LOCUS       NZ_CP113182             4935 bp    DNA     circular CON 14-JAN-2024
DEFINITION  Klebsiella pneumoniae strain SYCC1 plasmid pSYCC1_5, complete
            sequence.
ACCESSION   NZ_CP113182
VERSION     NZ_CP113182.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31836736
            Assembly: GCF_026626085.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4935)
  AUTHORS   Yin,Y. and Li,R.
  TITLE     Emergence and spread of tmexCD-toprJ in live poultry market in
            Yangzhou, China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4935)
  AUTHORS   Yin,Y. and Li,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-NOV-2022) College of Veterinary Medicine, Yangzhou
            univeristy, Shuangqiao, Yangzhou, Jiangsu 225009, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: SPAdes v. v. v3.12.0; unicycler v. v. v. v0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/14/2024 03:30:33
            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)                     :: 5,631
            CDSs (total)                      :: 5,507
            Genes (coding)                    :: 5,353
            CDSs (with protein)               :: 5,353
            Genes (RNA)                       :: 124
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 154
            CDSs (without protein)            :: 154
            Pseudo Genes (ambiguous residues) :: 0 of 154
            Pseudo Genes (frameshifted)       :: 61 of 154
            Pseudo Genes (incomplete)         :: 94 of 154
            Pseudo Genes (internal stop)      :: 26 of 154
            Pseudo Genes (multiple problems)  :: 22 of 154
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP113182.1.
            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..4935
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /strain="SYCC1"
                     /isolation_source="chicken"
                     /db_xref="taxon:573"
                     /plasmid="pSYCC1_5"
                     /geo_loc_name="China: Jiangsu"
                     /lat_lon="32.24 N 119.26 E"
                     /collection_date="2022-05"
                     /collected_by="Yayun Gao"
     gene            complement(join(4835..4935,1..145))
                     /locus_tag="OT490_RS28025"
                     /old_locus_tag="OT490_28030"
     CDS             complement(join(4835..4935,1..145))
                     /locus_tag="OT490_RS28025"
                     /old_locus_tag="OT490_28030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012848468.1"
                     /GO_component="GO:0110001 - toxin-antitoxin complex
                     [Evidence IEA]"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0097351 - toxin sequestering activity [Evidence IEA]"
                     /GO_process="GO:0045927 - positive regulation of growth
                     [Evidence IEA]; GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system Phd/YefM family
                     antitoxin"
                     /protein_id="WP_025987695.1"
                     /translation="MHAINFTDARKHFAETMKRVTDDAEPVRVMRRDAPDIVMIDAGEY
                     EALIETVYLFSNPANAEHINESMKQAERGEFVEVEY"
                     /name="type II toxin-antitoxin system Phd/YefM family
                     antitoxin"
     gene            382..543
                     /locus_tag="OT490_RS28030"
                     /old_locus_tag="OT490_28035"
     CDS             382..543
                     /locus_tag="OT490_RS28030"
                     /old_locus_tag="OT490_28035"
                     /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_162870772.1"
                     /translation="MAKHWSGQECPKTGTYGQYHDTDNSYAGSEYDRHVSKGDKFPPSK
                     NNHHFQEK"
                     /name="hypothetical protein"
     gene            complement(1344..1745)
                     /locus_tag="OT490_RS28035"
                     /old_locus_tag="OT490_28040"
     CDS             complement(1344..1745)
                     /locus_tag="OT490_RS28035"
                     /old_locus_tag="OT490_28040"
                     /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_045328244.1"
                     /translation="MTRVSISEAARLTGKSRTTLHRLIKTGELSTCSGERNKKMVDISE
                     LLRVFGPFDQPKNEHLTRQVPEQRDTAPADQSEHVIRQLKQQIEHLNILILSKDSHIDS
                     LKQAMLLLENHQAKLTEPPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            2071..2685
                     /locus_tag="OT490_RS28040"
                     /old_locus_tag="OT490_28045"
     CDS             2071..2685
                     /locus_tag="OT490_RS28040"
                     /old_locus_tag="OT490_28045"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012822468.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="TIR domain-containing protein"
                     /protein_id="WP_019725132.1"
                     /translation="MGKHKVFISYHHANDQYYKNALEKMNEEHEIFVNRSVSLGDIDED
                     EAPQKIREIIRDEYLRDTSVLILLVGTETKNRKHVDWELYSSMRDSTINKKSGILVVNL
                     PSTNTTYIRSTHGTNEKSEVHPTVTEWFSIDKRSTYEERFPYMPARIIDNFMKSGSYIS
                     VVNWNQIENNPETLRKLIDMTYNDREKATYDMSREMRMHNS"
                     /name="TIR domain-containing protein"
     gene            complement(2722..3429)
                     /locus_tag="OT490_RS28045"
                     /old_locus_tag="OT490_28050"
     CDS             complement(2722..3429)
                     /locus_tag="OT490_RS28045"
                     /old_locus_tag="OT490_28050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001258875.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004198042.1"
                     /translation="MKTFVTLWTIVFLAFIAVMCTVDISNYIPSVYTVFSKNRPLVTGA
                     LSILLISVFIWLMVSLYLLKKYSVKVEKLSLGGVNILFNESATLYKKSVKNHLDSKRAI
                     FKLRKNVDAFDEVISSYYQTYQFIRDEMKILNPKKDREIYDFSNEMLMVLNRFLTNYQN
                     NYKRWYKYISDKDEVVDRVSGDVMRFHATSINKIQMQYYDYERILKGFKDVNRFFVNDV
                     KPKFGINTDKWNW"
                     /name="hypothetical protein"
     gene            complement(3426..4331)
                     /locus_tag="OT490_RS28050"
                     /old_locus_tag="OT490_28055"
     CDS             complement(3426..4331)
                     /locus_tag="OT490_RS28050"
                     /old_locus_tag="OT490_28055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001697689.1"
                     /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_019725130.1"
                     /translation="MHNAALELFNERLPHKPYFSDDLHFGVRIAGKERAILAKYIQFNQ
                     PHAMFWLGFDVDRAGSSIDWSDRNAPAPTLTITNPENGHAHLLYALENSIRTAPDGKIK
                     PLRYAASVENALRKKLEADAGYSGLICKNPNHNHWKIAVWQPKLYTLDWLADFLDLNTG
                     NDKEIVADYGLGRNCTLFDKTRKWAYRAIRQGWPEYEQWLQACYERACAYNLQFARPLD
                     ENEVRGIAKSIAKWTSNKFSPEEFSKFVDITHSSEIQSKRGKKSGQSRRKGSLEEIKPW
                     VAMGISRRKYFYIKKNGEIR"
                     /name="replication initiation protein"
     gene            complement(4579..4854)
                     /locus_tag="OT490_RS28055"
                     /old_locus_tag="OT490_28060"
     CDS             complement(4579..4854)
                     /locus_tag="OT490_RS28055"
                     /old_locus_tag="OT490_28060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017412855.1"
                     /GO_process="GO:0008219 - cell death [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Txe/YoeB family addiction module toxin"
                     /protein_id="WP_019725129.1"
                     /translation="MSKWNIKFTRNGADDLNYWRDTDKKKFERIRQLLLSIEADPLTGI
                     GKPERLRHHKDPALYSRRIDQSHRLVYSIQNGEIIIYAARYHYGDK"
                     /name="Txe/YoeB family addiction module toxin"
ORIGIN
        1 ttagcgcctc atactctccc gcatcgatca taacaatatc aggcgcatca cggcgcatga
       61 cacgtaccgg ttcagcatca tcagtgacgc gcttcatcgt ctcggcaaaa tgtttacggg
      121 catcagtaaa attgattgca tgcatgttgt taacccccat ttgttggggc ttagcataga
      181 acatgtacgc aaataagtac ataaagatat ttccctaaaa acccacaacc aaatcagctc
      241 aaaatgtgaa ctcaatcgaa taaccacaaa aacaacaagt caatacattg aagcataatt
      301 tcaagcaatt acatttatga agtgcggcac aatttcgtac cgctaggagc ttagctccta
      361 aaacgagcaa aggaaaagta aatggcaaaa cattggtctg ggcaagaatg tccaaaaaca
      421 ggtacttacg gtcaatatca tgataccgac aactcatacg ctggttctga atatgatcgc
      481 catgtgagca agggtgataa gttccctccg agcaaaaaca accaccactt ccaagaaaaa
      541 taaaatatct tcagaagtct aaactaaaag ccctctgggg ctttttttgt acctgccatt
      601 cacttgattt accataacat ccgttatcag caccgcctga gaggccctca gggcgtttct
      661 gacgggaaac cggtaaaaca aggcaacaaa ccacccgaaa acccgccaga aacgcgcagg
      721 ctctgttttt acggcatgca tgagtatgcg cacaagtgca tagcgcggaa attgacacca
      781 ttcagccagg ggaagtcctg tttccggcgt tcttcccatc cgaaaacggt gaacggggac
      841 gcaatttatt gcgtggccgt gaagcgttgc cggcgcagcc ggaaaaccgg ttttcagcac
      901 gttcaggaat cggttcgtcc acggccggca atcacgttat ggcaagtcgc cggacgactc
      961 accacacgat tcaccggcga ctcttcacta gagtcgtacc cagagtcgcc gcgtctaaaa
     1021 aacaaccaaa cggggagtcg gatctagagt cgggtcgtta ttaactcatt gtttttatag
     1081 gcctgagtcg ttaccgactc tatgacgact cgccggggac tctatgacga gtcgtcatag
     1141 agtcggatct atataaataa aatttaaaaa acgaaatttc agtaaagtaa gctgctgata
     1201 ttaaatacaa atctgcaaaa ttttaatttt gcgtggggtg tgggtatttt tcgtggtgag
     1261 gagcgttcag agatctgacg attttcggga aggttcagga actccccgga atggccggag
     1321 aggaaaactg aagcatgacg gggtcaggat tttttccaga atttccacca cggcgccggg
     1381 ggttcagtta attttgcctg gtgattttca agaaggagca tggcctgttt caggctgtca
     1441 atgtgcgaat ccttggataa aatcaatatg ttaaggtgtt caatctgctg tttcagttga
     1501 cgaatgacat gttcactctg gtcagcaggc gctgtatcac gctgttcagg tacttgtcga
     1561 gtaaggtgtt cattcttcgg ttggtcaaac ggtccgaaaa cacgtaaaag ctctgatata
     1621 tcgaccattt ttttatttcg ttcaccgcta caagtggaca gttcacctgt tttgattaac
     1681 ctgtgcagcg ttgtccggct cttacccgtc agccgtgcag cctcactaat agacactctg
     1741 gtcatcagtt atcatccttt aatacattca gtctcaagga aacaggggcc agcttacgac
     1801 atactggtcc agaagtgatg tgtttttcgg aagggcgatg aaacacagga gtgaccgtgc
     1861 aaaatgcagg caacaaatga ctttccgctt cctcgcgcat tcgctcacta cgttcaacga
     1921 gcccgcccta aaccagtcat ggtgagacct tgctgaaggg accctatgtg tgctggctga
     1981 gaaaaaaaga gctctctaaa agagagctgt tatctgatat aggttcaagt gcaaaataga
     2041 gtgcacacaa acaaaaaaag gacaataaaa atgggaaagc ataaggtatt cattagctac
     2101 caccatgcga atgatcagta ctacaaaaac gcacttgaaa aaatgaatga ggaacatgaa
     2161 atattcgtga atcgctcagt atcattaggt gatatagatg aagatgaagc cccacaaaaa
     2221 ataagagaga taataagaga tgaatatctt agagatacat cagttcttat ccttcttgtt
     2281 ggaactgaaa caaaaaacag aaaacacgta gattgggaac tttactctag catgagagat
     2341 agtaccatta acaaaaaatc aggaatttta gtcgtcaatc tcccgtcaac aaatactacg
     2401 tacattcgtt caacacatgg aactaatgaa aaatcagaag ttcatcctac cgtaactgaa
     2461 tggttttcta ttgataagcg ctcaacttat gaggaaaggt tcccatatat gccagcaaga
     2521 ataatagaca acttcatgaa gagcgggtct tatatatcag tggtcaactg gaatcaaata
     2581 gaaaacaacc cagaaacact cagaaaatta atagacatga cttataacga tagagaaaaa
     2641 gcaacgtatg atatgtcgag agaaatgaga atgcataatt catagtacta tccaaggagt
     2701 agccttggct actcctttaa tttaccagtt ccacttatct gtattgattc caaacttagg
     2761 cttcacatca ttaacaaaga accggttaac atctttaaaa ccttttaaaa tacgctcata
     2821 atcataatac tgcatttgta ttttatttat gctggttgca tgaaatctca tgacatcacc
     2881 gctaacccta tcaacaacct catctttgtc tgatatgtac ttataccaac gcttgtagtt
     2941 gttctggtag ttagttagaa atctatttaa caccatgagc atctcattgc tgaaatcata
     3001 aatctcacga tcttttttag ggtttagtat tttcatttca tcacgaataa attggtaagt
     3061 ctgataatat gatgaaataa cctcatcaaa ggcatcaacg ttttttctta atttgaaaat
     3121 tgctcttttt gaatctaggt gattttttac actctttttg taaagtgtag cactctcatt
     3181 gaaaagtata ttcactccac caaggctaag tttctcaacc ttaaccgaat actttttaag
     3241 taagtagagg gataccatca gccaaataaa aacagatatc aaaagaatag aaagggcgcc
     3301 agttacaaga ggtctattct tactaaaaac tgtgtaaaca gacggaatgt aattagatat
     3361 atcaacagta cacatcacgg caataaatgc taaaaaaact atagtccaaa gagttacgaa
     3421 ggttttcatc ttatttcacc atttttcttg atataaaaat acttccgcct gcttattccc
     3481 atagctaccc aaggttttat ttcctctagg cttcctttcc tccttgactg ccctgacttt
     3541 ttccctctct ttgattgaat ttcagaggaa tgagtaatat caacaaattt actgaattct
     3601 tcaggtgaaa atttatttga tgtccattta gcaatgctct tagctatccc tcttacctca
     3661 ttttcatcca gaggccgtgc aaattgcagg ttgtatgcgc aagcgcgttc gtagcaggct
     3721 tgcagccact gctcatactc aggccagccc tgacggatgg cgcgatatgc ccacttacgg
     3781 gttttgtcga acaacgtgca gttacgacct aagccgtagt cggcaacgat ttccttgtca
     3841 ttccctgtgt tcagatcgag aaagtcggcc agccagtcca gagtgtagag cttcggttgc
     3901 cacacggcga ttttccagtg gttgtggttc ggatttttgc agatgagccc cgaatatcca
     3961 gcgtcagcct ctaatttttt acgtagcgca ttctccacgg aggcggcgta gcgtaacggt
     4021 tttattttgc cgtccggcgc ggtgcgtatc gagttttcca gcgcgtacag caggtgcgcg
     4081 tgtccgtttt cggggttagt tatggtcagc gtcggtgcag gcgcgttgcg gtcgctccag
     4141 tcgatggagg aaccggcgcg gtcaacgtca aatcccagcc agaacatggc gtgaggctga
     4201 ttgaactgga tatatttcgc cagaatagcg cgttccttac cggcgatacg gacaccaaag
     4261 tgcagatcgt ccgaaaagta cggcttgtgt ggtaagcgtt cgttgaaaag ttcgagtgcg
     4321 gcgttatgca atgtgccctg cgcttatggc gggctgttgt ctggcacggt tcatgtgcta
     4381 atatcctttc aaggtttcga cctagccctg gttatcatgc gatccgccaa gatatgacat
     4441 gatttccggg gctttgtttt ttctgaggct aacgttacac cgactttgcc tttgtgtcga
     4501 tctgacagcg acttacccta acatccgttg tacgccttgc atgaaaagct cgcatcaagc
     4561 gggctatatc gacttttgct atttgtcacc atagtgataa cgggctgcgt agatgatgat
     4621 ttctccgttc tggattgaat agaccagacg gtggctctga tcaatcctgc gggagtagag
     4681 tgccggatct ttgtggtgcc gcagccgttc gggttttcct atacctgtca gcggatcagc
     4741 ctcgatgctg agcaacagtt gccggatacg ctcaaacttc tttttgtcag tatcacgcca
     4801 gtagttaagg tcatcagcgc cattcctagt gaacttaata ttccacttcg acaaattcgc
     4861 cgcgctccgc ctgtttcatt gactcattga tatgctctgc gttcgccgga ttgctgaaca
     4921 gatagaccgt ttcga
//
