RubyGems - mspire - Versions diffs - 0.2.4 → 0.3.0 - Mend

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

data/INSTALL +1 -0
data/README +25 -0
data/Rakefile +129 -40
data/bin/{find_aa_freq.rb → aafreqs.rb} +2 -2
data/bin/bioworks_to_pepxml.rb +1 -0
data/bin/fasta_shaker.rb +1 -96
data/bin/filter_and_validate.rb +5 -0
data/bin/{mzxml_to_lmat.rb → ms_to_lmat.rb} +8 -7
data/bin/prob_validate.rb +6 -0
data/bin/raw_to_mzXML.rb +2 -2
data/bin/srf_group.rb +1 -0
data/bin/srf_to_sqt.rb +40 -0
data/changelog.txt +68 -0
data/lib/align/chams.rb +6 -6
data/lib/align.rb +4 -3
data/lib/bsearch.rb +120 -0
data/lib/fasta.rb +318 -86
data/lib/group_by.rb +10 -0
data/lib/index_by.rb +11 -0
data/lib/merge_deep.rb +21 -0
data/lib/{spec → ms/converter}/mzxml.rb +77 -109
data/lib/ms/gradient_program.rb +171 -0
data/lib/ms/msrun.rb +209 -0
data/lib/{spec/msrun.rb → ms/msrun_index.rb} +7 -40
data/lib/ms/parser/mzdata/axml.rb +12 -0
data/lib/ms/parser/mzdata/dom.rb +160 -0
data/lib/ms/parser/mzdata/libxml.rb +7 -0
data/lib/ms/parser/mzdata.rb +25 -0
data/lib/ms/parser/mzxml/axml.rb +11 -0
data/lib/ms/parser/mzxml/dom.rb +159 -0
data/lib/ms/parser/mzxml/hpricot.rb +253 -0
data/lib/ms/parser/mzxml/libxml.rb +15 -0
data/lib/ms/parser/mzxml/regexp.rb +122 -0
data/lib/ms/parser/mzxml/rexml.rb +72 -0
data/lib/ms/parser/mzxml/xmlparser.rb +248 -0
data/lib/ms/parser/mzxml.rb +175 -0
data/lib/ms/parser.rb +108 -0
data/lib/ms/precursor.rb +10 -0
data/lib/ms/scan.rb +81 -0
data/lib/ms/spectrum.rb +193 -0
data/lib/ms.rb +10 -0
data/lib/mspire.rb +4 -0
data/lib/roc.rb +61 -1
data/lib/sample_enzyme.rb +31 -8
data/lib/scan_i.rb +21 -0
data/lib/spec_id/aa_freqs.rb +7 -3
data/lib/spec_id/bioworks.rb +20 -14
data/lib/spec_id/digestor.rb +139 -0
data/lib/spec_id/mass.rb +116 -0
data/lib/spec_id/parser/proph.rb +236 -0
data/lib/spec_id/precision/filter/cmdline.rb +209 -0
data/lib/spec_id/precision/filter/interactive.rb +134 -0
data/lib/spec_id/precision/filter/output.rb +147 -0
data/lib/spec_id/precision/filter.rb +623 -0
data/lib/spec_id/precision/output.rb +60 -0
data/lib/spec_id/precision/prob/cmdline.rb +139 -0
data/lib/spec_id/precision/prob/output.rb +88 -0
data/lib/spec_id/precision/prob.rb +171 -0
data/lib/spec_id/proph/pep_summary.rb +92 -0
data/lib/spec_id/proph/prot_summary.rb +484 -0
data/lib/spec_id/proph.rb +2 -466
data/lib/spec_id/protein_summary.rb +2 -2
data/lib/spec_id/sequest/params.rb +316 -0
data/lib/spec_id/sequest/pepxml.rb +1513 -0
data/lib/spec_id/sequest.rb +2 -1672
data/lib/spec_id/srf.rb +445 -177
data/lib/spec_id.rb +183 -95
data/lib/spec_id_xml.rb +8 -10
data/lib/transmem/phobius.rb +147 -0
data/lib/transmem/toppred.rb +368 -0
data/lib/transmem.rb +157 -0
data/lib/validator/aa.rb +135 -0
data/lib/validator/background.rb +73 -0
data/lib/validator/bias.rb +95 -0
data/lib/validator/cmdline.rb +260 -0
data/lib/validator/decoy.rb +94 -0
data/lib/validator/digestion_based.rb +69 -0
data/lib/validator/probability.rb +48 -0
data/lib/validator/prot_from_pep.rb +234 -0
data/lib/validator/transmem.rb +272 -0
data/lib/validator/true_pos.rb +46 -0
data/lib/validator.rb +214 -0
data/lib/xml.rb +38 -0
data/lib/xml_style_parser.rb +105 -0
data/lib/xmlparser_wrapper.rb +19 -0
data/script/compile_and_plot_smriti_final.rb +97 -0
data/script/extract_gradient_programs.rb +56 -0
data/script/get_apex_values_rexml.rb +44 -0
data/script/mzXML2timeIndex.rb +1 -1
data/script/smriti_final_analysis.rb +103 -0
data/script/toppred_to_yaml.rb +47 -0
data/script/tpp_installer.rb +1 -1
data/{test/tc_align.rb → specs/align_spec.rb} +21 -27
data/{test/tc_bioworks_to_pepxml.rb → specs/bin/bioworks_to_pepxml_spec.rb} +25 -41
data/specs/bin/fasta_shaker_spec.rb +259 -0
data/specs/bin/filter_and_validate__multiple_vals_helper.yaml +202 -0
data/specs/bin/filter_and_validate_spec.rb +124 -0
data/specs/bin/ms_to_lmat_spec.rb +34 -0
data/specs/bin/prob_validate_spec.rb +62 -0
data/specs/bin/protein_summary_spec.rb +10 -0
data/{test/tc_fasta.rb → specs/fasta_spec.rb} +354 -310
data/specs/gi_spec.rb +22 -0
data/specs/load_bin_path.rb +7 -0
data/specs/merge_deep_spec.rb +13 -0
data/specs/ms/gradient_program_spec.rb +77 -0
data/specs/ms/msrun_spec.rb +455 -0
data/specs/ms/parser_spec.rb +92 -0
data/specs/ms/spectrum_spec.rb +89 -0
data/specs/roc_spec.rb +251 -0
data/specs/rspec_autotest.rb +149 -0
data/specs/sample_enzyme_spec.rb +41 -0
data/specs/spec_helper.rb +133 -0
data/specs/spec_id/aa_freqs_spec.rb +52 -0
data/{test/tc_bioworks.rb → specs/spec_id/bioworks_spec.rb} +56 -71
data/specs/spec_id/digestor_spec.rb +75 -0
data/specs/spec_id/precision/filter/cmdline_spec.rb +20 -0
data/specs/spec_id/precision/filter/output_spec.rb +31 -0
data/specs/spec_id/precision/filter_spec.rb +243 -0
data/specs/spec_id/precision/prob_spec.rb +111 -0
data/specs/spec_id/precision/prob_spec_helper.rb +0 -0
data/specs/spec_id/proph/pep_summary_spec.rb +143 -0
data/{test/tc_proph.rb → specs/spec_id/proph/prot_summary_spec.rb} +52 -32
data/{test/tc_protein_summary.rb → specs/spec_id/protein_summary_spec.rb} +85 -0
data/specs/spec_id/sequest/params_spec.rb +68 -0
data/specs/spec_id/sequest/pepxml_spec.rb +452 -0
data/specs/spec_id/sqt_spec.rb +138 -0
data/specs/spec_id/srf_spec.rb +209 -0
data/specs/spec_id/srf_spec_helper.rb +302 -0
data/specs/spec_id_helper.rb +33 -0
data/specs/spec_id_spec.rb +361 -0
data/specs/spec_id_xml_spec.rb +33 -0
data/specs/transmem/phobius_spec.rb +423 -0
data/specs/transmem/toppred_spec.rb +297 -0
data/specs/transmem_spec.rb +60 -0
data/specs/transmem_spec_shared.rb +64 -0
data/specs/validator/aa_spec.rb +107 -0
data/specs/validator/background_spec.rb +51 -0
data/specs/validator/bias_spec.rb +146 -0
data/specs/validator/decoy_spec.rb +51 -0
data/specs/validator/fasta_helper.rb +26 -0
data/specs/validator/prot_from_pep_spec.rb +141 -0
data/specs/validator/transmem_spec.rb +145 -0
data/specs/validator/true_pos_spec.rb +58 -0
data/specs/validator_helper.rb +33 -0
data/specs/xml_spec.rb +12 -0
data/test_files/000_pepxml18_small.xml +206 -0
data/test_files/020a.mzXML.timeIndex +4710 -0
data/test_files/4-03-03_mzXML/000.mzXML.timeIndex +3973 -0
data/test_files/4-03-03_mzXML/020.mzXML.timeIndex +3872 -0
data/test_files/4-03-03_small-prot.xml +321 -0
data/test_files/4-03-03_small.xml +3876 -0
data/test_files/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
data/test_files/bioworks-3.3_10prots.xml +5999 -0
data/test_files/bioworks31.params +77 -0
data/test_files/bioworks32.params +62 -0
data/test_files/bioworks33.params +63 -0
data/test_files/bioworks_single_run_small.xml +7237 -0
data/test_files/bioworks_small.fasta +212 -0
data/test_files/bioworks_small.params +63 -0
data/test_files/bioworks_small.phobius +109 -0
data/test_files/bioworks_small.toppred.out +2847 -0
data/test_files/bioworks_small.xml +5610 -0
data/test_files/bioworks_with_INV_small.xml +3753 -0
data/test_files/bioworks_with_SHUFF_small.xml +2503 -0
data/test_files/corrupted_900.srf +0 -0
data/test_files/head_of_7MIX.srf +0 -0
data/test_files/interact-opd1_mods_small-prot.xml +304 -0
data/test_files/messups.fasta +297 -0
data/test_files/opd1/000.my_answer.100lines.xml +101 -0
data/test_files/opd1/000.tpp_1.2.3.first10.xml +115 -0
data/test_files/opd1/000.tpp_2.9.2.first10.xml +126 -0
data/test_files/opd1/000.v2.1.mzXML.timeIndex +3748 -0
data/test_files/opd1/000_020-prot.png +0 -0
data/test_files/opd1/000_020_3prots-prot.mod_initprob.xml +62 -0
data/test_files/opd1/000_020_3prots-prot.xml +62 -0
data/test_files/opd1/opd1_cat_inv_small-prot.xml +139 -0
data/test_files/opd1/sequest.3.1.params +77 -0
data/test_files/opd1/sequest.3.2.params +62 -0
data/test_files/opd1/twenty_scans.mzXML +418 -0
data/test_files/opd1/twenty_scans.v2.1.mzXML +382 -0
data/test_files/opd1/twenty_scans_answ.lmat +0 -0
data/test_files/opd1/twenty_scans_answ.lmata +9 -0
data/test_files/opd1_020_beginning.RAW +0 -0
data/test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml +753 -0
data/test_files/orbitrap_mzData/000_cut.xml +1920 -0
data/test_files/pepproph_small.xml +4691 -0
data/test_files/phobius.small.noheader.txt +50 -0
data/test_files/phobius.small.small.txt +53 -0
data/test_files/s01_anC1_ld020mM.key.txt +25 -0
data/test_files/s01_anC1_ld020mM.meth +0 -0
data/test_files/small.fasta +297 -0
data/test_files/smallraw.RAW +0 -0
data/test_files/tf_bioworks2excel.bioXML +14340 -0
data/test_files/tf_bioworks2excel.txt.actual +1035 -0
data/test_files/toppred.small.out +416 -0
data/test_files/toppred.xml.out +318 -0
data/test_files/validator_hits_separate/bias_bioworks_small_HS.fasta +7 -0
data/test_files/validator_hits_separate/bioworks_small_HS.xml +5651 -0
data/test_files/yeast_gly_small-prot.xml +265 -0
data/test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes +6 -0
data/test_files/yeast_gly_small.xml +3807 -0
data/test_files/yeast_gly_small2.parentTimes +6 -0
metadata +273 -57
data/bin/filter.rb +0 -6
data/bin/precision.rb +0 -5
data/lib/spec/mzdata/parser.rb +0 -108
data/lib/spec/mzdata.rb +0 -48
data/lib/spec/mzxml/parser.rb +0 -449
data/lib/spec/scan.rb +0 -55
data/lib/spec_id/filter.rb +0 -797
data/lib/spec_id/precision.rb +0 -421
data/lib/toppred.rb +0 -18
data/script/filter-peps.rb +0 -164
data/test/tc_aa_freqs.rb +0 -59
data/test/tc_fasta_shaker.rb +0 -149
data/test/tc_filter.rb +0 -203
data/test/tc_filter_peps.rb +0 -46
data/test/tc_gi.rb +0 -17
data/test/tc_id_class_anal.rb +0 -70
data/test/tc_id_precision.rb +0 -89
data/test/tc_msrun.rb +0 -88
data/test/tc_mzxml.rb +0 -88
data/test/tc_mzxml_to_lmat.rb +0 -36
data/test/tc_peptide_parent_times.rb +0 -27
data/test/tc_precision.rb +0 -60
data/test/tc_roc.rb +0 -166
data/test/tc_sample_enzyme.rb +0 -32
data/test/tc_scan.rb +0 -26
data/test/tc_sequest.rb +0 -336
data/test/tc_spec.rb +0 -78
data/test/tc_spec_id.rb +0 -201
data/test/tc_spec_id_xml.rb +0 -36
data/test/tc_srf.rb +0 -262

data/test_files/bioworks_small.fasta ADDED Viewed

@@ -0,0 +1,212 @@
+>gi|49175991|ref|YP_025292.1| small toxic membrane polypeptide [Escherichia coli K12]
+MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVFTAYESE
+>gi|16128018|ref|NP_414565.1| unknown CDS [Escherichia coli K12]
+MCRHSLRSDGAGFYQLAGCEYSFSAIKIAAGGQFLPVICAMAMKSHFFLISVLNRRLTLTAVQGILGRFSLF
+>gi|16128024|ref|NP_414571.1| nucleoside hydrolase [Escherichia coli K12]
+MRLPIFLDTDPGIDDAVAIAAAIFAPELDLQLMTTVAGNVSVEKTTRNALQLLHFWNAEIPLAQGAAVPLVRAPRDAASVHGESGMAGYDFVEHNRKPLGIPAFLAIRDALMRAPEPVTLVAIGPLTNIALLLSQCPECKPYIRRLVIMGGSAGRGNCTPNAEFNIAADPEAAACVFRSGIEIVMCGLDVTNQAILTPDYLSTLPQLNRTGKMLHALFSHYRSGSMQSGLRMHDLCAIAWLVRPDLFTLKPCFVAVETQGEFTSGTTVVDIDGCLGKPANVQVALDLDVKGFQQWVAEVLALAS
+>gi|16128058|ref|NP_414606.1| transcriptional regulator for ara operon [Escherichia coli K12]
+MAEAQNDPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLLLRRMEAINESLHPPMDNRVREACQYISDHLADSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFRAGCEEKVNDVAVKLS
+>gi|16128092|ref|NP_414641.1| 7,8-dihydro-8-oxoguanine-triphosphatase, prefers dGTP [Escherichia coli K12]
+MKKLQIAVGIIRNENNEIFITRRAADAHMANKLEFPGGKIEMGETPEQAVVRELQEEVGITPQHFSLFEKLEYEFPDRHITLWFWLVERWEGEPWGKEGQPGEWMSLVGLNADDFPPANEPVIAKLKRL
+>gi|16128121|ref|NP_414670.1| putative transport protein (ABC superfamily, membrane) [Escherichia coli K12]
+MMHLYWVALKSIWAKEIHRFMRIWVQTLVPPVITMTLYFIIFGNLIGSRIGDMHGFSYMQFIVPGLIMMSVITNAYANVASSFFGAKFQRNIEELLVAPVPTHVIIAGYVGGGVARGLFVGILVTAISLFFVPFQVHSWVFVALTLVLTAVLFSLAGLLNGVFAKTFDDISLVPTFVLTPLTYLGGVFYSLTLLPPFWQGLSHLNPIVYMISGFRYGFLGINDVPLVTTFGVLVVFIVAFYLICWSLIQRGRGLRS
+>gi|90111097|ref|NP_414731.2| modulator of Rho-dependent transcription termination [Escherichia coli K12]
+MNDTYQPINCDDYDNLELACQHHLMLTLELKDGEKLQAKASDLVSRKNVEYLVVEAAGETRELRLDKITSFSHPEIGTVVVSES
+>gi|16128191|ref|NP_414740.1| D- and L-methionine transport protein (ABC superfamily, membrane) [Escherichia coli K12]
+MSEPMMWLLVRGVWETLAMTFVSGFFGFVIGLPVGVLLYVTRPGQIIANAKLYRTVSAIVNIFRSIPFIILLVWMIPFTRVIVGTSIGLQAAIVPLTVGAAPFIARMVENALLEIPTGLIEASRAMGATPMQIVRKVLLPEALPGLVNAATITLITLVGYSAMGGAVGAGGLGQIGYQYGYIGYNATVMNTVLVLLVILVYLIQFAGDRIVRAVTRK
+>gi|16128232|ref|NP_414781.1| CP4-6 prophage; putative DNA repair protein [Escherichia coli K12]
+MKQLSFLPGEMTPQDRRLIQRALRALDRHLHEPGVAFTSTHAVREWLRLHMAALEREEFRVLYLDNQNQLIAHETLFTGTINRTEVHPREVVKRALHFNAAAVILAHNHPSGETTPSQADKTLTQRLVQVLQLVDIRVPDHLIVGGRQIYSFAEHGLL
+>gi|16128248|ref|NP_414797.1| CP4-6 prophage; putative membrane component of ferric transport system [Escherichia coli K12]
+MESLPGQIDKSLDEASLSLRAGSLRTITHILLPLLRPAILSALIYSFVRAITTVSAIVFLVTPDTRVATAYILNRVEDGEYGVAIAYGSILIVVMLAIIFIFDWLIGESRTSRSKAKNQA
+>gi|90111117|ref|NP_414887.2| putative 3-hydroxyphenylpropionic transport protein (MFS family) [Escherichia coli K12]
+MSTRTPSSSSSRLMLTIGLCFLVALMEGLDLQAAGIAAGGIAQAFALDKMQMGWIFSAGILGLLPGALVGGMLADRYGRKRILIGSVALFGLFSLATAIAWDFPSLVFARLMTGVGLGAALPNLIALTSEAAGPRFRGTAVSLMYCGVPIGAALAATLGFAGANLAWQTVFWVGGVVPLILVPLLMRWLPESAVFAGEKQSAPPLRALFAPETATATLLLWLCYFFTLLVVYMLINWLPLLLVEQGFQPSQAAGVMFALQMGAASGTLMLGALMDKLRPVTMSLLIYSGMLASLLALGTVSSFNGMLLAGFVAGLFATGGQSVLYALAPLFYSSQIRATGVGTAVAVGRLGAMSGPLLAGKMLALGTGTVGVMAASAPGILVAGLAVFILMSRRSRIQPCADA
+>gi|16128374|ref|NP_414923.1| unknown CDS [Escherichia coli K12]
+MPTKPPYPREAYIVTIEKGKPGQTVTWYQLRADHPKPDSLISEHPTAQEAMDAKKRYEDPDKE
+>gi|16128403|ref|NP_414952.1| phosphatidylglycerophosphatase [Escherichia coli K12]
+MTILPRHKDVAKSRLKMSNPWHLLAVGFGSGLSPIVPGTMGSLAAIPFWYLMTFLPWQLYSLVVMLGICIGVYLCHQTAKDMGVHDHGSIVWDEFIGMWITLMALPTNDWQWVAAGFVIFRILDMWKPWPIRWFDRNVHGGMGIMIDDIVAGVISAGILYFIGHHWPLGILS
+>gi|16128443|ref|NP_414992.1| maltose O-acetyltransferase [Escherichia coli K12]
+MSTEKEKMIAGELYRSADETLSRDRLRARQLIHRYNHSLAEEHTLRQQILADLFGQVTEAYIEPTFRCDYGYNIFLGNNFFANFDCVMLDVCPIRIGDNCMLAPGVHIYTATHPIDPVARNSGAELGKPVTIGNNVWIGGRAVINPGVTIGDNVVVASGAVVTKDVPDNVVVGGNPARIIKKL
+>gi|16128499|ref|NP_415048.1| hypothetical protein b0515 [Escherichia coli K12]
+MGYLNNVTGYREDLLANRAIVKHGNFALLTPDGLVKNIIPGFENCDATILSTPKLGASFVDYLVTLHQNGGNQQGFGGEGIETFLYVISGNITAKAEGKTFALSEGGYLYCPPGSLMTFVNAQAEDSQIFLYKRRYVPVEGYAPWLVSGNASELERIHYEGMDDVILLDFLPKELGFDMNMHILSFAPGASHGYIETHVQEHGAYILSGQGVYNLDNNWIPVKKGDYIFMGAYSLQAGYGVGRGEAFSYIYSKDCNRDVEI
+>gi|16128537|ref|NP_415086.1| DLP12 prophage; putative lysis protein S, homolog of Rz of phage PA-2 [Escherichia coli K12]
+MKSMDKLTTGVAYGTSAGSAGYWFLQLLDKVTPSQWAAIGVLGSLVFGLLTYLTNLYFKIKEDKRKAARGE
+>gi|49176035|ref|YP_025295.1| small toxic membrane polypeptide [Escherichia coli K12]
+MLTKYALAAVIVLCLTVLGFTLLVGDSLCEFTVKERNIEFKAVLAYEPKK
+>gi|16128614|ref|NP_415164.1| hypothetical protein b0631 [Escherichia coli K12]
+MKTKLNELLEFPTPFTYKVMGQALPELVDQVVEVVQRHAPGDYTPTVKPSSKGNYHSVSITINATHIEQVETLYEELGKIDIVRMVL
+>gi|16128621|ref|NP_415171.1| homolog of Salmonella cobC, a phosphohistidine protein [Escherichia coli K12]
+MRLWLIRHGETQANIDGLYSGHAPTPLTARGIEQAQNLHTLLHGVSFDLVLCSELERAQHTARLVLSDRQLPVQIIPELNEMFFGDWEMRHHRDLMQEDAENYSAWCNDWQHAIPTNGEGFQAFSQRVERFIARLSEFQHYQNILVVSHQGVLSLLIARLIGMPAEAMWHFRVDQGCWSAIDINQKFATLRVLNSRAIGVENA
+>gi|16128710|ref|NP_415263.1| hypothetical protein b0735 [Escherichia coli K12]
+MSKIIATLYAVMDKRPLRALSFVMALLLAGCMFWDPSRFAAKTSELEIWHGLLLMWAVCAGVIHGVGFRPQKVLWQGIFCPLLADIVLIVGLIFFFF
+>gi|90111171|ref|NP_415327.2| hypothetical protein b0806 [Escherichia coli K12]
+MKKCLTLLIATVLSGISLTAYAAQPMSNLDSGQLRPAGTVSATGASNLSDLEDKLAEKAREQGAKGYVINSAGGNDQMFGTATIYK
+>gi|16128811|ref|NP_415364.1| unknown CDS [Escherichia coli K12]
+MIMKNCLLLGALLMGFTGVAMAQSVTVDVPSGYKVVVVPDSVSVPQAVSVATVPQTVYVAPAPAPAYRPHPYVRHLASVGEGMVIEHQIDDHHH
+>gi|16128871|ref|NP_415424.1| formate transport protein (formate channel 1) (FNT family) [Escherichia coli K12]
+MKADNPFDLLLPAAMAKVAEEAGVYKATKHPLKTFYLAITAGVFISIAFVFYITATTGTGTMPFGMAKLVGGICFSLGLILCVVCGADLFTSTVLIVVAKASGRITWGQLAKNWLNVYFGNLVGALLFVLLMWLSGEYMTANGQWGLNVLQTADHKVHHTFIEAVCLGILANLMVCLAVWMSYSGRSLMDKAFIMVLPVAMFVASGFEHSIANMFMIPMGIVIRDFASPEFWTAVGSAPENFSHLTVMNFITDNLIPVTIGNIIGGGLLVGLTYWVIYLRENDHH
+>gi|90111191|ref|NP_415463.2| putative fimbrial-like protein [Escherichia coli K12]
+MLKRIIWILFLLGLTWGCELFAHDGTVNISGSFRRNTCVLAQDSKQINVQLGDVSLTRFSHGNYGPEKSFIINLQDCGTDVSTVDVTFSGTPDGVQSEMLSIESGTDAASGLAIAILDDAKILIPLNQASKDYSLHSGKVPLTFYAQLRPVNSDVQSGKVNASATFVLHYD
+>gi|90111193|ref|NP_415466.4| hypothetical protein b0946 [Escherichia coli K12]
+MRIKPDDNWRWYYDEEHDRMMLDLANGMLFRSRFARKMLTPDAFSPAGFCVDDAALYFSFEEKCRDFNLSKEQKAELVLNALVAIRYLKPQMPKSWHFVSHGEMWVPMPGDAACVWLSDTHEQVNLLVVESGENAALCLLAQPCVVIAGRAMQLGDAIKIMNDRLKPQVNVDSFSLEQAV
+>gi|16128957|ref|NP_415511.1| suppresses fabA and ts growth mutation [Escherichia coli K12]
+MRRWISQNNIRLPRGAFFISALFFFNAVCIVSDNLLIIESFGEMAYNISYLTRVPGTNTLLACCCLLRPEEVNSEY
+>gi|16128974|ref|NP_415528.1| hypothetical protein b1008 [Escherichia coli K12]
+MNEAVSPGALSTLFTDARTHNGWRETPVSDETLREIYALMKWGPTSANCSPARIVFTRTAEGKERLRPALSSGNLQKTLTAPVTAIVAWDSEFYERLPLLFPHGDARSWFTSSPQLAEETAFRNSSMQAAYLIVACRALGLDTGPMSGFDRQHVDDAFFTGSTLKSNLLINIGYGDSSKLYARLPRLSFEEACGLL
+>gi|16129015|ref|NP_415570.1| unknown CDS [Escherichia coli K12]
+MEQSTSSSNTPGIELIFRLSYLQKRRISYPFP
+>gi|16129146|ref|NP_415701.1| SOS mutagenesis; error-prone repair; processed to UmuD'; forms complex with UmuC [Escherichia coli K12]
+MLFIKPADLREIVTFPLFSDLVQCGFPSPAADYVEQRIDLNQLLIQHPSATYFVKASGDSMIDGGISDGDLLIVDSAITASHGDIVIAAVDGEFTVKKLQLRPTVQLIPMNSAYSPITISSEDTLDVFGVVIHVVKAMR
+>gi|16129250|ref|NP_415805.1| hypothetical protein b1289 [Escherichia coli K12]
+MIDKIKSNARDLRRNLTLQERKLWRYLRSRRFSDFKFRRQHPVGSYILDFACCSARVVVELDGGQHDLAVAYDSRRTSWLESQGWTVLRFWNNEIDCNEETVLENILQELNRRSPSP
+>gi|16129266|ref|NP_415821.1| phage shock protein B [Escherichia coli K12]
+MSALFLAIPLTIFVLFVLPIWLWLHYSNRSGRSELSQSEQQRLAQLADEAKRMRERIQALESILDAEHPNWRDR
+>gi|16129267|ref|NP_415822.1| phage shock protein: activates phage shock-protein expression [Escherichia coli K12]
+MAGINLNKKLWRIPQQGMVRGVCAGIANYFDVPVKLVRILVVLSIFFGLALFTLVAYIILSFALDPMPDNMAFGEQLPSSSELLDEVDRELAASETRLREMERYVTSDTFTLRSRFRQL
+>gi|16129318|ref|NP_415875.1| Rac prophage; repressor protein [Escherichia coli K12]
+MKKENYSFKQACAVVGGQSAMARLLGVSPPSVNQWIKGVRQLPAERCPAIERATRGEVLCEELRPDIDWSYLRRSACCSQNMSVKQLNDSNKSSFDHT
+>gi|90111262|ref|NP_415894.4| conserved hypothetical protein, adenine nucleotide-binding domain [Escherichia coli K12]
+MNRTILVPIDISDSELTQRVISHVEEEAKIDDAEVHFLTVIPSLPYYASLGLAYSAELPAMDDLKAEAKSQLEEIIKKFKLPTDRVHVHVEEGSPKDRILELAKKIPAHMIIIASHRPDITTYLLGSNAAAVVRHAECSVLVVR
+>gi|16129357|ref|NP_415914.1| phenylacetic acid degradation protein [Escherichia coli K12]
+MSHKAWQNAHAMYENDACAKALGIDIISMDEGFAVVTMTVTAQMLNGHQSCHGGQLFSLADTAFAYACNSQGLAAVASACTIDFLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVNQQQKTVALFRGKSHRIGGTITGEA
+>gi|90111267|ref|NP_415926.4| putative enzyme [Escherichia coli K12]
+MTLYQIKPLFQSLLRPTMFWLYKHHVTANHITLAALALSLLTGLLLMLAAQPILFLLLPIVLFIRMALNALDGMLARECNQQTRLGAILNETGDVISDIALYLPFLFLPESNASLVILMLFCTILTEFCGLLAQTINGVRSYAGPFGKSDRALIFGLWGLAVAIYPQWMQWNNLLWSIASILLLWTAINRCRSVLLMSAEI
+>gi|16129388|ref|NP_415946.1| K+-tellurite ethidium and proflavin transport protein (TDT family) [Escherichia coli K12]
+MQSDKVLNLPAGYFGIVLGTIGMGFAWRYASQVWQVSHWLGDGLVILAMIIWGLLTSAFIARLIRFPHSVLAEVRHPVLSSFVSLFPATTMLVAIGFVPWFRPLAVCLFSFGVVVQLAYAAWQTAGLWRGSHPEEATTPGLYLPTVANNFISAMACGALGYTDAGLVFLGAGVFSWLSLEPVILQRLRSSGELPTALRTSLGIQLAPALVACSAWLSVNGGEGDTLAKMLFGYGLLQLLFMLRLMPWYLSQPFNASFWSFSFGVSALATTGLHLGSGSDNGFFHTLAVPLFIFTNFIIAILLIRTFALLMQGKLLVRTERAVLMKAEDKE
+>gi|16129463|ref|NP_416021.1| putative fimbrial-like protein [Escherichia coli K12]
+MKYNNIIFLGLCLGLTTYSALSADSVIKISGRVLDYGCTVSSDSLNFTVDLQKNSARQFPTTGSTSPAVPFQITLSECSKGTTGVRVAFNGIEDAENNTLLKLDEGSNTASGLGIEILDANMRPVKLNDLHAGMQWIPLVPEQNNILPYSARLKSTQKSVNPGLVRASATFTLEFQ
+>gi|16129488|ref|NP_416046.1| multiple antibiotic resistance protein [Escherichia coli K12]
+MLDLFKAIGLGLVVLLPLANPLTTVALFLGLAGNMNSAERNRQSLMASVYVFAIMMVAYYAGQLVMDTFGISIPGLRIAGGLIVAFIGFRMLFPQQKAIDSPEAKSKSEELEDEPSANIAFVPLAMPSTAGPGTIAMIISSASTVRQSSTFADWVLMVAPPLIFFLVAVILWGSLRSSGAIMRLVGKGGIEAISRLMGFLLVCMGVQFIINGILEIIKTYH
+>gi|90111295|ref|NP_416074.4| Qin prophage [Escherichia coli K12]
+MKSMDKLTTGVAYGTSAGNAGFWALQLLDKVTPSQWAAIGVLGSLVFGLLTYLTNLYFKIKEDRRKAARGE
+>gi|16129540|ref|NP_416099.1| hypothetical protein b1582 [Escherichia coli K12]
+MIKTTLLFFATALCEIIGCFLPWLWLKRNASIWLLLPAGISLALFVWLLTLHPAASGRVYAAYGGVYVCTALMWLRVVDGVKLTLYDWTGALIALCGMLIIVAGWGRT
+>gi|90111300|ref|NP_416103.2| hypothetical protein b1586 [Escherichia coli K12]
+MKLSTCCAALLLALASPAVLAAPGSCERIQSDISQRIINNGVPESSFTLSIVPNDQVDQPDSQVVGHCANDTHKILYTRTTSGNVSAPAQSSQDGAPAEPQ
+>gi|90111309|ref|NP_416156.4| hypothetical protein b1639 [Escherichia coli K12]
+MTMKKLLIIILPVLLSGCSAFNQLVERMQTDTLEYQCDEKPLTVKLNNPRQEVSFVYDNQLLHLKQGISASGARYTDGIYVFWSKGDEATVYKRDRIVLNNCQLQNPQR
+>gi|90111313|ref|NP_416166.2| hypothetical transcriptional regulator [Escherichia coli K12]
+MGLSELLKTAEVPKGSFYHYFRSKEAFGVAMLERHYAAYHQRLTELLQSGEGNYRDRILAYYQQTLNQFCQHGTISGCLTVKLSAEVCDLSEDMRSAMDKGARGVIALLSQALENGRENHCLTFCGEPLQQAQVLYALWLGANLQAKISRSFEPLENALAHVKNIIATPAV
+>gi|16129623|ref|NP_416182.1| protein ofunknown function [Escherichia coli K12]
+MATLLQLHFAFNGPFGDAMAEQLKPLAESINQEPGFLWKVWTESEKNHEAGGIYLFTDEKSALAYLEKHTARLKNLGVEEVVAKVFDVNEPLSQINQAKLA
+>gi|16129732|ref|NP_416292.1| methionine sulfoxide reductase B [Escherichia coli K12]
+MANKPSAEELKKNLSEMQFYVTQNHGTEPPFTGRLLHNKRDGVYHCLICDAPLFHSQTKYDSGCGWPSFYEPVSEESIRYIKDLSHGMQRIEIRCGNCDAHLGHVFPDGPQPTGERYCVNSASLRFTDGENGEEING
+>gi|90111344|ref|NP_416352.4| protein phosphatase 1 [Escherichia coli K12]
+MKQPAPVYQRIAGHQWRHIWLSGDIHGCLEQLRRKLWHCRFDPWRDLLISVGDVIDRGPQSLRCLQLLEQHWVCAVRGNHEQMAMDALASQQMSLWLMNGGDWFIALADNQQKQAKTALEKCQHLPFILEVHSRTGKHVIAHADYPDDVYEWQKDVDLHQVLWSRSRLGERQKGQGITGADHFWFGHTPLRHRVDIGNLHYIDTGAVFGGELTLVQLQ
+>gi|90111352|ref|NP_416389.4| hypothetical protein b1875 [Escherichia coli K12]
+MANWQSIDELQDIASDLPRFIHALDELSRRLGLNITPLTADHISLRCHQNATAERWRRGFEQCGELLSENMINGRPICLFKLHEPVQVAHWQFSIVELPWPGEKRYPHEGWEHIEIVLPGDPETLNARALALLSDEGLSLPGISVKTSSPKGEHERLPNPTLAVTDGKTTIKFHPWSIEEIVASEQSA
+>gi|16129855|ref|NP_416418.1| cytoplasmic ferritin (an iron storage protein) [Escherichia coli K12]
+MLKPEMIEKLNEQMNLELYSSLLYQQMSAWCSYHTFEGAAAFLRRHAQEEMTHMQRLFDYLTDTGNLPRINTVESPFAEYSSLDELFQETYKHEQLITQKINELAHAAMTNQDYPTFNFLQWYVSEQHEEEKLFKSIIDKLSLAGKSGEGLYFIDKELSTLDTQN
+>gi|16129862|ref|NP_416425.1| unknown CDS [Escherichia coli K12]
+MSTPDFSTAENNQELANEVSCLKAMLTLMLQAMGQADAGRVMLKMEKQLALIEDETQAAVFSKTVKQIKQAYRQ
+>gi|16129891|ref|NP_416454.1| flagellar biosynthesis protein [Escherichia coli K12]
+MTDYAISKKSKRSLWIPILVFITLAACASAGYSYWHSHQVAADDKAQQRVVPSPVFYALDTFTVNLGDADRVLYIGITLRLKDEATRSRLSEYLPEVRSRLLLLFSRQDAAVLATEEGKKNLIAEIKTTLSTPLVAGQPKQDVTDVLYTAFILR
+>gi|90111376|ref|NP_416555.2| GDP-mannose mannosyl hydrolase [Escherichia coli K12]
+MFLRQEDFATVVRSTPLVSLDFIVENSRGEFLLGKRTNRPAQGYWFVPGGRVQKDETLEAAFERLTMAELGLRLPITAGQFYGVWQHFYDDNFSGTDFTTHYVVLGFRFRVSEEELLLPDEQHDDYRWLTSDALLASDNVHANSRAYFLAEKRTGVPGL
+>gi|16130023|ref|NP_416587.1| putative phage protein (D protein) [Escherichia coli K12]
+MSGFKRVIDEQDWTITKVTHFLNNSGFTTSLELEVRLSDVGYETEDNE
+>gi|16130042|ref|NP_416607.1| hydroxyethylthiazole kinase [Escherichia coli K12]
+MQVDLLGSAQSAHALHLFHQHSPLVHCMTNDVVQTFTANTLLALGASPAMVIETEEASQFAAIASALLINVGTLTQPRAQAMRAAVEQAKSSQTPWTLDPVAVGALDYRRHFCHELLSFKPAAIRGNASEIMALAGIANGGRGVDTTDAAANAIPAAQTLARETGAIVVVTGEMDYVTDGHRIIGIHGGDPLMTKVVGTGCALSAVVAACCALPGDTLENVASACHWMKQAGERAVARSEGPGSFVPHFLDALWQLTQEVQA
+>gi|16130217|ref|NP_416785.1| NADH dehydrogenase subunit H [Escherichia coli K12]
+MSWISPELIEILLTILKAVVILLVVVTCGAFMSFGERRLLGLFQNRYGPNRVGWGGSLQLVADMIKMFFKEDWIPKFSDRVIFTLAPMIAFTSLLLAFAIVPVSPGWVVADLNIGILFFLMMAGLAVYAVLFAGWSSNNKYSLLGAMRASAQTLSYEVFLGLSLMGVVAQAGSFNMTDIVNSQAHVWNVIPQFFGFITFAIAGVAVCHRHPFDQPEAEQELADGYHIEYSGMKFGLFFVGEYIGIVTISALMVTLFFGGWQGPLLPPFIWFALKTAFFMMMFILIRASLPRPRYDQVMSFGWKICLPLTLINLLVTAAVILWQAQ
+>gi|16130268|ref|NP_416836.1| putative fimbrial-like protein [Escherichia coli K12]
+MNKSMIQSGGYVLLAGLILAMSSTLFAADNNLHFSGNLLSKSCALVVDGQYLAEVRFPTVSRQDLNVAGQSARVPVVFKLKDCKGPAGYNVKVTLTGVEDSEQPGFLALDTSSTAQGVGIGMEKTDGMQVAINNTNGATFALTNGNNDINFRAWLQAKSGRDVTIGEFTASLTATFEYI
+>gi|16130299|ref|NP_416868.1| multidrug resistance protein Y [Escherichia coli K12]
+MAITKSTPAPLTGGTLWCVTIALSLATFMQMLDSTISNVAIPTISGFLGASTDEGTWVITSFGVANAIAIPVTGRLAQRIGELRLFLLSVTFFSLSSLMCSLSTNLDVLIFFRVVQGLMAGPLIPLSQSLLLRNYPPEKRTFALALWSMTVIIAPICGPILGGYICDNFSWGWIFLINVPMGIIVLTLCLTLLKGRETETSPVKMNLPGLTLLVLGVGGLQIMLDKGRDLDWFNSSTIIILTVVSVISLISLVIWESTSENPILDLSLFKSRNFTIGIVSITCAYLFYSGAIVLMPQLLQETMGYNAIWAGLAYAPIGIMPLLISPLIGRYGNKIDMRLLVTFSFLMYAVCYYWRSVTFMPTIDFTGIILPQFFQGFAVACFFLPLTTISFSGLPDNKFANASSMSNFFRTLSGSVGTSLTMTLWGRRESLHHSQLTATIDQFNPVFNSSSQIMDKYYGSLSGVLNEINNEITQQSLSISANEIFRMAAIAFILLTVLVWFAKPPFTAKGVG
+>gi|90111436|ref|NP_416933.4| putative carboxysome structural protein, ethanolamine utilization [Escherichia coli K12]
+MINALGLLEVDGMVAAIDAADAMLKAANVRLLSHEVLDPGRLTLVVEGDLAACRAALDAGCAAAMRTGRVISRKEIGRPDDDTQWLVTGFNRQPKQPVREPDAPVIVAESADELLALLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSAGTLRKRSSRYRLKPH
+>gi|90111440|ref|NP_416957.4| putative carboxysome structural protein, ethanol utilization [Escherichia coli K12]
+MDKERIIQEFVPGKQVTLAHLIAHPGEELAKKIGVPDAGAIGIMTLTPGETAMIAGDLALKAADVHIGFLDRFSGALVIYGSVGAVEEALSQTVSGLGRLLNYTLCEMTKS
+>gi|90111445|ref|NP_416978.4| hydrogenase 4 membrane subunit [Escherichia coli K12]
+MRQTLCDGYLVIFALAQAVILLMLTPLFTGISRQIRARMHSRRGPGIWQDYRDIHKLFKRQEVAPTSSGLMFRLMPWVLISSMLVLAMALPLFITVSPFAGGGDLITLIYLLALFRFFFALSGLDTGSPFAGVGASRELTLGILVEPMLILSLLVLALIAGSTHIEMISNTLAMGWNSPLTTVLALLACGFACFIEMGKIPFDVAEAEQELQEGPLTEYSGAGLALAKWGLGLKQVVMASLFVALFLPFGRAQELSLACLLTSLVVTLLKVLLIFVLASIAENTLARGRFLLIHHVTWLGFSLAALAWVFWLTGL
+>gi|16130429|ref|NP_416999.1| unknown CDS [Escherichia coli K12]
+MSQATSMRKRHRFNSRMTRIVLLISFIFFFGRFIYSSVGAWQHHQSKKEAQQSTLSVESPVQR
+>gi|16130443|ref|NP_417013.1| nucleoside diphosphate kinase [Escherichia coli K12]
+MAIERTFSIIKPNAVAKNVIGNIFARFEAAGFKIVGTKMLHLTVEQARGFYAEHDGKPFFDGLVEFMTSGPIVVSVLEGENAVQRHRDLLGATNPANALAGTLRADYADSLTENGTHGSDSVESAAREIAYFFGEGEVCPRTR
+>gi|16130511|ref|NP_417081.1| hypothetical protein b2586 [Escherichia coli K12]
+MANDSWSGQDKAQHFIASAMLSAAGNEYSQHQGMSRDRSAMFGLMFSVSLGASKELWDSRPEGSGWSWKDLAWDVAGASTGYTVWQLTRH
+>gi|49176253|ref|YP_026176.1| CP4-57 prophage [Escherichia coli K12]
+MAAGFIADTASLPLIVSNLVNIVSADFFGLSFAQYASVMISVDAAAIAATLIMLYLFFRRVIPATY
+>gi|16130584|ref|NP_417156.1| hypothetical protein b2670 [Escherichia coli K12]
+MFSPQSRLRHAVADTFAMVVYCSVVNMCIEVFLSGMSFEQSFYSRLVAIPVNILIAWPYGMYRDLFMRAARKVSPSGWIKNLADILAYVTFQSPVYVAILLVVGADWHQIMAAVSSNIVVSMLMGAVYGYFLDYCRRLFKVSRYQQVKA
+>gi|16130625|ref|NP_417198.1| processing of HycE (part of the FHL complex) [Escherichia coli K12]
+MSEKVVFSQLSRKFIDENDATPAEAQQVVYYSLAIGHHLGVIDCLEAALTCPWDEYLAWIATLEAGSEARRKMEGVPKYGEIVIDINHVPMLANAFDKARAAQTSQQQEWSTMLLSMLHDIHQENAIYLMVRRLRD
+>gi|16130646|ref|NP_417219.1| putative epimerase/isomerase [Escherichia coli K12]
+MPRFAANLSMMFTEVPFIERFAAARKAGFDAVEFLFPYNYSTLQIQKQLEQNHLTLALFNTAPGDINAGEWGLSALPGREHEAHADIDLALEYALALNCEQVHVMAGVVPAGEDAERYRAVFIDNIRYAADRFAPHGKRILVEALSPGVKPHYLFSSQYQALAIVEEVARDNVFIQLDTFHAQKVDGNLTHLIRDYAGKYAHVQIAGLPDRHEPDDGEINYPWLFRLFDEVGYQGWIGCEYKPRGLTEEGLGWFDAWR
+>gi|16130699|ref|NP_417272.1| hypothetical protein b2792 [Escherichia coli K12]
+MTTHDRVRLQLQALEALLREHQHWRNDEPQPHQFNSTQPFFMDTMEPLEWLQWVLIPRMHDLLDNKQPLPGAFAVAPYYEMALATDHPQRALILAELEKLDALFADDAS
+>gi|16130761|ref|NP_417334.1| unknown CDS [Escherichia coli K12]
+MINDLKSILLKPSEEVDVFIKIFESWVTKLPSISGPVNLHIPTSFKDKSLEVESYFVDKSIWNVHITFHDDKRFVFFTDQFIAEFSPQEFVDNCEQYLINNHCFSPDKVNEICEQARHYLVEKMFETHSLDMNNSVLASPEDL
+>gi|16130806|ref|NP_417380.1| glycine cleavage system protein H [Escherichia coli K12]
+MSNVPAELKYSKEHEWLRKEADGTYTVGITEHAQELLGDMVFVDLPEVGATVSAGDDCAVAESVKAASDIYAPVSGEIVAVNDALSDSPELVNSEPYAGGWIFKIKASDESELESLLDATAYEALLEDE
+>gi|16130817|ref|NP_417391.1| chromosome replication initiation inhibitor protein [Escherichia coli K12]
+MKRPDYRTLQALDAVIRERGFERAAQKLCITQSAVSQRIKQLENMFGQPLLVRTVPPRPTEQGQKLLALLRQVELLEEEWLGDEQTGSTPLLLSLAVNADSLATWLLPALAPVLADSPIRLNLQVEDETRTQERLRRGEVVGAVSIQHQALPSCLVDKLGALDYLFVSSKPFAEKYFPNGVTRSALLKAPVVAFDHLDDMHQAFLQQNFDLPPGSVPCHIVNSSEAFVQLARQGTTCCMIPHLQIEKELASGELIDLTPGLFQRRMLYWHRFAPESRMMRKVTDALLDYGHKVLRQD
+>gi|16130835|ref|NP_417409.1| PTS family enzyme IIA, mannitol-specific, cryptic [Escherichia coli K12]
+MRLSDYFPESSISVIHSAKDWQEAIDFSMVSLLDKNYISENYIQAIKDSTINNGPYYILAPGVAMPHARPECGALKTGMSLTLLEQGVYFPGNDEPIKLLIGLSAADADSHIGAIQALSELLCEEEILEQLLTASSEKQLADIISRG
+>gi|16130863|ref|NP_417437.1| hypothetical protein b2962 [Escherichia coli K12]
+MSRTIFCTFLQREAEGQDFQLYPGELGKRIYNEISKEAWAQWQHKQTMLINEKKLNMMNAEHRKLLEQEMVNFLFEGKEVHIEGYTPEDKK
+>gi|16130867|ref|NP_417441.1| putative transport protein [Escherichia coli K12]
+MVIGPFINASAVLLGGVLGALLSQRLPERIRVSMTSIFGLASLGIGILLVVKCANLPAMVLATLLGALIGEICLLEKGVNTAVAKAQNLFRHSRKKPAHESFIQNYVAIIVLFCASGTGIFGAMNEGMTGDPSILIAKSFLDFFTAMIFACSLGIAVSVISIPLLIIQLTLAWAAALILPLTTPSMMADFSAVGGLLLLATGLRICGIKMFPVVNMLPALLLAMPLSAAWTAWFA
+>gi|16130900|ref|NP_417475.1| hypothetical protein b3002 [Escherichia coli K12]
+MERFLENAMYASRWLLAPVYFGLSLALVALALKFFQEIIHVLPNIFSMAESDLILVLLSLVDMTLVGGLLVMVMFSGYENFVSQLDISENKEKLNWLGKMDATSLKNKVAASIVAISSIHLLRVFMDAKNVPDNKLMWYVIIHLTFVLSAFVMGYLDRLTRHNH
+>gi|16130902|ref|NP_417477.1| unknown CDS [Escherichia coli K12]
+MNALSGLQTHEDSTCCNRFCRPDERSASGNSTLLRFGGFFADQTYLQVTRLMQRIHYLHQRLVIDGFVRSEEDGGVFLAFG
+>gi|16130905|ref|NP_417480.1| unknown CDS [Escherichia coli K12]
+MLVTFLLRKRKEKKAKVRQYANSNENDYQFDVVLILLCADFVTCVLEIHSG
+>gi|16130984|ref|NP_417560.1| Na+:serine/threonine symporter (DAACS family) [Escherichia coli K12]
+MTTQRSPGLFRRLAHGSLVKQILVGLVLGILLAWISKPAAEAVGLLGTLFVGALKAVAPILVLMLVMASIANHQHGQKTNIRPILFLYLLGTFSAALAAVVFSFAFPSTLHLSSSAGDISPPSGIVEVMRGLVMSMVSNPIDALLKGNYIGILVWAIGLGFALRHGNETTKNLVNDMSNAVTFMVKLVIRFAPIGIFGLVSSTLATTGFSTLWGYAQLLVVLVGCMLLVALVVNPLLVWWKIRRNPFPLVLLCLRESGVYAFFTRSSAANIPVNMALCEKLNLDRDTYSVSIPLGATINMAGAAITITVLTLAAVNTLGIPVDLPTALLLSVVASLCACGASGVAGGSLLLIPLACNMFGISNDIAMQVVAVGFIIGVLQDSCETALNSSTDVLFTAAACQAEDDRLANSALRN
+>gi|16131011|ref|NP_417588.1| transcriptional activator for amino acids degradation (LysR family) [Escherichia coli K12]
+MSTILLPKTQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVELVVRKNTGVTLTPAGQLLLSRSESITREMKNMVNEISGMSSEAVVEVSFGFPSLIGFTFMSGMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSAEMKLQDLHVEPLFESEFVLVASKSRTCTGTTTLESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNADFLTVIPCDMTSPFGSNQFITIPVEETLPVAQYAAVWSKNYRIKKAASVLVELAKEYSSYNGCRRRQLIEVG
+>gi|16131049|ref|NP_417626.1| hypothetical protein b3157 [Escherichia coli K12]
+MLDKLRSRIVHLGPSLLSVPVKLTPFALKRQVLEQVLSWQFRQALDDGELEFLEGRWLSIHVRDIDLQWFTSVVNGKLVVSQNAQADVSFSADASDLLMIAARKQDPDTLFFQRRLVIEGDTELGLYVKNLMDAIELEQMPKALRMMLLQLADFVEAGMKTAPETKQTSVGEPC
+>gi|16131065|ref|NP_417642.1| protein-export membrane protein [Escherichia coli K12]
+MYEALLVVFLIVAIGLVGLIMLQQGKGADMGASFGAGASATLFGSSGSGNFMTRMTALLATLFFIISLVLGNINSNKTNKGSEWENLSAPAKTEQTQPAAPAKPTSDIPN
+>gi|90111557|ref|NP_417676.2| sigma cross-reacting protein 27A (SCRP-27A) [Escherichia coli K12]
+MKKIGVILSGCGVYDGSEIHEAVLTLLAISRSGAQAVCFAPDKQQVDVINHLTGEAMTETRNVLIEAARITRGEIRPLAQADAAELDALIVPGGFGAAKNLSNFASLGSECTVDRELKALAQAMHQAGKPLGFMCIAPAMLPKIFDFPLRLTIGTDIDTAEVLEEMGAEHVPCPVDDIVVDEDNKIVTTPAYMLAQNIAEAASGIDKLVSRVLVLAE
+>gi|16131149|ref|NP_417727.1| DNA-binding protein Fis [Escherichia coli K12]
+MFEQRVNSDVLTVSTVNSQDQVTQKPLRDSVKQALKNYFAQLNGQDVNDLYELVLAEVEQPLLDMVMQYTRGNQTRAALMMGINRGTLRKKLKKYGMN
+>gi|16131155|ref|NP_417733.1| unknown CDS [Escherichia coli K12]
+MKRLIPVALLTALLAGCAHDSPCVPVYDDQGRLVHTNTCMKGTTQDNWETAGAIAGGAAAVAGLTMGIIALSK
+>gi|16131230|ref|NP_417810.1| glutathione-regulated potassium-efflux system ancillary protein [Escherichia coli K12]
+MMSQPAKVLLLYAHPESQDSVANRVLLKPATQLSNVTVHDLYAHYPDFFIDIPREQALLREHEVIVFQHPLYTYSCPALLKEWLDRVLSRGFASGPGGNQLAGKYWRSVITTGEPESAYRYDALNRYPMSDVLRPFELAAGMCRMHWLSPIIIYWARRQSAQELASHARAYGDWLANPLSPGGR
+>gi|90111586|ref|NP_417860.2| Hsp33-like chaperonin [Escherichia coli K12]
+MPQHDQLHRYLFENFAVRGELVTVSETLQQILENHDYPQPVKNVLAELLVATSLLTATLKFDGDITVQLQGDGPMNLAVINGNNNQQMRGVARVQGEIPENADLKTLVGNGYVVITITPSEGERYQGVVGLEGDTLAACLEDYFMRSEQLPTRLFIRTGDVDGKPAAGGMLLQVMPAQNAQQDDFDHLATLTETIKTEELLTLPANEVLWRLYHEEEVTVYDPQDVEFKCTCSRERCADALKTLPDEEVDSILAEDGEIDMHCDYCGNHYLFNAMDIAEIRNNASPADPQVH
+>gi|16131340|ref|NP_417925.1| putative enzyme [Escherichia coli K12]
+MLWSFIAVCLSAWLSVDASYRGPTWQRWVFKPLTLLLLLLLAWQAPMFDAISYLVLAGLCASLLGDALTLLPRQRLMYAIGAFFLSHLLYTIYFASQMTLSFFWPLPLVLLVLGALLLAIIWTRLEEYRWPICTFIGMTLVMVWLAGELWFFRPTAPALSAFVGASLLFISNFVWLGSHYRRRFRADNAIAAACYFAGHFLIVRSLYL
+>gi|16131343|ref|NP_417928.1| putative integral membrane protein [Escherichia coli K12]
+MNVFSQTQRYKALFWLSLFHLLVITSSNYLVQLPVSILGFHTTWGAFSFPFIFLATDLTVRIFGAPLARRIIFAVMIPALLISYVISSLFYMGSWQGFGALAHFNLFVARIATASFMAYALGQILDVHVFNRLRQSRRWWLAPTASTLFGNVSDTLAFFFIAFWRSPDAFMAEHWMEIALVDYCFKVLISIVFFLPMYGVLLNMLLKRLADKSEINALQAS
+>gi|90111596|ref|NP_417930.2| hypothetical protein b3473 [Escherichia coli K12]
+MPEPVAEPALNGLRLNLRIVSIVMFNFASYLTIGLPLAVLPGYVHDVMGFSAFWAGLVISLQYFATLLSRPHAGRYADSLGPKKIVVFGLCGCFLSGLGYLTAGLTASLPVISLLLLCLGRVILGIGQSFAGTGSTLWGVGVVGSLHIGRVISWNGIVTYGAMAMGAPLGVVFYHWGGLQALALIIMGVALVAILLAIPRPTVKASKGKPLPFRAVLGRVWLYGMALALASAGFGVIATFITLFYDAKGWDGAAFALTLFSCAFVGTRLLFPNGINRIGGLNVAMICFSVEIIGLLLVGVATMPWMAKIGVLLAGAGFSLVFPALGVVAVKAVPQQNQGAALATYTVFMDLSLGVTGPLAGLVMSWAGVPVIYLAAAGLVAIALLLTWRLKKRPPEHVPEAASSS
+>gi|16131350|ref|NP_417935.1| nickel transport proein (ABC superfamily, membrane) [Escherichia coli K12]
+MNFFLSSRWSVRLALIIIALLALIALTSQWWLPYDPQAIDLPSRLLSPDAQHWLGTDHLGRDIFSRLMAATRVSLGSVMACLLLVLTLGLVIGGSAGLIGGRVDQATMRVADMFMTFPTSILSFFMVGVLGTGLTNVIIAIALSHWAWYARMVRSLVISLRQREFVLASRLSGAGHVRVFVDHLAGAVIPSLLVLATLDIGHMMLHVAGMSFLGLGVTAPTAEWGVMINDARQYIWTQPLQMFWPGLALFISVMAFNLVGDALRDHLDPHLVTEHAH
+>gi|90111601|ref|NP_417948.2| putative transport protein [Escherichia coli K12]
+MNIYIGWLFKLIPLIMGLICIALGGFVLESSGQSEYFVAGHVLISLAAICLALFTTAFIIISQLTRGVNTFYNTLFPIIGYAGSIITMIWGWALLAGNDVMADEFVAGHVIFGVGMIAACVSTVAASSGHFLLIPKNAAGSKSDGTPVQAYSSLIGNCLIAVPVLLTLLGFIWSITLLRSADITPHYVAGHVLLGLTAICACLIGLVATIVHQTRNTFSTKEHWLWCYWVIFLGSITVLQGIYVLVSSDASARLAPGIILICLGMICYSIFSKVWLLALVWRRTCSLANRIPMIPVFTCLFCLFLASFLAEMAQTDMGYFIPSRVLVGLGAVCFTLFSIVSILEAGSAKK
+>gi|16131427|ref|NP_418012.1| cold shock protein 7.4, transcriptional activator of hns [Escherichia coli K12]
+MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL
+>gi|16131530|ref|NP_418116.1| putative membrane protein, transport [Escherichia coli K12]
+MGSTRKGMLNVLIAAVLWGSSGVCAQYIMEQSQMSSQFLTMTRLIFAGLILLTLSFVHGDKIFSIINNHKDAISLLIFSVVGALTVQLTFLLTIEKSNAATATVLQFLSPTIIVAWFSLVRKSRPGILVFCAILTSLVGTFLLVTHGNPTSLSISPAALFWGIASAFAAAFYTTYPSTLIARYGTLPVVGWSMLIGGLILLPFYARQGTNFVVNGSLILAFFYLVVIGTSLTFSLYLKGAQLIGGPKASILSCAEPLSSALLSLLLLGITFTLPDWLGTLLILSSVILISMDSRRRARKINRPARHK
+>gi|16131578|ref|NP_418166.1| drug/chloramphenicol transport protein (MFS family) [Escherichia coli K12]
+MSRFLICSFALVLLYPAGIDMYLVGLPRIAADLNASEAQLHIAFSVYLAGMAAAMLFAGKVADRSGRKPVAIPGAALFIIASVFCSLAETSTLFLAGRFLQGLGAGCCYVVAFAILRDTLDDRRRAKVLSLLNGITCIIPVLAPVLGHLIMLKFPWQSLFWAMAMMGIAVLMLSLFILKETRPAAPAASDKPRENSESLLNRFFLSRVVITTLSVSVILTFVNTSPVLLMEIMGFERGEYATIMALTAGVSMTVSFSTPFALGIFKPRTLMITSQVLFLAAGITLAVSPSHAVSLFGITLICAGFSVGFGVAMSQALGPFSLRAGVASSTLGIAQVCGSSLWIWLAAVVGIGAWNMLIGILIACSIVSLLLIMFVAPGRPVAAHEEIHHHA
+>gi|16131585|ref|NP_418173.1| hypothetical protein b3717 [Escherichia coli K12]
+MTQNIRPLPQFKYHPKPLETGAFEQDKTVECDCCEQQTSVYYSGPFYCVDEVEHLCPWCIADGSAAEKFAGSFQDDASIEGVEFEYDEEDEFAGIKNTYPDEMLKELVERTPGYHGWQQEFWLAHCGDFCVFIGYVGWNDIKDRLDEFANLEEDCENFGIRNSDLAKCLQKGGHCQGYLFRCLHCGKLRLWGDFS
+>gi|16131606|ref|NP_418194.1| ATP synthase subunit A [Escherichia coli K12]
+MASENMTPQDYIGHHLNNLQLDLRTFSLVDPQNPPATFWTINIDSMFFSVVLGLLFLVLFRSVAKKATSGVPGKFQTAIELVIGFVNGSVKDMYHGKSKLIAPLALTIFVWVFLMNLMDLLPIDLLPYIAEHVLGLPALRVVPSADVNVTLSMALGVFILILFYSIKMKGIGGFTKELTLQPFNHWAFIPVNLILEGVSLLSKPVSLGLRLFGNMYAGELIFILIAGLLPWWSQWILNVPWAIFHILIITLQAFIFMVLTIVYLSMASEEH
+>gi|67005950|ref|NP_418228.2| thioredoxin [Escherichia coli K12]
+MSDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA
+>gi|16131722|ref|NP_418318.1| putative dehydrogenase [Escherichia coli K12]
+MAAIAFIGLGQMGSPMASNLLQQGHQLRVFDVNAEAVRHLVDKGATPAANPAQAAKDAEFIITMLPNGDLVRNVLFGENGVCEGLSTDALVIDMSTIHPLQTDKLIADMQAKGFSMMDVPVGRTSANAITGTLLLLAGGTAEQVERATPILMAMGSELINAGGPGMGIRVKLINNYMSIALNALSAEAAVLCEALNLPFDVAVKVMSGTAAGKGHFTTSWPNKVLSGDLSPAFMIDLAHKDLGIALDVANQLHVPMPLGAASREVYSQARAAGRGRQDWSAILEQVRVSAGMTAKVKM
+>gi|16131732|ref|NP_418328.1| formate dehydrogenase, cytochrome B556 (FDO) subunit [Escherichia coli K12]
+MKRRDTIVRYTAPERINHWITAFCFILAAVSGLGFLFPSFNWLMQIMGTPQLARILHPFVGVVMFASFIIMFFRYWHHNLINRDDIFWAKNIRKIVVNEEVGDTGRYNFGQKCVFWAAIIFLVLLLVSGVIIWRPYFAPAFSIPVIRFALMLHSFAAVALIVVIMVHIYAALWVKGTITAMVEGWVTSAWAKKHHPRWYREVRKTTEKKAE
+>gi|16131829|ref|NP_418427.1| hypothetical protein b3999 [Escherichia coli K12]
+MLQNPIHLRLERLESWQHVTFMACLCERMYPNYAMFCQQTGFGDGQIYRRILDLIWETLTVKDAKVNFDSQLEKFEEAIPSADDFDLYGVYPAIDACVALSELVHSRLSGETLEHAVEVSKTSITTVAMLEMTQAGREMSDEELKENPAVEQEWDIQWEIFRLLAECEERDIELIKGLRADLREAGESNIGIIFQQ
+>gi|16131888|ref|NP_418486.1| regulation of superoxide response regulon [Escherichia coli K12]
+MSHQKIIQDLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSRVFRRQFDRTPSDYRHRL
+>gi|16131894|ref|NP_418492.1| hypothetical protein b4068 [Escherichia coli K12]
+MNGTIYQRIEDNAHFRELVEKRQRFATILSIIMLAVYIGFILLIAFAPGWLGTPLNPNTSVTRGIPIGVGVIVISFVLTGIYIWRANGEFDRLNNEVLHEVQAS
+>gi|16131928|ref|NP_418526.1| putative transcriptional regulator [Escherichia coli K12]
+MHLSTHPTSYPTRYQEIAAKLEQELRQHYRCGDYLPAEQQLAARFEVNRHTLRRAIDQLVEKGWVQRRQGVGVLVLMRPFDYPLNAQARFSQNLLDQGSHPTSEKLLSVLRPASGHVADALGITEGENVIHLRTLRRVNGVALCLIDHYFADLTLWPTLQRFDSGSLHDFLREQTGIALRRSQTRISARRAQAKECQRLEIPNMSPLLCVRTLNHRDGESSPAEYSVSLTRADMIEFTMEH
+>gi|16132032|ref|NP_418631.1| putative cationic amino acid transport protein [Escherichia coli K12]
+MPVMISGVLYALLAGLMWGLIFVGPLIVPEYPAMLQSMGRYLALGLIALPIAWLGRVRLRQLARRDWLTALMLTMMGNLIYYFCLASAIQRTGAPVSTMIIGTLPVVIPVFANLLYSQRDGKLAWGKLAPALICIGIGLACVNIAELNHGLPDFDWARYTSGIVLALVSVVCWAWYALRNARWLRENPDKHPMMWATAQALVTLPVSLIGYLVACYWLNTQTPDFSLPFGPRPLVFISLMVAIAVLCSWVGALCWNVASQLLPTVILGPLIVFETLAGLLYTFLLRQQMPPLMTLSGIALLVIGVVIAVRAKPEKPLTESVSES
+>gi|90111709|ref|NP_418651.2| putative sugar transport protein (ABC superfamily, membrane) [Escherichia coli K12]
+MPQSLPDTTTPKRRFRWPTGMPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALLAIGMTLVIATGGIDLSVGAVMAIAGATTAAMTVAGFSLPIVLLSALGTGILAGLWNGILVAILKIQPFVATLILMVAGRGVAQLITAGQIVTFNSPDLSWFGSGSLLFLPTPVIIAVLTLILFWLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPEMNQVVKAVVVLCVLIVQSQRFISLIKGVRSRDKT
+>gi|16132087|ref|NP_418686.1| L-idonate transport protein (GntP family) [Escherichia coli K12]
+MPLIIIAAGVALLLILMIGFKVNGFIALVLVAAVVGFAEGMDAQAVLHSIQNGIGSTLGGLAMILGFGAMLGKLISDTGAAQRIATTLIATFGKKRVQWALVITGLVVGLAMFFEVGFVLLLPLVFTIVASSGLPLLYVGVPMVAALSVTHCFLPPHPGPTAIATIFEANLGTTLLYGFIITIPTVIVAGPLFSKLLTRFEKAPPEGLFNPHLFSEEEMPSFWNSIFAAVIPVILMAIAAVCEITLPKTNTVRLFFEFVGNPAVALFIAIVIAIFTLGRRNGRTIEQIMDIIGDSIGAIAMIVFIIAGGGAFKQVLVDSGVGHYISHLMTGTTLSPLLMCWTVAALLRIALGSATVAAITTAGVVLPIINVTHADPALMVLATGAGSVIASHVNDPGFWLFKGYFNLTVGETLRTWTVMETLISIMGLLGVLAINAVLH

data/test_files/bioworks_small.params ADDED Viewed

@@ -0,0 +1,63 @@
+[SEQUEST]
+first_database_name = C:\Xcalibur\database\ecoli_K12_ncbi_20060321.fasta
+second_database_name =
+peptide_mass_tolerance = 25.0000
+peptide_mass_units = 2              ; 0=amu, 1=mmu, 2=ppm
+ion_series = 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0
+fragment_ion_tolerance = 1.0000          ; for trap data leave at 1.0, for accurate mass data use values < 1.0
+fragment_ion_units = 0              ; 0=amu, 1=mmu
+num_output_lines = 10                ; # peptide results to show
+num_results = 250                     ; # results to store
+num_description_lines = 5           ; # full protein descriptions to show for top N peptides
+show_fragment_ions = 0              ; 0=no, 1=yes
+print_duplicate_references = 40      ; number of duplicate references reported
+enzyme_info = Trypsin(KR/P) 1 1 KR P
+max_num_differential_per_peptide = 3           ; max # of diff. mod in a peptide
+diff_search_options = 15.999400 M 79.979900 STY 0.000000 M 0.000000 X 0.000000 T 0.000000 Y
+term_diff_search_options = 0.000000 0.000000
+nucleotide_reading_frame = 0        ; 0=protein db, 1-6, 7 = forward three, 8-reverse three, 9=all six
+mass_type_parent = 0                ; 0=average masses, 1=monoisotopic masses
+mass_type_fragment = 0              ; 0=average masses, 1=monoisotopic masses
+normalize_xcorr = 0                 ; use normalized xcorr values in the out file
+remove_precursor_peak = 0           ; 0=no, 1=yes
+ion_cutoff_percentage = 0.0000           ; prelim. score cutoff % as a decimal number i.e. 0.30 for 30%
+max_num_internal_cleavage_sites = 2           ; maximum value is 12
+protein_mass_filter = 0 0           ; enter protein mass min & max value ( 0 for both = unused)
+match_peak_count = 0                ; number of auto-detected peaks to try matching (max 5)
+match_peak_allowed_error = 1        ;  number of allowed errors in matching auto-detected peaks
+match_peak_tolerance = 1.0000            ; mass tolerance for matching auto-detected peaks
+partial_sequence =
+sequence_header_filter =
+digest_mass_range = 600.0 3500.0
+add_Cterm_peptide = 0.0000               ; added to each peptide C-terminus
+add_Cterm_protein = 0.0000               ; added to each protein C-terminus
+add_Nterm_peptide = 0.0000               ; added to each peptide N-terminus
+add_Nterm_protein = 0.0000               ; added to each protein N-terminus
+add_G_Glycine = 0.0000                   ; added to G
+add_A_Alanine = 0.0000                   ; added to A
+add_S_Serine = 0.0000                    ; added to S
+add_P_Proline = 0.0000                   ; added to P
+add_V_Valine = 0.0000                    ; added to V
+add_T_Threonine = 0.0000                 ; added to T
+add_C_Cysteine = 0.0000                  ; added to C
+add_L_Leucine = 0.0000                   ; added to L
+add_I_Isoleucine = 0.0000                ; added to I
+add_X_LorI = 0.0000                      ; added to X
+add_N_Asparagine = 0.0000                ; added to N
+add_O_Ornithine = 0.0000                 ; added to O
+add_B_avg_NandD = 0.0000                 ; added to B
+add_D_Aspartic_Acid = 0.0000             ; added to D
+add_Q_Glutamine = 0.0000                 ; added to Q
+add_K_Lysine = 0.0000                    ; added to K
+add_Z_avg_QandE = 0.0000                 ; added to Z
+add_E_Glutamic_Acid = 0.0000             ; added to E
+add_M_Methionine = 0.0000                ; added to M
+add_H_Histidine = 0.0000                 ; added to H
+add_F_Phenylalanine = 0.0000             ; added to F
+add_R_Arginine = 0.0000                  ; added to R
+add_Y_Tyrosine = 0.0000                  ; added to Y
+add_W_Tryptophan = 0.0000                ; added to W
+add_J_user_amino_acid = 0.0000           ; added to J
+add_U_user_amino_acid = 0.0000           ; added to U

data/test_files/bioworks_small.phobius ADDED Viewed

@@ -0,0 +1,109 @@
+Phobius prediction
+SEQENCE ID                     TM SP PREDICTION
+gi|49175991|ref|YP_025292.1|    0  Y n8-16c21/22o
+gi|16128018|ref|NP_414565.1|    0  0 i
+gi|16128024|ref|NP_414571.1|    0  0 i
+gi|16128058|ref|NP_414606.1|    0  0 i
+gi|16128092|ref|NP_414641.1|    0  0 i
+gi|16128121|ref|NP_414670.1|    7  Y n4-9c14/15o24-46i58-84o104-132i139-164o170-191i203-221o227-248i
+gi|90111097|ref|NP_414731.2|    0  0 i
+gi|16128191|ref|NP_414740.1|    5  0 o20-40i52-76o82-105i142-162o182-203i
+gi|16128232|ref|NP_414781.1|    0  0 i
+gi|16128248|ref|NP_414797.1|    2  0 i38-61o81-106i
+gi|90111117|ref|NP_414887.2|   11  Y n15-26c44/45o54-74i81-101o107-128i140-163o169-189i209-235o255-273i280-300o306-328i340-359o371-391i
+gi|16128374|ref|NP_414923.1|    0  0 i
+gi|16128403|ref|NP_414952.1|    5  0 i21-51o57-75i87-104o110-126i138-162o
+gi|16128443|ref|NP_414992.1|    0  0 i
+gi|16128499|ref|NP_415048.1|    0  0 i
+gi|16128537|ref|NP_415086.1|    2  0 i7-25o37-58i
+gi|49176035|ref|YP_025295.1|    0  Y n6-24c29/30o
+gi|16128614|ref|NP_415164.1|    0  0 i
+gi|16128621|ref|NP_415171.1|    0  0 i
+gi|16128710|ref|NP_415263.1|    3  0 o17-34i46-67o73-96i
+gi|90111171|ref|NP_415327.2|    0  Y n4-14c22/23o
+gi|16128811|ref|NP_415364.1|    0  Y n6-17c22/23o
+gi|16128871|ref|NP_415424.1|    6  0 i35-55o75-98i118-141o161-180i192-212o255-277i
+gi|90111191|ref|NP_415463.2|    0  Y n6-17c22/23o
+gi|90111193|ref|NP_415466.4|    0  0 i
+gi|16128957|ref|NP_415511.1|    0  Y n15-25c29/30o
+gi|16128974|ref|NP_415528.1|    0  0 i
+gi|16129015|ref|NP_415570.1|    0  0 i
+gi|16129146|ref|NP_415701.1|    0  0 i
+gi|16129250|ref|NP_415805.1|    0  0 i
+gi|16129266|ref|NP_415821.1|    1  0 o6-24i
+gi|16129267|ref|NP_415822.1|    1  0 o39-64i
+gi|16129318|ref|NP_415875.1|    0  0 i
+gi|90111262|ref|NP_415894.4|    0  0 i
+gi|16129357|ref|NP_415914.1|    0  0 i
+gi|90111267|ref|NP_415926.4|    5  0 o31-64i85-107o113-132i152-168o174-191i
+gi|16129388|ref|NP_415946.1|   10  0 i12-31o43-64i76-97o103-121i141-160o166-184i196-218o230-249i256-274o286-310i
+gi|16129463|ref|NP_416021.1|    0  Y n6-17c22/23o
+gi|16129488|ref|NP_416046.1|    5  0 o12-32i44-62o68-89i151-172o192-214i
+gi|90111295|ref|NP_416074.4|    1  Y n7-15c20/21o36-58i
+gi|16129540|ref|NP_416099.1|    4  0 o6-26i33-54o60-78i85-105o
+gi|90111300|ref|NP_416103.2|    0  Y n3-14c21/22o
+gi|90111309|ref|NP_416156.4|    0  Y n6-15c20/21o
+gi|90111313|ref|NP_416166.2|    0  0 i
+gi|16129623|ref|NP_416182.1|    0  Y n3-11c20/21o
+gi|16129732|ref|NP_416292.1|    0  0 i
+gi|90111344|ref|NP_416352.4|    0  0 i
+gi|90111352|ref|NP_416389.4|    0  0 i
+gi|16129855|ref|NP_416418.1|    0  0 i
+gi|16129862|ref|NP_416425.1|    0  0 i
+gi|16129891|ref|NP_416454.1|    1  0 i14-35o
+gi|90111376|ref|NP_416555.2|    0  0 i
+gi|16130023|ref|NP_416587.1|    0  0 i
+gi|16130042|ref|NP_416607.1|    0  0 i
+gi|16130217|ref|NP_416785.1|    9  0 i12-32o52-69i81-100o112-133i154-174o186-207i234-257o269-289i301-322o
+gi|16130268|ref|NP_416836.1|    0  Y n8-19c27/28o
+gi|16130299|ref|NP_416868.1|   13  0 i12-32o55-73i85-104o110-132i144-165o171-193i205-224o236-255i276-295o307-325i337-355o375-394i484-502o
+gi|90111436|ref|NP_416933.4|    0  0 i
+gi|90111440|ref|NP_416957.4|    0  0 i
+gi|90111445|ref|NP_416978.4|    8  0 o12-32i77-99o105-127i139-161o173-195i231-249o255-278i290-311o
+gi|16130429|ref|NP_416999.1|    0  Y n20-31c39/40o
+gi|16130443|ref|NP_417013.1|    0  0 i
+gi|16130511|ref|NP_417081.1|    0  0 i
+gi|49176253|ref|YP_026176.1|    2  0 i12-32o38-58i
+gi|16130584|ref|NP_417156.1|    4  0 i12-36o42-62i82-104o110-131i
+gi|16130625|ref|NP_417198.1|    0  0 i
+gi|16130646|ref|NP_417219.1|    0  0 i
+gi|16130699|ref|NP_417272.1|    0  0 i
+gi|16130761|ref|NP_417334.1|    0  0 i
+gi|16130806|ref|NP_417380.1|    0  0 i
+gi|16130817|ref|NP_417391.1|    0  0 i
+gi|16130835|ref|NP_417409.1|    0  0 i
+gi|16130863|ref|NP_417437.1|    0  Y n4-11c16/17o
+gi|16130867|ref|NP_417441.1|    8  0 o6-23i30-50o56-75i103-123o135-157i164-181o187-206i213-233o
+gi|16130900|ref|NP_417475.1|    4  0 o12-32i53-75o109-126i138-156o
+gi|16130902|ref|NP_417477.1|    0  0 i
+gi|16130905|ref|NP_417480.1|    0  0 i
+gi|16130984|ref|NP_417560.1|    8  0 i18-36o42-72i84-106o149-166i187-209o215-240i290-315o327-352i
+gi|16131011|ref|NP_417588.1|    0  0 i
+gi|16131049|ref|NP_417626.1|    0  0 i
+gi|16131065|ref|NP_417642.1|    1  Y n4-22c27/28o51-70i
+gi|90111557|ref|NP_417676.2|    0  0 i
+gi|16131149|ref|NP_417727.1|    0  0 i
+gi|16131155|ref|NP_417733.1|    1  Y n4-15c20/21o50-71i
+gi|16131230|ref|NP_417810.1|    0  0 i
+gi|90111586|ref|NP_417860.2|    0  0 i
+gi|16131340|ref|NP_417925.1|    6  Y n3-14c18/19o34-64i76-96o102-123i130-152o158-177i189-207o
+gi|16131343|ref|NP_417928.1|    6  0 i12-31o43-64i71-92o104-127i139-165o185-206i
+gi|90111596|ref|NP_417930.2|   12  0 i19-41o47-65i85-103o109-131i152-175o181-199i220-241o253-271i283-303o309-330i342-364o370-388i
+gi|16131350|ref|NP_417935.1|    6  0 i12-32o75-100i121-148o177-196i203-222o242-260i
+gi|90111601|ref|NP_417948.2|   10  0 i7-28o40-62i74-95o107-133i154-175o187-211i223-246o258-281i293-313o325-343i
+gi|16131427|ref|NP_418012.1|    0  0 i
+gi|16131530|ref|NP_418116.1|    9  Y n11-18c25/26o41-60i72-94o100-120i127-146o152-172i184-205o217-237i249-270o276-293i
+gi|16131578|ref|NP_418166.1|   11  Y n4-12c16/17o40-58i70-89o95-116i128-152o158-178i199-222o242-262i269-287o293-312i324-345o351-376i
+gi|16131585|ref|NP_418173.1|    0  0 i
+gi|16131606|ref|NP_418194.1|    5  0 o36-60i100-118o147-166i211-233o239-264i
+gi|67005950|ref|NP_418228.2|    0  0 i
+gi|16131722|ref|NP_418318.1|    0  Y n2-9c17/18o
+gi|16131732|ref|NP_418328.1|    4  0 i20-43o55-73i113-133o145-172i
+gi|16131829|ref|NP_418427.1|    0  0 i
+gi|16131888|ref|NP_418486.1|    0  0 i
+gi|16131894|ref|NP_418492.1|    2  0 i25-51o63-84i
+gi|16131928|ref|NP_418526.1|    0  0 i
+gi|16132032|ref|NP_418631.1|   10  0 i7-28o34-55i67-89o95-116i128-145o157-178i198-219o234-258i265-284o290-309i
+gi|90111709|ref|NP_418651.2|   10  0 i21-38o58-76i83-102o108-129i136-154o174-194i223-245o257-274i281-303o309-328i
+gi|16132087|ref|NP_418686.1|   12  0 i12-38o58-76i97-130o136-154i175-194o222-242i254-275o295-312i324-344o350-369i376-393o413-438i