LOCUS       NZ_CP116098             4036 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-S560 plasmid pDETEC70, complete
            sequence.
ACCESSION   NZ_CP116098
VERSION     NZ_CP116098.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988492
            Assembly: GCF_027944675.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4036)
  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  JOURNAL   Unpublished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 4036)
  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 02:00:16
            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)                     :: 5,033
            CDSs (total)                      :: 4,912
            Genes (coding)                    :: 4,656
            CDSs (with protein)               :: 4,656
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 256
            CDSs (without protein)            :: 256
            Pseudo Genes (ambiguous residues) :: 0 of 256
            Pseudo Genes (frameshifted)       :: 82 of 256
            Pseudo Genes (incomplete)         :: 173 of 256
            Pseudo Genes (internal stop)      :: 52 of 256
            Pseudo Genes (multiple problems)  :: 48 of 256
            Pseudo Genes (short protein)      :: 4 of 256
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116098.1.
            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..4036
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-S560"
                     /isolation_source="ICU staff rectal swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC70"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-09-01"
     gene            260..607
                     /gene="mobC"
                     /locus_tag="PIC78_RS25100"
                     /old_locus_tag="PIC78_25095"
     CDS             260..607
                     /gene="mobC"
                     /locus_tag="PIC78_RS25100"
                     /old_locus_tag="PIC78_25095"
                     /inference="COORDINATES: protein motif:HMM:NF039635.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_271287796.1"
                     /translation="MSYKDRYHRKHSVTLCFNDEEFKQVEELASMLKKPRAKAIRELIL
                     NKEFKLKKEISKNENGDVYYQLHKIGVNINQIARAINTDIDKFISHEFAEDFLNLFEEI
                     TNEIEEIKRRI"
                     /name="mobC"
     gene            609..2027
                     /locus_tag="PIC78_RS25105"
                     /old_locus_tag="PIC78_25100"
     CDS             609..2027
                     /locus_tag="PIC78_RS25105"
                     /old_locus_tag="PIC78_25100"
                     /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_271287797.1"
                     /translation="MYHKIIGGKKSKGQRNIKKSIEYLLREKNPEQQKDIKILSTTTKQ
                     DLINFENYILDKNKSNPYVCGVLSFEEKSISEELKTKLITEFEDVLFAGIEPENRPPVM
                     WVEHNDKGRVELNYLTFNSLQDRRSYTVYLDKRDRGLVNNYSEIINYENNLSSPFEEKE
                     NKNTLINKPKTNIPEDKKQFIENINTEIMALIINEELENREQTIKHIENMKGVKINRIR
                     KNQISIKSDLFDDDKPIVLKGDIYEEGRDYSDYRKEFNPKPTRDPELVREKLTELKRTF
                     AERIEKREIRNRSKFKKPSFKNLSENRQSIQREDQDIGYKYTNGDFINVSNNDGFSGMY
                     IRTDNMEIVNNESINTEYKTKTATEETAGTTRARDIEKINQQQQFVSSRLEEAGRKQQQ
                     FRKSIDTTEGRFGVCRRSVHSIISTFGRYIRTFSAYTRKNEHRQKFEKRRKIEEEKLKI
                     KNQGSYNRRRYKPY"
                     /name="hypothetical protein"
     gene            2624..4036
                     /locus_tag="PIC78_RS25110"
                     /old_locus_tag="PIC78_25105"
     CDS             2624..4036
                     /locus_tag="PIC78_RS25110"
                     /old_locus_tag="PIC78_25105"
                     /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_271287795.1"
                     /translation="MIRLKKVFNLTEEEIVLTNEIAEAISKEPKVETHEVNINFIDVLP
                     IIPNPHNLGLSENIDPLSLIYSKFVSETDIPPALPIFSFLSYLSAFSVNNNIMYKHPTS
                     PADYLNTWTLILAPSGAAKTTSAKIIESSIPKDIEEKPMIRPNFEGADGSAAFISELAK
                     AEKKIDNFGKPIQPIFWIEDEYSQFMKKLMPGGSMVETRKTMLKIHDNDKARRVTKNDT
                     IETESIVMSGLFLNTIDSFARNFDQESINDGLGRRHNFVYAERGEKVVPTWTVEEIIES
                     LKEGLDNFFSNVKTNVIYTYSPECRKIYDHFYMVYKEKFDHILGEETNGTFFRTYFMLS
                     WKYAAIYHILLKEEGTEIQAKSFDYGIKVSLMFLSSIKRFLDYKVDLKSGAKEVRKEYL
                     KKAAEKELNNLQKYKDFLLDNVEITLRDFNRKFSLKKVESLKVLKTIRENKLIKYHPLF
                     EVLAKEEAKAKK"
                     /name="hypothetical protein"
ORIGIN
        1 ctaccgcctt cacttcgttc agttggtcaa cccctcacaa aaaagccatt tgtaaaatgg
       61 ctttatttgt tcacggttat atataaaacc caaatttaaa ttgattattt tttattcagc
      121 tattgactta atttttatat gtattaatta atatataagt ggaaaactat ataacagcaa
      181 gctcagacaa tacttcgtat tgtcgcttgt gaggggttcc cccttcaatc cccttaaaac
      241 ccaacacagg aggcttacag tgagctacaa ggatagatac cataggaagc acagcgtcac
      301 gctatgcttc aatgacgaag aatttaaaca ggttgaagaa ctggcttcta tgctgaaaaa
      361 gccaagggcg aaagccataa gggagttaat actcaataaa gagtttaaac tcaaaaaaga
      421 aatttccaaa aatgaaaatg gtgatgtgta ttatcagctt cataaaatag gtgttaatat
      481 taaccagatt gcaagagcaa taaatactga tattgataaa tttatttctc atgagtttgc
      541 agaagatttt ttaaatttgt ttgaggaaat aacaaatgag atagaagaaa taaaaaggag
      601 aatataatat gtatcataaa ataataggag gtaaaaaaag caaaggtcaa aggaatataa
      661 aaaaaagtat tgaatattta ttgagagaga aaaacccaga acaacagaaa gacataaaga
      721 tattatcaac aaccacaaaa caagacctaa tcaattttga aaattatatt ttagataaaa
      781 acaaatcaaa tccatatgta tgtggtgttt tatcatttga agaaaaatcc atatcagaag
      841 aattaaaaac caaattaatt acagagtttg aagatgtttt atttgcagga attgaaccag
      901 aaaatagacc tccggttatg tgggtagaac acaacgacaa gggaagggta gagttaaatt
      961 atttaacatt taacagccta caagatagaa gatcatacac tgtatattta gataaaagag
     1021 atcgtggatt agtaaataat tactctgaaa taattaatta tgaaaataat ttatcaagtc
     1081 catttgaaga gaaagaaaat aaaaacacat taatcaacaa accaaaaacc aatattccag
     1141 aagataaaaa acaatttatt gaaaatatta acactgaaat aatggcatta attattaatg
     1201 aagagttgga aaatagagaa caaaccataa aacatattga aaatatgaaa ggtgttaaaa
     1261 taaacagaat acgaaaaaat caaatatcaa ttaaatctga tttgtttgat gacgataaac
     1321 ccattgtctt gaaaggagat atatatgaag agggaagaga ttacagcgat tatagaaaag
     1381 aattcaaccc aaaacctaca agagatccag agcttgttag agaaaaactc acagagctta
     1441 aaagaacatt tgcagaaaga attgaaaaac gagaaatcag aaatagatca aagtttaaaa
     1501 aaccatcgtt caaaaatcta tcagaaaata gacaaagtat tcaaagagaa gatcaagata
     1561 ttggatataa atatactaac ggcgatttta tcaatgttag taataacgat ggtttttcag
     1621 gtatgtatat tcgcactgat aatatggaga ttgtaaacaa tgagtcaatt aatacagaat
     1681 ataaaactaa aacagcaaca gaagaaacag caggaactac aagagcaaga gatattgaaa
     1741 aaattaatca gcaacaacaa tttgttagtt cgagacttga agaagctgga agaaaacaac
     1801 agcaattcag aaagtcgatt gatacaactg aaggaagatt tggagtatgt agaagatctg
     1861 tacactcaat tatttctact tttggaagat acatacgaac gttttcagca tatacaagga
     1921 agaatgaaca caggcagaaa ttcgaaaaaa gacgaaaaat cgaagaagaa aaactcaaaa
     1981 tcaaaaatca gggaagttac aacagaagac gatataaacc atattaaaaa tatgatgaca
     2041 acactactag atcactatga taaaacttta accgtgaaca agtgagaacc agccgtcagg
     2101 ctggttcttg cttgtgaggg gttgacctgt ccggtaggac ggttttctgt cataaggtgt
     2161 catagtgtca taaaaaccac aaaagaaaac gtcatatgtt ttgcagaaaa accatgacaa
     2221 caaaagtcaa aacaaaaaac atgatatttt ctgacaaatg agggctgaaa attgcctgtt
     2281 ttctttaaaa tccattttgt cagaaaagtt ctgacattct gacaagttaa ttttcctttt
     2341 ataatcaata tattacattt tttgtcatta gctttatcaa aagagtactg attttttctg
     2401 acaaatctct gacaaatttt ttttttaatc ctttaaaatc aatagtttac aagatttgtc
     2461 agaatgtcag agtgtcaaac aggggggggg tggtatgttt ttggcagtgc attttttggg
     2521 gctaaaatcc gacaaaataa aaaatgtctg atttttttta tgtaaacatt tgacaagtta
     2581 aaatcctatg ttataactgt atatataata ggaggattta attatgataa gattgaaaaa
     2641 ggtatttaat ttaacagaag aagaaatagt tttaacgaac gaaatagcag aagcaattag
     2701 caaagagcca aaagtagaaa ctcacgaagt gaatataaat tttattgatg ttttacctat
     2761 aataccaaac ccccataatt taggtttatc agaaaatata gatccattat ctttgatata
     2821 ttctaaattt gttagtgaaa ccgacatacc cccagcttta ccgatatttt catttttaag
     2881 ctatttaagt gcttttagtg ttaataacaa tataatgtat aagcatccta caagcccagc
     2941 ggattactta aatacttgga ctttaatact cgcaccttct ggtgcagcaa aaaccacatc
     3001 agcaaaaatt attgaaagtt ctataccaaa agatatagaa gaaaagccaa tgattagacc
     3061 taattttgaa ggtgctgacg gttcggcagc attcatttca gagttagcaa aagcagaaaa
     3121 gaaaattgat aatttcggaa aaccaataca gccgattttc tggatagaag acgaatactc
     3181 ccagtttatg aaaaaattaa tgccgggagg ttctatggtt gaaaccagaa aaacaatgtt
     3241 aaagatccat gataatgata aagcccgtag agttacgaag aacgatacta ttgaaactga
     3301 aagtatcgtt atgagtggtt tatttttgaa tactattgat agttttgcaa gaaactttga
     3361 tcaggaaagt attaatgatg gattaggaag aagacacaat tttgtttatg cagaaagagg
     3421 tgaaaaagtt gtcccaactt ggacagtgga agaaataatc gaatcactca aagagggatt
     3481 agataatttc ttttcaaatg taaaaacaaa tgtaatttat acatattcac cagaatgcag
     3541 aaaaatctat gaccattttt atatggttta taaagaaaaa tttgatcaca tattagggga
     3601 ggaaacaaac ggaacatttt tcagaacata ttttatgtta agttggaaat atgcagcaat
     3661 atatcatatt ttgctgaaag aagaaggaac cgaaattcag gcaaaatctt ttgactatgg
     3721 cataaaagtt tcattaatgt ttttatccag tataaaaaga tttttagatt acaaagtaga
     3781 tttaaaatct ggtgctaaag aagttagaaa ggaatattta aaaaaagcag cagaaaaaga
     3841 attaaacaac ttgcaaaaat acaaagattt tttgcttgat aatgtagaaa ttacattgcg
     3901 agattttaat aggaaattta gtcttaaaaa ggttgagagt ttaaaagtcc ttaaaacaat
     3961 cagagaaaac aaattaataa aataccatcc attgtttgaa gttttggcaa aagaagaagc
     4021 caaagcgaaa aaataa
//
