LOCUS       NZ_CP141252             5411 bp    DNA     circular CON 09-APR-2024
DEFINITION  Citrobacter freundii strain isolateG plasmid pIsolateG_F, complete
            sequence.
ACCESSION   NZ_CP141252
VERSION     NZ_CP141252.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37529178
            Assembly: GCF_032346775.2
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 5411)
  AUTHORS   Lerminiaux,N., Fakharuddin,K., Mulvey,M.R. and Mataseje,L.
  TITLE     Do we still need Illumina sequencing data?: Evaluating Oxford
            Nanopore Technologies R10.4.1 flow cells and v14 library prep kits
            for Gram negative bacteria whole genome assemblies
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5411)
  AUTHORS   Lerminiaux,N., Fakharuddin,K., Mulvey,M.R. and Mataseje,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-DEC-2023) National Microbiology Lab, Public Health
            Agency of Canada, 1015 Arlington Street, Winnipeg R3E3R2, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 22-NOV-2022
            Assembly Method :: Trycycler v. v0.5.0; Flye v. v2.9.2; Raven v.
            v1.8.1; Miniasm/minipolish v. v0.3_r179; Unicycler v. v0.5.0
            Assembly Name                     :: isolateG
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 227.0x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_032346775.2-RS_2024_04_09
            Annotation Date                   :: 04/09/2024 00:52:07
            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)                     :: 5,254
            CDSs (total)                      :: 5,128
            Genes (coding)                    :: 5,026
            CDSs (with protein)               :: 5,026
            Genes (RNA)                       :: 126
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 102
            CDSs (without protein)            :: 102
            Pseudo Genes (ambiguous residues) :: 0 of 102
            Pseudo Genes (frameshifted)       :: 27 of 102
            Pseudo Genes (incomplete)         :: 77 of 102
            Pseudo Genes (internal stop)      :: 18 of 102
            Pseudo Genes (multiple problems)  :: 18 of 102
            Pseudo Genes (short protein)      :: 1 of 102
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP141252.1.
            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..5411
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="isolateG"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pIsolateG_F"
                     /geo_loc_name="Canada: Ottawa"
                     /collection_date="2019"
     gene            complement(1079..1360)
                     /locus_tag="RRL16_RS26220"
                     /old_locus_tag="RRL16_26225"
     CDS             complement(1079..1360)
                     /locus_tag="RRL16_RS26220"
                     /old_locus_tag="RRL16_26225"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000594459.1"
                     /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_000594459.1"
                     /translation="MIKNIKHKGLRSFAENGNTAGIQPHLAKKLRMILTTLSTATCLQD
                     IVDVRALGCHPLKGERKGEFSVEVNGNWRVVFKVEEPNVLDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            1752..1991
                     /locus_tag="RRL16_RS26225"
                     /old_locus_tag="RRL16_26230"
     CDS             1752..1991
                     /locus_tag="RRL16_RS26225"
                     /old_locus_tag="RRL16_26230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609270.1"
                     /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_164525734.1"
                     /translation="MEPFEIPAAELADKLEVSQSALSRLLNGKTDLSYEMALRLSKVIG
                     RSAESWVNMQAQYSLSKSRKTLSETLEHLHPMFP"
                     /name="HigA family addiction module antitoxin"
     gene            complement(3524..3739)
                     /locus_tag="RRL16_RS26230"
                     /old_locus_tag="RRL16_26235"
     CDS             complement(3524..3739)
                     /locus_tag="RRL16_RS26230"
                     /old_locus_tag="RRL16_26235"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137422.1"
                     /translation="MTELEKQLLSALEQLQQDYSQRLDEWESAFAEWRSMCGLMQRENA
                     VLNERVSDLSTQVLSLSEQLRRLSGN"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3746..4237)
                     /locus_tag="RRL16_RS26235"
                     /old_locus_tag="RRL16_26240"
     CDS             complement(3746..4237)
                     /locus_tag="RRL16_RS26235"
                     /old_locus_tag="RRL16_26240"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_142991550.1"
                     /translation="MSSLLTLAKDLEQQSKAQQQSTGEMLKAAFSEHEQSVRAELSASA
                     RRISDAILAHEQSMSEAMEKNRRSVLRTAGRTWLTILMVSALLSGTSGSILWWQGQQIT
                     DNYTHLRQQEDTLAKMTARTWGVRYQESSDGRRFLILPPGIQTEAIPYDGTTWIRLKQE
                     "
                     /name="MbeB family mobilization protein"
     gene            complement(<4272..4976)
                     /locus_tag="RRL16_RS26240"
                     /old_locus_tag="RRL16_26245"
                     /pseudo=""
     CDS             complement(<4272..4976)
                     /locus_tag="RRL16_RS26240"
                     /old_locus_tag="RRL16_26245"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(4915..5238)
                     /locus_tag="RRL16_RS26245"
                     /old_locus_tag="RRL16_26250"
     CDS             complement(4915..5238)
                     /locus_tag="RRL16_RS26245"
                     /old_locus_tag="RRL16_26250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000957084.1"
                     /translation="MLTMWVTEDEHRRLLERCDGRQLAAWMRQICLDEKPARSGKLPSL
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(2..114)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.246"
                     /coverage="100.0"
                     /evalue="4.4999999999999994e-49"
     Typing          38..625
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.371"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(3433..4925)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.8"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgttggcac ggatgagggt gtcagtgaag tgcttcatgt ggcaggagaa aaaaggcggc
       61 accggtgcgt cagcagaata tgtgatacag gatatattcc gcttcctcgc tcactgactc
      121 gctgcgctcg gtcgttcggc tgcggcgagc ggaaatggct tacgaacggg gcggaaattt
      181 cctggaggat gctaggaaga agcttaacag ggaagcgaga aggccacggc aaagccgttt
      241 ttccataggc tccgcccccc tgacaaacat cacgaaatct gacgctcaaa tcagtggtgg
      301 cgaaacccga caggactata aagataccag gcgtttcccc ctggtggctc cctcgtgcgc
      361 tctcctgttc ctgcctttcg gtttaccggt gtcactccgc tgttatggcc gcgtttatct
      421 cattccacgc ctgacactca gttccgggaa ggcagttcgc tccaagctgg actgtatgca
      481 cgaacccccc gttcagtccg accgcagcgt cttatccggt aactatcgac ttgagtccaa
      541 cccggaaaga cacaacaaaa cgccactggc tgcggccatt ggtaagaggg tgtacaagag
      601 attactgatg cagagttctt gaagtcagag ccatactgag gctaaactgg aaggacagaa
      661 tttggtttca gcggtcttgt acaccctgtt accacggttc agaagttccc caacttactg
      721 aaccctcgaa aaaaccgcct ccccaggcgg ttttttcgtt tcgaacataa gatacgcttt
      781 gtcgatttaa tcagtcaagg aagaaccctg aaagcctcaa tcgcttacag aattattctt
      841 gttagagaca tgtttctgca ccgtatcaac accagtacac aaaacagctg caaacaggaa
      901 ccatccccac ccatctaggc cacgaacagc aagaacccca gcaatgacta cacaaagcaa
      961 agggaacaac aaaatcataa aggctctcat aaatcctcca gaggtactta tttttgaata
     1021 aagtccctaa tccatccata ttgccactag gatggattag taacttactt attgattact
     1081 aatggtaatc ttcaagatca acgtctaaga cgtttggttc ttccaccttg aaaaccaccc
     1141 tccagtttcc gttaacctct acggaaaact cacctttacg ttcacctttt agggggtgac
     1201 accccagcgc ccttacatcc acaatatctt gaagacatgt tgcggtgctt agcgtagtca
     1261 atatcatgcg aagttttttc gctaagtgag gctgaattcc ggcggtgtta ccgttttcag
     1321 caaaactccg aagcccttta tgctttatgt tttttatcat caatcatctc cataaaattt
     1381 tcgtcgatat ctatctctat aaacagaaaa caatttgaca gcgtccattt gaaccccttg
     1441 cattattaaa ataattgacg taactttgtc tctgaggtcg attacctcgt ttgacttcca
     1501 agagcgctaa ccgtacaata tggcgccttg aaaaagtcgg taaagacacc atatcagcgg
     1561 tagctttctg ctccaccgag catcctaaag cttactgctt tttttgtcaa taacagacac
     1621 ttgcgtattg tgcaatgcgc aacgcgaaag aaacaaaatg ttttgtgtaa tcaaatacaa
     1681 aaccaataga ggaaggcatg ataaatcttt acgatcctgt acaccccggt gaattcatca
     1741 gggaaatgtt catggaaccg ttcgaaatac ctgccgcaga gttagctgat aagcttgaag
     1801 tatcacaatc tgcattaagt agattgctca atggaaaaac tgatcttagt tatgagatgg
     1861 ctcttcgact atctaaagtt ataggccgct ctgcagagtc gtgggttaat atgcaggctc
     1921 agtacagcct ctcgaaaagt cgtaagactt tatccgagac gctagaacac cttcatccga
     1981 tgtttccata agtaaaagcc cgctcgtgcg ggctttttgc cgtaaaaccc cccgcatacc
     2041 tacctttagt ttgattttta gttcagttct tagatcttga aatgattgtt gtttgaacac
     2101 caataagatg cccatacaag gctctaaaaa ggagaacaaa atggcaattt atgtaggacc
     2161 acatggcaaa ataggtcgtg atggtggctc attccaagaa tgtgacatca acacaaacac
     2221 tcatactgtt acccgcaaat atggacgata ctgcaccatt cgcgataatg agttcgcacc
     2281 accaacgagc gcacctggca ggtactggct acagatctac cgaaccccag acaacactga
     2341 gtaacagaag cgccagtaac gacaaagccc gcataagcgg gctttgtctc ttacaaaatt
     2401 cctcgtcgtc gcaattcagc ttctatcgcc tcacatgcgg catccacaat ctccgtgttg
     2461 tagtacctgg acatgccact gctaatgata tcgtccatta gggcacggtt atgagctaag
     2521 gtacgtcgta agtattcagg ggtatgttgc tccatcggat tctccttttc atgactgagc
     2581 attattgctt acctgtattt atccccgtca gtgctggtca cgttgaaaag ccctaaaaaa
     2641 ccactttttt agctgcctta atcattgaaa aatggcactt aaatccacat ctatcgcgct
     2701 ggggaaatcg cccgcacaca gccactgata aaataaaagt gagataaaat ggatccaatg
     2761 gataagattt gcgatgtttg tgccctccct gccagcgcct gtacctgtgg cttctgcgat
     2821 gactgcaacg agaagctggc agactgcgtc tgtgagcgct gcagcgattg tggaaattta
     2881 gatgagcact gtagctgctc acgttgcgac gagtgcggtg aaaaactgga tgagtgcata
     2941 tgtgaggagt gcgaagaatg tctccgcagt ccacatgatt gtatctgcga aaactgacct
     3001 aaggccgaat tctctttcaa gagcgaccgg gacggtcgct cttatttacc ataacatccg
     3061 ttgggcgcac cgctgaaacg gggttggctg cgtttccggt gccagacgcg agaaagtggc
     3121 gacagacata acgaaaaaac accagaaacg cagccgctga atattacact ggtgcatagt
     3181 catgcagcca gatgcatgga tgttaaagtc acactaaaat ccgcgccaat gccttaaaaa
     3241 ccgacaaatg cttctccagc cagtcccaca gctccgccgc cagatacagg cagttaagca
     3301 atgattcaat aagatttaac agcttcattt cccgctcctg aataagtcgt gacctttttg
     3361 atcacgaacc tatttagcgg gagaaataag agcccctctt cgtgcgggtt gtcagctgcc
     3421 tggatggttt aaagtgtcgg cccgcggtag gttttctgcg gctggcgctc cagctccagt
     3481 gttttctgat actcattctc cctctgccgg agctcgatgg cattcagttc ccggacaagc
     3541 ggcgcagctg ctcgcttaaa ctcagcacct gcgtgctcaa gtccgacacg cgctcgttca
     3601 gcaccgcgtt ctcccgttgc ataagcccac acatgctccg ccattccgcg aaggcgctct
     3661 cccattcgtc cagcctttgc gagtagtcct gctgtagctg ctctaatgcg ctcagcaact
     3721 gcttttccag ctctgtcatt ttcagctact cctgtttcag gcggatccat gtcgtcccgt
     3781 cgtaagggat ggcttcggtt tgtatccccg gcggcaggat aagaaacctc cggccgtcgc
     3841 tgctctcctg atagcgcact ccccacgtcc tggcggtcat tttcgccagg gtatcttcct
     3901 gctgacgaag atgcgtgtaa ttgtcggtta tctgctgccc ctgccaccac agaatgctcc
     3961 cgctcgtgcc gctcagcagc gctgacacca tcaggatggt gagccatgtc cgcccggcag
     4021 tccgcagtac gctccgccgg tttttctcca tcgcctcgct catactctgc tcgtgggcga
     4081 ggatggcgtc gctgattctc ctcgcgcttg cgctcagttc cgctctgaca gactgctcgt
     4141 gctcgctgaa tgcggctttc agcatctcgc cggtactctg ctgctgcgct ttcgattgct
     4201 gctctaagtc cttcgccagc gttaaaagac tgctcataga tggctccctt cagtcggatg
     4261 tttcgccccc cgtccggatc ggcaatgctg atactgcttt tcgtggtgcg caccacctca
     4321 aaacctgcac cttcaagagt gtcagtgaca tcctgacggc ttttcagctc cccggacgaa
     4381 gcaagggtca gcagtccccg ggtaatggct tctgcggcct cctgcttcgt tttcggaagc
     4441 ccggacggcg tgaccagcgc ccggcggttt tccggcgcgt tcgggtcgtg cagccccagt
     4501 ctgccgttca cgatagtctg ccaggcatcg atgcgcggcc ggtcggcgcg gtcgtagtaa
     4561 ggctggagcc gcctgccggt cagcagctcg gtattgggga tcagaaagtt cagctccaga
     4621 cgccccttgt ccgcgtgctc cacccacaga atgctgtact gatctttatc gagtccgggc
     4681 atcagaaccc gctcgaagct ggccatcagt ttttcccgct ggccgggagg cagatcggcc
     4741 tccgcaaacg acagaacgcc ggaggtgtat ttcttaacgt aaggcgacgc gtcaatcagc
     4801 tcccggactt cttccggctt cccctgcagg acggtggcgc cttcacgctg ccggtcttta
     4861 cccagcagat agtccaccgg cccggcgcca ccgccgcggc cgcgcggatg aaatttaacg
     4921 atcatcgtcc gttcctttct caagaacggc gtgccgcagc cgctcaaggc cggcatcgat
     4981 ggccatcagc gccgccacaa tctgtaccct gtcatggccg gtgccgccgc cggcgttaac
     5041 acggcgggct atctggttca ggttattgcc catgccggca agctggcgca gcagcgccgg
     5101 cgagagtgag gggagctttc ctgaacgtgc cggcttttcg tccaggcaga tctgcctcat
     5161 ccacgccgcc agctgcctgc cgtcacagcg ctcgagcagc cgccggtgct cgtcctccgt
     5221 cacccacatg gtgagcatct tgctccgttt ctctgacaaa ccggcctcct gataacgccg
     5281 ggacgggcgg gaaagccttt cccggtcggc gcggggttgg acaaaccgca ggcgcgtcag
     5341 gcttttggcg ggtttcgggg cgcagccctg aaccagtcac gtagcgctag cggagtgtat
     5401 actggcttac t
//
