LOCUS       NZ_CP117051             6178 bp    DNA     linear   CON 11-MAR-2024
DEFINITION  Escherichia coli strain MLI106K4 plasmid p6_MLI106-4, complete
            sequence.
ACCESSION   NZ_CP117051
VERSION     NZ_CP117051.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29553889
            Assembly: GCF_024331525.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6178)
  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  JOURNAL   Unpublished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 6178)
  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 6178)
  AUTHORS   Zautner,A.E. and Riediger,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-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 05:25:21
            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)                     :: 5,063
            CDSs (total)                      :: 4,940
            Genes (coding)                    :: 4,671
            CDSs (with protein)               :: 4,671
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 269
            CDSs (without protein)            :: 269
            Pseudo Genes (ambiguous residues) :: 0 of 269
            Pseudo Genes (frameshifted)       :: 79 of 269
            Pseudo Genes (incomplete)         :: 197 of 269
            Pseudo Genes (internal stop)      :: 49 of 269
            Pseudo Genes (multiple problems)  :: 56 of 269
            Pseudo Genes (short protein)      :: 4 of 269
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP117051.1.
            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..6178
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MLI106K4"
                     /isolation_source="stool sample"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p6_MLI106-4"
                     /geo_loc_name="Mali: Koulikoro"
                     /lat_lon="12.52 N 7.34 W"
                     /collection_date="2014-06-24"
                     /collected_by="Bundeswehr Medical Service"
     gene            1..159
                     /locus_tag="NL407_RS01060"
                     /old_locus_tag="NL407_001060"
     CDS             1..159
                     /locus_tag="NL407_RS01060"
                     /old_locus_tag="NL407_001060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /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            619..1434
                     /gene="sul2"
                     /locus_tag="NL407_RS01065"
                     /old_locus_tag="NL407_001065"
     ARG             620..1431
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             1541..2298
                     /name="APH(3'')-Ib"
                     /gene="APH(3'')-Ib"
                     /gene_name="APH(3'')"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="99.21"
                     /coverage="94.38"
     ARG             1496..2295
                     /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            2298..3134
                     /locus_tag="NL407_RS01075"
                     /old_locus_tag="NL407_001075"
     CDS             2298..3134
                     /locus_tag="NL407_RS01075"
                     /old_locus_tag="NL407_001075"
                     /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(<3241..3645)
                     /locus_tag="NL407_RS01080"
                     /old_locus_tag="NL407_001080"
                     /pseudo=""
     CDS             complement(<3241..3645)
                     /locus_tag="NL407_RS01080"
                     /old_locus_tag="NL407_001080"
                     /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(3689..4078)
                     /locus_tag="NL407_RS01085"
                     /old_locus_tag="NL407_001085"
     CDS             complement(3689..4078)
                     /locus_tag="NL407_RS01085"
                     /old_locus_tag="NL407_001085"
                     /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            4296..4736
                     /locus_tag="NL407_RS01090"
                     /old_locus_tag="NL407_001090"
     CDS             4296..4736
                     /locus_tag="NL407_RS01090"
                     /old_locus_tag="NL407_001090"
                     /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(5459..5608)
                     /locus_tag="NL407_RS01095"
                     /old_locus_tag="NL407_001095"
     CDS             complement(5459..5608)
                     /locus_tag="NL407_RS01095"
                     /old_locus_tag="NL407_001095"
                     /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             2299..3131
                     /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(5644..5817)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          2..119
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.215"
                     /coverage="94.0"
                     /evalue="7.36e-44"
     Typing          5741..6178
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.403"
                     /coverage="99.0"
                     /evalue="1.5000000000000002e-168"
ORIGIN
        1 atgcacgaac cccccgttca gtccgaccgc tgcgccttgt ccggtaacta tcaacttgag
       61 tccaacccgg aaagacacga caaaacgcca ctggcagcag ccattagtaa caggagtgca
      121 cgagaagata gattaagagg tcttgaagta gaggcctgac tgcggctaca ctgaaagaac
      181 agttttggta atggcggtct cgtgaaccct gttaccgggt taagcagttc cccaactgac
      241 ttaaccttcg aacaaaccgc ctccccaggc ggttttttcg tttacagagc aagagattac
      301 gattcattga aaaggatctc aagaagatcc tttgtagatt actatcaatt aatcttccga
      361 acatgacacc agtcactgtt gattacggtt aaaccgctcc gtaacaggtt tccctcgtat
      421 tggtgacttg cagcaccaaa gaagcaaaaa agataaatat atctacttat tgagagatga
      481 tatatttatt tccaaaatgc tacagataca tcatcatgaa acggatcacc gcaaacaggt
      541 tactcgcctg gggattccct ttcgacccga gcatccgtat gagactcatg ctcgattatt
      601 attattatag aagcccccat gaataaatcg ctcatcattt tcggcatcgt caacataacc
      661 tcggacagtt tctccgatgg aggccggtat ctggcgccag acgcagccat tgcgcaggcg
      721 cgtaagctga tggccgaggg ggcagatgtg atcgacctcg gtccggcatc cagcaatccc
      781 gacgccgcgc ctgtttcgtc cgacacagaa atcgcgcgta tcgcgccggt gctggacgcg
      841 ctcaaggcag atggcattcc cgtctcgctc gacagttatc aacccgcgac gcaagcctat
      901 gccttgtcgc gtggtgtggc ctatctcaat gatattcgcg gttttccaga cgctgcgttc
      961 tatccgcaat tggcgaaatc atctgccaaa ctcgtcgtta tgcattcggt gcaagacggg
     1021 caggcagatc ggcgcgaggc acccgctggc gacatcatgg atcacattgc ggcgttcttt
     1081 gacgcgcgca tcgcggcgct gacgggtgcc ggtatcaaac gcaaccgcct tgtccttgat
     1141 cccggcatgg ggttttttct gggggctgct cccgaaacct cgctctcggt gctggcgcgg
     1201 ttcgatgaat tgcggctgcg cttcgatttg ccggtgcttc tgtctgtttc gcgcaaatcc
     1261 tttctgcgcg cgctcacagg ccgtggtccg ggggatgtcg gggccgcgac actcgctgca
     1321 gagcttgccg ccgccgcagg tggagctgac ttcatccgca cacacgagcc gcgccccttg
     1381 cgcgacgggc tggcggtatt ggcggcgctg aaagaaaccg caagaattcg ttaactgcac
     1441 attcgggata tttctctata ttcgcgcttc atcagaaaac tgaaggaacc tccattaaat
     1501 cgaactaata ttttttttgg tgaatcgcat tctgactggt tgcctgtcag aggcggagaa
     1561 tctggtgatt ttgtttttcg acgtggtgac gggcatgcct tcgcgaaaat cgcacctgct
     1621 tcccgccgcg gtgagctcgc tggagagcgt gaccgcctca tttggctcaa aggtcgaggt
     1681 gtggcttgcc ccgaggtcat caactggcag gaggaacagg agggtgcatg cttggtgata
     1741 acggcaattc cgggagtacc ggcggctgat ctgtctggag cggatttgct caaagcgtgg
     1801 ccgtcaatgg ggcagcaact tggcgctgtt cacagcctat cggttgatca atgtccgttt
     1861 gagcgcaggc tgtcgcgaat gttcggacgc gccgttgatg tggtgtcccg caatgccgtc
     1921 aatcccgact tcttaccgga cgaggacaag agtacgccgc agctcgatct tttggctcgt
     1981 gtcgaacgag agctaccggt gcggctcgac caagagcgca ccgatatggt tgtttgccat
     2041 ggtgatccct gcatgccgaa cttcatggtg gaccctaaaa ctcttcaatg cacgggtctg
     2101 atcgaccttg ggcggctcgg aacagcagat cgctatgccg atttggcact catgattgct
     2161 aacgccgaag agaactgggc agcgccagat gaagcagagc gcgccttcgc tgtcctattc
     2221 aatgtattgg ggatcgaagc ccccgaccgc gaacgccttg ccttctatct gcgattggac
     2281 cctctgactt ggggttgatg ttcatgccgc ctgtttttcc tgctcattgg cacgtttcgc
     2341 aacctgttct cattgcggac accttttcca gcctcgtttg gaaagtttca ttgccagacg
     2401 ggactcctgc aatcgtcaag ggattgaaac ctatagaaga cattgctgat gaactgcgcg
     2461 gggccgacta tctggtatgg cgcaatggga ggggagcagt ccggttgctc ggtcgtgaga
     2521 acaatctgat gttgctcgaa tatgccgggg agcgaatgct ctctcacatc gttgccgagc
     2581 acggcgacta ccaggcgacc gaaattgcag cggaactaat ggcgaagctg tatgccgcat
     2641 ctgaggaacc cctgccttct gcccttctcc cgatccggga tcgctttgca gctttgtttc
     2701 agcgggcgcg cgatgatcaa aacgcaggtt gtcaaactga ctacgtccac gcggcgatta
     2761 tagccgatca aatgatgagc aatgcctcgg aactgcgtgg gctacatggc gatctgcatc
     2821 atgaaaacat catgttctcc agtcgcggct ggctggtgat agatcccgtc ggtctggtcg
     2881 gtgaagtggg ctttggcgcc gccaatatgt tctacgatcc ggctgacaga gacgaccttt
     2941 gtctcgatcc tagacgcatt gcacagatgg cggacgcatt ctctcgtgcg ctggacgtcg
     3001 atccgcgtcg cctgctcgac caggcgtacg cttatgggtg cctttccgca gcttggaacg
     3061 cggatggaga agaggagcaa cgcgatctag ctatcgcggc cgcgatcaag caggtgcgac
     3121 agacgtcata ctagatatca agcgacttct cctatcccct gggaacacat caatctcacc
     3181 ggagaatatc gctggccaaa gccttagcgt aggattccgc cccttcccgc aaacgacccc
     3241 aaacaggaaa cgcagctgaa acgggaagct caacacccac tgacgcatgg gttgttcagg
     3301 cagtacttca tcaaccagca aggcggcact ttcggccatc cgccgcgccc cacagctcgg
     3361 gcagaaaccg cgacgcttac agctgaaagc gaccaggtgc tcggcgtggc aagactcgca
     3421 gcgaacccgt agaaagccat gctccagccg cccgcattgg agaaattctt caaattcccg
     3481 ttgcacatag cccggcaatt cctttccctg ctctgccata agcgcagcga atgccgggta
     3541 atactcgtca acgatctgat agagaagggt ttgctcgggt cggtggctct ggtaacgacc
     3601 agtatcccga tcccggctgg ccgtcctggc cgccacatga ggcatgttcc gcgtccttgc
     3661 aatactgtgt ttacatacag tctatcgctt agcggaaagt tcttttaccc tcagccgaaa
     3721 tgcctgccgt tgctagacat tgccagccag tgcccgtcac tcccactctt acattgttcg
     3781 cagtatctag gtacatgtta ttgcgtgcac cttcatgatg tataatgtta ttaatgacag
     3841 cagaaagatc gacagaatta atattcttcg tacctgggac agttatcggg tgtcggccag
     3901 tgatgagacc aaaggatgca gtataagatg aaccactact attatcatgg ccaccattac
     3961 caccaccgtt aaaactacct cccgaacttc cagagccgct atgaccatca ttgtaggggt
     4021 catttggtcc catgtgacca aaaccaccga cagtaccgct atttaactct gtactcataa
     4081 aattatcctc tttgactttt aaaaacagca aaaactgtat ttataacaat gtgtttatat
     4141 acagtattcg aaatactacg cccgtcaaaa ccacaccgtc aacaggtttt ttgtgtattt
     4201 ttcacgcctc acgggcagcc tcagaccttt tgtgttaaaa cagtaatatg ttctgctgtt
     4261 acaatacggt acacacagga gacactgtca cttttatggc atggcacaca gttcaagaga
     4321 cactgaaatt aacaggaaag tcgcgctcgc aattatatcg tgacatggct aaaggccttg
     4381 tcagctatcg cacaggaaaa aatgatcgcc gggagttcga gaccagtgaa ctgattcggg
     4441 cctatggcga gctgcgcact tctgagacac caaaaaggca caaggaggga cactccaaat
     4501 ctgtcgttag ccaggcggaa aatgctcagc tagacgtcat tcagcagaaa ctggacgctc
     4561 tgcagcagac tgttacccta atgcttgaag acaagatggc gcgggaagca gaaaaccgcc
     4621 tgcgaaatga ggagagggaa caactacagg ccgaaattag ccgtctggct gacgcgctgg
     4681 cacaggaaaa aaagcgggga ttctggtcgc ggctgtttcg ctccggttca gagtaacagt
     4741 gcaggtgact ctgatttacc ataacatctg ttatcagcac cgcctgagag gccctcaggg
     4801 cgtttctgac gggaaaccgg taaaacaggc aacaaaccac ccgaaaaccc gccagaaacg
     4861 cgcaggctct gtttttacgg catgcatgag tatgcgcaca agtgcatagc gcggaaattc
     4921 acaccattca gccggggtaa gtcctgtttc cggcgttctt cccatccgaa aacggtgaac
     4981 ggggacgcaa tttattgcgt ggccgtgaag cgttgccggc gcagccggaa aacccgctgt
     5041 cagcacgttc aggaaggggg tgatgtacaa atggcacaga ggatgaaagt gacgtatgag
     5101 ctgaaggaat gatgtaaaag tgatgtatga actgaaggag cgatgtaatt ctgtagtcag
     5161 gaagaataac ccgttcatgc aggcatgaac gatacagtga ggaacgcttt ttttgtcacg
     5221 atctcccctt aacctgcgta aatcacccgc catggttgat tatttttcaa cctcaaaatg
     5281 gtcatacacc taacgcagcc gcgattttca tcgcaactgc atgaattaaa agaaaaaaaa
     5341 ggaatatttc gttttcacga gtaatacccg ggtattaaaa atccactgta attacatgaa
     5401 aataaagaaa taaaaggtaa taccggagta ttaccacgta cgcgggcaag cgaaaaagct
     5461 ataacgcttc ccggccgaca ggcgacccaa aatccacagg ggcatgcagg ttctcttcag
     5521 taacctgcgc cattaaatca aaaaggtcat attcgccggg aagctgcgta tcagtcgaat
     5581 ccagttgttc atcatattca gatggcatgg ggtgatatcc agtagctgag aggttgttag
     5641 cgggtttcgg ggcgcagccc tgaaccagtc atgtagcgct agcggagtgt atactggctt
     5701 actatgttgc cacgattgcg aaaatcagtg aagtgcttca tgtggcagga gaaaaaaggc
     5761 agcaccggcg cgtcagcaga atatgcgata caggagatat tccgcttcct cgctcactga
     5821 ctcgctacgc tcggtcgttc ggctgcggcg agcggtaccg gcttacggac ggggacggaa
     5881 atttcctgga agataccagg aagacactta gcaaagaaga gataaggcca cggcgaagcc
     5941 gtttttccat aggctccgcc cccctgacaa gcatcgcaaa atctgacgct caaatcagtg
     6001 gtggcgaaac ccgacaggac tataaagatc ccaggcgttt ccccctggta gctccctcgt
     6061 gcgctctcct gttcctgcct ttcggtttac cggtgtcatt ccgctgttat ggccgcggtt
     6121 tctcattcca cgcctgacac tcagttccgt gaaggcagtt cgctccaagc tggactgt
//
