LOCUS       NZ_CP062785             5091 bp    DNA     circular CON 18-JUN-2023
DEFINITION  Escherichia coli O157:H7 strain Z869 plasmid pZ869-3, complete
            sequence.
ACCESSION   NZ_CP062785
VERSION     NZ_CP062785.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16327587
            Assembly: GCF_017165395.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli O157:H7
  ORGANISM  Escherichia coli O157:H7
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5091)
  AUTHORS   Fitzgerald,S., Lupolova,N., Shaaban,S., Dallman,T., Greig,D.,
            Allison,L., McNeilly,T., Bono,J.L. and Gally,D.L.
  TITLE     Large chromosomal rearrangements associated with recombination
            between homologous prophage regions are a common feature in E. coli
            O157 strains and promote phenotypic plasticity in the population
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5091)
  AUTHORS   Bono,J.L., Gally,D.L. and Fitzgerald,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-OCT-2020) Meat Safety and Quality Research Unit,
            United State Department of Agriculture, State Spur 18D, P.O. Box
            166, Clay Center, NE 68933, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. 3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 255.23561396321267x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/18/2023 01:59:00
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,916
            CDSs (total)                      :: 5,776
            Genes (coding)                    :: 5,456
            CDSs (with protein)               :: 5,456
            Genes (RNA)                       :: 140
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 110
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 320
            CDSs (without protein)            :: 320
            Pseudo Genes (ambiguous residues) :: 0 of 320
            Pseudo Genes (frameshifted)       :: 115 of 320
            Pseudo Genes (incomplete)         :: 189 of 320
            Pseudo Genes (internal stop)      :: 66 of 320
            Pseudo Genes (multiple problems)  :: 43 of 320
            Pseudo Genes (short protein)      :: 4 of 320
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP062785.1.
            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..5091
                     /organism="Escherichia coli O157:H7"
                     /mol_type="genomic DNA"
                     /strain="Z869"
                     /serotype="O157:H7"
                     /isolation_source="Bovine Faeces"
                     /db_xref="taxon:83334"
                     /plasmid="pZ869-3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2002"
                     /collected_by="IPRAVE Consortium"
     gene            join(4832..5091,1..187)
                     /locus_tag="ILQ35_RS29180"
                     /old_locus_tag="ILQ35_29195"
     CDS             join(4832..5091,1..187)
                     /locus_tag="ILQ35_RS29180"
                     /old_locus_tag="ILQ35_29195"
                     /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_000184721.1"
                     /translation="MTNREDWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPRNHPKWQEWEKRGKELLTKDSA"
                     /name="conjugal transfer protein TraD"
     gene            complement(381..1316)
                     /locus_tag="ILQ35_RS29185"
                     /old_locus_tag="ILQ35_29200"
     CDS             complement(381..1316)
                     /locus_tag="ILQ35_RS29185"
                     /old_locus_tag="ILQ35_29200"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011666805.1"
                     /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_059331890.1"
                     /translation="MSAALQYFDENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDSSVKA
                     LKYAAAIERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASA
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTPETFAQYVANTHTPEIQAKRGRKGGIAKGEAYADKRFMAL
                     CMLENGYSQKAIAAMLEVSTRTIRNWKSGK"
                     /name="replication initiation protein"
     gene            1843..2931
                     /locus_tag="ILQ35_RS29190"
                     /old_locus_tag="ILQ35_29205"
     CDS             1843..2931
                     /locus_tag="ILQ35_RS29190"
                     /old_locus_tag="ILQ35_29205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001340328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_059331889.1"
                     /translation="MNMNIKYILPLVSSFIISGCDSDGISKVKSSIDYSIDDSMTIGKA
                     FDTRSDCINGTWSEEEDSRGRTVVTYTCDISETGMKIINSEIIKGPESSLTGSIKNNNM
                     EIDNINKSIEMYKQQASLIEQTRKLMIEHVRKLENAFNEDPKISNNINIEPYLNKMLNI
                     ECHQRNEGYSCTTDEECRPYMNGLFSPNVSYDYLEESCQKHILPVYQSYIKNVLPLKSK
                     IKAISFTGMFNYCGRSSEECIKLIDDKFNGFSSYNQKQTQKISFYEDLNTRKNKTLNEC
                     KKILNISDVKLKYYWRVTDTGGVDYLSGELTYRINGENKSVAYNNNLVKYAYVNYTEKQ
                     IPSDYVNSILNQNYETIKNCSY"
                     /name="hypothetical protein"
     gene            complement(3110..4660)
                     /locus_tag="ILQ35_RS29195"
                     /old_locus_tag="ILQ35_29210"
     CDS             complement(3110..4660)
                     /locus_tag="ILQ35_RS29195"
                     /old_locus_tag="ILQ35_29210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001624483.1"
                     /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_059331891.1"
                     /translation="MASYHCTVKTGAKGAALKHADYISRSGEYKSYKSREDLEFSSSGN
                     MPSWAKKNPAELWKAADEFERKNGTAYREIEIALPRELTREQRIELVEDFVQKELGDRH
                     AYQYAIHNPPGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRANSKSPERGGAKKASI
                     PQTAGERKAALVALRSRWADVQNEHLARHGHESRVDHRSLKEQGINRTPEVHLGPVQAA
                     SLNGEQIVAIQERRNAERELKTARDAANAIQQEQEQKQKIKAVEPVRSARSPELLLQYR
                     KVMKTVIQGEARLARLGDANPNALKEHKLLQNAKAKKDSLSEWSRRIYEGARYLDKLGR
                     NVVSAQRELRELQEQRNALNGIRGLFRGADKREIDARILEQKSVLETAEHERNEFRNKL
                     QQAESEWDKENAAFKRTEGYKYVGDLDRYREREILAAASLENTRQKVAEEVSVARSQML
                     SLEPELSISGDEKAQMRHELLAEMAQERQQQEEKALRIQRSWAREASRSNERDQGMER"
                     /name="MobA/MobL family protein"
     Typing          complement(382..1316)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.186"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3114..4660)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.857"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 actctacaag gccgcaggcc tcatgattgt ggcaggactg gtggacagca aaaccggaaa
       61 accaaagttt agtgctgccg aactggtagg cgcactcgca ggaatcgcag agctaccgcg
      121 caaccatcca aaatggcagg aatgggaaaa acgcgggaaa gagctactca ccaaagacag
      181 tgcgtaagag cctccgttca cgttccggtt ccctggtgct tcctcgctca ttcgctcgct
      241 acgctcggtc atgagactgt ggcgagcacg accacctcaa tcatacggca agccgcacca
      301 ttgctgggct gaaaggagaa aaccgccgga aagcccgctg ctcaaaaaga cgccgaaaag
      361 gcgctgttat ctgatatagg ctattttccg cttttccaat tccgaatagt tcgagtggaa
      421 acctccaaca tcgccgcgat agctttctga gaatatccat tctccagcat acatagagcc
      481 atgaaacgct tgtcagcgta ggcttcgcct ttagcgatgc cacctttcct gcctctcttg
      541 gcctgtattt ctggcgtgtg cgtattagcc acatactgtg cgaaagtttc cggcgtgaag
      601 ttcctgtgcg tgtatttcgc aatgctcttg ccaatagccc gacattcagg cggagaaagc
      661 ggaacgggaa gcgatgcgtt gtacatttcg acacgctgaa tcacggcatc aagccactgt
      721 gagaatgctg gccagccctg acgaatcgcc ctgtaagccc atttgcgcgt catttcgaac
      781 aggtggcagt ttcgccccat cccgtaatgt ttatcgatgc tacgacgcgc tgaggcgctc
      841 aaatcgagat aatcagccag ttcatcgagg gtataggctt cctcgcgcca ctccatcacc
      901 tgccattcca ggtggaacgg atttttgcaa atcagtccgc tgtagttcac atcagcacaa
      961 agtttctcac acagcgaacg ttcaatcgca gcggcgtatt tcagcgcctt aaccgagctg
     1021 tccggcgcgg ttctcacggc gatattgagc gcgtagagca ggtgagcatg accgttcaca
     1081 ggatttttta cggtgatgtt cggcgcggga gcgttccggt cgctccagtc aatcgctgcc
     1141 ccctcgcggt caacgtcaaa aaccagccag aactgcgcat gaggctggtt ctgctggatg
     1201 taccgcgcaa gaagcgcacg ccctttgccg gagatgcgaa gaccaaaagc gagatcatcc
     1261 gtgtgatagg gacggtgggg taaattttcg tcgaagtatt gaagcgcggc gctcatgtgt
     1321 tacgattcct tccaggttat cgaccgacat cgcccctgta ttttcgtgaa agtcttggcg
     1381 gatagacacg aatttcaggg gcgtttgttt ttcagtcgct tacactaccc ccaacaacaa
     1441 aacctgtcga gccttcccgc aaaaccgatc catttaccat aactcccgtt gtacgtaccc
     1501 cgtaaaacgc cctcaatcgc tctctgacgc aaaaaacgca aaaagacaag gaaacaccag
     1561 ggtaaaacag aaaaatgcgt cagaattgtt ttcattggcc tgcataacta tgcacgaaag
     1621 cgatgcgcga tcggtttcga ccgcacaaag ctgcgaacgg gtcaaaaaga caaactttct
     1681 catccagaga acggtaaacg ggcgcgaaat cttttcgagc tcaatgaggc gctgagcacc
     1741 aaatagtaag tcggtttata cggtatgcat ggattccatt aacatattgt ttgtattaac
     1801 atatttgcgt tcgttattgt caaataagtc aaaagtgaaa agatgaatat gaacatcaaa
     1861 tacattcttc cattagtatc ttcatttatt atttcagggt gtgactctga tgggataagc
     1921 aaagtaaaat cttccataga ttattccatt gacgactcaa tgactattgg caaggctttt
     1981 gacacaagga gtgattgtat taatggaaca tggagtgaag aagaggatag tcgaggaaga
     2041 actgttgtta catatacttg tgacatcagt gaaaccggca tgaaaataat aaactcagaa
     2101 ataataaaag gccctgagag cagcctgaca ggctctataa aaaataacaa tatggaaata
     2161 gacaacatca ataaatcaat agagatgtac aaacagcaag catcattaat tgagcaaaca
     2221 agaaaactca tgatcgaaca cgtaaggaag ttagaaaacg ccttcaatga agatcccaaa
     2281 atatctaaca atattaatat tgaaccttac ctcaataaaa tgctaaacat agaatgtcat
     2341 cagagaaatg aaggctatag ctgcacaaca gatgaagagt gcaggccata tatgaacggc
     2401 ttgttttcac caaatgtatc atatgattac ttagaagaat catgtcaaaa acacatatta
     2461 ccagtatacc aatcatatat aaaaaatgta ttacccctaa aatctaaaat taaagcaata
     2521 agttttacag gtatgtttaa ctattgtggg agaagctctg aggaatgcat aaaattaata
     2581 gacgataaat ttaatggatt ttcatcttac aatcaaaaac aaactcaaaa aatatcattc
     2641 tacgaagatc taaacacaag aaaaaacaaa acattaaatg aatgcaagaa gatattaaat
     2701 atctcggatg ttaaactaaa atattactgg cgcgtaacag acaccggagg tgttgactat
     2761 ctgagtgggg agctaacata cagaattaac ggggaaaaca aatccgtagc atacaataac
     2821 aacctagtaa aatatgcata tgttaactac acagaaaaac aaataccatc agattatgtg
     2881 aattcaatac ttaaccaaaa ctatgagaca ataaagaact gcagctatta ataccacatc
     2941 tcacttactg gctgtttcac atataacgct tgttaatttc attaacacct gaacagtgag
     3001 tgaatcaaaa cgataaattt tctcattcag aaaacgcttc acgggacacg aaattttttc
     3061 gcgtcccgtg aagcgttggc ggggttcggg gcgcagtccc gatattgctt caacgctcca
     3121 taccttgatc acgttcgtta ctacgtgatg cctccctggc ccaggatcgc tgtatacgca
     3181 gtgccttttc ctcctgttgc tgccgttcct gagccatttc tgccagtaac tcatgtcgca
     3241 tttgagcttt ttcatctcca gatatactga gttcaggctc cagagataac atctggctac
     3301 gggcaacgga tacttcttca gcaacctttt gcctggtatt ctctaaagat gccgcggcca
     3361 gaatctcacg ttctctgtac ctgtccagat ccccaacgta cttatatccc tcggtacgct
     3421 taaaagcagc gttttctttg tcccactcgg attcagcttg ctgtagcttg ttcctgaatt
     3481 cattcctttc atgttcagcg gtttccagca cacttttttg ctccagaata cgcgcatcaa
     3541 tctccctttt gtcagccccc cgaaacaggc cacgaatccc attcaaagca ttgcgttgtt
     3601 cctgtagctc ccgcagctcc ctttgtgcgg aaacgacatt acgccccagt ttgtctaaat
     3661 accgtgctcc ttcatatatt cgcctgctcc attcggaaag agagtctttt ttagctttcg
     3721 cattctgaag cagcttatgt tctttgagcg cattgggatt ggcatcccct aaacgagcaa
     3781 gccttgcctc tccctgaatg accgttttca taaccttgcg gtactgaagc aataactccg
     3841 gtgaacgggc tgaacgaaca ggctcaactg ccttgatttt ttgcttttgc tcctgttcct
     3901 gctgaatggc atttgcggca tctctggcgg tcttgagttc ccgctcggca ttcctccgtt
     3961 cctggattgc aacaatctgc tcaccattca gactggcggc ctgaacgggg ccaagatgaa
     4021 cttctggcgt gcgattgata ccctgttctt tcagcgaacg atgatctacg cgcgactcgt
     4081 gaccgtgtcg cgcaaggtgc tcattctgca catcagccca gcgggaacgt agcgcaacaa
     4141 gggcggcttt tcgctctccg gcggtctggg gaatactcgc cttttttgcg cctccccgct
     4201 ccggtgattt gctgttggcg cgtttaaaaa attgctgcgg atcgcgttca ataccatcat
     4261 taatccgctc gcaaaacatg atatgcgcgt gtggctgttc ctttccgtcg attgcacctg
     4321 gcggattgtg gatcgcgtac tggtaggcat ggcgatcgcc aagttccttt tgcacgaaat
     4381 cttcaacaag ttctatccgt tgttcgcgtg tcagttcacg cggtaatgcg atctcaattt
     4441 cacggtatgc cgtcccgttt tttcgttcaa attcatctgc ggctttccac agttctgcgg
     4501 gatttttctt cgcccatgat ggcatgttac cggatgacga aaactccaga tcctcccgcg
     4561 atttgtagct cttatattcg ccggatctgg aaatgtaatc agcatgtttt aaggctgcgc
     4621 cttttgctcc ggttttaacg gtgcaatggt agcttgccat ctgcctttta gccctccgca
     4681 ggagcgcaca gtttcttgat gaaatcgaga aactactaag tgcgcatccc tgaataaatc
     4741 agggatgatt ttacgttctc acacgcaggc agacaaggtg atattatgca caataacaac
     4801 tcacattaac ggcaaaagtg cagaggtaag gatgacaaat cgtgaagact ggttaagtgc
     4861 aaaaattgcc tacatcaacg gactgaaatc accgtcagag cagcagagat tacttgtgtt
     4921 actggcagag aaaaaaaacc gaacaacgac ggatgaaaaa acgttgtccg cactgatacg
     4981 agcagaaaaa accgcagaga aagcagccgc agcaaaagcc agagtaacgg caatcatagc
     5041 ggcagaacgg aaggcagccg caagggcgga acgaaaggca cgagatcatg a
//
