LOCUS       NZ_AP022492             2929 bp    DNA     circular CON 30-JAN-2024
DEFINITION  Citrobacter portucalensis strain STN0717-27 plasmid pSTN0717-27-6,
            complete sequence.
ACCESSION   NZ_AP022492
VERSION     NZ_AP022492.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00195946
            Sequence Read Archive: DRR199751
            Assembly: GCF_015137095.1
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.
            STN0717-27 isolated from hospital sewage
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2929)
  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                   :: 734x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/30/2024 08:45:51
            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)                     :: 5,147
            CDSs (total)                      :: 5,032
            Genes (coding)                    :: 4,899
            CDSs (with protein)               :: 4,899
            Genes (RNA)                       :: 115
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 133
            CDSs (without protein)            :: 133
            Pseudo Genes (ambiguous residues) :: 0 of 133
            Pseudo Genes (frameshifted)       :: 35 of 133
            Pseudo Genes (incomplete)         :: 79 of 133
            Pseudo Genes (internal stop)      :: 31 of 133
            Pseudo Genes (multiple problems)  :: 11 of 133
            Pseudo Genes (short protein)      :: 1 of 133
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022492.1.
            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..2929
                     /organism="Citrobacter portucalensis"
                     /mol_type="genomic DNA"
                     /strain="STN0717-27"
                     /isolation_source="sewage"
                     /db_xref="taxon:1639133"
                     /plasmid="pSTN0717-27-6"
                     /geo_loc_name="Japan:Tokyo"
                     /collection_date="2018-07-17"
     gene            102..692
                     /locus_tag="JLF36_RS25580"
                     /old_locus_tag="STN0717CIT27_P60010"
     CDS             102..692
                     /locus_tag="JLF36_RS25580"
                     /old_locus_tag="STN0717CIT27_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_086642458.1"
                     /translation="MTKKNNVEILHKEKTNIENDSEIEHKKNPFVFNMSIDTKKKKLTV
                     DRGSEVETEEGVFTTTISQIQEVDREEFLKIFTGQIKFYFDLSQTGFKLFFIIMGLYQK
                     QIGGDEIYLNFETAKEEAEKYESAISKAVYYRGLKELLEKKMIAKSVKRYIFYINPAII
                     FNGDRARFVKEIKIKEEEKQQEENLKILRSKYA"
                     /name="hypothetical protein"
     gene            1074..1787
                     /locus_tag="JLF36_RS25585"
                     /old_locus_tag="STN0717CIT27_P60020"
     CDS             1074..1787
                     /locus_tag="JLF36_RS25585"
                     /old_locus_tag="STN0717CIT27_P60020"
                     /inference="COORDINATES: protein motif:HMM:NF013122.4"
                     /GO_function="GO:0008408 - 3'-5' exonuclease activity
                     [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="3'-5' exonuclease"
                     /protein_id="WP_064181260.1"
                     /translation="MATKIENDEVIPDEELNKIIEEINNEEDKRIKVIVDDYQQLTQNG
                     FFVLDTETTDLVGEVVSFSLIDDKNNILINEYCKPTRNKISKTAQSIHNISNKMIKDSR
                     NIISIYEDFLEIINREENKNKTIFIYNEGFDLSTIYRSLNYAGYKYKENNDFDDVEFRS
                     RCVMKDFAYYYGEHNEYYDTDKYKWKKLEFAANYFNIETKNLELHNSAVDCYLTLKVIE
                     NIRDHFKKENEYFSV"
                     /name="3'-5' exonuclease"
     gene            1799..2542
                     /locus_tag="JLF36_RS25590"
                     /old_locus_tag="STN0717CIT27_P60030"
     CDS             1799..2542
                     /locus_tag="JLF36_RS25590"
                     /old_locus_tag="STN0717CIT27_P60030"
                     /inference="COORDINATES: protein motif:HMM:NF012798.4"
                     /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: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific integrase"
                     /protein_id="WP_200926065.1"
                     /translation="MGNSKRNIKKLNDNFRESILDYAISHNLKCANALIALYATGCRPD
                     EIETGIKVNFDSKNNKLSFKIIGSKLNYQQKRGIRIREVTIKITDKNLQYYKPIIDIFE
                     KNPQAYDLKIKTESSKAFSGYITKISKKLWPRKKHHVSAYSFRHAKATELKNSENFDKE
                     EIAKIMGHASIRSQESYGRKNSRSKGGFDDITDVETSSKPRGGDRLLRFKIASKQQTAA
                     KIAAISTPPDVASAPPTAPVRSLKR"
                     /name="site-specific integrase"
ORIGIN
        1 tgttttcttg actagtctca aaaatctgtt aaaaaatgag aagaagagtc tcaccgagtg
       61 agaatttttt cggttatttt ttaaacagag agggtttgta tatgacaaag aaaaacaatg
      121 tagaaatttt acacaaagaa aaaactaata ttgaaaacga tagtgagatc gaacataaaa
      181 agaacccgtt tgttttcaat atgtctattg atactaaaaa gaaaaaacta actgttgatc
      241 ggggttcaga agtagaaaca gaagaggggg ttttcacaac aacaatatca caaattcaag
      301 aagttgatag ggaagaattt ttaaaaattt ttacaggaca aatcaaattc tattttgatt
      361 tgtctcaaac cggatttaaa ttgtttttca taattatggg tttgtatcaa aaacagatag
      421 gcggtgacga aatttattta aatttcgaaa cagcaaaaga agaagctgaa aaatacgagt
      481 cagcaatttc aaaagctgtc tactatagag gtttaaaaga attattagaa aagaaaatga
      541 tcgcaaaatc tgtaaaaaga tacatttttt atattaaccc ggcgatcatt ttcaatggcg
      601 atcgtgcaag atttgttaaa gaaattaaaa ttaaagaaga agaaaaacaa caagaagaaa
      661 atttaaaaat tcttcgctca aaatatgctt aaaaccgtcc tcgccggacg ggccaaatcc
      721 cttaaaaaat agaaaaaaat tctattttct aagggatttt tttattctca ttttctccac
      781 atttgagata ttgacattaa tttcaacccg gttatatcta tattatcttt tgttgtttct
      841 accccgattt tggggtggaa caacaaggca ttatgaaggg taagtttttt attacccgaa
      901 attatgccac ccccaaccgg gggtcattgt ttgaattttg aagcaacgcg aaaaatttaa
      961 ataatggggg gatggtttgg gttttacggt atttcaaatt tgagcaaagc gaatttttga
     1021 aatctccgga ttttgatgtt aacaatataa aaaacaataa atgaggtgaa attatggcaa
     1081 caaaaattga aaatgacgaa gtaattccag atgaggaatt aaataaaata atagaagaaa
     1141 taaacaatga ggaagataaa agaattaaag taattgttga tgactatcaa caacttacgc
     1201 aaaacggttt tttcgttctt gatacggaaa caacagatct tgttggtgaa gttgttagtt
     1261 tttcattgat tgacgacaaa aacaatatat taataaatga atattgcaaa cctactagaa
     1321 ataagatttc aaaaacagca cagtcaatac ataatatttc aaataaaatg atcaaagata
     1381 gtagaaatat aatttcaata tacgaagatt ttttagaaat aataaataga gaagaaaata
     1441 aaaataaaac tatttttatt tataatgagg gttttgatct ttcaacaatt tatagatctt
     1501 taaattatgc cggatataaa tataaagaaa ataacgattt cgacgatgta gaatttagat
     1561 ctcgttgcgt aatgaaagac tttgcctatt attacggaga acataatgag tactatgata
     1621 cagataaata taaatggaaa aaactcgaat tcgcagcaaa ttattttaat atcgaaacga
     1681 aaaacttaga attgcataat tccgccgtcg attgttattt gactttaaaa gtaattgaaa
     1741 acattagaga tcattttaaa aaagaaaacg agtatttttc tgtgtaggtg aaaaaaatat
     1801 gggtaattca aaaagaaata taaaaaaact aaatgataat tttcgagaga gtattttaga
     1861 ttatgcgatt tcgcataacc taaaatgcgc taacgccttg atcgcattat atgcgactgg
     1921 gtgtagacca gacgaaatag aaaccggaat taaagttaat tttgatagta aaaacaataa
     1981 gttaagtttc aaaattatag gttcaaaatt aaactatcaa caaaaaagag gtattagaat
     2041 tagagaagtt acgataaaaa tcacagataa aaatcttcaa tattacaaac ctataataga
     2101 tatttttgag aaaaaccctc aggcatatga tttaaaaatt aaaactgaaa gttctaaagc
     2161 attctccgga tatattacaa aaataagtaa aaaactttgg cccagaaaaa aacatcatgt
     2221 ttctgcatat agttttagac atgcaaaagc aacagaatta aaaaactcag agaattttga
     2281 taaggaagaa atcgctaaaa ttatgggcca tgcctcgatc agatctcaag aaagttacgg
     2341 aagaaagaac agcagaagca aaggtggatt tgacgacatt acagatgttg aaacaagctc
     2401 taagccccgt ggtggcgata gattgcttcg tttcaagatt gccagtaaac agcagacagc
     2461 cgcaaaaatc gcggctattt ccacccctcc agatgtagca agtgcacctc caacggctcc
     2521 cgttcgttca ttaaaacgct gagaagccac acagcaagct gtgtggcttt gaagtgttgg
     2581 cccgtccggc caggacggtt tttatagcaa aatcctccat attgcgaagc agggccccgg
     2641 aatcggggta actgggatgg ttttccagat ggtttttggt tttctattgc gaagcccagt
     2701 tatcacaatg ccgataaaaa ttttactcag agctaagcaa agcctcttag atcttatatt
     2761 tcttatattc ttatatgtct cgtaacccgc ataaacactg gatgtctagt ctctatagag
     2821 aaaaaaaatt ctctcaggag agaaaaaatt ctctctacag tgactaaatg tctcgatatt
     2881 gtgacttttt gtctcatttt ttttgtaaaa aatgagaata aatccaatg
//
