LOCUS       NZ_CP083781             3643 bp    DNA     circular CON 18-JUN-2023
DEFINITION  Klebsiella pneumoniae strain INF118 isolate INF118 plasmid
            pINF118_6, complete sequence.
ACCESSION   NZ_CP083781
VERSION     NZ_CP083781.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMEA3357001
            Assembly: GCF_020149875.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3643)
  AUTHORS   Hawkey,J., Cottingham,H., Tokolyi,A., Wick,R., Judd,L.M.,
            Cerdeira,L., de Oliveira Garcia,D., Wyres,K.L. and Holt,K.E.
  TITLE     Linear plasmids in Klebsiella and other Enterobacteriaceae
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3643)
  AUTHORS   Hawkey,J., Wyres,K.L., Judd,L.M., Jenney,A. and Holt,K.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-SEP-2021) Department of Infectious Diseases, Monash
            University, Level 2, The Burnet Institute, Melbourne, VIC 3004,
            Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 147x
            Sequencing Technology :: Illumina; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/18/2023 15:42:16
            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)                     :: 5,870
            CDSs (total)                      :: 5,748
            Genes (coding)                    :: 5,595
            CDSs (with protein)               :: 5,595
            Genes (RNA)                       :: 122
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 153
            CDSs (without protein)            :: 153
            Pseudo Genes (ambiguous residues) :: 0 of 153
            Pseudo Genes (frameshifted)       :: 67 of 153
            Pseudo Genes (incomplete)         :: 95 of 153
            Pseudo Genes (internal stop)      :: 23 of 153
            Pseudo Genes (multiple problems)  :: 26 of 153
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP083781.1.
            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..3643
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="INF118"
                     /isolate="INF118"
                     /isolation_source="wound swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pINF118_6"
                     /geo_loc_name="Australia"
                     /collection_date="2013-07"
     gene            join(3363..3643,1..61)
                     /locus_tag="LB478_RS29305"
                     /old_locus_tag="LB478_29305"
     CDS             join(3363..3643,1..61)
                     /locus_tag="LB478_RS29305"
                     /old_locus_tag="LB478_29305"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antitoxin"
                     /protein_id="WP_049087621.1"
                     /translation="MFTLQKPMHPGEFIREVYLEPLEIQISTFAEKIGVDTSTISRLVN
                     QKADLSYEMAIRLSKAFGRSAESWMKMQIAYGLYRAQDKVNLDEVETIYTPRNLDAAEM
                     QDHEPYINL"
                     /name="HigA family addiction module antitoxin"
     gene            342..551
                     /locus_tag="LB478_RS29310"
                     /old_locus_tag="LB478_29310"
     CDS             342..551
                     /locus_tag="LB478_RS29310"
                     /old_locus_tag="LB478_29310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005227293.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YdgH/BhsA/McbA-like domain containing protein"
                     /protein_id="WP_009310047.1"
                     /translation="MKSIKTFVAVAALSMMSFGAFAQSVSATASTLDRAEAKIAAQAAE
                     QGASYKITSAQFNNRVHMTAELTK"
                     /name="YdgH/BhsA/McbA-like domain containing protein"
     gene            complement(1394..1795)
                     /locus_tag="LB478_RS29315"
                     /old_locus_tag="LB478_29315"
     CDS             complement(1394..1795)
                     /locus_tag="LB478_RS29315"
                     /old_locus_tag="LB478_29315"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_009310048.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1795..1986)
                     /locus_tag="LB478_RS29320"
                     /old_locus_tag="LB478_29320"
     CDS             complement(1795..1986)
                     /locus_tag="LB478_RS29320"
                     /old_locus_tag="LB478_29320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_004187666.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2399..2512
                     /locus_tag="LB478_RS29325"
                     /old_locus_tag="LB478_29325"
     CDS             2399..2512
                     /locus_tag="LB478_RS29325"
                     /old_locus_tag="LB478_29325"
                     /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="replication initiation protein"
                     /protein_id="WP_077259703.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPKKHDKAPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(2821..3096)
                     /locus_tag="LB478_RS29330"
                     /old_locus_tag="LB478_29330"
     CDS             complement(2821..3096)
                     /locus_tag="LB478_RS29330"
                     /old_locus_tag="LB478_29330"
                     /inference="COORDINATES: protein motif:HMM:NF016875.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_049087620.1"
                     /translation="MIKSFKSKKLKQFSKGDTSKVAQAHKKKIEIILNALDTATSILDL
                     DLPGLDLHSYAEFTPVRWSLKVSANYRIFFEWDGANVNNVDYDDPH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     Typing          2107..2512
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.195"
                     /coverage="99.0"
                     /evalue="4.64e-162"
ORIGIN
        1 cactccgcgg aacctagatg ccgctgaaat gcaagatcat gaaccttata taaatctgta
       61 agcaacgcat ggttttgcat agacagaaaa gccctataga gggcttttct gtcttcgtta
      121 taccctctct atttatcatg cccacacttt caattctctc cattcagtcc acctggaacc
      181 aaagaatcat acttagcttt tatatgctca ctttttattc tatttttttg aatgacattc
      241 gcaaattgtt tcgattttaa tcagttcatg gtcgtcctat catttatcac atcagggcaa
      301 caacgcccca tacagaacaa aatgacttaa ggaatacgac catgaaatcc atcaaaactt
      361 tcgttgcagt tgccgctcta tccatgatgt ctttcggtgc ctttgctcag agcgtcagcg
      421 ctaccgcctc caccctggat cgtgctgaag caaaaattgc cgcacaggcc gctgaacaag
      481 gtgcgtcata caaaatcacc agcgctcagt tcaataaccg tgtccacatg acggctgaac
      541 tgaccaaata agatggtcgc agagggagct gccgaacagg tcgccgggag gcggcccgtt
      601 tcgtccctta gcaggaaaac cttcaggccc cttcgggggc ttttttgcac ctgtcattta
      661 acataaaggc atgattgtac gcaccgctaa aacggcctca gggcgtttct gacgggaaac
      721 cggtaaaaca ggcaacaaac cacccgaaaa cccgccagaa acgcgcaggc tctgttttta
      781 cggcatgcat gagtatgcac gcaagtgcat agcgcgaaaa ttcacgccat tcagccaggg
      841 taagtcctgt ttccggcgtt cttcctatcc gaaaacggtg aacggggacg caatttattg
      901 cgtggccgtg aagcgttgcc ggcgcagccg gaaaaccggt tttcagcacg atcaggaatc
      961 gggttcgtcg acggccggca atcacgttat ggcaagtcgc cggacgactc accagacaat
     1021 tcaccggcga ttcgactcgt gacttgactc tagagtcgtc aaggtcaaaa aaacaccaaa
     1081 atgacgattc gactctagag tcaagtcgtc ataagttact gatagtctta agtgagtcgt
     1141 cgatgactct atgacgagtc gtcggcaagt cgtacacgaa tcgccgacga cttggattca
     1201 ccttacagaa agtaatactg cgtaatttaa taacccacaa ctaactgata ttaatgagtt
     1261 atcttcaaaa ttttaatttt gcgtggggtg tgggtatttt tagtggtgag gagcgttcag
     1321 agatctgccg atttttggga aggttcagga actccccggg atggccggag aggaaaactg
     1381 aagcatgacg gggtcaggat tttttccaga atttccacca tggcgccggg gattcagtta
     1441 attttgcctg gtgattttca agaaggagca tggcctgttt caggctgtca atgtgcgaat
     1501 ccttggacaa aagtaaggtg ttcaggtgtt caatctcctg tttcagatga cgaatcacct
     1561 gttcactctg gtcagcagag gctgtatcac gctgttcaga gacctgtcca gaatggtgtt
     1621 cacccttcgg ttgttcaaag ggaccaaaga cacgtaaaag ctctgaagta tctaccattt
     1681 ttgcattgcg ttcaccgcta caggtggaca ggtcacctgc tttaattaac ctgtgcagtg
     1741 ttgttctact cttacccgtc agtcgggcag cctcactaat agacactctg gccatcagtt
     1801 accatcctgt aatgcatcca gtctcgagga cagtgtacgg aaaagatgct ccgcatcatc
     1861 gtggagtttc tcacaaaggt cggcttcgac atcgagatca agctcgttaa gcttctccaa
     1921 caggagcaga gactggttct ggatgaattt agccatattc agcgctgttt tctgttgttt
     1981 cgtcataaga agcctcagag cgtcagtgcc cagtgtaggg atgttctctt ttccgcttcc
     2041 tcgctcactc agtcgctacg ctcctgccgt tcggctgcgg cgagcggcag gaacatgcgt
     2101 ataaagctcg agaaaaccga gcgatcgcgt aaggggaaaa ggaaaggccg catggcggcc
     2161 gtttttccat aggctccgcc cccctgacaa gcatcacaaa atctgacgct caaatcagtg
     2221 gtggcgaaac ccgacaggac tataaagatc ccaggcgttt ccccctggta gctccctcgt
     2281 gcgctctcct gttcctgcct ttcggtttat cggtgtcatt ccgcagttat ggccgcggtt
     2341 tctcatacca cgccagacac tcgattccgg gtaggcagtt cgctccaagc tggactgtat
     2401 gcacgaaccc cccgttcagt ccgactgctg cgccttatcc ggtaactatc gtcttgagtc
     2461 caacccgaaa aagcacgaca aagcgccact ggcagcagcc actggtaact gatttagagg
     2521 agttagtctt gaagttatgc gtcagttaag gctaaactga aagaacaagt tttggtgact
     2581 aagctcctcc aagccagtta ccttggttca gaaacttgcc ggttactgaa ccttcgaaaa
     2641 aaccaccttg ccgggtggtt ttttcgtttg tggtttaaag atactctgca ccaacatcaa
     2701 tctcaagaaa ttatcctcac caagccattg acttaataaa aaaaacgcat ataatagacc
     2761 tcacggtctt ggttcggata accgaaccaa gaccgtgacc taagtcgttg attttattga
     2821 ttaatgtggg tcatcgtaat ccacattatt aacatttgcc ccatcccact caaagaaaat
     2881 acgatagttt gctgacacct tcagtgacca gcgaactgga gtgaactcag catacgagtg
     2941 aagatctaaa ccaggaaggt cgagatcaag aatggaagta gctgtatcta acgcgtttaa
     3001 gataatctct attttctttt tatgcgcttg tgctacctta cttgtatcgc ctttactgaa
     3061 ctgctttagc ttcttggatt taaaactttt aatcattgaa cttctccata tagttttttt
     3121 tagaagttct tcatgcaagg taaatgttct tgactcagtc ttatttatag gtagtattct
     3181 acgcctgcga agctttagaa ctatcaaata gacacatcaa gaacacaact gaagaaccgt
     3241 gtgtgttgcc gctaagaaaa aaaacacttc ccttaactaa atcattttac cacaaatgat
     3301 tttaaaagta aatagatttg cgctttgcgc aaggcgcaaa cagcaaaaaa ccaggaggtt
     3361 gcatgtttac attgcaaaaa cctatgcacc ccggcgagtt catccgcgaa gtatatttag
     3421 aacctttaga gattcagata agcacttttg cagagaagat cggggttgat acatcaacaa
     3481 tcagtcggtt ggttaaccaa aaagcagacc tgtcctacga gatggctatt cgcctatcaa
     3541 aagctttcgg tcgttccgcc gagtcatgga tgaaaatgca gatagcgtac ggcttatacc
     3601 gcgctcagga taaagtaaac cttgacgaag ttgaaaccat tta
//
