LOCUS       NZ_CP107191             4091 bp    DNA     circular CON 14-AUG-2023
DEFINITION  Escherichia coli strain R2 plasmid pR2-1030-3, complete sequence.
ACCESSION   NZ_CP107191
VERSION     NZ_CP107191.1
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 4091)
  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 4091)
  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
            CP107191.1.
            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..4091
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="R2"
                     /isolation_source="human"
                     /db_xref="taxon:562"
                     /plasmid="pR2-1030-3"
                     /geo_loc_name="Sweden: Gothenburg"
                     /collection_date="2017"
     gene            162..2309
                     /gene="mobQ"
                     /locus_tag="OGM32_RS25875"
                     /old_locus_tag="OGM32_25845"
     CDS             162..2309
                     /gene="mobQ"
                     /locus_tag="OGM32_RS25875"
                     /old_locus_tag="OGM32_25845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_139451126.1"
                     /translation="MAIYHLSMKILSRSKGYSAVASAAYRAGEKILDERTGVIHDYTRK
                     NGVASAVILTPANAPAWCANRAELWNAVEKAERRKNSQLAREFELAIPRELAQDAARET
                     VLNFVRENFVSRGMIADVAFHNLGGSNPHAHIMLSMRAITPDGFGEKVREWNDWTHAET
                     WRGSWADHANRALANAGYQEEIDHRSYERQGVEKKPGIHLGKSACAMEKWGIETERGEQ
                     NRLINRLNLEIQVSRDELRNSELTEPARRMADLLNIELPDNATSYILHDIIEALPTDSN
                     AAWKLTSKAMSMMADMQATRRRWEDLNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWV
                     APEYGREQEKIQSLSQRMEKLRQHHWKVEKQDIPASQKAFETQWQQWGASGLADLREQL
                     RKREEELRRKEQEETERRRAEQLRRNDNAVMDSGVLKAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRARIFESVDLMRDRSGYICERSEIGQRPPLQHVYSSATFEQ
                     LLTQVCQTWPQHTRDLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSMGGVVRLNGTLYPAFAVPTADNSQLVINALTDKGLRFA
                     GYGEAVNHDADSPARPAPELMQFHLKTWSEPLFAIVNTPEKQPDHLFRSLGFERTWDEW
                     QRDEYARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(2558..3259)
                     /locus_tag="OGM32_RS25880"
                     /old_locus_tag="OGM32_25850"
     CDS             complement(2558..3259)
                     /locus_tag="OGM32_RS25880"
                     /old_locus_tag="OGM32_25850"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_001281398.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGSDAESTEL
                     QKTMTVTAEEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLKPCVDELNQKSDLAVTLETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(3792..4082)
                     /locus_tag="OGM32_RS25885"
                     /old_locus_tag="OGM32_25855"
     CDS             complement(3792..4082)
                     /locus_tag="OGM32_RS25885"
                     /old_locus_tag="OGM32_25855"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001514113.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_021533561.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVREP
                     GETQLRAWLLHLLKTEVTRQADVSRIQPLIDELNALPKPVPKEVSENDQQA"
                     /name="hypothetical protein"
     Typing          complement(2..146)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.517"
                     /coverage="82.0"
                     /evalue="7.629999999999999e-52"
     Typing          complement(163..517)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2560..3259)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.158"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          121..2306
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.588"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccgtgcgcgg tgaaaaatcg cattttagcg cgtcactggt agtttaaaaa ctgaactggc
       61 ataatgcaca gcaaatcacg aagtgcgcac ttatacaaac tctccttcgt cgagtttgtg
      121 tgcgccctgc ggggctaaaa gaaaacggca acaacgacac gatggcaatt tatcatctca
      181 gcatgaagat tctttccaga agcaagggct acagcgccgt tgcttctgct gcctatcgtg
      241 ccggagaaaa aatactggat gagcgcaccg gagtgattca cgactacacc cgcaaaaacg
      301 gtgtagccag cgcagtgatt ctgacgccag caaacgcccc agcatggtgt gcgaaccgcg
      361 ccgaactctg gaatgctgtt gaaaaagccg agcggcggaa aaactcacaa cttgcgcggg
      421 agttcgaact cgccatcccc cgtgaactgg cgcaggatgc cgcacgggaa acagttctca
      481 acttcgtaag ggaaaacttt gtcagtcgcg gcatgatcgc cgacgtggcc tttcacaatc
      541 tgggcgggtc aaacccacac gcgcacatca tgctatccat gagggcaatc acgcctgacg
      601 gcttcgggga gaaagtccgt gagtggaatg actggactca cgccgaaaca tggcggggat
      661 catgggcaga ccatgcgaac agggcgctgg cgaacgccgg ttatcaggaa gagatagacc
      721 atcgttcata cgagcgacag ggggttgaga aaaagcctgg cattcacctc ggaaagtcgg
      781 cctgtgcgat ggaaaagtgg ggcatcgaaa cagaacgcgg cgaacagaat cgcctgatta
      841 acaggcttaa cctggaaata caggtttccc gcgacgaact caggaacagt gagctgacag
      901 agcccgcacg ccgtatggct gaccttctga atattgagct tcctgacaac gcaacttcgt
      961 acatactgca tgacatcatc gaagcgttgc cgacggacag taacgcagca tggaaactca
     1021 ccagtaaagc catgtcgatg atggcagata tgcaggcgac gcgcagacgc tgggaagatc
     1081 tgaacaccga acgaaaggaa gcgatgagcc atgctgccag cctgaaaaaa tcatcgccgt
     1141 tttcgtccgg tttttcccgt attcccctga tgcaatgggt tgcaccggaa tacggccgcg
     1201 aacaggaaaa aatccagtcg ttgagccagc gcatggaaaa attgcggcag catcactgga
     1261 aggttgagaa acaggacatt cccgcgagtc aaaaagcatt tgaaacacag tggcagcagt
     1321 ggggtgcatc tggccttgca gatctccgag aacagttgcg taaacgtgaa gaggaattgc
     1381 gccggaagga gcaggaggaa acagaacgtc gtcgggcgga gcagctcagg agaaatgaca
     1441 atgccgttat ggattcaggg gtactgaaag cagtcgttac ggggtatggc gaggccccca
     1501 tgccaggtaa cggggaaatg acctgttacc ttctgcttca caaccggaac ggagaatata
     1561 cgctctgggg gaacgaactg gagaaatacc gcgccagaat ttttgagagt gttgatttaa
     1621 tgcgtgacag gagtggttat atctgtgagc gaagcgaaat cggtcaacgt ccaccactgc
     1681 aacatgttta ttcctctgcg acctttgagc aactgctgac gcaggtttgc cagacatggc
     1741 cgcaacatac ccgcgatctc cgccagccga agacatggcc ggagtctttc tgtcttggag
     1801 aagaccgcca gccagccatg ccatcactgg cggcaaggaa ggtggatttt acgcagggac
     1861 gtctgccacc gactctgatg ccggtaatga gttctgtcga ccgtgaaacc cgccagcttc
     1921 agcttttgct ggtcatgggt gtggatgact ctatgggcgg tgttgtccgg cttaatggta
     1981 cgctgtatcc cgcgtttgcc gtccccacag ccgacaacag ccagctggta atcaatgcac
     2041 tgaccgacaa aggtttacgc tttgcaggct atggtgaagc ggtaaaccac gatgctgaca
     2101 gtccggcacg tcctgcgccg gaacttatgc agtttcatct gaaaacctgg agcgaaccgc
     2161 tttttgctat cgtcaacacg ccagaaaaac agccggatca tctgttccgc tcgctgggct
     2221 ttgagcgcac ctgggatgaa tggcaacgtg atgaatatgc ccgaacacac gccaccgaga
     2281 ggagacatga tcgcggttgg tcacagtgaa tgtgaccaat attttgtttt gtttaacatc
     2341 gtgttatgtt cgtcgatgtt catcgacagg gatgaatgca agaagcacac acataacaca
     2401 aatcaacttt atagttttcc cgcccccgaa aaattggggg ttcttttttc actgtgccag
     2461 agcgtttatg acgcaatttt ttacttcacc agtaccttcg catgccaaac acaaaaaaaa
     2521 cgcgtcagag agcgttttag aggccttaaa atcgattcta gatcgtcatc ttgatctgtt
     2581 tgtcttcctt gaagcgaaaa tgcagggcta caaccgtgcg ccccttcttg atcgtctcaa
     2641 gcgttacagc caagtcgctt ttttgattca gttcgtcaac gcaaggtttt aataattgct
     2701 ggttcagaga cttatatgtt tgatatttat gctctatatc aagcattgag cgaaaatcat
     2761 cgagggcgat aatacgttcc cctgtgctgc ggaattgctg gagaagttcg tatattctta
     2821 tgctgtaact tcttgataaa ttggagatgt tcttaattac aactctagta aattgcccct
     2881 tcaactgtgt cagataaggc atgaccgcat ctgaaaaagt gatttgggct ttgccctcac
     2941 ctttagcgta ctgtgcccga tactggatcc agcggaactc ctcgcgcttc tcatcgtcct
     3001 taaggatgat cgacctgtcc cacaaacgat caattgcttc ctgtagctga acctcggcat
     3061 ttttccgccc catatcaggg aatgagtcga aatactcttc ggcggtaaca gtcatggtct
     3121 tttgcaattc agtggattct gcatcagaac ccgacttcaa tcgaccaatg caaagtaaca
     3181 agaatcgctg ttcctgaaga gtcaatttat agctggcctc aaccagtgca ttggatttgt
     3241 aggcaatcag atccgacatt gtaaatccct caacctaagg taatgagtaa aatataaaca
     3301 ttccttaagg taaaggcaat atgatttaat tttaatatcc cttttcctgt gaatattacc
     3361 ttaaatcata ttgcctttac cttaaatcat attgcctatc caccttaaat catattgcct
     3421 ttaccttaaa ttatattacc tatagtcttc taaactcttg aatttcataa gaaaattcga
     3481 ccctaaaaca agtattaaaa acaagatctt aaaaacaaga tctaaaaact taacggcgag
     3541 cctgtggaaa acttggggtg ttcaaaacaa aaaatcatgg aaaacaacag gttacaaaaa
     3601 agcaggttcg caagttttag caaaaccccg ctcaaccctg tggaaatcca gtattcatgc
     3661 gggttcagcg catatcacct gtcgaaaaac cgtgcgtatg tgctcaatct ggcgacggat
     3721 tcacttccgc ttcctcgccc actcgctcgc taacgctcgg tcgctggggc tgcggcgagc
     3781 ggacggtgca ttcacgcctg ttggtcgttt tctgacactt ctttggggac tggttttggt
     3841 aacgcgttca gttcgtcaat caacggctgt atcctgctca catcagcctg ccgtgttacc
     3901 tctgtcttca ggagatgaag caaccaggct cgtagttgtg tttccccagg ctccctgacc
     3961 tttgccagca atgccgctcc cacaatgacc ttctgcgctg tgtccaggct cctgctcttc
     4021 gccttcagac gctgcaatct ggcctcagca tcggcaatct tctgttcgag tgttctactc
     4081 attccgtaac t
//
