LOCUS       NZ_CP083079             4167 bp    DNA     circular CON 10-FEB-2024
DEFINITION  Klebsiella pneumoniae strain 0113481141 plasmid p4-0113481141,
            complete sequence.
ACCESSION   NZ_CP083079
VERSION     NZ_CP083079.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21016545
            Assembly: GCF_021138155.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4167)
  AUTHORS   Campos-Madueno,E.I. and Endimiani,A.
  TITLE     A collection of hybrid assemblies of carbapenemase-producing
            Klebsiella pneumoniae clinical isolates from Switzerland
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4167)
  AUTHORS   Campos-Madueno,E.I. and Endimiani,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-SEP-2021) Institute for Infectious Diseases,
            University of Bern, Friedbuehlstrasse 51, Bern 3001, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 289.8651x
            Sequencing Technology :: Illumina NovaSeq and Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/10/2024 03:12:37
            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)                     :: 5,780
            CDSs (total)                      :: 5,658
            Genes (coding)                    :: 5,526
            CDSs (with protein)               :: 5,526
            Genes (RNA)                       :: 122
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 132
            CDSs (without protein)            :: 132
            Pseudo Genes (ambiguous residues) :: 0 of 132
            Pseudo Genes (frameshifted)       :: 57 of 132
            Pseudo Genes (incomplete)         :: 77 of 132
            Pseudo Genes (internal stop)      :: 22 of 132
            Pseudo Genes (multiple problems)  :: 20 of 132
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP083079.1.
            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..4167
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="0113481141"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p4-0113481141"
                     /geo_loc_name="Switzerland"
                     /lat_lon="46.188053 N 6.143417 E"
                     /collection_date="2020"
                     /collected_by="Dianalabs, Rue de la Colline 6, 1205 Geneva,
                     Switzerland"
     gene            complement(294..407)
                     /locus_tag="K9F42_RS28800"
                     /old_locus_tag="K9F42_28695"
                     /pseudo=""
     CDS             complement(294..407)
                     /locus_tag="K9F42_RS28800"
                     /old_locus_tag="K9F42_28695"
                     /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            823..1014
                     /locus_tag="K9F42_RS28805"
                     /old_locus_tag="K9F42_28700"
     CDS             823..1014
                     /locus_tag="K9F42_RS28805"
                     /old_locus_tag="K9F42_28700"
                     /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            1014..1415
                     /locus_tag="K9F42_RS28810"
                     /old_locus_tag="K9F42_28705"
     CDS             1014..1415
                     /locus_tag="K9F42_RS28810"
                     /old_locus_tag="K9F42_28705"
                     /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(1761..2003)
                     /locus_tag="K9F42_RS28815"
                     /old_locus_tag="K9F42_28710"
     CDS             complement(1761..2003)
                     /locus_tag="K9F42_RS28815"
                     /old_locus_tag="K9F42_28710"
                     /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(2369..3001)
                     /locus_tag="K9F42_RS28820"
                     /old_locus_tag="K9F42_28715"
     CDS             complement(2369..3001)
                     /locus_tag="K9F42_RS28820"
                     /old_locus_tag="K9F42_28715"
                     /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            complement(3001..4116)
                     /locus_tag="K9F42_RS28825"
                     /old_locus_tag="K9F42_28720"
     CDS             complement(3001..4116)
                     /locus_tag="K9F42_RS28825"
                     /old_locus_tag="K9F42_28720"
                     /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"
     Typing          complement(295..702)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.399"
                     /coverage="99.0"
                     /evalue="5.92e-171"
ORIGIN
        1 taataaaatg tacagctttc attgtgatta gctagacttt atgtcaaaga ttaactttga
       61 ttgcttgtgt tttaatcgat tttttttact ttcttcttga gattatctgg cagcagccgt
      121 aagcttccgg ctgtgaacga aaaaaaccgc cttggcgggc ggttttttcg aaaggttcag
      181 tagagttggc gctctatgaa ccgaggtaac tggcttaaag ggagcgcagt caccaaaact
      241 gttcgtttag tttagcttta actggcgtat aacttcaaga ctaactccct aaatcagtta
      301 ccagtggctg ctgccagtgg cgctttgtcg tgtctttccg ggttggactc aagacgatag
      361 ttaccggatt aggcgcagca gtcggactga acggggggtt cgtgcataca gtccagcttg
      421 gagcgaactg cctacccgga actgagtgtc aggcgtggaa tgagacaaac gcggccataa
      481 cagcggaatg acaccggtaa accgaaaggc aggaacagga gagcgcacga gggagccatc
      541 agggggaaac gcctggtatc tttatagtcc tgtcgggttt cgccaccact gatttgagcg
      601 tcagattccg tgatgctcgt caggggggcg gagcctatgg aaaaacggcc gctgtgcggc
      661 ctttccttct ttcctccatg cgattactcg gttttctcga gcgtttctac gcatgctcct
      721 gccgctcgcc gcagccgaac ggcaggagcg tagcgactga gtgagcgagg aagcggaaaa
      781 gaggagatcc ctacactgac cactgacgct ctgaggcctc ttatgacgaa acaacagaaa
      841 acagcgctga acatggctaa attcatccag aatcagtctc tgctcctgct ggagaagctt
      901 aacgagcttg atctcgatgt cgaggccgac ctttgtgaga aactccacga tgatgcggag
      961 catcttttcc gtacactgtc ctcgagactg gatgcattac aggatggtaa ctgatggcca
     1021 gagtgtctat tagtgaggct gcccgactga cgggtaagag tagaacaaca ctgcacaggt
     1081 taattaaagc aggtgacctg tccacctgta gcggtgagcg caatgcaaaa atggtagata
     1141 cttcagagct tttacgtgtc tttggcccct ttgagcaacc gaagggtgaa caccattctg
     1201 gacaggtctc tggacagcgt gatacagcct ctgctgacca gagtgaacag gtgatccgtc
     1261 atctgaaaca ggagattgaa cacctgaaca ccttactttt gtccaaggat tcgcacattg
     1321 acagcctgaa acaggccatg ctccttcttg aaaatcacca ggcaaaatta actgaatccc
     1381 cggcgccatg gtggaaattc tggaaaaaat cctgaccccg tcatgcttca gttttcctct
     1441 ccggccatcc cagggagttc ctgaaccttc ccaaaaatcg tcagatctct gaacgctcct
     1501 caccactaaa aatacccaca ccccacgcaa aattaaaatt ttgcagattc cttatttaca
     1561 acaatgggtt aatgaaaaat aaatgtgcgg tgatgtgtta caaagtgcag atccaagtcg
     1621 tggacgactc tatggcgaat cgctgacgaa ttgcccacga ttcatatgtg aatcacgctt
     1681 tattatcata ttgttatgat gaatcgactc ttgattcaat tcatcacttt gggtgttttt
     1741 tgctcatggt gactcttgat tcaattcacg attcgaatcg ccggtgaatc gtgtggtgag
     1801 tcgtccggcg acttgccata acgtgattgc cggccgtcga cgaacccgat tcctgaaggt
     1861 gctgaaaacc ggttttccgg ctgcgccggc aacgcttcac ggccacgcaa taaattgcgt
     1921 ccccgttcac cgttttcgga ggagaagaac gccggaaaca ggacttcccc tggctgaatg
     1981 gtgtgaattt ccgcgctatg cacttgcgcg catactcatg catgccgtaa aaacagagcc
     2041 tgcgcgtttc tggcgggttt tcgggtggtt tgttgcctgt tttaccggtt tcccgtcaga
     2101 aacgtcctga gtccgtttta gcggtgcgta caattatgat tttatgttaa attgttttaa
     2161 gtgaatagag agaatataac ttaagggagc atcttgtgct gggtctttta cattagatct
     2221 gcacaatcat tgttttggca tctggtgatg tctttaggac gtttgagatt gctgataact
     2281 aaagtgtatg atgctttcta tacgttatcc ggcgtttaat aacaccctgg tgataagcca
     2341 gcccgtgaag ggctggcttg atttggattt atatttttga aataaaatct tttatttcat
     2401 caaagcaatt gtctgctgtg tttattattc catttttcat ggatattcct attcttgagt
     2461 cggattctct attgcagcta agatagactt gtaccttagc ttttttttcg tttgttggat
     2521 aagtgtactc tttgtcactc gctgagatgt catctttatt atttttaatt ttttcgaaaa
     2581 attctattat gtattcatat aacgctcgag tgcttgcgtg ttcaattatc agatcttcaa
     2641 tggcaccttg cttgtctttt cctggcatta taaagaaaga aatttttgta ttgccattca
     2701 tagctatctc gttatgcgag ctgggggagg agatttgtag ttctcgcaat gtggcaatta
     2761 ttgatctttc tgtgtcagaa aatgatgtgt cagcatctaa tataataaaa atactttctt
     2821 tttcatcgaa agaatcaatg tttttgaatg ctctaagtgc ttgttttaat tttgattttc
     2881 catttatttt ttcgacaaaa acatcggtaa tgccttgtat ttcaagtagg ttgcatagaa
     2941 aatgaaaatc atcatcaccc tcaacgaaaa tgatcttttt gctattattt atgtctttca
     3001 ttatcttacc tcccagtcgt tctcaactga gtaggagaaa tcatccatat tgaattgtac
     3061 ggctgttggt tttagggagt tcttttctct tcctagtcta atataagcga tatcttcatt
     3121 tttgctatct atttcgttta ttgctcgtat cacatcttga ctatgagttg ttgcaaatat
     3181 ttgattgttg ttttgttttg cagatgaaat taatgatttt attatgtctt taattactga
     3241 gtaatgtatt ccgttctcga tttcatcaat aagaataatt gagttttcct gtaccagcac
     3301 tgagctgata aaagataatg ctcgactgat accctcgcca agcattgata tttcatttag
     3361 ctcactaaat ccaatgtcta aatatatttc cttattgtta cctatcgcag atattgctat
     3421 atctacaatt ctgtcatcta ttttttttaa gttttctagt atgtcttttt tccttttttg
     3481 tgttagtagg ctagatacat ttgtaattgt tgcctctttg tttatctttc tggatgttgt
     3541 tattattgtt gctgtcttaa atttataatt aatcccatcc ctttcgtttt ttatttcgga
     3601 ttttatttct acgccatctt ctttcaattg catagagaaa agcttattgg aaaccctgtt
     3661 tttcgcattg ggtgtctcgg tcacatttat ttttaaagag tttactgtgg cctgagaacc
     3721 gatagtttga cgaggtatgt tttggttaga tagtacggtg tcaacgttta gagacaaact
     3781 tgattctaat ctctgatttg tttctgtttc atatgtttgt gttacttcag agcgttcatc
     3841 tcgaatgact atggacatct tttgtgatgt gtccatatca tgaaagtaac taacccaaaa
     3901 tggcttgttt ttgtttattt ctgccatttc ttttctgaat gcttgaatgt ttaacaaaac
     3961 agccgggttt tttacatcat aaaaacaaaa aatagcatcc agtatagatg ttttcccgta
     4021 gttgtttttc ccagctatga tatttaaagt ctttaattgc tttagatata gctcattgaa
     4081 gcatttgaag ttctttaaac ttatttcctt tatcatgata gcctctgttc gtgtttttgt
     4141 tatatgccat acgatttgtt agtacct
//
