LOCUS       NZ_CP114315             3672 bp    DNA     circular CON 18-FEB-2024
DEFINITION  Klebsiella variicola strain 2022CK-00500 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP114315
VERSION     NZ_CP114315.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31152640
            Assembly: GCF_025579445.1
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-00500
  JOURNAL   Unpublished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
REFERENCE   3  (bases 1 to 3672)
  CONSRTM   Clinical and Environmental Microbiology Branch: Whole genome
            sequencing antimicrobial resistance pathogens in the healthcare
            setting
  TITLE     Direct Submission
  JOURNAL   Submitted (04-OCT-2022) Division of Healthcare Quality Promotion, US
            Centers for Disease Control and Prevention, 1600 Clifton Rd,
            Atlanta, GA, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 40.0x
            Sequencing Technology :: Oxford Nanopore GridION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/18/2024 04:49:08
            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)                     :: 5,848
            CDSs (total)                      :: 5,721
            Genes (coding)                    :: 5,560
            CDSs (with protein)               :: 5,560
            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
            CP114315.1.
            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-00500"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:244366"
                     /plasmid="unnamed3"
                     /geo_loc_name="USA"
                     /collection_date="2022-06-02"
     gene            135..326
                     /locus_tag="OEE47_RS29140"
                     /old_locus_tag="OEE47_29135"
     CDS             135..326
                     /locus_tag="OEE47_RS29140"
                     /old_locus_tag="OEE47_29135"
                     /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            326..727
                     /locus_tag="OEE47_RS29145"
                     /old_locus_tag="OEE47_29140"
     CDS             326..727
                     /locus_tag="OEE47_RS29145"
                     /old_locus_tag="OEE47_29140"
                     /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(1511..1813)
                     /locus_tag="OEE47_RS29150"
                     /old_locus_tag="OEE47_29145"
     CDS             complement(1511..1813)
                     /locus_tag="OEE47_RS29150"
                     /old_locus_tag="OEE47_29145"
                     /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(1877..2170)
                     /locus_tag="OEE47_RS29155"
                     /old_locus_tag="OEE47_29150"
     CDS             complement(1877..2170)
                     /locus_tag="OEE47_RS29155"
                     /old_locus_tag="OEE47_29150"
                     /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            2507..2788
                     /locus_tag="OEE47_RS29160"
                     /old_locus_tag="OEE47_29155"
     CDS             2507..2788
                     /locus_tag="OEE47_RS29160"
                     /old_locus_tag="OEE47_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            complement(3246..3392)
                     /locus_tag="OEE47_RS29165"
                     /old_locus_tag="OEE47_29160"
     CDS             complement(3246..3392)
                     /locus_tag="OEE47_RS29165"
                     /old_locus_tag="OEE47_29160"
                     /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"
     Typing          complement(3284..3672)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.675"
                     /coverage="95.0"
                     /evalue="0.0"
ORIGIN
        1 cggttttctc gagcttttat acgcatgctc ctgccgctcg ccgcagccga acggcaggag
       61 catagcgact gagtgagcga ggaagcggaa aagagaacat ccctacactg agcactgacg
      121 ctctgaggcc tcttatgacg aaacaacaga aaacagcgct gaacatggct aaattcatcc
      181 agaatcagtc tctgctcctg ctggagaagc ttaacgagct tgatcttgat gtcgaggccg
      241 acctttgtga gaaactccac gatgatgcgg agcatctttt ccgtacactg tcctcgagac
      301 tggatgcatt acaggatgat aactgatggc cagagtgtct attagtgagg ctgcccgact
      361 gacgggtaag agtagaacaa cactgcacag gttaattaaa gcaggtgacc tgtccacctg
      421 tagcggtgca cgtaatgcaa aaatggtaga tacttcagag cttttacgtg tctttggtcc
      481 ctttgagcaa ccgaagggtg aacaccattc tggacaggtc tctgaacagc gtgatacagc
      541 ctctgctgac cagagtgaac aggtgattcg tcatctgaaa caggagattg aacacctgaa
      601 caccttactt ttgtccaagg attcgcacat tgacagcctg aaacaggcca tgctccttct
      661 tgaaaatcac caggcaaaat taactgaatc cccggcgcca tggtggaaat tctggaaaaa
      721 atcctgaccg cgtcatgctt cagttttcct ctccggtcat tccggggagt tcctgaacct
      781 tcccaaaaat cgccagatct ctgagcactc ctcaccacga aaaataccca caccccacgc
      841 aaaattaaaa ttttgcagat agacctttag tttcaattag ttatctattg taaattacgc
      901 aattttattt tttgtaaggt gaatccgagt cgtgggcgac tctatggcga atcgctgacg
      961 aattgcccac gattcatatg tgaatcacgc tttattatca tatggttatg atgaattgac
     1021 tcttgattca attcatcact ttgggtgttt tttgttcatg gtgactcttg attcaattca
     1081 cgagtcgaat cgccggtgaa tcgtgtggtg agtcgtccgg cgacttgcca taacgtgatt
     1141 gccggccgtc gacgaacccg attcctgaac gtgctgaaaa cgggttttcc ggctgcgccg
     1201 gcaacggctc acgaccacgc aataaattgc gtccccgttc accgttttcg gatggaaaga
     1261 acgccggaaa caggacttac cctggctgaa tggcgtgaat tttcgagcta tgcacttgcg
     1321 tgcatactca tgcatgccgt aaaaacagag cctgcgcgtt tctggcgggt tttcgggtgg
     1381 tttgttgcct gttttaccgg tttcccgtca gaaacgccat gaggccgttt tagcggtgcg
     1441 tacaattatg actttatgtt aaatcattag ggaggggatt ctgctggaac ttagtggatg
     1501 ttattgcata tcagacaaat ttcggcagat ttcccaagtt atcgagttta gttttgtttg
     1561 gatctgtggt tatgtagcca tcgttcatcg cttccacttt ggctcctagg ttccacttac
     1621 cagtagagct gttctttaca actgtcataa agctggcttt tcccatgctg atcagctcgc
     1681 tgatgaattt gcgagagctg attgagccgg cagtgttcca tgagccatct cggtttattt
     1741 tatgaacttt tacgaattcg atgtgctgac cagcactgtc cattttgatt gctgagatat
     1801 agaaatctac catggttgcc tcctgatggc tgctgggtgt tttacgtaac aaaagcccgc
     1861 gttctgcggg cttttttcat ggaaacattg gatgcaagtg ttccagctct gccgctaaag
     1921 atttgcgact ttttgacagg ctgaattggg tctgcatgtt tacccacgac tctgcagagc
     1981 ggcctacgac cttcgacaat ctaagtgcca tttcatagct taagtctgtt ttcccattta
     2041 acagtctact taaggtagac tgggatacat caagtttatc ggctaactct gcggcaggta
     2101 tttcgaacgg ttccatgaac atttctctga taaactcacc aggatgaaca ggatcgtaaa
     2161 gatttatcat gccttcctct gtttgttttg tatttgatta tacaaaaaaa ttactgcctt
     2221 tcagtatgcg cattgcacaa tgtgcaagtt catgatattg acaaaaaaag cagtcagctt
     2281 taggatactc gttggagtca aagctactgc gtatgtatgg gcttttatgg ccttttcaag
     2341 gcgcagtatt ttacccttag gattcgttga agtcaaatga ggtgattgac ctcaagaaca
     2401 aacttacgtc aattgtttta ataaagcaag ggggcaaaat ggaactaatt aaaatgattt
     2461 taaaatatag atacaggtat agacgaaaaa aatatgggga ttgtagatga taaaaaacat
     2521 aaaacataaa ggacttagga gctttgctga agaaggtagc accgccggta ttcagcccag
     2581 tatggcgaaa agacttcgca tgattttgac tacgctaagc acagcaactt gcattcaaga
     2641 cgttgttgac gttagggcgt tagggtgcca ccccctaaag ggggagcgta aaggcgagta
     2701 ttccgttgaa gttaatggga actggcgggt agttttcaag gttgaggaac caaacgtctt
     2761 agacgttgat cttgaagatt atcattagtt atcaataagt aagttgctaa tccatccaag
     2821 tgaaagtacg gatggattag ggactttatt aaaaaagtaa cctctggaga aagtatgaga
     2881 tcctttatgg ttttattgtt cccgttgatt agcgtaacta ttgctggagt cctagctttt
     2941 cgtggtattg atggctgggg atggttcttg ttagctgctg tactttgtgc aggggctgat
     3001 actgtccaga agcatgtgtc taccaataaa aaggagcctg ctggtgagtg agctgtcttg
     3061 gttcttcctt gactgctttg aatgataaag cgtatcttac tcgccgagac gaaaaaaccg
     3121 cctggggagg cggttttttc gagggttcag taagttgggg aacttctgaa ccgtggtaac
     3181 agggtgtaca agaccgctga aaccaaattc tgtcctttca gtttagccgt agttgggctg
     3241 agacttcaag aactctgtat cagtaatctc ttgtacacct tcttaccagt ggctgctgcc
     3301 agtggcgctt gtgcgtgtct taccgggttg gactcaagac gatagttacc ggataaggcg
     3361 cagcagtcgg actgaacggg gggttcgtgc atacagtcca gcttggagcg aactgccttc
     3421 ccggaactga gtgtcaggcg tggaatgaga taaacgcggc cataacagcg gaatgacacc
     3481 ggtaaaccga atggcaggaa caggagagcg cacgagggag ccatcagggg gaaacgcctg
     3541 atatctttat agtcctgtcg ggtttcgcca ccactgattt gagcgtcagc tttgtgatgc
     3601 ttgtcagggg ggcggagcct atggaaaaac ggccgcttag cggcctttcc ttttccccgt
     3661 cacgcgaccg ct
//
