LOCUS       NZ_CP127513             6141 bp    DNA     circular CON 10-FEB-2024
DEFINITION  Klebsiella pneumoniae strain ER29693.4 plasmid pER29693_4A.2,
            complete sequence.
ACCESSION   NZ_CP127513
VERSION     NZ_CP127513.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35640678
            Assembly: GCF_036452095.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 6141)
  AUTHORS   Mushtaq,A., Alburquerque,B., Chung,M., Fabre,S., Sullivan,M.J.,
            Nowak,M., Sordillo,E.M., Polanco,J., van Bakel,H. and Gitman,M.R.
  TITLE     Clinical, microbiological and genomic characterization of
            Gram-negative bacteria with dual carbapenemases as identified by
            rapid molecular testing
  JOURNAL   JAC Antimicrob Resist 6 (1), dlad137 (2023)
   PUBMED   38161967
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 6141)
  AUTHORS   Alburquerque,B., Sullivan,M.J. and van Bakel,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-JUN-2023) Genetics and Genomic Sciences, Icahn School
            of Medicine, One Gustave L. Levy Place Box 1498, New York, NY 10029,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: FLYE v. 2.9.1-b1784
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 451.13x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/09/2024 11:00:02
            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)                     :: 5,614
            CDSs (total)                      :: 5,487
            Genes (coding)                    :: 5,373
            CDSs (with protein)               :: 5,373
            Genes (RNA)                       :: 127
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 114
            CDSs (without protein)            :: 114
            Pseudo Genes (ambiguous residues) :: 0 of 114
            Pseudo Genes (frameshifted)       :: 50 of 114
            Pseudo Genes (incomplete)         :: 65 of 114
            Pseudo Genes (internal stop)      :: 20 of 114
            Pseudo Genes (multiple problems)  :: 18 of 114
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP127513.1.
            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..6141
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="ER29693.4"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pER29693_4A.2"
                     /geo_loc_name="USA:New York City"
                     /lat_lon="40.7903114 N 73.9528738 W"
                     /collection_date="2014-09"
                     /collected_by="Mount Sinai Hospital"
     gene            join(5474..6141,1..280)
                     /locus_tag="QQ395_RS28040"
                     /old_locus_tag="QQ395_28005"
     CDS             join(5474..6141,1..280)
                     /locus_tag="QQ395_RS28040"
                     /old_locus_tag="QQ395_28005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014293673.1"
                     /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_015060053.1"
                     /translation="MRKCAQLELFRERLPRKPYYSDELTTGLRIADVARALGARYIQPN
                     GPTHRHWIVFDVDHAAATLSWDDVGAPAPNITVTNKANGHAHLIYGLDTPIRTAPDGNA
                     APLRYAAAIEAALREKLGADMGYSGLICKNPLHEHWLVQVWEPRLYDLAWLSDYLDLSS
                     YNGRKSLPEYGLGRNCTLFEKTRLWAYKAIRQGWPDYPEWLAACVDRASGYNAQFEQPL
                     PANEVRHTAKSIAKWTHQHLSPAGFREEQARRGAKGGKVSKGGGRPSNSGKDKSDLLPE
                     VLRLKAQGYTNRDIADDLQISPSTVSVYLKRDRP"
                     /name="replication initiation protein"
     gene            688..1080
                     /locus_tag="QQ395_RS28045"
                     /old_locus_tag="QQ395_28010"
     CDS             688..1080
                     /locus_tag="QQ395_RS28045"
                     /old_locus_tag="QQ395_28010"
                     /inference="COORDINATES: protein motif:HMM:NF037437.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="antitoxin VbhA family protein"
                     /protein_id="WP_043907050.1"
                     /translation="MSTTQIEKDSRRKAVNGVISSFQLEGEAITDEFKILLEDYINGKI
                     STDEVLAMVSDEPTTTEYDYEITPRTLGLGGGWNLRLLENGEEVGGGVFPLPEHCDFRD
                     EKALQTLLDSLYEDALAEASAWLASR"
                     /name="antitoxin VbhA family protein"
     gene            1062..1400
                     /locus_tag="QQ395_RS28050"
                     /old_locus_tag="QQ395_28015"
     CDS             1062..1400
                     /locus_tag="QQ395_RS28050"
                     /old_locus_tag="QQ395_28015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000502641.1"
                     /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_043907051.1"
                     /translation="MAGQPLKRLRSIKIRVSDAELERLRELCPKAQLAEWMREQCLGVA
                     QPQRRTPAPTVDPALLRQLAGMGNNLNQIARRVNSGEWGPLDRLRIIAELSAIGRELEE
                     LHHDHQIP"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1381..2835
                     /locus_tag="QQ395_RS28055"
                     /old_locus_tag="QQ395_28020"
     CDS             1381..2835
                     /locus_tag="QQ395_RS28055"
                     /old_locus_tag="QQ395_28020"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_064996073.1"
                     /translation="MIIKFHNRGVGRGSGPVGYLLGRDGNREGATLDRGNPAVIEALID
                     SSPYAKKYTSGVLSFAEADLPRATKDKLMSDFEKALLPGLEGNQYAVLWVEHRDKGRLE
                     LNFVVPNIELQSGKRLQPYFHKADNPRLDAWRTVVNGELKLHDPDDPLNRQAVITPKDL
                     PRGHKEAAQAITDGLLRMAGAGEIQSRDDVRKALQGAGFSVVRETKNSLSIADPDGGRN
                     IRLKGVLYEQDFRHGEGLRAELEAAGQRYREASDRRIHEARESYLRGVEIKRGENERRY
                     CRAQPENGLAVAQNVDLDAGQHRPVLERNERDPLVSGGIDSGAASHSPSLGREGRQAKA
                     DPVREEIGAPLRADLRPQSNRLGEGYLLDRAEGVLNDGIGAGIALRVRGFAERIRAAAQ
                     GMAGKLRELGEHVREHQTRGRDQQGSSRAIDEAGERLNAASGRLEQAAGGLDRASQQVA
                     KEREHRLLKALDRGWERGDRSRGFER"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(3117..3398)
                     /locus_tag="QQ395_RS28060"
                     /old_locus_tag="QQ395_28025"
     CDS             complement(3117..3398)
                     /locus_tag="QQ395_RS28060"
                     /old_locus_tag="QQ395_28025"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_043907053.1"
                     /translation="MGFFNLSKALEEVSDAFGAKETAIASAKLLGKGVVNLAHFAATTG
                     LDSVVKQTSNKVLNSESSTEEQREQAKKSAAWADARIAARNKAENTED"
                     /name="hypothetical protein"
     gene            3742..4539
                     /locus_tag="QQ395_RS28065"
                     /old_locus_tag="QQ395_28030"
     CDS             3742..4539
                     /locus_tag="QQ395_RS28065"
                     /old_locus_tag="QQ395_28030"
                     /EC_number="3.5.2.6"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011071128.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="OXA-48 family carbapenem-hydrolyzing class D
                     beta-lactamase OXA-232"
                     /protein_id="WP_043907054.1"
                     /translation="MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVV
                     LWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIAA
                     WNRDHDLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIR
                     ISATQQIAFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTSIEPKIGWW
                     VGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP"
                     /name="OXA-48 family carbapenem-hydrolyzing class D
                     beta-lactamase OXA-232"
     gene            complement(4946..>5098)
                     /locus_tag="QQ395_RS28070"
                     /old_locus_tag="QQ395_28035"
                     /pseudo=""
     CDS             complement(4946..>5098)
                     /locus_tag="QQ395_RS28070"
                     /old_locus_tag="QQ395_28035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015059985.1"
                     /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="EreA family erythromycin esterase"
                     /name="EreA family erythromycin esterase"
     ARG             3743..4536
                     /name="blaOXA-232"
                     /gene="blaOXA-232"
                     /gene_name="OXA-48 family carbapenem-hydrolyzing class D
                     beta-lactamase OXA-232"
                     /tool="amrfinderplus"
                     /drug_class="BETA-LACTAM"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          2..280
                     /name="ColKP3"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.87e-144"
     Typing          1382..2832
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.554"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 cgcaaacgaa gtccggcaca cggccaagtc cattgccaaa tggacgcacc agcacctaag
       61 ccccgcaggg ttcagagagg agcaggcccg gagaggtgcg aagggcggca aggtatccaa
      121 gggaggggga aggccgagca atagcggtaa ggacaagtcc gatctattgc cggaggttct
      181 gcggcttaag gctcaggggt acaccaaccg cgatatagcg gacgatcttc aaatctcccc
      241 cagtacggtg agcgtttacc taaagcgtga tcgtccgtga tcgaaacaag ccttatcaga
      301 taatagcccc ctttaggggg gttcctgcgc tcttgtcttt tagccttaaa aaatcctttt
      361 agcgcggatc tttggcgagg tggacaactg cgcctgtccg tccatcgccc ccctgttttt
      421 tcggggggtg tgggcggcag cagttatcca cggagccgct ctttcccttg atcttgctct
      481 agggcttgca gtatcccgcc catggttgaa taatgtacta agcaaggcta cacagaggcc
      541 cctctacctg cttcgcggtc tcgggcctct gtggccttgt tcaggggtgc tacgcccccc
      601 cgaaaccccc tgtggccccc gctcgatccg ccccttcggg acggtctgcg cggtggcttc
      661 ttggctctgg agaatggacg aggccctatg tcaacaacac agatagagaa agattcgaga
      721 aggaaggcag tcaatggcgt tatttctagt ttccaactag agggggaggc cataaccgat
      781 gaattcaaaa ttctacttga agattatatc aatggaaaaa tttccaccga tgaggtgtta
      841 gctatggtaa gtgacgaacc cacaacaacg gaatacgact acgaaatcac cccccgcact
      901 ctcggtcttg gcgggggctg gaatctgcgt ttgctggaga acggcgaaga ggtcggcggg
      961 ggtgttttcc ccttgccgga gcactgcgat tttcgggatg aaaaggcgct ccagacgcta
     1021 ctcgatagcc tctatgagga cgccttagcg gaggcctctg catggctggc cagccgttaa
     1081 agcgcctccg ctctatcaag atccgggtct cagatgcgga gcttgagcgc ctgcgggagc
     1141 tctgccccaa ggcccaactg gcggagtgga tgcgggagca atgtctcggt gttgcgcaac
     1201 cccagcgccg aacgccggcg cctaccgtag atccggcgct cttgcggcag ttggccggaa
     1261 tgggcaacaa cctgaaccag atcgcccggc gcgttaattc cggggagtgg gggccgttgg
     1321 atcggctgcg catcatagcg gagctgtccg ctataggccg cgagctggag gaactgcacc
     1381 atgatcatca aattccataa ccgtggggta ggccggggct ccgggcctgt tggctacttg
     1441 ttgggccgtg acgggaaccg ggaaggcgca acgctcgacc ggggcaaccc tgcggtgatt
     1501 gaagccctga ttgattccag tccctacgcc aaaaaataca cctctggcgt tctgtcgttt
     1561 gccgaggctg atttacccag ggcgaccaag gacaagctga tgagcgactt tgaaaaggcg
     1621 ctcctgcccg gactggaggg caaccagtac gctgttttgt gggtagagca ccgcgacaag
     1681 gggcggctgg agctgaattt tgtagtcccg aacatcgaat tgcagagcgg gaagcggctg
     1741 caaccctact tccacaaggc cgacaatccg cgcctcgatg cgtggcgaac cgtggtaaac
     1801 ggggagctga aattgcacga cccggacgat ccgttaaacc gtcaggccgt tatcacgcca
     1861 aaggatttgc cgagggggca caaggaggcc gctcaggcca ttacagacgg gcttttacgc
     1921 atggccggag caggggagat ccagagccgc gatgatgtgc gcaaagcctt gcagggtgcg
     1981 ggtttcagcg tggtacgcga aaccaaaaac agcctgagca ttgccgaccc ggacgggggg
     2041 cggaacatcc gattaaaggg ggtgctgtat gagcaagatt ttagacatgg cgaaggactt
     2101 cgagcagagc tcgaagcagc aggccaacgc tatcgagaag cgtctgaccg aagaattcac
     2161 gaggcacgag aaagctatct ccggggcgtt gaaatcaagc gaggagaaaa tgagcgccgc
     2221 tattgccgag cacagccaga aaatgggctg gctgttgctc aaaacgtgga tctggatgct
     2281 ggtcagcatc gtcctgttct tgagcgcaac gagcgggatc ctctggtatc agggggaatt
     2341 gatagcggag cggcaagcca ctctccaagc cttggcagag aagggcggca agctaaagct
     2401 gacccagtgc gggaagaaat tggagcacct ttgcgtgcag atctccgacc ccaatccaac
     2461 cgtttggggg aaggatacct attggatcgt gccgaagggg tactaaatga cgggattgga
     2521 gcgggaattg ctctgcgcgt tcgaggcttt gcagagcgca tacgagcagc agcacaaggc
     2581 atggcaggaa agctacgcga acttggcgag catgtacgag agcaccaaac aagaggccga
     2641 gatcagcagg gcagcagcag agcgattgac gaggcaggtg aacggcttaa cgcagcaagt
     2701 ggacggcttg agcaagcagc tggagggctt gaccgggcta gtcagcaagt tgcaaaagaa
     2761 agggaacaca ggctcctgaa ggcactggat cgaggctggg agcgtggaga cagatcgcga
     2821 ggctttgagc gttgacggaa caaaacggcc gtcagttata aaaaaaggaa agtgctatca
     2881 ctttcctttt atcggcggga attatcgttg agttcttcta tgccattttt catagtagta
     2941 actgtaatct tcatctctac caccagattc aatccagtca tcatactcag ggctattttt
     3001 gaaatctgaa tcagacatgc taactccttg ttattagttg gcttctatgg aagctagcgc
     3061 accgtgaagt tatgatcaac gatgtagtcc acatcattgt cgaaatgtgc gttcagctag
     3121 tcttcggtgt tttctgcttt atttctagcg gcgattctcg cgtctgccca tgcggcagac
     3181 tttttagcct gttctcgttg ttcttcggtt gaagactcgc tgttgagaac tttgttgctc
     3241 gtttgtttga ccaccgaatc caaacctgtt gttgctgcaa aatgagctag gttaacaact
     3301 cccttaccta acaacttggc actagcgatt gcggtttctt tagccccaaa agcatcagac
     3361 acctcctcaa gcgctttaga taggttaaaa aatcccatac tccccctaag aatatcatca
     3421 ataaaattga gtgttgctct gtggataact tgcagagttt attaagtatc attgcagcaa
     3481 agatgaaatc aatgatttat caaaaatgat tgaaaggtgg ttgtaaataa tgttacaatg
     3541 tgtgagaagc agtctaaatt cttcgtgaaa tagtgatttt tgaagctaat aaaaaacaca
     3601 cgtggaattt aggtaatagt taaagcttgt gcctgattgt tgccacaatt ggtcagcagt
     3661 ttgctaggga atgagagggc agagaatgat aagcttagca cttaatttgt atggatatat
     3721 tgcattaagc aaggggacgt tatgcgtgta ttagccttat cggctgtgtt tttggtggca
     3781 tcgattatcg gaatgccagc ggtagcaaag gaatggcaag aaaacaaaag ttggaatgct
     3841 cactttactg aacataaatc acagggcgta gttgtgctct ggaatgagaa taagcagcaa
     3901 ggatttacca ataatcttaa acgggcgaac caagcatttt tacccgcatc tacctttaaa
     3961 attcccaata gcttgatcgc cctcgatttg ggcgtggtta aggatgaaca ccaagtcttt
     4021 aagtgggatg gacagacgcg tgatatcgcc gcttggaatc gtgaccatga cttaattacc
     4081 gcgatgaagt actcagttgt gcctgtttat caagaatttg cccgccaaat tggtgaggca
     4141 cgtatgagta aaatgctgca cgccttcgat tatggcaatg aggatatctc gggcaatgta
     4201 gacagttttt ggctcgatgg tggtattcgc atttcggcta cccagcaaat cgctttttta
     4261 cgcaagctgt atcacaacaa gctgcacgtt tctgagcgta gtcagcgcat cgtgaaacaa
     4321 gccatgctga ccgaagccaa tggcgactat attattcggg ctaaaacggg atactcgact
     4381 agtatcgaac ctaagattgg ctggtgggtt ggttgggttg aacttgatga taatgtgtgg
     4441 ttttttgcga tgaatatgga tatgcccaca tcggatggtt tagggctgcg ccaagccatc
     4501 acaaaagaag tgctcaaaca ggagaaaatt attccctaga agtggttagc gcgtatttgt
     4561 gtgaaatagc cgtcatataa gctgtaaaga tatatggaca aaatgctgat gctcgatgcg
     4621 cttgtagtta atggctcata cttaatcggt caggcctaat cgacttaagc tccgcgcgtt
     4681 aactttcagc ctgagcatta gcatcacatt cctaaacgta aaaagcctag ccaatttgct
     4741 aggctttttt gttatctcaa tggccatggt cactcaacat gggggtgtga ataaaggagt
     4801 ggcgatgtca gtaaaggtga atgccgctgc gataaagtgc ctagcccatc aaggattgta
     4861 ggctttcttg gctgctaaag cgtttgacga aaaagtccaa gaaggcgctg atattggttc
     4921 tccatcattt tcatctaccg gtttactata ggtcaaccag gccgtccttg ccggcgcttg
     4981 ggacgcagac gatggcatca aatgcctcgc tcaaattcgt ttctacagag gcgctttggg
     5041 accgcattcg ctttgctttc atgggggcat ctgtcaatgt cagacatgaa tcctccgata
     5101 taggttgatt tttgatctct tcaacacttg gtgttgtccg actagagaga cttatatgga
     5161 tcagtattct tgcactgaca atggtgccac tcaatcccaa ggatcgacct agttagaggc
     5221 gtagatcaag caattcaaaa cagcgcagaa gcagaaggag gtggaaatat gttccagggt
     5281 gaaaggttac atgcaactaa cgttgctctc taggatgtgc ctgctgtaac gtattgtcca
     5341 gaaaagacaa ccccccgtta tcgcttgcat cttggcggag ctgcgaaaaa cgggggccgt
     5401 gacgaatcac aagagaagtc tatcacatgg atcatgccaa acaaccccac gccgccaata
     5461 agcgcggtgg tgcttgagaa agtgcgcaca gcttgagctg tttcgggagc gcctgccccg
     5521 gaaaccctac tattccgacg agcttacaac gggcctacgg attgcggatg ttgcccgcgc
     5581 ccttggtgcg cgttacatcc agccgaacgg gccaacgcac cgccactgga tcgtttttga
     5641 cgtagaccat gcagccgcta cgttatcttg ggatgacgta ggcgctccag cccctaacat
     5701 taccgtcacg aacaaggcca acggccacgc gcatctgatc tacggactgg atacgccgat
     5761 ccgcactgcc ccggatggaa atgcagcccc tctgcggtat gccgccgcca tcgaggccgc
     5821 gctccgggag aaattagggg cggatatggg ctactccggg ctgatctgca agaaccccct
     5881 gcatgagcac tggctggtgc aggtatggga accccggctc tacgatttag cctggctatc
     5941 cgattacctc gatctgagct cctacaatgg ccgcaaatcg cttcctgagt acgggcttgg
     6001 gcgaaactgt accctgttcg agaaaacgcg cctgtgggcc tataaagcga tccggcaggg
     6061 ctggccggat taccccgaat ggttggccgc ttgtgttgac cgggcatcag gatataacgc
     6121 ccagttcgag cagccgctcc c
//
