LOCUS       NZ_CP107130             6200 bp    DNA     circular CON 14-AUG-2023
DEFINITION  Escherichia coli strain S7 plasmid pS7-S3K40-2, complete sequence.
ACCESSION   NZ_CP107130
VERSION     NZ_CP107130.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31158880
            Assembly: GCF_030708235.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6200)
  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 6200)
  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                   :: 1326x
            Sequencing Technology :: Illumina NovaSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/11/2023 08:00:31
            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)                     :: 5,359
            CDSs (total)                      :: 5,244
            Genes (coding)                    :: 5,009
            CDSs (with protein)               :: 5,009
            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)              :: 235
            CDSs (without protein)            :: 235
            Pseudo Genes (ambiguous residues) :: 0 of 235
            Pseudo Genes (frameshifted)       :: 79 of 235
            Pseudo Genes (incomplete)         :: 174 of 235
            Pseudo Genes (internal stop)      :: 40 of 235
            Pseudo Genes (multiple problems)  :: 53 of 235
            Pseudo Genes (short protein)      :: 3 of 235
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP107130.1.
            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..6200
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="S7"
                     /isolation_source="human"
                     /db_xref="taxon:562"
                     /plasmid="pS7-S3K40-2"
                     /geo_loc_name="Sweden: Gothenburg"
                     /collection_date="2018"
     gene            complement(join(5996..6200,1..236))
                     /locus_tag="OGM49_RS26720"
                     /old_locus_tag="OGM49_26695"
     CDS             complement(join(5996..6200,1..236))
                     /locus_tag="OGM49_RS26720"
                     /old_locus_tag="OGM49_26695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011161230.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005119689.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="hypothetical protein"
     gene            454..843
                     /locus_tag="OGM49_RS26725"
                     /old_locus_tag="OGM49_26700"
     CDS             454..843
                     /locus_tag="OGM49_RS26725"
                     /old_locus_tag="OGM49_26700"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000102614.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            887..>1291
                     /locus_tag="OGM49_RS26730"
                     /old_locus_tag="OGM49_26705"
                     /pseudo=""
     CDS             887..>1291
                     /locus_tag="OGM49_RS26730"
                     /old_locus_tag="OGM49_26705"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /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="IS91 family transposase"
                     /name="IS91 family transposase"
     gene            complement(1398..2234)
                     /locus_tag="OGM49_RS26735"
                     /old_locus_tag="OGM49_26710"
     CDS             complement(1398..2234)
                     /locus_tag="OGM49_RS26735"
                     /old_locus_tag="OGM49_26710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000480972.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /protein_id="WP_000480968.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="aminoglycoside O-phosphotransferase APH(6)-Id"
     gene            complement(2234..3037)
                     /gene="aph(3'')-Ib"
                     /locus_tag="OGM49_RS26740"
                     /old_locus_tag="OGM49_26715"
     ARG             complement(2238..3037)
                     /name="aph(3'')-Ib"
                     /gene="aph(3'')-Ib"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3'')-Ib"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(3098..3913)
                     /gene="sul2"
                     /locus_tag="OGM49_RS26745"
                     /old_locus_tag="OGM49_26720"
     ARG             complement(3102..3913)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            5102..5251
                     /locus_tag="OGM49_RS26750"
                     /old_locus_tag="OGM49_26725"
     CDS             5102..5251
                     /locus_tag="OGM49_RS26750"
                     /old_locus_tag="OGM49_26725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     ARG             complement(1402..2234)
                     /name="aph(6)-Id"
                     /gene="aph(6)-Id"
                     /gene_name="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          4894..5067
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          complement(4365..4970)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 agctgagcat tttccgcctg gctaacgaca gatttggagt gtccctcctt gtgccttttt
       61 ggtgtctcag aagtgcgcag ctcgccatag gcccgaatca gttcactggt ctcgaactcc
      121 cggcgatcat tttttcctgt gcgatagctg acaaggcctt tagccatgtc acgatataat
      181 tgcgagcgcg actttcctgt taatttcagt gtctcttgaa ctgtgtgcca tgccataaaa
      241 gtgacagtgt ctcctgtgtg taccgtattg taacagcaga acatattact gttttaacac
      301 aaaaggtctg aggctgcccg tgaggcgtga aaaatacaca aaaaacctgt tgacggtgtg
      361 gttttgacgg gcgtagtatt tcgaatactg tatataaaca cattgttata aatacagttt
      421 ttgctgtttt taaaagtcaa agaggataat tttatgagta cagagttaaa tagcggtact
      481 gtcggtggtt ttggtcacat gggaccaaat gacccctaca atgatggtca tagcggctct
      541 ggaagttcgg gaggtagttt taacggtggt ggtaatggtg gccatgataa tagtagtggt
      601 tcatcttata ctgcatcctt tggtctcatc actggccgac acccgataac tgtcccaggt
      661 acgaagaata ttaattctgt cgatctttct gctgtcatta ataacattat acatcatgaa
      721 ggtgcacgca ataacatgta cctagatact gcgaacaatg taagagtggg agtgacgggc
      781 actggctggc aatgtctagc aacggcaggc atttcggctg agggtaaaag aactttccgc
      841 taagcgatag actgtatgta aacacagtat tgcaaggacg cggaacatgc ctcatgtggc
      901 ggccaggacg gccagccggg atcgggatac tggtcgttac cagagccacc gacccgagca
      961 aacccttctc tatcagatcg ttgacgagta ttacccggca ttcgctgcgc ttatggcaga
     1021 gcagggaaag gaattgccgg gctatgtgca acgggaattt gaagaatttc tccaatgcgg
     1081 gcggctggag catggctttc tacgggttcg ctgcgagtct tgccacgccg agcacctggt
     1141 cgctttcagc tgtaagcgtc gcggtttctg cccgagctgt ggggcgcggc ggatggccga
     1201 aagtgccgcc ttgctggttg atgaagtact gcctgaacaa cccatgcgtc agtgggtgtt
     1261 gagcttcccg tttcagctgc gtttcctgtt tggggtcgtt tgcgggaagg ggcggaatcc
     1321 tacgctaagg ctttggccag cgatattctc cggtgagatt gatgtgttcc caggggatag
     1381 gagaagtcgc ttgatatcta gtatgacgtc tgtcgcacct gcttgatcgc ggccgcgata
     1441 gctagatcgc gttgctcctc ttctccatcc gcgttccaag ctgcggaaag gcacccataa
     1501 gcgtacgcct ggtcgagcag gcgacgcgga tcgacgtcca gcgcacgaga gaatgcgtcc
     1561 gccatctgtg caatgcgtct aggatcgaga caaaggtcgt ctctgtcagc cggatcgtag
     1621 aacatattgg cggcgccaaa gcccacttca ccgaccagac cgacgggatc tatcaccagc
     1681 cagccgcgac tggagaacat gatgttttca tgatgcagat cgccatgtag cccacgcagt
     1741 tccgaggcat tgctcatcat ttgatcggct ataatcgccg cgtggacgta gtcagtttga
     1801 caacctgcgt tttgatcatc gcgcgcccgc tgaaacaaag ctgcaaagcg atcccggatc
     1861 gggagaaggg cagaaggcag gggttcctca gatgcggcat acagcttcgc cattagttcc
     1921 gctgcaattt cggtcgcctg gtagtcgccg tgctcggcaa cgatgtgaga gagcattcgc
     1981 tccccggcat attcgagcaa catcagattg ttctcacgac cgagcaaccg gactgctccc
     2041 ctcccattgc gccataccag atagtcggcc ccgcgcagtt catcagcaat gtcttctata
     2101 ggtttcaatc ccttgacgat tgcaggagtc ccgtctggca atgaaacttt ccaaacgagg
     2161 ctggaaaagg tgtccgcaat gagaacaggt tgcgaaacgt gccaatgagc aggaaaaaca
     2221 ggcggcatga acatcaaccc caagtcagag ggtccaatcg cagatagaag gcaaggcgtt
     2281 cgcggtcggg ggcttcgatc cccaatacat tgaataggac agcgaaggcg cgctctgctt
     2341 catctggcgc tgcccagttc tcttcggcgt tagcaatcat gagtgccaaa tcggcatagc
     2401 gatctgctgt tccgagccgc ccaaggtcga tcagacccgt gcattgaaga gttttagggt
     2461 ccaccatgaa gttcggcatg cagggatcac catggcaaac aaccatatcg gtgcgctctt
     2521 ggtcgagccg caccggtagc tctcgttcga cacgagccaa aagatcgagc tgcggcgtac
     2581 tcttgtcctc gtccggtaag aagtcgggat tgacggcatt gcgggacacc acatcaacgg
     2641 cgcgtccgaa cattcgcgac agcctgcgct caaacggaca ttgatcaacc gataggctgt
     2701 gaacagcgcc aagttgctgc cccattgacg gccacgcttt gagcaaatcc gctccagaca
     2761 gatcagccgc cggtactccc ggaattgccg ttatcaccaa gcatgcaccc tcctgttcct
     2821 cctgccagtt gatgacctcg gggcaagcca cacctcgacc tttgagccaa atgaggcggt
     2881 cacgctctcc agcgagctca ccgcggcggg aagcaggtgc gattttcgcg aaggcatgcc
     2941 cgtcaccacg tcgaaaaaca aaatcaccag attctccgcc tctgacaggc aaccagtcag
     3001 aatgcgattc accaaaaaaa atattagttc gattcaatgg aggttccttc agttttctga
     3061 tgaagcgcga atatagagaa atatcccgaa tgtgcagtta acgaattctt gcggtttctt
     3121 tcagcgccgc caataccgcc agcccgtcgc gcaaggggcg cggctcgtgt gtgcggatga
     3181 agtcagctcc acctgcggcg gcggcaagct ctgcagcgag tgtcgcggcc ccgacatccc
     3241 ccggaccacg gcctgtgagc gcgcgcagaa aggatttgcg cgaaacagac agaagcaccg
     3301 gcaaatcgaa gcgcagccgc aattcatcga accgcgccag caccgagagc gaggtttcgg
     3361 gagcagcccc cagaaaaaac cccatgccgg gatcaaggac aaggcggttg cgtttgatac
     3421 cggcacccgt cagcgccgcg atgcgcgcgt caaagaacgc cgcaatgtga tccatgatgt
     3481 cgccagcggg tgcctcgcgc cgatctgcct gcccgtcttg caccgaatgc ataacgacga
     3541 gtttggcaga tgatttcgcc aattgcggat agaacgcagc gtctggaaaa ccgcgaatat
     3601 cattgagata ggccacacca cgcgacaagg cataggcttg cgtcgcgggt tgataactgt
     3661 cgagcgagac gggaatgcca tctgccttga gcgcgtccag caccggcgcg atacgcgcga
     3721 tttctgtgtc ggacgaaaca ggcgcggcgt cgggattgct ggatgccgga ccgaggtcga
     3781 tcacatctgc cccctcggcc atcagcttac gcgcctgcgc aatggctgcg tctggcgcca
     3841 gataccggcc tccatcggag aaactgtccg aggttatgtt gacgatgccg aaaatgatga
     3901 gcgatttatt catgggggct tctataataa taataatcga gcatgagtct catacggatg
     3961 ctcgggtcga aagggaatcc ccaggcgagt aacctgtttg cggtgatccg tttcatgatg
     4021 atgtatctgt agcattttgg aaataaatat atcatctctc aataagtaga tatatttatc
     4081 ttttttgctt ctttggtgct gcaagtcacc aatacgaggg aaacctgtta cggagcggtt
     4141 taaccgtaat caacagtgac tggtgtcatg ttcggaagat taattgatag taatctacaa
     4201 aggatcttct tgagatcctt ttcaatgaat cgtaatctct tgctctgtaa acgaaaaaac
     4261 cgcctgggga ggcggtttgt tcgaaggtta agtcagttgg ggaactgctt aacccggtaa
     4321 cagggttcac gagaccgcca ttaccaaaac tgttctttca gtgtagccgc agtcaggcct
     4381 ctacttcaag acctcttaat ctatcttctc gtgcactcct gttactaatg gctgctgcca
     4441 gtggcgtttt gtcgtgtctt tccgggttgg actcaagttg atagttaccg gacaaggcgc
     4501 agcggtcgga ctgaacgggg ggttcgtgca tacagtccag cttggagcga actgccttca
     4561 cggaactgag tgtcaggcgt ggaatgagaa accgcggcca taacagcgga atgacaccgg
     4621 taaaccgaaa ggcaggaaca ggagagcgca cgagggagct accaggggga aacgcctggg
     4681 atctttatag tcctgtcggg tttcgccacc actgatttga gcgtcagatt ttgcgatgct
     4741 tgtcaggggg gcggagccta tggaaaaacg gcttcgccgt ggccttatct cttctttgct
     4801 aagtgtcttc ctggtatctt ccaggaaatt tccgtccccg tccgtaagcc ggtaccgctc
     4861 gccgcagccg aacgaccgag cgtagcgagt cagtgagcga ggaagcggaa tatctcctgt
     4921 atcgcatatt ctgctgacgc gccggtgctg ccttttttct cctgccacat gaagcacttc
     4981 actgattttc gcaatcgtgg caacatagta agccagtata cactccgcta gcgctacatg
     5041 actggttcag ggctgcgccc cgaaacccgc taacaacctc tcagctactg gatatcaccc
     5101 catgccatct gaatatgatg aacaactgga ttcgactgat acgcagcttc ccggcgaata
     5161 tgaccttttt gatttaatgg cgcaggttac tgaagagaac ctgcatgccc ctgtggattt
     5221 tgggtcgcct gtcggccggg aagcgttata gctttttcgc ttgcccgcgt acgtggtaat
     5281 actccggtat taccttttat ttctttattt tcatgtaatt acagtggatt tttaataccc
     5341 gggtattact cgtgaaaacg aaatattcct tttttttctt ttaattcatg cagttgcgat
     5401 gaaaatcgcg gctgcgttag gtgtatgacc attttgaggt tgaaaaataa tcaaccatgg
     5461 cgggtgattt acgcaggtta aggagagatc gtgacaaaaa aagcgttcct cactgtatcg
     5521 ttcatgcctg catgaacggg ttattcttcc tgactacaga attacatcgc tccttcagtt
     5581 catacatcac ttttacatca cttatacatc acttttacat cattccttca gctcatacgt
     5641 cactttcatc ctctgtgcca tttgtacatc acccccttcc tgaacgtgct gacagcgggt
     5701 tttccggctg cgccggcaac gcttcacggc cacgcaataa attgcgtccc cgttcaccgt
     5761 tttcggatgg gaagaacgcc ggaaacagga cttaccccgg ctgaatggtg tgaatttccg
     5821 cgctatgcac ttgtgcgcat actcatgcat gccgtaaaaa cagagcctgc gcgtttctgg
     5881 cgggttttcg ggtggtttgt tgcctgtttt accggtttcc cgtcagaaac gccctgaggg
     5941 cctctcaggc ggtgctgata acagatgtta tggtaaatca gagtcacctg cactgttact
     6001 ctgaaccgga gcgaaacagc cgcgaccaga atccccgctt tttttcctgt gccagcgcgt
     6061 cagccagacg gctaatttcg gcctgtagtt gttccctctc ctcatttcgc aggcggtttt
     6121 ctgcttcccg cgccatcttg tcttcaagca ttagggtaac agtctgctgc agagcgtcca
     6181 gtttctgctg aatgacgtct
//
