LOCUS       NZ_CP084396             4167 bp    DNA     circular CON 10-JAN-2024
DEFINITION  Klebsiella pneumoniae subsp. pneumoniae strain MRSN752019 plasmid
            unnamed2, complete sequence.
ACCESSION   NZ_CP084396
VERSION     NZ_CP084396.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18913844
            Assembly: GCF_018283505.2
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae subsp. pneumoniae
  ORGANISM  Klebsiella pneumoniae subsp. pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4167)
  AUTHORS   Martin,M.J., Corey,B.W., Sannio,F., MacDonald,U., Jones,B., Hall,L.,
            Mills,E., Stam,J., Ong,A., Kwak,Y., Bennett,J.W., Russo,T.A.,
            McGann,P.T., Lebreton,F. and Docquier,J.-D.
  TITLE     Anatomy of an Extensively Drug Resistant Klebsiella Pneumoniae
            Outbreak in Italy
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4167)
  AUTHORS   Martin,M.J., Corey,B.W., Sannio,F., MacDonald,U., Jones,B., Hall,L.,
            Mills,E., Stam,J., Ong,A., Kwak,Y., Bennett,J.W., Russo,T.A.,
            McGann,P.T., Lebreton,F. and Docquier,J.-D.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-SEP-2021) Multidrug-Resistant Organism Repository and
            Surveillance Network (MRSN), Walter Reed Army Institute of Research,
            503 Robert Grant Avenue, Silver Spring, MD 20910, USA
REFERENCE   3  (bases 1 to 4167)
  AUTHORS   Martin,M.J., Corey,B.W., Sannio,F., Macdonald,U., Jones,B., Hall,L.,
            Mills,E., Stam,J., Ong,A., Kwak,Y., Bennett,J.W., Russo,T.A.,
            Mcgann,P.T., Lebreton,F. and Docquier,J.-D.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-APR-2021) Multidrug-Resistant Organism Repository and
            Surveillance Network (MRSN), Walter Reed Army Institute of Research,
            503 Robert Grant Avenue, Silver Spring, MD 20910, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 08-SEP-2021
            Assembly Method                   :: Trycycler v. 0.4.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 600.0x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/10/2024 04:19:29
            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)                     :: 5,829
            CDSs (total)                      :: 5,705
            Genes (coding)                    :: 5,564
            CDSs (with protein)               :: 5,564
            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)              :: 141
            CDSs (without protein)            :: 141
            Pseudo Genes (ambiguous residues) :: 0 of 141
            Pseudo Genes (frameshifted)       :: 60 of 141
            Pseudo Genes (incomplete)         :: 87 of 141
            Pseudo Genes (internal stop)      :: 27 of 141
            Pseudo Genes (multiple problems)  :: 28 of 141
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP084396.1.
            Bacteria and source DNA available from Multidrug-Resistant Organism
            Repository and Surveillance Network (MRSN), Walter Reed Army
            Institute of Research.
            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..4167
                     /organism="Klebsiella pneumoniae subsp. pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="MRSN752019"
                     /isolation_source="Surveillance"
                     /host="Homo sapiens"
                     /sub_species="pneumoniae"
                     /db_xref="taxon:72407"
                     /plasmid="unnamed2"
                     /geo_loc_name="Italy: Siena"
                     /collection_date="2019-05-26"
                     /collected_by="University of Siena"
     gene            complement(join(4020..4167,1..44))
                     /locus_tag="KF608_RS02595"
                     /old_locus_tag="KF608_02600"
     CDS             complement(join(4020..4167,1..44))
                     /locus_tag="KF608_RS02595"
                     /old_locus_tag="KF608_02600"
                     /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_004187666.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            460..573
                     /locus_tag="KF608_RS02600"
                     /old_locus_tag="KF608_02605"
                     /pseudo=""
     CDS             460..573
                     /locus_tag="KF608_RS02600"
                     /old_locus_tag="KF608_02605"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="internal stop; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            918..2033
                     /locus_tag="KF608_RS02605"
                     /old_locus_tag="KF608_02610"
     CDS             918..2033
                     /locus_tag="KF608_RS02605"
                     /old_locus_tag="KF608_02610"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019405083.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0016887 - ATP hydrolysis activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ATP-binding protein"
                     /protein_id="WP_012579087.1"
                     /translation="MIKEISLKNFKCFNELYLKQLKTLNIIAGKNNYGKTSILDAIFCF
                     YDVKNPAVLLNIQAFRKEMAEINKNKPFWVSYFHDMDTSQKMSIVIRDERSEVTQTYET
                     ETNQRLESSLSLNVDTVLSNQNIPRQTIGSQATVNSLKINVTETPNAKNRVSNKLFSMQ
                     LKEDGVEIKSEIKNERDGINYKFKTATIITTSRKINKEATITNVSSLLTQKRKKDILEN
                     LKKIDDRIVDIAISAIGNNKEIYLDIGFSELNEISMLGEGISRALSFISSVLVQENSII
                     LIDEIENGIHYSVIKDIIKSLISSAKQNNNQIFATTHSQDVIRAINEIDSKNEDIAYIR
                     LGREKNSLKPTAVQFNMDDFSYSVENDWEVR"
                     /name="ATP-binding protein"
     gene            2033..2665
                     /locus_tag="KF608_RS02610"
                     /old_locus_tag="KF608_02615"
     CDS             2033..2665
                     /locus_tag="KF608_RS02610"
                     /old_locus_tag="KF608_02615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000804504.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3226 domain-containing protein"
                     /protein_id="WP_012579086.1"
                     /translation="MKDINNSKKIIFVEGDDDFHFLCNLLEIQGITDVFVEKINGKSKL
                     KQALRAFKNIDSFDEKESIFIILDADTSFSDTERSIIATLRELQISSPSSHNEIAMNGN
                     TKISFFIMPGKDKQGAIEDLIIEHASTRALYEYIIEFFEKIKNNKDDISASDKEYTYPT
                     NEKKAKVQVYLSCNRESDSRIGISMKNGIINTADNCFDEIKDFISKI"
                     /name="DUF3226 domain-containing protein"
     gene            3031..3273
                     /locus_tag="KF608_RS02615"
                     /old_locus_tag="KF608_02620"
     CDS             3031..3273
                     /locus_tag="KF608_RS02615"
                     /old_locus_tag="KF608_02620"
                     /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_098963735.1"
                     /translation="MHSAEIHTIQPGEVLFPAFFSSENGERGRNLLRGREALPAQPENR
                     FSAPSGIGFVDGRQSRYGKSPDDSPHDSPAIRIVN"
                     /name="hypothetical protein"
     gene            complement(3619..4020)
                     /locus_tag="KF608_RS02620"
                     /old_locus_tag="KF608_02625"
     CDS             complement(3619..4020)
                     /locus_tag="KF608_RS02620"
                     /old_locus_tag="KF608_02625"
                     /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_012579088.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSGQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     Typing          166..573
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.399"
                     /coverage="99.0"
                     /evalue="5.92e-171"
ORIGIN
        1 atgaatttag ccatgttcag cgctgttttc tgttgtttcg tcataagagg cctcagagcg
       61 tcagtggtca gtgtagggat ctcctctttt ccgcttcctc gctcactcag tcgctacgct
      121 cctgccgttc ggctgcggcg agcggcagga gcatgcgtag aaacgctcga gaaaaccgag
      181 taatcgcatg gaggaaagaa ggaaaggccg cacagcggcc gtttttccat aggctccgcc
      241 cccctgacga gcatcacgga atctgacgct caaatcagtg gtggcgaaac ccgacaggac
      301 tataaagata ccaggcgttt ccccctgatg gctccctcgt gcgctctcct gttcctgcct
      361 ttcggtttac cggtgtcatt ccgctgttat ggccgcgttt gtctcattcc acgcctgaca
      421 ctcagttccg ggtaggcagt tcgctccaag ctggactgta tgcacgaacc ccccgttcag
      481 tccgactgct gcgcctaatc cggtaactat cgtcttgagt ccaacccgga aagacacgac
      541 aaagcgccac tggcagcagc cactggtaac tgatttaggg agttagtctt gaagttatac
      601 gccagttaaa gctaaactaa acgaacagtt ttggtgactg cgctcccttt aagccagtta
      661 cctcggttca tagagcgcca actctactga acctttcgaa aaaaccgccc gccaaggcgg
      721 tttttttcgt tcacagccgg aagcttacgg ctgctgccag ataatctcaa gaagaaagta
      781 aaaaaaatcg attaaaacac aagcaatcaa agttaatctt tgacataaag tctagctaat
      841 cacaatgaaa gctgtacatt ttattaaggt actaacaaat cgtatggcat ataacaaaaa
      901 cacgaacaga ggctatcatg ataaaggaaa taagtttaaa gaacttcaaa tgcttcaatg
      961 agctatatct aaagcaatta aagactttaa atatcatagc tgggaaaaac aactacggga
     1021 aaacatctat actggatgct attttttgtt tttatgatgt aaaaaacccg gctgttttgt
     1081 taaacattca agcattcaga aaagaaatgg cagaaataaa caaaaacaag ccattttggg
     1141 ttagttactt tcatgatatg gacacatcac aaaagatgtc catagtcatt cgagatgaac
     1201 gctctgaagt aacacaaaca tatgaaacag aaacaaatca gagattagaa tcaagtttgt
     1261 ctctaaacgt tgacaccgta ctatctaacc aaaacatacc tcgtcaaact atcggttctc
     1321 aggccacagt aaactcttta aaaataaatg tgaccgagac acccaatgcg aaaaacaggg
     1381 tttccaataa gcttttctct atgcaattga aagaagatgg cgtagaaata aaatccgaaa
     1441 taaaaaacga aagggatggg attaattata aatttaagac agcaacaata ataacaacat
     1501 ccagaaagat aaacaaagag gcaacaatta caaatgtatc tagcctacta acacaaaaaa
     1561 ggaaaaaaga catactagaa aacttaaaaa aaatagatga cagaattgta gatatagcaa
     1621 tatctgcgat aggtaacaat aaggaaatat atttagacat tggatttagt gagctaaatg
     1681 aaatatcaat gcttggcgag ggtatcagtc gagcattatc ttttatcagc tcagtgctgg
     1741 tacaggaaaa ctcaattatt cttattgatg aaatcgagaa cggaatacat tactcagtaa
     1801 ttaaagacat aataaaatca ttaatttcat ctgcaaaaca aaacaacaat caaatatttg
     1861 caacaactca tagtcaagat gtgatacgag caataaacga aatagatagc aaaaatgaag
     1921 atatcgctta tattagacta ggaagagaaa agaactccct aaaaccaaca gccgtacaat
     1981 tcaatatgga tgatttctcc tactcagttg agaacgactg ggaggtaaga taatgaaaga
     2041 cataaataat agcaaaaaga tcattttcgt tgagggtgat gatgattttc attttctatg
     2101 caacctactt gaaatacaag gcattaccga tgtttttgtc gaaaaaataa atggaaaatc
     2161 aaaattaaaa caagcactta gagcattcaa aaacattgat tctttcgatg aaaaagaaag
     2221 tatttttatt atattagatg ctgacacatc attttctgac acagaaagat caataattgc
     2281 cacattgcga gaactacaaa tctcctcccc cagctcgcat aacgagatag ctatgaatgg
     2341 caatacaaaa atttctttct ttataatgcc aggaaaagac aagcaaggtg ccattgaaga
     2401 tctgataatt gaacacgcaa gcactcgagc gttatatgaa tacataatag aatttttcga
     2461 aaaaattaaa aataataaag atgacatctc agcgagtgac aaagagtaca cttatccaac
     2521 aaacgaaaaa aaagctaagg tacaagtcta tcttagctgc aatagagaat ccgactcaag
     2581 aataggaata tccatgaaaa atggaataat aaacacagca gacaattgct ttgatgaaat
     2641 aaaagatttt atttcaaaaa tataaatcca aatcaagcca gcccttcacg ggctggctta
     2701 tcaccagggt gttattaaac gccggataac gtatagaaag catcatacac tttagttatc
     2761 agcaatctca aacgtcctaa agacatcacc agatgccaaa acaatgattg tgcagatcta
     2821 atgtaaaaga cccagcacaa gatgctccct taagttatat tctctctatt cacttaaaac
     2881 aatttaacat aaaatcataa ttgtacgcac cgctaaaacg gactcaggac gtttctgacg
     2941 ggaaaccggt aaaacaggca acaaaccacc cgaaaacccg ccagaaacgc gcaggctctg
     3001 tttttacggc atgcatgagt atgcgcgcaa gtgcatagcg cggaaattca caccattcag
     3061 ccaggggaag tcctgtttcc ggcgttcttc tcctccgaaa acggtgaacg gggacgcaat
     3121 ttattgcgtg gccgtgaagc gttgccggcg cagccggaaa accggttttc agcaccttca
     3181 ggaatcgggt tcgtcgacgg ccggcaatca cgttatggca agtcgccgga cgactcacca
     3241 cacgattcac cggcgattcg aatcgtgaat tgaatcaaga gtcaccatga gcaaaaaaca
     3301 cccaaagtga tgaattgaat caagagtcga ttcatcataa caatatgata ataaagcgtg
     3361 attcacatat gaatcgtggg caattcgtca gcgattcgcc atagagtcgt ccacgacttg
     3421 gatctgcact ttgtaacaca tcaccgcaca tttatttttc attaacccat tgttgtaaat
     3481 aaggaatctg caaaatttta attttgcgtg gggtgtgggt atttttagtg gtgaggagcg
     3541 ttcagagatc tgacgatttt tgggaaggtt caggaactcc ctgggatggc cggagaggaa
     3601 aactgaagca tgacggggtc aggatttttt ccagaatttc caccatggcg ccggggattc
     3661 agttaatttt gcctggtgat tttcaagaag gagcatggcc tgtttcaggc tgtcaatgtg
     3721 cgaatccttg gacaaaagta aggtgttcag gtgttcaatc tcctgtttca gatgacggat
     3781 cacctgttca ctctggtcag cagaggctgt atcacgctgt ccagagacct gtccagaatg
     3841 gtgttcaccc ttcggttgct caaaggggcc aaagacacgt aaaagctctg aagtatctac
     3901 catttttgca ttgcgctcac cgctacaggt ggacaggtca cctgctttaa ttaacctgtg
     3961 cagtgttgtt ctactcttac ccgtcagtcg ggcagcctca ctaatagaca ctctggccat
     4021 cagttaccat cctgtaatgc atccagtctc gaggacagtg tacggaaaag atgctccgca
     4081 tcatcgtgga gtttctcaca aaggtcggcc tcgacatcga gatcaagctc gttaagcttc
     4141 tccagcagga gcagagactg attctgg
//
