LOCUS       CP091403                6760 bp    DNA     circular BCT 09-MAR-2022
DEFINITION  Escherichia coli strain 623214 plasmid p623214_2, complete sequence.
ACCESSION   CP091403
VERSION     CP091403.1
DBLINK      BioProject: PRJNA315192
            BioSample: SAMN10281498
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6760)
  AUTHORS   Bird,M.T., Greig,D.R., Nair,S., Jenkins,C., Godbole,G. and
            Gharbia,S.E.
  TITLE     Use of Nanopore sequencing to characterise the genomic architecture
            of mobile genetic elements encoding blaCTX-M-15 in Escherichia coli
            causing travellers diarrhoea
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6760)
  AUTHORS   Ashton,P.M., Dallman,T., Nair,S., De Pinna,E., Peters,T. and
            Grant,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-OCT-2018) Public Health England, 61 Colindale Avenue,
            London NW9 5EQ, United Kingdom
REFERENCE   3  (bases 1 to 6760)
  AUTHORS   Greig,D.R. and Jenkins,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-JAN-2022) Gastrointestinal Bacteria Reference Unit,
            Public Health England, 61 Colindale Avenue, London, London NW9 5EQ,
            United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 04-OCT-2020
            Assembly Method                   :: Flye v. v2.7
            Assembly Name                     :: 623214
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 81.86x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 01/24/2022 11:09:21
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 5.3
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 5,311
            CDSs (total)                      :: 5,184
            Genes (coding)                    :: 4,900
            CDSs (with protein)               :: 4,900
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 284
            CDSs (without protein)            :: 284
            Pseudo Genes (ambiguous residues) :: 0 of 284
            Pseudo Genes (frameshifted)       :: 139 of 284
            Pseudo Genes (incomplete)         :: 177 of 284
            Pseudo Genes (internal stop)      :: 62 of 284
            Pseudo Genes (multiple problems)  :: 76 of 284
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..6760
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="623214"
                     /serovar="Escherichia coli"
                     /isolation_source="human"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p623214_2"
                     /geo_loc_name="United Kingdom: United Kingdom"
                     /collection_date="2018-10"
                     /collected_by="PHE"
     gene            1..2637
                     /locus_tag="EBM07_26540"
     CDS             1..2637
                     /locus_tag="EBM07_26540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012443154.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DEAD/DEAH box helicase family protein"
                     /protein_id="UJY29265.1"
                     /translation="MAKKPKSAGREKLLFNKLKQFDEPGLFHDNYQTPDYIQANLKDIL
                     RPYQHSALRYLHYTQRKRDDALLHYRHLLFHMATGAGKTMVMAGTILYLFKEFGYQNFI
                     FFVHTDAIIQKTRENLLNPQSPKYLFSHELEIDGEKITIAPVDIFPSVPERNTIYLKLS
                     TIHKMHDELNSYRENSITYEDLKEIPLVLLGDEAHHFNAGTKARGKSKTSPENEEQTWE
                     RTIENILDLRPDNRLFEFTATIDLANKDIGQKYRDKVVYQYDLKQFMSDGYSKKVMLLE
                     ANQNDSDKMLDAVLLSQYRKLTAADHGITGFKPVILFKSNKIAISKAKQEEFSQLIAAM
                     TPESIRRHLANKKLQLSSDTSIWHKVIQRYADSDLVTVTGQIQEDFNDFNLLNVNKSDL
                     LEENPVLLNTLEEVDNPVRAVFAVAKVNEGWDVLNLYDIVRISEQASSSKTSTDSEAQL
                     IGRGARYYPFIYDGQRSFTRRFDNSTKDLSVLEQLHYHTINEPAYIKTLHASLEQADID
                     VHQDGGGTVEHARLKEDFKKSAVYQAGKLYFNEVEEIERSSRNWETYSLETRFEIQYQI
                     ACEESLDNLTGTKGGIIKPEPLVLDERFYRKAMQRISFYALDNLKRFFPKLTGIREFIR
                     SDAYLGKLKITVSVPQSLDFTTVPAKDKLHLLENVLLRISENVRRNDQKVKGTYRFISQ
                     PVKEVIKDYSLHIDPSVAINQKITAAPTIGKKWYVYDNAILNQLEHRLIKMLEAFMPKL
                     KARYDDIYVLRNDEQSTRFKLTEFGGVRGFMPDFIMILTRHSDNTYWQVFLEPKGDDRL
                     LDDAWKERMLETLNDRERIVIDENEHVRLVGIKFFANSQMDVFVSDMQNKLNDGESLET
                     SSLSLPL"
                     /name="DEAD/DEAH box helicase family protein"
     gene            complement(3039..3152)
                     /locus_tag="EBM07_26545"
     CDS             complement(3039..3152)
                     /locus_tag="EBM07_26545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="UJY29266.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLSPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(3817..4011)
                     /locus_tag="EBM07_26550"
     CDS             complement(3817..4011)
                     /locus_tag="EBM07_26550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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="UJY29263.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4891..6756
                     /locus_tag="EBM07_26555"
     CDS             4891..6756
                     /locus_tag="EBM07_26555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006816428.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific DNA-methyltransferase"
                     /protein_id="UJY29264.1"
                     /translation="MQTELIKELNKVLKAFPQFWNGEELQRSMVSDAISQKQPDLIKAL
                     VDNEKVRSVYGVDIDGIFIFDFDKLCGLLKYKEYWANSFTKYRNKVGLTSEGKYLDYSS
                     DVVLDFPFKDCILEGGMTKENQGKDEIYYNEIIAMDEVDSLLSPKAFTNAKRYTKEGVK
                     ENITKFNDDENLIIKGNNLIALHSIKKLYAGKVKLIYIDPPYNTGSDSFKYNDRFNRST
                     WLTFMKNRLEVAKEMLSDDGFIFIQCDDNESAYLKVLCDSIFGEENYRNSIYWHRTYAG
                     KTVKSKLPWNTDTILFYSKKESSLLEPYTAELSAADIKSYNKDDFDGRGKYNTVSLQKT
                     SSPGPQTTYDYIDNTGKKWSCPEKGWRMTKEKLKALENDNRLYITDKTIREKYYLKERK
                     EIGKQIDNFWHDIGNLNRVSDVAFIDGQKTEKLMQRIISLASKENDIVLDFHLGSGTSA
                     AAAHKMGRRYIGIEQMDYINEITVPRLQKVIEGEQGGISKDVNWQGSGSFVYVELVELN
                     AYFIHEIQKAQSTEELEKLFAVMKTEAYLNYQVALENVLSAEYEVDGILHKVAFSELEL
                     HEQKQLLIEILDKNQLYVNVSDMEDSDLNISESDKAFTRSFYGME"
                     /name="site-specific DNA-methyltransferase"
     Typing          3652..3737
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          4048..4146
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          4271..4526
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.86"
                     /coverage="89.0"
                     /evalue="1.25e-96"
     Typing          complement(3081..3634)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.075"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atggcgaaga aaccgaagtc agcaggtaga gagaagctgc tgtttaacaa gctgaagcag
       61 ttcgatgaac caggactgtt ccacgataac tatcagacgc cggactatat tcaggcaaac
      121 ctgaaagata tcctgcgtcc ctatcagcac agcgcactgc gttacctgca ttacacgcaa
      181 cgtaaacgtg atgacgcgct tctgcattac cgtcacctgc tgtttcacat ggcaaccggt
      241 gcagggaaaa cgatggttat ggcaggaacg atactctatc tatttaaaga gttcgggtat
      301 cagaacttca tctttttcgt acataccgac gcgattatcc agaaaacgcg agagaaccta
      361 cttaacccgc aatcgccgaa gtacctgttc agtcatgagc tggaaatcga cggggaaaaa
      421 atcaccatcg caccggtaga tatattcccg tccgtaccgg aacgcaacac gatttacctc
      481 aagctctcga ctatccataa gatgcacgat gagctgaaca gctatcgaga gaacagcatt
      541 acctacgagg atttaaaaga aatcccgctt gtgctactcg gtgacgaggc gcatcacttc
      601 aacgccggca ccaaagctag aggcaagtcg aaaacctcac cggagaacga ggagcagact
      661 tgggagcgta cgattgagaa catcctcgac ctgcgaccgg ataaccgcct gttcgagttc
      721 accgctacca ttgaccttgc aaacaaagat atcggacaga aataccgtga caaggtggta
      781 tatcagtatg atctgaagca gttcatgtca gacggttact cgaaaaaggt catgctgttg
      841 gaagcaaacc agaacgacag cgacaagatg ctcgatgcgg tactgttaag ccagtaccgt
      901 aaactgacgg cagcagatca cggcatcacc ggctttaaac cggtcattct gttcaagtcg
      961 aataagattg cgatatcaaa ggcgaagcag gaggagtttt cgcaactgat tgccgccatg
     1021 acacctgaga gcatcagacg tcatctggct aacaaaaaac tccagctcag ctctgacacc
     1081 agtatctggc ataaagtgat tcagcgttac gctgacagtg atttagtgac ggtgactgga
     1141 caaattcagg aggactttaa cgactttaac ctgctgaacg tcaacaagtc agacctgctg
     1201 gaggaaaacc ccgtcctgct gaatacactg gaagaagtcg ataatccagt gagagccgtc
     1261 tttgctgtcg cgaaggtgaa tgaaggctgg gacgtactta acctctacga tattgttcgc
     1321 ataagcgagc aggcgagcag cagcaaaacc agcacggaca gcgaagcgca gcttattggg
     1381 cgaggtgcgc gttactaccc gttcatttat gacggtcaac gtagcttcac ccgccgtttt
     1441 gataacagta cgaaggattt gagcgtactg gagcaactgc actatcacac catcaatgaa
     1501 ccggcgtaca tcaaaacact gcacgcctct ctggagcagg cggacattga cgtgcatcag
     1561 gatggcggag gtacggttga acacgccaga ttgaaagaag actttaaaaa gtccgccgtg
     1621 tatcaggcgg gtaagctgta ctttaacgaa gtggaagaga ttgagagaag cagccgaaac
     1681 tgggaaacct actcgctgga aacacgcttt gaaatacagt atcagatcgc ttgcgaggag
     1741 tcgctggaca acctgacagg cacaaagggg ggtatcataa aaccggaacc actggtactg
     1801 gacgagcgtt tttaccgcaa ggcgatgcaa agaatcagct tttacgcgct agataacctg
     1861 aaacgcttct tcccgaaact gacaggtatt cgggagttca tacgcagtga cgcctatctt
     1921 ggtaagctga aaatcaccgt cagcgtaccg cagtcactgg atttcaccac cgtaccggca
     1981 aaagataagc tgcacctact ggaaaacgtt ttgctgcgta tctcagagaa tgtgcgtcgc
     2041 aatgaccaga aggtaaaagg cacgtaccga tttatcagcc agccggtgaa agaggtgatt
     2101 aaagattaca gtttgcatat tgacccgtcg gtagccatta accagaaaat caccgccgct
     2161 cccaccattg gtaaaaaatg gtacgtgtac gataatgcga tactaaatca gcttgagcat
     2221 cgtctgataa aaatgctgga agcattcatg ccgaagctaa aagcgcgtta tgacgatatt
     2281 tacgtactgc gtaacgacga gcagtcaacg cgctttaagc tcacggagtt cggcggcgtg
     2341 cgtgggttta tgccagattt catcatgata ctgacgcgcc attcagacaa cacttactgg
     2401 caggtgttcc ttgaaccgaa gggggatgac cgtctgctgg atgacgcatg gaaagaacgg
     2461 atgctcgaaa cactgaatga cagggagcgc attgtaattg atgaaaatga gcacgtcaga
     2521 ctggttggga ttaaattctt tgccaatagc cagatggacg tttttgtcag cgacatgcag
     2581 aacaagctga atgatggaga atcgctcgaa acctcctcgc tctccctacc actgtaagtc
     2641 acgacaataa aataacggag cattacgctc cgttatttta ttgttatctc gaactacctc
     2701 ccagggaggt gatgattgct cctgtaatgg ttgcattgtt tgttcttgct gttgcgaatc
     2761 attagttttg aatggtggtt aaaaaccgtt cgctatgttt atgcctgggg gggggatgag
     2821 ggggaaaaga ttcaaggatc ctcttgtgat cctttttttc tgcgcgtaat ctgcagcctg
     2881 taaacgaaaa aaccaccctg gcaggtggtt tttcgaaggt tagctaatcc tggcagatta
     2941 tctaaccggg taactggctt ggaggagcgc agtcaccaaa atctgttctt tcagtttagc
     3001 cttaacaggt gcataacttc aagacaaact cctctaaatc agttaccagt ggctgctgcc
     3061 agtggcgata agtcgtgtct taccgggttg gactcaagac gatagttacc ggataaggcg
     3121 cagcggtcgg gctgaacggg gggttcgtgc acacagccca gcttggagcg aacgacctac
     3181 accgaaccga gataccaaca gcgtgagcta tgagaaagcg ccacgcttcc cgaagggaga
     3241 aaggcggaca ggtatccggt aagcggcagg gtcggaacag gagagcgcac gagggagctt
     3301 ccagggggaa acgcctggta tctttatagt cctgtcgggt ttcgccgact ctgacttgag
     3361 cgtcgatttt tgtgatgctc gtcagggggg cggagcctat ggaaaaacgc cagcggcgcg
     3421 gcctttttcc ggttcctgct cttttgctca catgttcttt ccggccttat cccctgattc
     3481 ggtggataat ctaattactg tctttgcgtg agttgatacc gctcgccgca gccgaacgac
     3541 cgagcgtagc gagtcagtga gcgaggaagc ggaagagcgt cggaagttgc attttctcct
     3601 tacgcatctg tgcggcattt cacatcggtt atggtgtact tttcatacaa tctgcactga
     3661 tgccgcatag ttaagccagt atacactccg ctatcgctac gtgactgggt catggctgcg
     3721 ccccgacacc cgctaaaacc ccctgacgcg ccctgacggg cttgtctgct gacgaaaacg
     3781 cccacgggaa agccgtgacc gcctccgtca gcttcgttat gttcctgttt cactttcggc
     3841 ctcaaagcga atctggatgc tgttctggag ttcttctgcg agttcgtgca gtcgttcgca
     3901 catggccgcc tgttcgtcgg catccagagc atccagtttt tcaagcagtg tcaggctctg
     3961 gcttttgata aatcgcgcca tattcagcgc agtttgttgt tgtttgttca ccttccgttg
     4021 ttctccgtca gttccgggtg tcggggggac cctgagcagg tggtaattgt aagacgttgc
     4081 gggcgacggt attacaattg cacatcctgt cctgtttctt taggacgtat catggcacag
     4141 catatcaact gataaataat ccctgtgcag tgcagccgct gttgcataaa atttcgctct
     4201 gcgtcgagtg tttcttaatc aataattcct ctgatactcc ggaaaaacgc gagtctgttc
     4261 tcatgcctga aatgcccaca ccccacgcaa aaacaagttt ttgctgattt ttctttataa
     4321 atagagagtt atgacaaatt agttcttctt gctctctttg tgatatttaa aaaagcggtg
     4381 ttggcgcagc tacaacaccg cgccgacacc gctttttagg ggtgttactg actattttca
     4441 taaaaaacat catcttatat taggggtgct gctagcggcg cggtgtgttt ttttacagga
     4501 cgcctctggg ggcgctgcta ggggtgtctg ttcagatatg tagcaatgag tcagggattc
     4561 acgaactgaa aatgtccgaa aatgtgtctc atgggtactg tatgcgccca aaccgatcgt
     4621 cattcacttt catgcatagc tatgcagtga gctgaaagcg atcctgacgc atttttccgg
     4681 tttaccccgg ggaaaacatc tctttttgcg gtgtttgcgg cagaatcgcg ttcagcgcgt
     4741 tttagcggtg cgcgcaagag cgtttatgtt aaatactact cgttctggtg cattttcccg
     4801 caactgaatc caactcatcg ctgttgggtt ccagcgccga acgctatacc ttacaatcat
     4861 tccaatattt aacagtcata aggccatgac atgcagaccg aattaataaa agaacttaac
     4921 aaggttttaa aagcgttccc gcaattctgg aatggagagg aattacaacg ttcaatggtg
     4981 agtgacgcta tcagtcaaaa gcagccagat cttatcaagg cattagtcga taatgaaaaa
     5041 gtccgctctg tttatggtgt ggatattgat ggcattttta tctttgattt tgacaaatta
     5101 tgtggtcttc taaaatacaa agaatattgg gctaatagct ttactaaata ccggaacaaa
     5161 gtgggattaa ctagcgaagg taaatacctt gattacagtt ctgatgtggt gctggatttt
     5221 cctttcaagg attgtattct tgaaggtgga atgaccaaag aaaatcaggg aaaagatgag
     5281 atttattata atgaaatcat agcaatggat gaagttgact ctttgctttc tcccaaggcg
     5341 ttcactaatg ctaagcgata taccaaagag ggggtaaaag aaaatatcac taaatttaac
     5401 gatgatgaaa atttaataat taagggaaac aatctcattg cactacattc aataaaaaaa
     5461 ctttacgcag gaaaagtaaa gttaatttat atagacccgc cttacaatac agggagtgat
     5521 agctttaagt ataatgatcg attcaatcgc tcaacatggt tgacattcat gaaaaatagg
     5581 cttgaggtgg ctaaagaaat gctttccgat gatggcttta tttttattca atgcgatgat
     5641 aatgaatcag catatcttaa agttttatgt gattcaattt ttggagaaga gaattataga
     5701 aactcaatct attggcatag aacctacgca gggaaaactg taaaaagtaa gttgccatgg
     5761 aatacagata caatattgtt ttattctaaa aaagaaagtt cattattaga gccatataca
     5821 gcagaactta gtgctgctga cattaaatcc tataacaagg atgattttga tggaaggggt
     5881 aaatacaaca ctgttagctt gcaaaaaaca agctctccag ggccgcaaac aacttatgat
     5941 tatatagata atacaggtaa gaaatggagt tgccctgaaa aagggtggag aatgacaaag
     6001 gaaaagttaa aggctttgga aaacgacaat aggctatata tcactgacaa aacaatacga
     6061 gaaaaatatt atcttaaaga aagaaaagag atcgggaaac aaatagataa tttttggcat
     6121 gacattggga atttaaatag ggtttccgat gttgctttta ttgatggaca aaaaactgaa
     6181 aaattaatgc aacggataat tagccttgct tccaaagaaa atgatatcgt cttggacttt
     6241 catctcggca gcggaactag cgcagcagca gcccataaaa tgggacgtcg ctatatcggt
     6301 attgagcaga tggattacat caatgagatc accgtgccac gtttgcaaaa agtcattgag
     6361 ggtgagcagg gaggtatctc aaaagacgtc aactggcagg ggagcggcag ctttgtctac
     6421 gttgaactag tggaactgaa cgcttacttc atacatgaaa tccagaaagc gcagtccacg
     6481 gaagaactcg aaaaactctt tgccgtgatg aagacagagg catatctcaa ctatcaggtg
     6541 gctctggaaa atgtgctgtc cgctgagtac gaagtggatg ggatcctcca taaggtagca
     6601 ttcagtgaac tggaactgca tgagcagaag cagcttttga ttgaaatcct agataagaac
     6661 cagctctacg tgaatgtctc tgatatggag gacagcgacc tgaacatttc agagagtgat
     6721 aaagccttta cccgcagctt ctacggaatg gagtgacggc
//
