LOCUS       CP056658                4315 bp    DNA     circular BCT 16-MAY-2022
DEFINITION  Escherichia coli strain RHBSTW-00204 plasmid pRHBSTW-00204_4,
            complete sequence.
ACCESSION   CP056658
VERSION     CP056658.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148538
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4315)
  AUTHORS   AbuOun,M., Jones,H., Stubberfield,E., Gilson,D., Shaw,L.P.,
            Hubbard,A.T.M., Chau,K.K., Sebra,R., Peto,T.E.A., Crook,D.W.,
            Read,D.S., Gweon,H.S., Walker,A.S., Stoesser,N., Smith,R.P.,
            Anjum,M.F. and On Behalf Of The Rehab,Consortium.
  TITLE     A genomic epidemiological study shows that prevalence of
            antimicrobial resistance in Enterobacterales is associated with the
            livestock host, as well as antimicrobial usage
  JOURNAL   Microb Genom 7 (10) (2021)
   PUBMED   34609275
REFERENCE   2  (bases 1 to 4315)
  AUTHORS   Shaw,L.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (12-JUN-2020) Nuffield Department of Medicine, University
            of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.7
            Assembly Name                     :: WTP3 T1-00204
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 111.15921851906x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 00:19:50
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.11
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 4,735
            CDSs (total)                      :: 4,617
            Genes (coding)                    :: 4,439
            CDSs (with protein)               :: 4,439
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 178
            CDSs (without protein)            :: 178
            Pseudo Genes (ambiguous residues) :: 0 of 178
            Pseudo Genes (frameshifted)       :: 63 of 178
            Pseudo Genes (incomplete)         :: 91 of 178
            Pseudo Genes (internal stop)      :: 42 of 178
            Pseudo Genes (multiple problems)  :: 17 of 178
            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..4315
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00204"
                     /isolation_source="Wastewater influent sample"
                     /db_xref="taxon:562"
                     /plasmid="pRHBSTW-00204_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(3691..4315,1..290))
                     /locus_tag="HV121_23610"
     CDS             complement(join(3691..4315,1..290))
                     /locus_tag="HV121_23610"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016243916.1"
                     /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="QLU12361.1"
                     /translation="MLNKIQLPDEIKKNTVTNGNSISLIKKLPSQYAHLILSDIPYGIG
                     AEDWDVLHNNSNNAYLGSSPAQKNAGAIFKKRGKPINGWSEADKKIPLEYQQWCEEWAT
                     EWFRVLKPGASAIIFAGRRFSHRCICAMEDAGFNLRDIIAWMRVKAPHRAQRLSCVYER
                     RGDTLNAEKWNGWRVGNLQPTFEPILWFSKPYKIGGTIADNAIIHGVGAYNQDAFVARN
                     GKPENVITAGFSSNESGLHPTQKPVALMKTLIELTTQKGQLVIDPFSGSGSTLVAAKDL
                     GRDYIGFEINPTYVETSIKRLNK"
                     /name="site-specific DNA-methyltransferase"
     gene            complement(1311..1505)
                     /locus_tag="HV121_23615"
     CDS             complement(1311..1505)
                     /locus_tag="HV121_23615"
                     /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="QLU12362.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2336..2629
                     /locus_tag="HV121_23620"
     CDS             2336..2629
                     /locus_tag="HV121_23620"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000129682.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QLU12363.1"
                     /translation="MNRSDMNYHDYSWTAVQGDNPRMTKLDATRFSRHEGYEVLDLINS
                     FQAKGGGALTLKSQQIIEWMLHERLPSNIQGRAQVKAWVVDNFSQMKDGYPF"
                     /name="hypothetical protein"
     gene            2767..3690
                     /locus_tag="HV121_23625"
     CDS             2767..3690
                     /locus_tag="HV121_23625"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000362418.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HindIII family type II restriction endonuclease"
                     /protein_id="QLU12364.1"
                     /translation="MDLTNIEFINDAAINRRRYWTNEIVKLSGHFVNDSSRVEEEIIYE
                     VSKSGSQALLDHLRLCTAIPESYEHDSSEEKLYSKYTDALISECFKFFGLNSIVLTERA
                     DAADVEVVCDSYSFVADAKVFRLSRTAKNQKDFKVQAMDGWRNTKDFAMVVCPIYQLPV
                     KSSQIYQQAILRNVCVFTYTHLAVLVKYADIVGSDVRILLEEIFRSVILMNPSKDSVQY
                     WTMINRTMLNYDKRIEKLWIDERIATSEGIYVLKKMAIEYLSSERGRILSMSREEAVRA
                     LIKMNKIESRIEQIKKVTDNNILSLK"
                     /name="HindIII family type II restriction endonuclease"
     Typing          1154..1238
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.349"
                     /coverage="100.0"
                     /evalue="1.42e-30"
     Typing          1542..1640
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          1765..2020
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(584..1143)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.204"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgctgatatt ctaatggtat tttcttatca gcctctgacc atccatttat tggttttcct
       61 ctttttttaa aaatagcacc tgcgtttttc tgcgcagggc ttgaacctag gtatgcgtta
      121 tttgagttat tatgtagcac atcccagtct tctgctccta tcccataagg gatatcactg
      181 agtattaaat gtgcatattg tgatgggagt ttttttatta atgatatcga gttaccattg
      241 gtaacggtat tcttttttat ttcatcaggt aattggatct tgtttaacat ctaaattcct
      301 gctctttcat agctttaaaa acacgctgat agtatacgtt aaagtacctt gacgcaggat
      361 tacctttcat cgtagccttt ctgaaaagaa aaaaccgcct tgcagggcgg ttttttcaag
      421 gttcaaagaa cttgcaggtt tttgaaccac ggtaactggc tttgtgggag cgcagtcacc
      481 aaaatctgtt ctttcagttt agccttaact ggcaagaaac ttcaagacca actcccataa
      541 aaccgttacc agtggctgct gccagtggcg ttaaggcgtg tcttaccggg ttggactcaa
      601 gacgatagtt accggataag gcgcagcggt cgggctgaac ggggggttcg tgcacacagc
      661 ccagcttgga gcgaacgacc tacaccgaac tgagatacca acagcgtgag ctatgagaaa
      721 gcgccacgct tcccgaaggg agaaaggcgg acaggtatcc ggtaagcggc agggtcggaa
      781 caggagagcg cacgagggag cttccagggg gaaacgcctg gtatctttat agtcctgtcg
      841 ggtttcgcca cctctgactt gagcgtcgat ttttgtgatg ctcgtcaggg gggcggagcc
      901 tatggaaaaa cgccagcggc gcggcctttt gtcctggctt tgcctttttg ctcacatgtt
      961 ctttccggcc ttatcccctg attctgtgga taactgtgtt accgtttttg tgtgagtcag
     1021 taccgctcgc cgcagccgaa cgaccgagcg tagcgagtca gtgagcgagg aagcggaaaa
     1081 gcgcctggac gtgcattttc tccttacgca tctgtgcggc atttcacacc cggcatgggg
     1141 cacttttcat acaatctgca ctgatgccgc atggttaagc cagtatacac tccgctgtcg
     1201 ctacgcgact gggtcagggt ttcgccccga cacccgctga cgcgccctgg cgggcttgtc
     1261 tgctgccgaa aacgctcgcg gacaagccgt gagcgcctcc gtcagcttcg ttatgttcct
     1321 gtttcacttt cagtctcaaa gcgaacctgg atgctgttct ggagttcttc cgcgagttcg
     1381 tgcagtcgtt cgcacatggc cgcctgttcg tcggcatcca gagcatccag tttttcaagc
     1441 agtgtcaggc tctggctttt gataaatcgc gccatattca gcgcagtttg ttgctgtttg
     1501 ttcaccttcc gttgttctcc gtcagtaccg ggtgtcgggt ggaccctgac caggtggtaa
     1561 ttgtaagacg ttgcgggcga cggtattaca attgcacatc ctgtcctgtt tttttaggac
     1621 gtatcatggc acagcatatc aactgataaa taatccctgt gcagtgcagc cgctgttgca
     1681 taaaatttcg ctctgcgtcg agtgtttctt aatcaataat tccgctgata ctccggaaaa
     1741 acgcgagtct gttctcatgc ctgaaatgcc cacaccccac gcaaaaacaa ttttttgctg
     1801 atttttcttt ataaatagag agttatgaca aattagttct tcttgctctc tttgtgatat
     1861 ttaaaaaagc ggtgtcggcg cggtgttgta gctgcgccaa caccgctttt taggggtggt
     1921 actgactatt ttcataaaaa acatcatttt atattagggg tgctgctagc ggcgcggtgt
     1981 gtttttttac aggacgcccc tgggggcgct gctaggggtg tctgttcaga tatgtagcaa
     2041 tgagtcaggg attcacgaac tgaaaatgtc cgaaaatgtg tctcatgggc accgtatgcg
     2101 cccaaaccga tcgccattca ctttcatgca tagctatgca gtgagctgaa agcgatcctg
     2161 acgcattttt ccggttttcg cttggtaaaa catctctttt tgcggtgttc gcggcagaat
     2221 cgcgttcagc gcgttttagc ggtgcgcgta atgcgacgtt atggtaaatg aggctgttga
     2281 gttattaatg ttatgtcgta atgtacgtat ataattcagg cgaagatgag aaaagatgaa
     2341 tagatctgat atgaattacc atgattactc atggacggct gtacaaggag ataatccacg
     2401 aatgactaag ctagatgcca cgcgctttag ccgtcatgag ggttatgagg tgttagattt
     2461 gattaattcc ttccaggcca aagggggtgg tgctctgacg ctaaaatcac agcagattat
     2521 cgagtggatg ctacatgaac gcctgccatc caatatccag gggcgagctc aggttaaagc
     2581 gtgggtggtt gataacttct cgcaaatgaa ggatggttat ccattctgat aaaaagcccg
     2641 ctacagcggg ctttttcatg agctgtgctc aatgaggcat tatggtaaat tgttatggag
     2701 tgggcatgtc tgtatatgat gcctggtggt atgattttgt ttgtaacact ggaaggttgt
     2761 tggaatatgg atttaacaaa tattgaattt attaatgatg ccgcaataaa taggaggcgt
     2821 tactggacta atgaaattgt caaattaagt gggcattttg ttaatgactc cagtagggtt
     2881 gaggaggaaa ttatttatga agtttccaaa tctggatctc aggctttatt ggaccacctt
     2941 cgattatgca cagccattcc tgaatcatat gagcatgatt caagcgaaga aaagttatat
     3001 tcaaagtata cagacgcatt gatttctgaa tgttttaagt tttttggttt gaatagcatt
     3061 gtgttaactg agagggctga tgcggcagat gtagaagttg tatgtgatag ttattctttt
     3121 gttgctgatg ctaaagtttt tcggttaagt cgaacagcta aaaatcagaa agattttaaa
     3181 gttcaagcaa tggatggttg gaggaatact aaagatttcg ccatggttgt ttgtccaata
     3241 tatcagctcc cagttaaatc aagtcaaata tatcaacaag ctattcttcg caatgtgtgt
     3301 gtgtttactt atactcattt agctgttctg gtaaagtatg ctgacattgt tggtagtgat
     3361 gttaggatat tgttagagga aatattcaga tctgtcatac tcatgaatcc aagtaaggat
     3421 agtgtgcagt actggactat gattaataga acgatgttga attatgataa gagaatagaa
     3481 aaactttgga ttgatgagcg aattgctaca tcagagggta tctatgtgct gaaaaagatg
     3541 gcaatagaat acctctcttc cgagagaggt agaattctaa gcatgagcag agaagaggct
     3601 gtaagagctt tgattaaaat gaataaaatt gaaagtagaa ttgagcagat taaaaaagtg
     3661 acagataata atattctgtc acttaaataa ttatttgttt aatctcttta tactggtctc
     3721 tacatatgta gggtttattt cgaaaccaat ataatcccta cctaaatctt tcgctgctac
     3781 caatgtagaa ccactgccac taaaagggtc aatgactaat tgaccttttt gtgttgttaa
     3841 ttctataagt gttttcatta aggctacagg tttttgtgtt gggtgtaatc cactttcatt
     3901 gctggaaaat ccagctgtaa tgacattttc aggtttgcca tttcttgcta caaatgcatc
     3961 ttgattataa gcaccgacac catgaataat tgcattatct gcaattgtgc cgccaatttt
     4021 atatggttta gagaaccata gtatgggttc aaaggttggt tgtagatttc caactcgcca
     4081 tccattccat ttttctgcgt ttaatgtatc cccgcgcctt tcgtaaacgc aactcaacct
     4141 ttgggctctg tgaggggctt ttactctcat ccatgcaatt atatcgcgaa gattgaatcc
     4201 agcatcttcc attgcacata tgcatcgatg agaaaatctt ctgcctgcaa aaataattgc
     4261 actggcacct ggttttaata ctctgaacca ttcagtagcc cattcttcac accat
//
