LOCUS       NZ_CP134373             4677 bp    DNA     circular CON 22-SEP-2023
DEFINITION  Escherichia coli strain TUM12357 plasmid pMTY12357_Col-pHAD28-like,
            complete sequence.
ACCESSION   NZ_CP134373
VERSION     NZ_CP134373.1
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 4677)
  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  JOURNAL   Unpublished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 4677)
  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
            CP134373.1.
            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..4677
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="TUM12357"
                     /isolation_source="Brazilian imported chicken meats"
                     /host="Chicken"
                     /db_xref="taxon:562"
                     /plasmid="pMTY12357_Col-pHAD28-like"
                     /geo_loc_name="Japan"
                     /collection_date="2012"
                     /collected_by="Toho University"
     gene            196..309
                     /locus_tag="RJ642_RS26225"
                     /old_locus_tag="RJ642_26200"
     CDS             196..309
                     /locus_tag="RJ642_RS26225"
                     /old_locus_tag="RJ642_26200"
                     /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="replication initiation protein"
                     /protein_id="WP_072101919.1"
                     /translation="MHEPPVQSDRCAFSGNYQLESNPERHDKTPMAAATGN"
                     /name="replication initiation protein"
     gene            complement(544..981)
                     /locus_tag="RJ642_RS26230"
                     /old_locus_tag="RJ642_26205"
     CDS             complement(544..981)
                     /locus_tag="RJ642_RS26230"
                     /old_locus_tag="RJ642_26205"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_052918195.1"
                     /translation="MPKRGKSIRSSSRNEETKPSKSTAKTTDRFISISFKHFHNVDDVG
                     QSINTWKDDGSLPDLIEKLVYLTANGITKVISDGVFTNYTRFPESAVNDFRCPDEISSD
                     EDWGVIKNIGGQKRRVAGFLRDNVFYIVFFDRDHRFWKSQK"
                     /name="hypothetical protein"
     gene            complement(986..2284)
                     /locus_tag="RJ642_RS26235"
                     /old_locus_tag="RJ642_26210"
     CDS             complement(986..2284)
                     /locus_tag="RJ642_RS26235"
                     /old_locus_tag="RJ642_26210"
                     /inference="COORDINATES: protein motif:HMM:NF024700.3"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ATP-binding protein"
                     /protein_id="WP_064987013.1"
                     /translation="MMVNFSLSNAFSFMEAQNMSMLAVSSSKDDINLANVVSVRDERIL
                     KSALIFGANASGKSNLMKTISLMKDIVLHSVQAIESGITKNVVPFLLDEAGPTKPSEME
                     MTFIADGIKYRYGLSLFQGKIKEEWLYYTPKTRETILFERDGQLIEINKAAFSESNLFI
                     KDGVIQKTREDVPFVSVVAGFNGEHSKRVVNWFSNVVFISGSNEGMFTGITMKLINESE
                     DFKAWLKKILPAFQINDIYLDEVAPEFPFGNIKTDDDNLKNLFSSIQNFAKNQKVFSLR
                     VVKKTANGEISVPIDFESEGTKKIVYLLGPIYNAMINNNLLLVDEFDSKFHTLLSKFLF
                     RIFHAQSEGFSQVIAAVQDVNLMNTDCFRRDQIWFVDKDVKSGSSHLYSLVEYKEKQRS
                     LKPSYGNDYLSGAFDAIPLFDNLNEFEKLMPEG"
                     /name="ATP-binding protein"
     gene            4042..4236
                     /locus_tag="RJ642_RS26240"
                     /old_locus_tag="RJ642_26215"
     CDS             4042..4236
                     /locus_tag="RJ642_RS26240"
                     /old_locus_tag="RJ642_26215"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041631.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(3528..3796)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="90.037"
                     /coverage="93.0"
                     /evalue="7.52e-94"
     Typing          complement(3908..4006)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(4310..4394)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.837"
                     /coverage="100.0"
                     /evalue="1.41e-35"
     Typing          18..513
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.28"
                     /coverage="99.0"
                     /evalue="1.36e-133"
     Typing          4405..4676
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.161"
                     /coverage="99.0"
                     /evalue="5.33e-113"
ORIGIN
        1 cgacgctcaa gtcagaggtg gcgaaacccg acaggactta aagataccag gcgtttcccc
       61 ctggtgactc cctcgtgcgc tctcctgttc ctgccattcg gtttaccggt gtcactccgc
      121 tgttatggcc gcgtttgtct cattccacgc ctgacactca gttccgggta ggcagttcgc
      181 tccaagctgg actgtatgca cgaacccccc gttcagtccg accgctgcgc cttttccggt
      241 aactatcaac ttgagtccaa cccggaaaga cacgacaaaa cgccaatggc agcagccact
      301 ggtaactgat ttagaggagt tagtcttgaa gttatgcgcc tgttaaggct aaactgaaag
      361 aacagatttg gttactgcgc tcctcataag ccagttacct tggttcacag agcgccaact
      421 cttagaaccg tcgaaaaacc gcccgccaag gcggtttttt cgtttacaga gcaagagatt
      481 acgacgagag catcacaatc tcaagaagat cttttcttaa catacaatac aactgtatct
      541 catctatttt tgactcttcc agaagcgatg atctctatca aaaaacacga tatagaacac
      601 attatctctc agaaatccgg cgactcttct tttctgcccg ccaatgtttt ttataacccc
      661 ccaatcctca tcagaggata tctcatctgg gcatctaaaa tcgtttacag ctgactcagg
      721 aaatcgagtg tagttagtaa acacaccgtc agaaatcact ttagtgattc cattcgccgt
      781 tagataaacc aatttttcaa tgagatcagg taggctacca tcatctttcc atgtatttat
      841 ggactgccca acatcatcga cgttatgaaa atgcttaaaa ctaatagata taaatctatc
      901 agtcgttttc gctgtgctct ttgaaggttt tgtttcctca ttcctcgaag agcttcgaat
      961 gcttttgcct ctctttggca tataatcatc cctcaggcat tagcttttca aattcattaa
     1021 gattatcaaa taacgggatt gcatcaaaag cacctgataa ataatcattc ccatatgatg
     1081 gcttcaatga tctttgtttc tctttgtact caaccaaaga ataaagatgg ctactccctg
     1141 actttacatc cttgtcaaca aaccaaattt ggtctcgtct aaagcaatca gtattcatta
     1201 aattaacatc ctgaactgca gcgattactt ggctaaaccc ttcactttgc gcatgaaata
     1261 tcctaaataa aaacttagat aaaagggtat ggaactttga atcgaactca tcaaccaata
     1321 ataagttatt gttaatcatg gcgttataaa taggcccaag gagatagact atctttttgg
     1381 tcccctctga ttcaaaatca atgggaaccg aaatctcccc attagcagtt tttttcacga
     1441 ctctaagaga aaatactttt tgattttttg caaaattctg aatcgagctg aataaatttt
     1501 ttaaattatc atcatctgtt tttatgttgc caaacgggaa ttcaggcgca acttcatcaa
     1561 gataaatatc attaatctga aaggctggta atattttttt tagccaagct ttaaaatctt
     1621 cagattcatt tataagcttc atggtaattc cagtaaacat tccttcgtta gaaccagaaa
     1681 taaataccac attactaaac caattcacaa cacgctttga gtgctcccca ttaaatccag
     1741 caacaacaga aacaaaggga acatcttctc ttgtcttctg aatgacccca tcctttataa
     1801 aaagatttga ctcgctaaat gctgctttat ttatttcaat aagttgacca tctcgctcaa
     1861 agagaatagt ctcccttgtt tttggcgtgt agtacaacca ctcttctttt atcttccctt
     1921 gaaataaaga taatccgtat ctgtatttaa tcccatccgc aataaaagtc atttccattt
     1981 cagatggttt agtaggcccc gcctcatcaa gtaaaaaagg gactacattc ttcgtaatgc
     2041 cactttcgat agcttgcaca gaatgcagga caatatcttt cattaaagat attgtcttca
     2101 tgagattaga ttttccgcta gcgttagctc cgaaaatcaa agcagacttc agtatccgct
     2161 catcccttac tgacactaca ttagccaagt ttatatcgtc tttcgatgac gacaccgcca
     2221 acatgctcat attttgagct tccatgaagg aaaatgcgtt tgaaagacta aagttaacca
     2281 tcataagaac acccctaaca acacccttaa actcaaaaat tgcacaatat tgacaaaatt
     2341 ctagattaag aatagcataa ccccgtacta aaacaacaaa agggtccaat agacagcaca
     2401 ttatgagtag ataagttaac gaccagctta aaaagaggtg tatatgaagt tttttctata
     2461 ccaaatggtc ccatttgcct cagtgattag ctcagcagtg ctggcttttc actcggtatc
     2521 tgggtgggga tggttccttt ttgtcgcgtt tatgctcagt ggcgctgaca ctgtaaaaaa
     2581 atacgtagag agtgaaacat gaatgaggag aagcaaaaat tgttgaagta agtgggttag
     2641 cctgtaccac cagaactaac ccgtaacaaa ccatacgcaa atgcggcgct tgagtaccac
     2701 ctcaagtgct ttgataaagc cagccacaag atctgttggt tgctacagta caattttgat
     2761 agcaaaaatc aacattcatg tggcgaaaat aggaaatgca acatgcagac ggacgagcct
     2821 caggcataca tttttcgccc ttacataacg gtaaagggca aacggataac ccgtcctaac
     2881 gggggaatgt ttaagatccc aattaatcgg gaaaagaaaa aacaataacc accgaagcat
     2941 gcaagcttcg gtccctaact tagtttatgt aaggaaagca acatggcctt ttatgtagat
     3001 agcacagcga aatttttaac aaaaacaacc gagcctgaag ggagtgtatg gcggtattac
     3061 tataagccgg gaaatacttg tccggcttcc ggcatttacc gctgcacgaa ctgtggtgat
     3121 gaagtgacgt gcaataaaga tgatcctttg ccaccgcaaa atcataggca gcataatgtc
     3181 ccaggtgaca tccgatggga attggtagtg atgacaaaga cgaagtaact tactaggccg
     3241 tctacggacg gcttttttat acctgccaat cagctggatt taccataaca tccgattgcg
     3301 cgcaccgcta aaacgcgctg aacgcgattc tgccgcaaac accgcaaaaa gagatgtttt
     3361 ccccggggta aaccggaaaa atgcgtcagg ctcgctttca gctcactgca tagctatgca
     3421 tgaaagtgaa tgacgatcgg tttgggcgca tacagtgccc atgagacaca ttttcggaca
     3481 ttttcagttc gtgaatccct gactcattgc tacatatctg aacagacacc cctggcagcg
     3541 cccccagggg cgtcctgtaa aaaaacacac cgcgcagcta gcagcacccc taatataaga
     3601 tgatgttttt tatgaaaata gtcagtacca cccctaaaaa gcggtgtcgg cgcggtgttg
     3661 tagctgcgcc aacaccgctt ttttaaatat cacaaagaga gcaagaagaa ctaatttgtc
     3721 ataactctct atttataaag aaaaatcagc aaaaaattgt ttttgcgtgg ggtgtgggca
     3781 tttcgggcat gagaacagac tcgcgttttt ccggagtatc agcggaatta ttgattaaga
     3841 aacactcgac gcagagcgaa attttatgca acagcggctg cactgcacag ggattattta
     3901 tcagttgata tgctgtgcca tgatacgtcc taaagaaaca ggacaggatg tgcaattgta
     3961 ataccgtcgc ccgcaacgtc ttacaattac cacctgctca gggtcccccc gacacccgga
     4021 actgacggag aacaacggaa ggtgaacaaa caacaacaaa ctgcgctgaa tatggcgcga
     4081 tttatcaaaa gccagagcct gacactgctt gaaaaactgg atgctctgga tgccgacgaa
     4141 caggcggcca tgtgcgaacg actgcacgaa ctcgcagaag aactccagaa cagcatccag
     4201 attcgctttg aggccgaaag tgaaacagga acataacgaa gctgacggag gcggtcacgg
     4261 ctttcccgtg ggcgttttcg tcagcagaca agcccgtcag ggcgcgtcag ggggtttcgg
     4321 ggcgaagccc tgaaccagtc acgtagcgat agcggagtgt atactggctt aaccatgcgg
     4381 catcagtgcg gattgtatga aaagtacgcc atgccgggtg tgaaatgccg cacagatgcg
     4441 taaggagaaa atgcatgtcc aggcgctttt ccgcttcctc gctcactgac tcgctacgct
     4501 cggtcgttcg actgcggcga gcggtactga ctcacacaaa aacggtaaca cagttatcca
     4561 cagaatcagg ggataaggcc ggaaagaaca tgtgagcaaa agaccaggaa caggaggaag
     4621 gccgcgccgc tggcgttttt ccataggctc cgcccccctg acgagcatca caaaaac
//
