LOCUS       NZ_CP115132             3066 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter freundii strain 2021CK-01443 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP115132
VERSION     NZ_CP115132.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22334928
            Assembly: GCF_020575245.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 3066)
  AUTHORS   Hergert,J., Casey,R., Wagner,J., Young,E.L. and Oakeson,K.F.
  TITLE     2021CK-01443
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3066)
  AUTHORS   Hergert,J., Casey,R., Wagner,J., Young,E.L. and Oakeson,K.F.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-DEC-2022) Utah Public Health Laboratory, Utah Public
            Health Laboratory Infectious Disease Submission Group, 4431 S 2700
            W, Salt Lake City, UT 84129, USA
REFERENCE   3  (bases 1 to 3066)
  CONSRTM   Clinical and Environmental Microbiology Branch: Whole genome
            sequencing antimicrobial resistance pathogens in the healthcare
            setting
  TITLE     Direct Submission
  JOURNAL   Submitted (21-OCT-2021) Division of Healthcare Quality Promotion, US
            Centers for Disease Control and Prevention, 1600 Clifton Rd,
            Atlanta, GA, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 20.0x
            Sequencing Technology :: Oxford Nanopore GridION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 11:47:45
            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)                     :: 5,528
            CDSs (total)                      :: 5,407
            Genes (coding)                    :: 5,262
            CDSs (with protein)               :: 5,262
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 145
            CDSs (without protein)            :: 145
            Pseudo Genes (ambiguous residues) :: 0 of 145
            Pseudo Genes (frameshifted)       :: 27 of 145
            Pseudo Genes (incomplete)         :: 114 of 145
            Pseudo Genes (internal stop)      :: 21 of 145
            Pseudo Genes (multiple problems)  :: 16 of 145
            Pseudo Genes (short protein)      :: 1 of 145
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP115132.1.
            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..3066
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="2021CK-01443"
                     /isolation_source="sputum"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="unnamed3"
                     /geo_loc_name="USA"
                     /collection_date="2021-09-11"
     gene            complement(689..964)
                     /locus_tag="O9240_RS27625"
                     /old_locus_tag="O9240_27605"
     CDS             complement(689..964)
                     /locus_tag="O9240_RS27625"
                     /old_locus_tag="O9240_27605"
                     /inference="COORDINATES: protein motif:HMM:NF016875.4"
                     /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_094544860.1"
                     /translation="MIKNFKSKKLKQFNSGDTSKVAQAHKKKIEIILNALDTATSINDL
                     DLPGLDLHSYAEYTPTRWSLKVSANYRIFFEWDGANVRNVDYDDPH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            1234..1575
                     /locus_tag="O9240_RS27630"
                     /old_locus_tag="O9240_27610"
     CDS             1234..1575
                     /locus_tag="O9240_RS27630"
                     /old_locus_tag="O9240_27610"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011330340.1"
                     /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_049592808.1"
                     /translation="MFTLQKPMHPGEFIREVYLEPLELQIGTFAEKLGVDTSTVSRLVN
                     QKADLSYEMALRLSKALGRSADSWMKMQIAYGLYRAQDKVNLEEVEVVYRPRNLDAPEK
                     QVHEFYENI"
                     /name="HigA family addiction module antitoxin"
     gene            2012..2200
                     /locus_tag="O9240_RS27635"
                     /old_locus_tag="O9240_27615"
     CDS             2012..2200
                     /locus_tag="O9240_RS27635"
                     /old_locus_tag="O9240_27615"
                     /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(2248..2475)
                     /locus_tag="O9240_RS27640"
                     /old_locus_tag="O9240_27620"
     CDS             complement(2248..2475)
                     /locus_tag="O9240_RS27640"
                     /old_locus_tag="O9240_27620"
                     /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_224019247.1"
                     /translation="MFGFSPGELMNLCPDERLLFVRMISAMLRRSGGDAGAVMFEAYRH
                     IVSDTNQARRSYMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     Typing          2..383
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.3"
                     /coverage="85.0"
                     /evalue="7.74e-171"
ORIGIN
        1 ccgcggcgct gccggttttc cataggctcc gcccccctga caagcatcac agaatctgac
       61 gctcaaatca gtggtggcga aacccgacag gactataaag atcccaggcg tttccccctg
      121 gtagctccct cgtgcgctct cctgttcctg cctttcggtt taccggtgtc actccgctgt
      181 tatggccgcg tttatctcat tccacgcctg acactcagtt ccgggtaggc agttcgctcc
      241 aagctggact gtatgcacga accccccgtt cagtccgacc gctgcgcctt ttccggtaac
      301 tatcgtcttg agtccaaccc ggaaaggcac gacttatcgc cactggcagc ggccactggt
      361 aagagggtgt acaagagatt actaatgcag agttcttgaa gtatcagcct aactacggct
      421 aaactggaag gacgtatttg gtggcagcgg tcttgtacac cctgttacca cggttcagaa
      481 gttccccaac ttgctgaacc ttcgaaaaac cacctcccca ggtggttttt tcgtttcagg
      541 attaaagata ctctgcgtcc cactcaatct caagaaatta tctttaccaa gccattgact
      601 taataaaaaa aaaccatata atagcctcat gggcttgaat cactttagtg attcaagccc
      661 atgacctaag tcattgattt aactgacatt aatgtggatc gtcgtaatcc acattacgga
      721 cgttggcacc atcccactca aagaaaatac gatagttcgc cgacaccttt aatgaccagc
      781 gggttggggt atattcagca tacgaatgaa gatccaaacc aggaaggtca agatcattta
      841 ttgaagtagc ggtatctaaa gcgtttaaga taatctctat tttcttttta tgcgcttgtg
      901 ctaccttact tgtatcacca ctgttaaatt gttttagttt tttggattta aaatttttaa
      961 tcattgaact tctccatatg aaaattttta tgttttagaa gttcttcttg tttagtaaag
     1021 tttcttgact gtgttctatt tataggtagt attctacgcc tgcgaagctt tagaactgcc
     1081 agatagtcac tacaagaaca aaacagaaga accaaactgt taacgttaag aaaaaattac
     1141 ccttaactaa tccattttat cacaaatgga ttgcttatgt caataggttt gcgcgttgcg
     1201 caaggcacaa aatcagagta tttaggaggt tgcatgttta cattgcaaaa acctatgcac
     1261 cccggcgagt ttatccgcga agtatattta gagccgttag agcttcaaat aggaacgttt
     1321 gcagaaaagc ttggggttga tacatcaacc gttagccggt tagtaaacca aaaagctgac
     1381 ctttcttatg aaatggcatt acgcctatca aaagccttag ggcgttctgc tgactcttgg
     1441 atgaaaatgc aaatagcata tggtttatat cgtgctcaag ataaagtaaa tcttgaagaa
     1501 gttgaggtgg tttaccgccc acggaacttg gatgctcctg aaaaacaggt ccatgaattt
     1561 tatgaaaata tctaaaaacg atatttcatt taggtaaaga aaagctccta accatagggg
     1621 ctttttgtct ctacacctgt gtatttatgt gaagacctaa cttgcactcg cagaggcggc
     1681 agcatcgtta ttcctgaaga tgcttaaaca gcgggtgttg agcctgtatc aaccattgat
     1741 agtgatctgt atatcctctt cactaacccc aaacttcata gccagccccc ttctatgctt
     1801 acctagagaa tttaccataa catccgttgc gtgcaccgcc tgagaggctc tcagggcgtt
     1861 tctacgacct cacctgcaaa agaacacatc ttaccccctg aaaaccgctc agaaacgcgc
     1921 tgatgatttc tgcgtacctg catggctatg cactcaagtg aatgaagtaa gatttcagtc
     1981 tgcgatcacc ataaaaccgg gaaaaagccg tatgacaaaa caggaatcag ccgcactgaa
     2041 catggcaaaa tttatccggg cgcagtcgct gctgctgctc gaaaaactcg acgtgctcga
     2101 tcttgatgac gaggcagccg actgtgagcg aatgcacgaa caggcagaag cgctttatca
     2161 gaagctgagc gcacgcttcg gtatacagga cggcgaataa agagacgaaa agaacgctca
     2221 cttagacgaa aagcgtatcc agggcaacta tgtatatcca ccgtgtacat agtcatgcct
     2281 gacgctttcg agcaggtcga gcatgtagga acgacgagct tgattggtat cggacacaat
     2341 atggcgatac gcctcaaaca taacagcacc cgcatcaccg cccgaacggc gaagcatagc
     2401 ggaaatcatc cgcacaaaga gcagacgttc atcggggcaa aggttcataa gttctcctgg
     2461 tgaaaaacca aacatgaaag cacccatcta ttaacgtcag ctgtgaacgc ttcattagaa
     2521 gaaaataggt aaacccggga aaaagatcca aacgttaaca tcacaggtaa acagaaacgt
     2581 cgggtcgatc gggaaattct ttcccggacg gcgcggggtt gggcaagccg caggcgcgtc
     2641 agtgctttta gcgggtgtcg gggcgcagcc ctgaaccagt cacgtagcgc tagcggagtg
     2701 tatactggct aaacttcaga gatgccaagg aagggacagg atatgttttg tagcaccgcc
     2761 accacggtgg cgatactcca aaacgcctgg tcagggcaca gccccgacac cccagagccg
     2821 actgtaggtc actggacgaa cgcggcggaa tgatgtcgga tgacgtcatt ttgcggcgtt
     2881 tgccctatcc tgcatcgtat taaaaaatgc agctatggcg cgtacggtgc caaagataag
     2941 cccggagata ttccgcttcc tcgctcactg actcgctacg ctcggtcgtt cggctgcggc
     3001 gagcggaagg agaatattca caaaggcata tggcgatgaa gacgagataa agcgagggag
     3061 gaaagg
//
