LOCUS       NZ_CP055680             3830 bp    DNA     circular CON 31-MAR-2024
DEFINITION  Escherichia fergusonii strain RHB28-C13 plasmid pRHB28-C13_6,
            complete sequence.
ACCESSION   NZ_CP055680
VERSION     NZ_CP055680.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148269
            Assembly: GCF_013596835.1
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-C13
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 159.376270081111x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013596835.1-RS_2024_03_31
            Annotation Date                   :: 03/31/2024 05:20:28
            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)                     :: 5,064
            CDSs (total)                      :: 4,940
            Genes (coding)                    :: 4,839
            CDSs (with protein)               :: 4,839
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 101
            CDSs (without protein)            :: 101
            Pseudo Genes (ambiguous residues) :: 0 of 101
            Pseudo Genes (frameshifted)       :: 31 of 101
            Pseudo Genes (incomplete)         :: 64 of 101
            Pseudo Genes (internal stop)      :: 18 of 101
            Pseudo Genes (multiple problems)  :: 13 of 101
            Pseudo Genes (short protein)      :: 2 of 101
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055680.1.
            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-C13"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB28-C13_6"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(2434..3830,1..508)
                     /locus_tag="HVY52_RS25145"
                     /old_locus_tag="HVY52_25135"
     CDS             join(2434..3830,1..508)
                     /locus_tag="HVY52_RS25145"
                     /old_locus_tag="HVY52_25135"
                     /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            798..986
                     /locus_tag="HVY52_RS25150"
                     /old_locus_tag="HVY52_25140"
     CDS             798..986
                     /locus_tag="HVY52_RS25150"
                     /old_locus_tag="HVY52_25140"
                     /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(1034..1300)
                     /locus_tag="HVY52_RS25155"
                     /old_locus_tag="HVY52_25145"
     CDS             complement(1034..1300)
                     /locus_tag="HVY52_RS25155"
                     /old_locus_tag="HVY52_25145"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_213069224.1"
                     /translation="MKRSQLTLIDGCFMFGFSPGELMNLCPDERLLFVRMISAMLRRSG
                     GDAGAVMFEAYRHIVSDTNQARRSCMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            1979..2128
                     /locus_tag="HVY52_RS25600"
     CDS             1979..2128
                     /locus_tag="HVY52_RS25600"
                     /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(1445..1617)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.379"
                     /coverage="100.0"
                     /evalue="9.47e-61"
     Typing          1542..2126
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.709"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 gagcatggcg gaaattcgtt cttccagcga gcagatttcc cagattgttg cgtcaattga
       61 tgagatttct ttccagacca acttgctggc gcttaacgcc gccgttgaag cggcacgtgc
      121 cggtgagctt ggcaaaggct ttgcggtagt ggcgacggag gtgcgtaacc tttcccagcg
      181 ctgtgcacga gaggccagtc agatccgtga gctgattaac cagaatatgg ataagattgg
      241 cgaaggggta gcacgagtca ccgcgtccgg caccgcgctg aaagcagcgg cggaaaatac
      301 cgggcggatg aaacagtacg tgagcgatat tgcccgtgcg gcgaatgagc agtcgcttgg
      361 cgtgtcgcag gtgcatcagg cactgaatca gctggagcag gtcactcagc aaaacgcagc
      421 gctggtctct caggcggcga gcgccagcca gatgctggac ggccagtctg aagcgatgtc
      481 cacgctggtc gatcgcttta ttgtctgata ctgccgttca gcatccggtc ttgataactt
      541 acaatcagaa aaaaccgcct aaaaggcggc ttttttatgc ctgcaaataa ctaggattta
      601 ccataacatc tgttgcgtgc accgcctgag aggctctgag agcgtttctg aggactccga
      661 cctgaaacat acacctttct gtgcccatat cgagaaaaaa cgcccctgat gatttctgcg
      721 tacctgcatg gctatgcact caagtgaatg aagtaagatt tcagtctgcg atcaccataa
      781 aaccgggaaa aagccgtatg acaaaacagg aatcagccgc actgaacatg gcaaaattta
      841 tccgggcgca gtcgctgctg ctgctcgaaa aactcgacgt gctcgatctt gatgacgagg
      901 cagccgactg tgagcgaatg cacgaacagg cagaagcgct ttatcagaag ctgagcgcac
      961 gcttcggtat acaggacggc gaataaagag acgaaaagaa cgctcactta gacgaaaagc
     1021 gtatccaggg caactatgta tatccaccgt gtacatagtc atgcctgacg ctttcgagca
     1081 ggtcgagcat gcaggaacga cgagcttgat tggtatcgga cacaatatgg cgatacgcct
     1141 caaacataac agcacccgca tcaccgcccg aacggcgaag catagcggaa atcatccgca
     1201 caaagagcag acgttcatcg gggcaaaggt tcataagttc tcctggtgaa aaaccaaaca
     1261 tgaagcaccc atctattaac gtcagctgtg aacgcttcat tacgcttcat taaaataggt
     1321 aaacccggga aaaagatcca aacgttaaca tcacaggtaa acagaaacgt cgggtcgatc
     1381 gggaaattct ttcccggacg gcgcggggtt gggcaagccg caggcgcgtc agtgctttta
     1441 gcgggtgtcg gggcgcagcc ctgaaccagt cacgtagcgc tagcggagtg tatactggct
     1501 tattatgtag gcacgggtgc gggaatcagt gaagtgcttc atgtggcagg aggaaaatgc
     1561 agcagcagag cgtaagcgga atatatgaga caggagatat tccgcttcct cgctcactga
     1621 ctcgctgcgc tcggtcgttc ggctgcggcg agcggtgcgg gattacgaat ggggcggaaa
     1681 tttcctggga gatgccagga agaaacttaa cagggaaacg gtaaggccgc ggcgaagccg
     1741 tttttccata ggctccgccc ccctgacaag catcacgaaa tctgacgctc aaatcagtgg
     1801 cggcgaaacc cgacaggact ataaagatcc caggcgtttc cccctggtag ctccctcgtg
     1861 cgctctcctg ttcctgcctt tcggtttacc ggtgtcattc cgctgttatg gccgcgttta
     1921 tctcattcca cgcctgacac tcagttccgg gaaggcagtt cgctccaagc tggactgtat
     1981 gcacgaaccc cccgttcagt ccgactgctg cgccttttcc ggtaactatc gtcttgagtc
     2041 caacccggaa agacacgaaa aatcgccact ggcagcggcc actggtaaac aggatgtgcg
     2101 agagatgtat cgagagttct tgaagtagtg gcctgactga ggctacacta gaaggacaaa
     2161 tttggtgaca tgtctcgcac aagactgtta ccacggttag agaatctgcc aggattatct
     2221 aaccttcgaa aaaccacctg caagggtggt tttttcgttt acagagcaag agattacgac
     2281 gatcgtcaaa ggatctcaag aagatccttt atggattgct accagcgcca ctgccgaatg
     2341 tggtgcccgt tcccccaaca ataaactata aagtttatgc atgtatctac cgatactcct
     2401 gcgatccctc aagaaagtaa ggaaagtatc gatatgtcat gggcttatcg tatttcaatg
     2461 caaatgaagt tgtttattgc attattcccg ctactgcttg ccttggtctg gttcgccggt
     2521 tcgggtattg tcagccgtat caataccgaa cagcagatga acaccattgg acagctcacc
     2581 acgctcgccc gcagcgcggg tgatgtggtg catcaactcc agagcgaacg tggaatgagc
     2641 gctggattta tcggcgcgcg cggccaaaag tttcgcgatg acttagctgc ccagcggcag
     2701 ttaaccgaca aggtgctggc aacatttaag cggttgctga ccgatacgaa taaggattta
     2761 ctccagggaa atattgccgc ccccctgaaa acgtttaatg aaagtattca gtttctcgac
     2821 tcaacccgta ccgccatcag cgaattaact atcgattcac caaaagcgag tcagttctat
     2881 acccaaacca tctctgacgt gctgaagttt gtcggcggga tggggcattt aagcacctca
     2941 ggctcgatgg tgaacgaact ggcggcttat tatagtctct tgaatttgaa ggagcaggct
     3001 ggtgtagaac gtgcgctgct gtccaatatc ttctcgatgg atcgctttga cgacggccag
     3061 ttcagcatgt ttagcgatgt ggtaggccag caggatgcct ggctgacggc agctcgcagc
     3121 tttagcacac ctgtgcaggc ggctgagctg gacaaatctc ttcagtccgc tgaagcaact
     3181 cgtgctcttg aactgcggga gacggctttt aataaagccg ccgaaggcgg atttggagtc
     3241 aacccgactg actggtttaa ccttcagacc cagcgtattg aaacgctgca aaaggtggaa
     3301 aatcgcgcgg tggatgcctt gcaggaacat gctgcgctgc ttgcccacaa tgcccgtgtc
     3361 gactggcagt ccttcctggt aatcagcctg gttgccctac tgattgctat cgcctttgcg
     3421 gtgatggtgg cacgcagtat ccagcagcaa ctgaacggta cgctgaaaac catcgcagag
     3481 atggacggcg acctgacacg tcgtcttgac gtccccggca gcgacgagct ctcagccctg
     3541 aaccgtgcct ataaccaagc gattgagaat attcagcata tcgtgcaaga aattaagtcc
     3601 ggtgcggtgg tgttgcgtag cgccagtagt gatatcgctg ccggtaatca ggatctggcc
     3661 cagcgtacgg atgaacaggc ggcatcgatt gtggaaacgg ccgccagcat ggagcagatt
     3721 tctactgcga tcacccagac cgccgataac gccagcgagg cggagcgtct gatacattcg
     3781 atggagcggg acgtactgga agctaatcgc gtctctaacg aggccagtca
//
