LOCUS       NZ_CP039276             2318 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Senftenberg str.
            CFSAN004025 plasmid pCFSAN004025.6, complete sequence.
ACCESSION   NZ_CP039276
VERSION     NZ_CP039276.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02352702
            Assembly: GCF_004798785.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Senftenberg str.
            CFSAN004025
  ORGANISM  Salmonella enterica subsp. enterica serovar Senftenberg str. CFS...
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 2318)
  AUTHORS   Robertson,J., Lin,J., Wren-Hedegus,A., Arya,G., Carrillo,C. and
            Nash,J.H.E.
  TITLE     Development of a multi-locus typing scheme for an Enterobacteriaceae
            linear plasmid that mediates inter-species transfer of flagella
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2318)
  AUTHORS   Robertson,J., Lin,J., Wren-Hedegus,A., Arya,G., Carrillo,C. and
            Nash,J.H.E.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-APR-2019) Public Health Agency of Canada, National
            Microbiology Laboratory at Guelph, 110 Stone Road West, Guelph,
            Ontario N1G3W4, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/24/2024 13:46:20
            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)                     :: 5,166
            CDSs (total)                      :: 5,046
            Genes (coding)                    :: 4,917
            CDSs (with protein)               :: 4,917
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 129
            CDSs (without protein)            :: 129
            Pseudo Genes (ambiguous residues) :: 0 of 129
            Pseudo Genes (frameshifted)       :: 51 of 129
            Pseudo Genes (incomplete)         :: 96 of 129
            Pseudo Genes (internal stop)      :: 24 of 129
            Pseudo Genes (multiple problems)  :: 34 of 129
            Pseudo Genes (short protein)      :: 1 of 129
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP039276.1.
            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..2318
                     /organism="Salmonella enterica subsp. enterica serovar
                     Senftenberg str. CFSAN004025"
                     /mol_type="genomic DNA"
                     /strain="CFSAN004025"
                     /serovar="Senftenberg"
                     /isolation_source="fish meal"
                     /sub_species="enterica"
                     /db_xref="taxon:1399047"
                     /plasmid="pCFSAN004025.6"
                     /geo_loc_name="Mexico"
                     /collection_date="2003-07-03"
                     /collected_by="FDA"
     gene            91..279
                     /locus_tag="CFSAN004025_RS26205"
                     /old_locus_tag="CFSAN004025_26500"
     CDS             91..279
                     /locus_tag="CFSAN004025_RS26205"
                     /old_locus_tag="CFSAN004025_26500"
                     /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(327..593)
                     /locus_tag="CFSAN004025_RS26210"
                     /old_locus_tag="CFSAN004025_26505"
     CDS             complement(327..593)
                     /locus_tag="CFSAN004025_RS26210"
                     /old_locus_tag="CFSAN004025_26505"
                     /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_223173001.1"
                     /translation="MKRSQLTLIDGCFMFGFSPGELMNLCPDERLLFVRMISAMLRRSG
                     GDAGAVMFEAYRHIVSDTNQARRSYMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     gene            complement(1614..1913)
                     /locus_tag="CFSAN004025_RS26230"
                     /old_locus_tag="CFSAN004025_26525"
     CDS             complement(1614..1913)
                     /locus_tag="CFSAN004025_RS26230"
                     /old_locus_tag="CFSAN004025_26525"
                     /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_016247612.1"
                     /translation="MKKILFCSLLLLSASSFAQQFHYQCEGRDLKIMLSPNAAFLDGKS
                     FEYKNGETNGETTKMTFFGPSGEVLKFLVNPVNNLYRMGLTSGATFEEINCTEI"
                     /name="hypothetical protein"
     gene            complement(1937..2176)
                     /locus_tag="CFSAN004025_RS26235"
                     /old_locus_tag="CFSAN004025_26530"
     CDS             complement(1937..2176)
                     /locus_tag="CFSAN004025_RS26235"
                     /old_locus_tag="CFSAN004025_26530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001560795.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001560795.1"
                     /translation="MIKKICITVIVVFLLLVGYGAWIGSEQNQRGVSLFEVAYTYNAMN
                     PISRIGYTFMLKRNHALVERAGEVKKSIDSMSGE"
                     /name="hypothetical protein"
     Typing          complement(738..910)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.954"
                     /coverage="100.0"
                     /evalue="2.04e-62"
     Typing          835..1381
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.091"
                     /coverage="90.0"
                     /evalue="0.0"
ORIGIN
        1 gatgatttct gcgtacctgc atggctatgc actcaagtga atgaagtaag atttcagtct
       61 gcgatcacca taaaaccggg aaaaagccgt atgacaaaac aggaatcagc cgcactgaac
      121 atggcaaaat ttatccgggc gcagtcgctg ctgctgctcg aaaaactcga cgtgctcgat
      181 cttgatgacg aggcagccga ctgtgagcga atgcacgaac aggcagaagc gctttatcag
      241 aagctgagcg cacgcttcgg tatacaggac ggcgaataaa gagacgaaaa gaacgctcac
      301 ttagacgaaa agcgtatcca aggcaactat gtatacccac cgtgtacata gtcatgcctg
      361 acgctttcga gcaggtcgag catgtaggaa cgacgagctt gattggtatc ggacacaata
      421 tggcgatacg cctcaaacat aacagcaccc gcatcaccgc ccgaacggcg aagcatagcg
      481 gaaatcatcc gcacaaagag cagacgttca tcggggcaaa ggttcataag ttctcctggt
      541 gaaaaaccaa acatgaagca cccatctatt aacgtcagct gtgaacgctt cattacgctt
      601 cattaaaata ggtaaacccg ggaaaaagat ccaaacatta acatcacagg taaacagaaa
      661 cgtcgggtcg atcgggaaat tctttcccgg acggcgcggg gttgggcaag ccgcaggcgc
      721 gtcagtgctt ttagcgggtg tcggggcgca gccctgaacc agtcacgtag cgctagcgga
      781 gtgtatactg gcttactatg taggcacggg tgcgggaatc agtgaagtgc ttcatgtggc
      841 aggaggaaaa tgcagcagca gagcgtaagc ggaatatatg agacaggaga tattccgctt
      901 cctcgctcac tgactcgctg cgctcggtcg ttcggctgcg gcgagcggtg cgggcttacg
      961 aatggggcgg aaatttcctg ggagatgcca ggaagaaact taacagggaa acgataaggc
     1021 cgcggcgaag ccgtttttcc ataggctccg cccccctgac aagcatcacg aaatctgacg
     1081 ctcaaatcag tggtggcgaa acccgacagg actataaaga taccaggcgt ttccccctgg
     1141 cggctccctc gtgcgctctc ctgttcctgc ctttcggttt accggtgtca ttccgctgtt
     1201 atggccgcgt ttgtctcatt ccacgcctga cactcagttc cgggtaggca gttcgctcca
     1261 agctggactg tatgcacgaa ccccccgttc agtccgaccg ctgcgcctta tccggtaact
     1321 atcgtcttga gtccaacccg gaaagacatg caaaagcacc actggcagca gccactggta
     1381 attgatttag aggagttagt cttgaagtca tgcgccggtt aaggctaaac tgaaaggaca
     1441 agttttggtg actgcgctcc tccaagccag ttacctcggt tcaaagagtt ggtagctcag
     1501 agaaccttcg aaaaaccgcc ctgcaaggcg gttttttcgt tttcagagca agagattacg
     1561 cgcagaccaa aacgatctca agaagatcat cttattaatc agataaaata tttctagatt
     1621 tcagtgcaat ttatctcttc aaatgtagca cctgaagtca gccccatacg atataagttg
     1681 ttgacaggat taaccaaaaa cttgagaacc tcaccagaag gaccaaagaa tgtcatcttt
     1741 gtcgtttccc cattcgtctc tccattctta tattcgaatg atttaccatc aagaaaagct
     1801 gcattaggtg aaagcattat ctttaaatct cgtccttcac actgataatg gaattgttgt
     1861 gcaaatgaac ttgcagaaag aagaagcagc gaacaaaaaa gtatcttttt catatcagtc
     1921 ctttaaattt aaaaaatcac tcaccactca tgctatcaat agatttctta acctctccag
     1981 ccctctcgac taaagcatga tttctcttca gcataaatgt atagccgatc cgactaattg
     2041 gattcattgc gttgtatgta tatgcaacct caaataaaga tactcctcgc tgattttgct
     2101 cagatccaat ccaagcacca tagccaacca acagcaaaaa aacgacgata acagtaatgc
     2161 agattttttt tatcattccc tatccagata atatgaagaa aacagaattg aacataacat
     2221 ccgttgcccg caccacctca ggcgccctca gggcgtttct gaggactccg gcctgaaaca
     2281 tacacctttc tgtgcccata tcgagaaaaa acgcccct
//
