LOCUS       NZ_CP056340             4167 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Citrobacter freundii strain RHBSTW-00697 plasmid pRHBSTW-00697_5,
            complete sequence.
ACCESSION   NZ_CP056340
VERSION     NZ_CP056340.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15148687
            Assembly: GCF_013738635.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 4167)
  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 4167)
  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                     :: WTP2 T2-00697
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 88.5090617777702x
            Sequencing Technology :: Hybrid: Illumina and OXFORD_NANOPORE
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 14:21:41
            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)                     :: 5,445
            CDSs (total)                      :: 5,326
            Genes (coding)                    :: 5,155
            CDSs (with protein)               :: 5,155
            Genes (RNA)                       :: 119
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 171
            CDSs (without protein)            :: 171
            Pseudo Genes (ambiguous residues) :: 0 of 171
            Pseudo Genes (frameshifted)       :: 53 of 171
            Pseudo Genes (incomplete)         :: 121 of 171
            Pseudo Genes (internal stop)      :: 31 of 171
            Pseudo Genes (multiple problems)  :: 29 of 171
            Pseudo Genes (short protein)      :: 1 of 171
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP056340.1.
            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..4167
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="RHBSTW-00697"
                     /isolation_source="Wastewater effluent sample"
                     /db_xref="taxon:546"
                     /plasmid="pRHBSTW-00697_5"
                     /geo_loc_name="United Kingdom"
                     /collection_date="2017"
     gene            join(3753..4167,1..200)
                     /locus_tag="HV270_RS27060"
                     /old_locus_tag="HV270_27070"
     CDS             join(3753..4167,1..200)
                     /locus_tag="HV270_RS27060"
                     /old_locus_tag="HV270_27070"
                     /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_038989285.1"
                     /translation="MTIEIIILANSIKHQACCVAGKTIAGEWVRIVADSSGKELTKEQA
                     SITNPYGTFLVKPLQKVLLNLTKHAPLLNQPENYINDPKSGWTQNFNLKFEDLSKYTDK
                     PNSLWGDNNDRIPYADITSSKIKIDSSLYLIEAKKATAYLNTYGKRRVSFSYNGLNYDL
                     PVTDPKFDTIEKDKVFESIYLCISLGEEYEGNCYKIVANIF"
                     /name="hypothetical protein"
     gene            211..651
                     /locus_tag="HV270_RS27065"
                     /old_locus_tag="HV270_27075"
     CDS             211..651
                     /locus_tag="HV270_RS27065"
                     /old_locus_tag="HV270_27075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001572619.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF488 domain-containing protein"
                     /protein_id="WP_038989283.1"
                     /translation="MNVFTIGFTKKSAEHFFNELKDNNVKKIIDVRLNNISQLSGFAKK
                     NDLIFFLEKLCGIDYIHLDELAPTKSILEPYQKKKITWEQYEIEFINLMERRSIEKSIN
                     IAEMDKSCLLCSEDKPHFCHRRLVLQYLNSKMDNIFKVRHLL"
                     /name="DUF488 domain-containing protein"
     gene            651..1244
                     /locus_tag="HV270_RS27070"
                     /old_locus_tag="HV270_27080"
     CDS             651..1244
                     /locus_tag="HV270_RS27070"
                     /old_locus_tag="HV270_27080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020580603.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF4326 domain-containing protein"
                     /protein_id="WP_012262159.1"
                     /translation="MNNLLVIYHEDFLCYEKLKRKIKNITINMDDFKITTTHDKRGILL
                     RLSTEITFELNIVKEVNLNDISHSIIFNCFNEYDEIITEIKEKNIPIRIINLKLAKAIN
                     IKGTTFGKGSSETYEYIGRGSKWGNPYSMYENGDDRDEVIRKFKYDFDFDKFLNVKKED
                     FIHLKGKKLGCFCKPQACHGDVIADYLNSLDDGE"
                     /name="DUF4326 domain-containing protein"
     gene            complement(1302..1772)
                     /locus_tag="HV270_RS27075"
                     /old_locus_tag="HV270_27085"
     CDS             complement(1302..1772)
                     /locus_tag="HV270_RS27075"
                     /old_locus_tag="HV270_27085"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016946649.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_012262160.1"
                     /translation="MQQAIRMRIEADSASGKMTETVRQSVNAALTQVEKELKQTGLEQQ
                     KPATDAFNQAAGTAKAMIHEMRREMSRYTWKSAIYIAMTMIAVMGGCLWGMYYFIDSGY
                     ARVAEMQHMEAVWQKKAPLADIKTCDGNPCVKVDISRTFGDKKDTYLIIKGK"
                     /name="hypothetical protein"
     gene            complement(1982..2128)
                     /locus_tag="HV270_RS27440"
                     /pseudo=""
     CDS             complement(1982..2128)
                     /locus_tag="HV270_RS27440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001717510.1"
                     /note="internal stop; 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            2728..2877
                     /locus_tag="HV270_RS27080"
                     /old_locus_tag="HV270_27090"
     CDS             2728..2877
                     /locus_tag="HV270_RS27080"
                     /old_locus_tag="HV270_27090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_162854494.1"
                     /translation="MPSEYDEQRDSTDTQLPGEYDLFDLMAKVTEENLHAPVDSGPPVG
                     REAL"
                     /name="hypothetical protein"
     Typing          2519..2735
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.14e-110"
     Typing          complement(1798..2307)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="83.144"
                     /coverage="99.0"
                     /evalue="1.77e-127"
ORIGIN
        1 aggcaacggc atacttaaac acatatggta aaagaagggt gtcgttctca tataatggat
       61 taaattatga cctacctgtt acagatccaa aatttgatac gatagaaaag gacaaggtgt
      121 ttgaaagcat ctacttgtgc attagtcttg gtgaagaata tgaaggcaac tgttataaaa
      181 tagttgcaaa cattttttaa ggtgctgttc atgaatgtat ttacaatagg atttacaaaa
      241 aaaagcgcag aacatttttt taatgaactg aaggataaca acgtaaaaaa aataatagat
      301 gtaaggttaa acaatatatc tcaactttct gggtttgcta aaaagaatga cttaatattc
      361 tttttagaaa aattgtgtgg tattgactac atacatttag atgagctggc cccaacaaaa
      421 tcaatactag aaccatatca aaaaaagaaa ataacttggg aacagtatga gattgaattt
      481 attaacctca tggaaagaag aagtattgaa aaatcaataa acatagcaga aatggataaa
      541 tcatgcctac tttgcagtga agacaaacct catttctgtc atcgcagact tgtgctacaa
      601 tacttaaact caaaaatgga caatatattt aaagtaaggc acctgctgta atgaacaact
      661 tgttagttat ctatcatgaa gacttccttt gctatgaaaa gctaaaaagg aaaataaaaa
      721 acataaccat aaacatggat gatttcaaaa taaccacaac tcacgataaa cgagggatct
      781 tattaaggtt atcaaccgaa attactttcg aattaaacat tgtaaaagaa gtaaacttaa
      841 acgatatatc tcattcaatt atattcaact gctttaatga atacgatgag ataataacag
      901 aaataaagga aaaaaacatt ccaattcgga ttataaatct aaagctagct aaagcaataa
      961 acataaaagg cacaactttt ggcaagggta gtagcgaaac atatgaatat attggaagag
     1021 gttctaagtg gggaaatcca tattcaatgt atgaaaatgg cgatgatagg gatgaagtta
     1081 ttaggaagtt taaatacgac ttcgattttg ataagttctt gaatgtgaag aaagaggact
     1141 tcattcatct aaaggggaaa aaattaggct gtttctgtaa acctcaagct tgtcatggtg
     1201 atgttattgc tgattatcta aattctctcg atgatggaga gtaattcatt acacccatca
     1261 ttcaaatcac attatttgaa tgatgggtgt aatgaatgca tttatttacc ttttataatc
     1321 agataagtat cttttttatc gccaaaggtt cggctgatat cgactttaac gcagggattt
     1381 ccgtcacacg tcttaatatc cgctaatggt gctttcttct gccagacggc ctccatatgc
     1441 tgcatttctg caacacgcgc atagccgctg tcgataaagt aatacatacc ccagagacaa
     1501 cctcccataa ctgcaatcat cgtcattgca atataaatcg ctgacttcca agtataacgc
     1561 gacatctcgc ggcgcatctc atggatcatc gctttcgccg tgccggcagc ctgattaaac
     1621 gcatctgtag ctggcttctg ctgctctagc ccagtctgct tcaactcttt ctcgacttgg
     1681 gttaaggccg cattaacaga ctgcctgacc gtttccgtca tcttgcctga ggcgctatcg
     1741 gcttcgattc tcatacggat ggcttgttgc atactttttg tagcccttca tgggggaaga
     1801 tcttcttgag atccttttat tctgcgcgta atctcttgtc ctgaaaacga aaaaaccacc
     1861 tggggaggtg gtttttcgaa ggttcagtaa gttggggaac ttctgaaccg tggtaacagg
     1921 gtgtacaaga ccgctgccac caaatacgtc ctttcagttt agccgtagtt aggcttcaac
     1981 ttcaagaact ctgcaccagt aatctcttgt acaccccttt accagtggct accgccaatg
     2041 gcgatttgac gtgtctgtaa gggttggact caagacgata gttaccttac atggcgcggt
     2101 agtcggactg aacggggggt tcgtgcatac agtccagctt ggagcgaact gcctacccgg
     2161 aactgagtgt caggcgtgga atgagacaaa cgcggccata acagcggaat gacaccggta
     2221 aaccgaatgg caggaacagg agagcgcacg agggagcgac ccatcggaaa cggtggggat
     2281 ctttaagtcc tgtcgggttt cgtcaccgct gtcggattca tggttgagct caggctccca
     2341 cagatgcacc gaaaaagtgt ctgtttatga attccggcag gggggcggag cctatgaaaa
     2401 aacggcaacg ccgcatcctt tttccggccc ttcctgattt gagcactgct tgcgtgtcct
     2461 gtcatctgtg agccggtaac gcccgccgca gtctcacggc aggagcgtag cgaccgagtg
     2521 agcgaggagg cgtcatttca tccttacctg catgttgcac ttacgcccgg tagccgcatt
     2581 ttttcccttg tcacatgaag cactttcata aatcaccact ccgccgtaac atatttagcc
     2641 agtatacact ccgctagcgc tacgtgactg gttcagggct gcgccccgaa acccgctaac
     2701 aacctctccg ctactggata tcaccccatg ccatctgaat atgatgaaca acgggattcg
     2761 actgatacgc agcttcccgg cgaatatgac ctttttgatt taatggcgaa ggttactgaa
     2821 gagaacctgc atgcccctgt ggattctggg ccgcctgtcg gccgggaagc gttatagctt
     2881 ttttcgcttg cccgcgtacg tggtaatacg ccggtattac atcttatttc tttattttca
     2941 tgtgattaca gatgatttta atacttgcgt attaccgtaa taaacggtgc atcccatttt
     3001 ttttatgtaa ttcatgcagt tgcgatgaaa atcgcggctg cgttaggtgt atagcaggtt
     3061 aagggataaa aaatcatctt ttttggtagg gcgctctccg taggttaagg gctatttggc
     3121 taaaaagcgt cctattcttt gatggtcatg cttgcatgac catctgagca accaaaaact
     3181 acagataaac tacaaaaaac gttttgcatt agtgatggca gactacaaaa aaactacaaa
     3241 aaccgtggca gactactaat agactacaag aaaactacag ataaactaca aagtaactac
     3301 cggattacct cagatccgtt ccctgaacca ttcgtacatc gacccccttc ctgaacgtgc
     3361 tgaaaacggg ttttccggct gcgccggcaa cgcttcacgg ccacgcaata aattgcgtcc
     3421 ccgttcaccg ttttccgatg ggaagaacgc cggaaacagg acttcccctg gctgaatggt
     3481 gtcaatttcc gtgctatgca cttgtgcgca tactcatgca tgccgtaaaa acagagcctg
     3541 cgcgtttctg gcgggttttc gggtggtttg ttgcctgttt taccggtttc ccgtcagaaa
     3601 cgccctcaga ggctctgagg cggtgccgat aagggatgtt atggtaaatg acaacaaccg
     3661 aaatactgtc gtgaatgtga tttttcgatt gaaaatcaca aaaaaatcaa caaatatcac
     3721 ctattctatc attcgacgtt agggaggatt aaatgactat tgaaattatt attttagcaa
     3781 actcaattaa acatcaggct tgttgtgttg caggaaaaac aatagcaggg gaatgggtta
     3841 gaattgtagc ggatagttca ggaaaagagt tgacaaaaga gcaagcctca ataacaaacc
     3901 cttacggtac attcttagta aaaccactgc aaaaagtact gttaaatctt acgaaacacg
     3961 ccccactttt aaatcaacca gaaaattata tcaatgatcc aaaatcagga tggactcaga
     4021 attttaattt gaaatttgaa gatctatcta aatatacaga caaacctaat agcttatggg
     4081 gtgataataa tgacaggatc ccatacgccg acataactag cagcaagatt aaaatagata
     4141 gctcactgta tttaattgag gctaaaa
//
