LOCUS       NZ_AP019540             5627 bp    DNA     circular CON 06-JUN-2024
DEFINITION  Escherichia coli strain THO-008 plasmid pTHO-008_2, complete
            sequence.
ACCESSION   NZ_AP019540
VERSION     NZ_AP019540.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00164371
            Sequence Read Archive: DRR170687, DRR170688
            Assembly: GCF_027943565.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Sekizuka,T., Katagiri,M., Segawa,T., Yatsu,K., Inamine,Y. and
            Kuroda,M.
  TITLE     complete genome sequences of Escherichia coli THO-008 carrying
            multi-copy IS26-mediated composite transposons harboring multi
            antimicrobial resistance genes including blaCTX-M-27 isolated from a
            patient in Japan
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5627)
  AUTHORS   Sekizuka,T., Katagiri,M., Segawa,T., Yatsu,K., Inamine,Y. and
            Kuroda,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-MAR-2019) Contact:Tsuyoshi Sekizuka National Institute
            of Infectious Diseases, Pathogen Genomics Center; 1-23-1 Toyama,
            Shinjuku-ku, Tokyo 162-8640, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Canu v. 1.4; minimap v. 0.2-r124; racon v. 1.1.0;
            circlator v. 1.5.3; Pilon v. 1.18; SPAdes v. 3.11.1; A5-miseq v.
            20140604
            Genome Coverage                   :: 200x
            Sequencing Technology             :: Sequel; NextSeq500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_027943565.1-RS_2024_06_06
            Annotation Date                   :: 06/06/2024 03:35:37
            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)                     :: 5,067
            CDSs (total)                      :: 4,939
            Genes (coding)                    :: 4,733
            CDSs (with protein)               :: 4,733
            Genes (RNA)                       :: 128
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 206
            CDSs (without protein)            :: 206
            Pseudo Genes (ambiguous residues) :: 0 of 206
            Pseudo Genes (frameshifted)       :: 67 of 206
            Pseudo Genes (incomplete)         :: 152 of 206
            Pseudo Genes (internal stop)      :: 28 of 206
            Pseudo Genes (multiple problems)  :: 37 of 206
            Pseudo Genes (short protein)      :: 1 of 206
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP019540.1.
            Annotated by DFAST v.1.0.8 (https://dfast.nig.ac.jp).
            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..5627
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="THO-008"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pTHO-008_2"
                     /geo_loc_name="Japan:Tokyo"
                     /collection_date="2018"
                     /note="Inc type: Col440I"
     gene            complement(101..292)
                     /locus_tag="QMN35_RS25250"
                     /old_locus_tag="ECTHO008_p20010"
     CDS             complement(101..292)
                     /locus_tag="QMN35_RS25250"
                     /old_locus_tag="ECTHO008_p20010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            356..679
                     /locus_tag="QMN35_RS25255"
                     /old_locus_tag="ECTHO008_p20020"
     CDS             356..679
                     /locus_tag="QMN35_RS25255"
                     /old_locus_tag="ECTHO008_p20020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            888..>1319
                     /locus_tag="QMN35_RS25260"
                     /pseudo=""
     CDS             888..>1319
                     /locus_tag="QMN35_RS25260"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            1357..1887
                     /locus_tag="QMN35_RS25265"
     CDS             1357..1887
                     /locus_tag="QMN35_RS25265"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_200922427.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNSKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            1894..2127
                     /locus_tag="QMN35_RS25270"
     CDS             1894..2127
                     /locus_tag="QMN35_RS25270"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2608..3660
                     /locus_tag="QMN35_RS25275"
                     /old_locus_tag="ECTHO008_p20040"
     CDS             2608..3660
                     /locus_tag="QMN35_RS25275"
                     /old_locus_tag="ECTHO008_p20040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001053268.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            3662..4528
                     /locus_tag="QMN35_RS25280"
                     /old_locus_tag="ECTHO008_p20050"
     CDS             3662..4528
                     /locus_tag="QMN35_RS25280"
                     /old_locus_tag="ECTHO008_p20050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     Typing          4912..5099
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          670..2231
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.808"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cccgacaccc gctaaaacct gctgacgcgc cctgacgggc ttgtcagctc ccggcatccg
       61 ctcacagaca agctgtgacc gtctccggga gctgcatgta tcagagattt tcaccgtcat
      121 ccccgaaacg tgcgaggcag ctgcggtaaa gctcatcggc gtggtcgtga agcgattcac
      181 aaatatcggc ctgttcatct gcgtccagtt cgttgagctt ctccagcagc gttaatgtct
      241 ggcttctgat aaagcgggcc atgttaaggg cggttttttc ctgtttagtc actgatgcct
      301 ccgtgtaagg gggatttctg ttcatggggt aatgataccg atgaaacgcg agaggatgct
      361 cacaatacgg gttactgatg atgaacatgc ccggttactt gaacgctgtg agggtaaaca
      421 actggcggta tggatgcggc gggtctgcct gggggagccg gttgcccgtt ccggaaaact
      481 gccgacactg gcaccgccgt tactgcgtca gctggccgcc atcggaaata acctgaatca
      541 gacagcccgt aaggtgaaca gcgggcagtg gtcttccggt gaccgggttc aggtggtggc
      601 cgcactgatg gccatcgggg atgagctgcg ccggctgcgt ctggccgtca gggaacaggg
      661 ggcgcgggat gatagttaaa tttcatgcca ggggaaaagg tggtggcagt ggtccggttg
      721 attacctgct ggggagggag cgtaaccgcg aaggcgcaac ggtgcttcag ggtaatccgg
      781 aagaagtccg ggaactcatc gatgccacgc catttgcgaa gaaatacacg tccggtgttc
      841 tgtcgttcgc ggagaaggag ctgccgccgg gaggacgtga aaaagtgatg gcgagctttg
      901 agcgtgtact gatgcccggt ctcgaaaaaa atcagtacag catcctgtgg gtggagcacc
      961 aggacaaggg acggcttgag ctgaattttg tcattccgaa catggagcta cagaccggaa
     1021 aacgcctcca gccgtactac gaccgcgcag acaggcctag aattgatgcc tggcagacgc
     1081 tggtgaatca ccattacggg ctgcatgacc cgaacgcccc ggagaaccgc cggacgctga
     1141 cccttcctga taacctgccg gaaacgaaac aggcgcttgc tgagggcgtc acacgcggga
     1201 tagacgcgct ttaccatgcc ggagagataa aaggccgtca ggatgtgatt caggcgctca
     1261 cagaggcggg gcttgaagtg gtcagggtga cgcgaagcag tatcagcatt gcagacccga
     1321 acggcgggag gaatatcaga ctgaaaggag cgttttatga gcaatctttt acagacgggc
     1381 gcggagttcg agaaaaagct gaaagagaga gccgaatcta cagagaaaat gctgaacgac
     1441 gagttcagga agctcgaaga atctgtaaac agggaactga cctcaaacga atctttaatc
     1501 aggaacgcta tcaacgacca tacaacagcc ctgaaagaac tgctggagag gtatcagaaa
     1561 acgaccgtcg atacgatgga cgcgcactgg aaaaccgtac tgaaaatgag cgtgaaacgc
     1621 tggctgtggc tgattatcgt ctcagtactg atgtttgcca cgaccgggag tctgctgtgg
     1681 taccagggca tgaagataaa cgcgaatatg aatattctcc gcgagcagaa agagagtctg
     1741 gagaagctga actcgaagac atggggcgtg cgttatcacg aggacagcaa cggacgtttt
     1801 ctggtgttgc cgaaggggat gaaagccgaa acgaactgga cgaaggacaa cggcaaactg
     1861 aacgcagtga gactggtgca ggagtgacag agcatgacgg agctggaaag acatttgctg
     1921 aacgcattag agcaactgca acaggactat atgcagcggc tgaacgaatg ggagaacgcc
     1981 ttcgtggaat tgcagaaaat gttttcgctt acgcaacggg acaacgcgat gctgaacggg
     2041 cgagtcatgc agttgagtca gcaggtgcag cacttgagcg agcggacaga acgcttgagc
     2101 cagttataca gcgagaacag gagataaggg atgaacggct gatgcaggaa cgcgaacatg
     2161 agttatctct ggagcgggag cgtcagccgg aaatccagga gcggacactg gatggccctt
     2221 cgctgggatg gtgaaaccat gaaaaatgac gtgttcagtg gattaaggcg ggctaatgtg
     2281 gcctgtagca tctggttgca taggtattca tgcggttaaa atttatcagg tgcgatcgcg
     2341 gcagtttttc gggtggtttg ttgccatttt tacctgtctg ctgccgtgat cgcaccgaac
     2401 gcgttttggc ggtgcgtaca atgcgacgtt atggtaaatg gagcggattt tcaggaagga
     2461 gtgatactaa caactcgaac actgtgcaaa taatgatttt tttaaaatat cggtaacgat
     2521 aataaattat ttcgttttac gccggtaata aatataatgt agtttcagta tataaaaaaa
     2581 tatatgaggt gtcttgtggg agctttcatg aatcttcaac aacgtataaa taaactacca
     2641 caattatcat ccagtttttc atttggaaaa gatattgata atattcattc atttatcttt
     2701 aacgaaactt ctaaagataa aattgaagat ttactaagaa aatgggtgtc aggcaatcag
     2761 ccctgtgtat ttggtaaatt ggcaagcaag aaaattaaag ggcttgattt ccatttatct
     2821 attgtaaata gcccccaact atataatgat gatggtcatt tgtttgattt tttgcgtaat
     2881 gaaagagttc gttttaaaga acgcgcaaga agaggagagg tcagtgcgca tctcatttat
     2941 tttattcatc cacaacttgc ctttgctcgt ccatcagaag agttagtgga catacaaaaa
     3001 tatatttgtt cgctgcatat gccagagtgc tatccaataa aagaggatgt tatttatact
     3061 gaaagcgtac catttcagga taaagatggg ctaaaaatat ataaggctgg tgttaatgtt
     3121 ttttactctt ctgctcatag aacaagaaat catgatagaa gaataccagg gggaatactt
     3181 atttctgtaa atgccccggg gcattttatg aggctggcga tagaaaaagg tttctataaa
     3241 gatcaagaac aagcgttagc ggatattcgt aacatgacta ttcagtctgt tggtaagggt
     3301 gggtattcac atccggaagg gatttctaca acatggcatt cagaatctaa tttggatcgt
     3361 tttggatgcc cagtgcacac cggtaatagt tcttattaca gcggttttta tcatactgat
     3421 gtattaattc caggggaatt aactaaggat gaaagattgc tccatgaaat agaaaatagt
     3481 gatccaatga tcttcaactg gaatgtattg ttttatgttt cattagaaga gtttcctata
     3541 gatgatcctt attatggaga gtttattggt attcctgtag atgatgcatc tatgtttttt
     3601 aactcctttc aaccaaggaa atttgaaaac aaaccccttt atgagaaaga ggatgattaa
     3661 tatgattaaa ggaatgcttt ttgctttttt agcagcgttc tcatgggggg cagctatcgt
     3721 aatgagcaaa aaaggagttg aagaactaga tgccggaggg gtgtttttct ggcagatttg
     3781 tagtgcagta atactatctt ggatagttct ttttataaaa agaaaaaaac tcccattaaa
     3841 ctcaaaagcg atacttgctt atgcgacagg cgtttttgaa ccattcttag cgtatacttt
     3901 tacactctac ggactttatt ttatttcagc aggaagcgca tcaattattt tttcacttga
     3961 atcagtgttt atattggtgt tgtctgttct tatttgctca gttaaaatta attccccgca
     4021 atattttata ttgttcctta taggtgcaat tgttggcagt attttggtag ccttgccaga
     4081 catcagtaat ggatcgaata atattgttgg atattgtctt gttgttgccg gtgtgttatc
     4141 ggcagcattt tatgttgtta tatcgtctcg ccttattaaa tcgtttgagc ctatcacatt
     4201 attgagcgga cagttgacat tctcccttat actgtcatcg ctctttattt ttatatctaa
     4261 atcatcaatt tatcttccgt tggaatccgt gattattgtt ttttcatctg gaatattaca
     4321 atatttttta gctttttgtt tttacttgaa ctccttgcgt tggctcccag ttcatttggc
     4381 agggataatg ttgtacttta ttccgctagt tgcattattt ttgtcatggt tgtttttgga
     4441 tgaacaattc acattcttac agggggtagg atttattgta actgtgctaa gtgtatattt
     4501 tcttaacaga aaatactcag aggagtaaca ttctgttcag gattgccccc cggcctccat
     4561 cgataccgtg ccaaatgcac gtaaaaaacg ggagcgtttc tggtgtcgga atgtaaccaa
     4621 gggggtcaga ggcgcgctaa aacgctctca ggggagtcaa atagagacgt ttgtaacaaa
     4681 aagatcaaag gatcctcttg agatcctttt tttctgcgcg taatctgctg cctgtaaacg
     4741 aaaaaaccgc cttgcagggc ggtttgatcg aaggttaagt cagcttgcag actgcttaac
     4801 caggtaactg tcttatgcga gacgagtcac caaaattgtt cttctagtgt agccgcactc
     4861 cggcagccac ttcaagtact ctctaaatat ctcgcacatg acttttacca atggctgctg
     4921 ccagtggcgc tttgtggtgt cttttccggg ttggacccaa gagaacagtt accggagaag
     4981 gcgcagcagt cgggctgaac ggggggttcc tgcatacagc ccagcccgga gcgaactgcc
     5041 taagtcgccc cgagatacca gaagacgtga gctatgagaa agcgccacgt gtcccgtaag
     5101 ggagaaaggc ggaaaaggta tccggtaatc gatatggcgg gaacgtgggg gcgcaggagg
     5161 gagcgattca ccggaaacgg tgatgatctt taagccacgt cgggtttcgc caccgctggc
     5221 ggatttcatg gttgagccgc aaggctccca cagatgcacc gaaaaagtgt ctgttttgtg
     5281 aagtccgtca ggggggcgga gcctatggaa aaagcgcctc cggcgcggcc tttcccgggg
     5341 tttcgttttt tgcgcacatg ttctttcctg gtttatcccc gggttctgtg gataacaggg
     5401 ttagcgtttt tgagaaagga gagtccgctc gccgcagccg aacgaccgag cgtagcgagt
     5461 cagtgagcga ggaagcggaa gagcgcctga actggcattt tctccttacg catctgtgcg
     5521 gcatttcaca ccggacatgg cgcacttttc atacaatccg cactgatgcc gaatggttaa
     5581 gccagtatac actccgctat cgctacgtga ctgggtcagg gccgcgc
//
