LOCUS       NZ_CP011613             5410 bp    DNA     circular CON 08-JAN-2024
DEFINITION  Klebsiella oxytoca strain CAV1335 plasmid pCAV1335-5410, complete
            sequence.
ACCESSION   NZ_CP011613
VERSION     NZ_CP011613.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03733750
            Assembly: GCF_001022115.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella oxytoca
  ORGANISM  Klebsiella oxytoca
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 5410)
  AUTHORS   Sheppard,A.E., Stoesser,N., Wilson,D., Sebra,R., Kasarskis,A.,
            Anson,L., Giess,A., Pankhurst,L., Vaughan,A., Grim,C.J., Cox,H.,
            Yeh,A., Sifri,C.D., Walker,S., Peto,T.E., Crook,D.W. and
            Mathers,A.J.
  TITLE     Rapid spread of a carbapenem resistance gene driven by multiple
            levels of genetic mobility
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5410)
  AUTHORS   Sheppard,A.E., Stoesser,N., Wilson,D., Sebra,R., Kasarskis,A.,
            Anson,L., Giess,A., Pankhurst,L., Vaughan,A., Grim,C.J., Cox,H.,
            Yeh,A., Sifri,C.D., Walker,S., Peto,T.E., Crook,D.W. and
            Mathers,A.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-JUN-2015) University of Oxford, John Radcliffe
            Hospital, Oxford OX39DU, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP3 v. 2.2.0
            Genome Coverage                   :: 51X
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/08/2024 01:56:29
            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)                     :: 6,456
            CDSs (total)                      :: 6,338
            Genes (coding)                    :: 6,217
            CDSs (with protein)               :: 6,217
            Genes (RNA)                       :: 118
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 121
            CDSs (without protein)            :: 121
            Pseudo Genes (ambiguous residues) :: 0 of 121
            Pseudo Genes (frameshifted)       :: 53 of 121
            Pseudo Genes (incomplete)         :: 77 of 121
            Pseudo Genes (internal stop)      :: 23 of 121
            Pseudo Genes (multiple problems)  :: 23 of 121
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP011613.1.
            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..5410
                     /organism="Klebsiella oxytoca"
                     /mol_type="genomic DNA"
                     /strain="CAV1335"
                     /isolation_source="Urine/Genitourinary"
                     /host="Homo sapiens"
                     /db_xref="taxon:571"
                     /plasmid="pCAV1335-5410"
                     /geo_loc_name="USA:Virginia"
                     /lat_lon="38.14 N 78.45 W"
                     /collection_date="2010-12"
                     /collected_by="Clinical Microbiology University of Virginia
                     Health System"
     gene            complement(1141..1434)
                     /locus_tag="AB181_RS00010"
                     /old_locus_tag="AB181_00010"
     CDS             complement(1141..1434)
                     /locus_tag="AB181_RS00010"
                     /old_locus_tag="AB181_00010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609270.1"
                     /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="HigA family addiction module antitoxin"
                     /protein_id="WP_000609279.1"
                     /translation="MINLYDPVHPGEFIREMFMEPFEIPAAELADKLEVSQSALSRLLN
                     GKTDLSYEMALRLSKVIGRSAESWVNMQAQYSLSKSRKTLSETLEHLHPMFP"
                     /name="HigA family addiction module antitoxin"
     gene            1772..2053
                     /locus_tag="AB181_RS00015"
                     /old_locus_tag="AB181_00015"
     CDS             1772..2053
                     /locus_tag="AB181_RS00015"
                     /old_locus_tag="AB181_00015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000594459.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_000594459.1"
                     /translation="MIKNIKHKGLRSFAENGNTAGIQPHLAKKLRMILTTLSTATCLQD
                     IVDVRALGCHPLKGERKGEFSVEVNGNWRVVFKVEEPNVLDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            3305..3628
                     /locus_tag="AB181_RS00030"
                     /old_locus_tag="AB181_00030"
     CDS             3305..3628
                     /locus_tag="AB181_RS00030"
                     /old_locus_tag="AB181_00030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_171853543.1"
                     /translation="MLTMWVTEDEHRRLLERCDGRQLAAWMRQICLDEKPARSGKLPSL
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMTIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3837..>4271
                     /locus_tag="AB181_RS35030"
                     /pseudo=""
     CDS             3837..>4271
                     /locus_tag="AB181_RS35030"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            4306..4797
                     /locus_tag="AB181_RS33660"
     CDS             4306..4797
                     /locus_tag="AB181_RS33660"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_045342089.1"
                     /translation="MSSLLTLAKDLEQQSKAQQQSTGEMLKAAFSEHEQSVRAELSASA
                     RRISDAILAHEQSMSEAMEKNRRSVLRTAGRTWLTILMVSALLIGTSGSILWWQGQQIT
                     DNYTHLRQQEDTLAKMTARTWGVRYQESSDGRRFLILPPGIQTEAIPYDGTTWIRLKQE
                     "
                     /name="MbeB family mobilization protein"
     gene            4804..5019
                     /locus_tag="AB181_RS33665"
     CDS             4804..5019
                     /locus_tag="AB181_RS33665"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137422.1"
                     /translation="MTELEKQLLSALEQLQQDYSQRLDEWESAFAEWRSMCGLMQRENA
                     VLNERVSDLSTQVLSLSEQLRRLSGN"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          3019..3192
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.857"
                     /coverage="100.0"
                     /evalue="5.54e-83"
     Typing          complement(2508..3095)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.54"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          3619..5111
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.2"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gttatgtctg tcgccacttt ctcgcgtctg gcaccggaaa cgcagccaac cccgtttcag
       61 cggtgcgccc aacggatgtt atggtaaata agagcgaccg tcccggtcgc tcttgaaaga
      121 gaattcggcc ttaggtcagt tttcgcagat acaatcatgt ggactgcgga gacattcttc
      181 gcactcctca catatgcact catccagttt ttcaccgcac tcgtcgcaac gtgagcagct
      241 acagtgctca tctaaatttc cacaatcgct gcagcgctca cagacgcagt ctgccagctt
      301 ctcgttgcag tcatcgcaga agccacaggt acaggcgctg gcagggaggg cacaaacatc
      361 gcaaatctta tccattggat ccattttatc tcacttttat tttatcagtg gctgtgtgcg
      421 ggcgatttcc ccagcgcgat agatgtggat ttaagtgcca tttttcaatg attaaggcag
      481 ctaaaaaagt ggttttttag ggcttttcaa cgtgaccagc actgacgggg ataaatacag
      541 gtaagcaata atgctcagtc atgaaaagga gaatccgatg gagcaacata cccctgaata
      601 cttacgacgt accttagctc ataaccgtgc cctaatggac gatatcatta gcagtggcat
      661 gtccaggtac tacaacacgg agattgtgga tgccgcatgt gaggcgatag aagctgaatt
      721 gcgacgacga ggaattttgt aagagacaaa gcccgcttat gcgggctttg tcgttactgg
      781 cgcttctgtt actcagtgtt gtctggggtt cggtagatct gtagccagta cctgccaggt
      841 gcgctcgttg gtggtgcgaa ctcattatcg cgaatggtgc agtatcgtcc atatttgcgg
      901 gtaacagtat gagtgtttgt gttgatgtca cattcttgga atgagccacc atcacgacct
      961 attttgccat gtggtcctac ataaattgcc attttgttct cctttttaga gccttgtatg
     1021 ggcatcttat tggtgttcaa acaacaatca tttcaagatc taagaactga actaaaaatc
     1081 aaactaaagg taggtatgcg ggggttttac ggcaaaaagc ccgcacgagc gggcttttac
     1141 ttatggaaac atcggatgaa ggtgttctag cgtctcggat aaagttttac gacttttcga
     1201 gaggctgtac tgagcctgca tattaaccca cgactctgca gagcggccta taactttaga
     1261 tagtcgaaga gccatctcat aactaagatc agtttttcca ttgagcaatc tacttaatgc
     1321 agattgtgat acttcaagct tatcagctaa ctctgcggca ggtatttcga acggttccat
     1381 gaacatttcc ctgatgaatt caccggggtg tacaggatcg taaagattta tcatgccttc
     1441 ctctattggt tttgtatttg attacacaaa acattttgtt tctttcgcgt tgcgcattgc
     1501 acaatacgca agtgtctgtt attgacaaaa aaagcagtaa gctttaggat gctcggtgga
     1561 gcagaaagct accgctgata tggtgtcttt accgactttt tcaaggcgcc atattgtacg
     1621 gttagcgctc ttggaagtca aacgaggtaa tcgacctcag agacaaagtt acgtcaatta
     1681 ttttaataat gcaaggggtt caaatggacg ctgtcaaatt gttttctgtt tatagagata
     1741 gatatcgacg aaaattttat ggagatgatt gatgataaaa aacataaagc ataaagggct
     1801 tcggagtttt gctgaaaacg gtaacaccgc cggaattcag cctcacttag cgaaaaaact
     1861 tcgcatgata ttgactacgc taagcaccgc aacatgtctt caagatattg tggatgtaag
     1921 ggcgctgggg tgtcaccccc taaaaggtga acgtaaaggt gagttttccg tagaggttaa
     1981 cggaaactgg agggtggttt tcaaggtgga agaaccaaac gtcttagacg ttgatcttga
     2041 agattaccat tagtaatcaa taagtaagtt actaatccat cctagtggca atatggatgg
     2101 attagggact ttattcaaaa ataagtacct ctggaggatt tatgagagcc tttatgattt
     2161 tgttgttccc tttgctttgt gtagtcattg ctggggttct tgctgttcgt ggcctagatg
     2221 ggtggggatg gttcctgttt gcagctgttt tgtgtactgg tgttgatacg gtgcagaaac
     2281 atgtctctaa caagaataat tctgtaagcg attgaggctt tcagggttct tccttgactg
     2341 attaaatcga caaagcgtat cttatgttcg aaacgaaaaa accgcctggg gaggcggttt
     2401 tttcgagggt tcagtaagtt ggggaacttc tgaaccgtgg taacagggtg tacaagaccg
     2461 ctgaaaccaa attctgtcct tccagtttag cctcagtatg gctctgactt caagaactct
     2521 gcatcagtaa tctcttgtac accctcttac caatggccgc agccagtggc gttttgttgt
     2581 gtctttccgg gttggactca agtcgatagt taccggataa gacgctgcgg tcggactgaa
     2641 cggggggttc gtgcatacag tccagcttgg agcgaactgc cttcccggaa ctgagtgtca
     2701 ggcgtggaat gagataaacg cggccataac agcggagtga caccggtaaa ccgaaaggca
     2761 ggaacaggag agcgcacgag ggagccacca gggggaaacg cctggtatct ttatagtcct
     2821 gtcgggtttc gccaccactg atttgagcgt cagatttcgt gatgcttgtc aggggggcgg
     2881 agcctatgga aaaacggctt tgtcgtggcc ttctcgcttc cctgttaagc ttcttcctgg
     2941 catcctccag gaaatttccg ccccgttcgt aagccatttc cgctcgccgc agccgaacga
     3001 ccgagcgcag cgagtcagtg agcgaggaag cggaatatat cctgtatcac atattctgct
     3061 gacgcaccgg tgccgccttt tttctcctgc cacatgaagc acttcactga caccctcatc
     3121 cgtgccaaca tagtaagcca gtatacactc cgctagcgct acgtgactgg ttcagggctg
     3181 cgccccgaaa cccgccaaaa gcctgacgcg cctgcggctt gtccaacccc gcgccgaccg
     3241 ggaaaggctt tcccgcccgt cccggcgtta tcaggaggcc ggtttgtcag agaaacggag
     3301 caagatgctc accatgtggg tgacggagga cgagcaccgg cggctgctcg agcgctgtga
     3361 cggcaggcag ctggcggcgt ggatgcggca gatctgcctg gacgaaaagc cggcacgttc
     3421 cggaaagctc ccctcactct cgccggcgct gctgcgccag cttgccggca tgggcaataa
     3481 cctgaaccag atagcccgcc gtgttaacgc cggcggcggc accggccatg acagggtaca
     3541 gattgtggcg gcgctgatga ccatcgatgc cggccttgag cggctgcggc acgccgttct
     3601 tgagaaagga acggacgatg atcgttaaat ttcatccgcg cggccgcggc ggtggcgccg
     3661 ggccggtgga ctatctgctg ggtaaagacc ggcagcgtga aggcgccacc gtcctgcagg
     3721 ggaagccgga agaagtccgg gagctgattg acgcgtcgcc ttacgttaag aaatacacct
     3781 ccggcgttct gtcgtttgcg gaggccgatc tgcctcccgg ccagcgggaa aaactgatgg
     3841 ccagcttcga gcgggttctg atgcccggac tcgataaaga tcagtacagc attctgtggg
     3901 tggagcacgc ggacaagggg cgtctggagc tgaactttct gatccccaat accgagctgc
     3961 tgaccggcag gcggctccag ccttactacg accgcgccga ccggccgcgc atcgatgcct
     4021 ggcagactat cgtgaacggc agactggggc tgcacgaccc gaacgcgccg gaaaaccgcc
     4081 gggctctggt cacgccgtcc gggctgccga aaacgaagca ggaggccgca gaagccatta
     4141 cccggggact gctgaccctt gcttcgtccg gggagctgaa aagccgtcag gatgtcactg
     4201 acactcttga aggtgcaggt tttgaggtgg tgcgcaccac gaaaagcagt atcagcattg
     4261 ccgacccgga cggggggcga aacatccgac tgaagggagc catctatgag cagtctttta
     4321 acgctggcga aggacttaga gcagcaatcg aaagcgcagc agcagagtac cggcgagatg
     4381 ctgaaagccg cattcagcga gcacgagcag tctgtcagag cggaactgag cgcaagcgcg
     4441 aggagaatca gcgacgccat cctcgcccac gagcagagta tgagcgaggc gatggagaaa
     4501 aaccggcgga gcgtactgcg gactgccggg cggacatggc tcaccatcct gatggtgtca
     4561 gcgctgctga tcggcacgag cgggagcatt ctgtggtggc aggggcagca gataaccgac
     4621 aattacacgc atcttcgtca gcaggaagat accctggcga aaatgaccgc ccggacgtgg
     4681 ggagtgcgct atcaggagag cagcgacggc cggaggtttc ttatcctgcc gccggggata
     4741 caaaccgaag ccatccctta cgacgggacg acatggatcc gcctgaaaca ggagtagctg
     4801 aaaatgacag agctggaaaa gcagttgctg agcgcattag agcagctaca gcaggactac
     4861 tcgcaaaggc tggacgaatg ggagagcgcc ttcgcggaat ggcggagcat gtgtgggctt
     4921 atgcaacggg agaacgcggt gctgaacgag cgcgtgtcgg acttgagcac gcaggtgctg
     4981 agtttaagcg agcagctgcg ccgcttgtcc gggaactgaa tgccatcgag ctccggcaga
     5041 gggagaatga gtatcagaaa acactggagc tggagcgcca gccgcagaaa acctaccgcg
     5101 ggccgacact ttaaaccatc caggcagctg acaacccgca cgaagagggg ctcttatttc
     5161 tcccgctaaa taggttcgtg atcaaaaagg tcacgactta ttcaggagcg ggaaatgaag
     5221 ctgttaaatc ttattgaatc attgcttaac tgcctgtatc tggcggcgga gctgtgggac
     5281 tggctggaga agcatttgtc ggtttttaag gcattggcgc ggattttagt gtgactttaa
     5341 catccatgca tctggctgca tgactatgca ccagtgtaat attcagcggc tgcgtttctg
     5401 gtgttttttc
//
