LOCUS       NZ_CP107161             1454 bp    DNA     circular CON 14-AUG-2023
DEFINITION  Escherichia coli strain R11 plasmid pR11-698-6, complete sequence.
ACCESSION   NZ_CP107161
VERSION     NZ_CP107161.1
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 1454)
  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 1454)
  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
            CP107161.1.
            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..1454
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="R11"
                     /isolation_source="human"
                     /db_xref="taxon:562"
                     /plasmid="pR11-698-6"
                     /geo_loc_name="Sweden: Gothenburg"
                     /collection_date="2018"
     gene            333..554
                     /locus_tag="OGM40_RS26465"
                     /old_locus_tag="OGM40_26435"
     CDS             333..554
                     /locus_tag="OGM40_RS26465"
                     /old_locus_tag="OGM40_26435"
                     /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_158414302.1"
                     /translation="MCKCNTVTRDDIPFAVWSGLRPDTPHQCVRAQCGFRFSSASSPTR
                     SLRSVAGAAASGVTSRMLSVIPLLFFRG"
                     /name="hypothetical protein"
     gene            complement(1001..1432)
                     /locus_tag="OGM40_RS26470"
                     /old_locus_tag="OGM40_26440"
     CDS             complement(1001..1432)
                     /locus_tag="OGM40_RS26470"
                     /old_locus_tag="OGM40_26440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001233485.1"
                     /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_063269671.1"
                     /translation="MRRVTQIDQESGEELGGFVAVIRPKQKSSFQRHFTMNQAALITIA
                     NELNHDQIRVLMALLADLDYENYIQVAQIDIADALKMQKTNVSRAIKNLIDFGIIIEGP
                     RIGRSKTYRLNPQFGWKGTVSNHRKALKNGLSVIQGGRV"
                     /name="helix-turn-helix domain-containing protein"
     Typing          complement(314..394)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.122"
                     /coverage="87.0"
                     /evalue="9.59e-28"
     Typing          508..766
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.0"
                     /coverage="99.0"
                     /evalue="1.09e-111"
ORIGIN
        1 atagttatct ctcaagataa ctaagttatc tctcaagata actatttgtc aaaagatccc
       61 gcttctggcg cggcttccag aagaccccct tctgtatctt attactctcg caaccaaaac
      121 aaagttttca tggggtgtcg gggcgaagcc ctgacccagt cacgtagcgc cagcggagtg
      181 tatactggct tattccgcta caagcctcgc ttattccgct acaagcctcg ccagccgtga
      241 tttttgccag atttcacgct ctcaacgctc aacagctcca tcatggtttt gccgtccgtt
      301 caccgctaaa acgcctcaga aatcgggaca ggatgtgcaa atgtaatacc gtcacccgcg
      361 acgatattcc gtttgccgtc tggtcagggc ttcgccccga caccccgcat cagtgcgtac
      421 gtgctcaatg tggtttccgg ttctcttccg cttcctcgcc cactcgctca ctacgttcgg
      481 tcgctggggc tgcggcgagc ggtgtcacct ctcgcatgtt gtcggtgatt ccgttgttgt
      541 tctttcgggg atgagtcgcc agatagcccc tcaaacgcgc tcagaagctc tcagacacac
      601 gaaacgggtt ttaaatgccc gtcagggcat ggaaggcgcg aaaaacgctt acagaggctc
      661 tcaggaggtc aggcgcgccg atacccctaa ccaggggctt tcaggtcgct aggaaccgcg
      721 tcagccccct gcaaagccta tttgcacggc acaggcagct attcggctgg ttggtggtcg
      781 tagaccgtcg gtgttacagc gatgggggtc tggggttctc cccagacggt ttccggttgc
      841 gctcaaggcg ctgccggaac cgtggcggcg cggtcgttct ggggatcggg gagcaaaaac
      901 aagcaaggga ttttgaggcg gcaaaagagc aatgcaggat agacaatcat ggtcaaaacg
      961 ttaacacgta gcccctgatt gtccgcctgc cgctggctct ttaaaccctg ccaccctgaa
     1021 tgacgctaag accattcttg agtgctttcc tgtgattgct taccgtccct ttccatccga
     1081 actgaggatt caagcgatag gttttactac gcccgatcct tggtccttcg atgatgatcc
     1141 caaaatcaat caagtttttt attgcgcgac tgacgttcgt tttttgcatt ttcaatgcat
     1201 ccgcaatatc gatttgcgca acttggatgt agttttcgta gtcaagatca gctagcaaag
     1261 ccattaaaac acgaatttga tcatgattaa gttcgtttgc aatcgtgatt aacgcagcct
     1321 gattcatcgt aaaatgcctc tgaaatgacg atttttgctt gggacgaata actgcaacaa
     1381 atccgcccaa ctcctctcct gactcttggt ctatctgtgt aactcttctc acggcttcct
     1441 ccgttctaga gaaa
//
