LOCUS       NZ_CP023915             3808 bp    DNA     circular CON 08-JAN-2024
DEFINITION  Klebsiella pneumoniae strain FDAARGOS_439 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP023915
VERSION     NZ_CP023915.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN07312483
            Assembly: GCF_002591075.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3808)
  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  JOURNAL   Unpublished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 3808)
  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                   :: 600.092x
            Sequencing Technology             :: PacBio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/08/2024 03:03:26
            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)                     :: 5,686
            CDSs (total)                      :: 5,564
            Genes (coding)                    :: 5,390
            CDSs (with protein)               :: 5,390
            Genes (RNA)                       :: 122
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 174
            CDSs (without protein)            :: 174
            Pseudo Genes (ambiguous residues) :: 0 of 174
            Pseudo Genes (frameshifted)       :: 70 of 174
            Pseudo Genes (incomplete)         :: 113 of 174
            Pseudo Genes (internal stop)      :: 29 of 174
            Pseudo Genes (multiple problems)  :: 33 of 174
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP023915.1.
            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..3808
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_439"
                     /isolation_source="Urine"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_439"
                     /db_xref="taxon:573"
                     /plasmid="unnamed4"
                     /geo_loc_name="Canada: BC"
                     /collection_date="2014-12"
                     /collected_by="BC Centre for Disease Control"
     gene            complement(join(3667..3808,1..281))
                     /locus_tag="CRN23_RS29650"
     CDS             complement(join(3667..3808,1..281))
                     /locus_tag="CRN23_RS29650"
                     /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_016809948.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKAIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTGVNSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEYNHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(281..472)
                     /locus_tag="CRN23_RS26760"
                     /old_locus_tag="CRN23_26750"
     CDS             complement(281..472)
                     /locus_tag="CRN23_RS26760"
                     /old_locus_tag="CRN23_26750"
                     /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_026056049.1"
                     /translation="MTKQQQTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            888..971
                     /locus_tag="CRN23_RS30705"
                     /old_locus_tag="CRN23_26760"
     CDS             888..971
                     /locus_tag="CRN23_RS30705"
                     /old_locus_tag="CRN23_26760"
                     /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="hypothetical protein"
                     /protein_id="WP_058655973.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPERHD"
                     /name="hypothetical protein"
     gene            complement(1233..1661)
                     /locus_tag="CRN23_RS26775"
                     /old_locus_tag="CRN23_26765"
     CDS             complement(1233..1661)
                     /locus_tag="CRN23_RS26775"
                     /old_locus_tag="CRN23_26765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000534558.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_016809951.1"
                     /translation="MGSGAGAQNPQLNIVSFSETFNLYYTSRFSAKTLDKIDDFIEHFE
                     KYNLFGDPLKKHPAWIGKVSPSWKVPDHYENKEAIELHARANKLWHAHLGDPVFKDTFH
                     GKYKVSDWVIHFQRLTPNHIKLLELGYHDPMELPQNFE"
                     /name="hypothetical protein"
     gene            complement(1625..1795)
                     /locus_tag="CRN23_RS30215"
     CDS             complement(1625..1795)
                     /locus_tag="CRN23_RS30215"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001531327.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_171482495.1"
                     /translation="MKTEQRHDLIKDTEVFGVSLSLLISRANEKSVTMPSGLSREQRRA
                     WAAEQVRKIHS"
                     /name="hypothetical protein"
     gene            1953..2381
                     /locus_tag="CRN23_RS26780"
                     /old_locus_tag="CRN23_26770"
     CDS             1953..2381
                     /locus_tag="CRN23_RS26780"
                     /old_locus_tag="CRN23_26770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000222531.1"
                     /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_016809950.1"
                     /translation="MTYSIEEKWKAGGLSLGWTAIPTVLFFIQNEKKLTSVAFNTLLNL
                     IVHWWNLQEWPHPSMESLAIRMGVSVRTVQRAINDLEKANLLDKKPTSKSDSRYGGRNI
                     YDLTKLVDYLDTMGPSVAEQVKKPRHKRPVYTVRKTTT"
                     /name="helix-turn-helix domain-containing protein"
     gene            2665..2865
                     /locus_tag="CRN23_RS26785"
                     /old_locus_tag="CRN23_26775"
     CDS             2665..2865
                     /locus_tag="CRN23_RS26785"
                     /old_locus_tag="CRN23_26775"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017802053.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="sigma-70 region 4 domain-containing protein"
                     /protein_id="WP_042918523.1"
                     /translation="MFGFGIQGTINKGFFLQMARRDQDAFLQYLYDQGYSAKDISKNFD
                     IPVPSVYNRINAHRGRGPLPN"
                     /name="sigma-70 region 4 domain-containing protein"
     Typing          521..997
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.797"
                     /coverage="91.0"
                     /evalue="4.61e-163"
ORIGIN
        1 tcagcttcta gtaaagcaat tctatgttgt aaatcatgta aaccaacgct gttaacacct
       61 gtagattctg cgtcactttt tacatcatat tttacagtat cgatgacacc atcaagagaa
      121 ccaaacactc taataagctc tgaggtatca ataactttaa tagccttccc gtgctttaca
      181 acagaggtgt aacttaactt cccactgtta atcatcttgt aaattgtggg gcgactaacc
      241 ttaacaagcc gtgccgcttc actaatagac actctggcca tcagttacca tcctgtaatt
      301 catccagtct cgaggacagt gtacggaaaa gatgctccgc atcatcgtgg agtttctcac
      361 aaaggtcggc ctctacatcg agatcaagct cgttaagctt ctccagcagg agcagagact
      421 gattctggat gaacttagcc atgtttagcg ccgtttgctg ttgtttcgtc ataaagagcc
      481 tcagagcgtc agtgctcaat gtaaaaactg tctcctttcc gcttcctcgc tcactcagtc
      541 gctacgctcc tgccgttcgg ctgcggcgag cggtcgcaac tcacgtataa gagcataaga
      601 cgacagggct gatagccgga ggggacaaaa taaggtcgcg gcgttgccgt ttttccatag
      661 gctccgcccc cctgacaagc atcacagaag cggacgctca aatcagtggt ggcgaaaccc
      721 gacaggacta taaagatacc tatcatttct gataggcggc tccctcgtgc gctctcctgt
      781 tcctgccttt cggtttaccg gtgtcattcc gctgttatgg ccgcgtttat ctcattccac
      841 gcctgacact cagttccggg taggcagttc gctccaagct ggactgtatg cacgaacccc
      901 ccgttcagtc cgaccgctgc gccttgtccg gtaactatcg tcttgagtcc aacccggaaa
      961 gacacgacta atcgccattg gcaacggcca ctggtaagca ggatgtgcga gagatgtatt
     1021 gagagttctt gaagtggcgg cctaactgag gctacactgg aaggacggat ttggtgacat
     1081 gtctcgcaca agactgttac cacggttaga taatctgcca ggattaaata accttcgaaa
     1141 aaccacctgc cagggtggtt ttttcgtttt cacaacagga gattacgacg aggttgaatg
     1201 aatctcaaga tttcatttag tctgctaccc gatcattcaa agttttgggg tagttccatc
     1261 gggtcatggt atcccagttc taaaagcttt atatggttcg gtgtcagccg ctggaaatgg
     1321 ataacccagt cagaaacctt gtatttccca tgaaacgtat ctttgaaaac cggatcgcct
     1381 aaatgagcat gccataactt gttagctcta gcgtgcagct caatagcttc tttgttttcg
     1441 taatgatcag gcactttcca cgacggcgat actttaccaa tccaagctgg atgttttttt
     1501 aaaggatcgc caaagaggtt atatttttcg aaatgctcaa tgaaatcatc gattttatcg
     1561 agtgtttttg cagaaaatcg ggatgtgtaa tagagattga aagtctcaga gaacgagaca
     1621 atattcaact gtggattttg cgcacctgct ccgctgccca tgctcttctc tgctccctac
     1681 ttagaccaga tggcattgta acagacttct cattcgctct ggaaatcaac agagacaagg
     1741 atacgccaaa tacttcagta tctttaataa gatcatgacg ttgttcggtt ttcatatcgt
     1801 taactccgta tctaattcag acaggaaaaa atcttttttc cgctttcaga gtagtctttt
     1861 gtagttgcac tataatggcg ttgatgtcac cctattcata tgaataatca tataatatat
     1921 acttcaaata tttttgtttt ttaggaaaat caatgactta ctctattgag gaaaaatgga
     1981 aggctggcgg tttgtctctt ggctggactg caatacctac tgtcttgttt tttatacaga
     2041 acgagaaaaa gctaacctcc gtagccttta acactctgct taacctgatc gttcattggt
     2101 ggaatttgca agaatggccg catccatcaa tggaaagcct agccatacgt atgggggttt
     2161 ctgtaaggac agttcagaga gctatcaatg atctggaaaa agctaatctc ttggacaaga
     2221 aaccaacgtc gaagagtgat agccgatatg gaggtcgtaa tatttatgat ctaacaaagc
     2281 tcgttgatta cctggataca atgggcccat cagtagctga acaggttaag aaaccccgtc
     2341 ataaaagacc ggtatatacc gtaagaaaaa caacaactta aaaaagagca attgcactgt
     2401 tcgaaggaaa aacgataact actctatggt attgcttgct gtataggtat tggtggtcct
     2461 gcggctggtt catcgcttca cggttaaaat agtcctgtaa gctgttaata tttaacataa
     2521 cactactacc acgaacctac gtaacaatcg ctaccaacac agaagtgaca aatttataaa
     2581 aaaacaaaaa ccataaaaaa acttgacttt atgttttttt tggctaattt ctttatcatt
     2641 tctttatcaa aaatagaggt ggctatgttt ggttttggaa ttcaaggtac tattaataaa
     2701 ggattttttc ttcagatggc tcgtagagat caggatgcat ttttgcaata tctctatgac
     2761 caagggtact cagcaaaaga tatcagcaag aacttcgata ttccggttcc tagcgtctac
     2821 aacagaatca acgctcaccg aggccgtgga cctcttccca attaatggtt cttctataca
     2881 aaaaagtcgc ctggataggc gactttttta actgaactct gtgtatagat ttaccataac
     2941 gtctcaattg tacgcaccgc taaaacggcc tcagggcgtt tctgacggaa aaccggcaaa
     3001 acaggcaaca aaccacccga aaacccgcca gaaacgcgca ggctccgttt ttacggcatg
     3061 catgagtatg cgcacaagtg catagcgcga aaactcacgc cattcagcca gggtaagtcc
     3121 tgtttccggc gttctttcca tccgaaaacg gtgaacgggg acgcaattta ttgcgtggcc
     3181 gtgaagcgtt gccggcgcag ccggaaaacc ggttttcagc acgttcagga atcgtgttcg
     3241 tcgacggccg gcaatcacgt tatggcaagt cgccggacga ctcaccacac gattcaccgg
     3301 cgactcttca ctagagtcgt acccagagtc gccgagtcta aaaaacaacc aaacggggag
     3361 tcgggtctag agtcgggtcg ttattaactc attgttttta tagtcctgag tcgttaccga
     3421 ctctatgacg actcgccggg gactctatga cgagtcgtca tagagtcgga tctatgtaaa
     3481 taaaatttaa aaaacgaaat ttcacgaaag taaaccactg atattaaata caaatctgca
     3541 aaattttaat tttgcgtagt gtgtgggtat ttttagtcgt gaggagcgtt cagagatctg
     3601 gcgatttttg ggaaggttca ggaactcccc gggatggccg gagaggaaaa ctgaagcatg
     3661 acggggtcag gattttttcc agaatttcca ccacggggaa tggggtggtg aagaaggttc
     3721 gtgattgtac tccagaagct gcatagcctg acgaagggaa tcaatatgct catctcgagc
     3781 cttaacagcc cctttaagac catcgttt
//
