LOCUS       NZ_CP107168             4082 bp    DNA     circular CON 14-AUG-2023
DEFINITION  Escherichia coli strain R9 plasmid pR9-658-4, complete sequence.
ACCESSION   NZ_CP107168
VERSION     NZ_CP107168.1
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 4082)
  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 4082)
  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
            CP107168.1.
            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..4082
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="R9"
                     /isolation_source="human"
                     /db_xref="taxon:562"
                     /plasmid="pR9-658-4"
                     /geo_loc_name="Sweden: Gothenburg"
                     /collection_date="2018"
     gene            complement(join(3407..4082,1..1484))
                     /gene="mobQ"
                     /locus_tag="OGM38_RS25820"
                     /old_locus_tag="OGM38_25790"
     CDS             complement(join(3407..4082,1..1484))
                     /gene="mobQ"
                     /locus_tag="OGM38_RS25820"
                     /old_locus_tag="OGM38_25790"
                     /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_241556012.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            1663..1917
                     /gene="mobC"
                     /locus_tag="OGM38_RS25825"
                     /old_locus_tag="OGM38_25795"
     CDS             1663..1917
                     /gene="mobC"
                     /locus_tag="OGM38_RS25825"
                     /old_locus_tag="OGM38_25795"
                     /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            2450..3151
                     /locus_tag="OGM38_RS25830"
                     /old_locus_tag="OGM38_25800"
     CDS             2450..3151
                     /locus_tag="OGM38_RS25830"
                     /old_locus_tag="OGM38_25800"
                     /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_001281397.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGADAESPKL
                     QKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEARAQITFSDAVMPYLTQLQGQFTRVVIKNISRLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCIDELNKKSDLAVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(1127..1485)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1486..1662
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2451..3151
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4..1571)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.853"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3411..4081)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="5.73e-149"
ORIGIN
        1 ctcctgtcac gcattaaatc aacacgctca aagattctgg tgcggtattt ctccagctcg
       61 ttcccccaga gcgtgtattc tccgttccgg ttgtgaagca gaaggtaaca ggtcatttcc
      121 ccgttaccag gcatgggggc ctcgccatac cccgtaacga ctgcgctcag tacccctgaa
      181 tccataacgg cattgtcatt tttcctgagc tgttccgctc gtcgctccgc gcgactacgt
      241 tctgtatcct cctgctcctt ccggcgcaat tcctcttcac gtttaagcaa ctggactctg
      301 agagctgcaa ggccggatgc cccccactgc tgccactgtt tttcaaatgc cgtctgactc
      361 gcgggaatgt cctgtttctc caccttccgg taatgctgtc gcaatttttc catttgctgg
      421 ctcagcgact ggatttttcc ctgttcgcta cggtattccg gtgccgccca ttgcatcagg
      481 ggaatacggg aaaaaccgga cgaaaacggc gatgattttt tcaggctggc agcatggctc
      541 atcgcttcct ttcgttcggt gttcagctct tcccagcgtc tgcgcgtcgc ctgcatatct
      601 gccatcatcg acatggcatt actggtgagt ttccatgccg agttactgtc cttcggcaac
      661 gcttcgataa tgtcacgtag tgtgtacgaa gttgcgttgt caggaagccc gatattcaga
      721 aggtcagcca cacggcgggc aggctctgtc agccctccgt tcctgagttc ggtgcgggaa
      781 atctgtattt ccaggttaag cctgttaatc agacgattct gttcgccgcg ttctgtttcg
      841 ataccgcgtg tttccatcgc acaggcagac tttccgaggt gaataccagg cgttttctca
      901 agcccctgtc gctcgtatga acgatggtct atctcttcct gataaccggc gttcgccagt
      961 gccctgtttg catggtcagc ccatgatgcc cgccacgtct cggcatgtgt ccggtcgttc
     1021 cagtccctga cctttccgct gaacccagca ggtccgatag ccctcgtggt cagcatgatg
     1081 tgcgcatggg gatttgtttt atccatgtga tggaacgcca catcagcaat catgccctga
     1141 ctgacaaagt tttctctgac aaaggcgaga acggtttccc gtgcggcatc ctgcggtagt
     1201 tcgcggggga tggcgagttc aatttcccgc gcaagttgtg agttcttccg gcgttcggcc
     1261 ttctcaacgg cattccagag ttcggcacgg ttcgtacacc aggcaggggc tgtcgcggga
     1321 gtcagaatca cagcttcagc cacaccgctt ttgcgggtgt agtcgtgagt cagtccggta
     1381 cgctcatcaa gcatcagtga accggaacga taggcagcag aagcaacggc gctgtagccg
     1441 ctgtttctgg agatgatttt catgctgaga tgataaatcg ccatttctgc cgtaatgcct
     1501 ttttgtggtt ttctttcagc cccgcagggc gcacacaatc gaaacggagt ggagattgta
     1561 taagtgcgca cttcgtgatt ttccgtgcat tatgccagct cagtttttaa actaccagtg
     1621 acgcgctaaa atgcgatttt tcatcgcgca cggagttaca tcatgagcag aacactcgaa
     1681 cagaagattg ctgatgctga ggccagatta cagcgcctga aggcgaagag caggagtctg
     1741 gacacagcgc agaaggtcat tgtgggtgca gcattgctgg caaaggtcag aaagccggag
     1801 gaggtgcagt tgcgtgcctg gttactccag ttcctgaagg cagaggtgac acgacaggct
     1861 gatgtgacgc gcatactgcc gctgattaac gagctggaag cgctgccagg acagtgattg
     1921 tatcgtccgc tcgccgcagt cccagcgacc gagcgttagc gagcgagtgg gcgaggaagc
     1981 ggaagtgaat ccgtcgcctg attgagcaca tacgcacggt ttttcgggag gtgatatgcg
     2041 ctgaacccgc atgaatactg gatttccaca gggttggagg gggtgtattc ggaacttgca
     2101 attctgcttt tttgcaacgc attgttttta ttggtttttt gttttcagca ctccaagtta
     2161 tccacaggct cgtcgttaag tttttagatc ttgtttttaa gatcttgttt ttaatacttg
     2221 ttttagcgcc aaaattcctt atagaaaaca aaatgttaca atgctatagg taatgtgatt
     2281 taaggtaaag gtaatatgat ttaaggtgtt taggtggggg aatttaaggt aaaggcaata
     2341 tgatttaagg taatattcac agaaaaaggg atattaaaat aaaaaggcat tgcctttcgt
     2401 tgagggtatg tttatctttt attcattacc ttttggggag ggatgctcta tgtcggatct
     2461 aattgcctat aaatccaatg cgctggttga agccagttat aaattgaccc tacaggaaca
     2521 gcgatttttg ttactttgca tcggtcgatt gaagtctggg gctgatgcag aatctccaaa
     2581 attgcaaaag acaatgacca ttacagctgc ggaatatttc gattcattcc ctgacatggg
     2641 gcggaaaaat gccgaggttc agttacagga agcaattgat cgtttgtggg acaggtcaat
     2701 cattctcaag gatgacgaga aacgtgagga gttccgctgg atccagtatc gggcacagta
     2761 cgctaaaggc gaggccagag cacaaataac attttctgac gcagtaatgc cttatttgac
     2821 acaactacaa gggcaattta ctagagttgt aatcaagaat atatctagat tatcaagaag
     2881 ttacagtata aggatatacg aactcctcca gcagttccgc agtactggcg aacgtattat
     2941 cgctctcgat gattttcgct caatgcttga tatagagcat aaatatcaaa catataaatc
     3001 acttaaccag caattattaa gaccctgcat tgacgaactg aacaaaaaaa gcgacctggc
     3061 tgtaacggtt gagacgatca aaaaggggcg cacggttgta gccctgcatt ttcgcttcaa
     3121 ggaagacaaa caaatcaaga tgacgatcta aaatcgattt taaggcacct aaaacgctcc
     3181 ctgctgcgtt ttttttgtgt tagtagtgcg aaggtactat tgaagtgaaa aattgcgtca
     3241 aaagcgctct aatgcagcga aaaaagaacc cccatttttt gggggcggaa aaacaaaact
     3301 atgcttgcat tatgtgtgtg cttcttgcat tcatccctgt cgatgaacat cgaagaacat
     3361 cgacgaacat aacacgatgt taaacaaaac aaaatattgt tcacattcac tgtgaccaac
     3421 cgcgatcatg tctcctctcg gtggcgtgtg ttcgtgcatc ttcctcgcgc cgccattcgt
     3481 cccaggtacg attaaaaccc agcgagcgga acagatgatc cggctgtttt tctggtgtgt
     3541 tgacggcagc aaaaagcggt gcctcacggg ttttcagatg aaactccata agttccggcg
     3601 caggtgatat gtggctgtct gcatcgtgat ttacggcaac accataccct gcataccgta
     3661 accccttatc ggtcagtgca ctgatgacca gctggctgtt atcggctgag ggaacggcaa
     3721 acgcgggata cagcgtacca ttaagccgga caacaccgcc cagagagtca tccacgccca
     3781 tgaccagcaa aagctgaagc tggcgggttt cccggtcgac agaactcatt accggcatca
     3841 gcgtcggtag cagacgtccc tgcgtaaaat ccaccttcct tgctgccagt gatggcatgg
     3901 ctggctggcg gtcttctcca agacagaaag actccggcca tgtcttcggc tggcggagat
     3961 tgcgggtata ttgcggccat gtctggcaaa cctgcgtcag aagttgctca aaggtcgcag
     4021 aggaataaac acgttgcagt ggtggatgtt gaccgatttc gcttcggtca cagatataac
     4081 ca
//
