LOCUS       NZ_CP082131             3684 bp    DNA     circular CON 11-OCT-2023
DEFINITION  Escherichia coli strain NDM_11.16372 plasmid unnamed1, complete
            sequence.
ACCESSION   NZ_CP082131
VERSION     NZ_CP082131.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN20857180
            Assembly: GCF_019844035.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3684)
  AUTHORS   Manyahi,J., Moyo,S.J., Blomberg,B., Langeland,N. and Robert,A.
  TITLE     NDM-5 Tanzania
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3684)
  AUTHORS   Manyahi,J., Moyo,S.J., Blomberg,B., Langeland,N. and Robert,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-AUG-2021) Clinical Science, University of Bergen,
            Haukelands veien 208, Bergen 5020, Norway
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicyler v. v0.4.8.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 76.3x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/11/2023 03:51:45
            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)                     :: 4,922
            CDSs (total)                      :: 4,802
            Genes (coding)                    :: 4,540
            CDSs (with protein)               :: 4,540
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 262
            CDSs (without protein)            :: 262
            Pseudo Genes (ambiguous residues) :: 0 of 262
            Pseudo Genes (frameshifted)       :: 87 of 262
            Pseudo Genes (incomplete)         :: 170 of 262
            Pseudo Genes (internal stop)      :: 56 of 262
            Pseudo Genes (multiple problems)  :: 49 of 262
            Pseudo Genes (short protein)      :: 4 of 262
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP082131.1.
            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..3684
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="NDM_11.16372"
                     /isolation_source="rectal swab from HIV infected patient"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed1"
                     /geo_loc_name="Tanzania:Dar es Salaam"
                     /lat_lon="6.7924 S 39.2083 E"
                     /collection_date="2018-02-03"
                     /collected_by="Joel Manyahi"
     gene            join(3484..3684,1..102)
                     /locus_tag="K5P77_RS24295"
                     /old_locus_tag="K5P77_24295"
     CDS             join(3484..3684,1..102)
                     /locus_tag="K5P77_RS24295"
                     /old_locus_tag="K5P77_24295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006326557.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3892 domain-containing protein"
                     /protein_id="WP_039023182.1"
                     /translation="MVDFYISAIKMDSAGQHIEFVKVHKINRDGSWNTAGSISSRKFIS
                     ELISMGKASFMTVVKNSSTGKWNLGAKVEAMDDGYITTDPNKTKLDNLGNLPKFV"
                     /name="DUF3892 domain-containing protein"
     gene            complement(887..1309)
                     /locus_tag="K5P77_RS24300"
                     /old_locus_tag="K5P77_24300"
     CDS             complement(887..1309)
                     /locus_tag="K5P77_RS24300"
                     /old_locus_tag="K5P77_24300"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_039023181.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVLKHGKTIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAGSTGVNSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPDSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1309..1500)
                     /locus_tag="K5P77_RS24305"
                     /old_locus_tag="K5P77_24305"
     CDS             complement(1309..1500)
                     /locus_tag="K5P77_RS24305"
                     /old_locus_tag="K5P77_24305"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /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_039023180.1"
                     /translation="MSKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1905..2051
                     /locus_tag="K5P77_RS24605"
     CDS             1905..2051
                     /locus_tag="K5P77_RS24605"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001717510.1"
                     /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_073545459.1"
                     /translation="MHEPPVQSDCCTLSGNYHLESNPVRHAQAPLAAATGKKVYKRLLI
                     QSS"
                     /name="replication initiation protein"
     gene            complement(2509..2790)
                     /locus_tag="K5P77_RS24310"
                     /old_locus_tag="K5P77_24310"
     CDS             complement(2509..2790)
                     /locus_tag="K5P77_RS24310"
                     /old_locus_tag="K5P77_24310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000594459.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_032440460.1"
                     /translation="MIKNIKHKGLRSFAEEGSTAGIQPSMAKRLRMILTTLSTATCIQD
                     VVDVRALGCHPLKGERKGEYSVEVNGNWRVVFKVEEPNVLDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            3127..3420
                     /locus_tag="K5P77_RS24315"
                     /old_locus_tag="K5P77_24315"
     CDS             3127..3420
                     /locus_tag="K5P77_RS24315"
                     /old_locus_tag="K5P77_24315"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609279.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antitoxin"
                     /protein_id="WP_023317864.1"
                     /translation="MINLYDPVHPGEFIREMFMEPFEIPAAELADKLDVSQSTLSRLLN
                     GKTDLSYEMALRLSKVVGRSAESWVNMQTQFSLSKSRKSLAAELEHLHPMFP"
                     /name="HigA family addiction module antitoxin"
     Typing          1642..2014
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.467"
                     /coverage="91.0"
                     /evalue="1.28e-167"
ORIGIN
        1 aacctaggag ccaaagtgga agcgatggac gatggctaca taaccacaga tccaaacaaa
       61 actaaactcg ataacttggg aaatctgccg aaatttgtct gatatgcaat aacatccact
      121 aagttccagc agaatcccct ccctaatgat ttaacataaa gtcataattg tacgcaccgc
      181 cagaacggcc tcagggcgtt tctgacagga aaccggtaaa acaggcaaca aaccacccga
      241 aaacccgtca gaaacgcgca ggctctgttt ttacggcatg catgagtatg cacgcaagtg
      301 catagcgcga aaattcacgc cattcagcca gggtaagtcc tgtttccggc gttcttccca
      361 tccgaaaacg gtgaacgggg acgcaattta ttgcgtggcc gtgaagcgtt gccggcgcag
      421 ccggaaaacc ggttttcagc acgttcagga atcgtgttcg tcgacggccg gcaatcacgt
      481 catggcaagt cgccggacga ctcaccacac gattcaccgg cgactcttca ctagagtcgt
      541 acccagagtc gccgagtcta aaaaacaacc aaacggggag tcgggtctag agtcgggtcg
      601 ttattaactc attgttttta tagctctgag tcgttaccga ctctatgacg actcgccggg
      661 gactctatga cgagtcgtca tagagtcgga tctatgtaaa taaaatttaa aaaccgaaac
      721 ttcaggaaag taagctactg atattaaata caaatctgca aaattttaat tttgcgtagt
      781 gtgtgggtat ttttagtcgt gaggagcgtt cagagatctg gcgatttttg ggaaggttca
      841 ggaactcccc gggatggccg gagaggaaaa cggaagcatg acggagtcag gattttttcc
      901 agaatttcca ccacggggaa tcgggtggtg aagaaggttc gtgcttgtgc tccagaagct
      961 gcatagcctg acgaagggaa tcaatatgct catctcgagc cttaacagcc cctttaagac
     1021 catcgttttc agcttctagt aaagcaattc tatgttgtaa atcatgtaaa ccaacgctgt
     1081 taacacctgt agatcctgcg tcacttttta catcatattt tacagtatcg atgacaccat
     1141 caagagaacc aaaaactcta ataagctctg aagtatcaat aactttaatg gtcttcccgt
     1201 gctttaaaac agaggtgtaa cttaacttcc cactgttaat catcttgtaa attgtggggc
     1261 gactaacctt aacaagccgt gccgcttcac taatagacac tctggccatc agttaccatc
     1321 ctgtaattca tccagtctcg aggacagtgt acggaaaaga tgctccgcat catcgtggag
     1381 tttctcacaa aggtcggcct ctgcatcaag atcaagctcg ttaagcttct ccagcaggag
     1441 cagagactga ttctggatga atttagccat gttcagcgct gttttctgtt gtttcgacat
     1501 aagaggcctc agagcgtcag tgctcagtgt aggtatgttc tcttttccgc ttcctcgctc
     1561 actcagtcgc tacgctcctg ccgttcggct gcggcgagcg gtcgcaatac acacataacg
     1621 acataggaca gacagcacgg agagggagaa ggccgcacac cggccgtttt tccataggct
     1681 ccgcccccct gacaagcatc acgaaatctg acgctcaaat cagtggtggc gaaccccgac
     1741 aggactataa agataccagg cgtttccccc tgatggctcc ctcgtgcgct ctcctgttcc
     1801 tgcctttcgg tttaccggtg tcattccgct gttatggccg cgtttatctc attccacgcc
     1861 agacactcag ttccgggtag gcagttcgct ccaagctgga ctgtatgcac gaaccccccg
     1921 ttcagtccga ctgctgcacc ttatccggta actatcatct tgagtccaac ccggtaagac
     1981 acgcacaagc gccactggca gcagccactg gtaagaaggt gtacaagaga ttactgatac
     2041 agagttcttg aagtctcagc ccaactacgg ctaaactgaa aggacagaat ttggtttcag
     2101 cggtcttgta caccctgtta ccacggttca gaagttcccc aacttactga accctcgaaa
     2161 aaaccgcctc cccaggcggt tttttcgtct cggcgagtaa gatacgcttt atcattcaaa
     2221 gcagtcaagg aagaaccaag acagctcact caccagcagg ctccttttta ttggtagaca
     2281 catgcttctg gacagtatca gcccctgcac aaagtacagc agctaacaag aaccatcccc
     2341 agccatcaat accacgaaaa gctaggactc cagcaatagt tacgctaatc aacgggaaca
     2401 ataaaaccat aaaggatctc atactttctc cagaggttac ttttttaata aagtccctaa
     2461 tccatccgta ctttcacttg gatggattag caacttactt attgataact aatgataatc
     2521 ttcaagatca acgtctaaga cgtttggttc ctcaaccttg aaaactaccc gccagttccc
     2581 attaacttca acggaatact cgcctttacg ctcccccttt agggggtggc accctaacgc
     2641 cctaacgtca acaacgtctt gaatgcaagt tgctgtgctt agcgtagtca aaatcatgcg
     2701 aagtcttttc gccatactgg gctgaatacc ggcggtgcta ccttcttcag caaagctcct
     2761 aagtccttta tgttttatgt tttttatcat ctacaatccc catatttttt tcgtctatac
     2821 ctgtatctat attttaaaat cattttaatt agttccattt tgcccccttg ctttattaaa
     2881 acaattgacg taagtttgtt cttgaggtca atcacctcat ttgacttcaa cgaatcctaa
     2941 gggtaaaata ctgcgccttg aaaaggccat aaaagcccat acatacgcag tagctttgac
     3001 tccaacgagt atcctaaagc tgactgcttt ttttgtcaat atcatgaact tgcacattgt
     3061 gcaatgcgca tactgaaagg cagtaatttt tttgtataat caaatacaaa acaaacagag
     3121 gaaggcatga taaatcttta cgatcctgtt catcctggtg agtttatcag agaaatgttc
     3181 atggaaccgt tcgaaatacc tgccgcagag ttagccgata aacttgatgt atcccagtct
     3241 accttaagta gactgttaaa tgggaaaaca gacttaagct atgaaatggc acttagattg
     3301 tcgaaggtcg taggccgctc tgcagagtcg tgggtaaaca tgcagaccca attcagcctg
     3361 tcaaaaagtc gcaaatcttt agcggcagag ctggaacact tgcatccaat gtttccatga
     3421 aaaaagcccg cagaacgcgg gcttttgtta cgtaaaacac ccagcagcca tcaggaggca
     3481 accatggtag atttctatat ctcagcaatc aaaatggaca gtgctggtca gcacatcgaa
     3541 ttcgtaaaag ttcataaaat aaaccgagat ggctcatgga acactgccgg ctcaatcagc
     3601 tctcgcaaat tcatcagcga gctgatcagc atgggaaaag ccagctttat gacagttgta
     3661 aagaacagct ctactggtaa gtgg
//
