LOCUS       CP057174                4154 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB34-C12 plasmid pRHB34-C12_2, complete
            sequence.
ACCESSION   CP057174
VERSION     CP057174.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148341
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4154)
  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 4154)
  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                     :: RH03 T3-C12
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 177.815528025207x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 06:37:07
            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)                     :: 4,550
            CDSs (total)                      :: 4,427
            Genes (coding)                    :: 4,318
            CDSs (with protein)               :: 4,318
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 109
            CDSs (without protein)            :: 109
            Pseudo Genes (ambiguous residues) :: 0 of 109
            Pseudo Genes (frameshifted)       :: 46 of 109
            Pseudo Genes (incomplete)         :: 51 of 109
            Pseudo Genes (internal stop)      :: 27 of 109
            Pseudo Genes (multiple problems)  :: 14 of 109
            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..4154
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB34-C12"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB34-C12_2"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(4070..4154,1..1058))
                     /gene="fepE"
                     /locus_tag="HVZ24_22730"
     CDS             complement(join(4070..4154,1..1058))
                     /gene="fepE"
                     /locus_tag="HVZ24_22730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010435173.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator"
                     /protein_id="QME05372.1"
                     /translation="MSAMDFKKNTDLDFPRYATPAVSTKEIDLLGLLDVLLAAKKRIVT
                     IVLAFAVVGLAIAFLIPQKWTSKAVITPAEQTQWNTLRQMMVTLQVLDVDAKVSRGDVF
                     NLFIKKFQSQSLLEEYMKTSPYVMSQLEGTEVDPLELHRAVVNIAEKMKATDNTQVKDA
                     DKAPYTSWTLSFTAPTAGDAQTVLEGYINYISRIVEQETMENIRNQITLKTKVVQQQLE
                     LDRVRLTNIHNTNLQRLNYSLEVANAAGIKKPVYSNGQAVKDDPDYSVALGADGIAQKL
                     QIEKNLKDVAELNADFQNREYYLTQLQKLSVEDVKLEPFRYQLSPSLPVKKDGPGKALI
                     VLLAGILGGLFACGSVLLREAMLSRNPLPEPITAVTPATE"
                     /name="fepE"
     gene            1217..1715
                     /locus_tag="HVZ24_22735"
                     /pseudo=""
     CDS             1217..1715
                     /locus_tag="HVZ24_22735"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_416498.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS5 family transposase"
                     /name="IS5 family transposase"
     gene            complement(2303..2416)
                     /locus_tag="HVZ24_22740"
     CDS             complement(2303..2416)
                     /locus_tag="HVZ24_22740"
                     /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="QME05371.1"
                     /translation="MHEPPVQSDRCVFSGNYRLESKPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(3602..3793)
                     /locus_tag="HVZ24_22745"
                     /pseudo=""
     CDS             complement(3602..3793)
                     /locus_tag="HVZ24_22745"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007798797.1"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="NINE protein"
                     /name="NINE protein"
     gene            3790..4032
                     /locus_tag="HVZ24_22750"
                     /pseudo=""
     CDS             3790..4032
                     /locus_tag="HVZ24_22750"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003862821.1"
                     /note="incomplete; partial on complete genome; missing
                     N-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="cupin domain-containing protein"
                     /name="cupin domain-containing protein"
     Typing          complement(2300..2685)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.373"
                     /coverage="90.0"
                     /evalue="1.04e-173"
ORIGIN
        1 caggcaaaca ggccgcccag aatccctgcc agcagcacaa tcagggcttt gcccggaccg
       61 tcttttttca ccggcagtga cggtgaaagc tgatacctga agggttcaag cttcacgtct
      121 tccacggaca gtttttgcaa ctgagtcaga tagtattcac ggttctggaa atccgcattc
      181 agctcggcca cgtccttcag attcttttca atctgcagct tttgcgcaat accgtcagca
      241 cccagcgcca cggagtagtc aggatcgtct tttaccgcct gtccgttgct gtaaaccggc
      301 ttcttaatgc ctgccgcgtt cgccacttcc agcgaatagt tgaggcgctg caggttggtg
      361 ttgtggatat tggtcagacg cacgcgatcc agctccagct gctgctgaac gactttcgtt
      421 ttcagcgtga tctggttacg gatattttcc atcgtctcct gctcaacaat gcgggagata
      481 tagttgatgt aaccttccag aaccgtctgc gcgtctcccg ccgtcggggc ggtaaagctc
      541 agcgtccatg aggtatacgg cgctttgtct gcgtctttaa cctgcgtgtt atctgtcgct
      601 ttcattttct cagcaatatt caccaccgcg cgatgcagct ccagcgggtc tacctcggtg
      661 ccttccagct gagacatcac gtacggggag gttttcatgt actcttcgag cagcgactgc
      721 gactgaaact ttttgatgaa caggttaaac acgtctccac ggctcacctt cgcgtcgacg
      781 tccagcacct gcagcgtcac catcatctgg cgcagcgtgt tccactgcgt ctgctcggcc
      841 ggcgtgatca cggctttact ggtccatttt tgcgggatta aaaacgcaat ggccaaccct
      901 actacggcga acgccaggac gatcgtcaca atacgttttt tggctgccag aagtacgtct
      961 aacaacccca ggagatctat ctctttggtg cttaccgccg gagtggcata acggggaaaa
     1021 tcgaggtccg tgtttttctt gaaatccatc gctgacataa ccgttcttct ttttggagcg
     1081 cagtaaattt ctgcctgatt ggttgcagtg gtcggatgat acaagaaagt aagaataatc
     1141 tgaacgccag attgatctat ctgtagaccg actatcagat ttagggaagg tgcgaacaag
     1201 tccctgatat gagatcatgt ttgtcatctg gagccatgga acagggttca tcatgagtca
     1261 tcaacttacc ttcgccgaca gtgaattcag cagtaagcgc cgtcagacca gaaaagagat
     1321 tttcttgtcc cgcatggagc agattctgcc atggcaaaac atggtggaag tcatcgagcc
     1381 gttttacccc aaggctggta atggccggcg accttatccg ctggaaacca tgctacgcat
     1441 tcactgcatg cagcattggt acaacctgag cgatggcgcg atcgaagatg ctctgtacga
     1501 aatcgcctcc atgcgtctgt ttgcccggtt acatgaaagc cagcatccgg gccaaggtgg
     1561 agcacccatt tcgcatcatc aagcgacagt tcggcttcgt gaaagccaga tacaaggggt
     1621 tgctgaaaaa cgataaccaa ctggcgatgt tattcacgct ggccaacctg tttcgggcgg
     1681 accaaatgat acgtcagtgg gagagatctc actaaaaact gggaataacg ccttaaatgg
     1741 cgaagaaacg gtctaaatag gctgattcaa ggcatttacg ggagaaaaaa atcggctcaa
     1801 acatgaagaa atgaaatgac tgagtcaacc gagaagaatt tccccgctta ttcgcacctt
     1861 ccctaatagc gcggctgcga ttctactttt ttcacctgaa cctgaagagg cgtttgtggc
     1921 tccgcagtgt gggcatgact ttgctgtttc gtgtatttcc ttgccgcatc ctcggcagta
     1981 aaccattgaa ctcatttttt atcctcgagc ttatttttag ttgggatgca taatatccga
     2041 tgttttataa cgatatgcat cctatatgct cgggtgggat agatttccat tatggtgaag
     2101 gatcttcttg agatcctttc tgtagcgtcg taatctcttg ctcagtaaac gaaaaaaccg
     2161 cccagcaagg cggtttttcg aaggttctca gagctgcaac tctttgaacc gtggtaactg
     2221 gcttatgagg agcgcagtaa ccaaatctgt tctttcagtt tagccttaac aggcgcataa
     2281 cttcaagact aactcctcta aatcagttac cagtggctgc tgccagtggc gctttgtcgt
     2341 gtctttccgg cttggactca agtcgatagt taccggagaa gacgcagcgg tcggactgaa
     2401 cggggggttc gtgcatacag tccagcttgg agcgaactgc ctacccggaa ctgagtgtca
     2461 ggcgtggaat gagataaacg cggccataac agcggaatga caccggtaaa ccgaaaggca
     2521 ggaacaggag agcgcacgag ggagccacca gggggaaacg cctggtatct ttaagtcctg
     2581 tcgggtttcg ccaccactga tttgagcgtc agattctgtg atgcttgtca ggggggcgga
     2641 gcctatggaa aaccggcaac gccgcggcct tttcttttgc ctctcgatcc tctctcattg
     2701 cctgtgcctt aatgtctccg ttccctccgc tcgccgcagc cgaacgaccg agcgtagcga
     2761 gtcagtgagc gaggaagcgg aatatccccg gacttatctt cggcaccgta cgcgccagtg
     2821 ctgcattttt taatacgatg caggataggg ctaacgccgc aaagtgacgt cacctgacgt
     2881 tcctggatta caaaggttaa agcagcggac aggaaatgtt ttgtgcccac agctatgctg
     2941 gcttattcac aaaacagcgg gacaagatgt gtttttggag taccgccggc ccgctaaaga
     3001 ctcctggtta gctcccgcat gtttgctatc tttttgctac cattttgcta cttttttgct
     3061 atctccagag tcttctggtc tttcggttgc tatccttttg ctactttttt gctatcaaaa
     3121 tgctacctct cccttcttgc aataaatgac caaggcacgt tagcgatgta tacatcgccg
     3181 cgccgcaagg gtgccccttc cgaatcccgt tcatcactgc gtgctgattc atccacgtta
     3241 aatccgaccc ccttagcaat aaatccagcc atgcctgacg gcctggccaa cgcctcacgg
     3301 ccgcacagta aactgcacac ccgtgaggcg ttattcgtga ggttcagtgg tgcttttggg
     3361 cgtccagccg gattttagcc gctaaaatcc cggccatgca tgtgtgtgca tagccatgca
     3421 gacgcgccag aatcatcagg cgcgtttttt cacgatatag gcacagggaa gtgtcggaaa
     3481 caggcaggaa gacccagaaa cgccctgaga gcctctcagg cggtgcacgc aacggatgtt
     3541 atggtaaatc tgcctcacag actggtacaa aaaaagcccc gcagggcttt tttgctatga
     3601 gttagccata ttttcttgcg aatttttcat cggaatcgca tagataaata ataaactcaa
     3661 taaactcaat aaacgcgatg atcgcgggta tgaatgtcca gcaaaaaatt agatacagga
     3721 atccctgtcc tattttacct aagtaaaatt tatgtacgcc aaatccacca aggaagaatg
     3781 ctaagaaaga tgatggcggt ggaggtcaat tttgagcagg gtgcgattgg cccgatgcac
     3841 aatcacccgc atgaacagct tacctatgtg ctctccgggg agttcgagtt tacgataggt
     3901 gaagaaaagc agatcgtgac ggcgggcgat acgctctata aagcgccgca cgtgatgcac
     3961 ggctgcattt gcctgaagcc cggcaccctt ctggatacct ttacgccggt gcgcgacgat
     4021 ttcctgaaat aaaaaaaggc gctgaatcag cgccttttta atatcgtcgt tactctgttg
     4081 ctggcgttac ggccgttatc ggctctggca acggattacg cgagagcatt gcctcacgca
     4141 gcagcacgct gccg
//
