LOCUS       NZ_CP098432             4167 bp    DNA     circular CON 22-OCT-2023
DEFINITION  Klebsiella pneumoniae strain 5844 plasmid p5844_5, complete
            sequence.
ACCESSION   NZ_CP098432
VERSION     NZ_CP098432.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28747375
            Assembly: GCF_032878755.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4167)
  AUTHORS   Bellinzona,G., Sassera,D., Corbella,M. and Merla,C.
  TITLE     Klebsiella pneumoniae AVI/CZA and CFDC resistant isolated in IRCCS
            Policlinico San Matteo
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4167)
  AUTHORS   Bellinzona,G., Sassera,D., Corbella,M. and Merla,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-MAY-2022) Biologia e Biotecnologie L. Spallanzani,
            University of Pavia, Via Ferrata, 9, Pavia, Italy 27100, Italy
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 83.42X
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/22/2023 13:13:07
            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)                     :: 5,506
            CDSs (total)                      :: 5,381
            Genes (coding)                    :: 5,255
            CDSs (with protein)               :: 5,255
            Genes (RNA)                       :: 125
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 126
            CDSs (without protein)            :: 126
            Pseudo Genes (ambiguous residues) :: 0 of 126
            Pseudo Genes (frameshifted)       :: 53 of 126
            Pseudo Genes (incomplete)         :: 75 of 126
            Pseudo Genes (internal stop)      :: 20 of 126
            Pseudo Genes (multiple problems)  :: 19 of 126
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP098432.1.
            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="5844"
                     /isolation_source="clinical isolate"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p5844_5"
                     /geo_loc_name="Italy: Pavia"
                     /lat_lon="45.19660 N 9.14881 E"
                     /collection_date="2021-02-22"
                     /collected_by="Fondazione IRCCS Policlinico San Matteo"
                     /genotype="ST101"
     gene            join(4166..4167,1..241)
                     /locus_tag="NCW68_RS27505"
                     /old_locus_tag="NCW68_27430"
     CDS             join(4166..4167,1..241)
                     /locus_tag="NCW68_RS27505"
                     /old_locus_tag="NCW68_27430"
                     /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(587..988)
                     /locus_tag="NCW68_RS27510"
                     /old_locus_tag="NCW68_27435"
     CDS             complement(587..988)
                     /locus_tag="NCW68_RS27510"
                     /old_locus_tag="NCW68_27435"
                     /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(988..1179)
                     /locus_tag="NCW68_RS27515"
                     /old_locus_tag="NCW68_27440"
     CDS             complement(988..1179)
                     /locus_tag="NCW68_RS27515"
                     /old_locus_tag="NCW68_27440"
                     /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            1595..1708
                     /locus_tag="NCW68_RS27520"
                     /old_locus_tag="NCW68_27445"
                     /pseudo=""
     CDS             1595..1708
                     /locus_tag="NCW68_RS27520"
                     /old_locus_tag="NCW68_27445"
                     /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            2053..3168
                     /locus_tag="NCW68_RS27525"
                     /old_locus_tag="NCW68_27450"
     CDS             2053..3168
                     /locus_tag="NCW68_RS27525"
                     /old_locus_tag="NCW68_27450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019405083.1"
                     /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"
     gene            3168..3800
                     /locus_tag="NCW68_RS27530"
                     /old_locus_tag="NCW68_27455"
     CDS             3168..3800
                     /locus_tag="NCW68_RS27530"
                     /old_locus_tag="NCW68_27455"
                     /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"
     Typing          1301..1708
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.399"
                     /coverage="99.0"
                     /evalue="5.92e-171"
ORIGIN
        1 gcatagcgcg gaaattcaca ccattcagcc aggggaagtc ctgtttccgg cgttcttctc
       61 ctccgaaaac ggtgaacggg gacgcaattt attgcgtggc cgtgaagcgt tgccggcgca
      121 gccggaaaac cggttttcag caccttcagg aatcgggttc gtcgacggcc ggcaatcacg
      181 ttatggcaag tcgccggacg actcaccaca cgattcaccg gcgattcgaa tcgtgaattg
      241 aatcaagagt caccatgagc aaaaaacacc caaagtgatg aattgaatca agagtcgatt
      301 catcataaca atatgataat aaagcgtgat tcacatatga atcgtgggca attcgtcagc
      361 gattcgccat agagtcgtcc acgacttgga tctgcacttt gtaacacatc accgcacatt
      421 tatttttcat taacccattg ttgtaaataa ggaatctgca aaattttaat tttgcgtggg
      481 gtgtgggtat ttttagtggt gaggagcgtt cagagatctg acgatttttg ggaaggttca
      541 ggaactccct gggatggccg gagaggaaaa ctgaagcatg acggggtcag gattttttcc
      601 agaatttcca ccatggcgcc ggggattcag ttaattttgc ctggtgattt tcaagaagga
      661 gcatggcctg tttcaggctg tcaatgtgcg aatccttgga caaaagtaag gtgttcaggt
      721 gttcaatctc ctgtttcaga tgacggatca cctgttcact ctggtcagca gaggctgtat
      781 cacgctgtcc agagacctgt ccagaatggt gttcaccctt cggttgctca aaggggccaa
      841 agacacgtaa aagctctgaa gtatctacca tttttgcatt gcgctcaccg ctacaggtgg
      901 acaggtcacc tgctttaatt aacctgtgca gtgttgttct actcttaccc gtcagtcggg
      961 cagcctcact aatagacact ctggccatca gttaccatcc tgtaatgcat ccagtctcga
     1021 ggacagtgta cggaaaagat gctccgcatc atcgtggagt ttctcacaaa ggtcggcctc
     1081 gacatcgaga tcaagctcgt taagcttctc cagcaggagc agagactgat tctggatgaa
     1141 tttagccatg ttcagcgctg ttttctgttg tttcgtcata agaggcctca gagcgtcagt
     1201 ggtcagtgta gggatctcct cttttccgct tcctcgctca ctcagtcgct acgctcctgc
     1261 cgttcggctg cggcgagcgg caggagcatg cgtagaaacg ctcgagaaaa ccgagtaatc
     1321 gcatggagga aagaaggaaa ggccgcacag cggccgtttt tccataggct ccgcccccct
     1381 gacgagcatc acggaatctg acgctcaaat cagtggtggc gaaacccgac aggactataa
     1441 agataccagg cgtttccccc tgatggctcc ctcgtgcgct ctcctgttcc tgcctttcgg
     1501 tttaccggtg tcattccgct gttatggccg cgtttgtctc attccacgcc tgacactcag
     1561 ttccgggtag gcagttcgct ccaagctgga ctgtatgcac gaaccccccg ttcagtccga
     1621 ctgctgcgcc taatccggta actatcgtct tgagtccaac ccggaaagac acgacaaagc
     1681 gccactggca gcagccactg gtaactgatt tagggagtta gtcttgaagt tatacgccag
     1741 ttaaagctaa actaaacgaa cagttttggt gactgcgctc cctttaagcc agttacctcg
     1801 gttcatagag cgccaactct actgaacctt tcgaaaaaac cgcccgccaa ggcggttttt
     1861 ttcgttcaca gccggaagct tacggctgct gccagataat ctcaagaaga aagtaaaaaa
     1921 aatcgattaa aacacaagca atcaaagtta atctttgaca taaagtctag ctaatcacaa
     1981 tgaaagctgt acattttatt aaggtactaa caaatcgtat ggcatataac aaaaacacga
     2041 acagaggcta tcatgataaa ggaaataagt ttaaagaact tcaaatgctt caatgagcta
     2101 tatctaaagc aattaaagac tttaaatatc atagctggga aaaacaacta cgggaaaaca
     2161 tctatactgg atgctatttt ttgtttttat gatgtaaaaa acccggctgt tttgttaaac
     2221 attcaagcat tcagaaaaga aatggcagaa ataaacaaaa acaagccatt ttgggttagt
     2281 tactttcatg atatggacac atcacaaaag atgtccatag tcattcgaga tgaacgctct
     2341 gaagtaacac aaacatatga aacagaaaca aatcagagat tagaatcaag tttgtctcta
     2401 aacgttgaca ccgtactatc taaccaaaac atacctcgtc aaactatcgg ttctcaggcc
     2461 acagtaaact ctttaaaaat aaatgtgacc gagacaccca atgcgaaaaa cagggtttcc
     2521 aataagcttt tctctatgca attgaaagaa gatggcgtag aaataaaatc cgaaataaaa
     2581 aacgaaaggg atgggattaa ttataaattt aagacagcaa caataataac aacatccaga
     2641 aagataaaca aagaggcaac aattacaaat gtatctagcc tactaacaca aaaaaggaaa
     2701 aaagacatac tagaaaactt aaaaaaaata gatgacagaa ttgtagatat agcaatatct
     2761 gcgataggta acaataagga aatatattta gacattggat ttagtgagct aaatgaaata
     2821 tcaatgcttg gcgagggtat cagtcgagca ttatctttta tcagctcagt gctggtacag
     2881 gaaaactcaa ttattcttat tgatgaaatc gagaacggaa tacattactc agtaattaaa
     2941 gacataataa aatcattaat ttcatctgca aaacaaaaca acaatcaaat atttgcaaca
     3001 actcatagtc aagatgtgat acgagcaata aacgaaatag atagcaaaaa tgaagatatc
     3061 gcttatatta gactaggaag agaaaagaac tccctaaaac caacagccgt acaattcaat
     3121 atggatgatt tctcctactc agttgagaac gactgggagg taagataatg aaagacataa
     3181 ataatagcaa aaagatcatt ttcgttgagg gtgatgatga ttttcatttt ctatgcaacc
     3241 tacttgaaat acaaggcatt accgatgttt ttgtcgaaaa aataaatgga aaatcaaaat
     3301 taaaacaagc acttagagca ttcaaaaaca ttgattcttt cgatgaaaaa gaaagtattt
     3361 ttattatatt agatgctgac acatcatttt ctgacacaga aagatcaata attgccacat
     3421 tgcgagaact acaaatctcc tcccccagct cgcataacga gatagctatg aatggcaata
     3481 caaaaatttc tttctttata atgccaggaa aagacaagca aggtgccatt gaagatctga
     3541 taattgaaca cgcaagcact cgagcgttat atgaatacat aatagaattt ttcgaaaaaa
     3601 ttaaaaataa taaagatgac atctcagcga gtgacaaaga gtacacttat ccaacaaacg
     3661 aaaaaaaagc taaggtacaa gtctatctta gctgcaatag agaatccgac tcaagaatag
     3721 gaatatccat gaaaaatgga ataataaaca cagcagacaa ttgctttgat gaaataaaag
     3781 attttatttc aaaaatataa atccaaatca agccagccct tcacgggctg gcttatcacc
     3841 agggtgttat taaacgccgg ataacgtata gaaagcatca tacactttag ttatcagcaa
     3901 tctcaaacgt cctaaagaca tcaccagatg ccaaaacaat gattgtgcag atctaatgta
     3961 aaagacccag cacaagatgc tcccttaagt tatattctct ctattcactt aaaacaattt
     4021 aacataaaat cataattgta cgcaccgcta aaacggactc aggacgtttc tgacgggaaa
     4081 ccggtaaaac aggcaacaaa ccacccgaaa acccgccaga aacgcgcagg ctctgttttt
     4141 acggcatgca tgagtatgcg cgcaagt
//
