LOCUS       NZ_CP011139             5164 bp    DNA     circular CON 01-JUN-2024
DEFINITION  Escherichia coli VR50 plasmid pVR50E, complete sequence.
ACCESSION   NZ_CP011139
VERSION     NZ_CP011139.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03371467
            Assembly: GCF_000968515.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli VR50
  ORGANISM  Escherichia coli VR50
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5164)
  AUTHORS   Beatson,S.A., Ben Zakour,N.L., Totsika,M., Forde,B.M., Watts,R.E.,
            Mabbett,A.N., Szubert,J.M., Sarkar,S., Phan,M.D., Peters,K.M.,
            Petty,N.K., Alikhan,N.F., Sullivan,M.J., Gawthorne,J.A.,
            Stanton-Cook,M., Nhu,N.T., Chong,T.M., Yin,W.F., Chan,K.G.,
            Hancock,V., Ussery,D.W., Ulett,G.C. and Schembri,M.A.
  TITLE     Molecular analysis of asymptomatic bacteriuria Escherichia coli
            strain VR50 reveals adaptation to the urinary tract by gene
            acquisition
  JOURNAL   Infect Immun 83 (5), 1749-1764 (2015)
   PUBMED   25667270
REFERENCE   2  (bases 1 to 5164)
  AUTHORS   Forde,B.M., Ben Zakour,N.L. and Beatson,S.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-APR-2015) School of Chemistry and Molecular
            Biosciences, University of Queensland, 76 Cooper road, Brisbane, QLD
            4072, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SMRTanalysis v. 2.0.0
            Genome Coverage                   :: 65x
            Sequencing Technology :: Pacific Biosciences SMRT sequencing
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_000968515.1-RS_2024_06_01
            Annotation Date                   :: 06/01/2024 04:12:53
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,102
            CDSs (total)                      :: 4,969
            Genes (coding)                    :: 4,733
            CDSs (with protein)               :: 4,733
            Genes (RNA)                       :: 133
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 18
            Pseudo Genes (total)              :: 236
            CDSs (without protein)            :: 236
            Pseudo Genes (ambiguous residues) :: 0 of 236
            Pseudo Genes (frameshifted)       :: 82 of 236
            Pseudo Genes (incomplete)         :: 158 of 236
            Pseudo Genes (internal stop)      :: 43 of 236
            Pseudo Genes (multiple problems)  :: 40 of 236
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP011139.1.
            Source DNA is available from Prof Mark Schembri
            (m.schembri@uq.edu.au).
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..5164
                     /organism="Escherichia coli VR50"
                     /mol_type="genomic DNA"
                     /strain="VR50"
                     /serotype="OR:K1:H-"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:941323"
                     /plasmid="pVR50E"
     gene            1046..1960
                     /locus_tag="ECVR50_RS26115"
                     /old_locus_tag="ECVR50_E002"
     CDS             1046..1960
                     /locus_tag="ECVR50_RS26115"
                     /old_locus_tag="ECVR50_E002"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001738986.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_001271363.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRSTVATSARTL
                     KPWEALGISRAWYYQLKKRGLVE"
                     /name="replication initiation protein"
     gene            complement(2164..2562)
                     /locus_tag="ECVR50_RS26120"
     CDS             complement(2164..2562)
                     /locus_tag="ECVR50_RS26120"
                     /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="WP_001222914.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLIDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKELKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            2739..3665
                     /locus_tag="ECVR50_RS26125"
                     /old_locus_tag="ECVR50_E003"
     CDS             2739..3665
                     /locus_tag="ECVR50_RS26125"
                     /old_locus_tag="ECVR50_E003"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /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="WP_001331297.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTAPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            3668..>4180
                     /locus_tag="ECVR50_RS26130"
                     /old_locus_tag="ECVR50_E004"
                     /pseudo=""
     CDS             3668..>4180
                     /locus_tag="ECVR50_RS26130"
                     /old_locus_tag="ECVR50_E004"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            complement(4264..4473)
                     /locus_tag="ECVR50_RS26135"
     CDS             complement(4264..4473)
                     /locus_tag="ECVR50_RS26135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001618649.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001096196.1"
                     /translation="MAKLGENTPHIIDATVDFMASSQAFREYLKKLPPDNTIPPALTDE
                     HVPLYIRRLEYYRLLYRPKQTESY"
                     /name="hypothetical protein"
     Typing          1047..1960
                     /name="rep_cluster_2131"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.909"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2740..3662
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gagtggaggt tgttacagtc gctttttata aaacaagcaa ccagtttttt tcaatagtct
       61 gatgatggtt gtgacagttt tgtgatattg ttcaaaatgt ttcttgttga atgtttgttt
      121 tttggtctat tggtgtctgg ttttattttt ttctgctatt acatatcaag aaatgtgatt
      181 ggtgtagcaa gagtggaatg cgatgtggat aaactaattg gttgtcgaat ctaatttact
      241 tagaaaacta cacttgtttt tgtgtatgaa tttagtgaat ttgtctgtct atgtgttttc
      301 gtgcatttat aaatccttcg tcaggatctt aaatttagtg ttgaatatgt agggcctgta
      361 cggtaattat tatttagcgt agctacttca tcgttgttcg aacacaacca acaacctgta
      421 attgttgttt ctcttggttc cccacttttg tggggttttt tatctcttcc gtgcatcgta
      481 aagcgcggac tccttctgga aaggttgttt tagggcatca ctgaggcatt ttttgcgttt
      541 gtgaatattg agcatccgat aactaaaata tttcccatag actctgattc ttgccaccga
      601 ccccaggtcg gttttttttt gtcctggcga gatgtgaagt ttggaaacag gaaaccccgt
      661 cagagcgcca cgcaccaggg gagaaaactt gtcgttttga gccgttcggt gttcagaacg
      721 cacgaaaccg atcgcacatc gctttcgtgc atagttatgc aacgccctga aaacgtttct
      781 gacgcgtttt tctggtttgg cctggtgttt tcttgtcttt ttgcgttttt tgcgccagaa
      841 agcgattgag ggcgttttac agggtacgta caacgggagt tatggtaaat ggatcggatt
      901 tgcgggaagg ctcgacaggt tttgtcgttg ggggtagtgt aagcgactga aaaacaaacg
      961 cccctgaaat tcgtgtctat ccgccaagac tttcacgaaa atacaggggc gatgtcggtc
     1021 gataacctgg aaggaatcgt aacacatgag cgccgcgctt caatacttcg aagaaaattt
     1081 accccaccgt ccctatcaca cggatgatct cgctttcggc cttcgtatct ccggcaaagg
     1141 gcgcgcgctt cttgcacggt atatccagca gaaccagcct catgcacagt tctggctggt
     1201 ttttgacgtt gaccgcgagg gggctgcgat tgactggagc gaccggaacg ctcccgcgcc
     1261 gaacatcacc gttaaaaatc ctgtgaacgg acacgctcac ctgctctacg cactcaacat
     1321 cgccgtgaga accgcgcctg atgcctcggt taaggcgctg aaatatgccg cagcggttga
     1381 acgttcgctg tgtgagaaac tttgtgcgga tgtgaactac agcggcctga tttgcaaaaa
     1441 tccgttccac ctggaatggc tggtgatgga gtggcgcgag gaagcctata ccctcgatga
     1501 actggctgat tatctcgatt tgagcgcctc agagcgtcgt agcatcgata aacattacgg
     1561 gatggggcga aactgccacc tgttcgaaat gacgcgcaaa tgggcttaca gggcgattcg
     1621 tcagggctgg ccagcgttct cacagtggct tgaagcggtg atccagcgtg tcgaaatgta
     1681 caatgcatcg cttcccgttc cgctttcact ggctgaatgt cgggctattg gcaagagcat
     1741 tgcgaaatac acgcacagga acttcacgcc ggaaactttc gcacagtatg tggctgatac
     1801 gcacacgcca gaaattcagg ctgcacgcgg tcgcaagggc ggttctaagt ctaagcgcag
     1861 cacagtagct acatctgcac gcacgctgaa accgtgggag gcattaggga tcagtcgcgc
     1921 ctggtattac caactgaaaa aacgaggtct cgtagagtag accaaataag cctatatcag
     1981 ataacagcgc ctttctggcg tctttttgag cagcaggttt tttgccgttt ttccccgttc
     2041 agccctgcaa tggcgcggct ttccgcgtga ttgtggtggt agtgctcgcc gcagtctcat
     2101 gaccgagcgt agcgagcgaa tgagcgagga agcaccaggg aatcggaaca cggatggagg
     2161 cacttacgcg tctgggtttg gggatgtctc cagatcgtac ttaagttcct taagtgcctg
     2221 taatatcctg tcttttttat agcatagctc gcctgttttt gtgtctacca gtcctgcttc
     2281 gatcagtagc ccagccgcga gaaagagccg gtgattgcgt tcccgtcgtt gtttttttcc
     2341 ctcgattcgt ttttggaccg cctgttttcg ttcgctctcc tgtgcctgta agtcgttttt
     2401 ttccgctgtt gccagtacgt ggagaagttt gcgttcctgt tctgtgagtc cggcttcgtt
     2461 gtcgatcagg tcaataatct gtctctgtcg tgcggtctgt tctccgagct tcctgatgaa
     2521 tccgatccgt ttcttcagcc attcgatgtt gctgatgcgc atgttcgtga tgctccctgg
     2581 tgtttttttg cggtgtgttg tggtcgtgca gtatatcgct tgcggtcggc gggtgcaggg
     2641 ggtatcttcc gtgctaattc gtaaaattag aaggaagcgc acttatatgt ttctctcctt
     2701 cgtcgagaaa cagtgcgctc ctgcagaggg ctgaaaccgt ggcaacctat cacctcagcg
     2761 ttaaatttgg tggcaagggg caggctgcaa accacgccga ttacatcgag cgcaaagaga
     2821 aataccgcga ccgtcaggat ttggaatatt ccgcacacgg aaacatgccg gaatgggcca
     2881 gggataatcc ttcccatttc tggcaggcgg ctgaccagtt tgaacgtgcg aacggttcga
     2941 cctataggga acttgaaatt gcattacccc gtgaactgac accggaacag cgccttgaac
     3001 tggtgcagga ttttgtacgt caggaagctg gcgaacggca cgcctggagt tttgccattc
     3061 acaatccgaa agcgagcatt gacggcggcg aacagcctca tgcgcatatc atgatgagtc
     3121 agcgtgtgaa tgatggcatt gaacgtacac cggaacagta tttccggcgc tataacgcca
     3181 ggtatcccga gcggggaggt gcgaaaaagg attccggaag cctgactctc actcagcaaa
     3241 aagagcagtt gcgggaattg cgaaaacgct gggaggtgaa gcacaacgaa catatgagaa
     3301 agcatggctt tgaaaggggc ttcattgact gccggacgct gaaagaacag ggcattgaac
     3361 gacgtcccga agtgcatctg ggttttgaag ctgccggacg gcttgatgat gcccagcgtc
     3421 atgacatcat gcaaaaacgg tctgaaccgg actattcccg ccatcttgaa caggcgcgaa
     3481 cggtcgggca tgacatcagg gaatggctgg acactccggt taagcaacat gaactggtca
     3541 gaaggctgca acatgatgtt gcgcgggagc atggctttga catgagagac agagtgagca
     3601 gacagaaccg aactgcacct gaacgggtta aatcaccgtc acgtggattt tctatgggat
     3661 tctgaacatg gccagcacag aagaaaaatt actcacgctc ctgttatcgg tggagcatct
     3721 gcaacatacc gcaatggagc aacagaaagc tgttgctgat tctctggctg tggcaaggga
     3781 aactcttcgc ggatatcggg atatttctga cggtgtggca aaacaggtca gggatgaagt
     3841 cagaaatgag gtgcagaagc tggacgtggc aggactgata ggtgagcgca tcagccagga
     3901 ttttcagcgg ctggaagagt cagtcgcaaa catgaaggca aacgcggatg ccctgaacag
     3961 ggatattgcg acaattcaca gcaatatcgt gcaggaatac aacaccctta aagggtatag
     4021 ctggaaatgg ctgggtgggg tgtcagtggc ttttctggtt atgttctgtg tgctcggatg
     4081 gggaatgaaa acaatactcg acaggaacta caacgccaca gcggcggtgt atcagaaagt
     4141 tgtgacactg gaagataaac tggtggagaa acctgtcacg gaagagccgg aaaaactgac
     4201 gcgcttcgct tgtccaacgc ctcacgaccc gcgaaaggat ttcgcgaacc gttcaccgtt
     4261 ttttcaatat gattctgtct gctttggtcg ataaagcaga cgatagtatt ccagccttcg
     4321 tatatataac ggtacgtgct catcagtaag agctggcggt attgtgttat cagggggaag
     4381 ttttttcaga tactcacgaa atgcctggct tgatgccata aaatctacag tagcatcgat
     4441 aatatgtggg gtgttttcac ctaattttgc catgatgata atccttatat tatcacggtt
     4501 tgtgaatgat agggtgtcac tattatttat gcgttagtga accagaaaaa atcccccgtt
     4561 ggcatagggg gatatgtaag gagaaataac ttcgcaggtg ttcttgtttg tataacgtga
     4621 aaagactgca cgcaacttaa taagtctgcc gtacttactt tcagttttca acataaggtt
     4681 tataacaatg tatggaatgg aagtgagctt taaggtttca gctctaaaaa ataaaatatt
     4741 tattagttgg ctggttgttg ttcttgttct gtatgtatat aaacactatc gacatattat
     4801 gaccgggaac attccttacc ccctctgcgc tcgcagaggt tttttttgtc attaattaat
     4861 aatgaactga aatgcagttc cgatacctcc atttgcacat tatccctgac atatggtacc
     4921 ggaaccgcat taattttatg ttataagagt ttatttttaa tgtccagatg gtttaatagt
     4981 atttatatgt aattagctgt atggatagta ctggttttat tgtataactt gtcgtttttt
     5041 ttattgtttt tgtgtggtgt gctaatcttt aagttataaa aaaacccctt ggaatacagg
     5101 ggcaaaagta aggaaaacaa atggatgctc agtttgtgtg acactttaaa ctaatggaac
     5161 tata
//
