INPUT SEQUENCE (A) : data/2IDB.code INPUT SEQUENCE (B) : data/target_ASTRAL.code SUBSEQUENCE OPTION : Whole sequence comparison EXEC OPTION : Naive Dynamic Programing RATIO : lcs/trimmed_seq_a = 0.542 (= 249/ 459), lcs/trimmed_seq_b = 0.771 (= 249/ 323) SEQ A : name = ./PDBdata/2IDB.pdb c1 SEQ A : residue = YNDLRDFLTLLEQQGELKRITLPVDPHLEITEIADRTLRAGGPALLFENPKGYSPVLCNLFGTPKRVAGGQEDVSALREVGKLLAFLKEPEPPKGFRDLPTKRLRGAPCQQKIVSGDDVDLNRIPITCWPEDAAPLITWGLTVTRGPHKERQNLGIYRQQLIGKNKLIRWLSHRGGALDYQEWCAAHPGERFPVSVALGADPATILGAVTPVPDTLSEYAFAGLLRGTKTEVVKCISNDLEVPASAEIVLEGYIEQGETAPEGPYGDHTGYYNEVDSFPVFTVTHITQREDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPEGCSYRLAVVTIKKQYAGHAKRVGVWSFLRQFYTKFVIVCDDDVNARDWNDVIWAITTRDPARDTVLVENTPIDYLDFASPVSGLGSKGLDATNKWPGETQREWGRPIKKDPDVVAHIDAIWDELAIF SEQ A : code = --0QAAAAAAAAABRRG000RG000RBRAAAAAAAAAABGR000000QG00RGO0001RQBRGQAAABQ20RGQAAAAAAAAAAAAAB00000QBBQB800000R00QABR00001R0R0QABGROG00QB0R0000000000000R00RG0000000000R0R0G000RRGRG0QAAAAAAAAAB00RG00000000000QAAAAAAGG000QBG0QAAAAAAABRG00000000R0R0000QB0R000000000R0000R00000QBRG000000000000R000000R00000000001R0QAAAAAAAAAAAAAAAAAAB0QBGR00000QABRR1R000000R0O00RQAABR3QB100QB9R0RG00000QBG0QBGQAAAAAAA8080QA88G0000R0000QBRQBGR00RG000000R00000AB0RG000000000QAAAAAAAABAAABR-- SEQ A : lcs = ----AAAAAAAAA---------------AAAAAAAAAAB--000000--00RG-000-R--RG--------R--------------------0QB----00000-00QAB-0000--0R0QAB-R--00--0R0000000000000R00RG0000000000-0R------R-RG-QAAAAAAAAAB--R-00000000000QAAAAA---0--QBG0QAAAAAAAB-----------0R00-----R000000000R0000-00000QBRG000000000---R-----0-0000000000--0QAAAAAAAAAAAAAAAAAAB--------------R-R000000-0-00-QAA----------------------------AAAAA---------------------BR----0-R------------0AB--G00000----QAAAA---------R-- SEQ B : name = ./pdbstyle-1.71/2a/d12asa_.ent c1 SEQ B : residue = AYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWNPVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQLPHIGQVQAGVWPAAVRESVPSLL SEQ B : code = --AAAAAAAAAAAAAAAAAAAAB0R0000000RG000PGRRGRR0RQBG0000000QABQBG00000R0RQAAAAAAAAABR000RG0000R00000QB0R000R000RG000R00000000RRRGQAAAAAAAAAAAAAAAAAAAAAB1BBR000000R000000QAAAAAB0QBG0QAAAAAAAAAB0R00R00000000RGRG0R00003G000RG000QBRG00RG0000000QABRG000000000000QAAAAAAAAABR0QAAABGQAAAAAABRRG000000000QAAAAAAABR0R0QAABG00000QAAAA0G0R-- SEQ B : lcs = ---AAAAAAAAAAAAAAAAAAAB0-0000000RG000--RRGR-0-QB-0000000QAB---00000R0-Q--------ABR000R-0000-00000--0-000R00-RG000-00000000RRRGQAAAAAAAAA---------------BR000000-00000-QAAAAA-0QBG0QAAAAAAA--B0R00R00000000----0R0000--000--00-QBRG00--0000000---R-000000000000QAAAAAAAAA----AAA---AAAAAABRR-000000000QAAAAAAABR0R0-A-BG00000QAAAA---R-- RATIO : lcs/trimmed_seq_a = 0.218 (= 100/ 459), lcs/trimmed_seq_b = 0.943 (= 100/ 106) SEQ A : name = ./PDBdata/2IDB.pdb c1 SEQ A : residue = YNDLRDFLTLLEQQGELKRITLPVDPHLEITEIADRTLRAGGPALLFENPKGYSPVLCNLFGTPKRVAGGQEDVSALREVGKLLAFLKEPEPPKGFRDLPTKRLRGAPCQQKIVSGDDVDLNRIPITCWPEDAAPLITWGLTVTRGPHKERQNLGIYRQQLIGKNKLIRWLSHRGGALDYQEWCAAHPGERFPVSVALGADPATILGAVTPVPDTLSEYAFAGLLRGTKTEVVKCISNDLEVPASAEIVLEGYIEQGETAPEGPYGDHTGYYNEVDSFPVFTVTHITQREDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPEGCSYRLAVVTIKKQYAGHAKRVGVWSFLRQFYTKFVIVCDDDVNARDWNDVIWAITTRDPARDTVLVENTPIDYLDFASPVSGLGSKGLDATNKWPGETQREWGRPIKKDPDVVAHIDAIWDELAIF SEQ A : code = --0QAAAAAAAAABRRG000RG000RBRAAAAAAAAAABGR000000QG00RGO0001RQBRGQAAABQ20RGQAAAAAAAAAAAAAB00000QBBQB800000R00QABR00001R0R0QABGROG00QB0R0000000000000R00RG0000000000R0R0G000RRGRG0QAAAAAAAAAB00RG00000000000QAAAAAAGG000QBG0QAAAAAAABRG00000000R0R0000QB0R000000000R0000R00000QBRG000000000000R000000R00000000001R0QAAAAAAAAAAAAAAAAAAB0QBGR00000QABRR1R000000R0O00RQAABR3QB100QB9R0RG00000QBG0QBGQAAAAAAA8080QA88G0000R0000QBRQBGR00RG000000R00000AB0RG000000000QAAAAAAAABAAABR-- SEQ A : lcs = ----------------------000----------------000000--00R--00--R--R--------0-----------------00000-----------R00--------1-0-0----R-G-----------00000000R0--G0000000---R-R0-000R-G--0------------------------------------------------------------------------------------------------------------------------------1-----------------------QBG-00000------R000000-0-0-R----R------------------------------------0QA-------------B---G----G000000R--------R-000000000----------------- SEQ B : name = ./pdbstyle-1.71/2c/d32c2a1.ent c1 SEQ B : residue = DIVLTQSPASLAVSLGQRATISCRASKSVSTSGYGYMHWNQQKPGQPPRLLIYLVSNLESGVPARFSGSGSGTDFTLNIHPVEEEDAATYYCQHIREPLTFGGGTKLEIK SEQ B : code = --00000O000000R00RR000000R0018100RG00000000R0G0000000RR0000RG01QBG00000R00000000RR0QABGG0000001R1R0000R00000-- SEQ B : lcs = --00000-000000R00RR000000R001--00RG00000000R0G0000000RR0000RG01QBG00000R00000000RR0QABGG000000-R-R0000-00000-- ...... ...... ...... RATIO : lcs/trimmed_seq_a = 0.231 (= 106/ 459), lcs/trimmed_seq_b = 0.883 (= 106/ 120) SEQ A : name = ./PDBdata/2IDB.pdb c1 SEQ A : residue = YNDLRDFLTLLEQQGELKRITLPVDPHLEITEIADRTLRAGGPALLFENPKGYSPVLCNLFGTPKRVAGGQEDVSALREVGKLLAFLKEPEPPKGFRDLPTKRLRGAPCQQKIVSGDDVDLNRIPITCWPEDAAPLITWGLTVTRGPHKERQNLGIYRQQLIGKNKLIRWLSHRGGALDYQEWCAAHPGERFPVSVALGADPATILGAVTPVPDTLSEYAFAGLLRGTKTEVVKCISNDLEVPASAEIVLEGYIEQGETAPEGPYGDHTGYYNEVDSFPVFTVTHITQREDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPEGCSYRLAVVTIKKQYAGHAKRVGVWSFLRQFYTKFVIVCDDDVNARDWNDVIWAITTRDPARDTVLVENTPIDYLDFASPVSGLGSKGLDATNKWPGETQREWGRPIKKDPDVVAHIDAIWDELAIF SEQ A : code = --0QAAAAAAAAABRRG000RG000RBRAAAAAAAAAABGR000000QG00RGO0001RQBRGQAAABQ20RGQAAAAAAAAAAAAAB00000QBBQB800000R00QABR00001R0R0QABGROG00QB0R0000000000000R00RG0000000000R0R0G000RRGRG0QAAAAAAAAAB00RG00000000000QAAAAAAGG000QBG0QAAAAAAABRG00000000R0R0000QB0R000000000R0000R00000QBRG000000000000R000000R00000000001R0QAAAAAAAAAAAAAAAAAAB0QBGR00000QABRR1R000000R0O00RQAABR3QB100QB9R0RG00000QBG0QBGQAAAAAAA8080QA88G0000R0000QBRQBGR00RG000000R00000AB0RG000000000QAAAAAAAABAAABR-- SEQ A : lcs = ---------------R-0--R-000----------------000000--00---000------------------------------------------------00QAB-0----R0R0----R--00--0R000---------------------------------------QAAA------B---G-----------QA-----GG----------------R-------------------------0000R0---R-----QB----------------------------------0QAAAAAA---------------B-R0000------1R-----0R0----QAAB-------------G00000---0------------0-0Q--------------B---------------R00000---R--------00QAAAA----BA--B--- SEQ B : name = ./zy/d1zyma2.ent c1 SEQ B : residue = SGILASPGIAFGKALLLKEKIIDLSAIQDEVILVAADLTPSETAQLNLKKVLGFITDAGGRTSHTSIMARSLELPAIVGTGSVTSQVKNDDYLILDAVNNQVYVNPTNEVIDKMRAVQEQVASE SEQ B : code = --R0R0000000000000PJ000QAB0R0R0R000R000QAHAABGRQAGGR0000R0R1QB0QAAAAHAABR00001R0R0QAABG00R000000QBR00000R00QAAAAGQB1RQABQA-- SEQ B : lcs = --R0R0000000000000--000QAB0R0R0R000R000QA-AABG-QAGGR0000R0R-QB0QAAAA-AABR00001R0R0QAABG00-000000QBR00000R00QAAAA--B---AB---- RATIO TABLE : range | frequency RATIO TABLE : --------------|-------------- RATIO RABLE : [0.9, 1.0] | 1 RATIO TABLE : [0.8, 0.9) | 9 RATIO TABLE : [0.7, 0.8) | 61 RATIO TABLE : [0.6, 0.7) | 265 RATIO TABLE : [0.5, 0.6) | 932 RATIO TABLE : [0.4, 0.5) | 1799 RATIO TABLE : [0.3, 0.4) | 2460 RATIO TABLE : [0.2, 0.3) | 4126 RATIO TABLE : [0.1, 0.2) | 2651 RATIO TABLE : [0.0, 0.1) | 701 RATIO : lcs/trimmed_seq_a = 0.904 (= 415/ 459), lcs/trimmed_seq_b = 0.293 (= 415/ 1415) SEQ A : name = ./PDBdata/2IDB.pdb c1 SEQ A : residue = YNDLRDFLTLLEQQGELKRITLPVDPHLEITEIADRTLRAGGPALLFENPKGYSPVLCNLFGTPKRVAGGQEDVSALREVGKLLAFLKEPEPPKGFRDLPTKRLRGAPCQQKIVSGDDVDLNRIPITCWPEDAAPLITWGLTVTRGPHKERQNLGIYRQQLIGKNKLIRWLSHRGGALDYQEWCAAHPGERFPVSVALGADPATILGAVTPVPDTLSEYAFAGLLRGTKTEVVKCISNDLEVPASAEIVLEGYIEQGETAPEGPYGDHTGYYNEVDSFPVFTVTHITQREDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPEGCSYRLAVVTIKKQYAGHAKRVGVWSFLRQFYTKFVIVCDDDVNARDWNDVIWAITTRDPARDTVLVENTPIDYLDFASPVSGLGSKGLDATNKWPGETQREWGRPIKKDPDVVAHIDAIWDELAIF SEQ A : code = --0QAAAAAAAAABRRG000RG000RBRAAAAAAAAAABGR000000QG00RGO0001RQBRGQAAABQ20RGQAAAAAAAAAAAAAB00000QBBQB800000R00QABR00001R0R0QABGROG00QB0R0000000000000R00RG0000000000R0R0G000RRGRG0QAAAAAAAAAB00RG00000000000QAAAAAAGG000QBG0QAAAAAAABRG00000000R0R0000QB0R000000000R0000R00000QBRG000000000000R000000R00000000001R0QAAAAAAAAAAAAAAAAAAB0QBGR00000QABRR1R000000R0O00RQAABR3QB100QB9R0RG00000QBG0QBGQAAAAAAA8080QA88G0000R0000QBRQBGR00RG000000R00000AB0RG000000000QAAAAAAAABAAABR-- SEQ A : lcs = --0Q----AAAAA-RRG000RG000RBRAAAAAAAAAABGR000000QG00RG-000-RQB-GQAAABQ-0RGQAAAAAAAAAAAAAB00000QBBQB-00000-00QAB-0000--0-0QABG--G00QB-R0000000000000R00RG0000000000R0R0-000R-GRG0QAAAAAAAA-B00--00000000000QAAAAAAGG000QBG0QAAAAAAAB--00000000R0R0000QB0R000000000R0000R00000--RG000000000000R000000R0000000000--0QAAAAAAAAAAAAAAAAAA-0QB-R00000QABRR--000000R0-00RQAABR-QB100QB-R0-G00000QB--QBGQAAAAAAA-0-0QA--G0000R0000QBRQBG-00RG000000R00000AB0RG000000000QAAAAAAAABAAABR-- SEQ B : name = ./tw/d1twfa_.ent c1 SEQ B : residue = VGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESL SEQ B : code = --RG00RG00000R00000000QAAAAAGG00000GRG01RRRR0RG00RG0R1R0G001RR0RG0RRG000QHBG000000000R00000QAHQAAAAAAAABG0RGRR00R00QBGQAAAAAABGRRQAAAAAAAAAAAABGRG00R0000RG0QBG00000RG00000R00000RG000000000000QG000000000QAAAAAAAABG0QAHAABGR00Q0000QAABG0R000000QAB000R0001RG0000QAAAAAAAAAAAAAAAAAHAAB000QAAAAAAAAAAAAAAAAAB00G0R000000RGQB00000QAAABR01AAAAAAAABRQB00RG00000000QBG0QBG0000QAAAABG0000000QB1QAAAAAAAAB0QGG1BG000000QBR0000QB00QGQBG00000R000R00000R00000001O0RGQABG0000000000000000QAAAAABR001R00000000000QAAAAAAAB0O0QAAHQG0QB0RG0RG0000QAAAAAAAABGQBG000QAAAAAAAABGQB0RR00000RGRGR0R000QAAAAAABG00R00000000R00QBRQBR000000RRG0300000QB0RGR00R0QAAAAAAB00QAAAAAAAAAAAAAAAAAAAAB00000QAABG00QAAAAAAAAAAAAAAAAAAAAAAAAABRRG0000RG0QAAAAAAAAAAAAAAAAAAAAAAAAABG0QBGQAAAAAABR0000QAAAAAB000R00000RRG000RRG0RGR0QBG00R0R0QAA0000RG0QAB000QAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAABQB0000QBR0000QBR00R0R00RQGR00QABG0000RQAGG00QAAAAAG0000QBGQA0000QAB0QBQAABGROQAAAAAAAAAAAAAAAAAAAAAAA0QBR00G00000RQAAAAAAAAAABR00QBG00R00QAAAAAAAAAAAAHR0R000RGQAAAAAAAAABQAAAAAAAAAB0QAAB000RR00QAAAAAAAAAAAAAAAABG001B0RQAAAAAAAAHAAAABG013RG000QAAAAAAABR0QG0R030000000QHBQBGQAAAAAAAAA0G000QAAGGR00000R03GQG00RGQAAAAAAAAABGO300RG0000000QAAAAABR00QAAAAAAAAAGB0QBG000000QBGRG0000000O2RRHQAAAAAAAAAB0RG0R0000RG00000000000000QB00000000000000000QB1AABG0RG0QA0000RBQAAAAB0R0QAAAAAAAAAAAAAAAAABR0000QAAAAAAAAABHQBRG000RORRGRG0R000QBG0R00RGQAAAAAAAAAJR000RRRGQAAAAABRG00RG0QBR0000001G-- SEQ B : lcs = ---------------------0QAAAAA--------R---R-----G-----------------------------------000R------------------G0----00R------------B-R--AAAAAAAAAA--BGR-00-0000---Q-G00---RG000--R-------------------Q-------------------BG-QA-AAB----Q0---------R------------------G----QAAAAAAAAAAAAA--------------------------------------------B00000Q---B-----------B-QB----------00---0---0000QA---B-000000-Q---A-------B--GG-------00QBR0000--00------------00-00000R00--------R----G0000000000-------------R0--R00---------------------------0--0RG-RG0---QAAAAAAAAB----000-------------0--00000-----0-000QAAAAAA-G----------------------------G----000QB--G-0---Q-----------------------AAAAAAAB00000--------------------------------------000R-0----------------------------------------R0000Q-----B0--R00000---000---0R--0---00-0R0---0000RG0---000--------------------------------------0000---0000--R00---------------0000R----00-------0000-----0000---0Q--------------AAAAAAAAAAAAAAAAAA0QBR00-000---QA---------BR-------R00---------------0-000R----------------------------000R---QAA--------------B------RQ-------------B--1----00Q-------BR0-G------00000Q-BQBGQAAAAAAA--0-0--QA-G--0000-R0------------------------------000Q-----BR---------------QBG----00---RG000000---R----------------------------------------------------00000---A-B-0RG0--0000-------------------------------0000QAAAAAAAA-B------------------------------AAA---------------------BR------------------- // [NOTE]: A trimmed sequence is the sequence obtained by removing residues of // irregular 5-tile codes, such as '-', where regular 5-tile codes are // {0, A, R, Q, B, G, 1, O, H, 3, J, 8, P, 9, 2, I}. Irregular 5-tile // codes are ommited during the LCS computation and LCSs consist of // regular 5-tile codes only.