Mercurial > repos > public-health-bioinformatics > match_plasmid_to_reference
comparison test-data/CP008719.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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| -1:000000000000 | 0:c917ef6807d7 |
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| 1 LOCUS CP008719 2101 bp DNA circular BCT 05-JAN-2016 | |
| 2 DEFINITION Escherichia coli strain ST648 plasmid pEC648_5, complete sequence. | |
| 3 ACCESSION CP008719 | |
| 4 VERSION CP008719.1 | |
| 5 DBLINK BioProject: PRJNA248607 | |
| 6 BioSample: SAMN02800875 | |
| 7 KEYWORDS . | |
| 8 SOURCE Escherichia coli | |
| 9 ORGANISM Escherichia coli | |
| 10 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; | |
| 11 Enterobacteriaceae; Escherichia. | |
| 12 REFERENCE 1 (bases 1 to 2101) | |
| 13 AUTHORS Gao,Z. | |
| 14 TITLE Complete Genome Sequence of Multiple Antibiotic Resistant | |
| 15 Escherichia coli Isolated from Pleural Effusion of Patients with | |
| 16 Empyema Thoracis | |
| 17 JOURNAL Unpublished | |
| 18 REFERENCE 2 (bases 1 to 2101) | |
| 19 AUTHORS Gao,Z. | |
| 20 TITLE Direct Submission | |
| 21 JOURNAL Submitted (09-JUN-2014) Department of Respiratory and Critical care | |
| 22 medicine, Peking University People's hospital, Xizhimen South | |
| 23 Street, Beijing, Beijing 100101, China | |
| 24 COMMENT Annotation was added by the NCBI Prokaryotic Genome Annotation | |
| 25 Pipeline (released 2013). Information about the Pipeline can be | |
| 26 found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/ | |
| 27 | |
| 28 ##Genome-Assembly-Data-START## | |
| 29 Assembly Method :: Newbler v. 2.3; Consed | |
| 30 Genome Coverage :: 40x; 350x | |
| 31 Sequencing Technology :: Roche 454 GS FLX; Illumina Hiseq 2000 | |
| 32 ##Genome-Assembly-Data-END## | |
| 33 | |
| 34 ##Genome-Annotation-Data-START## | |
| 35 Annotation Provider :: NCBI | |
| 36 Annotation Date :: 06/13/2014 09:01:46 | |
| 37 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation | |
| 38 Pipeline | |
| 39 Annotation Method :: Best-placed reference protein set; | |
| 40 GeneMarkS+ | |
| 41 Annotation Software revision :: 2.6 (rev. 437579) | |
| 42 Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; | |
| 43 repeat_region | |
| 44 Genes :: 4,807 | |
| 45 CDS :: 4,578 | |
| 46 Pseudo Genes :: 132 | |
| 47 CRISPR Arrays :: 2 | |
| 48 rRNAs :: 21 (5S, 16S, 23S) | |
| 49 tRNAs :: 72 | |
| 50 ncRNA :: 4 | |
| 51 Frameshifted Genes :: 116 | |
| 52 ##Genome-Annotation-Data-END## | |
| 53 FEATURES Location/Qualifiers | |
| 54 source 1..2101 | |
| 55 /organism="Escherichia coli" | |
| 56 /mol_type="genomic DNA" | |
| 57 /strain="ST648" | |
| 58 /db_xref="taxon:562" | |
| 59 /plasmid="pEC648_5" | |
| 60 gene join(1882..2101,1..47) | |
| 61 /locus_tag="FH07_00765" | |
| 62 CDS join(1882..2101,1..47) | |
| 63 /locus_tag="FH07_00765" | |
| 64 /inference="EXISTENCE: similar to AA | |
| 65 sequence:RefSeq:WP_001024536.1" | |
| 66 /note="Derived by automated computational analysis using | |
| 67 gene prediction method: Protein Homology." | |
| 68 /codon_start=1 | |
| 69 /transl_table=11 | |
| 70 /product="hypothetical protein" | |
| 71 /protein_id="ALV71377.1" | |
| 72 /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTF | |
| 73 GFHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS" | |
| 74 gene 913..1878 | |
| 75 /locus_tag="FH07_00775" | |
| 76 CDS 913..1878 | |
| 77 /locus_tag="FH07_00775" | |
| 78 /inference="EXISTENCE: similar to AA | |
| 79 sequence:RefSeq:WP_012421200.1" | |
| 80 /note="Derived by automated computational analysis using | |
| 81 gene prediction method: Protein Homology." | |
| 82 /codon_start=1 | |
| 83 /transl_table=11 | |
| 84 /product="Replication protein" | |
| 85 /protein_id="ALV71376.1" | |
| 86 /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRM | |
| 87 ASCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIV | |
| 88 VDYPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRG | |
| 89 KDGSAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGE | |
| 90 VVANVAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQL | |
| 91 DRETNEDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD" | |
| 92 ORIGIN | |
| 93 1 tagatttaaa cggtatcaag tttggatttt taagaacgca ttcttagttc tggaaaagag | |
| 94 61 ccagcggcag gctgaggtga taggtacgag attgcatgca atctctagtg ctctgtctat | |
| 95 121 cctgcattat cctcagcatt atcctcagca ttatcctcag ccttgccaac tcgacaccaa | |
| 96 181 tgcaggatag acaatccgat gtcaaatgtt aacactctgc gagtggtaca ttttccccgg | |
| 97 241 attatcgtcc tgagcctgcc gctggctctc tttctaccgc ctcgctttgc tcgttgctca | |
| 98 301 acgcctcaca gacacggatt aaaatccgca tccgttcacc gttttttaaa gtccgttaaa | |
| 99 361 agcatgatgc catctccgag agttaatctc gtcaaatgct aaatcgtggg ggtccccttt | |
| 100 421 ggggttccga tttagtgatt gacgacacca ccgattaaaa aacttatgcg gggtggatgg | |
| 101 481 tttcacgaag tgaggccatc cacctgtaag acagggtttt gtttttattc cctgttttgg | |
| 102 541 tgatcgggtg tgtggaaaag gttggggtaa gccgttcggg ggtgcttgtt ttggggggtt | |
| 103 601 aaaattgtgg ttattttttg cgcaattctc gcgcgtgatc cttgtattta tacttaaggg | |
| 104 661 ataaatggcg gatatgaaat agtggtttag cccagtaatg acgaggcttt gagtgggttt | |
| 105 721 tgacaggtca aagaaaatgg agcagaattg aggcgttttt aatcggcgtt ggggagtgcg | |
| 106 781 tcaacactcc ccaacatttc gaatgtgtca cctcagcggc aaactctggt gacatgtact | |
| 107 841 ggctcgcaat gcacaggtac gtgatgaata taccacatca aatcacagcc tgcccagatc | |
| 108 901 ggagcaggct taatgtcaga agataaattc ctttcggact acagcccccg tgatgcagtt | |
| 109 961 tgggataccc agcgcacgct taccgattct gtcgggggta tctaccagac tgctgctgaa | |
| 110 1021 ttcgagcgct atgcactccg tatggcctcc tgtagcggtt tgttacgttt tggttggtct | |
| 111 1081 accatcatgg aaaccggaga aacgcgccta cggcttcgta gtgcgcaatt ttgccgtgtc | |
| 112 1141 cgtcattgcc ctgtctgcca gtggagaaga accctcatgt ggcaagcccg tttttatcag | |
| 113 1201 gctctaccga aaatcgttgt ggattacccg tcttcccgat ggttgtttct gacgttaact | |
| 114 1261 gtcaggaact gcgagatagg tgaacttgga acagtcctta cagcaatgaa tgcggcgttt | |
| 115 1321 aagcgaatgg aaaagcgaaa ggagctatca cctgttcagg ggtggatcag ggctacggag | |
| 116 1381 gtgacgcgag gtaaggatgg cagcgcacat ccgcattttc actgtctgct gatggtgcaa | |
| 117 1441 ccttcttggt ttaaagggaa gaactacgtt aagcacgaac gttgggtaga actctggcgc | |
| 118 1501 gattgcttgc gggtgaacta tgagccgaat atcgatattc gggcagtaaa aactaagaca | |
| 119 1561 ggtgaggttg tggccaacgt tgccgagcaa ctgcaaagcg cggttgctga aacgctgaaa | |
| 120 1621 tactccgtta aaccggaaga tatggcaaac gatcctgagt ggtttcttga gctgacgcgg | |
| 121 1681 cagcttcaca agcgccgttt tatctcgacc ggtggggcgc taaaaaacgt cctccagttg | |
| 122 1741 gatcgagaaa ccaatgagga tcttgtcatt gccgacgatg taggggatgg cactgatgac | |
| 123 1801 gggaagcgga cggcgtttgt ctgggattca ggtaaacggc gttacaaacg cgcccctgag | |
| 124 1861 aaggataaat cggattaacg tatgaatatt aatattgaat acctgaatgg aaataagact | |
| 125 1921 attggtttat tttttttaag aagtgaagcg gtgattcctg acaggtttaa aaaccttatt | |
| 126 1981 ttgcttattg atggattaag ttttggcaca tttggttttc atccgcacga aggttttgag | |
| 127 2041 gatgaattaa ttttatatat tcagaaaaca aacgagaggg taaaaactct ttttgtgaaa | |
| 128 2101 a | |
| 129 // | |
| 130 |