LOCUS       NZ_OP242239             5440 bp    DNA     circular CON 23-MAR-2024
DEFINITION  Escherichia coli strain LA189 plasmid pLAO84, complete sequence.
ACCESSION   NZ_OP242239
VERSION     NZ_OP242239.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29363359
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5440)
  AUTHORS   Snaith,A.E., Dunn,S.J., Moran,R.A. and McNally,A.
  TITLE     Plasmids from ESBL+ E. coli from PDR Laos
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5440)
  AUTHORS   Snaith,A.E., Dunn,S.J., Moran,R.A. and McNally,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-AUG-2022) Institute of Microbiology and Infection,
            University of Birmingham, University of Birmingham, Birmingham B15
            2TT, United Kingdom
COMMENT     ##Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.7
            Sequencing Technology             :: Oxford Nanopore
            ##Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_028600235.1-RS_2024_03_23
            Annotation Date                   :: 03/23/2024 03:08:42
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 7
            CDSs (total)                      :: 7
            Genes (coding)                    :: 6
            CDSs (with protein)               :: 6
            Genes (RNA)                       :: 0
            tRNAs                             :: 0
            ncRNAs                            :: 0
            Pseudo Genes (total)              :: 1
            CDSs (without protein)            :: 1
            Pseudo Genes (ambiguous residues) :: 0 of 1
            Pseudo Genes (frameshifted)       :: 0 of 1
            Pseudo Genes (incomplete)         :: 1 of 1
            Pseudo Genes (internal stop)      :: 0 of 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            OP242239.1.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..5440
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LA189"
                     /isolation_source="Stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pLAO84"
     gene            13..240
                     /locus_tag="PUP04_RS00005"
     CDS             13..240
                     /locus_tag="PUP04_RS00005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011264024.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_052945622.1"
                     /translation="MDLARERQAHEAGARTRATAHERTPQQERQKAAREAERGREAWTL
                     GQGMKKPVAGCYGRLTRWKGGGDVVYMALL"
                     /name="hypothetical protein"
     gene            complement(272..922)
                     /gene="tetR(A)"
                     /locus_tag="PUP04_RS00010"
                     /old_locus_tag="OPJCHDDC_00001"
     CDS             complement(272..922)
                     /gene="tetR(A)"
                     /locus_tag="PUP04_RS00010"
                     /old_locus_tag="OPJCHDDC_00001"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000164043.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="tetracycline resistance transcriptional repressor
                     TetR(A)"
                     /protein_id="WP_001493764.1"
                     /translation="MTKLQPNTVIRAALDLLNEVGVDGLTTRKLAERLGVQQPALYWHF
                     RNKRALLDALAEAMLAENHTHSVPRADDDWRSFLIGNARSFRQALLAYRDGARIHAGTR
                     PGAPQMETADAQLRFLCEAGFSAGDAVNALMTISYFTVGAVLEEQAGDSDAGERGGTVE
                     QAPLSPLLRAAIDAFDEADPDAAFEQGLAVIVDGLAKRRLVVRNVEGPRKGDD"
                     /name="tetR(A)"
     ARG             954..2227
                     /name="tet(A)"
                     /gene="tet(A)"
                     /gene_name="major facilitator superfamily (MFS) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="tetracycline antibiotic"
                     /identity="98.33"
                     /coverage="100.0"
     ARG             1029..2224
                     /name="tet(A)"
                     /gene="tet(A)"
                     /gene_name="tetracycline efflux MFS transporter Tet(A)"
                     /tool="amrfinderplus"
                     /drug_class="TETRACYCLINE"
                     /identity="99.5"
                     /coverage="100.0"
     gene            complement(2259..>2609)
                     /locus_tag="PUP04_RS00020"
                     /old_locus_tag="OPJCHDDC_00003"
                     /pseudo=""
     CDS             complement(2259..>2609)
                     /locus_tag="PUP04_RS00020"
                     /old_locus_tag="OPJCHDDC_00003"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000058717.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="EamA family transporter"
                     /name="EamA family transporter"
     gene            3468..3695
                     /locus_tag="PUP04_RS00035"
     CDS             3468..3695
                     /locus_tag="PUP04_RS00035"
                     /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="WP_326465083.1"
                     /translation="MDRERCRKRRGRGRNALRASQGVRARDVMVNTYFILMEIILISGS
                     CLCGAVKFTIKNQPENFIDATVPYAEDSLE"
                     /name="hypothetical protein"
     gene            3713..4030
                     /locus_tag="PUP04_RS00025"
                     /old_locus_tag="OPJCHDDC_00005"
     CDS             3713..4030
                     /locus_tag="PUP04_RS00025"
                     /old_locus_tag="OPJCHDDC_00005"
                     /inference="COORDINATES: protein motif:HMM:NF016701.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="glutathione-dependent formaldehyde-activating
                     enzyme"
                     /protein_id="WP_240761615.1"
                     /translation="MVKVEDFDWQTSEELISSWKKESGYRNDFCKKCGSTVPNILRGQP
                     YVWLPLGLLNENIKADCCGDFCTDDSMMWDCVRSANSNKKAVSSLFDLLVMLNVEQAKL
                     E"
                     /name="glutathione-dependent formaldehyde-activating
                     enzyme"
     gene            4828..5019
                     /locus_tag="PUP04_RS00030"
                     /old_locus_tag="OPJCHDDC_00006"
     CDS             4828..5019
                     /locus_tag="PUP04_RS00030"
                     /old_locus_tag="OPJCHDDC_00006"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /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="WP_047402702.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNDQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(4330..4953)
                     /name="rep_cluster_2327"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.603"
                     /coverage="99.0"
                     /evalue="1.53e-168"
ORIGIN
        1 aagacggccg ccctggacct cgcccgcgag cgccaggcgc acgaggccgg cgcgcggacc
       61 cgcgccacgg cccacgagcg gacgccgcag caggagcgcc agaaggccgc cagagaggcc
      121 gagcgcggcc gtgaggcttg gacgctaggg cagggcatga aaaagcccgt agcgggctgc
      181 tacgggcgtc tgacgcggtg gaaaggggga ggggatgttg tctacatggc tctgctgtag
      241 tgagtgggtt gcgctccggc agcggtcctg atcaatcgtc accctttctc ggtccttcaa
      301 cgttcctgac aacgagcctc cttttcgcca atccatcgac aatcaccgcg agtccctgct
      361 cgaacgctgc gtccggatcg gcttcgtcga aggcgtctat cgcggcccgc aacagcggcg
      421 agagcggagc ctgttcaacg gtgccgccgc gctcgccggc atcgctgtcg ccggcctgct
      481 cctcaagcac ggccccaaca gtgaagtagc tgattgtcat cagcgcattg acggcgtccc
      541 cggccgaaaa acccgcctcg cagaggaagc gaagctgcgc gtcggccgtt tccatctgcg
      601 gtgcgcccgg tcgcgtgccg gcatggatgc gcgcgccatc gcggtaggcg agcagcgcct
      661 gcctgaagct gcgggcattc ccgatcagaa atgagcgcca gtcgtcgtcg gctctcggca
      721 ccgaatgcgt atgattctcc gccagcatgg cttcggccag tgcgtcgagc agcgcccgct
      781 tgttcctgaa gtgccagtaa agcgccggct gctgaacccc caaccgttcc gccagtttgc
      841 gtgtcgtcag accgtctacg ccgacctcgt tcaacaggtc cagggcggca cggatcactg
      901 tattcggctg caactttgtc atgcttgaca ctttatcact gataaacata atatgtccac
      961 caacttatca gtgataaaga atccgcgcgt tcaatcggac cagcggaggc tggtccggag
     1021 gccagacgtg aaacccaaca gacccctgat cgtaattctg agcactgtcg cgctcgacgc
     1081 tgtcggcatc ggcctgatta tgccggtgct gccgggcctc ctgcgcgatc tggttcactc
     1141 gaacgacgtc accgcccact atggcattct gctggcgctg tatgcgttga tgcaatttgc
     1201 ctgcgcacct gtgctgggcg cgctgtcgga tcgtttcggg cggcggccgg tcttgctcgt
     1261 ctcgctggcc ggcgctgctg tcgactacgc catcatggcg acgacgcctt tcctttgggt
     1321 tctctatatc gggcggatcg tggccggcat caccggggcg actggggcgg tagccggcgc
     1381 ttatattgcc gatatcactg atggcgatga gcgcgcgcgg cacttcggct tcatgagcgc
     1441 ctgtttcggg ttcgggatgg tcgcgggacc tgtgctcggt gggctgatgg gcggtttctc
     1501 cccccacgct ccgttcttcg ccgcggcagc cttgaacggc ctcaatttcc tgacgggctg
     1561 tttccttttg ccggagtcgc acaaaggcga acgccggccg ttacgccggg aggctctcaa
     1621 cccgctcgct tcgttccggt gggcccgggg catgaccgtc gtcgccgccc tgatggcggt
     1681 cttcttcatc atgcaacttg tcggacaggt gccggccgcg ctttgggtca ttttcggcga
     1741 ggatcgcttt cactgggacg cgaccacgat cggcatttcg cttgccgcat ttggcattct
     1801 gcattcactc gcccaggcaa tgatcaccgg ccctgtagcc gcccggctcg gcgaaaggcg
     1861 ggcactcatg ctcggaatga ttgccgacgg cacaggctac atcctgcttg ccttcgcgac
     1921 acggggatgg atggcgttcc cgatcatggt cctgcttgct tcgggtggca tcggaatgcc
     1981 ggcgctgcaa gcaatgttgt ccaggcaggt ggatgaggaa cgtcaggggc agctgcaagg
     2041 ctcactggcg gcgctcacca gcctgacctc gatcgtcgga cccctcctct tcacggcgat
     2101 ctatgcggct tctataacaa cgtggaacgg gtgggcatgg attgcaggcg ttgccctcta
     2161 cttgctctgc ctgccggcgc tgcgtcgcgg gctttggagc ggcgcagggc aacgagccga
     2221 tcgctgatcg tggaaacgat aggcctatgc catgcgggtc aaggcgactt ccggcaagct
     2281 atacgcgccc taggagtgcg gttggaacgt tggcccagcc agatactccc gatcacgagc
     2341 aggacgccga tgatttgaag cgcactcagc gtctgatcca agaacaacca tcctagcaac
     2401 acggcggtcc ccgggctgag aaagcccagt aaggaaacaa ctgtaggttc gagtcgcgag
     2461 atcccccgga accaaaggaa gtaggttaaa cccgctccga tcaggccgag ccacgccagg
     2521 ccgagaacat tggttcctgt aggcatcggg attggcggat caaacactaa agctactgga
     2581 acgagcagaa gtcctccggc cgccagttgg ggtcagtttg gatatagaga attattgtac
     2641 ggtaagcctg ttttttgaac agacttacct atagcaatag ggtgtactcc cgcgctatac
     2701 ggcattttca gaggtttgac cttaatcgga taacctaaat gcgatactgc aagagcgaca
     2761 acttaaaagc gataaccact gacgcaaaat caacccctta cgaaccaaga ttggttaaat
     2821 aatgcgctta acgtacaaaa aattccgatc tccaaactga ccccttcttc gcctcttatg
     2881 tttctcgaat gaatcgatgg ggacaggaaa tgttttgtgg ccaccgccgc ttcgccggca
     2941 ccacaaaact gtcggacaag atgtgttttt ggagtaccgc cggcaccaaa aacatttcat
     3001 caggcgcagc ctgataccct gaatttcgta cgcacgaaat tttgcttttg ttcagatcga
     3061 gggcaggatt cgcaaagtgc tggcgtttgt acccaccgga agctgccgcg cctggcggct
     3121 tggccaacgc ctcacggccg cacagtcaac tgtgcacccg ttcaccgtta ccagatcccc
     3181 tgattccggc cgggcctgcc tgcactggcc aaagccttaa aactgcgcaa tccgcagcgc
     3241 gggggcagtt gataaccact ttttactgtc atacttattt gccggctctc tgatcggtac
     3301 cggctgactg tttgtgcaaa ttttgtcgga catcctgacc ctcgatgtcc gttttttttg
     3361 ttcaaaattc gcctttagtg ccagcattcg tccgaaaccg gccgccattc acttccgtgc
     3421 atagccatgc aggcgcgcag aaatcatcag gcgcgttttt tcacgatatg gacagggaaa
     3481 ggtgccggaa acgcagagga cgcggcagaa acgcgctgag ggcctctcag ggggtgcggg
     3541 caagagatgt tatggtaaat acgtatttta ttttgatgga gattattttg attagtgggt
     3601 catgtttgtg tggtgctgtt aaattcacga taaaaaatca gcctgaaaat tttatagatg
     3661 ccactgttcc ctatgccgaa gacagtctgg agtaggtcat aacttagctg ccatagtgaa
     3721 agttgaggat tttgactggc aaacctcaga ggaattgatt tcttcatgga aaaaggaaag
     3781 tggttaccgt aacgatttct gcaaaaaatg tggttcgact gttccaaata ttttgagggg
     3841 gcagccttat gtgtggctac cacttgggct acttaacgag aatattaaag ctgactgctg
     3901 tggtgatttt tgtacagacg attcgatgat gtgggactgt gtgcgctcag cgaatagtaa
     3961 caaaaaagcg gtaagtagcc tgttcgactt attggttatg ctcaatgttg agcaggctaa
     4021 acttgaatag atagcgagca cgccttaggg atgttgctta atggattgta ttggaaagat
     4081 gcactgatgg atagttatct tgacctgata aggggttacc gcgtagatta gttgtcgcaa
     4141 acgaaaaaac cgccttgcag ggcggttttt cgaaggtact cagagctagc aactctttga
     4201 accgaggtaa ctggcttgga ggagcgcagt caccaaaact tgtcctttca gtttagcctt
     4261 aaccggcaca tgacttcaag tccatctcct ctaaatcagt taccagtggc tgctgccagt
     4321 ggcgctttgt cgtgtctttc cgggttggac tcaagatgat agttaccgga caaggcgcag
     4381 cggtcggact gaacgggggg ttcgtgcata cagtccagct tggagcgaac tgcctacccg
     4441 gaactgagtg tcaggcgtgg aatgagacaa acgcggccat aacagcggaa tgacaccggt
     4501 aaaccgaaag gcaggaacag gagagcgcac gagggagcca ccagggggaa acgcctggta
     4561 tctttatagt cctgtcgggt ttcgccacca ctgatttgag cgtccgattc tgtgatgctt
     4621 gtcagggggg cggagcctat ggaaaaacgc cccgccgggg cgtggccttt tcgcccttgt
     4681 ccttagcttt cgttatgctt accgttacgt tatctgctta tcctccctcc gctcgccgca
     4741 gactcatgac cgaacggagt gagcgaatga gcgaggaagc ggaaaaccat cagaacgtac
     4801 agtaagcact ttcgcgccgg ggccttcatg aacaaacaac aaaagacagc cgttaacatg
     4861 gctaaattca tccaggatca gtccctgctt cttctggaca ggcttaatga gctggatctg
     4921 gatcatgagg ctgatttctg cgagaaactc catgaggatg cggaacgcct ttaccgaagc
     4981 ctgtcagcgc gcctgaatga tcagcaggac ggtgcgtaat ggctccgttc tgggtattac
     5041 cggagtaata ccggcatcgc cttaattttc attgtcttgg tgcttaacat tattacccta
     5101 gtaataccca gaatcccttt attttttctt ttttatttat ttttcatgaa gttgcgataa
     5161 aaatcgcagc tgcgttaggt gtatggggtc agtttggata tagagaatta ttgtacggta
     5221 agcctgtttt ttgaacagac ttacctatag caatagggtg tactcccgcg ctatacggca
     5281 ttttcagagg tttgacctta atcggataac ctaaatgcga tactgcaaga gcgacaactt
     5341 aaaagcgata accactgacg caaaatcaac cccttacgaa ccaagattgg ttaaataatg
     5401 cgcttaacgt acaaaaaatt ccgatctcca aactgacccc
//
