LOCUS       NZ_CP101902             5207 bp    DNA     circular CON 10-OCT-2023
DEFINITION  Klebsiella pneumoniae strain 4011 plasmid pCol440II_4011, complete
            sequence.
ACCESSION   NZ_CP101902
VERSION     NZ_CP101902.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29397003
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5207)
  AUTHORS   Arcari,G., Carattoli,A., Bruno,F., Polani,R., Capitani,V.,
            Menichincheri,G., Sacco,F. and Raponi,G.
  TITLE     Ceftazidime-avibactam resistance in Klebsiella pneumoniae Sequence
            Type 37: a decade of persistence and concealed evolution
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5207)
  AUTHORS   Arcari,G., Carattoli,A., Bruno,F., Polani,R., Capitani,V.,
            Menichincheri,G., Sacco,F. and Raponi,G.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-JUN-2022) Molecular medicine, Sapienza University of
            Rome, Viale di Porta Tiburtina, Rome 00182, Italy
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 31x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/10/2023 01:59:35
            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)                     :: 7
            CDSs (total)                      :: 7
            Genes (coding)                    :: 6
            CDSs (with protein)               :: 6
            Genes (RNA)                       :: 0
            tRNAs                             :: 0
            ncRNAs                            :: 0
            Pseudo Genes (total)              :: 1
            CDSs (without protein)            :: 1
            Pseudo Genes (ambiguous residues) :: 0 of 1
            Pseudo Genes (frameshifted)       :: 0 of 1
            Pseudo Genes (incomplete)         :: 1 of 1
            Pseudo Genes (internal stop)      :: 0 of 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP101902.1.
            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..5207
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="4011"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pCol440II_4011"
                     /geo_loc_name="Italy: Rome"
                     /lat_lon="41.53 N 12.30 E"
                     /collection_date="2011-01-01"
                     /collected_by="Policlinico Umberto I Hospital"
     gene            603..944
                     /locus_tag="NKY01_RS00005"
     CDS             603..944
                     /locus_tag="NKY01_RS00005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006122514.1"
                     /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_071599364.1"
                     /translation="MADKRNKMLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPTR
                     AGRLPSISPALLRQLAGMGNNLNQIARKVNAGGAGHDRVQIVAALMAIDAGLERLRHAV
                     LEKGPDDDC"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1153..>1581
                     /locus_tag="NKY01_RS00010"
                     /pseudo=""
     CDS             1153..>1581
                     /locus_tag="NKY01_RS00010"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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            1622..2119
                     /locus_tag="NKY01_RS00015"
     CDS             1622..2119
                     /locus_tag="NKY01_RS00015"
                     /inference="COORDINATES: protein motif:HMM:NF016710.3"
                     /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_015328238.1"
                     /translation="MSSLLTASRDFEEKSKAQQQLTEERLKAAFSKHENVVKSELNASA
                     KRINDAISAHEQGMNAAMQSNRLSVLRMVGRTWLTITMVSGLLFASLSGVLWYQGNRIA
                     ANLAEIRQQRDTLSKLHMQTWGVTYLENRNGRFLVLPEGMKAETGRTVDNKTRNAVKLV
                     RE"
                     /name="MbeB family mobilization protein"
     gene            2126..2341
                     /locus_tag="NKY01_RS00020"
     CDS             2126..2341
                     /locus_tag="NKY01_RS00020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015328239.1"
                     /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_015328239.1"
                     /translation="MTELEKQLLSALEQLQQDYSRRLDEWESAFEEWRKMSGLMQRENA
                     ALSERVSGLSRQVQSLSEQLRRLSTG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            2793..4043
                     /locus_tag="NKY01_RS00025"
     CDS             2793..4043
                     /locus_tag="NKY01_RS00025"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015160339.1"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [Evidence IEA];
                     GO:0008168 - methyltransferase activity [Evidence IEA];
                     GO:1904047 - S-adenosyl-L-methionine binding [Evidence
                     IEA]"
                     /GO_process="GO:0006304 - DNA modification [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WP_001584442.1"
                     /translation="MTRPIAVDLFAGAGGLSLGFEQAGFDIMASVEIDPIHCSAHKYNF
                     PMCKTICRSVVDVTGEYVREVSGIGEKEIDVVIGGAPCQGFSLIGKRALDDDRNKLVYH
                     YVRLVLELKPKYFVFENVKGLTVGKHKQFLVEIMDAFKDGGYDVVSDYKVLNAADYGVP
                     QDRRRLFLMGGRKGIALPSYPEPLSIRTTVGDAIGDIPDAEKYPELWGRDWVYAKFGEQ
                     SLYSSYLHGVGKDPSDFSYPRIFNKDKLTCSLLTDHSDISRGRFVETLPDTVEPISRFK
                     KLSMNGLCNTLRAGTASDRGAFTSPRPIHPIYPRVITVREAARLHSYPDWFRFHVTKWH
                     GFRQVGNSVPPMLARSVGLQIMKVLGVTPKKPTKKIKLGDESLVAISMSDAASMFGVSS
                     NVIAKRIKNSNKEVVCE"
                     /name="DNA cytosine methyltransferase"
     gene            4036..4845
                     /locus_tag="NKY01_RS00030"
     CDS             4036..4845
                     /locus_tag="NKY01_RS00030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010222407.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032446875.1"
                     /translation="MSKDKKERSKNRYHQLVEKIFFDKYVDGDLEVLFERLDINSAAKD
                     LGIELPSNVGDVIYSIRFRTPMPESILLTQPEGKEWIIELAGRSKYRFRLVTISRILPN
                     PNMVAIKIPDNTPEIITGYSLDDEQALLAKVRYNRLIDIFLGITTYSLQNHLRTTVKGI
                     GQIEIDELYVGIDKYGCHYIIPVQAKGGTDQISMVQTSQDTAWCEQKYPNVRCRAISAQ
                     FVSSDLIALFELKIDEGQVKLIEERHYKLVPVKELDSSDISNYRMSV"
                     /name="hypothetical protein"
     gene            complement(5065..5196)
                     /locus_tag="NKY01_RS00035"
     CDS             complement(5065..5196)
                     /locus_tag="NKY01_RS00035"
                     /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="replication initiation protein"
                     /protein_id="WP_072007956.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPKRHAKAPLAAATGNRIHGAE"
                     /name="replication initiation protein"
     Typing          344..519
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="90.449"
                     /coverage="81.0"
                     /evalue="5.74e-59"
     Typing          complement(2..361)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.891"
                     /coverage="92.0"
                     /evalue="2.2499999999999998e-126"
     Typing          complement(4857..5207)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.818"
                     /coverage="99.0"
                     /evalue="4.12e-74"
     Typing          935..2457
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tggagcgaac tgcctacccg gaactgagtg tcaggcgtgg aatgagacaa acgcggccat
       61 aacagcggaa tgacaccggt aaaccgaaag gcaggaacag gagagcgcac gagggagcta
      121 ccagggggaa acgcctggga tctttatagt cctgtcgggt ttcgccacca ctgatttgag
      181 cgtcagattt tgtgatgctt gtcagggggg cggagcctat ggaaaaacgg caacgccgca
      241 tcctttttcc tgactttcct gacttgagcg cgatctcgtt atctcgtcct tcgtgagctg
      301 gtaacgcccg ccgcagtctc acggcaggag cgcagcgacc gagtgagcga ggaggcgtca
      361 tttcatcgtt acctgcattt tgcacttacg ccccgcagcc gtattttccc ccttgccaca
      421 tgaagcactt ccccgaatct ccatctcgcc gtaacatact aagccagtat acactccgct
      481 agcgctacgt gactggttca gggctgcgcc ccgaaacccc actgacgcgc ctgcggcttg
      541 tccaaccccg cgccgaccgg gaaaggcttt cccgtccgtc acggcgttat caggaggcga
      601 ttctggcaga taaacgcaac aagatgctca cgatgtgggt gacggaagac gaacaccggc
      661 ggttgcttga gcggtgcgac ggaaaacaac tggcggcgtg gatgcgccag acctgccttg
      721 atgagaaacc gacacgcgcc ggcaggcttc cctcgatttc gcccgcgctg ctgcgtcagc
      781 ttgccggcat gggcaataac ctgaaccaga tcgcccggaa agtgaacgcc ggtggtgccg
      841 gtcatgaccg ggtgcagatc gtggcagcgc tgatggcgat cgatgccggt ctggaacggt
      901 tgcggcatgc cgtactggaa aaagggccgg acgatgattg ttaaattcca tccccggggt
      961 cgcggcgggg gcgccggtcc tgtggattat cttctgggta aagaccggca gcgtgaaggt
     1021 gccagcgtcc tgcaggggaa gccggaagaa gtccgggagc tgattgatgc gtcgccgtat
     1081 gtgaaaaaat atacctccgg ggtgctgtca ttcgcggagg cggacctgcc gccgggtcag
     1141 cgtgaaaaac tgatggccag ctttgagcgg gttctgatgc ccggactcga taaagaccag
     1201 tacagcattc tgtgggtgga acacgcagac aagggtcgtc ttgagctgaa ttttctgatc
     1261 cccaataccg aattactgac ggggaaacgc ctccagccgt attacgatcg tgccgaccgg
     1321 ccgcgcatcg atgcgtggca gacagtggtc aacggcaggc tggggctaca tgatccgaac
     1381 gacccggaga accggcgggc gctggtcacg ccttcaggac tgccagaaac gaagcaggaa
     1441 gccgcagaga cgattacacg gggtttgctg atgttagcct catcaggaga gctgaaaacg
     1501 cgtgatgacg tcacaggggc gctcacagcg gccggttttg aggtggtcag aaccacaaaa
     1561 aacagtatca gcattgccga cccggacggg gggcgaaata tccgactgag gggagccatt
     1621 tatgagcagt cttttaacgg cctcgaggga cttcgaggag aaatcgaaag cacagcagca
     1681 gcttaccgaa gagaggctga aagccgcatt cagcaagcac gagaacgttg tcaaatcgga
     1741 actgaacgca agcgcgaaga gaatcaacga cgccatcagc gcccacgaac aggggatgaa
     1801 cgcggcgatg cagtcgaacc ggctgagcgt gctgcgaatg gtcgggcgga cgtggctgac
     1861 catcaccatg gtgtcagggc tgctgttcgc cagcctgagc ggggtgctgt ggtaccaggg
     1921 gaaccggata gcggcgaacc tggcggaaat caggcagcag agagatacgc tgtcgaaact
     1981 gcacatgcag acgtggggcg tgacctatct ggagaaccgc aacggacggt ttctggtgct
     2041 gccggagggg atgaaagccg aaacgggccg gacggtggac aacaagacgc ggaacgcggt
     2101 gaagctggta cgggagtaga gcagaatgac ggaactggaa aaacaattgc tgagcgcgtt
     2161 agagcagcta cagcaggact actcgagaag gctggacgag tgggagagcg ccttcgagga
     2221 atggcggaag atgtctggtc ttatgcaacg ggagaacgcg gcgctgagcg agcgcgtgtc
     2281 gggcttgagc aggcaggtgc agagtttgag cgagcagctg cgccggttat cgacaggctg
     2341 aatgagattg agcaacagcg atacgggcaa acaacggaaa aggaaccaga gaagacagca
     2401 gatctggtac cggaacggca acgcacatta tctcatggtg acagggagta tggagactga
     2461 taaacgcccg tctcaggtgg cctgagcgtg acggggatca tggccatttt ctgcgatttc
     2521 agcacacaga gagtcttttt taaccgaaat caccggctat gcagtgatgt gaataagtga
     2581 tgcatatgcg taaaataaat caggtgcgtt tctggtggtt ttcggtgtac ttgccaccac
     2641 cttttgcccg tcagccatca gaaacgccct gagtgcctcc ggcgcggtgc gggtaagaga
     2701 tgttatgttc aatcgaaatc agaaaaacga tcggtaaagc gatcgttttt ctgatagcat
     2761 catgttgatt ttatataacg tgggtgtaaa gaatgactag accgattgct gttgatttat
     2821 ttgctggagc gggtgggctg agtctcggtt tcgagcaagc tggctttgat ataatggcat
     2881 cagttgaaat agatccaata cattgctctg ctcacaaata taactttcct atgtgcaaaa
     2941 cgatatgtag aagtgttgtt gatgttaccg gagaatacgt tagggaagtt tcaggtattg
     3001 gtgagaaaga gattgatgta gtgatcggag gcgctccctg ccaaggcttt tcattaatag
     3061 gaaaacgcgc gcttgatgat gatagaaaca aactggtcta tcactatgta cggctggttc
     3121 ttgagctaaa gcctaaatac tttgtttttg aaaatgtaaa agggttgacg gttggtaagc
     3181 ataagcagtt tttagtagag ataatggatg catttaaaga tggcgggtac gacgttgtaa
     3241 gcgattataa agtgctaaac gcagctgatt atggagttcc tcaagatcgc cgtcgtcttt
     3301 tcttaatggg gggaaggaaa ggaattgctc tgccatcata ccctgagcca ttatccatta
     3361 gaacaacggt tggggacgct attggggata ttcctgatgc ggaaaaatat cctgagctat
     3421 ggggtagaga ttgggtttat gctaaatttg gtgagcaatc actatactca tcctatttgc
     3481 atggcgtagg aaaagatcct agtgatttta gctacccaag gatttttaat aaagacaaat
     3541 taacgtgttc tttactgaca gatcactctg acatttctag agggcggttt gttgaaactt
     3601 tgcctgacac ggtagaacca atcagcaggt ttaaaaagct ctcgatgaat gggctatgta
     3661 atactttaag ggcaggaaca gcaagtgaca gaggtgcttt tacatctcct cgtcctatac
     3721 atccgatcta tcctagggtc atcacggtca gagaggcagc aagactgcat tcatatcctg
     3781 attggttcag atttcatgtg actaagtggc atggatttag acaggtcggt aatagtgttc
     3841 ctcctatgct agctagaagt gttggcttgc agattatgaa ggttcttggt gttacgccaa
     3901 aaaaaccaac gaagaaaatc aaactcggtg atgaaagttt ggttgctatt tctatgtccg
     3961 atgctgcatc tatgtttggt gtgtcatcaa atgtaattgc taagagaata aaaaatagta
     4021 acaaggaggt tgtttgtgag taaggataaa aaagaaaggt ccaaaaatag ataccatcag
     4081 ttggtagaaa agatattttt cgataaatat gttgatggtg acttagaggt tttgtttgaa
     4141 aggttagata taaacagtgc tgcaaaagat ttaggtatag aactcccatc taatgttggt
     4201 gatgttatat attcaatcag atttagaacg cctatgccag aaagtattct gttgactcag
     4261 ccagaaggta aggagtggat tattgagctg gctggtaggt caaagtatcg atttagatta
     4321 gtaactatta gtaggatttt gccaaatcct aatatggtgg caataaaaat tccagacaat
     4381 accccggaga taattacagg ttattcttta gacgacgagc aggcattgct ggcgaaggtg
     4441 agatataacc ggctaataga tatatttcta ggtataacca catattcttt acagaatcat
     4501 ttaagaacta cggtgaaggg aattggtcaa atagagatcg atgaacttta tgtaggtata
     4561 gataaatacg gttgccatta tataatacca gttcaagcaa aaggtgggac agatcaaata
     4621 tcaatggtgc aaacatcgca agatacagcg tggtgtgaac aaaaataccc aaatgttaga
     4681 tgtagagcta tttccgctca gtttgtttcg agcgatttga ttgcactgtt tgagctaaag
     4741 atagacgaag gacaagtgaa attgattgag gaaaggcatt acaaactggt tccggtaaaa
     4801 gagttagata gctctgacat ctcaaactac cgcatgtctg tataatttct gagaggatct
     4861 tcttgagatc ctttcgttct agccgtaatc tcctaagccg taaacaaaaa aaccaccgct
     4921 accaacggtg gttcgtttgc cggaatttag agctaccaac tctttcttcc gaaggtaact
     4981 ggctttcacg gagcgcagat accaaaactg tcctttcagt gtagccgtag tcaggccacc
     5041 acttcaagaa ctctgtagat aactctactc cgctccgtga atccgattac cagtggctgc
     5101 tgccagtggc gcttttgcat gtcttttcgg gttggactca agacgatagt taccggacaa
     5161 ggcgcagcag tcggactgaa cggggggttc gtgcatacag tccagct
//
