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A brief instruction for the standalone US-align program:

Brief instruction, which can be obtained by running:

$ USalign -h

Usage: USalign PDB1.pdb PDB2.pdb [Options] Options: -mol Type of molecule(s) to align. auto: (default) align both protein and nucleic acids. prot: only align proteins in a structure. RNA : only align RNA and DNA in a structure. -mm Multimeric alignment option: 0: (default) alignment of two monomeric structures 1: alignment of two multi-chain oligomeric structures 2: alignment of individual chains to an oligomeric structure $ USalign -dir1 monomers/ list oligomer.pdb -ter 0 -mm 2 3: alignment of circularly permuted structure 4: alignment of multiple monomeric chains into a consensus alignment $ USalign -dir chains/ list -suffix .pdb -mm 4 To use -mm 1 or -mm 2, '-ter' option must be 0 or 1. -ter Number of chains to align. 3: only align the first chain, or the first segment of the first chain as marked by the 'TER' string in PDB file 2: (default) only align the first chain 1: align all chains of the first model (recommended for aligning asymmetric units) 0: align all chains from all models (recommended for aligning biological assemblies, i.e. biounits) -TMscore Whether to perform TM-score superposition without structure-based alignment. The same as -byresi. 0: (default) sequence independent structure alignment 1: superpose two structures by assuming that a pair of residues with the same residue index are equivalent between the two structures 2: superpose two structures, assuming that a pair of residues with the same residue index and the same chain ID are equivalent between the two structures 5: sequence dependent alignment: perform glocal sequence alignment followed by TM-score superposition. -byresi 5 is the same as -seq 6: superpose two complex structures by first deriving optimal chain mapping, followed by TM-score superposition for residues with the same residue ID -I Use the final alignment specified by FASTA file 'align.txt' -i Use alignment specified by 'align.txt' as an initial alignment -m Output rotation matrix for superposition -d TM-score scaled by an assigned d0, e.g., '-d 3.5' reports MaxSub score, where d0 is 3.5 Angstrom. -d does not change final alignment. -u TM-score normalized by an assigned length. It should be >= length of protein to avoid TM-score >1. -u does not change final alignment. -o Output superposed structure1 to sup.* for PyMOL viewing. $ USalign structure1.pdb structure2.pdb -o sup $ pymol -d @sup.pml # C-alpha trace aligned region $ pymol -d @sup_all.pml # C-alpha trace whole chain $ pymol -d @sup_atm.pml # full-atom aligned region $ pymol -d @sup_all_atm.pml # full-atom whole chain $ pymol -d @sup_all_atm_lig.pml # full-atom with all molecules -rasmol Output superposed structure1 to sup.* for RasMol viewing. $ USalign structure1.pdb structure2.pdb -rasmol sup $ rasmol -script sup # C-alpha trace aligned region $ rasmol -script sup_all # C-alpha trace whole chain $ rasmol -script sup_atm # full-atom aligned region $ rasmol -script sup_all_atm # full-atom whole chain $ rasmol -script sup_all_atm_lig # full-atom with all molecules -h Print the full help message, including additional options Example usages ('gunzip' program is needed to read .gz compressed files): USalign 101m.cif.gz 1mba.pdb # pairwise monomeric protein alignment USalign 1qf6.cif 5yyn.pdb.gz -mol RNA # pairwise monomeric RNA alignment USalign model.pdb native.pdb -TMscore 1 # calculate TM-score between two conformations of a monomer USalign 4v4a.cif 4v49.cif -mm 1 -ter 1 # oligomeric alignment for asymmetic units USalign 3ksc.pdb1 4lej.pdb1 -mm 1 -ter 0 # oligomeric alignment for biological units USalign 1ajk.pdb.gz 2ayh.pdb.gz -mm 3 # circular permutation alignment Additional options: -v Print the version of US-align -a TM-score normalized by the average length of two structures T or F, (default F). -a does not change the final alignment. -fast Fast but slightly inaccurate alignment -dir Perform all-against-all alignment among the list of PDB chains listed by 'chain_list' under 'chain_folder'. Note that the slash is necessary. $ USalign -dir chain_folder/ chain_list -dir1 Use chain2 to search a list of PDB chains listed by 'chain1_list' under 'chain1_folder'. Note that the slash is necessary. $ USalign -dir1 chain1_folder/ chain1_list chain2 -dir2 Use chain1 to search a list of PDB chains listed by 'chain2_list' under 'chain2_folder' $ USalign chain1 -dir2 chain2_folder/ chain2_list -suffix (Only when -dir1 and/or -dir2 are set, default is empty) add file name suffix to files listed by chain1_list or chain2_list -atom 4-character atom name used to represent a residue. Default is " C3'" for RNA/DNA and " CA " for proteins (note the spaces before and after CA). -split Whether to split PDB file into multiple chains 0: treat the whole structure as one single chain 1: treat each MODEL as a separate chain 2: (default) treat each chain as a separate chain -outfmt Output format 0: (default) full output 1: fasta format compact output 2: tabular format very compact output -1: full output, but without version or citation information -TMcut -1: (default) do not consider TMcut Values in [0.5,1): Do not proceed with TM-align for this structure pair if TM-score is unlikely to reach TMcut. TMcut is normalized as set by -a option: -2: normalized by longer structure length -1: normalized by shorter structure length 0: (default, same as F) normalized by second structure 1: same as T, normalized by average structure length -mirror Whether to align the mirror image of input structure 0: (default) do not align mirrored structure 1: align mirror of Structure_1 to origin Structure_2, which usually requires the '-het 1' option: $ USalign 4glu.pdb 3p9w.pdb -mirror 1 -het 1 -het Whether to align residues marked as 'HETATM' in addition to 'ATOM ' 0: (default) only align 'ATOM ' residues 1: align both 'ATOM ' and 'HETATM' residues 2: align both 'ATOM ' and MSE residues -se Do not perform superposition. Useful for extracting alignment from superposed structure pairs -infmt1 Input format for structure_11 -infmt2 Input format for structure_2 -1: (default) automatically detect PDB or PDBx/mmCIF format 0: PDB format 1: SPICKER format 3: PDBx/mmCIF format Advanced usage 1 (generate an image for a pair of superposed structures): USalign 1cpc.pdb 1mba.pdb -o sup pymol -c -d @sup_all_atm.pml -g sup_all_atm.png Advanced usage 2 (a quick search of query.pdb against I-TASSER PDB library): wget https://zhanggroup.org/library/PDB.tar.bz2 tar -xjvf PDB.tar.bz2 USalign query.pdb -dir2 PDB/ PDB/list -suffix .pdb -outfmt 2 -fast

An example of pairwise alignment between two monomeric proteins:

$ USalign 101m.cif 1mba.pdb

******************************************************************** * US-align (Version 20220126) * * Universal Structure Alignment of Proteins and Nucleic Acids * * Reference: C Zhang, M Shine, AM Pyle, Y Zhang. (2022) Submitted. * * Please email comments and suggestions to yangzhanglab@umich.edu * ******************************************************************** Name of Structure_1: 101m.cif:A (to be superimposed onto Structure_2) Name of Structure_2: 1mba.pdb:A Length of Structure_1: 154 residues Length of Structure_2: 146 residues Aligned length= 143, RMSD= 1.83, Seq_ID=n_identical/n_aligned= 0.245 TM-score= 0.81453 (normalized by length of Structure_1: L=154, d0=4.62) TM-score= 0.85377 (normalized by length of Structure_2: L=146, d0=4.50) (You should use TM-score normalized by length of the reference structure) (":" denotes residue pairs of d < 5.0 Angstrom, "." denotes other aligned residues) MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRVKHLKTEAEMKASEDLKKHGVTVLTALGAILKKK--G-HHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGNFGADAQGAMNKALELFRKDIAAKYKELGYQG :::::::::::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::::::::::::: : :::::::::::::: ::::::::::::::::::::::::: :::::::::::::::::::::: : :: -SLSAAEADLAGKSWAPVFANKNANGLDFLVALFEKFPDSANFFADFKGKS-VADIKASPKLRDVSSRIFTRLNEFVNNAANAGKMSAMLSQFAKEHV-GFGVGSAQFENVRSMFPGFVASVAA--PPAGADAAWTKLFGLIIDALKA-A-----GA #Total CPU time is 0.03 seconds

Visualizing the alignment in PyMOL:

$ USalign 101m.cif 1mba.pdb -o sup
$ pymol -d @sup_all_atm_lig.pml

Visualizing the alignment in RasMol:

$ USalign 101m.cif 1mba.pdb -rasmol sup
$ rasmol -script sup_all_atm_lig

An example of alignment between two oligomers:

$ USalign 4v4a.cif 4v49.cif

******************************************************************** * US-align (Version 20220126) * * Universal Structure Alignment of Proteins and Nucleic Acids * * Reference: C Zhang, M Shine, AM Pyle, Y Zhang. (2022) Submitted. * * Please email comments and suggestions to yangzhanglab@umich.edu * ******************************************************************** Name of Structure_1: 4v4a.cif:AA:AB:AC:AD:AE:AF:AG:AH:AI:AJ:AK:AL:AM:AN:AO:AP:AQ:AR:AS:AT:B0:B9:BA:BB:BC:BD:BE:BF:BG:BH:BI:BJ:BK:BL:BM:BN:BO:BP:BQ:BR:BS:BT:BU:BV:BW:BX:BY:BZ:B1:B2:B3:B4:B5::: (to be superimposed onto Structure_2) Name of Structure_2: 4v49.cif:AA:AB:AC:AD:AE:AF:AG:AH:AI:AJ:AK:AL:AM:AN:AO:AP:AQ:AR:AS:AT:B0:B9:BA:BB:BC:BD:BE:BF:BG:BH:BI:BJ:BK:BL:BM:BN:BO:BP:BQ:BR:BS:BT:BU:BV:BW:BX:BY:BZ:B1:B2:B3:B4:B5:AV:AU:AW Length of Structure_1: 10449 residues Length of Structure_2: 10604 residues Aligned length= 10443, RMSD= 0.91, Seq_ID=n_identical/n_aligned= 1.000 TM-score= 0.99814 (normalized by length of Structure_1: L=10449, d0=25.30) TM-score= 0.98356 (normalized by length of Structure_2: L=10604, d0=25.43) (You should use TM-score normalized by length of the reference structure) (":" denotes residue pairs of d < 5.0 Angstrom, "." denotes other aligned residues) uggagaguuugauccuggcucagggugaacgcuggcggcgugccuaagacaugcaagucgugcggauacgcgcggccccuuggggccgugcgucagcggcggacgggugaguaacgcgugggugaccuacccggaagagggggacaacccggggaaacucgggcuaaucccccauguggacgcaaguccaaagggggaagccuucgggucccccgcuuccggaugggcccgcgucccaucagcuaguuggugggguaauggcccaccaaggcgacgacggguagccggucugagaggauggccggccacaggggcacugagacacgggccccacuccuacgggaggcagcaguuaggaaucuuccgcaaugggcgcaagccugacggagcgacgccgcuuggaggaagaagcccuucgggguguaaacuccugaacccgggacgaaaccagggccacucauacuggcucugacugacgguaccgggguaauagcgccggccaacuccgugccagcagccgcgguaauacggagggcgcgagcguuacccggauucacugggcguaaagggcguguaggcggccuggggcgucccaugugaaagaccacggcucaaccgugggggagcgugggauacgcucaggcuagacggugggagagggugguggaauucccggaguagcggugaaaugcgcagauaccgggaggaacgccgauggcgaaggcagccaccugguccacccgugacgcugaggcgcgaaagcguggggagcaaaccggauuagauacccggguaguccacgcccuaaacgaugcgcgcuaggucucuggcggcucaaccgcugggggccgaagcuaacgcguuaagcgcgccgccuggggaguacggccgcaaggcugaaacucaaaggaauugacgggggcccgcacaagcgguggagcaugugguuuaauucgaagcaacgcgaagaaccuuaccaggccuugacaugcuagggaacccgggugaaagccuggggugccuucgggagcccuagcacaggugcugcauggccgucgucagcucgugccgugagguguuggguuaagucccgcaacgagcgcaacccccgccguuaguugccagcgguucggccgggcacucuaacgggacugcccgcgaaagcgggaggaaggaggggacgacgucuggucagcauggcccuuacggccugggcgacacacgugcuacaaugcccacuacaaagcgaugccacccggcaacggggagcuaaucgcaaaaaggugggcccaguucggauuggggucugcaacccgaccccaugaagccggaaucgcuaguaaucgcggaucagccaugccgcggugaauacguucccgggccuuguacacaccgcccgucacgccaugggagcgggcucuacccgaagucgccggguaaccuacgggaagcaggcgccgaggguagggcccgugacuggggcgaagucguaacaagguagcuguaccggaaggugcggcuggaucacuuucu*VKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKLFIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ*GNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRANIDYGFALARTTYGVLGVKAYIFLGEV*GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQLVIEFYSR*DFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELGSRNPINIAYATMEALRQLRTKADVERLRKG*MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA*ARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKVFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIAHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW*MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW*EQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFDAYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKARRAPQYSKR*KIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSREHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKT*KRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFRKAS*PTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPKEA*ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKKAPRK*ARKALIEKAKRTPKFKVRAYTRCVRCGRARSVYRFFGLCRICLRELAHKGQLPGVRKASW*PITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRALIEKLGIRG*MVKIRLARFGSKHNPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLKVDVERARYWLSVGAQPTDTARRLLRQAGVFRQE*PKKVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESRPISKRKRFRVLRLVESGRMDLVEKYLIRRQNYQSLSKRGGKA*PSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSGKEQRILAKTIKRARILGLLPFTEKLVRK*PRSLKKGVFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKLGEFAPTRTYR*RNLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAVQLAQEGKAEEALKIMRKAESLIDKAAKGSTLHKNAAARRKSRLMRKVRQLLEAAGAPLIGGGLSA*ggucaagauaguaaggguccacgguggaugcccuggcgcuggagccgaugaaggacgcgauuaccugcgaaaagccccgacgagcuggagauacgcuuugacucggggauguccgaauggggaaacccaccucguaagagguauccgcaaggaugggaacucagggaacugaaacaucucaguaccugaaggagaagaaagagaauucgauuccguuaguagcggcgagcgaacccggaucagcccaaauucaaccccucaagccgaaguggcuggaaagcuacaccucagaaggugagaguccuguaggcgaacgagcgguugacuguaaggucguuguucgugaaacgaugacugaauccgcgcggaccaccgcgcaaggcuaaauacucccagugaccgauagcgcauaguaccgugagggaaaggugaaaagaaccccgggaggggagugaaagagaaccugaaaccguggacuuacaagcagucauggcaccuuaugcguguuauggcgugccuauugaagcaugagccggcgacuuagaccugacgugcgagcuuaaguugaaaaacggaggcggagcgaaagcgaguccgaauagggcggcauuaguacgucgggcuagacucgaaaccaggugagcuaagcaugaccagguugaaacccccgugacagggggcggaggaccgaaccggugccugcugaaacagucucggaugaguuguguuuaggagugaaaagcuaaccgaaccuggagauagcuaguucuccccgaaauguauugagguacagccucggauguugaccauguccuguagagcacucacaaggcuaagggcacguaauguguucuaaaccuuaugaaacuccgaaggggcacgcguuuaguccgggagugaggcugcgagagcuaacuuccguagccgagagggaaacaacccagaccaucagcuaaggucccuaaaugaucgcucagugguuaaggaugugucgucgcauagacagccaggagguuggcuuagaagcagccacccuucaaagagugcguaauagcucacuggucgagugacgaugcgccgaaaaugaucggggcucaagugaucuaccgaagcuauggauucaacucgcgaagcgaguugucugguaggggagcguucaguccgcggagaagccauaccggaaggagugguggagccgacugaagugcggaugccggcaugaguaacgauaaaagaagugagaaucuucuucgccguaaggacaaggguuccuggggaagggucguccgcccagggaaagucgggaccuaaggugaggccgaacggcgcagccgauggacagcaggucaagauuccugcaccgaucauguggagugauggagggacgcauuacgcuauccaaugccaagcuauggcuaugcugguugguacgcucaagggcgaucgggucagaaaaucuaccggucacaugccucagacguaucgggagcuuccucggaagcgaaguuggaaacgcgacggugccaagaaaagcuucuaaacguugaaacaugauugcccguaccgcaaaccgacacagguguccgagugucaaugcacuaaggcgcgcgagagaacccucguuaaggaacuuugcaaucucaccccguaacuucggaagaagggguccccacgcuucgcguggggcgcagugaauaggcccaggcgacuguuuaccaaaaucacagcacucugccaacacgaacaguggacguauagggugugacgccugcccggugccggaaggucaaguggagcgguaagugcaagcaaagcugcgaaaugaagccccggugaacggcggccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaaaggcguaacgaucugggcgcugucucaacgagggacucggugaaauugaauuggcuguaaagaugcggccuacccguagcaggacgaaaagaccccguggagcuuuacuauagucuggcauucaacguugggacguggugcguaggauaggugggaggcgaagaacccuggcuacggcuggggggagccgccggugaaauaccacccucuacucuuugacguuguaaccugaaaaaucacuuucggggaccgugcuuggcggguaguuugacuggggcggucgccucccaaaauguaacggaggcgcccaaaggucaccucaagacgguuggaaaucgucuguagagcgcaaagguagaagguggcuugacugcgagacugacacgucgagcagggaggaaacucgggcuuagugaaccggugguaccguguggaagggccaucgaucaacggauaaaaguuaccccggggauaacaggcugaucucccccgagaguccauaucggcggggagguuuggcaccucgaugucggcucgucgcauccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaagcggcacgcgagcuggguucagaacgucgugagacaguucggucucuauccgcuacgggcgcaggagaauugaggggaguugcuccuaguacgagaggaccggagugaacggaccgcuggucucccugcugucguaccaacggcacaugcaggguagcuauguccggaacggauaaccgcugaaagcaucuaagcgggaagccagccccaagaugaguucucccacuguucagguaagacucccggaagaccaccggguuaagaggccaggcgugcacgcauagcaauguguucagcggacuggugcucaucagucgaggucuugacca*cccccgugcccauagcacuguggaaccaccccaccccaugccgaacugggucgugaaacacagcagcgccaaugauacucggaccgcagggucccggaaaagucggucagcgcggggg*KKYRPYTPSRRQMTTADFSGLTKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKRLYRIIDFKRRDKSGVNAKVAAIEYDPNRSARIALLHYADGEKRYILAPEGLTVGATVNAGPEAEPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGTSVQVQGKESDYVIVRLPSGELRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRTGAGRVPVTPWGKPTKGLKTRRKRKTSDRFIVTR*MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVNKPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRWNFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGENLILVKGAIPGANGGLVVLRSAAKAS*AQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAVDGFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDILRHDRLVIDAAALEIVEE*QQLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDKAAKELALITLQKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEKLINIGLPRIRDFRGINPNAFDGRGNYNLGIKEQLIFPEITYDMVDKTRGMDITIVTTAKTDEEARALLQSMGLPFRK*GKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQKHRALHGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAGVTFAVPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGKAGATGG*MQVILLEPSRLGKTGEVVSVKDGYARNWLIPQGLAVSATRTNMKTLEAQLRS*MKKVAGIVKLQLPAGKATPAPPVGPALGQYGANIMEFTKAFNAQTADKGDAIIPVEITIYADRSFTFITKTPPMSYLIRKAAGIGKGSSTPNKAKVGKLNWDQVLEIAKTKMPDLNAGSVEAAANTVAGTARSMGVTVEGGPN*VKTYIPKNDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVYTRYTGYQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPHSAQKPQVLKTQPL*IMPQSRLDVADNSGAREIMCIRVLNSGIGGKGLTTGGGGNKRYAHVGDIIVASVKDAAPRGAVKAGDVVKAVVVRTSHAIKRADGSTIRFDRNAAVIINNQGEPRGTRVFGPVARELRDRRFMKIVSLAPEV*HDLKPTPGSRKDRKRVGRGPGGTDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARLPKRGFNNVGTTYEVVKLSQLQDLEDTTFDRDTLEAYRLVRRKNRPVKLLASGEISRAVTVHVDAASAAAIKAVEAAGGRVVLPE*TKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRRGGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRLAGHKLPIQTK*HGKAGRKLNRNSSARVALARAQATALLREGRIQTTLTKAKELRPFVEQLITTAKGGDLHSRRLVAQDIHDKDVVRKVMDEVAPKYAERPGGYTRILRVGTRRGDGVTMALIELV*ATTIRRKLRTRRKVRTTTAASGRLRLSVYRSSKHIYAQIIDDSRGQTLAAASSAALKSGNKTDTAAAVGKALAAAAAEKGIKQVVFDRGSYKYHGRVKALADAAREGGLDF*QTHIKINRGELLRGIEQDHTRQLPDFRPGDTVRVDTKVREGNRTRSQAFEGVVIAINGSGSRKSFTVRKISFGEGVERVFPFASPLVNQVTIVERGKVRRAKLYYLRELRGKAARIKSDRSRVMK*PRAKTGIVRRRRHKKVLKRAKGFWGSRSKQYRNAFQTLLNAATYEYRDRRNKKRDFRRLWIQRINAGARLHGMNYSTFINGLKRANIDLNRKVLADIAAREPEAFKALVDASRNARQ*MFAIIQTGGKQYRVSEGDVIRVESLQGEAGDKVELKALFVGGEQTVFGEDAGKYTVQAEVVEHGRGKKIYIRKYKSGVQYRRRTGHRQNFTAIKILGIQG*EQTFRNKKQRKQQVKLRKPGFAVAKYVRMSPRKVRLVVDVIRGKSVQDAEDLLRFIPRSASEPVAKVLNSAKANALHNDEMLEDRLFVKEAYVDAGPTLKRLIPRARGSANIIKKRTSHITIIVAEKGNK*SHYDILQAPVISEKAYSAMERGVYSFWVSPKATKTEIKDAIQQAFGVRVIGISTMNVPGKRKRVGRFIGQRNDRKKAIVRLAEGQSIEALAGQ*PRPSAGSHHNDKLHFKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVEGVNVITKNVKPSMTNPQGGQEQRELALHASKVALVDPETGKATRVRKQIVDGKKVRVAVASGKTI*MELTAKPRTPKQKLDESMIAAVAYNKENNVSFALDRKAFDRAFRQQSTTGLFDITVEGGETFPALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGRSQGEVQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTLAADPELTVVSVLP*AHKKGVGSSKNGRDSNPKYLGVKKFGGEVVKAGNILVRQRGTKFKAGQGVGMGRDHTLFALSDGKVVFINKGKGARFISIEAAQTE*XXXXXXXXXXXXXXXX*KPSEMRNLQATDFAKEIDARKKELMELRFQAAAGQLAQPHRVRQLRREVAQLNTVKAELARKGEQ*MKIKLVRSVIGRPGNQVKTVQALGLRKIGDSREVSDTPAVRGMVKTVKHLLEVQE*MQKDLHPKAVPCKIIYQGQVVMETMSTRPEIHVDVWSGVHPFWTGEERFLDTEGRVDKFNKRFGDSYRRGSKK*AKHPVPKKKTSKSKRDMRRSHHALTAPNLTECPQCHGKKLSHHICPNCGYYDGRQVLA*AKDGPRIIVKMESSAGTGFYYTTTKNRRNTQAKLELKKYDPVAKKHVVFREKK*MKRTYQPNNRKRAKTHGFRARMKTKSGRNILARRRAKGRHQLTVSD*PKMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLAKAEWARMKLMLPR*KVRSSVKKMCDNCKVVRRHGRVLVICSNVKHKQRQ*MLADKESLIEALKLALSTEYNVKRNFTQSVEIILTFKGIDKKGDLKLREIVPLPKQPSKAKRVLVVPSSEQLEYAKKASPKVVITREELQKLQGQKRPVKKLARQNEWFLINQESALAGRILGPALGPRGKFPTPLPNTADISEYINRFKRSVLVKTKDQPQVQVFIGTEDKPEDLAENAIAVLNAIENKAKVETNLRNIYVKTTGKAVKVKR*----------------------------------------------------------------------------*---------*----------------------------------------------------------------------------* 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uggagaguuugauccuggcucagggugaacgcuggcggcgugccuaagacaugcaagucgugcggauacgcgcggccccuuggggccgugcgucagcggcggacgggugaguaacgcgugggugaccuacccggaagagggggacaacccggggaaacucgggcuaaucccccauguggacgcaaguccaaagggggaagccuucgggucccccgcuuccggaugggcccgcgucccaucagcuaguuggugggguaauggcccaccaaggcgacgacggguagccggucugagaggauggccggccacaggggcacugagacacgggccccacuccuacgggaggcagcaguuaggaaucuuccgcaaugggcgcaagccugacggagcgacgccgcuuggaggaagaagcccuucgggguguaaacuccugaacccgggacgaaaccagggccacucauacuggcucugacugacgguaccgggguaauagcgccggccaacuccgugccagcagccgcgguaauacggagggcgcgagcguuacccggauucacugggcguaaagggcguguaggcggccuggggcgucccaugugaaagaccacggcucaaccgugggggagcgugggauacgcucaggcuagacggugggagagggugguggaauucccggaguagcggugaaaugcgcagauaccgggaggaacgccgauggcgaaggcagccaccugguccacccgugacgcugaggcgcgaaagcguggggagcaaaccggauuagauacccggguaguccacgcccuaaacgaugcgcgcuaggucucuggcggcucaaccgcugggggccgaagcuaacgcguuaagcgcgccgccuggggaguacggccgcaaggcugaaacucaaaggaauugacgggggcccgcacaagcgguggagcaugugguuuaauucgaagcaacgcgaagaaccuuaccaggccuugacaugcuagggaacccgggugaaagccuggggugccuucgggagcccuagcacaggugcugcauggccgucgucagcucgugccgugagguguuggguuaagucccgcaacgagcgcaacccccgccguuaguugccagcgguucggccgggcacucuaacgggacugcccgcgaaagcgggaggaaggaggggacgacgucuggucagcauggcccuuacggccugggcgacacacgugcuacaaugcccacuacaaagcgaugccacccggcaacggggagcuaaucgcaaaaaggugggcccaguucggauuggggucugcaacccgaccccaugaagccggaaucgcuaguaaucgcggaucagccaugccgcggugaauacguucccgggccuuguacacaccgcccgucacgccaugggagcgggcucuacccgaagucgccggguaaccuacgggaagcaggcgccgaggguagggcccgugacuggggcgaagucguaacaagguagcuguaccggaaggugcggcuggauca------*VKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKLFIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ*GNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVAEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRANIDYGFALARTTYGVLGVKAYIFLGEV*GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQLVIEFYSR*DFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELGSRNPINIAYATMEALRQLRTKADVERLRKG*MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA*ARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKVFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIAHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW*MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW*EQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFDAYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKARRAPQYSKR*KIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSREHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKT*KRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFRKAS*PTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPKEA*ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKKAPRK*ARKALIEKAKRTPKFKVRAYTRCVRCGRARSVYRFFGLCRICLRELAHKGQLPGVRKASW*PITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRALIEKLGIRG*MVKIRLARFGSKHNPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLKVDVERARYWLSVGAQPTDTARRLLRQAGVFRQE*PKKVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIESRPISKRKRFRVLRLVESGRMDLVEKYLIRRQNYQSLSKRGGKA*PSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSGKEQRILAKTIKRARILGLLPFTEKLVRK*PRSLKKGVFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKLGEFAPTRTYR*RNLSALKRHRQSLKRRLRNKAKKSAIKTLSKKAVQLAQEGKAEEALKIMRKAESLIDKAAKGSTLHKNAAARRKSRLMRKVRQLLEAAGAPLIGGGLSA*ggucaagauaguaaggguccacgguggaugcccuggcgcuggagccgaugaaggacgcgauuaccugcgaaaagccccgacgagcuggagauacgcuuugacucggggauguccgaauggggaaacccaccucguaagagguauccgcaaggaugggaacucagggaacugaaacaucucaguaccugaaggagaagaaagagaauucgauuccguuaguagcggcgagcgaacccggaucagcccaaauucaaccccucaagccgaaguggcuggaaagcuacaccucagaaggugagaguccuguaggcgaacgagcgguugacuguaaggucguuguucgugaaacgaugacugaauccgcgcggaccaccgcgcaaggcuaaauacucccagugaccgauagcgcauaguaccgugagggaaaggugaaaagaaccccgggaggggagugaaagagaaccugaaaccguggacuuacaagcagucauggcaccuuaugcguguuauggcgugccuauugaagcaugagccggcgacuuagaccugacgugcgagcuuaaguugaaaaacggaggcggagcgaaagcgaguccgaauagggcggcauuaguacgucgggcuagacucgaaaccaggugagcuaagcaugaccagguugaaacccccgugacagggggcggaggaccgaaccggugccugcugaaacagucucggaugaguuguguuuaggagugaaaagcuaaccgaaccuggagauagcuaguucuccccgaaauguauugagguacagccucggauguugaccauguccuguagagcacucacaaggcuaagggcacguaauguguucuaaaccuuaugaaacuccgaaggggcacgcguuuaguccgggagugaggcugcgagagcuaacuuccguagccgagagggaaacaacccagaccaucagcuaaggucccuaaaugaucgcucagugguuaaggaugugucgucgcauagacagccaggagguuggcuuagaagcagccacccuucaaagagugcguaauagcucacuggucgagugacgaugcgccgaaaaugaucggggcucaagugaucuaccgaagcuauggauucaacucgcgaagcgaguugucugguaggggagcguucaguccgcggagaagccauaccggaaggagugguggagccgacugaagugcggaugccggcaugaguaacgauaaaagaagugagaaucuucuucgccguaaggacaaggguuccuggggaagggucguccgcccagggaaagucgggaccuaaggugaggccgaacggcgcagccgauggacagcaggucaagauuccugcaccgaucauguggagugauggagggacgcauuacgcuauccaaugccaagcuauggcuaugcugguugguacgcucaagggcgaucgggucagaaaaucuaccggucacaugccucagacguaucgggagcuuccucggaagcgaaguuggaaacgcgacggugccaagaaaagcuucuaaacguugaaacaugauugcccguaccgcaaaccgacacagguguccgagugucaaugcacuaaggcgcgcgagagaacccucguuaaggaacuuugcaaucucaccccguaacuucggaagaagggguccccacgcuucgcguggggcgcagugaauaggcccaggcgacuguuuaccaaaaucacagcacucugccaacacgaacaguggacguauagggugugacgccugcccggugccggaaggucaaguggagcgguaagugcaagcaaagcugcgaaaugaagccccggugaacggcggccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaaaggcguaacgaucugggcgcugucucaacgagggacucggugaaauugaauuggcuguaaagaugcggccuacccguagcaggacgaaaagaccccguggagcuuuacuauagucuggcauucaacguugggacguggugcguaggauaggugggaggcgaagaacccuggcuacggcuggggggagccgccggugaaauaccacccucuacucuuugacguuguaaccugaaaaaucacuuucggggaccgugcuuggcggguaguuugacuggggcggucgccucccaaaauguaacggaggcgcccaaaggucaccucaagacgguuggaaaucgucuguagagcgcaaagguagaagguggcuugacugcgagacugacacgucgagcagggaggaaacucgggcuuagugaaccggugguaccguguggaagggccaucgaucaacggauaaaaguuaccccggggauaacaggcugaucucccccgagaguccauaucggcggggagguuuggcaccucgaugucggcucgucgcauccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaagcggcacgcgagcuggguucagaacgucgugagacaguucggucucuauccgcuacgggcgcaggagaauugaggggaguugcuccuaguacgagaggaccggagugaacggaccgcuggucucccugcugucguaccaacggcacaugcaggguagcuauguccggaacggauaaccgcugaaagcaucuaagcgggaagccagccccaagaugaguucucccacuguucagguaagacucccggaagaccaccggguuaagaggccaggcgugcacgcauagcaauguguucagcggacuggugcucaucagucgaggucuugacca*cccccgugcccauagcacuguggaaccaccccaccccaugccgaacugggucgugaaacacagcagcgccaaugauacucggaccgcagggucccggaaaagucggucagcgcggggg*KKYRPYTPSRRQMTTADFSGLTKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKRLYRIIDFKRRDKSGVNAKVAAIEYDPNRSARIALLHYADGEKRYILAPEGLTVGATVNAGPEAEPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGTSVQVQGKESDYVIVRLPSGELRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRTGAGRVPVTPWGKPTKGLKTRRKRKTSDRFIVTR*MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVNKPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRWNFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGENLILVKGAIPGANGGLVVLRSAAKAS*AQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAVDGFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDILRHDRLVIDAAALEIVEE*QQLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDKAAKELALITLQKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEKLINIGLPRIRDFRGINPNAFDGRGNYNLGIKEQLIFPEITYDMVDKTRGMDITIVTTAKTDEEARALLQSMGLPFRK*GKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQKHRALHGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAGVTFAVPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGKAGATGG*MQVILLEPSRLGKTGEVVSVKDGYARNWLIPQGLAVSATRTNMKTLEAQLRS*MKKVAGIVKLQLPAGKATPAPPVGPALGQYGANIMEFTKAFNAQTADKGDAIIPVEITIYADRSFTFITKTPPMSYLIRKAAGIGKGSSTPNKAKVGKLNWDQVLEIAKTKMPDLNAGSVEAAANTVAGTARSMGVTVEGGPN*VKTYIPKNDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVYTRYTGYQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPHSAQKPQVLKTQPL*IMPQSRLDVADNSGAREIMCIRVLNSGIGGKGLTTGGGGNKRYAHVGDIIVASVKDAAPRGAVKAGDVVKAVVVRTSHAIKRADGSTIRFDRNAAVIINNQGEPRGTRVFGPVARELRDRRFMKIVSLAPEV*HDLKPTPGSRKDRKRVGRGPGGTDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARLPKRGFNNVGTTYEVVKLSQLQDLEDTTFDRDTLEAYRLVRRKNRPVKLLASGEISRAVTVHVDAASAAAIKAVEAAGGRVVLPE*TKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRRGGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRLAGHKLPIQTK*HGKAGRKLNRNSSARVALARAQATALLREGRIQTTLTKAKELRPFVEQLITTAKGGDLHSRRLVAQDIHDKDVVRKVMDEVAPKYAERPGGYTRILRVGTRRGDGVTMALIELV*ATTIRRKLRTRRKVRTTTAASGRLRLSVYRSSKHIYAQIIDDSRGQTLAAASSAALKSGNKTDTAAAVGKALAAAAAEKGIKQVVFDRGSYKYHGRVKALADAAREGGLDF*QTHIKINRGELLRGIEQDHTRQLPDFRPGDTVRVDTKVREGNRTRSQAFEGVVIAINGSGSRKSFTVRKISFGEGVERVFPFASPLVNQVTIVERGKVRRAKLYYLRELRGKAARIKSDRSRVMK*PRAKTGIVRRRRHKKVLKRAKGFWGSRSKQYRNAFQTLLNAATYEYRDRRNKKRDFRRLWIQRINAGARLHGMNYSTFINGLKRANIDLNRKVLADIAAREPEAFKALVDASRNARQ*MFAIIQTGGKQYRVSEGDVIRVESLQGEAGDKVELKALFVGGEQTVFGEDAGKYTVQAEVVEHGRGKKIYIRKYKSGVQYRRRTGHRQNFTAIKILGIQG*EQTFRNKKQRKQQVKLRKPGFAVAKYVRMSPRKVRLVVDVIRGKSVQDAEDLLRFIPRSASEPVAKVLNSAKANALHNDEMLEDRLFVKEAYVDAGPTLKRLIPRARGSANIIKKRTSHITIIVAEKGNK*SHYDILQAPVISEKAYSAMERGVYSFWVSPKATKTEIKDAIQQAFGVRVIGISTMNVPGKRKRVGRFIGQRNDRKKAIVRLAEGQSIEALAGQ*PRPSAGSHHNDKLHFKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVEGVNVITKNVKPSMTNPQGGQEQRELALHASKVALVDPETGKATRVRKQIVDGKKVRVAVASGKTI*MELTAKPRTPKQKLDESMIAAVAYNKENNVSFALDRKAFDRAFRQQSTTGLFDITVEGGETFPALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGRSQGEVQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTLAADPELTVVSVLP*AHKKGVGSSKNGRDSNPKYLGVKKFGGEVVKAGNILVRQRGTKFKAGQGVGMGRDHTLFALSDGKVVFINKGKGARFISIEAAQTE*XXXXXXXXXXXXXXXX*KPSEMRNLQATDFAKEIDARKKELMELRFQAAAGQLAQPHRVRQLRREVAQLNTVKAELARKGEQ*MKIKLVRSVIGRPGNQVKTVQALGLRKIGDSREVSDTPAVRGMVKTVKHLLEVQE*MQKDLHPKAVPCKIIYQGQVVMETMSTRPEIHVDVWSGVHPFWTGEERFLDTEGRVDKFNKRFGDSYRRGSKK*AKHPVPKKKTSKSKRDMRRSHHALTAPNLTECPQCHGKKLSHHICPNCGYYDGRQVLA*AKDGPRIIVKMESSAGTGFYYTTTKNRRNTQAKLELKKYDPVAKKHVVFREKK*MKRTYQPNNRKRAKTHGFRARMKTKSGRNILARRRAKGRHQLTVSD*PKMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLAKAEWARMKLMLPR*KVRSSVKKMCDNCKVVRRHGRVLVICSNVKHKQRQ*MLADKESLIEALKLALSTEYNVKRNFTQSVEIILTFKGIDKKGDLKLREIVPLPKQPSKAKRVLVVPSSEQLEYAKKASPKVVITREELQKLQGQKRPVKKLARQNEWFLINQESALAGRILGPALGPRGKFPTPLPNTADISEYINRFKRSVLVKTKDQPQVQVFIGTEDKPEDLAENAIAVLNAIENKAKVETNLRNIYVKTTGKAVKVKR*gcggauuuagcucaguugggagagcgccagacugaagaucuggagguccuguguucgauccacagaauucgcacca*auguucaaa*gcggauuuagcucaguugggagagcgccagacugaagaucuggagguccuguguucgauccacagaauucgcacca* #Total CPU time is 178.61 seconds

An example of multiple structure alignment (MSTA), i.e., aligning more than three monomers into one consensus alignment:

$ USalign -dir chains/ list -mm 4

******************************************************************** * US-align (Version 20220126) * * Universal Structure Alignment of Proteins and Nucleic Acids * * Reference: C Zhang, M Shine, AM Pyle, Y Zhang. (2022) Submitted. * * Please email comments and suggestions to yangzhanglab@umich.edu * ******************************************************************** Name of Structure_1: shorter (to be superimposed onto Structure_2) Name of Structure_2: longer Length of Structure_1: 84 residues Length of Structure_2: 92 residues Aligned length= 68, RMSD= 3.51, Seq_ID=n_identical/n_aligned= 0.491 TM-score= 0.46705 (normalized by length of Structure_1: L=84, d0=135.23) TM-score= 0.44992 (normalized by length of Structure_2: L=92, d0=3.24) TM-score= 0.45992 (normalized by user-specified L=88.00 and d0=3.11) (You should use TM-score normalized by length of the reference structure) (":" denotes residue pairs of d < 5.0 Angstrom, "." denotes other aligned residues) >3w3sB.pdb:B (L=98) * ---gggagagg-uuggccggcu---gg-ugccgcc-ccgg-ga----cuuc-----------------------aa-aucccgugggag---gucccgca-a-gg--gag-----c-uccggaggguucgauucccucccucucc----------cg--c---c- >6jxmB.pdb:B (L=97) ----gcggaag-uagu-uca-g-u-gg-uagaa-c-accc-ga----cagacgaagcgcuaaaacgug-ggauucu-gucgggggg---------------------------------ucgcggguucgagucccgucuuccgc----------uc--c---a- >1wz2C.pdb:C (L=88) ----gcggggg-uugc-cgagccu-ggucaaaggc-ggg--gg----acuca----------------------agauccccucc-----------------------cguaggg--guuccgggguucgaauccccgcccccgca------cca---------- >4v8bAB.pdb:V (L=87) ----gccgagg-uggu-ggaau-ug-gu-agacac-gcua--c----cuuga----------------------ggugguagugc----------------------ccaauagg--gcuuacggguucaagucccguccucggu----------acca------ >3q1qC.pdb:C (L=86) ----ggccagg-uagc-uc-ag-uugg-uaga-gc-acug-ga-----uaugggca----------ccccc-uaag--uccaggug---------------------------------ucggcgguucgauuccgccccuggccacca---------------- >4v8dAB.pdb:V (L=84) ----ggugggg-uucc-cgagc--g-gccaaaggg-agca--g----acugu----------------------aa-ucugccgu-----------------------c-aucga--cuucgaagguucgaauccuucccccacc----------acca------ >3am1B.pdb:B (L=81) ---ggcgcgggguaccgggcuu---gg-uagcccggggcu-uc-------------------------------------ggc-cgagg---gcga-----------gag-----cccuc--gggguucgauucccccccugcgc----------cg--c----- >5lzdy.pdb:y (L=91) ---ggaagauc-gucg-ucucc---gg--gaggcg-gcug-g----a---cu--------------------uc-aauc-caguuggggccg-------ccagcggu---------cccgggcagg--cgacuccugugaucuu-----------cc--gcca-- >6ah3T.pdb:T (L=80) agaagcggauu-uagc-ucagu-u-ggg-ag-agc-gcca--g----acuga----------------------agaucugg-agg---------------------------------uccuguguucgauccacagaauucgca---uuu------------- >3adbC.pdb:C (L=92) ---ggccgccgccacc-ggggu---gg-uccccgg-gccggacuuca---------------------------ga---uccggcgcgc---cccga------gu--ggg-----g-cgc--gggguucaauuccccgcggcggc-----------c--gc--ca #Total CPU time is 0.40 seconds

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