LOCUS       NZ_CP042538             4938 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter freundii strain E51 plasmid pE51_004, complete sequence.
ACCESSION   NZ_CP042538
VERSION     NZ_CP042538.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12289332
            Assembly: GCF_008931685.1
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  JOURNAL   Unpublished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 :: E51_oz_imp.uniclycerAssembly.fsa
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: na
            Genome Coverage                   :: 2513x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 13:51:31
            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)                     :: 5,506
            CDSs (total)                      :: 5,383
            Genes (coding)                    :: 5,273
            CDSs (with protein)               :: 5,273
            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)              :: 110
            CDSs (without protein)            :: 110
            Pseudo Genes (ambiguous residues) :: 0 of 110
            Pseudo Genes (frameshifted)       :: 35 of 110
            Pseudo Genes (incomplete)         :: 75 of 110
            Pseudo Genes (internal stop)      :: 23 of 110
            Pseudo Genes (multiple problems)  :: 21 of 110
            Pseudo Genes (short protein)      :: 1 of 110
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP042538.1.
            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="E51"
                     /isolation_source="Shower 3"
                     /db_xref="taxon:546"
                     /plasmid="pE51_004"
                     /geo_loc_name="Australia: Sydney"
                     /collection_date="2013-04-09"
                     /collected_by="Concord Repatriation Hospital Sydney
                     Australia"
     gene            complement(join(4221..4938,1..569))
                     /locus_tag="FR801_RS27700"
                     /old_locus_tag="FR801_27700"
     CDS             complement(join(4221..4938,1..569))
                     /locus_tag="FR801_RS27700"
                     /old_locus_tag="FR801_27700"
                     /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(1498..1713)
                     /locus_tag="FR801_RS27705"
                     /old_locus_tag="FR801_27705"
     CDS             complement(1498..1713)
                     /locus_tag="FR801_RS27705"
                     /old_locus_tag="FR801_27705"
                     /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(1720..2211)
                     /locus_tag="FR801_RS27710"
                     /old_locus_tag="FR801_27710"
     CDS             complement(1720..2211)
                     /locus_tag="FR801_RS27710"
                     /old_locus_tag="FR801_27710"
                     /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(<2246..2950)
                     /locus_tag="FR801_RS27715"
                     /old_locus_tag="FR801_27715"
                     /pseudo=""
     CDS             complement(<2246..2950)
                     /locus_tag="FR801_RS27715"
                     /old_locus_tag="FR801_27715"
                     /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(2889..3212)
                     /locus_tag="FR801_RS27720"
                     /old_locus_tag="FR801_27720"
     CDS             complement(2889..3212)
                     /locus_tag="FR801_RS27720"
                     /old_locus_tag="FR801_27720"
                     /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(3328..3500)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="9.14e-86"
     Typing          3425..3971
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.545"
                     /coverage="90.0"
                     /evalue="0.0"
     Typing          complement(1398..2899)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="83.692"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2896..3212)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.509"
                     /coverage="99.0"
                     /evalue="2.38e-59"
ORIGIN
        1 tattcatcac ttttgtaaag cgtctcggca cagaacagac gatgatgctt acctatgatt
       61 tcatcccgct tatagccagt ggcattgacg aaattttcat ttgcttcaag cacgatccct
      121 tcaggattga aggtgatgat ggccatagaa cggtttatgg catttacgac tgcttcctgc
      181 tcaagagcag aatgcacgcg ctcagaaata tcggcagcaa ttttaatgac tctgataaca
      241 cggccgcgcc tgtcagaaac ggggatataa ctggcttcaa gccatacgga acgatttccc
      301 tttgccagcc gcaggtactt gccactaaag ctttctcccc tggcaaggcg ctgccagaac
      361 tggctgtatt ccggtgaact taccagcgag ggcgggcaga atatacgatg gtggtgaccg
      421 attatttcat cagccctgta ccccatagtg gagagaaaaa gcgggctggc tttatttatc
      481 accccctccg gactgaactc aatgacaggc ttattctgac aaattgcgtc atacgaaatg
      541 gctgatcgct ggaggttcag ggagaacata tttttaagtg aaaacatatg aatcagattg
      601 cccggataat gtaagtactg ccatggttat cggctactcc ttatgtagcg ttatatatta
      661 ctgcgacagg gcgggaaaaa gcccgctctt cagccatgcc ggcatgatgt ccggctccgg
      721 atttcacgcg taaaaaaccc gccatcttta gcgggctgaa caataagaaa atgttcatat
      781 ttacggcaaa tccgccggct ccagcagaga agctggcgtc tatcaatctt ggaagaacca
      841 gcgcagctcc gcatgcatta acaggcatca gaaggcaaaa aaatggctca catccgggag
      901 ccggaaaaca ctcaactgcc tggatcgcag cacatccttt gtgaaggata atttaagtat
      961 cggccggatt gccgcgggca taagcccggc cggcataatt ttttccgtat ccgccagacc
     1021 tcggctttta acataacacc ccttgcccgc accgcagaaa cggggttggc tgcgtttccg
     1081 gtgccagacg cgagaaagtg gcgacagaca tgacgaaaaa acaccaaaaa cgcagccgct
     1141 ggatattaca ctgatgcata gtcatgcagc cagatgcatg cagcgtaaag tcacactaaa
     1201 atcagcgcga acgccttaaa aaccggcaaa tgcctctccg gcaactcaca cagctccatc
     1261 accaggtaaa aacagttcag cagggcttca ataacgttga gaattttcat cacttcctcc
     1321 gggataagtc actaccattc cggtagtcag cctatttagc aggaacgcga tgagcccttc
     1381 ttcgtgcggg ctgtcacctc atcttcggac catcgaaact cttctgcttc tgtcggagcg
     1441 tcagctccag ctcgttctga cgctgatact ccagtgcagc cttctcctcg atggcattca
     1501 gttcccggac aagcggcgca gctgctcgct taaactcagc acctgcgtgc tcaagtccga
     1561 cacgcgctcg ttcagcaccg cgttctcccg ttgcataagt ccacacatgc tccgccattc
     1621 cgcgaaggcg ctctcccatt cgtccagcct ttgcgagtag tcctgctgta gctgctctaa
     1681 tgcgctcagc aactgctttt ccagctctgt cattttccgc tactcctgtt tcaggcggat
     1741 ccaggtcgtc ccgtcgtagg ggatggcttc ggcttgcatc cccggcggca ggataaggaa
     1801 cctccggccg tcgttgctct cctgatagcg tactccccac gtccgggcgg tcattttcgc
     1861 cagggtatct tcctgctgac gaagatgtgt gtaattgtcg gttatctgcc gtccctgcca
     1921 ccacagaatg ctcccgctcg tggcgatcag cagcgctgac accatcagga tggtgagcca
     1981 tgtcctcccg gccgtcagca acacgctccg ccggtttttc tccatcgcct cgctcatact
     2041 ctgctcgtgg gcgctgatgg cgtcgctgat tctcctcgcg cttgcgttca gttccgctct
     2101 gacagactgc tcgtgctcgc tgaatgcggc tttcagcatc tcgccggtac tcttctgctg
     2161 cgctttcgat tgctgctcta agtccttcgc cagcgttaaa agactgctca tagatggctc
     2221 ccttcagtcg gatgtttcgc cccccgtcag ggtcggcaat gctgatactg cttttcgttg
     2281 tacgcaccac ctcaaaacct gcaccttcaa gagcctcagt gacgtcctga cggcttttca
     2341 gctccccgga cgaggctaag ctcagcagtc cacgggtgat ggcttctgcg gcttcctgct
     2401 tcgttttcgg cagtccggcc ggcgtgacca gcgcccggcg gttttccggc gcgttcggat
     2461 cgtgcagccc cagtctgccg ttcacgatgg tctgccaggc atcgatacgc ggccggtcgg
     2521 cgcggtcgta gtacggctgg agccgcctgc cggtcagcag ctcggtattg gggatcagaa
     2581 agttcagctc cagacgcccc ttgtcctcgt gctccaccca cagaatgctg tactgatctt
     2641 tatcaagtcc gggcatcaga acccgctcga agctggccat cagtttttcc cgctggccgg
     2701 gaggcagatc ggcctccgca aacgacagta cgccggaggt gtatttcttc acgtaaggcg
     2761 acgcgtcgat cagctcccgg acttcttccg gcttcccctg caggacgctg gcgccttcac
     2821 gctgccggtc tttacccagc agatagtcca ccggcccggc gccaccgccg cgaccgcgtg
     2881 gatgaaattt aacgatcatc gtccgttcct ttctcaagaa cggcgtgccg cagccgctca
     2941 agcccggcat cgatggccat cagcgccgcc acaatctgca cccggtcatg accggtaccg
     3001 acgccggcgt taacacggcg ggctatctgg ttcaggttgt tgcccatacc ggcaagctgg
     3061 cgcagcagcg ccggcgagat cgaaggaagt tttgcggtac gagccggctt ttcgtccagg
     3121 caggtctgcc gcatccacgc cgccagctgc ctgccgtcgc agcgctcaag tagccgcctg
     3181 tgctcatcct ccgtcaccca catggtgagc atcttgttcc gtttctctga caaaacagtc
     3241 tcctgataac cccgggacgg gcgggaaaac ctttcccggt cggcgcgggg ttggacaagc
     3301 cgcaggcgcg tcagtggctg ttagcgggtt tcggggcgca gccctgaacc agtcacgtag
     3361 cgctagcgga gtgtatactg gcttactatg ttggcacgga tgcgaatatc agtgaagtgc
     3421 ttcatgtggc aggagaaaaa tgcagcagcg gagcgtcagc agaatatgcg atacaggata
     3481 tattccgctt cctcgctcac tgactcgctg cgctcggtcg ttcggctgcg gcgagcggta
     3541 ccggcttaca ggcggggcgg aaatttcctg ggagatgcca gaaagaagct taacagggaa
     3601 gcgataaggc cgcggcgaag ccgtttttcc ataggctccg cccccctgac aagcatcacg
     3661 aaatctgacg ctcaaatcag tggtggcgaa acccgacagg actataaaga taccaggcgt
     3721 ttccccctgg tggctccctc gtgcgctctc ctgttcctgc ctttcggttt accggtgtca
     3781 ttccgctgtt atggccgcgt ttgtctcatt ccacgcctga cactcagttc cgggaaggca
     3841 gttcgctcca agctggactg tatgcacgaa ccccccgttc agtccgaccg ctgcgcctta
     3901 tccggtaact atcaacttga gtccaatccg gaaaaacacg acaaagcgcc actggcagca
     3961 gccactggta acaggtttag aggaggagag tcttgaagtt tcgggtgcga taaggctaca
     4021 ctgaaaggac agttttggtg actgtgctcc tccaagccag ttaccgcggt tcaaaagagc
     4081 gtcaactctt gcgaaccttc gaaaaagcca ccttgccggg tggttttttc gttttcagag
     4141 caagagatta cgacgcaacg gaaaggatct caagaagatc atctgtgatg ttcgacagat
     4201 atggggatat gcaccatggc ctatccggct ttaactgaaa tggcgacatc cttaaccgca
     4261 gtctcaaccc ctgcagcatt cctctgaatg ctggtcataa cttcacccgc ttcgcgcatg
     4321 agtgtaaccc cttcccgagt gttcatcagg ctgttttcaa tgccacagag aacatccttg
     4381 gccagttgac tattgctggc cacgacttgc tcaatttctt cagtcgcgct actgacgctc
     4441 gccgcaagat tacgcacttc tgcggcaaca accgcaaaac ttcttccgga tgcgccagcc
     4501 cttgctgctt caatcgcggc attcagtgca ataagtcttg tctgcatggc aaacttccgg
     4561 atggtttcca ccatatcgtc aatactttca gactgattgt tgagccgtga gatatcggtg
     4621 gagacagccc ccatcccctg cgcaattctg tcaatcataa ggatgctatt ttcaataaca
     4681 ttggcaccgt tctgcgcact ttctcgggtc tgcacggcca tatcccatgc atgcacagca
     4741 gcctcttgct ctctctggtt tcgcaggaca tcagccgtaa catctgtagc gaatttcaca
     4801 attttataaa gctgcccatc actgttaaag acagggttat aagttgcacg gaaccacaga
     4861 gagtctccct gacggttaag gcgtggaaac agaccagaaa aaaactcacc ttgattcaga
     4921 ctctcccaga aatgtcgg
//
