LOCUS       NZ_CP116928             5269 bp    DNA     linear   CON 11-MAR-2024
DEFINITION  Escherichia coli strain MLI105 plasmid p5_MLi105, complete sequence.
ACCESSION   NZ_CP116928
VERSION     NZ_CP116928.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29553885
            Assembly: GCF_024700835.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5269)
  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  JOURNAL   Unpublished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 5269)
  AUTHORS   Riediger,M. and Zautner,A.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-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 5269)
  AUTHORS   Zautner,A.E.
  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 05:17:12
            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)                     :: 4,532
            CDSs (total)                      :: 4,410
            Genes (coding)                    :: 4,206
            CDSs (with protein)               :: 4,206
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 204
            CDSs (without protein)            :: 204
            Pseudo Genes (ambiguous residues) :: 0 of 204
            Pseudo Genes (frameshifted)       :: 67 of 204
            Pseudo Genes (incomplete)         :: 140 of 204
            Pseudo Genes (internal stop)      :: 38 of 204
            Pseudo Genes (multiple problems)  :: 42 of 204
            Pseudo Genes (short protein)      :: 4 of 204
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116928.1.
            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..5269
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MLI105"
                     /isolation_source="stool sample"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p5_MLi105"
                     /geo_loc_name="Mali: Koulikoro"
                     /lat_lon="12.52 N 7.34 W"
                     /collection_date="2014-06-24"
                     /collected_by="Bundeswehr Medical Service"
     gene            75..233
                     /locus_tag="NL421_RS22620"
     CDS             75..233
                     /locus_tag="NL421_RS22620"
                     /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_171804822.1"
                     /translation="MHEPPVQPDCYALSGNYRLESNPVRHALTPLAAAIGNWTRWIEIL
                     RVLEVVA"
                     /name="replication initiation protein"
     gene            complement(469..1617)
                     /locus_tag="NL421_RS00120"
                     /old_locus_tag="NL421_000120"
     CDS             complement(469..1617)
                     /locus_tag="NL421_RS00120"
                     /old_locus_tag="NL421_000120"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001529706.1"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [Evidence IEA];
                     GO:0008168 - methyltransferase activity [Evidence IEA];
                     GO:1904047 - S-adenosyl-L-methionine binding [Evidence
                     IEA]"
                     /GO_process="GO:0006304 - DNA modification [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WP_040088069.1"
                     /translation="MRSLEIFSGAGGLAKGLELAGFQHVGFVELNKHACDSLRLNFDEE
                     KVFQGDIKNYDLSSIDKIDIVAGGPPCQPFSLGGKHKAHDDSRDMFPFAIKAIEVLQPK
                     AFIFENVKGLLRKSFADYFEYIILRLTYPCLSLSNVGDWRIHLDALRKARKDKHCGCTY
                     DVSFKLINAADYGVPQIRERVIIVGVRSDLNKKWSFPSVTHTQEKLLWEQHVTGDYWRK
                     HNIDAVIDKGISERLMKRFGIFPPSGKSWVTVRDALKNVPQPYESHGIGDHIFKDGARV
                     YPGHTGSYIDLPSKTLKAGAHGVPGGENMIRYEDGTVRYFTVYEGKLLQTFPREFLIAG
                     AWGEAMRQIGNAVPVLLAQKIGQQLYNLLNEEVEPLLCSNFN"
                     /name="DNA cytosine methyltransferase"
     gene            complement(1617..2261)
                     /locus_tag="NL421_RS00125"
                     /old_locus_tag="NL421_000125"
     CDS             complement(1617..2261)
                     /locus_tag="NL421_RS00125"
                     /old_locus_tag="NL421_000125"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001529705.1"
                     /GO_function="GO:0004518 - nuclease activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Eco29kI family restriction endonuclease"
                     /protein_id="WP_011017202.1"
                     /translation="MHNKKFDRSEHVYRNDSFLELIKDAVRFFSGTPVHSLPPPERFQG
                     AGVYALYYTGHYSLYDEYSRINRLAYNLPIYVGKAVPAGWRQSRISDHETRAGSELSNR
                     IREHSRNIAKTSNLNLCDFSCRFVIFEATGSDMISTVEAALIKIYKPLWNTVVDGFGNH
                     TPGAGRFAQAKSDWDVIHPGREWAEKCTGVHSEPYFIEERIKQYFSKSNFT"
                     /name="Eco29kI family restriction endonuclease"
     gene            complement(2661..2894)
                     /locus_tag="NL421_RS00130"
                     /old_locus_tag="NL421_000130"
     CDS             complement(2661..2894)
                     /locus_tag="NL421_RS00130"
                     /old_locus_tag="NL421_000130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_004026237.1"
                     /translation="MTELEIHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2901..3419)
                     /locus_tag="NL421_RS00135"
                     /old_locus_tag="NL421_000135"
     CDS             complement(2901..3419)
                     /locus_tag="NL421_RS00135"
                     /old_locus_tag="NL421_000135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_001749510.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQTNLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            complement(<3457..4155)
                     /locus_tag="NL421_RS22625"
                     /pseudo=""
     CDS             complement(<3457..4155)
                     /locus_tag="NL421_RS22625"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(4097..4420)
                     /locus_tag="NL421_RS00145"
                     /old_locus_tag="NL421_000145"
     CDS             complement(4097..4420)
                     /locus_tag="NL421_RS00145"
                     /old_locus_tag="NL421_000145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000956000.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4484..4675
                     /locus_tag="NL421_RS00150"
                     /old_locus_tag="NL421_000150"
     CDS             4484..4675
                     /locus_tag="NL421_RS00150"
                     /old_locus_tag="NL421_000150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(4761..4846)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          2..184
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.739"
                     /coverage="100.0"
                     /evalue="2.4000000000000003e-80"
     Typing          4868..5269
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.875"
                     /coverage="100.0"
                     /evalue="1.06e-164"
     Typing          complement(2558..4107)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.374"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcgtggcgct ttctcatagc tcacgctgtt ggtatctcag ttcggtgtag gtcgttcgct
       61 ccaagctggg ctgtgtgcac gaaccccccg ttcagcccga ctgctacgcc ttatccggta
      121 actatcgtct tgagtccaac ccggtaagac acgccttaac gccactggca gcagccattg
      181 gtaactggac aaggtggatt gagatattaa gagttcttga agtggtggcc taactgaggc
      241 tacactagaa ggacagtatt tggtatctgc gctccaccaa gccagttacc ttcgggaaaa
      301 agagttggta gctcttgatt ccggcaaacg aaccaccgtt ggtagcggtg gtttttttgt
      361 ttacaggcag cagattacgc gcagaaaaaa aggatctcaa gaagatcctt tgatcttttt
      421 ttgcaaattg cctctatggc tgtatcacca ccatagagac acaaactttt aattgaagtt
      481 agagcacaat aaaggctcaa cctcttcatt caataagtta tacaattgct gtcctatctt
      541 ctgagctagc aacacaggaa ctgcattacc aatctgcctc atagcctccc cccaagctcc
      601 tgcaatcaga aactctcgag gaaaagtctg aagaagcttc ccttcataaa ccgtaaaata
      661 acgaacagtc ccatcctcat acctaatcat attttcacct ccaggtacgc catgagcgcc
      721 agccttaagt gtttttgaag gcaaatcgat ataacttcca gtatgaccag gataaactcg
      781 agcgccatct ttaaagatat gatctccaat accatgtgac tcatatggtt gaggaacatt
      841 ctttaatgcg tccctaacag taacccagct tttccccgat ggggggaaaa taccaaaacg
      901 tttcattaaa cgctcagaaa tacctttatc tataaccgca tcaatattat gctttcgcca
      961 atagtcacca gtaacatgct gttcccacag taatttttct tgagtatgcg ttacgcttgg
     1021 aaaagaccat tttttattca aatcacttcg aacaccaaca attatgaccc gttccctaat
     1081 ttgtggaact ccataatcag ctgcattgat caatttaaaa ctgacatcat atgtacaccc
     1141 acagtgttta tccttgcgag cttttcttaa tgcatctaga tgtattctcc aatcacctac
     1201 attacttaac gataaacaag gataagtcaa acgaagaatt atgtattcaa aataatccgc
     1261 aaatgatttt ctaagcaacc ctttaacatt ttcaaaaata aaagcttttg gttgcaatac
     1321 ttcaattgct tttattgcaa atgggaacat atccctagag tcatcatgag ctttatgttt
     1381 tccgcccaat gaaaatggtt ggcagggagg cccgccagca acaatatcta ttttatctat
     1441 agatgaaagg tcataatttt taatatctcc ctgaaatacc ttctcctcat caaaattaag
     1501 tcgcaaagaa tcacatgcat gcttgtttaa ctcaacaaat cctacatgct gaaatcctgc
     1561 caactctaga cctttagcca aaccgccggc tcctgaaaaa atctctaatg atctcattat
     1621 gtaaaattac tcttagaaaa atactgttta attctctcct caataaagta tggctcagaa
     1681 tgaacacctg tacatttctc agcccactcc ctgccaggat gtattacatc ccaatcagat
     1741 ttagcttgcg caaatcgccc ggcaccaggg gtatgatttc caaagccatc aacaactgta
     1801 ttccacaaag gcttataaat tttaataaga gcggcctcaa ctgtactaat catatcagac
     1861 cccgtagcct caaatataac aaagcgacat gaaaaatcac acaaatttag attcgatgtt
     1921 tttgctatat ttcggctatg ttctctaatt ctattagata gttcagaacc agccctagtt
     1981 tcatgatcac taattctaga ctgacgccaa ccagcaggaa cagccttgcc aacataaata
     2041 ggaaggttat atgccaacct atttatacga gagtattcat catataatga ataatgccct
     2101 gtatagtaaa gagcatacac cccagcacct tgaaaccgtt ccggtggtgg taatgaatga
     2161 acaggcgtac cactaaaaaa acgaacggca tcttttatta actctaggaa agagtcattt
     2221 ctataaacat gctcagatct atcaaatttc ttattgtgca ttatgttttc cgaaaggttt
     2281 ttatattaac actcctactc aacatcacct atgatacgat cataaagctg atacccaaaa
     2341 ccatacgcat ttaccataac gtcgcattac gcgcaccgct aaaacgcgtt cagcgcgatc
     2401 acggcagcag acaggtaaaa atggcaacaa accacccgaa aaactgccgc gatcgcgcct
     2461 gataaatttt aaccgcatga atacctatgc aaccagatgg tacaggccac attaacccct
     2521 cttaatccac tgaagctgcc atttttcatg gtttcaccat cccagcgaag gaccatccag
     2581 cgtgcgttcc tgtatttccg gctgacgctc ccgttccagg gataacgcat gttcgcgctc
     2641 ctgtatcagc cgttcctctc ttatctccag ttctcgctgt ataactggct caagcgttct
     2701 gtctgctcgc tcaagtgctg cacctgctga ctcaactgca tgacccgctc gttcagcatc
     2761 gcgttgtccc gttgcgtaag cgaaaacatc ttctgcaatt ccacgaaggc gctctcccat
     2821 tcgctcagcc gctgcatata gtcctgttgc agctgctcta aggcgttcag caaatgtatt
     2881 tccagctctg tcactctgtg tcactccttc agatgtaccc actctttccc ctgaaaggga
     2941 atcacctccg ctgatttccc gtacggaagg acaaggaatt tcctgttccc gtcctgcaca
     3001 aactccacgc cccatgtctt cgcgttcagt ttctgcaatg tctcttcctg cttcctgatt
     3061 tcttccaggt tcgtctgtat ccgtccgcca agataccaga gcgtcccgcc actcgcggta
     3121 aacaggagaa agactatccc cagtaacatc atgcccgtat tccctgccag ctttaacacg
     3181 tccttcctgt gctgcatcat cgcctctttc accccttccc ggtgtttttc cagcgatttc
     3241 tctgtcgagg ctgtgaacag ggctatagcg tctctgattt tcgtctcgtt tgaggtcaca
     3301 gcctcgctga cagactcgcc gagcttcctg aactcgtcgt tcagcatttt ctctgtagat
     3361 tcggctctct ctttcagctt tttctcgaac tccgcgcccg tctgtaaaag attgctcata
     3421 aaatgctcct ttcagcctga tattcttccc gccgttcggg tctgaaatgc tgatactgct
     3481 tcgcgtcacc ctgaccactt caagccccgc ctctgtgagc gcctgaatca catcctgacg
     3541 gccttttatc tctccggcat ggtaaagtgc gtctataccg cgtgtaacgc tctcagcaag
     3601 tgcctgtttc gtttccggca ggttatcagg aagggtcagc gtccggcggt tctccggggc
     3661 gttggggtca tgcagtccgt aatggtgatt caccagcgtc tgccaggcat caattctcgg
     3721 cctgtctgcg cggtcgtagt acggctggag acgttttccg gtctgtagct ccatgttcgg
     3781 aatgacaaaa ttcagctcaa gccgtccctt gtcctggtgc tccacccaca ggatgctgta
     3841 ctgatttttt tcgagaccgg gcatcagtac acgctcaaag ctcgccatca ctttttcacg
     3901 tcctcccggt ggcagctcct tctccgcgaa cgacagcaca ccggacgtgt atttcttcgc
     3961 aaatggcgtg gcatcgatga gttcccgtac ttcttccgga ttaccctgaa gcaccgttgc
     4021 cccttcccgg ttacgctccc ttcccagcag gtaatcaacc ggaccactgc caccaccttt
     4081 tcccctggca tgaaacttaa ctatcatccc gcgtcccctg ttccctgacg gccagacgca
     4141 gccggcgcag ctcatccccg atggccatca gtgcggccac cacctgaacc cggtcaccgg
     4201 aagaccactg cccgctgttc accttacggg ctgtctgatt caggttattt ccgatggcgg
     4261 ccagctgacg cagtaacggc ggtgccagtg tcggcagttt tccggaacgg gcaaccggct
     4321 cacccaggca gacccgccgc atccataccg ccagttgttt accctcacag cgttcaagta
     4381 accgggcatg ttcatcatca gtaacccgta ttgtgagcat cctctcgcgt ttcatcggta
     4441 tcattacccc atgaacagaa atccccctta cacggaggca tcagtgacta aacaggaaaa
     4501 aaccgccctt aacatggccc gctttatcag aagccagaca ttaacgctgc tggagaagct
     4561 caacgaactg gacgcagatg aacaggccga tatttgtgaa tcgcttcacg accacgccga
     4621 tgagctttac cgcagctgcc tcgcacgttt cggggatgac ggtgaaaacc tctgacacat
     4681 gcagctcccg gagacggtca cagcttgtct gtgagcgaat gccgggagca gacaagcccg
     4741 tcagggcgcg tcagcaggtt ttagcgggtg tcggggcgca gccctgaccc agtcacgtag
     4801 cgatagcgga gtgtatactg gcttaaccat gcggcatcag tgcagataat aagaaaagag
     4861 caccatatac ggtgtgaaat accgcacaga tgcgtaagga gaaaatgccg catcaggcgc
     4921 tcttccgctt cctcgctcac tgactcgcta cgctcggtcg ttcggctgcg gcgagcggta
     4981 tcagctcact caaagacggt aatgcggtta tccacagaat caggggataa cgccaaaaga
     5041 aacatgtgag caaaaaacaa gaacccggaa aaggccacgc cgctggcgtt tttccatagg
     5101 ctccgccccc ctgacgagca tcacaaaaat cgacgctcaa gtcagaggtg gcgaaacccg
     5161 acaggactat aaagatacca ggcgtttccc cctggaagct ccctcgtgcg ctctcctgtt
     5221 ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc cttcgggaa
//
