SUPPLEMENTARY DATA Data in the Relational Database

Transkript

1 Probability-Based Scoring Function as a Software Tool Used The Open Bioinformatics Journal, 2009, Volume 3 i SUPPLEMENTARY DATA Data in the Relational Database Table B.1. Amino Acid Information Amino ID Amino Acid Mass 1 A C E D G F I H K M L N Q P S R T W V Y Table B.2. Enzyme Information EnzID EnzName CutPosition AA_Postion Exception Comment 1 Trypsin C-Terminal K, R P K, R not follow by P

2 ii The Open Bioinformatics Journal, 2009, Volume 3 Thammasorn et al. Table B.3. Post-Translational Modification Information ModID Category TypeMod Condition1 Condition2 Added Mass Comment 1 0 Acetyl (K) K modify K 2 0 Acetyl (N-term) NT every fragment(1) 3 0 Acetyl (Protein N-term) PNT st fragment of each protein(0) 4 0 Carbamidomethyl (C) C modify C 5 0 Carbamyl (K) K modify K 6 0 Carbamyl (N-term) NT every fragment 7 0 Carboxymethyl (C) C modify C 8 0 Guanidinyl (K) K modify K 9 1 ICAT-C (C) C modify C 10 1 ICAT-C:13C (9) (C) C modify C 11 1 ICPL (K) K modify K 12 1 ICPL (Protein N-term) PNT st fragment of each protein 13 1 ICPL:13C (6) (K) K modify K 14 1 ICPL:13C (6) (Protein N-term) PNT st fragment of each protein 15 1 ICPL:2H (4) (K) K modify K 16 1 ICPL:2H (4) (Protein N-term) PNT st fragment of each protein 17 1 itraq4plex (K) K modify K 18 1 itraq4plex (N-term) NT every fragment 19 1 itraq4plex (Y) Y modify Y 20 1 itraq8plex (K) K modify K 21 1 itraq8plex (N-term) NT every fragment 22 1 itraq8plex (Y) Y modify Y 23 0 Methyl (C-term) CT every fragment 24 0 Methyl (DE) D E modify D and E 25 0 Methylthio (C) C modify C 26 0 Oxidation (HW) H W modify H and W 27 0 Oxidation (M) M modify M 28 0 Phospho (ST) S T modify S and T 29 0 Phospho (Y) Y modify Y 30 0 Sulfo (S) S modify S 31 0 Sulfo (T) T modify T 32 0 Sulfo (Y) Y modify Y 33 1 TMT(K) K modify K 34 1 TMT (N-term) NT every fragment 35 1 TMT2plex (K) K modify K 36 1 TMT2plex (N-term) NT every fragment 37 1 TMT6plex (K) K modify K 38 1 TMT6plex (N-term) NT every fragment

3 Probability-Based Scoring Function as a Software Tool Used Table B.4. Protein Information of E. coli The Open Bioinformatics Journal, 2009, Volume 3 iii 1 YP_ thr operon leader peptide [Escherichia 2 YP_ fused aspartokinase I and homoserine dehydrogenase I [Escherichia coli str. 3 YP_ homoserine kinase [Escherichia coli str. 4 YP_ threonine synthase [Escherichia coli str. 5 YP_ hypothetical protein ECDH10B_ YP_ hypothetical protein ECDH10B_ YP_ transporter [Escherichia coli str. K-12 substr. 8 YP_ transaldolase B [Escherichia coli str. K- 12 substr. MKRISTTITTTITITTGNGAG MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQD ALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINA ALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCD PRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIG ASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSS EYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISA KFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGV GGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAK EPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMD YYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGK LDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLP AEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVD GNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLGRFADKLP SEPRENIVYQCWERFCQELGKQIPVAMTLEKNMPIGSGLGSSACSVVAALMAMNEHCG KPLNDTRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDIISQQVPGFDEWLWV LAYPGIKVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQPELAAKLMKDVIAEP YRERLLPGFRQARQAVAEIGAVASGISGSGPTLFALCDKPETAQRVADWLGKNYLQNQ EGFVHICRLDTAGARVLEN MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKIL SAFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLT HIAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIET VAIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQETR NQLVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQAT LSNAMDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDETTQQTMRELKELGYTSEPH AAVAYRALRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHN LPADFAALRKLMMNHQ MKKMQSIVLALSLVLVAPMAAQAAEITLVPSVKLQIGDRDNRGYYWDGGHWRDHGW WKQHYEWRGNRWHLHGPPPPPRHHKKAPHDHHGGHGPGKHHR MLILISPAKTLDYQSPLTTTRYTLPELLDNSQQLIHEARKLTPPQISTLMRISDKLAGINA ARFHDWQPDFTPANARQAILAFKGDVYTGLQAETFSEDDFDFAQQHLRMLSGLYGVL RPLDLMQPYRLEMGIRLENARGKDLYQFWGDIITNKLNEALAAQGDNVVINLASDEYF KSVKPKKLNAEIIKPVFLDEKNGKFKIISFYAKKARGLMSRFIIENRLTKPEQLTGFNSEG YFFDEDSSSNGELVFKRYEQR MPDFFSFINSVLWGSVMIYLLFGAGCWFTFRTGFVQFRYIRQFGKSLKNSIHPQPGGLTS FQSLCTSLAARVGSGNLAGVALAITAGGPGAVFWMWVAAFIGMATSFAECSLAQLYK ERDVNGQFRGGPAWYMARGLGMRWMGVLFAVFLLIAYGIIFSGVQANAVARALSFSF DFPPLVTGIILAVFTLLAITRGLHGVARLMQGFVPLMAIIWVLTSLVICVMNIGQLPHVI WSIFESAFGWQEAAGGAAGYTLSQAITNGFQRSMFSNEAGMGSTPNAAAAAASWPPH PAAQGIVQMIGIFIDTLVICTASAMLILLAGNGTTYMPLEGIQLIQKAMRVLMGSWGAE FVTLVVILFAFSSIVANYIYAENNLFFLRLNNPKAIWCLRICTFATVIGGTLLSLPLMWQL ADIIMACMAITNLTAILLLSPVVHTIASDYLRQRKLGVRPVFDPLRYPDIGRQLSPDAWD DVSQE MTDKLTSLRQYTTVVADTGDIAAMKLYQPQDATTNPSLILNAAQIPEYRKLIDDAVAW AKQQSNDRAQQIVDATDKLAVNIGLEILKLVPGRISTEVDARLSYDTEASIAKAKRLIKL YNDAGISNDRILIKLASTWQGIRAAEQLEKEGINCNLTLLFSFAQARACAEAGVFLISPF VGRILDWYKANTDKKEYAPAEDPGVVSVSEIYQYYKEHGYETVVMGASFRNIGEILEL AGCDRLTIAPALLKELAESEGAIERKLSYTGEVKARPARITESEFLWQHNQDPMAVDKL AEGIRKFAIDQEKLEKMIGDLL

4 iv The Open Bioinformatics Journal, 2009, Volume 3 Thammasorn et al. 9 YP_ molybdochelatase [Escherichia coli str. 10 YP_ inner membrane protein associated with acetate transport [Escherichia coli str. 11 YP_ hypothetical protein ECDH10B_ YP_ hypothetical protein ECDH10B_ YP_ hypothetical protein ECDH10B_ YP_ chaperone Hsp70, co-chaperone with DnaJ 15 YP_ chaperone Hsp40, co-chaperone with DnaK [Escherichia coli str. K-12 substr. 16 YP_ IS186/IS421 transposase [Escherichia 17 YP_ regulatory protein for HokC, overlaps CDS of hokc [Escherichia coli str. K- 12 substr. 18 YP_ toxic membrane protein, small 19 YP_ sodium-proton antiporter [Escherichia MNTLRIGLVSISDRASSGVYQDKGIPALEEWLTSALTTPFELETRLIPDEQAIIEQTLCELV DEMSCHLVLTTGGTGPARRDVTPDATLAVADREMPGFGEQMRQISLHFVPTAILSRQV GVIRKQALILNLPGQPKSIKETLEGVKDAEGNVVVHGIFASVPYCIQLLEGPYVETAPEV VAAFRPKSARRDVSE MGNTKLANPAPLGLMGFGMTTILLNLHNVGYFALDGIILAMGIFYGGIAQIFAGLLEYK KGNTFGLTAFTSYGSFWLTLVAILLMPKLGLTDAPNAQFLGVYLGLWGVFTLFMFFGT LKGARVLQFVFFSLTVLFALLAIGNIAGNAAIIHFAGWIGLICGASAIYLAMGEVLNEQF GRTVLPIGESH MNVNYLNDSDLDFLQHCSEEQLANFARLLTHNEKGKTRLSSVLMRNELFKSMEGHPE QHRRNWQLIAGELQHFGGDSIANKLRGHGKLYRAILLDVSKRLKLKADKEMSTFEIEQ QLLEQFLRNTWKKMDEEHKQEFLHAVDARVNELEELLPLLMKDKLLAKGVSHLLSSQ LTRILRTHAAMSVLGHGLLRGAGLGGPVGAALNGVKAVSGSAYRVTIPAVLQIACLRR MVSATQV MRVSWLESKCDTPFANNLSFISSGSSSSSSFTLASTACRNSCLCSSSIFFQVLRRNCSSNC CSISNVDISLSAFSFNRFETSSKMARYNLPCPRSLLAILSPPKCCNSPAISCQLRRCCSGCP SIDLNSSLRISTLERRVLPFSLWVSNRAKFANCSSLQC MKSVFTISASLAISLMLCCTAQANDHKLLGAIAMPRNETNDLALKLPVCRIVKRIQLSA DHGDLQLSGASVYFKAARSASQSLNIPSEIKEGQTTDWININSDNDNKRCVSKITFSGHT VNSSDMATLKIIGDD MGKIIGIDLGTTNSCVAIMDGTTPRVLENAEGDRTTPSIIAYTQDGETLVGQPAKRQAVT NPQNTLFAIKRLIGRRFQDEEVQRDVSIMPFKIIAADNGDAWVEVKGQKMAPPQISAEV LKKMKKTAEDYLGEPVTEAVITVPAYFNDAQRQATKDAGRIAGLEVKRIINEPTAAAL AYGLDKGTGNRTIAVYDLGGGTFDISIIEIDEVDGEKTFEVLATNGDTHLGGEDFDSRLI NYLVEEFKKDQGIDLRNDPLAMQRLKEAAEKAKIELSSAQQTDVNLPYITADATGPKH MNIKVTRAKLESLVEDLVNRSIEPLKVALQDAGLSVSDIDDVILVGGQTRMPMVQKKV AEFFGKEPRKDVNPDEAVAIGAAVQGGVLTGDVKDVLLLDVTPLSLGIETMGGVMTTL IAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMP QIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKF EELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAK MQELAQVSQKLMEIAQQQHAQQQTAGADASANNAKDDDVVDAEFEEVKDKK MAKQDYYEILGVSKTAEEREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVL TDSQKRAAYDQYGHAAFEQGGMGGGGFGGGADFSDIFGDVFGDIFGGGRGRQRAAR GADLRYNMELTLEEAVRGVTKEIRIPTLEECDVCHGSGAKPGTQPQTCPTCHGSGQVQ MRQGFFAVQQTCPHCQGRGTLIKDPCNKCHGHGRVERSKTLSVKIPAGVDTGDRIRLA GEGEAGEHGAPAGDLYVQVQVKQHPIFEREGNNLYCEVPINFAMAALGGEIEVPTLDG RVKLKVPGETQTGKLFRMRGKGVKSVRGGAQGDLLCRVVVETPVGLNERQKQLLQEL QESFGGPTGEHNSPRSKSFFDGVKKFFDDLTR MNYSHDNWSAILAHIGKPEELDTSARNAGALTRRREIRDAATLLRLGLAYGPGGMSLR EVTAWAQLHDVATLSDVALLKRLRNAADWFGILAAQTLAVRAAVTGCTSGKRLRLV DGTAISAPGGGSAEWRLHMGYDPHTCQFTDFELTDSRDAERLDRFAQTADEIRIADRGF GSRPECIRSLAFGEADYIVRVHWRGLRWLTAEGMRFDMMGFLRGLDCGKNGETTVMI GNSGNKKAGAPFPARLIAVSLPPEKALISKTRLLSENRRKGRVVQAETLEAAGHVLLLT SLPEDEYSAEQVADCYRLRWQIELAFKRLKSLLHLDALRAKEPELAKAWIFANLLAAFL IDDIIQPSLDFPPRSAGSEKKN MLNTCRVPLTDRKVKEKRAMKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQT EVAVFTAYESE MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVFTAYESE MKHLHRFFSSDASGGIILIIAAILAMIMANSGATSGWYHDFLETPVQLRVGSLEINKNML LWINDALMAVFFLLVGLEVKRELMQGSLASLRQAAFPVIAAIGGMIVPALLYLAFNYA DPITREGWAIPAATDIAFALGVLALLGSRVPLALKIFLMALAIIDDLGAIIIIALFYTNDLS MASLGVAAVAIAVLAVLNLCGARRTGVYILVGVVLWTAVLKSGVHATLAGVIVGFFIP LKEKHGRSPAKRLEHVLHPWVAYLILPLFAFANAGVSLQGVTLDGLTSILPLGIIAGLLI GKPLGISLFCWLALRLKLAHLPEGTTYQQIMVVGILCGIGFTMSIFIASLAFGSVDPELIN WAKLGILVGSISSAVIGYSWLRVRLRPSV

5 Probability-Based Scoring Function as a Software Tool Used The Open Bioinformatics Journal, 2009, Volume 3 v 20 YP_ DNA-binding transcriptional activator 21 YP_ IS1 transposase InsAB' [Escherichia 22 YP_ IS1 repressor protein InsA [Escherichia 23 YP_ S ribosomal subunit protein S20 24 YP_ hypothetical protein ECDH10B_ YP_ bifunctional riboflavin kinase and FAD synthetase [Escherichia coli str. K-12 substr. 26 YP_ isoleucyl-trna synthetase [Escherichia 27 YP_ prolipoprotein signal peptidase (signal peptidase II) [Escherichia coli str. K-12 substr. 28 YP_ FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase) [Escherichia coli str. 29 YP_ hydroxy-2-methyl-2-(E)-butenyl 4- diphosphate reductase, 4Fe-4S protein MSMSHINYNHLYYFWHVYKEGSVVGAAEALYLTPQTITGQIRALEERLQGKLFKRKGR GLEPSELGELVYRYADKMFTLSQEMLDIVNYRKESNLLFDVGVADALSKRLVSSVLNA AVVEGEPIHLRCFESTHEMLLEQLSQHKLDMIISDCPIDSTQQEGLFSVRIGECGVSFWC TNPPPEKPFPACLEERRLLIPGRRSMLGRKLLNWFNSQGLNVEILGEFDDAALMKAFGA MHNAIFVAPTLYAYDFYADKTVVEIGRVENVMEEYHAIFAERMIQHPAVQRICNTDYS ALFSPAVR MPGNSPHYGRWPQHDFTSLKKLRPQSVTSRIQPGSDVIVCAEMDEQWGYVGAKSRQR WLFYAYDSLRKTVVAHVFGERTMATLGRLMSLLSPFDVVIWMTDGWPLYESRLKGKL HVISKRYTQRIERHNLNLRQHLARLGRKSLSFSKSVELHDKVIGHYLNIKHYQ MASVSISCPSCSATDGVVRNGKSTAGHQRYLCSHCRKTWQLQFTYTASQPGTHQKIID MAMNGVGCRATARIMGVGLNTILRHLKNSGRSR MANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPI VDRQAAKGLIHKNKAARHKANLTAQINKLA MCRHSLRSDGAGFYQLAGCEYSFSAIKIAAGGQFLPVICAMAMKSHFFLISVLNRRLTL TAVQGILGRFSLF MKLIRGIHNLSQAPQEGCVLTIGNFDGVHRGHRALLQGLQEEGRKRNLPVMVMLFEPQ PLELFATDKAPARLTRLREKLRYLAECGVDYVLCVRFDRRFAALTAQNFISDLLVKHLR VKFLAVGDDFRFGAGREGDFLLLQKAGMEYGFDITSTQTFCEGGVRISSTAVRQALAD DNLALAESLLGHPFAISGRVVHGDELGRTIGFPTANVPLRRQVSPVKGVYAVEVLGLGE KPLPGVANIGTRPTVAGIRQQLEVHLLDVAMDLYGRHIQVVLRKKIRNEQRFASLDELK AQIARDELTAREFFGLTKPA MSDYKSTLNLPETGFPMRGDLAKREPGMLARWTDDDLYGIIRAAKKGKKTFILHDGPP YANGSIHIGHSVNKILKDIIVKSKGLSGYDSPYVPGWDCHGLPIELKVEQEYGKPGEKFT AAEFRAKCREYAATQVDGQRKDFIRLGVLGDWSHPYLTMDFKTEANIIRALGKIIGNG HLHKGAKPVHWCVDCRSALAEAEVEYYDKTSPSIDVAFQAVDQDALKAKFAVSNVN GPISLVIWTTTPWTLPANRAISIAPDFDYALVQIDGQAVILAKDLVESVMQRIGVTDYTIL GTVKGAELELLRFTHPFMGFDVPAILGDHVTLDAGTGAVHTAPGHGPDDYVIGQKYGL ETANPVGPDGTYLPGTYPTLDGVNVFKANDIVVALLQEKGALLHVEKMQHSYPCCWR HKTPIIFRATPQWFVSMDQKGLRAQSLKEIKGVQWIPDWGQARIESMVANRPDWCISR QRTWGVPMSLFVHKDTEELHPRTLELMEEVAKRVEVDGIQAWWDLDAKEILGDEADQ YVKVPDTLDVWFDSGSTHSSVVDVRPEFAGHAADMYLEGSDQHRGWFMSSLMISTA MKGKAPYRQVLTHGFTVDGQGRKMSKSIGNTVSPQDVMNKLGADILRLWVASTDYT GEMAVSDEILKRAADSYRRIRNTARFLLANLNGFDPAKDMVKPEEMVVLDRWAVGCA KAAQEDILKAYEAYDFHEVVQRLMRFCSVEMGSFYLDIIKDRQYTAKADSVARRSCQT ALYHIAEALVRWMAPILSFTADEVWGYLPGEREKYVFTGEWYEGLFGLADSEAMNDA FWDELLKVRGEVNKVIEQARADKKVGGSLEAAVTLYAEPELSAKLTALGDELRFVLLT SGATVADYNDAPADAQQSEVLKGLKVALSKAEGEKCPRCWHYTQDVGKVAEHAEIC GRCVSNVAGDGEKRKFA MSQSICSTGLRWLWLVVVVLIIDLGSKYLILQNFALGDTVPLFPSLNLHYARNYGAAFS FLADSGGWQRWFFAGIAIGISVILAVMMYRSKATQKLNNIAYALIIGGALGNLFDRLWH GFVVDMIDFYVGDWHFATFNLADTAICVGAALIVLEGFLPSRAKKQ MSESVQSNSAVLVHFTLKLDDGTTAESTRNNGKPALFRLGDASLSEGLEQHLLGLKVG DKTTFSLEPDAAFGVPSPDLIQYFSRREFMDAGEPEIGAIMLFTAMDGSEMPGVIREING DSITVDFNHPLAGQTVHFDIEVLEIDPALEA MQILLANPRGFCAGVDRAISIVENALAIYGAPIYVRHEVVHNRYVVDSLRERGAIFIEQIS EVPDGAILIFSAHGVSQAVRNEAKSRDLTVFDATCPLVTKVHMEVARASRRGEESILIG HAGHPEVEGTMGQYSNPEGGMYLVESPDDVWKLTVKNEEKLSFMTQTTLSVDDTSDV IDALRKRFPKIVGPRKDDICYATTNRQEAVRALAEQAEVVLVVGSKNSSNSNRLAELAQ RMGKRAFLIDDAKDIQEEWVKEVKCVGVTAGASAPDILVQNVVARLQQLGGGEAIPLE GREENIVFEVPKELRVDIREVD

6 vi The Open Bioinformatics Journal, 2009, Volume 3 Thammasorn et al. 30 YP_ ribonucleoside hydrolase 3 [Escherichia 31 YP_ dihydrodipicolinate reductase 32 YP_ carbamoyl phosphate synthetase small subunit, glutamine amidotransferase 33 YP_ carbamoyl-phosphate synthase large subunit [Escherichia coli str. K-12 substr. 34 YP_ DNA-binding transcriptional activator 35 YP_ acyl transferase [Escherichia coli str. K- 12 substr. 36 YP_ crotonobetainyl CoA hydratase MRLPIFLDTDPGIDDAVAIAAAIFAPELDLQLMTTVAGNVSVEKTTRNALQLLHFWNAE IPLAQGAAVPLVRAPRDAASVHGESGMAGYDFVEHNRKPLGIPAFLAIRDALMRAPEP VTLVAIGPLTNIALLLSQCPECKPYIRRLVIMGGSAGRGNCTPNAEFNIAADPEAAACVF RSGIEIVMCGLDVTNQAILTPDYLSTLPQLNRTGKMLHALFSHYRSGSMQSGLRMHDL CAIAWLVRPDLFTLKPCFVAVETQGEFTSGTTVVDIDGCLGKPANVQVALDLDVKGFQ QWVAEVLALAS MHDANIRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGK TGVTVQSSLDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIR DAAADIAIVFAANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALA MGEAIAHALDKDLKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERL EITHKASSRMTFANGAVRSALWLSGKESGLFDMRDVLDLNNL MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTL TGGLPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDG IFLSNGPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNH PVKDVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGH PEASPGPHDAAPLFDHFIELIEQYRKTAK MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGAT ADAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSG GGIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDA MGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVI EMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVT KIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSL DDPEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEE KVAEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDT CAAEFATDTAYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALR EDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKL ARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIG YPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAI CDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGL MNVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKE VIPPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMK KHGRALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGR PHIQDRIKNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNAD ATEKVISVQEMHAQIK MCEGYVEKPLYLLIAEWMMAENRWVIAREISIHFDIEHSKAVNTLTYILSEVTEISCEVK MIPNKLEGRGCQCQRLVKVVDIDEQIYARLRNNSREKLVGVRKTPRIPAVPLTELNREQ KWQMMLSKSMRR MSYYAFEGLIPVVHPTAFVHPSAVLIGDVIVGAGVYIGPLASLRGDYGRLIVQAGANIQ DGCIMHGYCDTDTIVGENGHIGHGAILHGCLIGRDALVGMNSVIMDGAVIGEESIVAA MSFVKAGFRGEKRQLLMGTPARAVRNVSDDELHWKRLNTKEYQDLVGRCHVSLHET QPLRQMEENRPRLQGTTDVTPKR MKQQGTTLPANNHTLKQYAFFAGMLSSLKKQKWRKGMSESLHLTRNGSILEITLDRPK ANAIDAKTSFEMGEVFLNFRDDPQLRVAIITGAGEKFFSAGWDLKAAAEGEAPDADFG PGGFAGLTEIFNLDKPVIAAVNGYAFGGGFELALAADFIVCADNASFALPEAKLGIVPDS GGVLRLPKILPPAIVNEMVMTGRRMGAEEALRWGIVNRVVSQAELMDNARELAQQLV NSAPLAIAALKEIYRTTSEMPVEEAYRYIRSGVLKHYPSVLHSEDAIEGPLAFAEKRDPV WKGR

7 Probability-Based Scoring Function as a Software Tool Used The Open Bioinformatics Journal, 2009, Volume 3 vii 37 YP_ crotonobetaine CoA ligase:carnitine CoA ligase [Escherichia coli str. K-12 substr. 38 YP_ crotonobetainyl CoA:carnitine CoA transferase [Escherichia coli str. K-12 substr. 39 YP_ crotonobetaine reductase subunit II, FAD-binding [Escherichia coli str. K- 12 substr. 40 YP_ transporter [Escherichia coli str. K-12 substr. 41 YP_ electron transfer flavoprotein subunit 42 YP_ electron transfer flavoprotein subunit 43 YP_ oxidoreductase [Escherichia coli str. K- 12 substr. 44 YP_ Fe-4S ferredoxin-type protein MDRGAMDIIGGQHLRQMWDDLADVYGHKTALICESSGGVVNRYSYLELNQEINRTAN LFYTLGIRKGDKVALHLDNCPEFIFCWFGLAKIGAIMVPINARLLCEESAWILQNSQACL LVTSAQFYPMYQQIQQEDATQLRHICLTDVALPADDGVSSFTQLKNQQPATLCYAPPLS TDDTAEILFTSGTTSRPKGVVITHYNLRFAGYYSAWQCALRDDDVYLTVMPAFHIDCQ CTAAMAAFSAGATFVLVEKYSARAFWGQVQKYRATVTECIPMMIRTLMVQPPSANDQ QHRLREVMFYLNLSEQEKDAFCERFGVRLLTSYGMTETIVGIIGDRPGDKRRWPSIGRV GFCYEAEIRDDHNRPLPAGEIGEICIKGIPGKTIFKEYFLNPQATAKVLEADGWLHTGDT GYRDEEDFFYFVDRRCNMIKRGGENVSCVELENIIAAHPKIQDIVVVGIKDSIRDEAIKA FVVLNEGETLSEEEFFRFCEQNMAKFKVPSYLEIRKDLPRNCSGKIIRKNLK MDHLPMPKFGPLAGLRVVFSGIEIAGPFAGQMFAEWGAEVIWIENVAWADTIRVQPNY PQLSRRNLHALSLNIFKDEGREAFLKLMETTDIFIEASKGPAFARRGITDEVLWQHNPKL VIAHLSGFGQYGTEEYTNLPAYNTIAQAFSGYLIQNGDVDQPMPAFPYTADYFSGLTAT TAALAALHKVRETGKGESIDIAMYEVMLRMGQYFMMDYFNGGEMCPRMSKGKDPYY AGCGLYKCADGYIVMELVGITQIEECFKDIGLAHLLGTPEIPEGTQLIHRIECPYGPLVEE KLDAWLATHTIAEVKERFAELNIACAKVLTVPELESNPQYVARESITQWQTMDGRTCK GPNIMPKFKNNPGQIWRGMPSHGMDTAAILKNIGYSENDIQELVSKGLAKVED MDFNLNDEQELFVAGIRELMASENWEAYFAECDRDSVYPERFVKALADMGIDSLLIPE EHGGLDAGFVTLAAVWMELGRLGAPTYVLYQLPGGFNTFLREGTQEQIDKIMAFRGT GKQMWNSAITEPGAGSDVGSLKTTYTRRNGKIYLNGSKCFITSSAYTPYIVVMARDGA SPDKPVYTEWFVDMSKPGIKVTKLEKLGLRMDSCCEITFDDVELDEKDMFGREGNGFN RVKEEFDHERFLVALTNYGTAMCAFEDAARYANQRVQFGEAIGRFQLIQEKFAHMAIK LNSMKNMLYEAAWKADNGTITSGDAAMCKYFCANAAFEVVDSAMQVLGGVGIAGN HRISRFWRDLRVDRVSGGSDEMQILTLGRAVLKQYR MKNEKRKTGIEPKVFFPPLIIVGILCWLTVRDLDAANVVINAVFSYVTNVWGWAFEWY MVVMLFGWFWLVFGPYAKKRLGNEPPEFSTASWIFMMFASCTSAAVLFWGSIEIYYYI STPPFGLEPNSTGAKELGLAYSLFHWGPLPWATYSFLSVAFAYFFFVRKMEVIRPSSTLV PLVGEKHAKGLFGTIVDNFYLVALIFAMGTSLGLATPLVTECMQWLFGIPHTLQLDAIII TCWIILNAICVACGLQKGVRIASDVRSYLSFLMLGWVFIVSGASFIMNYFTDSVGMLLM YLPRMLFYTDPIAKGGFPQGWTVFYWAWWVIYAIQMSIFLARISRGRTVRELCFGMVL GLTASTWILWTVLGSNTLLLIDKNIINIPNLIEQYGVARAIIETWAALPLSTATMWGFFIL CFIATVTLVNACSYTLAMSTCREVRDGEEPPLLVRIGWSILVGIIGIVLLALGGLKPIQTAI IAGGCPLFFVNIMVTLSFIKDAKQNWKD MKIITCYKCVPDEQDIAVNNADGSLDFSKADAKISQYDLNAIEAACQLKQQAAEAQVT ALSVGGKALTNAKGRKDVLSRGPDELIVVIDDQFEQALPQQTASALAAAAQKAGFDLI LCGDGSSDLYAQQVGLLVGEILNIPAVNGVSKIISLTADTLTVERELEDETETLSIPLPAV VAVSTDINSPQIPSMKAILGAAKKPVQVWSAADIGFNAEAAWSEQQVAAPKQRERQRI VIEGDGEEQIAAFAENLRKVI MNTFSQVWVFSDTPSRLPELMNGAQALANQINTFVLNDADGAQAIQLGANHVWKLNG KPDDRMIEDYAGVMADTIRQHGADGLVLLPNTRRGKLLAAKLGYRLKAAVSNDASTV SVQDGKATVKHMVYGGLAIGEERIATPYAVLTISSGTFDAAQPDASRTGETHTVEWQA PAVAITRTATQARQSNSVDLDKARLVVSVGRGIGSKENIALAEQLCKAIGAELACSRPV AENEKWMEHERYVGISNLMLKPELYLAVGISGQIQHMVGANASQTIFAINKDKNAPIFQ YADYGIVGDAVKILPALTAALAR MSEDIFDAIIVGAGLAGSVAALVLAREGAQVLVIERGNSAGAKNVTGGRLYAHSLEHII PGFADSAPVERLITHEKLAFMTEKSAMTMDYCNGDETSPSQRSYSVLRSKFDAWLMEQ AEEAGAQLITGIRVDNLVQRDGKVVGVEADGDVIEAKTVILADGVNSILAEKLGMAKR VKPTDVAVGVKELIELPKSVIEDRFQLQGNQGAACLFAGSPTDGLMGGGFLYTNENTL SLGLVCGLHHLHDAKKSVPQMLEDFKQHPAVAPLIAGGKLVEYSAHVVPEAGINMLPE LVGDGVLIAGDAAGMCMNLGFTIRGMDLAIAAGEAAAKTVLSAMKSDDFSKQKLAEY RQHLESGPLRDMRMYQKLPAFLDNPRMFSGYPELAVGVARDLFTIDGSAPELMRKKIL RHGKKVGFINLIKDGMKGVTVL MTSPVNVDVKLGVNKFNVDEEHPHIVVKADADKQALELLVKACPAGLYKKQDDGSV RFDYAGCLECGTCRILGLGSALEQWEYPRGTFGVEFRYG

8 viii The Open Bioinformatics Journal, 2009, Volume 3 Thammasorn et al. 45 YP_ transporter [Escherichia coli str. K-12 substr. 46 YP_ flavoprotein subunit for the KefC potassium efflux system [Escherichia MQPSRNFDDLKFSSIHRRILLWGSGGPFLDGYVLVMIGVALEQLTPALKLDADWIGLLG AGTLAGLFVGTSLFGYISDKVGRRKMFLIDIIAIGVISVATMFVSSPVELLVMRVLIGIVI GADYPIATSMITEFSSTRQRAFSISFIAAMWYVGATCADLVGYWLYDVEGGWRWMLG SAAIPCLLILIGRFELPESPRWLLRKGRVKECEEMMIKLFGEPVAFDEEQPQQTRFRDLF NRRHFPFVLFVAAIWTCQVIPMFAIYTFGPQIVGLLGLGVGKNAALGNVVISLFFMLGCI PPMLWLNTAGRRPLLIGSFAMMTLALAVLGLIPDMGIWLVVMAFAVYAFFSGGPGNL QWLYPNELFPTDIRASAVGVIMSLSRIGTIVSTWALPIFINNYGISNTMLMGAGISLFGLLI SVAFAPETRGMSLAQTSNMTIRGQRMG MILIIYAHPYPHHSHANKRMLEQARTLEGVEIRSLYQLYPDFNIDIAAEQEALSRADLIV WQHPMQWYSIPPLLKLWIDKVFSHGWAYGHGGTALHGKHLLWAVTTGGGESHFEIG AHPGFDVLSQPLQATAIYCGLNWLPPFAMHCTFICDDETLEGQARHYKQRLLEWQEAH HG