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["Table S4. R. etli plasmid p42a contains T-DNA border-like sequences"]
["name","inference","ftype","start","end","strand","locus_tag","gene","product","note","translation","sequence"]
["NC_007762","COORDINATES: similar to AA sequence:RefSeq:WP_076612082.1","CDS",81326,82390,"+","RHE_RS21460",null,"IS3-family-transposase","frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology."]
["NC_007762","COORDINATES: similar to AA sequence:RefSeq:WP_028755357.1","CDS",82452,82697,"+","RHE_RS31985",null,"transposase-domain-containing-protein","internal stop; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology."]
["NC_007762",null,"motif",82784,82808,"+",{"$nulls":3},"putative T-DNA border (1 mismatch versus left and right T-DNA consensus sequence)",null,"CGGCAGGATATATCCTGATGTATAT"]
["NC_007762",null,"motif",85354,85378,"+",{"$nulls":3},"putative T-DNA border (1 mismatch versus left T-DNA consensus sequence, 0 mismatches versus right T-DNA consensus sequence)",null,"TGGCAGGATATATAGACATGTCAAT"]
["NC_007762","COORDINATES: similar to AA sequence:RefSeq:WP_011970474.1","CDS",86505,86816,"+","RHE_RS31995",null,"IS21-family-transposase","incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology."]
["NC_007762","COORDINATES: similar to AA sequence:RefSeq:WP_003548555.1","CDS",86869,87750,"-","RHE_RS21480",null,"ATP-binding-protein","Derived by automated computational analysis using gene prediction method: Protein Homology.","MSATLDAIPSMIDRIRHDLVGLKMPRALEALDHVVRRLEHGELSALEAIDILLSEELTLRENSRIKTALRMGRLATIKTLAGFDFTFQPSLDRDRIFTLAQLGFVDRHEAVHFLGPPGTGKSHLATALGVEAVKAGKSVYFTNLADLIGSLARSEREGRLQERIRFFCRPSLLIVDEIGYLPVVQGGGNLFFQLVNARYERGAMILTSNRGFAEWGDVFGDPVVATALLDRLLHHAVVVQIEGSSYRLRQHAELMPEHVRSKALIAPPAFAPPQKPRGRPPKNPQFSLASTSA"]
["NC_007762","COORDINATES: similar to AA sequence:RefSeq:WP_013041153.1","CDS",87747,89004,"-","RHE_RS21485",null,"IS21-family-transposase","frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology."]
["NC_007762","COORDINATES: similar to AA sequence:RefSeq:WP_011970474.1","CDS",89147,89329,"+","RHE_RS32000",null,"IS21-family-transposase","incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology."]
["NC_007762","COORDINATES: similar to AA sequence:RefSeq:WP_011970475.1","CDS",89329,89906,"+","RHE_RS21490",null,"ATP-binding-protein","frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology."]
["NC_007762","COORDINATES: protein motif:HMM:NF013677.1","CDS",90837,91199,"+","RHE_RS21495",null,"IS66-family-insertion-sequence-hypothetical-protein","Derived by automated computational analysis using gene prediction method: Protein Homology.","MARIEIMSGTERRRRWSDEAKLRILAEADEPGARIGDVARRHDIHPGQIRLWRQSFNYADRPTVFLPVEITEEVGVSQPSTASTRPTIVEILLRNGRSLKVAVDVELKLLGPLVACVEAV"]
["NC_007762","COORDINATES: similar to AA sequence:RefSeq:WP_008555941.1","CDS",91196,91543,"+","RHE_RS21500","tnpB","IS66-family-insertion-sequence-element-accessory-protein-TnpB","Derived by automated computational analysis using gene prediction method: Protein Homology.","MIGPSGNVRVYLACGVTDMRRGIDGLSALVETVVREAPGSGAIFGFRGKRADRIKLLWWDGQGFCLFYKILERGYFPWPTAKEGVAHLTQAQLSMLVEGIDWRRPAWTSAPGRTG"]
["NC_007762","COORDINATES: similar to AA sequence:RefSeq:WP_009996985.1","CDS",91616,93181,"+","RHE_RS21505",null,"IS66-like-element-ISRel19-family-transposase","Derived by automated computational analysis using gene prediction method: Protein Homology.","METAPLDSQDELNTLRALVAEQAAKLESQEAEVIKRDSIIGLLRAQLELLRHRQHGASSEKIDRKIEQFELMLEEIEASRAEAEQRSGKPPLPELDDASEKPKRKPLPDDLTTEELVYAAPCNCPTCGGTSFLKAADRVVQVLEHVPASVKIVRHVEKRMICRECDTTVAGEMPTLPIERGKPGPGLLAHIMIAKFDDHIPLYRLSEMYDRLGIDISRSVMADWVGRVSALLTPLVLLIRAHIAALDRIHTDDTPVDVLDPGRGKTKTGRVWVYIFDGSGYQSATPAAIAYYYSPDRRGAHPADHLASFSGVMHADGYGGYKKLYGNQIIEAACMAHVRRKFHDVIKLKPSPIAEEALSRIGALYDIENRIRGMSADERRTLRQHHARPVLDELKAWIEATLSTLPQKQRLAEAMRYALSRWAALSVYIDDGRVEIDNNIAERAMRPLGIGRKNWLFAGSDKGGERIANILTIIETVKLQGHNPEVYLTDVLTRIQDHPEDRIEDLLPWNWTPAKARCEAA"]
["NC_007762","COORDINATES: similar to AA sequence:RefSeq:WP_011971014.1","CDS",93181,93477,"+","RHE_RS21510",null,"hypothetical-protein","incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology."]
["NC_007762","COORDINATES: similar to AA sequence:RefSeq:WP_011427378.1","CDS",93363,94322,"-","RHE_RS21515",null,"IS5-family-transposase","Derived by automated computational analysis using gene prediction method: Protein Homology.","MSWTAIARREHNRDVLRFPSDLKDREWALIKPLIPPARRGGRRRTTNMRSVAEAILYIASSGCQWRILPGDFPPVSTVRGYFYAWRAIGLWQSINQLLVMAAREIEGREAQPTAGIIDSQSVKATQSGGISGYDAGKKIKGRKRQIVTDTLGFLIFVFIHAADIQDRDGAPHVLKAIRRRFPWLRHIFADGGYAGAKLRRAMSGHGDWTIEIVKRSDHAKGFVVLPKRWVVERTFAWLGRCRRLAKDWEKSIESATAWAQIASIVSVRRTHFRVSRDGIYRPRFISSAMMRSIISGSHCVSMRNSRIPPSHVLMSASRL"]
["NC_007762",null,"motif",94407,94431,"+",{"$nulls":3},"putative T-DNA border (0 mismatches versus left and right T-DNA consensus sequence)",null,"TGGCAGGATATATCCTGATGTAAAA                                                                                "]
["NC_007762",null,"motif",96124,96148,"+",{"$nulls":3},"putative T-DNA border (1 mismatch versus right T-DNA consensus sequence)",null,"TGGCTGGATATATAGCTTTGTAGCC                                                                                "]
["NC_007762","COORDINATES: similar to AA sequence:RefSeq:WP_012556471.1","CDS",96241,97719,"+","RHE_RS21520",null,"trehalose-6-phosphate-synthase","Derived by automated computational analysis using gene prediction method: Protein Homology.","MKCVRPQNTLGSSTVNCSECCALTEHEFLGCPVDPIDTQGRLIVVSNRIRRDASPGNNSGGLAVAVNAALKLRGGIWMGWSGNTDAEATSTKMTREGNVTYVEVDLTTADVRDYYNGFSNQTLWPLFHSFKDRAVLSEDYEVAYRRVNATFAEILFPLWRPDDAVWVHDYHLIPLAEELRKLGSIGRVGFFLHVPWPKFEVLHDVPVHKLLLKAMSSYDVIGFQTRNDLTNFYEAVNCCNEGGKLENDVVLLFGRRIKLGAYAVSIETLNFAKSAAAAAKQPSMRQMVESLQGQTLIISVDRLDYTKGILERVRAYETFLKGNPSYLRKVTYLQIAPISRSDVLEYQQLQAAVAEAVGKANGAIGTADWTPLRYINSGSSRDELGALFRLARVGFVTPIRDGMNLVAKEYIAAQDAANPGVLIISGFAGAAQELSAGIIVDPRNIQSMAQAIADALEMPLTERKDRWRNMMTWLLEHDINYWTNTYLDDLFS"]
["NC_007762","COORDINATES: protein motif:HMM:NF013383.1,HMM:NF014381.1","CDS",98216,99271,"+","RHE_RS21525",null,"NAD/NADP-octopine/nopaline-dehydrogenase-family-protein","Derived by automated computational analysis using gene prediction method: Protein Homology.","MKVLIIGAGNLGNAFAADLSSRNHRVSIWTHPSHPGNSIKIANEGLEAKGAVVGHFYPTILPDLGHAVSEAEAIIVTIPAKAGVKEELKVRLAEHDLASKILIWVPGLLASLVGVKLSTAATFEASNSPYGCRIDEGKAFIKAFKKVIEIAAFDADSETEYRSQVEALFPSRLEWRANILDVAMHNTNFITHPVTVIENAQRILAGESFRFYRDGMTPSVCEKMEKLDELRMSVIAKFNFAGISHIGLVNRWYGRNEPNYLAFARNSPSHNATLGVPSDMQHRYLTEDCRMLPFYRGLAEKFGINAEIADWVLAQARALAGEDFEETGLTLAKLDMEGLSGDEIVAKWGAN"]
["NC_007762","COORDINATES: ab initio prediction:GeneMarkS-2+","CDS",100326,100631,"+","RHE_RS32005",null,"hypothetical-protein","Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.","MADNFKENVKDAYSIAERIALGYEPARDKPLLDAVGKRIMISKAVPNYPHIENLDQLKTFFIWFKQIKSFDNEPGCASGIANCFTFNHYLDATTTAQSLTQ"]
["NC_007762","COORDINATES: similar to AA sequence:RefSeq:WP_076611444.1","CDS",101211,102313,"+","RHE_RS21535",null,"IS3-like-element-ISRel21-family-transposase","programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.","MKASQFSDAQKAFILKQGDEGVSVAEICRKAGISQATYFNWKKKYAGMLPPEMKRLKQLEDENSRLKKIVADLTLDREMLQDVIRRKPLRPARKREMVKGMCCDWAISIRRACGALNFDRSTHHYTSRRADQAGLERRIREICEIRVRYGYRRVHVLLEREGWGTNIKRTYRIYRDLGLQLRNKTPKRRVKAKLREDRHMAVGPNDVWAMDFVHDQLAIGKKLRVLTVVDTFSRYVPVLDPRHSYRGEDVVQTLERVCQKAGYPKTIRVDQGTEFVSRDLDLWAYSKGVTLDFSRPGKPTDNAFIEAFNGRFRAECLNQHWFLTLADAREKMEDWRRYYNEERPHGAIGNKVPISLVNSGCATSPPP"]
["NC_007762",null,"motif",102413,102437,"+",{"$nulls":3},"putative T-DNA border (1 mismatch versus right T-DNA consensus sequence)",null,"TGACGGGATATATAGCGACGTAGAG"]
["NC_007762","COORDINATES: similar to AA sequence:RefSeq:WP_011427384.1","CDS",102550,103386,"+","RHE_RS21540",null,"IS5-like-element-ISRel20-family-transposase","Derived by automated computational analysis using gene prediction method: Protein Homology.","MSWTAIARREHNRDVLRFPSDLKDREWALIKPLIPPARRGGRRRTTNMRSVAEAILYIASSGCQWRILPGDFPPVSTVRGYFYAWRAIGLWQSINQLLVMAAREIEGREAQPTAGIIDSQSVKATQSGGISGYDAGKKIKGRKRQIVTDTLGFLIFVFIHAADIQDRDGAPHVLKAIRRRFPWLRHIFADGGYAGAKLRRAMSGHGDWTIEIVKRSDHAKGFVVLPKRWVVERTFAWLGRCRRLAKDWEKSIESATAWAQIASIRMLIRRIARYWIYE"]
["NC_007762","COORDINATES: similar to AA sequence:RefSeq:WP_012330183.1","CDS",103511,104359,"-","RHE_RS21545",null,"IS256-family-transposase","incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology."]
["NC_007762","COORDINATES: similar to AA sequence:RefSeq:WP_012650068.1","CDS",104412,105400,"-","RHE_RS21550",null,"IS5-family-transposase","frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology."]
[]
["The p42a sequence was screened for T-DNA left (NGGCAGGATNTATNNNNNTGTAANN) and right (TGNCAGGATNTATNNNNNNGTNNNN) border sequences"]
["A well matching sequence was found at 94407-94431 and four others almost matched the consensus sequences"]
["The annotation of the surrounding genes is from accession NC_007762 (annotated with NCBI Prokaryotic Genome Annotation Pipeline)"]
["The protein annotated as \"NAD/NADP-octopine/nopaline-dehydrogenase-family-protein\" (RHE_RS21525) has 69.9% sequence similarity to pTi-EU6 encoded D,L-succinamopine synthase (calculated by Needleman-Wunsch global alignment with EMBOSS needle tool)"]