LOCUS       NZ_CP016920             6139 bp    DNA     circular CON 05-MAR-2024
DEFINITION  Klebsiella pneumoniae isolate 11 plasmid pColKP3_DHQP1300920,
            complete sequence.
ACCESSION   NZ_CP016920
VERSION     NZ_CP016920.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN04448229
            Assembly: GCF_001709275.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 6139)
  AUTHORS   Lutgring,J.D., Zhu,W., de Man,T.J.B., Avillan,J., Anderson,K.F.,
            Lonsway,D.R., Rasheed,J.K. and Limbago,B.M.
  TITLE     DHQP1300920 Klebsiella pneumoniae chromosome + 4 plasmids
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6139)
  AUTHORS   de Man,T.J.B.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-AUG-2016) Division of Healthcare Quality Promotion,
            Centers for Disease Control and Prevention. Division of Healthcare
            Quality Promotion, 1600 Clifton Road NE, Atlanta, GA 30333, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. v. 3
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 139.0x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 03/04/2024 13:22:49
            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)                     :: 5,666
            CDSs (total)                      :: 5,545
            Genes (coding)                    :: 5,367
            CDSs (with protein)               :: 5,367
            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)              :: 178
            CDSs (without protein)            :: 178
            Pseudo Genes (ambiguous residues) :: 0 of 178
            Pseudo Genes (frameshifted)       :: 75 of 178
            Pseudo Genes (incomplete)         :: 98 of 178
            Pseudo Genes (internal stop)      :: 26 of 178
            Pseudo Genes (multiple problems)  :: 18 of 178
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP016920.1.
            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..6139
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /isolate="11"
                     /isolation_source="Urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pColKP3_DHQP1300920"
                     /geo_loc_name="USA: Pennsylvania"
                     /collection_date="2013-03-14"
                     /collected_by="PA State Health Department"
     gene            join(5762..6139,1..15)
                     /locus_tag="A8C11_RS00435"
                     /old_locus_tag="A8C11_00435"
     CDS             join(5762..6139,1..15)
                     /locus_tag="A8C11_RS00435"
                     /old_locus_tag="A8C11_00435"
                     /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="antitoxin VbhA family protein"
                     /protein_id="WP_043907050.1"
                     /translation="MSTTQIEKDSRRKAVNGVISSFQLEGEAITDEFKILLEDYINGKI
                     STDEVLAMVSDEPTTTEYDYEITPRTLGLGGGWNLRLLENGEEVGGGVFPLPEHCDFRD
                     EKALQTLLDSLYEDALAEASAWLASR"
                     /name="antitoxin VbhA family protein"
     gene            join(6136..6139,1..335)
                     /locus_tag="A8C11_RS32405"
                     /old_locus_tag="A8C11_00440"
     CDS             join(6136..6139,1..335)
                     /locus_tag="A8C11_RS32405"
                     /old_locus_tag="A8C11_00440"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_043907051.1"
                     /translation="MAGQPLKRLRSIKIRVSDAELERLRELCPKAQLAEWMREQCLGVA
                     QPQRRTPAPTVDPALLRQLAGMGNNLNQIARRVNSGEWGPLDRLRIIAELSAIGRELEE
                     LHHDHQIP"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            316..1770
                     /locus_tag="A8C11_RS32855"
     CDS             316..1770
                     /locus_tag="A8C11_RS32855"
                     /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(2052..2333)
                     /locus_tag="A8C11_RS00460"
                     /old_locus_tag="A8C11_00460"
     CDS             complement(2052..2333)
                     /locus_tag="A8C11_RS00460"
                     /old_locus_tag="A8C11_00460"
                     /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            2677..3474
                     /locus_tag="A8C11_RS00465"
                     /old_locus_tag="A8C11_00465"
     CDS             2677..3474
                     /locus_tag="A8C11_RS00465"
                     /old_locus_tag="A8C11_00465"
                     /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(3881..>4033)
                     /locus_tag="A8C11_RS30705"
                     /pseudo=""
     CDS             complement(3881..>4033)
                     /locus_tag="A8C11_RS30705"
                     /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            4409..5356
                     /locus_tag="A8C11_RS00470"
                     /old_locus_tag="A8C11_00470"
     CDS             4409..5356
                     /locus_tag="A8C11_RS00470"
                     /old_locus_tag="A8C11_00470"
                     /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"
     ARG             2678..3471
                     /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          4422..5343
                     /name="rep_cluster_1195"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.974"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          317..1767
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.554"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctggccagcc gttaaagcgc ctccgctcta tcaagatccg ggtctcagat gcggagcttg
       61 agcgcctgcg ggagctctgc cccaaggccc aactggcgga gtggatgcgg gagcaatgtc
      121 tcggtgttgc gcaaccccag cgccgaacgc cggcgcctac cgtagatccg gcgctcttgc
      181 ggcagttggc cggaatgggc aacaacctga accagatcgc ccggcgcgtt aattccgggg
      241 agtgggggcc gttggatcgg ctgcgcatca tagcggagct gtccgctata ggccgcgagc
      301 tggaggaact gcaccatgat catcaaattc cataaccgtg gggtaggccg gggctccggg
      361 cctgttggct acttgttggg ccgtgacggg aaccgggaag gcgcaacgct cgaccggggc
      421 aaccctgcgg tgattgaagc cctgattgat tccagtccct acgccaaaaa atacacctct
      481 ggcgttctgt cgtttgccga ggctgattta cccagggcga ccaaggacaa gctgatgagc
      541 gactttgaaa aggcgctcct gcccggactg gagggcaacc agtacgctgt tttgtgggta
      601 gagcaccgcg acaaggggcg gctggagctg aattttgtag tcccgaacat cgaattgcag
      661 agcgggaagc ggctgcaacc ctacttccac aaggccgaca atccgcgcct cgatgcgtgg
      721 cgaaccgtgg taaacgggga gctgaaattg cacgacccgg acgatccgtt aaaccgtcag
      781 gccgttatca cgccaaagga tttgccgagg gggcacaagg aggccgctca ggccattaca
      841 gacgggcttt tacgcatggc cggagcaggg gagatccaga gccgcgatga tgtgcgcaaa
      901 gccttgcagg gtgcgggttt cagcgtggta cgcgaaacca aaaacagcct gagcattgcc
      961 gacccggacg gggggcggaa catccgatta aagggggtgc tgtatgagca agattttaga
     1021 catggcgaag gacttcgagc agagctcgaa gcagcaggcc aacgctatcg agaagcgtct
     1081 gaccgaagaa ttcacgaggc acgagaaagc tatctccggg gcgttgaaat caagcgagga
     1141 gaaaatgagc gccgctattg ccgagcacag ccagaaaatg ggctggctgt tgctcaaaac
     1201 gtggatctgg atgctggtca gcatcgtcct gttcttgagc gcaacgagcg ggatcctctg
     1261 gtatcagggg gaattgatag cggagcggca agccactctc caagccttgg cagagaaggg
     1321 cggcaagcta aagctgaccc agtgcgggaa gaaattggag cacctttgcg tgcagatctc
     1381 cgaccccaat ccaaccgttt gggggaagga tacctattgg atcgtgccga aggggtacta
     1441 aatgacggga ttggagcggg aattgctctg cgcgttcgag gctttgcaga gcgcatacga
     1501 gcagcagcac aaggcatggc aggaaagcta cgcgaacttg gcgagcatgt acgagagcac
     1561 caaacaagag gccgagatca gcagggcagc agcagagcga ttgacgaggc aggtgaacgg
     1621 cttaacgcag caagtggacg gcttgagcaa gcagctggag ggcttgaccg ggctagtcag
     1681 caagttgcaa aagaaaggga acacaggctc ctgaaggcac tggatcgagg ctgggagcgt
     1741 ggagacagat cgcgaggctt tgagcgttga cggaacaaaa cggccgtcag ttataaaaaa
     1801 aggaaagtgc tatcactttc cttttatcgg cgggaattat cgttgagttc ttctatgcca
     1861 tttttcatag tagtaactgt aatcttcatc tctaccacca gattcaatcc agtcatcata
     1921 ctcagggcta tttttgaaat ctgaatcaga catgctaact ccttgttatt agttggcttc
     1981 tatggaagct agcgcaccgt gaagttatga tcaacgatgt agtccacatc attgtcgaaa
     2041 tgtgcgttca gctagtcttc ggtgttttct gctttatttc tagcggcgat tctcgcgtct
     2101 gcccatgcgg cagacttttt agcctgttct cgttgttctt cggttgaaga ctcgctgttg
     2161 agaactttgt tgctcgtttg tttgaccacc gaatccaaac ctgttgttgc tgcaaaatga
     2221 gctaggttaa caactccctt acctaacaac ttggcactag cgattgcggt ttctttagcc
     2281 ccaaaagcat cagacacctc ctcaagcgct ttagataggt taaaaaatcc catactcccc
     2341 ctaagaatat catcaataaa attgagtgtt gctctgtgga taacttgcag agtttattaa
     2401 gtatcattgc agcaaagatg aaatcaatga tttatcaaaa atgattgaaa ggtggttgta
     2461 aataatgtta caatgtgtga gaagcagtct aaattcttcg tgaaatagtg atttttgaag
     2521 ctaataaaaa acacacgtgg aatttaggta atagttaaag cttgtgcctg attgttgcca
     2581 caattggtca gcagtttgct agggaatgag agggcagaga atgataagct tagcacttaa
     2641 tttgtatgga tatattgcat taagcaaggg gacgttatgc gtgtattagc cttatcggct
     2701 gtgtttttgg tggcatcgat tatcggaatg ccagcggtag caaaggaatg gcaagaaaac
     2761 aaaagttgga atgctcactt tactgaacat aaatcacagg gcgtagttgt gctctggaat
     2821 gagaataagc agcaaggatt taccaataat cttaaacggg cgaaccaagc atttttaccc
     2881 gcatctacct ttaaaattcc caatagcttg atcgccctcg atttgggcgt ggttaaggat
     2941 gaacaccaag tctttaagtg ggatggacag acgcgtgata tcgccgcttg gaatcgtgac
     3001 catgacttaa ttaccgcgat gaagtactca gttgtgcctg tttatcaaga atttgcccgc
     3061 caaattggtg aggcacgtat gagtaaaatg ctgcacgcct tcgattatgg caatgaggat
     3121 atctcgggca atgtagacag tttttggctc gatggtggta ttcgcatttc ggctacccag
     3181 caaatcgctt ttttacgcaa gctgtatcac aacaagctgc acgtttctga gcgtagtcag
     3241 cgcatcgtga aacaagccat gctgaccgaa gccaatggcg actatattat tcgggctaaa
     3301 acgggatact cgactagtat cgaacctaag attggctggt gggttggttg ggttgaactt
     3361 gatgataatg tgtggttttt tgcgatgaat atggatatgc ccacatcgga tggtttaggg
     3421 ctgcgccaag ccatcacaaa agaagtgctc aaacaggaga aaattattcc ctagaagtgg
     3481 ttagcgcgta tttgtgtgaa atagccgtca tataagctgt aaagatatat ggacaaaatg
     3541 ctgatgctcg atgcgcttgt agttaatggc tcatacttaa tcggtcaggc ctaatcgact
     3601 taagctccgc gcgttaactt tcagcctgag cattagcatc acattcctaa acgtaaaaag
     3661 cctagccaat ttgctaggct tttttgttat ctcaatggcc atggtcactc aacatggggg
     3721 tgtgaataaa ggagtggcga tgtcagtaaa ggtgaatgcc gctgcgataa agtgcctagc
     3781 ccatcaagga ttgtaggctt tcttggctgc taaagcgttt gacgaaaaag tccaagaagg
     3841 cgctgatatt ggttctccat cattttcatc taccggttta ctataggtca accaggccgt
     3901 ccttgccggc gcttgggacg cagacgatgg catcaaatgc ctcgctcaaa ttcgtttcta
     3961 cagaggcgct ttgggaccgc attcgctttg ctttcatggg ggcatctgtc aatgtcagac
     4021 atgaatcctc cgatataggt tgatttttga tctcttcaac acttggtgtt gtccgactag
     4081 agagacttat atggatcagt attcttgcac tgacaatggt gccactcaat cccaaggatc
     4141 gacctagtta gaggcgtaga tcaagcaatt caaaacagcg cagaagcaga aggaggtgga
     4201 aatatgttcc agggtgaaag gttacatgca actaacgttg ctctctagga tgtgcctgct
     4261 gtaacgtatt gtccagaaaa gacaaccccc cgttatcgct tgcatcttgg cggagctgcg
     4321 aaaaacgggg gccgtgacga atcacaagag aagtctatca catggatcat gccaaacaac
     4381 cccacgccgc caataagcgc ggtggtgctt gagaaagtgc gcacagcttg agctgtttcg
     4441 ggagcgcctg ccccggaaac cctactattc cgacgagctt acaacgggcc tacggattgc
     4501 ggatgttgcc cgcgcccttg gtgcgcgtta catccagccg aacgggccaa cgcaccgcca
     4561 ctggatcgtt tttgacgtag accatgcagc cgctacgtta tcttgggatg acgtaggcgc
     4621 tccagcccct aacattaccg tcacgaacaa ggccaacggc cacgcgcatc tgatctacgg
     4681 actggatacg ccgatccgca ctgccccgga tggaaatgca gcccctctgc ggtatgccgc
     4741 cgccatcgag gccgcgctcc gggagaaatt aggggcggat atgggctact ccgggctgat
     4801 ctgcaagaac cccctgcatg agcactggct ggtgcaggta tgggaacccc ggctctacga
     4861 tttagcctgg ctatccgatt acctcgatct gagctcctac aatggccgca aatcgcttcc
     4921 tgagtacggg cttgggcgaa actgtaccct gttcgagaaa acgcgcctgt gggcctataa
     4981 agcgatccgg cagggctggc cggattaccc cgaatggttg gccgcttgtg ttgaccgggc
     5041 atcaggatat aacgcccagt tcgagcagcc gctccccgca aacgaagtcc ggcacacggc
     5101 caagtccatt gccaaatgga cgcaccagca cctaagcccc gcagggttca gagaggagca
     5161 ggcccggaga ggtgcgaagg gcggcaaggt atccaaggga gggggaaggc cgagcaatag
     5221 cggtaaggac aagtccgatc tattgccgga ggttctgcgg cttaaggctc aggggtacac
     5281 caaccgcgat atagcggacg atcttcaaat ctcccccagt acggtgagcg tttacctaaa
     5341 gcgtgatcgt ccgtgatcga aacaagcctt atcagataat agcccccttt aggggggttc
     5401 ctgcgctctt gtcttttagc cttaaaaaat ccttttagcg cggatctttg gcgaggtgga
     5461 caactgcgcc tgtccgtcca tcgcccccct gttttttcgg ggggtgtggg cggcagcagt
     5521 tatccacgga gccgctcttt cccttgatct tgctctaggg cttgcagtat cccgcccatg
     5581 gttgaataat gtactaagca aggctacaca gaggcccctc tacctgcttc gcggtctcgg
     5641 gcctctgtgg ccttgttcag gggtgctacg ccccccgaaa ccccctgtgg ccccgctcga
     5701 tccgcccctt cgggacggtc tgcgcggtgg cttcttggct ctggagaatg gacgaggccc
     5761 tatgtcaaca acacagatag agaaagattc gagaaggaag gcagtcaatg gcgttatttc
     5821 tagtttccaa ctagaggggg aggccataac cgatgaattc aaaattctac ttgaagatta
     5881 tatcaatgga aaaatttcca ccgatgaggt gttagctatg gtaagtgacg aacccacaac
     5941 aacggaatac gactacgaaa tcaccccccg cactctcggt cttggcgggg gctggaatct
     6001 gcgtttgctg gagaacggcg aagaggtcgg cgggggtgtt ttccccttgc cggagcactg
     6061 cgattttcgg gatgaaaagg cgctccagac gctactcgat agcctctatg aggacgcctt
     6121 agcggaggcc tctgcatgg
//
