LOCUS       NZ_CP035482             5632 bp    DNA     circular CON 18-JUN-2024
DEFINITION  Escherichia coli strain U13A plasmid pU13A_E, complete sequence.
ACCESSION   NZ_CP035482
VERSION     NZ_CP035482.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10817700
            Assembly: GCF_004135165.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5632)
  AUTHORS   Forde,B.M., Roberts,L.W., Phan,M.-D., Peters,K.M., Fleming,B.A.,
            Russell,C.W., Lenherr,S.M., Myers,J.B., Barker,A.P., Fisher,M.A.,
            Chong,T.-M., Yin,W.-F., Chan,K.-G., Schembri,M.A., Mulvey,M.A. and
            Beatson,S.A.
  TITLE     Personalised genomic investigation reveals strain heterogeneity
            during chronic infection with E. coli ST131
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5632)
  AUTHORS   Forde,B.M.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-JAN-2019) School of Chemistry and Molecular
            Biosciences, The University of Queensland, Building 76, Cooper Road,
            St Lucia, QLD 4072, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2017
            Assembly Method                   :: HGAP v. 2.3.0
            Assembly Name                     :: UTAH_U13A_1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 120.0x
            Sequencing Technology             :: PacBio RSII; Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_004135165.1-RS_2024_06_18
            Annotation Date                   :: 06/18/2024 04:39:49
            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)                     :: 5,276
            CDSs (total)                      :: 5,163
            Genes (coding)                    :: 4,925
            CDSs (with protein)               :: 4,925
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 238
            CDSs (without protein)            :: 238
            Pseudo Genes (ambiguous residues) :: 0 of 238
            Pseudo Genes (frameshifted)       :: 91 of 238
            Pseudo Genes (incomplete)         :: 176 of 238
            Pseudo Genes (internal stop)      :: 41 of 238
            Pseudo Genes (multiple problems)  :: 60 of 238
            Pseudo Genes (short protein)      :: 1 of 238
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP035482.1.
            Bacteria and source DNA available from Schembri lab, The University
            of Queensland, QLD 4072, Australia.
            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..5632
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="U13A"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pU13A_E"
                     /geo_loc_name="USA:Utah"
                     /collection_date="2013"
     gene            join(5493..5632,1..52)
                     /locus_tag="U13A_RS26820"
                     /pseudo=""
     CDS             join(5493..5632,1..52)
                     /locus_tag="U13A_RS26820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1255..2121)
                     /locus_tag="U13A_RS26835"
                     /old_locus_tag="U13A_E00001"
     CDS             complement(1255..2121)
                     /locus_tag="U13A_RS26835"
                     /old_locus_tag="U13A_E00001"
                     /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"
     gene            complement(2123..3175)
                     /locus_tag="U13A_RS26840"
                     /old_locus_tag="U13A_E00002"
     CDS             complement(2123..3175)
                     /locus_tag="U13A_RS26840"
                     /old_locus_tag="U13A_E00002"
                     /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_001053268.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            complement(3656..3889)
                     /locus_tag="U13A_RS27035"
     CDS             complement(3656..3889)
                     /locus_tag="U13A_RS27035"
                     /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            complement(3896..4426)
                     /locus_tag="U13A_RS27040"
     CDS             complement(3896..4426)
                     /locus_tag="U13A_RS27040"
                     /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            complement(<4464..5162)
                     /locus_tag="U13A_RS27925"
                     /pseudo=""
     CDS             complement(<4464..5162)
                     /locus_tag="U13A_RS27925"
                     /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            complement(5104..5427)
                     /locus_tag="U13A_RS26855"
                     /old_locus_tag="U13A_E00005"
     CDS             complement(5104..5427)
                     /locus_tag="U13A_RS26855"
                     /old_locus_tag="U13A_E00005"
                     /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_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(147..228)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(685..872)
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          complement(3553..5114)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gctttaccgc agttgcctcg cacgcttcgg ggatgacggt gaaaaccgct gacacatgca
       61 gctcccggag acggtcacag cttgtctgtg agcggatgcc gggagcagac aagcccgcca
      121 gggcgcgtca ggccgttgac ctttggggtg tcggggcgaa gccctgaccc agtcacgtag
      181 cgatagcgga gtgtatactg gcttaaccat tcggcatcag tgcggattgt atgaaaagtg
      241 cgccatgtcc ggtgtgaaat gccgcacaga tgcgtaagga gaaaatgcca gttcaggcgc
      301 tcttccgctt cctcgctcac tgactcgcta cgctcggtcg ttcggctgcg gcgagcggac
      361 tctcctttct caaaaacgct aaccctgtta tccacagaac ccggggataa accaggaaag
      421 aacatgtgcg caaaaaacga aaccccggga aaggccgcgc cggaggcgct ttttccatag
      481 gctccgcccc cctgacggac ttcacaaaac agacactttt tcggtgcatc tgtgggagcc
      541 ttgcggctca accatgaaat ccgccagcgg tggcgaaacc cgacgtggct taaagatcat
      601 caccgtttcc ggtgaatcgc tccctcctgc gcccccacgt tcccgccata tcgattaccg
      661 gatacctttt ccgcctttct cccttacggg acacgtggcg ctttctcata gctcacgtct
      721 tctggtatct cggggcgact taggcagttc gctccgggct gggctgtatg caggaacccc
      781 ccgttcagcc cgactgctgc gccttctccg gtaactgttc tcttgggtcc aacccggaaa
      841 agacaccaca aagcgccact ggcagcagcc attggtaaaa gtcatgtgcg agatatttag
      901 agagtacttg aagtggctgc cggagtgcgg ctacactaga agaacaattt tggtgactcg
      961 tctcgcataa gacagttacc tggttaagca gtctgcaagc tgacttaacc ttcgatcaaa
     1021 ccgccctgca aggcggtttt ttcgtttaca ggcagcagat tacgcgcaga aaaaaaggat
     1081 ctcaagagga tcctttgatc tttttgttac aaacgtctct atttgactcc cctgagagcg
     1141 ttttagcgcg cctctgaccc ccttggttac attccgacac cagaaacgct cccgtttttt
     1201 acgtgcattt ggcacggcat cgatggaggc cggggggcaa tcctgaacag aatgttactc
     1261 ctctgagtat tttctgttaa gaaaatatac acttagcaca gttacaataa atcctacccc
     1321 ctgtaagaat gtgaattgtt catccaaaaa caaccatgac aaaaataatg caactagcgg
     1381 aataaagtac aacattatcc ctgccaaatg aactgggagc caacgcaagg agttcaagta
     1441 aaaacaaaaa gctaaaaaat attgtaatat tccagatgaa aaaacaataa tcacggattc
     1501 caacggaaga taaattgatg atttagatat aaaaataaag agcgatgaca gtataaggga
     1561 gaatgtcaac tgtccgctca ataatgtgat aggctcaaac gatttaataa ggcgagacga
     1621 tataacaaca taaaatgctg ccgataacac accggcaaca acaagacaat atccaacaat
     1681 attattcgat ccattactga tgtctggcaa ggctaccaaa atactgccaa caattgcacc
     1741 tataaggaac aatataaaat attgcgggga attaatttta actgagcaaa taagaacaga
     1801 caacaccaat ataaacactg attcaagtga aaaaataatt gatgcgcttc ctgctgaaat
     1861 aaaataaagt ccgtagagtg taaaagtata cgctaagaat ggttcaaaaa cgcctgtcgc
     1921 ataagcaagt atcgcttttg agtttaatgg gagttttttt ctttttataa aaagaactat
     1981 ccaagatagt attactgcac tacaaatctg ccagaaaaac acccctccgg catctagttc
     2041 ttcaactcct tttttgctca ttacgatagc tgccccccat gagaacgctg ctaaaaaagc
     2101 aaaaagcatt cctttaatca tattaatcat cctctttctc ataaaggggt ttgttttcaa
     2161 atttccttgg ttgaaaggag ttaaaaaaca tagatgcatc atctacagga ataccaataa
     2221 actctccata ataaggatca tctataggaa actcttctaa tgaaacataa aacaatacat
     2281 tccagttgaa gatcattgga tcactatttt ctatttcatg gagcaatctt tcatccttag
     2341 ttaattctcc tggaattaat acatcagtat gataaaaacc gctgtaataa gaactattac
     2401 cggtgtgcac tgggcatcca aaacgatcca aattagattc tgaatgccat gttgtagaaa
     2461 tcccttccgg atgtgaatac ccacccttac caacagactg aatagtcatg ttacgaatat
     2521 ccgctaacgc ttgttcttga tctttataga aacctttttc tatcgccagc ctcataaaat
     2581 gccccggggc atttacagaa ataagtattc cccctggtat tcttctatca tgatttcttg
     2641 ttctatgagc agaagagtaa aaaacattaa caccagcctt atatattttt agcccatctt
     2701 tatcctgaaa tggtacgctt tcagtataaa taacatcctc ttttattgga tagcactctg
     2761 gcatatgcag cgaacaaata tatttttgta tgtccactaa ctcttctgat ggacgagcaa
     2821 aggcaagttg tggatgaata aaataaatga gatgcgcact gacctctcct cttcttgcgc
     2881 gttctttaaa acgaactctt tcattacgca aaaaatcaaa caaatgacca tcatcattat
     2941 atagttgggg gctatttaca atagataaat ggaaatcaag ccctttaatt ttcttgcttg
     3001 ccaatttacc aaatacacag ggctgattgc ctgacaccca ttttcttagt aaatcttcaa
     3061 ttttatcttt agaagtttcg ttaaagataa atgaatgaat attatcaata tcttttccaa
     3121 atgaaaaact ggatgataat tgtggtagtt tatttatacg ttgttgaaga ttcatgaaag
     3181 ctcccacaag acacctcata tattttttta tatactgaaa ctacattata tttattaccg
     3241 gcgtaaaacg aaataattta ttatcgttac cgatatttta aaaaaatcat tatttgcaca
     3301 gtgttcgagt tgttagtatc actccttcct gaaaatccgc tccatttacc ataacgtcgc
     3361 attgtacgca ccgccaaaac gcgttcggtg cgatcacggc agcagacagg taaaaatggc
     3421 aacaaaccac ccgaaaaact gccgcgatcg cacctgataa attttaaccg catgaatacc
     3481 tatgcaacca gatgctacag gccacattag cccgccttaa tccactgaac acgtcatttt
     3541 tcatggtttc accatcccag cgaagggcca tccagtgtcc gctcctggat ttccggctga
     3601 cgctcccgct ccagagataa ctcatgttcg cgttcctgca tcagccgttc atcccttatc
     3661 tcctgttctc gctgtataac tggctcaagc gttctgtccg ctcgctcaag tgctgcacct
     3721 gctgactcaa ctgcatgact cgcccgttca gcatcgcgtt gtcccgttgc gtaagcgaaa
     3781 acattttctg caattccacg aaggcgttct cccattcgtt cagccgctgc atatagtcct
     3841 gttgcagttg ctctaatgcg ttcagcaaat gtctttccag ctccgtcatg ctctgtcact
     3901 cctgcaccag tctcactgcg ttcagtttgc cgttgtcctt cgtccagttc gtttcggctt
     3961 tcatcccctt cggcaacacc agaaaacgtc cgttgctgtc ctcgtgataa cgcacgcccc
     4021 atgtcttcgc gttcagcttc tccagactct ctttctgctc gcggagaata ttcatattcg
     4081 cgtttatctt catgccctgg taccacagca gactcccggt cgtggcaaac atcagtactg
     4141 agacgataat cagccacagc cagcgtttca cgctcatttt cagtacggtt ttccagtgcg
     4201 cgtccatcgt atcgacggtc gttttctgat acctctccag cagttctttc agggctgttg
     4261 tatggtcgtt gatagcgttc ctgattaaag attcgtttga ggtcagttcc ctgtttacag
     4321 attcttcgag cttcctgaac tcgtcgttca gcattttctc tgtagattcg gctctctctt
     4381 tcagcttttt ctcgaactcc gcgcccgtct gtaaaagatt gctcataaaa cgctcctttc
     4441 agtctgatat tcctcccgcc gttcgggtct gcaatgctga tactgcttcg cgtcaccctg
     4501 accacttcaa gccccgcctc tgtgagcgcc tgaatcacat cctgacggcc ttttatctct
     4561 ccggcatggt aaagcgcgtc tatcccgcgt gtgacgccct cagcaagcgc ctgtttcgtt
     4621 tccggcaggt tatcaggaag ggtcagcgtc cggcggttct ccggggcgtt ggggtcatgc
     4681 agaccgtaat ggtgattcac cagcgtctgc caggcatcaa ttctcggcct gtctgcccgg
     4741 tcgtagtacg gctggaggcg ttttccggtc tgtagctcca tgttcggaat gacaaaattc
     4801 agctcaagcc gtcccttgtc ctggtgctcc acccacagga tgctgtactg atttttctcg
     4861 agaccgggca tcagtacacg ctcaaagctc gccatcactt tttcacgccc tccaggcggc
     4921 agctccttct ccgcgaacga cagaacacct gacgtgtatt tcttcgcaaa tggcgtggca
     4981 tcgatgagtt cccggacctc ttccggattc ccctgaagca ccgttgcccc ttcccggtta
     5041 cgctcccttc ccagcaggta atcaaccgga ccactgccac caccttttcc cctggcatga
     5101 aacttaacta tcatcccgcg ccccctgttc cctgaccgcc agacgcagcc ggcgcagctc
     5161 atccccgatg gccatcagtg cggccaccac ctgaacccgg tcaccggaag accactgccc
     5221 gctgttcacc ttcctcgctg tctggttaag gttattcccg atggcggcca gctgacgcag
     5281 taacggcggt gccagtgtcg gcagcttccc ggaacgggca accggctcac ccaggcagac
     5341 ccgccgcatc cataccgcca gttgtttacc ctcacagcgt tccagtaacc gggcatgttc
     5401 atcatcagta acccgtatcg tgagcatcct ctcgcgtttc atcggtatca ttacccccat
     5461 gaacagaacc ccccccttac acggaggcat cagtgaccaa acaggaaaaa accgccctta
     5521 acatggcccg cttcatcaga gccagacatt aacgctgctg gagaagctca acgaactgga
     5581 cgcggatgaa caggcagaca tctgtgaatc gcttcacgac cacgccgatg ag
//
