LOCUS       NZ_CP141908             4018 bp    DNA     circular CON 17-JAN-2024
DEFINITION  Klebsiella pneumoniae strain ST383 plasmid p4kb, complete sequence.
ACCESSION   NZ_CP141908
VERSION     NZ_CP141908.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39239327
            Assembly: GCF_035658215.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4018)
  AUTHORS   Gaibani,P. and Amadesi,S.
  TITLE     Complete genome sequence of Klebsiella pneumoniae clinical strain
            KPN1682 co-harboring NDM and OXA-48 carbapenemases isolated in
            Verona, Italy
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4018)
  AUTHORS   Gaibani,P. and Amadesi,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-JAN-2024) Microbiology, Policlinico
            Sant'Orsola-Malpighi, Via Massarenti 9, Bologna, BO 40138, Italy
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. v2.9.2
            Assembly Name                     :: KPN1682
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 75.0x
            Sequencing Technology :: Illumina iSeq 100; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/15/2024 22:53:09
            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)                     :: 5,667
            CDSs (total)                      :: 5,544
            Genes (coding)                    :: 5,375
            CDSs (with protein)               :: 5,375
            Genes (RNA)                       :: 123
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 169
            CDSs (without protein)            :: 169
            Pseudo Genes (ambiguous residues) :: 0 of 169
            Pseudo Genes (frameshifted)       :: 71 of 169
            Pseudo Genes (incomplete)         :: 91 of 169
            Pseudo Genes (internal stop)      :: 26 of 169
            Pseudo Genes (multiple problems)  :: 14 of 169
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP141908.1.
            Bacteria and source DNA available from Policlinico
            Sant'Orsola-Malpighi, Via Massarenti 9, 40138, Bologna (Italy).
            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..4018
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="ST383"
                     /isolation_source="Rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p4kb"
                     /geo_loc_name="Italy: Verona"
                     /lat_lon="45.45342827 N 10.98289984 E"
                     /collection_date="2021-05-14"
                     /collected_by="Azienda Ospedaliera Universitaria Integrata"
     gene            468..791
                     /locus_tag="VKC14_RS28305"
                     /old_locus_tag="VKC14_28340"
     CDS             468..791
                     /locus_tag="VKC14_RS28305"
                     /old_locus_tag="VKC14_28340"
                     /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_024191642.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQICLDEKPSRAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGTGHDRVQVVAVLMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1000..>1434
                     /locus_tag="VKC14_RS28310"
                     /old_locus_tag="VKC14_28345"
                     /pseudo=""
     CDS             1000..>1434
                     /locus_tag="VKC14_RS28310"
                     /old_locus_tag="VKC14_28345"
                     /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            1469..1954
                     /locus_tag="VKC14_RS28315"
                     /old_locus_tag="VKC14_28350"
     CDS             1469..1954
                     /locus_tag="VKC14_RS28315"
                     /old_locus_tag="VKC14_28350"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /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_061390563.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMISQTWLTIVLVSALLIASSAGILWWQGQQIL
                     DNYTTIQEQKSTQAMLSEKNNGVQLTTCGEERRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            1958..2173
                     /locus_tag="VKC14_RS28320"
                     /old_locus_tag="VKC14_28355"
     CDS             1958..2173
                     /locus_tag="VKC14_RS28320"
                     /old_locus_tag="VKC14_28355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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_072048928.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSDQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2302..2829
                     /locus_tag="VKC14_RS28325"
                     /old_locus_tag="VKC14_28360"
     CDS             2302..2829
                     /locus_tag="VKC14_RS28325"
                     /old_locus_tag="VKC14_28360"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004883515.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_016246513.1"
                     /translation="MKCFWACSVSVVLAMSFTVAAAENNDNVTYTKPSAGRDLYLTCKG
                     YQVKGASVINVEKPSYLEGTGEQVEFAIITPVGASDGLKVFFDSWGFSSFGLIESHVMH
                     EHWSLVHVGGRASVKGEKIDYSFVDNQPQEGGSYKPKTGVFLYGCMNSDKRPSWVEKIY
                     TRTGVFRGGIED"
                     /name="hypothetical protein"
     gene            3084..3296
                     /locus_tag="VKC14_RS28330"
                     /old_locus_tag="VKC14_28365"
     CDS             3084..3296
                     /locus_tag="VKC14_RS28330"
                     /old_locus_tag="VKC14_28365"
                     /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_034169353.1"
                     /translation="MGDFERTFGAGADFDRIIDENNSEYFREDRRKTKNSKKKFSSFQD
                     ALVWAKANPGKTIIRSPDGVGFIEK"
                     /name="hypothetical protein"
     gene            complement(3725..3838)
                     /locus_tag="VKC14_RS28335"
                     /old_locus_tag="VKC14_28370"
     CDS             complement(3725..3838)
                     /locus_tag="VKC14_RS28335"
                     /old_locus_tag="VKC14_28370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_072035093.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPERHDKTPLAAATGN"
                     /name="replication initiation protein"
     Typing          178..355
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.222"
                     /coverage="83.0"
                     /evalue="4.5e-50"
     Typing          complement(3..228)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="80.519"
                     /coverage="99.0"
                     /evalue="1.98e-37"
     Typing          complement(3522..4018)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.171"
                     /coverage="99.0"
                     /evalue="6.24e-142"
     Typing          782..2265
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.717"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 actgatttga gcgtcagatt tcgtgatgct tgtcaggggg gcggagccta tggaaaaacg
       61 gcaacgccgc atcctttttc cgccctttct gattgatttc cgcttagtct ctttatccag
      121 ccattcgtaa gctggcaacg cccgccgcag tctcacggca ggagcgcagc gaccgagtga
      181 gcgaggaggc gtcatttcac cgggatctgc atttcgcact tacgccccac agcagcattt
      241 tctccctgcc acatgaagca ctttcctgaa tccccactcc gatttaccat gttaagccag
      301 tatacactcc gctagcgcta cgtgactggt tcagggctgc gccccgaaac ccgctgaaaa
      361 gtactgccgc gccctgcggg cttgcccaac accgctccgg acaggaaaaa atttcccgcc
      421 cgaaccggtg ttatccggag gatggtttgg cagaaaagcg caacaaaatg ctcactatgt
      481 gggtgacaga agacgagcac cgccgacttc tggagcgctg tgagggtaaa caactcgcgg
      541 cctggatgcg ccagatatgc ctggacgaaa agccctcgcg tgctggcaaa cttccatcca
      601 tctcgccggc gctgcttcgt cagcttgccg gcatgggtaa caacctcaac cagattgccc
      661 ggcaggttaa cgccggtggc ggtactgggc acgatcgcgt gcaggttgtc gccgtgctga
      721 tggccattga tgccggactc gagcggctgc ggcacgccgt gctggaaaag ggggcagacg
      781 atgatcgtta agtttcatcc cagaggccgc ggcggtggcg gcggtccggt ggattatctg
      841 ctggggaaag accggcagcg cgacggcgcc agcgttctgc agggtaagcc ggaggaagtg
      901 cgggagctta ttgacgcctc gccttacgcc aagaaataca cctccggcgt gctgtctttt
      961 gccgaacagg atttgccgcc cggccagcgt gaaaagctga tggcgagctt tgagcgggtt
     1021 ctgatgcccg gactcgataa agaccagtac agcgtactgt gggttgagca ccgggacaaa
     1081 gggcggctgg agctgaactt cctgatcccg aacacggagc tgctgaccgg cagacgtctc
     1141 cagccgtatt acgaccgcgc cgaccgtccg cgcattgatg cctggcagac catagtgaac
     1201 ggcagactgg ggctgcacga cccgaacgcg ccggaaaacc ggcgggcgct ggttacaccg
     1261 tccgcgctgc cggaagcgaa gcaggaagcc gcccaggcga ttacgcgcgg cctactttcc
     1321 cttgcctcat ccggggagct gaaaacccgt caggacgtca ctgaggcgct ggaaagtgcg
     1381 ggttttgagg tggtgcgcac cacgaaaagc agcatcagca ttgccgaccc tgacgggggg
     1441 cgaaacatcc gactgaaggg agccatctat gaacagtctt ttaacgctgg cgaaggactt
     1501 agagcagaaa tcgaaagcgc agcagcagac taccggcgag atgctgaaag ccgcattcag
     1561 cgagcacgag aagtctgtca gagcggaact gagcgaaagc gagaagagaa tcagcgccgc
     1621 catcctcgac cacgaccgga agctgtcctc agccatgagc caacgcacga aagggatgct
     1681 gcgtatgatc agccagacgt ggctgaccat agtcctggtc tccgcgctac tgatcgcctc
     1741 gagcgcgggc attctgtggt ggcaggggca acagatactc gacaactaca cgaccatcca
     1801 ggaacagaag agcacgcagg ccatgctttc agagaagaac aacggcgtcc agctcacgac
     1861 ctgcggggag gagagacgcc gctgcgtgag ggtgaacccg gaagcgggaa gattcggaga
     1921 ggattcgagc tggatgatac tggcggggaa atagcacatg acggaactgg aaaaacagtt
     1981 gctgagcgca ttagagcagc tacagcagga ctactcgaaa aggctggacg agtgggagaa
     2041 cgccttcgcg gaatggcgga cgatgtctgg gcttatgcaa cgggagaacg cggcgctgag
     2101 cgagcgcgtc acgggcttga gcaggcaggt gcagagtttg agcgatcagc tgcgccgatt
     2161 gtcgcaaggc tgaatggcat cgaggcgcac cgggagcagg agcgcgcggc gcagcaccag
     2221 aaagcgctgg agctggaacg atcgcagcgg cagaaaggtt ttgagcttgg aatgtagtta
     2281 atcaatgaaa agggatgcgt tatgaaatgt ttctgggctt gctcagtctc ggtggttttg
     2341 gctatgtcat ttacagtcgc tgctgcggag aataacgaca acgttacata tacaaaaccg
     2401 tcagccggga gggacttata tcttacctgt aaaggttatc aggtgaaggg ggcatctgta
     2461 attaacgtcg agaaaccttc ttaccttgaa ggtactggtg agcaggttga atttgcaatc
     2521 attactcctg ttggtgcgtc tgacggactc aaggtctttt ttgattcatg gggtttttct
     2581 tcatttggat tgattgaaag ccatgtgatg catgagcact ggtctttagt tcatgttggg
     2641 gggcgtgctt cagtcaaagg tgaaaagatt gattattcat ttgtagataa ccagccacag
     2701 gaggggggga gctataaacc caaaacaggt gtgttcctgt acggctgcat gaactcggat
     2761 aaaagaccat cttgggtcga aaagatctac acaagaacag gtgtgtttcg agggggcata
     2821 gaagactaaa atactgctta cagcatgaaa atccattgaa cagagtgtca gttcatttcc
     2881 gtgcataact atgcataccg taagaactta cggggggcat ttatcggcgt ttttacgtgg
     2941 taagaggtgc tcttttgcgg ttcatggcgc agaacggtgc tgaggctgtc tgcggcggtg
     3001 cgaacaaggg atgttatggt aaataagagt gtcttttgga tattttaaat ctgttttttt
     3061 attaaattta atgggggcag aaaatggggg attttgagcg tacctttgga gctggtgctg
     3121 attttgatcg gataattgat gagaataaca gcgaatattt tcgagaagat cgccgaaaaa
     3181 ctaaaaattc aaaaaaaaaa ttctcttctt ttcaagatgc tttggtttgg gcgaaagcta
     3241 atcctggcaa aacgataata agatctccag acggtgtggg gtttattgaa aaatgaaaga
     3301 gtggattcac tgtaaaacaa cagtcatttt ttggacaaca ctgtctatat acgtactcat
     3361 atgtttcaca gtgtcgtatg ttggagtcta tgttacgtac gttgcagggc ctattttgtt
     3421 agttacaggc attcttgcat ggcttacgaa acctagctgt aatccaaagt gactgggcta
     3481 gacgaacttt atccccccat aaaacccgct tttttaaacg gatcttcttg agatcattca
     3541 tggagaatcg taatctctta gcactgtaaa cgaaaaaacc gcccagcaag gcggtttttt
     3601 cgaaggttct cagagcagca actctttgaa ccgaggtaac tggcttggag gagcacagtc
     3661 accaaaactt gtcctttcag tttagcctta accggcgcat aacttcaaga ctaactcctc
     3721 taaatcagtt accagtggct gctgccagtg gcgttttgtc gtgtctttcc gggttggact
     3781 caagtcgata gttaccggat aaggcgcagc ggtcggactg aacggggggt tcgtgcatac
     3841 agtccagctt ggagcgaact gcctacccgg aactgagtgt caggcgtgga attagataaa
     3901 cgcggccata acagcggaat gacaccggta aaccgaaagg caggaacagg agagcgcacg
     3961 agggagctac cagggggaaa cgcctgggat ctttatagtc ctgtcgggtt tcgccacc
//
