LOCUS       NZ_CP062777             3306 bp    DNA     circular CON 18-JUN-2023
DEFINITION  Escherichia coli O157:H7 strain Z563 plasmid pZ563-3, complete
            sequence.
ACCESSION   NZ_CP062777
VERSION     NZ_CP062777.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16327583
            Assembly: GCF_017165455.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli O157:H7
  ORGANISM  Escherichia coli O157:H7
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3306)
  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  JOURNAL   Unpublished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 3306)
  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                   :: 208.59433776286156x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/18/2023 02:11:55
            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)                     :: 5,652
            CDSs (total)                      :: 5,516
            Genes (coding)                    :: 5,211
            CDSs (with protein)               :: 5,211
            Genes (RNA)                       :: 136
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 106
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 305
            CDSs (without protein)            :: 305
            Pseudo Genes (ambiguous residues) :: 0 of 305
            Pseudo Genes (frameshifted)       :: 110 of 305
            Pseudo Genes (incomplete)         :: 177 of 305
            Pseudo Genes (internal stop)      :: 67 of 305
            Pseudo Genes (multiple problems)  :: 42 of 305
            Pseudo Genes (short protein)      :: 4 of 305
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP062777.1.
            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..3306
                     /organism="Escherichia coli O157:H7"
                     /mol_type="genomic DNA"
                     /strain="Z563"
                     /serotype="O157:H7"
                     /isolation_source="Bovine Faeces"
                     /db_xref="taxon:83334"
                     /plasmid="pZ563-3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2002"
                     /collected_by="IPRAVE Consortium"
     gene            complement(join(3253..3306,1..141))
                     /locus_tag="ILQ31_RS27915"
                     /old_locus_tag="ILQ31_27930"
     CDS             complement(join(3253..3306,1..141))
                     /locus_tag="ILQ31_RS27915"
                     /old_locus_tag="ILQ31_27930"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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="WP_001041624.1"
                     /translation="MNKQQQTALNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
                     EELQNSIQTRFEVENSTEI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            413..736
                     /gene="mobA"
                     /locus_tag="ILQ31_RS27920"
                     /old_locus_tag="ILQ31_27935"
     CDS             413..736
                     /gene="mobA"
                     /locus_tag="ILQ31_RS27920"
                     /old_locus_tag="ILQ31_27935"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            complement(971..1351)
                     /gene="lsoB"
                     /locus_tag="ILQ31_RS27925"
                     /old_locus_tag="ILQ31_27940"
     CDS             complement(971..1351)
                     /gene="lsoB"
                     /locus_tag="ILQ31_RS27925"
                     /old_locus_tag="ILQ31_27940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052605.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system antitoxin LsoB"
                     /protein_id="WP_000710826.1"
                     /translation="MKKDKKYQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKK
                     SKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNF
                     DKINVNLLSKATSFALKKGIPI"
                     /name="lsoB"
     gene            complement(1348..2388)
                     /gene="lsoA"
                     /locus_tag="ILQ31_RS27930"
                     /old_locus_tag="ILQ31_27945"
     CDS             complement(1348..2388)
                     /gene="lsoA"
                     /locus_tag="ILQ31_RS27930"
                     /old_locus_tag="ILQ31_27945"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052606.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system mRNA
                     endoribonuclease LsoA"
                     /protein_id="WP_000068433.1"
                     /translation="MAQNPFKALNINIDKIESALTQNGVTNYSSNVKNERETHISGTYK
                     GIDFLIKLMPSGGNTTIGRASGQNNTYFDEIALIIKENCLYSDTKNFEYTIPKFSDDDR
                     ANLFEFLSEEGITITEDNNNDPNCKHQYIMTTSNGDRVRAKIYKRGSIQFQGKYLQIAS
                     LINDFMCSILNMKEIVEQKNKEFNVDIKKETIESELHSKLPKSIDKIHEDIKKQLSCSL
                     IMKKIDVEMEDYSTYCFSALRAIEGFIYQILNDVCNPSSSKNLGEYFTENKPKYIIREI
                     HQETINGEIAEVLCECYTYWHENRHGLFHMKPGIADTKTINKLESIAIIDTVCQLIDGG
                     VARLKL"
                     /name="lsoA"
     gene            complement(2653..2766)
                     /locus_tag="ILQ31_RS28390"
     CDS             complement(2653..2766)
                     /locus_tag="ILQ31_RS28390"
                     /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="hypothetical protein"
                     /protein_id="WP_001459398.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLSPLAAAIGN"
                     /name="hypothetical protein"
     gene            2877..3125
                     /locus_tag="ILQ31_RS27935"
                     /old_locus_tag="ILQ31_27950"
     CDS             2877..3125
                     /locus_tag="ILQ31_RS27935"
                     /old_locus_tag="ILQ31_27950"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000919062.1"
                     /translation="MAGSEQESARGSFRGETPGIFIVLSGFATSGLSVDFCDARQGGGA
                     YGKTPAVLASSGALLFAHMFFPALSPDSVDNRITAFE"
                     /name="hypothetical protein"
     Typing          179..404
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="89.583"
                     /coverage="99.0"
                     /evalue="1.05e-76"
     Typing          complement(2695..3224)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.413"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          414..733
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="6.46e-64"
ORIGIN
        1 ttcttctgcg agttcgtgca gcttctcaca catggtggcc tgctcgtcag catcgagtgc
       61 gtccagtttt tcgagcagcg tcaggctctg gctttttatg aatcccgcca tgttgagtgc
      121 agtttgctgc tgcttgttca tctttctgtt ttctccgttc tgtctgtcat ctgcgtcgtg
      181 tgattatatc gcgcaccact tttcgaccgt cttaccgccg gtattctgcc gacggacatt
      241 tcagtcagac aacactgtca ctgccaaaaa acagcagtgc tttgttggta attcgaactt
      301 gcagacagga caggatgtgc aattgttata ccgcgcatac atgcacgcta ttacaattac
      361 cctggtcagg gcttcgcccc gacaccccat gtcagatacg gagccatgtt ttatgacaaa
      421 acgaagtgga agtaatacgc gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga
      481 agaagaccag gaaatcagaa aaagggctgc tgaatgcggc aagaccgttt ctggtttttt
      541 acgggcggca gctctcggta agaaagttaa ctcactgact gatgaccggg tgctgaaaga
      601 agttatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga
      661 cagagagtat gcggaggtgc tgatcgctat tacggagtat caccgtgccc tgttatccag
      721 gcttatggca gattagcttc ccggagagaa actgtcgaaa acagacggta tgaacgccgt
      781 aagcccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcga
      841 tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtctgcgtc
      901 agaatcgcgt tcagcgcgtt ttggcggtgc gcgtaatgag acgttatggt aaatgtcttc
      961 tggcttgata ttatattgga atgccttttt tcaaagcaaa tgatgtggct ttggatagaa
     1021 ggtttacgtt gatcttatca aagttttttt taaagaacga agccgagagc tcagataaat
     1081 cattatattc atcagttttc gtaactttgt ttaatgtgta acttgaaaac ttctcgccat
     1141 taaatgacgt atagacgtaa cgatcttttt ttccaccgtt aggaattatt aaatcaaaaa
     1201 aaacatcacc cttgcttttc tttttcttca agtcggattc gatttttgag aaaaattcgc
     1261 tcgggctata aatatcagta gcatagacaa taaataaagt tttatcttta ttttttattg
     1321 cttctatttg atatttttta tcttttttca taatttcaac ctagctacgc caccatctat
     1381 taattggcaa acggtatcga tgattgcgat tgattctaat ttgttaattg tcttcgtgtc
     1441 agctattcct ggtttcatat gaaacaaacc atgcctgttc tcatgccagt aagtgtagca
     1501 ttcacacaaa acttccgcta tttcaccatt tatagtttct tggtgtattt ctctgattat
     1561 atatttgggt ttgttttcag tgaagtattc gccaaggttc tttgatgatg atggattgca
     1621 aacatcatta agtatttgat atataaagcc ttctatggct cttaatgcag agaagcagta
     1681 tgttgagtaa tcttccattt cgacatctat ttttttcatt attagcgagc atgatagctg
     1741 ttttttgata tcttcatgga ttttatcgat gctttttggt agtttgctat gcaactcgga
     1801 ctcaatagtt tcttttttta tgtcaacatt aaattcttta tttttttgtt cgacaatctc
     1861 tttcatgttt agtattgagc acatgaaatc gttaatcaaa ctcgcgattt gaaggtattt
     1921 tccttggaat tgaatagagc cgcgcttgta aatttttgcc ctgaccctgt caccattgct
     1981 ggtggtcata atatattggt gtttacaatt aggatcgtta ttattatctt ctgttattgt
     2041 tatcccctct tcagaaagaa attcaaatag atttgccctg tcatcatcac tgaattttgg
     2101 aatggtgtat tcaaagttct ttgtgtctga atacaaacag ttttctttta taatcaaggc
     2161 gatttcatca aagtaagtgt tattttgccc agacgctctt ccgatagtgg tatttccgcc
     2221 tgatggcatt agttttatta agaagtctat tcctttatat gtgccagata tgtgagtttc
     2281 tctttcgttt tttacattag aggaatagtt tgtgacgcca ttctgcgtca gagcagactc
     2341 aatcttgtca atattgatat ttagtgcttt aaacgggttc tgtgccattg ggtcaatccg
     2401 ttgttttttt tgaatatgta cagatcttgt ttttttgtca acggaatagc tgttcgttga
     2461 cttgatagac cgattgattc atcatctcat aaataaagaa aaaccaccgc taccaacggt
     2521 ggttttctca aggttcgctg agctaccaac tctttgaacc aaggtaactg gcttggagga
     2581 gcgcagtcac caaaatctgt tctttcagtt tagccttaac aggtgcataa cttcaagaca
     2641 aactcctcta aatcagttac caatggctgc tgccagtggc gataagtcgt gtcttaccgg
     2701 gttggactca agacgatagt taccggataa ggcgcagcgg tcgggctgaa cggggggttc
     2761 gtgcacacag cccagcttgg agcgaacgac ctacaccgaa ctgagatacc aacagcgtga
     2821 gctatgagaa agcgccacgc ttcccgaagg gagaaaggcg gacaggtatc cggtaagtgg
     2881 cagggtcgga acaggagagc gcacgaggga gcttccgggg ggaaacgcct ggtatcttta
     2941 tagtcctgtc gggtttcgcc acctctggct tgagcgtcga tttttgtgat gctcgtcagg
     3001 ggggcggagc ctatggaaaa acgcctgcgg tgctggcttc ttccggtgct ttgctttttg
     3061 ctcacatgtt ctttccggct ttatcccctg attctgtgga taaccgtatt accgcctttg
     3121 agtgagctga caccgctcgc cgcagtcgaa cgaccgagcg tagcgagtca gtgagcgagg
     3181 aagcggaaga gcgccttatg tgacattttc tccttacgct ctgttgtgcc gttcggcatc
     3241 ctgccctgag cgttatatct ctgtgctatt ttctacttca aagcgtgtct gtatgctgtt
     3301 ctggag
//
