LOCUS       NZ_CP083060             4991 bp    DNA     circular CON 10-FEB-2024
DEFINITION  Klebsiella pneumoniae strain 1613258639 plasmid p5-1613258639,
            complete sequence.
ACCESSION   NZ_CP083060
VERSION     NZ_CP083060.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21016543
            Assembly: GCF_021137935.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4991)
  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  JOURNAL   Unpublished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 4991)
  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                   :: 266.8688x
            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 03:05:42
            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)                     :: 5,611
            CDSs (total)                      :: 5,484
            Genes (coding)                    :: 5,330
            CDSs (with protein)               :: 5,330
            Genes (RNA)                       :: 127
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 154
            CDSs (without protein)            :: 154
            Pseudo Genes (ambiguous residues) :: 0 of 154
            Pseudo Genes (frameshifted)       :: 67 of 154
            Pseudo Genes (incomplete)         :: 87 of 154
            Pseudo Genes (internal stop)      :: 23 of 154
            Pseudo Genes (multiple problems)  :: 20 of 154
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP083060.1.
            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..4991
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="1613258639"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p5-1613258639"
                     /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            join(4684..4991,1..94)
                     /locus_tag="K9F40_RS27915"
                     /old_locus_tag="K9F40_27895"
     CDS             join(4684..4991,1..94)
                     /locus_tag="K9F40_RS27915"
                     /old_locus_tag="K9F40_27895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /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_032489494.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQLKGEHHSGQVSEQRDTASVDQCEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            889..1293
                     /locus_tag="K9F40_RS27920"
                     /old_locus_tag="K9F40_27900"
     CDS             889..1293
                     /locus_tag="K9F40_RS27920"
                     /old_locus_tag="K9F40_27900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016529521.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF2251 domain-containing protein"
                     /protein_id="WP_008321396.1"
                     /translation="MTILVTIQAQLVVGEEQVIKSLAPEGMLAAVFEDDGRTGYFYALD
                     ESVEGNPIMDAVHIYNAEDVSDGHIPSDVKIGWSEDSQKCVLLINGYPHGAFDFVGKNG
                     YCRSGYPPPINKVWSLSGHEWSDSVDDFFR"
                     /name="DUF2251 domain-containing protein"
     gene            complement(1387..1818)
                     /locus_tag="K9F40_RS27925"
                     /old_locus_tag="K9F40_27905"
     CDS             complement(1387..1818)
                     /locus_tag="K9F40_RS27925"
                     /old_locus_tag="K9F40_27905"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001025244.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF6530 family protein"
                     /protein_id="WP_042109831.1"
                     /translation="MKIPAHLKHKPIIQVENYDRIDGPHADDTDAMGLSVGIAQWNTPG
                     WTELSAKVWRNTGEKWSRQSEELPLHRVIDLATLICITMDYSKNGRLSSSDDFPVTRST
                     DNPELAHHTEFMKKELKQNKSNLDVSLKRLSTELKRLGY"
                     /name="DUF6530 family protein"
     gene            2236..2493
                     /locus_tag="K9F40_RS27930"
                     /old_locus_tag="K9F40_27910"
     CDS             2236..2493
                     /locus_tag="K9F40_RS27930"
                     /old_locus_tag="K9F40_27910"
                     /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_042109830.1"
                     /translation="MGSNNNQNKDLQDKQADLLDQTYTLGWMDGYAEGYDDAIEDTQNA
                     LNKLENENELLTEVVESKDNVIKELASSAGRALQAVKKNK"
                     /name="hypothetical protein"
     gene            complement(2523..3581)
                     /locus_tag="K9F40_RS27935"
                     /old_locus_tag="K9F40_27915"
     CDS             complement(2523..3581)
                     /locus_tag="K9F40_RS27935"
                     /old_locus_tag="K9F40_27915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012508929.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ParA family protein"
                     /protein_id="WP_042109829.1"
                     /translation="MAIYAVWNNKGGVGKSYLTFQLASEYARQNPTKKVLVVDLCPQAN
                     SSSMLLGGMINGENTLNQIHSAIQRKTISGYIEDRIRSPYIPTNTGSSYVINVSTHNSK
                     VPNNLYLVTGDEQLELQASRVVGASFPGPHDAWRTVHLWINDLISDICNSWNNEDSCVF
                     IDCNPSFSIYTELALTAAERLLIPFSADGSSKRAVKAVLSLVYGERRHQNEPQSDFYLN
                     SNRYSMSLPQIYMYVGNRLTQMNNSSASAFKTVVTEIGDEIWKVWQTKPSLFCIHPNGS
                     STPNNKRSFRNMFQYEVNDANTASVVSGALGIPIATLTAGNKTVSGKIIKVNQTQLDKQ
                     VPNIVALAGMIE"
                     /name="ParA family protein"
     gene            complement(3911..4077)
                     /locus_tag="K9F40_RS28140"
                     /pseudo=""
     CDS             complement(3911..4077)
                     /locus_tag="K9F40_RS28140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505258.1"
                     /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            4493..4684
                     /locus_tag="K9F40_RS27940"
                     /old_locus_tag="K9F40_27920"
     CDS             4493..4684
                     /locus_tag="K9F40_RS27940"
                     /old_locus_tag="K9F40_27920"
                     /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_032489493.1"
                     /translation="MTKQQKTALNMAKFIQHQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(3970..4372)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.857"
                     /coverage="99.0"
                     /evalue="7.72e-165"
ORIGIN
        1 cagcctgaaa caggccatgc tccttcttga aaatcaccag gcaaaattaa ctgaatcccc
       61 ggcgccatgg tggaaattct ggaaaaaatc ctgaccctgt catgcttcag ttttcctctc
      121 cggccatccc ggggagttcc tgaaccttcc caaaaatagt cagatctctg aacgctcctc
      181 accactaaaa atacccacac cccacgcaaa attaaaattt tgcagatttg tatttaatat
      241 cagtagttta ctttcctgag atttcgtttt ttaaatttta tttatataga tccgactcta
      301 tgacgactcg tcatagagtc cccggcgagt cgtcatagag tcggtaacga ctcagggcta
      361 taaaaacaat gagttaataa cgacccgact ctagacccga ctccccgttt ggttgttttt
      421 tagtcgcggc gactctaggt acgactctag tgcagagtcg ccggtgaatc gtgtggtgag
      481 tcgtccggcg acttgccata acgtgattgc cggccgtcga cgaacccgat tcctgaacgt
      541 gctgaaaacc ggttttccgg ctgcgccggc aacgcttcac ggccacgcaa taaattgcgt
      601 ccccgttcac cgttttcgga tgggaagaac gccggaaaca ggacttaccc tgtctgaatg
      661 gcgtgaatat tcgcgctatg cacttgcgtg catactcatg catgccataa aaacagagcc
      721 tgcgcgtttc tggcgggttt tcgggtggtt tgttgcctgt tttaccggtt tcccgtcaga
      781 aacgccctca gcgcgtttct gacgatgctg ataacggatg ttatggtaaa ttatccgctt
      841 gtctgaaagc tggctgccga agcaaccaag gaaaggagaa cagacctgat gaccatttta
      901 gtgacgatac aggcccagct cgttgtcggg gaggaacagg ttataaagag cctcgctcct
      961 gagggcatgc tggccgccgt gttcgaagac gatggccgga ccgggtattt ctatgcgctc
     1021 gatgagtccg tcgagggaaa cccgattatg gacgcagtac acatctacaa tgccgaagac
     1081 gtttcagacg gtcacattcc ttctgatgtt aaaattggct ggtcagaaga cagtcagaag
     1141 tgcgtactcc tgatcaatgg atacccgcac ggggcattcg atttcgtggg aaaaaacggg
     1201 tactgcagga gtggttatcc tccccctata aacaaggtgt ggtctctttc cgggcatgag
     1261 tggagcgact ctgtggatga ttttttccgg tgaattacgg caggctatag cctgccatta
     1321 tggttcgaaa aacggatgtt atggtaaatt cgtctgtgaa gtaggtagac atttctaaag
     1381 ctagttttaa tagccaagtc tcttcaattc agtcgagagg cgtttgaggc ttacatcaag
     1441 attgctttta ttttgtttta actctttttt cataaactca gtgtgatgtg ctagctcagg
     1501 gttatcagtt gagcgagtca cgggaaaatc atcactggat gaaagtcgcc catttttact
     1561 gtagtccatg gtgatacaga tcagagttgc aaggtcgatt acccggtgaa gaggcagctc
     1621 ttctgattgt cttgaccatt tttctcctgt gtttcgccaa acctttgccg aaagctcagt
     1681 ccatccagga gtgttccatt gagcaatacc tacagatagc cccatagcat cagtgtcatc
     1741 ggcatgtggg ccgtcaatgc ggtcgtaatt ttcgacttga ataattggtt tatgcttcaa
     1801 atgcgcgggt attttcatca gttcgtcctt aggtaatgtt tgtgattatt aaattacatt
     1861 gtttttctaa ttataaaact cactaaatgt aagtaaatat taatatctat tgttatcatg
     1921 tgcttgtgat tttgtttttc caattttatg ttttttgctt ggagagtagc ggtgtttttt
     1981 tgtgtcaagt gttatgataa gccgtacgtt ttttttctgg tttatagttc ggttattcac
     2041 agcaatgggc gtggttttct atgactacag ataacgttag gaatattggc gactataaaa
     2101 agaaagatgt cggggtggat gctgactgta atccagtctc aggaaacaca ccaccagtca
     2161 gactaagtga gaaacttaga aatggaattc ctcctggttt gaaaactcag atgcgccaac
     2221 aaatgaggaa aaaacatggg ctctaacaat aatcagaata aagatctgca ggataagcaa
     2281 gctgatcttt tggaccaaac gtatactctt ggttggatgg atggctatgc cgaagggtat
     2341 gatgatgcta ttgaagatac tcagaacgct ttgaataaac tggaaaacga aaacgagttg
     2401 cttactgagg ttgttgaaag taaagataat gtaatcaaag agttggcctc tagtgctggc
     2461 agggcgctgc aagcagtaaa gaaaaacaaa taaaaaaagg cccttttaag ggccttgcta
     2521 ttttattcga tcataccagc gagagctaca atgttgggga cttgtttatc tagctgcgtc
     2581 tgattaacct ttattatttt tcctgaaaca gttttatttc ctgcagttaa tgtcgcgatt
     2641 ggaataccta aggctccaga tacgacagat gctgtgtttg catcatttac ttcatactga
     2701 aacatattcc tgaaagatct tttattattt ggcgttgagc tcccatttgg gtgaatacaa
     2761 aacagacttg gttttgtttg ccatactttc caaatttcat caccaatttc ggttactacc
     2821 gtcttaaatg cactggcaga tgaattgttc atttgcgtta atctatttcc aacatacata
     2881 tatatttgtg gtagcgacat agaataacga ttgctattaa gatagaaatc tgattgtggt
     2941 tcattctgat ggcgacgctc accataaact aaagaaagta cagccttaac tgctctcttt
     3001 gatgaaccat cggcagagaa aggaattaaa aggcgctctg ctgcggttaa agctaactct
     3061 gtataaatag agaagctagg gttgcagtca atgaatacgc agctatcttc attattccat
     3121 gagttgcaaa tgtcactgat taaatcatta atccagaggt gaacagtacg ccatgcatca
     3181 tggggacctg gaaatgatgc cccaacaact cttgatgctt ggagttctaa ttgttcatcg
     3241 ccagtgacaa gatatagatt atttggaact ttactattgt gtgtagatac atttattaca
     3301 tagctagaac cagtgttggt aggaatatat ggacttctga tcctatcctc aatatatcca
     3361 gatattgtct ttctctgtat tgctgaatga atctggttta gtgtgttttc gccatttatc
     3421 attccaccaa gtaacataga ggacgagttc gcttgtgggc acaggtcaac caccaggacc
     3481 tttttagtag ggttctgtct ggcatattca gaggctaact gaaaagtaag gtaacttttc
     3541 cctacaccac ccttgttatt ccatacggca tagatcgcca tctataactc ctaatctagt
     3601 tttgttgtta gcttagattc agggtactag agattattgt tctactgtta gtttctttca
     3661 gctgactgcc tttttttgga acgatattca gtcgaagggg ttggctggct caccatgact
     3721 tatctggagt tgtcgaattc cgattaaaag gatcttcttg agatcctaac ctgcgggatg
     3781 taatcttttg ctctgtaaac gaaaaaacca cctggggagg tggtttttcg aaggatcagt
     3841 aagttgggga acttctgaac cgtggtaaca gggtgtacaa gaccgctgcc accaaatctg
     3901 tcctttcagt ttagctgtag ttaggctgta acttcaagaa ctctgcacca gtaattcttg
     3961 tacacccctt accagtggct gctgccagtg gcgttttgtc gtgccttccg ggttggactc
     4021 aagtcgaaag ttaccggaac aggcgcagca gtcggactga acggggggtt cgtgcataca
     4081 gtccagcttg gagcgaactg cctacccgga actgagtgtc aggcgtggaa tgagacaaac
     4141 gcggccataa cagcggaatg acaccggtaa accgaaaggc aggaacagga gagcgcacga
     4201 gggagccatc agggggaaac gcctgatatc tttatagtcc tgtcgggttt cgccaccact
     4261 gatttgagcg tccgtttctg tgatgcttgt caggggggcg gagcctatgg aaaaacggcc
     4321 gctgtgcggc cttccctttt ctaaattacg tgatcgctcg gttttctcga gctttcatac
     4381 gcatgctcct gccgctcgcc gcagccgaac ggcaggagcg tagcgactga gtgagcgagg
     4441 aagcggaaaa gagaacatcc ctacactgag cactgacgct ctgaggcctc ttatgacgaa
     4501 acaacagaaa acagcgctga acatggctaa attcatccag catcaatctc tgctcctgct
     4561 ggagaagctt aacgagcttg atcttgatgt cgaggccgac ctttgtgaga aactccacga
     4621 tgatgcggag catcttttcc gtacactgtc ctcgagactg gatgcattac aggatggtaa
     4681 ctgatggcca gagtgtctat tagtgaggca gcccgactga cgggtaagag tagaacaaca
     4741 ctgcacaggt taattaaagc aggtgacctg tccacctgta gcggtgagcg caatgcaaaa
     4801 atggtagata cttcagagct tttacgtgtc tttggtccct ttgaacaact gaagggtgaa
     4861 caccattctg gacaggtctc tgaacagcgc gatacagcct ctgttgacca gtgtgaacag
     4921 gtgattcgtc atctgaaaca ggagattgaa cacctgaaca ctttactttt gtccaaagat
     4981 tcgcacattg a
//
