LOCUS       NZ_CP142969             4652 bp    DNA     circular CON 31-JAN-2024
DEFINITION  Klebsiella pneumoniae strain KP1906522 plasmid pKP1906522_4,
            complete sequence.
ACCESSION   NZ_CP142969
VERSION     NZ_CP142969.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39501656
            Assembly: GCF_036287765.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4652)
  AUTHORS   Maguire,M.
  TITLE     Spatiotemporal and genomic analysis of carbapenem resistance
            elements in Enterobacterales from hospital inpatients and natural
            water ecosystems of an Irish city
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4652)
  AUTHORS   Maguire,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-JAN-2024) Bacteriology, University of Galway,
            University Road, Galway, Galway 000000, Ireland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 106.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/31/2024 01:21:43
            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)                     :: 5,691
            CDSs (total)                      :: 5,566
            Genes (coding)                    :: 5,392
            CDSs (with protein)               :: 5,392
            Genes (RNA)                       :: 125
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 174
            CDSs (without protein)            :: 174
            Pseudo Genes (ambiguous residues) :: 0 of 174
            Pseudo Genes (frameshifted)       :: 92 of 174
            Pseudo Genes (incomplete)         :: 97 of 174
            Pseudo Genes (internal stop)      :: 31 of 174
            Pseudo Genes (multiple problems)  :: 38 of 174
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP142969.1.
            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..4652
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="KP1906522"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pKP1906522_4"
                     /geo_loc_name="Ireland"
                     /collection_date="2019"
     gene            join(4635..4652,1..95)
                     /locus_tag="VYI59_RS28410"
                     /old_locus_tag="VYI59_28415"
                     /pseudo=""
     CDS             join(4635..4652,1..95)
                     /locus_tag="VYI59_RS28410"
                     /old_locus_tag="VYI59_28415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="frameshifted; 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            complement(280..1008)
                     /locus_tag="VYI59_RS28415"
                     /old_locus_tag="VYI59_28420"
     CDS             complement(280..1008)
                     /locus_tag="VYI59_RS28415"
                     /old_locus_tag="VYI59_28420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001694614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_064182343.1"
                     /translation="MSNRLWLVVFILALLAFCGVFIVYFLWFKAWLNFHLSKNPEVWGQ
                     FGDFVGGVLNPILSFITVVILIITTIYQQKQYENSEKRELNKRFDDRFYGMISYQRDLV
                     ANFKLALPGNSDAGVKDAITYAEDVFFNTNDHSYINSQGFKEAIFPVVRTFYILIKMID
                     ESSEDEVSENIASKYYEWLVNLSDYHFLRLVFFCSFYYDGISSFDYIKSNKNIVSSLAK
                     MGWDKYTSEIIKRKHQLSIA"
                     /name="hypothetical protein"
     gene            complement(1005..1835)
                     /locus_tag="VYI59_RS28420"
                     /old_locus_tag="VYI59_28425"
     CDS             complement(1005..1835)
                     /locus_tag="VYI59_RS28420"
                     /old_locus_tag="VYI59_28425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001694615.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_064182342.1"
                     /translation="MAVTDVDFELKIESGANLVDMEYGLETMTGFSGAIAITADCILSN
                     EVPSKMSYSDNVRAKLMGACLGSYKQDFKLVISDPVKSANLERIGNSVLSELITYFICE
                     TMYVEPPALTKKAEKILSKMEKIESKVIDRIYERVKDMHKISRSNKYPVVLKRKTQLRN
                     FKLFEINENTASNLFNLTTDNNSVEIDAIVTRFNSFTGNGRLLADGDSVTIPFSFSGPY
                     SKVKASTKRLMSENLHDNNAVADELITRLKITANAKRNISGDIVKYMILSADKP"
                     /name="hypothetical protein"
     gene            complement(2804..3226)
                     /locus_tag="VYI59_RS28425"
                     /old_locus_tag="VYI59_28430"
     CDS             complement(2804..3226)
                     /locus_tag="VYI59_RS28425"
                     /old_locus_tag="VYI59_28430"
                     /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_024172727.1"
                     /translation="MARVSISEAAQLVKVSRPTIYKMINSGKLSYTSVVKHGKAIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3226..3417)
                     /locus_tag="VYI59_RS28430"
                     /old_locus_tag="VYI59_28435"
     CDS             complement(3226..3417)
                     /locus_tag="VYI59_RS28430"
                     /old_locus_tag="VYI59_28435"
                     /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_064182344.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EQLFRTLSSRLDVLQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(3897..4046)
                     /locus_tag="VYI59_RS28435"
                     /old_locus_tag="VYI59_28440"
     CDS             complement(3897..4046)
                     /locus_tag="VYI59_RS28435"
                     /old_locus_tag="VYI59_28440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_164699461.1"
                     /translation="MPSEYDEQRDSTDTQLPGEYDLFDLMAQVTEENLHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     Typing          2..95
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.75"
                     /coverage="100.0"
                     /evalue="1.08e-31"
     Typing          4379..4652
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.364"
                     /coverage="90.0"
                     /evalue="8.170000000000001e-125"
ORIGIN
        1 cagtccgacc gctgcgcctt aaccggtaac tatcatcttg agtccaaccc ggaaagacac
       61 gaaaaacgcc actggcagca gccactggta actgatttag aggagttagt cttgaagttg
      121 tgcgccagtt aaggctaaac tgaaagaaca agttttggtg actgcgctcc tccaagccag
      181 ttacctcggt tcaacgagcg ccaactccat gaaccttcga aaaaaccgcc cgccaaggcg
      241 gttttttcgt ttagccagac gatacatcct acgagagcat caagcaatac ttagctgatg
      301 ctttctttta attatttcag atgtgtattt gtcccacccc atttttgcca aactactaac
      361 aatgttttta ttcgacttta tataatcgaa tgaagatata ccatcataat aaaaagagca
      421 aaagaaaacg agcctcaaaa aatgataatc agacaagtta accaaccact cgtaatactt
      481 tgatgcaata ttttcactca cttcatcctc ggatgattca tcaatcattt tgatcaagat
      541 gtaaaatgtt cttacaaccg gaaagatggc ttccttaaac ccttgagaat taatataaga
      601 atggtcatta gtattaaaaa aaacatcttc ggcataagta atggcatctt tcacacctgc
      661 atcagagttc ccaggtaaag cgagtttaaa atttgccacc aaatctctct ggtaagagat
      721 catcccataa aatctatcat caaacctttt atttagttct cttttttccg agttctcata
      781 ctgtttttgc tggtaaatgg tggtgattat caatataaca acagtgataa aactgagtat
      841 cggatttaat acaccaccaa caaaatcacc gaattgcccc catacttcag gatttttaga
      901 taagtgaaaa ttaagccaag ctttaaacca tagaaaatat acaataaaaa caccgcaaaa
      961 ggccagcaaa gccagtataa aaacaactaa ccacaagcga ttactcatgg cttatccgca
     1021 ctcaatatca tatacttaac tatatcccct gatatattac gcttagcatt tgctgttatt
     1081 tttaatctcg ttattaactc atcagcaaca gcgttgttgt catgaaggtt ctcggacata
     1141 agcctctttg ttgacgcctt cactttacta taaggacccg aaaaactaaa tggtatagta
     1201 actgaatcac catcagcaag aagtcgccca ttccctgtga aggaattaaa tcttgtaacg
     1261 atcgcatcta tttcaacgga gttattatcc gtagttagat taaaaaggtt acttgcagta
     1321 ttttcattta tctcgaaaag cttaaaattc cttaattgcg tttttctttt caaaacaaca
     1381 ggatatttat tagaacggga aattttatgc atatctttca ctcgctcata aatcctatct
     1441 attactttac tttctatttt ctccatttta gataatattt tttcagcctt cttggttaaa
     1501 gctgggggtt caacatacat ggtttcacaa ataaagtacg ttattaactc agataaaaca
     1561 gagttaccta ttctttctag gttagcactt ttaacaggat ctgaaataac cagcttaaaa
     1621 tcttgcttat atgacccaag acaagccccc attagctttg ccctaacatt atcagagtag
     1681 ctcatttttg atggtacttc attagacaaa atacaatcag cggtaatagc aatggcacct
     1741 gagaaccccg tcatggtttc caagccatac tccatatcaa ccaagttagc tccagactct
     1801 atctttagct cgaaatccac atcagtgacc gccattgaag ttccttataa atccattcaa
     1861 ttcattaagt taagagcaaa tgttaattac tttgataata ctatctgaat aactcacctt
     1921 ccagaactta acaaacgtaa ccgtaaaaat cggtagtaaa gttagcatca catagccact
     1981 gatagatgtg atttaccaca ataaattcac tgtatgtcag tcacttaata cactctttgt
     2041 cccgtcatga cattttacgc ctgccattta acataacccc ctgattgtac gcaccgctaa
     2101 aacggcctca gggcgtttct gacgggaaac cggtaaaaca ggcaacaaac cacccgaaaa
     2161 cccgccagaa acgcgcaggc tctgttttta cggcatgcat gagtatgcac gcaagtgcat
     2221 agcgcgaaaa ttcacgccat tcagccaggg taagtcctgt ttccggcgtt ctttctatcc
     2281 gaaaacggtg aacggagacg caatttattg cgtggccgtg aagcgttgcc ggcgcagccg
     2341 gaaaaccggt tttcagcacg atcaggaatc gggttcgtcg acggccggca atcacgttat
     2401 ggcaagtcgc cggacgactc accagacaat tcaccggcga ttcgactcgt gacttgactc
     2461 tagagtcgtc aaggtcaaaa aaccaccaaa atgacgattc gactctagag tcaagtcgtc
     2521 ataagttact gatagtctta agcgagtcgt cgatgactct atgacgagtc gtcggcaagt
     2581 cgtacacgaa tcgccgacga cttggattca ccttacagaa agtaatactg cgtaatttaa
     2641 taacccacaa ctaactgata ttaatgagtt atcttcaaaa ttttaatttt gcgtggggtg
     2701 tggatatttt tagtggtgag gagcgttcag agatctgacg atttttggga aggttcacga
     2761 acgccccggc atggccggag aggaaaactc aagcatggcg ggatcaggat tttttccaga
     2821 atttccacca cggggaatgg ggtggtgaag aaggttcgtg cttgtgctcc agaagctgca
     2881 tagcctgacg aagggaatca atatgctcat ctcgagcctt aacagcccct ttaagaccat
     2941 cgttttcagc ttcaagtaaa gcgattctat gttgtaaatc atgtaaacca acgctgttaa
     3001 tacctgtaga ttctgcgtca ctttttacat catattttac agtatcgatt acaccatcaa
     3061 gagagccaaa caccctaata agctctgaag tatcaataac tttaatagcc ttcccgtgct
     3121 ttacaacaga ggtgtaactt aacttaccac tgttaatcat cttgtaaatc gtgggacgac
     3181 taaccttaac aagctgtgcc gcttcactaa tagacactct ggccatcagt taccatcctg
     3241 taatacatcc agtctcgagg acagtgtacg gaaaagttgc tccgcatcat cgtggagttt
     3301 ctcacaaagg tcggcctcga catcgagatc aagctcgtta agcttctcca gcaggagcag
     3361 agactgattc tggatgaatt tagccatgtt cagcgctgtt ttctgttgtt tcgtcataag
     3421 ggccctcaga gcatcagtgc tcagtgtaaa ccggtaaggg ggtcggatgt acaaatggtt
     3481 cagagaacgg atctgaggta atcctgtagt tattttgtag tttatctgta gtcatcgcac
     3541 taaaaatcag gattaagtca tcaacttttg tagtcttcct gtagtttacc tgtagtccgg
     3601 aaaaataatc cgttcatgca agcatgaacg aagcagttaa agacgctttt tcgtcgccgg
     3661 tgctccttaa cctgcgcaga taacgcggcc agaatgataa ttttttgccc cttaaatggt
     3721 catacaccta acgcagccgc gattttcatc gcaactgcat gaattaaaag gtaaaaactg
     3781 aaatctccgt ttatttatgt aatacgcaac gtattacaat cacctgtaat cacatgaaaa
     3841 taaagaaata aaatgtaata ccggcgtatt accacgtacg cgggcaagcg aaaaagctat
     3901 aacgcttccc ggccgacagg cggcccagaa tccacagggg cgtgcaggtt ctcttcagta
     3961 acctgcgcca ttaaatcaaa aaggtcatat tcgccgggaa gctgcgtatc agtcgaatcc
     4021 cgttgttcat catattcaga tggcatgggg tgatatccag tagctgagag gttgttagcg
     4081 ggtttctggg cgcagccctg aaccagtcaa gtagcactag cggagtgtgt acgggctcaa
     4141 tatgctacgg tggagtaaca cgttatgaaa gtgcttcatg tgacagagga aagtgcagcg
     4201 gcggggcgta cgggagaaaa tggaagcccg gggatatgac gcctcctcgc tcactcagtc
     4261 gcagacgctc ctgccgttcg gctgcggcgg gcgttacctg cgctcacaca acaagctcat
     4321 gatgaatcca cagattcagg ggagaaagcg ccacgcggca tgtgtgcaag aagagaaaaa
     4381 ggccgcgcac cggcgctttt tccataggct ccgcccccct gacaagcatc acaaaaactg
     4441 acgctcaaat cagtggtggc gaaacccgac aggactataa agatatcagg cgtttccccc
     4501 tgatggctcc ctcgtgcgct ctcctgttcc tgccattcgg tttaccggtg tcattccgct
     4561 gttatggccg cgtttgtctc attccacgcc tgacactcag ttccgggaag gcagttcgct
     4621 ccaagctgga ctgtatgcac gaaccccccg tt
//
