LOCUS       NZ_CP057214             4286 bp    DNA     circular CON 02-APR-2024
DEFINITION  Escherichia fergusonii strain RHB33-C07 plasmid pRHB33-C07_5,
            complete sequence.
ACCESSION   NZ_CP057214
VERSION     NZ_CP057214.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148326
            Assembly: GCF_013819085.1
KEYWORDS    RefSeq.
SOURCE      Escherichia fergusonii
  ORGANISM  Escherichia fergusonii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4286)
  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 4286)
  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                     :: RH14 T3-C07
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 151.359023831922x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013819085.1-RS_2024_04_02
            Annotation Date                   :: 04/02/2024 04:25:52
            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)                     :: 4,920
            CDSs (total)                      :: 4,796
            Genes (coding)                    :: 4,657
            CDSs (with protein)               :: 4,657
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 139
            CDSs (without protein)            :: 139
            Pseudo Genes (ambiguous residues) :: 0 of 139
            Pseudo Genes (frameshifted)       :: 48 of 139
            Pseudo Genes (incomplete)         :: 84 of 139
            Pseudo Genes (internal stop)      :: 23 of 139
            Pseudo Genes (multiple problems)  :: 17 of 139
            Pseudo Genes (short protein)      :: 2 of 139
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP057214.1.
            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..4286
                     /organism="Escherichia fergusonii"
                     /mol_type="genomic DNA"
                     /strain="RHB33-C07"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB33-C07_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(4192..4286,1..1153))
                     /locus_tag="HVZ09_RS24415"
                     /old_locus_tag="HVZ09_24365"
     CDS             complement(join(4192..4286,1..1153))
                     /locus_tag="HVZ09_RS24415"
                     /old_locus_tag="HVZ09_24365"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001522448.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WP_001522448.1"
                     /translation="MIKFVDLFSGTGGIRLGFEQAMKEIGLSTKCVKSSEIDKKACETY
                     KLNFDEESYCDIHDVDIDESFDVLLAGFPCQAFSYAGKQLGFADTRGTLFFEVERIIKK
                     NKPKLCLLENVRGLTSHDKGRTFSTILKSLHDLGYHVEYRLLNTSNFGVPQNRVRIYII
                     ASLKKEVTLTIPNDLGAKDTHNYKPSKGGHDFYTESKVSDILEDSPDKSYDCSDWFKQR
                     LEDIFKGDLNKVHGIRLIDTRNGNSLHSWDLGLKGECSNDEIAFMNSLIANRRKHIFGT
                     HQDGKALSKAQIETFFKHSETTNIIKNLIKKGYLKEKNGLYNPVCGNMSFEVFKFLDPN
                     KVSITLTASDANRLGVYHNNRLRRLTPRECARLQGYPDSYILHPKDSMAYKQLGNAVSV
                     PVIKNIFLDIMKNNFI"
                     /name="DNA cytosine methyltransferase"
     gene            complement(1150..2160)
                     /locus_tag="HVZ09_RS24420"
                     /old_locus_tag="HVZ09_24370"
     CDS             complement(1150..2160)
                     /locus_tag="HVZ09_RS24420"
                     /old_locus_tag="HVZ09_24370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000395670.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001522447.1"
                     /translation="MEFQELENSACLYWPKELAERAASISAISPLIETQDEFLSILTIS
                     TNKPTSCFDAVRLCNKISPNLFVKHLMVLSDIGGERLHRFFKDLDKIYPDRIMEFNIGN
                     NSYSYQFNSNRAWTTKNLNVEKSRLLQPVSDFTREMLDVCMLILWGGNTINNTNLPTEI
                     ENNCILGNLIGNKEAIEQFVKERYIMVSRQTGGATANDLGHICEIFIKEKLYKLIDDNI
                     SLDGHHIDGVTHNDKDLTTFDIVAKNTITKKCVGIEISFQVTTNSTIERKAGLAKSRRD
                     LLNSIGHKIAYVIDGSGNFQRSNAIKTIINHSDMTVNFSDNGINSLATFICETLK"
                     /name="hypothetical protein"
     gene            complement(2388..2519)
                     /locus_tag="HVZ09_RS24900"
     CDS             complement(2388..2519)
                     /locus_tag="HVZ09_RS24900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001318243.1"
                     /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_071791513.1"
                     /translation="MHEPPVQPDRCALSGNCRLESNPERHAKAPLAAAIGRGCTRNC"
                     /name="replication initiation protein"
     gene            complement(3183..3377)
                     /locus_tag="HVZ09_RS24425"
                     /old_locus_tag="HVZ09_24375"
     CDS             complement(3183..3377)
                     /locus_tag="HVZ09_RS24425"
                     /old_locus_tag="HVZ09_24375"
                     /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_001041631.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          3018..3103
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          3414..3512
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          3637..3892
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(2448..2996)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.414"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttgggtgtaa gatatatgag tctgggtaac cttgtagcct tgcacattct cttggtgtaa
       61 ggcgtcgcag tctattgttg tgatagactc caagtctatt ggcatcagat gcagtaagtg
      121 taattgacac tttatttggg tcaaggaatt tgaatacttc aaaagacata tttccgcaaa
      181 ctgggttgta tagtccgttt ttttctttaa ggtaaccctt tttaattaga ttttttatta
      241 tgttggtggt ttcgctatgt ttgaaaaatg tttcaatttg tgcttttgac aaagccttgc
      301 cgtcttggtg tgtgccaaaa atatgctttc tacgatttgc aattaatgaa ttcatgaaag
      361 ctatttcatc atttgagcac tcgcctttta gcccaagatc ccaagagtgc aaggagttgc
      421 cgttccttgt gtcaattagc ctgattccat gaactttatt caggtcacct ttaaaaatat
      481 cttcaaggcg ttgcttgaac caatcgctgc aatcatatga cttgtctgga ctatcctcta
      541 gtatgtcaga aacttttgat tctgtataaa aatcatgacc acctttggat ggtttgtaat
      601 tgtgcgtatc tttggctcca agatcattag gaatagtaag cgttacctct ttttttaatg
      661 aggctattat atatattcta accctatttt gagggacgcc aaaattactt gtatttaata
      721 gtctgtattc aacatgatac cctaaatcgt gaagggattt taatattgtt gaaaatgtcc
      781 ttcctttatc atgtgaagtt aatccacgta cattctccaa aagacacaat ttaggcttgt
      841 ttttctttat aattctttct acttcaaaaa ataatgtacc tcgggtgtct gcaaaaccaa
      901 gttgttttcc agcataagag aatgcttggc aaggaaatcc tgccaataaa acatcgaagc
      961 tttcatctat atcaacatca tgtatatcac aatatgattc ttcgtcgaag ttaagtttgt
     1021 atgtttcgca tgcttttttg tcaatttctg agctttttac acattttgtt gacaatccaa
     1081 tttctttcat ggcttgctca aaaccaagtc taataccacc tgtgccagaa aaaaggtcaa
     1141 caaatttaat catttcaatg tctcgcagat gaatgttgct agtgaattta taccattatc
     1201 tgaaaagtta acagtcatgt cactatggtt aattattgtt tttatggcat ttgagcgctg
     1261 aaaattacca gacccatcaa tcacatatgc tattttatgc cctattgaat tgagtaaatc
     1321 tcttctgctt ttggctaatc ctgcttttct ttctattgtt gagtttgttg taacttgaaa
     1381 acttatttca ataccaacac atttttttgt tatcgtgttt tttgctacaa tatcaaaagt
     1441 cgtaaggtct ttatcgttat gagttacacc atcgatatgg tgtccatcta gagatatatt
     1501 atcatcaata agtttataaa gtttttcttt tataaagatc tcgcatatgt gtccaagatc
     1561 atttgccgtt gcacctcctg tttgtctgct aaccattata tatctttctt ttacaaattg
     1621 ttctattgct tctttgttcc caattaaatt tcccaaaata cagttatttt ctatttcagt
     1681 tggaaggttt gtattgttta tagtgttacc tccccacagg atcagcatgc aaacatcaag
     1741 catttctcgt gtaaaatcac ttacaggttg caaaagtcgt gatttttcca cgtttaaatt
     1801 cttggttgtc catgctctat tgctattgaa ttggtaagag taagagttat tccctatatt
     1861 gaactccatt attctgtcag gatagatttt atctaaatct ttaaaaaagc gatgaagtct
     1921 ttcgcctcca atatctgaca aaaccattag gtgcttgaca aataggttgg gtgatatctt
     1981 attgcataac cgtacagcat caaaacaaga tgtaggctta tttgttgata ttgttagtat
     2041 tgataaaaat tcatcttggg tctctataag agggcttatg gcgctaatag atgctgctct
     2101 ttctgcaagt tctttgggcc agtataagca tgcgctattt tctaattctt ggaactccat
     2161 gattattcct tggtaaaact atccaaatag accttgagtt acacccctat gatgggtaat
     2221 ctctacgtgc gtaaacgaaa aaacccacgt tctcaggcgt gggtttttcg aaggttagaa
     2281 gtttctcagg ctttctaacc caaggtaaca gggcgtacaa gaccgctgcc accaaatctg
     2341 tcctttcagt gtagccgcag tcgggccttc acttcaagaa ctccgtatca gcaatttctt
     2401 gtacaccctc taccaatggc tgctgccagt ggtgcttttg catgtctttc cgggttggac
     2461 tcaagacgac agttaccgga taaggcgcag cggtcgggct gaacgggggg ttcgtgcaca
     2521 cagcccagct tggagcgaac gacctacacc gaactgagat accaacagcg tgagctatga
     2581 gaaagcgcca cgcttcccga agggagaaag gcggacaggt atccggtaag cggcagggtc
     2641 ggaacaggag agcgcacgag ggagcttcca gggggaaacg cctggtatct ttatagtcct
     2701 gtcgggtttc gccacctctg acttgagcgt cggtttttgt gatgctcgtc aggggggcgg
     2761 agcctatgga aaaacgccag cggcgtggcc ttttccgggt tctcgttttt tgctcacatg
     2821 tttcttttgg cgttatcccc tgattctgtg gataaccgca tctccgcttt tgagtgagcc
     2881 gacaccgctc gccgcagccg aacgaccgag cgtagcgagt cagtgagcga ggaagcggaa
     2941 gagcgccgga acgtgcattt tctccttacg catctgtgcg gcatttcaca ccgcatatgg
     3001 cgctcttttc ttacaatctg cactgatgcc gcatggttaa gccagtatac actccgctat
     3061 cgctacgtga ctgggtcatg gctgcgcccc gacacccgct aaaaccccct gacgcgccct
     3121 gacgggcttg tctgctgacg aaaacgccca cgggaaagcc gtgaccgcct ccgtcagctt
     3181 cgttatgttc ctgtttcact ttcggcctca aagcgaatct ggatgctgtt ctggagttct
     3241 tctgcgagtt cgtgcagtcg ttcgcacatg gccgcctgtt cgtcagcatc cagagcatcc
     3301 agtttttcaa gcagtgtcag gctctggctt ttgataaatc gcgccatatt cagcgcagtt
     3361 tgttgttgtt tgttcacctt ccgttgttct ccgtcagttc cgggtgtcgg ggggaccctg
     3421 agcaggtggt aattgtaaga cgttgcgggc gacggtatta caattgcaca tcctgtcctg
     3481 tttctttagg acgtatcatg gcacagcata tcaactgata aataatccct gtgcagtgca
     3541 gccgctgttg cataaaattt cgctctgcgt cgagtgtttc ttaatcaata attccgctga
     3601 tactccggaa aaacgcgagt ctgttctcat gcctgaaatg cccacacccc acgcaaaaac
     3661 aagtttttgc tgatttttct ttataaatag agagttatga caaattagtt cttcttgctc
     3721 tctttgtgat atttaaaaaa gcggtgtcgg cgcggtgttg tagctgcgcc aacaccgctt
     3781 tttaggggtg gtactgacta ttttcataaa aaacatcatc ttatattagg ggtgctgcta
     3841 gcggcgcggt gtgttttttt acaggacacc cctgggggcg ctgccagggg tgtctgttca
     3901 gatatgtagc aatgagtcag ggattcacga actgaaaatg tccgaaaatg tgtctcatgg
     3961 gcactgtatg cgcccaaacc gatcgtcatt cactttcatg catagctatg cagtgagctg
     4021 aaagcgatcc tgacgcattt ttccggttta ccccggggag aacatctctt tttgcggtgt
     4081 tcgcggcaga atcgcgttca gcgcgtttta gcggtgcgcg caatgcgaca ttatggtaaa
     4141 tctgttaaat ttaattaaat aaccatagag cagttttgct agtaatatag tttatatgaa
     4201 gttattcttc attatatcaa gaaaaatatt tttaatgact ggaacgctta cagcattccc
     4261 caattgttta tatgccatgc tatctt
//
