LOCUS       NZ_AP026959             2348 bp    DNA     circular CON 27-NOV-2023
DEFINITION  Salmonella enterica strain SE20-72C-2 plasmid pSE20-C72-2-11,
            complete sequence.
ACCESSION   NZ_AP026959
VERSION     NZ_AP026959.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00515066
            Sequence Read Archive: DRR396386, DRR396387
            Assembly: GCF_025999715.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica
  ORGANISM  Salmonella enterica
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1
  AUTHORS   Nakayama,T., Yamaguchi,T., Phuc,N.D., Chinh,D.V., Jinnai,M.,
            Kumeda,Y. and Hase,A.
  TITLE     Complete genome sequence of Salmonella enterica SE20-C72-2
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2348)
  AUTHORS   Nakayama,T. and Yamaguchi,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-OCT-2022) Contact:Tatsuya Nakayama Hiroshima
            University, Graduate School of Integrated Sciences for Life; 1-4-4
            Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Genome Coverage                   :: 187x
            Sequencing Technology             :: Illumina iseq; Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/27/2023 03:37:18
            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)                     :: 5,087
            CDSs (total)                      :: 4,969
            Genes (coding)                    :: 4,785
            CDSs (with protein)               :: 4,785
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 184
            CDSs (without protein)            :: 184
            Pseudo Genes (ambiguous residues) :: 0 of 184
            Pseudo Genes (frameshifted)       :: 66 of 184
            Pseudo Genes (incomplete)         :: 133 of 184
            Pseudo Genes (internal stop)      :: 28 of 184
            Pseudo Genes (multiple problems)  :: 40 of 184
            Pseudo Genes (short protein)      :: 1 of 184
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP026959.1.
            Annotated by DFAST https://dfast.ddbj.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..2348
                     /organism="Salmonella enterica"
                     /mol_type="genomic DNA"
                     /strain="SE20-72C-2"
                     /isolation_source="Gut content of Anabas testudineus"
                     /host="Anabas testudineus"
                     /db_xref="taxon:28901"
                     /plasmid="pSE20-C72-2-11"
                     /geo_loc_name="Viet Nam:Ho Chi Minh City"
                     /collection_date="2020-03-18"
     gene            211..957
                     /locus_tag="OO990_RS25405"
                     /old_locus_tag="SE2072C2_48890"
     CDS             211..957
                     /locus_tag="OO990_RS25405"
                     /old_locus_tag="SE2072C2_48890"
                     /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="helix-turn-helix domain-containing protein"
                     /protein_id="WP_071681991.1"
                     /translation="MDIGNILNESLNVEYSKLDLFLEKYDLTPEQKVEVYEFHAKASKK
                     NKTLVISETKENRFKSISEGVEYVHLFPKNLKILIKKYGLNTNELLVLTEIMESMLSHG
                     NLLINFSQKTLCELTEINKSTMSKTFKSLKQKQCLIEKNGHIYLNSVIFMKGLPHKLFI
                     QFRDHFLNSISYKLDDEEEFEKVFDDNFIKAYEKNLKEIKKKKQQIKEKKISKALDNFE
                     KEISEEWKEKFKDEEENFEFGFESEM"
                     /name="helix-turn-helix domain-containing protein"
     gene            1325..2053
                     /locus_tag="OO990_RS25410"
                     /old_locus_tag="SE2072C2_48900"
     CDS             1325..2053
                     /locus_tag="OO990_RS25410"
                     /old_locus_tag="SE2072C2_48900"
                     /inference="COORDINATES: protein motif:HMM:NF012798.3"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0015074 - DNA integration [Evidence IEA];
                     GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific integrase"
                     /protein_id="WP_097725005.1"
                     /translation="MGNSKRNIKKLNDNFREDILDYAFAHNLKCANALAILYATGCRPD
                     ELQTGVTVNYDSKKNEIEFRIIGSKLNRRMRRGIGVRKIKVKINNENARFFKNIVDKFI
                     ENPMSYDHKIKIESAKAFSGYITKISKKLWPRKTYHASAYSFRHAKATELKNSDYDKIE
                     IAQIMGHASVRSQQSYGRKSKKSKGGFDDIADVETNVKPRGGDRLLRFKIANKNKAAAK
                     IADTSTPSSPPPAPVRRFKM"
                     /name="site-specific integrase"
     Typing          2116..2298
                     /name="Col(IRGK)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.7e-91"
ORIGIN
        1 aaacttcaac cgtagttgtc aaattcgtca actctagttg tcaaattcgt caactgaggt
       61 tgtcaaatcc gacaactcta gccagtttcc aagtagaaac tacagtttca aaactgaaac
      121 tttttctacc ttttgcaact caatctattg actagttctt tataaatgtt aaaacatata
      181 tatagaaata aataaaaaga ggaggtttct atggatattg gaaatatatt aaatgagagt
      241 ttgaatgttg aatattcaaa attagatttg tttttagaaa aatatgattt aacacctgag
      301 caaaaagtag aagtttatga atttcacgcg aaagcgtcta agaaaaataa gactttagtt
      361 atttcagaaa caaaggaaaa tagatttaaa tctatttccg aaggtgttga atatgtgcat
      421 ttgtttccaa aaaacttaaa aatattaatt aaaaaatatg gtttaaacac aaatgaatta
      481 ttggttttaa cagaaataat ggaatcgatg ctttcacacg gaaatttatt aattaatttt
      541 tcacagaaaa cactctgtga attaacagaa attaataaat ctacaatgtc aaaaacattt
      601 aaaagcctta aacaaaagca atgtttaatt gagaaaaacg ggcatattta tttaaattct
      661 gtaatattta tgaaaggttt gcctcataaa ttgtttattc aatttagaga tcatttttta
      721 aattcaattt cttataaatt agatgatgaa gaagagtttg aaaaagtctt cgacgataat
      781 tttattaaag catatgaaaa aaatctcaaa gaaattaaaa agaaaaaaca acagataaaa
      841 gaaaagaaaa tatcaaaagc attagataat tttgaaaaag aaatttctga agaatggaaa
      901 gaaaaattta aagacgaaga ggaaaatttc gaatttggtt ttgaatctga aatgtaaaat
      961 cgccctcgcc gggcaggcga atcccttact gaaatagaat aaattctatt ccactaaggg
     1021 atttttttta tccattaatt ctccacattt caaatattga cagcattttc cacccggtta
     1081 taacagtact ataagtagtt gtttcaaccc gtctttttgg gtggaacaac aaggcatttt
     1141 agggatagag caaagcgaag gccataaaat tgccaccccc aaccgggggt cgttgttcga
     1201 tttgagcgat agcgaaaaat tgaacataag gggggagggt ttgggtttta cggtatttca
     1261 aatttgagca aagcgaattt ttgaaatttc cggttctttt aatttgcaat gaggaaaaat
     1321 caatatgggt aattcaaaaa gaaatataaa aaaactaaat gataatttta gagaggatat
     1381 tttagattat gcgttcgcgc acaatctaaa atgtgctaac gcacttgcta ttttatatgc
     1441 aacgggttgc cgtccggacg aactccaaac cggagttacg gtaaactatg acagcaaaaa
     1501 aaatgaaatt gaatttagaa taattggatc aaaactaaat agaagaatga gaagaggcat
     1561 aggggttaga aaaataaaag taaaaatcaa taatgaaaat gccaggtttt ttaaaaacat
     1621 tgttgataaa tttattgaaa acccaatgtc atatgatcac aaaatcaaaa ttgaaagtgc
     1681 caaagcattt tccgggtaca taacaaaaat atcgaaaaag ctatggccca ggaaaaccta
     1741 tcatgcttct gcatattctt ttagacatgc aaaagcaacg gaattgaaaa attccgatta
     1801 tgataaaatc gaaatagctc agattatggg ccatgcctca gttagatctc agcagagtta
     1861 cggaagaaag agcaaaaaaa gcaaaggtgg atttgatgac atcgcagatg tcgaaaccaa
     1921 tgttaaaccc cgtggcggtg atagattatt gagatttaag atcgcaaata aaaacaaagc
     1981 agcggcaaaa attgccgata cttccacccc cagcagtcct ccaccggctc ccgttcgtcg
     2041 cttcaaaatg tgaaccgtga gcagttcagg aggttccctc ctggactgtg aagggttggc
     2101 ccgtccggtc aggacggttt tacagcaaaa tcctccatag cgaagcagaa gcccggaacg
     2161 ggtaactgga tggttttccc ccgtggggga ttgatctgtt acttgaaaac caatgatctt
     2221 aaaagccatc tcaaaagttg aaaatttcac ccccttagtg ttcttaaaat tcttagatgt
     2281 tcttaggagt taaaaaacta ctctataacc attgatttta ctgacttttt aaaaaaggca
     2341 gttgtcaa
//
