LOCUS       NZ_CP116158             3263 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P61 plasmid pDETEC42, complete
            sequence.
ACCESSION   NZ_CP116158
VERSION     NZ_CP116158.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988466
            Assembly: GCF_027944855.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3263)
  AUTHORS   Moran,R.A., Baomo,L., Doughty,E.L., Guo,Y., Ba,X., van Schaik,W.,
            Zhuo,C. and McNally,A.
  TITLE     Extended-spectrum beta-lactamase genes traverse the Escherichia coli
            populations of ICU patients, staff and environment
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3263)
  AUTHORS   Moran,R.A., Baomo,L., Doughty,E.L., Guo,Y., Ba,X., van Schaik,W.,
            Zhuo,C. and McNally,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-JAN-2023) Institute of Microbiology and Infection,
            University of Birmingham, Institute of Microbiology and Infection,
            Birmingham B15 2TT, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 10x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/25/2024 01:59:19
            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)                     :: 4,937
            CDSs (total)                      :: 4,816
            Genes (coding)                    :: 4,535
            CDSs (with protein)               :: 4,535
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 281
            CDSs (without protein)            :: 281
            Pseudo Genes (ambiguous residues) :: 0 of 281
            Pseudo Genes (frameshifted)       :: 70 of 281
            Pseudo Genes (incomplete)         :: 207 of 281
            Pseudo Genes (internal stop)      :: 43 of 281
            Pseudo Genes (multiple problems)  :: 39 of 281
            Pseudo Genes (short protein)      :: 3 of 281
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116158.1.
            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..3263
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-P61"
                     /isolation_source="ICU patient rectal swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC42"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-08-01"
     gene            join(3164..3263,1..479)
                     /locus_tag="PIC71_RS24620"
                     /old_locus_tag="PIC71_24620"
     CDS             join(3164..3263,1..479)
                     /locus_tag="PIC71_RS24620"
                     /old_locus_tag="PIC71_24620"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_052266651.1"
                     /translation="MKSEIELKKTEHSSVEIPERILAIWGRSILNSGWTSVPNELLKNQ
                     SKLGIGNTELVLLINLISFMHHPDARVYPSISLLCERMNQDRRTIQRNLNKLVEMDILR
                     IKIRSTGKNSKGMTNLYDITPLMLKLINLKIPSLNTPDEKHTCPKCGKIAISREEITKE
                     FGFRTDTNGKMRTQSWCKDCRGRKIADLP"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(687..1010)
                     /gene="mobA"
                     /locus_tag="PIC71_RS24630"
                     /old_locus_tag="PIC71_24630"
     CDS             complement(687..1010)
                     /gene="mobA"
                     /locus_tag="PIC71_RS24630"
                     /old_locus_tag="PIC71_24630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            1283..1477
                     /locus_tag="PIC71_RS24635"
                     /old_locus_tag="PIC71_24635"
     CDS             1283..1477
                     /locus_tag="PIC71_RS24635"
                     /old_locus_tag="PIC71_24635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_001041643.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEVENSTEI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2312..2767)
                     /locus_tag="PIC71_RS24640"
                     /old_locus_tag="PIC71_24640"
     CDS             complement(2312..2767)
                     /locus_tag="PIC71_RS24640"
                     /old_locus_tag="PIC71_24640"
                     /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_039023474.1"
                     /translation="MTTKFNKFELHSAFRDGKLNEKYFVDLPYLKEEQRRALASFLGAI
                     TREEPLPGKNKPSWLDDNSIKISGTDAYEDGNYWHYHCGPYPEGVKLRSMTFNLGMNVA
                     GLTSAEVIHYQKLNDGTVFVVGFSPTHEPFPKSDAPHYNPLFTESDD"
                     /name="hypothetical protein"
     Typing          complement(1020..1246)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="88.797"
                     /coverage="99.0"
                     /evalue="6.34e-74"
     Typing          1507..2033
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.944"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          complement(691..1010)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="9.72e-63"
ORIGIN
        1 ggacatccgt ccccaatgaa ctattaaaaa accaatctaa gctaggaata ggaaacacag
       61 agcttgtact tttgattaat ctgatatctt tcatgcatca tcctgacgca agagtgtacc
      121 catcaatttc acttctatgc gaaagaatga atcaggacag acgaacaatt cagagaaatt
      181 taaacaagtt agtagaaatg gacattctga ggataaaaat acgctccacc ggcaaaaact
      241 ctaaaggaat gactaacttg tatgacataa cccctttaat gctgaagtta atcaacctaa
      301 aaataccatc tttaaatacg cccgatgaaa aacatacgtg tccaaaatgc ggaaaaatag
      361 ccatatcaag agaagaaata acaaaggagt ttggattcag aactgacact aatgggaaga
      421 tgagaacgca aagttggtgc aaggattgtc gaggtaggaa aattgcggat ttaccataac
      481 gtcgcattac gcgcaccgca gaaacgcgct gaacgcgatt ctgccgcaaa caccgcaaaa
      541 agagatgttt tccccggggt aaaccggaaa aatgcgtcag gattgttttc agcgcgttgc
      601 atgactatgc atgaaactga atggcgatcg gtttgggggc ttacggcgtt catatcgtct
      661 gttttcgaca gtttctctcc gggaagctaa tcagccataa gcctggataa cagggcacgg
      721 tgatactccg taatagcgat cagcacctcc gcatactccc tgtccccgac acgcttgccg
      781 tcgataaaga gttttttctg taacgccccc agtctcataa cttctttcag tacccgatca
      841 tcagtcagtg agttaacttt cttaccgaga gctgccgccc gtaaaaaacc ggaaacggtc
      901 ttgccacatt cagcagccct ttttctgatt tcctggtctt cttctgccgt cagacgaaca
      961 gggcgactga tagcccgcct gcgcgtatta cttccacttc gttttgtcat aaaacatggc
     1021 tccgtatctg acatggggtg tcggggcgaa gccctgacca gggtaattgt aatagcgtgc
     1081 atgtatgcgc ggtataacaa ttgcacatcc tgtcctgtct gcaagttcga attaccaaca
     1141 aagcactgct gtttttttgg cagtgacagt gttgtctgac tgaaatgtcc gtcggcagaa
     1201 taccggcggt aagacggtcc aaaagtggtg cgcgatataa tcacacgacg cagatgacag
     1261 acagaacgga gaaaacagaa agatgaacaa gcagcagcaa actgtactca acatggctgg
     1321 attcataaaa agccagagcc tgacgctgct cgaaaaactg gacgcactcg atgctgacga
     1381 gcaggccgcc atgtgtgaga agctgcacga actcgcagaa gaactccaga acagcataca
     1441 gacacgcttt gaagtagaaa atagcacaga gatataacgc tcagggcagg atgccgaacg
     1501 gcacaacaga gcgtaaggag aaaatgtcac ataaggcgct cttccgcttc ctcgctcact
     1561 gactcgctac gctcggtcgt tcgactgcgg cgagcggtgt cagctcactc aaaggcggta
     1621 atacggttat ccacagaatc aggggataaa gccggaaaga acatgtgagc aaaaagcaaa
     1681 gcaccggaag aagccagcac cgcaggcgtt tttccatagg ctccgccccc ctgacgagca
     1741 tcacaaaaat cgacgctcaa gtcagaggtg gcgaaacccg acaggactat aaagatacca
     1801 ggcgtttccc cctggaagct ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg
     1861 atacctgtcc gcctttctcc cttcgggaag cgtggcgctt tctcatagct cacgctgttg
     1921 gtatctcagt tcggtgtagg tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt
     1981 tcagcccgac cgctgcgcct tatccggtaa ctatcgtctt gagtccaacc cggaaagaca
     2041 cgacttatcg ccattggctg cggccattgg tagacaggat gtgcgagaga tgtatcgaga
     2101 gttcttgaag tggtggcctg actgcggcta cactgaaagg acagatttgg tgacatgtct
     2161 cgcacaagac tgttaccacg gttcagaagt tccccaactt actgaacctt cgaaaaacca
     2221 cctccccagg tggttttttc gtttctggaa aagagactac agctgagaga aaaaaatctc
     2281 aacatatcct taccagccac tattcagata tttaatcatc tgattcagtg aagagtgggt
     2341 tgtaatgcgg cgcatcagac ttagggaagg gctcatgtgt aggggagaag cctacgacaa
     2401 acaccgtgcc atcgttgagt ttttgatagt ggatcacttc agcggaggtt agccccgcaa
     2461 cgttcatacc caagttaaaa gtcatcgatc taagtttgac cccttctgga tatggaccgc
     2521 aatgataatg ccagtagttc ccgtcttcgt acgcatcagt accggaaatt ttaatggaat
     2581 tatcatcaag ccatgaaggc ttgtttttcc ctggaagagg ctcttcacga gttatcgcac
     2641 ccaagaaaga ggctaatgcc cggcgttgct cttctttgag gtagggtaaa tctacgaaat
     2701 acttttcatt cagcttcccg tctcggaaag ccgaatgaag ctcaaactta ttgaatttgg
     2761 ttgtcatcaa acactttcca cttaccttac tgagtaagta gatagcatat caaagatcga
     2821 ttcatcagac tgcggagaat cgcattttaa cgcttcatgt gcctgattct tgtatgaacg
     2881 cgagagcagc acttcgtcag cacgagattt gtactgctga cgacgttctg tatcgcagct
     2941 gtgattatca aatcgtacgt ttgccaacat gtcagtccta tgtttgaaga agtctgggaa
     3001 gataaaatct tactcaatta gatggtaaga gaggtccttt cccagtgcta gacattaggc
     3061 ctttttggtc aaattaaagg gcggcattga tgccgcccaa ataataaatc ataataacaa
     3121 tacctatata tataggtatt gttattatga ttggtgacag aaattgaaat cagaaatcga
     3181 actcaaaaaa acagaacact catcagtaga gatcccagaa aggatcttag ccatatgggg
     3241 gcgcagcatt ttaaactctg gct
//
