LOCUS       NZ_CP107124             4082 bp    DNA     circular CON 14-AUG-2023
DEFINITION  Escherichia coli strain S9 plasmid pS9-S4K58-2, complete sequence.
ACCESSION   NZ_CP107124
VERSION     NZ_CP107124.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31158882
            Assembly: GCF_030708195.1
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                   :: 436x
            Sequencing Technology :: Illumina NovaSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/11/2023 07:55:03
            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)                     :: 5,189
            CDSs (total)                      :: 5,077
            Genes (coding)                    :: 4,855
            CDSs (with protein)               :: 4,855
            Genes (RNA)                       :: 112
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 222
            CDSs (without protein)            :: 222
            Pseudo Genes (ambiguous residues) :: 0 of 222
            Pseudo Genes (frameshifted)       :: 79 of 222
            Pseudo Genes (incomplete)         :: 169 of 222
            Pseudo Genes (internal stop)      :: 35 of 222
            Pseudo Genes (multiple problems)  :: 53 of 222
            Pseudo Genes (short protein)      :: 3 of 222
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP107124.1.
            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="S9"
                     /isolation_source="human"
                     /db_xref="taxon:562"
                     /plasmid="pS9-S4K58-2"
                     /geo_loc_name="Sweden: Gothenburg"
                     /collection_date="2018"
     gene            complement(join(2544..4082,1..621))
                     /gene="mobQ"
                     /locus_tag="OGM51_RS25925"
                     /old_locus_tag="OGM51_25900"
     CDS             complement(join(2544..4082,1..621))
                     /gene="mobQ"
                     /locus_tag="OGM51_RS25925"
                     /old_locus_tag="OGM51_25900"
                     /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_001029343.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            800..1054
                     /gene="mobC"
                     /locus_tag="OGM51_RS25930"
                     /old_locus_tag="OGM51_25905"
     CDS             800..1054
                     /gene="mobC"
                     /locus_tag="OGM51_RS25930"
                     /old_locus_tag="OGM51_25905"
                     /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            1587..2288
                     /locus_tag="OGM51_RS25935"
                     /old_locus_tag="OGM51_25910"
     CDS             1587..2288
                     /locus_tag="OGM51_RS25935"
                     /old_locus_tag="OGM51_25910"
                     /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(264..622)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          623..799
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          1588..2288
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2..708)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.576"
                     /coverage="100.0"
                     /evalue="3.03e-155"
ORIGIN
        1 ggcagacttt ccgaggtgaa taccaggcgt tttctcaagc ccctgtcgct cgtatgaacg
       61 atggtctatc tcttcctgat aaccggcgtt cgccagtgcc ctgttcgcat ggtcagccca
      121 tgatgcacgc cacgtctcgg catgtgtccg gtcgttccag tccctgacct ttccaccgaa
      181 tccagcaggt ccgacagctc tcgtggtcag catgatgtgc gcatggggat ttgttttatc
      241 catgtgatgg aacgccacat cagcaatcat gccctgactg acaaagtttt ctctgacaaa
      301 ggcgagaacg gtttcccgtg cggcatcctg cggtagttcg cgggggatgg cgagttcaat
      361 ttcccgcgca agttgtgagt tcttccggcg ttcggccttc tcaacggcat tccagagttc
      421 ggcacggttc gtacaccagg caggggctgt cgcgggagtc agaatcacag cttcagccac
      481 accgcttttg cgggtgtagt cgtgagtcag tccggtacgc tcatcaagca tcagtgaacc
      541 ggaacgatag gcagcagaag caacggcgct gtagccgctg tttctggaga tgattttcat
      601 gctgagatga taaatcgcca tttctgccgt aatgcctttt tgtggttttc tttcagcccc
      661 gcagggcgca cacaatcgaa acggagtgga gattgtataa gtgcgcactt cgtgattttc
      721 cgtgcattat gccagctcag tttttaaact accagtgacg cgctaaaatg cgatttttca
      781 tcgcgcacgg agttacatca tgagcagaac actcgaacag aagattgctg atgctgaggc
      841 cagattacag cgcctgaagg cgaagagcag gagtctggac acagcgcaga aggtcattgt
      901 gggtgcagca ttgctggcaa aggtcagaaa gccggaggag gtgcagttgc gtgcctggtt
      961 actccagttc ctgaaggcag aggtgacacg acaggctgat gtgacgcgca tactgccgct
     1021 gattaacgag ctggaagcgc tgccaggaca gtgattgtat cgtccgctcg ccgcagtccc
     1081 agcgaccgag cgttagcgag cgagtgggcg aggaagcgga agtgaatccg tcgcctgatt
     1141 gagcacatac gcacggtttt tcgggaggtg atatgcgctg aacccgcatg aatactggat
     1201 ttccacaggg ttggaggggg tgtattcgga acttgcaatt ctgctttttt gcaacgcatt
     1261 gtttttattg gttttttgtt ttcagcactc caagttatcc acaggctcgt cgttaagttt
     1321 ttagatcttg tttttaagat cttgttttta atacttgttt tagcgccaaa attccttata
     1381 gaaaacaaaa tgttacaatg ctataggtaa tgtgatttaa ggtaaaggta atatgattta
     1441 aggtgtttag gtgggggaat ttaaggtaaa ggcaatatga tttaaggtaa tattcacaga
     1501 aaaagggata ttaaaataaa aaggcattgc ctttcgttga gggtatgttt atcttttatt
     1561 cattaccttt tggggaggga tgctctatgt cggatctaat tgcctataaa tccaatgcgc
     1621 tggttgaagc cagttataaa ttgaccctac aggaacagcg atttttgtta ctttgcatcg
     1681 gtcgattgaa gtctggggct gatgcagaat ctccaaaatt gcaaaagaca atgaccatta
     1741 cagctgcgga atatttcgat tcattccctg acatggggcg gaaaaatgcc gaggttcagt
     1801 tacaggaagc aattgatcgt ttgtgggaca ggtcaatcat tctcaaggat gacgagaaac
     1861 gtgaggagtt ccgctggatc cagtatcggg cacagtacgc taaaggcgag gccagagcac
     1921 aaataacatt ttctgacgca gtaatgcctt atttgacaca actacaaggg caatttacta
     1981 gagttgtaat caagaatata tctagattat caagaagtta cagtataagg atatacgaac
     2041 tcctccagca gttccgcagt actggcgaac gtattatcgc tctcgatgat tttcgctcaa
     2101 tgcttgatat agagcataaa tatcaaacat ataaatcact taaccagcaa ttattaagac
     2161 cctgcattga cgaactgaac aaaaaaagcg acctggctgt aacggttgag acgatcaaaa
     2221 aggggcgcac ggttgtagcc ctgcattttc gcttcaagga agacaaacaa atcaagatga
     2281 cgatctaaaa tcgattttaa ggcacctaaa acgctccctg ctgcgttttt tttgtgttag
     2341 tagtgcgaag gtactattga agtgaaaaat tgcgtcaaaa gcgctctaat gcagcgaaaa
     2401 aagaaccccc attttttggg ggcggaaaaa caaaactatg cttgcattat gtgtgtgctt
     2461 cttgcattca tccctgtcga tgaacatcga agaacatcga cgaacataac acgatgttaa
     2521 acaaaacaaa atattgttca cattcactgt gaccaaccgc gatcatgtct cctctcggtg
     2581 gcgtgtgttc gtgcatcttc ctcgcgccgc cattcgtccc aggtacgatt aaaacccagc
     2641 gagcggaaca gatgatccgg ctgtttttct ggtgtgttga cggcagcaaa aagcggtgcc
     2701 tcacgggttt tcagatgaaa ctccataagt tccggcgcag gtgatatgtg gctgtctgca
     2761 tcgtgattta cggcaacacc ataccctgca taccgtaacc ccttatcggt cagtgcactg
     2821 atgaccagct ggctgttatc ggctgaggga acggcaaacg cgggatacag cgtaccatta
     2881 agccggacaa caccgcccag agagtcatcc acgcccatga ccagcaaaag ctgaagctgg
     2941 cgggtttccc ggtcgacaga actcattacc ggcatcagcg tcggtagcag acgtccctgc
     3001 gtaaaatcca ccttccttgc tgccagtgat ggcatggctg gctggcggtc ttctccaaga
     3061 cagaaagact ccggccatgt cttcggctgg cggagattgc gggtatattg cggccatgtc
     3121 tggcaaacct gcgtcagaag ttgctcaaag gtcgcagagg aataaacacg ttgcagtggt
     3181 ggatgttgac cgatttcgct tcggtcacag atataaccac tcctgtcacg cattaaatca
     3241 acacgctcaa agattctggt gcggtatttc tccagctcgt tcccccagag cgtgtattct
     3301 ccgttccggt tgtgaagcag aaggtaacag gtcatttccc cgttaccagg catgggggcc
     3361 tcgccatacc ccgtaacgac tgcgctcagt acccctgaat ccataacggc attgtcattt
     3421 ttcctgagct gttccgctcg tcgctccgcg cgactacgtt ctgtatcctc ctgctccttc
     3481 cggcgcaatt cctcttcacg tttaagcaac tggactctga gagctgcaag gccggatgcc
     3541 ccccactgct gccactgttt ttcaaatgcc gtctgactcg cgggaatgtc ctgtttctcc
     3601 accttccggt aatgctgtcg caatttttcc atttgctggc tcagcgactg gatttttccc
     3661 tgttcgctac ggtattccgg tgccgcccat tgcatcaggg gaatacggga aaaaccggac
     3721 gaaaacggcg atgatttttt caggctggca gcatggctca tcgcttcctt tcgttcggtg
     3781 ttcagctctt cccagcgtct gcgcgtcgcc tgcatatctg ccatcatcga catggcatta
     3841 ctggtgagtt tccatgccgc attactgtcc ttcggcaacg cttcgatgat gtcacgtagt
     3901 gtgtacgaag ttgcgttgtc aggaagcacg atattcagaa ggtcagccac acggcgggca
     3961 ggctctgtca gcccgctgtt tctgagttcg gtacgggaaa tctgtatttc caggttaagt
     4021 ctgttaatca gacgattctg ttcgccgcgt tctgtttcga taccgcgtgt ttccatcgca
     4081 ca
//
