LOCUS       NZ_CP028552             4686 bp    DNA     circular CON 09-JAN-2024
DEFINITION  Klebsiella variicola strain WCHKP19 plasmid p4_020019, complete
            sequence.
ACCESSION   NZ_CP028552
VERSION     NZ_CP028552.2
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN06909163
            Assembly: GCF_002164805.3
KEYWORDS    RefSeq.
SOURCE      Klebsiella variicola
  ORGANISM  Klebsiella variicola
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4686)
  AUTHORS   Liu,L., Long,H., Feng,Y. and Zong,Z.
  TITLE     The complete genome of Klebsiella variicola strain SCKV020019
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4686)
  AUTHORS   Liu,L., Long,H., Feng,Y. and Zong,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-AUG-2019) Center of Infectious Diseases, West China
            Hospital, Sichuan University, Guoxuexiang 37, Chengdu, Sichuan
            610041, China
  REMARK    Sequence update by submitter
REFERENCE   3  (bases 1 to 4686)
  AUTHORS   Liu,L., Long,H., Feng,Y. and Zong,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-APR-2018) Center of Infectious Diseases, West China
            Hospital, Sichuan University, Guoxuexiang 37, Chengdu, Sichuan
            610041, China
REFERENCE   4  (bases 1 to 4686)
  AUTHORS   Liu,L., Feng,Y. and Zong,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-MAY-2017) Center of Infectious Diseases, West China
            Hospital, Sichuan University, Guoxuexiang 37, Chengdu, Sichuan
            610041, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200.0x
            Sequencing Technology             :: Illumina HiSeq; MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/09/2024 03:01:59
            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)                     :: 6,078
            CDSs (total)                      :: 5,951
            Genes (coding)                    :: 5,745
            CDSs (with protein)               :: 5,745
            Genes (RNA)                       :: 127
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 206
            CDSs (without protein)            :: 206
            Pseudo Genes (ambiguous residues) :: 0 of 206
            Pseudo Genes (frameshifted)       :: 75 of 206
            Pseudo Genes (incomplete)         :: 137 of 206
            Pseudo Genes (internal stop)      :: 48 of 206
            Pseudo Genes (multiple problems)  :: 47 of 206
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP028552.2.
            On Aug 26, 2019 this sequence version replaced NZ_CP028552.1.
            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..4686
                     /organism="Klebsiella variicola"
                     /mol_type="genomic DNA"
                     /strain="WCHKP19"
                     /host="Homo sapiens"
                     /db_xref="taxon:244366"
                     /plasmid="p4_020019"
                     /geo_loc_name="China: Meishan, Sichuan"
                     /collection_date="2016-10"
     gene            complement(782..1183)
                     /locus_tag="CAY66_RS02465"
                     /old_locus_tag="CAY66_02550"
     CDS             complement(782..1183)
                     /locus_tag="CAY66_RS02465"
                     /old_locus_tag="CAY66_02550"
                     /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_080843463.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1183..1374)
                     /locus_tag="CAY66_RS02470"
                     /old_locus_tag="CAY66_02555"
     CDS             complement(1183..1374)
                     /locus_tag="CAY66_RS02470"
                     /old_locus_tag="CAY66_02555"
                     /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_004187666.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1791..1937
                     /locus_tag="CAY66_RS31965"
                     /old_locus_tag="CAY66_02565"
     CDS             1791..1937
                     /locus_tag="CAY66_RS31965"
                     /old_locus_tag="CAY66_02565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /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_087499206.1"
                     /translation="MHDPPVQSDCCALSGNYHLESNPERRAKAPLAAATGKGVYKRLLV
                     QSS"
                     /name="replication initiation protein"
     gene            2301..3812
                     /locus_tag="CAY66_RS02485"
                     /old_locus_tag="CAY66_02570"
     CDS             2301..3812
                     /locus_tag="CAY66_RS02485"
                     /old_locus_tag="CAY66_02570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001577354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_087499205.1"
                     /translation="MTRINLDNILNEQGPCLTSELAETLVKNFGFTPAAARKRISRGTN
                     KIRKLSYIIFPHRARFIYLKKDYASEKYWNALYSSLRKENSSYYMAIRCIKSRGGMIKR
                     DEFGILCGSPFRQKNHIPYESIISSLIKSEIILEISSASGDRYLYLKEFEGSEHFLLEG
                     QNKKELISGIMIEQSRTWLKQLGLVSFGKVKAMGDDNNHPRVGTFEWHITGPSYTHPLT
                     KKYDNKTKPGFVVCDLNTQPITTLDDISIFIKKMDMTISMKNIGNCIFVYISNCYTEEA
                     LYLAKSKGVMAITYNNIFGKRNITAIDKISEILGNKWHDENLSGELARLTKELNERNGI
                     TQNLKGRLFEFICSDIKRRIEPTSRLILGREYITTQNERAEADITSIRDEVSISFIECK
                     GIKRESNLDDKQVDQWLDVRIPRLINYCKSHPDYKKLKKSFELWITGGLTEQSEIRIEH
                     FKKTHPKVDLIIKKPEDLIRHVKEINDRSIKKMLFEYFLKMERAQ"
                     /name="hypothetical protein"
     gene            3933..4019
                     /locus_tag="CAY66_RS02490"
                     /old_locus_tag="CAY66_02575"
     tRNA            3933..4019
                     /locus_tag="CAY66_RS02490"
                     /old_locus_tag="CAY66_02575"
                     /product="tRNA-Ile"
                     /inference="COORDINATES: profile:tRNAscan-SE:2.0.12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: tRNAscan-SE."
                     /anticodon=(pos:3967..3969,aa:Ile,seq:aat)
                     /name="tRNA-Ile"
     gene            4190..4265
                     /locus_tag="CAY66_RS02495"
                     /old_locus_tag="CAY66_02580"
     tRNA            4190..4265
                     /locus_tag="CAY66_RS02495"
                     /old_locus_tag="CAY66_02580"
                     /product="tRNA-Arg"
                     /inference="COORDINATES: profile:tRNAscan-SE:2.0.12"
                     /note="Derived by automated computational analysis using
                     gene prediction method: tRNAscan-SE."
                     /anticodon=(pos:4223..4225,aa:Arg,seq:tct)
                     /name="tRNA-Arg"
     gene            complement(4390..4662)
                     /locus_tag="CAY66_RS02500"
                     /old_locus_tag="CAY66_02585"
     CDS             complement(4390..4662)
                     /locus_tag="CAY66_RS02500"
                     /old_locus_tag="CAY66_02585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004897311.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_019405140.1"
                     /translation="MATDAQVKEINALIKKYPDSCSICHEVYDEDDVTYTVFGYDRKGK
                     IQVTTGCCAGMLTEPVLLGVCGCFDPEERDEIMQNHPMAKQFFTE"
                     /name="hypothetical protein"
     Typing          1420..1959
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.906"
                     /coverage="90.0"
                     /evalue="1.47e-178"
ORIGIN
        1 tcacaatccg ctgactctaa cacagactca ggcatccgcc gttgatttac cataacgtcc
       61 cattgtacgc accgctaaaa cggcctcagg gcgtttccga cgggaaaccg gtaaaacagg
      121 caacaaacca cccgaaaacc cgccagaaac gcgcaggctc tgtttttacg gcatgcatga
      181 gtatgcacgc aagtgcatag cgcgaaaatt cacgccattc agccagggta agtcctgttt
      241 ccggcgttct tcctatccga aaacggtgaa cggggacgca atttattgcg tggccgtgaa
      301 gcgttgccgg cgcagccgga aaaccggttt tcagcacgat caggaatcgg gttcgtcgac
      361 ggccggcaat cacgttatgg caagtcgccg gacgactcac cacacgattc accggcgatt
      421 cgactcgtga cttgactcta gagtcgtcaa ggtcaaaaaa acaccaaaat gacgattcga
      481 ctctagagtc aagtcgtcat aagttactga tagtcttaag tgagtcgtcg atgactctat
      541 gacgagtcgt cggcaagtcg tacacgaatc gccgacgact tggattcacc ttacagaaag
      601 taatactgcg taatgtaata acccacaact aactgatatt aatgagttat cttcaaaatt
      661 ttaattttgc gtggggtgtg ggtattttta gtggtgagga gcgttcagag atctgacgat
      721 ttttgggaag gttcaggaac tccccgggat ggccggagag gaaaactgaa gcatgacggg
      781 gtcaggattt tttccagaat ttccaccatg gcgacgggga ttcagttaat tttgcctggt
      841 gattttcaag aaggagcatg gcctgtttca ggctgtcaat gtgcgaatcc ttggacaaaa
      901 gtaaggtgtt caggtgttca atctcctgtt tcagatgacg aatcacctgt tcactctggt
      961 cagcagaggc tgtatcacgc tgttcagaga cctgtccaga atggtgttca cccttcggtt
     1021 gttcaaaggg accaaagaca cgtaaaagct ctgaagtatc taccattttt gcatttcgtt
     1081 caccgctaca ggtggacagg tcacctgctt taattaacct gtgcagtgtt gttctactct
     1141 tacccgtcag tcgggcagcc tcactaatag acactctggc catcagttac catcctgtaa
     1201 tgcatccagt ctcgaggaca gtgtacggaa aagatgctcc gcatcatcgt ggagtttctc
     1261 acaaaggtcg gcctcgacat cgagatcaag ctcgttaagc ttctccagca ggagcagaga
     1321 ctgattctgg atgaatttag ccatgttcag cgctgttttc tgttgtttcg tcataagagg
     1381 cctcagagcg tcagtgctca atgtagggat gttctctttt ccgcttcctc gctcactcag
     1441 tcgctacgct cctgccgttc ggctgcggcg agcggcaagg gcatgcgtgt aagaactcga
     1501 gaaaaccgag cggtaacgta agagagaaag tgtaaggccg agcgacggcc gttttttcca
     1561 taggctccgc ccccctgaca agcatcacaa aatctgacgc tcaaatcagt ggtggcgaaa
     1621 cccgacagga ctataaagat atcaggcgtt tccccctgat ggctccctcg tgcgctctcc
     1681 tgttcctgcc tttcggttta ccggtgtcat tccgctgtta tggccgcgtt tatctcattc
     1741 cacgcctgac actcagctcc gggtaggcag ttcgctccaa gctggactgt atgcacgacc
     1801 cccccgttca gtccgactgc tgcgccttat ccggtaacta tcatcttgag tccaatccgg
     1861 aaagacgcgc aaaagcgcca ctggcagcag ccactggtaa aggggtgtac aagagattac
     1921 tggtgcagag ttcttgaagt tgaagcctga ctacggctac actgaaagga cagatttggt
     1981 tgcagcggtc ttgtacaccc tgttaccacg gttcagaaac ttgcaggtct ctgatccttc
     2041 gaaaaagccg ccttgcaggg cggttttttc gtatctgaag ctaggttaat ctcatacatc
     2101 aattcgcgtc aagaaaacaa acctgcctca gcaagctcat ttacaggaaa aaaaatccta
     2161 ttgtgacgtt ttttgtagaa agtccagaat cccccctcta aaacccagtc tctatgcgcc
     2221 atcgctagaa ttttttttcg cttctgctag cctgcacgat agtgcagatt ataaatagcg
     2281 tagtgtgacg tgagcaaaaa atgaccagaa taaaccttga taatattttg aatgaacagg
     2341 gcccttgcct aacctccgaa cttgccgaaa cattggtaaa aaattttggt tttacaccgg
     2401 cagcagcgag gaaaaggata tctaggggga ctaataaaat tagaaaactc tcttacataa
     2461 tattccccca cagggctaga tttatttatc tgaaaaagga ctatgcgtca gaaaaatact
     2521 ggaatgctct atactcctca ttgaggaaag aaaactcctc ttattatatg gctatcagat
     2581 gcataaaaag cagaggagga atgataaaaa gagatgagtt tggtatttta tgcggctccc
     2641 cttttcggca gaaaaatcat ataccttacg aatcaataat atcctcacta ataaaatcag
     2701 aaataatatt agaaatatca agcgctagcg gagacagata tttatactta aaagagtttg
     2761 agggaagtga acattttcta ctagaagggc aaaacaaaaa agaattgatt tctgggataa
     2821 tgatagagca atccaggacc tggttaaagc agcttggttt agttagtttt ggaaaagtaa
     2881 aggcaatggg tgatgataac aaccatcctc gcgttggcac atttgaatgg catataactg
     2941 gaccatccta tactcaccct ctaacaaaaa aatacgataa caaaacgaaa ccaggattcg
     3001 ttgtttgcga cttaaacaca cagccaatca caacccttga cgatatatcc atttttataa
     3061 aaaaaatgga tatgacgata tcaatgaaga acatcggaaa ctgtatattt gtatacatat
     3121 caaattgtta cactgaagaa gctttgtacc ttgcaaaatc aaagggtgtg atggctataa
     3181 catataataa tatttttgga aaaagaaata taaccgcaat tgataaaata agcgagatat
     3241 tgggaaataa atggcatgat gaaaacttat caggagagtt agctagatta accaaagagc
     3301 taaatgaaag aaacggcata actcaaaatc taaaaggtag actctttgag ttcatttgct
     3361 cagatatcaa aaggcgcata gagccaacat ccagattgat attaggaagg gagtacataa
     3421 ccacacagaa tgaaagggca gaggcagata tcacatcgat aagggatgaa gtatcgatat
     3481 ccttcattga atgcaaagga ataaaaagag aaagtaatct tgatgataaa caagtagatc
     3541 aatggctaga tgtaaggata cctaggctta taaattattg taaatcacat cctgattaca
     3601 aaaaactaaa aaaatccttc gaactctgga ttacaggggg tttaacagag caatctgaaa
     3661 tcagaataga gcattttaaa aaaacgcacc caaaagtgga tttaattatt aaaaaaccag
     3721 aagacttgat ccgtcatgtt aaagaaataa atgatcgctc tataaagaaa atgctttttg
     3781 aatacttctt aaaaatggaa agggctcagt aaaattaaag ccttgcctca tagatgtagg
     3841 ttggtaaaaa cgtcaacaag aatgcatgat tgttactttt tttcatggac atcatctttc
     3901 cgacaatcaa taatggtcat cccccataca gtggagggat ggccgagttg gtgaaggcag
     3961 tcgcctaata agcgaccaaa cgctttgcgt ttcgcgggtt cgagtcccgc tccctattaa
     4021 aaaaaggcgc cctttagggc gcctttttgc atctgtctgt tttctaaagt tataataacg
     4081 tctcatcaca taccctgttc agccaccacc gataaccaca taaaaaactt cacaaaaata
     4141 atgcaatgat gttaaatcaa agacggtccc gactttgttg ggtccaaatg gggatatagc
     4201 tttaacggta gagcagcgga cttctaatct gatggttgtg ggttcaaatc ccattgtctc
     4261 caccaaaagc ctccccccct aaaaaggggg aggcaactat tctgttcaca gcatttacca
     4321 taacgcctaa tttcacgcag atatgaaaaa gcccgcacaa ggcgggcttc agactcaaca
     4381 gatacggaat cactctgtga aaaactgctt tgccatgggg tgattctgca tgatctcgtc
     4441 acgttcttcc gggtcaaagc acccacagac acccagcaga accggctctg tcagcattcc
     4501 ggcacagcat cccgtggtga cctgtatttt acctttccgg tcatacccaa aaacggtgta
     4561 ggtcacatca tcctcatcat agacttcatg acagatggag catgagtccg ggtatttttt
     4621 gatgagtgca ttaatttctt ttacctgagc gtcagtagcc aaaacatctc cctgagtcac
     4681 tgatta
//
