LOCUS       CP057728                5128 bp    DNA     circular BCT 13-MAY-2022
DEFINITION  Escherichia coli strain RHB16-C19 plasmid pRHB16-C19_4, complete
            sequence.
ACCESSION   CP057728
VERSION     CP057728.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148139
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5128)
  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 5128)
  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 T2-C19
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 78.8657885637409x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/19/2020 11:15:43
            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)                     :: 5,074
            CDSs (total)                      :: 4,955
            Genes (coding)                    :: 4,793
            CDSs (with protein)               :: 4,793
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 162
            CDSs (without protein)            :: 162
            Pseudo Genes (ambiguous residues) :: 0 of 162
            Pseudo Genes (frameshifted)       :: 48 of 162
            Pseudo Genes (incomplete)         :: 108 of 162
            Pseudo Genes (internal stop)      :: 36 of 162
            Pseudo Genes (multiple problems)  :: 25 of 162
            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..5128
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB16-C19"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB16-C19_4"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(170..301)
                     /locus_tag="HVX22_25330"
     CDS             complement(170..301)
                     /locus_tag="HVX22_25330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505258.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QMM04251.1"
                     /translation="MHEPPVQSDCCACSGNYRLESNPERHDKAPLAAAMSKGVYKIY"
                     /name="replication initiation protein"
     gene            complement(932..1123)
                     /locus_tag="HVX22_25335"
     CDS             complement(932..1123)
                     /locus_tag="HVX22_25335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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="QMM04252.1"
                     /translation="MTKQEKTAINMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1188..1511
                     /locus_tag="HVX22_25340"
     CDS             1188..1511
                     /locus_tag="HVX22_25340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="QMM04258.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1489..2211
                     /locus_tag="HVX22_25345"
                     /pseudo=""
     CDS             1489..2211
                     /locus_tag="HVX22_25345"
                     /inference="COORDINATES: protein motif:HMM:NF015397.1"
                     /note="incomplete; partial on complete genome; missing
                     C-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            2189..2707
                     /locus_tag="HVX22_25350"
     CDS             2189..2707
                     /locus_tag="HVX22_25350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="QMM04253.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVLFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     EKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            2714..2947
                     /gene="mbeD"
                     /locus_tag="HVX22_25355"
     CDS             2714..2947
                     /gene="mbeD"
                     /locus_tag="HVX22_25355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="QMM04254.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="mbeD"
     gene            complement(3540..3725)
                     /locus_tag="HVX22_25360"
     CDS             complement(3540..3725)
                     /locus_tag="HVX22_25360"
                     /inference="COORDINATES: protein motif:HMM:NF021447.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF2158 domain-containing protein"
                     /protein_id="QMM04255.1"
                     /translation="MPFNIGDIVYLKSESKAMTVIGYGSSQNNGYIDLANCAWLDKDNR
                     YCQILFLFQTIEKRIS"
                     /name="DUF2158 domain-containing protein"
     gene            complement(3767..4168)
                     /locus_tag="HVX22_25365"
     CDS             complement(3767..4168)
                     /locus_tag="HVX22_25365"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505260.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QMM04256.1"
                     /translation="MIDIQKLISWLGVEGAKAGLDKSEMTNAELIESFGNLLPKNPSKL
                     KRSDLVEEIILATRRMTHKSVEELMEMSKEDLYSYFHDQKYSRKELLDLLYTLEIRPGS
                     SAKKNLTEFTISEISDIGMYRRVAKGNHA"
                     /name="hypothetical protein"
     gene            complement(4165..5049)
                     /locus_tag="HVX22_25370"
     CDS             complement(4165..5049)
                     /locus_tag="HVX22_25370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505259.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ParA family protein"
                     /protein_id="QMM04257.1"
                     /translation="MAVTVGFISEKGGVGKTTSCYHIAEGLSRFHEKRVLVIDADYQRG
                     GITGRFFPKLIENFGNQAPQGTTLFNKYQQLYSAAQQTTDIDIIKFNSGIDVIPADPRL
                     STVSTDKLPSTNNIRSNNAILLQHLKTISAVLSPIADNYDYILIDSHPEVSDVMRSIIY
                     ASDYCVSPVKLDRQSSIGVATVIGEINNVNEDIEMLRKALQVGDSYKDTVFAGAMGMMA
                     REYAEELKQTEQYEYNRLRQAGDIFKHYITEGDGLRVAAAERVSVYDVQISNAYKQASQ
                     FKNLTIEFMRTCR"
                     /name="ParA family protein"
     Typing          664..837
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.571"
                     /coverage="100.0"
                     /evalue="1.23e-64"
     Typing          complement(154..740)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.723"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          1502..3051
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.412"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtactcttag ccatcaaacg aaaaaaaccg actggggagt cggttttttc gagggttcag
       61 taagttgggg aacttctgaa ccgtggtaac agggtgtaca agaccgctga aaccaaattc
      121 tgttattcca gtttagcctc tctaaggctg atacttcaag aactctcact cagtaaatct
      181 tgtacacccc tttactcatg gctgctgcca gtggcgcttt gtcgtgtctt tccgggttgg
      241 actcaagtcg atagttaccg gaacaggcgc agcagtcgga ctgaacgggg ggttcgtgca
      301 tacagtccag cttggagcga actgcctacc cggaactgag tgtcaggcgt ggaatgagat
      361 aaacgcggcc ataacagcgg aatgacaccg gtaaaccgaa aggcaggaac aggagagcgc
      421 acgagggagc caccaggggg aaacgcctgg tatctttata gtcctgtcgg gtttcgccac
      481 cactgatttg agcgtcagat ttcgtgatgc ttgtcagggg ggcggagcct atggaaaaac
      541 ggcttcgccg cgaccctatc gcttccctgt taagtatctt cctggcatct tccaggaaat
      601 ctccgccccg ttcgtaagcc atttccgctc gccgcagtcg aacgaccgag cgtagcgagt
      661 cagtgagcga ggaagcggaa tatatcctgt atcacatatt ctgctgacgc tccggtgccg
      721 ccttttttct cctgccacat gaagcacttt cctgataccc gcactcatgc caacatagta
      781 agccagtata cactccgcta tcgctacgtg actgggtcat ggctgcgccc cgacacccgc
      841 aaggtcaacg gcctgacgcg ccctgacggg cttgtctgct cccggcatcc gctcacagac
      901 aagctgtgac cgtctccggg agctgtatgt gtcagaggtt ttcaccgtca tccccgaagc
      961 gtgcgaggca gctgcggtaa agctcatcgg cgtggtcgtg aagcgattca cagatgtctg
     1021 cctgttcatc cgcgtccagt tcgttgagct tttccagcag cgttaatgtc tggcttctga
     1081 taaagcgggc catgttaatg gcggtttttt cctgtttagt cactgatgcc tccgtgtaag
     1141 gggggatttc tgttcatggg gtaatgatac cgatgaaacg cgagaggatg ctcacgatac
     1201 gggttactga tgatgaacat gcacggttac tggaacgctg tgagggtaaa cagctggcgg
     1261 tatggatgcg gcgggtctgt ctgggtgagc cggttgcccg ttccgggaag ctgccgacac
     1321 tggcaccgcc gttactgcgc cagctggctg ccatcgggaa taatctgaat cagacggcga
     1381 ggaaggtgaa cagcgggcag tggtcttccg gtgaccgggt tcaggtggtg gccgcactga
     1441 tggccatcga gagagagttg cgcagcttac ggcaggtcgt cagggaacat ggagcgcggg
     1501 atgatagtta agtttcatgc caggggaaaa ggcggtggca gtggtccggt tgattacctg
     1561 ctgggaaggg agcgtaaccg ggaaggggca acggtgcttc agggtaatcc ggaagaagtc
     1621 cgggaactca tcgatgccac gccatttgcg aagaaataca cgtcaggtgt tctgtcgttc
     1681 gcggagaagg agctgccgcc gggaggacgt gaaaaggtga tggcgagctt tgagcgtgta
     1741 ctgatgcccg gtctcgaaaa aaatcagtac agcatcctgt gggtggagca ccaggacaag
     1801 ggacggcttg agctgaattt tgtcattccg aacatggagc tacagagcgg aaaacgcctc
     1861 cagccgtact acgactgggc agacaggccg agaattgatg cctggcagac gctggttaat
     1921 caccattacg ggctgcatga ccccaacgcc ccggagaacc gccggatact gactctccct
     1981 gataacctgc cggaaacgaa acaggcgctt gcagagagcg tcacacgcgg gatagacgct
     2041 ctttatcatg tcggggagat aaaaggccgt caggatgtga ttcaggcgct cacagaggca
     2101 gggcttgaag tggtcagggt gacgcgaagc agtatcagca ttgcagaccc gaacggcggg
     2161 aagaatatca gactgaaagg agcattctat gagcaatctt ttacagacgg gcgcggagtt
     2221 cgagaaaaag ctgaaagaga gagccgaatc tacagagaca atgctgaacg acgagttcag
     2281 caagctcgaa aaatctgtaa gcaaggctgt gacatcaaac gagacgaaaa tcaaagacgc
     2341 tatagccctg ttcacagctt cgacagagga atcactgaaa aaacaccggg aaggggtgaa
     2401 agaggcgatg atgcagcaca ggaaggacgt gttaaagctg gcagggaata cgggcatgat
     2461 gttactgggg atggtccttt tcctgtttac cgtgagtggc gggacgctct ggtatcttgg
     2521 cgggcggata caggcgaacc tggaagaaat caggatacag gaagaaacat tgcagaaact
     2581 gaacgcgaag acatggggcg tggagtttgt gcaggacggg agaaggaaat ttctggtcct
     2641 tccgtacggg aaatcggcaa cggtgattcc ctatcaggag aaggactggg tacaactgac
     2701 ggagtgacac agagtgacgg agctggaaag acatttgctg aacgccttag agcaactgca
     2761 acaggactat atgcagcggc tgagcgaatg ggagagcgcc ttcgtggaat tgcagaaaat
     2821 gttttcgctt acgcaacggg acaacgcgat gctgaacgag caggtcatgc agttgagtca
     2881 gcaggtgcag cacttgagcg agcggacaga acgcttgagc cagttataca gcgagaacag
     2941 gagataaggg acgaacggct gatacaggag cgcgaacatg agttatccct ggagcgtgag
     3001 cgccagccgg aaatacagga atggacacag gatggccctt cgcttggatg gtaatcagag
     3061 acaggctaaa atgttgtcag cgcgtttccg gtgcattttt tgggataatg gttggttcgg
     3121 gggcaccggg aacgcgcttc agtcagacct tgctgaaaac acaggaacgc gttaaaacgc
     3181 atacgggcgc gattctggtg tgtcttttgt tgctgtgttt tgcctctatt gccagatcgc
     3241 gctcattccc ctgaacttct gttttcccgc tccggtcccc gtcttcttcg cttccgaaag
     3301 catgaaaaaa atccgtttca gctgtctctg gctggcaatt cctgcgtgat tcacatggct
     3361 gcatagctat gcatgtggtt aaaatttacc gggtgcgatc gcggcagttt ttcgggtggt
     3421 ttgttgccat ttttacctgt ctgctgccgt gatcgcaccg aacgcgtttc tgcggtgcgg
     3481 gcaacggatg ttatggtaaa taggttcgtc cggtatgctc aatgaagata agccagtttt
     3541 taactgattc ttttttcgat cgtttgaaac aagaatagta tttggcaata gcggttgtct
     3601 ttatctagcc aagcacaatt agctagatct atgtaaccgt tattttgaga cgatccatat
     3661 ccgatgaccg tcatcgcttt tgattctgac tttaagtaaa ctatatcgcc tatattaaat
     3721 ggcatttttt tatcctataa aaagccacct cacaggtggc ttttatttat gcatgattcc
     3781 ctttcgctac gcgacgatac atgccaatat cacttatctc acttattgtg aactcggtta
     3841 gatttttctt tgctgagctc ccaggtctga tttcaagagt atataacaaa tcaagaagtt
     3901 cttttctgct atatttctga tcgtggaaat atgaatacag atcttctttt gacatttcca
     3961 tcagttcttc aactgattta tgtgtcattc tccttgttgc taaaataatc tcctcaacga
     4021 gatcggagcg ttttaatttg cttgggttct ttggaagtaa attaccaaag gattcaatta
     4081 gctcggcatt agtcatttca cttttatcca agccagcttt agctccctca acgccaagcc
     4141 aagatatcag tttttggata tctatcatcg acaagtcctc ataaactcaa tcgtcaagtt
     4201 cttaaactgt gacgcttgtt tgtaagcgtt acttatctgt acatcataca ctgaaacgcg
     4261 ctctgctgca gctactctta gcccatcacc ttccgttatg tagtgcttga agatgtcacc
     4321 tgcttgccga agcctgttgt attcatattg ctctgtttgc ttcagttctt ctgcatattc
     4381 tctggccatc attcccattg ctccggcgaa aactgtgtcc ttatatgaat cgccgacttg
     4441 cagtgccttt cttagcattt caatatcttc atttacatta tttatctcac ctatgaccgt
     4501 ggccacacca atagatgatt gcctgtctag ttttaccggt gatacacaat aatctgatgc
     4561 gtagattata gagcgcatga catcagaaac ttcggggtgt gaatcaatca atatgtagtc
     4621 ataattatct gcaataggtg ataatacagc gcttatggtt tttaaatgct gtaaaagaat
     4681 ggcattgttc gatcttatat tgtttgtact aggtagctta tcagttgaaa cggttgataa
     4741 gcgagggtcg gctggaatga catcgatacc actattaaat ttaattatgt ctatgtcagt
     4801 cgtttgttgt gccgcgctat ataattgctg atacttgtta aataacgttg ttccttgcgg
     4861 tgcttgattt ccaaagtttt cgatcagttt agggaaaaat cttccagtta tacctccgcg
     4921 ttgataatct gcatctataa ctaaaacacg tttttcatga aaacgactaa gtccttcggc
     4981 aatgtgataa caggacgttg ttttaccaac cccacctttc tcactaataa acccaactgt
     5041 cacagccatt tttattcctt acaaatctct tttttttggt agagggaaca gcgtcaacgc
     5101 tttccttgac gttcagtata acgtcagc
//
