LOCUS       NZ_AP019693             4096 bp    DNA     circular CON 13-FEB-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Senftenberg strain
            SL180013 plasmid pSL180013-1, complete sequence.
ACCESSION   NZ_AP019693
VERSION     NZ_AP019693.1
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  JOURNAL   Unpublished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 4096)
  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
            AP019693.1.
            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..4096
                     /organism="Salmonella enterica subsp. enterica serovar
                     Senftenberg"
                     /mol_type="genomic DNA"
                     /strain="SL180013"
                     /serovar="Senftenberg"
                     /sub_species="enterica"
                     /db_xref="taxon:28150"
                     /plasmid="pSL180013-1"
                     /geo_loc_name="Japan"
                     /collection_date="2018"
     gene            625..948
                     /locus_tag="FNL84_RS24645"
                     /old_locus_tag="SL180013_P110"
     CDS             625..948
                     /locus_tag="FNL84_RS24645"
                     /old_locus_tag="SL180013_P110"
                     /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_001555769.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGSSGLDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1157..>1591
                     /locus_tag="FNL84_RS25260"
                     /pseudo=""
     CDS             1157..>1591
                     /locus_tag="FNL84_RS25260"
                     /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            1626..2111
                     /locus_tag="FNL84_RS24655"
                     /old_locus_tag="SL180013_P120"
     CDS             1626..2111
                     /locus_tag="FNL84_RS24655"
                     /old_locus_tag="SL180013_P120"
                     /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_012782630.1"
                     /translation="MNSLLTLAKDLEQKSKVQQQTTGEMLKAAFSEHEKSVRAELNESE
                     KRISAAIHDHDRMLSSAMSQRTKGMLRMVSQTWLTIVLVSVLLIASSAGILWWQGQQIL
                     DNYTTIREQKSTQAMLSERNSGVQLTTCGEERRRCVRVNPDAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            2115..2324
                     /locus_tag="FNL84_RS24660"
                     /old_locus_tag="SL180013_P130"
     CDS             2115..2324
                     /locus_tag="FNL84_RS24660"
                     /old_locus_tag="SL180013_P130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014538403.1"
                     /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_001632067.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWESAFAEWRTMCGLMQRENA
                     ALSERVTDLSTQVLSLSEQLRRLS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2854..3081)
                     /locus_tag="FNL84_RS24665"
                     /old_locus_tag="SL180013_P150"
     CDS             complement(2854..3081)
                     /locus_tag="FNL84_RS24665"
                     /old_locus_tag="SL180013_P150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010615788.1"
                     /GO_component="GO:0005886 - plasma membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YgdI/YgdR family lipoprotein"
                     /protein_id="WP_000719360.1"
                     /translation="MKKIFVSVFAAAVALSALTGCTRTSYAIHTNDGRTIVSDGKPTES
                     DSGLLGYKDANGVKQQINKADVKEVSEIPH"
                     /name="YgdI/YgdR family lipoprotein"
     gene            complement(3103..3336)
                     /locus_tag="FNL84_RS24670"
                     /old_locus_tag="SL180013_P160"
     CDS             complement(3103..3336)
                     /locus_tag="FNL84_RS24670"
                     /old_locus_tag="SL180013_P160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008461706.1"
                     /GO_component="GO:0005886 - plasma membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YgdI/YgdR family lipoprotein"
                     /protein_id="WP_001036746.1"
                     /translation="MNKKTLLAAMMVALVTFAAAGCSSNQEIKTTDDRTIVTDGKPKVD
                     SDTGLVSYKDAHTGRTEQINRDKITNMSELDN"
                     /name="YgdI/YgdR family lipoprotein"
     gene            3418..3687
                     /locus_tag="FNL84_RS24675"
     CDS             3418..3687
                     /locus_tag="FNL84_RS24675"
                     /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_079839079.1"
                     /translation="MNGQEFRLLLTEHGEKEAVLLFGKKSFVAVPDTQNLYGGCYYLYL
                     EDAHKNELLIELNESDLYPGGAIELQHNGGRKIHCEILKVRWSR"
                     /name="hypothetical protein"
     gene            complement(3924..4082)
                     /locus_tag="FNL84_RS25445"
     CDS             complement(3924..4082)
                     /locus_tag="FNL84_RS25445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032670878.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHEKSLLAAAISNWRYTRDKL
                     RGLEVWA"
                     /name="hypothetical protein"
     Typing          439..517
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.8899999999999995e-34"
     Typing          complement(2..363)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.906"
                     /coverage="93.0"
                     /evalue="6.530000000000004e-97"
     Typing          complement(3925..4082)
                     /name="rep_cluster_2406"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.79e-77"
     Typing          939..2434
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.998"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agcgaactgc cttcgcggaa ctgagtgtca ggcgtggaat gagaaaccgc ggccataaca
       61 gcggaatgac accggtaaac cgaaaggcag gaatgcgggg gagcacgagg gagccatcag
      121 ggggaaacgc ctggtatctt taagccgcat cgggtttcgc caccactgat ttgagcgtca
      181 gattctgtga tgcttgtcag gggggcggag cctatggaaa accggcagcg gcgcatcctt
      241 tcttcccctc ctgcattcac gtatttcccc gccacgtctt tatccgtgag tccgtaccgc
      301 tcgccgcagc cgaacgaccg agcgtagcga gtcagtgagc gaggaagcgg aatatccacc
      361 gggacaggca tcagcctctt acgcacctga gcctcatctc acagttttca tgactgacta
      421 tttcatcccg attcccgtcg tgccaccata gtaagccagt atacactccg ctagcgctac
      481 gtgactggtt cagggctgcg ccccgaaacc cgctaaatgc cactgacgcg cctgcggctt
      541 gcccaacacc gcgccgaccg ggaaaagatt tcccgcccgt cccggcgtta tcaggaggcc
      601 ggattggcag acaaacgcag caaaatgctc acgatgtggg taacagaaga tgagcaccgc
      661 cgtctgctgg aacgctgcga cggtaaacag ctcgcggcct ggatgcggca gacgtgcctg
      721 gacgagaagc ccgcccgggc cggcaaactt ccctcgatct cgccggcgct gcttcgtcag
      781 cttgccggca tggggaacaa cctcaaccag attgcccgcc aggttaacgc cggtggcagt
      841 agcggtctcg accgcgtgca ggtcgtcgcc gcgctgatgg ccatcgatgc cggactcgag
      901 cggctgcggc atgccgtact ggaaaagggg gctgacgatg atcgttaagt ttcatccccg
      961 gggacgcgga ggcggtgccg gcccggttga ttatctgctg gggaaagacc gccagcgcga
     1021 cggtgccagc gttcttcagg ggaagccgga ggaagtccgg gagcttatcg acgcctcgcc
     1081 ctacgccaaa aagtacacct ccggggtgct gtcctttgcc gaacaggact taccgcccgg
     1141 gcagcgtgaa acgctgatgg cgagcttcga gcgggttctg atgcccggac tcgataaaga
     1201 ccagtacagc gtgctgtggg ttgagcaccg ggacaagggg cggctggagc tgaacttcct
     1261 gatcccgaac acggagctgc tgaccggcaa acggctccag ccatactatg accgcgccga
     1321 ccgtcctcgc attgatgcct ggcagaccat cgtgaacggc agtctggggc tgcacgaccc
     1381 gaacgcgccg gaaaaccggc gggcactggt cacgccgtcc gcgctgccgg aaacgaagca
     1441 ggaagccgct caggcgatta cgcggggttt actggcctta gcctcgtccg gggagctgaa
     1501 aacgcgtcag gacgtcactg aggcgctgga aagcgcaggt tttgaggtgg ttcgcaccac
     1561 aaaaagcagc atcagcattg ccgacccgga cggggggcga aacatccgac tgaagggagc
     1621 catctatgaa cagtctttta acgctggcga aggacttaga gcagaaatcg aaagtgcagc
     1681 agcagactac cggcgagatg ctgaaagccg cattcagcga gcacgagaag tctgtcagag
     1741 cggaactgaa cgaaagcgag aagagaatca gcgccgccat ccacgaccac gaccggatgc
     1801 tgtcctcagc catgagccag cgtacgaaag ggatgctgcg catggtcagc cagacgtggc
     1861 tgaccatcgt cctggtctcc gtgctgctga tagcctcaag tgcgggcatt ctatggtggc
     1921 aggggcagca gatactcgac aattacacga ccatccggga gcagaagagc acgcaggcca
     1981 tgctgtccga gaggaacagc ggcgtgcagc tcacgacctg cggagaggaa cgacgccgct
     2041 gcgtgagggt gaacccggac gcgggacggt tcggagagga ttcgagctgg atgatactgg
     2101 cggggaaata gcacatgacg gaactggaaa aacagttgct gagcgcatta gagcagctac
     2161 agcaggacta ctcgaaaagg ctggacgagt gggagagcgc cttcgcggaa tggcggacga
     2221 tgtgtggtct tatgcaacgg gagaacgcag cgctgagcga gcgcgtcacg gacttgagca
     2281 cgcaggtgct gagtttaagc gagcagctgc gccggttgtc gtaaggctga acgacatcga
     2341 ggcacaccgg gagcaggagc gcgcagcgca gcaccagaaa gcgctggagc tggaacgatc
     2401 gcagcgtcag caggagtatg acggtccgtc gctgtgataa ccggataaaa cggggctttc
     2461 attgaggatc tgcgccgaaa cccggtgcca ttcacccggc tgcatggcta tgcagtcggg
     2521 tgagatttat caggcgcaga atgcacggtt tgcggggtgg tttactgtcg gttttgcagg
     2581 actgacgccg cattcgcgct gaacccgtcc ggagaggtgc gggcaaggga tgttatggta
     2641 aaagcatgat gcctggcggg tacggaaaaa ttgtggcgac cgagcctgca gacgcaaaaa
     2701 tccggcccat acttattcgt ctccttcatc aggaatgcag tactatccag ccactgcagg
     2761 tatttggccc ccagcggggg ctttttttgc ctgttgttgg ggcagataaa gaaaagggcc
     2821 gcattagcgg cccttttcgg agagagcgat gcctcaatgc ggaatttcag agacttcttt
     2881 aacgtcggct ttattgatct gctgtttgac accatttgcg tctttatagc ccagcaggcc
     2941 tgagtctgat tctgtaggct tgccgtcgct gacaattgta cgcccgtcgt tggtgtggat
     3001 ggcatagctt gtgcgcgtgc agccggttag ggctgaaagc gcaactgccg ctgcgaacac
     3061 tgaaacaaaa atctttttca aagccagctc cttttatccg tatcagttgt ctagttcact
     3121 catgttggta attttgtcac ggttgatctg ttcggttcgg cctgtatggg catctttgta
     3181 ggatactaat cccgtatcac tgtcaacttt gggtttgccg tctgtaacga tagtgcgatc
     3241 atctgtggtt tttatttctt ggtttgaaga acatccagca gcggcaaagg tcaccaacgc
     3301 gaccatcatg gccgccaaca gcgttttttt attcataata ggttccctgc ttaaaggtaa
     3361 agtggatatg gtcactaacc atctaagtat aggtcgtttt ttcatgcgaa aagaggattg
     3421 aatggacaag aatttcgatt attgctgaca gagcatggag aaaaagaggc tgttttactg
     3481 ttcggaaaga aatcttttgt tgccgtgcca gatacgcaga acctttatgg tgggtgttat
     3541 tacctttatt tagaggatgc tcacaagaac gagcttttaa ttgagttaaa cgaaagtgat
     3601 ttataccccg gtggcgcaat agaacttcaa cacaacggcg gtcggaagat tcattgcgag
     3661 atactaaaag taaggtggag tcgttaactc aagtaatgtt tcctaagtat gttgataggc
     3721 aaacatagtg gtagttagtc tctctgagta aatgatcttc ttgtgatcct gtcgttacag
     3781 tcgtaatctc ttgctctgaa aacgaaaaaa ccacctgggg aggtggtttg atcgaaggtt
     3841 aagtcagttg gggaactgct taaccaggta actgggtata cgagaccgca gaaaccaaaa
     3901 ctgttctttc agtgtagcct ctctcaggcc catacttcaa gacctcttaa tttgtctctc
     3961 gtatacctcc agttactaat ggctgctgcc agtagcgatt tttcgtgtct ttccgggttg
     4021 gactcaagac gatagttacc ggataaggcg cagcagtcgg actgaacggg gggttcgtgc
     4081 atacagtcaa tcctgg
//
