LOCUS       NZ_CP142947             6200 bp    DNA     circular CON 19-FEB-2024
DEFINITION  Escherichia coli strain B20159 plasmid pB20159_4, complete sequence.
ACCESSION   NZ_CP142947
VERSION     NZ_CP142947.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39500351
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6200)
  AUTHORS   Maguire,M.
  TITLE     Spatiotemporal and genomic analysis of carbapenem resistance
            elements in Enterobacterales from hospital inpatients and natural
            water ecosystems of an Irish city
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6200)
  AUTHORS   Maguire,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-JAN-2024) Bacteriology, University of Galway,
            University Road, Galway, Galway 000000, Ireland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 285.0x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/19/2024 10:32:49
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 8
            CDSs (total)                      :: 8
            Genes (coding)                    :: 7
            CDSs (with protein)               :: 7
            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
            CP142947.1.
            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..6200
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="B20159"
                     /isolation_source="seawater"
                     /db_xref="taxon:562"
                     /plasmid="pB20159_4"
                     /geo_loc_name="Ireland"
                     /collection_date="2020"
     ARG             complement(3..433)
                     /name="APH(3'')-Ib"
                     /gene="APH(3'')-Ib"
                     /gene_name="APH(3'')"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="99.31"
                     /coverage="53.93"
     ARG             complement(5831..6198)
                     /name="APH(3'')-Ib"
                     /gene="APH(3'')-Ib"
                     /gene_name="APH(3'')"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="100.0"
                     /coverage="45.69"
     gene            complement(494..1309)
                     /gene="sul2"
                     /locus_tag="VYI61_RS00010"
                     /old_locus_tag="VYI61_24820"
     ARG             complement(498..1309)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(1769..1927)
                     /locus_tag="VYI61_RS00015"
                     /old_locus_tag="VYI61_24825"
     CDS             complement(1769..1927)
                     /locus_tag="VYI61_RS00015"
                     /old_locus_tag="VYI61_24825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032287700.1"
                     /translation="MHEPPVQSDRCALSGNYQLESNPERHDKTPLAAAISNRSAREDRL
                     RGLEVEA"
                     /name="hypothetical protein"
     gene            2498..2647
                     /locus_tag="VYI61_RS00020"
                     /old_locus_tag="VYI61_24830"
     CDS             2498..2647
                     /locus_tag="VYI61_RS00020"
                     /old_locus_tag="VYI61_24830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(3392..3832)
                     /locus_tag="VYI61_RS00025"
                     /old_locus_tag="VYI61_24835"
     CDS             complement(3392..3832)
                     /locus_tag="VYI61_RS00025"
                     /old_locus_tag="VYI61_24835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011161230.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005119689.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="hypothetical protein"
     gene            4017..4439
                     /locus_tag="VYI61_RS00030"
                     /old_locus_tag="VYI61_24840"
     CDS             4017..4439
                     /locus_tag="VYI61_RS00030"
                     /old_locus_tag="VYI61_24840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_172684459.1"
                     /translation="MLFLKVKEDNFMSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGG
                     SFNGGGNGGHDNSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARN
                     NMYLDTANNVRVGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            4483..>4887
                     /locus_tag="VYI61_RS00035"
                     /old_locus_tag="VYI61_24845"
                     /pseudo=""
     CDS             4483..>4887
                     /locus_tag="VYI61_RS00035"
                     /old_locus_tag="VYI61_24845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS91 family transposase"
                     /name="IS91 family transposase"
     gene            complement(4994..5830)
                     /locus_tag="VYI61_RS00040"
                     /old_locus_tag="VYI61_24850"
     CDS             complement(4994..5830)
                     /locus_tag="VYI61_RS00040"
                     /old_locus_tag="VYI61_24850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000480972.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /protein_id="WP_000480968.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="aminoglycoside O-phosphotransferase APH(6)-Id"
     ARG             complement(4998..5830)
                     /name="aph(6)-Id"
                     /gene="aph(6)-Id"
                     /gene_name="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          2290..2463
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          complement(1761..2366)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cgggattgac ggcattgcgg gacaccacat caacggcgcg tccgaacatt cgcgacagcc
       61 tgcgctcaaa cggacattga tcaaccgata ggctgtgaac agcgccaagt tgctgcccca
      121 ttgacggcca cgctttgagc aaatccgctc cagacagatc agccgccggt actcccggaa
      181 ttgccgttat caccaagcat gcaccctcct gttcctcctg ccagttgatg acctcggggc
      241 aagccacacc tcgacctttg agccaaatga ggcggtcacg ctctccagcg agctcaccgc
      301 ggcgggaagc aggtgcgatt ttcgcgaagg catgcccgtc accacgtcga aaaacaaaat
      361 caccagattc tccgcctctg acaggcaacc agtcagaatg cgattcacca aaaaaaatat
      421 tagttcgatt caatggaggt tccttcagtt ttctgatgaa gcgcgaatat agagaaatat
      481 cccgaatgtg cagttaacga attcttgcgg tttctttcag cgccgccaat accgccagcc
      541 cgtcgcgcaa ggggcgcggc tcgtgtgtgc ggatgaagtc agctccacct gcggcggcgg
      601 caagctctgc agcgagtgtc gcggccccga catcccccgg accacggcct gtgagcgcgc
      661 gcagaaagga tttgcgcgaa acagacagaa gcaccggcaa atcgaagcgc agccgcaatt
      721 catcgaaccg cgccagcacc gagagcgagg tttcgggagc agcccccaga aaaaacccca
      781 tgccgggatc aaggacaagg cggttgcgtt tgataccggc acccgtcagc gccgcgatgc
      841 gcgcgtcaaa gaacgccgca atgtgatcca tgatgtcgcc agcgggtgcc tcgcgccgat
      901 ctgcctgccc gtcttgcacc gaatgcataa cgacgagttt ggcagatgat ttcgccaatt
      961 gcggatagaa cgcagcgtct ggaaaaccgc gaatatcatt gagataggcc acaccacgcg
     1021 acaaggcata ggcttgcgtc gcgggttgat aactgtcgag cgagacggga atgccatctg
     1081 ccttgagcgc gtccagcacc ggcgcgatac gcgcgatttc tgtgtcggac gaaacaggcg
     1141 cggcgtcggg attgctggat gccggaccga ggtcgatcac atctgccccc tcggccatca
     1201 gcttacgcgc ctgcgcaatg gctgcgtctg gcgccagata ccggcctcca tcggagaaac
     1261 tgtccgaggt tatgttgacg atgccgaaaa tgatgagcga tttattcatg ggggcttcta
     1321 taataataat aatcgagcat gagtctcata cggatgctcg ggtcgaaagg gaatccccag
     1381 gcgagtaacc tgtttgcggt gatccgtttc atgatgatgt atctgtagca ttttggaaat
     1441 aaatatatca tctctcaata agtagatata tttatctttt ttgcttcttt ggtgctgcaa
     1501 gtcaccaata cgagggaaac ctgttacgga gcggtttaac cgtaatcaac agtgactggt
     1561 gtcatgttcg gaagattaat tgatagtaat ctacaaagga tcttcttgag atccttttca
     1621 atgaatcgta atctcttgct ctgtaaacga aaaaaccgcc tggggaggcg gtttgttcga
     1681 aggttaagtc agttggggaa ctgcttaacc cggtaacagg gttcacgaga ccgccattac
     1741 caaaactgtt ctttcagtgt agccgcagtc aggcctctac ttcaagacct cttaatctat
     1801 cttctcgtgc actcctgtta ctaatggctg ctgccagtgg cgttttgtcg tgtctttccg
     1861 ggttggactc aagttgatag ttaccggaca aggcgcagcg gtcggactga acggggggtt
     1921 cgtgcataca gtccagcttg gagcgaactg ccttcacgga actgagtgtc aggcgtggaa
     1981 tgagaaaccg cggccataac agcggaatga caccggtaaa ccgaaaggca ggaacaggag
     2041 agcgcacgag ggagctacca gggggaaacg cctgggatct ttatagtcct gtcgggtttc
     2101 gccaccactg atttgagcgt cagattttgc gatgcttgtc aggggggcgg agcctatgga
     2161 aaaacggctt cgccgtggcc ttatctcttc tttgctaagt gtcttcctgg tatcttccag
     2221 gaaatttccg tccccgtccg taagccggta ccgctcgccg cagccgaacg accgagcgta
     2281 gcgagtcagt gagcgaggaa gcggaatatc tcctgtatcg catattctgc tgacgcgccg
     2341 gtgctgcctt ttttctcctg ccacatgaag cacttcactg attttcgcaa tcgtggcaac
     2401 atagtaagcc agtatacact ccgctagcgc tacatgactg gttcagggct gcgccccgaa
     2461 acccgctaac aacctctcag ctactggata tcaccccatg ccatctgaat atgatgaaca
     2521 actggattcg actgatacgc agcttcccgg cgaatatgac ctttttgatt taatggcgca
     2581 ggttactgaa gagaacctgc atgcccctgt ggattttggg tcgcctgtcg gccgggaagc
     2641 gttatagctt tttcgcttgc ccgcgtacgt ggtaatactc cggtattacc ttttatttct
     2701 ttattttcat gtaattacag tggattttta atacccgggt attactcgtg aaaacgaaat
     2761 attccttttt tttcttttaa ttcatgcagt tgcgatgaaa atcgcggctg cgttaggtgt
     2821 atgaccattt tgaggttgaa aaataatcaa ccatggcggg tgatttacgc aggttaaggg
     2881 gagatcgtga caaaaaaagc gttcctcact gtatcgttca tgcctgcatg aacgggttat
     2941 tcttcctgac tacagaatta catcgctcct tcagttcata catcactttt acatcactta
     3001 tacatcactt ttacatcatt ccttcagctc atacgtcact ttcatcctct gtgccatttg
     3061 tacatcaccc ccttcctgaa cgtgctgaca gcgggttttc cggctgcgcc ggcaacgctt
     3121 cacggccacg caataaattg cgtccccgtt caccgttttc ggatgggaag aacgccggaa
     3181 acaggactta ccccggctga atggtgtgaa tttccgcgct atgcacttgt gcgcatactc
     3241 atgcatgccg taaaaacaga gcctgcgcgt ttctggcggg ttttcgggtg gtttgttgcc
     3301 tgttttaccg gtttcccgtc agaaacgccc tgagggcctc tcaggcggtg ctgataacag
     3361 atgttatggt aaatcagagt cacctgcact gttactctga accggagcga aacagccgcg
     3421 accagaatcc ccgctttttt tcctgtgcca gcgcgtcagc cagacggcta atttcggcct
     3481 gtagttgttc cctctcctca tttcgcaggc ggttttctgc ttcccgcgcc atcttgtctt
     3541 caagcattag ggtaacagtc tgctgcagag cgtccagttt ctgctgaatg acgtctagct
     3601 gagcattttc cgcctggcta acgacagatt tggagtgtcc ctccttgtgc ctttttggtg
     3661 tctcagaagt gcgcagctcg ccataggccc gaatcagttc actggtctcg aactcccggc
     3721 gatcattttt tcctgtgcga tagctgacaa ggcctttagc catgtcacga tataattgcg
     3781 agcgcgactt tcctgttaat ttcagtgtct cttgaactgt gtgccatgcc ataaaagtga
     3841 cagtgtctcc tgtgtgtacc gtattgtaac agcagaacat attactgttt taacacaaaa
     3901 ggtctgaggc tgcccgtgag gcgtgaaaaa tacacaaaaa acctgttgac ggtgtggttt
     3961 tgacgggcgt agtatttcga atactgtata taaacacatt gttataaata cagtttttgc
     4021 tgtttttaaa agtcaaagag gataatttta tgagtacaga gttaaatagc ggtactgtcg
     4081 gtggttttgg tcacatggga ccaaatgacc cctacaatga tggtcatagc ggctctggaa
     4141 gttcgggagg tagttttaac ggtggtggta atggtggcca tgataatagt agtggttcat
     4201 cttatactgc atcctttggt ctcatcactg gccgacaccc gataactgtc ccaggtacga
     4261 agaatattaa ttctgtcgat ctttctgctg tcattaataa cattatacat catgaaggtg
     4321 cacgcaataa catgtaccta gatactgcga acaatgtaag agtgggagtg acgggcactg
     4381 gctggcaatg tctagcaacg gcaggcattt cggctgaggg taaaagaact ttccgctaag
     4441 cgatagactg tatgtaaaca cagtattgca aggacgcgga acatgcctca tgtggcggcc
     4501 aggacggcca gccgggatcg ggatactggt cgttaccaga gccaccgacc cgagcaaacc
     4561 cttctctatc agatcgttga cgagtattac ccggcattcg ctgcgcttat ggcagagcag
     4621 ggaaaggaat tgccgggcta tgtgcaacgg gaatttgaag aatttctcca atgcgggcgg
     4681 ctggagcatg gctttctacg ggttcgctgc gagtcttgcc acgccgagca cctggtcgct
     4741 ttcagctgta agcgtcgcgg tttctgcccg agctgtgggg cgcggcggat ggccgaaagt
     4801 gccgccttgc tggttgatga agtactgcct gaacaaccca tgcgtcagtg ggtgttgagc
     4861 ttcccgtttc agctgcgttt cctgtttggg gtcgtttgcg ggaaggggcg gaatcctacg
     4921 ctaaggcttt ggccagcgat attctccggt gagattgatg tgttcccagg ggataggaga
     4981 agtcgcttga tatctagtat gacgtctgtc gcacctgctt gatcgcggcc gcgatagcta
     5041 gatcgcgttg ctcctcttct ccatccgcgt tccaagctgc ggaaaggcac ccataagcgt
     5101 acgcctggtc gagcaggcga cgcggatcga cgtccagcgc acgagagaat gcgtccgcca
     5161 tctgtgcaat gcgtctagga tcgagacaaa ggtcgtctct gtcagccgga tcgtagaaca
     5221 tattggcggc gccaaagccc acttcaccga ccagaccgac gggatctatc accagccagc
     5281 cgcgactgga gaacatgatg ttttcatgat gcagatcgcc atgtagccca cgcagttccg
     5341 aggcattgct catcatttga tcggctataa tcgccgcgtg gacgtagtca gtttgacaac
     5401 ctgcgttttg atcatcgcgc gcccgctgaa acaaagctgc aaagcgatcc cggatcggga
     5461 gaagggcaga aggcaggggt tcctcagatg cggcatacag cttcgccatt agttccgctg
     5521 caatttcggt cgcctggtag tcgccgtgct cggcaacgat gtgagagagc attcgctccc
     5581 cggcatattc gagcaacatc agattgttct cacgaccgag caaccggact gctcccctcc
     5641 cattgcgcca taccagatag tcggccccgc gcagttcatc agcaatgtct tctataggtt
     5701 tcaatccctt gacgattgca ggagtcccgt ctggcaatga aactttccaa acgaggctgg
     5761 aaaaggtgtc cgcaatgaga acaggttgcg aaacgtgcca atgagcagga aaaacaggcg
     5821 gcatgaacat caaccccaag tcagagggtc caatcgcaga tagaaggcaa ggcgttcgcg
     5881 gtcgggggct tcgatcccca atacattgaa taggacagcg aaggcgcgct ctgcttcatc
     5941 tggcgctgcc cagttctctt cggcgttagc aatcatgagt gccaaatcgg catagcgatc
     6001 tgctgttccg agccgcccaa ggtcgatcag acccgtgcat tgaagagttt tagggtccac
     6061 catgaagttc ggcatgcagg gatcaccatg gcaaacaacc atatcggtgc gctcttggtc
     6121 gagccgcacc ggtagctctc gttcgacacg agccaaaaga tcgagctgcg gcgtactctt
     6181 gtcctcgtcc ggtaagaagt
//
