;Dbxref=taxon:83333;Is_circular=true;Name=F;gbkey=Src;genome=plasmid;mol_type=genomic DNA;plasmid-name=F;strain=K-12;substrain=CR63
4
+ NC_002483.1 RefSeq mobile_genetic_element 1 1258 . + . ID=id-NC_002483.1:1..1258;gbkey=mobile_element;mobile_element_type=insertion sequence:IS3a
5
+ NC_002483.1 RefSeq inverted_repeat 1 39 . + . ID=id-NC_002483.1:1..39;Note=IS3a 5' inverted repeat%3B~terminal repeat of IS3a;gbkey=repeat_region;rpt_type=inverted
6
+ NC_002483.1 RefSeq gene 66 365 . + . ID=gene-D616_p97047;Dbxref=GeneID:1263552;Name=yaaA;gbkey=Gene;gene=yaaA;gene_biotype=protein_coding;locus_tag=D616_p97047;old_locus_tag=Fpla001
7
+ NC_002483.1 RefSeq CDS 66 365 . + 0 ID=cds-NP_061380.1;Parent=gene-D616_p97047;Dbxref=Genbank:NP_061380.1,GeneID:1263552;Name=NP_061380.1;Note=100 pct identical to prf:1105313A[hypothetical protein of IS3];gbkey=CDS;gene=yaaA;locus_tag=D616_p97047;product=hypothetical protein;protein_id=NP_061380.1;transl_table=11
8
+ NC_002483.1 RefSeq gene 362 1228 . + . ID=gene-D616_p97046;Dbxref=GeneID:1263587;Name=yaaB;gbkey=Gene;gene=yaaB;gene_biotype=protein_coding;locus_tag=D616_p97046;old_locus_tag=Fpla002
9
+ NC_002483.1 RefSeq CDS 362 1228 . + 0 ID=cds-NP_061381.1;Parent=gene-D616_p97046;Dbxref=Genbank:NP_061381.1,GeneID:1263587;Name=NP_061381.1;Note=99 pct identical to sp:P05822[putative transposase for IS3];gbkey=CDS;gene=yaaB;locus_tag=D616_p97046;product=hypothetical protein;protein_id=NP_061381.1;transl_table=11
10
+ NC_002483.1 RefSeq inverted_repeat 1220 1258 . + . ID=id-NC_002483.1:1220..1258;Note=IS3a 3' inverted repeat%3B~terminal repeat of IS3a;gbkey=repeat_region;rpt_type=inverted
11
+ NC_002483.1 RefSeq sequence_difference 2059 2059 . + . ID=id-NC_002483.1:2059..2059;Note=conflict: A is changed to G in gb:X57429;compare=X57429.1;gbkey=misc_difference;replace=g
12
+ NC_002483.1 RefSeq gene 2110 2550 . + . ID=gene-D616_p97045;Dbxref=GeneID:1263579;Name=yacA;gbkey=Gene;gene=yacA;gene_biotype=protein_coding;locus_tag=D616_p97045;old_locus_tag=Fpla004
13
+ NC_002483.1 RefSeq CDS 2110 2550 . + 0 ID=cds-NP_061382.1;Parent=gene-D616_p97045;Dbxref=Genbank:NP_061382.1,GeneID:1263579;Name=NP_061382.1;gbkey=CDS;gene=yacA;locus_tag=D616_p97045;product=hypothetical protein;protein_id=NP_061382.1;transl_table=11
14
+ NC_002483.1 RefSeq gene 2821 2882 . - . ID=gene-D616_s97001;Dbxref=GeneID:1263526;Name=srnC;gbkey=Gene;gene=srnC;gene_biotype=antisense_RNA;locus_tag=D616_s97001;old_locus_tag=Fplas001
15
+ NC_002483.1 RefSeq antisense_RNA 2821 2882 . - . ID=rna-D616_s97001;Parent=gene-D616_s97001;Dbxref=GeneID:1263526;Note=antisense RNA of srnB mRNAs;gbkey=ncRNA;gene=srnC;locus_tag=D616_s97001
16
+ NC_002483.1 RefSeq exon 2821 2882 . - . ID=exon-D616_s97001-1;Parent=rna-D616_s97001;Dbxref=GeneID:1263526;Note=antisense RNA of srnB mRNAs;gbkey=ncRNA;gene=srnC;locus_tag=D616_s97001
17
+ NC_002483.1 RefSeq gene 2869 3075 . + . ID=gene-D616_p97087;Dbxref=GeneID:1263515;Name=srnB;gbkey=Gene;gene=srnB;gene_biotype=protein_coding;locus_tag=D616_p97087;old_locus_tag=Fpla005
18
+ NC_002483.1 RefSeq CDS 2869 3075 . + 0 ID=cds-NP_061383.1;Parent=gene-D616_p97087;Dbxref=Genbank:NP_061383.1,GeneID:1263515;Name=NP_061383.1;Note=100 pct identical to sp:P13970[SrnB of plasmid F];gbkey=CDS;gene=srnB;locus_tag=D616_p97087;product=hypothetical protein;protein_id=NP_061383.1;transl_table=11
19
+ NC_002483.1 RefSeq gene 2926 3075 . + . ID=gene-D616_p97086;Dbxref=GeneID:1263549;Name=srnB';gbkey=Gene;gene=srnB';gene_biotype=protein_coding;locus_tag=D616_p97086;old_locus_tag=Fpla006
20
+ NC_002483.1 RefSeq CDS 2926 3075 . + 0 ID=cds-NP_061384.1;Parent=gene-D616_p97086;Dbxref=Genbank:NP_061384.1,GeneID:1263549;Name=NP_061384.1;gbkey=CDS;gene=srnB';locus_tag=D616_p97086;product=hypothetical protein;protein_id=NP_061384.1;transl_table=11
21
+ NC_002483.1 RefSeq sequence_difference 3084 3084 . + . ID=id-NC_002483.1:3084..3084;Note=conflict: G is omitted from gb:M16168;compare=M16168.1;gbkey=misc_difference;replace=g
22
+ NC_002483.1 RefSeq sequence_difference 3089 3089 . + . ID=id-NC_002483.1:3089..3089;Note=conflict: G is changed to C in gb:M16168;compare=M16168.1;gbkey=misc_difference;replace=c
23
+ NC_002483.1 RefSeq gene 3359 3616 . + . ID=gene-D616_p97095;Dbxref=GeneID:1263536;Name=repA2;gbkey=Gene;gene=repA2;gene_biotype=protein_coding;locus_tag=D616_p97095
24
+ NC_002483.1 RefSeq CDS 3359 3616 . + 0 ID=cds-NP_061385.1;Parent=gene-D616_p97095;Dbxref=Genbank:NP_061385.1,GeneID:1263536;Name=NP_061385.1;Note=100 pct identical to sp:P13959[RepA2 of plasmid F];gbkey=CDS;gene=repA2;locus_tag=D616_p97095;product=replication regulatory protein;protein_id=NP_061385.1;transl_table=11
25
+ NC_002483.1 RefSeq gene 3747 3839 . - . ID=gene-D616_s97002;Dbxref=GeneID:14667383;Name=inc;gbkey=Gene;gene=inc;gene_biotype=antisense_RNA;locus_tag=D616_s97002
26
+ NC_002483.1 RefSeq antisense_RNA 3747 3839 . - . ID=rna-D616_s97002;Parent=gene-D616_s97002;Dbxref=GeneID:14667383;Note=inhibitor of RepFIC replication intiation protein synthesis;gbkey=ncRNA;gene=inc;locus_tag=D616_s97002
27
+ NC_002483.1 RefSeq exon 3747 3839 . - . ID=exon-D616_s97002-1;Parent=rna-D616_s97002;Dbxref=GeneID:14667383;Note=inhibitor of RepFIC replication intiation protein synthesis;gbkey=ncRNA;gene=inc;locus_tag=D616_s97002
28
+ NC_002483.1 RefSeq gene 3850 3924 . + . ID=gene-D616_p97091;Dbxref=GeneID:1263553;Name=repL;gbkey=Gene;gene=repL;gene_biotype=protein_coding;locus_tag=D616_p97091;old_locus_tag=Fpla008
29
+ NC_002483.1 RefSeq CDS 3850 3924 . + 0 ID=cds-NP_061386.1;Parent=gene-D616_p97091;Dbxref=Genbank:NP_061386.1,GeneID:1263553;Name=NP_061386.1;Note=92 pct identical to gp:P30REPFIC_2[leader peptide of repA1 of plasmid P307]%3B~positive regulator of RepFIC%3B~replication regulatory frame;gbkey=CDS;gene=repL;locus_tag=D616_p97091;product=hypothetical protein;protein_id=NP_061386.1;transl_table=11
30
+ NC_002483.1 RefSeq gene 3917 4190 . + . ID=gene-D616_p97096;Dbxref=GeneID:1263525;Name=repA1;end_range=4190,.;gbkey=Gene;gene=repA1;gene_biotype=other;locus_tag=D616_p97096;old_locus_tag=Fpla009;partial=true
31
+ NC_002483.1 RefSeq sequence_feature 3917 4190 . + . ID=id-D616_p97096;Dbxref=GeneID:1263525;Note=100 pct identical to sp:P13960[replication initiaion protein of plasmid F]%3B~inactivated by insertion sequence gamma delta(Tn1000);end_range=4190,.;gbkey=misc_feature;gene=repA1;locus_tag=D616_p97096;partial=true;product=RepFIC replication initiation protein
32
+ NC_002483.1 RefSeq mobile_genetic_element 4191 10171 . + . ID=id-NC_002483.1:4191..10171;Note=gamma delta(Tn1000);gbkey=mobile_element;mobile_element_type=transposon:Tn1000
33
+ NC_002483.1 RefSeq inverted_repeat 4191 4225 . + . ID=id-NC_002483.1:4191..4225;Note=gamma delta(Tn1000) 5' inverted repeat%3B~terminal repeat of Tn1000;gbkey=repeat_region;rpt_type=inverted
34
+ NC_002483.1 RefSeq gene 4303 6399 . - . ID=gene-D616_p97081;Dbxref=GeneID:1263581;Name=tnpX;gbkey=Gene;gene=tnpX;gene_biotype=protein_coding;locus_tag=D616_p97081;old_locus_tag=Fpla010
35
+ NC_002483.1 RefSeq CDS 4303 6399 . - 0 ID=cds-NP_061387.1;Parent=gene-D616_p97081;Dbxref=Genbank:NP_061387.1,GeneID:1263581;Name=NP_061387.1;Note=100 pct identical to gp:ECOTNPA_3[hypothetical protein of gamma delta(Tn1000)];gbkey=CDS;gene=tnpX;locus_tag=D616_p97081;product=hypothetical protein;protein_id=NP_061387.1;transl_table=11
36
+ NC_002483.1 RefSeq gene 6415 6966 . - . ID=gene-D616_p97083;Dbxref=GeneID:1263577;Name=tnpR;gbkey=Gene;gene=tnpR;gene_biotype=protein_coding;locus_tag=D616_p97083;old_locus_tag=Fpla011
37
+ NC_002483.1 RefSeq CDS 6415 6966 . - 0 ID=cds-NP_061388.1;Parent=gene-D616_p97083;Dbxref=Genbank:NP_061388.1,GeneID:1263577;Name=NP_061388.1;Note=100 pct identical to gp:ECOTNPA_2[gamma delta resolvase(Tn1000)];gbkey=CDS;gene=tnpR;locus_tag=D616_p97083;product=hypothetical protein;protein_id=NP_061388.1;transl_table=11
38
+ NC_002483.1 RefSeq gene 7130 10138 . + . ID=gene-D616_p97084;Dbxref=GeneID:1263527;Name=tnpA;gbkey=Gene;gene=tnpA;gene_biotype=protein_coding;locus_tag=D616_p97084;old_locus_tag=Fpla012
39
+ NC_002483.1 RefSeq CDS 7130 10138 . + 0 ID=cds-NP_061389.1;Parent=gene-D616_p97084;Dbxref=Genbank:NP_061389.1,GeneID:1263527;Name=NP_061389.1;Note=100 pct identical to gp:ECOTNPA_1[transposase of gamma delta(Tn1000)];gbkey=CDS;gene=tnpA;locus_tag=D616_p97084;product=hypothetical protein;protein_id=NP_061389.1;transl_table=11
40
+ NC_002483.1 RefSeq inverted_repeat 10137 10171 . + . ID=id-NC_002483.1:10137..10171;Note=gamma delta(Tn1000) 3' inverted repeat%3B~terminal repeat of Tn1000;gbkey=repeat_region;rpt_type=inverted
41
+ NC_002483.1 RefSeq gene 10729 11790 . - . ID=gene-D616_p97044;Dbxref=GeneID:1263551;Name=ybaA;gbkey=Gene;gene=ybaA;gene_biotype=protein_coding;locus_tag=D616_p97044;old_locus_tag=Fpla013
42
+ NC_002483.1 RefSeq CDS 10729 11790 . - 0 ID=cds-NP_061390.1;Parent=gene-D616_p97044;Dbxref=Genbank:NP_061390.1,GeneID:1263551;Name=NP_061390.1;Note=95 pct identical to gp:SMU26731_1[selenite dissimilatory reduction regulator protein];gbkey=CDS;gene=ybaA;locus_tag=D616_p97044;product=hypothetical protein;protein_id=NP_061390.1;transl_table=11
43
+ NC_002483.1 RefSeq gene 11900 12313 . - . ID=gene-D616_p97043;Dbxref=GeneID:1263533;Name=ybbA;gbkey=Gene;gene=ybbA;gene_biotype=protein_coding;locus_tag=D616_p97043;old_locus_tag=Fpla014
44
+ NC_002483.1 RefSeq CDS 11900 12313 . - 0 ID=cds-NP_061391.1;Parent=gene-D616_p97043;Dbxref=Genbank:NP_061391.1,GeneID:1263533;Name=NP_061391.1;gbkey=CDS;gene=ybbA;locus_tag=D616_p97043;product=hypothetical protein;protein_id=NP_061391.1;transl_table=11
45
+ NC_002483.1 RefSeq gene 12477 13040 . - . ID=gene-D616_p97042;Dbxref=GeneID:1263503;Name=ybcA;gbkey=Gene;gene=ybcA;gene_biotype=protein_coding;locus_tag=D616_p97042;old_locus_tag=Fpla015
46
+ NC_002483.1 RefSeq CDS 12477 13040 . - 0 ID=cds-NP_061392.1;Parent=gene-D616_p97042;Dbxref=Genbank:NP_061392.1,GeneID:1263503;Name=NP_061392.1;gbkey=CDS;gene=ybcA;locus_tag=D616_p97042;product=hypothetical protein;protein_id=NP_061392.1;transl_table=11
47
+ NC_002483.1 RefSeq gene 13047 13460 . - . ID=gene-D616_p97041;Dbxref=GeneID:1263519;Name=ybdA;gbkey=Gene;gene=ybdA;gene_biotype=protein_coding;locus_tag=D616_p97041;old_locus_tag=Fpla016
48
+ NC_002483.1 RefSeq CDS 13047 13460 . - 0 ID=cds-NP_061393.1;Parent=gene-D616_p97041;Dbxref=Genbank:NP_061393.1,GeneID:1263519;Name=NP_061393.1;gbkey=CDS;gene=ybdA;locus_tag=D616_p97041;product=hypothetical protein;protein_id=NP_061393.1;transl_table=11
49
+ NC_002483.1 RefSeq gene 13453 14055 . - . ID=gene-D616_p97040;Dbxref=GeneID:1263524;Name=ybdB;gbkey=Gene;gene=ybdB;gene_biotype=protein_coding;locus_tag=D616_p97040;old_locus_tag=Fpla017
50
+ NC_002483.1 RefSeq CDS 13453 14055 . - 0 ID=cds-NP_061394.1;Parent=gene-D616_p97040;Dbxref=Genbank:NP_061394.1,GeneID:1263524;Name=NP_061394.1;gbkey=CDS;gene=ybdB;locus_tag=D616_p97040;product=hypothetical protein;protein_id=NP_061394.1;transl_table=11
51
+ NC_002483.1 RefSeq mobile_genetic_element 15093 16350 . + . ID=id-NC_002483.1:15093..16350;gbkey=mobile_element;mobile_element_type=insertion sequence:IS3b
52
+ NC_002483.1 RefSeq inverted_repeat 15093 15131 . + . ID=id-NC_002483.1:15093..15131;Note=IS3b 5' inverted repeat%3B~terminal repeat of IS3b;gbkey=repeat_region;rpt_type=inverted
53
+ NC_002483.1 RefSeq gene 15158 15457 . + . ID=gene-D616_p97039;Dbxref=GeneID:1263530;Name=ybfA;gbkey=Gene;gene=ybfA;gene_biotype=protein_coding;locus_tag=D616_p97039;old_locus_tag=Fpla018
54
+ NC_002483.1 RefSeq CDS 15158 15457 . + 0 ID=cds-NP_061395.1;Parent=gene-D616_p97039;Dbxref=Genbank:NP_061395.1,GeneID:1263530;Name=NP_061395.1;Note=100 pct identical to prf:1105313A[hypothetical protein of IS3];gbkey=CDS;gene=ybfA;locus_tag=D616_p97039;product=hypothetical protein;protein_id=NP_061395.1;transl_table=11
55
+ NC_002483.1 RefSeq gene 15454 16320 . + . ID=gene-D616_p97038;Dbxref=GeneID:1263538;Name=ybfB;gbkey=Gene;gene=ybfB;gene_biotype=protein_coding;locus_tag=D616_p97038;old_locus_tag=Fpla019
56
+ NC_002483.1 RefSeq CDS 15454 16320 . + 0 ID=cds-NP_061396.1;Parent=gene-D616_p97038;Dbxref=Genbank:NP_061396.1,GeneID:1263538;Name=NP_061396.1;Note=98 pct identical to sp:P05822[putative transposase for IS3];gbkey=CDS;gene=ybfB;locus_tag=D616_p97038;product=hypothetical protein;protein_id=NP_061396.1;transl_table=11
57
+ NC_002483.1 RefSeq inverted_repeat 16312 16350 . + . ID=id-NC_002483.1:16312..16350;Note=IS3b 3' inverted repeat%3B~terminal repeat of IS3b;gbkey=repeat_region;rpt_type=inverted
58
+ NC_002483.1 RefSeq gene 16317 16571 . - . ID=gene-D616_p97037;Dbxref=GeneID:1263529;Name=ybgA;gbkey=Gene;gene=ybgA;gene_biotype=protein_coding;locus_tag=D616_p97037;old_locus_tag=Fpla020
59
+ NC_002483.1 RefSeq CDS 16317 16571 . - 0 ID=cds-NP_061397.1;Parent=gene-D616_p97037;Dbxref=Genbank:NP_061397.1,GeneID:1263529;Name=NP_061397.1;gbkey=CDS;gene=ybgA;locus_tag=D616_p97037;product=hypothetical protein;protein_id=NP_061397.1;transl_table=11
60
+ NC_002483.1 RefSeq gene 17216 17548 . + . ID=gene-D616_p97036;Dbxref=GeneID:1263520;Name=ybhA;gbkey=Gene;gene=ybhA;gene_biotype=protein_coding;locus_tag=D616_p97036;old_locus_tag=Fpla021
61
+ NC_002483.1 RefSeq CDS 17216 17548 . + 0 ID=cds-NP_061398.1;Parent=gene-D616_p97036;Dbxref=Genbank:NP_061398.1,GeneID:1263520;Name=NP_061398.1;Note=90 pct identical to 110 residues of 523 aa protein gp:AB024946_51[hypothetical protein of plasmid pB171];gbkey=CDS;gene=ybhA;locus_tag=D616_p97036;product=hypothetical protein;protein_id=NP_061398.1;transl_table=11
62
+ NC_002483.1 RefSeq mobile_genetic_element 17662 18992 . + . ID=id-NC_002483.1:17662..18992;gbkey=mobile_element;mobile_element_type=insertion sequence:IS2
63
+ NC_002483.1 RefSeq inverted_repeat 17662 17702 . + . ID=id-NC_002483.1:17662..17702;Note=IS2 5' inverted repeat%3B~terminal repeat of IS2;gbkey=repeat_region;rpt_type=inverted
64
+ NC_002483.1 RefSeq gene 17673 18578 . - . ID=gene-D616_p97035;Dbxref=GeneID:1263540;Name=ybhB;gbkey=Gene;gene=ybhB;gene_biotype=protein_coding;locus_tag=D616_p97035;old_locus_tag=Fpla022
65
+ NC_002483.1 RefSeq CDS 17673 18578 . - 0 ID=cds-NP_061399.1;Parent=gene-D616_p97035;Dbxref=Genbank:NP_061399.1,GeneID:1263540;Name=NP_061399.1;Note=100 pct identical to sp:P19777[IS2 hypothetical 34.4kD protein];gbkey=CDS;gene=ybhB;locus_tag=D616_p97035;product=hypothetical protein;protein_id=NP_061399.1;transl_table=11
66
+ NC_002483.1 RefSeq gene 18536 18946 . - . ID=gene-D616_p97034;Dbxref=GeneID:1263543;Name=ybiA;gbkey=Gene;gene=ybiA;gene_biotype=protein_coding;locus_tag=D616_p97034
67
+ NC_002483.1 RefSeq CDS 18536 18946 . - 0 ID=cds-NP_061400.3;Parent=gene-D616_p97034;Dbxref=Genbank:NP_061400.3,GeneID:1263543;Name=NP_061400.3;Note=100 pct identical to pir:S56497[IS2 hypothetical 13kD protein];gbkey=CDS;gene=ybiA;locus_tag=D616_p97034;product=hypothetical protein;protein_id=NP_061400.3;transl_table=11
68
+ NC_002483.1 RefSeq gene 18858 19142 . + . ID=gene-D616_p97033;Dbxref=GeneID:1263518;Name=ybiB;gbkey=Gene;gene=ybiB;gene_biotype=protein_coding;locus_tag=D616_p97033;old_locus_tag=Fpla024
69
+ NC_002483.1 RefSeq CDS 18858 19142 . + 0 ID=cds-NP_061401.1;Parent=gene-D616_p97033;Dbxref=Genbank:NP_061401.1,GeneID:1263518;Name=NP_061401.1;Note=86 pct identical to 50 residues of 523 aa protein gp:AB024946_31[hypothetical protein of plasmid pB171];gbkey=CDS;gene=ybiB;locus_tag=D616_p97033;product=hypothetical protein;protein_id=NP_061401.1;transl_table=11
70
+ NC_002483.1 RefSeq inverted_repeat 18951 18992 . + . ID=id-D616_p97033;Dbxref=GeneID:1263518;Note=IS2 3' inverted repeat%3B~terminal repeat of IS2;gbkey=repeat_region;gene=ybiB;locus_tag=D616_p97033;rpt_type=inverted
71
+ NC_002483.1 RefSeq gene 19245 19454 . + . ID=gene-D616_p97032;Dbxref=GeneID:1263539;Name=ybjA;gbkey=Gene;gene=ybjA;gene_biotype=protein_coding;locus_tag=D616_p97032;old_locus_tag=Fpla025
72
+ NC_002483.1 RefSeq CDS 19245 19454 . + 0 ID=cds-NP_061402.1;Parent=gene-D616_p97032;Dbxref=Genbank:NP_061402.1,GeneID:1263539;Name=NP_061402.1;Note=52 pct identical to 67 residues of 225 aa protein gp:ECEHECHEM_5[ORF5 gene product of plasmid pO157];gbkey=CDS;gene=ybjA;locus_tag=D616_p97032;product=hypothetical protein;protein_id=NP_061402.1;transl_table=11
73
+ NC_002483.1 RefSeq gene 20096 20791 . - . ID=gene-D616_p97031;Dbxref=GeneID:1263542;Name=ycaA;gbkey=Gene;gene=ycaA;gene_biotype=protein_coding;locus_tag=D616_p97031;old_locus_tag=Fpla026
74
+ NC_002483.1 RefSeq CDS 20096 20791 . - 0 ID=cds-NP_061403.1;Parent=gene-D616_p97031;Dbxref=Genbank:NP_061403.1,GeneID:1263542;Name=NP_061403.1;gbkey=CDS;gene=ycaA;locus_tag=D616_p97031;product=hypothetical protein;protein_id=NP_061403.1;transl_table=11
75
+ NC_002483.1 RefSeq gene 21222 21455 . - . ID=gene-D616_p97030;Dbxref=GeneID:1263501;Name=ycbA;gbkey=Gene;gene=ycbA;gene_biotype=protein_coding;locus_tag=D616_p97030;old_locus_tag=Fpla027
76
+ NC_002483.1 RefSeq CDS 21222 21455 . - 0 ID=cds-NP_061404.1;Parent=gene-D616_p97030;Dbxref=Genbank:NP_061404.1,GeneID:1263501;Name=NP_061404.1;gbkey=CDS;gene=ycbA;locus_tag=D616_p97030;product=hypothetical protein;protein_id=NP_061404.1;transl_table=11
77
+ NC_002483.1 RefSeq gene 21541 26817 . - . ID=gene-D616_p97029;Dbxref=GeneID:1263513;Name=ycbB;gbkey=Gene;gene=ycbB;gene_biotype=protein_coding;locus_tag=D616_p97029;old_locus_tag=Fpla028
78
+ NC_002483.1 RefSeq CDS 21541 26817 . - 0 ID=cds-NP_061405.1;Parent=gene-D616_p97029;Dbxref=Genbank:NP_061405.1,GeneID:1263513;Name=NP_061405.1;Note=23 pct identical(9 gaps) to 343 residues of 1286 aa protein sp:AIDA_ECOLI[Adhesin AidA-I precursor];gbkey=CDS;gene=ycbB;locus_tag=D616_p97029;product=hypothetical protein;protein_id=NP_061405.1;transl_table=11
79
+ NC_002483.1 RefSeq repeat_region 24085 24456 . + . ID=id-NC_002483.1:24085..24456;Note=repeat H;gbkey=repeat_region
80
+ NC_002483.1 RefSeq repeat_region 24457 24828 . + . ID=id-NC_002483.1:24457..24828;Note=repeat H;gbkey=repeat_region
81
+ NC_002483.1 RefSeq repeat_region 24829 25200 . + . ID=id-NC_002483.1:24829..25200;Note=repeat H;gbkey=repeat_region
82
+ NC_002483.1 RefSeq repeat_region 25201 25572 . + . ID=id-NC_002483.1:25201..25572;Note=repeat H;gbkey=repeat_region
83
+ NC_002483.1 RefSeq repeat_region 25573 25818 . + . ID=id-NC_002483.1:25573..25818;Note=repeat H;gbkey=repeat_region
84
+ NC_002483.1 RefSeq gene 26990 27259 . + . ID=gene-D616_p97028;Dbxref=GeneID:1263528;Name=ycgA;gbkey=Gene;gene=ycgA;gene_biotype=protein_coding;locus_tag=D616_p97028;old_locus_tag=Fpla029
85
+ NC_002483.1 RefSeq CDS 26990 27259 . + 0 ID=cds-NP_061406.1;Parent=gene-D616_p97028;Dbxref=Genbank:NP_061406.1,GeneID:1263528;Name=NP_061406.1;gbkey=CDS;gene=ycgA;locus_tag=D616_p97028;product=hypothetical protein;protein_id=NP_061406.1;transl_table=11
86
+ NC_002483.1 RefSeq gene 27486 31601 . - . ID=gene-D616_p97027;Dbxref=GeneID:1263499;Name=ychA;gbkey=Gene;gene=ychA;gene_biotype=protein_coding;locus_tag=D616_p97027;old_locus_tag=Fpla030
87
+ NC_002483.1 RefSeq CDS 27486 31601 . - 0 ID=cds-NP_061407.1;Parent=gene-D616_p97027;Dbxref=Genbank:NP_061407.1,GeneID:1263499;Name=NP_061407.1;Note=38 pct identical(7 gaps) to 456 residues of 1286 aa protein sp:AIDA_ECOLI[Adhesin AidA-I precursor];gbkey=CDS;gene=ychA;locus_tag=D616_p97027;product=hypothetical protein;protein_id=NP_061407.1;transl_table=11
88
+ NC_002483.1 RefSeq gene 32322 33269 . + . ID=gene-D616_p97100;Dbxref=GeneID:1263511;Name=ompP;gbkey=Gene;gene=ompP;gene_biotype=protein_coding;locus_tag=D616_p97100;old_locus_tag=Fpla031
89
+ NC_002483.1 RefSeq CDS 32322 33269 . + 0 ID=cds-NP_061408.1;Parent=gene-D616_p97100;Dbxref=Genbank:NP_061408.1,GeneID:1263511;Name=NP_061408.1;Note=100 pct identical to sp:OMPP_ECOLI[outer membrane protease OmpP precursor];gbkey=CDS;gene=ompP;locus_tag=D616_p97100;product=hypothetical protein;protein_id=NP_061408.1;transl_table=11
90
+ NC_002483.1 RefSeq gene 33362 34861 . + . ID=gene-D616_p97026;Dbxref=GeneID:1263517;Name=yddA;gbkey=Gene;gene=yddA;gene_biotype=protein_coding;locus_tag=D616_p97026;old_locus_tag=Fpla032
91
+ NC_002483.1 RefSeq CDS 33362 34861 . + 0 ID=cds-NP_061409.1;Parent=gene-D616_p97026;Dbxref=Genbank:NP_061409.1,GeneID:1263517;Name=NP_061409.1;Note=100 pct identical to 417 residues of 438 aa protein sp:YZZE_ECOLI[hypothetical 49.6 kD protein in ompP 3'region];gbkey=CDS;gene=yddA;locus_tag=D616_p97026;product=hypothetical protein;protein_id=NP_061409.1;transl_table=11
92
+ NC_002483.1 RefSeq gene 35217 35504 . + . ID=gene-D616_p97025;Dbxref=GeneID:1263502;Name=ydfA;gbkey=Gene;gene=ydfA;gene_biotype=protein_coding;locus_tag=D616_p97025;old_locus_tag=Fpla033
93
+ NC_002483.1 RefSeq CDS 35217 35504 . + 0 ID=cds-NP_061410.1;Parent=gene-D616_p97025;Dbxref=Genbank:NP_061410.1,GeneID:1263502;Name=NP_061410.1;gbkey=CDS;gene=ydfA;locus_tag=D616_p97025;product=hypothetical protein;protein_id=NP_061410.1;transl_table=11
94
+ NC_002483.1 RefSeq gene 35618 36358 . + . ID=gene-D616_p97101;Dbxref=GeneID:1263535;Name=int;gbkey=Gene;gene=int;gene_biotype=protein_coding;locus_tag=D616_p97101;old_locus_tag=Fpla034
95
+ NC_002483.1 RefSeq CDS 35618 36358 . + 0 ID=cds-NP_061411.1;Parent=gene-D616_p97101;Dbxref=Genbank:NP_061411.1,GeneID:1263535;Name=NP_061411.1;Note=98 pct identical to sp:Q47036[Int protein of E.coli];gbkey=CDS;gene=int;locus_tag=D616_p97101;product=hypothetical protein;protein_id=NP_061411.1;transl_table=11
96
+ NC_002483.1 RefSeq repeat_region 35982 36002 . - . ID=id-NC_002483.1:35982..36002;Note=RepFIB repeat sequence;gbkey=repeat_region
97
+ NC_002483.1 RefSeq repeat_region 36377 36397 . - . ID=id-NC_002483.1:36377..36397;Note=RepFIB repeat sequence;gbkey=repeat_region
98
+ NC_002483.1 RefSeq repeat_region 36407 36427 . - . ID=id-NC_002483.1:36407..36427;Note=RepFIB repeat sequence;gbkey=repeat_region
99
+ NC_002483.1 RefSeq repeat_region 36425 36445 . - . ID=id-NC_002483.1:36425..36445;Note=RepFIB repeat sequence;gbkey=repeat_region
100
+ NC_002483.1 RefSeq repeat_region 36552 36572 . - . ID=id-NC_002483.1:36552..36572;Note=RepFIB repeat sequence;gbkey=repeat_region
101
+ NC_002483.1 RefSeq repeat_region 36592 36612 . - . ID=id-NC_002483.1:36592..36612;Note=RepFIB repeat sequence;gbkey=repeat_region
102
+ NC_002483.1 RefSeq repeat_region 36622 36642 . + . ID=id-NC_002483.1:36622..36642;Note=RepFIB repeat sequence;gbkey=repeat_region
103
+ NC_002483.1 RefSeq gene 36643 37620 . - . ID=gene-D616_p97094;Dbxref=GeneID:1263561;Name=repB;gbkey=Gene;gene=repB;gene_biotype=protein_coding;locus_tag=D616_p97094;old_locus_tag=Fpla035
104
+ NC_002483.1 RefSeq CDS 36643 37620 . - 0 ID=cds-NP_061412.1;Parent=gene-D616_p97094;Dbxref=Genbank:NP_061412.1,GeneID:1263561;Name=NP_061412.1;Note=100 pct identical to pir:A32310[RepFIB replication protein of plasmid P307];gbkey=CDS;gene=repB;locus_tag=D616_p97094;product=hypothetical protein;protein_id=NP_061412.1;transl_table=11
105
+ NC_002483.1 RefSeq repeat_region 37816 37836 . + . ID=id-NC_002483.1:37816..37836;Note=RepFIB repeat sequence;gbkey=repeat_region
106
+ NC_002483.1 RefSeq repeat_region 37837 37857 . + . ID=id-NC_002483.1:37837..37857;Note=RepFIB repeat sequence;gbkey=repeat_region
107
+ NC_002483.1 RefSeq repeat_region 37858 37878 . + . ID=id-NC_002483.1:37858..37878;Note=RepFIB repeat sequence;gbkey=repeat_region
108
+ NC_002483.1 RefSeq gene 37942 38403 . - . ID=gene-D616_p97024;Dbxref=GeneID:1263505;Name=ydhA;gbkey=Gene;gene=ydhA;gene_biotype=protein_coding;locus_tag=D616_p97024;old_locus_tag=Fpla036
109
+ NC_002483.1 RefSeq CDS 37942 38403 . - 0 ID=cds-NP_061413.1;Parent=gene-D616_p97024;Dbxref=Genbank:NP_061413.1,GeneID:1263505;Name=NP_061413.1;Note=75 pct identical to 122 residues of 159 aa protein gp:FPLREPFIB_3[ORF2 of plasmid IncF];gbkey=CDS;gene=ydhA;locus_tag=D616_p97024;product=hypothetical protein;protein_id=NP_061413.1;transl_table=11
110
+ NC_002483.1 RefSeq repeat_region 38218 38238 . - . ID=id-D616_p97024;Dbxref=GeneID:1263505;Note=RepFIB repeat sequence;gbkey=repeat_region;gene=ydhA;locus_tag=D616_p97024
111
+ NC_002483.1 RefSeq gene 38460 39101 . - . ID=gene-D616_p97023;Dbxref=GeneID:1263508;Name=ydiA;gbkey=Gene;gene=ydiA;gene_biotype=protein_coding;locus_tag=D616_p97023;old_locus_tag=Fpla037
112
+ NC_002483.1 RefSeq CDS 38460 39101 . - 0 ID=cds-NP_061414.1;Parent=gene-D616_p97023;Dbxref=Genbank:NP_061414.1,GeneID:1263508;Name=NP_061414.1;gbkey=CDS;gene=ydiA;locus_tag=D616_p97023;product=hypothetical protein;protein_id=NP_061414.1;transl_table=11
113
+ NC_002483.1 RefSeq gene 39088 39318 . + . ID=gene-D616_p97022;Dbxref=GeneID:1263500;Name=ydjA;gbkey=Gene;gene=ydjA;gene_biotype=protein_coding;locus_tag=D616_p97022;old_locus_tag=Fpla038
114
+ NC_002483.1 RefSeq CDS 39088 39318 . + 0 ID=cds-NP_061415.1;Parent=gene-D616_p97022;Dbxref=Genbank:NP_061415.1,GeneID:1263500;Name=NP_061415.1;gbkey=CDS;gene=ydjA;locus_tag=D616_p97022;product=hypothetical protein;protein_id=NP_061415.1;transl_table=11
115
+ NC_002483.1 RefSeq gene 40634 40870 . - . ID=gene-D616_p97021;Dbxref=GeneID:1263506;Name=yeaA;gbkey=Gene;gene=yeaA;gene_biotype=protein_coding;locus_tag=D616_p97021;old_locus_tag=Fpla039
116
+ NC_002483.1 RefSeq CDS 40634 40870 . - 0 ID=cds-NP_061416.1;Parent=gene-D616_p97021;Dbxref=Genbank:NP_061416.1,GeneID:1263506;Name=NP_061416.1;gbkey=CDS;gene=yeaA;locus_tag=D616_p97021;product=hypothetical protein;protein_id=NP_061416.1;transl_table=11
117
+ NC_002483.1 RefSeq gene 41216 41506 . + . ID=gene-D616_p97020;Dbxref=GeneID:1263504;Name=yebA;gbkey=Gene;gene=yebA;gene_biotype=protein_coding;locus_tag=D616_p97020;old_locus_tag=Fpla040
118
+ NC_002483.1 RefSeq CDS 41216 41506 . + 0 ID=cds-NP_061417.1;Parent=gene-D616_p97020;Dbxref=Genbank:NP_061417.1,GeneID:1263504;Name=NP_061417.1;gbkey=CDS;gene=yebA;locus_tag=D616_p97020;product=hypothetical protein;protein_id=NP_061417.1;transl_table=11
119
+ NC_002483.1 RefSeq gene 41496 42395 . + . ID=gene-D616_p97019;Dbxref=GeneID:1263545;Name=yebB;gbkey=Gene;gene=yebB;gene_biotype=protein_coding;locus_tag=D616_p97019;old_locus_tag=Fpla041
120
+ NC_002483.1 RefSeq CDS 41496 42395 . + 0 ID=cds-NP_061418.1;Parent=gene-D616_p97019;Dbxref=Genbank:NP_061418.1,GeneID:1263545;Name=NP_061418.1;gbkey=CDS;gene=yebB;locus_tag=D616_p97019;product=hypothetical protein;protein_id=NP_061418.1;transl_table=11
121
+ NC_002483.1 RefSeq gene 42445 44670 . - . ID=gene-D616_p97099;Dbxref=GeneID:1263512;Name=pifA;gbkey=Gene;gene=pifA;gene_biotype=protein_coding;locus_tag=D616_p97099;old_locus_tag=Fpla042
122
+ NC_002483.1 RefSeq CDS 42445 44670 . - 0 ID=cds-NP_061419.1;Parent=gene-D616_p97099;Dbxref=Genbank:NP_061419.1,GeneID:1263512;Name=NP_061419.1;Note=100 pct identical to 290 residues of 307 aa protein gp:ECU89941_1[PifA of plasmid F];gbkey=CDS;gene=pifA;locus_tag=D616_p97099;product=hypothetical protein;protein_id=NP_061419.1;transl_table=11
123
+ NC_002483.1 RefSeq sequence_difference 43446 43446 . + . ID=id-NC_002483.1:43446..43446;Note=conflict: C is changed to A in gb:M12987;compare=M12987.1;gbkey=misc_difference;replace=a
124
+ NC_002483.1 RefSeq gene 44672 45763 . - . ID=gene-D616_p97093;Dbxref=GeneID:1263560;Name=repC;gbkey=Gene;gene=repC;gene_biotype=protein_coding;locus_tag=D616_p97093
125
+ NC_002483.1 RefSeq CDS 44672 45763 . - 0 ID=cds-NP_061420.1;Parent=gene-D616_p97093;Dbxref=Genbank:NP_061420.1,GeneID:1263560;Name=NP_061420.1;Note=100 pct identical to sp:PFC2_ECOLI[RepC of plasmid F];gbkey=CDS;gene=repC;locus_tag=D616_p97093;product=replication protein;protein_id=NP_061420.1;transl_table=11
126
+ NC_002483.1 RefSeq sequence_difference 44709 44709 . + . ID=id-NC_002483.1:44709..44709;Note=conflict: deletion%2C G is added to gb:M12987;compare=M12987.1;gbkey=misc_difference
127
+ NC_002483.1 RefSeq sequence_difference 44736 44736 . + . ID=id-NC_002483.1:44736..44736;Note=conflict: deletion%2C C is added to gb:M12987;compare=M12987.1;gbkey=misc_difference
128
+ NC_002483.1 RefSeq sequence_difference 44747 44747 . + . ID=id-NC_002483.1:44747..44747;Note=conflict: C is changed to G in gb:M12987;compare=M12987.1;gbkey=misc_difference;replace=g
129
+ NC_002483.1 RefSeq sequence_difference 44769 44769 . + . ID=id-NC_002483.1:44769..44769;Note=conflict: deletion%2C G is added to gb:M12987;compare=M12987.1;gbkey=misc_difference
130
+ NC_002483.1 RefSeq sequence_difference 44816 44816 . + . ID=id-NC_002483.1:44816..44816;Note=conflict: deletion%2C C is added to gb:M12987;compare=M12987.1;gbkey=misc_difference
131
+ NC_002483.1 RefSeq sequence_feature 45922 45949 . + . ID=id-NC_002483.1:45922..45949;Note=rfsF site;gbkey=misc_feature
132
+ NC_002483.1 RefSeq sequence_feature 45934 46135 . + . ID=id-NC_002483.1:45934..46135;Note=oriV(ori-1) region%3B~strart point of oriV is unclear between 45934 and 45974;gbkey=misc_feature
133
+ NC_002483.1 RefSeq gene 46340 46558 . + . ID=gene-D616_p97106;Dbxref=GeneID:1263592;Name=ccdA(letA);gbkey=Gene;gene=ccdA(letA);gene_biotype=protein_coding;locus_tag=D616_p97106;old_locus_tag=Fpla044
134
+ NC_002483.1 RefSeq CDS 46340 46558 . + 0 ID=cds-NP_061421.1;Parent=gene-D616_p97106;Dbxref=Genbank:NP_061421.1,GeneID:1263592;Name=NP_061421.1;Note=100 pct identical to sp:LTA1_ECOLI[CcdA of plasmid F];gbkey=CDS;gene=ccdA(letA);locus_tag=D616_p97106;product=hypothetical protein;protein_id=NP_061421.1;transl_table=11
135
+ NC_002483.1 RefSeq gene 46560 46865 . + . ID=gene-D616_p97105;Dbxref=GeneID:1263593;Name=ccdB(letD);gbkey=Gene;gene=ccdB(letD);gene_biotype=protein_coding;locus_tag=D616_p97105;old_locus_tag=Fpla045
136
+ NC_002483.1 RefSeq CDS 46560 46865 . + 0 ID=cds-NP_061422.1;Parent=gene-D616_p97105;Dbxref=Genbank:NP_061422.1,GeneID:1263593;Name=NP_061422.1;Note=100 pct identical to sp:LTB2_ECOLI[CcdB of plasmid F];gbkey=CDS;gene=ccdB(letD);locus_tag=D616_p97105;product=hypothetical protein;protein_id=NP_061422.1;transl_table=11
137
+ NC_002483.1 RefSeq gene 46866 47672 . + . ID=gene-D616_p97090;Dbxref=GeneID:1263556;Name=resD;gbkey=Gene;gene=resD;gene_biotype=protein_coding;locus_tag=D616_p97090;old_locus_tag=Fpla046
138
+ NC_002483.1 RefSeq CDS 46866 47672 . + 0 ID=cds-NP_061423.1;Parent=gene-D616_p97090;Dbxref=Genbank:NP_061423.1,GeneID:1263556;Name=NP_061423.1;Note=99 pct identical to sp:REDF_ECOLI[ResD of plasmid F];gbkey=CDS;gene=resD;locus_tag=D616_p97090;product=resolvase;protein_id=NP_061423.1;transl_table=11
139
+ NC_002483.1 RefSeq sequence_difference 47310 47311 . + . ID=id-D616_p97090;Dbxref=GeneID:1263556;Note=conflict: AC is changed to CA in gb:M12987;compare=M12987.1;gbkey=misc_difference;gene=resD;locus_tag=D616_p97090;replace=ca
140
+ NC_002483.1 RefSeq sequence_difference 48030 48030 . + . ID=id-NC_002483.1:48030..48030;Note=conflict: deletion%2C T is added to gb: M12987;compare=M12987.1;gbkey=misc_difference
141
+ NC_002483.1 RefSeq sequence_difference 48051 48052 . + . ID=id-NC_002483.1:48051..48052;Note=conflict: deletion%2C AG is added to gb: M12987;compare=M12987.1;gbkey=misc_difference
142
+ NC_002483.1 RefSeq sequence_feature 48136 48352 . + . ID=id-NC_002483.1:48136..48352;Note=oriS(ori-2) region;gbkey=misc_feature
143
+ NC_002483.1 RefSeq repeat_region 48254 48273 . + . ID=id-NC_002483.1:48254..48273;Note=IncB direct repeat;gbkey=repeat_region
144
+ NC_002483.1 RefSeq repeat_region 48275 48294 . + . ID=id-NC_002483.1:48275..48294;Note=IncB direct repeat;gbkey=repeat_region
145
+ NC_002483.1 RefSeq repeat_region 48308 48327 . + . ID=id-NC_002483.1:48308..48327;Note=IncB direct repeat;gbkey=repeat_region
146
+ NC_002483.1 RefSeq repeat_region 48330 48349 . + . ID=id-NC_002483.1:48330..48349;Note=IncB direct repeat;gbkey=repeat_region
147
+ NC_002483.1 RefSeq gene 48446 49201 . + . ID=gene-D616_p97092;Dbxref=GeneID:1263547;Name=repE;gbkey=Gene;gene=repE;gene_biotype=protein_coding;locus_tag=D616_p97092
148
+ NC_002483.1 RefSeq CDS 48446 49201 . + 0 ID=cds-NP_061424.1;Parent=gene-D616_p97092;Dbxref=Genbank:NP_061424.1,GeneID:1263547;Name=NP_061424.1;Note=100 pct identical to sp:REPE_ECOLI[RepE of plasmid F];gbkey=CDS;gene=repE;locus_tag=D616_p97092;product=replication initiation protein;protein_id=NP_061424.1;transl_table=11
149
+ NC_002483.1 RefSeq repeat_region 49204 49222 . + . ID=id-NC_002483.1:49204..49222;Note=IncC direct repeat;gbkey=repeat_region
150
+ NC_002483.1 RefSeq repeat_region 49226 49244 . + . ID=id-NC_002483.1:49226..49244;Note=IncC direct repeat;gbkey=repeat_region
151
+ NC_002483.1 RefSeq repeat_region 49259 49277 . + . ID=id-NC_002483.1:49259..49277;Note=IncC direct repeat;gbkey=repeat_region
152
+ NC_002483.1 RefSeq repeat_region 49350 49368 . + . ID=id-NC_002483.1:49350..49368;Note=IncC direct repeat;gbkey=repeat_region
153
+ NC_002483.1 RefSeq repeat_region 49433 49451 . + . ID=id-NC_002483.1:49433..49451;Note=IncC direct repeat;gbkey=repeat_region
154
+ NC_002483.1 RefSeq gene 49780 50955 . + . ID=gene-D616_p97089;Dbxref=GeneID:1263522;Name=sopA;gbkey=Gene;gene=sopA;gene_biotype=protein_coding;locus_tag=D616_p97089;old_locus_tag=Fpla048
155
+ NC_002483.1 RefSeq CDS 49780 50955 . + 0 ID=cds-NP_061425.3;Parent=gene-D616_p97089;Dbxref=Genbank:NP_061425.3,GeneID:1263522;Name=NP_061425.3;Note=100 pct identical to gp:FPLMCG_6[SopA of plasmid F];gbkey=CDS;gene=sopA;locus_tag=D616_p97089;product=hypothetical protein;protein_id=NP_061425.3;transl_table=11
156
+ NC_002483.1 RefSeq gene 50955 51926 . + . ID=gene-D616_p97088;Dbxref=GeneID:1263559;Name=sopB;gbkey=Gene;gene=sopB;gene_biotype=protein_coding;locus_tag=D616_p97088
157
+ NC_002483.1 RefSeq CDS 50955 51926 . + 0 ID=cds-NP_061426.1;Parent=gene-D616_p97088;Dbxref=Genbank:NP_061426.1,GeneID:1263559;Name=NP_061426.1;Note=100 pct identical to sp:SOPB_ECOLI[SopB of plasmid F];gbkey=CDS;gene=sopB;locus_tag=D616_p97088;product=hypothetical protein;protein_id=NP_061426.1;transl_table=11
158
+ NC_002483.1 RefSeq repeat_region 51999 52042 . + . ID=id-NC_002483.1:51999..52042;Note=IncD(sopC) direct repeat;gbkey=repeat_region
159
+ NC_002483.1 RefSeq repeat_region 52043 52085 . + . ID=id-NC_002483.1:52043..52085;Note=IncD(sopC) direct repeat;gbkey=repeat_region
160
+ NC_002483.1 RefSeq repeat_region 52086 52128 . + . ID=id-NC_002483.1:52086..52128;Note=IncD(sopC) direct repeat;gbkey=repeat_region
161
+ NC_002483.1 RefSeq repeat_region 52129 52171 . + . ID=id-NC_002483.1:52129..52171;Note=IncD(sopC) direct repeat;gbkey=repeat_region
162
+ NC_002483.1 RefSeq repeat_region 52172 52214 . + . ID=id-NC_002483.1:52172..52214;Note=IncD(sopC) direct repeat;gbkey=repeat_region
163
+ NC_002483.1 RefSeq repeat_region 52215 52257 . + . ID=id-NC_002483.1:52215..52257;Note=IncD(sopC) direct repeat;gbkey=repeat_region
164
+ NC_002483.1 RefSeq repeat_region 52258 52300 . + . ID=id-NC_002483.1:52258..52300;Note=IncD(sopC) direct repeat;gbkey=repeat_region
165
+ NC_002483.1 RefSeq repeat_region 52301 52343 . + . ID=id-NC_002483.1:52301..52343;Note=IncD(sopC) direct repeat;gbkey=repeat_region
166
+ NC_002483.1 RefSeq sequence_difference 52320 52320 . + . ID=id-NC_002483.1:52320..52320;Note=conflict: G is changed to A in gb:M12987;compare=M12987.1;gbkey=misc_difference;replace=a
167
+ NC_002483.1 RefSeq repeat_region 52344 52386 . + . ID=id-NC_002483.1:52344..52386;Note=IncD(sopC) direct repeat;gbkey=repeat_region
168
+ NC_002483.1 RefSeq repeat_region 52387 52429 . + . ID=id-NC_002483.1:52387..52429;Note=IncD(sopC) direct repeat;gbkey=repeat_region
169
+ NC_002483.1 RefSeq repeat_region 52430 52472 . + . ID=id-NC_002483.1:52430..52472;Note=IncD(sopC) direct repeat;gbkey=repeat_region
170
+ NC_002483.1 RefSeq gene 52569 52841 . + . ID=gene-D616_p97018;Dbxref=GeneID:1263598;Name=yfcA;gbkey=Gene;gene=yfcA;gene_biotype=protein_coding;locus_tag=D616_p97018;old_locus_tag=Fpla050
171
+ NC_002483.1 RefSeq CDS 52569 52841 . + 0 ID=cds-NP_061427.1;Parent=gene-D616_p97018;Dbxref=Genbank:NP_061427.1,GeneID:1263598;Name=NP_061427.1;Note=96 pct identical to gp:AB021078_30[YccA of plasmid ColIb-P9];gbkey=CDS;gene=yfcA;locus_tag=D616_p97018;product=hypothetical protein;protein_id=NP_061427.1;transl_table=11
172
+ NC_002483.1 RefSeq sequence_difference 52762 52762 . + . ID=id-D616_p97018;Dbxref=GeneID:1263598;Note=conflict: deletion%2C G is added to gb:M12987;compare=M12987.1;gbkey=misc_difference;gene=yfcA;locus_tag=D616_p97018
173
+ NC_002483.1 RefSeq gene 52855 53361 . + . ID=gene-D616_p97017;Dbxref=GeneID:1263495;Name=yfcB;gbkey=Gene;gene=yfcB;gene_biotype=protein_coding;locus_tag=D616_p97017;old_locus_tag=Fpla051
174
+ NC_002483.1 RefSeq CDS 52855 53361 . + 0 ID=cds-NP_061428.1;Parent=gene-D616_p97017;Dbxref=Genbank:NP_061428.1,GeneID:1263495;Name=NP_061428.1;Note=100 pct identical to gp:AF106329_1[orf168 of plasmid F];gbkey=CDS;gene=yfcB;locus_tag=D616_p97017;product=hypothetical protein;protein_id=NP_061428.1;transl_table=11
175
+ NC_002483.1 RefSeq gene 53343 53780 . + . ID=gene-D616_p97016;Dbxref=GeneID:1263599;Name=yfdA;gbkey=Gene;gene=yfdA;gene_biotype=protein_coding;locus_tag=D616_p97016;old_locus_tag=Fpla052
176
+ NC_002483.1 RefSeq CDS 53343 53780 . + 0 ID=cds-NP_061429.1;Parent=gene-D616_p97016;Dbxref=Genbank:NP_061429.1,GeneID:1263599;Name=NP_061429.1;Note=100 pct identical to gp:AF106329_2[orf145 of plasmid F];gbkey=CDS;gene=yfdA;locus_tag=D616_p97016;product=hypothetical protein;protein_id=NP_061429.1;transl_table=11
177
+ NC_002483.1 RefSeq sequence_difference 53741 53741 . + . ID=id-D616_p97016;Dbxref=GeneID:1263599;Note=conflict: G is changed to C in gb:AF106329;compare=AF106329.1;gbkey=misc_difference;gene=yfdA;locus_tag=D616_p97016;replace=c
178
+ NC_002483.1 RefSeq gene 53784 54089 . + . ID=gene-D616_p97015;Dbxref=GeneID:1263490;Name=yfdB;gbkey=Gene;gene=yfdB;gene_biotype=protein_coding;locus_tag=D616_p97015;old_locus_tag=Fpla053
179
+ NC_002483.1 RefSeq CDS 53784 54089 . + 0 ID=cds-NP_061430.1;Parent=gene-D616_p97015;Dbxref=Genbank:NP_061430.1,GeneID:1263490;Name=NP_061430.1;Note=100 pct identical to gp:AF106329_3[orf101 of plasmid F];gbkey=CDS;gene=yfdB;locus_tag=D616_p97015;product=hypothetical protein;protein_id=NP_061430.1;transl_table=11
180
+ NC_002483.1 RefSeq gene 54166 54849 . + . ID=gene-D616_p97014;Dbxref=GeneID:1263496;Name=yfeA;gbkey=Gene;gene=yfeA;gene_biotype=protein_coding;locus_tag=D616_p97014;old_locus_tag=Fpla054
181
+ NC_002483.1 RefSeq CDS 54166 54849 . + 0 ID=cds-NP_061431.1;Parent=gene-D616_p97014;Dbxref=Genbank:NP_061431.1,GeneID:1263496;Name=NP_061431.1;Note=100 pct identical to gp:AF106329_4[orf227 of plasmid F];gbkey=CDS;gene=yfeA;locus_tag=D616_p97014;product=hypothetical protein;protein_id=NP_061431.1;transl_table=11
182
+ NC_002483.1 RefSeq gene 54850 55071 . + . ID=gene-D616_p97013;Dbxref=GeneID:1263491;Name=yfeB;gbkey=Gene;gene=yfeB;gene_biotype=protein_coding;locus_tag=D616_p97013;old_locus_tag=Fpla055
183
+ NC_002483.1 RefSeq CDS 54850 55071 . + 0 ID=cds-NP_061432.1;Parent=gene-D616_p97013;Dbxref=Genbank:NP_061432.1,GeneID:1263491;Name=NP_061432.1;Note=100 pct identical to gp:AF106329_5[orf73 of plasmid F];gbkey=CDS;gene=yfeB;locus_tag=D616_p97013;product=hypothetical protein;protein_id=NP_061432.1;transl_table=11
184
+ NC_002483.1 RefSeq gene 55085 55519 . + . ID=gene-D616_p97012;Dbxref=GeneID:1263532;Name=yffA;gbkey=Gene;gene=yffA;gene_biotype=protein_coding;locus_tag=D616_p97012;old_locus_tag=Fpla056
185
+ NC_002483.1 RefSeq CDS 55085 55519 . + 0 ID=cds-NP_061433.1;Parent=gene-D616_p97012;Dbxref=Genbank:NP_061433.1,GeneID:1263532;Name=NP_061433.1;Note=100 pct identical to gp:AF106329_6[orf144 of plasmid F];gbkey=CDS;gene=yffA;locus_tag=D616_p97012;product=hypothetical protein;protein_id=NP_061433.1;transl_table=11
186
+ NC_002483.1 RefSeq gene 55565 56341 . + . ID=gene-D616_p97011;Dbxref=GeneID:1263492;Name=yffB;gbkey=Gene;gene=yffB;gene_biotype=protein_coding;locus_tag=D616_p97011;old_locus_tag=Fpla057
187
+ NC_002483.1 RefSeq CDS 55565 56341 . + 0 ID=cds-NP_061434.1;Parent=gene-D616_p97011;Dbxref=Genbank:NP_061434.1,GeneID:1263492;Name=NP_061434.1;Note=100 pct identical to gp:AF106329_7[orf248 of plasmid F];gbkey=CDS;gene=yffB;locus_tag=D616_p97011;product=hypothetical protein;protein_id=NP_061434.1;transl_table=11
188
+ NC_002483.1 RefSeq sequence_difference 56074 56074 . + . ID=id-D616_p97011;Dbxref=GeneID:1263492;Note=conflict: C is changed to G in gb:AF106329;compare=AF106329.1;gbkey=misc_difference;gene=yffB;locus_tag=D616_p97011;replace=g
189
+ NC_002483.1 RefSeq gene 56429 56740 . + . ID=gene-D616_p97010;Dbxref=GeneID:1263510;Name=yfgA;gbkey=Gene;gene=yfgA;gene_biotype=protein_coding;locus_tag=D616_p97010;old_locus_tag=Fpla058
190
+ NC_002483.1 RefSeq CDS 56429 56740 . + 0 ID=cds-NP_061435.1;Parent=gene-D616_p97010;Dbxref=Genbank:NP_061435.1,GeneID:1263510;Name=NP_061435.1;Note=98 pct identical to 101 residues of 156 aa protein gp:AB021078_37[YcgA of plasmid ColIb-P9];gbkey=CDS;gene=yfgA;locus_tag=D616_p97010;product=hypothetical protein;protein_id=NP_061435.1;transl_table=11
191
+ NC_002483.1 RefSeq gene 56755 57180 . + . ID=gene-D616_p97009;Dbxref=GeneID:1263597;Name=yfgB;gbkey=Gene;gene=yfgB;gene_biotype=protein_coding;locus_tag=D616_p97009;old_locus_tag=Fpla059
192
+ NC_002483.1 RefSeq CDS 56755 57180 . + 0 ID=cds-NP_061436.1;Parent=gene-D616_p97009;Dbxref=Genbank:NP_061436.1,GeneID:1263597;Name=NP_061436.1;Note=100 pct identical to gp:AF106329_9[orf141 of plasmid F];gbkey=CDS;gene=yfgB;locus_tag=D616_p97009;product=hypothetical protein;protein_id=NP_061436.1;transl_table=11
193
+ NC_002483.1 RefSeq gene 57227 57649 . + . ID=gene-D616_p97008;Dbxref=GeneID:1263596;Name=yfhA;gbkey=Gene;gene=yfhA;gene_biotype=protein_coding;locus_tag=D616_p97008;old_locus_tag=Fpla060
194
+ NC_002483.1 RefSeq CDS 57227 57649 . + 0 ID=cds-NP_061437.1;Parent=gene-D616_p97008;Dbxref=Genbank:NP_061437.1,GeneID:1263596;Name=NP_061437.1;Note=100 pct identical to gp:AF106329_10[orf140 of plasmid F];gbkey=CDS;gene=yfhA;locus_tag=D616_p97008;product=hypothetical protein;protein_id=NP_061437.1;transl_table=11
195
+ NC_002483.1 RefSeq gene 57956 58354 . + . ID=gene-D616_p97007;Dbxref=GeneID:1263590;Name=yfhB;gbkey=Gene;gene=yfhB;gene_biotype=protein_coding;locus_tag=D616_p97007;old_locus_tag=Fpla061
196
+ NC_002483.1 RefSeq CDS 57956 58354 . + 0 ID=cds-NP_061438.1;Parent=gene-D616_p97007;Dbxref=Genbank:NP_061438.1,GeneID:1263590;Name=NP_061438.1;Note=97 pct identical (1 gap) to pir:T00282[hypothetical protein of plasmid pO157];gbkey=CDS;gene=yfhB;locus_tag=D616_p97007;product=hypothetical protein;protein_id=NP_061438.1;transl_table=11
197
+ NC_002483.1 RefSeq direct_repeat 57997 58086 . + . ID=id-D616_p97007;Dbxref=GeneID:1263590;gbkey=repeat_region;gene=yfhB;locus_tag=D616_p97007;rpt_type=direct
198
+ NC_002483.1 RefSeq repeat_region 58081 58621 . + . ID=id-NC_002483.1:58081..58621;Note=repeat D;gbkey=repeat_region
199
+ NC_002483.1 RefSeq gene 58643 59182 . + . ID=gene-D616_p97085;Dbxref=GeneID:1263584;Name=ssb;gbkey=Gene;gene=ssb;gene_biotype=protein_coding;locus_tag=D616_p97085;old_locus_tag=Fpla062
200
+ NC_002483.1 RefSeq CDS 58643 59182 . + 0 ID=cds-NP_061439.1;Parent=gene-D616_p97085;Dbxref=Genbank:NP_061439.1,GeneID:1263584;Name=NP_061439.1;Note=100 pct identical to gp:AF106329_13[Ssb of plasmid F];gbkey=CDS;gene=ssb;locus_tag=D616_p97085;product=single-strand DNA binding protein;protein_id=NP_061439.1;transl_table=11
201
+ NC_002483.1 RefSeq gene 59233 59472 . + . ID=gene-D616_p97006;Dbxref=GeneID:1263591;Name=yfjA;gbkey=Gene;gene=yfjA;gene_biotype=protein_coding;locus_tag=D616_p97006;old_locus_tag=Fpla063
202
+ NC_002483.1 RefSeq CDS 59233 59472 . + 0 ID=cds-NP_061440.1;Parent=gene-D616_p97006;Dbxref=Genbank:NP_061440.1,GeneID:1263591;Name=NP_061440.1;Note=100 pct identical to gp:AF106329_14[orf77 of plasmid F];gbkey=CDS;gene=yfjA;locus_tag=D616_p97006;product=hypothetical protein;protein_id=NP_061440.1;transl_table=11
203
+ NC_002483.1 RefSeq gene 59538 61496 . + . ID=gene-D616_p97005;Dbxref=GeneID:1263594;Name=yfjB;gbkey=Gene;gene=yfjB;gene_biotype=protein_coding;locus_tag=D616_p97005;old_locus_tag=Fpla064
204
+ NC_002483.1 RefSeq CDS 59538 61496 . + 0 ID=cds-NP_061441.1;Parent=gene-D616_p97005;Dbxref=Genbank:NP_061441.1,GeneID:1263594;Name=NP_061441.1;Note=100 pct identical to gp:AF106329_15[orf652 of plasmid F];gbkey=CDS;gene=yfjB;locus_tag=D616_p97005;product=hypothetical protein;protein_id=NP_061441.1;transl_table=11
205
+ NC_002483.1 RefSeq gene 61551 61985 . + . ID=gene-D616_p97097;Dbxref=GeneID:1263521;Name=psiB;gbkey=Gene;gene=psiB;gene_biotype=protein_coding;locus_tag=D616_p97097;old_locus_tag=Fpla065
206
+ NC_002483.1 RefSeq CDS 61551 61985 . + 0 ID=cds-NP_061442.1;Parent=gene-D616_p97097;Dbxref=Genbank:NP_061442.1,GeneID:1263521;Name=NP_061442.1;Note=100 pct identical to sp:PSB1_ECOLI[PsiB of plasmid F];gbkey=CDS;gene=psiB;locus_tag=D616_p97097;product=hypothetical protein;protein_id=NP_061442.1;transl_table=11
207
+ NC_002483.1 RefSeq gene 61982 62701 . + . ID=gene-D616_p97098;Dbxref=GeneID:1263537;Name=psiA;gbkey=Gene;gene=psiA;gene_biotype=protein_coding;locus_tag=D616_p97098;old_locus_tag=Fpla066
208
+ NC_002483.1 RefSeq CDS 61982 62701 . + 0 ID=cds-NP_061443.1;Parent=gene-D616_p97098;Dbxref=Genbank:NP_061443.1,GeneID:1263537;Name=NP_061443.1;Note=100 pct identical to sp:PSA1_ECOLI[PsiA of plasmid F];gbkey=CDS;gene=psiA;locus_tag=D616_p97098;product=hypothetical protein;protein_id=NP_061443.1;transl_table=11
209
+ NC_002483.1 RefSeq repeat_region 62057 62066 . + . ID=id-D616_p97098;Dbxref=GeneID:1263537;Note=inverted repeat A;gbkey=repeat_region;gene=psiA;locus_tag=D616_p97098
210
+ NC_002483.1 RefSeq repeat_region 62107 62116 . + . ID=id-D616_p97098-2;Dbxref=GeneID:1263537;Note=inverted repeat A';gbkey=repeat_region;gene=psiA;locus_tag=D616_p97098
211
+ NC_002483.1 RefSeq gene 62827 62927 . - . ID=gene-D616_s97003;Dbxref=GeneID:1263558;Name=flmB;gbkey=Gene;gene=flmB;gene_biotype=antisense_RNA;locus_tag=D616_s97003;old_locus_tag=Fplas003
212
+ NC_002483.1 RefSeq antisense_RNA 62827 62927 . - . ID=rna-D616_s97003;Parent=gene-D616_s97003;Dbxref=GeneID:1263558;Note=antisense RNA of flmC mRNAs;gbkey=ncRNA;gene=flmB;locus_tag=D616_s97003
213
+ NC_002483.1 RefSeq exon 62827 62927 . - . ID=exon-D616_s97003-1;Parent=rna-D616_s97003;Dbxref=GeneID:1263558;Note=antisense RNA of flmC mRNAs;gbkey=ncRNA;gene=flmB;locus_tag=D616_s97003
214
+ NC_002483.1 RefSeq repeat_region 62880 62893 . + . ID=id-NC_002483.1:62880..62893;Note=inverted repeat I copy A;gbkey=repeat_region
215
+ NC_002483.1 RefSeq repeat_region 62899 62913 . + . ID=id-NC_002483.1:62899..62913;Note=inverted repeat I copy B;gbkey=repeat_region
216
+ NC_002483.1 RefSeq gene 62918 63130 . + . ID=gene-D616_p97102;Dbxref=GeneID:1263583;Name=flmC;gbkey=Gene;gene=flmC;gene_biotype=protein_coding;locus_tag=D616_p97102;old_locus_tag=Fpla067
217
+ NC_002483.1 RefSeq CDS 62918 63130 . + 0 ID=cds-NP_061444.1;Parent=gene-D616_p97102;Dbxref=Genbank:NP_061444.1,GeneID:1263583;Name=NP_061444.1;Note=100 pct identical to sp:FLCA1_ECOLI[FlmC of plasmid F];gbkey=CDS;gene=flmC;locus_tag=D616_p97102;product=hypothetical protein;protein_id=NP_061444.1;transl_table=11
218
+ NC_002483.1 RefSeq repeat_region 62942 62955 . + . ID=id-D616_p97102;Dbxref=GeneID:1263583;Note=inverted repeat II copy A;gbkey=repeat_region;gene=flmC;locus_tag=D616_p97102
219
+ NC_002483.1 RefSeq gene 62976 63134 . + . ID=gene-D616_p97103;Dbxref=GeneID:1263569;Name=flmA;gbkey=Gene;gene=flmA;gene_biotype=protein_coding;locus_tag=D616_p97103;old_locus_tag=Fpla068
220
+ NC_002483.1 RefSeq CDS 62976 63134 . + 0 ID=cds-NP_061445.1;Parent=gene-D616_p97103;Dbxref=Genbank:NP_061445.1,GeneID:1263569;Name=NP_061445.1;Note=100 pct identical to sp:FLMA_ECOLI[FlmA of plasmid F];gbkey=CDS;gene=flmA;locus_tag=D616_p97103;product=hypothetical protein;protein_id=NP_061445.1;transl_table=11
221
+ NC_002483.1 RefSeq repeat_region 62978 63136 . + . ID=id-NC_002483.1:62978..63136;Note=inverted repeat II copy B;gbkey=repeat_region
222
+ NC_002483.1 RefSeq repeat_region 63135 63152 . + . ID=id-NC_002483.1:63135..63152;Note=inverted repeat III copy A;gbkey=repeat_region
223
+ NC_002483.1 RefSeq repeat_region 63157 63174 . + . ID=id-NC_002483.1:63157..63174;Note=inverted repeat III copy B;gbkey=repeat_region
224
+ NC_002483.1 RefSeq repeat_region 63208 63221 . + . ID=id-NC_002483.1:63208..63221;Note=inverted repeat IV copy A;gbkey=repeat_region
225
+ NC_002483.1 RefSeq repeat_region 63226 63239 . + . ID=id-NC_002483.1:63226..63239;Note=inverted repeat IV copy B;gbkey=repeat_region
226
+ NC_002483.1 RefSeq gene 63372 63689 . - . ID=gene-D616_p97004;Dbxref=GeneID:1263498;Name=ygdA;gbkey=Gene;gene=ygdA;gene_biotype=protein_coding;locus_tag=D616_p97004;old_locus_tag=Fpla069
227
+ NC_002483.1 RefSeq CDS 63372 63689 . - 0 ID=cds-NP_061446.1;Parent=gene-D616_p97004;Dbxref=Genbank:NP_061446.1,GeneID:1263498;Name=NP_061446.1;Note=80 pct identical (1 gap) to 98 residues of 125 aa protein gp:AP000342_60[YehA of plasmid R100];gbkey=CDS;gene=ygdA;locus_tag=D616_p97004;product=hypothetical protein;protein_id=NP_061446.1;transl_table=11
228
+ NC_002483.1 RefSeq repeat_region 63469 64011 . + . ID=id-NC_002483.1:63469..64011;Note=repeat D;gbkey=repeat_region
229
+ NC_002483.1 RefSeq gene 64032 64319 . + . ID=gene-D616_p97003;Dbxref=GeneID:1263534;Name=ygeA;gbkey=Gene;gene=ygeA;gene_biotype=protein_coding;locus_tag=D616_p97003;old_locus_tag=Fpla070
230
+ NC_002483.1 RefSeq CDS 64032 64319 . + 0 ID=cds-NP_061447.1;Parent=gene-D616_p97003;Dbxref=Genbank:NP_061447.1,GeneID:1263534;Name=NP_061447.1;Note=100 pct identical to pir:S07013[hypothetical protein 95 (oriT 5' region) of plasmid F];gbkey=CDS;gene=ygeA;locus_tag=D616_p97003;product=hypothetical protein;protein_id=NP_061447.1;transl_table=11
231
+ NC_002483.1 RefSeq gene 64438 65259 . + . ID=gene-D616_p97002;Dbxref=GeneID:1263600;Name=ygeB;gbkey=Gene;gene=ygeB;gene_biotype=protein_coding;locus_tag=D616_p97002;old_locus_tag=Fpla071
232
+ NC_002483.1 RefSeq CDS 64438 65259 . + 0 ID=cds-NP_061448.1;Parent=gene-D616_p97002;Dbxref=Genbank:NP_061448.1,GeneID:1263600;Name=NP_061448.1;Note=99 pct identical to sp:G321_ECOLI[hypothetical protein 273 (oriT 5' region) of plasmid F];gbkey=CDS;gene=ygeB;locus_tag=D616_p97002;product=hypothetical protein;protein_id=NP_061448.1;transl_table=11
233
+ NC_002483.1 RefSeq sequence_difference 64598 64598 . + . ID=id-D616_p97002;Dbxref=GeneID:1263600;Note=conflict: A is changed to C in gb:AF106329;compare=AF106329.1;gbkey=misc_difference;gene=ygeB;locus_tag=D616_p97002;replace=c
234
+ NC_002483.1 RefSeq gene 65556 66065 . - . ID=gene-D616_p97001;Dbxref=GeneID:1263507;Name=ygfA;gbkey=Gene;gene=ygfA;gene_biotype=protein_coding;locus_tag=D616_p97001;old_locus_tag=Fpla072
235
+ NC_002483.1 RefSeq CDS 65556 66065 . - 0 ID=cds-NP_061449.1;Parent=gene-D616_p97001;Dbxref=Genbank:NP_061449.1,GeneID:1263507;Name=NP_061449.1;Note=100 pct identical to sp:X194_ECOLI[hypothetical protein 169 precursor (oriT 5' region) of plasmid F];gbkey=CDS;gene=ygfA;locus_tag=D616_p97001;product=hypothetical protein;protein_id=NP_061449.1;transl_table=11
236
+ NC_002483.1 RefSeq oriT 66118 66407 . + . ID=id-NC_002483.1:66118..66407;gbkey=oriT
237
+ NC_002483.1 RefSeq inverted_repeat 66130 66149 . + . ID=id-NC_002483.1:66130..66149;gbkey=repeat_region;rpt_type=inverted;rpt_unit_range=66130..66137
238
+ NC_002483.1 RefSeq inverted_repeat 66156 66173 . + . ID=id-NC_002483.1:66156..66173;Note=posssible TraI binding site;gbkey=repeat_region;rpt_type=inverted;rpt_unit_range=66156..66163
239
+ NC_002483.1 RefSeq sequence_feature 66157 66157 . + . ID=id-NC_002483.1:66157..66157;Note=nicking site;gbkey=misc_feature
240
+ NC_002483.1 RefSeq inverted_repeat 66250 66294 . + . ID=id-NC_002483.1:66250..66294;Note=sbmC%2C TraM binding site;gbkey=repeat_region;rpt_type=inverted;rpt_unit_range=66250..66267
241
+ NC_002483.1 RefSeq direct_repeat 66340 66407 . + . ID=id-NC_002483.1:66340..66407;Note=sbmB and sbmA%2C TraM binding site;gbkey=repeat_region;rpt_type=direct;rpt_unit_range=66340..66361
242
+ NC_002483.1 RefSeq gene 66479 66862 . + . ID=gene-D616_p97066;Dbxref=GeneID:1263565;Name=traM;gbkey=Gene;gene=traM;gene_biotype=protein_coding;locus_tag=D616_p97066
243
+ NC_002483.1 RefSeq CDS 66479 66862 . + 0 ID=cds-NP_061450.1;Parent=gene-D616_p97066;Dbxref=Genbank:NP_061450.1,GeneID:1263565;Name=NP_061450.1;Note=100 pct identical to sp:TRM1_ECOLI[TraM of plasmid F];gbkey=CDS;gene=traM;locus_tag=D616_p97066;product=hypothetical protein;protein_id=NP_061450.1;transl_table=11
244
+ NC_002483.1 RefSeq inverted_repeat 66944 66960 . + . ID=id-NC_002483.1:66944..66960;Note=possible CRP binding site;gbkey=repeat_region;rpt_type=inverted;rpt_unit_range=66944..66949
245
+ NC_002483.1 RefSeq gene 66977 67055 . - . ID=gene-D616_s97004;Dbxref=GeneID:14667384;Name=finP;gbkey=Gene;gene=finP;gene_biotype=antisense_RNA;locus_tag=D616_s97004
246
+ NC_002483.1 RefSeq antisense_RNA 66977 67055 . - . ID=rna-D616_s97004;Parent=gene-D616_s97004;Dbxref=GeneID:14667384;Note=antisense RNA of traY-Z mRNA;gbkey=ncRNA;gene=finP;locus_tag=D616_s97004
247
+ NC_002483.1 RefSeq exon 66977 67055 . - . ID=exon-D616_s97004-1;Parent=rna-D616_s97004;Dbxref=GeneID:14667384;Note=antisense RNA of traY-Z mRNA;gbkey=ncRNA;gene=finP;locus_tag=D616_s97004
248
+ NC_002483.1 RefSeq inverted_repeat 66985 67015 . + . ID=id-NC_002483.1:66985..67015;Note=FinP antisense RNA stem-loop 2;gbkey=repeat_region;rpt_type=inverted;rpt_unit_range=66985..66996
249
+ NC_002483.1 RefSeq inverted_repeat 67022 67051 . + . ID=id-NC_002483.1:67022..67051;Note=FinP antisense RNA stem-loop 1;gbkey=repeat_region;rpt_type=inverted;rpt_unit_range=67022..67032
250
+ NC_002483.1 RefSeq gene 67049 67738 . + . ID=gene-D616_p97072;Dbxref=GeneID:1263572;Name=traJ;gbkey=Gene;gene=traJ;gene_biotype=protein_coding;locus_tag=D616_p97072
251
+ NC_002483.1 RefSeq CDS 67049 67738 . + 0 ID=cds-NP_061451.1;Parent=gene-D616_p97072;Dbxref=Genbank:NP_061451.1,GeneID:1263572;Name=NP_061451.1;Note=100 pct identical to sp:TRAJ1_ECOLI[TraJ of plasmid F];gbkey=CDS;gene=traJ;locus_tag=D616_p97072;product=hypothetical protein;protein_id=NP_061451.1;transl_table=11
252
+ NC_002483.1 RefSeq inverted_repeat 67654 67674 . + . ID=id-D616_p97072;Dbxref=GeneID:1263572;Note=terminator of traJ mRNA;gbkey=repeat_region;gene=traJ;locus_tag=D616_p97072;rpt_type=inverted;rpt_unit_range=67654..67661
253
+ NC_002483.1 RefSeq gene 67837 68232 . + . ID=gene-D616_p97057;Dbxref=GeneID:1263531;Name=traY;gbkey=Gene;gene=traY;gene_biotype=protein_coding;locus_tag=D616_p97057;old_locus_tag=Fpla075
254
+ NC_002483.1 RefSeq CDS 67837 68232 . + 0 ID=cds-NP_061452.1;Parent=gene-D616_p97057;Dbxref=Genbank:NP_061452.1,GeneID:1263531;Name=NP_061452.1;Note=100 pct identical to sp:TRY1_ECOLI[TraY of plasmid F];gbkey=CDS;gene=traY;locus_tag=D616_p97057;product=hypothetical protein;protein_id=NP_061452.1;transl_table=11
255
+ NC_002483.1 RefSeq sequence_difference 67995 67995 . + . ID=id-D616_p97057;Dbxref=GeneID:1263531;Note=conflict: A is changed to G in gb:U01159;compare=U01159.2;gbkey=misc_difference;gene=traY;locus_tag=D616_p97057;replace=g
256
+ NC_002483.1 RefSeq gene 68265 68630 . + . ID=gene-D616_p97080;Dbxref=GeneID:1263548;Name=traA;gbkey=Gene;gene=traA;gene_biotype=protein_coding;locus_tag=D616_p97080;old_locus_tag=Fpla076
257
+ NC_002483.1 RefSeq CDS 68265 68630 . + 0 ID=cds-NP_061453.1;Parent=gene-D616_p97080;Dbxref=Genbank:NP_061453.1,GeneID:1263548;Name=NP_061453.1;Note=100 pct identical to sp:PIL1_ECOLI[TraA of plasmid F];gbkey=CDS;gene=traA;locus_tag=D616_p97080;product=prepropilin;protein_id=NP_061453.1;transl_table=11
258
+ NC_002483.1 RefSeq gene 68645 68956 . + . ID=gene-D616_p97069;Dbxref=GeneID:1263564;Name=traL;gbkey=Gene;gene=traL;gene_biotype=protein_coding;locus_tag=D616_p97069;old_locus_tag=Fpla077
259
+ NC_002483.1 RefSeq CDS 68645 68956 . + 0 ID=cds-NP_061454.1;Parent=gene-D616_p97069;Dbxref=Genbank:NP_061454.1,GeneID:1263564;Name=NP_061454.1;Note=99 pct identical to 103 aa protein sp:AP000342_68[TraL of plasmid R100];gbkey=CDS;gene=traL;locus_tag=D616_p97069;product=hypothetical protein;protein_id=NP_061454.1;transl_table=11
260
+ NC_002483.1 RefSeq sequence_difference 68914 68914 . + . ID=id-D616_p97069;Dbxref=GeneID:1263564;Note=conflict: T is omitted from in gb:U01159;compare=U01159.2;gbkey=misc_difference;gene=traL;locus_tag=D616_p97069;replace=t
261
+ NC_002483.1 RefSeq inverted_repeat 68648 68686 . + . ID=id-D616_p97069-2;Dbxref=GeneID:1263564;Note=tra mRNA core stability region;gbkey=repeat_region;gene=traL;locus_tag=D616_p97069;rpt_type=inverted;rpt_unit_range=68648..68652
262
+ NC_002483.1 RefSeq inverted_repeat 68700 68814 . + . ID=id-D616_p97069-3;Dbxref=GeneID:1263564;Note=tra mRNA core stability region;gbkey=repeat_region;gene=traL;locus_tag=D616_p97069;rpt_type=inverted;rpt_unit_range=68700..68726
263
+ NC_002483.1 RefSeq sequence_difference 68972 68972 . + . ID=id-NC_002483.1:68972..68972;Note=conflict: deletion%2C T is added to gb:U01159;compare=U01159.2;gbkey=misc_difference
264
+ NC_002483.1 RefSeq gene 68978 69544 . + . ID=gene-D616_p97074;Dbxref=GeneID:1263497;Name=traE;gbkey=Gene;gene=traE;gene_biotype=protein_coding;locus_tag=D616_p97074;old_locus_tag=Fpla078
265
+ NC_002483.1 RefSeq CDS 68978 69544 . + 0 ID=cds-NP_061455.1;Parent=gene-D616_p97074;Dbxref=Genbank:NP_061455.1,GeneID:1263497;Name=NP_061455.1;Note=98 pct identical to sp:TRE2_ECOLI[TraE of R1-19];gbkey=CDS;gene=traE;locus_tag=D616_p97074;product=hypothetical protein;protein_id=NP_061455.1;transl_table=11
266
+ NC_002483.1 RefSeq sequence_difference 69385 69385 . + . ID=id-D616_p97074;Dbxref=GeneID:1263497;Note=conflict: deletion%2C G is added to gb:U01159;compare=U01159.2;gbkey=misc_difference;gene=traE;locus_tag=D616_p97074
267
+ NC_002483.1 RefSeq sequence_difference 69409 69409 . + . ID=id-D616_p97074-2;Dbxref=GeneID:1263497;Note=conflict: T is omitted from gb:U01159;compare=U01159.2;gbkey=misc_difference;gene=traE;locus_tag=D616_p97074;replace=t
268
+ NC_002483.1 RefSeq gene 69531 70259 . + . ID=gene-D616_p97071;Dbxref=GeneID:1263586;Name=traK;gbkey=Gene;gene=traK;gene_biotype=protein_coding;locus_tag=D616_p97071;old_locus_tag=Fpla079
269
+ NC_002483.1 RefSeq CDS 69531 70259 . + 0 ID=cds-NP_061456.1;Parent=gene-D616_p97071;Dbxref=Genbank:NP_061456.1,GeneID:1263586;Name=NP_061456.1;Note=100 pct identical to sp:TRK1_ECOLI[TraK of plasmid F];gbkey=CDS;gene=traK;locus_tag=D616_p97071;product=hypothetical protein;protein_id=NP_061456.1;transl_table=11
270
+ NC_002483.1 RefSeq sequence_difference 69563 69563 . + . ID=id-D616_p97071;Dbxref=GeneID:1263586;Note=conflict: C is changed to G in gb:U01159;compare=U01159.2;gbkey=misc_difference;gene=traK;locus_tag=D616_p97071;replace=g
271
+ NC_002483.1 RefSeq gene 70259 71686 . + . ID=gene-D616_p97076;Dbxref=GeneID:1263578;Name=traB;gbkey=Gene;gene=traB;gene_biotype=protein_coding;locus_tag=D616_p97076;old_locus_tag=Fpla080
272
+ NC_002483.1 RefSeq CDS 70259 71686 . + 0 ID=cds-NP_061457.1;Parent=gene-D616_p97076;Dbxref=Genbank:NP_061457.1,GeneID:1263578;Name=NP_061457.1;Note=100 pct identical to sp:TRB1_ECOLI[TraB of plasmid F];gbkey=CDS;gene=traB;locus_tag=D616_p97076;product=hypothetical protein;protein_id=NP_061457.1;transl_table=11
273
+ NC_002483.1 RefSeq gene 71676 72266 . + . ID=gene-D616_p97064;Dbxref=GeneID:1263570;Name=traP;gbkey=Gene;gene=traP;gene_biotype=protein_coding;locus_tag=D616_p97064;old_locus_tag=Fpla081
274
+ NC_002483.1 RefSeq CDS 71676 72266 . + 0 ID=cds-NP_061458.1;Parent=gene-D616_p97064;Dbxref=Genbank:NP_061458.1,GeneID:1263570;Name=NP_061458.1;Note=100 pct identical to sp:TRAP_ECOLI[TraP of plasmid F];gbkey=CDS;gene=traP;locus_tag=D616_p97064;product=hypothetical protein;protein_id=NP_061458.1;transl_table=11
275
+ NC_002483.1 RefSeq gene 72253 72450 . + . ID=gene-D616_p97051;Dbxref=GeneID:1263494;Name=trbD;gbkey=Gene;gene=trbD;gene_biotype=protein_coding;locus_tag=D616_p97051;old_locus_tag=Fpla082
276
+ NC_002483.1 RefSeq CDS 72253 72450 . + 0 ID=cds-NP_061459.1;Parent=gene-D616_p97051;Dbxref=Genbank:NP_061459.1,GeneID:1263494;Name=NP_061459.1;Note=100 pct identical to sp:TRBD_ECOLI[TrbD of plasmid F];gbkey=CDS;gene=trbD;locus_tag=D616_p97051;product=hypothetical protein;protein_id=NP_061459.1;transl_table=11
277
+ NC_002483.1 RefSeq gene 72462 72713 . + . ID=gene-D616_p97049;Dbxref=GeneID:1263580;Name=trbG;gbkey=Gene;gene=trbG;gene_biotype=protein_coding;locus_tag=D616_p97049;old_locus_tag=Fpla083
278
+ NC_002483.1 RefSeq CDS 72462 72713 . + 0 ID=cds-NP_061460.1;Parent=gene-D616_p97049;Dbxref=Genbank:NP_061460.1,GeneID:1263580;Name=NP_061460.1;Note=100 pct identical to sp:TRBG_ECOLI[TrbG of plasmid F];gbkey=CDS;gene=trbG;locus_tag=D616_p97049;product=hypothetical protein;protein_id=NP_061460.1;transl_table=11
279
+ NC_002483.1 RefSeq gene 72710 73225 . + . ID=gene-D616_p97059;Dbxref=GeneID:1263566;Name=traV;gbkey=Gene;gene=traV;gene_biotype=protein_coding;locus_tag=D616_p97059;old_locus_tag=Fpla084
280
+ NC_002483.1 RefSeq CDS 72710 73225 . + 0 ID=cds-NP_061461.1;Parent=gene-D616_p97059;Dbxref=Genbank:NP_061461.1,GeneID:1263566;Name=NP_061461.1;Note=100 pct identical to sp:TRAV_ECOLI[TraV of plasmid F];gbkey=CDS;gene=traV;locus_tag=D616_p97059;product=hypothetical protein;protein_id=NP_061461.1;transl_table=11
281
+ NC_002483.1 RefSeq gene 73360 73581 . + . ID=gene-D616_p97062;Dbxref=GeneID:1263563;Name=traR;gbkey=Gene;gene=traR;gene_biotype=protein_coding;locus_tag=D616_p97062;old_locus_tag=Fpla085
282
+ NC_002483.1 RefSeq CDS 73360 73581 . + 0 ID=cds-NP_061462.1;Parent=gene-D616_p97062;Dbxref=Genbank:NP_061462.1,GeneID:1263563;Name=NP_061462.1;Note=100 pct identical to sp:TRAR_ECOLI[TraR of plasmid F];gbkey=CDS;gene=traR;locus_tag=D616_p97062;product=hypothetical protein;protein_id=NP_061462.1;transl_table=11
283
+ NC_002483.1 RefSeq gene 73741 76368 . + . ID=gene-D616_p97075;Dbxref=GeneID:1263568;Name=traC;gbkey=Gene;gene=traC;gene_biotype=protein_coding;locus_tag=D616_p97075;old_locus_tag=Fpla086
284
+ NC_002483.1 RefSeq CDS 73741 76368 . + 0 ID=cds-NP_061463.1;Parent=gene-D616_p97075;Dbxref=Genbank:NP_061463.1,GeneID:1263568;Name=NP_061463.1;Note=100 pct identical to sp:TRAC_ECOLI[TraC of plasmid F];gbkey=CDS;gene=traC;locus_tag=D616_p97075;product=hypothetical protein;protein_id=NP_061463.1;transl_table=11
285
+ NC_002483.1 RefSeq gene 76365 76751 . + . ID=gene-D616_p97048;Dbxref=GeneID:1263557;Name=trbI;gbkey=Gene;gene=trbI;gene_biotype=protein_coding;locus_tag=D616_p97048;old_locus_tag=Fpla087
286
+ NC_002483.1 RefSeq CDS 76365 76751 . + 0 ID=cds-NP_061464.1;Parent=gene-D616_p97048;Dbxref=Genbank:NP_061464.1,GeneID:1263557;Name=NP_061464.1;Note=99 pct identical to sp:TRBI_ECOLI[TrbI of plasmid F];gbkey=CDS;gene=trbI;locus_tag=D616_p97048;product=hypothetical protein;protein_id=NP_061464.1;transl_table=11
287
+ NC_002483.1 RefSeq sequence_difference 76701 76701 . + . ID=id-D616_p97048;Dbxref=GeneID:1263557;Note=conflict: A is changed to T in gb:U01159;compare=U01159.2;gbkey=misc_difference;gene=trbI;locus_tag=D616_p97048;replace=t
288
+ NC_002483.1 RefSeq gene 76748 77380 . + . ID=gene-D616_p97058;Dbxref=GeneID:1263571;Name=traW;gbkey=Gene;gene=traW;gene_biotype=protein_coding;locus_tag=D616_p97058;old_locus_tag=Fpla088
289
+ NC_002483.1 RefSeq CDS 76748 77380 . + 0 ID=cds-NP_061465.1;Parent=gene-D616_p97058;Dbxref=Genbank:NP_061465.1,GeneID:1263571;Name=NP_061465.1;Note=100 pct identical to sp:TRAW_ECOLI[TraW of plasmid F];gbkey=CDS;gene=traW;locus_tag=D616_p97058;product=hypothetical protein;protein_id=NP_061465.1;transl_table=11
290
+ NC_002483.1 RefSeq sequence_difference 77059 77059 . + . ID=id-D616_p97058;Dbxref=GeneID:1263571;Note=conflict: G is changed to C in gb:U01159;compare=U01159.2;gbkey=misc_difference;gene=traW;locus_tag=D616_p97058;replace=c
291
+ NC_002483.1 RefSeq gene 77377 78369 . + . ID=gene-D616_p97061;Dbxref=GeneID:1263544;Name=traU;gbkey=Gene;gene=traU;gene_biotype=protein_coding;locus_tag=D616_p97061;old_locus_tag=Fpla089
292
+ NC_002483.1 RefSeq CDS 77377 78369 . + 0 ID=cds-NP_061466.1;Parent=gene-D616_p97061;Dbxref=Genbank:NP_061466.1,GeneID:1263544;Name=NP_061466.1;Note=100 pct identical to sp:TRAU_ECOLI[TraU of plasmid F];gbkey=CDS;gene=traU;locus_tag=D616_p97061;product=hypothetical protein;protein_id=NP_061466.1;transl_table=11
293
+ NC_002483.1 RefSeq gene 78378 79016 . + . ID=gene-D616_p97053;Dbxref=GeneID:1263546;Name=trbC;gbkey=Gene;gene=trbC;gene_biotype=protein_coding;locus_tag=D616_p97053;old_locus_tag=Fpla090
294
+ NC_002483.1 RefSeq CDS 78378 79016 . + 0 ID=cds-NP_061467.1;Parent=gene-D616_p97053;Dbxref=Genbank:NP_061467.1,GeneID:1263546;Name=NP_061467.1;Note=100 pct identical to sp:TRBC_ECOLI[TrbC of plasmid F];gbkey=CDS;gene=trbC;locus_tag=D616_p97053;product=hypothetical protein;protein_id=NP_061467.1;transl_table=11
295
+ NC_002483.1 RefSeq gene 79013 80821 . + . ID=gene-D616_p97065;Dbxref=GeneID:1263575;Name=traN;gbkey=Gene;gene=traN;gene_biotype=protein_coding;locus_tag=D616_p97065;old_locus_tag=Fpla091
296
+ NC_002483.1 RefSeq CDS 79013 80821 . + 0 ID=cds-NP_061468.1;Parent=gene-D616_p97065;Dbxref=Genbank:NP_061468.1,GeneID:1263575;Name=NP_061468.1;Note=100 pct identical to sp:TRAN_ECOLI[TraN of plasmid F];gbkey=CDS;gene=traN;locus_tag=D616_p97065;product=hypothetical protein;protein_id=NP_061468.1;transl_table=11
297
+ NC_002483.1 RefSeq gene 80845 81105 . + . ID=gene-D616_p97050;Dbxref=GeneID:1263550;Name=trbE;gbkey=Gene;gene=trbE;gene_biotype=protein_coding;locus_tag=D616_p97050;old_locus_tag=Fpla092
298
+ NC_002483.1 RefSeq CDS 80845 81105 . + 0 ID=cds-NP_061469.1;Parent=gene-D616_p97050;Dbxref=Genbank:NP_061469.1,GeneID:1263550;Name=NP_061469.1;Note=100 pct identical to sp:TRBE_ECOLI[TrbE of plasmid F];gbkey=CDS;gene=trbE;locus_tag=D616_p97050;product=hypothetical protein;protein_id=NP_061469.1;transl_table=11
299
+ NC_002483.1 RefSeq gene 81068 81841 . + . ID=gene-D616_p97073;Dbxref=GeneID:1263589;Name=traF;gbkey=Gene;gene=traF;gene_biotype=protein_coding;locus_tag=D616_p97073;old_locus_tag=Fpla093
300
+ NC_002483.1 RefSeq CDS 81068 81841 . + 0 ID=cds-NP_061470.1;Parent=gene-D616_p97073;Dbxref=Genbank:NP_061470.1,GeneID:1263589;Name=NP_061470.1;Note=100 pct identical to pir:QUECTF[TraF of plasmid F];gbkey=CDS;gene=traF;locus_tag=D616_p97073;product=hypothetical protein;protein_id=NP_061470.1;transl_table=11
301
+ NC_002483.1 RefSeq gene 81857 82204 . + . ID=gene-D616_p97055;Dbxref=GeneID:1263573;Name=trbA;gbkey=Gene;gene=trbA;gene_biotype=protein_coding;locus_tag=D616_p97055;old_locus_tag=Fpla094
302
+ NC_002483.1 RefSeq CDS 81857 82204 . + 0 ID=cds-NP_061471.1;Parent=gene-D616_p97055;Dbxref=Genbank:NP_061471.1,GeneID:1263573;Name=NP_061471.1;Note=100 pct identical to sp:TRBA_ECOLI[TrbA of plasmid F];gbkey=CDS;gene=trbA;locus_tag=D616_p97055;product=hypothetical protein;protein_id=NP_061471.1;transl_table=11
303
+ NC_002483.1 RefSeq gene 82206 82520 . - . ID=gene-D616_p97107;Dbxref=GeneID:1263509;Name=artA;gbkey=Gene;gene=artA;gene_biotype=protein_coding;locus_tag=D616_p97107;old_locus_tag=Fpla095
304
+ NC_002483.1 RefSeq CDS 82206 82520 . - 0 ID=cds-NP_061472.1;Parent=gene-D616_p97107;Dbxref=Genbank:NP_061472.1,GeneID:1263509;Name=NP_061472.1;Note=100 pct identical to sp:ARTA_ECOLI[ArtA of plasmid F];gbkey=CDS;gene=artA;locus_tag=D616_p97107;product=hypothetical protein;protein_id=NP_061472.1;transl_table=11
305
+ NC_002483.1 RefSeq gene 82601 82885 . + . ID=gene-D616_p97070;Dbxref=GeneID:1263562;Name=traQ;gbkey=Gene;gene=traQ;gene_biotype=protein_coding;locus_tag=D616_p97070;old_locus_tag=Fpla096
306
+ NC_002483.1 RefSeq CDS 82601 82885 . + 0 ID=cds-NP_061473.1;Parent=gene-D616_p97070;Dbxref=Genbank:NP_061473.1,GeneID:1263562;Name=NP_061473.1;Note=100 pct identical to sp:TRAQ_ECOLI[TraQ of plasmid F];gbkey=CDS;gene=traQ;locus_tag=D616_p97070;product=hypothetical protein;protein_id=NP_061473.1;transl_table=11
307
+ NC_002483.1 RefSeq gene 82872 83417 . + . ID=gene-D616_p97060;Dbxref=GeneID:1263514;Name=trbB;gbkey=Gene;gene=trbB;gene_biotype=protein_coding;locus_tag=D616_p97060;old_locus_tag=Fpla097
308
+ NC_002483.1 RefSeq CDS 82872 83417 . + 0 ID=cds-NP_061474.1;Parent=gene-D616_p97060;Dbxref=Genbank:NP_061474.1,GeneID:1263514;Name=NP_061474.1;Note=99 pct identical to sp:TRBB_ECOLI[TrbB of plasmid F];gbkey=CDS;gene=trbB;locus_tag=D616_p97060;product=hypothetical protein;protein_id=NP_061474.1;transl_table=11
309
+ NC_002483.1 RefSeq sequence_difference 83304 83309 . + . ID=id-D616_p97060;Dbxref=GeneID:1263514;Note=conflict: deletion%2C GTCAAC is added to gb:U01159;compare=U01159.2;gbkey=misc_difference;gene=trbB;locus_tag=D616_p97060
310
+ NC_002483.1 RefSeq gene 83347 83688 . + . ID=gene-D616_p97052;Dbxref=GeneID:1263554;Name=trbJ;gbkey=Gene;gene=trbJ;gene_biotype=protein_coding;locus_tag=D616_p97052;old_locus_tag=Fpla098
311
+ NC_002483.1 RefSeq CDS 83347 83688 . + 0 ID=cds-NP_061475.1;Parent=gene-D616_p97052;Dbxref=Genbank:NP_061475.1,GeneID:1263554;Name=NP_061475.1;Note=100 pct identical to pir:QQEC25[TrbJ of plasmid F];gbkey=CDS;gene=trbJ;locus_tag=D616_p97052;product=hypothetical protein;protein_id=NP_061475.1;transl_table=11
312
+ NC_002483.1 RefSeq gene 83675 84055 . + . ID=gene-D616_p97056;Dbxref=GeneID:1263555;Name=trbF;gbkey=Gene;gene=trbF;gene_biotype=protein_coding;locus_tag=D616_p97056;old_locus_tag=Fpla099
313
+ NC_002483.1 RefSeq CDS 83675 84055 . + 0 ID=cds-NP_061476.1;Parent=gene-D616_p97056;Dbxref=Genbank:NP_061476.1,GeneID:1263555;Name=NP_061476.1;Note=100 pct identical to sp:TRBF_ECOLI[TrbF of plasmid F];gbkey=CDS;gene=trbF;locus_tag=D616_p97056;product=hypothetical protein;protein_id=NP_061476.1;transl_table=11
314
+ NC_002483.1 RefSeq gene 84052 85428 . + . ID=gene-D616_p97078;Dbxref=GeneID:1263523;Name=traH;gbkey=Gene;gene=traH;gene_biotype=protein_coding;locus_tag=D616_p97078;old_locus_tag=Fpla100
315
+ NC_002483.1 RefSeq CDS 84052 85428 . + 0 ID=cds-NP_061477.1;Parent=gene-D616_p97078;Dbxref=Genbank:NP_061477.1,GeneID:1263523;Name=NP_061477.1;Note=100 pct identical to sp:TRH1_ECOLI[TraH of plasmid F];gbkey=CDS;gene=traH;locus_tag=D616_p97078;product=hypothetical protein;protein_id=NP_061477.1;transl_table=11
316
+ NC_002483.1 RefSeq gene 85425 88241 . + . ID=gene-D616_p97079;Dbxref=GeneID:1263567;Name=traG;gbkey=Gene;gene=traG;gene_biotype=protein_coding;locus_tag=D616_p97079;old_locus_tag=Fpla101
317
+ NC_002483.1 RefSeq CDS 85425 88241 . + 0 ID=cds-NP_061478.1;Parent=gene-D616_p97079;Dbxref=Genbank:NP_061478.1,GeneID:1263567;Name=NP_061478.1;Note=100 pct identical to sp:TRG1_ECOLI[TraG of plasmid F];gbkey=CDS;gene=traG;locus_tag=D616_p97079;product=hypothetical protein;protein_id=NP_061478.1;transl_table=11
318
+ NC_002483.1 RefSeq gene 88274 88795 . + . ID=gene-D616_p97068;Dbxref=GeneID:1263588;Name=traS;gbkey=Gene;gene=traS;gene_biotype=protein_coding;locus_tag=D616_p97068;old_locus_tag=Fpla102
319
+ NC_002483.1 RefSeq CDS 88274 88795 . + 0 ID=cds-NP_061479.1;Parent=gene-D616_p97068;Dbxref=Genbank:NP_061479.1,GeneID:1263588;Name=NP_061479.1;Note=96 pct identical to 149aa protein sp:TRS1_ECOLI[TraS of plasmid F];gbkey=CDS;gene=traS;locus_tag=D616_p97068;product=surface exclusion protien;protein_id=NP_061479.1;transl_table=11
320
+ NC_002483.1 RefSeq sequence_difference 88699 88699 . + . ID=id-D616_p97068;Dbxref=GeneID:1263588;Note=conflict: C is omitted from gb:U01159;compare=U01159.2;gbkey=misc_difference;gene=traS;locus_tag=D616_p97068;replace=c
321
+ NC_002483.1 RefSeq inverted_repeat 88730 88768 . + . ID=id-D616_p97068-2;Dbxref=GeneID:1263588;function=traT mRNA leader;gbkey=repeat_region;gene=traS;locus_tag=D616_p97068;rpt_type=inverted;rpt_unit_range=88730..88747
322
+ NC_002483.1 RefSeq gene 88817 89551 . + . ID=gene-D616_p97067;Dbxref=GeneID:1263516;Name=traT;gbkey=Gene;gene=traT;gene_biotype=protein_coding;locus_tag=D616_p97067
323
+ NC_002483.1 RefSeq CDS 88817 89551 . + 0 ID=cds-NP_061480.1;Parent=gene-D616_p97067;Dbxref=Genbank:NP_061480.1,GeneID:1263516;Name=NP_061480.1;Note=99 pct identical to sp:TRT2_ECOLI[TraT of plasmid F];gbkey=CDS;gene=traT;locus_tag=D616_p97067;product=surface exclusion protien;protein_id=NP_061480.1;transl_table=11
324
+ NC_002483.1 RefSeq sequence_difference 89238 89238 . + . ID=id-D616_p97067;Dbxref=GeneID:1263516;Note=conflict: C is changed to G in gb:U01159;compare=U01159.2;gbkey=misc_difference;gene=traT;locus_tag=D616_p97067;replace=g
325
+ NC_002483.1 RefSeq sequence_difference 89565 89565 . + . ID=id-NC_002483.1:89565..89565;Note=conflict: deletion%2C G is added to gb:U01159;compare=U01159.2;gbkey=misc_difference
326
+ NC_002483.1 RefSeq inverted_repeat 89594 89688 . + . ID=id-NC_002483.1:89594..89688;Note=terminator of traT mRNA;gbkey=repeat_region;rpt_type=inverted;rpt_unit_range=89594..89635
327
+ NC_002483.1 RefSeq sequence_difference 89730 89732 . + . ID=id-NC_002483.1:89730..89732;Note=conflict: deletion%2C CGG is added to gb:U01159;compare=U01159.2;gbkey=misc_difference
328
+ NC_002483.1 RefSeq gene 89804 91957 . + . ID=gene-D616_p97082;Dbxref=GeneID:1263585;Name=traD;gbkey=Gene;gene=traD;gene_biotype=protein_coding;locus_tag=D616_p97082;old_locus_tag=Fpla104
329
+ NC_002483.1 RefSeq CDS 89804 91957 . + 0 ID=cds-NP_061481.1;Parent=gene-D616_p97082;Dbxref=Genbank:NP_061481.1,GeneID:1263585;Name=NP_061481.1;Note=100pct identical to gp:ECO011707_1[TraD of plasmid F];gbkey=CDS;gene=traD;locus_tag=D616_p97082;product=hypothetical protein;protein_id=NP_061481.1;transl_table=11
330
+ NC_002483.1 RefSeq sequence_difference 91955 91955 . + . ID=id-D616_p97082;Dbxref=GeneID:1263585;Note=conflict: deletion%2C T is added to gb: U01159;compare=U01159.2;gbkey=misc_difference;gene=traD;locus_tag=D616_p97082
331
+ NC_002483.1 RefSeq gene 91957 92676 . + . ID=gene-D616_p97054;Dbxref=GeneID:1263576;Name=trbH;gbkey=Gene;gene=trbH;gene_biotype=protein_coding;locus_tag=D616_p97054
332
+ NC_002483.1 RefSeq CDS 91957 92676 . + 0 ID=cds-NP_061482.1;Parent=gene-D616_p97054;Dbxref=Genbank:NP_061482.1,GeneID:1263576;Name=NP_061482.1;Note=99 pct identical to sp:TRBH_ECOLI[TrbH of plasmid F];gbkey=CDS;gene=trbH;locus_tag=D616_p97054;product=hypothetical protein;protein_id=NP_061482.1;transl_table=11
333
+ NC_002483.1 RefSeq sequence_difference 92597 92597 . + . ID=id-D616_p97054;Dbxref=GeneID:1263576;Note=conflict: G is changed to C in gb:U01159;compare=U01159.2;gbkey=misc_difference;gene=trbH;locus_tag=D616_p97054;replace=c
334
+ NC_002483.1 RefSeq gene 92673 97943 . + . ID=gene-D616_p97077;Dbxref=GeneID:1263574;Name=traI;gbkey=Gene;gene=traI;gene_biotype=protein_coding;locus_tag=D616_p97077;old_locus_tag=Fpla107
335
+ NC_002483.1 RefSeq CDS 92673 97943 . + 0 ID=cds-NP_061483.1;Parent=gene-D616_p97077;Dbxref=Genbank:NP_061483.1,GeneID:1263574;Name=NP_061483.1;Note=100 pct identical to sp:TRI1_ECOLI[TraI of plasmid F];gbkey=CDS;gene=traI;locus_tag=D616_p97077;product=hypothetical protein;protein_id=NP_061483.1;transl_table=11
336
+ NC_002483.1 RefSeq gene 97963 98709 . + . ID=gene-D616_p97063;Dbxref=GeneID:1263541;Name=traX;gbkey=Gene;gene=traX;gene_biotype=protein_coding;locus_tag=D616_p97063;old_locus_tag=Fpla108
337
+ NC_002483.1 RefSeq CDS 97963 98709 . + 0 ID=cds-NP_061484.1;Parent=gene-D616_p97063;Dbxref=Genbank:NP_061484.1,GeneID:1263541;Name=NP_061484.1;Note=100 pct identical to sp:TRX1_ECOLI[TraX of plasmid F];gbkey=CDS;gene=traX;locus_tag=D616_p97063;product=hypothetical protein;protein_id=NP_061484.1;transl_table=11
338
+ NC_002483.1 RefSeq gene 98764 99159 . + . Dbxref=GeneID:1498117;Name=finO;gbkey=Gene;gene=finO;gene_biotype=other;is_ordered=true;locus_tag=D616_p97104;old_locus_tag=Fpla003;part=1/2;partial=true
339
+ NC_002483.1 RefSeq gene 1259 1426 . + . Dbxref=GeneID:1498117;Name=finO;gbkey=Gene;gene=finO;gene_biotype=other;is_ordered=true;locus_tag=D616_p97104;old_locus_tag=Fpla003;part=2/2;partial=true
340
+ NC_002483.1 RefSeq sequence_difference 98794 98794 . + . ID=id-D616_p97104;Dbxref=GeneID:1498117;Note=conflict: C is changed to T in embl:X57429;compare=X57429.1;gbkey=misc_difference;gene=finO;locus_tag=D616_p97104;replace=t
341
+ NC_002483.1 RefSeq sequence_feature 98764 99159 . + . Dbxref=GeneID:1498117;Note=100%25 identical to gp:ECPTRAX3_2[FinO of plasmid F]%3B~interrupted by IS3;gbkey=misc_feature;gene=finO;locus_tag=D616_p97104;part=1/2
342
+ NC_002483.1 RefSeq sequence_feature 1259 1426 . + . Dbxref=GeneID:1498117;Note=100%25 identical to gp:ECPTRAX3_2[FinO of plasmid F]%3B~interrupted by IS3;gbkey=misc_feature;gene=finO;locus_tag=D616_p97104;part=2/2
343
+ NC_002483.1 RefSeq repeat_region 1259 1261 . + . ID=id-D616_p97104-3;Dbxref=GeneID:1498117;Note=duplicated sequence by insertion of IS3;gbkey=repeat_region;gene=finO;locus_tag=D616_p97104
344
+ NC_002483.1 RefSeq repeat_region 99157 99159 . + . ID=id-D616_p97104-4;Dbxref=GeneID:1498117;Note=duplicated sequence by insertion of IS3;gbkey=repeat_region;gene=finO;locus_tag=D616_p97104
345
+
data/lib/bioroebe/data/gff/sample.gff ADDED
@@ -0,0 +1,2 @@
1
+ 1 transcribed_unprocessed_pseudogene gene 11869 14409 . + . gene_id "ENSG00000223972"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene";
2
+ 1 processed_transcript transcript 11869 14409 . + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; gene_name "DDX11L1"; gene_sourc e "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-002"; transcript_source "havana";
data/lib/bioroebe/data/gff/test_gene.gff ADDED
@@ -0,0 +1,4 @@
1
+ ##gff-version 3
2
+ ##sequence-region ctg123 1 1497228
3
+ ctg123 . gene 900 9900 . + . ID=gene00001;Name=EDEN
4
+ ctg123 . gene 10900 19900 . - . ID=gene00002;Name=EDEN2
data/lib/bioroebe/data/gff/transcripts.gff ADDED
@@ -0,0 +1,16 @@
1
+ ## gff-version 3
2
+ ## sequence-region ctg123 1 1497228
3
+ ctg123 . mRNA 900 9200 . + . ID=mRNA00001;Name=EDEN.1
4
+ ctg123 . utr 900 1000 . + . ID=utr00001;Parent=mRNA00001
5
+ ctg123 . exon 1050 1500 . + . ID=exon00002;Parent=mRNA00001
6
+ ctg123 . exon 3000 3902 . + . ID=exon00003;Parent=mRNA00001
7
+ ctg123 . exon 5000 5500 . + . ID=exon00004;Parent=mRNA00001
8
+ ctg123 . exon 7000 9000 . + . ID=exon00005;Parent=mRNA00001
9
+ ctg123 . utr 9100 9200 . + . ID=utr00002;Parent=mRNA00001
10
+ ctg123 . mRNA 10900 19200 . - . ID=mRNA00002;Name=EDEN2.1
11
+ ctg123 . utr 10900 11000 . - . ID=utr00003;Parent=mRNA00002
12
+ ctg123 . exon 11050 11500 . - . ID=exon00006;Parent=mRNA00002
13
+ ctg123 . exon 13000 13902 . - . ID=exon00007;Parent=mRNA00002
14
+ ctg123 . exon 15000 15500 . - . ID=exon00008;Parent=mRNA00002
15
+ ctg123 . exon 17000 19000 . - . ID=exon00009;Parent=mRNA00002
16
+ ctg123 . utr 19100 19200 . - . ID=utr00004;Parent=mRNA00002
data/lib/bioroebe/data/gtf/README.md ADDED
@@ -0,0 +1 @@
1
+ This may store a few example .gtf (transcript) files.
data/lib/bioroebe/data/json/example_config.json ADDED
@@ -0,0 +1,48 @@
1
+ {
2
+ "Page":{"width":800, "height":800, "intervals":15},
3
+ "Tracks": [
4
+ {
5
+ "glyph":"generic",
6
+ "name":"Genes",
7
+ "label":true,
8
+ "file":"test_gene.gff",
9
+ "file_type":"gff",
10
+ "fill_color":"red",
11
+ "stroke_width":1,
12
+ "x_round":4,
13
+ "y_round":4
14
+ },
15
+ {
16
+ "glyph":"transcript",
17
+ "name":"Transcripts",
18
+ "label":true,
19
+ "file":"transcripts.gff",
20
+ "file_type":"gff",
21
+ "exon_fill_color":"green_white_radial",
22
+ "utr_fill_color":"blue_white_radial",
23
+ "stroke_width":1,
24
+ "gap_marker":"angled"
25
+ },
26
+ {
27
+ "glyph":"histogram",
28
+ "name":"Data",
29
+ "label":true,
30
+ "file":"data.txt",
31
+ "file_type":"data",
32
+ "track_height":100,
33
+ "fill_color":"yellow_white_radial",
34
+ "stroke_width":1
35
+ },
36
+ {
37
+ "glyph":"histogram",
38
+ "name":"Data with maxed-out scale",
39
+ "label":true,
40
+ "file":"data.txt",
41
+ "file_type":"data",
42
+ "track_height":100,
43
+ "fill_color":"red_white_radial",
44
+ "stroke_width":1,
45
+ "max_y":1000
46
+ }
47
+ ]
48
+ }