LOCUS       NZ_CP049850             5631 bp    DNA     circular CON 14-JUN-2024
DEFINITION  Escherichia coli strain UPEC-245U/190328 plasmid pEcoUTI1b, complete
            sequence.
ACCESSION   NZ_CP049850
VERSION     NZ_CP049850.1
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 5631)
  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  JOURNAL   Unpublished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 5631)
  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
            CP049850.1.
            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..5631
                     /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="pEcoUTI1b"
                     /geo_loc_name="Mexico: Mexico City"
                     /collection_date="2019-03-28"
                     /collected_by="Hospital Militar de Especialidades de la
                     mujer y neonatologia"
     gene            join(5096..5631,1..517)
                     /locus_tag="G9W35_RS26055"
                     /old_locus_tag="G9W35_25945"
     CDS             join(5096..5631,1..517)
                     /locus_tag="G9W35_RS26055"
                     /old_locus_tag="G9W35_25945"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_042011821.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPRGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            519..1385
                     /locus_tag="G9W35_RS26060"
                     /old_locus_tag="G9W35_25950"
     CDS             519..1385
                     /locus_tag="G9W35_RS26060"
                     /old_locus_tag="G9W35_25950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     gene            complement(2588..2779)
                     /locus_tag="G9W35_RS26065"
                     /old_locus_tag="G9W35_25955"
     CDS             complement(2588..2779)
                     /locus_tag="G9W35_RS26065"
                     /old_locus_tag="G9W35_25955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /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_000165975.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2844..3167
                     /locus_tag="G9W35_RS26070"
                     /old_locus_tag="G9W35_25960"
     CDS             2844..3167
                     /locus_tag="G9W35_RS26070"
                     /old_locus_tag="G9W35_25960"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3376..>3807
                     /locus_tag="G9W35_RS26075"
                     /pseudo=""
     CDS             3376..>3807
                     /locus_tag="G9W35_RS26075"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            3845..4375
                     /locus_tag="G9W35_RS26080"
                     /old_locus_tag="G9W35_25970"
     CDS             3845..4375
                     /locus_tag="G9W35_RS26080"
                     /old_locus_tag="G9W35_25970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_001673158.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            4382..4615
                     /locus_tag="G9W35_RS26085"
                     /old_locus_tag="G9W35_25975"
     CDS             4382..4615
                     /locus_tag="G9W35_RS26085"
                     /old_locus_tag="G9W35_25975"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          2413..2494
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          1769..1956
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          3158..4719
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aagaaatcat gatagaagaa taccaagggg aatacttatt tctgtaaatg ccccggggca
       61 ttttatgagg ctggcgatag aaaaaggttt ctataaagat caagaacaag cgttagcgga
      121 tattcgtaac atgactattc agtctgttgg taagggtggg tattcacatc cggaagggat
      181 ttctacaaca tggcattcag aatctaattt ggatcgtttt ggatgcccag tgcacaccgg
      241 taatagttct tattacagcg gtttttatca tactgatgta ttaattccag gagaattaac
      301 taaggatgaa agattgctcc atgaaataga aaatagtgat ccaatgatct tcaactggaa
      361 tgtattgttt tatgtttcat tagaagagtt tcctatagat gatccttatt atggagagtt
      421 tattggtatt cctgtagatg atgcatctat gttttttaac tcctttcaac caaggaaatt
      481 tgaaaacaaa cccctttatg agaaagagga tgattaatat gattaaagga atgctttttg
      541 cttttttagc agcgttctca tggggggcag ctatcgtaat gagcaaaaaa ggagttgaag
      601 aactagatgc cggaggggtg tttttctggc agatttgtag tgcagtaata ctatcttgga
      661 tagttctttt tataaaaaga aaaaaactcc cattaaactc aaaagcgata cttgcttatg
      721 cgacaggcgt ttttgaacca ttcttagcgt atacttttac actctacgga ctttatttta
      781 tttcagcagg aagcgcatca attatttttt cacttgaatc agtgtttata ttggtgttgt
      841 ctgttcttat ttgctcagtt aaaattaatt ccccgcaata ttttatattg ttccttatag
      901 gtgcaattgt tggcagtatt ttggtagcct tgccagacat cagtaatgga tcgaataata
      961 ttgttggata ttgtcttgtt gttgccggtg tgttatcggc agcattttat gttgttatat
     1021 cgtctcgcct tattaaatcg tttgagccta tcacattatt gagcggacag ttgacattct
     1081 cccttatact gtcatcgctc tttattttta tatctaaatc atcaatttat cttccgttgg
     1141 aatccgtgat tattgttttt tcatctggaa tattacaata ttttttagct ttttgttttt
     1201 acttgaactc cttgcgttgg ctcccagttc atttggcagg gataatgttg tactttattc
     1261 cgctagttgc attatttttg tcatggttgt ttttggatga acaattcaca ttcttacagg
     1321 gggtaggatt tattgtaact gtgctaagtg tatattttct taacagaaaa tactcagagg
     1381 agtaacattc tgttcaggat tgccccccgg cctccatcga taccgtgcca aatgcacgta
     1441 aaaaacggga gcgtttctgg tgtcggaatg taaccaaggg ggtcagaggc gcgctaaaac
     1501 gctctcaggg gagtcaaata gagacgtttg taacaaaaag atcaaaggat cctcttgaga
     1561 tccttttttt ctgcgcgtaa tctgctgcct gtaaacgaaa aaaccgcctt gcagggcggt
     1621 ttgatcgaag gttaagtcag cttgcagact gcttaaccag gtaactgtct tatgcgagac
     1681 gagtcaccaa aattgttctt ctagtgtagc cgcactccgg cagccacttc aagtactctc
     1741 taaatatctc gcacatgact tttaccaatg gctgctgcca gtggcgcttt gtggtgtctt
     1801 ttccgggttg gacccaagag aacagttacc ggagaaggcg cagcagtcgg gctgaacggg
     1861 gggttcctgc atacagccca gcccggagcg aactgcctaa gtcgccccga gataccagaa
     1921 gacgtgagct atgagaaagc gccacgtgtc ccgtaaggga gaaaggcgga aaaggtatcc
     1981 ggtaatcgat atggcgggaa cgtgggggcg caggagggag cgattcaccg gaaacggtga
     2041 tgatctttaa gccacgtcgg gtttcgccac cgctggcgga tttcatggtt gagccgcaag
     2101 gctcccacag atgcaccgaa aaagtgtctg ttttgtgaag tccgtcaggg gggcggagcc
     2161 tatggaaaaa gcgcctccgg cgcggccttt cccggggttt cgttttttgc gcacatgttc
     2221 tttcctggtt tatccccggg ttctgtggat aacagggtta gcgtttttga gaaaggagag
     2281 tccgctcgcc gcagccgaac gaccgagcgt agcgagtcag tgagcgagga agcggaagag
     2341 cgcctgaact ggcattttct ccttacgcat ctgtgcggca tttcacaccg gacatggcgc
     2401 acttttcata caatccgcac tgatgccgaa tggttaagcc agtatacact ccgctatcgc
     2461 tacgtgactg ggtcagggct tcgccccgac accccaaagg tcaacggcct gacgcgccct
     2521 ggcgggcttg tctgctcccg gcatccgctc acagacaagc tgtgaccgtc tccgggagct
     2581 gcatgtgtca gcggttttca ccgtcatccc cgaagcgtgc gaggcaactg cggtaaagct
     2641 catcggcgtg gtcgtgaagc gattcacaga tgtctgcctg ttcatccgcg tccagttcgt
     2701 tgagcttctc cagcagcgtt aatgtctggc ctctgatgaa gcgggccatg ttaagggcgg
     2761 ttttttcctg tttggtcact gatgcctccg tgtaaggggg ggttctgttc atgggggtaa
     2821 tgataccgat gaaacgcgag aggatgctca cgatacgggt tactgatgat gaacatgccc
     2881 ggttactgga acgctgtgag ggtaaacaac tggcggtatg gatgcggcgg gtctgcctgg
     2941 gtgagccggt tgcccgttcc gggaagctgc cgacactggc accgccgtta ctgcgtcagc
     3001 tggccgccat cgggaataac cttaaccaga cagcgaggaa ggtgaacagc gggcagtggt
     3061 cttccggtga ccgggttcag gtggtggccg cactgatggc catcggggat gagctgcgcc
     3121 ggctgcgtct ggcggtcagg gaacaggggg cgcgggatga tagttaagtt tcatgccagg
     3181 ggaaaaggtg gtggcagtgg tccggttgat tacctgctgg gaagggagcg taaccgggaa
     3241 ggggcaacgg tgcttcaggg gaatccggaa gaggtccggg aactcatcga tgccacgcca
     3301 tttgcgaaga aatacacgtc aggtgttctg tcgttcgcgg agaaggagct gccgcctgga
     3361 gggcgtgaaa aagtgatggc gagctttgag cgtgtactga tgcccggtct cgagaaaaat
     3421 cagtacagca tcctgtgggt ggagcaccag gacaagggac ggcttgagct gaattttgtc
     3481 attccgaaca tggagctaca gaccggaaaa cgcctccagc cgtactacga ccgggcagac
     3541 aggccgagaa ttgatgcctg gcagacgctg gtgaatcacc attacggtct gcatgacccc
     3601 aacgccccgg agaaccgccg gacgctgacc cttcctgata acctgccgga aacgaaacag
     3661 gcgcttgctg agggcgtcac acgcgggata gacgcgcttt accatgccgg agagataaaa
     3721 ggccgtcagg atgtgattca ggcgctcaca gaggcggggc ttgaagtggt cagggtgacg
     3781 cgaagcagta tcagcattgc agacccgaac ggcgggagga atatcagact gaaaggagcg
     3841 ttttatgagc aatcttttac agacgggcgc ggagttcgag aaaaagctga aagagagagc
     3901 cgaatctaca gagaaaatgc tgaacgacga gttcaggaag ctcgaagaat ctgtaaacag
     3961 ggaactgacc tcaaacgaat ctttaatcag gaacgctatc aacgaccata caacagccct
     4021 gaaagaactg ctggagaggt atcagaaaac gaccgtcgat acgatggacg cgcactggaa
     4081 aaccgtactg aaaatgagcg tgaaacgctg gctgtggctg attatcgtct cagtactgat
     4141 gtttgccacg accgggagtc tgctgtggta ccagggcatg aagataaacg cgaatatgaa
     4201 tattctccgc gagcagaaag agagtctgga gaagctgaac gcgaagacat ggggcgtgcg
     4261 ttatcacgag gacagcaacg gacgttttct ggtgttgccg aaggggatga aagccgaaac
     4321 gaactggacg aaggacaacg gcaaactgaa cgcagtgaga ctggtgcagg agtgacagag
     4381 catgacggag ctggaaagac atttgctgaa cgcattagag caactgcaac aggactatat
     4441 gcagcggctg aacgaatggg agaacgcctt cgtggaattg cagaaaatgt tttcgcttac
     4501 gcaacgggac aacgcgatgc tgaacgggcg agtcatgcag ttgagtcagc aggtgcagca
     4561 cttgagcgag cggacagaac gcttgagcca gttatacagc gagaacagga gataagggat
     4621 gaacggctga tgcaggaacg cgaacatgag ttatctctgg agcgggagcg tcagccggaa
     4681 atccaggagc ggacactgga tggcccttcg ctgggatggt gaaaccatga aaaatgacgt
     4741 gttcagtgga ttaaggcggg ctaatgtggc ctgtagcatc tggttgcata ggtattcatg
     4801 cggttaaaat ttatcaggtg cgatcgcggc agtttttcgg gtggtttgtt gccattttta
     4861 cctgtctgct gccgtgatcg caccgaacgc gttttggcgg tgcgtacaat gcgacgttat
     4921 ggtaaatgga gcggattttc aggaaggagt gatactaaca actcgaacac tgtgcaaata
     4981 atgatttttt taaaatatcg gtaacgataa taaattattt cgttttacgc cggtaataaa
     5041 tataatgtag tttcagtata taaaaaaata tatgaggtgt cttgtgggag ctttcatgaa
     5101 tcttcaacaa cgtataaata aactaccaca attatcatcc agtttttcat ttggaaaaga
     5161 tattgataat attcattcat ttatctttaa cgaaacttct aaagataaaa ttgaagattt
     5221 actaagaaaa tgggtgtcag gcaatcagcc ctgtgtattt ggtaaattgg caagcaagaa
     5281 aattaaaggg cttgatttcc atttatctat tgtaaatagc ccccaactat ataatgatga
     5341 tggtcatttg tttgattttt tgcgtaatga aagagttcgt tttaaagaac gcgcaagaag
     5401 aggagaggtc agtgcgcatc tcatttattt tattcatcca caacttgcct ttgctcgtcc
     5461 atcagaagag ttagtggaca tacaaaaata tatttgttcg ctgcatatgc cagagtgcta
     5521 tccaataaaa gaggatgtta tttatactga aagcgtacca tttcaggata aagatgggct
     5581 aaaaatatat aaggctggtg ttaatgtttt ttactcttct gctcatagaa c
//
