LOCUS       NZ_CP056972             3830 bp    DNA     circular CON 02-APR-2024
DEFINITION  Escherichia fergusonii strain RHB41-C15 plasmid pRHB41-C15_5,
            complete sequence.
ACCESSION   NZ_CP056972
VERSION     NZ_CP056972.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148427
            Assembly: GCF_013801845.1
KEYWORDS    RefSeq.
SOURCE      Escherichia fergusonii
  ORGANISM  Escherichia fergusonii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3830)
  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 3830)
  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                     :: RH01 T3-C15
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 148.040080997967x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013801845.1-RS_2024_04_02
            Annotation Date                   :: 04/02/2024 04:22:09
            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)                     :: 4,824
            CDSs (total)                      :: 4,701
            Genes (coding)                    :: 4,567
            CDSs (with protein)               :: 4,567
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 95
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 134
            CDSs (without protein)            :: 134
            Pseudo Genes (ambiguous residues) :: 0 of 134
            Pseudo Genes (frameshifted)       :: 54 of 134
            Pseudo Genes (incomplete)         :: 73 of 134
            Pseudo Genes (internal stop)      :: 23 of 134
            Pseudo Genes (multiple problems)  :: 17 of 134
            Pseudo Genes (short protein)      :: 2 of 134
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056972.1.
            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..3830
                     /organism="Escherichia fergusonii"
                     /mol_type="genomic DNA"
                     /strain="RHB41-C15"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB41-C15_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(3261..3830,1..1335))
                     /locus_tag="HV010_RS23945"
                     /old_locus_tag="HV010_23940"
     CDS             complement(join(3261..3830,1..1335))
                     /locus_tag="HV010_RS23945"
                     /old_locus_tag="HV010_23940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003839290.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="methyl-accepting chemotaxis protein"
                     /protein_id="WP_052895204.1"
                     /translation="MSWAYRISMQMKLFIALFPLLLALVWFAGSGIVSRINTEQQMNTI
                     GQLTTLARSAGDVVHQLQSERGMSAGFIGARGQKFRDDLAAQRQLTDKVLATFKRLLTD
                     TNKDLLQGNIAAPLKTFNESIQFLDSTRTAISELTIDSPKASQFYTQTISDVLKFVGGM
                     GHLSTSGSMVNELAAYYSLLNLKEQAGVERALLSNIFSMDRFDDGQFSMFSDVVGQQDA
                     WLTAARSFSTPVQAAELDKSLQSAEATRALELRETAFNKAAEGGFGVNPTDWFNLQTQR
                     IETLQKVENRAVDALQEHAALLAHNARVDWQSFLVISLVALLIAIAFAVMVARSIQQQL
                     NGTLKTIAEMDGDLTRRLDVPGSDELSALNRAYNQAIENIQHIVQEIKSGAVVLRSASS
                     DIAAGNQDLAQRTDEQAASIVETAASMEQISTAITQTADNASEAERLIHSMERDVLEAN
                     RVSNEASQSMAEIRSSSEQISQIVASIDEISFQTNLLALNAAVEAARAGELGKGFAVVA
                     TEVRNLSQRCAREASQIRELINQNMDKIGEGVARVTASGTALKAAAENTGRMKQYVSDI
                     ARAANEQSLGVSQVHQALNQLEQVTQQNAALVSQAASASQMLDGQSEAMSTLVDRFIV"
                     /name="methyl-accepting chemotaxis protein"
     gene            complement(1641..1790)
                     /locus_tag="HV010_RS24370"
     CDS             complement(1641..1790)
                     /locus_tag="HV010_RS24370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001333247.1"
                     /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_077464408.1"
                     /translation="MHEPPVQSDCCAFSGNYRLESNPERHEKSPLAAATGKQDVREMYR
                     EFLK"
                     /name="replication initiation protein"
     gene            2535..2735
                     /locus_tag="HV010_RS23950"
                     /old_locus_tag="HV010_23945"
     CDS             2535..2735
                     /locus_tag="HV010_RS23950"
                     /old_locus_tag="HV010_23945"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001046776.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_016236520.1"
                     /translation="MNLCPDERLLFVRMISAMLRRSGGDAGAVMFEAYRHIVSDTNQAR
                     RSCMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            complement(2783..2971)
                     /locus_tag="HV010_RS23955"
                     /old_locus_tag="HV010_23950"
     CDS             complement(2783..2971)
                     /locus_tag="HV010_RS23955"
                     /old_locus_tag="HV010_23950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /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_000165998.1"
                     /translation="MTKQESAALNMAKFIRAQSLLLLEKLDVLDLDDEAADCERMHEQA
                     EALYQKLSARFGIQDGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2153..2325
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.379"
                     /coverage="100.0"
                     /evalue="9.47e-61"
     Typing          complement(1632..2228)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.211"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 acgctccgcc tcgctggcgt tatcggcggt ctgggtgatc gcagtagaaa tctgctccat
       61 gctggcggcc gtttccacaa tcgatgccgc ctgttcatcc gtacgctggg ccagatcctg
      121 attaccggca gcgatatcac tactggcgct acgcaacacc accgcaccgg acttaatttc
      181 ttgcacgata tgctgaatat tctcaatcgc ttggttatag gcacggttca gggctgagag
      241 ctcgtcgctg ccggggacgt caagacgacg tgtcaggtcg ccgtccatct ctgcgatggt
      301 tttcagcgta ccgttcagtt gctgctggat actgcgtgcc accatcaccg caaaggcgat
      361 agcaatcagt agggcaacca ggctgattac caggaaggac tgccagtcga cacgggcatt
      421 gtgggcaagc agcgcagcat gttcctgcaa ggcatccacc gcgcgatttt ccaccttttg
      481 cagcgtttca atacgctggg tctgaaggtt aaaccagtca gtcgggttga ctccaaatcc
      541 gccttcggcg gctttattaa aagccgtctc ccgcagttca agagcacgag ttgcttcagc
      601 ggactgaaga gatttgtcca gctcagccgc ctgcacaggt gtgctaaagc tgcgagctgc
      661 cgtcagccag gcatcctgct ggcctaccac atcgctaaac atgctgaact ggccgtcgtc
      721 aaagcgatcc atcgagaaga tattggacag cagcgcacgt tctacaccag cctgctcctt
      781 caaattcaag agactataat aagccgccag ttcgttcacc atcgagcctg aggtgcttaa
      841 atgccccatc ccgccgacaa acttcagcac gtcagagatg gtttgggtat agaactgact
      901 cgcttttggt gaatcgatag ttaattcgct gatggcggta cgggttgagt cgagaaactg
      961 aatactttca ttaaacgttt tcaggggggc ggcaatattt ccctggagta aatccttatt
     1021 cgtatcggtc agcaaccgct taaatgttgc cagcaccttg tcggttaact gccgctgggc
     1081 agctaagtca tcgcgaaact tttggccgcg cgcgccgata aatccagcgc tcattccacg
     1141 ttcgctctgg agttgatgca ccacatcacc cgcgctgcgg gcgagcgtgg tgagctgtcc
     1201 aatggtgttc atctgctgtt cggtattgat acggctgaca atacccgaac cggcgaacca
     1261 gaccaaggca agcagtagcg ggaataatgc aataaacaac ttcatttgca ttgaaatacg
     1321 ataagcccat gacatatcga tactttcctt actttcttga gggatcgcag gagtatcggt
     1381 agatacatgc ataaacttta tagtttattg ttgggggaac gggcaccaca ttcggcagtg
     1441 gcgctggtag caatccataa aggatcttct tgagatcctt tgacgatcgt cgtaatctct
     1501 tgctctgtaa acgaaaaaac cacccttgca ggtggttttt cgaaggttag ataatcctgg
     1561 cagattctct aaccgtggta acagtcttgt gcgagacatg tcaccaaatt tgtccttcta
     1621 gtgtagcctc agtcaggcca ctacttcaag aactctcgat acatctctcg cacatcctgt
     1681 ttaccagtgg ccgctgccag tggcgatttt tcgtgtcttt ccgggttgga ctcaagacga
     1741 tagttaccgg aaaaggcgca gcagtcggac tgaacggggg gttcgtgcat acagtccagc
     1801 ttggagcgaa ctgccttccc ggaactgagt gtcaggcgtg gaatgagata aacgcggcca
     1861 taacagcgga atgacaccgg taaaccgaaa ggcaggaaca ggagagcgca cgagggagct
     1921 accaggggga aacgcctggg atctttatag tcctgtcggg tttcgccgcc actgatttga
     1981 gcgtcagatt tcgtgatgct tgtcaggggg gcggagccta tggaaaaacg gcttcgccgc
     2041 ggccttaccg tttccctgtt aagtttcttc ctggcatctc ccaggaaatt tccgccccat
     2101 tcgtaatccc gcaccgctcg ccgcagccga acgaccgagc gcagcgagtc agtgagcgag
     2161 gaagcggaat atctcctgtc tcatatattc cgcttacgct ctgctgctgc attttcctcc
     2221 tgccacatga agcacttcac tgattcccgc acccgtgcct acataataag ccagtataca
     2281 ctccgctagc gctacgtgac tggttcaggg ctgcgccccg acacccgcta aaagcactga
     2341 cgcgcctgcg gcttgcccaa ccccgcgccg tccgggaaag aatttcccga tcgacccgac
     2401 gtttctgttt acctgtgatg ttaacgtttg gatctttttc ccgggtttac ctattttaat
     2461 gaagcgtaat gaagcgttca cagctgacgt taatagatgg gtgcttcatg tttggttttt
     2521 caccaggaga acttatgaac ctttgccccg atgaacgtct gctctttgtg cggatgattt
     2581 ccgctatgct tcgccgttcg ggcggtgatg cgggtgctgt tatgtttgag gcgtatcgcc
     2641 atattgtgtc cgataccaat caagctcgtc gttcctgcat gctcgacctg ctcgaaagcg
     2701 tcaggcatga ctatgtacac ggtggatata catagttgcc ctggatacgc ttttcgtcta
     2761 agtgagcgtt cttttcgtct ctttattcgc cgtcctgtat accgaagcgt gcgctcagct
     2821 tctgataaag cgcttctgcc tgttcgtgca ttcgctcaca gtcggctgcc tcgtcatcaa
     2881 gatcgagcac gtcgagtttt tcgagcagca gcagcgactg cgcccggata aattttgcca
     2941 tgttcagtgc ggctgattcc tgttttgtca tacggctttt tcccggtttt atggtgatcg
     3001 cagactgaaa tcttacttca ttcacttgag tgcatagcca tgcaggtacg cagaaatcat
     3061 caggggcgtt ttttctcgat atgggcacag aaaggtgtat gtttcaggtc ggagtcctca
     3121 gaaacgctct cagagcctct caggcggtgc acgcaacaga tgttatggta aatcctagtt
     3181 atttgcaggc ataaaaaagc cgccttttag gcggtttttt ctgattgtaa gttatcaaga
     3241 ccggatgctg aacggcagta tcagacaata aagcgatcga ccagcgtgga catcgcttca
     3301 gactggccgt ccagcatctg gctggcgctc gccgcctgag agaccagcgc tgcgttttgc
     3361 tgagtgacct gctccagctg attcagtgcc tgatgcacct gcgacacgcc aagcgactgc
     3421 tcattcgccg cacgggcaat atcgctcacg tactgtttca tccgcccggt attttccgcc
     3481 gctgctttca gcgcggtgcc ggacgcggtg actcgtgcta ccccttcgcc aatcttatcc
     3541 atattctggt taatcagctc acggatctga ctggcctctc gtgcacagcg ctgggaaagg
     3601 ttacgcacct ccgtcgccac taccgcaaag cctttgccaa gctcaccggc acgtgccgct
     3661 tcaacggcgg cgttaagcgc cagcaagttg gtctggaaag aaatctcatc aattgacgca
     3721 acaatctggg aaatctgctc gctggaagaa cgaatttccg ccatgctctg actggcctcg
     3781 ttagagacgc gattagcttc cagtacgtcc cgctccatcg aatgtatcag
//
