LOCUS       NZ_CP092979             2959 bp    DNA     circular CON 24-MAY-2024
DEFINITION  Escherichia coli strain WCHEC005215 plasmid p3_005215, complete
            sequence.
ACCESSION   NZ_CP092979
VERSION     NZ_CP092979.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN06209720
            Assembly: GCF_022559685.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2959)
  AUTHORS   Long,H., Feng,Y. and Zong,Z.
  TITLE     The complete genome of Escherichia coli strain 005215
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2959)
  AUTHORS   Long,H., Feng,Y. and Zong,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-MAR-2022) Center of Infectious Diseases, West China
            Hospital, Sichuan University, Guoxuexiang 37, Chengdu, Sichuan
            610041, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Trycycler v. 0.5.3; Flye v. 2.9; Raven v. 1.8.0;
            Miniasm v. 0.3
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 150.0x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022559685.1-RS_2024_05_24
            Annotation Date                   :: 05/24/2024 04:43:40
            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)                     :: 5,008
            CDSs (total)                      :: 4,888
            Genes (coding)                    :: 4,629
            CDSs (with protein)               :: 4,629
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 259
            CDSs (without protein)            :: 259
            Pseudo Genes (ambiguous residues) :: 0 of 259
            Pseudo Genes (frameshifted)       :: 85 of 259
            Pseudo Genes (incomplete)         :: 175 of 259
            Pseudo Genes (internal stop)      :: 57 of 259
            Pseudo Genes (multiple problems)  :: 52 of 259
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP092979.1.
            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..2959
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WCHEC005215"
                     /isolation_source="Rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p3_005215"
                     /geo_loc_name="China: Sichuan, Chengdu"
                     /collection_date="2013-09"
     gene            complement(join(2906..2959,1..402))
                     /locus_tag="MM176_RS24865"
                     /old_locus_tag="MM176_24900"
     CDS             complement(join(2906..2959,1..402))
                     /locus_tag="MM176_RS24865"
                     /old_locus_tag="MM176_24900"
                     /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_061350436.1"
                     /translation="MTTKFNKFELHSAFRDGKLNEKHFVDLPYLKEEQLRALASFLGAI
                     TREEPLPGKNKPSWLDDDSIKISGTDAYEDGNYWHYHCGPYPESVKLRSMTFNLGMNVA
                     GLTSAEVIHYQKLNDGTVFVVGFSPTHEPFPKSDAPHYNPLFTESDD"
                     /name="hypothetical protein"
     gene            799..1377
                     /locus_tag="MM176_RS24870"
                     /old_locus_tag="MM176_24905"
     CDS             799..1377
                     /locus_tag="MM176_RS24870"
                     /old_locus_tag="MM176_24905"
                     /inference="COORDINATES: protein motif:HMM:NF025107.4"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /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_123906182.1"
                     /translation="MKSEIELKKTEHLSVEIPERILAIWGRSILNSGWTSVPNELLKNQ
                     SKLGIGNTELVLLINLISFMHHSDARVYPSISLLCERMNQDRRTIQRNLNKLVEMDILR
                     IKIRSTGKNSKGMTNLYDLTPLMLKLINLKIPSLNTPDEKHTCPKCGKIAISREEITKE
                     FGFRTDTNGKMRTQSWCKDCRGKKVADLP"
                     /name="helix-turn-helix domain-containing protein"
     Typing          2191..2684
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.237"
                     /coverage="96.0"
                     /evalue="2.76e-175"
ORIGIN
        1 gaagggctca tgtgtagggg agaagcctac gacaaacacc gtgccatcgt tgagtttttg
       61 atagtggatc acttctgcgg aggttagtcc agcaacgttc atacccaagt taaaagtcat
      121 cgatctaagt ttgaccgatt ctggatatgg accgcaatga taatgccagt agttcccgtc
      181 ttcgtaagca tcagtaccgg aaattttaat ggaatcatca tcaagccatg aaggcttgtt
      241 tttccctgga agaggctctt cacgagttat cgcacccaag aaagaggcta atgcccggag
      301 ttgttcttct ttgaggtagg gtaaatctac gaaatgcttt tcattcagct tcccgtctcg
      361 gaaagctgaa tgaagctcaa acttattgaa tttggttgtc atcaaacact ttccacttac
      421 cttactgagt aagcagatag catatcaaag atcgattcat cagacttcgg agaatcgcat
      481 tttaacgctt catgcgtctg attcttgtat gaacgcgaga gcagcacttc gtcagcacga
      541 gatttgtact gctgacgacg ttctgtatcg cagctgtgat tatcaaatcg tacgtttgcc
      601 aacatgtcag tcctatgttt gaagaaatct gggaagataa aatcttgctc aattcgatgg
      661 taagagaggt ctttccccgg tgctagacat taggcctttt tggtcaaata caagggcggc
      721 attgatgccg cccgaataat taatcataat aacaatacct atatatatag gtattgttat
      781 tatgattggt ggccgaagtt gaaatcagaa atcgaactaa aaaaaacaga acacttatca
      841 gtagagatcc ccgaaagaat cttagccata tgggggcgca gcattttaaa ctctggctgg
      901 acgtccgttc ccaatgaact attaaaaaac caatctaagc taggaatagg aaacacagag
      961 cttgtacttt tgattaacct gatctctttc atgcatcatt ctgacgcaag agtgtaccca
     1021 tcaatttcgc ttctatgcga aagaatgaat caagacagac gaacaattca gagaaattta
     1081 aacaagttag tagaaatgga cattctgagg ataaaaatac gttccaccgg taaaaactcc
     1141 aaaggaatga ctaacttgta tgacctcacc cctttaatgc tgaagctaat caacctaaaa
     1201 ataccatctt taaatacgcc cgatgaaaaa catacgtgtc caaaatgcgg gaaaatagcc
     1261 atatcaagag aagaaataac aaaagagttt ggattcagaa ctgacactaa tgggaagatg
     1321 agaacgcaaa gttggtgcaa agattgtcga ggcaagaaag ttgcggattt accataacat
     1381 ccgttggccg caccccctca gacgccctca gcgcatttct gcggcgggat gactgtttcc
     1441 ggcacttccc tatacctata tcgtgaaaaa acgcgcctga tgatttctgc gagtctgcat
     1501 ggctatgcac acacatgcat ggccgggatt ttagcggcta aaatccggca ggacgtccaa
     1561 aagcaccact taacctcacg aataacgcct cacgggtgcg cagtttactg tgcggccgtg
     1621 aggcgttggc caggccgtca ggcatggctg gatttattgc taagggggtc ggatttaacg
     1681 tggattaatc agcacgcagt gatgaacggg attcggaagg ggcacccttg cggcgcggcg
     1741 atgtatacat cgctaacgtg ccttggacat gcagagtaaa tcagtgagaa aacaggctat
     1801 aaacactgag caaacagatt cgggacaggt tgcaaacact tcctaaacag attcgggaca
     1861 gattgcaaac acttcctaaa cagattcggg acagattgca aacacttcct aaacaggttc
     1921 gggacagatt gcaaacactg attgctaagg gtatcgggca gagcatggtc atagcgtttt
     1981 ggagtatggg cggtactcca aaaacacatc ttgtcccgct gttttgtagc gctgacaaac
     2041 tggcggtgaa cacaaaacat atcctgtcat ctgctttaac tgttgtaatc cagaagtatc
     2101 aggtgacgtc actttacggc gttagcccta tcctgcatcg cattaaaaat gcagctatgg
     2161 cgtgtacggt gccaaagata agtacgaaga tattccgctt cctcgctcac tgactcgctg
     2221 cgctcggtcg ttcggctgcg gcgagcggag ggaacaggca catcaaaaga tgaagccatg
     2281 agggacgatg agggggaaaa aaacgccgcg gcgttgccga ttttccatag gctccgcccc
     2341 cctgacaagc atcacagaat ctgacgctca aatcagtggt ggcgaaaccc gacaggactt
     2401 aaagatacca ggcgtttccc cctggtggct ccctcgtgcg ctctcctgtt cctgcctttc
     2461 ggtttaccgg tgtcattccg ctgttatggc cgcgtttatc tcattccacg cctgacactc
     2521 gattccggga aggcagttcg ctccaagctg gactgtatgc acgaaccccc cgttcagtcc
     2581 gactgctgcg ccttttccgg taactatcaa cttgagtcca acccggaaag acacgacaaa
     2641 gcgccactgg cagcagccac tggtaaacag gatgtgcgag agatgtatcg agagttcttg
     2701 aagtggtggc ctgactgcgg ctacactgaa aggacagatt tggtgacatg tctcgcacaa
     2761 gactgttacc acggttagag aatctgccag gattaactaa ccttcgaaaa accacctgcc
     2821 agggtggttt tttcgtttca ggaaaagaga ctacagctga gagaaaaaaa tctcaacata
     2881 tccttaccag ccactattca gatatttaat catctgattc ggtgaagaga gggttgtaat
     2941 gcggcgcatc agacttagg
//
