LOCUS       CP044303                6471 bp    DNA     circular BCT 18-DEC-2019
DEFINITION  Escherichia coli strain P59A plasmid pP59A-5, complete sequence.
ACCESSION   CP044303
VERSION     CP044303.1
DBLINK      BioProject: PRJNA566431
            BioSample: SAMN12789773
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6471)
  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  JOURNAL   Unpublished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 6471)
  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..6471
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="P59A"
                     /isolation_source="Pork"
                     /db_xref="taxon:562"
                     /plasmid="pP59A-5"
                     /geo_loc_name="Cambodia"
                     /lat_lon="11.5564 N 104.9282 E"
                     /collection_date="2016"
                     /collected_by="Institut Pasteur du Cambodge"
     gene            complement(join(6343..6471,1..1995))
                     /locus_tag="F6P93_25295"
                     /pseudo=""
     CDS             complement(join(6343..6471,1..1995))
                     /locus_tag="F6P93_25295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001395566.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="DNA primase"
                     /name="DNA primase"
     gene            2195..2479
                     /locus_tag="F6P93_25300"
     CDS             2195..2479
                     /locus_tag="F6P93_25300"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000238497.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein C"
                     /protein_id="QGY23143.1"
                     /translation="MVKGSNKAADRLAKLEEQRARINAEIQRVRAREQQQERKNETRRK
                     VLVGAMILAKVNSSEWPEDRLMAAMDAYLERDHDRALFGLPPRQKDEPG"
                     /name="mobilization protein C"
     gene            complement(3149..4003)
                     /gene="estX"
                     /locus_tag="F6P93_25305"
     CDS             complement(3149..4003)
                     /gene="estX"
                     /locus_tag="F6P93_25305"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016242844.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="alpha/beta fold putative hydrolase EstX"
                     /protein_id="QGY23148.1"
                     /translation="MKEKVVVDKAISLHTESFGDPAHEPIILIMGAMASAVWWPDEFCS
                     QLAKMGRYVIRYDHRDTGKSTSYEPGQAPYSVEELADDVVRVIDGYGLEAAHLVGMSLG
                     GFLSQLVALKYPKRVKSLTLIASERLADADPDMPAFDPAIIEYHQRAESLDWSDRDAVV
                     AYQVGAWRIISGTAHAFDAEKIQNIAELDFDRTPNILTTFNHTTSGGGERSLERWLGRL
                     NEIAVPTLIIHGTEDPVLPYVHGLALKDAIRGSKMLTLEGTGHELHHEDWPRIIQAIKG
                     QTS"
                     /name="estX"
     gene            complement(4155..5006)
                     /locus_tag="F6P93_25310"
     CDS             complement(4155..5006)
                     /locus_tag="F6P93_25310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_569413.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication protein"
                     /protein_id="QGY23144.1"
                     /translation="MVKPKNKHSLSHVRHDPAHCLAPGLFRALKRGERKRSKLDVTYDY
                     GDGKRIEFSGPEPLGADDLRILQGLVAMAGPNGLVLGPEPKTEGGRQLRLFLEPKWEAV
                     TADAMVVKGSYRALAKEIGAEVDSGGALKHIQDCIERLWKVSIIAQNGRKRQGFRLLSE
                     YASDEADGRLYVALNPLIAQAVMGGGQHVRISMDEVRALDSETARLLHQRLCGWIDPGK
                     TGKASIDTLCGYVWPSEASGSTMRKRRQRVREALPELVALGWTVTEFAAGKYDITRPKA
                     AG"
                     /name="replication protein"
     gene            complement(4993..5832)
                     /locus_tag="F6P93_25315"
     CDS             complement(4993..5832)
                     /locus_tag="F6P93_25315"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001517559.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="regulatory protein RepA"
                     /protein_id="QGY23145.1"
                     /translation="MATHKPINILEAFAAAPPPLDYVLPNMVAGTVGALVSPGGAGKSM
                     LALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTAIHHRLHALGAHLSAEERQAVAD
                     GLLIQPLIGSLPNIMAPEWFDGLKRAAEGRRLMVLDTLRRFHIEEENASGPMAQVIGRM
                     EAIAADTGCSIVFLHHASKGAAMMGAGDQQQASRGSSVLVDNIRWQSYLSSMTSAEAEE
                     WGVDDDQRRFFVRFGVSKANYGAPFADRWFRRHDGGVLKPAVLERQRKSKGVPRGEA"
                     /name="regulatory protein RepA"
     gene            complement(5862..6068)
                     /locus_tag="F6P93_25320"
     CDS             complement(5862..6068)
                     /locus_tag="F6P93_25320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007857788.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QGY23146.1"
                     /translation="MKDQKDKQTGDLLASPDAVRQARYAERMKAKGMRQRKFWLTDDEY
                     EALRECLEELRAAQGGGSDPASA"
                     /name="hypothetical protein"
     gene            complement(6070..6282)
                     /locus_tag="F6P93_25325"
     CDS             complement(6070..6282)
                     /locus_tag="F6P93_25325"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QGY23147.1"
                     /translation="MEYEKSASGSVYLIKSDKGYWLPGGFGYTSNKAEAGRFSVADMAS
                     LNLDGCTLSLFREDKPFGPGKFLGD"
                     /name="hypothetical protein"
     Typing          complement(2085..2241)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.38e-77"
     Typing          complement(4994..5815)
                     /name="IncQ1"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          complement(2..1995)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="94.0"
                     /evalue="0.0"
ORIGIN
        1 ttcgtggccg ggcttgcgct ctgccagcgc tgggctggcc tcggccatgg ccttgccgat
       61 ttcctcggca ctgcggcccc ggctggccag cttctgcgcg gcgataaagt cgcacttgct
      121 gaggtcatca ccgaagcgct tgaccagccc ggccatctcg ctgcggtact cgtccagcgc
      181 cgtgcgccgg tggcggctaa gctgccgctc gggcagttcg aggctggcca gcctgcgggc
      241 cttctcctgc tgccgctggg cctgctcgat ctgctggcca gcctgctgca ccagcgccgg
      301 gccagcggtg gcggtcttgc ccttggattc acgcagcagc acccacggct gataaccggc
      361 gcgggtggtg tgcttgtcct tgcggttggt gaagcccgcc aagcggccat agtggcggct
      421 gtcggcgctg gccgggtcgg cgtcgtactc gctggccagc gtccgggcaa tctgcccccg
      481 aagttcaccg cctgcggcgt cggccacctt gacccatgcc tgatagttct tcgggctggt
      541 ttccactacc agggcaggct cccggccctc ggctttcatg tcatccaggt caaactcgct
      601 gaggtcgtcc accagcacca gaccatgccg ctcctgctcg gcgggcctga tatacacgtc
      661 attgccctgg gcattcatcc gcttgagcca tggcgtgttc tggagcactt cggcggctga
      721 ccattcccgg ttcatcatct ggccggtggt ggcgtccctg acgccgatat cgaagcgctc
      781 acagcccatg gccttgagct gtcggcctat ggcctgcaaa gtcctgtcgt tcttcatcgg
      841 gccaccaagc gcagccagat cgagccgtcc tcggttgtca gtggcgtcag gtcgagcaag
      901 agcaacgatg cgatcagcag caccaccgta ggcatcatgg aagccagcat cacggttagc
      961 catagcttcc agtgccaccc ccgcgacgcg ctccgggcgc tctgcgcggc gctgctcacc
     1021 tcggcggcta cctcccgcaa ctctttggcc agctccaccc atgccgcccc tgtctggcgc
     1081 tgggctttca gccactccgc cgcctgcgcc tcgctggcct gctgggtctg gctcatgacc
     1141 tgccgggctt cgtcggccag tgtcgccatg ctctgggcca gcggttcgat ctgctccgct
     1201 aactcgttga tgcctctgga tttcttcact ctgtcgattg cgttcatggt ctattgcctc
     1261 ccggtattcc tgtaagtcga tgatctgggc gttggcggtg tcgatgttca gggccacgtc
     1321 tgcccggtcg gtgcggatgc cccggccttc catctccacc acgttcggcc ccaggtgaac
     1381 accgggcagg cgctcgatgc cctgcgcctc aagtgttctg tggtcaatgc gggcgtcgtg
     1441 gccagcccgc tctaatgccc ggttggcatg gtcggcccat gcctcgcggg tctgctcaag
     1501 ccatgccttg ggcttgagcg cttcggtctt ctgtgccccg cccttctccg gggtcttgcc
     1561 gttgtaccgc ttgaaccact gagcggcggg ccgctcgatg ccgtcattga tccgctcgga
     1621 gatcatcagg tggcagtgcg ggttctcgcc gccaccggca tggatggcca gcgtatacgg
     1681 caggcgctcg gcaccagtca ggtgctgggc gaactcggac gccagcgcct tctgctggtc
     1741 gagggtcagc tcgaccggca gggcaaattc gacctccttg aacagccgcc cattggcgcg
     1801 ttcatacagg tcggcagcat cccagtagtc ggcgggccgc tcgacgaact ccggcatgtg
     1861 cccggattcg gcgtgcaaga cttcatccat gtcgcgggca tacttgcctt cgcgctggat
     1921 gtagtcggcc ttggccctgg ccgattggcc gcccgacctg ctgccggttt tcgccgtaag
     1981 gtgataaatc gccatgctgc ctcgctgttg cttttgcttt tcggctccat gcaatggccc
     2041 tcggagagcg caccgcccga agggtggccg ttaggccagt ttctcgaaga gaaaccggta
     2101 agtgcgccct ccccctacaa agtagggtcg ggattgccgc cgctgtgcct ccatgatagc
     2161 ctacgagaca gcacattaac aatggggtgt caagatggtt aaggggagca acaaggcggc
     2221 ggatcggctg gccaagctcg aagaacaacg agcgcgaatc aatgccgaaa ttcagcgggt
     2281 gcgggcaagg gaacagcagc aagagcgcaa gaacgaaaca aggcgcaagg tgctggtggg
     2341 ggccatgatt ttggccaagg tgaacagcag cgagtggccg gaggatcggc tcatggcggc
     2401 aatggatgcg taccttgaac gcgaccacga ccgcgccttg ttcggtctgc cgccacgcca
     2461 gaaggatgag ccgggctgaa tgatcgaccg agacaggccc tgcggggctg cacacgcgcc
     2521 cccacccttc gggtaggggg aaaggccgct aaagcggcta aaagcgctcc agcgtatttc
     2581 tgcggggttt ggtgtggggt ttagcgggct ttgcccgcct ttccccctgc cgcgcagcgg
     2641 tggggcggtg tgtagcctag cgcagcgaat agaccagcta tccggcctct ggccgggcat
     2701 attgggcaag ggcagcagcg ccccacaagg gcgctgataa ccgcgcctag tggattattc
     2761 ttagataatc atggatggat ttttccaaca ccccgccagc ccccgcccct gctgggtttg
     2821 caggtttggg ggcgtgacag ttattgcagg ggttcgtgac agttattgca ggggggcgtg
     2881 acagttattg caggggttcg tgacagttag tacgggagtg acgggcactg gctggcaatg
     2941 tctagcaacg gcaggcattt cggctgaggg taaaagaact ttccgctaag cgatagactg
     3001 tatgtaaaca cagtattgca aggacgcgga acatgcctca gcgatcaccg cttccctcat
     3061 gatgtttaac gccttgctca ccggaaaatt gcgagcgcag cgagtaattt ttacggtgca
     3121 gcaacttgtt gtacggtgca accgatagct atgacgtttg ccccttaatc gcctggataa
     3181 tcctcggcca gtcttcatga tgcaactcat gtcccgtgcc ttcgagtgtc agcatttttg
     3241 aaccacgaat cgcatctttc agtgccaacc catgcacata aggaagtaca ggatcctccg
     3301 tgccgtgaat gatcaaagtt ggtacagcta tctcatttaa tctcccgagc catctctcga
     3361 gcgatctctc gccaccacct gaagtagtgt ggttgaatgt tgtcaggata ttcggagtgc
     3421 gatcaaaatc taactcagcg atattttgta tcttctcagc gtcaaaagca tgcgcagtac
     3481 ctgagatgat tcgccacgct ccgacctgat acgcgacgac agcatctcta tcagaccaat
     3541 ccagcgattc cgcccgttgg tgatactcaa tgatggcagg atcaaaagcg ggcatatcag
     3601 gatctgcatc tgcaagccgt tctgaagcaa tcagcgtcaa gctcttcaca cgtttcggat
     3661 acttgagagc tacaagctgg gaaagaaatc cccccaaaga catgccgact aaatgagcag
     3721 cttccagacc ataaccatca atgacgcgaa ccacatcatc tgctaattct tcaacggaat
     3781 atggagcttg acctggctca tagcttgttg atttcccggt atcacggtgg tcgtaccgga
     3841 tcacatagcg acccattttg gctagttggg agcaaaactc atcaggccac cacaccgcag
     3901 acgccattgc ccccatgatc aggataatgg gttcatgggc cgggtcgccg aatgattcgg
     3961 tatggagtga aatcgcttta tcaacaacta ccttttcttt catactaaaa ttgccttcga
     4021 gttttacgta caacatttta ttcataggca tgctcatttt gccagttttg gctgcctgtt
     4081 aattgcgctc aaacatcccc aaccaattgt tttataaaga taaaaatgtc ttgtttacaa
     4141 tagagtgggg ggggtcagcc tgccgccttg ggccgggtga tgtcgtactt gcccgccgcg
     4201 aactcggtta ccgtccagcc cagcgcgacc agctccggca acgcctcgcg cacccgctgg
     4261 cggcgcttgc gcatggtcga accactggcc tctgacggcc agacatagcc gcacaaggta
     4321 tctatggaag ccttgccggt tttgccgggg tcgatccagc cacacagccg ctggtgcagc
     4381 aggcgggcgg tttcgctgtc cagcgcccgc acctcgtcca tgctgatgcg cacatgctgg
     4441 ccgccaccca tgacggcctg cgcgatcaag gggttcaggg ccacgtacag gcgcccgtcc
     4501 gcctcgtcgc tggcgtactc cgacagcagc cgaaacccct gccgcttgcg gccattctgg
     4561 gcgatgatgg ataccttcca aaggcgctcg atgcagtcct gtatgtgctt gagcgcccca
     4621 ccactatcga cctctgcccc gatttccttt gccagcgccc gatagctacc tttgaccacc
     4681 atggcatcag cggtgacggc ctcccacttg ggttccagga acagccggag ctgccgtccg
     4741 ccttcggtct tgggttccgg gccaagcact aggccattag gcccagccat ggccaccagc
     4801 ccttgcagga tgcgcagatc atcagcgccc agcggctccg ggccgctgaa ctcgatccgc
     4861 ttgccgtcgc cgtagtcata cgtcacgtcc agcttgctgc gcttgcgctc gccccgcttg
     4921 agggcacgga acaggccggg ggccagacag tgcgccgggt cgtgccggac gtggctgagg
     4981 ctgtgcttgt tcttaggctt caccacgggg cacccccttg ctcttgcgct gcctctccag
     5041 cacggcgggc ttgagcaccc cgccgtcatg ccgcctgaac caccgatcag cgaacggtgc
     5101 gccatagttg gccttgctca caccgaagcg gacgaagaac cggcgctggt cgtcgtccac
     5161 accccattcc tcggcctcgg cgctggtcat gctcgacagg taggactgcc agcggatgtt
     5221 atcgaccagt accgagctgc cccggctggc ctgctgctgg tcgcctgcgc ccatcatggc
     5281 cgcgcccttg ctggcatggt gcaggaacac gatagagcac ccggtatcgg cggcgatggc
     5341 ctccatgcga ccgatgacct gggccatggg gccgctggcg ttttcttcct cgatgtggaa
     5401 ccggcgcagc gtgtccagca ccatcaggcg gcggccctcg gcggcgcgct tgaggccgtc
     5461 gaaccactcc ggggccatga tgttgggcag gctgccgatc agcggctgga tcagcaggcc
     5521 gtcagccacg gcttgccgtt cctcggcgct gaggtgcgcc ccaagggcgt gcaggcggtg
     5581 atgaatggcg gtgggcgggt cttcggcggg caggtagatc accgggccgg tgggcagttc
     5641 gcccacctcc agcagatccg gcccgcctgc aatctgtgcg gccagttgca gggccagcat
     5701 ggatttaccg gcaccaccgg gcgacaccag cgccccgacc gtaccggcca ccatgttggg
     5761 caaaacgtag tccagcggtg gcggcgctgc tgcgaacgcc tccagaatat tgataggctt
     5821 atgggtagcc attgattgcc tcctttgcag gcagttggtg gttaggcgct ggcggggtca
     5881 ctacccccgc cctgcgccgc tctgagttct tccaggcact cgcgcagcgc ctcgtattcg
     5941 tcgtcggtca gccagaactt gcgctgacgc atccctttgg ccttcatgcg ctcggcatat
     6001 cgcgcttggc gtacagcgtc agggctggcc agcaggtcgc cggtctgctt gtccttttgg
     6061 tctttcatat cagtcaccga gaaacttgcc ggggccgaaa ggcttgtctt cgcggaacaa
     6121 ggacaaggtg cagccgtcaa ggttaaggct ggccatatca gcgactgaaa agcggccagc
     6181 ctcggccttg tttgacgtat aaccaaagcc accgggcaac caatagccct tgtcactttt
     6241 gatcaggtag accgaccctg aagcgctttt ttcgtattcc ataaaacccc cttctgtgcg
     6301 tgagtactca tagtataaca ggcgtgagta ctcacgcaag cactacatgc tgaaatctgg
     6361 cccgcccctg tccatgcctc gctggcggca agccgtttcc aaagtagttt ggcctgcgta
     6421 agctggatcg ctataggacc ggcgaccttt gttgatttgc gttcgataac t
//
