LOCUS       NZ_CP056507             4426 bp    DNA     circular CON 06-APR-2024
DEFINITION  Citrobacter freundii strain RHBSTW-00449 plasmid pRHBSTW-00449_3,
            complete sequence.
ACCESSION   NZ_CP056507
VERSION     NZ_CP056507.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148618
            Assembly: GCF_013748855.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 4426)
  AUTHORS   AbuOun,M., Jones,H., Stubberfield,E., Gilson,D., Shaw,L.P.,
            Hubbard,A.T.M., Chau,K.K., Sebra,R., Peto,T.E.A., Crook,D.W.,
            Read,D.S., Gweon,H.S., Walker,A.S., Stoesser,N., Smith,R.P.,
            Anjum,M.F. and On Behalf Of The Rehab,Consortium.
  TITLE     A genomic epidemiological study shows that prevalence of
            antimicrobial resistance in Enterobacterales is associated with the
            livestock host, as well as antimicrobial usage
  JOURNAL   Microb Genom 7 (10) (2021)
   PUBMED   34609275
REFERENCE   2  (bases 1 to 4426)
  AUTHORS   Shaw,L.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (12-JUN-2020) Nuffield Department of Medicine, University
            of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.7
            Assembly Name                     :: WTP5 T2-00449
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 107.375177636945x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013748855.1-RS_2024_04_06
            Annotation Date                   :: 04/06/2024 05:43:28
            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)                     :: 5,257
            CDSs (total)                      :: 5,142
            Genes (coding)                    :: 5,028
            CDSs (with protein)               :: 5,028
            Genes (RNA)                       :: 115
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 82
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 114
            CDSs (without protein)            :: 114
            Pseudo Genes (ambiguous residues) :: 0 of 114
            Pseudo Genes (frameshifted)       :: 37 of 114
            Pseudo Genes (incomplete)         :: 79 of 114
            Pseudo Genes (internal stop)      :: 18 of 114
            Pseudo Genes (multiple problems)  :: 21 of 114
            Pseudo Genes (short protein)      :: 2 of 114
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056507.1.
            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..4426
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00449"
                     /isolation_source="Wastewater influent sample"
                     /db_xref="taxon:546"
                     /plasmid="pRHBSTW-00449_3"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            129..344
                     /locus_tag="HV201_RS26115"
                     /old_locus_tag="HV201_26130"
     CDS             129..344
                     /locus_tag="HV201_RS26115"
                     /old_locus_tag="HV201_26130"
                     /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(1032..1247)
                     /locus_tag="HV201_RS26120"
                     /old_locus_tag="HV201_26135"
     CDS             complement(1032..1247)
                     /locus_tag="HV201_RS26120"
                     /old_locus_tag="HV201_26135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002241003.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_015387220.1"
                     /translation="MGFWETAGKIAKGAANALDEKAHELQATKMRLESKSSEELKRLIK
                     SDGFFGSASNTEKSMAMKILRERGDV"
                     /name="hypothetical protein"
     gene            1581..2042
                     /locus_tag="HV201_RS26125"
                     /old_locus_tag="HV201_26140"
     CDS             1581..2042
                     /locus_tag="HV201_RS26125"
                     /old_locus_tag="HV201_26140"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_128348982.1"
                     /translation="MVNTYYGYLLGVTLGEWAMGSDVQWQIDNGYLAQVMGDFSTESPS
                     FEMPMFGRYFDTFQAAIHVAKAFPGSTLQPSEYEDKTGMVIRHYYVDCHPYYDRLPPEK
                     SDDFQYDEYPSAIHVAACIDQASKELDELLFGGGYGENGEGHASPIILY"
                     /name="hypothetical protein"
     gene            complement(2298..2408)
                     /locus_tag="HV201_RS26475"
     CDS             complement(2298..2408)
                     /locus_tag="HV201_RS26475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505258.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_063858821.1"
                     /translation="MHEPPVQSDYHAHSGNYQLESNPERHDKIAIGGSHW"
                     /name="hypothetical protein"
     gene            3056..3379
                     /locus_tag="HV201_RS26135"
                     /old_locus_tag="HV201_26150"
     CDS             3056..3379
                     /locus_tag="HV201_RS26135"
                     /old_locus_tag="HV201_26150"
                     /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_126289757.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARTGKLPSI
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3588..>4022
                     /locus_tag="HV201_RS26480"
                     /pseudo=""
     CDS             3588..>4022
                     /locus_tag="HV201_RS26480"
                     /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"
     Typing          2770..2943
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.714"
                     /coverage="100.0"
                     /evalue="1.2e-79"
     Typing          complement(2242..2846)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.196"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3..436
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.621"
                     /coverage="99.0"
                     /evalue="4.53e-82"
     Typing          3057..3373
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.34"
                     /coverage="99.0"
                     /evalue="8.540000000000001e-63"
     Typing          3370..4424
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.739"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 cgtggggagt gcgctatcag gagagcagcg acggccggag gtttcttatc ctgccgccgg
       61 ggatgcaaac cgaagccatc ccttacgacg ggacgacatg gatccgcctg aaacaggagt
      121 agcggaaaat gacagagctg gaaaagcagt tgctgagcgc attagagcag ctacagcagg
      181 actactcgca aaggctggac gaatgggaga gcgccttcgc ggaatggcgg agcatgtgtg
      241 ggcttatgca acgggagaac gcggtgctga acgagcgcgt gtcggacttg agcacgcagg
      301 tgctgagttt aagcgagcag ctgcgccgct tgtccgggaa ctgaatgcca tcgagctccg
      361 gcagagggag aatgagtatc agaaaacact ggagctggag cgccagccgc agaaaaccta
      421 ccgcgggccg acactttaaa ccatccaggc agctgacaac ccgcacgaag aggggctctt
      481 acttctcccg ctaaataggt tcgtgatcaa aaaggtcacg acttattcag gagcgggaaa
      541 tgaagctgtt aaatcttatt gaatcattgc ttaactgcct gtatctggcg gcggagctgt
      601 gggactggct ggagaagcat ttgtcggttt ttaaggcgtt cgcgctgatt ttagtgtgac
      661 tttacgcgcc atgcatctgg ctgcatgact atgcatcagt gtaatatcca gcggctgcgt
      721 ttctggtgtt ttttcgtcat gtctgtcgcc actttctcgc gtctggcacc ggaaacgcag
      781 ccaaccccgt ttcagcggtg cgggcaatgg gacgttatgg taaataagtg ggcgtaaaaa
      841 agcccgggtt acgggcttct ggacgctatg acttaccacg acattctctg caccaacttt
      901 gattcgttgc accagaagga atggttctga atccgaatag agtttgcaac tcacctgcag
      961 tatgagcggt ggttcgcttg cagttagggc atgtatgagg aagattcacc gtgcctacca
     1021 tttttctatc cttaaacgtc tccgcgttct ctgagaattt tcattgccat gcttttttct
     1081 gtgttactgg ctgagccgaa aaaaccatca gatttaatga ggcgctttag ttcttcactg
     1141 cttttgcttt ctaagcgcat tttggttgcc tggagttcat gagctttttc atccaaagcg
     1201 ttagctgcgc cttttgcaat tttaccggcc gtttcccaaa atcccattta accactcctt
     1261 aatgcttatc caattggact tgttgtgatc cgacgactcc gacatttagg gcaataatca
     1321 ggcgtgccat aaccagtacg actggtccac tcatgcttac aatccaaaca cttagcccgg
     1381 tagattgtcg gtgccattga atactccatt gattttaaaa atatttgtat agtgcactaa
     1441 aattatcggc agtttttctc ggagcttgag aggtagataa ccctaagctg atatgttgcc
     1501 tttatgatgg ttttcgtgtg ccaaggttag ctaggtaagg gatttactgt gggaagtgct
     1561 ggttcgcgaa gtgaagcgtt atggtaaata catattatgg ttatttatta ggagtaactc
     1621 tgggagagtg ggctatggga tcagatgttc aatggcagat agataatggt tatttggcgc
     1681 aagttatggg ggatttttcg acagagtcgc ctagctttga aatgccaatg tttgggcgat
     1741 attttgatac ctttcaagct gctatacatg ttgcaaaagc tttcccaggg agtacgttgc
     1801 agccatcaga gtacgaagat aaaactggga tggtaatacg tcattattat gtggattgtc
     1861 atccgtatta tgatcgactt cctcctgaaa aaagcgatga ttttcagtat gatgaatacc
     1921 cttctgctat tcatgtggct gcgtgtattg atcaagccag caaagaactc gacgaactat
     1981 tgtttggtgg tggatatggg gaaaatggtg aggggcatgc aagcccgata attttatatt
     2041 agtgtgaggg ggcggaggga tattatccaa tttgtaaaat gatcttcttg agatcgtttt
     2101 gctctgcgcg taatctcttg ctctgaaaac gaaaaaacca cctggggagg tggtttttcg
     2161 aaggttcagt aagttgggga acttctgaac cgtggtaaca gtcttgtgcg agacgtgtca
     2221 ccaaatctgt ccttccagtg tagccgtagt ccggccacca cttcaagaac tctcgataca
     2281 tctctcgcac atcctgctta ccagtggcta ccgccaatgg cgattttgtc gtgtctttcc
     2341 gggttggact caagttgata gttaccggaa tgggcgtggt agtcggactg aacggggggt
     2401 tcgtgcatac agtccagctt ggagcgaact gcctacccgg aactgagtgt caggcgtgga
     2461 atgagacaaa cgcggccata acagcggagt gacaccggta aaccgaaagg caggaacagg
     2521 agagcgcacg agggagccgc cagggggaaa cgcctggtat ctttaagtcc tgtcgggttt
     2581 cgccaccact gatttgagcg tcagatttcg tgatgcttgt caggggggcg gagcctatgg
     2641 aaaaacggct tcgccgcggc cttctcgttt ccctgttaag tctcttcctc gcatctacca
     2701 ggaaatttcc gccccgctcg taagccattt ccgctcgccg cagccgaacg accgagcgca
     2761 gcgagtcagt gagcgaggaa gcggaatata tcctgtacca catattctgc tgacgcaccg
     2821 gtgccgcctt ttttctcctg ccacatgaag cacttcactg acaccctcat ccgtgccaac
     2881 atagtaagcc agtatacact ccgctagcgc ttcgtgactg gttcagggct gcgccccgaa
     2941 acccgccaaa agcctgacgc gcctgcggct tgtccaaccc cgcgccgacc gggaaagagg
     3001 ttcccgcccg tcccggcgtt atcaggagac cggtttgtca gagaaacgca gcaaaatgct
     3061 cacgatgtgg gtgaccgaag atgagcaccg ccgtctgctg gaacgctgcg acggtaaaca
     3121 gctcgcggcc tggatgcggc agacctgcct ggacgaaaag cctgcgcgca ccggaaagct
     3181 cccctcaatc tcgccggcgc tgctgcgcca gcttgccggc atgggcaata acctgaacca
     3241 gatagcccgc cgtgttaacg ccggcggcgg caccggccat gacagggtac agattgtggc
     3301 ggcgctgatg gccatcgatg ccgggcttga gcggctgcgg cacgccgttc ttgagaaagg
     3361 aacggacgat gatcgttaaa tttcatccac gcggtcgcgg cggtggcgcc gggccggtgg
     3421 actatcttct gggtaaagac cggcagcgtg aaggtgccag cgtcctgcag gggaagccgg
     3481 aagaagtccg ggagctgatt gacgcgtcgc cttacgtgaa gaaatacacc tccggcgtcc
     3541 tgtcgtttgc ggaggccgat ctgcctcccg gccagcggga aaaactgatg gccagcttcg
     3601 agcgggttct gatgcccgga cttgataaag atcagtacag cattctgtgg gtggagcacg
     3661 aggacaaggg gcgtctggag ctgaactttc tgatccccaa taccgagctg ctgaccggca
     3721 ggcggctcca gccgtactac gaccgcgccg accggccgcg tatcgatgcc tggcagacca
     3781 tcgtgaacgg cagactgggg ctgcacgacc cgaacgcacc ggaaaaccgc cgggcgctgg
     3841 tcacgccgtc cggactgccg aaaacgaagc aggaggccgc agaagccatc acgcgcggac
     3901 tgctgaccct tgcttcgtcc ggggagctga aaacccgtca ggacgtcact gaggcgctgg
     3961 aacggtcagg ttttgaggtg gtgcgcacca cgaaaagcag tatcagcatt gccgacccgg
     4021 acggggggcg aaacatccga ctgaagggag ccatctatga gcagtctttt aacgctggcg
     4081 aaggacttag agcagcaatc gaaagcgcag aagcagagta ccggcgagat gctgaaagcc
     4141 gcattcagcg agcacgagca gtctgtcaga gcggaactga gcgcaagcgc gaggagaatc
     4201 agcgacgcca tcctcgcaca cgagcagagt atgagcgagg cgatggagaa aaaccggcgg
     4261 agcgtactgc ggactgccgg gcggacatgg ctcaccatcc tgatggtgtc agcgctgctg
     4321 atcggcacga gcgggagcat actgtggtgg caggggcagc agataaccga caattacacg
     4381 catcttcgtc agcaggaaga taccctggcg aaaatgaccg cccgga
//
