LOCUS       NZ_CP083779             5521 bp    DNA     circular CON 18-JUN-2023
DEFINITION  Klebsiella pneumoniae strain INF118 isolate INF118 plasmid
            pINF118_4, complete sequence.
ACCESSION   NZ_CP083779
VERSION     NZ_CP083779.1
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 5521)
  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  JOURNAL   Unpublished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 5521)
  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
            CP083779.1.
            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..5521
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="INF118"
                     /isolate="INF118"
                     /isolation_source="wound swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pINF118_4"
                     /geo_loc_name="Australia"
                     /collection_date="2013-07"
     gene            complement(102..512)
                     /locus_tag="LB478_RS29250"
                     /old_locus_tag="LB478_29250"
     CDS             complement(102..512)
                     /locus_tag="LB478_RS29250"
                     /old_locus_tag="LB478_29250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /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_064353417.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKGIKVID
                     TSELIRVFGSLDGVIDDVKSDAESTGINSVGFHDLQHRIALLEAENDGLKGAVKARDEH
                     IDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(512..703)
                     /locus_tag="LB478_RS29255"
                     /old_locus_tag="LB478_29255"
     CDS             complement(512..703)
                     /locus_tag="LB478_RS29255"
                     /old_locus_tag="LB478_29255"
                     /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_032421723.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2000..>2559
                     /locus_tag="LB478_RS29260"
                     /old_locus_tag="LB478_29260"
                     /pseudo=""
     CDS             2000..>2559
                     /locus_tag="LB478_RS29260"
                     /old_locus_tag="LB478_29260"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558267.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="frameshifted; 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="IS1 family transposase"
                     /name="IS1 family transposase"
     gene            <2795..2959
                     /locus_tag="LB478_RS29265"
                     /old_locus_tag="LB478_29265"
                     /pseudo=""
     CDS             <2795..2959
                     /locus_tag="LB478_RS29265"
                     /old_locus_tag="LB478_29265"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076612230.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0004803 - transposase activity [Evidence IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /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="IS1 family transposase"
                     /name="IS1 family transposase"
     gene            complement(3100..3273)
                     /locus_tag="LB478_RS29270"
                     /old_locus_tag="LB478_29270"
     CDS             complement(3100..3273)
                     /locus_tag="LB478_RS29270"
                     /old_locus_tag="LB478_29270"
                     /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_158237476.1"
                     /translation="MSEDIGKVVDIFNEFTKVELPGGGGLETDSPVVEAAVAVGVLGAA
                     AYGLYKLFSSDD"
                     /name="hypothetical protein"
     gene            3883..4818
                     /locus_tag="LB478_RS29275"
                     /old_locus_tag="LB478_29275"
     CDS             3883..4818
                     /locus_tag="LB478_RS29275"
                     /old_locus_tag="LB478_29275"
                     /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_063259283.1"
                     /translation="MTAQDLINVLTILKANDSTSFSKIQRALKMSISQLEGIIDGLTAM
                     GIVYKSSFTSYSLTELTSKPVVSDGVRKAFEDIITNRGTYLSEELLQKVSTPFIPLMTH
                     EYKNAPVKVMIVGQETLGMEDAFSTIVSVDDYINESIESFNKFNFGEDLRNSHFWYAFD
                     EVVKYFNLPSRRHAYWTNLHKFQLIENDGDSVSISKLPSKDIMTMIHMQRELFLAEIKD
                     TKPDIIIYFTGGQTWVLDHYLNNGKKLAVKAIDERSHLGIIQTEFLHCPIAICTDHPSR
                     RGYTQAIVDHRANLLKYAADKFHASESAWF"
                     /name="hypothetical protein"
     Typing          complement(1051..1224)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          1148..1741
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.0"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 ggtatttttc gtggtgagga gtgttcccgg atctggcgat ttttgggaag gttcaggaac
       61 gccccgggat ggccggagag gaaaactcaa gcatggcggg atcaggattt tttccagaat
      121 ttccaccacg gggaatgggg tggtgaagaa ggttcgtgct tgtgctccag aagctgcata
      181 gcctgacgaa gggaatcaat atgctcatct cgagccttaa cagccccttt aagaccatcg
      241 ttttcagctt caagtaaagc gattctatgt tgtaaatcat gaaaaccaac gctgttaata
      301 cctgtagatt ctgcgtcact ttttacatca tcgatgacac catcaagaga accaaacact
      361 ctaataagct ctgatgtatc aataacttta atacccttcc cgtgctttac aacagaggtg
      421 taacttaact taccactgtt aatcatcttg taaatagtag ggcgactaac cttaacaagc
      481 cgtgctgctt cactaataga cactctggcc atcagttacc atcctgtaat tcatccagtc
      541 tcgaggacag tgtacggaaa agatgctccg catcatcgtg gagtttctca caaaggtcgg
      601 cctcagcatc gagatcaagc tcgttaagct tctccagcag gagcagagac tgattctgga
      661 tgaatttagc catgttcagc gctgttttct gttgtttcgt cataagggac ctcagagcat
      721 caatgctcag tgtaaaaccg gtaagggggt cggatgtacg aatggttcag agaacggatc
      781 tgaggtaatc ctgtagttat tttgtagttt atctgtagtc atcgcactaa aaatcaggat
      841 taagtcatca gcttttgtag tctttctgta gtttacctgt agtccggaaa aacaatccgt
      901 tcatgcgagc atgaacgagg tcgttagtaa cctgcgccat taaatcaaaa aggtcatatt
      961 cgccgggaag ctgcgtatca gtcgaatccc gttgttcatc atattcagat ggcatggggt
     1021 gatatccagt agctgagagg ttgttagagg gtttcggggc gcagccctga accagtcacg
     1081 tagcgctagc ggagtgtaaa ctggcttatt atgttggcac gggcacggaa atcagtgaag
     1141 tgcttcatgt ggcagaagaa aaaaggcggc accggcgcgt aagcagaata tgcgatacag
     1201 gagatattcc gcttcctcgc tcactgactc gctccgctcg gtcgttcggc tgcggcgagc
     1261 agtaccagct tactggcggg acggaaattt cctggtagat gccaggaagg aacgtaacag
     1321 ggaaacaata acgccgcggc aaagccgttt ttccataggc tccgcccccc tgacgagcat
     1381 cacagaatct gacactcaaa tcagtggtgg cgaaacccga caggactata aagatcccag
     1441 gcgtttcccc ctggtagctc cctcgtgcgc tctcctgttc ctgcctttcg gtgtaccggt
     1501 gtcattccgc tgttatggcc gcgtttatct cattccacgc ctgacactca gttccgggta
     1561 ggcagttcgc tccaagctgg actgtatgca cgaacccccc gttcagtccg accgctgcgc
     1621 cttatccggt aactatcatc ttgagtccaa cccggaaagg tacgaaaaaa cgccactggc
     1681 agcagccatt ggtaactgag atgtgcgaga gatttatctg gagttcttga agtgggagcc
     1741 tgagaacggc tacactggaa ggacagtttt ggtgactcgt ctcgcacaag acagttacct
     1801 ggttaagcag ttccccaact gacctaacct tcgatcaaac cacctcccca ggtggttttt
     1861 tcgtttcttg gagaagagac tacgacgaca aatgacggat ctcaagaaga tccttttaac
     1921 gtacaaaaat ttccgttctc caaaggtgat gctgccaact tactgattta gtgtatgatg
     1981 gtgtttttta ggtgctccag tggcttctgt ttctatcagc tgtccctcct gttcagctac
     2041 tgacggggtg gtgcgtaacg gcaaaagcac tgccggacat cagcgctatc tctgctctca
     2101 ctgccgtaaa acatggcagc tacagttcac ttacaccgcc tctcagcccg gtacgcacca
     2161 gaaaatcatt gatatggcca tgaatggcgt tggatgccgg gcaaccgccc gcattatggg
     2221 cgttggcctc aacacgattt tacgtcactt aaaaaactca gaccgcagtc ggtaacctcg
     2281 cgcatacaac cgggcagtga tgtgattgtc tgcgctgaaa tggacgaaca gtggggctac
     2341 gtcggtgcta aatcacgtca gcgctggctg ttttacgcgt atgacaggat acggaggacg
     2401 gttgtggcgc acgtcttcgg tgaacgcact ctggccacac tggagcgtct tctgagcctg
     2461 ctgtcggcct ttgaggtcgt ggtatggatg acggatggct ggccgctgta tgaatcacgc
     2521 ctgaagggaa agctgcacgt taacagcaag cgttacactg gggtcagttt ggagatcgga
     2581 aatttttgta cgttaagcgc attatttaac caatcttggt tcgtaagggg ttgattttgc
     2641 gtcagtggct atcgctttta agttgtcgct cttgcagtat cgcatttagg ttatccgatt
     2701 aaggtcaaac ctctgaaaat gccgtatagc gcgggagtac accctattgc tataggtaag
     2761 tctgttcaaa aaacaggctt gccgtacaat aattctctat atccaaactg acccctacac
     2821 tcaacgcatt gagcggcata acctgaatct gaggcagcac ctggcacggc atggacggaa
     2881 gtcgctgtcg ttctcaaaat cggtggagct gtatgacaaa gtcatcgggc attatctgaa
     2941 cataaaacac tatcaataag ttggagtcat tacctgaaat ggcaacagat agctgattct
     3001 ttgggttgtt cgtatcatgc agccgttgca ctatataagc gttatgagag attagatcta
     3061 aatgaaaagg cggggaaata aatccccacc gttaaataat taatcatcac tactaaatag
     3121 cttataaagc ccatatgctg cggcacctaa aacaccaaca gcaacagcag cctctacaac
     3181 agggctatcg gtctctaaac ctcctccacc aggaagttca accttcgtaa attcattaaa
     3241 aatatcaaca actttaccaa tatcttcact cataacaccc tcctttttga agaagtattt
     3301 tacttctaat caaaaaggta aaccatatca acccttcaaa ctaccaaaat aaattttgtt
     3361 agttttcagc gtttttattt aaataatgtt cacccttgat ttttaacatg tttttttgtg
     3421 attctgtcat gttatcaaca tacaacaatg cacctattac aagatttcta tttccatctt
     3481 ataatttaag acactctgcc ccaagaacga ttaaatcatg tgttcttttt cttctatctt
     3541 cgtttatttt cttctttctt agcatgttca acctattttg ggctgatgct atttgctgat
     3601 ctaaattttt actcataatc agaaacacca agataattac caacattcat aagaacaaaa
     3661 acatacgcta aattttctaa cacactaatc tctataagat tataatcaac agaagcatta
     3721 gctttaaaat attcaattcc caaaaagaca acatccctaa ctattttaat aatataagaa
     3781 tccctggtga tgctgccaac ttactgattt actgtactgc gaccgtcaga atgagttaaa
     3841 cgcgtatcta cattgaagca gttcaatatg aggaaaacag gaatgacagc acaagattta
     3901 atcaacgttc tcactattct taaggccaac gactcaacca gttttagcaa gattcaacgc
     3961 gcgttaaaga tgagtatttc gcagttggag ggcatcattg atgggttaac tgcaatggga
     4021 atagtgtata aatcatcatt cacttcatac agccttactg agttaacctc taaacctgtt
     4081 gttagtgacg gtgtaagaaa ggcattcgaa gatatcatta ccaatcgcgg tacttacctg
     4141 tcagaagaac tactacaaaa ggtaagtaca ccattcatcc cactgatgac gcacgaatac
     4201 aaaaatgccc cagttaaagt gatgatcgtg gggcaagaaa ctctgggaat ggaagatgct
     4261 ttcagtacca tcgtttcggt cgatgactac attaatgaga gcattgaatc cttcaataaa
     4321 ttcaattttg gtgaagattt aaggaatagc cacttttggt atgcatttga tgaagtagta
     4381 aagtatttta acctaccatc cagaaggcat gcttattgga ctaatcttca taagtttcaa
     4441 ttaattgaaa atgatggaga tagtgtcagc atttccaaac taccttcaaa agatatcatg
     4501 acaatgattc atatgcagcg tgaattattc ttggctgaaa ttaaagatac caagccagat
     4561 atcatcatct acttcacggg tgggcaaacc tgggtgttag atcattatct aaacaatggt
     4621 aaaaaattag cagttaaggc aatagatgaa cgctcgcatc tggggattat ccagacagaa
     4681 tttttgcatt gcccaatcgc tatatgtacc gaccatccta gtagaagggg atatactcaa
     4741 gccatcgtag atcatagagc taatctgctt aaatatgctg ctgacaaatt tcatgcaagt
     4801 gaatcggcat ggttctagcg aacacatgtc accgacagaa tatgaaaacc agtattatca
     4861 acggctcgga agtgtctaaa ttatccgtgg cgattcaatt taccataaca tccgttgcgt
     4921 gcaccgcctc agagcctctg aggacgtttc tgacgggaaa ccggtaaaac aggcaacaaa
     4981 ccacccgaaa acccgccaga aacgcgcagg ctctgttttt acggcatgca tgagtatgcg
     5041 cacaagtgca tagcgcggaa attcacgcca ttcagccggg gtaagtcctg tttccggcgt
     5101 tcttcccatc cgaaaacggt gaacggggac gcaatttatt gcgtggccgt gaagcgttgc
     5161 cggcgcagcc ggaaaaccgg ttttcagcac gttcaggaat cgggttcgtc gacggccggc
     5221 aatcacgtta tggcaagtcg ccggacgact caccggcgat tcgactcgtg acttgactct
     5281 agagtcaccg cggtcaaaaa aacgccaaag cgacgattcg actctagagt caagtcgtca
     5341 taagttactg atagtgtgga gtgagtcgtc gatgactcta tgacgagtcg tcggcaagtc
     5401 gtacacgaat caccgacgac ttggattgac cttacagaag gtaatactgc gtaatttaat
     5461 aaaacctaac caactgataa taaggagtta tctgcaaaat tttaattttg cgtggtgtgt
     5521 g
//
