LOCUS       NZ_AP022404             4907 bp    DNA     circular CON 30-JAN-2024
DEFINITION  Citrobacter portucalensis strain STW0522-30 plasmid pSTW0522-30-5,
            complete sequence.
ACCESSION   NZ_AP022404
VERSION     NZ_AP022404.1
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  JOURNAL   Unpublished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 4907)
  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
            AP022404.1.
            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..4907
                     /organism="Citrobacter portucalensis"
                     /mol_type="genomic DNA"
                     /strain="STW0522-30"
                     /isolation_source="sewage"
                     /db_xref="taxon:1639133"
                     /plasmid="pSTW0522-30-5"
                     /geo_loc_name="Japan:Tokyo"
                     /collection_date="2018-05-22"
     gene            complement(102..332)
                     /locus_tag="JLF43_RS26010"
                     /old_locus_tag="STW0522CIT30_P50010"
     CDS             complement(102..332)
                     /locus_tag="JLF43_RS26010"
                     /old_locus_tag="STW0522CIT30_P50010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001171587.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_200925417.1"
                     /translation="MHEQKDKKRRLGFMIGKSNATLPPDEQTQTEAELDQEVLKLFYPN
                     QCTKDTIERSEAGTDVFTASGSDDLFKKLKL"
                     /name="hypothetical protein"
     gene            631..1482
                     /locus_tag="JLF43_RS26015"
                     /old_locus_tag="STW0522CIT30_P50020"
     CDS             631..1482
                     /locus_tag="JLF43_RS26015"
                     /old_locus_tag="STW0522CIT30_P50020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000481810.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_200925416.1"
                     /translation="MFKIENNKDILKSQIPLKPYATNDLEFGLTIQNKNKALDMLYLQV
                     NHPLYLHTMVFDIDKENCFYEFENAHLPIPSFITKSPDSGRCHYGYMLNAPISSTEKSR
                     QKPVKFARAVYFNMANRLGADLGYAGLITKNPLNDHWSPFWSGADLYELNDLADCFDDL
                     EEPKKRENTGLAFGRNVEMFDTIRQWAYKNVLKYQSESSFNDFHNELLLKCQMHNAYLN
                     ADDLLPYNEIKATAKSIAKFCWKEFSEEKLNKIQSKKQSYRGKKNKGIVKSKTRKFLEA
                     IK"
                     /name="replication initiation protein"
     gene            1479..1751
                     /locus_tag="JLF43_RS26020"
                     /old_locus_tag="STW0522CIT30_P50030"
     CDS             1479..1751
                     /locus_tag="JLF43_RS26020"
                     /old_locus_tag="STW0522CIT30_P50030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000125721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid replication protein"
                     /protein_id="WP_074193887.1"
                     /translation="MKVKNRKRELTAKEYAEQYEISVRTVKRYFSQDREDYEKEAKQRR
                     LKAFVLRESGMKWSDVGIALGTTKHGAIALYKRYQQIDAPTTKEA"
                     /name="plasmid replication protein"
     gene            complement(1760..3235)
                     /locus_tag="JLF43_RS26025"
                     /old_locus_tag="STW0522CIT30_P50040"
     CDS             complement(1760..3235)
                     /locus_tag="JLF43_RS26025"
                     /old_locus_tag="STW0522CIT30_P50040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000678150.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_200927160.1"
                     /translation="MKGNVAKPGRSFKNRVDYILKDDHDFICSNMASDYNNVSDLTDEF
                     KTVSSFRQDIKKPVFHAFLSLPKNEHLTDEQWQEIAKDYLKEMNIDIDKHQYICVRHND
                     TDKEHIHIVANRVGLDGSVWLGQHSAFNTIAACERLEVKHGLTITQGLKGQKSDVSAPT
                     KAEIEQALRTGEKPARIVLQNALQAAMVGKPDLETFVERLQAVGIEPRFNVASTGNVAG
                     VSFSVGDVAFKGSQLGKKYSWNTIKGKVKYDKNRDDELVRRFSARKADDENSIGRSFVE
                     SNINDSRTSDRINDDIIGVGQYGIKSDATDINQSEQLIRSNNNRFKLSEKYNRPASHKV
                     RRTTQKAAQILNRVKKQYNKEPIKTYNKNGLNSWRDKSDSSSISRILDHAETANAATNN
                     FRLKGRGNINSRATKIEEIRERLEIKKPVVQPKNKEKIVKEEIKKKPLGLSMDENRFKS
                     KLKEALKKEKPKNETTPQQEDDQHLKPRGFKPR"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(3232..3603)
                     /gene="mobC"
                     /locus_tag="JLF43_RS26030"
                     /old_locus_tag="STW0522CIT30_P50050"
     CDS             complement(3232..3603)
                     /gene="mobC"
                     /locus_tag="JLF43_RS26030"
                     /old_locus_tag="STW0522CIT30_P50050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000379199.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_064374444.1"
                     /translation="MKTDRKRGRIELNHEVRRDISIQFRVNKAEFEYLKELVEASGLER
                     GHYIRREILNSEPIVKRKMPDFEQSLYKEIQHQGNNINQIAKKLNTNEDFKQSVAAEAN
                     FAIKQLMKRILKACEVYTI"
                     /name="mobC"
     gene            complement(3590..3841)
                     /locus_tag="JLF43_RS26035"
                     /old_locus_tag="STW0522CIT30_P50060"
     CDS             complement(3590..3841)
                     /locus_tag="JLF43_RS26035"
                     /old_locus_tag="STW0522CIT30_P50060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016241874.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_227524672.1"
                     /translation="MKLNVLARFFYYIEQDKDIPFDYSSYDEQGLCYFVANRYINENKA
                     DDLIQALIDTNDDDYIKAIRDYVQYTTLNEVRKKYEDR"
                     /name="hypothetical protein"
     gene            complement(3843..4109)
                     /locus_tag="JLF43_RS26040"
                     /old_locus_tag="STW0522CIT30_P50070"
     CDS             complement(3843..4109)
                     /locus_tag="JLF43_RS26040"
                     /old_locus_tag="STW0522CIT30_P50070"
                     /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_119913217.1"
                     /translation="MIDEMTQYRIRRFTQSQKSLLLKMIKESQRSDLEDNIKDILKDID
                     VSYSTGITKKASRKEEMIACREVHYIFSILTKRGINNDYRNEI"
                     /name="hypothetical protein"
     gene            complement(4116..4382)
                     /locus_tag="JLF43_RS26045"
                     /old_locus_tag="STW0522CIT30_P50080"
     CDS             complement(4116..4382)
                     /locus_tag="JLF43_RS26045"
                     /old_locus_tag="STW0522CIT30_P50080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001028448.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_200927159.1"
                     /translation="MKIVLSVSKCLYINDLDRLLSCDRFFVHLDYKDISKKESFEMNRH
                     DQESYKLIFDKLVGNDVMLAIDEDIYSEVVENLLYYSNKTYGD"
                     /name="hypothetical protein"
ORIGIN
        1 tatatactgc atcgagggtt ggccttctct caccgtccgg gtcggtttgg gtttgttcta
       61 ctggtgaaga tggccagctc tcccctgccc tacagcttca cctacagctt cagttttttg
      121 aacaggtcat cagaaccgga ggccgtgaaa acgtctgtac cggcttctga gcgttctatg
      181 gtgtctttag tgcattgatt aggataaaac agcttcagaa cttcctgatc aagctctgct
      241 tctgtttgtg tttgttcgtc tggtggcaat gttgcattgc tcttaccaat cataaaacct
      301 aaccgccgtt tcttgtcctt ctgttcgtgc atgatttacc tccccagcac agccagatcc
      361 tgcatatgaa gtttagtata cgttacagtg ttactttact ctgcagtagc cttcggcctg
      421 tgcttcgctg tggtgtaggg tccccaaaac tccgtctaat acctgatatt ggttaatggc
      481 acacataaca actttttttt gatggatcta ttgacaagat tatttgatat agtaaaactg
      541 taagagatta taaataaaag aaaagcccgc gtttcttgga aagtttggcg accaacaaga
      601 aacggggcat tacagaaagg atactgctat atgttcaaga tagaaaataa caaagatata
      661 ttaaaaagtc aaataccttt aaagccatat gctacaaatg atttagagtt cggattgact
      721 attcaaaata agaataaagc cttggatatg ctttatttac aagtaaatca cccgctttat
      781 cttcatacaa tggtatttga tatagacaaa gaaaactgct tttacgagtt tgaaaatgct
      841 catttgccca tcccgtcttt tataacaaaa agccctgata gtggacgttg tcattatggt
      901 tatatgctta atgctcctat atcctctacg gagaaaagca gacagaagcc tgtaaagttt
      961 gccagagctg tttattttaa tatggctaac cgtttaggtg ctgatctggg gtatgccgga
     1021 ctgattacaa aaaacccact caatgatcac tggtcgccgt tctggtcagg tgctgattta
     1081 tatgagttaa atgatttagc tgattgtttt gatgatttag aagaacccaa aaaacgagaa
     1141 aatacggggc ttgcttttgg tcgtaatgtt gaaatgttcg acacaataag gcagtgggct
     1201 tataaaaatg tgctaaaata tcagagtgaa agctcattta atgattttca caatgaacta
     1261 ttgctaaagt gtcaaatgca taatgcatat ttaaatgctg atgatttact gccatataat
     1321 gagataaaag ccacagcaaa aagcattgca aagttttgtt ggaaagaatt cagcgaagaa
     1381 aaactcaaca agatacagag taaaaaacag tcttaccgtg gaaagaaaaa caaaggaata
     1441 gtaaaaagta aaactcgtaa gtttttggag gccataaaat gaaagttaaa aatagaaaaa
     1501 gagaacttac tgcaaaagag tatgctgaac agtatgagat tagcgttaga acagtaaaaa
     1561 gatatttctc tcaagatcgt gaagactatg aaaaagaagc aaaacaaaga cgattaaaag
     1621 cttttgtatt acgtgaaagc ggtatgaaat ggtctgatgt tggtattgct cttggaacta
     1681 caaaacatgg tgctatagct ctttataaac gttatcaaca aatagacgca ccaacaacaa
     1741 aagaggctta aagcctcttt tatcttggtt taaaaccacg cggttttaaa tgctgatcgt
     1801 cttcctgctg tggtgttgtt tcattttttg gtttttcttt tttaagagct tcttttaact
     1861 tcgatttaaa tctattttca tccatactca aacctaacgg ctttttcttt atttcttctt
     1921 taactatttt ttctttattc tttggctgaa caactggttt ttttatttca agcctttctc
     1981 ttatctcttc gatcttagtt gctctactat tgatgttgcc acggcctttg agtctaaagt
     2041 tattcgtggc tgcgttggct gtttctgcat gatcaagtat cctactgata gaactgctat
     2101 cagatttatc acgccaacta ttgaggccat ttttattata agttttgatt ggttctttat
     2161 tgtattgttt tttaactctg ttgagtattt gtgcagcttt ttgtgttgtt cttctaactt
     2221 tatggcttgc tggtctatta tatttttcgc tgagtttaaa gcggttgttg ttgcttctaa
     2281 tgagttgttc actctggtta atgtctgttg cgtctgattt aatgccgtac tgaccgactc
     2341 cgataatatc atcattgatt ctgtcagagg ttctactgtc attgatattt gattcaacaa
     2401 atgatcgtcc aatactattt tcgtcatctg cttttcttgc tgagaatctt ctaacgagtt
     2461 catcatctct atttttgtca tatttcacct tacctttaat agtgttccaa ctgtattttt
     2521 tacccaactg tgagccttta aatgccacat ctccaacact gaatgaaacc cccgccacgt
     2581 tgccagtgct ggcaacattg aacctcggtt caatgcctac ggcctgcaga cgttctacga
     2641 acgtctcaag gtctggtttt cctaccatag cagcctgcaa tgcgttctgt agcacgatac
     2701 gagctggttt ttcaccagtg cggagggctt gctcgatctc agctttggtt ggtgctgata
     2761 cgtctgattt ttgaccttta agcccctgtg taatggttaa gccgtgtttt acttctaaac
     2821 gttcacaagc tgctattgtg ttaaatgctg agtgctgacc gagccataca gaaccatcaa
     2881 ggccaacacg attagctaca atatggatat gttctttatc tgtatcgtta tgacgaacac
     2941 aaatatattg atgtttgtct atatcaatat tcatttcttt caaatagtct tttgctatct
     3001 cttgccattg ttcatctgtt aaatgttcat tttttggaag agataaaaaa gcgtgaaata
     3061 ctggtttttt tatatcttgt ctaaagctgc ttacagtttt aaactcatca gttaaatcac
     3121 taacattatt ataatcactt gccatattgc tacatataaa atcgtggtca tctttaagaa
     3181 tgtaatcaac tctattttta aatgatcttc cgggttttgc tacatttcct ttcatatggt
     3241 ataaacctca caagccttta atattctttt cataagttgc tttatagcaa agttagcttc
     3301 tgcggctaca gattgtttaa agtcttcatt cgtatttagc tttttagcaa tctgatttat
     3361 attattacct tgatgttgta tttctttata caatgattgc tcaaaatccg gcatttttct
     3421 tttaacaata ggttcagagt ttaaaatctc tcttctaatg taatgacctc tttcaaggcc
     3481 agacgcctca acaagttctt ttaaatattc aaactctgct ttgtttactc taaactgtat
     3541 agatatatct ctacgtactt cgtgatttaa ctctatacgt cctctttttc tatctgtctt
     3601 catatttctt tctcacttca tttaaagttg tatactgaac ataatctctt atagctttta
     3661 tataatcatc gtcattagta tctatcaatg cctgtataag atcatcagct ttattttcgt
     3721 taatgtatct attagctaca aaataacata atccttgttc gtcatagctt gagtaatcaa
     3781 aaggtatatc tttatcttgt tctatgtaat agaaaaaacg tgctaataca ttaagtttca
     3841 tttcatattt catttctata atcattgtta atgcctcttt ttgttaatat actaaagatg
     3901 taatggactt cacgacaagc gatcatttct tcttttcttg atgctttctt tgttatgcca
     3961 gttgaataac taacatcaat atcttttaaa atatctttta tattatcttc taaatcgctt
     4021 cgctggcttt cttttatcat ctttagtagc aagctttttt gactttgtgt aaagcgtctt
     4081 attctgtatt gtgtcatttc atctatcatt ttatattaat ctccataagt cttatttgaa
     4141 taataaagta agttttcgac aacttcgctg tagatgtctt catcaatagc aagcattacg
     4201 tcattaccga caagcttatc aaagataagt ttgtagcttt cttggtcgtg tctattcatc
     4261 tcaaatgact cttttttgct aatatcttta taatctaaat gaacaaaaaa acgatcacac
     4321 gaaagtaagc gatctaaatc gtttatgtat aaacattttg atactgataa aactattttc
     4381 atatttattc cttttatttt gaagtgaact gtaaaactat ttaccgcttc cccttgatag
     4441 gggaataagc ggaagggtag atctttttca accctacgag caaagcgaga tagggccaat
     4501 cgaagattgg ggtataatac cggctacggg attacacctt gcctcagttt ccgaaaaaca
     4561 aaaataaagc tgaactcaac ctatatttaa ataaataacc gatccaaaaa gtttgtcaat
     4621 atagcggcta cataaataaa taccctgcac aacaaataaa atgcaaataa aaaatagggt
     4681 aaataatata ttgtcttgat gggtagctgt gcgtaatagg tagctttgcg taaaaaatgc
     4741 tgctgctacg tgaaatctgg aaaagttcgt gaccatcaga tcaccagatt ttaaggaatg
     4801 gggtttgatc ggcggcgaca gaaacgagta aaacttgctt ttgctcgttt gctggcgtct
     4861 atgggtttaa aatgctcata aaatcaacag actatagtat atattag
//
