LOCUS       NZ_CP011138             5631 bp    DNA     circular CON 01-JUN-2024
DEFINITION  Escherichia coli VR50 plasmid pVR50D, complete sequence.
ACCESSION   NZ_CP011138
VERSION     NZ_CP011138.1
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 5631)
  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 5631)
  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
            CP011138.1.
            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..5631
                     /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="pVR50D"
     gene            complement(1042..1233)
                     /locus_tag="ECVR50_RS26085"
                     /old_locus_tag="ECVR50_D004"
     CDS             complement(1042..1233)
                     /locus_tag="ECVR50_RS26085"
                     /old_locus_tag="ECVR50_D004"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /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="WP_000165975.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1298..1621
                     /locus_tag="ECVR50_RS26090"
                     /old_locus_tag="ECVR50_D005"
     CDS             1298..1621
                     /locus_tag="ECVR50_RS26090"
                     /old_locus_tag="ECVR50_D005"
                     /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="WP_046072959.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLCQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1830..>2261
                     /locus_tag="ECVR50_RS30770"
                     /pseudo=""
     CDS             1830..>2261
                     /locus_tag="ECVR50_RS30770"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            2299..2829
                     /locus_tag="ECVR50_RS30070"
     CDS             2299..2829
                     /locus_tag="ECVR50_RS30070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /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="WP_001673158.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            2836..3069
                     /locus_tag="ECVR50_RS30075"
     CDS             2836..3069
                     /locus_tag="ECVR50_RS30075"
                     /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="WP_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            3550..4602
                     /locus_tag="ECVR50_RS26105"
                     /old_locus_tag="ECVR50_D012"
     CDS             3550..4602
                     /locus_tag="ECVR50_RS26105"
                     /old_locus_tag="ECVR50_D012"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_046072960.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPEGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            4604..5470
                     /locus_tag="ECVR50_RS26110"
                     /old_locus_tag="ECVR50_D013"
     CDS             4604..5470
                     /locus_tag="ECVR50_RS26110"
                     /old_locus_tag="ECVR50_D013"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     Typing          867..948
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          223..410
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          1612..3173
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ggatcctctt gagatccttt ttttctgcgc gtaatctgct gcctgtaaac gaaaaaaccg
       61 ccttgcaggg cggtttgatc gaaggttaag tcagcttgca gactgcttaa ccaggtaact
      121 gtcttatgcg agacgagtca ccaaaattgt tcttctagtg tagccgcact ccggcagcca
      181 cttcaagtac tctctaaata tctcgcacat gacttttacc aatggctgct gccagtggcg
      241 ctttgtggtg tcttttccgg gttggaccca agagaacagt taccggagaa ggcgcagcag
      301 tcgggctgaa cggggggttc ctgcatacag cccagcccgg agcgaactgc ctaagtcgcc
      361 ccgagatacc agaagacgtg agctatgaga aagcgccacg tgtcccgtaa gggagaaagg
      421 cggaaaaggt atccggtaat cgatatggcg ggaacgtggg ggcgcaggag ggagcgattc
      481 accggaaacg gtgatgatct ttaagccacg tcgggtttcg ccaccgctgg cggatttcat
      541 ggttgagccg caaggctccc acagatgcac cgaaaaagtg tctgttttgt gaagtccgtc
      601 aggggggcgg agcctatgga aaaagcgcct ccggcgcggc ctttcccggg gtttcgtttt
      661 ttgcgcacat gttctttctt ggtttatccc cgggttctgt ggataacagg gttagcgttt
      721 ttgagaaagg agagtccgct cgccgcagcc gaacgaccga gcgtagcgag tcagtgagcg
      781 aggaagcgga agagcgcctg aactggcatt ttctccttac gcatctgtgc ggcatttcac
      841 accggacatg gcgcactttt catacaatcc gcactgatgc cgaatggtta agccagtata
      901 cactccgcta tcgctacgtg actgggtcag ggcttcgccc cgacacccca aaggtcaacg
      961 gcctgacgcg ccctggcggg cttgtctgct cccggcatcc gctcacagac aagctgtgac
     1021 cgtctccggg agctgcatgt gtcagcggtt ttcaccgtca tccccgaagc gtgcgaggca
     1081 actgcggtaa agctcatcgg cgtggtcgtg aagcgattca cagatgtctg cctgttcatc
     1141 cgcgtccagt tcgttgagct tctccagcag cgttaatgtc tggcctctga tgaagcgggc
     1201 catgttaagg gcggtttttt cctgtttggt cactgatgcc tccgtgtaag ggggggttct
     1261 gttcatgggg gtaatgatac cgatgaaacg cgagaggatg ctcacgatac gggttactga
     1321 tgatgaacat gcccggttac tggaacgctg tgagggtaaa caactggcgg tatggatgcg
     1381 gcgggtctgc ctgggtgagc cggttgcccg ttccgggaag ctgccgacac tggcaccgcc
     1441 gttactgtgt cagctggccg ccatcgggaa taaccttaac cagacagcga ggaaggtgaa
     1501 cagcgggcag tggtcttccg gtgaccgggt tcaggtggtg gccgcactga tggccatcgg
     1561 ggatgagctg cgccggctgc gtctggcggt cagggaacag ggggcgcggg atgatagtta
     1621 agtttcatgc caggggaaaa ggtggtggca gtggtccggt tgattacctg ctgggaaggg
     1681 agcgtaaccg ggaaggggca acggtgcttc aggggaatcc ggaagaggtc cgggaactca
     1741 tcgatgccac gccatttgcg aagaaataca cgtcaggtgt tctgtcgttc gcggagaagg
     1801 agctgccgcc tggagggcgt gaaaaagtga tggcgagctt tgagcgtgta ctgatgcccg
     1861 gtctcgagaa aaatcagtac agcatcctgt gggtggagca ccaggacaag ggacggcttg
     1921 agctgaattt tgtcattccg aacatggagc tacagaccgg aaaacgcctc cagccgtact
     1981 acgaccgggc agacaggccg agaattgatg cctggcagac gctggtgaat caccattacg
     2041 gtctgcatga ccccaacgcc ccggagaacc gccggacgct gacccttcct gataacctgc
     2101 cggaaacgaa acaggcgctt gctgagggcg tcacacgcgg gatagacgcg ctttaccatg
     2161 ccggagagat aaaaggccgt caggatgtga ttcaggcgct cacagaggcg gggcttgaag
     2221 tggtcagggt gacgcgaagc agtatcagca ttgcagaccc gaacggcggg aggaatatca
     2281 gactgaaagg agcgttttat gagcaatctt ttacagacgg gcgcggagtt cgagaaaaag
     2341 ctgaaagaga gagccgaatc tacagagaaa atgctgaacg acgagttcag gaagctcgaa
     2401 gaatctgtaa acagggaact gacctcaaac gaatctttaa tcaggaacgc tatcaacgac
     2461 catacaacag ccctgaaaga actgctggag aggtatcaga aaacgaccgt cgatacgatg
     2521 gacgcgcact ggaaaaccgt actgaaaatg agcgtgaaac gctggctgtg gctgattatc
     2581 gtctcagtac tgatgtttgc cacgaccggg agtctgctgt ggtaccaggg catgaagata
     2641 aacgcgaata tgaatattct ccgcgagcag aaagagagtc tggagaagct gaacgcgaag
     2701 acatggggcg tgcgttatca cgaggacagc aacggacgtt ttctggtgtt gccgaagggg
     2761 atgaaagccg aaacgaactg gacgaaggac aacggcaaac tgaacgcagt gagactggtg
     2821 caggagtgac agagcatgac ggagctggaa agacatttgc tgaacgcatt agagcaactg
     2881 caacaggact atatgcagcg gctgaacgaa tgggagaacg ccttcgtgga attgcagaaa
     2941 atgttttcgc ttacgcaacg ggacaacgcg atgctgaacg ggcgagtcat gcagttgagt
     3001 cagcaggtgc agcacttgag cgagcggaca gaacgcttga gccagttata cagcgagaac
     3061 aggagataag ggatgaacgg ctgatgcagg aacgcgaaca tgagttatct ctggagcggg
     3121 agcgtcagcc ggaaatccag gagcggacac tggatggccc ttcgctggga tggtgaaacc
     3181 atgaaaaatg acgtgttcag tggattaagg cgggctaatg tggcctgtag catctggttg
     3241 cataggtatt catgcggtta aaatttatca ggtgcgatcg cggcagtttt tcgggtggtt
     3301 tgttgccatt tttacctgtc tgctgccgtg atcgcaccga acgcgttttg gcggtgcgta
     3361 caatgcgacg ttatggtaaa tggagcggat tttcaggaag gagtgatact aacaactcga
     3421 acactgtgca aataatgatt tttttaaaat atcggtaacg ataataaatt atttcgtttt
     3481 acgccggtaa taaatataat gtagtttcag tatataaaaa aatatatgag gtgtcttgtg
     3541 ggagctttca tgaatcttca acaacgtata aataaactac cacaattatc atccagtttt
     3601 tcatttggaa aagatattga taatattcat tcatttatct ttaacgaaac ttctaaagat
     3661 aaaattgaag atttactaag aaaatgggtg tcaggcaatc agccctgtgt atttggtaaa
     3721 ttggcaagca agaaaattaa agggcttgat ttccatttat ctattgtaaa tagcccccaa
     3781 ctatataatg atgatggtca tttgtttgat tttttgcgta atgaaagagt tcgttttaaa
     3841 gaacgcgcaa gaagaggaga ggtcagtgcg catctcattt attttattca tccacaactt
     3901 gcctttgctc gtccatcaga agagttagtg gacatacaaa aatatatttg ttcgctgcat
     3961 atgccagagt gctatccaat aaaagaggat gttatttata ctgaaagcgt accatttcag
     4021 gataaagatg ggctaaaaat atataaggct ggtgttaatg ttttttactc ttctgctcat
     4081 agaacaagaa atcatgatag aagaatacca gagggaatac ttatttctgt aaatgccccg
     4141 gggcatttta tgaggctggc gatagaaaaa ggtttctata aagatcaaga acaagcgtta
     4201 gcggatattc gtaacatgac tattcagtct gttggtaagg gtgggtattc acatccggaa
     4261 gggatttcta caacatggca ttcagaatct aatttggatc gttttggatg cccagtgcac
     4321 accggtaata gttcttatta cagcggtttt tatcatactg atgtattaat tccaggagaa
     4381 ttaactaagg atgaaagatt gctccatgaa atagaaaata gtgatccaat gatcttcaac
     4441 tggaatgtat tgttttatgt ttcattagaa gagtttccta tagatgatcc ttattatgga
     4501 gagtttattg gtattcctgt agatgatgca tctatgtttt ttaactcctt tcaaccaagg
     4561 aaatttgaaa acaaacccct ttatgagaaa gaggatgatt aatatgatta aaggaatgct
     4621 ttttgctttt ttagcagcgt tctcatgggg ggcagctatc gtaatgagca aaaaaggagt
     4681 tgaagaacta gatgccggag gggtgttttt ctggcagatt tgtagtgcag taatactatc
     4741 ttggatagtt ctttttataa aaagaaaaaa actcccatta aactcaaaag cgatacttgc
     4801 ttatgcgaca ggcgtttttg aaccattctt agcgtatact tttacactct acggacttta
     4861 ttttatttca gcaggaagcg catcaattat tttttcactt gaatcagtgt ttatattggt
     4921 gttgtctgtt cttatttgct cagttaaaat taattccccg caatatttta tattgttcct
     4981 tataggtgca attgttggca gtattttggt agccttgcca gacatcagta atggatcgaa
     5041 taatattgtt ggatattgtc ttgttgttgc cggtgtgtta tcggcagcat tttatgttgt
     5101 tatatcgtct cgccttatta aatcgtttga gcctatcaca ttattgagcg gacagttgac
     5161 attctccctt atactgtcat cgctctttat ttttatatct aaatcatcaa tttatcttcc
     5221 gttggaatcc gtgattattg ttttttcatc tggaatatta caatattttt tagctttttg
     5281 tttttacttg aactccttgc gttggctccc agttcatttg gcagggataa tgttgtactt
     5341 tattccgcta gttgcattat ttttgtcatg gttgtttttg gatgaacaat tcacattctt
     5401 acagggggta ggatttattg taactgtgct aagtgtatat tttcttaaca gaaaatactc
     5461 agaggagtaa cattctgttc aggattgccc cccggcctcc atcgataccg tgccaaatgc
     5521 acgtaaaaaa cgggagcgtt tctggtgtcg gaatgtaacc aagggggtca gaggcgcgct
     5581 aaaacgctct caggggagtc aaatagagac gtttgtaaca aaaagatcaa a
//
