LOCUS       NZ_CP070183             5214 bp    DNA     circular CON 11-JAN-2024
DEFINITION  Klebsiella pneumoniae strain FDAARGOS_1330 plasmid unnamed4,
            complete sequence.
ACCESSION   NZ_CP070183
VERSION     NZ_CP070183.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16357472
            Assembly: GCF_016903515.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5214)
  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  JOURNAL   Unpublished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 5214)
  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                   :: SMRT v. 8.0.0, HGAP v. 4
            Genome Coverage                   :: 635.94x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/11/2024 06:11:10
            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)                     :: 5,373
            CDSs (total)                      :: 5,245
            Genes (coding)                    :: 5,139
            CDSs (with protein)               :: 5,139
            Genes (RNA)                       :: 128
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 107
            CDSs (without protein)            :: 106
            Pseudo Genes (ambiguous residues) :: 0 of 107
            Pseudo Genes (frameshifted)       :: 42 of 107
            Pseudo Genes (incomplete)         :: 56 of 107
            Pseudo Genes (internal stop)      :: 20 of 107
            Pseudo Genes (multiple problems)  :: 11 of 107
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP070183.1.
            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..5214
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_1330"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_1330"
                     /db_xref="taxon:573"
                     /plasmid="unnamed4"
                     /geo_loc_name="USA: WA"
                     /collected_by="ARMADA"
     gene            235..1485
                     /locus_tag="I6K60_RS26390"
                     /old_locus_tag="I6K60_26390"
     CDS             235..1485
                     /locus_tag="I6K60_RS26390"
                     /old_locus_tag="I6K60_26390"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015160339.1"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [Evidence IEA];
                     GO:0008168 - methyltransferase activity [Evidence IEA];
                     GO:1904047 - S-adenosyl-L-methionine binding [Evidence
                     IEA]"
                     /GO_process="GO:0006304 - DNA modification [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WP_138846454.1"
                     /translation="MTRPIAVDLFAGAGGLSLGFEQAGFDIMASVEIDPIHCSAHKYNF
                     PMCKTICRSVVDVTGEYVREVSGIGEKEIDVVIGGAPCQGFSLIGKRALDDDRNKLVYH
                     YVRLVLELKPKYFIFENVKGLTVGKHKQFLVEIMDAFKDGGYDVVSDYKVLNAADYGVP
                     QDRRRLFLMGGRKGIALPSYPEPLSIRTTVGDAIGDIPDAEKYPELWGRDWVYAKFGEQ
                     SLYSSYLHGVRKDPSDFSYPRIFNKDKLTCSLLTDHSDISRGRFVETLPDTVEPISRFK
                     KLSMNGLCNTLRAGTASDRGAFTSPRPIHPIYPRVITVREAARLHSYPDWFRFHVTKWH
                     GFRQVGNSVPPMLARSVGLQIMKVLGVTPKKPTKKIKLGDESLVAISMSDAASMFGVSS
                     NVIAKRIKNSNKEVVCE"
                     /name="DNA cytosine methyltransferase"
     gene            1478..2287
                     /locus_tag="I6K60_RS26395"
                     /old_locus_tag="I6K60_26395"
     CDS             1478..2287
                     /locus_tag="I6K60_RS26395"
                     /old_locus_tag="I6K60_26395"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010222407.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_044525163.1"
                     /translation="MSKDKKERSKNRYHQLVEKIFFDKYVDGDLEVLFERLEINSAAKD
                     LGIELPSNVGDVIYSIRFRTPMPESILLTQPEGKEWIIELAGRSKYRFRLVTISRILPN
                     PNMVAIKIPDNTPEIITGYSLDDEQALLAKVRYNRLIDIFLGITTYSLQNHLRTTVKGI
                     GQIEIDELYVGIDKYGCHYIIPVQAKGGTDQISMVQTSQDTAWCEQKYPNVRCRAISAQ
                     FVSSDLIALFELKIDEGQVKLIEERHYKLVPAKELDSSDISNYRMSV"
                     /name="hypothetical protein"
     gene            complement(2507..2638)
                     /locus_tag="I6K60_RS26960"
     CDS             complement(2507..2638)
                     /locus_tag="I6K60_RS26960"
                     /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="replication initiation protein"
                     /protein_id="WP_072007956.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPKRHAKAPLAAATGNRIHGAE"
                     /name="replication initiation protein"
     gene            3259..3600
                     /locus_tag="I6K60_RS26400"
                     /old_locus_tag="I6K60_26400"
     CDS             3259..3600
                     /locus_tag="I6K60_RS26400"
                     /old_locus_tag="I6K60_26400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006122514.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_071599364.1"
                     /translation="MADKRNKMLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPTR
                     AGRLPSISPALLRQLAGMGNNLNQIARKVNAGGAGHDRVQIVAALMAIDAGLERLRHAV
                     LEKGPDDDC"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3809..>4237
                     /locus_tag="I6K60_RS26965"
                     /pseudo=""
     CDS             3809..>4237
                     /locus_tag="I6K60_RS26965"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            4278..4775
                     /locus_tag="I6K60_RS26410"
                     /old_locus_tag="I6K60_26410"
     CDS             4278..4775
                     /locus_tag="I6K60_RS26410"
                     /old_locus_tag="I6K60_26410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020325392.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_015328238.1"
                     /translation="MSSLLTASRDFEEKSKAQQQLTEERLKAAFSKHENVVKSELNASA
                     KRINDAISAHEQGMNAAMQSNRLSVLRMVGRTWLTITMVSGLLFASLSGVLWYQGNRIA
                     ANLAEIRQQRDTLSKLHMQTWGVTYLENRNGRFLVLPEGMKAETGRTVDNKTRNAVKLV
                     RE"
                     /name="MbeB family mobilization protein"
     gene            4782..4997
                     /locus_tag="I6K60_RS26415"
                     /old_locus_tag="I6K60_26415"
     CDS             4782..4997
                     /locus_tag="I6K60_RS26415"
                     /old_locus_tag="I6K60_26415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015328239.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_015328239.1"
                     /translation="MTELEKQLLSALEQLQQDYSRRLDEWESAFEEWRKMSGLMQRENA
                     ALSERVSGLSRQVQSLSEQLRRLSTG"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          3001..3174
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.785"
                     /coverage="100.0"
                     /evalue="5.6599999999999995e-68"
     Typing          complement(2530..3015)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.238"
                     /coverage="80.0"
                     /evalue="0.0"
     Typing          3591..5113
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgcagtgat gtgaataagt gatgcatatg cgtaaaataa atcaggtgcg tttctggtgg
       61 ttttcggtgt acttgccacc accttttgcc cgtcagccat cagaaacgcc ctgagtgcct
      121 ccggcgcggt gcgggtaaga gatgttatgt tcaatcgaaa tcagaaaaac gatcggtaaa
      181 gcgatcgttt ttctgatagc atcatgttga ttttatataa cgtgggtgta aagaatgact
      241 agaccgattg ctgttgattt atttgctgga gcgggtgggc tgagtctcgg tttcgagcaa
      301 gctggctttg atataatggc atcagttgag atagatccaa tacattgctc tgctcacaaa
      361 tataactttc ctatgtgcaa aacgatatgt agaagtgttg ttgatgttac cggagaatac
      421 gttagggaag tttcaggtat tggtgagaaa gagattgatg tagtgatcgg aggcgctccc
      481 tgccaaggct tttcattaat aggaaaacgc gcgcttgatg atgatagaaa caaactggtc
      541 tatcactatg tacggctggt tcttgagcta aagcctaaat actttatttt tgaaaatgta
      601 aaagggttga cggttggtaa gcataagcag tttttagtag agataatgga tgcatttaaa
      661 gatggtgggt acgacgttgt aagcgattat aaagtgctaa acgcagctga ttatggagtt
      721 cctcaagatc gccgtcgtct tttcttaatg gggggaagga aaggaattgc tctgccatca
      781 taccctgagc cattatccat tagaacaacg gttggggacg ctattgggga tattcctgat
      841 gcggaaaaat atcctgagct atggggtaga gattgggttt atgctaaatt tggtgagcaa
      901 tcactatact catcctattt gcatggcgta agaaaagatc ctagtgattt tagctaccca
      961 aggattttta ataaagacaa attaacgtgt tctttactga cagatcactc tgacatttct
     1021 agagggcggt ttgttgaaac tttgcctgac acggtagaac caatcagcag gtttaaaaag
     1081 ctctcgatga atgggctatg taatacttta agggcaggaa cagcaagtga cagaggtgct
     1141 tttacatctc ctcgtcctat acatccgatc tatcctaggg tcatcacggt cagagaggca
     1201 gcaagactgc attcatatcc tgattggttc agatttcatg tgactaagtg gcatggattt
     1261 agacaggtcg gtaatagtgt tcctcctatg ctagctagaa gtgttggctt gcagattatg
     1321 aaggttcttg gtgttacgcc aaaaaaacca acgaagaaaa tcaaactcgg tgatgaaagt
     1381 ttggttgcta tttctatgtc cgatgctgca tctatgtttg gtgtgtcatc aaatgtaatt
     1441 gctaagagaa taaaaaatag taacaaggag gttgtttgtg agtaaggata aaaaagaaag
     1501 gtccaaaaat agataccatc agttggtaga aaagatattt ttcgataaat atgttgatgg
     1561 tgacttagag gttttgtttg aaaggttaga gataaacagt gctgcaaaag atttaggtat
     1621 agaactccca tctaatgttg gtgatgttat atattcaatc agatttagaa cgcctatgcc
     1681 agaaagtatt ctgttgactc agccagaagg taaggagtgg attattgagc tggctggtag
     1741 gtcaaagtat cgatttagat tagtaactat tagtaggatt ttgccaaatc ctaatatggt
     1801 ggcaataaaa attccagaca ataccccgga gataattaca ggttattctt tagacgacga
     1861 gcaggcattg ctggcgaagg tgagatataa ccggctaata gatatatttc taggtataac
     1921 cacatattct ttacagaatc atttaagaac tacggtgaag ggaattggtc aaatagagat
     1981 cgatgaactt tatgtaggta tagataaata cggttgccat tatataatac cagttcaagc
     2041 aaaaggtggg acagaccaaa tatcaatggt gcaaacatcg caagatacag cgtggtgtga
     2101 acaaaaatac ccaaatgtta gatgtagagc tatttccgct cagtttgttt cgagcgattt
     2161 gattgcactg tttgagctaa agatagacga aggacaagtg aaattgattg aggaaaggca
     2221 ttacaaactg gttccggcaa aagagttaga tagctctgac atctcaaact accgcatgtc
     2281 tgtataattt ctgagaggat cttcttgaga tcctttcgtt ctagccgtaa tctcctaagc
     2341 cgtaaacaaa aaaaccaccg ctaccaacgg tggttcgttt gccggaattt agagctacca
     2401 actctttctt ccgaaggtaa ctggctttca cggagcgcag ataccaaaac tgtcctttca
     2461 gtgtagccgt agtcaggcca ccacttcaag aactctgtag ataactctac tccgctccgt
     2521 gaatccgatt accagtggct gctgccagtg gcgcttttgc atgtcttttc gggttggact
     2581 caagacgata gttaccggac aaggcgcagc agtcggactg aacggggggt tcgtgcatac
     2641 agtccagctt ggagcgaact gcctacccgg aactgagtgt caggcgtgga atgagacaaa
     2701 cgcggccata acagcggaat gacaccggta aaccgaaagg caggaacagg agagcgcacg
     2761 agggagctac cagggggaaa cccttgggat ctttatagtc ctgtcgggtt tcgccgccac
     2821 tgatttgagc gtcagatttc gtgatgcttg tcaggggggc ggagcctatg gaaaaacggc
     2881 ttcgccgcag cctcatcgtt tccctgttaa gttccttcct ggcatccacc aggaaatttc
     2941 cacctcaccc gtaagccggt accgctcgcc gcagccgaac gaccgagcgc agcgagtcag
     3001 tgagcgagga agcggcacat ctcccgttac tacatgttct gctgacgcgc cggtgccgcc
     3061 tttttctcct gctacatgaa gcacttcccc gaatctccat ctcgccgtaa catactaagc
     3121 cagtatacac tccgctagcg ctacgtgact ggttcagggc tgcgccccga aaccccactg
     3181 acgcgcctgc ggcttgtcca accccgcgcc gaccgggaaa ggctttcccg tccgtcacgg
     3241 cgttatcagg aggcgattct ggcagataaa cgcaacaaga tgctcacgat gtgggtgacg
     3301 gaagacgaac accggcggtt gcttgagcgg tgcgacggaa aacaactggc ggcgtggatg
     3361 cgccagacct gccttgatga gaaaccgaca cgcgccggca ggcttccctc gatttcgccc
     3421 gcgctgctgc gtcagcttgc cggcatgggc aataacctga accagatcgc ccggaaagtg
     3481 aacgccggtg gtgccggtca tgaccgggtg cagatcgtgg cagcgctgat ggcgatcgat
     3541 gccggtctgg aacggttgcg gcatgccgta ctggaaaaag ggccggacga tgattgttaa
     3601 attccatccc cggggtcgcg gcgggggcgc cggtcctgtg gattatcttc tgggtaaaga
     3661 ccggcagcgt gaaggtgcca gcgtcctgca ggggaagccg gaagaagtcc gggagctgat
     3721 tgatgcgtcg ccgtatgtga aaaaatatac ctccggggtg ctgtcattcg cggaggcgga
     3781 cctgccgccg ggtcagcgtg aaaaactgat ggccagcttt gagcgggttc tgatgcccgg
     3841 actcgataaa gaccagtaca gcattctgtg ggtggaacac gcagacaagg gtcgtcttga
     3901 gctgaatttt ctgatcccca ataccgaatt actgacgggg aaacgcctcc agccgtatta
     3961 cgatcgtgcc gaccggccgc gcatcgatgc gtggcagaca gtggtcaacg gcaggctggg
     4021 gctacatgat ccgaacgacc cggagaaccg gcgggcgctg gtcacgcctt caggactgcc
     4081 agaaacgaag caggaagccg cagagacgat tacacggggt ttgctgatgt tagcctcatc
     4141 aggagagctg aaaacgcgtg atgacgtcac aggggcgctc acagcggccg gttttgaggt
     4201 ggtcagaacc acaaaaaaca gtatcagcat tgccgacccg gacggggggc gaaatatccg
     4261 actgagggga gccatttatg agcagtcttt taacggcctc gagggacttc gaggagaaat
     4321 cgaaagcaca gcagcagctt accgaagaga ggctgaaagc cgcattcagc aagcacgaga
     4381 acgttgtcaa atcggaactg aacgcaagcg cgaagagaat caacgacgcc atcagcgccc
     4441 acgaacaggg gatgaacgcg gcgatgcagt cgaaccggct gagcgtgctg cgaatggtcg
     4501 ggcggacgtg gctgaccatc accatggtgt cagggctgct gttcgccagc ctgagcgggg
     4561 tgctgtggta ccaggggaac cggatagcgg cgaacctggc ggaaatcagg cagcagagag
     4621 atacgctgtc gaaactgcac atgcagacgt ggggcgtgac ctatctggag aaccgcaacg
     4681 gacggtttct ggtgctgccg gaggggatga aagccgaaac gggccggacg gtggacaaca
     4741 agacgcggaa cgcggtgaag ctggtacggg agtagagcag aatgacggaa ctggaaaaac
     4801 aattgctgag cgcgttagag cagctacagc aggactactc gagaaggctg gacgagtggg
     4861 agagcgcctt cgaggaatgg cggaagatgt ctggtcttat gcaacgggag aacgcggcgc
     4921 tgagcgagcg cgtgtcgggc ttgagcaggc aggtgcagag tttgagcgag cagctgcgcc
     4981 ggttatcgac aggctgaatg agattgagca acagcgatac gggcaaacaa cggaaaagga
     5041 accagagaag acagcagatc tggtaccgga acggcaacgc acattatctc atggtgacag
     5101 ggagtatgga gactgataaa cgcccgtctc aggtggcctg agcgtgacgg ggatcatggc
     5161 cattttctgc gatttcagca cacagagagt cttttttaac cgaaatcacc ggct
//
