LOCUS       NZ_CP086420             5359 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Klebsiella pneumoniae strain AE-2247421-T20-ESBL plasmid
            p2247421-T20-ESBL_4, complete sequence.
ACCESSION   NZ_CP086420
VERSION     NZ_CP086420.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108735
            Assembly: GCF_022759985.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5359)
  AUTHORS   Moser,A.I., Endimiani,A., Campos-Madueno,E.I. and Vallone,A.
  TITLE     Genome plasticity in E. coli and K. pneumoniae: SNV accumulation
            over time
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5359)
  AUTHORS   Moser,A.I., Endimiani,A., Campos-Madueno,E.I. and Vallone,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-NOV-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                   :: 299x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759985.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:47:52
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,834
            CDSs (total)                      :: 5,713
            Genes (coding)                    :: 5,548
            CDSs (with protein)               :: 5,548
            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)              :: 165
            CDSs (without protein)            :: 165
            Pseudo Genes (ambiguous residues) :: 0 of 165
            Pseudo Genes (frameshifted)       :: 63 of 165
            Pseudo Genes (incomplete)         :: 98 of 165
            Pseudo Genes (internal stop)      :: 28 of 165
            Pseudo Genes (multiple problems)  :: 20 of 165
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086420.1.
            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..5359
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="AE-2247421-T20-ESBL"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p2247421-T20-ESBL_4"
                     /geo_loc_name="Switzerland"
                     /collection_date="2013"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            complement(join(5287..5359,1..59))
                     /locus_tag="LNN42_RS28985"
                     /old_locus_tag="LNN42_28990"
     CDS             complement(join(5287..5359,1..59))
                     /locus_tag="LNN42_RS28985"
                     /old_locus_tag="LNN42_28990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /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_072032592.1"
                     /translation="MHEPPVQSDRCAFSGNYRLESNPERHAKTPLAAATGNRIHGAE"
                     /name="replication initiation protein"
     gene            698..1018
                     /locus_tag="LNN42_RS28990"
                     /old_locus_tag="LNN42_28995"
     CDS             698..1018
                     /locus_tag="LNN42_RS28990"
                     /old_locus_tag="LNN42_28995"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_042863636.1"
                     /translation="MLTMWVTEDEHRRLLERCDGRQLAAWMRQTCLDEKPARAGRLPSI
                     SPALLRQLAGMGNNLNQIARKVNAGGAGHDRVQIVAALMAIDAGLERLRHAVLEKGGDD
                     DR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1227..>1658
                     /locus_tag="LNN42_RS28995"
                     /pseudo=""
     CDS             1227..>1658
                     /locus_tag="LNN42_RS28995"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            1696..2181
                     /locus_tag="LNN42_RS29000"
                     /old_locus_tag="LNN42_29005"
     CDS             1696..2181
                     /locus_tag="LNN42_RS29000"
                     /old_locus_tag="LNN42_29005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001749519.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_055314654.1"
                     /translation="MSSLLALAKDLEQQSKAQQQSTGEMLKAAFSEHEKSVKAELSASA
                     KRISDAISAHEQGMTAAMQSNRLSVLRMVGRTWLTITLVSVLLIAMSGSILWWQGQQIT
                     GNYQTIRAQERTQAMLSEKNHGVQLSLCGEKKLSCVKVNPKAGAYGEEGNWMVLERK"
                     /name="MbeB family mobilization protein"
     gene            2185..2397
                     /locus_tag="LNN42_RS29005"
                     /old_locus_tag="LNN42_29010"
     CDS             2185..2397
                     /locus_tag="LNN42_RS29005"
                     /old_locus_tag="LNN42_29010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137423.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137423.1"
                     /translation="MTELEKQLLTALEQLHQDYSQRLDEWESAFAEWQKMSGLMQRENA
                     ALNERVTRLSQQVANLSRQLQRLSQ"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2947..3210)
                     /locus_tag="LNN42_RS29010"
                     /old_locus_tag="LNN42_29015"
     CDS             complement(2947..3210)
                     /locus_tag="LNN42_RS29010"
                     /old_locus_tag="LNN42_29015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010891192.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_054175658.1"
                     /translation="MAAYTSETEKFLQSVSSDQTWWKSRYNPGDSVPHSGIYRCTVCGK
                     EITSNGSDPFPPQNHHQHSQQQAIKWQLIVRTDTKGDRFGIK"
                     /name="hypothetical protein"
     gene            complement(3628..4044)
                     /locus_tag="LNN42_RS29015"
                     /old_locus_tag="LNN42_29020"
     CDS             complement(3628..4044)
                     /locus_tag="LNN42_RS29015"
                     /old_locus_tag="LNN42_29020"
                     /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_032419562.1"
                     /translation="MSDQKNNLDIQKQTLESKWGKEALSMGWSAIPTSLFFLQGALNMT
                     PTTFNVLLHLIIHWWKPYDWPHPSQESIAVRMGVSSRTVQRSLQELENYGLLTKIRTSK
                     DNPKYKGRNIYDMSLLVKSLNILTPDLNAKLNEK"
                     /name="helix-turn-helix domain-containing protein"
     gene            4392..5066
                     /locus_tag="LNN42_RS29020"
                     /old_locus_tag="LNN42_29025"
     CDS             4392..5066
                     /locus_tag="LNN42_RS29020"
                     /old_locus_tag="LNN42_29025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001259273.1"
                     /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_032419561.1"
                     /translation="MRTIVYVDGFNFYHGLVKRSGYKWLDLYKLFEEQLLPIRARESQL
                     IQVKFFTAEIKAKFASRGELAHQAQQAYHRALVQIYGDKLQIIKGYYSERQECAMTFNE
                     GHPPSKTDRTTVWKLEEKQTDVRMALEMYRDAIRGEVEQLVLCTNDSDMIPPIEMIKAD
                     RPELKIGIVVPREQDTSRVISNLASLGDWSLPYVSYEALRLALLPDKVPTRRKPILKPN
                     HW"
                     /name="NYN domain-containing protein"
     Typing          410..590
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.978"
                     /coverage="83.0"
                     /evalue="2.08e-53"
     Typing          complement(2..460)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.478"
                     /coverage="88.0"
                     /evalue="0.0"
     Typing          1009..2513
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.622"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcaagacgat agttaccgga aaaggcgcag cggtcggact gaacgggggg ttcgtgcata
       61 cagtccagct tggagcgaac tgcctacccg gaactgagtg tcaggcgtgg aatgagacaa
      121 acgcggccat aacagcggaa tgacaccggt aaaccgaaag gcaggaacag gagagcgcac
      181 gagggagcca ccagggggaa acgcctggta tctttatagt cctgtcgggt ttcgccacca
      241 ctgatttgag cgtcagattt cgtgatgctt gtcagggggg cggagcctat ggaaaaacgg
      301 cagcgccgca tccttttccc gccctgcttg tcatgtcata tgcctttgct cttatccgtg
      361 tgtgcgtaac gcccgccgca gccgaacggc aggagcggaa gcgaccgagt gagcgaggag
      421 gcgtcatatc accgtaacct ccattttctc ctgtacgccc tgtagctgca ttttccccct
      481 gtcacatgaa gcactttcat aaagtgttac tcctccgtaa catattgagc cagtatacac
      541 tccgctagcg ctacgtgact ggttcagggc tgcgccccga aacccgctaa aagccactga
      601 cgcgcctgcg gcttgtccaa caccgtgccg accgggaaac atttcccgcc cgtcccggtg
      661 ttctcaggag gctactctgg cagacaaacg caacaagatg ctcacgatgt gggtgacgga
      721 agacgaacac cggcggctgc tcgagcggtg cgacggcagg cagctggcgg cgtggatgcg
      781 tcagacctgc ctcgatgaga agccggcgcg tgccggcaga ctgccgtcga tatcgccggc
      841 gctgctgcgc cagcttgccg gtatggggaa caacctgaac cagatcgccc ggaaagtgaa
      901 tgccggtggt gccggtcatg accgggtgca gattgtggcc gccctgatgg caatcgacgc
      961 gggactggag cggctgcggc atgcggtgct ggaaaaaggg ggggatgatg atcgttaaat
     1021 ttcacccccg ggggcgcggt ggtggtgccg gtccggtgga ttacctgctg ggaaaagacc
     1081 ggcagcgcga gggggcgacc gtgctgcagg gaaaaccgga ggaagtccgg gagcttatcg
     1141 atgcctcgcc gtatgcgaaa aagtacacct ccggcgtgct gtcgttcgcg gaggctgaac
     1201 tgccgcccgg gcagcgggag cagatcatgg ccagctttga gcgggttctg atgcccgggc
     1261 tcgataaaga ccagtacagc attctgtggg tggagcatac cgacaagggg aggctggagc
     1321 tgaatttcct gatccccaac actgaactgc tgaccgggaa acgcctgcag ccgtactacg
     1381 atcgcgccga ccggccgcgc atcgatgcct ggcagaccgt ggtgaacggc agactggggc
     1441 tgcatgatcc aaacgccccg gagaaccggc ggttactggt cacgccgtcc gcactgccgg
     1501 aaacgaagct ggaagccgct caggcgatta cacgggggtt gctggcctta gcctcatccg
     1561 gggagctcaa aacgcgcgag gacgtcacag gggcgctcac agcggcaggt tttgaggtgg
     1621 tccgcaccac aaaaaacagt atcagcattg ccgacccgga cggggggcga aacatccgac
     1681 tgaagggagc catttatgag cagtctttta gcgctggcga aggacttgga gcagcaatcg
     1741 aaagcgcagc agcagagtac cggcgagatg ctgaaagccg cattcagcga gcacgagaaa
     1801 tctgtaaaag cggaactgag cgcaagcgcg aagagaatca gcgacgccat cagcgcccac
     1861 gagcagggta tgaccgcggc gatgcagtcg aaccgcctga gcgtgctgcg tatggtcggc
     1921 cggacgtggc tgaccatcac cctggtctcg gtactgctga tcgccatgag cgggagcatt
     1981 ctgtggtggc aggggcagca gatcaccggg aattaccaga ctatccgggc gcaggagcgg
     2041 acgcaggcca tgttgtcgga gaaaaaccac ggcgttcagc tgtcgctctg cggggagaag
     2101 aaactgtcct gcgtcaaagt gaacccgaaa gcgggagctt acggggagga agggaactgg
     2161 atggtactgg agaggaaata gcccatgacg gaactggaaa aacagttgct gaccgcatta
     2221 gagcagctac atcaggacta ctcgcaaagg ctggacgagt gggagagcgc cttcgcggaa
     2281 tggcagaaga tgtctggtct tatgcaacgg gagaacgcgg cgctgaacga gcgcgtcacg
     2341 cgcttgagtc agcaggtggc gaacttgagc aggcagttac agcgtttgag ccagtagtgc
     2401 agcggcatga aatggcggtg gccgccgaac gggcatacga gcagcgacag cacgaaaaag
     2461 agctggcgga agcccgttcc cgtcagcgga gttatgacgg tccgacactg ggctgaacag
     2521 tatcatccgg tgacaggccg cacgaagaag ggctcttatt tctcccgcta aataggttcg
     2581 tgatcaaaaa gagcacggcc tatacctagg gggaattatg aaattgctta acgtcattga
     2641 agctgtactt aactgcctgt atctggcgac cgagctgtgg gactggctgg agaagcattt
     2701 tcctgttttt aaggcgttca tccggattct ggcctgaaat cagactgtat gcatctggct
     2761 gcatgaccat gcagccgggg aaaatttatc tgtcacgaac ggggcggtgt atcgggtggt
     2821 ttgttgccgg ttttacctga ctgccgtccc gtttgtggcg aacctgtccg gagcggtgcg
     2881 ggcaagggat gttatggtaa atatcttcga gcttcaggta caaaaaaagc cccggagggc
     2941 tctcaatcat ttgattccga aacggtcacc tttagtgtcc gttctgacaa tcaattgcca
     3001 tttgattgct tgttgctgac tgtgctgatg atggttttgc ggcgggaacg ggtcgctgcc
     3061 gttactggtg atctcttttc cgcagacggt acatcgataa attccagaat ggggaacgct
     3121 gtctcctgga ttatatcgtg acttccacca tgtttgatcg ctactgacgc tttgtaaaaa
     3181 cttctctgtt tcgctggtat atgcagccat ttagctttcc ttttctgaat ttatagggca
     3241 gagatagaaa agccgcccgc tggggcggct tttcgttgcc agtctaaata tcaagcatat
     3301 tgggttaaca tccaggttac agcctttcct gcgtacggag gcattacatt accttttgct
     3361 atcggggctg tagtggaagg ggttcctacg actttccaga caccactttc aggacacttt
     3421 tgtccggtag aagcagtcgt accaattggt gctttagaca tgctaattcc tctttttgtg
     3481 ttttgtccgt attgctgttt gtgtagcgat actgatgttt agtttagaaa ttagctttca
     3541 atagggagct gttgtcattt tctagaaatg tgatgctgaa caccttttgt acagtgatgt
     3601 gcgcgctttg gctgtcggaa tttttggtta cttttcgttt agtttggcgt tgaggtctgg
     3661 cgtaagaatg tttagtgact taactaaaag agacatatcg taaatgtttc gccctttgta
     3721 cttagggttg tccttgcttg tacgaatttt tgtaagcaat ccgtaatttt caagttcttg
     3781 gagtgagcgt tgaactgttc ttgatgaaac tcccattcta accgcgatgc tctcttgaga
     3841 tggatgtggc caatcatagg gtttccacca gtggataatt agatgaagta gcacattgaa
     3901 tgttgtgggg gtcatattga gtgcgccctg caggaagaaa agggatgtag gaatggctga
     3961 ccatcccatg cttaacgctt ccttccccca tttagactca agtgtctgtt tttgaatgtc
     4021 taaattattt ttttgatctg acatatacca acctgctaag ctgaagtctt cttagaagac
     4081 ttcagcttag caggttggta aattaattca tataattagt acgacaccag tgcgcttata
     4141 atatcattat atttaactat acttaatcta cactcacctc ttggtagcgc gattaagtta
     4201 cgcagctccc ttgaggctct aaacctccct ttaggtgggc agcgattaag ttacgcgtct
     4261 tccttcagga gcttgaaacc gccctctcgg ttagttttaa ccctgaggta ctacaactta
     4321 aactgtttgc taacgttagt ttttgttgtt aaaaccgccc ttagaggcgg tttttttatg
     4381 cgcgaaataa aatgagaaca atagtttacg tagatgggtt caatttttat cacggattgg
     4441 ttaagcgttc gggatataag tggttagacc tttataagct ctttgaagaa caactgcttc
     4501 cgataagagc acgagaatca cagttgattc aggtgaagtt ctttactgct gagatcaagg
     4561 caaagtttgc ttctcggggt gaattggcgc accaagctca gcaagcctac catcgagcat
     4621 tagtacagat ctatggcgat aagctacaga taataaaagg ttattactca gagcgtcagg
     4681 aatgtgcaat gacctttaat gaggggcatc ctccatcaaa aacggataga acaacggtct
     4741 ggaagttaga agaaaagcag acagacgtta gaatggcttt agaaatgtat cgcgatgcga
     4801 ttcgtggtga agtagaacaa ttggttctct gcactaacga ctcagatatg ataccgccaa
     4861 tagaaatgat aaaagctgat cggcctgagt taaaaatagg aatcgtagtg ccaagggaac
     4921 aggatactag tcgagtgatt agtaatctgg ctagtttagg ggattggagc ttgccatatg
     4981 tatcctatga agccttaaga ttagctttat tgccagataa agtccccact aggcggaagc
     5041 caatactgaa gccaaatcac tggtaaacag ccggatcttc ttgtgatcct tttactctcg
     5101 tcgtaatctc atgccctgca aacaaaaaaa ccaccgctac caacggtggt tcgtttgccg
     5161 gaatcaagag ctaccaactc tttttcccga aggtaactgg ctttcacgga gcgcagatac
     5221 caaaactgtc cttccagtgt agccgcagtc aggccaccac ttcaagaact ctgtagaagc
     5281 actctactac tctgctccgt gaatcctgtt accagtggct gctgccagtg gcgtttttgc
     5341 gtgtctttcc ggattggac
//
