LOCUS       NZ_CP057107             5603 bp    DNA     circular CON 30-MAR-2024
DEFINITION  Escherichia fergusonii strain RHB38-C01 plasmid pRHB38-C01_4,
            complete sequence.
ACCESSION   NZ_CP057107
VERSION     NZ_CP057107.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148383
            Assembly: GCF_013812875.1
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-C01
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 145.024101274844x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013812875.1-RS_2024_03_30
            Annotation Date                   :: 03/30/2024 05:12:01
            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)                     :: 4,733
            CDSs (total)                      :: 4,615
            Genes (coding)                    :: 4,527
            CDSs (with protein)               :: 4,527
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 88
            CDSs (without protein)            :: 88
            Pseudo Genes (ambiguous residues) :: 0 of 88
            Pseudo Genes (frameshifted)       :: 22 of 88
            Pseudo Genes (incomplete)         :: 57 of 88
            Pseudo Genes (internal stop)      :: 22 of 88
            Pseudo Genes (multiple problems)  :: 11 of 88
            Pseudo Genes (short protein)      :: 2 of 88
            CRISPR Arrays                     :: 4
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP057107.1.
            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-C01"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB38-C01_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(5273..5603,1..1574)
                     /locus_tag="HVZ66_RS23490"
                     /old_locus_tag="HVZ66_23490"
     CDS             join(5273..5603,1..1574)
                     /locus_tag="HVZ66_RS23490"
                     /old_locus_tag="HVZ66_23490"
                     /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            2004..2192
                     /locus_tag="HVZ66_RS23495"
                     /old_locus_tag="HVZ66_23495"
     CDS             2004..2192
                     /locus_tag="HVZ66_RS23495"
                     /old_locus_tag="HVZ66_23495"
                     /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            2202..3401
                     /locus_tag="HVZ66_RS23500"
                     /old_locus_tag="HVZ66_23500"
     CDS             2202..3401
                     /locus_tag="HVZ66_RS23500"
                     /old_locus_tag="HVZ66_23500"
                     /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"
     gene            complement(4099..4248)
                     /locus_tag="HVZ66_RS23505"
                     /old_locus_tag="HVZ66_23505"
     CDS             complement(4099..4248)
                     /locus_tag="HVZ66_RS23505"
                     /old_locus_tag="HVZ66_23505"
                     /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            4818..4967
                     /locus_tag="HVZ66_RS23860"
     CDS             4818..4967
                     /locus_tag="HVZ66_RS23860"
                     /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(4284..4456)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.379"
                     /coverage="100.0"
                     /evalue="9.47e-61"
     Typing          4381..4965
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.709"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 agggaaatat tgccgccccc ctgaaaacgt ttaatgaaag tattcagttt ctcgactcaa
       61 cccgtaccgc catcagcgaa ttaactatcg attcaccaaa agcgagtcag ttctataccc
      121 aaaccatctc tgacgtgctg aagtttgtcg gcgggatggg gcatttaagc acctcaggct
      181 cgatggtgaa cgaactggcg gcttattata gtctcttgaa tttgaaggag caggctggtg
      241 tagaacgtgc gctgctgtcc aatatcttct cgatggatcg ctttgacgac ggccagttca
      301 gcatgtttag cgatgtggta ggccagcagg atgcttggct gacggcagct cgcagcttta
      361 gcacacctgt gcaggcggct gagctggaca aatctcttca gtccgctgaa gcaactcgtg
      421 ctcttgaact gcgggagacg gcttttaata aagccgccga aggcggattt ggagtcaacc
      481 cgactgactg gtttaacctt cagacccagc gtattgaaac gctgcaaaag gtggaaaatc
      541 gcgcggtgga tgccttgcag gaacatgctg cgctgcttgc ccacaatgcc cgtgtcgact
      601 ggcagtcctt cctggtaatc agcctggttg ccctactgat tgctatcgcc tttgcggtga
      661 tggtggcacg cagtatccag cagcaactga acggtacgct gaaaaccatc gcagagatgg
      721 acggcgacct gacacgtcgt cttgacgtcc ccggcagcga cgagctctca gccctgaacc
      781 gtgcctataa ccaagcgatt gagaatattc agcatatcgt gcaagaaatt aagtccggtg
      841 cggtggtgtt gcgtagcgcc agtagtgata tcgctgccgg taatcaggat ctggcccagc
      901 gtacggatga acaggcggca tcgattgtgg aaacggccgc cagcatggag cagatttcta
      961 ctgcgatcac ccagaccgcc gataacgcca gcgaggcgga gcgtctgata cattcgatgg
     1021 agcgggacgt actggaagct aatcgcgtct ctaacgaggc cagtcagagc atggcggaaa
     1081 ttcgttcttc cagcgagcag atttcccaga ttgttgcgtc aattgatgag atttctttcc
     1141 agaccaactt gctggcgctt aacgccgccg ttgaagcggc acgtgccggt gagcttggca
     1201 aaggctttgc ggtagtggcg acggaggtgc gtaacctttc ccagcgctgt gcacgagagg
     1261 ccagtcagat ccgtgagctg attaaccaga atatggataa gattggcgaa ggggtagcac
     1321 gagtcaccgc gtccggcacc gcgctgaaag cagcggcgga aaataccggg cggatgaaac
     1381 agtacgtgag cgatattgcc cgtgcggcga atgagcagtc gcttggcgtg tcgcaggtgc
     1441 atcaggcact gaatcagctg gagcaggtca ctcagcaaaa cgcagcgctg gtctctcagg
     1501 cggcgagcgc cagccagatg ctggacggcc agtctgaagc gatgtccacg ctggtcgatc
     1561 gctttattgt ctgatactgc cgttcagcat ccggtcttga taacttacaa tcagaaaaaa
     1621 ccgcctaaaa ggcggctttt ttatgcctgc aaataactag gatttaccat aacatctgtt
     1681 atcagcaccg cctgagaggc cctcagggcg tttctgacgg gaaaccggta aaacaggcaa
     1741 caaaccaccc gaaaacccgc cagaaacgcg caggctctgt ttttacggca tgcatgagta
     1801 tgcgcacaag tgcatagcgc ggaaattcac accattcagc cggggtaagt cctgtttccg
     1861 gcgttcttcc catccgaaaa cggtgaacca cggcagcctg gcggctgcaa attgaaaacc
     1921 gccccggttc gtcctgttgt tgccgcacgc cccgcagaat atgtatgctc tgaggacctg
     1981 ttttattaag gactcatccc cttatgttga cccgcaaaag tatcgataca gttctgctct
     2041 ctgttggtgc tgagaagctc tcacaacgag aatgggactg gatgaaaatg ctcaaaccca
     2101 tggacccacc acctgcgatg gtgacgacct ccatcctgaa gcgccgtggc gatacagcag
     2161 cccttaccct gctacaggat accggggttt aatccatcct catgttgtcc ggttttactc
     2221 cccgccctct gaaacgtctg ttcacagcca accagtgctg gacgtccttc ctggatgcgg
     2281 gcggtctgcg cgatatcgag gttgaagccg tcaccaaaat gctggcctgc ggcacacgga
     2341 tactgggtgt aaaagagttc gggtgtgata acccggactg tcagcacgta aagtacctga
     2401 ccaactcatg cggcagccgt gcctgcccgt cctgcggaaa gaaggccaca gacctgtgga
     2461 cagcaacaca gctgaatcgt cttcctgact gcgactgggt acatctggtc ttcaccctgc
     2521 cggacacgct gtggccggtg ttcgaaagca accgctggct gctgaatgac gtgtgccgtc
     2581 tggcggtgga gaatctgctg tatgccgccc gaaaacgggg gctggaaccc ggtatcttct
     2641 gcgccatcca cacgtatggc cgtcgtctca actggcatcc gcatgtacat gtgtctgtaa
     2701 cctgtggagg tctgaataag catggtcagt ggaaaaagct gagcttcctg aaagacgcga
     2761 tgcgttcacg gtggatgtgg aatatgcggc agctgcttct gaaagcgtgg tcagagggga
     2821 tggcaatgcc ggagtcgttg tcacatatca cgacggaatc acagtggaga agcctggtgc
     2881 tgaaatccgg cggaaaatac tggcatgtgt acatgtcgaa gaagacagcc ggagggcgga
     2941 atacggcacg ctacctgggt cgttatctga agaagccacc aatagcggct tcccgactgg
     3001 ctcattacaa cggaggggca agcctgagct tccgttacct ggaccacaaa acgggagaaa
     3061 cggcgacgga aacgctgaca cagcgtgagc tggtcgcgag gctgaaacag cacatcccgg
     3121 agaagttttt taagatggtg aggtacttcg ggttccttgc caaccgtgtg tgtggagaga
     3181 agctgccgca ggtgtaccgt gcactgggga tggataaacc ggaaccagtg gcgaaagtgt
     3241 gctatgcaca aatggtgaaa cagttcctga gtcgtgaccc gttcgaatgc gtgctgtgtg
     3301 gctgccggat ggtataccgc cgggccattg cggggctgaa tgtatcaggg ctgaagaaaa
     3361 acgcgcggga tatcagtcta ctgaggtata tgccggcctg acacaggcta agtgtgcccg
     3421 ggaatcggtg aaagtataaa aaacagcctg ttacggtata aaaatcgacc atacagagag
     3481 ggaaaccacc ggagtggtgg gaaaagcaga aaggctcacg tggcataagg cgtggacaat
     3541 ggtatcgact ggtttttcaa tttcctatac gtgaacgggg acgcaattta ttgcgtggcc
     3601 gtgaagcgtt gccggcgcag ccggaaaacc cgctgtcagc acgttcagga agggggtgat
     3661 gtacaaatgg cacagaggat gaaagtgacg tatgagctga aggaatgatg taaaagtgat
     3721 gcataagtga tgtaaaagtg atgtataagt gatgtaaaag tgatgtatga actgaaggag
     3781 cgatgtaatt ctgtagtcag gaagaataac ccgttcatgc aggcatgaac gatacagtga
     3841 ggaacgcttt ttttgtcacg atctcccctt aacctgcgta aatcacccgc catggttgat
     3901 tatttttcaa cctcaaaatg gtcatacacc taacgcagcc gcgattttca tcgcaactgc
     3961 atgaattaaa agaaaaaaaa ggaatatttc gttttcacga gtaatacccg ggtattaaaa
     4021 atccactgta attacatgaa aataaagaaa taaaaggtaa taccggagta ttaccacgta
     4081 cgcgggcaag cgaaaaagct ataacgcttc ccggccgaca ggcgacccaa aatccacagg
     4141 ggcatgcagg ttctcttcag taacctgcgc cattaaatca aaaaggtcat attcgccggg
     4201 aagctgcgta tcagtcgaat ccagttgttc atcatattca gatggcatgg ggtgatatcc
     4261 agtagctgag aggttgttag cgggtttcgg ggcgcagccc tgaaccagtc atgtagcgct
     4321 agcggagtgt atactggctt attatgtagg cacgggtgcg ggaatcagtg aagtgcttca
     4381 tgtggcagga ggaaaatgca gcagcagagc gtaagcggaa tatatgagac aggagatatt
     4441 ccgcttcctc gctcactgac tcgctgcgct cggtcgttcg gctgcggcga gcggtgcggg
     4501 attacgaatg gggcggaaat ttcctgggag atgccaggaa gaaacttaac agggaaacgg
     4561 taaggccgcg gcgaagccgt ttttccatag gctccgcccc cctgacaagc atcacgaaat
     4621 ctgacgctca aatcagtggc ggcgaaaccc gacaggacta taaagatccc aggcgtttcc
     4681 ccctggtagc tccctcgtgc gctctcctgt tcctgccttt cggtttaccg gtgtcattcc
     4741 gctgttatgg ccgcgtttat ctcattccac gcctgacact cagttccggg aaggcagttc
     4801 gctccaagct ggactgtatg cacgaacccc ccgttcagtc cgactgctgc gccttttccg
     4861 gtaactatcg tcttgagtcc aacccggaaa gacacgaaaa atcgccactg gcagcggcca
     4921 ctggtaaaca ggatgtgcga gagatgtatc gagagttctt gaagtagtgg cctgactgag
     4981 gctacactag aaggacaaat ttggtgacat gtctcgcaca agactgttac cacggttaga
     5041 gaatctgcca ggattatcta accttcgaaa aaccacctgc aagggtggtt ttttcgttta
     5101 cagagcaaga gattacgacg atcgtcaaag gatctcaaga agatccttta tggattgcta
     5161 ccagcgccac tgccgaatgt ggtgcccgtt cccccaacaa taaactataa agtttatgca
     5221 tgtatctacc gatactcctg cgatccctca agaaagtaag gaaagtatcg atatgtcatg
     5281 ggtttatcgt atttcaatgc aaatgaagtt gtttattgca ttattcccgc tactgcttgc
     5341 cttggtctgg ttcgccggtt cgggtattgt cagccgtatc aataccgaac agcagatgaa
     5401 caccattgga cagctcacca cgctcgcccg cagcgcgggt gatgtggtgc atcaactcca
     5461 gagcgaacgt ggaatgagcg ctggatttat cggcgcgcgc ggccaaaagt ttcgcgatga
     5521 cttagctgcc cagcggcagt taaccgacaa ggtgctggca acatttaagc ggttgctgac
     5581 cgatacgaat aaggatttac tcc
//
