LOCUS       NZ_CP124808             3629 bp    DNA     circular CON 14-MAY-2024
DEFINITION  Klebsiella variicola strain J57 plasmid unnamed3, complete sequence.
ACCESSION   NZ_CP124808
VERSION     NZ_CP124808.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14640320
            Assembly: GCF_030007315.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella variicola
  ORGANISM  Klebsiella variicola
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3629)
  AUTHORS   Fernandez-Calvet,A., Toribio-Celestino,L., Alonso-del Valle,A.,
            Sastre-Dominguez,J., Valdes-Chiara,P., DelaFuente,J. and San
            Millan,A.
  TITLE     The distribution of fitness effects of plasmid pOXA-48 in clinical
            enterobacteria
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3629)
  AUTHORS   Toribio-Celestino,L. and San Millan,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-APR-2023) Microbial Biotechnology, Centro Nacional de
            Biotecnologia-CSIC, Darwin, 3, Madrid 28049, Spain
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology             :: Illumina HiSeq; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030007315.1-RS_2024_05_14
            Annotation Date                   :: 05/14/2024 05:15:43
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,826
            CDSs (total)                      :: 5,703
            Genes (coding)                    :: 5,538
            CDSs (with protein)               :: 5,538
            Genes (RNA)                       :: 123
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 165
            CDSs (without protein)            :: 165
            Pseudo Genes (ambiguous residues) :: 0 of 165
            Pseudo Genes (frameshifted)       :: 62 of 165
            Pseudo Genes (incomplete)         :: 97 of 165
            Pseudo Genes (internal stop)      :: 41 of 165
            Pseudo Genes (multiple problems)  :: 31 of 165
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP124808.1.
            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..3629
                     /organism="Klebsiella variicola"
                     /mol_type="genomic DNA"
                     /strain="J57"
                     /isolation_source="Human gut"
                     /host="Homo sapiens"
                     /db_xref="taxon:244366"
                     /plasmid="unnamed3"
                     /geo_loc_name="Spain"
                     /lat_lon="40.416500 N 3.702560 W"
                     /collection_date="2013-08-20"
                     /collected_by="Ramon y Cajal Health Research Institute
                     (IRYCIS)"
     gene            complement(424..825)
                     /locus_tag="QLG20_RS29075"
                     /old_locus_tag="QLG20_29065"
     CDS             complement(424..825)
                     /locus_tag="QLG20_RS29075"
                     /old_locus_tag="QLG20_29065"
                     /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_048270303.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKTGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNILLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(825..1016)
                     /locus_tag="QLG20_RS29080"
                     /old_locus_tag="QLG20_29070"
     CDS             complement(825..1016)
                     /locus_tag="QLG20_RS29080"
                     /old_locus_tag="QLG20_29070"
                     /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_049139654.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEELHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1431..1559
                     /locus_tag="QLG20_RS29085"
                     /old_locus_tag="QLG20_29075"
                     /pseudo=""
     CDS             1431..1559
                     /locus_tag="QLG20_RS29085"
                     /old_locus_tag="QLG20_29075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="internal stop; 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            1788..2228
                     /locus_tag="QLG20_RS29090"
                     /old_locus_tag="QLG20_29080"
     CDS             1788..2228
                     /locus_tag="QLG20_RS29090"
                     /old_locus_tag="QLG20_29080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002642251.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_019704629.1"
                     /translation="MSKYLITFDLDTTKLKTLYHGKNYNNAYYDIRSTLSRRGFENIQG
                     SVYLGQEGISEAHGTIAIQELTAKYSWFYECVSNIKFYRIESDLNAQFIADGVNEARKR
                     FYTQLEDMRKSLLSVGLTVEQVNEIIGQQQFKLESTISPDKM"
                     /name="hypothetical protein"
     gene            2297..2599
                     /locus_tag="QLG20_RS29095"
                     /old_locus_tag="QLG20_29085"
     CDS             2297..2599
                     /locus_tag="QLG20_RS29095"
                     /old_locus_tag="QLG20_29085"
                     /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_128316336.1"
                     /translation="MKIGSTREYGATKSHLLLMITTLPAGVGVFIYPIAEAVWGELPLL
                     KVVGYTALSLMIGGVVGNIVVRGLFSTSLGILFINPLAMISSLTGIAFLIVQYLP"
                     /name="hypothetical protein"
     Typing          1138..1541
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.912"
                     /coverage="99.0"
                     /evalue="1.01e-158"
ORIGIN
        1 acggccggca atcacgttat ggcaagtcac cgaacgactc accacacgat tcaccggcaa
       61 ctcttcacta gagtcgtacc cagagtcgcc acgcctaaaa aacaaccaaa cggggagtcg
      121 ggtctagagt cgggtcgtta ttaactcatt gtttttatag tcctgagtcg ttaccgactc
      181 tatgacgact cgccggggac tctatgacga gtcgtcatag agtcggatct atataaatca
      241 aatttaaaaa acaaaatttt acagacttaa actactgata ttaaatacaa atccgcaaaa
      301 ttttaatttt gcgtagtgtg tgggtatttt tagtggtgag gagcgttcag aaatccggcg
      361 attttttgga aggttcagga actccccggg atggccggag aggaaaacgg aagcatgacg
      421 gggtcaggat tttttccaga atttccacca tggcgccggg gattcagtta attttgcctg
      481 gtgattttca agaaggagca tggcctgttt caggctgtca atgtgcgaat ccttggacaa
      541 aagtaagata ttcaggtgtt caatctcctg tttcagatga cgaatcacct gttcactctg
      601 gtcagcagag gctgtatcac gctgttcaga gacctgtcca gaatggtgtt cacccttcgg
      661 ttgctcaaag ggaccaaaga cacgtaaaag ctctgaagta tctaccattt ttgcattgcg
      721 ctcaccacta caggtggaca ggtcacctgt tttaattaac ctgtgcagtg ttgtcctact
      781 cttgcccgtc agtcgggcag cctcactaat agacactctg gccatcagtt accatcctgt
      841 aatgcatcca gtctcgagga cagtgtacgg aaaagatgct ccgcatcatc gtggagttcc
      901 tcacaaaggt cggcctcgac atcgagatca agctcgttaa gcttctccag caggagcaga
      961 gactgattct ggatgaattt agccatgttc agcgctgttt tctgttgttt cgtcataaga
     1021 ggcctcagag cgtcagtgct cagtgtaggg atgttctctt ttccgcttcc tcgctcactc
     1081 agtcgctacg ctccggtcgt tcggctgcgg cgagcggcag gagcatgcgt ataagagctc
     1141 gagaaaaccg agaggtcaag gtaggggaaa acgggaggcc gcagcgcggc cgtttttcca
     1201 taggctccgc ccccctgaca agcatcacag aatttgacgc tcaaatcagt ggtggcgaaa
     1261 cccgacagga ctataaagat accaggcgtt tccccctgat ggctccctcg tgcgctctcc
     1321 tgttcctgcc attcggttta ccggtgtcat tccgctgtta tggccgcgtt tgtctcattc
     1381 cacgcctgac actcagttcc gggtaggcag ttcgctccaa gctggactgt atgcacgaac
     1441 cccccgttca gtccgactgc tgcgcctaat ccggtaacta tcgtcttgag tccaatccgg
     1501 aaagacgcga cttatcgcca ctggcagcag ccattggtaa cagaaccagg tggatttaga
     1561 tattaagagt cttgaagtga tggccctact gcggctacac tggaaggaca gtatttggta
     1621 tctgtgctcc accaagccag ttacccggtt aagcagttcc ccaactgact taacctttga
     1681 aaaaaccgcc tccccaggcg gtttttttcg tttaacgtcg gtaagatacg ctttagggtt
     1741 ccagctagtc aagctggcta ctaaaagtta ataagcgcag gaaaaatatg agcaaatacc
     1801 tgattacatt tgaccttgat acaacaaagt taaaaacctt gtatcacggc aagaactaca
     1861 ataatgctta ttacgatatt cgaagcacgt tgagccgacg cggctttgaa aacatacaag
     1921 gtagcgttta tttaggtcag gaaggtataa gtgaggctca cggaaccatt gcaattcaag
     1981 agctaacagc taaatacagc tggttctatg aatgcgtatc taacataaaa ttctatcgta
     2041 tagaatctga tttaaacgca cagtttatcg ctgatggcgt taacgaagcg agaaaaagat
     2101 tctataccca acttgaagat atgcgcaaaa gtttactatc cgttggttta acagtagaac
     2161 aagtaaacga aataataggt cagcaacaat tcaaattaga aagcacgata agccctgata
     2221 aaatgtgagc ataagtaaaa tggtttttct tcttataatg acgctatggt gggcatcctc
     2281 attcatcact catctaatga agattggtag caccagagag tacggtgcaa ctaaatctca
     2341 tttacttttg atgatcacca cacttcccgc tggagttggc gtctttatct acccaatagc
     2401 agaagctgta tggggtgagc taccgttact gaaagttgta ggctataccg ccttatccct
     2461 catgatagga ggggttgttg gcaacatagt tgttcgtgga ttattttcaa cttcgctggg
     2521 tattttgttt ataaaccccc tagcaatgat ctccagtctt acaggtatag cattcttaat
     2581 cgtgcaatac ttaccataac attaacccca acgcgcatga aaggcccgca ctgcgggctt
     2641 ttttttagaa gagatgtgcc ttcgtttcaa cttagcttca atagaggcac cggcaacata
     2701 caaaatatcc gtattttaat actagccacc gagcggtttc ctacgcatcg cgatcaaaaa
     2761 tgcacgagca atctgatcgg gcataaaatt tcagcaaccc actaaactca cccaaggaag
     2821 agtaaacata atctattgat aaaaaataat tttatatttt tagaaaagta ctgaatgttc
     2881 tttcgcggca aacggttcaa taaaaatgag catcagagca agttggaagg cacttttgag
     2941 tacttgatag gagactttaa aatgataatt acaattgagt taaaaggggc attgatggcc
     3001 aaaaatcact cagagtataa ggttttgttt gagggtaaat atctcgcggt aatatggata
     3061 ctatagattc gtcggcgaac gtcggcgaac gtcggcgaac gtcggcgaac gtcggcgaac
     3121 gtcggaataa gatcaattaa atattacatc aagataaaaa caataaaaaa ttaaaaaata
     3181 agtactgaat gttctttcgc ggcaaacggt tatataaaaa ttagcatcag agcaagttgg
     3241 aaggcacttt tgagtactaa caaacactca tctcactccg ctgtagggac cagtaacccc
     3301 aaccattcga tgtcatttaa cataaggccc tgattgtacg caccgctaaa acggcctcag
     3361 ggcgtttctg acgggaaacc ggtaaaacag gcaacaaacc acccgaaaac ccgccagaaa
     3421 cgcgcaggct ctgtttttac ggcatgcatg agtatgcacg caagtgcata gcgcgaaaat
     3481 tcacgccatt cagccagggt aagtcctgtt tcgggcgtac ttcccatccg aaaacggtga
     3541 acggggacgc aatttattgc gtggccgtga agcgttgccg gcgcagccgg aaaaccggtt
     3601 ttcagcacgt tcaggaatcc ggttcgtcg
//
