LOCUS       NZ_CP100519             3143 bp    DNA     circular CON 22-JUL-2023
DEFINITION  Klebsiella pneumoniae strain LH35-d plasmid pLH35-d-D, complete
            sequence.
ACCESSION   NZ_CP100519
VERSION     NZ_CP100519.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29499315
            Assembly: GCF_024227055.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3143)
  AUTHORS   Biggel,M.
  TITLE     ESBL-producing Enterobacteriaceae from poultry
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3143)
  AUTHORS   Biggel,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-JUL-2022) Institute for Food Safety and Hygiene,
            University of Zurich, Winterthurerstrasse 272, Zurich 8057,
            Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x, 100x
            Sequencing Technology :: Illumina MiniSeq, Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/22/2023 02:42:03
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,337
            CDSs (total)                      :: 5,216
            Genes (coding)                    :: 5,112
            CDSs (with protein)               :: 5,112
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 104
            CDSs (without protein)            :: 104
            Pseudo Genes (ambiguous residues) :: 0 of 104
            Pseudo Genes (frameshifted)       :: 51 of 104
            Pseudo Genes (incomplete)         :: 46 of 104
            Pseudo Genes (internal stop)      :: 19 of 104
            Pseudo Genes (multiple problems)  :: 11 of 104
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP100519.1.
            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..3143
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="LH35-d"
                     /isolation_source="pooled poultry feces"
                     /host="Gallus gallus domesticus"
                     /db_xref="taxon:573"
                     /plasmid="pLH35-d-D"
                     /geo_loc_name="Switzerland"
                     /collection_date="2022"
                     /collected_by="Institute for Food Safety and Hygiene,
                     University of Zurich"
     gene            join(3136..3143,1..106)
                     /locus_tag="NLZ11_RS26635"
                     /old_locus_tag="NLZ11_26635"
     CDS             join(3136..3143,1..106)
                     /locus_tag="NLZ11_RS26635"
                     /old_locus_tag="NLZ11_26635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_049026061.1"
                     /translation="MHEPPVQSDCCALSGNCHLESNPERHAKAPLAAATGN"
                     /name="hypothetical protein"
     gene            327..998
                     /locus_tag="NLZ11_RS26640"
                     /old_locus_tag="NLZ11_26640"
     CDS             327..998
                     /locus_tag="NLZ11_RS26640"
                     /old_locus_tag="NLZ11_26640"
                     /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_121560299.1"
                     /translation="MKSPHLISTQAAFFFEDTINRPDKLFNKINSDIGELIDSMPETIN
                     LPPIAPADIPRVVGHSSNGEYELSVSLNRVDIKKQYADPLLDQGSIEKFRAICKLIILS
                     VSSDMGISRIGLVSNLYIESSNPSLEISRKYLKKEDPNLLEINLRTNKESKEFGLSFNN
                     IILIQMGNVQSPSYNGKAIIVQVDTNTIETGGCIQKDIITDIFIKKSSIYNPATILERI
                     Q"
                     /name="hypothetical protein"
     gene            998..1408
                     /locus_tag="NLZ11_RS26645"
                     /old_locus_tag="NLZ11_26645"
     CDS             998..1408
                     /locus_tag="NLZ11_RS26645"
                     /old_locus_tag="NLZ11_26645"
                     /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_121560301.1"
                     /translation="MGWFGGKKDDSPSVSVRVYTTSTNTNTDTSSSSSSTNIAGDAFWE
                     RIDDLIEQKVNNNYKPKTKKEMDEESDRNIKKEAISIIKWTLIITLSGVVITFMYCTYQ
                     GKDIPEFAKTIFTVASTLAAGAGAFVFGNKSK"
                     /name="hypothetical protein"
     gene            complement(2139..2540)
                     /locus_tag="NLZ11_RS26650"
                     /old_locus_tag="NLZ11_26650"
     CDS             complement(2139..2540)
                     /locus_tag="NLZ11_RS26650"
                     /old_locus_tag="NLZ11_26650"
                     /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"
     gene            complement(2540..2731)
                     /locus_tag="NLZ11_RS26655"
                     /old_locus_tag="NLZ11_26655"
     CDS             complement(2540..2731)
                     /locus_tag="NLZ11_RS26655"
                     /old_locus_tag="NLZ11_26655"
                     /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_254541418.1"
                     /translation="MTRQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2..106
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.283"
                     /coverage="100.0"
                     /evalue="1.78e-39"
     Typing          2780..3143
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.8"
                     /coverage="92.0"
                     /evalue="4.8800000000000005e-123"
ORIGIN
        1 accccccgtt cagtccgact gctgcgcctt atccggtaac tgtcatcttg agtccaaccc
       61 ggaaaggcat gcaaaagcgc cactggcagc agccactggt aactgattta gaggagttag
      121 tcttgaagtt atgtgccagt taaggctaaa ctgaaagaac gaatttggtt actgcgctcc
      181 tccaagccag ttacctcggt tcaaagagcg ccaactcctc gaaccttcga aaaaaccgcc
      241 cgccaaggcg gttttttcgt attggagact accctctcag atatgctatc gtcaagggta
      301 ttaacaaata acaatagagg taaaaaatga aatcccctca cctaatatct actcaagcag
      361 cttttttctt tgaagataca ataaacagac ctgataagtt attcaataaa atcaactcgg
      421 atattggtga attaatagat tcaatgcctg agacaataaa ccttcctcct atagcccctg
      481 cggacattcc tagagtagtg ggtcactcat caaatggtga atatgaatta agcgtatcac
      541 tcaatcgagt ggatataaaa aaacaatatg ccgacccatt gctcgaccaa ggttcaattg
      601 aaaaattcag agcgatatgc aaacttataa tactatcggt atcttcagat atgggtatat
      661 ctcgaattgg gttagttagc aacctttaca ttgaaagcag caatccctct ttagaaatat
      721 cgaggaaata tttaaagaaa gaagatccaa acctccttga aataaaccta aggacgaata
      781 aagagagtaa agaatttggc ctgagcttta ataatataat tttaattcag atgggaaatg
      841 tacagtcccc aagctataac ggcaaagcaa tcattgtgca agttgacacc aatacgattg
      901 aaacaggtgg ctgcatacaa aaagatataa ttactgacat atttattaaa aaatcatcca
      961 tatataaccc tgctacaatt ttagaaagga tacagtgatg ggatggtttg gtggaaaaaa
     1021 agatgactca ccatctgtgt ctgtaagagt atataccaca tcaacaaaca ccaacacaga
     1081 tacctcttct tcttcatcat caacaaatat cgcaggtgat gcgttctggg agaggattga
     1141 cgacctcatt gaacaaaaag taaacaacaa ctataaacca aagacaaaaa aggaaatgga
     1201 tgaggaaagt gacagaaaca taaaaaaaga ggctatcagc ataataaaat ggacattaat
     1261 aataactcta agtggggttg ttattacatt catgtactgc acatatcaag ggaaagatat
     1321 ccctgagttt gcaaaaacaa tatttactgt tgccagcaca cttgctgcag gtgctggtgc
     1381 gtttgtcttt ggtaataaat caaagtagaa aacgagaggt tgatttaaca taactactta
     1441 attgtacgca ccgctaacac ggcctcaggg cgtttctgac gggaaaccgg taaaacaggc
     1501 aacaaaccac ccgaaaaccc gccagaaacg cgcaggctat gtttttacgg catgcatgag
     1561 tatgcacgca agtgcatagc gcgaaaactc acgccattca gccagggtaa gtcctgtttc
     1621 cggcgttcat accatccgaa aacggtgaac ggggacgcaa tttattgcgt ggccgtgaag
     1681 cgttgccggc gcagccggaa aaccggtttt cagcacgatc aggaatcggg ttcgtcgacg
     1741 gccggcaatc acgttatggc aagtcgccgg acgactcacc acacgattca ccggcgattc
     1801 gactcgtgac ttgactctag agtcgtcaag gtcaaaaaaa caccaaaatg acgattcgac
     1861 tctagagtca agtcgtcata agttactgat agtcttaagt gagtcgtcgg caagtcgtac
     1921 acgaatcgcc gacgacttgg attcatctta cagaaagtaa tactgcgtaa tttaataacc
     1981 cacaactaac tgatattaat gagttatctt caaaatttta attttgcgtg gggtgtgggt
     2041 atttttagtg gtgaggagcg ttcagagatc tgacgatttt tgggaaggtt caggaactcc
     2101 ccggcatggc cggagaggaa aactgaagca tgacggggtc aggatttttt ccagaatttc
     2161 caccatggcg ccggggattc agttaatttt gcctggtgat tttcaagaag gagcatggcc
     2221 tgtttcaggc tgtcaatgtg cgaatccttg gacaaaagta aggtgttcag gtgttcaatc
     2281 tcctgtttca gatgacggat cacctgttca ctctggtcag cagaggctgt atcacgctgt
     2341 ccagagacct gtccagaatg gtgttcaccc ttcggttgct caaaggggcc aaagacacgt
     2401 aaaagctctg aagtatctac catttttgca ttgcgctcac cgctacaggt ggacaggtca
     2461 cctgctttaa ttaacctgtg cagtgttgtt ctactcttac ccgtcagtcg ggcagcctca
     2521 ctaatagaca ctctggccat cagttaccat cctgtaatgc atccagtctc gaggacagtg
     2581 tacggaaaag atgctccgca tcatcgtgga gtttctcaca aaggtcggcc tcgacatcga
     2641 gatcaagctc gttaagcttc tccagcagga gcagagactg attctggatg aatttagcca
     2701 tgttcagcgc tgttttctgt tgtctcgtca taaggagcct cagagcgtca gtgcacagtg
     2761 taaaaccagt ctcttttccg cttcctcgct cactcagtcg ctacgctcct gccgttcggc
     2821 tgcggcgagc ggtcgcaacg cgcacataac ggcataggac agacagcacg gagagaaaga
     2881 aggcagcaca gcggccgttt ttccataggc tccgcccccc tgacaagcat cacagaattt
     2941 gacgctcaaa tcagtggtgg cgaaacccga caggactata aagataccag gcgtttcccc
     3001 ctgatggctc cctcgtgcgc tctcctgttc ctgccattcg gtttaccggt gtcattccgc
     3061 tgttatggcc gcgtttgtct cattccacgc ctgacactca gttccgggta ggcagttcgc
     3121 tccaagctgg actgtatgca cga
//
