Mercurial > repos > public-health-bioinformatics > match_plasmid_to_reference
diff test-data/JQ739157.gbk @ 0:c917ef6807d7 draft default tip
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
author | public-health-bioinformatics |
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date | Tue, 12 Nov 2019 22:47:36 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/JQ739157.gbk Tue Nov 12 22:47:36 2019 -0500 @@ -0,0 +1,214 @@ +LOCUS JQ739157 6544 bp DNA circular BCT 26-JUL-2016 +DEFINITION Acinetobacter pittii strain ABCA95 plasmid pABCA95, complete + sequence. +ACCESSION JQ739157 +VERSION JQ739157.2 +KEYWORDS . +SOURCE Acinetobacter pittii + ORGANISM Acinetobacter pittii + Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; + Moraxellaceae; Acinetobacter; Acinetobacter calcoaceticus/baumannii + complex. +REFERENCE 1 (bases 1 to 6544) + AUTHORS Fu,Y., Du,X., Ji,J., Chen,Y., Jiang,Y. and Yu,Y. + TITLE Epidemiological characteristics and genetic structure of blaNDM-1 + in non-baumannii Acinetobacter spp. in China + JOURNAL J. Antimicrob. Chemother. 67 (9), 2114-2122 (2012) + PUBMED 22604448 +REFERENCE 2 (bases 1 to 6544) + AUTHORS Fu,Y., Du,X., Ji,J., Chen,Y., Jiang,Y. and Yu,Y. + TITLE Direct Submission + JOURNAL Submitted (05-MAR-2012) Department of Infectious Diseases, Sir Run + Run Shaw Hospital, Affiliated with School of Medicine, Zhejiang + University, 3 East Qingchun Road, Hangzhou, Zhejiang 310016, China +REFERENCE 3 (bases 1 to 6544) + AUTHORS Fu,Y., Du,X., Ji,J., Chen,Y., Jiang,Y. and Yu,Y. + TITLE Direct Submission + JOURNAL Submitted (12-MAY-2014) Department of Infectious Diseases, Sir Run + Run Shaw Hospital, Affiliated with School of Medicine, Zhejiang + University, 3 East Qingchun Road, Hangzhou, Zhejiang 310016, China + REMARK Sequence update by submitter +COMMENT On May 12, 2014 this sequence version replaced JQ739157.1. +FEATURES Location/Qualifiers + source 1..6544 + /organism="Acinetobacter pittii" + /mol_type="genomic DNA" + /strain="ABCA95" + /db_xref="taxon:48296" + /plasmid="pABCA95" + gene 375..1031 + /gene="aphA6" + misc_feature 375..1031 + /gene="aphA6" + /note="similar to aphA6; aminoglycoside + 3'-phosphotransferase; 5' end of gene is missing" + mobile_element 1129..2215 + /mobile_element_type="insertion sequence:ISAba125" + repeat_region 1138..1154 + /note="IRL" + /rpt_type=inverted + CDS 1186..2211 + /codon_start=1 + /transl_table=11 + /product="Transposase" + /protein_id="AFK73837.1" + /translation="MEYIKLSYHHLNFEDRTALMLESRKEGFSARKFAELIKRHPSTI + YRELKRNSINDVYQARYASDNTFARRRRGHRKLKIDSILWKFIVEAIRCLWSPQQIAK + RLKTFPDLDQTMNVSHTTIYSTIRALPKGELKKDLLSCLRHENKKRKANGEPKKDSIL + QDIKTIHERPAEVQERKIPGHWEADLIKGKDNKSSIATLIERNTRLCILATLPDAKAE + SVRKALTEALKYLPAELRKTLTYDRGREMSEHKILEEDLGIDVYFCDPHSPWQKGTCE + NMNGLIRQYLPKGIDLNQADQHYLNQVAMSLNTRPRKALDWLTPLEKFAQLVDYHMAF + ETVAPHV" + repeat_region 2190..2206 + /note="IRL" + /rpt_type=inverted + gene 2312..3124 + /gene="blaNDM-1" + CDS 2312..3124 + /gene="blaNDM-1" + /codon_start=1 + /transl_table=11 + /product="metallo-beta-lactamase" + /protein_id="AFK73838.1" + /translation="MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQ + RFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQIL + NWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHS + LTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSL + GNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR" + gene 3128..3493 + /gene="bleo" + CDS 3128..3493 + /gene="bleo" + /note="involved in resistance to bleomycin" + /codon_start=1 + /transl_table=11 + /product="bleomycin resistance protein" + /protein_id="AFK73839.1" + /translation="MADHVTPNLPSRDFDVTEAFYAKLGFATSWKDRGWMILQRGGLQ + LEFFPYPDLDPATSSFGCCLRLDDLDAMVALVNAAGAEEKSTGWPRFKAPQLEASGLR + IGYLIDPDCTLVRLIQNPD" + gene 3498..4133 + /gene="trpF" + misc_feature 3498..4133 + /gene="trpF" + /note="similar to TrpF; phosphoribosyl anthranilate + isomerase; 3' end not present" + gene complement(4150..4830) + /gene="tat" + misc_feature complement(4150..4830) + /gene="tat" + /note="similar to TAT; twin-arginine translocation pathway + signal sequence protein; 5' end of gene is missing." +ORIGIN + 1 aagcttatag cagtgtcaca gatgcgaaaa agcaattaag tgcatatttt gagttttata + 61 atttgaaacg acctcattcg agtctagaca aaatgacacc aaatgagttt tactatgatc + 121 agctacccca acaaaacaag gtggcttaac tagagcggaa tatcacttat aaatacgctt + 181 ttagttgttc aaacaagtgg gaccacctct ctcgcatttg cggggttttt aatgctgaat + 241 aaaaggaaaa cttgatggaa ttgcccaata ttattcaaca atttattgga aacagcgttt + 301 tagagccaaa taaaattggt cagtcgccat cggatgttta ttcttttaat cgaaataatg + 361 aaactttttt tcttaagcga tctagcactt tatatacaga gaccacatac agtgtctctc + 421 gcgaagcgaa aatgttgagt tggctctctg agaaattaaa ggtgcctgaa ctcatcatga + 481 cttttcagga tgagcagttt gaattaatga tcactaaagc gatcaatgca aaaccaattt + 541 cagcgctttt tttaacagac caagaattgc ttgctatcta taaggaggca ctcaatctgt + 601 taaattcagt tgctattatt gattgtccat ttatttcaaa cattgatcat cggttaaaag + 661 agtcaaaatt ttttattgat aaccaactcc ttgacgatat agatcaagat gattttgacg + 721 ctgaattatg gggagaccat agaacttacc taagtctatg gaatgagtta actgagactc + 781 gtgttgaaga aagattggtt ttttctcatg gcgatatcac ggatagtaat atttttatag + 841 ataaattcaa tgaaatttac tttttagatc ttggccgtgc tgggttagct gatgaatttg + 901 tagatatatc ctttgttgaa cgttgcctaa gagaggatgc ctcggaggaa actgctaaaa + 961 tatttttaaa gcatttaaaa aatgatagac ctgacaaaag gaattatttt ttaaaacttg + 1021 atgaattgaa ttgattctaa gcattatcta aaaatactta attgtctttt aacgtcgcta + 1081 aattttaaat aaataagtga agagtgttag tggagccact gatttaaagt tggcagagta + 1141 aaacttgaag tgcgacataa accacctaat taatttaaag ggtttatgga gtatataaaa + 1201 ttgtcatacc atcatcttaa ctttgaagat cgtactgcat taatgcttga gtcaagaaaa + 1261 gaaggctttt cagccagaaa atttgctgaa ctcattaaaa gacatcctag tacgatctat + 1321 cgtgagctta aaagaaatag catcaatgac gtttatcaag ctcgatatgc ttctgataac + 1381 accttcgcta gacgtagacg tggtcacaga aaactcaaaa tcgattcaat cctctggaaa + 1441 tttattgttg aagcgatccg ttgtttatgg tctcctcagc aaatagcaaa gcgtttaaag + 1501 acatttcctg atttggatca aacaatgaat gtaagccata caacgattta ttcaacgata + 1561 cgagcattac caaagggtga gttgaaaaaa gacttattat cctgtctacg tcatgaaaat + 1621 aaaaagcgaa aagctaacgg tgaacctaaa aaagattcta tattacagga tattaaaact + 1681 attcatgagc gcccagccga agttcaagaa agaaaaatac cgggtcattg ggaagctgat + 1741 ttaattaaag gtaaagacaa taaaagttcg atagcaacac ttattgaacg aaatacacgg + 1801 ctctgtatct tggcaacatt acctgatgca aaggcagaat cagtgcgcaa ggctttaact + 1861 gaagctctga aatatttacc tgcagaactg cgtaaaacgt tgacctatga ccgtggacgt + 1921 gagatgtcag aacataaaat actcgaagaa gatttaggca tagatgtata tttctgtgac + 1981 ccacattcac cctggcaaaa aggcacatgc gaaaatatga atggtttaat taggcaatat + 2041 ttacctaaag ggattgattt aaatcaggca gatcagcatt atttaaatca agttgccatg + 2101 tcactgaata ctcgtcctag aaaggcgtta gattggctta caccattaga gaaatttgct + 2161 cagcttgttg attatcatat ggcttttgaa actgtcgcac ctcatgtttg aattcgcccc + 2221 atatttttgc tacagtgaac caaattaaga tcatctattt actaggcctc gcatttgcgg + 2281 ggtttttaat gctgaataaa aggaaaactt gatggaattg cccaatatta tgcacccggt + 2341 cgcgaagctg agcaccgcat tagccgctgc attgatgctg agcgggtgca tgcccggtga + 2401 aatccgcccg acgattggcc agcaaatgga aactggcgac caacggtttg gcgatctggt + 2461 tttccgccag ctcgcaccga atgtctggca gcacacttcc tatctcgaca tgccgggttt + 2521 cggggcagtc gcttccaacg gtttgatcgt cagggatggc ggccgcgtgc tggtggtcga + 2581 taccgcctgg accgatgacc agaccgccca gatcctcaac tggatcaagc aggagatcaa + 2641 cctgccggtc gcgctggcgg tggtgactca cgcgcatcag gacaagatgg gcggtatgga + 2701 cgcgctgcat gcggcgggga ttgcgactta tgccaatgcg ttgtcgaacc agcttgcccc + 2761 gcaagagggg atggttgcgg cgcaacacag cctgactttc gccgccaatg gctgggtcga + 2821 accagcaacc gcgcccaact ttggcccgct caaggtattt taccccggcc ccggccacac + 2881 cagtgacaat atcaccgttg ggatcgacgg caccgacatc gcttttggtg gctgcctgat + 2941 caaggacagc aaggccaagt cgctcggcaa tctcggtgat gccgacactg agcactacgc + 3001 cgcgtcagcg cgcgcgtttg gtgcggcgtt ccccaaggcc agcatgatcg tgatgagcca + 3061 ttccgccccc gatagccgcg ccgcaatcac tcatacggcc cgcatggccg acaagctgcg + 3121 ctgagccatg gctgaccacg tcacccccaa tctgccatcg cgcgatttcg atgtgacaga + 3181 ggcgttttat gcgaagctgg gctttgcgac gagttggaag gatcgcggct ggatgatcct + 3241 gcagcgcggc ggtttgcagc tcgaattctt cccctatcct gacctcgacc cagctacgag + 3301 ctcgttcggc tgttgcctgc ggttggatga tctcgatgcc atggtggcat tggtgaacgc + 3361 ggcgggagcc gaggaaaaaa gcaccggctg gccgcgcttc aaagctccgc aactggaggc + 3421 gagcggcctg aggatcggct acctgatcga tcccgactgc acgctggtgc ggctgatcca + 3481 gaaccccgac tgaccgcatg cccgcgaaaa tcaagatttg cgggatcagc acacccgagg + 3541 cgctcgatgc gaccatcgcg gcgcgggcgg actatgccgg gttggtgttc tatccagcgt + 3601 cgccccgtgc ggttacgtcg aatgtcgcgg gcgctttgac atcgcgcgca gctggccaga + 3661 tcgccatggt cggtttgttc gtcgatgcgg atgatgctgt catcgccgac gcactggtgg + 3721 cagccaagct gaacgcgctg cagctgcacg gttcggaatc gcccgaacgc gtggcccagt + 3781 tgcgcgcgcg gtttggcaag ccggtgtgga aggcgctgcc cgtcgccagc gccagcgatg + 3841 tcgcacgcgc cgcagcctat gccggggcgg cggacttgat cttgttcgac gccaagaccc + 3901 ccaaaggcgc gctgcccggc ggcatggggt tggcgttcga ctggtcgctg ctggccggat + 3961 atcgcggtgc cttgccgtgg gggctggcag gcgggctaaa tccgacgaat gttgccgagg + 4021 cgattgcgcg caccggagcg ccgctggtcg atacctccag cggcgtcgaa agcgcgccgg + 4081 gcgtcaagga taccgacaag attaccaatt tcgcctttgc ggtgcgcttg gcctaaatcg + 4141 cgtcgatcaa taggcgtcgt tcagcgcaaa gatcggcttg cgggtgcgcc actgccctcg + 4201 ggtgaagtcg ggaaaatcta acgtgcgatt gccctcagca atcgattgtt ccgacagagg + 4261 cgtgatcgcg ctccaggcca gcgcgtcgta aatgtcgatt ggcatcgggg ccttggcctt + 4321 cagcgcctcg acaaaagcgt ggatcacgaa ccagtccatc ccgccatgcc cggcccctgc + 4381 cgccagatcg gcgtagcgtt tccatagcgg gtgatcgtat ttcgcaaacc agccctcggc + 4441 aggctcccag cggtgcggct gtgggctctt gccctccaga tagatcgact tgttgacgtc + 4501 catccacagc ccctcggtgc cttgcacccg aaagccgaga gaataggggc gcggcagcga + 4561 ggtgtcgtgg cacagcatga tcgtttcacc attagtgcag ccgatcatgg tgttgaccac + 4621 atcacccagt gcgaatttca cctcggcgtt gggatgatcg gcagagccgt tcttgacgac + 4681 ataatcatgc agcccgcgcg ccttacagcc gaagccgcca gcgcccgctt cgcccggcaa + 4741 cgcgaccttc agggtgcggg tctgcggcgg gtagcacacg ccggcatcgg cgcagccctg + 4801 gtacttcacg gtcagggtgg tcgcgctcgc gccggccgcg ggcgtgccgg tgagggtgcc + 4861 gagcaattcc ttgcggtagg tttcgacgtc gccgaagaat tcgtcgcggt aggccttgcc + 4921 cttcggcagc gccatggtcg cgccggtgaa ggcggcatcg gccttgaccg aggtgcggtg + 4981 ccggtacagg taatagccgt cggcgatccg ccagcgcacc tcgatgcggt ccggcgcggt + 5041 ggcctgcgcg gacaggacga agacctcgtc gaccggcggc agttcgaagt cctgggcgac + 5101 ggccgaggtc gcgggcagcg caagcagcag ggcgagcccg gccagccagc ggcgcaggcg + 5161 gatcgtggat gcggtcattg gctcagttta ccggtcggct ctcggcggcc agccattgca + 5221 ggtattcggg caggccggac gcggcttcga ccgcgagcag ctccgggagt tcgtagggat + 5281 atagtatttt attaaattct tatgggaaat gacgaatgtt aaattatctt aagagcttta + 5341 ataatatcaa tacttatttg attttatcga taattctgct gttaatcata atatctctag + 5401 attatttcta aactgaatga atgtttataa tgagtgattc atattgctat tgaaatcgcc + 5461 ttctcacttt gaaagaaggc gaggatgagg gacttttatg ttgaattatc attttaaaaa + 5521 tgccttataa aagaagctta atgtgttttc ttatataggt ttaaacataa ttgttgtata + 5581 tcttaaatcc aattgatctt aaaattttcc tttatttttt gttatgagtg cgagaaaatt + 5641 gtcaaaaagg tcaatcagac tgggcgttaa tttgttttgc atactttttc ctatatcgaa + 5701 ttaaagtcat ataactaaca ccataatctt tagctatttg agtgaaaggg tatgaatcgt + 5761 ccttattttt aagggtatga attaactctt ttagtttttc ttctgtaatc gcaggcgatc + 5821 ttcccttgta tttacctttc ttttttttag ctaatttaat tccctctgct tgattctcac + 5881 taataatacc cctttcaagt tcagctacag cgcctaatac atggagttga aacttatcga + 5941 acttgtcatc tgaattgggg gtaaagttca ggttattttt gacaatatga acagacactc + 6001 cttttttatt tagcttttga acaatggtta caaggtcaat caagctacgt gccaatctaa + 6061 aaacatcatg agcgtacaca atgtccccac tacggacata atcgaacatt tcctgaagtg + 6121 cagggcgttt ggcagtcttt ccgctaaaat gatcaataaa agttttatct agctcaaagg + 6181 gtagatcatg gagctgtctt tcagggtttt ggtctttagt ggatacacgg atatacccca + 6241 ctctttgaaa gggtgtgttt ttaatttgat cttcaatatc taaattttct ttttccataa + 6301 ccagtataac aaaattagat aacctcaatg ttatatcaca ttagattaac aaaacaaccc + 6361 tattgttata gggtttttag ggtgtattat tatataacaa tagggtatac cctattgtta + 6421 tatatcttca ggtataagga aaaataacga tgattaattt taatgatcta agcgaatctg + 6481 aattattaag gattgcacag actggcatat caaaccgtat aggattgcgt acttcaggac + 6541 attg +// +