LOCUS       CP057376                3319 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB28-C15 plasmid pRHB28-C15_6, complete
            sequence.
ACCESSION   CP057376
VERSION     CP057376.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148271
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3319)
  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 3319)
  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 T2-C15
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 165.998511090652x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 08:18:12
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.11
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 4,909
            CDSs (total)                      :: 4,793
            Genes (coding)                    :: 4,638
            CDSs (with protein)               :: 4,638
            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)              :: 155
            CDSs (without protein)            :: 155
            Pseudo Genes (ambiguous residues) :: 0 of 155
            Pseudo Genes (frameshifted)       :: 59 of 155
            Pseudo Genes (incomplete)         :: 84 of 155
            Pseudo Genes (internal stop)      :: 29 of 155
            Pseudo Genes (multiple problems)  :: 15 of 155
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..3319
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB28-C15"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB28-C15_6"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(2828..3319,1..549)
                     /gene="lsoA"
                     /locus_tag="HVY54_24520"
     CDS             join(2828..3319,1..549)
                     /gene="lsoA"
                     /locus_tag="HVY54_24520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052606.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system mRNA
                     endoribonuclease LsoA"
                     /protein_id="QMG65719.1"
                     /translation="MAQNPFKALNINIDKIESALTQNGVTNYSSNVKNERETHISGTYK
                     GIDFLIKLMPSGGNTTIGRASGQNNTYFDEIALIIKENCLYSDTKNFEYTIPKFSDDDR
                     ANLFEFLSEEGITITEDNNNDPNCKHQYIMTTSNGDRVRAKIYKRGSIQFQGKYLQIAS
                     LINDFMCSILNMKEIVEQKNKEFNVDIKKETIESELHSKLPKSIDKIHEDIKKQLSCSL
                     IMKKIDVEMEDYSTYCFSALRAIEGFIYQILNDVCNPSSSKNLGEYFTENKPKYIIREI
                     HQETINGEIAEVLCECYTYWHENRHGLFHMKPGIADTKTINKLESIAIIDTVCQLIDGG
                     VARLKL"
                     /name="lsoA"
     gene            546..926
                     /gene="lsoB"
                     /locus_tag="HVY54_24525"
     CDS             546..926
                     /gene="lsoB"
                     /locus_tag="HVY54_24525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052605.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system antitoxin LsoB"
                     /protein_id="QMG65720.1"
                     /translation="MKKDKKYQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKK
                     SKGDVFFDLIIPNGGKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNF
                     DKINVNLLSKATSFALKKGIPI"
                     /name="lsoB"
     gene            complement(1161..1484)
                     /locus_tag="HVY54_24530"
     CDS             complement(1161..1484)
                     /locus_tag="HVY54_24530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nikA protein"
                     /protein_id="QMG65721.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     gene            1768..1962
                     /locus_tag="HVY54_24535"
     CDS             1768..1962
                     /locus_tag="HVY54_24535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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="QMG65722.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2450..2563
                     /locus_tag="HVY54_24540"
     CDS             2450..2563
                     /locus_tag="HVY54_24540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QMG65723.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPERHDLTPLAAAIGN"
                     /name="replication initiation protein"
     Typing          complement(1494..1733)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          1998..2519
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.437"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          complement(1165..1484)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.54e-62"
ORIGIN
        1 attaacgatt tcatgtgctc aatactaaac atgaaagaga ttgtcgaaca aaaaaataaa
       61 gaatttaatg ttgacataaa aaaagaaact attgagtccg agttgcatag caaactacca
      121 aaaagcatcg ataaaatcca tgaagatatc aaaaaacagc tatcatgctc gctaataatg
      181 aaaaaaatag atgtcgaaat ggaagattac tcaacatact gcttctctgc attaagagct
      241 atagaaggct ttatatatca aatacttaat gatgtttgca atccatcatc atcaaagaac
      301 cttggcgaat acttcactga aaacaaaccc aaatatataa tcagagaaat acaccaagaa
      361 actataaatg gtgaaatagc ggaagttttg tgtgaatgct acacttactg gcatgagaac
      421 aggcatggtt tgtttcatat gaaaccagga atagctgaca cgaagacaat taacaaatta
      481 gaatcaatcg caatcatcga taccgtttgc caattaatag atggtggcgt agctaggttg
      541 aaattatgaa aaaagataaa aaatatcaaa tagaagcaat aaaaaataaa gataaaactt
      601 tatttattgt ctatgctact gatatttata gcccgagcga atttttctca aaaatcgaat
      661 ccgacttgaa gaaaaagaaa agcaagggtg atgttttttt tgatttaata attcctaacg
      721 gtggaaaaaa agatcgttac gtctatacgt catttaatgg cgagaagttt tcaagttaca
      781 cattaaacaa agttacgaaa actgatgaat ataatgattt atctgagctc tcggcttcgt
      841 tctttaaaaa gaactttgat aagatcaacg taaaccttct atccaaagcc acatcatttg
      901 ctttgaaaaa aggcattcca atataatatc aagccagaag acatttacca taacgtctca
      961 ttacgcgcac cgctaaaacg cgctgaacgc gattctgacg cagacaccgc aaaaagagat
     1021 gttttacccc ggaaaaacag gaaggatgcg tcaggatcgt tttcagctca ctgcatagct
     1081 atgcatgaaa gtgaatggcg atcggtttgg ggacttacgg cgttcatacc gtctgttttc
     1141 gacagtttcc ctccgggaag ctaatctgcc ataagcctgg ataacagggc ccggtgatac
     1201 tccgtaatag ctatcagcac ctccgcatac tctctgtccc cgacacgctt gccgtcgata
     1261 aagagttttt tctgcaacgc ccccagtcgc atgacttctt tcagcacccg gtcatcagtc
     1321 agtgaattaa ctttcttacc gagagctgcc gcccgtaaaa aaccagaaac ggtcttgccg
     1381 cattcagcag ccctttttct gatttcctgg tcttcttctg ccgtcagacg aacagggcga
     1441 ctgatagccc gcctgcgcgt attacttcca cttcgttttg tcataaaaca tggctccgta
     1501 tctgacatgg gtgtcggggc aaagccctga ccagggtaat tgtaatagcg tgcatgtatg
     1561 cgcggtataa caattgcaca tcctgtcctg tcagcaagct cgaattaccg acaaaagcac
     1621 ggcagttttt tggcagtgac agtgttgtct gacagaaatg cccgtcaaag agtcagacag
     1681 cagaataccg gcggtaaaac agtcgaaaag tggtactcga tataatcaca caacgcagat
     1741 gacagaaaga acggagaaaa cagaaagatg aacaagcagc agcaaaccgt actcaacatg
     1801 gcgggattca taaaaagcca gagcctgacg ctgctcgaaa aactggacgc actcgatgct
     1861 gacgaacagg ccgccatgtg tgagaagctg cacgaactcg cggaagaact tcagaacagc
     1921 atacagacac gctttgaagc ggaaaatcgc accgggatat aacgcacccg gacaggatgc
     1981 agaacggcat agcggagcgt aaggagaaaa tgccacgtca gacgctcttc cgcttcctcg
     2041 ctcactgact cgctacgctc ggtcgttcga ctgcggcgag cggtgtcagc tcactcaaag
     2101 gcggtaatac ggttatccac agaatcaggg gataacgccg gaaagaacat gtgagcaaaa
     2161 agcaaagcac cggaacaagc cagcgccgat gccgtttttc cataggctcc gcccccctga
     2221 cgagcatcac aaaaatcgac gctcaagtca gaggtggcga aacccgacag gactataaag
     2281 ataccaggcg tttccccctg gaagctccct cgtgcgctct cctgttccga ccctgccgct
     2341 taccggatac ctgtccgcct ttctcccttc gggaagcgtg gcgctttctc atagctcacg
     2401 ctgttggtat ctcagttcgg tgtaggtcgt tcgctccaag ctgggctgtg tgcacgaacc
     2461 ccccgttcag cccgaccgct gcgccttatc cggtaactat cgtcttgagt ccaacccgga
     2521 aagacacgac ttaacgccac tggcagcagc cattggtaac tgatttagag gagtttgtct
     2581 tgaagttatg cacctgttaa ggctaaactg aaagaacaga ttttggtgac tgcgctcctc
     2641 caagccagtt accttggttc aaagagttgg tagctcagcg aaccttgaga aaaccaccgt
     2701 tggtagcggt ggtttttctt tatttatgag atgatgaatc aatcggtcta tcaagtcaac
     2761 gaacagctat tccgttgaca aaaaaacaag atctgtacat attcaaaaaa aacaacggat
     2821 tgacccaatg gcacagaacc cgtttaaagc actaaatatc aatattgaca agattgagtc
     2881 tgctctgacg cagaatggcg tcacaaacta ttcctctaat gtaaaaaacg aaagagaaac
     2941 tcacatatct ggcacatata aaggaataga cttcttaata aaactaatgc catcaggcgg
     3001 aaataccact atcggaagag cgtctgggca aaataacact tactttgatg aaatcgcctt
     3061 gattataaaa gaaaactgtt tgtattcaga cacaaagaac tttgaataca ccattccaaa
     3121 attcagtgat gatgacaggg caaatctatt tgaatttctt tctgaagagg ggataacaat
     3181 aacagaagat aataataacg atcctaattg taaacaccaa tatattatga ccaccagcaa
     3241 tggtgacagg gtcagggcaa aaatttacaa gcgcggctct attcaattcc aaggaaaata
     3301 ccttcaaatc gcgagtttg
//
