LOCUS       CP044304                4006 bp    DNA     circular BCT 18-DEC-2019
DEFINITION  Escherichia coli strain P59A plasmid pP59A-6, complete sequence.
ACCESSION   CP044304
VERSION     CP044304.1
DBLINK      BioProject: PRJNA566431
            BioSample: SAMN12789773
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4006)
  AUTHORS   Nadimpalli,M.
  TITLE     Shared mobile genetic elements are responsible for identical ESBL
            gene types among human- and animal-origin Enterobacteriaceae in
            Cambodia
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4006)
  AUTHORS   Nadimpalli,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-SEP-2019) Civil and Environmental Engineering, Tufts
            University, 200 College Avenue, Medford, MA 02155, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Unicycler v. 2018-07-01T00:00:00
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 20.0x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 09/24/2019 13:58:45
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.9
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 5,068
            CDSs (total)                      :: 4,958
            Genes (coding)                    :: 4,365
            CDSs (with protein)               :: 4,365
            Genes (RNA)                       :: 110
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 77
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 593
            CDSs (without protein)            :: 593
            Pseudo Genes (ambiguous residues) :: 0 of 593
            Pseudo Genes (frameshifted)       :: 387 of 593
            Pseudo Genes (incomplete)         :: 217 of 593
            Pseudo Genes (internal stop)      :: 189 of 593
            Pseudo Genes (multiple problems)  :: 174 of 593
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
FEATURES             Location/Qualifiers
     source          1..4006
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="P59A"
                     /isolation_source="Pork"
                     /db_xref="taxon:562"
                     /plasmid="pP59A-6"
                     /geo_loc_name="Cambodia"
                     /lat_lon="11.5564 N 104.9282 E"
                     /collection_date="2016"
                     /collected_by="Institut Pasteur du Cambodge"
     gene            complement(171..572)
                     /locus_tag="F6P93_25330"
     CDS             complement(171..572)
                     /locus_tag="F6P93_25330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="QGY23149.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVTRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(572..763)
                     /locus_tag="F6P93_25335"
     CDS             complement(572..763)
                     /locus_tag="F6P93_25335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="QGY23150.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCETLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2319..3340)
                     /gene="fepE"
                     /locus_tag="F6P93_25340"
                     /pseudo=""
     CDS             complement(2319..3340)
                     /gene="fepE"
                     /locus_tag="F6P93_25340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001421676.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator"
                     /name="fepE"
     Typing          complement(1375..1590)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="83.71"
                     /coverage="100.0"
                     /evalue="1.62e-49"
     Typing          1571..2099
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.545"
                     /coverage="89.0"
                     /evalue="1.2e-144"
ORIGIN
        1 aatttaataa cccacaacta actgatatta atgagttatc ttcaaaattt taattttgcg
       61 tagggtgtgg gtatttttag tggtgaggag cgttcagaga tctgacgatt tttgggaagg
      121 ttcaggaact ccccgggatg gccggagagg aaaactgaag catgacgggg tcaggatttt
      181 ttccagaatt tccaccatgg cgccggggat tcagttaatt ttgcctggtg attttcaaga
      241 aggagcatag cctgtttcag gctgtcaatg tgcgaatcct tggacaaaag taaggtgttc
      301 aggtgttcaa tctcctgttt cagatgacga gtcacctgtt cactctggtc agcagaggct
      361 gtatcacgct gttcagagac ctgtccagaa tggtgttcac ccttcggttg ttcaaaggga
      421 ccaaagacac gtaaaagctc tgaagtatct accatttttg cattgcgttc accgctacag
      481 gtggacaggt cacctgcttt aattaacctg tgcagtgttg ttctactctt acccgtcagt
      541 cgggcagcct cactaataga tactctggcc atcagttacc atcctgtaat gcatccaatc
      601 tcgaggacag tgtacggaaa agatgctccg catcatcgtg gagtgtctca caaaggtccg
      661 cctcaacatc gagatcaagc tcgttaagct tctccagcag gagcagagac tgattctgga
      721 tgaatttagc catgttcagc gctgttttct gttgtttcgt cataagggcc ctcagagcat
      781 cagtgctcag tataaaccgg taagggggtc ggatgtacga atggttcaga gaacggatct
      841 gaggttatcc tgtagttatt ttgtagttta tctgtagtca tcgcactaaa acgcaggatt
      901 aaatcatcaa cttttgtagt cttcctgtag tctggaaaaa taatccgttc atgcttgcat
      961 gaacgaagca gttaaagacg ctttttcgtc gccgatgatc cttaacctgc gcagatcacc
     1021 cagccagaat gataattttt tgccccttaa atggtcatac acctaacgca gccgcgattt
     1081 ttatcgcaac tgcatgaatt aaatgaaaaa aatggagtta tttcgtgtat tagcgtaata
     1141 cgcaacgtat tacaatcatc tgtaacaaca tgaaaataaa caaataacat gtaataccag
     1201 cgtattacat gtacgctggc cagcgaaaaa gctataacgc ttcccggccg acaggcgggc
     1261 cagaatccac cggggcgtgc aggttctctt cagtaacatg agccattaag tcaaaaaggt
     1321 catattcgcc gggaaacaga gcatcagtcg catccggttg ttcatcatac tcagatggca
     1381 tggtgtgata tccagtagct gaggggtgtt agcgggtttc ggggcgcagc cctgaaccag
     1441 tcacgtgagc gctagcggag tgcatactgg ctaaatattt taaaccgaag tggtgatttg
     1501 ccaaagtgct tcatgtggca ggagtgaaat gaggcttacc ggcgtcagga gaagatgctg
     1561 gttcaggtga tattccgctt cctcgctcac tgactcgctg cgctcggtcg ttcggctgcg
     1621 gcgagcggtg caggcttacg aatggggcgg aaatttattt cctggtggat gccaggaaga
     1681 aacttaacag ggatacgata aggccgcggc aaagccgttt ttccataggc tccgcccccc
     1741 tgacaagcat cacgaaatct gacgctcaaa tcagtggtgg cgaaacccga caggactata
     1801 aagataccag gcgtttcccc ctggtggctc cctcttgcgc tctcctgttc ccgtcctgcg
     1861 gcatccgtgt agtggtggaa gctttaccta aatcaccacg ccccgttccg tttagacagt
     1921 tcgctccaag ctgggctgta tgcaagaacc ccccgttcag cccgaccgct gcgccttatc
     1981 cggtaactat cgtcttgagt ccaacccggt aagacacgac ttaacgccat tggcagcggc
     2041 cactggtaaa caggatgtgc gagagatgta ttgagagttc ttgaagtggc agccttactg
     2101 aggctacact agaaggacag atttggtgac atgtctcgca caagactgtt accacggttc
     2161 agaagttccc caacttactg aaccttcgaa aaaccacctc cccaggtggt tttttcgttt
     2221 tctagagtag aagactacgg ctgtaaggga atgatctcaa gaagatcctt tgaacttttt
     2281 ataaaagttg cttataaaat gatgcatcag cacaactttt actcaatcac actcatcttt
     2341 ctggcctcca tggcatgacg taaaagtata tagccacatg caagcatccc tccaatgaca
     2401 gaagaaagaa ttacaattat ggcattactt ggcccatcct ttctgaccgg taacgttggg
     2461 ctcaattgat actgaaacgg cataaaatca acatccccca ctttcgccac aaccaattga
     2521 ttcacaatat attgacgatt tcgcaactcc ccactcaatt ccgaaacatc cttgattgat
     2581 tttttgatgt tcaatttagt tgctatacca tcagaaccga gagccacagg aaaatctgga
     2641 tcatccttca taatctgacc attgctgtat acaggttttt ttattccagc cgcattagca
     2701 acctccagtg aataattgag gcgtcgaata tctgcattca gctggtttct aatttttatc
     2761 tcatccagtg caagaatttc tttttcaaca ttagttttaa cttctagttc atttcttata
     2821 tcttccatca aatcccttac aacaagggaa gaaacataat taatataccc agacaacaca
     2881 tcgtgagctt ctttacttgt tggagcagta aaactcagag tccatgatac atacaatgat
     2941 gacgtggaac aatcaatgac tatatctatc aacccaacaa ttgcacgatg cagttcgaga
     3001 gcgctaatgt tcttcttttt aattatctcc ataacataag gagatgatct catatactca
     3061 ttcaacgaat taacggactg aaatttctta ataaacagag caaatgcgct atcacgattg
     3121 atatcaaaat ccactcccag aacatgaagc ttggaaagct ccttatttaa ttcactccat
     3181 tgaacagact cagcaggagt aaccacagca gaactagtcc attttggcca aacgaaaacc
     3241 gaagccattt tgaagcgaaa acgatcaccc aacaattttt tattttttgc tgccgtagtc
     3301 gagtcaaaag ttgatttcca tttactaatt ccggcagcat gttgtaatta gaaaatgttc
     3361 gatggatatc tttggtgctg ttgggaaaat acaatagcac tgtctatggt tttgttctcg
     3421 ataggaaaaa tcctaaaaat cattcagcag acatttaaca taacatttta attgtacgca
     3481 ccactaaaac ggcctcaggg cgtttctgac gggaaaccgg taaaacaggc aacaaaccac
     3541 ccgaaaaccc gccagaaacg cgcaggctct gtttttacgg catgcatgag tatgcacgca
     3601 aattactaac gcgaaattat tcagaagatt ccggtctaac ttcgcgtttg gctaatcgaa
     3661 aaccgacggg gttacggtat ttgcgatgac gcggaaggcg attcgccacg gcaaaccgga
     3721 aaaccggttt tcaacgatcg ggagtcccct gggttttcgc gtctgagcgt gactgataac
     3781 gttgctggca agtcgccgga cgactcacca gacaattcac cggcgattcg actcgtgact
     3841 tgactctaga gtcgtaaagg tcaaaaaaac accaaaatga cgattcaact ctagagtcaa
     3901 agtctgtcga tttgcgatag tctaggccag gtcgtcggta ttgactctaa caaacgagtg
     3961 cggaaatcgg cagagtgtgc aatgccgaca cggctgatta cgcctg
//
