LOCUS       NZ_CP107170             3373 bp    DNA     circular CON 14-AUG-2023
DEFINITION  Escherichia coli strain R9 plasmid pR9-658-6, complete sequence.
ACCESSION   NZ_CP107170
VERSION     NZ_CP107170.1
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 3373)
  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 3373)
  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
            CP107170.1.
            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..3373
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="R9"
                     /isolation_source="human"
                     /db_xref="taxon:562"
                     /plasmid="pR9-658-6"
                     /geo_loc_name="Sweden: Gothenburg"
                     /collection_date="2018"
     gene            complement(join(3325..3373,1..143))
                     /locus_tag="OGM38_RS25850"
                     /old_locus_tag="OGM38_25820"
     CDS             complement(join(3325..3373,1..143))
                     /locus_tag="OGM38_RS25850"
                     /old_locus_tag="OGM38_25820"
                     /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="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            207..530
                     /locus_tag="OGM38_RS25855"
                     /old_locus_tag="OGM38_25825"
     CDS             207..530
                     /locus_tag="OGM38_RS25855"
                     /old_locus_tag="OGM38_25825"
                     /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_001696562.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     APPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            739..>1179
                     /locus_tag="OGM38_RS25860"
                     /old_locus_tag="OGM38_25830"
                     /pseudo=""
     CDS             739..>1179
                     /locus_tag="OGM38_RS25860"
                     /old_locus_tag="OGM38_25830"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /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            1208..1768
                     /locus_tag="OGM38_RS25865"
                     /old_locus_tag="OGM38_25835"
     CDS             1208..1768
                     /locus_tag="OGM38_RS25865"
                     /old_locus_tag="OGM38_25835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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_000067486.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGMKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            1775..2008
                     /locus_tag="OGM38_RS25870"
                     /old_locus_tag="OGM38_25840"
     CDS             1775..2008
                     /locus_tag="OGM38_RS25870"
                     /old_locus_tag="OGM38_25840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /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_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          3161..3244
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.059"
                     /coverage="95.0"
                     /evalue="8.83e-18"
     Typing          521..2091
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.439"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agttcgtcgg cgtggtcgtg aagtgattcg cagatgtctg cctgttcgtc cgcgtccaga
       61 tcgttgagtt tttccagcag ggttagcgtc tggcttctga taaagcgagc catgttaagg
      121 gctgtttttt cctgtttggt catggtctta aggctccttg tatgggggat ttgttagggg
      181 gaatgatacc gatgaaacgc gagaagatgc tcacgatacg ggttaccgat gaggagcacg
      241 cccggttact ggaacgctgc gagggtaaac gactggcgga atggatgcgg cgggtctgtc
      301 tgggggagcc ggttgcacgc acaggaaaac tgccgacact ggcaccgcca ttgctgcggc
      361 atctggctgc catcgggaac aacctgaacc agacagcccg gaaggtgaac agcggccagt
      421 ggtcttcgat tgaccgggtt catgtggtgg ccgcactgat ggccatcgag ggtgaattgc
      481 gccagttgcg gcaggctgtc agggaacagg gggtacggga tgatagttaa atttcatgct
      541 agggggaaag gcggtggaag tggcccggtc gattacctgc tggggcggga gcgtaaccgc
      601 gaaggcgcaa cggtgctccg gggtaacccg gaagaagtgc gggaactcat tgattccacg
      661 ccattttcga agaaatacac gtcaggcgtt ctgtcgttcg cggagaagga gctaccaccg
      721 ggtgaacgcg aaagagtgat gacgagcttt gagcgtgttc ttatgcccgg tctcgaaaaa
      781 gaccagtaca gcattctctg ggtggaacac caggataagg ggcggctcga actgaatttt
      841 gtcatcccga acatggagct acagagcggt aagcgcctcc agccgtacta cgaccgtgcg
      901 gacaggccga ggataaatgc ctggcagacg ctggttaatc atcattacgg gctgcgtgac
      961 ccgaacgcac cggagaacag acggacgctt gtcacgccaa ataatctgcc aaaagcgaaa
     1021 caggaggccg cagaagcgat tacacggggt cttgaggctc tttaccatgc cggagcaata
     1081 aaaacgcgtc aggatgtcac agaggcgctt acagcggcag gttttgaggt ggtgaggaca
     1141 accaaaagca gcatcagtat tgccgacccg gagggggggc ggaatctcag gctaaagggg
     1201 gcgctgtatg agcaatcttt tacaaatggg aacagacttc gagaagaaac tgaaagagcg
     1261 agccgcttct accgagaaca tgctgaacag cgagttcagg aagctcgaag agtctgtaga
     1321 caaggcattg agcttaaaca ggcagaaaat cagagacgct atcagcgaac atacaacatc
     1381 cgtgaaaaag caactggata cgctgagcac caccgtgagc atgcagttca gcaccacaga
     1441 ggccgaactg tcccggcagc agaaaaaact gctctggcgg gtgatcaaag ggcggatact
     1501 gtttccggcg ctgaccgcgc tcagcgtcac gggcgggatt ttcctggggt gctgggggct
     1561 gatggagtgg caggaaagca agattgcgaa aaatatcctg actatcagag agcaggaaaa
     1621 cacgctggcg aaactcgagg caaaaacctg gggggtgacg ttcgtcaatg gcgagaacgg
     1681 gaaatttctg gtgttgccgg acgggatgaa aggggaaaac acctggacgg tgggcgacaa
     1741 gaacgccgtg aggctggtca gggagtaaac gagtatgacg gaactggaag ggcatttgct
     1801 gaacgcctta gagcatttgc aacaggacta tatgcggcgg ctgaacgagt gggagagcgc
     1861 cttcgcggaa ttgcagaaga tgcacgaggt tacgcaacgg aacaacgcga tactgaacga
     1921 gcgcgtcgtg atattgagtc agcaggtgca gagattagcc gggcaagtgg atcgcttgag
     1981 tcggttattt atcgcgaaca acagctaagg gatgaacagg agcgtgcccg gtacagacat
     2041 gaggtacagg aacgcgcggc acgggttcgg agtgggccat caatggagat gtgaccgggg
     2101 aagtgacgaa atcttgccat tttgacccgt tcgacggctg gggcgagcga aacaaatcgt
     2161 gtgccgtatt tgtgcatagc tatgcaacat cctgaaaacg catttcacgc gtttttgggg
     2221 attcagccag gggaaaacat ggttttttta ctttttgagc gtaaagacgt gaaaaatctc
     2281 gttattgcac ttgcgatctt tcgtcggcgg gcgtagaacg aaaacagctc gccaggaagg
     2341 cgagctgttt cgggttcatt gaggtctcta acctcctcaa tgttcctgtg gaaactgttg
     2401 agatccacaa cagaaaccag ttcattcagt ttgcatgagc cttctgtatt cttcaagaat
     2461 ttttcaacag cacagtctcc caggaacccc gaaaaaaacc tgtttttgca gatacttgcg
     2521 tatttgtgag aatcgtttgc ggttggggga gctgtgacga cggcgaccgc acgcgtgaga
     2581 gttccgctac cggcgcagag agtttcatcg acagcggaca cctgatgagt tgccacaaaa
     2641 accgtatgta gcgcggctag attggttgag ttagaccttg gcggcagttc ccggtatgtg
     2701 gtggcgtgac gggtgagatg gtgcggcgaa gacgcatacg tcacgcaggc gcgggttctt
     2761 ccactgacgc gccccgtgat cgatggcctt ggctccgtcc ggcatatcga gagcggcaaa
     2821 ctacccgtcc cttcactggg aggggtgagt tgttgccgtt ccctccgacc ttccaccatc
     2881 cagcatatcg cacgatccca tgtgcaccgc tactcctgat aactccagtg caaaaaaaaa
     2941 aacggatctg catcacaacg agagtgatcc caccgctcgc cgcagcccca gcgaccgaac
     3001 gtagtgagcg agtgggcgag gaagcggaag agtcacagag gcaagcattg tgcacttacg
     3061 cgcctgtgcc agtgtccgcg tgtgtgttgt ttatcgggcg cgctgttttt acgcatctgt
     3121 gcggcttttt actcctgaca tggtgcactt cccatccact ctgcaccgat gcaaaatgag
     3181 gtaagccagt atacacatcg ctatcgctct gtgaactggg tcagggctgc gccccgacac
     3241 ccgcactgac gcgccctggc gggcttgtct gctcccggca tccgctcaca ggcaagctgt
     3301 gaacgtctcc gggagctgca tgtttcagtt gctttcaccg tcatcgccga agcgtgcgag
     3361 gcaactgcgg tag
//
