LOCUS       NZ_CP107171             1822 bp    DNA     circular CON 14-AUG-2023
DEFINITION  Escherichia coli strain R9 plasmid pR9-658-7, complete sequence.
ACCESSION   NZ_CP107171
VERSION     NZ_CP107171.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31158869
            Assembly: GCF_030707935.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1822)
  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 1822)
  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                   :: 338x
            Sequencing Technology :: Illumina NovaSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/11/2023 07:51:19
            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)                     :: 5,176
            CDSs (total)                      :: 5,061
            Genes (coding)                    :: 4,871
            CDSs (with protein)               :: 4,871
            Genes (RNA)                       :: 115
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 190
            CDSs (without protein)            :: 190
            Pseudo Genes (ambiguous residues) :: 0 of 190
            Pseudo Genes (frameshifted)       :: 69 of 190
            Pseudo Genes (incomplete)         :: 138 of 190
            Pseudo Genes (internal stop)      :: 38 of 190
            Pseudo Genes (multiple problems)  :: 49 of 190
            Pseudo Genes (short protein)      :: 3 of 190
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP107171.1.
            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..1822
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="R9"
                     /isolation_source="human"
                     /db_xref="taxon:562"
                     /plasmid="pR9-658-7"
                     /geo_loc_name="Sweden: Gothenburg"
                     /collection_date="2018"
     gene            complement(join(1602..1822,1..67))
                     /locus_tag="OGM38_RS25875"
                     /old_locus_tag="OGM38_25845"
     CDS             complement(join(1602..1822,1..67))
                     /locus_tag="OGM38_RS25875"
                     /old_locus_tag="OGM38_25845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001220925.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023909281.1"
                     /translation="MRIKYESRWKLEELKLEICRSIDSLIDEYHIEYAMGINLYMNCED
                     KEFNPVDIVNEDGKNIMFVVSNNEKIQKPKKSAKKKIPAPVIELDKYRKK"
                     /name="hypothetical protein"
     gene            complement(80..613)
                     /locus_tag="OGM38_RS25880"
                     /old_locus_tag="OGM38_25850"
     CDS             complement(80..613)
                     /locus_tag="OGM38_RS25880"
                     /old_locus_tag="OGM38_25850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000893324.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_305773599.1"
                     /translation="MLERQFEDFEQQKRRDHQAQDQSKSAKQKRDRLNPPDWSQVTKAG
                     WNMLDSISEKVPRAFRLYSFFAQNIDKSCGAVVCDQKFLADYFGVSLRTIQYWIGDLES
                     IGAIVKIPVGIYYAYALDPYQVWRGYNKSKKYAAFNAKTLTQKDGVIDRKLRLMLSRRE
                     EFEGSLKTSNHDLD"
                     /name="replication/maintenance protein RepL"
     Typing          1100..1351
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.885"
                     /coverage="97.0"
                     /evalue="1.85e-99"
ORIGIN
        1 ctattgatct acatatttct aattttagtt cttctaattt ccaacgtgat tcatatttaa
       61 ttctcatagc gcatcatacc tagtccaagt catgattaga tgtcttaagc gagccttcaa
      121 actcttctct cctagagagc atgagccgca acttgcgatc aataacgcca tctttttgag
      181 ttaatgtttt tgcgttaaac gctgcatatt ttttagattt attatatccg cgccatacct
      241 gatacggatc taacgcataa gcataataga tacctactgg tattttcacg atggcaccaa
      301 tactttctaa atctccaatc caatattgga tcgtccttaa actaacaccg aaataatcag
      361 ctaagaattt ttggtcacat acaacagccc cacacgattt atctatattt tgagcaaaaa
      421 aagaatatag cctaaatgct ctgggaacct tctcagatat agagtccaac atattccagc
      481 ccgccttagt aacctgcgac cagtcaggtg gattcaaccg atctcgtttt tgcttagcac
      541 ttttggattg atcttgtgcc tgatgatctc gccgtttttg ctgttcgaaa tcttcaaatt
      601 gccgttccag catacttgca tccttacctg caacgttgtt tcgtacctta cgaaatttat
      661 atcgtacatt acgaaacaac acacgcaaac atgtttgcgt atacacatgc aaataacgtt
      721 tcgtatgttg gtgtcataat gctttgattt ttaagagaat gtcgattttt gctctaaaga
      781 tctatcaaag cacttttttg ctacacaaga tttaattagt tcatcgaaca tttggggtgt
      841 cggggcgaag ccctgaccca gtcacgtagc gatagcggag tgtatactgg cttactcttc
      901 tgcaagcctc gtcagccgtg attttgcccg atttcgcgct ctccacgttc aacagctcga
      961 tcatgttttt gcagtccgtt caccgctaaa acgccccgca tcagtgcgta cgtgctcaat
     1021 gtggtttccg gttctcttcc gcttcctcgc ccactcgctc actaacgttc ggtcgctggg
     1081 gctgcggcga gcggtgccac ctctcgcatg ttatcggtga ttccgctgtt gttctttcgg
     1141 ggatgagtcg ccagatagct cttcaaacgc tctcagaagc tctcagacgc acgaaacggg
     1201 ttttaaatgc ccatcagggc atggaaggcg cgaaaaacgc ttacagaggg ttttaggagg
     1261 tcaggcgcgc cgatacccct aaccagggga tttcaggtcg ccaggaaccg cgtcagcccc
     1321 ctgcaaagcc catttgcacg gaataggcag ccacgcggtt ggtaggtggt cgtagaccgt
     1381 cgatgttaca gcgatggggg tctggggttc tccccagacg gtttccggtt gcgctcaagg
     1441 cgctgccgga accgtggcgg ctcggtcgtt ctggaaaacg gggagcaaaa agacgcaagg
     1501 gattttgagg cggcaaaaga gcaatgcagg atagacaatc aactagaaat tgcatgcaat
     1561 gttctgtgga ttgtccgcct gccgctggct ctgtatggcc atcacttttt ccgatattta
     1621 tctaactcaa ttacaggtgc aggaattttt ttcttcgcac ttttttttgg tttttgtatt
     1681 ttttcattgt tgctaacaac aaacataata ttctttccat cttcattgac aatatcaacg
     1741 ggattaaact ccttatcttc acaattcata tatagattta ttcccattgc atattcgata
     1801 tgatattcat caattaacga at
//
