LOCUS       NZ_CP081310             2088 bp    DNA     circular CON 28-SEP-2023
DEFINITION  Escherichia coli strain Ec1079 plasmid pEc1079_4, complete sequence.
ACCESSION   NZ_CP081310
VERSION     NZ_CP081310.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN20802105
            Assembly: GCF_019720795.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2088)
  AUTHORS   Mahazu,S., Prah,I., Ayibieke,A., Sato,W., Iwasawa,M., Hayashi,T.,
            Suzuki,T., Iwanaga,S., Ablordey,A. and Saito,R.
  TITLE     Possible dissemination of E. coli sequence type (ST) 410 closely
            related to B4/H24RxC in Ghana
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2088)
  AUTHORS   Saito,R. and Mahazu,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-AUG-2021) Molecular Microbiology, Tokyo Medical and
            Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Tokyo,
            Please Select 272-0827, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: JUL-2021
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Oxford Nanopore; MGI DNBSEQ-G400FAST
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/28/2023 07:00:48
            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)                     :: 4,986
            CDSs (total)                      :: 4,865
            Genes (coding)                    :: 4,605
            CDSs (with protein)               :: 4,605
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 260
            CDSs (without protein)            :: 260
            Pseudo Genes (ambiguous residues) :: 0 of 260
            Pseudo Genes (frameshifted)       :: 81 of 260
            Pseudo Genes (incomplete)         :: 167 of 260
            Pseudo Genes (internal stop)      :: 50 of 260
            Pseudo Genes (multiple problems)  :: 34 of 260
            Pseudo Genes (short protein)      :: 4 of 260
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP081310.1.
            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..2088
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="Ec1079"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc1079_4"
                     /geo_loc_name="Ghana"
                     /lat_lon="9.3930 N 0.8235 W"
                     /collection_date="2015"
                     /collected_by="Tamale teaching hospital"
     gene            69..1034
                     /locus_tag="K5A55_RS24730"
                     /old_locus_tag="K5A55_24730"
     CDS             69..1034
                     /locus_tag="K5A55_RS24730"
                     /old_locus_tag="K5A55_24730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012421200.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_039064478.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLAIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
                     /name="protein rep"
     gene            1038..1304
                     /locus_tag="K5A55_RS24735"
                     /old_locus_tag="K5A55_24735"
     CDS             1038..1304
                     /locus_tag="K5A55_RS24735"
                     /old_locus_tag="K5A55_24735"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001024536.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001024536.1"
                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTFG
                     FHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
                     /name="hypothetical protein"
     Typing          463..694
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.05e-118"
ORIGIN
        1 cgcaatgcac aggtacgtga tgaatatacc acatcaaatc acagcctgcc cagatcggag
       61 caggcttaat gtcagaagat aaattccttt cggactacag cccccgtgat gcagtttggg
      121 atacccagcg cacgcttacc gattctgtcg ggggtatcta ccagactgct gctgaattcg
      181 agcgctatgc actccgtatg gcctcctgta gcggtttgtt acgttttggt tggtctacca
      241 tcatggaaac cggagaaacg cgcctacggc ttcgtagtgc gcaattttgc cgtgtccgtc
      301 attgccctgt ctgccagtgg agaagaaccc tcatgtggca agcccgtttt tatcaggctc
      361 taccgaaaat cgttgtggat tacccgtctt cccgatggtt gtttctgacg ttaactgtca
      421 ggaactgcga gataggtgaa cttggaacag tccttacagc aatgaatgcg gcgtttaagc
      481 gaatggaaaa gcgaaaggag ctatcacctg ttcaggggtg gatcagggct acggaggtga
      541 cgcgaggtaa ggatggcagc gcacatccgc attttcactg tctgctgatg gtgcaacctt
      601 cttggtttaa agggaagaac tacgttaagc acgaacgttg ggtagaactc tggcgcgatt
      661 gcttgcgggt gaactatgag ccgaatatcg atattcgggc agtaaaaact aagacaggtg
      721 aggttgtggc caacgttgcc gagcaactgc aaagcgcggt tgctgaaacg ctgaaatact
      781 ccgttaaacc ggaagatatg gcaaacgatc ctgagtggtt tcttgagctg acgcggcagc
      841 ttcacaagcg ccgttttatc tcgaccggtg gagcgctaaa aaacgtcctc cagttggatc
      901 gagaaaccaa tgaggatctt gccattgccg acgatgtagg ggatggcact gatgacggga
      961 agcggacggc gtttgtctgg gattcaggta aacggcgtta caaacgcgcc cctgagaagg
     1021 ataaatcgga ttaacgtatg aatattaata ttgaatacct gaatggaaat aagactattg
     1081 gtttattttt tttaagaagt gaagcggtga ttcctgacag gtttaaaaac cttattttgc
     1141 ttattgatgg attaagtttt ggcacatttg gttttcatcc gcacgaaggt tttgaggatg
     1201 aattaatttt atatattcag aaaacaaacg agagggtaaa aactcttttt gtgaaaatag
     1261 atttaaacgg tatcaagttt ggatttttaa gaacgcattc ttagttctgg aaaagagcca
     1321 gcggcaggct gaggtgatag gtacgagatt gcatgcaatc tctagtgctc tgtctatcct
     1381 gcattatcct cagcattatc ctcagccttg ccaactcgac accaatgcag gatagacaat
     1441 ccgatgtcaa atgttaacac tctgcgagtg gtacattttc cccggattat cgtcctgagc
     1501 ctgccgctgg ctctctttct accgcctcgc tttgctcgtt gctcaacgcc tcacagacac
     1561 ggattaaaat ccgcatccgt tcaccgtttt ttaaagtccg ttaaaagcat gatgccatct
     1621 ccgagagtta atctcgtcaa atgctaaatc gtgggggtcc cctttggggt tccgatttag
     1681 tgattgacga caccaccgat taaaaaactt atgcggggtg gatggtttca cgaagtgagg
     1741 ccatccacct gtaagacagg gttttgtttt tatcccctgt tttggtgatc gggtgtgtgg
     1801 aaaaggttgg ggtaagccgt tcggggtgct tgttttgggg ggttaaaatt gtggttattt
     1861 tttgcgcaat tctcgcgcgt gatccttgta tttatactta agggataaat ggcgggtatg
     1921 aaatagtggt ttagcccagt aatgacgagg ctttgagtgg gttttgacag gtcaaagaaa
     1981 atggagcaga attgaggcgt ttttaatcgg cgttggggag tgcgtcaaca ctccccaaca
     2041 tttcgaatgt gtcacctcag cggcaaactc tggtgacatg tactggct
//
