LOCUS       NZ_CP107125             1822 bp    DNA     circular CON 14-AUG-2023
DEFINITION  Escherichia coli strain S9 plasmid pS9-S4K58-3, complete sequence.
ACCESSION   NZ_CP107125
VERSION     NZ_CP107125.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31158882
            Assembly: GCF_030708195.1
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                   :: 436x
            Sequencing Technology :: Illumina NovaSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/11/2023 07:55:03
            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)                     :: 5,189
            CDSs (total)                      :: 5,077
            Genes (coding)                    :: 4,855
            CDSs (with protein)               :: 4,855
            Genes (RNA)                       :: 112
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 222
            CDSs (without protein)            :: 222
            Pseudo Genes (ambiguous residues) :: 0 of 222
            Pseudo Genes (frameshifted)       :: 79 of 222
            Pseudo Genes (incomplete)         :: 169 of 222
            Pseudo Genes (internal stop)      :: 35 of 222
            Pseudo Genes (multiple problems)  :: 53 of 222
            Pseudo Genes (short protein)      :: 3 of 222
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP107125.1.
            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="S9"
                     /isolation_source="human"
                     /db_xref="taxon:562"
                     /plasmid="pS9-S4K58-3"
                     /geo_loc_name="Sweden: Gothenburg"
                     /collection_date="2018"
     gene            complement(join(1575..1822,1..40))
                     /locus_tag="OGM51_RS25940"
                     /old_locus_tag="OGM51_25915"
     CDS             complement(join(1575..1822,1..40))
                     /locus_tag="OGM51_RS25940"
                     /old_locus_tag="OGM51_25915"
                     /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(53..586)
                     /locus_tag="OGM51_RS25945"
                     /old_locus_tag="OGM51_25920"
     CDS             complement(53..586)
                     /locus_tag="OGM51_RS25945"
                     /old_locus_tag="OGM51_25920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005707163.1"
                     /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_000893324.1"
                     /translation="MLEQQFEDFEQQKRRDHQAQDQSKSAKQKRDRLNPPDWSQVTKAG
                     WNMLDSISEKVPRAFRLYSFFAQNIDKSCGAVVCDQKFLADYFGVSLRTIQYWIGDLES
                     IGAIVKIPVGIYYAYALDPYQVWRGYNKSKKYAAFNAKTLTQKDGVIDRKLRLMLSRRE
                     EFEGSLKTSNHDLD"
                     /name="replication/maintenance protein RepL"
     Typing          1073..1324
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.885"
                     /coverage="97.0"
                     /evalue="1.85e-99"
ORIGIN
        1 gttcttctaa tttccaacgt gattcatatt taattctcat agcgcatcat acctagtcca
       61 agtcatgatt agatgtctta agcgagcctt caaactcttc tctcctagag agcatgagcc
      121 gcaacttgcg atcaataacg ccatcttttt gagttaatgt ttttgcgtta aacgctgcat
      181 attttttaga tttattatat ccgcgccata cctgatacgg atctaacgca taagcataat
      241 agatacctac tggtattttc acgatggcac caatactttc taaatctcca atccaatatt
      301 ggatcgtcct taaactaaca ccgaaataat cagctaagaa tttttggtca catacaacag
      361 ccccacacga tttatctata ttttgagcaa aaaaagaata tagcctaaat gctctgggaa
      421 ccttctcaga tatagagtcc aacatattcc agcccgcctt agtaacctgc gaccagtcag
      481 gtggattcaa ccgatctcgt ttttgcttag cacttttgga ttgatcttgt gcctgatgat
      541 ctcgccgttt ttgctgttcg aaatcttcaa attgctgttc cagcatactt gcatccttac
      601 ctgcaacgtt gtttcgtacc ttacgaaatt tatatcgtac attacgaaac aacacacgca
      661 aacatgtttg cgtatacaca tgcaaataac gtttcgtatg ttggtgtcat aatgctttga
      721 tttttaagag aatgtcgatt tttgctctaa agatctatca aagcactttt ttgctacaca
      781 agatttaatt agttcatcga acatttgggg tgtcggggcg aagccctgac ccagtcacgt
      841 agcgatagcg gagtgtatac tggcttactc ttctgcaagc ctcgtcagcc gtgattttgc
      901 ccgatttcgc gctctccacg ttcaacagct cgatcatgtt tttgcagtcc gttcaccgct
      961 aaaacgcccc gcatcagtgc gtacgtgctc aatgtggttt ccggttctct tccgcttcct
     1021 cgcccactcg ctcactaacg ttcggtcgct ggggctgcgg cgagcggtgc cacctctcgc
     1081 atgttatcgg tgattccgct gttgttcttt cggggatgag tcgccagata gctcttcaaa
     1141 cgctctcaga agctctcaga cgcacgaaac gggttttaaa tgcccatcag ggcatggaag
     1201 gcgcgaaaaa cgcttacaga gggttttagg aggtcaggcg cgccgatacc cctaaccagg
     1261 ggatttcagg tcgccaggaa ccgcgtcagc cccctgcaaa gcccatttgc acggaatagg
     1321 cagccacgcg gttggtaggt ggtcgtagac cgtcgatgtt acagcgatgg gggtctgggg
     1381 ttctccccag acggtttccg gttgcgctca aggcgctgcc ggaaccgtgg cggctcggtc
     1441 gttctggaaa acggggagca aaaagacgca agggattttg aggcggcaaa agagcaatgc
     1501 aggatagaca atcaactaga aattgcatgc aatgttctgt ggattgtccg cctgccgctg
     1561 gctctgtatg gccatcactt tttccgatat ttatctaact caattacagg tgcaggaatt
     1621 tttttcttcg cacttttttt tggtttttgt attttttcat tgttgctaac gacaaacata
     1681 atattctttc catcttcatt gacaatatca acgggattaa actccttatc ttcacaattc
     1741 atatatagat ttattcccat tgcatattcg atatgatatt catcaattaa cgaatctatt
     1801 gatctacata tttctaattt ta
//
