LOCUS       NZ_CP116157             4867 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P61 plasmid pDETEC41, complete
            sequence.
ACCESSION   NZ_CP116157
VERSION     NZ_CP116157.1
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 4867)
  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  JOURNAL   Unpublished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 4867)
  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
            CP116157.1.
            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..4867
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-P61"
                     /isolation_source="ICU patient rectal swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC41"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-08-01"
     gene            join(4696..4867,1..113)
                     /locus_tag="PIC71_RS24585"
                     /old_locus_tag="PIC71_24585"
     CDS             join(4696..4867,1..113)
                     /locus_tag="PIC71_RS24585"
                     /old_locus_tag="PIC71_24585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016149473.1"
                     /GO_function="GO:0008657 - DNA topoisomerase type II
                     (double strand cut, ATP-hydrolyzing) inhibitor activity
                     [Evidence IEA]; GO:0042803 - protein homodimerization
                     activity [Evidence IEA]"
                     /GO_process="GO:0030541 - plasmid partitioning [Evidence
                     IEA]; GO:0051290 - protein heterotetramerization [Evidence
                     IEA]"
                     /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_001554709.1"
                     /translation="MSYNLEFDPRALKEWRKLGDDVRLQFKKKLEQVLQHPRIDKNRLR
                     ELHDCYKIKLRASGYRLVYQVRDQTITVFVVAVGKRERSAAYDAADKRL"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(158..391)
                     /locus_tag="PIC71_RS24590"
                     /old_locus_tag="PIC71_24590"
     CDS             complement(158..391)
                     /locus_tag="PIC71_RS24590"
                     /old_locus_tag="PIC71_24590"
                     /inference="COORDINATES: protein motif:HMM:NF016769.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_001554708.1"
                     /translation="MTEMEQQLLSALESLQRHYEQQQQAWQDSYANLQRMFEVTSQELA
                     KNDRVCQALSMQVTGLAQQVESLNRTVRRLSN"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(<987..1625)
                     /locus_tag="PIC71_RS24720"
                     /pseudo=""
     CDS             complement(<987..1625)
                     /locus_tag="PIC71_RS24720"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(1615..1941)
                     /locus_tag="PIC71_RS24600"
                     /old_locus_tag="PIC71_24600"
     CDS             complement(1615..1941)
                     /locus_tag="PIC71_RS24600"
                     /old_locus_tag="PIC71_24600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006674374.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001554615.1"
                     /translation="MEKRTKEIKIRLTEAEHQRLLERCDRKHLAEWLRAVGLGESRTAR
                     RRPLPTVDPTLLRQVSGIGNNLNQIARYLNQHGLPPQERVSLLAVLNSIDQHLAELLEQ
                     HRDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2203..3267
                     /locus_tag="PIC71_RS24605"
                     /old_locus_tag="PIC71_24605"
     CDS             2203..3267
                     /locus_tag="PIC71_RS24605"
                     /old_locus_tag="PIC71_24605"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000849600.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="AAA family ATPase"
                     /protein_id="WP_032323124.1"
                     /translation="MKTISLFNNKGGVGKTTLTWNLSVSLSAKGKSVLLIDFDPQCNLS
                     IALLGETKFSELLEKDAANPYGKTIRAFCQPFIQQDITPTVHTFTPNYPMEEGSGRLDI
                     VPGDFWLNNLSDAISVGTDLIAGNAVTRFLIPSLIANKAQELNDCEYDYVLIDVPPSFN
                     TIVRSALYCSDYYLVPCTADVFSAYCIGLIGETLPKFRDDWEQGIRRSSAQSTPLISQK
                     GQPKFAGWIFNGFDKRKQPGHSIATEIAADAAHRDKIIESVKNDLRPKLSSIKTYPSVA
                     AFTPDTPVAKVEDLNVMAPDSILQGVPIRYLSSVRPTRDVLVRGAWSGPQKHLMQAMSD
                     EHDALADYIINNFV"
                     /name="AAA family ATPase"
     gene            complement(3294..4199)
                     /locus_tag="PIC71_RS24610"
                     /old_locus_tag="PIC71_24610"
     CDS             complement(3294..4199)
                     /locus_tag="PIC71_RS24610"
                     /old_locus_tag="PIC71_24610"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019725130.1"
                     /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_032323125.1"
                     /translation="MDNQALTLFNDRLPHKPYFSDDLQFGVRIAGKERALLAKYIQFNQ
                     PHAMYWLCFDVDRAGAAIDWADLGAPAPTLTIKNPENGHAHLLYALHTAVRTAPDGRAA
                     PLKYAAAIENALRKKLGADAGYSGLICKNPNHLHWQITVWQPELYTLDWLADYLDLGAA
                     NDREILPDYGLGRNCTLFDKTRKWAYRAIRQGWPQYDQWLQACIERAKAYNLQFSAPLE
                     ENEVMGIAKSVAKWTNKNLTESGFSEYVKKTHTPDIQAKRGRLGGEKSKGGGRPSTTGK
                     KWIEEGISRSSWYRKKATQL"
                     /name="replication initiation protein"
     gene            4464..4706
                     /locus_tag="PIC71_RS24615"
                     /old_locus_tag="PIC71_24615"
     CDS             4464..4706
                     /locus_tag="PIC71_RS24615"
                     /old_locus_tag="PIC71_24615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020301039.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelB/DinJ family
                     antitoxin"
                     /protein_id="WP_001554710.1"
                     /translation="MATINIRIDDELKSRSYAALEKLGVTPSEVLRQTLEYVAQSGRLP
                     FQQVLLTEDDADLMAIVRDRLENPQAGVKVSLDEL"
                     /name="type II toxin-antitoxin system RelB/DinJ family
                     antitoxin"
     Typing          complement(3425..4337)
                     /name="rep_cluster_2486"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.374"
                     /coverage="88.0"
                     /evalue="0.0"
     Typing          complement(112..1625)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.604"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccggttatcg cttggtctat caggttcgcg atcaaaccat tacggtattc gtggtggcgg
       61 tcggtaagcg cgagcgttct gccgcttacg atgcggccga taaacgctta taaactcatg
      121 ccgtgaccgc gagaataccg ctgttcgtgc cgcttggcta attgctcaag cggcgcactg
      181 ttctgtttaa gctctcgact tgctgcgcca agccggtgac ttgcatgctc aaggcctgac
      241 aaaccctgtc gtttttcgcc aactcctgcg aggtaacctc gaacatgcgc tgtaagttgg
      301 cgtagctgtc ctgccacgct tgctgctgtt gttcgtagtg cctctgtaag ctctctaatg
      361 cgctcagaag ctgctgctcc atttcggtca tgaatctctt caccctgata gataaaaccg
      421 cccagaatcg attctgtggc gtctgatgag gttatttggc gctgtacttg atgacctgac
      481 gatgttgagc gttcttgtac tcttcgatct tcttcgcccc ctgcggaagg atcaggtaat
      541 acacgctctt gttcttggaa tcgtgaatta tcgatacgcc ggctccggtc tggctcttta
      601 agtcctgcag gatctggctc tgctcgctga tttcgttctg gcgttcgacc acgatagtcc
      661 cgagatacca agctactcca atcaatatcg caaacaggat cccacttaat gccaggctgt
      721 acagccatgt cattccgact aagcggtgta tctgttttag ctggctgtcg ttctcttctt
      781 ggatagcggt ctgtatgttc cctgagctta atttcaaggc ctcggtgata cgtttctcgt
      841 gcttctcgaa tgcgttcgcg acgctcgttg cggtagtctt ggcttgctgc ttcgatttgc
      901 tctcgaactc ccgcgctaaa tttaaaatct cgctcataca gcactccttt taagcgaata
      961 ttcgggccac ctgccggatc agcaatactg atactggatt tggtttcccg tacgaccaac
     1021 aatccggcat cggtaaggtg ggaaatcacc cctttacgat ccgtaatttc tccctgctca
     1081 atcaagctga ttagcccttt ggtaatggct tccgctgcct gctgtttgtt gcgaggaagg
     1141 tcattagagg gggttaatgc tcggcgatta gcagggtcat tcgggtcgcg taacccaagc
     1201 cggtcattgg tgagggtttg ccatgcgtta acacgaggcc ggtcagcccg atcaaagtaa
     1261 ggttgtagcc gttttccgct ctgcaattcg atgttcggga taacaaaatt caattcaaga
     1321 cgccctttgt cctgatgttg aacccagagg caggcatact ggtctttatc tagaccggtc
     1381 atcaatgtct gctcccattc atccatcaat cgctgctttt cgccttcggg taaatcactc
     1441 tcctgaaaag agagcacgcc agaggtataa gttcgggcaa attcgcagcc atcaatcagc
     1501 tctttgacgt gctcagggtt accccgtaac accgtcgctt gttcgcgctg acgatcaggg
     1561 cccagaaggt aatcgacagg accactcccg ccaccggcac cacgaccatg aatcttaacg
     1621 atcacgatgt tgctccagca gttcggcaag atgttggtca atgctattga gcaccgctaa
     1681 caacgacacc cgttcttgcg gcggtaagcc atgctgattc aagtaacggg ctatttgatt
     1741 gaggttatta ccgatcccgc tgacctgacg taacaaggtc gggtctacgg taggtagcgg
     1801 acgacgccga gctgtacgcg attcgcctaa gccaacggct cgtaaccact cggccaaatg
     1861 cttacggtca cagcgttcaa gtagccgctg atgctccgct tcggtgagtc tgattttgat
     1921 ctctttggtg cgcttttcca tgagaatccg ctgagaaagt ttcgcaccca aagtgcgaat
     1981 tttcgcagtg gatgcaaggg gtttcggggg gcggcgagcc ccctgaacca gtcacagacg
     2041 gcacctcgca gaggggacgc tgtgtgtact ggcttaataa gctatagcat gtatagtcta
     2101 ctatcccgcg aaaaagaaga gaactcctag aaaggagctg ttatctgata taggcttgtt
     2161 ttgtctcacg tggcgaacta acgacgaata ataaagggaa aaatgaaaac aatatcgctg
     2221 ttcaataaca aggggggagt gggtaaaact actctaactt ggaatctaag tgtgtcccta
     2281 tcggctaagg gtaaatccgt tttactgata gacttcgacc cgcagtgtaa tttgtctatc
     2341 gcattactcg gagaaacaaa attctccgag ctattggaaa aagatgcggc gaatccgtat
     2401 ggcaagacca taagagcttt ttgccagcct tttattcaac aagacattac cccgacagtt
     2461 catactttca ctccgaatta tcctatggaa gaggggtcgg gacggttaga catagtccct
     2521 ggcgattttt ggttgaacaa cctttcagac gcaattagcg tgggtactga tctaatcgca
     2581 ggcaacgcag taacaaggtt tttaatccca agcttaatcg caaataaagc tcaagaatta
     2641 aacgactgtg agtatgatta tgtactcatt gatgtacctc catcatttaa tactattgtt
     2701 agatcagcac tgtattgctc tgattattat ttagttccat gtactgctga tgtgttctcc
     2761 gcttattgca taggtctaat tggtgaaacc ttgcccaaat ttagagacga ttgggagcag
     2821 ggaataagaa gaagttcagc tcaaagcaca cctcttatta gccaaaaagg acaaccaaaa
     2881 tttgctggtt ggatctttaa cggctttgac aagagaaaac agccaggtca ttcaatcgcg
     2941 acagaaattg cagccgatgc agcgcacaga gataaaatta ttgaatcagt caaaaatgac
     3001 cttcgaccta aactgtcatc aataaaaaca tatccatcag tagccgcctt tactcctgat
     3061 acccctgtag caaaagtaga ggatctcaac gtaatggctc cagatagtat tttgcagggc
     3121 gttcccattc gatatttgtc ttcagttcgc ccaacaagag atgtattagt aaggggcgct
     3181 tggtcaggac ctcagaaaca tttaatgcaa gcaatgtctg atgaacatga tgccctagcc
     3241 gattacataa tcaataactt cgtttaaaat caattacata taaagccgct cattcataac
     3301 tgagtggctt tttttctata ccatgagctt cggctaatac cttcttcgat ccatttcttt
     3361 cccgttgtgg acggccttcc accaccttta cttttttctc ctcctaaacg ccctcttttt
     3421 gcttgaatat caggagtatg tgtttttttt acatactcac taaaaccgct ctcagtaaga
     3481 ttcttatttg tccattttgc tacgcttttt gctatcccca tgacttcatt ctcctctaaa
     3541 ggtgcggaga actgcagatt gtaggcttta gcgcgttcaa tgcaggcttg tagccattgg
     3601 tcatactgcg gccagccttg gcggatagcg cggtaagccc acttgcgggt tttatcgaag
     3661 agggtgcagt tacggcctaa accgtagtcc ggcaggattt cgcggtcatt ggctgcgcca
     3721 aggtcgaggt aatcggctaa ccagtcaagg gtatagagct ctggctgcca gacggtgatc
     3781 tgccagtgca ggtggttcgg attcttgcaa attagccctg aataccccgc atctgcgccc
     3841 aattttttac gcagcgcatt ctcgatggcg gcggcgtatt taaggggggc agctcgacca
     3901 tccggcgcgg tacgtaccgc cgtatgcaag gcatacaaca ggtgagcatg tccgttctcg
     3961 gggtttttga tggtgagtgt gggcgcaggt gcccccagat cggcccaatc aatcgcggct
     4021 ccggctctgt ccacgtcaaa gcaaagccag tacatggcgt gaggctgatt aaactggatg
     4081 tattttgcga ggagagcacg ctctttaccg gcaatgcgaa caccaaactg taaatcatcg
     4141 gagaagtacg gcttgtgggg taaccggtcg ttaaaaagcg ttaaagcctg attatccaag
     4201 gctcccagcc ttatggcggg gctgttgttt tgcacgctgc atgtgctaat atcctttcta
     4261 ggtttcgacc tagccctgaa tgtcatgtcc gctcgccaaa gtagagcatg atttcggggc
     4321 tttgtttttt ctgccactaa gttacacctc aacaacggtt tttgtcatcc ccgacaatcc
     4381 gttattcctg cttgttctcg cacggcttta cgctcatact acttcttgta gatacacttg
     4441 tcactacatc aagaggtgag atgatggcca cgattaatat tcggatcgat gacgagctga
     4501 aaagccgctc ttatgccgca ctggaaaagc tgggcgtaac gccgtccgag gttctgcgcc
     4561 aaacactgga atatgtggcc caaagcggac gtttgccgtt ccagcaggtt ttgctgaccg
     4621 aggatgatgc cgatttgatg gctatcgttc gggatcgtct ggaaaaccca caggcgggcg
     4681 taaaggtgtc actggatgag ctataacctt gaatttgatc cccgagccct gaaggaatgg
     4741 cgcaagctcg gggatgatgt ccgtctgcag ttcaagaaaa aactcgagca ggttctacaa
     4801 cacccgcgga tcgataaaaa tcgcctgcga gagctgcatg actgctacaa aatcaagctc
     4861 cgtgcat
//
