LOCUS       NZ_CP113909             4448 bp    DNA     circular CON 02-APR-2024
DEFINITION  Klebsiella michiganensis strain PS_Koxy4 plasmid pPSKoxy4_5,
            complete sequence.
ACCESSION   NZ_CP113909
VERSION     NZ_CP113909.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12648330
            Assembly: GCF_014050515.2
KEYWORDS    RefSeq.
SOURCE      Klebsiella michiganensis
  ORGANISM  Klebsiella michiganensis
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 4448)
  AUTHORS   Shibu,P., McCuaig,F., McCartney,A.L., Kujawska,M., Hall,L.J. and
            Hoyles,L.
  TITLE     Improved molecular characterization of the Klebsiella oxytoca
            complex reveals the prevalence of the kleboxymycin biosynthetic gene
            cluster
  JOURNAL   Microb Genom 7 (6) (2021)
   PUBMED   34142942
REFERENCE   2  (bases 1 to 4448)
  AUTHORS   Hoyles,L.
  TITLE     Phage vB_KmiS-Kmi2C represents a novel genus of lytic bacteriophage
            that infects members of the Klebsiella oxytoca complex
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 4448)
  AUTHORS   Hoyles,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-DEC-2022) Biosciences, Nottingham Trent University,
            Clifton Lane, Nottingham NG11 8NS, United Kingdom
REFERENCE   4  (bases 1 to 4448)
  AUTHORS   Shibu,P., Mccartney,A.L., Kujawska,M., Hall,L.J. and Hoyles,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (28-AUG-2019) Biosciences, Nottingham Trent University,
            Clifton Lane, Nottingham NG11 8NS, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: NOV-2022
            Assembly Method                   :: Unicycler v. 0.4.0
            Assembly Name                     :: PS_Koxy4_hybrid
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 57.0x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_014050515.2-RS_2024_04_02
            Annotation Date                   :: 04/02/2024 06:27:22
            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)                     :: 6,156
            CDSs (total)                      :: 6,040
            Genes (coding)                    :: 5,888
            CDSs (with protein)               :: 5,888
            Genes (RNA)                       :: 116
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 152
            CDSs (without protein)            :: 152
            Pseudo Genes (ambiguous residues) :: 0 of 152
            Pseudo Genes (frameshifted)       :: 47 of 152
            Pseudo Genes (incomplete)         :: 119 of 152
            Pseudo Genes (internal stop)      :: 19 of 152
            Pseudo Genes (multiple problems)  :: 31 of 152
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP113909.1.
            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..4448
                     /organism="Klebsiella michiganensis"
                     /mol_type="genomic DNA"
                     /strain="PS_Koxy4"
                     /isolation_source="Rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1134687"
                     /plasmid="pPSKoxy4_5"
                     /geo_loc_name="United Kingdom: London"
                     /collection_date="2015-09"
                     /identified_by="P. Shibu"
     gene            join(4423..4448,1..133)
                     /locus_tag="F0A14_RS30690"
                     /old_locus_tag="F0A14_030685"
     CDS             join(4423..4448,1..133)
                     /locus_tag="F0A14_RS30690"
                     /old_locus_tag="F0A14_030685"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032670878.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHEKSLLAAAISNWRYTRDKL
                     RGLEVWA"
                     /name="hypothetical protein"
     gene            complement(370..738)
                     /locus_tag="F0A14_RS30695"
                     /old_locus_tag="F0A14_030690"
     CDS             complement(370..738)
                     /locus_tag="F0A14_RS30695"
                     /old_locus_tag="F0A14_030690"
                     /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_044704866.1"
                     /translation="MALLISLVVVAGLYYQFWYKPHRAPILRIWGIAPDGQEFRLLLTE
                     HGEKEAVLLFGKKSFVAVPDTQNLYGGCYYLYLEDAHKNELLIELNESDLYPGGAIELQ
                     HNGGRKIHCEILKVRWSR"
                     /name="hypothetical protein"
     gene            898..1131
                     /locus_tag="F0A14_RS30700"
                     /old_locus_tag="F0A14_030695"
     CDS             898..1131
                     /locus_tag="F0A14_RS30700"
                     /old_locus_tag="F0A14_030695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008461706.1"
                     /GO_component="GO:0005886 - plasma membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YgdI/YgdR family lipoprotein"
                     /protein_id="WP_044704865.1"
                     /translation="MNKKTLLAAMMVALVTFAAAGCSSNQEIKTTDGRTIVTDGKPKVD
                     SDTGLVSYKDAHTGRTEQINRDKITNMSELDN"
                     /name="YgdI/YgdR family lipoprotein"
     gene            1153..1380
                     /locus_tag="F0A14_RS30705"
                     /old_locus_tag="F0A14_030700"
     CDS             1153..1380
                     /locus_tag="F0A14_RS30705"
                     /old_locus_tag="F0A14_030700"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010615788.1"
                     /GO_component="GO:0005886 - plasma membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YgdI/YgdR family lipoprotein"
                     /protein_id="WP_000719360.1"
                     /translation="MKKIFVSVFAAAVALSALTGCTRTSYAIHTNDGRTIVSDGKPTES
                     DSGLLGYKDANGVKQQINKADVKEVSEIPH"
                     /name="YgdI/YgdR family lipoprotein"
     gene            complement(2072..2287)
                     /locus_tag="F0A14_RS30710"
                     /old_locus_tag="F0A14_030705"
     CDS             complement(2072..2287)
                     /locus_tag="F0A14_RS30710"
                     /old_locus_tag="F0A14_030705"
                     /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_044704874.1"
                     /translation="MTELEKQLLTALEQLHQDYSQRLDEWESAFAEWQKMSGLMQRENA
                     VLNERVSDLSTQVLSLSEQLRRLSGN"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2294..2785)
                     /locus_tag="F0A14_RS30715"
                     /old_locus_tag="F0A14_030710"
     CDS             complement(2294..2785)
                     /locus_tag="F0A14_RS30715"
                     /old_locus_tag="F0A14_030710"
                     /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_063844470.1"
                     /translation="MSSLLTLAKDLEQKSKAQQQSTGEMLKAAFSEHEQSVRAELSASA
                     RRISDAISAHEQSMSEAMEKNRRSVLLTAGRAWLTILMVSALLIATSGSILWWQGQQIT
                     DNYTHLRQQEDTLAKMTARTWGVRYQESSDGRRFLILPPGMQAEAIPYDGTTWIRLKQE
                     "
                     /name="MbeB family mobilization protein"
     gene            complement(<2820..3524)
                     /locus_tag="F0A14_RS30825"
                     /pseudo=""
     CDS             complement(<2820..3524)
                     /locus_tag="F0A14_RS30825"
                     /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            complement(3463..3786)
                     /locus_tag="F0A14_RS30725"
                     /old_locus_tag="F0A14_030720"
     CDS             complement(3463..3786)
                     /locus_tag="F0A14_RS30725"
                     /old_locus_tag="F0A14_030720"
                     /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_170949721.1"
                     /translation="MLTMWVTEDEHRRLLERCDGRQLAAWMRQTCLDEKPARTGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLEQLRHAVLEKGTD
                     DDH"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(3893..3971)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.75"
                     /coverage="100.0"
                     /evalue="2.7400000000000003e-32"
     Typing          2..133
                     /name="rep_cluster_2406"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="84.0"
                     /evalue="5.08e-63"
     Typing          4047..4448
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.122"
                     /coverage="94.0"
                     /evalue="8.28e-111"
     Typing          complement(1981..3473)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.8"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3470..3786)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="99.0"
                     /evalue="9.77e-61"
ORIGIN
        1 ctgctgcgcc ttatccggta actatcgtct tgagtccaac ccggaaagac acgaaaaatc
       61 gctactggca gcagccatta gtaactggag gtatacgaga gacaaattaa gaggtcttga
      121 agtatgggcc tgagagaggc tacactgaaa gaacattttt ggtttctgcg gtctcgtata
      181 cccagttacc tggttaagca gttccccaac tgacttaacc ttcgatcaaa ccacctcccc
      241 aggtggtttt ttcgttttca gagcaagaga ttacgactgt aacgacagga tcacaagaag
      301 atcatttact cagagagact aactaccact atgtttgcct atcaacatac ttaggaaaca
      361 ttacttgagt taacgactcc accttacttt tagtatctcg caatgaatct tccgaccgcc
      421 gttgtgttga agttctattg cgccaccggg gtataaatca ctttcgttta actcaattaa
      481 aagctcgttc ttgtgagcat cctctaaata aaggtaataa cacccaccat aaaggttctg
      541 cgtatctggc acggcaacaa aagatttctt tccgaacagt aaaacagcct ctttttctcc
      601 atgctctgtt agcaataatc gaaattcttg tccatcaggc gcgatccccc atatacgcaa
      661 gatcggcgct ctatgtggct tataccaaaa ttgatagtaa agacctgcca ctacaaccag
      721 tgaaattaat aaggccattt caatcctcaa aaacaagcaa cattccaaaa tcgtttttca
      781 ttcattttta ctgctgggca tgatgcccac cttcaatcct cttttcgcat gaaaaaacga
      841 cctatactta gatggttagt gaccatatcc actttacctt taagcaggga acctattatg
      901 aataaaaaaa cgctgttggc ggccatgatg gtcgcgttgg tgacctttgc cgctgctgga
      961 tgttcttcaa accaagaaat aaaaaccaca gatggtcgca ctatcgttac agacggcaaa
     1021 cccaaagttg acagtgatac ggggttagta tcctacaaag atgcccatac aggccgaacc
     1081 gaacagatca accgtgacaa aattaccaac atgagtgaac tagacaactg atacggataa
     1141 aaggagctgg ctttgaaaaa gatttttgtt tcagtgttcg cagcggcagt tgcgctttca
     1201 gccctaaccg gctgcacgcg cacaagctat gccatccaca ccaacgacgg gcgtacaatt
     1261 gtcagcgacg gcaagcctac agaatcagac tcaggcctgc tgggctataa agacgcaaat
     1321 ggtgtcaaac agcagatcaa taaagccgac gttaaagaag tctctgaaat tccgcattga
     1381 ggcatcgctc tctccgaaaa gggccgctaa tgcggccctt ttctttatct gccccaacaa
     1441 caggcaaaaa aagcccccgc tgggggccaa atacctgcag tggctggata gtactgcatt
     1501 cctgatgaag gagacgaata agtatgggcc ggatttttgc gtctgcaggc tcggtcgcca
     1561 caatttttcc gtacccgcca ggcatcatgc ttttaccata acatcccttg tctgcaccgc
     1621 cggatcggca ctgacggcgc agacggcacc aggcacccga aaacccggct taagcaacgc
     1681 tacatcctcc gttaagccgg gagataattt ttacccgact gcatagccat gcagccaggt
     1741 gaatgacggc aggattcagc ccaaaaacag cgtgaaggcc ccgaaaaccg gcaaatgctt
     1801 ttccagccac tcccacagtt ctgccgccag atgcaggcag ttaagtacag cttcaataac
     1861 attaagcagt ttcataattc cccctggtat aggccgtgat ctttgcatca cgacgtattt
     1921 agcggggaat ttcgcagccc ttcttcttgg ggtttatcac gggccggcat ccgtcagccc
     1981 agcgtcggtc ctttgtaggt tttctgcggc tggcgctcca gctccagtgt tttctgatac
     2041 tcattctccc cctgccggaa ctcggtggca ttcagttccc ggacaagcgg cgcagctgct
     2101 cgcttaaact cagcacctgc gtgctcaagt ccgacacgcg ctcgttcagc accgcgttct
     2161 cccgttgcat aagcccagac atcttctgcc attccgcgaa ggcgctctcc cattcgtcca
     2221 gcctttgcga gtagtcctga tgtagctgct ctaatgcggt cagcaactgc ttttccagct
     2281 ctgtcatttt ccgctactcc tgtttcaggc ggatccaggt cgtcccgtcg taggggatgg
     2341 cttcggcttg catccccggc ggcaggataa ggaacctccg gccgtcgctg ctctcctgat
     2401 agcgcactcc ccacgtccgg gcagtcattt tcgccagggt atcttcctgc tgacgaagat
     2461 gtgtgtaatt gtcggttatc tgctgcccct gccaccacag aatgctcccg ctcgtggcga
     2521 tcagcagcgc tgacaccatc aggatggtga gccatgccct cccggctgtc agcagcacgc
     2581 tccgccggtt tttctccatc gcctcgctca tactctgttc gtgggcgctg atggcgtcgc
     2641 tgattctcct cgcgcttgcg ctcagttccg ctctgacaga ctgctcgtgc tcgctgaatg
     2701 cggctttcag catctcgccg gtactctgct gctgcgcttt cgatttctgc tccaagtcct
     2761 tcgccagcgt taaaagactg ctcatagatg gctcccttca gtcggatgtt tcgccccccg
     2821 tccgggtcgg caatgctgat gctgcttttc gtgctgcgca ccacctcaaa acctgcgctt
     2881 tccagcgcct cagtgacgtc ctgacgggtt ttcagctccc cggatgaggc aagggcaagc
     2941 aggccgcgcg taatcgcctg ggcagcttcc tgcttcgctt ccggcagcgc ggacggcgtg
     3001 accagcgccc gccggttttc cggcgcgttc gggtcgtgca gccccagccg gccgttgacc
     3061 accgtctgcc aggcatcgat gcgcggccgg tcggcgcggt cgtagtacgg ctggagccgc
     3121 ctgccggtca gcagctcggt attggggatc agaaagttca gctccagacg ccccttgtcc
     3181 gcgtgctcca cccacagaat gctgtactga tctttatcga ggccgggcat cagaacacgc
     3241 tcgaagctgg ccatcagttt ttcccgctgg ccgggaggca gatctgcctc cgcaaacgac
     3301 agtacgccgg aggtgtattt cttcacgtaa ggcgacacat caatcagctc ccggacttct
     3361 tccggcttgc cctgcaggac ggtggcgcct tcacgctgcc ggtctttacc cagcaaatag
     3421 tccaccggcc cggcgccacc gccgcgaccg cgcggatgaa atttaatgat catcgtccgt
     3481 tcctttctca agaacggcgt gccgcagctg ctcaaggccg gcatcgattg ccatcagcgc
     3541 cgccacaatc tgcaccctgt catggccggt accgccgccg gcgttaacgc ggcgggctat
     3601 ctggttcagg ttgttgccca tgccggcaag ctggcgcagc agcgccggcg agatcgaggg
     3661 tagctttccg gtacgcgcag gcttttcatc aagacaggtc tgccgcatcc acgccgccag
     3721 ctgcctgccg tcacagcgtt cgagcagccg ccggtgctcg tcctccgtca cccacatggt
     3781 gagcatcttg ttccgtttct ctgacaaacc ggtctcctga taacgccggg acgggcggga
     3841 aagcctttcc cggtcggcgc ggggttggac aagccgcagg cgcgtcaggc ttttggcggg
     3901 tttcggggcg cagccctgaa ccagtcacgt agcgctagcg gagtgtatac tggcttacta
     3961 tggtggcacg acgggaatcg ggatgaaata gtcagtcata aaaactgtga gatgaggctc
     4021 aggtgcgtaa ggggctgatg cctgtcccgg tggatattcc gcttcctcgc tcactgactc
     4081 gctacgctcg gtcgttcggc tgcggcgagc ggtacggact cacggataaa gacgtggggg
     4141 ggaaatacgt gaatgcagga ggggaaaaaa ggatgcggcg ctgccggttt tccataggct
     4201 ccgcccccct gacaagcatc acagaatctg acgctcaaat cagtggtggc gaaacccgat
     4261 gcggcttaaa gataccaggc gtttccccct gatggctccc tcgtgctccc ccgcattcct
     4321 gcctttcggt ttaccggtgt cattccgctg ttatggccgc ggtttctcat tccacgcctg
     4381 acactcagtt ccgcgaaggc agttcgctcc aggattgact gtatgcacga accccccgtt
     4441 cagtccga
//
