LOCUS       NZ_CP055605             4664 bp    DNA     circular CON 01-APR-2024
DEFINITION  Escherichia fergusonii strain RHB41-C23 plasmid pRHB41-C23_7,
            complete sequence.
ACCESSION   NZ_CP055605
VERSION     NZ_CP055605.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148431
            Assembly: GCF_013591455.1
KEYWORDS    RefSeq.
SOURCE      Escherichia fergusonii
  ORGANISM  Escherichia fergusonii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4664)
  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 4664)
  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 T3-C23
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 145.857560681824x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013591455.1-RS_2024_04_01
            Annotation Date                   :: 04/01/2024 04:10:29
            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)                     :: 4,801
            CDSs (total)                      :: 4,683
            Genes (coding)                    :: 4,563
            CDSs (with protein)               :: 4,563
            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)              :: 120
            CDSs (without protein)            :: 120
            Pseudo Genes (ambiguous residues) :: 0 of 120
            Pseudo Genes (frameshifted)       :: 26 of 120
            Pseudo Genes (incomplete)         :: 84 of 120
            Pseudo Genes (internal stop)      :: 18 of 120
            Pseudo Genes (multiple problems)  :: 10 of 120
            Pseudo Genes (short protein)      :: 2 of 120
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055605.1.
            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..4664
                     /organism="Escherichia fergusonii"
                     /mol_type="genomic DNA"
                     /strain="RHB41-C23"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB41-C23_7"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(4100..4664,1..992))
                     /locus_tag="HV014_RS23790"
                     /old_locus_tag="HV014_23800"
     CDS             complement(join(4100..4664,1..992))
                     /locus_tag="HV014_RS23790"
                     /old_locus_tag="HV014_23800"
                     /EC_number="2.7.7.65"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015589620.1"
                     /GO_function="GO:0052621 - diguanylate cyclase activity
                     [Evidence IEA]; GO:0046872 - metal ion binding [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="sensor domain-containing diguanylate cyclase"
                     /protein_id="WP_225088504.1"
                     /translation="MRIKKPHLRPIVITLSVGGILLTSIFLIAVIMVFQRENIEKDLLY
                     ANSSYAMKMSDVMSGYIEMAQGELAYGAKKIKSTNDIDSLKDEADRLRLQSGMFNSVLV
                     VSNDAVVLATSPESLDLVGTRLNSSASKLAIEEKKPFISSPLKSVTGNLIILLSHPIYD
                     KGGNYIGYVGGSIYLKKHSLFGDVLSRHFFKNNTEISIVSDDGNVIFNNDKSAVDRPMV
                     MSDDLKSKLTASDRGEGAFFSSGHRYLLGYASMKNTTWNVLVYSRADSVTTILIAYAKS
                     VLVLLIIIIIVFSLISYFIASSISLPLEKLAISTNAKDIGASLVYIKAINAWYAEADRL
                     KKALFTYIKVMMERVDYLNEVALKDPLTGVNNRLGFLSKIQNHKRDSGYSVIVIDVDFF
                     KEINDSFGHGVGDEVLVSLAHIINSCCRSEDVVCRFGGEEFVVFLPNTSVVTAKCVAER
                     IRSVIESTVFPNNLRVTISAGVATQDDPLGRIDFLLKNADDALYQAKREGRNKVIVYSA
                     I"
                     /name="sensor domain-containing diguanylate cyclase"
     gene            complement(1338..1553)
                     /locus_tag="HV014_RS23795"
                     /old_locus_tag="HV014_23805"
     CDS             complement(1338..1553)
                     /locus_tag="HV014_RS23795"
                     /old_locus_tag="HV014_23805"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_015589619.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWESAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSSD"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1557..2042)
                     /locus_tag="HV014_RS23800"
                     /old_locus_tag="HV014_23810"
     CDS             complement(1557..2042)
                     /locus_tag="HV014_RS23800"
                     /old_locus_tag="HV014_23810"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_012565228.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQNTGEMLKAAFSEHEKSVKAELNESA
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     DNYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVKVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(<2077..2781)
                     /locus_tag="HV014_RS24305"
                     /old_locus_tag="HV014_23815"
                     /pseudo=""
     CDS             complement(<2077..2781)
                     /locus_tag="HV014_RS24305"
                     /old_locus_tag="HV014_23815"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(2720..3043)
                     /locus_tag="HV014_RS23810"
                     /old_locus_tag="HV014_23820"
     CDS             complement(2720..3043)
                     /locus_tag="HV014_RS23810"
                     /old_locus_tag="HV014_23820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_015059937.1"
                     /translation="MLTMWVTEGEHRRLLERCDGRQLAAWMRQTCLDEKPARSGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(3157..3329)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.701"
                     /coverage="100.0"
                     /evalue="4.2800000000000005e-79"
     Typing          3254..3805
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.639"
                     /coverage="91.0"
                     /evalue="0.0"
     Typing          complement(1235..2730)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.782"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2727..3043)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="99.0"
                     /evalue="1.9499999999999998e-60"
ORIGIN
        1 ttgatagctt taatataaac tagcgaagct ccgatatctt tagcattggt agatatagca
       61 agcttttcta aaggaagtga aatactggag gcaatgaaat atgaaataag tgaaaacaca
      121 ataattatta taattagcag aacaagtaca cttttagcat aagcaataag aatagtagtc
      181 acactgtcag cacgactata aaccaacaca ttccaagtag tatttttcat actagcataa
      241 ccaagaagat atctatgccc cgaagaaaaa aatgccccct cacctctatc agacgcagtt
      301 aactttgatt tcaaatcatc agacataacc ataggccgat caacagcact tttatcgtta
      361 ttaaagatca cattcccatc atcactaaca atgctaattt cagtgttgtt cttgaaaaaa
      421 tgcctgctca aaacatcgcc aaataaacta tgttttttta gatatataga cccaccgaca
      481 taccctatgt aattgccacc cttatcataa ataggatgtg acaacaaaat aatcaaattc
      541 ccagtaactg attttaacgg tgaagatatg aatggtttct tttcctcaat cgccaatttg
      601 ctggcacttg aattcaagcg ggtaccaact aaatcaagag attctggcga agtcgccaga
      661 acaacagcat cattactaac aacaagaact gaattaaaca taccagactg caatcttaac
      721 ctatccgcct catctttaag tgagtcaata tcattagttg attttatttt ttttgctcca
      781 tatgctaatt caccttgagc catttcaata taaccactca ttacatctga cattttcata
      841 gcgtacgatg aattagcata aagcaaatct ttttctatat tttcgcgctg aaaaaccata
      901 ataacggcaa tcagaaaaat agaagttaac aaaatcccac caacggacaa ggttatgact
      961 atcggacgaa ggtgaggctt tttaattctc ataaaaatac actccatata ataaaaaatg
     1021 ccgcatttac cataacatcc cttatcagca ccgccccgga cgggttcgga acaaatgcgg
     1081 cgtcagcccg gtaaaaccgg cagcaaactc tccgctaaac cgcgcattct gcgccagata
     1141 aatttcaccc ggctgcatgg ctatgcagtc gggtgaatgg ctccggcttt cagcgcagat
     1201 gtccgccgaa agccccgttt tatcaggtta tcacagtgaa gggctgttat acgtccgctg
     1261 tcgctgagat cgctccagct ccagcgcttt ctgatgctgc accacgcgct cctgctcccg
     1321 gtgcagctcg acggcattca gtcgctcgac aaccggcgca gctgctcgct caaactctgc
     1381 acctgcctgc tcaagcccgt gacgcgctcg ctcagcgctg cgttctcccg ttgcataaga
     1441 ccagacatcg tccgccattc cgcgaaggcg ctctcccact cgtccagcct tttcgagtag
     1501 tcctgctgta gctgctctaa tgcgctcagc aactgttttt ccagctccgt catgtgctat
     1561 ttccccgcca gtatcatcca gctcgaatcc tctccgaacc gtcccgcttc cgggttcacc
     1621 ttcacgcagc ggcgtctctg ctcgccgcag gtcgagagct gcacgccgct gttcctctct
     1681 gacagcatgg cctgcgtgct cttctgctcc cggatggtcg tgtagttgtc gagtatctgc
     1741 tgcccctgcc accacagaat gcccgcgctc gaggcgatca gcagcgcgga gaccaggacg
     1801 atggtcagcc acgtctggct gaccatgcgc accatgcctt tcgtgcgctg gctcatggct
     1861 gaggacagtt tccggtcgtg gtcgaggatg gcggcgctga ttctcttcgc gctttcgttc
     1921 agttccgctt ttacagattt ctcgtgctcg ctgaatgcgg ctttcagcat ctcgccggta
     1981 ttctgctgct gcgctttcga tttctgctct aagtccttcg ccagcgttaa aagactgttc
     2041 ataaatggct cccttcagtc ggatgtttcg ccccccgtcc gggtcggcaa tgctgatact
     2101 gctttttgtg gtgcggacca cctcaaaacc tgcgctttcc agcgcctcag tgacatcctg
     2161 acgggttttc agctccccgg atgaggcaag agcaagcaga ccgcgtgtaa tcgcttctgc
     2221 agcctcctgc ttcgctttag gcagtgcaga cggtgtgacc agtgcccgcc ggttctccgg
     2281 tgcgttcggg tcgtgcagcc ccagtctgcc gttcacgatg gtctgccagg catcgatgcg
     2341 tggacggtcg gcgcgatcgt aatacggctg gagccgtctg ccggtcagca gctccgtgct
     2401 cgggatcaga aaattcagct caagccgccc cttgtcacta tgctccaccc acaggatgct
     2461 gtactggtct ttatcaagtc cgggcatcag aacccgctca aagcttgcca tcagcttttc
     2521 ccgctggccg gaaggtaaat ccgcttccgc aaacgacagt accccggagg tgtatttctt
     2581 aacgtaaggc gacgcgtcaa tcagctcccg gacttcttcc ggcttcccct gcaggacggt
     2641 ggcgccttca cgctgccggt ctttacccag cagatagtcc accggcccgg cgccaccgcc
     2701 gcgaccgcgt ggatgaaatt taacgatcat cgtccgttcc tttctcaaga acggcgtgcc
     2761 gcagccgctc aagtccggca tcgatggcca tcagcgccgc aacaatctgc accctgtcat
     2821 ggccggtacc gccgccggcg ttaacacggc gggctatctg gttcaggtta ttgcccatgc
     2881 cggcaagctg gcgcagcagc gccggcgaga ttgagggaag ctttccggaa cgtgccggct
     2941 tttcgtccag gcaggtctgc cgcatccacg ccgccagctg cctgccgtca cagcgctcaa
     3001 gcagccgccg gtgctcgccc tccgtcaccc acatggtgag catcttgttc cgtttctctg
     3061 acaaaccggc ctcctgataa cgccgggacg ggcgggaaag gctttcccgg tcggcgcggg
     3121 gttggacaag ccgcaggcgc gtcaggcttt tggcgggttt cggggcgcag ccctgaacca
     3181 gtcacgtagc gctagcggag tgtatactgg cttactatgt tggcacggat gcgagtgtca
     3241 gtgaagtgtt tcatgtggca ggagaaaaat gcagcagcgg agcgtcagca gaatatgtga
     3301 tacaggatat attccgcttc ctcgctcact gactcgctgc gctcggtcgt tcggctgcgg
     3361 cgagcggtac cgacttacag gcggggcgga aatttcctgg gagatgccag gaagaagctt
     3421 aacagggaag cgataaggcc acggcgaagc cgtttttcca taggctccgc ccccctgaca
     3481 agcatcacga aatctgacgc tcaaatcagt ggtggcgaaa cccgacagga cttaaagata
     3541 ccaggcgttt ccccctggtg gctccctcgt gcgctctcct gttcctgcct ttcggtttac
     3601 cgatgtcaat ccgctgttat ggccgcgttt atctcattcc acgcctgaca ctcggttccg
     3661 ggaaggcagt tcgctccaag ctggactgta tgcacgaacc ccccgttcag cccgactacc
     3721 acgttgtccc ggtaactatc atcttgagtc caacccggaa cagacacgaa aaatcgccag
     3781 tggcggtagc cattagtaag aggattcacg gagcggagta gtagagtgtt ctacagagtt
     3841 cttgaagtgg tggcctgact gcggctacac tggaaggact gttttggtac ctgcgctccg
     3901 tgaaagccag ttaccttcgg aagaaagagt tggtagctct gaattccggc aaacgaacca
     3961 ccgttggtag cggtggtttt tttgtttaca gggtatgaga ttacgacgac atcgaaggga
     4021 taacaagagg atccgcttct tgcccactct tcgccacaaa aaaaacgaca cactagcgcg
     4081 taaagcatca tcaaaaaact caaatagcgc tatatacaat cactttatta cgcccctccc
     4141 ttttggcttg ataaagagca tcgtcagcat ttttcagcaa aaaatcgatc ctaccaagag
     4201 gatcatcttg tgttgccaca ccagcagata tggtgacccg caagttatta gggaagacag
     4261 tactttcaat aacactccta atacgctccg caacacactt agctgttacc acagatgtat
     4321 tcggcaggaa aacaacaaac tcttcgccac caaaccgaca aacaacatct tcactacggc
     4381 aacaggaatt aataatatga gccaaagaaa caagcacctc atctccgacc ccatgcccga
     4441 aactgtcatt tatctcttta aaaaaatcaa catcaattac aataactgaa taccctgaat
     4501 cccgcttatg attctgtatt ttacttaaaa accccaatct attgttcacg ccggtaaggg
     4561 gatctttaag cgccacctca tttagataat caactctttc catcattacc ttaatatacg
     4621 taaaaagcgc ctttttaagc ctatcagctt cggcatacca agca
//
