LOCUS       NZ_CP065166             5783 bp    DNA     circular CON 29-NOV-2023
DEFINITION  Klebsiella variicola strain KPN029 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP065166
VERSION     NZ_CP065166.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16685814
            Assembly: GCF_015694045.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella variicola
  ORGANISM  Klebsiella variicola
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5783)
  AUTHORS   Hawkey,J., Wyres,K.L., Judd,L., Jenney,A. and Holt,K.E.
  TITLE     Diversity and transmission of ESBL plasmids in a Melbourne hospital
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5783)
  AUTHORS   Hawkey,J., Wyres,K.L., Judd,L., Jenney,A. and Holt,K.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-NOV-2020) Department of Infectious Diseases, Monash
            University, Level 2, The Burnet Institute, Melbourne, VIC 3004,
            Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.7
            Assembly Name                     :: KPN029
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 101x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/29/2023 14:33:37
            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)                     :: 6,160
            CDSs (total)                      :: 6,035
            Genes (coding)                    :: 5,881
            CDSs (with protein)               :: 5,881
            Genes (RNA)                       :: 125
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 154
            CDSs (without protein)            :: 154
            Pseudo Genes (ambiguous residues) :: 0 of 154
            Pseudo Genes (frameshifted)       :: 56 of 154
            Pseudo Genes (incomplete)         :: 96 of 154
            Pseudo Genes (internal stop)      :: 27 of 154
            Pseudo Genes (multiple problems)  :: 22 of 154
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP065166.1.
            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..5783
                     /organism="Klebsiella variicola"
                     /mol_type="genomic DNA"
                     /strain="KPN029"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:244366"
                     /plasmid="unnamed4"
                     /geo_loc_name="Australia: Melbourne"
                     /lat_lon="37.8136 S 144.9631 E"
                     /collection_date="2017-03-28"
                     /collected_by="Microbiology Unit & Department of Infectious
                     Diseases, Alfred Hospital"
     gene            1..115
                     /locus_tag="I3U23_RS30565"
                     /old_locus_tag="I3U23_30565"
                     /pseudo=""
     CDS             1..115
                     /locus_tag="I3U23_RS30565"
                     /old_locus_tag="I3U23_30565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            complement(321..476)
                     /locus_tag="I3U23_RS30570"
                     /old_locus_tag="I3U23_30570"
     CDS             complement(321..476)
                     /locus_tag="I3U23_RS30570"
                     /old_locus_tag="I3U23_30570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008323621.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_071561715.1"
                     /translation="MKKLLFLGVVTVSVVLAACQVNNVRDTGGGAVSPSSTVTGVTLDS
                     GTNGNP"
                     /name="colicin release lysis protein"
     gene            complement(584..841)
                     /locus_tag="I3U23_RS30575"
                     /old_locus_tag="I3U23_30575"
     CDS             complement(584..841)
                     /locus_tag="I3U23_RS30575"
                     /old_locus_tag="I3U23_30575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015366249.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin immunity protein"
                     /protein_id="WP_010904244.1"
                     /translation="MANKTLADYTEQEFIEFIEKIKKADFATESEHDEAIYEFSQLTEH
                     PDGWDLIYHPQAGADNSPAGVVKTVKEWRAANGKPGFKKS"
                     /name="bacteriocin immunity protein"
     gene            complement(1023..1286)
                     /locus_tag="I3U23_RS30580"
                     /old_locus_tag="I3U23_30580"
     CDS             complement(1023..1286)
                     /locus_tag="I3U23_RS30580"
                     /old_locus_tag="I3U23_30580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015377593.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_064148700.1"
                     /translation="MSNPIEDIIKNESVSDVLRYFGPGRDISKIDRMYVSYKFEVISEG
                     VLLSEYKKLFDNGELKYDSNKNVIKGPNWKEPAFVTQKKYGI"
                     /name="hypothetical protein"
     gene            complement(1297..3639)
                     /locus_tag="I3U23_RS30585"
                     /old_locus_tag="I3U23_30585"
     CDS             complement(1297..3639)
                     /locus_tag="I3U23_RS30585"
                     /old_locus_tag="I3U23_30585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010904246.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="S-type pyocin domain-containing protein"
                     /protein_id="WP_181486822.1"
                     /translation="MGGGFNYNGEGATGTGLDRDPYVRDSNGNAIGVKSGYHAESYGTS
                     SPALGPNGAIQITAGVIAVPGDKPRPDGGSGGGNTVNTGPAGQLLVMNKGQLGYWETRS
                     TGAGNNEHNTSVFVAVGPSEAEKTASAEKALKEKQQAEAAAKDFAAKTAAASATAEKER
                     QQAIAAATAAGQHQSVSDARNSLNNATSDVSRLKSAADSALQEAKAKRKAAIDAVPVAT
                     QAENKYQELQQKIKGLKLKNGEYGTEKWEIIGSNKEHDHWGYRFYPSGITKAQVDVAQS
                     DAVNKRNQATSLASQATAAEQDSLKATAAYNAAETRRQAAQAALNSAEQAAAAERKRQE
                     AEAAAAAAAEKKRQADAVAKAAEEARAAAEKARLMQERQAAADKLKSTDIQSVRGIPST
                     ASPAASPISWAVASLGGISLDSVTAGKAWTQIAEVMAKLRGIAGASLVGPVVATAVGLF
                     WSRDVGIGSDVVPGRDISGLMPGDALSLPDLATLIKAADSKTGVSMPVRGRIIVREGDY
                     LESQFVRTPVAGSVPVVRATLDKATGYWGYTLPAIQGVPGQTILVSPSDAPGVNAPLGL
                     AGPVPLPETIIHTGGQTTVPQGGTVTVSPVIGEVDFRDLILVFPPESGLKPLYVMPVSP
                     YGDATEKGEHSGRPYNPDKAGGPVQNLNWRSAVINKAGIDKVKLHTGRFGESAANKVMI
                     DRLEKILSGQLQVTDTDKRFYTHELRELERYRALGVPDNVKPDDKGVTWNNTHTATLED
                     YKINEKTDPLYTKDAEEAEYKAELKNK"
                     /name="S-type pyocin domain-containing protein"
     gene            complement(4755..5177)
                     /locus_tag="I3U23_RS30590"
                     /old_locus_tag="I3U23_30590"
     CDS             complement(4755..5177)
                     /locus_tag="I3U23_RS30590"
                     /old_locus_tag="I3U23_30590"
                     /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_064148699.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKAIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(5177..5368)
                     /locus_tag="I3U23_RS30595"
                     /old_locus_tag="I3U23_30595"
     CDS             complement(5177..5368)
                     /locus_tag="I3U23_RS30595"
                     /old_locus_tag="I3U23_30595"
                     /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_023302508.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2..115
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.391"
                     /coverage="100.0"
                     /evalue="1.23e-47"
     Typing          5490..5783
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.271"
                     /coverage="99.0"
                     /evalue="2.9e-134"
ORIGIN
        1 atgcacgaac cccccgttca gtccgactgc tgcgccttga tccggtaact atcatcttga
       61 gtccaacccg gtaagacatg caaaagcacc actggcagca gccactggta actgatttag
      121 aggagttagt cttgaagtta tgcgccggtt aaggctaaac tgaaagaaca agttttggtt
      181 actgtgctcc tcataagcca gttacctcgg ttcaaagagc gccaactctt ggaaccttcg
      241 aaaaaccgcc cgccaaggcg gttttttcgt ttacagagca agagattacg acgatccaaa
      301 tgggatctca agaagatcct ttacggattg ccgttcgtac cgctatcaag cgtgactccg
      361 gtcaccgtcg atgaaggtga aacagcccca cctccggtgt cacgaacatt attgacctga
      421 catgccgcca gaaccacaga aacggtaaca acccccagga aaagtaattt tttcatatat
      481 caccttttat ttttattatt ctaagcaaat ggatacctag taattattat tcaaatccag
      541 agttaaaaat gtgcggattc atcacttgaa cccgcacatt caatcacgat tttttaaaac
      601 ctggcttacc gttagctgct cgccactctt ttactgtttt tacaacacca gcaggagagt
      661 tatcggctcc tgcttgagga tgataaataa gatcccaacc atctggatgt tcagtcaact
      721 ggctgaactc ataaatggcc tcatcatgct cagactcagt agcaaagtct gcttttttaa
      781 ttttttcgat aaactcaata aattcctgct ctgtatagtc agccaaagtt ttattagcca
      841 tttcagttcc cattatggat ttcaatatgg cgtttaggtt ttaatgcact cagcttaccc
      901 cagatattgt tgacctgaca tgctgccagt atcatcgaaa ccacgaccac tcaaaaaaga
      961 aacccttttc atatgtgagc tttaatcaaa gccctctttt caaagggctt catatgcaca
     1021 ctttaaatgc cgtatttttt ttgtgttaca aaagcaggct ctttccagtt aggcccctta
     1081 ataacatttt tattagagtc atactttagt tctccattgt cgaataactt tttgtattca
     1141 gataaaagaa cgccttcaga gatcacttca aacttatatg aaacatacat acggtcaatt
     1201 tttgaaatgt cgcgaccagg accaaagtag cgaagcacat cacttaccga ttcattttta
     1261 atgatgtctt caatcggatt actcattctc tccccctcat ttatttttta gctctgcttt
     1321 atactctgcc tcttcagcat cctttgtata gagcggatca gttttttcat taattttata
     1381 atcttccagc gttgctgtat gagtgttatt ccacgtaaca cctttatcat ctggcttcac
     1441 attatcaggg acccctaaag cacgataacg ttccagctct ctgagttcat gggtgtaaaa
     1501 ccgcttgtcc gtatcagtta cctgtaactg accgctcagg attttctcca gacggtcgat
     1561 cattactttg tttgctgctg attcaccaaa gcgaccggta tgtagcttca ccttatcaat
     1621 cccggccttg ttgatgactg cactacgcca gttaagattc tgtacaggac cacctgcctt
     1681 atccggatta taaggtcttc cgctgtgctc gcctttttct gttgcatctc cataagggct
     1741 aactggcatc acatataacg gctttaaccc tgactcagga gggaaaacaa ggataagatc
     1801 tcgaaaatca acttcaccaa taacaggaga tactgtcaca gtccccccct gagggaccgt
     1861 agtttgccca ccggtatgta taatagtttc aggcaaagga accggcccag caagtcccag
     1921 aggagcatta acgcccggcg catctgacgg acttaccagt attgtctgtc cgggcacgcc
     1981 ctgtatcgcc ggcaacgtat atccccagta accagtagct ttatccagag tagcccgaac
     2041 aaccggaaca ctaccggcaa caggtgttcg aacgaactga gactccagat aatcgccttc
     2101 acgcacgata atccggcctc gaaccggcat actgacaccc gttttactgt cagcagcttt
     2161 aatcaaagtg gccagatcag gtaatgacag tgcatcaccc ggcatcagcc cgctgatgtc
     2221 acgtccgggc accacatcac tgccaatacc aacatcacgt gaccaaaaca gccctacagc
     2281 agttgccacc acgggaccaa caagactcgc accggcaata cctcgcagtt tagccatcac
     2341 ctcagcaatc tgcgtccagg ctttccctgc agtaacacta tccagcgata taccaccaag
     2401 tgatgcaacg gcccaggaaa tgggtgacgc tgcaggcgat gccgtagacg ggatcccgcg
     2461 aacagactga atatctgtgg atttcagctt atctgctgct gcctgacgct cctgcatcag
     2521 cctggctttt tccgctgccg cacgcgcttc ctctgctgct tttgctactg cgtctgcctg
     2581 acgttttttc tcagcagcag ctgctgcagc cgcctcagct tcctgccgct tacgttcagc
     2641 agcagcagcc tgttcagcag aatttaacgc cgcctgagca gcctgacggc gcgtttctgc
     2701 cgcattatag gcagctgtag ctttcaggct gtcctgttct gctgctgttg cctgactggc
     2761 aagactggta gcctgatttc gcttattcac agcatcgctc tgcgccacat caacctgagc
     2821 tttggtaatt ccggatggat aaaacctgta tccccagtga tcatgctcct tattagagcc
     2881 aattatttcc catttttccg taccatactc accatttttc agcttcaggc ctttaatctt
     2941 ctgctgcagc tcctgatatt tattttccgc ctgggttgca acaggtacag catcaatagc
     3001 agccttccgt tttgcctttg cctcctgcag tgcactgtct gcagctgatt tcagacgaga
     3061 cacatctgac gtcgcgttat tcaggctatt acgggcatca gaaactgact gatgctgacc
     3121 cgctgcagtt gcagcagcaa ttgcctgctg gcgttctttt tccgccgtgg ctgatgcggc
     3181 agcagtttta gccgcaaagt cttttgctgc tgcttctgcc tgctgttttt cctttaacgc
     3241 cttctctgca gaagcagttt tttctgcctc agaaggacct acggcaacaa atacactcgt
     3301 attatgctca ttgttacccg cgcccgtaga acgagtttcc cagtatccaa gctgaccttt
     3361 attcatcacc aggagctgtc ctgccggtcc ggtgttaaca gtattcccac caccactacc
     3421 accgtcaggt cggggcttat ctccaggcac agcaataacc ccagcagtaa tctgaatagc
     3481 gccattaggc cctaaggctg gacttgaggt cccataggac tccgcgtgat agcctgattt
     3541 aacaccaata gcattaccat tgctgtcgcg aacatatgga tcacgatcca atccggtgcc
     3601 agtagcacct tccccgttat agttaaatcc accacccata actctctcct ttgttgttat
     3661 ttttatcgtt ttcctgcttg tcagaatctg gtgtgcggtt tatcgccttc gaacctgtat
     3721 ccggaggctg ttattagttc tctgccacac caagtactgt atataaatac atgtgtttat
     3781 atacagtact tgaatactac tcctgacatg agaactctgt caacacgcgg agagatacaa
     3841 ttatcttttg aattttcatt aagttaagcg taatagaaat gacaaaaccc agacaggacg
     3901 cggctcggca gagaaaaaaa attaacgata tgtgctctta aaaagggtgt gactgacgga
     3961 cagagacctg tacaaaaagt cttggtgtag agggtattcc gccacccgag cgcccccatt
     4021 taccataatc ccttaattgt acgcaccgct aaaacggcct cagggcgttt ctgacgggaa
     4081 accggtaaaa caggcaacaa accacccgaa aacccgccag aaacgcgcag gctctgtttt
     4141 tacggcatgc atgagtatgc gcgcaagtgc atagcgcgga aattcacgcc attcagccag
     4201 ggtaagtcct gtttccggcg ttcttctgat ccgaaaacgg tgaacgggga cgcaatttat
     4261 tgcgtggccg tgaggcgttg ccggcgcagc cggaaaaccg gttttcagca cgttcaggaa
     4321 tcgggttcgt cgacggccgg caatcacgtt atggcaagtc gccggacgac tcaccacacg
     4381 attcaccggc gattcgaatc gtgaattgaa tcaagagtca ccatgaacaa aaaacgccca
     4441 aattgatgaa ttgaatcaag agtcgattca tcataacaac atgataataa agcgtgattc
     4501 acatatgaat cgtgggcaat tcgtaaacga ttcgccatag agtcgtccac gacttggatc
     4561 tgcactttgt aacacatcac tgcacattaa tttttcatta accaattgtt ttaaataaag
     4621 aatctgcaaa attttaattt tgcgtagtgt gtgggtattt ttagtggtga ggagcgttca
     4681 gagatctggc gattttttgg aaggttcagg aactccccgg aatggccgga gaggaaaact
     4741 gaagcatgat ggggtcagga ttttttccag aatttccacc acggggaatg gggtggtgaa
     4801 gaaggttcgt gcttgtgctc cagaagctgc atagcctgac gaagggaatc aatatgctca
     4861 tctcgagcct taacagcccc tttaagacca tcgttttcag cttcaagtaa agcgattcta
     4921 tgttgtaaat catgtaaacc aacgctgtta atacctgtag attctgcgtc actttttaca
     4981 tcatatttta cagtatcgat tacaccatca agagaaccaa acactctaat aagctcagaa
     5041 gtatcaataa ctttaatagc cttcccgtgc tttacaacag aggtgtaact taacttccca
     5101 ctgttaatca tcttgtaaat tgtaggacga ctaaccttaa caagccgtgc cgcttcacta
     5161 atagacactc tggccatcag ttaccatcct gtaattcatc cagtctcgag gacagtgtac
     5221 ggaaaagatg ctccgcatca tcgtggagtt tctcacaaag gtcggcctcg acatcgagat
     5281 caagctcgtt aagcttctcc agcaggagca gagactgatt ctggatgaat ttagccatgt
     5341 tcagcgctgt tttctgttgt ttcgtcataa gaggcctcag agcgtcagtg ctcagtgtag
     5401 ggatgttctc ttttccgctt cctcgctcac tcagtcgcta cgctcctgcc gttcggctgc
     5461 ggcgagcggc aggagcatgc gtataaaagc tcgagaaaac cgagcgatcg cgtgatgggg
     5521 agaaggagag gccgcacagc ggccgttttt ccataggctc cgcccccctg acaagcatca
     5581 cagaatttga cgctcaaatc agtggtggcg aaacccgaca ggactataaa gataccaggc
     5641 gtttccccct gatggctccc tcgtgcgctc tcctgttcct gccattcggt ttaccggtgt
     5701 cattccgctg ttatggccgc gtttatctca ttccacgcct gacactcagt tccgggtagg
     5761 cagttcgctc caagctggac tgt
//
