LOCUS       NZ_AP022406             3075 bp    DNA     circular CON 30-JAN-2024
DEFINITION  Citrobacter portucalensis strain STW0522-30 plasmid pSTW0522-30-7,
            complete sequence.
ACCESSION   NZ_AP022406
VERSION     NZ_AP022406.1
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  JOURNAL   Unpublished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 3075)
  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
            AP022406.1.
            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..3075
                     /organism="Citrobacter portucalensis"
                     /mol_type="genomic DNA"
                     /strain="STW0522-30"
                     /isolation_source="sewage"
                     /db_xref="taxon:1639133"
                     /plasmid="pSTW0522-30-7"
                     /geo_loc_name="Japan:Tokyo"
                     /collection_date="2018-05-22"
     gene            102..1085
                     /locus_tag="JLF43_RS26060"
                     /old_locus_tag="STW0522CIT30_P70010"
     CDS             102..1085
                     /locus_tag="JLF43_RS26060"
                     /old_locus_tag="STW0522CIT30_P70010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000427687.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_032332413.1"
                     /translation="MGRLYNKKDNVKFENLSDRSEKDKVWDTQRKYCDLVSELYFQSAE
                     FERYFERMEDCSGRLEFNQLLDRETGEIKIKLTNAHFCRVRHCPVCQWRKSLMWKAKFY
                     KALPEIESEYKSARWMFLTLTVENCEITDLKNTLANMNKAFKKLIKRKHFLKYNLGFVK
                     TTEITKPKTKKDSNKAHPHFHILLMMKSTYFKDGYLKTEDWAEIWRDCLGVSYTPITDI
                     RKVRTKLTGEANRSALADAVAETLKYAVKPADMTRDREWFHELTRQVFKLRFVSTGGVL
                     KDLFKEDASEEDLLLLSEEEETDKELGSLYFNWYKTKSKYRRKVDK"
                     /name="protein rep"
     gene            1515..2705
                     /locus_tag="JLF43_RS26065"
                     /old_locus_tag="STW0522CIT30_P70020"
     CDS             1515..2705
                     /locus_tag="JLF43_RS26065"
                     /old_locus_tag="STW0522CIT30_P70020"
                     /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="plasmid recombination protein"
                     /protein_id="WP_025766524.1"
                     /translation="MSYQFIHIEDYSRTIAKKKKNDGKEKYNKETKGRSVRDIIAEAKR
                     EIGNCPHVENPKDPILLFGVDLDEVEKLAYEYHENTKLTDKNGKEKKLRSDANILLAGV
                     VSLNRENEDIWDEYKKDAIAFLSNKYGKKLVSVIEHTDEENPHFHFYVIQDVGKRFDLI
                     HDGKKALFENRDKKKHDQNIAYLNAMREMQERFWKVVSANYGLSKDGPKRQRLSRKDYF
                     KQKREIKLIKQAKEQAKTEGYKFAIDDFESKNWLNKIATSFTVKNSILHEAASRGDRYK
                     KGLSNTKKKLVNTEKDLEETEKELTSLKDNFKARVNNQTEILRNKNSYLENMNNNLNIE
                     NDKIKTENQKLLSENTSLKTENTEYKTFTDRVKKYFGDRFPEFLQKIKPKDRYTLK"
                     /name="plasmid recombination protein"
ORIGIN
        1 tttggagggg tgaaaaaaag tagaacgatt gacaaaaaaa aatcctctgt tagttttgaa
       61 cttgcgaagg tatcaaaaca aaacagagga tcggtgtttc tatgggaagg ttatataata
      121 aaaaagataa tgtcaagttt gaaaacttat cagatagatc agaaaaagat aaagtctggg
      181 atacacaaag aaaatattgt gatcttgttt ctgagttata ttttcaatcg gcagagttcg
      241 aaagatattt tgaacgaatg gaagattgct caggtcgttt agagtttaat caactgttag
      301 atcgtgaaac gggcgaaata aaaataaaac taacaaatgc tcatttttgt cgtgtaagac
      361 attgcccggt ttgtcagtgg agaaaatcgc ttatgtggaa agcaaagttt tataaagcac
      421 ttccagaaat cgaatcggaa tataaatctg ctcgttggat gtttttaact ctaacagtag
      481 aaaactgtga aataactgat ttaaaaaata ctcttgctaa tatgaataaa gcttttaaaa
      541 agctgataaa gagaaagcat tttttaaaat ataacttggg ttttgttaaa acaactgaaa
      601 tcacaaaacc gaaaacaaag aaagactcaa acaaagcaca tccgcacttt catattcttt
      661 tgatgatgaa aagtacctat tttaaagacg gttatttaaa aacggaagac tgggcggaga
      721 tatggagaga ttgtttaggt gtatcttata cacctataac cgatataaga aaagtaagaa
      781 ctaaactgac aggcgaggct aaccgttcgg ccttggctga tgcggttgct gagacgttga
      841 agtatgctgt aaagccagca gatatgacaa gggatcgtga gtggtttcac gaactaacaa
      901 gacaggtttt taagttacgt tttgtatcta ctggcggagt attgaaagat ttatttaaag
      961 aagatgcctc tgaagaagat ttattattat tgagtgaaga agaagaaaca gacaaagaac
     1021 ttggatcgtt atattttaac tggtataaaa caaaatcaaa atacagaaga aaagttgaca
     1081 agtgaaaaaa tacattatat ttagattgtg tagtttagtt tatttctgct tttacttgca
     1141 cgaagcgtca tttccttcca actcccagag atgaagaaat aaacttagta aaaagcagta
     1201 tggttctacg gctggctctt gatacaaagc atcctaagat gcaaaggaat gaccaaggat
     1261 taaaagccca tattgcttct acaaagttaa ctaataacca tagaacgatc atagatgatt
     1321 tgatcgggtt agtaaaaaag gcactcgcaa agagtgcttt ttttatgcct ttgattttag
     1381 cttccggcag gaccgcgttt attgtgaaac aataaacata gtcggtccct atgtatatta
     1441 aaacacgatt tacaaactat taaaacctgc taaaaatata atcatggaga atgaaaaaat
     1501 aagaggaaaa tataatgtca tatcagttta tacatattga agattactca agaacaatag
     1561 caaaaaagaa aaagaatgat gggaaggaaa aatataataa agagaccaaa ggaaggtccg
     1621 taagagatat tattgcagaa gctaaaagag aaataggaaa ctgtccacat gttgaaaatc
     1681 caaaagatcc tattttgctt tttggtgtag atttggatga agtagaaaaa ctcgcttatg
     1741 aatatcatga aaatacaaag ctaactgata aaaacggaaa agagaaaaag ctaagatctg
     1801 atgcaaatat attacttgcc ggggttgttt ctctgaacag ggaaaatgaa gatatttggg
     1861 atgagtataa aaaagatgcc atcgcttttc tttctaataa atatggtaaa aagttagttt
     1921 ctgtaataga gcatacagac gaagaaaacc cgcacttcca cttttacgtt attcaagacg
     1981 ttggaaagcg atttgattta atacacgacg gaaaaaaagc tttatttgaa aacagagaca
     2041 agaaaaaaca cgatcagaat atagcttatt taaatgctat gagagaaatg caagaaaggt
     2101 tctggaaagt agttagtgca aattatggtt tgtcaaaaga tggtccgaaa agacaaagat
     2161 taagccgtaa agattacttt aagcagaaaa gagagataaa actgattaaa caagcaaaag
     2221 aacaagcaaa aacagaaggt tataagtttg ctatagatga ttttgagagt aaaaactggt
     2281 taaacaagat tgcaacttct tttactgtta aaaacagtat attacatgaa gccgcatcga
     2341 gaggtgatag atataaaaaa ggactttcaa atacaaaaaa gaaacttgta aacacagaaa
     2401 aagatttaga agaaacagaa aaagaactta catcactaaa agataacttt aaagcaaggg
     2461 ttaataatca aactgaaata ctaagaaata aaaatagtta tcttgagaat atgaataata
     2521 atctgaatat tgaaaatgat aaaatcaaaa ctgaaaatca aaaactactc tctgaaaata
     2581 catctctaaa aactgaaaac actgaatata aaacatttac ggatagagta aaaaaatatt
     2641 ttggtgatcg ttttccagag ttcttacaga agataaaacc aaaagatcgc tacactctca
     2701 aatagtcaag aagaatggcg gggggtcccc gtttcggggt tccgctattg ttcttgacta
     2761 cacaacatag aaaaacactt gtacgggtgt aaggagaacg gagtgagcct tacacctgat
     2821 aaacccgcac ttatgcctta aaaccgctta gaactcgtta cagagcgtta cagaagccct
     2881 gtgggacggt ataaaaccgt cttggcttat ggatggaagg aacttccaga tcgtggtttt
     2941 ggtgtgggtt tttgtgtctt aaaatcagcc cgaaaagggc agatttcctt tacttgatac
     3001 cttaggcata aaagtcggaa gaaaaacggg tctttaatgt gcctctagcc cttgcggggc
     3061 aaggctttga agagt
//
