LOCUS       NZ_CP089004             4167 bp    DNA     circular CON 12-FEB-2024
DEFINITION  Klebsiella pneumoniae strain 56661 plasmid p56661-4.167, complete
            sequence.
ACCESSION   NZ_CP089004
VERSION     NZ_CP089004.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN23552368
            Assembly: GCF_021166135.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4167)
  AUTHORS   Chen,L., Hao,M., Lin,Y. and Kreiswirth,B.
  TITLE     Whole genome sequencing of K. pneumoniae isolates
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4167)
  AUTHORS   Chen,L., Hao,M., Lin,Y. and Kreiswirth,B.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-DEC-2021) HMH-CDI, Hackensack-Meridian Health Center
            for Discovery and Innovation, 111 Ideation Way, Nutley, NJ 07110,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-SEP-2021
            Assembly Method                   :: Unicycler v. v0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Oxford Nanopore MiniION and Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/12/2024 03:45:38
            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)                     :: 5,968
            CDSs (total)                      :: 5,844
            Genes (coding)                    :: 5,674
            CDSs (with protein)               :: 5,674
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 170
            CDSs (without protein)            :: 170
            Pseudo Genes (ambiguous residues) :: 0 of 170
            Pseudo Genes (frameshifted)       :: 70 of 170
            Pseudo Genes (incomplete)         :: 104 of 170
            Pseudo Genes (internal stop)      :: 30 of 170
            Pseudo Genes (multiple problems)  :: 31 of 170
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP089004.1.
            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="56661"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="p56661-4.167"
                     /geo_loc_name="Russia"
     gene            306..548
                     /locus_tag="LRZ77_RS26370"
                     /old_locus_tag="LRZ77_26370"
     CDS             306..548
                     /locus_tag="LRZ77_RS26370"
                     /old_locus_tag="LRZ77_26370"
                     /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(894..1295)
                     /locus_tag="LRZ77_RS26375"
                     /old_locus_tag="LRZ77_26375"
     CDS             complement(894..1295)
                     /locus_tag="LRZ77_RS26375"
                     /old_locus_tag="LRZ77_26375"
                     /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(1295..1486)
                     /locus_tag="LRZ77_RS26380"
                     /old_locus_tag="LRZ77_26380"
     CDS             complement(1295..1486)
                     /locus_tag="LRZ77_RS26380"
                     /old_locus_tag="LRZ77_26380"
                     /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            1902..2015
                     /locus_tag="LRZ77_RS26385"
                     /old_locus_tag="LRZ77_26385"
                     /pseudo=""
     CDS             1902..2015
                     /locus_tag="LRZ77_RS26385"
                     /old_locus_tag="LRZ77_26385"
                     /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            2360..3475
                     /locus_tag="LRZ77_RS26390"
                     /old_locus_tag="LRZ77_26390"
     CDS             2360..3475
                     /locus_tag="LRZ77_RS26390"
                     /old_locus_tag="LRZ77_26390"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019405083.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0016887 - ATP hydrolysis activity [Evidence IEA]"
                     /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            3475..4107
                     /locus_tag="LRZ77_RS26395"
                     /old_locus_tag="LRZ77_26395"
     CDS             3475..4107
                     /locus_tag="LRZ77_RS26395"
                     /old_locus_tag="LRZ77_26395"
                     /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          1608..2015
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.399"
                     /coverage="99.0"
                     /evalue="5.92e-171"
ORIGIN
        1 ataacgtata gaaagcatca tacactttag ttatcagcaa tctcaaacgt cctaaagaca
       61 tcaccagatg ccaaaacaat gattgtgcag atctaatgta aaagacccag cacaagatgc
      121 tcccttaagt tatattctct ctattcactt aaaacaattt aacataaaat cataattgta
      181 cgcaccgcta aaacggactc aggacgtttc tgacgggaaa ccggtaaaac aggcaacaaa
      241 ccacccgaaa acccgccaga aacgcgcagg ctctgttttt acggcatgca tgagtatgcg
      301 cgcaagtgca tagcgcggaa attcacacca ttcagccagg ggaagtcctg tttccggcgt
      361 tcttctcctc cgaaaacggt gaacggggac gcaatttatt gcgtggccgt gaagcgttgc
      421 cggcgcagcc ggaaaaccgg ttttcagcac cttcaggaat cgggttcgtc gacggccggc
      481 aatcacgtta tggcaagtcg ccggacgact caccacacga ttcaccggcg attcgaatcg
      541 tgaattgaat caagagtcac catgagcaaa aaacacccaa agtgatgaat tgaatcaaga
      601 gtcgattcat cataacaata tgataataaa gcgtgattca catatgaatc gtgggcaatt
      661 cgtcagcgat tcgccataga gtcgtccacg acttggatct gcactttgta acacatcacc
      721 gcacatttat ttttcattaa cccattgttg taaataagga atctgcaaaa ttttaatttt
      781 gcgtggggtg tgggtatttt tagtggtgag gagcgttcag agatctgacg atttttggga
      841 aggttcagga actccctggg atggccggag aggaaaactg aagcatgacg gggtcaggat
      901 tttttccaga atttccacca tggcgccggg gattcagtta attttgcctg gtgattttca
      961 agaaggagca tggcctgttt caggctgtca atgtgcgaat ccttggacaa aagtaaggtg
     1021 ttcaggtgtt caatctcctg tttcagatga cggatcacct gttcactctg gtcagcagag
     1081 gctgtatcac gctgtccaga gacctgtcca gaatggtgtt cacccttcgg ttgctcaaag
     1141 gggccaaaga cacgtaaaag ctctgaagta tctaccattt ttgcattgcg ctcaccgcta
     1201 caggtggaca ggtcacctgc tttaattaac ctgtgcagtg ttgttctact cttacccgtc
     1261 agtcgggcag cctcactaat agacactctg gccatcagtt accatcctgt aatgcatcca
     1321 gtctcgagga cagtgtacgg aaaagatgct ccgcatcatc gtggagtttc tcacaaaggt
     1381 cggcctcgac atcgagatca agctcgttaa gcttctccag caggagcaga gactgattct
     1441 ggatgaattt agccatgttc agcgctgttt tctgttgttt cgtcataaga ggcctcagag
     1501 cgtcagtggt cagtgtaggg atctcctctt ttccgcttcc tcgctcactc agtcgctacg
     1561 ctcctgccgt tcggctgcgg cgagcggcag gagcatgcgt agaaacgctc gagaaaaccg
     1621 agtaatcgca tggaggaaag aaggaaaggc cgcacagcgg ccgtttttcc ataggctccg
     1681 cccccctgac gagcatcacg gaatctgacg ctcaaatcag tggtggcgaa acccgacagg
     1741 actataaaga taccaggcgt ttccccctga tggctccctc gtgcgctctc ctgttcctgc
     1801 ctttcggttt accggtgtca ttccgctgtt atggccgcgt ttgtctcatt ccacgcctga
     1861 cactcagttc cgggtaggca gttcgctcca agctggactg tatgcacgaa ccccccgttc
     1921 agtccgactg ctgcgcctaa tccggtaact atcgtcttga gtccaacccg gaaagacacg
     1981 acaaagcgcc actggcagca gccactggta actgatttag ggagttagtc ttgaagttat
     2041 acgccagtta aagctaaact aaacgaacag ttttggtgac tgcgctccct ttaagccagt
     2101 tacctcggtt catagagcgc caactctact gaacctttcg aaaaaaccgc ccgccaaggc
     2161 ggtttttttc gttcacagcc ggaagcttac ggctgctgcc agataatctc aagaagaaag
     2221 taaaaaaaat cgattaaaac acaagcaatc aaagttaatc tttgacataa agtctagcta
     2281 atcacaatga aagctgtaca ttttattaag gtactaacaa atcgtatggc atataacaaa
     2341 aacacgaaca gaggctatca tgataaagga aataagttta aagaacttca aatgcttcaa
     2401 tgagctatat ctaaagcaat taaagacttt aaatatcata gctgggaaaa acaactacgg
     2461 gaaaacatct atactggatg ctattttttg tttttatgat gtaaaaaacc cggctgtttt
     2521 gttaaacatt caagcattca gaaaagaaat ggcagaaata aacaaaaaca agccattttg
     2581 ggttagttac tttcatgata tggacacatc acaaaagatg tccatagtca ttcgagatga
     2641 acgctctgaa gtaacacaaa catatgaaac agaaacaaat cagagattag aatcaagttt
     2701 gtctctaaac gttgacaccg tactatctaa ccaaaacata cctcgtcaaa ctatcggttc
     2761 tcaggccaca gtaaactctt taaaaataaa tgtgaccgag acacccaatg cgaaaaacag
     2821 ggtttccaat aagcttttct ctatgcaatt gaaagaagat ggcgtagaaa taaaatccga
     2881 aataaaaaac gaaagggatg ggattaatta taaatttaag acagcaacaa taataacaac
     2941 atccagaaag ataaacaaag aggcaacaat tacaaatgta tctagcctac taacacaaaa
     3001 aaggaaaaaa gacatactag aaaacttaaa aaaaatagat gacagaattg tagatatagc
     3061 aatatctgcg ataggtaaca ataaggaaat atatttagac attggattta gtgagctaaa
     3121 tgaaatatca atgcttggcg agggtatcag tcgagcatta tcttttatca gctcagtgct
     3181 ggtacaggaa aactcaatta ttcttattga tgaaatcgag aacggaatac attactcagt
     3241 aattaaagac ataataaaat cattaatttc atctgcaaaa caaaacaaca atcaaatatt
     3301 tgcaacaact catagtcaag atgtgatacg agcaataaac gaaatagata gcaaaaatga
     3361 agatatcgct tatattagac taggaagaga aaagaactcc ctaaaaccaa cagccgtaca
     3421 attcaatatg gatgatttct cctactcagt tgagaacgac tgggaggtaa gataatgaaa
     3481 gacataaata atagcaaaaa gatcattttc gttgagggtg atgatgattt tcattttcta
     3541 tgcaacctac ttgaaataca aggcattacc gatgtttttg tcgaaaaaat aaatggaaaa
     3601 tcaaaattaa aacaagcact tagagcattc aaaaacattg attctttcga tgaaaaagaa
     3661 agtattttta ttatattaga tgctgacaca tcattttctg acacagaaag atcaataatt
     3721 gccacattgc gagaactaca aatctcctcc cccagctcgc ataacgagat agctatgaat
     3781 ggcaatacaa aaatttcttt ctttataatg ccaggaaaag acaagcaagg tgccattgaa
     3841 gatctgataa ttgaacacgc aagcactcga gcgttatatg aatacataat agaatttttc
     3901 gaaaaaatta aaaataataa agatgacatc tcagcgagtg acaaagagta cacttatcca
     3961 acaaacgaaa aaaaagctaa ggtacaagtc tatcttagct gcaatagaga atccgactca
     4021 agaataggaa tatccatgaa aaatggaata ataaacacag cagacaattg ctttgatgaa
     4081 ataaaagatt ttatttcaaa aatataaatc caaatcaagc cagcccttca cgggctggct
     4141 tatcaccagg gtgttattaa acgccgg
//
