LOCUS       NZ_CP067264             4001 bp    DNA     circular CON 05-JAN-2024
DEFINITION  Klebsiella variicola strain E25 plasmid pE25c, complete sequence.
ACCESSION   NZ_CP067264
VERSION     NZ_CP067264.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17214842
            Assembly: GCF_017639085.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella variicola
  ORGANISM  Klebsiella variicola
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4001)
  AUTHORS   Biggel,M.
  TITLE     Characterization of fosA carrying plasmids from multidrug resistant
            Enterobacteriaceae food and environmental isolates
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4001)
  AUTHORS   Biggel,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-JAN-2021) Institute for Food Safety and Hygiene,
            University of Zurich, Winterthurerstrasse 272, Zurich 8057,
            Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Illumina MiniSeq, Oxford Nanopore MinIon
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/05/2024 08:05:16
            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)                     :: 5,490
            CDSs (total)                      :: 5,367
            Genes (coding)                    :: 5,254
            CDSs (with protein)               :: 5,254
            Genes (RNA)                       :: 123
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 113
            CDSs (without protein)            :: 113
            Pseudo Genes (ambiguous residues) :: 0 of 113
            Pseudo Genes (frameshifted)       :: 45 of 113
            Pseudo Genes (incomplete)         :: 62 of 113
            Pseudo Genes (internal stop)      :: 28 of 113
            Pseudo Genes (multiple problems)  :: 20 of 113
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP067264.1.
            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..4001
                     /organism="Klebsiella variicola"
                     /mol_type="genomic DNA"
                     /strain="E25"
                     /isolation_source="imported food: soy sprout"
                     /db_xref="taxon:244366"
                     /plasmid="pE25c"
                     /geo_loc_name="Switzerland: Zurich"
                     /collection_date="2014"
                     /collected_by="ILS, University of Zurich"
     gene            complement(join(3771..4001,1..492))
                     /locus_tag="JJB14_RS27310"
                     /old_locus_tag="JJB14_27305"
     CDS             complement(join(3771..4001,1..492))
                     /locus_tag="JJB14_RS27310"
                     /old_locus_tag="JJB14_27305"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_099119321.1"
                     /translation="MKKKSNNNQCELEHSRFNYDGISSGDVKSFFSSYDDEVLLLKNYT
                     SGSELFNNEDYDSRNLKYSDQDVVYKIEYDNACKPDGDIKEWSSWVGEFRKISGRIIDC
                     KIISDVIDVINDFNSLGLVELKLKDAFFGCESLPADIKTKKSLINFLKHYPELRKYSDT
                     ISVDYDLSLNVIAVSLRGDNHDGRYMNIQFESDGVITFFSKDADKDDSAYYISGRMFSA
                     KKVAKSYKIRSLFSILND"
                     /name="hypothetical protein"
     gene            complement(473..706)
                     /locus_tag="JJB14_RS27315"
                     /old_locus_tag="JJB14_27310"
     CDS             complement(473..706)
                     /locus_tag="JJB14_RS27315"
                     /old_locus_tag="JJB14_27310"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_069346841.1"
                     /translation="MSDEKQEMKRKMPHSFPLTIRVGATDEVAFVDFANRNGDDLEAFS
                     SVVLTKRVARNLIKQLSEFAGVEIVGNEEKIK"
                     /name="hypothetical protein"
     gene            complement(1741..2142)
                     /locus_tag="JJB14_RS27320"
                     /old_locus_tag="JJB14_27315"
     CDS             complement(1741..2142)
                     /locus_tag="JJB14_RS27320"
                     /old_locus_tag="JJB14_27315"
                     /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_069346840.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKDELHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNSLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(2142..2333)
                     /locus_tag="JJB14_RS27325"
                     /old_locus_tag="JJB14_27320"
     CDS             complement(2142..2333)
                     /locus_tag="JJB14_RS27325"
                     /old_locus_tag="JJB14_27320"
                     /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            2749..2861
                     /locus_tag="JJB14_RS27685"
                     /pseudo=""
     CDS             2749..2861
                     /locus_tag="JJB14_RS27685"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            complement(3147..3755)
                     /locus_tag="JJB14_RS27330"
                     /old_locus_tag="JJB14_27325"
     CDS             complement(3147..3755)
                     /locus_tag="JJB14_RS27330"
                     /old_locus_tag="JJB14_27325"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_138069329.1"
                     /translation="MTSVSSPYFGDDEDLVFDFSFDLDVSEKIKLIRQGLSNIDRLWRS
                     VRRKNCASNVSPAAFSLRVKFDGENVIWKEPALSFYEMIIKNDSDLQGEADSFMEFMIN
                     EGPFDVKSDVPVLLCLNGFFSCAEYSHVIYSFIDGISKTSPQKEQHTKAYHWDFEYVKQ
                     QDSLEIRSIMAHHSIAYLNNCLELNKEVMKQRKCKKLAH"
                     /name="hypothetical protein"
     Typing          2455..2861
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.088"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 aatagtatcg ctatattttc ttagctcagg atagtgtttc aagaagttga tgagtgattt
       61 ttttgtcttt atatctgccg gcaaactctc acacccaaaa aaggcatctt taagctttaa
      121 ctcaacaagc ccaagtgaat taaagtcatt tatcacatca ataacatcac ttattatttt
      181 acaatcaata atgcggccag atatttttct aaactcacca acccatgaag accactcctt
      241 aatatcgcca tcaggtttac acgcattatc gtattctatt ttgtagacga catcctggtc
      301 gctatacttt agattacgag agtcgtaatc ttcattatta aatagttcag agccagaggt
      361 gtaatttttc aaaagaagca cctcatcatc ataggatgaa aaaaaactct tcacatcacc
      421 cgagcttatc ccatcataat taaaacgcga gtgttctaat tcacattgat tattatttga
      481 ttttttcttc attgcctaca atctccacgc cggcaaattc agataattgt tttatcaagt
      541 ttcttgccac tcttttagtc aggacaacac ttgaaaaggc ctccaaatcg tcaccattgc
      601 ggttagcaaa atcaacaaaa gcaacctcat cagtagcccc gacacgaata gtcagaggga
      661 atgaatgagg catttttctt ttcatttctt gcttttcatc agacataaaa atctccacca
      721 ttataaaaaa agttttttac gcacatcaat tatcgcacat aatcacttga tctatagtgc
      781 atttttcaac ataaaattca ataatttaaa acaacagcct aaacatagca gctcgcacca
      841 accccagaat ccaaccctaa catttatttt attcgcgtct aaatgatata aattattccc
      901 cccccccaac gaagatggtc acaaaggaaa cagctaaaca ggtctacagg gggtcagtcc
      961 gcttcatcca taaagccact tcagtttttg ttgcgcctgt tatttaacat aaagccatga
     1021 ttgtacgcac cgctaaaacg gcctcagggc gtttctgacg ggaaaccggt aaaacaggca
     1081 acaaaccacc cgaaaacccg ccagaaacgc gcaggctctg tttttacggc atgcatgagt
     1141 atgcacgcaa gtgcatagcg cgaaaattca cgccattcag ccagagtaag tcctgtttcc
     1201 ggcgttcttt ccatccgaaa acggtgaacg gggacgcaat ttattgcgtg gccgtgaagc
     1261 gttgccggcg cagccggaaa accggttttc agcacgttca ggaatcgggt tcgtcgacgg
     1321 ccggcaatca cgttatggca agtcgccgga cgactcacca cacgactcta ggtacgactc
     1381 ttcactagag tcgtacctag agtcgctgcg tctaaaaaac aaccaaacgg ggagtcgtgt
     1441 ctagagtcgg gtcgttatta acttattgtt tttatagtcc tgagtcgtta ccgactctat
     1501 gacgactcgc cggggactct atgacgagtc gtcatagagt cggatctata taaataaaat
     1561 ttaaaaaacg aaatttcagt aaagtaacca actgatatta aatacaaatc tgcaaaatgt
     1621 taattttgcg tggggtgtgg gtatttttag tggtgaggag cgttcagaga tctgacgatt
     1681 tttgggaagg ttcaggaact ccccgggatg gccggagagg aaaacggaag catgacgggg
     1741 tcaggatttt ttccagaatt tccaccatgg cgccggggat tcagttaatt ttgcctggtg
     1801 attttcaaga aggagcatgg cctgtttcag gctgtcaatg tgcgaatcct tggacaaaag
     1861 taaggagttc aggtgttcaa tctcctgttt cagatgacga atcacctgtt cactctggtc
     1921 agcagaggct gtatcacgct gttcagagac ctgtccagaa tggagttcat ccttcggttg
     1981 ttcaaaggga ccaaagacac gcaaaagctc tgaagtatct accatttttg cattgcgttc
     2041 accgctacag gtggacaggt cacctgcttt aattaacctg tgtagtgttg ttctactctt
     2101 acccgtcagt cgggcagcct cactaataga cactctggcc atcagttacc atcctgtaat
     2161 gcatccagtc tcgaggacag tgtacggaaa agatgctccg catcatcgtg gagtttctca
     2221 caaaggtcgg cctctacatc aagatcaagc tcattaagct tctctagcag gagcagagac
     2281 tgattctgga tgaatttagc catgttcagc gctgttttct gttgtttcgt cataagaggc
     2341 ctcagagcgt cagtgctcag tgtagggatg ttctcttttc cgcttcctcg ctcactcagt
     2401 cgctatgctc ctgccgttcg gctgcggcga gcggcaggag catgcgtata aaagctcgag
     2461 aaaaccgagc ggtcgcgtga cgggaaaaag gaaaggccgc taagcggccg tttttccata
     2521 ggctccgccc ccctgacaag catcacagaa actgacgctc aaatcagtgg tggcgaaacc
     2581 cgacaggact ataaagatat caggcgtttc cccctgatgg ctccctcgtg cgctctcctg
     2641 ttcctgccat tcggtttacc ggtgtcattc cgctgttatg gccgcgttta tctcattcca
     2701 cgccagacac tcagttccgg gaaggcagtt cgctccaagc tggactgtat gcacgaaccc
     2761 cccgttcagt ccgaccgctg cgccttaacc ggtaactatc atcttgagtc caacccggaa
     2821 agacacgaaa aacgccactg gcagcagcca ttggtaactg atttagagga gatagtcttg
     2881 aagtcatgcg cctgttaagg ctaaactgaa agaacaagtt ttggtgactg cgctcctcca
     2941 agccagtaac cttggttcca ccacctgcaa gtggctgaac cttcgaagaa accgccctgc
     3001 aaggcggttt cttcgttttc gtccacagaa gattacaatt tgcgttgaag aagtacaagg
     3061 acaacaaagc aaaagaggtg attgactaaa aatcacccct tggattgaaa atgaaaaaac
     3121 accatcacaa caacaatgca aatacatcaa tgagctaatt ttttgcattt cctttgtttc
     3181 atcacttcct tatttaattc caggcaatta tttagatatg ctattgaatg gtgtgccata
     3241 atggaccgaa tctctaaaga gtcttgttgt tttacatatt caaaatccca gtgataagct
     3301 ttggtgtgct gttctttttg tggcgatgtc ttagatatac catcaataaa agaatatata
     3361 acatgtgaat actcagcgca ggaaaaaaaa ccatttagac acaaaagcac tggcacatca
     3421 gacttcacat caaaaggccc ctcatttatc atgaactcca taaaagaatc agcctcgccc
     3481 tgcaaatcac tatcattttt tattatcatt tcataaaaac ttaacgctgg ctctttccat
     3541 ataacatttt caccatcaaa tttaaccctc aaagaaaagg ctgcgggact aacattacta
     3601 gcgcaatttt ttcgtctcac agatcgccag agtctatcta tatttgatag accctgtctt
     3661 atcaatttta ttttttcgct gacatccaag tcaaaagaaa aatcaaaaac caaatcttca
     3721 tcatccccaa aatacggtga agaaacagaa gtcatatgtc gaccacctta ttaatcattg
     3781 agaatagaaa ataaacttct tattttgtaa gacttagcca ctttcttagc tgaaaacatc
     3841 ctcccagata tatagtaagc agagtcatct ttatcagcgt ctttggagaa gaatgttatg
     3901 actccatcac tctcaaactg tatattcata taccggccat cgtgattatc accacgcaaa
     3961 ctaacagcaa taacatttag agagaggtcg taatcaacag a
//
