LOCUS       NZ_CP057232             3257 bp    DNA     circular CON 01-APR-2024
DEFINITION  Escherichia fergusonii strain RHB32-C16 plasmid pRHB32-C16_4,
            complete sequence.
ACCESSION   NZ_CP057232
VERSION     NZ_CP057232.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148320
            Assembly: GCF_013820225.1
KEYWORDS    RefSeq.
SOURCE      Escherichia fergusonii
  ORGANISM  Escherichia fergusonii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3257)
  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 3257)
  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                     :: RH13 T3-C16
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 164.84135526264x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013820225.1-RS_2024_04_01
            Annotation Date                   :: 04/01/2024 04:17:56
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,694
            CDSs (total)                      :: 4,578
            Genes (coding)                    :: 4,454
            CDSs (with protein)               :: 4,454
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 124
            CDSs (without protein)            :: 124
            Pseudo Genes (ambiguous residues) :: 0 of 124
            Pseudo Genes (frameshifted)       :: 48 of 124
            Pseudo Genes (incomplete)         :: 64 of 124
            Pseudo Genes (internal stop)      :: 28 of 124
            Pseudo Genes (multiple problems)  :: 18 of 124
            Pseudo Genes (short protein)      :: 2 of 124
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP057232.1.
            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..3257
                     /organism="Escherichia fergusonii"
                     /mol_type="genomic DNA"
                     /strain="RHB32-C16"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB32-C16_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            129..425
                     /locus_tag="HVZ03_RS23210"
                     /old_locus_tag="HVZ03_23200"
     CDS             129..425
                     /locus_tag="HVZ03_RS23210"
                     /old_locus_tag="HVZ03_23200"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609270.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antitoxin"
                     /protein_id="WP_000609270.1"
                     /translation="MINLVDPVHPGVFIREMFMEPFEISAADLSEKLHVSPSTLSRVLN
                     GKADLSVEMALRLSRVLGRSAESWINMQTQYSLNASRKSPNVIKELDELVPIF"
                     /name="HigA family addiction module antitoxin"
     gene            complement(656..768)
                     /locus_tag="HVZ03_RS23710"
                     /pseudo=""
     CDS             complement(656..768)
                     /locus_tag="HVZ03_RS23710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            complement(1422..1616)
                     /locus_tag="HVZ03_RS23215"
                     /old_locus_tag="HVZ03_23205"
     CDS             complement(1422..1616)
                     /locus_tag="HVZ03_RS23215"
                     /old_locus_tag="HVZ03_23205"
                     /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="WP_001041633.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2760..3041)
                     /locus_tag="HVZ03_RS23220"
                     /old_locus_tag="HVZ03_23210"
     CDS             complement(2760..3041)
                     /locus_tag="HVZ03_RS23220"
                     /old_locus_tag="HVZ03_23210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000586174.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_000586174.1"
                     /translation="MIINIKHKGLRKFAETGNNAGIPQQFTQRLKLILTALSTATNLQD
                     MMDLKALRCHPLKGDRQGEYSLEVNGNWRVVFKLEEPNVFDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     Typing          1267..1349
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.81"
                     /coverage="100.0"
                     /evalue="1.76e-34"
     Typing          1653..1751
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          1876..2131
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(697..1254)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.464"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 acgcaccaat gtgcatcata atgtcattct tttttttagt caacaatgag ttgcgttatg
       61 cgcaatgcgc aatctgaaaa cgcaataggc ctatcttttt aaaactaata taggcttcag
      121 aggaaggtat gattaatctt gtcgatccag tacatccagg ggtttttatc cgtgagatgt
      181 ttatggaacc gtttgaaata tcagccgcgg acctgtctga aaaactgcat gtatcacctt
      241 ccactctaag tagagtgctg aatggaaaag ctgatttaag tgttgagatg gcattaaggc
      301 tttctcgagt tcttggtcgc agtgccgagt cgtggataaa catgcagact caatacagtc
      361 ttaacgcgag caggaagtca cctaatgtca ttaaggaatt agatgaattg gttcctatat
      421 tttgagaaaa gaaaaggccg ctatatgcgg cctttttctg tcttgactct caggcaactg
      481 gatcgtatcg tttctcgtaa acgaaaaaac cacccggcaa ggtggttttt tcgaaggttc
      541 agtaaccggc aagtttctga accagggtaa ctggcttgga ggagcgcagt caccaaaact
      601 tgttctttca gtttagcctt aactggcgca taacttcaag actaactcct ctaaatcagt
      661 taccagtggc tgctgccaat ggtgttttgc atgtctttcc gggttggact caagatgata
      721 gttaccggat aaggcgcagc ggtcgggctg aacggggggt tcgtgcacac agcccagctt
      781 ggagcgaacg acctacactg aaccgagata cctacagcgt gagctatgag aaagcgccac
      841 gcttcccgaa gggagaaagg cggacaggta tccggtaagc ggcagggtcg gaacaggaga
      901 gcgcacgagg gagccaccag ggggaaacgt ctggtatctt taagtcctgt cgggtttcgc
      961 cacctctgac ttgagcgtcg atttctgtga tgctcgtcag gggggcggag cctatggaaa
     1021 aacgcctgcg gcgcggcctt cttcctgttc ttggtctttt gctcacatgt tctttccggc
     1081 cttatcccct gattctgtgg ataaccgtgc tgccgttttt gtgtaagtca gtaccgctcg
     1141 ccgcagccga acgaccgagc gtagcgagtc agtgagcgag gaagcggaaa agcgcctgga
     1201 cgcgcatttt ctccttacgc atctgtgcgg aatttcacac ccggcatggg gcacttttca
     1261 tacaatctgc actgatgtcg catagttaag ccagtataca ctccgctatc gctacgtgac
     1321 tgggtcaggg cttcgccccg acacccgctg acgcgccctg gcgggcttgt ctgctgccga
     1381 aaacgctcgc ggacaagccg tgagcgcctc cgtcagcttc gttatgttcc tgtttcactt
     1441 tcggtctcaa agcgaacctg gatgctgttc tggagttctt ccgcgagttc gtgcagtcgt
     1501 tcgcacatgg ccgcctgttc gtcggcatcc agagcatcca gtttttcaag cagtgtcagg
     1561 ctctggcttt tgataaatcg cgccatattc agcgcagttt gttgctgttt gttcaccttc
     1621 cgttgttctc cgtcagtacc gggtgtcggg tggaccctga ccaggtggta attgtaagac
     1681 gttgcgggcg acggtattac aattgcacat cctgtcctgt ttttttagga cgtatcatgg
     1741 cacagcatat caactgataa ataatccctg tgcagtgcag ccgctgttgc ataaaatttc
     1801 gctctgcgtc gagtgtttct taatcaataa ttccgctgat actccggaaa aacgcgagtc
     1861 tgttctcatg cctgaaatgc ccacacccca cgcaaaaaca attttttgct gatttttctt
     1921 tataaataga gagttatgac aaattagttc ttcttgctct ctttgtgata tttaaaaaag
     1981 cggtgtcggc gcggtgttgt agctgcgcca acaccgcttt ttaggggtgg tactgactat
     2041 tttcataaaa aacatcattt tatattaggg gtgctgctag cggcgcggtg tgttttttta
     2101 caggacgccc ctgggggcgc tgctaggggt gtctgttcag atatgtagca atgagtcagg
     2161 gattcacgaa ctgaaaatgt ccgaaaatgt gtctcatggg caccgtatgc gcccaaaccg
     2221 atcgccattc actttcatgc atagctatgc agtgagctga aagcgatcct gacgcatttt
     2281 tccggttttc gcttggtaaa acatctcttt ttgcggtgtt cgcggcagaa tcgcgttcag
     2341 cgcgttttag cggtgcgcgt aatgcgacgt tatggtaaat gctgtgattt gcgggatggt
     2401 tttatctatg ttgatatcaa taccacctct tatggaggtg gcttacaccg atttttcctt
     2461 gttgtctgtt tcagaacaga tagaggcttt tttggcaatt atccaaccac tattgatagt
     2521 gtttattact acttagataa ctgagccttt actgtatctg cccctgcaag caggaaccca
     2581 acagttaaga accaccccca gccattgata ccttttagcg ctagaattgc tgcgcaaatg
     2641 atggctgcta tagggactat ctggtacaga aaatacttca tataacttac cccgaggttt
     2701 tgctttttta tgagacccta aagcatcgat actgtcactt tgatgcttta aggaccttct
     2761 tagtgataat cctcgagatc cacgtcaaag acgttaggtt cttcgagctt aaacactacg
     2821 cgccagtttc cattgacctc taacgaatac tctccttgac ggtctccctt caatggatgg
     2881 cagcgcaatg cctttaaatc catcatatcc tgcaagttcg tcgctgtgct taaggctgtt
     2941 aggatcagct tcagacgttg agtaaactgt tgcggaattc ctgcgttgtt acctgtttcg
     3001 gcaaacttac gcaaaccttt atgcttgata tttatgatca ttaatcacca tcccatattt
     3061 gtttagatag aaacatcgca gtttattttt ccggttcatc cgtatttcca ttgcaaaccc
     3121 cttgctctat ttgaataaat gacgtaggtt ttacttaacc aagtcgcatt ttaatctgtt
     3181 gacattggtt tgatgcgctg tacaatgccg gggccttgaa tttcacatca agtacccaca
     3241 tcataaggaa tgattag
//
