LOCUS       NZ_CP069923             5798 bp    DNA     linear   CON 03-DEC-2023
DEFINITION  Klebsiella oxytoca strain FDAARGOS_1334 plasmid unnamed13.
ACCESSION   NZ_CP069923
VERSION     NZ_CP069923.1
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 5798)
  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  JOURNAL   Unpublished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 5798)
  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
            CP069923.1.
            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..5798
                     /organism="Klebsiella oxytoca"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1334"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1334"
                     /db_xref="taxon:571"
                     /plasmid="unnamed13"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            <1..787
                     /locus_tag="I6K64_RS28770"
                     /old_locus_tag="I6K64_28765"
     CDS             <1..787
                     /locus_tag="I6K64_RS28770"
                     /old_locus_tag="I6K64_28765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_310916.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=2
                     /transl_table=11
                     /product="U32 family peptidase C-terminal domain-containing
                     protein"
                     /protein_id="WP_204724564.1"
                     /translation="CTNACRWEYNVQEGKEDDVGNIVHKYEPIPVQNVEPTLGIGAPTD
                     KVFMIEEAQRPGEYMTAFEDEHGTYIMNSKDLRAIAHVERLTKMGVHSLKIEGRTKSFY
                     YCARTAQVYRKAIDDAAAGKPFDTSLLETLEGLAHRGYTEGFLRRHTHDDYQNYEYGYS
                     VSDRQQFVGEFTGERKGDLAAAAVKNKFSVGDSLELMTPQGNINFTLEHMENAKGEAMP
                     VAPGDGYTVWIPVPQDLELNYALLMRNFSGETTRNPHGK"
                     /name="U32 family peptidase C-terminal domain-containing
                     protein"
     gene            complement(1281..1604)
                     /gene="yegR"
                     /locus_tag="I6K64_RS28775"
                     /old_locus_tag="I6K64_28770"
     CDS             complement(1281..1604)
                     /gene="yegR"
                     /locus_tag="I6K64_RS28775"
                     /old_locus_tag="I6K64_28770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_310918.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein YegR"
                     /protein_id="WP_021572871.1"
                     /translation="MKKIAAISLISVFLMSGCAVHNDETSIGKFGLAYKSNIQRKLDNQ
                     YYTEAEASLARGRISGAENIVKNDAAHFCVTQGKKMQIVDLKTEGAGLHGVARLTFKCG
                     ERE"
                     /name="yegR"
     gene            2018..2917
                     /gene="yegS"
                     /locus_tag="I6K64_RS28780"
                     /old_locus_tag="I6K64_28775"
     CDS             2018..2917
                     /gene="yegS"
                     /locus_tag="I6K64_RS28780"
                     /old_locus_tag="I6K64_28775"
                     /EC_number="2.7.1.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_310919.1"
                     /GO_function="GO:0001727 - lipid kinase activity [Evidence
                     IEA]; GO:0046872 - metal ion binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="lipid kinase YegS"
                     /protein_id="WP_000807362.1"
                     /translation="MAEFPASLLILNGKSTDNLPLREAIMLLREEGMTIHVRVTWEKGD
                     AARYVEEARKLGVATVIAGGGDGTINEVSTALIQCEGDDIPALGILPLGTANDFATSVG
                     IPEALDKALKLAIAGNAIAIDMAQVNKQTCFINMATGGFGTRITTETPEKLKAALGGVS
                     YIIHGLMRMDTLQPDRCEIRGENFHWQGDALVIGIGNGRQAGGGQQLCPNALINDGLLQ
                     LRIFTGDEILPALVSTLKSDEDNPNIIEGASSWFDIQAPHEITFNLDGEPLSGQNFHIE
                     ILPAALRCRLPPDCPLLR"
                     /name="yegS"
     gene            complement(2999..3772)
                     /locus_tag="I6K64_RS28785"
                     /old_locus_tag="I6K64_28780"
     CDS             complement(2999..3772)
                     /locus_tag="I6K64_RS28785"
                     /old_locus_tag="I6K64_28780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020077849.1"
                     /GO_function="GO:0003700 - DNA-binding transcription factor
                     activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DeoR/GlpR family DNA-binding transcription
                     regulator"
                     /protein_id="WP_001295426.1"
                     /translation="MNSFERRNKIIQLVNEQGTVLVQDLAGVFAASEATIRADLRFLEQ
                     KGVVTRFHGGAAKIMSGNSETETQEVGFKERFQLASAPKNRIAQAAVKMIHEGMTVILD
                     SGSTTMLIAEGLMTAKNITVITNSLPAAFALSENKDITLVVCGGTVRHKTRSMHGSIAE
                     RSLQDINADLMFVGADGIDAVNGITTFNEGYSISGAMVTAANKVIAVLDSSKFNRRGFN
                     QVLPIEKIDIIITDDAVSEVDKLALQKTRVKLITV"
                     /name="DeoR/GlpR family DNA-binding transcription
                     regulator"
     gene            complement(3878..4918)
                     /gene="gatD"
                     /locus_tag="I6K64_RS28790"
                     /old_locus_tag="I6K64_28785"
     CDS             complement(3878..4918)
                     /gene="gatD"
                     /locus_tag="I6K64_RS28790"
                     /old_locus_tag="I6K64_28785"
                     /EC_number="1.1.1.251"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_310921.1"
                     /GO_function="GO:0016491 - oxidoreductase activity
                     [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="galactitol-1-phosphate 5-dehydrogenase"
                     /protein_id="WP_000844236.1"
                     /translation="MKSVVNDTDGIVRVAESVIPEIKHQDEVRVKIASSGLCGSDLPRI
                     FKNGAHYYPITLGHEFSGYIDAVGSGVDDLHPGDAVACVPLLPCFTCPECLKGFYSQCA
                     KYDFIGSRRDGGFAEYIVVNRKNVFALPTDMPIEDGAFIEPITVGLHAFHLAQGCENKN
                     VIIIGAGTIGLLAIQCAVALGAKSVTAIDISSEKLALAKSFGAMQTFNSLEMSAPQMQG
                     ILRELRFNQLILETAGVPQTVELAVEIAGPHAQLALVGTLHQDLHLTSATFGKILRKEL
                     TVIGSWMNYSSPWPGQEWETASRLLTERKLSLEPLIAHRGSFESFAQAVRDIARNAMPG
                     KVLLIP"
                     /name="gatD"
     gene            complement(4966..>5798)
                     /locus_tag="I6K64_RS28795"
                     /old_locus_tag="I6K64_28790"
     CDS             complement(4966..>5798)
                     /locus_tag="I6K64_RS28795"
                     /old_locus_tag="I6K64_28790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_310922.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009401 - phosphoenolpyruvate-dependent
                     sugar phosphotransferase system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=3
                     /transl_table=11
                     /product="PTS transporter subunit IIC"
                     /protein_id="WP_320408377.1"
                     /translation="GIAIPHGTAAYMGPIAVLVDAIIEKIPGVNRIKFSADDIQRKFGP
                     FGEPVTVGFVMGLIIGILAGYDVKGVLQLAVKTAAVMLLMPRVIKPIMDGLTPIAKQAR
                     SRLQAKFGGQEFLIGLDPALLLGHTAVVSASLIFIPLTILIAVCVPGNQVLPFGDLATI
                     GFFVAMAVAVHRGNLFRTLISGVIIMSITLWIATQTIGLHTQLAANAGALKAGGMVASM
                     DQGGSPITWLLIQLFSPQNIPGFIIIGAIYLTGIFMTWRRARGFIKQEKAVLAE"
                     /name="PTS transporter subunit IIC"
ORIGIN
        1 ctgcaccaac gcctgccgct gggagtacaa cgtccaggaa gggaaagaag atgatgttgg
       61 caacatcgta cataagtacg agccgattcc ggtgcaaaat gttgagccga cgctgggtat
      121 cggcgcgcca accgacaaag tgtttatgat cgaagaagct cagcgtccgg gcgagtatat
      181 gactgcgttt gaagatgagc acggcactta catcatgaac tcgaaagatc tgcgcgctat
      241 cgcccacgtt gaacgcctga ccaaaatggg cgtgcattcg ctgaaaatcg aaggtcgtac
      301 aaaatctttc tactattgcg cacgcaccgc gcaggtttac cgtaaagcta tcgatgacgc
      361 agctgcggga aaaccattcg ataccagcct gctggaaact ctggaaggtc tggcgcatcg
      421 tggctatacc gaaggtttcc tgcgtcgtca tactcacgac gattatcaga actacgaata
      481 cggttattca gtttctgacc gccagcagtt tgttggtgag tttaccggtg agcgcaaggg
      541 cgacctcgcg gcggcagcgg tgaaaaataa attctccgtt ggcgacagcc ttgagctgat
      601 gacgccgcaa gggaacatta actttaccct tgagcatatg gaaaacgcca aaggcgaagc
      661 aatgccggtc gcaccgggcg atggttatac tgtgtggatc ccggtcccgc aggatcttga
      721 gctaaattac gcgctgctga tgcgtaattt ctccggggaa accacgcgta acccccacgg
      781 taagtgatta atttcgatta tttttcccgg atggaaaatt cttagaaacc gatcacatac
      841 agctgcattt attaaggtta tcatccgttt cgctgaaaaa cataacccat aaaatgctag
      901 ctgtaccagg aaccacctcc ttagcctgtg taatctccct tacacgggct tattttttac
      961 gcataagccc tatccctgat aaccgtcttc cattgaccac atcgatagaa tctcccttca
     1021 tagcacgatg cctttcacac aacggcatcg tgctcgccca ggttccggct acgcacagcc
     1081 agaacgcgca tgtttgacgc ttaccaaaaa atgaacctaa agcattggaa tatttttgac
     1141 atcattttct gatggcggca taaaataaaa atgctgcttt agtttcatct atctgtttgt
     1201 cattattact cacattcaat aatggtgttg aagaacaact atcagagata aaaatgaatg
     1261 tgtacatcgt agtcttgaat ctattctcgc tctccacatt tgaatgtcag acgagcgacg
     1321 ccatgtaatc ctgcaccttc tgtcttcagg tcaactatct gcattttttt gccctgagta
     1381 acacagaaat gagctgcatc attttttact atattttctg caccagaaat tctgcccctg
     1441 gctaaagaag cttcggcttc ggtgtagtat tggttatcga gtttacgctg aatattactt
     1501 ttatatgcaa gaccaaattt accgatactt gtctcatcat tatgtacagc acacccagac
     1561 ataagaaaaa cactaattaa tgatatagca gctatctttt tcatctcacc ttcccccatt
     1621 aaataccaac gacacgctct ggtgtttaaa tataataatg gcatgattat tataattgaa
     1681 taggattata ataaatgttc tgtacaacat ttcctacata agtaggaatt acatacacgg
     1741 atgccttccg ggtaacccca tgggggggtt aatatatttt taatagtata ttgaagatgc
     1801 cactgtttag ttgaatatta ggtatatgct cttttttgaa atttatcggt ggctgccgtt
     1861 aacattcact gtccccattg caagctcctg gtggtaacca ctgaatcctc tatacttgaa
     1921 ctgacttttt atcctccgac tttcatcctg ttctgactcc accttttctt ttctgctcta
     1981 cactatctac agaccaatca taaaggcaca tacgatcatg gcagaatttc ccgccagctt
     2041 actgattctt aatggcaaaa gtactgacaa tctacccttg cgcgaagcaa ttatgctgtt
     2101 gcgtgaggaa ggaatgacga tccatgtgcg ggtcacctgg gagaaaggcg atgccgcacg
     2161 atatgtagag gaggcccgga agttgggcgt cgcaacggtg attgccggtg gtggcgatgg
     2221 caccattaat gaagtttcta cggcgttgat tcaatgtgag ggggatgaca tacccgcgct
     2281 gggaattttg ccattaggaa ccgccaatga ttttgccacc agtgtaggga ttcctgaggc
     2341 actggataag gcgctgaaac tggcaattgc cggtaacgcc attgcgatag atatggcgca
     2401 ggtcaacaaa caaacctgtt ttattaatat ggcgacaggc gggtttggga cgcgtattac
     2461 cacagaaacg ccggaaaaat taaaagccgc gctgggtggc gtctcttaca tcattcatgg
     2521 cttaatgcgc atggacactc tgcaaccgga ccgttgtgaa atccgcggtg aaaactttca
     2581 ctggcaaggt gacgccctgg tcataggtat tggtaacggg cgtcaggccg gtggcggtca
     2641 gcaattgtgc ccgaacgcgt taattaacga tggcctgctg caactgcgca tttttaccgg
     2701 cgatgaaatt cttccagctc tcgtatcaac cttaaaatct gacgaagata acccgaatat
     2761 tatcgaaggc gcttcgtcgt ggtttgatat acaagcccca cacgaaatca cttttaatct
     2821 tgatggcgaa ccgttgagtg ggcaaaactt ccatattgaa atacttccgg cggcgttacg
     2881 ttgtcgatta ccaccagatt gtccattatt gcgttaatca aactattctc tcttgaacca
     2941 gggagaatcc gtaatgccgg atgcggtgta aaaaccttat ccggcataca gaacaatact
     3001 acaccgtaat taatttcacc cgtgtcttct gcaatgccag tttatccacc tctgacacag
     3061 catcgtcggt aataataatg tcgatttttt cgattggcag tacctgatta aaaccgcgac
     3121 gattaaattt cgatgaatcg agaacggcaa tcactttatt tgcggctgtg accatcgccc
     3181 cgctaatcga ataaccttca ttaaaggtcg taataccatt aaccgcatca ataccatcag
     3241 caccgacaaa cattaaatcg gcattaatat cctgcaatga acgctcggca atggaaccat
     3301 gcatcgagcg tgttttatgg cggacggtcc caccacagac gaccagagta atgtctttat
     3361 tttcggaaag ggcaaatgct gccgggagac tgttggtaat caccgtgata tttttggcgg
     3421 tcattaatcc ttcggcgata agcattgtgg tacttccgct gtcgagaata acggtcatcc
     3481 cttcgtggat cattttgact gccgcctgcg ctattctgtt ttttggcgca ctggcgagct
     3541 gaaatcgctc tttaaaccca acttcctggg tctcggtttc actattaccg gacattattt
     3601 tcgccgcacc gccatgaaag cgcgtaacca cgcctttttg ttcgagaaag cgcaaatcgg
     3661 cacggattgt cgcttccgag gcagcaaata ctcccgccag atcctgaaca agcacggttc
     3721 cctgttcatt cactaattgg atgatcttat tccttcgctc gaatgaattc atcgtcattt
     3781 acccatattc aattgtggct agtgtaaacg aagggggacc attggtgaat gatctgtttt
     3841 gcacaatacc gggccagcat cacgctggcc cgcggtttca gggaatgagc aacactttgc
     3901 ccggcatagc attacgagcg atgtcacgca ccgcctgggc gaagctttca aagcttccac
     3961 ggtgagcgat taatggctcc aggcttaact tacgttctgt cagcaaccgg ctcgccgttt
     4021 cccactcctg cccaggccaa gggctggagt agttcatcca actgccgata accgtcagct
     4081 ctttacgtaa tattttgcca aacgttgccg atgttaaatg caaatcttga tgcaacgtac
     4141 ccaccagcgc cagctgggca tgaggcccgg caatctctac cgccagttcg acggtttgcg
     4201 ggacgccagc cgtctcgagg ataagctgat taaagcgcag ctcgcgtaaa atgccctgca
     4261 tttgcggcgc gctcatttca aggctgttaa atgtttgcat cgcaccgaaa gattttgcca
     4321 gtgccagttt ttctgagcta atgtcgatag ccgtcacact ctttgctccc agcgcgacag
     4381 cgcactgaat ggccagcagg ccaatggttc cggcaccaat aataataacg tttttattct
     4441 cacaaccttg cgctaaatgg aaagcatgca ggccaacggt aatcggttca ataaaagccc
     4501 catcctcaat aggcatatcc gtgggtagag caaagacatt ttttcggtta acgacaatat
     4561 attcagcaaa tccaccatca cgccgcgagc caataaaatc atattttgcg cactgggaat
     4621 aaaacccttt caaacactct ggacaagtaa aacagggtaa taacggcaca caggcaaccg
     4681 catcgccagg gtgtaaatca tcaacaccgg atcccaccgc atcaatatag ccgctaaatt
     4741 catggcctaa cgttattgga taataatgtg caccattttt aaatatcctg ggtaaatcgg
     4801 aaccacataa gcccgagctg gcaattttta cccgtacctc atcctgatgt ttaatttcag
     4861 gaatgacgct ttctgcaacg cgcacgatac catcagtatc attcaccact gatttcataa
     4921 aaactcctga ttgttaaggg ggataaactc cccctcaggt aaaaattatt ctgcgagaac
     4981 ggctttctct tgtttaataa aaccacgcgc tctacgccag gtcatgaaaa taccggtaag
     5041 ataaattgcg ccgataataa tgaaaccggg aatattttgc ggggagaaaa gctgaatcag
     5101 taaccaggta atgggagaac cgccctgatc cattgaagcc accatacctc cggcttttaa
     5161 cgccccagca ttagccgcca gttgggtgtg caaaccaata gtttgcgtcg cgatccacag
     5221 ggtgatgctc ataatgatga cacccgagat caaggtgcgg aacagatttc cacgatgcac
     5281 ggcaactgcc atcgccacaa agaagccgat ggtggcaaga tcgccaaacg gcagtacctg
     5341 attacccgga acacaaacag caattaaaat ggtgagcggg ataaaaatca ggcttgccga
     5401 taccaccgcc gtatgcccca gcagtaatgc cggatccagg ccaatcagga actcctgacc
     5461 gccgaacttc gcctgcaaac ggctacgcgc ctgcttcgca ataggtgtta agccatccat
     5521 gatgggttta atcacccgtg gcatcagcag cataactgcc gccgtcttta ccgccagctg
     5581 caatacacct ttgacatcgt aacccgcgag gatgccgata atcagcccca tcacaaaacc
     5641 cacggtgaca ggttcgccaa atgggccaaa cttgcgctga atatcatcgg cactaaattt
     5701 aattcggtta acgcctggga ttttctcgat aatggcatcg accagcaccg caatcggccc
     5761 catatacgcc gccgtaccgt gcggaatagc aatgcctt
//
