LOCUS       NZ_AP024208             3397 bp    DNA     circular CON 07-JUL-2023
DEFINITION  Escherichia coli strain TA8571 plasmid pTMTA85713, complete
            sequence.
ACCESSION   NZ_AP024208
VERSION     NZ_AP024208.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00260480
            Sequence Read Archive: DRR258151, DRR258152
            Assembly: GCF_016629485.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Ariyoshi,T., Kubota,H. and Sadamasu,K.
  TITLE     Complete genome sequences of Escherichia coli strain TA8571
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3397)
  AUTHORS   Ariyoshi,T., Aoki,K., Kubota,H., Yokoyama,K., Ishii,Y., Tateda,K.
            and Sadamasu,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-DEC-2020) Contact:Tsukasa Ariyoshi Tokyo Metropolitan
            Institute of Public Health, Department of Microbiology; Hyakunincho
            3-24-1, Shinjuku-ku, Tokyo 169-0073, Japan URL
            :http://www.tokyo-eiken.go.jp/
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.9b
            Genome Coverage                   :: 289x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/07/2023 04:45:58
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,739
            CDSs (total)                      :: 4,620
            Genes (coding)                    :: 4,394
            CDSs (with protein)               :: 4,394
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 226
            CDSs (without protein)            :: 226
            Pseudo Genes (ambiguous residues) :: 0 of 226
            Pseudo Genes (frameshifted)       :: 65 of 226
            Pseudo Genes (incomplete)         :: 163 of 226
            Pseudo Genes (internal stop)      :: 35 of 226
            Pseudo Genes (multiple problems)  :: 38 of 226
            Pseudo Genes (short protein)      :: 5 of 226
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP024208.1.
            Annotated at DFAST 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..3397
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="TA8571"
                     /db_xref="taxon:562"
                     /plasmid="pTMTA85713"
                     /geo_loc_name="Japan"
                     /collection_date="2018"
     gene            complement(286..486)
                     /locus_tag="JG732_RS23310"
                     /old_locus_tag="ECTA8571_45450"
     CDS             complement(286..486)
                     /locus_tag="JG732_RS23310"
                     /old_locus_tag="ECTA8571_45450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001558245.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="antitoxin VbhA family protein"
                     /protein_id="WP_061585996.1"
                     /translation="MTDDRTLQLRLTGFRKAEASLRLEGMDPSGTPLYESVKTRILSGD
                     ITFDEGRTEIRAHYQKRANSN"
                     /name="antitoxin VbhA family protein"
     gene            1030..1174
                     /locus_tag="JG732_RS23790"
                     /pseudo=""
     CDS             1030..1174
                     /locus_tag="JG732_RS23790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001717510.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            1447..1617
                     /locus_tag="JG732_RS23390"
                     /old_locus_tag="ECTA8571_45460"
     CDS             1447..1617
                     /locus_tag="JG732_RS23390"
                     /old_locus_tag="ECTA8571_45460"
                     /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_153449163.1"
                     /translation="MSYVSERKSELVKAQQRKMDPSSPNSAPINQGLMDFILLAMKVDD
                     GFVQRGRIHGA"
                     /name="hypothetical protein"
     gene            complement(1621..2229)
                     /locus_tag="JG732_RS23315"
                     /old_locus_tag="ECTA8571_45470"
     CDS             complement(1621..2229)
                     /locus_tag="JG732_RS23315"
                     /old_locus_tag="ECTA8571_45470"
                     /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_063859057.1"
                     /translation="MAKCLLVKVRRETSVAVFRQCEIREKYLAIYKESFDEVITYLEKA
                     GALEPGVLRLTTIDDNAIRAWKSQWKGRSRKHAHGAWDWQNLVSKRARSCKRFDVAVWG
                     EDVLCGLSVGKLTRGKKTVRMDYLEACPTAHPLEKRITMIVVAVALSVAKKVGAQHVAI
                     FNPIKDKEEKVLKHYQSYGFTQRMLYGRFLKNVLYKEVV"
                     /name="hypothetical protein"
     gene            2469..2933
                     /locus_tag="JG732_RS23320"
     CDS             2469..2933
                     /locus_tag="JG732_RS23320"
                     /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_061583928.1"
                     /translation="MEDKNNLSSEVKNHVSKWGKTNISAGWTIIPNALLENQSRLGLSC
                     IDTMVLINLIMHWWEKDNPPRPSKKRLANMLGVSLKTVQRSFIHLEQCGAIKRIPRYKE
                     GKDNARTTNHYDLNGLVDLLEGFSKELIEEREANRKSEVNRPKKRGNPKS"
                     /name="hypothetical protein"
     Typing          538..1138
                     /name="rep_cluster_2324"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.05"
                     /coverage="92.0"
                     /evalue="0.0"
ORIGIN
        1 gcctttctgg taacggtgaa cgagtgcgca gtttactgtg cgttcgtgaa gcgttggcca
       61 agccgccagg cgcggcagat ttacagtggg tgcaaacgcc agcaatttgc gaatcctgct
      121 ctcgatctga acagcagcga aatttcgtac gtacgaaatt cagggtatcg ggcggggcct
      181 gatgaaacat tctggagtgc cggcggtact ccaaaaacac atcttgtccc gccattttgt
      241 ggcgccggcg cagcggcggt ggccacaaaa catttcctgt ccgcgtcagt tactgttcgc
      301 ccgcttctgg taatgagccc gtatctcagt gcggccttca tcgaaggtga tgtcaccgga
      361 aagaatcctt gtctttaccg attcataaag cggggttcct gatggatcca tcccttcaag
      421 cctgagagag gcctccgctt tacggaaccc tgtcaggcgc agttgcagtg tccgatcatc
      481 agtcatggtt tttcctttga gcagtcatgc gaataaggca ggcgtaaagt tagctaactt
      541 tacatgtcct gcccggatgt tgccgttgta tagctgtgca gggaaaagtg gaaaacgaca
      601 ggaaactgtt gcagccgggt gtgtaatcag ggaggaaacg tgtgtaccga gcgacacgat
      661 ccctgttcag cattacagac attacgcttc ctcggtcatt cgctcacttc gttcggtcat
      721 gacactgcgg cgagcgttac ctgctcaggc agaaggccat aaggaggttc tggggattgc
      781 cggttttcca taggcttcgc cctcctgaca agcttcacag aaatcaggtg atttccggcg
      841 ctcaaatcag aagtggcgaa acctgacagg acttaaagat ccccaccgtt tccgatgggt
      901 cgctccctcg tgcgctctcc tgttcccacc ctgaggttta cccgttgcag tccgccgtaa
      961 ggtggcgttt tctcattcct acccgtgcaa ctgggttcct tgtaggtggt tcgctccaag
     1021 ctgggctgta tgcacgaact ccccgttcag cccgactacc acgtctttat caggtaactg
     1081 tactcttgaa tccaaccctg aaagacacga caaagcgcca ctggcggtag ccattggtag
     1141 cagtgagtgc gagaggtgta tcgagagttc ttgaagttaa agcctgacta cagctacact
     1201 ggaaggacag atttggtgac acgtctcgca caagactgtt acctaggttc aaagagccgc
     1261 aaactcaatg aactggaaaa aaaccgcccc gcaaaggcgg tttttttctt ttgagagaaa
     1321 agagtacgct ttgcagaaga ggcgagtcaa caacagtcat ctctttttga aaatatagag
     1381 atctcgttat ttttttatcc acttgttata gtgtctacat ccccatacaa gacagagagt
     1441 cacaagatga gttatgtatc tgagcgcaaa agtgagctgg taaaggcaca gcaacgcaaa
     1501 atggatccat cctctcctaa ttcagctcca atcaatcagg gtcttatgga cttcatcctg
     1561 cttgctatga aagtagatga cggctttgtt caacgtggtc gtattcacgg cgcatagcta
     1621 tcaaacaact tctttgtaca gcacgttttt caaaaagcgt ccatacaaca ttctttgtgt
     1681 aaacccgtaa gactggtagt gttttaacac tttttcttct ttgtctttta tcgggttgaa
     1741 tatggctacg tgctgtgccc ctactttttt agctactgac agagccacag caaccacaat
     1801 cattgtgatt cgtttctcca acggatgagc tgttggacaa gcctctagat aatccattct
     1861 aactgtcttt ttaccacggg ttagctttcc aactgaaagc ccacaaagca catcctctcc
     1921 ccaaacagcc acatcaaatc ttttacaaga acgagctctc tttgatacaa ggttctgcca
     1981 atcccaagca ccatgagcgt gcttacgaga cctgcctttc cattggctct tccatgcacg
     2041 aatagcattg tcatcgattg tagtgagcct taaaacgccg ggctctaaag cacctgcctt
     2101 ctcaagataa gttataactt catcgaatga ctctttgtaa atcgcgagat atttttctct
     2161 aatttcgcat tgtctaaaaa ccgccacgct cgtctccctc ctgaccttga ccagtaaaca
     2221 ttttgccata aaaaaaccac tttaaatcat ttgctaacat tttggttagt ggtcaacaaa
     2281 gaccatatcc tatggtacat ttaaacccca ccctgtggac tttaaaaacc atagggtacg
     2341 gtctgatttg accacacaga aaaagatata gtgggacaat acgttaagac aatgacgcaa
     2401 ggtgaacggt aaaacgttca atatataaaa tgccctctag cctcagatga ccacaggatg
     2461 catgttttat ggaagacaaa aataacctgt cgagcgaagt aaagaaccac gtaagcaagt
     2521 gggggaagac aaacatttct gcaggatgga cgattatccc aaatgcctta ctggaaaatc
     2581 agtccaggtt gggtcttagc tgtattgata cgatggttct cataaacctc ataatgcatt
     2641 ggtgggaaaa agataacccc ccaagacctt cgaaaaagag actggcgaac atgctgggcg
     2701 tttcactaaa aaccgttcaa agaagtttta ttcatttgga acagtgtggt gccatcaagc
     2761 ggatacctcg atacaaagaa gggaaagaca atgccagaac aacaaaccat tacgatctga
     2821 acggactggt agacctgctg gaaggttttt cgaaagagct tatcgaagaa agagaggcga
     2881 atcgaaaaag tgaagttaat agacctaaga agcgcggtaa tccgaaaagt taataggctg
     2941 acaaacacac tctcctgtag agagtccaat ttaccataac atctcttgcc cgcaccccct
     3001 gagagcccct cagcgcgatc ctggggcgtc cgggccgttt ccggcacctt tccctgtcca
     3061 tactcctgaa aaacgcccct gatgattttt aggccgctgc atggctatgc acgagagtga
     3121 atgacgcgcg ccttcgctgc aaaacacctg cctgagcctc attttcagca cgaagcagtg
     3181 ctcattactt cacttttcgc cgcctaaaaa atttttttag aaaaactgat ttttctaccg
     3241 ctgaaaatta caaagtccct aatttcctga tccagaccca actccgtaca ggaaattttt
     3301 atatgcctaa atttttgaaa ctgataagcg tcatgctgaa ggtcatgaat gagctgcttg
     3361 atctcgtaga acgactgaaa gaattattcc cgcaatg
//
