LOCUS       NZ_CP061383             5488 bp    DNA     circular CON 10-JAN-2024
DEFINITION  Klebsiella pneumoniae strain NU-CRE236 plasmid pCRE-236-3, complete
            sequence.
ACCESSION   NZ_CP061383
VERSION     NZ_CP061383.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14453497
            Assembly: GCF_012029895.2
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5488)
  AUTHORS   Ozer,E.A., Krapp,F. and Hauser,A.R.
  TITLE     Carbapenem-resistant Klebsiella pneumoniae
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5488)
  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 5488)
  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
  REMARK    ?
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                   :: 133.76007750862843x
            Sequencing Technology :: Oxford Nanopore MiniION, Ilumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/10/2024 01:23:23
            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)                     :: 5,416
            CDSs (total)                      :: 5,293
            Genes (coding)                    :: 5,156
            CDSs (with protein)               :: 5,156
            Genes (RNA)                       :: 123
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 137
            CDSs (without protein)            :: 137
            Pseudo Genes (ambiguous residues) :: 0 of 137
            Pseudo Genes (frameshifted)       :: 59 of 137
            Pseudo Genes (incomplete)         :: 80 of 137
            Pseudo Genes (internal stop)      :: 30 of 137
            Pseudo Genes (multiple problems)  :: 30 of 137
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP061383.1.
            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..5488
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="NU-CRE236"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pCRE-236-3"
                     /geo_loc_name="USA: Chicago, IL"
                     /lat_lon="41.8945 N 87.6208 W"
     gene            join(4578..5488,1..910)
                     /locus_tag="HCV86_RS26910"
                     /old_locus_tag="HCV86_026905"
     CDS             join(4578..5488,1..910)
                     /locus_tag="HCV86_RS26910"
                     /old_locus_tag="HCV86_026905"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="Tn3 family transposase"
                     /protein_id="WP_001301408.1"
                     /translation="MAIRRRRRMFILFAERKVGEQHGPAAQGVLAAVQTLREMNADNLR
                     KVPADAPTAFIKPRWKPLVITPEGLDRKFYEICALSELKNALRSGDIWVKGSRQFRDFD
                     DYLLPAEKFAALKREQALPLAINPNSDQYLEERLQLLDEQLATVTRLAKDNELPDAILT
                     ESGLKITPLDAAVPDRAQALIDQTSQLLPRIKITELLMDVDDWTGFSRHFTHLKDGAEA
                     KDRTLLLSAILGDAINLGLTKMAESSPGLTYAKLSWLQAWHIRDETYSAALAELVNHQY
                     RHAFAAHWGDGTTSSSDGQRFRAGGRGESTGHVNPKYGSEPGRLFYTHISDQYAPFSTR
                     VVNVGVRDSTYVLDGLLYHESDLRIEEHYTDTAGFTDHVFALMHLLGFRFAPRIRDLGE
                     TKLYVPQGVQAYPTLRPLIGGTLNIKHVRAHWDDILRLASSIKQGTVTASLMLRKLGSY
                     PRQNGLAVALRELGRIERTLFILDWLQSVELRRRVHAGLNKGEARNSLARAVFFNRLGE
                     IRDRSFEQQRYRASGLNLVTAAIVLWNTVYLERATQGLVEAGKPVDGELLQFLSPLGWE
                     HINLTGDYVWRQSRRLEDGKFRPLRMPGKP"
                     /name="Tn3 family transposase"
     gene            968..1210
                     /locus_tag="HCV86_RS26915"
                     /old_locus_tag="HCV86_026910"
     CDS             968..1210
                     /locus_tag="HCV86_RS26915"
                     /old_locus_tag="HCV86_026910"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000844627.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="transposase"
                     /protein_id="WP_000844627.1"
                     /translation="MKTAALDLARERQAHEAGARTRATAHERTPQQERQKAAREAERGR
                     EAWTLGQGMKKPVAGCYGRLTRWKGGGDVVYMALL"
                     /name="transposase"
     gene            complement(1242..1892)
                     /gene="tetR(A)"
                     /locus_tag="HCV86_RS26920"
                     /old_locus_tag="HCV86_026915"
     CDS             complement(1242..1892)
                     /gene="tetR(A)"
                     /locus_tag="HCV86_RS26920"
                     /old_locus_tag="HCV86_026915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000164043.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="tetracycline resistance transcriptional repressor
                     TetR(A)"
                     /protein_id="WP_000164043.1"
                     /translation="MTKLQPNTVIRAALDLLNEVGVDGLTTRKLAERLGVQQPALYWHF
                     RNKRALLDALAEAMLAENHTHSVPRADDDWRSFLIGNARSFRQALLAYRDGARIHAGTR
                     PGAPQMETADAQLRFLCEAGFSAGDAVNALMTISYFTVGAVLEEQAGDSDAGERGGTVE
                     QAPLSPLLRAAIDAFDEAGPDAAFEQGLAVIVDGLAKRRLVVRNVEGPRKGDD"
                     /name="tetR(A)"
     gene            1998..3197
                     /gene="tet(A)"
                     /locus_tag="HCV86_RS26925"
                     /old_locus_tag="HCV86_026920"
     ARG             1999..3194
                     /name="tet(A)"
                     /gene="tet(A)"
                     /gene_name="tetracycline efflux MFS transporter Tet(A)"
                     /tool="amrfinderplus"
                     /drug_class="TETRACYCLINE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(3229..4113)
                     /locus_tag="HCV86_RS26930"
                     /old_locus_tag="HCV86_026925"
     CDS             complement(3229..4113)
                     /locus_tag="HCV86_RS26930"
                     /old_locus_tag="HCV86_026925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000058717.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EamA family transporter"
                     /protein_id="WP_000058717.1"
                     /translation="MSLRTPDLLFTAIAPAIWGSTYIVTTQYLPNFSPMTVAMLRALPA
                     GLLLVMIVRQIPTGIWWMRIFILGALNISLFWSLLFISVYRLPGGVAATVGAVQPLMVV
                     FISAALLGSPIRLMAVLGAICGTAGVALLVLTPNAALDPVGVAAGLAGAVSMAFGTVLT
                     RKWQPPVPLLTFTAWQLAAGGLLLVPVALVFDPPIPMPTGTNVLGLAWLGLIGAGLTYF
                     LWFRGISRLEPTVVSLLGFLSPGTAVLLGWLFLDQTLSALQIIGVLLVIGSIWLGQRSN
                     RTPRARIACRKSP"
                     /name="EamA family transporter"
     gene            complement(4251..4643)
                     /locus_tag="HCV86_RS26935"
                     /old_locus_tag="HCV86_026930"
     CDS             complement(4251..4643)
                     /locus_tag="HCV86_RS26935"
                     /old_locus_tag="HCV86_026930"
                     /EC_number="3.-.-.-"
                     /inference="COORDINATES: protein motif:HMM:NF013053.4"
                     /GO_function="GO:0016787 - hydrolase activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="isochorismatase family cysteine hydrolase"
                     /protein_id="WP_001351729.1"
                     /translation="MLFPNFSLGEEYEHAPPATNRQISPYLPSGRFRTGLPVEGLAIER
                     GDLFYACPRASVFYGTALDADLRTRGVSTLVMAGISTTGVVLSSVAWASDADYDVRLVQ
                     DCCYDPDRDAHEALLRSGFGGRVQVV"
                     /name="isochorismatase family cysteine hydrolase"
ORIGIN
        1 gggtggccgg ggcgagagca ccgggcacgt caacccgaag tacggtagcg agccgggacg
       61 gctgttctat acccatatct ccgaccagta cgcgccgttc agcacccgcg tggtgaatgt
      121 cggcgtccgc gattccacct atgtgctcga cggcctgctg taccacgagt ccgacctgcg
      181 gatcgaggag cactacaccg acacggccgg cttcaccgat cacgtctttg ccctgatgca
      241 cctgctaggc ttccgcttcg cgccgcgcat ccgcgacctc ggcgaaacca agctgtacgt
      301 gccgcagggc gtgcaagcct acccgacgtt gcgcccgctg atcggcggca ccctgaacat
      361 caagcacgtg cgtgcccact gggacgacat cctgcgcctg gccagctcga tcaagcaggg
      421 caccgtcacc gcctcgctga tgctgcgcaa gctcggcagc tacccgcgcc agaacggact
      481 ggccgtggcc ctgcgcgagc tgggccggat cgagcgcacg ctgttcatcc tggactggct
      541 gcaaagtgtt gaactgcgcc gccgcgtgca tgccggcctg aacaaaggtg aggcgcgcaa
      601 ctcgctggcc agggcggtgt tcttcaaccg ccttggggaa atcagggatc ggagcttcga
      661 gcagcagcgc taccgggcca gcggcctcaa cctggtgacg gcggctatcg tgctgtggaa
      721 cacggtgtac ctggaacgcg ccacccaggg gttggtcgag gccggcaagc cggtggacgg
      781 cgagctgctg caattcctgt cgccgctggg ctgggagcac atcaacctaa ccggcgatta
      841 cgtctggcgg cagagccgca gactggaaga cgggaagttt cggcccttac ggatgcccgg
      901 aaaaccttag cgtacgattt tttccgaatt ctgcgggctc ccctatctca tctgcgcaag
      961 gcagaacgtg aagacggccg ccctggacct cgcccgcgag cgccaggcgc acgaggccgg
     1021 cgcgcggacc cgcgccacgg cccacgagcg gacgccgcag caggagcgcc agaaggccgc
     1081 cagagaggcc gagcgcggcc gtgaggcttg gacgctaggg cagggcatga aaaagcccgt
     1141 agcgggctgc tacgggcgtc tgacgcggtg gaaaggggga ggggatgttg tctacatggc
     1201 tctgctgtag tgagtgggtt gcgctccggc agcggtcctg atcaatcgtc accctttctc
     1261 ggtccttcaa cgttcctgac aacgagcctc cttttcgcca atccatcgac aatcaccgcg
     1321 agtccctgct cgaacgctgc gtccggaccg gcttcgtcga aggcgtctat cgcggcccgc
     1381 aacagcggcg agagcggagc ctgttcaacg gtgccgccgc gctcgccggc atcgctgtcg
     1441 ccggcctgct cctcaagcac ggccccaaca gtgaagtagc tgattgtcat cagcgcattg
     1501 acggcgtccc cggccgaaaa acccgcctcg cagaggaagc gaagctgcgc gtcggccgtt
     1561 tccatctgcg gtgcgcccgg tcgcgtgccg gcatggatgc gcgcgccatc gcggtaggcg
     1621 agcagcgcct gcctgaagct gcgggcattc ccgatcagaa atgagcgcca gtcgtcgtcg
     1681 gctctcggca ccgaatgcgt atgattctcc gccagcatgg cttcggccag tgcgtcgagc
     1741 agcgcccgct tgttcctgaa gtgccagtaa agcgccggct gctgaacccc caaccgttcc
     1801 gccagtttgc gtgtcgtcag accgtctacg ccgacctcgt tcaacaggtc cagggcggca
     1861 cggatcactg tattcggctg caactttgtc atgcttgaca ctttatcact gataaacata
     1921 atatgtccac caacttatca gtgataaaga atccgcgcgt tcaatcggac cagcggaggc
     1981 tggtccggag gccagacgtg aaacccaaca gacccctgat cgtaattctg agcactgtcg
     2041 cgctcgacgc tgtcggcatc ggcctgatta tgccggtgct gccgggcctc ctgcgcgatc
     2101 tggttcactc gaacgacgtc accgcccact atggcattct gctggcgctg tatgcgttga
     2161 tgcaatttgc ctgcgcacct gtgctgggcg cgctgtcgga tcgtttcggg cggcggccgg
     2221 tcttgctcgt ctcgctggcc ggcgctgctg tcgactacgc catcatggcg acggcgcctt
     2281 tcctttgggt tctctatatc gggcggatcg tggccggcat caccggggcg actggggcgg
     2341 tagccggcgc ttatattgcc gatatcactg atggcgatga gcgcgcgcgg cacttcggct
     2401 tcatgagcgc ctgtttcggg ttcgggatgg tcgcgggacc tgtgctcggt gggctgatgg
     2461 gcggtttctc cccccacgct ccgttcttcg ccgcggcagc cttgaacggc ctcaatttcc
     2521 tgacgggctg tttccttttg ccggagtcgc acaaaggcga acgccggccg ttacgccggg
     2581 aggctctcaa cccgctcgct tcgttccggt gggcccgggg catgaccgtc gtcgccgccc
     2641 tgatggcggt cttcttcatc atgcaacttg tcggacaggt gccggccgcg ctttgggtca
     2701 ttttcggcga ggatcgcttt cactgggacg cgaccacgat cggcatttcg cttgccgcat
     2761 ttggcattct gcattcactc gcccaggcaa tgatcaccgg ccctgtagcc gcccggctcg
     2821 gcgaaaggcg ggcactcatg ctcggaatga ttgccgacgg cacaggctac atcctgcttg
     2881 ccttcgcgac acggggatgg atggcgttcc cgatcatggt cctgcttgct tcgggtggca
     2941 tcggaatgcc ggcgctgcaa gcaatgttgt ccaggcaggt ggatgaggaa cgtcaggggc
     3001 agctgcaagg ctcactggcg gcgctcacca gcctgacctc gatcgtcgga cccctcctct
     3061 tcacggcgat ctatgcggct tctataacaa cgtggaacgg gtgggcatgg attgcaggcg
     3121 ctgccctcta cttgctctgc ctgccggcgc tgcgtcgcgg gctttggagc ggcgcagggc
     3181 aacgagccga tcgctgatcg tggaaacgat aggcctatgc catgcgggtc aaggcgactt
     3241 ccggcaagct atacgcgccc taggagtgcg gttggaacgt tggcccagcc agatactccc
     3301 gatcacgagc aggacgccga tgatttgaag cgcactcagc gtctgatcca agaacaacca
     3361 tcctagcaac acggcggtcc ccgggctgag aaagcccagt aaggaaacaa ctgtaggttc
     3421 gagtcgcgag atcccccgga accaaaggaa gtaggttaaa cccgctccga tcaggccgag
     3481 ccacgccagg ccgagaacat tggttcctgt aggcatcggg attggcggat caaacactaa
     3541 agctactgga acgagcagaa gtcctccggc cgccagttgc caggcggtaa aggtgagcag
     3601 aggcacggga ggttgccact tgcgggtcag cacggttccg aacgccatgg aaaccgcccc
     3661 cgccaggccc gctgcgacgc cgacaggatc tagcgctgcg tttggtgtca acaccaacag
     3721 cgccacgccc gcagttccgc aaatagcccc caggaccgcc atcaatcgta tcgggctacc
     3781 tagcagagcg gcagagatga acacgaccat cagcggctgc acagcgccta ccgtcgccgc
     3841 gaccccgccc ggcaggcggt agaccgaaat aaacaacaag ctccagaata gcgaaatatt
     3901 aagtgcgccg aggatgaaga tgcgcatcca ccagattccc gttggaatct gtcggacgat
     3961 catcacgagc aataaacccg ccggcaacgc ccgcagcatc gcgaccgtca tcggtgagaa
     4021 gttcggcagg tattgggtgg tgacaatgta ggtgctgccc caaatggcag gtgctatcgc
     4081 tgtgaacaat aaatcgggcg tgcgtaatga catgcgatta caagacctcc gctacggcga
     4141 tgggtttttg agagttgcag gcgccgcgat gaccgcaccc tgacttggac tggccctgcc
     4201 tcgcaccaat ccacctgcgg ctatggccgc gatcatgcga ggcccgaaaa ttacacgacc
     4261 tgtacacgtc cgccgaaccc ggaacgcaac agagcttcgt gggcatcccg atccgggtcg
     4321 tagcagcagt cctggaccaa acgcacgtcg tagtccgcat cactagccca ggcgacgctt
     4381 gaaagaacaa cgccggtggt gcttatcccg gccatgacaa gcgtgcttac gccgcgcgtc
     4441 cgaaggtcgg cgtcgagcgc cgtgccataa aagacgctgg ctcgcggaca tgcatagaaa
     4501 aggtcgcccc gttcgatcgc aagcccttcg acgggcagac cggtgcgaaa tcgtccgctc
     4561 gggagatacg gtgagatttg gcgattcgtc gccggcggcg catgttcata ctcttcgccg
     4621 agcgaaaagt tggggaacag cacgggccgg ccgcgcaagg cgtgctggca gccgtgcaga
     4681 ccctgcgtga gatgaacgcc gacaacctgc gcaaggtgcc ggccgatgca cccacggcct
     4741 tcatcaagcc gcgctggaag ccgctggtga tcaccccgga aggcctcgac cggaaattct
     4801 acgaaatctg cgccctgtcc gagctgaaga acgccctgcg ctccggcgac atctgggtca
     4861 agggctcgcg gcagttccgc gacttcgacg actacctgct gccggccgag aagttcgccg
     4921 cactcaagcg cgagcaggcc ctgcccctgg cgatcaaccc gaacagcgac cagtacctgg
     4981 aagagcgttt gcagctgctg gacgagcagt tggccaccgt cacccgcctg gccaaggaca
     5041 acgagctgcc cgatgccatc ctcaccgagt cagggctgaa aatcaccccg ctggatgcgg
     5101 cggtgccgga tcgggcgcag gcgctgatcg accaaaccag ccagttactg ccgcgcatca
     5161 agatcaccga actgctgatg gacgtggacg actggacggg cttcagccgc cacttcaccc
     5221 acttgaagga cggggccgag gccaaagaca ggacgttgct gctgtccgca atcctcggtg
     5281 atgcgatcaa cctcgggctg accaagatgg ccgagtcgag ccccggcctg acctacgcca
     5341 agctgtcctg gctgcaagcc tggcacatcc gcgacgaaac ctattcggcg gccttggccg
     5401 agctggtcaa ccaccagtat cgccacgcct ttgccgccca ctggggcgac ggcacgacct
     5461 catcctccga tggccagcgc ttccgcgc
//
