LOCUS       NZ_AP022405             3087 bp    DNA     circular CON 30-JAN-2024
DEFINITION  Citrobacter portucalensis strain STW0522-30 plasmid pSTW0522-30-6,
            complete sequence.
ACCESSION   NZ_AP022405
VERSION     NZ_AP022405.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00195870
            Sequence Read Archive: DRR199675
            Assembly: GCF_015135215.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter portucalensis
  ORGANISM  Citrobacter portucalensis
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1
  AUTHORS   Sekizuka,T., Katagiri,M., Asai,K. and Kuroda,M.
  TITLE     complete genome sequences of Citrobacter portucalensis str.
            STW0522-30 isolated from hospital sewage
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3087)
  AUTHORS   Sekizuka,T., Katagiri,M., Asai,K. and Kuroda,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-FEB-2020) Contact:Tsuyoshi Sekizuka National Institute
            of Infectious Diseases, Pathogen Genomics Center; 1-23-1 Toyama,
            Shinjuku-ku, Tokyo 162-8640, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: flye v. 2.5; minimap v. 0.2-r124; racon v. 1.1.0;
            circlator v. 1.5.3; Pilon v. 1.18; SPAdes v. 3.11.1; A5-miseq v.
            20140604
            Genome Coverage                   :: 387x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/30/2024 09:04:00
            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)                     :: 5,249
            CDSs (total)                      :: 5,135
            Genes (coding)                    :: 4,958
            CDSs (with protein)               :: 4,958
            Genes (RNA)                       :: 114
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 82
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 177
            CDSs (without protein)            :: 177
            Pseudo Genes (ambiguous residues) :: 0 of 177
            Pseudo Genes (frameshifted)       :: 35 of 177
            Pseudo Genes (incomplete)         :: 134 of 177
            Pseudo Genes (internal stop)      :: 29 of 177
            Pseudo Genes (multiple problems)  :: 19 of 177
            Pseudo Genes (short protein)      :: 1 of 177
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022405.1.
            Annotated by DFAST v.1.2.3 (https://dfast.nig.ac.jp).
            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..3087
                     /organism="Citrobacter portucalensis"
                     /mol_type="genomic DNA"
                     /strain="STW0522-30"
                     /isolation_source="sewage"
                     /db_xref="taxon:1639133"
                     /plasmid="pSTW0522-30-6"
                     /geo_loc_name="Japan:Tokyo"
                     /collection_date="2018-05-22"
     gene            join(3066..3087,1..425)
                     /locus_tag="JLF43_RS26050"
                     /old_locus_tag="STW0522CIT30_P60010"
     CDS             join(3066..3087,1..425)
                     /locus_tag="JLF43_RS26050"
                     /old_locus_tag="STW0522CIT30_P60010"
                     /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_200924078.1"
                     /translation="MEEKIKKELESVYCEYWTEEFSVYAFGAYVAAAKKRLKADLMIDI
                     LYEIAKKEKIDLTYHTSLRICKIFMSRGILGDRLFSHFANVENKDGELTKREEKRTAKE
                     KVSIDYASIEYHYKEDVKNRLSDFDALFKHHNKAIKRRHIDAIR"
                     /name="hypothetical protein"
     gene            869..2041
                     /locus_tag="JLF43_RS26055"
                     /old_locus_tag="STW0522CIT30_P60020"
     CDS             869..2041
                     /locus_tag="JLF43_RS26055"
                     /old_locus_tag="STW0522CIT30_P60020"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0015074 - DNA integration [Evidence IEA];
                     GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific integrase"
                     /protein_id="WP_200924079.1"
                     /translation="MKVNLTRHQKGIADARLLMAQEQAMQAGSFLSVYVDKMIKDVINQ
                     VKIDASAESKEQYKTLYKSMISSNRGKSEQQILLSCNTRASFDKTRTAFRFCIVEQIKQ
                     LRREAEKLSKAKDYKGSQDLTVEAFKLSIKFEDEFLSDKRVLFSDVKSKIGYDKKSLSK
                     RKTAKNAPSSNEVLDNMKPAFFKRHSVCFSVINRFGIRPSEMQKGVKLQFENGRIFAVV
                     RGAKVAKDRGQQVRAIGYEPDLNNAADKLLLEAIENSPNKVFECVQTKKDYNALRKHFN
                     KYHEGFSLYSYRHAFASDLKKSGATRRQIAEAMGHRNTVSQEFYGYSKQGKGDREFVAK
                     ASNDIKVKPDIKEYIKSKSDAGSIGSKISQSKKSTGANLQSAPRTSIKPR"
                     /name="site-specific integrase"
ORIGIN
        1 aactcgaaag tgtttattgt gaatattgga ctgaagagtt ttcggtatat gcatttggtg
       61 cttatgtagc tgcagcaaaa aaaagattaa aggctgatct tatgattgac attttatatg
      121 aaatagcaaa aaaagaaaaa atagatctaa cctatcatac atcattgcgt atttgtaaga
      181 tttttatgtc tcgcggaatt ctaggagata ggttgttttc acatttcgct aatgttgaaa
      241 ataaagatgg tgaacttacc aaaagagaag aaaaaagaac agcaaaagaa aaagtttcta
      301 ttgactatgc aagcatagaa tatcattaca aagaagatgt taaaaataga ctttctgatt
      361 ttgatgcact ttttaaacat cataataaag caataaaaag acgacatatt gatgcaatca
      421 gatgacctgt cctacctgac cacgcaggta gattttaaag ctaacgtata tatattttag
      481 ctttacacaa tataaatgga aagttaacga atatatattt tagcgatacc ccgcaggagt
      541 taaaagctaa tatatatata ttttagcttg gtttagtgac ggcagatttg gcaatatttg
      601 acgaaatagc ggaaatgaaa tattaatata taagcggcaa gaaaaacatt attgcggatt
      661 tttattcgca ataatgtagg ttcgtttttt agtttttcga gtataagcga gaaaaaataa
      721 aaatggcggg cagccaagaa ccgttgccgt tcgacttttc ttcattgaga gcggagcgaa
      781 ctttgaagat taggagaaaa ggcaatgggt ttgatttttt gcgatagcga aaaataaacc
      841 cacaggaaga ctaaaagaga ggctggatat gaaagtaaac ttaaccagac accaaaaagg
      901 aatagctgat gcaaggttat tgatggcaca agagcaagca atgcaagctg gttcgttttt
      961 gagtgtttat gtagataaaa tgattaaaga tgtaataaat caagtaaaaa tagatgcatc
     1021 tgcagagtca aaagaacaat acaaaacatt atacaaatca atgatttcta gtaacagggg
     1081 gaaaagcgaa cagcaaatac ttttgtcgtg caacactcgt gcaagttttg acaaaacaag
     1141 aacagctttc cgcttttgta tagtagaaca aataaaacag ctacgccgtg aagctgaaaa
     1201 actatcaaag gcaaaagatt ataaaggttc tcaagatcta acagttgaag catttaaact
     1261 atctataaag tttgaggatg agtttttaag cgataagcga gttttatttt ctgacgtaaa
     1321 atcaaagatt ggttatgata aaaaatcatt aagtaaaagg aaaacggcaa aaaatgcacc
     1381 ttcctctaat gaggttttgg ataatatgaa acctgctttt tttaagcgtc attctgtttg
     1441 tttttctgta ataaatcgtt ttggtattag accatctgag atgcaaaaag gtgtcaaact
     1501 acaatttgaa aatgggcgta tttttgctgt tgttagaggt gctaaagttg ctaaagacag
     1561 ggggcaacag gtaagagcta taggatatga acctgattta aataatgcag ctgataagct
     1621 tttattggag gctatagaaa atagccccaa taaggttttt gaatgcgttc aaacaaaaaa
     1681 agattacaac gcattaagga agcattttaa taaataccat gaaggctttt ctttatattc
     1741 ttatcgtcat gcttttgcca gcgatttaaa aaaatcaggt gctacacgta ggcaaatagc
     1801 tgaagctatg gggcatagaa atactgtatc ccaagagttc tacggctatt ctaaacaggg
     1861 taaaggtgat cgagagtttg tagctaaagc gagtaatgat attaaagtaa agccggatat
     1921 taaagaatat ataaagtcta aaagtgatgc tggttctata ggtagcaaga tctcgcagtc
     1981 taaaaaatcg actggtgcaa atttgcagag tgctcccaga acgtcaatca aaccaagata
     2041 aagcgttcaa tatttttgat agagtattga cgtctaacgg atttcggtta taacagaaga
     2101 cagatacaac aaagccaacc tgtggaggtt ggctttgagg gactaaaaaa ggctagaacc
     2161 ttttgaagtc ttgtaatcaa gtgagttcag cacatgatta cgataggtaa gataaatcta
     2221 tcttacttct tcgtataagt caaacccatt tccttgcaag ccataaaaaa tctctagact
     2281 tttcaagtcc ttaagcacca atacgtttag ttaacgcatt gtatcgcgat ctacctgtgg
     2341 agccgccccg gatgagtctt gggcatgtgt atgttcgggt gggtgttggt gtaggacgaa
     2401 aacggggagt gctgcaaacg tccaaccggg aacgagttcc taaagtgctg atgagtatca
     2461 ggccagctat gagaaagccc atgccactaa atggggttag atactgtaag tgcattatgg
     2521 aacgacagcg ggggtgcagt agggtgccag ttcattggaa acgatgaaca gctctaagtc
     2581 gctgctcttt gggtgaagca caacaagaca ggctcaccaa aggatcgtca ctctgatagc
     2641 caaggctacc ggggaggcga aactttgggt gaaacacccg caagggtggc ttcgctgcct
     2701 cattgctgtt cttatggcgt agcacaggcc gataggctta tacagagtaa gtacaactaa
     2761 aagagataaa gaaaaacggc aacgctcgcc gcaagacaaa atattttatt ttgtcgagga
     2821 agcgtaagat ccacgataca aacataaagc acttactccc tgcatttaaa tataaaaccc
     2881 attttttttg gcgatgccac tttttgcctt cggccttttt tacgacctta ttttaagcta
     2941 acgtatatat cagatagcct tttataagcc attgttttaa gataaaaaat atatttgtta
     3001 gctcttgaca atgacactgt ttgcacggta ttgcatgcat gtgattatta tttatggggt
     3061 agcatatgga agaaaaaata aaaaaag
//
