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"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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LOCUS CP008719 2101 bp DNA circular BCT 05-JAN-2016 DEFINITION Escherichia coli strain ST648 plasmid pEC648_5, complete sequence. ACCESSION CP008719 VERSION CP008719.1 DBLINK BioProject: PRJNA248607 BioSample: SAMN02800875 KEYWORDS . SOURCE Escherichia coli ORGANISM Escherichia coli Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia. REFERENCE 1 (bases 1 to 2101) AUTHORS Gao,Z. TITLE Complete Genome Sequence of Multiple Antibiotic Resistant Escherichia coli Isolated from Pleural Effusion of Patients with Empyema Thoracis JOURNAL Unpublished REFERENCE 2 (bases 1 to 2101) AUTHORS Gao,Z. TITLE Direct Submission JOURNAL Submitted (09-JUN-2014) Department of Respiratory and Critical care medicine, Peking University People's hospital, Xizhimen South Street, Beijing, Beijing 100101, China COMMENT Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/ ##Genome-Assembly-Data-START## Assembly Method :: Newbler v. 2.3; Consed Genome Coverage :: 40x; 350x Sequencing Technology :: Roche 454 GS FLX; Illumina Hiseq 2000 ##Genome-Assembly-Data-END## ##Genome-Annotation-Data-START## Annotation Provider :: NCBI Annotation Date :: 06/13/2014 09:01:46 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline Annotation Method :: Best-placed reference protein set; GeneMarkS+ Annotation Software revision :: 2.6 (rev. 437579) Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes :: 4,807 CDS :: 4,578 Pseudo Genes :: 132 CRISPR Arrays :: 2 rRNAs :: 21 (5S, 16S, 23S) tRNAs :: 72 ncRNA :: 4 Frameshifted Genes :: 116 ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..2101 /organism="Escherichia coli" /mol_type="genomic DNA" /strain="ST648" /db_xref="taxon:562" /plasmid="pEC648_5" gene join(1882..2101,1..47) /locus_tag="FH07_00765" CDS join(1882..2101,1..47) /locus_tag="FH07_00765" /inference="EXISTENCE: similar to AA sequence:RefSeq:WP_001024536.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="hypothetical protein" /protein_id="ALV71377.1" /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTF GFHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS" gene 913..1878 /locus_tag="FH07_00775" CDS 913..1878 /locus_tag="FH07_00775" /inference="EXISTENCE: similar to AA sequence:RefSeq:WP_012421200.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="Replication protein" /protein_id="ALV71376.1" /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRM ASCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIV VDYPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRG KDGSAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGE VVANVAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQL DRETNEDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD" ORIGIN 1 tagatttaaa cggtatcaag tttggatttt taagaacgca ttcttagttc tggaaaagag 61 ccagcggcag gctgaggtga taggtacgag attgcatgca atctctagtg ctctgtctat 121 cctgcattat cctcagcatt atcctcagca ttatcctcag ccttgccaac tcgacaccaa 181 tgcaggatag acaatccgat gtcaaatgtt aacactctgc gagtggtaca ttttccccgg 241 attatcgtcc tgagcctgcc gctggctctc tttctaccgc ctcgctttgc tcgttgctca 301 acgcctcaca gacacggatt aaaatccgca tccgttcacc gttttttaaa gtccgttaaa 361 agcatgatgc catctccgag agttaatctc gtcaaatgct aaatcgtggg ggtccccttt 421 ggggttccga tttagtgatt gacgacacca ccgattaaaa aacttatgcg gggtggatgg 481 tttcacgaag tgaggccatc cacctgtaag acagggtttt gtttttattc cctgttttgg 541 tgatcgggtg tgtggaaaag gttggggtaa gccgttcggg ggtgcttgtt ttggggggtt 601 aaaattgtgg ttattttttg cgcaattctc gcgcgtgatc cttgtattta tacttaaggg 661 ataaatggcg gatatgaaat agtggtttag cccagtaatg acgaggcttt gagtgggttt 721 tgacaggtca aagaaaatgg agcagaattg aggcgttttt aatcggcgtt ggggagtgcg 781 tcaacactcc ccaacatttc gaatgtgtca cctcagcggc aaactctggt gacatgtact 841 ggctcgcaat gcacaggtac gtgatgaata taccacatca aatcacagcc tgcccagatc 901 ggagcaggct taatgtcaga agataaattc ctttcggact acagcccccg tgatgcagtt 961 tgggataccc agcgcacgct taccgattct gtcgggggta tctaccagac tgctgctgaa 1021 ttcgagcgct atgcactccg tatggcctcc tgtagcggtt tgttacgttt tggttggtct 1081 accatcatgg aaaccggaga aacgcgccta cggcttcgta gtgcgcaatt ttgccgtgtc 1141 cgtcattgcc ctgtctgcca gtggagaaga accctcatgt ggcaagcccg tttttatcag 1201 gctctaccga aaatcgttgt ggattacccg tcttcccgat ggttgtttct gacgttaact 1261 gtcaggaact gcgagatagg tgaacttgga acagtcctta cagcaatgaa tgcggcgttt 1321 aagcgaatgg aaaagcgaaa ggagctatca cctgttcagg ggtggatcag ggctacggag 1381 gtgacgcgag gtaaggatgg cagcgcacat ccgcattttc actgtctgct gatggtgcaa 1441 ccttcttggt ttaaagggaa gaactacgtt aagcacgaac gttgggtaga actctggcgc 1501 gattgcttgc gggtgaacta tgagccgaat atcgatattc gggcagtaaa aactaagaca 1561 ggtgaggttg tggccaacgt tgccgagcaa ctgcaaagcg cggttgctga aacgctgaaa 1621 tactccgtta aaccggaaga tatggcaaac gatcctgagt ggtttcttga gctgacgcgg 1681 cagcttcaca agcgccgttt tatctcgacc ggtggggcgc taaaaaacgt cctccagttg 1741 gatcgagaaa ccaatgagga tcttgtcatt gccgacgatg taggggatgg cactgatgac 1801 gggaagcgga cggcgtttgt ctgggattca ggtaaacggc gttacaaacg cgcccctgag 1861 aaggataaat cggattaacg tatgaatatt aatattgaat acctgaatgg aaataagact 1921 attggtttat tttttttaag aagtgaagcg gtgattcctg acaggtttaa aaaccttatt 1981 ttgcttattg atggattaag ttttggcaca tttggttttc atccgcacga aggttttgag 2041 gatgaattaa ttttatatat tcagaaaaca aacgagaggg taaaaactct ttttgtgaaa 2101 a //