LOCUS       NZ_AP019694             2345 bp    DNA     circular CON 13-FEB-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Senftenberg strain
            SL180013 plasmid pSL180013-2, complete sequence.
ACCESSION   NZ_AP019694
VERSION     NZ_AP019694.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMD00171749
            Sequence Read Archive: DRR178302
            Assembly: GCF_006741505.1
KEYWORDS    RefSeq; STANDARD_DRAFT.
SOURCE      Salmonella enterica subsp. enterica serovar Senftenberg
  ORGANISM  Salmonella enterica subsp. enterica serovar Senftenberg
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1
  AUTHORS   Morita,M., Shimada,K., Baba,H., Morofuji,K., Oda,S., Izumiya,H. and
            Ohnishi,M.
  TITLE     Genome sequence of a Salmonella enterica serotype Senftenberg strain
            lacking Salmonella pathogenicity island-1 in Japan
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2345)
  AUTHORS   Morita,M., Izumiya,H. and Ohnishi,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-MAY-2019) Contact:Masatomo Morita National Institute
            of Infectious Diseases, Department of Bacteriology I; Toyama 1-23-1,
            Shinjuku-ku, Tokyo 162-8640, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.4
            Genome Coverage                   :: 75x
            Sequencing Technology             :: Illumina MiSeq; ONT MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/13/2024 04:09:34
            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)                     :: 4,894
            CDSs (total)                      :: 4,772
            Genes (coding)                    :: 4,643
            CDSs (with protein)               :: 4,643
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 129
            CDSs (without protein)            :: 129
            Pseudo Genes (ambiguous residues) :: 0 of 129
            Pseudo Genes (frameshifted)       :: 41 of 129
            Pseudo Genes (incomplete)         :: 98 of 129
            Pseudo Genes (internal stop)      :: 18 of 129
            Pseudo Genes (multiple problems)  :: 24 of 129
            Pseudo Genes (short protein)      :: 1 of 129
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            AP019694.1.
            Annotated at DFAST 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..2345
                     /organism="Salmonella enterica subsp. enterica serovar
                     Senftenberg"
                     /mol_type="genomic DNA"
                     /strain="SL180013"
                     /serovar="Senftenberg"
                     /sub_species="enterica"
                     /db_xref="taxon:28150"
                     /plasmid="pSL180013-2"
                     /geo_loc_name="Japan"
                     /collection_date="2018"
     gene            57..245
                     /locus_tag="FNL84_RS24685"
                     /old_locus_tag="SL180013_P210"
     CDS             57..245
                     /locus_tag="FNL84_RS24685"
                     /old_locus_tag="SL180013_P210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /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_000165998.1"
                     /translation="MTKQESAALNMAKFIRAQSLLLLEKLDVLDLDDEAADCERMHEQA
                     EALYQKLSARFGIQDGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(293..520)
                     /locus_tag="FNL84_RS24690"
                     /old_locus_tag="SL180013_P220"
     CDS             complement(293..520)
                     /locus_tag="FNL84_RS24690"
                     /old_locus_tag="SL180013_P220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001046776.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_206659768.1"
                     /translation="MFGFSPGELMNLCPDERLLFVRMISAMLRRSGGDAGAVMFEAYRH
                     IVSDTNQARRSCMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            1374..1508
                     /locus_tag="FNL84_RS25450"
     CDS             1374..1508
                     /locus_tag="FNL84_RS25450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /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_072035952.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHDKAPLAAATGNRFRGGES"
                     /name="replication initiation protein"
     gene            complement(1929..2141)
                     /locus_tag="FNL84_RS24705"
                     /old_locus_tag="SL180013_P240"
     CDS             complement(1929..2141)
                     /locus_tag="FNL84_RS24705"
                     /old_locus_tag="SL180013_P240"
                     /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_039509481.1"
                     /translation="MGDFERTYGAGADFDRIIDENNSEYFRDERQKAKNSKKEFSSFQD
                     ALVWAKANPGKTIVRSPDGVGFIEK"
                     /name="hypothetical protein"
     Typing          994..1483
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.13"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 aagtgaatga agtaagattt cagtctgcga tcaccataaa accgggaaaa agccgtatga
       61 caaaacagga atcagccgca ctgaacatgg caaaatttat ccgggcgcag tcgctgctgc
      121 tgctcgaaaa actcgacgtg ctcgatcttg atgacgaggc agccgactgt gagcgaatgc
      181 acgaacaggc agaagcgctt tatcagaagc tgagcgcacg cttcggtata caggacggcg
      241 aataaagaga cgaaaagaac actcacttag acgaaaagcg tatccagggc aactatgtat
      301 atccaccgtg tacatagtca tgcctgacgc tttcgagcag gtcgagcatg caggaacgac
      361 gagcttgatt ggtatcggac acaatatggc gatacgcctc aaacataaca gcacccgcat
      421 caccgcccga acggcgaagc atagcggaaa tcatccgcac aaagagcaga cgttcatcgg
      481 ggcaaaggtt cataagttct cctggtgaaa aaccaaacat gaaagcaccc atctattaac
      541 gtcagctgtg aacgcttcat tagaagaaaa taggtaaacc cgggaaaaag atccaaacgt
      601 taacatcaca ggtaaacaga aacgtcgggt cgatcgggaa attctttccc ggacggcgcg
      661 gggttgggca agccgcaggc gcgtcagtgc ttttagcggg tgtcggggcg cagccctgaa
      721 ccagtcacgt agcgctagcg gagtgtatac tggctaaact tcagagatgc caaggaaggg
      781 acaggatatg ttttgtagca ccgccaccac ggtggcgata ctccaaaacg cctggtcagg
      841 gcacagcccc gacaccccag agccgactgt aggtcactgg acgaacgcgg cggaatgatg
      901 tcggatgacg tcattttgcg gcgtttgccc tatcctgcat cgtattaaaa aatgcagcta
      961 tggcgcgtac ggtgccaaag ataagcccgg agatattccg cttcctcgct cactgactcg
     1021 ctccgctcgg tcgttcggct gcggcgagcg gtaccggctt actggcgggg cggaaatttc
     1081 ctggcatctt ccaggaagaa gcttaacagg gaagcaagaa ggccacggcg aagccgtttt
     1141 tccataggct ccgcccccct gacaagcatc acgaaatctg acgctcaaat cagtggtggc
     1201 gaaacccgac aggacttaaa gataccaggc gtttccccct ggtggctccc tcgtgcgctc
     1261 tcctgttcct gcctttcggt ttaccggtgt cattccgctg ttatggccgc gtttatctca
     1321 ttccacgcct gacactcagt tccgggtagg cagttcgctc caagctggac tgtatgcacg
     1381 aaccccccgt tcagtccgac tgctgcgcct tatccggtaa ctatcgtctt gagtccaacc
     1441 cggaaagaca cgacaaagcg ccactggcag cagccactgg taacaggttt agaggaggag
     1501 agtcttgaaa tttcgggtgc gataaggcta cactgaaagg actattttgt gactgtgctc
     1561 ctccaagcca gttaccgcgg ttcaaaagag cgtcaactct tgcgaacctt cgaaaaagcc
     1621 accttgccgg gtggtttttt cgtttacaga gctaagagat tacgattctc cctaaatgat
     1681 ctcaagaaga tccgtttaaa aaagcgggtt ttatggttgg atgaagttcg tcttacccag
     1741 tcacatatta gatttatttg aattactact aggtttcgta agccatgcaa gaattcctgt
     1801 aactaacaaa ataggccctg caatgtacgt aacatagact ccaacatacg acactgtgaa
     1861 acatatgagt acgtatatag ccagtgttgt ccaaaaaatg actgccgttt tacagtgaat
     1921 ccactctttc atttttcaat aaatcccaca ccgtctggag atcttactat cgttttacca
     1981 ggattagctt tcgcccaaac caaagcatct tgaaaagaag agaattcttt tttcgaattt
     2041 ttagcttttt ggcgctcatc tcgaaaatat tcgctgttat tctcatcaat tatccgatca
     2101 aaatcagcac cagctccgta ggtacgctca aaatccccca tttcctaccc ccataaattt
     2161 aataaaaaaa cagatttaaa atatccaaca gacactctta tttaccataa catccgttgc
     2221 gtgcaccgcc tgagaggctc tcagggcgtt tctacgacct cacctgcaaa agaacacatc
     2281 ttaccccctg aaaaccgctc agaaacgcgc tgatgatttc tgcgtacctg catggctatg
     2341 cactc
//
