LOCUS       NZ_CP072861             6201 bp    DNA     linear   CON 11-FEB-2024
DEFINITION  Escherichia coli strain 184/2aE plasmid pEc184_3.
ACCESSION   NZ_CP072861
VERSION     NZ_CP072861.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18630606
            Assembly: GCF_018361365.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6201)
  AUTHORS   Santos Tufic-Garutti,S.D., de Araujo Longo,L.G., Fontana,H.,
            Garutti,L.H.G., de Carvalho Girao,V.B., Fuga,B., Lincopan,N., de
            Pinho Rodrigues,K.M. and Moreira,B.M.
  TITLE     OXA-181 carbapenemase carried on an IncX3 plasmid in high-risk
            Escherichia coli ST167 isolated from a traveler returning from
            Sub-Saharan Africa to Brazil
  JOURNAL   Diagn Microbiol Infect Dis 102 (1), 115570 (2022)
   PUBMED   34739936
REFERENCE   2  (bases 1 to 6201)
  AUTHORS   dos Santos Tufic-Garutti,S., de Araujo Longo,L.G., Fontana,H., Groto
            Garutti,L.H., Brigido de Carvalho Girao,V., Fuga,B., Lincopan,N., de
            Pinho Rodrigues,K.M. and Meurer Moreira,B.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-APR-2021) Medical Microbiology, Universidade Federal
            do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bloco I,
            Lab I2-59, Rio de Janeiro, Rio de Janeiro 21.941-902, Brazil
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 24-MAR-2020
            Assembly Method                   :: UNICYCLER v. 0.4.8
            Assembly Name                     :: Ec184_2aE
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 50.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/11/2024 09:00:58
            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)                     :: 4,845
            CDSs (total)                      :: 4,719
            Genes (coding)                    :: 4,486
            CDSs (with protein)               :: 4,486
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 233
            CDSs (without protein)            :: 233
            Pseudo Genes (ambiguous residues) :: 0 of 233
            Pseudo Genes (frameshifted)       :: 71 of 233
            Pseudo Genes (incomplete)         :: 162 of 233
            Pseudo Genes (internal stop)      :: 43 of 233
            Pseudo Genes (multiple problems)  :: 42 of 233
            Pseudo Genes (short protein)      :: 4 of 233
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP072861.1.
            Bacteria and source DNA available from Laboratorio de Investigacao
            em Microbiologia Medica, Avenida Carlos Chagas Filho, 373, CCS,
            Bloco I, Lab I2-59 Cidade Universitaria, Rio de Janeiro, RJ,
            Brasil.
            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..6201
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="184/2aE"
                     /isolation_source="Stool specimen"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc184_3"
                     /geo_loc_name="Brazil: Rio de Janeiro"
                     /lat_lon="22.95 S 43.17 W"
                     /altitude="15 m"
                     /collection_date="2017-12-10"
                     /collected_by="Instituto de Microbiologia Paulo de Goes"
     gene            371..520
                     /locus_tag="J9158_RS23860"
                     /old_locus_tag="J9158_23745"
     CDS             371..520
                     /locus_tag="J9158_RS23860"
                     /old_locus_tag="J9158_23745"
                     /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(1265..1705)
                     /locus_tag="J9158_RS23865"
                     /old_locus_tag="J9158_23750"
     CDS             complement(1265..1705)
                     /locus_tag="J9158_RS23865"
                     /old_locus_tag="J9158_23750"
                     /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            1923..2312
                     /locus_tag="J9158_RS23870"
                     /old_locus_tag="J9158_23755"
     CDS             1923..2312
                     /locus_tag="J9158_RS23870"
                     /old_locus_tag="J9158_23755"
                     /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            2356..>2760
                     /locus_tag="J9158_RS23875"
                     /old_locus_tag="J9158_23760"
                     /pseudo=""
     CDS             2356..>2760
                     /locus_tag="J9158_RS23875"
                     /old_locus_tag="J9158_23760"
                     /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(2867..3703)
                     /locus_tag="J9158_RS23880"
                     /old_locus_tag="J9158_23765"
     CDS             complement(2867..3703)
                     /locus_tag="J9158_RS23880"
                     /old_locus_tag="J9158_23765"
                     /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(3704..4461)
                     /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             complement(3707..4506)
                     /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            complement(4567..5382)
                     /gene="sul2"
                     /locus_tag="J9158_RS23890"
                     /old_locus_tag="J9158_23775"
     ARG             complement(4571..5382)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(5842..6000)
                     /locus_tag="J9158_RS24355"
     CDS             complement(5842..6000)
                     /locus_tag="J9158_RS24355"
                     /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             complement(2871..3703)
                     /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          163..336
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          complement(5..239)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.395"
                     /coverage="99.0"
                     /evalue="4.79e-69"
     Typing          complement(5673..6182)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.606"
                     /coverage="99.0"
                     /evalue="3.71e-149"
ORIGIN
        1 tgcgatgctt gtcagggggg cggagcctat ggaaaaacgg cttcgccgtg gccttatctc
       61 ttctttgcta agtgtcttcc tggtatcttc caggaaattt ccgtccccgt ccgtaagccg
      121 gtaccgctcg ccgcagccga acgaccgagc gtagcgagtc agtgagcgag gaagcggaat
      181 atctcctgta tcgcatattc tgctgacgcg ccggtgctgc cttttttctc ctgccacatg
      241 aagcacttca ctgattttcg caatcgtggc aacatagtaa gccagtatac actccgctag
      301 cgctacatga ctggttcagg gctgcgcccc gaaacccgct aacaacctct cagctactgg
      361 atatcacccc atgccatctg aatatgatga acaactggat tcgactgata cgcagcttcc
      421 cggcgaatat gacctttttg atttaatggc gcaggttact gaagagaacc tgcatgcccc
      481 tgtggatttt gggtcgcctg tcggccggga agcgttatag ctttttcgct tgcccgcgta
      541 cgtggtaata ctccggtatt accttttatt tctttatttt catgtaatta cagtggattt
      601 ttaatacccg ggtattactc gtgaaaacga aatattcctt ttttttcttt taattcatgc
      661 agttgcgatg aaaatcgcgg ctgcgttagg tgtatgacca ttttgaggtt gaaaaataat
      721 caaccatggc gggtgattta cgcaggttaa ggggagatcg tgacaaaaaa agcgttcctc
      781 actgtatcgt tcatgcctgc atgaacgggt tattcttcct gactacagaa ttacatcgct
      841 ccttcagttc atacatcact tttacatcac ttatacatca cttttacatc attccttcag
      901 ctcatacgtc actttcatcc tctgtgccat ttgtacatca cccccttcct gaacgtgctg
      961 acagcgggtt ttccggctgc gccggcaacg cttcacggcc acgcaataaa ttgcgtcccc
     1021 gttcaccgtt ttcggatggg aagaacgccg gaaacaggac ttaccccggc tgaatggtgt
     1081 gaatttccgc gctatgcact tgtgcgcata ctcatgcatg ccgtaaaaac agagcctgcg
     1141 cgtttctggc gggttttcgg gtggtttgtt gcctgtttta ccggtttccc gtcagaaacg
     1201 ccctgagggc ctctcaggcg gtgctgataa cagatgttat ggtaaatcag agtcacctgc
     1261 actgttactc tgaaccggag cgaaacagcc gcgaccagaa tccccgcttt ttttcctgtg
     1321 ccagcgcgtc agccagacgg ctaatttcgg cctgtagttg ttccctctcc tcatttcgca
     1381 ggcggttttc tgcttcccgc gccatcttgt cttcaagcat tagggtaaca gtctgctgca
     1441 gagcgtccag tttctgctga atgacgtcta gctgagcatt ttccgcctgg ctaacgacag
     1501 atttggagtg tccctccttg tgcctttttg gtgtctcaga agtgcgcagc tcgccatagg
     1561 cccgaatcag ttcactggtc tcgaactccc ggcgatcatt ttttcctgtg cgatagctga
     1621 caaggccttt agccatgtca cgatataatt gcgagcgcga ctttcctgtt aatttcagtg
     1681 tctcttgaac tgtgtgccat gccataaaag tgacagtgtc tcctgtgtgt accgtattgt
     1741 aacagcagaa catattactg ttttaacaca aaaggtctga ggctgcccgt gaggcgtgaa
     1801 aaatacacaa aaaacctgtt gacggtgtgg ttttgacggg cgtagtattt cgaatactgt
     1861 atataaacac attgttataa atacagtttt tgctgttttt aaaagtcaaa gaggataatt
     1921 ttatgagtac agagttaaat agcggtactg tcggtggttt tggtcacatg ggaccaaatg
     1981 acccctacaa tgatggtcat agcggctctg gaagttcggg aggtagtttt aacggtggtg
     2041 gtaatggtgg ccatgataat agtagtggtt catcttatac tgcatccttt ggtctcatca
     2101 ctggccgaca cccgataact gtcccaggta cgaagaatat taattctgtc gatctttctg
     2161 ctgtcattaa taacattata catcatgaag gtgcacgcaa taacatgtac ctagatactg
     2221 cgaacaatgt aagagtggga gtgacgggca ctggctggca atgtctagca acggcaggca
     2281 tttcggctga gggtaaaaga actttccgct aagcgataga ctgtatgtaa acacagtatt
     2341 gcaaggacgc ggaacatgcc tcatgtggcg gccaggacgg ccagccggga tcgggatact
     2401 ggtcgttacc agagccaccg acccgagcaa acccttctct atcagatcgt tgacgagtat
     2461 tacccggcat tcgctgcgct tatggcagag cagggaaagg aattgccggg ctatgtgcaa
     2521 cgggaatttg aagaatttct ccaatgcggg cggctggagc atggctttct acgggttcgc
     2581 tgcgagtctt gccacgccga gcacctggtc gctttcagct gtaagcgtcg cggtttctgc
     2641 ccgagctgtg gggcgcggcg gatggccgaa agtgccgcct tgctggttga tgaagtactg
     2701 cctgaacaac ccatgcgtca gtgggtgttg agcttcccgt ttcagctgcg tttcctgttt
     2761 ggggtcgttt gcgggaaggg gcggaatcct acgctaaggc tttggccagc gatattctcc
     2821 ggtgagattg atgtgttccc aggggatagg agaagtcgct tgatatctag tatgacgtct
     2881 gtcgcacctg cttgatcgcg gccgcgatag ctagatcgcg ttgctcctct tctccatccg
     2941 cgttccaagc tgcggaaagg cacccataag cgtacgcctg gtcgagcagg cgacgcggat
     3001 cgacgtccag cgcacgagag aatgcgtccg ccatctgtgc aatgcgtcta ggatcgagac
     3061 aaaggtcgtc tctgtcagcc ggatcgtaga acatattggc ggcgccaaag cccacttcac
     3121 cgaccagacc gacgggatct atcaccagcc agccgcgact ggagaacatg atgttttcat
     3181 gatgcagatc gccatgtagc ccacgcagtt ccgaggcatt gctcatcatt tgatcggcta
     3241 taatcgccgc gtggacgtag tcagtttgac aacctgcgtt ttgatcatcg cgcgcccgct
     3301 gaaacaaagc tgcaaagcga tcccggatcg ggagaagggc agaaggcagg ggttcctcag
     3361 atgcggcata cagcttcgcc attagttccg ctgcaatttc ggtcgcctgg tagtcgccgt
     3421 gctcggcaac gatgtgagag agcattcgct ccccggcata ttcgagcaac atcagattgt
     3481 tctcacgacc gagcaaccgg actgctcccc tcccattgcg ccataccaga tagtcggccc
     3541 cgcgcagttc atcagcaatg tcttctatag gtttcaatcc cttgacgatt gcaggagtcc
     3601 cgtctggcaa tgaaactttc caaacgaggc tggaaaaggt gtccgcaatg agaacaggtt
     3661 gcgaaacgtg ccaatgagca ggaaaaacag gcggcatgaa catcaacccc aagtcagagg
     3721 gtccaatcgc agatagaagg caaggcgttc gcggtcgggg gcttcgatcc ccaatacatt
     3781 gaataggaca gcgaaggcgc gctctgcttc atctggcgct gcccagttct cttcggcgtt
     3841 agcaatcatg agtgccaaat cggcatagcg atctgctgtt ccgagccgcc caaggtcgat
     3901 cagacccgtg cattgaagag ttttagggtc caccatgaag ttcggcatgc agggatcacc
     3961 atggcaaaca accatatcgg tgcgctcttg gtcgagccgc accggtagct ctcgttcgac
     4021 acgagccaaa agatcgagct gcggcgtact cttgtcctcg tccggtaaga agtcgggatt
     4081 gacggcattg cgggacacca catcaacggc gcgtccgaac attcgcgaca gcctgcgctc
     4141 aaacggacat tgatcaaccg ataggctgtg aacagcgcca agttgctgcc ccattgacgg
     4201 ccacgctttg agcaaatccg ctccagacag atcagccgcc ggtactcccg gaattgccgt
     4261 tatcaccaag catgcaccct cctgttcctc ctgccagttg atgacctcgg ggcaagccac
     4321 acctcgacct ttgagccaaa tgaggcggtc acgctctcca gcgagctcac cgcggcggga
     4381 agcaggtgcg attttcgcga aggcatgccc gtcaccacgt cgaaaaacaa aatcaccaga
     4441 ttctccgcct ctgacaggca accagtcaga atgcgattca ccaaaaaaaa tattagttcg
     4501 atttaatgga ggttccttca gttttctgat gaagcgcgaa tatagagaaa tatcccgaat
     4561 gtgcagttaa cgaattcttg cggtttcttt cagcgccgcc aataccgcca gcccgtcgcg
     4621 caaggggcgc ggctcgtgtg tgcggatgaa gtcagctcca cctgcggcgg cggcaagctc
     4681 tgcagcgagt gtcgcggccc cgacatcccc cggaccacgg cctgtgagcg cgcgcagaaa
     4741 ggatttgcgc gaaacagaca gaagcaccgg caaatcgaag cgcagccgca attcatcgaa
     4801 ccgcgccagc accgagagcg aggtttcggg agcagccccc agaaaaaacc ccatgccggg
     4861 atcaaggaca aggcggttgc gtttgatacc ggcacccgtc agcgccgcga tgcgcgcgtc
     4921 aaagaacgcc gcaatgtgat ccatgatgtc gccagcgggt gcctcgcgcc gatctgcctg
     4981 cccgtcttgc accgaatgca taacgacgag tttggcagat gatttcgcca attgcggata
     5041 gaacgcagcg tctggaaaac cgcgaatatc attgagatag gccacaccac gcgacaaggc
     5101 ataggcttgc gtcgcgggtt gataactgtc gagcgagacg ggaatgccat ctgccttgag
     5161 cgcgtccagc accggcgcga tacgcgcgat ttctgtgtcg gacgaaacag gcgcggcgtc
     5221 gggattgctg gatgccggac cgaggtcgat cacatctgcc ccctcggcca tcagcttacg
     5281 cgcctgcgca atggctgcgt ctggcgccag ataccggcct ccatcggaga aactgtccga
     5341 ggttatgttg acgatgccga aaatgatgag cgatttattc atgggggctt ctataataat
     5401 aataatcgag catgagtctc atacggatgc tcgggtcgaa agggaatccc caggcgagta
     5461 acctgtttgc ggtgatccgt ttcatgatga tgtatctgta gcattttgga aataaatata
     5521 tcatctctca ataagtagat atatttatct tttttgcttc tttggtgctg caagtcacca
     5581 atacgaggga aacctgttac ggagcggttt aaccgtaatc aacagtgact ggtgtcatgt
     5641 tcggaagatt aattgatagt aatctacaaa ggatcttctt gagatccttt tcaatgaatc
     5701 gtaatctctt gctctgtaaa cgaaaaaacc gcctggggag gcggtttgtt cgaaggttaa
     5761 gtcagttggg gaactgctta acccggtaac agggttcacg agaccgccat taccaaaact
     5821 gttctttcag tgtagccgca gtcaggcctc tacttcaaga cctcttaatc tatcttctcg
     5881 tgcactcctg ttactaatgg ctgctgccag tggcgttttg tcgtgtcttt ccgggttgga
     5941 ctcaagttga tagttaccgg acaaggcgca gcggtcggac tgaacggggg gttcgtgcat
     6001 acagtccagc ttggagcgaa ctgcctaccc ggaactgagt gtcaggcgtg gaatgagata
     6061 aacgcggcca taacagcgga atgacaccgg taaaccgaaa ggcaggaaca ggagagcgca
     6121 cgagggagcc accaggggga aacgcctggt atctttatag tcctgtcggg tttcgccacc
     6181 actgatttga gcgtcagatt t
//
