LOCUS       NZ_CP018665             2781 bp    DNA     circular CON 08-JAN-2024
DEFINITION  Klebsiella pneumoniae strain CAV1042 plasmid pCAV1042-2781, complete
            sequence.
ACCESSION   NZ_CP018665
VERSION     NZ_CP018665.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03024576
            Assembly: GCF_001908515.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 2781)
  AUTHORS   Mathers,A.J., Stoesser,N., Chai,W., Carroll,J., Barry,K.,
            Cherunvanky,A., Sebra,R., Kasarskis,A., Peto,T.E., Walker,A.S.,
            Sifri,C.D., Crook,D.W. and Sheppard,A.E.
  TITLE     Chromosomal Integration of the Klebsiella pneumoniae carbapenemase
            gene (blaKPC) in Klebsiella Species: Elusive but not Rare
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2781)
  AUTHORS   Mathers,A.J., Stoesser,N., Chai,W., Carroll,J., Barry,K.,
            Cherunvanky,A., Sebra,R., Kasarskis,A., Peto,T.E., Walker,A.S.,
            Sifri,C.D., Crook,D.W. and Sheppard,A.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-DEC-2016) Nuffield Department of Medicine, University
            of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. unspecified
            Genome Coverage                   :: 170x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/08/2024 03:09:05
            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)                     :: 5,702
            CDSs (total)                      :: 5,581
            Genes (coding)                    :: 5,419
            CDSs (with protein)               :: 5,419
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 162
            CDSs (without protein)            :: 162
            Pseudo Genes (ambiguous residues) :: 0 of 162
            Pseudo Genes (frameshifted)       :: 71 of 162
            Pseudo Genes (incomplete)         :: 98 of 162
            Pseudo Genes (internal stop)      :: 35 of 162
            Pseudo Genes (multiple problems)  :: 34 of 162
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP018665.1.
            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..2781
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="CAV1042"
                     /isolation_source="Urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pCAV1042-2781"
                     /geo_loc_name="USA:Virginia"
                     /lat_lon="38.14 N 78.45 W"
                     /collection_date="2008-04"
                     /collected_by="Clinical Microbiology University of Virginia
                     Health System"
     gene            complement(join(2511..2781,1..410))
                     /locus_tag="AGE78_RS00005"
                     /old_locus_tag="AGE78_00005"
     CDS             complement(join(2511..2781,1..410))
                     /locus_tag="AGE78_RS00005"
                     /old_locus_tag="AGE78_00005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001572662.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_072042463.1"
                     /translation="MGRKSREKKERHIKDRASPLKVYRFFKEKSHAEALCNGDVWLSTI
                     ETCRRYEDPLQGDPNEAIQTYSSGFISGGSDDSRFVSAAAHAGIHIGPGCSGITIQNCR
                     SFNKMPDAFVLCTTLEFQPENLNDTFGNYCVEISNVEEFFGLITKKLKGLLPIKLGAMG
                     EVRYGSHSFYGYQPPPGPIGFVKNRDKYSSQKEFRFLWVPETFDIQPRLVKCPELSYCC
                     RMIS"
                     /name="hypothetical protein"
     gene            complement(1172..1573)
                     /locus_tag="AGE78_RS00010"
                     /old_locus_tag="AGE78_00010"
     CDS             complement(1172..1573)
                     /locus_tag="AGE78_RS00010"
                     /old_locus_tag="AGE78_00010"
                     /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_074075293.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHYGQVSGQRDTASADQSEQVIRHLKQEIEHLNTLLSSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1573..1764)
                     /locus_tag="AGE78_RS00015"
                     /old_locus_tag="AGE78_00015"
     CDS             complement(1573..1764)
                     /locus_tag="AGE78_RS00015"
                     /old_locus_tag="AGE78_00015"
                     /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_032489493.1"
                     /translation="MTKQQKTALNMAKFIQHQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2179..2262
                     /locus_tag="AGE78_RS32300"
                     /old_locus_tag="AGE78_00025"
     CDS             2179..2262
                     /locus_tag="AGE78_RS32300"
                     /old_locus_tag="AGE78_00025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_072042462.1"
                     /translation="MHEPPVQSDCCASSGNYRLESNPERHD"
                     /name="replication initiation protein"
     Typing          1813..2292
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.32"
                     /coverage="92.0"
                     /evalue="9.970000000000001e-160"
ORIGIN
        1 atttccacac agtaatttcc aaaggtatcg ttcaagtttt ctggctgaaa ttccagtgtc
       61 gtacataaaa caaaggcgtc gggcatctta ttaaaagagc gacaattttg tatcgttatt
      121 ccactacagc caggtccaat atggattccg gcatgagctg cagcagagac aaaacggctg
      181 tcatcactgc cccctgagat aaaacccgag ctataggttt gaattgcttc attcggatct
      241 ccctgtaggg ggtcttcgta tcgtctacac gtttcaatag tgctcagcca aacatcgcca
      301 ttgcacaatg cctcagcatg actcttctct ttaaaaaacc tatatacttt aagggggctg
      361 gctctatctt taatatgcct ttcttttttc tctctacttt tcctacccat tgaaaaatat
      421 cctttttaaa ttttcattta ccataacatc tcttgcccgc accgctaaaa cggcctcagg
      481 gcgtttctga cgggaaaccg gtaaaacagg caacaaacca cccgaaaacc cgccagaaac
      541 gcgcaggctc tgtttttacg gcatgcatga gtatgcacgc aagtgcgtag cgcgaaaatt
      601 cacgccattc agccatggta agtcctgttt ccggcgttct tcccatccga aaacggtgaa
      661 cggggacgca atttattgcg tggccgtgaa gcgttgccgg cgcagccgga aaaccggttt
      721 tcagcacgtt caggaatcgt gttcgtcgac ggccggcaat cacgttatgg caagtcgccg
      781 gacgactcac cacacgattc cccggcgact cttcactaga gtcgtaccca gagtcgccga
      841 gtctaaaaag caaccaaacg gggagtcgtg tctagagtcg ggtcgttatt aactcattgt
      901 ttttatagtc ctgagtcgtt accgactcta tgacgactcg ccggggactc tatgacgagt
      961 cgtcatagag tcggatctat gtaaataaaa tttaaaaaac gaaatttcag gaaagtaaac
     1021 cactgatatt aaatacaaat ctgcaaaatt ttaattttgc gtagtgtgtg ggtattttta
     1081 gtcgtgagga gcgttcagag atctggcgat ttttgggaag gttcaggaac tccccgggat
     1141 ggccggagag gaaaactcaa gcatggcagg atcaggattt tttccagaat ttccaccatg
     1201 gcgccgggga ttcagttaat tttgcctggt gattttcaag aaggagcatg gcctgtttca
     1261 ggctgtcaat gtgcgaatcc ttggacgaaa gtaaggtgtt cagatgttca atctcctgtt
     1321 tcagatgacg aatcacctgt tcactctggt cagcagaggc tgtatcacgc tgtccagaga
     1381 cctgtccata atggtgttca cccttcggtt gctcaaaggg accaaagaca cgtaaaagct
     1441 ctgaagtatc taccattttt gcattgcgct caccgctaca ggtggacagg tcacctgctt
     1501 taattaacct gtgcagtgtt gttctactct tacccgtcag tcgggcagcc tcactaatag
     1561 acactctggc catcagttac catcctgtaa tgcatccagt ctcgaggaca gtgtacggaa
     1621 aagatgctcc gcatcatcgt ggagtttctc acaaaggtcg gcctcgacat cgagatcaag
     1681 ctcgttaagc ttctccagca ggagcagaga ctgatgctgg atgaatttag ccatgttcag
     1741 cgctgttttc tgttgtttcg tcataaatgg cctcagagcg tcagtgctca gtgtaaaacc
     1801 agtctctttt ccgcttcctc gctcactcag tcgctacgct ccggtcgttc ggctgcggcg
     1861 agcggcagga gcatgcgtat aaaaactcga gaagaccgag cggtcaaatg gggaagaagg
     1921 aaaggccgca aagcggccgt tttttcatag gctccgcccc ccctgacaag catcacggaa
     1981 tctgacgctc aaatcagtgg tggcgaaacc cgacaggact ataaagatac caggcgtttc
     2041 cccctggtgg ctccctcgtg cgctctcctg ttcctgcctt tcggtttacc ggtgtcattc
     2101 cgctgttatg gccgcgtttg tctcattcca cgcctgacac tcagttccgg gtaggcagtt
     2161 cgctccaagc tggactgtat gcacgaaccc cccgttcagt ccgactgctg cgcctcgtcc
     2221 ggtaactatc gtcttgagtc caacccggaa agacacgact aatcgccatt ggcagcagcc
     2281 actggtaatt gatttagagg agttagtctt gaagttatgc gccggttaag gctaaactga
     2341 aaggacaagt tttggttact gcgctcctcc aagccagtta ccgcggttca aagagttgct
     2401 gctctaagaa ccttcaaaag gaccgccttg ctgggcggtc tttttgtttc caaaggagat
     2461 tacgctggta acgtaatctc agtcaagaat tacactatgg aaaatgtcat ctaagatatc
     2521 attcggcaac aatatgaaag ctcagggcat ttgactaacc tgggttgaat atcaaatgtt
     2581 tctggcaccc aaagaaatct gaattctttc tgcgaagaat atttatctcg attttttaca
     2641 aacccaatcg gtcccggtgg aggctggtaa ccataaaaag aatgactccc atatctgacc
     2701 tcccccatag cacctaattt tataggtaat aaccccttta actttttagt aataagacca
     2761 aaaaactctt caacatttga t
//
