LOCUS       NZ_AP028313             3223 bp    DNA     circular CON 04-APR-2024
DEFINITION  Escherichia coli strain OIPH-1902-010 plasmid p1902-010-3, complete
            sequence.
ACCESSION   NZ_AP028313
VERSION     NZ_AP028313.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00622802
            Assembly: GCF_036508855.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Umeda,K., Anraku,M., Yamaguchi,T., Nakamura,H. and Kawahara,R.
  TITLE     Genetic characterization of KHM-1 metallo-beta-lactamase-producing
            isolates from inpatient sources in Osaka, Japan
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3223)
  AUTHORS   Umeda,K., Anraku,M., Yamaguchi,T., Nakamura,H. and Kawahara,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-JUN-2023) Contact:Kaoru Umeda Osaka Institute of
            Public Health; Higashinari-ku, Nakamichi 1-3-3, Osaka 537-8511,
            Japan:Osaka
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.4
            Genome Coverage                   :: 50X
            Sequencing Technology :: Illumina iSeq; Oxford Nanopore Technologies
            MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_036508855.1-RS_2024_04_04
            Annotation Date                   :: 04/04/2024 00:07:50
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,032
            CDSs (total)                      :: 4,917
            Genes (coding)                    :: 4,736
            CDSs (with protein)               :: 4,736
            Genes (RNA)                       :: 115
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 181
            CDSs (without protein)            :: 181
            Pseudo Genes (ambiguous residues) :: 0 of 181
            Pseudo Genes (frameshifted)       :: 67 of 181
            Pseudo Genes (incomplete)         :: 124 of 181
            Pseudo Genes (internal stop)      :: 32 of 181
            Pseudo Genes (multiple problems)  :: 37 of 181
            Pseudo Genes (short protein)      :: 4 of 181
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP028313.1.
            Annotated by DFAST https://dfast.ddbj.nig.ac.jp/
            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..3223
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="OIPH-1902-010"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p1902-010-3"
                     /geo_loc_name="Japan:Osaka"
                     /lat_lon="34.41 N 135.31 E"
                     /collection_date="2019"
                     /collected_by="Osaka Institute of Public Health"
                     /genotype="ST354"
     gene            complement(118..450)
                     /locus_tag="AABK08_RS25135"
     CDS             complement(118..450)
                     /locus_tag="AABK08_RS25135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008784643.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EmrE family multidrug efflux SMR transporter"
                     /protein_id="WP_001099531.1"
                     /translation="MNTYIFLGGAIVAEVIGTTFMKYSEGFTRLWPSVGTAISYCAAFY
                     LLSQTLENIPTGIAYAIWSGAGIVLISLAGWLVSGQKLDWPAIAGMFLICVGVLVINIF
                     SKSSAH"
                     /name="EmrE family multidrug efflux SMR transporter"
     gene            complement(618..833)
                     /locus_tag="AABK08_RS25140"
                     /old_locus_tag="OIPH1902010_48130"
     CDS             complement(618..833)
                     /locus_tag="AABK08_RS25140"
                     /old_locus_tag="OIPH1902010_48130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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_024195375.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLIQRENA
                     ALNERVTVLSRQVQSLSEQLRRLSKG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(837..1322)
                     /locus_tag="AABK08_RS25145"
                     /old_locus_tag="OIPH1902010_48140"
     CDS             complement(837..1322)
                     /locus_tag="AABK08_RS25145"
                     /old_locus_tag="OIPH1902010_48140"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /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_025367738.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGQFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(<1357..2061)
                     /locus_tag="AABK08_RS25150"
                     /pseudo=""
     CDS             complement(<1357..2061)
                     /locus_tag="AABK08_RS25150"
                     /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(2000..2323)
                     /locus_tag="AABK08_RS25155"
                     /old_locus_tag="OIPH1902010_48150"
     CDS             complement(2000..2323)
                     /locus_tag="AABK08_RS25155"
                     /old_locus_tag="OIPH1902010_48150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_004193914.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQIVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2962..3132
                     /locus_tag="AABK08_RS25160"
                     /old_locus_tag="OIPH1902010_48160"
     CDS             2962..3132
                     /locus_tag="AABK08_RS25160"
                     /old_locus_tag="OIPH1902010_48160"
                     /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="hypothetical protein"
                     /protein_id="WP_004193911.1"
                     /translation="MHEPPVQSDYHARSGNYQLESNPERHDKSPVAVAIGNWVHGAEIV
                     ENAYRVLEVKA"
                     /name="hypothetical protein"
     ARG             complement(119..450)
                     /name="qacG"
                     /gene="qacG"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="41.35"
                     /coverage="102.8"
     Typing          complement(2420..2611)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.308"
                     /coverage="89.0"
                     /evalue="3.38e-71"
     Typing          2591..3074
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.756"
                     /coverage="93.0"
                     /evalue="1.73e-132"
     Typing          complement(521..2010)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.784"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 caaacgaacc accgttggta gcggtggttt ttttgtttac agggaaaaag attacgcgca
       61 gaaagaaagg atctcaagga aatccttttg ctttggccaa tatgcttcgg taaaaagtta
      121 atgcgcagaa gattttgaaa aaatattaat aaccaaaact ccaacgcaaa taaggaacat
      181 tcctgcaatt gcaggccaat caagtttttg accgctaacc aaccaaccag ctaggcttat
      241 tagtacaatt cccgcaccag accaaattgc gtaagcaata ccggtaggta tattttccaa
      301 tgtttgggaa agcagataaa aggcagcgca ataacttatt gcagttccta cagacggcca
      361 caggcgtgta aatccttctg aatatttcat aaaggtggtg cctatgactt cagccacaat
      421 agcccctccc aggaaaatat atgtattcat aaaaatacct catgttgaaa aatttaaata
      481 tctttacata acaactaatt aatagaaccc ggcttatcat agcgaaggac catgatgctg
      541 ccactgcgat cgttccagct ccagcgcttt ctggtgctgc accgcccgct cctgctgccg
      601 gtgagtttct atcgcgttca gcctttcgac aaccggcgca gctgctcgct caaactctgc
      661 acctgcctgc tcaagaccgt gacgcgctcg ttcagcgccg cgttctcccg ttgaataaga
      721 ccagacatcg tccgccattc cgcgaaggcg ttctcccact cgtccagcct tttcgagtag
      781 tcctgctgta gctgctctaa tgcgctcagc aactgttttt ccagctccgt catgtgctat
      841 ttccccgcca gtatcatcca gctcgagtcc tctccgaact gtcccgcttc cgggttcacc
      901 ctcacgcagc ggcgtctctg ctcgccgcag gtcgagagct gtacgccgct gttcctctct
      961 gacagcatgg cctgcgtgct cttctgctcc cggatggtcg tatagttctc gagtatctgc
     1021 tgcccctgcc accacagaat gcccgcgctc gacgctatca gcagcgcgga gaccagaacg
     1081 atggtcagcc acgtctggct gaccatgcgc agcatccctt tcgtgcgctg gctcatggct
     1141 gaggacagct tccggtcgtg gtcgaggatg gcggcgctga ttctcttctc gctttcgctc
     1201 agttccgctc tgacagactt ctcgtgctcg ctgaatgcgg ctttcagcat ctcgccggta
     1261 gtctgctgct gcgctttcga tttctgctct aagtccttcg ccagcgttaa aagactgttc
     1321 atagatggct cccttcagtc ggatgtttcg ccccccgtcc gggtcggcaa tgctgatgct
     1381 gctttttgtg gtgcgcacca cctcaaaacc tgcgctttcc agcgcctcag tgacgtcctg
     1441 acgcgttttc agctccccgg atgaggcaag ggcaagcagg ccgctcgtaa tcgcctgggc
     1501 ggcttcctgc ttcgcttccg gcagcgcgga aggcgagacc agcacccgcc ggttctccgg
     1561 cgcgttcggg tcatgcagcc ccagcctgcc gttcactatg gtctgccagg catcgatgcg
     1621 cggacggtcg gcgcggtcgt aatacggctg tagccgcttg ccggtcagaa gctccgtgtt
     1681 cgggatcagg aagttcagct ccagccgccc cttgtcccgg tgctcaaccc acagcacgct
     1741 gtactggtct ttatcgagtc cgggcatcag aacccgctcg aaactcgcca tcagcttttc
     1801 gcgctggccg ggcggtaaat cctgttcggc aaaagacaga acgccggaag tgtacttttt
     1861 ggcgtagggc gaggcgtcga taagctcccg gacttcatcc ggcttcccct gcagaacgct
     1921 ggcgccgtcg cgctggcgat ctttacccag cagataatcg accggcccgc cgccgccgcc
     1981 gcgcccccga ggatgaaact taacgatcat catcagcacc cttttccagt acggcatgcc
     2041 gcaaccgctc gagtccggca tcgatggcca tcagcgcggc gacaatctgc acgcggtcgt
     2101 gtccgcttcc accaccggcg ttaacctggc gggcaatctg gttaaggttg ttccccatgc
     2161 cggcaagctg acgaagcagc gccggcgaga tcgacggaag tttgccggcg cgtgcgggct
     2221 tctcgtccag gcacgtctgc cgcatccagg ccgcgagttg cttaccctcg cagcgctcca
     2281 gcagacgccg gtgctcgtcc tcagtcaccc acatggtgag cattttgctg cgtttgtctg
     2341 ccaatccggc ctcctgataa cgccgggacg gacgggaaat cttttcccgg tcggcacggt
     2401 gttggacaag ccgcaggcgc ggcagtggtt ttagcgggtt tcggggcgca gccctgaacc
     2461 agtcacgtag cgctagcgga gtgtatactg gctaaacatg ttatgacgga gtggcaattt
     2521 atgaaagtgc ttcatgtgac aggggaaaaa tgcggctgcc gggcgtaagt gcaaaatgca
     2581 ggtggtgatg aaatgacgcc tcctcgctca ctcggtcgct acgctcctgc cgtgagactg
     2641 cggcgggcgt taccagctca cagattacgg gataagcaaa tgccgctcga agcaggaaag
     2701 gccaagaaaa ggatgcggag ttgccgtttt tccataggct ccgcccccct gacgagtatc
     2761 acgaaaatga cgctcaaatc agcggtggcg aaacccgatg cggcttaaag ataccaggcg
     2821 tttccccctg gtggctccct cgtgctcccc cgcattcctg cctttcggtt taccggtgtc
     2881 attccgctgt tatggccgcg gtttctcatt ccacgcctga aactcggttc cgggtaggca
     2941 gttcgctcca ggatggactg tatgcacgaa ccccccgttc agtccgacta ccacgcccgt
     3001 tccggtaact atcaacttga gtccaacccg gaaagacacg acaaatcgcc agtggcggta
     3061 gccattggta actgggttca cggagcagag attgtagaga atgcctacag agttcttgaa
     3121 gtgaaagcct gagtgcggct acactgaaag gacagtttag gtatctgcgc tccgtgaaag
     3181 ccagttacca tcggaacaaa gagttggtag ctctgaattc cgg
//
