LOCUS       NZ_CP057096             5603 bp    DNA     circular CON 02-APR-2024
DEFINITION  Escherichia fergusonii strain RHB38-C07 plasmid pRHB38-C07_4,
            complete sequence.
ACCESSION   NZ_CP057096
VERSION     NZ_CP057096.1
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 5603)
  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 5603)
  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
            CP057096.1.
            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..5603
                     /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_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(5577..5603,1..162))
                     /locus_tag="HVZ69_RS23620"
                     /old_locus_tag="HVZ69_23605"
     CDS             complement(join(5577..5603,1..162))
                     /locus_tag="HVZ69_RS23620"
                     /old_locus_tag="HVZ69_23605"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957857.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000957857.1"
                     /translation="MLTRKSIDTVLLSVGAEKLSQREWDWMKMLKPMDPPPAMVTTSIL
                     KRRGDTAALTLLQDTGV"
                     /name="hypothetical protein"
     gene            complement(592..2496)
                     /locus_tag="HVZ69_RS23625"
                     /old_locus_tag="HVZ69_23610"
     CDS             complement(592..2496)
                     /locus_tag="HVZ69_RS23625"
                     /old_locus_tag="HVZ69_23610"
                     /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_061202242.1"
                     /translation="MSWVYRISMQMKLFIALFPLLLALVWFAGSGIVSRINTEQQMNTI
                     GQLTTLARSAGDVVHQLQSERGMSAGFIGARGQKFRDDLAAQRQLTDKVLATFKRLLTD
                     TNKDLLQGNIAAPLKTFNESIQFLDSTRTAISELTIDSPKASQFYTQTISDVLKFVGGM
                     GHLSTSGSMVNELAAYYSLLNLKEQAGVERALLSNIFSMDRFDDGQFSMFSDVVGQQDA
                     WLTAARSFSTPVQAAELDKSLQSAEATRALELRETAFNKAAEGGFGVNPTDWFNLQTQR
                     IETLQKVENRAVDALQEHAALLAHNARVDWQSFLVISLVALLIAIAFAVMVARSIQQQL
                     NGTLKTIAEMDGDLTRRLDVPGSDELSALNRAYNQAIENIQHIVQEIKSGAVVLRSASS
                     DIAAGNQDLAQRTDEQAASIVETAASMEQISTAITQTADNASEAERLIHSMERDVLEAN
                     RVSNEASQSMAEIRSSSEQISQIVASIDEISFQTNLLALNAAVEAARAGELGKGFAVVA
                     TEVRNLSQRCAREASQIRELINQNMDKIGEGVARVTASGTALKAAAENTGRMKQYVSDI
                     ARAANEQSLGVSQVHQALNQLEQVTQQNAALVSQAASASQMLDGQSEAMSTLVDRFIV"
                     /name="methyl-accepting chemotaxis protein"
     gene            complement(2802..2951)
                     /locus_tag="HVZ69_RS24075"
     CDS             complement(2802..2951)
                     /locus_tag="HVZ69_RS24075"
                     /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            3521..3670
                     /locus_tag="HVZ69_RS23630"
                     /old_locus_tag="HVZ69_23615"
     CDS             3521..3670
                     /locus_tag="HVZ69_RS23630"
                     /old_locus_tag="HVZ69_23615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(4368..5567)
                     /locus_tag="HVZ69_RS23635"
                     /old_locus_tag="HVZ69_23620"
     CDS             complement(4368..5567)
                     /locus_tag="HVZ69_RS23635"
                     /old_locus_tag="HVZ69_23620"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000198547.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS91 family transposase"
                     /protein_id="WP_000948429.1"
                     /translation="MLSGFTPRPLKRLFTANQCWTSFLDAGGLRDIEVEAVTKMLACGT
                     RILGVKEFGCDNPDCQHVKYLTNSCGSRACPSCGKKATDLWTATQLNRLPDCDWVHLVF
                     TLPDTLWPVFESNRWLLNDVCRLAVENLLYAARKRGLEPGIFCAIHTYGRRLNWHPHVH
                     VSVTCGGLNKHGQWKKLSFLKDAMRSRWMWNMRQLLLKAWSEGMAMPESLSHITTESQW
                     RSLVLKSGGKYWHVYMSKKTAGGRNTARYLGRYLKKPPIAASRLAHYNGGASLSFRYLD
                     HKTGETATETLTQRELVARLKQHIPEKFFKMVRYFGFLANRVCGEKLPQVYRALGMDKP
                     EPVAKVCYAQMVKQFLSRDPFECVLCGCRMVYRRAIAGLNVSGLKKNARDISLLRYMPA
                     "
                     /name="IS91 family transposase"
     Typing          3314..3486
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.379"
                     /coverage="100.0"
                     /evalue="9.47e-61"
     Typing          complement(2793..3389)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.211"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aagggctgct gtatcgccac ggcgcttcag gatggaggtc gtcaccatcg caggtggtgg
       61 gtccatgggt ttgagcattt tcatccagtc ccattctcgt tgtgagagct tctcagcacc
      121 aacagagagc agaactgtat cgatactttt gcgggtcaac ataaggggat gagtccttaa
      181 taaaacaggt cctcagagca tacatattct gcggggcgtg cggcaacaac aggacgaacc
      241 ggggcggttt tcaatttgca gccgccaggc tgccgtggtt caccgttttc ggatgggaag
      301 aacgccggaa acaggactta ccccggctga atggtgtgaa tttccgcgct atgcacttgt
      361 gcgcatactc atgcatgccg taaaaacaga gcctgcgcgt ttctggcggg ttttcgggtg
      421 gtttgttgcc tgttttaccg gtttcccgtc agaaacgccc tgagggcctc tcaggcggtg
      481 ctgataacag atgttatggt aaatcctagt tatttgcagg cataaaaaag ccgcctttta
      541 ggcggttttt tctgattgta agttatcaag accggatgct gaacggcagt atcagacaat
      601 aaagcgatcg accagcgtgg acatcgcttc agactggccg tccagcatct ggctggcgct
      661 cgccgcctga gagaccagcg ctgcgttttg ctgagtgacc tgctccagct gattcagtgc
      721 ctgatgcacc tgcgacacgc caagcgactg ctcattcgcc gcacgggcaa tatcgctcac
      781 gtactgtttc atccgcccgg tattttccgc cgctgctttc agcgcggtgc cggacgcggt
      841 gactcgtgct accccttcgc caatcttatc catattctgg ttaatcagct cacggatctg
      901 actggcctct cgtgcacagc gctgggaaag gttacgcacc tccgtcgcca ctaccgcaaa
      961 gcctttgcca agctcaccgg cacgtgccgc ttcaacggcg gcgttaagcg ccagcaagtt
     1021 ggtctggaaa gaaatctcat caattgacgc aacaatctgg gaaatctgct cgctggaaga
     1081 acgaatttcc gccatgctct gactggcctc gttagagacg cgattagctt ccagtacgtc
     1141 ccgctccatc gaatgtatca gacgctccgc ctcgctggcg ttatcggcgg tctgggtgat
     1201 cgcagtagaa atctgctcca tgctggcggc cgtttccaca atcgatgccg cctgttcatc
     1261 cgtacgctgg gccagatcct gattaccggc agcgatatca ctactggcgc tacgcaacac
     1321 caccgcaccg gacttaattt cttgcacgat atgctgaata ttctcaatcg cttggttata
     1381 ggcacggttc agggctgaga gctcgtcgct gccggggacg tcaagacgac gtgtcaggtc
     1441 gccgtccatc tctgcgatgg ttttcagcgt accgttcagt tgctgctgga tactgcgtgc
     1501 caccatcacc gcaaaggcga tagcaatcag tagggcaacc aggctgatta ccaggaagga
     1561 ctgccagtcg acacgggcat tgtgggcaag cagcgcagca tgttcctgca aggcatccac
     1621 cgcgcgattt tccacctttt gcagcgtttc aatacgctgg gtctgaaggt taaaccagtc
     1681 agtcgggttg actccaaatc cgccttcggc ggctttatta aaagccgtct cccgcagttc
     1741 aagagcacga gttgcttcag cggactgaag agatttgtcc agctcagccg cctgcacagg
     1801 tgtgctaaag ctgcgagctg ccgtcagcca agcatcctgc tggcctacca catcgctaaa
     1861 catgctgaac tggccgtcgt caaagcgatc catcgagaag atattggaca gcagcgcacg
     1921 ttctacacca gcctgctcct tcaaattcaa gagactataa taagccgcca gttcgttcac
     1981 catcgagcct gaggtgctta aatgccccat cccgccgaca aacttcagca cgtcagagat
     2041 ggtttgggta tagaactgac tcgcttttgg tgaatcgata gttaattcgc tgatggcggt
     2101 acgggttgag tcgagaaact gaatactttc attaaacgtt ttcagggggg cggcaatatt
     2161 tccctggagt aaatccttat tcgtatcggt cagcaaccgc ttaaatgttg ccagcacctt
     2221 gtcggttaac tgccgctggg cagctaagtc atcgcgaaac ttttggccgc gcgcgccgat
     2281 aaatccagcg ctcattccac gttcgctctg gagttgatgc accacatcac ccgcgctgcg
     2341 ggcgagcgtg gtgagctgtc caatggtgtt catctgctgt tcggtattga tacggctgac
     2401 aatacccgaa ccggcgaacc agaccaaggc aagcagtagc gggaataatg caataaacaa
     2461 cttcatttgc attgaaatac gataaaccca tgacatatcg atactttcct tactttcttg
     2521 agggatcgca ggagtatcgg tagatacatg cataaacttt atagtttatt gttgggggaa
     2581 cgggcaccac attcggcagt ggcgctggta gcaatccata aaggatcttc ttgagatcct
     2641 ttgacgatcg tcgtaatctc ttgctctgta aacgaaaaaa ccacccttgc aggtggtttt
     2701 tcgaaggtta gataatcctg gcagattctc taaccgtggt aacagtcttg tgcgagacat
     2761 gtcaccaaat ttgtccttct agtgtagcct cagtcaggcc actacttcaa gaactctcga
     2821 tacatctctc gcacatcctg tttaccagtg gccgctgcca gtggcgattt ttcgtgtctt
     2881 tccgggttgg actcaagacg atagttaccg gaaaaggcgc agcagtcgga ctgaacgggg
     2941 ggttcgtgca tacagtccag cttggagcga actgccttcc cggaactgag tgtcaggcgt
     3001 ggaatgagat aaacgcggcc ataacagcgg aatgacaccg gtaaaccgaa aggcaggaac
     3061 aggagagcgc acgagggagc taccaggggg aaacgcctgg gatctttata gtcctgtcgg
     3121 gtttcgccgc cactgatttg agcgtcagat ttcgtgatgc ttgtcagggg ggcggagcct
     3181 atggaaaaac ggcttcgccg cggccttacc gtttccctgt taagtttctt cctggcatct
     3241 cccaggaaat ttccgcccca ttcgtaatcc cgcaccgctc gccgcagccg aacgaccgag
     3301 cgcagcgagt cagtgagcga ggaagcggaa tatctcctgt ctcatatatt ccgcttacgc
     3361 tctgctgctg cattttcctc ctgccacatg aagcacttca ctgattcccg cacccgtgcc
     3421 tacataataa gccagtatac actccgctag cgctacatga ctggttcagg gctgcgcccc
     3481 gaaacccgct aacaacctct cagctactgg atatcacccc atgccatctg aatatgatga
     3541 acaactggat tcgactgata cgcagcttcc cggcgaatat gacctttttg atttaatggc
     3601 gcaggttact gaagagaacc tgcatgcccc tgtggatttt gggtcgcctg tcggccggga
     3661 agcgttatag ctttttcgct tgcccgcgta cgtggtaata ctccggtatt accttttatt
     3721 tctttatttt catgtaatta cagtggattt ttaatacccg ggtattactc gtgaaaacga
     3781 aatattcctt ttttttcttt taattcatgc agttgcgatg aaaatcgcgg ctgcgttagg
     3841 tgtatgacca ttttgaggtt gaaaaataat caaccatggc gggtgattta cgcaggttaa
     3901 ggggagatcg tgacaaaaaa agcgttcctc actgtatcgt tcatgcctgc atgaacgggt
     3961 tattcttcct gactacagaa ttacatcgct ccttcagttc atacatcact tttacatcac
     4021 ttatacatca cttttacatc acttatgcat cacttttaca tcattccttc agctcatacg
     4081 tcactttcat cctctgtgcc atttgtacat cacccccttc ctgaacgtgc tgacagcggg
     4141 ttttccggct gcgccggcaa cgcttcacgg ccacgcaata aattgcgtcc ccgttcacgt
     4201 ataggaaatt gaaaaaccag tcgataccat tgtccacgcc ttatgccacg tgagcctttc
     4261 tgcttttccc accactccgg tggtttccct ctctgtatgg tcgattttta taccgtaaca
     4321 ggctgttttt tatactttca ccgattcccg ggcacactta gcctgtgtca ggccggcata
     4381 tacctcagta gactgatatc ccgcgcgttt ttcttcagcc ctgatacatt cagccccgca
     4441 atggcccggc ggtataccat ccggcagcca cacagcacgc attcgaacgg gtcacgactc
     4501 aggaactgtt tcaccatttg tgcatagcac actttcgcca ctggttccgg tttatccatc
     4561 cccagtgcac ggtacacctg cggcagcttc tctccacaca cacggttggc aaggaacccg
     4621 aagtacctca ccatcttaaa aaacttctcc gggatgtgct gtttcagcct cgcgaccagc
     4681 tcacgctgtg tcagcgtttc cgtcgccgtt tctcccgttt tgtggtccag gtaacggaag
     4741 ctcaggcttg cccctccgtt gtaatgagcc agtcgggaag ccgctattgg tggcttcttc
     4801 agataacgac ccaggtagcg tgccgtattc cgccctccgg ctgtcttctt cgacatgtac
     4861 acatgccagt attttccgcc ggatttcagc accaggcttc tccactgtga ttccgtcgtg
     4921 atatgtgaca acgactccgg cattgccatc ccctctgacc acgctttcag aagcagctgc
     4981 cgcatattcc acatccaccg tgaacgcatc gcgtctttca ggaagctcag ctttttccac
     5041 tgaccatgct tattcagacc tccacaggtt acagacacat gtacatgcgg atgccagttg
     5101 agacgacggc catacgtgtg gatggcgcag aagataccgg gttccagccc ccgttttcgg
     5161 gcggcataca gcagattctc caccgccaga cggcacacgt cattcagcag ccagcggttg
     5221 ctttcgaaca ccggccacag cgtgtccggc agggtgaaga ccagatgtac ccagtcgcag
     5281 tcaggaagac gattcagctg tgttgctgtc cacaggtctg tggccttctt tccgcaggac
     5341 gggcaggcac ggctgccgca tgagttggtc aggtacttta cgtgctgaca gtccgggtta
     5401 tcacacccga actcttttac acccagtatc cgtgtgccgc aggccagcat tttggtgacg
     5461 gcttcaacct cgatatcgcg cagaccgccc gcatccagga aggacgtcca gcactggttg
     5521 gctgtgaaca gacgtttcag agggcgggga gtaaaaccgg acaacatgag gatggattaa
     5581 accccggtat cctgtagcag ggt
//
