Mercurial > repos > public-health-bioinformatics > match_plasmid_to_reference
view test-data/outdir/reference_plasmid.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 |
---|---|
date | Tue, 12 Nov 2019 22:47:36 -0500 |
parents | |
children |
line wrap: on
line source
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 //