LOCUS       CP128763                5216 bp    DNA     circular BCT 03-JUL-2023
DEFINITION  Klebsiella pneumoniae strain CRE-118 plasmid pCRE-118_4, complete
            sequence.
ACCESSION   CP128763
VERSION     CP128763.1
DBLINK      BioProject: PRJNA788509
            BioSample: SAMN35878151
KEYWORDS    .
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5216)
  AUTHORS   Kochan,T.
  TITLE     Klebsiella pneumoniae Clinical Isolates with Features of Both
            Multidrug-Resistance and Hypervirulence Have Unexpectedly Low
            Virulence
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5216)
  AUTHORS   Kochan,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-JUN-2023) Microbiology & Immunology, Northwestern
            University, 303 E Chicago Ave, Ward 6-035, Chicago, IL 60611, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: trycycler v. v0.4.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 66.7372904980587x
            Sequencing Technology :: Oxford Nanopore MinION/GridION, Illumina
            NovaSeq/MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/26/2023 13:26:45
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,505
            CDSs (total)                      :: 5,381
            Genes (coding)                    :: 5,277
            CDSs (with protein)               :: 5,277
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 104
            CDSs (without protein)            :: 104
            Pseudo Genes (ambiguous residues) :: 0 of 104
            Pseudo Genes (frameshifted)       :: 42 of 104
            Pseudo Genes (incomplete)         :: 62 of 104
            Pseudo Genes (internal stop)      :: 14 of 104
            Pseudo Genes (multiple problems)  :: 14 of 104
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..5216
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="CRE-118"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pCRE-118_4"
                     /geo_loc_name="USA: Chicago"
                     /lat_lon="41.8945 N 87.6208 W"
     gene            complement(352..1161)
                     /locus_tag="QU716_27465"
     CDS             complement(352..1161)
                     /locus_tag="QU716_27465"
                     /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="WJU62926.1"
                     /translation="MSKDKKERSKNRYHQLVEKIFFDKYVDGDLEVLFERLDINSAAKD
                     LGIELPSNVGDVIYSIRFRTPMPESILLTQPEGKEWIIELAGRSKYRFRLVTISRILPN
                     PNMVAIKIPDNTPEIITGYSLDDEQALLAKVRYNRLIDIFLGITTYSLQNHLRTTVKGI
                     GQIEIDELYVGIDKYGCHYIIPVQAKGGTDQISMVQTSQDTAWCEQKYPNVRCRAISAQ
                     FVSSDLIALFELKIDEGQVKLIEERHYKLVPVKELDSSDISNYRMSV"
                     /name="hypothetical protein"
     gene            complement(1154..2404)
                     /locus_tag="QU716_27470"
     CDS             complement(1154..2404)
                     /locus_tag="QU716_27470"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015160339.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0003886 - DNA (cytosine-5-)-methyltransferase activity
                     [Evidence IEA]; GO_function: GO:0008168 - methyltransferase
                     activity [Evidence IEA]; GO_function: GO:1904047 -
                     S-adenosyl-L-methionine binding [Evidence IEA]; GO_process:
                     GO:0006304 - DNA modification [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WJU62927.1"
                     /translation="MTRPIAVDLFAGAGGLSLGFEQAGFDIMASVEIDPIHCSAHKYNF
                     PMCKTICRSVVDVTGEYVREVSGIGEKEIDVVIGGAPCQGFSLIGKRALDDDRNKLVYH
                     YVRLVLELKPKYFVFENVKGLTVGKHKQFLVEIMDAFKDGGYDVVSDYKVLNAADYGVP
                     QDRRRLFLMGGRKGIALPSYPEPLSIRTTVGDAIGDIPDAEKYPELWGRDWVYAKFGEQ
                     SLYSSYLHGVGKDPSDFSYPRIFNKDKLTCSLLTDHSDISRGRFVETLPDTVEPISRFK
                     KLSMNGLCNTLRAGTASDRGAFTSPRPIHPIYPRVITVREAARLHSYPDWFRFHVTKWH
                     GFRQVGNSVPPMLARSVGLQIMKVLGVTPKKPTKKIKLGDESLVAISMSDAASMFGVSS
                     NVIAKRIKNSNKEVVCE"
                     /name="DNA cytosine methyltransferase"
     gene            complement(2856..3071)
                     /locus_tag="QU716_27475"
     CDS             complement(2856..3071)
                     /locus_tag="QU716_27475"
                     /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="WJU62924.1"
                     /translation="MTELEKQLLSALEQLQQDYSRRLDEWESAFEEWRKMSGLMQRENA
                     ALSERVSGLSRQVQSLSEQLRRLSTG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3078..3575)
                     /locus_tag="QU716_27480"
     CDS             complement(3078..3575)
                     /locus_tag="QU716_27480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020325392.1"
                     /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="WJU62925.1"
                     /translation="MSSLLTASRDFEEKSKAQQQLTEERLKAAFSKHENVVKSELNASA
                     KRINDAISAHEQGMNAAMQSNRLSVLRMVGRTWLTITMVSGLLFASLSGVLWYQGNRIA
                     ANLAEIRQQRDTLSKLHMQTWGVTYLENRNGRFLVLPEGMKAETGRTVDNKTRNAVKLV
                     RE"
                     /name="MbeB family mobilization protein"
     gene            complement(3616..4044)
                     /locus_tag="QU716_27485"
                     /pseudo=""
     CDS             complement(3616..4044)
                     /locus_tag="QU716_27485"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial on complete genome; 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            complement(4253..4594)
                     /locus_tag="QU716_27490"
     CDS             complement(4253..4594)
                     /locus_tag="QU716_27490"
                     /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="WJU62928.1"
                     /translation="MADKRNKMLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPTR
                     AGRLPSISPALLRQLAGMGNNLNQIARKVNAGGAGHDRVQIVAALMAIDAGLERLRHAV
                     LEKGPDDDC"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(4679..4854)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="90.449"
                     /coverage="81.0"
                     /evalue="5.74e-59"
     Typing          2..341
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="81.25"
                     /coverage="99.0"
                     /evalue="5.37e-68"
     Typing          4801..5216
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.381"
                     /coverage="99.0"
                     /evalue="4.84e-128"
     Typing          complement(2741..4263)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.803"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4260..4573)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="99.0"
                     /evalue="1.04e-58"
ORIGIN
        1 atgcacgaac cccccgttca gtccgactgc tgcgccttgt ccggtaacta tcgtcttgag
       61 tccaacccga aaagacatgc aaaagcgcca ctggcagcag ccactggtaa tcggattcac
      121 ggagcggagt agagttatct acagagttct tgaagtggtg gcctgactac ggctacactg
      181 aaaggacagt tttggtatct gcgctccgtg aaagccagtt accttcggaa gaaagagttg
      241 gtagctctaa attccggcaa acgaaccacc gttggtagcg gtggtttttt tgtttacggc
      301 ttaggagatt acggctagaa cgaaaggatc tcaagaagat cctctcagaa attatacaga
      361 catgcggtag tttgagatgt cagagctatc taactctttt accggaacca gtttgtaatg
      421 cctttcctca atcaatttca cttgtccttc gtctatcttt agctcaaaca gtgcaatcaa
      481 atcgctcgaa acaaactgag cggaaatagc tctacatcta acatttgggt atttttgttc
      541 acaccacgct gtatcttgcg atgtttgcac cattgatatt tgatctgtcc caccttttgc
      601 ttgaactggt attatataat ggcaaccgta tttatctata cctacataaa gttcatcgat
      661 ctctatttga ccaattccct tcaccgtagt tcttaaatga ttctgtaaag aatatgtggt
      721 tatacctaga aatatatcta ttagccggtt atatctcacc ttcgccagca atgcctgctc
      781 gtcgtctaaa gaataacctg taattatctc cggggtattg tctggaattt ttattgccac
      841 catattagga tttggcaaaa tcctactaat agttactaat ctaaatcgat actttgacct
      901 accagccagc tcaataatcc actccttacc ttctggctga gtcaacagaa tactttctgg
      961 cataggcgtt ctaaatctga ttgaatatat aacatcacca acattagatg ggagttctat
     1021 acctaaatct tttgcagcac tgtttatatc taacctttca aacaaaacct ctaagtcacc
     1081 atcaacatat ttatcgaaaa atatcttttc taccaactga tggtatctat ttttggacct
     1141 ttctttttta tccttactca caaacaacct ccttgttact attttttatt ctcttagcaa
     1201 ttacatttga tgacacacca aacatagatg cagcatcgga catagaaata gcaaccaaac
     1261 tttcatcacc gagtttgatt ttcttcgttg gtttttttgg cgtaacacca agaaccttca
     1321 taatctgcaa gccaacactt ctagctagca taggaggaac actattaccg acctgtctaa
     1381 atccatgcca cttagtcaca tgaaatctga accaatcagg atatgaatgc agtcttgctg
     1441 cctctctgac cgtgatgacc ctaggataga tcggatgtat aggacgagga gatgtaaaag
     1501 cacctctgtc acttgctgtt cctgccctta aagtattaca tagcccattc atcgagagct
     1561 ttttaaacct gctgattggt tctaccgtgt caggcaaagt ttcaacaaac cgccctctag
     1621 aaatgtcaga gtgatctgtc agtaaagaac acgttaattt gtctttatta aaaatccttg
     1681 ggtagctaaa atcactagga tcttttccta cgccatgcaa ataggatgag tatagtgatt
     1741 gctcaccaaa tttagcataa acccaatctc taccccatag ctcaggatat ttttccgcat
     1801 caggaatatc cccaatagcg tccccaaccg ttgttctaat ggataatggc tcagggtatg
     1861 atggcagagc aattcctttc cttcccccca ttaagaaaag acgacggcga tcttgaggaa
     1921 ctccataatc agctgcgttt agcactttat aatcgcttac aacgtcgtac ccgccatctt
     1981 taaatgcatc cattatctct actaaaaact gcttatgctt accaaccgtc aaccctttta
     2041 cattttcaaa aacaaagtat ttaggcttta gctcaagaac cagccgtaca tagtgataga
     2101 ccagtttgtt tctatcatca tcaagcgcgc gttttcctat taatgaaaag ccttggcagg
     2161 gagcgcctcc gatcactaca tcaatctctt tctcaccaat acctgaaact tccctaacgt
     2221 attctccggt aacatcaaca acacttctac atatcgtttt gcacatagga aagttatatt
     2281 tgtgagcaga gcaatgtatt ggatctattt caactgatgc cattatatca aagccagctt
     2341 gctcgaaacc gagactcagc ccacccgctc cagcaaataa atcaacagca atcggtctag
     2401 tcattcttta cacccacgtt atataaaatc aacatgatgc tatcagaaaa acgatcgctt
     2461 taccgatcgt ttttctgatt tcgattgaac ataacatctc ttacccgcac cgcgccggag
     2521 gcactcaggg cgtttctgat ggctgacggg caaaaggtgg tggcaagtac accgaaaacc
     2581 accagaaacg cacctgattt attttacgca tatgcatcac ttattcacat cactgcatag
     2641 ccggtgattt cggttaaaaa agactctctg tgtgctgaaa tcgcagaaaa tggccatgat
     2701 ccccgtcacg ctcaggccac ctgagacggg cgtttatcag tctccatact ccctgtcacc
     2761 atgagataat gtgcgttgcc gttccggtac cagatctgct gtcttctctg gttccttttc
     2821 cgttgtttgc ccgtatcgct gttgctcaat ctcattcagc ctgtcgataa ccggcgcagc
     2881 tgctcgctca aactctgcac ctgcctgctc aagcccgaca cgcgctcgct cagcgccgcg
     2941 ttctcccgtt gcataagacc agacatcttc cgccattcct cgaaggcgct ctcccactcg
     3001 tccagccttc tcgagtagtc ctgctgtagc tgctctaacg cgctcaacaa ttgtttttcc
     3061 agttccgtca ttctgctcta ctcccgtacc agcttcaccg cgttccgcgt cttgttgtcc
     3121 accgtccggc ccgtttcggc tttcatcccc tccggcagca ccagaaaccg tccgttgcgg
     3181 ttctccagat aggtcacgcc ccacgtctgc atgtgcagtt tcgacagcgt atctctctgc
     3241 tgcctgattt ccgccaggtt cgccgctatc cggttcccct ggtaccacag caccccgctc
     3301 aggctggcga acagcagccc tgacaccatg gtgatggtca gccacgtccg cccgaccatt
     3361 cgcagcacgc tcagccggtt cgactgcatc gccgcgttca tcccctgttc gtgggcgctg
     3421 atggcgtcgt tgattctctt cgcgcttgcg ttcagttccg atttgacaac gttctcgtgc
     3481 ttgctgaatg cggctttcag cctctcttcg gtaagctgct gctgtgcttt cgatttctcc
     3541 tcgaagtccc tcgaggccgt taaaagactg ctcataaatg gctcccctca gtcggatatt
     3601 tcgccccccg tccgggtcgg caatgctgat actgtttttt gtggttctga ccacctcaaa
     3661 accggccgct gtgagcgccc ctgtgacgtc atcacgcgtt ttcagctctc ctgatgaggc
     3721 taacatcagc aaaccccgtg taatcgtctc tgcggcttcc tgcttcgttt ctggcagtcc
     3781 tgaaggcgtg accagcgccc gccggttctc cgggtcgttc ggatcatgta gccccagcct
     3841 gccgttgacc actgtctgcc acgcatcgat gcgcggccgg tcggcacgat cgtaatacgg
     3901 ctggaggcgt ttccccgtca gtaattcggt attggggatc agaaaattca gctcaagacg
     3961 acccttgtct gcgtgttcca cccacagaat gctgtactgg tctttatcga gtccgggcat
     4021 cagaacccgc tcaaagctgg ccatcagttt ttcacgctga cccggcggca ggtccgcctc
     4081 cgcgaatgac agcaccccgg aggtatattt tttcacatac ggcgacgcat caatcagctc
     4141 ccggacttct tccggcttcc cctgcaggac gctggcacct tcacgctgcc ggtctttacc
     4201 cagaagataa tccacaggac cggcgccccc gccgcgaccc cggggatgga atttaacaat
     4261 catcgtccgg ccctttttcc agtacggcat gccgcaaccg ttccagaccg gcatcgatcg
     4321 ccatcagcgc tgccacgatc tgcacccggt catgaccggc accaccggcg ttcactttcc
     4381 gggcgatctg gttcaggtta ttgcccatgc cggcaagctg acgcagcagc gcgggcgaaa
     4441 tcgagggaag cctgccggcg cgtgtcggtt tctcatcaag gcaggtctgg cgcatccacg
     4501 ccgccagttg ttttccgtcg caccgctcaa gcaaccgccg gtgttcgtct tccgtcaccc
     4561 acatcgtgag catcttgttg cgtttatctg ccagaatcgc ctcctgataa cgccgtgacg
     4621 gacgggaaag cctttcccgg tcggcgcggg gttggacaag ccgcaggcgc gtcagtgggg
     4681 tttcggggcg cagccctgaa ccagtcacgt agcgctagcg gagtgtatac tggcttagta
     4741 tgttacggcg agatggagat tcggggaagt gcttcatgtg gcaaggggga aaatacggct
     4801 gcggggcgta agtgcaaaat gcaggtaacg atgaaatgac gcctcctcgc tcactcggtc
     4861 gctgcgctcc tgccgtgaga ctgcggcggg cgttaccagc tcacgaagga cgagataacg
     4921 agatcgcgct caagtcagga aagtcaggaa agtcaggaaa aaggatgcgg cgttgccgtt
     4981 tttccatagg ctccgccccc ctgacaagca tcacaaaatc tgacgctcaa atcagtggtg
     5041 gcgaaacccg acaggactat aaagatccca ggcgtttccc cctggtagct ccctcgtgcg
     5101 ctctcctgtt cctgcctttc ggtttaccgg tgtcattccg ctgttatggc cgcgtttgtc
     5161 tcattccacg cctgacactc agttccgggt aggcagttcg ctccaagctg gactgt
//
