LOCUS       NZ_CP099293             3576 bp    DNA     circular CON 15-APR-2024
DEFINITION  Citrobacter freundii strain RHB03-E1-C03 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP099293
VERSION     NZ_CP099293.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15488495
            Assembly: GCF_029717865.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 3576)
  AUTHORS   Matlock,W.
  TITLE     Plasmid overlap and evolution between Enterobacterales isolates from
            bloodstream infections and non-human compartments
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3576)
  AUTHORS   Matlock,W.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-JUN-2022) Nuffield Department of Medicine, University
            of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.4
            Assembly Name                     :: RHB03-E1-C03
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 165x
            Sequencing Technology             :: Illumina/Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_029717865.1-RS_2024_04_14
            Annotation Date                   :: 04/14/2024 22:07:04
            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)                     :: 4,893
            CDSs (total)                      :: 4,772
            Genes (coding)                    :: 4,693
            CDSs (with protein)               :: 4,693
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 79
            CDSs (without protein)            :: 79
            Pseudo Genes (ambiguous residues) :: 0 of 79
            Pseudo Genes (frameshifted)       :: 19 of 79
            Pseudo Genes (incomplete)         :: 57 of 79
            Pseudo Genes (internal stop)      :: 12 of 79
            Pseudo Genes (multiple problems)  :: 9 of 79
            Pseudo Genes (short protein)      :: 1 of 79
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP099293.1.
            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="RHB03-E1-C03"
                     /isolation_source="Pooled sediment sample collected from
                     floor of pig farm"
                     /db_xref="taxon:546"
                     /plasmid="unnamed2"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            complement(join(3575..3576,1..187))
                     /locus_tag="NFJ31_RS24445"
                     /old_locus_tag="NFJ31_24420"
     CDS             complement(join(3575..3576,1..187))
                     /locus_tag="NFJ31_RS24445"
                     /old_locus_tag="NFJ31_24420"
                     /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            605..736
                     /locus_tag="NFJ31_RS24490"
     CDS             605..736
                     /locus_tag="NFJ31_RS24490"
                     /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"
     gene            complement(1046..1984)
                     /locus_tag="NFJ31_RS24450"
                     /old_locus_tag="NFJ31_24425"
     CDS             complement(1046..1984)
                     /locus_tag="NFJ31_RS24450"
                     /old_locus_tag="NFJ31_24425"
                     /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(3141..3572)
                     /locus_tag="NFJ31_RS24455"
                     /old_locus_tag="NFJ31_24430"
     CDS             complement(3141..3572)
                     /locus_tag="NFJ31_RS24455"
                     /old_locus_tag="NFJ31_24430"
                     /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"
     Typing          366..713
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.269"
                     /coverage="81.0"
                     /evalue="2.99e-149"
ORIGIN
        1 aatcctcttg aaaatcatcc agacgaatat ccagagtacg aaaaagcagt tccgcatcct
       61 catgcaattt ttcgcacaag ccggcttcag tatcgagatc ctgttcattg agattaccca
      121 gcaagaacag ggattgcgcc tgaatgaatt tcgccatatt cagtgccgtt ttctgttgtt
      181 tcgtcatcac agtgtcagtg ctccaaatga tatccggttc ttttccgctt cctcgaccgt
      241 tcgctcgcta cgctcggtca cttatctgcg gcgagcggac gcatcttcct aagagacaaa
      301 taacgtagac ggtaagcgta acgaaaagcc agaacaagaa cgataaagcc atgcccgacc
      361 agggcgtttt tccataggct tcgcccccct gacaagcatc acaaaatttg acgctcaaat
      421 cagtggtggc gaaacccgac aggactttaa agataccagg cgtttccccc tggtggctcc
      481 ctcgtgcgct ctcctgttcc tgcctttcgg tttaccggtg tcattccgct gttatggccg
      541 cggttctctc attccacgcc tgacactcag ttccgggtag gcagttcgct ccaagctgga
      601 ctgtatgcac gaaccccccg ttcagtccaa ccgctgcgcc ttatccggta actatcgtct
      661 tgagtccaac ccgaaaagac acgacaaaac gccactggca gcggccactg gtaatgggat
      721 gtacaagatt aactgaatga gagttcttga agtccgagct aaactacggc taaactgaaa
      781 ggacagatta cggtttcagc ggtcttgtac accctgttac cacggttcag aagttcccca
      841 acttgctgaa ccctcgaaaa aaccgactcc ccagtcggtt ttttcgtttc tggaacaaga
      901 gactacgacg agagacgaag gatctcaaga agatctcatc aatcaaacgc gtcaagtctc
      961 aaatttgacc atgattttcg cataacccca ttcgataact aacgatgtca aacaagtacc
     1021 gcacatacgg tacttgttcc ggaaactata aaaatccctt gtctgatagc catttcccaa
     1081 tatgagtgct gagggatgac tcaatatcga aaacatcaaa tggcttataa agtttacctg
     1141 ctaagtctgt atgtaatgaa cttagagtct tatcctttaa aagtaagacc tgcttcccca
     1201 ttcccatcat atatccaact tccaatgaaa cattagggtt aaaattatct tctgtaatcc
     1261 tctcaaaaat agcaataccg aaatcgcacc catacatata tgttttgata tttgaaaaga
     1321 gatcatccat atactcttta tcatcagccc ttaaagctat tatgttgtgt ttagacaact
     1381 ctttctttat tgcatcaaca agctttacgt gcgctgccgt gctaccaaac tgcatgatga
     1441 taaatgctgt ttttttccct tttggatagt cttttctgaa tttttcaagg ccagaagcta
     1501 tttcagggac attcatagcc tcttctgaaa ttctaccatc attgttatct ttactacttt
     1561 gaatttcaga ctgaatatat tcaatagaga gtttattaat atatgtatca agttcttccc
     1621 cggagagaga gactgggcaa gagaacgccc aaacaacatc accaacatca atccgaacct
     1681 gatggacgat actttgaagt tcaagctgtc tatattcaga taagtttcta tatactaaat
     1741 tattaccgcc accaggttta tcagcaaaca cgaaatgata agaaaaatcg tcttttgcga
     1801 caaacaaaaa tgaacattta tttattttga tattggatgc tggaatttgt aatgtcctag
     1861 catactctct caattttttg gcaaataatt taactatttc attagtatgt ttttgttctt
     1921 cttcagacag atctccacca atactagcca tcccaccgga agataaaaaa tccaaaacag
     1981 acatagttaa tttccttttt ccaattctaa agaacgcttg gcccggacat cccaaaacct
     2041 aaccactact taatggtaac atcacctatt cacttgataa tgatacaacc caccttgagt
     2101 ctactgccat ctatttaaca taagcactca ttacgcgcat cgctcagacg cactctgagc
     2161 gcttttgggg tgagtgcgtc gttttgtaca gtttacccgg gggaaaacgc tcagaacgcc
     2221 acagatgaat cctgagaggg tgaataacta tgctcccggc tgcatggtgc gtgatttgac
     2281 ggaaaacagc cgctaaaagg gagatttttc ccggtttact agcccgggaa tccgggattg
     2341 atgaagccta tttgttccgt cccataccat agggggtcag tttcccgtcc ctgatttgca
     2401 aagcgccccg tgctaacttc ccggccacgg aagaacggtg catctcatca tgtctccgtc
     2461 ggttctcctg agccgtcatc ggcctgatct ccagatccga aaactctctc ttaaactccg
     2521 cccccagaaa tttcaggtca tcgataaggg tcgcaaacca ttctttcacc tttttacctc
     2581 cacactagta agccattcag ataacagtct ggcacagact ggctaaagaa agcggtgaac
     2641 gggcacgcaa tttattgcgg ggtcgtgagg cgctggcagg gtgtcggggc gcatccatga
     2701 caggtctttt atctataaca ccgcgcaggg agagatactg atatcgcacc acacaaacag
     2761 aaaaagggta taccaagtgc aatcccttat cctgtgtggc actgaagccc tcagagcagc
     2821 ttttcaggta taccaagcca gttaccacct ggtatacccc ctacaggtct tgccagaact
     2881 ggctttaacc gcataaaaac agatgcgggt ataccatttc atacaagggg tggtataccc
     2941 ccggaagcct tgtcagcaaa ggcttccggc attagccgtg tatactgcgt ggggtgtgac
     3001 acgatttttt ggcctttatc agccatcaga aatcaaacat gcgggtaaag cggtcagatg
     3061 agaaagtata aacatccata tccggtgata gcctggtggc tggccgaacg ctatgaccgg
     3121 aatgcatgat tgataatgac tcaatgggat ttccagaact gccaccagga ctttgcagga
     3181 acattctgcg ggtcagaagt actctgttta tgctccagaa gttgcatggc ctgacgaagt
     3241 gaacttatat gctcatcccg tgcattcact gcatctttaa gcccggtatt ctccgcctgt
     3301 aaaagcgcca cttgatgctg taaagaatgt aaaaaatcac tgttaaccga cgtagtgaca
     3361 ccgtcaaatt ttacagtgtc acttttatca ccactgacaa catcaagagc accaaaaaga
     3421 cgaataagct cagctgtatc aatggtttta acgggttttc catgctttac aacggaggtg
     3481 tagctaagct caccagattt aagcagcttg taaatagtcg ggcgactgac actgacaaga
     3541 cgtgcagctt cactaatgga tacgcgagcc attact
//
