LOCUS       CP128764                4510 bp    DNA     circular BCT 03-JUL-2023
DEFINITION  Klebsiella pneumoniae strain CRE-118 plasmid pCRE-118_5, complete
            sequence.
ACCESSION   CP128764
VERSION     CP128764.1
DBLINK      BioProject: PRJNA788509
            BioSample: SAMN35878151
KEYWORDS    .
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4510)
  AUTHORS   Kochan,T.
  TITLE     Klebsiella pneumoniae Clinical Isolates with Features of Both
            Multidrug-Resistance and Hypervirulence Have Unexpectedly Low
            Virulence
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4510)
  AUTHORS   Kochan,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-JUN-2023) Microbiology & Immunology, Northwestern
            University, 303 E Chicago Ave, Ward 6-035, Chicago, IL 60611, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: trycycler v. v0.4.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 66.7372904980587x
            Sequencing Technology :: Oxford Nanopore MinION/GridION, Illumina
            NovaSeq/MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/26/2023 13:26:45
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,505
            CDSs (total)                      :: 5,381
            Genes (coding)                    :: 5,277
            CDSs (with protein)               :: 5,277
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 104
            CDSs (without protein)            :: 104
            Pseudo Genes (ambiguous residues) :: 0 of 104
            Pseudo Genes (frameshifted)       :: 42 of 104
            Pseudo Genes (incomplete)         :: 62 of 104
            Pseudo Genes (internal stop)      :: 14 of 104
            Pseudo Genes (multiple problems)  :: 14 of 104
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..4510
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="CRE-118"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pCRE-118_5"
                     /geo_loc_name="USA: Chicago"
                     /lat_lon="41.8945 N 87.6208 W"
     gene            1..114
                     /locus_tag="QU716_27495"
     CDS             1..114
                     /locus_tag="QU716_27495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WJU62932.1"
                     /translation="MHEPPVQSDCCVLSGNYRLESNPVRHAKAPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(414..770)
                     /locus_tag="QU716_27500"
     CDS             complement(414..770)
                     /locus_tag="QU716_27500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000075993.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0003677 - DNA binding [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antitoxin"
                     /protein_id="WJU62933.1"
                     /translation="MSQATRKPSTVGDIILYEYLEPSGLKINDLAEMLNVHRNSASALV
                     NNNRKLSTDMAFRLAKAFDTTAKFWLNIQQSVDLWEVTSSPRLQEEIERVTPAHEIIER
                     KHNAESLEKKHAVA"
                     /name="HigA family addiction module antitoxin"
     gene            complement(974..1294)
                     /locus_tag="QU716_27505"
     CDS             complement(974..1294)
                     /locus_tag="QU716_27505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001183575.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WJU62934.1"
                     /translation="MQQNHDSDDDCRIQFRDDWLYQFYKYGKANRKIPATISVSLGRKL
                     DMLNAADKIGDLRSPPGNRFENLNPPLTGYSSIRVNDKYRLIFKWGENGVEDLYLDPHD
                     YR"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            1477..1719
                     /locus_tag="QU716_27510"
     CDS             1477..1719
                     /locus_tag="QU716_27510"
                     /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="WJU62935.1"
                     /translation="MALVRSGNKTKIFEADPKFNPVFDTQHKPGDTCTYEGIYKCTGCG
                     KEVTIAGGKTLPPQNHHQHSPGQGDIRWQLFVYAE"
                     /name="protein L"
     gene            complement(2261..2707)
                     /locus_tag="QU716_27515"
     CDS             complement(2261..2707)
                     /locus_tag="QU716_27515"
                     /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="WJU62929.1"
                     /translation="MNDKSGFSFMKIGAGAKVTGLRMKRNVMVVDDLSHVESFVTVGER
                     GEVINLDADGNELHTPDSYREKLKIERGELQASLEKAKEEINSIDNDITSQKIKNQLSA
                     ALSQPMDAEGEWNTKRILQGVLDLSKQVGCGVLTAAITHYLGVS"
                     /name="hypothetical protein"
     gene            complement(3494..3904)
                     /locus_tag="QU716_27520"
     CDS             complement(3494..3904)
                     /locus_tag="QU716_27520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /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="WJU62930.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKIIKVID
                     TSELIRVFGSLDGVIDTVKSDAGSTGVNSVGLHDLQHRIALLEAENDGLKGAVKARDEH
                     IDSLRQAMQLLEHKHEPSSPPDSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3904..4095)
                     /locus_tag="QU716_27525"
     CDS             complement(3904..4095)
                     /locus_tag="QU716_27525"
                     /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="WJU62931.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2..114
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.368"
                     /coverage="100.0"
                     /evalue="1.23e-47"
     Typing          4215..4510
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.01e-153"
ORIGIN
        1 atgcacgaac cccccgttca gtccgactgc tgcgtcttat ccggtaacta tcgtcttgag
       61 tccaacccgg taagacatgc aaaagcgcca ctggcagcag ccactggtaa ctgatttaga
      121 ggagttagtc ttgaagtcat gcgcctgtta aggctaaact gaaagaacaa gttttggtga
      181 ctgcgctcct ccaagccagt taccttggtt caatcacctg caagtgtttg aaccttcgga
      241 aaaaccgccc tgcaaggcgg tttttccgtt tacagagcaa gagattacgc gtaccgaaac
      301 cggatctcaa gtgctcgtaa aagaaaatga tgatgacctt tagcggttac aaaaaaagaa
      361 ggcacactat tacagaggcc ttcttctagt ttggttaaat ttttttaaaa aaatcatgcg
      421 accgcatgtt ttttttccaa agattcagca ttgtgcttcc tttctataat ttcatgagcg
      481 ggagtgactc tttctatttc ttcctgaagg cgtgggctgc tcgtaacctc ccacaaatca
      541 acagactgct gtatatttaa ccagaactta gcggtagtat cgaatgcttt agctaaccga
      601 aacgccatat cggtagacag tttcctatta ttgttaacca aagcacttgc agaatttcta
      661 tgcacgttta acatttcagc caagtcattg atttttaaac cacttggctc gagatattca
      721 taaagaataa tatctcctac agtcgatggt tttctggttg cttgggacat gctttactcc
      781 tgaattggtc gcttctctct gttagatgag gaagataagt atttcttctg ttaccagctg
      841 tatcgattag taattatctt aaatatagtt acgtcgcgtt actttattaa tcattatttg
      901 tgatgacgtt ttaacgtagg tgaggaaatg cctcacctac ttgttttgta agataacagt
      961 tccggtctgt tacctatcgg taatcatgtg gatcgagata caaatcctcg actccgttct
     1021 caccccactt aaatatcaag cggtacttat cattcaccct tatagatgaa taccctgtca
     1081 atggagggtt gagattttca aatcggttcc ccgggggaga ccgtaaatct ccaattttat
     1141 cagcagcatt cagcatatcc agcttgcgac ctaatgaaac actaatcgta gctggaattt
     1201 ttcgattggc tttaccgtat ttataaaact ggtatagcca atcgtctcgg aactgaatgc
     1261 ggcaatcatc atcactatca tgattttgct gcatttttct tttacctcaa atgttgccgc
     1321 aacttggcaa gttctagatc accttttacc accaccatag tacaacaaac gccagaaatg
     1381 cacaatagca ctgtgcactt gtgcaaaaaa ccataatgat ataaaatgca caaaagcaca
     1441 gtgctactgt gcaaaaaaag aatagttgga ggtcatatgg cgcttgttcg ctcaggaaat
     1501 aaaaccaaga tttttgaagc agatccgaaa tttaacccag tttttgatac acaacacaag
     1561 cctggcgata cgtgcacgta tgaaggaatt tacaaatgca caggttgcgg taaagaagta
     1621 actatcgcag gagggaaaac acttccacca caaaatcatc atcaacatag tcccggacag
     1681 ggggacatcc gctggcaact atttgtttat gcagagtgag gtatgaaaat ggcagaccgt
     1741 agaccactta acccgcatgt cgtcgtccct aaaccaggag gcggaactca gccacgagat
     1801 cgtaataata atggaagagt ccgagagaaa cgttcagatg cgggaaaatc aagaaaataa
     1861 gaaaagccgc caaatagggg tcagtttgga tatcggaaac ttttgtacgt taagcgcatt
     1921 atttaaccaa tattgatgcg taagggattg attttacctc agctacgatc gcttttaagt
     1981 caccgctctt tctgtatcgc atttaggtta tccgattaag gaaaattcac gggaaacggc
     2041 gtatagcgcg ggagtacatc attgcgagag gtaagcctgt tcaaaacaca ggcttaccgt
     2101 acaataattc tctatatcca aactgacccc aagaagtctg acactaaccc cacacaaatc
     2161 gaatccgttg caagatgaga cacacaagaa aagagctaga cgaaggtcgc tccgctcccc
     2221 atggtttttg tatacccacc atgggggcat aggtagttta ttaactaact ccaagataat
     2281 gcgtgatcgc agccgtgagt acaccacagc ccacttgttt agataaatct aaaacccctt
     2341 gtaggattct cttagtgttc cactcacctt ctgcatccat tggttgagat agtgcagcac
     2401 tcaactggtt cttaatcttt tgcgaagtta tatcgttatc tattgagttg atttcctcct
     2461 tggctttctc caaggaagcc tggagttcac cgcgttctat ttttaacttt tcacgataac
     2521 tgtctggtgt gtgtagttcg ttcccatccg catcgagatt aataacttcg cctcgctcac
     2581 caacagtaac aaagctctct acgtgagaca gatcatcaac aaccatcaca ttccttttca
     2641 ttcttaaacc agtcactttt gcacctgcac cgatcttcat aaaactaaag cctgatttat
     2701 cgttcactca catcacctca taagataaaa atgttaataa cgttttcacg agcaattatt
     2761 taccataacg cctcattacg cgcaccgctc aaacgctcta gaaacgattc tggggcgtaa
     2821 tccattaaat cctacgtctt accccctgaa aacgcctcaa aatcgctcca gggcgtttta
     2881 cgggcatgaa ttgttatgca ccagactgac tggtggcgga tttcagcctg aattcaggcc
     2941 agacaactca aaacccgcac caaaccagac tgaaaacggt gaacggggac gcaatttatt
     3001 gcgtggccgt gaagcgttgc cggcgcagcc ggaaaaacgg ttttcagcac gttcaggaat
     3061 cgggttcgtc gacggccggc aatcacgtta tgcaagtcgc cggacgactc accacacgat
     3121 tcaccggcga ttcgactcgt gacttgactc tagagtcgcc aaggtcaaaa aaacaccaaa
     3181 atgacgattc gactctagag tcaagtcgtc ataagttact gatagtctta agtgagtcgt
     3241 cgatgactct atgacgagtc gtcggcaagt cgtacacgaa tcgccgacga cttggattca
     3301 ccttacagaa agtaatactg cgtaatgtaa taacccacaa ctaactgata ttaatgaatt
     3361 atcttcaaaa ttttaatttt gcgtggggtg tgggtatttt tagtggtgag gagcgttcag
     3421 agatctggcg atttttggga aggttcagga actccccggg atggccggag aggaaaacgg
     3481 aagcatgacg gagtcaggat tttttccaga atttccacca cggggaatcg ggtggtgaag
     3541 aaggttcgtg cttgtgctcc agaagctgca tagcctgacg aagggaatca atatgctcat
     3601 ctcgagcctt aacagcccct ttaagaccat cgttttcagc ttctagtaaa gcaattctat
     3661 gttgtaaatc atgtaaacca acgctgttaa cacctgtaga tcctgcgtca ctttttacag
     3721 tatcgatgac accatcaaga gaaccaaaaa ctctaataag ctctgaagta tcaataactt
     3781 taatgatctt cccgtgcttt acaacagagg tgtaacttaa cttcccactg ttaatcatct
     3841 tgtaaattgt ggggcgacta accttaacaa gccgtgccgc ttcactaata gacactctgg
     3901 ccatcagtta ccatcctgta attcatccag tctcgaggac agtgtacgga aaagatgctc
     3961 cgcatcatcg tggagtttct cacaaaggtc ggcctctgca tcaagatcaa gctcgttaag
     4021 cttctccagc aggagcagag actgattctg gatgaattta gccatgttca gcgctgtttt
     4081 ctgttgtttc gtcataagaa gcctcagagc gtcagtgctc agtgtaaaac cagtctcttt
     4141 tccgcttcct cgctcactca gtcgctacgc tcctgccgtt cggctgcggc gagcggtagg
     4201 actatgcgta taaatgctcg agaaaaccga gcggacgcgt gatgggcaga aggaaaggcc
     4261 gcttagcggc cgtttttcca taggctccgc ccccctgaca agcatcatag aaattgacgc
     4321 tcaaatcagt ggtggcgaaa cccgacagga ctataaagat atcaggcgtt tccccctgat
     4381 ggctccctcg tgcgctctcc tgttcctgcc attcggttta ccggtgtcat tccgctgtta
     4441 tggccgcgtt tatctcattc cacgccagac actcagttcc gggaaggcag ttcgctccaa
     4501 gctggactgt
//
