LOCUS       NZ_CP092978             3684 bp    DNA     circular CON 24-MAY-2024
DEFINITION  Escherichia coli strain WCHEC005215 plasmid p2_005215, complete
            sequence.
ACCESSION   NZ_CP092978
VERSION     NZ_CP092978.1
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 3684)
  AUTHORS   Long,H., Feng,Y. and Zong,Z.
  TITLE     The complete genome of Escherichia coli strain 005215
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3684)
  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
            CP092978.1.
            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..3684
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WCHEC005215"
                     /isolation_source="Rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p2_005215"
                     /geo_loc_name="China: Sichuan, Chengdu"
                     /collection_date="2013-09"
     gene            complement(301..603)
                     /locus_tag="MM176_RS24835"
                     /old_locus_tag="MM176_24870"
     CDS             complement(301..603)
                     /locus_tag="MM176_RS24835"
                     /old_locus_tag="MM176_24870"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006326557.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3892 domain-containing protein"
                     /protein_id="WP_039023182.1"
                     /translation="MVDFYISAIKMDSAGQHIEFVKVHKINRDGSWNTAGSISSRKFIS
                     ELISMGKASFMTVVKNSSTGKWNLGAKVEAMDDGYITTDPNKTKLDNLGNLPKFV"
                     /name="DUF3892 domain-containing protein"
     gene            complement(667..960)
                     /locus_tag="MM176_RS24840"
                     /old_locus_tag="MM176_24875"
     CDS             complement(667..960)
                     /locus_tag="MM176_RS24840"
                     /old_locus_tag="MM176_24875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609279.1"
                     /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="HigA family addiction module antitoxin"
                     /protein_id="WP_023317864.1"
                     /translation="MINLYDPVHPGEFIREMFMEPFEIPAAELADKLDVSQSTLSRLLN
                     GKTDLSYEMALRLSKVVGRSAESWVNMQTQFSLSKSRKSLAAELEHLHPMFP"
                     /name="HigA family addiction module antitoxin"
     gene            1297..1578
                     /locus_tag="MM176_RS24845"
                     /old_locus_tag="MM176_24880"
     CDS             1297..1578
                     /locus_tag="MM176_RS24845"
                     /old_locus_tag="MM176_24880"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000594459.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_032440460.1"
                     /translation="MIKNIKHKGLRSFAEEGSTAGIQPSMAKRLRMILTTLSTATCIQD
                     VVDVRALGCHPLKGERKGEYSVEVNGNWRVVFKVEEPNVLDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(2036..2182)
                     /locus_tag="MM176_RS24850"
                     /old_locus_tag="MM176_24885"
     CDS             complement(2036..2182)
                     /locus_tag="MM176_RS24850"
                     /old_locus_tag="MM176_24885"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001717510.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_073545459.1"
                     /translation="MHEPPVQSDCCTLSGNYHLESNPVRHAQAPLAAATGKKVYKRLLI
                     QSS"
                     /name="replication initiation protein"
     gene            2587..2778
                     /locus_tag="MM176_RS24855"
                     /old_locus_tag="MM176_24890"
     CDS             2587..2778
                     /locus_tag="MM176_RS24855"
                     /old_locus_tag="MM176_24890"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_039023180.1"
                     /translation="MSKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2778..3200
                     /locus_tag="MM176_RS24860"
                     /old_locus_tag="MM176_24895"
     CDS             2778..3200
                     /locus_tag="MM176_RS24860"
                     /old_locus_tag="MM176_24895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /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_039023181.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVLKHGKTIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAGSTGVNSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPDSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     Typing          complement(2074..2446)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.467"
                     /coverage="91.0"
                     /evalue="1.28e-167"
ORIGIN
        1 acggccacgc aataaattgc gtccccgttc accgttttcg gatgggaaga acgccggaaa
       61 caggacttac cctggctgaa tggcgtgaat tttcgcgcta tgcacttgcg tgcatactca
      121 tgcatgccgt aaaaacagag cctgcgcgtt tctgacgggt tttcgggtgg tttgttgcct
      181 gttttaccgg tttcctgtca gaaacgccct gaggccgttc tggcggtgcg tacaattatg
      241 actttatgtt aaatcattag ggaggggatt ctgctggaac ttagtggatg ttattgcata
      301 tcagacaaat ttcggcagat ttcccaagtt atcgagttta gttttgtttg gatctgtggt
      361 tatgtagcca tcgtccatcg cttccacttt ggctcctagg ttccacttac cagtagagct
      421 gttctttaca actgtcataa agctggcttt tcccatgctg atcagctcgc tgatgaattt
      481 gcgagagctg attgagccgg cagtgttcca tgagccatct cggtttattt tatgaacttt
      541 tacgaattcg atgtgctgac cagcactgtc cattttgatt gctgagatat agaaatctac
      601 catggttgcc tcctgatggc tgctgggtgt tttacgtaac aaaagcccgc gttctgcggg
      661 cttttttcat ggaaacattg gatgcaagtg ttccagctct gccgctaaag atttgcgact
      721 ttttgacagg ctgaattggg tctgcatgtt tacccacgac tctgcagagc ggcctacgac
      781 cttcgacaat ctaagtgcca tttcatagct taagtctgtt ttcccattta acagtctact
      841 taaggtagac tgggatacat caagtttatc ggctaactct gcggcaggta tttcgaacgg
      901 ttccatgaac atttctctga taaactcacc aggatgaaca ggatcgtaaa gatttatcat
      961 gccttcctct gtttgttttg tatttgatta tacaaaaaaa ttactgcctt tcagtatgcg
     1021 cattgcacaa tgtgcaagtt catgatattg acaaaaaaag cagtcagctt taggatactc
     1081 gttggagtca aagctactgc gtatgtatgg gcttttatgg ccttttcaag gcgcagtatt
     1141 ttacccttag gattcgttga agtcaaatga ggtgattgac ctcaagaaca aacttacgtc
     1201 aattgtttta ataaagcaag ggggcaaaat ggaactaatt aaaatgattt taaaatatag
     1261 atacaggtat agacgaaaaa aatatgggga ttgtagatga taaaaaacat aaaacataaa
     1321 ggacttagga gctttgctga agaaggtagc accgccggta ttcagcccag tatggcgaaa
     1381 agacttcgca tgattttgac tacgctaagc acagcaactt gcattcaaga cgttgttgac
     1441 gttagggcgt tagggtgcca ccccctaaag ggggagcgta aaggcgagta ttccgttgaa
     1501 gttaatggga actggcgggt agttttcaag gttgaggaac caaacgtctt agacgttgat
     1561 cttgaagatt atcattagtt atcaataagt aagttgctaa tccatccaag tgaaagtacg
     1621 gatggattag ggactttatt aaaaaagtaa cctctggaga aagtatgaga tcctttatgg
     1681 ttttattgtt cccgttgatt agcgtaacta ttgctggagt cctagctttt cgtggtattg
     1741 atggctgggg atggttcttg ttagctgctg tactttgtgc aggggctgat actgtccaga
     1801 agcatgtgtc taccaataaa aaggagcctg ctggtgagtg agctgtcttg gttcttcctt
     1861 gactgctttg aatgataaag cgtatcttac tcgccgagac gaaaaaaccg cctggggagg
     1921 cggttttttc gagggttcag taagttgggg aacttctgaa ccgtggtaac agggtgtaca
     1981 agaccgctga aaccaaattc tgtcctttca gtttagccgt agttgggctg agacttcaag
     2041 aactctgtat cagtaatctc ttgtacacct tcttaccagt ggctgctgcc agtggcgctt
     2101 gtgcgtgtct taccgggttg gactcaagat gatagttacc ggataaggtg cagcagtcgg
     2161 actgaacggg gggttcgtgc atacagtcca gcttggagcg aactgcctac ccggaactga
     2221 gtgtctggcg tggaatgaga taaacgcggc cataacagcg gaatgacacc ggtaaaccga
     2281 aaggcaggaa caggagagcg cacgagggag ccatcagggg gaaacgcctg gtatctttat
     2341 agtcctgtcg gggttcgcca ccactgattt gagcgtcaga tttcgtgatg cttgtcaggg
     2401 gggcggagcc tatggaaaaa cggccggtgt gcggccttct ccctctccgt gctgtctgtc
     2461 ctatgtcgtt atgtgtgtat tgcgaccgct cgccgcagcc gaacggcagg agcgtagcga
     2521 ctgagtgagc gaggaagcgg aaaagagaac atacctacac tgagcactga cgctctgagg
     2581 cctcttatgt cgaaacaaca gaaaacagcg ctgaacatgg ctaaattcat ccagaatcag
     2641 tctctgctcc tgctggagaa gcttaacgag cttgatcttg atgcagaggc cgacctttgt
     2701 gagaaactcc acgatgatgc ggagcatctt ttccgtacac tgtcctcgag actggatgaa
     2761 ttacaggatg gtaactgatg gccagagtgt ctattagtga agcggcacgg cttgttaagg
     2821 ttagtcgccc cacaatttac aagatgatta acagtgggaa gttaagttac acctctgttt
     2881 taaagcacgg gaagaccatt aaagttattg atacttcaga gcttattaga gtttttggtt
     2941 ctcttgatgg tgtcatcgat actgtaaaat atgatgtaaa aagtgacgca ggatctacag
     3001 gtgttaacag cgttggttta catgatttac aacatagaat tgctttacta gaagctgaaa
     3061 acgatggtct taaaggggct gttaaggctc gagatgagca tattgattcc cttcgtcagg
     3121 ctatgcagct tctggagcac aagcacgaac cttcttcacc acccgattcc ccgtggtgga
     3181 aattctggaa aaaatcctga ctccgtcatg cttccgtttt cctctccggc catcccgggg
     3241 agttcctgaa ccttcccaaa aatcgccaga tctctgaacg ctcctcacga ctaaaaatac
     3301 ccacacacta cgcaaaatta aaattttgca gatttgtatt taatatcagt agcttacttt
     3361 cctgaagttt cggtttttaa attttattta catagatccg actctatgac gactcgtcat
     3421 agagtccccg gcgagtcgtc atagagtcgg taacgactca gagctataaa aacaatgagt
     3481 taataacgac ccgactctag acccgactcc ccgtttggtt gttttttaga ctcggcgact
     3541 ctgggtacga ctctagtgaa gagtcgccgg tgaatcgtgt ggtgagtcgt ccggcgactt
     3601 gccatgacgt gattgccggc cgtcgacgaa cacgattcct gaacgtgctg aaaaccggtt
     3661 ttccggctgc gccggcaacg cttc
//
