LOCUS       NZ_CP103581             5466 bp    DNA     circular CON 20-SEP-2023
DEFINITION  Klebsiella pneumoniae strain 4014 plasmid pMB7964_2, complete
            sequence.
ACCESSION   NZ_CP103581
VERSION     NZ_CP103581.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28174049
            Assembly: GCF_024917415.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5466)
  AUTHORS   Shropshire,W.C., Konovalova,A., McDaneld,P.M., Gohel,M., Strope,B.,
            Sahasrabhojane,P., Tran,C.N., Greenberg,D.E., Kim,J., Zhan,X.,
            Aitken,S.L., Bhatti,M., Tor,S., Treangen,T., Hanson,B.M., Arias,C.A.
            and Shelburne,S.A.
  TITLE     Systematic Analysis of Mobile Genetic Elements Mediating
            Beta-lactamase Gene Amplification in Non-Carbapenemase-Producing
            Carbapenem Resistant Enterobacterales Bloodstream Infections
  JOURNAL   mSystems (2022) In press
REFERENCE   2  (bases 1 to 5466)
  AUTHORS   Shropshire,W.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-AUG-2022) Infectious Diseases and Infection Control,
            University of Texas MD Anderson Cancer Center, South Campus Research
            Building 4, Houston, TX 77054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.8.3-b1695
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 163x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/20/2023 05:46:43
            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)                     :: 5,348
            CDSs (total)                      :: 5,224
            Genes (coding)                    :: 5,103
            CDSs (with protein)               :: 5,103
            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)              :: 121
            CDSs (without protein)            :: 121
            Pseudo Genes (ambiguous residues) :: 0 of 121
            Pseudo Genes (frameshifted)       :: 43 of 121
            Pseudo Genes (incomplete)         :: 79 of 121
            Pseudo Genes (internal stop)      :: 15 of 121
            Pseudo Genes (multiple problems)  :: 14 of 121
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP103581.1.
            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..5466
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="4014"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pMB7964_2"
                     /geo_loc_name="USA: Houston"
                     /lat_lon="29.7068 N 95.3971 W"
                     /collection_date="2019-03-23"
                     /collected_by="MDACC"
                     /genotype="ST2004"
     gene            complement(join(5316..5466,1..230))
                     /locus_tag="M5S61_RS26665"
                     /old_locus_tag="M5S61_26665"
     CDS             complement(join(5316..5466,1..230))
                     /locus_tag="M5S61_RS26665"
                     /old_locus_tag="M5S61_26665"
                     /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_196536346.1"
                     /translation="MVNLTRTEVAKLIRNKLLNGGRLTPKQLDRILQKYGNHERSRVLE
                     LLRCKWGIPITIDSKGCYSITESDLRRFSDDPDDVLSGWKENAKKNREYRQLYRFVTAF
                     TGLTGISSETRREVLAAVKARI"
                     /name="hypothetical protein"
     gene            complement(223..429)
                     /locus_tag="M5S61_RS26670"
                     /old_locus_tag="M5S61_26670"
     CDS             complement(223..429)
                     /locus_tag="M5S61_RS26670"
                     /old_locus_tag="M5S61_26670"
                     /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_096835054.1"
                     /translation="MPQKYLVADDAAARLNISRARFFDFRRFIPTFPKPVKVRLNEGRP
                     RLVWTPAQLDAFALAFWGERSHG"
                     /name="hypothetical protein"
     gene            complement(684..1151)
                     /locus_tag="M5S61_RS26675"
                     /old_locus_tag="M5S61_26675"
     CDS             complement(684..1151)
                     /locus_tag="M5S61_RS26675"
                     /old_locus_tag="M5S61_26675"
                     /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_225541014.1"
                     /translation="MVNHLDFLAFQFFKLFAQYEYALKAMGYAKSGRDDSVQLDWDGFS
                     NDIGCLVLVDAEFPLQHAIDYIFDEPPRKQVLEDGKINWRKVNADQRSPQILFSHIRRV
                     RNNLYHGGKFNAHWLQPERSELLVKNSLIVLRALQGKHDGLAEAIRENRAS"
                     /name="hypothetical protein"
     gene            complement(1835..2272)
                     /locus_tag="M5S61_RS26680"
                     /old_locus_tag="M5S61_26680"
     CDS             complement(1835..2272)
                     /locus_tag="M5S61_RS26680"
                     /old_locus_tag="M5S61_26680"
                     /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_065800194.1"
                     /translation="MAVHTVTEAAKLAGVTRRTIYRYIKQGKLSSVVTDSNTTQIETSE
                     LLRVFGALSQPEGSQVSTGSQVEEPEYVTRLMAEMSQIRDLVQGQQQLLLEDKIETQKL
                     REQVTGLQNERDSVAQELDKVKAELEAERGKGFWKRLFRQG"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(2344..2982)
                     /locus_tag="M5S61_RS26685"
                     /old_locus_tag="M5S61_26685"
     CDS             complement(2344..2982)
                     /locus_tag="M5S61_RS26685"
                     /old_locus_tag="M5S61_26685"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001461243.1"
                     /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_065800192.1"
                     /translation="MKSNRVYSYLRASTSEQDASRAKEALQEFAKEHGYTIAAEFIENE
                     SGASLRRPELFNLLKVAQPGDVLLVEQVDRLSRLNAEDWQTLRQTISRKGIRVVALDLP
                     TSHMLLNTGDEFTSRMFEALNSMMLDMLAAIARKDYTDRQRRQAEGIKKAKEQGAYKGR
                     PVNEKLHKQILALREAGRSYSQIQELTGAARTTISKVLNGKNGSIDPSN"
                     /name="recombinase family protein"
     gene            3297..3509
                     /locus_tag="M5S61_RS26690"
                     /old_locus_tag="M5S61_26690"
     CDS             3297..3509
                     /locus_tag="M5S61_RS26690"
                     /old_locus_tag="M5S61_26690"
                     /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_114449708.1"
                     /translation="MKSKTGDSWAEFFAEVERETDKEIAEVSRQLALSEEEDKALLASL
                     EAEPLPELDLDLDLELDLLDIDFDW"
                     /name="hypothetical protein"
     gene            complement(4092..5174)
                     /locus_tag="M5S61_RS26695"
                     /old_locus_tag="M5S61_26695"
     CDS             complement(4092..5174)
                     /locus_tag="M5S61_RS26695"
                     /old_locus_tag="M5S61_26695"
                     /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_135723564.1"
                     /translation="MKRTGEDVTISRTPASRGKSRAGMPGKSTKVDGWTEKTLRGFKDF
                     VRGIDQDNFIGGHVSAITLTTGKRPSPELFKKMIAAVTNELNEMTGGKWVYCIEKTKNQ
                     KAPHVHLIAVFPDSCGDIDAKKVIAAWFKWAMKSNLVPSIENQDARDAWSPEGWMRYMA
                     KRDSKLIIHGTKELSVTKGCLPGVRMWGHGDGWTRTHEDIDLTDAAHRVITSMADAAID
                     IQLHDKGLQDKVVSSRKRRERYGNAAIVAPRSFQPSEMGVSIIKELAANPGLVFGGNGI
                     GFRPESRRECNILRRMLPLQIAREISQEEFDFLYGEISEHYDEEMKDMLADMREAEMED
                     RHRSGDIHIYDEQAHDAEWM"
                     /name="hypothetical protein"
ORIGIN
        1 gggtcatcgg aaaatcgtct taaatcgctc tcagtgatgc tgtaacagcc tttcgagtct
       61 atggtaatgg gtatacccca cttacagcgc aaaagctcca gaacgcggct acgttcgtga
      121 tttccgtatt tctgcaaaat ccggtcaagt tgctttggtg tcagcctacc gccgttcagc
      181 agcttattcc ggatcagctt ggctacttcg gttctggtca gattaaccat gtgagcgctc
      241 tccccagaaa gccaacgcga aggcgtcgag ctgtgcaggt gtccacacaa ggcgcggtct
      301 accctcgttg aggcgaactt tgacgggctt ggggaacgtt ggaataaatc gacggaagtc
      361 gaaaaaacgg gcgcggctga tattaaggcg tgcggctgca tcatctgcaa ccagatactt
      421 ctgaggcatt attacttcct tgtgaatgtt gccgcctaca tcctataagc ggatctggct
      481 tcctgccaga cataatcaag atatctgaac atttaagata aataaatact tattaagaaa
      541 ttggctgttc ttcatatctg aatctcagat tagtaaccag agtttactta aataggtcaa
      601 ccgttgaggc aatgagagtc agatgttatt gtcgccattt agtgctcgac gtatagaaat
      661 gaagactcga acactgcaat gattcacgag gctctatttt cacggatagc ctctgctaga
      721 ccgtcatgtt tcccctgtaa agcccgaaga actataaggg aattcttaac gagtaactcg
      781 cttcgttctg gctgaagcca atgagcatta aatttaccac catgatatag attgtttcgt
      841 accctccgaa tatgagaaaa caaaatctga ggtgagcgtt gatcagcgtt cacttttcgc
      901 caatttatct taccgtcttc cagaacttgc tttctaggcg gttcatcaaa gatataatca
      961 atagcatgtt gaagtggaaa ttcagcatcg accaaaacga gacaaccaat gtcattagaa
     1021 aagccgtccc aatcaagttg aacgctatca tcgcgccctg atttagcata ccccattgct
     1081 tttaaagcat attcatactg agcaaaaagt ttaaaaaatt ggaaagctaa gaaatcaaga
     1141 tgattaacca tacacactcc aagccaatga aaactaagta gcgaaaagaa aaaacgataa
     1201 aggagaaacg actttacaga aggcttcgcc cctcctgatg agcatcactg taaaggcgct
     1261 caaatcaaga gtaggcgaaa cccgacacag cttaaagatc ctcaccgttt ccgataagta
     1321 gctccctcgt gcgctcctgt gttcccacct taacgtttgc agccagcttt accgctcttt
     1381 ctaccttggg ggcgctaact ctcagcttcc cggtgctggt actgctcgtc ttaggtggtt
     1441 cgctccaagc tggatgatat gcacgaactc cccgtttcat ccgaccgttg cgcctgctgg
     1501 gtaactattc tcatgattcc aaccccagcg gacacggcaa agtgccgtca ttggcaacag
     1561 ccaatacggt aacgagtctt gagtgcggga actttgttga tatgcattcg ggcacaaaaa
     1621 cgcccgtctg tagcttgaat gctccgcgta aggcagatac actgagatca cgttttaggt
     1681 agctgttccc gctaaagact cagttacctg gtagacgagt cctgagaaaa cccgtttacc
     1741 cgttaaaacc cgcgcctgag aacgcgggtt ttttcgtttc tgagcaagag actacgctga
     1801 gaaacgaaat ataacaagag ccacaccacc aaacttagcc ttgcctaaac aaacgcttcc
     1861 aaaaaccttt cccacgttca gcctcaagtt ccgcctttac cttatccagc tcttgagcaa
     1921 ctgaatcacg ttcattctgc aacccggtca cctgttctcg cagcttttga gtctcaatct
     1981 tatcctcaag caataactgc tgctgccctt gaaccaaatc cctaatctgt gacatttccg
     2041 ccattaaacg tgtgacatac tcaggctctt caacctgtga tccagtggat acttgagagc
     2101 cttctggttg tgacagggcg ccaaaaactc gcaatagttc actggtctca atctgggttg
     2161 tattactgtc tgttacaact gatgagagct taccctgctt gatataacgg tatattgtcc
     2221 ttctagtgac acccgctagc ttagcggctt cagtgaccgt gtgtaccgcc atgtgacacc
     2281 ccttatcaat acagtgtgat cgattgtgac catgtttgtg acacggtcac taaaaaccta
     2341 ttattaattg gatgggtcaa tagagccatt tttgccatta aggactttac tgatagtggt
     2401 tctggctgct cctgttagct cctgtatctg gctatacgag cgcccagctt cacgcagcgc
     2461 caatatctgc ttgtgtagct tctcgttcac tggacgccct ttgtatgcgc cctgttcttt
     2521 ggctttctta ataccttcag cttggcggcg ttggcggtct gtgtaatctt tgcgagctat
     2581 tgccgccagc atatcgagca tcatcgaatt gagtgcctca aacatacgtg acgtaaattc
     2641 atcaccagta ttaagcaaca tgtgcgaagt tggcaggtct agcgctacaa ccctaattcc
     2701 ttttctgctt atcgtctggc gcagggtctg ccagtcttca gcgtttaaac gactcagacg
     2761 gtctacctgc tcgactaaca gcacgtcgcc cggttgcgcc actttcagca agttaaacag
     2821 ctctggacgc ctgagactcg ccccgctttc gttctcgata aattcagcgg cgattgtata
     2881 accgtgttct ttggcgaact cctgcaatgc ttccttagcg cggctggcgt cctgttccga
     2941 tgtggaggcg cggagatatg agtaaacacg attagatttc atggtgattg ctttgccggt
     3001 agtttttata tggtagccat attatcggta gcgttgaaat agtcaagact tattaaacta
     3061 ccacttaaag tggtcccttt tatcagtagc taataagtat acctaaaatg gactaccagt
     3121 atctaataat ccatttttgg ataacccatt gattctctca ataatcacca ttgggggatc
     3181 ttggataaca cccgacttct ccaccattgg gggaaaagcc ccgacgcggt gaggctggta
     3241 tgcgataatg atcgcgttgg gcaatggatg cccattaact aaaaaggatt tttgaaatga
     3301 aaagtaaaac cggtgattct tgggctgaat tttttgctga agtcgaacgt gaaaccgata
     3361 aagaaattgc tgaagtgagt aggcaactgg cattaagcga agaggaagat aaggcgcttc
     3421 ttgcttctct cgaagctgaa ccgctgccgg agttggattt ggatttggat ttggagctgg
     3481 atcttctgga tattgatttc gattggtgaa accaccagcg gcaattttta cgggttctga
     3541 gcggggtgaa attgcctcgc ttgttcttac agataaaaaa aggggcttgc cttgacctta
     3601 cgttgcaagg cttccactac gttccaccct ttcaagccac ggctggcgtg ctctcgcggg
     3661 acatcaagtc atgatcaagt cgttcttata gaaccgacgt ctaatgtcaa aaaattgacc
     3721 tccgatcatc gttaaaaagg tataagcatt ttctcttcaa cctgacttct ctcaacggat
     3781 gcccttcaga agggttagct ttttttctaa gactttggtt ttgttgtttg cgttctttct
     3841 caacgttggc gcggagcgcc gttattgaca gtgaactttc tgcgctggtg gcggtgaaac
     3901 cgccctgagt gataaacgaa ctacgatttt ttcgtcgtta taatttcctg cgacttgttt
     3961 tcttttgctt cgcctgtggc ggtgaaaccg ccgtttgcgg cttctttaac gaaatgactc
     4021 aacttactgt tgtaatagga tttttttacc ttattacccc cttactgtct ctactatata
     4081 tatatatacg ctcacatcca ctcggcatca tgcgcttgct catcatagat atgaatatcg
     4141 ccggaccgat gcctgtcctc catttctgcc tcccgcatgt ctgccaacat gtctttcatc
     4201 tcttcgtcgt aatgttcgga aatttcgcca tacagaaaat cgaactcttc ctgactaatt
     4261 tccctagcga tttgcaatgg aagcattctg cgtagaatgt tgcattcgcg gcggctttca
     4321 gggcgaaagc ctatcccgtt ccccccaaaa acaagacccg gatttgcagc cagctctttg
     4381 ataatggaaa cgcccatctc cgacggttgg aaagaccttg gggcgacaat agccgcatta
     4441 ccgtatctct cgcgcctttt ccgagaagat acaaccttat cctgcaaacc tttatcgtgt
     4501 aactggatgt cgatagcagc gtcagccatg gacgttatga cgcggtgagc ggcgtccgtt
     4561 aaatcgatat cttcatgcgt tcgcgtccac ccatcaccgt gtccccacat gcgaacgccc
     4621 ggcaaacagc ctttggttac ggaaagctcc tttgtgccgt gtatgatcaa cttgctatca
     4681 cgcttcgcca tgtagcgcat ccagccctct ggggaccatg cgtcccgtgc atcttgattt
     4741 tcaatcgacg gaacgagatt cgatttcatc gcccatttaa accaggctgc aattactttc
     4801 tttgcatcaa tatcaccgca tgaatcaggg aacacggcaa ttaagtgaac gtgcggagcc
     4861 ttctggttct tggttttttc aatacagtag acccattttc cgcccgtcat ttcgtttagc
     4921 tcattggtta cggcggcgat cattttctta aacaactcag gagatgggcg ctttcctgtc
     4981 gttagggtaa tagctgacac gtgtccgcca atgaagttgt cttgatcaat gcctcgaaca
     5041 aaatctttaa atccacgaag ggttttttca gtccagccgt cgaccttcgt tgacttgccc
     5101 ggcattcctg ctcgtgattt tccgcgtgat gcaggcgttc tcgatatcgt cacatcttcc
     5161 ccggtacgct tcatgcgtcc tgctggtggc gtgtgttttg ctaatgctgg ggtcgcctca
     5221 tctggcgtta tgtgatatga tttcattgta ttttttcgat acttccattt gtaaagtgtt
     5281 ctagcccgct ctgcgaaagc gggcttttct ttgtcttaaa ttctggcttt cactgctgcc
     5341 agcacctctc gtcttgtctc actgctgatt ccggtcaatc cagtaaacgc cgtaacaaac
     5401 cgataaagct ggcgatactc acgattcttt ttcgcgtttt ccttccagcc agatagaaca
     5461 tcatcg
//
