LOCUS       NZ_CP083794             5783 bp    DNA     circular CON 10-JAN-2024
DEFINITION  Klebsiella variicola strain INF352 plasmid pINF352_4, complete
            sequence.
ACCESSION   NZ_CP083794
VERSION     NZ_CP083794.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMEA3357250
            Assembly: GCF_020149805.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella variicola
  ORGANISM  Klebsiella variicola
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5783)
  AUTHORS   Hawkey,J., Cottingham,H., Tokolyi,A., Wick,R., Judd,L.M.,
            Cerdeira,L., de Oliveira Garcia,D., Wyres,K.L. and Holt,K.E.
  TITLE     Linear plasmids in Klebsiella and other Enterobacteriaceae
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5783)
  AUTHORS   Hawkey,J., Wyres,K.L., Judd,L.M., Jenney,A. and Holt,K.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-SEP-2021) Department of Infectious Diseases, Monash
            University, Level 2, The Burnet Institute, Melbourne, VIC 3004,
            Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 110x
            Sequencing Technology :: Illumina; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/10/2024 04:10:02
            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)                     :: 5,921
            CDSs (total)                      :: 5,798
            Genes (coding)                    :: 5,645
            CDSs (with protein)               :: 5,645
            Genes (RNA)                       :: 123
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 153
            CDSs (without protein)            :: 153
            Pseudo Genes (ambiguous residues) :: 0 of 153
            Pseudo Genes (frameshifted)       :: 52 of 153
            Pseudo Genes (incomplete)         :: 99 of 153
            Pseudo Genes (internal stop)      :: 23 of 153
            Pseudo Genes (multiple problems)  :: 19 of 153
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP083794.1.
            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..5783
                     /organism="Klebsiella variicola"
                     /mol_type="genomic DNA"
                     /strain="INF352"
                     /db_xref="taxon:244366"
                     /plasmid="pINF352_4"
     gene            join(4233..5783,1..792)
                     /locus_tag="LB484_RS29530"
                     /old_locus_tag="LB484_29530"
     CDS             join(4233..5783,1..792)
                     /locus_tag="LB484_RS29530"
                     /old_locus_tag="LB484_29530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010904246.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="S-type pyocin domain-containing protein"
                     /protein_id="WP_181486822.1"
                     /translation="MGGGFNYNGEGATGTGLDRDPYVRDSNGNAIGVKSGYHAESYGTS
                     SPALGPNGAIQITAGVIAVPGDKPRPDGGSGGGNTVNTGPAGQLLVMNKGQLGYWETRS
                     TGAGNNEHNTSVFVAVGPSEAEKTASAEKALKEKQQAEAAAKDFAAKTAAASATAEKER
                     QQAIAAATAAGQHQSVSDARNSLNNATSDVSRLKSAADSALQEAKAKRKAAIDAVPVAT
                     QAENKYQELQQKIKGLKLKNGEYGTEKWEIIGSNKEHDHWGYRFYPSGITKAQVDVAQS
                     DAVNKRNQATSLASQATAAEQDSLKATAAYNAAETRRQAAQAALNSAEQAAAAERKRQE
                     AEAAAAAAAEKKRQADAVAKAAEEARAAAEKARLMQERQAAADKLKSTDIQSVRGIPST
                     ASPAASPISWAVASLGGISLDSVTAGKAWTQIAEVMAKLRGIAGASLVGPVVATAVGLF
                     WSRDVGIGSDVVPGRDISGLMPGDALSLPDLATLIKAADSKTGVSMPVRGRIIVREGDY
                     LESQFVRTPVAGSVPVVRATLDKATGYWGYTLPAIQGVPGQTILVSPSDAPGVNAPLGL
                     AGPVPLPETIIHTGGQTTVPQGGTVTVSPVIGEVDFRDLILVFPPESGLKPLYVMPVSP
                     YGDATEKGEHSGRPYNPDKAGGPVQNLNWRSAVINKAGIDKVKLHTGRFGESAANKVMI
                     DRLEKILSGQLQVTDTDKRFYTHELRELERYRALGVPDNVKPDDKGVTWNNTHTATLED
                     YKINEKTDPLYTKDAEEAEYKAELKNK"
                     /name="S-type pyocin domain-containing protein"
     gene            803..1066
                     /locus_tag="LB484_RS29535"
                     /old_locus_tag="LB484_29535"
     CDS             803..1066
                     /locus_tag="LB484_RS29535"
                     /old_locus_tag="LB484_29535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015377593.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_064148700.1"
                     /translation="MSNPIEDIIKNESVSDVLRYFGPGRDISKIDRMYVSYKFEVISEG
                     VLLSEYKKLFDNGELKYDSNKNVIKGPNWKEPAFVTQKKYGI"
                     /name="hypothetical protein"
     gene            1248..1505
                     /locus_tag="LB484_RS29540"
                     /old_locus_tag="LB484_29540"
     CDS             1248..1505
                     /locus_tag="LB484_RS29540"
                     /old_locus_tag="LB484_29540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015366249.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin immunity protein"
                     /protein_id="WP_010904244.1"
                     /translation="MANKTLADYTEQEFIEFIEKIKKADFATESEHDEAIYEFSQLTEH
                     PDGWDLIYHPQAGADNSPAGVVKTVKEWRAANGKPGFKKS"
                     /name="bacteriocin immunity protein"
     gene            1613..1768
                     /locus_tag="LB484_RS29545"
                     /old_locus_tag="LB484_29545"
     CDS             1613..1768
                     /locus_tag="LB484_RS29545"
                     /old_locus_tag="LB484_29545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008323621.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_071561715.1"
                     /translation="MKKLLFLGVVTVSVVLAACQVNNVRDTGGGAVSPSSTVTGVTLDS
                     GTNGNP"
                     /name="colicin release lysis protein"
     gene            complement(1974..2088)
                     /locus_tag="LB484_RS29550"
                     /old_locus_tag="LB484_29550"
                     /pseudo=""
     CDS             complement(1974..2088)
                     /locus_tag="LB484_RS29550"
                     /old_locus_tag="LB484_29550"
                     /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            2504..2695
                     /locus_tag="LB484_RS29555"
                     /old_locus_tag="LB484_29555"
     CDS             2504..2695
                     /locus_tag="LB484_RS29555"
                     /old_locus_tag="LB484_29555"
                     /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_023302508.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2695..3117
                     /locus_tag="LB484_RS29560"
                     /old_locus_tag="LB484_29560"
     CDS             2695..3117
                     /locus_tag="LB484_RS29560"
                     /old_locus_tag="LB484_29560"
                     /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_064148699.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKAIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     Typing          complement(1975..2383)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.341"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ctggagtctc agttcgttcg aacacctgtt gccggtagtg ttccggttgt tcgggctact
       61 ctggataaag ctactggtta ctggggatat acgttgccgg cgatacaggg cgtgcccgga
      121 cagacaatac tggtaagtcc gtcagatgcg ccgggcgtta atgctcctct gggacttgct
      181 gggccggttc ctttgcctga aactattata cataccggtg ggcaaactac ggtccctcag
      241 ggggggactg tgacagtatc tcctgttatt ggtgaagttg attttcgaga tcttatcctt
      301 gttttccctc ctgagtcagg gttaaagccg ttatatgtga tgccagttag cccttatgga
      361 gatgcaacag aaaaaggcga gcacagcgga agaccttata atccggataa ggcaggtggt
      421 cctgtacaga atcttaactg gcgtagtgca gtcatcaaca aggccgggat tgataaggtg
      481 aagctacata ccggtcgctt tggtgaatca gcagcaaaca aagtaatgat cgaccgtctg
      541 gagaaaatcc tgagcggtca gttacaggta actgatacgg acaagcggtt ttacacccat
      601 gaactcagag agctggaacg ttatcgtgct ttaggggtcc ctgataatgt gaagccagat
      661 gataaaggtg ttacgtggaa taacactcat acagcaacgc tggaagatta taaaattaat
      721 gaaaaaactg atccgctcta tacaaaggat gctgaagagg cagagtataa agcagagcta
      781 aaaaataaat gagggggaga gaatgagtaa tccgattgaa gacatcatta aaaatgaatc
      841 ggtaagtgat gtgcttcgct actttggtcc tggtcgcgac atttcaaaaa ttgaccgtat
      901 gtatgtttca tataagtttg aagtgatctc tgaaggcgtt cttttatctg aatacaaaaa
      961 gttattcgac aatggagaac taaagtatga ctctaataaa aatgttatta aggggcctaa
     1021 ctggaaagag cctgcttttg taacacaaaa aaaatacggc atttaaagtg tgcatatgaa
     1081 gccctttgaa aagagggctt tgattaaagc tcacatatga aaagggtttc ttttttgagt
     1141 ggtcgtggtt tcgatgatac tggcagcatg tcaggtcaac aatatctggg gtaagctgag
     1201 tgcattaaaa cctaaacgcc atattgaaat ccataatggg aactgaaatg gctaataaaa
     1261 ctttggctga ctatacagag caggaattta ttgagtttat cgaaaaaatt aaaaaagcag
     1321 actttgctac tgagtctgag catgatgagg ccatttatga gttcagccag ttgactgaac
     1381 atccagatgg ttgggatctt atttatcatc ctcaagcagg agccgataac tctcctgctg
     1441 gtgttgtaaa aacagtaaaa gagtggcgag cagctaacgg taagccaggt tttaaaaaat
     1501 cgtgattgaa tgtgcgggtt caagtgatga atccgcacat ttttaactct ggatttgaat
     1561 aataattact aggtatccat ttgcttagaa taataaaaat aaaaggtgat atatgaaaaa
     1621 attacttttc ctgggggttg ttaccgtttc tgtggttctg gcggcatgtc aggtcaataa
     1681 tgttcgtgac accggaggtg gggctgtttc accttcatcg acggtgaccg gagtcacgct
     1741 tgatagcggt acgaacggca atccgtaaag gatcttcttg agatcccatt tggatcgtcg
     1801 taatctcttg ctctgtaaac gaaaaaaccg ccttggcggg cggtttttcg aaggttccaa
     1861 gagttggcgc tctttgaacc gaggtaactg gcttatgagg agcacagtaa ccaaaacttg
     1921 ttctttcagt ttagccttaa ccggcgcata acttcaagac taactcctct aaatcagtta
     1981 ccagtggctg ctgccagtgg tgcttttgca tgtcttaccg ggttggactc aagatgatag
     2041 ttaccggatc aaggcgcagc agtcggactg aacggggggt tcgtgcatac agtccagctt
     2101 ggagcgaact gcctacccgg aactgagtgt caggcgtgga atgagataaa cgcggccata
     2161 acagcggaat gacaccggta aaccgaatgg caggaacagg agagcgcacg agggagccat
     2221 cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt tcgccaccac tgatttgagc
     2281 gtcaaattct gtgatgcttg tcaggggggc ggagcctatg gaaaaacggc cgctgtgcgg
     2341 cctctccttc tccccatcac gcgatcgctc ggttttctcg agcttttata cgcatgctcc
     2401 tgccgctcgc cgcagccgaa cggcaggagc gtagcgactg agtgagcgag gaagcggaaa
     2461 agagaacatc cctacactga gcactgacgc tctgaggcct cttatgacga aacaacagaa
     2521 aacagcgctg aacatggcta aattcatcca gaatcagtct ctgctcctgc tggagaagct
     2581 taacgagctt gatctcgatg tcgaggccga cctttgtgag aaactccacg atgatgcgga
     2641 gcatcttttc cgtacactgt cctcgagact ggatgaatta caggatggta actgatggcc
     2701 agagtgtcta ttagtgaagc ggcacggctt gttaaggtta gtcgtcctac aatttacaag
     2761 atgattaaca gtgggaagtt aagttacacc tctgttgtaa agcacgggaa ggctattaaa
     2821 gttattgata cttctgagct tattagagtg tttggttctc ttgatggtgt aatcgatact
     2881 gtaaaatatg atgtaaaaag tgacgcagaa tctacaggta ttaacagcgt tggtttacat
     2941 gatttacaac atagaatcgc tttacttgaa gctgaaaacg atggtcttaa aggggctgtt
     3001 aaggctcgag atgagcatat tgattccctt cgtcaggcta tgcagcttct ggagcacaag
     3061 cacgaacctt cttcaccacc ccattccccg tggtggaaat tctggaaaaa atcctgaccc
     3121 catcatgctt cagttttcct ctccggccat tccggggagt tcctgaacct tccaaaaaat
     3181 cgccagatct ctgaacgctc ctcaccacta aaaataccca cacactacgc aaaattaaaa
     3241 ttttgcagat tctttattta aaacaattgg ttaatgaaaa attaatgtgc agtgatgtgt
     3301 tacaaagtgc agatccaagt cgtggacgac tctatggcga atcgtttacg aattgcccac
     3361 gattcatatg tgaatcacgc tttattatca tgttgttatg atgaatcgac tcttgattca
     3421 attcatcaat ttgggcgttt tttgttcatg gtgactcttg attcaattca cgattcgaat
     3481 cgccggtgaa tcgtgtggtg agtcgtccgg cgacttgcca taacgtgatt gccggccgtc
     3541 gacgaacccg attcctgaac gtgctgaaaa ccggttttcc ggctgcgccg gcaacgcctc
     3601 acggccacgc aataaattgc gtccccgttc accgttttcg gatcagaaga acgccggaaa
     3661 caggacttac cctggctgaa tggcgtgaat ttccgcgcta tgcacttgcg cgcatactca
     3721 tgcatgccgt aaaaacagag cctgcgcgtt tctggcgggt tttcgggtgg tttgttgcct
     3781 gttttaccgg tttcccgtca gaaacgccct gaggccgttt tagcggtgcg tacaattaag
     3841 ggattatggt aaatgggggc gctcgggtgg cggaataccc tctacaccaa gactttttgt
     3901 acaggtctct gtccgtcagt cacacccttt ttaagagcac atatcgttaa ttttttttct
     3961 ctgccgagcc gcgtcctgtc tgggttttgt catttctatt acgcttaact taatgaaaat
     4021 tcaaaagata attgtatctc tccgcgtgtt gacagagttc tcatgtcagg agtagtattc
     4081 aagtactgta tataaacaca tgtatttata tacagtactt ggtgtggcag agaactaata
     4141 acagcctccg gatacaggtt cgaaggcgat aaaccgcaca ccagattctg acaagcagga
     4201 aaacgataaa aataacaaca aaggagagag ttatgggtgg tggatttaac tataacgggg
     4261 aaggtgctac tggcaccgga ttggatcgtg atccatatgt tcgcgacagc aatggtaatg
     4321 ctattggtgt taaatcaggc tatcacgcgg agtcctatgg gacctcaagt ccagccttag
     4381 ggcctaatgg cgctattcag attactgctg gggttattgc tgtgcctgga gataagcccc
     4441 gacctgacgg tggtagtggt ggtgggaata ctgttaacac cggaccggca ggacagctcc
     4501 tggtgatgaa taaaggtcag cttggatact gggaaactcg ttctacgggc gcgggtaaca
     4561 atgagcataa tacgagtgta tttgttgccg taggtccttc tgaggcagaa aaaactgctt
     4621 ctgcagagaa ggcgttaaag gaaaaacagc aggcagaagc agcagcaaaa gactttgcgg
     4681 ctaaaactgc tgccgcatca gccacggcgg aaaaagaacg ccagcaggca attgctgctg
     4741 caactgcagc gggtcagcat cagtcagttt ctgatgcccg taatagcctg aataacgcga
     4801 cgtcagatgt gtctcgtctg aaatcagctg cagacagtgc actgcaggag gcaaaggcaa
     4861 aacggaaggc tgctattgat gctgtacctg ttgcaaccca ggcggaaaat aaatatcagg
     4921 agctgcagca gaagattaaa ggcctgaagc tgaaaaatgg tgagtatggt acggaaaaat
     4981 gggaaataat tggctctaat aaggagcatg atcactgggg atacaggttt tatccatccg
     5041 gaattaccaa agctcaggtt gatgtggcgc agagcgatgc tgtgaataag cgaaatcagg
     5101 ctaccagtct tgccagtcag gcaacagcag cagaacagga cagcctgaaa gctacagctg
     5161 cctataatgc ggcagaaacg cgccgtcagg ctgctcaggc ggcgttaaat tctgctgaac
     5221 aggctgctgc tgctgaacgt aagcggcagg aagctgaggc ggctgcagca gctgctgctg
     5281 agaaaaaacg tcaggcagac gcagtagcaa aagcagcaga ggaagcgcgt gcggcagcgg
     5341 aaaaagccag gctgatgcag gagcgtcagg cagcagcaga taagctgaaa tccacagata
     5401 ttcagtctgt tcgcgggatc ccgtctacgg catcgcctgc agcgtcaccc atttcctggg
     5461 ccgttgcatc acttggtggt atatcgctgg atagtgttac tgcagggaaa gcctggacgc
     5521 agattgctga ggtgatggct aaactgcgag gtattgccgg tgcgagtctt gttggtcccg
     5581 tggtggcaac tgctgtaggg ctgttttggt cacgtgatgt tggtattggc agtgatgtgg
     5641 tgcccggacg tgacatcagc gggctgatgc cgggtgatgc actgtcatta cctgatctgg
     5701 ccactttgat taaagctgct gacagtaaaa cgggtgtcag tatgccggtt cgaggccgga
     5761 ttatcgtgcg tgaaggcgat tat
//
