LOCUS       NZ_CP135453             4783 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Citrobacter freundii strain isolateL plasmid pIsolateL_C, complete
            sequence.
ACCESSION   NZ_CP135453
VERSION     NZ_CP135453.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37529183
            Assembly: GCF_032347795.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 4783)
  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  JOURNAL   Unpublished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 4783)
  AUTHORS   Lerminiaux,N., Fakharuddin,K., Mulvey,M.R. and Mataseje,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-SEP-2023) National Microbiology Lab, Public Health
            Agency of Canada, 1015 Arlington Street, Winnipeg R3E3R2, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 21-JUN-2023
            Assembly Method :: Trycycler v. v0.5.0; Flye v. v2.9.2; Raven v.
            v1.8.1; Miniasm/minipolish v. v0.3_r179
            Assembly Name                     :: isolateL
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 138X
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/07/2023 13:56:33
            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)                     :: 5,253
            CDSs (total)                      :: 5,133
            Genes (coding)                    :: 5,010
            CDSs (with protein)               :: 5,010
            Genes (RNA)                       :: 120
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 123
            CDSs (without protein)            :: 123
            Pseudo Genes (ambiguous residues) :: 0 of 123
            Pseudo Genes (frameshifted)       :: 32 of 123
            Pseudo Genes (incomplete)         :: 88 of 123
            Pseudo Genes (internal stop)      :: 23 of 123
            Pseudo Genes (multiple problems)  :: 18 of 123
            Pseudo Genes (short protein)      :: 1 of 123
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP135453.1.
            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..4783
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="isolateL"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pIsolateL_C"
                     /geo_loc_name="Canada: Ottawa"
                     /collection_date="2020"
     gene            476..>598
                     /locus_tag="RRL10_RS26230"
                     /old_locus_tag="RRL10_26230"
                     /pseudo=""
     CDS             476..>598
                     /locus_tag="RRL10_RS26230"
                     /old_locus_tag="RRL10_26230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001487656.1"
                     /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="replication initiation protein"
                     /name="replication initiation protein"
     gene            complement(918..1274)
                     /locus_tag="RRL10_RS26235"
                     /old_locus_tag="RRL10_26235"
     CDS             complement(918..1274)
                     /locus_tag="RRL10_RS26235"
                     /old_locus_tag="RRL10_26235"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000075993.1"
                     /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_023316024.1"
                     /translation="MSQATRKPSTVGDIILYEYLEPSGLKINDLAEMLNVHRNSASALV
                     NNNRKLSTDMAFRLAKAFDTTAKFWLNIQQSVDLWEVTSSPRLQEEIDRVIPAHEIIER
                     KHIVDSSEKKHAIA"
                     /name="HigA family addiction module antitoxin"
     gene            complement(1477..1794)
                     /locus_tag="RRL10_RS26240"
                     /old_locus_tag="RRL10_26240"
     CDS             complement(1477..1794)
                     /locus_tag="RRL10_RS26240"
                     /old_locus_tag="RRL10_26240"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001183575.1"
                     /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_023316025.1"
                     /translation="MQQDHEHDDCRIQFRDDWLYQFYKYGKANRKIPTAISASLGRKLD
                     MLNAADKVGDLRSPPGNRFENLNPPLTGYSSIRVNEKYRLIFKWGENGVEDLYLDPHDY
                     R"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            1981..2223
                     /locus_tag="RRL10_RS26245"
                     /old_locus_tag="RRL10_26245"
     CDS             1981..2223
                     /locus_tag="RRL10_RS26245"
                     /old_locus_tag="RRL10_26245"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001713065.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023316026.1"
                     /translation="MALVRSGNKSKIFEADTKFNSVFDTEYKPGETCEYEGIYKCTGCG
                     KEVTIAGGKTIPPQNHHQHTPAQGNIRWQLFVYAQ"
                     /name="hypothetical protein"
     gene            complement(2894..3109)
                     /locus_tag="RRL10_RS26250"
                     /old_locus_tag="RRL10_26250"
     CDS             complement(2894..3109)
                     /locus_tag="RRL10_RS26250"
                     /old_locus_tag="RRL10_26250"
                     /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(3116..3607)
                     /locus_tag="RRL10_RS26255"
                     /old_locus_tag="RRL10_26255"
     CDS             complement(3116..3607)
                     /locus_tag="RRL10_RS26255"
                     /old_locus_tag="RRL10_26255"
                     /inference="COORDINATES: protein motif:HMM:NF016710.3"
                     /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_032629998.1"
                     /translation="MSSLLTLAKDLEQQSKAQQQSTGEMLKAAFSEHEQSVRAELSASA
                     RRISDAILAHEQSMSEAMEKNRRSVLRTAGRTWFTILMVSALLIGTSGSILWWQGQQIT
                     DNYTHLRQQEDTLAKMTARTWGVRYQESSDGRRFLILPPGMQTEAIPYDGTTWIRLKQE
                     "
                     /name="MbeB family mobilization protein"
     gene            complement(<3642..4346)
                     /locus_tag="RRL10_RS26260"
                     /old_locus_tag="RRL10_26260"
                     /pseudo=""
     CDS             complement(<3642..4346)
                     /locus_tag="RRL10_RS26260"
                     /old_locus_tag="RRL10_26260"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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(4285..4608)
                     /locus_tag="RRL10_RS26265"
                     /old_locus_tag="RRL10_26265"
     CDS             complement(4285..4608)
                     /locus_tag="RRL10_RS26265"
                     /old_locus_tag="RRL10_26265"
                     /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_163063187.1"
                     /translation="MLTMWVTEGEHRRLLERCDGRPLAAWMRQTCLDEKPARTGKLPSL
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          38..585
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.559"
                     /coverage="90.0"
                     /evalue="0.0"
     Typing          complement(2803..4295)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.2"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4292..4608)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.453"
                     /coverage="99.0"
                     /evalue="1.45e-59"
ORIGIN
        1 atgttggcac ggatacggaa atcagtgaag tgcttcatgt ggcaggagaa aaaaggcggc
       61 aacggcgcgt cagcagaata tgcgatacag gatatattcc gcttcctcgc tcactgactc
      121 gctgcgctcg gtcgttcggc tgcggcgagc ggtgcgggct tacgaacggg gcggaaattt
      181 cctggaagat gccaggaaga aacttaacag ggaagcgata aggccacggc agagccggtt
      241 ttccataggc tccgcccccc tgacgagcat cacagaatct gacgctcaaa tcagtggtgg
      301 cgaaacccga caggactata aagataccag gcgtttcccc ctgatggctc cctcgtgcgc
      361 tctcctgttc ctgcctttcg gtttaccggt gtcattccgc tgttatggcc gcgtttgtct
      421 cattccacgc ctgacactcg gttccgggta ggcagttcgc tccaagctgg actgtatgca
      481 cgaacccccc gttcagtccg accgctgcgc ctgttccggt aactatcgac ttgagtccaa
      541 cccggaaaga cacgacaaaa cgccactggc agcagccact ggtaacagga ttagcagagc
      601 gaggtatgta ggcggtgcta cagagttctt gaagtggtgg cctaactacg gctacactgg
      661 aaggacagta tttggtatct gcgctctgct gaagccagtt accaggttaa gcagttcccc
      721 aactgactta accttcgaaa aaccgcctcc ccaggcggtt ttttcgttta cagagcaaga
      781 gattacgcgt acagagcacg gatctcaaga agatcgtaag aagaaagtta acatgagcgt
      841 ttttatccct caaaaagaag gcttctagtt atagaagcct tctttttgag ggataactta
      901 tattttttta aaaaaaatca tgcaatagca tgtttcttct cagaactatc aacaatgtgt
      961 ttcctttcta tgatttcatg agcgggaatc actctgtcta tttcttcttg caatcgaggg
     1021 ctactagtaa cctcccataa atcaacagac tgctgtatat ttagccagaa ctttgcagtg
     1081 gtatcgaagg ctttagccaa cctaaaagcc atatcggtag acagctttct attattgtta
     1141 actaaagcac tggcagagtt tctatgcaca ttcaacattt cagccaagtc attgattttt
     1201 aaaccacttg gttcgagata ttcataaaga ataatatccc ctacagttga tggctttcta
     1261 gttgcttggg acatgcttta ctcctaaatt ttttacttct ctctgttaga tgaggaagat
     1321 aagtatttcg tctattacca gctgtagcga tgagtaatta tcttaaatat agtcacgtca
     1381 ttttttttat taatcattat ttgtaatgac attttaatgt aggtgaggga acgcctcacc
     1441 tacttgtttt ataagataac agccacgacc tgttatctat cggtaatcat gtggatcgag
     1501 atacaaatcc tcgactccgt tttcacccca cttaaatatc aagcggtact tctcattcac
     1561 ccgtatggat gaataccctg tcaatggagg gttgagattc tcaaatcggt ttcccggggg
     1621 agaccgcaaa tctccaactt tatcagcagc attcagcata tccagcttgc gacctaatga
     1681 agcactaatc gcagttggaa tctttcgatt ggctttacca tatttgtaaa actggtatag
     1741 ccaatcgtct cgaaactgaa tgcggcaatc atcatgttca tgatcttgct gcatttttct
     1801 tttacctcaa tttttgccgc aacttggcaa ttttttcgat caccttctta cctccgatat
     1861 agtacagcaa acatatcaaa tgcacaacag cacagtgcac ttgtgcaatc aatggctatg
     1921 ctgtagaatg cactcatgca cagtgcaggt gtgcaaaata aatgataatt tggaggttgc
     1981 atggctcttg ttcgctcagg aaacaaaagc aagatttttg aagcagatac gaagtttaac
     2041 tcggtttttg acactgaata taagccggga gaaacatgtg aatatgaagg gatttataaa
     2101 tgtaccggtt gcggtaaaga agtaactatc gcaggcggga aaacaatccc accacaaaac
     2161 caccaccaac atacccccgc gcaagggaac attcgttggc aattgtttgt ttatgctcag
     2221 tgaggtatag aaaatggcag atcgtcgacc actcaaccca cacgttgtcg ttcctaaacc
     2281 aggcggcgga actcaacctc gtgaccgtaa caatgacgga agggtcagag gaaaacgctc
     2341 agatgcagga aagccacgaa aataacagca agccgccagc ctggcggctt ttttatatct
     2401 gcagctgata ctgatttacc ataacatccg ttgggcgcac cgctgaaacg gggttggctg
     2461 cgtttccggt gccagacgcg agaaagtggc gacagacata acgaaaaaac accagaaacg
     2521 cagccgctga atattacact ggtgcatagt catgcagcca gatgcatgga tgttaaagtc
     2581 acactaaaat ccgcgccaat gccttaaaaa ccgacaaatg cttctccagc cagtcccaca
     2641 gctccgccgc cagatacagg cagttaagca atgattcaat gagatttaac agcttcattt
     2701 cccgctcctg aataagtcgt gacctttttg atcacgaacc tatttagcgg gagaaataag
     2761 agcccctctt cgtgcgggtt gtcagctgcc tggatggttt aaagtgtcgg cccgcggtag
     2821 gttttctgcg gctggcgctc cagctccagt gttttctgat actcattctc cctctgccgg
     2881 agctcgatgg cattcagttc ccggacaagc ggcgcagctg ctcgcttaaa ctcagcacct
     2941 gcgtgctcaa gtccgacacg cgctcgttca gcaccgcgtt ctcccgttgc ataagcccac
     3001 acatgctccg ccattccgcg aaggcgctct cccattcgtc cagcctttgc gagtagtcct
     3061 gctgtagctg ctctaatgcg ctcagcaact gcttttccag ctctgtcatt ttccgctact
     3121 cctgtttcag gcggatccat gtcgtcccgt cgtaggggat ggcttcggtt tgcatcccgg
     3181 gcggcaggat aagaaacctc cggccgtcgc tgctctcctg atagcgcact ccccacgtcc
     3241 gggcagtcat tttcgccagg gtatcttcct gctgacgaag atgcgtgtaa ttgtcggtta
     3301 tctgctgccc ctgccaccac agtatgctcc cgctcgtgcc gatcagcagc gctgacacca
     3361 tcaggatggt gaaccatgtc cgcccggcag tccgcagtac gctccgccgg tttttctcca
     3421 tcgcctcgct catactctgc tcgtgtgcga ggatggcgtc gctgattctc ctcgcgcttg
     3481 cgctcagttc cgctctgaca gactgctcgt gctcgctgaa tgcggctttc agcatctcgc
     3541 cggtactctg ctgctgcgct ttcgattgct gctctaagtc cttcgccagc gttaaaagac
     3601 tgctcataga tggctccctt cagtcggatg tttcgccccc cgtccgggtc ggcaatgctg
     3661 atactgcttt tcgtggtgcg caccacctca aaacctgacc gttccagcgc ctcagtgacg
     3721 tcctgacggt ttttcagctc cccggacgaa gcaagggtca gcagtccgcg cgtgatggct
     3781 tcagtggcct cctgcttcgt tttcggcagt ccggacggcg tgaccagcgc ccggcggttt
     3841 tccggcgcgt tcgggtcatg cagccccagt ctgccgttca cgatggtctg ccaggcatcg
     3901 atgcgcggcc ggtcggcgcg gtcgtagtac ggctggagcc gcctgccggt cagcagttcg
     3961 gtattgggga tcagaaagtt cagctccaga cgccccttgt ccgcgtgctc cacccacaga
     4021 atgctgtact gatctttatc gagtccgggc atcagaaccc gctcgaagct ggccatcagt
     4081 ttttcccgct ggccgggagg cagatcggcc tccgcaaacg acagtacgcc ggaggtgtat
     4141 ttcttcacgt aaggcgacgc gtcaatcagc tcccggactt cttccggctt cccctgcagg
     4201 acgctggcgc cttcacgctg ccggtcttta cccagcagat agtccaccgg cccggcgcca
     4261 ccgccgcgac cgcgtggatg aaatttaacg atcatcgtcc gttcctttct caagaacggc
     4321 gtgccgcagc cgctcaagcc cggcatcgat ggccatcagc gccgccacaa tctgtaccct
     4381 gtcatggccg gtgccgccgc cggcgttaac acggcgggct atctggttca ggttattgcc
     4441 cataccggca agctggcgca gcagcgccgg cgagagtgag gggagctttc cggtgcgcgc
     4501 aggcttttcg tccaggcagg tctgccgcat ccacgccgcc agcggcctgc cgtcgcagcg
     4561 ctcaagcagc cgccggtgct cgccctccgt cacccacatg gtgagcatct tgttccgttt
     4621 ctctgacaaa ccggcctcct gataacgccg ggacgggcgg gaaagccttt cccggtcggc
     4681 gcggggttgg acaagccgca ggcgcgtcag tggcttttgg cgggtttcgg ggcgcagccc
     4741 tgaacccgtc acgtagcact agcggagtgt atactggctt aat
//
