LOCUS       NZ_CP075289             3991 bp    DNA     circular CON 05-JAN-2024
DEFINITION  Klebsiella pneumoniae strain YTF44-1 plasmid pYTF44-1-4k, complete
            sequence.
ACCESSION   NZ_CP075289
VERSION     NZ_CP075289.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN19107302
            Assembly: GCF_018449065.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3991)
  AUTHORS   Peng,K. and Li,R.
  TITLE     Plasmids shapes the current prevalence of tmexCD1-toprJ1 among
            Klebsiella pneumoniae in food production chain
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3991)
  AUTHORS   Peng,K. and Li,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-MAY-2021) College of Veterinary Medicine, Yangzhou
            University, No. 567, wenchang middle road, hanjiang district, yangz,
            yangzhou, jiangsu 225000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Oxford Nanopore MiniION; Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/05/2024 12:29:59
            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)                     :: 5,717
            CDSs (total)                      :: 5,592
            Genes (coding)                    :: 5,456
            CDSs (with protein)               :: 5,456
            Genes (RNA)                       :: 125
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 136
            CDSs (without protein)            :: 136
            Pseudo Genes (ambiguous residues) :: 0 of 136
            Pseudo Genes (frameshifted)       :: 53 of 136
            Pseudo Genes (incomplete)         :: 82 of 136
            Pseudo Genes (internal stop)      :: 17 of 136
            Pseudo Genes (multiple problems)  :: 15 of 136
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP075289.1.
            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="YTF44-1"
                     /isolation_source="a feces sample of swine origin"
                     /db_xref="taxon:573"
                     /plasmid="pYTF44-1-4k"
                     /geo_loc_name="China: Yangzhou, jiangsu province"
                     /lat_lon="32.40 N 119.40 E"
                     /collection_date="2020-07"
                     /collected_by="College of Veterinary Medicine, Yangzhou
                     University"
     gene            complement(join(3602..3991,1..33))
                     /locus_tag="KI725_RS28425"
                     /old_locus_tag="KI725_28425"
     CDS             complement(join(3602..3991,1..33))
                     /locus_tag="KI725_RS28425"
                     /old_locus_tag="KI725_28425"
                     /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(33..224)
                     /locus_tag="KI725_RS28430"
                     /old_locus_tag="KI725_28430"
     CDS             complement(33..224)
                     /locus_tag="KI725_RS28430"
                     /old_locus_tag="KI725_28430"
                     /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            632..744
                     /locus_tag="KI725_RS28730"
                     /pseudo=""
     CDS             632..744
                     /locus_tag="KI725_RS28730"
                     /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"
     gene            complement(971..1945)
                     /locus_tag="KI725_RS28435"
                     /old_locus_tag="KI725_28435"
     CDS             complement(971..1945)
                     /locus_tag="KI725_RS28435"
                     /old_locus_tag="KI725_28435"
                     /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(2526..2798)
                     /locus_tag="KI725_RS28440"
                     /old_locus_tag="KI725_28440"
     CDS             complement(2526..2798)
                     /locus_tag="KI725_RS28440"
                     /old_locus_tag="KI725_28440"
                     /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"
     Typing          273..744
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.777"
                     /coverage="92.0"
                     /evalue="7.8799999999999974e-146"
ORIGIN
        1 ccgtgccgct tcactaatag acactatggc catcagttac catcctgtaa ttcatccagt
       61 ctcgaggaca gtgtacggaa aagatgctcc gcatcatcat ggagtttctc acaaaggtcg
      121 gcctcgacat cgagatcaag ctcgttaagc ttatccagca ggagcagaga ctgattctgg
      181 atgaatttag ccatgttcag cgctgttttc tgttgttttg tcataagaag cctcagagcg
      241 tcagtgctca atgtcaaact agtctctttt ccgcttcctc gctcactcag tcgctacgct
      301 ccagccgttc ggctgcggcg agcggcagga gcgtgtacat aaaaacgtag gcaaccaaga
      361 tatgaggcag aaaagcaaag gccgccgaac ggctgttttt ccataggctc cgcccccctg
      421 acaagcatcg cggaaacgga cgctcaaatc agtggtggcg aaacccgaca ggacttaaag
      481 ataccaggcg tttccccctg gtggctccct cgtgcgctct cctgttcctg cctttcggtt
      541 taccggtgtc attccgctgt tatggccgcg ttttctcatt ccatgcctga tactcggctc
      601 cgggaaggca gttcgctcca agctggactg tatgcacgaa ccccccgttc agtccgactg
      661 ctgcgcccgt tccagtaact atctcttgag tccaacccgg aaagacacga cttatcgcca
      721 ttggcagcag ccactggtaa ttgatttaga ggagttagtc ttgaagttat gcgccagtta
      781 aggctaaact aaacgaactg ttttggtgac tgcgctcctc taagccagtt acctcggttc
      841 agaaacttgc cggttactga accttcgaaa aaccaccttg ccgggtggtt ttttcgtttg
      901 aggggtagag tacgctgcac ctcaaaggat cgtcaaggat ctttttggaa ttcatagagc
      961 tagccactgc ctatttgata gccaccttta attcctccag ctcagcgtca gtaaacaacc
     1021 cttcaagatc attatcttta tttcctatga ccttggttct tattttttct tgcctgcgaa
     1081 tgaattcagg atctgtaact ttaatagtca gagccctgcg aatcatatcc ttaatatcgg
     1141 agttatcagc ttggcaacga cgcaaaatat attgatagca agccttattg taaataagta
     1201 tagggttatc ctcattactc ataagtaact catccgtaat tgacagagca tcatcaatac
     1261 gatcaagtct tttcaaaata taagctttaa gcactaagag cttgtcgtag tcatccttag
     1321 ctacatcctc tcttttaaca agagacaatg attccgttac agcatctaat gcctcagtta
     1381 gttttttctt aacagaaaga gcctcatccg gaatggacat cattgattct gctttatcca
     1441 cagctgaaat ggctttaaag tatcctagct cgaattttgt tgttttctta tccatttcaa
     1501 gctgttctat cagctccttg ctcctatcaa gctcatcttt aaactcatct tgttcagcct
     1561 ccaaatcttg ttgcttttta tctataccgt ctacttgctc ttttaatact ttgttggcaa
     1621 gaccatccag taatgcgtac ccaagatacg cagagatccc cgaaacagaa ataagaagca
     1681 atatttgttc tatgaactta gttccaccac catcagccac aggaaatatt atacttgagt
     1741 aatcaacatg aagaaatgat gatatgaaag gaacacaaat aaatgcggat gctataccaa
     1801 atctataaac actagctctt ttattattct catccttatc ttttgaaaat ttattttggg
     1861 agtctcggca acctctggaa tagctcccca taacaccacc aaaacaaatt agagatgcaa
     1921 caaacaatag gttaaaaaaa gccatgagag aatccttgcg caaagcaaac aataaaactt
     1981 tgttcaggta agttaagata agctcaatca tatactaacc aataacaaaa aaggcagcct
     2041 tggctgcctt tttctgctga cttgacactt acaagtctgg acgctcatcg tgaagtttga
     2101 tttttttcat agagcacctc tcattaattg ttcctttgca agcccatgct tgcttagcgc
     2161 tgaatatagg gcataaaccc agcactcaca acaacaaaaa tgcttaaaat gataaaatca
     2221 acccatgtat tgacattggg tgaaaaaaaa agtataatgc actggtagcc aaaggggcgg
     2281 ggcttcgctt attcctaagg aataagcgaa gccccgcccc tttggctacc ataattaaat
     2341 gattgaattt aaaggatttt tttacaataa catccttcct ctcaatagtc atataaacat
     2401 gccccatgta ttcgtcattc tggatttttc aaaagaatga atgcgtgcat ttaccataac
     2461 gcctcatttc acgcagatat gaaaaagccc gcacaaggcg ggcttcagac tcaacagata
     2521 cggaatcact ctgtgaaaaa ctgctttgcc atggggtgat tctgcatgat ctcgtcacgt
     2581 tcttccgggt caaagcaccc acagacaccc agcagaaccg gctctgtcag cattccggca
     2641 cagcatcccg tggtgacctg tattttacct ttccggtcat acccaaaaac ggtgtaggtc
     2701 acatcatcct catcatagac ttcatgacag atggagcatg agtccgggta ttttttgatg
     2761 agtgcattaa tttcttttac ctgagcgtca gtagccaaaa catctccctg agtcactgat
     2821 tatcacaatc cgctgactct aacacagact caggcatccg ccgttgattt accataacgt
     2881 cccattacac gcaccgctaa aacggcctca gaacgattct ggggcgtaac ccattaaatc
     2941 ctacgtctta ccccctgaaa acgcctcaaa atcgctccag ggcgttttac gggcatgaat
     3001 cgttatgcac ttgactgact gtctggggat ttcagcctga attcaggcca ggcaactcaa
     3061 aacccgcacc aaaccagact gaaaacggtg aacgggtgcg caatttattg cgtggccgtg
     3121 aagcgttgcc ggcgcagccg gaaaaccggt tttcagcacg ttcaggaatc gggtttgtcg
     3181 agaccagcaa tcacattatg gcaagtcgcc ggacgactca ccacacgatt caccggcgat
     3241 tcgactcgtg acttgactct agagtcgcca tggtcaaaaa gccaccaacc cggcaagtcg
     3301 actctagagt caagtcatca taacgtactg attatatggc gtgattcaca tatgaatcgt
     3361 gggcaagtca tcggcgattc gccatagagt cgtccacgac tcggattcac cttacaaaaa
     3421 ataaaattgc gtaatttaaa atagataact gattgaaaat aaaggtctat ctgcaaaatt
     3481 ttaattttgc gtagtgtgtg ggtattttta gtggtgagga gcgttcaggg atctgacgat
     3541 ttttgggaag gttcaggaac tccccggaat ggccggagag caaaatggaa gcatggcggg
     3601 atcaggattt tttccagaat ttccaccacg gggaatgggg tggtgaagaa ggttcgtgct
     3661 tgtgctccag aagctgcata gcctgacgaa gggaatcaat atgctcatct cgagccttaa
     3721 cagccccttt aagaccatcg ttttcagctt caagtaaagc gattctatgt tgtaaatcat
     3781 gtaaaccaac gctgttaata cctgtagatt ctgcgtcact ttttacatca tattttacag
     3841 tatcgattac accatcaaga gaaccaaaca ctctaattag ctctgaagta tcaataactt
     3901 taatagcttt cccgtgcttt accacagagg tgtaacttaa cttcccactg ttaatcatct
     3961 tgtaaattgt ggggcgacta accttaacaa g
//
