LOCUS       NZ_CP114171             3672 bp    DNA     circular CON 06-FEB-2024
DEFINITION  Klebsiella variicola strain 2022CK-00565 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP114171
VERSION     NZ_CP114171.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31390135
            Assembly: GCF_026967755.1
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-00565
  JOURNAL   Unpublished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                   :: 26.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/06/2024 05:22:52
            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)                     :: 5,853
            CDSs (total)                      :: 5,726
            Genes (coding)                    :: 5,563
            CDSs (with protein)               :: 5,563
            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)              :: 163
            CDSs (without protein)            :: 163
            Pseudo Genes (ambiguous residues) :: 0 of 163
            Pseudo Genes (frameshifted)       :: 57 of 163
            Pseudo Genes (incomplete)         :: 103 of 163
            Pseudo Genes (internal stop)      :: 37 of 163
            Pseudo Genes (multiple problems)  :: 29 of 163
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP114171.1.
            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-00565"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:244366"
                     /plasmid="unnamed3"
                     /geo_loc_name="USA"
                     /collection_date="2022-09-04"
     gene            complement(69..371)
                     /locus_tag="OIX89_RS29160"
                     /old_locus_tag="OIX89_29160"
     CDS             complement(69..371)
                     /locus_tag="OIX89_RS29160"
                     /old_locus_tag="OIX89_29160"
                     /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(435..728)
                     /locus_tag="OIX89_RS29165"
                     /old_locus_tag="OIX89_29165"
     CDS             complement(435..728)
                     /locus_tag="OIX89_RS29165"
                     /old_locus_tag="OIX89_29165"
                     /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            1065..1346
                     /locus_tag="OIX89_RS29170"
                     /old_locus_tag="OIX89_29170"
     CDS             1065..1346
                     /locus_tag="OIX89_RS29170"
                     /old_locus_tag="OIX89_29170"
                     /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            complement(1804..1950)
                     /locus_tag="OIX89_RS29175"
                     /old_locus_tag="OIX89_29175"
     CDS             complement(1804..1950)
                     /locus_tag="OIX89_RS29175"
                     /old_locus_tag="OIX89_29175"
                     /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            2365..2556
                     /locus_tag="OIX89_RS29180"
                     /old_locus_tag="OIX89_29180"
     CDS             2365..2556
                     /locus_tag="OIX89_RS29180"
                     /old_locus_tag="OIX89_29180"
                     /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"
     gene            2556..2957
                     /locus_tag="OIX89_RS29185"
                     /old_locus_tag="OIX89_29185"
     CDS             2556..2957
                     /locus_tag="OIX89_RS29185"
                     /old_locus_tag="OIX89_29185"
                     /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"
     Typing          complement(1842..2244)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.79"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 caattatgac tttatgttaa atcattaggg aggggattct gctggaactt agtggatgtt
       61 attgcatatc agacaaattt cggcagattt cccaagttat cgagtttagt tttgtttgga
      121 tctgtggtta tgtagccatc gttcatcgct tccactttgg ctcctaggtt ccacttacca
      181 gtagagctgt tctttacaac tgtcataaag ctggcttttc ccatgctgat cagctcgctg
      241 atgaatttgc gagagctgat tgagccggca gtgttccatg agccatctcg gtttatttta
      301 tgaactttta cgaattcgat gtgctgacca gcactgtcca ttttgattgc tgagatatag
      361 aaatctacca tggttgcctc ctgatggctg ctgggtgttt tacgtaacaa aagcccgcgt
      421 tctgcgggct tttttcatgg aaacattgga tgcaagtgtt ccagctctgc cgctaaagat
      481 ttgcgacttt ttgacaggct gaattgggtc tgcatgttta cccacgactc tgcagagcgg
      541 cctacgacct tcgacaatct aagtgccatt tcatagctta agtctgtttt cccatttaac
      601 agtctactta aggtagactg ggatacatca agtttatcgg ctaactctgc ggcaggtatt
      661 tcgaacggtt ccatgaacat ttctctgata aactcaccag gatgaacagg atcgtaaaga
      721 tttatcatgc cttcctctgt ttgttttgta tttgattata caaaaaaatt actgcctttc
      781 agtatgcgca ttgcacaatg tgcaagttca tgatattgac aaaaaaagca gtcagcttta
      841 ggatactcgt tggagtcaaa gctactgcgt atgtatgggc ttttatggcc ttttcaaggc
      901 gcagtatttt acccttagga ttcgttgaag tcaaatgagg tgattgacct caagaacaaa
      961 cttacgtcaa ttgttttaat aaagcaaggg ggcaaaatgg aactaattaa aatgatttta
     1021 aaatatagat acaggtatag acgaaaaaaa tatggggatt gtagatgata aaaaacataa
     1081 aacataaagg acttaggagc tttgctgaag aaggtagcac cgccggtatt cagcccagta
     1141 tggcgaaaag acttcgcatg attttgacta cgctaagcac agcaacttgc attcaagacg
     1201 ttgttgacgt tagggcgtta gggtgccacc ccctaaaggg ggagcgtaaa ggcgagtatt
     1261 ccgttgaagt taatgggaac tggcgggtag ttttcaaggt tgaggaacca aacgtcttag
     1321 acgttgatct tgaagattat cattagttat caataagtaa gttgctaatc catccaagtg
     1381 aaagtacgga tggattaggg actttattaa aaaagtaacc tctggagaaa gtatgagatc
     1441 ctttatggtt ttattgttcc cgttgattag cgtaactatt gctggagtcc tagcttttcg
     1501 tggtattgat ggctggggat ggttcttgtt agctgctgta ctttgtgcag gggctgatac
     1561 tgtccagaag catgtgtcta ccaataaaaa ggagcctgct ggtgagtgag ctgtcttggt
     1621 tcttccttga ctgctttgaa tgataaagcg tatcttactc gccgagacga aaaaaccgcc
     1681 tggggaggcg gttttttcga gggttcagta agttggggaa cttctgaacc gtggtaacag
     1741 ggtgtacaag accgctgaaa ccaaattctg tcctttcagt ttagccgtag ttgggctgag
     1801 acttcaagaa ctctgtatca gtaatctctt gtacaccttc ttaccagtgg ctgctgccag
     1861 tggcgcttgt gcgtgtctta ccgggttgga ctcaagacga tagttaccgg ataaggcgca
     1921 gcagtcggac tgaacggggg gttcgtgcat acagtccagc ttggagcgaa ctgccttccc
     1981 ggaactgagt gtcaggcgtg gaatgagata aacgcggcca taacagcgga atgacaccgg
     2041 taaaccgaat ggcaggaaca ggagagcgca cgagggagcc atcaggggga aacgcctgat
     2101 atctttatag tcctgtcggg tttcgccacc actgatttga gcgtcagctt tgtgatgctt
     2161 gtcagggggg cggagcctat ggaaaaacgg ccgcttagcg gcctttcctt ttccccgtca
     2221 cgcgaccgct cggttttctc gagcttttat acgcatgctc ctgccgctcg ccgcagccga
     2281 acggcaggag catagcgact gagtgagcga ggaagcggaa aagagaacat ccctacactg
     2341 agcactgacg ctctgaggcc tcttatgacg aaacaacaga aaacagcgct gaacatggct
     2401 aaattcatcc agaatcagtc tctgctcctg ctggagaagc ttaacgagct tgatcttgat
     2461 gtcgaggccg acctttgtga gaaactccac gatgatgcgg agcatctttt ccgtacactg
     2521 tcctcgagac tggatgcatt acaggatgat aactgatggc cagagtgtct attagtgagg
     2581 ctgcccgact gacgggtaag agtagaacaa cactgcacag gttaattaaa gcaggtgacc
     2641 tgtccacctg tagcggtgca cgtaatgcaa aaatggtaga tacttcagag cttttacgtg
     2701 tctttggtcc ctttgagcaa ccgaagggtg aacaccattc tggacaggtc tctgaacagc
     2761 gtgatacagc ctctgctgac cagagtgaac aggtgattcg tcatctgaaa caggagattg
     2821 aacacctgaa caccttactt ttgtccaagg attcgcacat tgacagcctg aaacaggcca
     2881 tgctccttct tgaaaatcac caggcaaaat taactgaatc cccggcgcca tggtggaaat
     2941 tctggaaaaa atcctgaccg cgtcatgctt cagttttcct ctccggtcat tccggggagt
     3001 tcctgaacct tcccaaaaat cgccagatct ctgagcactc ctcaccacga aaaataccca
     3061 caccccacgc aaaattaaaa ttttgcagat agacctttag tttcaattag ttatctattg
     3121 taaattacgc aattttattt tttgtaaggt gaatccgagt cgtgggcgac tctatggcga
     3181 atcgctgacg aattgcccac gattcatatg tgaatcacgc tttattatca tatggttatg
     3241 atgaattgac tcttgattca attcatcact ttgggtgttt tttgttcatg gtgactcttg
     3301 attcaattca cgagtcgaat cgccggtgaa tcgtgtggtg agtcgtccgg cgacttgcca
     3361 taacgtgatt gccggccgtc gacgaacccg attcctgaac gtgctgaaaa cgggttttcc
     3421 ggctgcgccg gcaacggctc acgaccacgc aataaattgc gtccccgttc accgttttcg
     3481 gatggaaaga acgccggaaa caggacttac cctggctgaa tggcgtgaat tttcgagcta
     3541 tgcacttgcg tgcatactca tgcatgccgt aaaaacagag cctgcgcgtt tctggcgggt
     3601 tttcgggtgg tttgttgcct gttttaccgg tttcccgtca gaaacgccat gaggccgttt
     3661 tagcggtgcg ta
//
