LOCUS       NZ_AP022490             4987 bp    DNA     circular CON 30-JAN-2024
DEFINITION  Citrobacter portucalensis strain STN0717-27 plasmid pSTN0717-27-4,
            complete sequence.
ACCESSION   NZ_AP022490
VERSION     NZ_AP022490.1
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  JOURNAL   Unpublished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 4987)
  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
            AP022490.1.
            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..4987
                     /organism="Citrobacter portucalensis"
                     /mol_type="genomic DNA"
                     /strain="STN0717-27"
                     /isolation_source="sewage"
                     /db_xref="taxon:1639133"
                     /plasmid="pSTN0717-27-4"
                     /geo_loc_name="Japan:Tokyo"
                     /collection_date="2018-07-17"
     gene            102..434
                     /locus_tag="JLF36_RS25525"
                     /old_locus_tag="STN0717CIT27_P40010"
     CDS             102..434
                     /locus_tag="JLF36_RS25525"
                     /old_locus_tag="STN0717CIT27_P40010"
                     /inference="COORDINATES: protein motif:HMM:NF017757.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_045332894.1"
                     /translation="MSNDENEYTFKPVNAQAIKALKSLPEWVQAAFVHALDSVFYGVDP
                     GMSIAHLTVIGPGVVELRINGRPAYRCVYRSKAPGQVDLLHAFVKTCQGPDKKNMATTA
                     SRYKLL"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(450..758)
                     /locus_tag="JLF36_RS25530"
                     /old_locus_tag="STN0717CIT27_P40020"
     CDS             complement(450..758)
                     /locus_tag="JLF36_RS25530"
                     /old_locus_tag="STN0717CIT27_P40020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003341209.1"
                     /GO_function="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="helix-turn-helix transcriptional regulator"
                     /protein_id="WP_012477691.1"
                     /translation="MKNSFELISTDPVKFNTWSIKSKLIIIIRKLMIDNKWSQSEAAEK
                     LGISQPRVSNMLNGKLDKFSVDTLLEMVFKMGYKLDMDFTPLNTESPLTMVVKKAMV"
                     /name="helix-turn-helix transcriptional regulator"
     gene            complement(1108..1239)
                     /locus_tag="JLF36_RS25910"
     CDS             complement(1108..1239)
                     /locus_tag="JLF36_RS25910"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505258.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_058645281.1"
                     /translation="MHEPPVQSDCCACSGNYRLESNPEKHDLTPLAAATGKGCTRDN"
                     /name="hypothetical protein"
     gene            1888..2211
                     /locus_tag="JLF36_RS25535"
                     /old_locus_tag="STN0717CIT27_P40040"
     CDS             1888..2211
                     /locus_tag="JLF36_RS25535"
                     /old_locus_tag="STN0717CIT27_P40040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000957084.1"
                     /translation="MLTMWVTEDEHRRLLERCDGRQLAAWMRQICLDEKPARSGKLPSL
                     SPALLRQLAGMGNNLNQIARRVNAGGGTGHDRVQIVAALMAIDAGLERLRHAVLEKGTD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2420..>2854
                     /locus_tag="JLF36_RS25820"
                     /pseudo=""
     CDS             2420..>2854
                     /locus_tag="JLF36_RS25820"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            2889..3380
                     /locus_tag="JLF36_RS25545"
     CDS             2889..3380
                     /locus_tag="JLF36_RS25545"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_012564908.1"
                     /translation="MSSLLTLAKDLEQQSKAQQQSTGEMLKAVFSEHERSVRAELSASA
                     RRISDAILAHEQSMSEAMEKNRRSVLRTAGRTWLTILMVSALLIGTSGSILWWQGQQIT
                     DNYTHLRQQEDTLAKMTARTWGVRYQESSDGRRFLILPPGMQTEAIPYDGTTWIRLKQE
                     "
                     /name="MbeB family mobilization protein"
     gene            3387..3602
                     /locus_tag="JLF36_RS25550"
     CDS             3387..3602
                     /locus_tag="JLF36_RS25550"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137422.1"
                     /translation="MTELEKQLLSALEQLQQDYSQRLDEWESAFAEWRSMCGLMQRENA
                     VLNERVSDLSTQVLSLSEQLRRLSGN"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(4089..4316)
                     /locus_tag="JLF36_RS25555"
                     /old_locus_tag="STN0717CIT27_P40070"
     CDS             complement(4089..4316)
                     /locus_tag="JLF36_RS25555"
                     /old_locus_tag="STN0717CIT27_P40070"
                     /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_053504437.1"
                     /translation="MGYHYKELTVIELTAEEFELHKEGYSLELLTNMRNEEHTKYWEVC
                     PSCEGKMDPEENQGHEGYCATCWLDNPDWW"
                     /name="hypothetical protein"
     gene            complement(4452..4655)
                     /locus_tag="JLF36_RS25560"
                     /old_locus_tag="STN0717CIT27_P40080"
     CDS             complement(4452..4655)
                     /locus_tag="JLF36_RS25560"
                     /old_locus_tag="STN0717CIT27_P40080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017191052.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_071686691.1"
                     /translation="MAIYVGPHSKVGRNGGSFQECDINTTNHTVTRKYGRYCTIRDNEY
                     APPTSVPGRHWLQIFRTPDNTE"
                     /name="hypothetical protein"
     Typing          1602..1775
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.0"
                     /coverage="100.0"
                     /evalue="1.21e-74"
     Typing          complement(1109..1635)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.811"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2202..3694
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.8"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tggttttttt atgctcataa atcaatcaat cggagtttat atgcgaaacg ttttaacaat
       61 agttaagttg ctaaaaatca ataacctaga tgaggatgtt tatgtcaaac gacgaaaatg
      121 aatacacgtt caaacctgtt aatgcccagg ctatcaaggc attaaaatca ctcccagaat
      181 gggttcaggc tgcattcgtg cacgcattgg attcggtgtt ctacggggtg gatccgggga
      241 tgtccatcgc acacttgacg gtcatcggcc ccggcgttgt tgagttgaga atcaatggtc
      301 gcccagctta tcgctgtgta taccgcagta aggcacccgg ccaggtggac ttactgcatg
      361 cgtttgtgaa aacgtgccaa ggaccagata agaaaaacat ggcaaccaca gcttcgcgct
      421 acaagttgct ctaatcaaat tggcgatggt tacaccatcg ccttttttac aaccatagtc
      481 aggggcgact ctgtgtttaa tggagtgaag tccatatcca gcttgtaccc catcttgaaa
      541 accatttcca acagcgtatc gacggagaat ttgtccagtt ttccgttcag catattgctt
      601 actcttggtt gactgatacc taacttttct gccgcttctg attgcgacca tttgttatca
      661 atcattagtt ttctaattat gataatgagt tttgacttga tcgaccatgt attgaacttt
      721 actgggtctg tactgatcag ctcaaatgaa tttttcatag aacagctcca cttcggatta
      781 cctgtatcgc aatgataaaa gttccggcaa ggaactcctt atatatatat acgggcgggg
      841 cattatacaa gtaatgatat tgctttcaag aggaaaaagt gtaaagacat tttgatcttt
      901 taagtaaagc ttattgtgtt gacgtatcaa tccagcaaag agtagtcttt gcccataaac
      961 gaaaaaacca cccggcaagg tggtttttcg aaggttcatt aaaccggcaa gtttatgaac
     1021 cgtggtaaca gggtgtacaa gaccgctgcc acctaattcg tccttccagt ttagccgtag
     1081 ttggactgat acttcaagaa ctctgcatca gttatctctt gtacaccctt taccagtggc
     1141 tgccgccagt ggcgttaagt cgtgcttttc cgggttggac tcaagtcgat agttaccgga
     1201 acaggcgcag cagtcggact gaacgggggg ttcgtgcata cagtccagct tggagcgaac
     1261 tgccttcccg gaaccgagtg tcaggcgtgg aatgagataa acgcggccat aacagcggag
     1321 tgacaccggt aaaccgaaag gcaggaacag gagagcgcac gagggagcca ccagggggaa
     1381 acgcctggta tctttatagt cctgtcgggt ttcgccacca ctgatttgag cgtcagattt
     1441 tgtgatgctt gtcagggggg cggagcctat ggaaaaacgg cttcgccgcg gccttattgc
     1501 ttccctgcta agtttcttcc tggcatcttc caggacattt ccgccccgcc agtaagccat
     1561 ttccgctcgc cgcagccgaa cgaccgagcg cagcgagtca gtgagcgagg aagcggaata
     1621 tatcctgtat cgcatattct gctgacgcgc cggtgccgta ttttttctcc ttccacatga
     1681 agcacttcac tgacatccgc attcgtgcca acatagtaag ccagtgtaca ctccgctagc
     1741 gctacgtgac tggttcaggg ctgcgccccg aaacccgcca aaagcctgac gcgcctgcgg
     1801 cttgtccaac cccgcgccga ccgggaaagg ctttcccgcc cgtcccggcg ttatcaggag
     1861 gccggtttgt cagagaaacg gagcaagatg ctcaccatgt gggtgacgga ggacgagcac
     1921 cggcggctgc tcgagcgctg tgacggcagg cagctggcgg cgtggatgcg gcagatctgc
     1981 ctggacgaaa agccggcacg ttccggaaag ctcccctcac tctcgccggc gctgctgcgc
     2041 cagcttgccg gcatgggcaa taacctgaac cagatagccc gccgtgttaa cgccggcggc
     2101 ggcaccggcc atgacagggt acagattgtg gcggcgctga tggccatcga tgccggcctt
     2161 gagcggctgc ggcacgccgt tcttgagaaa ggaacggacg atgatcgtta aatttcatcc
     2221 gcgcggccgc ggcggtggcg ccgggccggt ggactatctg ctgggtaaag atcggcagcg
     2281 tgaaggcgcc accgtcctgc aggggaagcc ggaagaagtc cgggagctga ttgacgcgtc
     2341 gccttacgtt aagaaataca cctccggcgt tctgtcgttt gcggaggccg atctgcctcc
     2401 cggccagcgg gaaaaactga tggccagctt cgagcgggtt ctgatgcccg gactcgataa
     2461 agatcagtac agcattctgt gggtggagca cgcggacaag gggcgtctgg agctgaactt
     2521 tctgatcccc aataccgagc tgctgaccgg caggcggctc cagccttact acgaccgcgc
     2581 cgaccggccg cgcatcgatg cctggcagac tatcgtgaac ggcagactgg ggctgcacga
     2641 cccgaacgcg ccggaaaacc gccgggcgct ggtcacgccg tccgggctgc cgaaaacgaa
     2701 gcaggaggcc gcagaagcca ttacccgggg actgctgacc cttgcttcgt ccggggagct
     2761 gaaaagccgt caggatgtca ctgacactct tgaaggtgca ggttttgagg tggtgcgcac
     2821 cacgaaaagc agtatcagca ttgccgaccc ggacgggggg cgaaacatcc gactgaaggg
     2881 agccatctat gagcagtctt ttaacgctgg cgaaggactt agagcagcaa tcgaaagcgc
     2941 agcagcagag taccggcgag atgctgaaag ccgtattcag cgagcacgag cggtctgtca
     3001 gagcggaact gagcgcaagc gcgaggagaa tcagcgacgc catcctcgcc cacgagcaga
     3061 gtatgagcga ggcgatggag aaaaaccggc ggagcgtact gcggactgcc gggcggacat
     3121 ggctcaccat cctgatggtg tcagcgctgc tgatcggcac gagcgggagc attctgtggt
     3181 ggcaggggca gcagataacc gacaattaca cgcatcttcg tcagcaggaa gataccctgg
     3241 cgaaaatgac cgcccggacg tggggagtgc gctatcagga gagcagcgac ggccggaggt
     3301 ttcttatcct gccgccgggg atgcaaaccg aagccatccc ctacgacggg acgacatgga
     3361 tccgcctgaa acaggagtag cggaaaatga cagagctgga aaagcagttg ctgagcgcat
     3421 tagagcagct acagcaggac tactcgcaaa ggctggacga atgggagagc gccttcgcgg
     3481 aatggcggag catgtgtggg cttatgcaac gggagaacgc ggtgctgaac gagcgcgtgt
     3541 cggacttgag cacgcaggtg ctgagtttaa gcgagcagct gcgccgcttg tccgggaact
     3601 gaatgccacc gagttccggc agagggagaa tgagtatcag aaaacactgg agctggagcg
     3661 ccagccgcag aaaacctacc gcgggccgac actttaaacc atccaggcag ctgacaaccc
     3721 gcacgaagag gggctcttat ttctcccgct aaataggttc gtgatcaaaa aggtcacgac
     3781 ttattcagga gcgggaaatg aagctgttaa atcttattga atcattgctt aactgcctgt
     3841 atctggcggc ggagctgtgg gactggctgg agaagcattt gtcggttttt aaggcattgg
     3901 cgcggatttt agtgtgactt taacatccat gcatctggct gcatgactat gcaccagtgt
     3961 aatattcagc ggctgcgttt ctggtgtttt ttcgttatgt ctgtcgccac tttctcgcgt
     4021 ctggcaccgg aaacgcagcc aaccccgttt cagcggtgcg ggcaacggat gttatggtaa
     4081 attattaact accaccagtc agggttatcg agccagcatg tggcacagta accttcatgc
     4141 ccttgatttt cttctggatc catttttcct tcgcaggaag ggcaaacttc ccaatacttg
     4201 gtgtgttctt catttctcat gttagttaaa agctctaaag agtatccctc tttatgaagc
     4261 tcaaactctt ccgcagttaa ttcgatgacg gttaattcct tgtaatggta acccattcgc
     4321 ttgcctcgct ttatgcagct caatactaag atactgaaaa gcattaaatg tcagggtttt
     4381 cagtatctta caatgataat cctatccggt ttatacaagg gatattaccg ctttactaag
     4441 cagaagatga attactctgt gttatctggc gtgcggaaaa tttgcagcca atggcggcct
     4501 ggaacgctgg ttggaggggc gtactcatta tcgcggattg tgcagtagcg gccatatttt
     4561 cgggttaccg tatgattcgt tgtgttgata tcacattcct ggaatgaacc accattacga
     4621 cctactttgc tgtgaggacc aacataaata gccattctaa gctccttcgt cagatagttg
     4681 attaccagta tctaagtaga ttttattaat ttctatattt atcaatatca tagtgtgctt
     4741 tgttggcttt ccacattgcg tcgataaaat cctcatatct tgatgtaagg aaaaccaaca
     4801 catgtaactg ttaggtcttc tgcgcctaag tcaaattgat ttttttttat tcaaacagac
     4861 gtttgaagca ctaataagaa ttgatgacat ataagaattt atataggcat cgttggcgag
     4921 attgccaatg aattgttggt tcaacgagca ataaccatgc gcgcactttc ctaaatatag
     4981 ggcggtg
//
