LOCUS       NZ_CP114336             3672 bp    DNA     circular CON 18-FEB-2024
DEFINITION  Klebsiella variicola strain 2022CK-00505 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP114336
VERSION     NZ_CP114336.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31261057
            Assembly: GCF_025676845.1
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-00505
  JOURNAL   Unpublished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 (12-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                   :: 73.0x
            Sequencing Technology :: Oxford Nanopore GridION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/18/2024 04:48:14
            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)                     :: 5,894
            CDSs (total)                      :: 5,767
            Genes (coding)                    :: 5,609
            CDSs (with protein)               :: 5,609
            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)              :: 158
            CDSs (without protein)            :: 158
            Pseudo Genes (ambiguous residues) :: 0 of 158
            Pseudo Genes (frameshifted)       :: 58 of 158
            Pseudo Genes (incomplete)         :: 97 of 158
            Pseudo Genes (internal stop)      :: 37 of 158
            Pseudo Genes (multiple problems)  :: 29 of 158
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP114336.1.
            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-00505"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:244366"
                     /plasmid="unnamed4"
                     /geo_loc_name="USA"
                     /collection_date="2022-07-26"
     gene            complement(489..890)
                     /locus_tag="OGU18_RS29370"
                     /old_locus_tag="OGU18_29365"
     CDS             complement(489..890)
                     /locus_tag="OGU18_RS29370"
                     /old_locus_tag="OGU18_29365"
                     /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(890..1081)
                     /locus_tag="OGU18_RS29375"
                     /old_locus_tag="OGU18_29370"
     CDS             complement(890..1081)
                     /locus_tag="OGU18_RS29375"
                     /old_locus_tag="OGU18_29370"
                     /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            1496..1642
                     /locus_tag="OGU18_RS29380"
                     /old_locus_tag="OGU18_29375"
     CDS             1496..1642
                     /locus_tag="OGU18_RS29380"
                     /old_locus_tag="OGU18_29375"
                     /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(2100..2381)
                     /locus_tag="OGU18_RS29385"
                     /old_locus_tag="OGU18_29380"
     CDS             complement(2100..2381)
                     /locus_tag="OGU18_RS29385"
                     /old_locus_tag="OGU18_29380"
                     /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            2718..3011
                     /locus_tag="OGU18_RS29390"
                     /old_locus_tag="OGU18_29385"
     CDS             2718..3011
                     /locus_tag="OGU18_RS29390"
                     /old_locus_tag="OGU18_29385"
                     /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            3075..3377
                     /locus_tag="OGU18_RS29395"
                     /old_locus_tag="OGU18_29390"
     CDS             3075..3377
                     /locus_tag="OGU18_RS29395"
                     /old_locus_tag="OGU18_29390"
                     /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"
     Typing          1203..1605
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.79"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gtcgtgagcc gttgccggcg cagccggaaa acccgttttc agcacgttca ggaatcgggt
       61 tcgtcgacgg ccggcaatca cgttatggca agtcgccgga cgactcacca cacgattcac
      121 cggcgattcg actcgtgaat tgaatcaaga gtcaccatga acaaaaaaca cccaaagtga
      181 tgaattgaat caagagtcaa ttcatcataa ccatatgata ataaagcgtg attcacatat
      241 gaatcgtggg caattcgtca gcgattcgcc atagagtcgc ccacgactcg gattcacctt
      301 acaaaaaata aaattgcgta atttacaata gataactaat tgaaactaaa ggtctatctg
      361 caaaatttta attttgcgtg gggtgtgggt atttttcgtg gtgaggagtg ctcagagatc
      421 tggcgatttt tgggaaggtt caggaactcc ccggaatgac cggagaggaa aactgaagca
      481 tgacgcggtc aggatttttt ccagaatttc caccatggcg ccggggattc agttaatttt
      541 gcctggtgat tttcaagaag gagcatggcc tgtttcaggc tgtcaatgtg cgaatccttg
      601 gacaaaagta aggtgttcag gtgttcaatc tcctgtttca gatgacgaat cacctgttca
      661 ctctggtcag cagaggctgt atcacgctgt tcagagacct gtccagaatg gtgttcaccc
      721 ttcggttgct caaagggacc aaagacacgt aaaagctctg aagtatctac catttttgca
      781 ttacgtgcac cgctacaggt ggacaggtca cctgctttaa ttaacctgtg cagtgttgtt
      841 ctactcttac ccgtcagtcg ggcagcctca ctaatagaca ctctggccat cagttatcat
      901 cctgtaatgc atccagtctc gaggacagtg tacggaaaag atgctccgca tcatcgtgga
      961 gtttctcaca aaggtcggcc tcgacatcaa gatcaagctc gttaagcttc tccagcagga
     1021 gcagagactg attctggatg aatttagcca tgttcagcgc tgttttctgt tgtttcgtca
     1081 taagaggcct cagagcgtca gtgctcagtg tagggatgtt ctcttttccg cttcctcgct
     1141 cactcagtcg ctatgctcct gccgttcggc tgcggcgagc ggcaggagca tgcgtataaa
     1201 agctcgagaa aaccgagcgg tcgcgtgacg gggaaaagga aaggccgcta agcggccgtt
     1261 tttccatagg ctccgccccc ctgacaagca tcacaaagct gacgctcaaa tcagtggtgg
     1321 cgaaacccga caggactata aagatatcag gcgtttcccc ctgatggctc cctcgtgcgc
     1381 tctcctgttc ctgccattcg gtttaccggt gtcattccgc tgttatggcc gcgtttatct
     1441 cattccacgc ctgacactca gttccgggaa ggcagttcgc tccaagctgg actgtatgca
     1501 cgaacccccc gttcagtccg actgctgcgc cttatccggt aactatcgtc ttgagtccaa
     1561 cccggtaaga cacgcacaag cgccactggc agcagccact ggtaagaagg tgtacaagag
     1621 attactgata cagagttctt gaagtctcag cccaactacg gctaaactga aaggacagaa
     1681 tttggtttca gcggtcttgt acaccctgtt accacggttc agaagttccc caacttactg
     1741 aaccctcgaa aaaaccgcct ccccaggcgg ttttttcgtc tcggcgagta agatacgctt
     1801 tatcattcaa agcagtcaag gaagaaccaa gacagctcac tcaccagcag gctccttttt
     1861 attggtagac acatgcttct ggacagtatc agcccctgca caaagtacag cagctaacaa
     1921 gaaccatccc cagccatcaa taccacgaaa agctaggact ccagcaatag ttacgctaat
     1981 caacgggaac aataaaacca taaaggatct catactttct ccagaggtta cttttttaat
     2041 aaagtcccta atccatccgt actttcactt ggatggatta gcaacttact tattgataac
     2101 taatgataat cttcaagatc aacgtctaag acgtttggtt cctcaacctt gaaaactacc
     2161 cgccagttcc cattaacttc aacggaatac tcgcctttac gctccccctt tagggggtgg
     2221 caccctaacg ccctaacgtc aacaacgtct tgaatgcaag ttgctgtgct tagcgtagtc
     2281 aaaatcatgc gaagtctttt cgccatactg ggctgaatac cggcggtgct accttcttca
     2341 gcaaagctcc taagtccttt atgttttatg ttttttatca tctacaatcc ccatattttt
     2401 ttcgtctata cctgtatcta tattttaaaa tcattttaat tagttccatt ttgccccctt
     2461 gctttattaa aacaattgac gtaagtttgt tcttgaggtc aatcacctca tttgacttca
     2521 acgaatccta agggtaaaat actgcgcctt gaaaaggcca taaaagccca tacatacgca
     2581 gtagctttga ctccaacgag tatcctaaag ctgactgctt tttttgtcaa tatcatgaac
     2641 ttgcacattg tgcaatgcgc atactgaaag gcagtaattt ttttgtataa tcaaatacaa
     2701 aacaaacaga ggaaggcatg ataaatcttt acgatcctgt tcatcctggt gagtttatca
     2761 gagaaatgtt catggaaccg ttcgaaatac ctgccgcaga gttagccgat aaacttgatg
     2821 tatcccagtc taccttaagt agactgttaa atgggaaaac agacttaagc tatgaaatgg
     2881 cacttagatt gtcgaaggtc gtaggccgct ctgcagagtc gtgggtaaac atgcagaccc
     2941 aattcagcct gtcaaaaagt cgcaaatctt tagcggcaga gctggaacac ttgcatccaa
     3001 tgtttccatg aaaaaagccc gcagaacgcg ggcttttgtt acgtaaaaca cccagcagcc
     3061 atcaggaggc aaccatggta gatttctata tctcagcaat caaaatggac agtgctggtc
     3121 agcacatcga attcgtaaaa gttcataaaa taaaccgaga tggctcatgg aacactgccg
     3181 gctcaatcag ctctcgcaaa ttcatcagcg agctgatcag catgggaaaa gccagcttta
     3241 tgacagttgt aaagaacagc tctactggta agtggaacct aggagccaaa gtggaagcga
     3301 tgaacgatgg ctacataacc acagatccaa acaaaactaa actcgataac ttgggaaatc
     3361 tgccgaaatt tgtctgatat gcaataacat ccactaagtt ccagcagaat cccctcccta
     3421 atgatttaac ataaagtcat aattgtacgc accgctaaaa cggcctcatg gcgtttctga
     3481 cgggaaaccg gtaaaacagg caacaaacca cccgaaaacc cgccagaaac gcgcaggctc
     3541 tgtttttacg gcatgcatga gtatgcacgc aagtgcatag ctcgaaaatt cacgccattc
     3601 agccagggta agtcctgttt ccggcgttct ttccatccga aaacggtgaa cggggacgca
     3661 atttattgcg tg
//
