LOCUS       NZ_CP082125             4693 bp    DNA     circular CON 11-OCT-2023
DEFINITION  Escherichia coli strain PC-NDM34 plasmid unnamed1, complete
            sequence.
ACCESSION   NZ_CP082125
VERSION     NZ_CP082125.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN20857175
            Assembly: GCF_019843995.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4693)
  AUTHORS   Manyahi,J., Moyo,S.J., Blomberg,B., Langland,N. and Roberts,A.
  TITLE     NDM-5 Tanzania
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4693)
  AUTHORS   Manyahi,J., Moyo,S.J., Blomberg,B., Langland,N. and Roberts,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                   :: Unicycler v. v0.4.8.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 53.2x
            Sequencing Technology             :: Oxford Nanopore; Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/11/2023 03:44:53
            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)                     :: 5,102
            CDSs (total)                      :: 4,982
            Genes (coding)                    :: 4,783
            CDSs (with protein)               :: 4,783
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 199
            CDSs (without protein)            :: 199
            Pseudo Genes (ambiguous residues) :: 0 of 199
            Pseudo Genes (frameshifted)       :: 68 of 199
            Pseudo Genes (incomplete)         :: 124 of 199
            Pseudo Genes (internal stop)      :: 46 of 199
            Pseudo Genes (multiple problems)  :: 38 of 199
            Pseudo Genes (short protein)      :: 3 of 199
            CRISPR Arrays                     :: 4
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP082125.1.
            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..4693
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PC-NDM34"
                     /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="2018-02-20"
                     /collected_by="Joel Manyahi"
     gene            229..420
                     /locus_tag="K5P75_RS25280"
                     /old_locus_tag="K5P75_25280"
     CDS             229..420
                     /locus_tag="K5P75_RS25280"
                     /old_locus_tag="K5P75_25280"
                     /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_064765249.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLTSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            420..821
                     /locus_tag="K5P75_RS25285"
                     /old_locus_tag="K5P75_25285"
     CDS             420..821
                     /locus_tag="K5P75_RS25285"
                     /old_locus_tag="K5P75_25285"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /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="helix-turn-helix domain-containing protein"
                     /protein_id="WP_024623230.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQLKGEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1662..1871)
                     /locus_tag="K5P75_RS25290"
                     /old_locus_tag="K5P75_25290"
     CDS             complement(1662..1871)
                     /locus_tag="K5P75_RS25290"
                     /old_locus_tag="K5P75_25290"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005227293.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YdgH/BhsA/McbA-like domain containing protein"
                     /protein_id="WP_064765250.1"
                     /translation="MKTIKTFVAVATLSMMSFGAFAQSVSATASTLDRAEAKIAAQAAE
                     QGASYKITSAQFNNRVHMTAELTK"
                     /name="YdgH/BhsA/McbA-like domain containing protein"
     gene            complement(2312..2944)
                     /locus_tag="K5P75_RS25295"
                     /old_locus_tag="K5P75_25295"
     CDS             complement(2312..2944)
                     /locus_tag="K5P75_RS25295"
                     /old_locus_tag="K5P75_25295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012579086.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3226 domain-containing protein"
                     /protein_id="WP_064765251.1"
                     /translation="MKNINNSKKIIFVEGDDDFHFLCNLLEIQGITDVFVEKINGKSKL
                     KQALRAFKNIESFDEKESIFIILDADTSFTDTERSIIATLRELQISTPSAHNEIAMNGN
                     TKISFFIMPGKDKPGAIEDLIIEHASTRALYEYIIEFFEKIKNNKDNISASDEEYTYPT
                     NEKKAKVQVYLSCNRESDSRIGISMKNGIINTADNCFDEIKSFISKI"
                     /name="DUF3226 domain-containing protein"
     gene            complement(2944..4059)
                     /locus_tag="K5P75_RS25300"
                     /old_locus_tag="K5P75_25300"
     CDS             complement(2944..4059)
                     /locus_tag="K5P75_RS25300"
                     /old_locus_tag="K5P75_25300"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019405083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ATP-binding protein"
                     /protein_id="WP_064765252.1"
                     /translation="MIKEISLKNFKCFNELHLKQLKTLNIIAGKNNYGKTSILDAIFCF
                     YDVKNPAVLLNIQAFRKEMAEINKNKPFWVSYFHDMDTSQKMSIVIRDERSEVTQTYET
                     ETNQRLESSLSLNVDTVLSNQNIPRQTIGSQATVNSLKINVTETPNAKSRVSNKLFSMQ
                     LKEDGVEIKSEIKNERDGVNYKFKTATIITTSRKINKEATITNVSNLLTQKRKKDILEN
                     LRKIDDRIVDIAISAIGNNKEIYLDIGFSELNEISMLGEGISRALSFISSVLVQENSII
                     LIDEIENGIHYSVIKDIIKSLISSAKQNNNQIFATTHSQDVIRAINEIDSKNEDIAYIR
                     LGREKNSLKPTAVQFNMNDFSYSVENDWEVR"
                     /name="ATP-binding protein"
     gene            complement(4403..4516)
                     /locus_tag="K5P75_RS25740"
                     /pseudo=""
     CDS             complement(4403..4516)
                     /locus_tag="K5P75_RS25740"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="internal stop; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     Typing          complement(2..181)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.347"
                     /coverage="92.0"
                     /evalue="9.27e-31"
     Typing          complement(4404..4693)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.22"
                     /coverage="92.0"
                     /evalue="1.74e-131"
ORIGIN
        1 caccactgat ttgagcgtca gattctgtga tgcttgtcag gggggcggag cctatggaaa
       61 aacggccgct gtgctgcctt ctccctctcc gtgctgtctg ctctatgtcg ttatgtgcgc
      121 gttgcgaccg ctcgccgcag ccgaacggca ggagcgtagc gactgagtgg gcgaggaagc
      181 ggaaaagaga ctggttttac actgagcact gacgctccga ggcctcttat gacgaaacaa
      241 cagaaaacag cgctgaacat ggctaaattc atccagaatc agtctctgct cctgctggag
      301 aagcttaacg agcttgatct tgatgctgag gccgaccttt gtgagaaact ccacgatgat
      361 gcggagcatc ttttccgtac actgacctcg agactggatg cattacagga tggtaactga
      421 tggccagagt gtctattagt gaggctgccc gactgacggg taagagtaga acaacactgc
      481 acaggttaat taaagcaggt gacctgtcca cctgtagcgg tgaacgtaat gcaaaaatgg
      541 tagatacttc agagctttta cgtgtctttg gtccctttga acaactgaag ggtgaacacc
      601 attctggaca ggtctctgaa cagcgtgata cagcctctgc tgaccagagt gaacaggtga
      661 ttcgtcatct gaaacaggag attgaacacc tgaacacctt acttttgtcc aaggattcgc
      721 acattgacag cctgaaacag gccatgctcc ttcttgaaaa tcaccaggca aaattaactg
      781 aatccccggc gccatggtgg aaattctgga aaaaatcctg accccgtcat gctttagttt
      841 tcctctccgg ccattccggg gagttcctga accttcccaa aaatcgtcag atctctgaac
      901 gctcctcacc actaaaaata cccacacccc acgcaaaatt aaaattttga agataaccca
      961 ttaatatcag ttagttgttg gttattaaat tacgcagtat tactttctgt aaggtgaatc
     1021 caagtcgtcg gcaagtcgta gacgaatcgc cgacgacttg tcatagagtc atcgacgact
     1081 cacttaagac tatcagtaac ttatgacgac ttgactctag agtcgaatcg tcattttggt
     1141 gtttttttga ccttggcgac tctagagtca agtcacgagt cgaatcgccg gtgaatcgtg
     1201 tggtgagtcg tccggcgact tgcctaacgt gattgccggc cgtcgacgaa cccgattcct
     1261 gaacgtgatg aaaaccggtt ttccggctgc gccggcaacg cttcacggcc acgcaataaa
     1321 ttgcgtcccc gttcaccgtt ttcggatggg aagaacggtg gaaacaggac taaccctggc
     1381 taaatggcgt gaattttcgc gctatgcact tgcgtgcata ctcatgcatg ccgtaaaaac
     1441 agagcctgcg cgtttctggc ggggtttcgg gtggtttgtt gcctgttttg ccggtttccc
     1501 gtcagaaacg ccctgaggcc gttttagcgg tgcgtacaat catggcttta tgttaaatga
     1561 tagatgcaaa aaagccccga aggggcctga aggttttcct gctaaggggc gaaacgggcc
     1621 gccttccggc gacctgttcg gcagctccct ctgcgaccat cttatttggt cagttcagcc
     1681 gtcatgtgga cacggttatt gaactgagcg ctggtgattt tgtatgacgc accttgttca
     1741 gcggcctgtg cggcaatttt tgcttcagca cgatccaggg tggaggcggt agcgctgacg
     1801 ctctgagcaa acgcaccgaa agacatcatg gatagagtgg caactgcaac gaaagttttg
     1861 atggttttca tggtcgtatt ccttaagtaa ttttgttctg tatggggcgt tgttgccctg
     1921 atgtgataaa tgatagggcg accatgagct gattaaaatc gaaacaattt gcggatatca
     1981 ttcaaaaaaa tagaacaaaa aaatgagcac atcaaaacca ggtgtgagac tctgatttag
     2041 gggtgggcag gatgaatagc ctcgaggggt cgtaaaatta tggtcttatg taaaattttt
     2101 ttaagtgaat agagagaata taacttaagg gagcgccttg tgctgggtct tttacattag
     2161 atttgcacaa tcattgtttt ggcatctggt gatgtcttga ggacgtttga gattactgat
     2221 aactaaagta tatgatgctt tctatacgtt atccggcgtt taataacgct ctgggataag
     2281 ccagcctgtg aagggctggc ttaattttga tttatatttt tgaaataaaa ctttttattt
     2341 catcaaaaca attgtctgct gtgtttatta ttccattttt catggatatt cctatccttg
     2401 agtcggattc tctattgcag ctaagataga cttgtacctt agcttttttt tcgttggttg
     2461 gataagtgta ctcttcgtca ctcgctgaga tgttgtcttt attatttttg attttttcga
     2521 agaattctat tatgtattca tataacgctc gagtgcttgc gtgttcaatt atcagatctt
     2581 caatggcacc tggcttgtct tttcctggca ttataaagaa agaaattttt gtattgccat
     2641 tcatagctat ttcgttatgc gcgctggggg tggagatttg tagttctcgc aatgtggcaa
     2701 ttattgatct ttctgtgtca gtaaatgatg tatcagcatc taatataata aaaatgcttt
     2761 ctttttcatc gaaagactca atgtttttga atgctctaag tgcttgtttt aattttgatt
     2821 ttccatttat cttctcgaca aaaacatcgg taatgccttg tatttcaagt aggttgcata
     2881 gaaaatgaaa atcatcatca ccctcaacaa aaatgatctt cttgctattg tttatgtttt
     2941 tcattatctg acctcccagt cgttctctac cgagtaggaa aaatcattca tattgaattg
     3001 tacggctgtt ggttttaggg agttcttttc tcttcctagt ctaatgtaag cgatgtcttc
     3061 atttttgcta tctatttcgt ttattgctcg tatcacatct tgactatgag ttgttgcaaa
     3121 tatttgattg ttgttttgtt ttgcagatga aattaatgat tttattatgt ctttaattac
     3181 tgagtaatgt attccgttct cgatttcatc aataagaata attgagtttt cctgtaccaa
     3241 tactgagcta atgaaagata atgctcgact gataccctcg ccaagcattg atatttcatt
     3301 tagctcgcta aagccaatgt ctaaatatat ttccttgttg ttacctattg cagatattgc
     3361 tatatctaca attctgtcat ctatttttct taagttttct aatatatctt tttttctttt
     3421 ttgtgttagt agatttgata catttgtaat tgttgcctct ttgtttatct ttctggatgt
     3481 tgttattatc gttgctgtct taaatttata attaacccca tctctttcgt tttttatttc
     3541 tgattttatt tctacgccat cttctttcaa ttgcatagag aaaagcttat tggaaactct
     3601 gctttttgca ttgggtgtct cggtcacgtt tatttttaac gagtttactg tggcctgaga
     3661 accgatagtt tgacgaggta tgttttggtt agatagtacg gtgtcaacgt ttagagataa
     3721 acttgattct agtctctgat ttgtttctgt ttcatatgtt tgtgttactt cagagcgttc
     3781 atctcgaatg actatggaca tcttttgtga tgtgtccatg tcgtgaaagt aactaaccca
     3841 aaatggcttg tttttgttta tttctgccat ttcttttctg aatgcttgaa tgtttaacaa
     3901 gacggctggg ttttttacat cataaaaaca aaatatagca tccagtatag aggttttccc
     3961 gtagttgttt ttcccagcta tgatatttaa agtctttaat tgctttagat gtagctcatt
     4021 gaagcatttg aaattcttta aacttatttc ctttatcatg atagcctctg ttcgtgtttt
     4081 tgttatatgc catacgattt gttagtgcct taataaaatg tacagctttc attgtgatta
     4141 gctagacttt atgtcaaaga ttaactttga ttgcttgtgt tttaatcgat tttttttact
     4201 ttcttcttga gattatctgg cagcagccgt aagcttccgg ctgtgaacga aaaaaccgcc
     4261 ttggcgggcg gttttttcga aaggttcagt agagttggcg ctctatgaac cgaggtaact
     4321 ggcttaaagg gagcgcagtc accaaaactg ttcgtttagt ttagccttaa ctggcgtata
     4381 acttcaagac taactcccta aatcagttac cagtggctgc tgccagtggc gctttgtcgt
     4441 gtctttccgg gttggactca agacgatagt taccggatta ggcgcagcag taggactgaa
     4501 cggggggttc gtgcatacag tccagcttgg agcgaactgc cttcccggaa ctgagtgtca
     4561 ggcgtggaat gagacaaacg cggccataaa cagcggaatg acaccggtaa accgaatggc
     4621 aggaacagga gagcgcacga gggagccatc agggggaaac gcctggtatc tttatagtcc
     4681 tgtcgggttt cgc
//
