LOCUS       NZ_CP069910             5840 bp    DNA     circular CON 03-DEC-2023
DEFINITION  Klebsiella oxytoca strain FDAARGOS_1334 plasmid unnamed12, complete
            sequence.
ACCESSION   NZ_CP069910
VERSION     NZ_CP069910.1
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 5840)
  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  JOURNAL   Unpublished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 5840)
  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
            CP069910.1.
            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..5840
                     /organism="Klebsiella oxytoca"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1334"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1334"
                     /db_xref="taxon:571"
                     /plasmid="unnamed12"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            complement(join(5792..5840,1..209))
                     /locus_tag="I6K64_RS00005"
                     /old_locus_tag="I6K64_00005"
     CDS             complement(join(5792..5840,1..209))
                     /locus_tag="I6K64_RS00005"
                     /old_locus_tag="I6K64_00005"
                     /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="bacteriocin immunity protein"
                     /protein_id="WP_032413518.1"
                     /translation="MAGNKISDFTEEEFTAFVSKIIAADFPTDKENDDAIYSFAQLTEH
                     PAGWNLIFKPKIGEDSSAKGIVKTVKEWRAANGKPGFKKA"
                     /name="bacteriocin immunity protein"
     gene            complement(211..2229)
                     /locus_tag="I6K64_RS00010"
                     /old_locus_tag="I6K64_00010"
     CDS             complement(211..2229)
                     /locus_tag="I6K64_RS00010"
                     /old_locus_tag="I6K64_00010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004228432.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="S-type pyocin domain-containing protein"
                     /protein_id="WP_049245974.1"
                     /translation="MHNGQMGYWENRSSGAGNNEHTTRAFVAVGPSEAEKAARAEKVAQ
                     EKQQAEEAAKAFAAKTAAASAAAEKERQNAISAAAAAGQHQTVPDARNNLNQATAEASR
                     LKTVADNALNTAKNKRKEAIDAVPVATQAEKKYQDLQQSIKGLTLNNNGQYGTQKWEVI
                     SSNKEHDHWGYRFYPSGITKAQVDAAQNDAVNKRNAATSLASQATAAEQASLQASAAYN
                     AAETRRQAAQAALASAEQAAAAERKRHEAEAAAAAAAEKKRQADAAAKAAEEARAIAEK
                     AKALQARRTAADKLKSSEIQAVRGIPATAAPFAIPLTWSTASRGSFTLAADAAASLGAF
                     ISEALATLRVAVVANPVALTIAGLVLSKSVGVGSDMVPGRDISSMMPGDAFGLPDTAAL
                     NKAADQKTSVSMPVRGRLVMNDSGILDVQLVKTNTAGAVKVARAVLDKETGYWGYTLPA
                     VADVPAQTIFVSPADAPGANGPLTLSGPVPLPERILHTGDQISAPQATDKTVTPVADDL
                     DFDDIILVFPPESGLKPLYVMYRSPRNMPGTVSGKGQNVGNNWMGGASTGDGAPVPSQI
                     ADKLRGKTFGSFDSFRRAFWKAVADDSALSKQFSEADINQMKAGRAPTADFLESVGKRV
                     KIELHHEKEISQGGAVMDVDNIKALTPKNHIETHKGK"
                     /name="S-type pyocin domain-containing protein"
     gene            complement(2142..2534)
                     /locus_tag="I6K64_RS29765"
     CDS             complement(2142..2534)
                     /locus_tag="I6K64_RS29765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004152299.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_048981310.1"
                     /translation="MDLIITVRVLRAQALALLLPVMWLISLIVLVGRKSGHQMSRIFAV
                     MVMVGIWRIFGGRFTLCPLKKAQQLQQLSVASMVSAVLLPVMAEVRVGRGHRDSLSLCI
                     TGRWDTGKTDHPGLVITNILPALLWQ"
                     /name="hypothetical protein"
     gene            2909..3454
                     /locus_tag="I6K64_RS00015"
                     /old_locus_tag="I6K64_00015"
     CDS             2909..3454
                     /locus_tag="I6K64_RS00015"
                     /old_locus_tag="I6K64_00015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004178052.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_048981308.1"
                     /translation="MPLPERMKPARVTRKQMKELISQLNGILDHIDNGMDENNEELKQM
                     MADWNAKVVMPCGFSDFRDFSSWTSALDFTRMALNQEKYLDDFTWTELNDVINFIRKAE
                     GSESDHSYALQLLEINFKANPLDLIYHPDCWFNDEALFHARLTTEEIGGYLMKKSGRWL
                     NDAPDIQLVYAIPLDVYD"
                     /name="hypothetical protein"
     gene            complement(4203..4604)
                     /locus_tag="I6K64_RS00020"
                     /old_locus_tag="I6K64_00020"
     CDS             complement(4203..4604)
                     /locus_tag="I6K64_RS00020"
                     /old_locus_tag="I6K64_00020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /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_025714819.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADHSEQVISHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(4604..4795)
                     /locus_tag="I6K64_RS00025"
                     /old_locus_tag="I6K64_00025"
     CDS             complement(4604..4795)
                     /locus_tag="I6K64_RS00025"
                     /old_locus_tag="I6K64_00025"
                     /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_004187666.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            5211..5324
                     /locus_tag="I6K64_RS29770"
     CDS             5211..5324
                     /locus_tag="I6K64_RS29770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_049026061.1"
                     /translation="MHEPPVQSDCCALSGNCHLESNPERHAKAPLAAATGN"
                     /name="hypothetical protein"
     gene            complement(5529..5684)
                     /locus_tag="I6K64_RS00030"
                     /old_locus_tag="I6K64_00030"
     CDS             complement(5529..5684)
                     /locus_tag="I6K64_RS00030"
                     /old_locus_tag="I6K64_00030"
                     /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"
     Typing          4917..5324
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.161"
                     /coverage="99.0"
                     /evalue="5.8799999999999995e-176"
ORIGIN
        1 acggttttaa caatcccttt cgccgaagaa tcttcgccta tcttaggctt gaagatgagg
       61 ttccaaccag caggatgctc tgttagttgg gcgaacgaat aaatagcatc atcgttctct
      121 ttgtcagttg gaaaatcagc agcgattatt ttactaacaa aagcagtaaa ttcttcttcc
      181 gtaaaatctg aaattttatt accagccatt ttattttcct ttatgtgtct caatatgatt
      241 tttaggtgtt agcgccttaa tgttatcgac atccataaca gcccctcctt gagatatttc
      301 tttttcgtgg tgtaattcaa ttttaacacg tttccctact gattctaaaa agtccgcagt
      361 aggtgccctt ccagctttca tctgattaat atcagcttca ctaaattgct tgctcagtgc
      421 agaatcgtca gcaaccgctt tccagaacgc ccgacggaaa gaatcaaaac taccgaaagt
      481 cttcccgcgt aatttatccg caatctggga aggaacagga gcaccatccc cggtactggc
      541 cccccccatc cagttattgc caacgttctg ccctttgccg ctcactgtac cgggcatgtt
      601 acgagggcta cggtacatca catacagcgg ttttaggccg gattccggag gaaacaccag
      661 aataatatcg tcaaaatcga ggtcatccgc taccggcgtc acggttttat ctgtagcctg
      721 tggcgccgaa atctgatcac cggtatgcag aatacgctcc ggtagtggta ccggcccgct
      781 tagcgtcagt ggtccgtttg caccaggtgc gtcagccggg ctgacaaaaa tagtttgcgc
      841 cggaacatct gcgacagcgg gaagagtata gccccagtag ccggtttcct tatccagtac
      901 agcacgagcg accttcacgg caccggcagt attggttttg accagctgaa catccagaat
      961 gccgctatca ttcataacca gacggccacg aaccggcata ctgacagatg ttttctgatc
     1021 tgctgcttta ttcaatgccg cggtatcagg cagaccaaac gcatcgccag gcatcatcga
     1081 actgatatcc cgaccgggca ccatatcact accgacgcca actgatttcg ataacacaag
     1141 accggcaatg gttaatgcta ccgggttagc caccacagcg acacgtaacg tcgccagagc
     1201 ctcgctgatg aaagctccca ggctggccgc agcatcagcc gccagagtaa aacttccacg
     1261 tgacgcagtt gaccaggtca gaggaatagc aaaaggtgca gctgtagccg ggatacccct
     1321 gacagcctga atctctgaag atttcagttt atctgcggct gtacgacggg cctgcagcgc
     1381 ttttgctttt tcagcaatgg ctctggcctc ctcagcggct ttcgctgctg catcagcctg
     1441 tcgttttttt tctgccgcag cggcggctgc tgcttccgcc tcatggcgtt tacgttcagc
     1501 agcggcggct tgttctgcgg acgctaatgc agcctgggca gcctgacggc gcgtttctgc
     1561 agcattatag gcagctgatg cctgcagact ggcctgctca gcggccgttg cctgactggc
     1621 aagactggta gcagcatttc gtttgttcac cgcatcattc tgcgctgcat caacctgagc
     1681 ttttgtgatc ccagatggat agaaccggta tccccagtgg tcatgctctt tattcgaact
     1741 gataacctcc catttttggg taccgtattg gccgttatta tttagagtga ggcctttaat
     1801 gctttgctgc agatcctgat attttttctc agcctgagtt gctactggta cggcatcgat
     1861 agcttccttt cgcttattct tcgctgtatt aagggcatta tctgccactg ttttcaggcg
     1921 tgatgcttca gcagtcgcct gattcagatt attacgcgca tcaggaacag tttgatgttg
     1981 acctgcagca gccgcagcag aaatcgcatt ctgacgttct ttttcagcag cggcggatgc
     2041 cgctgctgtt ttcgctgcga atgcttttgc agcctcttct gcttgctgtt tttcctgagc
     2101 taccttctcc gctcgtgcag ctttttctgc ttctgatggg cctactgcca caaaagcgcg
     2161 ggtagtatgt tcgttattac cagccccgga tgatcggttt tcccagtatc ccatctgccc
     2221 gttatgcata acgagagact gtccctgtgg cccctgccca ccctgacttc cgccattacc
     2281 ggtagaagaa ctgcggacac catcgaagcc accgacagtt gttgaagttg ttgagccttc
     2341 ttcagaggac acagtgtgaa tctgcccccg aatatccgcc atatacccac cattaccatc
     2401 actgcgaata ttcgagacat ctgatgcccg gatttgcgtc ccaccaaaac tattaaactg
     2461 attagccaca tcactggcag aaggagagct aaggcctgag ctcgtagcac cctcaccgtt
     2521 ataattaaat ccacccatca cacatttcct tcttttgttt tttttgtttt ttttgttttc
     2581 cacttttctg aaatccggcg tgcggtttat tgcttcagga cagttatccg gaggctgtta
     2641 ttagttctct gccacgccaa actactgtat ataaaaacat gtgtttatat acagtagttt
     2701 gatactactc ttgacatgcc agctctgtca atatgcagac gtcaacaata tttttattta
     2761 ttttcaatcg gttaaaagtt acgacagagg taaatctgag gcagaatgcg gatcatcaga
     2821 aagaaaaaaa aacgatttgt gctctgattc atagcccgat agattactca gttcccccga
     2881 gtgcacgata aaaaagagag tatttctgat gccattacct gagcgaatga aacccgcacg
     2941 ggtcacccgt aaacagatga aagaactgat cagtcagctg aatggcattc tcgatcacat
     3001 cgataacggg atggacgaaa acaatgaaga actaaaacag atgatggcag actggaatgc
     3061 aaaggtcgtc atgccctgcg ggttctctga ttttcgtgat ttttcatcct ggacaagtgc
     3121 actagatttc accaggatgg cgcttaatca ggaaaaatac ctcgatgact ttacatggac
     3181 agaactgaac gacgttatca acttcatacg caaagcagaa ggtagtgaat ctgaccacag
     3241 ctatgcactc cagttactgg agattaattt caaggcaaac ccactggatc tcatctatca
     3301 ccctgactgc tggttcaatg atgaagcatt gtttcatgcc cggctgacta ccgaagaaat
     3361 tggtggctac ttaatgaaaa aatcaggtcg atggctcaac gatgcaccgg atatccaact
     3421 ggtgtatgcc atccccctgg atgtttatga ttaaccaagt caccatttac cataatccct
     3481 taattgtacg caccgctaaa acggcctcag ggcgtttccg acgggaaacc ggcaaaacag
     3541 gcaacaaacc acccgaaaac ccgccagaaa cgcgcaggct ctgtttttac ggcatgcatg
     3601 agtatgcacg caagtgcata gcgcgaaaat tcacaccatt cagccagggt aagtcctgtt
     3661 tccggcgttc ttcctatccg aaaacggtga acggggacgc aatttattgc gtggccgtga
     3721 agcgttgccg gcgcagccgg aaaaccggtt ttcatcacgt tcaggaatcg ggttcgtcga
     3781 cggccggcaa tcacgttatg gcaagtcacc ggacgactca ccacacgatt caccggcgat
     3841 tcgactcgtg acttgactct agagtcgcca aggtcaaaaa aaaaccaaaa tgacgactcg
     3901 actctagagt caagtcgtca taagttactg atagtcttaa gtgagtcgtc gatgactcta
     3961 tgacgagtca tcgacaagtc gtacgcgaat cgccgacgac ttggatttac cttacagaat
     4021 gtaatacagc gtaatttaat aacatctaac taactgatat taaggagtta tctgcaaaat
     4081 tttaattttg cgtagtgtgt gggtattttt agtcgtgagg agcgttcaga gatctggcga
     4141 tttttgggaa ggttcaggaa ctccccggga tggccggaga ggaaaacgga agcatgacgg
     4201 ggtcaggatt ttttccagaa tttccaccat ggcgccgggg attcagttaa ttttgcctgg
     4261 tgattttcaa gaaggagcat ggcctgtttc aggctgtcaa tgtgcgaatc cttggacaaa
     4321 agtaaggtat tcaggtgttc aatctcctgt ttcagatgac taatcacctg ttcactatgg
     4381 tcagcagagg ctgtatcacg ctgttcagag acctgtccag aatggtgttc acccttcggt
     4441 tgttcaaagg gaccaaagac acgtaaaagc tctgaagtat ctaccatttt tgcattgcgt
     4501 tcaccgctac aggtggacag gtcacctgct ttaattaacc tgtgcagtgt tgttctactc
     4561 ttacccgtca gtcgggcagc ctcactaata gacactctgg ccatcagtta ccatcctgta
     4621 atgcatccag tctcgaggac agtgtacgga aaagatgctc cgcatcatcg tggagtttct
     4681 cacaaaggtc ggcctctaca tcgagatcaa gctcgttaag cttctccagc aggagcagag
     4741 actgattctg gatgaattta gccatgttca gcgctgtttt ctgttgtttc gtcataagaa
     4801 gcctcagagc gtcagtgctc agtgtaagaa caatctcttt tccgcttcct cgctcactca
     4861 gtcgctacgc tccggtcgtt cggctgcggc gagcggcaag accgttctta taaaagctcg
     4921 agaaaaccga gcgatcaagg gaggcggaaa agaagaggcc gcccagcggc cgtttttcca
     4981 taggctccgc ccccctgaca agcatcacag aatttgacgc tcaaatcagt ggtggcgaaa
     5041 cccgacagga ctataaagat accaggcgtt tccccctgat ggctccctcg tgcgctctcc
     5101 tgttcctgcc attcggttta ccggtgtcat tccgctgtta tggccgcgtt tgtctcattc
     5161 cacgcctgac actcagttcc gggtaggcag ttcgctccaa gctggactgt atgcacgaac
     5221 cccccgttca gtccgactgc tgcgccttat ccggtaactg tcatcttgag tccaacccgg
     5281 aaaggcatgc aaaagcgcca ctggcagcag ccactggtaa ctgatttaga ggagttagtc
     5341 ttgaagttat gtgccagtta aggctaaact gaaagaacga atttggttac tgcgctcctc
     5401 taagccagtt acctcggttc aaagagcgcc aactcctcga accttcgaaa aaaccgcccg
     5461 ccaaggcggt tttttcgttt acagagcaag agattacgac gatccaaatg ggatctcaag
     5521 aagatccttt acggattgcc gttcgtaccg ctatcaagcg tgactccggt caccgtcgat
     5581 gaaggtgaaa cagccccacc tccggtgtct cgaacattat tgacctgaca tgctgccaga
     5641 accacagaaa cggtaacaac ccctaggaaa agtaattttt tcatatatca ccttttattt
     5701 ttattattct aggcaaatgg atatctagta attattcttc aaatccagag ttacaaatga
     5761 gcgggctcat aacttgaacc cgcaaattca atcacgcttt tttaaaacct ggcttaccgt
     5821 tagcagctcg ccattccttt
//
