LOCUS       NZ_CP049851             5119 bp    DNA     circular CON 14-JUN-2024
DEFINITION  Escherichia coli strain UPEC-245U/190328 plasmid pEcoUTI1a, complete
            sequence.
ACCESSION   NZ_CP049851
VERSION     NZ_CP049851.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14277527
            Assembly: GCF_023376095.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5119)
  AUTHORS   Velez-Sanchez,D., Ochoa,S.A., Cruz-Cordova,A., Lopez-Martinez,B.,
            Parra-Ortega,I., Escobedo-Munoz,A.S., Bustos,P., Cevallos,M.A. and
            Xicohtencatl-Cortes,J.
  TITLE     Comparative Genomics of Uropathogenic Escherichia coli Strains
            Isolated from Adult Women with Recurrent Urinary Tract Infections
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5119)
  AUTHORS   Velez-Sanchez,D., Ochoa,S.A., Cruz-Cordova,A., Lopez-Martinez,B.,
            Parra-Ortega,I., Escobedo-Munoz,A.S., Bustos,P., Cevallos,M.A. and
            Xicohtencatl-Cortes,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-MAR-2020) Centro de Ciencias Genomicas, Universidad
            Nacional Autonoma de Mexico, Circuito Universidad, Cuernavaca 66210,
            Mexico
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 19-FEB-2020
            Assembly Method                   :: Unicycler v. v0.4.1
            Assembly Name                     :: UTI-2_GENOME
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 208.905x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023376095.1-RS_2024_06_14
            Annotation Date                   :: 06/14/2024 05:43:47
            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)                     :: 5,247
            CDSs (total)                      :: 5,122
            Genes (coding)                    :: 4,924
            CDSs (with protein)               :: 4,924
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 198
            CDSs (without protein)            :: 198
            Pseudo Genes (ambiguous residues) :: 0 of 198
            Pseudo Genes (frameshifted)       :: 68 of 198
            Pseudo Genes (incomplete)         :: 124 of 198
            Pseudo Genes (internal stop)      :: 38 of 198
            Pseudo Genes (multiple problems)  :: 31 of 198
            Pseudo Genes (short protein)      :: 1 of 198
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP049851.1.
            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..5119
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="UPEC-245U/190328"
                     /isolation_source="bladder epithelial biopsy from
                     30-year-old female patient with recurrent urinary tract
                     infection"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEcoUTI1a"
                     /geo_loc_name="Mexico: Mexico City"
                     /collection_date="2019-03-28"
                     /collected_by="Hospital Militar de Especialidades de la
                     mujer y neonatologia"
     gene            join(5039..5119,1..63)
                     /locus_tag="G9W35_RS26315"
                     /old_locus_tag="G9W35_25980"
     CDS             join(5039..5119,1..63)
                     /locus_tag="G9W35_RS26315"
                     /old_locus_tag="G9W35_25980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_152896351.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAIGNWIVDLDTQ
                     NS"
                     /name="replication initiation protein"
     gene            complement(258..389)
                     /locus_tag="G9W35_RS26090"
                     /old_locus_tag="G9W35_25985"
     CDS             complement(258..389)
                     /locus_tag="G9W35_RS26090"
                     /old_locus_tag="G9W35_25985"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_072023513.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_077521118.1"
                     /translation="MKIIIFLITILFLSGCQANYIRDVQGGTVAPSSSSELTGIAVQ"
                     /name="colicin release lysis protein"
     gene            419..709
                     /gene="cki"
                     /locus_tag="G9W35_RS26095"
                     /old_locus_tag="G9W35_25990"
     CDS             419..709
                     /gene="cki"
                     /locus_tag="G9W35_RS26095"
                     /old_locus_tag="G9W35_25990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011264161.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin K immunity protein"
                     /protein_id="WP_011264161.1"
                     /translation="MHLKYYLHNLPESLIPWILILIFNDNDNTPLLFIFISSIHVLLYP
                     YSKLTISRYIKENTKLKKEPWYLCKLSALFYLLMAIPVGLPSFIYYTLKRN"
                     /name="cki"
     gene            complement(706..2178)
                     /locus_tag="G9W35_RS26100"
                     /old_locus_tag="G9W35_25995"
     CDS             complement(706..2178)
                     /locus_tag="G9W35_RS26100"
                     /old_locus_tag="G9W35_25995"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_159421185.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_function="GO:0140911 - pore-forming activity [Evidence
                     IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA];
                     GO:0050829 - defense response to Gram-negative bacterium
                     [Evidence IEA]; GO:0031640 - killing of cells of another
                     organism [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like pore-forming protein"
                     /protein_id="WP_221522800.1"
                     /translation="MDKVTDNSPDVESTESTEGSFPTVGVDTGDTITATLATGTENVGG
                     GGGAFGGASESSAAIHATAKWSTAQLKKHQTEQAARAAAAEAALAKAKSQRDALTQRLK
                     DIVNDALRANAARSPSVTDLAHANNMAMQAEAERLRLAKAEQKAREEAEAAEKALREAE
                     RQRDEIARQQAETAHLLAMAEAAEAEKNRQDSLDEEHRAVEVAEKKLAEAKAELAKAES
                     DVQSKQAIVSRVAGELENAQKSVDVKVTGFPGWRDVQKKLERQLQDKKNEYSSVTNALN
                     SAVSIRDAKKTDVQNAEIKLKEAKDALEKSQVKDSVDTMVGFYQYITEQYGEKYSRIAQ
                     DLAEKAKGSKFSSVDEALAAFEKYKNVLDKKISKVDRDAIFNALESVNYDELSKNLTKI
                     SKSLKITSRVSFLYDVGSDFKNAIETGNWRPLFVTLEKSAVDVGVAKIVALMFSFIVGV
                     PLGFWGIAIVTGIVSSYIGDDELNKLNELLGI"
                     /name="colicin-like pore-forming protein"
     gene            2423..2713
                     /locus_tag="G9W35_RS26105"
                     /old_locus_tag="G9W35_26000"
     CDS             2423..2713
                     /locus_tag="G9W35_RS26105"
                     /old_locus_tag="G9W35_26000"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001672407.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000047032.1"
                     /translation="MSKSPRHKLNKTDKRLLDTLVAAGYEHDKARDLIQKQVYTLTLAD
                     QRHVVSEISNGVNPTQAYSAVYQARRIRLARKYLNGKKVMEETGENTPPSA"
                     /name="hypothetical protein"
     gene            complement(2705..2983)
                     /locus_tag="G9W35_RS26110"
                     /old_locus_tag="G9W35_26005"
     CDS             complement(2705..2983)
                     /locus_tag="G9W35_RS26110"
                     /old_locus_tag="G9W35_26005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000710672.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000710675.1"
                     /translation="MKKCVPVLLFSVLSASVASHADSNVFQQKAEKTKNGIVADVNARQ
                     KMFSNRLKIQLQIDELRAELAGTRDAQKREDLRKKLESLERQKKSLR"
                     /name="hypothetical protein"
     gene            3105..3527
                     /locus_tag="G9W35_RS26115"
                     /old_locus_tag="G9W35_26010"
     CDS             3105..3527
                     /locus_tag="G9W35_RS26115"
                     /old_locus_tag="G9W35_26010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001255518.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="WP_021539380.1"
                     /translation="MRSAAARLLLIPLITATIALTGCTPKTSLERHTRHYVYASDDGFD
                     PNFYTQKADTIRMMLPFFQQFRDMGMKDKAAGVSAETAQQRVKEFHSEKFFHSLRSTTT
                     FAGRKYTNSDMPSPKKMKLMADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            complement(3751..4074)
                     /gene="mobA"
                     /locus_tag="G9W35_RS26120"
                     /old_locus_tag="G9W35_26015"
     CDS             complement(3751..4074)
                     /gene="mobA"
                     /locus_tag="G9W35_RS26120"
                     /old_locus_tag="G9W35_26015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            4358..4552
                     /locus_tag="G9W35_RS26125"
                     /old_locus_tag="G9W35_26020"
     CDS             4358..4552
                     /locus_tag="G9W35_RS26125"
                     /old_locus_tag="G9W35_26020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041639.1"
                     /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_001041621.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
                     EELQNSIQTRFEVENSTER"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(4084..4323)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          4582..5111
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.776"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(3755..4074)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="3.11e-62"
ORIGIN
        1 ttaacgccac tggcagcagc cattggtaac tggatagtgg atttagatac gcagaactct
       61 tgaagttgaa gccttatagc ggctacactg gaaggacagc atttggtatc tgtgctccac
      121 taaagccagt tacccggtta agcagtcccc aactgactta accttcgact aaaccgcctc
      181 cccaggcggt tttttcgttt acaggcagca gattacgcgc agaaaaaaag gatctcaaga
      241 agatcctttg atcttttcta ctgaaccgcg atccccgtca gttcagaaga cgaagatggt
      301 gcaacggttc ctccttgcac atcacgaata tagtttgctt gacatcctga caagaataat
      361 attgtaatta gaaaaattat tattttcata tttctttcca acaaaagtaa aaatacttat
      421 gcatttaaaa tactacctac ataatttacc tgaatcactt ataccatgga ttcttatttt
      481 aatatttaac gacaatgata acactccttt gttatttata tttatatcat caatacatgt
      541 attgctatat ccatactcta aattaaccat atctagatat atcaaagaaa atacaaagtt
      601 aaaaaaagaa ccctggtact tatgcaagtt atctgcattg ttttatttat taatggcaat
      661 cccagtagga ttgccaagtt tcatatatta cactctaaag agaaattaaa tccctaacaa
      721 ctcattaagt ttgttcaact catcatcccc tatgtaagaa gaaacaatac ctgtgacaat
      781 tgcaatcccc cagaaaccaa gaggcacacc aacaataaaa ctaaacatta atgccacaat
      841 ttttgccaca cctacatcga ccgcactttt ctccagcgtg acaaacaaag gtcgccagtt
      901 accagtttct attgcatttt taaaatcaga accaacatca tatagaaaag atactcgact
      961 agtgatttta agcgactttg atatcttcgt taaattctta gataactcat cataattaac
     1021 agactctaac gcattaaaaa tagcatcccg atcaacctta ctgattttct tatccagtac
     1081 atttttatac ttttcaaatg cagcaagagc ttcatcaaca ctactaaatt tactaccctt
     1141 cgccttttca gctaaatcct gagctattct ggaatatttt tccccatatt gttcggttat
     1201 atattgataa aacccaacca tagtatcaac agagtctttt acctgactct tctcaagagc
     1261 atccttagct tcttttaatt ttatctcagc attctgaaca tctgtttttt tagcatctct
     1321 aatgctaacc gcagaattaa gagcattcgt cactgacgaa tattcattct tcttatcctg
     1381 caattgtctc tccagttttt tctgaacatc acgccatcca ggaaatccag taaccttcac
     1441 atcaacactt ttttgagcgt tttcaagctc ccctgcaact ctggaaacaa tcgcttgctt
     1501 actctgtaca tcgctttcgg ccttcgccag ttcagcttta gcctcagcca gcttcttctc
     1561 tgccacttcc acagcccgat gctcttcatc aagagaatcc tgtcgatttt tctcagcctc
     1621 tgctgcctcc gccattgcta acaaatgcgc ggtttcagcc tgttggcggg caatctcatc
     1681 acgttggcgt tctgcttccc ggagcgcttt ttctgctgct tcagcttctt cacgggcttt
     1741 ttgctctgcc ttcgcaaggc gcaaacgctc agcctctgcc tgcattgcca tattattggc
     1801 atgagcaagg tcagttactg atggactacg agcggcatta gcacgtaaag cgtcattaac
     1861 aatatccttg agacgttgag tcagggcatc acgctgagat ttcgcttttg ccaatgctgc
     1921 ctcagccgca gcagcacggg cagcctgttc agtctgatgt tttttcaact gcgcggtaga
     1981 ccatttagcg gttgcatgta tcgcagcaga actttcactg gccccaccaa atgctccacc
     2041 gcctccacca acattttcag ttccagttgc aagcgtcgct gtaatcgtat cgccagtatc
     2101 aaccccaaca gttgggaatg acccctcagt agattctgtg ctctccacat ctggagaatt
     2161 atcagtgact ttatccataa agaaattcct ctttgataat taaaacaata aattaaaaac
     2221 aacatactgt acatataacc actggtttta tgtacagcaa aaacctacta ctcagcattg
     2281 tccatgtcaa gagcatggat tttcattttt gcaataagga tcacactatg gggaggcagg
     2341 cattgagaac gtcgaaacag aacaccggag caaatcagga tgagatataa aactgttgga
     2401 tcatgaaaaa acggagaacg atgtgagcaa atcaccccgc cataaactga acaaaacaga
     2461 caaacgactt ctcgacaccc ttgttgctgc cggatatgag catgacaaag cccgtgacct
     2521 catccagaaa caggtttaca cgctgacact ggcagatcag cgtcatgtgg tcagtgaaat
     2581 cagtaatggt gtgaatccca cccaggctta ctcggcggta taccaggcaa gacgcattcg
     2641 cctcgcccgt aaatatctga acggtaaaaa ggttatggaa gaaaccgggg aaaatacgcc
     2701 cccatcagcg taaggatttc ttttgccgct ccagagactc cagtttttta cgcaaatcct
     2761 ctcttttttg ggcatctctg gtgccagcca gctctgctct caactcatcg atctgaagtt
     2821 gtatcttcag tctgttactg aacattttct gtctggcatt aacatccgca acaatgccgt
     2881 tttttgtctt ctcggccttt tgttgaaaaa cattgctgtc cgcatgactg gcaaccgaag
     2941 cagaaagaac actaaaaagc aggactggca cacatttttt cacgggatta ttcctgactc
     3001 attgaccatc aaatcacatt gggagtaaac cgacgtatga taagagatac tcttcggaga
     3061 tataactccc tgagtatcaa gattaaaaac gcaaggagat gtttatgaga tctgccgctg
     3121 ccaggctgct tctgatacct ctgataacag caacaatagc tcttacagga tgcacaccaa
     3181 agaccagcct ggaacgacat acccggcatt atgtttatgc ttcagatgat ggatttgatc
     3241 ctaacttcta cacccagaaa gcagacacca tacgtatgat gctcccgttc tttcagcagt
     3301 tccgggatat ggggatgaaa gacaaagcag ccggagtatc agcagaaacg gcacagcaac
     3361 gtgtaaaaga attccactca gaaaaatttt ttcactcact ccggagcaca acaacctttg
     3421 ctggcagaaa atacacaaac agcgatatgc cttcgccgaa aaaaatgaaa ctaatggcag
     3481 acaccatttc tgcggtttat ctcgatggat acgagggcag acagtaaggg atttaccata
     3541 atcccttaat tgtacgcacc actgaaacgc gctgaacgcg attctgacgc agacaccgca
     3601 aaaagagatg ttttaccccg gaaaaacagg aaggatgcgt caggatcgtt ttcagctcgc
     3661 tgcatagcta tgcatgaaag cgaatggtga tcactttggg agcttacggt gttcataccg
     3721 tcagttttcg acagttttct ctccgggaag ctaatctgcc ataagcctgg ataacagggc
     3781 acggtgatac tccgtaatag cgatcagcac ctccgcatac tccctgtccc cgacacgctt
     3841 gccgtcgata aagagttttt tctgtaacgc ccccagtctc ataacttctt tcagtacccg
     3901 atcatcagtc agtgagttaa ctttcttacc gagagctgcc gcccgtaaaa aaccggaaac
     3961 ggtcttgccg cattcagcag ccctttttct gatttcctgg tcttcttctg ccgtcagacg
     4021 aacagggcga ctgatagccc gcctgcgcgt attacttcca cttcgttttg tcataaaaca
     4081 tggctccgta tctgacatgg gtgtcggggc aaagccctga ccagggtaat tgtaatagcg
     4141 tgcatgtatg cgcggtataa caattacaca tcctgtcctg tcagcaagtt cgaattaccg
     4201 acaaaggcac ggcagttttt tggcagtgac agtattgtca ggcagaaata cccgtcaaag
     4261 cgtcagacgg cagaataccg gcggtaaaac agtcgaaaag tggtacgcga tataatcaca
     4321 caacgcagat gacagacaga acggagaaaa cgaaaagatg aacaagcagc agcaagccgt
     4381 actcaacatg gcaggattca taaaaagcca aagcctgacg ctgctcgaaa agctggacgc
     4441 cctcgatgct gacgaacagg ctaccatgtg tgagaagctg cacgaactcg cagaagaact
     4501 ccagaacagc atccagacac gctttgaagt agaaaatagc acagagagat aacgctcagg
     4561 acaggatgcc gaacggcaca acagagcgta aggagaaaat gtcacataag gcgctcttcc
     4621 gcttcctcgc tcactgactc gctacgctcg gacgttcgac tgcggcgagc ggtgtcagct
     4681 cactcaaaag cagtaatacg gttatccaca gaatcagggg ataaagccgg aaagaacatg
     4741 tgagcaaaaa gcaaagcacc ggaagaagcc agcgccgcag gcgtttttcc ataggctccg
     4801 cccccctgac gagcatcaca aaaatcgacg ctcaagccag aggtggcgaa acccgacagg
     4861 actataaaga taccaggcgt ttccccctgg aagctccctc gtgcgctctc ctgttccgac
     4921 cctgccgctt accggatacc tgtccgcctt tctcccttcg ggaagcgtgg cgctttctca
     4981 tagctcacgc tgttggtatc tcagttcggt gtaggtcgtt cgctccaagc tgggctgtgt
     5041 gcacgaaccc cccgttcagc ccgaccgctg cgccttatcc ggtaactatc gtcttgagtc
     5101 caacccggta agacacgac
//
