LOCUS       NZ_CP060871             3684 bp    DNA     circular CON 24-MAY-2024
DEFINITION  Escherichia coli strain EC29 plasmid pEC29-5, complete sequence.
ACCESSION   NZ_CP060871
VERSION     NZ_CP060871.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15904668
            Assembly: GCF_022558645.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3684)
  AUTHORS   Ruan,Z.
  TITLE     Complete genome sequence of carbapenem resistant Escherichia coli
            isolates
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3684)
  AUTHORS   Ruan,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-AUG-2020) Department of Clinical laboratory, Sir Run
            Run Shaw Hospital, School of Medicine, Zhejiang University, 3
            Qingchun East Road, Hangzhou, Zhejiang 310016, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022558645.1-RS_2024_05_24
            Annotation Date                   :: 05/24/2024 04:06:56
            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)                     :: 5,039
            CDSs (total)                      :: 4,919
            Genes (coding)                    :: 4,647
            CDSs (with protein)               :: 4,647
            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)              :: 272
            CDSs (without protein)            :: 272
            Pseudo Genes (ambiguous residues) :: 0 of 272
            Pseudo Genes (frameshifted)       :: 95 of 272
            Pseudo Genes (incomplete)         :: 178 of 272
            Pseudo Genes (internal stop)      :: 55 of 272
            Pseudo Genes (multiple problems)  :: 50 of 272
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP060871.1.
            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="EC29"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEC29-5"
                     /geo_loc_name="China: Hangzhou"
                     /collection_date="2017-11-21"
                     /collected_by="Long Sun"
     gene            complement(join(3648..3684,1..266))
                     /locus_tag="H9211_RS24995"
                     /old_locus_tag="H9211_24755"
     CDS             complement(join(3648..3684,1..266))
                     /locus_tag="H9211_RS24995"
                     /old_locus_tag="H9211_24755"
                     /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(330..623)
                     /locus_tag="H9211_RS25000"
                     /old_locus_tag="H9211_24760"
     CDS             complement(330..623)
                     /locus_tag="H9211_RS25000"
                     /old_locus_tag="H9211_24760"
                     /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            960..1241
                     /locus_tag="H9211_RS25005"
                     /old_locus_tag="H9211_24765"
     CDS             960..1241
                     /locus_tag="H9211_RS25005"
                     /old_locus_tag="H9211_24765"
                     /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(1699..1845)
                     /locus_tag="H9211_RS25010"
     CDS             complement(1699..1845)
                     /locus_tag="H9211_RS25010"
                     /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            2250..2441
                     /locus_tag="H9211_RS25015"
                     /old_locus_tag="H9211_24770"
     CDS             2250..2441
                     /locus_tag="H9211_RS25015"
                     /old_locus_tag="H9211_24770"
                     /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            2441..2863
                     /locus_tag="H9211_RS25020"
                     /old_locus_tag="H9211_24775"
     CDS             2441..2863
                     /locus_tag="H9211_RS25020"
                     /old_locus_tag="H9211_24775"
                     /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(1737..2109)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.467"
                     /coverage="91.0"
                     /evalue="1.28e-167"
ORIGIN
        1 ttagttttgt ttggatctgt ggttatgtag ccatcgtcca tcgcttccac tttggctcct
       61 aggttccact taccagtaga gctgttcttt acaactgtca taaagctggc ttttcccatg
      121 ctgatcagct cgctgatgaa tttgcgagag ctgattgagc cggcagtgtt ccatgagcca
      181 tctcggttta ttttatgaac ttttacgaat tcgatgtgct gaccagcact gtccattttg
      241 attgctgaga tatagaaatc taccatggtt gcctcctgat ggctgctggg tgttttacgt
      301 aacaaaagcc cgcgttctgc gggctttttt catggaaaca ttggatgcaa gtgttccagc
      361 tctgccgcta aagatttgcg actttttgac aggctgaatt gggtctgcat gtttacccac
      421 gactctgcag agcggcctac gaccttcgac aatctaagtg ccatttcata gcttaagtct
      481 gttttcccat ttaacagtct acttaaggta gactgggata catcaagttt atcggctaac
      541 tctgcggcag gtatttcgaa cggttccatg aacatttctc tgataaactc accaggatga
      601 acaggatcgt aaagatttat catgccttcc tctgtttgtt ttgtatttga ttatacaaaa
      661 aaattactgc ctttcagtat gcgcattgca caatgtgcaa gttcatgata ttgacaaaaa
      721 aagcagtcag ctttaggata ctcgttggag tcaaagctac tgcgtatgta tgggctttta
      781 tggccttttc aaggcgcagt attttaccct taggattcgt tgaagtcaaa tgaggtgatt
      841 gacctcaaga acaaacttac gtcaattgtt ttaataaagc aagggggcaa aatggaacta
      901 attaaaatga ttttaaaata tagatacagg tatagacgaa aaaaatatgg ggattgtaga
      961 tgataaaaaa cataaaacat aaaggactta ggagctttgc tgaagaaggt agcaccgccg
     1021 gtattcagcc cagtatggcg aaaagacttc gcatgatttt gactacgcta agcacagcaa
     1081 cttgcattca agacgttgtt gacgttaggg cgttagggtg ccacccccta aagggggagc
     1141 gtaaaggcga gtattccgtt gaagttaatg ggaactggcg ggtagttttc aaggttgagg
     1201 aaccaaacgt cttagacgtt gatcttgaag attatcatta gttatcaata agtaagttgc
     1261 taatccatcc aagtgaaagt acggatggat tagggacttt attaaaaaag taacctctgg
     1321 agaaagtatg agatccttta tggttttatt gttcccgttg attagcgtaa ctattgctgg
     1381 agtcctagct tttcgtggta ttgatggctg gggatggttc ttgttagctg ctgtactttg
     1441 tgcaggggct gatactgtcc agaagcatgt gtctaccaat aaaaaggagc ctgctggtga
     1501 gtgagctgtc ttggttcttc cttgactgct ttgaatgata aagcgtatct tactcgccga
     1561 gacgaaaaaa ccgcctgggg aggcggtttt ttcgagggtt cagtaagttg gggaacttct
     1621 gaaccgtggt aacagggtgt acaagaccgc tgaaaccaaa ttctgtcctt tcagtttagc
     1681 cgtagttggg ctgagacttc aagaactctg tatcagtaat ctcttgtaca ccttcttacc
     1741 agtggctgct gccagtggcg cttgtgcgtg tcttaccggg ttggactcaa gatgatagtt
     1801 accggataag gtgcagcagt cggactgaac ggggggttcg tgcatacagt ccagcttgga
     1861 gcgaactgcc tacccggaac tgagtgtctg gcgtggaatg agataaacgc ggccataaca
     1921 gcggaatgac accggtaaac cgaaaggcag gaacaggaga gcgcacgagg gagccatcag
     1981 ggggaaacgc ctggtatctt tatagtcctg tcggggttcg ccaccactga tttgagcgtc
     2041 agatttcgtg atgcttgtca ggggggcgga gcctatggaa aaacggccgg tgtgcggcct
     2101 tctccctctc cgtgctgtct gtcctatgtc gttatgtgtg tattgcgacc gctcgccgca
     2161 gccgaacggc aggagcgtag cgactgagtg agcgaggaag cggaaaagag aacataccta
     2221 cactgagcac tgacgctctg aggcctctta tgtcgaaaca acagaaaaca gcgctgaaca
     2281 tggctaaatt catccagaat cagtctctgc tcctgctgga gaagcttaac gagcttgatc
     2341 ttgatgcaga ggccgacctt tgtgagaaac tccacgatga tgcggagcat cttttccgta
     2401 cactgtcctc gagactggat gaattacagg atggtaactg atggccagag tgtctattag
     2461 tgaagcggca cggcttgtta aggttagtcg ccccacaatt tacaagatga ttaacagtgg
     2521 gaagttaagt tacacctctg ttttaaagca cgggaagacc attaaagtta ttgatacttc
     2581 agagcttatt agagtttttg gttctcttga tggtgtcatc gatactgtaa aatatgatgt
     2641 aaaaagtgac gcaggatcta caggtgttaa cagcgttggt ttacatgatt tacaacatag
     2701 aattgcttta ctagaagctg aaaacgatgg tcttaaaggg gctgttaagg ctcgagatga
     2761 gcatattgat tcccttcgtc aggctatgca gcttctggag cacaagcacg aaccttcttc
     2821 accacccgat tccccgtggt ggaaattctg gaaaaaatcc tgactccgtc atgcttccgt
     2881 tttcctctcc ggccatcccg gggagttcct gaaccttccc aaaaatcgcc agatctctga
     2941 acgctcctca cgactaaaaa tacccacaca ctacgcaaaa ttaaaatttt gcagatttgt
     3001 atttaatatc agtagcttac tttcctgaag tttcggtttt taaattttat ttacatagat
     3061 ccgactctat gacgactcgt catagagtcc ccggcgagtc gtcatagagt cggtaacgac
     3121 tcagagctat aaaaacaatg agttaataac gacccgactc tagacccgac tccccgtttg
     3181 gttgtttttt agactcggcg actctgggta cgactctagt gaagagtcgc cggtgaatcg
     3241 tgtggtgagt cgtccggcga cttgccatga cgtgattgcc ggccgtcgac gaacacgatt
     3301 cctgaacgtg ctgaaaaccg gttttccggc tgcgccggca acgcttcacg gccacgcaat
     3361 aaattgcgtc cccgttcacc gttttcggat gggaagaacg ccggaaacag gacttaccct
     3421 ggctgaatgg cgtgaatttt cgcgctatgc acttgcgtgc atactcatgc atgccgtaaa
     3481 aacagagcct gcgcgtttct gacgggtttt cgggtggttt gttgcctgtt ttaccggttt
     3541 cctgtcagaa acgccctgag gccgttctgg cggtgcgtac aattatgact ttatgttaaa
     3601 tcattaggga ggggattctg ctggaactta gtggatgtta ttgcatatca gacaaatttc
     3661 ggcagatttc ccaagttatc gagt
//
