LOCUS       NZ_CP059123             6200 bp    DNA     circular CON 31-AUG-2023
DEFINITION  Escherichia coli strain Ec42 plasmid pEc42_4, complete sequence.
ACCESSION   NZ_CP059123
VERSION     NZ_CP059123.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15486687
            Assembly: GCF_019355455.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6200)
  AUTHORS   Mahazu,S., Wakano,S., Ayibieke,A., Prah,I., Ablordey,A. and Saito,R.
  TITLE     Whole genome analysis of ESBL producing E.coli ST131 from Ghana
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6200)
  AUTHORS   Mahazu,S., Wakano,S., Ayibieke,A., Prah,I., Ablordey,A. and Saito,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-JUL-2020) Molecular Microbiology, Tokyo Medical and
            Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2020
            Assembly Method                   :: Unicycler v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 1300x
            Sequencing Technology :: Oxford Nanopore MiniION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/29/2023 04:37:24
            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)                     :: 5,188
            CDSs (total)                      :: 5,067
            Genes (coding)                    :: 4,805
            CDSs (with protein)               :: 4,805
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 262
            CDSs (without protein)            :: 262
            Pseudo Genes (ambiguous residues) :: 0 of 262
            Pseudo Genes (frameshifted)       :: 90 of 262
            Pseudo Genes (incomplete)         :: 181 of 262
            Pseudo Genes (internal stop)      :: 50 of 262
            Pseudo Genes (multiple problems)  :: 56 of 262
            Pseudo Genes (short protein)      :: 4 of 262
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059123.1.
            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="Ec42"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc42_4"
                     /geo_loc_name="Ghana"
                     /collection_date="2016"
     gene            282..1097
                     /gene="sul2"
                     /locus_tag="H0X94_RS25605"
                     /old_locus_tag="H0X94_25485"
     ARG             283..1094
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             1204..1961
                     /name="APH(3'')-Ib"
                     /gene="APH(3'')-Ib"
                     /gene_name="APH(3'')"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="99.21"
                     /coverage="94.38"
     ARG             1159..1958
                     /name="aph(3'')-Ib"
                     /gene="aph(3'')-Ib"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3'')-Ib"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            1961..2797
                     /locus_tag="H0X94_RS25615"
                     /old_locus_tag="H0X94_25495"
     CDS             1961..2797
                     /locus_tag="H0X94_RS25615"
                     /old_locus_tag="H0X94_25495"
                     /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"
     gene            complement(<2904..3308)
                     /locus_tag="H0X94_RS25620"
                     /old_locus_tag="H0X94_25505"
                     /pseudo=""
     CDS             complement(<2904..3308)
                     /locus_tag="H0X94_RS25620"
                     /old_locus_tag="H0X94_25505"
                     /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(3352..3741)
                     /locus_tag="H0X94_RS25625"
                     /old_locus_tag="H0X94_25510"
     CDS             complement(3352..3741)
                     /locus_tag="H0X94_RS25625"
                     /old_locus_tag="H0X94_25510"
                     /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_000102614.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            3959..4399
                     /locus_tag="H0X94_RS25630"
                     /old_locus_tag="H0X94_25515"
     CDS             3959..4399
                     /locus_tag="H0X94_RS25630"
                     /old_locus_tag="H0X94_25515"
                     /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            complement(5144..5293)
                     /locus_tag="H0X94_RS25635"
                     /old_locus_tag="H0X94_25520"
     CDS             complement(5144..5293)
                     /locus_tag="H0X94_RS25635"
                     /old_locus_tag="H0X94_25520"
                     /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            5864..6022
                     /locus_tag="H0X94_RS26125"
     CDS             5864..6022
                     /locus_tag="H0X94_RS26125"
                     /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"
     ARG             1962..2794
                     /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          complement(5329..5502)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          5426..6031
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 attactatca attaatcttc cgaacatgac accagtcact gttgattacg gttaaaccgc
       61 tccgtaacag gtttccctcg tattggtgac ttgcagcacc aaagaagcaa aaaagataaa
      121 tatatctact tattgagaga tgatatattt atttccaaaa tgctacagat acatcatcat
      181 gaaacggatc accgcaaaca ggttactcgc ctggggattc cctttcgacc cgagcatccg
      241 tatgagactc atgctcgatt attattatta tagaagcccc catgaataaa tcgctcatca
      301 ttttcggcat cgtcaacata acctcggaca gtttctccga tggaggccgg tatctggcgc
      361 cagacgcagc cattgcgcag gcgcgtaagc tgatggccga gggggcagat gtgatcgacc
      421 tcggtccggc atccagcaat cccgacgccg cgcctgtttc gtccgacaca gaaatcgcgc
      481 gtatcgcgcc ggtgctggac gcgctcaagg cagatggcat tcccgtctcg ctcgacagtt
      541 atcaacccgc gacgcaagcc tatgccttgt cgcgtggtgt ggcctatctc aatgatattc
      601 gcggttttcc agacgctgcg ttctatccgc aattggcgaa atcatctgcc aaactcgtcg
      661 ttatgcattc ggtgcaagac gggcaggcag atcggcgcga ggcacccgct ggcgacatca
      721 tggatcacat tgcggcgttc tttgacgcgc gcatcgcggc gctgacgggt gccggtatca
      781 aacgcaaccg ccttgtcctt gatcccggca tggggttttt tctgggggct gctcccgaaa
      841 cctcgctctc ggtgctggcg cggttcgatg aattgcggct gcgcttcgat ttgccggtgc
      901 ttctgtctgt ttcgcgcaaa tcctttctgc gcgcgctcac aggccgtggt ccgggggatg
      961 tcggggccgc gacactcgct gcagagcttg ccgccgccgc aggtggagct gacttcatcc
     1021 gcacacacga gccgcgcccc ttgcgcgacg ggctggcggt attggcggcg ctgaaagaaa
     1081 ccgcaagaat tcgttaactg cacattcggg atatttctct atattcgcgc ttcatcagaa
     1141 aactgaagga acctccatta aatcgaacta atattttttt tggtgaatcg cattctgact
     1201 ggttgcctgt cagaggcgga gaatctggtg attttgtttt tcgacgtggt gacgggcatg
     1261 ccttcgcgaa aatcgcacct gcttcccgcc gcggtgagct cgctggagag cgtgaccgcc
     1321 tcatttggct caaaggtcga ggtgtggctt gccccgaggt catcaactgg caggaggaac
     1381 aggagggtgc atgcttggtg ataacggcaa ttccgggagt accggcggct gatctgtctg
     1441 gagcggattt gctcaaagcg tggccgtcaa tggggcagca acttggcgct gttcacagcc
     1501 tatcggttga tcaatgtccg tttgagcgca ggctgtcgcg aatgttcgga cgcgccgttg
     1561 atgtggtgtc ccgcaatgcc gtcaatcccg acttcttacc ggacgaggac aagagtacgc
     1621 cgcagctcga tcttttggct cgtgtcgaac gagagctacc ggtgcggctc gaccaagagc
     1681 gcaccgatat ggttgtttgc catggtgatc cctgcatgcc gaacttcatg gtggacccta
     1741 aaactcttca atgcacgggt ctgatcgacc ttgggcggct cggaacagca gatcgctatg
     1801 ccgatttggc actcatgatt gctaacgccg aagagaactg ggcagcgcca gatgaagcag
     1861 agcgcgcctt cgctgtccta ttcaatgtat tggggatcga agcccccgac cgcgaacgcc
     1921 ttgccttcta tctgcgattg gaccctctga cttggggttg atgttcatgc cgcctgtttt
     1981 tcctgctcat tggcacgttt cgcaacctgt tctcattgcg gacacctttt ccagcctcgt
     2041 ttggaaagtt tcattgccag acgggactcc tgcaatcgtc aagggattga aacctataga
     2101 agacattgct gatgaactgc gcggggccga ctatctggta tggcgcaatg ggaggggagc
     2161 agtccggttg ctcggtcgtg agaacaatct gatgttgctc gaatatgccg gggagcgaat
     2221 gctctctcac atcgttgccg agcacggcga ctaccaggcg accgaaattg cagcggaact
     2281 aatggcgaag ctgtatgccg catctgagga acccctgcct tctgcccttc tcccgatccg
     2341 ggatcgcttt gcagctttgt ttcagcgggc gcgcgatgat caaaacgcag gttgtcaaac
     2401 tgactacgtc cacgcggcga ttatagccga tcaaatgatg agcaatgcct cggaactgcg
     2461 tgggctacat ggcgatctgc atcatgaaaa catcatgttc tccagtcgcg gctggctggt
     2521 gatagatccc gtcggtctgg tcggtgaagt gggctttggc gccgccaata tgttctacga
     2581 tccggctgac agagacgacc tttgtctcga tcctagacgc attgcacaga tggcggacgc
     2641 attctctcgt gcgctggacg tcgatccgcg tcgcctgctc gaccaggcgt acgcttatgg
     2701 gtgcctttcc gcagcttgga acgcggatgg agaagaggag caacgcgatc tagctatcgc
     2761 ggccgcgatc aagcaggtgc gacagacgtc atactagata tcaagcgact tctcctatcc
     2821 cctgggaaca catcaatctc accggagaat atcgctggcc aaagccttag cgtaggattc
     2881 cgccccttcc cgcaaacgac cccaaacagg aaacgcagct gaaacgggaa gctcaacacc
     2941 cactgacgca tgggttgttc aggcagtact tcatcaacca gcaaggcggc actttcggcc
     3001 atccgccgcg ccccacagct cgggcagaaa ccgcgacgct tacagctgaa agcgaccagg
     3061 tgctcggcgt ggcaagactc gcagcgaacc cgtagaaagc catgctccag ccgcccgcat
     3121 tggagaaatt cttcaaattc ccgttgcaca tagcccggca attcctttcc ctgctctgcc
     3181 ataagcgcag cgaatgccgg gtaatactcg tcaacgatct gatagagaag ggtttgctcg
     3241 ggtcggtggc tctggtaacg accagtatcc cgatcccggc tggccgtcct ggccgccaca
     3301 tgaggcatgt tccgcgtcct tgcaatactg tgtttacata cagtctatcg cttagcggaa
     3361 agttctttta ccctcagccg aaatgcctgc cgttgctaga cattgccagc cagtgcccgt
     3421 cactcccact cttacattgt tcgcagtatc taggtacatg ttattgcgtg caccttcatg
     3481 atgtataatg ttattaatga cagcagaaag atcgacagaa ttaatattct tcgtacctgg
     3541 gacagttatc gggtgtcggc cagtgatgag accaaaggat gcagtataag atgaaccact
     3601 actattatca tggccaccat taccaccacc gttaaaacta cctcccgaac ttccagagcc
     3661 gctatgacca tcattgtagg ggtcatttgg tcccatgtga ccaaaaccac cgacagtacc
     3721 gctatttaac tctgtactca taaaattatc ctctttgact tttaaaaaca gcaaaaactg
     3781 tatttataac aatgtgttta tatacagtat tcgaaatact acgcccgtca aaaccacacc
     3841 gtcaacaggt tttttgtgta tttttcacgc ctcacgggca gcctcagacc ttttgtgtta
     3901 aaacagtaat atgttctgct gttacaatac ggtacacaca ggagacactg tcacttttat
     3961 ggcatggcac acagttcaag agacactgaa attaacagga aagtcgcgct cgcaattata
     4021 tcgtgacatg gctaaaggcc ttgtcagcta tcgcacagga aaaaatgatc gccgggagtt
     4081 cgagaccagt gaactgattc gggcctatgg cgagctgcgc acttctgaga caccaaaaag
     4141 gcacaaggag ggacactcca aatctgtcgt tagccaggcg gaaaatgctc agctagacgt
     4201 cattcagcag aaactggacg ctctgcagca gactgttacc ctaatgcttg aagacaagat
     4261 ggcgcgggaa gcagaaaacc gcctgcgaaa tgaggagagg gaacaactac aggccgaaat
     4321 tagccgtctg gctgacgcgc tggcacagga aaaaaagcgg ggattctggt cgcggctgtt
     4381 tcgctccggt tcagagtaac agtgcaggtg actctgattt accataacat ctgttatcag
     4441 caccgcctga gaggccctca gggcgtttct gacgggaaac cggtaaaaca ggcaacaaac
     4501 cacccgaaaa cccgccagaa acgcgcaggc tctgttttta cggcatgcat gagtatgcgc
     4561 acaagtgcat agcgcggaaa ttcacaccat tcagccgggg taagtcctgt ttccggcgtt
     4621 cttcccatcc gaaaacggtg aacggggacg caatttattg cgtggccgtg aagcgttgcc
     4681 ggcgcagccg gaaaacccgc tgtcagcacg ttcaggaagg gggtgatgta caaatggcac
     4741 agaggatgaa agtgacgtat gagctgaagg aatgatgtaa aagtgatgta taagtgatgt
     4801 aaaagtgatg tatgaactga aggagcgatg taattctgta gtcaggaaga ataacccgtt
     4861 catgcaggca tgaacgatac agtgaggaac gctttttttg tcacgatctc cccttaacct
     4921 gcgtaaatca cccgccatgg ttgattattt ttcaacctca aaatggtcat acacctaacg
     4981 cagccgcgat tttcatcgca actgcatgaa ttaaaagaaa aaaaaggaat atttcgtttt
     5041 cacgagtaat acccgggtat taaaaatcca ctgtaattac atgaaaataa agaaataaaa
     5101 ggtaataccg gagtattacc acgtacgcgg gcaagcgaaa aagctataac gcttcccggc
     5161 cgacaggcga cccaaaatcc acaggggcat gcaggttctc ttcagtaacc tgcgccatta
     5221 aatcaaaaag gtcatattcg ccgggaagct gcgtatcagt cgaatccagt tgttcatcat
     5281 attcagatgg catggggtga tatccagtag ctgagaggtt gttagcgggt ttcggggcgc
     5341 agccctgaac cagtcatgta gcgctagcgg agtgtatact ggcttactat gttgccacga
     5401 ttgcgaaaat cagtgaagtg cttcatgtgg caggagaaaa aaggcagcac cggcgcgtca
     5461 gcagaatatg cgatacagga gatattccgc ttcctcgctc actgactcgc tacgctcggt
     5521 cgttcggctg cggcgagcgg taccggctta cggacgggga cggaaatttc ctggaagata
     5581 ccaggaagac acttagcaaa gaagagataa ggccacggcg aagccgtttt tccataggct
     5641 ccgcccccct gacaagcatc gcaaaatctg acgctcaaat cagtggtggc gaaacccgac
     5701 aggactataa agatcccagg cgtttccccc tggtagctcc ctcgtgcgct ctcctgttcc
     5761 tgcctttcgg tttaccggtg tcattccgct gttatggccg cggtttctca ttccacgcct
     5821 gacactcagt tccgtgaagg cagttcgctc caagctggac tgtatgcacg aaccccccgt
     5881 tcagtccgac cgctgcgcct tgtccggtaa ctatcaactt gagtccaacc cggaaagaca
     5941 cgacaaaacg ccactggcag cagccattag taacaggagt gcacgagaag atagattaag
     6001 aggtcttgaa gtagaggcct gactgcggct acactgaaag aacagttttg gtaatggcgg
     6061 tctcgtgaac cctgttaccg ggttaagcag ttccccaact gacttaacct tcgaacaaac
     6121 cgcctcccca ggcggttttt tcgtttacag agcaagagat tacgattcat tgaaaaggat
     6181 ctcaagaaga tcctttgtag
//
