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/messups.fasta DELETED
@@ -1,297 +0,0 @@
1
- >gi|16127995|ref|NP_414542.1| thr operon leader peptide [Escherichia coli K12]
2
- MKRISTTITTTITITTGNGAG
3
- >gi|16127996|ref|NP_414543.1| bifunctional aspartokinase I/homeserine dehydrogenase I [Escherichia coli K12]
4
- MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERI
5
- FAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEA
6
- RGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYS
7
- AAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPC
8
- LIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLIT
9
- QSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL
10
- ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSW
11
- LKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAV
12
- ADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELM
13
- KFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIE
14
- IEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFK
15
- VKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV
16
- ">gi|16127997|ref|NP_414544.1| homoserine kinase [Escherichia coli K12]"
17
- MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLGRFADKLPSEPRENIVYQCWE
18
- RFCQELGKQIPVAMTLEKNMPIGSGLGSSACSVVAALMAMNEHCGKPLNDTRLLALMGELEGRISGSIHY
19
- DNVAPCFLGGMQLMIEENDIISQQVPGFDEWLWVLAYPGIKVSTAEARAILPAQYRRQDCIAHGRHLAGF
20
- IHACYSRQPELAAKLMKDVIAEPYRERLLPGFRQARQAVAEIGAVASGISGSGPTLFALCDKPETAQRVA
21
- DWLGKNYLQNQEGFVHICRLDTAGARVLEN
22
- ">gi|16127998|ref|NP_414545.1| threonine synthase [Escherichia coli K12]
23
- MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILSAFIGDEIPQE
24
- ILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTHIAGDKPVTILTATSGDTGAA
25
- VAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETVAIDGDFDACQALVKQAFDDEELKVALGLNS
26
- ANSINISRLLAQICYYFEAVAQLPQETRNQLVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVP
27
- RFLHDGQWSPKATQATLSNAMDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDETTQQTMRELKELGYTS
28
- EPHAAVAYRALRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHNLPADFAAL
29
- RKLMMNHQ
30
- >gi|16127999|ref|NP_414546.1| hypothetical protein b0005 [Escherichia coli K12]
31
- MKKMQSIVLALSLVLVAPMAAQAAEITLVPSVKLQIGDRDNRGYYWDGGHWRDHGWWKQHYEWRGNRWHL
32
- HGPPPPPRHHKKAPHDHHGGHGPGKHHR
33
- >gi|16128000|ref|NP_414547.1| hypothetical protein b0006 [Escherichia coli K12]
34
- MLILISPAKTLDYQSPLTTTRYTLPELLDNSQQLIHEARKLTPPQISTLMRISDKLAGINAARFHDWQPD
35
- FTPANARQAILAFKGDVYTGLQAETFSEDDFDFAQQHLRMLSGLYGVLRPLDLMQPYRLEMGIRLENARG
36
- KDLYQFWGDIITNKLNEALAAQGDNVVINLASDEYFKSVKPKKLNAEIIKPVFLDEKNGKFKIISFYAKK
37
- ARGLMSRFIIENRLTKPEQLTGFNSEGYFFDEDSSSNGELVFKRYEQR
38
- >gi|16128001|ref|NP_414548.1| inner membrane transport protein [Escherichia coli K12]
39
- MPDFFSFINSVLWGSVMIYLLFGAGCWFTFRTGFVQFRYIRQFGKSLKNSIHPQPGGLTSFQSLCTSLAA
40
- RVGSGNLAGVALAITAGGPGAVFWMWVAAFIGMATSFAECSLAQLYKERDVNGQFRGGPAWYMARGLGMR
41
- WMGVLFAVFLLIAYGIIFSGVQANAVARALSFSFDFPPLVTGIILAVFTLLAITRGLHGVARLMQGFVPL
42
- MAIIWVLTSLVICVMNIGQLPHVIWSIFESAFGWQEAAGGAAGYTLSQAITNGFQRSMFSNEAGMGSTPN
43
- AAAAAASWPPHPAAQGIVQMIGIFIDTLVICTASAMLILLAGNGTTYMPLEGIQLIQKAMRVLMGSWGAE
44
- FVTLVVILFAFSSIVANYIYAENNLFFLRLNNPKAIWCLRICTFATVIGGTLLSLPLMWQLADIIMACMA
45
- ITNLTAILLLSPVVHTIASDYLRQRKLGVRPVFDPLRYPDIGRQLSPDAWDDVSQE
46
- >gi|16128002|ref|NP_414549.1| transaldolase [Escherichia coli K12]
47
- MTDKLTSLRQYTTVVADTGDIAAMKLYQPQDATTNPSLILNAAQIPEYRKLIDDAVAWAKQQSNDRAQQI
48
- VDATDKLAVNIGLEILKLVPGRISTEVDARLSYDTEASIAKAKRLIKLYNDAGISNDRILIKLASTWQGI
49
- RAAEQLEKEGINCNLTLLFSFAQARACAEAGVFLISPFVGRILDWYKANTDKKEYAPAEDPGVVSVSEIY
50
- QYYKEHGYETVVMGASFRNIGEILELAGCDRLTIAPALLKELAESEGAIERKLSYTGEVKARPARITESE
51
- FLWQHNQDPMAVDKLAEGIRKFAIDQEKLEKMIGDLL
52
- >gi|16128003|ref|NP_414550.1| molybdenum cofactor biosynthesis protein [Escherichia coli K12]
53
- MNTLRIGLVSISDRASSGVYQDKGIPALEEWLTSALTTPFELETRLIPDEQAIIEQTLCELVDEMSCHLV
54
- LTTGGTGPARRDVTPDATLAVADREMPGFGEQMRQISLHFVPTAILSRQVGVIRKQALILNLPGQPKSIK
55
- ETLEGVKDAEGNVVVHGIFASVPYCIQLLEGPYVETAPEVVAAFRPKSARRDVSE
56
- >gi|16128004|ref|NP_414551.1| putative regulator, integral membrane protein [Escherichia coli K12]
57
- MGNTKLANPAPLGLMGFGMTTILLNLHNVGYFALDGIILAMGIFYGGIAQIFAGLLEYKKGNTFGLTAFT
58
- SYGSFWLTLVAILLMPKLGLTDAPNAQFLGVYLGLWGVFTLFMFFGTLKGARVLQFVFFSLTVLFALLAI
59
- GNIAGNAAIIHFAGWIGLICGASAIYLAMGEVLNEQFGRTVLPIGESH
60
- >gi|16128005|ref|NP_414552.1| hypothetical protein b0011 [Escherichia coli K12]
61
- MNVNYLNDSDLDFLQHCSEEQLANFARLLTHNEKGKTRLSSVLMRNELFKSMEGHPEQHRRNWQLIAGEL
62
- QHFGGDSIANKLRGHGKLYRAILLDVSKRLKLKADKEMSTFEIEQQLLEQFLRNTWKKMDEEHKQEFLHA
63
- VDARVNELEELLPLLMKDKLLAKGVSHLLSSQLTRILRTHAAMSVLGHGLLRGAGLGGPVGAALNGVKAV
64
- SGSAYRVTIPAVLQIACLRRMVSATQV
65
- >gi|90111078|ref|NP_414553.2| positive regulator for sigma 32 heat shock promoters [Escherichia coli K12]
66
- MRVSWLESKCDTPFANNLSFISSGSSSSSSFTLASTACRNSCLCSSSIFFQVLRRNCSSNCCSISNVDIS
67
- LSAFSFNRFETSSKMARYNLPCPRSLLAILSPPKCCNSPAISCQLRRCCSGCPSIDLNSSLRISTLERRV
68
- LPFSLWVSNRAKFANCSSLQC
69
- >gi|16128007|ref|NP_414554.1| hypothetical protein b0013 [Escherichia coli K12]
70
- MKSVFTISASLAISLMLCCTAQANDHKLLGAIAMPRNETNDLALKLPVCRIVKRIQLSADHGDLQLSGAS
71
- VYFKAARSASQSLNIPSEIKEGQTTDWININSDNDNKRCVSKITFSGHTVNSSDMATLKIIGDD
72
- >gi|16128008|ref|NP_414555.1| molecular chaperone DnaK [Escherichia coli K12]
73
- MGKIIGIDLGTTNSCVAIMDGTTPRVLENAEGDRTTPSIIAYTQDGETLVGQPAKRQAVTNPQNTLFAIK
74
- RLIGRRFQDEEVQRDVSIMPFKIIAADNGDAWVEVKGQKMAPPQISAEVLKKMKKTAEDYLGEPVTEAVI
75
- TVPAYFNDAQRQATKDAGRIAGLEVKRIINEPTAAALAYGLDKGTGNRTIAVYDLGGGTFDISIIEIDEV
76
- DGEKTFEVLATNGDTHLGGEDFDSRLINYLVEEFKKDQGIDLRNDPLAMQRLKEAAEKAKIELSSAQQTD
77
- VNLPYITADATGPKHMNIKVTRAKLESLVEDLVNRSIEPLKVALQDAGLSVSDIDDVILVGGQTRMPMVQ
78
- KKVAEFFGKEPRKDVNPDEAVAIGAAVQGGVLTGDVKDVLLLDVTPLSLGIETMGGVMTTLIAKNTTIPT
79
- KHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKD
80
- KNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPAD
81
- DKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQQQHAQQQTAGADASANNAKDDDVVDAE
82
- FEEVKDKK
83
- >gi|16128009|ref|NP_414556.1| chaperone with DnaK; heat shock protein [Escherichia coli K12]
84
- MAKQDYYEILGVSKTAEEREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVLTDSQKRAAYDQYG
85
- HAAFEQGGMGGGGFGGGADFSDIFGDVFGDIFGGGRGRQRAARGADLRYNMELTLEEAVRGVTKEIRIPT
86
- LEECDVCHGSGAKPGTQPQTCPTCHGSGQVQMRQGFFAVQQTCPHCQGRGTLIKDPCNKCHGHGRVERSK
87
- TLSVKIPAGVDTGDRIRLAGEGEAGEHGAPAGDLYVQVQVKQHPIFEREGNNLYCEVPINFAMAALGGEI
88
- EVPTLDGRVKLKVPGETQTGKLFRMRGKGVKSVRGGAQGDLLCRVVVETPVGLNERQKQLLQELQESFGG
89
- PTGEHNSPRSKSFFDGVKKFFDDLTR
90
- >gi|16128010|ref|NP_414557.1| IS186 hypothetical protein [Escherichia coli K12]
91
- MNYSHDNWSAILAHIGKPEELDTSARNAGALTRRREIRDAATLLRLGLAYGPGGMSLREVTAWAQLHDVA
92
- TLSDVALLKRLRNAADWFGILAAQTLAVRAAVTGCTSGKRLRLVDGTAISAPGGGSAEWRLHMGYDPHTC
93
- QFTDFELTDSRDAERLDRFAQTADEIRIADRGFGSRPECIRSLAFGEADYIVRVHWRGLRWLTAEGMRFD
94
- MMGFLRGLDCGKNGETTVMIGNSGNKKAGAPFPARLIAVSLPPEKALISKTRLLSENRRKGRVVQAETLE
95
- AAGHVLLLTSLPEDEYSAEQVADCYRLRWQIELAFKRLKSLLHLDALRAKEPELAKAWIFANLLAAFLID
96
- DIIQPSLDFPPRSAGSEKKN
97
- >gi|16128011|ref|NP_414558.1| IS186 and IS421 hypothetical protein [Escherichia coli K12]
98
- MPERELRLFYYLNCLSLQWFHRSYRNPARAENPSCQSAFLLQLTSAILASEPGRYNQLLQKQVSGYIRDA
99
- NRIPGQQCVSRLPFAQIGPAVQRLCCRLAQNQ
100
- >gi|16128012|ref|NP_414559.1| regulatory peptide whose translation enables hokC (gef) expression [Escherichia coli K12]
101
- MLNTCRVPLTDRKVKEKRAMKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVFTAYESE
102
- >gi|49175991|ref|YP_025292.1| small toxic membrane polypeptide [Escherichia coli K12]
103
- MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVFTAYESE
104
- >gi|16128013|ref|NP_414560.1| Na+/H antiporter, pH dependent [Escherichia coli K12]
105
- MKHLHRFFSSDASGGIILIIAAILAMIMANSGATSGWYHDFLETPVQLRVGSLEINKNMLLWINDALMAV
106
- FFLLVGLEVKRELMQGSLASLRQAAFPVIAAIGGMIVPALLYLAFNYADPITREGWAIPAATDIAFALGV
107
- LALLGSRVPLALKIFLMALAIIDDLGAIIIIALFYTNDLSMASLGVAAVAIAVLAVLNLCGARRTGVYIL
108
- VGVVLWTAVLKSGVHATLAGVIVGFFIPLKEKHGRSPAKRLEHVLHPWVAYLILPLFAFANAGVSLQGVT
109
- LDGLTSILPLGIIAGLLIGKPLGISLFCWLALRLKLAHLPEGTTYQQIMVVGILCGIGFTMSIFIASLAF
110
- GSVDPELINWAKLGILVGSISSAVIGYSWLRVRLRPSV
111
- >gi|16128014|ref|NP_414561.1| transcriptional activator of cation transport (LysR family) [Escherichia coli K12]
112
- MSMSHINYNHLYYFWHVYKEGSVVGAAEALYLTPQTITGQIRALEERLQGKLFKRKGRGLEPSELGELVY
113
- RYADKMFTLSQEMLDIVNYRKESNLLFDVGVADALSKRLVSSVLNAAVVEGEPIHLRCFESTHEMLLEQL
114
- SQHKLDMIISDCPIDSTQQEGLFSVRIGECGVSFWCTNPPPEKPFPACLEERRLLIPGRRSMLGRKLLNW
115
- FNSQGLNVEILGEFDDAALMKAFGAMHNAIFVAPTLYAYDFYADKTVVEIGRVENVMEEYHAIFAERMIQ
116
- HPAVQRICNTDYSALFSPAVR
117
- >gi|16128015|ref|NP_414562.1| IS1 protein InsB [Escherichia coli K12]
118
- MPGNSPHYGRWPQHDFTSLKKLRPQSVTSRIQPGSDVIVCAEMDEQWGYVGAKSRQRWLFYAYDSLRKTV
119
- VAHVFGERTMATLGRLMSLLSPFDVVIWMTDGWPLYESRLKGKLHVISKRYTQRIERHNLNLRQHLARLG
120
- RKSLSFSKSVELHDKVIGHYLNIKHYQ
121
- >gi|16128016|ref|NP_414563.1| IS1 protein InsA [Escherichia coli K12]
122
- MASVSISCPSCSATDGVVRNGKSTAGHQRYLCSHCRKTWQLQFTYTASQPGTHQKIIDMAMNGVGCRATA
123
- RIMGVGLNTILRHLKNSGRSR
124
- >gi|16128017|ref|NP_414564.1| 30S ribosomal protein S20 [Escherichia coli K12]
125
- MANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDRQAAKGLIHKN
126
- KAARHKANLTAQINKLA
127
- >gi|16128018|ref|NP_414565.1| unknown CDS [Escherichia coli K12]
128
- MCRHSLRSDGAGFYQLAGCEYSFSAIKIAAGGQFLPVICAMAMKSHFFLISVLNRRLTLTAVQGILGRFS
129
- LF
130
- >gi|16128019|ref|NP_414566.1| hypothetical protein b0025 [Escherichia coli K12]
131
- MKLIRGIHNLSQAPQEGCVLTIGNFDGVHRGHRALLQGLQEEGRKRNLPVMVMLFEPQPLELFATDKAPA
132
- RLTRLREKLRYLAECGVDYVLCVRFDRRFAALTAQNFISDLLVKHLRVKFLAVGDDFRFGAGREGDFLLL
133
- QKAGMEYGFDITSTQTFCEGGVRISSTAVRQALADDNLALAESLLGHPFAISGRVVHGDELGRTIGFPTA
134
- NVPLRRQVSPVKGVYAVEVLGLGEKPLPGVANIGTRPTVAGIRQQLEVHLLDVAMDLYGRHIQVVLRKKI
135
- RNEQRFASLDELKAQIARDELTAREFFGLTKPA
136
- >gi|16128020|ref|NP_414567.1| isoleucyl-tRNA synthetase [Escherichia coli K12]
137
- MSDYKSTLNLPETGFPMRGDLAKREPGMLARWTDDDLYGIIRAAKKGKKTFILHDGPPYANGSIHIGHSV
138
- NKILKDIIVKSKGLSGYDSPYVPGWDCHGLPIELKVEQEYGKPGEKFTAAEFRAKCREYAATQVDGQRKD
139
- FIRLGVLGDWSHPYLTMDFKTEANIIRALGKIIGNGHLHKGAKPVHWCVDCRSALAEAEVEYYDKTSPSI
140
- DVAFQAVDQDALKAKFAVSNVNGPISLVIWTTTPWTLPANRAISIAPDFDYALVQIDGQAVILAKDLVES
141
- VMQRIGVTDYTILGTVKGAELELLRFTHPFMGFDVPAILGDHVTLDAGTGAVHTAPGHGPDDYVIGQKYG
142
- LETANPVGPDGTYLPGTYPTLDGVNVFKANDIVVALLQEKGALLHVEKMQHSYPCCWRHKTPIIFRATPQ
143
- WFVSMDQKGLRAQSLKEIKGVQWIPDWGQARIESMVANRPDWCISRQRTWGVPMSLFVHKDTEELHPRTL
144
- ELMEEVAKRVEVDGIQAWWDLDAKEILGDEADQYVKVPDTLDVWFDSGSTHSSVVDVRPEFAGHAADMYL
145
- EGSDQHRGWFMSSLMISTAMKGKAPYRQVLTHGFTVDGQGRKMSKSIGNTVSPQDVMNKLGADILRLWVA
146
- STDYTGEMAVSDEILKRAADSYRRIRNTARFLLANLNGFDPAKDMVKPEEMVVLDRWAVGCAKAAQEDIL
147
- KAYEAYDFHEVVQRLMRFCSVEMGSFYLDIIKDRQYTAKADSVARRSCQTALYHIAEALVRWMAPILSFT
148
- ADEVWGYLPGEREKYVFTGEWYEGLFGLADSEAMNDAFWDELLKVRGEVNKVIEQARADKKVGGSLEAAV
149
- TLYAEPELSAKLTALGDELRFVLLTSGATVADYNDAPADAQQSEVLKGLKVALSKAEGEKCPRCWHYTQD
150
- VGKVAEHAEICGRCVSNVAGDGEKRKFA
151
- >gi|16128021|ref|NP_414568.1| signal peptidase II [Escherichia coli K12]
152
- MSQSICSTGLRWLWLVVVVLIIDLGSKYLILQNFALGDTVPLFPSLNLHYARNYGAAFSFLADSGGWQRW
153
- FFAGIAIGISVILAVMMYRSKATQKLNNIAYALIIGGALGNLFDRLWHGFVVDMIDFYVGDWHFATFNLA
154
- DTAICVGAALIVLEGFLPSRAKKQ
155
- >gi|16128022|ref|NP_414569.1| FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase) [Escherichia coli K12]
156
- MSESVQSNSAVLVHFTLKLDDGTTAESTRNNGKPALFRLGDASLSEGLEQHLLGLKVGDKTTFSLEPDAA
157
- FGVPSPDLIQYFSRREFMDAGEPEIGAIMLFTAMDGSEMPGVIREINGDSITVDFNHPLAGQTVHFDIEV
158
- LEIDPALEA
159
- >gi|16128023|ref|NP_414570.1| 4-hydroxy-3-methylbut-2-enyl diphosphate reductase [Escherichia coli K12]
160
- MQILLANPRGFCAGVDRAISIVENALAIYGAPIYVRHEVVHNRYVVDSLRERGAIFIEQISEVPDGAILI
161
- FSAHGVSQAVRNEAKSRDLTVFDATCPLVTKVHMEVARASRRGEESILIGHAGHPEVEGTMGQYSNPEGG
162
- MYLVESPDDVWKLTVKNEEKLSFMTQTTLSVDDTSDVIDALRKRFPKIVGPRKDDICYATTNRQEAVRAL
163
- AEQAEVVLVVGSKNSSNSNRLAELAQRMGKRAFLIDDAKDIQEEWVKEVKCVGVTAGASAPDILVQNVVA
164
- RLQQLGGGEAIPLEGREENIVFEVPKELRVDIREVD
165
- >gi|16128024|ref|NP_414571.1| nucleoside hydrolase [Escherichia coli K12]
166
- MRLPIFLDTDPGIDDAVAIAAAIFAPELDLQLMTTVAGNVSVEKTTRNALQLLHFWNAEIPLAQGAAVPL
167
- VRAPRDAASVHGESGMAGYDFVEHNRKPLGIPAFLAIRDALMRAPEPVTLVAIGPLTNIALLLSQCPECK
168
- PYIRRLVIMGGSAGRGNCTPNAEFNIAADPEAAACVFRSGIEIVMCGLDVTNQAILTPDYLSTLPQLNRT
169
- GKMLHALFSHYRSGSMQSGLRMHDLCAIAWLVRPDLFTLKPCFVAVETQGEFTSGTTVVDIDGCLGKPAN
170
- VQVALDLDVKGFQQWVAEVLALAS
171
- >gi|16128025|ref|NP_414572.1| dihydrodipicolinate reductase [Escherichia coli K12]
172
- MHDANIRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSSLDAVK
173
- DDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVFAANFSVGVNVMLKLL
174
- EKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKDLKDCAVYSREGHTGERVPGTIGFAT
175
- VRAGDIVGEHTAMFADIGERLEITHKASSRMTFANGAVRSALWLSGKESGLFDMRDVLDLNNL
176
- >gi|16128026|ref|NP_414573.1| carbamoyl-phosphate synthase small subunit [Escherichia coli K12]
177
- MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVGTNDADE
178
- ESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLREKGAQNGCIIAGDNPDA
179
- ALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGLPEAKKEDELPFHVVAYDFGAKRNILRMLV
180
- DRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASG
181
- AKTVKMKFGHHGGNHPVKDVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSF
182
- QGHPEASPGPHDAAPLFDHFIELIEQYRKTAK
183
- >gi|16128027|ref|NP_414574.1| carbamoyl-phosphate synthase large subunit [Escherichia coli K12]
184
- MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEMADATYIEPIH
185
- WEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATADAIDKAEDRRRFDVAMKKIG
186
- LETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGGIAYNREEFEEICARGLDLSPTKELLIDESL
187
- IGWKEYEMEVVRDKNDNCIIVCSIENFDAMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETG
188
- GSNVQFAVNPKNGRLIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEP
189
- SIDYVVTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA
190
- LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVGITGLNADFLR
191
- QLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEECEANPSTDRE
192
- KIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIV
193
- RIEKPKGVIVQYGGQTPLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEM
194
- AVEKAKEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDG
195
- EMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI
196
- EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKFPGVDPLLGPE
197
- MRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIV
198
- LGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFAT
199
- AMALNADATEKVISVQEMHAQIK
200
- >gi|90111079|ref|NP_414576.4| transcriptional regulator of cai operon [Escherichia coli K12]
201
- MCEGYVEKPLYLLIAEWMMAENRWVIAREISIHFDIEHSKAVNTLTYILSEVTEISCEVKMIPNKLEGRG
202
- CQCQRLVKVVDIDEQIYARLRNNSREKLVGVRKTPRIPAVPLTELNREQKWQMMLSKSMRR
203
- >gi|90111080|ref|NP_414577.2| possible synthesis of cofactor for carnitine racemase and dehydratase [Escherichia coli K12]
204
- MSYYAFEGLIPVVHPTAFVHPSAVLIGDVIVGAGVYIGPLASLRGDYGRLIVQAGANIQDGCIMHGYCDT
205
- DTIVGENGHIGHGAILHGCLIGRDALVGMNSVIMDGAVIGEESIVAAMSFVKAGFRGEKRQLLMGTPARA
206
- VRNVSDDELHWKRLNTKEYQDLVGRCHVSLHETQPLRQMEENRPRLQGTTDVTPKR
207
- >gi|16128030|ref|NP_414578.1| carnitinyl-CoA dehydratase [Escherichia coli K12]
208
- MKQQGTTLPANNHTLKQYAFFAGMLSSLKKQKWRKGMSESLHLTRNGSILEITLDRPKANAIDAKTSFEM
209
- GEVFLNFRDDPQLRVAIITGAGEKFFSAGWDLKAAAEGEAPDADFGPGGFAGLTEIFNLDKPVIAAVNGY
210
- AFGGGFELALAADFIVCADNASFALPEAKLGIVPDSGGVLRLPKILPPAIVNEMVMTGRRMGAEEALRWG
211
- IVNRVVSQAELMDNARELAQQLVNSAPLAIAALKEIYRTTSEMPVEEAYRYIRSGVLKHYPSVLHSEDAI
212
- EGPLAFAEKRDPVWKGR
213
- >gi|49175993|ref|NP_414579.3| crotonobetaine/carnitine-CoA ligase [Escherichia coli K12]
214
- MDRGAMDIIGGQHLRQMWDDLADVYGHKTALICESSGGVVNRYSYLELNQEINRTANLFYTLGIRKGDKV
215
- ALHLDNCPEFIFCWFGLAKIGAIMVPINARLLCEESAWILQNSQACLLVTSAQFYPMYQQIQQEDATQLR
216
- HICLTDVALPADDGVSSFTQLKNQQPATLCYAPPLSTDDTAEILFTSGTTSRPKGVVITHYNLRFAGYYS
217
- AWQCALRDDDVYLTVMPAFHIDCQCTAAMAAFSAGATFVLVEKYSARAFWGQVQKYRATVTECIPMMIRT
218
- LMVQPPSANDQQHRLREVMFYLNLSEQEKDAFCERFGVRLLTSYGMTETIVGIIGDRPGDKRRWPSIGRV
219
- GFCYEAEIRDDHNRPLPAGEIGEICIKGIPGKTIFKEYFLNPQATAKVLEADGWLHTGDTGYRDEEDFFY
220
- FVDRRCNMIKRGGENVSCVELENIIAAHPKIQDIVVVGIKDSIRDEAIKAFVVLNEGETLSEEEFFRFCE
221
- QNMAKFKVPSYLEIRKDLPRNCSGKIIRKNLK
222
- >gi|16128032|ref|NP_414580.1| crotonobetainyl-CoA:carnitineCoA-transferase [Escherichia coli K12]
223
- MDHLPMPKFGPLAGLRVVFSGIEIAGPFAGQMFAEWGAEVIWIENVAWADTIRVQPNYPQLSRRNLHALS
224
- LNIFKDEGREAFLKLMETTDIFIEASKGPAFARRGITDEVLWQHNPKLVIAHLSGFGQYGTEEYTNLPAY
225
- NTIAQAFSGYLIQNGDVDQPMPAFPYTADYFSGLTATTAALAALHKVRETGKGESIDIAMYEVMLRMGQY
226
- FMMDYFNGGEMCPRMSKGKDPYYAGCGLYKCADGYIVMELVGITQIEECFKDIGLAHLLGTPEIPEGTQL
227
- IHRIECPYGPLVEEKLDAWLATHTIAEVKERFAELNIACAKVLTVPELESNPQYVARESITQWQTMDGRT
228
- CKGPNIMPKFKNNPGQIWRGMPSHGMDTAAILKNIGYSENDIQELVSKGLAKVED
229
- >gi|16128033|ref|NP_414581.1| crotonobetainyl-CoA dehydrogenase [Escherichia coli K12]
230
- MDFNLNDEQELFVAGIRELMASENWEAYFAECDRDSVYPERFVKALADMGIDSLLIPEEHGGLDAGFVTL
231
- AAVWMELGRLGAPTYVLYQLPGGFNTFLREGTQEQIDKIMAFRGTGKQMWNSAITEPGAGSDVGSLKTTY
232
- TRRNGKIYLNGSKCFITSSAYTPYIVVMARDGASPDKPVYTEWFVDMSKPGIKVTKLEKLGLRMDSCCEI
233
- TFDDVELDEKDMFGREGNGFNRVKEEFDHERFLVALTNYGTAMCAFEDAARYANQRVQFGEAIGRFQLIQ
234
- EKFAHMAIKLNSMKNMLYEAAWKADNGTITSGDAAMCKYFCANAAFEVVDSAMQVLGGVGIAGNHRISRF
235
- WRDLRVDRVSGGSDEMQILTLGRAVLKQYR
236
- >gi|16128034|ref|NP_414582.1| L-carnitine/gamma-butyrobetaine antiporter [Escherichia coli K12]
237
- MKNEKRKTGIEPKVFFPPLIIVGILCWLTVRDLDAANVVINAVFSYVTNVWGWAFEWYMVVMLFGWFWLV
238
- FGPYAKKRLGNEPPEFSTASWIFMMFASCTSAAVLFWGSIEIYYYISTPPFGLEPNSTGAKELGLAYSLF
239
- HWGPLPWATYSFLSVAFAYFFFVRKMEVIRPSSTLVPLVGEKHAKGLFGTIVDNFYLVALIFAMGTSLGL
240
- ATPLVTECMQWLFGIPHTLQLDAIIITCWIILNAICVACGLQKGVRIASDVRSYLSFLMLGWVFIVSGAS
241
- FIMNYFTDSVGMLLMYLPRMLFYTDPIAKGGFPQGWTVFYWAWWVIYAIQMSIFLARISRGRTVRELCFG
242
- MVLGLTASTWILWTVLGSNTLLLIDKNIINIPNLIEQYGVARAIIETWAALPLSTATMWGFFILCFIATV
243
- TLVNACSYTLAMSTCREVRDGEEPPLLVRIGWSILVGIIGIVLLALGGLKPIQTAIIAGGCPLFFVNIMV
244
- TLSFIKDAKQNWKD
245
- >gi|90111081|ref|NP_414583.2| putative electron transfer flavoprotein subunit beta [Escherichia coli K12]
246
- MKIITCYKCVPDEQDIAVNNADGSLDFSKADAKISQYDLNAIEAACQLKQQAAEAQVTALSVGGKALTNA
247
- KGRKDVLSRGPDELIVVIDDQFEQALPQQTASALAAAAQKAGFDLILCGDGSSDLYAQQVGLLVGEILNI
248
- PAVNGVSKIISLTADTLTVERELEDETETLSIPLPAVVAVSTDINSPQIPSMKAILGAAKKPVQVWSAAD
249
- IGFNAEAAWSEQQVAAPKQRERQRIVIEGDGEEQIAAFAENLRKVI
250
- >gi|16128036|ref|NP_414584.1| putative electron transfer flavoprotein subunit alpha [Escherichia coli K12]
251
- MNTFSQVWVFSDTPSRLPELMNGAQALANQINTFVLNDADGAQAIQLGANHVWKLNGKPDDRMIEDYAGV
252
- MADTIRQHGADGLVLLPNTRRGKLLAAKLGYRLKAAVSNDASTVSVQDGKATVKHMVYGGLAIGEERIAT
253
- PYAVLTISSGTFDAAQPDASRTGETHTVEWQAPAVAITRTATQARQSNSVDLDKARLVVSVGRGIGSKEN
254
- IALAEQLCKAIGAELACSRPVAENEKWMEHERYVGISNLMLKPELYLAVGISGQIQHMVGANASQTIFAI
255
- NKDKNAPIFQYADYGIVGDAVKILPALTAALAR
256
- >gi|16128037|ref|NP_414585.1| carnitine metabolism related [Escherichia coli K12]
257
- MSEDIFDAIIVGAGLAGSVAALVLAREGAQVLVIERGNSAGAKNVTGGRLYAHSLEHIIPGFADSAPVER
258
- LITHEKLAFMTEKSAMTMDYCNGDETSPSQRSYSVLRSKFDAWLMEQAEEAGAQLITGIRVDNLVQRDGK
259
- VVGVEADGDVIEAKTVILADGVNSILAEKLGMAKRVKPTDVAVGVKELIELPKSVIEDRFQLQGNQGAAC
260
- LFAGSPTDGLMGGGFLYTNENTLSLGLVCGLHHLHDAKKSVPQMLEDFKQHPAVAPLIAGGKLVEYSAHV
261
- VPEAGINMLPELVGDGVLIAGDAAGMCMNLGFTIRGMDLAIAAGEAAAKTVLSAMKSDDFSKQKLAEYRQ
262
- HLESGPLRDMRMYQKLPAFLDNPRMFSGYPELAVGVARDLFTIDGSAPELMRKKILRHGKKVGFINLIKD
263
- GMKGVTVL
264
- >gi|16128038|ref|NP_414586.1| putative ferredoxin [Escherichia coli K12]
265
- MTSPVNVDVKLGVNKFNVDEEHPHIVVKADADKQALELLVKACPAGLYKKQDDGSVRFDYAGCLECGTCR
266
- ILGLGSALEQWEYPRGTFGVEFRYG
267
- >gi|16128039|ref|NP_414587.1| putative transport protein [Escherichia coli K12]
268
- MQPSRNFDDLKFSSIHRRILLWGSGGPFLDGYVLVMIGVALEQLTPALKLDADWIGLLGAGTLAGLFVGT
269
- SLFGYISDKVGRRKMFLIDIIAIGVISVATMFVSSPVELLVMRVLIGIVIGADYPIATSMITEFSSTRQR
270
- AFSISFIAAMWYVGATCADLVGYWLYDVEGGWRWMLGSAAIPCLLILIGRFELPESPRWLLRKGRVKECE
271
- EMMIKLFGEPVAFDEEQPQQTRFRDLFNRRHFPFVLFVAAIWTCQVIPMFAIYTFGPQIVGLLGLGVGKN
272
- AALGNVVISLFFMLGCIPPMLWLNTAGRRPLLIGSFAMMTLALAVLGLIPDMGIWLVVMAFAVYAFFSGG
273
- PGNLQWLYPNELFPTDIRASAVGVIMSLSRIGTIVSTWALPIFINNYGISNTMLMGAGISLFGLLISVAF
274
- APETRGMSLAQTSNMTIRGQRMG
275
- >gi|16128040|ref|NP_414588.1| glutathione-regulated potassium-efflux system ancillary protein [Escherichia coli K12]
276
- MILIIYAHPYPHHSHANKRMLEQARTLEGVEIRSLYQLYPDFNIDIAAEQEALSRADLIVWQHPMQWYSI
277
- PPLLKLWIDKVFSHGWAYGHGGTALHGKHLLWAVTTGGGESHFEIGAHPGFDVLSQPLQATAIYCGLNWL
278
- PPFAMHCTFICDDETLEGQARHYKQRLLEWQEAHHG
279
- >gi|16128041|ref|NP_414589.1| glutathione-regulated potassium-efflux system protein [Escherichia coli K12]
280
- MDSHTLIQALIYLGSAALIVPIAVRLGLGSVLGYLIAGCIIGPWGLRLVTDAESILHFAEIGVVLMLFII
281
- GLELDPQRLWKLRAAVFGCGALQMVICGGLLGLFCMLLGLRWQVAELIGMTLALSSTAIAMQAMNERNLM
282
- VTQMGRSAFAVLLFQDIAAIPLVAMIPLLATSSASTTMGAFALSALKVAGALVLVVLLGRYVTRPALRFV
283
- ARSGLREVFSAVALFLVFGFGLLLEEVGLSMAMGAFLAGVLLASSEYRHALESDIEPFKGLLLGLFFIGV
284
- GMSIDFGTLLENPLRIVILLLGFLIIKIAMLWLIARPLQVPNKQRRWFAVLLGQGSEFAFVVFGAAQMAN
285
- VLEPEWAKSLTLAVALSMAATPILLVILNRLEQSSTEEAREADEIDEEQPRVIIAGFGRFGQITGRLLLS
286
- SGVKMVVLDHDPDHIETLRKFGMKVFYGDATRMDLLESAGAAKAEVLINAIDDPQTNLQLTEMVKEHFPH
287
- LQIIARARDVDHYIRLRQAGVEKPERETFEGALKTGRLALESLGLGPYEARERADVFRRFNIQMVEEMAM
288
- VENDTKARAAVYKRTSAMLSEIITEDREHLSLIQRHGWQGTEEGKHTGNMADEPETKPSS
289
- >gi|16128042|ref|NP_414590.1| dihydrofolate reductase type I, trimethoprim resistance [Escherichia coli K12]
290
- MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDD
291
- RVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEF
292
- HDADAQNSHSYCFEILERR
293
- >gi|16128043|ref|NP_414591.1| diadenosinetetraphosphatase [Escherichia coli K12]
294
- MATYLIGDVHGCYDELIALLHKVEFTPGKDTLWLTGDLVARGPGSLDVLRYVKSLGDSVRLVLGNHDLHL
295
- LAVFAGISRNKPKDRLTPLLEAPDADELLNWLRRQPLLQIDEEKKLVMAHAGITPQWDLQTAKECARDVE
296
- AVLSSDSYPFFLDAMYGDMPNNWSPELRGLGRLRFITNAFTRMRFCFPNGQLDMYSKESPEEAPAPLKPW
297
- FAIPGPVAEEYSIAFGHWASLEGKGTPEGIYALDTGCCWGGTLTCLRWEDKQYFVQPSNRHKDLGEAAAS
data/test_files/opd1/000.my_answer.100lines.xml DELETED
@@ -1,101 +0,0 @@
1
- <?xml version="1.0" encoding="UTF-8"?>
2
- <?xml-stylesheet type="text/xsl" href="/tools/bin/TPP/tpp/schema/pepXML_std.xsl"?><msms_pipeline_analysis date="2007-1-3T17:3:33" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://regis-web.systemsbiology.net/pepXML /tools/bin/TPP/tpp/schema/pepXML_v18.xsd" summary_xml="000.xml">
3
- <msms_run_summary base_name="/blahblahblah/files/000" msManufacturer="ThermoFinnigan" msModel="LCQ Deca XP Plus" msIonization="ESI" msMassAnalyzer="Ion Trap" msDetector="UNKNOWN" raw_data_type="raw" raw_data=".mzXML">
4
- <sample_enzyme name="Trypsin">
5
- <specificity cut="KR" no_cut="" sense="C"/>
6
- </sample_enzyme>
7
- <search_summary base_name="/blahblah/files/000" search_engine="SEQUEST" precursor_mass_type="average" fragment_mass_type="average" out_data_type="out" out_data=".tgz" search_id="1">
8
- <search_database local_path="C:\Xcalibur\database\ecoli_K12.fasta" type="AA"/>
9
- <enzymatic_search_constraint enzyme="Trypsin" max_num_internal_cleavages="2" min_number_termini="2"/>
10
- <parameter name="diff_search_options" value="0.000000 S 0.000000 C 0.000000 M 0.000000 X 0.000000 T 0.000000 Y"/>
11
- <parameter name="digest_mass_range" value="600.0 3500.0"/>
12
- <parameter name="enzyme_info" value="Trypsin(KR) 1 1 KR -"/>
13
- <parameter name="first_database_name" value="C:\Xcalibur\database\ecoli_K12.fasta"/>
14
- <parameter name="fragment_ion_tolerance" value="1.0000"/>
15
- <parameter name="ion_cutoff_percentage" value="0.0000"/>
16
- <parameter name="ion_series" value="0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0"/>
17
- <parameter name="mass_type_fragment" value="0"/>
18
- <parameter name="mass_type_parent" value="0"/>
19
- <parameter name="match_peak_allowed_error" value="1"/>
20
- <parameter name="match_peak_count" value="0"/>
21
- <parameter name="match_peak_tolerance" value="1.0000"/>
22
- <parameter name="max_num_differential_per_peptide" value="3"/>
23
- <parameter name="max_num_internal_cleavage_sites" value="2"/>
24
- <parameter name="normalize_xcorr" value="0"/>
25
- <parameter name="nucleotide_reading_frame" value="0"/>
26
- <parameter name="num_description_lines" value="5"/>
27
- <parameter name="num_output_lines" value="10"/>
28
- <parameter name="num_results" value="500"/>
29
- <parameter name="partial_sequence" value=""/>
30
- <parameter name="peptide_mass_tolerance" value="1.5000"/>
31
- <parameter name="peptide_mass_units" value="0"/>
32
- <parameter name="print_duplicate_references" value="40"/>
33
- <parameter name="protein_mass_filter" value="0 0"/>
34
- <parameter name="remove_precursor_peak" value="0"/>
35
- <parameter name="search_engine" value="SEQUEST"/>
36
- <parameter name="second_database_name" value=""/>
37
- <parameter name="sequence_header_filter" value=""/>
38
- <parameter name="show_fragment_ions" value="1"/>
39
- <parameter name="term_diff_search_options" value="0.000000 0.000000"/>
40
- </search_summary>
41
- <spectrum_query spectrum="000.100.100.1" start_scan="100" end_scan="100" precursor_neutral_mass="1074.666926" assumed_charge="1" index="1">
42
- <search_result>
43
- <search_hit hit_rank="1" peptide="SIYFRNFK" peptide_prev_aa="R" peptide_next_aa="G" protein="gi|16130084|ref|NP_416651.1|" num_tot_proteins="1" num_matched_ions="4" tot_num_ions="14" calc_neutral_pep_mass="1074.23261" massdiff="+0.434316000000081" num_tol_term="2" num_missed_cleavages="1" is_rejected="0">
44
- <search_score name="xcorr" value="0.4"/>
45
- <search_score name="deltacn" value="0.023"/>
46
- <search_score name="deltacnstar" value="0"/>
47
- <search_score name="spscore" value="78.8"/>
48
- <search_score name="sprank" value="1"/>
49
- </search_hit>
50
- </search_result>
51
- </spectrum_query>
52
- <spectrum_query spectrum="000.1000.1000.1" start_scan="1000" end_scan="1000" precursor_neutral_mass="663.206111" assumed_charge="1" index="2">
53
- <search_result>
54
- <search_hit hit_rank="1" peptide="ALADFK" peptide_prev_aa="R" peptide_next_aa="S" protein="gi|16128765|ref|NP_415318.1|" num_tot_proteins="1" num_matched_ions="5" tot_num_ions="10" calc_neutral_pep_mass="663.76261" massdiff="-0.556499000000031" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
55
- <search_score name="xcorr" value="0.965"/>
56
- <search_score name="deltacn" value="0.132"/>
57
- <search_score name="deltacnstar" value="0"/>
58
- <search_score name="spscore" value="81.1"/>
59
- <search_score name="sprank" value="1"/>
60
- </search_hit>
61
- </search_result>
62
- </spectrum_query>
63
- <spectrum_query spectrum="000.1002.1002.1" start_scan="1002" end_scan="1002" precursor_neutral_mass="1291.663508" assumed_charge="1" index="3">
64
- <search_result>
65
- <search_hit hit_rank="1" peptide="EETEWRVQSK" peptide_prev_aa="R" peptide_next_aa="R" protein="gi|16128280|ref|NP_414829.1|" num_tot_proteins="1" num_matched_ions="10" tot_num_ions="18" calc_neutral_pep_mass="1291.37261" massdiff="+0.29089799999997" num_tol_term="2" num_missed_cleavages="1" is_rejected="0">
66
- <search_score name="xcorr" value="0.904"/>
67
- <search_score name="deltacn" value="0.041"/>
68
- <search_score name="deltacnstar" value="0"/>
69
- <search_score name="spscore" value="140.0"/>
70
- <search_score name="sprank" value="1"/>
71
- </search_hit>
72
- </search_result>
73
- </spectrum_query>
74
- <spectrum_query spectrum="000.1003.1003.1" start_scan="1003" end_scan="1003" precursor_neutral_mass="769.421687" assumed_charge="1" index="4">
75
- <search_result>
76
- <search_hit hit_rank="1" peptide="NIGLLNK" peptide_prev_aa="R" peptide_next_aa="I" protein="gi|16129238|ref|NP_415793.1|" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="12" calc_neutral_pep_mass="770.92261" massdiff="-1.50092299999994" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
77
- <search_score name="xcorr" value="0.887"/>
78
- <search_score name="deltacn" value="0.115"/>
79
- <search_score name="deltacnstar" value="0"/>
80
- <search_score name="spscore" value="153.1"/>
81
- <search_score name="sprank" value="2"/>
82
- </search_hit>
83
- </search_result>
84
- </spectrum_query>
85
- <spectrum_query spectrum="000.1004.1004.2" start_scan="1004" end_scan="1004" precursor_neutral_mass="1252.326528" assumed_charge="2" index="5">
86
- <search_result>
87
- <search_hit hit_rank="1" peptide="QLTYTAHGPHK" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|16131568|ref|NP_418155.1|" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="20" calc_neutral_pep_mass="1252.38261" massdiff="-0.0560820000000604" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
88
- <search_score name="xcorr" value="1.066"/>
89
- <search_score name="deltacn" value="0.172"/>
90
- <search_score name="deltacnstar" value="0"/>
91
- <search_score name="spscore" value="125.2"/>
92
- <search_score name="sprank" value="10"/>
93
- </search_hit>
94
- </search_result>
95
- </spectrum_query>
96
- <spectrum_query spectrum="000.1004.1004.3" start_scan="1004" end_scan="1004" precursor_neutral_mass="1878.489792" assumed_charge="3" index="6">
97
- <search_result>
98
- <search_hit hit_rank="1" peptide="AGNARVVNSNAMSFLAQK" peptide_prev_aa="K" peptide_next_aa="G" protein="gi|16131337|ref|NP_417922.1|" num_tot_proteins="1" num_matched_ions="16" tot_num_ions="68" calc_neutral_pep_mass="1878.12261" massdiff="+0.367181999999957" num_tol_term="2" num_missed_cleavages="1" is_rejected="0">
99
- <search_score name="xcorr" value="1.37"/>
100
- <search_score name="deltacn" value="0.199"/>
101
- <search_score name="deltacnstar" value="0"/>
data/test_files/opd1/000.tpp_1.2.3.first10.xml DELETED
@@ -1,115 +0,0 @@
1
- <?xml version="1.0" encoding="UTF-8"?>
2
- <!DOCTYPE msms_pipeline_analysis SYSTEM "/usr/bin/msms_analysis3.dtd">
3
- <?xml-stylesheet type="text/xsl" href="/isb/std_xsl/pepXML_std.xsl"?>
4
- <msms_pipeline_analysis date="Tue Aug 15 20:43:02 2006" summary_xml="000.xml">
5
- <msms_run_summary base_name="/work/john/TPP_pepxml_prep_opd00001/run_000_020_ready/000" search_engine="SEQUEST" database="C:\Xcalibur\database\ecoli_K12.fasta" raw_data_type="mzXML" raw_data=".mzXML" out_data_type="out" out_data=".tgz" sample_enzyme="tryptic">
6
- <search_summary base_name="/work/john/TPP_pepxml_prep_opd00001/run_000_020_ready/000" search_engine="SEQUEST" precursor_mass_type="average" fragment_mass_type="average">
7
- <enzymatic_search_constraint enzyme="tryptic" max_num_internal_cleavages="2" min_number_termini="2"/>
8
- <sequence_search_constraint sequence="0"/>
9
- <sequence_search_constraint sequence="0"/>
10
- <parameter name="peptide_mass_tol" value="1.500"/>
11
- <parameter name="fragment_ion_tol" value="0.000"/>
12
- <parameter name="ion_series" value=" 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0
13
- <parameter name="max_num_differential_AA_per_mod" value="4"/>
14
- <parameter name="nucleotide_reading_frame" value="0"/>
15
- <parameter name="num_output_lines" value="10"/>
16
- <parameter name="remove_precursor_peak" value="0"/>
17
- <parameter name="ion_cutoff_percentage" value="0.0"/>
18
- <parameter name="match_peak_count" value="0"/>
19
- <parameter name="match_peak_allowed_error" value="1"/>
20
- <parameter name="match_peak_tolerance" value="1.0"/>
21
- <parameter name="protein_mass_filter" value="0 0"/>
22
- <parameter name="sequence_header_filter" value=""/>
23
- </search_summary>
24
- <search_result spectrum="000.100.100.1" start_scan="100" end_scan="100" precursor_neutral_mass="1074.5920" assumed_charge="1" index="1">
25
- <search_hit hit_rank="1" peptide="SIYFRNFK" peptide_prev_aa="R" peptide_next_aa="G" protein="gi|16130084|ref|NP_416651.1|" num_tot_proteins="1" num_matched_ions=" 4" tot_num_ions=" 14" calc_neutral_pep_mass="1074.1920" massdiff="+0.4" num_tol_term="2" num_missed_cleavages="-1" is_rejected="0">
26
- <search_score name="xcorr" value="0.400"/>
27
- <search_score name="deltacn" value="0.023"/>
28
- <search_score name="deltacnstar" value="0"/>
29
- <search_score name="spscore" value="78.8"/>
30
- <search_score name="sprank" value="1"/>
31
- </search_hit>
32
- </search_result>
33
- <search_result spectrum="000.1000.1000.1" start_scan="1000" end_scan="1000" precursor_neutral_mass="663.1920" assumed_charge="1" index="2">
34
- <search_hit hit_rank="1" peptide="ALADFK" peptide_prev_aa="R" peptide_next_aa="S" protein="gi|16128765|ref|NP_415318.1|" num_tot_proteins="1" num_matched_ions=" 5" tot_num_ions=" 10" calc_neutral_pep_mass="663.7920" massdiff="-0.6" num_tol_term="2" num_missed_cleavages="-1" is_rejected="0">
35
- <search_score name="xcorr" value="0.965"/>
36
- <search_score name="deltacn" value="0.132"/>
37
- <search_score name="deltacnstar" value="0"/>
38
- <search_score name="spscore" value="81.1"/>
39
- <search_score name="sprank" value="1"/>
40
- </search_hit>
41
- </search_result>
42
- <search_result spectrum="000.1002.1002.1" start_scan="1002" end_scan="1002" precursor_neutral_mass="1291.6920" assumed_charge="1" index="3">
43
- <search_hit hit_rank="1" peptide="EETEWRVQSK" peptide_prev_aa="R" peptide_next_aa="R" protein="gi|16128280|ref|NP_414829.1|" num_tot_proteins="1" num_matched_ions=" 10" tot_num_ions=" 18" calc_neutral_pep_mass="1291.3920" massdiff="+0.3" num_tol_term="2" num_missed_cleavages="1" is_rejected="0">
44
- <search_score name="xcorr" value="0.904"/>
45
- <search_score name="deltacn" value="0.041"/>
46
- <search_score name="deltacnstar" value="0"/>
47
- <search_score name="spscore" value="140.0"/>
48
- <search_score name="sprank" value="1"/>
49
- </search_hit>
50
- </search_result>
51
- <search_result spectrum="000.1003.1003.1" start_scan="1003" end_scan="1003" precursor_neutral_mass="769.3920" assumed_charge="1" index="4">
52
- <search_hit hit_rank="1" peptide="NIGLLNK" peptide_prev_aa="R" peptide_next_aa="I" protein="gi|16129238|ref|NP_415793.1|" num_tot_proteins="1" num_matched_ions=" 8" tot_num_ions=" 12" calc_neutral_pep_mass="770.8920" massdiff="-1.5" num_tol_term="2" num_missed_cleavages="-1" is_rejected="0">
53
- <search_score name="xcorr" value="0.887"/>
54
- <search_score name="deltacn" value="0.115"/>
55
- <search_score name="deltacnstar" value="0"/>
56
- <search_score name="spscore" value="153.1"/>
57
- <search_score name="sprank" value="2"/>
58
- </search_hit>
59
- </search_result>
60
- <search_result spectrum="000.1004.1004.2" start_scan="1004" end_scan="1004" precursor_neutral_mass="1252.2920" assumed_charge="2" index="5">
61
- <search_hit hit_rank="1" peptide="QLTYTAHGPHK" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|16131568|ref|NP_418155.1|" num_tot_proteins="1" num_matched_ions=" 7" tot_num_ions=" 20" calc_neutral_pep_mass="1252.3920" massdiff="-0.1" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
62
- <search_score name="xcorr" value="1.066"/>
63
- <search_score name="deltacn" value="0.172"/>
64
- <search_score name="deltacnstar" value="0"/>
65
- <search_score name="spscore" value="125.2"/>
66
- <search_score name="sprank" value="10"/>
67
- </search_hit>
68
- </search_result>
69
- <search_result spectrum="000.1004.1004.3" start_scan="1004" end_scan="1004" precursor_neutral_mass="1878.4920" assumed_charge="3" index="6">
70
- <search_hit hit_rank="1" peptide="AGNARVVNSNAMSFLAQK" peptide_prev_aa="K" peptide_next_aa="G" protein="gi|16131337|ref|NP_417922.1|" num_tot_proteins="1" num_matched_ions=" 16" tot_num_ions=" 68" calc_neutral_pep_mass="1878.0920" massdiff="+0.4" num_tol_term="2" num_missed_cleavages="1" is_rejected="0">
71
- <search_score name="xcorr" value="1.370"/>
72
- <search_score name="deltacn" value="0.199"/>
73
- <search_score name="deltacnstar" value="0"/>
74
- <search_score name="spscore" value="245.0"/>
75
- <search_score name="sprank" value="2"/>
76
- </search_hit>
77
- </search_result>
78
- <search_result spectrum="000.1006.1006.2" start_scan="1006" end_scan="1006" precursor_neutral_mass="888.1920" assumed_charge="2" index="7">
79
- <search_hit hit_rank="1" peptide="GNSRDIVK" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|16131041|ref|NP_417618.1|" num_tot_proteins="1" num_matched_ions=" 9" tot_num_ions=" 14" calc_neutral_pep_mass="887.9920" massdiff="+0.2" num_tol_term="2" num_missed_cleavages="-1" is_rejected="0">
80
- <search_score name="xcorr" value="0.982"/>
81
- <search_score name="deltacn" value="0.006"/>
82
- <search_score name="deltacnstar" value="0"/>
83
- <search_score name="spscore" value="267.3"/>
84
- <search_score name="sprank" value="6"/>
85
- </search_hit>
86
- </search_result>
87
- <search_result spectrum="000.1006.1006.3" start_scan="1006" end_scan="1006" precursor_neutral_mass="1332.2920" assumed_charge="3" index="8">
88
- <search_hit hit_rank="1" peptide="MAAGENPAAEMIK" peptide_prev_aa="K" peptide_next_aa="S" protein="gi|16132265|ref|NP_418563.1|" num_tot_proteins="2" num_matched_ions=" 16" tot_num_ions=" 48" calc_neutral_pep_mass="1332.5920" massdiff="-0.3" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
89
- <search_score name="xcorr" value="1.058"/>
90
- <search_score name="deltacn" value="0.191"/>
91
- <search_score name="deltacnstar" value="0"/>
92
- <search_score name="spscore" value="177.5"/>
93
- <search_score name="sprank" value="8"/>
94
- </search_hit>
95
- </search_result>
96
- <search_result spectrum="000.1007.1007.1" start_scan="1007" end_scan="1007" precursor_neutral_mass="867.2920" assumed_charge="1" index="9">
97
- <search_hit hit_rank="1" peptide="GALLHVEK" peptide_prev_aa="K" peptide_next_aa="M" protein="gi|16128020|ref|NP_414567.1|" num_tot_proteins="1" num_matched_ions=" 4" tot_num_ions=" 14" calc_neutral_pep_mass="865.9920" massdiff="+1.3" num_tol_term="2" num_missed_cleavages="-1" is_rejected="0">
98
- <search_score name="xcorr" value="0.467"/>
99
- <search_score name="deltacn" value="0.011"/>
100
- <search_score name="deltacnstar" value="0"/>
101
- <search_score name="spscore" value="39.4"/>
102
- <search_score name="sprank" value="30"/>
103
- </search_hit>
104
- </search_result>
105
- <search_result spectrum="000.1008.1008.2" start_scan="1008" end_scan="1008" precursor_neutral_mass="691.0920" assumed_charge="2" index="10">
106
- <search_hit hit_rank="1" peptide="RLFTR" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|16130457|ref|NP_417027.1|" num_tot_proteins="1" num_matched_ions=" 5" tot_num_ions=" 8" calc_neutral_pep_mass="691.7920" massdiff="-0.7" num_tol_term="2" num_missed_cleavages="-1" is_rejected="0">
107
- <search_score name="xcorr" value="0.903"/>
108
- <search_score name="deltacn" value="0.333"/>
109
- <search_score name="deltacnstar" value="0"/>
110
- <search_score name="spscore" value="172.8"/>
111
- <search_score name="sprank" value="1"/>
112
- </search_hit>
113
- </search_result>
114
- </msms_run_summary>
115
- </msms_pipeline_analysis>