LOCUS       NZ_CP054229             6431 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain EcPF15 plasmid p2, complete sequence.
ACCESSION   NZ_CP054229
VERSION     NZ_CP054229.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15075995
            Assembly: GCF_013372365.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6431)
  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  JOURNAL   Unpublished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 6431)
  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.0.4.11
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 70x, 250x
            Sequencing Technology             :: Illumina NextSeq, ONT MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 02:37:40
            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)                     :: 4,702
            CDSs (total)                      :: 4,583
            Genes (coding)                    :: 4,462
            CDSs (with protein)               :: 4,462
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 121
            CDSs (without protein)            :: 121
            Pseudo Genes (ambiguous residues) :: 0 of 121
            Pseudo Genes (frameshifted)       :: 30 of 121
            Pseudo Genes (incomplete)         :: 90 of 121
            Pseudo Genes (internal stop)      :: 18 of 121
            Pseudo Genes (multiple problems)  :: 18 of 121
            Pseudo Genes (short protein)      :: 4 of 121
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054229.1.
            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..6431
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EcPF15"
                     /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="2018-06"
                     /collected_by="UT Southwestern Medical Center/ UT Dallas"
     gene            <1005..1595
                     /locus_tag="HR073_RS23255"
                     /old_locus_tag="HR073_23255"
                     /pseudo=""
     CDS             <1005..1595
                     /locus_tag="HR073_RS23255"
                     /old_locus_tag="HR073_23255"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001697689.1"
                     /note="internal stop; incomplete; partial in the middle of
                     a contig; missing N-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            1592..3271
                     /locus_tag="HR073_RS23260"
                     /old_locus_tag="HR073_23260"
     CDS             1592..3271
                     /locus_tag="HR073_RS23260"
                     /old_locus_tag="HR073_23260"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000598747.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0016887 - ATP hydrolysis activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="AAA family ATPase"
                     /protein_id="WP_001774712.1"
                     /translation="MIKVQLPTREHRLHELNLNYGDVVFFIGQNGSGKSSLLNNLFQKI
                     GSQSSVYVLAHRKNTFSSDIIDFSNSEYKNAQGWIFNEIKGSQCRYRVNYDSQMVAIPI
                     VKLKNKVIARALSFVDSFKSNNNQPAELIKSEVDVLNMVFADAKLSIEFFLDDEANVMA
                     RNIKGENPDVYPISMLSDGEKSALIIASEIICADENTTIFLDEPERHMHRSIVSPLLSS
                     LMKYRRDCVFFVATHELSLPAFFDNVKVVNVKNCYFSEQREPIYWDFNVVEDYDELFNG
                     VDEQTKIDILGARDKVLFVEGVTSSLDRDLYSAIFPMVSVVSKQKCDLVELAVKGLRLN
                     DEIHRVSAFGIIDNDNKVQAKVDNLKKDFIFSLDVHSIESIYYHPRMIKFVIDFVKEAN
                     GIDNVDALFMEIHDFAIDAINEKRDHLCCRAVEKTIRADLMSAIPKQQDIKNRIKFNKE
                     IDIECYVNKEIAAFDAMIAERNLDALVSRYPIRETNLLAHVAKKCGFADRSRYELNVIR
                     TIKSNADARAFVLSLLGGLDEAILGCSDTENSPADTHTVFAM"
                     /name="AAA family ATPase"
     gene            complement(3508..3702)
                     /locus_tag="HR073_RS23265"
                     /old_locus_tag="HR073_23265"
     CDS             complement(3508..3702)
                     /locus_tag="HR073_RS23265"
                     /old_locus_tag="HR073_23265"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041636.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADVQAAMCERLHELA
                     EELQNSIQVHFEAENETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(4496..5206)
                     /locus_tag="HR073_RS23270"
                     /old_locus_tag="HR073_23270"
     CDS             complement(4496..5206)
                     /locus_tag="HR073_RS23270"
                     /old_locus_tag="HR073_23270"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000967646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000967645.1"
                     /translation="MLYWKKMPSLWIGNRIAEFSDLDTAKAIAALKIYLTFCLFCKESD
                     SGHRTVELTFSNLCEIASLSRSLVNEGLKILYAKELIKNISPTARKKIYTVDVLENHND
                     GWCKLPFKGVVDEDKKISAFQSMHNRYPFELLALQTYMYLLYARDNNSDYTLARKKTIC
                     KKLKCKLPELNKAITYLIHIGLLDRVVKKSIENIPLEMFHDSYYFYIKTGSKSALTYRR
                     KSEPPVIPEADLPF"
                     /name="hypothetical protein"
     gene            complement(5620..6135)
                     /locus_tag="HR073_RS23275"
                     /old_locus_tag="HR073_23275"
     CDS             complement(5620..6135)
                     /locus_tag="HR073_RS23275"
                     /old_locus_tag="HR073_23275"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000675351.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
                     /protein_id="WP_000675351.1"
                     /translation="MKFYTISSRYIEYLKGFEDKVPNSEDPNYQNPKAFIGIVLEIQGH
                     KYLAPLTSPKPWHSTIKESSPSFFKLHENGVPENQLGLINLKFMIPIIEAEVSLLDLNG
                     MPNTAYKRMLYKQLQFIRVNSDKIAEKSELLRKLVLQGKMQGTCNFSLLEEKYRDFGKE
                     ANDTEEGE"
                     /name="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
     Typing          3739..3838
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.02"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          3963..4218
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.574"
                     /coverage="89.0"
                     /evalue="2.65e-108"
     Typing          complement(274..846)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.828"
                     /coverage="90.0"
                     /evalue="5.34e-173"
ORIGIN
        1 ccctcaaaat gtcatttgag gcttttttaa agtactgatt ccagagttga ctgttttttt
       61 catcagttca gtgtgggggg gggtaagttg ggttatgaca tgaatcaaaa aggatctgct
      121 tgagatcctt tttttctacg cgtaatctct tgctctgaaa acgaaaaaac cacctgggga
      181 ggtggttttt cgatggttca gtaagttggg gaacttctga accgtggtaa cagggtgtac
      241 aagaccgctg ccaccaaatt cgtccttcca gtttagccgt agtttggttc taacttcaag
      301 aactctgcat cagtaatctc ttgtacaccc cttaccaatg gccgcagcca gtggcgataa
      361 gtcgtgtctt tccgggttgg actcaagatg atagttaccg gacaaggcgc agcggtcgga
      421 ctgaacgggg gggtcgtgca tacagtccag cttggagcga actgcctacc cggaaccgag
      481 tgtcaggcgt ggaatgagat aaacgcggcc ataacagcgg aatgacaccg gtaaaccgaa
      541 aggcaggaac aggagagcgc acgagggagc caccaggggg aaacgcctgg tatctttaag
      601 tcctgtcggg tttcgccacc actgatttga gcgtcagatt ctgtgatgct tgtcaggggg
      661 gcggagccta tggaaaaacg ccagcggcgc ggccttttgc cctggctttg cctttttgct
      721 cacatgttct ttccggcctt atcccctgat tctgtggata accgtattac cgtctctgag
      781 tgagctgata ccgctcgccg cagccgaacg accgagcgca gcgagttagt gagcgaggaa
      841 gcggaagagc gtaggcattt gcattttctc cttacgcatc tgtgcggcat ttcacaccgt
      901 caatagcgca cttttcatac aatccgcact gataccgcat agttaagtca gtactcacag
      961 cgtcccctct gcgaggtgcc ttctgtgact ggttcagggg gcttgccgcc cccctcaaat
     1021 atgcagccgt cattgagaat gcgctgcgta aaaaattggg cgccgatgcg gggtattcag
     1081 ggctaatttg cgagaatccg aaccacctgc actggcagat caccgtttgg cagcctgagc
     1141 tctacaccct cgactgatta gccgactacc tcgaccttgg cgcagctaat gaccgcgaaa
     1201 tcctaccgga ctacggttta ggccgtaact gcaccctctt cgataaaacc cgcaagtggg
     1261 cttaccgcgc tatccaccaa ggctggccgc agtatgacca atggctacaa gcttgctttg
     1321 aacgcgctaa agcctacaac ctgcagttct ccgcaccttt agacgagaac gaagtcatgg
     1381 gtattgccaa aagtgtagct aagtggacta ataaaaattt tacagagtca tcatttgatg
     1441 attttataaa aaagacccat tcggcagaca tccaatctct atgtgggaaa aaaagtaaag
     1501 gaggaggtag gccttcatta aactctccat ggattaattt aggaattagt cgttcaacgt
     1561 attttagatt aaaagctaaa gagaaaggaa aatgataaaa gttcagttac ctactagaga
     1621 acatcgtctt catgagctta atcttaatta tggcgatgtc gtttttttta ttggtcagaa
     1681 tggtagtggt aaatccagcc tattaaataa tctttttcaa aaaataggat ctcaatcatc
     1741 agtatatgtt ttagcgcata gaaaaaatac attcagcagc gacattattg atttcagtaa
     1801 tagtgagtat aaaaatgcgc agggatggat ttttaatgaa attaaaggca gtcaatgtag
     1861 atacagagtt aattatgact cacagatggt tgccatacct atagtaaaat taaaaaacaa
     1921 agtgatagcc agggctttaa gtttcgtaga ttcatttaaa tcaaataaca atcagccggc
     1981 agagttaata aagtcagagg ttgatgttct aaacatggtt tttgctgatg ccaaattatc
     2041 tattgagttc tttctagatg atgaagccaa cgttatggca aggaatatta aaggtgaaaa
     2101 tcctgatgtt tatcctatat caatgctttc tgacggtgaa aaaagtgcac taattattgc
     2161 cagtgagatt atttgcgctg atgaaaacac aactattttc ttagatgagc ctgagcgaca
     2221 tatgcacaga agcattgtgt ctccgctgct ttcatcttta atgaaatatc gtagagattg
     2281 tgtttttttt gttgccaccc acgagttaag cttgcctgcg ttttttgata acgtgaaagt
     2341 ggttaacgtt aaaaactgct atttttccga acaaagagaa ccgatatact gggatttcaa
     2401 tgttgttgag gattatgacg aattattcaa tggtgttgat gagcaaacta aaatagatat
     2461 acttggcgct agggataagg ttctatttgt tgaaggtgtt acgtctagcc ttgaccgtga
     2521 tttatattcg gccatatttc ctatggtttc agttgtatct aaacaaaaat gtgatttggt
     2581 tgaattggcg gtaaaaggct tgagactaaa tgacgaaatt catcgagtat cggcgtttgg
     2641 tatcattgat aatgataaca aggtgcaggc gaaggtcgat aacttaaaga aagacttcat
     2701 ttttagtctc gacgttcatt ctattgagtc gatttattat catcctagaa tgattaagtt
     2761 tgtcattgac tttgtaaaag aggctaatgg gatagataat gttgatgcct tatttatgga
     2821 aattcatgac ttcgctattg atgccataaa tgaaaagcgc gatcacttat gctgccgtgc
     2881 agttgaaaaa acaataaggg cagacttaat gtcggccata ccaaaacagc aagatattaa
     2941 gaaccgcatt aagtttaata aagaaattga tattgaatgt tatgttaata aagaaattgc
     3001 tgcatttgat gcaatgatcg cggaacgaaa tttggatgcg ttagtctcac gctaccctat
     3061 ccgagaaaca aatttgttgg cacatgtagc taaaaaatgt ggttttgccg atcgctctag
     3121 atatgagtta aacgtgattc gtacgatcaa gagtaatgct gacgctagag catttgtttt
     3181 atccctcctc ggagggttag atgaagctat tttgggatgt tcagatacgg aaaatagccc
     3241 agctgatacc catacagttt ttgctatgtg agactaaaca acctatatca gataacagcc
     3301 ctgcttttgc ggggcttttt gtttgtgcgt gacttgaccg cgatgtacga tagttgctgt
     3361 attaagtcag tatacactcc gctatcgcta cgtgactggg tcagggctgc gccccgacac
     3421 ccgttaaaac ccgctgacgc gccctgacgg gcttgtctgc tgacgaaaat gctcacgggc
     3481 aagccgtgac cgccttcgtc agcttcgtta tgttcctgtt tcattttcgg cctcaaagtg
     3541 aacctggatg ctgttctgga gttcttctgc gagttcgtgc agtcgttcac acatggccgc
     3601 ctgtacgtcg gcatccagag catccagttt ttcaagcagt gtcaggctct ggcttttgat
     3661 aaatcgcgcc atattcagcg cagtttgttg ctgtttgttc accttccgtt gttctccgtc
     3721 agtaccgggt gtcgggtgga ccctgactag gtggtaattg taagacgttg cgggcgacgg
     3781 tattacaatt gcacatcctg tcctgttttt tttaggacgt atcatggcac agcatatcaa
     3841 ctgataaata atccctgtgc agtgcagccg ctgttgcata aaatttcgct ctgcgtcgag
     3901 tgtttcttaa tcaataattc cgctgatact ccggaaaaac gcgagtctgt tctcatgcct
     3961 gaaatgccca caccccacgc aaaaacaatt ttttgctgat ttttctttat aaatagagag
     4021 ttatgacaaa ttagtttctc ttgctctctt tgtgatattt aaaaaagcgg tgtcggcgcg
     4081 gctacaacac cgcgccgaca ccgctttgta ggggtggtac tgactatttt cataaaaaac
     4141 atcattttat attaggggtg ctgctagcgg cgcggtgtgt ttttttacag gatgcccctg
     4201 ggggcgctgc taggggtgtc tgttcagata tgtagcaatg agtcagggat tcacgaactg
     4261 aaaatgtccg aaaatgtgtc tcatgggcac cgtatgcgcc caaaccgttc gccattcact
     4321 ttcatgcata gctatgcagc gagctgaaaa cgatcctgac gcattttttc ggtttacctt
     4381 ggggaaaaca tctctttttg cggtatttgc gtcagaatcg cgttcagcgc gtttctgagg
     4441 tgcgggcaac ggatgttatg ttcaatccgt gtgataattg gtgtggaata aacaatcaaa
     4501 atggtaagtc ggcttctgga ataactggcg gttctgattt ccttctgtag gttagagcgc
     4561 tcttactgcc tgtttttata tagaaatagt acgagtcatg aaacatctct agaggtatgt
     4621 tttctatgga ttttttcaca actctatcaa gcaaacctat atggataagg taggtgattg
     4681 ctttgtttag ttcaggtaat ttgcatttca attttttgca tatggtcttt ttcctagcca
     4741 gtgtgtagtc gctgttatta tcacgagcgt aaagaagata catgtaagtt tgtaaggcta
     4801 gtaactcaaa gggatatctg ttgtgcatgg attgaaatgc acttattttt ttgtcctcgt
     4861 cgacaactcc tttaaatgga agcttgcacc atccatcatt atgattttct agcacatcca
     4921 cggtataaat cttttttcgt gcagtcggcg atatgttttt tatcagctct tttgcataaa
     4981 gaattttaag gccttcgttc accaaggaac ggcttaatga cgctatctcg caaaggttgc
     5041 taaaggttaa ctcaaccgtt ctgtggccag agtctgactc tttgcaaaac aggcagaatg
     5101 ttaaataaat ttttaatgcc gctatagctt ttgctgtatc aagatcgctg aattcagcga
     5161 tcctatttcc tatccatagt gaaggcattt ttttccagta cagcatgaat cacctcaagg
     5221 ccaagttttg aaagatgaaa tagaccaatc ccaatataga aagtgagagc acaaggttag
     5281 ttattaccgc tgcgactttc gcaagcctct caaccagata cacgcctttc tcaaacattt
     5341 ttcacccctc gtaatcgctt cttgttgttt ttattatctc agggtgtgaa ggcgttgtaa
     5401 cgccttcaca aaaatctatc tagaaagata aaagtgatgt taatttttta tcttgttgtt
     5461 tttaacggtt ttttatttga gttttggtat ttgtattaat cataatatgg ttcaccgtga
     5521 actatgtatg tgagtcgaac cgttgagttt tgaatattag acctgaatag tgtccaagat
     5581 cactcggttt cggacactat tcaggatggc aatgaagcgt tactcgcctt cttccgtgtc
     5641 attagcttct ttgccgaaat ctcggtattt ttcttctaac agggaaaaat tacatgttcc
     5701 ttgcattttt ccttgcagga cgagcttcct taaaagctct gatttctcag ctattttgtc
     5761 tgaatttaca cgaataaact ggagctgctt atagagcatt ctcttgtagg cggtattcgg
     5821 cataccgttc aagtcaagta aggatacttc ggcttcgatg attggaatca tgaacttcag
     5881 attaatcaat ccgagctgat tttcggggac accattttca tggagcttaa agaagctagg
     5941 cgatgattct ttaatagtgc tatgccatgg ctttggggat gttaaagggg ctagatactt
     6001 atgcccttga atctctaaca caatgccaat gaaagctttc ggattctgat agttaggatc
     6061 ttcgctattg ggaactttgt cttcgaatcc ctttaggtat tcaatgtatc tgcttgatat
     6121 agtgtaaaat ttcatttttt tctcgtaaaa aaggcgactg tgtagtcgcc tcttttactg
     6181 tattacttta aggtagtaaa tgacctaaat ttctagctgc acttaaggta gcaaatcacc
     6241 tgaatttcta gctgcactta aaggtagcaa atcacctgaa tttctagctg cacttaaagg
     6301 tagcaaatca cctgaatttc tagctgcact taaaggtagc aaatcacctt gattcgagta
     6361 tacctgatct tcgcctaggc ttacaactag gtaacttgca gctgtgtagt tgtagccctt
     6421 gccgctgtat c
//
