LOCUS       NZ_CP107190             4593 bp    DNA     circular CON 14-AUG-2023
DEFINITION  Escherichia coli strain R2 plasmid pR2-1030-2, complete sequence.
ACCESSION   NZ_CP107190
VERSION     NZ_CP107190.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31158863
            Assembly: GCF_030708055.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4593)
  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 4593)
  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                   :: 1378x
            Sequencing Technology :: Illumina NovaSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/11/2023 07:56:32
            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)                     :: 5,177
            CDSs (total)                      :: 5,064
            Genes (coding)                    :: 4,853
            CDSs (with protein)               :: 4,853
            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)              :: 211
            CDSs (without protein)            :: 211
            Pseudo Genes (ambiguous residues) :: 0 of 211
            Pseudo Genes (frameshifted)       :: 81 of 211
            Pseudo Genes (incomplete)         :: 155 of 211
            Pseudo Genes (internal stop)      :: 40 of 211
            Pseudo Genes (multiple problems)  :: 58 of 211
            Pseudo Genes (short protein)      :: 3 of 211
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP107190.1.
            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..4593
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="R2"
                     /isolation_source="human"
                     /db_xref="taxon:562"
                     /plasmid="pR2-1030-2"
                     /geo_loc_name="Sweden: Gothenburg"
                     /collection_date="2017"
     gene            join(4433..4593,1..31)
                     /locus_tag="OGM32_RS25845"
                     /old_locus_tag="OGM32_25815"
     CDS             join(4433..4593,1..31)
                     /locus_tag="OGM32_RS25845"
                     /old_locus_tag="OGM32_25815"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001677262.1"
                     /translation="MTKQEKTAINMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1042..1881
                     /locus_tag="OGM32_RS25850"
                     /old_locus_tag="OGM32_25820"
     CDS             1042..1881
                     /locus_tag="OGM32_RS25850"
                     /old_locus_tag="OGM32_25820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001354646.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     gene            complement(2569..2802)
                     /locus_tag="OGM32_RS25855"
                     /old_locus_tag="OGM32_25825"
     CDS             complement(2569..2802)
                     /locus_tag="OGM32_RS25855"
                     /old_locus_tag="OGM32_25825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_000137388.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2809..3369)
                     /locus_tag="OGM32_RS25860"
                     /old_locus_tag="OGM32_25830"
     CDS             complement(2809..3369)
                     /locus_tag="OGM32_RS25860"
                     /old_locus_tag="OGM32_25830"
                     /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_000067488.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<3404..3838)
                     /locus_tag="OGM32_RS25865"
                     /old_locus_tag="OGM32_25835"
                     /pseudo=""
     CDS             complement(<3404..3838)
                     /locus_tag="OGM32_RS25865"
                     /old_locus_tag="OGM32_25835"
                     /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            complement(4047..4370)
                     /locus_tag="OGM32_RS25870"
                     /old_locus_tag="OGM32_25840"
     CDS             complement(4047..4370)
                     /locus_tag="OGM32_RS25870"
                     /old_locus_tag="OGM32_25840"
                     /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_001677263.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(120..204)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          215..770
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.907"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2472..4057)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 acgcttcggc gatgacggtg aaagcaactg aaacatgcag ctcccggaga cgttcacagc
       61 ttgcctgtga gcggatgccg ggagcagaca agcccgtcag ggcgcgtcag cgggttttag
      121 cgggtgtcgg ggcgcagccc tgacccagtc acgtagcgat agcggagtgt atactggctt
      181 aactatgtgg catcagtgcg gattataaga aaagtgcacc atatgcggtg tgaaataccg
      241 cacagatgcg taaggagaaa atgccgcatc aggcgctctt ccgcttcctc gctcactgac
      301 tcgctacgct cggtcgttcg gctgcggcga gcggtatcag ctcactcaaa gacggtgatg
      361 cggttatcca cagaatcagg ggataacgcc aaaagaaaca tgtgagcaaa aggccaggaa
      421 caggaagaag gccgcgccgc tggcgttttt ccataggctc cgcccccctg acgagcatca
      481 caaaaacaga tgctcaagtc agaggtggcg aaacccgaca ggactataaa gataccaggc
      541 gtttccccct ggaagctccc tcgtgcgctc tcctgttccg accctgccgc ttaccggata
      601 cctgtccgcc tttctccctt cgggaagcgt ggcgctttct catagctcac gctgttggta
      661 tctcggcccg gtgtaggtcg ttcgctccaa gctgggctgt gtgcacgaac cccccgttca
      721 gcccgaccgc tgcgccttat ccggtaacta tcgtcttgag tccaacccgg aaagacacgt
      781 aaaaacgcca ctggcagcag ccattggtaa ccgtttagag gagttagtct tgaagttatg
      841 cgccggttaa ggctaaactg aaaggacaga tttggtggct gtgctcctcc aagccagtta
      901 ccttggttca aagagttgct gctctgagaa ccttcgaaaa gccgccttgc tgggcggttt
      961 tttcgtttac ggacaagact accttcagga tcgttagatc tcaagacaat catgcatagt
     1021 gagcatacac aggagccgaa cttgcttaca ctgttcatct tttttgtttt attaatagct
     1081 gcatgtttct tttgttttgc tccaccacga agaggatatg acagaaatga gatcattcca
     1141 tacaaaataa aactatcaat aaataaatat cgcctttaca tatactcatc gggaaaggta
     1201 agacaatacc ttttattttt agttatttta tcactgtact actccatagc ggaaccattt
     1261 aagtctgagt taataaaaaa catatcatat tcactgatgg ctgcatttat ttttgataca
     1321 gggcttaatt ttagcaagga gaatataact aaaggagtga tttcaacaag gtggcataat
     1381 gacctatatt catcatttga gagaatgaaa gcaattaata aaatttacta cccatccaac
     1441 aaagagataa acacagaagg tctatccaaa gccatcacat catctctttt caatgatgac
     1501 gcgaactcgt tcgcaaagag agattttcgc ttgatgtggg acttatcttc tgaaaaatat
     1561 ctttcctata aagaaataat aataagaaaa ggcgataagc ttgacgctgt atgcttgaga
     1621 tttataaatg atgactacaa gtttttagtt aatttcaaca gagatgaaga ggttttcaaa
     1681 tactttccat ctataatgca accttcactc aaaacatata gagcgttatc aagactagta
     1741 aactcaatca aagatccttc tagatttaag ttcacgacag agtcattaga aatggagtta
     1801 ctagaatact tagagttaag aaatgaatta ttcaatgaca tagaagaagt aatgggtagc
     1861 tatgctcaga gggcaccata gttcatgata gccctcgata gtacttactt atatttttag
     1921 agaggtttaa gtgtaagtag agggagtaac acctggtttt tcagcatcca ctccaatgaa
     1981 tgctgacacc gatacgcgat aattctcttt atcgtagcaa aatcatcctc cagattgcgg
     2041 ttgagaatag gttcatggtg cgcaatacga ttgcgcagtt ttctcacggg acttgttagc
     2101 agtaatgctt ccccccgggg acaaacgaca gagatataca acaaaggccc gcaattaaaa
     2161 tactccgtat ttaccataac gtcgcattgc gcgtaccgct taaacgcgtt cagcgcgatc
     2221 acggcagcag acaggtaaaa acagcaacaa accacccgaa aaactgccgc gatcgcgcct
     2281 ggtaaatttt aacctcatgc atagttatgc gcgaaactga atgacgatca gtttcgcacg
     2341 ttccagccgt cgaacggggc aaaatgggga ggtttggata ttgttaatgc taatgtacgt
     2401 acattaacat tggcgccatc cgggtagggc gtgccacaaa ctggctcgat ttcagggggt
     2461 accccggtca catccccatt gacgggccac gccagatccg cgcttcgggt tcctgctctt
     2521 catgccagcg ccgggcaagc tcctgcgcct gacgctcctg ttcatccctt atctgttgtt
     2581 cgtgataaat aaccgactca agcggtcgac ttgtccggct aatagctgca cctgctgact
     2641 caagttcacg acacgctcgt tcagtatcgc gttgttctgt tgcgtaaccg cgtgcatctt
     2701 ctgcaattct gcgaaggcgc tctcccactc gttcagccgc cgcatatagt cctgttgcaa
     2761 atgctctaag gcgttcagca aatgcccttc cagttccgtc atactcgttt actccctgac
     2821 cagcctcacg gcgttcttgt cgcccaccgt ccaggtgttt tcccctttca ccccgtccgg
     2881 cagcaccaga aatttcccgt tctcgccatt gacgaacgtc accccccagg tttttgcctc
     2941 gagtttcgcc agcgtgtttt cctgctctct gatggtcaag atatttttcg caatcctgct
     3001 ttcctgccac tgaatcagcc cccagcaccc caggaaaatg ccgcccgtga cgctgagcgc
     3061 ggtcagcgcc ggaaacagta cccgcccttt gatcacctgc cagagcaggt ttttctgctg
     3121 ccgggacagt tcggcctctg tggtgctgag ctgcgtgctc acggtggtgc tcagcgtatc
     3181 cagttgctgt ttcacggatg ttgtatgttc gctgatagcg tctctgattt tctgcctgtt
     3241 taagctcagt gccttgtcta cagactcttc tagcttcctg aactcgctgt tcagcatgtt
     3301 ctcggtagaa gcggctcgct ctttcagttt cttctcgaag tccgttccca tttgtaaaag
     3361 attgctcata cagcgccccc tttagcctga gattccgccc cccctccggg tcggcaatac
     3421 tgatactgct tctggttgtc ctcaccacct caaaacctgc cgctgtgagc gcctcagtga
     3481 catcctgacg cgtttttatt gctccggcac ggtaaagcgc ctcaagaccc cgtgtaatcg
     3541 cttctgcggc ctcctgtttc gcttttggca gattattcgg tgtgacaagc gtccgtctgt
     3601 tctccggtgc gttcgggtca cgcagcccgt aatgatgatt aaccagcgtc tgccaggcat
     3661 ttatcctcgg cctgtccgca cggtcgtagt acggctggag gcgcttaccg ctctgtagtt
     3721 ccatgttcgg aatgacaaaa ttcagttcga gccgcccctt atcctggtgt tccacccaga
     3781 gaatgctgta ctggtctttt tcgagaccgg gcataagaac acgctcaaag ctcgtcatca
     3841 ctctttcgcg ttcacccggc ggtaactcct tctccgcgaa cgacagaacg cctgacgtgt
     3901 atttcttcga aaatggcgtg gcatcaatga gttcccggat ttcttccggg ttaccccgga
     3961 gcaccgttgc gccttcgcgg ttacgctccc gccccagcag gtaatcgacc gggccacttc
     4021 caccgccttt ccccctggca tgaaatttaa ctatcatccc gtcccccctg ttccctgaca
     4081 gcctgccgca actggcgcaa ttcaccctcg atggccatca gagcggccac cacatgaacc
     4141 cggtcaatcg aagaccagtg gccgctgttc accttccggg ctgtctggtt cagattgttc
     4201 ccgatggcag ccagatgccg cagcaatggc ggcgatagtg tcggcagttt tcctgtgcgc
     4261 gcaaccggct cccccagaca gacccgccgc atccattctg ccagtcgttt accctcgcag
     4321 cgttccagta accgggcgtg ctcctcatcg ctaacccgta ttgtgagcat cttctcgcgt
     4381 ttcatcggta tcattccccc taaaaaatcc cctattaagg agccttaaga ccatgaccaa
     4441 acaggaaaaa acagccatta acatggcccg ctttatcaga agccagacgc tgaccctgct
     4501 ggaaaaactc aacgagctgg acgcggacga acaggcagac atctgcgaat cacttcacga
     4561 ccacgccgac gaactctacc gtagttgcct cgc
//
