LOCUS       NZ_CP116149             5167 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P622 plasmid pDETEC27, complete
            sequence.
ACCESSION   NZ_CP116149
VERSION     NZ_CP116149.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988467
            Assembly: GCF_027944835.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5167)
  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  JOURNAL   Unpublished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 5167)
  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 01:51:10
            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)                     :: 5,207
            CDSs (total)                      :: 5,096
            Genes (coding)                    :: 4,860
            CDSs (with protein)               :: 4,860
            Genes (RNA)                       :: 111
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 236
            CDSs (without protein)            :: 236
            Pseudo Genes (ambiguous residues) :: 0 of 236
            Pseudo Genes (frameshifted)       :: 76 of 236
            Pseudo Genes (incomplete)         :: 179 of 236
            Pseudo Genes (internal stop)      :: 36 of 236
            Pseudo Genes (multiple problems)  :: 49 of 236
            Pseudo Genes (short protein)      :: 3 of 236
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116149.1.
            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..5167
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-P622"
                     /isolation_source="ICU patient rectal swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC27"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-09-03"
     gene            224..1138
                     /locus_tag="PIB88_RS25965"
                     /old_locus_tag="PIB88_25965"
     CDS             224..1138
                     /locus_tag="PIB88_RS25965"
                     /old_locus_tag="PIB88_25965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001738986.1"
                     /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_001271348.1"
                     /translation="MSAALQYFDENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRSTVATSARTL
                     KPWEALGISRAWYYQLKKRGLVE"
                     /name="replication initiation protein"
     gene            complement(1342..1740)
                     /locus_tag="PIB88_RS25970"
                     /old_locus_tag="PIB88_25970"
     CDS             complement(1342..1740)
                     /locus_tag="PIB88_RS25970"
                     /old_locus_tag="PIB88_25970"
                     /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_001222914.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLIDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKELKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            1917..2843
                     /locus_tag="PIB88_RS25975"
                     /old_locus_tag="PIB88_25975"
     CDS             1917..2843
                     /locus_tag="PIB88_RS25975"
                     /old_locus_tag="PIB88_25975"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_001331297.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTAPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            2846..3379
                     /locus_tag="PIB88_RS25980"
                     /old_locus_tag="PIB88_25980"
     CDS             2846..3379
                     /locus_tag="PIB88_RS25980"
                     /old_locus_tag="PIB88_25980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000168770.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            complement(3445..3654)
                     /locus_tag="PIB88_RS25985"
                     /old_locus_tag="PIB88_25985"
     CDS             complement(3445..3654)
                     /locus_tag="PIB88_RS25985"
                     /old_locus_tag="PIB88_25985"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001618649.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001096196.1"
                     /translation="MAKLGENTPHIIDATVDFMASSQAFREYLKKLPPDNTIPPALTDE
                     HVPLYIRRLEYYRLLYRPKQTESY"
                     /name="hypothetical protein"
     Typing          225..999
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.778"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          1918..2840
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gttttttgcg ccagaaagcg actgagggcg ttttaagggg ggcgtacaac gggagttatg
       61 gtaaatggat cgggttttcg ggaaggttcg acaggatttg ccgttgggtg tagtgtaagc
      121 gactgaaaaa caaacgcccc tgaaatcatg tccagatccg gcaagattca acatgaaata
      181 cagagggcgt gtaggtcgca taacccggag agaatcgtaa cacatgagcg ccgcgcttca
      241 atacttcgac gaaaatttac cccatcgtcc ctatcacacg gatgatctcg cttttggtct
      301 tcgcatctcc ggcaaagggc gtgcgcttct tgcgcggtac atacagcaga accagcctca
      361 tgcgcagttc tggctggttt ttgacgttga ccgcgagggg gctgcgattg actggagcga
      421 ccggaacgct cccgcgccga acatcaccgt taaaaatcct gtgaacggac acgctcacct
      481 gctctacgca ctcaacatcg ccgtgagaac cgcgcctgat gcctcggtta aggcgctgaa
      541 atatgccgca gcggttgaac gttcgctgtg tgagaaactt tgtgcggatg tgaactacag
      601 cggcctgatt tgcaaaaatc cgttccacct ggaatggctg gtgatggagt ggcgcgagga
      661 agcctatacc ctcgatgaac tggctgatta tctcgatttg agcgcctcag agcgtcgtag
      721 catcgataaa cattacggga tggggcgaaa ctgccacctg ttcgaaatga cgcgcaaatg
      781 ggcttacagg gcgattcgtc agggctggcc agcgttctca cagtggcttg aagcggtgat
      841 ccagcgtgtc gaaatgtaca atgcatcgct tcccgttccg ctttcactgg ctgaatgtcg
      901 ggctattggc aagagcattg cgaaatacac gcacaggaac ttcacgccgg aaactttcgc
      961 acagtatgtg gctgatacgc acacgccaga aattcaggct gcacgcggtc gcaagggcgg
     1021 ttctaagtct aagcgcagca cagtagctac atctgcacgc acgctgaaac cgtgggaggc
     1081 attagggatc agtcgcgcct ggtattacca actgaaaaaa cgaggtctcg tagagtagac
     1141 caaataagcc tatatcagat aacagcgcct ttctggcgtc tttttgagca gcaggttttt
     1201 tgccgttttt ccccgttcag ccctgcaatg gcgcggcttt ccgcgtgatt gtggtggtag
     1261 tgctcgccgc agtctcatga ccgagcgtag cgagcgaatg agcgaggaag caccagggaa
     1321 tcggaacacg gatggaggca cttacgcgtc tgggtttggg gatgtctcca gatcgtactt
     1381 aagttcctta agtgcttgta atatcctgtc ttttttatag catagctcgc ctgtttttgt
     1441 gtctaccagt cctgcttcga tcagtagccc agccgcgaga aagagccggt gattgcgttc
     1501 ccgtcgttgt ttttttccct cgattcgttt ttggaccgcc tgttttcgtt cgctctcctg
     1561 tgcctgtaag tcgttttttt ccgctgttgc cagtacgtgg agaagtttgc gttcctgttc
     1621 tgtgagtccg gcttcgttgt cgatcaggtc aataatctgt ctctgtcgtg cggtctgttc
     1681 tccgagcttc ctgatgaatc cgatccgttt cttcagccat tcgatgttgc tgatgcgcat
     1741 gttcgtgatg ctccctggtg tttttttgcg gtgtgttgtg gtcgtgcagt atatcgcttg
     1801 cggtcggcgg gtgcaggggg tatcttccgt gctaattcgt aaaattagaa ggaagcgcac
     1861 ttatatgttt ctctccttcg tcgagaaaca gtgcgctcct gcagagggct gaaaccgtgg
     1921 caacctatca cctcagcgtt aaatttggtg gcaaggggca ggctgcaaac cacgccgatt
     1981 acatcgagcg caaagagaaa taccgcgacc gtcaggattt ggaatattcc gcacacggaa
     2041 acatgccgga atgggccagg gataatcctt cccatttctg gcaggcggct gaccagtttg
     2101 aacgtgcgaa cggttcgacc tatagggaac ttgaaattgc attaccccgt gaactgacac
     2161 cggaacagcg ccttgaactg gtgcaggatt ttgtacgtca ggaagctggc gaacggcacg
     2221 cctggagttt tgccattcac aatccgaaag cgagcattga cggcggcgaa cagcctcatg
     2281 cgcatatcat gatgagtcag cgtgtgaatg atggcattga acgtacaccg gaacagtatt
     2341 tccggcgcta taacgccagg tatcccgagc ggggaggtgc gaaaaaggat tccggaagcc
     2401 tgactctcac tcagcaaaaa gagcagttgc gggaattgcg aaaacgctgg gaggtgaagc
     2461 acaacgaaca tatgagaaag catggctttg aaaggggctt cattgactgc cggacgctga
     2521 aagaacaggg cattgaacga cgtcccgaag tgcatctggg ttttgaagct gccggacggc
     2581 ttgatgatgc ccagcgtcat gacatcatgc aaaaacggtc tgaaccggac tattcccgcc
     2641 atcttgaaca ggcgcgaacg gtcgggcatg acatcaggga atggctggac actccggtta
     2701 agcaacatga actggtcaga aggctgcaac atgatgttgc gcgggagcat ggctttgaca
     2761 tgagagacag agtgagcaga cagaaccgaa ctgcacctga acgggttaaa tcaccgtcac
     2821 gtggattttc tatgggattc tgaacatggc cagcacagaa gaaaaattac ttacgctcct
     2881 gttatcggtg gagcatctgc aacataccgc aatggagcaa cagaaagctg ttgctgattc
     2941 tctggctgtg gcaagggaaa ctcttcgcgg atatcgggat atttctgacg gtgtggcaaa
     3001 acaggtcagg gatgaagtca gaaatgaggt gcagaagctg gacgtggcag gactgatagg
     3061 tgagcgcatc agccaggatt ttcagcggct ggaagagtca gtcgcaaaca tgaaggcaaa
     3121 cgcggatgcc ctgaacaggg atattgcgac aattcacagc aatatcgtgc aggaatacaa
     3181 cacccttaaa gggtatagct ggaaatggct gggtggggtg tcagtggctt ttctggttat
     3241 gttctgtgtg ctcggatggg gaatgaaaac aatactcgac aggaactaca acgccacagc
     3301 ggcggtgtat cagaaagttg tgacactgga agataaactg gtggagaaac ctgtcacggg
     3361 gaagagccgg aaaaactgac gcgcttcgct tgtccaacgc ctcacgaccc gcgaaagaat
     3421 ttcgcgaacc gttcaccgtt tttttcaata tgattctgtc tgctttggtc gataaagcag
     3481 acgatagtat tccagccttc gtatatataa cggtacgtgc tcatcagtaa gagctggcgg
     3541 tattgtgtta tcagggggaa gttttttcag atactcacga aatgcctggc ttgatgccat
     3601 aaaatctaca gtagcatcga taatatgtgg ggtgttttca cctaattttg ccatgatgat
     3661 aatccttata ttatcacggt ttgtgaatga tagggtgtca ctattattta tgcgttagtg
     3721 aaccagaaaa aatcccccgt tggcataggg ggatatgtaa ggagaaataa cttcgcaggt
     3781 gttcttgttt gtataacgtg aaaagactgc acgcaactta ataagtctgc cgtacttact
     3841 ttcagttttc aacataaggt ttataacaat gtatggaatg gaagtgagct ttaaggtttc
     3901 agctctaaaa aataaaatat ttattagttg gctggttgtt gttcttgttc tgtatgtata
     3961 taaacactat cgacatatta tgaccgggaa cattccttac cccctctgcg ctcgcagagg
     4021 ttttttttgt cattaattaa taatgaactg aaatgcagtt ccgatacctc catttgcaca
     4081 ttatccctga catatggtac cggaaccgca ttaattttat gttataagag tttattttta
     4141 atgtccagat ggtttaatag tatttatatg taattagctg tatggatagt actggtttta
     4201 ttgtataact tgtcgttttt ttttattgtt tttgtgtggt gtgctaatct ttaagttata
     4261 aaaaaacccc ttggaataca ggggcaaaag taaggaaaac aaatggatgc tcagtttgtg
     4321 tgacacttta aactaatgga actatagagt ggaggttgtt acagtcgctt ttataaaaca
     4381 gcaaccagtt tttttcaata gtctgatgat ggttgtgaca gttttgtgat attgttcaaa
     4441 atgtttcttg ttgaatgttt gttttttggt ctattggtgt ctggttttat tttttctgct
     4501 attacatatc aagaaatgtg attggtgtag caagagtgga atgcgatgtg gataaactaa
     4561 ttggttgtcg aatctaattt acttagaaaa ctacacttgt ttttgtgtat gaatttagtg
     4621 aatttgtctg tctatgtgtt ttcgtgcatt tataaatcct tcgtcaggat cttaaattta
     4681 gtgttgaata tgtagggcct gtacggtaat tattatttag cgtagctact tcatcgttgt
     4741 tcgaacacaa ccaacaacct gtaattgttg tttctcttgg ttccccactt ttgtggggtt
     4801 ttttatctct tccgtgcatc gtaaagcgcg gactccttct ggaaaggttg ttttagggca
     4861 tcactgaggc attttttgcg tttgtgaata ttgagcatcc gataactaaa atatttccca
     4921 tagactctga ttcttgccac cgaccccagg tcggtttttt tttgtcctgg cgagatgtga
     4981 agtttggaaa caggaaaccc cgtcagagcg ccacgcacca ggggagaaaa cttgtcgttt
     5041 tgagccgttc ggtgttcaga acgcacgaaa ccgatcgcac atcgctttcg tgcatagtta
     5101 tgcaacgccc tgaaaacgat tctgacgcgt ttttctggtt tggcctggtg ttttcttgtc
     5161 tttttgc
//
