mspire 0.4.9 → 0.5.0

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Files changed (255) hide show
  1. data/README +27 -17
  2. data/changelog.txt +31 -62
  3. data/lib/ms/calc.rb +32 -0
  4. data/lib/ms/data/interleaved.rb +60 -0
  5. data/lib/ms/data/lazy_io.rb +73 -0
  6. data/lib/ms/data/lazy_string.rb +15 -0
  7. data/lib/ms/data/simple.rb +59 -0
  8. data/lib/ms/data/transposed.rb +41 -0
  9. data/lib/ms/data.rb +57 -0
  10. data/lib/ms/format/format_error.rb +12 -0
  11. data/lib/ms/spectrum.rb +25 -384
  12. data/lib/ms/support/binary_search.rb +126 -0
  13. data/lib/ms.rb +10 -10
  14. metadata +38 -350
  15. data/INSTALL +0 -58
  16. data/README.rdoc +0 -18
  17. data/Rakefile +0 -330
  18. data/bin/aafreqs.rb +0 -23
  19. data/bin/bioworks2excel.rb +0 -14
  20. data/bin/bioworks_to_pepxml.rb +0 -148
  21. data/bin/bioworks_to_pepxml_gui.rb +0 -225
  22. data/bin/fasta_shaker.rb +0 -5
  23. data/bin/filter_and_validate.rb +0 -5
  24. data/bin/gi2annot.rb +0 -14
  25. data/bin/id_class_anal.rb +0 -112
  26. data/bin/id_precision.rb +0 -172
  27. data/bin/ms_to_lmat.rb +0 -67
  28. data/bin/pepproph_filter.rb +0 -16
  29. data/bin/prob_validate.rb +0 -6
  30. data/bin/protein_summary.rb +0 -6
  31. data/bin/protxml2prots_peps.rb +0 -32
  32. data/bin/raw_to_mzXML.rb +0 -55
  33. data/bin/run_percolator.rb +0 -122
  34. data/bin/sqt_group.rb +0 -26
  35. data/bin/srf_group.rb +0 -27
  36. data/bin/srf_to_sqt.rb +0 -40
  37. data/lib/align/chams.rb +0 -78
  38. data/lib/align.rb +0 -154
  39. data/lib/archive/targz.rb +0 -94
  40. data/lib/bsearch.rb +0 -120
  41. data/lib/core_extensions.rb +0 -16
  42. data/lib/fasta.rb +0 -626
  43. data/lib/gi.rb +0 -124
  44. data/lib/group_by.rb +0 -10
  45. data/lib/index_by.rb +0 -11
  46. data/lib/merge_deep.rb +0 -21
  47. data/lib/ms/converter/mzxml.rb +0 -77
  48. data/lib/ms/gradient_program.rb +0 -170
  49. data/lib/ms/msrun.rb +0 -244
  50. data/lib/ms/msrun_index.rb +0 -108
  51. data/lib/ms/parser/mzdata/axml.rb +0 -67
  52. data/lib/ms/parser/mzdata/dom.rb +0 -175
  53. data/lib/ms/parser/mzdata/libxml.rb +0 -7
  54. data/lib/ms/parser/mzdata.rb +0 -31
  55. data/lib/ms/parser/mzxml/axml.rb +0 -70
  56. data/lib/ms/parser/mzxml/dom.rb +0 -182
  57. data/lib/ms/parser/mzxml/hpricot.rb +0 -253
  58. data/lib/ms/parser/mzxml/libxml.rb +0 -19
  59. data/lib/ms/parser/mzxml/regexp.rb +0 -122
  60. data/lib/ms/parser/mzxml/rexml.rb +0 -72
  61. data/lib/ms/parser/mzxml/xmlparser.rb +0 -248
  62. data/lib/ms/parser/mzxml.rb +0 -282
  63. data/lib/ms/parser.rb +0 -108
  64. data/lib/ms/precursor.rb +0 -25
  65. data/lib/ms/scan.rb +0 -81
  66. data/lib/mspire.rb +0 -4
  67. data/lib/pi_zero.rb +0 -244
  68. data/lib/qvalue.rb +0 -161
  69. data/lib/roc.rb +0 -187
  70. data/lib/sample_enzyme.rb +0 -160
  71. data/lib/scan_i.rb +0 -21
  72. data/lib/spec_id/aa_freqs.rb +0 -170
  73. data/lib/spec_id/bioworks.rb +0 -497
  74. data/lib/spec_id/digestor.rb +0 -138
  75. data/lib/spec_id/mass.rb +0 -179
  76. data/lib/spec_id/parser/proph.rb +0 -335
  77. data/lib/spec_id/precision/filter/cmdline.rb +0 -218
  78. data/lib/spec_id/precision/filter/interactive.rb +0 -134
  79. data/lib/spec_id/precision/filter/output.rb +0 -148
  80. data/lib/spec_id/precision/filter.rb +0 -637
  81. data/lib/spec_id/precision/output.rb +0 -60
  82. data/lib/spec_id/precision/prob/cmdline.rb +0 -160
  83. data/lib/spec_id/precision/prob/output.rb +0 -94
  84. data/lib/spec_id/precision/prob.rb +0 -249
  85. data/lib/spec_id/proph/pep_summary.rb +0 -104
  86. data/lib/spec_id/proph/prot_summary.rb +0 -484
  87. data/lib/spec_id/proph.rb +0 -4
  88. data/lib/spec_id/protein_summary.rb +0 -489
  89. data/lib/spec_id/sequest/params.rb +0 -316
  90. data/lib/spec_id/sequest/pepxml.rb +0 -1458
  91. data/lib/spec_id/sequest.rb +0 -33
  92. data/lib/spec_id/sqt.rb +0 -349
  93. data/lib/spec_id/srf.rb +0 -973
  94. data/lib/spec_id.rb +0 -778
  95. data/lib/spec_id_xml.rb +0 -99
  96. data/lib/transmem/phobius.rb +0 -147
  97. data/lib/transmem/toppred.rb +0 -368
  98. data/lib/transmem.rb +0 -157
  99. data/lib/validator/aa.rb +0 -48
  100. data/lib/validator/aa_est.rb +0 -112
  101. data/lib/validator/background.rb +0 -77
  102. data/lib/validator/bias.rb +0 -95
  103. data/lib/validator/cmdline.rb +0 -431
  104. data/lib/validator/decoy.rb +0 -107
  105. data/lib/validator/digestion_based.rb +0 -70
  106. data/lib/validator/probability.rb +0 -51
  107. data/lib/validator/prot_from_pep.rb +0 -234
  108. data/lib/validator/q_value.rb +0 -32
  109. data/lib/validator/transmem.rb +0 -272
  110. data/lib/validator/true_pos.rb +0 -46
  111. data/lib/validator.rb +0 -197
  112. data/lib/xml.rb +0 -38
  113. data/lib/xml_style_parser.rb +0 -119
  114. data/lib/xmlparser_wrapper.rb +0 -19
  115. data/release_notes.txt +0 -2
  116. data/script/compile_and_plot_smriti_final.rb +0 -97
  117. data/script/create_little_pepxml.rb +0 -61
  118. data/script/degenerate_peptides.rb +0 -47
  119. data/script/estimate_fpr_by_cysteine.rb +0 -226
  120. data/script/extract_gradient_programs.rb +0 -56
  121. data/script/find_cysteine_background.rb +0 -137
  122. data/script/genuine_tps_and_probs.rb +0 -136
  123. data/script/get_apex_values_rexml.rb +0 -44
  124. data/script/histogram_probs.rb +0 -61
  125. data/script/mascot_fix_pepxml.rb +0 -123
  126. data/script/msvis.rb +0 -42
  127. data/script/mzXML2timeIndex.rb +0 -25
  128. data/script/peps_per_bin.rb +0 -67
  129. data/script/prep_dir.rb +0 -121
  130. data/script/simple_protein_digestion.rb +0 -27
  131. data/script/smriti_final_analysis.rb +0 -103
  132. data/script/sqt_to_meta.rb +0 -24
  133. data/script/top_hit_per_scan.rb +0 -67
  134. data/script/toppred_to_yaml.rb +0 -47
  135. data/script/tpp_installer.rb +0 -249
  136. data/specs/align_spec.rb +0 -79
  137. data/specs/bin/bioworks_to_pepxml_spec.rb +0 -79
  138. data/specs/bin/fasta_shaker_spec.rb +0 -259
  139. data/specs/bin/filter_and_validate__multiple_vals_helper.yaml +0 -199
  140. data/specs/bin/filter_and_validate_spec.rb +0 -180
  141. data/specs/bin/ms_to_lmat_spec.rb +0 -34
  142. data/specs/bin/prob_validate_spec.rb +0 -86
  143. data/specs/bin/protein_summary_spec.rb +0 -14
  144. data/specs/fasta_spec.rb +0 -354
  145. data/specs/gi_spec.rb +0 -22
  146. data/specs/load_bin_path.rb +0 -7
  147. data/specs/merge_deep_spec.rb +0 -13
  148. data/specs/ms/gradient_program_spec.rb +0 -77
  149. data/specs/ms/msrun_spec.rb +0 -498
  150. data/specs/ms/parser_spec.rb +0 -92
  151. data/specs/ms/spectrum_spec.rb +0 -87
  152. data/specs/pi_zero_spec.rb +0 -115
  153. data/specs/qvalue_spec.rb +0 -39
  154. data/specs/roc_spec.rb +0 -251
  155. data/specs/rspec_autotest.rb +0 -149
  156. data/specs/sample_enzyme_spec.rb +0 -126
  157. data/specs/spec_helper.rb +0 -135
  158. data/specs/spec_id/aa_freqs_spec.rb +0 -52
  159. data/specs/spec_id/bioworks_spec.rb +0 -148
  160. data/specs/spec_id/digestor_spec.rb +0 -75
  161. data/specs/spec_id/precision/filter/cmdline_spec.rb +0 -20
  162. data/specs/spec_id/precision/filter/output_spec.rb +0 -31
  163. data/specs/spec_id/precision/filter_spec.rb +0 -246
  164. data/specs/spec_id/precision/prob_spec.rb +0 -44
  165. data/specs/spec_id/precision/prob_spec_helper.rb +0 -0
  166. data/specs/spec_id/proph/pep_summary_spec.rb +0 -98
  167. data/specs/spec_id/proph/prot_summary_spec.rb +0 -128
  168. data/specs/spec_id/protein_summary_spec.rb +0 -189
  169. data/specs/spec_id/sequest/params_spec.rb +0 -68
  170. data/specs/spec_id/sequest/pepxml_spec.rb +0 -374
  171. data/specs/spec_id/sequest_spec.rb +0 -38
  172. data/specs/spec_id/sqt_spec.rb +0 -246
  173. data/specs/spec_id/srf_spec.rb +0 -172
  174. data/specs/spec_id/srf_spec_helper.rb +0 -139
  175. data/specs/spec_id_helper.rb +0 -33
  176. data/specs/spec_id_spec.rb +0 -366
  177. data/specs/spec_id_xml_spec.rb +0 -33
  178. data/specs/transmem/phobius_spec.rb +0 -425
  179. data/specs/transmem/toppred_spec.rb +0 -298
  180. data/specs/transmem_spec.rb +0 -60
  181. data/specs/transmem_spec_shared.rb +0 -64
  182. data/specs/validator/aa_est_spec.rb +0 -66
  183. data/specs/validator/aa_spec.rb +0 -40
  184. data/specs/validator/background_spec.rb +0 -67
  185. data/specs/validator/bias_spec.rb +0 -122
  186. data/specs/validator/decoy_spec.rb +0 -51
  187. data/specs/validator/fasta_helper.rb +0 -26
  188. data/specs/validator/prot_from_pep_spec.rb +0 -141
  189. data/specs/validator/transmem_spec.rb +0 -146
  190. data/specs/validator/true_pos_spec.rb +0 -58
  191. data/specs/validator_helper.rb +0 -33
  192. data/specs/xml_spec.rb +0 -12
  193. data/test_files/000_pepxml18_small.xml +0 -206
  194. data/test_files/020a.mzXML.timeIndex +0 -4710
  195. data/test_files/4-03-03_mzXML/000.mzXML.timeIndex +0 -3973
  196. data/test_files/4-03-03_mzXML/020.mzXML.timeIndex +0 -3872
  197. data/test_files/4-03-03_small-prot.xml +0 -321
  198. data/test_files/4-03-03_small.xml +0 -3876
  199. data/test_files/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
  200. data/test_files/bioworks-3.3_10prots.xml +0 -5999
  201. data/test_files/bioworks31.params +0 -77
  202. data/test_files/bioworks32.params +0 -62
  203. data/test_files/bioworks33.params +0 -63
  204. data/test_files/bioworks_single_run_small.xml +0 -7237
  205. data/test_files/bioworks_small.fasta +0 -212
  206. data/test_files/bioworks_small.params +0 -63
  207. data/test_files/bioworks_small.phobius +0 -109
  208. data/test_files/bioworks_small.toppred.out +0 -2847
  209. data/test_files/bioworks_small.xml +0 -5610
  210. data/test_files/bioworks_with_INV_small.xml +0 -3753
  211. data/test_files/bioworks_with_SHUFF_small.xml +0 -2503
  212. data/test_files/corrupted_900.srf +0 -0
  213. data/test_files/head_of_7MIX.srf +0 -0
  214. data/test_files/interact-opd1_mods_small-prot.xml +0 -304
  215. data/test_files/messups.fasta +0 -297
  216. data/test_files/opd1/000.my_answer.100lines.xml +0 -101
  217. data/test_files/opd1/000.tpp_1.2.3.first10.xml +0 -115
  218. data/test_files/opd1/000.tpp_2.9.2.first10.xml +0 -126
  219. data/test_files/opd1/000.v2.1.mzXML.timeIndex +0 -3748
  220. data/test_files/opd1/000_020-prot.png +0 -0
  221. data/test_files/opd1/000_020_3prots-prot.mod_initprob.xml +0 -62
  222. data/test_files/opd1/000_020_3prots-prot.xml +0 -62
  223. data/test_files/opd1/opd1_cat_inv_small-prot.xml +0 -139
  224. data/test_files/opd1/sequest.3.1.params +0 -77
  225. data/test_files/opd1/sequest.3.2.params +0 -62
  226. data/test_files/opd1/twenty_scans.mzXML +0 -418
  227. data/test_files/opd1/twenty_scans.v2.1.mzXML +0 -382
  228. data/test_files/opd1/twenty_scans_answ.lmat +0 -0
  229. data/test_files/opd1/twenty_scans_answ.lmata +0 -9
  230. data/test_files/opd1_020_beginning.RAW +0 -0
  231. data/test_files/opd1_2runs_2mods/data/020.mzData.xml +0 -683
  232. data/test_files/opd1_2runs_2mods/data/020.readw.mzXML +0 -382
  233. data/test_files/opd1_2runs_2mods/data/040.mzData.xml +0 -683
  234. data/test_files/opd1_2runs_2mods/data/040.readw.mzXML +0 -382
  235. data/test_files/opd1_2runs_2mods/data/README.txt +0 -6
  236. data/test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml +0 -753
  237. data/test_files/orbitrap_mzData/000_cut.xml +0 -1920
  238. data/test_files/pepproph_small.xml +0 -4691
  239. data/test_files/phobius.small.noheader.txt +0 -50
  240. data/test_files/phobius.small.small.txt +0 -53
  241. data/test_files/s01_anC1_ld020mM.key.txt +0 -25
  242. data/test_files/s01_anC1_ld020mM.meth +0 -0
  243. data/test_files/small.fasta +0 -297
  244. data/test_files/small.sqt +0 -87
  245. data/test_files/smallraw.RAW +0 -0
  246. data/test_files/tf_bioworks2excel.bioXML +0 -14340
  247. data/test_files/tf_bioworks2excel.txt.actual +0 -1035
  248. data/test_files/toppred.small.out +0 -416
  249. data/test_files/toppred.xml.out +0 -318
  250. data/test_files/validator_hits_separate/bias_bioworks_small_HS.fasta +0 -7
  251. data/test_files/validator_hits_separate/bioworks_small_HS.xml +0 -5651
  252. data/test_files/yeast_gly_small-prot.xml +0 -265
  253. data/test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes +0 -6
  254. data/test_files/yeast_gly_small.xml +0 -3807
  255. data/test_files/yeast_gly_small2.parentTimes +0 -6
data/test_files/bioworks_small.fasta DELETED
@@ -1,212 +0,0 @@
1
- >gi|49175991|ref|YP_025292.1| small toxic membrane polypeptide [Escherichia coli K12]
2
- MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVFTAYESE
3
- >gi|16128018|ref|NP_414565.1| unknown CDS [Escherichia coli K12]
4
- MCRHSLRSDGAGFYQLAGCEYSFSAIKIAAGGQFLPVICAMAMKSHFFLISVLNRRLTLTAVQGILGRFSLF
5
- >gi|16128024|ref|NP_414571.1| nucleoside hydrolase [Escherichia coli K12]
6
- MRLPIFLDTDPGIDDAVAIAAAIFAPELDLQLMTTVAGNVSVEKTTRNALQLLHFWNAEIPLAQGAAVPLVRAPRDAASVHGESGMAGYDFVEHNRKPLGIPAFLAIRDALMRAPEPVTLVAIGPLTNIALLLSQCPECKPYIRRLVIMGGSAGRGNCTPNAEFNIAADPEAAACVFRSGIEIVMCGLDVTNQAILTPDYLSTLPQLNRTGKMLHALFSHYRSGSMQSGLRMHDLCAIAWLVRPDLFTLKPCFVAVETQGEFTSGTTVVDIDGCLGKPANVQVALDLDVKGFQQWVAEVLALAS
7
- >gi|16128058|ref|NP_414606.1| transcriptional regulator for ara operon [Escherichia coli K12]
8
- MAEAQNDPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLLLRRMEAINESLHPPMDNRVREACQYISDHLADSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFRAGCEEKVNDVAVKLS
9
- >gi|16128092|ref|NP_414641.1| 7,8-dihydro-8-oxoguanine-triphosphatase, prefers dGTP [Escherichia coli K12]
10
- MKKLQIAVGIIRNENNEIFITRRAADAHMANKLEFPGGKIEMGETPEQAVVRELQEEVGITPQHFSLFEKLEYEFPDRHITLWFWLVERWEGEPWGKEGQPGEWMSLVGLNADDFPPANEPVIAKLKRL
11
- >gi|16128121|ref|NP_414670.1| putative transport protein (ABC superfamily, membrane) [Escherichia coli K12]
12
- MMHLYWVALKSIWAKEIHRFMRIWVQTLVPPVITMTLYFIIFGNLIGSRIGDMHGFSYMQFIVPGLIMMSVITNAYANVASSFFGAKFQRNIEELLVAPVPTHVIIAGYVGGGVARGLFVGILVTAISLFFVPFQVHSWVFVALTLVLTAVLFSLAGLLNGVFAKTFDDISLVPTFVLTPLTYLGGVFYSLTLLPPFWQGLSHLNPIVYMISGFRYGFLGINDVPLVTTFGVLVVFIVAFYLICWSLIQRGRGLRS
13
- >gi|90111097|ref|NP_414731.2| modulator of Rho-dependent transcription termination [Escherichia coli K12]
14
- MNDTYQPINCDDYDNLELACQHHLMLTLELKDGEKLQAKASDLVSRKNVEYLVVEAAGETRELRLDKITSFSHPEIGTVVVSES
15
- >gi|16128191|ref|NP_414740.1| D- and L-methionine transport protein (ABC superfamily, membrane) [Escherichia coli K12]
16
- MSEPMMWLLVRGVWETLAMTFVSGFFGFVIGLPVGVLLYVTRPGQIIANAKLYRTVSAIVNIFRSIPFIILLVWMIPFTRVIVGTSIGLQAAIVPLTVGAAPFIARMVENALLEIPTGLIEASRAMGATPMQIVRKVLLPEALPGLVNAATITLITLVGYSAMGGAVGAGGLGQIGYQYGYIGYNATVMNTVLVLLVILVYLIQFAGDRIVRAVTRK
17
- >gi|16128232|ref|NP_414781.1| CP4-6 prophage; putative DNA repair protein [Escherichia coli K12]
18
- MKQLSFLPGEMTPQDRRLIQRALRALDRHLHEPGVAFTSTHAVREWLRLHMAALEREEFRVLYLDNQNQLIAHETLFTGTINRTEVHPREVVKRALHFNAAAVILAHNHPSGETTPSQADKTLTQRLVQVLQLVDIRVPDHLIVGGRQIYSFAEHGLL
19
- >gi|16128248|ref|NP_414797.1| CP4-6 prophage; putative membrane component of ferric transport system [Escherichia coli K12]
20
- MESLPGQIDKSLDEASLSLRAGSLRTITHILLPLLRPAILSALIYSFVRAITTVSAIVFLVTPDTRVATAYILNRVEDGEYGVAIAYGSILIVVMLAIIFIFDWLIGESRTSRSKAKNQA
21
- >gi|90111117|ref|NP_414887.2| putative 3-hydroxyphenylpropionic transport protein (MFS family) [Escherichia coli K12]
22
- MSTRTPSSSSSRLMLTIGLCFLVALMEGLDLQAAGIAAGGIAQAFALDKMQMGWIFSAGILGLLPGALVGGMLADRYGRKRILIGSVALFGLFSLATAIAWDFPSLVFARLMTGVGLGAALPNLIALTSEAAGPRFRGTAVSLMYCGVPIGAALAATLGFAGANLAWQTVFWVGGVVPLILVPLLMRWLPESAVFAGEKQSAPPLRALFAPETATATLLLWLCYFFTLLVVYMLINWLPLLLVEQGFQPSQAAGVMFALQMGAASGTLMLGALMDKLRPVTMSLLIYSGMLASLLALGTVSSFNGMLLAGFVAGLFATGGQSVLYALAPLFYSSQIRATGVGTAVAVGRLGAMSGPLLAGKMLALGTGTVGVMAASAPGILVAGLAVFILMSRRSRIQPCADA
23
- >gi|16128374|ref|NP_414923.1| unknown CDS [Escherichia coli K12]
24
- MPTKPPYPREAYIVTIEKGKPGQTVTWYQLRADHPKPDSLISEHPTAQEAMDAKKRYEDPDKE
25
- >gi|16128403|ref|NP_414952.1| phosphatidylglycerophosphatase [Escherichia coli K12]
26
- MTILPRHKDVAKSRLKMSNPWHLLAVGFGSGLSPIVPGTMGSLAAIPFWYLMTFLPWQLYSLVVMLGICIGVYLCHQTAKDMGVHDHGSIVWDEFIGMWITLMALPTNDWQWVAAGFVIFRILDMWKPWPIRWFDRNVHGGMGIMIDDIVAGVISAGILYFIGHHWPLGILS
27
- >gi|16128443|ref|NP_414992.1| maltose O-acetyltransferase [Escherichia coli K12]
28
- MSTEKEKMIAGELYRSADETLSRDRLRARQLIHRYNHSLAEEHTLRQQILADLFGQVTEAYIEPTFRCDYGYNIFLGNNFFANFDCVMLDVCPIRIGDNCMLAPGVHIYTATHPIDPVARNSGAELGKPVTIGNNVWIGGRAVINPGVTIGDNVVVASGAVVTKDVPDNVVVGGNPARIIKKL
29
- >gi|16128499|ref|NP_415048.1| hypothetical protein b0515 [Escherichia coli K12]
30
- MGYLNNVTGYREDLLANRAIVKHGNFALLTPDGLVKNIIPGFENCDATILSTPKLGASFVDYLVTLHQNGGNQQGFGGEGIETFLYVISGNITAKAEGKTFALSEGGYLYCPPGSLMTFVNAQAEDSQIFLYKRRYVPVEGYAPWLVSGNASELERIHYEGMDDVILLDFLPKELGFDMNMHILSFAPGASHGYIETHVQEHGAYILSGQGVYNLDNNWIPVKKGDYIFMGAYSLQAGYGVGRGEAFSYIYSKDCNRDVEI
31
- >gi|16128537|ref|NP_415086.1| DLP12 prophage; putative lysis protein S, homolog of Rz of phage PA-2 [Escherichia coli K12]
32
- MKSMDKLTTGVAYGTSAGSAGYWFLQLLDKVTPSQWAAIGVLGSLVFGLLTYLTNLYFKIKEDKRKAARGE
33
- >gi|49176035|ref|YP_025295.1| small toxic membrane polypeptide [Escherichia coli K12]
34
- MLTKYALAAVIVLCLTVLGFTLLVGDSLCEFTVKERNIEFKAVLAYEPKK
35
- >gi|16128614|ref|NP_415164.1| hypothetical protein b0631 [Escherichia coli K12]
36
- MKTKLNELLEFPTPFTYKVMGQALPELVDQVVEVVQRHAPGDYTPTVKPSSKGNYHSVSITINATHIEQVETLYEELGKIDIVRMVL
37
- >gi|16128621|ref|NP_415171.1| homolog of Salmonella cobC, a phosphohistidine protein [Escherichia coli K12]
38
- MRLWLIRHGETQANIDGLYSGHAPTPLTARGIEQAQNLHTLLHGVSFDLVLCSELERAQHTARLVLSDRQLPVQIIPELNEMFFGDWEMRHHRDLMQEDAENYSAWCNDWQHAIPTNGEGFQAFSQRVERFIARLSEFQHYQNILVVSHQGVLSLLIARLIGMPAEAMWHFRVDQGCWSAIDINQKFATLRVLNSRAIGVENA
39
- >gi|16128710|ref|NP_415263.1| hypothetical protein b0735 [Escherichia coli K12]
40
- MSKIIATLYAVMDKRPLRALSFVMALLLAGCMFWDPSRFAAKTSELEIWHGLLLMWAVCAGVIHGVGFRPQKVLWQGIFCPLLADIVLIVGLIFFFF
41
- >gi|90111171|ref|NP_415327.2| hypothetical protein b0806 [Escherichia coli K12]
42
- MKKCLTLLIATVLSGISLTAYAAQPMSNLDSGQLRPAGTVSATGASNLSDLEDKLAEKAREQGAKGYVINSAGGNDQMFGTATIYK
43
- >gi|16128811|ref|NP_415364.1| unknown CDS [Escherichia coli K12]
44
- MIMKNCLLLGALLMGFTGVAMAQSVTVDVPSGYKVVVVPDSVSVPQAVSVATVPQTVYVAPAPAPAYRPHPYVRHLASVGEGMVIEHQIDDHHH
45
- >gi|16128871|ref|NP_415424.1| formate transport protein (formate channel 1) (FNT family) [Escherichia coli K12]
46
- MKADNPFDLLLPAAMAKVAEEAGVYKATKHPLKTFYLAITAGVFISIAFVFYITATTGTGTMPFGMAKLVGGICFSLGLILCVVCGADLFTSTVLIVVAKASGRITWGQLAKNWLNVYFGNLVGALLFVLLMWLSGEYMTANGQWGLNVLQTADHKVHHTFIEAVCLGILANLMVCLAVWMSYSGRSLMDKAFIMVLPVAMFVASGFEHSIANMFMIPMGIVIRDFASPEFWTAVGSAPENFSHLTVMNFITDNLIPVTIGNIIGGGLLVGLTYWVIYLRENDHH
47
- >gi|90111191|ref|NP_415463.2| putative fimbrial-like protein [Escherichia coli K12]
48
- MLKRIIWILFLLGLTWGCELFAHDGTVNISGSFRRNTCVLAQDSKQINVQLGDVSLTRFSHGNYGPEKSFIINLQDCGTDVSTVDVTFSGTPDGVQSEMLSIESGTDAASGLAIAILDDAKILIPLNQASKDYSLHSGKVPLTFYAQLRPVNSDVQSGKVNASATFVLHYD
49
- >gi|90111193|ref|NP_415466.4| hypothetical protein b0946 [Escherichia coli K12]
50
- MRIKPDDNWRWYYDEEHDRMMLDLANGMLFRSRFARKMLTPDAFSPAGFCVDDAALYFSFEEKCRDFNLSKEQKAELVLNALVAIRYLKPQMPKSWHFVSHGEMWVPMPGDAACVWLSDTHEQVNLLVVESGENAALCLLAQPCVVIAGRAMQLGDAIKIMNDRLKPQVNVDSFSLEQAV
51
- >gi|16128957|ref|NP_415511.1| suppresses fabA and ts growth mutation [Escherichia coli K12]
52
- MRRWISQNNIRLPRGAFFISALFFFNAVCIVSDNLLIIESFGEMAYNISYLTRVPGTNTLLACCCLLRPEEVNSEY
53
- >gi|16128974|ref|NP_415528.1| hypothetical protein b1008 [Escherichia coli K12]
54
- MNEAVSPGALSTLFTDARTHNGWRETPVSDETLREIYALMKWGPTSANCSPARIVFTRTAEGKERLRPALSSGNLQKTLTAPVTAIVAWDSEFYERLPLLFPHGDARSWFTSSPQLAEETAFRNSSMQAAYLIVACRALGLDTGPMSGFDRQHVDDAFFTGSTLKSNLLINIGYGDSSKLYARLPRLSFEEACGLL
55
- >gi|16129015|ref|NP_415570.1| unknown CDS [Escherichia coli K12]
56
- MEQSTSSSNTPGIELIFRLSYLQKRRISYPFP
57
- >gi|16129146|ref|NP_415701.1| SOS mutagenesis; error-prone repair; processed to UmuD'; forms complex with UmuC [Escherichia coli K12]
58
- MLFIKPADLREIVTFPLFSDLVQCGFPSPAADYVEQRIDLNQLLIQHPSATYFVKASGDSMIDGGISDGDLLIVDSAITASHGDIVIAAVDGEFTVKKLQLRPTVQLIPMNSAYSPITISSEDTLDVFGVVIHVVKAMR
59
- >gi|16129250|ref|NP_415805.1| hypothetical protein b1289 [Escherichia coli K12]
60
- MIDKIKSNARDLRRNLTLQERKLWRYLRSRRFSDFKFRRQHPVGSYILDFACCSARVVVELDGGQHDLAVAYDSRRTSWLESQGWTVLRFWNNEIDCNEETVLENILQELNRRSPSP
61
- >gi|16129266|ref|NP_415821.1| phage shock protein B [Escherichia coli K12]
62
- MSALFLAIPLTIFVLFVLPIWLWLHYSNRSGRSELSQSEQQRLAQLADEAKRMRERIQALESILDAEHPNWRDR
63
- >gi|16129267|ref|NP_415822.1| phage shock protein: activates phage shock-protein expression [Escherichia coli K12]
64
- MAGINLNKKLWRIPQQGMVRGVCAGIANYFDVPVKLVRILVVLSIFFGLALFTLVAYIILSFALDPMPDNMAFGEQLPSSSELLDEVDRELAASETRLREMERYVTSDTFTLRSRFRQL
65
- >gi|16129318|ref|NP_415875.1| Rac prophage; repressor protein [Escherichia coli K12]
66
- MKKENYSFKQACAVVGGQSAMARLLGVSPPSVNQWIKGVRQLPAERCPAIERATRGEVLCEELRPDIDWSYLRRSACCSQNMSVKQLNDSNKSSFDHT
67
- >gi|90111262|ref|NP_415894.4| conserved hypothetical protein, adenine nucleotide-binding domain [Escherichia coli K12]
68
- MNRTILVPIDISDSELTQRVISHVEEEAKIDDAEVHFLTVIPSLPYYASLGLAYSAELPAMDDLKAEAKSQLEEIIKKFKLPTDRVHVHVEEGSPKDRILELAKKIPAHMIIIASHRPDITTYLLGSNAAAVVRHAECSVLVVR
69
- >gi|16129357|ref|NP_415914.1| phenylacetic acid degradation protein [Escherichia coli K12]
70
- MSHKAWQNAHAMYENDACAKALGIDIISMDEGFAVVTMTVTAQMLNGHQSCHGGQLFSLADTAFAYACNSQGLAAVASACTIDFLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVNQQQKTVALFRGKSHRIGGTITGEA
71
- >gi|90111267|ref|NP_415926.4| putative enzyme [Escherichia coli K12]
72
- MTLYQIKPLFQSLLRPTMFWLYKHHVTANHITLAALALSLLTGLLLMLAAQPILFLLLPIVLFIRMALNALDGMLARECNQQTRLGAILNETGDVISDIALYLPFLFLPESNASLVILMLFCTILTEFCGLLAQTINGVRSYAGPFGKSDRALIFGLWGLAVAIYPQWMQWNNLLWSIASILLLWTAINRCRSVLLMSAEI
73
- >gi|16129388|ref|NP_415946.1| K+-tellurite ethidium and proflavin transport protein (TDT family) [Escherichia coli K12]
74
- MQSDKVLNLPAGYFGIVLGTIGMGFAWRYASQVWQVSHWLGDGLVILAMIIWGLLTSAFIARLIRFPHSVLAEVRHPVLSSFVSLFPATTMLVAIGFVPWFRPLAVCLFSFGVVVQLAYAAWQTAGLWRGSHPEEATTPGLYLPTVANNFISAMACGALGYTDAGLVFLGAGVFSWLSLEPVILQRLRSSGELPTALRTSLGIQLAPALVACSAWLSVNGGEGDTLAKMLFGYGLLQLLFMLRLMPWYLSQPFNASFWSFSFGVSALATTGLHLGSGSDNGFFHTLAVPLFIFTNFIIAILLIRTFALLMQGKLLVRTERAVLMKAEDKE
75
- >gi|16129463|ref|NP_416021.1| putative fimbrial-like protein [Escherichia coli K12]
76
- MKYNNIIFLGLCLGLTTYSALSADSVIKISGRVLDYGCTVSSDSLNFTVDLQKNSARQFPTTGSTSPAVPFQITLSECSKGTTGVRVAFNGIEDAENNTLLKLDEGSNTASGLGIEILDANMRPVKLNDLHAGMQWIPLVPEQNNILPYSARLKSTQKSVNPGLVRASATFTLEFQ
77
- >gi|16129488|ref|NP_416046.1| multiple antibiotic resistance protein [Escherichia coli K12]
78
- MLDLFKAIGLGLVVLLPLANPLTTVALFLGLAGNMNSAERNRQSLMASVYVFAIMMVAYYAGQLVMDTFGISIPGLRIAGGLIVAFIGFRMLFPQQKAIDSPEAKSKSEELEDEPSANIAFVPLAMPSTAGPGTIAMIISSASTVRQSSTFADWVLMVAPPLIFFLVAVILWGSLRSSGAIMRLVGKGGIEAISRLMGFLLVCMGVQFIINGILEIIKTYH
79
- >gi|90111295|ref|NP_416074.4| Qin prophage [Escherichia coli K12]
80
- MKSMDKLTTGVAYGTSAGNAGFWALQLLDKVTPSQWAAIGVLGSLVFGLLTYLTNLYFKIKEDRRKAARGE
81
- >gi|16129540|ref|NP_416099.1| hypothetical protein b1582 [Escherichia coli K12]
82
- MIKTTLLFFATALCEIIGCFLPWLWLKRNASIWLLLPAGISLALFVWLLTLHPAASGRVYAAYGGVYVCTALMWLRVVDGVKLTLYDWTGALIALCGMLIIVAGWGRT
83
- >gi|90111300|ref|NP_416103.2| hypothetical protein b1586 [Escherichia coli K12]
84
- MKLSTCCAALLLALASPAVLAAPGSCERIQSDISQRIINNGVPESSFTLSIVPNDQVDQPDSQVVGHCANDTHKILYTRTTSGNVSAPAQSSQDGAPAEPQ
85
- >gi|90111309|ref|NP_416156.4| hypothetical protein b1639 [Escherichia coli K12]
86
- MTMKKLLIIILPVLLSGCSAFNQLVERMQTDTLEYQCDEKPLTVKLNNPRQEVSFVYDNQLLHLKQGISASGARYTDGIYVFWSKGDEATVYKRDRIVLNNCQLQNPQR
87
- >gi|90111313|ref|NP_416166.2| hypothetical transcriptional regulator [Escherichia coli K12]
88
- MGLSELLKTAEVPKGSFYHYFRSKEAFGVAMLERHYAAYHQRLTELLQSGEGNYRDRILAYYQQTLNQFCQHGTISGCLTVKLSAEVCDLSEDMRSAMDKGARGVIALLSQALENGRENHCLTFCGEPLQQAQVLYALWLGANLQAKISRSFEPLENALAHVKNIIATPAV
89
- >gi|16129623|ref|NP_416182.1| protein ofunknown function [Escherichia coli K12]
90
- MATLLQLHFAFNGPFGDAMAEQLKPLAESINQEPGFLWKVWTESEKNHEAGGIYLFTDEKSALAYLEKHTARLKNLGVEEVVAKVFDVNEPLSQINQAKLA
91
- >gi|16129732|ref|NP_416292.1| methionine sulfoxide reductase B [Escherichia coli K12]
92
- MANKPSAEELKKNLSEMQFYVTQNHGTEPPFTGRLLHNKRDGVYHCLICDAPLFHSQTKYDSGCGWPSFYEPVSEESIRYIKDLSHGMQRIEIRCGNCDAHLGHVFPDGPQPTGERYCVNSASLRFTDGENGEEING
93
- >gi|90111344|ref|NP_416352.4| protein phosphatase 1 [Escherichia coli K12]
94
- MKQPAPVYQRIAGHQWRHIWLSGDIHGCLEQLRRKLWHCRFDPWRDLLISVGDVIDRGPQSLRCLQLLEQHWVCAVRGNHEQMAMDALASQQMSLWLMNGGDWFIALADNQQKQAKTALEKCQHLPFILEVHSRTGKHVIAHADYPDDVYEWQKDVDLHQVLWSRSRLGERQKGQGITGADHFWFGHTPLRHRVDIGNLHYIDTGAVFGGELTLVQLQ
95
- >gi|90111352|ref|NP_416389.4| hypothetical protein b1875 [Escherichia coli K12]
96
- MANWQSIDELQDIASDLPRFIHALDELSRRLGLNITPLTADHISLRCHQNATAERWRRGFEQCGELLSENMINGRPICLFKLHEPVQVAHWQFSIVELPWPGEKRYPHEGWEHIEIVLPGDPETLNARALALLSDEGLSLPGISVKTSSPKGEHERLPNPTLAVTDGKTTIKFHPWSIEEIVASEQSA
97
- >gi|16129855|ref|NP_416418.1| cytoplasmic ferritin (an iron storage protein) [Escherichia coli K12]
98
- MLKPEMIEKLNEQMNLELYSSLLYQQMSAWCSYHTFEGAAAFLRRHAQEEMTHMQRLFDYLTDTGNLPRINTVESPFAEYSSLDELFQETYKHEQLITQKINELAHAAMTNQDYPTFNFLQWYVSEQHEEEKLFKSIIDKLSLAGKSGEGLYFIDKELSTLDTQN
99
- >gi|16129862|ref|NP_416425.1| unknown CDS [Escherichia coli K12]
100
- MSTPDFSTAENNQELANEVSCLKAMLTLMLQAMGQADAGRVMLKMEKQLALIEDETQAAVFSKTVKQIKQAYRQ
101
- >gi|16129891|ref|NP_416454.1| flagellar biosynthesis protein [Escherichia coli K12]
102
- MTDYAISKKSKRSLWIPILVFITLAACASAGYSYWHSHQVAADDKAQQRVVPSPVFYALDTFTVNLGDADRVLYIGITLRLKDEATRSRLSEYLPEVRSRLLLLFSRQDAAVLATEEGKKNLIAEIKTTLSTPLVAGQPKQDVTDVLYTAFILR
103
- >gi|90111376|ref|NP_416555.2| GDP-mannose mannosyl hydrolase [Escherichia coli K12]
104
- MFLRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHYVVLGFRFRVSEEELLLPDEQHDDYRWLTSDALLASDNVHANSRAYFLAEKRTGVPGL
105
- >gi|16130023|ref|NP_416587.1| putative phage protein (D protein) [Escherichia coli K12]
106
- MSGFKRVIDEQDWTITKVTHFLNNSGFTTSLELEVRLSDVGYETEDNE
107
- >gi|16130042|ref|NP_416607.1| hydroxyethylthiazole kinase [Escherichia coli K12]
108
- MQVDLLGSAQSAHALHLFHQHSPLVHCMTNDVVQTFTANTLLALGASPAMVIETEEASQFAAIASALLINVGTLTQPRAQAMRAAVEQAKSSQTPWTLDPVAVGALDYRRHFCHELLSFKPAAIRGNASEIMALAGIANGGRGVDTTDAAANAIPAAQTLARETGAIVVVTGEMDYVTDGHRIIGIHGGDPLMTKVVGTGCALSAVVAACCALPGDTLENVASACHWMKQAGERAVARSEGPGSFVPHFLDALWQLTQEVQA
109
- >gi|16130217|ref|NP_416785.1| NADH dehydrogenase subunit H [Escherichia coli K12]
110
- MSWISPELIEILLTILKAVVILLVVVTCGAFMSFGERRLLGLFQNRYGPNRVGWGGSLQLVADMIKMFFKEDWIPKFSDRVIFTLAPMIAFTSLLLAFAIVPVSPGWVVADLNIGILFFLMMAGLAVYAVLFAGWSSNNKYSLLGAMRASAQTLSYEVFLGLSLMGVVAQAGSFNMTDIVNSQAHVWNVIPQFFGFITFAIAGVAVCHRHPFDQPEAEQELADGYHIEYSGMKFGLFFVGEYIGIVTISALMVTLFFGGWQGPLLPPFIWFALKTAFFMMMFILIRASLPRPRYDQVMSFGWKICLPLTLINLLVTAAVILWQAQ
111
- >gi|16130268|ref|NP_416836.1| putative fimbrial-like protein [Escherichia coli K12]
112
- MNKSMIQSGGYVLLAGLILAMSSTLFAADNNLHFSGNLLSKSCALVVDGQYLAEVRFPTVSRQDLNVAGQSARVPVVFKLKDCKGPAGYNVKVTLTGVEDSEQPGFLALDTSSTAQGVGIGMEKTDGMQVAINNTNGATFALTNGNNDINFRAWLQAKSGRDVTIGEFTASLTATFEYI
113
- >gi|16130299|ref|NP_416868.1| multidrug resistance protein Y [Escherichia coli K12]
114
- MAITKSTPAPLTGGTLWCVTIALSLATFMQMLDSTISNVAIPTISGFLGASTDEGTWVITSFGVANAIAIPVTGRLAQRIGELRLFLLSVTFFSLSSLMCSLSTNLDVLIFFRVVQGLMAGPLIPLSQSLLLRNYPPEKRTFALALWSMTVIIAPICGPILGGYICDNFSWGWIFLINVPMGIIVLTLCLTLLKGRETETSPVKMNLPGLTLLVLGVGGLQIMLDKGRDLDWFNSSTIIILTVVSVISLISLVIWESTSENPILDLSLFKSRNFTIGIVSITCAYLFYSGAIVLMPQLLQETMGYNAIWAGLAYAPIGIMPLLISPLIGRYGNKIDMRLLVTFSFLMYAVCYYWRSVTFMPTIDFTGIILPQFFQGFAVACFFLPLTTISFSGLPDNKFANASSMSNFFRTLSGSVGTSLTMTLWGRRESLHHSQLTATIDQFNPVFNSSSQIMDKYYGSLSGVLNEINNEITQQSLSISANEIFRMAAIAFILLTVLVWFAKPPFTAKGVG
115
- >gi|90111436|ref|NP_416933.4| putative carboxysome structural protein, ethanolamine utilization [Escherichia coli K12]
116
- MINALGLLEVDGMVAAIDAADAMLKAANVRLLSHEVLDPGRLTLVVEGDLAACRAALDAGCAAAMRTGRVISRKEIGRPDDDTQWLVTGFNRQPKQPVREPDAPVIVAESADELLALLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSAGTLRKRSSRYRLKPH
117
- >gi|90111440|ref|NP_416957.4| putative carboxysome structural protein, ethanol utilization [Escherichia coli K12]
118
- MDKERIIQEFVPGKQVTLAHLIAHPGEELAKKIGVPDAGAIGIMTLTPGETAMIAGDLALKAADVHIGFLDRFSGALVIYGSVGAVEEALSQTVSGLGRLLNYTLCEMTKS
119
- >gi|90111445|ref|NP_416978.4| hydrogenase 4 membrane subunit [Escherichia coli K12]
120
- MRQTLCDGYLVIFALAQAVILLMLTPLFTGISRQIRARMHSRRGPGIWQDYRDIHKLFKRQEVAPTSSGLMFRLMPWVLISSMLVLAMALPLFITVSPFAGGGDLITLIYLLALFRFFFALSGLDTGSPFAGVGASRELTLGILVEPMLILSLLVLALIAGSTHIEMISNTLAMGWNSPLTTVLALLACGFACFIEMGKIPFDVAEAEQELQEGPLTEYSGAGLALAKWGLGLKQVVMASLFVALFLPFGRAQELSLACLLTSLVVTLLKVLLIFVLASIAENTLARGRFLLIHHVTWLGFSLAALAWVFWLTGL
121
- >gi|16130429|ref|NP_416999.1| unknown CDS [Escherichia coli K12]
122
- MSQATSMRKRHRFNSRMTRIVLLISFIFFFGRFIYSSVGAWQHHQSKKEAQQSTLSVESPVQR
123
- >gi|16130443|ref|NP_417013.1| nucleoside diphosphate kinase [Escherichia coli K12]
124
- MAIERTFSIIKPNAVAKNVIGNIFARFEAAGFKIVGTKMLHLTVEQARGFYAEHDGKPFFDGLVEFMTSGPIVVSVLEGENAVQRHRDLLGATNPANALAGTLRADYADSLTENGTHGSDSVESAAREIAYFFGEGEVCPRTR
125
- >gi|16130511|ref|NP_417081.1| hypothetical protein b2586 [Escherichia coli K12]
126
- MANDSWSGQDKAQHFIASAMLSAAGNEYSQHQGMSRDRSAMFGLMFSVSLGASKELWDSRPEGSGWSWKDLAWDVAGASTGYTVWQLTRH
127
- >gi|49176253|ref|YP_026176.1| CP4-57 prophage [Escherichia coli K12]
128
- MAAGFIADTASLPLIVSNLVNIVSADFFGLSFAQYASVMISVDAAAIAATLIMLYLFFRRVIPATY
129
- >gi|16130584|ref|NP_417156.1| hypothetical protein b2670 [Escherichia coli K12]
130
- MFSPQSRLRHAVADTFAMVVYCSVVNMCIEVFLSGMSFEQSFYSRLVAIPVNILIAWPYGMYRDLFMRAARKVSPSGWIKNLADILAYVTFQSPVYVAILLVVGADWHQIMAAVSSNIVVSMLMGAVYGYFLDYCRRLFKVSRYQQVKA
131
- >gi|16130625|ref|NP_417198.1| processing of HycE (part of the FHL complex) [Escherichia coli K12]
132
- MSEKVVFSQLSRKFIDENDATPAEAQQVVYYSLAIGHHLGVIDCLEAALTCPWDEYLAWIATLEAGSEARRKMEGVPKYGEIVIDINHVPMLANAFDKARAAQTSQQQEWSTMLLSMLHDIHQENAIYLMVRRLRD
133
- >gi|16130646|ref|NP_417219.1| putative epimerase/isomerase [Escherichia coli K12]
134
- MPRFAANLSMMFTEVPFIERFAAARKAGFDAVEFLFPYNYSTLQIQKQLEQNHLTLALFNTAPGDINAGEWGLSALPGREHEAHADIDLALEYALALNCEQVHVMAGVVPAGEDAERYRAVFIDNIRYAADRFAPHGKRILVEALSPGVKPHYLFSSQYQALAIVEEVARDNVFIQLDTFHAQKVDGNLTHLIRDYAGKYAHVQIAGLPDRHEPDDGEINYPWLFRLFDEVGYQGWIGCEYKPRGLTEEGLGWFDAWR
135
- >gi|16130699|ref|NP_417272.1| hypothetical protein b2792 [Escherichia coli K12]
136
- MTTHDRVRLQLQALEALLREHQHWRNDEPQPHQFNSTQPFFMDTMEPLEWLQWVLIPRMHDLLDNKQPLPGAFAVAPYYEMALATDHPQRALILAELEKLDALFADDAS
137
- >gi|16130761|ref|NP_417334.1| unknown CDS [Escherichia coli K12]
138
- MINDLKSILLKPSEEVDVFIKIFESWVTKLPSISGPVNLHIPTSFKDKSLEVESYFVDKSIWNVHITFHDDKRFVFFTDQFIAEFSPQEFVDNCEQYLINNHCFSPDKVNEICEQARHYLVEKMFETHSLDMNNSVLASPEDL
139
- >gi|16130806|ref|NP_417380.1| glycine cleavage system protein H [Escherichia coli K12]
140
- MSNVPAELKYSKEHEWLRKEADGTYTVGITEHAQELLGDMVFVDLPEVGATVSAGDDCAVAESVKAASDIYAPVSGEIVAVNDALSDSPELVNSEPYAGGWIFKIKASDESELESLLDATAYEALLEDE
141
- >gi|16130817|ref|NP_417391.1| chromosome replication initiation inhibitor protein [Escherichia coli K12]
142
- MKRPDYRTLQALDAVIRERGFERAAQKLCITQSAVSQRIKQLENMFGQPLLVRTVPPRPTEQGQKLLALLRQVELLEEEWLGDEQTGSTPLLLSLAVNADSLATWLLPALAPVLADSPIRLNLQVEDETRTQERLRRGEVVGAVSIQHQALPSCLVDKLGALDYLFVSSKPFAEKYFPNGVTRSALLKAPVVAFDHLDDMHQAFLQQNFDLPPGSVPCHIVNSSEAFVQLARQGTTCCMIPHLQIEKELASGELIDLTPGLFQRRMLYWHRFAPESRMMRKVTDALLDYGHKVLRQD
143
- >gi|16130835|ref|NP_417409.1| PTS family enzyme IIA, mannitol-specific, cryptic [Escherichia coli K12]
144
- MRLSDYFPESSISVIHSAKDWQEAIDFSMVSLLDKNYISENYIQAIKDSTINNGPYYILAPGVAMPHARPECGALKTGMSLTLLEQGVYFPGNDEPIKLLIGLSAADADSHIGAIQALSELLCEEEILEQLLTASSEKQLADIISRG
145
- >gi|16130863|ref|NP_417437.1| hypothetical protein b2962 [Escherichia coli K12]
146
- MSRTIFCTFLQREAEGQDFQLYPGELGKRIYNEISKEAWAQWQHKQTMLINEKKLNMMNAEHRKLLEQEMVNFLFEGKEVHIEGYTPEDKK
147
- >gi|16130867|ref|NP_417441.1| putative transport protein [Escherichia coli K12]
148
- MVIGPFINASAVLLGGVLGALLSQRLPERIRVSMTSIFGLASLGIGILLVVKCANLPAMVLATLLGALIGEICLLEKGVNTAVAKAQNLFRHSRKKPAHESFIQNYVAIIVLFCASGTGIFGAMNEGMTGDPSILIAKSFLDFFTAMIFACSLGIAVSVISIPLLIIQLTLAWAAALILPLTTPSMMADFSAVGGLLLLATGLRICGIKMFPVVNMLPALLLAMPLSAAWTAWFA
149
- >gi|16130900|ref|NP_417475.1| hypothetical protein b3002 [Escherichia coli K12]
150
- MERFLENAMYASRWLLAPVYFGLSLALVALALKFFQEIIHVLPNIFSMAESDLILVLLSLVDMTLVGGLLVMVMFSGYENFVSQLDISENKEKLNWLGKMDATSLKNKVAASIVAISSIHLLRVFMDAKNVPDNKLMWYVIIHLTFVLSAFVMGYLDRLTRHNH
151
- >gi|16130902|ref|NP_417477.1| unknown CDS [Escherichia coli K12]
152
- MNALSGLQTHEDSTCCNRFCRPDERSASGNSTLLRFGGFFADQTYLQVTRLMQRIHYLHQRLVIDGFVRSEEDGGVFLAFG
153
- >gi|16130905|ref|NP_417480.1| unknown CDS [Escherichia coli K12]
154
- MLVTFLLRKRKEKKAKVRQYANSNENDYQFDVVLILLCADFVTCVLEIHSG
155
- >gi|16130984|ref|NP_417560.1| Na+:serine/threonine symporter (DAACS family) [Escherichia coli K12]
156
- MTTQRSPGLFRRLAHGSLVKQILVGLVLGILLAWISKPAAEAVGLLGTLFVGALKAVAPILVLMLVMASIANHQHGQKTNIRPILFLYLLGTFSAALAAVVFSFAFPSTLHLSSSAGDISPPSGIVEVMRGLVMSMVSNPIDALLKGNYIGILVWAIGLGFALRHGNETTKNLVNDMSNAVTFMVKLVIRFAPIGIFGLVSSTLATTGFSTLWGYAQLLVVLVGCMLLVALVVNPLLVWWKIRRNPFPLVLLCLRESGVYAFFTRSSAANIPVNMALCEKLNLDRDTYSVSIPLGATINMAGAAITITVLTLAAVNTLGIPVDLPTALLLSVVASLCACGASGVAGGSLLLIPLACNMFGISNDIAMQVVAVGFIIGVLQDSCETALNSSTDVLFTAAACQAEDDRLANSALRN
157
- >gi|16131011|ref|NP_417588.1| transcriptional activator for amino acids degradation (LysR family) [Escherichia coli K12]
158
- MSTILLPKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELVVRKNTGVTLTPAGQLLLSRSESITREMKNMVNEISGMSSEAVVEVSFGFPSLIGFTFMSGMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSAEMKLQDLHVEPLFESEFVLVASKSRTCTGTTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNADFLTVIPCDMTSPFGSNQFITIPVEETLPVAQYAAVWSKNYRIKKAASVLVELAKEYSSYNGCRRRQLIEVG
159
- >gi|16131049|ref|NP_417626.1| hypothetical protein b3157 [Escherichia coli K12]
160
- MLDKLRSRIVHLGPSLLSVPVKLTPFALKRQVLEQVLSWQFRQALDDGELEFLEGRWLSIHVRDIDLQWFTSVVNGKLVVSQNAQADVSFSADASDLLMIAARKQDPDTLFFQRRLVIEGDTELGLYVKNLMDAIELEQMPKALRMMLLQLADFVEAGMKTAPETKQTSVGEPC
161
- >gi|16131065|ref|NP_417642.1| protein-export membrane protein [Escherichia coli K12]
162
- MYEALLVVFLIVAIGLVGLIMLQQGKGADMGASFGAGASATLFGSSGSGNFMTRMTALLATLFFIISLVLGNINSNKTNKGSEWENLSAPAKTEQTQPAAPAKPTSDIPN
163
- >gi|90111557|ref|NP_417676.2| sigma cross-reacting protein 27A (SCRP-27A) [Escherichia coli K12]
164
- MKKIGVILSGCGVYDGSEIHEAVLTLLAISRSGAQAVCFAPDKQQVDVINHLTGEAMTETRNVLIEAARITRGEIRPLAQADAAELDALIVPGGFGAAKNLSNFASLGSECTVDRELKALAQAMHQAGKPLGFMCIAPAMLPKIFDFPLRLTIGTDIDTAEVLEEMGAEHVPCPVDDIVVDEDNKIVTTPAYMLAQNIAEAASGIDKLVSRVLVLAE
165
- >gi|16131149|ref|NP_417727.1| DNA-binding protein Fis [Escherichia coli K12]
166
- MFEQRVNSDVLTVSTVNSQDQVTQKPLRDSVKQALKNYFAQLNGQDVNDLYELVLAEVEQPLLDMVMQYTRGNQTRAALMMGINRGTLRKKLKKYGMN
167
- >gi|16131155|ref|NP_417733.1| unknown CDS [Escherichia coli K12]
168
- MKRLIPVALLTALLAGCAHDSPCVPVYDDQGRLVHTNTCMKGTTQDNWETAGAIAGGAAAVAGLTMGIIALSK
169
- >gi|16131230|ref|NP_417810.1| glutathione-regulated potassium-efflux system ancillary protein [Escherichia coli K12]
170
- MMSQPAKVLLLYAHPESQDSVANRVLLKPATQLSNVTVHDLYAHYPDFFIDIPREQALLREHEVIVFQHPLYTYSCPALLKEWLDRVLSRGFASGPGGNQLAGKYWRSVITTGEPESAYRYDALNRYPMSDVLRPFELAAGMCRMHWLSPIIIYWARRQSAQELASHARAYGDWLANPLSPGGR
171
- >gi|90111586|ref|NP_417860.2| Hsp33-like chaperonin [Escherichia coli K12]
172
- MPQHDQLHRYLFENFAVRGELVTVSETLQQILENHDYPQPVKNVLAELLVATSLLTATLKFDGDITVQLQGDGPMNLAVINGNNNQQMRGVARVQGEIPENADLKTLVGNGYVVITITPSEGERYQGVVGLEGDTLAACLEDYFMRSEQLPTRLFIRTGDVDGKPAAGGMLLQVMPAQNAQQDDFDHLATLTETIKTEELLTLPANEVLWRLYHEEEVTVYDPQDVEFKCTCSRERCADALKTLPDEEVDSILAEDGEIDMHCDYCGNHYLFNAMDIAEIRNNASPADPQVH
173
- >gi|16131340|ref|NP_417925.1| putative enzyme [Escherichia coli K12]
174
- MLWSFIAVCLSAWLSVDASYRGPTWQRWVFKPLTLLLLLLLAWQAPMFDAISYLVLAGLCASLLGDALTLLPRQRLMYAIGAFFLSHLLYTIYFASQMTLSFFWPLPLVLLVLGALLLAIIWTRLEEYRWPICTFIGMTLVMVWLAGELWFFRPTAPALSAFVGASLLFISNFVWLGSHYRRRFRADNAIAAACYFAGHFLIVRSLYL
175
- >gi|16131343|ref|NP_417928.1| putative integral membrane protein [Escherichia coli K12]
176
- MNVFSQTQRYKALFWLSLFHLLVITSSNYLVQLPVSILGFHTTWGAFSFPFIFLATDLTVRIFGAPLARRIIFAVMIPALLISYVISSLFYMGSWQGFGALAHFNLFVARIATASFMAYALGQILDVHVFNRLRQSRRWWLAPTASTLFGNVSDTLAFFFIAFWRSPDAFMAEHWMEIALVDYCFKVLISIVFFLPMYGVLLNMLLKRLADKSEINALQAS
177
- >gi|90111596|ref|NP_417930.2| hypothetical protein b3473 [Escherichia coli K12]
178
- MPEPVAEPALNGLRLNLRIVSIVMFNFASYLTIGLPLAVLPGYVHDVMGFSAFWAGLVISLQYFATLLSRPHAGRYADSLGPKKIVVFGLCGCFLSGLGYLTAGLTASLPVISLLLLCLGRVILGIGQSFAGTGSTLWGVGVVGSLHIGRVISWNGIVTYGAMAMGAPLGVVFYHWGGLQALALIIMGVALVAILLAIPRPTVKASKGKPLPFRAVLGRVWLYGMALALASAGFGVIATFITLFYDAKGWDGAAFALTLFSCAFVGTRLLFPNGINRIGGLNVAMICFSVEIIGLLLVGVATMPWMAKIGVLLAGAGFSLVFPALGVVAVKAVPQQNQGAALATYTVFMDLSLGVTGPLAGLVMSWAGVPVIYLAAAGLVAIALLLTWRLKKRPPEHVPEAASSS
179
- >gi|16131350|ref|NP_417935.1| nickel transport proein (ABC superfamily, membrane) [Escherichia coli K12]
180
- MNFFLSSRWSVRLALIIIALLALIALTSQWWLPYDPQAIDLPSRLLSPDAQHWLGTDHLGRDIFSRLMAATRVSLGSVMACLLLVLTLGLVIGGSAGLIGGRVDQATMRVADMFMTFPTSILSFFMVGVLGTGLTNVIIAIALSHWAWYARMVRSLVISLRQREFVLASRLSGAGHVRVFVDHLAGAVIPSLLVLATLDIGHMMLHVAGMSFLGLGVTAPTAEWGVMINDARQYIWTQPLQMFWPGLALFISVMAFNLVGDALRDHLDPHLVTEHAH
181
- >gi|90111601|ref|NP_417948.2| putative transport protein [Escherichia coli K12]
182
- MNIYIGWLFKLIPLIMGLICIALGGFVLESSGQSEYFVAGHVLISLAAICLALFTTAFIIISQLTRGVNTFYNTLFPIIGYAGSIITMIWGWALLAGNDVMADEFVAGHVIFGVGMIAACVSTVAASSGHFLLIPKNAAGSKSDGTPVQAYSSLIGNCLIAVPVLLTLLGFIWSITLLRSADITPHYVAGHVLLGLTAICACLIGLVATIVHQTRNTFSTKEHWLWCYWVIFLGSITVLQGIYVLVSSDASARLAPGIILICLGMICYSIFSKVWLLALVWRRTCSLANRIPMIPVFTCLFCLFLASFLAEMAQTDMGYFIPSRVLVGLGAVCFTLFSIVSILEAGSAKK
183
- >gi|16131427|ref|NP_418012.1| cold shock protein 7.4, transcriptional activator of hns [Escherichia coli K12]
184
- MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL
185
- >gi|16131530|ref|NP_418116.1| putative membrane protein, transport [Escherichia coli K12]
186
- MGSTRKGMLNVLIAAVLWGSSGVCAQYIMEQSQMSSQFLTMTRLIFAGLILLTLSFVHGDKIFSIINNHKDAISLLIFSVVGALTVQLTFLLTIEKSNAATATVLQFLSPTIIVAWFSLVRKSRPGILVFCAILTSLVGTFLLVTHGNPTSLSISPAALFWGIASAFAAAFYTTYPSTLIARYGTLPVVGWSMLIGGLILLPFYARQGTNFVVNGSLILAFFYLVVIGTSLTFSLYLKGAQLIGGPKASILSCAEPLSSALLSLLLLGITFTLPDWLGTLLILSSVILISMDSRRRARKINRPARHK
187
- >gi|16131578|ref|NP_418166.1| drug/chloramphenicol transport protein (MFS family) [Escherichia coli K12]
188
- MSRFLICSFALVLLYPAGIDMYLVGLPRIAADLNASEAQLHIAFSVYLAGMAAAMLFAGKVADRSGRKPVAIPGAALFIIASVFCSLAETSTLFLAGRFLQGLGAGCCYVVAFAILRDTLDDRRRAKVLSLLNGITCIIPVLAPVLGHLIMLKFPWQSLFWAMAMMGIAVLMLSLFILKETRPAAPAASDKPRENSESLLNRFFLSRVVITTLSVSVILTFVNTSPVLLMEIMGFERGEYATIMALTAGVSMTVSFSTPFALGIFKPRTLMITSQVLFLAAGITLAVSPSHAVSLFGITLICAGFSVGFGVAMSQALGPFSLRAGVASSTLGIAQVCGSSLWIWLAAVVGIGAWNMLIGILIACSIVSLLLIMFVAPGRPVAAHEEIHHHA
189
- >gi|16131585|ref|NP_418173.1| hypothetical protein b3717 [Escherichia coli K12]
190
- MTQNIRPLPQFKYHPKPLETGAFEQDKTVECDCCEQQTSVYYSGPFYCVDEVEHLCPWCIADGSAAEKFAGSFQDDASIEGVEFEYDEEDEFAGIKNTYPDEMLKELVERTPGYHGWQQEFWLAHCGDFCVFIGYVGWNDIKDRLDEFANLEEDCENFGIRNSDLAKCLQKGGHCQGYLFRCLHCGKLRLWGDFS
191
- >gi|16131606|ref|NP_418194.1| ATP synthase subunit A [Escherichia coli K12]
192
- MASENMTPQDYIGHHLNNLQLDLRTFSLVDPQNPPATFWTINIDSMFFSVVLGLLFLVLFRSVAKKATSGVPGKFQTAIELVIGFVNGSVKDMYHGKSKLIAPLALTIFVWVFLMNLMDLLPIDLLPYIAEHVLGLPALRVVPSADVNVTLSMALGVFILILFYSIKMKGIGGFTKELTLQPFNHWAFIPVNLILEGVSLLSKPVSLGLRLFGNMYAGELIFILIAGLLPWWSQWILNVPWAIFHILIITLQAFIFMVLTIVYLSMASEEH
193
- >gi|67005950|ref|NP_418228.2| thioredoxin [Escherichia coli K12]
194
- MSDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA
195
- >gi|16131722|ref|NP_418318.1| putative dehydrogenase [Escherichia coli K12]
196
- MAAIAFIGLGQMGSPMASNLLQQGHQLRVFDVNAEAVRHLVDKGATPAANPAQAAKDAEFIITMLPNGDLVRNVLFGENGVCEGLSTDALVIDMSTIHPLQTDKLIADMQAKGFSMMDVPVGRTSANAITGTLLLLAGGTAEQVERATPILMAMGSELINAGGPGMGIRVKLINNYMSIALNALSAEAAVLCEALNLPFDVAVKVMSGTAAGKGHFTTSWPNKVLSGDLSPAFMIDLAHKDLGIALDVANQLHVPMPLGAASREVYSQARAAGRGRQDWSAILEQVRVSAGMTAKVKM
197
- >gi|16131732|ref|NP_418328.1| formate dehydrogenase, cytochrome B556 (FDO) subunit [Escherichia coli K12]
198
- MKRRDTIVRYTAPERINHWITAFCFILAAVSGLGFLFPSFNWLMQIMGTPQLARILHPFVGVVMFASFIIMFFRYWHHNLINRDDIFWAKNIRKIVVNEEVGDTGRYNFGQKCVFWAAIIFLVLLLVSGVIIWRPYFAPAFSIPVIRFALMLHSFAAVALIVVIMVHIYAALWVKGTITAMVEGWVTSAWAKKHHPRWYREVRKTTEKKAE
199
- >gi|16131829|ref|NP_418427.1| hypothetical protein b3999 [Escherichia coli K12]
200
- MLQNPIHLRLERLESWQHVTFMACLCERMYPNYAMFCQQTGFGDGQIYRRILDLIWETLTVKDAKVNFDSQLEKFEEAIPSADDFDLYGVYPAIDACVALSELVHSRLSGETLEHAVEVSKTSITTVAMLEMTQAGREMSDEELKENPAVEQEWDIQWEIFRLLAECEERDIELIKGLRADLREAGESNIGIIFQQ
201
- >gi|16131888|ref|NP_418486.1| regulation of superoxide response regulon [Escherichia coli K12]
202
- MSHQKIIQDLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSRVFRRQFDRTPSDYRHRL
203
- >gi|16131894|ref|NP_418492.1| hypothetical protein b4068 [Escherichia coli K12]
204
- MNGTIYQRIEDNAHFRELVEKRQRFATILSIIMLAVYIGFILLIAFAPGWLGTPLNPNTSVTRGIPIGVGVIVISFVLTGIYIWRANGEFDRLNNEVLHEVQAS
205
- >gi|16131928|ref|NP_418526.1| putative transcriptional regulator [Escherichia coli K12]
206
- MHLSTHPTSYPTRYQEIAAKLEQELRQHYRCGDYLPAEQQLAARFEVNRHTLRRAIDQLVEKGWVQRRQGVGVLVLMRPFDYPLNAQARFSQNLLDQGSHPTSEKLLSVLRPASGHVADALGITEGENVIHLRTLRRVNGVALCLIDHYFADLTLWPTLQRFDSGSLHDFLREQTGIALRRSQTRISARRAQAKECQRLEIPNMSPLLCVRTLNHRDGESSPAEYSVSLTRADMIEFTMEH
207
- >gi|16132032|ref|NP_418631.1| putative cationic amino acid transport protein [Escherichia coli K12]
208
- MPVMISGVLYALLAGLMWGLIFVGPLIVPEYPAMLQSMGRYLALGLIALPIAWLGRVRLRQLARRDWLTALMLTMMGNLIYYFCLASAIQRTGAPVSTMIIGTLPVVIPVFANLLYSQRDGKLAWGKLAPALICIGIGLACVNIAELNHGLPDFDWARYTSGIVLALVSVVCWAWYALRNARWLRENPDKHPMMWATAQALVTLPVSLIGYLVACYWLNTQTPDFSLPFGPRPLVFISLMVAIAVLCSWVGALCWNVASQLLPTVILGPLIVFETLAGLLYTFLLRQQMPPLMTLSGIALLVIGVVIAVRAKPEKPLTESVSES
209
- >gi|90111709|ref|NP_418651.2| putative sugar transport protein (ABC superfamily, membrane) [Escherichia coli K12]
210
- MPQSLPDTTTPKRRFRWPTGMPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALLAIGMTLVIATGGIDLSVGAVMAIAGATTAAMTVAGFSLPIVLLSALGTGILAGLWNGILVAILKIQPFVATLILMVAGRGVAQLITAGQIVTFNSPDLSWFGSGSLLFLPTPVIIAVLTLILFWLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPEMNQVVKAVVVLCVLIVQSQRFISLIKGVRSRDKT
211
- >gi|16132087|ref|NP_418686.1| L-idonate transport protein (GntP family) [Escherichia coli K12]
212
- MPLIIIAAGVALLLILMIGFKVNGFIALVLVAAVVGFAEGMDAQAVLHSIQNGIGSTLGGLAMILGFGAMLGKLISDTGAAQRIATTLIATFGKKRVQWALVITGLVVGLAMFFEVGFVLLLPLVFTIVASSGLPLLYVGVPMVAALSVTHCFLPPHPGPTAIATIFEANLGTTLLYGFIITIPTVIVAGPLFSKLLTRFEKAPPEGLFNPHLFSEEEMPSFWNSIFAAVIPVILMAIAAVCEITLPKTNTVRLFFEFVGNPAVALFIAIVIAIFTLGRRNGRTIEQIMDIIGDSIGAIAMIVFIIAGGGAFKQVLVDSGVGHYISHLMTGTTLSPLLMCWTVAALLRIALGSATVAAITTAGVVLPIINVTHADPALMVLATGAGSVIASHVNDPGFWLFKGYFNLTVGETLRTWTVMETLISIMGLLGVLAINAVLH
data/test_files/bioworks_small.params DELETED
@@ -1,63 +0,0 @@
1
- [SEQUEST]
2
- first_database_name = C:\Xcalibur\database\ecoli_K12_ncbi_20060321.fasta
3
- second_database_name =
4
- peptide_mass_tolerance = 25.0000
5
- peptide_mass_units = 2 ; 0=amu, 1=mmu, 2=ppm
6
- ion_series = 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0
7
- fragment_ion_tolerance = 1.0000 ; for trap data leave at 1.0, for accurate mass data use values < 1.0
8
- fragment_ion_units = 0 ; 0=amu, 1=mmu
9
- num_output_lines = 10 ; # peptide results to show
10
- num_results = 250 ; # results to store
11
- num_description_lines = 5 ; # full protein descriptions to show for top N peptides
12
- show_fragment_ions = 0 ; 0=no, 1=yes
13
- print_duplicate_references = 40 ; number of duplicate references reported
14
- enzyme_info = Trypsin(KR/P) 1 1 KR P
15
- max_num_differential_per_peptide = 3 ; max # of diff. mod in a peptide
16
- diff_search_options = 15.999400 M 79.979900 STY 0.000000 M 0.000000 X 0.000000 T 0.000000 Y
17
- term_diff_search_options = 0.000000 0.000000
18
- nucleotide_reading_frame = 0 ; 0=protein db, 1-6, 7 = forward three, 8-reverse three, 9=all six
19
- mass_type_parent = 0 ; 0=average masses, 1=monoisotopic masses
20
- mass_type_fragment = 0 ; 0=average masses, 1=monoisotopic masses
21
- normalize_xcorr = 0 ; use normalized xcorr values in the out file
22
- remove_precursor_peak = 0 ; 0=no, 1=yes
23
- ion_cutoff_percentage = 0.0000 ; prelim. score cutoff % as a decimal number i.e. 0.30 for 30%
24
- max_num_internal_cleavage_sites = 2 ; maximum value is 12
25
- protein_mass_filter = 0 0 ; enter protein mass min & max value ( 0 for both = unused)
26
- match_peak_count = 0 ; number of auto-detected peaks to try matching (max 5)
27
- match_peak_allowed_error = 1 ; number of allowed errors in matching auto-detected peaks
28
- match_peak_tolerance = 1.0000 ; mass tolerance for matching auto-detected peaks
29
- partial_sequence =
30
- sequence_header_filter =
31
- digest_mass_range = 600.0 3500.0
32
-
33
- add_Cterm_peptide = 0.0000 ; added to each peptide C-terminus
34
- add_Cterm_protein = 0.0000 ; added to each protein C-terminus
35
- add_Nterm_peptide = 0.0000 ; added to each peptide N-terminus
36
- add_Nterm_protein = 0.0000 ; added to each protein N-terminus
37
- add_G_Glycine = 0.0000 ; added to G
38
- add_A_Alanine = 0.0000 ; added to A
39
- add_S_Serine = 0.0000 ; added to S
40
- add_P_Proline = 0.0000 ; added to P
41
- add_V_Valine = 0.0000 ; added to V
42
- add_T_Threonine = 0.0000 ; added to T
43
- add_C_Cysteine = 0.0000 ; added to C
44
- add_L_Leucine = 0.0000 ; added to L
45
- add_I_Isoleucine = 0.0000 ; added to I
46
- add_X_LorI = 0.0000 ; added to X
47
- add_N_Asparagine = 0.0000 ; added to N
48
- add_O_Ornithine = 0.0000 ; added to O
49
- add_B_avg_NandD = 0.0000 ; added to B
50
- add_D_Aspartic_Acid = 0.0000 ; added to D
51
- add_Q_Glutamine = 0.0000 ; added to Q
52
- add_K_Lysine = 0.0000 ; added to K
53
- add_Z_avg_QandE = 0.0000 ; added to Z
54
- add_E_Glutamic_Acid = 0.0000 ; added to E
55
- add_M_Methionine = 0.0000 ; added to M
56
- add_H_Histidine = 0.0000 ; added to H
57
- add_F_Phenylalanine = 0.0000 ; added to F
58
- add_R_Arginine = 0.0000 ; added to R
59
- add_Y_Tyrosine = 0.0000 ; added to Y
60
- add_W_Tryptophan = 0.0000 ; added to W
61
- add_J_user_amino_acid = 0.0000 ; added to J
62
- add_U_user_amino_acid = 0.0000 ; added to U
63
-
data/test_files/bioworks_small.phobius DELETED
@@ -1,109 +0,0 @@
1
- Phobius prediction
2
-
3
- SEQENCE ID TM SP PREDICTION
4
- gi|49175991|ref|YP_025292.1| 0 Y n8-16c21/22o
5
- gi|16128018|ref|NP_414565.1| 0 0 i
6
- gi|16128024|ref|NP_414571.1| 0 0 i
7
- gi|16128058|ref|NP_414606.1| 0 0 i
8
- gi|16128092|ref|NP_414641.1| 0 0 i
9
- gi|16128121|ref|NP_414670.1| 7 Y n4-9c14/15o24-46i58-84o104-132i139-164o170-191i203-221o227-248i
10
- gi|90111097|ref|NP_414731.2| 0 0 i
11
- gi|16128191|ref|NP_414740.1| 5 0 o20-40i52-76o82-105i142-162o182-203i
12
- gi|16128232|ref|NP_414781.1| 0 0 i
13
- gi|16128248|ref|NP_414797.1| 2 0 i38-61o81-106i
14
- gi|90111117|ref|NP_414887.2| 11 Y n15-26c44/45o54-74i81-101o107-128i140-163o169-189i209-235o255-273i280-300o306-328i340-359o371-391i
15
- gi|16128374|ref|NP_414923.1| 0 0 i
16
- gi|16128403|ref|NP_414952.1| 5 0 i21-51o57-75i87-104o110-126i138-162o
17
- gi|16128443|ref|NP_414992.1| 0 0 i
18
- gi|16128499|ref|NP_415048.1| 0 0 i
19
- gi|16128537|ref|NP_415086.1| 2 0 i7-25o37-58i
20
- gi|49176035|ref|YP_025295.1| 0 Y n6-24c29/30o
21
- gi|16128614|ref|NP_415164.1| 0 0 i
22
- gi|16128621|ref|NP_415171.1| 0 0 i
23
- gi|16128710|ref|NP_415263.1| 3 0 o17-34i46-67o73-96i
24
- gi|90111171|ref|NP_415327.2| 0 Y n4-14c22/23o
25
- gi|16128811|ref|NP_415364.1| 0 Y n6-17c22/23o
26
- gi|16128871|ref|NP_415424.1| 6 0 i35-55o75-98i118-141o161-180i192-212o255-277i
27
- gi|90111191|ref|NP_415463.2| 0 Y n6-17c22/23o
28
- gi|90111193|ref|NP_415466.4| 0 0 i
29
- gi|16128957|ref|NP_415511.1| 0 Y n15-25c29/30o
30
- gi|16128974|ref|NP_415528.1| 0 0 i
31
- gi|16129015|ref|NP_415570.1| 0 0 i
32
- gi|16129146|ref|NP_415701.1| 0 0 i
33
- gi|16129250|ref|NP_415805.1| 0 0 i
34
- gi|16129266|ref|NP_415821.1| 1 0 o6-24i
35
- gi|16129267|ref|NP_415822.1| 1 0 o39-64i
36
- gi|16129318|ref|NP_415875.1| 0 0 i
37
- gi|90111262|ref|NP_415894.4| 0 0 i
38
- gi|16129357|ref|NP_415914.1| 0 0 i
39
- gi|90111267|ref|NP_415926.4| 5 0 o31-64i85-107o113-132i152-168o174-191i
40
- gi|16129388|ref|NP_415946.1| 10 0 i12-31o43-64i76-97o103-121i141-160o166-184i196-218o230-249i256-274o286-310i
41
- gi|16129463|ref|NP_416021.1| 0 Y n6-17c22/23o
42
- gi|16129488|ref|NP_416046.1| 5 0 o12-32i44-62o68-89i151-172o192-214i
43
- gi|90111295|ref|NP_416074.4| 1 Y n7-15c20/21o36-58i
44
- gi|16129540|ref|NP_416099.1| 4 0 o6-26i33-54o60-78i85-105o
45
- gi|90111300|ref|NP_416103.2| 0 Y n3-14c21/22o
46
- gi|90111309|ref|NP_416156.4| 0 Y n6-15c20/21o
47
- gi|90111313|ref|NP_416166.2| 0 0 i
48
- gi|16129623|ref|NP_416182.1| 0 Y n3-11c20/21o
49
- gi|16129732|ref|NP_416292.1| 0 0 i
50
- gi|90111344|ref|NP_416352.4| 0 0 i
51
- gi|90111352|ref|NP_416389.4| 0 0 i
52
- gi|16129855|ref|NP_416418.1| 0 0 i
53
- gi|16129862|ref|NP_416425.1| 0 0 i
54
- gi|16129891|ref|NP_416454.1| 1 0 i14-35o
55
- gi|90111376|ref|NP_416555.2| 0 0 i
56
- gi|16130023|ref|NP_416587.1| 0 0 i
57
- gi|16130042|ref|NP_416607.1| 0 0 i
58
- gi|16130217|ref|NP_416785.1| 9 0 i12-32o52-69i81-100o112-133i154-174o186-207i234-257o269-289i301-322o
59
- gi|16130268|ref|NP_416836.1| 0 Y n8-19c27/28o
60
- gi|16130299|ref|NP_416868.1| 13 0 i12-32o55-73i85-104o110-132i144-165o171-193i205-224o236-255i276-295o307-325i337-355o375-394i484-502o
61
- gi|90111436|ref|NP_416933.4| 0 0 i
62
- gi|90111440|ref|NP_416957.4| 0 0 i
63
- gi|90111445|ref|NP_416978.4| 8 0 o12-32i77-99o105-127i139-161o173-195i231-249o255-278i290-311o
64
- gi|16130429|ref|NP_416999.1| 0 Y n20-31c39/40o
65
- gi|16130443|ref|NP_417013.1| 0 0 i
66
- gi|16130511|ref|NP_417081.1| 0 0 i
67
- gi|49176253|ref|YP_026176.1| 2 0 i12-32o38-58i
68
- gi|16130584|ref|NP_417156.1| 4 0 i12-36o42-62i82-104o110-131i
69
- gi|16130625|ref|NP_417198.1| 0 0 i
70
- gi|16130646|ref|NP_417219.1| 0 0 i
71
- gi|16130699|ref|NP_417272.1| 0 0 i
72
- gi|16130761|ref|NP_417334.1| 0 0 i
73
- gi|16130806|ref|NP_417380.1| 0 0 i
74
- gi|16130817|ref|NP_417391.1| 0 0 i
75
- gi|16130835|ref|NP_417409.1| 0 0 i
76
- gi|16130863|ref|NP_417437.1| 0 Y n4-11c16/17o
77
- gi|16130867|ref|NP_417441.1| 8 0 o6-23i30-50o56-75i103-123o135-157i164-181o187-206i213-233o
78
- gi|16130900|ref|NP_417475.1| 4 0 o12-32i53-75o109-126i138-156o
79
- gi|16130902|ref|NP_417477.1| 0 0 i
80
- gi|16130905|ref|NP_417480.1| 0 0 i
81
- gi|16130984|ref|NP_417560.1| 8 0 i18-36o42-72i84-106o149-166i187-209o215-240i290-315o327-352i
82
- gi|16131011|ref|NP_417588.1| 0 0 i
83
- gi|16131049|ref|NP_417626.1| 0 0 i
84
- gi|16131065|ref|NP_417642.1| 1 Y n4-22c27/28o51-70i
85
- gi|90111557|ref|NP_417676.2| 0 0 i
86
- gi|16131149|ref|NP_417727.1| 0 0 i
87
- gi|16131155|ref|NP_417733.1| 1 Y n4-15c20/21o50-71i
88
- gi|16131230|ref|NP_417810.1| 0 0 i
89
- gi|90111586|ref|NP_417860.2| 0 0 i
90
- gi|16131340|ref|NP_417925.1| 6 Y n3-14c18/19o34-64i76-96o102-123i130-152o158-177i189-207o
91
- gi|16131343|ref|NP_417928.1| 6 0 i12-31o43-64i71-92o104-127i139-165o185-206i
92
- gi|90111596|ref|NP_417930.2| 12 0 i19-41o47-65i85-103o109-131i152-175o181-199i220-241o253-271i283-303o309-330i342-364o370-388i
93
- gi|16131350|ref|NP_417935.1| 6 0 i12-32o75-100i121-148o177-196i203-222o242-260i
94
- gi|90111601|ref|NP_417948.2| 10 0 i7-28o40-62i74-95o107-133i154-175o187-211i223-246o258-281i293-313o325-343i
95
- gi|16131427|ref|NP_418012.1| 0 0 i
96
- gi|16131530|ref|NP_418116.1| 9 Y n11-18c25/26o41-60i72-94o100-120i127-146o152-172i184-205o217-237i249-270o276-293i
97
- gi|16131578|ref|NP_418166.1| 11 Y n4-12c16/17o40-58i70-89o95-116i128-152o158-178i199-222o242-262i269-287o293-312i324-345o351-376i
98
- gi|16131585|ref|NP_418173.1| 0 0 i
99
- gi|16131606|ref|NP_418194.1| 5 0 o36-60i100-118o147-166i211-233o239-264i
100
- gi|67005950|ref|NP_418228.2| 0 0 i
101
- gi|16131722|ref|NP_418318.1| 0 Y n2-9c17/18o
102
- gi|16131732|ref|NP_418328.1| 4 0 i20-43o55-73i113-133o145-172i
103
- gi|16131829|ref|NP_418427.1| 0 0 i
104
- gi|16131888|ref|NP_418486.1| 0 0 i
105
- gi|16131894|ref|NP_418492.1| 2 0 i25-51o63-84i
106
- gi|16131928|ref|NP_418526.1| 0 0 i
107
- gi|16132032|ref|NP_418631.1| 10 0 i7-28o34-55i67-89o95-116i128-145o157-178i198-219o234-258i265-284o290-309i
108
- gi|90111709|ref|NP_418651.2| 10 0 i21-38o58-76i83-102o108-129i136-154o174-194i223-245o257-274i281-303o309-328i
109
- gi|16132087|ref|NP_418686.1| 12 0 i12-38o58-76i97-130o136-154i175-194o222-242i254-275o295-312i324-344o350-369i376-393o413-438i