LOCUS       NZ_CP028575             1564 bp    DNA     circular CON 17-JUN-2024
DEFINITION  Escherichia coli strain WCHEC005784 plasmid p1_005784, complete
            sequence.
ACCESSION   NZ_CP028575
VERSION     NZ_CP028575.2
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN06209728
            Assembly: GCF_003051985.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1564)
  AUTHORS   Feng,Y., Long,H. and Zong,Z.
  TITLE     The complete genome of Escherichia coli strain WCHEC005784
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1564)
  AUTHORS   Feng,Y., Long,H. and Zong,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-JUL-2018) Center of Infectious Diseases, West China
            Hospital, Sichuan University, Guoxuexiang 37, Chengdu, Sichuan
            610041, China
  REMARK    Sequence update by submitter
REFERENCE   3  (bases 1 to 1564)
  AUTHORS   Feng,Y., Long,H. and Zong,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-APR-2018) Center of Infectious Diseases, West China
            Hospital, Sichuan University, Guoxuexiang 37, Chengdu, Sichuan
            610041, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200.0x
            Sequencing Technology             :: Illumina HiSeq; MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_003051985.2-RS_2024_06_17
            Annotation Date                   :: 06/17/2024 04:26:30
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,913
            CDSs (total)                      :: 4,791
            Genes (coding)                    :: 4,552
            CDSs (with protein)               :: 4,552
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 239
            CDSs (without protein)            :: 239
            Pseudo Genes (ambiguous residues) :: 0 of 239
            Pseudo Genes (frameshifted)       :: 75 of 239
            Pseudo Genes (incomplete)         :: 176 of 239
            Pseudo Genes (internal stop)      :: 39 of 239
            Pseudo Genes (multiple problems)  :: 47 of 239
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP028575.2.
            On Jul 15, 2018 this sequence version replaced NZ_CP028575.1.
            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..1564
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WCHEC005784"
                     /isolation_source="Rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p1_005784"
                     /geo_loc_name="China: Sichuan, Chengdu"
                     /collection_date="2014-08"
     gene            complement(join(1516..1564,1..431))
                     /locus_tag="DBQ99_RS00005"
                     /old_locus_tag="DBQ99_00015"
     CDS             complement(join(1516..1564,1..431))
                     /locus_tag="DBQ99_RS00005"
                     /old_locus_tag="DBQ99_00015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001620079.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_000275450.1"
                     /translation="MYIGTEEQRKKRLKELEKLNKESESDPKNNGPFTQVYQKGWERIR
                     ELSKDKQGVVAIPLYSFLAEHIDPSCGAVVADQQFLADKLGVSRSTIKRWLNYLESKNA
                     LVRIPVAGKVCAYALDPHEVWKGYNTSKNYAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     gene            831..1052
                     /locus_tag="DBQ99_RS26635"
     CDS             831..1052
                     /locus_tag="DBQ99_RS26635"
                     /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_250111760.1"
                     /translation="MCKRNTVTRDDIPFAVWSGLRPDTPHQCVRAQCGFRFSSASSPTR
                     SLRSVAGAAASGVTSRMLSVIPLLFFRG"
                     /name="hypothetical protein"
     Typing          complement(812..892)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.683"
                     /coverage="87.0"
                     /evalue="2.08e-24"
     Typing          1006..1266
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.275"
                     /coverage="100.0"
                     /evalue="1.83e-109"
ORIGIN
        1 ttgaccagtg ttttagtgac aaacgccgcg tagtttttag atgtgttgta tcccttccag
       61 acttcatgtg gatcgagtgc atacgcacaa accttaccag caacaggaat tctgactaac
      121 gcgttttttg attctaagta gttgagccag cgcttaattg tgcttcggct aacacccaat
      181 ttatctgcta aaaactgctg atcggcaaca acagcaccgc atgagggatc tatgtgctca
      241 gctaaaaacg agtaaagcgg tattgctaca actccctgct tgtccttcga cagttctcgg
      301 atcctttccc agcccttctg ataaacctgg gtgaatgggc cgttattttt cggatctgat
      361 tccgattctt tgtttaattt ttccagttct tttagacgct tttttcgctg ctcttcagtc
      421 ccgatataca tggtaaatct ccacggtcta atgatggctc aaatataagc catcatagct
      481 caaacgtaaa ccatgatagg tcgacctagc tcacacatgc gtgagctaac cttagaccac
      541 acatgcgtga gctaacccat aatgcaagta gctaaaaaat caataactta caaaatcgcc
      601 cttaaatatc ttttctgctg aaagtgttgc gcgaagcgga acactttttt ggggtgtcgg
      661 ggcgaagccc tgacccagtc acgtagcgat agcggagtgt atactggctt attccgctac
      721 aagcctcgcc agccgtgatt tttgccagat ttcacgctct caacgctcaa cagctccatc
      781 atggttttgc cgtccgttca ccgctaaaac gcctcagaaa tcgggacagg atgtgcaaac
      841 ggaataccgt cacccgcgac gatattccgt ttgccgtctg gtcagggctt cgccccgaca
      901 ccccgcatca gtgcgtacgt gctcaatgtg gtttccggtt ctcttccgct tcctcgccca
      961 ctcgctcact acgttcggtc gctggggctg cggcgagcgg tgtcacctct cgcatgttgt
     1021 cggtgattcc gttgttgttc tttcggggat gagtcgccag atagcccctc aaacgcgctc
     1081 agaagctctc agacacacga aacgggtttt aaatgcccgt cagggcatgg aaggcgcgaa
     1141 aaacgcttac agagcgtttc aggaggtcag gcgcgccgat acccctagcc aggggctttc
     1201 aggtcgccag gaaccgcgcc agccccctgc aaagcccatt tgcacggtac aggcagccac
     1261 tcggttggta ggtggtcgta gaccgtcggt gttacagcga tgggggtctg gggttctccc
     1321 cagacggttt ccggttgcgc tcaaggcgct gccggaaccg tggcggctcg atcgttctgg
     1381 agatcgggga gcaaaaacac gcaagggatt ttgaggcggc aaaagagcaa tgcaggatag
     1441 acaacccgat gtcaaatgtt aacatttgaa tcagattgtc caaaaacggg gtttttgcct
     1501 gtgcctgccg ctggctcaat ttgaaaacat ggccatgatt cggcgctgaa tatcaccgtc
     1561 tttg
//
