LOCUS       NZ_CP097241             6141 bp    DNA     circular CON 11-JUN-2024
DEFINITION  Klebsiella pneumoniae strain 1 plasmid p6.1, complete sequence.
ACCESSION   NZ_CP097241
VERSION     NZ_CP097241.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN27722563
            Assembly: GCF_023374245.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 6141)
  AUTHORS   Luo,T.L., Corey,B.W., Snesrud,E., Iovleva,A., McElheny,C.L.,
            Preston,L., Bennett,J.W., McGann,P.T. and Lebreton,F.
  TITLE     IS26-mediated plasmid and toxin-antitoxin gene convergence in
            Klebsiella pneumoniae resulting in antibiotic resistance gene loss
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6141)
  AUTHORS   Luo,T.L., Corey,B.W., Snesrud,E., Iovleva,A., McElheny,C.L.,
            Preston,L., Bennett,J.W., McGann,P.T. and Lebreton,F.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-MAY-2022) Bioinformatics, Walter Reed Army Institute
            of Research, 503 Robert Grant Ave, Silver Spring, MD 20910, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Newbler v. 2.9
            Assembly Name                     :: MRSN546052
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 113x
            Sequencing Technology             :: Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023374245.1-RS_2024_06_11
            Annotation Date                   :: 06/11/2024 04:57:04
            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)                     :: 5,667
            CDSs (total)                      :: 5,546
            Genes (coding)                    :: 5,378
            CDSs (with protein)               :: 5,378
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 168
            CDSs (without protein)            :: 168
            Pseudo Genes (ambiguous residues) :: 0 of 168
            Pseudo Genes (frameshifted)       :: 62 of 168
            Pseudo Genes (incomplete)         :: 103 of 168
            Pseudo Genes (internal stop)      :: 25 of 168
            Pseudo Genes (multiple problems)  :: 19 of 168
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP097241.1.
            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="1"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p6.1"
                     /geo_loc_name="USA: Pittsburgh"
                     /lat_lon="40.4406 N 79.9959 W"
                     /collection_date="2013-03-06"
                     /collected_by="UPMC"
                     /genotype="ST14"
     gene            complement(11..>163)
                     /locus_tag="M4268_RS28215"
                     /old_locus_tag="M4268_28225"
                     /pseudo=""
     CDS             complement(11..>163)
                     /locus_tag="M4268_RS28215"
                     /old_locus_tag="M4268_28225"
                     /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"
     gene            539..1486
                     /locus_tag="M4268_RS28220"
                     /old_locus_tag="M4268_28230"
     CDS             539..1486
                     /locus_tag="M4268_RS28220"
                     /old_locus_tag="M4268_28230"
                     /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            1894..2286
                     /locus_tag="M4268_RS28225"
                     /old_locus_tag="M4268_28235"
     CDS             1894..2286
                     /locus_tag="M4268_RS28225"
                     /old_locus_tag="M4268_28235"
                     /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            2268..2606
                     /locus_tag="M4268_RS28230"
                     /old_locus_tag="M4268_28240"
     CDS             2268..2606
                     /locus_tag="M4268_RS28230"
                     /old_locus_tag="M4268_28240"
                     /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            2587..4041
                     /locus_tag="M4268_RS28235"
                     /old_locus_tag="M4268_28245"
     CDS             2587..4041
                     /locus_tag="M4268_RS28235"
                     /old_locus_tag="M4268_28245"
                     /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(4323..4604)
                     /locus_tag="M4268_RS28240"
                     /old_locus_tag="M4268_28250"
     CDS             complement(4323..4604)
                     /locus_tag="M4268_RS28240"
                     /old_locus_tag="M4268_28250"
                     /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            4948..5745
                     /locus_tag="M4268_RS28245"
                     /old_locus_tag="M4268_28255"
     CDS             4948..5745
                     /locus_tag="M4268_RS28245"
                     /old_locus_tag="M4268_28255"
                     /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"
     ARG             4949..5742
                     /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          552..1473
                     /name="rep_cluster_1195"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.974"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          2588..4038
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.554"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 taccggttta ctataggtca accaggccgt ccttgccggc gcttgggacg cagacgatgg
       61 catcaaatgc ctcgctcaaa ttcgtttcta cagaggcgct ttgggaccgc attcgctttg
      121 ctttcatggg ggcatctgtc aatgtcagac atgaatcctc cgatataggt tgatttttga
      181 tctcttcaac acttggtgtt gtccgactag agagacttat atggatcagt attcttgcac
      241 tgacaatggt gccactcaat cccaaggatc gacctagtta gaggcgtaga tcaagcaatt
      301 caaaacagcg cagaagcaga aggaggtgga aatatgttcc agggtgaaag gttacatgca
      361 actaacgttg ctctctagga tgtgcctgct gtaacgtatt gtccagaaaa gacaaccccc
      421 cgttatcgct tgcatcttgg cggagctgcg aaaaacgggg gccgtgacga atcacaagag
      481 aagtctatca catggatcat gccaaacaac cccacgccgc caataagcgc ggtggtgctt
      541 gagaaagtgc gcacagcttg agctgtttcg ggagcgcctg ccccggaaac cctactattc
      601 cgacgagctt acaacgggcc tacggattgc ggatgttgcc cgcgcccttg gtgcgcgtta
      661 catccagccg aacgggccaa cgcaccgcca ctggatcgtt tttgacgtag accatgcagc
      721 cgctacgtta tcttgggatg acgtaggcgc tccagcccct aacattaccg tcacgaacaa
      781 ggccaacggc cacgcgcatc tgatctacgg actggatacg ccgatccgca ctgccccgga
      841 tggaaatgca gcccctctgc ggtatgccgc cgccatcgag gccgcgctcc gggagaaatt
      901 aggggcggat atgggctact ccgggctgat ctgcaagaac cccctgcatg agcactggct
      961 ggtgcaggta tgggaacccc ggctctacga tttagcctgg ctatccgatt acctcgatct
     1021 gagctcctac aatggccgca aatcgcttcc tgagtacggg cttgggcgaa actgtaccct
     1081 gttcgagaaa acgcgcctgt gggcctataa agcgatccgg cagggctggc cggattaccc
     1141 cgaatggttg gccgcttgtg ttgaccgggc atcaggatat aacgcccagt tcgagcagcc
     1201 gctccccgca aacgaagtcc ggcacacggc caagtccatt gccaaatgga cgcaccagca
     1261 cctaagcccc gcagggttca gagaggagca ggcccggaga ggtgcgaagg gcggcaaggt
     1321 atccaaggga gggggaaggc cgagcaatag cggtaaggac aagtccgatc tattgccgga
     1381 ggttctgcgg cttaaggctc aggggtacac caaccgcgat atagcggacg atcttcaaat
     1441 ctcccccagt acggtgagcg tttacctaaa gcgtgatcgt ccgtgatcga aacaagcctt
     1501 atcagataat agcccccttt aggggggttc ctgcgctctt gtcttttagc cttaaaaaat
     1561 ccttttagcg cggatctttg gcgaggtgga caactgcgcc tgtccgtcca tcgcccccct
     1621 gttttttcgg ggggtgtggg cggcagcagt tatccacgga gccgctcttt cccttgatct
     1681 tgctctaggg cttgcagtat cccgcccatg gttgaataat gtactaagca aggctacaca
     1741 gaggcccctc tacctgcttc gcggtctcgg gcctctgtgg ccttgttcag gggtgctacg
     1801 cccccccgaa accccctgtg gcccccgctc gatccgcccc ttcgggacgg tctgcgcggt
     1861 ggcttcttgg ctctggagaa tggacgaggc cctatgtcaa caacacagat agagaaagat
     1921 tcgagaagga aggcagtcaa tggcgttatt tctagtttcc aactagaggg ggaggccata
     1981 accgatgaat tcaaaattct acttgaagat tatatcaatg gaaaaatttc caccgatgag
     2041 gtgttagcta tggtaagtga cgaacccaca acaacggaat acgactacga aatcaccccc
     2101 cgcactctcg gtcttggcgg gggctggaat ctgcgtttgc tggagaacgg cgaagaggtc
     2161 ggcgggggtg ttttcccctt gccggagcac tgcgattttc gggatgaaaa ggcgctccag
     2221 acgctactcg atagcctcta tgaggacgcc ttagcggagg cctctgcatg gctggccagc
     2281 cgttaaagcg cctccgctct atcaagatcc gggtctcaga tgcggagctt gagcgcctgc
     2341 gggagctctg ccccaaggcc caactggcgg agtggatgcg ggagcaatgt ctcggtgttg
     2401 cgcaacccca gcgccgaacg ccggcgccta ccgtagatcc ggcgctcttg cggcagttgg
     2461 ccggaatggg caacaacctg aaccagatcg cccggcgcgt taattccggg gagtgggggc
     2521 cgttggatcg gctgcgcatc atagcggagc tgtccgctat aggccgcgag ctggaggaac
     2581 tgcaccatga tcatcaaatt ccataaccgt ggggtaggcc ggggctccgg gcctgttggc
     2641 tacttgttgg gccgtgacgg gaaccgggaa ggcgcaacgc tcgaccgggg caaccctgcg
     2701 gtgattgaag ccctgattga ttccagtccc tacgccaaaa aatacacctc tggcgttctg
     2761 tcgtttgccg aggctgattt acccagggcg accaaggaca agctgatgag cgactttgaa
     2821 aaggcgctcc tgcccggact ggagggcaac cagtacgctg ttttgtgggt agagcaccgc
     2881 gacaaggggc ggctggagct gaattttgta gtcccgaaca tcgaattgca gagcgggaag
     2941 cggctgcaac cctacttcca caaggccgac aatccgcgcc tcgatgcgtg gcgaaccgtg
     3001 gtaaacgggg agctgaaatt gcacgacccg gacgatccgt taaaccgtca ggccgttatc
     3061 acgccaaagg atttgccgag ggggcacaag gaggccgctc aggccattac agacgggctt
     3121 ttacgcatgg ccggagcagg ggagatccag agccgcgatg atgtgcgcaa agccttgcag
     3181 ggtgcgggtt tcagcgtggt acgcgaaacc aaaaacagcc tgagcattgc cgacccggac
     3241 ggggggcgga acatccgatt aaagggggtg ctgtatgagc aagattttag acatggcgaa
     3301 ggacttcgag cagagctcga agcagcaggc caacgctatc gagaagcgtc tgaccgaaga
     3361 attcacgagg cacgagaaag ctatctccgg ggcgttgaaa tcaagcgagg agaaaatgag
     3421 cgccgctatt gccgagcaca gccagaaaat gggctggctg ttgctcaaaa cgtggatctg
     3481 gatgctggtc agcatcgtcc tgttcttgag cgcaacgagc gggatcctct ggtatcaggg
     3541 ggaattgata gcggagcggc aagccactct ccaagccttg gcagagaagg gcggcaagct
     3601 aaagctgacc cagtgcggga agaaattgga gcacctttgc gtgcagatct ccgaccccaa
     3661 tccaaccgtt tgggggaagg atacctattg gatcgtgccg aaggggtact aaatgacggg
     3721 attggagcgg gaattgctct gcgcgttcga ggctttgcag agcgcatacg agcagcagca
     3781 caaggcatgg caggaaagct acgcgaactt ggcgagcatg tacgagagca ccaaacaaga
     3841 ggccgagatc agcagggcag cagcagagcg attgacgagg caggtgaacg gcttaacgca
     3901 gcaagtggac ggcttgagca agcagctgga gggcttgacc gggctagtca gcaagttgca
     3961 aaagaaaggg aacacaggct cctgaaggca ctggatcgag gctgggagcg tggagacaga
     4021 tcgcgaggct ttgagcgttg acggaacaaa acggccgtca gttataaaaa aaggaaagtg
     4081 ctatcacttt ccttttatcg gcgggaatta tcgttgagtt cttctatgcc atttttcata
     4141 gtagtaactg taatcttcat ctctaccacc agattcaatc cagtcatcat actcagggct
     4201 atttttgaaa tctgaatcag acatgctaac tccttgttat tagttggctt ctatggaagc
     4261 tagcgcaccg tgaagttatg atcaacgatg tagtccacat cattgtcgaa atgtgcgttc
     4321 agctagtctt cggtgttttc tgctttattt ctagcggcga ttctcgcgtc tgcccatgcg
     4381 gcagactttt tagcctgttc tcgttgttct tcggttgaag actcgctgtt gagaactttg
     4441 ttgctcgttt gtttgaccac cgaatccaaa cctgttgttg ctgcaaaatg agctaggtta
     4501 acaactccct tacctaacaa cttggcacta gcgattgcgg tttctttagc cccaaaagca
     4561 tcagacacct cctcaagcgc tttagatagg ttaaaaaatc ccatactccc cctaagaata
     4621 tcatcaataa aattgagtgt tgctctgtgg ataacttgca gagtttatta agtatcattg
     4681 cagcaaagat gaaatcaatg atttatcaaa aatgattgaa aggtggttgt aaataatgtt
     4741 acaatgtgtg agaagcagtc taaattcttc gtgaaatagt gatttttgaa gctaataaaa
     4801 aacacacgtg gaatttaggt aatagttaaa gcttgtgcct gattgttgcc acaattggtc
     4861 agcagtttgc tagggaatga gagggcagag aatgataagc ttagcactta atttgtatgg
     4921 atatattgca ttaagcaagg ggacgttatg cgtgtattag ccttatcggc tgtgtttttg
     4981 gtggcatcga ttatcggaat gccagcggta gcaaaggaat ggcaagaaaa caaaagttgg
     5041 aatgctcact ttactgaaca taaatcacag ggcgtagttg tgctctggaa tgagaataag
     5101 cagcaaggat ttaccaataa tcttaaacgg gcgaaccaag catttttacc cgcatctacc
     5161 tttaaaattc ccaatagctt gatcgccctc gatttgggcg tggttaagga tgaacaccaa
     5221 gtctttaagt gggatggaca gacgcgtgat atcgccgctt ggaatcgtga ccatgactta
     5281 attaccgcga tgaagtactc agttgtgcct gtttatcaag aatttgcccg ccaaattggt
     5341 gaggcacgta tgagtaaaat gctgcacgcc ttcgattatg gcaatgagga tatctcgggc
     5401 aatgtagaca gtttttggct cgatggtggt attcgcattt cggctaccca gcaaatcgct
     5461 tttttacgca agctgtatca caacaagctg cacgtttctg agcgtagtca gcgcatcgtg
     5521 aaacaagcca tgctgaccga agccaatggc gactatatta ttcgggctaa aacgggatac
     5581 tcgactagta tcgaacctaa gattggctgg tgggttggtt gggttgaact tgatgataat
     5641 gtgtggtttt ttgcgatgaa tatggatatg cccacatcgg atggtttagg gctgcgccaa
     5701 gccatcacaa aagaagtgct caaacaggag aaaattattc cctagaagtg gttagcgcgt
     5761 atttgtgtga aatagccgtc atataagctg taaagatata tggacaaaat gctgatgctc
     5821 gatgcgcttg tagttaatgg ctcatactta atcggtcagg cctaatcgac ttaagctccg
     5881 cgcgttaact ttcagcctga gcattagcat cacattccta aacgtaaaaa gcctagccaa
     5941 tttgctaggc ttttttgtta tctcaatggc catggtcact caacatgggg gtgtgaataa
     6001 aggagtggcg atgtcagtaa aggtgaatgc cgctgcgata aagtgcctag cccatcaagg
     6061 attgtaggct ttcttggctg ctaaagcgtt tgacgaaaaa gtccaagaag gcgctgatat
     6121 tggttctcca tcattttcat c
//
