LOCUS       NZ_CP116173             5728 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P1056 plasmid pDETEC84, complete
            sequence.
ACCESSION   NZ_CP116173
VERSION     NZ_CP116173.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988445
            Assembly: GCF_027944915.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5728)
  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  JOURNAL   Unpublished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 5728)
  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 01:49:26
            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)                     :: 4,863
            CDSs (total)                      :: 4,743
            Genes (coding)                    :: 4,559
            CDSs (with protein)               :: 4,559
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 184
            CDSs (without protein)            :: 184
            Pseudo Genes (ambiguous residues) :: 0 of 184
            Pseudo Genes (frameshifted)       :: 64 of 184
            Pseudo Genes (incomplete)         :: 109 of 184
            Pseudo Genes (internal stop)      :: 47 of 184
            Pseudo Genes (multiple problems)  :: 37 of 184
            Pseudo Genes (short protein)      :: 3 of 184
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116173.1.
            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..5728
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-P1056"
                     /isolation_source="ICU patient rectal swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC84"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-10-22"
     gene            329..1252
                     /locus_tag="PIC86_RS24225"
                     /old_locus_tag="PIC86_24220"
     CDS             329..1252
                     /locus_tag="PIC86_RS24225"
                     /old_locus_tag="PIC86_24220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016237866.1"
                     /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_062859337.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLSASARR
                     SIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSPAE
                     CRAIGKSIAKYTYRKFSPEGFSAVQAARGRKGGNANSSENQAIKGQKSKRVAVATSART
                     LKPWVTLGISRATYYRKLKCDPDLAK"
                     /name="replication initiation protein"
     gene            complement(1459..1905)
                     /locus_tag="PIC86_RS24230"
                     /old_locus_tag="PIC86_24225"
     CDS             complement(1459..1905)
                     /locus_tag="PIC86_RS24230"
                     /old_locus_tag="PIC86_24225"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000184721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_271292795.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAILAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGITELPRNHPKWQEWERRGKELLTKDSA"
                     /name="conjugal transfer protein TraD"
     gene            2077..3171
                     /locus_tag="PIC86_RS24235"
                     /old_locus_tag="PIC86_24230"
     CDS             2077..3171
                     /locus_tag="PIC86_RS24235"
                     /old_locus_tag="PIC86_24230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016230929.1"
                     /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_000179381.1"
                     /translation="MASYHCTVKTGAKGVALKHADYISRSGEYKNYKSREDLEFSSSGN
                     MPSWAKKNPAELWKAADEFERKNGTAYREIEIALPRELTREQRIELVEDFVQKELGDRH
                     AYQYAIHNPPGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRANSKSPERGGAKKARF
                     GETQQERKSALVALRSHWADVQNEHLARHGHQSRVDHRSLKEQGIKRTPEVHLGPVRVA
                     VMNADQVCAILAWRNAEREKLEAEKERDSIIDLKTTLKEALAERDNMPPTLDELGAELK
                     AFVESSFDELNEVMQLNSLIDGALDTMMKQFQVEEERKLQQERLIQAARDEAEKQRELE
                     RERVRRRAYSSPAPSRSRDYGMSR"
                     /name="MobA/MobL family protein"
     gene            3193..3909
                     /locus_tag="PIC86_RS24240"
                     /old_locus_tag="PIC86_24235"
     CDS             3193..3909
                     /locus_tag="PIC86_RS24240"
                     /old_locus_tag="PIC86_24235"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016235968.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001175446.1"
                     /translation="MQLDEHSRKIAALVAYNEKQIKEINRIITLLNERVNDLNTFTDTL
                     EREGKVVSGISYSLRDSVSHVDFYLNKGMEEVSCKLQKSVSDTLTSLLREKLSFTLNDV
                     RQEWTDFEEQTSKEIKESLKQTTRDAEVATGIIRKTMEKYTVTRIVEKVLVLLVLFLLL
                     MIAPSFYAEYLKMNIGSLMEEQKKHESMLKEWKEKAPLAEFSKCGEYRDVCVLVDDKSG
                     YYSNEQTPNKKYAILK"
                     /name="hypothetical protein"
     gene            complement(3967..4539)
                     /locus_tag="PIC86_RS24245"
                     /old_locus_tag="PIC86_24240"
     CDS             complement(3967..4539)
                     /locus_tag="PIC86_RS24245"
                     /old_locus_tag="PIC86_24240"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001681717.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LysE family translocator"
                     /protein_id="WP_196611317.1"
                     /translation="MEYSTLFSFAIVTLSQTISIGPGVALVINNAFSQGLKSSIKTSIY
                     IRAGEAIVMVISLFTLSSTSSIEQHFYIIKILGGSYLIYIGVMGLINKKNKKSKVQKPL
                     LIPLLNPKAYLFFAALIPAFIDDNTNIALNFFILGVLFIFISFLTDIIYIAIVLTIRDK
                     LTPSFSRYISICSSIFILGTGIYFILT"
                     /name="LysE family translocator"
     gene            complement(4546..5496)
                     /locus_tag="PIC86_RS24250"
                     /old_locus_tag="PIC86_24245"
     CDS             complement(4546..5496)
                     /locus_tag="PIC86_RS24250"
                     /old_locus_tag="PIC86_24245"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000997639.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000997639.1"
                     /translation="MNDFINECISAPRINGMEEFFSSTASGEKHKPFRLVEIDERLFHS
                     YDYIKFGKNLTKNSGPFVNHYFCSIPYSKEEECRLGTTVIKYATTLNKKLNAWCLGMAE
                     GAMARTISELSKGNIQTLTTSPTKENEHAFFNYGSSENAYFICTPFFLLEEKLKKSNLN
                     QFNQGFDIIIEDTTFQMYSPNRSGQINHVKRLLNNDGIFIFTEKHSSEHDEYQKREIQK
                     DYSFKQRYFSKDEINTKKEIVLNTMNLNEVSVDDMISAIKQHFKYASIYWNSGNFYSIA
                     ASNSLKHISTFINLLPKAAIPMEYVYEKLPRNISW"
                     /name="hypothetical protein"
     Typing          567..1029
                     /name="rep_cluster_2131"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.745"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          2078..3168
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.055"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aggggggaaa ccgatcatga atcgcttttg tgcatagtta tgcaggccca taaaaacgat
       61 tctgacgcgt ttttatggtt taccctagtg ttttcttgtc tttttgagtt ttttgcgtca
      121 gaaagcgatt gagagcgttt tagagggtac gtacaacagg agttatggta aatggatcgg
      181 gtttgcggga agactcgaca ggttttgtcg ttgggggtag tgtaagcgac tgaaaaacaa
      241 acgcccctga aattcgtgcc tctccgccaa gattgtcacg agaatacagg ggcgaggtcg
      301 gtcgataacc tggaaggaat cgtaacacat gagcgccgcg cttcaatact tcgaagaaaa
      361 tttacctcac cgcccctatc acacagatga tctcgctttc ggccttcgca tctccggcaa
      421 agggcgtgcg cttcttgcgc ggtacatcca gcagaaccag cctcatgcgc agttctggct
      481 ggtttttgac gttgaccgcg agggggcagc gattgactgg agcgaccgga acgcccccgc
      541 gccgaacatc accgttaaaa atcctgtgaa cggacacgct cacctgctct atgcactcaa
      601 tatcgccgtg agaaccgcgc ctgatgcgtc ggttaaggcg ctgaaatatg ccgcagcggt
      661 tgaacgttcg ctgtgtgaga aactttgtgc tgatgtgaac tacagcggac tgatttgcaa
      721 aaatccgttc cacctggaat ggcaggtgat ggagtggcgc gaggaagcct ataccctcga
      781 tgaactggct gattatttga gcgcctcagc gcgtcgtagc atcgataaac attacgggat
      841 ggggcgaaac tgccacctgt tcgaaatgac gcgcaaatgg gcttacaggg cgattcgtca
      901 gggctggcca gcattctcac agtggcttga tgccgtgatt cagcgtgtcg aaatgtacaa
      961 cgcatcgctt cccgttccgc tttctccggc tgaatgtcgg gctattggca agagtattgc
     1021 gaaatacacc taccgcaaat tctctcctga aggcttttcc gcagtacagg ctgctcgagg
     1081 tcgtaagggc ggtaatgcaa attcatcaga aaatcaggct attaaaggtc agaaatcaaa
     1141 gcgtgtagcc gttgccacat cggcacgaac tctgaagccg tgggtgacgt tagggatcag
     1201 tcgtgccaca tactatcgaa aactaaaatg tgatccagat ctcgcaaaat gagaccagat
     1261 aacaagcctt atcagataac agcgcctgta ggcgtttttt tgagcgggta ggtttggggt
     1321 gatttcccgt gtttcgtttg gcaatggttt tagcgtctgt gtgtgagtgg tggttgtgct
     1381 cgccgcagtc tcaatgaccg agcgtagcga gcgaatgagc gaggaagcac cagggaacgg
     1441 gaacgagaac gaaggcactt acgcactgtc tttggttagt agctccttcc cgcgtctttc
     1501 ccattcctgc cattttggat ggttgcgcgg tagctctgtg attcctgcga gtgcgcctac
     1561 cagttcggca gcactaaact ttggttttcc ggttttgctg tccaccagtc ctgccacaat
     1621 catgaggcct gcggccttgt agagttcatg atcccgcgcc tttcgttccg cccttgcggc
     1681 tgccttccgt tctgctgcta ggattgccgt taccctggct tttgctgcgg ctgctttctc
     1741 tgcggttttt tctgcccgta tcagtgcgga caacgttttt tcatccgtcg ttgttcggtt
     1801 ttttttctct gccagtaaca caagtaatct ctgctgctct gacggtgatt tcagtccgtt
     1861 gatgtaggca atttttgcac ttaaccactc ttcacgattt gtcattctta cctctgcact
     1921 tttgccgtta atgtgagttg ttattgtgca taatatcacc ttgtctgcct gcgtgtgaga
     1981 ccgtaaaatc atccctgatt aattcaggga tgcgcactta gacgtttctc tccttcgtcg
     2041 agaaacagtg cgctcctgcg gagggcttaa cggcagatgg caagctacca ttgcacagtt
     2101 aaaactggag caaaaggcgt agccttaaaa catgctgatt acatttccag atccggcgaa
     2161 tataaaaact ataaatcgcg ggaggatctg gaattttctt catccggtaa catgccatca
     2221 tgggcgaaga aaaatcccgc agaactgtgg aaagctgctg atgaatttga acgaaaaaac
     2281 gggacggcat accgtgaaat tgagatcgca ttaccgcgag aactgacacg tgaacaacgg
     2341 atagagcttg ttgaagattt cgtgcaaaag gaacttggtg atcgccatgc ctatcagtac
     2401 gcgatccaca atccaccagg tgcaattgac gggaaggaac agccacacgc gcatatcatg
     2461 ttttgcgaac ggattaatga tggtattgaa cgcgatccgc agcagttttt taaacgtgcc
     2521 aacagcaaat caccagagcg ggggggcgca aaaaaggcac gctttggcga gacacaacaa
     2581 gagcgaaaat cagccctggt tgcgctacgc tctcactggg ctgatgtgca gaatgaacac
     2641 cttgcgcgac acggccacca gtcgcgcgtt gatcatcgtt cgctgaaaga acagggtatc
     2701 aagcgtacgc cggaggtgca tcttggtccc gttcgtgttg ctgttatgaa cgctgatcag
     2761 gtttgtgcaa ttctggcatg gagaaatgcg gaacgggaga agctggaggc cgagaaggaa
     2821 cgggacagca tcattgacct taaaacgacc ttgaaggaag cgttagctga acgggataac
     2881 atgccaccaa ccctggatga gcttggggca gaattgaaag cgtttgttga aagctcgttt
     2941 gatgaactca atgaggtaat gcagcttaat tcattgattg acggtgcgct ggacacaatg
     3001 atgaagcaat tccaggtgga agaggagcgg aagttgcaac aggaacgact aattcaggct
     3061 gcgcgagatg aagccgaaaa gcaaagagag ctggagaggg aaagagtgcg ccggcgtgcg
     3121 tattcttcac cagcaccatc acgttcacgc gattatggta tgagccgtta agcactggag
     3181 gttttttatt ttatgcaatt ggatgaacat tcaagaaaaa ttgctgccct tgttgcgtat
     3241 aatgaaaagc aaataaaaga aataaacagg ataattactc tgcttaatga aagagtgaat
     3301 gacttaaata cctttacaga tactcttgaa cgtgaaggta aagttgtatc tggaatttct
     3361 tattccttga gggatagtgt gtctcatgtt gatttttatc ttaataaagg aatggaagaa
     3421 gtatcctgta aattacagaa atctgtctca gacacactaa catcattact ccgtgaaaaa
     3481 ttatctttca cacttaatga tgtaaggcaa gagtggactg attttgaaga gcaaacaagt
     3541 aaagagataa aggaatcatt aaagcagacg accagagatg ctgaagttgc gacaggtata
     3601 attagaaaaa caatggagaa gtatacagta acaaggatag tcgaaaaggt acttgtgttg
     3661 cttgtattat ttttattgtt aatgattgct cctagttttt atgctgaata tctcaaaatg
     3721 aatatcggtt ctctaatgga agaacagaaa aaacatgaat ctatgttaaa agagtggaag
     3781 gaaaaagcac cattggcaga gttctctaag tgtggagagt atagggacgt atgcgtgtta
     3841 gttgatgata aaagcggata ttattccaat gaacaaaccc caaataaaaa atatgccata
     3901 ctgaaatagt gttaagtaac tcatgccgtc ttatgactaa ggctgtatga gtataaaaac
     3961 ggcgtttcac gtcaagataa aataaatacc tgtacctaat ataaaaatgg agctacatat
     4021 acttatgtac cttgagaatg acggagttaa tttatccctt atcgtcaaga caatagctat
     4081 gtaaataata tctgtcagga atgatataaa tataaacaaa acacccaata taaagaaatt
     4141 taatgcgata tttgtattat catctataaa tgctggtatt aatgccgcaa agaataaata
     4201 cgcctttggg tttaataatg gtataagtaa aggtttttgt actttgcttt ttttgttttt
     4261 tttattaatt aaacccatta cccctatgta tattaaatag cttccaccta agatctttat
     4321 aatgtaaaag tgttgttcta tgctggatgt tgaagataac gtgaaaagag atattaccat
     4381 gacgattgct tcgccagctc ttatgtatat acttgttttt attgatgatt taagtccttg
     4441 tgaaaaggcg ttgtttataa ccaatgcaac accaggtcct attgatatag tttgagataa
     4501 agttacgata gcaaatgaaa ataatgttga atattccata tttacttacc atgatatatt
     4561 tcgcgggagc ttttcatata catattccat aggaattgcg gctttcggta ataaatttat
     4621 aaatgtggat atgtgcttta gtgaattgct ggcggcgatt gagtaaaaat ttccgctatt
     4681 ccaatatatt gatgcgtatt taaaatgttg tttaattgcg gaaatcatat catcaacact
     4741 aacttcattt aaattcattg tgttgagtac gatttccttt tttgtgttaa tctcatcttt
     4801 cgagaaatac ctttgtttga atgagtaatc tttttggatt tctctttttt gatattcatc
     4861 atgttctgag ctatgttttt ctgtaaatat gaaaatacca tcattattta atagtctttt
     4921 tacgtggttt atttgaccag atctgtttgg tgagtacatt tgaaatgtgg tatcttctat
     4981 tataatatcg aatccttgat taaattggtt aaggtttgat tttttcagtt tttcttccaa
     5041 caggaaaaaa ggagtgcaaa taaaataagc attttcactt gagccataat taaaaaatgc
     5101 atgttcattt tcttttgttg gactggttgt taatgtttgt atgtttcctt ttgataattc
     5161 tgaaatggtt cttgccattg ctccctcagc cataccaaga caccatgcgt ttaatttttt
     5221 atttagtgtt gttgcgtatt ttattactgt tgttcctaat ctgcattctt cttccttgct
     5281 gtatggtatg ctgcaaaaat aatgattaac gaaagggccg ctgttttttg tgaggttttt
     5341 gccaaactta atgtaatcat aagaatgaaa aagccgctca tctatttcta ctagtctaaa
     5401 aggtttgtgt ttttcccctg atgcagttga tgagaaaaat tcttccatgc catttattct
     5461 cggagcggat atacattcat ttataaagtc attcattttt ctatcctctg gtctgagttt
     5521 ttgcatttgt tgttatgact atttaatgct aattatcaga taaccttttt tacacgccat
     5581 aaacacgatt atgattgatg ttttatattg tcgatatttc gttgtccaga ctgtatatgt
     5641 ttggaaattt gtttgcatac gggttcgttc cgtttagctg gctttttgga tgagaaagtt
     5701 tgctgttttg acccgttcgc gcttctga
//
