LOCUS       NZ_CP069929             4311 bp    DNA     linear   CON 03-DEC-2023
DEFINITION  Klebsiella oxytoca strain FDAARGOS_1334 plasmid unnamed20.
ACCESSION   NZ_CP069929
VERSION     NZ_CP069929.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357476
            Assembly: GCF_016903415.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella oxytoca
  ORGANISM  Klebsiella oxytoca
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4311)
  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  JOURNAL   Unpublished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 4311)
  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                   :: Canu v. 1.8
            Genome Coverage                   :: 591.2x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 12/03/2023 03:56:31
            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)                     :: 5,915
            CDSs (total)                      :: 5,798
            Genes (coding)                    :: 5,689
            CDSs (with protein)               :: 5,689
            Genes (RNA)                       :: 117
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 109
            CDSs (without protein)            :: 109
            Pseudo Genes (ambiguous residues) :: 0 of 109
            Pseudo Genes (frameshifted)       :: 47 of 109
            Pseudo Genes (incomplete)         :: 70 of 109
            Pseudo Genes (internal stop)      :: 26 of 109
            Pseudo Genes (multiple problems)  :: 29 of 109
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP069929.1.
            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..4311
                     /organism="Klebsiella oxytoca"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1334"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1334"
                     /db_xref="taxon:571"
                     /plasmid="unnamed20"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            complement(<1..1103)
                     /gene="emrD"
                     /locus_tag="I6K64_RS29200"
                     /old_locus_tag="I6K64_29195"
     ARG             complement(4..1103)
                     /name="emrD"
                     /gene="emrD"
                     /gene_name="multidrug efflux MFS transporter EmrD"
                     /tool="amrfinderplus"
                     /drug_class="EFFLUX"
                     /identity="100.0"
                     /coverage="93.15"
     gene            1185..1259
                     /gene="ysdE"
                     /locus_tag="I6K64_RS29700"
     CDS             1185..1259
                     /gene="ysdE"
                     /locus_tag="I6K64_RS29700"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_010051212.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein YsdE"
                     /protein_id="WP_211180519.1"
                     /translation="MNVSQIYARNGELFSGRICKQKRQ"
                     /name="ysdE"
     gene            complement(1383..1472)
                     /gene="tisB"
                     /locus_tag="I6K64_RS29205"
                     /old_locus_tag="I6K64_29200"
     CDS             complement(1383..1472)
                     /gene="tisB"
                     /locus_tag="I6K64_RS29205"
                     /old_locus_tag="I6K64_29200"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_001165331.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type I toxin-antitoxin system toxin TisB"
                     /protein_id="WP_001054909.1"
                     /translation="MNLVDIAILILKLIVAALQLLDAVLKYLK"
                     /name="tisB"
     gene            2037..2135
                     /gene="ivbL"
                     /locus_tag="I6K64_RS29210"
                     /old_locus_tag="I6K64_29205"
     CDS             2037..2135
                     /gene="ivbL"
                     /locus_tag="I6K64_RS29210"
                     /old_locus_tag="I6K64_29205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_418128.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ilvB operon leader peptide IvbL"
                     /protein_id="WP_001300753.1"
                     /translation="MTTSMLNAKLLPTAPSAAVVVVRVVVVVGNAP"
                     /name="ivbL"
     gene            2241..3929
                     /gene="ilvB"
                     /locus_tag="I6K64_RS29215"
                     /old_locus_tag="I6K64_29210"
     CDS             2241..3929
                     /gene="ilvB"
                     /locus_tag="I6K64_RS29215"
                     /old_locus_tag="I6K64_29210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_418127.1"
                     /GO_function="GO:0003984 - acetolactate synthase activity
                     [Evidence IEA]; GO:0050660 - flavin adenine dinucleotide
                     binding [Evidence IEA]; GO:0000287 - magnesium ion binding
                     [Evidence IEA]; GO:0030976 - thiamine pyrophosphate binding
                     [Evidence IEA]"
                     /GO_process="GO:0009082 - branched-chain amino acid
                     biosynthetic process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="acetolactate synthase large subunit"
                     /protein_id="WP_000168475.1"
                     /translation="MASSGTTSTRKRFTGAEFIVHFLEQQGIKIVTGIPGGSILPVYDA
                     LSQSTQIRHILARHEQGAGFIAQGMARTDGKPAVCMACSGPGATNLVTAIADARLDSIP
                     LICITGQVPASMIGTDAFQEVDTYGISIPITKHNYLVRHIEELPQVMSDAFRIAQSGRP
                     GPVWIDIPKDVQTAVFEIETQPAMAEKAAAPAFSEESIRDAAAMINAAKRPVLYLGGGV
                     INAPARVRELAEKAQLPTTMTLMALGMLPKAHPLSLGMLGMHGVRSTNYILQEADLLIV
                     LGARFDDRAIGKTEQFCPNAKIIHVDIDRAELGKIKQPHVAIQADVDDVLAQLIPLVEA
                     QPRAEWHQLVADLQREFPCPIPKACDPLSHYGLINAVAACVDDNAIITTDVGQHQMWTA
                     QAYPLNRPRQWLTSGGLGTMGFGLPAAIGAALANPDRKVLCFSGDGSLMMNIQEMATAS
                     ENQLDVKIILMNNEALGLVHQQQSLFYEQGVFAATYPGKINFMQIAAGFGLETCDLNNE
                     ADPQASLQEIINRPGPALIHVRIDAEEKVYPMVPPGAANTEMVGE"
                     /name="ilvB"
     gene            3933..4223
                     /gene="ilvN"
                     /locus_tag="I6K64_RS29220"
                     /old_locus_tag="I6K64_29215"
     CDS             3933..4223
                     /gene="ilvN"
                     /locus_tag="I6K64_RS29220"
                     /old_locus_tag="I6K64_29215"
                     /EC_number="2.2.1.6"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_312638.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="acetolactate synthase small subunit"
                     /protein_id="WP_001181706.1"
                     /translation="MQNTTHDNVILELTVRNHPGVMTHVCGLFARRAFNVEGILCLPIQ
                     DSDKSHIWLLVNDDQRLEQMISQIDKLEDVVKVQRNQSDPTMFNKIAVFFQ"
                     /name="ilvN"
ORIGIN
        1 aacaacccca ggctgccctg accggtttgc ggcaacatcg cagagagcga cgccagcacg
       61 ccggaaccaa tgttttgcag accgccgacc agcgcgccag ccgtgcccgc caggaagggg
      121 aacggctcca tcgcgccgct ggtcgccagc ggaaacagca tcccggcacc gaaaaagaac
      181 agcgcggcgg gaacgagcag cgtccagaca ttcatcacgc caaaccagtc ggggatccac
      241 atcagcaagc cagccagcag gcagcagata accgactgcc acattaacgt ggagaagcgt
      301 ttattgggac gtccggcaaa ccatgcgcca aaaaacgctg ccggaatcgg cagaataaac
      361 aaaatactga ccgtcatact gctcagccct aacaccgcgc ccatcagcac gccggagcag
      421 gcttcaaagg cggcaatccc ggccagaccg ccaatcagca tcagcaaata acagttaaaa
      481 ccgctgttac cgaaaagcgt tttataactg gtaagcaggc gcgtgcgcgg tgcatcgacc
      541 ggacgcgttt ccggcatcca gcgggccata ctgaaggtca caccagcaca aagaaccaac
      601 aaaaagagat aacaggcgcg ccagttccac atcgtatcca gcagaccgcc gattagcggt
      661 gcgagcaacg gactgacgag aatccccatg tttaacaggc tgttagcatg gcgcaactgt
      721 gtccgttcat ataaatctcg cggtaaagta cgcgccatta cgccgccaac gccggtgccc
      781 atcccctgca tcgcgctggc ggcaatcaac accgtcaaac tggaggtcgt gaccgcgacc
      841 agcgttgcca gcataaaaat ggacattccg acgaggatca ccggtcggcg gcccacgcgg
      901 tcggaaatcg ggccataaaa cagctgtgag acaccgtaag tcagcagata agcgcccatt
      961 acgctctgca ccgccccttc acggacgttg agatcgcgcg ccatatcggc aatagctgga
     1021 atataaatgg tttgcgccat ctgaccgacg gccacgagta ataccaacat caataacaaa
     1081 ttgacgtttc tttgcctttt cattatcacg gatgctttta taaaaataat tagaataagt
     1141 cactacgcat tcccataaat gcgggagagg aatctatcac attgatgaat gttagccaga
     1201 tatacgccag gaatggggaa ttgtttagcg gcagaatatg taaacaaaag cggcaataaa
     1261 tgttgccggg agagatggta gggcggataa gatgcgtcag catcgcatcc gacaccaacc
     1321 cgcacgctaa atataaaagg ggagcggttt cccgctcccc tttggtgcga cttgaatctg
     1381 aattacttca ggtatttcag aacagcatca agcagttgca gtgctgcaac aatgagtttg
     1441 aggataagaa tggcgatatc caccaggttc atacgcgtct cctgtggttc aggagcactg
     1501 ccagctgacg tacctttccg ctgcctgttg ccagctgttg tgcacgcggt atctcaagga
     1561 gaaacgttgt gcttgttgac ataacacagt gtgctcacgc ggggttaagg cgctgacggc
     1621 accacccgtt tcagccagga cttagtgcgc cgggtaacga tgcggccccc gcataacaca
     1681 ttgcgtacag tgatattata gaagtttact gtataaataa acagtaatat ttggacaaaa
     1741 cgcaaactgt gatcgatact caactatgca ctaaatacgt caaaattcgt gccgaaattg
     1801 cgcgttctgc gcggaacacg tatactttca gtgttgacat aatacagtgt gctttgcggt
     1861 taccagccgc aggcgactga cgaaacctcg ctccggcggg gttttttgtt atctgcaatt
     1921 cagtacaaaa cgtgatcaac ccctcaattt tcccttgctg aaaaattttc cattgtctcc
     1981 cctgtaaagc tgtgcttgta taaatattgt taaacacaaa accaacaagg tccccaatga
     2041 ctacttccat gctcaacgca aaactactac caactgcgcc atccgccgca gtggtcgtcg
     2101 tgcgtgtggt ggtggtcgtc ggcaatgcgc cgtagggact ggaacaacac acgattccaa
     2161 aaccccgccg gcgcaaaccg ggcggggttt ttcgtttaag cacctcccgg aaagtcggcc
     2221 cagaagaaaa ggactggagc atggcaagtt cgggcacaac atcgacgcgt aagcgcttta
     2281 ccggcgcaga atttatcgtt catttcctgg aacagcaggg cattaagatt gtgacaggca
     2341 ttccgggcgg ttctatcctg cctgtttacg atgccttaag ccaaagcacg caaatccgcc
     2401 atattctggc ccgtcatgaa cagggcgcgg gctttatcgc tcagggaatg gcgcgcaccg
     2461 acggtaaacc ggcggtctgt atggcctgta gcggaccggg tgcgactaac ctggtgaccg
     2521 ccattgccga tgcgcggctg gactccatcc cgctgatttg catcactggt caggttcccg
     2581 cctcgatgat cggcaccgac gccttccagg aagtggacac ctacggcatc tctatcccca
     2641 tcaccaaaca caactatctg gtcagacata tcgaagaact cccgcaggtc atgagcgatg
     2701 ccttccgcat tgcgcaatca ggccgcccag gcccggtgtg gatagacatt cctaaggatg
     2761 tgcaaacggc agtttttgag attgaaacac agcccgctat ggcagaaaaa gccgccgccc
     2821 ccgcctttag cgaagaaagc attcgtgacg cagcggcgat gattaacgct gccaaacgcc
     2881 cggtgcttta tctgggcggc ggtgtgatca atgcgcccgc acgggtgcgt gaactggcgg
     2941 agaaagcgca actgcctacc accatgactt taatggcgct gggcatgttg ccaaaagcgc
     3001 atccgttgtc gctgggtatg ctggggatgc acggcgtgcg cagcaccaac tatattttgc
     3061 aggaggcgga tttgttgata gtgctcggtg cgcgttttga tgaccgggcg attggcaaaa
     3121 ccgagcagtt ctgtccgaat gccaaaatca ttcatgtcga tatcgaccgt gcagagctgg
     3181 gtaaaatcaa gcagccgcac gtggcgattc aggcggatgt tgatgacgtg ctggcgcagt
     3241 tgatcccgct ggtggaagcg caaccgcgtg cagagtggca ccagttggta gcggatttgc
     3301 agcgtgagtt tccgtgtcca atcccgaaag cgtgcgatcc gttaagccat tacggcctga
     3361 tcaacgccgt tgccgcctgt gtcgatgaca atgcaattat caccaccgac gttggtcagc
     3421 atcagatgtg gaccgcgcaa gcttatccgc tcaatcgccc acgccagtgg ctgacctccg
     3481 gtgggctggg cacgatgggt tttggcctgc ctgcggcgat tggcgctgcg ctggcgaacc
     3541 cggatcgcaa agtgttgtgt ttctccggcg acggcagcct gatgatgaat attcaggaga
     3601 tggcgaccgc cagtgaaaat cagctggatg tcaaaatcat tctgatgaac aacgaagcgc
     3661 tggggctggt gcatcagcaa cagagtctgt tctacgagca aggcgttttt gccgccacct
     3721 atccgggcaa aatcaacttt atgcagattg ccgccggatt cggcctcgaa acctgtgatt
     3781 tgaataacga agccgatccg caggcttcat tgcaggaaat catcaatcgc cctggcccgg
     3841 cgctgatcca tgtgcgcatt gatgccgaag aaaaagttta cccgatggtg ccgccaggtg
     3901 cggcgaatac tgaaatggtg ggggaataag ccatgcaaaa cacaactcat gacaacgtaa
     3961 ttctggagct caccgttcgc aaccatccgg gcgtaatgac ccacgtttgt ggcctttttg
     4021 cccgccgcgc ttttaacgtt gaaggcattc tttgtctgcc gattcaggac agcgacaaaa
     4081 gccatatctg gctactggtc aatgacgacc agcgtctgga gcagatgata agccaaatcg
     4141 ataagctgga agatgtcgtg aaagtgcagc gtaatcagtc cgatccgacg atgtttaaca
     4201 agatcgcggt gttttttcag taaccgctca aggcttgaac aacatcgcgc ttatcgctaa
     4261 ggtaagcgcg tgttttttta cccgccagga caagaccatg atcaccgttg c
//
