LOCUS       NZ_CP039275             3270 bp    DNA     circular CON 26-JAN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Senftenberg str.
            CFSAN004025 plasmid pCFSAN004025.5, complete sequence.
ACCESSION   NZ_CP039275
VERSION     NZ_CP039275.1
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 3270)
  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  JOURNAL   Unpublished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 3270)
  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
            CP039275.1.
            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..3270
                     /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="pCFSAN004025.5"
                     /geo_loc_name="Mexico"
                     /collection_date="2003-07-03"
                     /collected_by="FDA"
     gene            complement(join(2607..3270,1..374))
                     /locus_tag="CFSAN004025_RS26185"
                     /old_locus_tag="CFSAN004025_26480"
     CDS             complement(join(2607..3270,1..374))
                     /locus_tag="CFSAN004025_RS26185"
                     /old_locus_tag="CFSAN004025_26480"
                     /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="type II toxin-antitoxin system RnlA family toxin"
                     /protein_id="WP_079849605.1"
                     /translation="MAQNPFKALNINTDKIEAALTQNGVTNFSSIVRNERETHLSGTYK
                     EIDFLIKLMPSGGNTTIGRASGQNNTYFDEIAGIIKENCLYSDKKTFEYTIPRFSDENK
                     EMLFAFLTEENVKIEEDKNNDPNCKHQYIMTTGNGDRVRAKIYNRGSIQFQGKYLQIAS
                     LINDFMCTILDMKEIIEQKNQEFNVDIKKETIESELHSKLPKSIDLIHDDIKKQLSCSL
                     IMKQIDVEMEDYSTYCFSALRSIEGFIYQLLGSVCNPSSSRNLGEYFTENNPKYIIRDI
                     HQETINGEIAEVLCECYTYWHENRHGLFHMKPGVADTKTIDKAESIEIIDTVCQLIDKG
                     MARLK"
                     /name="type II toxin-antitoxin system RnlA family toxin"
     gene            1315..1464
                     /locus_tag="CFSAN004025_RS26430"
     CDS             1315..1464
                     /locus_tag="CFSAN004025_RS26430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001442891.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGPPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(2227..2607)
                     /locus_tag="CFSAN004025_RS26200"
                     /old_locus_tag="CFSAN004025_26495"
     CDS             complement(2227..2607)
                     /locus_tag="CFSAN004025_RS26200"
                     /old_locus_tag="CFSAN004025_26495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052605.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RnlB family
                     antitoxin"
                     /protein_id="WP_079849606.1"
                     /translation="MKINKKYQIEVIKDKDKTLFIVYATDIYSPSEFFSKIESDLKKKK
                     VGGDVFFDLIIPNGGKKDRYVHTSFNGERLTSYTLNKVTETDKYKSLSERSASFFKNNF
                     NNINANLLSKATSFALKQGIPI"
                     /name="type II toxin-antitoxin system RnlB family
                     antitoxin"
     Typing          1107..1322
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="88.636"
                     /coverage="100.0"
                     /evalue="7.33e-68"
     Typing          complement(640..1157)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.095"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tcgttgtttt tatcttcttc tatttttacg ttttcttcag taagaaatgc aaacaacatt
       61 tccttatttt catcgctgaa tcttgggatt gtgtattcaa acgttttttt atctgaatac
      121 aaacagtttt cttttataat gccagcgatc tcatcaaagt aagtgttgtt ttgtcctgat
      181 gcccttccta tagtggtgtt tccacctgat ggcattagct ttattaaaaa atctatttct
      241 ttatatgtcc ctgataaatg tgtttctctt tcgtttctca cgatagaaga aaagtttgtg
      301 acgccattct gcgtcaaggc agcttcaatc ttgtctgtat taatatttag tgctttaaat
      361 gggttctgtg ccattgcctc aatccgttgt tttttctgaa tatgtacaga tcttgttttt
      421 ttgtcaatgg aagcgcggtt cgttgacttg atagactgat tgattcatca tcgcataaag
      481 aaaaaaccac cgctaccaac ggtggttttc tcaaggttcg ttgagctacc aactctttga
      541 accgaggtaa ctggctttcg cagagcacag aaaccaaatt cgttattaca gtgtagctgt
      601 acttcacctc acacttcaac acttctttgt tctgcgaatc cgttaccagt ggctgctgcc
      661 agtggcgctt tgtcgtgcct ttccgggttg gactcaagat gatagttacc ggacaaggcg
      721 cagcggtcgg actgaacggg gggttcgtgc atacagtcca gcttggagcg aactgcctac
      781 ccggaactga gtgtcaggcg tggaatgaga taaacgcggc cataacagcg gaatgacacc
      841 ggtaaaccga aaggcaggaa caggagagcg cacgagggag ccatcagggg gaaacgcctg
      901 gtatctttat agtcctgtcg ggtttcgcca ccactgattt gagcgtcaga tttcgtgatg
      961 cttgtcaggg gggcggagcc tatggaaaaa cggcagcgcc gcatcctttt tccggccttt
     1021 cctgacttga gtgccatctc tttatcttgt cgtttgtgag caggtaacgc ccgccgcagc
     1081 ctcacggcag gagcgtagcg accgagtgag cgaggaggcg tcatatcacc gtaactccca
     1141 ttttctccct tacgccctgt agctgcattt tcccctgtca catgaagcac tttcattagg
     1201 tgctactccg ccgtaacata ttcagccact gtacactccg ctagcgctac gtgactggtt
     1261 cagggctgcg ctccgaaacc cgctaacaac ctctccgcta ctggatatca ccccatgcca
     1321 tctgaatatg atgaacaact ggattcgact gatacgcagc ttcccggcga atatgacctt
     1381 tttgatttaa tggcgcaggt tactgaagag aacctgcacg ccccggtgga ttttgggccg
     1441 cctgtcggcc gggaagcgtt atagcttttt cgcttacccg cgtacgtgta atacgccggt
     1501 attacatctt atttctttat tttcatgtga ttacaggtgg ttgtaatacg ttgcgtatta
     1561 cataaataaa cgggaacttc actttttacc ttttaattca tgcaattgcg atgaaaatcg
     1621 cggttgcgta tggtgtatgg ccatttaagg gataaagaat catctcctta ccgggctgag
     1681 ctttgcctat tctgaggaga tctgtgaaaa aaagcgtcca taactagctc gttcatactt
     1741 gtatgaacag cttattcctc ctgactacta ataaactaca gcgtcactac tgatttacta
     1801 ctgatttact actgatttac tacaaatcgg aggaggatga ctacttatct actactgatt
     1861 tactactgaa ttactactga attacgtcag aacagttctc tgaaccattc gtacatccga
     1921 cccccttatc ttcatgcttg atgttcttgc caacgcctca cggccacgca ataaattgcg
     1981 tccccgttca ccgttttcgg gtgggaagaa cgccggaaac aggacttacc ccggctgaat
     2041 ggcgtgaatt ttcgcactat gcacttgcgc gcatactcat gcatgccgta aaaacagagc
     2101 ctgcgcgttt ctggcgggtt ttcgggtggt ttgttgcctg ttttaccggt ttcccgtcag
     2161 aaacgccctg agagcctctc aggcggtgca cgcaacggat gttatgttca atatctgaac
     2221 ttgcttttat attggaatac cttgttttaa agcaaatgat gtggctttag atagaaggtt
     2281 tgcattaata ttattaaagt tattcttaaa gaacgaagct gagcgttccg ataaggattt
     2341 atacttatct gtttccgtaa ctttgtttaa tgtgtagctt gtcaatcgct cgccgttgaa
     2401 tgatgtatgg acgtaacggt ctttttttcc accattagga attattaaat caaaaaaaac
     2461 atcgccacca actttctttt tctttaaatc agactcgatt ttagagaaaa attcgctcgg
     2521 gctataaata tctgtagcgt agacaatgaa taaagtttta tctttatcct ttatcacctc
     2581 tatttgatat tttttgttta ttttcattat ttcaacctag ccatgccttt atctatcaac
     2641 tgacatacag tatcgataat ttcaatagat tctgctttgt caattgtctt agtgtcagcc
     2701 acacctggtt tcatatggaa caagccatgt ctgttttcat gccagtaagt gtagcactca
     2761 cacaaaactt ctgctatttc accattaata gtttcttggt gtatatctct tattatgtat
     2821 ttcgggttat tctcagtgaa gtactcgcca agattccttg atgatgatgg gttgcatacg
     2881 cttccaagta gttgatatat aaagccttct atggatctca aggctgagaa acaatatgtt
     2941 gagtaatctt ccatttcgac atctatttgt ttcattatga gcgagcagga tagctgtttt
     3001 ttgatgtcgt catggattag gtcgatgctt tttggtagtt tactatgtaa ttctgactca
     3061 attgtttctt tttttatgtc aacattaaat tcttgattct tctgttctat aatctctttc
     3121 atgtccagta tggtgcacat gaaatcatta atcaaacttg cgatttgaag atatttacct
     3181 tggaattgaa ttgagccacg gttgtaaatt tttgctctga ctctgtcacc attgccagtg
     3241 gtcatgatgt attgatgttt acagttgggg
//
