LOCUS       NZ_CP054300             2155 bp    DNA     circular CON 12-MAY-2024
DEFINITION  Citrobacter freundii strain IDR1800045912-01-00 plasmid p1C2,
            complete sequence.
ACCESSION   NZ_CP054300
VERSION     NZ_CP054300.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15086845
            Assembly: GCF_014170055.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 2155)
  AUTHORS   Prussing,C., Snavely,E., Singh,N., Lapierre,P.,
            Lasek-Nesselquist,E., Mitchell,K., Haas,W., Owsiak,R., Nazarian,E.
            and Musser,K.
  TITLE     Nanopore MinION sequencing reveals possible transfer of blaKPC-2
            plasmids across bacterial species in two healthcare facilities
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2155)
  AUTHORS   Prussing,C., Snavely,E., Singh,N., Lapierre,P.,
            Lasek-Nesselquist,E., Mitchell,K., Haas,W., Owsiak,R., Nazarian,E.
            and Musser,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-JUN-2020) Division of Infectious Diseases, Wadsworth
            Center, New York State Department of Health, 120 New Scotland Ave,
            Albany, NY 12208, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 02-OCT-2019
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 183x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_014170055.1-RS_2024_05_12
            Annotation Date                   :: 05/12/2024 03:50:50
            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)                     :: 5,127
            CDSs (total)                      :: 5,006
            Genes (coding)                    :: 4,896
            CDSs (with protein)               :: 4,896
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 110
            CDSs (without protein)            :: 110
            Pseudo Genes (ambiguous residues) :: 0 of 110
            Pseudo Genes (frameshifted)       :: 27 of 110
            Pseudo Genes (incomplete)         :: 75 of 110
            Pseudo Genes (internal stop)      :: 21 of 110
            Pseudo Genes (multiple problems)  :: 13 of 110
            Pseudo Genes (short protein)      :: 1 of 110
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054300.1.
            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..2155
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="IDR1800045912-01-00"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="p1C2"
                     /geo_loc_name="USA:Maine"
                     /lat_lon="45 N 69 W"
                     /collection_date="2018-10"
                     /collected_by="Maine Center for Disease Control and
                     Prevention"
     gene            join(2052..2155,1..199)
                     /locus_tag="HS089_RS25510"
                     /old_locus_tag="HS089_25515"
     CDS             join(2052..2155,1..199)
                     /locus_tag="HS089_RS25510"
                     /old_locus_tag="HS089_25515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005161566.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="TM2 domain-containing protein"
                     /protein_id="WP_023207139.1"
                     /translation="MSSMVYCRGCGKEIHETAKSCPHCGATNASSGSGEKSRIAAALLA
                     FFLGGFGVHKFYLGKIGQGFLYLIFCWTFIPAIIAFIEFIIYLCDSDEKFARKYG"
                     /name="TM2 domain-containing protein"
     gene            454..642
                     /locus_tag="HS089_RS25515"
                     /old_locus_tag="HS089_25520"
     CDS             454..642
                     /locus_tag="HS089_RS25515"
                     /old_locus_tag="HS089_25520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /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_000165998.1"
                     /translation="MTKQESAALNMAKFIRAQSLLLLEKLDVLDLDDEAADCERMHEQA
                     EALYQKLSARFGIQDGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(690..890)
                     /locus_tag="HS089_RS25520"
                     /old_locus_tag="HS089_25525"
     CDS             complement(690..890)
                     /locus_tag="HS089_RS25520"
                     /old_locus_tag="HS089_25525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001046776.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024148903.1"
                     /translation="MNLCPDERLLFVRMISAMLRRSGGDAGAVMFEAYRHIVSDTNQAR
                     RSYMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            1631..1744
                     /locus_tag="HS089_RS25525"
                     /old_locus_tag="HS089_25530"
     CDS             1631..1744
                     /locus_tag="HS089_RS25525"
                     /old_locus_tag="HS089_25530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_072202106.1"
                     /translation="MHEPPVQSDCCAFSGNYQLESNPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     Typing          complement(1097..1269)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.954"
                     /coverage="100.0"
                     /evalue="2.04e-62"
     Typing          1194..1740
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.625"
                     /coverage="90.0"
                     /evalue="0.0"
ORIGIN
        1 aaaaagtaga atcgcagccg cgctattagc attcttcctt ggtggatttg gcgtacataa
       61 attttactta ggtaaaatag gacagggatt cctgtatcta attttttgct ggacattcat
      121 acccgcgatc atcgcgttta ttgagtttat tatttatcta tgcgattccg atgaaaaatt
      181 cgcaagaaaa tatggctaac tcatagcaaa aaagccctgc ggggcttttt ttgtaccagt
      241 ctgtgaggca gatttaccat aacatccgtt gcccgcaccg cctgagacgc cctcagcgcg
      301 tttctgagga ctccggcctg aaacatacac ctttctgtgc ccatatcgag aaaaaacgcc
      361 cctgatgatt tctgcgtacc tgcatggcta tgcactcaag tgaatgaagt aagatttcag
      421 tctgcgatca ccataaaacc gggaaaaagc cgtatgacaa aacaggaatc agccgcactg
      481 aacatggcaa aatttatccg ggcgcagtcg ctgctgctgc tcgaaaaact cgacgtgctc
      541 gatcttgatg acgaggcagc cgactgtgag cgaatgcacg aacaggcaga agcgctttat
      601 cagaagctga gcgcacgctt cggtatacag gacggcgaat aaagagacga aaagaacgct
      661 cacttagacg aaaagcgtat ccagggcaac tatgtatatc caccgtgtac atagtcatgc
      721 ctgacgcttt cgagcaggtc gagcatgtag gaacgacgag cttgattggt atcggacaca
      781 atatggcgat acgcctcaaa cataacagca cccgcatcac cgcccgaacg gcgaagcata
      841 gcggaaatca tccgcacaaa gagcagacgt tcatcggggc aaaggttcat aagttctcct
      901 ggtgaaaaac caaacatgaa agcacccatc tattaacgtc agctgtgaac gcttcattag
      961 aagaaaatag gtaaacccgg gaaaaagatc caaacgttaa catcacaggt aaacagaaac
     1021 gtcgggtcga tcgggaaatt ctttcccgga cggcgcgggg ttgggcaagc cgcaggcgcg
     1081 tcagtgcttt tagcgggtgt cggggcgcag ccctgaacca gtcacgtagc gctagcggag
     1141 tgtatactgg cttactatgt aggcacgggt gcgggaatca gtgaagtgct tcatgtggca
     1201 ggaggaaaat gcagcagcag agcgtaagcg gaatatatga gacaggagat attccgcttc
     1261 ctcgctcact gactcgctgc gctcggtcgt tcggctgcgg cgagcggtgc gggcttacga
     1321 atggggcgga aatctcctgg gagatgccag gaagaaactt aacagggaaa cgataaggcc
     1381 gcggcgaagc cgtttttcca taggctccgc ccccctgaca agcatcacga aatctgacgc
     1441 tcaaatcagt ggcggcgaaa cccgacagga ctataaagat cccaggcgtt tccccctggt
     1501 agctccctcg tgcgctctcc tgttcctgcc tttcggttta ccggtgtcat tccgctgtta
     1561 tggccgcgtt tatctcattc cacgcctgac actcagttcc gggaaggcag ttcgctccaa
     1621 gctggactgt atgcacgaac cccccgttca gtccgactgc tgcgcctttt ccggtaacta
     1681 tcaacttgag tccaacccgg aaagacacga caaagcgcca ctggcagcag ccactggtaa
     1741 ctgatttaga ggagttagtc ttgaagttat gcgcctgtta aggctaaact gaaagaacag
     1801 atttggttcc tgcgctcctc gtaagccagt taccacggtt caaagagttg ctgctctgag
     1861 aaccttcgaa aaaccgcctt gctgggcggt tttttcgttt acagagcaag agattacgac
     1921 gctacagaaa ggatctcaag aagatccttc accataatgg aaatctatcc cacccgagca
     1981 tataggatgc atatcgttat aaaacatcgg atattatgca tcccaactaa aaataagctc
     2041 gaggataaaa aatgagttca atggtttact gccgaggatg cggcaaggaa atacacgaaa
     2101 cagcaaagtc atgcccacac tgcggagcca caaacgcctc ttcaggttca ggtga
//
