LOCUS       NZ_AP022393             2830 bp    DNA     circular CON 30-JAN-2024
DEFINITION  Citrobacter portucalensis strain STW0522-26 plasmid pSTW0522-26-4,
            complete sequence.
ACCESSION   NZ_AP022393
VERSION     NZ_AP022393.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00195867
            Sequence Read Archive: DRR199672
            Assembly: GCF_015134935.1
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.
            STW0522-26 isolated from hospital sewage
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2830)
  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                   :: 165x
            Sequencing Technology             :: Sequel; NextSeq 500
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/30/2024 08:57:10
            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)                     :: 5,122
            CDSs (total)                      :: 5,012
            Genes (coding)                    :: 4,883
            CDSs (with protein)               :: 4,883
            Genes (RNA)                       :: 110
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 78
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 129
            CDSs (without protein)            :: 129
            Pseudo Genes (ambiguous residues) :: 0 of 129
            Pseudo Genes (frameshifted)       :: 33 of 129
            Pseudo Genes (incomplete)         :: 80 of 129
            Pseudo Genes (internal stop)      :: 29 of 129
            Pseudo Genes (multiple problems)  :: 12 of 129
            Pseudo Genes (short protein)      :: 1 of 129
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP022393.1.
            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..2830
                     /organism="Citrobacter portucalensis"
                     /mol_type="genomic DNA"
                     /strain="STW0522-26"
                     /isolation_source="sewage"
                     /db_xref="taxon:1639133"
                     /plasmid="pSTW0522-26-4"
                     /geo_loc_name="Japan:Tokyo"
                     /collection_date="2018-05-22"
     gene            101..1084
                     /locus_tag="JLF45_RS25485"
                     /old_locus_tag="STW0522CIT26_P40010"
     CDS             101..1084
                     /locus_tag="JLF45_RS25485"
                     /old_locus_tag="STW0522CIT26_P40010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000427687.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_200921660.1"
                     /translation="MDNVGNKNNKVKYENLADRSDKDQIWDHHRKETDLVSVLYEQEKE
                     FYRYFERMEDCSGRLEFSQLVNKDTGEMKIKLKSAHFCRVRHCPVCQWRKSLMWKARYW
                     KALPEIQSKYPSGRWLFFTLTVRNCEITEVKNTIQNMHKAFIKLIQRKHFKTYNLGFIK
                     TTEITRSKTGTAHPHFHVLLFMKSTYFNIGYMKNEAWSELWRDCLGVDYTPSVKIKTVR
                     NKKTGEVVKMGEDGMEHAVAETLKYSVKPADMYADREWFHEMTRQVHKMRFVSTGGVLK
                     DIFSEDVSEEEMLLLNDEEETDEDLNNNIFFNWHKKNSKYRRKIVE"
                     /name="protein rep"
     gene            1261..2436
                     /locus_tag="JLF45_RS25490"
                     /old_locus_tag="STW0522CIT26_P40020"
     CDS             1261..2436
                     /locus_tag="JLF45_RS25490"
                     /old_locus_tag="STW0522CIT26_P40020"
                     /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_200921661.1"
                     /translation="MSYQFIHIEDYSKVISKKRGNGGKGKYNEETKGRSVRDIIAEAKR
                     EEGNCPHVENPKPPLLLYGKNLDEVEKLAYEYHENTKLTDKNGKEKKLRSDANILLAGV
                     VSLNRENEDIWDEYKNDAIAFLSNKYGKKLVSVIEHTDEANPHFHFYVIQEPGKRFDLI
                     HDGKKALFENRDKKKHDQNIAYLNAMRKVQEDFFRVVSSNYGLSKDGPKRKRTSRKDYF
                     KQKREIKLIQQVKEQAKIDGYNFAVDDFHGKSWLNKVVTSFTVKNSTLQEAIARGDRYK
                     KGLSSTKKKLKNTESDLEETEKELSSLKDNFKERVNNQTSLLKDKNNKLTVENENIKKQ
                     NEQLEHENKNLKTILEESLPLYELLKNKYGDRFEEWKESLFNTMKTKLKLK"
                     /name="plasmid recombination protein"
ORIGIN
        1 aaagaaattt gcaagatcgg gtatctattg acaaaaaaaa tcctcttgtt aagtttgcaa
       61 ttgtctaggt cgcaaaaaat aacaagagga tcacgttttc atggataatg taggtaataa
      121 aaataataaa gtcaagtacg aaaacttggc agatcgatct gataaagatc aaatatggga
      181 tcatcataga aaagaaactg accttgtttc tgttttatat gaacaggaaa aagagtttta
      241 tcgttatttc gaaagaatgg aagattgttc cggtcgttta gagttttcac agcttgtaaa
      301 taaagacact ggagaaatga agattaaatt aaaatctgct catttctgtc gagttcgtca
      361 ctgccctgtg tgccagtggc gaaaatcttt gatgtggaaa gccagatatt ggaaagcact
      421 tcctgagata caatcaaaat atccttctgg taggtggcta ttttttactt taacagttag
      481 aaactgtgaa ataacagaag taaaaaacac aatccaaaat atgcataaag cattcattaa
      541 actaatccag agaaaacatt ttaaaactta taatctgggt tttatcaaga caactgaaat
      601 aacaagatcg aagacgggaa cggcacaccc tcactttcat gtattattat tcatgaagtc
      661 tacttatttt aatatcggtt atatgaaaaa tgaggcttgg agtgaacttt ggagggattg
      721 tttaggtgtg gattacacac cgtcagtaaa gattaaaaca gtcaggaaca agaagacggg
      781 tgaagtggtc aagatgggtg aagacggcat ggaacatgct gttgcagaga ctttgaagta
      841 ttcagtaaag ccagcagata tgtatgcaga tcgtgaatgg ttccatgaga tgacaagaca
      901 agtccataag atgagatttg tctctacggg tggagtgctg aaagatatat tcagcgaaga
      961 tgtatcagaa gaagaaatgt tattattgaa tgacgaggaa gaaacagacg aggatttaaa
     1021 taataatata ttctttaact ggcataagaa aaacagcaaa tatagacgaa agattgtaga
     1081 gtaaaaaagg caccgctaag gtgctttttt tatgcctttg acttttcccc gtaggggccg
     1141 gcgtttattg cgaagcaata aacatagtcg gtccctatgt ttattaaaac gggatttaca
     1201 aactattaaa atatgctaaa aataaaacat tggggaaata aaatataagg ggaaaatata
     1261 atgtcatatc agtttataca tattgaagat tactctaaag taatatcaaa aaaaagaggc
     1321 aatggcggca agggaaaata taacgaagaa acaaaaggga gatctgtaag agatattata
     1381 gctgaagcaa aaagagagga agggaactgt ccacatgttg aaaatcccaa acctcctctt
     1441 ttgttgtatg gtaaaaattt agatgaggtt gaaaagttag cttatgaata tcatgaaaat
     1501 acaaagctaa ctgataagaa cggaaaagaa aaaaagttaa gatctgatgc aaatatatta
     1561 cttgctggtg ttgtttcttt gaatagggaa aatgaagaca tttgggatga gtataaaaac
     1621 gatgccatcg cttttctttc aaataaatat ggtaaaaagt tagtttctgt aatagagcat
     1681 actgacgaag caaatccaca ctttcacttt tatgttattc aagaacccgg aaaacgattt
     1741 gatttaatac atgatggaaa aaaagcttta tttgaaaaca gagacaagaa aaaacacgat
     1801 cagaatatag cttatttaaa tgccatgaga aaagttcaag aagatttttt tcgtgtcgta
     1861 tcttctaact atggtttatc aaaggatggt ccgaagagaa aaaggaccag ccgaaaggat
     1921 tattttaagc aaaaaagaga aataaaactt attcagcaag taaaagaaca ggcaaaaata
     1981 gatggttata attttgcagt ggatgatttt catgggaaaa gctggttaaa caaggtcgta
     2041 acttctttta ctgttaaaaa cagcacctta caggaagcca tcgccagagg tgataggtat
     2101 aaaaaaggac tttccagcac aaaaaagaaa cttaaaaata cagagagtga tttagaagaa
     2161 acagaaaaag aactatcttc actaaaagat aactttaaag aaagagtgaa taatcaaaca
     2221 tcattactta aagataaaaa taataaacta actgttgaga atgagaatat aaaaaaacaa
     2281 aatgagcagt tagagcatga aaataaaaac ctaaaaacca ttttggaaga gtctcttcct
     2341 ctctacgagc ttttgaaaaa taaatatgga gatcgctttg aagaatggaa agaaagttta
     2401 tttaacacca tgaaaaccaa actgaaactt aaatagtcaa taagaaaatc gggggttccc
     2461 tgaaagggtt ccgattttgt tgttgactac gcacaaaaat aaaacttgtt agggttgaag
     2521 gtgaacaaag tgagccttca acctgataaa ctgtttttct gccctttgag ccgtttcggg
     2581 gtggtttctg gtggctcata gtggcagaac cccgtaaaac tcgttacagg ccgttttagg
     2641 ggccttcctg acggtcctaa accgtcatgg ccctgagctg gaagagtctt ccagtggggt
     2701 ggttttgggg tttgattttg gaccggaacg ggccggtttt acctcatctt gatacctgag
     2761 ggataacgtg gatttcaaaa agtggcttga agccttgtgg cagtaggctt ggagtgggtt
     2821 ttggagtgtg
//
