bio 1.3.1 → 1.4.0

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  1. data/ChangeLog +2105 -3728
  2. data/KNOWN_ISSUES.rdoc +35 -3
  3. data/README.rdoc +8 -2
  4. data/RELEASE_NOTES.rdoc +166 -0
  5. data/bin/bioruby +4 -1
  6. data/bioruby.gemspec +146 -1
  7. data/bioruby.gemspec.erb +3 -1
  8. data/doc/ChangeLog-before-1.3.1 +3961 -0
  9. data/doc/Tutorial.rd +154 -22
  10. data/doc/Tutorial.rd.html +125 -68
  11. data/lib/bio.rb +21 -6
  12. data/lib/bio/appl/bl2seq/report.rb +11 -202
  13. data/lib/bio/appl/blast/format0.rb +0 -193
  14. data/lib/bio/appl/blast/report.rb +2 -147
  15. data/lib/bio/appl/blast/wublast.rb +0 -208
  16. data/lib/bio/appl/fasta.rb +4 -19
  17. data/lib/bio/appl/fasta/format10.rb +0 -14
  18. data/lib/bio/appl/genscan/report.rb +0 -176
  19. data/lib/bio/appl/hmmer.rb +1 -15
  20. data/lib/bio/appl/hmmer/report.rb +0 -100
  21. data/lib/bio/appl/meme/mast.rb +156 -0
  22. data/lib/bio/appl/meme/mast/report.rb +91 -0
  23. data/lib/bio/appl/meme/motif.rb +48 -0
  24. data/lib/bio/appl/psort.rb +0 -111
  25. data/lib/bio/appl/psort/report.rb +1 -45
  26. data/lib/bio/appl/pts1.rb +2 -4
  27. data/lib/bio/appl/sosui/report.rb +5 -54
  28. data/lib/bio/appl/targetp/report.rb +1 -104
  29. data/lib/bio/appl/tmhmm/report.rb +0 -36
  30. data/lib/bio/command.rb +94 -10
  31. data/lib/bio/data/aa.rb +1 -77
  32. data/lib/bio/data/codontable.rb +1 -95
  33. data/lib/bio/data/na.rb +1 -26
  34. data/lib/bio/db/aaindex.rb +1 -38
  35. data/lib/bio/db/fasta.rb +1 -134
  36. data/lib/bio/db/fasta/format_qual.rb +204 -0
  37. data/lib/bio/db/fasta/qual.rb +102 -0
  38. data/lib/bio/db/fastq.rb +645 -0
  39. data/lib/bio/db/fastq/fastq_to_biosequence.rb +40 -0
  40. data/lib/bio/db/fastq/format_fastq.rb +175 -0
  41. data/lib/bio/db/genbank/genbank.rb +1 -86
  42. data/lib/bio/db/gff.rb +0 -17
  43. data/lib/bio/db/go.rb +4 -72
  44. data/lib/bio/db/kegg/common.rb +112 -0
  45. data/lib/bio/db/kegg/compound.rb +29 -20
  46. data/lib/bio/db/kegg/drug.rb +74 -34
  47. data/lib/bio/db/kegg/enzyme.rb +26 -5
  48. data/lib/bio/db/kegg/genes.rb +128 -15
  49. data/lib/bio/db/kegg/genome.rb +3 -41
  50. data/lib/bio/db/kegg/glycan.rb +19 -24
  51. data/lib/bio/db/kegg/orthology.rb +16 -56
  52. data/lib/bio/db/kegg/reaction.rb +81 -28
  53. data/lib/bio/db/kegg/taxonomy.rb +1 -52
  54. data/lib/bio/db/litdb.rb +1 -16
  55. data/lib/bio/db/phyloxml/phyloxml.xsd +582 -0
  56. data/lib/bio/db/phyloxml/phyloxml_elements.rb +1174 -0
  57. data/lib/bio/db/phyloxml/phyloxml_parser.rb +954 -0
  58. data/lib/bio/db/phyloxml/phyloxml_writer.rb +228 -0
  59. data/lib/bio/db/prosite.rb +2 -95
  60. data/lib/bio/db/rebase.rb +5 -6
  61. data/lib/bio/db/sanger_chromatogram/abif.rb +120 -0
  62. data/lib/bio/db/sanger_chromatogram/chromatogram.rb +133 -0
  63. data/lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb +32 -0
  64. data/lib/bio/db/sanger_chromatogram/scf.rb +210 -0
  65. data/lib/bio/io/das.rb +0 -44
  66. data/lib/bio/io/ddbjxml.rb +1 -181
  67. data/lib/bio/io/flatfile.rb +1 -7
  68. data/lib/bio/io/flatfile/autodetection.rb +6 -0
  69. data/lib/bio/io/keggapi.rb +0 -442
  70. data/lib/bio/io/ncbirest.rb +130 -132
  71. data/lib/bio/io/ncbisoap.rb +2 -1
  72. data/lib/bio/io/pubmed.rb +0 -88
  73. data/lib/bio/location.rb +0 -73
  74. data/lib/bio/pathway.rb +0 -171
  75. data/lib/bio/sequence.rb +18 -1
  76. data/lib/bio/sequence/adapter.rb +3 -0
  77. data/lib/bio/sequence/format.rb +16 -0
  78. data/lib/bio/sequence/quality_score.rb +205 -0
  79. data/lib/bio/tree.rb +70 -5
  80. data/lib/bio/util/restriction_enzyme/single_strand.rb +3 -2
  81. data/lib/bio/util/sirna.rb +1 -23
  82. data/lib/bio/version.rb +1 -1
  83. data/sample/demo_aaindex.rb +67 -0
  84. data/sample/demo_aminoacid.rb +101 -0
  85. data/sample/demo_bl2seq_report.rb +220 -0
  86. data/sample/demo_blast_report.rb +285 -0
  87. data/sample/demo_codontable.rb +119 -0
  88. data/sample/demo_das.rb +105 -0
  89. data/sample/demo_ddbjxml.rb +212 -0
  90. data/sample/demo_fasta_remote.rb +51 -0
  91. data/sample/demo_fastaformat.rb +105 -0
  92. data/sample/demo_genbank.rb +132 -0
  93. data/sample/demo_genscan_report.rb +202 -0
  94. data/sample/demo_gff1.rb +49 -0
  95. data/sample/demo_go.rb +98 -0
  96. data/sample/demo_hmmer_report.rb +149 -0
  97. data/sample/demo_kegg_compound.rb +57 -0
  98. data/sample/demo_kegg_drug.rb +65 -0
  99. data/sample/demo_kegg_genome.rb +74 -0
  100. data/sample/demo_kegg_glycan.rb +72 -0
  101. data/sample/demo_kegg_orthology.rb +62 -0
  102. data/sample/demo_kegg_reaction.rb +66 -0
  103. data/sample/demo_kegg_taxonomy.rb +92 -0
  104. data/sample/demo_keggapi.rb +502 -0
  105. data/sample/demo_litdb.rb +42 -0
  106. data/sample/demo_locations.rb +99 -0
  107. data/sample/demo_ncbi_rest.rb +130 -0
  108. data/sample/demo_nucleicacid.rb +49 -0
  109. data/sample/demo_pathway.rb +196 -0
  110. data/sample/demo_prosite.rb +120 -0
  111. data/sample/demo_psort.rb +138 -0
  112. data/sample/demo_psort_report.rb +70 -0
  113. data/sample/demo_pubmed.rb +118 -0
  114. data/sample/demo_sirna.rb +63 -0
  115. data/sample/demo_sosui_report.rb +89 -0
  116. data/sample/demo_targetp_report.rb +135 -0
  117. data/sample/demo_tmhmm_report.rb +68 -0
  118. data/sample/pmfetch.rb +13 -4
  119. data/sample/pmsearch.rb +15 -4
  120. data/sample/test_phyloxml_big.rb +205 -0
  121. data/test/bioruby_test_helper.rb +61 -0
  122. data/test/data/KEGG/1.1.1.1.enzyme +935 -0
  123. data/test/data/KEGG/C00025.compound +102 -0
  124. data/test/data/KEGG/D00063.drug +104 -0
  125. data/test/data/KEGG/G00024.glycan +47 -0
  126. data/test/data/KEGG/G01366.glycan +18 -0
  127. data/test/data/KEGG/K02338.orthology +902 -0
  128. data/test/data/KEGG/R00006.reaction +14 -0
  129. data/test/data/fastq/README.txt +109 -0
  130. data/test/data/fastq/error_diff_ids.fastq +20 -0
  131. data/test/data/fastq/error_double_qual.fastq +22 -0
  132. data/test/data/fastq/error_double_seq.fastq +22 -0
  133. data/test/data/fastq/error_long_qual.fastq +20 -0
  134. data/test/data/fastq/error_no_qual.fastq +20 -0
  135. data/test/data/fastq/error_qual_del.fastq +20 -0
  136. data/test/data/fastq/error_qual_escape.fastq +20 -0
  137. data/test/data/fastq/error_qual_null.fastq +0 -0
  138. data/test/data/fastq/error_qual_space.fastq +21 -0
  139. data/test/data/fastq/error_qual_tab.fastq +21 -0
  140. data/test/data/fastq/error_qual_unit_sep.fastq +20 -0
  141. data/test/data/fastq/error_qual_vtab.fastq +20 -0
  142. data/test/data/fastq/error_short_qual.fastq +20 -0
  143. data/test/data/fastq/error_spaces.fastq +20 -0
  144. data/test/data/fastq/error_tabs.fastq +21 -0
  145. data/test/data/fastq/error_trunc_at_plus.fastq +19 -0
  146. data/test/data/fastq/error_trunc_at_qual.fastq +19 -0
  147. data/test/data/fastq/error_trunc_at_seq.fastq +18 -0
  148. data/test/data/fastq/error_trunc_in_plus.fastq +19 -0
  149. data/test/data/fastq/error_trunc_in_qual.fastq +20 -0
  150. data/test/data/fastq/error_trunc_in_seq.fastq +18 -0
  151. data/test/data/fastq/error_trunc_in_title.fastq +17 -0
  152. data/test/data/fastq/illumina_full_range_as_illumina.fastq +8 -0
  153. data/test/data/fastq/illumina_full_range_as_sanger.fastq +8 -0
  154. data/test/data/fastq/illumina_full_range_as_solexa.fastq +8 -0
  155. data/test/data/fastq/illumina_full_range_original_illumina.fastq +8 -0
  156. data/test/data/fastq/longreads_as_illumina.fastq +40 -0
  157. data/test/data/fastq/longreads_as_sanger.fastq +40 -0
  158. data/test/data/fastq/longreads_as_solexa.fastq +40 -0
  159. data/test/data/fastq/longreads_original_sanger.fastq +120 -0
  160. data/test/data/fastq/misc_dna_as_illumina.fastq +16 -0
  161. data/test/data/fastq/misc_dna_as_sanger.fastq +16 -0
  162. data/test/data/fastq/misc_dna_as_solexa.fastq +16 -0
  163. data/test/data/fastq/misc_dna_original_sanger.fastq +16 -0
  164. data/test/data/fastq/misc_rna_as_illumina.fastq +16 -0
  165. data/test/data/fastq/misc_rna_as_sanger.fastq +16 -0
  166. data/test/data/fastq/misc_rna_as_solexa.fastq +16 -0
  167. data/test/data/fastq/misc_rna_original_sanger.fastq +16 -0
  168. data/test/data/fastq/sanger_full_range_as_illumina.fastq +8 -0
  169. data/test/data/fastq/sanger_full_range_as_sanger.fastq +8 -0
  170. data/test/data/fastq/sanger_full_range_as_solexa.fastq +8 -0
  171. data/test/data/fastq/sanger_full_range_original_sanger.fastq +8 -0
  172. data/test/data/fastq/solexa_full_range_as_illumina.fastq +8 -0
  173. data/test/data/fastq/solexa_full_range_as_sanger.fastq +8 -0
  174. data/test/data/fastq/solexa_full_range_as_solexa.fastq +8 -0
  175. data/test/data/fastq/solexa_full_range_original_solexa.fastq +8 -0
  176. data/test/data/fastq/wrapping_as_illumina.fastq +12 -0
  177. data/test/data/fastq/wrapping_as_sanger.fastq +12 -0
  178. data/test/data/fastq/wrapping_as_solexa.fastq +12 -0
  179. data/test/data/fastq/wrapping_original_sanger.fastq +24 -0
  180. data/test/data/meme/db +0 -0
  181. data/test/data/meme/mast +0 -0
  182. data/test/data/meme/mast.out +13 -0
  183. data/test/data/meme/meme.out +3 -0
  184. data/test/data/phyloxml/apaf.xml +666 -0
  185. data/test/data/phyloxml/bcl_2.xml +2097 -0
  186. data/test/data/phyloxml/made_up.xml +144 -0
  187. data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +65 -0
  188. data/test/data/phyloxml/phyloxml_examples.xml +415 -0
  189. data/test/data/sanger_chromatogram/test_chromatogram_abif.ab1 +0 -0
  190. data/test/data/sanger_chromatogram/test_chromatogram_scf_v2.scf +0 -0
  191. data/test/data/sanger_chromatogram/test_chromatogram_scf_v3.scf +0 -0
  192. data/test/functional/bio/appl/test_pts1.rb +7 -5
  193. data/test/functional/bio/io/test_ensembl.rb +4 -3
  194. data/test/functional/bio/io/test_pubmed.rb +9 -3
  195. data/test/functional/bio/io/test_soapwsdl.rb +5 -4
  196. data/test/functional/bio/io/test_togows.rb +5 -4
  197. data/test/functional/bio/sequence/test_output_embl.rb +6 -4
  198. data/test/functional/bio/test_command.rb +54 -5
  199. data/test/runner.rb +5 -3
  200. data/test/unit/bio/appl/bl2seq/test_report.rb +5 -4
  201. data/test/unit/bio/appl/blast/test_ncbioptions.rb +4 -2
  202. data/test/unit/bio/appl/blast/test_report.rb +5 -4
  203. data/test/unit/bio/appl/blast/test_rpsblast.rb +5 -4
  204. data/test/unit/bio/appl/gcg/test_msf.rb +5 -5
  205. data/test/unit/bio/appl/genscan/test_report.rb +8 -9
  206. data/test/unit/bio/appl/hmmer/test_report.rb +5 -4
  207. data/test/unit/bio/appl/iprscan/test_report.rb +6 -5
  208. data/test/unit/bio/appl/mafft/test_report.rb +6 -5
  209. data/test/unit/bio/appl/meme/mast/test_report.rb +46 -0
  210. data/test/unit/bio/appl/meme/test_mast.rb +103 -0
  211. data/test/unit/bio/appl/meme/test_motif.rb +38 -0
  212. data/test/unit/bio/appl/paml/codeml/test_rates.rb +5 -4
  213. data/test/unit/bio/appl/paml/codeml/test_report.rb +5 -4
  214. data/test/unit/bio/appl/paml/test_codeml.rb +5 -4
  215. data/test/unit/bio/appl/sim4/test_report.rb +5 -4
  216. data/test/unit/bio/appl/sosui/test_report.rb +6 -5
  217. data/test/unit/bio/appl/targetp/test_report.rb +5 -3
  218. data/test/unit/bio/appl/test_blast.rb +5 -4
  219. data/test/unit/bio/appl/test_fasta.rb +4 -2
  220. data/test/unit/bio/appl/test_pts1.rb +4 -2
  221. data/test/unit/bio/appl/tmhmm/test_report.rb +6 -5
  222. data/test/unit/bio/data/test_aa.rb +5 -3
  223. data/test/unit/bio/data/test_codontable.rb +5 -4
  224. data/test/unit/bio/data/test_na.rb +5 -3
  225. data/test/unit/bio/db/biosql/tc_biosql.rb +5 -1
  226. data/test/unit/bio/db/embl/test_common.rb +4 -2
  227. data/test/unit/bio/db/embl/test_embl.rb +6 -6
  228. data/test/unit/bio/db/embl/test_embl_rel89.rb +6 -6
  229. data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +7 -8
  230. data/test/unit/bio/db/embl/test_sptr.rb +6 -8
  231. data/test/unit/bio/db/embl/test_uniprot.rb +6 -5
  232. data/test/unit/bio/db/fasta/test_format_qual.rb +346 -0
  233. data/test/unit/bio/db/kegg/test_compound.rb +146 -0
  234. data/test/unit/bio/db/kegg/test_drug.rb +194 -0
  235. data/test/unit/bio/db/kegg/test_enzyme.rb +241 -0
  236. data/test/unit/bio/db/kegg/test_genes.rb +32 -4
  237. data/test/unit/bio/db/kegg/test_glycan.rb +260 -0
  238. data/test/unit/bio/db/kegg/test_orthology.rb +50 -0
  239. data/test/unit/bio/db/kegg/test_reaction.rb +96 -0
  240. data/test/unit/bio/db/pdb/test_pdb.rb +4 -2
  241. data/test/unit/bio/db/sanger_chromatogram/test_abif.rb +76 -0
  242. data/test/unit/bio/db/sanger_chromatogram/test_scf.rb +98 -0
  243. data/test/unit/bio/db/test_aaindex.rb +6 -6
  244. data/test/unit/bio/db/test_fasta.rb +5 -46
  245. data/test/unit/bio/db/test_fastq.rb +829 -0
  246. data/test/unit/bio/db/test_gff.rb +4 -2
  247. data/test/unit/bio/db/test_lasergene.rb +7 -5
  248. data/test/unit/bio/db/test_medline.rb +4 -2
  249. data/test/unit/bio/db/test_newick.rb +6 -6
  250. data/test/unit/bio/db/test_nexus.rb +4 -2
  251. data/test/unit/bio/db/test_phyloxml.rb +769 -0
  252. data/test/unit/bio/db/test_phyloxml_writer.rb +328 -0
  253. data/test/unit/bio/db/test_prosite.rb +6 -5
  254. data/test/unit/bio/db/test_qual.rb +63 -0
  255. data/test/unit/bio/db/test_rebase.rb +5 -3
  256. data/test/unit/bio/db/test_soft.rb +7 -6
  257. data/test/unit/bio/io/flatfile/test_autodetection.rb +6 -7
  258. data/test/unit/bio/io/flatfile/test_buffer.rb +6 -5
  259. data/test/unit/bio/io/flatfile/test_splitter.rb +4 -4
  260. data/test/unit/bio/io/test_ddbjxml.rb +4 -3
  261. data/test/unit/bio/io/test_ensembl.rb +5 -3
  262. data/test/unit/bio/io/test_fastacmd.rb +4 -3
  263. data/test/unit/bio/io/test_flatfile.rb +6 -5
  264. data/test/unit/bio/io/test_soapwsdl.rb +4 -3
  265. data/test/unit/bio/io/test_togows.rb +4 -2
  266. data/test/unit/bio/sequence/test_aa.rb +5 -3
  267. data/test/unit/bio/sequence/test_common.rb +4 -2
  268. data/test/unit/bio/sequence/test_compat.rb +4 -2
  269. data/test/unit/bio/sequence/test_dblink.rb +5 -3
  270. data/test/unit/bio/sequence/test_na.rb +4 -2
  271. data/test/unit/bio/sequence/test_quality_score.rb +330 -0
  272. data/test/unit/bio/shell/plugin/test_seq.rb +5 -3
  273. data/test/unit/bio/test_alignment.rb +5 -3
  274. data/test/unit/bio/test_command.rb +4 -3
  275. data/test/unit/bio/test_db.rb +5 -3
  276. data/test/unit/bio/test_feature.rb +4 -2
  277. data/test/unit/bio/test_location.rb +4 -2
  278. data/test/unit/bio/test_map.rb +5 -3
  279. data/test/unit/bio/test_pathway.rb +4 -2
  280. data/test/unit/bio/test_reference.rb +4 -2
  281. data/test/unit/bio/test_sequence.rb +5 -3
  282. data/test/unit/bio/test_shell.rb +5 -3
  283. data/test/unit/bio/test_tree.rb +6 -6
  284. data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +4 -2
  285. data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +4 -2
  286. data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +4 -2
  287. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +4 -2
  288. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +4 -2
  289. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +4 -2
  290. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +4 -2
  291. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +4 -2
  292. data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +4 -2
  293. data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +4 -2
  294. data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +4 -2
  295. data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +4 -2
  296. data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +17 -13
  297. data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +17 -13
  298. data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +4 -2
  299. data/test/unit/bio/util/test_color_scheme.rb +5 -3
  300. data/test/unit/bio/util/test_contingency_table.rb +5 -3
  301. data/test/unit/bio/util/test_restriction_enzyme.rb +4 -2
  302. data/test/unit/bio/util/test_sirna.rb +6 -4
  303. metadata +147 -2
data/test/data/KEGG/C00025.compound ADDED
@@ -0,0 +1,102 @@
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+ ENTRY C00025 Compound
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+ NAME L-Glutamate;
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+ L-Glutamic acid;
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+ L-Glutaminic acid;
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+ Glutamate
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+ FORMULA C5H9NO4
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+ MASS 147.0532
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+ REMARK Same as: D00007
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+ COMMENT The name "glutamate" also means DL-Glutamate (see [CPD:C00302])
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+ REACTION R00021 R00093 R00114 R00239 R00241 R00243 R00245 R00248
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+ R00250 R00251 R00253 R00254 R00256 R00257 R00258 R00259
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+ R00260 R00261 R00262 R00263 R00355 R00372 R00411 R00457
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+ R00494 R00525 R00573 R00575 R00578 R00609 R00667 R00668
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+ R00684 R00694 R00707 R00708 R00734 R00768 R00894 R00895
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+ R00908 R00942 R00986 R01072 R01090 R01155 R01161 R01214
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+ R01231 R01339 R01585 R01586 R01648 R01654 R01684 R01716
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+ R01939 R01956 R02040 R02077 R02199 R02237 R02274 R02282
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+ R02283 R02285 R02287 R02313 R02315 R02433 R02619 R02700
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+ R02772 R02773 R02929 R02930 R03053 R03120 R03189 R03207
20
+ R03243 R03248 R03266 R03651 R03905 R03916 R03952 R03970
21
+ R03971 R04028 R04029 R04051 R04171 R04173 R04188 R04212
22
+ R04217 R04234 R04241 R04269 R04338 R04438 R04463 R04467
23
+ R04475 R04529 R04558 R04776 R05052 R05085 R05197 R05207
24
+ R05224 R05225 R05507 R05578 R05815 R06423 R06426 R06844
25
+ R06977 R07275 R07276 R07277 R07396 R07414 R07419 R07456
26
+ R07613 R07643 R07659 R08244
27
+ PATHWAY PATH: ko00250 Alanine, aspartate and glutamate metabolism
28
+ PATH: ko00330 Arginine and proline metabolism
29
+ PATH: ko00340 Histidine metabolism
30
+ PATH: ko00471 D-Glutamine and D-glutamate metabolism
31
+ PATH: ko00480 Glutathione metabolism
32
+ PATH: ko00650 Butanoate metabolism
33
+ PATH: ko00660 C5-Branched dibasic acid metabolism
34
+ PATH: ko00860 Porphyrin and chlorophyll metabolism
35
+ PATH: ko00910 Nitrogen metabolism
36
+ PATH: ko00970 Aminoacyl-tRNA biosynthesis
37
+ PATH: map01060 Biosynthesis of plant secondary metabolites
38
+ PATH: ko01064 Biosynthesis of alkaloids derived from ornithine,
39
+ lysine and nicotinic acid
40
+ PATH: ko01100 Metabolic pathways
41
+ PATH: ko02010 ABC transporters
42
+ PATH: ko04080 Neuroactive ligand-receptor interaction
43
+ PATH: ko04540 Gap junction
44
+ PATH: ko04720 Long-term potentiation
45
+ PATH: ko04730 Long-term depression
46
+ PATH: ko04742 Taste transduction
47
+ PATH: ko05014 Amyotrophic lateral sclerosis (ALS)
48
+ PATH: ko05016 Huntington's disease
49
+ ENZYME 1.4.1.2 1.4.1.3 1.4.1.4 1.4.1.13
50
+ 1.4.1.14 1.4.3.11 1.4.7.1 1.5.1.9
51
+ 1.5.1.10 1.5.1.12 1.5.99.5 2.1.1.21
52
+ 2.1.2.5 2.3.1.1 2.3.1.14 2.3.1.35
53
+ 2.3.2.2 2.3.2.- 2.4.2.14 2.4.2.-
54
+ 2.6.1.1 2.6.1.2 2.6.1.3 2.6.1.4
55
+ 2.6.1.5 2.6.1.6 2.6.1.7 2.6.1.8
56
+ 2.6.1.9 2.6.1.11 2.6.1.13 2.6.1.16
57
+ 2.6.1.17 2.6.1.19 2.6.1.22 2.6.1.23
58
+ 2.6.1.24 2.6.1.26 2.6.1.27 2.6.1.29
59
+ 2.6.1.33 2.6.1.34 2.6.1.36 2.6.1.38
60
+ 2.6.1.39 2.6.1.40 2.6.1.42 2.6.1.48
61
+ 2.6.1.49 2.6.1.52 2.6.1.55 2.6.1.57
62
+ 2.6.1.59 2.6.1.65 2.6.1.67 2.6.1.68
63
+ 2.6.1.72 2.6.1.75 2.6.1.76 2.6.1.79
64
+ 2.6.1.80 2.6.1.81 2.6.1.82 2.6.1.83
65
+ 2.6.1.85 2.6.1.- 2.7.2.11 2.7.2.13
66
+ 3.5.1.2 3.5.1.38 3.5.1.55 3.5.1.65
67
+ 3.5.1.68 3.5.1.87 3.5.1.94 3.5.1.96
68
+ 3.5.2.9 3.5.3.8 4.1.1.15 4.1.3.27
69
+ 4.1.3.- 5.1.1.3 5.4.99.1 6.1.1.17
70
+ 6.1.1.24 6.3.1.2 6.3.1.6 6.3.1.11
71
+ 6.3.1.- 6.3.2.2 6.3.2.12 6.3.2.17
72
+ 6.3.2.18 6.3.4.2 6.3.4.12 6.3.5.1
73
+ 6.3.5.2 6.3.5.3 6.3.5.4 6.3.5.5
74
+ 6.3.5.6 6.3.5.7 6.3.5.9 6.3.5.10
75
+ DBLINKS CAS: 56-86-0
76
+ PubChem: 3327
77
+ ChEBI: 16015
78
+ KNApSAcK: C00001358
79
+ PDB-CCD: GLU
80
+ 3DMET: B00007
81
+ NIKKAJI: J9.171E
82
+ ATOM 10
83
+ 1 C1c C 23.8372 -17.4608
84
+ 2 C1b C 25.0252 -16.7233
85
+ 3 C6a C 22.6023 -16.7994
86
+ 4 N1a N 23.8781 -18.8595
87
+ 5 C1b C 26.2601 -17.3788
88
+ 6 O6a O 21.4434 -17.5954
89
+ 7 O6a O 22.6198 -15.4007
90
+ 8 C6a C 27.4482 -16.6414
91
+ 9 O6a O 28.6830 -17.3028
92
+ 10 O6a O 27.4714 -15.2426
93
+ BOND 9
94
+ 1 1 2 1
95
+ 2 1 3 1
96
+ 3 1 4 1 #Down
97
+ 4 2 5 1
98
+ 5 3 6 1
99
+ 6 3 7 2
100
+ 7 5 8 1
101
+ 8 8 9 1
102
+ 9 8 10 2
data/test/data/KEGG/D00063.drug ADDED
@@ -0,0 +1,104 @@
1
+ ENTRY D00063 Drug
2
+ NAME Tobramycin (JP15/USP);
3
+ TOB;
4
+ Tobracin (TN);
5
+ Tobrex (TN)
6
+ FORMULA C18H37N5O9
7
+ MASS 467.2591
8
+ SOURCE Streptomyces tenebrarius [TAX:1933]
9
+ TARGET 16S rRNA of 30S ribosomal subunit, protein synthesis inhibitor
10
+ [BR:ko03011(16S)]
11
+ ACTIVITY Antibacterial
12
+ REMARK Same as: C00397
13
+ Therapeutic category: 1317 6123
14
+ ATC code: J01GB01 S01AA12
15
+ COMMENT natural product
16
+ PATHWAY PATH: map07021 Aminoglycosides
17
+ PRODUCTS TOBI (Novartis Pharma) 94F9E516-6BF6-4E30-8DDE-8833C25C2560
18
+ TOBRAMYCIN (Bristol-Myers Squibb) 7305F9BB-622B-43C0-981A-56E2F226CFD7
19
+ TOBRAMYCIN (Hospira) C5A005B0-7B6F-4E30-DF92-9A20B1CA66A1
20
+ Tobramycin (Akorn-Strides) 49151A62-191A-4BA8-8B8C-BD8535F2FDB3
21
+ Tobramycin (Bausch and Lomb) A5693EC9-D2F7-4D45-90B0-A113C54840D7
22
+ Tobramycin (Falcon Pharma) 27E2C16E-19B0-4745-93EB-5CF99F94BB92
23
+ Tobramycin (Hospira) 4E115874-3637-4AED-B6AF-77D53A850208
24
+ Tobramycin (Hospira) EB02166C-18F6-4BE0-F493-AC89D65DA759
25
+ Tobramycin (X-Gen Pharma) A384641C-04E3-4AB5-B152-7408CD07B64D
26
+ Tobramycin in Sodium Chloride (Hospira) EE907146-E4A8-4578-A9B0-C8E9790E3D55
27
+ Tobrex (Alcon Lab) 4B8716C4-0FFD-49AA-9006-A3BF5B6D19A6
28
+ Tobrex (Alcon Lab) CDD423C5-A231-47D4-BF51-00B5C29E6A60
29
+ DBLINKS CAS: 32986-56-4
30
+ PubChem: 7847131
31
+ ChEBI: 28864
32
+ DrugBank: DB00684
33
+ PDB-CCD: TOY
34
+ LigandBox: D00063
35
+ NIKKAJI: J4.533K
36
+ ATOM 32
37
+ 1 C1y C 20.6560 -20.0968
38
+ 2 C1y C 20.6560 -21.4973
39
+ 3 C1y C 21.8689 -22.1975
40
+ 4 C1y C 23.0818 -21.4973
41
+ 5 C1y C 23.0818 -20.0968
42
+ 6 O2x O 21.8689 -19.3965
43
+ 7 C1b C 19.4432 -19.3965
44
+ 8 O1a O 18.2473 -20.0872
45
+ 9 O1a O 19.4432 -22.1975
46
+ 10 N1a N 21.8689 -23.5978
47
+ 11 O1a O 24.3134 -22.2085
48
+ 12 O2a O 24.3134 -19.3855
49
+ 13 C1y C 25.4878 -18.6963
50
+ 14 C1y C 26.7056 -19.3879
51
+ 15 C1x C 27.9134 -18.6791
52
+ 16 C1y C 27.9035 -17.2786
53
+ 17 C1y C 26.6857 -16.5869
54
+ 18 C1y C 25.4779 -17.2958
55
+ 19 N1a N 26.7157 -20.7965
56
+ 20 N1a N 29.0779 -16.5893
57
+ 21 O1a O 24.2675 -16.6084
58
+ 22 O2a O 26.6757 -15.1950
59
+ 23 C1y C 27.8854 -14.4851
60
+ 24 O2x O 29.0946 -15.1718
61
+ 25 C1y C 30.3025 -14.4631
62
+ 26 C1y C 30.2926 -13.0626
63
+ 27 C1x C 29.0835 -12.3758
64
+ 28 C1y C 27.8755 -13.0846
65
+ 29 C1b C 31.5468 -15.1693
66
+ 30 N1a N 31.5569 -16.5953
67
+ 31 O1a O 31.5060 -12.3503
68
+ 32 N1a N 26.6567 -12.3923
69
+ BOND 34
70
+ 1 1 2 1
71
+ 2 2 3 1
72
+ 3 3 4 1
73
+ 4 4 5 1
74
+ 5 5 6 1
75
+ 6 1 6 1
76
+ 7 1 7 1 #Up
77
+ 8 7 8 1
78
+ 9 2 9 1 #Down
79
+ 10 3 10 1 #Up
80
+ 11 4 11 1 #Down
81
+ 12 5 12 1 #Down
82
+ 13 13 12 1 #Down
83
+ 14 13 14 1
84
+ 15 14 15 1
85
+ 16 15 16 1
86
+ 17 16 17 1
87
+ 18 17 18 1
88
+ 19 13 18 1
89
+ 20 14 19 1 #Up
90
+ 21 16 20 1 #Up
91
+ 22 18 21 1 #Up
92
+ 23 17 22 1 #Down
93
+ 24 23 22 1 #Down
94
+ 25 23 24 1
95
+ 26 24 25 1
96
+ 27 25 26 1
97
+ 28 26 27 1
98
+ 29 27 28 1
99
+ 30 23 28 1
100
+ 31 25 29 1 #Up
101
+ 32 29 30 1
102
+ 33 26 31 1 #Down
103
+ 34 28 32 1 #Down
104
+ ///
data/test/data/KEGG/G00024.glycan ADDED
@@ -0,0 +1,47 @@
1
+ ENTRY G00024 Glycan
2
+ NAME T antigen
3
+ COMPOSITION (Gal)1 (GalNAc)1 (Ser/Thr)1
4
+ MASS 365.3 (Ser/Thr)
5
+ CLASS Glycoprotein; O-Glycan
6
+ Neoglycoconjugate
7
+ REMARK Same as: C04750 C04776
8
+ REFERENCE 1 [PMID:12950230]
9
+ Backstrom M, Link T, Olson FJ, Karlsson H, Graham R, Picco G,
10
+ Burchell J, Taylor-Papadimitriou J, Noll T, Hansson GC.
11
+ Recombinant MUC1 mucin with a breast cancer-like O-glycosylation
12
+ produced in large amounts in Chinese-hamster ovary cells.
13
+ Biochem. J. 376 (2003) 677-86.
14
+ 2 [PMID:14631106]
15
+ Wu AM.
16
+ Carbohydrate structural units in glycoproteins and polysaccharides
17
+ as important ligands for Gal and GalNAc reactive lectins.
18
+ J. Biomed. Sci. 10 (2003) 676-88.
19
+ REACTION R05908 R05912 R05913 R06140
20
+ PATHWAY PATH: ko00512 O-Glycan biosynthesis
21
+ PATH: ko01100 Metabolic pathways
22
+ ENZYME 2.4.1.102 2.4.1.122 2.4.99.4 3.2.1.97
23
+ ORTHOLOGY KO: K00727 beta-1,3-galactosyl-O-glycosyl-glycoprotein
24
+ beta-1,6-N-acetylglucosaminyltransferase [EC:2.4.1.102]
25
+ KO: K00731 glycoprotein-N-acetylgalactosamine
26
+ 3-beta-galactosyltransferase [EC:2.4.1.122]
27
+ KO: K00780 beta-galactoside alpha-2,3-sialyltransferase
28
+ (sialyltransferase 4A) [EC:2.4.99.4]
29
+ KO: K03368 beta-galactoside alpha-2,3-sialyltransferase
30
+ (sialyltransferase 4B) [EC:2.4.99.4]
31
+ DBLINKS CCSD: 98 99 100 2225 2236 2237 2238 2239 2240 2241 2242 2243 3406
32
+ 5035 5038 5887 14321 18613 25363 27572 28182 29046 29092 29175
33
+ 29393 29521 29554 30734 30735 30848 30849 30850 30917 32646
34
+ 33022 33851 33878 33952 34823 34829 34986 34995 35029 35050
35
+ 35107 35108 35805 35833 35991 36236 36826 36863 37982 38587
36
+ 38640 38672 42797 43915 44029 44775 45346 46438 46466 47186
37
+ 48015 48891 49283 49293 50466 50469 50477
38
+ GlycomeDB: 475
39
+ JCGGDB: JCGG-STR025711
40
+ NODE 3
41
+ 1 Ser/Thr 8 0
42
+ 2 GalNAc -1 0
43
+ 3 Gal -9 0
44
+ EDGE 2
45
+ 1 2:a1 1
46
+ 2 3:b1 2:3
47
+ ///
data/test/data/KEGG/G01366.glycan ADDED
@@ -0,0 +1,18 @@
1
+ ENTRY G01366 Glycan
2
+ COMPOSITION (4dlyxHex)1 (GlcNAc)1 (Man)2
3
+ MASS 691.6
4
+ CLASS Glycoprotein; N-Glycan
5
+ COMMENT synthetic (CCSD:2549)
6
+ DBLINKS CCSD: 2549 2550 16559 25204
7
+ GlycomeDB: 5567
8
+ JCGGDB: JCGG-STR026574
9
+ NODE 4
10
+ 1 GlcNAc 11.4 0
11
+ 2 4dlyxHex -0.6 0
12
+ 3 Man -10.6 5
13
+ 4 Man -10.6 -5
14
+ EDGE 3
15
+ 1 2:b1 1:4
16
+ 2 3:a1 2:6
17
+ 3 4:a1 2:3
18
+ ///
data/test/data/KEGG/K02338.orthology ADDED
@@ -0,0 +1,902 @@
1
+ ENTRY K02338 KO
2
+ NAME DPO3B, dnaN
3
+ DEFINITION DNA polymerase III subunit beta [EC:2.7.7.7]
4
+ CLASS Metabolism; Nucleotide Metabolism; Purine metabolism [PATH:ko00230]
5
+ Metabolism; Nucleotide Metabolism; Pyrimidine metabolism
6
+ [PATH:ko00240]
7
+ Genetic Information Processing; Replication and Repair; DNA
8
+ replication [PATH:ko03030]
9
+ Genetic Information Processing; Replication and Repair; Mismatch
10
+ repair [PATH:ko03430]
11
+ Genetic Information Processing; Replication and Repair; Homologous
12
+ recombination [PATH:ko03440]
13
+ Protein Families; Genetic Information Processing; DNA replication
14
+ proteins [BR:ko03032]
15
+ Protein Families; Genetic Information Processing; DNA repair and
16
+ recombination proteins [BR:ko03400]
17
+ DBLINKS RN: R00375 R00376 R00377 R00378
18
+ COG: COG0592
19
+ GO: 0003887
20
+ GENES ECO: b3701(dnaN)
21
+ ECJ: JW3678(dnaN)
22
+ ECD: ECDH10B_3887(dnaN)
23
+ EBW: BWG_3391(dnaN)
24
+ ECE: Z5192(dnaN)
25
+ ECS: ECs4636
26
+ ECF: ECH74115_5129(dnaN)
27
+ ETW: ECSP_4747(dnaN)
28
+ ECG: E2348C_4012(dnaN)
29
+ ECC: c4623(dnaN)
30
+ ECI: UTI89_C4251(dnaN)
31
+ ECP: ECP_3902
32
+ ECV: APECO1_2756(dnaN)
33
+ ECW: EcE24377A_4211(dnaN)
34
+ ECX: EcHS_A3914(dnaN)
35
+ ECM: EcSMS35_4066(dnaN)
36
+ ECY: ECSE_3987
37
+ ECL: EcolC_0002
38
+ ECK: EC55989_4170(dnaN)
39
+ ECQ: ECED1_4392(dnaN)
40
+ ECR: ECIAI1_3879(dnaN)
41
+ ECT: ECIAI39_4305(dnaN)
42
+ ECZ: ECS88_4124(dnaN)
43
+ EUM: ECUMN_4232(dnaN)
44
+ ELF: LF82_0508(dnaN)
45
+ EBL: B21_03528(dnaN)
46
+ EBD: ECBD_0002
47
+ EBR: ECB_03584(dnaN)
48
+ EFE: EFER_3996(dnaN)
49
+ STY: STY3941(dnaN)
50
+ STT: t3682(dnaN)
51
+ SPT: SPA3681(dnaN)
52
+ SEK: SSPA3436
53
+ SPQ: SPAB_04776
54
+ SEI: SPC_3924(dnaN)
55
+ SEC: SC3755(dnaN)
56
+ SEH: SeHA_C4171(dnaN)
57
+ SEE: SNSL254_A4122(dnaN)
58
+ SEW: SeSA_A4049(dnaN)
59
+ SEA: SeAg_B4065(dnaN)
60
+ SED: SeD_A4229(dnaN)
61
+ SEG: SG3594(dnaN)
62
+ SET: SEN3654(dnaN)
63
+ SES: SARI_03808
64
+ STM: STM3837(dnaN)
65
+ YPE: YPO4096(dnaN)
66
+ YPK: y4112(dnaN)
67
+ YPM: YP_4004(dnaN)
68
+ YPA: YPA_4142
69
+ YPN: YPN_3954
70
+ YPP: YPDSF_0002
71
+ YPG: YpAngola_A4176(dnaN)
72
+ YPS: YPTB3942(dnaN)
73
+ YPI: YpsIP31758_4152(dnaN)
74
+ YPY: YPK_0002
75
+ YPB: YPTS_0002
76
+ YEN: YE4172(dnaN)
77
+ SFL: SF3763(dnaN)
78
+ SFX: S4008(dnaN)
79
+ SFV: SFV_3811(dnaN)
80
+ SSN: SSON_3651(dnaN)
81
+ SBO: SBO_3676(dnaN)
82
+ SBC: SbBS512_E4224(dnaN)
83
+ SDY: SDY_4183(dnaN)
84
+ ECA: ECA4440(dnaN)
85
+ PCT: PC1_0002
86
+ ETA: ETA_34520(dnaN)
87
+ PLU: plu0002(dnaN)
88
+ PAY: PAU_00002(dnaN)
89
+ BUC: BU011(dnaN)
90
+ BAS: BUsg011(dnaN)
91
+ BAB: bbp011(dnaN)
92
+ BCC: BCc_003(dnaN)
93
+ BAP: BUAP5A_011(dnaN)
94
+ BAU: BUAPTUC7_011(dnaN)
95
+ WBR: WGLp015(dnaN)
96
+ SGL: SG0002
97
+ ENT: Ent638_0002
98
+ ESA: ESA_03975
99
+ KPN: KPN_04104(dnaN)
100
+ KPE: KPK_0002(dnaN)
101
+ KPU: KP1_5482(dnaN)
102
+ CKO: CKO_00047
103
+ SPE: Spro_0033
104
+ PMR: PMI3133(dnaN)
105
+ EIC: NT01EI_0002
106
+ BFL: Bfl016(dnaN)
107
+ BPN: BPEN_015(dnaN)
108
+ HDE: HDEF_1740(dnaN)
109
+ DDA: Dd703_0002
110
+ DZE: Dd1591_0002
111
+ HIN: HI0992(dnaN)
112
+ HIT: NTHI1166(dnaN)
113
+ HIP: CGSHiEE_07005
114
+ HIQ: CGSHiGG_08555
115
+ HDU: HD0850(dnaN)
116
+ HAP: HAPS_1502(dnaN)
117
+ HSO: HS_0137(dnaN)
118
+ HSM: HSM_0002
119
+ PMU: PM1160(dnaN)
120
+ MSU: MS0486(dnaN)
121
+ APL: APL_0002(dnaN)
122
+ APJ: APJL_0002(dnaN)
123
+ APA: APP7_0002
124
+ ASU: Asuc_0002
125
+ AAP: NT05HA_0052
126
+ XFA: XF0002
127
+ XFT: PD0002(dnaN)
128
+ XFM: Xfasm12_0002
129
+ XFN: XfasM23_0002
130
+ XCC: XCC0002(dnaN)
131
+ XCB: XC_0002
132
+ XCA: xccb100_0002(dnaN)
133
+ XCV: XCV0002(dnaN)
134
+ XAC: XAC0002(dnaN)
135
+ XOO: XOO0002(dnaN)
136
+ XOM: XOO_0002
137
+ XOP: PXO_03482(dnaN)
138
+ SML: Smlt0002(dnaN)
139
+ SMT: Smal_0002
140
+ VCH: VC0013
141
+ VCO: VC0395_A2506(dnaN)
142
+ VCM: VCM66_0013(dnaN)
143
+ VCJ: VCD_001481
144
+ VVU: VV1_0998
145
+ VVY: VV0012
146
+ VPA: VP0012
147
+ VHA: VIBHAR_00443
148
+ VSP: VS_0011
149
+ VFI: VF_0010(dnaN)
150
+ VFM: VFMJ11_0010(dnaN)
151
+ VSA: VSAL_I0010(dnaN)
152
+ PPR: PBPRA0009
153
+ PAE: PA0002(dnaN)
154
+ PAU: PA14_00020(dnaN)
155
+ PAP: PSPA7_0002(dnaN)
156
+ PAG: PLES_00011(dnaN)
157
+ PPU: PP_0011(dnaN)
158
+ PPF: Pput_0002
159
+ PPG: PputGB1_0004
160
+ PPW: PputW619_0002
161
+ PST: PSPTO_0002(dnaN)
162
+ PSB: Psyr_0002
163
+ PSP: PSPPH_0002(dnaN)
164
+ PFL: PFL_0002(dnaN)
165
+ PFO: Pfl01_0002
166
+ PFS: PFLU0002(dnaN)
167
+ PEN: PSEEN0002(dnaN)
168
+ PMY: Pmen_0002
169
+ PSA: PST_0002(dnaN)
170
+ CJA: CJA_0002(dnaN)
171
+ AVN: Avin_00020
172
+ PAR: Psyc_0002(dnaN)
173
+ PCR: Pcryo_0004
174
+ PRW: PsycPRwf_0003
175
+ ACI: ACIAD0002(dnaN)
176
+ ACB: A1S_0002
177
+ ABM: ABSDF0002(dnaN)
178
+ ABY: ABAYE0002(dnaN)
179
+ ABC: ACICU_00004
180
+ ABN: AB57_0019(dnaN)
181
+ ABB: ABBFA_000002(dnaN)
182
+ SON: SO_0009(dnaN)
183
+ SDN: Sden_0002
184
+ SFR: Sfri_0002
185
+ SAZ: Sama_0014
186
+ SBL: Sbal_0002
187
+ SBM: Shew185_0002
188
+ SBN: Sbal195_0002
189
+ SBP: Sbal223_0002
190
+ SLO: Shew_0002
191
+ SPC: Sputcn32_0002
192
+ SSE: Ssed_0007
193
+ SPL: Spea_0002
194
+ SHE: Shewmr4_0002
195
+ SHM: Shewmr7_0002
196
+ SHN: Shewana3_0010
197
+ SHW: Sputw3181_0002
198
+ SHL: Shal_0002
199
+ SWD: Swoo_0002
200
+ SWP: swp_0016
201
+ ILO: IL0002(dnaN)
202
+ CPS: CPS_0002(dnaN)
203
+ PHA: PSHAa0002(dnaN)
204
+ PAT: Patl_0002
205
+ SDE: Sde_0002
206
+ MAQ: Maqu_0002
207
+ AMC: MADE_00003
208
+ PIN: Ping_3715
209
+ TTU: TERTU_0003(dnaN)
210
+ CBU: CBU_0002(dnaN)
211
+ CBS: COXBURSA331_A0002(dnaN)
212
+ CBD: CBUD_0002(dnaN)
213
+ CBG: CbuG_0003
214
+ CBC: CbuK_0002
215
+ LPN: lpg0002
216
+ LPF: lpl0002(dnaN)
217
+ LPP: lpp0002(dnaN)
218
+ LPC: LPC_0002(dnaN)
219
+ MCA: MCA3032(dnaN)
220
+ FTU: FTT0002(dnaN)
221
+ FTF: FTF0002(dnaN)
222
+ FTW: FTW_0002(dnaN)
223
+ FTL: FTL_0002
224
+ FTH: FTH_0002(dnaN)
225
+ FTA: FTA_0003(dnaN)
226
+ FTM: FTM_0002(dnaN)
227
+ FTN: FTN_0002(dnaN)
228
+ FPH: Fphi_0843
229
+ TCX: Tcr_0002
230
+ NOC: Noc_0002
231
+ AEH: Mlg_0002
232
+ HHA: Hhal_1226
233
+ TGR: Tgr7_0002
234
+ HCH: HCH_00003(dnaN)
235
+ CSA: Csal_0002
236
+ ABO: ABO_0002(dnaN)
237
+ MMW: Mmwyl1_0002
238
+ AHA: AHA_0002(dnaN)
239
+ ASA: ASA_0002(dnaN)
240
+ TAU: Tola_0002
241
+ DNO: DNO_0002(dnaN)
242
+ AFE: Lferr_0002
243
+ AFR: AFE_0001(dnaN)
244
+ BCI: BCI_0132(dnaN)
245
+ RMA: Rmag_0002
246
+ VOK: COSY_0002(dnaN)
247
+ KKO: Kkor_0002
248
+ NME: NMB1902(dnaN)
249
+ NMA: NMA0553(dnaN)
250
+ NMC: NMC0321(dnaN)
251
+ NMN: NMCC_0318(dnaN)
252
+ NMI: NMO_0268(dnaN)
253
+ NGO: NGO0002
254
+ NGK: NGK_0002
255
+ CVI: CV_0002(dnaN)
256
+ LHK: LHK_03241(dnaN)
257
+ RSO: RSc3441(dnaN)
258
+ RPI: Rpic_0002
259
+ RPF: Rpic12D_0002
260
+ REU: Reut_A0002
261
+ REH: H16_A0002(dnaN)
262
+ RME: Rmet_0002
263
+ CTI: RALTA_A0002(dnaN)
264
+ BMA: BMA0002(dnaN)
265
+ BMV: BMASAVP1_A2849(dnaN)
266
+ BML: BMA10229_A2236(dnaN)
267
+ BMN: BMA10247_0002(dnaN)
268
+ BPS: BPSL0074(dnaN)
269
+ BPM: BURPS1710b_0300(dnaN)
270
+ BPL: BURPS1106A_0102(dnaN)
271
+ BPD: BURPS668_0088(dnaN)
272
+ BPR: GBP346_A4277(dnaN)
273
+ BTE: BTH_I3240(dnaN)
274
+ BVI: Bcep1808_0002
275
+ BUR: Bcep18194_A3183
276
+ BCN: Bcen_2554
277
+ BCH: Bcen2424_0002
278
+ BCM: Bcenmc03_0002
279
+ BCJ: BCAL0422(dnaN)
280
+ BAM: Bamb_0002
281
+ BAC: BamMC406_0002
282
+ BMU: Bmul_0002
283
+ BMJ: BMULJ_00069(dnaN)
284
+ BXE: Bxe_A4461
285
+ BPH: Bphy_0002
286
+ BPY: Bphyt_0002
287
+ BGL: bglu_1g00020
288
+ PNU: Pnuc_0002
289
+ PNE: Pnec_0002
290
+ BPE: BP0490(dnaN)
291
+ BPA: BPP4400(dnaN)
292
+ BBR: BB4988(dnaN)
293
+ BPT: Bpet0002(dnaN)
294
+ BAV: BAV3411(dnaN)
295
+ RFR: Rfer_0002 Rfer_4311
296
+ POL: Bpro_0002
297
+ PNA: Pnap_4118
298
+ AAV: Aave_0002
299
+ AJS: Ajs_4145
300
+ VEI: Veis_0002
301
+ DAC: Daci_0002
302
+ DIA: Dtpsy_0002
303
+ VAP: Vapar_0002
304
+ MPT: Mpe_A0002
305
+ HAR: HEAR0003(dnaN)
306
+ MMS: mma_0002(dnaN)
307
+ LCH: Lcho_0002
308
+ NEU: NE0002(dnaN)
309
+ NET: Neut_0002
310
+ NMU: Nmul_A0002
311
+ EBA: ebA2847(dnaN)
312
+ AZO: azo0002(dnaN)
313
+ DAR: Daro_0002
314
+ TMZ: Tmz1t_0002
315
+ TBD: Tbd_0002
316
+ MFA: Mfla_0002
317
+ MMB: Mmol_0002
318
+ MEI: Msip34_0002
319
+ HPY: HP0500
320
+ HPJ: jhp0452(dnaN)
321
+ HPA: HPAG1_0476
322
+ HPS: HPSH_04415
323
+ HPG: HPG27_460(dnaN)
324
+ HPP: HPP12_0508(dnaN)
325
+ HPB: HELPY_0852(dnaN)
326
+ HHE: HH1126(dnaN)
327
+ HAC: Hac_0821(dnaN)
328
+ WSU: WS0001(dnaN)
329
+ TDN: Suden_0002
330
+ CJE: Cj0002(dnaN)
331
+ CJR: CJE0002(dnaN)
332
+ CJJ: CJJ81176_0028(dnaN)
333
+ CJU: C8J_0002(dnaN)
334
+ CJD: JJD26997_0002(dnaN)
335
+ CFF: CFF8240_0002(dnaN)
336
+ CCV: CCV52592_2055(dnaN)
337
+ CHA: CHAB381_0003(dnaN)
338
+ CCO: CCC13826_1851(dnaN)
339
+ CLA: Cla_0002(dnaN)
340
+ ABU: Abu_0002(dnaN)
341
+ NIS: NIS_0002(dnaN)
342
+ SUN: SUN_0002(dnaN)
343
+ NAM: NAMH_0002(dnaN)
344
+ GSU: GSU0001(dnaN)
345
+ GME: Gmet_0002
346
+ GUR: Gura_0002
347
+ GLO: Glov_0002
348
+ GBM: Gbem_0002
349
+ GEO: Geob_0002
350
+ GEM: GM21_0002
351
+ PCA: Pcar_0002(dnaN)
352
+ PPD: Ppro_0002
353
+ DVU: DVU0002(dnaN)
354
+ DVL: Dvul_0006
355
+ DVM: DvMF_2082
356
+ DDE: Dde_0002
357
+ DDS: Ddes_0004
358
+ DMA: DMR_00020(dnaN)
359
+ LIP: LI0786(dnaN)
360
+ DBA: Dbac_3096
361
+ BBA: Bd0002(dnaN)
362
+ DPS: DP0648
363
+ DOL: Dole_0094
364
+ DAL: Dalk_0275 Dalk_4110
365
+ DAT: HRM2_00010(dnaN)
366
+ ADE: Adeh_0002
367
+ ACP: A2cp1_0002
368
+ AFW: Anae109_0002
369
+ ANK: AnaeK_0002
370
+ MXA: MXAN_0236(dnaN)
371
+ SCL: sce8164(dnaN)
372
+ SAT: SYN_02050
373
+ SFU: Sfum_2688
374
+ RPR: RP419
375
+ RTY: RT0405(dnaN)
376
+ RCM: A1E_03260
377
+ RCO: RC0583(dnaN)
378
+ RFE: RF_0649(dnaN)
379
+ RAK: A1C_03150
380
+ RRI: A1G_03290
381
+ RRJ: RrIowa_0695
382
+ RMS: RMA_0600(dnaN)
383
+ RPK: RPR_05615
384
+ RBE: RBE_0656(dnaN)
385
+ RBO: A1I_04260
386
+ OTS: OTBS_0002(dnaN)
387
+ OTT: OTT_1572(dnaN)
388
+ WOL: WD1067(dnaN)
389
+ WBM: Wbm0429
390
+ WRI: WRi_011020(dnaN)
391
+ WPI: WPa_0934(dnaN)
392
+ AMA: AM1014(dnaN)
393
+ AMF: AMF_773(dnaN)
394
+ APH: APH_1097(dnaN)
395
+ ERU: Erum7880(dnaN)
396
+ ERW: ERWE_CDS_08330(dnaN)
397
+ ERG: ERGA_CDS_08230(dnaN)
398
+ ECN: Ecaj_0815
399
+ ECH: ECH_1009(dnaN) ECH_1010
400
+ NSE: NSE_0170(dnaN)
401
+ NRI: NRI_0166(dnaN)
402
+ PUB: SAR11_0411(dnaN)
403
+ MLO: mll5580
404
+ MES: Meso_0002
405
+ PLA: Plav_0004
406
+ SME: SMc00415(dnaN)
407
+ SMD: Smed_3543
408
+ ATU: Atu0301(dnaN)
409
+ ATC: AGR_C_520
410
+ ARA: Arad_0542(dnaN)
411
+ AVI: Avi_0351(dnaN)
412
+ RET: RHE_CH00318(dnaN)
413
+ REC: RHECIAT_CH0000356(dnaN)
414
+ RLE: RL0334(dnaN)
415
+ RLT: Rleg2_4329
416
+ RLG: Rleg_4592
417
+ RHI: NGR_c36750(dnaN)
418
+ LAS: CLIBASIA_01695
419
+ BME: BMEI1942
420
+ BMF: BAB1_0002(dnaN)
421
+ BMB: BruAb1_0002(dnaN)
422
+ BMC: BAbS19_I00020
423
+ BMS: BR0002(dnaN)
424
+ BMT: BSUIS_A0002(dnaN)
425
+ BOV: BOV_0002(dnaN)
426
+ BCS: BCAN_A0002(dnaN)
427
+ BMR: BMI_I2(dnaN)
428
+ OAN: Oant_0004
429
+ BJA: bll0829(dnaN)
430
+ BRA: BRADO0002(dnaN)
431
+ BBT: BBta_0002(dnaN)
432
+ RPA: RPA0002(dnaN)
433
+ RPB: RPB_0002
434
+ RPC: RPC_0002
435
+ RPD: RPD_0002
436
+ RPE: RPE_0002
437
+ RPT: Rpal_0002
438
+ NWI: Nwi_0002
439
+ NHA: Nham_0002
440
+ OCA: OCAR_4536(dnaN)
441
+ BHE: BH01190(dnaN)
442
+ BQU: BQ01120(dnaN)
443
+ BBK: BARBAKC583_1278(dnaN)
444
+ BTR: Btr_0130(dnaN)
445
+ BGR: Bgr_01170(dnaN)
446
+ XAU: Xaut_0002
447
+ AZC: AZC_1013
448
+ MEX: Mext_0002
449
+ MEA: Mex_1p0002(dnaN)
450
+ MDI: METDI0002(dnaN)
451
+ MRD: Mrad2831_2239
452
+ MET: M446_0002
453
+ MPO: Mpop_0003
454
+ MCH: Mchl_0003
455
+ MNO: Mnod_0002
456
+ BID: Bind_3047
457
+ MSL: Msil_3705
458
+ CCR: CC_0156
459
+ CCS: CCNA_00155
460
+ CAK: Caul_0162
461
+ PZU: PHZ_c3468(dnaN)
462
+ SIL: SPO0150(dnaN)
463
+ SIT: TM1040_0002
464
+ RSP: RSP_1343
465
+ RSH: Rsph17029_0012
466
+ RSQ: Rsph17025_0003
467
+ RSK: RSKD131_2743
468
+ JAN: Jann_0002
469
+ RDE: RD1_0209(dnaN)
470
+ PDE: Pden_0342 Pden_0970 Pden_2834
471
+ DSH: Dshi_3374
472
+ MMR: Mmar10_0002
473
+ HNE: HNE_0563(dnaN)
474
+ HBA: Hbal_3037
475
+ ZMO: ZMO0980(dnaN)
476
+ NAR: Saro_0639 Saro_1429
477
+ SAL: Sala_0708
478
+ SWI: Swit_2795
479
+ ELI: ELI_07330
480
+ GOX: GOX0002
481
+ GBE: GbCGDNIH1_0319
482
+ ACR: Acry_1437
483
+ GDI: GDI1772(dnaN)
484
+ GDJ: Gdia_0002
485
+ RRU: Rru_A0002
486
+ RCE: RC1_3063(dnaN)
487
+ MAG: amb0637
488
+ MGM: Mmc1_0002
489
+ ABA: Acid345_0002
490
+ ACA: ACP_2196(dnaN)
491
+ SUS: Acid_0002
492
+ BSU: BSU00020(dnaN)
493
+ BHA: BH0002(dnaN)
494
+ BAN: BA0002(dnaN-1) BA2684(dnaN-2)
495
+ BAR: GBAA0002(dnaN-1) GBAA2684(dnaN-2)
496
+ BAA: BA_0597 BA_3202
497
+ BAT: BAS0002 BAS2499
498
+ BAH: BAMEG_0002(dnaN1) BAMEG_1910(dnaN2)
499
+ BAI: BAA_0002(dnaN1) BAA_2748(dnaN2)
500
+ BCE: BC0002 BC2693
501
+ BCA: BCE_0002(dnaN) BCE_2720(dnaN) BCE_A0091(dnaN)
502
+ BCZ: BCZK0002(dnaN) BCZK2430(dnaN)
503
+ BCR: BCAH187_A0002(dnaN1) BCAH187_A2750(dnaN2) BCAH187_C0074(dnaN)
504
+ BCB: BCB4264_A0002(dnaN1) BCB4264_A2706(dnaN2)
505
+ BCU: BCAH820_0002(dnaN1) BCAH820_2699(dnaN2) BCAH820_B0051(dnaN)
506
+ BCG: BCG9842_B2604(dnaN2) BCG9842_B5318(dnaN1)
507
+ BCQ: BCQ_0002(dnaN) BCQ_2544(dnaN-2) BCQ_PI001
508
+ BCX: BCA_0002(dnaN1) BCA_2773(dnaN2)
509
+ BCY: Bcer98_0002
510
+ BTK: BT9727_0002(dnaN) BT9727_2460(dnaN)
511
+ BTL: BALH_0002(dnaN) BALH_2417
512
+ BWE: BcerKBAB4_0002 BcerKBAB4_2456
513
+ BLI: BL00077(dnaN)
514
+ BLD: BLi00002(dnaN)
515
+ BCL: ABC0002(dnaN)
516
+ BAY: RBAM_000020(dnaN)
517
+ BPU: BPUM_0002(dnaN)
518
+ OIH: OB0002(dnaN)
519
+ GKA: GK0002(dnaN)
520
+ GTN: GTNG_0002
521
+ GWC: GWCH70_0002
522
+ AFL: Aflv_0002(dnaN)
523
+ SAU: SA0002(dnaN)
524
+ SAV: SAV0002(dnaN)
525
+ SAW: SAHV_0002(dnaN)
526
+ SAM: MW0002(dnaN)
527
+ SAR: SAR0002(dnaN)
528
+ SAS: SAS0002
529
+ SAC: SACOL0002(dnaN)
530
+ SAB: SAB0002(dnaN)
531
+ SAA: SAUSA300_0002(dnaN)
532
+ SAX: USA300HOU_0002(dnaN)
533
+ SAO: SAOUHSC_00002
534
+ SAJ: SaurJH9_0002
535
+ SAH: SaurJH1_0002
536
+ SAE: NWMN_0002(dnaN)
537
+ SEP: SE0002
538
+ SER: SERP2552(dnaN)
539
+ SHA: SH0002(dnaN)
540
+ SSP: SSP0002
541
+ SCA: Sca_2473(dnaN)
542
+ LMO: lmo0002(dnaN)
543
+ LMF: LMOf2365_0002(dnaN)
544
+ LMH: LMHCC_2662(dnaN)
545
+ LMC: Lm4b_00002(dnaN)
546
+ LIN: lin0002(dnaN)
547
+ LWE: lwe0002(dnaN)
548
+ LSP: Bsph_0005(dnaN) Bsph_p018
549
+ ESI: Exig_0002
550
+ EAT: EAT1b_1729
551
+ MCL: MCCL_0002(dnaN)
552
+ BBE: BBR47_00020(dnaN)
553
+ LLA: L0275(dnaN)
554
+ LLC: LACR_0002
555
+ LLM: llmg_0002(dnaN)
556
+ SPY: SPy_0003(dnaN)
557
+ SPZ: M5005_Spy_0002(dnaN)
558
+ SPM: spyM18_0002(dnaN)
559
+ SPG: SpyM3_0002(dnaN)
560
+ SPS: SPs0002
561
+ SPH: MGAS10270_Spy0002(dnaN)
562
+ SPI: MGAS10750_Spy0002(dnaN)
563
+ SPJ: MGAS2096_Spy0002(dnaN)
564
+ SPK: MGAS9429_Spy0002(dnaN)
565
+ SPF: SpyM50002(dnaN)
566
+ SPA: M6_Spy0002
567
+ SPB: M28_Spy0002(dnaN)
568
+ SOZ: Spy49_0002(dnaN)
569
+ SPN: SP_0002
570
+ SPD: SPD_0002(dnaN)
571
+ SPR: spr0002(dnaN)
572
+ SPW: SPCG_0002(dnaN)
573
+ SPX: SPG_0002(dnaN)
574
+ SNE: SPN23F_00020(dnaN)
575
+ SPV: SPH_0002(dnaN)
576
+ SNM: SP70585_0002(dnaN)
577
+ SJJ: SPJ_0002(dnaN)
578
+ SPP: SPP_0002(dnaN)
579
+ SNT: SPT_0002(dnaN)
580
+ SAG: SAG0002(dnaN)
581
+ SAN: gbs0002(dnaN)
582
+ SAK: SAK_0002(dnaN)
583
+ SMU: SMU.02(dnaN)
584
+ STC: str0002(dnaN)
585
+ STL: stu0002(dnaN)
586
+ STE: STER_0002
587
+ SSA: SSA_0002(dnaN)
588
+ SSU: SSU05_0002
589
+ SSV: SSU98_0002 SSU98_0003
590
+ SSB: SSUBM407_0002(dnaN)
591
+ SSI: SSU0002(dnaN)
592
+ SSS: SSUSC84_0002(dnaN)
593
+ SGO: SGO_0002(dnaN)
594
+ SEQ: SZO_00020
595
+ SEZ: Sez_0002(dnaN)
596
+ SEU: SEQ_0002
597
+ SUB: SUB0002(dnaN)
598
+ SDS: SDEG_0002(dnaN)
599
+ LPL: lp_0002(dnaN)
600
+ LPJ: JDM1_0002(dnaN)
601
+ LJO: LJ0002
602
+ LAC: LBA0002(dnaN)
603
+ LSA: LSA0002(dnaN)
604
+ LSL: LSL_0002(dnaN)
605
+ LDB: Ldb0002(dnaN)
606
+ LBU: LBUL_0002
607
+ LBR: LVIS_0002
608
+ LCA: LSEI_0002
609
+ LCB: LCABL_00020(dnaN)
610
+ LGA: LGAS_0002
611
+ LRE: Lreu_0002
612
+ LRF: LAR_0002
613
+ LHE: lhv_0002
614
+ LFE: LAF_0002
615
+ PPE: PEPE_0002
616
+ EFA: EF0002(dnaN)
617
+ OOE: OEOE_0002
618
+ LME: LEUM_0002
619
+ LCI: LCK_00002(dnaN)
620
+ CAC: CAC0002(dnaN)
621
+ CPE: CPE0002(dnaN)
622
+ CPF: CPF_0002(dnaN)
623
+ CPR: CPR_0002(dnaN)
624
+ CTC: CTC00093
625
+ CNO: NT01CX_0866(dnaN)
626
+ CTH: Cthe_2372
627
+ CDF: CD0002(dnaN)
628
+ CBO: CBO0002(dnaG)
629
+ CBA: CLB_0002(dnaN)
630
+ CBH: CLC_0002(dnaN)
631
+ CBY: CLM_0002(dnaN)
632
+ CBL: CLK_3134(dnaN) CLK_A0115(dnaN)
633
+ CBK: CLL_A0002(dnaN)
634
+ CBB: CLD_0824(dnaN) CLD_A0160(dnaN)
635
+ CBI: CLJ_B0002(dnaN_1)
636
+ CBT: CLH_0002(dnaN)
637
+ CBF: CLI_0002(dnaN)
638
+ CBE: Cbei_0002
639
+ CKL: CKL_0002(dnaN)
640
+ CKR: CKR_0002
641
+ CPY: Cphy_0002
642
+ CCE: Ccel_0002
643
+ AMT: Amet_0002
644
+ AOE: Clos_0002
645
+ STH: STH2
646
+ SWO: Swol_0002
647
+ ATE: Athe_0003
648
+ DSY: DSY0002(dnaN)
649
+ DHD: Dhaf_0002
650
+ DRM: Dred_0002
651
+ PTH: PTH_0002(dnaN)
652
+ DAU: Daud_0002
653
+ HMO: HM1_0904(dnaN)
654
+ FMA: FMG_0002
655
+ EEL: EUBELI_00002
656
+ ERE: EUBREC_0002
657
+ TTE: TTE0002(dnaN)
658
+ TEX: Teth514_0002
659
+ TPD: Teth39_0002
660
+ CHY: CHY_2709(dnaN)
661
+ MTA: Moth_0003
662
+ CSC: Csac_0002
663
+ CPO: COPRO5265_0066(dnaN)
664
+ NTH: Nther_0002
665
+ HOR: Hore_00020
666
+ MGE: MG_001(dnaN)
667
+ MPN: MPN001(dnaN)
668
+ MPU: MYPU_0020(dnaN)
669
+ MPE: MYPE20(dnaN)
670
+ MGA: MGA_0618(dnaN)
671
+ MMY: MSC_0002(dnaN)
672
+ MMO: MMOB0020(dnaN)
673
+ MHY: mhp002(dnaN)
674
+ MHJ: MHJ_0002(dnaN)
675
+ MHP: MHP7448_0002(dnaN)
676
+ MSY: MS53_0002(dnaN)
677
+ MCP: MCAP_0002(dnaN)
678
+ MAA: MAG_0020(dnaN)
679
+ MAT: MARTH_orf003(dnaN)
680
+ MCO: MCJ_000020(dnaN)
681
+ UUR: UU079(dnaN)
682
+ UPA: UPA3_0078(dnaN)
683
+ UUE: UUR10_0085(dnaN)
684
+ POY: PAM002(dnaN)
685
+ AYW: AYWB_002(dnaN)
686
+ PML: ATP_00194(dnaN)
687
+ PAL: PAa_0002(dnaN)
688
+ MFL: Mfl002
689
+ MTU: Rv0002(dnaN)
690
+ MTC: MT0002(dnaN)
691
+ MRA: MRA_0002(dnaN)
692
+ MTF: TBFG_10002
693
+ MTB: TBMG_00002(TBMG_00002.1)
694
+ MBO: Mb0002(dnaN)
695
+ MBB: BCG_0002(dnaN_1) BCG_0032(dnaN_2)
696
+ MBT: JTY_0002(dnaN)
697
+ MLE: ML0002(dnaN)
698
+ MLB: MLBr_00002(dnaN)
699
+ MPA: MAP0002(dnaN)
700
+ MAV: MAV_0002(dnaN)
701
+ MSM: MSMEG_0001(dnaN)
702
+ MUL: MUL_0002(dnaN)
703
+ MVA: Mvan_0002
704
+ MGI: Mflv_0826
705
+ MAB: MAB_0002(dnaN)
706
+ MMC: Mmcs_0002
707
+ MKM: Mkms_0010
708
+ MJL: Mjls_0002
709
+ MMI: MMAR_0002(dnaN)
710
+ CGL: NCgl0002(cgl0003)
711
+ CGB: cg0004(dnaN)
712
+ CGT: cgR_0003
713
+ CEF: CE0003
714
+ CDI: DIP0002(dnaN)
715
+ CJK: jk0002(dnaN)
716
+ CUR: cur_0002
717
+ CAR: cauri_0002(dnaN)
718
+ CKP: ckrop_0001
719
+ NFA: nfa20(dnaN) nfa39660(dnaN2)
720
+ RHA: RHA1_ro03667(dnaN)
721
+ RER: RER_00020(dnaN)
722
+ ROP: ROP_34840(dnaN)
723
+ SCO: SCO3878(dnaN) SCP1.119(dnaN)
724
+ SMA: SAV_3362(dnaN2) SAV_4317(dnaN1)
725
+ SGR: SGR_3397(dnaN2) SGR_3701(dnaN)
726
+ TWH: TWT002(dnaN)
727
+ TWS: TW002(dnaN)
728
+ LXX: Lxx00020(dnaN)
729
+ CMI: CMM_0002(dnaN)
730
+ CMS: CMS_0002(dnaN)
731
+ ART: Arth_0002
732
+ AAU: AAur_0002(dnaN)
733
+ ACH: Achl_0002
734
+ RSA: RSal33209_0002
735
+ KRH: KRH_00020(dnaN)
736
+ MLU: Mlut_00020
737
+ BCV: Bcav_0002
738
+ BFA: Bfae_00020
739
+ JDE: Jden_0002
740
+ KSE: Ksed_00020
741
+ PAC: PPA0002
742
+ NCA: Noca_0002
743
+ TFU: Tfu_0002 Tfu_0086
744
+ FRA: Francci3_0003 Francci3_0738 Francci3_1710
745
+ FRE: Franean1_0003 Franean1_2567 Franean1_5871
746
+ FAL: FRAAL0004(dnaN) FRAAL1257
747
+ ACE: Acel_0002
748
+ KRA: Krad_0002 Krad_1769
749
+ SEN: SACE_0003(dnaN) SACE_0327(dnaN)
750
+ AMI: Amir_0002 Amir_0251
751
+ STP: Strop_0003
752
+ SAQ: Sare_0002
753
+ BLO: BL0638(dnaN)
754
+ BLJ: BLD_1435(dnaN)
755
+ BLN: Blon_0003
756
+ BAD: BAD_0002(dnaN)
757
+ BLA: BLA_0002(dnaN)
758
+ BLC: Balac_0002
759
+ BLT: Balat_0002
760
+ RXY: Rxyl_0002
761
+ AFO: Afer_0002
762
+ CCU: Ccur_00020
763
+ FNU: FN0536 FN0617
764
+ LBA: Lebu_1267
765
+ GAU: GAU_0002(dnaN)
766
+ RBA: RB10108(dnaN)
767
+ OTE: Oter_0953
768
+ MIN: Minf_0002(dnaN)
769
+ AMU: Amuc_0816
770
+ CTR: CT075(dnaN)
771
+ CTA: CTA_0080(dnaN)
772
+ CTB: CTL0331(dnaN)
773
+ CTL: CTLon_0326(dnaN)
774
+ CTJ: JALI_0741(dnaN)
775
+ CMU: TC0347(dnaN)
776
+ CPN: CPn0338(dnaN)
777
+ CPA: CP0419
778
+ CPJ: CPj0338(dnaN)
779
+ CPT: CpB0347
780
+ CCA: CCA00445(dnaN)
781
+ CAB: CAB431(dnaN)
782
+ CFE: CF0562(dnaN)
783
+ PCU: pc1705(dnaN)
784
+ BBU: BB0438
785
+ BBZ: BbuZS7_0444(dnaN)
786
+ BGA: BG0445(dnaN)
787
+ BAF: BAPKO_0460(dnaN)
788
+ BTU: BT0438
789
+ BHR: BH0438
790
+ BDU: BDU_435(dnaN)
791
+ BRE: BRE_438(dnaN)
792
+ TPA: TP0002
793
+ TPP: TPASS_0002(dnaN)
794
+ TDE: TDE0231(dnaN)
795
+ LIL: LA0002(dnaN)
796
+ LIC: LIC10002(dnaN)
797
+ LBJ: LBJ_0005(dnaN)
798
+ LBL: LBL_0005(dnaN)
799
+ LBI: LEPBI_I0002(dnaN)
800
+ LBF: LBF_0005(dnaN)
801
+ BHY: BHWA1_01258(dnaN)
802
+ SYN: slr0965(dnaN)
803
+ SYW: SYNW0001(dnaN)
804
+ SYC: syc1496_c(dnaN)
805
+ SYF: Synpcc7942_0001
806
+ SYD: Syncc9605_0001
807
+ SYE: Syncc9902_0001
808
+ SYG: sync_0001(dnaN)
809
+ SYR: SynRCC307_0001(dnaN)
810
+ SYX: SynWH7803_0001(dnaN)
811
+ SYP: SYNPCC7002_A1263(dnaN)
812
+ CYA: CYA_1647(dnaN)
813
+ CYB: CYB_1539(dnaN)
814
+ TEL: tll2349(dnaN)
815
+ MAR: MAE_38670(dnaN)
816
+ CYT: cce_1864(dnaN1) cce_4866(dnaN2)
817
+ CYP: PCC8801_1016
818
+ CYC: PCC7424_0340
819
+ CYN: Cyan7425_0199
820
+ GVI: gvip446(dnaN)
821
+ ANA: alr2010(dnaN) alr7569
822
+ NPU: Npun_R0034
823
+ AVA: Ava_0002 Ava_C0075
824
+ PMA: Pro0001(dnaN)
825
+ PMM: PMM0001(dnaN)
826
+ PMT: PMT0001(dnaN)
827
+ PMN: PMN2A_1328
828
+ PMI: PMT9312_0001
829
+ PMB: A9601_00001(dnaN)
830
+ PMC: P9515_00001(dnaN)
831
+ PMF: P9303_00001(dnaN)
832
+ PMG: P9301_00001(dnaN)
833
+ PMH: P9215_00001(dnaN)
834
+ PMJ: P9211_00001
835
+ PME: NATL1_00001(dnaN)
836
+ TER: Tery_0008
837
+ AMR: AM1_3096(dnaN)
838
+ BTH: BT_1364
839
+ BFR: BF2981
840
+ BFS: BF2857
841
+ BVU: BVU_2894
842
+ PGI: PG1853(dnaN)
843
+ PGN: PGN_1786
844
+ PDI: BDI_0694
845
+ APS: CFPG_644
846
+ SRU: SRU_0002(dnaN)
847
+ CHU: CHU_1549(dnaN)
848
+ CPI: Cpin_0616
849
+ GFO: GFO_1914(dnaN)
850
+ FJO: Fjoh_2720
851
+ FPS: FP1091(dnaN)
852
+ FBA: FIC_00920
853
+ COC: Coch_1752
854
+ SMG: SMGWSS_005(dnaN)
855
+ SMS: SMDSEM_005(dnaN)
856
+ AAS: Aasi_0152
857
+ CTE: CT0001(dnaN)
858
+ CPC: Cpar_0002
859
+ CCH: Cag_0002
860
+ CPH: Cpha266_0002
861
+ CPB: Cphamn1_0002
862
+ CLI: Clim_0002
863
+ PVI: Cvib_0002
864
+ PLT: Plut_0001
865
+ PPH: Ppha_0002
866
+ PAA: Paes_0002
867
+ CTS: Ctha_0842
868
+ DET: DET1227(dnaN)
869
+ DEH: cbdb_A1145(dnaN)
870
+ DEB: DehaBAV1_1036
871
+ RRS: RoseRS_4406
872
+ RCA: Rcas_0749
873
+ CAU: Caur_2639
874
+ CAG: Cagg_0019
875
+ CHL: Chy400_2852
876
+ HAU: Haur_1513
877
+ TRO: trd_0714(dnaN)
878
+ EMI: Emin_0003
879
+ RSD: TGRD_004
880
+ DRA: DR_0001
881
+ DGE: Dgeo_0003 Dgeo_3063
882
+ DDR: Deide_00020(dnaN)
883
+ TTH: TTC1609
884
+ TTJ: TTHA0001
885
+ AAE: aq_1882(dnaN)
886
+ HYA: HY04AAS1_1088
887
+ SUL: SYO3AOP1_0963
888
+ SAF: SULAZ_0725(dnaN)
889
+ PMX: PERMA_1539(dnaN)
890
+ TMA: TM0262
891
+ TPT: Tpet_0662
892
+ TLE: Tlet_0486
893
+ TRQ: TRQ2_0686
894
+ TNA: CTN_0424
895
+ TME: Tmel_0535
896
+ TAF: THA_1368(dnaN)
897
+ FNO: Fnod_1203
898
+ PMO: Pmob_1171
899
+ KOL: Kole_1868
900
+ DTH: DICTH_1442(dnaN)
901
+ DTU: Dtur_1551
902
+ TYE: THEYE_A0016(dnaN)