LOCUS       NZ_CP070107             6169 bp    DNA     linear   CON 05-JAN-2024
DEFINITION  Klebsiella pneumoniae strain FDAARGOS_1314 plasmid unnamed2.
ACCESSION   NZ_CP070107
VERSION     NZ_CP070107.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357456
            Assembly: GCF_016904415.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 6169)
  AUTHORS   Sokurenko,E., Tallon,L., Sadzewicz,L., Zhao,X., Boylan,J., Ott,S.,
            Bowen,H., Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S.,
            Yan,Y. and Sichtig,H.
  TITLE     FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS):
            Supporting development and validation of Infectious Disease Dx tests
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6169)
  AUTHORS   Sokurenko,E., Tallon,L., Sadzewicz,L., Zhao,X., Boylan,J., Ott,S.,
            Bowen,H., Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S.,
            Yan,Y. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-FEB-2021) Institute for Genome Sciences, University of
            Maryland School of Medicine, BioPark II, 801 W. Baltimore St., Suite
            619, Baltimore, MD 21201, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SMRT v. 8.0.0, HGAP v. 4
            Genome Coverage                   :: 1159.81x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/05/2024 07:47:05
            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)                     :: 5,696
            CDSs (total)                      :: 5,573
            Genes (coding)                    :: 5,417
            CDSs (with protein)               :: 5,417
            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)              :: 156
            CDSs (without protein)            :: 156
            Pseudo Genes (ambiguous residues) :: 0 of 156
            Pseudo Genes (frameshifted)       :: 71 of 156
            Pseudo Genes (incomplete)         :: 86 of 156
            Pseudo Genes (internal stop)      :: 27 of 156
            Pseudo Genes (multiple problems)  :: 25 of 156
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP070107.1.
            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/
FEATURES             Location/Qualifiers
     source          1..6169
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1314"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1314"
                     /db_xref="taxon:573"
                     /plasmid="unnamed2"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            53..505
                     /gene="arr"
                     /locus_tag="I6K44_RS26765"
                     /old_locus_tag="I6K44_26765"
     CDS             53..505
                     /gene="arr"
                     /locus_tag="I6K44_RS26765"
                     /old_locus_tag="I6K44_26765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000237816.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NAD(+)--rifampin ADP-ribosyltransferase"
                     /protein_id="WP_204753002.1"
                     /translation="MVKDWIPISHDNYKQVQGPFYHGTKANLAIGDLLTTGFISHFEDG
                     RILKHIYFSALMEPAVWGAELAMSLSGLEGPGYIYIVEPTGPFEDDPNLTNKRFPGNPT
                     QSYRTCEPLRIVGVVEDWEGHPVELIRGMLDSLEDLKARGLHVIED"
                     /name="arr"
     ARG             579..1111
                     /name="dfrA27"
                     /gene="dfrA27"
                     /gene_name="trimethoprim resistant dihydrofolate reductase
                     dfr"
                     /tool="rgi"
                     /drug_class="diaminopyrimidine antibiotic"
                     /identity="99.36"
                     /coverage="112.74"
     ARG             639..1108
                     /name="dfrA27"
                     /gene="dfrA27"
                     /gene_name="trimethoprim-resistant dihydrofolate reductase
                     DfrA27"
                     /tool="amrfinderplus"
                     /drug_class="TRIMETHOPRIM"
                     /identity="100.0"
                     /coverage="100.0"
     gene            1292..2137
                     /locus_tag="I6K44_RS26775"
                     /old_locus_tag="I6K44_26775"
     CDS             1292..2137
                     /locus_tag="I6K44_RS26775"
                     /old_locus_tag="I6K44_26775"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_048608579.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ANT(3'')-Ia family aminoglycoside
                     nucleotidyltransferase AadA16"
                     /protein_id="WP_001749984.1"
                     /translation="MSNAVPAEISVQLSQALNVIEHHLGSTLLAVHLYGSALDGGLKPC
                     SDIDLLVTVTAQLDETVRQALFVDFLEVSASPGQSEALRALEVTIVVYGDVVPWRYPAR
                     RELQFGEWQRKDILAGIFEPATTDVDLAILLTKARQHSLALAGSAAEDFFNSVPESDLF
                     KALADTLKLWNSQPDWAGDERNVVLTLSRIWYSAATGKIAPKDVAANWVMERLPVQHQP
                     VLLEAQQAYLGQGMDCLASRADQLTAFIYFVKHEAASLLGSTPMMSNSSFKPTPLRGAA
                     "
                     /name="ANT(3'')-Ia family aminoglycoside
                     nucleotidyltransferase AadA16"
     gene            2254..2601
                     /locus_tag="I6K44_RS26780"
                     /old_locus_tag="I6K44_26780"
     CDS             2254..2601
                     /locus_tag="I6K44_RS26780"
                     /old_locus_tag="I6K44_26780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000679427.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quaternary ammonium compound efflux SMR
                     transporter QacE delta 1"
                     /protein_id="WP_000679427.1"
                     /translation="MKGWLFLVIAIVGEVIATSALKSSEGFTKLAPSAVVIIGYGIAFY
                     FLSLVLKSIPVGVAYAVWSGLGVVIITAIAWLLHGQKLDAWGFVGMGLIIAAFLLARSP
                     SWKSLRRPTPW"
                     /name="quaternary ammonium compound efflux SMR transporter
                     QacE delta 1"
     gene            2595..3434
                     /gene="sul1"
                     /locus_tag="I6K44_RS26785"
                     /old_locus_tag="I6K44_26785"
     ARG             2596..3431
                     /name="sul1"
                     /gene="sul1"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul1"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            3839..5380
                     /locus_tag="I6K44_RS26790"
                     /old_locus_tag="I6K44_26790"
     CDS             3839..5380
                     /locus_tag="I6K44_RS26790"
                     /old_locus_tag="I6K44_26790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000050481.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS91-like element ISCR1 family transposase"
                     /protein_id="WP_000050481.1"
                     /translation="MSLARNATASQSPTQTNGYERHQPDQTLLYQLVEQHYPAFKASLE
                     AQGQHLPRYIQQEFNDLLQCGRLEYGFMRVRCEDCHHERLVAFSCKRRGFCPSCGARRM
                     AESAALLIDEVFPKEPIRQWVLSFPFQLRFLLARHPQLMGQVLSIVYRTLSTHLIKKAG
                     YTKASAQTGSVTLIQRFGSALNLNVHYHMLFLDGVYAEDDYGKQRFHRVKAPTYDELNT
                     LAHTLSHRIARCMEKRGILERDAENTWLTLEEGEDDTLTQLHGASVTYRIAVGPQQGRK
                     VFTLQTLPGREDKADSSSRVANHAGFSLHAGVMAEAHQRDKLERLCRYISRPAVSEKRL
                     ALTANGQVRYELKTPYRNGTTHVIFEPLDFIAKLAALVPKPRVNLTRFHGVFAPNSKHR
                     VQVTPAKRGKKPDKSEGLDTNWRDKSPAERHRAMTWMQRLKRVFNIDIEVCEHCGGHVK
                     VIASIEDPKVIEQILKHLKQKTAKANAAKQRELPPERAPPLTPSLFDPSQSRLFD"
                     /name="IS91-like element ISCR1 family transposase"
     gene            complement(<5613..6152)
                     /locus_tag="I6K44_RS26795"
                     /old_locus_tag="I6K44_26795"
                     /pseudo=""
     CDS             complement(<5613..6152)
                     /locus_tag="I6K44_RS26795"
                     /old_locus_tag="I6K44_26795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_460650.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="ABC transporter substrate-binding protein"
                     /name="ABC transporter substrate-binding protein"
     ARG             2255..2598
                     /name="qacEdelta1"
                     /gene="qacEdelta1"
                     /gene_name="quaternary ammonium compound efflux SMR
                     transporter QacE delta 1"
                     /tool="amrfinderplus"
                     /drug_class="QUATERNARY AMMONIUM"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             54..502
                     /name="arr-3"
                     /gene="arr-3"
                     /gene_name="NAD(+)--rifampin ADP-ribosyltransferase Arr-3"
                     /tool="amrfinderplus"
                     /drug_class="RIFAMYCIN"
                     /identity="98.67"
                     /coverage="100.0"
     ARG             1293..2134
                     /name="aadA16"
                     /gene="aadA16"
                     /gene_name="ANT(3'')-Ia family aminoglycoside
                     nucleotidyltransferase AadA16"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
ORIGIN
        1 cccctcatgt caaacgttat gcagccaaat cccaacaatt aagggtctta aaatggtaaa
       61 agattggatt cccatctctc atgataatta caagcaggtg caaggaccgt tctatcatgg
      121 aaccaaagcc aatttggcga ttggtgactt gctaaccaca gggttcatct ctcatttcga
      181 ggacggtcgt attcttaagc acatctactt ttccgccttg atggagccag cagtttgggg
      241 agctgaactt gctatgtcac tgtctggcct cgagggtccg ggctacatat acatagttga
      301 gccaacagga ccgttcgaag acgatccgaa tcttacgaac aaaagatttc ccggtaatcc
      361 aacacagtcc tatagaacct gcgaaccctt gagaattgtt ggcgttgttg aagactggga
      421 ggggcatcct gttgaattaa taaggggaat gttggattcg ttggaggact taaaggcccg
      481 tggtttacac gtcattgaag actagtcctt tgcataacaa agccatcaaa ccggacgcca
      541 gagattccgc gcctgttgcg catggcttcg ccattttatg cgcaataggc gcgccaccct
      601 gtcgccgttt atggcggcgt taacccaaag gagtatcgtg aaaatatcac taatggctgc
      661 aaaagcaaga aatggggtta ttggctgcgg ctcggatatc ccgtggaacg ctaaaggtga
      721 gcagctgctt tttaaagcaa taacttacaa tcaatggctc ttagtcggcc gtaaaacatt
      781 tgaggcaatg ggggctctcc caaatagaaa gtatgcagtt gtcagccgct caggatcggt
      841 agctactaac gatgatgtgg ttgtgtttcc atctatagaa gcagcaatga gggagctaaa
      901 gactcttacg aaccatgttg ttgtttctgg tggtggagag atctacaaga gtctgatcgc
      961 ccatgccgac acgctacata tctcgacaat agattccgag ccagagggca atgttttctt
     1021 tccggaaatc cccaaagagt tcaatgtggt gttcgagcag gaatttcatt caaatataaa
     1081 ttatcgctat caaatctggc aaaggggtta accatccaag ccatcggaca cattttgctt
     1141 cgctgcgctc aaaacgcaaa atgtgccgct gcttagcggc gttagatgca ctaagcacat
     1201 aattgctcac agccaaacta tcaggtcaag tctgctttta ttatttttaa gcgtgcataa
     1261 taagccctac acaaattggg agttagacat catgagcaac gcagtgcccg ccgagatttc
     1321 ggtacagcta tcacaggcac tcaacgtcat cgagcatcat ctgggatcga cgttgctggc
     1381 cgtgcatttg tacggctctg cactcgacgg tggcctgaag ccatgcagtg atattgattt
     1441 gctggttact gtgactgcac agctcgatga gactgtgcgg caggctctgt tcgtagattt
     1501 cctggaagtt tccgcttctc ccggccaaag tgaagctctc cgtgccttgg aagttaccat
     1561 cgtcgtgtac ggcgatgttg ttccttggcg ttatccagcc agacgggaac tgcaattcgg
     1621 ggagtggcag cgcaaggaca ttcttgcggg catcttcgag cccgcgacaa ccgatgttga
     1681 tctggctatt ctgctaacta aagcaaggca acacagcctt gccttggcag gttcggccgc
     1741 ggaagatttc ttcaactcag tcccggaaag cgatctattc aaagcactgg ccgacacctt
     1801 gaaactatgg aactcacaac cggattgggc aggcgacgag cggaatgtag tgcttacttt
     1861 gtctcgcatt tggtacagcg cagcaaccgg caagatcgcg ccgaaggatg tagctgccaa
     1921 ctgggtaatg gaacgcctgc ccgtccaaca tcagcccgtg ctgcttgaag cccagcaggc
     1981 ttaccttgga caagggatgg attgcttggc ctcacgcgct gatcagttga ctgcgttcat
     2041 ttactttgtg aagcacgaag ccgccagtct gctcggctcc acgccaatga tgtctaacag
     2101 ttcattcaag ccgacgccgc ttcgcggcgc agcttaattc aggcgttaga tgcactaagc
     2161 acataattgc tcacagccaa actatcaggt caagtctgct tttattattt ttaagcgtgc
     2221 ataataagcc ctacacaaat tgggagatat atcatgaaag gctggctttt tcttgttatc
     2281 gcaatagttg gcgaagtaat cgcaacatcc gcattaaaat ctagcgaggg ctttactaag
     2341 cttgcccctt ccgccgttgt cataatcggt tatggcatcg cattttattt tctttctctg
     2401 gttctgaaat ccatccctgt cggtgttgct tatgcagtct ggtcgggact cggcgtcgtc
     2461 ataattacag ccattgcctg gttgcttcat gggcaaaagc ttgatgcgtg gggctttgta
     2521 ggtatggggc tcataattgc tgcctttttg ctcgcccgat ccccatcgtg gaagtcgctg
     2581 cggaggccga cgccatggtg acggtgttcg gcattctgaa tctcaccgag gactccttct
     2641 tcgatgagag ccggcggcta gaccccgccg gcgctgtcac cgcggcgatc gaaatgctgc
     2701 gagtcggatc agacgtcgtg gatgtcggac cggccgccag ccatccggac gcgaggcctg
     2761 tatcgccggc cgatgagatc agacgtattg cgccgctctt agacgccctg tccgatcaga
     2821 tgcaccgtgt ttcaatcgac agcttccaac cggaaaccca gcgctatgcg ctcaagcgcg
     2881 gcgtgggcta cctgaacgat atccaaggat ttcctgaccc tgcgctctat cccgatattg
     2941 ctgaggcgga ctgcaggctg gtggttatgc actcagcgca gcgggatggc atcgccaccc
     3001 gcaccggtca ccttcgaccc gaagacgcgc tcgacgagat tgtgcggttc ttcgaggcgc
     3061 gggtttccgc cttgcgacgg agcggggtcg ctgccgaccg gctcatcctc gatccgggga
     3121 tgggattttt cttgagcccc gcaccggaaa catcgctgca cgtgctgtcg aaccttcaaa
     3181 agctgaagtc ggcgttgggg cttccgctat tggtctcggt gtcgcggaaa tccttcttgg
     3241 gcgccaccgt tggccttcct gtaaaggatc tgggtccagc gagccttgcg gcggaacttc
     3301 acgcgatcgg caatggcgct gactacgtcc gcacccacgc gcctggagat ctgcgaagcg
     3361 caatcacctt ctcggaaacc ctcgcgaaat ttcgcagtcg cgacgccaga gaccgagggt
     3421 tagatcatgc ctagcattca ccttccggcc gcccgctaaa tatctccttt tgggttgtta
     3481 ataaaacatc caataagttg actgtgcgtg aaaaagaaag ttttgtgtga tggcgttgaa
     3541 gatcgcaccg ttaagctctt atgtgggatg gtgcagagct cgacgactac cgataaaacg
     3601 caaccgccgc aaacagacaa gaaaaagccc caactgataa cagttggggc ttcagtattg
     3661 tgattggtgg agcaatagca ccctgaaccc aaaaccttct cgctcaaccg gtagtggctg
     3721 ataacaactc gtgagggcta ttgcgggtta agcatttagc gatgtctagg gccagactgg
     3781 acgtctgaac gcaagccgct gatactgtac ataaccacag tatcagcgga ggatacccat
     3841 gtcgctggca aggaacgcca cggcgagtca atcgcccact caaacaaacg gttacgaacg
     3901 ccaccaaccc gaccagacgc tgctctacca gctggttgag cagcactacc cagccttcaa
     3961 agcctcactc gaagcccaag gtcaacacct gcctcgctac atccaacaag aattcaacga
     4021 cctcctccaa tgtggccgtc tggagtatgg tttcatgcgg gttcgctgcg aggattgtca
     4081 tcacgagcgt ctggtcgcct tcagctgtaa acgacgcggc ttttgcccta gctgcggtgc
     4141 ccgccggatg gccgagagtg cggcgctgct gatagacgaa gtcttcccca aggagcccat
     4201 tcgccagtgg gtgctcagct ttcctttcca gctacgcttt ttgctggctc gccatcccca
     4261 gctgatgggc caggtcttga gtatcgtcta tcgtacactc tcaactcatc tgatcaaaaa
     4321 agccggttac accaaagcct ctgcacaaac tggctcagtg actcttatcc aacgctttgg
     4381 ctccgcgcta aatctcaatg tccactacca catgctgttt ctcgatggtg tctatgccga
     4441 agatgactat ggcaagcaac gcttccatcg tgtcaaggca cccacttacg atgagctgaa
     4501 tacgctcgct cacaccctca gccatcgcat cgctcgctgc atggaaaagc gtgggatttt
     4561 ggagcgtgat gccgagaata cgtggttgac actggaagag ggcgaagacg atacgctgac
     4621 tcaattacat ggtgcttcgg ttacgtatcg cattgccgtc ggcccccagc aagggcgcaa
     4681 agtcttcacc ctgcaaacct tgccagggcg tgaggataaa gccgactcaa gcagtcgagt
     4741 agccaaccat gctggtttct cgctacacgc cggtgtgatg gccgaagcgc atcagcggga
     4801 taagcttgag cgcttgtgtc gctacattag tcggccagcg gtttcagaaa aacgtctggc
     4861 attaaccgcc aatgggcagg tgcgttacga gctcaaaact ccgtaccgca atggcaccac
     4921 ccatgtgatc ttcgagccgc tggacttcat cgccaaactc gctgcgttgg tacctaagcc
     4981 gcgagtcaac ctcacacgct tccacggcgt ctttgcaccg aacagcaaac accgagttca
     5041 agtaacaccc gccaagcggg gcaagaagcc cgacaaatcg gaaggtctcg atactaactg
     5101 gcgtgacaag agtcctgcag agcgccaccg cgccatgacc tggatgcaac gcctcaagcg
     5161 agtcttcaat attgatattg aagtctgcga acactgcggc ggtcacgtca aagtgattgc
     5221 cagcatcgaa gatccgaagg tcattgagca gattctcaag catctgaaac agaaaacagc
     5281 caaggcgaat gccgccaagc agcgtgagct gccaccagaa cgagcgccgc cactgactcc
     5341 cagcctgttc gatccatcac agagtcgtct ctttgactga cgaccccaaa tccaacactg
     5401 ctcaacactg ccaactttta aacggggcgg tggggcagtt tgtatctctc gagctatcag
     5461 gctagagatt ttaccgccaa atcgaacctt attagagcgg tttaggctgg accggcagtt
     5521 aaaattgggg cttgagcggt aaacgagtga gggaatttca ggtaagatac ttcggatgag
     5581 gagcaaaaag gtggtttata cttcctatac cccataaagg aggcatccgg ttgcgttaag
     5641 cggaattcaa cggtgttgtt gtccagtttg cgcacgcttt ggacgttatc ggcaaactgc
     5701 aggctgtcga agtaggggaa actgctgccg ttcacattgt gccacggatg gtggcgatca
     5761 aagatgcgct cgaaggtaaa caccacatcg tctgcattca gtttgcgggt gggggtgaac
     5821 caggccgtct tctgaaactg aacgtcacga cgcagatgga agcggtaggt tgcgccgtta
     5881 tccagcacct cccagctttc agcaagctca ggcaccagcc gataggtgta gggatctaca
     5941 tcaagcagtc ggtcatacaa ttgggccgct aacgtatcga cgatgagacc gctgctcgtt
     6001 ttttgtgggt tgaacgtatt gacttgcccg ctgacgcaat agacaaaccc actgtcacgg
     6061 atatcagcgt gcggagcttg ctcaggcgca gcagcagcct gaccactcag aaatccagcc
     6121 atcacgatca gagatgataa aaccaggcgc ataattttaa tggattata
//
