LOCUS       NZ_CP054299             3576 bp    DNA     circular CON 12-MAY-2024
DEFINITION  Citrobacter freundii strain IDR1800045912-01-00 plasmid p1C4,
            complete sequence.
ACCESSION   NZ_CP054299
VERSION     NZ_CP054299.1
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 3576)
  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  JOURNAL   Unpublished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 3576)
  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
            CP054299.1.
            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..3576
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="IDR1800045912-01-00"
                     /isolation_source="urine"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="p1C4"
                     /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            complement(96..1034)
                     /locus_tag="HS089_RS25490"
                     /old_locus_tag="HS089_25495"
     CDS             complement(96..1034)
                     /locus_tag="HS089_RS25490"
                     /old_locus_tag="HS089_25495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013185833.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_200002678.1"
                     /translation="MSVLDFLSSGGMASIGGDLSEEEQKHTNEIVKLFAKKLREYARTL
                     QIPASNIKINKCSFLFVAKDDFSYHFVFADKPGGGNNLVYRNLSEYRQLELQSIVHQVR
                     IDVGDVVWAFSCPVSLSGEELDTYINKLSIEYIQSEIQSSKDNNDGRISEEAMNVPEIA
                     SGLEKFRKDYPKGKKTAFIIMQFGSTAAHVKLVDAIKKELSKHNIIALRADDKEYMDDL
                     FSNIKTYMYGCDFGIAIFERITEDNFNPNVSLEVGYMMGMGKQVLLLKDKTLSSLHTDL
                     AGKLYKPFDVFDIESSLSTHIGKWLSDKGFL"
                     /name="hypothetical protein"
     gene            complement(2191..2622)
                     /locus_tag="HS089_RS25495"
                     /old_locus_tag="HS089_25500"
     CDS             complement(2191..2622)
                     /locus_tag="HS089_RS25495"
                     /old_locus_tag="HS089_25500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000135004.1"
                     /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_044703046.1"
                     /translation="MARVSISEAARLVSVSRPTIYKLLKSGELSYTSVVKHGKPVKTID
                     TAELIRLFGALDVVSGDKSDTVKFDGVTTSVNSDFLHSLQHQVALLQAENTGLKDAVNA
                     RDEHISSLRQAMQLLEHKQSTSDPQNVPAKSWWQFWKSH"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(2625..2813)
                     /locus_tag="HS089_RS25500"
                     /old_locus_tag="HS089_25505"
     CDS             complement(2625..2813)
                     /locus_tag="HS089_RS25500"
                     /old_locus_tag="HS089_25505"
                     /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_044703047.1"
                     /translation="MTKQQKTALNMAKFIQAQSLFLLGNLNEQDLDTEAGLCEKLHEDA
                     ELLFRTLDIRLDDFQED"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3231..3362
                     /locus_tag="HS089_RS25505"
                     /old_locus_tag="HS089_25510"
     CDS             3231..3362
                     /locus_tag="HS089_RS25505"
                     /old_locus_tag="HS089_25510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /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_072052181.1"
                     /translation="MHEPPVQSNRCALSGNYRLESNPKRHDKTPLAAATGNGMYKIN"
                     /name="replication initiation protein"
     Typing          2992..3339
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.269"
                     /coverage="81.0"
                     /evalue="2.99e-149"
ORIGIN
        1 gtcaagtctc aaatttgacc atgattttcg cataacccca ttcgataact aacgatgtca
       61 aacaagtacc gcacatacgg tacttgttcc ggaaactata aaaatccctt gtctgatagc
      121 catttcccaa tatgagtgct gagggatgac tcaatatcga aaacatcaaa tggcttataa
      181 agtttacctg ctaagtctgt atgtaatgaa cttagagtct tatcctttaa aagtaaaacc
      241 tgcttcccca ttcccatcat atatccaact tccaatgaaa cattagggtt aaaattatct
      301 tctgtaatcc tctcaaaaat agcaataccg aaatcgcacc catacatata tgttttgata
      361 tttgaaaaga gatcatccat atactcttta tcatcagccc ttaaagctat tatgttgtgt
      421 ttagacaact ctttctttat tgcatcaaca agctttacgt gcgctgccgt gctaccaaac
      481 tgcatgatga taaatgctgt ttttttccct tttggatagt cttttctgaa tttttcaagg
      541 ccagaagcta tttcagggac attcatagcc tcttctgaaa ttctaccatc attgttatct
      601 ttactacttt gaatttcaga ctgaatatat tcaatagaga gtttattaat atatgtatca
      661 agttcttccc cggagagaga gactgggcaa gagaacgccc aaacaacatc accaacatca
      721 atccgaacct gatggacgat actttgaagt tcaagctgtc tatattcaga taagtttcta
      781 tatactaaat tattaccgcc accaggttta tcagcaaaca cgaaatgata agaaaaatcg
      841 tcttttgcga caaacaaaaa tgaacattta tttattttga tattggatgc tggaatttgt
      901 aatgtcctag catactctct caattttttg gcaaataatt taactatttc attagtatgt
      961 ttttgttctt cttcagacag atctccacca atactagcca tcccaccgga agataaaaaa
     1021 tccaaaacag acatagttaa tttccttttt ccaattctaa agaacgcttg gcccggacat
     1081 cccaaaacct aaccactact taatggtaac atcacctatt cacttgataa tgatacaacc
     1141 caccttgagt ctactgccat ctatttaaca taagcactca ttacgcgcat cgctcagacg
     1201 cactctgagc gcttttgggg tgagtgcgtc gttttgtaca gtttacccgg gggaaaacgc
     1261 tcagaacgcc acagatgaat cctgagaggg tgaataacta tgctcccggc tgcatggtgc
     1321 gtgatttgac ggaaaacagc cgctaaaagg gagatttttc ccggtttact agcccgggaa
     1381 tccgggattg atgaagccta tttgttccgt cccataccat agggggtcag tttcccgtcc
     1441 ctgatttgca aagcgccccg tgctaacttc ccggccacgg aagaacggtg catctcatca
     1501 tgtctccgtc ggttctcctg agccgtcatc ggcctgatct ccagatccga aaactctctc
     1561 ttaaactccg cccccagaaa tttcaggtca tcgataaggg tcgcaaacca ttctttcacc
     1621 tttttacctc cacactagta agccattcag ataacagtct ggcacagact ggctaaagaa
     1681 agcggtgaac gggcacgcaa tttattgcgg ggtcgtgagg cgctggcagg gtgtcggggc
     1741 gcatccatga caggtctttt atctataaca ccgcgcaggg agagatactg atatcgcacc
     1801 acacaaacag aaaaagggta taccaagtgc aatcccttat cctgtgtggc actgaagccc
     1861 tcagagcagc ttttcaggta taccaagcca gttaccacct ggtatacccc ctacaggtct
     1921 tgccagaact ggctttaacc gcataaaaac agatgcgggt ataccatttc atacaagggg
     1981 tggtataccc ccggaagcct tgtcagcaaa ggcttccggc attagccgtg tatactgcgt
     2041 ggggtgtgac acgatttttt ggcctttatc agccatcaga aatcaaacat gcgggtaaag
     2101 cggtcagatg agaaagtata aacatccata tccggtgata gcctggtggc tggccgaacg
     2161 ctatgaccgg aatgcatgat tgataatgac tcaatgggat ttccagaact gccaccagga
     2221 ctttgcagga acattctgcg ggtcagaagt actctgttta tgctccagaa gttgcatggc
     2281 ctgacgaagt gaacttatat gctcatcccg tgcattcact gcatctttaa gcccggtatt
     2341 ctccgcctgt aaaagcgcca cttgatgctg taaagaatgt aaaaaatcac tgttaaccga
     2401 cgtagtgaca ccgtcaaatt ttacagtgtc acttttatca ccactgacaa catcaagagc
     2461 accaaaaaga cgaataagct cagctgtatc aatggtttta acgggttttc catgctttac
     2521 aacggaggtg tagctaagct caccagattt aagcagcttg taaatagtcg ggcgactgac
     2581 actgacaaga cgtgcagctt cactaatgga tacgcgagcc attactaatc ctcttgaaaa
     2641 tcatccagac gaatatccag agtacgaaaa agcagttccg catcctcatg caatttttcg
     2701 cacaagccgg cttcagtatc gagatcctgt tcattgagat tacccagcaa gaacagggat
     2761 tgcgcctgaa tgaatttcgc catattcagt gccgttttct gttgtttcgt catcacagtg
     2821 tcagtgctcc aaatgatatc cggttctttt ccgcttcctc gaccgttcgc tcgctacgct
     2881 cggtcactta tctgcggcga gcggacgcat cttcctaaga gacaaataac gtagacggta
     2941 agcgtaacga aaagccagaa caagaacgat aaagccatgc ccgaccaggg cgtttttcca
     3001 taggcttcgc ccccctgaca agcatcacaa aatttgacgc tcaaatcagt ggtggcgaaa
     3061 cccgacagga ctttaaagat accaggcgtt tccccctggt ggctccctcg tgcgctctcc
     3121 tgttcctgcc tttcggttta ccggtgtcat tccgctgtta tggccgcggt tctctcattc
     3181 cacgcctgac actcagttcc gggtaggcag ttcgctccaa gctggactgt atgcacgaac
     3241 cccccgttca gtccaaccgc tgcgccttat ccggtaacta tcgtcttgag tccaacccga
     3301 aaagacacga caaaacgcca ctggcagcgg ccactggtaa tgggatgtac aagattaact
     3361 gaatgagagt tcttgaagtc cgagctaaac tacggctaaa ctgaaaggac agattacggt
     3421 ttcagcggtc ttgtacaccc tgttaccacg gttcagaagt tccccaactt gctgaaccct
     3481 cgaaaaaacc gactccccag tcggtttttt cgtttctgga acaagagact acgacgagag
     3541 acgaaggatc tcaagaagat ctcatcaatc aaacgc
//
