LOCUS       NZ_CP035483             1506 bp    DNA     circular CON 18-JUN-2024
DEFINITION  Escherichia coli strain U13A plasmid pU13A_F, complete sequence.
ACCESSION   NZ_CP035483
VERSION     NZ_CP035483.1
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 1506)
  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  JOURNAL   Unpublished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 1506)
  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
            CP035483.1.
            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..1506
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="U13A"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pU13A_F"
                     /geo_loc_name="USA:Utah"
                     /collection_date="2013"
     gene            join(1146..1506,1..299)
                     /locus_tag="U13A_RS27685"
     CDS             join(1146..1506,1..299)
                     /locus_tag="U13A_RS27685"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001490767.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_021534844.1"
                     /translation="MCKCNTVTRDDIPFAIWSGLHPDTPHQCVRAQCGFRFSSASSPTR
                     SLTFGRWGCGERCHLSHVIGDSAVVLSGMSRQIALQTLSEALRRTKRVLNARQGMEGAK
                     NAYRGFQEVRRADTPNQGLSGRQEPRQPPAKPICTALAAIQLVGGRRPSMLQRWGSGVL
                     PRRFPVALKALPEPWQLRRFGDYRAKVANDVNDVILRRLPYPASHRTDMRQKSNAG"
                     /name="hypothetical protein"
     gene            complement(357..797)
                     /locus_tag="U13A_RS26865"
                     /old_locus_tag="U13A_F00001"
     CDS             complement(357..797)
                     /locus_tag="U13A_RS26865"
                     /old_locus_tag="U13A_F00001"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000031238.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000031238.1"
                     /translation="MSKDVERITQINDQGEIIGGFVAVIRPKQKSAFQRHFTMNQDALR
                     ILAKELTGEQFKVLMLMLADLDYENFIQIAQADIAETLGMQKTNVSRAVRALLDVGVIF
                     EGPKVGRSKTYRLNEQFGWKGTVTNHKKALKNGFSVIQGGRI"
                     /name="hypothetical protein"
ORIGIN
        1 aggggctttc aggtcgccag gaaccgcgtc agccccctgc aaagcccatt tgcacggcac
       61 tggcagctat tcagctggtt ggtggtcgta gaccgtcgat gttacagcga tgggggtctg
      121 gggttctccc cagacggttt ccggttgcgc tcaaggcgct gccggaaccg tggcagctca
      181 gacgttttgg agattatcgg gcaaaggttg cgaatgacgt caatgacgtc attttgcggc
      241 gtttgcccta tcctgcatcg catcgaactg acatgcggca aaagagcaat gcaggataga
      301 caatcatggt caaaacgtta acacgtagcc ctgattgtcc gcctgccgct ggctctttaa
      361 atccggccgc cctgaatgac actaaagccg tttttgagtg cctttttgtg gttggttacg
      421 gtgcctttcc aaccaaattg ttcattcagc cggtatgttt ttgatctgcc aactttaggt
      481 ccctcaaaga tcaccccaac atccagtagc gcgcgaacgg cgcgactaac attcgttttc
      541 tgcatcccta aagtttcagc aatatctgct tgggcgatct gaatgaagtt ttcgtaatcc
      601 agatctgcaa gcatcagcat taagaccttg aattgctccc cggttaattc cttagccaag
      661 atccgtaatg cgtcttgatt catggtgaaa tgcctctgaa atgctgattt ttgtttaggg
      721 cggataacgg caacgaagcc gccgataatc tcaccctggt catttatctg agtgattctc
      781 tcgacatcct tactcatctt tgaaccctat ttgagttatc aataatgata acagtgttat
      841 cattattgat aactatgtca actgtaaccc ttagattttg ttaatgtttt tattctcctt
      901 tctgtatctt tatattaggc gtctaacgca ttgattccat tagatattta tcctagctac
      961 tctttggggt gtcggggcga agccctgacc cagtcacgta acgatagcgg agtgtatact
     1021 ggcttaatcc tctgcaagcc tcgtcagccg tgatttttgc cagatttcga ggttttcacg
     1081 ttcaacagct cctgcacgtt ttttgccgtc cgttcaccgt taaactccgc agaaatcggg
     1141 acaggatgtg caaatgtaat accgtcaccc gcgacgatat tccgtttgcc atctggtcag
     1201 ggcttcaccc cgacaccccg catcagtgcg tacgtgctca atgtggtttc cggttctctt
     1261 ccgcttcctc gcccactcgc tcactaacgt tcggtcgctg gggctgcggc gagcggtgcc
     1321 acctctcgca tgttatcggt gattccgctg ttgttctttc ggggatgagt cgccagatag
     1381 ctcttcaaac gctctcagaa gctctcaggc gcacgaaacg ggttttaaat gcccgtcagg
     1441 gcatggaagg cgcgaaaaac gcttacagag ggtttcagga ggtcaggcgc gccgataccc
     1501 ctaacc
//
