LOCUS       NZ_CP069927             5069 bp    DNA     linear   CON 03-DEC-2023
DEFINITION  Klebsiella oxytoca strain FDAARGOS_1334 plasmid unnamed18.
ACCESSION   NZ_CP069927
VERSION     NZ_CP069927.1
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 5069)
  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  JOURNAL   Unpublished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 5069)
  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
            CP069927.1.
            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..5069
                     /organism="Klebsiella oxytoca"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1334"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1334"
                     /db_xref="taxon:571"
                     /plasmid="unnamed18"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            complement(<1..622)
                     /gene="cutC"
                     /locus_tag="I6K64_RS28905"
                     /old_locus_tag="I6K64_28900"
     CDS             complement(<1..622)
                     /gene="cutC"
                     /locus_tag="I6K64_RS28905"
                     /old_locus_tag="I6K64_28900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_025309.2"
                     /GO_function="GO:0005507 - copper ion binding [Evidence
                     IEA]"
                     /GO_process="GO:0055070 - copper ion homeostasis [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="copper homeostasis protein CutC"
                     /protein_id="WP_204724567.1"
                     /translation="MALLEICCYSMECALTAQQNGADRVELCAAPKEGGLTPSLGVLKS
                     VRQRVTIPVHPIIRPRGGDFCYSDGEFAAILEDVRTVRELGFPGLVTGVLDVDGNVDMP
                     RMEKIMAAAGPLAVTFHRAFDMCANPLYTLNNLAELGIARVLTSGQKSDALQGLSKIME
                     LIAHRDAPIIMAGAGVRAENLHHFLDAGVLEVHSSAGAWQASPM"
                     /name="cutC"
     gene            complement(636..1202)
                     /locus_tag="I6K64_RS28910"
                     /old_locus_tag="I6K64_28905"
     CDS             complement(636..1202)
                     /locus_tag="I6K64_RS28910"
                     /old_locus_tag="I6K64_28905"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_416389.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="VOC family protein"
                     /protein_id="WP_001326725.1"
                     /translation="MANWQSIDELQDIASDLPRFIHALDELSRRLGLNITPLTADHISL
                     RCHQNATAERWRRGFEQCGELLSENMINGRPICLFKLHEPVQVAHWQFSIVELPWPGEK
                     RYPHEGWEHIEIVLPGDPETLNARALALLSDEGLSLPGISVKTSSPKGEHERLPNPTLA
                     VTDGKTTIKFHPWSIEEIVASEQSA"
                     /name="VOC family protein"
     gene            1418..3151
                     /gene="argS"
                     /locus_tag="I6K64_RS28915"
                     /old_locus_tag="I6K64_28910"
     CDS             1418..3151
                     /gene="argS"
                     /locus_tag="I6K64_RS28915"
                     /old_locus_tag="I6K64_28910"
                     /EC_number="6.1.1.19"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001025321.1"
                     /GO_component="GO:0005737 - cytoplasm [Evidence IEA]"
                     /GO_function="GO:0004814 - arginine-tRNA ligase activity
                     [Evidence IEA]"
                     /GO_process="GO:0006420 - arginyl-tRNA aminoacylation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="arginine--tRNA ligase"
                     /protein_id="WP_001025322.1"
                     /translation="MNIQALLSEKVRQAMIAAGAPADCEPQVRQSAKVQFGDYQANGMM
                     AVAKKLGMAPRQLAEQVLTHLDLNGIASKVEIAGPGFINIFLDPAFLAEHVQQALASDR
                     LGVATPEKQTIVVDYSAPNVAKEMHVGHLRSTIIGDAAVRTLEFLGHKVIRANHVGDWG
                     TQFGMLIAWLEKQQQENAGEMELADLEGFYRDAKKHYDEDEEFAERARNYVVKLQSGDE
                     YFREMWRKLVDITMTQNQITYDRLNVTLTRDDVMGESLYNPMLPGIVADLKAKGLAVES
                     EGATVVFLDEFKNKEGEPMGVIIQKKDGGYLYTTTDIACAKYRYETLHADRVLYYIDSR
                     QHQHLMQAWAIVRKAGYVPESVPLEHHMFGMMLGKDGKPFKTRAGGTVKLADLLDEALE
                     RARRLVAEKNPDMPADELEKLANAVGIGAVKYADLSKNRTTDYIFDWDNMLAFEGNTAP
                     YMQYAYTRVLSVFRKAEIDEEQLAAAPVIIREDREAQLAARLLQFEETLTVVAREGTPH
                     VMCAYLYDLAGLFSGFYEHCPILSAENEEVRNSRLKLAQLTAKTLKLGLDTLGIETVER
                     M"
                     /name="argS"
     gene            complement(3193..3237)
                     /gene="yecV"
                     /locus_tag="I6K64_RS29680"
     CDS             complement(3193..3237)
                     /gene="yecV"
                     /locus_tag="I6K64_RS29680"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_010051188.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein YecV"
                     /protein_id="WP_211180499.1"
                     /translation="MSIFRIHLDGNKKA"
                     /name="yecV"
     gene            3328..3816
                     /locus_tag="I6K64_RS28920"
                     /old_locus_tag="I6K64_28915"
     CDS             3328..3816
                     /locus_tag="I6K64_RS28920"
                     /old_locus_tag="I6K64_28915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_416391.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="lysozyme inhibitor LprI family protein"
                     /protein_id="WP_001299676.1"
                     /translation="MFKFLVLTLGIISCQAYAEDTVIVNDHDISAIKDCWQKNSDDDTD
                     VNVIKSCLRQEYNLVDAQLNKAYGEAYRYIEQVPRTGVKKPDTEQLNLLKKSQRAWLDF
                     RDKECELILSNEDVQDLSDPYSESEWLSCMIIQTNTRTRQLQLYRNSEDFYPSPLTRG"
                     /name="lysozyme inhibitor LprI family protein"
     gene            complement(3936..4328)
                     /gene="flhe"
                     /locus_tag="I6K64_RS28925"
                     /old_locus_tag="I6K64_28920"
     CDS             complement(3936..4328)
                     /gene="flhe"
                     /locus_tag="I6K64_RS28925"
                     /old_locus_tag="I6K64_28920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_416392.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="flagellar protein FlhE"
                     /protein_id="WP_001259583.1"
                     /translation="MRTLLAILLFPLLVQAAGEGMWQASSVGITLNHRGESMSSAPLST
                     RQPASGLMTLVAWRYQLIGPTPSGLRVRLCSQSRCVELEGQSGTTVAFSGIAAAEPLRF
                     IWEVPGGGRLIPPLKVQRNEVIVNYR"
                     /name="flhe"
     gene            complement(4328..>5069)
                     /locus_tag="I6K64_RS28930"
                     /old_locus_tag="I6K64_28925"
     CDS             complement(4328..>5069)
                     /locus_tag="I6K64_RS28930"
                     /old_locus_tag="I6K64_28925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_310616.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009306 - protein secretion [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=2
                     /transl_table=11
                     /product="FHIPEP family type III secretion protein"
                     /protein_id="WP_204724568.1"
                     /translation="GTLPGEATVDPAFGLNAIWIESALKEQAQIQGYTVVEASTVVATH
                     LNHLISQHAAELFGRQEAQQLLDRVAQEMPKLTEDLVPGVVTLTTLHKVLQNLLDEKVP
                     IRDMRTILETLAEHAPIQSDPHELTAVVRVALGRAITQQWFPGKDEVHVIGLDTPLERL
                     LLQALQGGGGLEPGLADRLLAQTQEALSRQEMLGAPPVLLVNHALRPLLSRFLRRSLPQ
                     LVVLSNLELSDNRHIRMTATIGGK"
                     /name="FHIPEP family type III secretion protein"
ORIGIN
        1 gcatcggtga ggcttgccac gctcccgcgg agctatggac ttccagcact ccggcatcga
       61 ggaagtggtg caggttttct gcacggactc ctgctccggc cataatgatt ggagcatcac
      121 gatgggcaat aagttccata atttttgata aaccttgcag tgcgtctgat ttttgccctg
      181 atgtcagtac ccgggcaatg cccaattccg caagattatt gagtgtatat aaagggttag
      241 cgcacatatc gaaggcgcga tgaaaagtca ctgccagcgg accggcagca gccattattt
      301 tttccattcg tggcatatcg acattcccgt caacatcgag aacgcccgtc accagtccag
      361 gaaaacctaa ttcgcggacc gtgcgcacat cctcaagaat ggcggcaaac tcaccgtcgc
      421 tgtagcaaaa atcaccaccg cgtgggcgaa ttatcggatg cacagggatc gtcacccgct
      481 ggcgcacgga tttcagtaca cccaacgacg gcgttaagcc cccctctttt ggggctgcgc
      541 ataattcaac tctgtctgcg ccgttttgct gcgccgttag tgcacattcc atgctgtaac
      601 agcaaatttc cagtaatgcc atttttactc cttaattacg ccgactgctc gctggcaacg
      661 atctcttcaa tggaccacgg atgaaactta atagttgttt tgccatcggt gaccgccagc
      721 gtcggattcg gtaatcgctc atgctcacct tttggcgaac tggttttcac tgagatcccc
      781 ggtaggctga gtccttcatc agaaagcaat gccagcgcac gggcattcag cgtttctgga
      841 tcacccggca gaacgatttc aatatgttcc caaccttcgt gtgggtaacg tttttccccg
      901 ggccacggta gctccacaat agaaaactgc cagtgcgcaa cctgtaccgg ttcatgcaat
      961 ttaaacagac aaatcggtct gccattgatc atattttctg acaaaagctc gccacactgt
     1021 tcaaacccgc gacgccagcg ttcagcagtg gcgttttgat ggcaacgcaa agaaatgtga
     1081 tcggcagtca gcggagtgat attcaacccc agacggcggg aaagttcatc taatgcgtgg
     1141 ataaatcgcg gtaaatccga tgcaatatcc tgcagctcgt cgatagattg ccagttcgcc
     1201 ataatcactc ttcgtctttc agtaaaagcg ttaatttacc ctgttgccct gtgccaacca
     1261 accgctgatt tcacgccgct tctgatgcaa tagtgaaaac ggcaatacgc cacgcgcacg
     1321 ttgctgacga aaacagccat ttgcagtata ctcccgccct aatttcttta actggtgcgg
     1381 gcaatttttg ctcgcttcat caatgtaagg tattccggtg aatattcagg ctcttctctc
     1441 agaaaaagtc cgtcaggcca tgattgcggc aggcgcgcct gcggattgcg aaccgcaggt
     1501 tcgtcagtca gcaaaagttc agttcggcga ctatcaggct aacggcatga tggcagttgc
     1561 taaaaaactg ggtatggcac cgcgacaatt agcagagcag gtgctgactc atctggatct
     1621 taacggtatc gccagcaaag ttgagatcgc cgggccaggc tttatcaaca ttttccttga
     1681 tccggcattc ctggctgaac atgttcagca ggcgctggcg tccgatcgtc tcggtgttgc
     1741 tacgccagaa aaacagacca ttgtggttga ctactctgcg ccaaacgtgg cgaaagagat
     1801 gcatgtcggt cacctgcgct ctaccattat tggtgacgca gcagtgcgta ctctggagtt
     1861 cctcggtcac aaagtgattc gcgcaaacca cgtcggcgac tggggcactc agttcggtat
     1921 gctgattgca tggctggaaa agcagcagca ggaaaacgcc ggtgaaatgg agctggctga
     1981 ccttgaaggt ttctaccgcg atgcgaaaaa gcattacgat gaagatgaag agttcgccga
     2041 gcgcgcacgt aactacgtgg taaaactgca aagcggtgac gaatatttcc gcgagatgtg
     2101 gcgcaaactg gtcgacatca ccatgacgca gaaccagatc acctacgatc gtctcaacgt
     2161 gacgctgacc cgtgatgacg tgatgggcga aagcctttac aacccgatgc tgccaggaat
     2221 tgtggcggat ctcaaagcca aaggtctggc agtagaaagc gaaggggcga ccgtcgtatt
     2281 ccttgatgag tttaaaaaca aggaaggcga accgatgggc gtgatcattc agaagaaaga
     2341 tggcggctat ctctacacca ccactgatat cgcctgtgcg aaatatcgtt atgaaacact
     2401 gcatgccgat cgcgtgctgt attacatcga ctcccgtcag catcaacacc tgatgcaggc
     2461 atgggcgatc gtccgtaaag caggctatgt accggaatcc gtaccgctgg aacaccacat
     2521 gttcggcatg atgctgggta aagacggcaa accgttcaaa acccgcgcgg gtggtacagt
     2581 gaaactggcc gatctgctgg atgaagccct ggaacgtgca cgccgtctgg tggcagaaaa
     2641 gaacccggat atgccagccg acgagctgga aaaactggct aacgcggttg gtattggtgc
     2701 ggtgaaatat gcggatctct ccaaaaaccg caccacggac tacatcttcg actgggacaa
     2761 catgctggcg tttgagggta ataccgcgcc atacatgcag tatgcataca cgcgtgtatt
     2821 gtccgtgttc cgtaaagcag aaattgacga agagcaactg gctgcagctc cggttatcat
     2881 ccgtgaagat cgtgaagcgc aactggcagc tcgcctgctg cagtttgaag aaaccctcac
     2941 cgtggttgcc cgtgaaggca cgccgcatgt aatgtgtgct tacctgtacg atctggccgg
     3001 tctgttctct ggcttctacg agcactgccc gatcctcagc gcagaaaacg aagaagtgcg
     3061 taacagccgt ctaaaactgg cacaactgac ggcgaagacg ctgaagctgg gtctggatac
     3121 gctgggtatt gagactgtag agcgtatgta atcgattttt cgtgagagtg aagcctgatc
     3181 agggttagcc gatcaggctt ttttattgcc atctaaatgt attctgaaaa tggacatgcc
     3241 attgttttct cactgttgga taagaggcca gaagcgtaat atccggcccc agggaaacga
     3301 taacggttga atttaaggaa taccgcagtg tttaaatttc ttgtattaac attaggcatt
     3361 atctcttgcc aggcttacgc agaagatacg gttatagtaa acgaccatga catttcagcc
     3421 atcaaagatt gttggcaaaa aaattcagat gatgatactg acgttaacgt gatcaaatca
     3481 tgcctgcgac aagaatacaa tctcgtcgat gcgcaattaa ataaagccta tggtgaagct
     3541 tatcgttata tagaacaagt gccacgcaca ggtgtaaaaa aacctgatac cgaacaactt
     3601 aacttgctta aaaaatcaca gcgagcctgg ctggatttta gggacaaaga atgtgaatta
     3661 atcctttcaa atgaggacgt tcaggattta agtgaccctt attctgaatc agaatggctc
     3721 tcatgtatga tcatacagac caatacgcga actcgccagt tgcagctata ccgtaactct
     3781 gaagattttt atccaagccc tttgacaaga ggataattca catctttttg gcatgttttg
     3841 ttgcaagcta ttcctgataa ataattgcaa caagacatcg agcctttttc actgagttat
     3901 taaacatact cgcgagcgcg taattttttt gtccttcagc gataattcac aatcacttca
     3961 ttacgttgta cctttagcgg tggaattaac cgcccaccgc ctggcacttc ccagataaat
     4021 cgcaacggtt ctgctgccgc tataccggaa aaggccacgg tggttccgct ctgcccctct
     4081 aattcgacac aacgagattg cgaacacaag cgaacccgca gtcctgaagg tgtcgggccg
     4141 ataagctgat aacgccacgc taccagcgtc atcaatcctg aagcaggttg tcgcgtagaa
     4201 agaggcgcag acgacatcga ctcaccgcga tgatttagcg taattcctac actacttgcc
     4261 tgccacatcc cctccccggc ggcttgcacc agcagcggaa acaataatat tgctaataag
     4321 gttctcatta tttgccgcca attgtcgccg tcatgcggat atgtcggtta tcagacagtt
     4381 ccagattcga caggaccact aactgcggca agctgcggcg caggaagcga gacaataatg
     4441 gtcgcagcgc gtggttcacc aacaatactg gcggcgcacc cagcatctcc tgacgggata
     4501 gcgcttcctg agtttgcgcc agtaaacgat ccgccagccc tggctccagt cctcccccgc
     4561 cctgcagcgc ctgtagtaac aaacgttcca gcggtgtatc gaggccaata acatggactt
     4621 catctttgcc aggaaaccac tgctgggtaa tcgcccgtcc caacgccacg cgcacgacgg
     4681 cggttaattc atgtggatcg ctttggatgg gcgcatgttc cgccagcgtt tcgagaatgg
     4741 tgcgcatatc gcgaatcggt actttttcat cgaggagatt ttgcagcact ttatgcagtg
     4801 tggtgagcgt gacgacgcca ggaacgagat cttccgtcag ctttggcatc tcctgggcga
     4861 cgcgatccaa cagctgttgc gcctcctgac gaccaaacag ctctgcggca tgctggctaa
     4921 tgaggtggtt aagatgcgtt gctaccaccg tgctggcctc aaccactgtg tacccctgaa
     4981 tctgcgcctg ttcttttagc gcactttcaa tccagatagc attcaggcca aatgccggat
     5041 cgacggtcgc ctcaccaggt aacgtcccg
//
