LOCUS       NZ_CP054226             5658 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain EcPF16 plasmid p2, complete sequence.
ACCESSION   NZ_CP054226
VERSION     NZ_CP054226.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15075996
            Assembly: GCF_013372345.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5658)
  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  JOURNAL   Unpublished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 5658)
  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.0.4.12
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 231x, 197x
            Sequencing Technology             :: Illumina NextSeq, ONT MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 02:14:44
            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)                     :: 4,756
            CDSs (total)                      :: 4,644
            Genes (coding)                    :: 4,362
            CDSs (with protein)               :: 4,362
            Genes (RNA)                       :: 112
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 81
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 282
            CDSs (without protein)            :: 282
            Pseudo Genes (ambiguous residues) :: 0 of 282
            Pseudo Genes (frameshifted)       :: 70 of 282
            Pseudo Genes (incomplete)         :: 211 of 282
            Pseudo Genes (internal stop)      :: 42 of 282
            Pseudo Genes (multiple problems)  :: 42 of 282
            Pseudo Genes (short protein)      :: 5 of 282
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054226.1.
            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..5658
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EcPF16"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p2"
                     /geo_loc_name="USA: Dallas, Texas"
                     /lat_lon="32.77 N 96.79 W"
                     /collection_date="2018-07"
                     /collected_by="UT Southwestern Medical Center/ UT Dallas"
     gene            complement(join(4220..5658,1..67))
                     /locus_tag="HR074_RS23530"
                     /old_locus_tag="HR074_23510"
     CDS             complement(join(4220..5658,1..67))
                     /locus_tag="HR074_RS23530"
                     /old_locus_tag="HR074_23510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001577354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_176321127.1"
                     /translation="MSKLDLEKILAANGPCLSSELADILVEQFGLTPAAARKRISRGSQ
                     NLKKLSYIIFPHRARFVYLKNDYASTKYWKALYSSLKKENSSYYMAIDSIRTRGGMIRK
                     DEFGIICGSPVRQKNHIPYESLMLSLMKAEILLETSNENGGNYLYLKECEGHEHLLIES
                     QNKKELINGIMIEQARTWLKQLGLVSYGKTKAMGDETKNPMVGTFEWHITGPSYIHPLT
                     KNSINEKKPGFIVCDLNTTPSATLDDIDTFIRKMDMTLSLKNIGDCFFVYISNAYTEKA
                     LYKAKSKGVLAITFSNIFGKRNTVAAERLGDILNNRDINQIQASEIIKLTKELNERNGI
                     TQNLKGKLFEFICADMKKKIDISSRILIGREYITSQGDKAEADITSIRDDISICFIECK
                     AIKRESTLDDEQVDRWLDVRIPRLLNYCKSHTDYKHLKKTFELWVTGNLSENSNHRIND
                     FISKNPKIKITIKKPRELLKDVKDINDRALKNLLFNYFLKREK"
                     /name="hypothetical protein"
     gene            987..1178
                     /locus_tag="HR074_RS23535"
                     /old_locus_tag="HR074_23515"
     CDS             987..1178
                     /locus_tag="HR074_RS23535"
                     /old_locus_tag="HR074_23515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166327.1"
                     /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_001737777.1"
                     /translation="MTKQEKTALNMAKFIQGQSLLLLDKLNELNLDIEADMCEKLHEDA
                     EMLCRTLYGRLNALQDVG"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1178..1564
                     /locus_tag="HR074_RS23540"
                     /old_locus_tag="HR074_23520"
     CDS             1178..1564
                     /locus_tag="HR074_RS23540"
                     /old_locus_tag="HR074_23520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016162088.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_032328203.1"
                     /translation="MAKISISEAARLTGKSRTTLHRLIKTGELSTCHGARNARMVDISE
                     LIRVFGPLEHRPSEQFAAQVSEHSDTGVSAQTEQVIAQLRQEVEHLKTLVSAKDSHIDS
                     LKQAMLLIEHKHTGDSSWWKFWKR"
                     /name="helix-turn-helix domain-containing protein"
     gene            2560..2853
                     /locus_tag="HR074_RS23545"
                     /old_locus_tag="HR074_23525"
     CDS             2560..2853
                     /locus_tag="HR074_RS23545"
                     /old_locus_tag="HR074_23525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001414864.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_240532970.1"
                     /translation="MAYKNKNGQPRERAMVAAYSLVTQFGGKQQDVAKVLGCSPSTIHQ
                     WVKEIGYKKEIAGLKQELSDANEYIEELADNLGLEYHPDEPEENDYDDEDDR"
                     /name="helix-turn-helix domain-containing protein"
     gene            3514..3783
                     /locus_tag="HR074_RS23550"
                     /old_locus_tag="HR074_23530"
     CDS             3514..3783
                     /locus_tag="HR074_RS23550"
                     /old_locus_tag="HR074_23530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012822261.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024167138.1"
                     /translation="MSITMSQKSAREGLGNPELFQGGVYVTKNGLAELFVQTAEEREAE
                     LRERERERQSNALLKLVMAAKREIKNGRGMSPEDAMRRLREART"
                     /name="hypothetical protein"
     gene            3798..4142
                     /locus_tag="HR074_RS23555"
                     /old_locus_tag="HR074_23535"
     CDS             3798..4142
                     /locus_tag="HR074_RS23555"
                     /old_locus_tag="HR074_23535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014542127.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024167139.1"
                     /translation="MANSFNVTIAEAALWSLQDAESFKSNYTDSVQAASWADDLLASSV
                     KAISQDPARYRYNAMLADKGISIRERLDPDNQYRCLYDFDEQNGVIEILLFVSTKQDLE
                     KMLYRYLVVK"
                     /name="hypothetical protein"
     Typing          2068..2146
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="89.024"
                     /coverage="89.0"
                     /evalue="2.54e-18"
     Typing          complement(452..810)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.028"
                     /coverage="84.0"
                     /evalue="2.95e-159"
ORIGIN
        1 cagccagctc tgagcttaaa catggcccat tagcggccaa gattttttct agatctagtt
       61 tgctcatttt ttatccttgt cacactacgc tatttataat cagcactatc gtgctggcta
      121 tgagcagcga aaaaactctc tcgcaaagtc gctctgtggc tggctttatg ggaggctgtt
      181 tttgtctaaa ccctaaaaac gtcacaatac atcaattgtt gatgaaaatg aggtggttga
      241 ggtgggtttg ttttcttgac gtgaattgag gtatgagatt aacctagcct cagatacgaa
      301 aaaaccgcct tgcagggcgg ttttttcaac ggttcaagaa cttgcaggtt ttgaaccgag
      361 gtaactggct tggaggagca cagtcaccaa aacttgttct ttcagtttag ccttaaccgg
      421 cgcataactt caagaccaac tcctctagaa cagttaccag tggctgctgc cagtggcgct
      481 ttgtcgtgtc tttccgggtt ggactcaagt tgatagttac cggaagaggc gcagcagtcg
      541 gactgaacgg ggggttcgtg catacagtcc agcttggagc gaactgcctt cccggaactg
      601 agtgtcaggc gtggaatgag aaaccgcggc cataactgcg gaatgacacc ggcaaaccga
      661 aaggcaggaa caggagagcg cacgagggag ccaccagggg gaaacgcctg gtatctttaa
      721 gtcctgtcgg gtttcgccac cactgatttg agcgtcagat ttcgtgatgc ttgtcagggg
      781 ggcgaagcct atggaaaaac ggcaacgccg ttaccttacc ctttttcctc acatctttcc
      841 tagtaggtta cctcctgaat ctgtggctaa ctttgtcagt ctgtactgct cgccgcagac
      901 ccgtgaccga gcattgcgag cgaacgggcg aggaagcaga atggagcctg tcttaacatt
      961 aagcacgtac gtactgaggc ctgttcatga ctaaacaaga gaaaaccgcg ctgaatatgg
     1021 cgaagttcat ccaggggcag tcccttttgt tgctggataa gctgaatgag ctcaatctcg
     1081 acattgaggc ggacatgtgt gaaaaacttc atgaggatgc agagatgctc tgcaggactt
     1141 tatatgggcg gttaaatgct ctacaggatg tgggttaatg gccaagatat cgatcagtga
     1201 ggccgctcgg ctgactggga agagtcggac aacgctgcac aggttgatta aaacaggtga
     1261 actgtccacc tgtcatggtg caaggaacgc cagaatggta gatatttcgg agcttatccg
     1321 tgtttttggc cctctggagc atcgtccgtc tgaacagttc gctgcacagg tctctgaaca
     1381 ctctgacaca ggtgtttccg cgcagactga acaggtcatt gcgcagctgc ggcaggaagt
     1441 ggaacacctg aaaacattag tttcagccaa ggattcacac atcgacagcc tcaaacaagc
     1501 gatgctgttg attgagcaca agcataccgg ggattcatcc tggtggaagt tctggaaacg
     1561 ctgagaacgc ctcagttgcc ggcggggctt gtctgattta ctgaatgact tagcacaaac
     1621 ctgttttttc ggactatcca cacagcgcga tagccgctct gtgtggatag ggacaaaaca
     1681 tcacacccca cgcaagactt cgccttgcag atttatcttt ttatatcaaa atgataagta
     1741 taaatatttc agtcgattta catttacccc gaaaagtatc acacatttag cacacctcca
     1801 ggtgtcggta ccggcactgt catatcgccg gattgtggct atcgctattt ttcagtgcct
     1861 tacatgtcac acaatccggc actggtgccg gatccacaca cctgtatatc cgcgagcagt
     1921 gccggatccg cccacatgat atttatccag gtggccggat tgtgtgactg atttatatcc
     1981 agtgtggtgc cggatccggc actgtggctt gccggcattt tcagggtctt ttcatggctt
     2041 cagttttttt gagggtgtca gcgccacggg acaggatgtg catttgtaat accgcgcact
     2101 cgcggcatgg caaatgctcc tgtcagggct cgccgccccg acaccctgca agcgcttcac
     2161 ggtcacgcaa taaattgcgc gcccgttcac cactaccttt ttctcagcgt gattttgcgc
     2221 atgcgcaaaa tcacctgcca gaaatgcacg ccagcaggcc cggaaagtgt gaaaaagaag
     2281 ggttatgggg tatatccgga gccgaaatca gagccattca cctggctgca taggcattca
     2341 ctgtgccaga attcatcccc tgcgtttctg gcggttttcc gggtggtttg ttgcctgttt
     2401 taccgttctg ccgtcagaaa cgcgctgagg ccgtctgagc ggtgcgcgta atgcggcgtt
     2461 atggtaaatg cggttttttt attgtgtcgc ttacttgtgc ttatcatcag cctcttttaa
     2521 aatttaaaat tcgaatttta aattttaaaa gaggctggca tggcttacaa aaacaaaaat
     2581 ggtcaaccaa gagagcgagc catggttgcc gcgtattctt tggtaacgca gtttggtggc
     2641 aaacagcagg atgtagctaa agtacttggt tgttcaccat ctacgattca tcagtgggta
     2701 aaagagattg gttataaaaa agagatcgcg ggactgaagc aagaacttag tgatgcgaat
     2761 gaatacatcg aagagctagc tgataatctc ggacttgaat accatccaga tgaaccggaa
     2821 gagaatgatt atgacgatga ggatgaccgt tagctcatcc tttcgttctc gctatgaaaa
     2881 ggcccgcaag tgcgggcctt ttcaattaac catttaaggg atgaccattg cagttttcaa
     2941 caggccttcc gcatattggg caaaagagag cgtccttttt ctgtatctta ttgattttca
     3001 ttaattaact ccgttttgtg ctggtttttg taggttagct gcaacgtttt tcaagttttg
     3061 aacaatgtgc gcttctgcat ttacggcagt atgactgagg gatttttctg ccgtcagaca
     3121 tctctctaaa gccgaagatc tcgtctatct ctttaacatc cctacctgcg gttactttgc
     3181 aacacggaca ttcagcgccc atttcatacg gcatacccat ctccccgttt ttggaagata
     3241 cagtcggtac tgtatccact tctcttatgt gggtttaatc gatttttttc aagcaatagt
     3301 ggttagttga agctcagaaa gtttatgctt aaatgttggt gtacaaattc aacataaatt
     3361 tgtacaccaa tatgggtttt gatacaatgt aaatgctact caccctaagt ggcagcaaga
     3421 tatgaggttt ttttgacctc tttttttatt caggagttag ttgcttatgc ttaatcttgc
     3481 gtgtaagtga ctgttttaac taaaggtata catatgtcta taactatgtc tcagaagtca
     3541 gcccgcgaag gtcttggcaa ccctgaacta ttccaaggag gcgtttatgt tacgaaaaat
     3601 ggtttagcag aactgttcgt acagaccgca gaagagagag aggccgagct gcgtgaaaga
     3661 gaaagagaac ggcaatcaaa tgctcttttg aagctagtaa tggctgcaaa aagagagata
     3721 aaaaatggtc gtggaatgtc ccccgaagat gctatgcgga ggttacgtga agcgcgaact
     3781 taatataagg agccaacttg gcaaattcat tcaatgtaac gatcgcggaa gcggcactat
     3841 ggtccctgca agatgcagaa tccttcaaat caaactacac ggatagtgtt caagctgctt
     3901 cgtgggctga tgatctttta gcatcatcgg taaaggccat ttctcaagat cctgctcgtt
     3961 atcgctacaa tgctatgtta gcagataagg gaatatcgat ccgtgagcgc ttggaccctg
     4021 ataaccagta ccgttgttta tatgattttg atgagcaaaa tggtgtcatt gagatattgc
     4081 ttttcgttag tactaagcaa gaccttgaga aaatgcttta tcgatacctt gttgttaagt
     4141 aattgtgaaa atgcccactt ttatagtggg cattttcgtg tggttcttat agcgaggcat
     4201 tatggtaaag ccaagctttt tatttctctc tttttaaaaa atagttaaag agtaggtttt
     4261 taagagccct gtcgtttata tcctttacat ctttaagaag ttctctaggt ttttttattg
     4321 ttatttttat tttggggttt ttacttataa aatcatttat cctatgattt gaattttcgc
     4381 ttaagttacc agttacccaa agctcgaatg ttttttttaa gtgtttgtaa tccgtgtgtg
     4441 acttgcaata gttcaaaagt cttgggatcc tgacatcaag ccatctatca acctgttcgt
     4501 catcaagagt actttctctt tttattgcct tacattctat gaaacatata gaaatgtcat
     4561 ctctgataga cgtgatatca gcctcggctt tatctccttg gcttgtaata tattctctgc
     4621 ctatcagtat ccttgaggag atgtcaattt ttttcttcat gtccgcacag ataaactcaa
     4681 aaagttttcc ttttaaattt tgagttatcc cattcctctc atttaattcc tttgtaagct
     4741 ttattatttc tgacgcctgt atttggttaa tatctctatt atttaatata tctcctaacc
     4801 tttccgcagc gactgtgttt ctttttccaa atatattgct gaaagttata gccagcacgc
     4861 cttttgattt agctttgtat aatgcttttt cggtgtatgc atttgatatg taaacaaaaa
     4921 aacaatcacc tatatttttt aatgataatg tcatatccat ctttcttatg aatgtgtcga
     4981 tatcatccaa tgtggctgat ggtgttgtgt ttaaatcaca gacaataaac cctggttttt
     5041 tttcattgat gctgttttta gtcaatggat gaatgtatga ggggcctgtt atatgccatt
     5101 cgaaagttcc aaccattggg ttttttgttt catcacccat ggcttttgtt ttcccataac
     5161 tcactaagcc taattgtttt agccatgttc tagcttgctc aatcattatc ccgttaatga
     5221 gttctttttt gttttggctt tctattaaca ggtgttcatg accctcgcac tctttaaggt
     5281 ataaataatt accaccattt tcattagatg tttctaaaag tatttccgct ttcattaatg
     5341 ataacattaa cgattcataa ggaatgtggt ttttttgcct tactggagaa ccacagatta
     5401 ttccaaactc gtctttcctg atcattcctc ctcttgttct aatggaatct atcgccatat
     5461 agtatgagga gttttctttt tttaatgatg agtatagggc tttccaatat ttagttgaag
     5521 cgtagtcatt tttcaaataa acgaatctgg ctctgtgcgg gaaaattatg tatgaaagct
     5581 tttttaaatt ttgtgaacct ctggatattc tttttctagc agcagcaggc gtaagaccaa
     5641 attgctcaac caaaatgt
//
