LOCUS       NZ_CP034042             5010 bp    DNA     circular CON 26-NOV-2023
DEFINITION  Klebsiella pneumoniae subsp. pneumoniae strain CRK0298 plasmid p3,
            complete sequence.
ACCESSION   NZ_CP034042
VERSION     NZ_CP034042.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN08579613
            Assembly: GCF_002970375.3
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae subsp. pneumoniae
  ORGANISM  Klebsiella pneumoniae subsp. pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5010)
  AUTHORS   Fouts,D., White,R., nguyen,K., Singh,I. and D'Souza,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-NOV-2018) Informatics Core Services, JCVI, 9605
            Medical Center Drive, Rockville, MD 20850, USA
REFERENCE   2  (bases 1 to 5010)
  AUTHORS   Vanduin,D., Fouts,D., Sutton,G., Nguyen,K., Hujer,A., Hujer,K. and
            Bonomo,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-OCT-2018) Informatics Core Services, JCVI, 9605
            Medical Center Drive, Rockville, MD 20850, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: OCT-2018
            Assembly Method                   :: Unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 121.2238x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/26/2023 02:31:17
            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)                     :: 5,746
            CDSs (total)                      :: 5,628
            Genes (coding)                    :: 5,518
            CDSs (with protein)               :: 5,518
            Genes (RNA)                       :: 118
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 82
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 110
            CDSs (without protein)            :: 110
            Pseudo Genes (ambiguous residues) :: 0 of 110
            Pseudo Genes (frameshifted)       :: 43 of 110
            Pseudo Genes (incomplete)         :: 61 of 110
            Pseudo Genes (internal stop)      :: 19 of 110
            Pseudo Genes (multiple problems)  :: 11 of 110
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP034042.1.
            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..5010
                     /organism="Klebsiella pneumoniae subsp. pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="CRK0298"
                     /isolation_source="miscellaneous body fluid"
                     /host="Homo sapiens"
                     /sub_species="pneumoniae"
                     /db_xref="taxon:72407"
                     /plasmid="p3"
                     /geo_loc_name="USA: Ohio"
                     /collection_date="2015"
     gene            1..906
                     /locus_tag="C5X33_RS29215"
                     /old_locus_tag="C5X33_29215"
     CDS             1..906
                     /locus_tag="C5X33_RS29215"
                     /old_locus_tag="C5X33_29215"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001697689.1"
                     /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_019725130.1"
                     /translation="MHNAALELFNERLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRAGSSIDWSDRNAPAPTLTITNPENGHAHLLYALENSIRTAPDGKIK
                     PLRYAASVENALRKKLEADAGYSGLICKNPNHNHWKIAVWQPKLYTLDWLADFLDLNTG
                     NDKEIVADYGLGRNCTLFDKTRKWAYRAIRQGWPEYEQWLQACYERACAYNLQFARPLD
                     ENEVRGIAKSIAKWTSNKFSPEEFSKFVDITHSSEIQSKRGKKSGQSRRKGSLEEIKPW
                     VAMGISRRKYFYIKKNGEIR"
                     /name="replication initiation protein"
     gene            903..1610
                     /locus_tag="C5X33_RS29220"
                     /old_locus_tag="C5X33_29220"
     CDS             903..1610
                     /locus_tag="C5X33_RS29220"
                     /old_locus_tag="C5X33_29220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001258875.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004198042.1"
                     /translation="MKTFVTLWTIVFLAFIAVMCTVDISNYIPSVYTVFSKNRPLVTGA
                     LSILLISVFIWLMVSLYLLKKYSVKVEKLSLGGVNILFNESATLYKKSVKNHLDSKRAI
                     FKLRKNVDAFDEVISSYYQTYQFIRDEMKILNPKKDREIYDFSNEMLMVLNRFLTNYQN
                     NYKRWYKYISDKDEVVDRVSGDVMRFHATSINKIQMQYYDYERILKGFKDVNRFFVNDV
                     KPKFGINTDKWNW"
                     /name="hypothetical protein"
     gene            complement(1647..2261)
                     /locus_tag="C5X33_RS29225"
                     /old_locus_tag="C5X33_29225"
     CDS             complement(1647..2261)
                     /locus_tag="C5X33_RS29225"
                     /old_locus_tag="C5X33_29225"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012822468.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="TIR domain-containing protein"
                     /protein_id="WP_019725132.1"
                     /translation="MGKHKVFISYHHANDQYYKNALEKMNEEHEIFVNRSVSLGDIDED
                     EAPQKIREIIRDEYLRDTSVLILLVGTETKNRKHVDWELYSSMRDSTINKKSGILVVNL
                     PSTNTTYIRSTHGTNEKSEVHPTVTEWFSIDKRSTYEERFPYMPARIIDNFMKSGSYIS
                     VVNWNQIENNPETLRKLIDMTYNDREKATYDMSREMRMHNS"
                     /name="TIR domain-containing protein"
     gene            2663..3064
                     /locus_tag="C5X33_RS29230"
                     /old_locus_tag="C5X33_29230"
     CDS             2663..3064
                     /locus_tag="C5X33_RS29230"
                     /old_locus_tag="C5X33_29230"
                     /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_019725133.1"
                     /translation="MTRVSISEAARLTGKSRTTLHRLIKTGELSTCSGERNTKMVDISE
                     LLRVFGPFDQPKNEHLTRQVPEQRDTAPADQSEHVIRQLKQQIEHLNILILSKDSHIDS
                     LKQAMLLLENHQAKLTEPPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3864..4025)
                     /locus_tag="C5X33_RS30415"
     CDS             complement(3864..4025)
                     /locus_tag="C5X33_RS30415"
                     /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_162870772.1"
                     /translation="MAKHWSGQECPKTGTYGQYHDTDNSYAGSEYDRHVSKGDKFPPSK
                     NNHHFQEK"
                     /name="hypothetical protein"
     gene            4262..4507
                     /locus_tag="C5X33_RS29235"
                     /old_locus_tag="C5X33_29235"
     CDS             4262..4507
                     /locus_tag="C5X33_RS29235"
                     /old_locus_tag="C5X33_29235"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012848468.1"
                     /GO_component="GO:0110001 - toxin-antitoxin complex
                     [Evidence IEA]"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0097351 - toxin sequestering activity [Evidence IEA]"
                     /GO_process="GO:0045927 - positive regulation of growth
                     [Evidence IEA]; GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system Phd/YefM family
                     antitoxin"
                     /protein_id="WP_025987695.1"
                     /translation="MHAINFTDARKHFAETMKRVTDDAEPVRVMRRDAPDIVMIDAGEY
                     EALIETVYLFSNPANAEHINESMKQAERGEFVEVEY"
                     /name="type II toxin-antitoxin system Phd/YefM family
                     antitoxin"
     gene            4488..4763
                     /locus_tag="C5X33_RS29240"
                     /old_locus_tag="C5X33_29240"
     CDS             4488..4763
                     /locus_tag="C5X33_RS29240"
                     /old_locus_tag="C5X33_29240"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017412855.1"
                     /GO_process="GO:0008219 - cell death [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Txe/YoeB family addiction module toxin"
                     /protein_id="WP_019725129.1"
                     /translation="MSKWNIKFTRNGADDLNYWRDTDKKKFERIRQLLLSIEADPLTGI
                     GKPERLRHHKDPALYSRRIDQSHRLVYSIQNGEIIIYAARYHYGDK"
                     /name="Txe/YoeB family addiction module toxin"
ORIGIN
        1 ttgcataacg ccgcactcga acttttcaac gaacgcttac cacacaagcc gtacttttcg
       61 gacgatctgc actttggtgt ccgtatcgcc ggtaaggaac gcgctattct ggcgaaatat
      121 atccagttca atcagcctca cgccatgttc tggctgggat ttgacgttga ccgcgccggt
      181 tcctccatcg actggagcga ccgcaacgcg cctgcaccga cgctgaccat aactaacccc
      241 gaaaacggac acgcgcacct gctgtacgcg ctggaaaact cgatacgcac cgcgccggac
      301 ggcaaaataa aaccgttacg ctacgccgcc tccgtggaga atgcgctacg taaaaaatta
      361 gaggctgacg ctggatattc ggggctcatc tgcaaaaatc cgaaccacaa ccactggaaa
      421 atcgccgtgt ggcagccgaa gctctacact ctggactggc tggccgactt tctcgatctg
      481 aacacaggga atgacaagga aatcgttgcc gactacggct taggccgtaa ctgcacgttg
      541 ttcgacaaaa cccgtaagtg ggcatatcgc gccatccgtc agggctggcc tgagtatgag
      601 cagtggctgc aagcctgcta cgaacgcgct tgcgcataca acctgcaatt tgcacggcct
      661 ctggatgaaa atgaggtaag agggatagct aagagcattg ctaaatggac atcaaataaa
      721 ttttcacctg aagaattcag taaatttgtt gatattactc attcctctga aattcaatca
      781 aagagaggga aaaagtcagg acagtcaagg aggaaaggaa gcctagagga aataaaacct
      841 tgggtagcta tgggaataag caggcggaag tatttttata tcaagaaaaa tggtgaaata
      901 agatgaaaac cttcgtaact ctttggacta tagttttttt agcatttatt gccgtgatgt
      961 gtactgttga tatatctaat tacattccgt ctgtttacac agtttttagt aagaatagac
     1021 ctcttgtaac tggcgccctt tctattcttt tgatatctgt ttttatttgg ctgatggtat
     1081 ccctctactt acttaaaaag tattcggtta aggttgagaa acttagcctt ggtggagtga
     1141 atatactttt caatgagagt gctacacttt acaaaaagag tgtaaaaaat cacctagatt
     1201 caaaaagagc aattttcaaa ttaagaaaaa acgttgatgc ctttgatgag gttatttcat
     1261 catattatca gacttaccaa tttattcgtg atgaaatgaa aatactaaac cctaaaaaag
     1321 atcgtgagat ttatgatttc agcaatgaga tgctcatggt gttaaataga tttctaacta
     1381 actaccagaa caactacaag cgttggtata agtacatatc agacaaagat gaggttgttg
     1441 atagggttag cggtgatgtc atgagatttc atgcaaccag cataaataaa atacaaatgc
     1501 agtattatga ttatgagcgt attttaaaag gttttaaaga tgttaaccgg ttctttgtta
     1561 atgatgtgaa gcctaagttt ggaatcaata cagataagtg gaactggtaa attaaaggag
     1621 tagccaaggc tactccttgg atagtactat gaattatgca ttctcatttc tctcgacata
     1681 tcatacgttg ctttttctct atcgttataa gtcatgtcta ttaattttct gagtgtttct
     1741 gggttgtttt ctatttgatt ccagttgacc actgatatat aagacccgct cttcatgaag
     1801 ttgtctatta ttcttgctgg catatatggg aacctttcct cataagttga gcgcttatca
     1861 atagaaaacc attcagttac ggtaggatga acttctgatt tttcattagt tccatgtgtt
     1921 gaacgaatgt acgtagtatt tgttgacggg agattgacga ctaaaattcc tgattttttg
     1981 ttaatggtac tatctctcat gctagagtaa agttcccaat ctacgtgttt tctgtttttt
     2041 gtttcagttc caacaagaag gataagaact gatgtatctc taagatattc atctcttatt
     2101 atctctctta ttttttgtgg ggcttcatct tcatctatat cacctaatga tactgagcga
     2161 ttcacgaata tttcatgttc ctcattcatt ttttcaagtg cgtttttgta gtactgatca
     2221 ttcgcatggt ggtagctaat gaatacctta tgctttccca tttttattgt cctttttttg
     2281 tttgtgtgca ctctattttg cacttgaacc tatatcagat aacagctctc ttttagagag
     2341 ctcttttttt ctcagccagc acacataggg tcccttcagc aaggtctcgc catgactggt
     2401 ttagggcggg ctcgttgctt ccctaaacgc cttgagaaga gagctatcac ctcactttat
     2461 tcttacgtac cgctcgccgc agtcttatga ccgaacgtag tgagcgaatg cgcgaggaag
     2521 cggaaagtca tttgttgcct gcattttgca cggtcactcc tgtgtttcat cgcccttctg
     2581 aaaaacacat cacttctgga ccagtatgtc gtaagctggc ccctgtttcc ttgagactga
     2641 atgtattaaa ggatgataac tgatgaccag agtgtctatt agtgaggctg cacggctgac
     2701 gggtaagagc cggacaacgc tgcacaggtt aatcaaaaca ggtgaactgt ccacttgtag
     2761 cggtgaacga aatacaaaaa tggtcgatat atcagagctt ttacgtgttt tcggaccgtt
     2821 tgaccaaccg aagaatgaac accttactcg acaagtacct gaacagcgtg atacagcgcc
     2881 tgctgaccag agtgaacatg tcattcgtca actgaaacag cagattgaac accttaacat
     2941 attgatttta tcgaaggatt cgcacattga cagcctgaaa caggccatgc tccttcttga
     3001 aaatcaccag gcaaaattaa ctgaaccccc ggcgccgtgg tggaaattct ggaaaaaatc
     3061 ctgaccccgt catgcttcag ttttcctctc cggccattcc ggggagttcc tgaaccttcc
     3121 cgaaaatcgt cagatctctg aacgctcctc accacgaaaa atacccacac cccacgcaaa
     3181 attttaattt tgcagatttg tatttaatat cagcagctta ctttactgaa atttcgtttt
     3241 ttaaatttta tttatataga tccgactcta tgacgagtcg tcatagagtc cccggcgagt
     3301 cgtcatagag tcggtaacga ctcaggccta taaaaacaat gagttaataa cgacccgact
     3361 ctagatccga ctccccgttt ggttgttttt tagacgtggc gactctgggt acgactctag
     3421 tgaagagtcg ccggggaatc gtgtggtgag tcgtccggcg acttgccata acgtgattgc
     3481 cggccgtgga cgaaccgatt cctgaacgtg ctgaaaaccg gttttccggc tgcgccggca
     3541 acgcttcacg gccacgcaat aaattgcgtc cccgttcacc gttttcggat gggaagaacg
     3601 ccggaaacag gacttcccct ggctgaatgg tgtcaatttc cgcgctatgc acttgtgcgc
     3661 atactcatgc atgccgtaaa aacagagcct gcgcgtttct ggcgggtttt cgggtggttt
     3721 gttgccttgt ttaccggttt cccgtcagaa acgccctgag ggcatctcag gcggtgctga
     3781 taacggatgt tatggtaaat caagtgaatg gcaggtacaa aaaaagcccc agagggcttt
     3841 tagtttagac ttctgaagat attttatttt tcttggaagt ggtggttgtt tttgctcgga
     3901 gggaacttat cacccttgct cacatggcga tcatattcag aaccagcgta tgagttgtcg
     3961 gtatcatgat attgaccgta agtacctgtt tttggacatt cttgcccaga ccaatgtttt
     4021 gccatttact tttcctttgc tcgttttagg agctaagctc ctagcggtac gaaattgtgc
     4081 cgcacttcat aaatgtaatt gcttgaaatt atgcttcaat gtattgactt gttgtttttg
     4141 tggttattcg attgagttca cattttgagc tgatttggtt gtgggttttt agggaaatat
     4201 ctttatgtac ttatttgcgt acatgttcta tgctaagccc caacaaatgg gggttaacaa
     4261 catgcatgca atcaatttta ctgatgcccg taaacatttt gccgagacga tgaagcgcgt
     4321 cactgatgat gctgaaccgg tacgtgtcat gcgccgtgat gcgcctgata ttgttatgat
     4381 cgatgcggga gagtatgagg cgctaatcga aacggtctat ctgttcagca atccggcgaa
     4441 cgcagagcat atcaatgagt caatgaaaca ggcggagcgc ggcgaatttg tcgaagtgga
     4501 atattaagtt cactaggaat ggcgctgatg accttaacta ctggcgtgat actgacaaaa
     4561 agaagtttga gcgtatccgg caactgttgc tcagcatcga ggctgatccg ctgacaggta
     4621 taggaaaacc cgaacggctg cggcaccaca aagatccggc actctactcc cgcaggattg
     4681 atcagagcca ccgtctggtc tattcaatcc agaacggaga aatcatcatc tacgcagccc
     4741 gttatcacta tggtgacaaa tagcaaaagt cgatatagcc cgcttgatgc gggcttttca
     4801 tgcaaggcgt acaacggatg ttagggtaag tcgctgtcag atcgacacaa aggcaaagtc
     4861 ggtgtaacgt tagcctcaga aaaaacaaag ccccggaaat catgtcatat cttggcggat
     4921 cgcatgataa ccagggctag gtcgaaacct tgaaaggata ttagcacatg aaccgtgcca
     4981 gacaacagcc cgccataagc gcagggcaca
//
