LOCUS       NZ_CP057362             3830 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia fergusonii strain RHB28-C21 plasmid pRHB28-C21_6,
            complete sequence.
ACCESSION   NZ_CP057362
VERSION     NZ_CP057362.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148274
            Assembly: GCF_013829265.1
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 T2-C21
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 152.972283596324x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013829265.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 05:13:08
            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)                     :: 4,953
            CDSs (total)                      :: 4,834
            Genes (coding)                    :: 4,677
            CDSs (with protein)               :: 4,677
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 157
            CDSs (without protein)            :: 157
            Pseudo Genes (ambiguous residues) :: 0 of 157
            Pseudo Genes (frameshifted)       :: 36 of 157
            Pseudo Genes (incomplete)         :: 109 of 157
            Pseudo Genes (internal stop)      :: 22 of 157
            Pseudo Genes (multiple problems)  :: 12 of 157
            Pseudo Genes (short protein)      :: 2 of 157
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP057362.1.
            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="RHB28-C21"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB28-C21_6"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(2911..3830,1..985)
                     /locus_tag="HVY57_RS24525"
                     /old_locus_tag="HVY57_24475"
     CDS             join(2911..3830,1..985)
                     /locus_tag="HVY57_RS24525"
                     /old_locus_tag="HVY57_24475"
                     /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            1275..1463
                     /locus_tag="HVY57_RS24530"
                     /old_locus_tag="HVY57_24480"
     CDS             1275..1463
                     /locus_tag="HVY57_RS24530"
                     /old_locus_tag="HVY57_24480"
                     /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"
     gene            complement(1511..1738)
                     /locus_tag="HVY57_RS24535"
                     /old_locus_tag="HVY57_24485"
     CDS             complement(1511..1738)
                     /locus_tag="HVY57_RS24535"
                     /old_locus_tag="HVY57_24485"
                     /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_206659768.1"
                     /translation="MFGFSPGELMNLCPDERLLFVRMISAMLRRSGGDAGAVMFEAYRH
                     IVSDTNQARRSCMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            2456..2605
                     /locus_tag="HVY57_RS24985"
     CDS             2456..2605
                     /locus_tag="HVY57_RS24985"
                     /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"
     Typing          complement(1922..2094)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.379"
                     /coverage="100.0"
                     /evalue="9.47e-61"
     Typing          2019..2603
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.709"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 ccgtgtcgac tggcagtcct tcctggtaat cagcctggtt gccctactga ttgctatcgc
       61 ctttgcggtg atggtggcac gcagtatcca gcagcaactg aacggtacgc tgaaaaccat
      121 cgcagagatg gacggcgacc tgacacgtcg tcttgacgtc cccggcagcg acgagctctc
      181 agccctgaac cgtgcctata accaagcgat tgagaatatt cagcatatcg tgcaagaaat
      241 taagtccggt gcggtggtgt tgcgtagcgc cagtagtgat atcgctgccg gtaatcagga
      301 tctggcccag cgtacggatg aacaggcggc atcgattgtg gaaacggccg ccagcatgga
      361 gcagatttct actgcgatca cccagaccgc cgataacgcc agcgaggcgg agcgtctgat
      421 acattcgatg gagcgggacg tactggaagc taatcgcgtc tctaacgagg ccagtcagag
      481 catggcggaa attcgttctt ccagcgagca gatttcccag attgttgcgt caattgatga
      541 gatttctttc cagaccaact tgctggcgct taacgccgcc gttgaagcgg cacgtgccgg
      601 tgagcttggc aaaggctttg cggtagtggc gacggaggtg cgtaaccttt cccagcgctg
      661 tgcacgagaa gccagtcaga tccgtgagct gattaaccag aatatggata agattggcga
      721 aggggtagca cgagtcaccg cgtccggcac cgcgctgaaa gcagcggcgg aaaataccgg
      781 gcggatgaaa cagtacgtga gcgatattgc ccgtgcggcg aatgagcagt cgcttggcgt
      841 gtcgcaggtg catcaggcac tgaatcagct ggagcaggtc actcagcaaa acgcagcgct
      901 ggtctctcag gcggcgagcg ccagccagat gctggacggc cagtctgaag cgatgtccac
      961 gctggtcgat cgctttattg tctgatactg ccgttcagca tccggtcttg ataacttaca
     1021 atcagaaaaa accgcctaaa aggcggcttt tttatgcctg caaataacta ggatttacca
     1081 taacatctgt tgcgtgcacc gcctgagagg ctctgagagc gtttctgagg actccgacct
     1141 gaaacataca cctttctgtg cccatatcga gaaaaaacgc ccctgatgat ttctgcgtac
     1201 ctgcatggct atgcactcaa gtgaatgaag taagatttca gtctgcgatc accataaaac
     1261 cgggaaaaag ccgtatgaca aaacaggaat cagccgcact gaacatggca aaatttatcc
     1321 gggcgcagtc gctgctgctg ctcgaaaaac tcgacgtgct cgatcttgat gacgaggcag
     1381 ccgactgtga gcgaatgcac gaacaggcag aagcgcttta tcagaagctg agcgcacgct
     1441 tcggtataca ggacggcgaa taaagagacg aaaagaacgc tcacttagac gaaaagcgta
     1501 tccagggcaa ctatgtatat ccaccgtgta catagtcatg cctgacgctt tcgagcaggt
     1561 cgagcatgca ggaacgacga gcttgattgg tatcggacac aatatggcga tacgcctcaa
     1621 acataacagc acccgcatca ccgcccgaac ggcgaagcat agcggaaatc atccgcacaa
     1681 agagcagacg ttcatcgggg caaaggttca taagttctcc tggtgaaaaa ccaaacatga
     1741 agcacccatc tattaacgtc agctgtgaac gcttcattac gcttcattaa aataggtaaa
     1801 cccgggaaaa agatccaaac gttaacatca caggtaaaca gaaacgtcgg gtcgatcggg
     1861 aaattctttc ccggacggcg cggggttggg caagccgcag gcgcgtcagt gcttttagcg
     1921 ggtgtcgggg cgcagccctg aaccagtcac gtagcgctag cggagtgtat actggcttat
     1981 tatgtaggca cgggtgcggg aatcagtgaa gtgcttcatg tggcaggagg aaaatgcagc
     2041 agcagagcgt aagcggaata tatgagacag gagatattcc gcttcctcgc tcactgactc
     2101 gctgcgctcg gtcgttcggc tgcggcgagc ggtgcgggat tacgaatggg gcggaaattt
     2161 cctgggagat gccaggaaga aacttaacag ggaaacggta aggccgcggc gaagccgttt
     2221 ttccataggc tccgcccccc tgacaagcat cacgaaatct gacgctcaaa tcagtggcgg
     2281 cgaaacccga caggactata aagatcccag gcgtttcccc ctggtagctc cctcgtgcgc
     2341 tctcctgttc ctgcctttcg gtttaccggt gtcattccgc tgttatggcc gcgtttatct
     2401 cattccacgc ctgacactca gttccgggaa ggcagttcgc tccaagctgg actgtatgca
     2461 cgaacccccc gttcagtccg actgctgcgc cttttccggt aactatcgtc ttgagtccaa
     2521 cccggaaaga cacgaaaaat cgccactggc agcggccact ggtaaacagg atgtgcgaga
     2581 gatgtatcga gagttcttga agtagtggcc tgactgaggc tacactagaa ggacaaattt
     2641 ggtgacatgt ctcgcacaag actgttacca cggttagaga atctgccagg attatctaac
     2701 cttcgaaaaa ccacctgcaa gggtggtttt ttcgtttaca gagcaagaga ttacgacgat
     2761 cgtcaaagga tctcaagaag atcctttatg gattgctacc agcgccactg ccgaatgtgg
     2821 tgcccgttcc cccaacaata aactataaag tttatgcatg tatctaccga tactcctgcg
     2881 atccctcaag aaagtaagga aagtatcgat atgtcatggg cttatcgtat ttcaatgcaa
     2941 atgaagttgt ttattgcatt attcccgcta ctgcttgcct tggtctggtt cgccggttcg
     3001 ggtattgtca gccgtatcaa taccgaacag cagatgaaca ccattggaca gctcaccacg
     3061 ctcgcccgca gcgcgggtga tgtggtgcat caactccaga gcgaacgtgg aatgagcgct
     3121 ggatttatcg gcgcgcgcgg ccaaaagttt cgcgatgact tagctgccca gcggcagtta
     3181 accgacaagg tgctggcaac atttaagcgg ttgctgaccg atacgaataa ggatttactc
     3241 cagggaaata ttgccgcccc cctgaaaacg tttaatgaaa gtattcagtt tctcgactca
     3301 acccgtaccg ccatcagcga attaactatc gattcaccaa aagcgagtca gttctatacc
     3361 caaaccatct ctgacgtgct gaagtttgtc ggcgggatgg ggcatttaag cacctcaggc
     3421 tcgatggtga acgaactggc ggcttattat agtctcttga atttgaagga gcaggctggt
     3481 gtagaacgtg cgctgctgtc caatatcttc tcgatggatc gctttgacga cggccagttc
     3541 agcatgttta gcgatgtggt aggccagcag gatgcctggc tgacggcagc tcgcagcttt
     3601 agcacacctg tgcaggcggc tgagctggac aaatctcttc agtccgctga agcaactcgt
     3661 gctcttgaac tgcgggagac ggcttttaat aaagccgccg aaggcggatt tggagtcaac
     3721 ccgactgact ggtttaacct tcagacccag cgtattgaaa cgctgcaaaa ggtggaaaat
     3781 cgcgcggtgg atgccttgca ggaacatgct gcgctgcttg cccacaatgc
//
