LOCUS       NZ_CP097414             3991 bp    DNA     circular CON 16-JUN-2024
DEFINITION  Klebsiella pneumoniae strain K165-2 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP097414
VERSION     NZ_CP097414.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28404993
            Assembly: GCF_023538935.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3991)
  AUTHORS   DelaFuente,J., Toribio-Celestino,L., Santos-Lopez,A.,
            Leon-Sampedro,R., Alonso-del Valle,A., Costas,C., Cui,L.,
            Rodriguez-Beltran,J., Bikard,D., Canton,R. and San Millan,A.
  TITLE     Within-patient evolution of plasmid-mediated antimicrobial
            resistance
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3991)
  AUTHORS   DelaFuente,J., Toribio-Celestino,L., Santos-Lopez,A.,
            Leon-Sampedro,R., Alonso-del Valle,A., Costas,C., Cui,L.,
            Rodriguez-Beltran,J., Bikard,D., Canton,R. and San Millan,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (16-MAY-2022) Microbial Biotechnology, Centro Nacional de
            Biotecnologia-CSIC, Darwin, 3, Madrid 28049, Spain
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Oxford Nanopore; Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023538935.1-RS_2024_06_16
            Annotation Date                   :: 06/16/2024 05:37:10
            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)                     :: 5,559
            CDSs (total)                      :: 5,435
            Genes (coding)                    :: 5,320
            CDSs (with protein)               :: 5,320
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 115
            CDSs (without protein)            :: 115
            Pseudo Genes (ambiguous residues) :: 0 of 115
            Pseudo Genes (frameshifted)       :: 51 of 115
            Pseudo Genes (incomplete)         :: 65 of 115
            Pseudo Genes (internal stop)      :: 16 of 115
            Pseudo Genes (multiple problems)  :: 15 of 115
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP097414.1.
            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..3991
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="K165-2"
                     /isolation_source="Human gut"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /plasmid="unnamed3"
                     /geo_loc_name="Spain: Madrid"
                     /lat_lon="40.48 N 3.69 W"
                     /collection_date="2014-03-04/2016-03-31"
                     /collected_by="Ramon y Cajal Health Research Institute
                     (IRYCIS)"
     gene            complement(join(3540..3991,1..523))
                     /locus_tag="M8Y69_RS27685"
                     /old_locus_tag="M8Y69_27685"
     CDS             complement(join(3540..3991,1..523))
                     /locus_tag="M8Y69_RS27685"
                     /old_locus_tag="M8Y69_27685"
                     /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_114269875.1"
                     /translation="MAFFNLLFVASLICFGGVMGSYSRGCRDSQNKFSKDKDENNKRAS
                     VYRFGIASAFICVPFISSFLHVDYSSIIFPVADGGGTKFIEQILLLISVSGISAYLGYA
                     LLDGLANKVLKEQVDGIDKKQQDLEAEQDEFKDELDRSKELIEQLEMDKKTTKFELGYF
                     KAISAVDKAESMMSIPDEALSVKKKLTEALDAVTESLSLVKREDVAKDDYDKLLVLKAY
                     ILKRLDRIDDALSITDELLMSNEDNPILIYNKACYQYILRRCQADNSDIKDMIRRALTI
                     KVTDPEFIRRQEKIRTKVIGNKDNDLEGLFTDAELEELKVAIK"
                     /name="hypothetical protein"
     gene            complement(1104..1376)
                     /locus_tag="M8Y69_RS27690"
                     /old_locus_tag="M8Y69_27690"
     CDS             complement(1104..1376)
                     /locus_tag="M8Y69_RS27690"
                     /old_locus_tag="M8Y69_27690"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004897311.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_019405140.1"
                     /translation="MATDAQVKEINALIKKYPDSCSICHEVYDEDDVTYTVFGYDRKGK
                     IQVTTGCCAGMLTEPVLLGVCGCFDPEERDEIMQNHPMAKQFFTE"
                     /name="hypothetical protein"
     gene            complement(2180..2602)
                     /locus_tag="M8Y69_RS27695"
                     /old_locus_tag="M8Y69_27695"
     CDS             complement(2180..2602)
                     /locus_tag="M8Y69_RS27695"
                     /old_locus_tag="M8Y69_27695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /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_040214596.1"
                     /translation="MAIVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKAIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(2602..2793)
                     /locus_tag="M8Y69_RS27700"
                     /old_locus_tag="M8Y69_27700"
     CDS             complement(2602..2793)
                     /locus_tag="M8Y69_RS27700"
                     /old_locus_tag="M8Y69_27700"
                     /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_040198051.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLDKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3201..3313
                     /locus_tag="M8Y69_RS27705"
                     /old_locus_tag="M8Y69_27705"
                     /pseudo=""
     CDS             3201..3313
                     /locus_tag="M8Y69_RS27705"
                     /old_locus_tag="M8Y69_27705"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="frameshifted; 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"
     Typing          2842..3313
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.777"
                     /coverage="92.0"
                     /evalue="7.8799999999999974e-146"
ORIGIN
        1 ttgattctgc tttatccaca gctgaaatgg ctttaaagta tcctagctcg aattttgttg
       61 ttttcttatc catttcaagc tgttctatca gctccttgct cctatcaagc tcatctttaa
      121 actcatcttg ttcagcctcc aaatcttgtt gctttttatc tataccgtct acttgctctt
      181 ttaatacttt gttggcaaga ccatccagta atgcgtaccc aagatacgca gagatccccg
      241 aaacagaaat aagaagcaat atttgttcta tgaacttagt tccaccacca tcagccacag
      301 gaaatattat acttgagtaa tcaacatgaa gaaatgatga tatgaaagga acacaaataa
      361 atgcggatgc tataccaaat ctataaacac tagctctttt attattctca tccttatctt
      421 ttgaaaattt attttgggag tctcggcaac ctctggaata gctccccata acaccaccaa
      481 aacaaattag agatgcaaca aacaataggt taaaaaaagc catgagagaa tccttgcgca
      541 aagcaaacaa taaaactttg ttcaggtaag ttaagataag ctcaatcata tactaaccaa
      601 taacaaaaaa ggcagccttg gctgcctttt tctgctgact tgacacttac aagtctggac
      661 gctcatcgtg aagtttgatt tttttcatag agcacctctc attaattgtt cctttgcaag
      721 cccatgcttg cttagcgctg aatatagggc ataaacccag cactcacaac aacaaaaatg
      781 cttaaaatga taaaatcaac ccatgtattg acattgggtg aaaaaaaaag tataatgcac
      841 tggtagccaa aggggcgggg cttcgcttat tccttaggaa taagcgaagc cccgcccctt
      901 tggctaccat aattaaatga ttgaatttaa aggatttttt tacaataaca tccttcctct
      961 caatagtcat ataaacatgc cccatgtatt cgtcattctg gatttttcaa aagaatgaat
     1021 gcgtgcattt accataacgc ctcatttcac gcagatatga aaaagcccgc acaaggcggg
     1081 cttcagactc aacagatacg gaatcactct gtgaaaaact gctttgccat ggggtgattc
     1141 tgcatgatct cgtcacgttc ttccgggtca aagcacccac agacacccag cagaaccggc
     1201 tctgtcagca ttccggcaca gcatcccgtg gtgacctgta ttttaccttt ccggtcatac
     1261 ccaaaaacgg tgtaggtcac atcatcctca tcatagactt catgacagat ggagcatgag
     1321 tccgggtatt ttttgatgag tgcattaatt tcttttacct gagcgtcagt agccaaaaca
     1381 tctccctgag tcactgatta tcacaatccg ctgactctaa cacagactca ggcatccgcc
     1441 gttgatttac cataacgtcc cattacacgc accgctaaaa cggcctcaga acgattctgg
     1501 ggcgtaaccc attaaatcct acgtcttacc ccctgaaaac gcctcaaaat cgctccaggg
     1561 cgttttacgg gcatgaatcg ttatgcactt gactgactgt ctggggattt cagcctgaat
     1621 tcaggccagg caactcaaaa cccgcaccaa accagactga aaacggtgaa cgggtgcgca
     1681 atttattgcg tggccgtgaa gcgttgccgg cgcagccgga aaaccggttt tcagcacgtt
     1741 caggaatcgg gtttgtcgag accagcaatc acattatggc aagtcgccgg acgactcacc
     1801 acacgattca ccggcgattc gactcgtgac ttgactctag agtcgccatg gtcaaaaagc
     1861 caccaacccg gcaagtcgac tctagagtca agtcatcata acgtactgat tatatggcgt
     1921 gattcacata tgaatcgtgg gcaagtcatc ggcgattcgc catagagtcg tccacgactc
     1981 ggattcacct tacaaaaaat aaaattgcgt aatttaaaat agataactga ttgaaaataa
     2041 aggtctatct gcaaaatttt aattttgcgt agtgtgtggg tatttttagt ggtgaggagc
     2101 gttcagggat ctgacgattt ttgggaaggt tcaggaactc cccggaatgg ccggagagca
     2161 aaatggaagc atggcgggat caggattttt tccagaattt ccaccacggg gaatggggtg
     2221 gtgaagaagg ttcgtgcttg tgctccagaa gctgcatagc ctgacgaagg gaatcaatat
     2281 gctcatctcg agccttaaca gcccctttaa gaccatcgtt ttcagcttca agtaaagcga
     2341 ttctatgttg taaatcatgt aaaccaacgc tgttaatacc tgtagattct gcgtcacttt
     2401 ttacatcata ttttacagta tcgattacac catcaagaga accaaacact ctaattagct
     2461 ctgaagtatc aataacttta atagctttcc cgtgctttac cacagaggtg taacttaact
     2521 tcccactgtt aatcatcttg taaattgtgg ggcgactaac cttaacaagc cgtgccgctt
     2581 cactaataga cactatggcc atcagttacc atcctgtaat tcatccagtc tcgaggacag
     2641 tgtacggaaa agatgctccg catcatcatg gagtttctca caaaggtcgg cctcgacatc
     2701 gagatcaagc tcgttaagct tatccagcag gagcagagac tgattctgga tgaatttagc
     2761 catgttcagc gctgttttct gttgttttgt cataagaagc ctcagagcgt cagtgctcaa
     2821 tgtcaaacta gtctcttttc cgcttcctcg ctcactcagt cgctacgctc cagccgttcg
     2881 gctgcggcga gcggcaggag cgtgtacata aaaacgtagg caaccaagat atgaggcaga
     2941 aaagcaaagg ccgccgaacg gctgtttttc cataggctcc gcccccctga caagcatcgc
     3001 ggaaacggac gctcaaatca gtggtggcga aacccgacag gacttaaaga taccaggcgt
     3061 ttccccctgg tggctccctc gtgcgctctc ctgttcctgc ctttcggttt accggtgtca
     3121 ttccgctgtt atggccgcgt tttctcattc catgcctgat actcggctcc gggaaggcag
     3181 ttcgctccaa gctggactgt atgcacgaac cccccgttca gtccgactgc tgcgcccgtt
     3241 ccagtaacta tctcttgagt ccaacccgga aagacacgac ttatcgccat tggcagcagc
     3301 cactggtaat tgatttagag gagttagtct tgaagttatg cgccagttaa ggctaaacta
     3361 aacgaactgt tttggtgact gcgctcctct aagccagtta cctcggttca gaaacttgcc
     3421 ggttactgaa ccttcgaaaa accaccttgc cgggtggttt tttcgtttga ggggtagagt
     3481 acgctgcacc tcaaaggatc gtcaaggatc tttttggaat tcatagagct agccactgcc
     3541 tatttgatag ccacctttaa ttcctccagc tcagcgtcag taaacaaccc ttcaagatca
     3601 ttatctttat ttcctatgac cttggttctt attttttctt gcctgcgaat gaattcagga
     3661 tctgtaactt taatagtcag agccctgcga atcatatcct taatatcgga gttatcagct
     3721 tggcaacgac gcaaaatata ttgatagcaa gccttattgt aaataagtat agggttatcc
     3781 tcattactca taagtaactc atccgtaatt gacagagcat catcaatacg atcaagtctt
     3841 ttcaaaatat aagctttaag cactaagagc ttgtcgtagt catccttagc tacatcctct
     3901 cttttaacaa gagacaatga ttccgttaca gcatctaatg cctcagttag ttttttctta
     3961 acagaaagag cctcatccgg aatggacatc a
//
