LOCUS       NZ_CP057219             4286 bp    DNA     circular CON 02-APR-2024
DEFINITION  Escherichia fergusonii strain RHB33-C04 plasmid pRHB33-C04_5,
            complete sequence.
ACCESSION   NZ_CP057219
VERSION     NZ_CP057219.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148325
            Assembly: GCF_013819325.1
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-C04
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 138.730801885388x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013819325.1-RS_2024_04_02
            Annotation Date                   :: 04/02/2024 04:35:31
            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)                     :: 4,913
            CDSs (total)                      :: 4,789
            Genes (coding)                    :: 4,649
            CDSs (with protein)               :: 4,649
            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)              :: 140
            CDSs (without protein)            :: 140
            Pseudo Genes (ambiguous residues) :: 0 of 140
            Pseudo Genes (frameshifted)       :: 48 of 140
            Pseudo Genes (incomplete)         :: 85 of 140
            Pseudo Genes (internal stop)      :: 23 of 140
            Pseudo Genes (multiple problems)  :: 17 of 140
            Pseudo Genes (short protein)      :: 2 of 140
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP057219.1.
            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-C04"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB33-C04_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(4162..4286,1..7))
                     /locus_tag="HVZ08_RS24840"
     CDS             complement(join(4162..4286,1..7))
                     /locus_tag="HVZ08_RS24840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /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(671..865)
                     /locus_tag="HVZ08_RS24375"
                     /old_locus_tag="HVZ08_24380"
     CDS             complement(671..865)
                     /locus_tag="HVZ08_RS24375"
                     /old_locus_tag="HVZ08_24380"
                     /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"
     gene            complement(1680..2927)
                     /locus_tag="HVZ08_RS24380"
                     /old_locus_tag="HVZ08_24385"
     CDS             complement(1680..2927)
                     /locus_tag="HVZ08_RS24380"
                     /old_locus_tag="HVZ08_24385"
                     /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(2924..3934)
                     /locus_tag="HVZ08_RS24385"
                     /old_locus_tag="HVZ08_24390"
     CDS             complement(2924..3934)
                     /locus_tag="HVZ08_RS24385"
                     /old_locus_tag="HVZ08_24390"
                     /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"
     Typing          506..591
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          902..1000
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          1125..1380
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(2..484)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.07"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4186..4286)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.157"
                     /coverage="89.0"
                     /evalue="1.26e-32"
ORIGIN
        1 cgtgcacaca gcccagcttg gagcgaacga cctacaccga actgagatac caacagcgtg
       61 agctatgaga aagcgccacg cttcccgaag ggagaaaggc ggacaggtat ccggtaagcg
      121 gcagggtcgg aacaggagag cgcacgaggg agcttccagg gggaaacgcc tggtatcttt
      181 atagtcctgt cgggtttcgc cacctctgac ttgagcgtcg gtttttgtga tgctcgtcag
      241 gggggcggag cctatggaaa aacgccagcg gcgtggcctt ttccgggttc tcgttttttg
      301 ctcacatgtt tcttttggcg ttatcccctg attctgtgga taaccgcatc tccgcttttg
      361 agtgagccga caccgctcgc cgcagccgaa cgaccgagcg tagcgagtca gtgagcgagg
      421 aagcggaaga gcgccggaac gtgcattttc tccttacgca tctgtgcggc atttcacacc
      481 gcatatggcg ctcttttctt acaatctgca ctgatgccgc atggttaagc cagtatacac
      541 tccgctatcg ctacgtgact gggtcatggc tgcgccccga cacccgctaa aaccccctga
      601 cgcgccctga cgggcttgtc tgctgacgaa aacgcccacg ggaaagccgt gaccgcctcc
      661 gtcagcttcg ttatgttcct gtttcacttt cggcctcaaa gcgaatctgg atgctgttct
      721 ggagttcttc tgcgagttcg tgcagtcgtt cgcacatggc cgcctgttcg tcagcatcca
      781 gagcatccag tttttcaagc agtgtcaggc tctggctttt gataaatcgc gccatattca
      841 gcgcagtttg ttgttgtttg ttcaccttcc gttgttctcc gtcagttccg ggtgtcgggg
      901 ggaccctgag caggtggtaa ttgtaagacg ttgcgggcga cggtattaca attgcacatc
      961 ctgtcctgtt tctttaggac gtatcatggc acagcatatc aactgataaa taatccctgt
     1021 gcagtgcagc cgctgttgca taaaatttcg ctctgcgtcg agtgtttctt aatcaataat
     1081 tccgctgata ctccggaaaa acgcgagtct gttctcatgc ctgaaatgcc cacaccccac
     1141 gcaaaaacaa gtttttgctg atttttcttt ataaatagag agttatgaca aattagttct
     1201 tcttgctctc tttgtgatat ttaaaaaagc ggtgtcggcg cggtgttgta gctgcgccaa
     1261 caccgctttt taggggtggt actgactatt ttcataaaaa acatcatctt atattagggg
     1321 tgctgctagc ggcgcggtgt gtttttttac aggacacccc tgggggcgct gccaggggtg
     1381 tctgttcaga tatgtagcaa tgagtcaggg attcacgaac tgaaaatgtc cgaaaatgtg
     1441 tctcatgggc actgtatgcg cccaaaccga tcgtcattca ctttcatgca tagctatgca
     1501 gtgagctgaa agcgatcctg acgcattttt ccggtttacc ccggggagaa catctctttt
     1561 tgcggtgttc gcggcagaat cgcgttcagc gcgttttagc ggtgcgcgca atgcgacatt
     1621 atggtaaatc tgttaaattt aattaaataa ccatagagca gttttgctag taatatagtt
     1681 tatatgaagt tattcttcat tatatcaaga aaaatatttt taatgactgg aacgcttaca
     1741 gcattcccca attgtttata tgccatgcta tcttttgggt gtaagatata tgagtctggg
     1801 taaccttgta gccttgcaca ttctcttggt gtaaggcgtc gcagtctatt gttgtgatag
     1861 actccaagtc tattggcatc agatgcagta agtgtaattg acactttatt tgggtcaagg
     1921 aatttgaata cttcaaaaga catatttccg caaactgggt tgtatagtcc gtttttttct
     1981 ttaaggtaac cctttttaat tagatttttt attatgttgg tggtttcgct atgtttgaaa
     2041 aatgtttcaa tttgtgcttt tgacaaagcc ttgccgtctt ggtgtgtgcc aaaaatatgc
     2101 tttctacgat ttgcaattaa tgaattcatg aaagctattt catcatttga gcactcgcct
     2161 tttagcccaa gatcccaaga gtgcaaggag ttgccgttcc ttgtgtcaat tagcctgatt
     2221 ccatgaactt tattcaggtc acctttaaaa atatcttcaa ggcgttgctt gaaccaatcg
     2281 ctgcaatcat atgacttgtc tggactatcc tctagtatgt cagaaacttt tgattctgta
     2341 taaaaatcat gaccaccttt ggatggtttg taattgtgcg tatctttggc tccaagatca
     2401 ttaggaatag taagcgttac ctcttttttt aatgaggcta ttatatatat tctaacccta
     2461 ttttgaggga cgccaaaatt acttgtattt aatagtctgt attcaacatg ataccctaaa
     2521 tcgtgaaggg attttaatat tgttgaaaat gtccttcctt tatcatgtga agttaatcca
     2581 cgtacattct ccaaaagaca caatttaggc ttgtttttct ttataattct ttctacttca
     2641 aaaaataatg tacctcgggt gtctgcaaaa ccaagttgtt ttccagcata agagaatgct
     2701 tggcaaggaa atcctgccaa taaaacatcg aagctttcat ctatatcaac atcatgtata
     2761 tcacaatatg attcttcgtc gaagttaagt ttgtatgttt cgcatgcttt tttgtcaatt
     2821 tctgagcttt ttacacattt tgttgacaat ccaatttctt tcatggcttg ctcaaaacca
     2881 agtctaatac cacctgtgcc agaaaaaagg tcaacaaatt taatcatttc aatgtctcgc
     2941 agatgaatgt tgctagtgaa tttataccat tatctgaaaa gttaacagtc atgtcactat
     3001 ggttaattat tgtttttatg gcatttgagc gctgaaaatt accagaccca tcaatcacat
     3061 atgctatttt atgccctatt gaattgagta aatctcttct gcttttggct aatcctgctt
     3121 ttctttctat tgttgagttt gttgtaactt gaaaacttat ttcaatacca acacattttt
     3181 ttgttatcgt gttttttgct acaatatcaa aagtcgtaag gtctttatcg ttatgagtta
     3241 caccatcgat atggtgtcca tctagagata tattatcatc aataagttta taaagttttt
     3301 cttttataaa gatctcgcat atgtgtccaa gatcatttgc cgttgcacct cctgtttgtc
     3361 tgctaaccat tatatatctt tcttttacaa attgttctat tgcttctttg ttcccaatta
     3421 aatttcccaa aatacagtta ttttctattt cagttggaag gtttgtattg tttatagtgt
     3481 tacctcccca caggatcagc atgcaaacat caagcatttc tcgtgtaaaa tcacttacag
     3541 gttgcaaaag tcgtgatttt tccacgttta aattcttggt tgtccatgct ctattgctat
     3601 tgaattggta agagtaagag ttattcccta tattgaactc cattattctg tcaggataga
     3661 ttttatctaa atctttaaaa aagcgatgaa gtctttcgcc tccaatatct gacaaaacca
     3721 ttaggtgctt gacaaatagg ttgggtgata tcttattgca taaccgtaca gcatcaaaac
     3781 aagatgtagg cttatttgtt gatattgtta gtattgataa aaattcatct tgggtctcta
     3841 taagagggct tatggcgcta atagatgctg ctctttctgc aagttctttg ggccagtata
     3901 agcatgcgct attttctaat tcttggaact ccatgattat tccttggtaa aactatccaa
     3961 atagaccttg agttacaccc ctatgatggg taatctctac gtgcgtaaac gaaaaaaccc
     4021 acgttctcag gcgtgggttt ttcgaaggtt agaagtttct caggctttct aacccaaggt
     4081 aacagggcgt acaagaccgc tgccaccaaa tctgtccttt cagtgtagcc gcagtcgggc
     4141 cttcacttca agaactccgt atcagcaatt tcttgtacac cctctaccaa tggctgctgc
     4201 cagtggtgct tttgcatgtc tttccgggtt ggactcaaga cgacagttac cggataaggc
     4261 gcagcggtcg ggctgaacgg ggggtt
//
