LOCUS       NZ_CP056965             3830 bp    DNA     circular CON 02-APR-2024
DEFINITION  Escherichia fergusonii strain RHB41-C20 plasmid pRHB41-C20_5,
            complete sequence.
ACCESSION   NZ_CP056965
VERSION     NZ_CP056965.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148429
            Assembly: GCF_013801425.1
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 T3-C20
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 132.253115999787x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013801425.1-RS_2024_04_02
            Annotation Date                   :: 04/02/2024 04:40:09
            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)                     :: 4,826
            CDSs (total)                      :: 4,703
            Genes (coding)                    :: 4,568
            CDSs (with protein)               :: 4,568
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 95
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 135
            CDSs (without protein)            :: 135
            Pseudo Genes (ambiguous residues) :: 0 of 135
            Pseudo Genes (frameshifted)       :: 54 of 135
            Pseudo Genes (incomplete)         :: 74 of 135
            Pseudo Genes (internal stop)      :: 23 of 135
            Pseudo Genes (multiple problems)  :: 17 of 135
            Pseudo Genes (short protein)      :: 2 of 135
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056965.1.
            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="RHB41-C20"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB41-C20_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            737..937
                     /locus_tag="HV012_RS23940"
                     /old_locus_tag="HV012_23945"
     CDS             737..937
                     /locus_tag="HV012_RS23940"
                     /old_locus_tag="HV012_23945"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001046776.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_016236520.1"
                     /translation="MNLCPDERLLFVRMISAMLRRSGGDAGAVMFEAYRHIVSDTNQAR
                     RSCMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            complement(985..1173)
                     /locus_tag="HV012_RS23945"
                     /old_locus_tag="HV012_23950"
     CDS             complement(985..1173)
                     /locus_tag="HV012_RS23945"
                     /old_locus_tag="HV012_23950"
                     /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(1463..3367)
                     /locus_tag="HV012_RS23950"
                     /old_locus_tag="HV012_23955"
     CDS             complement(1463..3367)
                     /locus_tag="HV012_RS23950"
                     /old_locus_tag="HV012_23955"
                     /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            complement(3673..3822)
                     /locus_tag="HV012_RS24380"
     CDS             complement(3673..3822)
                     /locus_tag="HV012_RS24380"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505258.1"
                     /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          355..527
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.379"
                     /coverage="100.0"
                     /evalue="9.47e-61"
     Typing          complement(2..430)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.575"
                     /coverage="99.0"
                     /evalue="1.49e-173"
     Typing          complement(3496..3830)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.844"
                     /coverage="99.0"
                     /evalue="8.92e-71"
ORIGIN
        1 gcttggagcg aactgccttc ccggaactga gtgtcaggcg tggaatgaga taaacgcggc
       61 cataacagcg gaatgacacc ggtaaaccga aaggcaggaa caggagagcg cacgagggag
      121 ctaccagggg gaaacgcctg ggatctttat agtcctgtcg ggtttcgccg ccactgattt
      181 gagcgtcaga tttcgtgatg cttgtcaggg gggcggagcc tatggaaaaa cggcttcgcc
      241 gcggccttac cgtttccctg ttaagtttct tcctggcatc tcccaggaaa tttccgcccc
      301 attcgtaatc ccgcaccgct cgccgcagcc gaacgaccga gcgcagcgag tcagtgagcg
      361 aggaagcgga atatctcctg tctcatatat tccgcttacg ctctgctgct gcattttcct
      421 cctgccacat gaagcacttc actgattccc gcacccgtgc ctacataata agccagtata
      481 cactccgcta gcgctacgtg actggttcag ggctgcgccc cgacacccgc taaaagcact
      541 gacgcgcctg cggcttgccc aaccccgcgc cgtccgggaa agaatttccc gatcgacccg
      601 acgtttctgt ttacctgtga tgttaacgtt tggatctttt tcccgggttt acctatttta
      661 atgaagcgta atgaagcgtt cacagctgac gttaatagat gggtgcttca tgtttggttt
      721 ttcaccagga gaacttatga acctttgccc cgatgaacgt ctgctctttg tgcggatgat
      781 ttccgctatg cttcgccgtt cgggcggtga tgcgggtgct gttatgtttg aggcgtatcg
      841 ccatattgtg tccgatacca atcaagctcg tcgttcctgc atgctcgacc tgctcgaaag
      901 cgtcaggcat gactatgtac acggtggata tacatagttg ccctggatac gcttttcgtc
      961 taagtgagcg ttcttttcgt ctctttattc gccgtcctgt ataccgaagc gtgcgctcag
     1021 cttctgataa agcgcttctg cctgttcgtg cattcgctca cagtcggctg cctcgtcatc
     1081 aagatcgagc acgtcgagtt tttcgagcag cagcagcgac tgcgcccgga taaattttgc
     1141 catgttcagt gcggctgatt cctgttttgt catacggctt tttcccggtt ttatggtgat
     1201 cgcagactga aatcttactt cattcacttg agtgcatagc catgcaggta cgcagaaatc
     1261 atcaggggcg ttttttctcg atatgggcac agaaaggtgt atgtttcagg tcggagtcct
     1321 cagaaacgct ctcagagcct ctcaggcggt gcacgcaaca gatgttatgg taaatcctag
     1381 ttatttgcag gcataaaaaa gccgcctttt aggcggtttt ttctgattgt aagttatcaa
     1441 gaccggatgc tgaacggcag tatcagacaa taaagcgatc gaccagcgtg gacatcgctt
     1501 cagactggcc gtccagcatc tggctggcgc tcgccgcctg agagaccagc gctgcgtttt
     1561 gctgagtgac ctgctccagc tgattcagtg cctgatgcac ctgcgacacg ccaagcgact
     1621 gctcattcgc cgcacgggca atatcgctca cgtactgttt catccgcccg gtattttccg
     1681 ccgctgcttt cagcgcggtg ccggacgcgg tgactcgtgc taccccttcg ccaatcttat
     1741 ccatattctg gttaatcagc tcacggatct gactggcctc tcgtgcacag cgctgggaaa
     1801 ggttacgcac ctccgtcgcc actaccgcaa agcctttgcc aagctcaccg gcacgtgccg
     1861 cttcaacggc ggcgttaagc gccagcaagt tggtctggaa agaaatctca tcaattgacg
     1921 caacaatctg ggaaatctgc tcgctggaag aacgaatttc cgccatgctc tgactggcct
     1981 cgttagagac gcgattagct tccagtacgt cccgctccat cgaatgtatc agacgctccg
     2041 cctcgctggc gttatcggcg gtctgggtga tcgcagtaga aatctgctcc atgctggcgg
     2101 ccgtttccac aatcgatgcc gcctgttcat ccgtacgctg ggccagatcc tgattaccgg
     2161 cagcgatatc actactggcg ctacgcaaca ccaccgcacc ggacttaatt tcttgcacga
     2221 tatgctgaat attctcaatc gcttggttat aggcacggtt cagggctgag agctcgtcgc
     2281 tgccggggac gtcaagacga cgtgtcaggt cgccgtccat ctctgcgatg gttttcagcg
     2341 taccgttcag ttgctgctgg atactgcgtg ccaccatcac cgcaaaggcg atagcaatca
     2401 gtagggcaac caggctgatt accaggaagg actgccagtc gacacgggca ttgtgggcaa
     2461 gcagcgcagc atgttcctgc aaggcatcca ccgcgcgatt ttccaccttt tgcagcgttt
     2521 caatacgctg ggtctgaagg ttaaaccagt cagtcgggtt gactccaaat ccgccttcgg
     2581 cggctttatt aaaagccgtc tcccgcagtt caagagcacg agttgcttca gcggactgaa
     2641 gagatttgtc cagctcagcc gcctgcacag gtgtgctaaa gctgcgagct gccgtcagcc
     2701 aggcatcctg ctggcctacc acatcgctaa acatgctgaa ctggccgtcg tcaaagcgat
     2761 ccatcgagaa gatattggac agcagcgcac gttctacacc agcctgctcc ttcaaattca
     2821 agagactata ataagccgcc agttcgttca ccatcgagcc tgaggtgctt aaatgcccca
     2881 tcccgccgac aaacttcagc acgtcagaga tggtttgggt atagaactga ctcgcttttg
     2941 gtgaatcgat agttaattcg ctgatggcgg tacgggttga gtcgagaaac tgaatacttt
     3001 cattaaacgt tttcaggggg gcggcaatat ttccctggag taaatcctta ttcgtatcgg
     3061 tcagcaaccg cttaaatgtt gccagcacct tgtcggttaa ctgccgctgg gcagctaagt
     3121 catcgcgaaa cttttggccg cgcgcgccga taaatccagc gctcattcca cgttcgctct
     3181 ggagttgatg caccacatca cccgcgctgc gggcgagcgt ggtgagctgt ccaatggtgt
     3241 tcatctgctg ttcggtattg atacggctga caatacccga accggcgaac cagaccaagg
     3301 caagcagtag cgggaataat gcaataaaca acttcatttg cattgaaata cgataagccc
     3361 atgacatatc gatactttcc ttactttctt gagggatcgc aggagtatcg gtagatacat
     3421 gcataaactt tatagtttat tgttggggga acgggcacca cattcggcag tggcgctggt
     3481 agcaatccat aaaggatctt cttgagatcc tttgacgatc gtcgtaatct cttgctctgt
     3541 aaacgaaaaa accacccttg caggtggttt ttcgaaggtt agataatcct ggcagattct
     3601 ctaaccgtgg taacagtctt gtgcgagaca tgtcaccaaa tttgtccttc tagtgtagcc
     3661 tcagtcaggc cactacttca agaactctcg atacatctct cgcacatcct gtttaccagt
     3721 ggccgctgcc agtggcgatt tttcgtgtct ttccgggttg gactcaagac gatagttacc
     3781 ggaaaaggcg cagcagtcgg actgaacggg gggttcgtgc atacagtcca
//
