LOCUS       NZ_CP134374             4237 bp    DNA     circular CON 22-SEP-2023
DEFINITION  Escherichia coli strain TUM12357 plasmid pMTY12357_Col-MG828-like,
            complete sequence.
ACCESSION   NZ_CP134374
VERSION     NZ_CP134374.1
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 4237)
  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  JOURNAL   Unpublished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 4237)
  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
            CP134374.1.
            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..4237
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="TUM12357"
                     /isolation_source="Brazilian imported chicken meats"
                     /host="Chicken"
                     /db_xref="taxon:562"
                     /plasmid="pMTY12357_Col-MG828-like"
                     /geo_loc_name="Japan"
                     /collection_date="2012"
                     /collected_by="Toho University"
     gene            613..1128
                     /locus_tag="RJ642_RS26245"
                     /old_locus_tag="RJ642_26220"
     CDS             613..1128
                     /locus_tag="RJ642_RS26245"
                     /old_locus_tag="RJ642_26220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000097059.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_000097059.1"
                     /translation="MSSLSLQRYETNPFLELMTIPMKGKRIQVSRLGRDDNVLVNQNTG
                     EKFGTHVTTFKRVDSEQFVKLFTANIGLTFDLSSAGIKAFNVLLWAVQKQAFAKDQVLL
                     DSRALDDFLKSYDSLKLSYATLKRGINELEKAQIIAKTMRKGFYFINPNFVFNGDRIAF
                     TTLIERDC"
                     /name="replication/maintenance protein RepL"
     gene            1191..1598
                     /locus_tag="RJ642_RS26250"
                     /old_locus_tag="RJ642_26225"
     CDS             1191..1598
                     /locus_tag="RJ642_RS26250"
                     /old_locus_tag="RJ642_26225"
                     /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_310995232.1"
                     /translation="MSKNDVFACACRRLLEVVAGEQKWRFVRLLITTTWLEVFMTKHDA
                     IRISQLHQIFYDDDGLIDSEKNVTILYSIGFTVDEIAHFRNSTPNTVAAQLLNARVKLG
                     CASVSSLKPMILLRLLLNIKEIRFGFETDCK"
                     /name="hypothetical protein"
     gene            1686..1949
                     /locus_tag="RJ642_RS26255"
                     /old_locus_tag="RJ642_26230"
     CDS             1686..1949
                     /locus_tag="RJ642_RS26255"
                     /old_locus_tag="RJ642_26230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001677227.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EexN family lipoprotein"
                     /protein_id="WP_000717655.1"
                     /translation="MKKICTLLMSIFILSACGEDTKSSDWWLNHPKEATEKYKECKKSG
                     EDSVNCQNVKKVAGIIGRTYGPMLEILKAESAEYDKQHGLNR"
                     /name="EexN family lipoprotein"
     gene            1954..2952
                     /locus_tag="RJ642_RS26260"
                     /old_locus_tag="RJ642_26235"
     CDS             1954..2952
                     /locus_tag="RJ642_RS26260"
                     /old_locus_tag="RJ642_26235"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000012467.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_052978250.1"
                     /translation="MSGFFEKFNSEVVSKIEEMTKPLQSQLGQDMLSLLSAGISVYILW
                     VGYQILAGKRQTPLQDLVWDLSKFAIILTFVSNADGYLTAAMDAIKSMKDGFLGKPVWA
                     TLDTMWSTTQLLADKVYAMDQSKYVSVEGGIGSMLVWGGSILIMSVAAVIYMLADVTMQ
                     LAILVAPIFIGCYMFGFTRVMFNNWLGILFSSVFTVIFAGVLVKIGTEFQTDMLSQISR
                     DANSTNILTMGAMAFVIGVLIAVFVWKSSSFAQQLAGAGVEGTLQGMALLGIGVAGMAV
                     EKTRNQMKRGTRTAAEWAGEKGEQKRASIGALGMEARRRASLEKARARNSA"
                     /name="type IV secretion system protein"
     gene            2949..3662
                     /locus_tag="RJ642_RS26265"
                     /old_locus_tag="RJ642_26240"
     CDS             2949..3662
                     /locus_tag="RJ642_RS26265"
                     /old_locus_tag="RJ642_26240"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001590713.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV secretion system protein"
                     /protein_id="WP_001590713.1"
                     /translation="MNKKLIFSVLLCLFSFGSVAGIPVAIDASPEWAVEATRWTERLKQ
                     WSETARHYQSQIQAYKDQLATATGIRNIAAFTNELSNLQSELANIYKQGNSYISDFTSN
                     PEGALSSQAKNLFSKYGAFNMCSTGIESSDNLCKARIVSTAASIEQGNEINKQLSSAMS
                     QIQSLSNRIESSKDMKESQDLANALQAQSLKIQAIKMQYDVWDSKNRADAEMLKEQKYA
                     EYRLRQKNAKIPSFE"
                     /name="type IV secretion system protein"
     Typing          1955..2757
                     /name="MPF_T"
                     /typing="mate-pair-formation"
                     /tool="MOB-suite"
                     /identity="89.552"
                     /coverage="91.0"
                     /evalue="1.41e-160"
ORIGIN
        1 tcgctgtaac atcgacggtc tacgaccacc taccaaccgt gtggctacct gttccgtgct
       61 aatgggcttt gcagggggct ggcgcggttc ctggcgacct gaaagcccct ggttaggggt
      121 atcggcgcgc ctgacctcct gaaaccctct gtaagcattt ttcgcgcctt ccatgccctg
      181 acgggcatct aaagcccgtt tcgtgcgtct gagcgcgttt taagagctaa gacgactaaa
      241 acattaccaa cacctgaaaa tcgcgttctg gtgctctgga tggcccacag aacgcatttt
      301 cgaacagaac agcaacggca tttctgacaa catgcgagag gtgatcccgc tcgccgcagc
      361 cccagcgacc gaacgtagtg agcgagtggg cgaggaagcg gaagagaatt gatagccata
      421 attgagcacc tacgctcctt agttaagaac taagaaggga aattctcgga acccgcatga
      481 atcctagaaa gtggtgatca ggatctgtac cttgtaagct cagatccggt accttacagg
      541 ctcaaaaatt gcttgatttt gagcttatga ggatttattg tgaatctcca aagcccaaaa
      601 aaggatgcaa taatgagctc gctaagctta cagagatacg aaacaaaccc gtttttagag
      661 cttatgacga tcccgatgaa agggaaacgg atacaagtat ctcgtcttgg gcgggatgac
      721 aatgttttgg ttaatcaaaa cacgggagaa aagtttggaa cacatgtaac cacttttaag
      781 cgtgtagata gtgagcaatt tgttaagttg tttactgcga atattgggtt aacgtttgat
      841 ttatcatcgg caggaattaa agcttttaat gttcttttat gggctgttca aaaacaagcc
      901 tttgcaaagg atcaggttct tttggattca agggctcttg atgacttttt aaaaagctat
      961 gatagcttaa aacttagtta tgctacgtta aagagaggaa ttaacgagtt agaaaaagct
     1021 cagattatag caaagacaat gcgtaaagga ttttatttta taaaccccaa ttttgtattt
     1081 aatggagatc gaatagcatt tacaacccta attgagaggg attgttaatc gatagaacaa
     1141 tacaatgcag gatagacaat ccgatgtcaa atgttaacat ttgaatcaga ttgtccaaaa
     1201 acgatgtttt tgcctgtgcc tgccgcaggc tactagaagt agtcgcaggc gaacaaaagt
     1261 ggcgttttgt tcgcctgcta atcacaacaa cctggctaga ggtttttatg actaaacatg
     1321 atgctatacg catttctcaa cttcatcaaa ttttttacga tgatgatgga ttaattgatt
     1381 cagaaaagaa cgtgactatt ttatacagta taggatttac agttgatgaa atagctcatt
     1441 ttagaaattc aacaccaaac acagttgcgg ctcagctatt aaatgcaagg gttaaattag
     1501 gttgcgcctc ggtttcatct ttaaagccaa tgatcttatt aagattgctt ttgaacataa
     1561 aagagattcg ttttggattc gaaactgatt gcaaataata tagttcaata ggtatttttg
     1621 ctcttgacta gaattacaat tgctgattgt atcagcaatt gtaatgtcca tacgaggaat
     1681 caaagatgaa aaaaatttgt acgctcttaa tgtctatttt cattctttcc gcatgtggtg
     1741 aagatacaaa atcatcagat tggtggctta atcatcccaa agaagcgacg gagaaatata
     1801 aggagtgtaa aaagtcaggg gaagattctg ttaattgtca aaatgttaaa aaagttgccg
     1861 gaattattgg tagaacctat ggccctatgc ttgaaatact taaggctgag tcagctgaat
     1921 atgataagca acatggattg aacaggtgat aacatgtctg gtttctttga aaagtttaat
     1981 agcgaagttg ttagtaaaat cgaagagatg accaaaccac ttcaaagtca attaggtcag
     2041 gatatgttat ctcttctaag tgcaggtatt agcgtttata tcctctgggt tggctatcaa
     2101 atattggcag ggaaacgcca gaccccatta caagatctcg tctgggatct atcaaaattt
     2161 gccattattt taacattcgt aagcaatgct gatggctatc tgacggcagc aatggatgct
     2221 attaaatcta tgaaggatgg gttccttggt aaacctgtat gggcaacgct agataccatg
     2281 tggagtacaa ctcagctttt ggctgacaaa gtttatgcta tggatcaatc caaatatgtg
     2341 tcagttgaag gtggaatcgg gtcaatgttg gtttggggag gaagtatcct gattatgtct
     2401 gtagcggctg ttatttacat gcttgccgat gtaacaatgc agttagctat tcttgtagct
     2461 ccgatattta tcggttgtta tatgtttgga ttcactagag taatgtttaa taactggctt
     2521 ggtatattat tttctagtgt atttactgtt atttttgctg gagttctcgt caaaattggt
     2581 accgagtttc aaactgatat gcttagtcag atatcgagag atgctaactc aacaaatatt
     2641 ttaacaatgg gcgcaatggc atttgtaatt ggagttctga ttgctgtctt tgtctggaaa
     2701 tcatcgagtt tcgcgcagca gcttgccggt gcaggtgttg aaggtactct tcagggaatg
     2761 gctcttttag ggattggggt tgctggaatg gccgtagaga aaacgagaaa ccagatgaaa
     2821 cgtggaacgc gaacagccgc cgaatgggca ggtgaaaaag gggagcagaa acgggcttca
     2881 ataggcgcat tgggaatgga agcaagaaga cgagcatccc tggaaaaagc acgtgcgagg
     2941 aattcagcat gaacaaaaaa ctaatttttt cagtactttt gtgcttattt tcatttggtt
     3001 ctgtcgcagg tattccggtt gctattgatg ccagtccgga atgggctgtt gaagccacaa
     3061 gatggacaga acgactcaaa caatggtctg aaacagcgcg gcattatcaa agtcagattc
     3121 aggcatataa agaccagtta gccacggcaa caggtataag gaatattgcg gcattcacaa
     3181 atgaactaag taacctacaa tcagagctgg caaacattta taagcagggg aacagttata
     3241 tttctgattt taccagtaat cctgaaggtg cattaagtag tcaggcgaaa aatctgttca
     3301 gcaagtatgg tgcttttaat atgtgttcta caggcattga aagttctgat aacctttgta
     3361 aggccagaat agtttcaacg gccgctagca ttgaacaggg aaatgagata aataagcagc
     3421 tatcaagtgc aatgtctcag attcagagtt taagtaaccg aattgagtct tcaaaggata
     3481 tgaaagaatc ccaggatttg gctaacgcat tgcaggcgca gtcgttaaaa atacaggcaa
     3541 ttaaaatgca gtatgatgta tgggatagta aaaacagggc tgatgcggaa atgttgaaag
     3601 agcaaaagta tgctgagtat cgcctgcgtc agaaaaatgc aaagataccg agtttcgaat
     3661 gatatgataa agctaaataa gctaaaagaa tgggtagata atcattggtc tagattgaat
     3721 agtaccggtt ctacaccgcc gccactgtta atctcgctac caatcatagt tattgtttta
     3781 agtgtggagc ttacgttaaa gctggttaat gctttaatgt attatggtac attgcaattt
     3841 atcactgata aaattgaaaa gaggtttgtt cccagcggtg gtataaaaga aagactcctt
     3901 tttacgttaa agctgttttg tattttactt ctgttattaa tagtaatgcg attttcaatg
     3961 aagtaaaaaa taaaggtcat cgaatagatg gccttttcta ttctaaattc taaatataga
     4021 gcctgcggca ggcacaggca aaaacatcgt ttttggacaa tcatggataa aatgttaaca
     4081 ttttgaccat gattgtctat cctgcattgc tcttttgccg acctcaaaac ccctagcgtg
     4141 tttttgtttc ccgatctcta gaaccaccga gccgccacgg ttccggcagc gccttgagcg
     4201 caaccggaaa ccgtctgggg agaaccccag accccca
//
