LOCUS       CP139236                5216 bp    DNA     circular BCT 04-DEC-2023
DEFINITION  Klebsiella pneumoniae strain ARLG-3484 plasmid pARLG-3484-5,
            complete sequence.
ACCESSION   CP139236
VERSION     CP139236.1
DBLINK      BioProject: PRJNA658369
            BioSample: SAMN15868158
KEYWORDS    .
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5216)
  AUTHORS   Jiang,J., Chen,L. and Kreiswirth,B.
  TITLE     Genomic characteristics of 6 CR-HvKP strains in the US
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5216)
  AUTHORS   Jiang,J., Chen,L. and Kreiswirth,B.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-NOV-2023) HMH-CDI, Hackensack-Meridian Health Center
            for Discovery and Innovation, 340 Kingsland Street, Building 102,
            Nutley, NJ 07110, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 11/28/2023 20:13:58
            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)                     :: 5,869
            CDSs (total)                      :: 5,746
            Genes (coding)                    :: 5,571
            CDSs (with protein)               :: 5,571
            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)              :: 175
            CDSs (without protein)            :: 175
            Pseudo Genes (ambiguous residues) :: 0 of 175
            Pseudo Genes (frameshifted)       :: 72 of 175
            Pseudo Genes (incomplete)         :: 107 of 175
            Pseudo Genes (internal stop)      :: 24 of 175
            Pseudo Genes (multiple problems)  :: 27 of 175
            CRISPR Arrays                     :: 1
            ##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="ARLG-3484"
                     /isolation_source="respiratory"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="pARLG-3484-5"
                     /geo_loc_name="USA: South"
                     /collection_date="2016"
                     /collected_by="MDRO network"
     gene            complement(join(5212..5216,1..805))
                     /locus_tag="JJW40_29315"
     CDS             complement(join(5212..5216,1..805))
                     /locus_tag="JJW40_29315"
                     /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="WPQ29329.1"
                     /translation="MSKDKKERSKNRYHQLVEKIFFDKYVDGDLEVLFERLDINSAAKD
                     LGIELPSNVGDVIYSIRFRTPMPESILLTQPEGKEWIIELAGRSKYRFRLVTISRILPN
                     PNMVAIKIPDNTPEIITGYSLDDEQALLAKVRYNRLIDIFLGITTYSLQNHLRTTVKGI
                     GQIEIDELYVGIDKYGCHYIIPVQAKGGTDQISMVQTSQDTAWCEQKYPNVRCRAISAQ
                     FVSSDLIALFELKIDEGQVKLIEERHYKLVPVKELDSSDISNYRMSV"
                     /name="hypothetical protein"
     gene            complement(798..2048)
                     /locus_tag="JJW40_29320"
     CDS             complement(798..2048)
                     /locus_tag="JJW40_29320"
                     /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="WPQ29330.1"
                     /translation="MTRPIAVDLFAGAGGLSLGFEQAGFDIMASVEIDPIHCSAHKYNF
                     PMCKTICRSVVDVTGEYVREVSGIGEKEIDVVIGGAPCQGFSLIGKRALDDDRNKLVYH
                     YVRLVLELKPKYFVFENVKGLTVGKHKQFLVEIMDAFKDGGYDVVSDYKVLNAADYGVP
                     QDRRRLFLMGGRKGIALPSYPEPLSIRTTVGDAIGDIPDAEKYPELWGRDWVYAKFGEQ
                     SLYSSYLHGVGKDPSDFSYPRIFNKDKLTCSLLTDHSDISRGRFVETLPDTVEPISRFK
                     KLSMNGLCNTLRAGTASDRGAFTSPRPIHPIYPRVITVREAARLHSYPDWFRFHVTKWH
                     GFRQVGNSVPPMLARSVGLQIMKVLGVTPKKPTKKIKLGDESLVAISMSDAASMFGVSS
                     NVIAKRIKNSNKEVVCE"
                     /name="DNA cytosine methyltransferase"
     gene            complement(2500..2715)
                     /locus_tag="JJW40_29325"
     CDS             complement(2500..2715)
                     /locus_tag="JJW40_29325"
                     /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="WPQ29331.1"
                     /translation="MTELEKQLLSALEQLQQDYSRRLDEWESAFEEWRKMSGLMQRENA
                     ALSERVSGLSRQVQSLSEQLRRLSTG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2722..3219)
                     /locus_tag="JJW40_29330"
     CDS             complement(2722..3219)
                     /locus_tag="JJW40_29330"
                     /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="WPQ29327.1"
                     /translation="MSSLLTASRDFEEKSKAQQQLTEERLKAAFSKHENVVKSELNASA
                     KRINDAISAHEQGMNAAMQSNRLSVLRMVGRTWLTITMVSGLLFASLSGVLWYQGNRIA
                     ANLAEIRQQRDTLSKLHMQTWGVTYLENRNGRFLVLPEGMKAETGRTVDNKTRNAVKLV
                     RE"
                     /name="MbeB family mobilization protein"
     gene            complement(3260..3958)
                     /locus_tag="JJW40_29335"
                     /pseudo=""
     CDS             complement(3260..3958)
                     /locus_tag="JJW40_29335"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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(3897..4238)
                     /locus_tag="JJW40_29340"
     CDS             complement(3897..4238)
                     /locus_tag="JJW40_29340"
                     /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="WPQ29332.1"
                     /translation="MADKRNKMLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPTR
                     AGRLPSISPALLRQLAGMGNNLNQIARKVNAGGAGHDRVQIVAALMAIDAGLERLRHAV
                     LEKGPDDDC"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4861..4992
                     /locus_tag="JJW40_29345"
     CDS             4861..4992
                     /locus_tag="JJW40_29345"
                     /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="WPQ29328.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPKRHAKAPLAAATGNRIHGAE"
                     /name="replication initiation protein"
     Typing          complement(4323..4498)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="90.449"
                     /coverage="81.0"
                     /evalue="5.74e-59"
     Typing          4445..4970
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.434"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2385..3907)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3904..4217)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="99.0"
                     /evalue="1.04e-58"
ORIGIN
        1 cagacatgcg gtagtttgag atgtcagagc tatctaactc ttttaccgga accagtttgt
       61 aatgcctttc ctcaatcaat ttcacttgtc cttcgtctat ctttagctca aacagtgcaa
      121 tcaaatcgct cgaaacaaac tgagcggaaa tagctctaca tctaacattt gggtattttt
      181 gttcacacca cgctgtatct tgcgatgttt gcaccattga tatttgatct gtcccacctt
      241 ttgcttgaac tggtattata taatggcaac cgtatttatc tatacctaca taaagttcat
      301 cgatctctat ttgaccaatt cccttcaccg tagttcttaa atgattctgt aaagaatatg
      361 tggttatacc tagaaatata tctattagcc ggttatatct caccttcgcc agcaatgcct
      421 gctcgtcgtc taaagaataa cctgtaatta tctccggggt attgtctgga atttttattg
      481 ccaccatatt aggatttggc aaaatcctac taatagttac taatctaaat cgatactttg
      541 acctaccagc cagctcaata atccactcct taccttctgg ctgagtcaac agaatacttt
      601 ctggcatagg cgttctaaat ctgattgaat atataacatc accaacatta gatgggagtt
      661 ctatacctaa atcttttgca gcactgttta tatctaacct ttcaaacaaa acctctaagt
      721 caccatcaac atatttatcg aaaaatatct tttctaccaa ctgatggtat ctatttttgg
      781 acctttcttt tttatcctta ctcacaaaca acctccttgt tactattttt tattctctta
      841 gcaattacat ttgatgacac accaaacata gatgcagcat cggacataga aatagcaacc
      901 aaactttcat caccgagttt gattttcttc gttggttttt ttggcgtaac accaagaacc
      961 ttcataatct gcaagccaac acttctagct agcataggag gaacactatt accgacctgt
     1021 ctaaatccat gccacttagt cacatgaaat ctgaaccaat caggatatga atgcagtctt
     1081 gctgcctctc tgaccgtgat gaccctagga tagatcggat gtataggacg aggagatgta
     1141 aaagcacctc tgtcacttgc tgttcctgcc cttaaagtat tacatagccc attcatcgag
     1201 agctttttaa acctgctgat tggttctacc gtgtcaggca aagtttcaac aaaccgccct
     1261 ctagaaatgt cagagtgatc tgtcagtaaa gaacacgtta atttgtcttt attaaaaatc
     1321 cttgggtagc taaaatcact aggatctttt cctacgccat gcaaatagga tgagtatagt
     1381 gattgctcac caaatttagc ataaacccaa tctctacccc atagctcagg atatttttcc
     1441 gcatcaggaa tatccccaat agcgtcccca accgttgttc taatggataa tggctcaggg
     1501 tatgatggca gagcaattcc tttccttccc cccattaaga aaagacgacg gcgatcttga
     1561 ggaactccat aatcagctgc gtttagcact ttataatcgc ttacaacgtc gtacccgcca
     1621 tctttaaatg catccattat ctctactaaa aactgcttat gcttaccaac cgtcaaccct
     1681 tttacatttt caaaaacaaa gtatttaggc tttagctcaa gaaccagccg tacatagtga
     1741 tagaccagtt tgtttctatc atcatcaagc gcgcgttttc ctattaatga aaagccttgg
     1801 cagggagcgc ctccgatcac tacatcaatc tctttctcac caatacctga aacttcccta
     1861 acgtattctc cggtaacatc aacaacactt ctacatatcg ttttgcacat aggaaagtta
     1921 tatttgtgag cagagcaatg tattggatct atttcaactg atgccattat atcaaagcca
     1981 gcttgctcga aaccgagact cagcccaccc gctccagcaa ataaatcaac agcaatcggt
     2041 ctagtcattc tttacaccca cgttatataa aatcaacatg atgctatcag aaaaacgatc
     2101 gctttaccga tcgtttttct gatttcgatt gaacataaca tctcttaccc gcaccgcgcc
     2161 ggaggcactc agggcgtttc tgatggctga cgggcaaaag gtggtggcaa gtacaccgaa
     2221 aaccaccaga aacgcacctg atttatttta cgcatatgca tcacttattc acatcactgc
     2281 atagccggtg atttcggtta aaaaagactc tctgtgtgct gaaatcgcag aaaatggcca
     2341 tgatccccgt cacgctcagg ccacctgaga cgggcgttta tcagtctcca tactccctgt
     2401 caccatgaga taatgtgcgt tgccgttccg gtaccagatc tgctgtcttc tctggttcct
     2461 tttccgttgt ttgcccgtat cgctgttgct caatctcatt cagcctgtcg ataaccggcg
     2521 cagctgctcg ctcaaactct gcacctgcct gctcaagccc gacacgcgct cgctcagcgc
     2581 cgcgttctcc cgttgcataa gaccagacat cttccgccat tcctcgaagg cgctctccca
     2641 ctcgtccagc cttctcgagt agtcctgctg tagctgctct aacgcgctca gcaattgttt
     2701 ttccagttcc gtcattctgc tctactcccg taccagcttc accgcgttcc gcgtcttgtt
     2761 gtccaccgtc cggcccgttt cggctttcat cccctccggc agcaccagaa accgtccgtt
     2821 gcggttctcc agataggtca cgccccacgt ctgcatgtgc agtttcgaca gcgtatctct
     2881 ctgctgcctg atttccgcca ggttcgccgc tatccggttc ccctggtacc acagcacccc
     2941 gctcaggctg gcgaacagca gccctgacac catggtgatg gtcagccacg tccgcccgac
     3001 cattcgcagc acgctcagcc ggttcgactg catcgccgcg ttcatcccct gttcgtgggc
     3061 gctgatggcg tcgttgattc tcttcgcgct tgcgttcagt tccgatttga caacgttctc
     3121 gtgcttgctg aatgcggctt tcagcctctc ttcggtaagc tgctgctgtg ctttcgattt
     3181 ctcctcgaag tccctcgagg ccgttaaaag actgctcata aatggctccc ctcagtcgga
     3241 tatttcgccc cccgtccggg tcggcaatgc tgatactgtt ttttgtggtt ctgaccacct
     3301 caaaaccggc cgctgtgagc gcccctgtga cgtcatcacg cgttttcagc tctcctgatg
     3361 aggctaacat cagcaaaccc cgtgtaatcg tctctgcggc ttcctgcttc gtttctggca
     3421 gtcctgaagg cgtgaccagc gcccgccggt tctccgggtc gttcggatca tgtagcccca
     3481 gcctgccgtt gaccactgtc tgccacgcat cgatgcgcgg ccggtcggca cgatcgtaat
     3541 acggctggag gcgtttcccc gtcagtaatt cggtattggg gatcagaaaa ttcagctcaa
     3601 gacgaccctt gtctgcgtgt tccacccaca gaatgctgta ctggtcttta tcgagtccgg
     3661 gcatcagaac ccgctcaaag ctggccatca gtttttcacg ctgacccggc ggcaggtccg
     3721 cctccgcgaa tgacagcacc ccggaggtat attttttcac atacggcgac gcatcaatca
     3781 gctcccggac ttcttccggc ttcccctgca ggacgctggc accttcacgc tgccggtctt
     3841 tacccagaag ataatccaca ggaccggcgc ccccgccgcg accccgggga tggaatttaa
     3901 caatcatcgt ccggcccttt ttccagtacg gcatgccgca accgttccag accggcatcg
     3961 atcgccatca gcgctgccac gatctgcacc cggtcatgac cggcaccacc ggcgttcact
     4021 ttccgggcga tctggttcag gttattgccc atgccggcaa gctgacgcag cagcgcgggc
     4081 gaaatcgagg gaagcctgcc ggcgcgtgtc ggtttctcat caaggcaggt ctggcgcatc
     4141 cacgccgcca gttgttttcc gtcgcaccgc tcaagcaacc gccggtgttc gtcttccgtc
     4201 acccacatcg tgagcatctt gttgcgttta tctgccagaa tcgcctcctg ataacgccgt
     4261 gacggacggg aaagcctttc ccggtcggcg cggggttgga caagccgcag gcgcgtcagt
     4321 ggggtttcgg ggcgcagccc tgaaccagtc acgtagcgct agcggagtgt atactggctt
     4381 agtatgttac ggcgagatgg agattcgggg aagtgcttca tgtggcaagg gggaaaatac
     4441 ggctgcgggg cgtaagtgca aaatgcaggt aacgatgaaa tgacgcctcc tcgctcactc
     4501 ggtcgctgcg ctcctgccgt gagactgcgg cgggcgttac cagctcacga aggacgagat
     4561 aacgagatcg cgctcaagtc aggaaagtca ggaaagtcag gaaaaaggat gcggcgttgc
     4621 cgtttttcca taggctccgc ccccctgaca agcatcacaa aatctgacgc tcaaatcagt
     4681 ggtggcgaaa cccgacagga ctataaagat cccaggcgtt tccccctggt agctccctcg
     4741 tgcgctctcc tgttcctgcc tttcggttta ccggtgtcat tccgctgtta tggccgcgtt
     4801 tgtctcattc cacgcctgac actcagttcc gggtaggcag ttcgctccaa gctggactgt
     4861 atgcacgaac cccccgttca gtccgactgc tgcgccttgt ccggtaacta tcgtcttgag
     4921 tccaacccga aaagacatgc aaaagcgcca ctggcagcag ccactggtaa tcggattcac
     4981 ggagcggagt agagttatct acagagttct tgaagtggtg gcctgactac ggctacactg
     5041 aaaggacagt tttggtatct gcgctccgtg aaagccagtt accttcggaa gaaagagttg
     5101 gtagctctaa attccggcaa acgaaccacc gttggtagcg gtggtttttt tgtttacggc
     5161 ttaggagatt acggctagaa cgaaaggatc tcaagaagat cctctcagaa attata
//
