LOCUS       NZ_CP033778             4565 bp    DNA     linear   CON 08-JAN-2024
DEFINITION  Klebsiella pneumoniae strain FDAARGOS_531 plasmid unnamed4.
ACCESSION   NZ_CP033778
VERSION     NZ_CP033778.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10163226
            Assembly: GCF_003812105.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4565)
  AUTHORS   Campos,J., Goldberg,B., Tallon,L., Sadzewicz,L., Zhao,X.,
            Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S., Geyer,C.,
            Nandy,P., 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  JOURNAL   Unpublished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 4565)
  AUTHORS   Campos,J., Goldberg,B., Tallon,L., Sadzewicz,L., Zhao,X.,
            Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S., Geyer,C.,
            Nandy,P., Yan,Y. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-NOV-2018) 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. 3.0, SPAdes v. 3.6.0
            Genome Coverage                   :: 620.460689310345x
            Sequencing Technology             :: PacBio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/08/2024 04:11:16
            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)                     :: 5,634
            CDSs (total)                      :: 5,510
            Genes (coding)                    :: 5,349
            CDSs (with protein)               :: 5,349
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 161
            CDSs (without protein)            :: 161
            Pseudo Genes (ambiguous residues) :: 0 of 161
            Pseudo Genes (frameshifted)       :: 91 of 161
            Pseudo Genes (incomplete)         :: 81 of 161
            Pseudo Genes (internal stop)      :: 21 of 161
            Pseudo Genes (multiple problems)  :: 29 of 161
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP033778.1.
            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..4565
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_531"
                     /isolation_source="Bronchoalveolar lavage from right lung"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_531"
                     /db_xref="taxon:573"
                     /plasmid="unnamed4"
                     /collection_date="2016-04-07"
                     /collected_by="Children's National Hospital"
     gene            51..164
                     /locus_tag="EGX99_RS29985"
                     /old_locus_tag="EGX99_28855"
     CDS             51..164
                     /locus_tag="EGX99_RS29985"
                     /old_locus_tag="EGX99_28855"
                     /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_080882241.1"
                     /translation="MHEPPVQSDCCVLSGNYHLESNPVRHAKAPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(368..2023)
                     /locus_tag="EGX99_RS28925"
                     /old_locus_tag="EGX99_28865"
     CDS             complement(368..2023)
                     /locus_tag="EGX99_RS28925"
                     /old_locus_tag="EGX99_28865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001697690.1"
                     /GO_function="GO:0019239 - deaminase activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="anti-phage dCTP deaminase"
                     /protein_id="WP_223340786.1"
                     /translation="MSLARKLREKRSNPIHSANEDSSGGDSINQITSRQSMDLVIGFCG
                     AVGSGIKSIVDVTEEELDDLGYDVYRIRVSELMQKLFSEWRDDIVTPFDRYHKLQDFGD
                     ALRNKYYPHILSEAVIHEIKIEKGIDTSSKKNKKAFLVDQLKHQDEIELLRMVYQHNFY
                     LLGVIRSEVERKRNLRDEGLSKSEVDIVIHHDRKSESDYGQQTAKAILDSDYFVKNNQG
                     QRAHLKAKVKRFIGLIHGLNGLTPTTYEKGMYAAHSASLQSACLSRQVGAAILDVNGNL
                     ISVGRNDVPKFNGGLYSADDGVNDHRCVYKGGKCYNEVRKLKIKSKISQILMSESACEL
                     GVKLTEDQAEQLADVIYKKTPVSSIIEYSRSIHAEMDAITSLARLGNGGFSDKVLYTTT
                     FPCHNCARHIVAVGITKVVYIEPYEKSLALELHDDAITEVNEHGKVIFESFEGVSPRRY
                     QKFFFSTDERKDSFGNAEKYSTKYKNHIDIQFIDSYLDFENRVVDIFRTNTNIDSGNHV
                     GRTDSTINLSSQPVPPVPPVPPVPPVPPVPPDSK"
                     /name="anti-phage dCTP deaminase"
     gene            complement(2036..2218)
                     /locus_tag="EGX99_RS28930"
                     /old_locus_tag="EGX99_28870"
     CDS             complement(2036..2218)
                     /locus_tag="EGX99_RS28930"
                     /old_locus_tag="EGX99_28870"
                     /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_080882243.1"
                     /translation="MGKELSLNKIYDKNSRYINDSRGHELGKEKKVFDFEVEMIKKRRE
                     DAIRKIIEDSKSLKW"
                     /name="hypothetical protein"
     gene            2606..2815
                     /locus_tag="EGX99_RS28935"
                     /old_locus_tag="EGX99_28875"
     CDS             2606..2815
                     /locus_tag="EGX99_RS28935"
                     /old_locus_tag="EGX99_28875"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005227293.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YdgH/BhsA/McbA-like domain containing protein"
                     /protein_id="WP_009310047.1"
                     /translation="MKSIKTFVAVAALSMMSFGAFAQSVSATASTLDRAEAKIAAQAAE
                     QGASYKITSAQFNNRVHMTAELTK"
                     /name="YdgH/BhsA/McbA-like domain containing protein"
     gene            complement(3658..4059)
                     /locus_tag="EGX99_RS28945"
                     /old_locus_tag="EGX99_28885"
     CDS             complement(3658..4059)
                     /locus_tag="EGX99_RS28945"
                     /old_locus_tag="EGX99_28885"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /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_116953876.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASAHQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(4059..4250)
                     /locus_tag="EGX99_RS28950"
                     /old_locus_tag="EGX99_28890"
     CDS             complement(4059..4250)
                     /locus_tag="EGX99_RS28950"
                     /old_locus_tag="EGX99_28890"
                     /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_023302508.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2..164
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.951"
                     /coverage="87.0"
                     /evalue="1.9e-71"
     Typing          4299..4565
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="83.088"
                     /coverage="82.0"
                     /evalue="1.1500000000000001e-59"
ORIGIN
        1 cacgcctgac actcagttcc gggtaggcag ttcgctccaa gctggactgt atgcacgaac
       61 cccccgttca gtccgactgc tgcgtcttat ccggtaacta tcatcttgag tccaacccgg
      121 taagacatgc aaaagcacca ctggcagcag ccaccggtaa ctgatttaga ggagttagtc
      181 ttgaagttat gcgccagtta aggctaaact gaaagaacaa gttttggtga ctgcgctcct
      241 ccaagccagt taccttggtt catagagccg caaactctag aaccttaaaa aaaccgcccc
      301 gcaaaggcgg tttttttctt tctcgtctca aggttaagct ctgtataaca tcagagtcaa
      361 cagatcttca tttcgagtct ggtggtactg gtggtactgg tggtactggc ggcacgggcg
      421 gcacgggcgg tacgggctgg gaagataaat taatagtcga atcagttctc ccgacatgat
      481 tgccagaatc aatatttgtg ttagttctaa aaatatcaac gactcgattt tcgaaatcta
      541 aatagctatc aataaactgt atatcaatgt gatttttata tttagtggag tacttttctg
      601 cgttaccgaa actatctttc ctttcatctg tagaaaagaa gaatttttga tacctacgag
      661 gtgatacacc ttcaaaggac tcaaatataa ccttcccatg ctcattcacc tcggttatag
      721 catcatcatg caattctaaa gcgaggcttt tttcatatgg ctctatataa acaacttttg
      781 ttattccaac agcaacaata tgtctcgcgc agttatgaca aggaaatgtg gttgtatata
      841 aaactttatc agaaaaacct ccattaccta gtctagctaa tgatgtaata gcatccatct
      901 ctgcatgaat tgagcgagag tactctataa tagaagatac tggtgttttt ttatatatta
      961 catcagccag ttgctctgct tgatcttctg ttaatttaac accaagttca caagcgcttt
     1021 ccgacataag tatttgtgaa attttgcttt taatctttag ttttctaact tcattataac
     1081 atttaccacc tttgtataca caacgatgat cattgacacc atcatccgca ctataaagcc
     1141 caccattgaa tttaggtaca tcattacgcc caacggaaat cagattccca ttaacatcca
     1201 atatagcagc accaacttga cgagaaaggc atgcagattg cagagatgct gaatgagctg
     1261 catacatacc tttttcatac gtggttggag ttaaaccatt tagcccatgt atcaagccaa
     1321 taaaacgctt aaccttagcc ttaaggtgcg ccctttgtcc ttgattattc ttaacaaaat
     1381 aatcagagtc aagtatagct ttcgcagtct gctgaccata atcgctctct gattttctat
     1441 cgtgatgaat aactatatcg acttctgact tactcagccc ttcatctcta agattacgct
     1501 ttctttctac ttcacttcta attacaccta gtaaataaaa attatgttgg tagaccattc
     1561 ttaaaagttc aatttcatcc tgatgcttca actgatcgac caaaaaagcc tttttatttt
     1621 ttttacttga ggtgtcaatg cctttttcta tttttatttc atggattaca gcttcagata
     1681 gtatatgtgg gtaatattta tttcttaacg catcaccaaa atcttgcagc ttatgatatc
     1741 tatcaaacgg agtaacaata tcatcacgcc attctgaaaa aagtttttgc ataagctcgc
     1801 taactcttat gcgataaaca tcatatccta gatcatctag ttcttcttca gtcacatcaa
     1861 caattgactt tattcctgag ccaacagcac cgcaaaatcc tataacaaga tccatagact
     1921 gtctggaggt tatttggttt atgctatccc ctccagagga gtcctcgtta gcactatgaa
     1981 tcggattact tcttttttct cttaactttc tagccaggct cataaaagac ctcacttacc
     2041 attttaatga ttttgaatcc tcaattatct tccttatagc gtcctctctt ctttttttaa
     2101 tcatttcaac ttcaaaatcg aaaactttct tttcctttcc cagctcatgc cctctagaat
     2161 cattaatata tctagaattc ttatcataaa ttttatttag agatagctct ttacccatca
     2221 caccctcctg caagacgcat ggattttact gttatcttta taacaggcaa tagccaagaa
     2281 acgtaatcga tagagatttt tttttcttat cctaaacatt aggaaattcg gcaagagaaa
     2341 agcaagagag atcacgccaa actaaccatt atttttcaat ttgttaaaat aaaatcatca
     2401 atgttaacat ttctatccac cacctcattt ggtacctaga atccagagat aaacctctgg
     2461 tcttgatgcg ctcaattctt gttctttttt tttgaatgat atccgcaaat tgtttcgatt
     2521 ttaatcagtc catggtcgtc ctatcattta tcacatcagg gcaacaacgc cccatacaga
     2581 acaaaattac ttaaggaata cgaccatgaa atccatcaaa actttcgttg cagttgccgc
     2641 actatccatg atgtctttcg gtgcctttgc tcagagcgtc agcgctaccg cctccaccct
     2701 ggatcgtgct gaagcaaaaa ttgccgcaca ggccgctgaa caaggtgcgt catacaaaat
     2761 caccagcgct cagttcaata accgtgtcca catgacggct gaactgacca aataagatgg
     2821 tcgcagaggg agctgccgaa caggtcgccg ggaggcggcc cgtttcgtcc cttagcagga
     2881 aaaccttcag gccccttcgg gggctttttt gcatctgtca tttaacataa aggtatgatt
     2941 gtacgcaccg ctaaaacggt ctcagggcgt ttctgacggg aaaccggtaa aacaggcaac
     3001 aaaccacccg aaaacccgcc agaaacgcgc aggctctgtt tttacggcat gcatgagtat
     3061 gcacgcaagt gcatagcgcg aaaattcacg ccattcagcc agagtaagtc ctgtttccgg
     3121 cgttctttcc atccgaaaac ggtgaacggg gacgcaattt attgcgtggc cgtgaagcgt
     3181 tgccggcgca gccggaaaac cggttttcag cacgttcagg aatcgggttc gtcgacggcc
     3241 ggcaatcacg ttatggcaag tcgccggacg actcaccaca cgattcaccg gcgactcttc
     3301 actagagtcg tacccagagt cgccgcgtct aaaaaacaac caaacgggga gtcgtgtcta
     3361 gagtcgggtc gttattaact tattgttttt atagtcctga gtcgttaccg actctatgac
     3421 gactcgccgg ggactctatg acgagtcgtc atagagtcgg atctatgtaa ataaatttta
     3481 aaaaccgaaa tttcaggaaa gtaagctact gatattaaat acaaatctgc aaaattttaa
     3541 ttttgcgtag tgtgtgggta tttttagtcg tggggagcgt tcagagatct ggcgattttt
     3601 gggaaggttc aggaactccc cgggatggcc ggagaggaaa actgaagcat gacggggtca
     3661 ggattttttc cagaatttcc accatggcgc cggggattca gttaattttg cctggtgatt
     3721 ttcaagaagg agcatggcct gtttcaggct gtcaatgtgc gaatccttgg acaaaagtaa
     3781 ggtgttcagg tgttcaatct cctgtttcag atgacgaatc acctgttcac tctggtgagc
     3841 agaggctgta tcacgttgtt cagagacctg tccagaatgg tgttcaccct tcggttgctc
     3901 aaagggacca aagacacgta aaagctctga agtatctacc atttttgcat tgcgttcacc
     3961 gctacaggtg gacaggtcac ctgctttaat caacctgtgc agtgttgttc tactcttacc
     4021 cgtcagtcgg gcagcctcac taatagacac tctggccatc agttaccatc ctgtaattca
     4081 tccagtctcg aggacagtgt acggaaaaga tgctccgcat catcgtggag tttctcacaa
     4141 aggtcggcct caacatcgag atcaagctcg ttaagcttct ccagcaggag cagagactga
     4201 ttctggatga atttagccat gttcagcgct gttttctgtt gtttcgtcat aagaagcctc
     4261 agagcgtcag tgctcagtgt aagaacagtc tcttttccgc ttcctcgctc actcagtcgc
     4321 tacgctcctg ccgttcggct gcggcgagcg gcaggagcat gcgtgtaaaa gctcgagaaa
     4381 accgagcagt ctcgtgatgg ggaaaaggaa aggccgcaca gcggccgttt ttccataggc
     4441 tccgcccccc tgacgagcat cacggaatct gacgctcaaa tcagtggcgg cgaaacccga
     4501 caggactata aagataccag gcgtttcccc ctgatggctc cctcgtgcgc tctcctgttc
     4561 ctgcc
//
