LOCUS       NZ_CP058060             5264 bp    DNA     circular CON 01-APR-2024
DEFINITION  Escherichia fergusonii strain RHB02-C22 plasmid pRHB02-C22_4,
            complete sequence.
ACCESSION   NZ_CP058060
VERSION     NZ_CP058060.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15147971
            Assembly: GCF_013923185.1
KEYWORDS    RefSeq.
SOURCE      Escherichia fergusonii
  ORGANISM  Escherichia fergusonii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5264)
  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 5264)
  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                     :: RH02 T1-C22
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 117.004931831572x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013923185.1-RS_2024_04_01
            Annotation Date                   :: 04/01/2024 04:20:42
            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)                     :: 4,813
            CDSs (total)                      :: 4,694
            Genes (coding)                    :: 4,592
            CDSs (with protein)               :: 4,592
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 102
            CDSs (without protein)            :: 102
            Pseudo Genes (ambiguous residues) :: 0 of 102
            Pseudo Genes (frameshifted)       :: 37 of 102
            Pseudo Genes (incomplete)         :: 57 of 102
            Pseudo Genes (internal stop)      :: 20 of 102
            Pseudo Genes (multiple problems)  :: 13 of 102
            Pseudo Genes (short protein)      :: 2 of 102
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058060.1.
            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..5264
                     /organism="Escherichia fergusonii"
                     /mol_type="genomic DNA"
                     /strain="RHB02-C22"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:564"
                     /plasmid="pRHB02-C22_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(5231..5264,1..353)
                     /locus_tag="HVV54_RS23845"
                     /old_locus_tag="HVV54_23845"
     CDS             join(5231..5264,1..353)
                     /locus_tag="HVV54_RS23845"
                     /old_locus_tag="HVV54_23845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000147848.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000147848.1"
                     /translation="MTGRSRSQFYRDMRAGLVSYRTGRDGRREFETSELIRAYGELKQN
                     ETPERHSEGHAENPHDQQTERILRELNELKQCLTLMLEDKQAQDMDRRRQEAEREQLQN
                     EIAQLRQALELEKKRGFWSRLFGR"
                     /name="hypothetical protein"
     gene            434..853
                     /locus_tag="HVV54_RS23850"
                     /old_locus_tag="HVV54_23850"
     CDS             434..853
                     /locus_tag="HVV54_RS23850"
                     /old_locus_tag="HVV54_23850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016247941.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="WP_001254967.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQQFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            1623..1817
                     /locus_tag="HVV54_RS23855"
                     /old_locus_tag="HVV54_23855"
     CDS             1623..1817
                     /locus_tag="HVV54_RS23855"
                     /old_locus_tag="HVV54_23855"
                     /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_052962668.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EEIQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2472..2630
                     /locus_tag="HVV54_RS24360"
     CDS             2472..2630
                     /locus_tag="HVV54_RS24360"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /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_071531517.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHALTPLAAATGNRISRAMMA
                     QTVLQSS"
                     /name="replication initiation protein"
     gene            complement(2829..2966)
                     /locus_tag="HVV54_RS24365"
                     /old_locus_tag="HVV54_23860"
     CDS             complement(2829..2966)
                     /locus_tag="HVV54_RS24365"
                     /old_locus_tag="HVV54_23860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405930.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_001405930.1"
                     /translation="MRKRFFVGIFAINLLVGCQANYIRDVQGGTIAPSSSSKLTGIAVQ
                     "
                     /name="colicin release lysis protein"
     gene            3128..3355
                     /locus_tag="HVV54_RS23865"
                     /old_locus_tag="HVV54_23865"
     CDS             3128..3355
                     /locus_tag="HVV54_RS23865"
                     /old_locus_tag="HVV54_23865"
                     /inference="COORDINATES: protein motif:HMM:NF015489.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin E1 immunity protein"
                     /protein_id="WP_231370010.1"
                     /translation="MLYAIVISTILCPYSKYAIEYIAFNFIKKVFFERRKNLNNAPVAK
                     LNLFMLYNLLCLVLAIPFGLLGLFISIKNN"
                     /name="colicin E1 immunity protein"
     gene            complement(3352..4920)
                     /gene="cea"
                     /locus_tag="HVV54_RS23870"
                     /old_locus_tag="HVV54_23870"
     CDS             complement(3352..4920)
                     /gene="cea"
                     /locus_tag="HVV54_RS23870"
                     /old_locus_tag="HVV54_23870"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000447006.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="pore-forming bacteriocin colicin E1"
                     /protein_id="WP_000447006.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGTPDGSGSGGGGGKGGSKS
                     ESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQRLKDIVNEALRH
                     NASRTPSATELAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKAFQEAEQRRKEIERE
                     KAETERQLKLAEAEEKRLAALSEEAKAVEIAQKKLSAAQSEVVKMDGEIKTLNSRLSSS
                     IHARDAEMKTLAGKRNELAQASAKYKELDELVKKLSPRANDPLQNRPFFEATRRRVGAG
                     KIREEKQKQVTASETRINRINADITQIQKAISQVSNNRNAGIARVHEAEENLKKAQNNL
                     LNSQIKDAVDATVSFYQTLTEKYGEKYSKMAQELADKSKGKKIGNVNEALAAFEKYKDV
                     LNKKFSKADRDAIFNALASVKYDDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDTG
                     DWKPLFLTLEKKAADAGVSYVVALLFSLLAGTTLGIWGIAIVTGILCSYIDKNKLNTIN
                     EVLGI"
                     /name="cea"
     Typing          complement(1109..1364)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.899"
                     /coverage="89.0"
                     /evalue="2.61e-118"
     Typing          complement(1489..1587)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(1891..1975)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.186"
                     /coverage="100.0"
                     /evalue="6.62e-29"
     Typing          1986..2544
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.365"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atatgcgcgc aggccttgtc agttaccgta ccggcaggga cggacgacgg gagtttgaaa
       61 ccagtgaact gatccgggca tacggcgaat taaagcagaa tgagacacca gaaaggcaca
      121 gtgagggaca tgcagaaaat ccacatgatc agcagacaga acgcattctc cgggagctga
      181 atgagctgaa acaatgcctg acgctgatgc ttgaggataa acaggcacag gatatggatc
      241 gcagacgcca ggaagcagaa cgggaacagc tacaaaatga gatagcccag ctcaggcagg
      301 cactggaact ggaaaagaaa cggggattct ggtccaggtt gttcggtcgc tgaacgctgt
      361 cagagactga tgataaaata gtcttcggat aataactcac cgagaataaa tactttaagg
      421 tagggagaca ctcatgagac gtaccggaaa caaactttgt cttatcgcca tgataacagc
      481 aacagtagct ctcacagcct gtaccccaaa gggcagcgtg gaacaacata cccggcatta
      541 cgtatatgct tctgatgacg gttttgatcc caacttttcc acccaaaaag ccgacacaac
      601 acgaatgatg gtgccttttt ttcggcagtt ctgggatatg ggagctaaag ataaagcgac
      661 aggaaaatca cggagtgatg tgcaacaacg cattcagcag tttcacagcc aggaattttt
      721 aaactcactc cggggcacaa ctcaatttgc gggtactgat taccgcagca aagaccttac
      781 cccgaaaaaa tccaggctgc tggctgacac gatttctgcg gtttatctcg atggctacga
      841 gggcagacag taagtggatt taccataatc ccttaattgt acgcaccgct aaaacgcgct
      901 gaacgcgatt ctgccgcaaa caccgcaaaa agagatgttt tccccggggt aaaccggaaa
      961 aatgcgtcag gatcgctttc agctcactgc atagctatgc atgaaagtga atgacgatcg
     1021 gtttgggcgc atacagtgcc catgagacac attttcggac attttcagtt cgtgaatccc
     1081 tgactcattg ctatatatct gaatagacac ccctagcagc gcccccaggg gcatcctgta
     1141 aaaaaacaca ccgcgccgct agcagcaccc ctaatataag atgatgtttt ttatgaaaat
     1201 agtcagtacc acccctaaaa agcggtgttg gcgcagctac aacaccgcgc cgacaccgct
     1261 tttttaaata tcacaaagag agcaagaaga actaatttgt cataactctc tatttataaa
     1321 gaaaaatcag caaaaacttg tttttgcgtg gggtgtgggc atttcaggca tgagaacaga
     1381 ctcgcgtttt tccggagtat cagcggaatt attgattaag aaacactcga cgcagagcga
     1441 aattttatgc aacagcggct gcactgcaca gggattattt atcagttgat atgctgtgcc
     1501 atgatacgtc ctaaagaaac aggacaggat gtgtaattgt aataccgtcg cccgcaacgt
     1561 cttacaatta ccacctggtc agggtccacc cgacacccgg tactgacgga gaacaacgga
     1621 aggtgaacaa acagcaacaa actgcgctga atatggcgcg atttatcaaa agccagagcc
     1681 tgacactact tgaaaaactg gatgctctgg atgccgacga acaggcggcc atgtgcgaac
     1741 gactgcacga actcgcggaa gagatccaga acagcatcca ggttcgcttt gagaccgaaa
     1801 gtgaaacagg gacataacga ggctgacgga ggcgctcacg gcttgtccgc gagcgttttc
     1861 ggcagcagac aagcccgcca gggcgcgtca gggggtttcg gggcaaagcc ctgaaccagt
     1921 cacagagcga tagcgatgtg tatactggct taactatgcg gcatcagtgc agattgtatg
     1981 aaaagtgccc catgccgggt gtgaaatgcc gcacagatgc gtaaggagaa aatgcgcgtc
     2041 caggcgcttt tccgcttcct cgctcactga ctcgctacgc tcggtcgttc gactgcggcg
     2101 agcggtactg actcacacaa aaacggtaac acagttatcc acagaatcag gggataaggc
     2161 cggaaagaac atgtgagcaa aagaccagga acaggaagaa ggccacgtag caggcgtttt
     2221 tccataggct ccgcccccct gacgagcatc acaaaaatag acgctcaagt cagaggtggc
     2281 gaaacccgac aggactataa agataccagg cgtttccccc tggaagctcc ctcgtgcgct
     2341 ctcctgttcc gaccctgccg cttaccggat acctgtccgc ctttctccct tcgggaagcg
     2401 tggcgctttc tcatagctca cgctgttggt atctcagttc ggtgtaggtc gttcgctcca
     2461 agctgggctg tgtgcacgaa ccccccgttc agcccgaccg ctgcgcctta tccggtaact
     2521 atcgtcttga gtccaacccg gtaaggcacg ccttaacgcc actggcagca gccactggta
     2581 accggattag cagagcgatg atggcacaaa cggtgctaca gagttcttga agtagtggcc
     2641 cgactacggc tacactagaa ggacagtatt tggtatctgc gctctgctga agccagttac
     2701 cttcggaaaa agagttggta gctcttgatc cggcaaacaa accaccgttg gtagcggtgg
     2761 tttttttgtt tgcaagcagc agattacgcg cagaaaaaaa ggatctcaag aagatccttt
     2821 gatcttttct actgaaccgc gatccccgtc agtttagaag aggaggatgg tgcgatggtc
     2881 cctccctgaa catcacgtat atagttagcc tgacatccaa caaggaggtt tatcgcgaat
     2941 attcccacaa aaaatctttt cctcataact cgatccttat aaaatgaaaa gaatatatgg
     3001 cgaggtttaa tttatgagct taagatacta cataaaaaat attttatttg gcctgtactg
     3061 cacacttata tatatatacc ttataacaaa aaacagcgaa gggtattatt tccttgtgtc
     3121 agataagatg ctatatgcaa tagtgataag cactattcta tgtccatatt caaaatatgc
     3181 tattgaatac atagctttta acttcataaa gaaagttttt ttcgaaagaa gaaaaaacct
     3241 aaataacgcc cccgtagcaa aattaaacct atttatgcta tataatctac tttgtttggt
     3301 cctagcaatc ccatttggat tgctaggact ttttatatca ataaagaata attaaatccc
     3361 taacacctca tttatagtat taagtttatt cttatcaata taggagcata gaattcctgt
     3421 aacaatagca ataccccaaa tacctaatgt agttccagca agcaagctaa aaagtaaagc
     3481 aacaacataa ctcacccctg catctgcagc tttcttctct aatgtaagaa atagtggctt
     3541 ccagtcacct gtatccttaa tttttaggat atcagatacc acatcatatc caaaagaaac
     3601 atgccccgta atcttcaagt acttggcaaa ctgatctaaa tgtttagccc agtcatcata
     3661 cttcaccgat gccaacgcat taaaaatagc atcacgatcg gctttgctga atttcttatt
     3721 taaaacatcc ttgtattttt caaaagcagc gagagcttca ttcacattgc cgattttctt
     3781 acctttagac ttatcagcaa gttcctgtgc cattttcgaa tatttttcac catatttttc
     3841 agtcagcgtt tgataaaagc taactgttgc atcaacagca tccttaatct gtgaattaag
     3901 gagattattc tgtgcttttt tcaaattttc ttcagcttca tgaacacgag cgataccggc
     3961 attacgatta ttactgacct gagaaatagc cttctggatc tgagttatat cagcatttat
     4021 ccggttaata cgtgtttctg atgctgttac ctgtttttgt ttttcttctc taatcttacc
     4081 ggccccaacc cgtcgtctgg ttgcttcaaa aaaaggacgg ttctgaagcg gatcattggc
     4141 tcttggtgat agttttttga ccagctcatc cagttcttta tatttagcgg atgcctgagc
     4201 cagttcattt cgttttccag cgagcgtttt catttctgca tcacgggcat ggatactgga
     4261 gcttaaacga gaattgagag tcttaatctc tccatccatt ttcaccactt cagattgtgc
     4321 agcagaaagt tttttttggg cgatctcaac agctttagct tcttcactca atgcagccag
     4381 tcgtttctct tcagcttcag ccagtttcaa ctggcgttct gtttcagcct tctcccgttc
     4441 aatctcttta cgtcgttgtt ctgcttcctg aaaagccttt tctgctgctt ccgcttcttt
     4501 acgggctttt tcttctgctt tcgcaaggcg caaacgctct gcttccgcct gcatagctgc
     4561 attattagca tgagcaagct ctgttgctga aggcgtacgt gaggcattgt gacgaagagc
     4621 ctcattcacg atatccttca ggcgctgagt cagcgcatcc ctgtttgcct ttgctttcgc
     4681 ctgtgcttcc gctgcagctt ttgcccgggc agcctgctct gcctgtgttt tctttaattg
     4741 agcagtagac catttagcag ttgcatgaat agctgcagaa ctttcacttt tactgcctcc
     4801 ttttccacct ccgccgccag agccactccc gtcaggagta ccattcaaaa gagtaataat
     4861 tacctgtccc ttatcatcat aaggaacacc atctttatag tacgctaccg cggtttccat
     4921 tataaaatcc tctttgactt ttaaaacaat aagttaaaaa taaatactgt acatataacc
     4981 actggtttta tatacagcat aaaagctacg ccgctgcatt ttccctgtca agactgtgga
     5041 cttccatttt tgtgaaaacg atcaaaaaaa cagtctttca caccacgcgc tattctcgcc
     5101 cgatgccaca aaaaccagca caaacattac cgttctcaga cctcattatg ttttactgaa
     5161 actatgagat gagacatcta tgggacactg tcactttatg gcatggcaca cactccggga
     5221 cgcactaaaa atgacaggca gatcgcgttc acagttttac cgtg
//
