LOCUS       NZ_CP116998             6222 bp    DNA     linear   CON 07-JUN-2024
DEFINITION  Escherichia coli strain MLI108K2 plasmid p6_MLI108-2, complete
            sequence.
ACCESSION   NZ_CP116998
VERSION     NZ_CP116998.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29553892
            Assembly: GCF_024331375.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6222)
  AUTHORS   Riediger,M. and Zautner,A.E.
  TITLE     Molecular epidemiology of Escherichia coli with resistance against
            third-generation cephalosporins isolated from stool samples of
            European soldiers with diarrhea on deployment in Western African
            Mali
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6222)
  AUTHORS   Riediger,M. and Zautner,A.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (29-JAN-2023) Institute of Medical Microbiology and
            Hospital Hygiene, Medical Faculty, Otto-von-Guericke University
            Magdeburg, Leipziger Strasze 44, Magdeburg, Saxony-Anhalt 39120,
            Germany
REFERENCE   3  (bases 1 to 6222)
  AUTHORS   Zautner,A.E. and Riediger,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-JUL-2022) Institute of Medical Microbiology and
            Hospital Hygiene, Medical Faculty, Otto-von-Guericke University
            Magdeburg, Leipziger Strasze 44, Magdeburg, Saxony-Anhalt 39120,
            Germany
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 25-JAN-2023
            Assembly Method :: trycycler v. 0.5.3; unicycler v. 0.5.0; skesa v.
            2.4.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_024331375.2-RS_2024_06_07
            Annotation Date                   :: 06/07/2024 03:09:32
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,991
            CDSs (total)                      :: 4,866
            Genes (coding)                    :: 4,605
            CDSs (with protein)               :: 4,605
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 261
            CDSs (without protein)            :: 261
            Pseudo Genes (ambiguous residues) :: 0 of 261
            Pseudo Genes (frameshifted)       :: 84 of 261
            Pseudo Genes (incomplete)         :: 184 of 261
            Pseudo Genes (internal stop)      :: 54 of 261
            Pseudo Genes (multiple problems)  :: 54 of 261
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116998.1.
            Bacteria and source DNA available from Institute of Medical
            Microbiology and Hospital Hygiene Medical Faculty Otto-von-Guericke
            University Magdeburg 39120 Magdeburg, Germany.
            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..6222
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MLI108K2"
                     /isolation_source="stool sample"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p6_MLI108-2"
                     /geo_loc_name="Mali: Koulikoro"
                     /lat_lon="12.52 N 7.34 W"
                     /collection_date="2014-07-24"
                     /collected_by="Bundeswehr Medical Service"
     gene            91..249
                     /locus_tag="NL410_RS24930"
     CDS             91..249
                     /locus_tag="NL410_RS24930"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032287700.1"
                     /translation="MHEPPVQSDRCALSGNYQLESNPERHDKTPLAAAISNRSAREDRL
                     RGLEVEA"
                     /name="hypothetical protein"
     gene            709..1524
                     /gene="sul2"
                     /locus_tag="NL410_RS01690"
                     /old_locus_tag="NL410_001685"
     ARG             710..1521
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            1585..2388
                     /gene="aph(3'')-Ib"
                     /locus_tag="NL410_RS01695"
                     /old_locus_tag="NL410_001690"
     ARG             1586..2385
                     /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            2388..3224
                     /locus_tag="NL410_RS01700"
                     /old_locus_tag="NL410_001695"
     CDS             2388..3224
                     /locus_tag="NL410_RS01700"
                     /old_locus_tag="NL410_001695"
                     /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(<3331..3735)
                     /locus_tag="NL410_RS01705"
                     /old_locus_tag="NL410_001700"
                     /pseudo=""
     CDS             complement(<3331..3735)
                     /locus_tag="NL410_RS01705"
                     /old_locus_tag="NL410_001700"
                     /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(3779..4168)
                     /locus_tag="NL410_RS01710"
                     /old_locus_tag="NL410_001705"
     CDS             complement(3779..4168)
                     /locus_tag="NL410_RS01710"
                     /old_locus_tag="NL410_001705"
                     /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            4386..4826
                     /locus_tag="NL410_RS01715"
                     /old_locus_tag="NL410_001710"
     CDS             4386..4826
                     /locus_tag="NL410_RS01715"
                     /old_locus_tag="NL410_001710"
                     /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            complement(5593..5742)
                     /locus_tag="NL410_RS01720"
                     /old_locus_tag="NL410_001715"
     CDS             complement(5593..5742)
                     /locus_tag="NL410_RS01720"
                     /old_locus_tag="NL410_001715"
                     /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"
     gene            complement(5948..>6222)
                     /locus_tag="NL410_RS01725"
                     /old_locus_tag="NL410_001720"
                     /pseudo=""
     CDS             complement(5948..>6222)
                     /locus_tag="NL410_RS01725"
                     /old_locus_tag="NL410_001720"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000919062.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=3
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     ARG             2389..3221
                     /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          complement(5778..5951)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          2..419
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.922"
                     /coverage="99.0"
                     /evalue="1.44e-93"
     Typing          6055..6222
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.266"
                     /coverage="85.0"
                     /evalue="1.2e-68"
ORIGIN
        1 accggtgtca ttccgctgtt atggccgcgg tttctcattc cacgcctgac actcagttcc
       61 gtgaaggcag ttcgctccaa gctggactgt atgcacgaac cccccgttca gtccgaccgc
      121 tgcgccttgt ccggtaacta tcaacttgag tccaacccgg aaagacacga caaaacgcca
      181 ctggcagcag ccattagtaa caggagtgca cgagaagata gattaagagg tcttgaagta
      241 gaggcctgac tgcggctaca ctgaaagaac agttttggta atggcggtct cgtgaaccct
      301 gttaccgggt taagcagttc cccaactgac ttaaccttcg aacaaaccgc ctccccaggc
      361 ggttttttcg tttacagagc aagagattac gattcattga aaaggatctc aagaagatcc
      421 tttgtagatt actatcaatt aatcttccga acatgacacc agtcactgtt gattacggtt
      481 aaaccgctcc gtaacaggtt tccctcgtat tggttacttg cagcaccaaa gaagcaaaaa
      541 agataaatat atctacttat tgagagatga tatatttatt tccaaaatgc tacagataca
      601 tcatcatgaa acggatcacc gcaaacaggt tactcgcctg gggattccct ttcgacccga
      661 gcatccgtat gagactcatg ctcgattatt attattatag aagcccccat gaataaatcg
      721 ctcatcattt tcggcatcgt caacataacc tcggacagtt tctccgatgg aggccggtat
      781 ctggcgccag acgcagccat tgcgcaggcg cgtaagctga tggccgaggg ggcagatgtg
      841 atcgacctcg gtccggcatc cagcaatccc gacgccgcgc ctgtttcgtc cgacacagaa
      901 atcgcgcgta tcgcgccggt gctggacgcg ctcaaggcag atggcattcc cgtctcgctc
      961 gacagttatc aacccgcgac gcaagcctat gccttgtcgc gtggtgtggc ctatctcaat
     1021 gatattcgcg gttttccaga cgctgcgttc tatccgcaat tggcgaaatc atctgccaaa
     1081 ctcgtcgtta tgcattcggt gcaagacggg caggcagatc ggcgcgaggc acccgctggc
     1141 gacatcatgg atcacattgc ggcgttcttt gacgcgcgca tcgcggcgct gacgggtgcc
     1201 ggtatcaaac gcaaccgcct tgtccttgat cccggcatgg ggttttttct gggggctgct
     1261 cccgaaacct cgctctcggt gctggcgcgg ttcgatgaat tgcggctgcg cttcgatttg
     1321 ccggtgcttc tgtctgtttc gcgcaaatcc tttctgcgcg cgctcacagg ccgtggtccg
     1381 ggggatgtcg gggccgcgac actcgctgca gagcttgccg ccgccgcagg tggagctgac
     1441 ttcatccgca cacacgagcc gcgccccttg cgcgacgggc tggcggtatt ggcggcgctg
     1501 aaagaaaccg caagaattcg ttaactgcac attcgggata tttctctata ttcgcgcttc
     1561 atcagaaaac tgaaggaacc tccattgaat cgaactaata ttttttttgg tgaatcgcat
     1621 tctgactggt tgcctgtcag aggcggagaa tctggtgatt ttgtttttcg acgtggtgac
     1681 gggcatgcct tcgcgaaaat cgcacctgct tcccgccgcg gtgagctcgc tggagagcgt
     1741 gaccgcctca tttggctcaa aggtcgaggt gtggcttgcc ccgaggtcat caactggcag
     1801 gaggaacagg agggtgcatg cttggtgata acggcaattc cgggagtacc ggcggctgat
     1861 ctgtctggag cggatttgct caaagcgtgg ccgtcaatgg ggcagcaact tggcgctgtt
     1921 cacagcctat cggttgatca atgtccgttt gagcgcaggc tgtcgcgaat gttcggacgc
     1981 gccgttgatg tggtgtcccg caatgccgtc aatcccgact tcttaccgga cgaggacaag
     2041 agtacgccgc agctcgatct tttggctcgt gtcgaacgag agctaccggt gcggctcgac
     2101 caagagcgca ccgatatggt tgtttgccat ggtgatccct gcatgccgaa cttcatggtg
     2161 gaccctaaaa ctcttcaatg cacgggtctg atcgaccttg ggcggctcgg aacagcagat
     2221 cgctatgccg atttggcact catgattgct aacgccgaag agaactgggc agcgccagat
     2281 gaagcagagc gcgccttcgc tgtcctattc aatgtattgg ggatcgaagc ccccgaccgc
     2341 gaacgccttg ccttctatct gcgattggac cctctgactt ggggttgatg ttcatgccgc
     2401 ctgtttttcc tgctcattgg cacgtttcgc aacctgttct cattgcggac accttttcca
     2461 gcctcgtttg gaaagtttca ttgccagacg ggactcctgc aatcgtcaag ggattgaaac
     2521 ctatagaaga cattgctgat gaactgcgcg gggccgacta tctggtatgg cgcaatggga
     2581 ggggagcagt ccggttgctc ggtcgtgaga acaatctgat gttgctcgaa tatgccgggg
     2641 agcgaatgct ctctcacatc gttgccgagc acggcgacta ccaggcgacc gaaattgcag
     2701 cggaactaat ggcgaagctg tatgccgcat ctgaggaacc cctgccttct gcccttctcc
     2761 cgatccggga tcgctttgca gctttgtttc agcgggcgcg cgatgatcaa aacgcaggtt
     2821 gtcaaactga ctacgtccac gcggcgatta tagccgatca aatgatgagc aatgcctcgg
     2881 aactgcgtgg gctacatggc gatctgcatc atgaaaacat catgttctcc agtcgcggct
     2941 ggctggtgat agatcccgtc ggtctggtcg gtgaagtggg ctttggcgcc gccaatatgt
     3001 tctacgatcc ggctgacaga gacgaccttt gtctcgatcc tagacgcatt gcacagatgg
     3061 cggacgcatt ctctcgtgcg ctggacgtcg atccgcgtcg cctgctcgac caggcgtacg
     3121 cttatgggtg cctttccgca gcttggaacg cggatggaga agaggagcaa cgcgatctag
     3181 ctatcgcggc cgcgatcaag caggtgcgac agacgtcata ctagatatca agcgacttct
     3241 cctatcccct gggaacacat caatctcacc ggagaatatc gctggccaaa gccttagcgt
     3301 aggattccgc cccttcccgc aaacgacccc aaacaggaaa cgcagctgaa acgggaagct
     3361 caacacccac tgacgcatgg gttgttcagg cagtacttca tcaaccagca aggcggcact
     3421 ttcggccatc cgccgcgccc cacagctcgg gcagaaaccg cgacgcttac agctgaaagc
     3481 gaccaggtgc tcggcgtggc aagactcgca gcgaacccgt agaaagccat gctccagccg
     3541 cccgcattgg agaaattctt caaattcccg ttgcacatag cccggcaatt cctttccctg
     3601 ctctgccata agcgcagcga atgccgggta atactcgtca acgatctgat agagaagggt
     3661 ttgctcgggt cggtggctct ggtaacgacc agtatcccga tcccggctgg ccgtcctggc
     3721 cgccacatga ggcatgttcc gcgtccttgc aatactgtgt ttacatacag tctatcgctt
     3781 agcggaaagt tcttttaccc tcagccgaaa tgcctgccgt tgctagacat tgccagccag
     3841 tgcccgtcac tcccactctt acattgttcg cagtatctag gtacatgtta ttgcgtgcac
     3901 cttcatgatg tataatgtta ttaatgacag cagaaagatc gacagaatta atattcttcg
     3961 tacctgggac agttatcggg tgtcggccag tgatgagacc aaaggatgca gtataagatg
     4021 aaccactact attatcatgg ccaccattac caccaccgtt aaaactacct cccgaacttc
     4081 cagagccgct atgaccatca ttgtaggggt catttggtcc catgtgacca aaaccaccga
     4141 cagtaccgct atttaactct gtactcataa aattatcctc tttgactttt aaaaacagca
     4201 aaaactgtat ttataacaat gtgtttatat acagtattcg aaatactacg cccgtcaaaa
     4261 ccacaccgtc aacaggtttt ttgtgtattt ttcacgcctc acgggcagcc tcagaccttt
     4321 tgtgttaaaa cagtaatatg ttctgctgtt acaatacggt acacacagga gacactgtca
     4381 cttttatggc atggcacaca gttcaagaga cactgaaatt aacaggaaag tcgcgctcgc
     4441 aattatatcg tgacatggct aaaggccttg tcagctatcg cacaggaaaa aatgatcgcc
     4501 gggagttcga gaccagtgaa ctgattcggg cctatggcga gctgcgcact tctgagacac
     4561 caaaaaggca caaggaggga cactccaaat ctgtcgttag ccaggcggaa aatgctcagc
     4621 tagacgtcat tcagcagaaa ctggacgctc tgcagcagac tgttacccta atgcttgaag
     4681 acaagatggc gcgggaagca gaaaaccgcc tgcgaaatga ggagagggaa caactacagg
     4741 ccgaaattag ccgtctggct gacgcgctgg cacaggaaaa aaagcgggga ttctggtcgc
     4801 ggctgtttcg ctccggttca gagtaacagt gcaggtgact ctgatttacc ataacatctg
     4861 ttatcagcac cgcctgagag gccctcaggg cgtttctgac gggaaaccgg taaaacaggc
     4921 aacaaaccac ccgaaaaccc gccagaaacg cgcaggctct gtttttacgg catgcatgag
     4981 tatgcgcaca agtgcatagc gcggaaattc acaccattca gccggggtaa gtcctgtttc
     5041 cggcgttctt cccatccgaa aacggtgaac ggggacgcaa tttattgcgt ggccgtgaag
     5101 cgttgccggc gcagccggaa aacccgctgt cagcacgttc aggaaggggg tgatgtacaa
     5161 atggcacaga ggatgaaagt gacgtatgag ctgaaggaat gatgtaaaag tgatgtataa
     5221 gtgatgtaaa agtgatgtat aagtgatgta aaagtgatgt atgaactgaa ggagcgatgt
     5281 aattctgtag tcaggaagaa taacccgttc atgcaggcat gaacgataca gtgaggaacg
     5341 ctttttttgt cacgatctcc ccttaacctg cgtaaatcac ccgccatggt tgattatttt
     5401 tcaacctcaa aatggtcata cacctaacgc agccgcgatt ttcatcgcaa ctgcatgaat
     5461 taaaagaaaa aaaaggaata tttcgttttc acgagtaata cccgggtatt aaaaatccac
     5521 tgtaattaca tgaaaataaa gaaataaaag gtaataccgg agtattacca cgtacgcggg
     5581 caagcgaaaa agctataacg cttcccggcc gacaggcgac ccaaaatcca caggggcatg
     5641 caggttctct tcagtaacct gcgccattaa atcaaaaagg tcatattcgc cgggaagctg
     5701 cgtatcagtc gaatccagtt gttcatcata ttcagatggc atggggtgat atccagtagc
     5761 tgagaggttg ttagcgggtt tcggggcgca gccctgaacc agtcatgtag cgctagcgga
     5821 gtgtatactg gcttactatg ttgccacgat tgcgaaaatc agtgaagtgc ttcatgtggc
     5881 aggagaaaaa aggcagcacc ggcgcgtcag cagaatatgc gatacaggag atattccgct
     5941 tcctcgctca ctgactcgct acgctcggtc gttcggctgc ggcgagcggt accggcttac
     6001 ggacggggac ggaaatttcc tggaagatac caggaagaca cttagcaaag aagagataag
     6061 gccacggcga agccgttttt ccataggctc cgcccccctg acaagcatcg caaaatctga
     6121 cgctcaaatc agtggtggcg aaacccgaca ggactataaa gatcccaggc gtttccccct
     6181 ggtagctccc tcgtgcgctc tcctgttcct gcctttcggt tt
//
