LOCUS       NZ_CP011140             4075 bp    DNA     circular CON 01-JUN-2024
DEFINITION  Escherichia coli VR50 plasmid pVR50F, complete sequence.
ACCESSION   NZ_CP011140
VERSION     NZ_CP011140.1
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 4075)
  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 4075)
  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
            CP011140.1.
            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..4075
                     /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="pVR50F"
     gene            164..871
                     /locus_tag="ECVR50_RS26140"
                     /old_locus_tag="ECVR50_F001"
     CDS             164..871
                     /locus_tag="ECVR50_RS26140"
                     /old_locus_tag="ECVR50_F001"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001296720.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1113..3266)
                     /gene="mobQ"
                     /locus_tag="ECVR50_RS26145"
                     /old_locus_tag="ECVR50_F002"
     CDS             complement(1113..3266)
                     /gene="mobQ"
                     /locus_tag="ECVR50_RS26145"
                     /old_locus_tag="ECVR50_F002"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001029350.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_001029350.1"
                     /translation="MAIYHLSMKIISRSNGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPEDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGESGLAALRSQL
                     LKREEELRRKELEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQHPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMEFHLKTREAPLFAVVNTPEKQPDHLFRSLGFNRTWDEW
                     RREEDARTHATERRPDRGWSQGM"
                     /name="mobQ"
     gene            3454..3708
                     /gene="mobC"
                     /locus_tag="ECVR50_RS26150"
                     /old_locus_tag="ECVR50_F003"
     CDS             3454..3708
                     /gene="mobC"
                     /locus_tag="ECVR50_RS26150"
                     /old_locus_tag="ECVR50_F003"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091749.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          complement(2909..3267)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.222"
                     /coverage="100.0"
                     /evalue="3.97e-172"
     Typing          3268..3447
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.2299999999999998e-89"
     Typing          165..871
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1123..3353)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.46"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 taaaggtgat ataatttaag gtgcttgggt gaggtaattt aaggtaaagg tgaggagatt
       61 taaggtaata ttcacaggaa aatggggggt gaaaatataa ttgctcacca atgctaaagg
      121 tgataggttt ttatttcacc tcatttttgg cctggtggtt aaaatgacat caaaccctct
      181 gatagcctat aagtccaatg cgctggttga ggccagttac aagctaactt tacaagaaca
      241 gcgtttctta ttgctctgca taagccgact taactccggt actgacgtag cttcacctga
      301 attgcaaaag acaatgacca ttacagctgc ggaatatttt gattcattcc ctgatatggg
      361 gcggaaaaat gccgaggttc agctacagga agcgatcgat cgtttgtggg acaggtcgat
      421 cattctcaag gacgacgaga agcgcgagga gttccgctgg attcagtatc gggcacagta
      481 cgcgagggga gaggggaaag cacaaatcac tttttctgac gcggtaatgc cttatctgac
      541 acagttgaag gggcaattca ccagagtcgt cattaaaaat atttctaatt tatcaagaag
      601 ttacagcata agaatatacg aaattctcca gcaattccgc agtactgggg aacgtattat
      661 cgccctcgat gattttaaat catcactgat gcttgatggt aaatataaag atttcaaaac
      721 gttaaacagg gatctaataa aaccctgtgt tgacgaactg aacaaaaaaa gcgacctggc
      781 tgtaacggtt gagacgatca aaaaggggcg cacggttgta gccctgcatt ttcgcttcaa
      841 ggaagacaaa cagatcaaga tgacgatcta gaatcgattt taaggcacct aaaacgctca
      901 ctgtcgcgtt tttcttgtgt caggaatgcg aaggtactat tgaagtgaaa agttgcgtca
      961 aaaacgctct gatgcagcaa aaaaagaacc cccaattttt gggggcggaa aaacaaaact
     1021 atgtttgcgc tatgtgagtg tgcttcttgc attcatccct gtcgatgaac atcgacgaac
     1081 ataacacgat gttaaacaaa acaaaatatt gttcacattc cctgtgacca accgcgatca
     1141 ggtctcctct cggtggcgtg tgttcgtgca tcttcctcgc gccgccattc gtcccaggta
     1201 cgattgaaac ccagcgagcg gaacagatga tccggctgtt tttctggtgt gttgacgaca
     1261 gcaaaaagcg gtgcctcacg ggttttcaga tgaaactcca taagttccgg cgcaggtgat
     1321 atgtggctgt ctgcatcgtg atttacggca acaccatacc ctgcataccg taacccctta
     1381 tcggtcagtg cactgatgac cagctggctg ttatcggctg agggaacggc aaacgcggga
     1441 tacagcgtac cattaagccg gacaacaccg cccagagagt catccacgcc catgaccagc
     1501 aaaagctgaa gctggcgggt ttcccggtcg acagaactca tgaccggcat cagcgtcggt
     1561 ggcagacgtc cctgcgtaaa atccaccttc cttgctgcca gtgatggcat ggctggctgg
     1621 cggtcttctc caagacagaa agactccggc catgtcttcg gttggcggag attgcgggta
     1681 tgttgcggcc atgtctggca aacctgcgtc agaagttgct caaaggtcgc agaggaataa
     1741 acacgttgca gtggtggatg ttgaccgatt tcgcttcggt cacagatata accactcctg
     1801 tcacgcatta aatcaacact ctcaaagatc ctggtgcggt atttctccag ctcgttcccc
     1861 cagagcgtat attctccgtt ccggttgtga agcagaaggt aacaggtcat ttccccgtta
     1921 ccaggcatgg gagcctcgcc ataccccgta acgactgctc tcagcacccc tgaatccata
     1981 acggcattgt cattttttct gagctgctcc gcgcgactac gttctgtatc ctccagctcc
     2041 ttccggcgca attcctcttc acgtttaagc aactgggatc tgagagctgc aaggccggat
     2101 tccccccact gctgccactg tttttcaaat gccgtctgac tcgcgggaat gtcctgtttc
     2161 tccaccttcc ggtaatgctg tcgcaatttt tccatttgct ggctcagaga ctggattttt
     2221 ccctgctcac tacggtattc cggtgcagcc cattgcatca ggggaatacg ggaaaaaccg
     2281 gacgaaaacg gcgatgattt tttcaggctg gcagcatggc tcatcgcttc ctttcgttcg
     2341 gtgttcagct cttcccagcg tctgcgcgtc gcctgcatat ctgccatcat cgacatggcg
     2401 ttactggtga gtttccatgc cgcgttactg tcctccggca acgcttcgat gatgtcacgt
     2461 agtgtgtacg aagttgcgtt gtcaggaagc ccgatattca gaaggtcagc cacacggcgg
     2521 gcaggctctg tcagcccgct gttcctgagt tcggtgcggg aaatctgtat ttccaggtta
     2581 agcctgttaa tcagacgatt ctgttcgccg cgttctgttt cgataccgcg tgtttccatc
     2641 gcacaggcag actttccgag gtgaatacca ggcgttttct caagcccctg tcgctcgtat
     2701 gaacgatggt ctatctcttc ctgataaccg gcgttcgcca gtgccctgtt tgcatggtca
     2761 gcccatgatg cacgccacgt ctcggcatgt gtccggtcgt tccagtccct gacctttccg
     2821 ccgaacccag caggtccgac agccctcgtg gtcagcatga tgtgcgcatg gggatttgtt
     2881 ttatccatgt gatggaacgc cacatcagca atcatgccct gactgacaaa gttttctctg
     2941 acaaaggcga gaacggtttc ccgtgcggca tcctgcggca gttcacgggg gatagcgagt
     3001 tcaatttccc gcgcaagttg tgagttcttc cggcgttcgg ccttctcaac ggcattccag
     3061 agttcggcac ggttcgtaca ccaggcaggg gctgtcgcgg gggtcagaat cacagcctca
     3121 gccacaccgc ttttgcgggt gtagtcgtga gtcagtccgg tacgctcatc aagcattagt
     3181 gaaccagaac gataggcagc agaagcaacg gcgctgtagc cgttgcttct ggagatgatt
     3241 ttcatactga gatgataaat cgccatttct gccgtaatgc ctttttgcag ttttctttca
     3301 gccccgcagg gcgcacacaa tcgaaacgga gtggagattg tataagtgcg cacttcgtgc
     3361 acttcgtgat ttgccgtgca ttatgccagc tcagttttta aactaccagt gacgcgctaa
     3421 aatgcgattt ttcaccgcgc acggagtcac gaaatgagca gaacactcga acagaagatt
     3481 gccgaagctg aggccagatt acagcgcctg aaggcgaaga gccggagcct ggacacagcg
     3541 cagaaggtca ttgtgggtgc agcattgctg gcaaaggtca gaaagccgga ggaagtgcag
     3601 ttgcgagctt ggttactcca gttcctgaag gcagaggtga cacggcaggc tgatgtgacg
     3661 cgaatactgc cgctgattaa cgagctggag gcgctgccag agcagtgatt gtatcgtccg
     3721 ctcgccgcag cccagcgacc gaacgttagc gagcgagtgg gcgaggaagc ggaagtgaat
     3781 cagtcgccag gttgagcaca tacgcacggt ttttcgacag gtgatatgcg ctgaacccgc
     3841 atgaatactg gatttccaca gggttggagg gggtgtattc ggaattttca atcctgattt
     3901 tttgcaatac attgttttta tttgattttt attttcagca ccccaagtta tccacaggct
     3961 cgccgttaag tttttagatc ttgtttttaa gatcttgttt ttaatacttg ttttagggtc
     4021 gaaattcctg attaaaaaca atgcgttaca cgtgcatagg tgggggaatt taagg
//
