LOCUS       CP055728                6746 bp    DNA     circular BCT 16-MAY-2022
DEFINITION  Escherichia coli strain RHB13-C14 plasmid pRHB13-C14_5, complete
            sequence.
ACCESSION   CP055728
VERSION     CP055728.1
DBLINK      BioProject: PRJNA605147
            BioSample: SAMN15148098
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6746)
  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 6746)
  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 T1-C14
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 84.3972219793898x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/18/2020 17:04:29
            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)                     :: 5,159
            CDSs (total)                      :: 5,038
            Genes (coding)                    :: 4,830
            CDSs (with protein)               :: 4,830
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 208
            CDSs (without protein)            :: 208
            Pseudo Genes (ambiguous residues) :: 0 of 208
            Pseudo Genes (frameshifted)       :: 85 of 208
            Pseudo Genes (incomplete)         :: 110 of 208
            Pseudo Genes (internal stop)      :: 38 of 208
            Pseudo Genes (multiple problems)  :: 24 of 208
            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..6746
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="RHB13-C14"
                     /isolation_source="Pooled pig faecal samples collected from
                     floor of farm"
                     /db_xref="taxon:562"
                     /plasmid="pRHB13-C14_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(5662..6746,1..1135)
                     /locus_tag="HVW81_25660"
     CDS             join(5662..6746,1..1135)
                     /locus_tag="HVW81_25660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001029330.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="QLM74955.1"
                     /translation="MAIYHLSMKIISRKNGYSAVASAAYRSGSVIPDDRTGLIHDYTRK
                     RGVDDAVILTPANAPSWCGDRSVLWNAVEKAEQRRNSQLAREIELAIPREISREAARET
                     VLAFVRENFVSRGMIADVAFHHMDRTNPHAHIMLTTRAVGETGFAGKVRDWNDRALAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKAPGLHLGKAACAMEKRGMETERGEQ
                     NRLINSLNLEIQVSRTQLALRTVQEAQRKRELSDAARRAAEALNLTIPAANASADTLRE
                     FIATLPQECGNAWEMTPEFLAMNGKANDIKREGNALVKERDILEKEMTGLRKARPVASI
                     LSELPLMTWAEPEYRKRQLRFWKLGKQIESLSRTYRAVKERDIPARRQAFETQWNTWIA
                     PGMAELKEKLSAREAERRREEAEAEARRKEQEHEARLKRHDNHRLSRETALVGVITELG
                     RAREPGTGRITRYMMLSNRAGEFTVWGDELAHYPRSVHDPVNVYLSPGGAVMVTDIHAG
                     RPESHETMARPERVRMYSGATVRHVLEQMRQGWPSYGFPALPHHWPDNFYFSNDRRPVA
                     SPLPSAHRVDITADAAPEQLMPVVFSREGNSRTLNLLLCKGPEEMLVGFVRREGGFCPV
                     LVLPSPDYSHLMVSTITENGVCLAGYGEAINHDEDTPYPPEPHLMQFRLKGHHDRLLAA
                     VHKPEEMPDYLFRQLGFNQTWHEWKQDEQHRQQQRRPGHYRGMSM"
                     /name="MobA/MobL family protein"
     gene            1268..1965
                     /locus_tag="HVW81_25665"
                     /pseudo=""
     CDS             1268..1965
                     /locus_tag="HVW81_25665"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076612230.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS1-like element IS1A family transposase"
                     /name="IS1-like element IS1A family transposase"
     gene            complement(1976..2650)
                     /locus_tag="HVW81_25670"
     CDS             complement(1976..2650)
                     /locus_tag="HVW81_25670"
                     /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="QLM74956.1"
                     /translation="MFDVQQHRYNYFYNMATVVENLIPEDICDTLVSRINELISEGAVD
                     HVKHSGLGNNAVSDLGGDYNHHIFKGPDIRKHLPELNAIYHAILPLISIITCTDTITSP
                     YELSDVNIKAYPPNGGTLGLHYDTNGITVLLSLMDNKEAPLRIQIPRSHPSKKESWIEH
                     KEIYAKKGGLLIMQGRKVLHDSAPTQTEQKISVIYNYYERHDTYRHKDFDNFVYFGIKP
                     DG"
                     /name="hypothetical protein"
     gene            2790..3671
                     /locus_tag="HVW81_25675"
     CDS             2790..3671
                     /locus_tag="HVW81_25675"
                     /inference="COORDINATES: protein motif:HMM:NF013088.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EamA family transporter"
                     /protein_id="QLM74957.1"
                     /translation="MSKSVDIFIGFLVTVLWGANFVVIDVGLRDLDPFALTFLRFLFCA
                     IPLCFFIKRPREMSLVYVSIYGVIFGVGLWWLVNYAMYNGLAAGVSSVFLQFSAFFTII
                     LSAFIFGEKINKVHAVGMIVSFLGLVMMITSSDDSSTIYGIFLVILAALAWALCNMIVK
                     MKKPSDMVGFIVWSSIFSAPSVLILTVIAKGWGPIISIKDNISFASAFSVLFQAYITTV
                     IGYMIWNNLMKKYPATEIAPLSLFVPVSGLTASFFLLDEKLSVFQLIAVVVVCVGIFIF
                     LNASRIKKWINL"
                     /name="EamA family transporter"
     gene            4066..5001
                     /locus_tag="HVW81_25680"
     CDS             4066..5001
                     /locus_tag="HVW81_25680"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011666805.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QLM74958.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAIERALCEKLGADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASA
                     RRSIDKHYGMGRNCYLFEMTRKWAYRAIRQGWPVFSQWLDAVIQRVEMYNASLPVPLSP
                     AECRAIGKSIAKYTHRNFTPETFAQYVATTHTPEIQAARGRKGGIAKGAGYEDKRSTAL
                     EMLVNGCTQKAIAEMLGVSDRTIRNWKSGK"
                     /name="replication initiation protein"
     gene            complement(5208..5483)
                     /locus_tag="HVW81_25685"
     CDS             complement(5208..5483)
                     /locus_tag="HVW81_25685"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091757.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /protein_id="QLM74959.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAAMLARVRRP
                     EEAQLRAFLLQFLRKEVTRQADMNRLQPLINELEKLPKPPAKPQNH"
                     /name="mobilization protein"
     Typing          complement(5488..5661)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.571"
                     /coverage="98.0"
                     /evalue="2.65e-76"
     Typing          complement(5662..6020)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.722"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4067..5001
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.132"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3..1132
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.082"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          5663..6744
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.507"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gaaactcggg aaacagattg aatctctcag ccgcacttac agggccgtga aagaacggga
       61 cattcctgcc cgtcgtcagg cctttgaaac gcagtggaat acatggattg cgccgggaat
      121 ggcagagctg aaagaaaaac tgtcagcacg ggaagcggag cggcgcaggg aggaagccga
      181 agcggaagcg cgccggaagg aacaggagca tgaggcgcgg ctgaaacgtc atgataacca
      241 ccgtctgagc cgtgaaacgg cattagtcgg ggttattacg gagctggggc gtgccagaga
      301 gccgggaacg ggcaggataa cccgctacat gatgctgagt aacagggcag gagaattcac
      361 ggtatggggt gatgagctgg cgcattaccc ccggagtgtt catgacccgg tgaatgttta
      421 tctgtcgcct ggcggggctg tgatggtcac ggatatacac gcagggcggc ctgaatctca
      481 tgagacaatg gcgcggcctg agcgtgtgag aatgtattcc ggtgcgacgg tccggcatgt
      541 actggaacag atgcgccagg ggtggccctc ttacggtttt ccggcgctgc cgcatcactg
      601 gccggataat ttttatttca gcaacgaccg caggcccgta gcctctccgc taccgtcagc
      661 gcaccgggtg gatatcaccg ctgatgcggc accggaacaa ctcatgcctg ttgtattttc
      721 gagagaggga aacagcagga cgctgaatct gttgttgtgc aaagggccgg aggaaatgct
      781 tgtcgggttt gttcgccggg aaggagggtt ttgccccgtt cttgtgcttc cgtcgccgga
      841 ttacagtcat ctgatggtca gcaccatcac ggagaacggg gtatgcctgg caggttacgg
      901 agaagctata aaccatgatg aggatactcc gtacccaccg gaaccgcacc tgatgcagtt
      961 ccggctcaaa ggccatcatg acaggctttt ggctgctgtc cacaaaccgg aagagatgcc
     1021 ggattatctc ttccgtcaac tcggttttaa tcagacctgg catgagtgga agcaggacga
     1081 acagcacagg caacaacaac gacgcccggg acactatcgg ggcatgagta tgtaaaagta
     1141 aataagacta ttttatctgg ctatttttgt taaaacagcc agataatgca tactattcta
     1201 aatcatctgg ttggtgatgc tgccaactta ctgatttagt gtatgatggt gtttttgagg
     1261 tgctccagtg gcttctgttt ctatcagctg tccctcctgt tcagctactg acggggtggt
     1321 gcgtaacggc aaaagcaccg ccggacatca gcgctatctc tgctctcact gccgtaaaac
     1381 atggcaactg cagttcactt acaccgcttc tcaacccggt acgcaccaga aaatcattga
     1441 tatggccatg aatggcgttg gatgccgggc aactgcccgc attatgggcg ttggtctcaa
     1501 cacgatttta cgtcacttaa aaaactcagg ccgcagtcgg taacctcgcg catacagccg
     1561 ggcagtgacg tcatcgtctg cgcggaaatg gacgaacagt ggggctatgt cggggctaaa
     1621 tcgcgccagc gctggctgtt ttacgcgtat gacagtctcc ggaagacggt tgttgcgcac
     1681 gtattcggtg aacgcactat ggcgacgctg gggcgtctta tgagcctgct gtcacccttt
     1741 gacgtggtga tatggatgac ggatggctgg ccgctgtatg aatcccgcct gaagggaaag
     1801 ctgcacgtaa tcagcaagcg atatacgcag cgaattgagc ggcataacct gaatctgagg
     1861 cagcacctgg cacggctggg acggaagtcg ctgtcgttct caaaatcggt ggagctgcat
     1921 gacaaagtca tcgggcatta tctgaacata aaacactatc aataagttgg agtcattacc
     1981 catctggttt tataccaaaa tagacaaaat tatcaaaatc tttatgtcta taagtgtcgt
     2041 gcctttcata gtaattgtaa ataacggata ttttttgctc cgtttgggtc ggggcgctat
     2101 catgtaatac ctttcttcct tgcattataa gaaggcctcc tttttttgca tatatttctt
     2161 tatgttctat ccatgattcc tttttgcttg gatggcttct aggaatttgt attcttaatg
     2221 gagcttcttt gttatccatt agagataata aaacagttat accatttgtg tcgtagtgca
     2281 accctaatgt tccaccattt ggagggtatg cttttatgtt gacatctgac agttcataag
     2341 gtgaagtgat ggtatctgtg catgttataa tgcttattaa aggtaagatt gcatgatata
     2401 tggcgtttaa ctcaggaaga tgcttcctta tatctggccc cttgaatata tgatgattgt
     2461 agtcacctcc aagatctgaa actgcattgt tacctaatcc tgagtgctta acgtgatcta
     2521 cagctccttc actgattagt tcgtttattc ttgatactag agtatcacaa atatcttcgg
     2581 gtatcaggtt ttcaacaact gttgccatgt tataaaagta gttatatctg tgttgttgca
     2641 catcaaacat attcttttcc ttttatggtt gttgattttt tgtaacataa tcgtgatggt
     2701 gtgttgtgtc aatgtttttg ttgtgtttgt tttttgtttg tggtaggtaa tccttgattg
     2761 ttgattactt attgtttttt aggtgattta tgagcaagag cgttgatatc tttattggtt
     2821 ttttggtcac ggttttgtgg ggagctaatt ttgttgtcat tgatgttgga ttaagggatt
     2881 tagacccctt tgctttaact tttttacgat ttttattttg cgcaatacca ttgtgttttt
     2941 ttattaaacg ccccagagaa atgtctttag tatatgtgtc tatttatggt gtgatttttg
     3001 gagtcgggtt gtggtggctt gtaaattatg ccatgtacaa tgggttagct gctggggttt
     3061 cttctgtgtt tttacaattt agtgcatttt ttacaattat tttaagtgct tttatattcg
     3121 gcgagaaaat aaataaggtt catgcggttg gtatgattgt gtctttttta gggttggtta
     3181 tgatgatcac ctcatcagat gatagttcta ctatttatgg tatttttcta gttatattgg
     3241 ctgcgttggc atgggcgttg tgcaatatga tcgttaagat gaaaaaacca tctgatatgg
     3301 ttggcttcat agtttggtca agtatttttt ctgctccttc tgttttgatt ttaactgtta
     3361 ttgctaaagg ctgggggccg attatatcta taaaagataa tatatcattt gcttctgctt
     3421 tttctgttct ttttcaggca tatattacaa cagtaatagg gtatatgatc tggaacaact
     3481 taatgaagaa gtatccagca acagaaattg cccctctgtc tttgttcgtt ccagtatctg
     3541 gtttgacagc atcattcttt ttgctagatg aaaaactatc cgtatttcaa ttaatcgctg
     3601 tggttgttgt ctgtgtcggt atatttatct ttttaaacgc atccagaata aaaaaatgga
     3661 taaatttata actaaacccc gtgcggaacc ttctatggag agagaaactt gtcattttga
     3721 cccgttcgcc cttcggaacg gtcgaaatcg atcgcgcatc gctttcgtga atagttatgc
     3781 aggctcatga aaacaattct gacgcgtttt tctggctttg cctggtgttt ccttgtcttt
     3841 ttgagttttt tgcgtcagaa agcgtctgag ggcgttttaa ggggtacgta caacaggagt
     3901 tatggtaaat ggatcgggtt ttcgggaagg ttcgacagga tttgccgttg ggtgtagtgt
     3961 aagcgactga aaaacaaacg cccctgaaat tcgtgtctct ccgccaagat tgtcacgaga
     4021 atacaggggc gaggtcggtc gataacctgg aaggaatcgt aacacatgag cgccgcgctt
     4081 caatacttcg aagaaaattt accccaccgt ccctatcaca cggatgatct cgcttttggt
     4141 cttcgcatct ccggcaaagg gcgtgcgctt cttgcgcggt acatccagca gaaccagcct
     4201 catgcgcagt tctggctggt ttttgacgtt gaccgcgagg gggctgcgat tgactggagc
     4261 gaccggaacg cccccgcgcc gaacatcacc gtaaaaaatc ccgtgaacgg tcatgctcac
     4321 ctgctctatg cactcaacat cgccgtgaga accgcgcctg atgcgtcggt taaggcactg
     4381 aagtacgctg ccgcgataga gcgtgcgctg tgtgagaaac ttggtgcaga tgtgaactac
     4441 agcggactga tttgcaaaaa tccgttccac ctggaatggc tggtgatgga gtggcgcgag
     4501 gaagcctata ccctcgatga actggctgat tatctcgatt tgagcgcctc agcgcgccgt
     4561 agcatcgata aacattacgg gatggggcga aactgctacc tgttcgaaat gacgcgcaaa
     4621 tgggcttaca gggcgattcg tcagggctgg cctgtattct cacaatggct tgatgccgtg
     4681 atccagcgtg tcgaaatgta caacgcatca cttcccgttc cgctttctcc ggctgaatgt
     4741 cgggctattg gcaagagcat agcgaaatac acgcacagga acttcacgcc ggaaactttc
     4801 gcacagtatg tggcgacaac gcacacgccg gaaattcaag ctgcccgagg ccgtaaaggt
     4861 ggtatagcca aaggggctgg ctatgaggat aagcgcagca ccgcgctgga aatgttggtg
     4921 aatgggtgta ctcaaaaggc tatagctgaa atgttaggtg tttccgatcg cactattcga
     4981 aactggaaaa gcggaaaata gcctatatca gataacagcg ccttttcggc gcttttttga
     5041 gcttttggtg ttcctgtggt ttttccggtt ccgtccagca atggcgctgg tttcctcgtg
     5101 attgcggtgg cagcgctcgc cgcagtctca tgaccgagcg tagcgagcga atgagcgagg
     5161 aagcgcaaag gcgtccggtg gtgcatgtgg cacttacgcg ccggggctta gtggttctgc
     5221 ggtttcgcag gtggtttggg tagcttctcc agctcgttaa tcagcggttg tagccggttc
     5281 atatcggcct gtcttgtgac ttcctttcgc aggaactgga gcaggaacgc tcgcagttgc
     5341 gcttcttccg gcctccgtac ccttgccagc atggctgccc ccacaatgac tttttgcgct
     5401 gtgtccaggc tccggctctt cgccttcagg cgctgtaatc gggcctcagc gtcggcaatc
     5461 ttctgttcga gtgttctgct catttcgtga ctccgtgcgc ggtgaaaaat cgcattttag
     5521 cgcgtcactg gtagtttaaa aactgaactg gcataatgca cggaacatca cgaagtgcgc
     5581 acttatacaa tctccactcc gtttcgattg tgtgcgccct gcggggctga aagaaaacgg
     5641 caaaaaggca ttacggcaga aatggcgatt tatcatctca gcatgaaaat catttcgcga
     5701 aaaaacggct acagtgccgt tgcttctgct gcctaccgtt ccggctctgt catacccgat
     5761 gaccgtaccg gattaatcca cgattacacc cgtaaacgcg gcgttgatga tgcggtcatt
     5821 ctcacccctg cgaatgcacc gtcctggtgt ggtgaccgtt ccgttctctg gaatgcggtc
     5881 gagaaagccg aacagcgccg gaactcccag ctggcaaggg agattgaact cgccattccc
     5941 cgtgagattt cccgcgaggc cgcacgggag accgttctcg cttttgtccg ggaaaacttt
     6001 gtcagtcggg gcatgattgc cgatgtggcg ttccatcaca tggaccggac caatccccat
     6061 gcgcacatca tgctgaccac gagagctgtc ggggaaacgg gattcgcagg aaaggtcagg
     6121 gactggaacg accgggcact cgccgagacg tggcgcgcat catgggctga ccatgcgaac
     6181 agagcgcttg cgaacgccgg ctaccaggaa gagatagacc atcgttcata cgagcgtcag
     6241 ggactggaga aagcgccggg ccttcacctc ggaaaggctg cctgtgcgat ggaaaaacgg
     6301 ggaatggaaa cagaacgcgg tgagcagaac cgtctgatta acagccttaa cctggaaata
     6361 caggtttccc gcacgcagct tgctctcagg acggttcagg aagcgcagcg taagcgggaa
     6421 ctcagcgatg ctgcacgtcg tgcagcggaa gcccttaacc tgaccattcc cgctgcgaat
     6481 gcctcagcgg ataccctgcg ggaatttatc gccacactgc cgcaggaatg cgggaacgca
     6541 tgggagatga ccccggagtt cctggcgatg aacgggaagg caaacgacat caaacgtgag
     6601 gggaatgcgc tggtgaaaga gcgggatatt ctcgaaaaag agatgaccgg actcagaaaa
     6661 gcccgtccgg tagcgtccat cctgtcagag cttcccctga tgacatgggc tgaaccggaa
     6721 taccgcaaaa gacaactccg cttctg
//
