bio 1.3.1 → 1.4.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (303) hide show
  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 @@
1
+ ENTRY C00025 Compound
2
+ NAME L-Glutamate;
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+ L-Glutamic acid;
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+ L-Glutaminic acid;
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+ Glutamate
6
+ FORMULA C5H9NO4
7
+ MASS 147.0532
8
+ REMARK Same as: D00007
9
+ COMMENT The name "glutamate" also means DL-Glutamate (see [CPD:C00302])
10
+ REACTION R00021 R00093 R00114 R00239 R00241 R00243 R00245 R00248
11
+ R00250 R00251 R00253 R00254 R00256 R00257 R00258 R00259
12
+ R00260 R00261 R00262 R00263 R00355 R00372 R00411 R00457
13
+ R00494 R00525 R00573 R00575 R00578 R00609 R00667 R00668
14
+ R00684 R00694 R00707 R00708 R00734 R00768 R00894 R00895
15
+ R00908 R00942 R00986 R01072 R01090 R01155 R01161 R01214
16
+ R01231 R01339 R01585 R01586 R01648 R01654 R01684 R01716
17
+ R01939 R01956 R02040 R02077 R02199 R02237 R02274 R02282
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+ R02283 R02285 R02287 R02313 R02315 R02433 R02619 R02700
19
+ 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)