LOCUS       NZ_OV049812             5590 bp    DNA     circular CON 01-FEB-2024
DEFINITION  Klebsiella pneumoniae strain DJ isolate DJ plasmid DJ_4_ColRNA,
            complete sequence.
ACCESSION   NZ_OV049812
VERSION     NZ_OV049812.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMEA7556989
            Sequence Read Archive: ERR4824536, ERR4824554
            Assembly: GCF_920103885.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1
  AUTHORS   Brisse,S. and Rodrigues,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-NOV-2021) Institut Pasteur, Biodiversity &
            Epidemiology of Bacterial Pathogens, CNRS UMR3525, 25 rue Dr Roux,
            75724 Paris, France
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/01/2024 04:09:12
            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)                     :: 5,765
            CDSs (total)                      :: 5,639
            Genes (coding)                    :: 5,420
            CDSs (with protein)               :: 5,420
            Genes (RNA)                       :: 126
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 219
            CDSs (without protein)            :: 219
            Pseudo Genes (ambiguous residues) :: 0 of 219
            Pseudo Genes (frameshifted)       :: 114 of 219
            Pseudo Genes (incomplete)         :: 119 of 219
            Pseudo Genes (internal stop)      :: 28 of 219
            Pseudo Genes (multiple problems)  :: 38 of 219
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            OV049812.1.
            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..5590
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="DJ"
                     /isolate="DJ"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="DJ_4_ColRNA"
                     /geo_loc_name="India"
                     /collection_date="2016"
     gene            complement(join(5240..5590,1..606))
                     /locus_tag="LRA90_RS26940"
     CDS             complement(join(5240..5590,1..606))
                     /locus_tag="LRA90_RS26940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014640333.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0009036 - type II site-specific deoxyribonuclease
                     activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II restriction endonuclease"
                     /protein_id="WP_223673566.1"
                     /translation="MKKLSSRYKRLFFMQRLSPGEFKTLISKERKSHFITPFALVYKTF
                     CDLGYDQKNSDYFLNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYLIDEERIKDMSPY
                     DAIRDFTMEYPTHIYDLALSNTQSRRSRAGKEFESILELLMMGAGIPVDVQGAIGKSFF
                     QKNQIGKLVDLVMPGVVQYTSNKRNTMLISAKTTLRERWQEVPEEVNRTGIREMYLATL
                     DDSFSEETINILYEANVVVVTTIENKNFKYKNNNRVLTFEDMLQSAMELSRKWNNVSYT
                     DSEKEEIQQSILKQIEKYSDFPYVVNYYRNRLSALFD"
                     /name="type II restriction endonuclease"
     gene            677..1816
                     /gene="dcm"
                     /locus_tag="LRA90_RS26945"
     CDS             677..1816
                     /gene="dcm"
                     /locus_tag="LRA90_RS26945"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000131511.1"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [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-5-)-methyltransferase"
                     /protein_id="WP_000131512.1"
                     /translation="MTDNIAATIKGKRERLHMTQKEFADALGLSKYGDRTIRRWERGET
                     KPTGAELKAVMDFPDTPPYPNNENGRYRMIDLFAGIGGTRLGFHQTNAVNVVFSSEWDK
                     FAQKTYHANYGDFPDGDITKIDEKDIPDHEILVGGFPCVAFSQAGLKKGFNDTRGTLFF
                     DIARIIKEKKPHAFLLENVKNLLGHDKGRTFSIIKNTLEELNYTVYYNIFAAKDFGVPQ
                     NRERIYIVGFNKEKVRNHEHFTFPTPLKTKTRVGDILEKSVDNKYTLSDALWNGHQRRK
                     LVNAAAGKGFGYGLFNENSPYTNTISARYYKDGSEILIEQKGSNPRKITPREASRLQGF
                     PSDFIIPVSDTQAYKQFGNSVAVPVINAIAEKIISTLDS"
                     /name="dcm"
     gene            complement(2181..2435)
                     /locus_tag="LRA90_RS26950"
     CDS             complement(2181..2435)
                     /locus_tag="LRA90_RS26950"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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_040088071.1"
                     /translation="MTELEIHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2442..2960)
                     /locus_tag="LRA90_RS26955"
     CDS             complement(2442..2960)
                     /locus_tag="LRA90_RS26955"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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="WP_001749510.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQTNLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            complement(<2998..3696)
                     /locus_tag="LRA90_RS28880"
                     /pseudo=""
     CDS             complement(<2998..3696)
                     /locus_tag="LRA90_RS28880"
                     /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            complement(3638..3961)
                     /locus_tag="LRA90_RS26965"
     CDS             complement(3638..3961)
                     /locus_tag="LRA90_RS26965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4025..4216
                     /locus_tag="LRA90_RS26970"
     CDS             4025..4216
                     /locus_tag="LRA90_RS26970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4886..5047
                     /locus_tag="LRA90_RS28885"
     CDS             4886..5047
                     /locus_tag="LRA90_RS28885"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /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_071596883.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHALTPLAAATGNRISRARFI
                     QMLTEFLK"
                     /name="replication initiation protein"
     Typing          complement(4302..4389)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.753"
                     /coverage="100.0"
                     /evalue="1.48e-35"
     Typing          4413..4958
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.353"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2078..3648)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.328"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccatcgctcc ctcagcgttg ttttagcgga aatcaacatt gtatttcttt tgttagatgt
       61 gtactggact acacctggca taacaagatc tacaagttta cctatttggt ttttttgaaa
      121 aaatgacttc ccaatagccc cctgcacatc aacaggaatt cctgccccca tcattaatag
      181 ctcaagaata gactcaaact cttttcctgc cctgctacgt ctggattgag tgttagacag
      241 tgccaaatca tatatgtgtg tagggtattc catcgtaaaa tcacgaatgg catcataagg
      301 actcatatct tttattcttt cttcatcaat aagatatgat aacattcttg ttgtgaattc
      361 tttttcaaat ggttcaaatt ctttccaaca gttttttctc attgcaatta tatattcact
      421 tggattattc aaaaaataat cactattttt ttgatcatac cctaaatcac aaaatgtttt
      481 ataaaccaaa gcaaatggcg taataaaatg cgactttctc tctttagaaa ttagagtttt
      541 aaattcacca ggactcaatc tttgcataaa aaataacctt ttatatctac ttgaaagttt
      601 tttcatgcac gttcataatt ggaatcaaaa caggacaaat tgtcctaaaa ccaacactta
      661 attctggtag acatgcatga ctgataatat cgcagcaaca atcaaaggaa aaagagaaag
      721 acttcatatg actcaaaaag agtttgcaga cgcccttggt ctttcaaaat atggagacag
      781 aaccataaga agatgggagc gcggggaaac aaaacctact ggggcggaac taaaagcagt
      841 tatggacttt ccagacacac caccttaccc aaacaacgag aatggcagat atcgcatgat
      901 cgatttattt gctggaatcg gtggaaccag acttggattt catcaaacta acgctgtaaa
      961 tgttgttttt tccagcgaat gggataagtt tgctcaaaag acatatcatg caaattatgg
     1021 tgatttccct gatggggaca taacaaaaat cgatgaaaaa gatattcctg atcatgaaat
     1081 tcttgtcggt gggtttcctt gcgtagcatt ctctcaagca gggctcaaaa aaggatttaa
     1141 tgatacaaga ggaactttgt tttttgatat agcaaggata ataaaggaaa aaaaacctca
     1201 tgctttttta cttgaaaatg taaaaaactt gctaggacat gataaaggta gaactttttc
     1261 aataataaaa aacacacttg aagaattgaa ttacactgtg tattacaata tcttcgctgc
     1321 aaaagacttt ggtgttccac aaaatagaga acgcatatac attgtaggct ttaataaaga
     1381 aaaagtaaga aatcatgaac attttacttt tccaacccca ttaaaaacaa aaacaagagt
     1441 tggagatatt cttgaaaaga gcgtagacaa taaatatacg ctatcagatg cgctctggaa
     1501 tggacaccaa cgcaggaaac ttgtaaatgc agcagccggt aaaggctttg ggtatggttt
     1561 atttaatgaa aatagcccat atactaatac cataagtgcg aggtactata aagatggtag
     1621 cgaaatatta atagagcaaa aaggaagtaa cccaagaaaa ataactccgc gggaagcgtc
     1681 aagacttcaa gggtttccta gtgattttat tatccctgta tcggatacac aggcttataa
     1741 gcaatttggg aattcagtcg cagtccctgt tatcaatgca atagcagaaa aaatcatatc
     1801 gaccttagat tcataaacta agtcataagg acacaatgcg gcccagaatc caattccccc
     1861 ccatatggat ttaccataac gtcgcattac acgcaccgct aaaacgcgtt cagcgcgatc
     1921 acggcagcag acaggtaaaa atggcaacaa accacccgaa aaactgccgc gatcgcgcct
     1981 gataaatttt aaccgcatga atacctatgc aaccagatgg tacaggccac attaacccct
     2041 cttaatccac tgaagctgcc atttttcatg gtttcaccat cccagcgaag gaccatccag
     2101 cgtgcgttcc tgtatttccg gctgacgctc ccgttccagg gataacgcat gttcgcgctc
     2161 ctgtatcagc cgtgcctctc ttatctccag ttctcgctgt ataactggct caagcgttct
     2221 gtctgctcgc tcaagcgttc tgtctgctcg ctcaagtgct gcacctgctg actcaactgc
     2281 atgacccgct cgttcagcat cgcgttgtcc cgttgcgtaa gcgaaaacat cttctgcaat
     2341 tccacgaagg cgctctccca ttcgctcagc cgctgcatat agtcctgttg cagctgctct
     2401 aaggcgttca gcaaatgtat ttccagctct gtcactctga gtcactcctt cagatgtacc
     2461 cactctttcc cctgaaaggg aatcacctcc gctgatttcc cgtacggaag gacaaggaat
     2521 ttcctgttcc cgtcctgcac aaactccacg ccccatgtct tcgcgttcag tttctgcaat
     2581 gtctcttcct gcttcctgat ttcttccagg ttcgtctgta tccgtccgcc aagataccag
     2641 agcgtcccgc cactcgcggt aaacaggaga aagactatcc ccagtaacat catgcccgta
     2701 ttccctgcca gctttaacac gtccttcctg tgctgcatca tcgcctcttt caccccttcc
     2761 cggtgttttt ccagcgattt ctctgtcgag gctgtgaaca gggctatagc gtctctgatt
     2821 ttcgtctcgt ttgaggtcac agcctcgctg acagactcgc cgagcttcct gaactcgtcg
     2881 ttcagcattt tctctgtaga ttcggctctc tctttcagct ttttctcgaa ctccgcgccc
     2941 gtctgtaaaa gattgctcat aaaacgctcc tttcagtctg atattcctcc cgccgttcgg
     3001 gtctgcaatg ctgatactgc ttcgcgtcac cctgaccact tcaagccccg cctctgtgag
     3061 cgcctgaatc acatcctgac gtccttttat ctctccggca tggtaaagtg cgtctatacc
     3121 gcatgtaacg ctctcagcaa gtgcctgttt cgtttccggc aggttatcag gaagggtcag
     3181 cgtccggcgg ttctccgggg cgttggggtc atgcagtccg taatggtgat tcaccagcgt
     3241 ctgccaggca tcaattctcg gcctgtctgc gcggtcgtag tacggctgga gacgttttcc
     3301 ggtctgtagc tccatgttcg gaatgacaaa attcagctca agccgtccct tgtcctggtg
     3361 ctccacccac aggatgctgt actgattttt ttcgagaccg ggcatcagta cacgctcaaa
     3421 gctcgccatc actttttcac gtcctcccgg cggcagctcc ttctccgcga acgacagaac
     3481 accggacgtg tatttcttcg caaatggcgt ggcatcgatg agttcccgga cttcttccgg
     3541 attaccctga agcaccgttg cgccttcgcg gttacgctcc ctccccagca ggtaatcaac
     3601 cggaccactg ccaccacctt ttcccctggc atgaaattta actatcatcc cgcgccccct
     3661 gttccctgac ggccagacgc agccggcgca gctcatcccc gatggccatc agtgcggcca
     3721 ctacctgaac ccggtcaccg gaagaccact gcccgctgtt caccttacgg gctgtctgat
     3781 tcaggttatt tccgatggcg gccagctgac gcagtaacgg cggtgccagt gtcggcagtt
     3841 tcccggaacg ggcaaccggc tctcccaggc agacccgccg catccatacc gccagttgtt
     3901 taccctcaca gcgttcaagt aacctggcat gttcatcatc agtaacccgt atcgtgagca
     3961 tcctctcgcg tttcatcggt atcattaccc catgaacaga aatccccctt acacggaggc
     4021 atcagtgact aaacaggaaa aaacagccct taacatggcg cgctttatca gaagccagac
     4081 attaacgctg ctggaaaagc tcaacgaact ggacgcggat gaacaggcag acatctgtga
     4141 atcgcttcac gaccacgccg atgagcttta ccgcagctgc ctcgcacgtt tcggggatga
     4201 cggtgaaaac ctctgacaca tgcagctccc ggagacggtc acagcttgtc tgtgagcgga
     4261 tgccgggagc agacaagccc gtcaggacgc gtcagcaggt tttagggggt gtcggggcgc
     4321 agccctgacc cagtcacgta gcgatagcgg agtgtatact ggcttaacta tgcggcatca
     4381 gtgcggattg tatgaaaagc acgccatgtc gggtgtgaaa tgccgcacag atgcgtaagg
     4441 agaacatacc gcatcaggcg ctcttccgct tcctcgctca ctgactcgct gcgctcggtc
     4501 gttcggctgc ggcaagcggt gccggctcac tcaaaggcgg aaatacggtt atccacagaa
     4561 tcaggggata aggccggaaa gaacatgtga gtaaaaaggc aaagggcaac aaaaggccgc
     4621 gccgctggcg tttttccata ggctccgccc ccctgacgag catcacaaaa atcgacgctc
     4681 aagtcagagg tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctggaag
     4741 ctccctcgtg cgctctcctg ttccgaccct gccgcttacc ggatacctgt ccgcctttct
     4801 cccttcggga agcgtggcgc tttctcatag ctcacgctgt tggtatctcg gcccggtgta
     4861 ggtcgttcgc tccaagctgg gctgtgtgca cgaacccccc gttcagcccg accgctgcgc
     4921 cttatccggt aactatcgtc ttgagtccaa cccagtaaga cacgccttaa cgccactggc
     4981 agcagccact ggtaaccgga ttagcagagc gagatttatc cagatgctta cagagttctt
     5041 gaagtgatgg cctaactacg gctacactgg aaggacagta tttggtatct gtgctctgct
     5101 gaagccagat tacctcggtt agataatctg ccaggattag ctaaccttcg aaaaaaccac
     5161 ctgccagggt ggtttttttc gtttacaggt ccaagattac gcgcagaaaa aaaggatctc
     5221 aagagatcct tttagttttt tagtcaaaaa gagcactaag cctatttcta taataattaa
     5281 caacataagg gaaatcacta tatttttcta tttgttttaa tattgactgt tgaatttcct
     5341 ctttttcaga gtctgtgtaa cttacattat tccactttct tgataattcc attgctgact
     5401 gtagcatatc ttcaaaggtt agcaccctat tattattttt atatttgaaa tttttatttt
     5461 ctatcgtcgt tacaacgacc acattagcct cgtataatat atttattgtc tcctcgctaa
     5521 aagaatcatc tagtgtagct agatacattt ctctaatacc tgttctatta acctcttcag
     5581 gtacttcttg
//
