LOCUS       NZ_CP054218             2113 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain EcPF40 plasmid p4, complete sequence.
ACCESSION   NZ_CP054218
VERSION     NZ_CP054218.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15075998
            Assembly: GCF_013372305.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2113)
  AUTHORS   Sharon,B.M., Nguyen,A., Arute,A.P., Hulyalkar,N.V., Nguyen,V.H.,
            Zimmern,P.E. and De Nisco,N.J.
  TITLE     Complete Genome Sequences of Seven Uropathogenic Escherichia coli
            Strains Isolated from Postmenopausal Women Suffering from Recurrent
            Urinary Tract Infection
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2113)
  AUTHORS   Sharon,B.M., Nguyen,A., Arute,A.P., Hulyalkar,N.V., Nguyen,V.H.,
            Zimmern,P.E. and De Nisco,N.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-JUN-2020) Biological Sciences, University of Texas at
            Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v.0.4.14
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 64x, 315x
            Sequencing Technology             :: Illumina NextSeq, ONT MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 02:34:47
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,134
            CDSs (total)                      :: 5,019
            Genes (coding)                    :: 4,806
            CDSs (with protein)               :: 4,806
            Genes (RNA)                       :: 115
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 213
            CDSs (without protein)            :: 213
            Pseudo Genes (ambiguous residues) :: 0 of 213
            Pseudo Genes (frameshifted)       :: 79 of 213
            Pseudo Genes (incomplete)         :: 143 of 213
            Pseudo Genes (internal stop)      :: 36 of 213
            Pseudo Genes (multiple problems)  :: 42 of 213
            Pseudo Genes (short protein)      :: 4 of 213
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054218.1.
            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..2113
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EcPF40"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p4"
                     /geo_loc_name="USA: Dallas, Texas"
                     /lat_lon="32.77 N 96.79 W"
                     /collection_date="2019-04"
                     /collected_by="UT Southwestern Medical Center/ UT Dallas"
     gene            complement(join(1504..2113,1..356))
                     /locus_tag="HR076_RS25375"
                     /old_locus_tag="HR076_25400"
     CDS             complement(join(1504..2113,1..356))
                     /locus_tag="HR076_RS25375"
                     /old_locus_tag="HR076_25400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012421200.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001287824.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
                     /name="protein rep"
     gene            complement(1234..1500)
                     /locus_tag="HR076_RS25380"
                     /old_locus_tag="HR076_25405"
     CDS             complement(1234..1500)
                     /locus_tag="HR076_RS25380"
                     /old_locus_tag="HR076_25405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001024536.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001024536.1"
                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTFG
                     FHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
                     /name="hypothetical protein"
     Typing          complement(1845..2076)
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.05e-118"
ORIGIN
        1 ttcctgacag ttaacgtcag aaacaaccat cgggaagacg ggtaatccac aacgattttc
       61 ggtagagcct gataaaaacg ggcttgccac atgagggttc ttctccactg gcagacaggg
      121 caatgacgga cacggcaaaa ttgcgcacta cgaagccgta ggcgcgtttc tccggtttcc
      181 atgatggtag accaaccaaa acgtaacaaa ccgctacagg aggccatacg gagtgcatag
      241 cgctcgaatt cagcagcagt ctggtagata cccccgacag aatcggtaag cgtgcgctgg
      301 gtatcccaaa ctgcatcacg ggggctgtag tccgaaagga atttatcttc tgacattaag
      361 cctgctccga tctgggcagg ctgtgatttg atgtggtata ttcatcacgt acctgtgcat
      421 tgcgagccag tacatgtcac cagagtttgc cgctgaggtg acacattcga aatgttgggg
      481 agtgttgacg cactccccaa cgccgattaa aaacgcctca attctgctcc attttctttg
      541 acctgtcaaa acccactcaa agcctcgtca ttactgggct aaaccactat ttcatatccg
      601 ccatttatcc cttaagtata aatacaagga tcacgcgcga gaattgcgca aaaaataacc
      661 acaattttaa ccccccaaaa caagcacccc cgaacggctt accccaacct tttccacaca
      721 cccgatcacc aaaacaggga ataaaaacaa aaccctgtct tacaggtgga tggcctcact
      781 tcgtgaaacc atccaccccg cataagtttt ttaatcggtg gtgtcgtcaa tcactaaatc
      841 ggaaccccaa aggggacccc cacgatttag catttgacga gattaactct cggagatggc
      901 atcatgcttt taacggactt taaaaaacgg tgaacggatg cggattttaa tccgtgtctg
      961 tgaggcgttg agcaacgagc aaagcgaggc ggtagaaaga gagccagcgg caggctcagg
     1021 acgataatcc ggggaaaatg taccactcgc agagtgttaa catttgacat cggattgtct
     1081 atcctgcatt ggtgtcgagt tggcaaggct gaggataatg ctgaggataa tgctgaggat
     1141 aatgctgagg ataatgcagg atagacagag cactagagat tgcatgcaat ctcgtaccta
     1201 tcacctcagc ctgccgctgg ctcttttcca gaactaagaa tgcgttctta aaaatccaaa
     1261 cttgataccg tttaaatcta ttttcacaaa aagagttttt accctctcgt ttgttttctg
     1321 aatatataaa attaattcat cctcaaaacc ttcgtgcgga tgaaaaccaa atgtgccaaa
     1381 acttaatcca tcaataagca aaataaggtt tttaaacctg tcaggaatca ccgcttcact
     1441 tcttaaaaaa aataaaccaa tagtcttatt tccattcagg tattcaatat taatattcat
     1501 acgttaatcc gatttatcct tctcaggggc gcgtttgtaa cgccgtttac ctgaatccca
     1561 gacaaacgcc gtccgcttcc cgtcatcagt gccatcccct acatcgtcgg caatgacaag
     1621 atcctcattg gtttctcgat ccaactggag gacgtttttt agcgccccac cggtcgagat
     1681 aaaacggcgc ttgtgaagct gccgcgtcag ctcaagaaac cactcaggat cgtttgccat
     1741 atcttccggt ttaacggagt atttcagcgt ttcagcaacc gcgctttgca gttgctcggc
     1801 aacgttggcc acaacctcac ctgtcttagt ttttactgcc cgaatatcga tattcggctc
     1861 atagttcacc cgcaagcaat cgcgccagag ttctacccaa cgttcgtgct taacgtagtt
     1921 cttcccttta aaccaagaag gttgcaccat cagcagacag tgaaaatgcg gatgtgcgct
     1981 gccatcctta cctcgcgtca cctccgtagc cctgatccac ccctgaacag gtgatagctc
     2041 ctttcgcttt tccattcgct taaacgccgc attcattgct gtaaggactg ttccaagttc
     2101 acctatctcg cag
//
