LOCUS       NZ_CP133850             4448 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter freundii strain CF2 plasmid unnamed3, complete sequence.
ACCESSION   NZ_CP133850
VERSION     NZ_CP133850.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37200065
            Assembly: GCF_031432815.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 4448)
  AUTHORS   Turton,J.F. and Turton,J.A.
  TITLE     Plasmid analysis using q20 nanopore sequencing
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4448)
  AUTHORS   Turton,J.F. and Turton,J.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-SEP-2023) HCAI, Fungal, AMR, AMU & Sepsis Division,
            United Kingdom Health Security Agency, 61 Colindale Avenue, London,
            London NW9 5EQ, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2023
            Assembly Method :: Flye v. 2.9.1-b1780; Medaka v. 1.7.2
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 33x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 11:57:23
            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)                     :: 5,426
            CDSs (total)                      :: 5,298
            Genes (coding)                    :: 5,130
            CDSs (with protein)               :: 5,130
            Genes (RNA)                       :: 128
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 16
            Pseudo Genes (total)              :: 168
            CDSs (without protein)            :: 168
            Pseudo Genes (ambiguous residues) :: 0 of 168
            Pseudo Genes (frameshifted)       :: 88 of 168
            Pseudo Genes (incomplete)         :: 77 of 168
            Pseudo Genes (internal stop)      :: 24 of 168
            Pseudo Genes (multiple problems)  :: 18 of 168
            Pseudo Genes (short protein)      :: 1 of 168
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP133850.1.
            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="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="CF2"
                     /isolation_source="drain"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="unnamed3"
                     /geo_loc_name="United Kingdom: England"
                     /collection_date="2022-10"
                     /genotype="ST162"
     gene            join(3927..4448,1..57)
                     /locus_tag="RHA96_RS02175"
                     /old_locus_tag="RHA96_02175"
     CDS             join(3927..4448,1..57)
                     /locus_tag="RHA96_RS02175"
                     /old_locus_tag="RHA96_02175"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310049.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_265453801.1"
                     /translation="MAKLPLPPLPLPIAPPSTVKNSGSERAKKSGRRTLSAKRKTLLEE
                     LWGDELEQLKVWNRHEHDGYTTVPRTLTYISRILDYLGGTGLPLSQTYLALWCRVFDEG
                     FVEIRDKDGFAYEAGFSGQRAVTTWTGRMRKLRDLGFITTKPGTSGEFQYVILLNPLTV
                     IKELYEGKEKDERYNALVGRMQEVGAKWE"
                     /name="hypothetical protein"
     gene            61..606
                     /locus_tag="RHA96_RS02180"
                     /old_locus_tag="RHA96_02180"
     CDS             61..606
                     /locus_tag="RHA96_RS02180"
                     /old_locus_tag="RHA96_02180"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310050.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_265453802.1"
                     /translation="MASYFPTLEISGEEFDFTHLEPFIMHVNSDMAKKVLKVHVRFTNH
                     CFTKGYESFYHPEGEPIIYDHSGNGRTFCPIRYRLSLALPEIINRLCDPAEKVYQTSAK
                     RNWAYSITIDDPEGPYHLFFEIRRASRDERHLQDLNVVIESAYPEDRGYGPPSLLGRIG
                     FVGLCGRVFCGKPLATKR"
                     /name="hypothetical protein"
     gene            complement(2053..2484)
                     /locus_tag="RHA96_RS02185"
                     /old_locus_tag="RHA96_02185"
     CDS             complement(2053..2484)
                     /locus_tag="RHA96_RS02185"
                     /old_locus_tag="RHA96_02185"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000135004.1"
                     /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="excisionase family DNA-binding protein"
                     /protein_id="WP_265453800.1"
                     /translation="MARVSISEAARLVSVSRPTIYKLLKSGELSYTSVVKHGKSVKTID
                     TAELIRVFGAIEGVSIGQSDTVKFDDMSTSVNSDFLQSLQHRLTLLQAENAGLKDAVNA
                     RDEHISSLRQAMQLLEHKQSASDPQSVPAKSWWQFWKSH"
                     /name="excisionase family DNA-binding protein"
     gene            complement(2484..2675)
                     /locus_tag="RHA96_RS02190"
                     /old_locus_tag="RHA96_02190"
     CDS             complement(2484..2675)
                     /locus_tag="RHA96_RS02190"
                     /old_locus_tag="RHA96_02190"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166327.1"
                     /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_048234308.1"
                     /translation="MTKQQRTALNMAKFIQAQSLLLLEKLNELDLDTEADLCEKLHEDA
                     EQLFRTLAIRLDDFQEDL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3092..3204
                     /locus_tag="RHA96_RS02195"
                     /old_locus_tag="RHA96_02195"
                     /pseudo=""
     CDS             3092..3204
                     /locus_tag="RHA96_RS02195"
                     /old_locus_tag="RHA96_02195"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     Typing          2911..3405
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.048"
                     /coverage="99.0"
                     /evalue="1.31e-158"
ORIGIN
        1 gaaaggtaca acgcattagt gggccgtatg caggaggttg gcgctaaatg ggagtaattc
       61 atggctagct atttcccaac gttagaaata tctggagaag agttcgattt cactcacctt
      121 gagccattca ttatgcacgt aaatagtgac atggctaaaa aggtactaaa agtacacgtg
      181 agattcacaa accattgttt cacaaaaggt tatgagtctt tttatcatcc agaaggagag
      241 ccgataattt acgaccatag cgggaatggg agaacgtttt gcccaatcag atatagatta
      301 tctttggcgt tgcctgagat tatcaaccgt ctatgtgatc cagcagaaaa agtgtatcaa
      361 acatcggcaa agagaaactg ggcctactcc attacaattg atgatccgga ggggccatat
      421 cacttatttt ttgaaataag acgcgcctcg cgtgatgaga gacacctgca agatttgaat
      481 gttgttatcg agagtgccta tcctgaggat cgagggtacg gacctccgtc cttactaggc
      541 cgaattggtt ttgtaggttt atgcggtagg gtattttgtg gaaagcctct ggcgactaaa
      601 agatgaaaaa aaagcacctg aaaggtgcct tttttctgct tctttggtaa tcgttccgga
      661 caccactagc ttttgcttag gttcgccttg cgcgaacaca ggaacaagat ttgccctgct
      721 gggtagcgct caatctcatc cggtcagtcg ctacgatgta aacaatataa caaaaccaat
      781 tacgcaattc agcaccaccg attcaatgta atgcttcgat agacatggag caccttgagt
      841 acagaaacta tagttaacca actgaattta aagaagcata tgaatattat aatacaactc
      901 agatgatgag ttgcattata aaacacatat gcctttgtgg ttcaccatga tttcactaca
      961 ataaacatgc ggatcattgc acccagcttg ttcaggtcta ccgtttacgg cttatagcat
     1021 tcggcggatt taccataacg cctcattacg cgcaccgttc agacgacctc agcgcgcttt
     1081 gagcgtgaag ccgatgaaaa ccccagctta cccggcgaaa agcccgcaaa acggcgcaga
     1141 tgaatcctga gaggctgaat ggctatgcac ccgactgcat ggcgcgggtt ttgacggtaa
     1201 acagacagtg aaagggaggt tttaccctgt tttcttatca ggatatccgg gggggcgata
     1261 aagcctacct gtcacgcctc atgccataaa aggtcagttc cccgtccctg atttgcaaaa
     1321 cgccccgtgc taacttcccg gccacggaag aacggtgcat ctcatcatgt ctacgccgga
     1381 cctcctcagc cgtcatcggc ctgatctcca gatccgaaaa ctctctctta aactccgccc
     1441 ccagaaattt caggtcatcg ataagggtcg caaaccattc tttcatcgtt ctgcctccgc
     1501 gctattaaag ccattcagat aacagtctgg cacagactgg cgaaagaaag cggtgaacgg
     1561 gcacgcaatt tattgcggga tcgtgaagcg ctggcagggt gtcggggcgc agccatgaca
     1621 ggtcttttat ccattacacc gcgcagggag agaggctgat atagcgtcac acaagcagga
     1681 taagggtata cctgccgcaa tcccttatcc tgtgcggcat ttcagcccca gatcagtgtt
     1741 tcaggtatac catgccagtc aacacctggt ataccgccta caggccttgc cacgactggc
     1801 tttaacggta taaaaacaga tgggggtata ccatttcata caaggggtgg tatacccccg
     1861 gaagcctttg ctggcaaggc ttccggctga gcagtgtata ctgcgtgggg tgtgacacga
     1921 ttttttggcc tttatcagcc atcagaaatc aaacatgcgg gcaaagcagt ccgatgggaa
     1981 agtataaact tccatatcag gtgatagtct ggctgctggg cgaacgctat gaccggaatg
     2041 cgtagtaatg actcaatggg atttccagaa ctgccaccag gactttgcag gaacactctg
     2101 cgggtcagag gcgctctgtt tatgctccag aagttgcatg gcctgacgaa gtgaactgat
     2161 gtgctcatcc cgtgcattca ccgcatcttt gagcccggca ttctccgcct gtaaaagcgt
     2221 taaccgatgc tgtaaagact gtaaaaaatc actattaacc gatgtagaca tgtcgtcaaa
     2281 ttttacagtg tcactttgac caatacttac accctcaata gcaccaaaaa cacgaataag
     2341 ctcagcggta tcaatggttt ttacggattt gccatgcttt acaactgagg tgtaacttag
     2401 ttcaccagac ttaagtagct tgtaaattgt cggacgactg acactgacaa gacgtgccgc
     2461 ttcgctaatg gatacacggg ccattacaaa tcctcttgaa aatcatccag acgaatagcc
     2521 agagtgcgaa agagctgttc cgcatcctca tgcagttttt cgcacaggtc ggcctcagta
     2581 tcgagatcca gttcgttgag cttctccagc aaaagcaggg attgcgcctg aatgaattta
     2641 gccatattca atgccgttct ctgttgcttt gtcatcacag cgtcagtgct ccaagtcatc
     2701 tccggttctt ttccgcttcc tcgaccgttc gctcgctacg ctcggtcact tgtctgcggc
     2761 gagcggacgg atctttctaa gtgataaata aggttggcag taagcgtaac caaaagacag
     2821 gtcaggaacg agaaggccac gcccaacagg ccgtttttcc ataggcttcg cccccctgac
     2881 gagcatcacg taatcagacg ctcaaatcag tggtggcgaa acccgacagg actataaaga
     2941 taccaggcgt ttccccctgg cggctccctc gtgcgctctc ctgttcctgc ctttcggttt
     3001 accggtgtca ttccgctgtt atggccgcgg ttctctcatt ccacgccaga cactcagttc
     3061 cgggaaggca gttcgctcca agctggactg tatgcacgaa ccccccgttc agtccgactg
     3121 ctgcgcctta tccggtaact atctcttgag tccaacccgg aaggacacga cttatcgcca
     3181 ctggcagcag ccactggtaa ttgatttaga ggagttagtc ttgaagttat gcgccagtta
     3241 aggctaaact aaacgaacag ttttggtgac tgcgctcctc taagccagtt acctcggttc
     3301 agaaacttgc cggttgctga accttcgaaa aaccaccttg ccgggtggtt ttttcgttta
     3361 cagagcaaga gattacgcgc agaaaaaaag gatctcaaga agatcctttt ttaaatgttc
     3421 actggaacga aataacccgt aaagctcaaa acccttaacg tagggtaatg tctgttttcc
     3481 aagcggaccc catcaacacc cacacatagc tctcacgtca cctcaggcac gctcaagcaa
     3541 gagccaagcc atttcctgct aaaaccccca tatcggcaaa atcgcacaca gggcacagtg
     3601 agcagccatt tcgctttgta ttaaatggct gtcgaaaatt attgccttgc ccccttgcat
     3661 ccccattcag cacagcgagc acattcagca catatcagca cattcagcac agcgagcaca
     3721 gaaacaggtc ataactcatt gaataacagc tatcacatgc tgtatttatt acaactcacg
     3781 cattgagatg taataaatag atattcataa gatgtctata ggttgatagg caacatcaca
     3841 accaaacgca aaacaacaca taactcgttg ttttgaaaga gaaaatgact acaataaccg
     3901 tatattaaat gattttggag aaactaatgg cgaagttacc actgccacca ctgccactac
     3961 cgatagcgcc accgtcaaca gtaaagaata gtggttcaga aagagcgaag aagtcaggaa
     4021 ggagaactct ttcagcaaaa aggaaaacct tgttagaaga gctatgggga gacgagcttg
     4081 aacaactcaa ggtatggaat cgccatgaac atgacgggta tacaacagtg ccaagaacgc
     4141 tgacatatat cagtcgaatc ctcgattacc tcggaggaac gggcctgcca ttgtcccaaa
     4201 catatctggc tctttggtgc agagtatttg atgaaggatt tgtggagata agggataaag
     4261 atggatttgc ttatgaggct ggttttagtg gacaacgagc agtaaccaca tggacaggga
     4321 ggatgagaaa actaagagat ttaggtttca taactacaaa acccggcacg tcaggtgaat
     4381 ttcaatatgt gattttgctt aacccgctga ctgtcattaa agagttatac gaaggtaagg
     4441 aaaaagat
//
