LOCUS       NZ_CP116992             3133 bp    DNA     linear   CON 11-MAR-2024
DEFINITION  Escherichia coli strain MLI108K1 plasmid p3_MLI108-1, complete
            sequence.
ACCESSION   NZ_CP116992
VERSION     NZ_CP116992.1
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 3133)
  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  JOURNAL   Unpublished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 3133)
  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 3133)
  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
            CP116992.1.
            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..3133
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MLI108K1"
                     /isolation_source="stool sample"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p3_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(<1..746)
                     /locus_tag="NL409_RS01725"
                     /old_locus_tag="NL409_001715"
     CDS             complement(<1..746)
                     /locus_tag="NL409_RS01725"
                     /old_locus_tag="NL409_001715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001127762.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_272789942.1"
                     /translation="MDTTSLISSISVPRLSFYETFLGCATDQEKVGAYVAYQDLSGDFF
                     CLVQMIEVALRNAINNTIKANHGPAWYDSIPQTKKSQDLVLNAKQKALDECGVRYTDDD
                     VICRLTFGFWVYMLDAPYRDTQRPCYIWTPENKAKTFPHAKNPLGGGDMKVKALFDEFH
                     KVLLFRNRLFHHEPIWKKHHCKSHSQAINNMLKEFNFLMNALSIVSNEKKELIEFIGHD
                     RRFYERCTIEYVMGIIGRIKCRELKVA"
                     /name="hypothetical protein"
     gene            complement(1205..1528)
                     /gene="mobA"
                     /locus_tag="NL409_RS01730"
                     /old_locus_tag="NL409_001720"
     CDS             complement(1205..1528)
                     /gene="mobA"
                     /locus_tag="NL409_RS01730"
                     /old_locus_tag="NL409_001720"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            1813..2007
                     /locus_tag="NL409_RS01735"
                     /old_locus_tag="NL409_001725"
     CDS             1813..2007
                     /locus_tag="NL409_RS01735"
                     /old_locus_tag="NL409_001725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041623.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_025492124.1"
                     /translation="MNKQQQTALNMAKFIKSQSLTLLEKLDSLDADAQAAMCEKLHELA
                     EELQNSIQTRFESESGTGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2484..2597
                     /locus_tag="NL409_RS24910"
     CDS             2484..2597
                     /locus_tag="NL409_RS24910"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_071790583.1"
                     /translation="MHEPPVQSDYCALSGNYRLESNPERHDLSPLAAATGN"
                     /name="replication initiation protein"
     gene            2959..3102
                     /locus_tag="NL409_RS01740"
                     /old_locus_tag="NL409_001730"
     CDS             2959..3102
                     /locus_tag="NL409_RS01740"
                     /old_locus_tag="NL409_001730"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_152918943.1"
                     /translation="MNTKVLFVKKALKSITCAILSLLPALSRAVTELRSLSAARLKAGK
                     SF"
                     /name="hypothetical protein"
     Typing          complement(1538..1775)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.75"
                     /coverage="99.0"
                     /evalue="1e-116"
     Typing          2306..2755
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.494"
                     /coverage="90.0"
                     /evalue="1.02e-154"
     Typing          complement(1209..1528)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.32e-62"
ORIGIN
        1 gctaccttaa gctccctgca cttaatcctc cctataatcc ccataacata ctctatcgtg
       61 cagcgttcat aaaagcgcct atcgtgccca ataaactcaa taagttcctt tttctcgtta
      121 gagacgatac tcaaggcatt cattaaaaaa ttgaactctt tcaacatatt atttatggct
      181 tgactatgcg acttgcagtg gtgttttttc caaataggct catggtgaaa aagtcgattc
      241 ctaaacaaaa gaactttatg aaactcgtca aacaacgctt taaccttcat atccccccca
      301 cccaaaggat tcttcgcatg aggaaatgtt tttgccttgt tctctggagt ccagatgtag
      361 cacggccttt gcgtatccct atatggggca tctaacatat aaacccaaaa gccaaaggtt
      421 agacggcaaa taacatcatc atccgtatac cttacgccac actcatctag cgctttttgt
      481 ttcgcattta aaacaagatc ctgagatttc tttgtttgag gtatagagtc gtaccaagca
      541 ggcccatgat tagctttgat tgtattgttt atcgcattac gcagagcaac ctcaatcatc
      601 tggacaagac aaaaaaaatc gccagacaga tcttggtagg caacgtatgc cccaaccttt
      661 tcttgatcag tagcgcaccc aagaaatgtt tcatagaaag ataatcttgg tacagaaatt
      721 gagctaatta aacttgttgt atccatgaaa actcacttat ctctttacta tgaatatttt
      781 tcagactacc attacaacat tcgaggagca ggcgaactac cgtttttctg tgtacctcta
      841 gagcgtaaaa tataacaaaa aagcccacta cagagtgggc ttttttgtta tatttatcta
      901 tatgaaacaa ccagttatag ttattgtttc ataataagaa ttgaatactc ttcacaatcc
      961 acaacatcag aaaatacttt gctgccaatt taccataact ccccttacgc gcaccgctaa
     1021 aacgcgctga acgcgattct gccgcaaaca ccgcaaaaag agatgtttta cccagtgaaa
     1081 accggaaaaa tgcgtcagga ccgttttcag ctcactgcat agctatgcat gaaagtgaat
     1141 ggcgatcggt ttggggcctt acggcgttca taccgtctgt tttcgacagt ttctctccgg
     1201 gaagctaatc tgccataagc ctggataaca gggcccggtg atactccgta atagcgatca
     1261 gcacctccgc atactctctg tccccgacac gcttgccgtc gataaagagt tttttctgta
     1321 acgcccccag tctcataact tctttcagta cccgatcatc agtcagtgag ttaactttct
     1381 taccgagagc tgccgcccgt aaaaaaccgg aaacggtctt gccgcattca gcagcccttt
     1441 ttctgatttc ctggtcttct tctgccgtca gacgaacagg gcgactgata gcccgcctgc
     1501 gcgtattact tccacttcgt tttgtcataa aacatggctc cgtatctgac atggggtgtc
     1561 ggggcgaagc cctgaccagg gtaattgtaa tagcgcgcat gtatgcgcgg tataacaatt
     1621 acacatcctg tcctgtcagc aagttcgaat taccgacaaa ggcacggcag ttttttggca
     1681 gtgacagtat tgtcaggcag aaatgcccgt caaagagtca gacgacagaa taccggcggc
     1741 aaaactgtcg aaaagtggta cgcgatataa tcacacgacg cagatgacag acagaacgga
     1801 gaaaacagaa agatgaacaa gcagcagcaa accgcactta acatggcaaa attcataaaa
     1861 agccagagcc tgacgctgct cgaaaaactg gactcactcg atgctgatgc acaggccgcc
     1921 atgtgtgaga aactgcacga actcgcagaa gaactccaga acagcataca gacacgcttt
     1981 gaatcggaaa gtggcaccgg ggaataacag tgttcctaca ccagacagga tgcagaacga
     2041 tataccggtg cgtaaggaga aaataccaca taaggcgctc ttccgcttcc tcgctcacta
     2101 actcgctacg ctcggtcgtt cggctgcggc gagcggtatc agctcactca aagacggtaa
     2161 tgaggttatc cacagaatca ggggataacg ccaaaagaaa catgtgagca aaaaacaaga
     2221 acccgaaaaa ggccgcgccg gtggcgtttt tccataggct ccgcccccct gacgagcatc
     2281 acaaaaatcg acgctcaagt cagaggtggc gaaacccgac aggactataa agataccagg
     2341 cgtttccccc tgatggctcc ctcgtgcgct ctcctgttcc tgcctttcgg tttaccggtg
     2401 tcattccgct gttatggccg cgttatctca ttccacgcct gacactcagt tccgggtagg
     2461 cagttcgctc caagctggac tgtatgcacg aaccccccgt tcagtccgac tactgcgcct
     2521 tatccggtaa ctatcgtctt gagtccaacc cggaaaggca cgacttatcg ccattggcag
     2581 cagccactgg taactgattt agaggagtta gtcttgaagt tacgtgccag ttaaggctaa
     2641 actggaagaa caagttttgg tgactgcgct cctcttaagc cagttaccga ggttcagaaa
     2701 cttgccggtt gctgaacctt cgaaaaacca ccttgccggg tggttttttc gtttttaaga
     2761 ttacgatggg cgcgatatga actcaaggaa atccgcaatt aaattataaa agtttgtgga
     2821 ttaatggaaa aactgatgtg aatcagctat ttatccttaa gatttgatgt cagatatggt
     2881 ataattaacc attcaaatag atggaataaa aagtcaacgc tgccattaga acggcataag
     2941 aaatagagga ttatgaaaat gaatactaaa gttctttttg tgaaaaaagc cttgaaatca
     3001 attacttgcg caattctttc gctcttaccg gctttaagtc gcgcagtaac agagttacgt
     3061 agcctttcgg ctgcgcgact taaagccggt aagagctttt gattgtatca catttttcct
     3121 taaaagtcaa ccg
//
