mspire 0.2.4 → 0.3.0

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Files changed (233) hide show
  1. data/INSTALL +1 -0
  2. data/README +25 -0
  3. data/Rakefile +129 -40
  4. data/bin/{find_aa_freq.rb → aafreqs.rb} +2 -2
  5. data/bin/bioworks_to_pepxml.rb +1 -0
  6. data/bin/fasta_shaker.rb +1 -96
  7. data/bin/filter_and_validate.rb +5 -0
  8. data/bin/{mzxml_to_lmat.rb → ms_to_lmat.rb} +8 -7
  9. data/bin/prob_validate.rb +6 -0
  10. data/bin/raw_to_mzXML.rb +2 -2
  11. data/bin/srf_group.rb +1 -0
  12. data/bin/srf_to_sqt.rb +40 -0
  13. data/changelog.txt +68 -0
  14. data/lib/align/chams.rb +6 -6
  15. data/lib/align.rb +4 -3
  16. data/lib/bsearch.rb +120 -0
  17. data/lib/fasta.rb +318 -86
  18. data/lib/group_by.rb +10 -0
  19. data/lib/index_by.rb +11 -0
  20. data/lib/merge_deep.rb +21 -0
  21. data/lib/{spec → ms/converter}/mzxml.rb +77 -109
  22. data/lib/ms/gradient_program.rb +171 -0
  23. data/lib/ms/msrun.rb +209 -0
  24. data/lib/{spec/msrun.rb → ms/msrun_index.rb} +7 -40
  25. data/lib/ms/parser/mzdata/axml.rb +12 -0
  26. data/lib/ms/parser/mzdata/dom.rb +160 -0
  27. data/lib/ms/parser/mzdata/libxml.rb +7 -0
  28. data/lib/ms/parser/mzdata.rb +25 -0
  29. data/lib/ms/parser/mzxml/axml.rb +11 -0
  30. data/lib/ms/parser/mzxml/dom.rb +159 -0
  31. data/lib/ms/parser/mzxml/hpricot.rb +253 -0
  32. data/lib/ms/parser/mzxml/libxml.rb +15 -0
  33. data/lib/ms/parser/mzxml/regexp.rb +122 -0
  34. data/lib/ms/parser/mzxml/rexml.rb +72 -0
  35. data/lib/ms/parser/mzxml/xmlparser.rb +248 -0
  36. data/lib/ms/parser/mzxml.rb +175 -0
  37. data/lib/ms/parser.rb +108 -0
  38. data/lib/ms/precursor.rb +10 -0
  39. data/lib/ms/scan.rb +81 -0
  40. data/lib/ms/spectrum.rb +193 -0
  41. data/lib/ms.rb +10 -0
  42. data/lib/mspire.rb +4 -0
  43. data/lib/roc.rb +61 -1
  44. data/lib/sample_enzyme.rb +31 -8
  45. data/lib/scan_i.rb +21 -0
  46. data/lib/spec_id/aa_freqs.rb +7 -3
  47. data/lib/spec_id/bioworks.rb +20 -14
  48. data/lib/spec_id/digestor.rb +139 -0
  49. data/lib/spec_id/mass.rb +116 -0
  50. data/lib/spec_id/parser/proph.rb +236 -0
  51. data/lib/spec_id/precision/filter/cmdline.rb +209 -0
  52. data/lib/spec_id/precision/filter/interactive.rb +134 -0
  53. data/lib/spec_id/precision/filter/output.rb +147 -0
  54. data/lib/spec_id/precision/filter.rb +623 -0
  55. data/lib/spec_id/precision/output.rb +60 -0
  56. data/lib/spec_id/precision/prob/cmdline.rb +139 -0
  57. data/lib/spec_id/precision/prob/output.rb +88 -0
  58. data/lib/spec_id/precision/prob.rb +171 -0
  59. data/lib/spec_id/proph/pep_summary.rb +92 -0
  60. data/lib/spec_id/proph/prot_summary.rb +484 -0
  61. data/lib/spec_id/proph.rb +2 -466
  62. data/lib/spec_id/protein_summary.rb +2 -2
  63. data/lib/spec_id/sequest/params.rb +316 -0
  64. data/lib/spec_id/sequest/pepxml.rb +1513 -0
  65. data/lib/spec_id/sequest.rb +2 -1672
  66. data/lib/spec_id/srf.rb +445 -177
  67. data/lib/spec_id.rb +183 -95
  68. data/lib/spec_id_xml.rb +8 -10
  69. data/lib/transmem/phobius.rb +147 -0
  70. data/lib/transmem/toppred.rb +368 -0
  71. data/lib/transmem.rb +157 -0
  72. data/lib/validator/aa.rb +135 -0
  73. data/lib/validator/background.rb +73 -0
  74. data/lib/validator/bias.rb +95 -0
  75. data/lib/validator/cmdline.rb +260 -0
  76. data/lib/validator/decoy.rb +94 -0
  77. data/lib/validator/digestion_based.rb +69 -0
  78. data/lib/validator/probability.rb +48 -0
  79. data/lib/validator/prot_from_pep.rb +234 -0
  80. data/lib/validator/transmem.rb +272 -0
  81. data/lib/validator/true_pos.rb +46 -0
  82. data/lib/validator.rb +214 -0
  83. data/lib/xml.rb +38 -0
  84. data/lib/xml_style_parser.rb +105 -0
  85. data/lib/xmlparser_wrapper.rb +19 -0
  86. data/script/compile_and_plot_smriti_final.rb +97 -0
  87. data/script/extract_gradient_programs.rb +56 -0
  88. data/script/get_apex_values_rexml.rb +44 -0
  89. data/script/mzXML2timeIndex.rb +1 -1
  90. data/script/smriti_final_analysis.rb +103 -0
  91. data/script/toppred_to_yaml.rb +47 -0
  92. data/script/tpp_installer.rb +1 -1
  93. data/{test/tc_align.rb → specs/align_spec.rb} +21 -27
  94. data/{test/tc_bioworks_to_pepxml.rb → specs/bin/bioworks_to_pepxml_spec.rb} +25 -41
  95. data/specs/bin/fasta_shaker_spec.rb +259 -0
  96. data/specs/bin/filter_and_validate__multiple_vals_helper.yaml +202 -0
  97. data/specs/bin/filter_and_validate_spec.rb +124 -0
  98. data/specs/bin/ms_to_lmat_spec.rb +34 -0
  99. data/specs/bin/prob_validate_spec.rb +62 -0
  100. data/specs/bin/protein_summary_spec.rb +10 -0
  101. data/{test/tc_fasta.rb → specs/fasta_spec.rb} +354 -310
  102. data/specs/gi_spec.rb +22 -0
  103. data/specs/load_bin_path.rb +7 -0
  104. data/specs/merge_deep_spec.rb +13 -0
  105. data/specs/ms/gradient_program_spec.rb +77 -0
  106. data/specs/ms/msrun_spec.rb +455 -0
  107. data/specs/ms/parser_spec.rb +92 -0
  108. data/specs/ms/spectrum_spec.rb +89 -0
  109. data/specs/roc_spec.rb +251 -0
  110. data/specs/rspec_autotest.rb +149 -0
  111. data/specs/sample_enzyme_spec.rb +41 -0
  112. data/specs/spec_helper.rb +133 -0
  113. data/specs/spec_id/aa_freqs_spec.rb +52 -0
  114. data/{test/tc_bioworks.rb → specs/spec_id/bioworks_spec.rb} +56 -71
  115. data/specs/spec_id/digestor_spec.rb +75 -0
  116. data/specs/spec_id/precision/filter/cmdline_spec.rb +20 -0
  117. data/specs/spec_id/precision/filter/output_spec.rb +31 -0
  118. data/specs/spec_id/precision/filter_spec.rb +243 -0
  119. data/specs/spec_id/precision/prob_spec.rb +111 -0
  120. data/specs/spec_id/precision/prob_spec_helper.rb +0 -0
  121. data/specs/spec_id/proph/pep_summary_spec.rb +143 -0
  122. data/{test/tc_proph.rb → specs/spec_id/proph/prot_summary_spec.rb} +52 -32
  123. data/{test/tc_protein_summary.rb → specs/spec_id/protein_summary_spec.rb} +85 -0
  124. data/specs/spec_id/sequest/params_spec.rb +68 -0
  125. data/specs/spec_id/sequest/pepxml_spec.rb +452 -0
  126. data/specs/spec_id/sqt_spec.rb +138 -0
  127. data/specs/spec_id/srf_spec.rb +209 -0
  128. data/specs/spec_id/srf_spec_helper.rb +302 -0
  129. data/specs/spec_id_helper.rb +33 -0
  130. data/specs/spec_id_spec.rb +361 -0
  131. data/specs/spec_id_xml_spec.rb +33 -0
  132. data/specs/transmem/phobius_spec.rb +423 -0
  133. data/specs/transmem/toppred_spec.rb +297 -0
  134. data/specs/transmem_spec.rb +60 -0
  135. data/specs/transmem_spec_shared.rb +64 -0
  136. data/specs/validator/aa_spec.rb +107 -0
  137. data/specs/validator/background_spec.rb +51 -0
  138. data/specs/validator/bias_spec.rb +146 -0
  139. data/specs/validator/decoy_spec.rb +51 -0
  140. data/specs/validator/fasta_helper.rb +26 -0
  141. data/specs/validator/prot_from_pep_spec.rb +141 -0
  142. data/specs/validator/transmem_spec.rb +145 -0
  143. data/specs/validator/true_pos_spec.rb +58 -0
  144. data/specs/validator_helper.rb +33 -0
  145. data/specs/xml_spec.rb +12 -0
  146. data/test_files/000_pepxml18_small.xml +206 -0
  147. data/test_files/020a.mzXML.timeIndex +4710 -0
  148. data/test_files/4-03-03_mzXML/000.mzXML.timeIndex +3973 -0
  149. data/test_files/4-03-03_mzXML/020.mzXML.timeIndex +3872 -0
  150. data/test_files/4-03-03_small-prot.xml +321 -0
  151. data/test_files/4-03-03_small.xml +3876 -0
  152. data/test_files/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
  153. data/test_files/bioworks-3.3_10prots.xml +5999 -0
  154. data/test_files/bioworks31.params +77 -0
  155. data/test_files/bioworks32.params +62 -0
  156. data/test_files/bioworks33.params +63 -0
  157. data/test_files/bioworks_single_run_small.xml +7237 -0
  158. data/test_files/bioworks_small.fasta +212 -0
  159. data/test_files/bioworks_small.params +63 -0
  160. data/test_files/bioworks_small.phobius +109 -0
  161. data/test_files/bioworks_small.toppred.out +2847 -0
  162. data/test_files/bioworks_small.xml +5610 -0
  163. data/test_files/bioworks_with_INV_small.xml +3753 -0
  164. data/test_files/bioworks_with_SHUFF_small.xml +2503 -0
  165. data/test_files/corrupted_900.srf +0 -0
  166. data/test_files/head_of_7MIX.srf +0 -0
  167. data/test_files/interact-opd1_mods_small-prot.xml +304 -0
  168. data/test_files/messups.fasta +297 -0
  169. data/test_files/opd1/000.my_answer.100lines.xml +101 -0
  170. data/test_files/opd1/000.tpp_1.2.3.first10.xml +115 -0
  171. data/test_files/opd1/000.tpp_2.9.2.first10.xml +126 -0
  172. data/test_files/opd1/000.v2.1.mzXML.timeIndex +3748 -0
  173. data/test_files/opd1/000_020-prot.png +0 -0
  174. data/test_files/opd1/000_020_3prots-prot.mod_initprob.xml +62 -0
  175. data/test_files/opd1/000_020_3prots-prot.xml +62 -0
  176. data/test_files/opd1/opd1_cat_inv_small-prot.xml +139 -0
  177. data/test_files/opd1/sequest.3.1.params +77 -0
  178. data/test_files/opd1/sequest.3.2.params +62 -0
  179. data/test_files/opd1/twenty_scans.mzXML +418 -0
  180. data/test_files/opd1/twenty_scans.v2.1.mzXML +382 -0
  181. data/test_files/opd1/twenty_scans_answ.lmat +0 -0
  182. data/test_files/opd1/twenty_scans_answ.lmata +9 -0
  183. data/test_files/opd1_020_beginning.RAW +0 -0
  184. data/test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml +753 -0
  185. data/test_files/orbitrap_mzData/000_cut.xml +1920 -0
  186. data/test_files/pepproph_small.xml +4691 -0
  187. data/test_files/phobius.small.noheader.txt +50 -0
  188. data/test_files/phobius.small.small.txt +53 -0
  189. data/test_files/s01_anC1_ld020mM.key.txt +25 -0
  190. data/test_files/s01_anC1_ld020mM.meth +0 -0
  191. data/test_files/small.fasta +297 -0
  192. data/test_files/smallraw.RAW +0 -0
  193. data/test_files/tf_bioworks2excel.bioXML +14340 -0
  194. data/test_files/tf_bioworks2excel.txt.actual +1035 -0
  195. data/test_files/toppred.small.out +416 -0
  196. data/test_files/toppred.xml.out +318 -0
  197. data/test_files/validator_hits_separate/bias_bioworks_small_HS.fasta +7 -0
  198. data/test_files/validator_hits_separate/bioworks_small_HS.xml +5651 -0
  199. data/test_files/yeast_gly_small-prot.xml +265 -0
  200. data/test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes +6 -0
  201. data/test_files/yeast_gly_small.xml +3807 -0
  202. data/test_files/yeast_gly_small2.parentTimes +6 -0
  203. metadata +273 -57
  204. data/bin/filter.rb +0 -6
  205. data/bin/precision.rb +0 -5
  206. data/lib/spec/mzdata/parser.rb +0 -108
  207. data/lib/spec/mzdata.rb +0 -48
  208. data/lib/spec/mzxml/parser.rb +0 -449
  209. data/lib/spec/scan.rb +0 -55
  210. data/lib/spec_id/filter.rb +0 -797
  211. data/lib/spec_id/precision.rb +0 -421
  212. data/lib/toppred.rb +0 -18
  213. data/script/filter-peps.rb +0 -164
  214. data/test/tc_aa_freqs.rb +0 -59
  215. data/test/tc_fasta_shaker.rb +0 -149
  216. data/test/tc_filter.rb +0 -203
  217. data/test/tc_filter_peps.rb +0 -46
  218. data/test/tc_gi.rb +0 -17
  219. data/test/tc_id_class_anal.rb +0 -70
  220. data/test/tc_id_precision.rb +0 -89
  221. data/test/tc_msrun.rb +0 -88
  222. data/test/tc_mzxml.rb +0 -88
  223. data/test/tc_mzxml_to_lmat.rb +0 -36
  224. data/test/tc_peptide_parent_times.rb +0 -27
  225. data/test/tc_precision.rb +0 -60
  226. data/test/tc_roc.rb +0 -166
  227. data/test/tc_sample_enzyme.rb +0 -32
  228. data/test/tc_scan.rb +0 -26
  229. data/test/tc_sequest.rb +0 -336
  230. data/test/tc_spec.rb +0 -78
  231. data/test/tc_spec_id.rb +0 -201
  232. data/test/tc_spec_id_xml.rb +0 -36
  233. data/test/tc_srf.rb +0 -262
data/test_files/bioworks_small.fasta ADDED
@@ -0,0 +1,212 @@
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 ADDED
@@ -0,0 +1,63 @@
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 ADDED
@@ -0,0 +1,109 @@
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