LOCUS       NZ_CP122466             4018 bp    DNA     circular CON 30-MAY-2024
DEFINITION  Klebsiella pneumoniae subsp. pneumoniae strain IITJ_U23 plasmid
            pU23UNK1, complete sequence.
ACCESSION   NZ_CP122466
VERSION     NZ_CP122466.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN34035886
            Assembly: GCF_029834625.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae subsp. pneumoniae
  ORGANISM  Klebsiella pneumoniae subsp. pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4018)
  AUTHORS   Chakrabortty,A., Kapoor,A., Khochare,S., Dey,T., Arora,L., Tak,V.,
            Nag,V.L., Sivashanmugam,K. and Shankar,M.
  TITLE     Genome sequence of two ST16 strains causing ICU-acquired infections
            in Jodhpur India
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4018)
  AUTHORS   Chakrabortty,A., Kapoor,A., Khochare,S., Dey,T., Arora,L., Tak,V.,
            Nag,V.L., Sivashanmugam,K. and Shankar,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-APR-2023) Department of Bioscience & Bioengineering,
            Indian Institute of Technology Jodhpur, NH65, Nagaur Road, Karwar,
            Jodhpur, Rajasthan 342030, India
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Assembly Name                     :: IITJ_GMPL_KpnU23v1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 166x
            Sequencing Technology :: Illumina NovaSeq and Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_029834625.1-RS_2024_05_30
            Annotation Date                   :: 05/30/2024 05:01:51
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,816
            CDSs (total)                      :: 5,681
            Genes (coding)                    :: 5,520
            CDSs (with protein)               :: 5,520
            Genes (RNA)                       :: 135
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 95
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 161
            CDSs (without protein)            :: 161
            Pseudo Genes (ambiguous residues) :: 0 of 161
            Pseudo Genes (frameshifted)       :: 70 of 161
            Pseudo Genes (incomplete)         :: 90 of 161
            Pseudo Genes (internal stop)      :: 17 of 161
            Pseudo Genes (multiple problems)  :: 15 of 161
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122466.1.
            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..4018
                     /organism="Klebsiella pneumoniae subsp. pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="IITJ_U23"
                     /isolation_source="Urine of ICU admitted patient"
                     /host="Homo sapiens"
                     /sub_species="pneumoniae"
                     /db_xref="taxon:72407"
                     /plasmid="pU23UNK1"
                     /geo_loc_name="India: Jodhpur"
                     /collection_date="2020-08-02"
                     /collected_by="AIIMS Jodhpur"
                     /identified_by="Prof. Vijaya Lakshmi Nag"
     gene            complement(join(3812..4018,1..9))
                     /locus_tag="P9M41_RS28995"
                     /old_locus_tag="P9M41_28995"
     CDS             complement(join(3812..4018,1..9))
                     /locus_tag="P9M41_RS28995"
                     /old_locus_tag="P9M41_28995"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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_072048928.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSDQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(13..498)
                     /locus_tag="P9M41_RS29000"
                     /old_locus_tag="P9M41_29000"
     CDS             complement(13..498)
                     /locus_tag="P9M41_RS29000"
                     /old_locus_tag="P9M41_29000"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /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_061390563.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMISQTWLTIVLVSALLIASSAGILWWQGQQIL
                     DNYTTIQEQKSTQAMLSEKNNGVQLTTCGEERRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(<533..1237)
                     /locus_tag="P9M41_RS29125"
                     /pseudo=""
     CDS             complement(<533..1237)
                     /locus_tag="P9M41_RS29125"
                     /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(1176..1499)
                     /locus_tag="P9M41_RS29010"
                     /old_locus_tag="P9M41_29010"
     CDS             complement(1176..1499)
                     /locus_tag="P9M41_RS29010"
                     /old_locus_tag="P9M41_29010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_024191642.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQICLDEKPSRAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGTGHDRVQVVAVLMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2147..2260
                     /locus_tag="P9M41_RS29130"
     CDS             2147..2260
                     /locus_tag="P9M41_RS29130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_072035093.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPERHDKTPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(2689..2901)
                     /locus_tag="P9M41_RS29015"
                     /old_locus_tag="P9M41_29015"
     CDS             complement(2689..2901)
                     /locus_tag="P9M41_RS29015"
                     /old_locus_tag="P9M41_29015"
                     /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_034169353.1"
                     /translation="MGDFERTFGAGADFDRIIDENNSEYFREDRRKTKNSKKKFSSFQD
                     ALVWAKANPGKTIIRSPDGVGFIEK"
                     /name="hypothetical protein"
     gene            complement(3156..3683)
                     /locus_tag="P9M41_RS29020"
                     /old_locus_tag="P9M41_29020"
     CDS             complement(3156..3683)
                     /locus_tag="P9M41_RS29020"
                     /old_locus_tag="P9M41_29020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004883515.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_016246513.1"
                     /translation="MKCFWACSVSVVLAMSFTVAAAENNDNVTYTKPSAGRDLYLTCKG
                     YQVKGASVINVEKPSYLEGTGEQVEFAIITPVGASDGLKVFFDSWGFSSFGLIESHVMH
                     EHWSLVHVGGRASVKGEKIDYSFVDNQPQEGGSYKPKTGVFLYGCMNSDKRPSWVEKIY
                     TRTGVFRGGIED"
                     /name="hypothetical protein"
     Typing          complement(1613..1790)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.222"
                     /coverage="83.0"
                     /evalue="4.5e-50"
     Typing          1737..2260
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.434"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3..1186)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.405"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ttccgtcatg tgctatttcc ccgccagtat catccagctc gaatcctctc cgaatcttcc
       61 cgcttccggg ttcaccctca cgcagcggcg tctctcctcc ccgcaggtcg tgagctggac
      121 gccgttgttc ttctctgaaa gcatggcctg cgtgctcttc tgttcctgga tggtcgtgta
      181 gttgtcgagt atctgttgcc cctgccacca cagaatgccc gcgctcgagg cgatcagtag
      241 cgcggagacc aggactatgg tcagccacgt ctggctgatc atacgcagca tccctttcgt
      301 gcgttggctc atggctgagg acagcttccg gtcgtggtcg aggatggcgg cgctgattct
      361 cttctcgctt tcgctcagtt ccgctctgac agacttctcg tgctcgctga atgcggcttt
      421 cagcatctcg ccggtagtct gctgctgcgc tttcgatttc tgctctaagt ccttcgccag
      481 cgttaaaaga ctgttcatag atggctccct tcagtcggat gtttcgcccc ccgtcagggt
      541 cggcaatgct gatgctgctt ttcgtggtgc gcaccacctc aaaacccgca ctttccagcg
      601 cctcagtgac gtcctgacgg gttttcagct ccccggatga ggcaagggaa agtaggccgc
      661 gcgtaatcgc ctgggcggct tcctgcttcg cttccggcag cgcggacggt gtaaccagcg
      721 cccgccggtt ttccggcgcg ttcgggtcgt gcagccccag tctgccgttc actatggtct
      781 gccaggcatc aatgcgcgga cggtcggcgc ggtcgtaata cggctggaga cgtctgccgg
      841 tcagcagctc cgtgttcggg atcaggaagt tcagctccag ccgccctttg tcccggtgct
      901 caacccacag tacgctgtac tggtctttat cgagtccggg catcagaacc cgctcaaagc
      961 tcgccatcag cttttcacgc tggccgggcg gcaaatcctg ttcggcaaaa gacagcacgc
     1021 cggaggtgta tttcttggcg taaggcgagg cgtcagtaag ctcccgcact tcctccggct
     1081 taccctgcag aacgctggcg ccgtcgcgct gccggtcttt ccccagcaga taatccaccg
     1141 gaccgccgcc accgccgcgg cctctgggat gaaacttaac gatcatcgtc tgcccccttt
     1201 tccagcacgg cgtgccgcag ccgctcgagt ccggcatcaa tggccatcag cacggcgaca
     1261 acctgcacgc gatcgtgccc agtaccgcca ccggcgttaa cctgccgggc aatctggttg
     1321 aggttgttac ccatgccggc aagctgacga agcagcgccg gcgagatgga tggaagtttg
     1381 ccagcacgcg agggcttttc gtccaggcat atctggcgca tccaggccgc gagttgttta
     1441 ccctcacagc gctccagaag tcggcggtgc tcgtcttctg tcacccacat agtgagcatt
     1501 ttgttgcgct tttctgccaa accatcctcc ggataacacc ggttcgggcg ggaaattttt
     1561 tcctgtccgg agcggtgttg ggcaagcccg cagggcgcgg cagtactttt cagcgggttt
     1621 cggggcgcag ccctgaacca gtcacgtagc gctagcggag tgtatactgg cttaacatgg
     1681 taaatcggag tggggattca ggaaagtgct tcatgtggca gggagaaaat gctgctgtgg
     1741 ggcgtaagtg cgaaatgcag atcccggtga aatgacgcct cctcgctcac tcggtcgctg
     1801 cgctcctgcc gtgagactgc ggcgggcgtt gccagcttac gaatggctgg ataaagagac
     1861 taagcggaaa tcaatcagaa agggcggaaa aaggatgcgg cgttgccgtt tttccatagg
     1921 ctccgccccc ctgacaagca tcacgaaatc tgacgctcaa atcagtggtg gcgaaacccg
     1981 acaggactat aaagatccca ggcgtttccc cctggtagct ccctcgtgcg ctctcctgtt
     2041 cctgcctttc ggtttaccgg tgtcattccg ctgttatggc cgcgtttatc taattccacg
     2101 cctgacactc agttccgggt aggcagttcg ctccaagctg gactgtatgc acgaaccccc
     2161 cgttcagtcc gaccgctgcg ccttatccgg taactatcga cttgagtcca acccggaaag
     2221 acacgacaaa acgccactgg cagcagccac tggtaactga tttagaggag ttagtcttga
     2281 agttatgcgc cggttaaggc taaactgaaa ggacaagttt tggtgactgt gctcctccaa
     2341 gccagttacc tcggttcaaa gagttgctgc tctgagaacc ttcgaaaaaa ccgccttgct
     2401 gggcggtttt ttcgtttaca gtgctaagag attacgattc tccatgaatg atctcaagaa
     2461 gatccgttta aaaaagcggg ttttatgggg ggataaagtt cgtctagccc agtcactttg
     2521 gattacagct aggtttcgta agccatgcaa gaatgcctgt aactaacaaa ataggccctg
     2581 caacgtacgt aacatagact ccaacatacg acactgtgaa acatatgagt acgtatatag
     2641 acagtgttgt ccaaaaaatg actgttgttt tacagtgaat ccactctttc atttttcaat
     2701 aaaccccaca ccgtctggag atcttattat cgttttgcca ggattagctt tcgcccaaac
     2761 caaagcatct tgaaaagaag agaatttttt ttttgaattt ttagtttttc ggcgatcttc
     2821 tcgaaaatat tcgctgttat tctcatcaat tatccgatca aaatcagcac cagctccaaa
     2881 ggtacgctca aaatccccca ttttctgccc ccattaaatt taataaaaaa acagatttaa
     2941 aatatccaaa agacactctt atttaccata acatcccttg ttcgcaccgc cgcagacagc
     3001 ctcagcaccg ttctgcgcca tgaaccgcaa aagagcacct cttaccacgt aaaaacgccg
     3061 ataaatgccc cccgtaagtt cttacggtat gcatagttat gcacggaaat gaactgacac
     3121 tctgttcaat ggattttcat gctgtaagca gtattttagt cttctatgcc ccctcgaaac
     3181 acacctgttc ttgtgtagat cttttcgacc caagatggtc ttttatccga gttcatgcag
     3241 ccgtacagga acacacctgt tttgggttta tagctccccc cctcctgtgg ctggttatct
     3301 acaaatgaat aatcaatctt ttcacctttg actgaagcac gccccccaac atgaactaaa
     3361 gaccagtgct catgcatcac atggctttca atcaatccaa atgaagaaaa accccatgaa
     3421 tcaaaaaaga ccttgagtcc gtcagacgca ccaacaggag taatgattgc aaattcaacc
     3481 tgctcaccag taccttcaag gtaagaaggt ttctcgacgt taattacaga tgcccccttc
     3541 acctgataac ctttacaggt aagatataag tccctcccgg ctgacggttt tgtatatgta
     3601 acgttgtcgt tattctccgc agcagcgact gtaaatgaca tagccaaaac caccgagact
     3661 gagcaagccc agaaacattt cataacgcat cccttttcat tgattaacta cattccaagc
     3721 tcaaaacctt tctgccgctg cgatcgttcc agctccagcg ctttctggtg ctgcgccgcg
     3781 cgctcctgct cccggtgcgc ctcgatgcca ttcagccttg cgacaatcgg cgcagctgat
     3841 cgctcaaact ctgcacctgc ctgctcaagc ccgtgacgcg ctcgctcagc gccgcgttct
     3901 cccgttgcat aagcccagac atcgtccgcc attccgcgaa ggcgttctcc cactcgtcca
     3961 gccttttcga gtagtcctgc tgtagctgct ctaatgcgct cagcaactgt ttttccag
//
