LOCUS       NZ_CP116991             6222 bp    DNA     linear   CON 11-MAR-2024
DEFINITION  Escherichia coli strain MLI108K1 plasmid p6_MLI108-1, complete
            sequence.
ACCESSION   NZ_CP116991
VERSION     NZ_CP116991.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29553891
            Assembly: GCF_024700875.2
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  JOURNAL   Unpublished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 Date                   :: 03/11/2024 05:22:30
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,988
            CDSs (total)                      :: 4,863
            Genes (coding)                    :: 4,603
            CDSs (with protein)               :: 4,603
            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)              :: 260
            CDSs (without protein)            :: 260
            Pseudo Genes (ambiguous residues) :: 0 of 260
            Pseudo Genes (frameshifted)       :: 83 of 260
            Pseudo Genes (incomplete)         :: 179 of 260
            Pseudo Genes (internal stop)      :: 53 of 260
            Pseudo Genes (multiple problems)  :: 51 of 260
            Pseudo Genes (short protein)      :: 3 of 260
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116991.1.
            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="MLI108K1"
                     /isolation_source="stool sample"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p6_MLI108-1"
                     /geo_loc_name="Mali: Koulikoro"
                     /lat_lon="12.52 N 7.34 W"
                     /collection_date="2014-07-24"
                     /collected_by="Bundeswehr Medical Service"
     gene            complement(64..504)
                     /locus_tag="NL409_RS01690"
                     /old_locus_tag="NL409_001680"
     CDS             complement(64..504)
                     /locus_tag="NL409_RS01690"
                     /old_locus_tag="NL409_001680"
                     /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            722..1111
                     /locus_tag="NL409_RS01695"
                     /old_locus_tag="NL409_001685"
     CDS             722..1111
                     /locus_tag="NL409_RS01695"
                     /old_locus_tag="NL409_001685"
                     /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            1155..>1559
                     /locus_tag="NL409_RS01700"
                     /old_locus_tag="NL409_001690"
                     /pseudo=""
     CDS             1155..>1559
                     /locus_tag="NL409_RS01700"
                     /old_locus_tag="NL409_001690"
                     /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(1666..2502)
                     /locus_tag="NL409_RS01705"
                     /old_locus_tag="NL409_001695"
     CDS             complement(1666..2502)
                     /locus_tag="NL409_RS01705"
                     /old_locus_tag="NL409_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(2502..3305)
                     /gene="aph(3'')-Ib"
                     /locus_tag="NL409_RS01710"
                     /old_locus_tag="NL409_001700"
     ARG             complement(2506..3305)
                     /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(3366..4181)
                     /gene="sul2"
                     /locus_tag="NL409_RS01715"
                     /old_locus_tag="NL409_001705"
     ARG             complement(3370..4181)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(4641..4799)
                     /locus_tag="NL409_RS24905"
     CDS             complement(4641..4799)
                     /locus_tag="NL409_RS24905"
                     /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            5370..5519
                     /locus_tag="NL409_RS01720"
                     /old_locus_tag="NL409_001710"
     CDS             5370..5519
                     /locus_tag="NL409_RS01720"
                     /old_locus_tag="NL409_001710"
                     /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(1670..2502)
                     /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          5162..5335
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          complement(4633..5238)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cctgagggcc tctcaggcgg tgctgataac agatgttatg gtaaatcaga gtcacctgca
       61 ctgttactct gaaccggagc gaaacagccg cgaccagaat ccccgctttt tttcctgtgc
      121 cagcgcgtca gccagacggc taatttcggc ctgtagttgt tccctctcct catttcgcag
      181 gcggttttct gcttcccgcg ccatcttgtc ttcaagcatt agggtaacag tctgctgcag
      241 agcgtccagt ttctgctgaa tgacgtctag ctgagcattt tccgcctggc taacgacaga
      301 tttggagtgt ccctccttgt gcctttttgg tgtctcagaa gtgcgcagct cgccataggc
      361 ccgaatcagt tcactggtct cgaactcccg gcgatcattt tttcctgtgc gatagctgac
      421 aaggccttta gccatgtcac gatataattg cgagcgcgac tttcctgtta atttcagtgt
      481 ctcttgaact gtgtgccatg ccataaaagt gacagtgtct cctgtgtgta ccgtattgta
      541 acagcagaac atattactgt tttaacacaa aaggtctgag gctgcccgtg aggcgtgaaa
      601 aatacacaaa aaacctgttg acggtgtggt tttgacgggc gtagtatttc gaatactgta
      661 tataaacaca ttgttataaa tacagttttt gctgttttta aaagtcaaag aggataattt
      721 tatgagtaca gagttaaata gcggtactgt cggtggtttt ggtcacatgg gaccaaatga
      781 cccctacaat gatggtcata gcggctctgg aagttcggga ggtagtttta acggtggtgg
      841 taatggtggc catgataata gtagtggttc atcttatact gcatcctttg gtctcatcac
      901 tggccgacac ccgataactg tcccaggtac gaagaatatt aattctgtcg atctttctgc
      961 tgtcattaat aacattatac atcatgaagg tgcacgcaat aacatgtacc tagatactgc
     1021 gaacaatgta agagtgggag tgacgggcac tggctggcaa tgtctagcaa cggcaggcat
     1081 ttcggctgag ggtaaaagaa ctttccgcta agcgatagac tgtatgtaaa cacagtattg
     1141 caaggacgcg gaacatgcct catgtggcgg ccaggacggc cagccgggat cgggatactg
     1201 gtcgttacca gagccaccga cccgagcaaa cccttctcta tcagatcgtt gacgagtatt
     1261 acccggcatt cgctgcgctt atggcagagc agggaaagga attgccgggc tatgtgcaac
     1321 gggaatttga agaatttctc caatgcgggc ggctggagca tggctttcta cgggttcgct
     1381 gcgagtcttg ccacgccgag cacctggtcg ctttcagctg taagcgtcgc ggtttctgcc
     1441 cgagctgtgg ggcgcggcgg atggccgaaa gtgccgcctt gctggttgat gaagtactgc
     1501 ctgaacaacc catgcgtcag tgggtgttga gcttcccgtt tcagctgcgt ttcctgtttg
     1561 gggtcgtttg cgggaagggg cggaatccta cgctaaggct ttggccagcg atattctccg
     1621 gtgagattga tgtgttccca ggggatagga gaagtcgctt gatatctagt atgacgtctg
     1681 tcgcacctgc ttgatcgcgg ccgcgatagc tagatcgcgt tgctcctctt ctccatccgc
     1741 gttccaagct gcggaaaggc acccataagc gtacgcctgg tcgagcaggc gacgcggatc
     1801 gacgtccagc gcacgagaga atgcgtccgc catctgtgca atgcgtctag gatcgagaca
     1861 aaggtcgtct ctgtcagccg gatcgtagaa catattggcg gcgccaaagc ccacttcacc
     1921 gaccagaccg acgggatcta tcaccagcca gccgcgactg gagaacatga tgttttcatg
     1981 atgcagatcg ccatgtagcc cacgcagttc cgaggcattg ctcatcattt gatcggctat
     2041 aatcgccgcg tggacgtagt cagtttgaca acctgcgttt tgatcatcgc gcgcccgctg
     2101 aaacaaagct gcaaagcgat cccggatcgg gagaagggca gaaggcaggg gttcctcaga
     2161 tgcggcatac agcttcgcca ttagttccgc tgcaatttcg gtcgcctggt agtcgccgtg
     2221 ctcggcaacg atgtgagaga gcattcgctc cccggcatat tcgagcaaca tcagattgtt
     2281 ctcacgaccg agcaaccgga ctgctcccct cccattgcgc cataccagat agtcggcccc
     2341 gcgcagttca tcagcaatgt cttctatagg tttcaatccc ttgacgattg caggagtccc
     2401 gtctggcaat gaaactttcc aaacgaggct ggaaaaggtg tccgcaatga gaacaggttg
     2461 cgaaacgtgc caatgagcag gaaaaacagg cggcatgaac atcaacccca agtcagaggg
     2521 tccaatcgca gatagaaggc aaggcgttcg cggtcggggg cttcgatccc caatacattg
     2581 aataggacag cgaaggcgcg ctctgcttca tctggcgctg cccagttctc ttcggcgtta
     2641 gcaatcatga gtgccaaatc ggcatagcga tctgctgttc cgagccgccc aaggtcgatc
     2701 agacccgtgc attgaagagt tttagggtcc accatgaagt tcggcatgca gggatcacca
     2761 tggcaaacaa ccatatcggt gcgctcttgg tcgagccgca ccggtagctc tcgttcgaca
     2821 cgagccaaaa gatcgagctg cggcgtactc ttgtcctcgt ccggtaagaa gtcgggattg
     2881 acggcattgc gggacaccac atcaacggcg cgtccgaaca ttcgcgacag cctgcgctca
     2941 aacggacatt gatcaaccga taggctgtga acagcgccaa gttgctgccc cattgacggc
     3001 cacgctttga gcaaatccgc tccagacaga tcagccgccg gtactcccgg aattgccgtt
     3061 atcaccaagc atgcaccctc ctgttcctcc tgccagttga tgacctcggg gcaagccaca
     3121 cctcgacctt tgagccaaat gaggcggtca cgctctccag cgagctcacc gcggcgggaa
     3181 gcaggtgcga ttttcgcgaa ggcatgcccg tcaccacgtc gaaaaacaaa atcaccagat
     3241 tctccgcctc tgacaggcaa ccagtcagaa tgcgattcac caaaaaaaat attagttcga
     3301 ttcaatggag gttccttcag ttttctgatg aagcgcgaat atagagaaat atcccgaatg
     3361 tgcagttaac gaattcttgc ggtttctttc agcgccgcca ataccgccag cccgtcgcgc
     3421 aaggggcgcg gctcgtgtgt gcggatgaag tcagctccac ctgcggcggc ggcaagctct
     3481 gcagcgagtg tcgcggcccc gacatccccc ggaccacggc ctgtgagcgc gcgcagaaag
     3541 gatttgcgcg aaacagacag aagcaccggc aaatcgaagc gcagccgcaa ttcatcgaac
     3601 cgcgccagca ccgagagcga ggtttcggga gcagccccca gaaaaaaccc catgccggga
     3661 tcaaggacaa ggcggttgcg tttgataccg gcacccgtca gcgccgcgat gcgcgcgtca
     3721 aagaacgccg caatgtgatc catgatgtcg ccagcgggtg cctcgcgccg atctgcctgc
     3781 ccgtcttgca ccgaatgcat aacgacgagt ttggcagatg atttcgccaa ttgcggatag
     3841 aacgcagcgt ctggaaaacc gcgaatatca ttgagatagg ccacaccacg cgacaaggca
     3901 taggcttgcg tcgcgggttg ataactgtcg agcgagacgg gaatgccatc tgccttgagc
     3961 gcgtccagca ccggcgcgat acgcgcgatt tctgtgtcgg acgaaacagg cgcggcgtcg
     4021 ggattgctgg atgccggacc gaggtcgatc acatctgccc cctcggccat cagcttacgc
     4081 gcctgcgcaa tggctgcgtc tggcgccaga taccggcctc catcggagaa actgtccgag
     4141 gttatgttga cgatgccgaa aatgatgagc gatttattca tgggggcttc tataataata
     4201 ataatcgagc atgagtctca tacggatgct cgggtcgaaa gggaatcccc aggcgagtaa
     4261 cctgtttgcg gtgatccgtt tcatgatgat gtatctgtag cattttggaa ataaatatat
     4321 catctctcaa taagtagata tatttatctt ttttgcttct ttggtgctgc aagtaaccaa
     4381 tacgagggaa acctgttacg gagcggttta accgtaatca acagtgactg gtgtcatgtt
     4441 cggaagatta attgatagta atctacaaag gatcttcttg agatcctttt caatgaatcg
     4501 taatctcttg ctctgtaaac gaaaaaaccg cctggggagg cggtttgttc gaaggttaag
     4561 tcagttgggg aactgcttaa cccggtaaca gggttcacga gaccgccatt accaaaactg
     4621 ttctttcagt gtagccgcag tcaggcctct acttcaagac ctcttaatct atcttctcgt
     4681 gcactcctgt tactaatggc tgctgccagt ggcgttttgt cgtgtctttc cgggttggac
     4741 tcaagttgat agttaccgga caaggcgcag cggtcggact gaacgggggg ttcgtgcata
     4801 cagtccagct tggagcgaac tgccttcacg gaactgagtg tcaggcgtgg aatgagaaac
     4861 cgcggccata acagcggaat gacaccggta aaccgaaagg caggaacagg agagcgcacg
     4921 agggagctac cagggggaaa cgcctgggat ctttatagtc ctgtcgggtt tcgccaccac
     4981 tgatttgagc gtcagatttt gcgatgcttg tcaggggggc ggagcctatg gaaaaacggc
     5041 ttcgccgtgg ccttatctct tctttgctaa gtgtcttcct ggtatcttcc aggaaatttc
     5101 cgtccccgtc cgtaagccgg taccgctcgc cgcagccgaa cgaccgagcg tagcgagtca
     5161 gtgagcgagg aagcggaata tctcctgtat cgcatattct gctgacgcgc cggtgctgcc
     5221 ttttttctcc tgccacatga agcacttcac tgattttcgc aatcgtggca acatagtaag
     5281 ccagtataca ctccgctagc gctacatgac tggttcaggg ctgcgccccg aaacccgcta
     5341 acaacctctc agctactgga tatcacccca tgccatctga atatgatgaa caactggatt
     5401 cgactgatac gcagcttccc ggcgaatatg acctttttga tttaatggcg caggttactg
     5461 aagagaacct gcatgcccct gtggattttg ggtcgcctgt cggccgggaa gcgttatagc
     5521 tttttcgctt gcccgcgtac gtggtaatac tccggtatta ccttttattt ctttattttc
     5581 atgtaattac agtggatttt taatacccgg gtattactcg tgaaaacgaa atattccttt
     5641 tttttctttt aattcatgca gttgcgatga aaatcgcggc tgcgttaggt gtatgaccat
     5701 tttgaggttg aaaaataatc aaccatggcg ggtgatttac gcaggttaag gggagatcgt
     5761 gacaaaaaaa gcgttcctca ctgtatcgtt catgcctgca tgaacgggtt attcttcctg
     5821 actacagaat tacatcgctc cttcagttca tacatcactt ttacatcact tatacatcac
     5881 ttttacatca cttatacatc acttttacat cattccttca gctcatacgt cactttcatc
     5941 ctctgtgcca tttgtacatc acccccttcc tgaacgtgct gacagcgggt tttccggctg
     6001 cgccggcaac gcttcacggc cacgcaataa attgcgtccc cgttcaccgt tttcggatgg
     6061 gaagaacgcc ggaaacagga cttaccccgg ctgaatggtg tgaatttccg cgctatgcac
     6121 ttgtgcgcat actcatgcat gccgtaaaaa cagagcctgc gcgtttctgg cgggttttcg
     6181 ggtggtttgt tgcctgtttt accggtttcc cgtcagaaac gc
//
