LOCUS       CP056982                2601 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB41-C14 plasmid pRHB41-C14_9, complete
            sequence.
ACCESSION   CP056982
VERSION     CP056982.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148426
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2601)
  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 2601)
  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-C14
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 173.996160485263x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 03:28:15
            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)                     :: 5,152
            CDSs (total)                      :: 5,031
            Genes (coding)                    :: 4,749
            CDSs (with protein)               :: 4,749
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 282
            CDSs (without protein)            :: 282
            Pseudo Genes (ambiguous residues) :: 0 of 282
            Pseudo Genes (frameshifted)       :: 99 of 282
            Pseudo Genes (incomplete)         :: 175 of 282
            Pseudo Genes (internal stop)      :: 42 of 282
            Pseudo Genes (multiple problems)  :: 32 of 282
            CRISPR Arrays                     :: 1
            ##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..2601
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB41-C14"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB41-C14_9"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(2307..2601,1..371)
                     /locus_tag="HV009_25740"
     CDS             join(2307..2601,1..371)
                     /locus_tag="HV009_25740"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMB17744.1"
                     /translation="MVHVMSFQLAIFFKQHITRPDHFFSSINDAAGNLFDRMPQIIPLP
                     DEVPPEIPRVAATNMSGTYNFNISLNRLDFTLNVSDSQFKEPEALSDFALKSKLIVKNI
                     PTEIEIIRIGIIGNYFELERLPAIALAKKYSKKDLGNISEFNFRYNKISQEFGYSFNNV
                     FSISNAEINTKGIVSDGVFIQKDINNNPSGLSIKKDMVMEIITKKIKELSTSGLEGIS"
                     /name="hypothetical protein"
     gene            371..736
                     /locus_tag="HV009_25745"
     CDS             371..736
                     /locus_tag="HV009_25745"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMB17742.1"
                     /translation="MPPQNRSSSSSSYSSPSVNSGSSSALQIDAAWASFEAMIERRLEE
                     IKPKTPAQIKANGDSRNKTIVISALVVILAIIVIYIGAIYIIDSVTGKEFTSSLMPVIT
                     AIISGVLGYLSGEKSSK"
                     /name="hypothetical protein"
     gene            1972..2121
                     /locus_tag="HV009_25750"
     CDS             1972..2121
                     /locus_tag="HV009_25750"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QMB17743.1"
                     /translation="MHEPPVQSDCCACPGNYRLESNPERHDKAPLAAATGNGLEELSLD
                     VMRL"
                     /name="replication initiation protein"
     Typing          1594..2082
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.901"
                     /coverage="95.0"
                     /evalue="0.0"
ORIGIN
        1 taattgtaaa aaacattcct accgaaattg agattatccg gattggaata atcggcaatt
       61 atttcgaatt agaaagactt ccagctatag ccttagcaaa aaaatactcc aaaaaagatc
      121 ttggaaacat aagtgagttt aatttccgat acaataaaat atctcaggaa ttcggatata
      181 gttttaataa tgttttctcg attagcaatg cagagataaa cactaaggga atagtctcag
      241 atggagtatt tatacaaaaa gacataaaca acaatccatc aggattatca ataaaaaaag
      301 acatggtaat ggaaataata actaagaaaa tcaaggagtt gtcaacaagt ggcttagagg
      361 ggatatccta atgcctccac agaaccgttc atcatccagc tcgtcataca gttcaccaag
      421 tgtgaattct ggtagctcgt ctgctttgca aatagatgct gcatgggctt ctttcgaagc
      481 aatgatagaa agaagactgg aagagataaa acctaagacg ccagcacaaa tcaaagcaaa
      541 tggtgacagc agaaataaaa ccattgtcat atctgcttta gttgtaatat tagctataat
      601 agttatatat attggagcaa tatacataat tgattctgtc actgggaagg agttcacgtc
      661 ctcacttatg cccgtaataa ccgcaataat aagtggcgta cttggatatc tttctggaga
      721 gaaatcatcc aaataaaaaa taagcgctgc tgtattaaga tatggcagca cttattatcc
      781 caaacataaa actacaaatt tattaacatg tggtgaaatt aacttcaatt taccataaca
      841 tccgttgccc gcaccttctc agacggcctg aaggcgtttc tgcctcgtcc ggccgatttc
      901 cggcaccttt ccctatccca aacactgaaa aacgcccctg atgatttttg cgcagctgca
      961 tggctatgca cagacatgcc tggcctccat tttagcggct aaaatccggc gagcgccctg
     1021 aaagccatca tgaaccaccc tgataacggt gaacgggtgc gcagtttact gtgcggccgt
     1081 gaggcgttgg ccaggccgtc aggcatggca ggatttattg ctaagggggg tcggatttaa
     1141 cctggggtga tcagcgcgca gagatgaacg ggattcggaa ggggaaccct tgcggcgcgg
     1201 cgatgtatac atcgctaacg tgccttggtc atttattgca agaagggaga ggtagcattt
     1261 tgatagcaaa aaagtagcaa aaggatagca accgaaagac cagaagactc tggagatagc
     1321 aaaaaagtag caaaaagata gcaaaaagat agcaaaaaga tagcaaacat gcgggagcta
     1381 accaggagtc tttagcgggc cggcggtact ccaaaaacac atcttgtccc gctgttttgt
     1441 gaataagcca gcatagctgt gggcacaaaa catctcctgt ccgctgcttt aacctttgta
     1501 atccaagaac gtcaggtgac gtcactttgc ggcgttcgcc ctatcctgca tcgtattaaa
     1561 aaatgcagct atggcgcgta cggtgccaaa gagaagcccg cagatattcc gcttcctcgc
     1621 tcactgactc gctccgctcg gtcgttcggc tgcggcgagc gttacctgca cacggataag
     1681 gacaaaggca tacggcgtga caggcagggc aggaaaagga tgcggcgctg ccgtttttcc
     1741 ataggctccg cccccctgac aagcatcacg aaatctgacg ctcaaatcag tggtggcgaa
     1801 acccgacagg actataaaga taccaggcgt ttccccctgg tggctccctc gtgcgctctc
     1861 ctgttcctgc ctttcggttt accggtgtca ttccgctgtt atggccgcgt ttatctcatt
     1921 ccacgcctga cactcagttc cgggtaggca gttcgctcca agctggactg tatgcacgaa
     1981 ccccccgttc agtccgactg ctgcgcctgt cccggtaact atcgtcttga gtccaacccg
     2041 gaaagacacg acaaagcgcc actggcagca gccactggta acggattaga ggaattgagt
     2101 cttgatgtga tgcgcctgta aaggctaaac taaaagaaca agttttggtg actgcgctcc
     2161 ctctaagcca gttacctcgg ttagttagat ttcctaggtc tttctaacct ctaaaaaacc
     2221 gcctgccagg gcggtttttt ttcttcgtaa gaagattacc tttcgcttta tacttcagtc
     2281 aagacactaa taaaaatgga gttgaaatgg tacatgtcat gagtttccag ttggctatct
     2341 tttttaagca gcatataaca agaccggatc attttttttc cagtattaat gatgccgctg
     2401 gcaatttatt tgataggatg cctcaaatta tcccacttcc agatgaggta ccaccagaga
     2461 tacctagagt ggcagcaaca aatatgtcgg gaacatataa ctttaacata tcactcaaca
     2521 gattagattt cacattaaat gtatccgatt ctcaatttaa agagccagaa gctttaagtg
     2581 actttgcact aaagtcaaaa c
//
