LOCUS       NZ_CP142913             5339 bp    DNA     circular CON 31-JAN-2024
DEFINITION  Klebsiella pneumoniae strain KP1902196 plasmid pKP1902196_3,
            complete sequence.
ACCESSION   NZ_CP142913
VERSION     NZ_CP142913.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39500185
            Assembly: GCF_036287625.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5339)
  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  JOURNAL   Unpublished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 5339)
  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                   :: 73.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/30/2024 12:27:10
            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)                     :: 5,766
            CDSs (total)                      :: 5,643
            Genes (coding)                    :: 5,517
            CDSs (with protein)               :: 5,517
            Genes (RNA)                       :: 123
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 126
            CDSs (without protein)            :: 126
            Pseudo Genes (ambiguous residues) :: 0 of 126
            Pseudo Genes (frameshifted)       :: 58 of 126
            Pseudo Genes (incomplete)         :: 75 of 126
            Pseudo Genes (internal stop)      :: 15 of 126
            Pseudo Genes (multiple problems)  :: 19 of 126
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP142913.1.
            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..5339
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="KP1902196"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pKP1902196_3"
                     /geo_loc_name="Ireland"
                     /collection_date="2019"
     gene            162..320
                     /locus_tag="VYI53_RS28750"
                     /old_locus_tag="VYI53_28755"
     CDS             162..320
                     /locus_tag="VYI53_RS28750"
                     /old_locus_tag="VYI53_28755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005019281.1"
                     /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_071606098.1"
                     /translation="MHEPPVQSDRCAFSGNYHLESNPERHDKTPLAAATGKQDVREMYQ
                     EFLKWRP"
                     /name="replication initiation protein"
     gene            586..1584
                     /locus_tag="VYI53_RS28755"
                     /old_locus_tag="VYI53_28760"
     CDS             586..1584
                     /locus_tag="VYI53_RS28755"
                     /old_locus_tag="VYI53_28760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001082277.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0008170 - N-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0006306 - DNA methylation [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA methyltransferase"
                     /protein_id="WP_021197943.1"
                     /translation="MNRTEALKKIQIEVEEFVTYADNEQLIINNDCLTVLKKIPNNTVS
                     LILTDPPYHATQKKNIYGDTQFKKDDEYINWMEEISIEWRRILKPNGSLYCFCDSSMSA
                     RLEVMLSKRFNILNHIVWTKPNQPGFDGWKGKMNKESLRQWYGHSERIIFCEPAKDGNL
                     HRSSFGELLKKKRTEAGLSGNKLTELTGAYGKVNHGGAVSNWETGRNIPSREQYKKIKE
                     AILSTGKVDFMPEYEDAIRPFIISKNVEYTDVWNFESVRPYKGKHPAEKPQDMLNHIIM
                     ASSYEEDIVLDCFSGSGSTALAAKRNRRKCISIDIDMHWTDYTEKRLNELF"
                     /name="DNA methyltransferase"
     gene            complement(1598..2584)
                     /locus_tag="VYI53_RS28760"
                     /old_locus_tag="VYI53_28765"
     CDS             complement(1598..2584)
                     /locus_tag="VYI53_RS28760"
                     /old_locus_tag="VYI53_28765"
                     /EC_number="3.1.21.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000533217.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="BstXI family restriction endonuclease"
                     /protein_id="WP_071606097.1"
                     /translation="MARNVKLPHLLSRKIYKTGQTRGADDDVIYQNRVSRNSTVLIPFE
                     LILSEGNRDVLRKDYDNGYIVLIPPDYLFGERRNETLSIMNDCELILGVNCLVFYSQRY
                     QYVDYNPRDFGLRSTQPMNRTGDLGGDYVCRISGTTSENMGRISFGYNITTSKGAGIRV
                     FEYADKEVIEKARIQLEAIYWLCHDSLDAAIEYGMPPEDAEERKRLALEAANQQGLLNE
                     IDLISNRIIDVDKDTVCPLCLAKISAKGFFSKVEQQEFRRVHDLTITEINLFHINELRY
                     GHFNHKPYNLGWGHHHCNVVVKDSGIENTLEWMHEVLVRNERLNRAP"
                     /name="BstXI family restriction endonuclease"
     gene            complement(2577..3029)
                     /locus_tag="VYI53_RS28765"
                     /old_locus_tag="VYI53_28770"
     CDS             complement(2577..3029)
                     /locus_tag="VYI53_RS28765"
                     /old_locus_tag="VYI53_28770"
                     /inference="COORDINATES: protein motif:HMM:NF013540.4"
                     /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 transcriptional regulator"
                     /protein_id="WP_225522248.1"
                     /translation="MPVLPVSRQKRAEGLSGGADNGCYGKFACNKGYKKPPSNYESMIN
                     VTYSPCDYSQHEGIIILSTTNRKILIMESLLLSKVSFVIKKIRLEKGMTQEDLAYKSNL
                     DRTYISGVERNSRNITIKTLALIIKGLGVSDVIFFELLIKEISTHG"
                     /name="helix-turn-helix transcriptional regulator"
     gene            complement(3687..4109)
                     /locus_tag="VYI53_RS28770"
                     /old_locus_tag="VYI53_28775"
     CDS             complement(3687..4109)
                     /locus_tag="VYI53_RS28770"
                     /old_locus_tag="VYI53_28775"
                     /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_004207907.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKDIKVID
                     VSELIRVFGSLDGVTDTVKYDVKSDAISTEVNTIGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHDPSSPAHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(4109..4300)
                     /locus_tag="VYI53_RS28775"
                     /old_locus_tag="VYI53_28780"
     CDS             complement(4109..4300)
                     /locus_tag="VYI53_RS28775"
                     /old_locus_tag="VYI53_28780"
                     /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_004207910.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDSLQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(4924..5139)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="84.091"
                     /coverage="100.0"
                     /evalue="3.48e-51"
     Typing          2..459
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.866"
                     /coverage="90.0"
                     /evalue="3.65e-159"
     Typing          5125..5339
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.667"
                     /coverage="88.0"
                     /evalue="1.7e-78"
ORIGIN
        1 actataaaga tcccaggcgt ttccccctgg tagctccctc gtgcgctctc ctgttcctgc
       61 ctttcggttt accggtgtca ttccgctgtt atggccgcgt ttgtctcatt ccacgcctga
      121 cactcagttc cgggtaggca gttcgctcca agctggactg tatgcacgaa ccccccgttc
      181 agtccgaccg ctgcgccttc tccggtaact atcatcttga gtccaacccg gagaggcacg
      241 acaaaacgcc actggcagca gccactggta agcaggatgt gcgagagatg tatcaagagt
      301 tcttgaagtg gaggccttag tgaggctaca ctggaaggac agatttggtg acatgtctcg
      361 cacaagactg ttaccacggt tcagaaactt gccggtttac tgaaccttcg aaaaaccacc
      421 ttgccgggtg gttttttcgt ttacatagca agagattaca tctcactgat taggatctca
      481 agaggatcta ctccactgca cttatctatc aagtaattaa aacattgaaa aagaaatctt
      541 agatgcttag aatgttgact atagtcaaca aaagaaatag tatttatgaa tagaactgaa
      601 gctttaaaaa aaatccagat tgaagtcgaa gagttcgtca cttatgcaga taacgagcaa
      661 ttaataatca acaatgactg tttaactgta ttaaaaaaga tcccaaacaa cacagtctct
      721 ttgatactta ctgatccacc atatcatgcg acacagaaga aaaatattta tggcgatact
      781 caatttaaaa aagatgatga atatataaat tggatggaag aaatctccat tgaatggaga
      841 agaatattaa aaccaaatgg ttcactttat tgcttctgtg actcatcaat gtctgcacga
      901 ttagaagtca tgctatctaa aaggtttaac atattaaatc atattgtgtg gaccaagcca
      961 aaccaacctg gctttgatgg ctggaaaggg aaaatgaata aagaatcatt acgtcagtgg
     1021 tatgggcatt cagaaagaat tatcttttgc gagcctgcaa aagatgggaa tttacatcgc
     1081 tcttcttttg gcgagttatt aaagaaaaag agaacagaag cgggtcttag cggaaataag
     1141 ctaaccgaat taacaggtgc ttatggaaaa gttaatcatg gcggagctgt gtctaactgg
     1201 gagacaggaa gaaacatacc aagtcgcgaa caatacaaaa aaataaaaga agcgatattg
     1261 agcactggaa aagtggactt tatgcctgaa tatgaagatg caatacgacc ttttattata
     1321 tcgaaaaatg tagaatacac tgacgtttgg aatttcgaat ctgtcaggcc atataaggga
     1381 aagcatccag cagaaaaacc ccaagatatg ttaaatcata ttataatggc tagctcttat
     1441 gaagaagaca tagttttgga ttgtttttct ggctctggca gcacggcatt agccgcgaaa
     1501 aggaataggc ggaagtgcat atctatcgat atagatatgc actggacgga ttatacagaa
     1561 aaaagattaa atgagctttt ttaaaagcag agcgccttta tggcgctcta ttaagccttt
     1621 catttctaac caaaacttca tgcatccatt ctaatgtatt ttctatgccg gaatctttta
     1681 ctaccacatt gcaatgatga tgaccccacc ctaaattata cggcttatga ttaaaatgac
     1741 cataccttaa ctcattgata tggaagagat taatctcggt aattgtaaga tcatgtactc
     1801 gcctaaactc ttgttgctct acctttgaaa aaaaaccttt agctgatatt tttgctaaac
     1861 acaatggaca aacagtgtct ttatcaacat caataattct attacttatt aaatcaattt
     1921 catttaatag cccctgttga tttgctgcct caagagccaa cctttttctt tcttccgcat
     1981 cttctggtgg cattccatat tctatagcgg catctaatga atcatggcac aaccaatata
     2041 tcgcctcaag ttgaatacga gctttttcta taacttcttt atcagcatat tcaaacaccc
     2101 taatcccggc acctttagat gtagtaatat tatacccaaa ggatattcta cccatatttt
     2161 cagaagttgt tccagaaatc ctgcaaacat aatcgccacc aagatcccca gttcgattca
     2221 ttggctgggt agacctaaga ccaaaatccc ttggattata atcgacatac tggtaccttt
     2281 ggctataaaa aaccaagcaa ttaacaccta aaattaactc acaatcattc ataatagaga
     2341 gagtttcgtt acgcctctcc ccaaacaaat aatcaggcgg aattagaaca atataaccat
     2401 tatcatagtc ctttcttaac acatccctat taccttcaga taatattagt tcaaaaggaa
     2461 ttaaaacagt actatttcgt gaaactctat tctggtaaat aacatcatca tcagccccgc
     2521 gagtttgacc tgttttatat attttacgtg acaacagatg tgggagttta acattcctag
     2581 ccatgcgttg aaatctcctt tataagcagt tcaaaaaata taacatctga cacccccaag
     2641 ccctttataa ttaacgcaag ggtttttatt gttatatttc tggaattcct ctcaaccccg
     2701 gaaatataag ttctatctag gtttgattta tatgctaaat cttcttgagt cattcctttt
     2761 tctaacctta ttttttttat tacaaaggat acttttgata aaagaagact ttccataatt
     2821 aatatttttc tgttcgttgt tgataggata ataatgcctt catgttgact ataatcacac
     2881 ggactataag tcacattaat catcgattca taattcgaag gaggcttttt ataaccttta
     2941 ttacacgcaa atttaccata acatccgtta tcagcaccgc ctgagaggcc ctcagcgcgt
     3001 ttctgacggg aaaccggtaa aacaggcaac aaaccacccg aaaacccgcc agaaacgcgc
     3061 aggctctgtt tttacggcat gcatgagtat gcgcgcaagt gcatagcgcg gaaattcaca
     3121 ccattcagcc ggggtaagtc ctgtttccgg cgttcttccc atccgaaaac ggtgaacggg
     3181 gacgcaattt attgcgtggc cgtgaagcgt tgccggcgca gccggaaaac cggttttcag
     3241 cacgttcagg aatcgggttc gtcgacggcc ggcaatcacg ttatggcaag tcaccggacg
     3301 acttagcaca cgattcaccg gcgattcgaa tcgtgaattg aatcaagagt caccatgaac
     3361 aaaaaacacc caaagtgatg aattgaatca agagtcgatt catcataaca atatgataat
     3421 aaagcgtgat tcacatatga atcgtgggca attcgtcagc gattcgccat agagtcgtcc
     3481 acgacttgga tctgcacttt gtaacacatc accgcacatt tatttttcat taaaccattg
     3541 ttgtaaataa ggaatctgca aaattttaat tttgcgtggg gtgtgggtat ttttagtggt
     3601 gaggagcgtt cagagatctg gcgatttttg ggaaggttca ggaactcccc gggatcgccg
     3661 gagagcaaaa ctgaaacatg gcaggatcag gattttttcc agaatttcca ccacggagaa
     3721 tgagccggtg aagaggggtc gtgcttgtgc tccaaaagct gcatagcctg gcgaagggaa
     3781 tcaatatgct catcgcgtgc tttaacagcc cctttaagac catcgttttc agcttcaagt
     3841 aaagcgattc tatgttgtaa atcatgtaaa ccaatggtgt taacctctgt agaaattgcg
     3901 tcacttttta catcatattt tacagtatca gttacaccat caagagaacc aaacacccta
     3961 ataagctcgg atacatcaat aactttaata tccttcccgt gctttacaac agaggtataa
     4021 cttaacttcc cgctgttaat catcttgtaa atagtgggac gactaacctt aacaagccgt
     4081 gcagcttcac taatagacac tctggccatc agttaccatc ctgtaatgaa tccagtctcg
     4141 aggagagtgt acggaaaaga tgctctgcat catcgtggag tttctcacaa aggtcggcct
     4201 cagcatcgag atcaagctcg ttaagcttct ccagcaggag cagagactga ttctggatga
     4261 atttagccat gttcagcgct gttttctgtt gtttcgtcat aagggacctc agagcatcaa
     4321 tgctcagtgt aaaaccggta agggggtcgg atgtacgaat ggttcagaga acggatctga
     4381 ggtaatcctg tagttatgtt gtagtttatc tgtagtcatc gcactaaaaa tcaggattaa
     4441 gtcatcagct tttgtagtct ttctgtagtt tacctgtagt ccggaaaaac aatccgttca
     4501 tgcgagcatg aacgaggtcg ttaatgacgt ttttttgtca ccgacgcccc ttaacctccg
     4561 cagatcaccc ggcaagaatg ataatttttt ggccattaaa tggtcataca cctaacgcag
     4621 ccgcgatttt catcgcaact gcatgaatta aaaagtaaaa actgaaatct ccgtttattt
     4681 atgtaatacg caacgtatta caatcacctg taattacatg aaaataaaga aataaaatgt
     4741 aataccggcg tattaccacg tacgcgggta agcgaaaaag ctataacgct tcccggccga
     4801 caggcggccc aaaatccacc ggggcgtgca ggttctcttc agtaacctgc gccattaaat
     4861 caaaaaggtc atattcgccg ggaagctgcg tatcagtcga atcccgttgt tcatcatatt
     4921 cagatggcat ggggtgatat ccagtagctg agaggttgtt agagggtttc ggggcgcagc
     4981 cctgaaccag tcacgtagca ctagcggagt gtatatgggc tcaatatgct acggtgaagt
     5041 aacactttat gaaagtgctt catgtggcag gagaaaaagg tggcaccggc gcgtcagcag
     5101 aacatgtagt aacgggagat gtgccgcttc ctcgctcact gactcgctac gctcggtcgt
     5161 tcggctgcgg cgagcggtac cggcttacga atggggcgga aatttccggg tagatgccag
     5221 gagggaactt aacagggaaa cgataaggcc gcggcgctgc cgtttttcca taggctccgc
     5281 ccccctgaca agcatcacga aatctgacgc tcaaatcagt ggcggcgaaa cccgacagg
//
