LOCUS       NZ_AP022517             3087 bp    DNA     circular CON 30-JAN-2024
DEFINITION  Citrobacter portucalensis strain STN0717-72 plasmid pSTN0717-72-4,
            complete sequence.
ACCESSION   NZ_AP022517
VERSION     NZ_AP022517.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00195990
            Sequence Read Archive: DRR199795
            Assembly: GCF_015138175.1
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.
            STN0717-72 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  JOURNAL   Unpublished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                   :: 877x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/30/2024 09:07:39
            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)                     :: 5,251
            CDSs (total)                      :: 5,137
            Genes (coding)                    :: 4,941
            CDSs (with protein)               :: 4,941
            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)              :: 196
            CDSs (without protein)            :: 196
            Pseudo Genes (ambiguous residues) :: 0 of 196
            Pseudo Genes (frameshifted)       :: 35 of 196
            Pseudo Genes (incomplete)         :: 147 of 196
            Pseudo Genes (internal stop)      :: 33 of 196
            Pseudo Genes (multiple problems)  :: 17 of 196
            Pseudo Genes (short protein)      :: 1 of 196
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022517.1.
            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="STN0717-72"
                     /isolation_source="sewage"
                     /db_xref="taxon:1639133"
                     /plasmid="pSTN0717-72-4"
                     /geo_loc_name="Japan:Tokyo"
                     /collection_date="2018-07-17"
     gene            102..548
                     /locus_tag="JLF48_RS26145"
                     /old_locus_tag="STN0717CIT72_P40010"
     CDS             102..548
                     /locus_tag="JLF48_RS26145"
                     /old_locus_tag="STN0717CIT72_P40010"
                     /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            992..2164
                     /locus_tag="JLF48_RS26150"
                     /old_locus_tag="STN0717CIT72_P40020"
     CDS             992..2164
                     /locus_tag="JLF48_RS26150"
                     /old_locus_tag="STN0717CIT72_P40020"
                     /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 taagccattg ttttaagata aaaaatatat ttgttagctc ttgacaatga cactgtttgc
       61 acggtattgc atgcatgtga ttattattta tggggtagca tatggaagaa aaaataaaaa
      121 aagaactcga aagtgtttat tgtgaatatt ggactgaaga gttttcggta tatgcatttg
      181 gtgcttatgt agctgcagca aaaaaaagat taaaggctga tcttatgatt gacattttat
      241 atgaaatagc aaaaaaagaa aaaatagatc taacctatca tacatcattg cgtatttgta
      301 agatttttat gtctcgcgga attctaggag ataggttgtt ttcacatttc gctaatgttg
      361 aaaataaaga tggtgaactt accaaaagag aagaaaaaag aacagcaaaa gaaaaagttt
      421 ctattgacta tgcaagcata gaatatcatt acaaagaaga tgttaaaaat agactttctg
      481 attttgatgc actttttaaa catcataata aagcaataaa aagacgacat attgatgcaa
      541 tcagatgacc tgtcctacct gaccacgcag gtagatttta aagctaacgt atatatattt
      601 tagctttaca caatataaat ggaaagttaa cgaatatata ttttagcgat accccgcagg
      661 agttaaaagc taatatatat atattttagc ttggtttagt gacggcagat ttggcaatat
      721 ttgacgaaat agcggaaatg aaatattaat atataagcgg caagaaaaac attattgcgt
      781 atttttattc gcaataatgt aggttcgttt tttagttttt cgagtataag cgagaaaaaa
      841 taaaaatggc gggcagccaa gaaccgttgc cgttcgactt ttcttcattg agagcggagc
      901 gaactttgaa gattaggaga aaaggcaatg ggtttgattt tttgcgatag cgaaaaataa
      961 acccacagga agactaaaag agaggctgga tatgaaagta aacttaacca gacaccaaaa
     1021 aggaatagct gatgcaaggt tattgatggc acaagagcaa gcaatgcaag ctggttcgtt
     1081 tttgagtgtt tatgtagata aaatgattaa agatgtaata aatcaagtaa aaatagatgc
     1141 atctgcagag tcaaaagaac aatacaaaac attatacaaa tcaatgattt ctagtaacag
     1201 ggggaaaagc gaacagcaaa tacttttgtc gtgcaacact cgtgcaagtt ttgacaaaac
     1261 aagaacagct ttccgctttt gtatagtaga acaaataaaa cagctacgcc gtgaagctga
     1321 aaaactatca aaggcaaaag attataaagg ttctcaagat ctaacagttg aagcatttaa
     1381 actatctata aagtttgagg atgagttttt aagcgataag cgagttttat tttctgacgt
     1441 aaaatcaaag attggttatg ataaaaaatc attaagtaaa aggaaaacgg caaaaaatgc
     1501 accttcctct aatgaggttt tggataatat gaaacctgct ttttttaagc gtcattctgt
     1561 ttgtttttct gtaataaatc gttttggtat tagaccatct gagatgcaaa aaggtgtcaa
     1621 actacaattt gaaaatgggc gtatttttgc tgttgttaga ggtgctaaag ttgctaaaga
     1681 cagggggcaa caggtaagag ctataggata tgaacctgat ttaaataatg cagctgataa
     1741 gcttttattg gaggctatag aaaatagccc caataaggtt tttgaatgcg ttcaaacaaa
     1801 aaaagattac aacgcattaa ggaagcattt taataaatac catgaaggct tttctttata
     1861 ttcttatcgt catgcttttg ccagcgattt aaaaaaatca ggtgctacac gtaggcaaat
     1921 agctgaagct atggggcata gaaatactgt atcccaagag ttctacggct attctaaaca
     1981 gggtaaaggt gatcgagagt ttgtagctaa agcgagtaat gatattaaag taaagccgga
     2041 tattaaagaa tatataaagt ctaaaagtga tgctggttct ataggtagca agatctcgca
     2101 gtctaaaaaa tcgactggtg caaatttgca gagtgctccc agaacgtcaa tcaaaccaag
     2161 ataaagcgtt caatattttt gatagagtat tgacgtctaa cggatttcgg ttataacaga
     2221 agacagatac aacaaagcca acctgtggag gttggctttg agggactaaa aaaggctgga
     2281 accttttgaa gtcttgtaat caagtgagtt cagcacatga ttacgatagg taagataaat
     2341 ctatcttact tcttcgtata agtcaaaccc atttccttgc aagccataaa aaatctctag
     2401 acttttcaag tccttaagca ccaatacgtt tagttaacgc attgtatcgc gatctacctg
     2461 tggagccgcc ccggatgagt cttgggcatg tgtatgttcg ggtgggtgtt ggtgtaggac
     2521 gaaaacgggg agtgctgcaa acgtccaacc gggaacgagt tcctaaagtg ctgatgagta
     2581 tcaggccagc tatgagaaag cccatgccac taaatggggt tagatactgt aagtgcatta
     2641 tggaacgaca gcgggggtgc agtagggtgc cagttcattg gaaacgatga acagctctaa
     2701 gtcgctgctc tttgggtgaa gcacaacaag acaggctcac caaaggatcg tcactctgat
     2761 agccaaggct accggggagg cgaaactttg ggtgaaacac ccgcaagggt ggcttcgctg
     2821 cctcattgct gttcttatgg cgtagcacag gccgataggc ttatacagag taagtacaac
     2881 taaaagagat aaagaaaaac ggcaacgctc gccgcaagac aaaatatttt attttgtcga
     2941 ggaagcgtaa gatccacgat acaaacataa agcacttact ccctgcattt aaatataaaa
     3001 cccatttttt ttggcgatgc cactttttgc cttcggcctt ttttacgacc ttattttaag
     3061 ctaacgtata tatcagatag cctttta
//
