LOCUS       NZ_AP026793             1661 bp    DNA     circular CON 27-NOV-2023
DEFINITION  Escherichia coli strain IPCEC42 plasmid pIPCEC42_5, complete
            sequence.
ACCESSION   NZ_AP026793
VERSION     NZ_AP026793.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00533654
            Sequence Read Archive: DRR403238, DRR403241
            Assembly: GCF_026001125.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Suzuki,M., Tran,H.H. and Shibayama,K.
  TITLE     Complete genome sequence of Escherichia coli IPCEC42
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1661)
  AUTHORS   Suzuki,M., Tran,H.H. and Shibayama,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-SEP-2022) Contact:Masato Suzuki National Institute of
            Infectious Diseases, Antimicrobial Resistance Research Center; 4-2-1
            Aobacho, Higashimurayama, Tokyo 189-0002, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8.0
            Genome Coverage                   :: 343x
            Sequencing Technology             :: Illumina MiSeq; ONT MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/27/2023 03:47:39
            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)                     :: 5,417
            CDSs (total)                      :: 5,313
            Genes (coding)                    :: 5,051
            CDSs (with protein)               :: 5,051
            Genes (RNA)                       :: 104
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 77
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 262
            CDSs (without protein)            :: 262
            Pseudo Genes (ambiguous residues) :: 0 of 262
            Pseudo Genes (frameshifted)       :: 106 of 262
            Pseudo Genes (incomplete)         :: 183 of 262
            Pseudo Genes (internal stop)      :: 46 of 262
            Pseudo Genes (multiple problems)  :: 60 of 262
            Pseudo Genes (short protein)      :: 3 of 262
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP026793.1.
            Annotated by DFAST https://dfast.ddbj.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..1661
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="IPCEC42"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pIPCEC42_5"
                     /geo_loc_name="Cambodia:Phnom Penh"
                     /collection_date="2016"
     gene            complement(64..219)
                     /locus_tag="OPA56_RS26980"
                     /old_locus_tag="IPCEC42_51860"
     CDS             complement(64..219)
                     /locus_tag="OPA56_RS26980"
                     /old_locus_tag="IPCEC42_51860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001302705.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001358489.1"
                     /translation="MNHFIGGKSGGSIYYKPIQCPTGFIMTGTRMYGIGDGVDEEHVDA
                     YCCPFG"
                     /name="hypothetical protein"
     gene            complement(258..389)
                     /locus_tag="OPA56_RS26985"
     CDS             complement(258..389)
                     /locus_tag="OPA56_RS26985"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001425347.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_256465069.1"
                     /translation="MAMGSVVHLLFFLSEQCYLMPFSTYRIGTGLRANPVGGLVAIK"
                     /name="hypothetical protein"
     gene            complement(577..906)
                     /locus_tag="OPA56_RS26990"
     CDS             complement(577..906)
                     /locus_tag="OPA56_RS26990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001199278.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001141248.1"
                     /translation="MPSTHRIGTEASANPVRGKKLAQVIAKLLPLQLLRGVGLEQRQHV
                     HLARKSLVEAVNADQIPDLYGSHVPCLQATMHGLPVATRPKIKMVQLQFTPFASDDTYH
                     WQTTM"
                     /name="hypothetical protein"
     gene            <882..1105
                     /locus_tag="OPA56_RS27155"
                     /pseudo=""
     CDS             <882..1105
                     /locus_tag="OPA56_RS27155"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012565250.1"
                     /note="frameshifted; internal stop; incomplete; partial in
                     the middle of a contig; missing N-terminus; Derived by
                     automated computational analysis using gene prediction
                     method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="shufflon system plasmid conjugative transfer
                     pilus tip adhesin PilV"
                     /name="shufflon system plasmid conjugative transfer pilus
                     tip adhesin PilV"
ORIGIN
        1 gggaaattat gagtccggcg gcacaattac tgttacatgc ctgaatcttc ctggtgctgg
       61 gatttaaccg aaggggcaac aataagcatc aacgtgttcc tcatcaacgc catcaccaat
      121 gccatacatg cgtgtacctg tcatgataaa tccggtcggg cattgaatgg gtttgtagta
      181 gatagatcct ccacttttcc cgccaatgaa gtgattcatt gctacagatg attgatacca
      241 cttacaggcg gagtagttca ctttattgcc accagaccac cgaccggatt ggcacggagg
      301 ccagtgccaa tccggtacgt ggagaagggc atcaggtagc actgttctga caggaaaaat
      361 agcaaatgga caacagatcc cattgccatc tggtttttct gccagccagt gtacctggag
      421 tgtcagtaat gcagaaaatc cgcacgggtg gaagccgaat tattttgcgg ggtcagttgc
      481 aacctatgat gccaatcgaa ttgtgaaatg cggcttctat gacgaataca acttttatgg
      541 cggtactcac cgaactgacc tgtcggggaa atgtagttac atcgtggttt gccagtgata
      601 agtatcgtca ctggcaaatg gcgtaaactg taattgaacc attttgatct tcggtcgtgt
      661 cgcaactggc agtccatgca ttgttgcctg aaggcatgga acgtgtgagc catataaatc
      721 cggtatttga tctgcattga ccgcctccac caatgacttt cttgccagat ggacatgttg
      781 ccgttgctcc aggccaacgc cacgcagtag ctgaagcggt aacaatttgg ctatcacctg
      841 cgccaatttt tttccacgta ccggattggc actggcctcc gtgccaatcc ggtgtgtgga
      901 gggcattagg tggaaagctc aaggttactc aactttccag cactggttac ttggggcaat
      961 ttgacttttt gtgccattgc tgtgaatggg aaatgctgag gattctcatt actgccaggt
     1021 agtcgagagt ccatctggtt cacgaaaatg gtacaaatac gagcacaaga caggttgtat
     1081 tgcgtcctgt gtaactctca attaagtttg gtatccaaat actgaaaata ccctgagcca
     1141 caagagtagt ttttgggccg gataagaggt gatctgataa gttgcgccag cagggacagc
     1201 aaaagagatg aatgctgtct tcccataaga tgggttatta ctcgcatttg tgctaatcaa
     1261 tgcccctgca acgtatcctg caatctggat gtgttagcac aatctccccc ggcggaacca
     1321 ccattccctc cagaggcgta aacaaacagc gtaccacttc ccgtattgcg accagtaaat
     1381 gatcctcggt gtgatccaag attactgtaa ctaccgttag aggaaccgga agttctccac
     1441 acaccggatt ggcactggcc tccgtgccaa tccggtatct ggacaacggc aaaagtgaac
     1501 ttcactacca gtacgtacaa tatcgggaaa aacacccgaa atctgagcat tggcgtacat
     1561 gcgtactgtt cgtggacata ccttaatggt gcgccttttg gtgggtttca gcaggtatac
     1621 tccgaccaaa acaaggtttg gtatgtgaat aattatgcgt g
//
