LOCUS       NZ_CP044042             3439 bp    DNA     linear   CON 09-JAN-2024
DEFINITION  Klebsiella pneumoniae strain FDAARGOS_630 plasmid unnamed7.
ACCESSION   NZ_CP044042
VERSION     NZ_CP044042.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11056345
            Assembly: GCF_008693405.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3439)
  AUTHORS   Bachman,M., Young,C., Tallon,L., Sadzewicz,L., Vavikolanu,K.,
            Mehta,A., Aluvathingal,J., Nadendla,S., Nandy,P., Geyer,C., 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  JOURNAL   Unpublished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 3439)
  AUTHORS   Bachman,M., Young,C., Tallon,L., Sadzewicz,L., Vavikolanu,K.,
            Mehta,A., Aluvathingal,J., Nadendla,S., Nandy,P., Geyer,C., Yan,Y.
            and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-SEP-2019) 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                   :: canu v. 1.4
            Genome Coverage                   :: 695.31x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/09/2024 02:59:27
            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)                     :: 5,547
            CDSs (total)                      :: 5,425
            Genes (coding)                    :: 5,285
            CDSs (with protein)               :: 5,285
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 140
            CDSs (without protein)            :: 140
            Pseudo Genes (ambiguous residues) :: 0 of 140
            Pseudo Genes (frameshifted)       :: 59 of 140
            Pseudo Genes (incomplete)         :: 86 of 140
            Pseudo Genes (internal stop)      :: 22 of 140
            Pseudo Genes (multiple problems)  :: 24 of 140
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP044042.1.
            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..3439
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_630"
                     /isolation_source="clinical isolate"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_630"
                     /db_xref="taxon:573"
                     /plasmid="unnamed7"
                     /geo_loc_name="USA: MI"
                     /collected_by="University of Michigan Health System"
     gene            complement(84..506)
                     /locus_tag="FOB38_RS28030"
                     /old_locus_tag="FOB38_28030"
     CDS             complement(84..506)
                     /locus_tag="FOB38_RS28030"
                     /old_locus_tag="FOB38_28030"
                     /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(506..697)
                     /locus_tag="FOB38_RS28035"
                     /old_locus_tag="FOB38_28035"
     CDS             complement(506..697)
                     /locus_tag="FOB38_RS28035"
                     /old_locus_tag="FOB38_28035"
                     /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            1113..1196
                     /locus_tag="FOB38_RS28985"
                     /old_locus_tag="FOB38_28045"
     CDS             1113..1196
                     /locus_tag="FOB38_RS28985"
                     /old_locus_tag="FOB38_28045"
                     /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(1458..1886)
                     /locus_tag="FOB38_RS28050"
                     /old_locus_tag="FOB38_28050"
     CDS             complement(1458..1886)
                     /locus_tag="FOB38_RS28050"
                     /old_locus_tag="FOB38_28050"
                     /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(1850..2020)
                     /locus_tag="FOB38_RS28570"
     CDS             complement(1850..2020)
                     /locus_tag="FOB38_RS28570"
                     /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            2178..2606
                     /locus_tag="FOB38_RS28055"
                     /old_locus_tag="FOB38_28055"
     CDS             2178..2606
                     /locus_tag="FOB38_RS28055"
                     /old_locus_tag="FOB38_28055"
                     /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            2890..3090
                     /locus_tag="FOB38_RS28060"
                     /old_locus_tag="FOB38_28060"
     CDS             2890..3090
                     /locus_tag="FOB38_RS28060"
                     /old_locus_tag="FOB38_28060"
                     /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"
     gene            complement(3196..>3439)
                     /locus_tag="FOB38_RS28840"
     CDS             complement(3196..>3439)
                     /locus_tag="FOB38_RS28840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001415424.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=2
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_223856701.1"
                     /translation="TGFPAAPATLHGHAINCVPVHRFRMERTPETGLTLAEWREFSRYA
                     LVRILMHAVKTEPARFWRVFGWFVACFAGFPSETP"
                     /name="hypothetical protein"
     Typing          746..1222
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.797"
                     /coverage="91.0"
                     /evalue="4.61e-163"
ORIGIN
        1 gagcgttcag agatctggcg atttttggga aggttcagga actccccggg atggccggag
       61 aggaaaactg aagcatgacg gggtcaggat tttttccaga atttccacca cggggaatgg
      121 ggtggtgaag aaggttcgtg attgtactcc agaagctgca tagcctgacg aagggaatca
      181 atatgctcat ctcgagcctt aacagcccct ttaagaccat cgttttcagc ttctagtaaa
      241 gcaattctat gttgtaaatc atgtaaacca acgctgttaa cacctgtaga ttctgcgtca
      301 ctttttacat catattttac agtatcgatg acaccatcaa gagaaccaaa cactctaata
      361 agctctgagg tatcaataac tttaatagcc ttcccgtgct ttacaacaga ggtgtaactt
      421 aacttcccac tgttaatcat cttgtaaatt gtggggcgac taaccttaac aagccgtgcc
      481 gcttcactaa tagacactct ggccatcagt taccatcctg taattcatcc agtctcgagg
      541 acagtgtacg gaaaagatgc tccgcatcat cgtggagttt ctcacaaagg tcggcctcta
      601 catcgagatc aagctcgtta agcttctcca gcaggagcag agactgattc tggatgaact
      661 tagccatgtt tagcgccgtt tgctgttgtt tcgtcataaa gagcctcaga gcgtcagtgc
      721 tcaatgtaaa aactgtctcc tttccgcttc ctcgctcact cagtcgctac gctcctgccg
      781 ttcggctgcg gcgagcggtc gcaactcacg tataagagca taagacgaca gggctgatag
      841 ccggagggga caaaataagg tcgcggcgtt gccgtttttc cataggctcc gcccccctga
      901 caagcatcac agaagcggac gctcaaatca gtggtggcga aacccgacag gactataaag
      961 atacctatca tttctgatag gcggctccct cgtgcgctct cctgttcctg cctttcggtt
     1021 taccggtgtc attccgctgt tatggccgcg tttatctcat tccacgcctg acactcagtt
     1081 ccgggtaggc agttcgctcc aagctggact gtatgcacga accccccgtt cagtccgacc
     1141 gctgcgcctt gtccggtaac tatcgtcttg agtccaaccc ggaaagacac gactaatcgc
     1201 cattggcaac ggccactggt aagcaggatg tgcgagagat gtattgagag ttcttgaagt
     1261 ggcggcctaa ctgaggctac actggaagga cggatttggt gacatgtctc gcacaagact
     1321 gttaccacgg ttagataatc tgccaggatt aaataacctt cgaaaaacca cctgccaggg
     1381 tggttttttc gttttcacaa caggagatta cgacgaggtt gaatgaatct caagatttca
     1441 tttagtctgc tacccgatca ttcaaagttt tggggtagtt ccatcgggtc atggtatccc
     1501 agttctaaaa gctttatatg gttcggtgtc agccgctgga aatggataac ccagtcagaa
     1561 accttgtatt tcccatgaaa cgtatctttg aaaaccggat cgcctaaatg agcatgccat
     1621 aacttgttag ctctagcgtg cagctcaata gcttctttgt tttcgtaatg atcaggcact
     1681 ttccacgacg gcgatacttt accaatccaa gctggatgtt tttttaaagg atcgccaaag
     1741 aggttatatt tttcgaaatg ctcaatgaaa tcatcgattt tatcgagtgt ttttgcagaa
     1801 aatcgggatg tgtaatagag attgaaagtc tcagagaacg agacaatatt caactgtgga
     1861 ttttgcgcac ctgctccgct gcccatgctc ttctctgctc cctacttaga ccagatggca
     1921 ttgtaacaga cttctcattc gctctggaaa tcaacagaga caaggatacg ccaaatactt
     1981 cagtatcttt aataagatca tgacgttgtt cggttttcat atcgttaact ccgtatctaa
     2041 ttcagacagg aaaaaatctt ttttccgctt tcagagtagt cttttgtagt tgcactataa
     2101 tggcgttgat gtcaccctat tcatatgaat aatcatataa tatatacttc aaatattttt
     2161 gttttttagg aaaatcaatg acttactcta ttgaggaaaa atggaaggct ggcggtttgt
     2221 ctcttggctg gactgcaata cctactgtct tgttttttat acagaacgag aaaaagctaa
     2281 cctccgtagc ctttaacact ctgcttaacc tgatcgttca ttggtggaat ttgcaagaat
     2341 ggccgcatcc atcaatggaa agcctagcca tacgtatggg ggtttctgta aggacagttc
     2401 agagagctat caatgatctg gaaaaagcta atctcttgga caagaaacca acgtcgaaga
     2461 gtgatagccg atatggaggt cgtaatattt atgatctaac aaagctcgtt gattacctgg
     2521 atacaatggg cccatcagta gctgaacagg ttaagaaacc ccgtcataaa agaccggtat
     2581 ataccgtaag aaaaacaaca acttaaaaaa gagcaattgc actgttcgaa ggaaaaacga
     2641 taactactct atggtattgc ttgctgtata ggtattggtg gtcctgcggc tggttcatcg
     2701 cttcacggtt aaaatagtcc tgtaagctgt taatatttaa cataacacta ctaccacgaa
     2761 cctacgtaac aatcgctacc aacacagaag tgacaaattt ataaaaaaac aaaaaccata
     2821 aaaaaacttg actttatgtt ttttttggct aatttcttta tcatttcttt atcaaaaata
     2881 gaggtggcta tgtttggttt tggaattcaa ggtactatta ataaaggatt ttttcttcag
     2941 atggctcgta gagatcagga tgcatttttg caatatctct atgaccaagg gtactcagca
     3001 aaagatatca gcaagaactt cgatattccg gttcctagcg tctacaacag aatcaacgct
     3061 caccgaggcc gtggacctct tcccaattaa tggttcttct atacaaaaaa gtcgcctgga
     3121 taggcgactt ttttaactga actctgtgta tagatttacc ataacgtctc aattgtacgc
     3181 accgctaaaa cggcctcagg gcgtttctga cggaaaaccg gcaaaacagg caacaaacca
     3241 cccgaaaacc cgccagaaac gcgcaggctc cgtttttacg gcatgcatga gtatgcgcac
     3301 aagtgcatag cgcgaaaact cacgccattc agccagggta agtcctgttt ccggcgttct
     3361 ttccatccga aaacggtgaa cggggacgca atttattgcg tggccgtgaa gcgttgccgg
     3421 cgcagccgga aaaccggtt
//
