LOCUS       NZ_CP041106             5733 bp    DNA     circular CON 08-JAN-2024
DEFINITION  Klebsiella pneumoniae subsp. pneumoniae strain KPCTRSRTH07 plasmid
            unnamed7, complete sequence.
ACCESSION   NZ_CP041106
VERSION     NZ_CP041106.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN07450602
            Assembly: GCF_002248115.2
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 5733)
  AUTHORS   Fouts,D., Sutton,G., Nguyen,K., White,R., D'Souza,R. and
            Thamlikitkul,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-JUN-2019) Bioinformatics, JCVI, 9605 Medical Center
            Drive, Suite 150, Rockville, MD 20850, USA
REFERENCE   2  (bases 1 to 5733)
  AUTHORS   Fouts,D., Sutton,G., Nguyen,K., White,R., D'Souza,R. and
            Thamlikitkul,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-JUN-2019) Bioinformatics, JCVI, 9605 Medical Center
            Drive, Suite 150, Rockville, MD 20850, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 23-MAY-2019
            Assembly Method                   :: Unicycler v. v0.4.7
            Assembly Name                     :: KPCTRSRTH07
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: NA
            Genome Coverage                   :: 161.03x
            Sequencing Technology :: Illumina NextSeq 500, Oxford Nanopore
            MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/08/2024 05:19:52
            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)                     :: 5,806
            CDSs (total)                      :: 5,682
            Genes (coding)                    :: 5,535
            CDSs (with protein)               :: 5,535
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 147
            CDSs (without protein)            :: 147
            Pseudo Genes (ambiguous residues) :: 0 of 147
            Pseudo Genes (frameshifted)       :: 70 of 147
            Pseudo Genes (incomplete)         :: 80 of 147
            Pseudo Genes (internal stop)      :: 20 of 147
            Pseudo Genes (multiple problems)  :: 19 of 147
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP041106.1.
            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..5733
                     /organism="Klebsiella pneumoniae subsp. pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="KPCTRSRTH07"
                     /isolation_source="Rectal swab"
                     /host="Swine"
                     /sub_species="pneumoniae"
                     /db_xref="taxon:72407"
                     /plasmid="unnamed7"
                     /geo_loc_name="Thailand: Nakhon Pathom"
                     /lat_lon="13.8199 N 100.0622 E"
                     /collection_date="2016-11-04"
     gene            complement(150..458)
                     /locus_tag="CI661_RS29305"
                     /old_locus_tag="CI661_0029305"
     CDS             complement(150..458)
                     /locus_tag="CI661_RS29305"
                     /old_locus_tag="CI661_0029305"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012564913.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_060628143.1"
                     /translation="MTEKLKGTASVLHETKTYEELVEKHSVEVANGLLANAINTALPNA
                     GITSNDVAGFSKVTIALRTGEVDLAKTAKEANADAAAVSANIIAGLKASQKSKDEIK"
                     /name="hypothetical protein"
     gene            complement(1239..1655)
                     /locus_tag="CI661_RS29310"
                     /old_locus_tag="CI661_0029310"
     CDS             complement(1239..1655)
                     /locus_tag="CI661_RS29310"
                     /old_locus_tag="CI661_0029310"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001283459.1"
                     /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_060628320.1"
                     /translation="MSDQKNNFNLQKQTLESKWGKEALSMGWSAIPTSLFFLQGALNMT
                     PTTFNVLLHLIIHWWKPYDWPHPSQESIAVRMGVSSRTVQRSLQELENYGLLTKIRTSK
                     DNPKYKGRNIYDMSLLVKSLNILTPDLNAKLNEK"
                     /name="helix-turn-helix domain-containing protein"
     gene            2003..2677
                     /locus_tag="CI661_RS29315"
                     /old_locus_tag="CI661_0029315"
     CDS             2003..2677
                     /locus_tag="CI661_RS29315"
                     /old_locus_tag="CI661_0029315"
                     /inference="COORDINATES: protein motif:HMM:NF014045.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="WP_001259273.1"
                     /translation="MRTIVYVDGFNFYHGLVKRSGYKWLDLYKLFEEQLLPIRARESQL
                     IQVKFFTAEIKAKFATRGELAHQAQQAYHRALLQIYGEKLQIIKGYYSERQECAMTFNE
                     GYPPSKTDRTTVWKLEEKQTDVRMALEMYRDAIRGEAEQLVLCTNDSDMIPPIEMIKAD
                     RPELKIGIVVPREQDTSRVISSLASLGDWSLPYVSYEALRLALLPDKVPTRRKPILKPN
                     HW"
                     /name="NYN domain-containing protein"
     gene            3444..3635
                     /locus_tag="CI661_RS29320"
                     /old_locus_tag="CI661_0029320"
     CDS             3444..3635
                     /locus_tag="CI661_RS29320"
                     /old_locus_tag="CI661_0029320"
                     /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            3635..4036
                     /locus_tag="CI661_RS29325"
                     /old_locus_tag="CI661_0029325"
     CDS             3635..4036
                     /locus_tag="CI661_RS29325"
                     /old_locus_tag="CI661_0029325"
                     /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_060628044.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVAEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            4998..5690
                     /locus_tag="CI661_RS29330"
                     /old_locus_tag="CI661_0029330"
     CDS             4998..5690
                     /locus_tag="CI661_RS29330"
                     /old_locus_tag="CI661_0029330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000550475.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3800 domain-containing protein"
                     /protein_id="WP_071556240.1"
                     /translation="MHLLYVDESGTPSDPTLNHFVLSGISVFEKQTHWIEQEMNAIAAR
                     FNTDDPYERELHGSPMRGGRDGWKNFPFDDRKQAIKDCLTLLTQKHRDIRIFACVVPKG
                     SLGGKDVITESFYQISSRFDMYLSRLHYQGATSRGVAIFDKSSTEKSIQSLARTFKDTG
                     YGYGKLRNFSEVPLFLDSKASRLIQLADLVSYSIFRKFELNDDEFYKIIEHSFDYNNGK
                     VHGLYVAH"
                     /name="DUF3800 domain-containing protein"
     Typing          complement(2920..3323)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.103"
                     /coverage="99.0"
                     /evalue="4.61e-167"
ORIGIN
        1 tagccactat cttccatcga tgcagggcct acgactgaag cctgcattgc attttctcat
       61 tagcatcgca caacggatgt tatagtgagt acagcccgtt atggacataa aaaagccacc
      121 attcaggtgg ctttttaccc tgctgataat cactttattt catccttgct cttttgtgat
      181 gctttcaatc ccgcaataat atttgctgaa acagctgcag catcagcgtt cgcttctttc
      241 gctgttttgg ctagatcaac ttctcctgtg cgcaaggcta tcgtcacctt gctgaatccg
      301 gcgacgtcat ttgaagttat tcctgcgtta ggcaaagcag tattgatcgc atttgccagc
      361 aagccgttag cgacttctac tgaatgcttc tcaaccaatt cctcataagt tttggtttca
      421 tgcagaacac tagccgttcc tttcagtttc tcggtcatgt aaacctcttg tctgtgataa
      481 tttagatgtg ggattttaca tattgttttg attttaaatg gataaatccc acgttatgga
      541 atttatctca gatgtaacag agatcatttt gtctcaaatt cgtcaaccca taaccctttg
      601 ttatcttgaa agtatttatc taattcggca tgcatcgaga tactcattgc taggcattcc
      661 tagtcctagc tttgctcacc caatcagcca cactagtgat gtttactctc tttgaacccc
      721 ctctttttta gccagtaatt aagttcgtgt tcttgctttt tcgatacgtg ctttcctact
      781 gggtgtgaca ttttccccct tacgatgggg aaaacttacg ctgacacatg gagcatttta
      841 gagatccatt cgtaccatct ttgaacagtg tcattgtctt acaaaatgga cattgcttac
      901 ctcttccgcc ccggccttcg tttggtggtg ttctcactac agcattgcaa gaagtacagc
      961 tgtttccgaa gagggtcagc ttgttacaga aggggcactt ttttccaggc atttaaggct
     1021 ttccattaaa tattcatttt atttaatgaa tatattatta agatgttttg cttgtaaagc
     1081 actatcttag atcatctttc gtggtgatta aattttgatc taaggtgagt gcagagtgtg
     1141 ccggcaatcc cctgttcatc ttggcggagt ccgagataca gacctgataa atggtaaacc
     1201 tgctacgacg gtggcctgat tttaaatgta ttttgcggtt atttttcgtt cagtttggcg
     1261 ttaaggtcag gagtaagaat atttagtgac ttaaccaaaa gagacatatc gtaaatgttt
     1321 cttcctttgt acttagggtt gtccttactt gtacgaattt ttgtaagcaa tccgtagttt
     1381 tcaagttctt ggagtgagcg ttgcactgtt cttgatgaaa cacccattct aactgcaatg
     1441 ctctcctgag agggatgtgg ccaatcgtag ggtttccacc agtggataat tagatggagt
     1501 aagacattga atgttgtggg tgtcatattg agcgcaccct gtaagaagaa aagtgatgta
     1561 ggaatagctg accagcccat gcttaatgct tcctttcccc atttagattc aagtgtttgt
     1621 ttttgaaggt taaaattatt tttttgatct gacatatacc aacctgctaa gctgaagtct
     1681 tcttagaaga cttcagctta gcaggttggt aaattaattc atataattag tacgacacca
     1741 gcgcgcttat aatatcatta tattcaacta tacttaatct acactcacct cttggtagcg
     1801 cgattaagtt acgcggctcc cttgaggctc taaacctccc tttaggtggg cagcgattaa
     1861 gttacgcgtc ttccttcagg agcttgaaac cgctctctcg gttagtttta accctgagga
     1921 actacaactt aaactgtttg ctaacgttag tttttgttgt taaaaccgcc cttagaggcg
     1981 gtttttttat gcgtgaaata aaatgagaac aatagtttac gtagatgggt tcaattttta
     2041 ccatggattg gtcaaacgtt cgggatataa gtggctggac ctttataagc tctttgaaga
     2101 acaactactt ccgataagag caagagagtc acagttgatt caggtgaagt tcttcactgc
     2161 tgagatcaaa gctaaatttg ctacccgagg tgagttagct caccaggctc agcaagctta
     2221 ccatcgagca ttactgcaga tttatggcga gaagctacaa ataatcaaag ggtactactc
     2281 agaacgtcag gaatgtgcga tgaccttcaa tgaggggtat cctccatcga aaacggatag
     2341 aacaacggtc tggaagttag aagaaaagca gactgacgtt agaatggctt tagaaatgta
     2401 tcgcgatgcg attcgtggtg aggcagagca gttggttctc tgtactaacg attcggatat
     2461 gataccgcca atagaaatga taaaagccga tcgacctgaa ttgaaaattg gaatcgtagt
     2521 accaagggag caagatacta gtcgagttat tagtagtctg gctagtttag gggattggag
     2581 cctgccatat gtatcctacg aagctttgag attagcgcta ttaccagata aggttcccac
     2641 tagacggaaa ccaatactga agccaaatca ctggtaaaca gccggatctt cttgtgatcc
     2701 ttttactctc gtcgtaatct catgccctgc aaacaaaaaa accaccgcta ccaacggtgg
     2761 ttcgtttgcc ggaatcaaga gctaccaact ctttcttccg aaggtaactg gctttcacgg
     2821 agcgcaggta ccaaaactgt ccttccagtg tagccgcagt caggcctcca cttcaagaac
     2881 tctgtagaac actctactac tccgctccgt gaatcctctt actaatggct accgccactg
     2941 gcgatttttc gtgtctgttc cgggttggac tcaagatgat agttaccggg acaacgtggt
     3001 agtcgggctg aacggggggt tcgtgcatac agtccagctt ggagcgaact gcctacccgg
     3061 aactgagtgt caggcgtgga atgagataaa cgcggccata acagcggaat gacaccggta
     3121 aaccgaatgg caggaacagg agagcgcacg agggagccat cagggggaaa cgcctgatat
     3181 ctttatagtc ctgtcgggtt tcgccaccac tgatttgagc gtcagcttct gtgatgcttg
     3241 tcaggggggc ggagcctatg gaaaaacggc cgctaagcgg cctttccttt tccccgtcac
     3301 gcgaccgctc ggttttctcg agcttttaca cgcatgctcc tgccgctcgc cgcagccgaa
     3361 cggcaggagc atagcgactg agtgagcgag gaagcggaaa agagaacatc cctacactga
     3421 gcactgacgc tctgaggcct cttatgacga aacaacagaa aacagcgctg aacatggcta
     3481 aattcatcca gaatcagtct ctgctcctgc tggagaagct taacgagctt gatctcgatg
     3541 tcgaggccga cctttgtgag aaactccacg atgatgcgga gcatcttttc cgtacactgt
     3601 cctcaagact ggatgcatta caggatggta actgatggcc agagtttcta ttagtgaggc
     3661 tgcccgactg acgggtaaga gtagaacaac actgcacagg ttaattaaag caggtgacct
     3721 gtccacctgt agcggtgaac gcaatgcaaa aatggtagat acttcagagc ttttacgtgt
     3781 ctttggtccc tttgaacaac cgaagggtga acaccattct ggacaggtcg ctgaacagcg
     3841 tgatacagcc tctgctgacc agagtgaaca ggtgattcgt catctgaaac aggagattga
     3901 acacctgaac accttacttt tgtccaagga ttcgcacatt gacagcctca aacaggccat
     3961 gctccttctt gaaaatcacc aggcaaaatt aactgaatcc ccggcgccat ggtggaaatt
     4021 ctggaaaaaa tcctgacccc gtcatgcttc agttttcctc tccggccatc ccggggagtt
     4081 cctgaacctt cccaaaaatc gtcagatctc tgaacgcacc tcaccactaa aaatacccac
     4141 accccacgca aaattaaaat tttgaagata actcattaat atcagttatt tgtgggttat
     4201 taaattacgc agtattactt tctgtaaggt gaatccaagt cgtcggcgat tcgtgtacga
     4261 cttgccgacg actcgtcata gagtcatcga cgactcactc cacactatca gtaacttatg
     4321 acgacttgac tctagagtcg aatcgtcgct ttggcgtttt tttgaccgta gtgactctag
     4381 agtcaagtca cgagtcgaat cgccggtgaa tcgtgtggtg agtcgtctgg tgacttgcca
     4441 taacgtgatt gccggccgtc gacgaacctg attcctgaac gtgctgaaaa ccggttttcc
     4501 ggctgcgccg gcaacgcttc acggccacgc aataaattgc gtccccgttc accgttttcg
     4561 gaggagaaga acgccggaaa caggacttcc cctggctgaa tggtgtcaat ttccgcgcta
     4621 tgcacttgtg cgcatactca tgcatgccgt aaaaacagag cctgtgcgtt tctggcgggt
     4681 tttcgggtgg tttgttgcct gttttaccgg ttttccgtca gaaacgctct gagggcctct
     4741 caggcggtgc tgataacgga tgttatggta aataagagtg acgatgaagc aactatccga
     4801 ttgaatttat gttatttaat tgctcatgat tatgatatgt gtataaatta ttttggtaaa
     4861 tatgcgtttg cctgttatgc tcaacactga gtcagttcgc tgcccatagc ggtgtatgcg
     4921 atttttatcg cactggcttg cctaatttat gaaaaggccg cgcatttgcg cggccttttt
     4981 cgtttaagga atcttcgatg catctcttat acgttgatga gtctggtaca ccatcagacc
     5041 ctacacttaa tcattttgtc ctttctggta tctcagtgtt tgaaaagcag actcattgga
     5101 tagagcaaga gatgaatgct atcgcagcca gatttaatac tgatgatccg tatgaaagag
     5161 aattgcatgg ttcgcctatg agaggtgggc gagatggctg gaaaaatttt cctttcgatg
     5221 acaggaaaca agcgatcaaa gattgcctaa cactcctgac tcaaaagcat cgggatatcc
     5281 gtatatttgc gtgtgttgta cccaagggat ccttaggtgg aaaggacgta ataacagaat
     5341 ctttttatca gatatcgtct cgtttcgaca tgtatttgag ccgattacat taccaaggag
     5401 caacatctcg aggggtggcc atttttgata aatcgtcaac agagaaaagt attcagtctc
     5461 ttgctcgtac gtttaaagat actggatatg gatatggaaa acttcgtaac ttctctgaag
     5521 tgcctttgtt tttggattcc aaggcgtcaa ggttgattca gcttgcggat cttgtatcgt
     5581 actcaatttt caggaagttt gagctcaatg atgatgagtt ctacaagatt attgagcatt
     5641 cctttgacta caataatggt aaagttcacg gactttacgt agctcactaa ttgaatcgct
     5701 gtggataggt tgtctccggg tcagatgccg ctg
//
