LOCUS       NZ_CP031820             6211 bp    DNA     circular CON 18-JUN-2023
DEFINITION  Klebsiella pneumoniae strain INF235 isolate INF235 plasmid unnamed3,
            complete sequence.
ACCESSION   NZ_CP031820
VERSION     NZ_CP031820.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMEA3357198
            Assembly: GCF_003590665.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 6211)
  AUTHORS   Wyres,K.L., Wick,R., Judd,L.M., Froumine,R., Tokolyi,A., Gorrie,C.,
            Lam,M.C., Duchene,S., Jenney,A. and Holt,K.E.
  TITLE     Distinct evolutionary dynamics of horizontal gene transfer in drug
            resistant and virulent clones of Klebsiella pneumoniae
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6211)
  AUTHORS   Wyres,K.L., Wick,R., Judd,L.M., Froumine,R., Tokolyi,A., Gorrie,C.,
            Lam,M.C., Duchene,S., Jenney,A. and Holt,K.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-AUG-2018) Department of Biochemistry and Molecular
            Biology; Bio21 Molecular Science and Biotechnology Institute,
            University of Melbourne, University of Melbourne, Parkville, VIC
            3010, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.2.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 119x
            Sequencing Technology :: Nanopore minION; Illumina HiSeq 2000
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/18/2023 11:32:07
            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)                     :: 5,453
            CDSs (total)                      :: 5,329
            Genes (coding)                    :: 5,136
            CDSs (with protein)               :: 5,136
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 193
            CDSs (without protein)            :: 193
            Pseudo Genes (ambiguous residues) :: 0 of 193
            Pseudo Genes (frameshifted)       :: 77 of 193
            Pseudo Genes (incomplete)         :: 119 of 193
            Pseudo Genes (internal stop)      :: 48 of 193
            Pseudo Genes (multiple problems)  :: 41 of 193
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP031820.1.
            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..6211
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="INF235"
                     /isolate="INF235"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="unnamed3"
                     /geo_loc_name="Australia"
                     /collection_date="2013-11"
     gene            complement(71..232)
                     /locus_tag="D0898_RS29055"
     CDS             complement(71..232)
                     /locus_tag="D0898_RS29055"
                     /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_162870772.1"
                     /translation="MAKHWSGQECPKTGTYGQYHDTDNSYAGSEYDRHVSKGDKFPPSK
                     NNHHFQEK"
                     /name="hypothetical protein"
     gene            469..714
                     /locus_tag="D0898_RS27950"
                     /old_locus_tag="D0898_28015"
     CDS             469..714
                     /locus_tag="D0898_RS27950"
                     /old_locus_tag="D0898_28015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012848468.1"
                     /GO_component="GO:0110001 - toxin-antitoxin complex
                     [Evidence IEA]"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0097351 - toxin sequestering activity [Evidence IEA]"
                     /GO_process="GO:0045927 - positive regulation of growth
                     [Evidence IEA]; GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system Phd/YefM family
                     antitoxin"
                     /protein_id="WP_025987695.1"
                     /translation="MHAINFTDARKHFAETMKRVTDDAEPVRVMRRDAPDIVMIDAGEY
                     EALIETVYLFSNPANAEHINESMKQAERGEFVEVEY"
                     /name="type II toxin-antitoxin system Phd/YefM family
                     antitoxin"
     gene            695..970
                     /locus_tag="D0898_RS27955"
                     /old_locus_tag="D0898_28020"
     CDS             695..970
                     /locus_tag="D0898_RS27955"
                     /old_locus_tag="D0898_28020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017412855.1"
                     /GO_process="GO:0008219 - cell death [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Txe/YoeB family addiction module toxin"
                     /protein_id="WP_019725129.1"
                     /translation="MSKWNIKFTRNGADDLNYWRDTDKKKFERIRQLLLSIEADPLTGI
                     GKPERLRHHKDPALYSRRIDQSHRLVYSIQNGEIIIYAARYHYGDK"
                     /name="Txe/YoeB family addiction module toxin"
     gene            1218..2123
                     /locus_tag="D0898_RS27960"
                     /old_locus_tag="D0898_28025"
     CDS             1218..2123
                     /locus_tag="D0898_RS27960"
                     /old_locus_tag="D0898_28025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001697689.1"
                     /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_019725130.1"
                     /translation="MHNAALELFNERLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRAGSSIDWSDRNAPAPTLTITNPENGHAHLLYALENSIRTAPDGKIK
                     PLRYAASVENALRKKLEADAGYSGLICKNPNHNHWKIAVWQPKLYTLDWLADFLDLNTG
                     NDKEIVADYGLGRNCTLFDKTRKWAYRAIRQGWPEYEQWLQACYERACAYNLQFARPLD
                     ENEVRGIAKSIAKWTSNKFSPEEFSKFVDITHSSEIQSKRGKKSGQSRRKGSLEEIKPW
                     VAMGISRRKYFYIKKNGEIR"
                     /name="replication initiation protein"
     gene            2120..2827
                     /locus_tag="D0898_RS27965"
                     /old_locus_tag="D0898_28030"
     CDS             2120..2827
                     /locus_tag="D0898_RS27965"
                     /old_locus_tag="D0898_28030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001258875.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004198042.1"
                     /translation="MKTFVTLWTIVFLAFIAVMCTVDISNYIPSVYTVFSKNRPLVTGA
                     LSILLISVFIWLMVSLYLLKKYSVKVEKLSLGGVNILFNESATLYKKSVKNHLDSKRAI
                     FKLRKNVDAFDEVISSYYQTYQFIRDEMKILNPKKDREIYDFSNEMLMVLNRFLTNYQN
                     NYKRWYKYISDKDEVVDRVSGDVMRFHATSINKIQMQYYDYERILKGFKDVNRFFVNDV
                     KPKFGINTDKWNW"
                     /name="hypothetical protein"
     gene            complement(2864..3478)
                     /locus_tag="D0898_RS27970"
                     /old_locus_tag="D0898_28035"
     CDS             complement(2864..3478)
                     /locus_tag="D0898_RS27970"
                     /old_locus_tag="D0898_28035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012822468.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="TIR domain-containing protein"
                     /protein_id="WP_019725132.1"
                     /translation="MGKHKVFISYHHANDQYYKNALEKMNEEHEIFVNRSVSLGDIDED
                     EAPQKIREIIRDEYLRDTSVLILLVGTETKNRKHVDWELYSSMRDSTINKKSGILVVNL
                     PSTNTTYIRSTHGTNEKSEVHPTVTEWFSIDKRSTYEERFPYMPARIIDNFMKSGSYIS
                     VVNWNQIENNPETLRKLIDMTYNDREKATYDMSREMRMHNS"
                     /name="TIR domain-containing protein"
     gene            3880..4281
                     /locus_tag="D0898_RS27975"
                     /old_locus_tag="D0898_28040"
     CDS             3880..4281
                     /locus_tag="D0898_RS27975"
                     /old_locus_tag="D0898_28040"
                     /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_019725133.1"
                     /translation="MTRVSISEAARLTGKSRTTLHRLIKTGELSTCSGERNTKMVDISE
                     LLRVFGPFDQPKNEHLTRQVPEQRDTAPADQSEHVIRQLKQQIEHLNILILSKDSHIDS
                     LKQAMLLLENHQAKLTEPPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            5134..6114
                     /locus_tag="D0898_RS27980"
                     /old_locus_tag="D0898_28045"
     CDS             5134..6114
                     /locus_tag="D0898_RS27980"
                     /old_locus_tag="D0898_28045"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000082736.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS5-like element ISEc68 family transposase"
                     /protein_id="WP_000082736.1"
                     /translation="MSQQLTFADSEFSSKRRQTRKEVFLGRMDDLLPWDKLLGVIEPVY
                     PKAGNGRRPYPLETMLRIHCMQQWYNLSDEAMEDALYEIASMRQFARLSLDKAIPDRTT
                     IMNFRHLLEQHELARKIFSTVNHWLAECGVLMTQGTLVDATIIQAPSSTKNKHNSRDED
                     MHQTKKGNQWYFGMKAHIGVDAKSGLTHSLVTTAANEHDLNQVGKLLHGDEEFISADAG
                     YQGAEKRDELSDVSADWLIAKRPGKVNALKQHPRKNKLAIRYEYLKASIRAKVEHPFRI
                     VKCQFGFVKARYKGLAKNDSQLAMLFTLANLVRVDQLIRAQARST"
                     /name="IS5-like element ISEc68 family transposase"
ORIGIN
        1 acggtttggg gcgtcatatc gggagctgcg gaccacttaa tcgcaacttc cttagacttc
       61 tgaagatatt ttatttttct tggaagtggt ggttgttttt gctcggaggg aacttatcac
      121 ccttgctcac atggcgatca tattcagaac cagcgtatga gttgtcggta tcatgatatt
      181 gaccgtaagt acctgttttt ggacattctt gcccagacca atgttttgcc atttactttt
      241 cctttgctcg ttttaggagc taagctccta gcggtacgaa attgtgccgc acttcataaa
      301 tgtaattgct tgaaattatg cttcaatgta ttgacttgtt gtttttgtgg ttattcgatt
      361 gagttcacat tttgagctga tttggttgtg ggtttttagg gaaatatctt tatgtactta
      421 tttgcgtaca tgttctatgc taagccccaa caaatggggg ttaacaacat gcatgcaatc
      481 aattttactg atgcccgtaa acattttgcc gagacgatga agcgcgtcac tgatgatgct
      541 gaaccggtac gtgtcatgcg ccgtgatgcg cctgatattg ttatgatcga tgcgggagag
      601 tatgaggcgc taatcgaaac ggtctatctg ttcagcaatc cggcgaacgc agagcatatc
      661 aatgagtcaa tgaaacaggc ggagcgcggc gaatttgtcg aagtggaata ttaagttcac
      721 taggaatggc gctgatgacc ttaactactg gcgtgatact gacaaaaaga agtttgagcg
      781 tatccggcaa ctgttgctca gcatcgaggc tgatccgctg acaggtatag gaaaacccga
      841 acggctgcgg caccacaaag atccggcact ctactcccgc aggattgatc agagccaccg
      901 tctggtctat tcaatccaga acggagaaat catcatctac gcagcccgtt atcactatgg
      961 tgacaaatag caaaagtcga tatagcccgc ttgatgcggg cttttcatgc aaggcgtaca
     1021 acggatgtta gggtaagtcg ctgtcagatc gacacaaagg caaagtcggt gtaacgttag
     1081 cctcagaaaa aacaaagccc cggaaatcat gtcatatctt ggcggatcgc atgataacca
     1141 gggctaggtc gaaaccttga aaggatatta gcacatgaac cgtgccagac aacagcccgc
     1201 cataagcgca gggcacattg cataacgccg cactcgaact tttcaacgaa cgcttaccac
     1261 acaagccgta cttttcggac gatctgcact ttggtgtccg tatcgccggt aaggaacgcg
     1321 ctattctggc gaaatatatc cagttcaatc agcctcacgc catgttctgg ctgggatttg
     1381 acgttgaccg cgccggttcc tccatcgact ggagcgaccg caacgcgcct gcaccgacgc
     1441 tgaccataac taaccccgaa aacggacacg cgcacctgct gtacgcgctg gaaaactcga
     1501 tacgcaccgc gccggacggc aaaataaaac cgttacgcta cgccgcctcc gtggagaatg
     1561 cgctacgtaa aaaattagag gctgacgctg gatattcggg gctcatctgc aaaaatccga
     1621 accacaacca ctggaaaatc gccgtgtggc agccgaagct ctacactctg gactggctgg
     1681 ccgactttct cgatctgaac acagggaatg acaaggaaat cgttgccgac tacggcttag
     1741 gccgtaactg cacgttgttc gacaaaaccc gtaagtgggc atatcgcgcc atccgtcagg
     1801 gctggcctga gtatgagcag tggctgcaag cctgctacga acgcgcttgc gcatacaacc
     1861 tgcaatttgc acggcctctg gatgaaaatg aggtaagagg gatagctaag agcattgcta
     1921 aatggacatc aaataaattt tcacctgaag aattcagtaa atttgttgat attactcatt
     1981 cctctgaaat tcaatcaaag agagggaaaa agtcaggaca gtcaaggagg aaaggaagcc
     2041 tagaggaaat aaaaccttgg gtagctatgg gaataagcag gcggaagtat ttttatatca
     2101 agaaaaatgg tgaaataaga tgaaaacctt cgtaactctt tggactatag tttttttagc
     2161 atttattgcc gtgatgtgta ctgttgatat atctaattac attccgtctg tttacacagt
     2221 ttttagtaag aatagacctc ttgtaactgg cgccctttct attcttttga tatctgtttt
     2281 tatttggctg atggtatccc tctacttact taaaaagtat tcggttaagg ttgagaaact
     2341 tagccttggt ggagtgaata tacttttcaa tgagagtgct acactttaca aaaagagtgt
     2401 aaaaaatcac ctagattcaa aaagagcaat tttcaaatta agaaaaaacg ttgatgcctt
     2461 tgatgaggtt atttcatcat attatcagac ttaccaattt attcgtgatg aaatgaaaat
     2521 actaaaccct aaaaaagatc gtgagattta tgatttcagc aatgagatgc tcatggtgtt
     2581 aaatagattt ctaactaact accagaacaa ctacaagcgt tggtataagt acatatcaga
     2641 caaagatgag gttgttgata gggttagcgg tgatgtcatg agatttcatg caaccagcat
     2701 aaataaaata caaatgcagt attatgatta tgagcgtatt ttaaaaggtt ttaaagatgt
     2761 taaccggttc tttgttaatg atgtgaagcc taagtttgga atcaatacag ataagtggaa
     2821 ctggtaaatt aaaggagtag ccaaggctac tccttggata gtactatgaa ttatgcattc
     2881 tcatttctct cgacatatca tacgttgctt tttctctatc gttataagtc atgtctatta
     2941 attttctgag tgtttctggg ttgttttcta tttgattcca gttgaccact gatatataag
     3001 acccgctctt catgaagttg tctattattc ttgctggcat atatgggaac ctttcctcat
     3061 aagttgagcg cttatcaata gaaaaccatt cagttacggt aggatgaact tctgattttt
     3121 cattagttcc atgtgttgaa cgaatgtacg tagtatttgt tgacgggaga ttgacgacta
     3181 aaattcctga ttttttgtta atggtactat ctctcatgct agagtaaagt tcccaatcta
     3241 cgtgttttct gttttttgtt tcagttccaa caagaaggat aagaactgat gtatctctaa
     3301 gatattcatc tcttattatc tctcttattt tttgtggggc ttcatcttca tctatatcac
     3361 ctaatgatac tgagcgattc acgaatattt catgttcctc attcattttt tcaagtgcgt
     3421 ttttgtagta ctgatcattc gcatggtggt agctaatgaa taccttatgc tttcccattt
     3481 ttattgtcct ttttttgttt gtgtgcactc tattttgcac ttgaacctat atcagataac
     3541 agctctcttt tagagagctc tttttttctc agccagcaca catagggtcc cttcagcaag
     3601 gtctcgccat gactggttta gggcgggctc gttgcttccc taaacgcctt gagaagagag
     3661 ctatcacctc actttattct tacgtaccgc tcgccgcagt cttatgaccg aacgtagtga
     3721 gcgaatgcgc gaggaagcgg aaagtcattt gttgcctgca ttttgcacgg tcactcctgt
     3781 gtttcatcgc ccttctgaaa aacacatcac ttctggacca gtatgtcgta agctggcccc
     3841 tgtttccttg agactgaatg tattaaagga tgataactga tgaccagagt gtctattagt
     3901 gaggctgcac ggctgacggg taagagccgg acaacgctgc acaggttaat caaaacaggt
     3961 gaactgtcca cttgtagcgg tgaacgaaat acaaaaatgg tcgatatatc agagctttta
     4021 cgtgttttcg gaccgtttga ccaaccgaag aatgaacacc ttactcgaca agtacctgaa
     4081 cagcgtgata cagcgcctgc tgaccagagt gaacatgtca ttcgtcaact gaaacagcag
     4141 attgaacacc ttaacatatt gattttatcg aaggattcgc acattgacag cctgaaacag
     4201 gccatgctcc ttcttgaaaa tcaccaggca aaattaactg aacccccggc gccgtggtgg
     4261 aaattctgga aaaaatcctg accccgtcat gcttcagttt tcctctccgg ccattccggg
     4321 gagttcctga accttcccga aaatcgtcag atctctgaac gctcctcacc acgaaaaata
     4381 cccacacccc acgcaaaatt ttaattttgc agatttgtat ttaatatcag cagcttactt
     4441 tactgaaatt tcgtttttta aattttattt atatagatcc gactctatga cgagtcgtca
     4501 tagagtcccc ggcgagtcgt catagagtcg gtaacgactc aggcctataa aaacaatgag
     4561 ttaataacga cccgactcta gatccgactc cccgtttggt tgttttttag acgtggcgac
     4621 tctgggtacg actctagtga agagtcgccg gggaatcgtg tggtgagtcg tccggcgact
     4681 tgccataacg tgattgccgg ccgtggacga accgattcct gaacgtgctg aaaaccggtt
     4741 ttccggctgc gccggcaacg cttcacggcc acgcaataaa ttgcgtcccc gttcaccgtt
     4801 ttcggatggg aagaacgccg gaaacaggac ttcccctggc tgaatggtgt caatttccgc
     4861 gctatgcact tgtgcgcata ctcatgcatg ccgtaaaaac agagcctgcg cgtttctggc
     4921 gggttttcgg gtggtttgtt gccttgttta ccggtttccc gtcagaaacg ccctgagggc
     4981 atctcaggcg gtgctgataa cggatgttat ggtaaatcaa gtgaatggca ggtacaaaaa
     5041 aagccccaga gggcttttag tttagggaag gtgcgaataa gtccgagatg tgagatcatc
     5101 gtgttgtaac ctgaacccag aatgagtaac cggatgagcc agcaactgac ttttgccgac
     5161 agtgagtttt ccagtaaacg ccgccagacc cgcaaagaag ttttccttgg cagaatggat
     5221 gacttgcttc cctgggacaa attacttggc gttatcgagc ctgtgtatcc caaggccggt
     5281 aatggtcgca ggccctatcc gctggaaacc atgctgcgta ttcactgcat gcagcaatgg
     5341 tacaacctga gcgatgaggc catggaagat gccctctatg aaatcgcctc catgcgccaa
     5401 tttgctcgcc tgtcactgga taaagccatt ccagaccgca ctaccatcat gaatttccgg
     5461 catttgctgg agcagcatga actggcccgc aaaatcttca gtaccgttaa tcactggcta
     5521 gcagagtgtg gcgttctaat gacccagggc accttggtgg atgccaccat cattcaagcc
     5581 cccagctcta ccaaaaacaa acacaacagc cgtgatgaag acatgcacca gaccaagaaa
     5641 ggtaaccagt ggtacttcgg catgaaagcg cacattggcg tggacgccaa aagtggcctg
     5701 acccacagtc tggtgaccac ggcggctaac gagcacgacc tcaatcaggt tggcaagtta
     5761 ctgcatggcg atgaagaatt tatctcagcc gatgctggtt atcagggggc cgaaaagcgc
     5821 gatgagctca gcgatgtcag cgcagactgg cttatcgcca agcgtcccgg caaagtgaat
     5881 gcattgaagc aacacccgcg caagaacaag ctggccatcc gttacgaata cctgaaagcg
     5941 agtatccgag cgaaggttga gcatccattt cggatagtaa aatgtcagtt tggtttcgtc
     6001 aaagccaggt acaaggggct ggctaaaaat gacagtcaac tggcgatgtt attcaccctg
     6061 gcgaacctgg ttcgagttga ccaattgata cgggcacagg cgagatctac ctgaaatgag
     6121 gaaattggcc tgaaacaggg ccaaaatcag ccacgaagag acgattttgg gctgaaaatt
     6181 ggaaaattga gccacaggac gtcgataaag g
//
