LOCUS       NZ_CP107159             4088 bp    DNA     circular CON 14-AUG-2023
DEFINITION  Escherichia coli strain R11 plasmid pR11-698-4, complete sequence.
ACCESSION   NZ_CP107159
VERSION     NZ_CP107159.1
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 4088)
  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 4088)
  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
            CP107159.1.
            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..4088
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="R11"
                     /isolation_source="human"
                     /db_xref="taxon:562"
                     /plasmid="pR11-698-4"
                     /geo_loc_name="Sweden: Gothenburg"
                     /collection_date="2018"
     gene            complement(join(3192..4088,1..1263))
                     /gene="mobQ"
                     /locus_tag="OGM40_RS26445"
                     /old_locus_tag="OGM40_26415"
     CDS             complement(join(3192..4088,1..1263))
                     /gene="mobQ"
                     /locus_tag="OGM40_RS26445"
                     /old_locus_tag="OGM40_26415"
                     /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_001029344.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALVNAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            1442..1696
                     /gene="mobC"
                     /locus_tag="OGM40_RS26450"
                     /old_locus_tag="OGM40_26420"
     CDS             1442..1696
                     /gene="mobC"
                     /locus_tag="OGM40_RS26450"
                     /old_locus_tag="OGM40_26420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091745.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            2229..2936
                     /locus_tag="OGM40_RS26455"
                     /old_locus_tag="OGM40_26425"
     CDS             2229..2936
                     /locus_tag="OGM40_RS26455"
                     /old_locus_tag="OGM40_26425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /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_001296720.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(906..1264)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1265..1441
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2230..2935
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.859"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2..1263)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.05"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(3196..4088)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcgctccgcg cgactacgtt ctgtatcctc ctgctccttc cggcgcaatt cctcttcacg
       61 tttaagcaac tggactctga gagctgcaag gccggatgcc ccccactgct gccactgttt
      121 ttcaaatgcc gtctgactcg cgggaatgtc ctgtttctcc accttccggt aatgctgtcg
      181 caatttttcc atttgctggc tcagcgactg gatttttccc tgttcgctac ggtattccgg
      241 tgccgcccat tgcatcaggg gaatacggga aaaaccggac gaaaacggcg atgatttttt
      301 caggctggca gcatggctca tcgcttcctt tcgttcggtg ttcagctctt cccagcgtct
      361 gcgcgtcgcc tgcatatctg ccatcatcga catggcatta ctggtgagtt tccatgccgc
      421 attactgtcc ttcggcaacg cttcgatgat gtcacgtagt gtgtacgaag ttgcgttgtc
      481 aggaagcacg atattcagaa ggtcagccac acggcgggca ggctctgtca gcccgctgtt
      541 tctgagttcg gtacgggaaa tctgtatttc caggttaagt ctgttaatca gacgattctg
      601 ttcgccgcgt tctgtttcga taccgcgtgt ttccatcgca caggcagact ttccgaggtg
      661 aataccaggc gttttctcaa gcccctgtcg ctcgtatgaa cgatggtcta tctcttcctg
      721 ataaccggcg ttcaccagtg ccctgttcgc atggtcagcc catgatgcac gccacgtctc
      781 ggcatgtgtc cggtcgttcc agtccctgac ctttccaccg aatccagcag gtccgacagc
      841 tctcgtggtc agcatgatgt gcgcatgggg atttgtttta tccatgtgat ggaacgccac
      901 atcagcaatc atgccctgac tgacaaagtt ttctctgaca aaggcgagaa cggtttcccg
      961 tgcggcatcc tgcggtagtt cgcgggggat ggcgagttca atttcccgcg caagttgtga
     1021 gttcttccgg cgttcggcct tctcaacggc attccagagt tcggcacggt tcgtacacca
     1081 ggcaggggct gtcgcgggag tcagaatcac agcttcagcc acaccgcttt tgcgggtgta
     1141 gtcgtgagtc agtccggtac gctcatcaag catcagtgaa ccggaacgat aggcagcaga
     1201 agcaacggcg ctgtagccgc tgtttctgga gatgattttc atgctgagat gataaatcgc
     1261 catttctgcc gtaatgcctt tttgtggttt tctttcagcc ccgcagggcg cacacaatcg
     1321 aaacggagtg gagattgtat aagtgcgcac ttcgtgattt tccgtgcatt atgccagctc
     1381 agtttttaaa ctaccagtga cgcgctaaaa tgcgattttt catcgcgcac ggagttacat
     1441 catgagcaga acactcgaac agaagattgc tgatgctgag gccagattac agcgcctgaa
     1501 ggcgaagagc aggagtctgg acacagcgca gaaggtcatt gtgggtgcag cattgctggc
     1561 aaaggtcaga aagccggagg aggtgcagtt gcgtgcctgg ttactccagt tcctgaaggc
     1621 agaggtgaca cgacaggctg atgtgacgcg catactgccg ctgattaacg agctggaagc
     1681 gctgccagga cagtgattgt atcgtccgct cgccgcagtc ccagcgaccg agcgttagcg
     1741 agcgagtggg cgaggaagcg gaagtgaatc cgtcgcctga ttgagcacat acgcacggtt
     1801 tttcgggagg tgatatgcgc tgaacccgca tgaatactgg atttccacag ggttggaggg
     1861 ggtgtattcg gaacttgcaa ttctgctttt tttgcaacgc attgttttta ttggtttttt
     1921 gttttcagca ctccaagtta tccacaggct cgtcgttaag tttttagatc ttgtttttaa
     1981 gatcttgttt ttaatacttg ttttagcgcc aaaattcctt atagaaaaca aaatgttaca
     2041 atgctatagg taatatgatt taaggtaaag gtgatataat ttaaggtgct tgggtgaggt
     2101 aatttaaggt aaaggtgagg agatttaagg taatattcac aggaaaatgg ggggtgaaaa
     2161 tataattgct caccaatgct aaaggtgata ggtttttatt tcacctcatt tttggcctgg
     2221 tggttaaaat gacatcaaac cctctgatag cctataagtc caatgcgctg gttgaggcca
     2281 gttacaagct aactttacaa gaacagcgtt tcttattgct ctgcataagc cgacttaact
     2341 ccggtactga cgtagcttca cctgaattgc aaaagacaat gaccattaca gctgcggaat
     2401 attttgattc attccctgat atggggcgga aaaatgccga ggttcagcta caggaagcga
     2461 tcgatcgttt gtgggacagg tcgatcattc tcaaggacga cgagaagcgc gaggagttcc
     2521 gctggattca gtatcgggca cagtacgcga ggggagaggg gaaagcacaa atcacttttt
     2581 ctgacgcggt aatgccttat ctgacacagt tgaaggggca attcaccaga gtcgtcatta
     2641 aaaatatttc taatttatca agaagttaca gcataagaat atacgaaatt ctccagcaat
     2701 tccgcagtac tggggaacgt attatcgccc tcgatgattt taaatcatca ctgatgcttg
     2761 atggtaaata taaagatttc aaaacgttaa acagggatct aataaaaccc tgtgttgacg
     2821 aactgaacaa aaaaagcgac ctggctgtaa cggttgagac gatcaaaaag gggcgcacgg
     2881 ttgtagccct gcattttcgc ttcaaggaag acaaacaaat caagatgacg atctaaaatc
     2941 gattttaagg cacctaaaac gctccctgct gcgttttttt tgtgttagta gtgcgaaggt
     3001 actattgaag tgaaaaattg cgtcaaaagc gctctaatgc agcgaaaaaa gaacccccat
     3061 tttttggggg cggaaaaaca aaactatgct tgcattatgt gtgtgcttct tgcattcatc
     3121 cctgtcgatg aacatcgaag aacatcgacg aacataacac gatgttaaac aaaacaaaat
     3181 attgttcaca ttcactgtga ccaaccgcga tcatgtctcc tctcggtggc gtgtgttcgt
     3241 gcatcttcct cgcgccgcca ttcgtcccag gtacgattaa aacccagcga gcggaacaga
     3301 tgatccggct gtttttctgg tgtgttgacg gcagcaaaaa gcggtgcctc acgggttttc
     3361 agatgaaact ccataagttc cggcgcaggt gatatgtggc tgtctgcatc gtgatttacg
     3421 gcaacaccat accctgcata ccgtaacccc ttatcggtca gtgcactgat gaccagctgg
     3481 ctgttatcgg ctgagggaac ggcaaacgcg ggatacagcg taccattaag ccggacaaca
     3541 ccgcccagag agtcatccac gcccatgacc agcaaaagct gaagctggcg ggtttcccgg
     3601 tcgacagaac tcattaccgg catcagcgtc ggtagcagac gtccctgcgt aaaatccacc
     3661 ttccttgctg ccagtgatgg catggctggc tggcggtctt ctccaagaca gaaagactcc
     3721 ggccatgtct tcggctggcg gagattgcgg gtatattgcg gccatgtctg gcaaacctgc
     3781 gtcagaagtt gctcaaaggt cgcagaggaa taaacacgtt gcagtggtgg atgttgaccg
     3841 atttcgcttc ggtcacagat ataaccactc ctgtcacgca ttaaatcaac acgctcaaag
     3901 attctggtgc ggtatttctc cagctcgttc ccccagagcg tgtattctcc gttccggttg
     3961 tgaagcagaa ggtaacaggt catttccccg ttaccaggca tgggggcctc gccatacccc
     4021 gtaacgactg cgctcagtac ccctgaatcc ataacggcat tgtcattttt cctgagctgt
     4081 tccgctcg
//
