LOCUS       CP056960                4073 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB41-C22 plasmid pRHB41-C22_6, complete
            sequence.
ACCESSION   CP056960
VERSION     CP056960.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148430
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4073)
  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 4073)
  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-C22
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 147.446626226081x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 03:49:53
            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)                     :: 4,816
            CDSs (total)                      :: 4,694
            Genes (coding)                    :: 4,558
            CDSs (with protein)               :: 4,558
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 136
            CDSs (without protein)            :: 136
            Pseudo Genes (ambiguous residues) :: 0 of 136
            Pseudo Genes (frameshifted)       :: 52 of 136
            Pseudo Genes (incomplete)         :: 82 of 136
            Pseudo Genes (internal stop)      :: 22 of 136
            Pseudo Genes (multiple problems)  :: 20 of 136
            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..4073
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB41-C22"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB41-C22_6"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(385..978)
                     /locus_tag="HV013_24070"
     CDS             complement(385..978)
                     /locus_tag="HV013_24070"
                     /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="replication protein"
                     /protein_id="QMA99504.1"
                     /translation="MSGRKFGRLPNWWARSSWLVNNVRSNEIGGGIASMKCLLALSVLI
                     DFHSRTASVSFTGMERLTGLSRPMIVKGVAKLEKDGLIKIDREMFVNSYELTVQPNDDR
                     WAKVPVDTIRKKLNTISNRGMAPFVALKLYLTIISLRYQSNNTVKVTHETLRSYTGVQP
                     NQIRFGLDVLYCSRLIHLQPKEDRESNIYEIIGL"
                     /name="replication protein"
     gene            complement(1572..2486)
                     /locus_tag="HV013_24075"
     CDS             complement(1572..2486)
                     /locus_tag="HV013_24075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001448734.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Abi family protein"
                     /protein_id="QMA99505.1"
                     /translation="MPNTIHYPHVIPFISQGKINAIKSTFGNNLSDRECYGIYIWSQKA
                     SSAIYPLLQQLEVTLRNSIDKEATKLIGQKWWDNVYTDTSKSKHGDFIHNINKAIRRYE
                     NEFKKKNPSMANTKIIAPHDDIIAHTDFYTWQAVLSDAFHTQSRSEASRALWPRLTYRV
                     LKGLDRSKDEGTARIDFLNELNEIRNYRNRLSHNDCIWIKIHSKNLQSAVETIREKINK
                     IEGLIKTINPQVHLSLTKWGSFYHAKRICSQKEAELHLGKGIINSTTDEMNTILDQLYA
                     LTADGKLTGVVKRNTNNIAFHKF"
                     /name="Abi family protein"
     gene            complement(3491..3685)
                     /locus_tag="HV013_24080"
     CDS             complement(3491..3685)
                     /locus_tag="HV013_24080"
                     /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="QMA99506.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2..127
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.913"
                     /coverage="88.0"
                     /evalue="2.24e-44"
     Typing          3324..3410
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          3722..3820
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          3945..4073
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.656"
                     /coverage="89.0"
                     /evalue="2.22e-49"
     Typing          complement(2754..3313)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.204"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcgccgacac cgctttgtag gggtggtact gactattttt ataaaaaaca tcattttata
       61 tcaggggtgc tgctagcggc gcggtgtgtt tttttacagg acgcccctgg gggcgctgcc
      121 aggggtgtct gttcagatat gtagcaatga gtcagggatt cacgaactga aaatgtccga
      181 aaatgtgtct catgggcacc gtatgcgccc aaaccgttcg tcattcattt tcatgcatag
      241 ctatgcagtg ggctgaaaac gatcctgacg cattttttcg gttttcactg ggtaaaacat
      301 ctctttttgc ggtatctgcg tcagaatcgc gttcagtgcg ttttagcggt gcgcgtaatg
      361 cgacgttatg gtaaatgcat ttcctcatag gccgattatt tcatagatgt ttgactctct
      421 atcttctttt ggttgcagat gtatcaggcg actacagtac agtacatcta agccgaacct
      481 aatctggttt ggctggacac ctgtatagct tctcagtgtt tcatgtgtca ccttaacagt
      541 attatttgac tgataacgaa ggcttataat tgttaaatat agttttaatg ccacaaatgg
      601 ggccatcccc ctgttcgata tggtgtttag ttttttcctg atagtatcta ctggtacttt
      661 tgcccaccta tcatcatttg gctgtactgt taattcatag gagttaacaa acatctctct
      721 atctatcttt ataagaccat ctttctcaag tttggctact cctttcacta tcatggggcg
      781 gcttagtcca gtcagtcttt ccattccggt aaatgatact gaggctgttc ttgaatggaa
      841 atcaatcaag acggatagag ctaacaagca tttcattgat gcaatgccgc cccctatctc
      901 atttgaacga acattgttta caagccatga gcttcgggcc caccagtttg gaagcctgcc
      961 aaattttcta ccgctcattt ttaccccatt ttcggtcaag gagagatata aatagcttta
     1021 ttatcatata catgaaaacc attgcaccta aagatacaac agaaaccaaa acctccggct
     1081 ttgcggaagt tagcgttacc agcaaattgt tgagggtttc caattggtcc tccagtcgca
     1141 tactaagttg ttgtgtttta actttatata cgcttattag aataaatcta gataaagcaa
     1201 tatttggtgg ttgcttgttt tcccatataa aacatgatgt tatcttgttt ttatcgtttt
     1261 ttaactggta aatgtaaatt tgataatgct ggtttaatcg gcgtttttag ttatttttgt
     1321 tgtgtgtttt ttgatctatt ggtaaatggt ggatggtaag ctttggcgtg atcatgggaa
     1381 atagtttgct ctttttcctg atgatgatgt atcatgtatg gcagtgaagc cttgagcttt
     1441 cgctttaatg cattgtgaaa tttttataga ttcacaatga cattaaggcc acgctccacc
     1501 gaaaggtgat aatggcaaga gatttggatg aggctcgaca ggaaactgtc gggccttttc
     1561 tattttgtga tctaaaactt gtgaaatgcg atattgttgg tatttcgttt tacaacaccc
     1621 gttagctttc cgtcagcagt tagtgcgtat agttgatcta gaattgtgtt catctcatct
     1681 gttgtgctat tgattattcc tttgcctaga tgcaattcgg cctctttttg agaacatatt
     1741 cttttggcgt gataaaagga accccacttc gttaatgata ggtgtacctg tgggtttatc
     1801 gtttttatca gtccttctat tttgtttatt ttttctctta ttgtttctac tgcagattgc
     1861 aaatttttag agtgtatttt tatccatatg caatcattat gcgataacct atttctgtag
     1921 tttctgatct cattcagctc gtttaagaaa tcaattctgg ctgtgccttc atctttgctt
     1981 ctatctaatc ccttcagtac tctgtaggtg agcctgggcc ataaggctct tgatgcttca
     2041 gatcttgatt gtgtatgaaa agcatcgctc aaaaccgctt gccatgtgta aaaatctgtg
     2101 tgtgcaatga tgtcatcatg aggtgcaatt attttggtat ttgccattga tgggtttttt
     2161 ttcttgaatt cattctcata tcttcttatt gctttgttta tattatgtat gaagtcaccg
     2221 tgtttgcttt ttgatgtgtc ggtgtataca ttatcccacc atttttggcc tattagtttt
     2281 gtcgcttctt tatcaatcga gtttctcaaa gtaacttcga gttgttgcag taatggatat
     2341 atggcagatg aggctttctg gctccatata tatatcccgt agcactccct atcagacagg
     2401 ttattaccaa acgtgctttt tatagcattt atttttcctt gggatataaa tggtattaca
     2461 tgagggtaat gaattgtatt tggcatatcc atctctatca tacacttagt ggtgattgga
     2521 tgttgccata cacgtatgga tagttgtaga gtgttaaacg aaaaaaccgc cttggcgggc
     2581 ggtttttcga aggttcaaag agttggcgct ctgtgaacca aggtaactgg cttggaggag
     2641 cgcagtcacc aaaatctgtt ctttcagttt agccttaaca ggtgcataac ttcaagacaa
     2701 actcctctaa atcagttacc agtggctgct gccagtggcg ttaaggcgtg ccttaccggg
     2761 ttggactcaa gacgatagtt accggataag gcgcagcggt cgggctgaac ggggggttcg
     2821 tgcacacagc ccagcttgga gcgaacgacc tacaccgaac tgagatacca acagcgtgag
     2881 ctatgagaaa gcgccacgct tcccgaaggg agaaaggcgg acaggtatcc ggtaagcggc
     2941 agggtcggaa caggagagcg cacgagggag cttccagggg gaaacgcctg gtatctttat
     3001 agtcctgtcg ggtttcgcca cctctgactt gagcgtcggt ttttgtgatg ctcgtcaggg
     3061 gggcggagcc tatggaaaaa cgccagcggc gcggcctttt gtcctggctt tgccttgttg
     3121 ctcacatgtt ctttccggtc ttatcccctg attctgtgga taactgtgtt accgtttttg
     3181 tgtgagtcag taccgctcgc cgcagccgaa cgaccgagcg tagcgagtca gtgagcgagg
     3241 aagcggaaaa gcgcctggac gtgcattttc tccttacgca tctgtgcggc atttcacacc
     3301 cggcatgggg cacttttcat acaatccgca ctgatgccgc atggttaagc cagtatacac
     3361 tccgctatcg ctacgtgact gggtcatggc tgcgccccga cacccgctaa aaccccctga
     3421 cgcgccctga cgggcttgtc tgctgccgaa aacgctcgcg gacaagccgt gagcgcctcc
     3481 gtcagcttcg ttatgttcct gtttcacttt cggtctcaaa gcgaacctgg atgctgttct
     3541 ggagttcttc cgcgagttcg tgcagtcgtt cgcacatggc tgcctgttcg tcggcatcca
     3601 gagcatccag tttttcaagc agtgtcaggc tctggctttt gataaatcgc gccatattca
     3661 gcgcagtttg ttgttgtttg ttcaccttcc gttgttctcc gtcagttccg ggtgtcgggg
     3721 ggaccctgag cagctggtaa ttgtaagacg ttgcgggcga cggtattaca attgcacatc
     3781 ctgtcctgtt tttttaggac gtatcatggc acagcatatc aactgataaa taatccctgt
     3841 gcagtgcagc cgctgttgca taaaatttcg ctctgcgtcg agtgtttctt aatcaataat
     3901 tccgctgata ctccggaaaa acgcgagtct gttctcattc ctgaaatgcc cacaccccac
     3961 gcaaaaacaa gtttttgctg atttttcttt ataaatagag agttatgaaa aattagtttc
     4021 tcttgctctc tttgcgatat ttaaaaaagc ggtgccggcg cagctacaac acc
//
