LOCUS       NZ_CP057241             3257 bp    DNA     circular CON 01-APR-2024
DEFINITION  Escherichia fergusonii strain RHB32-C09 plasmid pRHB32-C09_4,
            complete sequence.
ACCESSION   NZ_CP057241
VERSION     NZ_CP057241.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148317
            Assembly: GCF_013820465.1
KEYWORDS    RefSeq.
SOURCE      Escherichia fergusonii
  ORGANISM  Escherichia fergusonii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3257)
  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 3257)
  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                     :: RH13 T3-C09
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 126.590727368132x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013820465.1-RS_2024_04_01
            Annotation Date                   :: 04/01/2024 04:19:13
            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)                     :: 4,694
            CDSs (total)                      :: 4,578
            Genes (coding)                    :: 4,454
            CDSs (with protein)               :: 4,454
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 124
            CDSs (without protein)            :: 124
            Pseudo Genes (ambiguous residues) :: 0 of 124
            Pseudo Genes (frameshifted)       :: 48 of 124
            Pseudo Genes (incomplete)         :: 64 of 124
            Pseudo Genes (internal stop)      :: 28 of 124
            Pseudo Genes (multiple problems)  :: 18 of 124
            Pseudo Genes (short protein)      :: 2 of 124
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP057241.1.
            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..3257
                     /organism="Escherichia fergusonii"
                     /mol_type="genomic DNA"
                     /strain="RHB32-C09"
                     /isolation_source="Pooled sheep faecal samples collected
                     from floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB32-C09_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(540..821)
                     /locus_tag="HVZ00_RS23210"
                     /old_locus_tag="HVZ00_23205"
     CDS             complement(540..821)
                     /locus_tag="HVZ00_RS23210"
                     /old_locus_tag="HVZ00_23205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000586174.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_000586174.1"
                     /translation="MIINIKHKGLRKFAETGNNAGIPQQFTQRLKLILTALSTATNLQD
                     MMDLKALRCHPLKGDRQGEYSLEVNGNWRVVFKLEEPNVFDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            1166..1462
                     /locus_tag="HVZ00_RS23215"
                     /old_locus_tag="HVZ00_23210"
     CDS             1166..1462
                     /locus_tag="HVZ00_RS23215"
                     /old_locus_tag="HVZ00_23210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609270.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antitoxin"
                     /protein_id="WP_000609270.1"
                     /translation="MINLVDPVHPGVFIREMFMEPFEISAADLSEKLHVSPSTLSRVLN
                     GKADLSVEMALRLSRVLGRSAESWINMQTQYSLNASRKSPNVIKELDELVPIF"
                     /name="HigA family addiction module antitoxin"
     gene            complement(1693..1805)
                     /locus_tag="HVZ00_RS23710"
                     /pseudo=""
     CDS             complement(1693..1805)
                     /locus_tag="HVZ00_RS23710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            complement(2459..2653)
                     /locus_tag="HVZ00_RS23220"
                     /old_locus_tag="HVZ00_23215"
     CDS             complement(2459..2653)
                     /locus_tag="HVZ00_RS23220"
                     /old_locus_tag="HVZ00_23215"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041633.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2304..2386
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.81"
                     /coverage="100.0"
                     /evalue="1.76e-34"
     Typing          2690..2788
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          2913..3168
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(1734..2291)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.464"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atcgccattc actttcatgc atagctatgc agtgagctga aagcgatcct gacgcatttt
       61 tccggttttc gcttggtaaa acatctcttt ttgcggtgtt cgcggcagaa tcgcgttcag
      121 cgcgttttag cggtgcgcgt aatgcgacgt tatggtaaat gctgtgattt gcgggatggt
      181 tttatctatg ttgatatcaa taccacctct tatggaggtg gcttacaccg atttttcctt
      241 gttgtctgtt tcagaacaga tagaggcttt tttggcaatt atccaaccac tattgatagt
      301 gtttattact acttagataa ctgagccttt actgtatctg cccctgcaag caggaaccca
      361 acagttaaga accaccccca gccattgata ccttttagcg ctagaattgc tgcgcaaatg
      421 atggctgcta tagggactat ctggtacaga aaatacttca tataacttac cccgaggttt
      481 tgctttttta tgagacccta aagcatcgat actgtcactt tgatgcttta aggaccttct
      541 tagtgataat cctcgagatc cacgtcaaag acgttaggtt cttcgagctt aaacactacg
      601 cgccagtttc cattgacctc taacgaatac tctccttgac ggtctccctt caatggatgg
      661 cagcgcaatg cctttaaatc catcatatcc tgcaagttcg tcgctgtgct taaggctgtt
      721 aggatcagct tcagacgttg agtaaactgt tgcggaattc ctgcgttgtt acctgtttcg
      781 gcaaacttac gcaaaccttt atgcttgata tttatgatca ttaatcacca tcccatattt
      841 gtttagatag aaacatcgca gtttattttt ccggttcatc cgtatttcca ttgcaaaccc
      901 cttgctctat ttgaataaat gacgtaggtt ttacttaacc aagtcgcatt ttaatctgtt
      961 gacattggtt tgatgcgctg tacaatgccg gggccttgaa tttcacatca agtacccaca
     1021 tcataaggaa tgattagacg caccaatgtg catcataatg tcattctttt ttttagtcaa
     1081 caatgagttg cgttatgcgc aatgcgcaat ctgaaaacgc aataggccta tctttttaaa
     1141 actaatatag gcttcagagg aaggtatgat taatcttgtc gatccagtac atccaggggt
     1201 ttttatccgt gagatgttta tggaaccgtt tgaaatatca gccgcggacc tgtctgaaaa
     1261 actgcatgta tcaccttcca ctctaagtag agtgctgaat ggaaaagctg atttaagtgt
     1321 tgagatggca ttaaggcttt ctcgagttct tggtcgcagt gccgagtcgt ggataaacat
     1381 gcagactcaa tacagtctta acgcgagcag gaagtcacct aatgtcatta aggaattaga
     1441 tgaattggtt cctatatttt gagaaaagaa aaggccgcta tatgcggcct ttttctgtct
     1501 tgactctcag gcaactggat cgtatcgttt ctcgtaaacg aaaaaaccac ccggcaaggt
     1561 ggttttttcg aaggttcagt aaccggcaag tttctgaacc agggtaactg gcttggagga
     1621 gcgcagtcac caaaacttgt tctttcagtt tagccttaac tggcgcataa cttcaagact
     1681 aactcctcta aatcagttac cagtggctgc tgccaatggt gttttgcatg tctttccggg
     1741 ttggactcaa gatgatagtt accggataag gcgcagcggt cgggctgaac ggggggttcg
     1801 tgcacacagc ccagcttgga gcgaacgacc tacactgaac cgagatacct acagcgtgag
     1861 ctatgagaaa gcgccacgct tcccgaaggg agaaaggcgg acaggtatcc ggtaagcggc
     1921 agggtcggaa caggagagcg cacgagggag ccaccagggg gaaacgtctg gtatctttaa
     1981 gtcctgtcgg gtttcgccac ctctgacttg agcgtcgatt tctgtgatgc tcgtcagggg
     2041 ggcggagcct atggaaaaac gcctgcggcg cggccttctt cctgttcttg gtcttttgct
     2101 cacatgttct ttccggcctt atcccctgat tctgtggata accgtgctgc cgtttttgtg
     2161 taagtcagta ccgctcgccg cagccgaacg accgagcgta gcgagtcagt gagcgaggaa
     2221 gcggaaaagc gcctggacgc gcattttctc cttacgcatc tgtgcggaat ttcacacccg
     2281 gcatggggca cttttcatac aatctgcact gatgtcgcat agttaagcca gtatacactc
     2341 cgctatcgct acgtgactgg gtcagggctt cgccccgaca cccgctgacg cgccctggcg
     2401 ggcttgtctg ctgccgaaaa cgctcgcgga caagccgtga gcgcctccgt cagcttcgtt
     2461 atgttcctgt ttcactttcg gtctcaaagc gaacctggat gctgttctgg agttcttccg
     2521 cgagttcgtg cagtcgttcg cacatggccg cctgttcgtc ggcatccaga gcatccagtt
     2581 tttcaagcag tgtcaggctc tggcttttga taaatcgcgc catattcagc gcagtttgtt
     2641 gctgtttgtt caccttccgt tgttctccgt cagtaccggg tgtcgggtgg accctgacca
     2701 ggtggtaatt gtaagacgtt gcgggcgacg gtattacaat tgcacatcct gtcctgtttt
     2761 tttaggacgt atcatggcac agcatatcaa ctgataaata atccctgtgc agtgcagccg
     2821 ctgttgcata aaatttcgct ctgcgtcgag tgtttcttaa tcaataattc cgctgatact
     2881 ccggaaaaac gcgagtctgt tctcatgcct gaaatgccca caccccacgc aaaaacaatt
     2941 ttttgctgat ttttctttat aaatagagag ttatgacaaa ttagttcttc ttgctctctt
     3001 tgtgatattt aaaaaagcgg tgtcggcgcg gtgttgtagc tgcgccaaca ccgcttttta
     3061 ggggtggtac tgactatttt cataaaaaac atcattttat attaggggtg ctgctagcgg
     3121 cgcggtgtgt ttttttacag gacgcccctg ggggcgctgc taggggtgtc tgttcagata
     3181 tgtagcaatg agtcagggat tcacgaactg aaaatgtccg aaaatgtgtc tcatgggcac
     3241 cgtatgcgcc caaaccg
//
