LOCUS       NZ_CP042528             4938 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter freundii strain E11 plasmid pE11_004, complete sequence.
ACCESSION   NZ_CP042528
VERSION     NZ_CP042528.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12289395
            Assembly: GCF_008931625.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 4938)
  AUTHORS   Phan,H.T.T., Stoesser,N., Gordon,K.A., Crook,D., Walker,S.A.,
            Mathers,A.J., Peto,T.E.A., George,S. and Lipworth,S.I.
  TITLE     Genomic Dynamics of Species and Mobile Genetic Elements in a
            Prolonged blaIMP-4-associated Carbapenemase Outbreak in an
            Australian Hospital
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4938)
  AUTHORS   Phan,H.T.T.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-AUG-2019) Nuffield Department of Micriobiology,
            University of Oxford, Headley Way, Oxford, Oxford OX3 7BN, United
            Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: SEP-2017
            Assembly Method                   :: Unicycler v. SEP-2017
            Assembly Name :: E11_oz_imp.uniclycerAssembly.fsa
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: na
            Genome Coverage                   :: 2355x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 13:57:49
            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)                     :: 5,367
            CDSs (total)                      :: 5,244
            Genes (coding)                    :: 5,140
            CDSs (with protein)               :: 5,140
            Genes (RNA)                       :: 123
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 104
            CDSs (without protein)            :: 104
            Pseudo Genes (ambiguous residues) :: 0 of 104
            Pseudo Genes (frameshifted)       :: 37 of 104
            Pseudo Genes (incomplete)         :: 64 of 104
            Pseudo Genes (internal stop)      :: 26 of 104
            Pseudo Genes (multiple problems)  :: 19 of 104
            Pseudo Genes (short protein)      :: 1 of 104
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP042528.1.
            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..4938
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="E11"
                     /isolation_source="Shower 3"
                     /db_xref="taxon:546"
                     /plasmid="pE11_004"
                     /geo_loc_name="Australia: Sydney"
                     /collection_date="2012-07-03"
                     /collected_by="Concord Repatriation Hospital Sydney
                     Australia"
     gene            join(4841..4938,1..37)
                     /locus_tag="FR864_RS27155"
                     /old_locus_tag="FR864_27040"
     CDS             join(4841..4938,1..37)
                     /locus_tag="FR864_RS27155"
                     /old_locus_tag="FR864_27040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_039269308.1"
                     /translation="MHEPPVQSDRCALSGNYQLESNPEKHDKAPLAAATGNRFRGGES"
                     /name="hypothetical protein"
     gene            complement(262..1548)
                     /locus_tag="FR864_RS26630"
                     /old_locus_tag="FR864_27050"
     CDS             complement(262..1548)
                     /locus_tag="FR864_RS26630"
                     /old_locus_tag="FR864_27050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007899670.1"
                     /GO_process="GO:0006935 - chemotaxis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="PAS domain-containing methyl-accepting chemotaxis
                     protein"
                     /protein_id="WP_225986332.1"
                     /translation="MFSLNLQRSAISYDAICQNKPVIEFSPEGVINKASPLFLSTMGYR
                     ADEIIGHHHRIFCPPSLVSSPEYSQFWQRLARGESFSGKYLRLAKGNRSVWLEASYIPV
                     SDRRGRVIRVIKIAADISERVHSALEQEAVVNAINRSMAIITFNPEGIVLEANENFVNA
                     TGYKRDEIIGKHHRLFCAETLYKSDEYRHFWESLNQGEFFSGLFPRLNRQGDSLWFRAT
                     YNPVFNSDGQLYKIVKFATDVTADVLRNQREQEAAVHAWDMAVQTRESAQNGANVIENS
                     ILMIDRIAQGMGAVSTDISRLNNQSESIDDMVETIRKFAMQTRLIALNAAIEAARAGAS
                     GRSFAVVAAEVRNLAASVSSATEEIEQVVASNSQLAKDVLCGIENSLMNTREGVTLMRE
                     AGEVMTSIQRNAAGVETAVKDVAISVKAG"
                     /name="PAS domain-containing methyl-accepting chemotaxis
                     protein"
     gene            complement(2477..2692)
                     /locus_tag="FR864_RS26635"
                     /old_locus_tag="FR864_27055"
     CDS             complement(2477..2692)
                     /locus_tag="FR864_RS26635"
                     /old_locus_tag="FR864_27055"
                     /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(2699..3190)
                     /locus_tag="FR864_RS26640"
                     /old_locus_tag="FR864_27060"
     CDS             complement(2699..3190)
                     /locus_tag="FR864_RS26640"
                     /old_locus_tag="FR864_27060"
                     /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_016355729.1"
                     /translation="MSSLLTLAKDLEQQSKAQQKSTGEMLKAAFSEHEQSVRAELNASA
                     RRISDAISAHEQSMSEAMEKNRRSVLLTAGRTWLTILMVSALLIATSGSILWWQGRQIT
                     DNYTHLRQQEDTLAKMTARTWGVRYQESNDGRRFLILPPGMQAEAIPYDGTTWIRLKQE
                     "
                     /name="MbeB family mobilization protein"
     gene            complement(<3225..3929)
                     /locus_tag="FR864_RS27160"
                     /old_locus_tag="FR864_27065"
                     /pseudo=""
     CDS             complement(<3225..3929)
                     /locus_tag="FR864_RS27160"
                     /old_locus_tag="FR864_27065"
                     /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(3868..4191)
                     /locus_tag="FR864_RS26650"
                     /old_locus_tag="FR864_27070"
     CDS             complement(3868..4191)
                     /locus_tag="FR864_RS26650"
                     /old_locus_tag="FR864_27070"
                     /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_007899679.1"
                     /translation="MLTMWVTEDEHRRLLERCDGRQLAAWMRQTCLDEKPARTAKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGVGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(4307..4479)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="9.14e-86"
     Typing          53..221
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="83.908"
                     /coverage="85.0"
                     /evalue="9.37e-36"
     Typing          4404..4938
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.424"
                     /coverage="88.0"
                     /evalue="0.0"
     Typing          complement(2377..3878)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="83.692"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3875..4191)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.509"
                     /coverage="99.0"
                     /evalue="2.38e-59"
ORIGIN
        1 agccactggt aacaggttta gaggaggaga gtcttgaagt ttcgggtgcg ataaggctac
       61 actgaaagga cagttttggt gactgtgctc ctccaagcca gttaccgcgg ttcaaaagag
      121 cgtcaactct tgcgaacctt cgaaaaagcc accttgccgg gtggtttttt cgttttcaga
      181 gcaagagatt acgacgcaac ggaaaggatc tcaagaagat catctgtgat gttcgacaga
      241 tatggggata tgcaccatgg cctatccggc tttaactgaa atggcgacat ccttaaccgc
      301 agtctcaacc cctgcagcat tcctctgaat gctggtcata acttcacccg cttcgcgcat
      361 gagtgtaacc ccttcccgag tgttcatcag gctgttttca atgccacaga gaacatcctt
      421 ggccagttga ctattgctgg ccacgacttg ctcaatttct tcagtcgcgc tactgacgct
      481 cgccgcaaga ttacgcactt ctgcggcaac aaccgcaaaa cttcttccgg atgcgccagc
      541 ccttgctgct tcaatcgcgg cattcagtgc aataagtctt gtctgcatgg caaacttccg
      601 gatggtttcc accatatcgt caatactttc agactgattg ttgagccgtg agatatcggt
      661 ggagacagcc cccatcccct gcgcaattct gtcaatcata aggatgctat tttcaataac
      721 attggcaccg ttctgcgcac tttctcgggt ctgcacggcc atatcccatg catgcacagc
      781 agcctcttgc tctctctggt ttcgcaggac atcagccgta acatctgtag cgaatttcac
      841 aattttataa agctgcccat cactgttaaa gacagggtta taagttgcac ggaaccacag
      901 agagtctccc tgacggttaa ggcgtggaaa cagaccagaa aaaaactcac cttgattcag
      961 actctcccag aaatgtcggt attcatcact tttgtaaagc gtctcggcac agaacagacg
     1021 atgatgctta cctatgattt catcccgctt atagccagtg gcattgacga aattttcatt
     1081 tgcttcaagc acgatccctt caggattgaa ggtgatgatg gccatagaac ggtttatggc
     1141 atttacgact gcttcctgct caagagcaga atgcacgcgc tcagaaatat cggcagcaat
     1201 tttaatgact ctgataacac ggccgcgcct gtcagaaacg gggatataac tggcttcaag
     1261 ccatacggaa cgatttccct ttgccagccg caggtacttg ccactaaagc tttctcccct
     1321 ggcaaggcgc tgccagaact ggctgtattc cggtgaactt accagcgagg gcgggcagaa
     1381 tatacgatgg tggtgaccga ttatttcatc agccctgtac cccatagtgg agagaaaaag
     1441 cgggctggct ttatttatca ccccctccgg actgaactca atgacaggct tattctgaca
     1501 aattgcgtca tacgaaatgg ctgatcgctg gaggttcagg gagaacatat ttttaagtga
     1561 aaacatatga atcagattgc ccggataatg taagtactgc catggttatc ggctactcct
     1621 tatgtagcgt tatatattac tgcgacaggg cgggaaaaag cccgctcttc agccatgccg
     1681 gcatgatgtc cggctccgga tttcacgcgt aaaaaacccg ccatctttag cgggctgaac
     1741 aataagaaaa tgttcatatt tacggcaaat ccgccggctc cagcagagaa gctggcgtct
     1801 atcaatcttg gaagaaccag cgcagctccg catgcattaa caggcatcag aaggcaaaaa
     1861 aatggctcac atccgggagc cggaaaacac tcaactgcct ggatcgcagc acatcctttg
     1921 tgaaggataa tttaagtatc ggccggattg ccgcgggcat aagcccggcc ggcataattt
     1981 tttccgtatc cgccagacct cggcttttaa cataacaccc cttgcccgca ccgcagaaac
     2041 ggggttggct gcgtttccgg tgccagacgc gagaaagtgg cgacagacat gacgaaaaaa
     2101 caccaaaaac gcagccgctg gatattacac tgatgcatag tcatgcagcc agatgcatgc
     2161 agcgtaaagt cacactaaaa tcagcgcgaa cgccttaaaa accggcaaat gcctctccgg
     2221 caactcacac agctccatca ccaggtaaaa acagttcagc agggcttcaa taacgttgag
     2281 aattttcatc acttcctccg ggataagtca ctaccattcc ggtagtcagc ctatttagca
     2341 ggaacgcgat gagcccttct tcgtgcgggc tgtcacctca tcttcggacc atcgaaactc
     2401 ttctgcttct gtcggagcgt cagctccagc tcgttctgac gctgatactc cagtgcagcc
     2461 ttctcctcga tggcattcag ttcccggaca agcggcgcag ctgctcgctt aaactcagca
     2521 cctgcgtgct caagtccgac acgcgctcgt tcagcaccgc gttctcccgt tgcataagtc
     2581 cacacatgct ccgccattcc gcgaaggcgc tctcccattc gtccagcctt tgcgagtagt
     2641 cctgctgtag ctgctctaat gcgctcagca actgcttttc cagctctgtc attttccgct
     2701 actcctgttt caggcggatc caggtcgtcc cgtcgtaggg gatggcttcg gcttgcatcc
     2761 ccggcggcag gataaggaac ctccggccgt cgttgctctc ctgatagcgt actccccacg
     2821 tccgggcggt cattttcgcc agggtatctt cctgctgacg aagatgtgtg taattgtcgg
     2881 ttatctgccg tccctgccac cacagaatgc tcccgctcgt ggcgatcagc agcgctgaca
     2941 ccatcaggat ggtgagccat gtcctcccgg ccgtcagcaa cacgctccgc cggtttttct
     3001 ccatcgcctc gctcatactc tgctcgtggg cgctgatggc gtcgctgatt ctcctcgcgc
     3061 ttgcgttcag ttccgctctg acagactgct cgtgctcgct gaatgcggct ttcagcatct
     3121 cgccggtact cttctgctgc gctttcgatt gctgctctaa gtccttcgcc agcgttaaaa
     3181 gactgctcat agatggctcc cttcagtcgg atgtttcgcc ccccgtcagg gtcggcaatg
     3241 ctgatactgc ttttcgttgt acgcaccacc tcaaaacctg caccttcaag agcctcagtg
     3301 acgtcctgac ggcttttcag ctccccggac gaggctaagc tcagcagtcc acgggtgatg
     3361 gcttctgcgg cttcctgctt cgttttcggc agtccggccg gcgtgaccag cgcccggcgg
     3421 ttttccggcg cgttcggatc gtgcagcccc agtctgccgt tcacgatggt ctgccaggca
     3481 tcgatacgcg gccggtcggc gcggtcgtag tacggctgga gccgcctgcc ggtcagcagc
     3541 tcggtattgg ggatcagaaa gttcagctcc agacgcccct tgtcctcgtg ctccacccac
     3601 agaatgctgt actgatcttt atcaagtccg ggcatcagaa cccgctcgaa gctggccatc
     3661 agtttttccc gctggccggg aggcagatcg gcctccgcaa acgacagtac gccggaggtg
     3721 tatttcttca cgtaaggcga cgcgtcgatc agctcccgga cttcttccgg cttcccctgc
     3781 aggacgctgg cgccttcacg ctgccggtct ttacccagca gatagtccac cggcccggcg
     3841 ccaccgccgc gaccgcgtgg atgaaattta acgatcatcg tccgttcctt tctcaagaac
     3901 ggcgtgccgc agccgctcaa gcccggcatc gatggccatc agcgccgcca caatctgcac
     3961 ccggtcatga ccggtaccga cgccggcgtt aacacggcgg gctatctggt tcaggttgtt
     4021 gcccataccg gcaagctggc gcagcagcgc cggcgagatc gaaggaagtt ttgcggtacg
     4081 agccggcttt tcgtccaggc aggtctgccg catccacgcc gccagctgcc tgccgtcgca
     4141 gcgctcaagt agccgcctgt gctcatcctc cgtcacccac atggtgagca tcttgttccg
     4201 tttctctgac aaaacagtct cctgataacc ccgggacggg cgggaaaacc tttcccggtc
     4261 ggcgcggggt tggacaagcc gcaggcgcgt cagtggctgt tagcgggttt cggggcgcag
     4321 ccctgaacca gtcacgtagc gctagcggag tgtatactgg cttactatgt tggcacggat
     4381 gcgaatatca gtgaagtgct tcatgtggca ggagaaaaat gcagcagcgg agcgtcagca
     4441 gaatatgcga tacaggatat attccgcttc ctcgctcact gactcgctgc gctcggtcgt
     4501 tcggctgcgg cgagcggtac cggcttacag gcggggcgga aatttcctgg gagatgccag
     4561 aaagaagctt aacagggaag cgataaggcc gcggcgaagc cgtttttcca taggctccgc
     4621 ccccctgaca agcatcacga aatctgacgc tcaaatcagt ggtggcgaaa cccgacagga
     4681 ctataaagat accaggcgtt tccccctggt ggctccctcg tgcgctctcc tgttcctgcc
     4741 tttcggttta ccggtgtcat tccgctgtta tggccgcgtt tgtctcattc cacgcctgac
     4801 actcagttcc gggaaggcag ttcgctccaa gctggactgt atgcacgaac cccccgttca
     4861 gtccgaccgc tgcgccttat ccggtaacta tcaacttgag tccaatccgg aaaaacacga
     4921 caaagcgcca ctggcagc
//
