LOCUS       NZ_CP107160             1552 bp    DNA     circular CON 14-AUG-2023
DEFINITION  Escherichia coli strain R11 plasmid pR11-698-5, complete sequence.
ACCESSION   NZ_CP107160
VERSION     NZ_CP107160.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31158871
            Assembly: GCF_030707895.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1552)
  AUTHORS   Jaen-Luchoro,D., Kahnamouei,A., Yazdanshenas,S., Lindblom,A.,
            Samuelsson,E., Ahren,C. and Karami,N.
  TITLE     Comparative Genomic Analysis of ST131 Subclade C2 of ESBL-Producing
            E. coli Isolates from Patients with Recurrent and Sporadic Urinary
            Tract Infections
  JOURNAL   Microorganisms 11 (7), 1622 (2023)
   PUBMED   37512795
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1552)
  AUTHORS   Jaen-Luchoro,D., Kahnamouei,A., Yazdanshenas,S., Lindblom,A.,
            Samuelsson,E., Ahren,C. and Karami,N.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-OCT-2022) Infectious Diseases, University of
            Gothenburg - CCUG, Guldhedsgatan 10a, Box 7193, Gothenburg, Vastra
            Gotaland 40234, Sweden
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 392x
            Sequencing Technology :: Illumina NovaSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/11/2023 07:50:53
            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)                     :: 5,294
            CDSs (total)                      :: 5,181
            Genes (coding)                    :: 4,975
            CDSs (with protein)               :: 4,975
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 206
            CDSs (without protein)            :: 206
            Pseudo Genes (ambiguous residues) :: 0 of 206
            Pseudo Genes (frameshifted)       :: 71 of 206
            Pseudo Genes (incomplete)         :: 151 of 206
            Pseudo Genes (internal stop)      :: 38 of 206
            Pseudo Genes (multiple problems)  :: 48 of 206
            Pseudo Genes (short protein)      :: 3 of 206
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP107160.1.
            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..1552
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="R11"
                     /isolation_source="human"
                     /db_xref="taxon:562"
                     /plasmid="pR11-698-5"
                     /geo_loc_name="Sweden: Gothenburg"
                     /collection_date="2018"
     gene            1..477
                     /locus_tag="OGM40_RS26460"
                     /old_locus_tag="OGM40_26430"
     CDS             1..477
                     /locus_tag="OGM40_RS26460"
                     /old_locus_tag="OGM40_26430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /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_000469298.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     Typing          complement(1367..1475)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="90.909"
                     /coverage="100.0"
                     /evalue="9.29e-34"
     Typing          complement(709..969)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.748"
                     /coverage="100.0"
                     /evalue="8.56e-103"
ORIGIN
        1 atgtttattg attcagaaaa acgactgaaa caactttcag atgaggcaaa gaaaaacacc
       61 gaggatctcg aagaagcaaa gaaaaattca aggtttacac aggtatctcc aaaaggttgg
      121 gagcgcgttc gagagctgct gaaggatagc caaggcatat cagcactgaa gctgtactca
      181 tttttagcgg agcatatcga tccgacatgt ggcgctgtcg ttgcggatca gcaattctta
      241 gctgaaaaac ttggagttag cagaagcaca attattcgtt ggctcaatta cttagaatca
      301 aaaaacgcat tagttagaat ccctgttgct ggtaaggtat gtgcgtatgc cctcgatcca
      361 catgaagtct ggaagggata caacaccacg aaaaaccatg cagcgtttgt cactaaaaca
      421 ctggttaaca aagacggtga tattcagcgc cgaatcatgg ccatgttttc aaattgagcc
      481 agcggcaggc ggacaatcca cagaacattg catgcaattt ctagtggatt gtctatcctg
      541 cattgctctt ttgccgacct caaaacccct cgcgtgtttt tgtttcccga tctccagaac
      601 gaccgcgctg ccacggttcc ggcagcgcct tgagcgcaac cggaaaccgt ctggggagaa
      661 ccccagaccc ccatcgctgt aacatcgacg gtctacgacc acctaccaac cgcgtggctg
      721 cctattccgt gcaaatgggc tttgcagggg gctgacgcgg ttcctggcga cctgaaagcc
      781 cctggttagg ggtatcggcg cgcctgacct cctaaaaccc tctgtaagcg tttttcgcgc
      841 cttccatgcc ctgacgggca tttaaaaccc gtttcgtgcg tctgagagct tctgagagcg
      901 tttgaagagc tatctggcga ctcatccccg aaagaacaac agcggaatca ccgataacat
      961 gcgagaggtg gcaccgctcg ccgcagcccc agcgaccgaa cgttagtgag cgagtgggcg
     1021 aggaagcgga agagaaccgg aaaccacatt gagcacgtac gcactgatgc ggggtgtcgg
     1081 ggtgaaactc tgaccagatg gcaaacggaa tatcgtcgcg ggtgacggta ttacatttgc
     1141 acatcctgtc ccgatttctg cggagtttaa cggtgaacgg acggcaaaaa acgtgcagga
     1201 gctgttgaac gtgaaaacca cgaaatctgg caaaaatcac agctgacgag gcttgcagaa
     1261 gagtaagcca gtatacactc cgctatcgct acgtgactgg gtcagggctt cgccccgaca
     1321 cccctaaagg gtgttgcgtg gcccgcaaca cccttgccta gaatagatct tttgcggcga
     1381 tttgtaagcc attgtttttt tagagtgttt tttatttacc tgtcgcatgc agggtgacac
     1441 aacgttgtcg catcctgtat gcgacaacat gcaacaaggt gttgcatgga tgtgtcatga
     1501 tggtttagat ttgagccaac gttagtgcat gggattttca gagggaaaaa tc
//
