LOCUS       NZ_CP073059             5657 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Klebsiella pneumoniae strain MGH83 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP073059
VERSION     NZ_CP073059.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03280386
            Assembly: GCF_001185665.2
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5657)
  AUTHORS   Earl,A.M., Manson,A.L., Bhattacharyya,R., Brennan-Krohn,T.,
            Cosimi,L., Delaney,M., Ferraro,M.J., Gilmore,M., Gussin,G.,
            Hooper,D., Huang,S., Kim,D., Kirby,J., Onderdonk,A., Peterson,E.,
            Pierce,V., Shenoy,E., Wurster,J., Shea,T.D., Chapman,S., Howe,W.,
            Walker,B. and Birren,B.W.
  TITLE     Multi-genus dynamics of carbapenem resistance within hospitals
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5657)
  AUTHORS   Earl,A.M., Manson,A.L., Bhattacharyya,R., Brennan-Krohn,T.,
            Cosimi,L., Delaney,M., Ferraro,M.J., Gilmore,M., Gussin,G.,
            Hooper,D., Huang,S., Kim,D., Kirby,J., Onderdonk,A., Peterson,E.,
            Pierce,V., Shenoy,E., Wurster,J., Shea,T.D., Chapman,S., Howe,W.,
            Walker,B. and Birren,B.W.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-MAY-2021) Infectious Disease and Microbiome Program,
            Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
  REMARK    Sequence update by submitter
REFERENCE   3  (bases 1 to 5657)
  AUTHORS   Earl,A.M., Manson,A.L., Bhattacharyya,R., Brennan-Krohn,T.,
            Cosimi,L., Delaney,M., Ferraro,M.J., Gilmore,M., Gussin,G.,
            Hooper,D., Huang,S., Kim,D., Kirby,J., Onderdonk,A., Peterson,E.,
            Pierce,V., Shenoy,E., Wurster,J., Shea,T.D., Chapman,S., Howe,W.,
            Walker,B. and Birren,B.W.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-AUG-2020) Infectious Disease and Microbiome Program,
            Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
REFERENCE   4  (bases 1 to 5657)
  AUTHORS   Earl,A.M., Onderdonk,A.B., Kirby,J., Ferraro,M.J., Huang,S.,
            Spencer,M., Fodor,A., Hooper,D., Dekker,J., O'Brien,T., Quan,V.,
            Gombosev,A., Delaney,M., Dubois,A., Ernst,C., Kim,D.S., Rossman,W.,
            Gohs,F., Petruso,H., Nozar,T., Mougeot,F., Manson-Mcguire,A.,
            Young,S., Abouelleil,A., Cao,P., Chapman,S.B., Griggs,A., Priest,M.,
            Shea,T., Wortman,I., Wortman,J.R., Nusbaum,C. and Birren,B.
  CONSRTM   The Broad Institute Genomics Platform, The Broad Institute Genome
            Sequencing Center for Infectious Disease
  TITLE     Direct Submission
  JOURNAL   Submitted (10-JUN-2015) Broad Institute of MIT and Harvard, 7
            Cambridge Center, Cambridge, MA 02142, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.3
            Assembly Name                     :: MGH83
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 189x
            Sequencing Technology             :: Illumina; Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 14:23:05
            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)                     :: 5,956
            CDSs (total)                      :: 5,829
            Genes (coding)                    :: 5,689
            CDSs (with protein)               :: 5,689
            Genes (RNA)                       :: 127
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 140
            CDSs (without protein)            :: 140
            Pseudo Genes (ambiguous residues) :: 0 of 140
            Pseudo Genes (frameshifted)       :: 57 of 140
            Pseudo Genes (incomplete)         :: 85 of 140
            Pseudo Genes (internal stop)      :: 25 of 140
            Pseudo Genes (multiple problems)  :: 24 of 140
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP073059.1.
            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..5657
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="MGH83"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="unnamed5"
                     /collection_date="2014"
     gene            complement(join(5430..5657,1..888))
                     /locus_tag="SM57_RS29610"
     CDS             complement(join(5430..5657,1..888))
                     /locus_tag="SM57_RS29610"
                     /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_123677980.1"
                     /translation="MKVYHPAPEEPKLKSVFKYNDYYARVSTYRAGHTISAGHQASLAA
                     GKPKRIAGKLPHSMAKKRTFKENRFDIDPASTPGTPYFFTLKPFSEIEPEHFSEALKAL
                     ISMLKAKKTQYIYMLEWAEHEKMPHIHLVANIHGEMSEDLEAFATSVKLHWSKKTCGSH
                     LAEARQHHEPVYDACGVFGYMSKQSPDEFNDRAIATGKDWSVISVTGCSRGWKKPSLEV
                     CEVSPEVGLDIKRGMKRIVEARGVKLSKVSKGCDSEAKRVISEVSPFTISGLSREESRR
                     LRDQVIDSQPLKERRYLIVMRDLYHRAHELDSQEVKGEVERLLLDKGYDMRHMFPDWEK
                     PKMSMAERYKTVPVYRLLRKTKKAIMAAREK"
                     /name="hypothetical protein"
     gene            complement(961..1341)
                     /locus_tag="SM57_RS29615"
     CDS             complement(961..1341)
                     /locus_tag="SM57_RS29615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001516808.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_050849818.1"
                     /translation="MANLTRTEVAKLIRNKLLNGSKLTPKQFDRILHKHGNHERSRVLE
                     LLRCKWGIPIITDRKGCYSVDESHLRRFADDADDAMSGWKDEAKRKREYRQLYRFVATL
                     SGLTGISCEARSEVLAAVEARI"
                     /name="hypothetical protein"
     gene            complement(1334..1540)
                     /locus_tag="SM57_RS29620"
     CDS             complement(1334..1540)
                     /locus_tag="SM57_RS29620"
                     /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_050849819.1"
                     /translation="MTQKYLIADEAAAYLNISRARFFDFRRFIPAFPKPIKIRLNEGRP
                     RLVWTPEQLDTFSLSFWGDRSHG"
                     /name="hypothetical protein"
     gene            complement(1830..2030)
                     /locus_tag="SM57_RS29625"
     CDS             complement(1830..2030)
                     /locus_tag="SM57_RS29625"
                     /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_123677981.1"
                     /translation="MLKKDDIILIKSYGNEKIKIFLRGVNEVLMIDASFEEVKFAINND
                     LQDLQDLQGMQAVSAPLKIVT"
                     /name="hypothetical protein"
     gene            complement(3154..3591)
                     /locus_tag="SM57_RS29630"
     CDS             complement(3154..3591)
                     /locus_tag="SM57_RS29630"
                     /inference="COORDINATES: protein motif:HMM:TIGR01764.1"
                     /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_050849814.1"
                     /translation="MAVHTVTEAAKLAGVTRRTIYRYIKQGKLSTVVTGSDSAQIETSE
                     LLRVFGNLSHPEESKVSTGSHQKEPEYVTRLMAEMSQIRDLVQGQQQLLLEDKLKTQKL
                     REQVTGLQNERDAATQELDKVKAELEAERGKGFWKRLFRQG"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3751..4299)
                     /locus_tag="SM57_RS29635"
     CDS             complement(3751..4299)
                     /locus_tag="SM57_RS29635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001273871.1"
                     /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_050849815.1"
                     /translation="MANIGYIRVSSIQQNTERQLAGLALDKVFEEKASGKNIEREQFKA
                     MMDYVREGDTLHVHSIDRLCRKTSDLLATVEELTKRGVIVQFHKEGFKTGKESAFGNFM
                     LTVLAGVAQMEREFMLERQREGYEAAKQAGRIAGRGKSSTIDRRAVRGDLQSGMSIRKT
                     AEKHGISTQTVMKIKSELI"
                     /name="recombinase family protein"
     gene            4568..4885
                     /locus_tag="SM57_RS29640"
     CDS             4568..4885
                     /locus_tag="SM57_RS29640"
                     /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_050849816.1"
                     /translation="MKSKTADSWAELDREIDEVIAKLNAEQPELDLDKLLAVSEEEGKA
                     LLASLEAEPLPELDLDLELNNLDKLLAASEEVNEALLASLEAEPLIELPELDLELLDCA
                     W"
                     /name="hypothetical protein"
ORIGIN
        1 tcgccgctct ttcagtggct ggctgtcgat gacctgatca cgcagccgcc tagactcttc
       61 gcgcgacaac ccggagatgg tgaagggcga aacctctgag atgactctct ttgcctcgct
      121 gtcgcagcct ttggatacct tgctcagctt cacacctctg gcttcgacaa tgcgcttcat
      181 tccccgtttt atgtctaacc caacctctgg actcacctcg cagacttcga gactgggttt
      241 cttccagcct cttgagcaac ccgttacgct aattacagac cagtccttgc ctgtcgctat
      301 tgctctgtcg ttgaactcgt ccggcgactg tttcgacatg tagccaaaca caccacaagc
      361 atcatagaca ggctcatggt gctgcctcgc ctcagcaagg tggctgccgc aagtcttctt
      421 cgaccagtgg agttttacgc tcgttgcgaa tgcctcaagg tcttctgaca tttccccgtg
      481 gatattggca acaaggtgga tgtgcggcat tttctcgtgt tctgcccatt cgagcatgta
      541 gatatattgc gtttttttag ctttcagcat cgagatcagc gctttcaatg cttcggaaaa
      601 gtgttctggc tctatttcag aaaagggctt cagtgtgaag aaataaggcg taccgggggt
      661 gcttgccgga tcaatatcaa accggttttc tttaaacgtt ctcttctttg ccatgctgtg
      721 cgggagcttg ccggctattc ttttgggttt gcctgctgcc aatgacgctt gatgccccgc
      781 tgaaatggtg tgtcccgctc tgtacgtgga cactctggca tagtagtcgt tgtatttgaa
      841 aacgctcttt aattttggtt cttctggtgc agggtggtat actttcacgg tattttgccg
      901 aatacttgtc aattagtaat tgttactagc ccgctctgct aaagcgggct tttctttgtc
      961 ttaaatcctg gcttccactg ctgccagcac ttcgcttctt gcctcacagc tgatcccggt
     1021 taaaccggaa agcgtcgcaa caaaccggta aagctggcga tattcacgct tcctcttcgc
     1081 ttcatccttc cagccagaca tggcatcatc tgcatcatcg gcaaaccgtc gtaaatggct
     1141 ctcatcgacg ctgtaacagc ctttccggtc tgtgatgata ggaatccccc acttacagcg
     1201 caaaagctcc agaacgcggc tacgctcgtg atttccgtgt ttatgcaata tgcggtcaaa
     1261 ttgcttaggg gtcagtttac tgccattcag cagcttgttt cgaatcagct tggctacttc
     1321 ggttcttgtc agattagcca tgtgaacgat ccccccagaa agataacgag aaggtatcaa
     1381 gctgttcagg cgtccaaaca aggcgcggtc tgccttcatt cagtctgatc ttgattggct
     1441 tggggaacgc ggggatgaat cggcggaaat cgaaaaatcg agcgcggctg atattgagat
     1501 aggcggctgc ctcgtctgca atgaggtatt tctgggtcat gatcatttcc ttttgaatgt
     1561 tactgcctac atcctgtaag cagtgtcggg ctttctgcct gacaatgtca gaataacaat
     1621 aaaatacaga catttaaagc cgtactgacg tactgagatt catttactct caatgggata
     1681 acaaacaata aaatgaatca tgccaccaaa acacatcaga acgattctga gagttttttt
     1741 tggggttcag acgggaaaat cgcgcacagt ccgtttcagc ggtgcgcgca acggatgtta
     1801 tggtaaatgt tgagtgctct tactaaaaat caggttacta tttttagcgg tgcgcttact
     1861 gcctgcattc cctgaagatc ctgaagatcc tgaaggtcat tattgatagc aaactttacc
     1921 tcttcaaagc tcgcgtcaat cattagaacc tcattcacac cccgtaaaaa tatttttatt
     1981 ttttcgttac catatgattt tattaggata atatcatctt tttttagcat gatactttcg
     2041 ttacttattg ttttgagatg aagcatcgtc atggtttttt ttgcatgtgc ttgttaaggg
     2101 gattgagatt attcctaaat ccttgagttt gtacatacaa aaaaaacaaa aaaatcctaa
     2161 tgccccgtgg tgggtatata aaaatcacgg ggagcggagc gaccttcgtc cagctcgttt
     2221 cttgtttttc ttaccctgca aaaggtttga tggtgtgggc actgtgctca cgtcggagaa
     2281 tcacactttg ccgcttactg ctgccttgtt cgctcatttt atcaggtgcc agttatcgta
     2341 ctgcgagacg gggtagagct taactctttc gcggttaagt tacgtaccca ccgtttgcct
     2401 gtttatcctg ccggagtccg gggcgtagac ctgagcgtct aaggtgcaga tatgatttta
     2461 atgtcgttga atggtattaa gctggtagtg acaaggctag ccagccctgc gaacgacagt
     2521 aaccaatctc ctttacagaa ggcttcgccc ctcctgacga gcatcacaaa aaagacgctc
     2581 aaatcaagag taggcgaaac ccgacacagc ttaaagatcc tcaccgtttc cgataagtag
     2641 ctccctcgtg cgctcctgtg ttcccacctt aacgtttgca gccagctttg ccgctctttc
     2701 tactttgggg gcgctaactc tcagcttccc tgtgctggca ctgctcgtct taggtggttc
     2761 gctccaagct ggatgatatg cacgaactcc ccgtttcatc cgaccgttgc gcctgctgga
     2821 taactattct cacgattcca accccagcag acacggcaaa acgccgtcat tggcaacagc
     2881 caatacggta acgagtcttg agtgcgggaa ctttgttgat atgcattcgg gcacaaaaac
     2941 gcccgtctgt agcttgaatg ctccgcgtaa ggcagataca ctgatatcac gttttaggta
     3001 gctgttcccg ctaaagactc agttacctgg tagacgagtc ctgagaaaac ccgtttaccc
     3061 gataaatccc gcgcctgaga acgcgggttt tttcgtttct gagcaagaga ttacgctgag
     3121 aaacaaaata taacaagagc cacaccacca aacttagcct tgcctaaaca aacgtttcca
     3181 aaaccccttt ccgcgctcag cctcaagctc cgccttcacc ttgtccagtt cctgagtcgc
     3241 agcatcacgt tcattctgca acccggtcac ctgttctcgc agcttttgag tcttaagctt
     3301 atcctcaagc aataactgct gctgcccttg gaccaaatcc ctgatctgtg acatttcagc
     3361 cattaaacgt gtgacatatt caggctcttt ttggtgtgat ccggtggata ctttagactc
     3421 ttctgggtgt gacaggttgc caaaaacccg tagcaattcg ctggtttcaa tctgggcaga
     3481 gtcactacct gtcactaccg ttgagagctt accctgcttg atatagcggt atattgtacg
     3541 cctagtgaca ccagctaatt tagcggcttc agtgaccgtg tgtaccgcca tgtgacaccc
     3601 cttatcaata cagtgtgatc gattgtgacc atgtttgtga cacggtcact aaccaaacat
     3661 tattaaatag atgggtcaat agtgccatgt ttgcagctaa tcaccttgct gatagtggtt
     3721 ctgtctgctc ggcaagtgct aatgattatc tcaaataagc tcggatttta ttttcatcac
     3781 ggtctgtgtg ctgatgccat gcttttccgc tgtctttctg atagacatcc cggactgtaa
     3841 atcgcctctg acagctctac gatcgattgt ggagcttttt ccacgtccag caatacgtcc
     3901 agcttgctta gctgcttcgt agccttctcg ctgtcgttca agcataaatt cacgctccat
     3961 ctgggctact ccagcaagaa cagtcagcat gaagttgccg aaagcgcttt ctttgccagt
     4021 tttgaaacct tctttgtgaa actggacgat tacgccacgt ttggtaagtt cttcaacggt
     4081 tgccagcaaa tcagaagttt tacgacaaag acgatcgatg ctgtgaacat gcaaggtgtc
     4141 gccctcacgc acataatcca tcatggcttt gaactgttcg cgctcaatgt tttttccgct
     4201 cgctttttct tcaaacactt tatcaagtgc aagaccagcc aactggcgtt ctgtgttctg
     4261 ctggatggat gacacgcgga tgtaaccaat attagccatg caaaaacctt tcgtagtgat
     4321 ttacttcaat gcccaaacac tacggctgta tcacataaaa atcaagacaa atcactacgg
     4381 tttatttcaa ctttaagcgt ggtgaaatag ggtgctttat tagaacggcg ctggtctgct
     4441 ggtggcttgt tatttttaga gaaaccacca atggtgtaaa agccgaaaac acccgacacg
     4501 gtgcgggcta tgtgggataa tcatctggtc tggcaatgat gccactaaca ctaaaaggat
     4561 ttttaacatg aaaagtaaaa ccgctgattc ttgggctgag ctggaccgtg aaattgatga
     4621 ggtaattgct aagctgaatg ctgaacagcc agagctggac ttggacaagc ttctggcagt
     4681 aagcgaagag gaaggcaagg cgcttcttgc ctctcttgag gctgagccgc tgccggagtt
     4741 ggatctggac ttggagttga ataacctgga taagcttctg gcagcaagcg aagaggtgaa
     4801 cgaggcgctt cttgcttctc ttgaggctga gccgctaata gaactgccag agttggattt
     4861 agagcttctg gattgtgctt ggtaaatcca ccagcaccga tttctacggg ttctgagtgg
     4921 ggtgatttaa ccccgctcgt acttacagat aaaaaatccg tttctgttcg accttacgtt
     4981 gcaaggcttc cacgtcattt aagcccctca caccgcatct ggcgtgctct cgctggacat
     5041 caaatgatga tcaaacagct cttatacaac tgaggtttta acgtcatttt ttgacatttt
     5101 aacgtcaact taaaagtata agaactaact acccaaccca gtttctacga aaggatgccc
     5161 ttcgaagtaa gccccttttt ttctaggact ttaactgtgc ccttcccgtt cggtttcaac
     5221 tttggcgcgg agcgccgtta ttgacactga acgattcgcg ccattggcgg tgaaaccgcc
     5281 ctgagcgcag acaaacgact atcaggattc acgcctttct tctctcgctg atggcggttt
     5341 caccgccgtt tgcggctact tttccttgat gattctctgg ttgataaata aacgatttat
     5401 ctctccttca cactactaac agtaacagac tacttctctc tggctgccat tatcgctttt
     5461 ttggttttgc gcaatagcct gtataccgga actgttttgt atctttcagc catgctcatc
     5521 ttcggcttct cccaatcagg gaacatatgg cgcatatcat agcccttatc gagtaatagc
     5581 cgttctactt cgccttttac ctcttgagaa tccagctcat gcgctcgatg atacaagtca
     5641 cgcattacta tgagata
//
