mspire 0.2.4 → 0.3.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (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/messups.fasta ADDED
@@ -0,0 +1,297 @@
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 ADDED
@@ -0,0 +1,101 @@
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 ADDED
@@ -0,0 +1,115 @@
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>