LOCUS       NZ_CP114167             3672 bp    DNA     circular CON 06-FEB-2024
DEFINITION  Klebsiella variicola strain 2022CK-00564 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP114167
VERSION     NZ_CP114167.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31390134
            Assembly: GCF_026967735.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella variicola
  ORGANISM  Klebsiella variicola
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3672)
  AUTHORS   Hergert,J., Casey,R., Wagner,J., Young,E.L. and Oakeson,K.F.
  TITLE     2022CK-00564
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3672)
  AUTHORS   Hergert,J., Casey,R., Wagner,J., Young,E.L. and Oakeson,K.F.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-DEC-2022) Utah Public Health Laboratory, Utah Public
            Health Laboratory Infectious Disease submission group, 4431 S 2700
            W, Salt Lake City, UT 84129, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 23.0x
            Sequencing Technology :: Oxford Nanopore GridION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/06/2024 05:22:49
            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)                     :: 5,852
            CDSs (total)                      :: 5,725
            Genes (coding)                    :: 5,564
            CDSs (with protein)               :: 5,564
            Genes (RNA)                       :: 127
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 161
            CDSs (without protein)            :: 161
            Pseudo Genes (ambiguous residues) :: 0 of 161
            Pseudo Genes (frameshifted)       :: 59 of 161
            Pseudo Genes (incomplete)         :: 100 of 161
            Pseudo Genes (internal stop)      :: 37 of 161
            Pseudo Genes (multiple problems)  :: 30 of 161
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP114167.1.
            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..3672
                     /organism="Klebsiella variicola"
                     /mol_type="genomic DNA"
                     /strain="2022CK-00564"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:244366"
                     /plasmid="unnamed3"
                     /geo_loc_name="USA"
                     /collection_date="2022-09-08"
     gene            270..416
                     /locus_tag="OIX91_RS29150"
                     /old_locus_tag="OIX91_29150"
     CDS             270..416
                     /locus_tag="OIX91_RS29150"
                     /old_locus_tag="OIX91_29150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001487656.1"
                     /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_269136674.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPVRHAQAPLAAATGKKVYKRLLI
                     QSS"
                     /name="replication initiation protein"
     gene            complement(874..1155)
                     /locus_tag="OIX91_RS29155"
                     /old_locus_tag="OIX91_29155"
     CDS             complement(874..1155)
                     /locus_tag="OIX91_RS29155"
                     /old_locus_tag="OIX91_29155"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000594459.1"
                     /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_032440460.1"
                     /translation="MIKNIKHKGLRSFAEEGSTAGIQPSMAKRLRMILTTLSTATCIQD
                     VVDVRALGCHPLKGERKGEYSVEVNGNWRVVFKVEEPNVLDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            1492..1785
                     /locus_tag="OIX91_RS29160"
                     /old_locus_tag="OIX91_29160"
     CDS             1492..1785
                     /locus_tag="OIX91_RS29160"
                     /old_locus_tag="OIX91_29160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609279.1"
                     /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="HigA family addiction module antitoxin"
                     /protein_id="WP_023317864.1"
                     /translation="MINLYDPVHPGEFIREMFMEPFEIPAAELADKLDVSQSTLSRLLN
                     GKTDLSYEMALRLSKVVGRSAESWVNMQTQFSLSKSRKSLAAELEHLHPMFP"
                     /name="HigA family addiction module antitoxin"
     gene            1849..2151
                     /locus_tag="OIX91_RS29165"
                     /old_locus_tag="OIX91_29165"
     CDS             1849..2151
                     /locus_tag="OIX91_RS29165"
                     /old_locus_tag="OIX91_29165"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006326557.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3892 domain-containing protein"
                     /protein_id="WP_023317863.1"
                     /translation="MVDFYISAIKMDSAGQHIEFVKVHKINRDGSWNTAGSISSRKFIS
                     ELISMGKASFMTVVKNSSTGKWNLGAKVEAMNDGYITTDPNKTKLDNLGNLPKFV"
                     /name="DUF3892 domain-containing protein"
     gene            complement(2935..3336)
                     /locus_tag="OIX91_RS29170"
                     /old_locus_tag="OIX91_29170"
     CDS             complement(2935..3336)
                     /locus_tag="OIX91_RS29170"
                     /old_locus_tag="OIX91_29170"
                     /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_040242827.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGARNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3336..3527)
                     /locus_tag="OIX91_RS29175"
                     /old_locus_tag="OIX91_29175"
     CDS             complement(3336..3527)
                     /locus_tag="OIX91_RS29175"
                     /old_locus_tag="OIX91_29175"
                     /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_040242829.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDDN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2..379
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.842"
                     /coverage="92.0"
                     /evalue="2.7200000000000002e-179"
ORIGIN
        1 gacggggaaa aggaaaggcc gctaagcggc cgtttttcca taggctccgc ccccctgaca
       61 agcatcacaa agctgacgct caaatcagtg gtggcgaaac ccgacaggac tataaagata
      121 tcaggcgttt ccccctgatg gctccctcgt gcgctctcct gttcctgcca ttcggtttac
      181 cggtgtcatt ccgctgttat ggccgcgttt atctcattcc acgcctgaca ctcagttccg
      241 ggaaggcagt tcgctccaag ctggactgta tgcacgaacc ccccgttcag tccgactgct
      301 gcgccttatc cggtaactat cgtcttgagt ccaacccggt aagacacgca caagcgccac
      361 tggcagcagc cactggtaag aaggtgtaca agagattact gatacagagt tcttgaagtc
      421 tcagcccaac tacggctaaa ctgaaaggac agaatttggt ttcagcggtc ttgtacaccc
      481 tgttaccacg gttcagaagt tccccaactt actgaaccct cgaaaaaacc gcctccccag
      541 gcggtttttt cgtctcggcg agtaagatac gctttatcat tcaaagcagt caaggaagaa
      601 ccaagacagc tcactcacca gcaggctcct ttttattggt agacacatgc ttctggacag
      661 tatcagcccc tgcacaaagt acagcagcta acaagaacca tccccagcca tcaataccac
      721 gaaaagctag gactccagca atagttacgc taatcaacgg gaacaataaa accataaagg
      781 atctcatact ttctccagag gttacttttt taataaagtc cctaatccat ccgtactttc
      841 acttggatgg attagcaact tacttattga taactaatga taatcttcaa gatcaacgtc
      901 taagacgttt ggttcctcaa ccttgaaaac tacccgccag ttcccattaa cttcaacgga
      961 atactcgcct ttacgctccc cctttagggg gtggcaccct aacgccctaa cgtcaacaac
     1021 gtcttgaatg caagttgctg tgcttagcgt agtcaaaatc atgcgaagtc ttttcgccat
     1081 actgggctga ataccggcgg tgctaccttc ttcagcaaag ctcctaagtc ctttatgttt
     1141 tatgtttttt atcatctaca atccccatat ttttttcgtc tatacctgta tctatatttt
     1201 aaaatcattt taattagttc cattttgccc ccttgcttta ttaaaacaat tgacgtaagt
     1261 ttgttcttga ggtcaatcac ctcatttgac ttcaacgaat cctaagggta aaatactgcg
     1321 ccttgaaaag gccataaaag cccatacata cgcagtagct ttgactccaa cgagtatcct
     1381 aaagctgact gctttttttg tcaatatcat gaacttgcac attgtgcaat gcgcatactg
     1441 aaaggcagta atttttttgt ataatcaaat acaaaacaaa cagaggaagg catgataaat
     1501 ctttacgatc ctgttcatcc tggtgagttt atcagagaaa tgttcatgga accgttcgaa
     1561 atacctgccg cagagttagc cgataaactt gatgtatccc agtctacctt aagtagactg
     1621 ttaaatggga aaacagactt aagctatgaa atggcactta gattgtcgaa ggtcgtaggc
     1681 cgctctgcag agtcgtgggt aaacatgcag acccaattca gcctgtcaaa aagtcgcaaa
     1741 tctttagcgg cagagctgga acacttgcat ccaatgtttc catgaaaaaa gcccgcagaa
     1801 cgcgggcttt tgttacgtaa aacacccagc agccatcagg aggcaaccat ggtagatttc
     1861 tatatctcag caatcaaaat ggacagtgct ggtcagcaca tcgaattcgt aaaagttcat
     1921 aaaataaacc gagatggctc atggaacact gccggctcaa tcagctctcg caaattcatc
     1981 agcgagctga tcagcatggg aaaagccagc tttatgacag ttgtaaagaa cagctctact
     2041 ggtaagtgga acctaggagc caaagtggaa gcgatgaacg atggctacat aaccacagat
     2101 ccaaacaaaa ctaaactcga taacttggga aatctgccga aatttgtctg atatgcaata
     2161 acatccacta agttccagca gaatcccctc cctaatgatt taacataaag tcataattgt
     2221 acgcaccgct aaaacggcct catggcgttt ctgacgggaa accggtaaaa caggcaacaa
     2281 accacccgaa aacccgccag aaacgcgcag gctctgtttt tacggcatgc atgagtatgc
     2341 acgcaagtgc atagctcgaa aattcacgcc attcagccag ggtaagtcct gtttccggcg
     2401 ttctttccat ccgaaaacgg tgaacgggga cgcaatttat tgcgtggtcg tgagccgttg
     2461 ccggcgcagc cggaaaaccc gttttcagca cgttcaggaa tcgggttcgt cgacggccgg
     2521 caatcacgtt atggcaagtc gccggacgac tcaccacacg attcaccggc gattcgactc
     2581 gtgaattgaa tcaagagtca ccatgaacaa aaaacaccca aagtgatgaa ttgaatcaag
     2641 agtcaattca tcataaccat atgataataa agcgtgattc acatatgaat cgtgggcaat
     2701 tcgtcagcga ttcgccatag agtcgcccac gactcggatt caccttacaa aaaataaaat
     2761 tgcgtaattt acaatagata actaattgaa actaaaggtc tatctgcaaa attttaattt
     2821 tgcgtggggt gtgggtattt ttcgtggtga ggagtgctca gagatctggc gatttttggg
     2881 aaggttcagg aactccccgg aatgaccgga gaggaaaact gaagcatgac gcggtcagga
     2941 ttttttccag aatttccacc atggcgccgg ggattcagtt aattttgcct ggtgattttc
     3001 aagaaggagc atggcctgtt tcaggctgtc aatgtgcgaa tccttggaca aaagtaaggt
     3061 gttcaggtgt tcaatctcct gtttcagatg acgaatcacc tgttcactct ggtcagcaga
     3121 ggctgtatca cgctgttcag agacctgtcc agaatggtgt tcacccttcg gttgctcaaa
     3181 gggaccaaag acacgtaaaa gctctgaagt atctaccatt tttgcattac gtgcaccgct
     3241 acaggtggac aggtcacctg ctttaattaa cctgtgcagt gttgttctac tcttacccgt
     3301 cagtcgggca gcctcactaa tagacactct ggccatcagt tatcatcctg taatgcatcc
     3361 agtctcgagg acagtgtacg gaaaagatgc tccgcatcat cgtggagttt ctcacaaagg
     3421 tcggcctcga catcaagatc aagctcgtta agcttctcca gcaggagcag agactgattc
     3481 tggatgaatt tagccatgtt cagcgctgtt ttctgttgtt tcgtcataag aggcctcaga
     3541 gcgtcagtgc tcagtgtagg gatgttctct tttccgcttc ctcgctcact cagtcgctat
     3601 gctcctgccg ttcggctgcg gcgagcggca ggagcatgcg tataaaagct cgagaaaacc
     3661 gagcggtcgc gt
//
