LOCUS       NZ_AP022391             3961 bp    DNA     circular CON 30-JAN-2024
DEFINITION  Citrobacter portucalensis strain STW0522-26 plasmid pSTW0522-26-2,
            complete sequence.
ACCESSION   NZ_AP022391
VERSION     NZ_AP022391.1
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  JOURNAL   Unpublished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 3961)
  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
            AP022391.1.
            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..3961
                     /organism="Citrobacter portucalensis"
                     /mol_type="genomic DNA"
                     /strain="STW0522-26"
                     /isolation_source="sewage"
                     /db_xref="taxon:1639133"
                     /plasmid="pSTW0522-26-2"
                     /geo_loc_name="Japan:Tokyo"
                     /collection_date="2018-05-22"
     gene            complement(102..512)
                     /locus_tag="JLF45_RS25425"
                     /old_locus_tag="STW0522CIT26_P20010"
     CDS             complement(102..512)
                     /locus_tag="JLF45_RS25425"
                     /old_locus_tag="STW0522CIT26_P20010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_048295909.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKGIKVID
                     TSELIRVFGSLDGVIDDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKARDEH
                     IDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(512..703)
                     /locus_tag="JLF45_RS25430"
                     /old_locus_tag="STW0522CIT26_P20020"
     CDS             complement(512..703)
                     /locus_tag="JLF45_RS25430"
                     /old_locus_tag="STW0522CIT26_P20020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_032421723.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1174..1365)
                     /locus_tag="JLF45_RS25435"
                     /old_locus_tag="STW0522CIT26_P20030"
     CDS             complement(1174..1365)
                     /locus_tag="JLF45_RS25435"
                     /old_locus_tag="STW0522CIT26_P20030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041614.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1784..1915
                     /locus_tag="JLF45_RS25440"
     CDS             1784..1915
                     /locus_tag="JLF45_RS25440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005019281.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_047741455.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHAKAPLAAATGKQDVREM"
                     /name="hypothetical protein"
     gene            2240..3175
                     /locus_tag="JLF45_RS25445"
                     /old_locus_tag="STW0522CIT26_P20040"
     CDS             2240..3175
                     /locus_tag="JLF45_RS25445"
                     /old_locus_tag="STW0522CIT26_P20040"
                     /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_087777346.1"
                     /translation="MTAQDLINVLTILKANDSTSFSKIQRALKMSISQLEGIIDGLTAM
                     GIVYKSSFTSYSLTELTSKPVVSDGVRKAFEDIITNRGTYLSEELLQKVSTPFIPLMTH
                     EYKNAPVKVMIVGQETLGMEDAFSTIVSVDDYINESIESFNKFNFGEDLRNSHFWYAFD
                     EVVKYFNLPSRRHAYWTNLHKFQLIENDGDSVSISKLPSKDIMTMIHMQRELFLAEIKD
                     TKPDIIIYFTGGQTWVLDHYLNNGKKLAVKAIDERSHLGIIQTEFLHCPIAICTDHPSR
                     RGYTQAIVDHRANLLKYAADKFHASESARV"
                     /name="hypothetical protein"
     gene            <3204..3307
                     /locus_tag="JLF45_RS25450"
                     /pseudo=""
     CDS             <3204..3307
                     /locus_tag="JLF45_RS25450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558297.1"
                     /GO_process="GO:0015074 - DNA integration [Evidence IEA]"
                     /note="frameshifted; incomplete; partial in the middle of a
                     contig; missing N-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS3 family transposase"
                     /name="IS3 family transposase"
     gene            complement(3367..3684)
                     /locus_tag="JLF45_RS25455"
     CDS             complement(3367..3684)
                     /locus_tag="JLF45_RS25455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001415424.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_200921657.1"
                     /translation="MVSRPATCHNVIAGRRRTRFLNVLKTGFPAAPATLHGHAINCVPV
                     HRFRMGRTPETGLTPAEWREFPRYALARILMHAVKTKPARFWRVFGWFVACFVGFLPET
                     P"
                     /name="hypothetical protein"
     Typing          1241..1860
                     /name="rep_cluster_2327"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.772"
                     /coverage="99.0"
                     /evalue="1.1900000000000001e-169"
ORIGIN
        1 ggtatttttc gtggtgagga gtgttcccgg atctggcgat ttttgggaag gttcaggaac
       61 gccccgggat ggccggagag gaaaactcaa gcatggcggg atcaggattt tttccagaat
      121 ttccaccacg gggaatgggg tggtgaagaa ggttcgtgct tgtgctccag aagctgcata
      181 gcctgacgaa gggaatcaat atgctcatct cgagccttaa cagccccttt aagaccatcg
      241 ttttcagctt caagtaaagc gattctatgt tgtaaatcat gtaaaccaac gctgttaata
      301 cctgtagatt ctgcgtcact ttttacatca tcgatgacac catcaagaga accaaaaact
      361 ctaataagct ctgatgtatc aataacttta atacccttcc cgtgctttac aacagaggtg
      421 taacttaact taccactgtt aatcatcttg taaatagtag ggcgactaac cttaacaagc
      481 cgtgctgctt cactaataga cactctggcc atcagttacc atcctgtaat tcatccagtc
      541 tcgaggacag tgtacggaaa agatgctccg catcatcgtg gagtttctca caaaggtcgg
      601 cctcagcatc gagatcaagc tcgttaagct tctccagcag gagcagagac tgattctgga
      661 tgaatttagc catgttcagc gctgttttct gttgtttcgt cataagggac ctcagagcat
      721 cagtgctcag tgtaaaaccg gtaagggggt cggatgtacg aatggttcag agaacggatc
      781 tgaggtaatc ctgtagttat tttgtagttt atctgtagtc atcgcactaa aaatcaggat
      841 taagtcatca gcttttgtag tctttctgta gtttacctgt agtccggaaa aataatccgt
      901 tcatgctcgc atgaacgagg tcgttaatga cgtttttttg tcaccgacgc cccttaacct
      961 gcgtaaatca cccgccatgg ttgattattt ttcaacctca aaatggtcat acacctaacg
     1021 cagctgcgat tttcatcgca acttcatgaa aaataaataa aaaagaaaaa atacagggat
     1081 tgtgggtatt accggggtaa taatgttaag cgccaagaca atgaaaatta aggcgatgcc
     1141 ggtattactc cggtaatacc cacaacggag ccattacgca ccgtcctgct gctcattcag
     1201 gcgcgctgac aggcttcggt aaaggcgttc cgcatcctca tggagtttct cgcagaaatc
     1261 agcctcatga tccagatcca gctcattaag cctgtccaga agaagcaggg actgatcctg
     1321 gatgaattta gccatgttaa cggcagtctt ttgttgtttg ttcatgaagg ccccggcgcg
     1381 aaagtgctta ctgtacgttc tgatggtttt ccgcttcctc gctcattcgc tcactccgtt
     1441 cggtcatgag tctgcggcga gcggagggaa gataagcaga taacgtaacg gtaagcataa
     1501 cgaaagctaa ggacaagggc gaaaaggcca cgccccgccg gggcgttttt ccataggctc
     1561 cgcccccctg acaagcatca cgaaatctga cgctcaaatc agtggtggcg aaacccgaca
     1621 ggactataaa gataccaggc gtttccccct gatggctccc tcgtgcgctc tcctgttcct
     1681 gcctttcggt ttaccggtgt cactccgctg ttatggccgc gtttatctca ttccacgcct
     1741 gacactcagt tccgggtagg cagttcgctc caagctggac tgtatgcacg aaccccccgt
     1801 tcagtccgac tgctgcgcct tatccggtaa ctatcgtctt gagtccaacc cggaaagaca
     1861 tgcaaaagcg ccactggcag cagccactgg taagcaggat gtgcgagaga tgtagtaaga
     1921 gttcttgaag tgatggcctg agtgcggcta cactgaaagg acaaatttgg tgacatgtct
     1981 cgcacaagac tgttacctgg ttaagcagtt ccccaactga cctaaccttc gatcaaacca
     2041 cctccccagg tggttttttc gtttcttgga gaagagacta cgacgacaaa tgacggatct
     2101 caagaagatc cttttaacgt acaaaaattt ccgttctcca aaggtgatgc tgccaactta
     2161 ctgatttagt gtactgcgac cgtcagaatg agttaaacgc gtatctacat tgaagcagtt
     2221 caatatgagg aaaacaggaa tgacagcaca agatttaatc aacgttctca ctattcttaa
     2281 ggccaacgac tcaaccagtt ttagcaagat tcaacgcgcg ttaaagatga gtatttcgca
     2341 gttggagggc atcattgatg ggttaactgc aatgggaata gtgtataaat catcattcac
     2401 ttcatacagc cttactgagt taacctctaa acctgttgtt agtgacggtg taagaaaggc
     2461 attcgaagat atcattacca atcgcggtac ttacctgtca gaagaactac tacaaaaggt
     2521 aagtacacca ttcatcccac tgatgacgca cgaatacaaa aatgccccag ttaaagtgat
     2581 gatcgtgggg caagaaactc tgggaatgga agatgctttc agtaccatcg tttcggtcga
     2641 tgactacatt aatgagagca ttgaatcctt caataaattc aattttggtg aagatttaag
     2701 gaatagccac ttttggtatg catttgatga agtagtaaag tattttaacc taccatccag
     2761 aaggcatgct tattggacta atcttcataa gtttcaatta attgaaaatg atggagatag
     2821 tgtcagcatt tccaaactac cttcaaaaga tatcatgaca atgattcata tgcagcgtga
     2881 attattcttg gctgaaatta aagataccaa gccagatatc atcatctact tcacgggtgg
     2941 gcaaacctgg gtgttagatc attatctaaa caatggtaaa aaattagcag ttaaggcaat
     3001 agatgaacgc tcgcatctgg ggattatcca gacagaattt ttgcattgcc caatcgctat
     3061 atgtaccgac catcctagta gaaggggata tactcaagcc atcgtagatc atagagctaa
     3121 tctgcttaaa tatgctgctg acaaatttca tgcaagtgaa tcggcacggg tttaacagcc
     3181 ccccagagtc atttaagatc gcttacatcg aaatgtttta taacagtaac gtcggcatgg
     3241 ttctagcgaa cacatgtcac cgacagaata tgaaaaccag tattatcaac ggctcggaag
     3301 tgtctagatt atccgtggcg attcaattta ccataacatc cgttatcagc accgcctgag
     3361 aggctctcag ggcgtttctg gcaggaaacc gacaaaacag gcaacaaacc atccgaaaac
     3421 ccgccagaaa cgcgcaggct ttgtttttac ggcatgcatg agtatgcgcg caagtgcata
     3481 gcgcggaaat tcacgccatt cagccggggt aagtcctgtt tccggcgttc ttcccatccg
     3541 aaaacggtga acggggacgc aatttattgc gtggccgtga agcgttgccg gcgcagccgg
     3601 aaaaccggtt ttcagcacgt tcaggaatcg ggttcgtcga cggccggcaa tcacgttatg
     3661 gcaagtcgcc ggacgactca ccacacgatt caccggcgat tcgactcgtg acttgactct
     3721 agagtcacca cggtcataaa aacgccaaag cgacgattcg actctagagt caagtcgtca
     3781 taagttactg atagtgtgga gtgagtcgtc gatgactcta tgacgagtcg tcggcaagtc
     3841 gtacacgaat caccgacgac ttggattgac cttacagaag gtaatactgc gtaatttaat
     3901 aaaacctaac caactgataa taaggagtta tctgcaaaat tttaattttg cgtggtgtgt
     3961 g
//
