LOCUS       NZ_AP022392             3944 bp    DNA     circular CON 30-JAN-2024
DEFINITION  Citrobacter portucalensis strain STW0522-26 plasmid pSTW0522-26-3,
            complete sequence.
ACCESSION   NZ_AP022392
VERSION     NZ_AP022392.1
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  JOURNAL   Unpublished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 3944)
  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
            AP022392.1.
            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..3944
                     /organism="Citrobacter portucalensis"
                     /mol_type="genomic DNA"
                     /strain="STW0522-26"
                     /isolation_source="sewage"
                     /db_xref="taxon:1639133"
                     /plasmid="pSTW0522-26-3"
                     /geo_loc_name="Japan:Tokyo"
                     /collection_date="2018-05-22"
     gene            102..968
                     /locus_tag="JLF45_RS25460"
                     /old_locus_tag="STW0522CIT26_P30010"
     CDS             102..968
                     /locus_tag="JLF45_RS25460"
                     /old_locus_tag="STW0522CIT26_P30010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000586611.1"
                     /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_200921658.1"
                     /translation="MIIQEEHNIDFFKNQMPNKPYCTNNLDMGLSIRNKAKALEMLYLQ
                     ANQPAIQTCLLFDLDKKNSFYTFEKVGLPIPHFITKTPKTGRCHYGYMLKAGVCKTQQA
                     RLKPLKYAAAVEMAMAKKLKADLGFAGLITKNPLNDHWSPFWSGADLYDLDYLADFVDL
                     EKPQIQEKKSEAYGLGRNVNLFEDLRQYAYRTVLNFKKISTFEKFENELLLKAQGLNNF
                     CNPQNPLQYKEIKATVRSVARWTWKNFDSHTFSLIQSARGLKNKGKAKKTTNKNIKSML
                     DFIGGEK"
                     /name="replication initiation protein"
     gene            965..1234
                     /locus_tag="JLF45_RS25465"
                     /old_locus_tag="STW0522CIT26_P30020"
     CDS             965..1234
                     /locus_tag="JLF45_RS25465"
                     /old_locus_tag="STW0522CIT26_P30020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001549724.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="response regulator transcription factor"
                     /protein_id="WP_200921659.1"
                     /translation="MRRSTIRKGLTQKEMAQRFNISIKTVKKYTSEPREQYEQTAADRR
                     RQAYELRSQGLKWQQVADKMGCSYHGAVALYRRYVALDMPQNSL"
                     /name="response regulator transcription factor"
     gene            complement(1471..1755)
                     /locus_tag="JLF45_RS25470"
                     /old_locus_tag="STW0522CIT26_P30030"
     CDS             complement(1471..1755)
                     /locus_tag="JLF45_RS25470"
                     /old_locus_tag="STW0522CIT26_P30030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001549726.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_079843899.1"
                     /translation="MSKSTAQQIADLQNKLQALRTKKARQDRREETRQKIILGAEVAKV
                     LGKKPEEINKALILGLLSKINELDEEEKQEFTRLGLNILEEWKNENRKP"
                     /name="conjugal transfer protein TraD"
     gene            complement(1752..2141)
                     /locus_tag="JLF45_RS25475"
                     /old_locus_tag="STW0522CIT26_P30040"
     CDS             complement(1752..2141)
                     /locus_tag="JLF45_RS25475"
                     /old_locus_tag="STW0522CIT26_P30040"
                     /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_181547849.1"
                     /translation="MNKLITEAEGARIESVFKYILEASESILIEHGHVITGQIIKNKKF
                     FADNGHKDFERLEYYLSSAISSLVEDKVTEGIKDINTDENLVFKKINELSDKEKLILAE
                     CIIKHFEYSNIRGMQKAFNIFGGDK"
                     /name="hypothetical protein"
     gene            2387..3547
                     /gene="mobQ"
                     /locus_tag="JLF45_RS25480"
                     /old_locus_tag="STW0522CIT26_P30050"
     CDS             2387..3547
                     /gene="mobQ"
                     /locus_tag="JLF45_RS25480"
                     /old_locus_tag="STW0522CIT26_P30050"
                     /inference="COORDINATES: protein motif:HMM:NF041496.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_117059963.1"
                     /translation="MAIYHLSFKLCKRSEGKSSVYLAAYQNRNKFTDNRTGAVWNYSKK
                     EGFDGSLILAPPQAPGWLVKSSEALWNEVERTERQKNGQTARYFDVALPVELDDKQKKD
                     LLIKYCQDNFVDEGMIADIAFHDLNSKNPHAHVMLTMKNVGPEGFLTKNREWNDKKCLE
                     AWRQNWEVITNEALKKYGHKSRIDSRSLEEQKEEADRKAKVAKTPQAKAAWIAKSIRLD
                     RTPMTRIHRHNWKTGQKLRKLEQEERKILYKKASLTYHQITKPIEPEQSMKIEKSQIAQ
                     KIKSIFETAKNKLNSKIADFFKPKPKKETPEKFVSSYEIDELGNHILKKEAENWDQKNN
                     DKIKKQVREKKEKEESERLRLKEEDEKLKNSSKPIQQNNNHRKLKR"
                     /name="mobQ"
     Typing          2388..3544
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.705"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tacaggattg aaaaacctat aaaaataaaa accccaccct ctgcgatttt gttttggcga
       61 cagaaaacag agagtagggc cagataaaaa ggactggaaa aatgataata caagaagaac
      121 ataacatcga tttttttaaa aatcaaatgc ctaacaagcc ttattgtaca aataacctcg
      181 atatgggatt aagcataagg aacaaggcaa aagccttaga aatgctgtat ttacaggcaa
      241 atcagccagc aatccaaact tgcttactct ttgatttaga taagaaaaac tcattctata
      301 catttgagaa ggtgggctta cccatacctc actttattac aaaaacacca aagacaggtc
      361 gttgccatta cgggtacatg cttaaagccg gtgtttgtaa gacacaacaa gcaaggttga
      421 agccgttgaa gtatgccgct gccgttgaaa tggctatggc gaaaaaactt aaagcagatc
      481 tggggtttgc tggattgatt acaaaaaatc cactcaatga tcactggtcg ccgttctggt
      541 caggtgctga cctttacgac ctggattatt tagctgattt tgtggactta gaaaaacctc
      601 aaatacaaga gaaaaaaagc gaggcttatg gtttaggtcg caatgttaat ttgtttgaag
      661 atctacgaca atatgcttac agaacggttt taaatttcaa aaaaatatct actttcgaga
      721 aattcgaaaa cgaactacta ttaaaggcac agggtttaaa taatttttgc aatccacaaa
      781 acccgttaca atacaaagag ataaaagcaa cagttagaag tgtagcccgt tggacctgga
      841 aaaattttga tagtcataca tttagtttaa ttcaatctgc acgaggttta aaaaataaag
      901 gaaaggctaa aaaaacaaca aataaaaata ttaagtctat gcttgatttt ataggaggtg
      961 aaaaatgaga agaagcacaa taagaaaagg tttaactcaa aaagaaatgg ctcaaagatt
     1021 taatatctct attaaaacgg taaaaaaata tacatccgaa cctcgtgaac aatacgaaca
     1081 aacagcggct gatcgtcgtc gtcaggctta cgaactacga agccaggggc tgaaatggca
     1141 acaggtagcc gacaaaatgg gctgttcgta tcacggagcc gttgccctgt atcgtcgtta
     1201 tgttgctttg gatatgcctc aaaacagcct gtaacgactt ctaagcagtt tttcccccta
     1261 acctaaccaa accctccacc cctgggggga ttttttcccc tttccccgta tccgggcttg
     1321 tgtctggata gttgagggac actctggtac caacaaatca acaaacccac ccagccacca
     1381 gaggccctct ggcaacctta aaacctccag cctacggctg gcaacccttc acaatgaaaa
     1441 accagccaag atcggctggt tttttattgt tcacggttta cgattttcat tcttccactc
     1501 ttctaaaata tttaatccta atcgtgtgaa ttcttgtttt tcttcttcgt caagttcatt
     1561 tattttactt aacaatccaa gaattaaagc cttgttaatt tcctctggtt ttttacctaa
     1621 aaccttagcc acttctgcac ccaggattat tttttgtctt gtttcttccc ttctgtcctg
     1681 tcttgctttt tttgttctta atgcttgtag tttattttgc aaatctgcga tctgctgtgc
     1741 agtagattta ctcatttatc acccccaaaa atattaaaag ctttttgcat tcctctaata
     1801 tttgaatatt caaaatgttt aataatacac tcagctaaaa ttaatttttc cttatcactc
     1861 aattcattta tttttttaaa aacaaggttc tcatccgtgt taatgtcttt aatgccttct
     1921 gttaccttat cctcgacaag agaactaatt gccgagctaa ggtaatactc taacctttca
     1981 aaatctttat gcccgttatc agcaaagaac tttttgtttt ttattatttg ccccgtaata
     2041 acatgcccat gctctattaa tatgctttca gatgcctcta atatgtattt aaaaacactt
     2101 tcgattcttg caccttctgc ctctgttata agtttattca taataccctc ctaattattt
     2161 attttgttat ttattacctc cattatttac tttagtcaaa tatattttag aataaaataa
     2221 ataatattta atattgggcg aagcctgggt ttattacttt attattttga gatgcaatcg
     2281 aaaaaataat attagtaatg cccacttata cactcgttcc gagtgtgtgg gccctgcggg
     2341 gctaaaaccc aaaattcaaa agataaaaaa agtaaggggg tagcctatgg ctatatatca
     2401 tttaagtttt aaattgtgca aaaggtcaga aggtaaatct tccgtctatt tggctgcata
     2461 tcagaataga aataaattta ccgataatag aacgggtgcc gtatggaatt acagcaaaaa
     2521 agaaggcttt gacggttcgt taatcctggc accaccacaa gcaccaggat ggcttgtgaa
     2581 gtcgtctgag gccctatgga atgaggttga gaggacagaa cgacagaaga acggacagac
     2641 tgccaggtac ttcgatgtcg ccttgccggt ggagctggac gacaaacaaa aaaaagacct
     2701 tttaataaaa tactgtcagg ataattttgt agatgaggga atgattgccg atattgcatt
     2761 ccacgatcta aatagtaaaa atccccatgc ccatgtaatg ttaacaatga aaaatgttgg
     2821 gccagaggga tttttaacaa aaaacagaga atggaacgat aagaaatgtt tagaagcctg
     2881 gaggcaaaat tgggaagtta ttacaaatga ggcattaaaa aaatatggtc ataaatcccg
     2941 tattgattcc cgttcattgg aagaacaaaa agaagaggct gacagaaaag caaaagttgc
     3001 aaaaactcca caggcaaaag ctgcctggat tgctaaatct atccgtctgg acagaacgcc
     3061 aatgacccgc attcacaggc ataattggaa aactgggcag aaattaagaa aattggagca
     3121 agaagaaagg aagattttat ataaaaaggc ttcgttaaca tatcaccaaa taactaaacc
     3181 aattgagcct gagcaatcta tgaaaataga aaaatcacaa atagctcaaa aaataaaatc
     3241 tatattcgaa actgccaaaa ataaattaaa ttcgaaaatc gctgactttt tcaagcctaa
     3301 acccaaaaaa gaaactcctg aaaaatttgt cagtagttat gaaattgacg agttaggaaa
     3361 tcacatattg aaaaaagagg ctgaaaattg ggatcagaaa aacaatgata aaattaaaaa
     3421 gcaggttcgt gagaaaaaag aaaaagaaga atccgaaagg ttgaggctta aagaagagga
     3481 tgagaaatta aaaaatagct ccaagccaat tcagcaaaat aacaatcata ggaaattaaa
     3541 gcgatagtat atattgctat atactacaat atactatact acattttcaa aattgttact
     3601 ctggctggct ctaactcacc tttgtgaatt ttcacagctt cattaactga cttcataagc
     3661 attttaaaaa atttactatg cttattttta tttcttcttt ttttcttctg caatttcttt
     3721 tttttcataa tttcaccaaa aaaaatcgaa tcgccaattt ttcttcgaac aatcctcttt
     3781 tttctttttt tattgttttt ctatcttcgg taatgcttcg caccatagat ctgatagtaa
     3841 tgctttgctg ccgtatgtaa agaactgccc caacttcgtt gggctgttat ctgatatggt
     3901 taaggttcac tacttgacaa atttttaaga tcggttagaa ctgg
//
