LOCUS       NZ_CP018667             5566 bp    DNA     circular CON 08-JAN-2024
DEFINITION  Klebsiella pneumoniae strain CAV1042 plasmid pCAV1042-5566, complete
            sequence.
ACCESSION   NZ_CP018667
VERSION     NZ_CP018667.1
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 5566)
  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  JOURNAL   Unpublished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 5566)
  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
            CP018667.1.
            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..5566
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="CAV1042"
                     /isolation_source="Urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pCAV1042-5566"
                     /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(5177..5566,1..153))
                     /locus_tag="AGE78_RS00055"
                     /old_locus_tag="AGE78_00055"
     CDS             complement(join(5177..5566,1..153))
                     /locus_tag="AGE78_RS00055"
                     /old_locus_tag="AGE78_00055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001696621.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="stationary phase growth adaptation protein"
                     /protein_id="WP_110204878.1"
                     /translation="MNIDEVAKWRPFTDPDGNIWDLSFLDAHEVTYTHCAPGKPDIVYK
                     FTVSYSFHCFCKDYPEQTEEEKLSLMYDAGKDARPFCKIRYALARDKLRAIIEGLGNAK
                     VIHAGYGSYAVVEITVNEGESEFYFVPFKVYRERKKLRLHVTSAYPVNERPSGKPVSFF
                     KIAHNLLRGQPLPKPHM"
                     /name="stationary phase growth adaptation protein"
     gene            921..1163
                     /locus_tag="AGE78_RS00065"
                     /old_locus_tag="AGE78_00065"
     CDS             921..1163
                     /locus_tag="AGE78_RS00065"
                     /old_locus_tag="AGE78_00065"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001713065.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein L"
                     /protein_id="WP_074075294.1"
                     /translation="MALVKHGSRHLIGEAGAQHNGTYDRKYRSGDTCQFEGIYKCAGCG
                     KEITLAKGKTFPPQNHHQHSLLSGAIEWQLLVFAQ"
                     /name="protein L"
     gene            complement(1211..1660)
                     /locus_tag="AGE78_RS00070"
                     /old_locus_tag="AGE78_00070"
     CDS             complement(1211..1660)
                     /locus_tag="AGE78_RS00070"
                     /old_locus_tag="AGE78_00070"
                     /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="helix-turn-helix domain-containing protein"
                     /protein_id="WP_077274101.1"
                     /translation="MSKQSQNLLNLTQAAEAVGITRKTLYSHIDKGLVSVTRQQGKRYI
                     DVSELIRHYGSVSLPEEEVNTVTRSQDKHDGDTILAMQRELVELRKLIEKQQLLLEDKR
                     EADRLREQVTGLQNERDAASLELGKVKAELEMERKKGFWERLFGK"
                     /name="helix-turn-helix domain-containing protein"
     gene            2270..2776
                     /locus_tag="AGE78_RS00075"
                     /old_locus_tag="AGE78_00075"
     CDS             2270..2776
                     /locus_tag="AGE78_RS00075"
                     /old_locus_tag="AGE78_00075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007373079.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_074075295.1"
                     /translation="MTKKTAQSAADSDLQAFLSEAAERFKPDATVLAARIDTAVQRYTA
                     TSRTQRFNAPAVLAMQQLQDRILEGWRYDIGIPQSVYLAGSSGNMAITLRKPESLMEQE
                     IADLKRQIEDAYHNELAAAMEREVDMLVQDAANEAQQRAEETAATERDAMRKLLRNMLL
                     TEATA"
                     /name="hypothetical protein"
     gene            3049..3711
                     /locus_tag="AGE78_RS00080"
                     /old_locus_tag="AGE78_00080"
     CDS             3049..3711
                     /locus_tag="AGE78_RS00080"
                     /old_locus_tag="AGE78_00080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008320537.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="inovirus-type Gp2 protein"
                     /protein_id="WP_074075296.1"
                     /translation="MTHAVTSHYDNGRYHLINSANYTFNDNTYSLNFKPDSKRHAPIRQ
                     EIIDSFITQLCAMQSHYSKIFAFRFDLSVPAGMPVSESNKLVSELFTKLRGKFTAKRWN
                     GQPIKKFAYGWVREKEKAKQVHYHCWIALPHFQVRVAGFGNEGTYGLINTLWSELTAQA
                     GRAHLCDGTYTINRDDHSSLVELVERVSYLAKARGKYSTGDGQRMFSASKLKIHANA"
                     /name="inovirus-type Gp2 protein"
     gene            complement(3927..4559)
                     /locus_tag="AGE78_RS00085"
                     /old_locus_tag="AGE78_00085"
     CDS             complement(3927..4559)
                     /locus_tag="AGE78_RS00085"
                     /old_locus_tag="AGE78_00085"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015689667.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0000150 - DNA strand exchange activity [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="recombinase family protein"
                     /protein_id="WP_074075297.1"
                     /translation="MTSRVYAYLRASTKEQDASRAREQLDEFANSKGMTIATYFTENES
                     GASLQRPELFRLLAIAQKGDVLLVEQVDRLSRLSGDDWNKLRALINKKGVRVVALDLPT
                     SHQLIRSGDEFTDRMLESLNGMMLDMLAAIARKDYTDRKRRQSQGISKAKAAGKFKGRP
                     EDAQRNEKIGKLLKAGMSYTDIMGTVNCSRATVAKVSKSLKDTAITG"
                     /name="recombinase family protein"
ORIGIN
        1 cgagtaagaa acagtgaact tgtacacgat gtcaggttta ccgggagcgc aatgagtata
       61 agtaacctca tgtgcatcaa gaaatgacaa atcccatatg ttgccatcag gatccgtaaa
      121 aggacgccac ttagcaactt catcaatgtt cacgaaaaga gcctcgatac ccggatggca
      181 gaatccgcac attctaccag agaaaagaca agcggaagga gcgcgggaaa aaagaagggt
      241 caggacttta cagaaggctt cgcccctcct gacgagcatc acaatacaga cgctcaaatc
      301 aagagtggcg aaacccgaca cagcttaaag atcccaggtg tttccccctg gtagctccct
      361 cgtgcgctcc tgtgttccca ccttgacgtt tgcagccagc cttgccgctc tttctacttt
      421 gggggcgcta actctcagct tccctatgct ggcactgctc gttttaggtg gttcgctcca
      481 agctggatga tatgcacgaa ctccccgttt catccgaccg ttgcgcctgc tgggtaactc
      541 ttctcatgat tccaacccca gcagacacgg caaagtgccg ctaatggcaa cagccaatac
      601 ggtaacgcgt tctattgggg gatttcgtcg gtaggtcttg aagtgtgcgc ctgaatgcgg
      661 ctacactgag aatactgatt taggtgacgt cgttcccccg aacacgttac ctggctgatc
      721 agtcctgaga aaactggtca acccgataaa gcccgcgcct gagaacgcgg gttttttcgt
      781 ttcagggata atgcacctgg atccgtgagc atgtcaaacg cctacaaata gattccttac
      841 tattcagtgt tccccactat tactcatgtt taaaaaaaca gtataatgac caaaaagcaa
      901 ccattgaaag gcgacgtaat atggctctgg taaaacatgg tagtaggcat ttaattggcg
      961 aggctggcgc acaacataat ggaacttacg accgtaaata tcgttcaggt gatacctgtc
     1021 agtttgaagg gatttataaa tgcgccggtt gtggtaaaga aataactctg gcaaaaggaa
     1081 aaactttccc gccacagaat caccatcaac actcgttgct ttcaggagca attgagtggc
     1141 aactacttgt atttgcacaa taaaaaccat gaaggtataa ataccgcctg caaaggcggt
     1201 tccttttcat ctatttacca aaaagtcttt cccaaaaacc cttcttcctc tccatctcaa
     1261 gctccgcctt cacctttccc agctccaagg atgctgcgtc acgctcattt tgcaacccgg
     1321 tcacctgttc ccgcagccgg tcggcctccc gcttatcctc aagcaacaat tgctgtttct
     1381 cgatcagctt ccgcagctct accaactccc gctgcatagc caatattgta tcgccatcat
     1441 gtttatcttg tgaccgtgta acggtgttta cttcttcctc aggaagggat acagatccgt
     1501 aatgcctgat tagctcggat acgtcgatat atcgtttacc ttgctggcga gtaacactca
     1561 ccaaaccctt atcaatatgg gaatagagcg ttttccgtgt gatgcctacc gcctcagcag
     1621 cctgtgtaag gttgagtaga ttctggctct gcttactcac tgtataccct ccattttatc
     1681 actgtgttta ctctgggtag tatacacata aaaaaacagc acgctcgcac ttgataatgc
     1741 ttctcattca aaacgtcttg tgataaaata accgaaggcc aataaacaaa aaacaggaga
     1801 cacattgcat gtaacgccca cgccagccgc tttcacatcg ccgaccgatg acgagcgtat
     1861 ccaactggca acactactga ataccgttga cctacgcgcg acaactccaa ggatcaacgt
     1921 cttgcacttt ctgaatatcg cagatgctcc ggtgacagcc gtaacggtta gccactgcct
     1981 tgacctgcct ctgtctactg catatcgagc attgacggca cttgaggtta ataaccttgc
     2041 aggtgtgaca tttggacgct ccgaagtaac gcgttggttt cggttcctac cgaacaagcc
     2101 tcagcattgc caatcttgtg ggcagagctt ctacacagag tacgcataag ccgtacacat
     2161 aaacactgac gagatgatcg cactatacgg tcacaacaaa tgacgctcac cacagagcgc
     2221 cagcggccct ctatggcctt tatttaccga ttgcagagaa gaattacaca tgacaaagaa
     2281 gacagcacag agcgccgctg atagcgatct acaggcattc ctgagcgaag ccgcagaacg
     2341 attcaaacct gacgccaccg tactggcagc gcggattgat accgccgttc aaaggtacac
     2401 agccaccagc agaacacagc gtttcaacgc cccggcagtc ctggcaatgc aacagctaca
     2461 ggatcggatt ctggagggct ggcggtacga tatcggtatt ccccaatcgg tgtatctcgc
     2521 tggtagttcg gggaatatgg caatcacgct ccgcaaaccg gagtcgctaa tggaacaaga
     2581 aattgccgac ctaaaacgac agattgagga tgcttaccac aacgaactcg ccgccgcgat
     2641 ggaacgcgag gtagatatgc tggttcagga cgccgccaac gaagcccagc aacgtgcaga
     2701 ggaaaccgca gccacagaac gggacgctat gcgtaagctc ctacgcaata tgctccttac
     2761 tgaggcgacc gcatgaccgt cattaagaag gggccaccat gccccgctta catcgaccct
     2821 gacgcactgg aaagagccat tgccgccgct cggaaaatca gtgaagccaa cccggaacgg
     2881 tataaatctg ttcccgcctc gccgaaactt ttctgagtga aaactatggc aattggtacg
     2941 actccacgcc agcagcggcg cggcataggg atgctttact tacgcaataa acatactggt
     3001 tattactaat acctgtatct gtacatacca aacatcaatc ggaggaacat gactcatgca
     3061 gtaaccagcc actacgacaa tggcagatat caccttatca actcagctaa ctacaccttc
     3121 aacgacaaca cgtatagcct gaacttcaaa cctgacagca aacgccatgc gccgatccgt
     3181 caggaaataa tcgacagctt cattacccaa ctctgcgcga tgcagtccca ttacagcaaa
     3241 atcttcgctt tccggttcga tctgtcagtc ccggcaggaa tgccagtatc tgagagcaat
     3301 aagctggtca gtgagctgtt caccaagcta cgcggcaagt tcactgcaaa gcgatggaat
     3361 ggacagccga tcaagaaatt cgcatatggc tgggtaaggg aaaaagagaa ggccaagcag
     3421 gttcattacc attgctggat agccttgcct cacttccaag tcagagttgc tggattcggc
     3481 aatgagggaa catacggcct gataaacact ctttggagtg aactcacagc ccaagcgggt
     3541 cgcgcccact tatgtgatgg tacatacacc atcaacaggg atgatcactc atcgctggta
     3601 gagctggttg aacgggtttc ctaccttgcc aaggcgcgtg ggaaatattc cactggggac
     3661 gggcaacgaa tgttttcagc atcaaaactg aaaatacacg ccaatgctta accgggttcg
     3721 cctctaccgg gcaagccata cgcacaagaa aaatatctgg ggcatttccc atgacaaatt
     3781 tgtcaccagc aggcacacca acgcccacag cgatccacgc gccgccggtt ttctcacatt
     3841 aaacaggcaa taaaaatccc cgcacatggc gagggtctca atacgccgac tgtcttaggt
     3901 cggtgctttt gattgtggac ggctgattag cctgtgatag cggtatcttt cagactcttg
     3961 ctcactttgg caaccgtcgc acgggaacag ttcaccgttc ccatgatgtc ggtgtacgac
     4021 atacccgctt tcagcaactt accaatcttc tcgttgcgct gggcatcttc cgggcgacct
     4081 ttgaatttgc cagccgcctt tgccttactg attccctgag actgacggcg cttacggtcg
     4141 gtgtagtcct tacgtgcaat ggcagccagc atatccagca tcatcccgtt caatgattcc
     4201 agcatacggt cagtaaactc atcaccggac cggatcagct ggtggctggt tggcaagtct
     4261 aaagcaacca ctcttacacc cttcttattg atcaatgccc gtaatttgtt ccagtcatca
     4321 ccgcttaaac gcgacaggcg gtctacctgc tccaccagca atacgtcacc cttctgtgcg
     4381 atagccagca gccggaacaa ctcaggacgc tgcaatgacg ctcccgactc gttctctgtg
     4441 aaataggtgg cgatggtcat ccctttagaa ttagcaaact catcaagctg ctctctggcg
     4501 cgtgatgcgt cctgctcttt ggtagaggct ctgaggtagg cgtaaacacg tgatgtcatg
     4561 gtggcgtccc ttaatagtct gtttttagtg gttcaacaat atcagtctat taagagtggt
     4621 tcaataaatt cttttcccgg cctgattggt tcaataaatc ggtacctctt gaagtatacc
     4681 taaaacagac cacatgacag gcagcatatc gacaacccac cggcagatat ttctggaaga
     4741 tccgggcaac actgatctca gccagcaaaa cgctgagcac cgcagtccat gcgccagagg
     4801 tacaatcacc ggcaggatat ttgcagccgc cggtttacat atgtgggggt atcagcgatc
     4861 ccgcgccggg ggggggttat aaatatgcaa cacgtgatat caggttaggc tttaggttct
     4921 ctttagtcgg ctatttcaag aaagccagat acagcaaggg attgcgggga gatcgagaaa
     4981 agttagtata taggtgcaac caaaatgttg gttgcaaatc tacatcacac tacctacaat
     5041 tgctttaagg atgcagcaga ctggtaatac cagacatccc actaccaaca gcaatgttgg
     5101 tcgaggccaa gcccggtaaa ggtgttctga ataccagaag aaatttctgg cgaagcccgc
     5161 gactaagcgg gctttgttac atatggggtt taggtaatgg ctgcccgcgt agaagattgt
     5221 gagctatctt gaaaaagcta actggcttac ctgacggtct ctcattgaca ggataagcac
     5281 ttgttacatg aaggcgcagc tttttacgct cacgatatac cttaaaaggc acaaagtaga
     5341 actcactttc accttcattc accgtaatct ctacaacagc ataactgcca tagccagcat
     5401 ggataacctt cgcgttaccc aatccttcaa tgatggctct cagcttgtct cgagcaagag
     5461 catatcggat cttacaaaat ggcctcgcgt ctttgcctgc gtcatacatc aacgataatt
     5521 tttcttcctc agtctgctca ggataatcct tgcaaaaaca atggaa
//
