LOCUS       NZ_CP057097             5440 bp    DNA     circular CON 02-APR-2024
DEFINITION  Escherichia fergusonii strain RHB38-C07 plasmid pRHB38-C07_5,
            complete sequence.
ACCESSION   NZ_CP057097
VERSION     NZ_CP057097.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148386
            Assembly: GCF_013813205.1
KEYWORDS    RefSeq.
SOURCE      Escherichia fergusonii
  ORGANISM  Escherichia fergusonii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5440)
  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 5440)
  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                     :: RH04 T3-C07
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 148.110310255315x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013813205.1-RS_2024_04_02
            Annotation Date                   :: 04/02/2024 04:20:15
            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)                     :: 4,766
            CDSs (total)                      :: 4,646
            Genes (coding)                    :: 4,502
            CDSs (with protein)               :: 4,502
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 144
            CDSs (without protein)            :: 144
            Pseudo Genes (ambiguous residues) :: 0 of 144
            Pseudo Genes (frameshifted)       :: 52 of 144
            Pseudo Genes (incomplete)         :: 85 of 144
            Pseudo Genes (internal stop)      :: 27 of 144
            Pseudo Genes (multiple problems)  :: 21 of 144
            Pseudo Genes (short protein)      :: 2 of 144
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP057097.1.
            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..5440
                     /organism="Escherichia fergusonii"
                     /mol_type="genomic DNA"
                     /strain="RHB38-C07"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB38-C07_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     ARG             4..911
                     /name="tet(A)"
                     /gene="tet(A)"
                     /gene_name="major facilitator superfamily (MFS) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="tetracycline antibiotic"
                     /identity="98.32"
                     /coverage="71.23"
     ARG             5153..5439
                     /name="tet(A)"
                     /gene="tet(A)"
                     /gene_name="major facilitator superfamily (MFS) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="tetracycline antibiotic"
                     /identity="96.88"
                     /coverage="22.64"
     gene            complement(943..>1293)
                     /locus_tag="HVZ69_RS23645"
                     /old_locus_tag="HVZ69_23630"
                     /pseudo=""
     CDS             complement(943..>1293)
                     /locus_tag="HVZ69_RS23645"
                     /old_locus_tag="HVZ69_23630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000058717.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="EamA family transporter"
                     /name="EamA family transporter"
     gene            2397..2714
                     /locus_tag="HVZ69_RS23650"
                     /old_locus_tag="HVZ69_23635"
     CDS             2397..2714
                     /locus_tag="HVZ69_RS23650"
                     /old_locus_tag="HVZ69_23635"
                     /inference="COORDINATES: protein motif:HMM:NF016701.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="glutathione-dependent formaldehyde-activating
                     enzyme"
                     /protein_id="WP_240761615.1"
                     /translation="MVKVEDFDWQTSEELISSWKKESGYRNDFCKKCGSTVPNILRGQP
                     YVWLPLGLLNENIKADCCGDFCTDDSMMWDCVRSANSNKKAVSSLFDLLVMLNVEQAKL
                     E"
                     /name="glutathione-dependent formaldehyde-activating
                     enzyme"
     gene            complement(2980..3093)
                     /locus_tag="HVZ69_RS23655"
                     /old_locus_tag="HVZ69_23640"
     CDS             complement(2980..3093)
                     /locus_tag="HVZ69_RS23655"
                     /old_locus_tag="HVZ69_23640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_059446996.1"
                     /translation="MHEPPVQSDRCALSGNYHLESNPERHDKAPLAAATGN"
                     /name="hypothetical protein"
     gene            3512..3703
                     /locus_tag="HVZ69_RS23660"
                     /old_locus_tag="HVZ69_23645"
     CDS             3512..3703
                     /locus_tag="HVZ69_RS23660"
                     /old_locus_tag="HVZ69_23645"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /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_047402702.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNDQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4137..4364
                     /locus_tag="HVZ69_RS23665"
                     /old_locus_tag="HVZ69_23650"
     CDS             4137..4364
                     /locus_tag="HVZ69_RS23665"
                     /old_locus_tag="HVZ69_23650"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011264024.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_052945622.1"
                     /translation="MDLARERQAHEAGARTRATAHERTPQQERQKAAREAERGREAWTL
                     GQGMKKPVAGCYGRLTRWKGGGDVVYMALL"
                     /name="hypothetical protein"
     gene            complement(4396..5046)
                     /gene="tetR(A)"
                     /locus_tag="HVZ69_RS23670"
                     /old_locus_tag="HVZ69_23655"
     CDS             complement(4396..5046)
                     /gene="tetR(A)"
                     /locus_tag="HVZ69_RS23670"
                     /old_locus_tag="HVZ69_23655"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000164043.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="tetracycline resistance transcriptional repressor
                     TetR(A)"
                     /protein_id="WP_001493764.1"
                     /translation="MTKLQPNTVIRAALDLLNEVGVDGLTTRKLAERLGVQQPALYWHF
                     RNKRALLDALAEAMLAENHTHSVPRADDDWRSFLIGNARSFRQALLAYRDGARIHAGTR
                     PGAPQMETADAQLRFLCEAGFSAGDAVNALMTISYFTVGAVLEEQAGDSDAGERGGTVE
                     QAPLSPLLRAAIDAFDEADPDAAFEQGLAVIVDGLAKRRLVVRNVEGPRKGDD"
                     /name="tetR(A)"
     Typing          complement(3014..3637)
                     /name="rep_cluster_2327"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.603"
                     /coverage="99.0"
                     /evalue="1.53e-168"
ORIGIN
        1 gggttctcta tatcgggcgg atcgtggccg gcatcaccgg ggcgactggg gcggtagccg
       61 gcgcttatat tgccgatatc actgatggcg atgagcgcgc gcggcacttc ggcttcatga
      121 gcgcctgttt cgggttcggg atggtcgcgg gacctgtgct cggtgggctg atgggcggtt
      181 tctcccccca cgctccgttc ttcgccgcgg cagccttgaa cggcctcaat ttcctgacgg
      241 gctgtttcct tttgccggag tcgcacaaag gcgaacgccg gccgttacgc cgggaggctc
      301 tcaacccgct cgcttcgttc cggtgggccc ggggcatgac cgtcgtcgcc gccctgatgg
      361 cggtcttctt catcatgcaa cttgtcggac aggtgccggc cgcgctttgg gtcattttcg
      421 gcgaggatcg ctttcactgg gacgcgacca cgatcggcat ttcgcttgcc gcatttggca
      481 ttctgcattc actcgcccag gcaatgatca ccggccctgt agccgcccgg ctcggcgaaa
      541 ggcgggcact catgctcgga atgattgccg acggcacagg ctacatcctg cttgccttcg
      601 cgacacgggg atggatggcg ttcccgatca tggtcctgct tgcttcgggt ggcatcggaa
      661 tgccggcgct gcaagcaatg ttgtccaggc aggtggatga ggaacgtcag gggcagctgc
      721 aaggctcact ggcggcgctc accagcctga cctcgatcgt cggacccctc ctcttcacgg
      781 cgatctatgc ggcttctata acaacgtgga acgggtgggc atggattgca ggcgctgccc
      841 tctacttgct ctgcctgccg gcgctgcgtc gcgggctttg gagcggcgca gggcaacgag
      901 ccgatcgctg atcgtggaaa cgataggcct atgccatgcg ggtcaaggcg acttccggca
      961 agctatacgc gccctaggag tgcggttgga acgttggccc agccagatac tcccgatcac
     1021 gagcaggacg ccgatgattt gaagcgcact cagcgtctga tccaagaaca accatcctag
     1081 caacacggcg gtccccgggc tgagaaagcc cagtaaggaa acaactgtag gttcgagtcg
     1141 cgagatcccc cggaaccaaa ggaagtaggt taaacccgct ccgatcaggc cgagccacgc
     1201 caggccgaga acattggttc ctgtaggcat cgggattggc ggatcaaaca ctaaagctac
     1261 tggaacgagc agaagtcctc cggccgccag ttggggtcag tttggatata gagaattatt
     1321 gtacggtaag cctgtttttt gaacagactt acctatagca atagggtgta ctcccgcgct
     1381 atacggcatt ttcagaggtt tgaccttaat cggataacct aaatgcgata ctgcaagagc
     1441 gacaacttaa aagcgataac cactgacgca aaatcaaccc cttacgaacc aagattggtt
     1501 aaataatgcg cttaacgtac aaaaaattcc gatctccaaa ctgacccctt cttcgcctct
     1561 tatgtttctc gaatgaatcg atggggacag gaaatgtttt gtggccaccg ccgcttcgcc
     1621 ggcaccacaa aactgtcgga caagatgtgt ttttggagta ccgccggcac caaaaacatt
     1681 tcatcaggcg cagcctgata ccctgaattt cgtacgcacg aaattttgct tttgttcaga
     1741 tcgagggcag gattcgcaaa gtgctggcgt ttgtacccac cggaagctgc cgcgcctggc
     1801 ggcttggcca acgcctcacg gccgcacagt caactgtgca cccgttcacc gttaccagat
     1861 cccctgattc cggccgggcc tgcctgcact ggccaaagcc ttaaaactgc gcaatccgca
     1921 gcgcgggggc agttgataac cactttttac tgtcatactt atttgccggc tctctgatcg
     1981 gtaccggctg actgtttgtg caaattttgt cggacatcct gaccctcgat gtccgttttt
     2041 tttgttcaaa attcgccttt agtgccagca ttcgtccgaa accggccgcc attcacttcc
     2101 gtgcatagcc atgcaggcgc gcagaaatca tcaggcgcgt tttttcacga tatggacagg
     2161 gaaaggtgcc ggaaacgcag aggacgcggc agaaacgcgc tgagggcctc tcagggggtg
     2221 cgggcaagag atgttatggt aaatacgtat tttattttga tggagattat tttgattagt
     2281 gggtcatgtt tgtgtggtgc tgttaaattc acgataaaaa atcagcctga aaattttata
     2341 gatgccactg ttccctatgc cgaagacagt ctggagtagg tcataactta gctgccatag
     2401 tgaaagttga ggattttgac tggcaaacct cagaggaatt gatttcttca tggaaaaagg
     2461 aaagtggtta ccgtaacgat ttctgcaaaa aatgtggttc gactgttcca aatattttga
     2521 gggggcagcc ttatgtgtgg ctaccacttg ggctacttaa cgagaatatt aaagctgact
     2581 gctgtggtga tttttgtaca gacgattcga tgatgtggga ctgtgtgcgc tcagcgaata
     2641 gtaacaaaaa agcggtaagt agcctgttcg acttattggt tatgctcaat gttgagcagg
     2701 ctaaacttga atagatagcg agcacgcctt agggatgttg cttaatggat tgtattggaa
     2761 agatgcactg atggatagtt atcttgacct gataaggggt taccgcgtag attagttgtc
     2821 gcaaacgaaa aaaccgcctt gcagggcggt ttttcgaagg tactcagagc tagcaactct
     2881 ttgaaccgag gtaactggct tggaggagcg cagtcaccaa aacttgtcct ttcagtttag
     2941 ccttaaccgg cacatgactt caagtccatc tcctctaaat cagttaccag tggctgctgc
     3001 cagtggcgct ttgtcgtgtc tttccgggtt ggactcaaga tgatagttac cggacaaggc
     3061 gcagcggtcg gactgaacgg ggggttcgtg catacagtcc agcttggagc gaactgccta
     3121 cccggaactg agtgtcaggc gtggaatgag acaaacgcgg ccataacagc ggaatgacac
     3181 cggtaaaccg aaaggcagga acaggagagc gcacgaggga gccaccaggg ggaaacgcct
     3241 ggtatcttta tagtcctgtc gggtttcgcc accactgatt tgagcgtccg attctgtgat
     3301 gcttgtcagg ggggcggagc ctatggaaaa acgccccgcc ggggcgtggc cttttcgccc
     3361 ttgtccttag ctttcgttat gcttaccgtt acgttatctg cttatcctcc ctccgctcgc
     3421 cgcagactca tgaccgaacg gagtgagcga atgagcgagg aagcggaaaa ccatcagaac
     3481 gtacagtaag cactttcgcg ccggggcctt catgaacaaa caacaaaaga cagccgttaa
     3541 catggctaaa ttcatccagg atcagtccct gcttcttctg gacaggctta atgagctgga
     3601 tctggatcat gaggctgatt tctgcgagaa actccatgag gatgcggaac gcctttaccg
     3661 aagcctgtca gcgcgcctga atgatcagca ggacggtgcg taatggctcc gttctgggta
     3721 ttaccggagt aataccggca tcgccttaat tttcattgtc ttggtgctta acattattac
     3781 cctagtaata cccagaatcc ctttattttt tcttttttat ttatttttca tggagttgcg
     3841 ataaaaatcg cagctgcgtt aggtgtatgg ggtcagtttg gatatagaga attattgtac
     3901 ggtaagcctg ttttttgaac agacttacct atagcaatag ggtgtactcc cgcgctatac
     3961 ggcattttca gaggtttgac cttaatcgga taacctaaat gcgatactgc aagagcgaca
     4021 acttaaaagc gataaccact gacgcaaaat caacccctta cgaaccaaga ttggttaaat
     4081 aatgcgctta acgtacaaaa aattccgatc tccaaactga ccccaagacg gccgccctgg
     4141 acctcgcccg cgagcgccag gcgcacgagg ccggcgcgcg gacccgcgcc acggcccacg
     4201 agcggacgcc gcagcaggag cgccagaagg ccgccagaga ggccgagcgc ggccgtgagg
     4261 cttggacgct agggcagggc atgaaaaagc ccgtagcggg ctgctacggg cgtctgacgc
     4321 ggtggaaagg gggaggggat gttgtctaca tggctctgct gtagtgagtg ggttgcgctc
     4381 cggcagcggt cctgatcaat cgtcaccctt tctcggtcct tcaacgttcc tgacaacgag
     4441 cctccttttc gccaatccat cgacaatcac cgcgagtccc tgctcgaacg ctgcgtccgg
     4501 atcggcttcg tcgaaggcgt ctatcgcggc ccgcaacagc ggcgagagcg gagcctgttc
     4561 aacggtgccg ccgcgctcgc cggcatcgct gtcgccggcc tgctcctcaa gcacggcccc
     4621 aacagtgaag tagctgattg tcatcagcgc attgacggcg tccccggccg aaaaacccgc
     4681 ctcgcagagg aagcgaagct gcgcgtcggc cgtttccatc tgcggtgcgc ccggtcgcgt
     4741 gccggcatgg atgcgcgcgc catcgcggta ggcgagcagc gcctgcctga agctgcgggc
     4801 attcccgatc agaaatgagc gccagtcgtc gtcggctctc ggcaccgaat gcgtatgatt
     4861 ctccgccagc atggcttcgg ccagtgcgtc gagcagcgcc cgcttgttcc tgaagtgcca
     4921 gtaaagcgcc ggctgctgaa cccccaaccg ttccgccagt ttgcgtgtcg tcagaccgtc
     4981 tacgccgacc tcgttcaaca ggtccagggc ggcacggatc actgtattcg gctgcaactt
     5041 tgtcatgctt gacactttat cactgataaa cataatatgt ccaccaactt atcagtgata
     5101 aagaatccgc gcgttcaatc ggaccagcgg aggctggtcc ggaggccaga cgtgaaaccc
     5161 aacagacccc tgatcgtaat tctgagcact gtcgcgctcg acgctgtcgg catcggcctg
     5221 attatgccgg tgctgccggg cctcctgcgc gatctggttc actcgaacga cgtctccgcc
     5281 cactatggca ttctgctggc gctgtatgcg ttgatgcaat ttgcctgcgc acctgtgctg
     5341 ggcgcgctgt cggatcgttt cgggcggcgg ccggtcttgc tcgtctcgct ggccggcgct
     5401 gctgtcgact acgccatcat ggcgacgacg cctttccttt
//
