LOCUS       NZ_CP061403             3549 bp    DNA     circular CON 10-JAN-2024
DEFINITION  Klebsiella pneumoniae strain NU-CRE085 plasmid pCRE-085-4, complete
            sequence.
ACCESSION   NZ_CP061403
VERSION     NZ_CP061403.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14453493
            Assembly: GCF_012029975.2
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3549)
  AUTHORS   Ozer,E.A., Krapp,F. and Hauser,A.R.
  TITLE     Carbapenem-resistant Klebsiella pneumoniae
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3549)
  AUTHORS   Ozer,E.A., Krapp,F. and Hauser,A.R.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-SEP-2020) Medicine, Northwestern University Feinberg
            School of Medicine, 645 N Michigan Ave, Suite 900, Chicago, IL
            60611, USA
REFERENCE   3  (bases 1 to 3549)
  AUTHORS   Ozer,E.A., Lopez,F. and Hauser,A.R.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-MAR-2020) Medicine, Northwestern University Feinberg
            School of Medicine, 645 N. Michigan Ave., Suite 900, Chicago, IL
            60611, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 20-AUG-2020
            Assembly Method :: Flye, Unicicyler v. 2.7.1, 0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 470.0953392789152x
            Sequencing Technology :: Oxford Nanopore MiniION, Ilumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/10/2024 01:19:29
            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)                     :: 5,671
            CDSs (total)                      :: 5,547
            Genes (coding)                    :: 5,416
            CDSs (with protein)               :: 5,416
            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)              :: 131
            CDSs (without protein)            :: 131
            Pseudo Genes (ambiguous residues) :: 0 of 131
            Pseudo Genes (frameshifted)       :: 49 of 131
            Pseudo Genes (incomplete)         :: 88 of 131
            Pseudo Genes (internal stop)      :: 14 of 131
            Pseudo Genes (multiple problems)  :: 19 of 131
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP061403.1.
            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..3549
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="NU-CRE085"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pCRE-085-4"
                     /geo_loc_name="USA: Chicago, IL"
                     /lat_lon="41.8945 N 87.6208 W"
     gene            complement(734..>1075)
                     /locus_tag="HCV82_RS28150"
                     /old_locus_tag="HCV82_028145"
                     /pseudo=""
     CDS             complement(734..>1075)
                     /locus_tag="HCV82_RS28150"
                     /old_locus_tag="HCV82_028145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004178052.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            <1074..1676
                     /locus_tag="HCV82_RS28155"
                     /old_locus_tag="HCV82_028150"
                     /pseudo=""
     CDS             <1074..1676
                     /locus_tag="HCV82_RS28155"
                     /old_locus_tag="HCV82_028150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004178051.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="klebicin B-related nuclease bacteriocin"
                     /name="klebicin B-related nuclease bacteriocin"
     gene            1678..1935
                     /locus_tag="HCV82_RS28160"
                     /old_locus_tag="HCV82_028155"
     CDS             1678..1935
                     /locus_tag="HCV82_RS28160"
                     /old_locus_tag="HCV82_028155"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013365855.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin immunity protein"
                     /protein_id="WP_025714833.1"
                     /translation="MAGNKISDFTEEEFTAFVSKIIAADFPTDKENDDAIYSFAQLTEH
                     PAGWNLIFKPKVGEDSSAKGIVKTVKEWRAANGKPGFKKA"
                     /name="bacteriocin immunity protein"
     gene            2043..2198
                     /locus_tag="HCV82_RS28165"
                     /old_locus_tag="HCV82_028160"
     CDS             2043..2198
                     /locus_tag="HCV82_RS28165"
                     /old_locus_tag="HCV82_028160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008323621.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_071561715.1"
                     /translation="MKKLLFLGVVTVSVVLAACQVNNVRDTGGGAVSPSSTVTGVTLDS
                     GTNGNP"
                     /name="colicin release lysis protein"
     gene            complement(2356..2517)
                     /locus_tag="HCV82_RS28670"
     CDS             complement(2356..2517)
                     /locus_tag="HCV82_RS28670"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_049165871.1"
                     /translation="MHEPPVQSDCCVLSGNYHLESNPERHDKAPLAAATGNGFRGVGLE
                     VMRLLRLN"
                     /name="hypothetical protein"
     gene            2922..3113
                     /locus_tag="HCV82_RS28170"
                     /old_locus_tag="HCV82_028165"
     CDS             2922..3113
                     /locus_tag="HCV82_RS28170"
                     /old_locus_tag="HCV82_028165"
                     /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_023302508.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3113..3535
                     /locus_tag="HCV82_RS28175"
                     /old_locus_tag="HCV82_028170"
     CDS             3113..3535
                     /locus_tag="HCV82_RS28175"
                     /old_locus_tag="HCV82_028170"
                     /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="WP_025714834.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKAIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTSINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKREPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     Typing          complement(2405..2874)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.834"
                     /coverage="92.0"
                     /evalue="2.73e-170"
ORIGIN
        1 agttttcctc tccggccatc ccagggagtt cctgaacctt cccaaaaatc gccagatctc
       61 tgaacgctcc tcacgactaa aaatacccac acactacgca aaattaaaat tttgcagatt
      121 ccttatttaa aacaattggt taatgaaaaa ttaatgtgca gtgatgtgtt acaaagtgca
      181 gatccaagtc gtggacgact ctatggcgaa tcgtttacga attgcccacg attcatatgt
      241 gaatcacgct ttattatcat gttgttatga tgaatcgact cttgattcaa ttcatcaatt
      301 tgggcgtttt ttgttcatgg tgactcttga ttcaattcac gattcgaatc gccggtgaat
      361 cgtgtggtga gtcgtccggc gacttgccat aacgtgattg ccggccgtcg acgaacccga
      421 ttcctgaacg tgctgaaaac cggttttccg gctgcgccgg caacgcctca cggccacgca
      481 ataaattgcg tccccgttca ccgttttcgg atcagaagaa cgccggaaac aggacttacc
      541 ctggctgaat ggcgtgaatt tccgcgctat gcacttgcgc gcatactcat gcatgccgta
      601 aaaacagagc ctgcgcgttt ctggcgggtt ttcgggtggt ttgttgcctg ttttaccggt
      661 ttcccgtcag aaacgtcctg aggccgtttt agcggtgcgt acaattaagg gattatggta
      721 aatggtgact tggttaatca taaacatcct gggggatggc atacaccagt tggatatccg
      781 gtgcatcgtt gagccatcga cctgattttt tcattaagta gccaccaatt tcttcggtag
      841 tcagccgggc atgaaacaat gcttcatcat tgaaccagca gtcagggtga tagatgagat
      901 ccagtgggtt tgccttgaaa ttaatctcca gtaactggag tgcatagctg tggtcagatg
      961 cactaccttc tgctttgcgt atgaagttga taacgtcgtt cagttctttc catgtaaagt
     1021 catcgaggta tttttcctga ttaagcgcca tcctggtgaa atctagtgca cttgacgcac
     1081 ctggtgcaaa cggaccactg acgctaagcg ggccggtacc actaccggag cgtattctgc
     1141 ataccggtga tcagatttcg gcgccacagg ctacagataa aaccgtgacg ccggtagcgg
     1201 atgacctcga ttttgacgat attattctgg tgtttcctcc ggaatccggc ctaaaaccgc
     1261 tgtatgtgat gtaccgtagc cctcgtaaca tgcccggtac agtgagcggc aaagggcaga
     1321 acgttggcaa taactggatg gggggggcca gtaccgggga tggtgctcct gttccttccc
     1381 agattgcgga taaattacgc gggaagactt tcggtagttt tgattctttc cgtcgggcgt
     1441 tctggaaagc ggttgctgac gattctgcac tgagcaagca atttagtgaa gctgatatta
     1501 atcagatgaa agctggaagg gcacctactg cggacttttt agaatcagta gggaaacgtg
     1561 ttaaaattga attacaccac gaaaaagaaa tatctcaagg aggggctgtt atggatgtcg
     1621 ataacattaa ggcgctaaca cctaaaaatc atattgagac acataaagga aaataaaatg
     1681 gctggtaata aaatttcaga ttttacggaa gaagaattta ctgcttttgt tagtaaaata
     1741 atcgctgctg attttccaac tgacaaagag aacgatgatg ctatttattc gttcgcccaa
     1801 ctaacagagc atcctgctgg ttggaacctc atcttcaagc ctaaggtagg cgaagattct
     1861 tcggcgaaag gaattgttaa aaccgtaaag gaatggcgag ctgctaacgg taagccaggt
     1921 tttaaaaaag cgtgattgaa tttgcgggtt caagttatga gcccgctcat ttgtaactct
     1981 ggatttgaag aataattact agatatccat ttgcctagaa taataaaaat aaaaggtgat
     2041 atatgaaaaa attacttttc ctaggggttg ttaccgtttc tgtggttctg gcagcatgtc
     2101 aggtcaataa tgttcgagac accggaggtg gggctgtttc accttcatcg acggtgaccg
     2161 gagtcacgct tgatagcggt acgaacggca atccgtaaag gatcttcttg agatcccatt
     2221 tggatcgtcg taatctcttg ctctgtaaac gaaaaaaccg ccttgcaagg cggttttttc
     2281 gaaggttcaa acacttgcag gtgattgaac caaggtaact ggcttagagg agcgcagtca
     2341 ccaaaacttg ttctttcagt ttagccttaa caggcgcatg acttcaagac caactcctct
     2401 aaatccgtta ccagtggctg ctgccagtgg cgctttgtcg tgtctttccg ggttggactc
     2461 aagatgatag ttaccggata agacgcagca gtcggactga acggggggtt cgtgcataca
     2521 gtccagcttg gagcgaactg cctacccgga actgagtgtc aggcgtggaa tgagacaaac
     2581 gcggccataa cagcggaatg acaccggtaa accgaatggc aggaacagga gagcgcacga
     2641 gggagccatc agggggaaac gcctggtatc tttatagtcc tgtcgggttt cgccaccact
     2701 gatttgagcg tcaaattctg tgatgcttgt caggggggcg gagcctatgg aaaaacggcc
     2761 gctgtgctgc cttctccctc tccgagctgt ctgctctatg tcgttatgtg cgcgttgcga
     2821 ccgctcgccg cagccgaacg gcaggagcgt agcgactgag tgagcgagga agcggaaaag
     2881 agaacatccc tacactgagc actgacgctg tgaggcctct tatgacgaaa caacagaaaa
     2941 cagcgctgaa tatggcaaaa ttcatccaga atcagtctct gctcctgctg gagaagctta
     3001 acgagcttga tctcgatgtc gaggccgacc tttgtgagaa actccacgat gatgcggagc
     3061 atcttttccg tacactgtcc tcgagactgg atgaattaca ggatggcaat tgatggccag
     3121 agtgtctatt agtgaagcgg cacggcttgt taaggttagc cgtcccacaa tttacaagat
     3181 gattaacagt gggaagttaa gttacacctc tgttgtaaag cacgggaagg ctattaaagt
     3241 tattgatact tcagagctta ttagagtttt tggttctctt gatggtgtca tcgatactgt
     3301 aaaatatgat gtaaaaagtg acgcagaatc tacaagtatt aacagcgttg gtttacatga
     3361 tttacaacat agaatcgctc tacttgaagc tgaaaacgat ggtcttaaag gggctgttaa
     3421 ggctcgagat gagcatattg attcccttcg tcaggctatg cagcttctgg agcacaagcg
     3481 cgagccttct tcaccacccc attccccgtg gtggaaattc tggaaaaaat cctgatcctg
     3541 ccatgcttg
//
