LOCUS       NZ_CP134375             3374 bp    DNA     circular CON 22-SEP-2023
DEFINITION  Escherichia coli strain TUM12357 plasmid pMTY12357_5, complete
            sequence.
ACCESSION   NZ_CP134375
VERSION     NZ_CP134375.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37323659
            Assembly: GCF_031663975.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3374)
  AUTHORS   Aoki,K.
  TITLE     Visualization of food-borne spreading blaCTX-M trafficking to human
            using blaCTX-M-8 as an indicator: blaCTX-M-8-carrying IncI-1/pST113
            plasmid was transferring host from chicken E. coli to human E. coli
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3374)
  AUTHORS   Aoki,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-SEP-2023) Department of Microbiology and Infectious
            Diseases, Toho University, 5-21-16, Omori-nishi, Ota-ku, Tokyo
            143-8540, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.5.0
            Assembly Name                     :: TUM12357
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 107x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/22/2023 09:45:49
            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)                     :: 5,258
            CDSs (total)                      :: 5,138
            Genes (coding)                    :: 4,794
            CDSs (with protein)               :: 4,794
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 344
            CDSs (without protein)            :: 344
            Pseudo Genes (ambiguous residues) :: 0 of 344
            Pseudo Genes (frameshifted)       :: 99 of 344
            Pseudo Genes (incomplete)         :: 259 of 344
            Pseudo Genes (internal stop)      :: 64 of 344
            Pseudo Genes (multiple problems)  :: 69 of 344
            Pseudo Genes (short protein)      :: 4 of 344
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP134375.1.
            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..3374
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="TUM12357"
                     /isolation_source="Brazilian imported chicken meats"
                     /host="Chicken"
                     /db_xref="taxon:562"
                     /plasmid="pMTY12357_5"
                     /geo_loc_name="Japan"
                     /collection_date="2012"
                     /collected_by="Toho University"
     gene            complement(join(3110..3374,1..59))
                     /locus_tag="RJ642_RS26270"
                     /old_locus_tag="RJ642_26245"
     CDS             complement(join(3110..3374,1..59))
                     /locus_tag="RJ642_RS26270"
                     /old_locus_tag="RJ642_26245"
                     /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_001696562.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     APPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            123..314
                     /locus_tag="RJ642_RS26275"
                     /old_locus_tag="RJ642_26250"
     CDS             123..314
                     /locus_tag="RJ642_RS26275"
                     /old_locus_tag="RJ642_26250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1632..1865)
                     /locus_tag="RJ642_RS26280"
                     /old_locus_tag="RJ642_26255"
     CDS             complement(1632..1865)
                     /locus_tag="RJ642_RS26280"
                     /old_locus_tag="RJ642_26255"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /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_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1872..2432)
                     /locus_tag="RJ642_RS26285"
                     /old_locus_tag="RJ642_26260"
     CDS             complement(1872..2432)
                     /locus_tag="RJ642_RS26285"
                     /old_locus_tag="RJ642_26260"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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_000067486.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGMKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<2461..3120)
                     /locus_tag="RJ642_RS26290"
                     /old_locus_tag="RJ642_26265"
                     /pseudo=""
     CDS             complement(<2461..3120)
                     /locus_tag="RJ642_RS26290"
                     /old_locus_tag="RJ642_26265"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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"
     Typing          complement(396..476)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.805"
                     /coverage="93.0"
                     /evalue="8.68e-18"
     Typing          complement(1550..3120)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.439"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccctcgcagc gttccagtaa ccgggcgtgc tcctcatcgg taacccgtat cgtgagcatc
       61 ttctcgcgtt tcatcggtat cattccccct aacaaatccc ccatacaagg agccttaaga
      121 ccatgaccaa acaggaaaaa acagccctta acatggctcg ctttatcaga agccagacgc
      181 taaccctgct ggaaaaactc aacgatctgg acgcggacga acaggcagac atctgcgaat
      241 cacttcacga ccacgccgac gaactctacc gcagttgcct cgcacgcttc ggcgatgacg
      301 gtgaaagcaa ctgaaacatg cagctcccgg agacgttcac agcttgcctg tgagcggatg
      361 ccgggagcag acaagcccgc cagggcgcgt cagtgcgggt gtcggggcgc agccctgacc
      421 cagttcacag agcgatagcg atgtgtatac tggcttacct cattttgcat cggtgcagag
      481 tggatgggaa gtgcaccatg tcaggagtaa aaagccgcac agatgcgtaa aaacagcgcg
      541 cccgataaac aacacacacg cggacactgg cacaggcgcg taagtgcaca atgcttgcct
      601 ctgtgactct tccgcttcct cgcccactcg ctcactacgt tcggtcgctg gggctgcggc
      661 gagcggtggg atcactctcg ttgtgatgca gatccgtttt ttttttttgc actggagtta
      721 tcaggagtag cggtgcacat gggttcgtgc gatatgctgg atggtggaag gtcggaggga
      781 acggcaacaa ctcacccctc ccagtgaagg gacgggtagt ttgccgctct cgatatgccg
      841 gacggagcca aggccatcga tcacggggcg cgtcagtgga agaacccgcg cctgcgtgac
      901 gtatgcgtct tcgccgcacc atctcacccg tcacgccacc acataccggg aactgccgcc
      961 aaggtctaac tcaaccaatc tagccgcgct acatacggtt tttgtggcaa ctcatcaggt
     1021 gtccgctgtc gatgaaactc tctgcgccgg tagcggaact ctcacgcgtg cggtcgccgt
     1081 cgtcacagct cccccaaccg caaacgattc tcgcaaatac gcaagtatct gcaaaaacag
     1141 gtttttttcg gggttcctgg gagactgtgc tgttgaaaaa ttcttgaaga atacagaagg
     1201 ctcatgcaaa ctgaatgaac tggtttctgt tgtggatctc aacagtttcc acaggaacat
     1261 tgaggaggtc agagacctca atgaacccga aacagctcgc cttcctggcg agctgttttc
     1321 gttctacgcc cgccgacgaa agatcgcaag tgcaataacg agatttttca cgtctttacg
     1381 ctcaaaaagt aaaaaaacca tgttttcccc tggctgaatc cccaaaaacg cgtgaaatgc
     1441 gttttcagga tgttgcatag ctatgcacaa atacggcaca cgatttgttt cgctcgcccc
     1501 agccgtcgaa cgggtcaaaa tggcaagatt tcgtcacttc cccggtcaca tctccattga
     1561 tggcccactc cgaacccgtg ccgcgcgttc ctgtacctca tgtctgtacc gggcacgctc
     1621 ctgttcatcc cttagctgtt gttcgcgata aataaccgac tcaagcgatc cacttgcccg
     1681 gctaatctct gcacctgctg actcaatatc acgacgcgct cgttcagtat cgcgttgttc
     1741 cgttgcgtaa cctcgtgcat cttctgcaat tccgcgaagg cgctctccca ctcgttcagc
     1801 cgccgcatat agtcctgttg caaatgctct aaggcgttca gcaaatgccc ttccagttcc
     1861 gtcatactcg tttactccct gaccagcctc acggcgttct tgtcgcccac cgtccaggtg
     1921 ttttcccctt tcatcccgtc cggcaacacc agaaatttcc cgttctcgcc attgacgaac
     1981 gtcacccccc aggtttttgc ctcgagtttc gccagcgtgt tttcctgctc tctgatagtc
     2041 aggatatttt tcgcaatctt gctttcctgc cactccatca gcccccagca ccccaggaaa
     2101 atcccgcccg tgacgctgag cgcggtcagc gccggaaaca gtatccgccc tttgatcacc
     2161 cgccagagca gttttttctg ctgccgggac agttcggcct ctgtggtgct gaactgcatg
     2221 ctcacggtgg tgctcagcgt atccagttgc tttttcacgg atgttgtatg ttcgctgata
     2281 gcgtctctga ttttctgcct gtttaagctc aatgccttgt ctacagactc ttcgagcttc
     2341 ctgaactcgc tgttcagcat gttctcggta gaagcggctc gctctttcag tttcttctcg
     2401 aagtctgttc ccatttgtaa aagattgctc atacagcgcc ccctttagcc tgagattccg
     2461 ccccccctcc gggtcggcaa tactgatgct gcttttggtt gtcctcacca cctcaaaacc
     2521 tgccgctgta agcgcctctg tgacatcctg acgcgttttt attgctccgg catggtaaag
     2581 agcctcaaga ccccgtgtaa tcgcttctgc ggcctcctgt ttcgcttttg gcagattatt
     2641 tggcgtgaca agcgtccgtc tgttctccgg tgcgttcggg tcacgcagcc cgtaatgatg
     2701 attaaccagc gtctgccagg catttatcct cggcctgtcc gcacggtcgt agtacggctg
     2761 gaggcgctta ccgctctgta gctccatgtt cgggatgaca aaattcagtt cgagccgccc
     2821 cttatcctgg tgttccaccc agagaatgct gtactggtct ttttcgagac cgggcataag
     2881 aacacgctca aagctcgtca tcactctttc gcgttcaccc ggtggtagct ccttctccgc
     2941 gaacgacaga acgcctgacg tgtatttctt cgaaaatggc gtggaatcaa tgagttcccg
     3001 cacttcttcc gggttacccc ggagcaccgt tgcgccttcg cggttacgct cccgccccag
     3061 caggtaatcg accgggccac ttccaccgcc tttccccctg gcatgaaatt taactatcat
     3121 cccgtacccc ctgttccctg acagcctgcc gcaactggcg caattcaccc tcgatggcca
     3181 tcagtgcggc caccacatga acccggtcaa tcgaagacca ctggccgctg ttcaccttcc
     3241 gggctgtctg gttcaggttg ttcccgatgg cagccagatg ccgcagcaat ggcggtgcca
     3301 gtgtcggcag ttttcctgtg cgtgcaaccg gctcccccag acagacccgc cgcatccatt
     3361 ccgccagtcg ttta
//
