LOCUS       NZ_CP070145             3336 bp    DNA     circular CON 05-JAN-2024
DEFINITION  Klebsiella oxytoca strain FDAARGOS_1331 plasmid unnamed1, complete
            sequence.
ACCESSION   NZ_CP070145
VERSION     NZ_CP070145.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357473
            Assembly: GCF_016904515.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella oxytoca
  ORGANISM  Klebsiella oxytoca
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3336)
  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  JOURNAL   Unpublished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 3336)
  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                   :: 904.14x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/05/2024 07:44:36
            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)                     :: 5,691
            CDSs (total)                      :: 5,575
            Genes (coding)                    :: 5,481
            CDSs (with protein)               :: 5,481
            Genes (RNA)                       :: 116
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 94
            CDSs (without protein)            :: 94
            Pseudo Genes (ambiguous residues) :: 0 of 94
            Pseudo Genes (frameshifted)       :: 37 of 94
            Pseudo Genes (incomplete)         :: 55 of 94
            Pseudo Genes (internal stop)      :: 23 of 94
            Pseudo Genes (multiple problems)  :: 18 of 94
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP070145.1.
            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..3336
                     /organism="Klebsiella oxytoca"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1331"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1331"
                     /db_xref="taxon:571"
                     /plasmid="unnamed1"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            complement(103..>351)
                     /locus_tag="I6K61_RS28240"
                     /old_locus_tag="I6K61_28245"
                     /pseudo=""
     CDS             complement(103..>351)
                     /locus_tag="I6K61_RS28240"
                     /old_locus_tag="I6K61_28245"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004178052.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            <350..832
                     /locus_tag="I6K61_RS28245"
                     /old_locus_tag="I6K61_28250"
                     /pseudo=""
     CDS             <350..832
                     /locus_tag="I6K61_RS28245"
                     /old_locus_tag="I6K61_28250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004178051.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="S-type pyocin domain-containing protein"
                     /name="S-type pyocin domain-containing protein"
     gene            834..1091
                     /locus_tag="I6K61_RS28250"
                     /old_locus_tag="I6K61_28255"
     CDS             834..1091
                     /locus_tag="I6K61_RS28250"
                     /old_locus_tag="I6K61_28255"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013365855.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin immunity protein"
                     /protein_id="WP_025714833.1"
                     /translation="MAGNKISDFTEEEFTAFVSKIIAADFPTDKENDDAIYSFAQLTEH
                     PAGWNLIFKPKVGEDSSAKGIVKTVKEWRAANGKPGFKKA"
                     /name="bacteriocin immunity protein"
     gene            1199..1354
                     /locus_tag="I6K61_RS28255"
                     /old_locus_tag="I6K61_28260"
     CDS             1199..1354
                     /locus_tag="I6K61_RS28255"
                     /old_locus_tag="I6K61_28260"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008323621.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_071561715.1"
                     /translation="MKKLLFLGVVTVSVVLAACQVNNVRDTGGGAVSPSSTVTGVTLDS
                     GTNGNP"
                     /name="colicin release lysis protein"
     gene            complement(1512..1673)
                     /locus_tag="I6K61_RS28730"
     CDS             complement(1512..1673)
                     /locus_tag="I6K61_RS28730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_049165871.1"
                     /translation="MHEPPVQSDCCVLSGNYHLESNPERHDKAPLAAATGNGFRGVGLE
                     VMRLLRLN"
                     /name="hypothetical protein"
     gene            2078..2269
                     /locus_tag="I6K61_RS28260"
                     /old_locus_tag="I6K61_28265"
     CDS             2078..2269
                     /locus_tag="I6K61_RS28260"
                     /old_locus_tag="I6K61_28265"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_023302508.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2269..2691
                     /locus_tag="I6K61_RS28265"
                     /old_locus_tag="I6K61_28270"
     CDS             2269..2691
                     /locus_tag="I6K61_RS28265"
                     /old_locus_tag="I6K61_28270"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /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_025714834.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKAIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTSINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKREPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     Typing          complement(1561..2030)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.834"
                     /coverage="92.0"
                     /evalue="2.73e-170"
ORIGIN
        1 tcgggtggtt tgttgcctgt tttaccggtt tcccgtcaga aacgtcctga ggccgtttta
       61 gcggtgcgta caattaaggg attatggtaa atggtgactt ggttaatcat aaacatcctg
      121 ggggatggca tacaccagtt ggatatccgg tgcatcgttg agccatcgac ctgatttttt
      181 cattaagtag ccaccaattt cttcggtagt cagccgggca tgaaacaatg cttcatcatt
      241 gaaccagcag tcagggtgat agatgagatc cagtgggttt gccttgaaat taatctccag
      301 taactggagt gcatagctgt ggtcagatgc actaccttct gcttttcgta tggcggatga
      361 cctcgatttt gacgatatta ttctggtgtt tcctccggaa tccggcctaa aaccgctgta
      421 tgtgatgtac cgtagccctc gtaacatgcc cggtacagtg agcggcaaag ggcagaacgt
      481 tggcaataac tggatggggg gggccagtac cggggatggt gctcctgttc cttcccagat
      541 tgcggataaa ttacgcggga agactttcgg tagttttgat tctttccgtc gggcgttctg
      601 gaaagcggtt gctgacgatt ctgcactgag caagcaattt agtgaagctg atattaatca
      661 gatgaaagct ggaagggcac ctactgcgga ctttttagaa tcagtaggga aacgtgttaa
      721 aattgaatta caccacgaaa aagaaatatc tcaaggaggg gctgttatgg atgtcgataa
      781 cattaaggcg ctaacaccta aaaatcatat tgagacacat aaaggaaaat aaaatggctg
      841 gtaataaaat ttcagatttt acggaagaag aatttactgc ttttgttagt aaaataatcg
      901 ctgctgattt tccaactgac aaagagaacg atgatgctat ttattcgttc gcccaactaa
      961 cagagcatcc tgctggttgg aacctcatct tcaagcctaa ggtaggcgaa gattcttcgg
     1021 cgaaaggaat tgttaaaacc gtaaaggaat ggcgagctgc taacggtaag ccaggtttta
     1081 aaaaagcgtg attgaatttg cgggttcaag ttatgagccc gctcatttgt aactctggat
     1141 ttgaagaata attactagat atccatttgc ctagaataat aaaaataaaa ggtgatatat
     1201 gaaaaaatta cttttcctag gggttgttac cgtttctgtg gttctggcag catgtcaggt
     1261 caataatgtt cgagacaccg gaggtggggc tgtttcacct tcatcgacgg tgaccggagt
     1321 cacgcttgat agcggtacga acggcaatcc gtaaaggatc ttcttgagat cccatttgga
     1381 tcgtcgtaat ctcttgctct gtaaacgaaa aaaccgcctt gcagggcggt ttttccgaag
     1441 gttcaaacac ttgcaggtga ttgaaccaag gtaactggct tggaggagcg cagtcaccaa
     1501 aacttgttct ttcagtttag ccttaacagg cgcatgactt caagaccaac tcctctaaat
     1561 ccgttaccag tggctgctgc cagtggcgct ttgtcgtgtc tttccgggtt ggactcaaga
     1621 tgatagttac cggataagac gcagcagtcg gactgaacgg ggggttcgtg catacagtcc
     1681 agcttggagc gaactgccta cccggaactg agtgtcaggc gtggaatgag acaaacgcgg
     1741 ccataacagc ggaatgacac cggtaaaccg aatggcagga acaggagagc gcacgaggga
     1801 gccatcaggg ggaaacgcct ggtatcttta tagtcctgtc gggtttcgcc accactgatt
     1861 tgagcgtcaa attctgtgat gcttgtcagg ggggcggagc ctatggaaaa acggccgctg
     1921 tgctgccttc tccctctccg agctgtctgc tctatgtcgt tatgtgcgcg ttgcgaccgc
     1981 tcgccgcagc cgaacggcag gagcgtagcg actgagtgag cgaggaagcg gaaaagagat
     2041 ctgtctgaca ttgagcactg acgctctgag gccctttatg acgaaacaac agaaaacagc
     2101 gctgaacatg gctaaattca tccagaatca gtctctgctc ctgctggaga agcttaacga
     2161 gcttgatctc gatgttgagg ccgacctttg tgagaaactc cacgatgatg cggagcatct
     2221 tttccgtaca ctgtcctcga gactggatga attacaggat ggtaattgat ggccagagtg
     2281 tctattagtg aagcggcacg gcttgttaag gttagccgtc ccacaattta caagatgatt
     2341 aacagtggga agttaagtta cacctctgtt gtaaagcacg ggaaggctat taaagttatt
     2401 gatacttcag agcttattag agtgtttggt tctcttgatg gtgtcatcga tactgtaaaa
     2461 tatgatgtaa aaagtgacgc agaatctaca agtattaaca gcgttggttt acatgattta
     2521 caacatagaa tcgctctact tgaagctgaa aacgatggtc ttaaaggggc tgttaaggct
     2581 cgagatgagc atattgattc ccttcgtcag gctatgcagc ttctggagca caagcgcgag
     2641 ccttcttcac caccccattc cccgtggtgg aaattctgga aaaaatcctg atcctgccat
     2701 gcttgagttt tcctctccgg ccatcccagg gagttcctga accttcccaa aaatcgccag
     2761 atctctgaac gctcctcacg actaaaaata cccacacact acgcaaaatt aaaattttgc
     2821 agattcctta tttaaaacaa ctggttaatg aaaaattaat gtgcagtgat gtgttacaaa
     2881 gtgcagatcc aagtcgtgga cgactctatg gcgaatcgtt tacgaattgc ccacgattca
     2941 tatgtgaatc acgctttatt atcatgttgt tatgatgaat cgactcttga ttcaattcat
     3001 caatttgggc gttttttgtt catggtgact cttgattcaa ttcacgattc gaatcgccgg
     3061 tgaatcgtgt ggtgagtcgt ccggcgactt gccataacgt gattgccggc cgtcgacgaa
     3121 cccgattcct gaacgtgctg aaaaccggtt ttccggctgc gccggcaacg cctcacggcc
     3181 acgcaataaa ttgcgtcccc gttcaccgtt ttcggatcag aagaacgccg gaaacaggac
     3241 ttaccctggc tgaatggcgt gaatttccgc gctatgcact tgcgcgcata ctcatgcatg
     3301 ccgtaaaaac agagcctgcg cgtttctggc gggttt
//
