LOCUS       NZ_CP023945             4163 bp    DNA     linear   CON 08-JAN-2024
DEFINITION  Klebsiella pneumoniae strain FDAARGOS_446 plasmid unnamed3.
ACCESSION   NZ_CP023945
VERSION     NZ_CP023945.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN07312490
            Assembly: GCF_002587885.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4163)
  AUTHORS   Croxen,M., Tallon,L.J., Sadzewicz,L., Ott,S., Zhao,X., Nagaraj,S.,
            Vavikolanu,K., Aluvathingal,J., Nadendla,S., Geyer,C. 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  JOURNAL   Unpublished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 4163)
  AUTHORS   Croxen,M., Tallon,L.J., Sadzewicz,L., Ott,S., Zhao,X., Nagaraj,S.,
            Vavikolanu,K., Aluvathingal,J., Nadendla,S., Geyer,C. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-OCT-2017) Center for Devices and Radiological Health,
            US Food and Drug Administration, 10903 New Hampshire Avenue, Silver
            Spring, MD 20993-0002, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: SMRT v. 2.3.0, HGAP v. 3, SPAdes v. 3.6.0
            Genome Coverage                   :: 475.368x
            Sequencing Technology             :: PacBio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/08/2024 02:52:43
            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)                     :: 5,775
            CDSs (total)                      :: 5,652
            Genes (coding)                    :: 5,500
            CDSs (with protein)               :: 5,500
            Genes (RNA)                       :: 123
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 152
            CDSs (without protein)            :: 152
            Pseudo Genes (ambiguous residues) :: 0 of 152
            Pseudo Genes (frameshifted)       :: 62 of 152
            Pseudo Genes (incomplete)         :: 92 of 152
            Pseudo Genes (internal stop)      :: 16 of 152
            Pseudo Genes (multiple problems)  :: 17 of 152
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP023945.1.
            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..4163
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_446"
                     /isolation_source="Rectal"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_446"
                     /db_xref="taxon:573"
                     /plasmid="unnamed3"
                     /geo_loc_name="Canada: BC"
                     /collection_date="2014-01"
                     /collected_by="BC Centre for Disease Control"
     gene            38..439
                     /locus_tag="CRN69_RS00005"
                     /old_locus_tag="CRN69_00005"
     CDS             38..439
                     /locus_tag="CRN69_RS00005"
                     /old_locus_tag="CRN69_00005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="transcriptional regulator"
                     /protein_id="WP_039817125.1"
                     /translation="MARVSISEASRLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKSEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="transcriptional regulator"
     gene            complement(1336..1635)
                     /locus_tag="CRN69_RS29630"
     CDS             complement(1336..1635)
                     /locus_tag="CRN69_RS29630"
                     /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="hypothetical protein"
                     /protein_id="WP_125564845.1"
                     /translation="MSNPPFEFVIRYHDLSPEQVRSFIDDAFHRVDLVLEKQLSDRPGF
                     FIPTCKSLTTNPSLSEIAIAVYNTYAVTEMIKDQLLRQSSNITLIKDIREIFVS"
                     /name="hypothetical protein"
     gene            complement(1726..1986)
                     /locus_tag="CRN69_RS00010"
                     /old_locus_tag="CRN69_00010"
     CDS             complement(1726..1986)
                     /locus_tag="CRN69_RS00010"
                     /old_locus_tag="CRN69_00010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010891192.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein L"
                     /protein_id="WP_072016306.1"
                     /translation="MAAYTEKTEQFLQRVTHTQTWWTSTYDPSDTVPVSGIYRCTVCGK
                     EITSNKNDPFPPQNHHQHSQKQNVKWQLIVRTDTNGDKFGN"
                     /name="protein L"
     gene            2464..2799
                     /locus_tag="CRN69_RS00015"
                     /old_locus_tag="CRN69_00015"
     CDS             2464..2799
                     /locus_tag="CRN69_RS00015"
                     /old_locus_tag="CRN69_00015"
                     /inference="COORDINATES: protein motif:HMM:NF017757.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_077255464.1"
                     /translation="MSASEMKEICLDVTGVDKELKSLPIDKALAFLHNLKLVAAGIEPE
                     LKVEHLKVVAPGVIELKINGSPAYRCVYTIKSPGKVIVLRVFKKTTNGPARKDLEVVKQ
                     RLKNLKI"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(2819..3130)
                     /locus_tag="CRN69_RS00020"
                     /old_locus_tag="CRN69_00020"
     CDS             complement(2819..3130)
                     /locus_tag="CRN69_RS00020"
                     /old_locus_tag="CRN69_00020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017134632.1"
                     /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 transcriptional regulator"
                     /protein_id="WP_039817123.1"
                     /translation="MSNQNIFEILTSDPVSLNMWNLKSNLILAIHKTVRDNGWNQTEAA
                     AHLGISQPRVSNMLKGKLDKFSTDSLLEIMFKLGYKLDMQVHPSSEVILEMGMKKAML"
                     /name="helix-turn-helix transcriptional regulator"
     gene            complement(3488..3601)
                     /locus_tag="CRN69_RS31010"
                     /old_locus_tag="CRN69_00025"
     CDS             complement(3488..3601)
                     /locus_tag="CRN69_RS31010"
                     /old_locus_tag="CRN69_00025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_072016307.1"
                     /translation="MHEPPVQSDCCALSGNYHLESNPVRHAKAPLAAAIGN"
                     /name="replication initiation protein"
     gene            4010..>4163
                     /locus_tag="CRN69_RS00035"
                     /old_locus_tag="CRN69_00035"
     CDS             4010..>4163
                     /locus_tag="CRN69_RS00035"
                     /old_locus_tag="CRN69_00035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_065874968.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(3489..3962)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.627"
                     /coverage="92.0"
                     /evalue="9.83e-170"
ORIGIN
        1 tgtcctcgag actggatgca ttacaggatg gtaactgatg gcccgagtgt ctattagtga
       61 ggcttcccga ctgacgggta agagtagaac aacactgcac aggttaatta aagcaggtga
      121 cctgtccacc tgtagcggtg aacgtaatgc aaaaatggta gatacttcag agcttttacg
      181 tgtctttggt ccctttgagc aaccgaagag tgaacaccat tctggacagg tctctgaaca
      241 gcgtgataca gcctctgctg accagagtga acaggtgatt cgtcatctga aacaggagat
      301 tgaacacctg aacaccttac ttttgtccaa ggattcgcac attgatagcc tgaaacaggc
      361 catgctcctt cttgaaaatc accaggcaaa attaactgaa tccccggcgc catggtggaa
      421 attctggaaa aaatcctgac cccgtcatgc ttcagttttc ctctccggcc atcccgggga
      481 gttcctgaac cttcccaaaa atcgccagat ctctgaacgc tcctcaccac taaaaatatc
      541 cacaccccac gcaaaattaa aattttgcag atttgtattt tatatcagca gcttacgttc
      601 tataaatttc gtttttttaa ttttatttat acagatccga ctctatgacg agtcgtcata
      661 gagtccccgg cgagtcgtca tagagtcggt aacgactcag gactataaaa acaataagtt
      721 aacaacgacc cgactctaga cccgactccc cgtttggttg ttttttagac gtgacgactc
      781 tgggtacgac tctagtgaag agtcgccggt gaatcgtgtg gtgagtcgtc cggcgacttg
      841 ccataacgtg attgccggcc gtcgacgaac ccgattcctg aacgtgctga aaaccggttt
      901 tccggctgcg ccggcaacgc ttcacggcca cgcaataaat tgcgtccccg ttcaccgttt
      961 tcggatggga agaacgccgg aaacaggact taccctggct gaatggcgtg aattttcgcg
     1021 ctatgcactt gcgtgcatac tcatgcatgc cgtaaaaaca gagcctgcgc gtttctggcg
     1081 ggttttcggg tggtttgttg cctgttttac cggtttcccg tcagaaacgc cctgaggccg
     1141 ttttagcggt gcgtacaatc atacctttat gttaaatgat agatgtaaaa agccccgatt
     1201 ggtctgatgg atttcctgct gaggtgcgaa gcggtccacc tcccggcgac ctgttcggaa
     1261 actccctctg cgccagtctt gtttggccaa ataagctgtt atgagataag cacttgtggt
     1321 gtggtagaga agatcctagc tgacaaagat ctctcttatg tctttaatga gagtgatatt
     1381 ggaagattgt cgaagcaatt ggtcctttat catttcagta acggcatatg tgttgtaaac
     1441 agcgatagct atttcagata aagacggatt agtagttagt gacttacatg taggaataaa
     1501 aaagcctgga cgatcggata actgtttttc tagaacgaga tcaacacgat gaaaagcatc
     1561 gtcaataaag ctccgcactt gctctggaga caggtcatga taacgaatga caaattcaaa
     1621 aggtggatta gacataagac ctcagatcgt ggattgtttg gtacgagtga gtaatgagac
     1681 tttctggtaa atcactgagg gaaagccccg aagggcttcc gtgtctcagt taccaaattt
     1741 atcaccgttt gtgtctgtcc tcacaattag ctgccattta acattttgtt tttgactatg
     1801 ttgatgatgg ttttgtgggg ggaaaggatc gtttttatta ctagttatct ctttaccgca
     1861 tacggtacag cgataaatgc ctgatactgg aactgtatcg cttggatcgt atgttgatgt
     1921 ccaccaagtc tgtgtgtgtg taactcgctg taagaactgc tctgtttttt ccgtatatgc
     1981 agccattctt ttacctttct tatcgtttat tttcttggtt ttcctgcgtc tgagcgtttt
     2041 ttgcgcaccg ttccgtcatt gtttctgtct ctgggctggg ttccgccacc aggctttggc
     2101 actaccacat ctttgtttag cggtcttcta tctgccatct cttaactcct tctttcagtt
     2161 gtgatgcttt acggagactt ttagcttcga tggaggatta ctttcgtaaa cagctgatag
     2221 cttatttatt gagctaacgg catgcgcaag cgaagcggca tattgttagt ttatacaact
     2281 tagagtatat tgatgcaatg gatattgcct aaagcagtgt cctgaaccac tgaaattaaa
     2341 tgcctctacc tggtgaatct catcaggcgt agaggtttgg ttttttagtg aggttttttt
     2401 aatcggagta tcaaatgaga aatttaattg ttcgaccact aaaccccaac aaaggaggac
     2461 actatgtccg caagcgaaat gaaagagatt tgtctagacg taactggtgt tgataaagag
     2521 ctaaagtctt tacctattga taaagcttta gcttttttgc acaacttgaa gttggttgcc
     2581 gctggaattg aaccagaact gaaagttgaa cacctgaaag tagttgctcc aggcgtgatt
     2641 gagttgaaga taaatggtag ccctgcttat cgttgtgtgt acacgataaa atcacccggc
     2701 aaggtgatcg tgttacgtgt cttcaagaaa acgactaacg gacctgcacg caaagactta
     2761 gaagtcgtga agcaacggct gaaaaatctc aaaatatagt atccactcaa ggcgatgttc
     2821 acagcatcgc ctttttcatg cccatctcta aaattacttc agaggatggg tgtacttgca
     2881 tgtctaattt gtaacccagc ttgaacatga tttccagtag tgaatctgta gaaaacttgt
     2941 ccagcttccc tttcagcatg ttgctaaccc taggttggct tatgcctaga tgtgcggccg
     3001 cctctgtttg gttccagccg ttatctctta ccgtcttatg tatggcgagg atcaggtttg
     3061 atttcaggtt ccacatgttt agggataccg gatcactcgt tagtatttcg aatatgtttt
     3121 gattgctcat aattttcatc tcctatctga atgcgagcat ttagttgtca caagacaata
     3181 ggaacgatta ttagcttaca ctaaagtttg cggattatac aagttacagt atgcatgaca
     3241 agatgtagat ggggttttat ttgtaaattt aaagcattct aacaacactt gttgactgga
     3301 tcttggtcgt cagcgtagtc ttcatttgtt ttaaaaagaa aaaccgcctg gggaggcggt
     3361 ttttcaaggt tcatcaaacc ggcaagttta tgaaccgagg taactggctt agaggagcac
     3421 agtcaccaaa tctgttttat cagtgtagcc gtatagtacg tgtcttttca agacttcact
     3481 cctctaatca gttaccaatg gctgctgcca gtggcgcttt tgcatgtctt accgggttgg
     3541 actcaagatg atagttaccg gataaggcgc agcagtcgga ctgaacgggg ggttcgtgca
     3601 tacagtccag cttggagcga actgcctacc cggaactgag tgtcaggcgt ggaatgagat
     3661 aaacgcggcc ataactgcgg aatgacaccg gtaaaccgaa aggcaggaac aggagagcgc
     3721 acgagggagc catcaggggg aaacgcctgg tatctttaga gtcctgtcgg gtttcgccac
     3781 cactgatttg agcgtctgtt tttgtgatgc ttatcagggg ggcggagcct atggaaaaac
     3841 ggcaacgccg cggccttccg ttgtcctttc cgagctgtct gtcctatgcc cttatgtgtg
     3901 cgttgcgacc gctcgccgca gccgaacggt aggagcgtag cgactgagtg agcgaggaag
     3961 cggaaaagag accggtttta cattgagcac tgacgctctg aggcccttta tgacgaaaca
     4021 acagaaaacg gcgctgaaca tggctaagtt catccagaat cagtccctgc tcctgctgga
     4081 gaagcttaac gagcttgatc tcgatgctga ggctgacctt tgtgagaaac tccacgatga
     4141 tgcggagcat cttttccgta cac
//
