LOCUS       NZ_CP074453             3953 bp    DNA     circular CON 22-FEB-2024
DEFINITION  Klebsiella michiganensis strain S4_CRE4 plasmid pCRE4_4, complete
            sequence.
ACCESSION   NZ_CP074453
VERSION     NZ_CP074453.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16387624
            Assembly: GCF_027595545.1
KEYWORDS    RefSeq.
SOURCE      Klebsiella michiganensis
  ORGANISM  Klebsiella michiganensis
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
REFERENCE   1  (bases 1 to 3953)
  AUTHORS   Elam,L.P., Chittur,K., Addison,R.M., Lewis,S., Smith,B.A.,
            Anderson,D.J. and Sysoeva,T.A.
  TITLE     Characterization Of Recent Carbapenem-Resistant Enterobacteriaceae
            Isolates From A Large Tertiary Care US Hospital
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3953)
  AUTHORS   Elam,L.P., Chittur,K., Addison,R.M., Lewis,S., Smith,B.A.,
            Anderson,D.J. and Sysoeva,T.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-MAY-2021) Biological Sciences, University of Alabama
            in Huntsville, 301 Sparkman Dr, Huntsville, AL 35899, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 395x
            Sequencing Technology             :: Illumina NextSeq; PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/22/2024 01:40:53
            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)                     :: 5,825
            CDSs (total)                      :: 5,707
            Genes (coding)                    :: 5,580
            CDSs (with protein)               :: 5,580
            Genes (RNA)                       :: 118
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 127
            CDSs (without protein)            :: 127
            Pseudo Genes (ambiguous residues) :: 0 of 127
            Pseudo Genes (frameshifted)       :: 41 of 127
            Pseudo Genes (incomplete)         :: 93 of 127
            Pseudo Genes (internal stop)      :: 19 of 127
            Pseudo Genes (multiple problems)  :: 23 of 127
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP074453.1.
            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..3953
                     /organism="Klebsiella michiganensis"
                     /mol_type="genomic DNA"
                     /strain="S4_CRE4"
                     /isolation_source="urine, clean catch"
                     /host="Homo sapiens"
                     /db_xref="taxon:1134687"
                     /plasmid="pCRE4_4"
                     /geo_loc_name="USA: Durham, NC"
                     /lat_lon="36.0075 N 78.9384 W"
                     /collection_date="2017-01-26"
                     /collected_by="Rachel Addison"
     gene            join(3798..3953,1..36)
                     /locus_tag="KHV91_RS29075"
                     /old_locus_tag="KHV91_28995"
     CDS             join(3798..3953,1..36)
                     /locus_tag="KHV91_RS29075"
                     /old_locus_tag="KHV91_28995"
                     /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_004187666.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            36..437
                     /locus_tag="KHV91_RS29080"
                     /old_locus_tag="KHV91_29000"
     CDS             36..437
                     /locus_tag="KHV91_RS29080"
                     /old_locus_tag="KHV91_29000"
                     /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_023287146.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIRAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSEQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1304..1459)
                     /locus_tag="KHV91_RS29085"
                     /old_locus_tag="KHV91_29005"
     CDS             complement(1304..1459)
                     /locus_tag="KHV91_RS29085"
                     /old_locus_tag="KHV91_29005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010251985.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF1508 domain-containing protein"
                     /protein_id="WP_064761103.1"
                     /translation="MNDTWDFYTDGKGEWRWRRTASNGRIVGASSQGYVNRADCIANAR
                     RNGYTG"
                     /name="DUF1508 domain-containing protein"
     gene            1935..2702
                     /locus_tag="KHV91_RS29090"
                     /old_locus_tag="KHV91_29010"
     CDS             1935..2702
                     /locus_tag="KHV91_RS29090"
                     /old_locus_tag="KHV91_29010"
                     /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_094543585.1"
                     /translation="MRFLWRPLPYSRLRECDFLNCIDENDSSSWIAALKIFICIVIKSD
                     LDENGEYCAMITYPQVQKMTGMSRQLICCGFDKLKFYKMISSEGVRKKKYSLLTCEKGS
                     TRQKPLTKRFDGLSTGRWCKFPLKGLIDDDGVIPSFLAMSNRNINDLHALRLFIYLLSV
                     RRHGDVFIVVKAETLMKKLRLKRVQLTLALAHMSALGLIVKERYREGDFLSLNKTPAYA
                     FLLCGWDALEWNHNRIKESNWRNDYLESFDNWV"
                     /name="hypothetical protein"
     gene            complement(2723..2896)
                     /locus_tag="KHV91_RS29095"
                     /old_locus_tag="KHV91_29015"
     CDS             complement(2723..2896)
                     /locus_tag="KHV91_RS29095"
                     /old_locus_tag="KHV91_29015"
                     /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_153848860.1"
                     /translation="MDIKTKLKRSLDSVESAISSLKRARGQTTDAYHEINKAIRELEDA
                     EYNIRKSIREME"
                     /name="hypothetical protein"
     gene            complement(3233..3382)
                     /locus_tag="KHV91_RS29170"
     CDS             complement(3233..3382)
                     /locus_tag="KHV91_RS29170"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001396189.1"
                     /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_077253766.1"
                     /translation="MHEPPVQSDCCACSGNYQLESNPERHDKAPLAAATGKQDVREMYL
                     EFLK"
                     /name="replication initiation protein"
     Typing          complement(3274..3676)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.545"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 tcctcgagac tggatgcatt acaggatggt aactgatggc cagagtgtct attagtgagg
       61 ctgcccgact gacgggtaag agtagaacaa cactgcacag gttaattaga gcaggtgacc
      121 tgtccacctg tagcggtgaa cgcaatgcaa aaatggtaga tacttcagag cttttgcgtg
      181 tctttggtcc ctttgagcaa ccgaagggtg aacaccattc tggacaggtc tctgaacagc
      241 gtgatacagc ctctgctgac cagagtgaac aggtgattcg tcatctgaaa caggagattg
      301 aacacctgaa caccttactt ttgtccaagg attcgcacat tgacagcctg aaacaggcca
      361 tgctccttct tgaaaatcac caggcaaaat taactgaatc cccggcgcca tggtggaaat
      421 tctggaaaaa atcctgatcc tgccatgctt gagttttcct ctccggccat cccggggagt
      481 tcctgaacct tcccaaaaat cgccagatct ctgaacgctc ctcacgacta aaaataccca
      541 cacactacgc aaaattaaaa ttttgcagat ttgtatttaa tatcagttgt ttactttcct
      601 gaaatttcgt tttttaaatt ttatttacat agatccgact ctatgacgac tcgtcataga
      661 gtccccggcg agtcgtcata gagtcggtaa cgactcagga ctataaaaac aataagttaa
      721 taacgacccg actctagaca cgactccccg tttggttgtt ttttagacgc ggcgactctg
      781 ggtacgactc tagtgaagag tcgccggtga atcgtgtggt gagtcgtccg gcgacttgcc
      841 ataacgtgat tgccggccgt cgacgaaccc gattcctgaa cgtgctgaaa accggttttc
      901 cggctgcgcc ggcaacgctt cacggccacg caataaattg cgtccccgtt caccgttttc
      961 ggatgggaag aacgccggaa acaggactta ccctggctga atggcgtgaa ttttcgcgct
     1021 atgcacttgc gtgcatactc atgcatgccg taaaaacaga gcctgcgcgt ttctggcggg
     1081 ttttcgggtg gtttgttgcc tgttttaccg gtttcccgtc agaaacgccc tgaggccgtt
     1141 ttagcggtgc gtacaatcat gcctttatgt taaatgacaa atgcaaaaaa gcccccgaag
     1201 gggcctgaag gttttcctgt atagggagga aaaataggtg ccctgtttgg cagtacccgt
     1261 taccggctga cagccacatt ccagtcgtat acctgattca ggactagccg gtgtaaccat
     1321 tgcggcgggc attagcgatg caatccgctc ggtttacata gccctgactg gatgcaccaa
     1381 caatacgacc attgctggcc gttctgcgcc agcgccattc gcctttacca tcagtataaa
     1441 aatcccatgt atcgttcatt ctgtttttat cctgtgctgt gtggggatcc ccaaggttga
     1501 tataaagcat tcctcctctt tttcaatcga taagagtgtg ttttgcgatg cgagtacgat
     1561 aggaatttct gttacatgtt actcatgcaa tgccgtctca ttaggtctaa aggcttcttg
     1621 tgatgcacat agactatctt ggtatcttaa tagactatct tttgttgtta taacattgat
     1681 tttaaaggtt tttgtatttt gttatattct agaaagatta taataaaaag acttataagt
     1741 ctttttatta tgtgtcatga ttttttcaag atttgagcag aggtgttttc gggaggagag
     1801 tatcatgagt ctagaaaagt atgtgaagtt actcgagaga gttgcagcga tttctggtga
     1861 gttaacccag cttgtaatct ctgtgacgtt attaataatt tcttggtatc ttattaaata
     1921 attaaggtga agctatgcgg tttttatgga ggcctttgcc ttactctagg ttaagggaat
     1981 gtgatttttt aaactgtatt gatgagaatg attcgtcttc atggatagcc gcattgaaaa
     2041 tattcatttg cattgttatt aaatctgatc tggatgagaa tggagagtat tgtgcaatga
     2101 ttacgtatcc tcaagtccag aaaatgacag ggatgagtag gcagttaata tgttgtggtt
     2161 ttgataagct gaagttttat aaaatgatat ctagcgaggg tgttaggaaa aaaaagtatt
     2221 cattattaac ttgtgaaaaa ggctccacta gacaaaaacc tttgacgaaa aggtttgatg
     2281 ggctatccac ggggagatgg tgtaagttcc cgttaaaagg attgattgat gatgatggtg
     2341 taatcccttc ttttctggct atgagcaata gaaatattaa cgaccttcat gcattgcggt
     2401 tgtttatcta tttattgtca gtgaggaggc atggtgatgt ttttattgtt gtaaaagcag
     2461 aaacgctgat gaaaaaatta cgacttaaaa gagttcaact aacattggct ttagctcata
     2521 tgtcagcttt ggggttgata gttaaagagc gatataggga gggcgatttt ttgagtttaa
     2581 ataaaacgcc tgcatatgct tttttattgt gtggatggga tgctcttgag tggaatcaca
     2641 atagaataaa agagagtaac tggagaaatg attatttaga gtcgtttgat aactgggttt
     2701 gaagcccagt tatctatata actcactcca tctcacgaat ggatttcctt atgttgtact
     2761 cggcatcctc aagttcacga attgctttgt ttatttcatg gtatgcatcc gtagtttgcc
     2821 ctcttgcacg ctttaaagat gaaattgcac tttccacaga atctaaagaa cgtttaagct
     2881 ttgtcttgat atccatattg aacctctgtt ttttatctgc tgctagggtg attgtggaac
     2941 accctaatga atttgtttta tttaaataaa atcaatatga tacgtctttt tttgaagtct
     3001 attggtattg ttaagtggtg ctggtttggt tttgatatat gtctatgtat ctaacggatt
     3061 tgcttgtgat cctttcctcg gcgtcgtagt ctcttgctct gtaaacgaaa aaaccacccg
     3121 gcaaggtggt ttttcgaagg ttcattaacc ggcaagttta tgaaccgtgg taacagtctt
     3181 gtgcgagaca tgtcaccaaa tccgtccttc cagtgtagcc tcagttaggt cttcacttca
     3241 agaactctaa atacatctct cgcacatcct gtttaccagt ggctgctgcc agtggcgctt
     3301 tgtcgtgtct ttccgggttg gactcaagtt gatagttacc ggaacaggcg cagcagtcgg
     3361 actgaacggg gggttcgtgc atacagtcca gcttggagcg aactgccttc ccggaactga
     3421 gtgtcaggcg tggaatgaga taaacgcggc cataacagcg gaatgacacc ggtaaaccga
     3481 atggcaggaa caggagagcg cacgagggag ccatcagggg gaaacgcctg atatctttat
     3541 agtcctgtcg ggtttcgcca ccactgattt gagcgtcagt ttctgtgatg cttgtcaggg
     3601 gggcggagcc tatggaaaaa cggccgcaaa gcggcctttc cttttccccg tcacgcgatc
     3661 gctcggtttt ctcgagtttt tacacgcatg ctcctgccgc tcgccgcagc cgaacggcag
     3721 gagcatagcg actgagtgag cgaggaagcg gaaaagagaa catccctaca ctgcgcactg
     3781 acgctctgag gcctcttatg acgaaacaac agaaaacagc gcttaacatg gctaaattca
     3841 tccagaatca gtctctgctc ctgctggaga agcttaatga gcttgatctc gatgtcgagg
     3901 ccgacctttg tgagaaactc cacgatgatg cggagcatct tttccgtaca ctg
//
