LOCUS       NZ_CP049971             4145 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain ARL09/232 plasmid pCO_Eco4457-4, complete
            sequence.
ACCESSION   NZ_CP049971
VERSION     NZ_CP049971.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14351533
            Assembly: GCF_013376575.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4145)
  AUTHORS   Olivera,C.D. and Rakonjac,J.
  TITLE     Complete genome assembly of New Delhi metallo-beta-lactamase-1
            (NDM-1)- producing Escherichia coli human isolate from New Zealand
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4145)
  AUTHORS   Olivera,C.D. and Rakonjac,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-MAR-2020) School of Fundamental Science, Massey
            University, Tennent Drive, Palmerston North 4442, New Zealand
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: MAR-2020
            Assembly Method                   :: Unicycler v. MAR-2020
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 02:37:54
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,280
            CDSs (total)                      :: 5,159
            Genes (coding)                    :: 4,937
            CDSs (with protein)               :: 4,937
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 222
            CDSs (without protein)            :: 222
            Pseudo Genes (ambiguous residues) :: 0 of 222
            Pseudo Genes (frameshifted)       :: 77 of 222
            Pseudo Genes (incomplete)         :: 134 of 222
            Pseudo Genes (internal stop)      :: 53 of 222
            Pseudo Genes (multiple problems)  :: 41 of 222
            Pseudo Genes (short protein)      :: 2 of 222
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP049971.1.
            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..4145
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ARL09/232"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /culture_collection="NZRM:4457"
                     /db_xref="taxon:562"
                     /plasmid="pCO_Eco4457-4"
                     /geo_loc_name="New Zealand"
                     /collection_date="2009"
                     /collected_by="Institute of Environmental Science and
                     Research (ESR)"
     gene            join(4031..4145,1..1028)
                     /gene="wzz(fepE)"
                     /locus_tag="G9448_RS26080"
                     /old_locus_tag="G9448_26150"
     CDS             join(4031..4145,1..1028)
                     /gene="wzz(fepE)"
                     /locus_tag="G9448_RS26080"
                     /old_locus_tag="G9448_26150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010435173.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WP_021544858.1"
                     /translation="MSAMDFKKNTDLDFPRYATPAVSTKEIDLLGLLDVLLAAKKRIVT
                     IVLAFAVVGLAIAFLIPQKWTSKAVITPAEQTQWNTLRQMMVTLQVLDVDAKVSRGDVF
                     NLFIKKFQSQSLLEEYMKTSPYVMSQLEGTEVDPLELHRAVVNIAEKMKATDNTQVKDA
                     DKAPYTSWTLSFTAPTAGDAQTVLEGYINYISRIVEQETMENIRNQITLKTKVVQQQLE
                     LDRVRLTNIHNTNLQRLNYSLEVANAAGIKKPVYSNGQAVKDDPDYSVALGADGIAQKL
                     QIEKNLKDVAELNADFQNREYYLTQLQKLSVEDVKLEPFRYQLSPSLPVKKDGPGKALI
                     VLLAGILGGLFACGSVLLREAMLSRNPLPEPITAVTPATE"
                     /name="wzz(fepE)"
     gene            complement(1066..>1308)
                     /locus_tag="G9448_RS26085"
                     /old_locus_tag="G9448_26155"
                     /pseudo=""
     CDS             complement(1066..>1308)
                     /locus_tag="G9448_RS26085"
                     /old_locus_tag="G9448_26155"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003862821.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="cupin domain-containing protein"
                     /name="cupin domain-containing protein"
     gene            <1305..1487
                     /locus_tag="G9448_RS26090"
                     /old_locus_tag="G9448_26160"
                     /pseudo=""
     CDS             <1305..1487
                     /locus_tag="G9448_RS26090"
                     /old_locus_tag="G9448_26160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007798797.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="NINE protein"
                     /name="NINE protein"
     gene            2673..2786
                     /locus_tag="G9448_RS26095"
                     /old_locus_tag="G9448_26170"
     CDS             2673..2786
                     /locus_tag="G9448_RS26095"
                     /old_locus_tag="G9448_26170"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_071778980.1"
                     /translation="MHEPPVQSDRCVFSGNYRLESKPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     gene            3094..>3225
                     /locus_tag="G9448_RS26630"
                     /old_locus_tag="G9448_26175"
                     /pseudo=""
     CDS             3094..>3225
                     /locus_tag="G9448_RS26630"
                     /old_locus_tag="G9448_26175"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013578013.1"
                     /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="zinc-ribbon domain-containing protein"
                     /name="zinc-ribbon domain-containing protein"
     gene            complement(3374..3490)
                     /locus_tag="G9448_RS26635"
     CDS             complement(3374..3490)
                     /locus_tag="G9448_RS26635"
                     /inference="COORDINATES: protein motif:HMM:NF013752.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001407452.1"
                     /translation="MKARYKGLLKNDNQLAMLFTLANLFRADQMIRQWERSH"
                     /name="hypothetical protein"
     gene            complement(3453..3836)
                     /locus_tag="G9448_RS26100"
                     /old_locus_tag="G9448_26180"
     CDS             complement(3453..3836)
                     /locus_tag="G9448_RS26100"
                     /old_locus_tag="G9448_26180"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003117291.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS5/IS1182 family transposase"
                     /protein_id="WP_021544857.1"
                     /translation="MSHQLTFADSEFSSKRRQTRKEIFLSRMEQILPWQNMVEVIEPFY
                     PKAGNGRRPYPLETMLRIHCMQHWYNLSDGAIEDALYEIASMRLFARLHESQHPGQGGA
                     PISHHQATVRLRESQIQGVAEKR"
                     /name="IS5/IS1182 family transposase"
     Typing          2402..2790
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.153"
                     /coverage="91.0"
                     /evalue="1.04e-173"
ORIGIN
        1 ccaaaaaacg tattgtgacg atcgtcctgg cgttcgccgt agtagggttg gccattgcgt
       61 ttttaatccc gcaaaaatgg accagtaaag ccgtgatcac gccggccgag cagacgcagt
      121 ggaacacgct gcgccagatg atggtgacgc tgcaggtgct ggacgtcgac gcgaaggtga
      181 gccgtggaga cgtgtttaac ctgttcatca aaaagtttca gtcgcagtcg ctgctcgaag
      241 agtacatgaa aacctccccg tacgtgatgt ctcagctgga aggcaccgag gtagacccgc
      301 tggagctgca tcgcgcggtg gtgaatattg ctgagaaaat gaaagcgaca gataacacgc
      361 aggttaaaga cgcagacaaa gcgccgtata cctcatggac gctgagcttt accgccccga
      421 cggcgggaga cgcgcagacg gttctggaag gttacatcaa ctatatctcc cgcattgttg
      481 agcaggagac gatggaaaat atccgtaacc agatcacgct gaaaacgaaa gtcgttcagc
      541 agcagctgga gctggatcgc gtgcgtctga ccaatatcca caacaccaac ctgcagcgcc
      601 tcaactattc gctggaagtg gcgaacgcgg caggcattaa gaagccggtt tacagcaacg
      661 gacaggcggt aaaagacgat cctgactact ccgtggcgct gggtgctgac ggtattgcgc
      721 aaaagctgca gattgaaaag aatctgaagg acgtggccga gctgaatgcg gatttccaga
      781 accgtgaata ctatctgact cagttgcaaa aactgtccgt ggaagacgtg aagcttgaac
      841 ccttcaggta tcagctttca ccgtcactgc cggtgaaaaa agacggtccg ggcaaagccc
      901 tgattgtgct gctggcaggg attctgggcg gcctgtttgc ctgcggcagc gtgctgctgc
      961 gtgaggcaat gctctcgcgt aatccgttgc cagagccgat aacggccgta acgccagcaa
     1021 cagagtaacg acgatattaa aaaggcgctg attcagcgcc tttttttatt tcaggaaatc
     1081 gtcgcgcacc ggcgtaaagg tatccagaag ggtgccgggc ttcaggcaaa tgcagccgtg
     1141 catcacgtgc ggcgctttat agagcgtatc gcccgccgtc acgatctgct tttcttcacc
     1201 tatcgtaaac tcgaactccc cggagagcac ataggtaagc tgttcatgcg ggtgattgtg
     1261 catcgggcca atcgcaccct gctcaaaatt gacctccacc gccatcatct ttcttagcat
     1321 tcttccttgg tggatttggc gtacataaat tttacttagg taaaatagga cagggattcc
     1381 tgtatctaat tttttgctgg acattcatac ccgcgatcat cgcgtttatt gagtttatta
     1441 tttatctatg cgattccgat gaaaaattcg caagaaaata tggctaactc atagcaaaaa
     1501 agccctgcgg ggcttttttt gtaccagtct gtgaggcaga tttaccataa catccgttgc
     1561 gtgcaccgcc tgagaggctc tcagggcgtt tctgggtctt cctgcctgtt tccgacactt
     1621 ccctgtgcct atatcgtgaa aaaacgcgcc tgatgattct ggcgcgtctg catggctatg
     1681 cacacacatg catggccggg attttagcgg ctaaaatccg gctggacgcc caaaagcacc
     1741 actgaacctc acgaataacg cctcacgggt gtgcagttta ctgtgcggcc gtgaggcgtt
     1801 ggccaggccg tcaggcatgg ctggatttat tgctaagggg gtcggattta acgtggatga
     1861 atcagcacgc agtgatgaac gggattcgga aggggcaccc ttgcggcgcg gcgatgtata
     1921 catcgctaac gtgccttggt catttattgc aagaagggag aggtagcatt ttgatagcaa
     1981 aaaagtagca aaaggatagc aaccgaaaga ccagaagact ctggagatag caaaaaagta
     2041 gcaaaatggt agcaaaaaga tagcaaacat gcgggagcta accaggagtc tttagcgggc
     2101 cggcggtact ccaaaaacac atcttgtccc gctgttttgt gaataagcca gcatagctgt
     2161 gggcacaaaa catttcctgt ccgctgcttt aacctttgta atccaggaac gtcaggtgac
     2221 gtcactttgc ggcgttagcc ctatcctgca tcgtattaaa aaatgcagca ctggcgcgta
     2281 cggtgccgaa gataagtccg gggatattcc gcttcctcgc tcactgactc gctacgctcg
     2341 gtcgttcggc tgcggcgagc ggagggaacg gagacattaa ggcacaggca atgagagagg
     2401 atcgagaggc aaaagaaaag gccgcggcgt tgccggtttt ccataggctc cgcccccctg
     2461 acaagcatca cagaatctga cgctcaaatc agtggtggcg aaacccgaca ggacttaaag
     2521 ataccaggcg tttccccctg gtggctccct cgtgcgctct cctgttcctg cctttcggtt
     2581 taccggtgtc attccgctgt tatggccgcg tttatctcat tccacgcctg acactcagtt
     2641 ccgggtaggc agttcgctcc aagctggact gtatgcacga accccccgtt cagtccgacc
     2701 gctgcgtctt ctccggtaac tatcgacttg agtccaagcc ggaaagacac gacaaagcgc
     2761 cactggcagc agccactggt aactgattta gaggagttag tcttgaagtt atgcgcctgt
     2821 taaggctaaa ctgaaagaac agatttggtt actgcgctcc tcataagcca gttaccacgg
     2881 ttcaaagagt tgcagctctg agaaccttcg aaaaaccgcc ttgctgggcg gttttttcgt
     2941 ttactgagca agagattacg acgctacaga aaggatctca agaagatcct tcaccataat
     3001 ggaaatctat cccacccgag catataggat gcatatcgtt ataaaacatc ggatattatg
     3061 catcccaact aaaaataagc tcgaggataa aaaatgagtt caatggttta ctgccgagga
     3121 tgcggcaagg aaatacacga aacagcaaag tcatgcccac actgcggagc cacaaacgcc
     3181 tcttcaggtt caggtgaaaa aagtagaatc gcagccgcgc tattagggaa ggtgcgaata
     3241 agcggggaaa ttcttctcgg ttgactcagt catttcattt cttcatgttt gagccgattt
     3301 ttttctcccg taaatgcctt gaatcagcct atttagaccg tttcttcgcc atttaaggcg
     3361 ttattcccag tttttagtga gatctctccc actgacgtat catttggtcc gcccgaaaca
     3421 ggttggccag cgtgaataac atcgccagtt ggttatcgtt tttcagcaac cccttgtatc
     3481 tggctttcac gaagccgaac tgtcgcttga tgatgcgaaa tgggtgctcc accttggccc
     3541 ggatgctggc tttcatgtaa ccgggcaaac agacgcatgg aggcgatttc gtacagagca
     3601 tcttcgatcg cgccatcgct caggttgtac caatgctgca tgcagtgaat gcgtagcatg
     3661 gtttccagcg gataaggtcg ccggccatta ccagccttgg ggtaaaacgg ctcgatgact
     3721 tccaccatgt tttgccatgg cagaatctgc tccatgcggg acaagaaaat ctcttttctg
     3781 gtctgacggc gcttactgct gaattcactg tcggcgaagg taagttgatg actcatgatg
     3841 aaccctgttc catggctcca gatgacaaac atgatctcat atcagggact tgttcgcacc
     3901 ttccctaaat ctgatagtcg gtctacagat agatcaatct ggcgttcaga ttattcttac
     3961 tttcttgtat catccgacca ctgcaaccaa tcaggcagaa atttactgcg ctccaaaaag
     4021 aagaacggtt atgtcagcga tggatttcaa gaaaaacacg gacctcgatt ttccccgtta
     4081 tgccactccg gcggtaagca ccaaagagat agatctcctg gggttgttag acgtacttct
     4141 ggcag
//
